From c9ff7531683e2e8c4ba271c5826f3b00eb33c980 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 15 Oct 2009 21:52:32 +0000 Subject: [PATCH 001/446] Added documentation for the save() function for domains. Made the save function for domains use a const solution vector. --- Cantera/src/oneD/Domain1D.h | 992 +++++++++++++++--------------- Cantera/src/oneD/Inlet1D.h | 14 +- Cantera/src/oneD/Resid1D.h | 14 +- Cantera/src/oneD/Solid1D.cpp | 2 +- Cantera/src/oneD/Solid1D.h | 10 +- Cantera/src/oneD/StFlow.cpp | 4 +- Cantera/src/oneD/StFlow.h | 10 +- Cantera/src/oneD/Surf1D.h | 2 +- Cantera/src/oneD/boundaries1D.cpp | 20 +- 9 files changed, 554 insertions(+), 514 deletions(-) diff --git a/Cantera/src/oneD/Domain1D.h b/Cantera/src/oneD/Domain1D.h index 004742be2..b201fe304 100644 --- a/Cantera/src/oneD/Domain1D.h +++ b/Cantera/src/oneD/Domain1D.h @@ -21,501 +21,513 @@ namespace Cantera { - // domain types - const int cFlowType = 50; - const int cConnectorType = 100; - const int cSurfType = 102; - const int cInletType = 104; - const int cSymmType = 105; - const int cOutletType = 106; - const int cEmptyType = 107; - const int cOutletResType = 108; - const int cPorousType = 109; + // domain types + const int cFlowType = 50; + const int cConnectorType = 100; + const int cSurfType = 102; + const int cInletType = 104; + const int cSymmType = 105; + const int cOutletType = 106; + const int cEmptyType = 107; + const int cOutletResType = 108; + const int cPorousType = 109; - class MultiJac; - class OneDim; + class MultiJac; + class OneDim; + + + /** + * Base class for one-dimensional domains. + */ + class Domain1D { + public: + + /** + * Constructor. + * @param nv Number of variables at each grid point. + * @param points Number of grid points. + */ + Domain1D(int nv=1, int points=1, + doublereal time = 0.0) : + m_rdt(0.0), + m_time(time), + m_container(0), + m_index(-1), + m_type(0), + m_iloc(0), + m_jstart(0), + m_left(0), + m_right(0), + m_id("-"), m_desc("-"), + m_refiner(0), m_bw(-1) { + resize(nv, points); + } + + /// Destructor. Does nothing + virtual ~Domain1D(){ delete m_refiner; } + + /// Domain type flag. + const int domainType() { return m_type; } + + /** + * The left-to-right location of this domain. + */ + const int domainIndex() { return m_index; } + + /** + * True if the domain is a connector domain. + */ + bool isConnector() { return (m_type >= cConnectorType); } + + /** + * The container holding this domain. + */ + const OneDim& container() const { return *m_container; } + + /** + * Specify the container object for this domain, and the + * position of this domain in the list. + */ + void setContainer(OneDim* c, int index){ + m_container = c; + m_index = index; + } + + /* + * Set the Jacobian bandwidth. See the discussion of method bandwidth. + */ + void setBandwidth(int bw = -1) { + m_bw = bw; + } + + /** + * Set the Jacobian bandwith for this domain. When class + * OneDim computes the bandwidth of the overall multi-domain + * problem (in OneDim::resize()), it calls this method for the + * bandwidth of each domain. If setBandwidth has not been + * called, then a negative bandwidth is returned, in which + * case OneDim assumes that this domain is dense -- that is, + * at each point, all components depend on the value of all + * other components at that point. In this case, the bandwidth + * is bw = 2*nComponents() - 1. However, if this domain + * contains some components that are uncoupled from other + * components at the same point, then this default bandwidth + * may greatly overestimate the true bandwidth, with a + * substantial penalty in performance. For such domains, use + * method setBandwidth to specify the bandwidth before passing + * this domain to the Sim1D or OneDim constructor. + */ + int bandwidth() { return m_bw; } + + /** + * Initialize. This method is called by OneDim::init() for + * each domain once at the beginning of a simulation. Base + * class method does nothing, but may be overloaded. + */ + virtual void init(){ } + + virtual void setInitialState(doublereal* xlocal = 0){} + virtual void setState(int point, const doublereal* state, doublereal* x) {} + + /** + * Resize the domain to have nv components and np grid points. + * This method is virtual so that subclasses can perform other + * actions required to resize the domain. + */ + virtual void resize(int nv, int np) { + // if the number of components is being changed, then a + // new grid refiner is required. + if (nv != m_nv || !m_refiner) { + m_nv = nv; + delete m_refiner; + m_refiner = new Refiner(*this); + } + m_nv = nv; + m_td.resize(m_nv, 1); + m_name.resize(m_nv,""); + m_max.resize(m_nv, 0.0); + m_min.resize(m_nv, 0.0); + m_rtol_ss.resize(m_nv, 1.0e-8); + m_atol_ss.resize(m_nv, 1.0e-15); + m_rtol_ts.resize(m_nv, 1.0e-8); + m_atol_ts.resize(m_nv, 1.0e-15); + m_points = np; + m_z.resize(np, 0.0); + m_slast.resize(m_nv * m_points, 0.0); + locate(); + } + + /// Return a reference to the grid refiner. + Refiner& refiner() { return *m_refiner; } + + /// Number of components at each grid point. + int nComponents() const { return m_nv; } + + /// Number of grid points in this domain. + int nPoints() const { return m_points; } + + /// Name of the nth component. May be overloaded. + virtual std::string componentName(int n) const { + if (m_name[n] != "") return m_name[n]; + else return "component " + int2str(n); + } + + void setComponentName(int n, std::string name) { + m_name[n] = name; + } + + void setComponentType(int n, int ctype) { + if (ctype == 0) setAlgebraic(n); + } + + /// index of component with name \a name. + int componentIndex(std::string name) const { + int nc = nComponents(); + for (int n = 0; n < nc; n++) { + if (name == componentName(n)) return n; + } + throw CanteraError("Domain1D::componentIndex", + "no component named "+name); + } + + /** + * Set the lower and upper bounds for each solution component. + */ + void setBounds(int nl, const doublereal* lower, + int nu, const doublereal* upper) { + if (nl < m_nv || nu < m_nv) + throw CanteraError("Domain1D::setBounds", + "wrong array size for solution bounds. " + "Size should be at least "+int2str(m_nv)); + std::copy(upper, upper + m_nv, m_max.begin()); + std::copy(lower, lower + m_nv, m_min.begin()); + } + + void setBounds(int n, doublereal lower, doublereal upper) { + m_min[n] = lower; + m_max[n] = upper; + } + + /// set the error tolerances for all solution components. + void setTolerances(int nr, const doublereal* rtol, + int na, const doublereal* atol, int ts = 0); + + /// set the error tolerances for solution component \a n. + void setTolerances(int n, doublereal rtol, doublereal atol, int ts = 0); + + //added by Karl Meredith + /// set scalar error tolerances. All solution components will + /// have the same relative and absolute error tolerances. + void setTolerances(doublereal rtol, doublereal atol,int ts=0); + + //added by Karl Meredith + void setTolerancesTS(doublereal rtol, doublereal atol); + + //added by Karl Meredith + void setTolerancesSS(doublereal rtol, doublereal atol); + + /// Relative tolerance of the nth component. + doublereal rtol(int n) { return (m_rdt == 0.0 ? m_rtol_ss[n] : m_rtol_ts[n]); } + + /// Absolute tolerance of the nth component. + doublereal atol(int n) { return (m_rdt == 0.0 ? m_atol_ss[n] : m_atol_ts[n]); } + + /// Upper bound on the nth component. + doublereal upperBound(int n) const { return m_max[n]; } + + /// Lower bound on the nth component + doublereal lowerBound(int n) const { return m_min[n]; } /** - * Base class for one-dimensional domains. + * Prepare to do time stepping with time step dt. Copy the + * internally-stored solution at the last time step to array + * x0. */ - class Domain1D { - public: - - /** - * Constructor. - * @param nv Number of variables at each grid point. - * @param points Number of grid points. - */ - Domain1D(int nv=1, int points=1, - doublereal time = 0.0) : - m_rdt(0.0), - m_time(time), - m_container(0), - m_index(-1), - m_type(0), - m_iloc(0), - m_jstart(0), - m_left(0), - m_right(0), - m_id("-"), m_desc("-"), - m_refiner(0), m_bw(-1) { - resize(nv, points); - } - - /// Destructor. Does nothing - virtual ~Domain1D(){ delete m_refiner; } - - /// Domain type flag. - const int domainType() { return m_type; } - - /** - * The left-to-right location of this domain. - */ - const int domainIndex() { return m_index; } - - /** - * True if the domain is a connector domain. - */ - bool isConnector() { return (m_type >= cConnectorType); } - - /** - * The container holding this domain. - */ - const OneDim& container() const { return *m_container; } - - /** - * Specify the container object for this domain, and the - * position of this domain in the list. - */ - void setContainer(OneDim* c, int index){ - m_container = c; - m_index = index; - } - - /* - * Set the Jacobian bandwidth. See the discussion of method bandwidth. - */ - void setBandwidth(int bw = -1) { - m_bw = bw; - } - - /** - * Set the Jacobian bandwith for this domain. When class - * OneDim computes the bandwidth of the overall multi-domain - * problem (in OneDim::resize()), it calls this method for the - * bandwidth of each domain. If setBandwidth has not been - * called, then a negative bandwidth is returned, in which - * case OneDim assumes that this domain is dense -- that is, - * at each point, all components depend on the value of all - * other components at that point. In this case, the bandwidth - * is bw = 2*nComponents() - 1. However, if this domain - * contains some components that are uncoupled from other - * components at the same point, then this default bandwidth - * may greatly overestimate the true bandwidth, with a - * substantial penalty in performance. For such domains, use - * method setBandwidth to specify the bandwidth before passing - * this domain to the Sim1D or OneDim constructor. - */ - int bandwidth() { return m_bw; } - - /** - * Initialize. This method is called by OneDim::init() for - * each domain once at the beginning of a simulation. Base - * class method does nothing, but may be overloaded. - */ - virtual void init(){ } - - virtual void setInitialState(doublereal* xlocal = 0){} - virtual void setState(int point, const doublereal* state, doublereal* x) {} - - /** - * Resize the domain to have nv components and np grid points. - * This method is virtual so that subclasses can perform other - * actions required to resize the domain. - */ - virtual void resize(int nv, int np) { - // if the number of components is being changed, then a - // new grid refiner is required. - if (nv != m_nv || !m_refiner) { - m_nv = nv; - delete m_refiner; - m_refiner = new Refiner(*this); - } - m_nv = nv; - m_td.resize(m_nv, 1); - m_name.resize(m_nv,""); - m_max.resize(m_nv, 0.0); - m_min.resize(m_nv, 0.0); - m_rtol_ss.resize(m_nv, 1.0e-8); - m_atol_ss.resize(m_nv, 1.0e-15); - m_rtol_ts.resize(m_nv, 1.0e-8); - m_atol_ts.resize(m_nv, 1.0e-15); - m_points = np; - m_z.resize(np, 0.0); - m_slast.resize(m_nv * m_points, 0.0); - locate(); - } - - /// Return a reference to the grid refiner. - Refiner& refiner() { return *m_refiner; } - - /// Number of components at each grid point. - int nComponents() const { return m_nv; } - - /// Number of grid points in this domain. - int nPoints() const { return m_points; } - - /// Name of the nth component. May be overloaded. - virtual std::string componentName(int n) const { - if (m_name[n] != "") return m_name[n]; - else return "component " + int2str(n); - } - - void setComponentName(int n, std::string name) { - m_name[n] = name; - } - - void setComponentType(int n, int ctype) { - if (ctype == 0) setAlgebraic(n); - } - - /// index of component with name \a name. - int componentIndex(std::string name) const { - int nc = nComponents(); - for (int n = 0; n < nc; n++) { - if (name == componentName(n)) return n; - } - throw CanteraError("Domain1D::componentIndex", - "no component named "+name); - } - - /** - * Set the lower and upper bounds for each solution component. - */ - void setBounds(int nl, const doublereal* lower, - int nu, const doublereal* upper) { - if (nl < m_nv || nu < m_nv) - throw CanteraError("Domain1D::setBounds", - "wrong array size for solution bounds. " - "Size should be at least "+int2str(m_nv)); - std::copy(upper, upper + m_nv, m_max.begin()); - std::copy(lower, lower + m_nv, m_min.begin()); - } - - void setBounds(int n, doublereal lower, doublereal upper) { - m_min[n] = lower; - m_max[n] = upper; - } - - /// set the error tolerances for all solution components. - void setTolerances(int nr, const doublereal* rtol, - int na, const doublereal* atol, int ts = 0); - - /// set the error tolerances for solution component \a n. - void setTolerances(int n, doublereal rtol, doublereal atol, int ts = 0); - - //added by Karl Meredith - /// set scalar error tolerances. All solution components will - /// have the same relative and absolute error tolerances. - void setTolerances(doublereal rtol, doublereal atol,int ts=0); - - //added by Karl Meredith - void setTolerancesTS(doublereal rtol, doublereal atol); - - //added by Karl Meredith - void setTolerancesSS(doublereal rtol, doublereal atol); - - /// Relative tolerance of the nth component. - doublereal rtol(int n) { return (m_rdt == 0.0 ? m_rtol_ss[n] : m_rtol_ts[n]); } - - /// Absolute tolerance of the nth component. - doublereal atol(int n) { return (m_rdt == 0.0 ? m_atol_ss[n] : m_atol_ts[n]); } - - /// Upper bound on the nth component. - doublereal upperBound(int n) const { return m_max[n]; } - - /// Lower bound on the nth component - doublereal lowerBound(int n) const { return m_min[n]; } - - - /** - * Prepare to do time stepping with time step dt. Copy the - * internally-stored solution at the last time step to array - * x0. - */ - void initTimeInteg(doublereal dt, const doublereal* x0) { - std::copy(x0 + loc(), x0 + loc() + size(), m_slast.begin()); - m_rdt = 1.0/dt; - } - - /** - * Prepare to solve the steady-state problem. - * Set the internally-stored reciprocal of the time step to 0,0 - */ - void setSteadyMode() { m_rdt = 0.0; } - - /// True if in steady-state mode - bool steady() { return (m_rdt == 0.0); } - - /// True if not in steady-state mode - bool transient() { return (m_rdt != 0.0); } - - /** - * Set this if something has changed in the governing - * equations (e.g. the value of a constant has been changed, - * so that the last-computed Jacobian is no longer valid. - * Note: see file OneDim.cpp for the implementation of this method. - */ - void needJacUpdate(); - - /** - * Evaluate the steady-state residual at all points, even if in - * transient mode. Used only to print diagnostic output. - */ - void evalss(doublereal* x, doublereal* r, integer* mask) { - eval(-1,x,r,mask,0.0); - } - - //! Evaluate the residual function at point j. If j < 0, - //! evaluate the residual function at all points. - /*! - * @param j Grid point j - * @param x Soln vector. This is the input. - * @param r residual this is the output. - */ - virtual void eval(int j, doublereal* x, doublereal* r, - integer* mask, doublereal rdt=0.0); - - virtual doublereal residual(doublereal* x, int n, int j) { - throw CanteraError("Domain1D::residual","residual function must be overloaded in derived class "+id()); - } - - int timeDerivativeFlag(int n) { return m_td[n];} - void setAlgebraic(int n) { m_td[n] = 0; } - - /** - * Does nothing. - */ - virtual void update(doublereal* x) {} - - doublereal time() const { return m_time;} - void incrementTime(doublereal dt) { m_time += dt; } - size_t index(int n, int j) const { return m_nv*j + n; } - doublereal value(const doublereal* x, int n, int j) const { - return x[index(n,j)]; - } - - virtual void setJac(MultiJac* jac){} - virtual void save(XML_Node& o, doublereal* sol) { - throw CanteraError("Domain1D::save","base class method called"); - } - - int size() const { return m_nv*m_points; } - - /** - * Find the index of the first grid point in this domain, and - * the start of its variables in the global solution vector. - */ - void locate() { - - if (m_left) { - // there is a domain on the left, so the first grid point - // in this domain is one more than the last one on the left - m_jstart = m_left->lastPoint() + 1; - - // the starting location in the solution vector - m_iloc = m_left->loc() + m_left->size(); - } - else { - // this is the left-most domain - m_jstart = 0; - m_iloc = 0; - } - // if there is a domain to the right of this one, then - // repeat this for it - if (m_right) m_right->locate(); - } - - /** - * Location of the start of the local solution vector in the global - * solution vector, - */ - virtual int loc(int j = 0) const { return m_iloc; } - - /** - * The index of the first (i.e., left-most) grid point - * belonging to this domain. - */ - int firstPoint() const { return m_jstart; } - - /** - * The index of the last (i.e., right-most) grid point - * belonging to this domain. - */ - int lastPoint() const { return m_jstart + m_points - 1; } - - /** - * Set the left neighbor to domain 'left.' Method 'locate' is - * called to update the global positions of this domain and - * all those to its right. - */ - void linkLeft(Domain1D* left) { - m_left = left; - locate(); - } - - /** - * Set the right neighbor to domain 'right.' - */ - void linkRight(Domain1D* right) { m_right = right; } - - /** - * Append domain 'right' to this one, and update all links. - */ - void append(Domain1D* right) { - linkRight(right); - right->linkLeft(this); - } - - /** - * Return a pointer to the left neighbor. - */ - Domain1D* left() const { return m_left; } - - /** - * Return a pointer to the right neighbor. - */ - Domain1D* right() const { return m_right; } - - /** - * Value of component n at point j in the previous solution. - */ - double prevSoln(int n, int j) const { - return m_slast[m_nv*j + n]; - } - - /** - * Specify an identifying tag for this domain. - */ - void setID(const std::string& s) {m_id = s;} - - std::string id() { - if (m_id != "") return m_id; - else return std::string("domain ") + int2str(m_index); - } - - /** - * Specify descriptive text for this domain. - */ - void setDesc(const std::string& s) {m_desc = s;} - const std::string& desc() { return m_desc; } - - virtual void getTransientMask(integer* mask){} - - virtual void showSolution_s(std::ostream& s, const doublereal* x) {} - virtual void showSolution(const doublereal* x); - - virtual void restore(const XML_Node& dom, doublereal* soln) {} - - doublereal z(int jlocal) const { - return m_z[jlocal]; - } - doublereal zmin() const { return m_z[0]; } - doublereal zmax() const { return m_z[m_points - 1]; } - - - void setProfile(std::string name, doublereal* values, doublereal* soln) { - int n, j; - for (n = 0; n < m_nv; n++) { - if (name == componentName(n)) { - for (j = 0; j < m_points; j++) { - soln[index(n, j) + m_iloc] = values[j]; - } - return; - } - } - throw CanteraError("Domain1D::setProfile", - "unknown component: "+name); - } - - vector_fp& grid() { return m_z; } - const vector_fp& grid() const { return m_z; } - doublereal grid(int point) { return m_z[point]; } - - virtual void setupGrid(int n, const doublereal* z); - - void setGrid(int n, const doublereal* z); - - /** - * Writes some or all initial solution values into the global - * solution array, beginning at the location pointed to by - * x. This method is called by the Sim1D constructor, and - * allows default values or ones that have been set locally - * prior to installing this domain into the container to be - * written to the global solution vector. - */ - virtual void _getInitialSoln(doublereal* x); - - /** - * Initial value of solution component \a n at grid point \a j. - */ - virtual doublereal initialValue(int n, int j); - - /** - * In some cases, a domain may need to set parameters that - * depend on the initial solution estimate. In such cases, the - * parameters may be set in method _finalize. This method is - * called just before the Newton solver is called, and the x - * array is guaranteed to be the local solution vector for - * this domain that will be used as the initial guess. If no - * such parameters need to be set, then method _finalize does - * not need to be overloaded. - */ - virtual void _finalize(const doublereal* x) {} - - //added by Karl Meredith - doublereal m_zfixed; - doublereal m_tfixed; - - bool m_adiabatic; - - protected: - - doublereal m_rdt; - int m_nv; - int m_points; - vector_fp m_slast; - doublereal m_time; - vector_fp m_max; - vector_fp m_min; - vector_fp m_rtol_ss, m_rtol_ts; - vector_fp m_atol_ss, m_atol_ts; - vector_fp m_z; - OneDim* m_container; - int m_index; - int m_type; - - //! Starting location within the solution vector for unknowns - //! that correspond to this domain - /*! - * Remember there may be multiple domains associated with - * this problem - */ - int m_iloc; - - int m_jstart; - - Domain1D *m_left, *m_right; - std::string m_id, m_desc; - Refiner* m_refiner; - vector_int m_td; - std::vector m_name; - int m_bw; - - private: - - }; + void initTimeInteg(doublereal dt, const doublereal* x0) { + std::copy(x0 + loc(), x0 + loc() + size(), m_slast.begin()); + m_rdt = 1.0/dt; + } + + /** + * Prepare to solve the steady-state problem. + * Set the internally-stored reciprocal of the time step to 0,0 + */ + void setSteadyMode() { m_rdt = 0.0; } + + /// True if in steady-state mode + bool steady() { return (m_rdt == 0.0); } + + /// True if not in steady-state mode + bool transient() { return (m_rdt != 0.0); } + + /** + * Set this if something has changed in the governing + * equations (e.g. the value of a constant has been changed, + * so that the last-computed Jacobian is no longer valid. + * Note: see file OneDim.cpp for the implementation of this method. + */ + void needJacUpdate(); + + /** + * Evaluate the steady-state residual at all points, even if in + * transient mode. Used only to print diagnostic output. + */ + void evalss(doublereal* x, doublereal* r, integer* mask) { + eval(-1,x,r,mask,0.0); + } + + //! Evaluate the residual function at point j. If j < 0, + //! evaluate the residual function at all points. + /*! + * @param j Grid point j + * @param x Soln vector. This is the input. + * @param r residual this is the output. + */ + virtual void eval(int j, doublereal* x, doublereal* r, + integer* mask, doublereal rdt=0.0); + + virtual doublereal residual(doublereal* x, int n, int j) { + throw CanteraError("Domain1D::residual","residual function must be overloaded in derived class "+id()); + } + + int timeDerivativeFlag(int n) { return m_td[n];} + void setAlgebraic(int n) { m_td[n] = 0; } + + /** + * Does nothing. + */ + virtual void update(doublereal* x) {} + + doublereal time() const { return m_time;} + void incrementTime(doublereal dt) { m_time += dt; } + size_t index(int n, int j) const { return m_nv*j + n; } + doublereal value(const doublereal* x, int n, int j) const { + return x[index(n,j)]; + } + + virtual void setJac(MultiJac* jac){} + + //! Save the current solution for this domain into an XML_Node + /*! + * Base class version of the general domain1D save function. This + * base class version will throw an error condition. Inherited classes + * will know how to save the solution vector. + * + * @param o XML_Node to save the solution to. + * @param sol Current value of the solution vector. + * The object will pick out which part of the solution + * vector pertains to this object. + */ + virtual void save(XML_Node& o, const doublereal * const sol) { + throw CanteraError("Domain1D::save","base class method called"); + } + + int size() const { return m_nv*m_points; } + + /** + * Find the index of the first grid point in this domain, and + * the start of its variables in the global solution vector. + */ + void locate() { + + if (m_left) { + // there is a domain on the left, so the first grid point + // in this domain is one more than the last one on the left + m_jstart = m_left->lastPoint() + 1; + + // the starting location in the solution vector + m_iloc = m_left->loc() + m_left->size(); + } + else { + // this is the left-most domain + m_jstart = 0; + m_iloc = 0; + } + // if there is a domain to the right of this one, then + // repeat this for it + if (m_right) m_right->locate(); + } + + /** + * Location of the start of the local solution vector in the global + * solution vector, + */ + virtual int loc(int j = 0) const { return m_iloc; } + + /** + * The index of the first (i.e., left-most) grid point + * belonging to this domain. + */ + int firstPoint() const { return m_jstart; } + + /** + * The index of the last (i.e., right-most) grid point + * belonging to this domain. + */ + int lastPoint() const { return m_jstart + m_points - 1; } + + /** + * Set the left neighbor to domain 'left.' Method 'locate' is + * called to update the global positions of this domain and + * all those to its right. + */ + void linkLeft(Domain1D* left) { + m_left = left; + locate(); + } + + /** + * Set the right neighbor to domain 'right.' + */ + void linkRight(Domain1D* right) { m_right = right; } + + /** + * Append domain 'right' to this one, and update all links. + */ + void append(Domain1D* right) { + linkRight(right); + right->linkLeft(this); + } + + /** + * Return a pointer to the left neighbor. + */ + Domain1D* left() const { return m_left; } + + /** + * Return a pointer to the right neighbor. + */ + Domain1D* right() const { return m_right; } + + /** + * Value of component n at point j in the previous solution. + */ + double prevSoln(int n, int j) const { + return m_slast[m_nv*j + n]; + } + + /** + * Specify an identifying tag for this domain. + */ + void setID(const std::string& s) {m_id = s;} + + std::string id() { + if (m_id != "") return m_id; + else return std::string("domain ") + int2str(m_index); + } + + /** + * Specify descriptive text for this domain. + */ + void setDesc(const std::string& s) {m_desc = s;} + const std::string& desc() { return m_desc; } + + virtual void getTransientMask(integer* mask){} + + virtual void showSolution_s(std::ostream& s, const doublereal* x) {} + virtual void showSolution(const doublereal* x); + + virtual void restore(const XML_Node& dom, doublereal* soln) {} + + doublereal z(int jlocal) const { + return m_z[jlocal]; + } + doublereal zmin() const { return m_z[0]; } + doublereal zmax() const { return m_z[m_points - 1]; } + + + void setProfile(std::string name, doublereal* values, doublereal* soln) { + int n, j; + for (n = 0; n < m_nv; n++) { + if (name == componentName(n)) { + for (j = 0; j < m_points; j++) { + soln[index(n, j) + m_iloc] = values[j]; + } + return; + } + } + throw CanteraError("Domain1D::setProfile", + "unknown component: "+name); + } + + vector_fp& grid() { return m_z; } + const vector_fp& grid() const { return m_z; } + doublereal grid(int point) { return m_z[point]; } + + virtual void setupGrid(int n, const doublereal* z); + + void setGrid(int n, const doublereal* z); + + /** + * Writes some or all initial solution values into the global + * solution array, beginning at the location pointed to by + * x. This method is called by the Sim1D constructor, and + * allows default values or ones that have been set locally + * prior to installing this domain into the container to be + * written to the global solution vector. + */ + virtual void _getInitialSoln(doublereal* x); + + /** + * Initial value of solution component \a n at grid point \a j. + */ + virtual doublereal initialValue(int n, int j); + + /** + * In some cases, a domain may need to set parameters that + * depend on the initial solution estimate. In such cases, the + * parameters may be set in method _finalize. This method is + * called just before the Newton solver is called, and the x + * array is guaranteed to be the local solution vector for + * this domain that will be used as the initial guess. If no + * such parameters need to be set, then method _finalize does + * not need to be overloaded. + */ + virtual void _finalize(const doublereal* x) {} + + //added by Karl Meredith + doublereal m_zfixed; + doublereal m_tfixed; + + bool m_adiabatic; + + protected: + + doublereal m_rdt; + int m_nv; + int m_points; + vector_fp m_slast; + doublereal m_time; + vector_fp m_max; + vector_fp m_min; + vector_fp m_rtol_ss, m_rtol_ts; + vector_fp m_atol_ss, m_atol_ts; + vector_fp m_z; + OneDim* m_container; + int m_index; + int m_type; + + //! Starting location within the solution vector for unknowns + //! that correspond to this domain + /*! + * Remember there may be multiple domains associated with + * this problem + */ + int m_iloc; + + int m_jstart; + + Domain1D *m_left, *m_right; + std::string m_id, m_desc; + Refiner* m_refiner; + vector_int m_td; + std::vector m_name; + int m_bw; + + private: + + }; } #endif diff --git a/Cantera/src/oneD/Inlet1D.h b/Cantera/src/oneD/Inlet1D.h index 75bea5332..b12fc99a3 100644 --- a/Cantera/src/oneD/Inlet1D.h +++ b/Cantera/src/oneD/Inlet1D.h @@ -162,7 +162,7 @@ namespace Cantera { virtual void init(); virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); protected: @@ -196,7 +196,7 @@ namespace Cantera { virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); virtual void _finalize(const doublereal* x) {} virtual void _getInitialSoln(doublereal* x) { @@ -227,7 +227,7 @@ namespace Cantera { virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); virtual void _finalize(const doublereal* x) { ; //m_temp = x[0]; @@ -259,7 +259,7 @@ namespace Cantera { virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); virtual void _finalize(const doublereal* x) { ; //m_temp = x[0]; @@ -306,7 +306,7 @@ namespace Cantera { virtual void init(); virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); protected: @@ -340,7 +340,7 @@ namespace Cantera { virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); virtual void _getInitialSoln(doublereal* x) { @@ -400,7 +400,7 @@ namespace Cantera { virtual void eval(int jg, doublereal* xg, doublereal* rg, integer* diagg, doublereal rdt); - virtual void save(XML_Node& o, doublereal* soln); + virtual void save(XML_Node& o, const doublereal * const soln); virtual void restore(const XML_Node& dom, doublereal* soln); virtual void _getInitialSoln(doublereal* x) { diff --git a/Cantera/src/oneD/Resid1D.h b/Cantera/src/oneD/Resid1D.h index 26eeed9aa..34dcda18e 100644 --- a/Cantera/src/oneD/Resid1D.h +++ b/Cantera/src/oneD/Resid1D.h @@ -221,7 +221,19 @@ namespace Cantera { } virtual void setJac(MultiJac* jac){} - virtual void save(XML_Node& o, doublereal* sol) { + + //! Save the current solution for this domain into an XML_Node + /*! + * Base class version of the general domain1D save function. This + * base class version will throw an error condition. Inherited classes + * will know how to save the solution vector. + * + * @param o XML_Node to save the solution to. + * @param sol Current value of the solution vector. + * The object will pick out which part of the solution + * vector pertains to this object. + */ + virtual void save(XML_Node& o, const doublereal * const sol) { throw CanteraError("Resid1D::save","base class method called"); } diff --git a/Cantera/src/oneD/Solid1D.cpp b/Cantera/src/oneD/Solid1D.cpp index 42e6b5c3c..c9797b7fa 100644 --- a/Cantera/src/oneD/Solid1D.cpp +++ b/Cantera/src/oneD/Solid1D.cpp @@ -544,7 +544,7 @@ namespace Cantera { - void Solid1D::save(XML_Node& o, doublereal* sol) { + void Solid1D::save(XML_Node& o, const doublereal * const sol) { int k; ArrayViewer soln(m_nv, m_points, sol + loc()); diff --git a/Cantera/src/oneD/Solid1D.h b/Cantera/src/oneD/Solid1D.h index 967f7c353..70c4cf64f 100644 --- a/Cantera/src/oneD/Solid1D.h +++ b/Cantera/src/oneD/Solid1D.h @@ -197,7 +197,15 @@ namespace Cantera { virtual void showSolution(const doublereal* x); - virtual void save(XML_Node& o, doublereal* sol); + //! Save the current solution for this domain into an XML_Node + /*! + * + * @param o XML_Node to save the solution to. + * @param sol Current value of the solution vector. + * The object will pick out which part of the solution + * vector pertains to this object. + */ + virtual void save(XML_Node& o, const doublereal * const sol); virtual void restore(XML_Node& dom, doublereal* soln); diff --git a/Cantera/src/oneD/StFlow.cpp b/Cantera/src/oneD/StFlow.cpp index 84a388030..826cfd3f7 100644 --- a/Cantera/src/oneD/StFlow.cpp +++ b/Cantera/src/oneD/StFlow.cpp @@ -1154,10 +1154,10 @@ namespace Cantera { - void StFlow::save(XML_Node& o, doublereal* sol) { + void StFlow::save(XML_Node& o, const doublereal * const sol) { int k; - ArrayViewer soln(m_nv, m_points, sol + loc()); + ArrayViewer soln(m_nv, m_points, const_cast(sol) + loc()); XML_Node& flow = (XML_Node&)o.addChild("domain"); flow.addAttribute("type",flowType()); diff --git a/Cantera/src/oneD/StFlow.h b/Cantera/src/oneD/StFlow.h index 1b608927d..ffab5c402 100644 --- a/Cantera/src/oneD/StFlow.h +++ b/Cantera/src/oneD/StFlow.h @@ -182,7 +182,15 @@ namespace Cantera { virtual void showSolution(const doublereal* x); - virtual void save(XML_Node& o, doublereal* sol); + //! Save the current solution for this domain into an XML_Node + /*! + * + * @param o XML_Node to save the solution to. + * @param sol Current value of the solution vector. + * The object will pick out which part of the solution + * vector pertains to this object. + */ + virtual void save(XML_Node& o, const doublereal * const sol); virtual void restore(const XML_Node& dom, doublereal* soln); diff --git a/Cantera/src/oneD/Surf1D.h b/Cantera/src/oneD/Surf1D.h index 44e8013e4..d450253a2 100644 --- a/Cantera/src/oneD/Surf1D.h +++ b/Cantera/src/oneD/Surf1D.h @@ -273,7 +273,7 @@ namespace Cantera { } } - virtual void save(XML_Node& o, doublereal* soln) { + virtual void save(XML_Node& o, const doublereal * const soln) { doublereal* s = soln + loc(); XML_Node& surf = o.addChild("surface"); for (int k = 0; k < m_nsp; k++) { diff --git a/Cantera/src/oneD/boundaries1D.cpp b/Cantera/src/oneD/boundaries1D.cpp index 31a17c903..678f07f6f 100644 --- a/Cantera/src/oneD/boundaries1D.cpp +++ b/Cantera/src/oneD/boundaries1D.cpp @@ -242,8 +242,8 @@ namespace Cantera { } void Inlet1D:: - save(XML_Node& o, doublereal* soln) { - doublereal* s = soln + loc(); + save(XML_Node& o, const doublereal* const soln) { + const doublereal* s = soln + loc(); XML_Node& inlt = o.addChild("domain"); inlt.addAttribute("id",id()); inlt.addAttribute("points",1); @@ -305,7 +305,7 @@ namespace Cantera { } void Empty1D:: - save(XML_Node& o, doublereal* soln) { + save(XML_Node& o, const doublereal * const soln) { XML_Node& symm = o.addChild("domain"); symm.addAttribute("id",id()); symm.addAttribute("points",1); @@ -385,7 +385,7 @@ namespace Cantera { void Symm1D:: - save(XML_Node& o, doublereal* soln) { + save(XML_Node& o, const doublereal * const soln) { XML_Node& symm = o.addChild("domain"); symm.addAttribute("id",id()); symm.addAttribute("points",1); @@ -480,7 +480,7 @@ namespace Cantera { void Outlet1D:: - save(XML_Node& o, doublereal* soln) { + save(XML_Node& o, const doublereal * const soln) { XML_Node& outlt = o.addChild("domain"); outlt.addAttribute("id",id()); outlt.addAttribute("points",1); @@ -617,7 +617,7 @@ namespace Cantera { void OutletRes1D:: - save(XML_Node& o, doublereal* soln) { + save(XML_Node& o, const doublereal * const soln) { XML_Node& outlt = o.addChild("domain"); outlt.addAttribute("id",id()); outlt.addAttribute("points",1); @@ -691,8 +691,8 @@ namespace Cantera { } void Surf1D:: - save(XML_Node& o, doublereal* soln) { - doublereal* s = soln + loc(); + save(XML_Node& o, const doublereal * const soln) { + const doublereal* s = soln + loc(); //XML_Node& inlt = o.addChild("inlet"); XML_Node& inlt = o.addChild("domain"); inlt.addAttribute("id",id()); @@ -851,8 +851,8 @@ namespace Cantera { } void ReactingSurf1D:: - save(XML_Node& o, doublereal* soln) { - doublereal* s = soln + loc(); + save(XML_Node& o, const doublereal * const soln) { + const doublereal* s = soln + loc(); //XML_Node& inlt = o.addChild("inlet"); XML_Node& inlt = o.addChild("domain"); inlt.addAttribute("id",id()); From 48261703d43d4017b68b55ad96c9a0c88e6f55d3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 20 Oct 2009 22:26:24 +0000 Subject: [PATCH 002/446] Added the object PDSS_SSVol. This has more functionality than PDSS_ConstVol in that there are a range of models for fitting the standard state volume. Removed executable flags. removed the function pdssType. --- Cantera/src/thermo/ConstDensityThermo.cpp | 0 Cantera/src/thermo/ConstDensityThermo.h | 0 Cantera/src/thermo/Constituents.cpp | 0 Cantera/src/thermo/Constituents.h | 0 Cantera/src/thermo/NasaPoly1.h | 0 Cantera/src/thermo/NasaThermo.h | 0 Cantera/src/thermo/PDSS_ConstVol.h | 1 - Cantera/src/thermo/PDSS_HKFT.h | 1 - Cantera/src/thermo/PDSS_IdealGas.h | 2 - Cantera/src/thermo/PDSS_IonsFromNeutral.h | 2 - Cantera/src/thermo/PDSS_SSVol.cpp | 427 ++++++++++++++++++ Cantera/src/thermo/PDSS_SSVol.h | 452 ++++++++++++++++++++ Cantera/src/thermo/Phase.cpp | 0 Cantera/src/thermo/Phase.h | 0 Cantera/src/thermo/ShomatePoly.h | 0 Cantera/src/thermo/ShomateThermo.h | 0 Cantera/src/thermo/SpeciesThermo.h | 0 Cantera/src/thermo/SpeciesThermoFactory.cpp | 0 Cantera/src/thermo/SpeciesThermoFactory.h | 0 Cantera/src/thermo/SpeciesThermoMgr.h | 0 Cantera/src/thermo/State.h | 0 Cantera/src/thermo/ThermoPhase.h | 0 Cantera/src/thermo/VPSSMgr_General.cpp | 10 + Cantera/src/thermo/mix_defs.h | 18 + Cantera/src/thermo/speciesThermoTypes.h | 0 25 files changed, 907 insertions(+), 6 deletions(-) mode change 100755 => 100644 Cantera/src/thermo/ConstDensityThermo.cpp mode change 100755 => 100644 Cantera/src/thermo/ConstDensityThermo.h mode change 100755 => 100644 Cantera/src/thermo/Constituents.cpp mode change 100755 => 100644 Cantera/src/thermo/Constituents.h mode change 100755 => 100644 Cantera/src/thermo/NasaPoly1.h mode change 100755 => 100644 Cantera/src/thermo/NasaThermo.h create mode 100644 Cantera/src/thermo/PDSS_SSVol.cpp create mode 100644 Cantera/src/thermo/PDSS_SSVol.h mode change 100755 => 100644 Cantera/src/thermo/Phase.cpp mode change 100755 => 100644 Cantera/src/thermo/Phase.h mode change 100755 => 100644 Cantera/src/thermo/ShomatePoly.h mode change 100755 => 100644 Cantera/src/thermo/ShomateThermo.h mode change 100755 => 100644 Cantera/src/thermo/SpeciesThermo.h mode change 100755 => 100644 Cantera/src/thermo/SpeciesThermoFactory.cpp mode change 100755 => 100644 Cantera/src/thermo/SpeciesThermoFactory.h mode change 100755 => 100644 Cantera/src/thermo/SpeciesThermoMgr.h mode change 100755 => 100644 Cantera/src/thermo/State.h mode change 100755 => 100644 Cantera/src/thermo/ThermoPhase.h mode change 100755 => 100644 Cantera/src/thermo/mix_defs.h mode change 100755 => 100644 Cantera/src/thermo/speciesThermoTypes.h diff --git a/Cantera/src/thermo/ConstDensityThermo.cpp b/Cantera/src/thermo/ConstDensityThermo.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/ConstDensityThermo.h b/Cantera/src/thermo/ConstDensityThermo.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/Constituents.cpp b/Cantera/src/thermo/Constituents.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/NasaPoly1.h b/Cantera/src/thermo/NasaPoly1.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/NasaThermo.h b/Cantera/src/thermo/NasaThermo.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/PDSS_ConstVol.h b/Cantera/src/thermo/PDSS_ConstVol.h index 0d668f1db..eaea66322 100644 --- a/Cantera/src/thermo/PDSS_ConstVol.h +++ b/Cantera/src/thermo/PDSS_ConstVol.h @@ -99,7 +99,6 @@ namespace Cantera { * @name Utilities * @{ */ - virtual int pdssType() const { return -1; } /** * @} diff --git a/Cantera/src/thermo/PDSS_HKFT.h b/Cantera/src/thermo/PDSS_HKFT.h index cdb95103d..987005f72 100644 --- a/Cantera/src/thermo/PDSS_HKFT.h +++ b/Cantera/src/thermo/PDSS_HKFT.h @@ -126,7 +126,6 @@ namespace Cantera { * @name Utilities * @{ */ - virtual int pdssType() const { return -1; } /** * @} diff --git a/Cantera/src/thermo/PDSS_IdealGas.h b/Cantera/src/thermo/PDSS_IdealGas.h index 9cd996f51..909581ec0 100644 --- a/Cantera/src/thermo/PDSS_IdealGas.h +++ b/Cantera/src/thermo/PDSS_IdealGas.h @@ -101,8 +101,6 @@ namespace Cantera { * @name Utilities * @{ */ - virtual int pdssType() const { return -1; } - /** * @} diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.h b/Cantera/src/thermo/PDSS_IonsFromNeutral.h index 8c545355c..7399c6953 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.h +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.h @@ -103,8 +103,6 @@ namespace Cantera { * @name Utilities * @{ */ - virtual int pdssType() const { return -1; } - /** * @} diff --git a/Cantera/src/thermo/PDSS_SSVol.cpp b/Cantera/src/thermo/PDSS_SSVol.cpp new file mode 100644 index 000000000..78a4260dd --- /dev/null +++ b/Cantera/src/thermo/PDSS_SSVol.cpp @@ -0,0 +1,427 @@ +/** + * @file PDSS_SSVol.cpp + * Implementation of a pressure dependent standard state + * virtual function. + */ +/* + * Copywrite (2006) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Id: PDSS_SSVol.cpp,v 1.10 2009/01/04 06:34:20 hkmoffa Exp $ + */ + +#include "ct_defs.h" +#include "xml.h" +#include "ctml.h" +#include "PDSS_SSVol.h" +#include "ThermoFactory.h" + +#include "VPStandardStateTP.h" + +using namespace std; + +namespace Cantera { + /** + * Basic list of constructors and duplicators + */ + + PDSS_SSVol::PDSS_SSVol(VPStandardStateTP *tp, int spindex) : + PDSS(tp, spindex), + volumeModel_(cSSVOLUME_CONSTANT), + m_constMolarVolume(-1.0) + { + m_pdssType = cPDSS_SSVOL; + TCoeff_[0] = 0.0; + TCoeff_[1] = 0.0; + TCoeff_[2] = 0.0; + } + + + PDSS_SSVol::PDSS_SSVol(VPStandardStateTP *tp, int spindex, std::string inputFile, std::string id) : + PDSS(tp, spindex), + volumeModel_(cSSVOLUME_CONSTANT), + m_constMolarVolume(-1.0) + { + + m_pdssType = cPDSS_SSVOL; + constructPDSSFile(tp, spindex, inputFile, id); + } + + PDSS_SSVol::PDSS_SSVol(VPStandardStateTP *tp, int spindex, + const XML_Node& speciesNode, + const XML_Node& phaseRoot, + bool spInstalled) : + PDSS(tp, spindex), + volumeModel_(cSSVOLUME_CONSTANT), + m_constMolarVolume(-1.0) + { + m_pdssType = cPDSS_SSVOL; + constructPDSSXML(tp, spindex, speciesNode, phaseRoot, spInstalled) ; + } + + + PDSS_SSVol::PDSS_SSVol(const PDSS_SSVol &b) : + PDSS(b), + volumeModel_(cSSVOLUME_CONSTANT), + m_constMolarVolume(-1.0) + { + /* + * Use the assignment operator to do the brunt + * of the work for the copy construtor. + */ + *this = b; + } + + /* + * Assignment operator + */ + PDSS_SSVol& PDSS_SSVol::operator=(const PDSS_SSVol&b) { + if (&b == this) return *this; + PDSS::operator=(b); + volumeModel_ = b.volumeModel_; + m_constMolarVolume = b.m_constMolarVolume; + TCoeff_ = b.TCoeff_; + return *this; + } + + PDSS_SSVol::~PDSS_SSVol() { + } + + //! Duplicator + PDSS* PDSS_SSVol::duplMyselfAsPDSS() const { + PDSS_SSVol * idg = new PDSS_SSVol(*this); + return (PDSS *) idg; + } + + /** + * constructPDSSXML: + * + * Initialization of a PDSS_SSVol object using an + * xml file. + * + * This routine is a precursor to initThermo(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void PDSS_SSVol::constructPDSSXML(VPStandardStateTP *tp, int spindex, + const XML_Node& speciesNode, + const XML_Node& phaseNode, bool spInstalled) { + PDSS::initThermo(); + SpeciesThermo &sp = m_tp->speciesThermo(); + m_p0 = sp.refPressure(m_spindex); + + if (!spInstalled) { + throw CanteraError("PDSS_SSVol::constructPDSSXML", "spInstalled false not handled"); + } + + const XML_Node *ss = speciesNode.findByName("standardState"); + if (!ss) { + throw CanteraError("PDSS_SSVol::constructPDSSXML", + "no standardState Node for species " + speciesNode.name()); + } + std::string model = (*ss)["model"]; + if (model == "constant_incompressible" || model == "constant") { + volumeModel_ = cSSVOLUME_CONSTANT; + m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI"); + } else if (model == "temperature_polynomial") { + volumeModel_ = cSSVOLUME_TPOLY; + getFloatArray(*ss, TCoeff_, true, "", "floatArray"); + } else if (model == "density_temperature_polynomial") { + volumeModel_ = cSSVOLUME_DENSITY_TPOLY; + getFloatArray(*ss, TCoeff_, true, "", "floatArray"); + } else { + throw CanteraError("PDSS_SSVol::initThermoXML", + "standardState model for species isn't constant_incompressible: " + speciesNode.name()); + } + std::string id = ""; + + } + + + /** + * constructPDSSFile(): + * + * Initialization of a PDSS_SSVol object using an + * xml file. + * + * This routine is a precursor to initThermo(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void PDSS_SSVol::constructPDSSFile(VPStandardStateTP *tp, int spindex, + std::string inputFile, std::string id) { + + if (inputFile.size() == 0) { + throw CanteraError("PDSS_SSVol::initThermo", + "input file is null"); + } + std::string path = findInputFile(inputFile); + ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("PDSS_SSVol::initThermo","could not open " + +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("PDSS_SSVol::initThermo", + "ERROR: Can not find phase named " + + id + " in file named " + inputFile); + } + + XML_Node& speciesList = fxml_phase->child("speciesArray"); + XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"], + &(fxml_phase->root())); + const vector&sss = tp->speciesNames(); + const XML_Node* s = speciesDB->findByAttr("name", sss[spindex]); + + constructPDSSXML(tp, spindex, *s, *fxml_phase, true); + delete fxml; + } + + void PDSS_SSVol::initThermoXML(const XML_Node& phaseNode, std::string& id) { + PDSS::initThermoXML(phaseNode, id); + m_minTemp = m_spthermo->minTemp(m_spindex); + m_maxTemp = m_spthermo->maxTemp(m_spindex); + m_p0 = m_spthermo->refPressure(m_spindex); + m_mw = m_tp->molecularWeight(m_spindex); + } + + void PDSS_SSVol::initThermo() { + PDSS::initThermo(); + SpeciesThermo &sp = m_tp->speciesThermo(); + m_p0 = sp.refPressure(m_spindex); + m_V0_ptr[m_spindex] = m_constMolarVolume; + m_Vss_ptr[m_spindex] = m_constMolarVolume; + } + + doublereal + PDSS_SSVol::enthalpy_mole() const { + doublereal val = enthalpy_RT(); + doublereal RT = GasConstant * m_temp; + return (val * RT); + } + + doublereal + PDSS_SSVol::enthalpy_RT() const { + doublereal val = m_hss_RT_ptr[m_spindex]; + return (val); + } + + + doublereal + PDSS_SSVol::intEnergy_mole() const { + doublereal pVRT = (m_pres * m_Vss_ptr[m_spindex]) / (GasConstant * m_temp); + doublereal val = m_h0_RT_ptr[m_spindex] - pVRT; + doublereal RT = GasConstant * m_temp; + return (val * RT); + } + + + doublereal + PDSS_SSVol::entropy_mole() const { + doublereal val = entropy_R(); + return (val * GasConstant); + } + + doublereal + PDSS_SSVol::entropy_R() const { + doublereal val = m_sss_R_ptr[m_spindex]; + return (val); + } + + /** + * Calculate the Gibbs free energy in mks units of + * J kmol-1 K-1. + */ + doublereal + PDSS_SSVol::gibbs_mole() const { + doublereal val = gibbs_RT(); + doublereal RT = GasConstant * m_temp; + return (val * RT); + } + + doublereal + PDSS_SSVol::gibbs_RT() const { + doublereal val = m_gss_RT_ptr[m_spindex]; + return (val); + } + + doublereal + PDSS_SSVol::cp_mole() const { + doublereal val = m_cpss_R_ptr[m_spindex]; + return (val * GasConstant); + } + + doublereal + PDSS_SSVol::cp_R() const { + doublereal val = m_cpss_R_ptr[m_spindex]; + return (val); + } + + doublereal + PDSS_SSVol::cv_mole() const { + doublereal val = (cp_mole() - m_V0_ptr[m_spindex]); + return (val); + } + + doublereal + PDSS_SSVol::molarVolume() const { + doublereal val = m_Vss_ptr[m_spindex]; + return (val); + } + + doublereal + PDSS_SSVol::density() const { + doublereal val = m_Vss_ptr[m_spindex]; + return (m_mw/val); + } + + doublereal + PDSS_SSVol::gibbs_RT_ref() const { + doublereal val = m_g0_RT_ptr[m_spindex]; + return (val); + } + + doublereal PDSS_SSVol::enthalpy_RT_ref() const { + doublereal val = m_h0_RT_ptr[m_spindex]; + return (val); + } + + doublereal PDSS_SSVol::entropy_R_ref() const { + doublereal val = m_s0_R_ptr[m_spindex]; + return (val); + } + + doublereal PDSS_SSVol::cp_R_ref() const { + doublereal val = m_cp0_R_ptr[m_spindex]; + return (val); + } + + doublereal PDSS_SSVol::molarVolume_ref() const { + doublereal val = m_V0_ptr[m_spindex]; + return (val); + } + + void PDSS_SSVol::calcMolarVolume() const { + if (volumeModel_ == cSSVOLUME_CONSTANT ) { + m_Vss_ptr[m_spindex] = m_constMolarVolume; + } else if (volumeModel_ == cSSVOLUME_TPOLY) { + m_Vss_ptr[m_spindex] = TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * TCoeff_[2]); + dVdT_ = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2]; + d2VdT2_ = 2.0 * TCoeff_[2]; + } else if (volumeModel_ == cSSVOLUME_DENSITY_TPOLY) { + doublereal dens = (TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * TCoeff_[2])); + m_Vss_ptr[m_spindex] = m_mw / dens; + doublereal dens2 = dens * dens; + doublereal ddensdT = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2]; + doublereal d2densdT2 = 2.0 * TCoeff_[2]; + dVdT_ = - m_mw / (dens2) * (ddensdT); + d2VdT2_ = 2.0 * m_mw / (dens2 * dens) * ddensdT * ddensdT - m_mw / dens2 * d2densdT2; + } else { + throw CanteraError("PDSS_SSVol::calcMolarVolume", "unimplemented"); + } + } + + + /// critical temperature + doublereal PDSS_SSVol::critTemperature() const { + throw CanteraError("PDSS_SSVol::critTemperature()", "unimplemented"); + return (0.0); + } + + /// critical pressure + doublereal PDSS_SSVol::critPressure() const { + throw CanteraError("PDSS_SSVol::critPressure()", "unimplemented"); + return (0.0); + } + + /// critical density + doublereal PDSS_SSVol::critDensity() const { + throw CanteraError("PDSS_SSVol::critDensity()", "unimplemented"); + return (0.0); + } + + + + void PDSS_SSVol::setPressure(doublereal p) { + m_pres = p; + doublereal deltaP = m_pres - m_p0; + if (fabs(deltaP) < 1.0E-10) { + m_hss_RT_ptr[m_spindex] = m_h0_RT_ptr[m_spindex]; + m_sss_R_ptr[m_spindex] = m_s0_R_ptr[m_spindex]; + m_gss_RT_ptr[m_spindex] = m_hss_RT_ptr[m_spindex] - m_sss_R_ptr[m_spindex]; + m_cpss_R_ptr[m_spindex] = m_cp0_R_ptr[m_spindex]; + } else { + doublereal del_pRT = deltaP / (GasConstant * m_temp); + doublereal sV_term = - deltaP / (GasConstant) * dVdT_; + m_hss_RT_ptr[m_spindex] = m_h0_RT_ptr[m_spindex] + sV_term + del_pRT * (m_Vss_ptr[m_spindex]); + m_sss_R_ptr[m_spindex] = m_s0_R_ptr[m_spindex] + sV_term; + m_gss_RT_ptr[m_spindex] = m_hss_RT_ptr[m_spindex] - m_sss_R_ptr[m_spindex]; + m_cpss_R_ptr[m_spindex] = m_cp0_R_ptr[m_spindex] - m_temp * deltaP * d2VdT2_; + } + } + + void PDSS_SSVol::setTemperature(doublereal temp) { + m_temp = temp; + m_spthermo->update_one(m_spindex, temp, m_cp0_R_ptr, m_h0_RT_ptr, m_s0_R_ptr); + calcMolarVolume(); + m_g0_RT_ptr[m_spindex] = m_h0_RT_ptr[m_spindex] - m_s0_R_ptr[m_spindex]; + doublereal deltaP = m_pres - m_p0; + if (fabs(deltaP) < 1.0E-10) { + m_hss_RT_ptr[m_spindex] = m_h0_RT_ptr[m_spindex]; + m_sss_R_ptr[m_spindex] = m_s0_R_ptr[m_spindex]; + m_gss_RT_ptr[m_spindex] = m_hss_RT_ptr[m_spindex] - m_sss_R_ptr[m_spindex]; + m_cpss_R_ptr[m_spindex] = m_cp0_R_ptr[m_spindex]; + } else { + doublereal del_pRT = deltaP / (GasConstant * m_temp); + doublereal sV_term = - deltaP / (GasConstant) * dVdT_; + m_hss_RT_ptr[m_spindex] = m_h0_RT_ptr[m_spindex] + sV_term + del_pRT * (m_Vss_ptr[m_spindex]); + m_sss_R_ptr[m_spindex] = m_s0_R_ptr[m_spindex] + sV_term; + m_gss_RT_ptr[m_spindex] = m_hss_RT_ptr[m_spindex] - m_sss_R_ptr[m_spindex]; + m_cpss_R_ptr[m_spindex] = m_cp0_R_ptr[m_spindex] - m_temp * deltaP * d2VdT2_; + } + } + + + void PDSS_SSVol::setState_TP(doublereal temp, doublereal pres) { + m_pres = pres; + setTemperature(temp); + } + + + void PDSS_SSVol::setState_TR(doublereal temp, doublereal rho) { + doublereal rhoStored = m_mw / m_constMolarVolume; + if (fabs(rhoStored - rho) / (rhoStored + rho) > 1.0E-4) { + throw CanteraError("PDSS_SSVol::setState_TR", + "Inconsistent supplied rho"); + } + setTemperature(temp); + } + + /// saturation pressure + doublereal PDSS_SSVol::satPressure(doublereal t){ + return (1.0E-200); + } + +} diff --git a/Cantera/src/thermo/PDSS_SSVol.h b/Cantera/src/thermo/PDSS_SSVol.h new file mode 100644 index 000000000..422c28ed6 --- /dev/null +++ b/Cantera/src/thermo/PDSS_SSVol.h @@ -0,0 +1,452 @@ +/** + * @file PDSS_SSVol.h + * Declarations for the class PDSS_SSVol (pressure dependent standard state) + * which handles calculations for a single species with an expression for the molar volume in a phase + * given by an enumerated data type + * (see class \ref pdssthermo and \link Cantera::PDSS_SSVol PDSS_SSVol\endlink). + */ +/* + * Copywrite (2006) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Id: PDSS_SSVol.h,v 1.6 2008/10/13 21:01:48 hkmoffa Exp $ + */ + +#ifndef CT_PDSS_SSVOL_H +#define CT_PDSS_SSVOL_H + +#include "PDSS.h" + +namespace Cantera { + class XML_Node; + class VPStandardStateTP; + + //! Class for pressure dependent standard states that use a constant volume model + /*! + * Class for pressure dependent standard states that use a constant volume model. + * + * + * @ingroup pdssthermo + */ + class PDSS_SSVol : public PDSS { + + public: + + /** + * @name Constructors + * @{ + */ + + //! Constructor + /*! + * @param tp Pointer to the ThermoPhase object pertaining to the phase + * @param spindex Species index of the species in the phase + */ + PDSS_SSVol(VPStandardStateTP *tp, int spindex); + + + //! Constructor that initializes the object by examining the input file + //! of the ThermoPhase object + /*! + * This function calls the constructPDSSFile member function. + * + * @param tp Pointer to the ThermoPhase object pertaining to the phase + * @param spindex Species index of the species in the phase + * @param inputFile String name of the input file + * @param id String name of the phase in the input file. The default + * is the empty string, in which case the first phase in the + * file is used. + */ + PDSS_SSVol(VPStandardStateTP *tp, int spindex, + std::string inputFile, std::string id = ""); + + //! Constructor that initializes the object by examining the input file + //! of the ThermoPhase object + /*! + * This function calls the constructPDSSXML member function. + * + * @param vptp_ptr Pointer to the ThermoPhase object pertaining to the phase + * @param spindex Species index of the species in the phase + * @param speciesNode Reference to the species XML tree. + * @param phaseRef Reference to the XML tree containing the phase information. + * @param spInstalled Boolean indicating whether the species is installed yet + * or not. + */ + PDSS_SSVol(VPStandardStateTP *vptp_ptr, int spindex, const XML_Node& speciesNode, + const XML_Node& phaseRef, bool spInstalled); + + //! Copy Constructur + /*! + * @param b Object to be copied + */ + PDSS_SSVol(const PDSS_SSVol &b); + + //! Assignment operator + /*! + * @param b Object to be copeid + */ + PDSS_SSVol& operator=(const PDSS_SSVol&b); + + //! Destructor + virtual ~PDSS_SSVol(); + + //! Duplicator + virtual PDSS *duplMyselfAsPDSS() const; + + /** + * @} + * @name Utilities + * @{ + */ + + /** + * @} + * @name Molar Thermodynamic Properties of the Species Standard State + * in the Solution + * @{ + */ + + //! Return the molar enthalpy in units of J kmol-1 + /*! + * Returns the species standard state enthalpy in J kmol-1 at the + * current temperature and pressure. + * + * @return returns the species standard state enthalpy in J kmol-1 + */ + virtual doublereal enthalpy_mole() const; + + //! Return the standard state molar enthalpy divided by RT + /*! + * Returns the species standard state enthalpy divided by RT at the + * current temperature and pressure. + * + * @return returns the species standard state enthalpy in unitless form + */ + virtual doublereal enthalpy_RT() const; + + //! Return the molar internal Energy in units of J kmol-1 + /*! + * Returns the species standard state internal Energy in J kmol-1 at the + * current temperature and pressure. + * + * @return returns the species standard state internal Energy in J kmol-1 + */ + virtual doublereal intEnergy_mole() const; + + //! Return the molar entropy in units of J kmol-1 K-1 + /*! + * Returns the species standard state entropy in J kmol-1 K-1 at the + * current temperature and pressure. + * + * @return returns the species standard state entropy in J kmol-1 K-1 + */ + virtual doublereal entropy_mole() const; + + //! Return the standard state entropy divided by RT + /*! + * Returns the species standard state entropy divided by RT at the + * current temperature and pressure. + * + * @return returns the species standard state entropy divided by RT + */ + virtual doublereal entropy_R() const; + + //! Return the molar gibbs free energy in units of J kmol-1 + /*! + * Returns the species standard state gibbs free energy in J kmol-1 at the + * current temperature and pressure. + * + * @return returns the species standard state gibbs free energy in J kmol-1 + */ + virtual doublereal gibbs_mole() const; + + //! Return the molar gibbs free energy divided by RT + /*! + * Returns the species standard state gibbs free energy divided by RT at the + * current temperature and pressure. + * + * @return returns the species standard state gibbs free energy divided by RT + */ + virtual doublereal gibbs_RT() const; + + //! Return the molar const pressure heat capacity in units of J kmol-1 K-1 + /*! + * Returns the species standard state Cp in J kmol-1 K-1 at the + * current temperature and pressure. + * + * @return returns the species standard state Cp in J kmol-1 K-1 + */ + virtual doublereal cp_mole() const; + + //! Return the molar const pressure heat capacity divided by RT + /*! + * Returns the species standard state Cp divided by RT at the + * current temperature and pressure. + * + * @return returns the species standard state Cp divided by RT + */ + virtual doublereal cp_R() const; + + //! Return the molar const volume heat capacity in units of J kmol-1 K-1 + /*! + * Returns the species standard state Cv in J kmol-1 K-1 at the + * current temperature and pressure. + * + * @return returns the species standard state Cv in J kmol-1 K-1 + */ + virtual doublereal cv_mole() const; + + //! Return the molar volume at standard state + /*! + * Returns the species standard state molar volume at the + * current temperature and pressure + * + * @return returns the standard state molar volume divided by R + * units are m**3 kmol-1. + */ + virtual doublereal molarVolume() const; + + //! Return the standard state density at standard state + /*! + * Returns the species standard state density at the + * current temperature and pressure + * + * @return returns the standard state density + * units are kg m-3 + */ + virtual doublereal density() const; + + /** + * @} + * @name Properties of the Reference State of the Species + * in the Solution + * @{ + */ + + //! Return the molar gibbs free energy divided by RT at reference pressure + /*! + * Returns the species reference state gibbs free energy divided by RT at the + * current temperature. + * + * @return returns the reference state gibbs free energy divided by RT + */ + virtual doublereal gibbs_RT_ref() const; + + //! Return the molar enthalpy divided by RT at reference pressure + /*! + * Returns the species reference state enthalpy divided by RT at the + * current temperature. + * + * @return returns the reference state enthalpy divided by RT + */ + virtual doublereal enthalpy_RT_ref() const; + + //! Return the molar entropy divided by R at reference pressure + /*! + * Returns the species reference state entropy divided by R at the + * current temperature. + * + * @return returns the reference state entropy divided by R + */ + virtual doublereal entropy_R_ref() const; + + //! Return the molar heat capacity divided by R at reference pressure + /*! + * Returns the species reference state heat capacity divided by R at the + * current temperature. + * + * @return returns the reference state heat capacity divided by R + */ + virtual doublereal cp_R_ref() const; + + //! Return the molar volume at reference pressure + /*! + * Returns the species reference state molar volume at the + * current temperature. + * + * @return returns the reference state molar volume divided by R + * units are m**3 kmol-1. + */ + virtual doublereal molarVolume_ref() const; + + private: + + //! Does the internal calculation of the volume + /*! + * + */ + void calcMolarVolume() const; + + /** + * @} + * @name Mechanical Equation of State Properties + * @{ + */ + + //! Sets the pressure in the object + /*! + * Currently, this sets the pressure in the PDSS object. + * It is indeterminant what happens to the owning VPStandardStateTP + * object and to the VPSSMgr object. + * + * @param pres Pressure to be set (Pascal) + */ + virtual void setPressure(doublereal pres); + + //! Set the internal temperature + /*! + * @param temp Temperature (Kelvin) + */ + virtual void setTemperature(doublereal temp); + + //! Set the internal temperature and pressure + /*! + * @param temp Temperature (Kelvin) + * @param pres pressure (Pascals) + */ + virtual void setState_TP(doublereal temp, doublereal pres); + + + //! Set the internal temperature and density + /*! + * @param temp Temperature (Kelvin) + * @param rho Density (kg m-3) + */ + virtual void setState_TR(doublereal temp, doublereal rho); + + /** + * @} + * @name Miscellaneous properties of the standard state + * @{ + */ + + /// critical temperature + virtual doublereal critTemperature() const; + + /// critical pressure + virtual doublereal critPressure() const; + + /// critical density + virtual doublereal critDensity() const; + + /// saturation pressure + /*! + * @param t Temperature (kelvin) + */ + virtual doublereal satPressure(doublereal t); + + /** + * @} + * @name Initialization of the Object + * @{ + */ + + //! Initialization routine for all of the shallow pointers + /*! + * This is a cascading call, where each level should call the + * the parent level. + * + * The initThermo() routines get called before the initThermoXML() routines + * from the constructPDSSXML() routine. + * + * + * Calls initPtrs(); + */ + virtual void initThermo(); + + //! Initialization of a PDSS object using an + //! input XML file. + /*! + * + * This routine is a precursor to constructPDSSXML(XML_Node*) + * routine, which does most of the work. + * + * @param vptp_ptr Pointer to the Variable pressure %ThermoPhase object + * This object must have already been malloced. + * + * @param spindex Species index within the phase + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPDSSFile(VPStandardStateTP *vptp_ptr, int spindex, + std::string inputFile, std::string id); + + //! Initialization of a PDSS object using an xml tree + /*! + * This routine is a driver for the initialization of the + * object. + * + * basic logic: + * initThermo() (cascade) + * getStuff from species Part of XML file + * initThermoXML(phaseNode) (cascade) + * + * @param vptp_ptr Pointer to the Variable pressure %ThermoPhase object + * This object must have already been malloced. + * + * @param spindex Species index within the phase + * + * @param speciesNode XML Node containing the species information + * + * @param phaseNode Reference to the phase Information for the phase + * that owns this species. + * + * @param spInstalled Boolean indicating whether the species is + * already installed. + */ + void constructPDSSXML(VPStandardStateTP *vptp_ptr, int spindex, + const XML_Node& speciesNode, + const XML_Node& phaseNode, bool spInstalled); + + //! Initialization routine for the PDSS object based on the phaseNode + /*! + * This is a cascading call, where each level should call the + * the parent level. + * + * @param phaseNode Reference to the phase Information for the phase + * that owns this species. + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + virtual void initThermoXML(const XML_Node& phaseNode, std::string& id); + + //@} + + private: + + //! Enumerated data type describing the type of volume model + //! used to calculate the standard state volume of the species + SSVolume_Model_enumType volumeModel_; + + //! Value of the constant molar volume for the species + /*! + * m3 / kmol + */ + doublereal m_constMolarVolume; + + //! coefficients for the temperature representation + vector_fp TCoeff_; + + //! Derivative of the volume wrt temperature + mutable doublereal dVdT_; + + //! 2nd derivative of the volume wrt temperature + mutable doublereal d2VdT2_; + + }; + +} + +#endif + + + diff --git a/Cantera/src/thermo/Phase.cpp b/Cantera/src/thermo/Phase.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/ShomatePoly.h b/Cantera/src/thermo/ShomatePoly.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/ShomateThermo.h b/Cantera/src/thermo/ShomateThermo.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/SpeciesThermo.h b/Cantera/src/thermo/SpeciesThermo.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/SpeciesThermoFactory.h b/Cantera/src/thermo/SpeciesThermoFactory.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/SpeciesThermoMgr.h b/Cantera/src/thermo/SpeciesThermoMgr.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h old mode 100755 new mode 100644 diff --git a/Cantera/src/thermo/VPSSMgr_General.cpp b/Cantera/src/thermo/VPSSMgr_General.cpp index 043310b8a..f75c9ad27 100644 --- a/Cantera/src/thermo/VPSSMgr_General.cpp +++ b/Cantera/src/thermo/VPSSMgr_General.cpp @@ -30,6 +30,7 @@ #include "PDSS_IdealGas.h" #include "PDSS_Water.h" #include "PDSS_ConstVol.h" +#include "PDSS_SSVol.h" #include "PDSS_HKFT.h" #include "PDSS_IonsFromNeutral.h" #include "GeneralSpeciesThermo.h" @@ -159,6 +160,9 @@ namespace Cantera { if (model == "constant_incompressible") { VPSSMgr::installSTSpecies(k, speciesNode, phaseNode_ptr); kPDSS = new PDSS_ConstVol(m_vptp_ptr, k, speciesNode, *phaseNode_ptr, true); + if (!kPDSS) { + throw CanteraError("VPSSMgr_General::returnPDSS_ptr", "new PDSS_ConstVol failed"); + } } else if (model == "waterIAPWS" || model == "waterPDSS") { // VPSSMgr::installSTSpecies(k, speciesNode, phaseNode_ptr); kPDSS = new PDSS_Water(m_vptp_ptr, 0); @@ -190,6 +194,12 @@ namespace Cantera { } genSpthermo->installPDSShandler(k, kPDSS, this); + } else if (model == "constant" || model == "temperature_polynomial" || model == "density_temperature_polynomial") { + VPSSMgr::installSTSpecies(k, speciesNode, phaseNode_ptr); + kPDSS = new PDSS_SSVol(m_vptp_ptr, k, speciesNode, *phaseNode_ptr, true); + if (!kPDSS) { + throw CanteraError("VPSSMgr_General::returnPDSS_ptr", "new PDSS_SSVol failed"); + } } else { throw CanteraError("VPSSMgr_General::returnPDSS_ptr", "unknown standard state formulation: " + model); diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h old mode 100755 new mode 100644 index 05954fada..adee9aeba --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -83,11 +83,29 @@ namespace Cantera { const int cVPSS_DebyeHuckel = 1050; const int cVPSS_MolalSoln = 1060; + //! Types of general formulations for the specification of the standard state volume + enum SSVolume_Model_enumType { + //! This approximation is for a constant volume + cSSVOLUME_CONSTANT = 0, + //! This approximation is for a species with a quadratic polynomial in temperature + /*! + * V^ss_i = ai + bi T + ci T2 + */ + cSSVOLUME_TPOLY, + //! This approximation is for a species where the density is expressed as a + //! quadratic polynomial in temperature + /*! + * V^ss_i = M_i / (ai + bi T + ci T2) + */ + cSSVOLUME_DENSITY_TPOLY + }; + //! Types of PDSS's enum PDSS_enumType { cPDSS_UNDEF = 100, cPDSS_IDEALGAS, cPDSS_CONSTVOL, + cPDSS_SSVOL, cPDSS_MOLAL_CONSTVOL, cPDSS_WATER, cPDSS_MOLAL_HKFT, diff --git a/Cantera/src/thermo/speciesThermoTypes.h b/Cantera/src/thermo/speciesThermoTypes.h old mode 100755 new mode 100644 From 60c4b40d32bb69411509030146cbee191f6a34dd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 20 Oct 2009 23:46:29 +0000 Subject: [PATCH 003/446] Bug fixes to the PDSS_SSVol object. --- Cantera/src/base/ctml.cpp | 31 +- Cantera/src/base/ctml.h | 3 +- Cantera/src/oneD/Domain1D.h | 15 +- Cantera/src/oneD/StFlow.cpp | 1940 ++++++++++++------------- Cantera/src/thermo/PDSS_SSVol.cpp | 26 +- Cantera/src/thermo/VPSSMgrFactory.cpp | 12 + 6 files changed, 1032 insertions(+), 995 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index d11ad58a6..b705927c0 100755 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -883,17 +883,27 @@ namespace ctml { * units converter is used. * @param nodeName XML Name of the XML node to read. * The default value for the node name is floatArray + * + * @return Returns the number of floats read */ - void getFloatArray(const Cantera::XML_Node& node, vector_fp& v, const bool convert, + int getFloatArray(const Cantera::XML_Node& node, vector_fp& v, const bool convert, const std::string unitsString, const std::string nodeName) { string::size_type icom; string numstr; doublereal dtmp; string nn = node.name(); - if (nn != nodeName) - throw CanteraError("getFloatArray", - "wrong xml element type/name: was expecting " + const Cantera::XML_Node *readNode = &node; + if (nn != nodeName) { + vector ll; + node.getChildren(nodeName, ll); + if (ll.size() == 0) { + throw CanteraError("getFloatArray", + "wrong xml element type/name: was expecting " + nodeName + "but accessed " + node.name()); + } else { + readNode = ll[0]; + } + } v.clear(); doublereal vmin = Undef, vmax = Undef; @@ -902,7 +912,7 @@ namespace ctml { /* * Get the attributes field, units, from the XML node */ - std::string units = node["units"]; + std::string units = (*readNode)["units"]; if (units != "" && convert) { if (unitsString == "actEnergy" && units != "") { funit = actEnergyToSI(units); @@ -911,13 +921,13 @@ namespace ctml { } } - if (node["min"] != "") - vmin = atofCheck(node["min"].c_str()); - if (node["max"] != "") - vmax = atofCheck(node["max"].c_str()); + if ((*readNode)["min"] != "") + vmin = atofCheck((*readNode)["min"].c_str()); + if ((*readNode)["max"] != "") + vmax = atofCheck((*readNode)["max"].c_str()); doublereal vv; - std::string val = node.value(); + std::string val = readNode->value(); while (1 > 0) { icom = val.find(','); if (icom != string::npos) { @@ -956,6 +966,7 @@ namespace ctml { for (int n = 0; n < nv; n++) { v[n] *= funit; } + return v.size(); } // This routine is used to interpret the value portions of XML diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 4b3d4ebd9..25fbe3a9c 100755 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -363,8 +363,9 @@ namespace ctml { * units converter is used. * @param nodeName XML Name of the XML node to read. * The default value for the node name is floatArray + * @return Returns the number of floats read into v. */ - void getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, + int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, const bool convert=true, const std::string typeString="", const std::string nodeName = "floatArray"); diff --git a/Cantera/src/oneD/Domain1D.h b/Cantera/src/oneD/Domain1D.h index b201fe304..7d57583ec 100644 --- a/Cantera/src/oneD/Domain1D.h +++ b/Cantera/src/oneD/Domain1D.h @@ -58,7 +58,7 @@ namespace Cantera { m_jstart(0), m_left(0), m_right(0), - m_id("-"), m_desc("-"), + m_id(""), m_desc(""), m_refiner(0), m_bw(-1) { resize(nv, points); } @@ -412,9 +412,11 @@ namespace Cantera { */ void setID(const std::string& s) {m_id = s;} - std::string id() { - if (m_id != "") return m_id; - else return std::string("domain ") + int2str(m_index); + std::string id() const { + if (m_id != "") + return m_id; + else + return std::string("domain ") + int2str(m_index); } /** @@ -519,7 +521,10 @@ namespace Cantera { int m_jstart; Domain1D *m_left, *m_right; - std::string m_id, m_desc; + + //! Identity tag for the domain + std::string m_id; + std::string m_desc; Refiner* m_refiner; vector_int m_td; std::vector m_name; diff --git a/Cantera/src/oneD/StFlow.cpp b/Cantera/src/oneD/StFlow.cpp index 826cfd3f7..29fc73328 100644 --- a/Cantera/src/oneD/StFlow.cpp +++ b/Cantera/src/oneD/StFlow.cpp @@ -32,1170 +32,1170 @@ using namespace std; namespace Cantera { - //------------------- importSolution ------------------------ + //------------------- importSolution ------------------------ - /** - * Import a previous solution to use as an initial estimate. The - * previous solution may have been computed using a different - * reaction mechanism. Species in the old and new mechanisms are - * matched by name, and any species in the new mechanism that were - * not in the old one are set to zero. The new solution is created - * with the same number of grid points as in the old solution. - */ - void importSolution(int points, - doublereal* oldSoln, igthermo_t& oldmech, - int size_new, doublereal* newSoln, igthermo_t& newmech) { + /** + * Import a previous solution to use as an initial estimate. The + * previous solution may have been computed using a different + * reaction mechanism. Species in the old and new mechanisms are + * matched by name, and any species in the new mechanism that were + * not in the old one are set to zero. The new solution is created + * with the same number of grid points as in the old solution. + */ + void importSolution(int points, + doublereal* oldSoln, igthermo_t& oldmech, + int size_new, doublereal* newSoln, igthermo_t& newmech) { - // Number of components in old and new solutions - int nv_old = oldmech.nSpecies() + 4; - int nv_new = newmech.nSpecies() + 4; + // Number of components in old and new solutions + int nv_old = oldmech.nSpecies() + 4; + int nv_new = newmech.nSpecies() + 4; - if (size_new < nv_new*points) { - throw CanteraError("importSolution", - "new solution array must have length "+ - int2str(nv_new*points)); - } + if (size_new < nv_new*points) { + throw CanteraError("importSolution", + "new solution array must have length "+ + int2str(nv_new*points)); + } - int n, j, knew; - string nm; + int n, j, knew; + string nm; - // copy u,V,T,lambda - for (j = 0; j < points; j++) - for (n = 0; n < 4; n++) - newSoln[nv_new*j + n] = oldSoln[nv_old*j + n]; + // copy u,V,T,lambda + for (j = 0; j < points; j++) + for (n = 0; n < 4; n++) + newSoln[nv_new*j + n] = oldSoln[nv_old*j + n]; - // copy mass fractions - int nsp0 = oldmech.nSpecies(); - //int nsp1 = newmech.nSpecies(); + // copy mass fractions + int nsp0 = oldmech.nSpecies(); + //int nsp1 = newmech.nSpecies(); - // loop over the species in the old mechanism - for (int k = 0; k < nsp0; k++) { - nm = oldmech.speciesName(k); // name + // loop over the species in the old mechanism + for (int k = 0; k < nsp0; k++) { + nm = oldmech.speciesName(k); // name - // location of this species in the new mechanism. - // If < 0, then the species is not in the new mechanism. - knew = newmech.speciesIndex(nm); + // location of this species in the new mechanism. + // If < 0, then the species is not in the new mechanism. + knew = newmech.speciesIndex(nm); - // copy this species from the old to the new solution vectors - if (knew >= 0) { - for (j = 0; j < points; j++) { - newSoln[nv_new*j + 4 + knew] = oldSoln[nv_old*j + 4 + k]; - } - } - } - - - // normalize mass fractions - for (j = 0; j < points; j++) { - newmech.setMassFractions(&newSoln[nv_new*j + 4]); - newmech.getMassFractions(&newSoln[nv_new*j + 4]); - } + // copy this species from the old to the new solution vectors + if (knew >= 0) { + for (j = 0; j < points; j++) { + newSoln[nv_new*j + 4 + knew] = oldSoln[nv_old*j + 4 + k]; + } + } } - static void st_drawline() { - writelog("\n-------------------------------------" - "------------------------------------------"); + // normalize mass fractions + for (j = 0; j < points; j++) { + newmech.setMassFractions(&newSoln[nv_new*j + 4]); + newmech.getMassFractions(&newSoln[nv_new*j + 4]); + } + } + + + static void st_drawline() { + writelog("\n-------------------------------------" + "------------------------------------------"); + } + + StFlow::StFlow(igthermo_t* ph, int nsp, int points) : + Domain1D(nsp+4, points), + m_inlet_u(0.0), + m_inlet_V(0.0), + m_inlet_T(-1.0), + m_surface_T(-1.0), + m_press(-1.0), + m_nsp(nsp), + m_thermo(0), + m_kin(0), + m_trans(0), + m_jac(0), + m_ok(false), + m_do_soret(false), + m_transport_option(-1), + m_efctr(0.0) + { + m_type = cFlowType; + + m_points = points; + m_thermo = ph; + + if (ph == 0) return; // used to create a dummy object + + int nsp2 = m_thermo->nSpecies(); + if (nsp2 != m_nsp) { + m_nsp = nsp2; + Domain1D::resize(m_nsp+4, points); } - StFlow::StFlow(igthermo_t* ph, int nsp, int points) : - Domain1D(nsp+4, points), - m_inlet_u(0.0), - m_inlet_V(0.0), - m_inlet_T(-1.0), - m_surface_T(-1.0), - m_press(-1.0), - m_nsp(nsp), - m_thermo(0), - m_kin(0), - m_trans(0), - m_jac(0), - m_ok(false), - m_do_soret(false), - m_transport_option(-1), - m_efctr(0.0) - { - m_type = cFlowType; - m_points = points; - m_thermo = ph; + // make a local copy of the species molecular weight vector + m_wt = m_thermo->molecularWeights(); - if (ph == 0) return; // used to create a dummy object + // the species mass fractions are the last components in the solution + // vector, so the total number of components is the number of species + // plus the offset of the first mass fraction. + m_nv = c_offset_Y + m_nsp; - int nsp2 = m_thermo->nSpecies(); - if (nsp2 != m_nsp) { - m_nsp = nsp2; - Domain1D::resize(m_nsp+4, points); - } + // enable all species equations by default + m_do_species.resize(m_nsp, true); + + // but turn off the energy equation at all points + m_do_energy.resize(m_points,false); + + m_diff.resize(m_nsp*m_points); + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_flux.resize(m_nsp,m_points); + m_wdot.resize(m_nsp,m_points, 0.0); + m_surfdot.resize(m_nsp, 0.0); + m_ybar.resize(m_nsp); - // make a local copy of the species molecular weight vector - m_wt = m_thermo->molecularWeights(); + //-------------- default solution bounds -------------------- - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - m_nv = c_offset_Y + m_nsp; - - // enable all species equations by default - m_do_species.resize(m_nsp, true); - - // but turn off the energy equation at all points - m_do_energy.resize(m_points,false); - - m_diff.resize(m_nsp*m_points); - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_surfdot.resize(m_nsp, 0.0); - m_ybar.resize(m_nsp); - - - //-------------- default solution bounds -------------------- - - vector_fp vmin(m_nv), vmax(m_nv); + vector_fp vmin(m_nv), vmax(m_nv); - // no bounds on u - vmin[0] = -1.e20; - vmax[0] = 1.e20; + // no bounds on u + vmin[0] = -1.e20; + vmax[0] = 1.e20; - // V - vmin[1] = -1.e20; - vmax[1] = 1.e20; + // V + vmin[1] = -1.e20; + vmax[1] = 1.e20; - // temperature bounds - vmin[2] = 200.0; - vmax[2]= 1.e9; + // temperature bounds + vmin[2] = 200.0; + vmax[2]= 1.e9; - // lamda should be negative - vmin[3] = -1.e20; - vmax[3] = 1.e20; + // lamda should be negative + vmin[3] = -1.e20; + vmax[3] = 1.e20; - // mass fraction bounds - int k; - for (k = 0; k < m_nsp; k++) { - vmin[4+k] = -1.0e-5; - vmax[4+k] = 1.0e5; - } - setBounds(vmin.size(), DATA_PTR(vmin), vmax.size(), DATA_PTR(vmax)); - - - //-------------------- default error tolerances ---------------- - vector_fp rtol(m_nv, 1.0e-8); - vector_fp atol(m_nv, 1.0e-15); - setTolerances(rtol.size(), DATA_PTR(rtol), atol.size(), DATA_PTR(atol),false); - setTolerances(rtol.size(), DATA_PTR(rtol), atol.size(), DATA_PTR(atol),true); - - //-------------------- grid refinement ------------------------- - m_refiner->setActive(0, false); - m_refiner->setActive(1, false); - m_refiner->setActive(2, false); - m_refiner->setActive(3, false); - - vector_fp gr; - for (int ng = 0; ng < m_points; ng++) gr.push_back(1.0*ng/m_points); - setupGrid(m_points, DATA_PTR(gr)); - setID("stagnation flow"); + // mass fraction bounds + int k; + for (k = 0; k < m_nsp; k++) { + vmin[4+k] = -1.0e-5; + vmax[4+k] = 1.0e5; } + setBounds(vmin.size(), DATA_PTR(vmin), vmax.size(), DATA_PTR(vmax)); - /** - * Change the grid size. Called after grid refinement. - */ - void StFlow::resize(int ncomponents, int points) { - Domain1D::resize(ncomponents, points); - m_rho.resize(m_points, 0.0); - m_wtm.resize(m_points, 0.0); - m_cp.resize(m_points, 0.0); - m_enth.resize(m_points, 0.0); - m_visc.resize(m_points, 0.0); - m_tcon.resize(m_points, 0.0); + //-------------------- default error tolerances ---------------- + vector_fp rtol(m_nv, 1.0e-8); + vector_fp atol(m_nv, 1.0e-15); + setTolerances(rtol.size(), DATA_PTR(rtol), atol.size(), DATA_PTR(atol),false); + setTolerances(rtol.size(), DATA_PTR(rtol), atol.size(), DATA_PTR(atol),true); - if (m_transport_option == c_Mixav_Transport) { - m_diff.resize(m_nsp*m_points); - } - else { - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_diff.resize(m_nsp*m_points); - } - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_do_energy.resize(m_points,false); + //-------------------- grid refinement ------------------------- + m_refiner->setActive(0, false); + m_refiner->setActive(1, false); + m_refiner->setActive(2, false); + m_refiner->setActive(3, false); - m_fixedy.resize(m_nsp, m_points); - m_fixedtemp.resize(m_points); + vector_fp gr; + for (int ng = 0; ng < m_points; ng++) gr.push_back(1.0*ng/m_points); + setupGrid(m_points, DATA_PTR(gr)); + setID("stagnation flow"); + } - m_dz.resize(m_points-1); - m_z.resize(m_points); - } + + /** + * Change the grid size. Called after grid refinement. + */ + void StFlow::resize(int ncomponents, int points) { + Domain1D::resize(ncomponents, points); + m_rho.resize(m_points, 0.0); + m_wtm.resize(m_points, 0.0); + m_cp.resize(m_points, 0.0); + m_enth.resize(m_points, 0.0); + m_visc.resize(m_points, 0.0); + m_tcon.resize(m_points, 0.0); + + if (m_transport_option == c_Mixav_Transport) { + m_diff.resize(m_nsp*m_points); + } + else { + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_diff.resize(m_nsp*m_points); + } + m_flux.resize(m_nsp,m_points); + m_wdot.resize(m_nsp,m_points, 0.0); + m_do_energy.resize(m_points,false); + + m_fixedy.resize(m_nsp, m_points); + m_fixedtemp.resize(m_points); + + m_dz.resize(m_points-1); + m_z.resize(m_points); + } - void StFlow::setupGrid(int n, const doublereal* z) { - resize(m_nv, n); - int j; + void StFlow::setupGrid(int n, const doublereal* z) { + resize(m_nv, n); + int j; - m_z[0] = z[0]; - for (j = 1; j < m_points; j++) { - m_z[j] = z[j]; - m_dz[j-1] = m_z[j] - m_z[j-1]; - } + m_z[0] = z[0]; + for (j = 1; j < m_points; j++) { + m_z[j] = z[j]; + m_dz[j-1] = m_z[j] - m_z[j-1]; } + } - /** - * Install a transport manager. - */ - void StFlow::setTransport(Transport& trans, bool withSoret) { - m_trans = &trans; - m_do_soret = withSoret; + /** + * Install a transport manager. + */ + void StFlow::setTransport(Transport& trans, bool withSoret) { + m_trans = &trans; + m_do_soret = withSoret; - if (m_trans->model() == cMulticomponent) { - m_transport_option = c_Multi_Transport; - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_diff.resize(m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } - else if (m_trans->model() == cMixtureAveraged) { - m_transport_option = c_Mixav_Transport; - m_diff.resize(m_nsp*m_points); - if (withSoret) - throw CanteraError("setTransport", - "Thermal diffusion (the Soret effect) " - "requires using a multicomponent transport model."); - } - else - throw CanteraError("setTransport","unknown transport model."); + if (m_trans->model() == cMulticomponent) { + m_transport_option = c_Multi_Transport; + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_diff.resize(m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); } - - void StFlow::enableSoret(bool withSoret) { - if (m_transport_option == c_Multi_Transport) - m_do_soret = withSoret; - else { - throw CanteraError("setTransport", - "Thermal diffusion (the Soret effect) " - "requires using a multicomponent transport model."); - } + else if (m_trans->model() == cMixtureAveraged) { + m_transport_option = c_Mixav_Transport; + m_diff.resize(m_nsp*m_points); + if (withSoret) + throw CanteraError("setTransport", + "Thermal diffusion (the Soret effect) " + "requires using a multicomponent transport model."); } + else + throw CanteraError("setTransport","unknown transport model."); + } - - /** - * Set the gas object state to be consistent with the solution at - * point j. - */ - void StFlow::setGas(const doublereal* x,int j) { - m_thermo->setTemperature(T(x,j)); - const doublereal* yy = x + m_nv*j + c_offset_Y; - m_thermo->setMassFractions_NoNorm(yy); - m_thermo->setPressure(m_press); + void StFlow::enableSoret(bool withSoret) { + if (m_transport_option == c_Multi_Transport) + m_do_soret = withSoret; + else { + throw CanteraError("setTransport", + "Thermal diffusion (the Soret effect) " + "requires using a multicomponent transport model."); } + } - /** - * Set the gas state to be consistent with the solution at the - * midpoint between j and j + 1. - */ - void StFlow::setGasAtMidpoint(const doublereal* x,int j) { - m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); - const doublereal* yyj = x + m_nv*j + c_offset_Y; - const doublereal* yyjp = x + m_nv*(j+1) + c_offset_Y; - for (int k = 0; k < m_nsp; k++) - m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); - m_thermo->setMassFractions_NoNorm(DATA_PTR(m_ybar)); - m_thermo->setPressure(m_press); + /** + * Set the gas object state to be consistent with the solution at + * point j. + */ + void StFlow::setGas(const doublereal* x,int j) { + m_thermo->setTemperature(T(x,j)); + const doublereal* yy = x + m_nv*j + c_offset_Y; + m_thermo->setMassFractions_NoNorm(yy); + m_thermo->setPressure(m_press); + } + + + /** + * Set the gas state to be consistent with the solution at the + * midpoint between j and j + 1. + */ + void StFlow::setGasAtMidpoint(const doublereal* x,int j) { + m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); + const doublereal* yyj = x + m_nv*j + c_offset_Y; + const doublereal* yyjp = x + m_nv*(j+1) + c_offset_Y; + for (int k = 0; k < m_nsp; k++) + m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); + m_thermo->setMassFractions_NoNorm(DATA_PTR(m_ybar)); + m_thermo->setPressure(m_press); + } + + + void StFlow::_finalize(const doublereal* x) { + int k, j; + doublereal zz, tt; + int nz = m_zfix.size(); + bool e = m_do_energy[0]; + for (j = 0; j < m_points; j++) { + if (e || nz == 0) + setTemperature(j, T(x, j)); + else { + zz = (z(j) - z(0))/(z(m_points - 1) - z(0)); + tt = linearInterp(zz, m_zfix, m_tfix); + setTemperature(j, tt); + } + for (k = 0; k < m_nsp; k++) { + setMassFraction(j, k, Y(x, k, j)); + } } + if (e) solveEnergyEqn(); + } - void StFlow::_finalize(const doublereal* x) { - int k, j; - doublereal zz, tt; - int nz = m_zfix.size(); - bool e = m_do_energy[0]; - for (j = 0; j < m_points; j++) { - if (e || nz == 0) - setTemperature(j, T(x, j)); - else { - zz = (z(j) - z(0))/(z(m_points - 1) - z(0)); - tt = linearInterp(zz, m_zfix, m_tfix); - setTemperature(j, tt); - } - for (k = 0; k < m_nsp; k++) { - setMassFraction(j, k, Y(x, k, j)); - } - } - if (e) solveEnergyEqn(); - } + //------------------------------------------------------ + /** + * Evaluate the residual function for axisymmetric stagnation + * flow. If jpt is less than zero, the residual function is + * evaluated at all grid points. If jpt >= 0, then the residual + * function is only evaluated at grid points jpt-1, jpt, and + * jpt+1. This option is used to efficiently evaluate the + * Jacobian numerically. + * + */ - //------------------------------------------------------ + void AxiStagnFlow::eval(int jg, doublereal* xg, + doublereal* rg, integer* diagg, doublereal rdt) { - /** - * Evaluate the residual function for axisymmetric stagnation - * flow. If jpt is less than zero, the residual function is - * evaluated at all grid points. If jpt >= 0, then the residual - * function is only evaluated at grid points jpt-1, jpt, and - * jpt+1. This option is used to efficiently evaluate the - * Jacobian numerically. - * - */ + // if evaluating a Jacobian, and the global point is outside + // the domain of influence for this domain, then skip + // evaluating the residual + if (jg >=0 && (jg < firstPoint() - 1 || jg > lastPoint() + 1)) return; - void AxiStagnFlow::eval(int jg, doublereal* xg, - doublereal* rg, integer* diagg, doublereal rdt) { + // if evaluating a Jacobian, compute the steady-state residual + if (jg >= 0) rdt = 0.0; - // if evaluating a Jacobian, and the global point is outside - // the domain of influence for this domain, then skip - // evaluating the residual - if (jg >=0 && (jg < firstPoint() - 1 || jg > lastPoint() + 1)) return; - - // if evaluating a Jacobian, compute the steady-state residual - if (jg >= 0) rdt = 0.0; - - // start of local part of global arrays - doublereal* x = xg + loc(); - doublereal* rsd = rg + loc(); - integer* diag = diagg + loc(); + // start of local part of global arrays + doublereal* x = xg + loc(); + doublereal* rsd = rg + loc(); + integer* diag = diagg + loc(); - int jmin, jmax, jpt; - jpt = jg - firstPoint(); + int jmin, jmax, jpt; + jpt = jg - firstPoint(); - if (jg < 0) { // evaluate all points - jmin = 0; - jmax = m_points - 1; - } - else { // evaluate points for Jacobian - jmin = max(jpt-1, 0); - jmax = min(jpt+1,m_points-1); - } + if (jg < 0) { // evaluate all points + jmin = 0; + jmax = m_points - 1; + } + else { // evaluate points for Jacobian + jmin = max(jpt-1, 0); + jmax = min(jpt+1,m_points-1); + } - // properties are computed for grid points from j0 to j1 - int j0 = max(jmin-1,0); - int j1 = min(jmax+1,m_points-1); + // properties are computed for grid points from j0 to j1 + int j0 = max(jmin-1,0); + int j1 = min(jmax+1,m_points-1); - int j, k; + int j, k; - //----------------------------------------------------- - // update properties - //----------------------------------------------------- + //----------------------------------------------------- + // update properties + //----------------------------------------------------- - // update thermodynamic properties only if a Jacobian is not - // being evaluated - if (jpt < 0) { //if (jpt < 0 || (m_transport_option == c_Multi_Transport)) { - updateThermo(x, j0, j1); + // update thermodynamic properties only if a Jacobian is not + // being evaluated + if (jpt < 0) { //if (jpt < 0 || (m_transport_option == c_Multi_Transport)) { + updateThermo(x, j0, j1); - // update transport properties only if a Jacobian is not being - // evaluated - updateTransport(x, j0, j1); - } + // update transport properties only if a Jacobian is not being + // evaluated + updateTransport(x, j0, j1); + } - // update the species diffusive mass fluxes whether or not a - // Jacobian is being evaluated - updateDiffFluxes(x, j0, j1); + // update the species diffusive mass fluxes whether or not a + // Jacobian is being evaluated + updateDiffFluxes(x, j0, j1); - //---------------------------------------------------- - // evaluate the residual equations at all required - // grid points - //---------------------------------------------------- + //---------------------------------------------------- + // evaluate the residual equations at all required + // grid points + //---------------------------------------------------- - doublereal sum, sum2, dtdzj; + doublereal sum, sum2, dtdzj; - for (j = jmin; j <= jmax; j++) { + for (j = jmin; j <= jmax; j++) { - //---------------------------------------------- - // left boundary - //---------------------------------------------- + //---------------------------------------------- + // left boundary + //---------------------------------------------- - if (j == 0) { + if (j == 0) { - // these may be modified by a boundary object + // these may be modified by a boundary object - // Continuity. This propagates information right-to-left, - // since rho_u at point 0 is dependent on rho_u at point 1, - // but not on mdot from the inlet. - rsd[index(c_offset_U,0)] = - -(rho_u(x,1) - rho_u(x,0))/m_dz[0] - -(density(1)*V(x,1) + density(0)*V(x,0)); + // Continuity. This propagates information right-to-left, + // since rho_u at point 0 is dependent on rho_u at point 1, + // but not on mdot from the inlet. + rsd[index(c_offset_U,0)] = + -(rho_u(x,1) - rho_u(x,0))/m_dz[0] + -(density(1)*V(x,1) + density(0)*V(x,0)); - // the inlet (or other) object connected to this one - // will modify these equations by subtracting its values - // for V, T, and mdot. As a result, these residual equations - // will force the solution variables to the values for - // the boundary object - rsd[index(c_offset_V,0)] = V(x,0); - rsd[index(c_offset_T,0)] = T(x,0); - rsd[index(c_offset_L,0)] = -rho_u(x,0); + // the inlet (or other) object connected to this one + // will modify these equations by subtracting its values + // for V, T, and mdot. As a result, these residual equations + // will force the solution variables to the values for + // the boundary object + rsd[index(c_offset_V,0)] = V(x,0); + rsd[index(c_offset_T,0)] = T(x,0); + rsd[index(c_offset_L,0)] = -rho_u(x,0); - // The default boundary condition for species is zero - // flux. However, the boundary object may modify - // this. - sum = 0.0; - for (k = 0; k < m_nsp; k++) { - sum += Y(x,k,0); - rsd[index(c_offset_Y + k, 0)] = - -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); - } - rsd[index(c_offset_Y, 0)] = 1.0 - sum; - } + // The default boundary condition for species is zero + // flux. However, the boundary object may modify + // this. + sum = 0.0; + for (k = 0; k < m_nsp; k++) { + sum += Y(x,k,0); + rsd[index(c_offset_Y + k, 0)] = + -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); + } + rsd[index(c_offset_Y, 0)] = 1.0 - sum; + } - //---------------------------------------------- - // - // right boundary - // - //---------------------------------------------- + //---------------------------------------------- + // + // right boundary + // + //---------------------------------------------- - else if (j == m_points - 1) { + else if (j == m_points - 1) { - // the boundary object connected to the right of this - // one may modify or replace these equations. The - // default boundary conditions are zero u, V, and T, - // and zero diffusive flux for all species. + // the boundary object connected to the right of this + // one may modify or replace these equations. The + // default boundary conditions are zero u, V, and T, + // and zero diffusive flux for all species. - rsd[index(0,j)] = rho_u(x,j); - rsd[index(1,j)] = V(x,j); - rsd[index(2,j)] = T(x,j); - rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); - diag[index(c_offset_L, j)] = 0; - doublereal sum = 0.0; - for (k = 0; k < m_nsp; k++) { - sum += Y(x,k,j); - rsd[index(k+4,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); - } - rsd[index(4,j)] = 1.0 - sum; - diag[index(4,j)] = 0; + rsd[index(0,j)] = rho_u(x,j); + rsd[index(1,j)] = V(x,j); + rsd[index(2,j)] = T(x,j); + rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); + diag[index(c_offset_L, j)] = 0; + doublereal sum = 0.0; + for (k = 0; k < m_nsp; k++) { + sum += Y(x,k,j); + rsd[index(k+4,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); + } + rsd[index(4,j)] = 1.0 - sum; + diag[index(4,j)] = 0; - } + } - //------------------------------------------ - // interior points - //------------------------------------------ + //------------------------------------------ + // interior points + //------------------------------------------ - else { + else { - //---------------------------------------------- - // Continuity equation - // - // Note that this propagates the mass flow rate - // information to the left (j+1 -> j) from the - // value specified at the right boundary. The - // lambda information propagates in the opposite - // direction. - // - // d(\rho u)/dz + 2\rho V = 0 - // - //------------------------------------------------ + //---------------------------------------------- + // Continuity equation + // + // Note that this propagates the mass flow rate + // information to the left (j+1 -> j) from the + // value specified at the right boundary. The + // lambda information propagates in the opposite + // direction. + // + // d(\rho u)/dz + 2\rho V = 0 + // + //------------------------------------------------ - rsd[index(c_offset_U,j)] = - -(rho_u(x,j+1) - rho_u(x,j))/m_dz[j] - -(density(j+1)*V(x,j+1) + density(j)*V(x,j)); + rsd[index(c_offset_U,j)] = + -(rho_u(x,j+1) - rho_u(x,j))/m_dz[j] + -(density(j+1)*V(x,j+1) + density(j)*V(x,j)); - //algebraic constraint - diag[index(c_offset_U, j)] = 0; + //algebraic constraint + diag[index(c_offset_U, j)] = 0; - //------------------------------------------------ - // Radial momentum equation - // - // \rho u dV/dz + \rho V^2 = d(\mu dV/dz)/dz - lambda - // - //------------------------------------------------- - rsd[index(c_offset_V,j)] - = (shear(x,j) - lambda(x,j) - rho_u(x,j)*dVdz(x,j) - - m_rho[j]*V(x,j)*V(x,j))/m_rho[j] - - rdt*(V(x,j) - V_prev(j)); - diag[index(c_offset_V, j)] = 1; + //------------------------------------------------ + // Radial momentum equation + // + // \rho u dV/dz + \rho V^2 = d(\mu dV/dz)/dz - lambda + // + //------------------------------------------------- + rsd[index(c_offset_V,j)] + = (shear(x,j) - lambda(x,j) - rho_u(x,j)*dVdz(x,j) + - m_rho[j]*V(x,j)*V(x,j))/m_rho[j] + - rdt*(V(x,j) - V_prev(j)); + diag[index(c_offset_V, j)] = 1; - //------------------------------------------------- - // Species equations - // - // \rho u dY_k/dz + dJ_k/dz + M_k\omega_k - // - //------------------------------------------------- - getWdot(x,j); + //------------------------------------------------- + // Species equations + // + // \rho u dY_k/dz + dJ_k/dz + M_k\omega_k + // + //------------------------------------------------- + getWdot(x,j); - doublereal convec, diffus; - for (k = 0; k < m_nsp; k++) { - convec = rho_u(x,j)*dYdz(x,k,j); - diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) - /(z(j+1) - z(j-1)); - rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j) ) - - convec - diffus)/m_rho[j] - - rdt*(Y(x,k,j) - Y_prev(k,j)); - diag[index(c_offset_Y + k, j)] = 1; - } + doublereal convec, diffus; + for (k = 0; k < m_nsp; k++) { + convec = rho_u(x,j)*dYdz(x,k,j); + diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) + /(z(j+1) - z(j-1)); + rsd[index(c_offset_Y + k, j)] + = (m_wt[k]*(wdot(k,j) ) + - convec - diffus)/m_rho[j] + - rdt*(Y(x,k,j) - Y_prev(k,j)); + diag[index(c_offset_Y + k, j)] = 1; + } - //----------------------------------------------- - // energy equation - //----------------------------------------------- + //----------------------------------------------- + // energy equation + //----------------------------------------------- - if (m_do_energy[j]) { + if (m_do_energy[j]) { - setGas(x,j); + setGas(x,j); - // heat release term - const vector_fp& h_RT = m_thermo->enthalpy_RT_ref(); - const vector_fp& cp_R = m_thermo->cp_R_ref(); + // heat release term + const vector_fp& h_RT = m_thermo->enthalpy_RT_ref(); + const vector_fp& cp_R = m_thermo->cp_R_ref(); - sum = 0.0; - sum2 = 0.0; - doublereal flxk; - for (k = 0; k < m_nsp; k++) { - flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); - sum += wdot(k,j)*h_RT[k]; - sum2 += flxk*cp_R[k]/m_wt[k]; - } - sum *= GasConstant * T(x,j); - dtdzj = dTdz(x,j); - sum2 *= GasConstant * dtdzj; + sum = 0.0; + sum2 = 0.0; + doublereal flxk; + for (k = 0; k < m_nsp; k++) { + flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); + sum += wdot(k,j)*h_RT[k]; + sum2 += flxk*cp_R[k]/m_wt[k]; + } + sum *= GasConstant * T(x,j); + dtdzj = dTdz(x,j); + sum2 *= GasConstant * dtdzj; - rsd[index(c_offset_T, j)] = - - m_cp[j]*rho_u(x,j)*dtdzj - - divHeatFlux(x,j) - sum - sum2; - rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); + rsd[index(c_offset_T, j)] = + - m_cp[j]*rho_u(x,j)*dtdzj + - divHeatFlux(x,j) - sum - sum2; + rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); - rsd[index(c_offset_T, j)] = - rsd[index(c_offset_T, j)] + m_efctr*(T_fixed(j) - T(x,j)); + rsd[index(c_offset_T, j)] = + rsd[index(c_offset_T, j)] + m_efctr*(T_fixed(j) - T(x,j)); - rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); - diag[index(c_offset_T, j)] = 1; - } + rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); + diag[index(c_offset_T, j)] = 1; + } - // residual equations if the energy equation is disabled + // residual equations if the energy equation is disabled - if (!m_do_energy[j]) { - rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); - diag[index(c_offset_T, j)] = 0; - } + if (!m_do_energy[j]) { + rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); + diag[index(c_offset_T, j)] = 0; + } - rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); - diag[index(c_offset_L, j)] = 0; - } - } + rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); + diag[index(c_offset_L, j)] = 0; + } } + } - /** - * Update the transport properties at grid points in the range - * from j0 to j1, based on solution x. - */ - void StFlow::updateTransport(doublereal* x,int j0, int j1) { - int j,k,m; + /** + * Update the transport properties at grid points in the range + * from j0 to j1, based on solution x. + */ + void StFlow::updateTransport(doublereal* x,int j0, int j1) { + int j,k,m; - if (m_transport_option == c_Mixav_Transport) { - for (j = j0; j < j1; j++) { - setGasAtMidpoint(x,j); - m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); - m_trans->getMixDiffCoeffs(DATA_PTR(m_diff) + j*m_nsp); - m_tcon[j] = m_trans->thermalConductivity(); - } - } - else if (m_transport_option == c_Multi_Transport) { - doublereal sum, sumx, wtm, dz; - doublereal eps = 1.0e-12; - for (m = j0; m < j1; m++) { - setGasAtMidpoint(x,m); - dz = m_z[m+1] - m_z[m]; - wtm = m_thermo->meanMolecularWeight(); - - m_visc[m] = (m_dovisc ? m_trans->viscosity() : 0.0); - - m_trans->getMultiDiffCoeffs(m_nsp, - DATA_PTR(m_multidiff) + mindex(0,0,m)); - - for (k = 0; k < m_nsp; k++) { - sum = 0.0; - sumx = 0.0; - for (j = 0; j < m_nsp; j++) { - if (j != k) { - sum += m_wt[j]*m_multidiff[mindex(k,j,m)]* - ((X(x,j,m+1) - X(x,j,m))/dz + eps); - sumx += (X(x,j,m+1) - X(x,j,m))/dz; - } - } - m_diff[k + m*m_nsp] = sum/(wtm*(sumx+eps)); - } - - m_tcon[m] = m_trans->thermalConductivity(); - if (m_do_soret) { - m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + m*m_nsp); - } - } - } + if (m_transport_option == c_Mixav_Transport) { + for (j = j0; j < j1; j++) { + setGasAtMidpoint(x,j); + m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); + m_trans->getMixDiffCoeffs(DATA_PTR(m_diff) + j*m_nsp); + m_tcon[j] = m_trans->thermalConductivity(); + } } + else if (m_transport_option == c_Multi_Transport) { + doublereal sum, sumx, wtm, dz; + doublereal eps = 1.0e-12; + for (m = j0; m < j1; m++) { + setGasAtMidpoint(x,m); + dz = m_z[m+1] - m_z[m]; + wtm = m_thermo->meanMolecularWeight(); + + m_visc[m] = (m_dovisc ? m_trans->viscosity() : 0.0); + + m_trans->getMultiDiffCoeffs(m_nsp, + DATA_PTR(m_multidiff) + mindex(0,0,m)); + + for (k = 0; k < m_nsp; k++) { + sum = 0.0; + sumx = 0.0; + for (j = 0; j < m_nsp; j++) { + if (j != k) { + sum += m_wt[j]*m_multidiff[mindex(k,j,m)]* + ((X(x,j,m+1) - X(x,j,m))/dz + eps); + sumx += (X(x,j,m+1) - X(x,j,m))/dz; + } + } + m_diff[k + m*m_nsp] = sum/(wtm*(sumx+eps)); + } + + m_tcon[m] = m_trans->thermalConductivity(); + if (m_do_soret) { + m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + m*m_nsp); + } + } + } + } - //------------------------------------------------------ + //------------------------------------------------------ - /** - * Evaluate the residual function for axisymmetric stagnation - * flow. If jpt is less than zero, the residual function is - * evaluated at all grid points. If jpt >= 0, then the residual - * function is only evaluated at grid points jpt-1, jpt, and - * jpt+1. This option is used to efficiently evaluate the - * Jacobian numerically. - * - */ + /** + * Evaluate the residual function for axisymmetric stagnation + * flow. If jpt is less than zero, the residual function is + * evaluated at all grid points. If jpt >= 0, then the residual + * function is only evaluated at grid points jpt-1, jpt, and + * jpt+1. This option is used to efficiently evaluate the + * Jacobian numerically. + * + */ - void FreeFlame::eval(int jg, doublereal* xg, - doublereal* rg, integer* diagg, doublereal rdt) { + void FreeFlame::eval(int jg, doublereal* xg, + doublereal* rg, integer* diagg, doublereal rdt) { - // if evaluating a Jacobian, and the global point is outside - // the domain of influence for this domain, then skip - // evaluating the residual - if (jg >=0 && (jg < firstPoint() - 1 || jg > lastPoint() + 1)) return; + // if evaluating a Jacobian, and the global point is outside + // the domain of influence for this domain, then skip + // evaluating the residual + if (jg >=0 && (jg < firstPoint() - 1 || jg > lastPoint() + 1)) return; - // if evaluating a Jacobian, compute the steady-state residual - if (jg >= 0) rdt = 0.0; + // if evaluating a Jacobian, compute the steady-state residual + if (jg >= 0) rdt = 0.0; - // start of local part of global arrays - doublereal* x = xg + loc(); - doublereal* rsd = rg + loc(); - integer* diag = diagg + loc(); + // start of local part of global arrays + doublereal* x = xg + loc(); + doublereal* rsd = rg + loc(); + integer* diag = diagg + loc(); - int jmin, jmax, jpt; - jpt = jg - firstPoint(); + int jmin, jmax, jpt; + jpt = jg - firstPoint(); - if (jg < 0) { // evaluate all points - jmin = 0; - jmax = m_points - 1; - } - else { // evaluate points for Jacobian - jmin = max(jpt-1, 0); - jmax = min(jpt+1,m_points-1); - } + if (jg < 0) { // evaluate all points + jmin = 0; + jmax = m_points - 1; + } + else { // evaluate points for Jacobian + jmin = max(jpt-1, 0); + jmax = min(jpt+1,m_points-1); + } - // properties are computed for grid points from j0 to j1 - int j0 = max(jmin-1,0); - int j1 = min(jmax+1,m_points-1); + // properties are computed for grid points from j0 to j1 + int j0 = max(jmin-1,0); + int j1 = min(jmax+1,m_points-1); - int j, k; + int j, k; - //----------------------------------------------------- - // update properties - //----------------------------------------------------- + //----------------------------------------------------- + // update properties + //----------------------------------------------------- - // update thermodynamic properties only if a Jacobian is not - // being evaluated - if (jpt < 0) { - updateThermo(x, j0, j1); - updateTransport(x, j0, j1); - } + // update thermodynamic properties only if a Jacobian is not + // being evaluated + if (jpt < 0) { + updateThermo(x, j0, j1); + updateTransport(x, j0, j1); + } - // update the species diffusive mass fluxes whether or not a - // Jacobian is being evaluated - updateDiffFluxes(x, j0, j1); + // update the species diffusive mass fluxes whether or not a + // Jacobian is being evaluated + updateDiffFluxes(x, j0, j1); - //---------------------------------------------------- - // evaluate the residual equations at all required - // grid points - //---------------------------------------------------- + //---------------------------------------------------- + // evaluate the residual equations at all required + // grid points + //---------------------------------------------------- - doublereal sum, sum2, dtdzj; + doublereal sum, sum2, dtdzj; - for (j = jmin; j <= jmax; j++) { + for (j = jmin; j <= jmax; j++) { - //---------------------------------------------- - // left boundary - //---------------------------------------------- + //---------------------------------------------- + // left boundary + //---------------------------------------------- - if (j == 0) { + if (j == 0) { - // these may be modified by a boundary object + // these may be modified by a boundary object - // Continuity. This propagates information right-to-left, - // since rho_u at point 0 is dependent on rho_u at point 1, - // but not on mdot from the inlet. - rsd[index(c_offset_U,0)] = - -(rho_u(x,1) - rho_u(x,0))/m_dz[0] - -(density(1)*V(x,1) + density(0)*V(x,0)); + // Continuity. This propagates information right-to-left, + // since rho_u at point 0 is dependent on rho_u at point 1, + // but not on mdot from the inlet. + rsd[index(c_offset_U,0)] = + -(rho_u(x,1) - rho_u(x,0))/m_dz[0] + -(density(1)*V(x,1) + density(0)*V(x,0)); - // the inlet (or other) object connected to this one - // will modify these equations by subtracting its values - // for V, T, and mdot. As a result, these residual equations - // will force the solution variables to the values for - // the boundary object - rsd[index(c_offset_V,0)] = V(x,0); - rsd[index(c_offset_T,0)] = T(x,0); - rsd[index(c_offset_L,0)] = -rho_u(x,0); + // the inlet (or other) object connected to this one + // will modify these equations by subtracting its values + // for V, T, and mdot. As a result, these residual equations + // will force the solution variables to the values for + // the boundary object + rsd[index(c_offset_V,0)] = V(x,0); + rsd[index(c_offset_T,0)] = T(x,0); + rsd[index(c_offset_L,0)] = -rho_u(x,0); - // The default boundary condition for species is zero - // flux - sum = 0.0; - for (k = 0; k < m_nsp; k++) { - sum += Y(x,k,0); - rsd[index(c_offset_Y + k, 0)] = - -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); - } - rsd[index(c_offset_Y, 0)] = 1.0 - sum; - } + // The default boundary condition for species is zero + // flux + sum = 0.0; + for (k = 0; k < m_nsp; k++) { + sum += Y(x,k,0); + rsd[index(c_offset_Y + k, 0)] = + -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); + } + rsd[index(c_offset_Y, 0)] = 1.0 - sum; + } - //---------------------------------------------- - // - // right boundary - // - //---------------------------------------------- + //---------------------------------------------- + // + // right boundary + // + //---------------------------------------------- - else if (j == m_points - 1) { + else if (j == m_points - 1) { - // the boundary object connected to the right of this - // one may modify or replace these equations. The - // default boundary conditions are zero u, V, and T, - // and zero diffusive flux for all species. + // the boundary object connected to the right of this + // one may modify or replace these equations. The + // default boundary conditions are zero u, V, and T, + // and zero diffusive flux for all species. - // zero gradient - rsd[index(0,j)] = rho_u(x,j) - rho_u(x,j-1); - rsd[index(1,j)] = V(x,j); - rsd[index(2,j)] = T(x,j) - T(x,j-1); - doublereal sum = 0.0; - rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); - diag[index(c_offset_L, j)] = 0; - for (k = 0; k < m_nsp; k++) { - sum += Y(x,k,j); - rsd[index(k+4,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); - } - rsd[index(4,j)] = 1.0 - sum; - diag[index(4,j)] = 0; - } + // zero gradient + rsd[index(0,j)] = rho_u(x,j) - rho_u(x,j-1); + rsd[index(1,j)] = V(x,j); + rsd[index(2,j)] = T(x,j) - T(x,j-1); + doublereal sum = 0.0; + rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); + diag[index(c_offset_L, j)] = 0; + for (k = 0; k < m_nsp; k++) { + sum += Y(x,k,j); + rsd[index(k+4,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); + } + rsd[index(4,j)] = 1.0 - sum; + diag[index(4,j)] = 0; + } - //------------------------------------------ - // interior points - //------------------------------------------ + //------------------------------------------ + // interior points + //------------------------------------------ - else { + else { - //---------------------------------------------- - // Continuity equation - //---------------------------------------------- + //---------------------------------------------- + // Continuity equation + //---------------------------------------------- - if (grid(j) > m_zfixed){ - rsd[index(c_offset_U,j)] = - - (rho_u(x,j) - rho_u(x,j-1))/m_dz[j-1] - - (density(j-1)*V(x,j-1) + density(j)*V(x,j)); - } + if (grid(j) > m_zfixed){ + rsd[index(c_offset_U,j)] = + - (rho_u(x,j) - rho_u(x,j-1))/m_dz[j-1] + - (density(j-1)*V(x,j-1) + density(j)*V(x,j)); + } - else if (grid(j) == m_zfixed){ - if (m_do_energy[j]) { - rsd[index(c_offset_U,j)] = (T(x,j) - m_tfixed); - } - else { - rsd[index(c_offset_U,j)] = (rho_u(x,j) - - m_rho[0]*0.3); - } - } - else if(grid(j) < m_zfixed){ - rsd[index(c_offset_U,j)] = - - (rho_u(x,j+1) - rho_u(x,j))/m_dz[j] - - (density(j+1)*V(x,j+1) + density(j)*V(x,j)); - } - //algebraic constraint - diag[index(c_offset_U, j)] = 0; + else if (grid(j) == m_zfixed){ + if (m_do_energy[j]) { + rsd[index(c_offset_U,j)] = (T(x,j) - m_tfixed); + } + else { + rsd[index(c_offset_U,j)] = (rho_u(x,j) + - m_rho[0]*0.3); + } + } + else if(grid(j) < m_zfixed){ + rsd[index(c_offset_U,j)] = + - (rho_u(x,j+1) - rho_u(x,j))/m_dz[j] + - (density(j+1)*V(x,j+1) + density(j)*V(x,j)); + } + //algebraic constraint + diag[index(c_offset_U, j)] = 0; - //------------------------------------------------ - // Radial momentum equation - // - // \rho u dV/dz + \rho V^2 = d(\mu dV/dz)/dz - lambda - // - //------------------------------------------------- - rsd[index(c_offset_V,j)] - = (shear(x,j) - lambda(x,j) - rho_u(x,j)*dVdz(x,j) - - m_rho[j]*V(x,j)*V(x,j))/m_rho[j] - - rdt*(V(x,j) - V_prev(j)); - diag[index(c_offset_V, j)] = 1; + //------------------------------------------------ + // Radial momentum equation + // + // \rho u dV/dz + \rho V^2 = d(\mu dV/dz)/dz - lambda + // + //------------------------------------------------- + rsd[index(c_offset_V,j)] + = (shear(x,j) - lambda(x,j) - rho_u(x,j)*dVdz(x,j) + - m_rho[j]*V(x,j)*V(x,j))/m_rho[j] + - rdt*(V(x,j) - V_prev(j)); + diag[index(c_offset_V, j)] = 1; - //------------------------------------------------- - // Species equations - // - // \rho u dY_k/dz + dJ_k/dz + M_k\omega_k - // - //------------------------------------------------- - getWdot(x,j); + //------------------------------------------------- + // Species equations + // + // \rho u dY_k/dz + dJ_k/dz + M_k\omega_k + // + //------------------------------------------------- + getWdot(x,j); - doublereal convec, diffus; - for (k = 0; k < m_nsp; k++) { - convec = rho_u(x,j)*dYdz(x,k,j); - diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) - /(z(j+1) - z(j-1)); - rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j) ) - - convec - diffus)/m_rho[j] - - rdt*(Y(x,k,j) - Y_prev(k,j)); - diag[index(c_offset_Y + k, j)] = 1; - } + doublereal convec, diffus; + for (k = 0; k < m_nsp; k++) { + convec = rho_u(x,j)*dYdz(x,k,j); + diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) + /(z(j+1) - z(j-1)); + rsd[index(c_offset_Y + k, j)] + = (m_wt[k]*(wdot(k,j) ) + - convec - diffus)/m_rho[j] + - rdt*(Y(x,k,j) - Y_prev(k,j)); + diag[index(c_offset_Y + k, j)] = 1; + } - //----------------------------------------------- - // energy equation - //----------------------------------------------- + //----------------------------------------------- + // energy equation + //----------------------------------------------- - if (m_do_energy[j]) { + if (m_do_energy[j]) { - setGas(x,j); + setGas(x,j); - // heat release term - const vector_fp& h_RT = m_thermo->enthalpy_RT_ref(); - const vector_fp& cp_R = m_thermo->cp_R_ref(); + // heat release term + const vector_fp& h_RT = m_thermo->enthalpy_RT_ref(); + const vector_fp& cp_R = m_thermo->cp_R_ref(); - sum = 0.0; - sum2 = 0.0; - doublereal flxk; - for (k = 0; k < m_nsp; k++) { - flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); - sum += wdot(k,j)*h_RT[k]; - sum2 += flxk*cp_R[k]/m_wt[k]; - } - sum *= GasConstant * T(x,j); - dtdzj = dTdz(x,j); - sum2 *= GasConstant * dtdzj; + sum = 0.0; + sum2 = 0.0; + doublereal flxk; + for (k = 0; k < m_nsp; k++) { + flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); + sum += wdot(k,j)*h_RT[k]; + sum2 += flxk*cp_R[k]/m_wt[k]; + } + sum *= GasConstant * T(x,j); + dtdzj = dTdz(x,j); + sum2 *= GasConstant * dtdzj; - rsd[index(c_offset_T, j)] = - - m_cp[j]*rho_u(x,j)*dtdzj - - divHeatFlux(x,j) - sum - sum2; - rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); + rsd[index(c_offset_T, j)] = + - m_cp[j]*rho_u(x,j)*dtdzj + - divHeatFlux(x,j) - sum - sum2; + rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); - rsd[index(c_offset_T, j)] = - rsd[index(c_offset_T, j)] + m_efctr*(T_fixed(j) - T(x,j)); + rsd[index(c_offset_T, j)] = + rsd[index(c_offset_T, j)] + m_efctr*(T_fixed(j) - T(x,j)); - rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); - diag[index(c_offset_T, j)] = 1; - } - // residual equations if the energy equation is disabled - else { - rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); - diag[index(c_offset_T, j)] = 0; - } + rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); + diag[index(c_offset_T, j)] = 1; + } + // residual equations if the energy equation is disabled + else { + rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); + diag[index(c_offset_T, j)] = 0; + } - rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); - diag[index(c_offset_L, j)] = 0; - } - } + rsd[index(c_offset_L, j)] = lambda(x,j) - lambda(x,j-1); + diag[index(c_offset_L, j)] = 0; + } } + } - /** - * Print the solution. - */ - void StFlow::showSolution(const doublereal* x) { - int nn = m_nv/5; - int i, j, n; - //char* buf = new char[100]; - char buf[100]; + /** + * Print the solution. + */ + void StFlow::showSolution(const doublereal* x) { + int nn = m_nv/5; + int i, j, n; + //char* buf = new char[100]; + char buf[100]; - // The mean molecular weight is needed to convert - updateThermo(x, 0, m_points-1); + // The mean molecular weight is needed to convert + updateThermo(x, 0, m_points-1); - sprintf(buf, " Pressure: %10.4g Pa \n", m_press); - writelog(buf); - for (i = 0; i < nn; i++) { - st_drawline(); - sprintf(buf, "\n z "); - writelog(buf); - for (n = 0; n < 5; n++) { - sprintf(buf, " %10s ",componentName(i*5 + n).c_str()); - writelog(buf); - } - st_drawline(); - for (j = 0; j < m_points; j++) { - sprintf(buf, "\n %10.4g ",m_z[j]); - writelog(buf); - for (n = 0; n < 5; n++) { - sprintf(buf, " %10.4g ",component(x, i*5+n,j)); - writelog(buf); - } - } - writelog("\n"); - } - int nrem = m_nv - 5*nn; - st_drawline(); - sprintf(buf, "\n z "); - writelog(buf); - for (n = 0; n < nrem; n++) { - sprintf(buf, " %10s ", componentName(nn*5 + n).c_str()); - writelog(buf); - } - st_drawline(); - for (j = 0; j < m_points; j++) { - sprintf(buf, "\n %10.4g ",m_z[j]); - writelog(buf); - for (n = 0; n < nrem; n++) { - sprintf(buf, " %10.4g ",component(x, nn*5+n,j)); - writelog(buf); - } - } - writelog("\n"); + sprintf(buf, " Pressure: %10.4g Pa \n", m_press); + writelog(buf); + for (i = 0; i < nn; i++) { + st_drawline(); + sprintf(buf, "\n z "); + writelog(buf); + for (n = 0; n < 5; n++) { + sprintf(buf, " %10s ",componentName(i*5 + n).c_str()); + writelog(buf); + } + st_drawline(); + for (j = 0; j < m_points; j++) { + sprintf(buf, "\n %10.4g ",m_z[j]); + writelog(buf); + for (n = 0; n < 5; n++) { + sprintf(buf, " %10.4g ",component(x, i*5+n,j)); + writelog(buf); + } + } + writelog("\n"); } + int nrem = m_nv - 5*nn; + st_drawline(); + sprintf(buf, "\n z "); + writelog(buf); + for (n = 0; n < nrem; n++) { + sprintf(buf, " %10s ", componentName(nn*5 + n).c_str()); + writelog(buf); + } + st_drawline(); + for (j = 0; j < m_points; j++) { + sprintf(buf, "\n %10.4g ",m_z[j]); + writelog(buf); + for (n = 0; n < nrem; n++) { + sprintf(buf, " %10.4g ",component(x, nn*5+n,j)); + writelog(buf); + } + } + writelog("\n"); + } - /** - * Update the diffusive mass fluxes. - */ - void StFlow::updateDiffFluxes(const doublereal* x, int j0, int j1) { - int j, k, m; - doublereal sum, wtm, rho, dz, gradlogT; + /** + * Update the diffusive mass fluxes. + */ + void StFlow::updateDiffFluxes(const doublereal* x, int j0, int j1) { + int j, k, m; + doublereal sum, wtm, rho, dz, gradlogT; - switch (m_transport_option) { + switch (m_transport_option) { - case c_Mixav_Transport: - case c_Multi_Transport: - for (j = j0; j < j1; j++) { - sum = 0.0; - wtm = m_wtm[j]; - rho = density(j); - dz = z(j+1) - z(j); + case c_Mixav_Transport: + case c_Multi_Transport: + for (j = j0; j < j1; j++) { + sum = 0.0; + wtm = m_wtm[j]; + rho = density(j); + dz = z(j+1) - z(j); - for (k = 0; k < m_nsp; k++) { - m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm); - m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz; - sum -= m_flux(k,j); - } - // correction flux to insure that \sum_k Y_k V_k = 0. - for (k = 0; k < m_nsp; k++) m_flux(k,j) += sum*Y(x,k,j); - } - break; + for (k = 0; k < m_nsp; k++) { + m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm); + m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz; + sum -= m_flux(k,j); + } + // correction flux to insure that \sum_k Y_k V_k = 0. + for (k = 0; k < m_nsp; k++) m_flux(k,j) += sum*Y(x,k,j); + } + break; - default: - throw CanteraError("updateDiffFluxes","unknown transport model"); - } - - if (m_do_soret) { - for (m = j0; m < j1; m++) { - gradlogT = 2.0*(T(x,m+1) - T(x,m))/(T(x,m+1) + T(x,m)); - for (k = 0; k < m_nsp; k++) { - m_flux(k,m) -= m_dthermal(k,m)*gradlogT; - } - } - } + default: + throw CanteraError("updateDiffFluxes","unknown transport model"); } - - string StFlow::componentName(int n) const { - switch(n) { - case 0: return "u"; - case 1: return "V"; - case 2: return "T"; - case 3: return "lambda"; - default: - if (n >= (int) c_offset_Y && n < (int) (c_offset_Y + m_nsp)) { - return m_thermo->speciesName(n - c_offset_Y); - } - else - return ""; - } + if (m_do_soret) { + for (m = j0; m < j1; m++) { + gradlogT = 2.0*(T(x,m+1) - T(x,m))/(T(x,m+1) + T(x,m)); + for (k = 0; k < m_nsp; k++) { + m_flux(k,m) -= m_dthermal(k,m)*gradlogT; + } + } } + } - //added by Karl Meredith - int StFlow::componentIndex(string name) const { + string StFlow::componentName(int n) const { + switch(n) { + case 0: return "u"; + case 1: return "V"; + case 2: return "T"; + case 3: return "lambda"; + default: + if (n >= (int) c_offset_Y && n < (int) (c_offset_Y + m_nsp)) { + return m_thermo->speciesName(n - c_offset_Y); + } + else + return ""; + } + } + + + //added by Karl Meredith + int StFlow::componentIndex(string name) const { - if(name=="u") {return 0;} - else if (name=="V") {return 1;} - else if (name=="T") {return 2;} - else if (name=="lambda") {return 3;} - else { - for (int n=4;n ignored; - int nsp = m_thermo->nSpecies(); - vector_int did_species(nsp, 0); - - vector str; - dom.getChildren("string",str); - int nstr = static_cast(str.size()); - for (int istr = 0; istr < nstr; istr++) { - const XML_Node& nd = *str[istr]; - writelog(nd["title"]+": "+nd.value()+"\n"); - } - - //map params; - double pp = -1.0; - pp = getFloat(dom, "pressure", "pressure"); - setPressure(pp); + return -1; + } - vector d; - dom.child("grid_data").getChildren("floatArray",d); - int nd = static_cast(d.size()); + void StFlow::restore(const XML_Node& dom, doublereal* soln) { - vector_fp x; - int n, np = 0, j, ks, k; - string nm; - bool readgrid = false, wrote_header = false; - for (n = 0; n < nd; n++) { - const XML_Node& fa = *d[n]; - nm = fa["title"]; - if (nm == "z") { - getFloatArray(fa,x,false); - np = x.size(); - writelog("Grid contains "+int2str(np)+ - " points.\n"); - readgrid = true; - setupGrid(np, DATA_PTR(x)); - } - } - if (!readgrid) { - throw CanteraError("StFlow::restore", - "domain contains no grid points."); - } + vector ignored; + int nsp = m_thermo->nSpecies(); + vector_int did_species(nsp, 0); - writelog("Importing datasets:\n"); - for (n = 0; n < nd; n++) { - const XML_Node& fa = *d[n]; - nm = fa["title"]; - getFloatArray(fa,x,false); - if (nm == "u") { - writelog("axial velocity "); - if ((int) x.size() == np) { - for (j = 0; j < np; j++) { - soln[index(0,j)] = x[j]; - } - } - else { - goto error; - } - } - else if (nm == "z") { - ; // already read grid - } - else if (nm == "V") { - writelog("radial velocity "); - if ((int) x.size() == np) { - for (j = 0; j < np; j++) - soln[index(1,j)] = x[j]; - } - else goto error; - } - else if (nm == "T") { - writelog("temperature "); - if ((int) x.size() == np) { - for (j = 0; j < np; j++) - soln[index(2,j)] = x[j]; - - // For fixed-temperature simulations, use the - // imported temperature profile by default. If - // this is not desired, call setFixedTempProfile - // *after* restoring the solution. - - vector_fp zz(np); - for (int jj = 0; jj < np; jj++) - zz[jj] = (grid(jj) - zmin())/(zmax() - zmin()); - setFixedTempProfile(zz, x); - } - else goto error; - } - else if (nm == "L") { - writelog("lambda "); - if ((int) x.size() == np) { - for (j = 0; j < np; j++) - soln[index(3,j)] = x[j]; - } - else goto error; - } - else if (m_thermo->speciesIndex(nm) >= 0) { - writelog(nm+" "); - if ((int) x.size() == np) { - k = m_thermo->speciesIndex(nm); - did_species[k] = 1; - for (j = 0; j < np; j++) - soln[index(k+4,j)] = x[j]; - } - } - else - ignored.push_back(nm); - } - - if (ignored.size() != 0) { - writelog("\n\n"); - writelog("Ignoring datasets:\n"); - int nn = static_cast(ignored.size()); - for (int n = 0; n < nn; n++) { - writelog(ignored[n]+" "); - } - } - - for (ks = 0; ks < nsp; ks++) { - if (did_species[ks] == 0) { - if (!wrote_header) { - writelog("Missing data for species:\n"); - wrote_header = true; - } - writelog(m_thermo->speciesName(ks)+" "); - } - } - - return; - error: - throw CanteraError("StFlow::restore","Data size error"); + vector str; + dom.getChildren("string",str); + int nstr = static_cast(str.size()); + for (int istr = 0; istr < nstr; istr++) { + const XML_Node& nd = *str[istr]; + writelog(nd["title"]+": "+nd.value()+"\n"); } + //map params; + double pp = -1.0; + pp = getFloat(dom, "pressure", "pressure"); + setPressure(pp); - void StFlow::save(XML_Node& o, const doublereal * const sol) { - int k; + vector d; + dom.child("grid_data").getChildren("floatArray",d); + int nd = static_cast(d.size()); - ArrayViewer soln(m_nv, m_points, const_cast(sol) + loc()); - - XML_Node& flow = (XML_Node&)o.addChild("domain"); - flow.addAttribute("type",flowType()); - flow.addAttribute("id",m_id); - flow.addAttribute("points",m_points); - flow.addAttribute("components",m_nv); - - if (m_desc != "") addString(flow,"description",m_desc); - XML_Node& gv = flow.addChild("grid_data"); - addFloat(flow, "pressure", m_press, "Pa", "pressure"); - addFloatArray(gv,"z",m_z.size(),DATA_PTR(m_z), - "m","length"); - vector_fp x(static_cast(soln.nColumns())); - - soln.getRow(0,DATA_PTR(x)); - addFloatArray(gv,"u",x.size(),DATA_PTR(x),"m/s","velocity"); - - soln.getRow(1,DATA_PTR(x)); - addFloatArray(gv,"V", - x.size(),DATA_PTR(x),"1/s","rate"); - - soln.getRow(2,DATA_PTR(x)); - addFloatArray(gv,"T",x.size(),DATA_PTR(x),"K","temperature",0.0); - - soln.getRow(3,DATA_PTR(x)); - addFloatArray(gv,"L",x.size(),DATA_PTR(x),"N/m^4"); - - for (k = 0; k < m_nsp; k++) { - soln.getRow(4+k,DATA_PTR(x)); - addFloatArray(gv,m_thermo->speciesName(k), - x.size(),DATA_PTR(x),"","massFraction",0.0,1.0); - } + vector_fp x; + int n, np = 0, j, ks, k; + string nm; + bool readgrid = false, wrote_header = false; + for (n = 0; n < nd; n++) { + const XML_Node& fa = *d[n]; + nm = fa["title"]; + if (nm == "z") { + getFloatArray(fa,x,false); + np = x.size(); + writelog("Grid contains "+int2str(np)+ + " points.\n"); + readgrid = true; + setupGrid(np, DATA_PTR(x)); + } + } + if (!readgrid) { + throw CanteraError("StFlow::restore", + "domain contains no grid points."); } + writelog("Importing datasets:\n"); + for (n = 0; n < nd; n++) { + const XML_Node& fa = *d[n]; + nm = fa["title"]; + getFloatArray(fa,x,false); + if (nm == "u") { + writelog("axial velocity "); + if ((int) x.size() == np) { + for (j = 0; j < np; j++) { + soln[index(0,j)] = x[j]; + } + } + else { + goto error; + } + } + else if (nm == "z") { + ; // already read grid + } + else if (nm == "V") { + writelog("radial velocity "); + if ((int) x.size() == np) { + for (j = 0; j < np; j++) + soln[index(1,j)] = x[j]; + } + else goto error; + } + else if (nm == "T") { + writelog("temperature "); + if ((int) x.size() == np) { + for (j = 0; j < np; j++) + soln[index(2,j)] = x[j]; - void StFlow::setJac(MultiJac* jac) { - m_jac = jac; + // For fixed-temperature simulations, use the + // imported temperature profile by default. If + // this is not desired, call setFixedTempProfile + // *after* restoring the solution. + + vector_fp zz(np); + for (int jj = 0; jj < np; jj++) + zz[jj] = (grid(jj) - zmin())/(zmax() - zmin()); + setFixedTempProfile(zz, x); + } + else goto error; + } + else if (nm == "L") { + writelog("lambda "); + if ((int) x.size() == np) { + for (j = 0; j < np; j++) + soln[index(3,j)] = x[j]; + } + else goto error; + } + else if (m_thermo->speciesIndex(nm) >= 0) { + writelog(nm+" "); + if ((int) x.size() == np) { + k = m_thermo->speciesIndex(nm); + did_species[k] = 1; + for (j = 0; j < np; j++) + soln[index(k+4,j)] = x[j]; + } + } + else + ignored.push_back(nm); } + if (ignored.size() != 0) { + writelog("\n\n"); + writelog("Ignoring datasets:\n"); + int nn = static_cast(ignored.size()); + for (int n = 0; n < nn; n++) { + writelog(ignored[n]+" "); + } + } + + for (ks = 0; ks < nsp; ks++) { + if (did_species[ks] == 0) { + if (!wrote_header) { + writelog("Missing data for species:\n"); + wrote_header = true; + } + writelog(m_thermo->speciesName(ks)+" "); + } + } + + return; + error: + throw CanteraError("StFlow::restore","Data size error"); + } + + + + void StFlow::save(XML_Node& o, const doublereal * const sol) { + int k; + + ArrayViewer soln(m_nv, m_points, const_cast(sol) + loc()); + + XML_Node& flow = (XML_Node&)o.addChild("domain"); + flow.addAttribute("type",flowType()); + flow.addAttribute("id",m_id); + flow.addAttribute("points",m_points); + flow.addAttribute("components",m_nv); + + if (m_desc != "") addString(flow,"description",m_desc); + XML_Node& gv = flow.addChild("grid_data"); + addFloat(flow, "pressure", m_press, "Pa", "pressure"); + addFloatArray(gv,"z",m_z.size(),DATA_PTR(m_z), + "m","length"); + vector_fp x(static_cast(soln.nColumns())); + + soln.getRow(0,DATA_PTR(x)); + addFloatArray(gv,"u",x.size(),DATA_PTR(x),"m/s","velocity"); + + soln.getRow(1,DATA_PTR(x)); + addFloatArray(gv,"V", + x.size(),DATA_PTR(x),"1/s","rate"); + + soln.getRow(2,DATA_PTR(x)); + addFloatArray(gv,"T",x.size(),DATA_PTR(x),"K","temperature",0.0); + + soln.getRow(3,DATA_PTR(x)); + addFloatArray(gv,"L",x.size(),DATA_PTR(x),"N/m^4"); + + for (k = 0; k < m_nsp; k++) { + soln.getRow(4+k,DATA_PTR(x)); + addFloatArray(gv,m_thermo->speciesName(k), + x.size(),DATA_PTR(x),"","massFraction",0.0,1.0); + } + } + + + void StFlow::setJac(MultiJac* jac) { + m_jac = jac; + } + } // namespace diff --git a/Cantera/src/thermo/PDSS_SSVol.cpp b/Cantera/src/thermo/PDSS_SSVol.cpp index 78a4260dd..21ec884a6 100644 --- a/Cantera/src/thermo/PDSS_SSVol.cpp +++ b/Cantera/src/thermo/PDSS_SSVol.cpp @@ -133,12 +133,20 @@ namespace Cantera { m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI"); } else if (model == "temperature_polynomial") { volumeModel_ = cSSVOLUME_TPOLY; - getFloatArray(*ss, TCoeff_, true, "", "floatArray"); + int num = getFloatArray(*ss, TCoeff_, true, "", "volumeTemperaturePolynomial"); + if (num != 4) { + throw CanteraError("PDSS_SSVol::constructPDSSXML", + " Didn't get 3 density polynomial numbers for species " + speciesNode.name()); + } } else if (model == "density_temperature_polynomial") { volumeModel_ = cSSVOLUME_DENSITY_TPOLY; - getFloatArray(*ss, TCoeff_, true, "", "floatArray"); + int num = getFloatArray(*ss, TCoeff_, true, "", "densityTemperaturePolynomial"); + if (num != 4) { + throw CanteraError("PDSS_SSVol::constructPDSSXML", + " Didn't get 3 density polynomial numbers for species " + speciesNode.name()); + } } else { - throw CanteraError("PDSS_SSVol::initThermoXML", + throw CanteraError("PDSS_SSVol::constructPDSSXML", "standardState model for species isn't constant_incompressible: " + speciesNode.name()); } std::string id = ""; @@ -327,15 +335,15 @@ namespace Cantera { if (volumeModel_ == cSSVOLUME_CONSTANT ) { m_Vss_ptr[m_spindex] = m_constMolarVolume; } else if (volumeModel_ == cSSVOLUME_TPOLY) { - m_Vss_ptr[m_spindex] = TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * TCoeff_[2]); - dVdT_ = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2]; - d2VdT2_ = 2.0 * TCoeff_[2]; + m_Vss_ptr[m_spindex] = TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * (TCoeff_[2] + m_temp * TCoeff_[3])); + dVdT_ = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2] + 3.0 * m_temp * m_temp * TCoeff_[3]; + d2VdT2_ = 2.0 * TCoeff_[2] + 6.0 * m_temp * TCoeff_[3]; } else if (volumeModel_ == cSSVOLUME_DENSITY_TPOLY) { - doublereal dens = (TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * TCoeff_[2])); + doublereal dens = TCoeff_[0] + m_temp * (TCoeff_[1] + m_temp * (TCoeff_[2] + m_temp * TCoeff_[3])); m_Vss_ptr[m_spindex] = m_mw / dens; doublereal dens2 = dens * dens; - doublereal ddensdT = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2]; - doublereal d2densdT2 = 2.0 * TCoeff_[2]; + doublereal ddensdT = TCoeff_[1] + 2.0 * m_temp * TCoeff_[2] + 3.0 * m_temp * m_temp * TCoeff_[3]; + doublereal d2densdT2 = 2.0 * TCoeff_[2] + 6.0 * m_temp * TCoeff_[3]; dVdT_ = - m_mw / (dens2) * (ddensdT); d2VdT2_ = 2.0 * m_mw / (dens2 * dens) * ddensdT * ddensdT - m_mw / dens2 * d2densdT2; } else { diff --git a/Cantera/src/thermo/VPSSMgrFactory.cpp b/Cantera/src/thermo/VPSSMgrFactory.cpp index 0993635bb..186bf5576 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.cpp +++ b/Cantera/src/thermo/VPSSMgrFactory.cpp @@ -114,6 +114,10 @@ namespace Cantera { } else if (ssModel == "constant_incompressible" || ssModel == "constantVolume") { has_nasa_constVol++; + } else if (ssModel == "temperature_polynomial" || + ssModel == "density_temperature_polynomial" || + ssModel == "constant") { + has_other++; } else { throw UnknownVPSSMgrModel("getVPSSMgrTypes:", spNode->attrib("name")); @@ -126,6 +130,10 @@ namespace Cantera { } else if (ssModel == "constant_incompressible" || ssModel == "constantVolume") { has_shomate_constVol++; + } else if (ssModel == "temperature_polynomial" || + ssModel == "density_temperature_polynomial" || + ssModel == "constant") { + has_other++; } else { throw UnknownVPSSMgrModel("getVPSSMgrTypes:", spNode->attrib("name")); @@ -138,6 +146,10 @@ namespace Cantera { } else if (ssModel == "constant_incompressible" || ssModel == "constantVolume") { has_simple_constVol++; + } else if (ssModel == "temperature_polynomial" || + ssModel == "density_temperature_polynomial" || + ssModel == "constant") { + has_other++; } else { throw UnknownVPSSMgrModel("getVPSSMgrTypes:", spNode->attrib("name")); From e64a38175483ab2ae049c2f83d4d41ef19ec0045 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 00:10:48 +0000 Subject: [PATCH 004/446] Doxygen update. --- Cantera/src/thermo/HMWSoln.h | 4 ++-- Cantera/src/thermo/PDSS_SSVol.h | 9 +++++---- Cantera/src/thermo/WaterProps.cpp | 4 ++-- Cantera/src/thermo/WaterPropsIAPWS.cpp | 2 +- Cantera/src/thermo/WaterPropsIAPWS.h | 2 +- Cantera/src/thermo/WaterPropsIAPWSphi.cpp | 2 +- Cantera/src/thermo/WaterPropsIAPWSphi.h | 2 +- 7 files changed, 13 insertions(+), 12 deletions(-) diff --git a/Cantera/src/thermo/HMWSoln.h b/Cantera/src/thermo/HMWSoln.h index 7c55e8ab4..7b146f554 100644 --- a/Cantera/src/thermo/HMWSoln.h +++ b/Cantera/src/thermo/HMWSoln.h @@ -104,7 +104,7 @@ namespace Cantera { * water (IAPWS 1995 formulation) is used as its standard state. * All standard state properties for the solvent are based on * this real model for water, and involve function calls - * to the object that handles the real water model, #WaterPropsIAPWS. + * to the object that handles the real water model, #Cantera::WaterPropsIAPWS. * * The standard states for solutes are on the unit molality basis. * Therefore, in the documentation below, the normal \f$ o \f$ @@ -507,7 +507,7 @@ namespace Cantera { * \f] * * - *

Activity of the Water Solvent

+ *

Activity of the Water Solvent

* * The activity for the solvent water,\f$ a_o \f$, is not independent and must be * determined either from the Gibbs-Duhem relation or from taking the appropriate derivative diff --git a/Cantera/src/thermo/PDSS_SSVol.h b/Cantera/src/thermo/PDSS_SSVol.h index 422c28ed6..16dba893b 100644 --- a/Cantera/src/thermo/PDSS_SSVol.h +++ b/Cantera/src/thermo/PDSS_SSVol.h @@ -1,12 +1,12 @@ /** * @file PDSS_SSVol.h * Declarations for the class PDSS_SSVol (pressure dependent standard state) - * which handles calculations for a single species with an expression for the molar volume in a phase + * which handles calculations for a single species with an expression for the standard state molar volume in a phase * given by an enumerated data type * (see class \ref pdssthermo and \link Cantera::PDSS_SSVol PDSS_SSVol\endlink). */ /* - * Copywrite (2006) Sandia Corporation. Under the terms of + * Copywrite (2009) Sandia Corporation. Under the terms of * Contract DE-AC04-94AL85000 with Sandia Corporation, the * U.S. Government retains certain rights in this software. */ @@ -23,9 +23,10 @@ namespace Cantera { class XML_Node; class VPStandardStateTP; - //! Class for pressure dependent standard states that use a constant volume model + //! Class for pressure dependent standard states that uses a standard state volume + //! model of some sort. /*! - * Class for pressure dependent standard states that use a constant volume model. + * * * * @ingroup pdssthermo diff --git a/Cantera/src/thermo/WaterProps.cpp b/Cantera/src/thermo/WaterProps.cpp index 662fed741..64ed23fa1 100644 --- a/Cantera/src/thermo/WaterProps.cpp +++ b/Cantera/src/thermo/WaterProps.cpp @@ -495,7 +495,7 @@ namespace Cantera { // Parameters for the viscosityWater() function - + //@{ const double H[4] = {1., 0.978197, 0.579829, @@ -514,7 +514,7 @@ namespace Cantera { const double rhoStar = 317.763; // kg / m3 const double presStar = 22.115E6; // Pa const double muStar = 55.071E-6; //Pa s - + //@} // Returns the viscosity of water at the current conditions // (kg/m/s) diff --git a/Cantera/src/thermo/WaterPropsIAPWS.cpp b/Cantera/src/thermo/WaterPropsIAPWS.cpp index 652bbda7a..60f2a5fee 100644 --- a/Cantera/src/thermo/WaterPropsIAPWS.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWS.cpp @@ -2,7 +2,7 @@ * @file WaterPropsIAPWS.cpp * Definitions for a class for calculating the equation of state of water * from the IAPWS 1995 Formulation based on the steam tables thermodynamic - * basis (See class \link WaterPropsIAPWS WaterPropsIAPWS\endlink). + * basis (See class \link Cantera::WaterPropsIAPWS WaterPropsIAPWS\endlink). */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/WaterPropsIAPWS.h b/Cantera/src/thermo/WaterPropsIAPWS.h index 003441167..023d076a9 100644 --- a/Cantera/src/thermo/WaterPropsIAPWS.h +++ b/Cantera/src/thermo/WaterPropsIAPWS.h @@ -2,7 +2,7 @@ * @file WaterPropsIAPWS.h * Headers for a class for calculating the equation of state of water * from the IAPWS 1995 Formulation based on the steam tables thermodynamic - * basis (See class \link WaterPropsIAPWS WaterPropsIAPWS\endlink). + * basis (See class \link Cantera::WaterPropsIAPWS WaterPropsIAPWS\endlink). */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp index c8ee6dcfc..4299b97cd 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp @@ -1,7 +1,7 @@ /** * @file WaterPropsIAPWSphi.cpp * Definitions for Lowest level of the classes which support a real water model - * (see class #WaterPropsIAPWS and class #WaterPropsIAPWSphi). + * (see class \link Cantera::WaterPropsIAPWS WaterPropsIAPWS\endlink and class #WaterPropsIAPWSphi). */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.h b/Cantera/src/thermo/WaterPropsIAPWSphi.h index 7bdf45ca2..6a5b0ca87 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.h +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.h @@ -1,7 +1,7 @@ /** * @file WaterPropsIAPWSphi.h * Header for Lowest level of the classes which support a real water model - * (see class #WaterPropsIAPWS and class #WaterPropsIAPWSphi). + * (see class \link Cantera::WaterPropsIAPWS WaterPropsIAPWS\endlink and class \link WaterPropsIAPWSphi WaterPropsIAPWSphi\endlink). * * This class calculates dimensionless quantitites. */ From f38d72ddf983bff65be7ea6ccbbd84feb0b31251 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 00:11:16 +0000 Subject: [PATCH 005/446] Added new files. --- tools/doc/Cantera.cfg.in | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index 31d7c80bf..da93749d5 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -143,6 +143,7 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ VPSSMgr_General.h VPSSMgr_General.cpp \ VPSSMgrFactory.h VPSSMgrFactory.cpp \ PDSS_ConstVol.h PDSS_ConstVol.cpp \ + PDSS_SSVol.h PDSS_SSVol.cpp \ PDSS_IdealGas.h PDSS_IdealGas.cpp \ PDSS_Water.h PDSS_Water.cpp \ PDSS_HKFT.h PDSS_HKFT.cpp \ From ea7f8508307a668c887e546449908669ae33f634 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 00:53:56 +0000 Subject: [PATCH 006/446] Adding in more files. --- tools/doc/Cantera.cfg.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index da93749d5..fc66616e8 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -135,6 +135,8 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ DebyeHuckel.h DebyeHuckel.cpp \ MineralEQ3.h MineralEQ3.cpp \ HMWSoln.h HMWSoln.cpp HMWSoln_input.cpp \ + GibbsExcessVPSSTP.h GibbsExcessVPSSTP.cpp \ + MargulesVPSSTP.h MargulesVPSSTP.cpp \ VPSSMgr.h VPSSMgr.cpp VPSSMgr_types.h \ VPSSMgr_ConstVol.h VPSSMgr_ConstVol.cpp \ VPSSMgr_IdealGas.h VPSSMgr_IdealGas.cpp \ From 70ea5d84d26d57888b573cece8a95f3ebd887a79 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 01:02:02 +0000 Subject: [PATCH 007/446] Added files in ther thermo directory --- tools/doc/Cantera.cfg.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index fc66616e8..e0e0a72dc 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -137,6 +137,7 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ HMWSoln.h HMWSoln.cpp HMWSoln_input.cpp \ GibbsExcessVPSSTP.h GibbsExcessVPSSTP.cpp \ MargulesVPSSTP.h MargulesVPSSTP.cpp \ + IonsFromNeutralVPSSTP.h IonsFromNeutralVPSSTP.cpp \ VPSSMgr.h VPSSMgr.cpp VPSSMgr_types.h \ VPSSMgr_ConstVol.h VPSSMgr_ConstVol.cpp \ VPSSMgr_IdealGas.h VPSSMgr_IdealGas.cpp \ @@ -149,6 +150,7 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ PDSS_IdealGas.h PDSS_IdealGas.cpp \ PDSS_Water.h PDSS_Water.cpp \ PDSS_HKFT.h PDSS_HKFT.cpp \ + PDSS_IonsFromNeutral.h PDSS_IonsFromNeutral.cpp \ IdealSolnGasVPSS.h IdealSolnGasVPSS.cpp \ ConstDensityThermo.h ConstDensityThermo.cpp \ WaterPropsIAPWSphi.h WaterPropsIAPWSphi.cpp \ From d5b74320acf6171ee6b596d861f88fdadd2ac204 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 01:02:44 +0000 Subject: [PATCH 008/446] Doxygen updates Started to document new PDSS formulations --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 10 +--------- Cantera/src/thermo/GibbsExcessVPSSTP.h | 8 ++++++-- Cantera/src/thermo/MargulesVPSSTP.h | 2 +- Cantera/src/thermo/PDSS.h | 15 +++++++++++++++ 4 files changed, 23 insertions(+), 12 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 6958d2b6b..4019c3886 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -257,15 +257,7 @@ namespace Cantera { return 0; } - //@} - /// @name Properties of the Standard State of the Species in the Solution - //@{ - - - - //@} - /// @name Thermodynamic Values for the Species Reference States - //@{ + double GibbsExcessVPSSTP::checkMFSum(const doublereal * const x) const { doublereal norm = accumulate(x, x + m_kk, 0.0); diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 75242aec8..c9d27094f 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -1,9 +1,9 @@ /** - * @file gibbsExcessVPSSTP.h + * @file GibbsExcessVPSSTP.h * Header for intermediate ThermoPhase object for phases which * employ gibbs excess free energy based formulations * (see \ref thermoprops - * and class \link Cantera::gibbsExcessVPSSTP gibbsExcessVPSSTP\endlink). + * and class \link Cantera::GibbsExcessVPSSTP GibbsExcessVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating @@ -517,6 +517,10 @@ namespace Cantera { protected: + //! utility routine to check mole fraction sum + /*! + * @param x vector of mole fractions. + */ double checkMFSum(const doublereal * const x) const; protected: diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 5f78c12fb..128caa440 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -1,5 +1,5 @@ /** - * @file Margules.h + * @file MargulesVPSSTP.h * Header for intermediate ThermoPhase object for phases which * employ gibbs excess free energy based formulations * (see \ref thermoprops diff --git a/Cantera/src/thermo/PDSS.h b/Cantera/src/thermo/PDSS.h index 1f542c417..ad989cfe8 100644 --- a/Cantera/src/thermo/PDSS.h +++ b/Cantera/src/thermo/PDSS.h @@ -100,6 +100,21 @@ namespace Cantera { * pressure dependencies to these thermo functions. * . * + * - PDSS_SSVol + * - standardState model = "constant_incompressible" || model == "constant" + * - standardState model = "temperature_polynomial" + * - standardState model = "density_temperature_polynomial" + * - This model assumes that the species in the phase obey a + * fairly general equation of state, but one that separates out + * the calculation of the standard state density and/or volume. + * Models include a cubic polynomial in temperature for either + * the standard state volume or the standard state density. + * The manager uses a SimpleThermo object to handle the + * calculation of the reference state. This object then adds the + * pressure dependencies and the volume terms to these thermo functions + * to complete the representation. + * . + * * - PDSS_Water_ * - standardState model = "Water" * - This model assumes that From 23732968c6ba6385b6f5ca17e457a9c2a5eeebfd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 14:26:07 +0000 Subject: [PATCH 009/446] doxygen warning messages removed. --- Cantera/src/thermo/MargulesVPSSTP.h | 79 ++++++++++++++++++++++------- 1 file changed, 61 insertions(+), 18 deletions(-) diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 128caa440..e69bda3a3 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -336,10 +336,11 @@ namespace Cantera { //! Special constructor for a hard-coded problem /*! - * - * LiKCl treating the PseudoBinary layer as passthrough. - * -> test to predict the eutectic and liquidus correctly. - * + * + * @param testProb Hard-coded value. Only the value of 1 is + * used. It's for + * a LiKCl system + * -> test to predict the eutectic and liquidus correctly. */ MargulesVPSSTP(int testProb); @@ -350,7 +351,7 @@ namespace Cantera { * * @param b class to be copied */ - MargulesVPSSTP(const MargulesVPSSTP&b); + MargulesVPSSTP(const MargulesVPSSTP& b); //! Assignment operator /*! @@ -537,6 +538,9 @@ namespace Cantera { * \f[ * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] + * + * @param hbar Vector of returned partial molar enthalpies + * (length m_kk, units = J/kmol) */ virtual void getPartialMolarEnthalpies(doublereal* hbar) const; @@ -554,6 +558,9 @@ namespace Cantera { * - R \ln( \gamma_k X_k) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] + * + * @param sbar Vector of returned partial molar entropies + * (length m_kk, units = J/kmol/K) */ virtual void getPartialMolarEntropies(doublereal* sbar) const; @@ -567,7 +574,7 @@ namespace Cantera { * Units: J/kmol * * @param mu output vector containing the species electrochemical potentials. - * Length: m_kk. + * Length: m_kk., units = J/kmol */ void getElectrochemPotentials(doublereal* mu) const; @@ -581,6 +588,10 @@ namespace Cantera { * * @param dlnActCoeffdT Output vector of temperature derivatives of the * log Activity Coefficients. length = m_kk + * + * @param dlnActCoeffdT Vector of returned derivatives of + * ln (actCoeff) wrt temperature. + * (length m_kk, units = 1/K) */ virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const; @@ -692,11 +703,16 @@ namespace Cantera { * This function reads the XML file and writes the coefficients * it finds to an internal data structures. * - * @param BinSalt reference to the XML_Node named "binaryNeutralSpeciesParameters" - * containing the binary interaction + * @param xmlBinarySpecies Reference to the XML_Node named "binaryNeutralSpeciesParameters" + * containing the binary interaction */ - void readXMLBinarySpecies(XML_Node &xmLBinarySpecies); + void readXMLBinarySpecies(XML_Node &xmlBinarySpecies); + //! Resize internal arrays within the object that depend upon the number + //! of binary Margules interaction terms + /*! + * @param num Number of binary Margules interaction terms + */ void resizeNumInteractions(const int num); @@ -711,11 +727,11 @@ namespace Cantera { */ void s_update_lnActCoeff() const; - // Update the derivative of the log of the activity coefficients wrt T - /* + //! Update the derivative of the log of the activity coefficients wrt T + /*! * This function will be called to update the internally storred - * natural logarithm of the activity coefficients - * + * derivative of the natural logarithm of the activity coefficients + * wrt temperature. */ void s_update_dlnActCoeff_dT() const; @@ -733,30 +749,57 @@ namespace Cantera { //! number of binary interaction expressions - int numBinaryInteractions_; + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_HE_b_ij; + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_HE_c_ij; + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_HE_d_ij; - + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_SE_b_ij; + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_SE_c_ij; + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression mutable vector_fp m_SE_d_ij; + //! vector of species indices representing species A in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species A. + */ vector_int m_pSpecies_A_ij; + + //! vector of species indices representing species B in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species B. + */ vector_int m_pSpecies_B_ij; - + //! form of the Margules interaction expression + /*! + * Currently there is only one form. + */ int formMargules_; - int formTempModel_; - private: + //! form of the temperatuer dependence of the Margules interaction expression + /*! + * Currently there is only one form -> constant wrt temperature. + */ + int formTempModel_; }; From 6de5cb2e99e930dbec854630741780fb306b0e60 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 15:09:55 +0000 Subject: [PATCH 010/446] Doxygen update - Still lots to do here. --- Cantera/src/transport/AqueousTransport.cpp | 4 +- Cantera/src/transport/AqueousTransport.h | 2 +- Cantera/src/transport/DustyGasTransport.cpp | 32 +-- Cantera/src/transport/DustyGasTransport.h | 203 ++++++++++---------- Cantera/src/transport/MixTransport.h | 26 ++- Cantera/src/transport/MultiTransport.cpp | 7 +- Cantera/src/transport/MultiTransport.h | 16 +- Cantera/src/transport/TransportBase.h | 25 ++- Cantera/src/transport/WaterTransport.h | 3 +- 9 files changed, 159 insertions(+), 159 deletions(-) diff --git a/Cantera/src/transport/AqueousTransport.cpp b/Cantera/src/transport/AqueousTransport.cpp index 55e820462..8e730600b 100644 --- a/Cantera/src/transport/AqueousTransport.cpp +++ b/Cantera/src/transport/AqueousTransport.cpp @@ -1,6 +1,6 @@ /** - * @file MixTransport.cpp - * Mixture-averaged transport properties for ideal gas mixtures. + * @file AqueousTransport.cpp + * Transport properties for aqueous systems */ /* * $Revision: 1.4 $ diff --git a/Cantera/src/transport/AqueousTransport.h b/Cantera/src/transport/AqueousTransport.h index 1d593bd16..7179fe5e9 100644 --- a/Cantera/src/transport/AqueousTransport.h +++ b/Cantera/src/transport/AqueousTransport.h @@ -1,5 +1,5 @@ /** - * @file LiquidTransport.h + * @file AqueousTransport.h * Header file defining class AqueousTransport */ /* diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index f16d2f3b5..c62e91bea 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -148,35 +148,11 @@ namespace Cantera { } } -// void DustyGasTransport::getMolarFluxes(const double* grad_conc, -// double grad_P, double* fluxes) { -// updateMultiDiffCoeffs(); -// copy(grad_conc, grad_conc + m_nsp, m_spwork.begin()); -// multiply(m_multidiff, m_spwork.begin(), fluxes); -// m_thermo->getConcentrations(m_spwork.begin()); -// divide_each(m_spwork.begin(), m_spwork.end(), m_dk.begin()); + void DustyGasTransport::getMolarFluxes(const doublereal* const state1, + const doublereal * const state2, + const doublereal delta, + doublereal * const fluxes) { -// // if no permeability has been specified, use result for -// // close-packed spheres -// double b = 0.0; -// if (m_perm < 0.0) { -// double p = m_porosity; -// double d = m_diam; -// double t = m_tortuosity; -// b = p*p*p*d*d/(72.0*t*(1.0-p)*(1.0-p)); -// } -// else { -// b = m_perm; -// } -// b *= grad_P / m_gastran->viscosity(); -// scale(m_spwork.begin(), m_spwork.end(), m_spwork.begin(), b); -// increment(m_multidiff, m_spwork.begin(), fluxes); -// scale(fluxes, fluxes + m_nsp, fluxes, -1.0); -// } - - - void DustyGasTransport::getMolarFluxes(const doublereal* state1, - const doublereal* state2, double delta, double* fluxes) { int k; doublereal conc1, conc2; doublereal* cbar = DATA_PTR(m_spwork); diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index e28fa4ae5..bad14bc4f 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -19,143 +19,152 @@ namespace Cantera { - /// - /// Class DustyGasTransport implements the Dusty Gas model for - /// transport in porous media. As implemented here, only species - /// transport is handled. The viscosity, thermal conductivity, and - /// thermal diffusion coefficients are not implemented. - /// - class DustyGasTransport : public Transport { + /// + /// Class DustyGasTransport implements the Dusty Gas model for + /// transport in porous media. As implemented here, only species + /// transport is handled. The viscosity, thermal conductivity, and + /// thermal diffusion coefficients are not implemented. + /// + class DustyGasTransport : public Transport { - public: + public: - /// default constructor - DustyGasTransport(thermo_t* thermo=0); + /// default constructor + DustyGasTransport(thermo_t* thermo=0); - /// Destructor. Does nothing, since class allocates no memory - /// on the heap. - virtual ~DustyGasTransport() {} + /// Destructor. Does nothing, since class allocates no memory + /// on the heap. + virtual ~DustyGasTransport() {} - //--------------------------------------------------------- - // overloaded base class methods + //--------------------------------------------------------- + // overloaded base class methods - virtual int model() const { return cDustyGasTransport; } + virtual int model() const { return cDustyGasTransport; } - virtual void setParameters(const int type, const int k, const doublereal* const p); + virtual void setParameters(const int type, const int k, const doublereal* const p); - virtual void getMultiDiffCoeffs(const int ld, doublereal* const d); + virtual void getMultiDiffCoeffs(const int ld, doublereal* const d); - virtual void getMolarFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, - doublereal* fluxes); + //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic + //! state at two nearby points. + /*! + * @param state1 Array of temperature, density, and mass + * fractions for state 1. + * @param state2 Array of temperature, density, and mass + * fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). + */ + virtual void getMolarFluxes(const doublereal * const state1, + const doublereal* const state2, const doublereal delta, + doublereal* const fluxes); - //----------------------------------------------------------- - // new methods added in this class + //----------------------------------------------------------- + // new methods added in this class - /// Set the porosity (dimensionless) - void setPorosity(doublereal porosity) { - m_porosity = porosity; - m_knudsen_ok = false; - m_bulk_ok = false; - } + /// Set the porosity (dimensionless) + void setPorosity(doublereal porosity) { + m_porosity = porosity; + m_knudsen_ok = false; + m_bulk_ok = false; + } - /// Set the tortuosity (dimensionless) - void setTortuosity(doublereal tort) { - m_tortuosity = tort; - m_knudsen_ok = false; - m_bulk_ok = false; - } + /// Set the tortuosity (dimensionless) + void setTortuosity(doublereal tort) { + m_tortuosity = tort; + m_knudsen_ok = false; + m_bulk_ok = false; + } - /// Set the mean pore radius (m) - void setMeanPoreRadius(doublereal rbar) { - m_pore_radius = rbar; - m_knudsen_ok = false; - } + /// Set the mean pore radius (m) + void setMeanPoreRadius(doublereal rbar) { + m_pore_radius = rbar; + m_knudsen_ok = false; + } - /// Set the mean particle diameter - void setMeanParticleDiameter(doublereal dbar) { - m_diam = dbar; - } + /// Set the mean particle diameter + void setMeanParticleDiameter(doublereal dbar) { + m_diam = dbar; + } - /// Set the permeability. If not set, the value for - /// close-packed spheres will be used by default. - void setPermeability(doublereal B) { - m_perm = B; - } + /// Set the permeability. If not set, the value for + /// close-packed spheres will be used by default. + void setPermeability(doublereal B) { + m_perm = B; + } - /// Return a reference to the transport manager used to compute the gas - /// binary diffusion coefficients and the visdcosity. - Transport& gasTransport() { return *m_gastran; } + /// Return a reference to the transport manager used to compute the gas + /// binary diffusion coefficients and the visdcosity. + Transport& gasTransport() { return *m_gastran; } - friend class TransportFactory; + friend class TransportFactory; - protected: + protected: - // called by TransportFactory - void initialize(ThermoPhase* phase, Transport* gastr); + // called by TransportFactory + void initialize(ThermoPhase* phase, Transport* gastr); - private: + private: - void updateTransport_T(); - void updateTransport_C(); + void updateTransport_T(); + void updateTransport_C(); - void updateBinaryDiffCoeffs(); - void updateMultiDiffCoeffs(); - void updateKnudsenDiffCoeffs(); - void eval_H_matrix(); + void updateBinaryDiffCoeffs(); + void updateMultiDiffCoeffs(); + void updateKnudsenDiffCoeffs(); + void eval_H_matrix(); - // gas attributes - int m_nsp; - doublereal m_tmin, m_tmax; - vector_fp m_mw; + // gas attributes + int m_nsp; + doublereal m_tmin, m_tmax; + vector_fp m_mw; - // property values + // property values - /// binary diffusion coefficients - DenseMatrix m_d; + /// binary diffusion coefficients + DenseMatrix m_d; - /// mole fractions - vector_fp m_x; + /// mole fractions + vector_fp m_x; - /// Knudsen diffusion coefficients - vector_fp m_dk; + /// Knudsen diffusion coefficients + vector_fp m_dk; - /// temperature - doublereal m_temp; + /// temperature + doublereal m_temp; - /// multicomponent diffusion coefficients - DenseMatrix m_multidiff; + /// multicomponent diffusion coefficients + DenseMatrix m_multidiff; - // work space - vector_fp m_spwork; - vector_fp m_spwork2; + // work space + vector_fp m_spwork; + vector_fp m_spwork2; - // concentration gradients - //vector_fp m_gradConc; - //vector_fp m_conc; + // concentration gradients + //vector_fp m_gradConc; + //vector_fp m_conc; - doublereal m_gradP; /// pressure gradient + doublereal m_gradP; /// pressure gradient - bool m_knudsen_ok; - bool m_bulk_ok; - bool m_conc_set; - bool m_gradConc_set; - bool m_gradP_set; + bool m_knudsen_ok; + bool m_bulk_ok; + bool m_conc_set; + bool m_gradConc_set; + bool m_gradP_set; - doublereal m_porosity; /// porosity - doublereal m_tortuosity; /// tortuosity - doublereal m_pore_radius; /// pore radius (m) - doublereal m_diam; /// particle diameter (m) - doublereal m_perm; /// permeability + doublereal m_porosity; /// porosity + doublereal m_tortuosity; /// tortuosity + doublereal m_pore_radius; /// pore radius (m) + doublereal m_diam; /// particle diameter (m) + doublereal m_perm; /// permeability - Transport* m_gastran; /// pointer to gas transport manager + Transport* m_gastran; /// pointer to gas transport manager - }; + }; } #endif diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 18a781577..55b49503a 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -1,20 +1,20 @@ /** * @file MixTransport.h - * Header file defining class MixTransport + * Headers for the MixTransport object, which models transport properties + * in ideal gas solutions using a mixture averaged approximation + * (see \ref tranprops and \link Cantera::MixTransport MixTransport \endlink) . + * */ - /* $Author: hkmoffa $ * $Revision: 1.11 $ * $Date: 2009/03/27 18:24:39 $ */ - // Copyright 2001 California Institute of Technology #ifndef CT_MIXTRAN_H #define CT_MIXTRAN_H - // turn off warnings under Windows #ifdef WIN32 #pragma warning(disable:4786) @@ -28,8 +28,6 @@ #include #include -using namespace std; - // Cantera includes #include "TransportBase.h" #include "DenseMatrix.h" @@ -152,9 +150,9 @@ namespace Cantera { vector_fp m_mw; // polynomial fits - vector m_visccoeffs; - vector m_condcoeffs; - vector m_diffcoeffs; + std::vector m_visccoeffs; + std::vector m_condcoeffs; + std::vector m_diffcoeffs; vector_fp m_polytempvec; // property values @@ -165,11 +163,11 @@ namespace Cantera { array_fp m_molefracs; - vector > m_poly; - vector m_astar_poly; - vector m_bstar_poly; - vector m_cstar_poly; - vector m_om22_poly; + std::vector > m_poly; + std::vector m_astar_poly; + std::vector m_bstar_poly; + std::vector m_cstar_poly; + std::vector m_om22_poly; DenseMatrix m_astar; DenseMatrix m_bstar; DenseMatrix m_cstar; diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index 1f9e443c0..e3b83db98 100755 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -672,9 +672,10 @@ namespace Cantera { } } - void MultiTransport::getMolarFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, - doublereal* fluxes) { + void MultiTransport::getMolarFluxes(const doublereal* const state1, + const doublereal * const state2, + const doublereal delta, + doublereal * const fluxes) { getMassFluxes(state1, state2, delta, fluxes); int k, nsp = m_thermo->nSpecies(); for (k = 0; k < nsp; k++) { diff --git a/Cantera/src/transport/MultiTransport.h b/Cantera/src/transport/MultiTransport.h index 5979b8ce9..03bb146ee 100644 --- a/Cantera/src/transport/MultiTransport.h +++ b/Cantera/src/transport/MultiTransport.h @@ -139,9 +139,19 @@ namespace Cantera { int ldf, doublereal* fluxes); - virtual void getMolarFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, - doublereal* fluxes); + //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic + //! state at two nearby points. + /*! + * @param state1 Array of temperature, density, and mass + * fractions for state 1. + * @param state2 Array of temperature, density, and mass + * fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). + */ + virtual void getMolarFluxes(const doublereal* const state1, + const doublereal* const state2, + const doublereal delta, + doublereal* const fluxes); virtual void getMassFluxes(const doublereal* state1, const doublereal* state2, doublereal delta, diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 864469f8c..12309ec30 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -1,5 +1,9 @@ /** * @file TransportBase.h + * Headers for the Transport object, which is the virtual base class + * for all transport property evaluators and also includes the tranprops group definition + * (see \ref tranprops and \link Cantera::Transport Transport \endlink) . + * * Provides class Transport. */ @@ -301,18 +305,21 @@ namespace Cantera { getSpeciesFluxes( ndim, grad_T, ldx, grad_X, ldf, fluxes ); } - /** - * Get the molar fluxes [kmol/m^2/s], given the thermodynamic - * state at two nearby points. + + //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic + //! state at two nearby points. + /*! * @param state1 Array of temperature, density, and mass - * fractions for state 1. + * fractions for state 1. * @param state2 Array of temperature, density, and mass - * fractions for state 2. - * @param delta Distance from state 1 to state 2 (m). + * fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). */ - virtual void getMolarFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, - doublereal* fluxes) { err("getMolarFluxes"); } + virtual void getMolarFluxes(const doublereal * const state1, + const doublereal * const state2, const doublereal delta, + doublereal * const fluxes) { + err("getMolarFluxes"); + } /** * Get the mass fluxes [kg/m^2/s], given the thermodynamic diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index 31d89966a..cd858ee8d 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -1,6 +1,5 @@ /** - * - * @file LiquidTransport.h + * @file WaterTransport.h * Header file defining class LiquidTransport */ /* From 4776ef8f8d8d15c9505a7993b84620ec7176fb32 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Oct 2009 15:10:27 +0000 Subject: [PATCH 011/446] Added all of the files in the transport directory. --- tools/doc/Cantera.cfg.in | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index e0e0a72dc..e56d4f6dc 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -163,7 +163,16 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ Nasa9PolyMultiTempRegion.h Nasa9PolyMultiTempRegion.cpp \ vcs_internal.h vcs_defs.h \ vcs_MultiPhaseEquil.h vcs_MultiPhaseEquil.cpp \ - FalloffFactory.h FalloffFactory.cpp + FalloffFactory.h FalloffFactory.cpp \ + TransportBase.h TransportBase.cpp TransportParams.h \ + MMCollisionInt.h L_matrix.h MMCollisionInt.cpp FtnTransport.h \ + TransportFactory.h TransportFactory.cpp \ + MultiTransport.h MultiTransport.cpp MixTransport.h MixTransport.cpp \ + DustyGasTransport.h DustyGasTransport.cpp \ + SolidTransport.h SolidTransport.cpp \ + SimpleTransport.h SimpleTransport.cpp \ + LiquidTransport.h LiquidTransportParams.h LiquidTransport.cpp \ + AqueousTransport.h AqueousTransport.cpp WaterTransport.h WaterTransport.cpp RECURSIVE = NO EXCLUDE = CVS examples converters zeroD EXCLUDE_SYMLINKS = NO From d641b8f49256ee762b62de339d81297ec63dd973 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 18:23:15 +0000 Subject: [PATCH 012/446] TransportFactory.h, TransportFactory.cpp TransportFactory::setupLiquidTransport: Removed "transport_database" argument since this can equally well be pulled from thermo object also passed. The "transport_databse" is now called species_database (since it holds the vector of species nodes. The method getLiquidTransportData is renamed to getLiquidSpeciesTransportData to reflect the fact that it just parses the species node parts of the transport data. A new XML_Node, called phase_database and corresponding to the phase, is defined. If this has a child "transport" node, this node is passed to the new method. void TransportFactory::getLiquidInteractionsTransportData( const XML_Node &transportNode, XML_Node& log, const std::vector& names, LiquidTransportParams& tr); This method, largely unfilled, will parse models for species-species interactions in the liquid phase. TransportFactory::getLiquidSpeciesTransportData Largely minor changes to the parsing of the species transport properties, but allow all temperature dependence models for hydrodynamic radius just for generality. LiquidTransportData objects are now pushed directly onto LiquidTransportParams instead of filling members of LiquidTransportParams. Removed most of the unit conversion and will rely largely on the parser unit conversions. Need to be careful here, especially with the hydrodynamic radius which will likely be given in Angstroms and not meters. --- Cantera/src/transport/TransportFactory.cpp | 201 +++++++++++++-------- Cantera/src/transport/TransportFactory.h | 17 +- 2 files changed, 136 insertions(+), 82 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 3fce58ea3..180651b0e 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -521,9 +521,11 @@ namespace Cantera { * viscosity transport data is provided in Arhennius form. */ void TransportFactory::setupLiquidTransport(std::ostream &flog, - const std::vector &transport_database, thermo_t* thermo, int log_level, LiquidTransportParams& trParam) { + const std::vector & species_database = thermo->speciesData(); + const XML_Node* phase_database = &thermo->xml(); + // constant mixture attributes trParam.thermo = thermo; trParam.nsp_ = trParam.thermo->nSpecies(); @@ -539,22 +541,27 @@ namespace Cantera { trParam.thermo->molecularWeights().end(), trParam.mw.begin()); // Resize all other vectors in trParam - trParam.visc_A.resize(nsp, 0.0); - trParam.visc_n.resize(nsp, 0.0); - trParam.visc_Tact.resize(nsp, 0.0); - trParam.thermCond_A.resize(nsp, 0.0); - trParam.thermCond_n.resize(nsp, 0.0); - trParam.thermCond_Tact.resize(nsp, 0.0); - trParam.visc_Eij.resize(nsp, nsp, 0.0); - trParam.visc_Sij.resize(nsp, nsp, 0.0); - trParam.hydroRadius.resize(nsp, 0.0); - trParam.A_k_cond.resize(nsp, 0.0); - trParam.B_k_cond.resize(nsp, 0.0); trParam.LTData.resize(nsp); + // Need to identify a method to obtain interaction matrices. + // This will fill LiquidTransportParams members visc_Eij, visc_Sij + trParam.visc_Eij.resize(nsp,nsp); + trParam.visc_Sij.resize(nsp,nsp); + cout << "Still no support for species viscosity interactions in TransportFactory.cpp" << endl; + XML_Node root, log; - getLiquidTransportData(transport_database, log, - trParam.thermo->speciesNames(), trParam); + // Note that getLiquidSpeciesTransportData just populates the pure species transport data. + getLiquidSpeciesTransportData(species_database, log, + trParam.thermo->speciesNames(), trParam); + + // getLiquidInteractionsTransportData() populates the + // species-species interaction models parameters + // like visc_Eij + if (phase_database->hasChild("transport")) { + XML_Node& transportNode = phase_database->child("transport"); + getLiquidInteractionsTransportData(transportNode, log, + trParam.thermo->speciesNames(), trParam); + } } @@ -596,8 +603,6 @@ namespace Cantera { thermo_t* thermo, int log_level) { - const std::vector & transport_database = thermo->speciesData(); - LiquidTransportParams trParam; #ifdef DEBUG_MODE ofstream flog("transport_log.xml"); @@ -609,7 +614,7 @@ namespace Cantera { // create the object, but don't associate it with a file std::ostream &flog(std::cout); #endif - setupLiquidTransport(flog, transport_database, thermo, log_level, trParam); + setupLiquidTransport(flog, thermo, log_level, trParam); // do model-specific initialization tran->initLiquid(trParam); #ifdef DEBUG_MODE @@ -838,7 +843,7 @@ namespace Cantera { * instance of TransportParams containing the transport data for * these species read from the file. */ - void TransportFactory::getLiquidTransportData( const std::vector &xspecies, + void TransportFactory::getLiquidSpeciesTransportData( const std::vector &xspecies, XML_Node& log, const std::vector &names, LiquidTransportParams& trParam) @@ -848,9 +853,7 @@ namespace Cantera { * Create a map of species names versus liquid transport data parameters */ std::map datatable; - doublereal A_visc, n_visc, Tact_visc, hydrodynamic_radius; - doublereal A_thcond, n_thcond, Tact_thcond; - doublereal A_spdiff, n_spdiff, Tact_spdiff; + doublereal A_k, n_k, Tact_k; int nsp = static_cast(xspecies.size()); std::cout << "Size of xspecies " << nsp << std::endl; @@ -882,20 +885,56 @@ namespace Cantera { * hydrodynamic radius * * format: - * 3.0 + * 3.0 * 3.0 + * + * 1.0 + * 2.0 + * 3.0 + * + * + * + * 0.0. 1.0, 2.0, 3.0, 4.0 + * + * */ if (trNode.hasChild("hydrodynamic_radius")) { XML_Node& hnode = trNode.child("hydrodynamic_radius"); + std::string units = lowercase(hnode["units"]); + if ( units == "" ) + cout << "Warning::hydrodynamic_radius units not given for " + << name << endl + << " Units assumed to be meters." << endl; std::string model = lowercase(hnode["model"]); if (model == "" || model == "constant") { - hydrodynamic_radius = hnode.fp_value(); - if (hydrodynamic_radius > 0.0) data.hydroradius = hydrodynamic_radius; - else throw TransportDBError(linenum, + A_k = getFloat(trNode, "hydrodynamic_radius", "toSI"); + //A_k = hnode.fp_value(); + //// Angstroms -> meters + //A_k = 1.e-10 * A_k; + if (A_k > 0.0) { + (data.hydroRadiusCoeffs).push_back(A_k); + } else throw TransportDBError(linenum, "negative or zero hydrodynamic radius"); data.model_hydroradius = LTR_MODEL_CONSTANT; + } else if (model == "arrhenius") { + getArrhenius(hnode, A_k, n_k, Tact_k); + if (A_k <= 0.0) { + throw TransportDBError(linenum, "negative or zero viscosity"); + } + // Angstroms -> meters + //already done in getArrhenius??? + //A_k = 1.e-10 * A_k; + (data.hydroRadiusCoeffs).push_back(A_k); + (data.hydroRadiusCoeffs).push_back(n_k); + (data.hydroRadiusCoeffs).push_back(Tact_k); + data.model_hydroradius = LTR_MODEL_ARRHENIUS; + } else if (model == "coeff") { + getFloatArray(hnode, vCoeff, true); // if units labeled, convert Angstroms -> meters + data.hydroRadiusCoeffs = vCoeff; + vCoeff.clear(); + data.model_hydroradius = LTR_MODEL_POLY; } else { - throw CanteraError(" TransportFactory::getLiquidTransportData", + throw CanteraError(" TransportFactory::getLiquidSpeciesTransportData", "Unknown model for hydrodynamic_radius:" + model); } } @@ -921,27 +960,27 @@ namespace Cantera { XML_Node& vnode = trNode.child("viscosity"); std::string model = lowercase(vnode["model"]); if (model == "" || model == "constant") { - A_visc = ctml::getFloatCurrent(vnode, "toSI"); - if (A_visc > 0.0) (data.viscCoeffs).push_back(A_visc); + A_k = ctml::getFloatCurrent(vnode, "toSI"); + if (A_k > 0.0) (data.viscCoeffs).push_back(A_k); else throw TransportDBError(linenum, "negative or zero viscosity"); data.model_viscosity = LTR_MODEL_CONSTANT; } else if (model == "arrhenius") { - getArrhenius(vnode, A_visc, n_visc, Tact_visc); - if (A_visc <= 0.0) { + getArrhenius(vnode, A_k, n_k, Tact_k); + if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero viscosity"); } - (data.viscCoeffs).push_back(A_visc); - (data.viscCoeffs).push_back(n_visc); - (data.viscCoeffs).push_back(Tact_visc); + (data.viscCoeffs).push_back(A_k); + (data.viscCoeffs).push_back(n_k); + (data.viscCoeffs).push_back(Tact_k); data.model_viscosity = LTR_MODEL_ARRHENIUS; } else if (model == "coeff") { getFloatArray(vnode, vCoeff, true); data.viscCoeffs = vCoeff; vCoeff.clear(); - data.model_viscosity = LTR_MODEL_COEFF; + data.model_viscosity = LTR_MODEL_POLY; } else { - throw CanteraError(" TransportFactory::getLiquidTransportData", + throw CanteraError(" TransportFactory::getLiquidSpeciesTransportData", "Unknown model for viscosity:" + vnode["model"]); } } @@ -967,27 +1006,27 @@ namespace Cantera { XML_Node& tnode = trNode.child("thermalConductivity"); std::string model = lowercase(tnode["model"]); if (model == "" || model == "constant") { - A_thcond = ctml::getFloatCurrent(tnode, "toSI"); - if (A_thcond > 0.0) (data.thermalCondCoeffs).push_back(A_thcond); + A_k = ctml::getFloatCurrent(tnode, "toSI"); + if (A_k > 0.0) (data.thermalCondCoeffs).push_back(A_k); else throw TransportDBError(linenum, "negative or zero thermalConductivity"); data.model_thermalCond = LTR_MODEL_CONSTANT; } else if (model == "arrhenius") { - getArrhenius(tnode, A_thcond, n_thcond, Tact_thcond); - if (A_thcond <= 0.0) { + getArrhenius(tnode, A_k, n_k, Tact_k); + if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero thermalConductivity"); } - (data.thermalCondCoeffs).push_back(A_thcond); - (data.thermalCondCoeffs).push_back(n_thcond); - (data.thermalCondCoeffs).push_back(Tact_thcond); + (data.thermalCondCoeffs).push_back(A_k); + (data.thermalCondCoeffs).push_back(n_k); + (data.thermalCondCoeffs).push_back(Tact_k); data.model_thermalCond = LTR_MODEL_ARRHENIUS; } else if (model == "coeff") { getFloatArray(tnode, vCoeff, true); data.thermalCondCoeffs = vCoeff; vCoeff.clear(); - data.model_thermalCond = LTR_MODEL_COEFF; + data.model_thermalCond = LTR_MODEL_POLY; } else { - throw CanteraError(" TransportFactory::getLiquidTransportData", + throw CanteraError(" TransportFactory::getLiquidSpeciesTransportData", "Unknown model for thermalConductivity:" + tnode["model"]); } } @@ -1014,26 +1053,26 @@ namespace Cantera { XML_Node& dnode = trNode.child("speciesDiffusivity"); std::string model = lowercase(dnode["model"]); if (model == "" || model == "constant") { - A_spdiff = ctml::getFloatCurrent(dnode, "toSI"); - if (A_spdiff > 0.0) (data.speciesDiffusivityCoeffs).push_back(A_spdiff); + A_k = ctml::getFloatCurrent(dnode, "toSI"); + if (A_k > 0.0) (data.speciesDiffusivityCoeffs).push_back(A_k); else throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); data.model_speciesDiffusivity = LTR_MODEL_CONSTANT; } else if (model == "arrhenius") { - getArrhenius(dnode, A_spdiff, n_spdiff, Tact_spdiff); - if (A_spdiff <= 0.0) { + getArrhenius(dnode, A_k, n_k, Tact_k); + if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); } - (data.speciesDiffusivityCoeffs).push_back(A_spdiff); - (data.speciesDiffusivityCoeffs).push_back(n_spdiff); - (data.speciesDiffusivityCoeffs).push_back(Tact_spdiff); + (data.speciesDiffusivityCoeffs).push_back(A_k); + (data.speciesDiffusivityCoeffs).push_back(n_k); + (data.speciesDiffusivityCoeffs).push_back(Tact_k); data.model_speciesDiffusivity = LTR_MODEL_ARRHENIUS; } else if (model == "coeff") { getFloatArray(dnode, vCoeff, true); data.speciesDiffusivityCoeffs = vCoeff; - data.model_speciesDiffusivity = LTR_MODEL_COEFF; + data.model_speciesDiffusivity = LTR_MODEL_POLY; } else { - throw CanteraError(" TransportFactory::getLiquidTransportData", + throw CanteraError(" TransportFactory::getLiquidSpeciesTransportData", "Unknown model for speciesDiffusivity:" + dnode["model"]); } } @@ -1054,45 +1093,47 @@ namespace Cantera { // 'datatable' returns a default TransportData object if // the species name is not one in the transport database. // This can be detected by examining 'geometry'. - if (trdat.viscCoeffs[0] < 0) { - throw TransportDBError(0,"no transport data found for species " + if (trdat.viscCoeffs[0] <= 0.0 ) { + throw TransportDBError(0,"no viscosity transport data found for species " + names[i]); + cout << "No viscosity seen for " << names[i] + << "but this might not be required depending on what you are trying to do." + << endl; } - // parameters should be converted to SI units before storing - if (trdat.viscCoeffs.size() > 0) { - trParam.visc_A[i] = trdat.viscCoeffs[0] ; - } - if (trdat.viscCoeffs.size() > 2) { - trParam.visc_n[i] = trdat.viscCoeffs[1] ; - trParam.visc_Tact[i] = trdat.viscCoeffs[2] ; - } - - if (trdat.thermalCondCoeffs.size() > 0) { - trParam.thermCond_A[i] = trdat.thermalCondCoeffs[0] ; - } - if (trdat.thermalCondCoeffs.size() > 2) { - trParam.thermCond_n[i] = trdat.thermalCondCoeffs[1] ; - trParam.thermCond_Tact[i] = trdat.thermalCondCoeffs[2] ; - } - - // Angstroms -> meters - trParam.hydroRadius[i] = 1.e-10 * trdat.hydroradius; - /* * this is a much more general way to handle the transfer * -> calling the default copy constructor for LiquidTransportData */ trParam.LTData.push_back(trdat); } - - // Need to identify a method to obtain interaction matrices. - // This will fill LiquidTransportParams members visc_Eij, visc_Sij - trParam.visc_Eij.resize(trParam.nsp_,trParam.nsp_); - //cout << "No support for species viscosity interactions in TransportFactory.cpp" << endl; } + /** + * Read transport property data from a file for interactions + * between species in a liquid. + * Given the name of a file containing transport property + * parameters and a list of species names, this method returns an + * instance of TransportParams containing the transport data for + * these species read from the file. + */ + void TransportFactory::getLiquidInteractionsTransportData( const XML_Node &transportNode, + XML_Node& log, + const std::vector &names, + LiquidTransportParams& trParam) + { + + if ( transportNode.hasChild("viscosity")) { + XML_Node& viscosityNode = transportNode.child("viscosity"); + string viscosityModel = viscosityNode.attrib("model"); + if (viscosityModel == "") { + throw CanteraError("LiquidTransport::initLiquid", + "transport::visosity XML node doesn't have a model string"); + } + } + } + /********************************************************* * * Polynomial fitting diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index d38603557..3c016ad3b 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -186,7 +186,20 @@ namespace Cantera { * these species read from the file. * */ - void getLiquidTransportData(const std::vector &db, + void getLiquidSpeciesTransportData(const std::vector &db, + XML_Node& log, const std::vector& names, + LiquidTransportParams& tr); + + //! Read transport property data from a file for a list of species. + /*! + * + * Given the name of a file containing transport property + * parameters and a list of species names, this method returns an + * instance of TransportParams containing the transport data for + * these species read from the file. + * + */ + void getLiquidInteractionsTransportData(const XML_Node &db, XML_Node& log, const std::vector& names, LiquidTransportParams& tr); @@ -205,7 +218,7 @@ namespace Cantera { GasTransportParams& tr); - void setupLiquidTransport(std::ostream &flog, const std::vector &transport_database, + void setupLiquidTransport(std::ostream &flog, thermo_t* thermo, int log_level, LiquidTransportParams& tr); From 2492db97507bd1835cc8f75c10ae44a67cb577c2 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 18:30:21 +0000 Subject: [PATCH 013/446] TransportParams.h, LiquidTransportParams.h, LiquidTransportData.h Moved temperature fits polynomials for viscosity, conductivity, diffusivity from TransportParams to GasTransportParams. Defined mixing model enumeration for liquid species-species interactions in LiquidTransportParams enum LiquidTranMixingModel { LTR_MIXMODEL_NOTSET=-1, LTR_MIXMODEL_SOLVENT, LTR_MIXMODEL_MOLEFRACS, LTR_MIXMODEL_MASSFRACS, LTR_MIXMODEL_LOG_MOLEFRACS, LTR_PAIRWISE_INTERACTIONS }; Removed species Arrhenius parameters from LiquidTransportParams. These are now held in LiquidTransportData obejcts which are stored as a vector in LiquidTransportParams In LiquidTransportData, the hydrodynamic radius now holds coefficients for temperature dependent models instead of just a constant value. Also changed enumeration for polynomial from LTR_MODEL_COEFF to LTR_MODEL_POLY. --- Cantera/src/transport/LiquidTransportData.h | 26 +++++--- Cantera/src/transport/LiquidTransportParams.h | 62 ++++++------------- Cantera/src/transport/TransportParams.h | 17 +++-- 3 files changed, 47 insertions(+), 58 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index a664bedc1..ee1faa948 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -33,12 +33,21 @@ namespace Cantera { enum LiquidTR_Model { + //! Temperature dependence type for pure (liquid) species properties + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature (only one implemented so far) + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ LTR_MODEL_NOTSET=-1, LTR_MODEL_CONSTANT, LTR_MODEL_ARRHENIUS, - LTR_MODEL_COEFF + LTR_MODEL_POLY }; + //! Class LiquidTransportData holds transport parameters for a + //! specific liquid-phase species. class LiquidTransportData { public: @@ -46,7 +55,6 @@ namespace Cantera { LiquidTransportData() : speciesName("-"), model_hydroradius(LTR_MODEL_NOTSET), - hydroradius(-1.0), model_viscosity(LTR_MODEL_NOTSET), model_thermalCond(LTR_MODEL_NOTSET), model_speciesDiffusivity(LTR_MODEL_NOTSET) @@ -58,21 +66,25 @@ namespace Cantera { //! Model type for the hydroradius LiquidTR_Model model_hydroradius; - //! Actual value of the hydroradius - doublereal hydroradius; + //! Ceofficients for the hydroradius model + vector_fp hydroRadiusCoeffs; - //! Model type for the hydroradius + //! Model type for the viscosity LiquidTR_Model model_viscosity; + + //! Ceofficients for the viscosity model vector_fp viscCoeffs; - //! Model type for the hydroradius + //! Model type for the thermal conductivity LiquidTR_Model model_thermalCond; + //! Ceofficients for the thermal conductivity model vector_fp thermalCondCoeffs; - //! Model type for the hydroradius + //! Model type for the speciesDiffusivity LiquidTR_Model model_speciesDiffusivity; + //! Ceofficients for the species diffusivity model vector_fp speciesDiffusivityCoeffs; }; diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 713ab1c52..faf08edb6 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -12,6 +12,26 @@ namespace Cantera { + + //! Composition dependence type for liquid mixture transport properties + /*! + * Types of temperature dependencies: + * 0 - Use solvent (species 0) properties + * 1 - Properties weighted linearly by mole fractions + * 2 - Properties weighted linearly by mass fractions + * 3 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * 4 - Interactions given pairwise between each possible species (i.e. D_ij) + */ + enum LiquidTranMixingModel { + LTR_MIXMODEL_NOTSET=-1, + LTR_MIXMODEL_SOLVENT, + LTR_MIXMODEL_MOLEFRACS, + LTR_MIXMODEL_MASSFRACS, + LTR_MIXMODEL_LOG_MOLEFRACS, + LTR_PAIRWISE_INTERACTIONS + }; + + /** * Holds transport model parameters relevant to transport in * liquids for which activated jump processes limit transport @@ -25,25 +45,6 @@ namespace Cantera { LiquidTransportParams() {} ~LiquidTransportParams() {} - - //section for liquid transport properties - - //Arrhenius parameters for transport coefficients: - - //!Arrhenius pre-exponential parameter for viscosity. - vector_fp visc_A; - //!Temperature exponent for viscosity. - vector_fp visc_n; - //!Arrhenius activation temperature for viscosity. - vector_fp visc_Tact; - - //!Arrhenius pre-exponential parameter for thermal conductivity. - vector_fp thermCond_A; - //!Temperature exponent for thermal conductivity. - vector_fp thermCond_n; - //!Arrhenius activation temperature for thermal conductivity. - vector_fp thermCond_Tact; - //! Energies of molecular interaction associated with viscosity. /** * These multiply the mixture viscosity by @@ -59,29 +60,6 @@ namespace Cantera { //! Entropies of molecular interaction associated with viscosity. DenseMatrix visc_Sij; - //Hydrodynamic radius of transported molecule - vector_fp hydroRadius; - - //! Coefficients for the limiting conductivity of ions - //! in solution: A_k - /*! - * This is used in the following formula for the - * limiting conductivity of the kth ion. - * - * ln (lambda^o_k nu_solv) = A_k + B_k / T - * - * nu_solv is the pure component solvent viscosity - * - * Note the limiting conductivities of ions will also - * be used to input the diffusion coefficients. - */ - vector_fp A_k_cond; - - //! Coefficients for the limiting conductivity of ions - //! in solution: B_k - vector_fp B_k_cond; - - std::vector LTData; }; diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 24eeaa1cd..7c1bc6817 100755 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -26,15 +26,6 @@ namespace Cantera { thermo_t* thermo; vector_fp mw; - // polynomial fits - //temperature-fit viscosity - std::vector visccoeffs; - //temperature-fit heat conduction - std::vector condcoeffs; - //temperature-fit diffusivity - std::vector diffcoeffs; - vector_fp polytempvec; - //minimum and maximum temperatures for parameter fits doublereal tmax, tmin; int mode_; @@ -56,6 +47,14 @@ namespace Cantera { GasTransportParams() {} ~GasTransportParams() {} + // polynomial fits + //temperature-fit viscosity + std::vector visccoeffs; + //temperature-fit heat conduction + std::vector condcoeffs; + //temperature-fit diffusivity + std::vector diffcoeffs; + vector_fp polytempvec; std::vector > poly; std::vector omega22_poly; From dbef25a481c80a7f86553aedaf11a0cd625cdca3 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 18:59:18 +0000 Subject: [PATCH 014/446] LiquidTransport.h LiquidTransport.cpp Changed order of some prototypes in LiquidTransport.h to group public, protected and private members better. Renamed methods (consistency with other transport models) like virtual void update_temp() to virtual bool update_T() //note boolean return value Added method getSpeciesHydrodynamicRadius(doublereal* const radius); to fill the hydrodynamic radius array. Added protected member vectors to hold information on temperature-dependent species transport properties: (1) model enumeration like vector m_viscTempDepType_Ns; (2) coefficients of temperature-dependent properties like vector m_coeffVisc_Ns; These replace sets of variables like m_visc_A, m_visc_n, m_visc_Tact. These are filled in LiquidTransport::initLiquid using LiquidTransportData vector held within LiquidTransportParams Species thermal conductivity variables now use "lambda" instead of "cond" for simplicity. Still need to work on species-species interactions. Variables like int m_compositionDepType will need to be replaced by property-specific (i.e. viscosity, thermal conductivity) variables. Major changes to LiquidTransport::initLiquid(LiquidTransportParams& tr) - starting to bring in species-species interactions, but not there yet. - complete rewrite of filling temperture-dependent property variables. - added hydrodynamic radius and species diffusivity property parsing. - LiquidTransport::thermalConductivity() now uses mass-fraction weighted mixing rule. Generality will follow. LiquidTransport::updateViscosity LiquidTransport::updateCond_T() hava been updated to use new temperture-dependent property coefficients (m_lambdaTempDepType_Ns and m_coeffLambda_Ns). LiquidTransport::updateDiff() now computes Stefan-Maxwell interaction parameters (D_ij) using Stokes-Einstein reltion. --- Cantera/src/transport/LiquidTransport.cpp | 457 ++++++++++++++++------ Cantera/src/transport/LiquidTransport.h | 313 ++++++++++----- 2 files changed, 556 insertions(+), 214 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 903b1298f..3f185f77f 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -36,6 +36,7 @@ namespace Cantera { m_nsp(0), m_tmin(-1.0), m_tmax(100000.), + m_compositionDepType(-1), m_iStateMF(-1), m_temp(-1.0), m_logt(0.0), @@ -60,6 +61,7 @@ namespace Cantera { m_nsp(0), m_tmin(-1.0), m_tmax(100000.), + m_compositionDepType(-1), m_iStateMF(-1), m_temp(-1.0), m_logt(0.0), @@ -92,17 +94,17 @@ namespace Cantera { m_tmin = right.m_tmin; m_tmax = right.m_tmax; m_mw = right.m_mw; - m_visc_A = right.m_visc_A; - m_visc_logA = right.m_visc_logA; - m_visc_n = right.m_visc_n; - m_visc_Tact = right.m_visc_Tact; + m_viscTempDepType_Ns = right.m_viscTempDepType_Ns; + m_lambdaTempDepType_Ns = right.m_lambdaTempDepType_Ns; + m_diffTempDepType_Ns = right.m_diffTempDepType_Ns; + m_radiusTempDepType_Ns = right.m_radiusTempDepType_Ns; + m_coeffVisc_Ns = right.m_coeffVisc_Ns; + m_coeffLambda_Ns = right.m_coeffLambda_Ns; + m_coeffDiff_Ns = right.m_coeffDiff_Ns; + m_coeffRadius_Ns = right.m_coeffRadius_Ns; m_visc_Eij = right.m_visc_Eij; m_visc_Sij = right.m_visc_Sij; - m_thermCond_A = right.m_thermCond_A; - m_thermCond_n = right.m_thermCond_n; - m_thermCond_Tact = right.m_thermCond_Tact; m_hydrodynamic_radius = right.m_hydrodynamic_radius; - m_diffcoeffs = right.m_diffcoeffs; m_Grad_X = right.m_Grad_X; m_Grad_T = right.m_Grad_T; m_Grad_V = right.m_Grad_V; @@ -110,7 +112,7 @@ namespace Cantera { m_bdiff = right.m_bdiff; m_viscSpecies = right.m_viscSpecies; m_logViscSpecies = right.m_logViscSpecies; - m_condSpecies = right.m_condSpecies; + m_lambdaSpecies = right.m_lambdaSpecies; m_iStateMF = -1; m_molefracs = right.m_molefracs; m_concentrations = right.m_concentrations; @@ -134,7 +136,6 @@ namespace Cantera { m_cond_temp_ok = false; m_cond_mix_ok = false; m_mode = right.m_mode; - m_diam = right.m_diam; m_debug = right.m_debug; m_nDim = right.m_nDim; @@ -153,45 +154,214 @@ namespace Cantera { */ bool LiquidTransport::initLiquid(LiquidTransportParams& tr) { + int k; // constant substance attributes m_thermo = tr.thermo; m_nsp = m_thermo->nSpecies(); m_tmin = m_thermo->minTemp(); m_tmax = m_thermo->maxTemp(); + /* + * Read the transport block in the phase XML Node + * It's not an error if this block doesn't exist. Just use the defaults + */ + XML_Node &phaseNode = m_thermo->xml(); + if (phaseNode.hasChild("transport")) { + XML_Node& transportNode = phaseNode.child("transport"); + if ( transportNode.hasChild("viscosity")) { + XML_Node& viscosityNode = transportNode.child("viscosity"); + string viscosityModel = viscosityNode.attrib("model"); + if (viscosityModel == "") { + throw CanteraError("LiquidTransport::initLiquid", + "transport::visosity XML node doesn't have a model string"); + } + } + + + + string transportModel = transportNode.attrib("model"); + if (transportModel == "LiquidTransport") { + /* + * + * or + * + */ + std::string modelName = ""; + if (getOptionalModel(transportNode, "compositionDependence", + modelName)) { + modelName = lowercase(modelName); + if (modelName == "solvent_only") { + m_compositionDepType = 0; + } else if (modelName == "mixture_averaged") { + m_compositionDepType = 1; + } else { + throw CanteraError("LiquidTransport::initLiquid", "Unknown compositionDependence Model: " + modelName); + } + } + + + + + } + } + // make a local copy of the molecular weights m_mw.resize(m_nsp); copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin()); - // copy parameters into local storage - m_visc_A = tr.visc_A ; - m_visc_n = tr.visc_n ; - m_visc_Tact = tr.visc_Tact ; + /* + * Get the input Viscosities + */ + m_viscSpecies.resize(m_nsp); + m_coeffVisc_Ns.clear(); + m_coeffVisc_Ns.resize(m_nsp); + m_viscTempDepType_Ns.resize(m_nsp); - //The following two are not yet filled in LiquidTransportParams - m_visc_Eij = tr.visc_Eij ; - m_visc_Sij = tr.visc_Sij ; + //for each species, assign viscosity model and coefficients + for (k = 0; k < m_nsp; k++) { + Cantera::LiquidTransportData <d = tr.LTData[k]; + //specify temperature dependence + m_viscTempDepType_Ns[k] = ltd.model_viscosity; + //vector kentry corresponds to the k-th entry of m_coeffVisc_Ns + vector_fp &kentry = m_coeffVisc_Ns[k]; - //save logarithm of pre-exponential for easier computation - m_visc_logA.resize(m_nsp); - for ( int i = 0; i < m_nsp; i++ ) - m_visc_logA[i] = log( m_visc_A[i] ); + if ( m_viscTempDepType_Ns[k] == LTR_MODEL_CONSTANT + || m_viscTempDepType_Ns[k] == LTR_MODEL_POLY ) { + kentry = ltd.viscCoeffs; - m_thermCond_A = tr.thermCond_A ; - m_thermCond_n = tr.thermCond_n ; - m_thermCond_Tact = tr.thermCond_Tact ; - - m_hydrodynamic_radius = tr.hydroRadius ; + } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + kentry = ltd.viscCoeffs; + //for Arrhenius form, also carry the logarithm of the pre-exponential + kentry[3] = log( kentry[0] ); + } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + //we might be OK with viscosity not being set so + // this error is repeated in updateViscosity_T() + // and can be deleted from here if appropriate + throw CanteraError("LiquidTransport::initLiquid", + "Viscosity Model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::initLiquid", + "Viscosity Model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); + } + } - //m_diffcoeffs = tr.diffcoeffs; + /* + * Get the input Thermal Conductivities + */ + m_lambdaSpecies.resize(m_nsp); + m_coeffLambda_Ns.clear(); + m_coeffLambda_Ns.resize(m_nsp); + m_lambdaTempDepType_Ns.resize(m_nsp); + + //for each species, assign viscosity model and coefficients + for (k = 0; k < m_nsp; k++) { + Cantera::LiquidTransportData <d = tr.LTData[k]; + //specify temperature dependence + m_lambdaTempDepType_Ns[k] = ltd.model_thermalCond; + //vector kentry corresponds to the k-th entry of m_coeffLambda_Ns + vector_fp &kentry = m_coeffLambda_Ns[k]; + + if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_CONSTANT + || m_lambdaTempDepType_Ns[k] == LTR_MODEL_POLY ) { + kentry = ltd.thermalCondCoeffs; + + } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + kentry = ltd.thermalCondCoeffs; + //for Arrhenius form, also carry the logarithm of the pre-exponential + kentry[3] = log( kentry[0] ); + + } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + throw CanteraError("LiquidTransport::initLiquid", + "Thermal conductivity model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::initLiquid", + "Thermal conductivity model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); + } + } + + /* + * Get the input Hydrodynamic Radii + */ + m_hydrodynamic_radius.resize(m_nsp); + m_coeffRadius_Ns.clear(); + m_coeffRadius_Ns.resize(m_nsp); + m_radiusTempDepType_Ns.resize(m_nsp); + + //for each species, assign viscosity model and coefficients + for (k = 0; k < m_nsp; k++) { + Cantera::LiquidTransportData <d = tr.LTData[k]; + //specify temperature dependence + m_radiusTempDepType_Ns[k] = ltd.model_hydroradius; + //vector kentry corresponds to the k-th entry of m_coeffRadius_Ns + vector_fp &kentry = m_coeffRadius_Ns[k]; + + if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_CONSTANT + || m_radiusTempDepType_Ns[k] == LTR_MODEL_POLY ) { + kentry = ltd.hydroRadiusCoeffs; + + } else if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + kentry = ltd.hydroRadiusCoeffs; + //for Arrhenius form, also carry the logarithm of the pre-exponential + kentry[3] = log( kentry[0] ); + + } else if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + throw CanteraError("LiquidTransport::initLiquid", + "Hydrodynamic radius model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::initLiquid", + "Hydrodynamic radius model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); + } + } + + /* + * Get the input Species Diffusivities + * Note that species diffusivities are not what is needed. + * Rather the Stefan Boltzmann interaction parameters are + * needed for the current model. This section may, therefore, + * be extraneous. + */ + // m_viscSpecies.resize(m_nsp); + m_coeffDiff_Ns.clear(); + m_coeffDiff_Ns.resize(m_nsp); + m_diffTempDepType_Ns.resize(m_nsp); + + //for each species, assign viscosity model and coefficients + for (k = 0; k < m_nsp; k++) { + Cantera::LiquidTransportData <d = tr.LTData[k]; + //specify temperature dependence + if ( ltd.model_speciesDiffusivity >= 0 + || ltd.speciesDiffusivityCoeffs.size() > 0 ) { + cout << "Warning: diffusion coefficient data for " + << m_thermo->speciesName(k) + << endl + << "in the input file is not used for LiquidTransport model." + << endl + << "LiquidTransport model uses hydrodynamicRadius, viscosity " + << endl + << "and the Stokes-Einstein equation." + << endl; + } + } m_mode = tr.mode_; m_viscSpecies.resize(m_nsp); m_logViscSpecies.resize(m_nsp); - m_condSpecies.resize(m_nsp); + m_lambdaSpecies.resize(m_nsp); m_bdiff.resize(m_nsp, m_nsp); m_molefracs.resize(m_nsp); @@ -237,22 +407,23 @@ namespace Cantera { */ doublereal LiquidTransport::viscosity() { - update_temp(); - update_conc(); + update_T(); + update_C(); if (m_visc_mix_ok) return m_viscmix; // update m_viscSpecies[] if necessary if (!m_visc_temp_ok) { - updateViscosity_temp(); + updateViscosity_T(); } if (!m_visc_conc_ok) { - updateViscosities_conc(); + updateViscosities_C(); } /* We still need to implement interaction parameters */ /* This constant viscosity model has no input */ + if (viscosityModel_ == LVISC_CONSTANT) { err("constant viscosity not implemented for LiquidTransport."); @@ -272,15 +443,17 @@ namespace Cantera { * ( m_visc_Sij(i,j) + m_visc_Eij(i,j) / m_temp ); m_viscmix = exp( interaction ); + } else { + err("Unknown viscosity model in LiquidTransport::viscosity()."); } return m_viscmix; } void LiquidTransport::getSpeciesViscosities(doublereal* visc) { - update_temp(); + update_T(); if (!m_visc_temp_ok) { - updateViscosity_temp(); + updateViscosity_T(); } copy(m_viscSpecies.begin(), m_viscSpecies.end(), visc); } @@ -292,19 +465,23 @@ namespace Cantera { void LiquidTransport::getBinaryDiffCoeffs(int ld, doublereal* d) { int i,j; - update_temp(); + if ( ld != m_nsp ) + throw CanteraError("LiquidTransport::getBinaryDiffCoeffs", + "First argument does not correspond to number of species in model.\nDiff Coeff matrix may be misdimensioned"); + update_T(); // if necessary, evaluate the binary diffusion coefficents // from the polynomial fits - if (!m_diff_temp_ok) updateDiff_temp(); - doublereal pres = m_thermo->pressure(); + if (!m_diff_temp_ok) updateDiff_T(); - doublereal rp = 1.0/pres; for (i = 0; i < m_nsp; i++) for (j = 0; j < m_nsp; j++) { - d[ld*j + i] = rp * m_bdiff(i,j); + d[ld*j + i] = m_bdiff(i,j); + } } + + //================================================================================================ // Get the electrical Mobilities (m^2/V/s). /* @@ -378,30 +555,33 @@ namespace Cantera { update_Grad_lnAC(); } //================================================================================================ - /****************** thermal conductivity **********************/ - + /****************** thermal conductivity **********************/ /* * The thermal conductivity is computed from the following mixture rule: - * \[ - * \lambda = 0.5 \left( \sum_k X_k \lambda_k - * + \frac{1}{\sum_k X_k/\lambda_k}\right) - * \] + * \[ + * \lambda = \left( \sum_k Y_k \lambda_k \right) + * \] */ doublereal LiquidTransport::thermalConductivity() { - update_temp(); - update_conc(); + update_T(); + update_C(); if (!m_cond_temp_ok) { - updateCond_temp(); + updateCond_T(); } if (!m_cond_mix_ok) { - doublereal sum1 = 0.0, sum2 = 0.0; - for (int k = 0; k < m_nsp; k++) { - sum1 += m_molefracs[k] * m_condSpecies[k]; - sum2 += m_molefracs[k] / m_condSpecies[k]; + + // mass-fraction weighted thermal conductivity + { + doublereal sum1 = 0.0, sum2 = 0.0; + for (int k = 0; k < m_nsp; k++) { + sum1 += m_molefracs[k] * m_mw[k] * m_lambdaSpecies[k]; + sum2 += m_molefracs[k] * m_mw[k] ; + } + m_lambda = sum1 / sum2 ; } - m_lambda = 0.5*(sum1 + 1.0/sum2); + m_cond_mix_ok = true; } @@ -455,8 +635,8 @@ namespace Cantera { void LiquidTransport::getSpeciesFluxesExt(int ldf, doublereal* fluxes) { int n, k; - update_temp(); - update_conc(); + update_T(); + update_C(); getMixDiffCoeffs(DATA_PTR(m_spwork)); @@ -491,12 +671,12 @@ namespace Cantera { */ void LiquidTransport::getMixDiffCoeffs(doublereal* const d) { - update_temp(); - update_conc(); + update_T(); + update_C(); // update the binary diffusion coefficients if necessary if (!m_diff_temp_ok) { - updateDiff_temp(); + updateDiff_T(); } int k, j; @@ -534,20 +714,20 @@ namespace Cantera { * This is called whenever a transport property is * requested. * The first task is to check whether the temperature has changed - * since the last call to update_temp(). + * since the last call to update_T(). * If it hasn't then an immediate return is carried out. * * @internal */ - void LiquidTransport::update_temp() + bool LiquidTransport::update_T() { // First make a decision about whether we need to recalculate doublereal t = m_thermo->temperature(); - if (t == m_temp) return; + if (t == m_temp) return false; // Next do a reality check on temperature value if (t < 0.0) { - throw CanteraError("LiquidTransport::update_temp()", + throw CanteraError("LiquidTransport::update_T()", "negative temperature "+fp2str(t)); } @@ -570,7 +750,7 @@ namespace Cantera { m_visc_mix_ok = false; m_diff_mix_ok = false; // m_cond_mix_ok = false; (don't need it because a lower lvl flag is set - + return true; } @@ -586,7 +766,7 @@ namespace Cantera { * * @internal */ - void LiquidTransport::update_conc() { + bool LiquidTransport::update_C() { // If the pressure has changed then the concentrations // have changed. doublereal pres = m_thermo->pressure(); @@ -613,7 +793,7 @@ namespace Cantera { concTot_tran_ *= concTot_; } if (qReturn) { - return; + return false; } // signal that concentration-dependent quantities will need to @@ -625,6 +805,8 @@ namespace Cantera { m_visc_mix_ok = false; m_diff_mix_ok = false; m_cond_mix_ok = false; + + return true; } @@ -680,71 +862,84 @@ namespace Cantera { /************************************************************************* * - * methods to update temperature-dependent properties + * methods to update species temperature-dependent properties * *************************************************************************/ /** - * Update the temperature-dependent parts of the mixture-averaged + * Update the temperature-dependent parts of the species * thermal conductivity. */ - void LiquidTransport::updateCond_temp() { + void LiquidTransport::updateCond_T() { + int k; - /* - if (m_mode == CK_Mode) { - for (k = 0; k < m_nsp; k++) { - m_condSpecies[k] = exp(m_condcoeffs[k]); - } - } else { - for (k = 0; k < m_nsp; k++) { - m_condSpecies[k] = m_sqrt_t * m_condcoeffs[k]; + for (k = 0; k < m_nsp; k++) { + vector_fp &coeffk = m_coeffLambda_Ns[k]; + + if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_CONSTANT ) { + m_lambdaSpecies[k] = coeffk[0] ; + + } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + //m_coeffLambda_Ns[k][0] holds A + //m_coeffLambda_Ns[k][1] holds n + //m_coeffLambda_Ns[k][2] holds Tact + //m_coeffLambda_Ns[k][3] holds log(A) + m_lambdaSpecies[k] = coeffk[0] * exp( coeffk[1] * m_logt + - coeffk[2] / m_temp ); + + } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_POLY ) { + m_lambdaSpecies[k] = coeffk[0] + + coeffk[1] * m_temp + + coeffk[2] * m_temp * m_temp + + coeffk[3] * m_temp * m_temp * m_temp + + coeffk[4] * m_temp * m_temp * m_temp * m_temp; + + } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + throw CanteraError("LiquidTransport::updateCond_T", + "Conductivity Model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::updateCond_T", + "Conductivity Model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); } } m_cond_temp_ok = true; m_cond_mix_ok = false; - */ } + //! Update the StefanMaxwell interaction parameters. /** - * Update the binary diffusion coefficients. These are evaluated - * from the polynomial fits at unit pressure (1 Pa). + * These are evaluated using the Stokes-Einstein + * relation from the viscosity and hydrodynamic radius. */ - void LiquidTransport::updateDiff_temp() { + void LiquidTransport::updateDiff_T() { - // evaluate binary diffusion coefficients at unit pressure + double *viscSpec = new double(m_nsp); + double *radiusSpec = new double(m_nsp); + getSpeciesViscosities( viscSpec ); + getSpeciesHydrodynamicRadius( radiusSpec ); - /* - if (m_mode == CK_Mode) { - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - m_bdiff(i,j) = exp(m_diffcoeffs[ic]); - m_bdiff(j,i) = m_bdiff(i,j); - ic++; - } + int i,j; + for (i = 0; i < m_nsp; i++) + for (j = 0; j < m_nsp; j++) { + m_DiffCoeff_StefMax(i,j) = m_bdiff(i,j) = GasConstant * m_temp + / ( 6.0 * Pi * radiusSpec[i] * viscSpec[j] ) ; + cout << " D_ij = " << m_bdiff(i,j) << " for " + << m_thermo->speciesName(i) << ", " + << m_thermo->speciesName(j) << endl; } - } - else { - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - m_bdiff(i,j) = m_temp * m_sqrt_t*m_diffcoeffs[ic]; - m_bdiff(j,i) = m_bdiff(i,j); - ic++; - } - } - } - m_diff_temp_ok = true; m_diff_mix_ok = false; - */ } - /** - * Update the pure-species viscosities. - */ - void LiquidTransport::updateViscosities_conc() { + //! Update the pure-species viscosities functional dependence on concentration. + void LiquidTransport::updateViscosities_C() { m_visc_conc_ok = true; } @@ -755,20 +950,47 @@ namespace Cantera { * weighting functions in the viscosity mixture rule. * The flag m_visc_ok is set to true. */ - void LiquidTransport::updateViscosity_temp() { + void LiquidTransport::updateViscosity_T() { int k; for (k = 0; k < m_nsp; k++) { - m_logViscSpecies[k] = m_visc_logA[k] + m_visc_n[k] * m_logt - + m_visc_Tact[k] / m_temp ; - m_viscSpecies[k] = exp( m_logViscSpecies[k] ); + vector_fp &coeffk = m_coeffVisc_Ns[k]; + + if ( m_viscTempDepType_Ns[k] == LTR_MODEL_CONSTANT ) { + m_logViscSpecies[k] = log( coeffk[0] ); + m_viscSpecies[k] = coeffk[0] ; + + } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + //m_coeffVisc_Ns[k][0] holds A + //m_coeffVisc_Ns[k][1] holds n + //m_coeffVisc_Ns[k][2] holds Tact + //m_coeffVisc_Ns[k][3] holds log(A) + m_logViscSpecies[k] = coeffk[3] + coeffk[1] * m_logt + - coeffk[2] / m_temp ; + m_viscSpecies[k] = exp( m_logViscSpecies[k] ); + + } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_POLY ) { + m_viscSpecies[k] = coeffk[0] + + coeffk[1] * m_temp + + coeffk[2] * m_temp * m_temp + + coeffk[3] * m_temp * m_temp * m_temp + + coeffk[4] * m_temp * m_temp * m_temp * m_temp; + m_logViscSpecies[k] = log( m_viscSpecies[k] ); + + } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + throw CanteraError("LiquidTransport::updateViscosity_T", + "Viscosity Model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::updateViscosity_T", + "Viscosity Model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); + } + m_visc_temp_ok = true; + m_visc_mix_ok = false; } - //for (k = 0; k < m_nsp; k++) { - //m_viscSpecies[k] = m_visc_A[k] * exp( m_visc_n[k] * m_logt - // + m_visc_Tact[k] / m_temp ); - //} - m_visc_temp_ok = true; - m_visc_mix_ok = false; } @@ -787,9 +1009,10 @@ namespace Cantera { /* - * Update the concentrations in the mixture. + * Update the concentrations and diffusion coefficients in the mixture. */ - update_conc(); + update_C(); + if ( !m_diff_temp_ok ) updateDiff_T(); double T = m_thermo->temperature(); diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index c3df40c3f..4d6c43638 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -34,9 +34,9 @@ namespace Cantera { const int LVISC_INTERACTION = 1; const int LVISC_AVG_ENERGIES = 2; - const int LDIFF_MIXDIFF_UNCORRECTED = 0; - const int LDIFF_MIXDIFF_FLUXCORRECTED = 1; - const int LDIFF_MULTICOMP_STEFANMAXWELL = 2; + const int LDIFF_CONSTANT = 0; + const int LDIFF_ARHENNIUS = 1; + const int LDIFF_STOKES_EINSTEIN = 2; @@ -136,6 +136,9 @@ namespace Cantera { class LiquidTransport : public Transport { public: + typedef vector_fp Coeff_T_; + + //! Default constructor. /*! * This requires call to initLiquid(LiquidTransportParams& tr) @@ -222,10 +225,18 @@ namespace Cantera { */ virtual void getSpeciesViscosities(doublereal* const visc); + //! Returns the hydrodynamic radius for all species + /*! + * The pure species viscosities are to be given in an Arrhenius + * form in accordance with activated-jump-process dominated transport. + */ + virtual void getSpeciesHydrodynamicRadius(doublereal* const radius); + //! Returns the binary diffusion coefficients /*! - * @param ld - * @param d + * @param ld number of species in system + * @param d vector of mixture diffusion coefficients + * units = m2 s-1. length = ld*ld = (number of species)^2 */ virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d); @@ -237,14 +248,19 @@ namespace Cantera { virtual void getMixDiffCoeffs(doublereal* const d); + //! Return the thermal diffusion coefficients + /*! + * These are all zero for this simple implementaion + * + * @param dt thermal diffusion coefficients + */ virtual void getThermalDiffCoeffs(doublereal* const dt); //! Return the thermal conductivity of the solution /*! * The thermal conductivity is computed from the following mixture rule: * \f[ - * \lambda = 0.5 \left( \sum_k X_k \lambda_k - * + \frac{1}{\sum_k X_k/\lambda_k}\right) + * \lambda = \left( \sum_k Y_k \lambda_k \right) * \f] * * Controlling update boolean = m_condmix_ok @@ -309,14 +325,84 @@ namespace Cantera { */ virtual void set_Grad_X(const doublereal* const grad_X); - virtual void update_Grad_lnAC(); + + //! Updates the internal value of the gradient of the logarithm of the + //! activity coefficients, which is used in the gradient of the chemical potential. + /*! The gradient of the chemical potential can be written in terms of + * gradient of the logarithm of the mole fraction times a correction + * associated with the gradient of the activity coefficient relative to + * that of the mole fraction. Specifically, the gradients of the + * logarithms of each are involved according to the formula + + * \f[ + * \nabla \mu_k = RT \nabla ( \ln X_k ) + * \[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \] + * \f] + * + * The quantity within the square brackets is computed within + * this method. + */ + virtual void update_Grad_lnAC(); + + /** + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) + * @param ldx Leading dimension of the grad_X array. + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * + * + * The diffusive mass flux of species \e k is computed from + * + * + */ + virtual void getSpeciesFluxes(int ndim, + const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, doublereal* fluxes); + + //! Return the species diffusive mass fluxes wrt to + //! the mass averaged velocity, + /*! + * + * units = kg/m2/s + * + * Internally, gradients in the in mole fraction, temperature + * and electrostatic potential contribute to the diffusive flux + * + * + * The diffusive mass flux of species \e k is computed from the following + * formula + * + * \f[ + * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * V_c = - \sum_j {\rho M_j D_j \nabla X_j} + * \f] + * + * @param ldf stride of the fluxes array. Must be equal to + * or greater than the number of species. + * @param fluxes Vector of calculated fluxes + */ + virtual void getSpeciesFluxesExt(int ldf, doublereal* fluxes); protected: - //! Handles the effects of changes in the Temperature, internally - //! within the object. + //! Returns true if temperature has changed, + //! in which case flags are set to recompute transport properties. /*! - * This is called whenever a transport property is - * requested. + * This is called whenever a transport property is requested. * The first task is to check whether the temperature has changed * since the last call to update_T(). * If it hasn't then an immediate return is carried out. @@ -326,10 +412,13 @@ namespace Cantera { * part of all of the interfaces. * * @internal - */ - virtual void update_temp(); + * + * @return Returns true if the temperature has changed, and false otherwise + */ + virtual bool update_T(); - //! Handles the effects of changes in the mixture concentration + //! Returns true if mixture composition has changed, + //! in which case flags are set to recompute transport properties. /*! * This is called for every interface call to check whether * the concentrations have changed. Concentrations change @@ -340,43 +429,47 @@ namespace Cantera { * part of all of the interfaces. * * @internal + * + * @return Returns true if the mixture composition has changed, and false otherwise. */ - virtual void update_conc(); - - public: - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * - */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes); - - - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * - */ - virtual void getSpeciesFluxesExt(int ldf, doublereal* fluxes); - + virtual bool update_C(); //! Solve the stefan_maxell equations for the diffusive fluxes. void stefan_maxwell_solve(); + //! Update the temperature-dependent viscosity terms. + //! Updates the array of pure species viscosities, and the + //! weighting functions in the viscosity mixture rule. + /*! + * The flag m_visc_ok is set to true. + */ + void updateViscosity_T(); + + //! Update the temperature-dependent parts of the mixture-averaged + //! thermal conductivity. + void updateCond_T(); + + //! Update the concentration parts of the viscosities + /*! + * Internal routine is run whenever the update_boolean + * m_visc_conc_ok is false. This routine will calculate + * internal values for the species viscosities. + * + * @internal + */ + void updateViscosities_C(); + + //! Update the binary diffusion coefficients wrt T. + /*! + * These are evaluated + * from the polynomial fits at unit pressure (1 Pa). + */ + void updateDiff_T(); + + private: - - //! Number of species in the mixture int m_nsp; @@ -392,11 +485,17 @@ namespace Cantera { */ vector_fp m_mw; - //! Pure species viscosities in Arrhenius temperature-dependent form. - vector_fp m_visc_A; - vector_fp m_visc_logA; //logarithm of coefficient - vector_fp m_visc_n; - vector_fp m_visc_Tact; + //! Viscosity temperature dependence type + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature (only one implemented so far) + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ + vector m_viscTempDepType_Ns; + + //! Pure species viscosities in temperature-dependent form. + std::vector m_coeffVisc_Ns; //! Molecular interaction energies associated with viscosity /** @@ -412,22 +511,76 @@ namespace Cantera { */ DenseMatrix m_visc_Sij; - //! Pure species thermal conductivities in Arrhenius temperature-dependent form. - vector_fp m_thermCond_A; - vector_fp m_thermCond_n; - vector_fp m_thermCond_Tact; + + + //! Thermal conductivity temperature dependence type + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature (only one implemented so far) + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ + vector m_lambdaTempDepType_Ns; + + //! Pure species thermal conductivities in temperature-dependent form. + std::vector m_coeffLambda_Ns; + + //! Diffusion coefficient temperature dependence type + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature (only one implemented so far) + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ + vector m_diffTempDepType_Ns; + + //! Pure species diffusvities in temperature-dependent form. + std::vector m_coeffDiff_Ns; + + + vector useHydroRadius_; + + //!Hydrodynamic radius temperature dependence type + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ + vector m_radiusTempDepType_Ns; + + //! Pure hydrodynamic radius in temperature-dependent form. + std::vector m_coeffRadius_Ns; //! Species hydrodynamic radius vector_fp m_hydrodynamic_radius; + + //! Composition dependence of the transport properties + /*! + * The following coefficients are allowed to have simple + * composition dependencies + * mixture viscosity + * mixture thermal conductivity + * + * + * Types of composition dependencies + * 0 - Solvent values (i.e., species 0) contributes only + * 1 - linear combination of mole fractions; + */ + int m_compositionDepType; + //! Polynomial coefficients of the binary diffusion coefficients /*! * These express the temperature dependendence of the * binary diffusivities. An overall pressure dependence is then * added. */ + /* vector m_diffcoeffs; + */ + //! Internal value of the gradient of the mole fraction vector /*! @@ -532,7 +685,7 @@ namespace Cantera { * * controlling update boolean -> m_cond_temp_ok */ - vector_fp m_condSpecies; + vector_fp m_lambdaSpecies; //! State of the mole fraction vector. int m_iStateMF; @@ -587,7 +740,10 @@ namespace Cantera { */ doublereal concTot_tran_; + //! Mean molecular mass doublereal meanMolecularWeight_; + + //! Density doublereal dens_; //! Local copy of the charge of each species @@ -651,39 +807,13 @@ namespace Cantera { //! Saved value of the mixture viscosity doublereal m_viscmix; - // work space + //! work space + /*! + * Length is equal to m_nsp + */ vector_fp m_spwork; - //! Internal Function - protected: - //! Update the temperature-dependent viscosity terms. - //! Updates the array of pure species viscosities, and the - //! weighting functions in the viscosity mixture rule. - /*! - * The flag m_visc_ok is set to true. - */ - void updateViscosity_temp(); - //! Update the temperature-dependent parts of the mixture-averaged - //! thermal conductivity. - void updateCond_temp(); - - //! Update the concentration parts of the viscosities - /*! - * Internal routine is run whenever the update_boolean - * m_visc_conc_ok is false. This routine will calculate - * internal values for the species viscosities. - * - * @internal - */ - void updateViscosities_conc(); - - //! Update the binary diffusion coefficients wrt T. - /*! - * These are evaluated - * from the polynomial fits at unit pressure (1 Pa). - */ - void updateDiff_temp(); private: //! Boolean indicating that the top-level mixture viscosity is current @@ -696,7 +826,7 @@ namespace Cantera { bool m_visc_temp_ok; //! Flag to indicate that the pure species viscosities - //! are current wrt the temperature + //! are current wrt the concentration bool m_visc_conc_ok; //! Boolean indicating that mixture diffusion coeffs are current @@ -712,18 +842,9 @@ namespace Cantera { //! Boolean indicating that mixture conductivity is current bool m_cond_mix_ok; - //! Mode for fitting the species viscosities - /*! - * Either its CK_Mode or its cantera mode - * in CK_Mode visc is fitted to a polynomial - * in Cantera mode sqrt(visc) is fitted. - */ + //! Mode indicator for transport models -- currently unused. int m_mode; - //! Internal storage for the diameter - diameter - //! species interactions - DenseMatrix m_diam; - //! Debugging flags /*! * Turn on to get debugging information @@ -736,8 +857,6 @@ namespace Cantera { */ int m_nDim; - private: - //! Throw an exception if this method is invoked. /*! * This probably indicates something is not yet implemented. From e52797d335ac32deb8730e9b9164c8a24c16082d Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 19:03:02 +0000 Subject: [PATCH 015/446] Minor changes to reflect changes in LiquidTransportParams, LiquidTransportData and TransportParams. However, the last set of changes broke AqueosTransport because it uses the same property coefficient vectors as those now moved to GasTransportParams. --- Cantera/src/transport/AqueousTransport.cpp | 9 ++++++--- Cantera/src/transport/SimpleTransport.cpp | 2 +- Cantera/src/transport/SimpleTransport.h | 4 ++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/Cantera/src/transport/AqueousTransport.cpp b/Cantera/src/transport/AqueousTransport.cpp index 8e730600b..3b7033dfa 100644 --- a/Cantera/src/transport/AqueousTransport.cpp +++ b/Cantera/src/transport/AqueousTransport.cpp @@ -87,9 +87,12 @@ namespace Cantera { m_thermo->molecularWeights().end(), m_mw.begin()); // copy polynomials and parameters into local storage - m_visccoeffs = tr.visccoeffs; - m_condcoeffs = tr.condcoeffs; - m_diffcoeffs = tr.diffcoeffs; + //m_visccoeffs = tr.visccoeffs; + //m_condcoeffs = tr.condcoeffs; + //m_diffcoeffs = tr.diffcoeffs; + cout << "In AqueousTransport::initLiquid we need to replace" << endl + << "LiquidTransportParams polyniomial coefficients with" << endl + << "those in LiquidTransportData as in SimpleTransport." << endl; m_mode = tr.mode_; diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index 569f6a2ab..d9aa801f6 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -296,7 +296,7 @@ namespace Cantera { "hydroradius model is not constant for species " + spName0); } vector_fp &kentry = m_coeffHydroRadius_Ns[k]; - kentry.push_back(ltd.hydroradius); + kentry = ltd.hydroRadiusCoeffs; } else { if (dm != dm0) { throw CanteraError(" SimpleTransport::initLiquid", diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 35eb9560f..875403a01 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -310,7 +310,7 @@ namespace Cantera { */ virtual void getFluidMobilities(doublereal* const mobil_f); - //! Specify the valpdaue of the gradient of the voltage + //! Specify the value of the gradient of the voltage /*! * * @param grad_V Gradient of the voltage (length num dimensions); @@ -450,7 +450,7 @@ namespace Cantera { * Types of temperature dependencies: * 0 - Independent of temperature (only one implemented so far) * 1 - extended arrhenius form - * 2 - power law form + * 2 - polynomial in temperature form */ int tempDepType_; From c5b90826cb736f4d8960050e0d2eb13d2b321aa5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 23 Oct 2009 19:11:14 +0000 Subject: [PATCH 016/446] Added a missing function as a shell. --- Cantera/src/transport/LiquidTransport.cpp | 46 +++++++++++++---------- 1 file changed, 27 insertions(+), 19 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 3f185f77f..5c47c4b8e 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -188,7 +188,7 @@ namespace Cantera { */ std::string modelName = ""; if (getOptionalModel(transportNode, "compositionDependence", - modelName)) { + modelName)) { modelName = lowercase(modelName); if (modelName == "solvent_only") { m_compositionDepType = 0; @@ -457,7 +457,15 @@ namespace Cantera { } copy(m_viscSpecies.begin(), m_viscSpecies.end(), visc); } - + //==================================================================================================================== + // Returns the hydrodynamic radius for all species + /* + * The pure species viscosities are to be given in an Arrhenius + * form in accordance with activated-jump-process dominated transport. + */ + void LiquidTransport::getSpeciesHydrodynamicRadius(doublereal* const radius) { + } + //==================================================================================================================== /******************* binary diffusion coefficients **************/ @@ -482,7 +490,7 @@ namespace Cantera { } - //================================================================================================ + //================================================================================================ // Get the electrical Mobilities (m^2/V/s). /* * This function returns the mobilities. In some formulations @@ -836,15 +844,15 @@ namespace Cantera { } double mag = 1.0E-7 / sum; - for (k = 0; k < m_nsp; k++) { - Xdelta_[k] = m_molefracs[k] + mag * ma_Grad_X[k]; - if (Xdelta_[k] > 1.0) { - Xdelta_[k] = 1.0; - } - if (Xdelta_[k] < 0.0) { - Xdelta_[k] = 0.0; - } + for (k = 0; k < m_nsp; k++) { + Xdelta_[k] = m_molefracs[k] + mag * ma_Grad_X[k]; + if (Xdelta_[k] > 1.0) { + Xdelta_[k] = 1.0; } + if (Xdelta_[k] < 0.0) { + Xdelta_[k] = 0.0; + } + } m_thermo->setMoleFractions(DATA_PTR(Xdelta_)); m_thermo->getActivityCoefficients(DATA_PTR(lnActCoeffMolarDelta_)); for (k = 0; k < m_nsp; k++) { @@ -886,7 +894,7 @@ namespace Cantera { //m_coeffLambda_Ns[k][2] holds Tact //m_coeffLambda_Ns[k][3] holds log(A) m_lambdaSpecies[k] = coeffk[0] * exp( coeffk[1] * m_logt - - coeffk[2] / m_temp ); + - coeffk[2] / m_temp ); } else if ( m_lambdaTempDepType_Ns[k] == LTR_MODEL_POLY ) { m_lambdaSpecies[k] = coeffk[0] @@ -1163,14 +1171,14 @@ namespace Cantera { * Throw an exception if this method is invoked. * This probably indicates something is not yet implemented. */ - doublereal LiquidTransport::err(std::string msg) const { - throw CanteraError("Liquid Transport Class", - "\n\n\n**** Method "+ msg +" not implemented in model " - + int2str(model()) + " ****\n" - "(Did you forget to specify a transport model?)\n\n\n"); + doublereal LiquidTransport::err(std::string msg) const { + throw CanteraError("Liquid Transport Class", + "\n\n\n**** Method "+ msg +" not implemented in model " + + int2str(model()) + " ****\n" + "(Did you forget to specify a transport model?)\n\n\n"); - return 0.0; - } + return 0.0; + } } From 60c94463405389b51e25066353ca070c9a1e3b5d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 23 Oct 2009 19:12:45 +0000 Subject: [PATCH 017/446] Added corrected doxygen information. --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 93dd6402f..bf39f3397 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -1,9 +1,9 @@ /** - * @file PseudoBinaryVPSSTP.cpp - * Definitions for intermediate ThermoPhase object for phases which - * employ excess gibbs free energy formulations + * @file IonsFromNeutralVPSSTP.cpp + * Definitions for the object which treats ionic liquids as made of ions as species + * even though the thermodynamics is obtained from the neutral molecule representation. * (see \ref thermoprops - * and class \link Cantera::PseudoBinaryVPSSTP PseudoBinaryVPSSTP\endlink). + * and class \link Cantera::IonsFromNeutralVPSSTP IonsFromNeutralVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating @@ -21,7 +21,6 @@ * $Revision: 1.2 $ */ - #include "IonsFromNeutralVPSSTP.h" #include "ThermoFactory.h" From 45c2e077d12d10f62f22d894f39dec17470b0942 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 22:34:08 +0000 Subject: [PATCH 018/446] LiquidTransport.h LiquidTransport.cpp Added methods void getSpeciesHydrodynamicRadius() -- similar to getSpeciesViscosities() void updateHydrodynamicRadius_T() -- similar to updateViscosities_T() void updateHydrodynamicRadius_C() Added private members bool m_radi_temp_ok; bool m_radi_conc_ok; --- Cantera/src/transport/LiquidTransport.cpp | 76 ++++++++++++++++++++++- Cantera/src/transport/LiquidTransport.h | 30 ++++++++- 2 files changed, 101 insertions(+), 5 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 5c47c4b8e..d581b3215 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -46,6 +46,8 @@ namespace Cantera { m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), + m_radi_temp_ok(false), + m_radi_conc_ok(false), m_diff_mix_ok(false), m_diff_temp_ok(false), m_cond_temp_ok(false), @@ -71,6 +73,8 @@ namespace Cantera { m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), + m_radi_temp_ok(false), + m_radi_conc_ok(false), m_diff_mix_ok(false), m_diff_temp_ok(false), m_cond_temp_ok(false), @@ -112,6 +116,7 @@ namespace Cantera { m_bdiff = right.m_bdiff; m_viscSpecies = right.m_viscSpecies; m_logViscSpecies = right.m_logViscSpecies; + m_hydrodynamic_radius = right.m_hydrodynamic_radius; m_lambdaSpecies = right.m_lambdaSpecies; m_iStateMF = -1; m_molefracs = right.m_molefracs; @@ -131,6 +136,8 @@ namespace Cantera { m_visc_mix_ok = false; m_visc_temp_ok = false; m_visc_conc_ok = false; + m_radi_temp_ok = false; + m_radi_conc_ok = false; m_diff_mix_ok = false; m_diff_temp_ok = false; m_cond_temp_ok = false; @@ -378,7 +385,8 @@ namespace Cantera { m_visc_mix_ok = false; m_visc_temp_ok = false; m_visc_conc_ok = false; - + m_radi_temp_ok = false; + m_radi_conc_ok = false; m_cond_temp_ok = false; m_cond_mix_ok = false; m_diff_temp_ok = false; @@ -457,15 +465,23 @@ namespace Cantera { } copy(m_viscSpecies.begin(), m_viscSpecies.end(), visc); } - //==================================================================================================================== + + //=============================================================== // Returns the hydrodynamic radius for all species /* * The pure species viscosities are to be given in an Arrhenius * form in accordance with activated-jump-process dominated transport. */ void LiquidTransport::getSpeciesHydrodynamicRadius(doublereal* const radius) { + update_T(); + if (!m_radi_temp_ok) { + updateHydrodynamicRadius_T(); + } + copy(m_hydrodynamic_radius.begin(), m_hydrodynamic_radius.end(), radius); + } - //==================================================================================================================== + + //================================================================ /******************* binary diffusion coefficients **************/ @@ -746,6 +762,7 @@ namespace Cantera { // temperature has changed so temp flags are flipped m_visc_temp_ok = false; + m_radi_temp_ok = false; m_diff_temp_ok = false; // temperature has changed, so polynomial temperature @@ -1002,6 +1019,59 @@ namespace Cantera { } + //! Update the pure-species viscosities functional dependence on concentration. + void LiquidTransport::updateHydrodynamicRadius_C() { + m_visc_conc_ok = true; + } + + + /** + * Update the temperature-dependent hydrodynamic radius terms. + * Updates the array of pure species viscosities, and the + * weighting functions in the viscosity mixture rule. + * The flag m_visc_ok is set to true. + */ + void LiquidTransport::updateHydrodynamicRadius_T() { + int k; + + for (k = 0; k < m_nsp; k++) { + vector_fp &coeffk = m_coeffRadius_Ns[k]; + + if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_CONSTANT ) { + m_hydrodynamic_radius[k] = coeffk[0] ; + + } else if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_ARRHENIUS ) { + //m_coeffRadius_Ns[k][0] holds A + //m_coeffRadius_Ns[k][1] holds n + //m_coeffRadius_Ns[k][2] holds Tact + //m_coeffRadius_Ns[k][3] holds log(A) + m_hydrodynamic_radius[k] = coeffk[0] * exp( coeffk[1] * m_logt + - coeffk[2] / m_temp ); + + } else if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_POLY ) { + m_hydrodynamic_radius[k] = coeffk[0] + + coeffk[1] * m_temp + + coeffk[2] * m_temp * m_temp + + coeffk[3] * m_temp * m_temp * m_temp + + coeffk[4] * m_temp * m_temp * m_temp * m_temp; + + } else if ( m_radiusTempDepType_Ns[k] == LTR_MODEL_NOTSET ) { + throw CanteraError("LiquidTransport::updateHydrodynamicRadius_T", + "Hydrodynamic Radius Model is not set for species " + + m_thermo->speciesName(k) + + " in the input file"); + } else { + throw CanteraError("LiquidTransport::updateHydrodynamicRadius_T", + "Hydrodynamic Radius Model for species " + + m_thermo->speciesName(k) + + " is not handled by this object"); + } + m_radi_temp_ok = true; + m_diff_mix_ok = false; + } + } + + /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 4d6c43638..b56129fce 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -446,6 +446,13 @@ namespace Cantera { */ void updateViscosity_T(); + //! Update the temperature-dependent hydrodynamic radius terms + //! for each species + /*! + * The flag m_radi_temp_ok is set to true. + */ + void updateHydrodynamicRadius_T(); + //! Update the temperature-dependent parts of the mixture-averaged //! thermal conductivity. void updateCond_T(); @@ -453,13 +460,23 @@ namespace Cantera { //! Update the concentration parts of the viscosities /*! * Internal routine is run whenever the update_boolean - * m_visc_conc_ok is false. This routine will calculate - * internal values for the species viscosities. + * m_visc_conc_ok is false. Currently there is no concentration + * dependence for the pure species viscosities. * * @internal */ void updateViscosities_C(); + //! Update the concentration dependence of the hydrodynamic radius + /*! + * Internal routine is run whenever the update_boolean + * m_radi_conc_ok is false. Currently there is no concentration + * dependence for the hydrodynamic radius. + * + * @internal + */ + void updateHydrodynamicRadius_C(); + //! Update the binary diffusion coefficients wrt T. /*! * These are evaluated @@ -535,6 +552,7 @@ namespace Cantera { vector m_diffTempDepType_Ns; //! Pure species diffusvities in temperature-dependent form. + //! Not currently used since we get diffusivity from hydrodynamic radius. std::vector m_coeffDiff_Ns; @@ -829,6 +847,14 @@ namespace Cantera { //! are current wrt the concentration bool m_visc_conc_ok; + //! Boolean indicating that temperature dependence of + //! hydrodynamic radius is current + bool m_radi_temp_ok; + + //! Flag to indicate that the hydrodynamic radius is current + //! is current wrt the concentration + bool m_radi_conc_ok; + //! Boolean indicating that mixture diffusion coeffs are current bool m_diff_mix_ok; From 9c989652258812263772fb78511d235116e01226 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 23 Oct 2009 22:52:26 +0000 Subject: [PATCH 019/446] Added PDSS_SSVol.cpp to Makefile.in --- Cantera/src/thermo/Makefile.in | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index 3a31d01d4..fee9e7dfc 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -40,7 +40,7 @@ THERMO_OBJ = State.o Elements.o Constituents.o Phase.o \ ThermoFactory.o phasereport.o SpeciesThermoInterpType.o \ VPSSMgr.o VPSSMgrFactory.o VPSSMgr_General.o IdealSolnGasVPSS.o \ VPSSMgr_IdealGas.o VPSSMgr_ConstVol.o PDSS_ConstVol.o PDSS_IdealGas.o \ - @phase_object_files@ + PDSS_SSVol.o @phase_object_files@ THERMO_H = State.h Elements.h Constituents.h Phase.h mix_defs.h \ ThermoPhase.h IdealGasPhase.h ConstDensityThermo.h \ @@ -54,7 +54,7 @@ THERMO_H = State.h Elements.h Constituents.h Phase.h mix_defs.h \ EdgePhase.h \ VPSSMgr.h VPSSMgrFactory.h VPSSMgr_General.h IdealSolnGasVPSS.h \ VPSSMgr_IdealGas.h VPSSMgr_ConstVol.h PDSS_ConstVol.h PDSS_IdealGas.h \ - @phase_header_files@ + PDSS_SSVol.h @phase_header_files@ # Extended Cantera Thermodynamics Object Files From d06773652b71ac99e08f6e74ebe5cc9490e3222d Mon Sep 17 00:00:00 2001 From: John Hewson Date: Sat, 24 Oct 2009 00:57:49 +0000 Subject: [PATCH 020/446] Minor changes: Added examples for transport mixing model XML Changed "arrhenius" to "Arrhenius" is XML. --- Cantera/src/transport/LiquidTransportParams.h | 42 ++++++++++++++++++- Cantera/src/transport/TransportFactory.cpp | 30 ++++++------- 2 files changed, 56 insertions(+), 16 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index faf08edb6..1dd99b5d7 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -21,14 +21,54 @@ namespace Cantera { * 2 - Properties weighted linearly by mass fractions * 3 - Properties weighted logarithmically by mole fractions (interaction energy weighting) * 4 - Interactions given pairwise between each possible species (i.e. D_ij) + * + * + * + * + * + * LiCl(L) + * KCl(L) + * -1.0 + * 1.0E-1 + * + * + * + * + * + * + * Li+ + * K+ + * 1.5 + * + * + * K+ + * Cl- + * 1.0 + * + * + * Li+ + * Cl- + * 1.2 + * + * + * + * + * + * + * + * + * + * + * */ enum LiquidTranMixingModel { LTR_MIXMODEL_NOTSET=-1, + LTR_MIXMODEL_NONE, LTR_MIXMODEL_SOLVENT, LTR_MIXMODEL_MOLEFRACS, LTR_MIXMODEL_MASSFRACS, LTR_MIXMODEL_LOG_MOLEFRACS, - LTR_PAIRWISE_INTERACTIONS + LTR_PAIRWISE_INTERACTION }; diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 180651b0e..1d1ec5ffb 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -885,29 +885,29 @@ namespace Cantera { * hydrodynamic radius * * format: - * 3.0 - * 3.0 - * + * 3.0 + * 3.0 + * * 1.0 * 2.0 * 3.0 - * + * * - * + * * 0.0. 1.0, 2.0, 3.0, 4.0 - * + * * */ - if (trNode.hasChild("hydrodynamic_radius")) { - XML_Node& hnode = trNode.child("hydrodynamic_radius"); + if (trNode.hasChild("hydrodynamicRadius")) { + XML_Node& hnode = trNode.child("hydrodynamicRadius"); std::string units = lowercase(hnode["units"]); if ( units == "" ) - cout << "Warning::hydrodynamic_radius units not given for " + cout << "Warning::hydrodynamicRadius units not given for " << name << endl << " Units assumed to be meters." << endl; std::string model = lowercase(hnode["model"]); if (model == "" || model == "constant") { - A_k = getFloat(trNode, "hydrodynamic_radius", "toSI"); + A_k = getFloat(trNode, "hydrodynamicRadius", "toSI"); //A_k = hnode.fp_value(); //// Angstroms -> meters //A_k = 1.e-10 * A_k; @@ -916,7 +916,7 @@ namespace Cantera { } else throw TransportDBError(linenum, "negative or zero hydrodynamic radius"); data.model_hydroradius = LTR_MODEL_CONSTANT; - } else if (model == "arrhenius") { + } else if (model == "Arrhenius") { getArrhenius(hnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero viscosity"); @@ -935,7 +935,7 @@ namespace Cantera { data.model_hydroradius = LTR_MODEL_POLY; } else { throw CanteraError(" TransportFactory::getLiquidSpeciesTransportData", - "Unknown model for hydrodynamic_radius:" + model); + "Unknown model for hydrodynamicRadius:" + model); } } @@ -965,7 +965,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero viscosity"); data.model_viscosity = LTR_MODEL_CONSTANT; - } else if (model == "arrhenius") { + } else if (model == "Arrhenius") { getArrhenius(vnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero viscosity"); @@ -1011,7 +1011,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero thermalConductivity"); data.model_thermalCond = LTR_MODEL_CONSTANT; - } else if (model == "arrhenius") { + } else if (model == "Arrhenius") { getArrhenius(tnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero thermalConductivity"); @@ -1058,7 +1058,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); data.model_speciesDiffusivity = LTR_MODEL_CONSTANT; - } else if (model == "arrhenius") { + } else if (model == "Arrhenius") { getArrhenius(dnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); From 217a0b49821f39f7633bfc2b23824dea450e3724 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Sat, 24 Oct 2009 02:04:06 +0000 Subject: [PATCH 021/446] Slowly adding species-species transport interactions. --- Cantera/src/transport/LiquidTransport.cpp | 10 +++++++++- Cantera/src/transport/TransportFactory.cpp | 21 ++++++++++++++++++--- 2 files changed, 27 insertions(+), 4 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index d581b3215..ce9b75e9b 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -974,6 +974,14 @@ namespace Cantera { * Updates the array of pure species viscosities, and the * weighting functions in the viscosity mixture rule. * The flag m_visc_ok is set to true. + * + * Note that for viscosity, a positive activation energy + * corresponds to the typical case of a positive argument + * to the exponential so that the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( + E / R T ) + * \f] */ void LiquidTransport::updateViscosity_T() { int k; @@ -991,7 +999,7 @@ namespace Cantera { //m_coeffVisc_Ns[k][2] holds Tact //m_coeffVisc_Ns[k][3] holds log(A) m_logViscSpecies[k] = coeffk[3] + coeffk[1] * m_logt - - coeffk[2] / m_temp ; + + coeffk[2] / m_temp ; m_viscSpecies[k] = exp( m_logViscSpecies[k] ); } else if ( m_viscTempDepType_Ns[k] == LTR_MODEL_POLY ) { diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 1d1ec5ffb..d3d96f53c 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1126,10 +1126,25 @@ namespace Cantera { if ( transportNode.hasChild("viscosity")) { XML_Node& viscosityNode = transportNode.child("viscosity"); - string viscosityModel = viscosityNode.attrib("model"); - if (viscosityModel == "") { - throw CanteraError("LiquidTransport::initLiquid", + if ( viscosityNode.hasChild("compositionDependence") ) { + string viscosityModel = viscosityNode.child("compositionDependence").attrib("model"); + if (viscosityModel == "") { + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "transport::visosity XML node doesn't have a model string"); + } else if ( viscosityModel == "none"){ + ; + } else if ( viscosityModel == "solvent"){ + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "solvent interactions not implemented"); + } else if ( viscosityModel == "moleFractions"){ + ; + } else if ( viscosityModel == "massFractions"){ + ; + } else if ( viscosityModel == "logMoleFractions"){ + ; + } else if ( viscosityModel == "pairwiseInteractionEnergy"){ + ; + } } } } From cc07e10207a9c77c4e8ae35a86fc57a5212b9cd8 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 28 Oct 2009 01:05:45 +0000 Subject: [PATCH 022/446] LiquidTransport.cpp Removed XML node processing of transport model (species interaction part) from initLiquid(). m_molefracs_tran and m_concentrations are now properly dimensioned and copied. TransportFactory.cpp Corrections to XML node processing in getLiquidSpeciesTransportData and getLiquidSpeciesInteractionData --- Cantera/src/transport/LiquidTransport.cpp | 62 ++++++------------- Cantera/src/transport/TransportFactory.cpp | 69 +++++++++++----------- 2 files changed, 52 insertions(+), 79 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index ce9b75e9b..1dc7a0409 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -120,6 +120,7 @@ namespace Cantera { m_lambdaSpecies = right.m_lambdaSpecies; m_iStateMF = -1; m_molefracs = right.m_molefracs; + m_molefracs_tran = right.m_molefracs_tran; m_concentrations = right.m_concentrations; m_chargeSpecies = right.m_chargeSpecies; m_DiffCoeff_StefMax = right.m_DiffCoeff_StefMax; @@ -168,50 +169,6 @@ namespace Cantera { m_tmin = m_thermo->minTemp(); m_tmax = m_thermo->maxTemp(); - /* - * Read the transport block in the phase XML Node - * It's not an error if this block doesn't exist. Just use the defaults - */ - XML_Node &phaseNode = m_thermo->xml(); - if (phaseNode.hasChild("transport")) { - XML_Node& transportNode = phaseNode.child("transport"); - if ( transportNode.hasChild("viscosity")) { - XML_Node& viscosityNode = transportNode.child("viscosity"); - string viscosityModel = viscosityNode.attrib("model"); - if (viscosityModel == "") { - throw CanteraError("LiquidTransport::initLiquid", - "transport::visosity XML node doesn't have a model string"); - } - } - - - - string transportModel = transportNode.attrib("model"); - if (transportModel == "LiquidTransport") { - /* - * - * or - * - */ - std::string modelName = ""; - if (getOptionalModel(transportNode, "compositionDependence", - modelName)) { - modelName = lowercase(modelName); - if (modelName == "solvent_only") { - m_compositionDepType = 0; - } else if (modelName == "mixture_averaged") { - m_compositionDepType = 1; - } else { - throw CanteraError("LiquidTransport::initLiquid", "Unknown compositionDependence Model: " + modelName); - } - } - - - - - } - } - // make a local copy of the molecular weights m_mw.resize(m_nsp); copy(m_thermo->molecularWeights().begin(), @@ -359,11 +316,24 @@ namespace Cantera { << endl << "LiquidTransport model uses hydrodynamicRadius, viscosity " << endl - << "and the Stokes-Einstein equation." + << "and the Stokes-Einstein equation or Interaction Model." << endl; } } + + + /* + * Read the transport block in the phase XML Node + * It's not an error if this block doesn't exist. Just use the defaults + */ + + //HERE WE NEED TO GET THINGS FROM + //TransportFactory::getLiquidInteractionsTransportData + + + + m_mode = tr.mode_; m_viscSpecies.resize(m_nsp); @@ -372,6 +342,8 @@ namespace Cantera { m_bdiff.resize(m_nsp, m_nsp); m_molefracs.resize(m_nsp); + m_molefracs_tran.resize(m_nsp); + m_concentrations.resize(m_nsp); m_spwork.resize(m_nsp); // resize the internal gradient variables diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index d3d96f53c..69a468feb 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -43,7 +43,7 @@ #include -using namespace std; +//using namespace std; /** * polynomial degree used for fitting collision integrals @@ -68,7 +68,7 @@ namespace Cantera { */ class TransportDBError : public CanteraError { public: - TransportDBError(int linenum, string msg) + TransportDBError(int linenum, std::string msg) : CanteraError("getTransportData", "error reading transport data: " + msg + "\n") {} @@ -77,7 +77,7 @@ namespace Cantera { class NotImplemented : public CanteraError { public: - NotImplemented(string method) : CanteraError("Transport", + NotImplemented(std::string method) : CanteraError("Transport", "\n\n\n**** Method "+method+" not implemented. ****\n" "(Did you forget to specify a transport model?)\n\n\n") {} }; @@ -376,7 +376,7 @@ namespace Cantera { "no transport XML node"); } XML_Node& transportNode = phaseNode.child("transport"); - string transportModel = transportNode.attrib("model"); + std::string transportModel = transportNode.attrib("model"); if (transportModel == "") { throw CanteraError("TransportFactory::newTransport", "transport XML node doesn't have a model string"); @@ -547,7 +547,7 @@ namespace Cantera { // This will fill LiquidTransportParams members visc_Eij, visc_Sij trParam.visc_Eij.resize(nsp,nsp); trParam.visc_Sij.resize(nsp,nsp); - cout << "Still no support for species viscosity interactions in TransportFactory.cpp" << endl; + std::cout << "Still no support for species viscosity interactions in TransportFactory.cpp" << std::endl; XML_Node root, log; // Note that getLiquidSpeciesTransportData just populates the pure species transport data. @@ -724,7 +724,7 @@ namespace Cantera { void TransportFactory::getTransportData(const std::vector &xspecies, XML_Node& log, const std::vector &names, GasTransportParams& tr) { - string name; + std::string name; int geom; std::map datatable; doublereal welldepth, diam, dipole, polar, rot; @@ -735,8 +735,8 @@ namespace Cantera { // errors. Note that this procedure validates all entries, not // only those for the species listed in 'names'. - string val, type; - map gindx; + std::string val, type; + map gindx; gindx["atom"] = 100; gindx["linear"] = 101; gindx["nonlinear"] = 102; @@ -753,7 +753,7 @@ namespace Cantera { XML_Node& tr = sp.child("transport"); getString(tr, "geometry", val, type); geom = gindx[val] - 100; - map fv; + map fv; welldepth = getFloat(tr, "LJ_welldepth"); diam = getFloat(tr, "LJ_diameter"); @@ -893,7 +893,7 @@ namespace Cantera { * 3.0 * * - * + * * 0.0. 1.0, 2.0, 3.0, 4.0 * * @@ -902,8 +902,8 @@ namespace Cantera { XML_Node& hnode = trNode.child("hydrodynamicRadius"); std::string units = lowercase(hnode["units"]); if ( units == "" ) - cout << "Warning::hydrodynamicRadius units not given for " - << name << endl + std::cout << "Warning::hydrodynamicRadius units not given for " + << name << std::endl << " Units assumed to be meters." << endl; std::string model = lowercase(hnode["model"]); if (model == "" || model == "constant") { @@ -916,10 +916,10 @@ namespace Cantera { } else throw TransportDBError(linenum, "negative or zero hydrodynamic radius"); data.model_hydroradius = LTR_MODEL_CONSTANT; - } else if (model == "Arrhenius") { + } else if (model == "arrhenius") { getArrhenius(hnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { - throw TransportDBError(linenum, "negative or zero viscosity"); + throw TransportDBError(linenum, "negative or zero hydrodynamic radius"); } // Angstroms -> meters //already done in getArrhenius??? @@ -928,7 +928,7 @@ namespace Cantera { (data.hydroRadiusCoeffs).push_back(n_k); (data.hydroRadiusCoeffs).push_back(Tact_k); data.model_hydroradius = LTR_MODEL_ARRHENIUS; - } else if (model == "coeff") { + } else if (model == "coeffs") { getFloatArray(hnode, vCoeff, true); // if units labeled, convert Angstroms -> meters data.hydroRadiusCoeffs = vCoeff; vCoeff.clear(); @@ -951,7 +951,7 @@ namespace Cantera { * 3.0 * * - * + * * 0.0. 1.0, 2.0, 3.0, 4.0 * * @@ -965,7 +965,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero viscosity"); data.model_viscosity = LTR_MODEL_CONSTANT; - } else if (model == "Arrhenius") { + } else if (model == "arrhenius") { getArrhenius(vnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero viscosity"); @@ -974,7 +974,7 @@ namespace Cantera { (data.viscCoeffs).push_back(n_k); (data.viscCoeffs).push_back(Tact_k); data.model_viscosity = LTR_MODEL_ARRHENIUS; - } else if (model == "coeff") { + } else if (model == "coeffs") { getFloatArray(vnode, vCoeff, true); data.viscCoeffs = vCoeff; vCoeff.clear(); @@ -1011,7 +1011,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero thermalConductivity"); data.model_thermalCond = LTR_MODEL_CONSTANT; - } else if (model == "Arrhenius") { + } else if (model == "arrhenius") { getArrhenius(tnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero thermalConductivity"); @@ -1020,7 +1020,7 @@ namespace Cantera { (data.thermalCondCoeffs).push_back(n_k); (data.thermalCondCoeffs).push_back(Tact_k); data.model_thermalCond = LTR_MODEL_ARRHENIUS; - } else if (model == "coeff") { + } else if (model == "coeffs") { getFloatArray(tnode, vCoeff, true); data.thermalCondCoeffs = vCoeff; vCoeff.clear(); @@ -1044,7 +1044,7 @@ namespace Cantera { * 3.0 * * - * + * * 0.0. 1.0, 2.0, 3.0, 4.0 * * @@ -1058,7 +1058,7 @@ namespace Cantera { else throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); data.model_speciesDiffusivity = LTR_MODEL_CONSTANT; - } else if (model == "Arrhenius") { + } else if (model == "arrhenius") { getArrhenius(dnode, A_k, n_k, Tact_k); if (A_k <= 0.0) { throw TransportDBError(linenum, "negative or zero speciesDiffusivity"); @@ -1067,7 +1067,7 @@ namespace Cantera { (data.speciesDiffusivityCoeffs).push_back(n_k); (data.speciesDiffusivityCoeffs).push_back(Tact_k); data.model_speciesDiffusivity = LTR_MODEL_ARRHENIUS; - } else if (model == "coeff") { + } else if (model == "coeffs") { getFloatArray(dnode, vCoeff, true); data.speciesDiffusivityCoeffs = vCoeff; data.model_speciesDiffusivity = LTR_MODEL_POLY; @@ -1096,9 +1096,9 @@ namespace Cantera { if (trdat.viscCoeffs[0] <= 0.0 ) { throw TransportDBError(0,"no viscosity transport data found for species " + names[i]); - cout << "No viscosity seen for " << names[i] + std::cout << "No viscosity seen for " << names[i] << "but this might not be required depending on what you are trying to do." - << endl; + << std::endl; } /* @@ -1127,22 +1127,23 @@ namespace Cantera { if ( transportNode.hasChild("viscosity")) { XML_Node& viscosityNode = transportNode.child("viscosity"); if ( viscosityNode.hasChild("compositionDependence") ) { - string viscosityModel = viscosityNode.child("compositionDependence").attrib("model"); - if (viscosityModel == "") { + XML_Node& compositionNode = viscosityNode.child("compositionDependence"); + std::string compositionModel = compositionNode.attrib("model"); + if ( compositionModel == "" ) { throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", - "transport::visosity XML node doesn't have a model string"); - } else if ( viscosityModel == "none"){ + "transport::viscosity XML node doesn't have a model string"); + } else if ( compositionModel == "none"){ ; - } else if ( viscosityModel == "solvent"){ + } else if ( compositionModel == "solvent"){ throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "solvent interactions not implemented"); - } else if ( viscosityModel == "moleFractions"){ + } else if ( compositionModel == "moleFractions"){ ; - } else if ( viscosityModel == "massFractions"){ + } else if ( compositionModel == "massFractions"){ ; - } else if ( viscosityModel == "logMoleFractions"){ + } else if ( compositionModel == "logMoleFractions"){ ; - } else if ( viscosityModel == "pairwiseInteractionEnergy"){ + } else if ( compositionModel == "pairwiseInteractionEnergy"){ ; } } From a4b9fd56c4f6077ef9163fcca4acc64bad7ab578 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 28 Oct 2009 02:30:59 +0000 Subject: [PATCH 023/446] Added following members in LiquidTransport.cpp and LiquidTransport.h associated with transport coefficient mixing properties: + LiquidTranMixingModel m_viscMixModel; + LiquidTranMixingModel m_lambdaMixModel; + DenseMatrix m_lambda_Aij; + LiquidTranMixingModel m_diffMixModel; + DenseMatrix m_diff_Dij; + LiquidTranMixingModel m_radiusMixModel; Removed - int m_compositionDepType; since it is replaced by the above property-dependent model specifications. Similarly in LiquidTransportParams.h added following + LiquidTranMixingModel model_viscosity; + LiquidTranMixingModel model_thermalCond; + DenseMatrix thermalCond_Aij; + LiquidTranMixingModel model_speciesDiffusivity; + DenseMatrix diff_Dij; + LiquidTranMixingModel model_hydroradius; Added some processing of the above variables from the XML file in LiquidTransport::getLiquidInteractionsTransportData. --- Cantera/src/transport/LiquidTransport.cpp | 30 ++++++++++- Cantera/src/transport/LiquidTransport.h | 54 +++++++++++++------ Cantera/src/transport/LiquidTransportParams.h | 52 +++++++++++++++--- Cantera/src/transport/TransportFactory.cpp | 10 ++-- 4 files changed, 117 insertions(+), 29 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 1dc7a0409..dbcd6798e 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -36,7 +36,9 @@ namespace Cantera { m_nsp(0), m_tmin(-1.0), m_tmax(100000.), - m_compositionDepType(-1), + m_viscMixModel(LTR_MIXMODEL_NOTSET), + m_lambdaMixModel(LTR_MIXMODEL_NOTSET), + m_diffMixModel(LTR_MIXMODEL_NOTSET), m_iStateMF(-1), m_temp(-1.0), m_logt(0.0), @@ -63,7 +65,6 @@ namespace Cantera { m_nsp(0), m_tmin(-1.0), m_tmax(100000.), - m_compositionDepType(-1), m_iStateMF(-1), m_temp(-1.0), m_logt(0.0), @@ -118,6 +119,9 @@ namespace Cantera { m_logViscSpecies = right.m_logViscSpecies; m_hydrodynamic_radius = right.m_hydrodynamic_radius; m_lambdaSpecies = right.m_lambdaSpecies; + m_viscMixModel = right.m_viscMixModel; + m_lambdaMixModel = right.m_lambdaMixModel; + m_diffMixModel = right.m_diffMixModel; m_iStateMF = -1; m_molefracs = right.m_molefracs; m_molefracs_tran = right.m_molefracs_tran; @@ -330,6 +334,28 @@ namespace Cantera { //HERE WE NEED TO GET THINGS FROM //TransportFactory::getLiquidInteractionsTransportData + /* + * Viscosity mixing rules + */ + m_viscMixModel = tr.model_viscosity; + m_visc_Eij.resize(m_nsp,m_nsp); + m_visc_Sij.resize(m_nsp,m_nsp); + + + + /* + * Thermal conductivity mixing rules + */ + m_lambdaMixModel = tr.model_viscosity; + m_lambda_Aij.resize(m_nsp,m_nsp); + + /* + * Species Diffusivity binary diffusion coefficients + * for Stefan Maxwell equation or "mixing rules" + */ + m_diffMixModel = tr.model_viscosity; + m_diff_Dij.resize(m_nsp,m_nsp); + diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index b56129fce..f570932b9 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -514,6 +514,15 @@ namespace Cantera { //! Pure species viscosities in temperature-dependent form. std::vector m_coeffVisc_Ns; + //! Viscosity mixing model type + /*! + * Types of mixing models supported: + * 2 - Mole fraction weighting of species viscosities + * 3 - Mass fraction weighting of species viscosities + * 4 - Mole fraction weighting of logarithms of species viscosities + */ + LiquidTranMixingModel m_viscMixModel; + //! Molecular interaction energies associated with viscosity /** * These multiply the viscosity according to @@ -528,8 +537,6 @@ namespace Cantera { */ DenseMatrix m_visc_Sij; - - //! Thermal conductivity temperature dependence type /*! * Types of temperature dependencies: @@ -542,6 +549,21 @@ namespace Cantera { //! Pure species thermal conductivities in temperature-dependent form. std::vector m_coeffLambda_Ns; + //! Thermal conductivity mixing model type + /*! + * Types of mixing models supported: + * 2 - Mole fraction weighting of species viscosities + * 3 - Mass fraction weighting of species viscosities + */ + LiquidTranMixingModel m_lambdaMixModel; + + //! Molecular interaction associated with thermal conductivity + /** + * These multiply the viscosity according to + * \f[ exp( \sum_{i} \sum{j} X_i X_j S_{i,j} \f]. + */ + DenseMatrix m_lambda_Aij; + //! Diffusion coefficient temperature dependence type /*! * Types of temperature dependencies: @@ -555,6 +577,16 @@ namespace Cantera { //! Not currently used since we get diffusivity from hydrodynamic radius. std::vector m_coeffDiff_Ns; + //! Species diffusivity mixing model type + /*! + * Types of mixing models supported: + * 5 - Pairwise interactions -- Setfan-Maxwell diffusion coefficients + */ + LiquidTranMixingModel m_diffMixModel; + + //! Setfan-Maxwell diffusion coefficients + DenseMatrix m_diff_Dij; + vector useHydroRadius_; @@ -573,21 +605,13 @@ namespace Cantera { //! Species hydrodynamic radius vector_fp m_hydrodynamic_radius; - - - //! Composition dependence of the transport properties + //! Hydrodynamic radius mixing model type /*! - * The following coefficients are allowed to have simple - * composition dependencies - * mixture viscosity - * mixture thermal conductivity - * - * - * Types of composition dependencies - * 0 - Solvent values (i.e., species 0) contributes only - * 1 - linear combination of mole fractions; + * Types of mixing models supported: + * 0 - No mixing model allowed */ - int m_compositionDepType; + LiquidTranMixingModel m_radiusMixModel; + //! Polynomial coefficients of the binary diffusion coefficients /*! diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 1dd99b5d7..e1790c266 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -16,11 +16,12 @@ namespace Cantera { //! Composition dependence type for liquid mixture transport properties /*! * Types of temperature dependencies: - * 0 - Use solvent (species 0) properties - * 1 - Properties weighted linearly by mole fractions - * 2 - Properties weighted linearly by mass fractions - * 3 - Properties weighted logarithmically by mole fractions (interaction energy weighting) - * 4 - Interactions given pairwise between each possible species (i.e. D_ij) + * 0 - Mixture calculations with this property are not allowed + * 1 - Use solvent (species 0) properties + * 2 - Properties weighted linearly by mole fractions + * 3 - Properties weighted linearly by mass fractions + * 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * 5 - Interactions given pairwise between each possible species (i.e. D_ij) * * * @@ -68,7 +69,7 @@ namespace Cantera { LTR_MIXMODEL_MOLEFRACS, LTR_MIXMODEL_MASSFRACS, LTR_MIXMODEL_LOG_MOLEFRACS, - LTR_PAIRWISE_INTERACTION + LTR_MIXMODEL_PAIRWISE_INTERACTION }; @@ -85,6 +86,13 @@ namespace Cantera { LiquidTransportParams() {} ~LiquidTransportParams() {} + //! Species transport parameters + std::vector LTData; + + //! Model for species interaction effects for viscosity + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel model_viscosity; + //! Energies of molecular interaction associated with viscosity. /** * These multiply the mixture viscosity by @@ -100,8 +108,38 @@ namespace Cantera { //! Entropies of molecular interaction associated with viscosity. DenseMatrix visc_Sij; - std::vector LTData; + //! Model for species interaction effects for thermal conductivity + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel model_thermalCond; + //! Interaction associated with linear weighting of + //! thermal conductivity. + /** + * This is used for either LTR_MIXMODEL_MASSFRACS + * or LTR_MIXMODEL_MOLEFRACS. + * The overall formula for the mixture viscosity is + * + * \f[ \eta_{mix} = \sum_i X_i \eta_i + * + \sum_i \sum_j X_i X_j A_{i,j} \f]. + */ + DenseMatrix thermalCond_Aij; + + //! Model for species interaction effects for mass diffusivity + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel model_speciesDiffusivity; + + //! Interaction associated with linear weighting of + //! thermal conductivity. + /** + * This is used for either LTR_MIXMODEL_PAIRWISE_INTERACTION. + * These provide species interaction coefficients associated with + * the Stefan-Maxwell formulation. + */ + DenseMatrix diff_Dij; + + //! Model for species interaction effects for hydrodynamic radius + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel model_hydroradius; }; } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 69a468feb..e7cb2dde7 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1133,18 +1133,18 @@ namespace Cantera { throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "transport::viscosity XML node doesn't have a model string"); } else if ( compositionModel == "none"){ - ; + trParam.model_viscosity = LTR_MIXMODEL_NONE; } else if ( compositionModel == "solvent"){ throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "solvent interactions not implemented"); } else if ( compositionModel == "moleFractions"){ - ; + trParam.model_viscosity = LTR_MIXMODEL_MOLEFRACS; } else if ( compositionModel == "massFractions"){ - ; + trParam.model_viscosity = LTR_MIXMODEL_MASSFRACS; } else if ( compositionModel == "logMoleFractions"){ - ; + trParam.model_viscosity = LTR_MIXMODEL_LOG_MOLEFRACS; } else if ( compositionModel == "pairwiseInteractionEnergy"){ - ; + trParam.model_viscosity = LTR_MIXMODEL_PAIRWISE_INTERACTION; } } } From 33cf246c2563c502d70d656205c499016d814c58 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 28 Oct 2009 04:02:28 +0000 Subject: [PATCH 024/446] LiquidTransportParams.h TransportFactory.cpp Filled out TransportFactory::getLiquidInteractionsTransportData to parse interaction parameters. About 220 lines of XML node extraction added. LiquidTransport.h LiquidTransport.cpp Near the end of LiquidTransport::initLiquid, added the copying of interaction parameters from the LiquidTransportParams object to members: + m_visc_Eij = tr.visc_Eij; + m_visc_Sij = tr.visc_Sij; + m_lambda_Aij = tr.thermalCond_Aij; + m_diff_Dij = tr.diff_Dij; + m_radius_Aij = tr.radius_Aij; Note that the last member was added to allow for hydrodynamic radius mixing rules. --- Cantera/src/transport/LiquidTransport.cpp | 25 +- Cantera/src/transport/LiquidTransport.h | 3 + Cantera/src/transport/LiquidTransportParams.h | 22 +- Cantera/src/transport/TransportFactory.cpp | 236 ++++++++++++++++-- 4 files changed, 248 insertions(+), 38 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index dbcd6798e..fe61d4d43 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -325,37 +325,40 @@ namespace Cantera { } } - - /* - * Read the transport block in the phase XML Node - * It's not an error if this block doesn't exist. Just use the defaults + * Here we get interaction parameters from LiquidTransportParams + * that were filled in TransportFactory::getLiquidInteractionsTransportData */ - - //HERE WE NEED TO GET THINGS FROM - //TransportFactory::getLiquidInteractionsTransportData /* * Viscosity mixing rules */ m_viscMixModel = tr.model_viscosity; m_visc_Eij.resize(m_nsp,m_nsp); m_visc_Sij.resize(m_nsp,m_nsp); - - + m_visc_Eij = tr.visc_Eij; + m_visc_Sij = tr.visc_Sij; /* * Thermal conductivity mixing rules */ - m_lambdaMixModel = tr.model_viscosity; + m_lambdaMixModel = tr.model_thermalCond; m_lambda_Aij.resize(m_nsp,m_nsp); + m_lambda_Aij = tr.thermalCond_Aij; /* * Species Diffusivity binary diffusion coefficients * for Stefan Maxwell equation or "mixing rules" */ - m_diffMixModel = tr.model_viscosity; + m_diffMixModel = tr.model_speciesDiffusivity; m_diff_Dij.resize(m_nsp,m_nsp); + m_diff_Dij = tr.diff_Dij; + /* + * Hydrodynamic radius mixing model rules + */ + m_radiusMixModel = tr.model_radius; + m_radius_Aij.resize(m_nsp,m_nsp); + m_radius_Aij = tr.radius_Aij; diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index f570932b9..4af44619b 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -612,6 +612,9 @@ namespace Cantera { */ LiquidTranMixingModel m_radiusMixModel; + //! Hydrodynamic radius mixing model interaction parameters + DenseMatrix m_radius_Aij; + //! Polynomial coefficients of the binary diffusion coefficients /*! diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index e1790c266..157c372f1 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -27,8 +27,8 @@ namespace Cantera { * * * - * LiCl(L) - * KCl(L) + * LiCl(L) + * KCl(L) * -1.0 * 1.0E-1 * @@ -37,18 +37,18 @@ namespace Cantera { * * * - * Li+ - * K+ + * Li+ + * K+ * 1.5 * * - * K+ - * Cl- + * K+ + * Cl- * 1.0 * * - * Li+ - * Cl- + * Li+ + * Cl- * 1.2 * * @@ -140,6 +140,12 @@ namespace Cantera { //! Model for species interaction effects for hydrodynamic radius //! Takes enum LiquidTranMixingModel LiquidTranMixingModel model_hydroradius; + + //! Interaction associated with hydrodynamic radius. + /** + * Not yet implemented + */ + DenseMatrix radius_Aij; }; } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index e7cb2dde7..533e08230 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1124,30 +1124,228 @@ namespace Cantera { LiquidTransportParams& trParam) { - if ( transportNode.hasChild("viscosity")) { - XML_Node& viscosityNode = transportNode.child("viscosity"); - if ( viscosityNode.hasChild("compositionDependence") ) { - XML_Node& compositionNode = viscosityNode.child("compositionDependence"); - std::string compositionModel = compositionNode.attrib("model"); - if ( compositionModel == "" ) { + std::string type; + std::string speciesA; + std::string speciesB; + /* + * Viscosity + */ + if ( transportNode.hasChild("viscosity")) { + XML_Node& viscosityNode = transportNode.child("viscosity"); + if ( viscosityNode.hasChild("compositionDependence") ) { + XML_Node& compositionNode = viscosityNode.child("compositionDependence"); + std::string compositionModel = compositionNode.attrib("model"); + if ( compositionModel == "" ) { throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "transport::viscosity XML node doesn't have a model string"); - } else if ( compositionModel == "none"){ - trParam.model_viscosity = LTR_MIXMODEL_NONE; - } else if ( compositionModel == "solvent"){ - throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + } else if ( compositionModel == "none"){ + trParam.model_viscosity = LTR_MIXMODEL_NONE; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_NONE interactions not implemented for viscosity"); + } else if ( compositionModel == "solvent"){ + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", "solvent interactions not implemented"); - } else if ( compositionModel == "moleFractions"){ - trParam.model_viscosity = LTR_MIXMODEL_MOLEFRACS; - } else if ( compositionModel == "massFractions"){ - trParam.model_viscosity = LTR_MIXMODEL_MASSFRACS; - } else if ( compositionModel == "logMoleFractions"){ - trParam.model_viscosity = LTR_MIXMODEL_LOG_MOLEFRACS; - } else if ( compositionModel == "pairwiseInteractionEnergy"){ - trParam.model_viscosity = LTR_MIXMODEL_PAIRWISE_INTERACTION; - } + } else if ( compositionModel == "moleFractions"){ + trParam.model_viscosity = LTR_MIXMODEL_MOLEFRACS; + } else if ( compositionModel == "massFractions"){ + trParam.model_viscosity = LTR_MIXMODEL_MASSFRACS; + } else if ( compositionModel == "logMoleFractions"){ + trParam.model_viscosity = LTR_MIXMODEL_LOG_MOLEFRACS; + } else if ( compositionModel == "pairwiseInteractionEnergy"){ + trParam.model_viscosity = LTR_MIXMODEL_PAIRWISE_INTERACTION; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_PAIRWISE_INTERACTION interactions not implemented for viscosity"); + } + int num = compositionNode.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = compositionNode.child(iChild); + std::string nodeName = lowercase( xmlChild.name() ); + if ( nodeName != "interaction" ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "expected element and got " + nodeName ); + getString( xmlChild, "speciesA", speciesA, type ); + getString( xmlChild, "speciesB", speciesB, type ); + int iSpecies = trParam.thermo->speciesIndex( speciesA ); + if ( iSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesA ); + int jSpecies = trParam.thermo->speciesIndex( speciesB ); + if ( jSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesB ); + trParam.visc_Eij(iSpecies,jSpecies) = getFloat( xmlChild, "Eij", "toSI" ); + trParam.visc_Eij(jSpecies,iSpecies) = trParam.visc_Eij(iSpecies,jSpecies) ; + trParam.visc_Sij(iSpecies,jSpecies) = getFloat( xmlChild, "Sij", "toSI" ); + trParam.visc_Sij(jSpecies,iSpecies) = trParam.visc_Sij(iSpecies,jSpecies) ; } } + } + + + /* + * Thermal conductivity + */ + if ( transportNode.hasChild("thermalConductivity")) { + XML_Node& thermCondNode = transportNode.child("thermalConductivity"); + if ( thermCondNode.hasChild("compositionDependence") ) { + XML_Node& compositionNode = thermCondNode.child("compositionDependence"); + std::string compositionModel = compositionNode.attrib("model"); + if ( compositionModel == "" ) { + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "transport::thermalConductivity XML node doesn't have a model string"); + } else if ( compositionModel == "none"){ + trParam.model_thermalCond = LTR_MIXMODEL_NONE; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_NONE interactions not implemented for thermalConductivity"); + } else if ( compositionModel == "solvent"){ + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "solvent interactions not implemented"); + } else if ( compositionModel == "moleFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_MOLEFRACS; + } else if ( compositionModel == "massFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_MASSFRACS; + } else if ( compositionModel == "logMoleFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_LOG_MOLEFRACS; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_LOG_MOLEFRACS interactions not implemented for thermalConductivity"); + } else if ( compositionModel == "pairwiseInteractionEnergy"){ + trParam.model_thermalCond = LTR_MIXMODEL_PAIRWISE_INTERACTION; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_PAIRWISE_INTERACTION interactions not implemented for thermalConductivity"); + } + int num = compositionNode.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = compositionNode.child(iChild); + std::string nodeName = lowercase( xmlChild.name() ); + if ( nodeName != "interaction" ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "expected element and got <" + nodeName + ">" ); + getString( xmlChild, "speciesA", speciesA, type ); + getString( xmlChild, "speciesB", speciesB, type ); + int iSpecies = trParam.thermo->speciesIndex( speciesA ); + if ( iSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesA ); + int jSpecies = trParam.thermo->speciesIndex( speciesB ); + if ( jSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesB ); + trParam.thermalCond_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); + trParam.thermalCond_Aij(jSpecies,iSpecies) = trParam.thermalCond_Aij(iSpecies,jSpecies) ; + } + } + } + + + /* + * Species Diffusivity + */ + if ( transportNode.hasChild("speciesDiffusivity")) { + XML_Node& diffusivityNode = transportNode.child("speciesDiffusivity"); + if ( diffusivityNode.hasChild("compositionDependence") ) { + XML_Node& compositionNode = diffusivityNode.child("compositionDependence"); + std::string compositionModel = compositionNode.attrib("model"); + if ( compositionModel == "" ) { + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "transport::speciesDiffusivity XML node doesn't have a model string"); + } else if ( compositionModel == "none"){ + trParam.model_speciesDiffusivity = LTR_MIXMODEL_NONE; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_NONE interactions not implemented for speciesDiffusivity"); + } else if ( compositionModel == "solvent"){ + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "solvent interactions not implemented"); + } else if ( compositionModel == "moleFractions"){ + trParam.model_speciesDiffusivity = LTR_MIXMODEL_MOLEFRACS; + } else if ( compositionModel == "massFractions"){ + trParam.model_speciesDiffusivity = LTR_MIXMODEL_MASSFRACS; + } else if ( compositionModel == "logMoleFractions"){ + trParam.model_speciesDiffusivity = LTR_MIXMODEL_LOG_MOLEFRACS; + } else if ( compositionModel == "pairwiseInteractionEnergy"){ + trParam.model_speciesDiffusivity = LTR_MIXMODEL_PAIRWISE_INTERACTION; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_PAIRWISE_INTERACTION interactions not implemented for speciesDiffusivity"); + } + int num = compositionNode.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = compositionNode.child(iChild); + std::string nodeName = lowercase( xmlChild.name() ); + if ( nodeName != "interaction" ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "expected element and got " + nodeName ); + getString( xmlChild, "speciesA", speciesA, type ); + getString( xmlChild, "speciesB", speciesB, type ); + int iSpecies = trParam.thermo->speciesIndex( speciesA ); + if ( iSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesA ); + int jSpecies = trParam.thermo->speciesIndex( speciesB ); + if ( jSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesB ); + trParam.diff_Dij(iSpecies,jSpecies) = getFloat( xmlChild, "Dij", "toSI" ); + trParam.diff_Dij(jSpecies,iSpecies) = trParam.diff_Dij(iSpecies,jSpecies) ; + } + } + } + + /* + * Hydrodynamic radius + */ + if ( transportNode.hasChild("hydrodynamicRadius")) { + XML_Node& radiusNode = transportNode.child("hydrodynamicRadius"); + if ( radiusNode.hasChild("compositionDependence") ) { + XML_Node& compositionNode = radiusNode.child("compositionDependence"); + std::string compositionModel = compositionNode.attrib("model"); + if ( compositionModel == "" ) { + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "transport::hydrodynamicRadius XML node doesn't have a model string"); + } else if ( compositionModel == "none"){ + trParam.model_thermalCond = LTR_MIXMODEL_NONE; + } else if ( compositionModel == "solvent"){ + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "solvent interactions not implemented"); + } else if ( compositionModel == "moleFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_MOLEFRACS; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_MOLEFRACS interactions not implemented for hydrodynamicRadius"); + } else if ( compositionModel == "massFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_MASSFRACS; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_MASSFRACS interactions not implemented for hydrodynamicRadius"); + } else if ( compositionModel == "logMoleFractions"){ + trParam.model_thermalCond = LTR_MIXMODEL_LOG_MOLEFRACS; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_LOG_MOLEFRACS interactions not implemented for hydrodynamicRadius"); + } else if ( compositionModel == "pairwiseInteractionEnergy"){ + trParam.model_thermalCond = LTR_MIXMODEL_PAIRWISE_INTERACTION; + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "LTR_MIXMODEL_PAIRWISE_INTERACTION interactions not implemented for hydrodynamicRadius"); + } + int num = compositionNode.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = compositionNode.child(iChild); + std::string nodeName = lowercase( xmlChild.name() ); + if ( nodeName != "interaction" ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "expected element and got <" + nodeName + ">" ); + getString( xmlChild, "speciesA", speciesA, type ); + getString( xmlChild, "speciesB", speciesB, type ); + int iSpecies = trParam.thermo->speciesIndex( speciesA ); + if ( iSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesA ); + int jSpecies = trParam.thermo->speciesIndex( speciesB ); + if ( jSpecies < 0 ) + throw CanteraError("LiquidTransport::getLiquidInteractionsTransportData", + "Unknown species " + speciesB ); + trParam.radius_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); + trParam.radius_Aij(jSpecies,iSpecies) = trParam.radius_Aij(iSpecies,jSpecies) ; + } + } + } + + } /********************************************************* From 0d6d5642b17eaa8d192d5c450532979c3ec51486 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Nov 2009 22:55:34 +0000 Subject: [PATCH 025/446] Added keywords property --- Cantera/src/thermo/MargulesVPSSTP.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index e69bda3a3..fdbfa8434 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -17,7 +17,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: MargulesVPSSTP.h,v 1.1 2009/03/03 21:08:31 hkmoffa Exp $ + * $Id$ */ #ifndef CT_MARGULESVPSSTP_H From 35e4c9ea453f5c2e8ba5850cb2ef975c9e2ff4f8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Nov 2009 23:36:49 +0000 Subject: [PATCH 026/446] Turned on Keyword substition in all files. --- Cantera/Makefile.in | 6 +++--- Cantera/clib/src/Cabinet.h | 2 +- Cantera/clib/src/Makefile.in | 6 +++--- Cantera/clib/src/Storage.cpp | 2 +- Cantera/clib/src/Storage.h | 2 +- Cantera/clib/src/clib_defs.h | 2 +- Cantera/clib/src/ct.cpp | 2 +- Cantera/clib/src/ct.h | 2 +- Cantera/clib/src/ctbdry.cpp | 2 +- Cantera/clib/src/ctbdry.h | 2 +- Cantera/clib/src/ctfunc.cpp | 2 +- Cantera/clib/src/ctfunc.h | 2 +- Cantera/clib/src/ctmultiphase.cpp | 2 +- Cantera/clib/src/ctmultiphase.h | 2 +- Cantera/clib/src/ctnum.h | 2 +- Cantera/clib/src/ctonedim.cpp | 2 +- Cantera/clib/src/ctonedim.h | 2 +- Cantera/clib/src/ctreactor.cpp | 2 +- Cantera/clib/src/ctreactor.h | 2 +- Cantera/clib/src/ctrpath.cpp | 2 +- Cantera/clib/src/ctrpath.h | 2 +- Cantera/clib/src/ctstagn.h | 2 +- Cantera/clib/src/ctsurf.cpp | 2 +- Cantera/clib/src/ctsurf.h | 2 +- Cantera/clib/src/ctxml.cpp | 2 +- Cantera/clib/src/ctxml.h | 2 +- Cantera/cxx/Makefile.in | 6 +++--- Cantera/cxx/demos/kinetics1/kinetics1.cpp | 6 +++--- Cantera/cxx/include/Cantera.h | 4 ++-- Cantera/cxx/include/Cantera.mak.in | 2 +- Cantera/cxx/include/Cantera_bt.mak.in | 2 +- Cantera/cxx/include/GRI30.h | 2 +- Cantera/cxx/include/Interface.h | 2 +- Cantera/cxx/include/PureFluid.h | 2 +- Cantera/cxx/include/equilibrium.h | 2 +- Cantera/cxx/include/kinetics.h | 2 +- Cantera/cxx/include/zerodim.h | 2 +- Cantera/cxx/src/Makefile.in | 6 +++--- Cantera/fortran/src/Makefile.in | 6 +++--- Cantera/fortran/src/fct.cpp | 2 +- Cantera/fortran/src/fctxml.cpp | 4 ++-- Cantera/matlab/Makefile.in | 6 +++--- Cantera/matlab/cantera/Contents.m | 2 +- Cantera/matlab/cantera/private/ctfunctions.cpp | 2 +- Cantera/matlab/cantera/private/mixturemethods.cpp | 2 +- Cantera/matlab/cantera/private/mllogger.h | 2 +- Cantera/matlab/cantera/private/phasemethods.cpp | 2 +- Cantera/matlab/cantera/private/reactormethods.cpp | 2 +- Cantera/matlab/cantera/private/reactornetmethods.cpp | 2 +- Cantera/matlab/cantera/private/thermomethods.cpp | 2 +- Cantera/matlab/cantera/private/wallmethods.cpp | 2 +- Cantera/matlab/cantera/private/xmlmethods.cpp | 2 +- Cantera/matlab/setup_winmatlab.py | 2 +- Cantera/python/Cantera/Edge.py | 2 +- Cantera/python/Cantera/Interface.py | 2 +- Cantera/python/Cantera/Phase.py | 2 +- Cantera/python/Cantera/importFromFile.py | 2 +- Cantera/python/Makefile.in | 6 +++--- Cantera/python/ctml_writer.py | 2 +- Cantera/python/src/Makefile.in | 6 +++--- Cantera/python/src/ctkinetics_methods.cpp | 2 +- Cantera/python/src/ctonedim_methods.cpp | 2 +- Cantera/src/Makefile.in | 6 +++--- Cantera/src/base/Array.h | 6 +++--- Cantera/src/base/LogPrintCtrl.cpp | 6 +++--- Cantera/src/base/LogPrintCtrl.h | 4 ++-- Cantera/src/base/Makefile.in | 6 +++--- Cantera/src/base/PrintCtrl.cpp | 6 +++--- Cantera/src/base/PrintCtrl.h | 4 ++-- Cantera/src/base/checkFinite.cpp | 4 ++-- Cantera/src/base/clockWC.cpp | 6 +++--- Cantera/src/base/clockWC.h | 6 +++--- Cantera/src/base/ct2ctml.cpp | 4 ++-- Cantera/src/base/ct_defs.h | 4 ++-- Cantera/src/base/ctexceptions.h | 4 ++-- Cantera/src/base/ctml.cpp | 4 ++-- Cantera/src/base/ctml.h | 4 ++-- Cantera/src/base/global.h | 4 ++-- Cantera/src/base/logger.h | 2 +- Cantera/src/base/mdp_allo.cpp | 4 ++-- Cantera/src/base/mdp_allo.h | 4 ++-- Cantera/src/base/misc.cpp | 2 +- Cantera/src/base/plots.cpp | 4 ++-- Cantera/src/base/plots.h | 4 ++-- Cantera/src/base/stringUtils.cpp | 2 +- Cantera/src/base/stringUtils.h | 4 ++-- Cantera/src/base/units.h | 2 +- Cantera/src/base/utilities.h | 2 +- Cantera/src/base/vec_functions.h | 4 ++-- Cantera/src/base/xml.cpp | 4 ++-- Cantera/src/base/xml.h | 4 ++-- Cantera/src/converters/CKParser.cpp | 2 +- Cantera/src/converters/Makefile.in | 6 +++--- Cantera/src/converters/NASA9Parser.cpp | 2 +- Cantera/src/converters/Species.h | 2 +- Cantera/src/converters/ck2ct.cpp | 2 +- Cantera/src/equil/BasisOptimize.cpp | 2 +- Cantera/src/equil/ChemEquil.cpp | 2 +- Cantera/src/equil/ChemEquil.h | 6 +++--- Cantera/src/equil/Makefile.in | 6 +++--- Cantera/src/equil/MultiPhase.cpp | 4 ++-- Cantera/src/equil/MultiPhase.h | 4 ++-- Cantera/src/equil/MultiPhaseEquil.cpp | 2 +- Cantera/src/equil/PropertyCalculator.h | 6 +++--- Cantera/src/equil/equil.h | 6 +++--- Cantera/src/equil/equilibrate.cpp | 2 +- Cantera/src/equil/vcs_DoubleStarStar.cpp | 6 +++--- Cantera/src/equil/vcs_DoubleStarStar.h | 6 +++--- Cantera/src/equil/vcs_Exception.h | 2 +- Cantera/src/equil/vcs_Gibbs.cpp | 2 +- Cantera/src/equil/vcs_IntStarStar.cpp | 6 +++--- Cantera/src/equil/vcs_IntStarStar.h | 6 +++--- Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 2 +- Cantera/src/equil/vcs_MultiPhaseEquil.h | 6 +++--- Cantera/src/equil/vcs_SpeciesProperties.h | 2 +- Cantera/src/equil/vcs_TP.cpp | 6 +++--- Cantera/src/equil/vcs_VolPhase.cpp | 2 +- Cantera/src/equil/vcs_VolPhase.h | 2 +- Cantera/src/equil/vcs_defs.h | 2 +- Cantera/src/equil/vcs_elem.cpp | 2 +- Cantera/src/equil/vcs_elem_rearrange.cpp | 6 +++--- Cantera/src/equil/vcs_equilibrate.cpp | 2 +- Cantera/src/equil/vcs_inest.cpp | 6 +++--- Cantera/src/equil/vcs_internal.h | 2 +- Cantera/src/equil/vcs_linmaxc.cpp | 6 +++--- Cantera/src/equil/vcs_nondim.cpp | 2 +- Cantera/src/equil/vcs_phaseStability.cpp | 4 ++-- Cantera/src/equil/vcs_prep.cpp | 6 +++--- Cantera/src/equil/vcs_prob.cpp | 2 +- Cantera/src/equil/vcs_prob.h | 2 +- Cantera/src/equil/vcs_rearrange.cpp | 2 +- Cantera/src/equil/vcs_report.cpp | 2 +- Cantera/src/equil/vcs_root1d.cpp | 2 +- Cantera/src/equil/vcs_rxnadj.cpp | 2 +- Cantera/src/equil/vcs_setMolesLinProg.cpp | 2 +- Cantera/src/equil/vcs_solve.cpp | 2 +- Cantera/src/equil/vcs_solve.h | 2 +- Cantera/src/equil/vcs_solve_TP.cpp | 2 +- Cantera/src/equil/vcs_species_thermo.cpp | 2 +- Cantera/src/equil/vcs_species_thermo.h | 2 +- Cantera/src/equil/vcs_util.cpp | 2 +- Cantera/src/equil/vcs_xerror.c | 6 +++--- Cantera/src/kinetics/AqueousKinetics.cpp | 4 ++-- Cantera/src/kinetics/AqueousKinetics.h | 6 +++--- Cantera/src/kinetics/EdgeKinetics.h | 6 +++--- Cantera/src/kinetics/Enhanced3BConc.h | 6 +++--- Cantera/src/kinetics/FalloffFactory.cpp | 6 +++--- Cantera/src/kinetics/FalloffFactory.h | 4 ++-- Cantera/src/kinetics/FalloffMgr.h | 6 +++--- Cantera/src/kinetics/GasKinetics.h | 6 +++--- Cantera/src/kinetics/GasKineticsWriter.h | 6 +++--- Cantera/src/kinetics/Group.cpp | 6 +++--- Cantera/src/kinetics/Group.h | 6 +++--- Cantera/src/kinetics/ImplicitChem.cpp | 6 +++--- Cantera/src/kinetics/ImplicitChem.h | 6 +++--- Cantera/src/kinetics/ImplicitSurfChem.cpp | 6 +++--- Cantera/src/kinetics/ImplicitSurfChem.h | 6 +++--- Cantera/src/kinetics/InterfaceKinetics.h | 6 +++--- Cantera/src/kinetics/Kinetics.cpp | 4 ++-- Cantera/src/kinetics/Kinetics.h | 4 ++-- Cantera/src/kinetics/KineticsFactory.cpp | 6 +++--- Cantera/src/kinetics/KineticsFactory.h | 6 +++--- Cantera/src/kinetics/Makefile.in | 6 +++--- Cantera/src/kinetics/RateCoeffMgr.h | 6 +++--- Cantera/src/kinetics/ReactionData.h | 6 +++--- Cantera/src/kinetics/ReactionPath.cpp | 6 +++--- Cantera/src/kinetics/ReactionPath.h | 6 +++--- Cantera/src/kinetics/ReactionStoichMgr.cpp | 6 +++--- Cantera/src/kinetics/ReactionStoichMgr.h | 6 +++--- Cantera/src/kinetics/RxnRates.h | 6 +++--- Cantera/src/kinetics/StoichManager.h | 6 +++--- Cantera/src/kinetics/ThirdBodyMgr.h | 6 +++--- Cantera/src/kinetics/importKinetics.cpp | 6 +++--- Cantera/src/kinetics/importKinetics.h | 6 +++--- Cantera/src/kinetics/reaction_defs.h | 6 +++--- Cantera/src/kinetics/solveSP.cpp | 2 +- Cantera/src/kinetics/solveSP.h | 2 +- Cantera/src/numerics/ArrayViewer.h | 6 +++--- Cantera/src/numerics/BandMatrix.h | 6 +++--- Cantera/src/numerics/CVodeInt.cpp | 2 +- Cantera/src/numerics/CVodeInt.h | 6 +++--- Cantera/src/numerics/CVodesIntegrator.h | 4 ++-- Cantera/src/numerics/DAE_Solver.h | 4 ++-- Cantera/src/numerics/DASPK.cpp | 4 ++-- Cantera/src/numerics/DASPK.h | 4 ++-- Cantera/src/numerics/DenseMatrix.h | 6 +++--- Cantera/src/numerics/Func1.h | 6 +++--- Cantera/src/numerics/IDA_Solver.h | 6 +++--- Cantera/src/numerics/Integrator.h | 6 +++--- Cantera/src/numerics/Makefile.in | 6 +++--- Cantera/src/numerics/NonlinearSolver.cpp | 4 ++-- Cantera/src/numerics/NonlinearSolver.h | 4 ++-- Cantera/src/numerics/ResidEval.h | 4 ++-- Cantera/src/numerics/ResidJacEval.cpp | 4 ++-- Cantera/src/numerics/ResidJacEval.h | 4 ++-- Cantera/src/numerics/SquareMatrix.cpp | 4 ++-- Cantera/src/numerics/SquareMatrix.h | 4 ++-- Cantera/src/numerics/ctlapack.h | 6 +++--- Cantera/src/numerics/funcs.cpp | 6 +++--- Cantera/src/numerics/funcs.h | 6 +++--- Cantera/src/numerics/polyfit.h | 6 +++--- Cantera/src/numerics/sort.cpp | 2 +- Cantera/src/numerics/sort.h | 2 +- Cantera/src/oneD/Domain1D.h | 6 +++--- Cantera/src/oneD/Inlet1D.h | 6 +++--- Cantera/src/oneD/Makefile.in | 6 +++--- Cantera/src/oneD/MultiJac.cpp | 6 +++--- Cantera/src/oneD/MultiJac.h | 6 +++--- Cantera/src/oneD/MultiNewton.cpp | 6 +++--- Cantera/src/oneD/MultiNewton.h | 6 +++--- Cantera/src/oneD/Resid1D.h | 6 +++--- Cantera/src/oneD/Solid1D.cpp | 6 +++--- Cantera/src/oneD/Solid1D.h | 6 +++--- Cantera/src/oneD/StFlow.cpp | 6 +++--- Cantera/src/oneD/StFlow.h | 6 +++--- Cantera/src/oneD/boundaries1D.cpp | 6 +++--- Cantera/src/spectra/Makefile.in | 6 +++--- Cantera/src/thermo/AdsorbateThermo.h | 6 +++--- Cantera/src/thermo/ConstCpPoly.cpp | 6 +++--- Cantera/src/thermo/ConstCpPoly.h | 6 +++--- Cantera/src/thermo/ConstDensityThermo.cpp | 2 +- Cantera/src/thermo/ConstDensityThermo.h | 6 +++--- Cantera/src/thermo/Constituents.cpp | 4 ++-- Cantera/src/thermo/Constituents.h | 4 ++-- Cantera/src/thermo/Crystal.h | 6 +++--- Cantera/src/thermo/DebyeHuckel.cpp | 2 +- Cantera/src/thermo/DebyeHuckel.h | 2 +- Cantera/src/thermo/EdgePhase.h | 6 +++--- Cantera/src/thermo/Elements.cpp | 6 +++--- Cantera/src/thermo/Elements.h | 6 +++--- Cantera/src/thermo/GeneralSpeciesThermo.cpp | 2 +- Cantera/src/thermo/GeneralSpeciesThermo.h | 6 +++--- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 4 ++-- Cantera/src/thermo/GibbsExcessVPSSTP.h | 2 +- Cantera/src/thermo/HMWSoln.cpp | 2 +- Cantera/src/thermo/HMWSoln.h | 2 +- Cantera/src/thermo/HMWSoln_input.cpp | 2 +- Cantera/src/thermo/IdealGasPhase.cpp | 2 +- Cantera/src/thermo/IdealGasPhase.h | 6 +++--- Cantera/src/thermo/IdealMolalSoln.cpp | 4 ++-- Cantera/src/thermo/IdealMolalSoln.h | 6 +++--- Cantera/src/thermo/IdealSolidSolnPhase.cpp | 2 +- Cantera/src/thermo/IdealSolidSolnPhase.h | 6 +++--- Cantera/src/thermo/IdealSolnGasVPSS.cpp | 6 +++--- Cantera/src/thermo/IdealSolnGasVPSS.h | 6 +++--- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 4 ++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 2 +- Cantera/src/thermo/LatticePhase.cpp | 2 +- Cantera/src/thermo/LatticePhase.h | 6 +++--- Cantera/src/thermo/LatticeSolidPhase.cpp | 2 +- Cantera/src/thermo/LatticeSolidPhase.h | 6 +++--- Cantera/src/thermo/Makefile.in | 6 +++--- Cantera/src/thermo/MargulesVPSSTP.cpp | 4 ++-- Cantera/src/thermo/MetalPhase.h | 6 +++--- Cantera/src/thermo/MineralEQ3.cpp | 2 +- Cantera/src/thermo/MineralEQ3.h | 4 ++-- Cantera/src/thermo/MolalityVPSSTP.cpp | 6 +++--- Cantera/src/thermo/MolalityVPSSTP.h | 2 +- Cantera/src/thermo/Mu0Poly.cpp | 6 +++--- Cantera/src/thermo/Mu0Poly.h | 6 +++--- Cantera/src/thermo/Nasa9Poly1.cpp | 6 +++--- Cantera/src/thermo/Nasa9Poly1.h | 4 ++-- Cantera/src/thermo/Nasa9PolyMultiTempRegion.cpp | 6 +++--- Cantera/src/thermo/Nasa9PolyMultiTempRegion.h | 6 +++--- Cantera/src/thermo/NasaPoly1.h | 6 +++--- Cantera/src/thermo/NasaPoly2.h | 6 +++--- Cantera/src/thermo/NasaThermo.h | 4 ++-- Cantera/src/thermo/PDSS.cpp | 2 +- Cantera/src/thermo/PDSS.h | 2 +- Cantera/src/thermo/PDSSFactory.cpp | 2 +- Cantera/src/thermo/PDSS_ConstVol.cpp | 2 +- Cantera/src/thermo/PDSS_ConstVol.h | 2 +- Cantera/src/thermo/PDSS_HKFT.cpp | 2 +- Cantera/src/thermo/PDSS_HKFT.h | 4 ++-- Cantera/src/thermo/PDSS_IdealGas.cpp | 2 +- Cantera/src/thermo/PDSS_IdealGas.h | 2 +- Cantera/src/thermo/PDSS_IonsFromNeutral.cpp | 2 +- Cantera/src/thermo/PDSS_IonsFromNeutral.h | 2 +- Cantera/src/thermo/PDSS_SSVol.cpp | 2 +- Cantera/src/thermo/PDSS_SSVol.h | 2 +- Cantera/src/thermo/PDSS_Water.cpp | 2 +- Cantera/src/thermo/PDSS_Water.h | 6 +++--- Cantera/src/thermo/Phase.h | 6 +++--- Cantera/src/thermo/PseudoBinaryVPSSTP.cpp | 4 ++-- Cantera/src/thermo/PseudoBinaryVPSSTP.h | 2 +- Cantera/src/thermo/PureFluidPhase.cpp | 2 +- Cantera/src/thermo/PureFluidPhase.h | 6 +++--- Cantera/src/thermo/SemiconductorPhase.h | 6 +++--- Cantera/src/thermo/ShomatePoly.h | 6 +++--- Cantera/src/thermo/ShomateThermo.h | 2 +- Cantera/src/thermo/SimpleThermo.h | 2 +- Cantera/src/thermo/SingleSpeciesTP.cpp | 6 +++--- Cantera/src/thermo/SingleSpeciesTP.h | 6 +++--- Cantera/src/thermo/SpeciesThermo.h | 6 +++--- Cantera/src/thermo/SpeciesThermoFactory.cpp | 4 ++-- Cantera/src/thermo/SpeciesThermoFactory.h | 4 ++-- Cantera/src/thermo/SpeciesThermoInterpType.cpp | 6 +++--- Cantera/src/thermo/SpeciesThermoInterpType.h | 6 +++--- Cantera/src/thermo/SpeciesThermoMgr.h | 6 +++--- Cantera/src/thermo/State.cpp | 4 ++-- Cantera/src/thermo/State.h | 4 ++-- Cantera/src/thermo/StoichSubstance.cpp | 4 ++-- Cantera/src/thermo/StoichSubstance.h | 4 ++-- Cantera/src/thermo/StoichSubstanceSSTP.cpp | 2 +- Cantera/src/thermo/StoichSubstanceSSTP.h | 4 ++-- Cantera/src/thermo/SurfPhase.cpp | 4 ++-- Cantera/src/thermo/SurfPhase.h | 4 ++-- Cantera/src/thermo/ThermoFactory.cpp | 4 ++-- Cantera/src/thermo/ThermoFactory.h | 6 +++--- Cantera/src/thermo/ThermoPhase.cpp | 6 +++--- Cantera/src/thermo/ThermoPhase.h | 4 ++-- Cantera/src/thermo/VPSSMgr.cpp | 6 +++--- Cantera/src/thermo/VPSSMgr.h | 6 +++--- Cantera/src/thermo/VPSSMgrFactory.cpp | 2 +- Cantera/src/thermo/VPSSMgrFactory.h | 4 ++-- Cantera/src/thermo/VPSSMgr_ConstVol.cpp | 6 +++--- Cantera/src/thermo/VPSSMgr_ConstVol.h | 6 +++--- Cantera/src/thermo/VPSSMgr_General.cpp | 6 +++--- Cantera/src/thermo/VPSSMgr_General.h | 4 ++-- Cantera/src/thermo/VPSSMgr_IdealGas.cpp | 6 +++--- Cantera/src/thermo/VPSSMgr_IdealGas.h | 6 +++--- Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp | 4 ++-- Cantera/src/thermo/VPSSMgr_Water_ConstVol.h | 4 ++-- Cantera/src/thermo/VPSSMgr_Water_HKFT.cpp | 4 ++-- Cantera/src/thermo/VPSSMgr_Water_HKFT.h | 4 ++-- Cantera/src/thermo/VPSSMgr_types.h | 6 +++--- Cantera/src/thermo/VPStandardStateTP.cpp | 6 +++--- Cantera/src/thermo/VPStandardStateTP.h | 4 ++-- Cantera/src/thermo/WaterProps.cpp | 2 +- Cantera/src/thermo/WaterProps.h | 2 +- Cantera/src/thermo/WaterPropsIAPWS.cpp | 2 +- Cantera/src/thermo/WaterPropsIAPWS.h | 2 +- Cantera/src/thermo/WaterPropsIAPWSphi.cpp | 2 +- Cantera/src/thermo/WaterPropsIAPWSphi.h | 2 +- Cantera/src/thermo/WaterSSTP.cpp | 2 +- Cantera/src/thermo/WaterSSTP.h | 2 +- Cantera/src/thermo/electrolytes.h | 2 +- Cantera/src/thermo/phasereport.cpp | 4 ++-- Cantera/src/thermo/speciesThermoTypes.h | 6 +++--- Cantera/src/transport/AqueousTransport.cpp | 4 ++-- Cantera/src/transport/AqueousTransport.h | 4 ++-- Cantera/src/transport/DustyGasTransport.cpp | 6 +++--- Cantera/src/transport/LiquidTransport.cpp | 4 ++-- Cantera/src/transport/LiquidTransport.h | 4 ++-- Cantera/src/transport/LiquidTransportData.h | 6 +++--- Cantera/src/transport/MMCollisionInt.cpp | 6 +++--- Cantera/src/transport/MMCollisionInt.h | 6 +++--- Cantera/src/transport/Makefile.in | 4 ++-- Cantera/src/transport/MixTransport.cpp | 6 +++--- Cantera/src/transport/MixTransport.h | 6 +++--- Cantera/src/transport/MultiTransport.cpp | 6 +++--- Cantera/src/transport/SimpleTransport.cpp | 4 ++-- Cantera/src/transport/SimpleTransport.h | 4 ++-- Cantera/src/transport/SolidTransport.cpp | 6 +++--- Cantera/src/transport/SolidTransport.h | 6 +++--- Cantera/src/transport/TransportBase.cpp | 4 ++-- Cantera/src/transport/TransportBase.h | 4 ++-- Cantera/src/transport/TransportFactory.h | 6 +++--- Cantera/src/transport/WaterTransport.h | 4 ++-- Cantera/src/zeroD/ConstPressureReactor.h | 6 +++--- Cantera/src/zeroD/FlowDevice.h | 6 +++--- Cantera/src/zeroD/FlowReactor.h | 6 +++--- Cantera/src/zeroD/Makefile.in | 6 +++--- Cantera/src/zeroD/PID_Controller.h | 6 +++--- Cantera/src/zeroD/Reactor.h | 6 +++--- Cantera/src/zeroD/ReactorBase.cpp | 6 +++--- Cantera/src/zeroD/ReactorBase.h | 6 +++--- Cantera/src/zeroD/ReactorFactory.cpp | 6 +++--- Cantera/src/zeroD/ReactorFactory.h | 6 +++--- Cantera/src/zeroD/ReactorNet.h | 6 +++--- Cantera/src/zeroD/Reservoir.h | 6 +++--- Cantera/src/zeroD/Wall.h | 6 +++--- Cantera/src/zeroD/flowControllers.h | 6 +++--- Cantera/user/Makefile.in | 6 +++--- Makefile.in | 2 +- apps/bvp/stagnation.cpp | 6 +++--- data/transport/misc_tran.dat | 6 +++--- examples/cxx/equil_example1.cpp | 6 +++--- examples/cxx/kinetics_example1.cpp | 6 +++--- examples/cxx/kinetics_example2.cpp | 6 +++--- examples/cxx/kinetics_example3.cpp | 6 +++--- examples/cxx/rxnpath_example1.cpp | 6 +++--- examples/cxx/transport_example1.cpp | 6 +++--- examples/cxx/transport_example2.cpp | 6 +++--- ext/Makefile.in | 6 +++--- ext/blas/Makefile.in | 2 +- ext/cvode/Makefile.in | 6 +++--- ext/f2c_blas/Makefile.in | 4 ++-- ext/f2c_lapack/Makefile.in | 6 +++--- ext/f2c_libs/Makefile.in | 6 +++--- ext/f2c_math/Makefile.in | 6 +++--- ext/f2c_recipes/Makefile.in | 6 +++--- ext/lapack/Makefile.in | 2 +- ext/math/Makefile.in | 6 +++--- ext/recipes/Makefile.in | 2 +- ext/tpx/Makefile.in | 2 +- test_problems/ChemEquil_gri_matrix/gri_matrix.cpp | 6 +++--- test_problems/ChemEquil_gri_pairs/gri_pairs.cpp | 6 +++--- test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp | 6 +++--- test_problems/ChemEquil_red1/basopt_red1.cpp | 6 +++--- test_problems/CpJump/CpJump.cpp | 6 +++--- test_problems/Makefile.in | 6 +++--- test_problems/VCSnonideal/Makefile.in | 6 +++--- test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml | 2 +- test_problems/VCSnonideal/NaCl_equil/nacl_equil.cpp | 6 +++--- test_problems/VPsilane_test/silane_equil.cpp | 6 +++--- test_problems/cathermo/DH_graph_1/DH_graph_1.cpp | 6 +++--- test_problems/cathermo/DH_graph_NM/DH_graph_1.cpp | 6 +++--- test_problems/cathermo/DH_graph_Pitzer/DH_graph_1.cpp | 6 +++--- test_problems/cathermo/DH_graph_acommon/DH_graph_1.cpp | 6 +++--- test_problems/cathermo/DH_graph_bdotak/DH_graph_1.cpp | 6 +++--- .../cathermo/HMW_dupl_test/HMW_NaCl_sp1977_alt.xml | 2 +- test_problems/cathermo/HMW_dupl_test/HMW_dupl_test.cpp | 6 +++--- test_problems/cathermo/HMW_dupl_test/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_dupl_test/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_dupl_test/sortAlgorithms.h | 6 +++--- .../cathermo/HMW_graph_CpvT/HMW_NaCl_sp1977_alt.xml | 2 +- test_problems/cathermo/HMW_graph_CpvT/HMW_graph_CpvT.cpp | 6 +++--- test_problems/cathermo/HMW_graph_CpvT/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_graph_CpvT/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_graph_CpvT/sortAlgorithms.h | 6 +++--- test_problems/cathermo/HMW_graph_GvI/HMW_NaCl.xml | 2 +- test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp | 6 +++--- test_problems/cathermo/HMW_graph_GvI/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_graph_GvI/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_graph_GvI/sortAlgorithms.h | 6 +++--- .../cathermo/HMW_graph_GvT/HMW_NaCl_sp1977_alt.xml | 2 +- test_problems/cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp | 6 +++--- test_problems/cathermo/HMW_graph_GvT/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_graph_GvT/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_graph_GvT/sortAlgorithms.h | 6 +++--- .../cathermo/HMW_graph_HvT/HMW_NaCl_sp1977_alt.xml | 2 +- test_problems/cathermo/HMW_graph_HvT/HMW_graph_HvT.cpp | 6 +++--- test_problems/cathermo/HMW_graph_HvT/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_graph_HvT/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_graph_HvT/sortAlgorithms.h | 6 +++--- .../cathermo/HMW_graph_VvT/HMW_NaCl_sp1977_alt.xml | 2 +- test_problems/cathermo/HMW_graph_VvT/HMW_graph_VvT.cpp | 6 +++--- test_problems/cathermo/HMW_graph_VvT/TemperatureTable.h | 2 +- test_problems/cathermo/HMW_graph_VvT/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/HMW_graph_VvT/sortAlgorithms.h | 6 +++--- test_problems/cathermo/HMW_test_1/HMW_test_1.cpp | 6 +++--- test_problems/cathermo/HMW_test_3/HMW_test_3.cpp | 6 +++--- test_problems/cathermo/Makefile.in | 6 +++--- test_problems/cathermo/VPissp/ISSPTester.cpp | 2 +- test_problems/cathermo/ims/IMSTester.cpp | 2 +- test_problems/cathermo/issp/ISSPTester.cpp | 2 +- test_problems/cathermo/stoichSubSSTP/TemperatureTable.h | 2 +- test_problems/cathermo/stoichSubSSTP/sortAlgorithms.cpp | 6 +++--- test_problems/cathermo/stoichSubSSTP/sortAlgorithms.h | 6 +++--- test_problems/cathermo/stoichSubSSTP/stoichSubSSTP.cpp | 6 +++--- test_problems/cathermo/testIAPWS/testIAPWSphi.cpp | 2 +- test_problems/cathermo/testWaterPDSS/testWaterPDSS.cpp | 2 +- test_problems/cathermo/testWaterTP/testWaterSSTP.cpp | 2 +- test_problems/cathermo/wtWater/wtWater.cpp | 2 +- test_problems/ck2cti_test/Makefile.in | 6 +++--- test_problems/ck2cti_test/runtest.in | 2 +- test_problems/cxx_ex/Makefile.in | 6 +++--- test_problems/cxx_ex/runtest | 2 +- test_problems/min_python/Makefile.in | 6 +++--- test_problems/min_python/negATest/negATest.cpp | 6 +++--- test_problems/nasa9_reader/Makefile.in | 6 +++--- test_problems/nasa9_reader/runtest.in | 2 +- test_problems/negATest/negATest.cpp | 6 +++--- test_problems/printUtilUnitTest/pUtest.cpp | 2 +- test_problems/pureFluidTest/testPureWater.cpp | 2 +- test_problems/silane_equil/silane_equil.cpp | 6 +++--- test_problems/surfkin/surfdemo.cpp | 2 +- tools/Makefile.in | 6 +++--- tools/bin/cvs2cl.pl | 8 ++++---- tools/doc/Makefile.in | 6 +++--- tools/src/ck2cti.cpp | 2 +- tools/testtools/csvdiff.cpp | 8 ++++---- tools/testtools/mdp_allo.cpp | 6 +++--- tools/testtools/mdp_allo.h | 6 +++--- tools/testtools/tok_input_util.cpp | 8 ++++---- tools/testtools/tok_input_util.h | 8 ++++---- win32/vc7/Sundials/sundials/sundials_config.h | 4 ++-- win32/vc9/Sundials/SUNDIALS_SHARED/sundials_config.h | 4 ++-- 479 files changed, 1023 insertions(+), 1023 deletions(-) diff --git a/Cantera/Makefile.in b/Cantera/Makefile.in index 1d0500e66..8af85d494 100755 --- a/Cantera/Makefile.in +++ b/Cantera/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2007/05/06 17:16:43 $ -# $Revision: 1.8 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # See file License.txt for licensing information diff --git a/Cantera/clib/src/Cabinet.h b/Cantera/clib/src/Cabinet.h index 02ef05032..0369cbf72 100755 --- a/Cantera/clib/src/Cabinet.h +++ b/Cantera/clib/src/Cabinet.h @@ -2,7 +2,7 @@ * @file Cabinet.h */ /* - * $Id: Cabinet.h,v 1.9 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/Makefile.in b/Cantera/clib/src/Makefile.in index af4229a15..d42de7845 100755 --- a/Cantera/clib/src/Makefile.in +++ b/Cantera/clib/src/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.19 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # diff --git a/Cantera/clib/src/Storage.cpp b/Cantera/clib/src/Storage.cpp index d5462bccb..fea7dc4ad 100755 --- a/Cantera/clib/src/Storage.cpp +++ b/Cantera/clib/src/Storage.cpp @@ -2,7 +2,7 @@ * @file Storage.cpp */ /* - * $Id: Storage.cpp,v 1.6 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/Storage.h b/Cantera/clib/src/Storage.h index 62db86fd5..159570e84 100755 --- a/Cantera/clib/src/Storage.h +++ b/Cantera/clib/src/Storage.h @@ -2,7 +2,7 @@ * @file Storage.h */ /* - * $Id: Storage.h,v 1.4 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_STORAGE_H diff --git a/Cantera/clib/src/clib_defs.h b/Cantera/clib/src/clib_defs.h index ba18a4811..f3fa601f7 100755 --- a/Cantera/clib/src/clib_defs.h +++ b/Cantera/clib/src/clib_defs.h @@ -2,7 +2,7 @@ * @file clib_defs.h */ /* - * $Id: clib_defs.h,v 1.5 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/ct.cpp b/Cantera/clib/src/ct.cpp index a0464f2bf..e6c33cbe8 100755 --- a/Cantera/clib/src/ct.cpp +++ b/Cantera/clib/src/ct.cpp @@ -8,7 +8,7 @@ * pointers are passed to or from the calling application. */ -/* $Id: ct.cpp,v 1.45 2009/07/22 01:23:40 hkmoffa Exp $ */ +/* $Id$ */ // turn off warnings under Windows #ifdef WIN32 diff --git a/Cantera/clib/src/ct.h b/Cantera/clib/src/ct.h index 4d91d4b05..8aa59bec3 100755 --- a/Cantera/clib/src/ct.h +++ b/Cantera/clib/src/ct.h @@ -2,7 +2,7 @@ * @file ct.h */ /* - * $Id: ct.h,v 1.24 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_CT_H diff --git a/Cantera/clib/src/ctbdry.cpp b/Cantera/clib/src/ctbdry.cpp index ca15f1c1b..76a4e188b 100755 --- a/Cantera/clib/src/ctbdry.cpp +++ b/Cantera/clib/src/ctbdry.cpp @@ -2,7 +2,7 @@ * @file ctbdry.cpp */ /* - * $Id: ctbdry.cpp,v 1.7 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/ctbdry.h b/Cantera/clib/src/ctbdry.h index be287776a..700901cf3 100755 --- a/Cantera/clib/src/ctbdry.h +++ b/Cantera/clib/src/ctbdry.h @@ -2,7 +2,7 @@ * @file ctbdry.h */ /* - * $Id: ctbdry.h,v 1.4 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_BDRY_H diff --git a/Cantera/clib/src/ctfunc.cpp b/Cantera/clib/src/ctfunc.cpp index 5f5aaede9..8e7fd442a 100755 --- a/Cantera/clib/src/ctfunc.cpp +++ b/Cantera/clib/src/ctfunc.cpp @@ -2,7 +2,7 @@ * @file ctfunc.cpp */ /* - * $Id: ctfunc.cpp,v 1.10 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifdef WIN32 diff --git a/Cantera/clib/src/ctfunc.h b/Cantera/clib/src/ctfunc.h index 0b451ac19..8c60483ac 100755 --- a/Cantera/clib/src/ctfunc.h +++ b/Cantera/clib/src/ctfunc.h @@ -2,7 +2,7 @@ * @file ctfunc.h */ /* - * $Id: ctfunc.h,v 1.4 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_FUNC1_H diff --git a/Cantera/clib/src/ctmultiphase.cpp b/Cantera/clib/src/ctmultiphase.cpp index cf3692b62..e37c1dd5e 100644 --- a/Cantera/clib/src/ctmultiphase.cpp +++ b/Cantera/clib/src/ctmultiphase.cpp @@ -2,7 +2,7 @@ * @file ctmultiphase.cpp */ /* - * $Id: ctmultiphase.cpp,v 1.15 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/ctmultiphase.h b/Cantera/clib/src/ctmultiphase.h index ec3364e46..81c99c623 100644 --- a/Cantera/clib/src/ctmultiphase.h +++ b/Cantera/clib/src/ctmultiphase.h @@ -2,7 +2,7 @@ * @file ctmultiphase.h */ /* - * $Id: ctmultiphase.h,v 1.7 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_MULTIPHASE_H diff --git a/Cantera/clib/src/ctnum.h b/Cantera/clib/src/ctnum.h index 977c67a7b..791a302bf 100755 --- a/Cantera/clib/src/ctnum.h +++ b/Cantera/clib/src/ctnum.h @@ -2,7 +2,7 @@ * @file ctnum.h */ /* - * $Id: ctnum.h,v 1.2 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_CTNUM_H diff --git a/Cantera/clib/src/ctonedim.cpp b/Cantera/clib/src/ctonedim.cpp index b411fb85f..e1da6fa52 100644 --- a/Cantera/clib/src/ctonedim.cpp +++ b/Cantera/clib/src/ctonedim.cpp @@ -2,7 +2,7 @@ * @file ctonedim.cpp */ /* - * $Id: ctonedim.cpp,v 1.25 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ // turn off warnings under Windows diff --git a/Cantera/clib/src/ctonedim.h b/Cantera/clib/src/ctonedim.h index 1fa45c80e..8bf95e442 100644 --- a/Cantera/clib/src/ctonedim.h +++ b/Cantera/clib/src/ctonedim.h @@ -2,7 +2,7 @@ * @file ctonedim.h */ /* - * $Id: ctonedim.h,v 1.16 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_ONEDIM_H diff --git a/Cantera/clib/src/ctreactor.cpp b/Cantera/clib/src/ctreactor.cpp index 05d4976f7..0e8fff638 100755 --- a/Cantera/clib/src/ctreactor.cpp +++ b/Cantera/clib/src/ctreactor.cpp @@ -2,7 +2,7 @@ * @file ctreactor.cpp */ /* - * $Id: ctreactor.cpp,v 1.19 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/ctreactor.h b/Cantera/clib/src/ctreactor.h index a54ce3225..2ab223c07 100755 --- a/Cantera/clib/src/ctreactor.h +++ b/Cantera/clib/src/ctreactor.h @@ -2,7 +2,7 @@ * @file ctreactor.h */ /* - * $Id: ctreactor.h,v 1.7 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_REACTOR_H diff --git a/Cantera/clib/src/ctrpath.cpp b/Cantera/clib/src/ctrpath.cpp index 21cd23559..8de8aa1ef 100755 --- a/Cantera/clib/src/ctrpath.cpp +++ b/Cantera/clib/src/ctrpath.cpp @@ -2,7 +2,7 @@ * @file ctrpath.cpp */ /* - * $Id: ctrpath.cpp,v 1.4 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #define CANTERA_USE_INTERNAL diff --git a/Cantera/clib/src/ctrpath.h b/Cantera/clib/src/ctrpath.h index 5c51ca1e6..c2af32904 100755 --- a/Cantera/clib/src/ctrpath.h +++ b/Cantera/clib/src/ctrpath.h @@ -2,7 +2,7 @@ * @file ctrpath.h */ /* - * $Id: ctrpath.h,v 1.2 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_RXNPATH_H diff --git a/Cantera/clib/src/ctstagn.h b/Cantera/clib/src/ctstagn.h index 156f8732b..4b4b721bf 100755 --- a/Cantera/clib/src/ctstagn.h +++ b/Cantera/clib/src/ctstagn.h @@ -2,7 +2,7 @@ * @file ctstagn.h */ /* - * $Id: ctstagn.h,v 1.2 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_STAGN_H diff --git a/Cantera/clib/src/ctsurf.cpp b/Cantera/clib/src/ctsurf.cpp index 984c700b0..b7a5f9d93 100755 --- a/Cantera/clib/src/ctsurf.cpp +++ b/Cantera/clib/src/ctsurf.cpp @@ -2,7 +2,7 @@ * @file ctsurf.cpp */ /* - * $Id: ctsurf.cpp,v 1.6 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ // turn off warnings under Windows diff --git a/Cantera/clib/src/ctsurf.h b/Cantera/clib/src/ctsurf.h index 19cb35d6f..610422696 100755 --- a/Cantera/clib/src/ctsurf.h +++ b/Cantera/clib/src/ctsurf.h @@ -2,7 +2,7 @@ * @file ctsurf.h */ /* - * $Id: ctsurf.h,v 1.3 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_SURF_H diff --git a/Cantera/clib/src/ctxml.cpp b/Cantera/clib/src/ctxml.cpp index 5d008c9b0..57b237293 100644 --- a/Cantera/clib/src/ctxml.cpp +++ b/Cantera/clib/src/ctxml.cpp @@ -2,7 +2,7 @@ * @file ctxml.cpp */ /* - * $Id: ctxml.cpp,v 1.13 2009/07/22 01:21:35 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/clib/src/ctxml.h b/Cantera/clib/src/ctxml.h index e3b67313d..7629c8465 100644 --- a/Cantera/clib/src/ctxml.h +++ b/Cantera/clib/src/ctxml.h @@ -2,7 +2,7 @@ * @file ctxml.h */ /* - * $Id: ctxml.h,v 1.6 2009/07/11 17:16:09 hkmoffa Exp $ + * $Id$ */ #ifndef CTC_XML_H diff --git a/Cantera/cxx/Makefile.in b/Cantera/cxx/Makefile.in index b142632e9..9bac968f9 100644 --- a/Cantera/cxx/Makefile.in +++ b/Cantera/cxx/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/04/04 03:27:43 $ -# $Revision: 1.14 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # See file License.txt for licensing information diff --git a/Cantera/cxx/demos/kinetics1/kinetics1.cpp b/Cantera/cxx/demos/kinetics1/kinetics1.cpp index e78d95096..b8e440838 100644 --- a/Cantera/cxx/demos/kinetics1/kinetics1.cpp +++ b/Cantera/cxx/demos/kinetics1/kinetics1.cpp @@ -2,9 +2,9 @@ // // zero-dimensional kinetics example program // -// $Author: hkmoffa $ -// $Revision: 1.2 $ -// $Date: 2009/05/13 21:52:29 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/Cantera/cxx/include/Cantera.h b/Cantera/cxx/include/Cantera.h index 15c32a444..0093fe998 100755 --- a/Cantera/cxx/include/Cantera.h +++ b/Cantera/cxx/include/Cantera.h @@ -5,8 +5,8 @@ */ /* - * $Revision: 1.11 $ - * $Date: 2009/01/05 23:34:40 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in index cb0cfec51..67b6b1885 100644 --- a/Cantera/cxx/include/Cantera.mak.in +++ b/Cantera/cxx/include/Cantera.mak.in @@ -15,7 +15,7 @@ # # ##################################################################### -# $Id: Cantera.mak.in,v 1.5 2009/01/09 23:26:41 hkmoffa Exp $ +# $Id$ # # # This variable determines whether we are making this example in the diff --git a/Cantera/cxx/include/Cantera_bt.mak.in b/Cantera/cxx/include/Cantera_bt.mak.in index f9566f2bf..54c124c6e 100644 --- a/Cantera/cxx/include/Cantera_bt.mak.in +++ b/Cantera/cxx/include/Cantera_bt.mak.in @@ -15,7 +15,7 @@ # # ##################################################################### -# $Id: Cantera_bt.mak.in,v 1.2 2008/01/21 21:17:52 hkmoffa Exp $ +# $Id$ # # # This variable determines whether we are making this example in the diff --git a/Cantera/cxx/include/GRI30.h b/Cantera/cxx/include/GRI30.h index 04de8f887..6bc28cb26 100644 --- a/Cantera/cxx/include/GRI30.h +++ b/Cantera/cxx/include/GRI30.h @@ -1,5 +1,5 @@ /* - * $Id: GRI30.h,v 1.8 2008/02/16 21:35:30 hkmoffa Exp $ + * $Id$ */ #ifndef CXX_GRI30H #define CXX_GRI30H diff --git a/Cantera/cxx/include/Interface.h b/Cantera/cxx/include/Interface.h index 3dff74dac..0734fd233 100644 --- a/Cantera/cxx/include/Interface.h +++ b/Cantera/cxx/include/Interface.h @@ -5,7 +5,7 @@ */ /* - * $Id: Interface.h,v 1.10 2008/01/09 13:43:26 dggoodwin Exp $ + * $Id$ */ #ifndef CXX_INTERFACE diff --git a/Cantera/cxx/include/PureFluid.h b/Cantera/cxx/include/PureFluid.h index 7b16fb675..ce7ec4c9e 100644 --- a/Cantera/cxx/include/PureFluid.h +++ b/Cantera/cxx/include/PureFluid.h @@ -1,5 +1,5 @@ /* - * $Id: PureFluid.h,v 1.7 2007/12/21 02:58:41 hkmoffa Exp $ + * $Id$ */ #ifndef CXX_PUREFLUID #define CXX_PUREFLUID diff --git a/Cantera/cxx/include/equilibrium.h b/Cantera/cxx/include/equilibrium.h index 618495d48..1de354127 100755 --- a/Cantera/cxx/include/equilibrium.h +++ b/Cantera/cxx/include/equilibrium.h @@ -4,7 +4,7 @@ * (see \ref equilfunctions) */ /* - * $Id: equilibrium.h,v 1.11 2009/04/04 03:27:43 hkmoffa Exp $ + * $Id$ */ #ifndef CT_EQUIL_INCL #define CT_EQUIL_INCL diff --git a/Cantera/cxx/include/kinetics.h b/Cantera/cxx/include/kinetics.h index 137599144..f19fd9114 100644 --- a/Cantera/cxx/include/kinetics.h +++ b/Cantera/cxx/include/kinetics.h @@ -1,5 +1,5 @@ /* - * $Id: kinetics.h,v 1.4 2007/05/04 15:18:41 dggoodwin Exp $ + * $Id$ */ #ifndef CXX_INCL_KINETICS #define CXX_INCL_KINETICS diff --git a/Cantera/cxx/include/zerodim.h b/Cantera/cxx/include/zerodim.h index 34d932c4d..168039815 100644 --- a/Cantera/cxx/include/zerodim.h +++ b/Cantera/cxx/include/zerodim.h @@ -1,5 +1,5 @@ /* - * $Id: zerodim.h,v 1.8 2009/07/22 01:21:35 hkmoffa Exp $ + * $Id$ */ #ifndef CT_INCL_ZERODIM_H #define CT_INCL_ZERODIM_H diff --git a/Cantera/cxx/src/Makefile.in b/Cantera/cxx/src/Makefile.in index 05eaa3c6e..01e78a4ac 100644 --- a/Cantera/cxx/src/Makefile.in +++ b/Cantera/cxx/src/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.17 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # diff --git a/Cantera/fortran/src/Makefile.in b/Cantera/fortran/src/Makefile.in index 15f80f708..66f59382f 100644 --- a/Cantera/fortran/src/Makefile.in +++ b/Cantera/fortran/src/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/04/04 03:23:32 $ -# $Revision: 1.21 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # diff --git a/Cantera/fortran/src/fct.cpp b/Cantera/fortran/src/fct.cpp index e7dcf99fd..7b746d9d6 100644 --- a/Cantera/fortran/src/fct.cpp +++ b/Cantera/fortran/src/fct.cpp @@ -7,7 +7,7 @@ * pointers are passed to or from the calling application. */ /* - * $Id: fct.cpp,v 1.14 2009/07/23 16:56:48 hkmoffa Exp $ + * $Id$ */ // turn off warnings under Windows diff --git a/Cantera/fortran/src/fctxml.cpp b/Cantera/fortran/src/fctxml.cpp index 17c96f165..93efbc8a3 100644 --- a/Cantera/fortran/src/fctxml.cpp +++ b/Cantera/fortran/src/fctxml.cpp @@ -4,8 +4,8 @@ */ /* - * $Revision: 1.9 $ - * $Date: 2009/07/23 17:03:04 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/matlab/Makefile.in b/Cantera/matlab/Makefile.in index fa4000812..0bfbed956 100644 --- a/Cantera/matlab/Makefile.in +++ b/Cantera/matlab/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/07/06 23:52:40 $ -# $Revision: 1.33 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001-2004 California Institute of Technology # See file License.txt for licensing information diff --git a/Cantera/matlab/cantera/Contents.m b/Cantera/matlab/cantera/Contents.m index c5a94f3e5..5a4f155ec 100755 --- a/Cantera/matlab/cantera/Contents.m +++ b/Cantera/matlab/cantera/Contents.m @@ -33,7 +33,7 @@ % ctclear - Clear all objects from memory. % % Copyright 2002 California Institute of Technology -% $Revision: 1.1.1.1 $ $Date: 2003/04/14 17:57:49 $ +% $Revision$ $Date$ diff --git a/Cantera/matlab/cantera/private/ctfunctions.cpp b/Cantera/matlab/cantera/private/ctfunctions.cpp index 49c4edcad..f6b937e22 100644 --- a/Cantera/matlab/cantera/private/ctfunctions.cpp +++ b/Cantera/matlab/cantera/private/ctfunctions.cpp @@ -2,7 +2,7 @@ * @file ctfunctions.cpp */ /* - * $Id: ctfunctions.cpp,v 1.10 2009/07/11 16:43:12 hkmoffa Exp $ + * $Id$ */ #include "mex.h" diff --git a/Cantera/matlab/cantera/private/mixturemethods.cpp b/Cantera/matlab/cantera/private/mixturemethods.cpp index 671c8d901..fc0018012 100644 --- a/Cantera/matlab/cantera/private/mixturemethods.cpp +++ b/Cantera/matlab/cantera/private/mixturemethods.cpp @@ -2,7 +2,7 @@ * @file mixturemethods.cpp */ /* - * $Id: mixturemethods.cpp,v 1.3 2009/07/11 16:43:12 hkmoffa Exp $ + * $Id$ */ #include "mex.h" #include "../../../clib/src/ctmultiphase.h" diff --git a/Cantera/matlab/cantera/private/mllogger.h b/Cantera/matlab/cantera/private/mllogger.h index 2c4ac8d96..30d0e2dd3 100644 --- a/Cantera/matlab/cantera/private/mllogger.h +++ b/Cantera/matlab/cantera/private/mllogger.h @@ -2,7 +2,7 @@ * @file mlloger.h */ /* - * $Id: mllogger.h,v 1.5 2009/07/11 16:43:12 hkmoffa Exp $ + * $Id$ */ #ifndef MLLOGGER_H diff --git a/Cantera/matlab/cantera/private/phasemethods.cpp b/Cantera/matlab/cantera/private/phasemethods.cpp index df75fa57e..3a958f1df 100644 --- a/Cantera/matlab/cantera/private/phasemethods.cpp +++ b/Cantera/matlab/cantera/private/phasemethods.cpp @@ -2,7 +2,7 @@ * @file phasemethods.cpp */ /* - * $Id: phasemethods.cpp,v 1.5 2009/07/11 16:43:12 hkmoffa Exp $ + * $Id$ */ #include "mex.h" diff --git a/Cantera/matlab/cantera/private/reactormethods.cpp b/Cantera/matlab/cantera/private/reactormethods.cpp index b22cf37fb..49bad594c 100644 --- a/Cantera/matlab/cantera/private/reactormethods.cpp +++ b/Cantera/matlab/cantera/private/reactormethods.cpp @@ -2,7 +2,7 @@ * @file reactormethods.cpp */ /* - * $Id: reactormethods.cpp,v 1.5 2009/07/11 16:43:12 hkmoffa Exp $ + * $Id$ */ #include "mex.h" diff --git a/Cantera/matlab/cantera/private/reactornetmethods.cpp b/Cantera/matlab/cantera/private/reactornetmethods.cpp index 27b678809..766ae885f 100644 --- a/Cantera/matlab/cantera/private/reactornetmethods.cpp +++ b/Cantera/matlab/cantera/private/reactornetmethods.cpp @@ -2,7 +2,7 @@ * @file reactornetmethods.cpp */ /* - * $Id: reactornetmethods.cpp,v 1.4 2009/07/11 16:43:13 hkmoffa Exp $ + * $Id$ */ #include "mex.h" diff --git a/Cantera/matlab/cantera/private/thermomethods.cpp b/Cantera/matlab/cantera/private/thermomethods.cpp index c2fb43512..02286ed88 100644 --- a/Cantera/matlab/cantera/private/thermomethods.cpp +++ b/Cantera/matlab/cantera/private/thermomethods.cpp @@ -2,7 +2,7 @@ * @file thermomethods.cpp */ /* - * $Id: thermomethods.cpp,v 1.11 2009/07/11 16:43:13 hkmoffa Exp $ + * $Id$ */ #include "mex.h" #include "../../../clib/src/ct.h" diff --git a/Cantera/matlab/cantera/private/wallmethods.cpp b/Cantera/matlab/cantera/private/wallmethods.cpp index 004b4c652..1b7cf7e20 100644 --- a/Cantera/matlab/cantera/private/wallmethods.cpp +++ b/Cantera/matlab/cantera/private/wallmethods.cpp @@ -2,7 +2,7 @@ * @file wallmethods.cpp */ /* - * $Id: wallmethods.cpp,v 1.5 2009/07/11 16:43:13 hkmoffa Exp $ + * $Id$ */ #include "mex.h" #include "../../../clib/src/ctreactor.h" diff --git a/Cantera/matlab/cantera/private/xmlmethods.cpp b/Cantera/matlab/cantera/private/xmlmethods.cpp index 5cc4ed959..00397e429 100644 --- a/Cantera/matlab/cantera/private/xmlmethods.cpp +++ b/Cantera/matlab/cantera/private/xmlmethods.cpp @@ -2,7 +2,7 @@ * @file xmlmethods.cpp */ /* - * $Id: xmlmethods.cpp,v 1.5 2009/07/11 16:43:13 hkmoffa Exp $ + * $Id$ */ #include "mex.h" diff --git a/Cantera/matlab/setup_winmatlab.py b/Cantera/matlab/setup_winmatlab.py index 6207f9815..c41132377 100644 --- a/Cantera/matlab/setup_winmatlab.py +++ b/Cantera/matlab/setup_winmatlab.py @@ -1,7 +1,7 @@ # # python script to create a few key files for the windows build # -# $Id: setup_winmatlab.py,v 1.29 2009/07/20 19:38:53 hkmoffa Exp $ +# $Id$ # import sys import os diff --git a/Cantera/python/Cantera/Edge.py b/Cantera/python/Cantera/Edge.py index 32a8c512f..a6c661186 100644 --- a/Cantera/python/Cantera/Edge.py +++ b/Cantera/python/Cantera/Edge.py @@ -7,7 +7,7 @@ from SurfacePhase import EdgePhase from Kinetics import Kinetics import XML -__revision__ = "$Id: Edge.py,v 1.1 2006/04/23 07:27:10 dggoodwin Exp $" +__revision__ = "$Id$" class Edge(EdgePhase, Kinetics): """ diff --git a/Cantera/python/Cantera/Interface.py b/Cantera/python/Cantera/Interface.py index 7a7307966..8a26d8f61 100644 --- a/Cantera/python/Cantera/Interface.py +++ b/Cantera/python/Cantera/Interface.py @@ -7,7 +7,7 @@ from SurfacePhase import SurfacePhase, EdgePhase from Kinetics import Kinetics import XML -__revision__ = "$Id: Interface.py,v 1.8 2007/02/17 10:48:09 dggoodwin Exp $" +__revision__ = "$Id$" class Interface(SurfacePhase, Kinetics): """ diff --git a/Cantera/python/Cantera/Phase.py b/Cantera/python/Cantera/Phase.py index c5cc1fdba..ed65174e8 100755 --- a/Cantera/python/Cantera/Phase.py +++ b/Cantera/python/Cantera/Phase.py @@ -10,7 +10,7 @@ import types from Cantera.num import asarray from exceptions import CanteraError -__revision__ = "$Id: Phase.py,v 1.9 2007/05/25 14:17:38 dggoodwin Exp $" +__revision__ = "$Id$" # return true is x is a sequence def _isseq(n, x): diff --git a/Cantera/python/Cantera/importFromFile.py b/Cantera/python/Cantera/importFromFile.py index 448d13074..4d9f3ae5f 100755 --- a/Cantera/python/Cantera/importFromFile.py +++ b/Cantera/python/Cantera/importFromFile.py @@ -8,7 +8,7 @@ import Interface import Edge import XML -__revision__ = "$Id: importFromFile.py,v 1.12 2007/02/17 10:48:09 dggoodwin Exp $" +__revision__ = "$Id$" def importPhase(file, name = '', loglevel = 0, debug = 0): """Import one phase from an input file. If 'name' is specified, the diff --git a/Cantera/python/Makefile.in b/Cantera/python/Makefile.in index f4f268608..9d83154b3 100755 --- a/Cantera/python/Makefile.in +++ b/Cantera/python/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/04/19 21:11:51 $ -# $Revision: 1.31 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # See file License.txt for licensing information diff --git a/Cantera/python/ctml_writer.py b/Cantera/python/ctml_writer.py index 1d78f79cd..9754a7d53 100644 --- a/Cantera/python/ctml_writer.py +++ b/Cantera/python/ctml_writer.py @@ -16,7 +16,7 @@ # # -# $Id: ctml_writer.py,v 1.25 2007/12/30 04:19:38 dggoodwin Exp $ +# $Id$ import string diff --git a/Cantera/python/src/Makefile.in b/Cantera/python/src/Makefile.in index 4791f646d..2a68ff12f 100755 --- a/Cantera/python/src/Makefile.in +++ b/Cantera/python/src/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: dggoodwin $ -# $Date: 2003/04/14 17:57:50 $ -# $Revision: 1.1.1.1 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # diff --git a/Cantera/python/src/ctkinetics_methods.cpp b/Cantera/python/src/ctkinetics_methods.cpp index 45cd77c19..a9309a4b0 100644 --- a/Cantera/python/src/ctkinetics_methods.cpp +++ b/Cantera/python/src/ctkinetics_methods.cpp @@ -4,7 +4,7 @@ */ /* - * $Id: ctkinetics_methods.cpp,v 1.8 2009/04/19 21:03:10 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/python/src/ctonedim_methods.cpp b/Cantera/python/src/ctonedim_methods.cpp index 397419f1d..d1ac71e89 100644 --- a/Cantera/python/src/ctonedim_methods.cpp +++ b/Cantera/python/src/ctonedim_methods.cpp @@ -1,6 +1,6 @@ /* - * $Id: ctonedim_methods.cpp,v 1.12 2009/03/24 19:13:02 hkmoffa Exp $ + * $Id$ */ diff --git a/Cantera/src/Makefile.in b/Cantera/src/Makefile.in index 4408231f2..01072f159 100755 --- a/Cantera/src/Makefile.in +++ b/Cantera/src/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: dggoodwin $ -# $Date: 2007/12/15 17:15:50 $ -# $Revision: 1.58 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2001 California Institute of Technology # diff --git a/Cantera/src/base/Array.h b/Cantera/src/base/Array.h index 003700a8c..22c508748 100755 --- a/Cantera/src/base/Array.h +++ b/Cantera/src/base/Array.h @@ -4,9 +4,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2009/01/15 23:05:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/LogPrintCtrl.cpp b/Cantera/src/base/LogPrintCtrl.cpp index fac746ece..34cef0ba6 100644 --- a/Cantera/src/base/LogPrintCtrl.cpp +++ b/Cantera/src/base/LogPrintCtrl.cpp @@ -4,9 +4,9 @@ * (see \ref Cantera::LogPrintCtrl). */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2008/04/08 20:19:26 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/LogPrintCtrl.h b/Cantera/src/base/LogPrintCtrl.h index 80aa5a8bf..889298e2b 100644 --- a/Cantera/src/base/LogPrintCtrl.h +++ b/Cantera/src/base/LogPrintCtrl.h @@ -4,8 +4,8 @@ * (see \ref Cantera::LogPrintCtrl). */ /* - * $Revision: 1.2 $ - * $Date: 2009/01/15 20:08:50 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/Makefile.in b/Cantera/src/base/Makefile.in index 73c81a191..7d00cb58a 100644 --- a/Cantera/src/base/Makefile.in +++ b/Cantera/src/base/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/02/11 19:55:56 $ -# $Revision: 1.8 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/base/PrintCtrl.cpp b/Cantera/src/base/PrintCtrl.cpp index f40824fb4..973b248b2 100644 --- a/Cantera/src/base/PrintCtrl.cpp +++ b/Cantera/src/base/PrintCtrl.cpp @@ -4,9 +4,9 @@ * (see \ref Cantera::PrintCtrl). */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2009/03/14 00:27:10 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/PrintCtrl.h b/Cantera/src/base/PrintCtrl.h index 50e224bc5..cce65457f 100644 --- a/Cantera/src/base/PrintCtrl.h +++ b/Cantera/src/base/PrintCtrl.h @@ -4,8 +4,8 @@ * (see \ref Cantera::PrintCtrl). */ /* - * $Revision: 1.3 $ - * $Date: 2009/03/14 00:27:10 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/checkFinite.cpp b/Cantera/src/base/checkFinite.cpp index f4f2f2601..b20096b99 100644 --- a/Cantera/src/base/checkFinite.cpp +++ b/Cantera/src/base/checkFinite.cpp @@ -4,8 +4,8 @@ * check for the presence of NaNs in the code. */ /* - * $Revision: 1.2 $ - * $Date: 2009/03/27 00:39:43 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/clockWC.cpp b/Cantera/src/base/clockWC.cpp index 6c823ca7d..7b7bd7936 100644 --- a/Cantera/src/base/clockWC.cpp +++ b/Cantera/src/base/clockWC.cpp @@ -4,9 +4,9 @@ * (see \ref Cantera::clockWC). */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2007/06/11 15:20:03 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/clockWC.h b/Cantera/src/base/clockWC.h index d9888ed99..8d3ad1654 100644 --- a/Cantera/src/base/clockWC.h +++ b/Cantera/src/base/clockWC.h @@ -4,9 +4,9 @@ * (see \ref Cantera::clockWC). */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2007/06/11 15:20:03 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/ct2ctml.cpp b/Cantera/src/base/ct2ctml.cpp index da2fb958b..591d599fb 100644 --- a/Cantera/src/base/ct2ctml.cpp +++ b/Cantera/src/base/ct2ctml.cpp @@ -5,8 +5,8 @@ */ /* - * $Revision: 1.14 $ - * $Date: 2009/07/13 16:47:40 $ + * $Revision$ + * $Date$ */ // Copyright 2001-2005 California Institute of Technology diff --git a/Cantera/src/base/ct_defs.h b/Cantera/src/base/ct_defs.h index 3b8cb52db..c394cadb7 100755 --- a/Cantera/src/base/ct_defs.h +++ b/Cantera/src/base/ct_defs.h @@ -10,8 +10,8 @@ */ /* - * $Revision: 1.9 $ - * $Date: 2009/01/24 00:15:00 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/ctexceptions.h b/Cantera/src/base/ctexceptions.h index 80b787814..1c29cbd36 100755 --- a/Cantera/src/base/ctexceptions.h +++ b/Cantera/src/base/ctexceptions.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/02/11 19:55:57 $ - * $Revision: 1.7 $ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index b705927c0..9e0cf934b 100755 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -5,8 +5,8 @@ */ /* - * $Revision: 1.24 $ - * $Date: 2009/03/13 03:18:08 $ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 25fbe3a9c..5cfe45417 100755 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -6,8 +6,8 @@ */ /* - * $Revision: 1.22 $ - * $Date: 2009/07/11 17:20:19 $ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/base/global.h b/Cantera/src/base/global.h index d3b02c924..c0386d8fc 100755 --- a/Cantera/src/base/global.h +++ b/Cantera/src/base/global.h @@ -17,8 +17,8 @@ */ /* - * $Revision: 1.8 $ - * $Date: 2009/07/06 23:52:40 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/logger.h b/Cantera/src/base/logger.h index fcc93b0ca..d4b508aa3 100644 --- a/Cantera/src/base/logger.h +++ b/Cantera/src/base/logger.h @@ -4,7 +4,7 @@ * (see \ref textlogs and class \link Cantera::Logger Logger\endlink). */ /* - * $Id: logger.h,v 1.3 2008/12/17 17:13:35 hkmoffa Exp $ + * $Id$ */ #ifndef CT_LOGGER_H diff --git a/Cantera/src/base/mdp_allo.cpp b/Cantera/src/base/mdp_allo.cpp index 745601491..1d9f90e3f 100644 --- a/Cantera/src/base/mdp_allo.cpp +++ b/Cantera/src/base/mdp_allo.cpp @@ -3,8 +3,8 @@ * Definitions for dynamic allocation of multidimensional pointer arrays */ /* - * $Revision: 1.3 $ - * $Date: 2009/07/22 01:21:35 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/mdp_allo.h b/Cantera/src/base/mdp_allo.h index 03c969fef..ef41f9b95 100644 --- a/Cantera/src/base/mdp_allo.h +++ b/Cantera/src/base/mdp_allo.h @@ -5,8 +5,8 @@ * one call. */ /* - * $Revision: 1.2 $ - * $Date: 2009/03/27 00:39:43 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index f0a9d8e8e..30d8d9a90 100755 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -10,7 +10,7 @@ * HTML_logs */ /* - * $Id: misc.cpp,v 1.16 2009/07/13 16:47:40 hkmoffa Exp $ + * $Id$ */ #ifdef WIN32 diff --git a/Cantera/src/base/plots.cpp b/Cantera/src/base/plots.cpp index de293ba48..fe093e030 100755 --- a/Cantera/src/base/plots.cpp +++ b/Cantera/src/base/plots.cpp @@ -3,8 +3,8 @@ */ /* - * $Revision: 1.2 $ - * $Date: 2009/01/14 23:16:24 $ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/base/plots.h b/Cantera/src/base/plots.h index 794680d37..5c2a0a186 100755 --- a/Cantera/src/base/plots.h +++ b/Cantera/src/base/plots.h @@ -5,8 +5,8 @@ */ /* - * $Revision: 1.2 $ - * $Date: 2009/01/14 23:16:24 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/stringUtils.cpp b/Cantera/src/base/stringUtils.cpp index a8f61444a..54eb66d32 100755 --- a/Cantera/src/base/stringUtils.cpp +++ b/Cantera/src/base/stringUtils.cpp @@ -5,7 +5,7 @@ */ /* - * $Id: stringUtils.cpp,v 1.22 2009/01/15 20:08:50 hkmoffa Exp $ + * $Id$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/stringUtils.h b/Cantera/src/base/stringUtils.h index 367affb23..4dc6c7dbf 100755 --- a/Cantera/src/base/stringUtils.h +++ b/Cantera/src/base/stringUtils.h @@ -5,8 +5,8 @@ */ /* - * $Revision: 1.15 $ - * $Date: 2009/01/15 20:08:50 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/units.h b/Cantera/src/base/units.h index 81be47535..6e3ac70a5 100644 --- a/Cantera/src/base/units.h +++ b/Cantera/src/base/units.h @@ -7,7 +7,7 @@ * This header is included only by file misc.cpp. */ /* - * $Id: units.h,v 1.5 2007/12/15 17:15:50 dggoodwin Exp $ + * $Id$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/base/utilities.h b/Cantera/src/base/utilities.h index a608789f5..7b5221555 100755 --- a/Cantera/src/base/utilities.h +++ b/Cantera/src/base/utilities.h @@ -6,7 +6,7 @@ // Copyright 2001 California Institute of Technology /* - * $Id: utilities.h,v 1.9 2008/08/22 14:41:07 hkmoffa Exp $ + * $Id$ */ /** diff --git a/Cantera/src/base/vec_functions.h b/Cantera/src/base/vec_functions.h index 3b74ca33c..c3b14fff1 100755 --- a/Cantera/src/base/vec_functions.h +++ b/Cantera/src/base/vec_functions.h @@ -3,8 +3,8 @@ * Templates for operations on vector-like objects. */ /* - * $Date: 2009/01/15 20:08:50 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index ad52226e8..d4c6f0e80 100755 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -6,8 +6,8 @@ */ /* - * $Revision: 1.27 $ - * $Date: 2009/07/22 01:21:35 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index 392da867d..b66567446 100755 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -6,8 +6,8 @@ */ /* - * $Revision: 1.23 $ - * $Date: 2009/07/22 01:21:35 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/converters/CKParser.cpp b/Cantera/src/converters/CKParser.cpp index 3efea5455..b51b408ea 100755 --- a/Cantera/src/converters/CKParser.cpp +++ b/Cantera/src/converters/CKParser.cpp @@ -5,7 +5,7 @@ // Copyright 2001 California Institute of Technology // -// $Id: CKParser.cpp,v 1.23 2009/03/13 03:26:18 hkmoffa Exp $ +// $Id$ // turn off warnings about truncating long names under Windows #ifdef WIN32 diff --git a/Cantera/src/converters/Makefile.in b/Cantera/src/converters/Makefile.in index 9290b1ad7..d491f2f59 100644 --- a/Cantera/src/converters/Makefile.in +++ b/Cantera/src/converters/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.19 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/converters/NASA9Parser.cpp b/Cantera/src/converters/NASA9Parser.cpp index 8b917c78d..cb4f7069a 100644 --- a/Cantera/src/converters/NASA9Parser.cpp +++ b/Cantera/src/converters/NASA9Parser.cpp @@ -5,7 +5,7 @@ // Copyright 2001 California Institute of Technology // -// $Id: NASA9Parser.cpp,v 1.2 2009/03/13 03:26:18 hkmoffa Exp $ +// $Id$ // diff --git a/Cantera/src/converters/Species.h b/Cantera/src/converters/Species.h index 9b0b84e99..9b82c7d3a 100755 --- a/Cantera/src/converters/Species.h +++ b/Cantera/src/converters/Species.h @@ -3,7 +3,7 @@ * */ /* - * $Id: Species.h,v 1.2 2007/09/13 15:05:39 hkmoffa Exp $ + * $Id$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/converters/ck2ct.cpp b/Cantera/src/converters/ck2ct.cpp index a9b178586..464ab8283 100644 --- a/Cantera/src/converters/ck2ct.cpp +++ b/Cantera/src/converters/ck2ct.cpp @@ -3,7 +3,7 @@ * Convert CK-format reaction mechanism files to Cantera input format. */ /* - * $Id: ck2ct.cpp,v 1.27 2009/01/10 18:03:31 hkmoffa Exp $ + * $Id$ * */ #ifdef WIN32 diff --git a/Cantera/src/equil/BasisOptimize.cpp b/Cantera/src/equil/BasisOptimize.cpp index 809cd2050..b98d36ff4 100644 --- a/Cantera/src/equil/BasisOptimize.cpp +++ b/Cantera/src/equil/BasisOptimize.cpp @@ -5,7 +5,7 @@ */ /* - * $Id: BasisOptimize.cpp,v 1.9 2009/01/05 23:20:43 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/equil/ChemEquil.cpp b/Cantera/src/equil/ChemEquil.cpp index 25b3145ab..d78714575 100755 --- a/Cantera/src/equil/ChemEquil.cpp +++ b/Cantera/src/equil/ChemEquil.cpp @@ -8,7 +8,7 @@ /* * * - * $Id: ChemEquil.cpp,v 1.15 2009/03/14 03:28:04 hkmoffa Exp $ + * $Id$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/equil/ChemEquil.h b/Cantera/src/equil/ChemEquil.h index d40d1ef77..f39244292 100755 --- a/Cantera/src/equil/ChemEquil.h +++ b/Cantera/src/equil/ChemEquil.h @@ -3,9 +3,9 @@ * * Chemical equilibrium. * - * $Author: hkmoffa $ - * $Date: 2008/09/04 17:03:42 $ - * $Revision: 1.6 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/equil/Makefile.in b/Cantera/src/equil/Makefile.in index 1ef465f86..363c44348 100644 --- a/Cantera/src/equil/Makefile.in +++ b/Cantera/src/equil/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.16 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index 7d8567f72..81dcb4865 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -5,8 +5,8 @@ */ /* * - * $Date: 2009/04/17 00:40:48 $ - * $Revision: 1.15 $ + * $Date$ + * $Revision$ */ #include "MultiPhase.h" diff --git a/Cantera/src/equil/MultiPhase.h b/Cantera/src/equil/MultiPhase.h index 7dfa0a5a3..fa96148c3 100644 --- a/Cantera/src/equil/MultiPhase.h +++ b/Cantera/src/equil/MultiPhase.h @@ -5,8 +5,8 @@ */ /* - * $Date: 2009/04/17 00:40:48 $ - * $Revision: 1.11 $ + * $Date$ + * $Revision$ */ // Copyright 2004 California Institute of Technology diff --git a/Cantera/src/equil/MultiPhaseEquil.cpp b/Cantera/src/equil/MultiPhaseEquil.cpp index db5e786d4..0d70eaae5 100644 --- a/Cantera/src/equil/MultiPhaseEquil.cpp +++ b/Cantera/src/equil/MultiPhaseEquil.cpp @@ -2,7 +2,7 @@ * @file MultiPhaseEquil.cpp */ /* - * $Id: MultiPhaseEquil.cpp,v 1.12 2009/04/22 00:33:35 hkmoffa Exp $ + * $Id$ */ #include "MultiPhaseEquil.h" diff --git a/Cantera/src/equil/PropertyCalculator.h b/Cantera/src/equil/PropertyCalculator.h index f5ae87345..cb37cbcbb 100755 --- a/Cantera/src/equil/PropertyCalculator.h +++ b/Cantera/src/equil/PropertyCalculator.h @@ -1,9 +1,9 @@ /** * @file PropertyCalculator.h * - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2008/12/17 16:56:43 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/equil/equil.h b/Cantera/src/equil/equil.h index e43f1471a..937b70a4a 100644 --- a/Cantera/src/equil/equil.h +++ b/Cantera/src/equil/equil.h @@ -1,8 +1,8 @@ /*********************************************************************** * $RCSfile: equil.h,v $ - * $Author: hkmoffa $ - * $Date: 2008/04/11 22:44:49 $ - * $Revision: 1.3 $ + * $Author$ + * $Date$ + * $Revision$ ***********************************************************************/ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/equil/equilibrate.cpp b/Cantera/src/equil/equilibrate.cpp index 3c50e5cca..548df4f68 100644 --- a/Cantera/src/equil/equilibrate.cpp +++ b/Cantera/src/equil/equilibrate.cpp @@ -4,7 +4,7 @@ * */ /* - * $Id: equilibrate.cpp,v 1.11 2009/03/18 17:27:20 hkmoffa Exp $ + * $Id$ */ #include "equil.h" #include "ChemEquil.h" diff --git a/Cantera/src/equil/vcs_DoubleStarStar.cpp b/Cantera/src/equil/vcs_DoubleStarStar.cpp index 0b72701eb..4a95e111b 100644 --- a/Cantera/src/equil/vcs_DoubleStarStar.cpp +++ b/Cantera/src/equil/vcs_DoubleStarStar.cpp @@ -5,9 +5,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2008/08/01 16:05:38 $ + * $Author$ + * $Revision$ + * $Date$ */ #include "vcs_DoubleStarStar.h" diff --git a/Cantera/src/equil/vcs_DoubleStarStar.h b/Cantera/src/equil/vcs_DoubleStarStar.h index cb6060f69..79db395ea 100644 --- a/Cantera/src/equil/vcs_DoubleStarStar.h +++ b/Cantera/src/equil/vcs_DoubleStarStar.h @@ -5,9 +5,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2008/08/01 16:05:38 $ + * $Author$ + * $Revision$ + * $Date$ */ #ifndef VCS_DOUBLESTARSTAR_H diff --git a/Cantera/src/equil/vcs_Exception.h b/Cantera/src/equil/vcs_Exception.h index 3ee7fbacb..c08216868 100644 --- a/Cantera/src/equil/vcs_Exception.h +++ b/Cantera/src/equil/vcs_Exception.h @@ -2,7 +2,7 @@ * @file vcs_Exception.h */ /* - * $Id: vcs_Exception.h,v 1.2 2008/07/22 16:23:55 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_Gibbs.cpp b/Cantera/src/equil/vcs_Gibbs.cpp index 224095eae..f427da1a3 100644 --- a/Cantera/src/equil/vcs_Gibbs.cpp +++ b/Cantera/src/equil/vcs_Gibbs.cpp @@ -3,7 +3,7 @@ * Functions which calculate the extrinsic Gibbs Free energies */ /* - * $Id: vcs_Gibbs.cpp,v 1.12 2009/03/27 21:32:33 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_IntStarStar.cpp b/Cantera/src/equil/vcs_IntStarStar.cpp index c356298f0..772ade325 100644 --- a/Cantera/src/equil/vcs_IntStarStar.cpp +++ b/Cantera/src/equil/vcs_IntStarStar.cpp @@ -5,9 +5,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2007/12/19 21:19:28 $ + * $Author$ + * $Revision$ + * $Date$ */ #include "vcs_IntStarStar.h" diff --git a/Cantera/src/equil/vcs_IntStarStar.h b/Cantera/src/equil/vcs_IntStarStar.h index bde2bcf02..653f42bb7 100644 --- a/Cantera/src/equil/vcs_IntStarStar.h +++ b/Cantera/src/equil/vcs_IntStarStar.h @@ -5,9 +5,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2007/12/19 21:19:28 $ + * $Author$ + * $Revision$ + * $Date$ */ #ifndef VCS_INTSTARSTAR_H diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index e394ddf53..9d8863917 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -3,7 +3,7 @@ * Driver routine for the VCSnonideal equilibrium solver package */ /* - * $Id: vcs_MultiPhaseEquil.cpp,v 1.48 2009/03/28 03:07:23 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.h b/Cantera/src/equil/vcs_MultiPhaseEquil.h index 4ef1a8857..3b35973a4 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.h +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.h @@ -4,9 +4,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.12 $ - * $Date: 2008/05/06 16:53:37 $ + * $Author$ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/equil/vcs_SpeciesProperties.h b/Cantera/src/equil/vcs_SpeciesProperties.h index 13d8ec9d3..7a3457a6d 100644 --- a/Cantera/src/equil/vcs_SpeciesProperties.h +++ b/Cantera/src/equil/vcs_SpeciesProperties.h @@ -1,5 +1,5 @@ -/* $Id: vcs_SpeciesProperties.h,v 1.1 2007/12/19 21:19:28 hkmoffa Exp $ */ +/* $Id$ */ #ifndef VCS_SPECIES_PROPERTIES_H #define VCS_SPECIES_PROPERTIES_H diff --git a/Cantera/src/equil/vcs_TP.cpp b/Cantera/src/equil/vcs_TP.cpp index 4b9f2e0ff..83f3e3248 100644 --- a/Cantera/src/equil/vcs_TP.cpp +++ b/Cantera/src/equil/vcs_TP.cpp @@ -3,9 +3,9 @@ /* | RCS Head Information on zuzax.pchem.sandia.gov | */ /* -------------------------------------------------- */ /* $RCSfile: vcs_TP.cpp,v $ */ -/* $Author: hkmoffa $ */ -/* $Date: 2008/12/17 16:34:18 $ */ -/* $Revision: 1.14 $ */ +/* $Author$ */ +/* $Date$ */ +/* $Revision$ */ /* ======================================================================= */ #include "vcs_solve.h" diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index cdac4b681..760f919ff 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -2,7 +2,7 @@ * @file vcs_VolPhase.cpp */ -/* $Id: vcs_VolPhase.cpp,v 1.37 2009/07/23 14:41:40 hkmoffa Exp $ */ +/* $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 6de83bdeb..808558a16 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -3,7 +3,7 @@ * Header for the object representing each phase within vcs */ /* - * $Id: vcs_VolPhase.h,v 1.29 2009/04/18 00:42:50 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_defs.h b/Cantera/src/equil/vcs_defs.h index 28e46c17c..056859ff6 100644 --- a/Cantera/src/equil/vcs_defs.h +++ b/Cantera/src/equil/vcs_defs.h @@ -3,7 +3,7 @@ * Defines and definitions within the vcs package */ /* - * $Id: vcs_defs.h,v 1.14 2009/04/18 00:42:51 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_elem.cpp b/Cantera/src/equil/vcs_elem.cpp index 0c293f710..0d6d37ef8 100644 --- a/Cantera/src/equil/vcs_elem.cpp +++ b/Cantera/src/equil/vcs_elem.cpp @@ -5,7 +5,7 @@ * of the element abundances constraints. */ /* - * $Id: vcs_elem.cpp,v 1.12 2008/10/23 01:13:35 hkmoffa Exp $ + * $Id$ */ #include "vcs_solve.h" diff --git a/Cantera/src/equil/vcs_elem_rearrange.cpp b/Cantera/src/equil/vcs_elem_rearrange.cpp index c86d7d8ba..95e94feaa 100644 --- a/Cantera/src/equil/vcs_elem_rearrange.cpp +++ b/Cantera/src/equil/vcs_elem_rearrange.cpp @@ -3,9 +3,9 @@ * Contains implementations for rearranging the element columns, and * it contains the algorithm for choosing the rearrangement. */ -/* $Author: hkmoffa $ - * $Date: 2008/12/17 16:56:43 $ - * $Revision: 1.13 $ +/* $Author$ + * $Date$ + * $Revision$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_equilibrate.cpp b/Cantera/src/equil/vcs_equilibrate.cpp index 6039c65d0..ed46e6c14 100644 --- a/Cantera/src/equil/vcs_equilibrate.cpp +++ b/Cantera/src/equil/vcs_equilibrate.cpp @@ -4,7 +4,7 @@ */ /* * - * $Id: vcs_equilibrate.cpp,v 1.7 2009/03/18 17:27:20 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_inest.cpp b/Cantera/src/equil/vcs_inest.cpp index e45505cad..f071a044a 100644 --- a/Cantera/src/equil/vcs_inest.cpp +++ b/Cantera/src/equil/vcs_inest.cpp @@ -2,9 +2,9 @@ * @file vcs_inest.cpp * Implementation methods for obtaining a good initial guess */ -/* $Author: hkmoffa $ - * $Date: 2009/03/27 22:36:20 $ - * $Revision: 1.35 $ +/* $Author$ + * $Date$ + * $Revision$ */ /* diff --git a/Cantera/src/equil/vcs_internal.h b/Cantera/src/equil/vcs_internal.h index 6756c4a7a..b816240e2 100644 --- a/Cantera/src/equil/vcs_internal.h +++ b/Cantera/src/equil/vcs_internal.h @@ -3,7 +3,7 @@ * Internal declarations for the VCSnonideal package */ /* - * $Id: vcs_internal.h,v 1.20 2009/04/18 00:42:51 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_linmaxc.cpp b/Cantera/src/equil/vcs_linmaxc.cpp index 20c2b0398..813324eb7 100644 --- a/Cantera/src/equil/vcs_linmaxc.cpp +++ b/Cantera/src/equil/vcs_linmaxc.cpp @@ -1,6 +1,6 @@ -/* $Author: hkmoffa $ - * $Date: 2008/12/17 16:34:18 $ - * $Revision: 1.5 $ +/* $Author$ + * $Date$ + * $Revision$ */ /* diff --git a/Cantera/src/equil/vcs_nondim.cpp b/Cantera/src/equil/vcs_nondim.cpp index cd0a31b16..16d44448d 100644 --- a/Cantera/src/equil/vcs_nondim.cpp +++ b/Cantera/src/equil/vcs_nondim.cpp @@ -3,7 +3,7 @@ * Nondimensionalization routines within VCSnonideal */ /* - * $Id: vcs_nondim.cpp,v 1.17 2008/12/17 16:56:43 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2007) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index 7193015d7..a0a560abf 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -1,7 +1,7 @@ /* ======================================================================= */ /* $RCSfile: vcs_phaseStability.cpp,v $ */ -/* $Date: 2009/04/18 00:42:51 $ */ -/* $Revision: 1.8 $ */ +/* $Date$ */ +/* $Revision$ */ /* ======================================================================= */ diff --git a/Cantera/src/equil/vcs_prep.cpp b/Cantera/src/equil/vcs_prep.cpp index eee8a75a2..5579f2211 100644 --- a/Cantera/src/equil/vcs_prep.cpp +++ b/Cantera/src/equil/vcs_prep.cpp @@ -4,9 +4,9 @@ */ /* $RCSfile: vcs_prep.cpp,v $ */ -/* $Author: hkmoffa $ */ -/* $Date: 2008/12/17 16:34:18 $ */ -/* $Revision: 1.25 $ */ +/* $Author$ */ +/* $Date$ */ +/* $Revision$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of * Contract DE-AC04-94AL85000 with Sandia Corporation, the diff --git a/Cantera/src/equil/vcs_prob.cpp b/Cantera/src/equil/vcs_prob.cpp index 0993faa3c..6d1891b4c 100644 --- a/Cantera/src/equil/vcs_prob.cpp +++ b/Cantera/src/equil/vcs_prob.cpp @@ -5,7 +5,7 @@ */ /* - * $Id: vcs_prob.cpp,v 1.22 2008/12/17 16:56:43 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_prob.h b/Cantera/src/equil/vcs_prob.h index d235c392d..70905a50b 100644 --- a/Cantera/src/equil/vcs_prob.h +++ b/Cantera/src/equil/vcs_prob.h @@ -4,7 +4,7 @@ */ /* - * $Id: vcs_prob.h,v 1.6 2008/05/06 16:53:38 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_rearrange.cpp b/Cantera/src/equil/vcs_rearrange.cpp index 4d556c784..e12310c55 100644 --- a/Cantera/src/equil/vcs_rearrange.cpp +++ b/Cantera/src/equil/vcs_rearrange.cpp @@ -3,7 +3,7 @@ * implementation file for rearranging species. */ /* - * $Id: vcs_rearrange.cpp,v 1.5 2008/12/17 16:34:18 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2007) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_report.cpp b/Cantera/src/equil/vcs_report.cpp index 9beb9a1f2..94dde2c62 100644 --- a/Cantera/src/equil/vcs_report.cpp +++ b/Cantera/src/equil/vcs_report.cpp @@ -1,5 +1,5 @@ /* - * $Id: vcs_report.cpp,v 1.38 2009/04/01 01:16:40 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_root1d.cpp b/Cantera/src/equil/vcs_root1d.cpp index b7bdf4085..bb8116b96 100644 --- a/Cantera/src/equil/vcs_root1d.cpp +++ b/Cantera/src/equil/vcs_root1d.cpp @@ -3,7 +3,7 @@ * Code for a one dimensional root finder program. */ /* - * $Id: vcs_root1d.cpp,v 1.5 2008/12/17 16:34:18 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_rxnadj.cpp b/Cantera/src/equil/vcs_rxnadj.cpp index 72d14fb55..0a4983045 100644 --- a/Cantera/src/equil/vcs_rxnadj.cpp +++ b/Cantera/src/equil/vcs_rxnadj.cpp @@ -3,7 +3,7 @@ * Routines for carrying out various adjustments to the reaction steps */ /* - * $Id: vcs_rxnadj.cpp,v 1.34 2009/04/18 00:42:51 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2006) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_setMolesLinProg.cpp b/Cantera/src/equil/vcs_setMolesLinProg.cpp index bd3e64d51..425600cae 100644 --- a/Cantera/src/equil/vcs_setMolesLinProg.cpp +++ b/Cantera/src/equil/vcs_setMolesLinProg.cpp @@ -3,7 +3,7 @@ * */ /* - * $Id: vcs_setMolesLinProg.cpp,v 1.11 2008/12/17 16:34:18 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 354a7e16a..108d1dcbc 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -3,7 +3,7 @@ * Header file for the internal class that holds the problem. */ /* - * $Id: vcs_solve.cpp,v 1.60 2008/12/17 16:56:43 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 2337632cc..64acf7ee0 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -3,7 +3,7 @@ * Header file for the internal object that holds the problem */ /* - * $Id: vcs_solve.h,v 1.75 2009/04/18 00:42:51 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index cff79e653..5d8bae98b 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -3,7 +3,7 @@ * main algorithm for finding an equilibrium */ /* - * $Id: vcs_solve_TP.cpp,v 1.93 2009/04/18 00:42:51 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_species_thermo.cpp b/Cantera/src/equil/vcs_species_thermo.cpp index c51507d3b..1a33fcf80 100644 --- a/Cantera/src/equil/vcs_species_thermo.cpp +++ b/Cantera/src/equil/vcs_species_thermo.cpp @@ -3,7 +3,7 @@ * Implementation for the VCS_SPECIES_THERMO object. */ /* - * $Id: vcs_species_thermo.cpp,v 1.18 2008/12/17 16:34:18 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_species_thermo.h b/Cantera/src/equil/vcs_species_thermo.h index 047cc4c20..268b9731f 100644 --- a/Cantera/src/equil/vcs_species_thermo.h +++ b/Cantera/src/equil/vcs_species_thermo.h @@ -1,5 +1,5 @@ /* - * $Id: vcs_species_thermo.h,v 1.3 2008/04/28 16:08:35 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/equil/vcs_util.cpp b/Cantera/src/equil/vcs_util.cpp index a39ea4915..ae34e3a12 100644 --- a/Cantera/src/equil/vcs_util.cpp +++ b/Cantera/src/equil/vcs_util.cpp @@ -3,7 +3,7 @@ * Internal definitions for utility functions for the VCSnonideal package */ /* - * $Id: vcs_util.cpp,v 1.13 2009/07/06 22:30:58 hkmoffa Exp $ + * $Id$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/equil/vcs_xerror.c b/Cantera/src/equil/vcs_xerror.c index 32b0dd269..a7d98d18a 100644 --- a/Cantera/src/equil/vcs_xerror.c +++ b/Cantera/src/equil/vcs_xerror.c @@ -21,9 +21,9 @@ static integer c__1 = 1; /* -------------------------------------------------- */ /* | CVS Head Information | */ /* -------------------------------------------------- */ -/* $Author: hkmoffa $ */ -/* $Date: 2008/01/03 21:38:25 $ */ -/* $Revision: 1.1 $ */ +/* $Author$ */ +/* $Date$ */ +/* $Revision$ */ /* ======================================================================= */ /* Subroutine */ int s88fmt_(integer *n, integer *ivalue, integer *ifmt) diff --git a/Cantera/src/kinetics/AqueousKinetics.cpp b/Cantera/src/kinetics/AqueousKinetics.cpp index 7590bba54..0559dec2b 100644 --- a/Cantera/src/kinetics/AqueousKinetics.cpp +++ b/Cantera/src/kinetics/AqueousKinetics.cpp @@ -11,8 +11,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/02/11 01:50:54 $ - * $Revision: 1.1 $ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/kinetics/AqueousKinetics.h b/Cantera/src/kinetics/AqueousKinetics.h index bcdd1d9e7..a23bc0626 100644 --- a/Cantera/src/kinetics/AqueousKinetics.h +++ b/Cantera/src/kinetics/AqueousKinetics.h @@ -3,9 +3,9 @@ * * @ingroup chemkinetics * - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2009/02/11 01:50:57 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/EdgeKinetics.h b/Cantera/src/kinetics/EdgeKinetics.h index c5e2168ca..b19e7b3e6 100644 --- a/Cantera/src/kinetics/EdgeKinetics.h +++ b/Cantera/src/kinetics/EdgeKinetics.h @@ -5,9 +5,9 @@ * @ingroup electrochem */ -/* $Author: hkmoffa $ - * $Revision: 1.4 $ - * $Date: 2008/12/16 20:32:18 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/Enhanced3BConc.h b/Cantera/src/kinetics/Enhanced3BConc.h index 7d927eafd..0aa892a64 100644 --- a/Cantera/src/kinetics/Enhanced3BConc.h +++ b/Cantera/src/kinetics/Enhanced3BConc.h @@ -2,9 +2,9 @@ * @file Enhanced3BConc.h */ -/* $Author: dggoodwin $ - * $Date: 2007/05/04 14:27:23 $ - * $Revision: 1.1 $ +/* $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/FalloffFactory.cpp b/Cantera/src/kinetics/FalloffFactory.cpp index 1e9108df7..fa3f41cf0 100644 --- a/Cantera/src/kinetics/FalloffFactory.cpp +++ b/Cantera/src/kinetics/FalloffFactory.cpp @@ -2,9 +2,9 @@ * @file FalloffFactory.cpp */ -/* $Author: hkmoffa $ - * $Date: 2008/12/29 21:34:08 $ - * $Revision: 1.6 $ +/* $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/FalloffFactory.h b/Cantera/src/kinetics/FalloffFactory.h index fd1605cd7..cbf3a88af 100644 --- a/Cantera/src/kinetics/FalloffFactory.h +++ b/Cantera/src/kinetics/FalloffFactory.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2008/12/29 21:34:08 $ - * $Revision: 1.4 $ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/FalloffMgr.h b/Cantera/src/kinetics/FalloffMgr.h index d09cff962..a36d7bcce 100644 --- a/Cantera/src/kinetics/FalloffMgr.h +++ b/Cantera/src/kinetics/FalloffMgr.h @@ -1,9 +1,9 @@ /** * @file FalloffMgr.h * - * $Author: dggoodwin $ - * $Date: 2007/05/10 03:28:32 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/GasKinetics.h b/Cantera/src/kinetics/GasKinetics.h index bd2c55d0b..7dee80dcd 100644 --- a/Cantera/src/kinetics/GasKinetics.h +++ b/Cantera/src/kinetics/GasKinetics.h @@ -3,9 +3,9 @@ * * @ingroup chemkinetics * - * $Author: hkmoffa $ - * $Revision: 1.8 $ - * $Date: 2008/12/29 21:34:08 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/GasKineticsWriter.h b/Cantera/src/kinetics/GasKineticsWriter.h index fe3be0de0..88b07a213 100644 --- a/Cantera/src/kinetics/GasKineticsWriter.h +++ b/Cantera/src/kinetics/GasKineticsWriter.h @@ -2,9 +2,9 @@ * * @file GasKineticsWriter.h * - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/17 17:09:37 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/Group.cpp b/Cantera/src/kinetics/Group.cpp index b799def71..4c58727d0 100644 --- a/Cantera/src/kinetics/Group.cpp +++ b/Cantera/src/kinetics/Group.cpp @@ -3,9 +3,9 @@ * * Implementation file for the Group class used in reaction path analysis. * - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2008/12/29 21:34:08 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/Group.h b/Cantera/src/kinetics/Group.h index c1e2ebdca..82e13b74f 100644 --- a/Cantera/src/kinetics/Group.h +++ b/Cantera/src/kinetics/Group.h @@ -1,9 +1,9 @@ /** * @file Group.h * - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ + * $Author$ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/kinetics/ImplicitChem.cpp b/Cantera/src/kinetics/ImplicitChem.cpp index 57cad99db..5a05e2f76 100644 --- a/Cantera/src/kinetics/ImplicitChem.cpp +++ b/Cantera/src/kinetics/ImplicitChem.cpp @@ -2,9 +2,9 @@ * @file ImplicitChem.cpp */ -/* $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ImplicitChem.h b/Cantera/src/kinetics/ImplicitChem.h index 7d17c06b3..96180bdee 100644 --- a/Cantera/src/kinetics/ImplicitChem.h +++ b/Cantera/src/kinetics/ImplicitChem.h @@ -1,9 +1,9 @@ /** * @file ImplicitChem.h * - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ImplicitSurfChem.cpp b/Cantera/src/kinetics/ImplicitSurfChem.cpp index 1801b7001..28e82d45a 100644 --- a/Cantera/src/kinetics/ImplicitSurfChem.cpp +++ b/Cantera/src/kinetics/ImplicitSurfChem.cpp @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.4 $ - * $Date: 2007/08/29 19:57:48 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ImplicitSurfChem.h b/Cantera/src/kinetics/ImplicitSurfChem.h index 57b233998..adc0fcdce 100644 --- a/Cantera/src/kinetics/ImplicitSurfChem.h +++ b/Cantera/src/kinetics/ImplicitSurfChem.h @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2007/08/23 21:43:07 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 261947bf9..3de46a1f1 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -4,9 +4,9 @@ * @ingroup chemkinetics */ /* - * $Author: hkmoffa $ - * $Revision: 1.11 $ - * $Date: 2008/12/17 17:09:37 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/Kinetics.cpp b/Cantera/src/kinetics/Kinetics.cpp index f7ac93ff7..38ea75fe0 100644 --- a/Cantera/src/kinetics/Kinetics.cpp +++ b/Cantera/src/kinetics/Kinetics.cpp @@ -7,8 +7,8 @@ * Kinetics managers calculate rates of progress of species due to homogeneous or heterogeneous kinetics. */ /* - * $Date: 2008/12/16 20:32:18 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ */ // Copyright 2001-2004 California Institute of Technology diff --git a/Cantera/src/kinetics/Kinetics.h b/Cantera/src/kinetics/Kinetics.h index 69c6ebca8..25ca5305f 100644 --- a/Cantera/src/kinetics/Kinetics.h +++ b/Cantera/src/kinetics/Kinetics.h @@ -4,8 +4,8 @@ * module documentation (see \ref kineticsmgr and class * \link Cantera::Kinetics Kinetics\endlink). * - * $Date: 2008/12/16 20:32:18 $ - * $Revision: 1.8 $ + * $Date$ + * $Revision$ */ // Copyright 2001-2004 California Institute of Technology diff --git a/Cantera/src/kinetics/KineticsFactory.cpp b/Cantera/src/kinetics/KineticsFactory.cpp index 142bdc36f..0d811f63e 100644 --- a/Cantera/src/kinetics/KineticsFactory.cpp +++ b/Cantera/src/kinetics/KineticsFactory.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.4 $ - * $Date: 2009/02/11 20:01:45 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/KineticsFactory.h b/Cantera/src/kinetics/KineticsFactory.h index 4fdc9c6be..f4336c96d 100644 --- a/Cantera/src/kinetics/KineticsFactory.h +++ b/Cantera/src/kinetics/KineticsFactory.h @@ -3,9 +3,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2009/02/11 01:50:58 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/Makefile.in b/Cantera/src/kinetics/Makefile.in index 19700d7d6..cfd625c43 100644 --- a/Cantera/src/kinetics/Makefile.in +++ b/Cantera/src/kinetics/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/02/11 01:50:58 $ -# $Revision: 1.10 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/kinetics/RateCoeffMgr.h b/Cantera/src/kinetics/RateCoeffMgr.h index fba1ae9d4..792c14617 100644 --- a/Cantera/src/kinetics/RateCoeffMgr.h +++ b/Cantera/src/kinetics/RateCoeffMgr.h @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ReactionData.h b/Cantera/src/kinetics/ReactionData.h index 6c7665a31..99541ed14 100644 --- a/Cantera/src/kinetics/ReactionData.h +++ b/Cantera/src/kinetics/ReactionData.h @@ -3,9 +3,9 @@ * */ /* - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2007/06/04 23:05:07 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ReactionPath.cpp b/Cantera/src/kinetics/ReactionPath.cpp index 4b2feb41f..af42f38a2 100644 --- a/Cantera/src/kinetics/ReactionPath.cpp +++ b/Cantera/src/kinetics/ReactionPath.cpp @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.2 $ - * $Date: 2008/02/05 23:36:12 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ReactionPath.h b/Cantera/src/kinetics/ReactionPath.h index 5100648b7..f2ccf67d6 100644 --- a/Cantera/src/kinetics/ReactionPath.h +++ b/Cantera/src/kinetics/ReactionPath.h @@ -3,9 +3,9 @@ * * Classes for reaction path analysis. * - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ReactionStoichMgr.cpp b/Cantera/src/kinetics/ReactionStoichMgr.cpp index dca9fc3b5..67f09f37a 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.cpp +++ b/Cantera/src/kinetics/ReactionStoichMgr.cpp @@ -5,9 +5,9 @@ /// //------------------------------------------------ -// $Author: dggoodwin $ -// $Revision: 1.1 $ -// $Date: 2007/05/04 15:48:44 $ +// $Author$ +// $Revision$ +// $Date$ // turn off warnings under Windows #ifdef WIN32 diff --git a/Cantera/src/kinetics/ReactionStoichMgr.h b/Cantera/src/kinetics/ReactionStoichMgr.h index d8121d700..203bfc5e4 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.h +++ b/Cantera/src/kinetics/ReactionStoichMgr.h @@ -5,9 +5,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2007/06/12 14:20:02 $ + * $Author$ + * $Revision$ + * $Date$ */ #ifndef CT_RXN_STOICH diff --git a/Cantera/src/kinetics/RxnRates.h b/Cantera/src/kinetics/RxnRates.h index a17f549d7..44f0c6a70 100644 --- a/Cantera/src/kinetics/RxnRates.h +++ b/Cantera/src/kinetics/RxnRates.h @@ -3,9 +3,9 @@ * */ -/* $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/StoichManager.h b/Cantera/src/kinetics/StoichManager.h index d699c68d9..826ae9ee8 100644 --- a/Cantera/src/kinetics/StoichManager.h +++ b/Cantera/src/kinetics/StoichManager.h @@ -1,9 +1,9 @@ /** * @file StoichManager.h * - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2007/05/17 21:17:16 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/ThirdBodyMgr.h b/Cantera/src/kinetics/ThirdBodyMgr.h index 63ccea4f8..33ab92c22 100644 --- a/Cantera/src/kinetics/ThirdBodyMgr.h +++ b/Cantera/src/kinetics/ThirdBodyMgr.h @@ -1,9 +1,9 @@ /** * @file ThirdBodyMgr.h * - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:27:23 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/kinetics/importKinetics.cpp b/Cantera/src/kinetics/importKinetics.cpp index 7641bdd9b..5313286ab 100644 --- a/Cantera/src/kinetics/importKinetics.cpp +++ b/Cantera/src/kinetics/importKinetics.cpp @@ -10,9 +10,9 @@ * from the ctml tree structures. */ -/* $Author: hkmoffa $ - * $Revision: 1.10 $ - * $Date: 2009/03/13 03:23:20 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/kinetics/importKinetics.h b/Cantera/src/kinetics/importKinetics.h index 8735ac18d..404937bc7 100644 --- a/Cantera/src/kinetics/importKinetics.h +++ b/Cantera/src/kinetics/importKinetics.h @@ -10,9 +10,9 @@ * from the ctml tree structures. */ /* - * $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2007/06/04 23:09:19 $ + * $Author$ + * $Revision$ + * $Date$ * */ diff --git a/Cantera/src/kinetics/reaction_defs.h b/Cantera/src/kinetics/reaction_defs.h index 8e6123915..eb36dc544 100644 --- a/Cantera/src/kinetics/reaction_defs.h +++ b/Cantera/src/kinetics/reaction_defs.h @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Date: 2007/05/04 14:27:24 $ - * $Revision: 1.1 $ + * $Author$ + * $Date$ + * $Revision$ * */ diff --git a/Cantera/src/kinetics/solveSP.cpp b/Cantera/src/kinetics/solveSP.cpp index a91f0a3c9..a44757365 100644 --- a/Cantera/src/kinetics/solveSP.cpp +++ b/Cantera/src/kinetics/solveSP.cpp @@ -2,7 +2,7 @@ * @file: solveSP.cpp Implicit surface site concentration solver */ /* - * $Id: solveSP.cpp,v 1.4 2008/12/17 17:09:37 hkmoffa Exp $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/kinetics/solveSP.h b/Cantera/src/kinetics/solveSP.h index 7caf9b334..f4d679d3e 100644 --- a/Cantera/src/kinetics/solveSP.h +++ b/Cantera/src/kinetics/solveSP.h @@ -4,7 +4,7 @@ * (see \ref chemkinetics and class \link Cantera::solveSP solveSP\endlink). */ /* - * $Id: solveSP.h,v 1.3 2007/12/30 04:19:38 dggoodwin Exp $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/ArrayViewer.h b/Cantera/src/numerics/ArrayViewer.h index cc6bcfbe5..112648530 100755 --- a/Cantera/src/numerics/ArrayViewer.h +++ b/Cantera/src/numerics/ArrayViewer.h @@ -4,9 +4,9 @@ * Header file for class ArrayViewer */ -/* $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:40:26 $ +/* $Author$ + * $Revision$ + * $Date$ * */ diff --git a/Cantera/src/numerics/BandMatrix.h b/Cantera/src/numerics/BandMatrix.h index 3d5512108..d3f7fdd3e 100755 --- a/Cantera/src/numerics/BandMatrix.h +++ b/Cantera/src/numerics/BandMatrix.h @@ -5,9 +5,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:40:26 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/numerics/CVodeInt.cpp b/Cantera/src/numerics/CVodeInt.cpp index 74e77b4ec..658094a5e 100644 --- a/Cantera/src/numerics/CVodeInt.cpp +++ b/Cantera/src/numerics/CVodeInt.cpp @@ -1,7 +1,7 @@ /** * @file CVodeInt.cpp * - * $Id: CVodeInt.cpp,v 1.1 2009/07/17 15:32:51 hkmoffa Exp $ + * $Id$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/numerics/CVodeInt.h b/Cantera/src/numerics/CVodeInt.h index 7a909ff39..ac1836b1a 100644 --- a/Cantera/src/numerics/CVodeInt.h +++ b/Cantera/src/numerics/CVodeInt.h @@ -2,9 +2,9 @@ * @file CVodeInt.h */ -/* $Author: hkmoffa $ - * $Date: 2009/07/17 15:32:51 $ - * $Revision: 1.1 $ +/* $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/numerics/CVodesIntegrator.h b/Cantera/src/numerics/CVodesIntegrator.h index a72a8ff12..99a0a9cbb 100644 --- a/Cantera/src/numerics/CVodesIntegrator.h +++ b/Cantera/src/numerics/CVodesIntegrator.h @@ -3,8 +3,8 @@ */ /* - * $Date: 2009/03/27 21:32:33 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ */ // Copyright 2005 California Institute of Technology diff --git a/Cantera/src/numerics/DAE_Solver.h b/Cantera/src/numerics/DAE_Solver.h index 332950a0c..4d570cca7 100644 --- a/Cantera/src/numerics/DAE_Solver.h +++ b/Cantera/src/numerics/DAE_Solver.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/03/27 23:39:26 $ - * $Revision: 1.4 $ + * $Date$ + * $Revision$ * * Copyright 2006 California Institute of Technology * diff --git a/Cantera/src/numerics/DASPK.cpp b/Cantera/src/numerics/DASPK.cpp index 08e75495c..301131946 100755 --- a/Cantera/src/numerics/DASPK.cpp +++ b/Cantera/src/numerics/DASPK.cpp @@ -3,8 +3,8 @@ * */ /* - * $Date: 2009/03/27 23:39:26 $ - * $Revision: 1.2 $ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/numerics/DASPK.h b/Cantera/src/numerics/DASPK.h index 1ef8c80e2..7ae5ccc0c 100755 --- a/Cantera/src/numerics/DASPK.h +++ b/Cantera/src/numerics/DASPK.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/03/27 23:39:26 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index 0473b8885..613bb948b 100755 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -5,9 +5,9 @@ */ /* - * $Author: dggoodwin $ - * $Date: 2008/02/05 23:36:12 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * */ diff --git a/Cantera/src/numerics/Func1.h b/Cantera/src/numerics/Func1.h index b6a6b2504..fa3e6b23f 100644 --- a/Cantera/src/numerics/Func1.h +++ b/Cantera/src/numerics/Func1.h @@ -1,9 +1,9 @@ /** * @file Func1.h * - * $Author: hkmoffa $ - * $Date: 2009/03/23 23:25:31 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/numerics/IDA_Solver.h b/Cantera/src/numerics/IDA_Solver.h index d981a850f..59546d991 100644 --- a/Cantera/src/numerics/IDA_Solver.h +++ b/Cantera/src/numerics/IDA_Solver.h @@ -5,9 +5,9 @@ * Header file for class IDA_Solver */ -/* $Author: hkmoffa $ - * $Date: 2008/04/08 20:19:27 $ - * $Revision: 1.3 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2006 California Institute of Technology * diff --git a/Cantera/src/numerics/Integrator.h b/Cantera/src/numerics/Integrator.h index 2006f62e8..6b498dc0a 100644 --- a/Cantera/src/numerics/Integrator.h +++ b/Cantera/src/numerics/Integrator.h @@ -1,9 +1,9 @@ /** * @file Integrator.h * - * $Author: hkmoffa $ - * $Date: 2009/05/13 21:49:11 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * */ diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index 39c86c8de..bffd2a159 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/07/17 15:32:51 $ -# $Revision: 1.13 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index d8200fd00..caae05959 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/03/27 21:32:33 $ - * $Revision: 1.5 $ + * $Date$ + * $Revision$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index e51819965..420ce23e1 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/02/14 18:02:22 $ - * $Revision: 1.4 $ + * $Date$ + * $Revision$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index 03b30a0d9..ec61bd2d2 100755 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -3,8 +3,8 @@ * */ /* - * $Date: 2009/02/11 19:57:24 $ - * $Revision: 1.2 $ + * $Date$ + * $Revision$ */ // Copyright 2006 California Institute of Technology diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 124534fe4..18168c055 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -3,8 +3,8 @@ * */ /* - * $Revision: 1.2 $ - * $Date: 2009/03/03 17:55:25 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 52f950d29..daa3bb6aa 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -5,8 +5,8 @@ */ /* - * $Date: 2009/04/02 14:24:05 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ * */ /* diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 35d3e86a3..8b34c083f 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -3,8 +3,8 @@ * */ /* - * $Revision: 1.1 $ - * $Date: 2009/01/27 15:59:13 $ + * $Revision$ + * $Date$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index 26de64517..d6c767952 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -4,8 +4,8 @@ */ /* - * $Date: 2009/03/03 21:20:32 $ - * $Revision: 1.2 $ + * $Date$ + * $Revision$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index c3dda9959..0b5a6da3a 100755 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -2,9 +2,9 @@ * @file ctlapack.h */ -/* $Author: dggoodwin $ - * $Revision: 1.2 $ - * $Date: 2008/02/05 23:36:12 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology. diff --git a/Cantera/src/numerics/funcs.cpp b/Cantera/src/numerics/funcs.cpp index c1276244d..81ce55810 100755 --- a/Cantera/src/numerics/funcs.cpp +++ b/Cantera/src/numerics/funcs.cpp @@ -3,9 +3,9 @@ * numerical functions. */ /* - * $Author: hkmoffa $ - * $Date: 2008/07/30 16:48:25 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001-2003 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/numerics/funcs.h b/Cantera/src/numerics/funcs.h index b12f80306..8774f195e 100644 --- a/Cantera/src/numerics/funcs.h +++ b/Cantera/src/numerics/funcs.h @@ -3,9 +3,9 @@ * numerical functions. */ /* - * $Author: hkmoffa $ - * $Date: 2008/07/30 16:48:25 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001-2003 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/numerics/polyfit.h b/Cantera/src/numerics/polyfit.h index 99645f83f..b8436ae34 100755 --- a/Cantera/src/numerics/polyfit.h +++ b/Cantera/src/numerics/polyfit.h @@ -2,9 +2,9 @@ * @file polyfit.h C interface for Fortran DPOLFT subroutine */ /* - * $Author: hkmoffa $ - * $Date: 2008/07/30 16:48:25 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001-2003 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/numerics/sort.cpp b/Cantera/src/numerics/sort.cpp index 66120c70c..ed6fc21c4 100755 --- a/Cantera/src/numerics/sort.cpp +++ b/Cantera/src/numerics/sort.cpp @@ -1,7 +1,7 @@ /** * @file sort.cpp * - * $Id: sort.cpp,v 1.1 2007/05/04 14:40:27 dggoodwin Exp $ + * $Id$ */ #ifdef WIN32 diff --git a/Cantera/src/numerics/sort.h b/Cantera/src/numerics/sort.h index 1e33851e5..e83ab53b0 100755 --- a/Cantera/src/numerics/sort.h +++ b/Cantera/src/numerics/sort.h @@ -1,7 +1,7 @@ /** * @file sort.h * - * $Id: sort.h,v 1.1 2007/05/04 14:40:27 dggoodwin Exp $ + * $Id$ */ #ifndef CT_SORT_H diff --git a/Cantera/src/oneD/Domain1D.h b/Cantera/src/oneD/Domain1D.h index 7d57583ec..256432431 100644 --- a/Cantera/src/oneD/Domain1D.h +++ b/Cantera/src/oneD/Domain1D.h @@ -1,9 +1,9 @@ /** * @file Domain1D.h * - * $Author: hkmoffa $ - * $Date: 2009/05/31 16:24:35 $ - * $Revision: 1.26 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/oneD/Inlet1D.h b/Cantera/src/oneD/Inlet1D.h index b12fc99a3..373aaafde 100644 --- a/Cantera/src/oneD/Inlet1D.h +++ b/Cantera/src/oneD/Inlet1D.h @@ -6,9 +6,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.20 $ - * $Date: 2007/05/04 14:41:27 $ + * $Author$ + * $Revision$ + * $Date$ * * Copyright 2002-3 California Institute of Technology */ diff --git a/Cantera/src/oneD/Makefile.in b/Cantera/src/oneD/Makefile.in index 9afea4ab5..ad4c6a0a5 100644 --- a/Cantera/src/oneD/Makefile.in +++ b/Cantera/src/oneD/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.16 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/oneD/MultiJac.cpp b/Cantera/src/oneD/MultiJac.cpp index eead1da28..69003381c 100644 --- a/Cantera/src/oneD/MultiJac.cpp +++ b/Cantera/src/oneD/MultiJac.cpp @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2008/12/17 17:13:03 $ - * $Revision: 1.13 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/oneD/MultiJac.h b/Cantera/src/oneD/MultiJac.h index a91ea804e..a99a24a09 100644 --- a/Cantera/src/oneD/MultiJac.h +++ b/Cantera/src/oneD/MultiJac.h @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Date: 2007/05/04 14:41:27 $ - * $Revision: 1.3 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/oneD/MultiNewton.cpp b/Cantera/src/oneD/MultiNewton.cpp index c9cb239aa..e85f4da54 100644 --- a/Cantera/src/oneD/MultiNewton.cpp +++ b/Cantera/src/oneD/MultiNewton.cpp @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2008/12/17 17:13:03 $ - * $Revision: 1.20 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/oneD/MultiNewton.h b/Cantera/src/oneD/MultiNewton.h index 95c90c516..8a4298981 100644 --- a/Cantera/src/oneD/MultiNewton.h +++ b/Cantera/src/oneD/MultiNewton.h @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Date: 2006/11/27 21:43:34 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/oneD/Resid1D.h b/Cantera/src/oneD/Resid1D.h index 34dcda18e..58f089ba7 100644 --- a/Cantera/src/oneD/Resid1D.h +++ b/Cantera/src/oneD/Resid1D.h @@ -1,9 +1,9 @@ /** * @file Resid1D.h * - * $Author: dggoodwin $ - * $Date: 2006/11/27 21:43:34 $ - * $Revision: 1.4 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/oneD/Solid1D.cpp b/Cantera/src/oneD/Solid1D.cpp index c9797b7fa..4f6be4b61 100644 --- a/Cantera/src/oneD/Solid1D.cpp +++ b/Cantera/src/oneD/Solid1D.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.4 $ - * $Date: 2004/08/28 16:12:41 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2003 California Institute of Technology diff --git a/Cantera/src/oneD/Solid1D.h b/Cantera/src/oneD/Solid1D.h index 70c4cf64f..c0f32964f 100644 --- a/Cantera/src/oneD/Solid1D.h +++ b/Cantera/src/oneD/Solid1D.h @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2006/11/27 21:43:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/oneD/StFlow.cpp b/Cantera/src/oneD/StFlow.cpp index 29fc73328..16d39d5c4 100644 --- a/Cantera/src/oneD/StFlow.cpp +++ b/Cantera/src/oneD/StFlow.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.32 $ - * $Date: 2007/05/04 14:41:27 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/oneD/StFlow.h b/Cantera/src/oneD/StFlow.h index ffab5c402..83437325d 100644 --- a/Cantera/src/oneD/StFlow.h +++ b/Cantera/src/oneD/StFlow.h @@ -4,9 +4,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.18 $ - * $Date: 2007/05/22 20:16:47 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/oneD/boundaries1D.cpp b/Cantera/src/oneD/boundaries1D.cpp index 678f07f6f..d788cf99d 100644 --- a/Cantera/src/oneD/boundaries1D.cpp +++ b/Cantera/src/oneD/boundaries1D.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.18 $ - * $Date: 2006/11/27 21:43:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2002-3 California Institute of Technology diff --git a/Cantera/src/spectra/Makefile.in b/Cantera/src/spectra/Makefile.in index e612622e9..fc124f288 100644 --- a/Cantera/src/spectra/Makefile.in +++ b/Cantera/src/spectra/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/04/04 03:08:28 $ -# $Revision: 1.7 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2007 California Institute of Technology # diff --git a/Cantera/src/thermo/AdsorbateThermo.h b/Cantera/src/thermo/AdsorbateThermo.h index 88457697e..1d8230ffd 100644 --- a/Cantera/src/thermo/AdsorbateThermo.h +++ b/Cantera/src/thermo/AdsorbateThermo.h @@ -8,9 +8,9 @@ * */ -/* $Author: dggoodwin $ - * $Revision: 1.2 $ - * $Date: 2007/12/24 15:32:30 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2007 California Institute of Technology diff --git a/Cantera/src/thermo/ConstCpPoly.cpp b/Cantera/src/thermo/ConstCpPoly.cpp index 868fafea9..2cfcd2a37 100644 --- a/Cantera/src/thermo/ConstCpPoly.cpp +++ b/Cantera/src/thermo/ConstCpPoly.cpp @@ -5,9 +5,9 @@ * \link Cantera::ConstCpPoly ConstCpPoly \endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/17 17:04:46 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/ConstCpPoly.h b/Cantera/src/thermo/ConstCpPoly.h index b46ccd8bb..7577769c5 100644 --- a/Cantera/src/thermo/ConstCpPoly.h +++ b/Cantera/src/thermo/ConstCpPoly.h @@ -5,9 +5,9 @@ * \link Cantera::ConstCpPoly ConstCpPoly\endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/13 01:59:49 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/ConstDensityThermo.cpp b/Cantera/src/thermo/ConstDensityThermo.cpp index a8d442957..b0adfaca1 100644 --- a/Cantera/src/thermo/ConstDensityThermo.cpp +++ b/Cantera/src/thermo/ConstDensityThermo.cpp @@ -5,7 +5,7 @@ \endlink). */ /* - * $Id: ConstDensityThermo.cpp,v 1.5 2008/12/17 17:04:47 hkmoffa Exp $ + * $Id$ * * Copyright 2002 California Institute of Technology */ diff --git a/Cantera/src/thermo/ConstDensityThermo.h b/Cantera/src/thermo/ConstDensityThermo.h index 809323156..f462516c5 100644 --- a/Cantera/src/thermo/ConstDensityThermo.h +++ b/Cantera/src/thermo/ConstDensityThermo.h @@ -4,9 +4,9 @@ * (see \ref thermoprops and \link Cantera::ConstDensityThermo ConstDensityThermo\endlink). */ /* - * $Author: hkmoffa $ - * $Date: 2008/12/10 16:42:48 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/thermo/Constituents.cpp b/Cantera/src/thermo/Constituents.cpp index 54a9e220f..2d42d9564 100644 --- a/Cantera/src/thermo/Constituents.cpp +++ b/Cantera/src/thermo/Constituents.cpp @@ -5,8 +5,8 @@ */ /* - * $Date: 2009/01/04 21:28:02 $ - * $Revision: 1.7 $ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h index e386ee935..a38622906 100644 --- a/Cantera/src/thermo/Constituents.h +++ b/Cantera/src/thermo/Constituents.h @@ -5,8 +5,8 @@ */ /* - * $Date: 2009/02/23 20:41:03 $ - * $Revision: 1.7 $ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/Crystal.h b/Cantera/src/thermo/Crystal.h index efe4a8c3b..3e6652137 100644 --- a/Cantera/src/thermo/Crystal.h +++ b/Cantera/src/thermo/Crystal.h @@ -1,9 +1,9 @@ /** * @file Crystal.h * - * $Author: dggoodwin $ - * $Date: 2007/05/04 14:02:40 $ - * $Revision: 1.1 $ + * $Author$ + * $Date$ + * $Revision$ */ #ifndef CT_CRYSTAL_H #define CT_CRYSTAL_H diff --git a/Cantera/src/thermo/DebyeHuckel.cpp b/Cantera/src/thermo/DebyeHuckel.cpp index 9c4d78919..91546cf6d 100644 --- a/Cantera/src/thermo/DebyeHuckel.cpp +++ b/Cantera/src/thermo/DebyeHuckel.cpp @@ -13,7 +13,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: DebyeHuckel.cpp,v 1.33 2009/03/27 00:38:56 hkmoffa Exp $ + * $Id$ */ //! Max function #ifndef MAX diff --git a/Cantera/src/thermo/DebyeHuckel.h b/Cantera/src/thermo/DebyeHuckel.h index 1467ec860..16e3b5dc8 100644 --- a/Cantera/src/thermo/DebyeHuckel.h +++ b/Cantera/src/thermo/DebyeHuckel.h @@ -15,7 +15,7 @@ */ /* - * $Id: DebyeHuckel.h,v 1.31 2009/03/27 00:38:57 hkmoffa Exp $ + * $Id$ */ #ifndef CT_DEBYEHUCKEL_H diff --git a/Cantera/src/thermo/EdgePhase.h b/Cantera/src/thermo/EdgePhase.h index 8acafc6bf..176e9afb8 100644 --- a/Cantera/src/thermo/EdgePhase.h +++ b/Cantera/src/thermo/EdgePhase.h @@ -4,9 +4,9 @@ * between two surfaces (see \ref thermoprops and \link Cantera::EdgePhase EdgePhase\endlink). */ -/* $Author: hkmoffa $ - * $Date: 2008/10/08 22:11:08 $ - * $Revision: 1.3 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/thermo/Elements.cpp b/Cantera/src/thermo/Elements.cpp index 073e3c443..61e4a260b 100644 --- a/Cantera/src/thermo/Elements.cpp +++ b/Cantera/src/thermo/Elements.cpp @@ -9,9 +9,9 @@ /**************************************************************************** * $RCSfile: Elements.cpp,v $ - * $Author: hkmoffa $ - * $Date: 2009/03/13 03:21:34 $ - * $Revision: 1.7 $ + * $Author$ + * $Date$ + * $Revision$ * * ****************************************************************************/ diff --git a/Cantera/src/thermo/Elements.h b/Cantera/src/thermo/Elements.h index 298450eb3..148cf2abf 100644 --- a/Cantera/src/thermo/Elements.h +++ b/Cantera/src/thermo/Elements.h @@ -7,9 +7,9 @@ */ /*********************************************************************** * $RCSfile: Elements.h,v $ - * $Author: hkmoffa $ - * $Date: 2008/12/04 02:02:45 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ ***********************************************************************/ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/GeneralSpeciesThermo.cpp b/Cantera/src/thermo/GeneralSpeciesThermo.cpp index 683ae3c74..b96fd7bbe 100644 --- a/Cantera/src/thermo/GeneralSpeciesThermo.cpp +++ b/Cantera/src/thermo/GeneralSpeciesThermo.cpp @@ -5,7 +5,7 @@ * \link Cantera::GeneralSpeciesThermo GeneralSpeciesThermo\endlink). */ /* - * $Id: GeneralSpeciesThermo.cpp,v 1.10 2008/12/13 01:59:49 hkmoffa Exp $ + * $Id$ */ // Copyright 2001-2004 California Institute of Technology diff --git a/Cantera/src/thermo/GeneralSpeciesThermo.h b/Cantera/src/thermo/GeneralSpeciesThermo.h index 4cbe211f3..0697d7e9d 100644 --- a/Cantera/src/thermo/GeneralSpeciesThermo.h +++ b/Cantera/src/thermo/GeneralSpeciesThermo.h @@ -8,9 +8,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.7 $ - * $Date: 2008/12/13 01:59:49 $ + * $Author$ + * $Revision$ + * $Date$ */ #ifndef CT_GENERALSPECIESTHERMO_H diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 4019c3886..e45bd5243 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -17,8 +17,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/03/03 21:08:31 $ - * $Revision: 1.3 $ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index c9d27094f..59b456232 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -17,7 +17,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: GibbsExcessVPSSTP.h,v 1.3 2009/03/03 21:08:31 hkmoffa Exp $ + * $Id$ */ #ifndef CT_GIBBSEXCESSVPSSTP_H diff --git a/Cantera/src/thermo/HMWSoln.cpp b/Cantera/src/thermo/HMWSoln.cpp index c221ab0cf..073eeaddf 100644 --- a/Cantera/src/thermo/HMWSoln.cpp +++ b/Cantera/src/thermo/HMWSoln.cpp @@ -18,7 +18,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: HMWSoln.cpp,v 1.53 2009/03/27 00:38:57 hkmoffa Exp $ + * $Id$ */ //@{ #ifndef MAX diff --git a/Cantera/src/thermo/HMWSoln.h b/Cantera/src/thermo/HMWSoln.h index 7b146f554..40cce6f86 100644 --- a/Cantera/src/thermo/HMWSoln.h +++ b/Cantera/src/thermo/HMWSoln.h @@ -14,7 +14,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: HMWSoln.h,v 1.62 2009/03/27 00:38:57 hkmoffa Exp $ + * $Id$ */ #ifndef CT_HMWSOLN_H diff --git a/Cantera/src/thermo/HMWSoln_input.cpp b/Cantera/src/thermo/HMWSoln_input.cpp index 534684626..bca1ae93f 100644 --- a/Cantera/src/thermo/HMWSoln_input.cpp +++ b/Cantera/src/thermo/HMWSoln_input.cpp @@ -13,7 +13,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: HMWSoln_input.cpp,v 1.33 2009/01/29 02:07:05 hkmoffa Exp $ + * $Id$ */ #include "HMWSoln.h" diff --git a/Cantera/src/thermo/IdealGasPhase.cpp b/Cantera/src/thermo/IdealGasPhase.cpp index a07107628..b442f540b 100644 --- a/Cantera/src/thermo/IdealGasPhase.cpp +++ b/Cantera/src/thermo/IdealGasPhase.cpp @@ -7,7 +7,7 @@ * */ /* - * $Id: IdealGasPhase.cpp,v 1.3 2008/08/23 00:53:54 hkmoffa Exp $ + * $Id$ */ #ifdef WIN32 diff --git a/Cantera/src/thermo/IdealGasPhase.h b/Cantera/src/thermo/IdealGasPhase.h index c9d069943..cc676a8a4 100644 --- a/Cantera/src/thermo/IdealGasPhase.h +++ b/Cantera/src/thermo/IdealGasPhase.h @@ -6,9 +6,9 @@ * */ -/* $Author: hkmoffa $ - * $Date: 2009/07/05 18:07:18 $ - * $Revision: 1.5 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/thermo/IdealMolalSoln.cpp b/Cantera/src/thermo/IdealMolalSoln.cpp index 280e0060a..0c560636a 100644 --- a/Cantera/src/thermo/IdealMolalSoln.cpp +++ b/Cantera/src/thermo/IdealMolalSoln.cpp @@ -19,8 +19,8 @@ */ /* * - * $Date: 2009/03/27 00:51:38 $ - * $Revision: 1.27 $ + * $Date$ + * $Revision$ */ #include "IdealMolalSoln.h" diff --git a/Cantera/src/thermo/IdealMolalSoln.h b/Cantera/src/thermo/IdealMolalSoln.h index 4a5118762..737fe349a 100644 --- a/Cantera/src/thermo/IdealMolalSoln.h +++ b/Cantera/src/thermo/IdealMolalSoln.h @@ -19,9 +19,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/03/27 00:51:38 $ - * $Revision: 1.24 $ + * $Author$ + * $Date$ + * $Revision$ */ #ifndef CT_IDEALMOLALSOLN_H diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.cpp b/Cantera/src/thermo/IdealSolidSolnPhase.cpp index 5ca849645..ccc8aa17b 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.cpp +++ b/Cantera/src/thermo/IdealSolidSolnPhase.cpp @@ -5,7 +5,7 @@ * \link Cantera::IdealSolidSolnPhase IdealSolidSolnPhase\endlink). */ /* - * $Id: IdealSolidSolnPhase.cpp,v 1.11 2009/03/27 00:51:39 hkmoffa Exp $ + * $Id$ */ /* * Copywrite 2006 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.h b/Cantera/src/thermo/IdealSolidSolnPhase.h index 77df55a8d..a9f87b29c 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.h +++ b/Cantera/src/thermo/IdealSolidSolnPhase.h @@ -10,9 +10,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2009/03/27 00:51:39 $ - * $Revision: 1.18 $ + * $Author$ + * $Date$ + * $Revision$ */ /* * Copywrite 2006 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/thermo/IdealSolnGasVPSS.cpp b/Cantera/src/thermo/IdealSolnGasVPSS.cpp index 308d5f612..a3943247b 100644 --- a/Cantera/src/thermo/IdealSolnGasVPSS.cpp +++ b/Cantera/src/thermo/IdealSolnGasVPSS.cpp @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2008/09/16 14:38:13 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/IdealSolnGasVPSS.h b/Cantera/src/thermo/IdealSolnGasVPSS.h index be8623de0..4be4e7a09 100644 --- a/Cantera/src/thermo/IdealSolnGasVPSS.h +++ b/Cantera/src/thermo/IdealSolnGasVPSS.h @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2008/08/23 00:53:54 $ - * $Revision: 1.1 $ + * $Author$ + * $Date$ + * $Revision$ */ #ifndef CT_IDEALSOLNGASVPSS_H diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index bf39f3397..d848b7f97 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -17,8 +17,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/03/27 01:08:55 $ - * $Revision: 1.2 $ + * $Date$ + * $Revision$ */ #include "IonsFromNeutralVPSSTP.h" diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 66da9ddf0..955c88694 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -17,7 +17,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: $ + * $Id$ */ #ifndef CT_IONSFROMNEUTRALVPSSTP_H diff --git a/Cantera/src/thermo/LatticePhase.cpp b/Cantera/src/thermo/LatticePhase.cpp index 46a951e9c..00942edfb 100644 --- a/Cantera/src/thermo/LatticePhase.cpp +++ b/Cantera/src/thermo/LatticePhase.cpp @@ -8,7 +8,7 @@ * */ /* - * $Id: LatticePhase.cpp,v 1.8 2009/01/02 22:34:41 hkmoffa Exp $ + * $Id$ */ #include "config.h" diff --git a/Cantera/src/thermo/LatticePhase.h b/Cantera/src/thermo/LatticePhase.h index 465d28187..7c160560c 100644 --- a/Cantera/src/thermo/LatticePhase.h +++ b/Cantera/src/thermo/LatticePhase.h @@ -6,9 +6,9 @@ * (see \ref thermoprops and class \link Cantera::LatticePhase LatticePhase\endlink). * */ -/* $Author: hkmoffa $ - * $Date: 2008/12/13 01:59:49 $ - * $Revision: 1.7 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2005 California Institute of Technology * diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index e0e13dddf..e9671db02 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -2,7 +2,7 @@ * * @file LatticeSolidPhase.cpp * - * $Id: LatticeSolidPhase.cpp,v 1.4 2008/10/08 22:11:08 hkmoffa Exp $ + * $Id$ */ #ifdef WIN32 diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index 8f765e894..d97116f3b 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -7,9 +7,9 @@ */ -/* $Author: hkmoffa $ - * $Date: 2008/12/13 01:59:49 $ - * $Revision: 1.5 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2005 California Institute of Technology * diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index fee9e7dfc..b45d3eb44 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2009/03/03 21:08:31 $ -# $Revision: 1.30 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index c19956c1b..d2f6ebdce 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -12,8 +12,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/03/03 21:08:31 $ - * $Revision: 1.1 $ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/thermo/MetalPhase.h b/Cantera/src/thermo/MetalPhase.h index 3d4163252..32ad3431d 100644 --- a/Cantera/src/thermo/MetalPhase.h +++ b/Cantera/src/thermo/MetalPhase.h @@ -4,9 +4,9 @@ * */ -/* $Author: hkmoffa $ - * $Date: 2009/03/24 20:36:05 $ - * $Revision: 1.4 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2003 California Institute of Technology * diff --git a/Cantera/src/thermo/MineralEQ3.cpp b/Cantera/src/thermo/MineralEQ3.cpp index 849d03e32..1758f95de 100644 --- a/Cantera/src/thermo/MineralEQ3.cpp +++ b/Cantera/src/thermo/MineralEQ3.cpp @@ -14,7 +14,7 @@ */ /* - * $Id: MineralEQ3.cpp,v 1.2 2008/12/27 00:27:55 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/MineralEQ3.h b/Cantera/src/thermo/MineralEQ3.h index 83077d219..f75f28a9e 100644 --- a/Cantera/src/thermo/MineralEQ3.h +++ b/Cantera/src/thermo/MineralEQ3.h @@ -14,8 +14,8 @@ */ /* - * $Date: 2009/01/04 19:21:28 $ - * $Revision: 1.4 $ + * $Date$ + * $Revision$ */ #ifndef CT_MINERALEQ3_H diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp index c526ebcce..285289a9e 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.cpp +++ b/Cantera/src/thermo/MolalityVPSSTP.cpp @@ -17,9 +17,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/01/16 16:24:35 $ - * $Revision: 1.23 $ + * $Author$ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h index a635e3091..f9eb439d9 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.h +++ b/Cantera/src/thermo/MolalityVPSSTP.h @@ -17,7 +17,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: MolalityVPSSTP.h,v 1.20 2009/01/20 21:48:54 hkmoffa Exp $ + * $Id$ */ #ifndef CT_MOLALITYVPSSTP_H diff --git a/Cantera/src/thermo/Mu0Poly.cpp b/Cantera/src/thermo/Mu0Poly.cpp index 59cf05441..81cfc3333 100644 --- a/Cantera/src/thermo/Mu0Poly.cpp +++ b/Cantera/src/thermo/Mu0Poly.cpp @@ -6,9 +6,9 @@ * (see \ref spthermo and class \link Cantera::Mu0Poly Mu0Poly\endlink). */ /* - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/05/04 14:02:42 $ + * $Author$ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/thermo/Mu0Poly.h b/Cantera/src/thermo/Mu0Poly.h index ad926486f..b3eee75ba 100644 --- a/Cantera/src/thermo/Mu0Poly.h +++ b/Cantera/src/thermo/Mu0Poly.h @@ -6,9 +6,9 @@ * (see \ref spthermo and class \link Cantera::Mu0Poly Mu0Poly\endlink). */ -/* $Author: hkmoffa $ - * $Revision: 1.2 $ - * $Date: 2007/09/13 15:05:39 $ +/* $Author$ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/thermo/Nasa9Poly1.cpp b/Cantera/src/thermo/Nasa9Poly1.cpp index dc22c741a..61ecd735f 100644 --- a/Cantera/src/thermo/Nasa9Poly1.cpp +++ b/Cantera/src/thermo/Nasa9Poly1.cpp @@ -10,9 +10,9 @@ * This parameterization has one NASA temperature region. */ -/* $Author: hkmoffa $ - * $Revision: 1.4 $ - * $Date: 2007/12/27 19:09:38 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2007 Sandia National Laboratories diff --git a/Cantera/src/thermo/Nasa9Poly1.h b/Cantera/src/thermo/Nasa9Poly1.h index b3447851c..2b8bd5244 100644 --- a/Cantera/src/thermo/Nasa9Poly1.h +++ b/Cantera/src/thermo/Nasa9Poly1.h @@ -19,8 +19,8 @@ #define CT_NASA9POLY1_H /* - * $Revision: 1.4 $ - * $Date: 2009/01/04 19:21:28 $ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/thermo/Nasa9PolyMultiTempRegion.cpp b/Cantera/src/thermo/Nasa9PolyMultiTempRegion.cpp index 4de34c16f..47c5788e0 100644 --- a/Cantera/src/thermo/Nasa9PolyMultiTempRegion.cpp +++ b/Cantera/src/thermo/Nasa9PolyMultiTempRegion.cpp @@ -11,9 +11,9 @@ * This parameterization has one NASA temperature region. */ -/* $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2008/03/04 23:40:18 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2007 Sandia National Laboratories diff --git a/Cantera/src/thermo/Nasa9PolyMultiTempRegion.h b/Cantera/src/thermo/Nasa9PolyMultiTempRegion.h index b24e83cc9..b29d138f5 100644 --- a/Cantera/src/thermo/Nasa9PolyMultiTempRegion.h +++ b/Cantera/src/thermo/Nasa9PolyMultiTempRegion.h @@ -14,9 +14,9 @@ #ifndef CT_NASA9POLYMULTITEMPREGION_H #define CT_NASA9POLYMULTITEMPREGION_H -/* $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2007/12/27 19:09:38 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2007 Sandia National Laboratories diff --git a/Cantera/src/thermo/NasaPoly1.h b/Cantera/src/thermo/NasaPoly1.h index 17df3a245..60736ecca 100644 --- a/Cantera/src/thermo/NasaPoly1.h +++ b/Cantera/src/thermo/NasaPoly1.h @@ -14,9 +14,9 @@ #define CT_NASAPOLY1_H -/* $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/13 01:59:49 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/NasaPoly2.h b/Cantera/src/thermo/NasaPoly2.h index 0c542abf9..3e885f561 100644 --- a/Cantera/src/thermo/NasaPoly2.h +++ b/Cantera/src/thermo/NasaPoly2.h @@ -8,9 +8,9 @@ * Two zoned Nasa polynomial parameterization */ -/* $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/13 01:59:49 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/NasaThermo.h b/Cantera/src/thermo/NasaThermo.h index 438a6a71b..46cf02a71 100644 --- a/Cantera/src/thermo/NasaThermo.h +++ b/Cantera/src/thermo/NasaThermo.h @@ -7,8 +7,8 @@ */ /* - * $Revision: 1.7 $ - * $Date: 2009/01/04 19:21:28 $ + * $Revision$ + * $Date$ */ // Copyright 2003 California Institute of Technology diff --git a/Cantera/src/thermo/PDSS.cpp b/Cantera/src/thermo/PDSS.cpp index 64a5301b7..8409882fe 100644 --- a/Cantera/src/thermo/PDSS.cpp +++ b/Cantera/src/thermo/PDSS.cpp @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS.cpp,v 1.17 2009/01/04 06:34:19 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS.h b/Cantera/src/thermo/PDSS.h index ad989cfe8..0ca22eb30 100644 --- a/Cantera/src/thermo/PDSS.h +++ b/Cantera/src/thermo/PDSS.h @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS.h,v 1.16 2009/01/04 19:21:28 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PDSS_H diff --git a/Cantera/src/thermo/PDSSFactory.cpp b/Cantera/src/thermo/PDSSFactory.cpp index b8e87c564..b1c27f784 100644 --- a/Cantera/src/thermo/PDSSFactory.cpp +++ b/Cantera/src/thermo/PDSSFactory.cpp @@ -5,7 +5,7 @@ * (see \ref pdssthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink); */ /* - * $Id: PDSSFactory.cpp,v 1.2 2008/10/13 21:01:48 hkmoffa Exp $ + * $Id$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/PDSS_ConstVol.cpp b/Cantera/src/thermo/PDSS_ConstVol.cpp index 557be556f..5eff50510 100644 --- a/Cantera/src/thermo/PDSS_ConstVol.cpp +++ b/Cantera/src/thermo/PDSS_ConstVol.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_ConstVol.cpp,v 1.10 2009/01/04 06:34:20 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS_ConstVol.h b/Cantera/src/thermo/PDSS_ConstVol.h index eaea66322..87815b047 100644 --- a/Cantera/src/thermo/PDSS_ConstVol.h +++ b/Cantera/src/thermo/PDSS_ConstVol.h @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_ConstVol.h,v 1.6 2008/10/13 21:01:48 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PDSS_CONSTVOL_H diff --git a/Cantera/src/thermo/PDSS_HKFT.cpp b/Cantera/src/thermo/PDSS_HKFT.cpp index b78dc22bf..313e140d3 100644 --- a/Cantera/src/thermo/PDSS_HKFT.cpp +++ b/Cantera/src/thermo/PDSS_HKFT.cpp @@ -7,7 +7,7 @@ */ /* - * $Id: PDSS_HKFT.cpp,v 1.22 2009/03/13 03:21:34 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/thermo/PDSS_HKFT.h b/Cantera/src/thermo/PDSS_HKFT.h index 987005f72..99202cf7b 100644 --- a/Cantera/src/thermo/PDSS_HKFT.h +++ b/Cantera/src/thermo/PDSS_HKFT.h @@ -7,8 +7,8 @@ */ /* - * $Date: 2009/01/04 19:21:28 $ - * $Revision: 1.14 $ + * $Date$ + * $Revision$ */ /* diff --git a/Cantera/src/thermo/PDSS_IdealGas.cpp b/Cantera/src/thermo/PDSS_IdealGas.cpp index b34376aa3..48be63302 100644 --- a/Cantera/src/thermo/PDSS_IdealGas.cpp +++ b/Cantera/src/thermo/PDSS_IdealGas.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_IdealGas.cpp,v 1.8 2009/01/04 06:34:20 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS_IdealGas.h b/Cantera/src/thermo/PDSS_IdealGas.h index 909581ec0..5c2ae566d 100644 --- a/Cantera/src/thermo/PDSS_IdealGas.h +++ b/Cantera/src/thermo/PDSS_IdealGas.h @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_IdealGas.h,v 1.4 2008/10/13 21:01:48 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PDSS_IDEALGAS_H diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp index 1c598b04a..f768a4e89 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_IonsFromNeutral.cpp,v 1.8 2009/01/04 06:34:20 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.h b/Cantera/src/thermo/PDSS_IonsFromNeutral.h index 7399c6953..58d963a15 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.h +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.h @@ -11,7 +11,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_IdealGas.h,v 1.4 2008/10/13 21:01:48 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PDSS_IONSFROMNEUTRAL_H diff --git a/Cantera/src/thermo/PDSS_SSVol.cpp b/Cantera/src/thermo/PDSS_SSVol.cpp index 21ec884a6..c99a1a537 100644 --- a/Cantera/src/thermo/PDSS_SSVol.cpp +++ b/Cantera/src/thermo/PDSS_SSVol.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_SSVol.cpp,v 1.10 2009/01/04 06:34:20 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS_SSVol.h b/Cantera/src/thermo/PDSS_SSVol.h index 16dba893b..a2755fbf0 100644 --- a/Cantera/src/thermo/PDSS_SSVol.h +++ b/Cantera/src/thermo/PDSS_SSVol.h @@ -11,7 +11,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_SSVol.h,v 1.6 2008/10/13 21:01:48 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PDSS_SSVOL_H diff --git a/Cantera/src/thermo/PDSS_Water.cpp b/Cantera/src/thermo/PDSS_Water.cpp index 50beffd50..9a6170521 100644 --- a/Cantera/src/thermo/PDSS_Water.cpp +++ b/Cantera/src/thermo/PDSS_Water.cpp @@ -8,7 +8,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PDSS_Water.cpp,v 1.15 2008/12/22 22:40:44 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/PDSS_Water.h b/Cantera/src/thermo/PDSS_Water.h index 06425eb0b..e01871252 100644 --- a/Cantera/src/thermo/PDSS_Water.h +++ b/Cantera/src/thermo/PDSS_Water.h @@ -9,9 +9,9 @@ * Contract DE-AC04-94AL85000 with Sandia Corporation, the * U.S. Government retains certain rights in this software. */ -/* $Author: hkmoffa $ - * $Date: 2009/01/03 03:59:39 $ - * $Revision: 1.11 $ +/* $Author$ + * $Date$ + * $Revision$ */ #ifndef CT_PDSS_WATER_H diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index 12bdf7e90..8512f8aae 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -8,9 +8,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2008/02/03 20:59:18 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp b/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp index 12ee677af..f909098a6 100644 --- a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp +++ b/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp @@ -17,8 +17,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/03/27 01:08:55 $ - * $Revision: 1.2 $ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/thermo/PseudoBinaryVPSSTP.h b/Cantera/src/thermo/PseudoBinaryVPSSTP.h index b62053e8c..3cc9a9d5b 100644 --- a/Cantera/src/thermo/PseudoBinaryVPSSTP.h +++ b/Cantera/src/thermo/PseudoBinaryVPSSTP.h @@ -17,7 +17,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: PseudoBinaryVPSSTP.h,v 1.1 2009/03/03 21:08:31 hkmoffa Exp $ + * $Id$ */ #ifndef CT_PSEUDOBINARYVPSSTP_H diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 5ce137eee..a0748e18c 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -6,7 +6,7 @@ * and class \link Cantera::PureFluidPhase PureFluidPhase\endlink). */ /* - * $Id: PureFluidPhase.cpp,v 1.5 2009/03/13 03:21:34 hkmoffa Exp $ + * $Id$ */ #include "xml.h" #include "PureFluidPhase.h" diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index a1f674f38..2e2c626c1 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -10,9 +10,9 @@ * It inherits from ThermoPhase, but is built on top of the tpx package. */ -/* $Author: dggoodwin $ - * $Date: 2007/12/24 15:32:30 $ - * $Revision: 1.7 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2003 California Institute of Technology */ diff --git a/Cantera/src/thermo/SemiconductorPhase.h b/Cantera/src/thermo/SemiconductorPhase.h index c82fbbd8b..561d7df0b 100644 --- a/Cantera/src/thermo/SemiconductorPhase.h +++ b/Cantera/src/thermo/SemiconductorPhase.h @@ -4,9 +4,9 @@ * */ -/* $Author: dggoodwin $ - * $Date: 2007/11/27 13:26:08 $ - * $Revision: 1.2 $ +/* $Author$ + * $Date$ + * $Revision$ * * Copyright 2003 California Institute of Technology * diff --git a/Cantera/src/thermo/ShomatePoly.h b/Cantera/src/thermo/ShomatePoly.h index 25745a4aa..2937d8f0b 100644 --- a/Cantera/src/thermo/ShomatePoly.h +++ b/Cantera/src/thermo/ShomatePoly.h @@ -8,9 +8,9 @@ * Shomate polynomial expressions. */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2008/12/13 01:59:49 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/ShomateThermo.h b/Cantera/src/thermo/ShomateThermo.h index 3d7869f2a..c37822801 100644 --- a/Cantera/src/thermo/ShomateThermo.h +++ b/Cantera/src/thermo/ShomateThermo.h @@ -6,7 +6,7 @@ * \link Cantera::ShomateThermo ShomateThermo\endlink). */ /* - * $Id: ShomateThermo.h,v 1.6 2008/12/13 01:59:49 hkmoffa Exp $ + * $Id$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/SimpleThermo.h b/Cantera/src/thermo/SimpleThermo.h index c64c8da5e..2a548c739 100644 --- a/Cantera/src/thermo/SimpleThermo.h +++ b/Cantera/src/thermo/SimpleThermo.h @@ -6,7 +6,7 @@ * \link Cantera::SimpleThermo SimpleThermo\endlink). */ /* - * $Id: SimpleThermo.h,v 1.9 2008/12/13 01:59:49 hkmoffa Exp $ + * $Id$ */ #ifndef CT_SIMPLETHERMO_H diff --git a/Cantera/src/thermo/SingleSpeciesTP.cpp b/Cantera/src/thermo/SingleSpeciesTP.cpp index 5b89c2d6b..e9980ada2 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.cpp +++ b/Cantera/src/thermo/SingleSpeciesTP.cpp @@ -12,9 +12,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2007/06/05 15:17:15 $ - * $Revision: 1.10 $ + * $Author$ + * $Date$ + * $Revision$ */ #include "SingleSpeciesTP.h" diff --git a/Cantera/src/thermo/SingleSpeciesTP.h b/Cantera/src/thermo/SingleSpeciesTP.h index 56ffa94ce..59e726bf2 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.h +++ b/Cantera/src/thermo/SingleSpeciesTP.h @@ -13,9 +13,9 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/12/13 01:59:49 $ - * $Revision: 1.13 $ + * $Author$ + * $Date$ + * $Revision$ * */ diff --git a/Cantera/src/thermo/SpeciesThermo.h b/Cantera/src/thermo/SpeciesThermo.h index d34cf2ecd..35b8c8edb 100644 --- a/Cantera/src/thermo/SpeciesThermo.h +++ b/Cantera/src/thermo/SpeciesThermo.h @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.10 $ - * $Date: 2008/12/13 01:59:49 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index 89bea1928..06c48c269 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -5,8 +5,8 @@ * (see \ref spthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink); */ /* - * $Revision: 1.20 $ - * $Date: 2008/12/29 21:35:15 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/SpeciesThermoFactory.h b/Cantera/src/thermo/SpeciesThermoFactory.h index 7d7af60e7..172b0f939 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.h +++ b/Cantera/src/thermo/SpeciesThermoFactory.h @@ -7,8 +7,8 @@ */ /* - * $Revision: 1.11 $ - * $Date: 2009/02/11 20:03:08 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/SpeciesThermoInterpType.cpp b/Cantera/src/thermo/SpeciesThermoInterpType.cpp index ce6de7c43..7b7fa5365 100644 --- a/Cantera/src/thermo/SpeciesThermoInterpType.cpp +++ b/Cantera/src/thermo/SpeciesThermoInterpType.cpp @@ -3,9 +3,9 @@ * Definitions for a */ -/* $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2009/01/04 06:34:20 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2007 Sandia National Laboratories diff --git a/Cantera/src/thermo/SpeciesThermoInterpType.h b/Cantera/src/thermo/SpeciesThermoInterpType.h index a1b22903c..6e8f83b04 100644 --- a/Cantera/src/thermo/SpeciesThermoInterpType.h +++ b/Cantera/src/thermo/SpeciesThermoInterpType.h @@ -5,9 +5,9 @@ * (see \ref spthermo and class \link Cantera::SpeciesThermoInterpType SpeciesThermoInterpType \endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.8 $ - * $Date: 2008/12/13 01:59:49 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/SpeciesThermoMgr.h b/Cantera/src/thermo/SpeciesThermoMgr.h index 3728dbdb1..14d5347c3 100644 --- a/Cantera/src/thermo/SpeciesThermoMgr.h +++ b/Cantera/src/thermo/SpeciesThermoMgr.h @@ -7,9 +7,9 @@ * \link Cantera::SpeciesThermoDuo SpeciesThermoDuo\endlink and * \link Cantera::SpeciesThermo1 SpeciesThermo1\endlink) * - * $Author: hkmoffa $ - * $Revision: 1.12 $ - * $Date: 2009/02/11 20:03:08 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/State.cpp b/Cantera/src/thermo/State.cpp index d31c4f774..5fcdbbfa8 100644 --- a/Cantera/src/thermo/State.cpp +++ b/Cantera/src/thermo/State.cpp @@ -7,8 +7,8 @@ /* * - * $Date: 2009/03/03 19:53:34 $ - * $Revision: 1.8 $ + * $Date$ + * $Revision$ * * Copyright 2003-2004 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h index b5bd5eca8..21248e8d3 100644 --- a/Cantera/src/thermo/State.h +++ b/Cantera/src/thermo/State.h @@ -6,8 +6,8 @@ */ /* - * $Date: 2009/02/15 17:33:06 $ - * $Revision: 1.6 $ + * $Date$ + * $Revision$ * * Copyright 2001-2003 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/thermo/StoichSubstance.cpp b/Cantera/src/thermo/StoichSubstance.cpp index 964e040aa..7770c149a 100644 --- a/Cantera/src/thermo/StoichSubstance.cpp +++ b/Cantera/src/thermo/StoichSubstance.cpp @@ -5,8 +5,8 @@ * ThermoPhase class. */ /* - * $Date: 2009/01/04 21:28:02 $ - * $Revision: 1.8 $ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/thermo/StoichSubstance.h b/Cantera/src/thermo/StoichSubstance.h index b1b8ffa26..991ef4962 100644 --- a/Cantera/src/thermo/StoichSubstance.h +++ b/Cantera/src/thermo/StoichSubstance.h @@ -5,8 +5,8 @@ */ /* - * $Date: 2009/01/04 21:28:02 $ - * $Revision: 1.8 $ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/thermo/StoichSubstanceSSTP.cpp b/Cantera/src/thermo/StoichSubstanceSSTP.cpp index 7c4a6ee93..565e7cfc5 100644 --- a/Cantera/src/thermo/StoichSubstanceSSTP.cpp +++ b/Cantera/src/thermo/StoichSubstanceSSTP.cpp @@ -14,7 +14,7 @@ */ /* - * $Id: StoichSubstanceSSTP.cpp,v 1.13 2009/01/02 20:04:17 hkmoffa Exp $ + * $Id$ */ #include "ct_defs.h" diff --git a/Cantera/src/thermo/StoichSubstanceSSTP.h b/Cantera/src/thermo/StoichSubstanceSSTP.h index 0f59c7888..59b5598c4 100644 --- a/Cantera/src/thermo/StoichSubstanceSSTP.h +++ b/Cantera/src/thermo/StoichSubstanceSSTP.h @@ -12,8 +12,8 @@ */ /* - * $Date: 2009/01/02 20:04:17 $ - * $Revision: 1.12 $ + * $Date$ + * $Revision$ */ #ifndef CT_STOICHSUBSTANCESSTP_H diff --git a/Cantera/src/thermo/SurfPhase.cpp b/Cantera/src/thermo/SurfPhase.cpp index 4d58bb9d2..44fea43fd 100644 --- a/Cantera/src/thermo/SurfPhase.cpp +++ b/Cantera/src/thermo/SurfPhase.cpp @@ -7,8 +7,8 @@ */ /* - * $Revision: 1.13 $ - * $Date: 2009/01/24 00:15:00 $ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/Cantera/src/thermo/SurfPhase.h b/Cantera/src/thermo/SurfPhase.h index 978c1f760..2872c9db4 100644 --- a/Cantera/src/thermo/SurfPhase.h +++ b/Cantera/src/thermo/SurfPhase.h @@ -7,8 +7,8 @@ */ /* - * $Date: 2009/01/04 21:28:02 $ - * $Revision: 1.11 $ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 70ad4164d..5cc165beb 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -6,8 +6,8 @@ */ /* - * $Revision: 1.20 $ - * $Date: 2009/03/13 03:21:34 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/ThermoFactory.h b/Cantera/src/thermo/ThermoFactory.h index 77dccd54e..b9a034086 100644 --- a/Cantera/src/thermo/ThermoFactory.h +++ b/Cantera/src/thermo/ThermoFactory.h @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.10 $ - * $Date: 2009/02/11 20:03:08 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 1e6e1fddd..eb0e60250 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -6,9 +6,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2009/03/03 19:53:34 $ - * $Revision: 1.18 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 9df05133b..d6c7a64a1 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -7,8 +7,8 @@ */ /* - * $Date: 2009/02/18 22:31:32 $ - * $Revision: 1.26 $ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/Cantera/src/thermo/VPSSMgr.cpp b/Cantera/src/thermo/VPSSMgr.cpp index 403117bef..1f8e451d8 100644 --- a/Cantera/src/thermo/VPSSMgr.cpp +++ b/Cantera/src/thermo/VPSSMgr.cpp @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.8 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr.h b/Cantera/src/thermo/VPSSMgr.h index 9b2d913c2..5be3b3217 100644 --- a/Cantera/src/thermo/VPSSMgr.h +++ b/Cantera/src/thermo/VPSSMgr.h @@ -8,9 +8,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2009/05/28 23:08:06 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/VPSSMgrFactory.cpp b/Cantera/src/thermo/VPSSMgrFactory.cpp index 186bf5576..6e3962fb6 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.cpp +++ b/Cantera/src/thermo/VPSSMgrFactory.cpp @@ -6,7 +6,7 @@ * \link Cantera::VPSSMgrFactory VPSSMgrFactory\endlink); */ /* - * $Id: VPSSMgrFactory.cpp,v 1.8 2009/03/04 01:01:57 hkmoffa Exp $ + * $Id$ */ /* diff --git a/Cantera/src/thermo/VPSSMgrFactory.h b/Cantera/src/thermo/VPSSMgrFactory.h index 9d55d7957..5683608b3 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.h +++ b/Cantera/src/thermo/VPSSMgrFactory.h @@ -6,8 +6,8 @@ */ /* - * $Revision: 1.5 $ - * $Date: 2009/02/11 20:03:08 $ + * $Revision$ + * $Date$ */ /* diff --git a/Cantera/src/thermo/VPSSMgr_ConstVol.cpp b/Cantera/src/thermo/VPSSMgr_ConstVol.cpp index bf05a8640..12bc083be 100644 --- a/Cantera/src/thermo/VPSSMgr_ConstVol.cpp +++ b/Cantera/src/thermo/VPSSMgr_ConstVol.cpp @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.4 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr_ConstVol.h b/Cantera/src/thermo/VPSSMgr_ConstVol.h index 14a867530..52ead4294 100644 --- a/Cantera/src/thermo/VPSSMgr_ConstVol.h +++ b/Cantera/src/thermo/VPSSMgr_ConstVol.h @@ -6,9 +6,9 @@ * \link Cantera::VPSSMgr_ConstVol VPSSMgr_ConstVol \endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2009/05/28 23:08:06 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/VPSSMgr_General.cpp b/Cantera/src/thermo/VPSSMgr_General.cpp index f75c9ad27..fc90e6e4e 100644 --- a/Cantera/src/thermo/VPSSMgr_General.cpp +++ b/Cantera/src/thermo/VPSSMgr_General.cpp @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr_General.h b/Cantera/src/thermo/VPSSMgr_General.h index 32e2011d2..458c5e5c4 100644 --- a/Cantera/src/thermo/VPSSMgr_General.h +++ b/Cantera/src/thermo/VPSSMgr_General.h @@ -7,8 +7,8 @@ * class \link Cantera::VPSSMgr_General VPSSMgr_General\endlink). */ /* - * $Revision: 1.4 $ - * $Date: 2009/05/28 23:08:06 $ + * $Revision$ + * $Date$ */ /* * Copywrite (2007) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/VPSSMgr_IdealGas.cpp b/Cantera/src/thermo/VPSSMgr_IdealGas.cpp index 7eedbc033..34ef28457 100644 --- a/Cantera/src/thermo/VPSSMgr_IdealGas.cpp +++ b/Cantera/src/thermo/VPSSMgr_IdealGas.cpp @@ -12,9 +12,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.3 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr_IdealGas.h b/Cantera/src/thermo/VPSSMgr_IdealGas.h index ee123a3aa..146fa3e0a 100644 --- a/Cantera/src/thermo/VPSSMgr_IdealGas.h +++ b/Cantera/src/thermo/VPSSMgr_IdealGas.h @@ -7,9 +7,9 @@ * class \link Cantera::VPSSMgr_IdealGas VPSSMgr_IdealGas\endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.3 $ - * $Date: 2009/05/28 23:08:06 $ + * $Author$ + * $Revision$ + * $Date$ */ /* diff --git a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp index 5a156420a..40a65a8eb 100644 --- a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp +++ b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp @@ -15,8 +15,8 @@ */ /* - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.9 $ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.h b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.h index 7d8a248de..057a1d6f9 100644 --- a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.h +++ b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.h @@ -9,8 +9,8 @@ */ /* - * $Revision: 1.7 $ - * $Date: 2009/05/28 23:08:06 $ + * $Revision$ + * $Date$ */ /* diff --git a/Cantera/src/thermo/VPSSMgr_Water_HKFT.cpp b/Cantera/src/thermo/VPSSMgr_Water_HKFT.cpp index ac725e84b..0b33cdd63 100644 --- a/Cantera/src/thermo/VPSSMgr_Water_HKFT.cpp +++ b/Cantera/src/thermo/VPSSMgr_Water_HKFT.cpp @@ -15,8 +15,8 @@ */ /* - * $Date: 2009/05/28 23:08:06 $ - * $Revision: 1.13 $ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPSSMgr_Water_HKFT.h b/Cantera/src/thermo/VPSSMgr_Water_HKFT.h index d54d7dd99..462eae89c 100644 --- a/Cantera/src/thermo/VPSSMgr_Water_HKFT.h +++ b/Cantera/src/thermo/VPSSMgr_Water_HKFT.h @@ -8,8 +8,8 @@ */ /* - * $Revision: 1.7 $ - * $Date: 2009/05/28 23:08:06 $ + * $Revision$ + * $Date$ */ /* diff --git a/Cantera/src/thermo/VPSSMgr_types.h b/Cantera/src/thermo/VPSSMgr_types.h index 9d7512563..4d55e1eff 100644 --- a/Cantera/src/thermo/VPSSMgr_types.h +++ b/Cantera/src/thermo/VPSSMgr_types.h @@ -8,9 +8,9 @@ * class \link Cantera::VPSSMgr VPSSMgr\endlink). */ /* - * $Author: hkmoffa $ - * $Revision: 1.1 $ - * $Date: 2008/08/23 00:53:55 $ + * $Author$ + * $Revision$ + * $Date$ */ /* * Copywrite (2005) Sandia Corporation. Under the terms of diff --git a/Cantera/src/thermo/VPStandardStateTP.cpp b/Cantera/src/thermo/VPStandardStateTP.cpp index 6a79674aa..0c4dd874e 100644 --- a/Cantera/src/thermo/VPStandardStateTP.cpp +++ b/Cantera/src/thermo/VPStandardStateTP.cpp @@ -11,9 +11,9 @@ * U.S. Government retains certain rights in this software. */ /* - * $Author: hkmoffa $ - * $Date: 2009/01/04 06:34:20 $ - * $Revision: 1.16 $ + * $Author$ + * $Date$ + * $Revision$ */ // turn off warnings under Windows diff --git a/Cantera/src/thermo/VPStandardStateTP.h b/Cantera/src/thermo/VPStandardStateTP.h index f9097565d..4df17709c 100644 --- a/Cantera/src/thermo/VPStandardStateTP.h +++ b/Cantera/src/thermo/VPStandardStateTP.h @@ -14,8 +14,8 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date: 2009/03/27 00:38:57 $ - * $Revision: 1.20 $ + * $Date$ + * $Revision$ */ #ifndef CT_VPSTANDARDSTATETP_H diff --git a/Cantera/src/thermo/WaterProps.cpp b/Cantera/src/thermo/WaterProps.cpp index 64ed23fa1..5501a7129 100644 --- a/Cantera/src/thermo/WaterProps.cpp +++ b/Cantera/src/thermo/WaterProps.cpp @@ -7,7 +7,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterProps.cpp,v 1.9 2008/12/17 17:04:47 hkmoffa Exp $ + * $Id$ */ //@{ diff --git a/Cantera/src/thermo/WaterProps.h b/Cantera/src/thermo/WaterProps.h index f3ca51cbb..b6099f7df 100644 --- a/Cantera/src/thermo/WaterProps.h +++ b/Cantera/src/thermo/WaterProps.h @@ -11,7 +11,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterProps.h,v 1.5 2008/08/23 00:53:55 hkmoffa Exp $ + * $Id$ */ #ifndef CT_WATERPROPS_H diff --git a/Cantera/src/thermo/WaterPropsIAPWS.cpp b/Cantera/src/thermo/WaterPropsIAPWS.cpp index 60f2a5fee..0a7a83f9c 100644 --- a/Cantera/src/thermo/WaterPropsIAPWS.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWS.cpp @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterPropsIAPWS.cpp,v 1.17 2008/12/17 17:01:29 hkmoffa Exp $ + * $Id$ */ #include "WaterPropsIAPWS.h" diff --git a/Cantera/src/thermo/WaterPropsIAPWS.h b/Cantera/src/thermo/WaterPropsIAPWS.h index 023d076a9..b3c722b1d 100644 --- a/Cantera/src/thermo/WaterPropsIAPWS.h +++ b/Cantera/src/thermo/WaterPropsIAPWS.h @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterPropsIAPWS.h,v 1.16 2008/09/29 20:03:57 hkmoffa Exp $ + * $Id$ */ #ifndef WATERPROPSIAPWS_H diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp index 4299b97cd..d91bce64b 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterPropsIAPWSphi.cpp,v 1.12 2008/12/29 22:53:36 hkmoffa Exp $ + * $Id$ */ #include "WaterPropsIAPWSphi.h" diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.h b/Cantera/src/thermo/WaterPropsIAPWSphi.h index 6a5b0ca87..1691214ae 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.h +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.h @@ -11,7 +11,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterPropsIAPWSphi.h,v 1.8 2008/09/12 21:51:04 hkmoffa Exp $ + * $Id$ */ #ifndef WATERPROPSIAPWSPHI_H diff --git a/Cantera/src/thermo/WaterSSTP.cpp b/Cantera/src/thermo/WaterSSTP.cpp index af1922645..863d96803 100644 --- a/Cantera/src/thermo/WaterSSTP.cpp +++ b/Cantera/src/thermo/WaterSSTP.cpp @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterSSTP.cpp,v 1.17 2009/03/27 00:38:58 hkmoffa Exp $ + * $Id$ */ #include "xml.h" diff --git a/Cantera/src/thermo/WaterSSTP.h b/Cantera/src/thermo/WaterSSTP.h index bbc46b18a..b4add6b2f 100644 --- a/Cantera/src/thermo/WaterSSTP.h +++ b/Cantera/src/thermo/WaterSSTP.h @@ -9,7 +9,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: WaterSSTP.h,v 1.13 2009/03/27 00:38:58 hkmoffa Exp $ + * $Id$ */ #ifndef CT_WATERSSTP_H diff --git a/Cantera/src/thermo/electrolytes.h b/Cantera/src/thermo/electrolytes.h index 97bf75bef..eecd6f878 100644 --- a/Cantera/src/thermo/electrolytes.h +++ b/Cantera/src/thermo/electrolytes.h @@ -10,7 +10,7 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id: electrolytes.h,v 1.1 2006/07/06 15:41:15 hkmoffa Exp $ + * $Id$ */ #ifndef CT_ELECTROLYTES_H #define CT_ELECTROLYTES_H diff --git a/Cantera/src/thermo/phasereport.cpp b/Cantera/src/thermo/phasereport.cpp index 8a5830d6c..af3dfdacc 100644 --- a/Cantera/src/thermo/phasereport.cpp +++ b/Cantera/src/thermo/phasereport.cpp @@ -4,8 +4,8 @@ */ /* - * $Date: 2009/01/14 22:46:33 $ - * $Revision: 1.8 $ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/thermo/speciesThermoTypes.h b/Cantera/src/thermo/speciesThermoTypes.h index 2e570ba5b..f8e742821 100644 --- a/Cantera/src/thermo/speciesThermoTypes.h +++ b/Cantera/src/thermo/speciesThermoTypes.h @@ -4,9 +4,9 @@ * reference-state thermodynamics managers (see \ref spthermo) */ /* - * $Author: hkmoffa $ - * $Revision: 1.6 $ - * $Date: 2008/09/29 20:03:57 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/transport/AqueousTransport.cpp b/Cantera/src/transport/AqueousTransport.cpp index 3b7033dfa..df6fdf188 100644 --- a/Cantera/src/transport/AqueousTransport.cpp +++ b/Cantera/src/transport/AqueousTransport.cpp @@ -3,8 +3,8 @@ * Transport properties for aqueous systems */ /* - * $Revision: 1.4 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ diff --git a/Cantera/src/transport/AqueousTransport.h b/Cantera/src/transport/AqueousTransport.h index 7179fe5e9..f5bfc3d8f 100644 --- a/Cantera/src/transport/AqueousTransport.h +++ b/Cantera/src/transport/AqueousTransport.h @@ -3,8 +3,8 @@ * Header file defining class AqueousTransport */ /* - * $Revision: 1.4 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index c62e91bea..fee667dde 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -8,9 +8,9 @@ */ /* - * $Author: hkmoffa $ - * $Date: 2009/03/27 18:24:39 $ - * $Revision: 1.12 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2003 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index fe61d4d43..cd196c725 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -3,8 +3,8 @@ * Mixture-averaged transport properties for ideal gas mixtures. */ /* - * $Revision: 1.10 $ - * $Date: 2009/03/24 20:44:30 $ + * $Revision$ + * $Date$ */ #include "ThermoPhase.h" diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 4af44619b..a8be0e628 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -4,8 +4,8 @@ * Header file defining class LiquidTransport */ /* - * $Revision: 1.9 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ #ifndef CT_LIQUIDTRAN_H diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index ee1faa948..7b3d28609 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -4,9 +4,9 @@ * (see \link Cantera::TransportFactory TransportFactory\endlink) */ /* - * $Author: hkmoffa $ - * $Date: 2008/12/24 18:19:01 $ - * $Revision: 1.14 $ + * $Author$ + * $Date$ + * $Revision$ * * * diff --git a/Cantera/src/transport/MMCollisionInt.cpp b/Cantera/src/transport/MMCollisionInt.cpp index 6639c9c9d..c50855c32 100755 --- a/Cantera/src/transport/MMCollisionInt.cpp +++ b/Cantera/src/transport/MMCollisionInt.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.11 $ - * $Date: 2008/12/17 17:06:24 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology */ diff --git a/Cantera/src/transport/MMCollisionInt.h b/Cantera/src/transport/MMCollisionInt.h index 0a915a0f9..797a30ea5 100755 --- a/Cantera/src/transport/MMCollisionInt.h +++ b/Cantera/src/transport/MMCollisionInt.h @@ -3,9 +3,9 @@ * Monk and Monchick collision integrals */ /* - * $Author: hkmoffa $ - * $Revision: 1.5 $ - * $Date: 2007/07/26 21:55:32 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index 9f52f08e1..8302e9a54 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### # -# $Date: 2009/02/15 19:41:33 $ -# $Revision: 1.22 $ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 2dd2da5da..4f70664af 100755 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -3,9 +3,9 @@ * Mixture-averaged transport properties for ideal gas mixtures. */ -/* $Author: hkmoffa $ - * $Revision: 1.16 $ - * $Date: 2009/03/27 18:24:39 $ +/* $Author$ + * $Revision$ + * $Date$ */ // copyright 2001 California Institute of Technology diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 55b49503a..8ef0ef52a 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -5,9 +5,9 @@ * (see \ref tranprops and \link Cantera::MixTransport MixTransport \endlink) . * */ -/* $Author: hkmoffa $ - * $Revision: 1.11 $ - * $Date: 2009/03/27 18:24:39 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index e3b83db98..4bc72954c 100755 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -5,9 +5,9 @@ * * @ingroup transportProps * - * $Author: hkmoffa $ - * $Date: 2009/03/27 18:24:39 $ - * $Revision: 1.17 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * See file License.txt for licensing information diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index d9aa801f6..69d4a8628 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -3,8 +3,8 @@ * Simple mostly constant transport properties */ /* - * $Revision: 1.10 $ - * $Date: 2009/03/24 20:44:30 $ + * $Revision$ + * $Date$ */ #include "ThermoPhase.h" diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 875403a01..ba13dacb6 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -4,8 +4,8 @@ * Header file defining class SimpleTransport */ /* - * $Revision: 1.9 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ #ifndef CT_SIMPLETRAN_H diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index 36c6b92f9..6401d7f45 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -3,9 +3,9 @@ * @file SolidTransport.cpp */ -/* $Author: hkmoffa $ - * $Revision: 1.10 $ - * $Date: 2009/03/27 18:24:39 $ +/* $Author$ + * $Revision$ + * $Date$ */ // copyright 2008 California Institute of Technology diff --git a/Cantera/src/transport/SolidTransport.h b/Cantera/src/transport/SolidTransport.h index 76e18f943..31e5fe0a1 100644 --- a/Cantera/src/transport/SolidTransport.h +++ b/Cantera/src/transport/SolidTransport.h @@ -4,9 +4,9 @@ * Header file defining class SolidTransport */ -/* $Author: hkmoffa $ - * $Revision: 1.7 $ - * $Date: 2009/03/27 18:24:39 $ +/* $Author$ + * $Revision$ + * $Date$ */ // Copyright 2003 California Institute of Technology diff --git a/Cantera/src/transport/TransportBase.cpp b/Cantera/src/transport/TransportBase.cpp index 75da215b7..f0c881907 100644 --- a/Cantera/src/transport/TransportBase.cpp +++ b/Cantera/src/transport/TransportBase.cpp @@ -3,8 +3,8 @@ * Mixture-averaged transport properties for ideal gas mixtures. */ /* - * $Revision: 1.1 $ - * $Date: 2009/02/15 19:41:33 $ + * $Revision$ + * $Date$ */ #include "ThermoPhase.h" diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 12309ec30..1d9070555 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -8,8 +8,8 @@ */ /* - * $Revision: 1.23 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ // Copyright 2001-2003 California Institute of Technology diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 3c016ad3b..d41e23d21 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -4,9 +4,9 @@ * (see \link Cantera::TransportFactory TransportFactory\endlink) */ /* - * $Author: hkmoffa $ - * $Date: 2008/12/24 18:19:01 $ - * $Revision: 1.14 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2001 California Institute of Technology * diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index cd858ee8d..b4ad85348 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -3,8 +3,8 @@ * Header file defining class LiquidTransport */ /* - * $Revision: 1.9 $ - * $Date: 2009/03/27 18:24:39 $ + * $Revision$ + * $Date$ */ #ifndef CT_WATERTRAN_H diff --git a/Cantera/src/zeroD/ConstPressureReactor.h b/Cantera/src/zeroD/ConstPressureReactor.h index 432b9bed7..0e82d1306 100644 --- a/Cantera/src/zeroD/ConstPressureReactor.h +++ b/Cantera/src/zeroD/ConstPressureReactor.h @@ -1,9 +1,9 @@ /** * @file Reactor.h * - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2006/11/27 21:43:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/FlowDevice.h b/Cantera/src/zeroD/FlowDevice.h index 8eea2d59a..3273f5c5e 100644 --- a/Cantera/src/zeroD/FlowDevice.h +++ b/Cantera/src/zeroD/FlowDevice.h @@ -1,9 +1,9 @@ /** * @file FlowDevice.h * - * $Author: dggoodwin $ - * $Date: 2007/05/04 14:41:28 $ - * $Revision: 1.6 $ + * $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/FlowReactor.h b/Cantera/src/zeroD/FlowReactor.h index e6fa4cb8a..e6b750d79 100644 --- a/Cantera/src/zeroD/FlowReactor.h +++ b/Cantera/src/zeroD/FlowReactor.h @@ -1,9 +1,9 @@ /** * @file FlowReactor.h * - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2006/11/27 21:43:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/Makefile.in b/Cantera/src/zeroD/Makefile.in index 30bd426bd..8c3000018 100644 --- a/Cantera/src/zeroD/Makefile.in +++ b/Cantera/src/zeroD/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/12/30 21:49:41 $ -# $Revision: 1.17 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Cantera/src/zeroD/PID_Controller.h b/Cantera/src/zeroD/PID_Controller.h index 91b3850d7..77560dfd0 100644 --- a/Cantera/src/zeroD/PID_Controller.h +++ b/Cantera/src/zeroD/PID_Controller.h @@ -1,9 +1,9 @@ /** * @file PID_Controller.h * - * $Author: dggoodwin $ - * $Revision: 1.2 $ - * $Date: 2005/06/18 17:01:12 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/Reactor.h b/Cantera/src/zeroD/Reactor.h index e5e515b04..aca2506ce 100644 --- a/Cantera/src/zeroD/Reactor.h +++ b/Cantera/src/zeroD/Reactor.h @@ -1,9 +1,9 @@ /** * @file Reactor.h * - * $Author: dggoodwin $ - * $Revision: 1.11 $ - * $Date: 2007/05/04 14:41:28 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/ReactorBase.cpp b/Cantera/src/zeroD/ReactorBase.cpp index 60314a488..9348e6d66 100644 --- a/Cantera/src/zeroD/ReactorBase.cpp +++ b/Cantera/src/zeroD/ReactorBase.cpp @@ -1,9 +1,9 @@ /** * @file ReactorBase.cpp * - * $Author: dggoodwin $ - * $Revision: 1.11 $ - * $Date: 2006/11/27 21:43:34 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/ReactorBase.h b/Cantera/src/zeroD/ReactorBase.h index 3558e099f..047265478 100644 --- a/Cantera/src/zeroD/ReactorBase.h +++ b/Cantera/src/zeroD/ReactorBase.h @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.14 $ - * $Date: 2007/07/27 03:38:24 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/ReactorFactory.cpp b/Cantera/src/zeroD/ReactorFactory.cpp index 073add4ad..ee07a21f3 100644 --- a/Cantera/src/zeroD/ReactorFactory.cpp +++ b/Cantera/src/zeroD/ReactorFactory.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2007/05/10 03:28:32 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2006 California Institute of Technology diff --git a/Cantera/src/zeroD/ReactorFactory.h b/Cantera/src/zeroD/ReactorFactory.h index 30c29c6b1..d1da8024f 100644 --- a/Cantera/src/zeroD/ReactorFactory.h +++ b/Cantera/src/zeroD/ReactorFactory.h @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2007/05/10 03:28:32 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/ReactorNet.h b/Cantera/src/zeroD/ReactorNet.h index f7265c0a0..021610a23 100644 --- a/Cantera/src/zeroD/ReactorNet.h +++ b/Cantera/src/zeroD/ReactorNet.h @@ -3,9 +3,9 @@ */ /* - * $Author: hkmoffa $ - * $Revision: 1.16 $ - * $Date: 2009/07/11 17:35:05 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2004 California Institute of Technology diff --git a/Cantera/src/zeroD/Reservoir.h b/Cantera/src/zeroD/Reservoir.h index 7ae625f61..d60539df3 100644 --- a/Cantera/src/zeroD/Reservoir.h +++ b/Cantera/src/zeroD/Reservoir.h @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.3 $ - * $Date: 2005/06/18 17:01:12 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/src/zeroD/Wall.h b/Cantera/src/zeroD/Wall.h index c07ef168c..4afeb4b3f 100644 --- a/Cantera/src/zeroD/Wall.h +++ b/Cantera/src/zeroD/Wall.h @@ -3,9 +3,9 @@ * Header file for class Wall. */ -/* $Author: dggoodwin $ - * $Date: 2007/05/04 14:41:28 $ - * $Revision: 1.9 $ +/* $Author$ + * $Date$ + * $Revision$ */ // Copyright 2001-2004 California Institute of Technology diff --git a/Cantera/src/zeroD/flowControllers.h b/Cantera/src/zeroD/flowControllers.h index 177e33bba..07799d48e 100644 --- a/Cantera/src/zeroD/flowControllers.h +++ b/Cantera/src/zeroD/flowControllers.h @@ -3,9 +3,9 @@ * * Some flow devices derived from class FlowDevice. * - * $Author: dggoodwin $ - * $Revision: 1.6 $ - * $Date: 2007/05/04 14:41:28 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2001 California Institute of Technology diff --git a/Cantera/user/Makefile.in b/Cantera/user/Makefile.in index 2160a2aa5..42548c761 100644 --- a/Cantera/user/Makefile.in +++ b/Cantera/user/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh ############################################################### -# $Author: hkmoffa $ -# $Date: 2008/01/01 19:19:50 $ -# $Revision: 1.7 $ +# $Author$ +# $Date$ +# $Revision$ # # Copyright 2002 California Institute of Technology # diff --git a/Makefile.in b/Makefile.in index 7fa9e0934..410fee99d 100755 --- a/Makefile.in +++ b/Makefile.in @@ -1,6 +1,6 @@ #!/bin/sh # -# $Id: Makefile.in,v 1.96 2009/03/25 01:11:48 hkmoffa Exp $ +# $Id$ # export_dir = $(HOME)/sfdist version = @ctversion@ diff --git a/apps/bvp/stagnation.cpp b/apps/bvp/stagnation.cpp index ac885ae38..e0357b63c 100644 --- a/apps/bvp/stagnation.cpp +++ b/apps/bvp/stagnation.cpp @@ -3,9 +3,9 @@ */ /* - * $Author: dggoodwin $ - * $Revision: 1.1 $ - * $Date: 2007/11/06 21:13:09 $ + * $Author$ + * $Revision$ + * $Date$ */ // Copyright 2002 California Institute of Technology diff --git a/data/transport/misc_tran.dat b/data/transport/misc_tran.dat index 586df5bea..71bce0d79 100644 --- a/data/transport/misc_tran.dat +++ b/data/transport/misc_tran.dat @@ -3,9 +3,9 @@ ! ! Miscellaneous collection of transport parameters ! -! $Author: hkmoffa $ -! $Date: 2003/09/05 14:45:59 $ -! $Revision: 1.1 $ +! $Author$ +! $Date$ +! $Revision$ ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! diff --git a/examples/cxx/equil_example1.cpp b/examples/cxx/equil_example1.cpp index 1d812033d..d188be7f0 100755 --- a/examples/cxx/equil_example1.cpp +++ b/examples/cxx/equil_example1.cpp @@ -2,9 +2,9 @@ // // chemical equilibrium // -// $Author: hkmoffa $ -// $Revision: 1.15 $ -// $Date: 2008/02/16 21:33:37 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/examples/cxx/kinetics_example1.cpp b/examples/cxx/kinetics_example1.cpp index 74500c287..ed8172356 100755 --- a/examples/cxx/kinetics_example1.cpp +++ b/examples/cxx/kinetics_example1.cpp @@ -2,9 +2,9 @@ // // zero-dimensional kinetics example program // -// $Author: hkmoffa $ -// $Revision: 1.13 $ -// $Date: 2009/07/11 17:25:05 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/examples/cxx/kinetics_example2.cpp b/examples/cxx/kinetics_example2.cpp index 391a7b7ea..2aa5ee684 100755 --- a/examples/cxx/kinetics_example2.cpp +++ b/examples/cxx/kinetics_example2.cpp @@ -2,9 +2,9 @@ // // zero-dimensional kinetics example program // -// $Author: hkmoffa $ -// $Revision: 1.8 $ -// $Date: 2009/07/11 17:25:05 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/examples/cxx/kinetics_example3.cpp b/examples/cxx/kinetics_example3.cpp index e2be7ff7b..ab2932cfb 100644 --- a/examples/cxx/kinetics_example3.cpp +++ b/examples/cxx/kinetics_example3.cpp @@ -2,9 +2,9 @@ // // zero-dimensional kinetics example program // -// $Author: hkmoffa $ -// $Revision: 1.5 $ -// $Date: 2009/07/11 17:25:05 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2006 // diff --git a/examples/cxx/rxnpath_example1.cpp b/examples/cxx/rxnpath_example1.cpp index 9a7756aad..5ad7690ae 100755 --- a/examples/cxx/rxnpath_example1.cpp +++ b/examples/cxx/rxnpath_example1.cpp @@ -2,9 +2,9 @@ // // reaction path diagrams // -// $Author: hkmoffa $ -// $Revision: 1.9 $ -// $Date: 2009/07/11 17:25:05 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/examples/cxx/transport_example1.cpp b/examples/cxx/transport_example1.cpp index 65fd37499..d483c70b0 100755 --- a/examples/cxx/transport_example1.cpp +++ b/examples/cxx/transport_example1.cpp @@ -2,9 +2,9 @@ // // mixture-averaged transport properties // -// $Author: hkmoffa $ -// $Revision: 1.7 $ -// $Date: 2008/02/16 21:33:37 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/examples/cxx/transport_example2.cpp b/examples/cxx/transport_example2.cpp index 83086651b..e5ac40030 100755 --- a/examples/cxx/transport_example2.cpp +++ b/examples/cxx/transport_example2.cpp @@ -2,9 +2,9 @@ // // mixture-averaged transport properties // -// $Author: hkmoffa $ -// $Revision: 1.6 $ -// $Date: 2008/02/16 21:33:38 $ +// $Author$ +// $Revision$ +// $Date$ // // copyright California Institute of Technology 2002 // diff --git a/ext/Makefile.in b/ext/Makefile.in index d902d6cfe..6189ca913 100755 --- a/ext/Makefile.in +++ b/ext/Makefile.in @@ -1,9 +1,9 @@ #/bin/sh # # $Source: /cvsroot/cantera/cantera/ext/Makefile.in,v $ -# $Author: dggoodwin $ -# $Revision: 1.10 $ -# $Date: 2008/02/13 06:43:27 $ +# $Author$ +# $Revision$ +# $Date$ # # Makefile for ext directory # diff --git a/ext/blas/Makefile.in b/ext/blas/Makefile.in index caef518a0..e9417b30f 100755 --- a/ext/blas/Makefile.in +++ b/ext/blas/Makefile.in @@ -1,7 +1,7 @@ #/bin/sh # $License$ # -# $Id: Makefile.in,v 1.8 2008/12/30 21:49:41 hkmoffa Exp $ +# $Id$ # do_ranlib = @DO_RANLIB@ BLASLIB = @buildlib@/libctblas.a diff --git a/ext/cvode/Makefile.in b/ext/cvode/Makefile.in index ef438dc2b..494dc2185 100755 --- a/ext/cvode/Makefile.in +++ b/ext/cvode/Makefile.in @@ -1,8 +1,8 @@ # # $Source: /cvsroot/cantera/cantera/ext/cvode/Makefile.in,v $ -# $Author: hkmoffa $ -# $Revision: 1.10 $ -# $Date: 2008/12/30 21:49:42 $ +# $Author$ +# $Revision$ +# $Date$ # #---------------------------------------------------------------------------- # CVODE diff --git a/ext/f2c_blas/Makefile.in b/ext/f2c_blas/Makefile.in index e10e9f192..8c33bf26e 100755 --- a/ext/f2c_blas/Makefile.in +++ b/ext/f2c_blas/Makefile.in @@ -1,8 +1,8 @@ #/bin/sh #/bin/sh # -# $Revision: 1.10 $ -# $Date: 2009/01/12 19:34:14 $ +# $Revision$ +# $Date$ # .SUFFIXES : diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 732ad0f0d..f85c8c20a 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -1,9 +1,9 @@ #/bin/sh # # $Source: /cvsroot/cantera/cantera/ext/f2c_lapack/Makefile.in,v $ -# $Author: hkmoffa $ -# $Revision: 1.9 $ -# $Date: 2009/01/12 19:34:14 $ +# $Author$ +# $Revision$ +# $Date$ # .SUFFIXES : diff --git a/ext/f2c_libs/Makefile.in b/ext/f2c_libs/Makefile.in index 708e973f2..714b7a4b0 100755 --- a/ext/f2c_libs/Makefile.in +++ b/ext/f2c_libs/Makefile.in @@ -1,8 +1,8 @@ # # $Source: /cvsroot/cantera/cantera/ext/f2c_libs/Makefile.in,v $ -# $Author: dggoodwin $ -# $Revision: 1.13 $ -# $Date: 2008/02/05 23:36:13 $ +# $Author$ +# $Revision$ +# $Date$ # # Unix makefile: see README. # For C++, first "make hadd". diff --git a/ext/f2c_math/Makefile.in b/ext/f2c_math/Makefile.in index 35ead9668..5c74cc4bf 100644 --- a/ext/f2c_math/Makefile.in +++ b/ext/f2c_math/Makefile.in @@ -1,9 +1,9 @@ #/bin/sh # # $Source: /cvsroot/cantera/cantera/ext/f2c_math/Makefile.in,v $ -# $Author: hkmoffa $ -# $Revision: 1.10 $ -# $Date: 2008/12/30 21:49:42 $ +# $Author$ +# $Revision$ +# $Date$ # .SUFFIXES : diff --git a/ext/f2c_recipes/Makefile.in b/ext/f2c_recipes/Makefile.in index daaf914a0..1ed83b9d8 100644 --- a/ext/f2c_recipes/Makefile.in +++ b/ext/f2c_recipes/Makefile.in @@ -1,9 +1,9 @@ #/bin/sh # # $Source: /cvsroot/cantera/cantera/ext/f2c_recipes/Makefile.in,v $ -# $Author: hkmoffa $ -# $Revision: 1.5 $ -# $Date: 2008/12/30 21:49:42 $ +# $Author$ +# $Revision$ +# $Date$ # .SUFFIXES : diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index ce5e6e97e..48b38590c 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -1,5 +1,5 @@ # $License$ -# $Id: Makefile.in,v 1.10 2008/12/30 21:58:10 hkmoffa Exp $ +# $Id$ # #/bin/sh diff --git a/ext/math/Makefile.in b/ext/math/Makefile.in index aba77e6e2..4fdfdb9a3 100755 --- a/ext/math/Makefile.in +++ b/ext/math/Makefile.in @@ -1,8 +1,8 @@ # # $Source: /cvsroot/cantera/cantera/ext/math/Makefile.in,v $ -# $Author: hkmoffa $ -# $Revision: 1.13 $ -# $Date: 2008/12/30 21:58:10 $ +# $Author$ +# $Revision$ +# $Date$ # .SUFFIXES : diff --git a/ext/recipes/Makefile.in b/ext/recipes/Makefile.in index dc81b0417..54f8922fb 100755 --- a/ext/recipes/Makefile.in +++ b/ext/recipes/Makefile.in @@ -1,6 +1,6 @@ # $License$ # -# $Id: Makefile.in,v 1.8 2008/12/30 21:49:42 hkmoffa Exp $ +# $Id$ # #/bin/sh .SUFFIXES : diff --git a/ext/tpx/Makefile.in b/ext/tpx/Makefile.in index bf0ebca96..3284b2a74 100755 --- a/ext/tpx/Makefile.in +++ b/ext/tpx/Makefile.in @@ -1,6 +1,6 @@ #/bin/sh # -# $Id: Makefile.in,v 1.17 2009/03/28 19:10:17 hkmoffa Exp $ +# $Id$ # .SUFFIXES : .SUFFIXES : .cpp .d .o diff --git a/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp b/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp index 4a5176c6b..8b016a734 100644 --- a/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp +++ b/test_problems/ChemEquil_gri_matrix/gri_matrix.cpp @@ -1,7 +1,7 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/02/16 21:41:06 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp b/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp index 3e14cd6d2..ac6090ae3 100644 --- a/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp +++ b/test_problems/ChemEquil_gri_pairs/gri_pairs.cpp @@ -1,7 +1,7 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/02/16 21:40:10 $ - * $Revision: 1.3 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp b/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp index b5e836263..bcfa933b6 100644 --- a/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp +++ b/test_problems/ChemEquil_ionizedGas/ionizedGasEquil.cpp @@ -1,7 +1,7 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/02/16 21:43:06 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ * * */ diff --git a/test_problems/ChemEquil_red1/basopt_red1.cpp b/test_problems/ChemEquil_red1/basopt_red1.cpp index 3630cbaca..7c9bea129 100644 --- a/test_problems/ChemEquil_red1/basopt_red1.cpp +++ b/test_problems/ChemEquil_red1/basopt_red1.cpp @@ -1,7 +1,7 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/02/16 21:44:47 $ - * $Revision: 1.5 $ + * $Author$ + * $Date$ + * $Revision$ * */ diff --git a/test_problems/CpJump/CpJump.cpp b/test_problems/CpJump/CpJump.cpp index 0081d69f2..dd5205d2a 100644 --- a/test_problems/CpJump/CpJump.cpp +++ b/test_problems/CpJump/CpJump.cpp @@ -1,7 +1,7 @@ /* - * $Author: hkmoffa $ - * $Date: 2008/02/16 21:46:15 $ - * $Revision: 1.2 $ + * $Author$ + * $Date$ + * $Revision$ * * Copyright 2002 California Institute of Technology * diff --git a/test_problems/Makefile.in b/test_problems/Makefile.in index b2c381ba2..16b923a8f 100644 --- a/test_problems/Makefile.in +++ b/test_problems/Makefile.in @@ -1,7 +1,7 @@ # -# $Revision: 1.36 $ -# $Author: hkmoffa $ -# $Date: 2009/03/25 01:03:05 $ +# $Revision$ +# $Author$ +# $Date$ # # test_python=@BUILD_PYTHON@ diff --git a/test_problems/VCSnonideal/Makefile.in b/test_problems/VCSnonideal/Makefile.in index 704cb03d3..f5ea312c3 100644 --- a/test_problems/VCSnonideal/Makefile.in +++ b/test_problems/VCSnonideal/Makefile.in @@ -1,7 +1,7 @@ # -# $Revision: 1.1 $ -# $Author: hkmoffa $ -# $Date: 2007/12/20 23:47:41 $ +# $Revision$ +# $Author$ +# $Date$ # # test_vcs_nonideal=@COMPILE_VCSNONIDEAL@ diff --git a/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml b/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml index 59c471cf9..75cbc0e7f 100644 --- a/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml +++ b/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml @@ -1,6 +1,6 @@ + * + * + */ + if ( tranTypeNode.hasChild("velocityBasis")) { + std::string velocityBasis = + tranTypeNode.child("velocityBasis").attrib("basis"); + if ( velocityBasis == "mass" ) + trParam.velocityBasis = VB_MASSAVG; + else if ( velocityBasis == "mole" ) + trParam.velocityBasis = VB_MOLEAVG; + else if ( trParam.thermo->speciesIndex( velocityBasis ) > 0 ) + trParam.velocityBasis = trParam.thermo->speciesIndex( velocityBasis ) ; + else { + int linenum; + throw TransportDBError( linenum, "Unknown attribute " + velocityBasis + " for node. "); + } + + + } } } diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 5fe1ef3d8..63c4b9f0b 100755 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -19,7 +19,7 @@ namespace Cantera { public: - TransportParams() : thermo(0), xml(0) {} + TransportParams() : thermo(0), xml(0), velocityBasis(VB_MASSAVG) {} virtual ~TransportParams(); int nsp_; @@ -27,6 +27,10 @@ namespace Cantera { thermo_t* thermo; vector_fp mw; + //! A basis for the average velocity can be specified. + //! Valid bases include "mole" "mass" and species names. + int velocityBasis; + //minimum and maximum temperatures for parameter fits doublereal tmax, tmin; int mode_; From c0249fa3d21d43814bfa55bc20404f022d8211eb Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 2 Dec 2009 02:07:02 +0000 Subject: [PATCH 046/446] Modified TransportParams to eliminate a warning message due to the constructor initialization list being out of order. --- Cantera/src/transport/TransportFactory.cpp | 6 - Cantera/src/transport/TransportParams.h | 156 +++++++++++++-------- 2 files changed, 100 insertions(+), 62 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index e9c40e42d..72902ec87 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -90,12 +90,6 @@ namespace Cantera { const doublereal FiveThirds = 5.0/3.0; - TransportParams::~TransportParams(){ -#ifdef DEBUG_MODE - delete xml; -#endif - }; - //////////////////// class TransportFactory methods ////////////// diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 63c4b9f0b..119f6a7d6 100755 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -11,77 +11,121 @@ namespace Cantera { - /** - * Base class to hold transport model parameters. - * Used by TransportFactory. - */ - class TransportParams { + /** + * Base class to hold transport model parameters. + * Used by TransportFactory. + */ + class TransportParams { - public: + public: - TransportParams() : thermo(0), xml(0), velocityBasis(VB_MASSAVG) {} - virtual ~TransportParams(); - int nsp_; + TransportParams() : + nsp_(0), + thermo(0), + mw(0), + velocityBasis(VB_MASSAVG), + tmax(1000000.), + tmin(10.), + mode_(0), + xml(0), + log_level(-1) + { + } - // phase_t* mix; - thermo_t* thermo; - vector_fp mw; + virtual ~TransportParams() + { +#ifdef DEBUG_MODE + delete xml; +#endif + } - //! A basis for the average velocity can be specified. - //! Valid bases include "mole" "mass" and species names. - int velocityBasis; + int nsp_; - //minimum and maximum temperatures for parameter fits - doublereal tmax, tmin; - int mode_; - XML_Writer* xml; - int log_level; + // phase_t* mix; + thermo_t* thermo; + vector_fp mw; - }; + //! A basis for the average velocity can be specified. + //! Valid bases include "mole" "mass" and species names. + int velocityBasis; + + //minimum and maximum temperatures for parameter fits + doublereal tmax; + doublereal tmin; + int mode_; + XML_Writer* xml; + int log_level; + + }; - /** - * Holds transport model parameters relevant to transport in ideal - * gases with a kinetic theory of gases derived transport model. - * Used by TransportFactory. - */ - class GasTransportParams : public TransportParams { + /** + * Holds transport model parameters relevant to transport in ideal + * gases with a kinetic theory of gases derived transport model. + * Used by TransportFactory. + */ + class GasTransportParams : public TransportParams { - public: + public: - GasTransportParams() {} - ~GasTransportParams() {} + GasTransportParams() : + TransportParams(), + visccoeffs(0), + condcoeffs(0), + diffcoeffs(0), + polytempvec(0), + poly(0), + omega22_poly(0), + astar_poly(0), + bstar_poly(0), + cstar_poly(0), + zrot(0), + crot(0), + polar(0), + alpha(0), + fitlist(0), + eps(0), + sigma(0), + reducedMass(0, 0), + diam(0, 0), + epsilon(0, 0), + dipole(0, 0), + delta(0, 0) + { + } - // polynomial fits - //temperature-fit viscosity - std::vector visccoeffs; - //temperature-fit heat conduction - std::vector condcoeffs; - //temperature-fit diffusivity - std::vector diffcoeffs; - vector_fp polytempvec; + virtual ~GasTransportParams() {} - std::vector > poly; - std::vector omega22_poly; - std::vector astar_poly; - std::vector bstar_poly; - std::vector cstar_poly; + // polynomial fits + //temperature-fit viscosity + std::vector visccoeffs; + //temperature-fit heat conduction + std::vector condcoeffs; + //temperature-fit diffusivity + std::vector diffcoeffs; + vector_fp polytempvec; - vector_fp zrot; - vector_fp crot; + std::vector > poly; + std::vector omega22_poly; + std::vector astar_poly; + std::vector bstar_poly; + std::vector cstar_poly; - std::vector polar; - vector_fp alpha; - vector_fp fitlist; - vector_fp eps; - vector_fp sigma; - DenseMatrix reducedMass; - DenseMatrix diam; - DenseMatrix epsilon; - DenseMatrix dipole; - DenseMatrix delta; + vector_fp zrot; + vector_fp crot; - }; + std::vector polar; + vector_fp alpha; + vector_fp fitlist; + vector_fp eps; + vector_fp sigma; + DenseMatrix reducedMass; + DenseMatrix diam; + DenseMatrix epsilon; + DenseMatrix dipole; + DenseMatrix delta; + + }; } From 1f9d937d152a154e4cf3f93766ae2d9a02e5edf2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 2 Dec 2009 18:06:09 +0000 Subject: [PATCH 047/446] Fixed errors in the copy and assignment operator functions for the IonsFromNeutralVPSSTP object. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 8 ++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 46 ++++++++++++++------ Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 26 +++++++---- Cantera/src/thermo/MargulesVPSSTP.cpp | 8 ++-- Cantera/src/thermo/VPStandardStateTP.cpp | 2 +- 5 files changed, 61 insertions(+), 29 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index f8606c1d3..e5f9f5754 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -45,7 +45,7 @@ namespace Cantera { GibbsExcessVPSSTP::GibbsExcessVPSSTP(const GibbsExcessVPSSTP &b) : VPStandardStateTP() { - *this = operator=(b); + GibbsExcessVPSSTP::operator=(b); } /* @@ -56,10 +56,12 @@ namespace Cantera { */ GibbsExcessVPSSTP& GibbsExcessVPSSTP:: operator=(const GibbsExcessVPSSTP &b) { - if (&b != this) { - VPStandardStateTP::operator=(b); + if (&b == this) { + return *this; } + VPStandardStateTP::operator=(b); + moleFractions_ = b.moleFractions_; lnActCoeff_Scaled_ = b.lnActCoeff_Scaled_; dlnActCoeffdT_Scaled_ = b.dlnActCoeffdT_Scaled_; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 636940c6b..0dabe7ae4 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -141,7 +141,7 @@ namespace Cantera { neutralMoleculePhase_(0), IOwnNThermoPhase_(true) { - *this = operator=(b); + IonsFromNeutralVPSSTP::operator=(b); } /* @@ -152,14 +152,18 @@ namespace Cantera { */ IonsFromNeutralVPSSTP& IonsFromNeutralVPSSTP:: operator=(const IonsFromNeutralVPSSTP &b) { - if (&b != this) { - GibbsExcessVPSSTP::operator=(b); - } + if (&b == this) { + return *this; + } + + GibbsExcessVPSSTP::operator=(b); ionSolnType_ = b.ionSolnType_; numNeutralMoleculeSpecies_ = b.numNeutralMoleculeSpecies_; indexSpecialSpecies_ = b.indexSpecialSpecies_; indexSecondSpecialSpecies_ = b.indexSecondSpecialSpecies_; + fm_neutralMolec_ions_ = b.fm_neutralMolec_ions_; + fm_invert_ionForNeutral = b.fm_invert_ionForNeutral; NeutralMolecMoleFractions_ = b.NeutralMolecMoleFractions_; cationList_ = b.cationList_; numCationSpecies_ = b.numCationSpecies_; @@ -167,21 +171,35 @@ namespace Cantera { numAnionSpecies_ = b.numAnionSpecies_; passThroughList_ = b.passThroughList_; numPassThroughSpecies_ = b.numPassThroughSpecies_; - /* - * This is a shallow copy. We need to figure this out - */ - neutralMoleculePhase_ = b.neutralMoleculePhase_; - if (neutralMoleculePhase_) { - exit(-1); - } - IOwnNThermoPhase_ = b.IOwnNThermoPhase_; + /* + * If we own the underlying neutral molecule phase, then we do a deep + * copy. If not, we do a shallow copy. + */ + if (IOwnNThermoPhase_) { + if (b.neutralMoleculePhase_) { + if (neutralMoleculePhase_) { + delete neutralMoleculePhase_; + } + neutralMoleculePhase_ = (b.neutralMoleculePhase_)->duplMyselfAsThermoPhase(); + } else { + neutralMoleculePhase_ = 0; + } + } else { + neutralMoleculePhase_ = b.neutralMoleculePhase_; + } + + IOwnNThermoPhase_ = b.IOwnNThermoPhase_; moleFractionsTmp_ = b.moleFractionsTmp_; + muNeutralMolecule_ = b.muNeutralMolecule_; + gammaNeutralMolecule_ = b.gammaNeutralMolecule_; + dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_; + dlnActCoeffdlnC_NeutralMolecule_ = b.dlnActCoeffdlnC_NeutralMolecule_; return *this; } - /** + /* * * ~IonsFromNeutralVPSSTP(): (virtual) * @@ -191,7 +209,7 @@ namespace Cantera { IonsFromNeutralVPSSTP::~IonsFromNeutralVPSSTP() { if (IOwnNThermoPhase_) { delete neutralMoleculePhase_; - neutralMoleculePhase_=0; + neutralMoleculePhase_ = 0; } } diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 965087d34..f9070fa0c 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -152,9 +152,9 @@ namespace Cantera { /// Destructor. virtual ~IonsFromNeutralVPSSTP(); - //! Duplication routine for objects which inherit from ThermoPhase. + //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ @@ -720,7 +720,7 @@ namespace Cantera { //! Index of special species int indexSpecialSpecies_; - //! Index of special species + //! Index of special species int indexSecondSpecialSpecies_; //! Formula Matrix for composition of neutral molecules @@ -768,7 +768,7 @@ namespace Cantera { int numCationSpecies_; //! List of the species in this ThermoPhase which are anion species - std::vectoranionList_; + std::vector anionList_; //! Number of anion species int numAnionSpecies_; @@ -785,9 +785,22 @@ namespace Cantera { int numPassThroughSpecies_; public: + //! This is a pointer to the neutral Molecule Phase + /*! + * If the variable, IOwnNThermoPhase_ is true, then we own + * the pointer. If not, then this is considered a shallow pointer. + */ ThermoPhase *neutralMoleculePhase_; - protected: + + private: + + //! If true then we own the underlying neutral Molecule Phase + /*! + * If this is false, then the neutral molecule phase is considered + * as a shallow pointer. + */ bool IOwnNThermoPhase_; + //! ThermoPhase for the cation lattice /*! * Currently this is unimplemented and may be deleted @@ -808,9 +821,6 @@ namespace Cantera { mutable std::vector dlnActCoeffdT_NeutralMolecule_; mutable std::vector dlnActCoeffdlnC_NeutralMolecule_; - private: - - }; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 21af0007d..2017d8357 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -75,7 +75,7 @@ namespace Cantera { MargulesVPSSTP::MargulesVPSSTP(const MargulesVPSSTP &b) : GibbsExcessVPSSTP() { - *this = operator=(b); + MargulesVPSSTP::operator=(b); } /* @@ -86,9 +86,11 @@ namespace Cantera { */ MargulesVPSSTP& MargulesVPSSTP:: operator=(const MargulesVPSSTP &b) { - if (&b != this) { - GibbsExcessVPSSTP::operator=(b); + if (&b == this) { + return *this; } + + GibbsExcessVPSSTP::operator=(b); numBinaryInteractions_ = b.numBinaryInteractions_ ; m_HE_b_ij = b.m_HE_b_ij; diff --git a/Cantera/src/thermo/VPStandardStateTP.cpp b/Cantera/src/thermo/VPStandardStateTP.cpp index 0c4dd874e..bc4b85b4d 100644 --- a/Cantera/src/thermo/VPStandardStateTP.cpp +++ b/Cantera/src/thermo/VPStandardStateTP.cpp @@ -60,7 +60,7 @@ namespace Cantera { m_P0(OneAtm), m_VPSS_ptr(0) { - *this = b; + VPStandardStateTP::operator=(b); } /* From 9a142cfd87beb86f73e7ce783a474074710ee322 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 2 Dec 2009 23:07:43 +0000 Subject: [PATCH 048/446] Added "LiquidTransport.h" to the files included under transport.h --- Cantera/cxx/include/transport.h | 1 + 1 file changed, 1 insertion(+) diff --git a/Cantera/cxx/include/transport.h b/Cantera/cxx/include/transport.h index be76ab861..035753e74 100755 --- a/Cantera/cxx/include/transport.h +++ b/Cantera/cxx/include/transport.h @@ -13,4 +13,5 @@ #include "kernel/DustyGasTransport.h" #include "kernel/MultiTransport.h" #include "kernel/MixTransport.h" +#include "kernel/LiquidTransport.h" #endif From 951420155d2988057d0f8e1624e357f303160afa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:52:04 +0000 Subject: [PATCH 049/446] Added more initializations --- Cantera/src/base/Array.h | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/Cantera/src/base/Array.h b/Cantera/src/base/Array.h index 22c508748..bde5f28c6 100755 --- a/Cantera/src/base/Array.h +++ b/Cantera/src/base/Array.h @@ -56,8 +56,11 @@ namespace Cantera { /** * Default constructor. Create an empty array. */ - Array2D() : m_nrows(0), m_ncols(0) { - m_data.clear(); + Array2D() : + m_data(0), + m_nrows(0), + m_ncols(0) + { } //! Constructor. @@ -70,7 +73,7 @@ namespace Cantera { * @param v Default fill value. The default is 0.0 */ Array2D(const int m, const int n, const doublereal v = 0.0) - : m_nrows(m), m_ncols(n) { + : m_data(0), m_nrows(m), m_ncols(n) { m_data.resize(n*m); std::fill(m_data.begin(), m_data.end(), v); } @@ -79,7 +82,11 @@ namespace Cantera { /*! * @param y Array2D to make the copy from */ - Array2D(const Array2D& y) { + Array2D(const Array2D& y) : + m_data(0), + m_nrows(0), + m_ncols(0) + { m_nrows = y.m_nrows; m_ncols = y.m_ncols; m_data.resize(m_nrows*m_ncols); From 4f3715e119b3d33a7ac16800dea9d3503514d009 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:52:51 +0000 Subject: [PATCH 050/446] Added more initializations --- Cantera/src/base/units.h | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Cantera/src/base/units.h b/Cantera/src/base/units.h index 6e3ac70a5..9aa3a3355 100644 --- a/Cantera/src/base/units.h +++ b/Cantera/src/base/units.h @@ -177,7 +177,10 @@ namespace Cantera { * Units class constructor, containing the default mappings between * strings and units. */ - Unit(){ + Unit() : + m_u(), + m_act_u() + { // length m_u["m"] = 1.0; From 55a743c2c0587f7179d5b06bf05e02b27d9c46a6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:53:44 +0000 Subject: [PATCH 051/446] Added more initializations --- Cantera/src/base/misc.cpp | 65 +++++++++++++++++++++++++++++++++++---- 1 file changed, 59 insertions(+), 6 deletions(-) diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index 30d8d9a90..7aa434eb2 100755 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -176,15 +176,62 @@ namespace Cantera { * constructor for the Messages class which is a subclass * of the Application class. */ - Messages() { + Messages() : + errorMessage(0), + errorRoutine(0), + logwriter(0) +#ifdef WITH_HTML_LOGS + ,xmllog(0), + current(0), + loglevel(0), + loglevels(0), + loggroups(0) +#endif + { // install a default logwriter that writes to standard // output / standard error logwriter = new Logger(); + } + + //! Copy Constructor for the Messages class + /*! + * constructor for the Messages class which is a subclass + * of the Application class. + */ + Messages(const Messages &r) : + errorMessage(r.errorMessage), + errorRoutine(r.errorRoutine), + logwriter(0) #ifdef WITH_HTML_LOGS - xmllog = 0; - current = 0; - loglevel = 0; + , xmllog(r.xmllog), + current(r.current), + loglevel(r.loglevel), + loglevels(r.loglevels), + loggroups(r.loggroups) #endif + { + // install a default logwriter that writes to standard + // output / standard error + logwriter = new Logger(*(r.logwriter)); + } + + //! Assignment operator + Messages & operator=(const Messages &r) + { + if (this == &r) { + return *this; + } + errorMessage = r.errorMessage; + errorRoutine = r.errorRoutine; + logwriter = new Logger(*(r.logwriter)); +#ifdef WITH_HTML_LOGS + xmllog = r.xmllog; + current = r.current; + loglevel = r.loglevel; + loglevels = r.loglevels; + loggroups = r.loggroups; +#endif + return *this; } //! Destructor for the Messages class @@ -484,8 +531,14 @@ namespace Cantera { protected: //RFB Protected ctor access thru static member function Instance //! Constructor for class sets up the initial conditions - Application() : /*linelen(0),*/ stop_on_error(false), - tmp_dir("."), m_sleep("1") + Application() : + inputDirs(0), + stop_on_error(false), + options(), + tmp_dir("."), + xmlfiles(), + m_sleep("1"), + pMessenger(0) { #if !defined( THREAD_SAFE_CANTERA ) pMessenger = std::auto_ptr(new Messages()); From ae22fd8aca512f45dd12129be885746af06d7586 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:54:24 +0000 Subject: [PATCH 052/446] Added more initializations --- Cantera/src/base/xml.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index d4c6f0e80..a3cd5423e 100755 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -51,7 +51,8 @@ namespace Cantera { * @param line Number number where the error occurred. */ XML_Error(int line=0) : - m_line(line) + m_line(line), + m_msg(0) { m_msg = "Error in XML file"; if (line > 0) { @@ -392,7 +393,8 @@ namespace Cantera { ////////////////////////// XML_Node ///////////////////////////////// XML_Node::XML_Node(const char * cnm) - : m_value(""), + : m_name(""), + m_value(""), m_parent(0), m_locked(false), m_nchildren(0), From 1a3af47eb9759c7feea05323f5dd2ce8e71c1389 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:55:43 +0000 Subject: [PATCH 053/446] took out checkMFSum() which is inappropriate in that context. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index e5f9f5754..fd7e460c3 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -96,33 +96,21 @@ namespace Cantera { */ void GibbsExcessVPSSTP::setMassFractions(const doublereal* const y) { -#if DEBUG_MODE - checkMFSum(y); -#endif State::setMassFractions(y); getMoleFractions(DATA_PTR(moleFractions_)); } void GibbsExcessVPSSTP::setMassFractions_NoNorm(const doublereal* const y) { -#if DEBUG_MODE - checkMFSum(y); -#endif State::setMassFractions_NoNorm(y); getMoleFractions(DATA_PTR(moleFractions_)); } void GibbsExcessVPSSTP::setMoleFractions(const doublereal* const x) { -#if DEBUG_MODE - checkMFSum(x); -#endif State::setMoleFractions(x); getMoleFractions(DATA_PTR(moleFractions_)); } void GibbsExcessVPSSTP::setMoleFractions_NoNorm(const doublereal* const x) { -#if DEBUG_MODE - checkMFSum(x); -#endif State::setMoleFractions_NoNorm(x); getMoleFractions(DATA_PTR(moleFractions_)); } @@ -265,8 +253,8 @@ namespace Cantera { double GibbsExcessVPSSTP::checkMFSum(const doublereal * const x) const { doublereal norm = accumulate(x, x + m_kk, 0.0); if (fabs(norm - 1.0) > 1.0E-9) { - throw CanteraError("GibbsExcessVPSSTP::checkMFSun", - "MF sum exceeded tolerance of 1.0E-9:" + fp2str(norm)); + throw CanteraError("GibbsExcessVPSSTP::checkMFSum", + "(MF sum - 1) exceeded tolerance of 1.0E-9:" + fp2str(norm)); } return norm; } From 4f66d852b565697d72944d1d41810f957c7bc51a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:56:45 +0000 Subject: [PATCH 054/446] Added more expressive comments. --- Cantera/src/thermo/State.h | 32 ++++++++++++++++++++++---------- 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h index 21248e8d3..4d403d4aa 100644 --- a/Cantera/src/thermo/State.h +++ b/Cantera/src/thermo/State.h @@ -123,14 +123,18 @@ namespace Cantera { */ doublereal moleFraction(const int k) const; - /** - * Set the mole fractions to the specified values, and then - * normalize them so that they sum to 1.0. + + //! Set the mole fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! * @param x Array of unnormalized mole fraction values (input). - * Must have a length greater than or equal to the number of - * species. + * Must have a length greater than or equal to the number of + * species. * - * @param x Input vector of mole fractions. + * @param x Input vector of mole fractions. There is no restriction + * on the sum of the mole fraction vector. Internally, + * the State object will normalize this vector before + * storring its contents. * Length is m_kk. */ virtual void setMoleFractions(const doublereal* const x); @@ -176,7 +180,10 @@ namespace Cantera { * Must have a length greater than or equal to the number of * species. * - * @param y Input vector of mass fractions. + * @param y Input vector of mass fractions. There is no restriction + * on the sum of the mass fraction vector. Internally, + * the State object will normalize this vector before + * storring its contents. * Length is m_kk. */ virtual void setMassFractions(const doublereal* const y); @@ -209,9 +216,14 @@ namespace Cantera { */ doublereal concentration(const int k) const; - /** - * Set the concentrations to the specified values within the - * phase. + + //! Set the concentrations to the specified values within the + //! phase. + /* + * We set the concentrations here and therefore we set the + * overall density of the phase. We hold the temperature constant + * during this operation. Therefore, we have possibly changed + * the pressure of the phase by calling this routine. * * @param c The input vector to this routine is in dimensional * units. For volumetric phases c[k] is the From 05753b6ef1cdae2d1a4fcecd11f96e1d9b4bd47a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:58:08 +0000 Subject: [PATCH 055/446] Fixed an Error in the assignment operator. --- Cantera/src/thermo/PDSS_IonsFromNeutral.cpp | 46 +++++++++++++++------ 1 file changed, 34 insertions(+), 12 deletions(-) diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp index f768a4e89..28fa361de 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp @@ -37,8 +37,7 @@ namespace Cantera { { m_pdssType = cPDSS_IONSFROMNEUTRAL; } - - + //==================================================================================================================== PDSS_IonsFromNeutral::PDSS_IonsFromNeutral(VPStandardStateTP *tp, int spindex, std::string inputFile, std::string id) : PDSS(tp, spindex), @@ -50,8 +49,7 @@ namespace Cantera { m_pdssType = cPDSS_IONSFROMNEUTRAL; constructPDSSFile(tp, spindex, inputFile, id); } - - + //==================================================================================================================== PDSS_IonsFromNeutral::PDSS_IonsFromNeutral(VPStandardStateTP *tp, int spindex, const XML_Node& speciesNode, const XML_Node& phaseRoot, bool spInstalled) : @@ -68,8 +66,7 @@ namespace Cantera { std::string id = ""; constructPDSSXML(tp, spindex, speciesNode, phaseRoot, id); } - - + //==================================================================================================================== PDSS_IonsFromNeutral::PDSS_IonsFromNeutral(const PDSS_IonsFromNeutral &b) : PDSS(b) @@ -80,35 +77,57 @@ namespace Cantera { */ *this = b; } - - /** + //==================================================================================================================== + /* * Assignment operator */ PDSS_IonsFromNeutral& PDSS_IonsFromNeutral::operator=(const PDSS_IonsFromNeutral&b) { - if (&b == this) return *this; + if (&b == this) { + return *this; + } + PDSS::operator=(b); m_tmin = b.m_tmin; m_tmax = b.m_tmax; + + /* + * The shallow pointer copy in the next step will be insufficient in most cases. However, its + * functionally the best we can do for this assignment operator. We fix up the pointer in the + * initAllPtrs() function. + */ neutralMoleculePhase_ = b.neutralMoleculePhase_; + numMult_ = b.numMult_; idNeutralMoleculeVec = b.idNeutralMoleculeVec; factorVec = b.factorVec; add2RTln2_ = b.add2RTln2_; + tmpNM = b.tmpNM; specialSpecies_ = b.specialSpecies_; return *this; } - + //==================================================================================================================== PDSS_IonsFromNeutral::~PDSS_IonsFromNeutral() { } - + //==================================================================================================================== //! Duplicator PDSS* PDSS_IonsFromNeutral::duplMyselfAsPDSS() const { PDSS_IonsFromNeutral * idg = new PDSS_IonsFromNeutral(*this); return (PDSS *) idg; } + //==================================================================================================================== + void PDSS_IonsFromNeutral::initAllPtrs(VPStandardStateTP *tp, VPSSMgr *vpssmgr_ptr, + SpeciesThermo* spthermo) { + PDSS::initAllPtrs(tp, vpssmgr_ptr, spthermo); + IonsFromNeutralVPSSTP *ionPhase = dynamic_cast(tp); + if (!ionPhase) { + throw CanteraError("PDSS_IonsFromNeutral::initAllPts", "Dynamic cast failed"); + } + neutralMoleculePhase_ = ionPhase->neutralMoleculePhase_; + } + //==================================================================================================================== /** * constructPDSSXML: * @@ -140,6 +159,9 @@ namespace Cantera { } IonsFromNeutralVPSSTP *ionPhase = dynamic_cast(tp); + if (!ionPhase) { + throw CanteraError("PDSS_IonsFromNeutral::constructPDSSXML", "Dynamic cast failed"); + } neutralMoleculePhase_ = ionPhase->neutralMoleculePhase_; std::vector key; @@ -172,7 +194,7 @@ namespace Cantera { } } - + //==================================================================================================================== void PDSS_IonsFromNeutral::constructPDSSFile(VPStandardStateTP *tp, int spindex, std::string inputFile, std::string id) { From 646d31f8be2922d06ca276b7d1dbc89ac7e2e39f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 17:59:27 +0000 Subject: [PATCH 056/446] Fixed an error in the assignment operator. --- Cantera/src/thermo/VPStandardStateTP.cpp | 27 ++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/Cantera/src/thermo/VPStandardStateTP.cpp b/Cantera/src/thermo/VPStandardStateTP.cpp index bc4b85b4d..8331f6d86 100644 --- a/Cantera/src/thermo/VPStandardStateTP.cpp +++ b/Cantera/src/thermo/VPStandardStateTP.cpp @@ -85,9 +85,9 @@ namespace Cantera { m_Plast_ss = b.m_Plast_ss; m_P0 = b.m_P0; - - - // copy the pdss objects + /* + * Duplicate the pdss objects + */ if (m_PDSS_storage.size() > 0) { for (int k = 0; k < (int) m_PDSS_storage.size(); k++) { delete(m_PDSS_storage[k]); @@ -99,21 +99,36 @@ namespace Cantera { m_PDSS_storage[k] = ptmp->duplMyselfAsPDSS(); } + /* + * Duplicate the VPSS Manager object that conducts the calculations + */ if (m_VPSS_ptr) { delete m_VPSS_ptr; m_VPSS_ptr = 0; } m_VPSS_ptr = (b.m_VPSS_ptr)->duplMyselfAsVPSSMgr(); - m_VPSS_ptr->initAllPtrs(this, m_spthermo); + /* + * The VPSSMgr object contains shallow pointers. Whenever you have shallow + * pointers, they have to be fixed up to point to the correct objects refering + * back to this ThermoPhase's properties. + */ + m_VPSS_ptr->initAllPtrs(this, m_spthermo); + /* + * The PDSS objects contains shallow pointers. Whenever you have shallow + * pointers, they have to be fixed up to point to the correct objects refering + * back to this ThermoPhase's properties. This function also sets m_VPSS_ptr + * so it occurs after m_VPSS_ptr is set. + */ for (int k = 0; k < m_kk; k++) { - PDSS *ptmp = b.m_PDSS_storage[k]; + PDSS *ptmp = m_PDSS_storage[k]; ptmp->initAllPtrs(this, m_VPSS_ptr, m_spthermo); } + } return *this; } - + //==================================================================================================================== /* * ~VPStandardStateTP(): (virtual) * From fe6f8a29d03a18c00a93cb733953b83ab23e7dd1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:00:18 +0000 Subject: [PATCH 057/446] Fixed error in the assignment operator. --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 49 +++++++++++--------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 0dabe7ae4..aaa88fe7c 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -155,6 +155,26 @@ namespace Cantera { if (&b == this) { return *this; } + + /* + * If we own the underlying neutral molecule phase, then we do a deep + * copy. If not, we do a shallow copy. We get a valid pointer for + * neutralMoleculePhase_ first, because we need it to assign the pointers + * within the PDSS_IonsFromNeutral object. which is done in the + * GibbsExcessVPSSTP::operator=(b) step. + */ + if (IOwnNThermoPhase_) { + if (b.neutralMoleculePhase_) { + if (neutralMoleculePhase_) { + delete neutralMoleculePhase_; + } + neutralMoleculePhase_ = (b.neutralMoleculePhase_)->duplMyselfAsThermoPhase(); + } else { + neutralMoleculePhase_ = 0; + } + } else { + neutralMoleculePhase_ = b.neutralMoleculePhase_; + } GibbsExcessVPSSTP::operator=(b); @@ -172,23 +192,6 @@ namespace Cantera { passThroughList_ = b.passThroughList_; numPassThroughSpecies_ = b.numPassThroughSpecies_; - /* - * If we own the underlying neutral molecule phase, then we do a deep - * copy. If not, we do a shallow copy. - */ - if (IOwnNThermoPhase_) { - if (b.neutralMoleculePhase_) { - if (neutralMoleculePhase_) { - delete neutralMoleculePhase_; - } - neutralMoleculePhase_ = (b.neutralMoleculePhase_)->duplMyselfAsThermoPhase(); - } else { - neutralMoleculePhase_ = 0; - } - } else { - neutralMoleculePhase_ = b.neutralMoleculePhase_; - } - IOwnNThermoPhase_ = b.IOwnNThermoPhase_; moleFractionsTmp_ = b.moleFractionsTmp_; muNeutralMolecule_ = b.muNeutralMolecule_; @@ -824,21 +827,21 @@ namespace Cantera { neutralMoleculePhase_->setMoleFractions(DATA_PTR(NeutralMolecMoleFractions_)); } - void IonsFromNeutralVPSSTP::setMoleFractions(const doublereal* const y) { - GibbsExcessVPSSTP::setMoleFractions(y); + void IonsFromNeutralVPSSTP::setMoleFractions(const doublereal* const x) { + GibbsExcessVPSSTP::setMoleFractions(x); calcNeutralMoleculeMoleFractions(); neutralMoleculePhase_->setMoleFractions(DATA_PTR(NeutralMolecMoleFractions_)); } - void IonsFromNeutralVPSSTP::setMoleFractions_NoNorm(const doublereal* const y) { - GibbsExcessVPSSTP::setMoleFractions_NoNorm(y); + void IonsFromNeutralVPSSTP::setMoleFractions_NoNorm(const doublereal* const x) { + GibbsExcessVPSSTP::setMoleFractions_NoNorm(x); calcNeutralMoleculeMoleFractions(); neutralMoleculePhase_->setMoleFractions(DATA_PTR(NeutralMolecMoleFractions_)); } - void IonsFromNeutralVPSSTP::setConcentrations(const doublereal* const y) { - GibbsExcessVPSSTP::setConcentrations(y); + void IonsFromNeutralVPSSTP::setConcentrations(const doublereal* const c) { + GibbsExcessVPSSTP::setConcentrations(c); calcNeutralMoleculeMoleFractions(); neutralMoleculePhase_->setMoleFractions(DATA_PTR(NeutralMolecMoleFractions_)); } From 1756f4a65ef6fc96ec866b5b88cef33e1ea38665 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:01:43 +0000 Subject: [PATCH 058/446] changes in comments. --- Cantera/src/thermo/VPSSMgr.cpp | 26 +++++++++++++++++++++----- Cantera/src/thermo/VPSSMgr.h | 4 ++-- 2 files changed, 23 insertions(+), 7 deletions(-) diff --git a/Cantera/src/thermo/VPSSMgr.cpp b/Cantera/src/thermo/VPSSMgr.cpp index 1f8e451d8..64ec7e22c 100644 --- a/Cantera/src/thermo/VPSSMgr.cpp +++ b/Cantera/src/thermo/VPSSMgr.cpp @@ -74,12 +74,30 @@ namespace Cantera { *this = right; } + //==================================================================================================================== + /* + * Assigment operator + * We use a shallow copy strategy here. Note, this will have to be fixed up later. + */ VPSSMgr& VPSSMgr::operator=(const VPSSMgr &right) { if (&right == this) { return *this; } m_kk = right.m_kk; + /* + * What we are doing here is to make a shallow copy of the VPStandardStateTP + * pointer in the "new" VPSSMgr object using the value from the "old" + * VPSSMgr object. This is not appropriate if we are making a copy of a ThermoPhase + * object and the VPSSMgr objects are owned by the ThermoPhase object. + * + * The new object will want to have a different value of m_vptp_ptr than the + * value this is being copied here. It will want to refer to the copy of the + * VPStandardStateTP object being made that will own the new VPSSMgr object. + * However, the assignment object is not the place to carry out this fixup. + * + * We will have to "fix" up the shallow copies later. + */ m_vptp_ptr = right.m_vptp_ptr; m_spthermo = right.m_spthermo; m_tlast = -1.0; @@ -113,13 +131,12 @@ namespace Cantera { return *this; } - + //==================================================================================================================== VPSSMgr *VPSSMgr::duplMyselfAsVPSSMgr() const { VPSSMgr *vp = new VPSSMgr(*this); return vp; } - - + //==================================================================================================================== void VPSSMgr::initAllPtrs(VPStandardStateTP *vp_ptr, SpeciesThermo *sp_ptr) { m_vptp_ptr = vp_ptr; @@ -141,8 +158,7 @@ namespace Cantera { } } - - /*****************************************************************/ + //==================================================================================================================== // Standard States void diff --git a/Cantera/src/thermo/VPSSMgr.h b/Cantera/src/thermo/VPSSMgr.h index 5be3b3217..b57751883 100644 --- a/Cantera/src/thermo/VPSSMgr.h +++ b/Cantera/src/thermo/VPSSMgr.h @@ -772,11 +772,11 @@ namespace Cantera { const XML_Node * const phaseNode_ptr); - //! Initialize the internal pointers in this object + //! Initialize the internal shallow pointers in this object /*! * There are a bunch of internal shallow pointers that point to the owning * VPStandardStateTP and SpeciesThermo objects. This function reinitializes - * them. + * them. This function is called like an onion. * * @param vp_ptr Pointer to the VPStandardStateTP standard state * @param sp_ptr Poitner to the SpeciesThermo standard state From a6a6761eae16f741f61fb9200af8221a8f36f556 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:02:24 +0000 Subject: [PATCH 059/446] added another function --- Cantera/src/thermo/PDSS_IonsFromNeutral.h | 49 ++++++++++++++++------- 1 file changed, 35 insertions(+), 14 deletions(-) diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.h b/Cantera/src/thermo/PDSS_IonsFromNeutral.h index 58d963a15..4b95fd6c2 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.h +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.h @@ -48,18 +48,6 @@ namespace Cantera { */ PDSS_IonsFromNeutral(VPStandardStateTP *tp, int spindex); - //! Copy Constructur - /*! - * @param b Object to be copied - */ - PDSS_IonsFromNeutral(const PDSS_IonsFromNeutral& b); - - //! Assignment operator - /*! - * @param b Object to be copeid - */ - PDSS_IonsFromNeutral& operator=(const PDSS_IonsFromNeutral& b); - //! Constructor that initializes the object by examining the input file //! of the ThermoPhase object /*! @@ -91,13 +79,43 @@ namespace Cantera { PDSS_IonsFromNeutral(VPStandardStateTP *vptp_ptr, int spindex, const XML_Node& speciesNode, const XML_Node& phaseRef, bool spInstalled); + //! Copy Constructor + /*! + * @param b Object to be copied + */ + PDSS_IonsFromNeutral(const PDSS_IonsFromNeutral& b); + + //! Assignment operator + /*! + * @param b Object to be copeid + */ + PDSS_IonsFromNeutral& operator=(const PDSS_IonsFromNeutral& b); //! Destructor virtual ~PDSS_IonsFromNeutral(); //! Duplicator virtual PDSS *duplMyselfAsPDSS() const; - + + //! Initialize or Reinitialize all shallow pointers in the object + /*! + * This command is called to reinitialize all shallow pointers in the + * object. It's needed for the duplicator capability. + * We need to have an inherited function here to set neutralMoleculePhase_ properly. + * + * @param vptp_ptr Pointer to the Variable pressure %ThermoPhase object + * This object must have already been malloced. + * + * @param vpssmgr_ptr Pointer to the variable pressure standard state + * calculator for this phase + * + * @param spthermo_ptr Pointer to the optional SpeciesThermo object + * that will handle the calculation of the reference + * state thermodynamic coefficients. + */ + virtual void initAllPtrs(VPStandardStateTP *vptp_ptr, VPSSMgr *vpssmgr_ptr, + SpeciesThermo* spthermo_ptr); + /** * @} * @name Utilities @@ -436,7 +454,10 @@ namespace Cantera { doublereal m_tmax; - //! Pointer to the Neutral Molecule thermophase object + //! Pointer to the Neutral Molecule ThermoPhase object + /*! + * This is a shallow pointer. + */ ThermoPhase *neutralMoleculePhase_; public: From 380a10a863a5cedfda069008db380a3bb41f2482 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:03:35 +0000 Subject: [PATCH 060/446] Added another function initAllPts() to handle shallow pointer concerns. --- Cantera/src/thermo/Phase.h | 1 + Cantera/src/thermo/VPSSMgr_General.cpp | 42 +++++++++++++++++++++++--- Cantera/src/thermo/VPSSMgr_General.h | 15 +++++++-- 3 files changed, 50 insertions(+), 8 deletions(-) diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index 8512f8aae..60c5ec06a 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -502,6 +502,7 @@ namespace Cantera { * base classes become hidden. */ int m_kk; + /** * m_ndim is the dimensionality of the phase. Volumetric * phases have dimensionality 3 and surface phases have diff --git a/Cantera/src/thermo/VPSSMgr_General.cpp b/Cantera/src/thermo/VPSSMgr_General.cpp index fc90e6e4e..442eeda59 100644 --- a/Cantera/src/thermo/VPSSMgr_General.cpp +++ b/Cantera/src/thermo/VPSSMgr_General.cpp @@ -63,12 +63,23 @@ namespace Cantera { m_useTmpRefStateStorage = true; *this = right; } - - + //==================================================================================================================== VPSSMgr_General& VPSSMgr_General::operator=(const VPSSMgr_General &b) { - if (&b == this) return *this; + if (&b == this) { + return *this; + } VPSSMgr::operator=(b); + /* + * Must fill in the shallow pointers. These must have already been transfered + * and storred in the owning VPStandardStateTP class. Note we are aware that at this point + * m_vptr_ptr may refer back to the wrong ThermoPhase object. However, the shallow copy + * performed here is consistent with the assignment operator's general functionality. + */ + m_PDSS_ptrs.resize(m_kk); + for (int k = 0; k < m_kk; k++) { + m_PDSS_ptrs[k] = m_vptp_ptr->providePDSS(k); + } return *this; } @@ -76,8 +87,29 @@ namespace Cantera { VPSSMgr_General *vpm = new VPSSMgr_General(*this); return (VPSSMgr *) vpm; } - - + //==================================================================================================================== + // Initialize the internal shallow pointers in this object + /* + * There are a bunch of internal shallow pointers that point to the owning + * VPStandardStateTP and SpeciesThermo objects. This function reinitializes + * them. This function is called like an onion. + * + * @param vp_ptr Pointer to the VPStandardStateTP standard state + * @param sp_ptr Poitner to the SpeciesThermo standard state + */ + void VPSSMgr_General::initAllPtrs(VPStandardStateTP *vp_ptr, SpeciesThermo *sp_ptr) + { + VPSSMgr::initAllPtrs(vp_ptr, sp_ptr); + /* + * Must fill in the shallow pointers. These must have already been transfered + * and storred in the owning VPStandardStateTP class. + */ + m_PDSS_ptrs.resize(m_kk); + for (int k = 0; k < m_kk; k++) { + m_PDSS_ptrs[k] = m_vptp_ptr->providePDSS(k); + } + } + //==================================================================================================================== void VPSSMgr_General::_updateRefStateThermo() const { if (m_useTmpRefStateStorage) { diff --git a/Cantera/src/thermo/VPSSMgr_General.h b/Cantera/src/thermo/VPSSMgr_General.h index 458c5e5c4..fe43a307b 100644 --- a/Cantera/src/thermo/VPSSMgr_General.h +++ b/Cantera/src/thermo/VPSSMgr_General.h @@ -266,8 +266,18 @@ namespace Cantera { */ virtual VPSSMgr_enumType reportVPSSMgrType() const ; - - protected: + //! Initialize the internal shallow pointers in this object + /*! + * There are a bunch of internal shallow pointers that point to the owning + * VPStandardStateTP and SpeciesThermo objects. This function reinitializes + * them. This function is called like an onion. + * + * @param vp_ptr Pointer to the VPStandardStateTP standard state + * @param sp_ptr Poitner to the SpeciesThermo standard state + */ + virtual void initAllPtrs(VPStandardStateTP *vp_ptr, SpeciesThermo *sp_ptr); + + private: //! Shallow pointers containing the PDSS objects for the species //! in this phase. @@ -276,7 +286,6 @@ namespace Cantera { */ std::vector m_PDSS_ptrs; - private: //! VPStandardStateTP has its own err routine /*! From 6842b761db03cadf72072fe80aede308d2882000 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:13:11 +0000 Subject: [PATCH 061/446] Added more ignore files. From 443ccf0af5e3f1973c074e95a62f98b50a9f61b6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 18:14:40 +0000 Subject: [PATCH 062/446] Added ignore files. From da0cb495c270ad7590020e7200516e93698eb024 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Dec 2009 19:04:54 +0000 Subject: [PATCH 063/446] Merging trunk changes into the branch --- .../cygwin_gcc344_dbg_f2c_numeric.sh | 164 +++++++++++++++++ .../cygwin_gcc344_dbg_f2c_numpy.sh | 167 ++++++++++++++++++ ... => linux_32_gcc343_dbg_python235_numeric} | 0 ... => linux_32_gcc343_opt_python235_numeric} | 0 ...py => linux_64_gcc424_dbg_python252_numpy} | 0 ...py => linux_64_gcc424_opt_python252_numpy} | 0 ...on251_numpy => mac_gcc401_python251_numpy} | 0 .../sol10_64bit_CC57_dbg_py24_numarray | 141 +++++++++++++++ 8 files changed, 472 insertions(+) create mode 100755 docs/install_examples/cygwin_gcc344_dbg_f2c_numeric.sh create mode 100755 docs/install_examples/cygwin_gcc344_dbg_f2c_numpy.sh rename docs/install_examples/{linux.32_gcc343_python235_numeric => linux_32_gcc343_dbg_python235_numeric} (100%) rename docs/install_examples/{linux.32_gcc343_opt_python235_numeric => linux_32_gcc343_opt_python235_numeric} (100%) rename docs/install_examples/{linux.64_gcc424_python252_numpy => linux_64_gcc424_dbg_python252_numpy} (100%) rename docs/install_examples/{linux.64_gcc424_opt_python252_numpy => linux_64_gcc424_opt_python252_numpy} (100%) rename docs/install_examples/{mac.gcc401_python251_numpy => mac_gcc401_python251_numpy} (100%) create mode 100755 docs/install_examples/sol10_64bit_CC57_dbg_py24_numarray diff --git a/docs/install_examples/cygwin_gcc344_dbg_f2c_numeric.sh b/docs/install_examples/cygwin_gcc344_dbg_f2c_numeric.sh new file mode 100755 index 000000000..9c4450748 --- /dev/null +++ b/docs/install_examples/cygwin_gcc344_dbg_f2c_numeric.sh @@ -0,0 +1,164 @@ +#!/bin/sh +# ------------------------------------------------------------------------------ +# +# Example Cantera pre-preconfig configuration script +# 10/20/09 +# +# Platform: cygwin +# Compiler: gcc v. 3.4.4 +# Optimization: Debug version +# python: v. 2.5.2 (full installation) +# matlab: no +# f2c: yes +# num python numeric +# +# +# --------------------------------------------------------------------------- +# The only place where the User must custimize this installation +# is located at the top here: +# +# Specify the installation directory here: +# +Cantera_Install_Dir='/cygdrive/c/cygwin_env/arch/cygwin/cantera-1.8_develop' +# +# Specify the Sundials installation directory here (leave it as a null script +# if you don't want to link sundials in +# +# Sundials_Home='' +Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.3.0_dbg' +# +# Specify the Sundials version number (either 2.2, 2.3, or 2.4) +Sundials_Version='2.3' +# Sundials_Version=2.4' +# ----------------------------------------------------------------------------- +# +# User may optionally customize below this line (but doesn't have to) -- +# +CANTERA_CONFIG_PREFIX=$Cantera_Install_Dir +export CANTERA_CONFIG_PREFIX + +SET_PYTHON_SITE_PACKAGE_TOPDIR=y +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_CMD=/usr/bin/python +export PYTHON_CMD + +# +# The full python package works within cygwin. Minimal is needed at the least +# +PYTHON_PACKAGE='full' +#PYTHON_PACKAGE='minimal' +export PYTHON_PACKAGE + +WITH_IDEAL_SOLUTIONS="y" +export WITH_IDEAL_SOLUTIONS + +WITH_ELECTROLYTES="y" +export WITH_ELECTROLYTES + +WITH_VCSNONIDEAL="y" +export WITH_VCSNONIDEAL + +# +# Matlab on the pc is supported through the windows vc++ 8.0 compilation +# environment +# +BUILD_MATLAB_TOOLBOX="n" +export BUILD_MATLAB_TOOLBOX + +NUMARRAY_HOME='' +export NUMARRAY_HOME +# +# Turns on extra debugging +# +DEBUG_MODE='y' +export DEBUG_MODE +# +# Numeric must have already been installed in the +# /usr/lib/python2.5/site-packages +# directory before the Cantera installation. If not, you can always +# do a minimal python installation and forego forming Cantera's python interface. +# +USE_NUMERIC="y" +export USE_NUMERIC +# +# We use F2C with the cygwin installation. However, the g77 interface should +# work too. +# +BUILD_WITH_F2C="y" +export BUILD_WITH_F2C + +BITCOMPILE="32" +export BITCOMPILE +# +# We use the default gcc compilers that come with cygwin. Currently, this +# is gcc v. 3.4.4. +# +CXX='g++' +export CXX +# +CC='gcc' +export CC +# +F77='g77' +export F77 +# +# Debug options +# +# -DDEBUG_HKM +# -DDEBUG_BASISOPTIMIZE +# -DDEBUG_CHEMEQUIL +# +CXXFLAGS="-g -Wall " +export CXXFLAGS + +CFLAGS=$CXXFLAGS +export CFLAGS + +FFLAGS="-g " +export FFLAGS + +LDFLAGS='-g' +export LDFLAGS + +LCXX_END_LIBS="-lm -lstdc++" +export LCXX_END_LIBS + +# The gcc compiler in cygwin will put a .exe extension on anyway. So, +# we might as well define this field as .exe. cygwin will automagically +# equate executable files with no extension as having an .exe extension. +# This is very mysterious. However, the mystery goes away if you define +# these files to have a .exe suffix from the getgo. +EXE_EXT=".exe" +export EXE_EXT + +EXTRA_LINK="" +export EXTRA_LINK + +MAKE=make +export MAKE +# +# Specify the SUNDIALS option +# +if test -n "$Sundials_Home" +then + USE_SUNDIALS='y' + SUNDIALS_VERSION=$Sundials_Version +else + USE_SUNDIALS='n' +fi +export USE_SUNDIALS +export SUNDIALS_VERSION +# +# Specify where to find the sundials installation directories +# +SUNDIALS_HOME=$Sundials_Home +export SUNDIALS_HOME +# +# Ok, fire off the main preconfig script +# +./preconfig + diff --git a/docs/install_examples/cygwin_gcc344_dbg_f2c_numpy.sh b/docs/install_examples/cygwin_gcc344_dbg_f2c_numpy.sh new file mode 100755 index 000000000..b00277856 --- /dev/null +++ b/docs/install_examples/cygwin_gcc344_dbg_f2c_numpy.sh @@ -0,0 +1,167 @@ +#!/bin/sh +# ------------------------------------------------------------------------------ +# +# Example Cantera pre-preconfig configuration script +# 10/20/09 +# +# Platform: cygwin +# Compiler: gcc v. 3.4.4 +# Optimization: Debug version +# python: v. 2.5.2 (full installation) +# matlab: no +# f2c: yes +# num python: numpy, which is distributed with cygwin +# +# +# --------------------------------------------------------------------------- +# The only place where the User must custimize this installation +# is located at the top here: +# +# Specify the installation directory here: +# +Cantera_Install_Dir='/cygdrive/c/cygwin_env/arch/cygwin/cantera-1.8_develop' +# +# Specify the Sundials installation directory here (leave it as a null script +# if you don't want to link sundials in +# +# Sundials_Home='' +Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.3.0_dbg' +# +# Specify the Sundials version number (either 2.2, 2.3, or 2.4) +Sundials_Version='2.3' +# Sundials_Version=2.4' +# ----------------------------------------------------------------------------- +# +CANTERA_CONFIG_PREFIX=$Cantera_Install_Dir +export CANTERA_CONFIG_PREFIX + +SET_PYTHON_SITE_PACKAGE_TOPDIR=y +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_CMD=/usr/bin/python +export PYTHON_CMD + +# +# The full python package works within cygwin. Minimal is needed at the least +# +PYTHON_PACKAGE='full' +#PYTHON_PACKAGE='minimal' +export PYTHON_PACKAGE + +WITH_IDEAL_SOLUTIONS="y" +export WITH_IDEAL_SOLUTIONS + +WITH_ELECTROLYTES="y" +export WITH_ELECTROLYTES + +WITH_VCSNONIDEAL="y" +export WITH_VCSNONIDEAL + +# +# Matlab on the pc is supported through the windows vc++ 8.0 compilation +# environment. Therefore, we turn it off here. +# +BUILD_MATLAB_TOOLBOX="n" +export BUILD_MATLAB_TOOLBOX + +NUMARRAY_HOME='' +export NUMARRAY_HOME +# +# Turns on extra debugging +# +DEBUG_MODE='y' +export DEBUG_MODE +# +# Numpy must have already been installed in the +# /usr/lib/python2.5/site-packages +# directory before the Cantera installation. If not, you can always +# do a minimal python installation and forego forming Cantera's python interface. +# +USE_NUMPY="y" +export USE_NUMPY +# +# Specify where to find the include files within the numpy distribution +# +NUMPY_INC_DIR="/usr/lib/python2.5/site-packages/numpy/core/include" +export NUMPY_INC_DIR +# +# We use F2C with the cygwin installation. However, the g77 interface should +# work too. +# +BUILD_WITH_F2C="y" +export BUILD_WITH_F2C + +BITCOMPILE="32" +export BITCOMPILE +# +# We use the default gcc compilers that come with cygwin. Currently, this +# is gcc v. 3.4.4. +# +CXX='g++' +export CXX +# +CC='gcc' +export CC +# +F77='g77' +export F77 +# +# Debug options +# +# -DDEBUG_HKM +# -DDEBUG_BASISOPTIMIZE +# -DDEBUG_CHEMEQUIL +# +CXXFLAGS="-g -Wall " +export CXXFLAGS + +CFLAGS=$CXXFLAGS +export CFLAGS + +FFLAGS="-g " +export FFLAGS + +LDFLAGS='-g' +export LDFLAGS + +LCXX_END_LIBS="-lm -lstdc++" +export LCXX_END_LIBS + +# The gcc compiler in cygwin will put a .exe extension on anyway. So, +# we might as well define this field as .exe. cygwin will automagically +# equate executable files with no extension as having an .exe extension. +# This is very mysterious. However, the mystery goes away if you define +# these files to have a .exe suffix from the getgo. +EXE_EXT=".exe" +export EXE_EXT + +EXTRA_LINK="" +export EXTRA_LINK + +MAKE=make +export MAKE +# +# Specify the SUNDIALS option +# +if test -n "$Sundials_Home" +then + USE_SUNDIALS='y' + SUNDIALS_VERSION=$Sundials_Version +else + USE_SUNDIALS='n' +fi +export USE_SUNDIALS +export SUNDIALS_VERSION +# +# Specify where to find the sundials installation directories +# +SUNDIALS_HOME=$Sundials_Home +export SUNDIALS_HOME +# +# Ok, fire off the main preconfig script +# +./preconfig + diff --git a/docs/install_examples/linux.32_gcc343_python235_numeric b/docs/install_examples/linux_32_gcc343_dbg_python235_numeric similarity index 100% rename from docs/install_examples/linux.32_gcc343_python235_numeric rename to docs/install_examples/linux_32_gcc343_dbg_python235_numeric diff --git a/docs/install_examples/linux.32_gcc343_opt_python235_numeric b/docs/install_examples/linux_32_gcc343_opt_python235_numeric similarity index 100% rename from docs/install_examples/linux.32_gcc343_opt_python235_numeric rename to docs/install_examples/linux_32_gcc343_opt_python235_numeric diff --git a/docs/install_examples/linux.64_gcc424_python252_numpy b/docs/install_examples/linux_64_gcc424_dbg_python252_numpy similarity index 100% rename from docs/install_examples/linux.64_gcc424_python252_numpy rename to docs/install_examples/linux_64_gcc424_dbg_python252_numpy diff --git a/docs/install_examples/linux.64_gcc424_opt_python252_numpy b/docs/install_examples/linux_64_gcc424_opt_python252_numpy similarity index 100% rename from docs/install_examples/linux.64_gcc424_opt_python252_numpy rename to docs/install_examples/linux_64_gcc424_opt_python252_numpy diff --git a/docs/install_examples/mac.gcc401_python251_numpy b/docs/install_examples/mac_gcc401_python251_numpy similarity index 100% rename from docs/install_examples/mac.gcc401_python251_numpy rename to docs/install_examples/mac_gcc401_python251_numpy diff --git a/docs/install_examples/sol10_64bit_CC57_dbg_py24_numarray b/docs/install_examples/sol10_64bit_CC57_dbg_py24_numarray new file mode 100755 index 000000000..98d450e33 --- /dev/null +++ b/docs/install_examples/sol10_64bit_CC57_dbg_py24_numarray @@ -0,0 +1,141 @@ +#!/bin/sh +# +# Sierra 64 bit setup: +# -xO4 -xtarget=native64 -xarch=native64 -xcode=pic32 -DSUN10 -library=stlport4 +# +# Sierra warnings setup: +# +w2 -errtags -erroff=doubunder,reftotemp,ppextraw,inllargeint,inllargeuse,wnoelseretvalue,truncwarn,diffenumtype,notused,wvarhid enmem,badcastw,hidef -errwarn=%all,no%wunreachable,no%partinit +# +# Notes: +# When you add flsgs with % in them python won't build, because there is an +# error in the python distutils routines. I am currently manually +# fixing these. +# +# Program Names: +# +MAKE=gmake +export MAKE + +# +# Pointers to the 64 bit python built with Sunpro compilers +PYTHON_DIR=${HOME}/arch/sol_py64 +export PYTHON_DIR +PYTHON_CMD=${HOME}/arch/sol_py64/bin/python +export PYTHON_CMD + +# +# Use the CC compiler for C++ code +CXX=CC +export CXX +# +# Specification of the c compiler +# +CC=cc +export CC + +CXX_DEPENDS='CC -xM1' +export CXX_DEPENDS + +USE_NUMERIC='n' +export USE_NUMERIC + +# +# HKM 7/22/09 +# The matlab option is currently not working. Matlab uses the gcc +# compiler. This setup uses the solaris compiler. I can get +# the matlab extensions to compile. But, when I run matlab +# I get an unsatisfied external +# When I add the commands: +# -l/opt/SUNWspro/lib/f9 -lCrun -lCstd -lfsu +# to the matlab build, I can get rid of the runtime unsatisfied +# external. However, I immediate crash dump matlab. This +# suggests that there are duplicate Cstd routines from gcc and +# from the solaris compilers fighting it out. +# I believe the solution will involve compiling everything +# with gcc in order to get matlab on solaris to work. +# +BUILD_MATLAB_TOOLBOX="n" +export BUILD_MATLAB_TOOLBOX + +DEBUG_MODE="y" +export DEBUG_MODE + +# +# Compiler Flags +# +BITCOMPILE="64" +export BITCOMPILE +# +# remember the issue with % and python +# +EFLAGS=" +w2 -errtags -erroff=doubunder,reftotemp,ppextraw,inllargeint,inllargeuse,wnoelseretvalue,truncwarn,diffenumtype,notused,wvarhidenmem,badcastw,hidef -errwarn=%all,no%wunreachable,no%partinit" +#AFLAGS=" -xtarget=native64 -xarch=native64 -xcode=pic32 -library=stlport4" +AFLAGS=" -xtarget=native64 -xarch=native64 -xcode=pic32" +export AFLAGS + +F77=f77 +export F77 + +F90=f95 +export F90 + +FFLAGS="-g -xtarget=native64 -xarch=native64 -xcode=pic32 " +export FFLAGS + +CFLAGS="-g -xtarget=native64 -xarch=native64 -xcode=pic32 -v " +export CFLAGS + +CXXFLAGS="-g $AFLAGS $EFLAGS -DDEBUG_HKM" +export CXXFLAGS + +LCXX_END_LIBS="-lm " +export LCXX_END_LIBS + +# other useful endlibs for solaris 64 bit are +# -mt -lsunmath -lfsu + +USE_SUNDIALS='n' +export USE_SUNDIALS + +WITH_VCSNONIDEAL='y' +export WITH_VCSNONIDEAL + +# +# Location Variables - set the directory to point to +# a 64-bit specific directory. +# +CANTERA_INSTALL_DIR=${HOME}/arch/sol_py64/cantera-1.8 +export CANTERA_INSTALL_DIR + +CANTERA_CONFIG_PREFIX=${HOME}/arch/sol_py64/cantera-1.8 +export CANTERA_CONFIG_PREFIX + +#CANTERA_PYTHON_HOME=${CANTERA_PYTHON_HOME:="$HOME/python_modules"} +#export CANTERA_PYTHON_HOME + +SET_PYTHON_SITE_PACKAGE_TOPDIR="y" +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=${HOME}"/arch/sol_py64/cantera-1.8" +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_PACKAGE="full" +#PYTHON_PACKAGE="minimal" +#PYTHON_PACKAGE="none" +export PYTHON_PACKAGE + +BUILD_WITH_F2C="n" +export BUILD_WITH_F2C + +# +# Archive commands +# +ARCHIVE="CC -xar -xcode=pic32 -o " +export ARCHIVE + + +# +# Invoke the regular configure script +# +./preconfig + From 47aba7b3fdd6cf4f9ff844a0e09b384ffaa4417b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 7 Dec 2009 17:36:29 +0000 Subject: [PATCH 064/446] Took out the FtnTransport.h file. It's no longer used --- tools/doc/Cantera.cfg.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index e56d4f6dc..72b352910 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -165,7 +165,7 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ vcs_MultiPhaseEquil.h vcs_MultiPhaseEquil.cpp \ FalloffFactory.h FalloffFactory.cpp \ TransportBase.h TransportBase.cpp TransportParams.h \ - MMCollisionInt.h L_matrix.h MMCollisionInt.cpp FtnTransport.h \ + MMCollisionInt.h L_matrix.h MMCollisionInt.cpp \ TransportFactory.h TransportFactory.cpp \ MultiTransport.h MultiTransport.cpp MixTransport.h MixTransport.cpp \ DustyGasTransport.h DustyGasTransport.cpp \ From 0e85b295cc688decff7b8b433f2e99cf957c514a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 8 Dec 2009 17:33:06 +0000 Subject: [PATCH 065/446] An initial implementation of a string function that returns the eosType(). This is something that we've been lacking. --- Cantera/src/thermo/ThermoFactory.cpp | 20 ++++++++++++++++++++ Cantera/src/thermo/ThermoFactory.h | 10 ++++++++++ 2 files changed, 30 insertions(+) diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 5cc165beb..c1e33c528 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -218,6 +218,26 @@ namespace Cantera { return th; } + // Translate the eosType id into a string + /* + * Returns a string representation of the eosType id for a phase. + * @param ieos eosType id of the phase. This is unique for the phase + * @param length maximum length of the return string. Defaults to 100 + * + * @return returns a string representation. + */ + std::string eosTypeString(int ieos, int length) + { + std::string ss = "UnknownPhaseType"; + // bool found = false; + for (int n = 0; n < ntypes; n++) { + if (_itypes[n] == ieos) { + ss = _types[n]; + //found = true; + } + } + return ss; + } /* diff --git a/Cantera/src/thermo/ThermoFactory.h b/Cantera/src/thermo/ThermoFactory.h index b9a034086..01ec78d12 100644 --- a/Cantera/src/thermo/ThermoFactory.h +++ b/Cantera/src/thermo/ThermoFactory.h @@ -143,6 +143,16 @@ namespace Cantera { return f->newThermoPhase(model); } + //! Translate the eosType id into a string + /*! + * Returns a string representation of the eosType id for a phase. + * @param ieos eosType id of the phase. This is unique for the phase + * @param length maximum length of the return string. Defaults to 100 + * + * @return returns a string representation. + */ + std::string eosTypeString(int ieos, int length = 100); + /*! * This routine first looks up the From 1687ecaf1b3e22c162d4ceef848974c3e9ee8b0b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 9 Dec 2009 16:52:16 +0000 Subject: [PATCH 066/446] Bug fix involving kinetics operators that use HMWSoln. The member function getActivityConcentration() calculated the standard concentrations for solute species incorrectly. This caused the reaction rates of progress for kinetics operations involving HMWSoln to be calculated incorrectly. In particular, equilibrium constants (which were and are correct) were not compatible with forward vs. reverse ROP's. I fixed this error, and worked on more documentation of generalized activity concentrations. --- Cantera/src/thermo/HMWSoln.cpp | 10 ++- Cantera/src/thermo/HMWSoln.h | 135 +++++++++++++++++++++++++++------ 2 files changed, 118 insertions(+), 27 deletions(-) diff --git a/Cantera/src/thermo/HMWSoln.cpp b/Cantera/src/thermo/HMWSoln.cpp index 073eeaddf..8e30b0ac5 100644 --- a/Cantera/src/thermo/HMWSoln.cpp +++ b/Cantera/src/thermo/HMWSoln.cpp @@ -917,10 +917,14 @@ namespace Cantera { * reaction rate expressions within the phase. */ void HMWSoln::getActivityConcentrations(doublereal* c) const { - double c_solvent = standardConcentration(); + double cs_solvent = standardConcentration(); getActivities(c); - for (int k = 0; k < m_kk; k++) { - c[k] *= c_solvent; + c[0] *= cs_solvent; + if (m_kk > 1) { + double cs_solute = standardConcentration(1); + for (int k = 1; k < m_kk; k++) { + c[k] *= cs_solute; + } } } diff --git a/Cantera/src/thermo/HMWSoln.h b/Cantera/src/thermo/HMWSoln.h index 40cce6f86..f174a9469 100644 --- a/Cantera/src/thermo/HMWSoln.h +++ b/Cantera/src/thermo/HMWSoln.h @@ -1027,10 +1027,12 @@ namespace Cantera { * this phase equal to the default concentration of the solvent at the system temperature * and pressure multiplied by Mnaught (kg solvent / gmol solvent). The solvent * standard concentration is just equal to its standard state concentration. + * + * * This means that the - * kinetics operator essentially works on an generalized concentration basis (kg / m3), + * kinetics operator essentially works on an generalized concentration basis (kmol / m3), * with units for the kinetic rate constant specified - * as if all reactants (solvent or solute) are on a concentration basis (kg /m3). + * as if all reactants (solvent or solute) are on a concentration basis (kmol /m3). * The concentration will be modified by the activity coefficients. * * For example, a bulk-phase binary reaction between liquid solute species @@ -1039,39 +1041,50 @@ namespace Cantera { * following equation for its rate of progress variable, \f$ R^1 \f$, which has * units of kmol m-3 s-1. * + * \f[ + * R^1 = k^1 C_j^a C_k^a = k^1 (C^o_o \tilde{M}_o a_j) (C^o_o \tilde{M}_o a_k) + * \f] + * + * where * * \f[ - * R^1 = k^1 C_j^a C_k^a = k^1 (C_o \tilde{M}_o a_j) (C_o \tilde{M}_o a_k) - * \f] - * where - * \f[ - * C_j^a = C_o \tilde{M}_o a_j \quad and \quad C_k^a = C_o \tilde{M}_o a_k + * C_j^a = C^o_o \tilde{M}_o a_j \quad and \quad C_k^a = C^o_o \tilde{M}_o a_k * \f] * * \f$ C_j^a \f$ is the activity concentration of species j, and - * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C_o \f$ - * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ is + * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^o_o \f$ + * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ * has units of kg solvent per gmol solvent and is equal to * * \f[ * \tilde{M}_o = \frac{M_o}{1000} * \f] * - * * \f$ a_j \f$ is * the activity of species j at the current temperature and pressure * and concentration of the liquid phase is given by the molality based * activity coefficient multiplied by the molality of the jth species. * * \f[ - * a_j = \gamma_j^\triangle m_j + * a_j = \gamma_j^\triangle m_j = \gamma_j^\triangle \frac{n_j}{\tilde{M}_o n_o} * \f] * * \f$k^1 \f$ has units of m3 kmol-1 s-1. * + * Therefore the generalized activity concentration of a solute species has the following form + * + * \f[ + * C_j^a = C^o_o \frac{\gamma_j^\triangle n_j}{n_o} + * \f] + * + * The generalized activity concentration of the solvent has the same units, but its a simpler form + * + * \f[ + * C_o^a = C^o_o a_o + * \f] * * The reverse rate constant can then be obtained from the law of microscopic reversibility - * and the equilibrium expression for the system. + * and the equilibrium expression for the system. * * \f[ * \frac{a_j a_k}{ a_l} = K^{o,1} = \exp(\frac{\mu^o_l - \mu^o_j - \mu^o_k}{R T} ) @@ -1587,18 +1600,31 @@ namespace Cantera { * @{ */ - /** - * This method returns an array of generalized concentrations - * \f$ C_k\f$ that are defined such that - * \f$ a_k = C_k / C^0_k, \f$ where \f$ C^0_k \f$ + + //! This method returns an array of generalized activity concentrations + /*! + * The generalized activity concentrations, \f$ C_k^a\f$, are defined such that + * \f$ a_k = C^a_k / C^0_k, \f$ where \f$ C^0_k \f$ * is a standard concentration * defined below. These generalized concentrations are used * by kinetics manager classes to compute the forward and * reverse rates of elementary reactions. * + * The generalized activity concentration of a solute species has the following form + * + * \f[ + * C_j^a = C^o_o \frac{\gamma_j^\triangle n_j}{n_o} + * \f] + * + * The generalized activity concentration of the solvent has the same units, but its a simpler form + * + * \f[ + * C_o^a = C^o_o a_o + * \f] + * + * * @param c Array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. + * units are kmol m-3 for both the solvent and the solute species */ virtual void getActivityConcentrations(doublereal* c) const; @@ -1607,12 +1633,73 @@ namespace Cantera { * The standard concentration \f$ C^0_k \f$ used to normalize * the activity (i.e., generalized) concentration for use * - * For the time being, we will use the concentration of pure - * solvent at the temperature and pressure of the solution - * for the the standard concentration of all species. - * This has the effect of making mass-action reaction rates - * based on the molality of species proportional to the - * molality of the species. + * We have set the standard concentration for all solute species in + * this phase equal to the default concentration of the solvent at the system temperature + * and pressure multiplied by Mnaught (kg solvent / gmol solvent). The solvent + * standard concentration is just equal to its standard state concentration. + * + * \f[ + * C_j^0 = C^o_o \tilde{M}_o \quad and C_o^0 = C^o_o + * \f] + * + * The consequence of this is that the standard concentrations have unequal units + * between the solvent and the solute. However, both the solvent and the solute + * activity concentrations will have the same units of kmol kg-3. + * + * This means that the + * kinetics operator essentially works on an generalized concentration basis (kmol / m3), + * with units for the kinetic rate constant specified + * as if all reactants (solvent or solute) are on a concentration basis (kmol /m3). + * The concentration will be modified by the activity coefficients. + * + * For example, a bulk-phase binary reaction between liquid solute species + * j and k, producing + * a new liquid solute species l would have the + * following equation for its rate of progress variable, \f$ R^1 \f$, which has + * units of kmol m-3 s-1. + * + * \f[ + * R^1 = k^1 C_j^a C_k^a = k^1 (C^o_o \tilde{M}_o a_j) (C^o_o \tilde{M}_o a_k) + * \f] + * + * where + * + * \f[ + * C_j^a = C^o_o \tilde{M}_o a_j \quad and \quad C_k^a = C^o_o \tilde{M}_o a_k + * \f] + * + * \f$ C_j^a \f$ is the activity concentration of species j, and + * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^o_o \f$ + * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ + * has units of kg solvent per gmol solvent and is equal to + * + * \f[ + * \tilde{M}_o = \frac{M_o}{1000} + * \f] + * + * \f$ a_j \f$ is + * the activity of species j at the current temperature and pressure + * and concentration of the liquid phase is given by the molality based + * activity coefficient multiplied by the molality of the jth species. + * + * \f[ + * a_j = \gamma_j^\triangle m_j = \gamma_j^\triangle \frac{n_j}{\tilde{M}_o n_o} + * \f] + * + * \f$k^1 \f$ has units of m3 kmol-1 s-1. + * + * Therefore the generalized activity concentration of a solute species has the following form + * + * \f[ + * C_j^a = C^o_o \frac{\gamma_j^\triangle n_j}{n_o} + * \f] + * + * The generalized activity concentration of the solvent has the same units, but its a simpler form + * + * \f[ + * C_o^a = C^o_o a_o + * \f] + * * * @param k Optional parameter indicating the species. The default * is to assume this refers to species 0. From 6b1a1ac27f4fe9c9df5f09fbccbf3d1efbbec4fa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 11 Dec 2009 15:27:02 +0000 Subject: [PATCH 067/446] Merged changes from the trunk. --- Cantera/src/thermo/IdealGasPhase.h | 2 +- Cantera/src/thermo/Makefile.in | 4 +- Cantera/src/thermo/MetalSHEelectrons.cpp | 546 +++++++++++++++++++++ Cantera/src/thermo/MetalSHEelectrons.h | 565 ++++++++++++++++++++++ Cantera/src/thermo/SingleSpeciesTP.cpp | 26 +- Cantera/src/thermo/ThermoFactory.cpp | 9 +- Cantera/src/thermo/WaterProps.cpp | 1 + Cantera/src/thermo/WaterPropsIAPWSphi.cpp | 544 ++++++++++----------- Cantera/src/thermo/WaterPropsIAPWSphi.h | 68 +-- Cantera/src/thermo/mix_defs.h | 2 +- 10 files changed, 1450 insertions(+), 317 deletions(-) create mode 100644 Cantera/src/thermo/MetalSHEelectrons.cpp create mode 100644 Cantera/src/thermo/MetalSHEelectrons.h diff --git a/Cantera/src/thermo/IdealGasPhase.h b/Cantera/src/thermo/IdealGasPhase.h index cc676a8a4..b83cec970 100644 --- a/Cantera/src/thermo/IdealGasPhase.h +++ b/Cantera/src/thermo/IdealGasPhase.h @@ -252,7 +252,7 @@ namespace Cantera { * * where we can use the concept of microscopic reversibility to * write the reverse rate constant in terms of the - * forward reate constant and the concentration equilibrium + * forward rate constant and the concentration equilibrium * constant, \f$ K_c \f$. * * \f[ diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index b45d3eb44..73669357e 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -66,7 +66,7 @@ ELECTRO_OBJ = MolalityVPSSTP.o VPStandardStateTP.o \ WaterPropsIAPWSphi.o WaterPropsIAPWS.o WaterProps.o \ PDSS.o PDSS_Water.o PDSS_HKFT.o \ HMWSoln.o HMWSoln_input.o DebyeHuckel.o \ - WaterSSTP.o \ + WaterSSTP.o MetalSHEelectrons.o \ VPSSMgr_Water_ConstVol.o VPSSMgr_Water_HKFT.o ELECTRO_H = MolalityVPSSTP.h VPStandardStateTP.h \ @@ -74,7 +74,7 @@ ELECTRO_H = MolalityVPSSTP.h VPStandardStateTP.h \ WaterPropsIAPWSphi.h WaterPropsIAPWS.h WaterProps.h \ PDSS.h PDSS_Water.h PDSS_HKFT.h \ HMWSoln.h electrolytes.h \ - DebyeHuckel.h WaterSSTP.h VPSSMgr_Water_HKFT.h \ + DebyeHuckel.h WaterSSTP.h MetalSHEelectrons.h VPSSMgr_Water_HKFT.h \ VPSSMgr_Water_ConstVol.h endif ifeq ($(do_issp),1) diff --git a/Cantera/src/thermo/MetalSHEelectrons.cpp b/Cantera/src/thermo/MetalSHEelectrons.cpp new file mode 100644 index 000000000..221fa5ae9 --- /dev/null +++ b/Cantera/src/thermo/MetalSHEelectrons.cpp @@ -0,0 +1,546 @@ +/** + * @file MetalSHEelectrons.cpp + * Definition file for the %MetalSHEElectrons class, which represents the + * electrons in a metal that are consistent with the + * SHE electrode (see \ref thermoprops and + * class \link Cantera::MetalSHEelectrons MetalSHEelectrons\endlink) + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + * + */ + +/* + * $Id: MetalSHEelectrons.cpp 279 2009-12-05 19:08:43Z hkmoffa $ + */ + +#include "ct_defs.h" + +#include "MetalSHEelectrons.h" +#include "SingleSpeciesTP.h" +#include "ThermoFactory.h" + +#include +using namespace std; +using namespace Cantera; + +namespace Cantera { + + /* + * ---- Constructors ------- + */ + //==================================================================================================================== + /* + * Default Constructor for the MetalSHEelectrons class + */ + MetalSHEelectrons::MetalSHEelectrons(): + SingleSpeciesTP(), + xdef_(0) + { + } + //==================================================================================================================== + // Create and initialize a MetalSHEelectrons ThermoPhase object + // from an asci input file + /* + * @param infile name of the input file + * @param id name of the phase id in the file. + * If this is blank, the first phase in the file is used. + */ + MetalSHEelectrons::MetalSHEelectrons(std::string infile, std::string id) : + SingleSpeciesTP(), + xdef_(0) + { + XML_Node* root; + if (infile == "MetalSHEelectrons_default.xml") { + xdef_ = MetalSHEelectrons::makeDefaultXMLTree(); + root = xdef_; + } else { + root = get_XML_File(infile); + } + if (id == "-") id = ""; + XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, root); + if (!xphase) { + throw CanteraError("MetalSHEelectrons::MetalSHEelectrons", + "Couldn't find phase name in file:" + id); + } + // Check the model name to ensure we have compatibility + const XML_Node& th = xphase->child("thermo"); + std::string model = th["model"]; + if (model != "MetalSHEelectrons") { + throw CanteraError("MetalSHEelectrons::MetalSHEelectrons", + "thermo model attribute must be MetalSHEelectrons"); + } + importPhase(*xphase, this); + } + //==================================================================================================================== + // Full Constructor. + /* + * @param phaseRef XML node pointing to a MetalSHEelectrons description + * @param id Id of the phase. + */ + MetalSHEelectrons::MetalSHEelectrons(XML_Node& xmlphase, std::string id) : + SingleSpeciesTP(), + xdef_(0) + { + if (id != "") { + std::string idxml = xmlphase["id"]; + if (id != idxml) { + throw CanteraError("MetalSHEelectrons::MetalSHEelectrons", + "id's don't match"); + } + } + const XML_Node& th = xmlphase.child("thermo"); + std::string model = th["model"]; + if (model != "MetalSHEelectrons") { + throw CanteraError("MetalSHEelectrons::MetalSHEelectrons", + "thermo model attribute must be MetalSHEelectrons"); + } + importPhase(xmlphase, this); + } + //==================================================================================================================== + // Copy constructor + /* + * @param right Object to be copied + */ + MetalSHEelectrons::MetalSHEelectrons(const MetalSHEelectrons &right) : + SingleSpeciesTP() + { + operator=(right); + } + //==================================================================================================================== + /* + * Destructor for the routine (virtual) + * + */ + MetalSHEelectrons::~MetalSHEelectrons() + { + if (xdef_) { + delete xdef_; + } + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + MetalSHEelectrons & + MetalSHEelectrons::operator=(const MetalSHEelectrons & right) + { + if (&right != this) { + SingleSpeciesTP::operator=(right); + } + + if (xdef_) { + delete xdef_; + } + xdef_ = new XML_Node(*right.xdef_); + + return *this; + } + //==================================================================================================================== + // Duplication function + /* + * This virtual function is used to create a duplicate of the + * current phase. It's used to duplicate the phase when given + * a ThermoPhase pointer to the phase. + * + * @return It returns a ThermoPhase pointer. + */ + ThermoPhase *MetalSHEelectrons::duplMyselfAsThermoPhase() const { + MetalSHEelectrons *stp = new MetalSHEelectrons(*this); + return (ThermoPhase *) stp; + } + //==================================================================================================================== + + /* + * ---- Utilities ----- + */ + + /* + * Equation of state flag. Returns the value cStoichSubstance, + * defined in mix_defs.h. + */ + int MetalSHEelectrons::eosType() const { + return cMetalSHEelectrons; + } + //==================================================================================================================== + + /* + * ---- Molar Thermodynamic properties of the solution ---- + */ + + /** + * ----- Mechanical Equation of State ------ + */ + //==================================================================================================================== + /* + * Pressure. Units: Pa. + * For an incompressible substance, the density is independent + * of pressure. This method simply returns the stored + * pressure value. + */ + doublereal MetalSHEelectrons::pressure() const { + return m_press; + } + //==================================================================================================================== + /* + * Set the pressure at constant temperature. Units: Pa. + * For an incompressible substance, the density is + * independent of pressure. Therefore, this method only + * stores the specified pressure value. It does not + * modify the density. + */ + void MetalSHEelectrons::setPressure(doublereal p) { + m_press = p; + } + //==================================================================================================================== + /* + * The isothermal compressibility. Units: 1/Pa. + * The isothermal compressibility is defined as + * \f[ + * \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T + * \f] + * + * It's equal to zero for this model, since the molar volume + * doesn't change with pressure or temperature. + */ + doublereal MetalSHEelectrons::isothermalCompressibility() const { + return -1.0/pressure(); + } + //==================================================================================================================== + /* + * The thermal expansion coefficient. Units: 1/K. + * The thermal expansion coefficient is defined as + * + * \f[ + * \beta = \frac{1}{v}\left(\frac{\partial v}{\partial T}\right)_P + * \f] + * + * It's equal to zero for this model, since the molar volume + * doesn't change with pressure or temperature. + */ + doublereal MetalSHEelectrons::thermalExpansionCoeff() const { + return 1.0/temperature(); + + } + //==================================================================================================================== + /* + * ---- Chemical Potentials and Activities ---- + */ + //==================================================================================================================== + /* + * This method returns the array of generalized + * concentrations. For a stoichiomeetric substance, there is + * only one species, and the generalized concentration is 1.0. + */ + void MetalSHEelectrons:: + getActivityConcentrations(doublereal* c) const { + c[0] = 1.0; + } + //==================================================================================================================== + /* + * The standard concentration. This is defined as the concentration + * by which the generalized concentration is normalized to produce + * the activity. + */ + doublereal MetalSHEelectrons::standardConcentration(int k) const { + return 1.0; + } + //==================================================================================================================== + /* + * Returns the natural logarithm of the standard + * concentration of the kth species + */ + doublereal MetalSHEelectrons::logStandardConc(int k) const { + return 0.0; + } + //==================================================================================================================== + /* + * Returns the units of the standard and generalized + * concentrations Note they have the same units, as their + * ratio is defined to be equal to the activity of the kth + * species in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + */ + void MetalSHEelectrons:: + getUnitsStandardConc(doublereal *uA, int k, int sizeUA) const { + for (int i = 0; i < 6; i++) { + uA[i] = 0; + } + } + //==================================================================================================================== + /* + * ---- Partial Molar Properties of the Solution ---- + */ + + //==================================================================================================================== + + /* + * ---- Properties of the Standard State of the Species in the Solution + * ---- + */ + //==================================================================================================================== + /* + * Get the array of chemical potentials at unit activity + * \f$ \mu^0_k \f$. + * + * For a stoichiometric substance, there is no activity term in + * the chemical potential expression, and therefore the + * standard chemical potential and the chemical potential + * are both equal to the molar Gibbs function. + */ + void MetalSHEelectrons:: + getStandardChemPotentials(doublereal* mu0) const { + getGibbs_RT(mu0); + mu0[0] *= GasConstant * temperature(); + } + //==================================================================================================================== + /* + * Get the nondimensional Enthalpy functions for the species + * at their standard states at the current + * T and P of the solution. + * Molar enthalpy. Units: J/kmol. For an incompressible, + * stoichiometric substance, the internal energy is + * independent of pressure, and therefore the molar enthalpy + * is \f[ \hat h(T, P) = \hat u(T) + P \hat v \f], where the + * molar specific volume is constant. + */ + void MetalSHEelectrons::getEnthalpy_RT(doublereal* hrt) const { + getEnthalpy_RT_ref(hrt); + } + //==================================================================================================================== + /* + * Get the array of nondimensional Entropy functions for the + * standard state species + * at the current T and P of the solution. + */ + void MetalSHEelectrons::getEntropy_R(doublereal* sr) const { + getEntropy_R_ref(sr); + doublereal tmp = log (pressure() / m_p0); + sr[0] -= tmp; + } + //==================================================================================================================== + /* + * Get the nondimensional Gibbs functions for the species + * at their standard states of solution at the current T and P + * of the solution + */ + void MetalSHEelectrons::getGibbs_RT(doublereal* grt) const { + getGibbs_RT_ref(grt); + doublereal tmp = log (pressure() / m_p0); + grt[0] += tmp; + } + //==================================================================================================================== + /* + * Get the nondimensional Gibbs functions for the standard + * state of the species at the current T and P. + */ + void MetalSHEelectrons::getCp_R(doublereal* cpr) const { + _updateThermo(); + cpr[0] = m_cp0_R[0]; + } + //==================================================================================================================== + /* + * Molar internal energy (J/kmol). + * For an incompressible, + * stoichiometric substance, the molar internal energy is + * independent of pressure. Since the thermodynamic properties + * are specified by giving the standard-state enthalpy, the + * term \f$ P_0 \hat v\f$ is subtracted from the specified molar + * enthalpy to compute the molar internal energy. + */ + void MetalSHEelectrons::getIntEnergy_RT(doublereal* urt) const { + getEnthalpy_RT(urt); + urt[0] -= 1.0; + } + //==================================================================================================================== + /* + * ---- Thermodynamic Values for the Species Reference States ---- + */ + /* + * Molar internal energy or the reference state at the current + * temperature, T (J/kmol). + * For an incompressible, + * stoichiometric substance, the molar internal energy is + * independent of pressure. Since the thermodynamic properties + * are specified by giving the standard-state enthalpy, the + * term \f$ P_0 \hat v\f$ is subtracted from the specified molar + * enthalpy to compute the molar internal energy. + * + * Note, this is equal to the standard state internal energy + * evaluated at the reference pressure. + */ + void MetalSHEelectrons::getIntEnergy_RT_ref(doublereal* urt) const { + _updateThermo(); + doublereal RT = GasConstant * temperature(); + doublereal PV = m_p0 / molarDensity(); + urt[0] = m_h0_RT[0] - PV / RT; + } + + /* + * ---- Saturation Properties + */ + + + + /* + * ---- Initialization and Internal functions + */ + //==================================================================================================================== + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + void MetalSHEelectrons::initThermo() { + /* + * Call the base class thermo initializer + */ + SingleSpeciesTP::initThermo(); + } + //==================================================================================================================== + + void MetalSHEelectrons::initThermoXML(XML_Node& phaseNode, std::string id) { + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("MetalSHEelectrons::initThermoXML", + "no thermo XML node"); + } + XML_Node &tnode = phaseNode.child("thermo"); + doublereal dens = 2.65E3; + if (tnode.hasChild("density")) { + dens = getFloatDefaultUnits(tnode, "density", "kg/m3"); + } + setDensity(dens); + SingleSpeciesTP::initThermoXML(phaseNode, id); + } + //==================================================================================================================== + XML_Node *MetalSHEelectrons::makeDefaultXMLTree() + { + XML_Node *xtop = new XML_Node("ctml", 0); + XML_Node &xv = xtop->addChild("validate"); + xv.addAttribute("reactions", "yes"); + xv.addAttribute("species", "yes"); + + XML_Node &xp = xtop->addChild("phase"); + xp.addAttribute("dim", "3"); + xp.addAttribute("id", "MetalSHEelectrons"); + XML_Node &xe = xp.addChild("elementArray", "E"); + xe.addAttribute("datasrc", "elements.xml"); + XML_Node &xs = xp.addChild("speciesArray", "she_electron"); + xs.addAttribute("datasrc", "#species_Metal_SHEelectrons"); + XML_Node &xt = xp.addChild("thermo"); + xt.addAttribute("model", "metalSHEelectrons"); + XML_Node &xtr = xp.addChild("transport"); + xtr.addAttribute("model", "none"); + XML_Node &xk = xp.addChild("kinetics"); + xk.addAttribute("model", "none"); + + XML_Node &xsd = xtop->addChild("speciesData"); + xsd.addAttribute("id", "species_Metal_SHEelectrons"); + + XML_Node &xsp = xsd.addChild("species"); + xsp.addAttribute("name", "she_electron"); + xsp.addChild("atomArray", "E:1"); + xsp.addChild("charge", "-1"); + XML_Node &xspt = xsp.addChild("thermo"); + + XML_Node &xN1 = xspt.addChild("NASA"); + xN1.addAttribute("Tmax", "1000."); + xN1.addAttribute("Tmin", "200."); + xN1.addAttribute("P0", "100000.0"); + XML_Node &xF1 = xsd.addChild("floatArray", + "1.172165560E+00, 3.990260375E-03, -9.739075500E-06, " + "1.007860470E-08, -3.688058805E-12, -4.589675865E+02, 3.415051190E-01" ); + xF1.addAttribute("name", "coeffs"); + xF1.addAttribute("size", "7"); + + XML_Node &xN2 = xspt.addChild("NASA"); + xN2.addAttribute("Tmax", "6000."); + xN2.addAttribute("Tmin", "1000."); + xN2.addAttribute("P0", "100000.0"); + XML_Node &xF2 = xsd.addChild("floatArray", + "1.466432895E+00, 4.133039835E-04, -7.320116750E-08, 7.705017950E-12," + "-3.444022160E-16, -4.065327985E+02, -5.121644350E-01"); + xF2.addAttribute("name", "coeffs"); + xF2.addAttribute("size", "7"); + + return xtop; + } + //==================================================================================================================== + /* + * setParameters: + * + * Generic routine that is used to set the parameters used + * by this model. + * C[0] = density of phase [ kg/m3 ] + */ + void MetalSHEelectrons::setParameters(int n, doublereal * const c) { + doublereal rho = c[0]; + setDensity(rho); + } + //==================================================================================================================== + /* + * getParameters: + * + * Generic routine that is used to get the parameters used + * by this model. + * n = 1 + * C[0] = density of phase [ kg/m3 ] + */ + void MetalSHEelectrons::getParameters(int &n, doublereal * const c) const { + doublereal rho = density(); + n = 1; + c[0] = rho; + } + //==================================================================================================================== + /* + * Reads an xml data block for the parameters needed by this + * routine. eosdata is a reference to the xml thermo block, and looks + * like this: + * + * + * + * 3.52 + * + * + */ + void MetalSHEelectrons::setParametersFromXML(const XML_Node& eosdata) { + std::string model = eosdata["model"]; + if (model != "MetalSHEelectrons") { + throw CanteraError("MetalSHEelectrons::setParametersFromXML", + "thermo model attribute must be MetalSHEelectrons"); + } + doublereal rho = 2.65E3; + if (eosdata.hasChild("density")) { + rho = getFloat(eosdata, "density", "toSI"); + } + setDensity(rho); + } + //==================================================================================================================== + +} diff --git a/Cantera/src/thermo/MetalSHEelectrons.h b/Cantera/src/thermo/MetalSHEelectrons.h new file mode 100644 index 000000000..424e91f2c --- /dev/null +++ b/Cantera/src/thermo/MetalSHEelectrons.h @@ -0,0 +1,565 @@ +/** + * @file MetalSHEelectrons.h + * Header file for the %MetalSHEElectrons class, which represents the + * electrons in a metal that are consistent with the + * SHE electrode (see \ref thermoprops and + * class \link Cantera::MetalSHEelectrons MetalSHEelectrons\endlink) + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Date: 2009-12-05 12:08:43 -0700 (Sat, 05 Dec 2009) $ + * $Revision: 279 $ + */ + +#ifndef CT_METALSHEELECTRONS_H +#define CT_METALSHEELECTRONS_H + +#include "mix_defs.h" +#include "SingleSpeciesTP.h" +//#include "SpeciesThermo.h" + +namespace Cantera { + + //! Class %MetalSHEelectrons represents electrons within + //! a metal, adjacent to an aqueous electrolyte, that are consistent with the SHE reference electrode. + /*! + * The class is based on the electron having a chemical potential + * equal to one-half of the entropy of the H2 gas at the system pressure + * + * + * Specification of Species Standard %State Properties + * + * This class inherits from SingleSpeciesTP. + * It is assumed that the reference state thermodynamics may be + * obtained by a pointer to a populated species thermodynamic property + * manager class (see ThermoPhase::m_spthermo). How to relate pressure + * changes to the reference state thermodynamics is resolved at this level. + * + * The enthalpy function is given by the following relation. + * + * \f[ + * h^o_k(T,P) = h^{ref}_k(T) + * \f] + * + * The standard state constant-pressure heat capacity is independent of pressure: + * + * \f[ + * Cp^o_k(T,P) = Cp^{ref}_k(T) + * \f] + * + * The standard state entropy depends in the following fashion on pressure: + * + * \f[ + * S^o_k(T,P) = S^{ref}_k(T) - R \ln(\frac{P}{P_{ref}}) + * \f] + * + * The standard state gibbs free energy is obtained from the enthalpy and entropy + * functions: + * + * \f[ + * \mu^o_k(T,P) = h^o_k(T,P) - S^o_k(T,P) T + * \f] + * + * \f[ + * \mu^o_k(T,P) = \mu^{ref}_k(T) + R T \ln( \frac{P}{P_{ref}}) + * \f] + * + * where + * \f[ + * \mu^{ref}_k(T) = h^{ref}_k(T) - T S^{ref}_k(T) + * \f] + * + * The standard state internal energy is obtained from the enthalpy function also + * + * \f[ + * u^o_k(T,P) = h^o_k(T) - R T + * \f] + * + * + * Specification of Solution Thermodynamic Properties + * + * All solution properties are obtained from the standard state + * species functions, since there is only one species in the phase. + * + * %Application within %Kinetics Managers + * + * The standard concentration is equal to 1.0. This means that the + * kinetics operator works on an activities basis. Since this + * is a stoichiometric substance, this means that the concentration + * of this phase drops out of kinetics expressions since the activity is + * always equal to one. + * + * This is what is expected of electrons. The only effect that this class will + * have on reactions is in terms of the standard state chemical potential, which + * is equal to 1/2 of the H2 gas chemical potential, and the voltage assigned + * to the electron, which is the voltage of the metal. + * + * + * Instanteation of the Class + * + * The constructor for this phase is located in the default ThermoFactory + * for %Cantera. A new %MetalSHEelectrons object may be created by + * the following code snippets, where the file metalSHEelectrons.xml exists + * in a local directory: + * + * @code + * MetalSHEelectrons *eMetal = new MetalSHEelectrons("metalSHEelectrons.xml", ""); + * @endcode + * + * or by the following call to importPhase(): + * + * @code + * sprintf(file_ID,"%s#MetalSHEelectrons", iFile); + * XML_Node *xm = get_XML_NameID("phase", file_ID, 0); + * MetalSHEelectrons eMetal; + * importPhase(*xm, &eMetal); + * @endcode + * + * @code + * ThermoPhase *eMetal = newPhase(" MetalSHEelectrons.xml", "MetalSHEelectrons"); + * @endcode + * + * Additionally, this phase may be created without including an xml file with + * the special command, where the default file is embedded into this object. + * + * @code + * MetalSHEelectrons *eMetal = new MetalSHEelectrons("MetalSHEelectrons_default.xml", ""); + * @endcode + * + * + * + * XML Example + * + * The phase model name for this is called %MetalSHEelectrons. It must be supplied + * as the model attribute of the thermo XML element entry. + * Within the phase XML block, + * the density of the phase must be specified though it's not used. An example of an XML file + * this phase is given below. + * + * @verbatim + + + + + + + E + + she_electron + + 2.165 + + + + + + + + + E:1 + -1 + + + + 1.172165560E+00, 3.990260375E-03, -9.739075500E-06, 1.007860470E-08, + -3.688058805E-12, -4.589675865E+02, 3.415051190E-01 + + + + + 1.466432895E+00, 4.133039835E-04, -7.320116750E-08, 7.705017950E-12, + -3.444022160E-16, -4.065327985E+02, -5.121644350E-01 + + + + 2.165 + + + +@endverbatim + * + * The model attribute, "MetalSHEelectrons", on the thermo element + * identifies the phase as being a %MetalSHEelectrons object. + * + * @ingroup thermoprops + */ + class MetalSHEelectrons : public SingleSpeciesTP { + + public: + + //! Default constructor for the MetalSHEelectrons class + MetalSHEelectrons(); + + //! Construct and initialize a %MetalSHEelectrons %ThermoPhase object + //! directly from an asci input file + /*! + * @param infile name of the input file + * @param id name of the phase id in the file. + * If this is blank, the first phase in the file is used. + */ + MetalSHEelectrons(std::string infile, std::string id = ""); + + //! Construct and initialize a MetalSHEelectrons ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML node pointing to a MetalSHEelectrons description + * @param id Id of the phase. + */ + MetalSHEelectrons(XML_Node& phaseRef, std::string id = ""); + + //! Copy constructor + /*! + * @param right Object to be copied + */ + MetalSHEelectrons(const MetalSHEelectrons &right); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + MetalSHEelectrons & operator=(const MetalSHEelectrons & right); + + //! Destructor for the routine (virtual) + virtual ~MetalSHEelectrons(); + + //! Duplication function + /*! + * This virtual function is used to create a duplicate of the + * current phase. It's used to duplicate the phase when given + * a ThermoPhase pointer to the phase. + * + * @return It returns a ThermoPhase pointer. + */ + ThermoPhase *duplMyselfAsThermoPhase() const; + + /** + * + * @name Utilities + * @{ + */ + + /** + * Equation of state flag. + * + * Returns the value cStoichSubstance, defined in mix_defs.h. + */ + virtual int eosType() const; + + /** + * @} + * @name Molar Thermodynamic Properties of the Solution + * @{ + */ + + /** + * @} + * @name Mechanical Equation of State + * @{ + */ + + + //! Report the Pressure. Units: Pa. + /*! + * For an incompressible substance, the density is independent + * of pressure. This method simply returns the storred + * pressure value. + */ + virtual doublereal pressure() const; + + //! Set the pressure at constant temperature. Units: Pa. + /*! + * For an incompressible substance, the density is + * independent of pressure. Therefore, this method only + * stores the specified pressure value. It does not + * modify the density. + * + * @param p Pressure (units - Pa) + */ + virtual void setPressure(doublereal p); + + //! Returns the isothermal compressibility. Units: 1/Pa. + /*! + * The isothermal compressibility is defined as + * \f[ + * \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T + * \f] + */ + virtual doublereal isothermalCompressibility() const; + + //! Return the volumetric thermal expansion coefficient. Units: 1/K. + /*! + * The thermal expansion coefficient is defined as + * \f[ + * \beta = \frac{1}{v}\left(\frac{\partial v}{\partial T}\right)_P + * \f] + */ + virtual doublereal thermalExpansionCoeff() const ; + + /** + * @} + * @name Activities, Standard States, and Activity Concentrations + * + * This section is largely handled by parent classes, since there + * is only one species. Therefore, the activity is equal to one. + * @{ + */ + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. + * + * For a stoichiomeetric substance, there is + * only one species, and the generalized concentration is 1.0. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + //! Return the standard concentration for the kth species + /*! + * The standard concentration \f$ C^0_k \f$ used to normalize + * the activity (i.e., generalized) concentration. + * This phase assumes that the kinetics operator works on an + * dimensionless basis. Thus, the standard concentration is + * equal to 1.0. + * + * @param k Optional parameter indicating the species. The default + * is to assume this refers to species 0. + * @return + * Returns The standard Concentration as 1.0 + */ + virtual doublereal standardConcentration(int k=0) const; + + //! Natural logarithm of the standard concentration of the kth species. + /*! + * @param k index of the species (defaults to zero) + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Get the array of chemical potentials at unit activity for the species + //! at their standard states at the current T and P of the solution. + /*! + * For a stoichiometric substance, there is no activity term in + * the chemical potential expression, and therefore the + * standard chemical potential and the chemical potential + * are both equal to the molar Gibbs function. + * + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution + * + * @param mu0 Output vector of chemical potentials. + * Length: m_kk. + */ + virtual void getStandardChemPotentials(doublereal* mu0) const; + + //! Returns the units of the standard and generalized concentrations. + /*! + * Note they have the same units, as their + * ratio is defined to be equal to the activity of the kth + * species in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * The base %ThermoPhase class assigns thedefault quantities + * of (kmol/m3) for all species. + * Inherited classes are responsible for overriding the default + * values if necessary. + * + * @param uA Output vector containing the units + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + * @param k species index. Defaults to 0. + * @param sizeUA output int containing the size of the vector. + * Currently, this is equal to 6. + */ + virtual void getUnitsStandardConc(doublereal *uA, int k = 0, + int sizeUA = 6) const; + + //@} + /// @name Partial Molar Properties of the Solution + /// + /// These properties are handled by the parent class, + /// SingleSpeciesTP + //@{ + + + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + //! Get the nondimensional Enthalpy functions for the species + //! at their standard states at the current T and P of the solution. + /*! + * @param hrt Output vector of nondimensional standard state enthalpies. + * Length: m_kk. + */ + virtual void getEnthalpy_RT(doublereal* hrt) const; + + //! Get the array of nondimensional Entropy functions for the + //! standard state species at the current T and P of the solution. + /*! + * @param sr Output vector of nondimensional standard state entropies. + * Length: m_kk. + */ + virtual void getEntropy_R(doublereal* sr) const; + + //! Get the nondimensional Gibbs functions for the species + //! in their standard states at the current T and P of the solution. + /*! + * @param grt Output vector of nondimensional standard state gibbs free energies + * Length: m_kk. + */ + virtual void getGibbs_RT(doublereal* grt) const; + + //! Get the nondimensional Heat Capacities at constant + //! pressure for the species standard states + //! at the current T and P of the solution + /*! + * @param cpr Output vector of nondimensional standard state heat capacities + * Length: m_kk. + */ + virtual void getCp_R(doublereal* cpr) const; + + //! Returns the vector of nondimensional Internal Energies of the standard + //! state species at the current T and P of the solution + /*! + * For an incompressible, + * stoichiometric substance, the molar internal energy is + * independent of pressure. Since the thermodynamic properties + * are specified by giving the standard-state enthalpy, the + * term \f$ P_{ref} \hat v\f$ is subtracted from the specified reference molar + * enthalpy to compute the standard state molar internal energy. + * + * @param urt output vector of nondimensional standard state + * internal energies of the species. Length: m_kk. + */ + virtual void getIntEnergy_RT(doublereal* urt) const; + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + //! Returns the vector of nondimensional + //! internal Energies of the reference state at the current temperature + //! of the solution and the reference pressure for each species. + /*! + * @param urt Output vector of nondimensional reference state + * internal energies of the species. + * Length: m_kk + */ + virtual void getIntEnergy_RT_ref(doublereal *urt) const; + + /* + * ---- Critical State Properties + */ + + + /* + * ---- Saturation Properties + */ + + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + virtual void initThermoXML(XML_Node& phaseNode, std::string id); + + //! Make the default XML tree + /*! + * @return Returns a malloced XML tree containing the + * default info. + */ + static XML_Node *makeDefaultXMLTree(); + + //! Set the equation of state parameters + /*! + * @internal + * The number and meaning of these depends on the subclass. + * + * @param n number of parameters + * @param c array of \a n coefficients + * c[0] = density of phase [ kg/m3 ] + */ + virtual void setParameters(int n, doublereal * const c); + + //! Get the equation of state parameters in a vector + /*! + * @internal + * + * @param n number of parameters + * @param c array of \a n coefficients + * + * For this phase: + * - n = 1 + * - c[0] = density of phase [ kg/m3 ] + */ + virtual void getParameters(int &n, doublereal * const c) const; + + //! Set equation of state parameter values from XML entries. + /*! + * This method is called by function importPhase() in + * file importCTML.cpp when processing a phase definition in + * an input file. It should be overloaded in subclasses to set + * any parameters that are specific to that particular phase + * model. Note, this method is called before the phase is + * initialzed with elements and/or species. + * + * For this phase, the density of the phase is specified in this block. + * + * @param eosdata An XML_Node object corresponding to + * the "thermo" entry for this phase in the input file. + * + * eosdata points to the thermo block, and looks like this: + * + * @verbatim + + + 3.52 + + @endverbatim + * + */ + virtual void setParametersFromXML(const XML_Node& eosdata); + + protected: + + XML_Node *xdef_; + }; + + +} +#endif diff --git a/Cantera/src/thermo/SingleSpeciesTP.cpp b/Cantera/src/thermo/SingleSpeciesTP.cpp index e9980ada2..3bdfe52b3 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.cpp +++ b/Cantera/src/thermo/SingleSpeciesTP.cpp @@ -543,13 +543,33 @@ namespace Cantera { * @see importCTML.cpp */ void SingleSpeciesTP::initThermo() { + /* - * Check to make sure that there is one and only one species - * in this phase. + * Make sure there is one and only one species in this phase. */ + m_kk = nSpecies(); if (m_kk != 1) { - err("singleSpeciesTP ERROR m_kk != 1"); + throw CanteraError("initThermo", + "stoichiometric substances may only contain one species."); } + doublereal tmin = m_spthermo->minTemp(); + doublereal tmax = m_spthermo->maxTemp(); + if (tmin > 0.0) m_tmin = tmin; + if (tmax > 0.0) m_tmax = tmax; + + /* + * Store the reference pressure in the variables for the class. + */ + m_p0 = refPressure(); + + /* + * Resize temporary arrays. + */ + int leng = 1; + m_h0_RT.resize(leng); + m_cp0_R.resize(leng); + m_s0_R.resize(leng); + /* * Make sure the species mole fraction is equal to 1.0; */ diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index c1e33c528..7913d50d4 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -59,6 +59,7 @@ #ifdef WITH_STOICH_SUBSTANCE #include "MineralEQ3.h" +#include "MetalSHEelectrons.h" #endif //#include "importCTML.h" @@ -93,7 +94,7 @@ namespace Cantera { "PureFluid", "LatticeSolid", "Lattice", "HMW", "IdealSolidSolution", "DebyeHuckel", "IdealMolalSolution", "IdealGasVPSS", - "MineralEQ3", "electrodeElectron", "Margules", + "MineralEQ3", "MetalSHEelectrons", "Margules", "IonsFromNeutralMolecule" }; @@ -102,7 +103,7 @@ namespace Cantera { cPureFluid, cLatticeSolid, cLattice, cHMW, cIdealSolidSolnPhase, cDebyeHuckel, cIdealMolalSoln, cVPSS_IdealGas, - cMineralEQ3, cElectrodeElectron, + cMineralEQ3, cMetalSHEelectrons, cMargulesVPSSTP, cIonsFromNeutral }; @@ -173,8 +174,8 @@ namespace Cantera { #endif #ifdef WITH_STOICH_SUBSTANCE - case cElectrodeElectron: - th = new electrodeElectron(); + case cMetalSHEelectrons: + th = new MetalSHEelectrons(); break; #endif diff --git a/Cantera/src/thermo/WaterProps.cpp b/Cantera/src/thermo/WaterProps.cpp index 5501a7129..061499a92 100644 --- a/Cantera/src/thermo/WaterProps.cpp +++ b/Cantera/src/thermo/WaterProps.cpp @@ -495,6 +495,7 @@ namespace Cantera { // Parameters for the viscosityWater() function + //@{ const double H[4] = {1., 0.978197, diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp index d91bce64b..5f8a382de 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp @@ -29,10 +29,10 @@ using std::fabs; * routine, except for internal checks. All calculations here are done * in dimensionless units. */ -static const double T_c = 647.096; // Kelvin -static const double P_c = 22.064E6; // Pascals -static const double Rho_c = 322.; // kg m-3 -static const double M_water = 18.015268; // kg kmol-1 +static const doublereal T_c = 647.096; // Kelvin +static const doublereal P_c = 22.064E6; // Pascals +static const doublereal Rho_c = 322.; // kg m-3 +static const doublereal M_water = 18.015268; // kg kmol-1 /* * The added constants were calculated so that u = s = 0 @@ -42,7 +42,7 @@ static const double M_water = 18.015268; // kg kmol-1 * H didn't turn out to be .611872 J/kg, but .611782 J/kg. * There may be a slight error here somehow. */ -static const double ni0[9] = { +static const doublereal ni0[9] = { 0.0, -8.32044648201 - 0.000000001739715, 6.6832105268 + 0.000000000793232, @@ -54,7 +54,7 @@ static const double ni0[9] = { 0.24873 }; -static const double gammi0[9] = { +static const doublereal gammi0[9] = { 0.0, 0.0, 0.0, @@ -241,7 +241,7 @@ static const int tiR[55] = { 4 // 54 }; -static const double ni[57] = { +static const doublereal ni[57] = { +0.0, +0.12533547935523E-1, // 1 +0.78957634722828E1, // 2 @@ -302,61 +302,61 @@ static const double ni[57] = { }; -static const double alphai[3] = { +static const doublereal alphai[3] = { +20., +20., +20. }; -static const double betai[3] = { +static const doublereal betai[3] = { +150., +150., +250. }; -static const double gammai[3] = { +static const doublereal gammai[3] = { +1.21, +1.21, +1.25 }; -static const double epsi[3] = { +static const doublereal epsi[3] = { +1.0, +1.0, +1.0 }; -static const double ai[2] = { +static const doublereal ai[2] = { +3.5, +3.5 }; -static const double bi[2] = { +static const doublereal bi[2] = { +0.85, +0.95 }; -static const double Bi[2] = { +static const doublereal Bi[2] = { +0.2, +0.2 }; -static const double Ci[2] = { +static const doublereal Ci[2] = { +28.0, +32.0 }; -static const double Di[2] = { +static const doublereal Di[2] = { +700., +800. }; -static const double Ai[2] = { +static const doublereal Ai[2] = { +0.32, +0.32 }; -static const double Bbetai[2] = { +static const doublereal Bbetai[2] = { +0.3, +0.3 }; @@ -382,20 +382,20 @@ WaterPropsIAPWSphi::WaterPropsIAPWSphi() : * prints out the result. It's used for conducting the internal * check. */ -void WaterPropsIAPWSphi::intCheck(double tau, double delta) { +void WaterPropsIAPWSphi::intCheck(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0(); - double res = phiR(); - double res_d = phiR_d(); - double nau_d = phi0_d(); - double res_dd = phiR_dd(); - double nau_dd = phi0_dd(); - double res_t = phiR_t(); - double nau_t = phi0_t(); - double res_tt = phiR_tt(); - double nau_tt = phi0_tt(); - double res_dt = phiR_dt(); - double nau_dt = phi0_dt(); + doublereal nau = phi0(); + doublereal res = phiR(); + doublereal res_d = phiR_d(); + doublereal nau_d = phi0_d(); + doublereal res_dd = phiR_dd(); + doublereal nau_dd = phi0_dd(); + doublereal res_t = phiR_t(); + doublereal nau_t = phi0_t(); + doublereal res_tt = phiR_tt(); + doublereal nau_tt = phi0_tt(); + doublereal res_dt = phiR_dt(); + doublereal nau_dt = phi0_dt(); std::printf("nau = %20.12e\t\tres = %20.12e\n", nau, res); std::printf("nau_d = %20.12e\t\tres_d = %20.12e\n", nau_d, res_d); @@ -406,19 +406,19 @@ void WaterPropsIAPWSphi::intCheck(double tau, double delta) { } void WaterPropsIAPWSphi::check1() { - double T = 500.; - double rho = 838.025; - double tau = T_c/T; - double delta = rho / Rho_c; + doublereal T = 500.; + doublereal rho = 838.025; + doublereal tau = T_c/T; + doublereal delta = rho / Rho_c; printf(" T = 500 K, rho = 838.025 kg m-3\n"); intCheck(tau, delta); } void WaterPropsIAPWSphi::check2() { - double T = 647; - double rho = 358.0; - double tau = T_c/T; - double delta = rho / Rho_c; + doublereal T = 647; + doublereal rho = 358.0; + doublereal tau = T_c/T; + doublereal delta = rho / Rho_c; printf(" T = 647 K, rho = 358.0 kg m-3\n"); intCheck(tau, delta); } @@ -427,7 +427,7 @@ void WaterPropsIAPWSphi::check2() { * Calculate the polynomials in tau and delta, and store them in static * storage. */ -void WaterPropsIAPWSphi::tdpolycalc(double tau, double delta) { +void WaterPropsIAPWSphi::tdpolycalc(doublereal tau, doublereal delta) { if ((tau != TAUsave) || 1) { TAUsave = tau; TAUsqrt = sqrt(tau); @@ -449,10 +449,10 @@ void WaterPropsIAPWSphi::tdpolycalc(double tau, double delta) { * Calculate Eqn. 6.5 for phi0, the ideal gas part of the * dimensionless Helmholtz free energy. */ -double WaterPropsIAPWSphi::phi0() const { - double tau = TAUsave; - double delta = DELTAsave; - double retn = log(delta) + ni0[1] + ni0[2]*tau + ni0[3]*log(tau); +doublereal WaterPropsIAPWSphi::phi0() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; + doublereal retn = log(delta) + ni0[1] + ni0[2]*tau + ni0[3]*log(tau); retn += ni0[4] * log(1.0 - exp(-gammi0[4]*tau)); retn += ni0[5] * log(1.0 - exp(-gammi0[5]*tau)); @@ -469,16 +469,16 @@ double WaterPropsIAPWSphi::phi0() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = (ni[1] * delta / TAUsqrt + + doublereal T375 = pow(tau, 0.375); + doublereal val = (ni[1] * delta / TAUsqrt + ni[2] * delta * TAUsqrt * T375 + ni[3] * delta * tau + ni[4] * DELTAp[2] * TAUsqrt + @@ -497,8 +497,8 @@ double WaterPropsIAPWSphi::phiR() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; val += (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); } @@ -508,16 +508,16 @@ double WaterPropsIAPWSphi::phiR() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; - double atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; + doublereal atmp = 0.5 / Bbetai[j]; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); + doublereal triagtmp = pow(triag, bi[j]); - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); val += (ni[i] * triagtmp * delta * phi); } @@ -528,11 +528,11 @@ double WaterPropsIAPWSphi::phiR() const { * Calculate the Phi function, which is basically the helmholtz free energy * Eqn. (6.4) */ -double WaterPropsIAPWSphi::phi(double tau, double delta) { +doublereal WaterPropsIAPWSphi::phi(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0(); - double res = phiR(); - double retn = nau + res; + doublereal nau = phi0(); + doublereal res = phiR(); + doublereal retn = nau + res; return retn; } @@ -544,16 +544,16 @@ double WaterPropsIAPWSphi::phi(double tau, double delta) { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR_d() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR_d() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = (ni[1] / TAUsqrt + + doublereal T375 = pow(tau, 0.375); + doublereal val = (ni[1] / TAUsqrt + ni[2] * TAUsqrt * T375 + ni[3] * tau + ni[4] * 2.0 * delta * TAUsqrt + @@ -573,9 +573,9 @@ double WaterPropsIAPWSphi::phiR_d() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; - double tmp = (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; + doublereal tmp = (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); val += tmp * (diR[i]/delta - 2.0 * alphai[j] * dtmp); } @@ -585,27 +585,27 @@ double WaterPropsIAPWSphi::phiR_d() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; - double atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; + doublereal atmp = 0.5 / Bbetai[j]; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); - double triagtmpm1 = pow(triag, bi[j]-1.0); - double atmpM1 = atmp - 1.0; - double ptmp = pow(dtmp2,atmpM1); - double p2tmp = pow(dtmp2, ai[j]-1.0); - double dtriagddelta = + doublereal triagtmp = pow(triag, bi[j]); + doublereal triagtmpm1 = pow(triag, bi[j]-1.0); + doublereal atmpM1 = atmp - 1.0; + doublereal ptmp = pow(dtmp2,atmpM1); + doublereal p2tmp = pow(dtmp2, ai[j]-1.0); + doublereal dtriagddelta = deltam1 *(Ai[j] * theta * 2.0 / Bbetai[j] * ptmp + 2.0*Bi[j]*ai[j]*p2tmp); - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); - double dphiddelta = -2.0*Ci[j]*deltam1*phi; - double dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal dphiddelta = -2.0*Ci[j]*deltam1*phi; + doublereal dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; - double tmp = ni[i] * (triagtmp * (phi + delta*dphiddelta) + + doublereal tmp = ni[i] * (triagtmp * (phi + delta*dphiddelta) + dtriagtmpddelta * delta * phi); val += tmp; } @@ -620,8 +620,8 @@ double WaterPropsIAPWSphi::phiR_d() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phi0_d() const { - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phi0_d() const { + doublereal delta = DELTAsave; return (1.0/delta); } @@ -630,11 +630,11 @@ double WaterPropsIAPWSphi::phi0_d() const { * of helmholtz free energy wrt delta * Eqn. (6.4) */ -double WaterPropsIAPWSphi::phi_d(double tau, double delta) { +doublereal WaterPropsIAPWSphi::phi_d(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0_d(); - double res = phiR_d(); - double retn = nau + res; + doublereal nau = phi0_d(); + doublereal res = phiR_d(); + doublereal retn = nau + res; return retn; } @@ -645,10 +645,10 @@ double WaterPropsIAPWSphi::phi_d(double tau, double delta) { * * note: this is done so much, we have a seperate routine. */ -double WaterPropsIAPWSphi::pressureM_rhoRT(double tau, double delta) { +doublereal WaterPropsIAPWSphi::pressureM_rhoRT(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double res = phiR_d(); - double retn = 1.0 + delta * res; + doublereal res = phiR_d(); + doublereal retn = 1.0 + delta * res; return retn; } @@ -659,17 +659,17 @@ double WaterPropsIAPWSphi::pressureM_rhoRT(double tau, double delta) { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR_dd() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR_dd() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; - double atmp; + doublereal atmp; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = (ni[4] * 2.0 * TAUsqrt + + doublereal T375 = pow(tau, 0.375); + doublereal val = (ni[4] * 2.0 * TAUsqrt + ni[5] * 2.0 * T375 * T375 + ni[6] * 6.0 * delta * T375 + ni[7] * 12.0 * DELTAp[2] * tau); @@ -677,8 +677,8 @@ double WaterPropsIAPWSphi::phiR_dd() const { * Next, do polynomial contributions 8 to 51 */ for (i = 8; i <= 51; i++) { - double dtmp = DELTAp[ciR[i]]; - double tmp = ni[i] * exp(-dtmp) * TAUp[tiR[i]]; + doublereal dtmp = DELTAp[ciR[i]]; + doublereal tmp = ni[i] * exp(-dtmp) * TAUp[tiR[i]]; if (diR[i] == 1) { atmp = 1.0/delta; } else { @@ -694,14 +694,14 @@ double WaterPropsIAPWSphi::phiR_dd() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; - double tmp = (ni[i] * TAUp[tiR[i]] * + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; + doublereal tmp = (ni[i] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); - double deltmp = DELTAp[diR[i]]; - double deltmpM1 = deltmp/delta; - double deltmpM2 = deltmpM1 / delta; - double d2tmp = dtmp * dtmp; + doublereal deltmp = DELTAp[diR[i]]; + doublereal deltmpM1 = deltmp/delta; + doublereal deltmpM2 = deltmpM1 / delta; + doublereal d2tmp = dtmp * dtmp; val += tmp * (-2.0*alphai[j]*deltmp + 4.0 * alphai[j] * alphai[j] * deltmp * d2tmp - @@ -714,41 +714,41 @@ double WaterPropsIAPWSphi::phiR_dd() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); - double triagtmpm1 = pow(triag, bi[j]-1.0); - double atmpM1 = atmp - 1.0; - double ptmp = pow(dtmp2,atmpM1); - double p2tmp = pow(dtmp2, ai[j]-1.0); - double dtriagddelta = + doublereal triagtmp = pow(triag, bi[j]); + doublereal triagtmpm1 = pow(triag, bi[j]-1.0); + doublereal atmpM1 = atmp - 1.0; + doublereal ptmp = pow(dtmp2,atmpM1); + doublereal p2tmp = pow(dtmp2, ai[j]-1.0); + doublereal dtriagddelta = deltam1 *(Ai[j] * theta * 2.0 / Bbetai[j] * ptmp + 2.0*Bi[j]*ai[j]*p2tmp); - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); - double dphiddelta = -2.0*Ci[j]*deltam1*phi; - double dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal dphiddelta = -2.0*Ci[j]*deltam1*phi; + doublereal dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; - double d2phiddelta2 = 2.0 * Ci[j] * phi * (2.0*Ci[j]*dtmp2 - 1.0); + doublereal d2phiddelta2 = 2.0 * Ci[j] * phi * (2.0*Ci[j]*dtmp2 - 1.0); - double pptmp = ptmp / dtmp2; - double d2triagddelta2 = dtriagddelta / deltam1; + doublereal pptmp = ptmp / dtmp2; + doublereal d2triagddelta2 = dtriagddelta / deltam1; d2triagddelta2 += dtmp2 *(4.0*Bi[j]*ai[j]*(ai[j]-1.0)*pow(dtmp2,ai[j]-2.0) + 2.0*Ai[j]*Ai[j]/(Bbetai[j]*Bbetai[j])*ptmp*ptmp + Ai[j]*theta*4.0/Bbetai[j]*(atmp-1.0)*pptmp); - double d2triagtmpd2delta = + doublereal d2triagtmpd2delta = bi[j] * (triagtmpm1 * d2triagddelta2 + (bi[j]-1.0)*triagtmpm1/triag*dtriagddelta*dtriagddelta); - double ctmp = (triagtmp * (2.0*dphiddelta + delta*d2phiddelta2) + + doublereal ctmp = (triagtmp * (2.0*dphiddelta + delta*d2phiddelta2) + 2.0*dtriagtmpddelta*(phi + delta * dphiddelta) + d2triagtmpd2delta * delta * phi); @@ -765,8 +765,8 @@ double WaterPropsIAPWSphi::phiR_dd() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phi0_dd() const { - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phi0_dd() const { + doublereal delta = DELTAsave; return (-1.0/(delta*delta)); } @@ -775,36 +775,36 @@ double WaterPropsIAPWSphi::phi0_dd() const { * of helmholtz free energy wrt delta * Eqn. (6.4) */ -double WaterPropsIAPWSphi::phi_dd(double tau, double delta) { +doublereal WaterPropsIAPWSphi::phi_dd(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0_dd(); - double res = phiR_dd(); - double retn = nau + res; + doublereal nau = phi0_dd(); + doublereal res = phiR_dd(); + doublereal retn = nau + res; return retn; } -double WaterPropsIAPWSphi::dimdpdrho(double tau, double delta) { +doublereal WaterPropsIAPWSphi::dimdpdrho(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double res1 = phiR_d(); - double res2 = phiR_dd(); - double retn = 1.0 + delta * (2.0*res1 + delta*res2); + doublereal res1 = phiR_d(); + doublereal res2 = phiR_dd(); + doublereal retn = 1.0 + delta * (2.0*res1 + delta*res2); return retn; } -double WaterPropsIAPWSphi::dimdpdT(double tau, double delta) { +doublereal WaterPropsIAPWSphi::dimdpdT(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double res1 = phiR_d(); - double res2 = phiR_dt(); - double retn = (1.0 + delta * res1) - tau * delta * (res2); + doublereal res1 = phiR_d(); + doublereal res2 = phiR_dt(); + doublereal retn = (1.0 + delta * res1) - tau * delta * (res2); return retn; } /* * Calculate d_phi0/d(tau) */ -double WaterPropsIAPWSphi::phi0_t() const { - double tau = TAUsave; - double retn = ni0[2] + ni0[3]/tau;; +doublereal WaterPropsIAPWSphi::phi0_t() const { + doublereal tau = TAUsave; + doublereal retn = ni0[2] + ni0[3]/tau;; retn += (ni0[4] * gammi0[4] * (1.0/(1.0 - exp(-gammi0[4]*tau)) - 1.0)); retn += (ni0[5] * gammi0[5] * (1.0/(1.0 - exp(-gammi0[5]*tau)) - 1.0)); retn += (ni0[6] * gammi0[6] * (1.0/(1.0 - exp(-gammi0[6]*tau)) - 1.0)); @@ -820,17 +820,17 @@ double WaterPropsIAPWSphi::phi0_t() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR_t() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR_t() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; - double atmp, tmp; + doublereal atmp, tmp; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = ((-0.5) *ni[1] * delta / TAUsqrt / tau + + doublereal T375 = pow(tau, 0.375); + doublereal val = ((-0.5) *ni[1] * delta / TAUsqrt / tau + ni[2] * delta * 0.875 / TAUsqrt * T375 + ni[3] * delta + ni[4] * DELTAp[2] * 0.5 / TAUsqrt + @@ -850,8 +850,8 @@ double WaterPropsIAPWSphi::phiR_t() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; tmp = (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); val += tmp *(tiR[i]/tau - 2.0 * betai[j]*ttmp); @@ -862,21 +862,21 @@ double WaterPropsIAPWSphi::phiR_t() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); + doublereal triagtmp = pow(triag, bi[j]); - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); - double dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; + doublereal dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; - double dphidtau = - 2.0 * Di[j] * ttmp * phi; + doublereal dphidtau = - 2.0 * Di[j] * ttmp * phi; val += ni[i] * delta * (dtriagtmpdtau * phi + triagtmp * dphidtau); } @@ -889,21 +889,21 @@ double WaterPropsIAPWSphi::phiR_t() const { * of helmholtz free energy wrt tau * Eqn. (6.4) */ -double WaterPropsIAPWSphi::phi_t(double tau, double delta) { +doublereal WaterPropsIAPWSphi::phi_t(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0_t(); - double res = phiR_t(); - double retn = nau + res; + doublereal nau = phi0_t(); + doublereal res = phiR_t(); + doublereal retn = nau + res; return retn; } /* * Calculate d2_phi0/dtau2 */ -double WaterPropsIAPWSphi::phi0_tt() const { - double tau = TAUsave; - double tmp, itmp; - double retn = - ni0[3]/(tau * tau); +doublereal WaterPropsIAPWSphi::phi0_tt() const { + doublereal tau = TAUsave; + doublereal tmp, itmp; + doublereal retn = - ni0[3]/(tau * tau); for (int i = 4; i <= 8; i++) { tmp = exp(-gammi0[i]*tau); itmp = 1.0 - tmp; @@ -919,17 +919,17 @@ double WaterPropsIAPWSphi::phi0_tt() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR_tt() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR_tt() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; - double atmp, tmp; + doublereal atmp, tmp; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = ((-0.5) * (-1.5) * ni[1] * delta / (TAUsqrt * tau * tau) + + doublereal T375 = pow(tau, 0.375); + doublereal val = ((-0.5) * (-1.5) * ni[1] * delta / (TAUsqrt * tau * tau) + ni[2] * delta * 0.875 * (-0.125) * T375 / (TAUsqrt * tau) + ni[4] * DELTAp[2] * 0.5 * (-0.5)/ (TAUsqrt * tau) + ni[5] * DELTAp[2] * 0.75 *(-0.25) * T375 * T375 / (tau * tau) + @@ -949,8 +949,8 @@ double WaterPropsIAPWSphi::phiR_tt() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; tmp = (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); atmp = tiR[i]/tau - 2.0 * betai[j]*ttmp; @@ -962,28 +962,28 @@ double WaterPropsIAPWSphi::phiR_tt() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); - double triagtmpM1 = triagtmp / triag; + doublereal triagtmp = pow(triag, bi[j]); + doublereal triagtmpM1 = triagtmp / triag; - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); - double dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; + doublereal dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; - double dphidtau = - 2.0 * Di[j] * ttmp * phi; + doublereal dphidtau = - 2.0 * Di[j] * ttmp * phi; - double d2triagtmpdtau2 = + doublereal d2triagtmpdtau2 = (2 * bi[j] * triagtmpM1 + 4 * theta * theta * bi[j] * (bi[j]-1.0) * triagtmpM1 / triag); - double d2phidtau2 = 2.0*Di[j]*phi *(2.0*Di[j]*ttmp*ttmp - 1.0); + doublereal d2phidtau2 = 2.0*Di[j]*phi *(2.0*Di[j]*ttmp*ttmp - 1.0); tmp = (d2triagtmpdtau2 * phi + 2 * dtriagtmpdtau * dphidtau + @@ -999,18 +999,18 @@ double WaterPropsIAPWSphi::phiR_tt() const { * of helmholtz free energy wrt tau * Eqn. (6.4) */ -double WaterPropsIAPWSphi::phi_tt(double tau, double delta) { +doublereal WaterPropsIAPWSphi::phi_tt(doublereal tau, doublereal delta) { tdpolycalc(tau, delta); - double nau = phi0_tt(); - double res = phiR_tt(); - double retn = nau + res; + doublereal nau = phi0_tt(); + doublereal res = phiR_tt(); + doublereal retn = nau + res; return retn; } /** * Calculate d2_phi0/dtauddelta */ -double WaterPropsIAPWSphi::phi0_dt() const { +doublereal WaterPropsIAPWSphi::phi0_dt() const { return 0.0; } @@ -1021,16 +1021,16 @@ double WaterPropsIAPWSphi::phi0_dt() const { * tau = dimensionless temperature * delta = dimensionless pressure */ -double WaterPropsIAPWSphi::phiR_dt() const { - double tau = TAUsave; - double delta = DELTAsave; +doublereal WaterPropsIAPWSphi::phiR_dt() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; int i, j; - double tmp; + doublereal tmp; /* * Write out the first seven polynomials in the expression */ - double T375 = pow(tau, 0.375); - double val = (ni[1] * (-0.5) / (TAUsqrt * tau) + + doublereal T375 = pow(tau, 0.375); + doublereal val = (ni[1] * (-0.5) / (TAUsqrt * tau) + ni[2] * (0.875) * T375 / TAUsqrt + ni[3] + ni[4] * 2.0 * delta * (0.5) / TAUsqrt + @@ -1051,8 +1051,8 @@ double WaterPropsIAPWSphi::phiR_dt() const { */ for (j = 0; j < 3; j++) { i = 52 + j; - double dtmp = delta - epsi[j]; - double ttmp = tau - gammai[j]; + doublereal dtmp = delta - epsi[j]; + doublereal ttmp = tau - gammai[j]; tmp = (ni[i] * DELTAp[diR[i]] * TAUp[tiR[i]] * exp(-alphai[j]*dtmp*dtmp - betai[j]*ttmp*ttmp)); val += tmp * ((diR[i]/delta - 2.0 * alphai[j] * dtmp) * @@ -1064,39 +1064,39 @@ double WaterPropsIAPWSphi::phiR_dt() const { */ for (j = 0; j < 2; j++) { i = 55 + j; - double deltam1 = delta - 1.0; - double dtmp2 = deltam1 * deltam1; - double atmp = 0.5 / Bbetai[j]; - double theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); - double triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); - double ttmp = tau - 1.0; + doublereal deltam1 = delta - 1.0; + doublereal dtmp2 = deltam1 * deltam1; + doublereal atmp = 0.5 / Bbetai[j]; + doublereal theta = (1.0 - tau) + Ai[j] * pow(dtmp2, atmp); + doublereal triag = theta * theta + Bi[j] * pow(dtmp2, ai[j]); + doublereal ttmp = tau - 1.0; - double triagtmp = pow(triag, bi[j]); - double triagtmpm1 = pow(triag, bi[j]-1.0); - double atmpM1 = atmp - 1.0; - double ptmp = pow(dtmp2,atmpM1); - double p2tmp = pow(dtmp2, ai[j]-1.0); - double dtriagddelta = + doublereal triagtmp = pow(triag, bi[j]); + doublereal triagtmpm1 = pow(triag, bi[j]-1.0); + doublereal atmpM1 = atmp - 1.0; + doublereal ptmp = pow(dtmp2,atmpM1); + doublereal p2tmp = pow(dtmp2, ai[j]-1.0); + doublereal dtriagddelta = deltam1 *(Ai[j] * theta * 2.0 / Bbetai[j] * ptmp + 2.0*Bi[j]*ai[j]*p2tmp); - double phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); - double dphiddelta = -2.0*Ci[j]*deltam1*phi; - double dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; + doublereal phi = exp(-Ci[j]*dtmp2 - Di[j]*ttmp*ttmp); + doublereal dphiddelta = -2.0*Ci[j]*deltam1*phi; + doublereal dtriagtmpddelta = bi[j] * triagtmpm1 * dtriagddelta; - double dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; + doublereal dtriagtmpdtau = -2.0*theta * bi[j] * triagtmp / triag; - double dphidtau = - 2.0 * Di[j] * ttmp * phi; + doublereal dphidtau = - 2.0 * Di[j] * ttmp * phi; - double d2phiddeltadtau = 4.0 * Ci[j] * Di[j] * deltam1 * ttmp * phi; + doublereal d2phiddeltadtau = 4.0 * Ci[j] * Di[j] * deltam1 * ttmp * phi; - double d2triagtmpddeltadtau = + doublereal d2triagtmpddeltadtau = ( -Ai[j] * bi[j] * 2.0 / Bbetai[j] * triagtmpm1 * deltam1 * ptmp -2.0 * theta * bi[j] * (bi[j] - 1.0) * triagtmpm1 / triag * dtriagddelta); - double tmp = ni[i] * (triagtmp * (dphidtau + delta*d2phiddeltadtau) + + doublereal tmp = ni[i] * (triagtmp * (dphidtau + delta*d2phiddeltadtau) + delta * dtriagtmpddelta * dphidtau + dtriagtmpdtau * (phi + delta * dphiddelta) + d2triagtmpddeltadtau * delta * phi); @@ -1113,30 +1113,30 @@ double WaterPropsIAPWSphi::phiR_dt() const { * critical point. * */ -double WaterPropsIAPWSphi::dfind(double p_red, double tau, double deltaGuess) { - double dd = deltaGuess; +doublereal WaterPropsIAPWSphi::dfind(doublereal p_red, doublereal tau, doublereal deltaGuess) { + doublereal dd = deltaGuess; bool conv = false; - double deldd = dd; - double pcheck = 1.0E-30 + 1.0E-8 * p_red; + doublereal deldd = dd; + doublereal pcheck = 1.0E-30 + 1.0E-8 * p_red; for (int n = 0; n < 200; n++) { /* * Calculate the internal polynomials, and then calculate the * phi deriv functions needed by this routine. */ tdpolycalc(tau, dd); - double q1 = phiR_d(); - double q2 = phiR_dd(); + doublereal q1 = phiR_d(); + doublereal q2 = phiR_dd(); /* * Calculate the predicted reduced pressure, pred0, based on the * current tau and dd. */ - double pred0 = dd + dd * dd * q1; + doublereal pred0 = dd + dd * dd * q1; /* * Calculate the derivative of the predicted reduced pressure * wrt the reduced density, dd, This is dpddelta */ - double dpddelta = 1.0 + 2.0 * dd * q1 + dd * dd * q2; + doublereal dpddelta = 1.0 + 2.0 * dd * q1 + dd * dd * q2; /* * If dpddelta is negative, then we are in the middle of the * 2 phase region, beyond the stability curve. We need to adjust @@ -1158,7 +1158,7 @@ double WaterPropsIAPWSphi::dfind(double p_red, double tau, double deltaGuess) { /* * Dampen and crop the update */ - double dpdx = dpddelta; + doublereal dpdx = dpddelta; if (n < 10) { dpdx = dpddelta * 1.1; } @@ -1200,74 +1200,74 @@ double WaterPropsIAPWSphi::dfind(double p_red, double tau, double deltaGuess) { /** * Calculate the dimensionless gibbs free energy g/RT. */ -double WaterPropsIAPWSphi::gibbs_RT() const { - double delta = DELTAsave; - double rd = phiR_d(); - double g = 1.0 + phi0() + phiR() + delta * rd; +doublereal WaterPropsIAPWSphi::gibbs_RT() const { + doublereal delta = DELTAsave; + doublereal rd = phiR_d(); + doublereal g = 1.0 + phi0() + phiR() + delta * rd; return g; } /** * Calculate the dimensionless enthalpy h/RT. */ -double WaterPropsIAPWSphi::enthalpy_RT() const { - double delta = DELTAsave; - double tau = TAUsave; - double rd = phiR_d(); - double nt = phi0_t(); - double rt = phiR_t(); - double hRT = 1.0 + tau * (nt + rt) + delta * rd; +doublereal WaterPropsIAPWSphi::enthalpy_RT() const { + doublereal delta = DELTAsave; + doublereal tau = TAUsave; + doublereal rd = phiR_d(); + doublereal nt = phi0_t(); + doublereal rt = phiR_t(); + doublereal hRT = 1.0 + tau * (nt + rt) + delta * rd; return hRT; } /* * Calculate the dimensionless entropy s/R. */ -double WaterPropsIAPWSphi::entropy_R() const { - double tau = TAUsave; - double nt = phi0_t(); - double rt = phiR_t(); - double p0 = phi0(); - double pR = phiR(); - double sR = tau * (nt + rt) - p0 - pR; +doublereal WaterPropsIAPWSphi::entropy_R() const { + doublereal tau = TAUsave; + doublereal nt = phi0_t(); + doublereal rt = phiR_t(); + doublereal p0 = phi0(); + doublereal pR = phiR(); + doublereal sR = tau * (nt + rt) - p0 - pR; return sR; } /* * Calculate the dimensionless internal energy, u/RT. */ -double WaterPropsIAPWSphi::intEnergy_RT() const { - double tau = TAUsave; - double nt = phi0_t(); - double rt = phiR_t(); - double uR = tau * (nt + rt); +doublereal WaterPropsIAPWSphi::intEnergy_RT() const { + doublereal tau = TAUsave; + doublereal nt = phi0_t(); + doublereal rt = phiR_t(); + doublereal uR = tau * (nt + rt); return uR; } /* * Calculate the dimensionless constant volume Heat Capacity, Cv/R */ -double WaterPropsIAPWSphi::cv_R() const { - double tau = TAUsave; - double ntt = phi0_tt(); - double rtt = phiR_tt(); - double cvR = - tau * tau * (ntt + rtt); +doublereal WaterPropsIAPWSphi::cv_R() const { + doublereal tau = TAUsave; + doublereal ntt = phi0_tt(); + doublereal rtt = phiR_tt(); + doublereal cvR = - tau * tau * (ntt + rtt); return cvR; } /* * Calculate the dimensionless constant pressure Heat Capacity, Cp/R */ -double WaterPropsIAPWSphi::cp_R() const { - double tau = TAUsave; - double delta = DELTAsave; - double cvR = cv_R(); - //double nd = phi0_d(); - double rd = phiR_d(); - double rdd = phiR_dd(); - double rdt = phiR_dt(); - double num = (1.0 + delta * rd - delta * tau * rdt); - double cpR = cvR + (num * num / +doublereal WaterPropsIAPWSphi::cp_R() const { + doublereal tau = TAUsave; + doublereal delta = DELTAsave; + doublereal cvR = cv_R(); + //doublereal nd = phi0_d(); + doublereal rd = phiR_d(); + doublereal rdd = phiR_dd(); + doublereal rdt = phiR_dt(); + doublereal num = (1.0 + delta * rd - delta * tau * rdt); + doublereal cpR = cvR + (num * num / (1.0 + 2.0 * delta * rd + delta * delta * rdd)); return cpR; } diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.h b/Cantera/src/thermo/WaterPropsIAPWSphi.h index 1691214ae..cbd905d21 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.h +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.h @@ -45,35 +45,35 @@ public: * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double phi(double tau, double delta); + doublereal phi(doublereal tau, doublereal delta); //! Delta derivative of phi /*! * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double phi_d(double tau, double delta); + doublereal phi_d(doublereal tau, doublereal delta); //! 2nd derivative of phi wrt delta /*! * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double phi_dd(double tau, double delta); + double phi_dd(doublereal tau, doublereal delta); //! First derivative of phi wrt tau /*! * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double phi_t(double tau, double delta); + doublereal phi_t(doublereal tau, doublereal delta); //! Second derivative of phi wrt tau /*! * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double phi_tt(double tau, double delta); + doublereal phi_tt(doublereal tau, doublereal delta); //! Internal check # 1 void check1(); @@ -91,7 +91,7 @@ public: * * note: this is done so much, we have a seperate routine. */ - double pressureM_rhoRT(double tau, double delta); + doublereal pressureM_rhoRT(doublereal tau, doublereal delta); //! Dimensionless derivative of p wrt rho at constant T /*! @@ -101,7 +101,7 @@ public: * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double dimdpdrho(double tau, double delta); + doublereal dimdpdrho(doublereal tau, doublereal delta); //! Dimensionless derivative of p wrt T at constant rho /*! @@ -111,7 +111,7 @@ public: * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - double dimdpdT(double tau, double delta); + doublereal dimdpdT(doublereal tau, doublereal delta); /** * This program computes the reduced density, given the reduced pressure @@ -126,37 +126,37 @@ public: * @return * Returns the dimensionless density. */ - double dfind(double p_red, double tau, double deltaGuess); + doublereal dfind(doublereal p_red, doublereal tau, doublereal deltaGuess); /** * Calculate the dimensionless gibbs free energy */ - double gibbs_RT() const; + doublereal gibbs_RT() const; /** * Calculate the dimensionless enthalpy, h/RT */ - double enthalpy_RT() const; + doublereal enthalpy_RT() const; /** * Calculate the dimensionless entropy, s/R */ - double entropy_R() const; + doublereal entropy_R() const; /** * Calculate the dimensionless internal energy, u/RT */ - double intEnergy_RT() const; + doublereal intEnergy_RT() const; /** * Calculate the dimensionless constant volume heat capacity, Cv/R */ - double cv_R() const; + doublereal cv_R() const; /** * Calculate the dimensionless constant pressure heat capacity, Cv/R */ - double cp_R() const; + doublereal cp_R() const; //! Calculates internal polynomials in tau and delta. @@ -167,35 +167,35 @@ public: * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - void tdpolycalc(double tau, double delta); + void tdpolycalc(doublereal tau, doublereal delta); //! Return the value of phiR(), res - double phiR() const; + doublereal phiR() const; private: //! nau calculation - double phi0() const; + doublereal phi0() const; //! calculation of d_phiR/d_d - double phiR_d() const; + doublereal phiR_d() const; //! calculation of d_nau/d_d - double phi0_d() const; + doublereal phi0_d() const; //! calculation of d2_res/d_dd - double phiR_dd() const; + doublereal phiR_dd() const; //! calculation of d2_nau/d_dd - double phi0_dd() const; + doublereal phi0_dd() const; //! calculation of d_nau/d_t - double phi0_t() const; + doublereal phi0_t() const; //! calculation of d_res/d_t - double phiR_t() const; + doublereal phiR_t() const; //! calculation of d2_res/d_tt - double phiR_tt() const; + doublereal phiR_tt() const; //! calculation of d2_nau/d_tt - double phi0_tt() const; + doublereal phi0_tt() const; //! calculation of d2_res/d_dt - double phiR_dt() const; + doublereal phiR_dt() const; //! calculation of d2_nau/d_dt - double phi0_dt() const; + doublereal phi0_dt() const; /** * intCheck() calculates all of the functions at a one point and @@ -205,23 +205,23 @@ private: * @param tau Dimensionless temperature = T_c/T * @param delta Dimensionless density = delta = rho / Rho_c */ - void intCheck(double tau, double delta); + void intCheck(doublereal tau, doublereal delta); private: //! Value of internally calculated polynomials of powers of TAU - double TAUp[52]; + doublereal TAUp[52]; //! Value of internally calculated polynomials of powers of delta - double DELTAp[16]; + doublereal DELTAp[16]; //! Last tau that was used to calculate polynomials - double TAUsave; + doublereal TAUsave; //! sqrt of TAU - double TAUsqrt; + doublereal TAUsqrt; //! Last delta that was used to calculate polynomials - double DELTAsave; + doublereal DELTAsave; }; #endif diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index adee9aeba..50482d169 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -44,7 +44,7 @@ namespace Cantera { const int cSemiconductor = 7; const int cMineralEQ3 = 8; // MineralEQ3 in MineralEQ3.h - const int cElectrodeElectron = 9; // electrodeElectron + const int cMetalSHEelectrons = 9; // SHE electrode electrons const int cLatticeSolid = 20; // LatticeSolidPhase.h const int cLattice = 21; From d99352f3d19103da0057a9bd6bdcd3474c75d56d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 12 Dec 2009 00:15:00 +0000 Subject: [PATCH 068/446] Doxygen Updates - no changes to the code --- Cantera/src/transport/FtnTransport.h | 1 + Cantera/src/transport/L_matrix.h | 0 Cantera/src/transport/MMCollisionInt.cpp | 977 ++++++++++++----------- Cantera/src/transport/MMCollisionInt.h | 25 +- Cantera/src/transport/MixTransport.cpp | 0 Cantera/src/transport/MultiTransport.cpp | 0 Cantera/src/transport/TransportParams.h | 0 7 files changed, 516 insertions(+), 487 deletions(-) mode change 100755 => 100644 Cantera/src/transport/FtnTransport.h mode change 100755 => 100644 Cantera/src/transport/L_matrix.h mode change 100755 => 100644 Cantera/src/transport/MMCollisionInt.cpp mode change 100755 => 100644 Cantera/src/transport/MMCollisionInt.h mode change 100755 => 100644 Cantera/src/transport/MixTransport.cpp mode change 100755 => 100644 Cantera/src/transport/MultiTransport.cpp mode change 100755 => 100644 Cantera/src/transport/TransportParams.h diff --git a/Cantera/src/transport/FtnTransport.h b/Cantera/src/transport/FtnTransport.h old mode 100755 new mode 100644 index 7df1de947..793a1352d --- a/Cantera/src/transport/FtnTransport.h +++ b/Cantera/src/transport/FtnTransport.h @@ -38,6 +38,7 @@ extern "C" { + doublereal __VISC__(doublereal* t, doublereal* p, doublereal* x); doublereal __BULKVISC__(doublereal* t, doublereal* p, doublereal* x); doublereal __TCON__(doublereal* t, doublereal* p, doublereal* x); diff --git a/Cantera/src/transport/L_matrix.h b/Cantera/src/transport/L_matrix.h old mode 100755 new mode 100644 diff --git a/Cantera/src/transport/MMCollisionInt.cpp b/Cantera/src/transport/MMCollisionInt.cpp old mode 100755 new mode 100644 index c50855c32..42e6c267a --- a/Cantera/src/transport/MMCollisionInt.cpp +++ b/Cantera/src/transport/MMCollisionInt.cpp @@ -27,519 +27,530 @@ using namespace std; namespace Cantera { - const int DeltaDegree = 6; + const int DeltaDegree = 6; - double MMCollisionInt::delta[8] = {0.0, 0.25, 0.50, 0.75, 1.0, - 1.5, 2.0, 2.5}; + double MMCollisionInt::delta[8] = {0.0, 0.25, 0.50, 0.75, 1.0, + 1.5, 2.0, 2.5}; - doublereal quadInterp(doublereal x0, doublereal* x, doublereal* y) { - doublereal dx21, dx32, dx31, dy32, dy21, a; - dx21 = x[1] - x[0]; - dx32 = x[2] - x[1]; - dx31 = dx21 + dx32; - dy32 = y[2] - y[1]; - dy21 = y[1] - y[0]; - a = (dx21*dy32 - dy21*dx32)/(dx21*dx31*dx32); - return a*(x0 - x[0])*(x0 - x[1]) + (dy21/dx21)*(x0 - x[1]) + y[1]; - } + doublereal quadInterp(doublereal x0, doublereal* x, doublereal* y) { + doublereal dx21, dx32, dx31, dy32, dy21, a; + dx21 = x[1] - x[0]; + dx32 = x[2] - x[1]; + dx31 = dx21 + dx32; + dy32 = y[2] - y[1]; + dy21 = y[1] - y[0]; + a = (dx21*dy32 - dy21*dx32)/(dx21*dx31*dx32); + return a*(x0 - x[0])*(x0 - x[1]) + (dy21/dx21)*(x0 - x[1]) + y[1]; + } - double MMCollisionInt::tstar22[37] = + double MMCollisionInt::tstar22[37] = {0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.5, 3.0, 3.5, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 12.0, 14.0, 16.0, 18.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0, 75.0, 100.0}; - double MMCollisionInt::omega22_table[37*8] = { - 4.1005, 4.266, 4.833, 5.742, 6.729, 8.624, 10.34, 11.89, - 3.2626, 3.305, 3.516, 3.914, 4.433, 5.57, 6.637, 7.618, - 2.8399, 2.836, 2.936, 3.168, 3.511, 4.329, 5.126, 5.874, - 2.531, 2.522, 2.586, 2.749, 3.004, 3.64, 4.282, 4.895, - 2.2837, 2.277, 2.329, 2.46, 2.665, 3.187, 3.727, 4.249, - 2.0838, 2.081, 2.13, 2.243, 2.417, 2.862, 3.329, 3.786, - 1.922, 1.924, 1.97, 2.072, 2.225, 2.614, 3.028, 3.435, - 1.7902, 1.795, 1.84, 1.934, 2.07, 2.417, 2.788, 3.156, - 1.6823, 1.689, 1.733, 1.82, 1.944, 2.258, 2.596, 2.933, - 1.5929, 1.601, 1.644, 1.725, 1.838, 2.124, 2.435, 2.746, - 1.4551, 1.465, 1.504, 1.574, 1.67, 1.913, 2.181, 2.451, - 1.3551, 1.365, 1.4, 1.461, 1.544, 1.754, 1.989, 2.228, - 1.28, 1.289, 1.321, 1.374, 1.447, 1.63, 1.838, 2.053, - 1.2219, 1.231, 1.259, 1.306, 1.37, 1.532, 1.718, 1.912, - 1.1757, 1.184, 1.209, 1.251, 1.307, 1.451, 1.618, 1.795, - 1.0933, 1.1, 1.119, 1.15, 1.193, 1.304, 1.435, 1.578, - 1.0388, 1.044, 1.059, 1.083, 1.117, 1.204, 1.31, 1.428, - 0.99963, 1.004, 1.016, 1.035, 1.062, 1.133, 1.22, 1.319, - 0.96988, 0.9732, 0.983, 0.9991, 1.021, 1.079, 1.153, 1.236, - 0.92676, 0.9291, 0.936, 0.9473, 0.9628, 1.005, 1.058, 1.121, - 0.89616, 0.8979, 0.903, 0.9114, 0.923, 0.9545, 0.9955, 1.044, - 0.87272, 0.8741, 0.878, 0.8845, 0.8935, 0.9181, 0.9505, 0.9893, - 0.85379, 0.8549, 0.858, 0.8632, 0.8703, 0.8901, 0.9164, 0.9482, - 0.83795, 0.8388, 0.8414, 0.8456, 0.8515, 0.8678, 0.8895, 0.916, - 0.82435, 0.8251, 0.8273, 0.8308, 0.8356, 0.8493, 0.8676, 0.8901, - 0.80184, 0.8024, 0.8039, 0.8065, 0.8101, 0.8201, 0.8337, 0.8504, - 0.78363, 0.784, 0.7852, 0.7872, 0.7899, 0.7976, 0.8081, 0.8212, - 0.76834, 0.7687, 0.7696, 0.7712, 0.7733, 0.7794, 0.7878, 0.7983, - 0.75518, 0.7554, 0.7562, 0.7575, 0.7592, 0.7642, 0.7711, 0.7797, - 0.74364, 0.7438, 0.7445, 0.7455, 0.747, 0.7512, 0.7569, 0.7642, - 0.71982, 0.72, 0.7204, 0.7211, 0.7221, 0.725, 0.7289, 0.7339, - 0.70097, 0.7011, 0.7014, 0.7019, 0.7026, 0.7047, 0.7076, 0.7112, - 0.68545, 0.6855, 0.6858, 0.6861, 0.6867, 0.6883, 0.6905, 0.6932, - 0.67232, 0.6724, 0.6726, 0.6728, 0.6733, 0.6743, 0.6762, 0.6784, - 0.65099, 0.651, 0.6512, 0.6513, 0.6516, 0.6524, 0.6534, 0.6546, - 0.61397, 0.6141, 0.6143, 0.6145, 0.6147, 0.6148, 0.6148, 0.6147, - 0.5887, 0.5889, 0.5894, 0.59, 0.5903, 0.5901, 0.5895, 0.5885 - }; + double MMCollisionInt::omega22_table[37*8] = { + 4.1005, 4.266, 4.833, 5.742, 6.729, 8.624, 10.34, 11.89, + 3.2626, 3.305, 3.516, 3.914, 4.433, 5.57, 6.637, 7.618, + 2.8399, 2.836, 2.936, 3.168, 3.511, 4.329, 5.126, 5.874, + 2.531, 2.522, 2.586, 2.749, 3.004, 3.64, 4.282, 4.895, + 2.2837, 2.277, 2.329, 2.46, 2.665, 3.187, 3.727, 4.249, + 2.0838, 2.081, 2.13, 2.243, 2.417, 2.862, 3.329, 3.786, + 1.922, 1.924, 1.97, 2.072, 2.225, 2.614, 3.028, 3.435, + 1.7902, 1.795, 1.84, 1.934, 2.07, 2.417, 2.788, 3.156, + 1.6823, 1.689, 1.733, 1.82, 1.944, 2.258, 2.596, 2.933, + 1.5929, 1.601, 1.644, 1.725, 1.838, 2.124, 2.435, 2.746, + 1.4551, 1.465, 1.504, 1.574, 1.67, 1.913, 2.181, 2.451, + 1.3551, 1.365, 1.4, 1.461, 1.544, 1.754, 1.989, 2.228, + 1.28, 1.289, 1.321, 1.374, 1.447, 1.63, 1.838, 2.053, + 1.2219, 1.231, 1.259, 1.306, 1.37, 1.532, 1.718, 1.912, + 1.1757, 1.184, 1.209, 1.251, 1.307, 1.451, 1.618, 1.795, + 1.0933, 1.1, 1.119, 1.15, 1.193, 1.304, 1.435, 1.578, + 1.0388, 1.044, 1.059, 1.083, 1.117, 1.204, 1.31, 1.428, + 0.99963, 1.004, 1.016, 1.035, 1.062, 1.133, 1.22, 1.319, + 0.96988, 0.9732, 0.983, 0.9991, 1.021, 1.079, 1.153, 1.236, + 0.92676, 0.9291, 0.936, 0.9473, 0.9628, 1.005, 1.058, 1.121, + 0.89616, 0.8979, 0.903, 0.9114, 0.923, 0.9545, 0.9955, 1.044, + 0.87272, 0.8741, 0.878, 0.8845, 0.8935, 0.9181, 0.9505, 0.9893, + 0.85379, 0.8549, 0.858, 0.8632, 0.8703, 0.8901, 0.9164, 0.9482, + 0.83795, 0.8388, 0.8414, 0.8456, 0.8515, 0.8678, 0.8895, 0.916, + 0.82435, 0.8251, 0.8273, 0.8308, 0.8356, 0.8493, 0.8676, 0.8901, + 0.80184, 0.8024, 0.8039, 0.8065, 0.8101, 0.8201, 0.8337, 0.8504, + 0.78363, 0.784, 0.7852, 0.7872, 0.7899, 0.7976, 0.8081, 0.8212, + 0.76834, 0.7687, 0.7696, 0.7712, 0.7733, 0.7794, 0.7878, 0.7983, + 0.75518, 0.7554, 0.7562, 0.7575, 0.7592, 0.7642, 0.7711, 0.7797, + 0.74364, 0.7438, 0.7445, 0.7455, 0.747, 0.7512, 0.7569, 0.7642, + 0.71982, 0.72, 0.7204, 0.7211, 0.7221, 0.725, 0.7289, 0.7339, + 0.70097, 0.7011, 0.7014, 0.7019, 0.7026, 0.7047, 0.7076, 0.7112, + 0.68545, 0.6855, 0.6858, 0.6861, 0.6867, 0.6883, 0.6905, 0.6932, + 0.67232, 0.6724, 0.6726, 0.6728, 0.6733, 0.6743, 0.6762, 0.6784, + 0.65099, 0.651, 0.6512, 0.6513, 0.6516, 0.6524, 0.6534, 0.6546, + 0.61397, 0.6141, 0.6143, 0.6145, 0.6147, 0.6148, 0.6148, 0.6147, + 0.5887, 0.5889, 0.5894, 0.59, 0.5903, 0.5901, 0.5895, 0.5885 + }; - //----------------------------- + //----------------------------- - // changed upper limit to 500 from 1.0e10 dgg 5/21/04 - double MMCollisionInt::tstar[39] = { - 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, - 1.2, 1.4, 1.6, 1.8, 2.0, 2.5, 3.0, 3.5, 4.0, - 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 12.0, 14.0, 16.0, - 18.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0, 75.0, 100.0, 500.0}; + // changed upper limit to 500 from 1.0e10 dgg 5/21/04 + double MMCollisionInt::tstar[39] = { + 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, + 1.2, 1.4, 1.6, 1.8, 2.0, 2.5, 3.0, 3.5, 4.0, + 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 12.0, 14.0, 16.0, + 18.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0, 75.0, 100.0, 500.0}; - double MMCollisionInt::astar_table[39*8] = { - 1.0065, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, - 1.0231, 1.0660, 1.0380, 1.0400, 1.0430, 1.0500, 1.0520, 1.0510, - 1.0424, 1.0450, 1.0480, 1.0520, 1.0560, 1.0650, 1.0660, 1.0640, - 1.0719, 1.0670, 1.0600, 1.0550, 1.0580, 1.0680, 1.0710, 1.0710, - 1.0936, 1.0870, 1.0770, 1.0690, 1.0680, 1.0750, 1.0780, 1.0780, - 1.1053, 1.0980, 1.0880, 1.0800, 1.0780, 1.0820, 1.0840, 1.0840, - 1.1104, 1.1040, 1.0960, 1.0890, 1.0860, 1.0890, 1.0900, 1.0900, - 1.1114, 1.1070, 1.1000, 1.0950, 1.0930, 1.0950, 1.0960, 1.0950, - 1.1104, 1.1070, 1.1020, 1.0990, 1.0980, 1.1000, 1.1000, 1.0990, - 1.1086, 1.1060, 1.1020, 1.1010, 1.1010, 1.1050, 1.1050, 1.1040, - 1.1063, 1.1040, 1.1030, 1.1030, 1.1040, 1.1080, 1.1090, 1.1080, - 1.1020, 1.1020, 1.1030, 1.1050, 1.1070, 1.1120, 1.1150, 1.1150, - 1.0985, 1.0990, 1.1010, 1.1040, 1.1080, 1.1150, 1.1190, 1.1200, - 1.0960, 1.0960, 1.0990, 1.1030, 1.1080, 1.1160, 1.1210, 1.1240, - 1.0943, 1.0950, 1.0990, 1.1020, 1.1080, 1.1170, 1.1230, 1.1260, - 1.0934, 1.0940, 1.0970, 1.1020, 1.1070, 1.1160, 1.1230, 1.1280, - 1.0926, 1.0940, 1.0970, 1.0990, 1.1050, 1.1150, 1.1230, 1.1300, - 1.0934, 1.0950, 1.0970, 1.0990, 1.1040, 1.1130, 1.1220, 1.1290, - 1.0948, 1.0960, 1.0980, 1.1000, 1.1030, 1.1120, 1.1190, 1.1270, - 1.0965, 1.0970, 1.0990, 1.1010, 1.1040, 1.1100, 1.1180, 1.1260, - 1.0997, 1.1000, 1.1010, 1.1020, 1.1050, 1.1100, 1.1160, 1.1230, - 1.1025, 1.1030, 1.1040, 1.1050, 1.1060, 1.1100, 1.1150, 1.1210, - 1.1050, 1.1050, 1.1060, 1.1070, 1.1080, 1.1110, 1.1150, 1.1200, - 1.1072, 1.1070, 1.1080, 1.1080, 1.1090, 1.1120, 1.1150, 1.1190, - 1.1091, 1.1090, 1.1090, 1.1100, 1.1110, 1.1130, 1.1150, 1.1190, - 1.1107, 1.1110, 1.1110, 1.1110, 1.1120, 1.1140, 1.1160, 1.1190, - 1.1133, 1.1140, 1.1130, 1.1140, 1.1140, 1.1150, 1.1170, 1.1190, - 1.1154, 1.1150, 1.1160, 1.1160, 1.1160, 1.1170, 1.1180, 1.1200, - 1.1172, 1.1170, 1.1170, 1.1180, 1.1180, 1.1180, 1.1190, 1.1200, - 1.1186, 1.1190, 1.1190, 1.1190, 1.1190, 1.1190, 1.1200, 1.1210, - 1.1199, 1.1200, 1.1200, 1.1200, 1.1200, 1.1210, 1.1210, 1.1220, - 1.1223, 1.1220, 1.1220, 1.1220, 1.1220, 1.1230, 1.1230, 1.1240, - 1.1243, 1.1240, 1.1240, 1.1240, 1.1240, 1.1240, 1.1250, 1.1250, - 1.1259, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, - 1.1273, 1.1270, 1.1270, 1.1270, 1.1270, 1.1270, 1.1270, 1.1280, - 1.1297, 1.1300, 1.1300, 1.1300, 1.1300, 1.1300, 1.1300, 1.1290, - 1.1339, 1.1340, 1.1340, 1.1350, 1.1350, 1.1340, 1.1340, 1.1320, - 1.1364, 1.1370, 1.1370, 1.1380, 1.1390, 1.1380, 1.1370, 1.1350, - 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, - 1.14187 }; + double MMCollisionInt::astar_table[39*8] = { + 1.0065, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, 1.0840, + 1.0231, 1.0660, 1.0380, 1.0400, 1.0430, 1.0500, 1.0520, 1.0510, + 1.0424, 1.0450, 1.0480, 1.0520, 1.0560, 1.0650, 1.0660, 1.0640, + 1.0719, 1.0670, 1.0600, 1.0550, 1.0580, 1.0680, 1.0710, 1.0710, + 1.0936, 1.0870, 1.0770, 1.0690, 1.0680, 1.0750, 1.0780, 1.0780, + 1.1053, 1.0980, 1.0880, 1.0800, 1.0780, 1.0820, 1.0840, 1.0840, + 1.1104, 1.1040, 1.0960, 1.0890, 1.0860, 1.0890, 1.0900, 1.0900, + 1.1114, 1.1070, 1.1000, 1.0950, 1.0930, 1.0950, 1.0960, 1.0950, + 1.1104, 1.1070, 1.1020, 1.0990, 1.0980, 1.1000, 1.1000, 1.0990, + 1.1086, 1.1060, 1.1020, 1.1010, 1.1010, 1.1050, 1.1050, 1.1040, + 1.1063, 1.1040, 1.1030, 1.1030, 1.1040, 1.1080, 1.1090, 1.1080, + 1.1020, 1.1020, 1.1030, 1.1050, 1.1070, 1.1120, 1.1150, 1.1150, + 1.0985, 1.0990, 1.1010, 1.1040, 1.1080, 1.1150, 1.1190, 1.1200, + 1.0960, 1.0960, 1.0990, 1.1030, 1.1080, 1.1160, 1.1210, 1.1240, + 1.0943, 1.0950, 1.0990, 1.1020, 1.1080, 1.1170, 1.1230, 1.1260, + 1.0934, 1.0940, 1.0970, 1.1020, 1.1070, 1.1160, 1.1230, 1.1280, + 1.0926, 1.0940, 1.0970, 1.0990, 1.1050, 1.1150, 1.1230, 1.1300, + 1.0934, 1.0950, 1.0970, 1.0990, 1.1040, 1.1130, 1.1220, 1.1290, + 1.0948, 1.0960, 1.0980, 1.1000, 1.1030, 1.1120, 1.1190, 1.1270, + 1.0965, 1.0970, 1.0990, 1.1010, 1.1040, 1.1100, 1.1180, 1.1260, + 1.0997, 1.1000, 1.1010, 1.1020, 1.1050, 1.1100, 1.1160, 1.1230, + 1.1025, 1.1030, 1.1040, 1.1050, 1.1060, 1.1100, 1.1150, 1.1210, + 1.1050, 1.1050, 1.1060, 1.1070, 1.1080, 1.1110, 1.1150, 1.1200, + 1.1072, 1.1070, 1.1080, 1.1080, 1.1090, 1.1120, 1.1150, 1.1190, + 1.1091, 1.1090, 1.1090, 1.1100, 1.1110, 1.1130, 1.1150, 1.1190, + 1.1107, 1.1110, 1.1110, 1.1110, 1.1120, 1.1140, 1.1160, 1.1190, + 1.1133, 1.1140, 1.1130, 1.1140, 1.1140, 1.1150, 1.1170, 1.1190, + 1.1154, 1.1150, 1.1160, 1.1160, 1.1160, 1.1170, 1.1180, 1.1200, + 1.1172, 1.1170, 1.1170, 1.1180, 1.1180, 1.1180, 1.1190, 1.1200, + 1.1186, 1.1190, 1.1190, 1.1190, 1.1190, 1.1190, 1.1200, 1.1210, + 1.1199, 1.1200, 1.1200, 1.1200, 1.1200, 1.1210, 1.1210, 1.1220, + 1.1223, 1.1220, 1.1220, 1.1220, 1.1220, 1.1230, 1.1230, 1.1240, + 1.1243, 1.1240, 1.1240, 1.1240, 1.1240, 1.1240, 1.1250, 1.1250, + 1.1259, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, 1.1260, + 1.1273, 1.1270, 1.1270, 1.1270, 1.1270, 1.1270, 1.1270, 1.1280, + 1.1297, 1.1300, 1.1300, 1.1300, 1.1300, 1.1300, 1.1300, 1.1290, + 1.1339, 1.1340, 1.1340, 1.1350, 1.1350, 1.1340, 1.1340, 1.1320, + 1.1364, 1.1370, 1.1370, 1.1380, 1.1390, 1.1380, 1.1370, 1.1350, + 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, 1.14187, + 1.14187 }; - double MMCollisionInt::bstar_table[39*8] = { - 1.1852, 1.2963, 1.2963, 1.2963, 1.2963, 1.2963,1.2963, 1.2963, - 1.1960, 1.216, 1.237, 1.269, 1.285, 1.290, 1.297, 1.294, - 1.2451, 1.257, 1.340, 1.389, 1.366, 1.327, 1.314, 1.278, - 1.2900, 1.294, 1.272, 1.258, 1.262, 1.282, 1.290, 1.299, - 1.2986, 1.291, 1.284, 1.278, 1.277, 1.288, 1.294, 1.297, - 1.2865, 1.281, 1.276, 1.272, 1.277, 1.286, 1.292, 1.298, - 1.2665, 1.264, 1.261, 1.263, 1.269, 1.284, 1.292, 1.298, - 1.2455, 1.244, 1.248, 1.255, 1.262, 1.278, 1.289, 1.296, - 1.2253, 1.225, 1.234, 1.240, 1.252, 1.271, 1.284, 1.295, - 1.2078, 1.210, 1.216, 1.227, 1.242, 1.264, 1.281, 1.292, - 1.1919, 1.192, 1.205, 1.216, 1.230, 1.256, 1.273, 1.287, - 1.1678, 1.172, 1.181, 1.195, 1.209, 1.237, 1.261, 1.277, - 1.1496, 1.155, 1.161, 1.174, 1.189, 1.221, 1.246, 1.266, - 1.1366, 1.141, 1.147, 1.159, 1.174, 1.202, 1.231, 1.256, - 1.1270, 1.130, 1.138, 1.148, 1.162, 1.191, 1.218, 1.242, - 1.1197, 1.122, 1.129, 1.140, 1.149, 1.178, 1.205, 1.231, - 1.1080, 1.110, 1.116, 1.122, 1.132, 1.154, 1.180, 1.205, - 1.1016, 1.103, 1.107, 1.112, 1.120, 1.138, 1.160, 1.183, - 1.0980, 1.099, 1.102, 1.106, 1.112, 1.127, 1.145, 1.165, - 1.0958, 1.097, 1.099, 1.102, 1.107, 1.119, 1.135, 1.153, - 1.0935, 1.094, 1.095, 1.097, 1.100, 1.109, 1.120, 1.134, - 1.0925, 1.092, 1.094, 1.095, 1.098, 1.104, 1.112, 1.122, - 1.0922, 1.092, 1.093, 1.094, 1.096, 1.100, 1.106, 1.115, - 1.0922, 1.092, 1.093, 1.093, 1.095, 1.098, 1.103, 1.110, - 1.0923, 1.092, 1.093, 1.093, 1.094, 1.097, 1.101, 1.106, - 1.0923, 1.092, 1.092, 1.093, 1.094, 1.096, 1.099, 1.103, - 1.0927, 1.093, 1.093, 1.093, 1.094, 1.095, 1.098, 1.101, - 1.0930, 1.093, 1.093, 1.093, 1.094, 1.094, 1.096, 1.099, - 1.0933, 1.094, 1.093, 1.094, 1.094, 1.095, 1.096, 1.098, - 1.0937, 1.093, 1.094, 1.094, 1.094, 1.094, 1.096, 1.097, - 1.0939, 1.094, 1.094, 1.094, 1.094, 1.095, 1.095, 1.097, - 1.0943, 1.094, 1.094, 1.094, 1.095, 1.095, 1.096, 1.096, - 1.0944, 1.095, 1.094, 1.094, 1.094, 1.095, 1.095, 1.096, - 1.0944, 1.094, 1.095, 1.094, 1.094, 1.095, 1.096, 1.096, - 1.0943, 1.095, 1.094, 1.094, 1.095, 1.095, 1.095, 1.095, - 1.0941, 1.094, 1.094, 1.094, 1.094, 1.094, 1.094, 1.096, - 1.0947, 1.095, 1.094, 1.094, 1.093, 1.093, 1.094, 1.095, - 1.0957, 1.095, 1.094, 1.093, 1.092, 1.093, 1.093, 1.094, - 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, - 1.10185}; + double MMCollisionInt::bstar_table[39*8] = { + 1.1852, 1.2963, 1.2963, 1.2963, 1.2963, 1.2963,1.2963, 1.2963, + 1.1960, 1.216, 1.237, 1.269, 1.285, 1.290, 1.297, 1.294, + 1.2451, 1.257, 1.340, 1.389, 1.366, 1.327, 1.314, 1.278, + 1.2900, 1.294, 1.272, 1.258, 1.262, 1.282, 1.290, 1.299, + 1.2986, 1.291, 1.284, 1.278, 1.277, 1.288, 1.294, 1.297, + 1.2865, 1.281, 1.276, 1.272, 1.277, 1.286, 1.292, 1.298, + 1.2665, 1.264, 1.261, 1.263, 1.269, 1.284, 1.292, 1.298, + 1.2455, 1.244, 1.248, 1.255, 1.262, 1.278, 1.289, 1.296, + 1.2253, 1.225, 1.234, 1.240, 1.252, 1.271, 1.284, 1.295, + 1.2078, 1.210, 1.216, 1.227, 1.242, 1.264, 1.281, 1.292, + 1.1919, 1.192, 1.205, 1.216, 1.230, 1.256, 1.273, 1.287, + 1.1678, 1.172, 1.181, 1.195, 1.209, 1.237, 1.261, 1.277, + 1.1496, 1.155, 1.161, 1.174, 1.189, 1.221, 1.246, 1.266, + 1.1366, 1.141, 1.147, 1.159, 1.174, 1.202, 1.231, 1.256, + 1.1270, 1.130, 1.138, 1.148, 1.162, 1.191, 1.218, 1.242, + 1.1197, 1.122, 1.129, 1.140, 1.149, 1.178, 1.205, 1.231, + 1.1080, 1.110, 1.116, 1.122, 1.132, 1.154, 1.180, 1.205, + 1.1016, 1.103, 1.107, 1.112, 1.120, 1.138, 1.160, 1.183, + 1.0980, 1.099, 1.102, 1.106, 1.112, 1.127, 1.145, 1.165, + 1.0958, 1.097, 1.099, 1.102, 1.107, 1.119, 1.135, 1.153, + 1.0935, 1.094, 1.095, 1.097, 1.100, 1.109, 1.120, 1.134, + 1.0925, 1.092, 1.094, 1.095, 1.098, 1.104, 1.112, 1.122, + 1.0922, 1.092, 1.093, 1.094, 1.096, 1.100, 1.106, 1.115, + 1.0922, 1.092, 1.093, 1.093, 1.095, 1.098, 1.103, 1.110, + 1.0923, 1.092, 1.093, 1.093, 1.094, 1.097, 1.101, 1.106, + 1.0923, 1.092, 1.092, 1.093, 1.094, 1.096, 1.099, 1.103, + 1.0927, 1.093, 1.093, 1.093, 1.094, 1.095, 1.098, 1.101, + 1.0930, 1.093, 1.093, 1.093, 1.094, 1.094, 1.096, 1.099, + 1.0933, 1.094, 1.093, 1.094, 1.094, 1.095, 1.096, 1.098, + 1.0937, 1.093, 1.094, 1.094, 1.094, 1.094, 1.096, 1.097, + 1.0939, 1.094, 1.094, 1.094, 1.094, 1.095, 1.095, 1.097, + 1.0943, 1.094, 1.094, 1.094, 1.095, 1.095, 1.096, 1.096, + 1.0944, 1.095, 1.094, 1.094, 1.094, 1.095, 1.095, 1.096, + 1.0944, 1.094, 1.095, 1.094, 1.094, 1.095, 1.096, 1.096, + 1.0943, 1.095, 1.094, 1.094, 1.095, 1.095, 1.095, 1.095, + 1.0941, 1.094, 1.094, 1.094, 1.094, 1.094, 1.094, 1.096, + 1.0947, 1.095, 1.094, 1.094, 1.093, 1.093, 1.094, 1.095, + 1.0957, 1.095, 1.094, 1.093, 1.092, 1.093, 1.093, 1.094, + 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, 1.10185, + 1.10185}; - double MMCollisionInt::cstar_table[39*8] = { - 0.8889, 0.77778, 0.77778,0.77778,0.77778,0.77778,0.77778,0.77778, - 0.88575, 0.8988, 0.8378, 0.8029, 0.7876, 0.7805, 0.7799, 0.7801, - 0.87268, 0.8692,0.8647,0.8479,0.8237,0.7975,0.7881,0.7784, - 0.85182, 0.8525,0.8366,0.8198,0.8054,0.7903,0.7839,0.782, - 0.83542, 0.8362,0.8306,0.8196,0.8076,0.7918,0.7842,0.7806, - 0.82629, 0.8278,0.8252,0.8169,0.8074,0.7916,0.7838,0.7802, - 0.82299, 0.8249,0.823,0.8165,0.8072,0.7922,0.7839,0.7798, - 0.82357, 0.8257,0.8241,0.8178,0.8084,0.7927,0.7839,0.7794, - 0.82657, 0.828,0.8264,0.8199,0.8107,0.7939,0.7842,0.7796, - 0.8311, 0.8234,0.8295,0.8228,0.8136,0.796,0.7854,0.7798, - 0.8363, 0.8366,0.8342,0.8267,0.8168,0.7986,0.7864,0.7805, - 0.84762, 0.8474,0.8438,0.8358,0.825,0.8041,0.7904,0.7822, - 0.85846, 0.8583,0.853,0.8444,0.8336,0.8118,0.7957,0.7854, - 0.8684, 0.8674,0.8619,0.8531,0.8423,0.8186,0.8011,0.7898, - 0.87713, 0.8755,0.8709,0.8616,0.8504,0.8265,0.8072,0.7939, - 0.88479, 0.8831,0.8779,0.8695,0.8578,0.8338,0.8133,0.799, - 0.89972, 0.8986,0.8936,0.8846,0.8742,0.8504,0.8294,0.8125, - 0.91028, 0.9089,0.9043,0.8967,0.8869,0.8649,0.8438,0.8253, - 0.91793, 0.9166,0.9125,0.9058,0.897,0.8768,0.8557,0.8372, - 0.92371, 0.9226,0.9189,0.9128,0.905,0.8861,0.8664,0.8484, - 0.93135, 0.9304,0.9274,0.9226,0.9164,0.9006,0.8833,0.8662, - 0.93607, 0.9353,0.9329,0.9291,0.924,0.9109,0.8958,0.8802, - 0.93927, 0.9387,0.9366,0.9334,0.9292,0.9162,0.905,0.8911, - 0.94149, 0.9409,0.9393,0.9366,0.9331,0.9236,0.9122,0.8997, - 0.94306, 0.9426,0.9412,0.9388,0.9357,0.9276,0.9175,0.9065, - 0.94419, 0.9437,0.9425,0.9406,0.938,0.9308,0.9219,0.9119, - 0.94571, 0.9455,0.9445,0.943,0.9409,0.9353,0.9283,0.9201, - 0.94662, 0.9464,0.9456,0.9444,0.9428,0.9382,0.9325,0.9258, - 0.94723, 0.9471,0.9464,0.9455,0.9442,0.9405,0.9355,0.9298, - 0.94764, 0.9474,0.9469,0.9462,0.945,0.9418,0.9378,0.9328, - 0.9479, 0.9478,0.9474,0.9465,0.9457,0.943,0.9394,0.9352, - 0.94827, 0.9481,0.948,0.9472,0.9467,0.9447,0.9422,0.9391, - 0.94842, 0.9484,0.9481,0.9478,0.9472,0.9458,0.9437,0.9415, - 0.94852, 0.9484,0.9483,0.948,0.9475,0.9465,0.9449,0.943, - 0.94861, 0.9487,0.9484,0.9481,0.9479,0.9468,0.9455,0.943, - 0.94872, 0.9486,0.9486,0.9483,0.9482,0.9475,0.9464,0.9452, - 0.94881, 0.9488,0.9489,0.949,0.9487,0.9482,0.9476,0.9468, - 0.94863, 0.9487,0.9489,0.9491,0.9493,0.9491,0.9483,0.9476, - 0.94444, 0.94444,0.94444,0.94444,0.94444,0.94444,0.94444,0.94444}; + double MMCollisionInt::cstar_table[39*8] = { + 0.8889, 0.77778, 0.77778,0.77778,0.77778,0.77778,0.77778,0.77778, + 0.88575, 0.8988, 0.8378, 0.8029, 0.7876, 0.7805, 0.7799, 0.7801, + 0.87268, 0.8692,0.8647,0.8479,0.8237,0.7975,0.7881,0.7784, + 0.85182, 0.8525,0.8366,0.8198,0.8054,0.7903,0.7839,0.782, + 0.83542, 0.8362,0.8306,0.8196,0.8076,0.7918,0.7842,0.7806, + 0.82629, 0.8278,0.8252,0.8169,0.8074,0.7916,0.7838,0.7802, + 0.82299, 0.8249,0.823,0.8165,0.8072,0.7922,0.7839,0.7798, + 0.82357, 0.8257,0.8241,0.8178,0.8084,0.7927,0.7839,0.7794, + 0.82657, 0.828,0.8264,0.8199,0.8107,0.7939,0.7842,0.7796, + 0.8311, 0.8234,0.8295,0.8228,0.8136,0.796,0.7854,0.7798, + 0.8363, 0.8366,0.8342,0.8267,0.8168,0.7986,0.7864,0.7805, + 0.84762, 0.8474,0.8438,0.8358,0.825,0.8041,0.7904,0.7822, + 0.85846, 0.8583,0.853,0.8444,0.8336,0.8118,0.7957,0.7854, + 0.8684, 0.8674,0.8619,0.8531,0.8423,0.8186,0.8011,0.7898, + 0.87713, 0.8755,0.8709,0.8616,0.8504,0.8265,0.8072,0.7939, + 0.88479, 0.8831,0.8779,0.8695,0.8578,0.8338,0.8133,0.799, + 0.89972, 0.8986,0.8936,0.8846,0.8742,0.8504,0.8294,0.8125, + 0.91028, 0.9089,0.9043,0.8967,0.8869,0.8649,0.8438,0.8253, + 0.91793, 0.9166,0.9125,0.9058,0.897,0.8768,0.8557,0.8372, + 0.92371, 0.9226,0.9189,0.9128,0.905,0.8861,0.8664,0.8484, + 0.93135, 0.9304,0.9274,0.9226,0.9164,0.9006,0.8833,0.8662, + 0.93607, 0.9353,0.9329,0.9291,0.924,0.9109,0.8958,0.8802, + 0.93927, 0.9387,0.9366,0.9334,0.9292,0.9162,0.905,0.8911, + 0.94149, 0.9409,0.9393,0.9366,0.9331,0.9236,0.9122,0.8997, + 0.94306, 0.9426,0.9412,0.9388,0.9357,0.9276,0.9175,0.9065, + 0.94419, 0.9437,0.9425,0.9406,0.938,0.9308,0.9219,0.9119, + 0.94571, 0.9455,0.9445,0.943,0.9409,0.9353,0.9283,0.9201, + 0.94662, 0.9464,0.9456,0.9444,0.9428,0.9382,0.9325,0.9258, + 0.94723, 0.9471,0.9464,0.9455,0.9442,0.9405,0.9355,0.9298, + 0.94764, 0.9474,0.9469,0.9462,0.945,0.9418,0.9378,0.9328, + 0.9479, 0.9478,0.9474,0.9465,0.9457,0.943,0.9394,0.9352, + 0.94827, 0.9481,0.948,0.9472,0.9467,0.9447,0.9422,0.9391, + 0.94842, 0.9484,0.9481,0.9478,0.9472,0.9458,0.9437,0.9415, + 0.94852, 0.9484,0.9483,0.948,0.9475,0.9465,0.9449,0.943, + 0.94861, 0.9487,0.9484,0.9481,0.9479,0.9468,0.9455,0.943, + 0.94872, 0.9486,0.9486,0.9483,0.9482,0.9475,0.9464,0.9452, + 0.94881, 0.9488,0.9489,0.949,0.9487,0.9482,0.9476,0.9468, + 0.94863, 0.9487,0.9489,0.9491,0.9493,0.9491,0.9483,0.9476, + 0.94444, 0.94444,0.94444,0.94444,0.94444,0.94444,0.94444,0.94444}; + //==================================================================================================================== + MMCollisionInt::MMCollisionInt() + { + } + //==================================================================================================================== + MMCollisionInt::~MMCollisionInt() + { + } + //==================================================================================================================== - void MMCollisionInt::init(XML_Writer* xml, - doublereal tsmin, doublereal tsmax, int log_level) { -#ifdef DEBUG_MODE - ostream& logfile = xml->output(); - m_xml = xml; + void MMCollisionInt::init(XML_Writer* xml, + doublereal tsmin, doublereal tsmax, int log_level) { +#ifdef DEBUG_MODE + if (!xml) { + throw CanteraError("MMCollisionInt::init", "pointer to xml file is zero"); + } + ostream& logfile = xml->output(); + m_xml = xml; #else - m_xml = 0; + m_xml = 0; + log_level = 0; #endif - m_loglevel = log_level; + m_loglevel = log_level; #ifdef DEBUG_MODE - if (m_loglevel > 0) { - m_xml->XML_comment(logfile, "Collision Integral Polynomial Fits"); - } - char p[200]; + if (m_loglevel > 0) { + m_xml->XML_comment(logfile, "Collision Integral Polynomial Fits"); + } + char p[200]; #endif - m_nmin = -1; - m_nmax = -1; + m_nmin = -1; + m_nmax = -1; - for (int n = 0; n < 37; n++) { - if (tsmin > tstar[n+1]) m_nmin = n; - if (tsmax > tstar[n+1]) m_nmax = n+1; - } - if (m_nmin < 0 || m_nmin >= 36 || m_nmax < 0 || m_nmax > 36) { - m_nmin = 0; - m_nmax = 36; - } -#ifdef DEBUG_MODE - if (m_loglevel > 0) { - m_xml->XML_item(logfile, "Tstar_min", tstar[m_nmin + 1]); - m_xml->XML_item(logfile, "Tstar_max", tstar[m_nmax + 1]); - } -#endif - m_logTemp.resize(37); - doublereal rmserr, e22 = 0.0, ea = 0.0, eb = 0.0, ec = 0.0; - -#ifdef DEBUG_MODE - if (m_loglevel > 0) { - m_xml->XML_open(logfile, "dstar_fits"); - m_xml->XML_comment(logfile, "Collision integral fits at each " - "tabulated T* vs. delta*.\n" - "These polynomial fits are used to interpolate between " - "columns (delta*)\n in the Monchick and Mason tables." - " They are only used for nonzero delta*."); - if (log_level < 4) { - m_xml->XML_comment(logfile, - "polynomial coefficients not printed (log_level < 4)"); - } - } -#endif - - string indent = " "; - for (int i = 0; i < 37; i++) - { - m_logTemp[i] = log(tstar[i+1]); - vector_fp c(DeltaDegree+1); - - rmserr = fitDelta(0, i, DeltaDegree, DATA_PTR(c)); -#ifdef DEBUG_MODE - if (log_level > 3) { - sprintf(p, " Tstar=\"%12.6g\"", tstar[i+1]); - m_xml->XML_open(logfile, "dstar_fit", p); - m_xml->XML_item(logfile, "Tstar", tstar[i+1]); - m_xml->XML_writeVector(logfile, indent, "omega22", - c.size(), DATA_PTR(c)); - } -#endif - m_o22poly.push_back(c); - if (rmserr > e22) e22 = rmserr; - - rmserr = fitDelta(1, i, DeltaDegree, DATA_PTR(c)); - m_apoly.push_back(c); -#ifdef DEBUG_MODE - if (log_level > 3) - m_xml->XML_writeVector(logfile, indent, "astar", - c.size(), DATA_PTR(c)); -#endif - if (rmserr > ea) ea = rmserr; - - rmserr = fitDelta(2, i, DeltaDegree, DATA_PTR(c)); - m_bpoly.push_back(c); -#ifdef DEBUG_MODE - if (log_level > 3) - m_xml->XML_writeVector(logfile, indent, "bstar", - c.size(), DATA_PTR(c)); -#endif - if (rmserr > eb) eb = rmserr; - - rmserr = fitDelta(3, i, DeltaDegree, DATA_PTR(c)); - m_cpoly.push_back(c); -#ifdef DEBUG_MODE - if (log_level > 3) { - m_xml->XML_writeVector(logfile, indent, "cstar", - c.size(), DATA_PTR(c)); - } -#endif - if (rmserr > ec) ec = rmserr; - -#ifdef DEBUG_MODE - if (log_level > 3) { - m_xml->XML_close(logfile, "dstar_fit"); - } - - if (log_level > 0) { - sprintf(p, - "max RMS errors in fits vs. delta*:\n" - " omega_22 = %12.6g \n" - " A* = %12.6g \n" - " B* = %12.6g \n" - " C* = %12.6g \n", e22, ea, eb, ec); - m_xml->XML_comment(logfile, p); - m_xml->XML_close(logfile, "dstar_fits"); - } -#endif - } + for (int n = 0; n < 37; n++) { + if (tsmin > tstar[n+1]) m_nmin = n; + if (tsmax > tstar[n+1]) m_nmax = n+1; } - - MMCollisionInt::~MMCollisionInt() {} - - - - doublereal MMCollisionInt::fitDelta(int table, int ntstar, - int degree, doublereal* c) { - vector_fp w(8); - doublereal* begin = 0; - int ndeg=0; - switch (table) { - case 0: - begin = omega22_table + 8*ntstar; break; - case 1: - begin = astar_table + 8*(ntstar + 1); break; - case 2: - begin = bstar_table + 8*(ntstar + 1); break; - case 3: - begin = cstar_table + 8*(ntstar + 1); break; - default: - return 0.0; - } - w[0] = -1.0; - return polyfit(8, delta, begin, DATA_PTR(w), degree, ndeg, 0.0, c); + if (m_nmin < 0 || m_nmin >= 36 || m_nmax < 0 || m_nmax > 36) { + m_nmin = 0; + m_nmax = 36; } - - doublereal MMCollisionInt::omega22(double ts, double deltastar) { - int i; - for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; - int i1, i2; - i1 = i - 1; - if (i1 < 0) i1 = 0; - i2 = i1+3; - if (i2 > 36) { - i2 = 36; - i1 = i2 - 3; - } - vector_fp values(3); - for (i = i1; i < i2; i++) { - if (deltastar == 0.0) values[i-i1] = omega22_table[8*i]; - else values[i-i1] = poly5(deltastar, DATA_PTR(m_o22poly[i])); - } - return quadInterp(log(ts), DATA_PTR(m_logTemp) - + i1, DATA_PTR(values)); - } - - doublereal MMCollisionInt::astar(double ts, double deltastar) { - int i; - for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; - int i1, i2; - i1 = i - 1; - if (i1 < 0) i1 = 0; - i2 = i1+3; - if (i2 > 36) { - i2 = 36; - i1 = i2 - 3; - } - vector_fp values(3); - for (i = i1; i < i2; i++) { - if (deltastar == 0.0) values[i-i1] = astar_table[8*(i + 1)]; - else values[i-i1] = poly5(deltastar, DATA_PTR(m_apoly[i])); - } - return quadInterp(log(ts), DATA_PTR(m_logTemp) - + i1, DATA_PTR(values)); - } - - - doublereal MMCollisionInt::bstar(double ts, double deltastar) { - int i; - for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; - int i1, i2; - i1 = i - 1; - if (i1 < 0) i1 = 0; - i2 = i1+3; - if (i2 > 36) { - i2 = 36; - i1 = i2 - 3; - } - vector_fp values(3); - for (i = i1; i < i2; i++) { - if (deltastar == 0.0) values[i-i1] = bstar_table[8*(i + 1)]; - else values[i-i1] = poly5(deltastar, DATA_PTR(m_bpoly[i])); - } - return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, - DATA_PTR(values)); - } - - - doublereal MMCollisionInt::cstar(double ts, double deltastar) { - int i; - for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; - int i1, i2; - i1 = i - 1; - if (i1 < 0) i1 = 0; - i2 = i1+3; - if (i2 > 36) { - i2 = 36; - i1 = i2 - 3; - } - vector_fp values(3); - for (i = i1; i < i2; i++) { - if (deltastar == 0.0) values[i-i1] = cstar_table[8*(i + 1)]; - else values[i-i1] = poly5(deltastar, DATA_PTR(m_cpoly[i])); - } - return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, - DATA_PTR(values)); } - - - void MMCollisionInt::fit_omega22(ostream& logfile, int degree, - doublereal deltastar, doublereal* o22) - { - - int i, n = m_nmax - m_nmin + 1; - int ndeg=0; - string indent = " "; - vector_fp values(n); - doublereal rmserr; - vector_fp w(n); - doublereal* logT = DATA_PTR(m_logTemp) + m_nmin; - for (i = 0; i < n; i++) { - if (deltastar == 0.0) values[i] = omega22_table[8*(i + m_nmin)]; - else values[i] = poly5(deltastar, DATA_PTR(m_o22poly[i+m_nmin])); - } - w[0]= -1.0; - rmserr = polyfit(n, logT, DATA_PTR(values), - DATA_PTR(w), degree, ndeg, 0.0, o22); #ifdef DEBUG_MODE - if (m_loglevel > 0 && rmserr > 0.01) { - char p[100]; - sprintf(p, "Warning: RMS error = %12.6g in omega_22 fit" - "with delta* = %12.6g\n", rmserr, deltastar); - m_xml->XML_comment(logfile, p); - } -#endif + if (m_loglevel > 0) { + m_xml->XML_item(logfile, "Tstar_min", tstar[m_nmin + 1]); + m_xml->XML_item(logfile, "Tstar_max", tstar[m_nmax + 1]); } +#endif + m_logTemp.resize(37); + doublereal rmserr, e22 = 0.0, ea = 0.0, eb = 0.0, ec = 0.0; - void MMCollisionInt::fit(ostream& logfile, int degree, - doublereal deltastar, doublereal* a, doublereal* b, doublereal* c) - { - int i, n = m_nmax - m_nmin + 1; - int ndeg=0; - //char s[100]; - string indent = " "; - vector_fp values(n); - doublereal rmserr; - vector_fp w(n); - doublereal* logT = DATA_PTR(m_logTemp) + m_nmin; - for (i = 0; i < n; i++) { - if (deltastar == 0.0) values[i] = astar_table[8*(i + m_nmin + 1)]; - else values[i] = poly5(deltastar, DATA_PTR(m_apoly[i+m_nmin])); - } - w[0]= -1.0; - rmserr = polyfit(n, logT, DATA_PTR(values), - DATA_PTR(w), degree, ndeg, 0.0, a); +#ifdef DEBUG_MODE + if (m_loglevel > 0) { + m_xml->XML_open(logfile, "dstar_fits"); + m_xml->XML_comment(logfile, "Collision integral fits at each " + "tabulated T* vs. delta*.\n" + "These polynomial fits are used to interpolate between " + "columns (delta*)\n in the Monchick and Mason tables." + " They are only used for nonzero delta*."); + if (log_level < 4) { + m_xml->XML_comment(logfile, + "polynomial coefficients not printed (log_level < 4)"); + } + } +#endif + + string indent = " "; + for (int i = 0; i < 37; i++) + { + m_logTemp[i] = log(tstar[i+1]); + vector_fp c(DeltaDegree+1); + + rmserr = fitDelta(0, i, DeltaDegree, DATA_PTR(c)); +#ifdef DEBUG_MODE + if (log_level > 3) { + sprintf(p, " Tstar=\"%12.6g\"", tstar[i+1]); + m_xml->XML_open(logfile, "dstar_fit", p); + m_xml->XML_item(logfile, "Tstar", tstar[i+1]); + m_xml->XML_writeVector(logfile, indent, "omega22", + c.size(), DATA_PTR(c)); + } +#endif + m_o22poly.push_back(c); + if (rmserr > e22) e22 = rmserr; + + rmserr = fitDelta(1, i, DeltaDegree, DATA_PTR(c)); + m_apoly.push_back(c); +#ifdef DEBUG_MODE + if (log_level > 3) + m_xml->XML_writeVector(logfile, indent, "astar", + c.size(), DATA_PTR(c)); +#endif + if (rmserr > ea) ea = rmserr; + + rmserr = fitDelta(2, i, DeltaDegree, DATA_PTR(c)); + m_bpoly.push_back(c); +#ifdef DEBUG_MODE + if (log_level > 3) + m_xml->XML_writeVector(logfile, indent, "bstar", + c.size(), DATA_PTR(c)); +#endif + if (rmserr > eb) eb = rmserr; + + rmserr = fitDelta(3, i, DeltaDegree, DATA_PTR(c)); + m_cpoly.push_back(c); +#ifdef DEBUG_MODE + if (log_level > 3) { + m_xml->XML_writeVector(logfile, indent, "cstar", + c.size(), DATA_PTR(c)); + } +#endif + if (rmserr > ec) ec = rmserr; + +#ifdef DEBUG_MODE + if (log_level > 3) { + m_xml->XML_close(logfile, "dstar_fit"); + } + + if (log_level > 0) { + sprintf(p, + "max RMS errors in fits vs. delta*:\n" + " omega_22 = %12.6g \n" + " A* = %12.6g \n" + " B* = %12.6g \n" + " C* = %12.6g \n", e22, ea, eb, ec); + m_xml->XML_comment(logfile, p); + m_xml->XML_close(logfile, "dstar_fits"); + } +#endif + } + } + + + + doublereal MMCollisionInt::fitDelta(int table, int ntstar, + int degree, doublereal* c) { + vector_fp w(8); + doublereal* begin = 0; + int ndeg=0; + switch (table) { + case 0: + begin = omega22_table + 8*ntstar; break; + case 1: + begin = astar_table + 8*(ntstar + 1); break; + case 2: + begin = bstar_table + 8*(ntstar + 1); break; + case 3: + begin = cstar_table + 8*(ntstar + 1); break; + default: + return 0.0; + } + w[0] = -1.0; + return polyfit(8, delta, begin, DATA_PTR(w), degree, ndeg, 0.0, c); + } + + doublereal MMCollisionInt::omega22(double ts, double deltastar) { + int i; + for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; + int i1, i2; + i1 = i - 1; + if (i1 < 0) i1 = 0; + i2 = i1+3; + if (i2 > 36) { + i2 = 36; + i1 = i2 - 3; + } + vector_fp values(3); + for (i = i1; i < i2; i++) { + if (deltastar == 0.0) values[i-i1] = omega22_table[8*i]; + else values[i-i1] = poly5(deltastar, DATA_PTR(m_o22poly[i])); + } + return quadInterp(log(ts), DATA_PTR(m_logTemp) + + i1, DATA_PTR(values)); + } + + doublereal MMCollisionInt::astar(double ts, double deltastar) { + int i; + for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; + int i1, i2; + i1 = i - 1; + if (i1 < 0) i1 = 0; + i2 = i1+3; + if (i2 > 36) { + i2 = 36; + i1 = i2 - 3; + } + vector_fp values(3); + for (i = i1; i < i2; i++) { + if (deltastar == 0.0) values[i-i1] = astar_table[8*(i + 1)]; + else values[i-i1] = poly5(deltastar, DATA_PTR(m_apoly[i])); + } + return quadInterp(log(ts), DATA_PTR(m_logTemp) + + i1, DATA_PTR(values)); + } + + + doublereal MMCollisionInt::bstar(double ts, double deltastar) { + int i; + for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; + int i1, i2; + i1 = i - 1; + if (i1 < 0) i1 = 0; + i2 = i1+3; + if (i2 > 36) { + i2 = 36; + i1 = i2 - 3; + } + vector_fp values(3); + for (i = i1; i < i2; i++) { + if (deltastar == 0.0) values[i-i1] = bstar_table[8*(i + 1)]; + else values[i-i1] = poly5(deltastar, DATA_PTR(m_bpoly[i])); + } + return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, + DATA_PTR(values)); + } + + + doublereal MMCollisionInt::cstar(double ts, double deltastar) { + int i; + for (i = 0; i < 37; i++) if (ts < tstar22[i]) break; + int i1, i2; + i1 = i - 1; + if (i1 < 0) i1 = 0; + i2 = i1+3; + if (i2 > 36) { + i2 = 36; + i1 = i2 - 3; + } + vector_fp values(3); + for (i = i1; i < i2; i++) { + if (deltastar == 0.0) values[i-i1] = cstar_table[8*(i + 1)]; + else values[i-i1] = poly5(deltastar, DATA_PTR(m_cpoly[i])); + } + return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, + DATA_PTR(values)); } + + + void MMCollisionInt::fit_omega22(ostream& logfile, int degree, + doublereal deltastar, doublereal* o22) + { + + int i, n = m_nmax - m_nmin + 1; + int ndeg=0; + string indent = " "; + vector_fp values(n); + doublereal rmserr; + vector_fp w(n); + doublereal* logT = DATA_PTR(m_logTemp) + m_nmin; + for (i = 0; i < n; i++) { + if (deltastar == 0.0) values[i] = omega22_table[8*(i + m_nmin)]; + else values[i] = poly5(deltastar, DATA_PTR(m_o22poly[i+m_nmin])); + } + w[0]= -1.0; + rmserr = polyfit(n, logT, DATA_PTR(values), + DATA_PTR(w), degree, ndeg, 0.0, o22); +#ifdef DEBUG_MODE + if (m_loglevel > 0 && rmserr > 0.01) { + char p[100]; + sprintf(p, "Warning: RMS error = %12.6g in omega_22 fit" + "with delta* = %12.6g\n", rmserr, deltastar); + m_xml->XML_comment(logfile, p); + } +#endif + } + + void MMCollisionInt::fit(ostream& logfile, int degree, + doublereal deltastar, doublereal* a, doublereal* b, doublereal* c) + { + int i, n = m_nmax - m_nmin + 1; + int ndeg=0; + //char s[100]; + string indent = " "; + vector_fp values(n); + doublereal rmserr; + vector_fp w(n); + doublereal* logT = DATA_PTR(m_logTemp) + m_nmin; + for (i = 0; i < n; i++) { + if (deltastar == 0.0) values[i] = astar_table[8*(i + m_nmin + 1)]; + else values[i] = poly5(deltastar, DATA_PTR(m_apoly[i+m_nmin])); + } + w[0]= -1.0; + rmserr = polyfit(n, logT, DATA_PTR(values), + DATA_PTR(w), degree, ndeg, 0.0, a); - for (i = 0; i < n; i++) { - if (deltastar == 0.0) values[i] = bstar_table[8*(i + m_nmin + 1)]; - else values[i] = poly5(deltastar, DATA_PTR(m_bpoly[i+m_nmin])); - } - w[0]= -1.0; - rmserr = polyfit(n, logT, DATA_PTR(values), - DATA_PTR(w), degree, ndeg, 0.0, b); - - for (i = 0; i < n; i++) { - if (deltastar == 0.0) values[i] = cstar_table[8*(i + m_nmin + 1)]; - else values[i] = poly5(deltastar, DATA_PTR(m_cpoly[i+m_nmin])); - } - w[0]= -1.0; - rmserr = polyfit(n, logT, DATA_PTR(values), - DATA_PTR(w), degree, ndeg, 0.0, c); -#ifdef DEBUG_MODE - if (m_loglevel > 2) { - char p[100]; - sprintf(p, " dstar=\"%12.6g\"", deltastar); - m_xml->XML_open(logfile, "tstar_fit", p); - - m_xml->XML_writeVector(logfile, indent, "astar", degree+1, a); - if (rmserr > 0.01) { - sprintf(p, "Warning: RMS error = %12.6g for A* fit", rmserr); - m_xml->XML_comment(logfile, p); - } - - m_xml->XML_writeVector(logfile, indent, "bstar", degree+1, b); - if (rmserr > 0.01) { - sprintf(p, "Warning: RMS error = %12.6g for B* fit", rmserr); - m_xml->XML_comment(logfile, p); - } - - m_xml->XML_writeVector(logfile, indent, "cstar", degree+1, c); - - if (rmserr > 0.01) { - sprintf(p, "Warning: RMS error = %12.6g for C* fit", rmserr); - m_xml->XML_comment(logfile, p); - } - m_xml->XML_close(logfile, "tstar_fit"); - } -#endif + for (i = 0; i < n; i++) { + if (deltastar == 0.0) values[i] = bstar_table[8*(i + m_nmin + 1)]; + else values[i] = poly5(deltastar, DATA_PTR(m_bpoly[i+m_nmin])); } + w[0]= -1.0; + rmserr = polyfit(n, logT, DATA_PTR(values), + DATA_PTR(w), degree, ndeg, 0.0, b); + + for (i = 0; i < n; i++) { + if (deltastar == 0.0) values[i] = cstar_table[8*(i + m_nmin + 1)]; + else values[i] = poly5(deltastar, DATA_PTR(m_cpoly[i+m_nmin])); + } + w[0]= -1.0; + rmserr = polyfit(n, logT, DATA_PTR(values), + DATA_PTR(w), degree, ndeg, 0.0, c); +#ifdef DEBUG_MODE + if (m_loglevel > 2) { + char p[100]; + sprintf(p, " dstar=\"%12.6g\"", deltastar); + m_xml->XML_open(logfile, "tstar_fit", p); + + m_xml->XML_writeVector(logfile, indent, "astar", degree+1, a); + if (rmserr > 0.01) { + sprintf(p, "Warning: RMS error = %12.6g for A* fit", rmserr); + m_xml->XML_comment(logfile, p); + } + + m_xml->XML_writeVector(logfile, indent, "bstar", degree+1, b); + if (rmserr > 0.01) { + sprintf(p, "Warning: RMS error = %12.6g for B* fit", rmserr); + m_xml->XML_comment(logfile, p); + } + + m_xml->XML_writeVector(logfile, indent, "cstar", degree+1, c); + + if (rmserr > 0.01) { + sprintf(p, "Warning: RMS error = %12.6g for C* fit", rmserr); + m_xml->XML_comment(logfile, p); + } + m_xml->XML_close(logfile, "tstar_fit"); + } +#endif + } } // namespace diff --git a/Cantera/src/transport/MMCollisionInt.h b/Cantera/src/transport/MMCollisionInt.h old mode 100755 new mode 100644 index 797a30ea5..4bc0c3e17 --- a/Cantera/src/transport/MMCollisionInt.h +++ b/Cantera/src/transport/MMCollisionInt.h @@ -3,7 +3,6 @@ * Monk and Monchick collision integrals */ /* - * $Author$ * $Revision$ * $Date$ */ @@ -41,8 +40,10 @@ namespace Cantera { }; - /** - * Collision integrals. This class provides functions that + + //! Calculation of Collision integrals + /*! + * This class provides functions that * interpolate the tabulated collision integrals in Monchick and * Mason, "Transport Properties of Polar Gases," J. Chem. Phys. (1961) * @@ -52,11 +53,27 @@ namespace Cantera { public: - MMCollisionInt(){} + //! Default Constructor + MMCollisionInt(); + + //! Destructor virtual ~MMCollisionInt(); + + + //! Initialize the object for calculation + /*! + * + * @param xml Pointer to the log file that will receive the debug output + * messages + * @param tsmin Minimum value of Tstar to carry out the fitting + * @param tsmax Maximum value of Tstar to carry out the fitting + * @param loglevel Set the loglevel for the object. The default + * loglevel is zero, indicating no output. + */ void init(XML_Writer* xml, doublereal tsmin, doublereal tsmax, int loglevel = 0); + doublereal omega22(double ts, double deltastar); doublereal astar(double ts, double deltastar); doublereal bstar(double ts, double deltastar); diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h old mode 100755 new mode 100644 From ccd01f5125cf3798338598d6e8b92566f76b9071 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 13 Dec 2009 17:30:36 +0000 Subject: [PATCH 069/446] Doxygen update -> no source code changed. --- Cantera/src/transport/SimpleTransport.h | 7 +++++-- Cantera/src/transport/TransportBase.h | 25 +++++++++++++++++++++---- 2 files changed, 26 insertions(+), 6 deletions(-) diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 0eeb13fcd..2e892b142 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -1,7 +1,10 @@ /** * * @file SimpleTransport.h - * Header file defining class SimpleTransport + * Header file for the class SimpleTransport which provides simple + * transport properties for liquids and solids + * (see \ref tranprops and \link Cantera::SimpleTransport SimpleTransport \endlink) . + */ /* * $Revision$ @@ -123,7 +126,7 @@ namespace Cantera { * In the second part, a mixing rule is applied, based on the * Wilkes correlation, to yield the mixture viscosity. * - * + * @ingroup tranprops * */ class SimpleTransport : public Transport { diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 414c82d12..9b203ab71 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -1,7 +1,8 @@ /** * @file TransportBase.h * Headers for the Transport object, which is the virtual base class - * for all transport property evaluators and also includes the tranprops group definition + * for all transport property evaluators and also includes the + * tranprops group definition * (see \ref tranprops and \link Cantera::Transport Transport \endlink) . * * Provides class Transport. @@ -74,6 +75,10 @@ namespace Cantera { * Transport is meant to be used as a base class only. It is * possible to instantiate it, but its methods throw exceptions if * called. + * + * All member functions are virtual, unless otherwise stated. + * + * @ingroup tranprops */ class Transport { @@ -456,9 +461,21 @@ namespace Cantera { { err("getMixDiffCoeffs"); } - /** - * Set transport model parameters. This method may be - * overloaded in subclasses to set model-specific parameters. + + //! Set transport model parameters. + /*! + * This method may be + * overloaded in subclasses to set model-specific parameters. + * The primary use of this class is to set parameters while in the + * middle of a calculation. + * + * @param type Specifies the type of parameters to set + * 0 : Diffusion coefficient + * 1 : Thermal Conductivity + * The rest are currently unused. + * @param k Species index to set the parameters on + * @param p Vector of parameters. The length of the vector + * varies with the parameterization */ virtual void setParameters(const int type, const int k, const doublereal* const p); From 0d6e6bd10bd215c93c99c7b591ed32bf04de7ea9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 13 Dec 2009 18:03:53 +0000 Subject: [PATCH 070/446] Doxygen update - No code changes were made. --- Cantera/src/transport/LiquidTransport.h | 16 ++- Cantera/src/transport/TransportBase.h | 160 +++++++++++++++++------- 2 files changed, 120 insertions(+), 56 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 177293afe..468555b52 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -1,5 +1,4 @@ /** - * * @file LiquidTransport.h * Header file defining class LiquidTransport */ @@ -121,7 +120,7 @@ namespace Cantera { * Wilkes correlation, to yield the mixture viscosity. * * - * + * @ingroup tranprops */ class LiquidTransport : public Transport { public: @@ -141,7 +140,7 @@ namespace Cantera { */ LiquidTransport(thermo_t* thermo = 0, int ndim = 1); - //!Copy Constructor for the %LiquidThermo object. + //! Copy Constructor for the %LiquidThermo object. /*! * @param right %LiquidTransport to be copied */ @@ -190,7 +189,6 @@ namespace Cantera { return cLiquidTransport; } - //! overloaded base class methods //! Returns the viscosity of the solution /*! @@ -355,11 +353,11 @@ namespace Cantera { * length = ldx * ndim */ virtual void getSpeciesVdiff(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - doublereal* Vdiff) ; + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + doublereal* Vdiff); //! Get the species diffusive mass fluxes wrt to //! the mass averaged velocity, diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 9b203ab71..0d3ff8749 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -147,26 +147,45 @@ namespace Cantera { */ bool ready(); - /** - * Returns an integer index number. This is for internal use - * of Cantera, and may be removed in the future. + + //! Returns an integer index number. + /*! + * This is for internal use + * of Cantera, and may be removed in the future. + * + * @return Returns the index number + * + * @deprecated */ int index() const ; - /** - * Set an integer index number. This is for internal use of - * Cantera, and may be removed in the future. + + //! Set an integer index number. + /*! + * This is for internal use of + * Cantera, and may be removed in the future. + * + * @param i index value + * + * @deprecated */ void setIndex(int i); //! Set the number of dimensions to be expected in flux expressions /*! - * Internal memory will be set with this value + * Internal memory will be set with this value. + * + * @param ndim Number of dimensions in flux expressions */ void setNDim(const int ndim); - //! return the number of dimensions - int nDim() const { return m_nDim; } + //! Return the number of dimensions in flux expressions + /*! + * @return Returns the number of dimensions + */ + int nDim() const { + return m_nDim; + } /** * @name Transport Properties @@ -343,11 +362,11 @@ namespace Cantera { * length = ldx * ndim */ virtual void getSpeciesVdiff(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - doublereal* Vdiff) { + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + doublereal* Vdiff) { err("getSpeciesVdiff"); } @@ -375,12 +394,12 @@ namespace Cantera { * length = ldx * ndim */ virtual void getSpeciesVdiffES(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_Phi, - doublereal* Vdiff) { + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_Phi, + doublereal* Vdiff) { getSpeciesVdiff( ndim, grad_T, ldx, grad_X, ldf, Vdiff ); } @@ -480,10 +499,30 @@ namespace Cantera { virtual void setParameters(const int type, const int k, const doublereal* const p); - - void setVelocityBasis( int ivb ) { m_velocityBasis = ivb; } + //! Sets the velocity basis + /*! + * What the transport object does with this parameter is up to the + * individual operator. Currently, this is not functional for most + * transport operators including all of the gas-phase operators. + * + * @param ivb Species the velocity basis + */ + void setVelocityBasis(int ivb) + { + m_velocityBasis = ivb; + } - int getVelocityBasis( ) { return m_velocityBasis; } + //! Gets the velocity basis + /*! + * What the transport object does with this parameter is up to the + * individual operator. Currently, this is not functional for most + * transport operators including all of the gas-phase operators. + * + * @return Returns the velocity basis + */ + int getVelocityBasis( ) const { + return m_velocityBasis; + } friend class TransportFactory; @@ -502,29 +541,46 @@ namespace Cantera { //virtual bool init(TransportParams& tr) //{ err("init"); return false; } - /** - * Called by TransportFactory to set parameters. + + //! Called by TransportFactory to set parameters. + /*! + * This is called by classes that use the gas phase parameter + * list to initialize themselves. + * + * @param tr Reference to the parameter list that will be used + * to initialize the class */ - virtual bool initGas( GasTransportParams& tr ) - { err("initGas"); return false; } + virtual bool initGas(GasTransportParams& tr) + { + err("initGas"); + return false; + } - /** - * Called by TransportFactory to set parameters. - */ - virtual bool initLiquid( LiquidTransportParams& tr ) - { err("initLiquid"); return false; } - - - - - /** - * Set the phase object. + //! Called by TransportFactory to set parameters. + /*! + * This is called by classes that use the liquid phase parameter + * list to initialize themselves. + * + * @param tr Reference to the parameter list that will be used + * to initialize the class */ + virtual bool initLiquid(LiquidTransportParams& tr) + { + err("initLiquid"); + return false; + } + + //! Specifies the %ThermPhase object. + /*! + * @param thermo Reference to the ThermoPhase object that + * the transport object will use + */ void setThermo(thermo_t& thermo); - - /** - * Enable for use. Once finalize() has been called, the + + //! Enable the transport object for use. + /*! + * Once finalize() has been called, the * transport manager should be ready to compute any supported * transport property, and no further modifications to the * model parameters should be made. @@ -533,18 +589,27 @@ namespace Cantera { //@} + //! pointer to the object representing the phase + thermo_t* m_thermo; - thermo_t* m_thermo; ///< pointer to the object representing the phase - bool m_ready; ///< true if finalize has been called - size_t m_nmin; ///< number of species + //! true if finalize has been called + bool m_ready; + + //! Number of species + size_t m_nmin; + + //! Value of the internal index + /*! + * @deprecated + */ int m_index; //! Number of dimensions used in flux expresions int m_nDim; - //! velocity basis from which diffusion velocities are computed. - //! Defaults to mass averaged = -2 - int m_velocityBasis; + //! Celocity basis from which diffusion velocities are computed. + //! Defaults to the mass averaged basis = -2 + int m_velocityBasis; private: @@ -564,6 +629,7 @@ namespace Cantera { }; + //! general definition for the transport class typedef Transport transport_t; } From debcff82d97890f660e387b710b4c479741da23c Mon Sep 17 00:00:00 2001 From: John Hewson Date: Tue, 15 Dec 2009 21:43:34 +0000 Subject: [PATCH 071/446] Added a pointer to a Transport object to the Phase class. This allows a ThermoPhase object to know what Transport object it is associated with. --- Cantera/src/thermo/Phase.h | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index 60c5ec06a..7395d9933 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -26,6 +26,7 @@ using namespace ctml; namespace Cantera { + class Transport; //forward declaration /** * @defgroup phases Models of Phases of Matter @@ -221,6 +222,9 @@ namespace Cantera { */ void setName(std::string nm); + //! Attach a Transport object pointer to this Phase + void setTransport( Transport* tr ) { m_trans = tr; } + //! Returns the index of the phase /*! * The index is used in the Python and matlab interfaces to @@ -434,6 +438,9 @@ namespace Cantera { */ void getMoleFractionsByName(compositionMap& x) const; + //! Get a Transport object pointer attached to this Phase + Transport* getTransport( ) { return m_trans; } + //! Return the mole fraction of a single species /*! * @param k String name of the species @@ -515,6 +522,13 @@ namespace Cantera { */ int m_index; + /** + * A Transport object pointer attached to this Phase + */ + Transport *m_trans; + + + private: //! This stores the initial state of the system From 8e8c7ec38f0f5cbe8853d1e3533714521287a11d Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 16 Dec 2009 00:27:39 +0000 Subject: [PATCH 072/446] Added methods to compute current and conductivity. Fixed bug in Stefan_Maxwell_Solve Adding lots of comments to LiquidTransport --- Cantera/src/transport/LiquidTransport.cpp | 737 ++++++++++++++-------- Cantera/src/transport/LiquidTransport.h | 572 +++++++++++------ Cantera/src/transport/TransportBase.h | 24 +- 3 files changed, 876 insertions(+), 457 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index e2a23fe29..6f0a401db 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -38,7 +38,6 @@ namespace Cantera { m_tmax(100000.), m_iStateMF(-1), m_temp(-1.0), - m_logt(0.0), m_press(-1.0), m_lambda(-1.0), m_viscmix(-1.0), @@ -66,7 +65,6 @@ namespace Cantera { m_tmax(100000.), m_iStateMF(-1), m_temp(-1.0), - m_logt(0.0), m_press(-1.0), m_lambda(-1.0), m_viscmix(-1.0), @@ -129,7 +127,6 @@ namespace Cantera { m_B = right.m_B; m_A = right.m_A; m_temp = right.m_temp; - m_logt = right.m_logt; m_press = right.m_press; m_flux = right.m_flux; m_Vdiff = right.m_Vdiff; @@ -176,9 +173,16 @@ namespace Cantera { } - // Initialize the object + // Initialize the transport object /* - * This is where we dimension everything. + * Here we change all of the internal dimensions to be sufficient. + * We get the object ready to do property evaluations. + * A lot of the input required to do property evaluations is + * contained in the LiquidTransportParams class that is + * filled in TransportFactory. + * + * @param tr Transport parameters for all of the species + * in the phase. */ bool LiquidTransport::initLiquid(LiquidTransportParams& tr) { @@ -311,19 +315,12 @@ namespace Cantera { /****************** viscosity ******************************/ + // Returns the viscosity of the solution /* - * The viscosity is computed using the Wilke mixture rule. - * \f[ - * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. - * \f] - * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, - * and - * \f[ - * \Phi_{k,j} = \frac{\left[1 - * + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2} - * {\sqrt{8}\sqrt{1 + M_k/M_j}} - * \f] - * @see updateViscosity_T(); + * The viscosity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species viscosities. */ doublereal LiquidTransport::viscosity() { @@ -332,6 +329,12 @@ namespace Cantera { if (m_visc_mix_ok) return m_viscmix; + ////// LiquidTranInteraction method + m_viscmix = m_viscMixModel->getMixTransProp( m_viscTempDep_Ns ); + + return m_viscmix; + + /* // update m_viscSpecies[] if necessary if (!m_visc_temp_ok) { updateViscosity_T(); @@ -340,13 +343,18 @@ namespace Cantera { if (!m_visc_conc_ok) { updateViscosities_C(); } - - ////// LiquidTranInteraction method - m_viscmix = m_viscMixModel->getMixTransProp( m_viscTempDep_Ns ); - - return m_viscmix; + */ } + // Returns the pure species viscosities for all species + /* + * The pure species viscosities are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param visc array of length "number of species" + * to hold returned viscosities. + */ void LiquidTransport::getSpeciesViscosities(doublereal* visc) { update_T(); if (!m_visc_temp_ok) { @@ -358,8 +366,12 @@ namespace Cantera { //=============================================================== // Returns the hydrodynamic radius for all species /* - * The pure species viscosities are to be given in an Arrhenius - * form in accordance with activated-jump-process dominated transport. + * The species hydrodynamic radii are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param radius array of length "number of species" + * to hold returned radii. */ void LiquidTransport::getSpeciesHydrodynamicRadius(doublereal* const radius) { update_T(); @@ -372,9 +384,55 @@ namespace Cantera { //================================================================ + // Return the thermal conductivity of the solution + /* + * The thermal conductivity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species thermal condictivities. + */ + doublereal LiquidTransport::thermalConductivity() { + + update_T(); + update_C(); + + if (!m_cond_mix_ok) { + m_lambda = m_lambdaMixModel->getMixTransProp( m_lambdaTempDep_Ns ); + m_cond_mix_ok = true; + } + + return m_lambda; + } + + + /****************** thermal diffusion coefficients ************/ + + //! Return the thermal diffusion coefficients + /*! + * These are all zero for this simple implementaion + * + * @param dt thermal diffusion coefficients + */ + void LiquidTransport::getThermalDiffCoeffs(doublereal* const dt) { + for (int k = 0; k < m_nsp; k++) { + dt[k] = 0.0; + } + } + /******************* binary diffusion coefficients **************/ + // Returns the binary diffusion coefficients + /* + * The binary diffusion coefficients are specified in the input + * file through the LiquidTransportInteractions class. These + * are the binary interaction coefficients employed in the + * Stefan-Maxwell equation. + * + * @param ld number of species in system + * @param d vector of binary diffusion coefficients + * units = m2 s-1. length = ld*ld = (number of species)^2 + */ void LiquidTransport::getBinaryDiffCoeffs(int ld, doublereal* d) { int i,j; @@ -396,19 +454,32 @@ namespace Cantera { //================================================================================================ - // Get the electrical Mobilities (m^2/V/s). + // Get the Electrical mobilities (m^2/V/s). /* - * This function returns the mobilities. In some formulations - * this is equal to the normal mobility multiplied by faraday's constant. + * The electrical mobilities are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the electrical mobilities + * are calculated from the mixture-averaged + * diffusion coefficients through a call to getMixDiffCoeffs() + * using the Einstein relation * - * Frequently, but not always, the mobility is calculated from the - * diffusion coefficient using the Einstein relation - * - * \f[ + * \f[ * \mu^e_k = \frac{F D_k}{R T} * \f] * - * @param mobil_e Returns the mobilities of + * Note that this call to getMixDiffCoeffs() requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a {\em slow} method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. + * + * @param mobil_e Returns the electrical mobilities of * the species in array \c mobil_e. The array must be * dimensioned at least as large as the number of species. */ @@ -422,22 +493,33 @@ namespace Cantera { } //================================================================================================ - //! Get the fluid mobilities (s kmol/kg). - /*! - * This function returns the fluid mobilities. Usually, you have - * to multiply Faraday's constant into the resulting expression - * to general a species flux expression. - * - * Frequently, but not always, the mobility is calculated from the - * diffusion coefficient using the Einstein relation + // Get the fluid mobilities (s kmol/kg). + /* + * The fluid mobilities are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the fluid mobilities + * are calculated from the mixture-averaged + * diffusion coefficients through a call to getMixDiffCoeffs() + * using the Einstein relation * * \f[ * \mu^f_k = \frac{D_k}{R T} * \f] * + * Note that this call to getMixDiffCoeffs() requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a {\em slow} method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. * - * @param mobil_f Returns the mobilities of - * the species in array \c mobil. The array must be + * @param mobil_f Returns the fluid mobilities of + * the species in array \c mobil_f. The array must be * dimensioned at least as large as the number of species. */ void LiquidTransport::getFluidMobilities(doublereal* const mobil_f) { @@ -448,18 +530,32 @@ namespace Cantera { } } //============================================================== + //! Specify the value of the gradient of the temperature + /*! + * @param grad_T Gradient of the temperature (length num dimensions); + */ void LiquidTransport::set_Grad_T(const doublereal* const grad_T) { for (int a = 0; a < m_nDim; a++) { m_Grad_T[a] = grad_T[a]; } } //============================================================== + //! Specify the value of the gradient of the voltage + /*! + * + * @param grad_V Gradient of the voltage (length num dimensions); + */ void LiquidTransport::set_Grad_V(const doublereal* const grad_V) { for (int a = 0; a < m_nDim; a++) { m_Grad_V[a] = grad_V[a]; } } //============================================================== + //! Specify the value of the gradient of the MoleFractions + /*! + * + * @param grad_X Gradient of the mole fractions(length nsp * num dimensions); + */ void LiquidTransport::set_Grad_X(const doublereal* const grad_X) { int itop = m_nDim * m_nsp; for (int i = 0; i < itop; i++) { @@ -467,63 +563,131 @@ namespace Cantera { } } //============================================================== - /****************** thermal conductivity **********************/ + + // Compute the mixture electrical conductivity from + // the Stefan-Maxwell equation. /* - * The thermal conductivity is computed from the following mixture rule: - * \[ - * \lambda = \left( \sum_k Y_k \lambda_k \right) - * \] + * To compute the mixture electrical conductance, the Stefan + * Maxwell equation is solved for zero species gradients and + * for unit potential gradient, \f$ \nabla V \f$. + * The species fluxes are converted to current by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species i. + * The conductance, \f$ \kappa \f$ is obtained from + * \f[ + * \kappa = \vec{i} / \nabla V. + * \f] */ - doublereal LiquidTransport::thermalConductivity() { - - update_T(); - update_C(); - - if (!m_cond_temp_ok) { - updateCond_T(); - } - if (!m_cond_mix_ok) { - - // mass-fraction weighted thermal conductivity - { - doublereal sum1 = 0.0, sum2 = 0.0; - for (int k = 0; k < m_nsp; k++) { - sum1 += m_molefracs[k] * m_mw[k] * m_lambdaSpecies[k]; - sum2 += m_molefracs[k] * m_mw[k] ; - } - m_lambda = sum1 / sum2 ; - } - - m_cond_mix_ok = true; + doublereal LiquidTransport::getElectricConduct( ) { + doublereal gradT = 0.0; + doublereal gradX[m_nDim * m_nsp]; + doublereal gradV[m_nDim]; + for (int i = 0; i < m_nDim; i++) { + for (int k = 0; k < m_nsp; k++) + gradX[ i*m_nDim + k] = 0.0; + gradV[i] = 1.0; } - return m_lambda; - } + set_Grad_T(&gradT); + set_Grad_X(gradX); + set_Grad_V(gradV); + doublereal *fluxes = new doublereal( m_nsp * m_nDim ); + doublereal current; - /****************** thermal diffusion coefficients ************/ + getSpeciesFluxesExt(m_nDim, fluxes); - /** - * Thermal diffusion is not considered in this mixture-averaged - * model. To include thermal diffusion, use transport manager - * MultiTransport instead. This methods fills out array dt with - * zeros. - */ - void LiquidTransport::getThermalDiffCoeffs(doublereal* const dt) { - for (int k = 0; k < m_nsp; k++) { - dt[k] = 0.0; + //sum over species charges, fluxes, Faraday to get current + // Since we want the scalar conductivity, we need only consider one-dim + for (int i = 0; i < 1; i++) { + current = 0.0; + for (int k = 0; k < m_nsp; k++) + current += m_chargeSpecies[k] * Faraday * fluxes[k] / m_mw[k]; + //divide by unit potential gradient + current /= - gradV[i]; } + delete fluxes; + return current; + } + //! Compute the electric current density in A/m^2 /** + * The electric current is computed first by computing the + * species diffusive fluxes using the Stefan Maxwell solution + * and then the current, \f$ \vec{i} \f$ by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species i. + * * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * @param grad_T The temperature gradient (ignored in this model). + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. + */ + void LiquidTransport::getElectricCurrent(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current) { + + set_Grad_T(grad_T); + set_Grad_X(grad_X); + set_Grad_V(grad_V); + + doublereal *fluxes = new doublereal( m_nsp * m_nDim ); + + getSpeciesFluxesExt(ldf, fluxes); + + //sum over species charges, fluxes, Faraday to get current + for (int i = 0; i < m_nDim; i++) { + current[i] = 0.0; + for (int k = 0; k < m_nsp; k++) + current[i] += m_chargeSpecies[k] * Faraday * fluxes[k] / m_mw[k]; + //divide by unit potential gradient + } + delete fluxes; + + } + + // Get the species diffusive velocities wrt to + // the averaged velocity, + // given the gradients in mole fraction and temperature + /* + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * + * Units for the returned fluxes are kg m-2 s-1. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void LiquidTransport::getSpeciesVdiff(int ndim, const doublereal* grad_T, @@ -557,15 +721,54 @@ namespace Cantera { getSpeciesVdiffExt(ldf, Vdiff); } - /** + // Return the species diffusive mass fluxes wrt to + // the averaged velocity in [kmol/m^2/s]. + /* + * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * Note that for this method, there is no argument for the + * gradient of the electric potential (voltage). Electric + * potential gradients can be set with set_Grad_V() or + * method getSpeciesFluxesES() can be called.x + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * length = ndim + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void LiquidTransport::getSpeciesFluxes(int ndim, const doublereal* grad_T, @@ -576,15 +779,49 @@ namespace Cantera { getSpeciesFluxesExt(ldf, fluxes); } - /** + // Return the species diffusive mass fluxes wrt to + // the averaged velocity in [kmol/m^2/s]. + /* + * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * length = ndim + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void LiquidTransport::getSpeciesFluxesES(int ndim, const doublereal* grad_T, @@ -599,15 +836,18 @@ namespace Cantera { getSpeciesFluxesExt(ldf, fluxes); } - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + // Return the species diffusive velocities relative to + // the averaged velocity. + /* + * This method acts similarly to getSpeciesVdiffES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesVdiffES() for details. + * + * @param ldf Leading dimension of the Vdiff array. + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void LiquidTransport::getSpeciesVdiffExt(int ldf, doublereal* Vdiff) { int n, k; @@ -626,15 +866,20 @@ namespace Cantera { } } - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from + // Return the species diffusive fluxes relative to + // the averaged velocity. + /* + * This method acts similarly to getSpeciesFluxesES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesFluxesES() for details. + * + * units = kg/m2/s * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * @param ldf Leading dimension of the Vdiff array. + * @param fluxes Output of the diffusive fluxes. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void LiquidTransport::getSpeciesFluxesExt(int ldf, doublereal* fluxes) { int n, k; @@ -651,68 +896,58 @@ namespace Cantera { fluxes[n*ldf + k] = m_flux(k,n); } } - /* - getMixDiffCoeffs(DATA_PTR(m_spwork)); - const array_fp& mw = m_thermo->molecularWeights(); - const doublereal* y = m_thermo->massFractions(); - doublereal rhon = m_thermo->molarDensity(); - // Unroll wrt ndim - vector_fp sum(m_nDim,0.0); - for (n = 0; n < m_nDim; n++) { - for (k = 0; k < m_nsp; k++) { - fluxes[n*ldf + k] = -rhon * mw[k] * m_spwork[k] * m_Grad_X[n*m_nsp + k]; - sum[n] += fluxes[n*ldf + k]; - } - } - for (n = 0; n < m_nDim; n++) - for (k = 0; k < m_nsp; k++) - fluxes[n*ldf + k] -= sum[n]; - */ - } - /** - * Mixture-averaged diffusion coefficients [m^2/s]. - * - * For the single species case or the pure fluid case - * the routine returns the self-diffusion coefficient. - * This is need to avoid a Nan result in the formula - * below. + // Get the Mixture diffusion coefficients [m^2/s] + /* + * The mixture diffusion coefficients are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the mixture diffusion coefficients + * are defined according to Ficks law: + * \f[ + * X_i \vec{V_i} = -D_i \nabla X_i. + * \f] + * Solving Ficks Law for \f$ D_i \f$ gives a mixture diffusion + * coefficient + * \f[ + * D_i = - X_i \vec{V_i} / ( \nabla X_i ). + * \f] + * If \f$ \nabla X_i = 0 \f$ this is undefined and the + * nonsensical value -1 is returned. + * + * Note that this evaluation of \f$ \vec{V_i} \f$ requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a {\em slow} method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. + * + * @param d vector of mixture diffusion coefficients + * units = m2 s-1. length = number of species */ void LiquidTransport::getMixDiffCoeffs(doublereal* const d) { update_T(); update_C(); - // update the binary diffusion coefficients if necessary - if (!m_diff_temp_ok) { - updateDiff_T(); - } - - int k, j; - doublereal mmw = m_thermo->meanMolecularWeight(); - doublereal sumxw_tran = 0.0; - doublereal sum2; - - if (m_nsp == 1) { - d[0] = m_bdiff(0,0); - } else { + update_Grad_lnAC(); + + stefan_maxwell_solve(); + + for (n = 0; n < m_nDim; n++) { for (k = 0; k < m_nsp; k++) { - sumxw_tran += m_molefracs_tran[k] * m_mw[k]; - } - for (k = 0; k < m_nsp; k++) { - sum2 = 0.0; - for (j = 0; j < m_nsp; j++) { - if (j != k) { - sum2 += m_molefracs_tran[j] / m_bdiff(j,k); - } + if ( m_Grad_X[n*m_nsp + k] != 0.0 ) { + d[n*ldf + k] = - m_Vdiff(k,n) * m_molefracs[k] + / m_Grad_X[n*m_nsp + k]; + } else { + //avoid divide by zero with nonsensical response + d[n*ldf + k] = - 1.0; } - // Because we use m_molefracs_tran, sum2 must be positive definate - // if (sum2 <= 0.0) { - // d[k] = m_bdiff(k,k); - // } else { - d[k] = (sumxw_tran - m_molefracs_tran[k] * m_mw[k])/(mmw * sum2); - // } } } } @@ -743,8 +978,6 @@ namespace Cantera { // Compute various direct functions of temperature m_temp = t; - m_logt = log(m_temp); - m_kbt = Boltzmann * m_temp; // temperature has changed so temp flags are flipped m_visc_temp_ok = false; @@ -822,87 +1055,6 @@ namespace Cantera { return true; } - - // We formulate the directional derivative - /* - * We only calculate the change in ac due to composition. - * The pressure and the temperature are taken care of in - * other parts of the expression. - * - */ - /* - void LiquidTransport::update_Grad_lnAC() { - int k; - - for (int a = 0; a < m_nDim; a++) { - // We form the directional derivative - double * ma_Grad_X = &m_Grad_X[a*m_nsp]; - double sum = 0.0; - for (k = 0; k < m_nsp; k++) { - sum += ma_Grad_X[k] * ma_Grad_X[k]; - } - if (sum == 0.0) { - for (k = 0; k < m_nsp; k++) { - m_Grad_lnAC[m_nsp * a + k] = 0.0; - } - continue; - } - double mag = 1.0E-7 / sum; - - for (k = 0; k < m_nsp; k++) { - Xdelta_[k] = m_molefracs[k] + mag * ma_Grad_X[k]; - if (Xdelta_[k] > 1.0) { - Xdelta_[k] = 1.0; - } - if (Xdelta_[k] < 0.0) { - Xdelta_[k] = 0.0; - } - } - m_thermo->setMoleFractions(DATA_PTR(Xdelta_)); - m_thermo->getActivityCoefficients(DATA_PTR(lnActCoeffMolarDelta_)); - for (k = 0; k < m_nsp; k++) { - lnActCoeffMolarDelta_[k] = log(lnActCoeffMolarDelta_[k]); - } - - for (k = 0; k < m_nsp; k++) { - m_Grad_lnAC[m_nsp * a + k] = - sum * (lnActCoeffMolarDelta_[k] - log(actCoeffMolar_[k])) / mag; - } - } - m_thermo->setMoleFractions(DATA_PTR(m_molefracs)); - - } - */ - - //! Evaluate the gradient of the activity coefficients - //! as they alter the diffusion coefficient. - /** - * The required quantity is the derivitive of the logarithm of the - * activity coefficient with respect to the derivative of the - * logarithm of the mole fraction (or whatever concentration - * variable we are using to express chemical potential. - * - * Returns the vector over species i: - * \[ - * 1 + \partial \left[ \ln ( \gamma_i ) \right] - * / \partial \left[ \ln ( \X_i ) \right] - * \] - */ - void LiquidTransport::update_Grad_lnAC() { - - int k; - - vector_fp grad_lnAC(m_nsp); - m_thermo->getdlnActCoeffdlnC( DATA_PTR(grad_lnAC) ); - - for (k = 0; k < m_nsp; k++) { - m_Grad_lnAC[k] = grad_lnAC[k]; - // std::cout << k << " m_Grad_lnAC = " << m_Grad_lnAC[k] << std::endl; - } - - return; - } - /************************************************************************* * * methods to update species temperature-dependent properties @@ -991,12 +1143,87 @@ namespace Cantera { m_radi_mix_ok = false; } + //! Updates the internal value of the gradient of the + //! logarithm of the activity coefficients, which is + //! used in the gradient of the chemical potential. + /** + * Evaluate the gradients of the activity coefficients + * as they alter the diffusion coefficient. + * + * The gradient of the chemical potential can be written in terms of + * gradient of the logarithm of the mole fraction times a correction + * associated with the gradient of the activity coefficient relative to + * that of the mole fraction. Specifically, the gradients of the + * logarithms of each are involved according to the formula + + * \f[ + * \nabla \mu_k = RT \nabla ( \ln X_k ) + * \left[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \right] + * \f] + * + * The required quantity is the derivitive of the logarithm of the + * activity coefficient with respect to the derivative of the + * logarithm of the mole fraction (or whatever concentration + * variable we are using to express chemical potential. + * + * Updates the vector over species i: + * \[ + * \partial \left[ \ln ( \gamma_i ) \right] + * / \partial \left[ \ln ( \X_i ) \right] + * \] + */ + void LiquidTransport::update_Grad_lnAC() { + + int k; + + vector_fp grad_lnAC(m_nsp); + m_thermo->getdlnActCoeffdlnC( DATA_PTR(grad_lnAC) ); + + for (k = 0; k < m_nsp; k++) { + m_Grad_lnAC[k] = grad_lnAC[k]; + // std::cout << k << " m_Grad_lnAC = " << m_Grad_lnAC[k] << std::endl; + } + + return; + } + /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations * */ + //! Solve the stefan_maxell equations for the diffusive fluxes. + /* + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + * + * One of the Stefan Maxwell equations is replaced by the appropriate + * definition of the mass-averaged velocity, the mole-averaged velocity + * or the specification that velocities are relative to that + * of one species. + */ void LiquidTransport::stefan_maxwell_solve() { int i, j, a; doublereal tmp; @@ -1098,8 +1325,8 @@ namespace Cantera { throw CanteraError("LiquidTransport::stefan_maxwell_solve", "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); - m_A(i,i) += tmp; - m_A(i,j) = - tmp; + m_A(i,i) -= tmp; + m_A(i,j) = + tmp; } } } @@ -1135,8 +1362,8 @@ namespace Cantera { throw CanteraError("LiquidTransport::stefan_maxwell_solve", "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); - m_A(i,i) += tmp; - m_A(i,j) = - tmp; + m_A(i,i) -= tmp; + m_A(i,j) = + tmp; } } } @@ -1176,8 +1403,8 @@ namespace Cantera { throw CanteraError("LiquidTransport::stefan_maxwell_solve", "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); - m_A(i,i) += tmp; - m_A(i,j) = - tmp; + m_A(i,i) -= tmp; + m_A(i,j) = + tmp; } } } diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 468555b52..a14034c65 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -32,92 +32,56 @@ namespace Cantera { class LiquidTransportParams; - //! Class LiquidTransport implements mixture-averaged transport - //! properties for liquid phases. + //! Class LiquidTransport implements models for transport + //! properties for liquid phases. /*! - * The model is based on that - * described by Newman, Electrochemical Systems + * Liquid Transport is set up with some flexibility in + * this class. Transport properties like viscostiy + * and thermal conductivity are allowed flexibility within + * the constraints of the LiquidTransportProperty and + * LiquidTransportInteractions classes. For species + * diffusion, the LiquidTransport class focuses on + * the Stefan-Maxwell equation to determine the diffusion + * velocities. Other options for liquid diffusion include + * solvent-dominated diffusion, and a class SolventTransport + * should be forthcoming. * - * The velocity of species i may be described by the - * following equation p. 297 (12.1) - * - * \f[ - * c_i \nabla \mu_i = R T \sum_j \frac{c_i c_j}{c_T D_{ij}} - * (\mathbf{v}_j - \mathbf{v}_i) - * \f] - * - * This as written is degenerate by 1 dof. - * - * To fix this we must add in the definition of the mass averaged - * velocity of the solution. We will call the simple bold-faced - * \f$\mathbf{v} \f$ - * symbol the mass-averaged velocity. Then, the relation - * between \f$\mathbf{v}\f$ and the individual species velocities is - * \f$\mathbf{v}_i\f$ - * - * \f[ - * \rho_i \mathbf{v}_i = \rho_i \mathbf{v} + \mathbf{j}_i - * \f] - * where \f$\mathbf{j}_i\f$ are the diffusional fluxes of species i - * with respect to the mass averaged velocity and - * - * \f[ - * \sum_i \mathbf{j}_i = 0 - * \f] + * The class LiquidTransport has several roles. + * -# It brings together the individual species transport + * properties, expressed as subclasses of LTPspecies + * (Liquid Transport Properties of Species), with + * models for the composition dependence of liquid + * transport properties expressed as subclasses of + * LiquidTranInteraction. * - * and - * - * \f[ - * \sum_i \rho_i \mathbf{v}_i = \rho \mathbf{v} - * \f] + * -# It calculates the bulk velocity \f$ \vec{v} \f$ and + * individual species diffusion velocities, \f$ \vec{V_i} \f$ + * using the Stefan-Maxwell equations. It is + * possible to set a flag to calculate relative to a + * mass-averaged bulk velocity, relative to a mole-averaged + * bulk velocity or relative to a single species velocity + * using the keyword. + * Mass-averaged velocities are the default for which the + * diffusion velocities satisfy + * \f[ + * \sum_{i} Y_i \vec{V_i} = 0 + * \f] + * for mass fraction \f$ Y_i \f$. For mole-averaged velocities + * \f[ + * \sum_{i} X_i \vec{V_i} = 0 + * \f] + * for mole fraction \f$ X_i \f$. * - * Using these definitions, we can write - * - * \f[ - * \mathbf{v}_i = \mathbf{v} + \frac{\mathbf{j}_i}{\rho_i} - * \f] - * - * - * \f[ - * c_i \nabla \mu_i = R T \sum_j \frac{c_i c_j}{c_T D_{ij}} - * (\frac{\mathbf{j}_j}{\rho_j} - \frac{\mathbf{j}_i}{\rho_i}) - * = R T \sum_j \frac{1}{D_{ij}} - * (\frac{x_i \mathbf{j}_j}{M_j} - \frac{x_j \mathbf{j}_i}{M_i}) - * \f] - * - * The equations that we actually solve are - * - * \f[ - * c_i \nabla \mu_i = - * = R T \sum_j \frac{1}{D_{ij}} - * (\frac{x_i \mathbf{j}_j}{M_j} - \frac{x_j \mathbf{j}_i}{M_i}) - * \f] - * and we replace the 0th equation with the following: - * - * \f[ - * \sum_i \mathbf{j}_i = 0 - * \f] - * - * When there are charged species, we replace the rhs with the - * gradient of the electrochemical potential to obtain the - * modified equation + * -# It provides acccess to a number of derived quantities + * related to transport properties as described in the + * various methods below. + * * - * \f[ - * c_i \nabla \mu_i + c_i F z_i \nabla \Phi - * = R T \sum_j \frac{1}{D_{ij}} - * (\frac{x_i \mathbf{j}_j}{M_j} - \frac{x_j \mathbf{j}_i}{M_i}) - * \f] - * - * With this formulation we may solve for the diffusion velocities, - * without having to worry about what the mass averaged velocity - * is. - * - *

Viscosity Calculation

- * - * The viscosity calculation may be broken down into two parts. - * In the first part, the viscosity of the pure species are calculated - * In the second part, a mixing rule is applied, based on the - * Wilkes correlation, to yield the mixture viscosity. + * Within LiquidTransport, the state is presumed to be + * defined in terms of the species mole fraction, + * temperature and pressure. Charged species are expected + * and quantities like the electric current are computed + * based on a combined electrochemcial potential. * * * @ingroup tranprops @@ -175,6 +139,9 @@ namespace Cantera { /*! * Here we change all of the internal dimensions to be sufficient. * We get the object ready to do property evaluations. + * A lot of the input required to do property evaluations is + * contained in the LiquidTransportParams class that is + * filled in TransportFactory. * * @param tr Transport parameters for all of the species * in the phase. @@ -192,44 +159,77 @@ namespace Cantera { //! Returns the viscosity of the solution /*! - * The viscosity is computed using mixture averaging plus - * any information on interaction parameters - * \f[ - * \mu = \sum_k {\mu_k X_k} {\sum_j \sum_k {G_{j,k} X_k X_j} }. - * \f] - * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, - * and \f$ G_{k,j} \f$ is the interaction parameter. - - * @see updateViscosity_T(); - * - * Controlling update boolean m_viscmix_ok + * The viscosity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species viscosities. */ virtual doublereal viscosity(); - //! Returns the pure species viscosities + //! Returns the pure species viscosities for all species /*! - * The pure species viscosities are to be given in an Arrhenius - * form in accordance with activated-jump-process dominated transport. + * The pure species viscosities are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param visc array of length "number of species" + * to hold returned viscosities. */ virtual void getSpeciesViscosities(doublereal* const visc); //! Returns the hydrodynamic radius for all species /*! - * The pure species viscosities are to be given in an Arrhenius - * form in accordance with activated-jump-process dominated transport. + * The species hydrodynamic radii are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param radius array of length "number of species" + * to hold returned radii. */ virtual void getSpeciesHydrodynamicRadius(doublereal* const radius); //! Returns the binary diffusion coefficients /*! + * The binary diffusion coefficients are specified in the input + * file through the LiquidTransportInteractions class. These + * are the binary interaction coefficients employed in the + * Stefan-Maxwell equation. + * * @param ld number of species in system - * @param d vector of mixture diffusion coefficients + * @param d vector of binary diffusion coefficients * units = m2 s-1. length = ld*ld = (number of species)^2 */ virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d); //! Get the Mixture diffusion coefficients /*! + * The mixture diffusion coefficients are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the mixture diffusion coefficients + * are defined according to Ficks law: + * \f[ + * X_i \vec{V_i} = -D_i \nabla X_i. + * \f] + * Solving Ficks Law for \f$ D_i \f$ gives a mixture diffusion + * coefficient + * \f[ + * D_i = - X_i \vec{V_i} / ( \nabla X_i ). + * \f] + * If \f$ \nabla X_i = 0 \f$ this is undefined and the + * nonsensical value -1 is returned. + * + * Note that this evaluation of \f$ \vec{V_i} \f$ requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a \e slow method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. + * * @param d vector of mixture diffusion coefficients * units = m2 s-1. length = number of species */ @@ -246,27 +246,38 @@ namespace Cantera { //! Return the thermal conductivity of the solution /*! - * The thermal conductivity is computed from the following mixture rule: - * \f[ - * \lambda = \left( \sum_k Y_k \lambda_k \right) - * \f] - * - * Controlling update boolean = m_condmix_ok - */ + * The thermal conductivity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species thermal condictivities. + */ virtual doublereal thermalConductivity(); //! Get the Electrical mobilities (m^2/V/s). /*! - * This function returns the mobilities. In some formulations - * this is equal to the normal mobility multiplied by faraday's constant. - * - * The mobility is calculated from the - * diffusion coefficient using the Einstein relation + * The electrical mobilities are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the electrical mobilities + * are calculated from the mixture-averaged + * diffusion coefficients through a call to getMixDiffCoeffs() + * using the Einstein relation * * \f[ * \mu^e_k = \frac{F D_k}{R T} * \f] * + * Note that this call to getMixDiffCoeffs() requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a \e slow method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. + * * @param mobil_e Returns the electrical mobilities of * the species in array \c mobil_e. The array must be * dimensioned at least as large as the number of species. @@ -275,17 +286,29 @@ namespace Cantera { //! Get the fluid mobilities (s kmol/kg). /*! - * This function returns the fluid mobilities. Usually, you have - * to multiply Faraday's constant into the resulting expression - * to general a species flux expression. - * - * The mobility is calculated from the - * diffusion coefficient using the Einstein relation + * The fluid mobilities are not well defined + * in the context of LiquidTransport because the Stefan Maxwell + * equation is solved. Here the fluid mobilities + * are calculated from the mixture-averaged + * diffusion coefficients through a call to getMixDiffCoeffs() + * using the Einstein relation * * \f[ * \mu^f_k = \frac{D_k}{R T} * \f] * + * Note that this call to getMixDiffCoeffs() requires + * a solve of the Stefan Maxwell equation making this + * determination of the mixture averaged diffusion coefficients + * a \e slow method for obtaining diffusion coefficients. + * + * Also note that the Stefan Maxwell solve will be based upon + * the thermodynamic state (including gradients) most recently + * set. Gradients can be set specifically using set_Grad_V, + * set_Grad_X and set_Grad_T or through calls to + * getSpeciesFluxes, getSpeciesFluxesES, getSpeciesVdiff, + * getSpeciesVdiffES, etc. + * * @param mobil_f Returns the fluid mobilities of * the species in array \c mobil_f. The array must be * dimensioned at least as large as the number of species. @@ -301,7 +324,6 @@ namespace Cantera { //! Specify the value of the gradient of the temperature /*! - * * @param grad_T Gradient of the temperature (length num dimensions); */ virtual void set_Grad_T(const doublereal* const grad_T); @@ -313,29 +335,68 @@ namespace Cantera { */ virtual void set_Grad_X(const doublereal* const grad_X); - - //! Updates the internal value of the gradient of the logarithm of the - //! activity coefficients, which is used in the gradient of the chemical potential. - /*! The gradient of the chemical potential can be written in terms of - * gradient of the logarithm of the mole fraction times a correction - * associated with the gradient of the activity coefficient relative to - * that of the mole fraction. Specifically, the gradients of the - * logarithms of each are involved according to the formula + //! Compute the mixture electrical conductivity from + //! the Stefan-Maxwell equation. + /** + * To compute the mixture electrical conductance, the Stefan + * Maxwell equation is solved for zero species gradients and + * for unit potential gradient, \f$ \nabla V \f$. + * The species fluxes are converted to current by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species i. + * The conductance, \f$ \kappa \f$ is obtained from + * \f[ + * \kappa = \vec{i} / \nabla V. + * \f] + * + */ + doublereal getElectricConduct( ); + + //! Compute the electric current density in A/m^2 + /** + * The electric current is computed first by computing the + * species diffusive fluxes using the Stefan Maxwell solution + * and then the current, \f$ \vec{i} \f$ by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species i. + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_T The temperature gradient (ignored in this model). + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. + */ + void getElectricCurrent(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current) ; + - * \f[ - * \nabla \mu_k = RT \nabla ( \ln X_k ) - * \left[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \right] - * \f] - * - * The quantity within the square brackets is computed within - * this method. - */ - virtual void update_Grad_lnAC(); //! Get the species diffusive velocities wrt to - //! the mass averaged velocity, + //! the averaged velocity, //! given the gradients in mole fraction and temperature /*! + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * * Units for the returned fluxes are kg m-2 s-1. * * @param ndim Number of dimensions in the flux expressions @@ -360,10 +421,15 @@ namespace Cantera { doublereal* Vdiff); //! Get the species diffusive mass fluxes wrt to - //! the mass averaged velocity, + //! the averaged velocity, //! given the gradients in mole fraction, temperature //! and electrostatic potential. /*! + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * * Units for the returned fluxes are kg m-2 s-1. * * @param ndim Number of dimensions in the flux expressions @@ -390,34 +456,41 @@ namespace Cantera { const doublereal* grad_Phi, doublereal* Vdiff) ; - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * (length = ndim) - * @param ldx Leading dimension of the grad_X array. - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * - * - * The diffusive mass flux of species \e k is computed from - * - * - */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes); + //! Return the species diffusive mass fluxes wrt to - //! the mole averaged velocity, + //! the averaged velocity in [kmol/m^2/s]. /** + * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * Note that for this method, there is no argument for the + * gradient of the electric potential (voltage). Electric + * potential gradients can be set with set_Grad_V() or + * method getSpeciesFluxesES() can be called.x + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). * (length = ndim) @@ -433,11 +506,55 @@ namespace Cantera { * @param fluxes Output of the diffusive mass fluxes * Flat vector with the m_nsp in the inner loop. * length = ldx * ndim + */ + virtual void getSpeciesFluxes(int ndim, + const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, doublereal* fluxes); + + //! Return the species diffusive mass fluxes wrt to + //! the averaged velocity in [kmol/m^2/s]. + /** * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. * - * The diffusive mass flux of species \e k is computed from - * - * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) + * @param ldx Leading dimension of the grad_X array. + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * length = ndim + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ virtual void getSpeciesFluxesES(int ndim, const doublereal* grad_T, @@ -447,38 +564,36 @@ namespace Cantera { const doublereal* grad_Phi, doublereal* fluxes); - //! Return the species diffusive velocities relative to - //! the (mass) averaged velocity. - //! See getSpeciesFluxesExt for further details. + //! Return the species diffusive velocities relative to + //! the averaged velocity. + /** + * This method acts similarly to getSpeciesVdiffES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesVdiffES() for details. + * + * @param ldf Leading dimension of the Vdiff array. + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ virtual void getSpeciesVdiffExt(int ldf, doublereal* Vdiff); - //! Return the species diffusive mass fluxes wrt to - //! the mass averaged velocity, - /*! - * - * units = kg/m2/s - * - * Internally, gradients in the in mole fraction, temperature - * and electrostatic potential contribute to the diffusive flux - * - * - * The diffusive mass flux of species \e k is computed from the following - * formula - * - * \f[ - * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c - * \f] - * - * where V_c is the correction velocity - * - * \f[ - * V_c = - \sum_j {\rho M_j D_j \nabla X_j} - * \f] - * - * @param ldf stride of the fluxes array. Must be equal to - * or greater than the number of species. - * @param fluxes Vector of calculated fluxes - */ + //! Return the species diffusive fluxes relative to + //! the averaged velocity. + /** + * This method acts similarly to getSpeciesFluxesES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesFluxesES() for details. + * + * units = kg/m2/s + * + * @param ldf Leading dimension of the Vdiff array. + * @param fluxes Output of the diffusive fluxes. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ virtual void getSpeciesFluxesExt(int ldf, doublereal* fluxes); protected: @@ -517,7 +632,70 @@ namespace Cantera { */ virtual bool update_C(); + + //! Updates the internal value of the gradient of the + //! logarithm of the activity coefficients, which is + //! used in the gradient of the chemical potential. + /** + * Evaluate the gradients of the activity coefficients + * as they alter the diffusion coefficient. + * + * The gradient of the chemical potential can be written in terms of + * gradient of the logarithm of the mole fraction times a correction + * associated with the gradient of the activity coefficient relative to + * that of the mole fraction. Specifically, the gradients of the + * logarithms of each are involved according to the formula + + * \f[ + * \nabla \mu_k = RT \nabla ( \ln X_k ) + * \left[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \right] + * \f] + * + * The required quantity is the derivitive of the logarithm of the + * activity coefficient with respect to the derivative of the + * logarithm of the mole fraction (or whatever concentration + * variable we are using to express chemical potential. + * + * Updates the vector over species i: + * \[ + * \partial \left[ \ln ( \gamma_i ) \right] + * / \partial \left[ \ln ( \X_i ) \right] + * \] + */ + virtual void update_Grad_lnAC(); + + //! Solve the stefan_maxell equations for the diffusive fluxes. + /** + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. + * + * One of the Stefan Maxwell equations is replaced by the appropriate + * definition of the mass-averaged velocity, the mole-averaged velocity + * or the specification that velocities are relative to that + * of one species. + */ void stefan_maxwell_solve(); //! Update the temperature-dependent viscosity terms. @@ -892,12 +1070,6 @@ namespace Cantera { */ doublereal m_temp; - //! Current log(T) - doublereal m_logt; - - //! Current value of kT - doublereal m_kbt; - //! Current value of the pressure doublereal m_press; diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 0d3ff8749..544fe3898 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -276,8 +276,28 @@ namespace Cantera { //@} - - + + //! Compute the mixture electrical conductivity + doublereal getElectricConduct( ); + + //! Compute the electric current + /** + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_T The temperature gradient (ignored in this model). + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. + */ + void getElectricCurrent(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current) ; + //! Get the species diffusive mass fluxes wrt to //! the mass averaged velocity, //! given the gradients in mole fraction and temperature From 9782ac76e8b582497fbd424e2cbd7329fd18d07b Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 16 Dec 2009 00:29:32 +0000 Subject: [PATCH 073/446] Minor edits --- .../src/transport/LiquidTransportParams.cpp | 6 +++-- Cantera/src/transport/LiquidTransportParams.h | 23 ++++++++++++++++--- Cantera/src/transport/TransportFactory.cpp | 10 +------- Cantera/src/transport/TransportParams.h | 1 - 4 files changed, 25 insertions(+), 15 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index b811eefa4..7aafc4859 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -350,10 +350,12 @@ namespace Cantera { void LTI_Pairwise_Interaction::setParameters( LiquidTransportParams& trParam ) { int nsp = m_thermo->nSpecies(); + m_diagonals.resize(nsp); for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; - m_diagonals[k] = ltd.speciesDiffusivity; + if ( ltd.speciesDiffusivity ) + m_diagonals[k] = ltd.speciesDiffusivity; } } @@ -398,7 +400,7 @@ namespace Cantera { tmp(i,j) = tmp(j,i) = m_Dij(i,j) * exp( - m_Eij(i,j) / temp ); for ( int i = 0; i < nsp; i++ ) - if ( tmp(i,i) == 0.0 && !(m_diagonals[i]) ) + if ( tmp(i,i) == 0.0 && m_diagonals[i] ) tmp(i,i) = m_diagonals[i]->getSpeciesTransProp() ; return tmp; diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index b4ab26a22..4e0656ac9 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -25,6 +25,14 @@ namespace Cantera { + class NotImplemented : public CanteraError { + public: + NotImplemented(std::string method) : CanteraError("Transport", + "\n\n**** Method "+method+" not implemented. ****\n" + "(Did you forget to specify a transport model?)\n\n") {} + }; + + //! Composition dependence type for liquid mixture transport properties /*! * Types of temperature dependencies: @@ -116,9 +124,18 @@ namespace Cantera { //! Return the mixture transport property value. //! (Must be implemented in subclasses.) - virtual doublereal getMixTransProp( doublereal* speciesValues, doublereal *weightSpecies = 0 ) { return 0.0; } - virtual doublereal getMixTransProp( std::vector LTPptrs ) { return 0.0; } - virtual DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Dij; } + virtual doublereal getMixTransProp( doublereal* speciesValues, doublereal *weightSpecies = 0 ) { + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } + + virtual doublereal getMixTransProp( std::vector LTPptrs ) { + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } + + virtual DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { + //return m_Dij; + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } protected: //! Model for species interaction effects diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 72902ec87..921ee4236 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -75,14 +75,6 @@ namespace Cantera { }; - class NotImplemented : public CanteraError { - public: - NotImplemented(std::string method) : CanteraError("Transport", - "\n\n\n**** Method "+method+" not implemented. ****\n" - "(Did you forget to specify a transport model?)\n\n\n") {} - }; - - /////////////////////////// constants ////////////////////////// const doublereal ThreeSixteenths = 3.0/16.0; @@ -373,7 +365,7 @@ namespace Cantera { lti->setParameters( trParam ); break; default: - throw CanteraError("newLTI","unknown transport model: " + model ); + // throw CanteraError("newLTI","unknown transport model: " + model ); lti = new LiquidTranInteraction( tp_ind ); lti->init( trNode, thermo ); } diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 119f6a7d6..563c6d9ca 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -40,7 +40,6 @@ namespace Cantera { } int nsp_; - // phase_t* mix; thermo_t* thermo; vector_fp mw; From d38eea717a57fe652ed4c43c3357a9f2e25a4fad Mon Sep 17 00:00:00 2001 From: John Hewson Date: Thu, 17 Dec 2009 19:07:53 +0000 Subject: [PATCH 074/446] Updating Doxygen comments --- Cantera/src/transport/LiquidTransport.cpp | 36 ++-- Cantera/src/transport/LiquidTransport.h | 155 +++++++++--------- Cantera/src/transport/LiquidTransportData.h | 35 +++- Cantera/src/transport/LiquidTransportParams.h | 6 +- 4 files changed, 123 insertions(+), 109 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 6f0a401db..779000a66 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -169,7 +169,7 @@ namespace Cantera { if ( m_viscMixModel ) delete m_viscMixModel; if ( m_lambdaMixModel ) delete m_lambdaMixModel; if ( m_diffMixModel ) delete m_diffMixModel; - if ( m_radiusMixModel ) delete m_radiusMixModel; + //if ( m_radiusMixModel ) delete m_radiusMixModel; } @@ -265,7 +265,7 @@ namespace Cantera { */ m_viscMixModel = tr.viscosity; m_lambdaMixModel = tr.thermalCond; - m_radiusMixModel = tr.hydroRadius; + //m_radiusMixModel = tr.hydroRadius; m_diffMixModel = tr.speciesDiffusivity; m_bdiff.resize(m_nsp,m_nsp); //Don't really need to update this here. @@ -939,14 +939,14 @@ namespace Cantera { stefan_maxwell_solve(); - for (n = 0; n < m_nDim; n++) { - for (k = 0; k < m_nsp; k++) { + for ( int n = 0; n < m_nDim; n++) { + for (int k = 0; k < m_nsp; k++) { if ( m_Grad_X[n*m_nsp + k] != 0.0 ) { - d[n*ldf + k] = - m_Vdiff(k,n) * m_molefracs[k] + d[n*m_nsp + k] = - m_Vdiff(k,n) * m_molefracs[k] / m_Grad_X[n*m_nsp + k]; } else { //avoid divide by zero with nonsensical response - d[n*ldf + k] = - 1.0; + d[n*m_nsp + k] = - 1.0; } } } @@ -1063,7 +1063,8 @@ namespace Cantera { /** * Update the temperature-dependent parts of the species - * thermal conductivity. + * thermal conductivity internally using calls to the + * appropriate LTPspecies subclass. */ void LiquidTransport::updateCond_T() { @@ -1077,11 +1078,8 @@ namespace Cantera { } - //! Update the StefanMaxwell interaction parameters. - /** - * These are evaluated using the Stokes-Einstein - * relation from the viscosity and hydrodynamic radius. - */ + //! Update the binary Stefan-Maxwell diffusion coefficients + //! wrt T using calls to the appropriate LTPspecies subclass void LiquidTransport::updateDiff_T() { m_bdiff = m_diffMixModel->getMatrixTransProp(); @@ -1097,9 +1095,8 @@ namespace Cantera { /** - * Update the temperature-dependent viscosity terms. - * Updates the array of pure species viscosities, and the - * weighting functions in the viscosity mixture rule. + * Updates the array of pure species viscosities internally + * using calls to the appropriate LTPspecies subclass. * The flag m_visc_ok is set to true. * * Note that for viscosity, a positive activation energy @@ -1127,12 +1124,9 @@ namespace Cantera { } - /** - * Update the temperature-dependent hydrodynamic radius terms. - * Updates the array of pure species viscosities, and the - * weighting functions in the viscosity mixture rule. - * The flag m_visc_ok is set to true. - */ + //! Update the temperature-dependent hydrodynamic radius terms + //! for each species internally using calls to the + //! appropriate LTPspecies subclass void LiquidTransport::updateHydrodynamicRadius_T() { int k; diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index a14034c65..767629bcf 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -698,23 +698,29 @@ namespace Cantera { */ void stefan_maxwell_solve(); - //! Update the temperature-dependent viscosity terms. - //! Updates the array of pure species viscosities, and the - //! weighting functions in the viscosity mixture rule. + //! Updates the array of pure species viscosities internally. /*! * The flag m_visc_ok is set to true. + * + * Note that for viscosity, a positive activation energy + * corresponds to the typical case of a positive argument + * to the exponential so that the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( + E / R T ) + * \f] */ void updateViscosity_T(); //! Update the temperature-dependent hydrodynamic radius terms - //! for each species + //! for each species internally /*! * The flag m_radi_temp_ok is set to true. */ void updateHydrodynamicRadius_T(); //! Update the temperature-dependent parts of the mixture-averaged - //! thermal conductivity. + //! thermal conductivity internally void updateCond_T(); //! Update the concentration parts of the viscosities @@ -737,11 +743,8 @@ namespace Cantera { */ void updateHydrodynamicRadius_C(); - //! Update the binary diffusion coefficients wrt T. - /*! - * These are evaluated - * from the polynomial fits at unit pressure (1 Pa). - */ + //! Update the binary Stefan-Maxwell diffusion coefficients + //! wrt T using calls to the appropriate LTPspecies subclass void updateDiff_T(); @@ -762,54 +765,64 @@ namespace Cantera { */ vector_fp m_mw; - //! Viscosity temperature dependence type + //! Viscosity for each species expressed as an appropriate subclass + //! of LTPspecies /*! - * Types of temperature dependencies: - * 0 - Independent of temperature (only one implemented so far) - * 1 - extended arrhenius form - * 2 - polynomial in temperature form + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). */ std::vector m_viscTempDep_Ns; - //! Viscosity mixing model type + //! Viscosity of the mixture expressed as a subclass of + //! LiquidTranInteraction /*! - * Types of mixing models supported: - * 2 - Mole fraction weighting of species viscosities - * 3 - Mass fraction weighting of species viscosities - * 4 - Mole fraction weighting of logarithms of species viscosities + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). */ LiquidTranInteraction *m_viscMixModel; - //! Thermal conductivity temperature dependence type + //! Thermal conductivity for each species expressed as an + //! appropriate subclass of LTPspecies /*! - * Types of temperature dependencies: - * 0 - Independent of temperature (only one implemented so far) - * 1 - extended arrhenius form - * 2 - polynomial in temperature form + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). */ std::vector m_lambdaTempDep_Ns; - //! Thermal conductivity mixing model type + //! Thermal conductivity of the mixture expressed as a subclass of + //! LiquidTranInteraction /*! - * Types of mixing models supported: - * 2 - Mole fraction weighting of species viscosities - * 3 - Mass fraction weighting of species viscosities + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). */ LiquidTranInteraction *m_lambdaMixModel; - //! Diffusion coefficient temperature dependence type + //! (NOT USED IN LiquidTransport.) + //! Diffusion coefficient model for each species expressed as an + //! appropriate subclass of LTPspecies /*! - * Types of temperature dependencies: - * 0 - Independent of temperature (only one implemented so far) - * 1 - extended arrhenius form - * 2 - polynomial in temperature form + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). + * + * Since the LiquidTransport class uses the Stefan-Maxwell equation + * to describe species diffusivity, the species-specific + * diffusivity is irrelevant. */ std::vector m_diffTempDep_Ns; - //! Species diffusivity mixing model type + //! Species diffusivity of the mixture expressed as a subclass of + //! LiquidTranInteraction. This will return an array of + //! Stefan-Maxwell interaction parameters for use in the + //! Stefan-Maxwell solution. /*! - * Types of mixing models supported: - * 5 - Pairwise interactions -- Setfan-Maxwell diffusion coefficients + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). */ LiquidTranInteraction *m_diffMixModel; @@ -817,37 +830,29 @@ namespace Cantera { DenseMatrix m_diff_Dij; - std::vector useHydroRadius_; - - //!Hydrodynamic radius temperature dependence type + //!Hydrodynamic radius for each species expressed as an + //! appropriate subclass of LTPspecies /*! - * Types of temperature dependencies: - * 0 - Independent of temperature - * 1 - extended arrhenius form - * 2 - polynomial in temperature form + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). */ std::vector m_radiusTempDep_Ns; + //! (Not used in LiquidTransport) + //! Hydrodynamic radius of the mixture expressed as a subclass of + //! LiquidTranInteraction + /*! + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). + */ + LiquidTranInteraction *m_radiusMixModel; + //! Species hydrodynamic radius vector_fp m_hydrodynamic_radius; - //! Hydrodynamic radius mixing model type - /*! - * Types of mixing models supported: - * 0 - No mixing model allowed - */ - LiquidTranInteraction *m_radiusMixModel; - - - //! Polynomial coefficients of the binary diffusion coefficients - /*! - * These express the temperature dependendence of the - * binary diffusivities. An overall pressure dependence is then - * added. - */ - /* - std::vector m_diffcoeffs; - */ + //! Hydrodynamic radius //! Internal value of the gradient of the mole fraction vector @@ -874,10 +879,10 @@ namespace Cantera { * It multiplies the gradient of the mole fraction, and in this way * serves to "modify" the diffusion coefficient. * - * m_Grad_X[k] = 1 + \partial \left[ \ln ( \gamma_i ) \right] + * m_Grad_lnAC[k] = \partial \left[ \ln ( \gamma_i ) \right] * / \partial \left[ \ln ( \X_i ) \right] * - * Note that where "molefraction is used here, whatever + * Note that where "mole fraction" is used here, whatever * concentration-related variable applies, so that if * molality is the concentration variable, the gradient of the * activity coefficient should be with respect to the molality. @@ -937,8 +942,8 @@ namespace Cantera { //! Array of Binary Diffusivities /*! - * Depends on the temperature. We have set the pressure dependence - * to zero for this liquid phase constituitve model + * These are evaluated according to the subclass of + * LiquidTranInteraction stored in m_diffMixModel. * * This has a size equal to nsp x nsp * It is a symmetric matrix. @@ -949,13 +954,12 @@ namespace Cantera { */ DenseMatrix m_bdiff; - //! Species viscosities and their logarithm + //! Internal value of the species viscosities /*! - * Viscosity of the species and its logarithm - * Length = number of species + * Viscosity of the species evaluated using subclass of LTPspecies + * held in m_viscTempDep_Ns. * - * Depends on the temperature. We have set the pressure dependence - * to zero for this liquid phase constituitve model + * Length = number of species * * controlling update boolean -> m_visc_temp_ok */ @@ -963,12 +967,11 @@ namespace Cantera { //! Internal value of the species individual thermal conductivities /*! - * Then a mixture rule is applied to get the solution conductivities + * Thermal conductivities of the species evaluated using subclass + * of LTPspecies held in m_lambdaTempDep_Ns. * - * Depends on the temperature and perhaps pressure, but - * not the species concentrations + * Length = number of species * - * controlling update boolean -> m_cond_temp_ok */ vector_fp m_lambdaSpecies; @@ -1014,8 +1017,6 @@ namespace Cantera { */ vector_fp m_molefracs_tran; - vector_fp Xdelta_; - //! Local copy of the concentrations of the species in the phase /*! * The concentrations are consistent with the m_molefracs @@ -1073,7 +1074,7 @@ namespace Cantera { //! Current value of the pressure doublereal m_press; - //! Solution of the flux system + //! Solution of the Stefan Maxwell equation in terms of flux /*! * This is the mass flux of species k * in units of kg m-3 s-1. diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index 733f0b463..3f2be9bfa 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -29,6 +29,19 @@ namespace Cantera { + /** + * Enumeration of the types of transport properties that can be + * handled by the variables in the various Transport classes. + * Not all of these are handled by each class and each class + * should handle exceptions where the transport property is not handled. + * + * Tranport properties currently on the list + * 0 - viscosity + * 1 - thermal conductivity + * 2 - species diffusivity + * 3 - hydrodynamic radius + * 4 - thermal conductivity + */ enum TransportPropertyList { TP_UNKNOWN = -1, TP_VISCOSITY = 0, @@ -38,14 +51,14 @@ namespace Cantera { TP_ELECTCOND }; + //! Temperature dependence type for pure (liquid) species properties + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ enum LiquidTR_Model { - //! Temperature dependence type for pure (liquid) species properties - /*! - * Types of temperature dependencies: - * 0 - Independent of temperature (only one implemented so far) - * 1 - extended arrhenius form - * 2 - polynomial in temperature form - */ LTR_MODEL_NOTSET=-1, LTR_MODEL_CONSTANT, LTR_MODEL_ARRHENIUS, @@ -72,7 +85,7 @@ namespace Cantera { /** * The transport property is constructed from the * XML node, propNode, that is a child of the - * node and specifies a type of + * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity). */ LTPspecies( const XML_Node &propNode = 0, @@ -150,7 +163,11 @@ namespace Cantera { //! Class LiquidTransportData holds transport parameters for a - //! specific liquid-phase species. + //! specific liquid-phase species. + /** + * This class is mainly used to collect transport properties + * from the parse phase and transfer them to the Transport class. + */ class LiquidTransportData { public: diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 4e0656ac9..709b68ef4 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -42,7 +42,8 @@ namespace Cantera { * 3 - Properties weighted linearly by mass fractions * 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) * 5 - Interactions given pairwise between each possible species (i.e. D_ij) - * + * + * \verbatim * * * @@ -80,6 +81,7 @@ namespace Cantera { * * * + * \endverbatim * */ enum LiquidTranMixingModel { @@ -114,7 +116,7 @@ namespace Cantera { //! initialize LiquidTranInteraction objects with thermo and XML node /** - * @param compModelNode XML node + * @param compModelNode \verbatim \endverbatim XML node * @param thermo Pointer to thermo object */ virtual void init( const XML_Node &compModelNode = 0, From 1ab5f6725a485fd6d988cc58127f073913068e06 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 17 Dec 2009 22:13:14 +0000 Subject: [PATCH 075/446] Utility commit - doxygen updates - started filling in copy constructors, assignment operator, and dupl function. --- Cantera/src/transport/SolidTransport.cpp | 225 ++++++++++++++--------- Cantera/src/transport/SolidTransport.h | 112 ++++++++--- 2 files changed, 227 insertions(+), 110 deletions(-) diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index ee20c52b6..de1925eb1 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -1,14 +1,15 @@ /** - * * @file SolidTransport.cpp + * Definition file for the class SolidTransport, which handles transport + * of ions within solid phases + * (see \ref tranprops and \link Cantera::SolidTransport SolidTransport \endlink). */ - /* $Author$ * $Revision$ * $Date$ */ -// copyright 2008 California Institute of Technology +// Copyright 2008 California Institute of Technology // turn off warnings under Windows @@ -27,92 +28,152 @@ using namespace std; namespace Cantera { - SolidTransport::SolidTransport() {} + //==================================================================================================================== + SolidTransport::SolidTransport() : + Transport() , + m_nmobile(0.0), + m_Adiff(0), + m_Ndiff(0), + m_Ediff(0), + m_sp(0), + m_Alam(0), + m_Nlam(0), + m_Elam(0) + { + } + //==================================================================================================================== + SolidTransport::~SolidTransport() + { + } + //==================================================================================================================== + SolidTransport::SolidTransport(const SolidTransport &right) : + Transport(), + m_nmobile(0.0), + m_Adiff(0), + m_Ndiff(0), + m_Ediff(0), + m_sp(0), + m_Alam(0), + m_Nlam(0), + m_Elam(0) + { + /* + * Use the assignment operator to do the brunt + * of the work for the copy construtor. + */ + *this = right; + } + //==================================================================================================================== + SolidTransport& SolidTransport::operator=(const SolidTransport& b) + { + if (&b != this) { + return *this; + } + Transport::operator=(b); - void SolidTransport::setParameters(const int n, const int k, const double* const p) { - switch (n) { + m_nmobile = b.m_nmobile; + m_Adiff = b.m_Adiff; + m_Ndiff = b.m_Ndiff; + m_Ediff = b.m_Ediff; + m_sp = b.m_sp; + m_Alam = b.m_Alam; + m_Nlam = b.m_Nlam; + m_Elam = b.m_Elam; + + return *this; + } + //==================================================================================================================== + Transport *SolidTransport::duplMyselfAsTransport() const + { + SolidTransport* tr = new SolidTransport(*this); + return (dynamic_cast(tr)); + } + //==================================================================================================================== + void SolidTransport::setParameters(const int n, const int k, const double* const p) { + switch (n) { - case 0: - // set the Arrhenius parameters for the diffusion coefficient - // of species k. - m_sp.push_back(k); - m_Adiff.push_back(p[0]); - m_Ndiff.push_back(p[1]); - m_Ediff.push_back(p[2]); - m_nmobile = m_sp.size(); - break; + case 0: + // set the Arrhenius parameters for the diffusion coefficient + // of species k. + m_sp.push_back(k); + m_Adiff.push_back(p[0]); + m_Ndiff.push_back(p[1]); + m_Ediff.push_back(p[2]); + m_nmobile = m_sp.size(); + break; - case 1: - // set the thermal conductivity Arrhenius parameters. - m_Alam = p[0]; - m_Nlam = p[2]; - m_Elam = p[2]; - break; + case 1: + // set the thermal conductivity Arrhenius parameters. + m_Alam = p[0]; + m_Nlam = p[2]; + m_Elam = p[2]; + break; - default: - ; - } + default: + ; } - - /** - * Compute the mobilities of the species from the diffusion coefficients, - * using the Einstein relation. - */ - void SolidTransport::getMobilities(doublereal* const mobil) { - int k; - getMixDiffCoeffs(mobil); - doublereal t = m_thermo->temperature(); - int nsp = m_thermo->nSpecies(); - doublereal c1 = ElectronCharge / (Boltzmann * t); - for (k = 0; k < nsp; k++) { - mobil[k] *= c1 * fabs(m_thermo->charge(k)); - } - } - - /** - * Thermal Conductivity. - * \f[ - * \lambda = A T^n \exp(-E/RT) - * \f] - */ - doublereal SolidTransport::thermalConductivity() { - doublereal t = m_thermo->temperature(); - return m_Alam *pow(t, m_Nlam) * exp(-m_Elam/t); + m_work.resize(m_thermo->nSpecies()); + } + //==================================================================================================================== + /* + * Compute the mobilities of the species from the diffusion coefficients, + * using the Einstein relation. + */ + void SolidTransport::getMobilities(doublereal* const mobil) { + int k; + getMixDiffCoeffs(mobil); + doublereal t = m_thermo->temperature(); + int nsp = m_thermo->nSpecies(); + doublereal c1 = ElectronCharge / (Boltzmann * t); + for (k = 0; k < nsp; k++) { + mobil[k] *= c1 * fabs(m_thermo->charge(k)); } + } + //==================================================================================================================== + /** + * Thermal Conductivity. + * \f[ + * \lambda = A T^n \exp(-E/RT) + * \f] + */ + doublereal SolidTransport::thermalConductivity() { + doublereal t = m_thermo->temperature(); + return m_Alam *pow(t, m_Nlam) * exp(-m_Elam/t); + } + //==================================================================================================================== - - /** - * The diffusion coefficients are computed from - * - * \f[ - * D_k = A_k T^{n_k} \exp(-E_k/RT). - * \f] - * - * The diffusion coefficients are only non-zero for species for - * which parameters have been specified using method - * setParameters. - */ - void SolidTransport::getMixDiffCoeffs(doublereal* const d) { - doublereal temp = m_thermo->temperature(); - int nsp = m_thermo->nSpecies(); - int k; - for (k = 0; k < nsp; k++) d[k] = 0.0; - for (k = 0; k < m_nmobile; k++) { - d[m_sp[k]] = - m_Adiff[k] * pow(temp, m_Ndiff[k]) * exp(-m_Ediff[k]/temp); - } + /** + * The diffusion coefficients are computed from + * + * \f[ + * D_k = A_k T^{n_k} \exp(-E_k/RT). + * \f] + * + * The diffusion coefficients are only non-zero for species for + * which parameters have been specified using method + * setParameters. + */ + void SolidTransport::getMixDiffCoeffs(doublereal* const d) { + doublereal temp = m_thermo->temperature(); + int nsp = m_thermo->nSpecies(); + int k; + for (k = 0; k < nsp; k++) d[k] = 0.0; + for (k = 0; k < m_nmobile; k++) { + d[m_sp[k]] = + m_Adiff[k] * pow(temp, m_Ndiff[k]) * exp(-m_Ediff[k]/temp); } - -// void SolidTransport::electricalConductivity() { -// getMobilities(m_work.begin()); -// int nsp = m_thermo->nSpecies(); -// int k; -// doublereal sum = 0.0; -// for (k = 0; k < nsp; n++) { -// sum += m_thermo->charge(k)*m_thermo->moleFraction(k)*m_work[k]; -// } -// return sum * m_thermo->molarDensity(); -// } - + } + //==================================================================================================================== + doublereal SolidTransport::electricalConductivity() + { + getMobilities(&m_work[0]); + int nsp = m_thermo->nSpecies(); + doublereal sum = 0.0; + for (int k = 0; k < nsp; k++) { + sum += m_thermo->charge(k) * m_thermo->moleFraction(k) * m_work[k]; + } + return sum * m_thermo->molarDensity(); + } + //==================================================================================================================== } diff --git a/Cantera/src/transport/SolidTransport.h b/Cantera/src/transport/SolidTransport.h index 31e5fe0a1..8c6be50d2 100644 --- a/Cantera/src/transport/SolidTransport.h +++ b/Cantera/src/transport/SolidTransport.h @@ -1,10 +1,11 @@ /** - * * @file SolidTransport.h - * Header file defining class SolidTransport + * Header file for defining the class SolidTransport, which handles transport + * of ions within solid phases + * (see \ref tranprops and \link Cantera::SolidTransport SolidTransport \endlink). */ -/* $Author$ +/* * $Revision$ * $Date$ */ @@ -37,40 +38,95 @@ namespace Cantera { - /** - * Class SolidTransport implements transport - * properties for solids. + + //! Class SolidTransport implements transport properties for solids. + /*! + * + * + * + */ + class SolidTransport : public Transport { + + public: + + //! Default constructor + SolidTransport(); + + //! Copy Constructor + /*! + * @param right Object to be copied */ - class SolidTransport : public Transport { + SolidTransport(const SolidTransport &right); - public: -virtual ~SolidTransport() {} + //! Destructor + virtual ~SolidTransport(); - virtual int model() const { return cSolidTransport; } + //! Assignment operator + /*! + * This is NOT a virtual function. + * + * @param right Reference to Transport object to be copied into the + * current one. + */ + SolidTransport& operator=(const SolidTransport& right); - virtual doublereal thermalConductivity(); - virtual void getMixDiffCoeffs(doublereal* const d); - virtual void getMobilities(doublereal* const mobil); - virtual void setParameters(const int n, const int k, const doublereal* const p); + //! Duplication routine for objects which inherit from + //! %Transport + /*! + * This virtual routine can be used to duplicate %Transport objects + * inherited from %Transport even if the application only has + * a pointer to %Transport to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + */ + virtual Transport *duplMyselfAsTransport() const; - friend class TransportFactory; - protected: + virtual int model() const { return cSolidTransport; } - /// default constructor - SolidTransport(); + virtual doublereal thermalConductivity(); + virtual void getMixDiffCoeffs(doublereal* const d); - private: + //! Compute the electrical mobilities of the species from the diffusion coefficients, + //! using the Einstein relation. + /*! + * Frequently, but not always, the mobility is calculated from the + * diffusion coefficient using the Einstein relation + * + * \f[ + * \mu^e_k = \frac{F D_k}{R T} + * \f] + * + * units (m^2/V/s). + * @param mobil Returns the mobilities of + * the species in array \c mobil_e. The array must be + * dimensioned at least as large as the number of species. + */ + virtual void getMobilities(doublereal* const mobil); - int m_nmobile; // number of mobile species - vector_fp m_Adiff; - vector_fp m_Ndiff; - vector_fp m_Ediff; - vector_int m_sp; - doublereal m_Alam; - doublereal m_Nlam; - doublereal m_Elam; - }; + virtual void setParameters(const int n, const int k, const doublereal* const p); + + friend class TransportFactory; + + /** + * The electrical conductivity (Siemens/m). + */ + virtual doublereal electricalConductivity(); + + + private: + + int m_nmobile; // number of mobile species + vector_fp m_Adiff; + vector_fp m_Ndiff; + vector_fp m_Ediff; + vector_int m_sp; + doublereal m_Alam; + doublereal m_Nlam; + doublereal m_Elam; + vector_fp m_work; + }; } #endif From 39ea7fdeab1369332d83deec3366307b450ec5ec Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 18 Dec 2009 16:43:20 +0000 Subject: [PATCH 076/446] Doxygen update. Worked on general information for the Transport classes. --- Cantera/src/transport/SolidTransport.cpp | 7 +-- Cantera/src/transport/TransportBase.h | 73 +++++++++++++++++++----- 2 files changed, 61 insertions(+), 19 deletions(-) diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index de1925eb1..0e723aad6 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -131,7 +131,7 @@ namespace Cantera { } } //==================================================================================================================== - /** + /* * Thermal Conductivity. * \f[ * \lambda = A T^n \exp(-E/RT) @@ -139,11 +139,10 @@ namespace Cantera { */ doublereal SolidTransport::thermalConductivity() { doublereal t = m_thermo->temperature(); - return m_Alam *pow(t, m_Nlam) * exp(-m_Elam/t); + return m_Alam * pow(t, m_Nlam) * exp(-m_Elam/t); } //==================================================================================================================== - - /** + /* * The diffusion coefficients are computed from * * \f[ diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 544fe3898..152e9a936 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -69,25 +69,61 @@ namespace Cantera { VB_MASSAVG = -1 }; - /** - * Base class for transport property managers. All classes that - * compute transport properties derive from this class. Class - * Transport is meant to be used as a base class only. It is - * possible to instantiate it, but its methods throw exceptions if - * called. + //! Base class for transport property managers. + /*! + * All classes that compute transport properties for a single phase + * derive from this class. Class + * %Transport is meant to be used as a base class only. It is + * possible to instantiate it, but its methods throw exceptions if + * called. + * + * Note, transport properties for multiphase situations have yet to be + * fully developed within Cantera. * * All member functions are virtual, unless otherwise stated. * + *
+ *

Relationship of the %Transport class to the %ThermoPhase Class

+ *
+ * + * This section describes how calculations are carried out within + * the %Transport class. The %Transport class and derived classes of the + * the %Transport class necessarily use the %ThermoPhase class to obtain + * the list of species and the thermodynamic state of the phase. + * + * No state information is storred within %Transport classes. + * Queries to the underlying ThermoPhase object must be made to obtain + * the state of the system. + * + * An exception to this however is the state information concerning the + * the gradients of variables. This information is not storred within + * the ThermoPhase objects. It may be collected within the Transport objects. + * In fact, the meaning of const operations within the Transport class + * refers to calculations which do not change the state of the + * system nor the state of the first order gradients of the system. + * + * When a const operation is evoked within the Transport class, it is + * also implicitly assumed that the underlying state within the ThermoPhase + * object has not changed its values. + * + * @todo Provide a general mechanism to store the gradients of state variables + * within the system. + * * @ingroup tranprops */ class Transport { public: - - /** - * Constructor. New transport managers should be created using + //! Constructor. + /*! + * New transport managers should be created using * TransportFactory, not by calling the constructor directly. + * + * @param thermo Pointer to the ThermoPhase class representing + * this phase. + * @param ndim Dimension of the flux vector used in the calculation. + * * @see TransportFactory */ Transport(thermo_t* thermo=0, int ndim = 1); @@ -123,7 +159,6 @@ namespace Cantera { // Note ->need working copy constructors and operator=() functions for all first virtual Transport *duplMyselfAsTransport() const; - /** * Transport model. The transport model is the set of * equations used to compute the transport properties. This @@ -159,7 +194,6 @@ namespace Cantera { */ int index() const ; - //! Set an integer index number. /*! * This is for internal use of @@ -489,19 +523,23 @@ namespace Cantera { { err("getMultiDiffCoeffs"); } + //! Returns a vector of mixture averaged diffusion coefficients /** * Mixture-averaged diffusion coefficients [m^2/s]. If the + * * transport manager implements a mixture-averaged diffusion * model, then this method returns the array of * mixture-averaged diffusion coefficients. Otherwise it * throws an exception. + * + * @param d Return vector of mixture averaged diffusion coefficients + * Units = m2/s. Length = n_sp */ virtual void getMixDiffCoeffs(doublereal* const d) { err("getMixDiffCoeffs"); } - - //! Set transport model parameters. + //! Set model parameters for derived classes /*! * This method may be * overloaded in subclasses to set model-specific parameters. @@ -627,13 +665,14 @@ namespace Cantera { //! Number of dimensions used in flux expresions int m_nDim; - //! Celocity basis from which diffusion velocities are computed. + //! Velocity basis from which diffusion velocities are computed. //! Defaults to the mass averaged basis = -2 int m_velocityBasis; private: - /** + //! Error routine + /*! * Throw an exception if a method of this class is * invoked. This probably indicates that a transport manager * is being used that does not implement all virtual methods, @@ -644,6 +683,10 @@ namespace Cantera { * meaningless. If the application invokes the viscosity() * method, the base class method will be called, resulting in * an exception being thrown. + * + * @param msg Descriptive message string to add to the error report + * + * @return returns a double, though we will never get there */ doublereal err(std::string msg) const; From b4032c9d9a0ce97acb35a4ef7fa9e418b4c56b99 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 18 Dec 2009 21:28:25 +0000 Subject: [PATCH 077/446] Updating Doxygen comments --- Cantera/src/transport/LiquidTransportData.cpp | 24 ++-- Cantera/src/transport/LiquidTransportData.h | 112 ++++++++++++--- Cantera/src/transport/LiquidTransportParams.h | 133 ++++++++++++++---- 3 files changed, 213 insertions(+), 56 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 6357231a9..531763b51 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -92,8 +92,9 @@ namespace Cantera { //! Construct an LTPspecies object for a liquid tranport property //! expressed as a constant value. - /** The transport property is constructed from the XML node, propNode, - * that is a child of the node and specifies a type of + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ LTPspecies_Const::LTPspecies_Const( const XML_Node &propNode, @@ -139,9 +140,10 @@ namespace Cantera { /////////////////////////////////////////////////////////////// //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a constant value. - /** The transport property is constructed from the XML node, propNode, - * that is a child of the node and specifies a type of + //! expressed in extended Arrhenius form. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ LTPspecies_Arrhenius::LTPspecies_Arrhenius( const XML_Node &propNode, @@ -190,7 +192,7 @@ namespace Cantera { return *this; } - //! Return the value for this transport property evaluated + //! Return the pure species value for this transport property evaluated //! from the Arrhenius expression /** * In general the Arrhenius expression is @@ -207,6 +209,9 @@ namespace Cantera { * \f[ * \mu = A T^n \exp( + E / R T ). * \f] + * + * Any temperature and composition dependence will be + * adjusted internally according to the information provided. */ doublereal LTPspecies_Arrhenius::getSpeciesTransProp( ) { @@ -236,9 +241,10 @@ namespace Cantera { /////////////////////////////////////////////////////////////// //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a constant value. - /** The transport property is constructed from the XML node, propNode, - * that is a child of the node and specifies a type of + //! expressed as a polynomial in temperature. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ LTPspecies_Poly::LTPspecies_Poly( const XML_Node &propNode, diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index 3f2be9bfa..29fb0bbc9 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -70,23 +70,22 @@ namespace Cantera { //! specific liquid-phase species. /** * Subclasses handle different means of specifying transport properties - * like constant, Arrhenius or polynomial fits. In its current state, + * like constant, %Arrhenius or polynomial fits. In its current state, * it is primarily suitable for specifying temperature dependence, but * the adjustCoeffsForComposition() method can be implemented to * adjust for composition dependence. * Mixing rules for computing mixture transport properties are handled - * separately in + * separately in LiquidTranInteraction subclasses. */ class LTPspecies { public: //! Construct an LTPspecies object for a liquid tranport property. - /** - * The transport property is constructed from the - * XML node, propNode, that is a child of the + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity). + * transport property (like viscosity) */ LTPspecies( const XML_Node &propNode = 0, std::string name = "-", @@ -115,7 +114,7 @@ namespace Cantera { * The pure species transport property (i.e. pure species viscosity) * is returned. Any temperature and composition dependence will be * adjusted internally according to the information provided by the - * thermo object. + * subclass object. */ virtual doublereal getSpeciesTransProp( ) { return 0.0; } @@ -165,8 +164,14 @@ namespace Cantera { //! Class LiquidTransportData holds transport parameters for a //! specific liquid-phase species. /** + * A LiquidTransportData object is created for each species. + * * This class is mainly used to collect transport properties - * from the parse phase and transfer them to the Transport class. + * from the parse phase in the TranportFactory and transfer + * them to the Transport class. Transport properties are + * expressed by subclasses of LTPspecies. + * One may need to be careful about deleting pointers to LTPspecies + * objects created in the TransportFactory. */ class LiquidTransportData { @@ -176,12 +181,14 @@ namespace Cantera { speciesName("-") { } - //! copy constructor + //! Copy constructor LiquidTransportData( const LiquidTransportData &right ) ; //! Assignment operator LiquidTransportData& operator=(const LiquidTransportData& right ); + //! A LiquidTransportData object is instantiated for each species. + //! This is the species name for which this object is instantiated. std::string speciesName; //! Model type for the hydroradius @@ -206,6 +213,22 @@ namespace Cantera { //! Class LTPspecies_Const holds transport parameters for a //! specific liquid-phase species when the transport property //! is just a constant value. + /** + * As an example of the input required for LTPspecies_Const + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * 1.000 + * + * + * + * + * \endverbatim + */ class LTPspecies_Const : public LTPspecies{ public: @@ -227,8 +250,7 @@ namespace Cantera { /*! * The pure species transport property (i.e. pure species viscosity) * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided by the - * thermo object. + * adjusted internally according to the information provided. */ doublereal getSpeciesTransProp( ); @@ -246,7 +268,26 @@ namespace Cantera { //! Class LTPspecies_Arrhenius holds transport parameters for a //! specific liquid-phase species when the transport property - //! is just a constant value. + //! is expressed in Arrhenius form. + /** + * As an example of the input required for LTPspecies_Arrhenius + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * + * 6.578e-5 + * 0.0 + * 23788.e3 + * + * + * + * + * \endverbatim + */ class LTPspecies_Arrhenius : public LTPspecies{ public: @@ -264,12 +305,26 @@ namespace Cantera { virtual ~LTPspecies_Arrhenius( ) { } - //! Returns the pure species tranport property - /*! - * The pure species transport property (i.e. pure species viscosity) - * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided by the - * thermo object. + //! Return the pure species value for this transport property evaluated + //! from the Arrhenius expression + /** + * In general the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( - E / R T ). + * \f] + * + * Note that for viscosity, the convention is such that + * a positive activation energy corresponds to the typical + * case of a positive argument to the exponential so that + * the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( + E / R T ). + * \f] + * + * Any temperature and composition dependence will be + * adjusted internally according to the information provided. */ doublereal getSpeciesTransProp( ); @@ -299,7 +354,23 @@ namespace Cantera { //! Class LTPspecies_Poly holds transport parameters for a //! specific liquid-phase species when the transport property - //! is just a constant value. + //! is expressed as a polynomial in temperature. + /** + * As an example of the input required for LTPspecies_Poly + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * 0.6, -15.0e-5 + * + * + * + * + * \endverbatim + */ class LTPspecies_Poly : public LTPspecies{ public: @@ -321,8 +392,7 @@ namespace Cantera { /*! * The pure species transport property (i.e. pure species viscosity) * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided by the - * thermo object. + * adjusted internally according to the information provided. */ doublereal getSpeciesTransProp( ); diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 709b68ef4..9267999c4 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -36,12 +36,12 @@ namespace Cantera { //! Composition dependence type for liquid mixture transport properties /*! * Types of temperature dependencies: - * 0 - Mixture calculations with this property are not allowed - * 1 - Use solvent (species 0) properties - * 2 - Properties weighted linearly by mole fractions - * 3 - Properties weighted linearly by mass fractions - * 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) - * 5 - Interactions given pairwise between each possible species (i.e. D_ij) + * - 0 - Mixture calculations with this property are not allowed + * - 1 - Use solvent (species 0) properties + * - 2 - Properties weighted linearly by mole fractions + * - 3 - Properties weighted linearly by mass fractions + * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) * * \verbatim * @@ -96,6 +96,26 @@ namespace Cantera { }; + //! Base class to handle transport property evaluation in a mixture. + /** + * In a mixture, the mixture transport properties will generally depend on + * the contributions of each of the pure species transport properties. + * Many composition dependencies are possible. This class, + * LiquidTranInteraction, is designed to be a base class for the + * implementation of various models for the mixing of pure species + * transport properties. + * + * There are two very broad types of transport properties to consider. + * First, there are properties for which a mixture value can be + * obtained through some mixing rule. These are obtained using the + * method getMixTransProp(). Viscosity is typical of this. + * Second there are properties for which a matrix of properties may + * exist. This matrix of properties is obtained from the method + * getMatrixTransProp(). Diffusion coefficients are of this type. + * Subclasses should implement the appropriate one or both of + * these methods. + * + */ class LiquidTranInteraction { public: @@ -192,25 +212,6 @@ namespace Cantera { //! Takes enum LiquidTranMixingModel LiquidTranMixingModel model_viscosity; - //! Energies of molecular interaction associated with viscosity. - /** - * These multiply the mixture viscosity by - * \f[ \exp( \sum_{i} \sum_{j} X_i X_j ( S_{i,j} + E_{i,j} / T ) ) \f]. - * - * The overall formula for the logarithm of the mixture viscosity is - * - * \f[ \ln \eta_{mix} = \sum_i X_i \ln \eta_i - * + \sum_i \sum_j X_i X_j ( S_{i,j} + E_{i,j} / T ) \f]. - */ - DenseMatrix visc_Eij; - - //! Entropies of molecular interaction associated with viscosity. - DenseMatrix visc_Sij; - - //! Model for species interaction effects for thermal conductivity - //! Takes enum LiquidTranMixingModel - LiquidTranMixingModel model_thermalCond; - //! Interaction associated with linear weighting of //! thermal conductivity. /** @@ -286,7 +287,15 @@ namespace Cantera { }; - + //! Simple mole fraction weighting of transport properties + /** + * This model weights the transport property by the mole + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ \eta_{mix} = \sum_i X_i \eta_i + * + \sum_i \sum_j X_i X_j A_{i,j} \f]. + */ class LTI_MoleFracs : public LiquidTranInteraction { public: @@ -321,6 +330,15 @@ namespace Cantera { }; + //! Simple mass fraction weighting of transport properties + /** + * This model weights the transport property by the mass + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ \eta_{mix} = \sum_i Y_i \eta_i + * + \sum_i \sum_j Y_i Y_j A_{i,j} \f]. + */ class LTI_MassFracs : public LiquidTranInteraction { public: @@ -355,6 +373,46 @@ namespace Cantera { }; + //! Mixing rule using logarithms of the mole fractions + /** + * This model is based on the idea that liquid molecules are + * generally interacting with some energy and entropy of interaction. + * For transport properties that depend on these energies of + * interaction, the mixture transport property can be written + * in terms of its logarithm + * + * \f[ \ln \eta_{mix} = \sum_i X_i \ln \eta_i + * + \sum_i \sum_j X_i X_j ( S_{i,j} + E_{i,j} / T ) + * \f]. + * + * These additional interaction terms multiply the mixture property by + * \f[ \exp( \sum_{i} \sum_{j} X_i X_j ( S_{i,j} + E_{i,j} / T ) ) \f] + * so that the self-interaction terms \f$ S_{i,j} \f$ and + * \f$ E_{i,j} \f$ should be zero. + * + * Note that the energies and entropies of interaction should be + * a function of the composition themselves, but this is not yet + * implemented. (We might follow the input of Margules model + * thermodynamic data for the purpose of implementing this.) + * + * Sample input for this method is + * \verbatim + * + * + * + * + * + * -1.0e3 + * 80.0e-5 + * + * + * + * + * \endverbatim + */ class LTI_Log_MoleFracs : public LiquidTranInteraction { public: @@ -389,6 +447,29 @@ namespace Cantera { }; + //! Transport properties that act like pairwise interactions + //! as in binary diffusion coefficients. + /** + * This class holds parameters for transport properties expressed + * as a matrix of pairwise interaction parameters. + * Input can be provided for constant or Arrhenius forms of the + * separate parameters. + * + * Sample input for this method is + * \verbatim + * + * + * + * + * 1.0e-8 + * 24.0e6 + * + * + * + * + * \endverbatim + * + */ class LTI_Pairwise_Interaction : public LiquidTranInteraction { public: From cb5e85ed5cd867671f950abf65be47bbbbcd5de8 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 18 Dec 2009 21:30:24 +0000 Subject: [PATCH 078/446] Removed parsing for old Liquid Transport Interaction models --- Cantera/src/transport/TransportFactory.cpp | 222 --------------------- 1 file changed, 222 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 921ee4236..5b56670dd 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1133,229 +1133,7 @@ namespace Cantera { catch(CanteraError) { ; } - return; - - std::string type; - std::string speciesA; - std::string speciesB; - /* - * Viscosity - */ - if ( transportNode.hasChild("viscosity")) { - XML_Node& viscosityNode = transportNode.child("viscosity"); - if ( viscosityNode.hasChild("compositionDependence") ) { - XML_Node& compositionNode = viscosityNode.child("compositionDependence"); - std::string compositionModel = compositionNode.attrib("model"); - if ( compositionModel == "" ) { - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "transport::viscosity XML node doesn't have a model string"); - } else if ( compositionModel == "none"){ - trParam.model_viscosity = LTI_MODEL_NONE; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_NONE interactions not implemented for viscosity"); - } else if ( compositionModel == "solvent"){ - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "solvent interactions not implemented"); - } else if ( compositionModel == "moleFractions"){ - trParam.model_viscosity = LTI_MODEL_MOLEFRACS; - } else if ( compositionModel == "massFractions"){ - trParam.model_viscosity = LTI_MODEL_MASSFRACS; - } else if ( compositionModel == "logMoleFractions"){ - trParam.model_viscosity = LTI_MODEL_LOG_MOLEFRACS; - } else if ( compositionModel == "pairwiseInteraction"){ - trParam.model_viscosity = LTI_MODEL_PAIRWISE_INTERACTION; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_PAIRWISE_INTERACTION interactions not implemented for viscosity"); - } - int num = compositionNode.nChildren(); - for (int iChild = 0; iChild < num; iChild++) { - XML_Node &xmlChild = compositionNode.child(iChild); - std::string nodeName = lowercase( xmlChild.name() ); - if ( nodeName != "interaction" ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "expected element and got " + nodeName ); - speciesA = xmlChild.attrib("speciesA"); - speciesB = xmlChild.attrib("speciesB"); - int iSpecies = trParam.thermo->speciesIndex( speciesA ); - if ( iSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesA ); - int jSpecies = trParam.thermo->speciesIndex( speciesB ); - if ( jSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesB ); - trParam.visc_Eij(iSpecies,jSpecies) = getFloat( xmlChild, "Eij", "toSI" ); - trParam.visc_Eij(jSpecies,iSpecies) = trParam.visc_Eij(iSpecies,jSpecies) ; - trParam.visc_Sij(iSpecies,jSpecies) = getFloat( xmlChild, "Sij", "toSI" ); - trParam.visc_Sij(jSpecies,iSpecies) = trParam.visc_Sij(iSpecies,jSpecies) ; - } - } - } - - - /* - * Thermal conductivity - */ - if ( transportNode.hasChild("thermalConductivity")) { - XML_Node& thermCondNode = transportNode.child("thermalConductivity"); - if ( thermCondNode.hasChild("compositionDependence") ) { - XML_Node& compositionNode = thermCondNode.child("compositionDependence"); - std::string compositionModel = compositionNode.attrib("model"); - if ( compositionModel == "" ) { - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "transport::thermalConductivity XML node doesn't have a model string"); - } else if ( compositionModel == "none"){ - trParam.model_thermalCond = LTI_MODEL_NONE; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_NONE interactions not implemented for thermalConductivity"); - } else if ( compositionModel == "solvent"){ - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "solvent interactions not implemented"); - } else if ( compositionModel == "moleFractions"){ - trParam.model_thermalCond = LTI_MODEL_MOLEFRACS; - } else if ( compositionModel == "massFractions"){ - trParam.model_thermalCond = LTI_MODEL_MASSFRACS; - } else if ( compositionModel == "logMoleFractions"){ - trParam.model_thermalCond = LTI_MODEL_LOG_MOLEFRACS; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_LOG_MOLEFRACS interactions not implemented for thermalConductivity"); - } else if ( compositionModel == "pairwiseInteraction"){ - trParam.model_thermalCond = LTI_MODEL_PAIRWISE_INTERACTION; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_PAIRWISE_INTERACTION interactions not implemented for thermalConductivity"); - } - int num = compositionNode.nChildren(); - for (int iChild = 0; iChild < num; iChild++) { - XML_Node &xmlChild = compositionNode.child(iChild); - std::string nodeName = lowercase( xmlChild.name() ); - if ( nodeName != "interaction" ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "expected element and got <" + nodeName + ">" ); - speciesA = xmlChild.attrib("speciesA"); - speciesB = xmlChild.attrib("speciesB"); - int iSpecies = trParam.thermo->speciesIndex( speciesA ); - if ( iSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesA ); - int jSpecies = trParam.thermo->speciesIndex( speciesB ); - if ( jSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesB ); - trParam.thermalCond_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); - trParam.thermalCond_Aij(jSpecies,iSpecies) = trParam.thermalCond_Aij(iSpecies,jSpecies) ; - } - } - } - - - /* - * Species Diffusivity - */ - if ( transportNode.hasChild("speciesDiffusivity")) { - XML_Node& diffusivityNode = transportNode.child("speciesDiffusivity"); - if ( diffusivityNode.hasChild("compositionDependence") ) { - XML_Node& compositionNode = diffusivityNode.child("compositionDependence"); - std::string compositionModel = compositionNode.attrib("model"); - if ( compositionModel == "" ) { - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "transport::speciesDiffusivity XML node doesn't have a model string"); - } else if ( compositionModel == "none"){ - trParam.model_speciesDiffusivity = LTI_MODEL_NONE; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_NONE interactions not implemented for speciesDiffusivity"); - } else if ( compositionModel == "solvent"){ - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "solvent interactions not implemented"); - } else if ( compositionModel == "moleFractions"){ - trParam.model_speciesDiffusivity = LTI_MODEL_MOLEFRACS; - } else if ( compositionModel == "massFractions"){ - trParam.model_speciesDiffusivity = LTI_MODEL_MASSFRACS; - } else if ( compositionModel == "logMoleFractions"){ - trParam.model_speciesDiffusivity = LTI_MODEL_LOG_MOLEFRACS; - } else if ( compositionModel == "pairwiseInteraction"){ - trParam.model_speciesDiffusivity = LTI_MODEL_PAIRWISE_INTERACTION; - } - int num = compositionNode.nChildren(); - for (int iChild = 0; iChild < num; iChild++) { - XML_Node &xmlChild = compositionNode.child(iChild); - std::string nodeName = lowercase( xmlChild.name() ); - if ( nodeName != "interaction" ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "expected element and got " + nodeName ); - speciesA = xmlChild.attrib("speciesA"); - speciesB = xmlChild.attrib("speciesB"); - int iSpecies = trParam.thermo->speciesIndex( speciesA ); - if ( iSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesA ); - int jSpecies = trParam.thermo->speciesIndex( speciesB ); - if ( jSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesB ); - trParam.diff_Dij(iSpecies,jSpecies) = getFloat( xmlChild, "Dij", "toSI" ); - trParam.diff_Dij(jSpecies,iSpecies) = trParam.diff_Dij(iSpecies,jSpecies) ; - } - } - } - - /* - * Hydrodynamic radius - */ - if ( transportNode.hasChild("hydrodynamicRadius")) { - XML_Node& radiusNode = transportNode.child("hydrodynamicRadius"); - if ( radiusNode.hasChild("compositionDependence") ) { - XML_Node& compositionNode = radiusNode.child("compositionDependence"); - std::string compositionModel = compositionNode.attrib("model"); - if ( compositionModel == "" ) { - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "transport::hydrodynamicRadius XML node doesn't have a model string"); - } else if ( compositionModel == "none"){ - trParam.model_thermalCond = LTI_MODEL_NONE; - } else if ( compositionModel == "solvent"){ - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "solvent interactions not implemented"); - } else if ( compositionModel == "moleFractions"){ - trParam.model_thermalCond = LTI_MODEL_MOLEFRACS; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_MOLEFRACS interactions not implemented for hydrodynamicRadius"); - } else if ( compositionModel == "massFractions"){ - trParam.model_thermalCond = LTI_MODEL_MASSFRACS; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_MASSFRACS interactions not implemented for hydrodynamicRadius"); - } else if ( compositionModel == "logMoleFractions"){ - trParam.model_thermalCond = LTI_MODEL_LOG_MOLEFRACS; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_LOG_MOLEFRACS interactions not implemented for hydrodynamicRadius"); - } else if ( compositionModel == "pairwiseInteraction"){ - trParam.model_thermalCond = LTI_MODEL_PAIRWISE_INTERACTION; - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "LTI_MODEL_PAIRWISE_INTERACTION interactions not implemented for hydrodynamicRadius"); - } - int num = compositionNode.nChildren(); - for (int iChild = 0; iChild < num; iChild++) { - XML_Node &xmlChild = compositionNode.child(iChild); - std::string nodeName = lowercase( xmlChild.name() ); - if ( nodeName != "interaction" ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "expected element and got <" + nodeName + ">" ); - speciesA = xmlChild.attrib("speciesA"); - speciesB = xmlChild.attrib("speciesB"); - int iSpecies = trParam.thermo->speciesIndex( speciesA ); - if ( iSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesA ); - int jSpecies = trParam.thermo->speciesIndex( speciesB ); - if ( jSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesB ); - trParam.radius_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); - trParam.radius_Aij(jSpecies,iSpecies) = trParam.radius_Aij(iSpecies,jSpecies) ; - } - } - } - - } /********************************************************* From 7bf73c7db23e0171e308125b11bea50046bafe49 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:29:11 +0000 Subject: [PATCH 079/446] Reduced warning messages by adding operator precedence parenthesis. --- ext/f2c_math/ddaspk.c | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ext/f2c_math/ddaspk.c b/ext/f2c_math/ddaspk.c index 44ffb2319..052eb72cd 100644 --- a/ext/f2c_math/ddaspk.c +++ b/ext/f2c_math/ddaspk.c @@ -8561,7 +8561,7 @@ L30: } i__2 = km1; for (j = 1; j <= i__2; ++j) { - i__ = (j - 1 << 1) + 1; + i__ = ((j - 1) << 1) + 1; t1 = a[j + k * a_dim1]; t2 = a[j + 1 + k * a_dim1]; c__ = q[i__]; @@ -8617,7 +8617,7 @@ L70: /* ----------------------------------------------------------------------- */ i__1 = nm1; for (k = 1; k <= i__1; ++k) { - i__ = (k - 1 << 1) + 1; + i__ = ((k - 1) << 1) + 1; t1 = a[k + *n * a_dim1]; t2 = a[k + 1 + *n * a_dim1]; c__ = q[i__]; @@ -8745,7 +8745,7 @@ L130: i__1 = *n; for (k = 1; k <= i__1; ++k) { kp1 = k + 1; - iq = (k - 1 << 1) + 1; + iq = ((k - 1) << 1) + 1; c__ = q[iq]; s = q[iq + 1]; t1 = b[k]; From 0708f2b9426711b045df5de8f2eb0bfaa1f9500d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:31:52 +0000 Subject: [PATCH 080/446] Added parenthesis to reduce warning messages. || logical element always takes the least precedence. --- ext/f2c_math/xermsg.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ext/f2c_math/xermsg.c b/ext/f2c_math/xermsg.c index b1eac2ab1..2f23e5844 100644 --- a/ext/f2c_math/xermsg.c +++ b/ext/f2c_math/xermsg.c @@ -364,7 +364,7 @@ static logical c_true = TRUE_; /* THEN WHETHER THE PROGRAM WILL CONTINUE. */ - if (mkntrl == 2 && *level >= 1 || mkntrl == 1 && *level == 2) { + if ((mkntrl == 2 && *level >= 1) || (mkntrl == 1 && *level == 2)) { i__1 = ltemp; s_copy(temp + i__1, " PROG ABORTED,", ltemp + 14 - i__1, (ftnlen) 14); @@ -437,7 +437,7 @@ L20: /* CONTROL FLAG IS SET FOR RECOVERY, THEN RETURN. */ L30: - if (*level <= 0 || *level == 1 && mkntrl <= 1) { + if ((*level <= 0) || (*level == 1 && mkntrl <= 1)) { return 0; } From 24f94885c4db2dfc0384f5390171c7d7d4c7f319 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:34:13 +0000 Subject: [PATCH 081/446] Added parenthesis to reduce warning messages --- ext/f2c_math/j4save.c | 2 +- ext/f2c_math/xersve.c | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ext/f2c_math/j4save.c b/ext/f2c_math/j4save.c index 733e9e848..db219b885 100644 --- a/ext/f2c_math/j4save.c +++ b/ext/f2c_math/j4save.c @@ -69,7 +69,7 @@ integer j4save_(integer *iwhich, integer *ivalue, logical *iset) /* ***END PROLOGUE J4SAVE */ /* SAVE IPARAM */ /* ***FIRST EXECUTABLE STATEMENT J4SAVE */ - ret_val = iparam[(0 + (0 + (*iwhich - 1 << 2))) / 4]; + ret_val = iparam[(0 + (0 + ((*iwhich - 1) << 2))) / 4]; if (*iset) { iparam[*iwhich - 1] = *ivalue; } diff --git a/ext/f2c_math/xersve.c b/ext/f2c_math/xersve.c index 3c93c4161..94735e8e2 100644 --- a/ext/f2c_math/xersve.c +++ b/ext/f2c_math/xersve.c @@ -143,8 +143,8 @@ static integer c__1 = 1; for (i__ = 1; i__ <= i__2; ++i__) { io___9.ciunit = iunit; s_wsfe(&io___9); - do_fio(&c__1, libtab + (i__ - 1 << 3), (ftnlen)8); - do_fio(&c__1, subtab + (i__ - 1 << 3), (ftnlen)8); + do_fio(&c__1, libtab + ((i__ - 1) << 3), (ftnlen)8); + do_fio(&c__1, subtab + ((i__ - 1) << 3), (ftnlen)8); do_fio(&c__1, mestab + (i__ - 1) * 20, (ftnlen)20); do_fio(&c__1, (char *)&nertab[i__ - 1], (ftnlen)sizeof( integer)); @@ -187,8 +187,8 @@ static integer c__1 = 1; s_copy(mes, messg, (ftnlen)20, messg_len); i__1 = nmsg; for (i__ = 1; i__ <= i__1; ++i__) { - if (s_cmp(lib, libtab + (i__ - 1 << 3), (ftnlen)8, (ftnlen)8) == - 0 && s_cmp(sub, subtab + (i__ - 1 << 3), (ftnlen)8, ( + if (s_cmp(lib, libtab + ((i__ - 1) << 3), (ftnlen)8, (ftnlen)8) == + 0 && s_cmp(sub, subtab + ((i__ - 1) << 3), (ftnlen)8, ( ftnlen)8) == 0 && s_cmp(mes, mestab + (i__ - 1) * 20, ( ftnlen)20, (ftnlen)20) == 0 && *nerr == nertab[i__ - 1] && *level == levtab[i__ - 1]) { @@ -204,8 +204,8 @@ static integer c__1 = 1; /* Empty slot found for new message. */ ++nmsg; - s_copy(libtab + (i__ - 1 << 3), lib, (ftnlen)8, (ftnlen)8); - s_copy(subtab + (i__ - 1 << 3), sub, (ftnlen)8, (ftnlen)8); + s_copy(libtab + ((i__ - 1) << 3), lib, (ftnlen)8, (ftnlen)8); + s_copy(subtab + ((i__ - 1) << 3), sub, (ftnlen)8, (ftnlen)8); s_copy(mestab + (i__ - 1) * 20, mes, (ftnlen)20, (ftnlen)20); nertab[i__ - 1] = *nerr; levtab[i__ - 1] = *level; From a7fd7aa131cc3eb5d0e5a7c065733f24be22de43 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:41:37 +0000 Subject: [PATCH 082/446] Added parenthesis to reduce warning levels. --- ext/f2c_libs/lbitbits.c | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ext/f2c_libs/lbitbits.c b/ext/f2c_libs/lbitbits.c index 5b6ccf72d..2f44abf9d 100644 --- a/ext/f2c_libs/lbitbits.c +++ b/ext/f2c_libs/lbitbits.c @@ -44,11 +44,11 @@ lbit_cshift(integer a, integer b, integer len) full_len: if (b >= 0) { b %= LONGBITS; - return (integer)(x << b | x >> LONGBITS -b ); + return (integer)(x << b | x >> (LONGBITS -b) ); } b = -b; b %= LONGBITS; - return (integer)(x << LONGBITS - b | x >> b); + return (integer)(x << (LONGBITS - b) | x >> b); } y = z = (unsigned long)-1; y <<= len; @@ -57,11 +57,11 @@ lbit_cshift(integer a, integer b, integer len) x &= z; if (b >= 0) { b %= len; - return (integer)(y | z & (x << b | x >> len - b)); + return (integer)((y) | (z & (x << b | x >> (len - b)))); } b = -b; b %= len; - return (integer)(y | z & (x >> b | x << len - b)); + return (integer)((y) | (z & (x >> b | x << (len - b)))); } #ifdef __cplusplus } From 5c644ca58f0557ac17adc58e714bb5f76212eefc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:45:29 +0000 Subject: [PATCH 083/446] Adding parenthesis to reduce warnings --- ext/f2c_libs/dfe.c | 4 ++-- ext/f2c_libs/due.c | 4 ++-- ext/f2c_libs/endfile.c | 2 +- ext/f2c_libs/iio.c | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ext/f2c_libs/dfe.c b/ext/f2c_libs/dfe.c index c6b10d0e9..cd2e673d6 100644 --- a/ext/f2c_libs/dfe.c +++ b/ext/f2c_libs/dfe.c @@ -101,7 +101,7 @@ integer s_rdfe(cilist *a) int n; if(!f__init) f_init(); f__reading=1; - if(n=c_dfe(a))return(n); + if((n=c_dfe(a))) return(n); if(f__curunit->uwrt && f__nowreading(f__curunit)) err(a->cierr,errno,"read start"); f__getn = y_getc; @@ -123,7 +123,7 @@ integer s_wdfe(cilist *a) int n; if(!f__init) f_init(); f__reading=0; - if(n=c_dfe(a)) return(n); + if((n=c_dfe(a))) return(n); if(f__curunit->uwrt != 1 && f__nowwriting(f__curunit)) err(a->cierr,errno,"startwrt"); f__putn = x_putc; diff --git a/ext/f2c_libs/due.c b/ext/f2c_libs/due.c index a7f4cec46..e463448f8 100644 --- a/ext/f2c_libs/due.c +++ b/ext/f2c_libs/due.c @@ -37,7 +37,7 @@ integer s_rdue(cilist *a) { int n; f__reading=1; - if(n=c_due(a)) return(n); + if((n=c_due(a))) return(n); if(f__curunit->uwrt && f__nowreading(f__curunit)) err(a->cierr,errno,"read start"); return(0); @@ -50,7 +50,7 @@ integer s_wdue(cilist *a) { int n; f__reading=0; - if(n=c_due(a)) return(n); + if((n=c_due(a))) return(n); if(f__curunit->uwrt != 1 && f__nowwriting(f__curunit)) err(a->cierr,errno,"write start"); return(0); diff --git a/ext/f2c_libs/endfile.c b/ext/f2c_libs/endfile.c index 04020d380..8d7b7ea33 100644 --- a/ext/f2c_libs/endfile.c +++ b/ext/f2c_libs/endfile.c @@ -43,7 +43,7 @@ integer f_end(alist *a) if(b->ufd==NULL) { char nbuf[10]; sprintf(nbuf,"fort.%ld",(long)a->aunit); - if (tf = FOPEN(nbuf, f__w_mode[0])) + if ((tf = FOPEN(nbuf, f__w_mode[0]))) fclose(tf); return(0); } diff --git a/ext/f2c_libs/iio.c b/ext/f2c_libs/iio.c index 8553efcf9..6641f6ead 100644 --- a/ext/f2c_libs/iio.c +++ b/ext/f2c_libs/iio.c @@ -88,7 +88,7 @@ integer s_rsfi(a) icilist *a; integer s_rsfi(icilist *a) #endif { int n; - if(n=c_si(a)) return(n); + if((n=c_si(a))) return(n); f__reading=1; f__doed=rd_ed; f__doned=rd_ned; @@ -120,7 +120,7 @@ integer s_wsfi(a) icilist *a; integer s_wsfi(icilist *a) #endif { int n; - if(n=c_si(a)) return(n); + if((n=c_si(a))) return(n); f__reading=0; f__doed=w_ed; f__doned=w_ned; From 44dc8c9084f9ee2f51fc8bc6e542515a7710dab0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:53:44 +0000 Subject: [PATCH 084/446] Added parentheses to avind warning messages. --- ext/f2c_libs/inquire.c | 49 +++++++++++++++++++++++++++--------------- 1 file changed, 32 insertions(+), 17 deletions(-) diff --git a/ext/f2c_libs/inquire.c b/ext/f2c_libs/inquire.c index 5936a674c..033e9c019 100644 --- a/ext/f2c_libs/inquire.c +++ b/ext/f2c_libs/inquire.c @@ -63,55 +63,70 @@ integer f_inqu(inlist *a) p=NULL; } } - if(a->inex!=NULL) - if(byfile && x != -1 || !byfile && p!=NULL) - *a->inex=1; - else *a->inex=0; - if(a->inopen!=NULL) + if(a->inex!=NULL) { + if((byfile && x != -1) || (!byfile && p!=NULL)) { + *a->inex=1; + } else { + *a->inex=0; + } + } + if(a->inopen!=NULL) { if(byfile) *a->inopen=(p!=NULL); else *a->inopen=(p!=NULL && p->ufd!=NULL); + } if(a->innum!=NULL) *a->innum= p-f__units; - if(a->innamed!=NULL) - if(byfile || p!=NULL && p->ufnm!=NULL) + if(a->innamed!=NULL) { + if(byfile || (p!=NULL && p->ufnm!=NULL)) *a->innamed=1; else *a->innamed=0; - if(a->inname!=NULL) + } + if(a->inname!=NULL) { if(byfile) b_char(buf,a->inname,a->innamlen); else if(p!=NULL && p->ufnm!=NULL) b_char(p->ufnm,a->inname,a->innamlen); - if(a->inacc!=NULL && p!=NULL && p->ufd!=NULL) + } + if(a->inacc!=NULL && p!=NULL && p->ufd!=NULL) { if(p->url) b_char("DIRECT",a->inacc,a->inacclen); else b_char("SEQUENTIAL",a->inacc,a->inacclen); - if(a->inseq!=NULL) + } + if(a->inseq!=NULL) { if(p!=NULL && p->url) b_char("NO",a->inseq,a->inseqlen); else b_char("YES",a->inseq,a->inseqlen); - if(a->indir!=NULL) + } + if(a->indir!=NULL) { if(p==NULL || p->url) b_char("YES",a->indir,a->indirlen); else b_char("NO",a->indir,a->indirlen); - if(a->infmt!=NULL) + } + if(a->infmt!=NULL) { if(p!=NULL && p->ufmt==0) b_char("UNFORMATTED",a->infmt,a->infmtlen); else b_char("FORMATTED",a->infmt,a->infmtlen); - if(a->inform!=NULL) + } + if(a->inform!=NULL) { if(p!=NULL && p->ufmt==0) b_char("NO",a->inform,a->informlen); else b_char("YES",a->inform,a->informlen); - if(a->inunf) + } + if(a->inunf) { if(p!=NULL && p->ufmt==0) b_char("YES",a->inunf,a->inunflen); - else if (p!=NULL) b_char("NO",a->inunf,a->inunflen); - else b_char("UNKNOWN",a->inunf,a->inunflen); + else { + if (p!=NULL) b_char("NO",a->inunf,a->inunflen); + else b_char("UNKNOWN",a->inunf,a->inunflen); + } + } if(a->inrecl!=NULL && p!=NULL) *a->inrecl=p->url; if(a->innrec!=NULL && p!=NULL && p->url>0) *a->innrec=(ftnint)(FTELL(p->ufd)/p->url+1); - if(a->inblank && p!=NULL && p->ufmt) + if(a->inblank && p!=NULL && p->ufmt) { if(p->ublnk) b_char("ZERO",a->inblank,a->inblanklen); else b_char("NULL",a->inblank,a->inblanklen); + } return(0); } From ee684289513efbb7b34a117dee3052df931300df Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 17:56:40 +0000 Subject: [PATCH 085/446] Added parenthesis to avoid warning messages. --- ext/f2c_libs/lread.c | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/ext/f2c_libs/lread.c b/ext/f2c_libs/lread.c index bf54a2e41..c23c0ad58 100644 --- a/ext/f2c_libs/lread.c +++ b/ext/f2c_libs/lread.c @@ -107,7 +107,7 @@ flag f__lquit; int f__lcount,f__ltype,nml_read; char *f__lchar; double f__lx,f__ly; -#define ERR(x) if(n=(x)) return(n) +#define ERR(x) if((n=(x))) return(n) #define GETC(x) (x=(*l_getc)()) #define Ungetc(x,y) (*l_ungetc)(x,y) @@ -292,11 +292,12 @@ l_C(Void) f__lquit = 2; return 0; } - if (rd_count(ch)) + if (rd_count(ch)) { if(!f__cf || !feof(f__cf)) errfl(f__elist->cierr,112,"complex format"); else err(f__elist->cierr,(EOF),"lread"); + } if(GETC(ch)!='*') { if(!f__cf || !feof(f__cf)) @@ -315,7 +316,7 @@ l_C(Void) Ungetc(ch,f__cf); nml_save = nml_read; nml_read = 0; - if (ch = l_R(1,0)) + if ((ch = l_R(1,0))) return ch; if (!f__ltype) errfl(f__elist->cierr,112,"no real part"); @@ -327,7 +328,7 @@ l_C(Void) } while(iswhit(GETC(ch))); (void) Ungetc(ch,f__cf); - if (ch = l_R(1,0)) + if ((ch = l_R(1,0))) return ch; if (!f__ltype) errfl(f__elist->cierr,112,"no imaginary part"); @@ -354,7 +355,7 @@ l_C(Void) nmL_getc(Void) { int rv; - if (rv = *nmL_next++) + if ((rv = *nmL_next++)) return rv; l_getc = nmL_getc_save; l_ungetc = nmL_ungetc_save; @@ -436,11 +437,12 @@ l_L(Void) if(isdigit(ch)) { rd_count(ch); - if(GETC(ch)!='*') + if(GETC(ch)!='*') { if(!f__cf || !feof(f__cf)) errfl(f__elist->cierr,112,"no star"); else err(f__elist->cierr,(EOF),"lread"); + } GETC(ch); } sawdot = 0; @@ -788,7 +790,7 @@ integer s_rsle(cilist *a) f__reading=1; f__external=1; f__formatted=1; - if(n=c_le(a)) return(n); + if((n=c_le(a))) return(n); f__lioproc = l_read; f__lquit = 0; f__lcount = 0; From c865e0e4d776c7b32e642381e0d33735a448f0a5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 18:15:15 +0000 Subject: [PATCH 086/446] Changes to allow the program to compile! visc_Eij and visc_Sij seem to have been taken out. And, the code no longer needs to resize them. Also took out some warning messages --- Cantera/src/transport/LiquidTransportData.cpp | 2 +- Cantera/src/transport/SolidTransport.cpp | 4 ++-- Cantera/src/transport/TransportFactory.cpp | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 531763b51..17ba9f1e0 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -295,7 +295,7 @@ namespace Cantera { doublereal t = m_thermo->temperature(); if (t != m_temp) { double tempN = 1.0; - for ( int i = 0; i < m_coeffs.size() ; i++ ) { + for (int i = 0; i < (int) m_coeffs.size() ; i++) { m_prop += m_coeffs[i] * tempN; tempN *= m_temp; } diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index 0e723aad6..35d12d54e 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -31,7 +31,7 @@ namespace Cantera { //==================================================================================================================== SolidTransport::SolidTransport() : Transport() , - m_nmobile(0.0), + m_nmobile(0), m_Adiff(0), m_Ndiff(0), m_Ediff(0), @@ -48,7 +48,7 @@ namespace Cantera { //==================================================================================================================== SolidTransport::SolidTransport(const SolidTransport &right) : Transport(), - m_nmobile(0.0), + m_nmobile(0), m_Adiff(0), m_Ndiff(0), m_Ediff(0), diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 5b56670dd..7ae020cda 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -626,8 +626,8 @@ namespace Cantera { // Need to identify a method to obtain interaction matrices. // This will fill LiquidTransportParams members visc_Eij, visc_Sij - trParam.visc_Eij.resize(nsp,nsp); - trParam.visc_Sij.resize(nsp,nsp); + // trParam.visc_Eij.resize(nsp,nsp); + // trParam.visc_Sij.resize(nsp,nsp); trParam.thermalCond_Aij.resize(nsp,nsp); trParam.diff_Dij.resize(nsp,nsp); trParam.radius_Aij.resize(nsp,nsp); From ec3c7e37c7a1be0137db23e29acdcce6bc3c8cbc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Dec 2009 20:21:40 +0000 Subject: [PATCH 087/446] Fixed an error that caused sundials version 2.3 not to work as intended. --- Cantera/src/numerics/CVodesIntegrator.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Cantera/src/numerics/CVodesIntegrator.cpp b/Cantera/src/numerics/CVodesIntegrator.cpp index bf651bfea..15c545188 100644 --- a/Cantera/src/numerics/CVodesIntegrator.cpp +++ b/Cantera/src/numerics/CVodesIntegrator.cpp @@ -238,7 +238,7 @@ namespace Cantera { int flag; -#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION23) +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) flag = CVodeSensMalloc(m_cvode_mem, m_np, CV_STAGGERED, m_yS); if (flag != CV_SUCCESS) { throw CVodesErr("Error in CVodeSensMalloc"); @@ -291,7 +291,7 @@ namespace Cantera { if (!m_cvode_mem) throw CVodesErr("CVodeCreate failed."); int flag = 0; -#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION23) +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) if (m_itol == CV_SV) { // vector atol flag = CVodeMalloc(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol, @@ -370,7 +370,7 @@ namespace Cantera { m_fdata = new FuncData(&func, func.nparams()); //m_data = (void*)&func; -#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION23) +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) flag = CVodeSetFdata(m_cvode_mem, (void*)m_fdata); if (flag != CV_SUCCESS) { throw CVodesErr("CVodeSetFdata failed."); @@ -410,7 +410,7 @@ namespace Cantera { int result, flag; -#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION23) +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) if (m_itol == CV_SV) { result = CVodeReInit(m_cvode_mem, cvodes_rhs, m_t0, nv(m_y), m_itol, m_reltol, @@ -465,15 +465,15 @@ namespace Cantera { { double t; int flag; - double tretn; flag = CVode(m_cvode_mem, tout, nv(m_y), &t, CV_NORMAL); if (flag != CV_SUCCESS) throw CVodesErr(" CVodes error encountered."); -#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION23) +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) if (m_np > 0) { CVodeGetSens(m_cvode_mem, tout, m_yS); } #elif defined(SUNDIALS_VERSION_24) + double tretn; if (m_np > 0) { CVodeGetSens(m_cvode_mem, &tretn, m_yS); if (fabs(tretn - tout) > 1.0E-5) { From a7a59b84b8a2b96bc390c03aa846f5c693d9908a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 22 Dec 2009 22:23:53 +0000 Subject: [PATCH 088/446] Fixed an error in the assignment operator. The internal state of the VPSSMgr object must be resynced by calling stateState_TP() after the new VMSSMgr object is set up. --- Cantera/src/thermo/VPStandardStateTP.cpp | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/VPStandardStateTP.cpp b/Cantera/src/thermo/VPStandardStateTP.cpp index 8331f6d86..2c1da45e1 100644 --- a/Cantera/src/thermo/VPStandardStateTP.cpp +++ b/Cantera/src/thermo/VPStandardStateTP.cpp @@ -74,7 +74,7 @@ namespace Cantera { if (&b != this) { /* * Mostly, this is a passthrough to the underlying - * assignment operator for the ThermoPhae parent object. + * assignment operator for the ThermoPhase parent object. */ ThermoPhase::operator=(b); /* @@ -124,7 +124,12 @@ namespace Cantera { PDSS *ptmp = m_PDSS_storage[k]; ptmp->initAllPtrs(this, m_VPSS_ptr, m_spthermo); } - + /* + * Ok, the VPSSMgr object is ready for business. + * We need to resync the temperature and the pressure of the new standard states + * with what is storred in this object. + */ + m_VPSS_ptr->setState_TP(m_Tlast_ss, m_Plast_ss); } return *this; } From b0a7626dccd6c282f0a02335afe5e99dcdfb8980 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 23 Dec 2009 01:52:40 +0000 Subject: [PATCH 089/446] Doxygen update. No code changed. --- Cantera/src/transport/TransportBase.h | 92 +++++++++++++++++---------- 1 file changed, 57 insertions(+), 35 deletions(-) diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 152e9a936..097db665d 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -315,11 +315,11 @@ namespace Cantera { doublereal getElectricConduct( ); //! Compute the electric current - /** + /*! * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). * @param ldx Leading dimension of the grad_X array. - * @param grad_T The temperature gradient (ignored in this model). + * @param grad_X The gradient of the mole fraction * @param ldf Leading dimension of the grad_V and current vectors. * @param grad_V The electrostatic potential gradient. * @param current The electric current in A/m^2. @@ -349,8 +349,8 @@ namespace Cantera { * @param ldf Leading dimension of the fluxes array * (usually equal to m_nsp but not always) * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ virtual void getSpeciesFluxes(int ndim, const doublereal* grad_T, @@ -399,7 +399,7 @@ namespace Cantera { //! the mass averaged velocity, //! given the gradients in mole fraction and temperature /*! - * Units for the returned fluxes are kg m-2 s-1. + * Units for the returned velocities are m s-1 * * @param ndim Number of dimensions in the flux expressions * @param grad_T Gradient of the temperature @@ -411,9 +411,11 @@ namespace Cantera { * length = ldx * ndim * @param ldf Leading dimension of the fluxes array * (usually equal to m_nsp but not always) - * @param Vdiff Output of the diffusive velocities. - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param Vdiff Output of the diffusive velocities wrt the mass-averaged + * velocity + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * units are m / s. */ virtual void getSpeciesVdiff(int ndim, const doublereal* grad_T, @@ -424,12 +426,11 @@ namespace Cantera { err("getSpeciesVdiff"); } - //! Get the species diffusive mass fluxes wrt to - //! the mass averaged velocity, - //! given the gradients in mole fraction, temperature + //! Get the species diffusive velocities wrt to the mass averaged velocity, + //! given the gradients in mole fraction, temperature, //! and electrostatic potential. /*! - * Units for the returned fluxes are kg m-2 s-1. + * Units for the returned velocities are m s-1. * * @param ndim Number of dimensions in the flux expressions * @param grad_T Gradient of the temperature @@ -443,9 +444,10 @@ namespace Cantera { * (usually equal to m_nsp but not always) * @param grad_Phi Gradients of the electrostatic potential * (length = ndim) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param Vdiff Output of the diffusive velocities wrt the mass-averaged velocity + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * units are m / s. */ virtual void getSpeciesVdiffES(int ndim, const doublereal* grad_T, @@ -466,58 +468,78 @@ namespace Cantera { * @param state2 Array of temperature, density, and mass * fractions for state 2. * @param delta Distance from state 1 to state 2 (m). + * @param cfluxes Output array containing the diffusive molar fluxes of species + * from state1 to state2. This is a flat vector with the + * m_nsp in the inner loop. + * length = ldx * ndim. + * Units are [kmol/m^2/s]. */ virtual void getMolarFluxes(const doublereal * const state1, const doublereal * const state2, const doublereal delta, - doublereal * const fluxes) { + doublereal * const cfluxes) { err("getMolarFluxes"); } - /** - * Get the mass fluxes [kg/m^2/s], given the thermodynamic - * state at two nearby points. + + //! Get the mass fluxes [kg/m^2/s], given the thermodynamic + //! state at two nearby points. + /*! * @param state1 Array of temperature, density, and mass * fractions for state 1. * @param state2 Array of temperature, density, and mass * fractions for state 2. * @param delta Distance from state 1 to state 2 (m). + * @param mfluxes Output array containing the diffusive mass fluxes of species + * from state1 to state2. This is a flat vector with the + * m_nsp in the inner loop. + * length = ldx * ndim. + * Units are [kg/m^2/s]. */ virtual void getMassFluxes(const doublereal* state1, const doublereal* state2, doublereal delta, - doublereal* fluxes) { err("getMassFluxes"); } - - /** - * Thermal diffusion coefficients [kg/m/sec]. + doublereal* mfluxes) { + err("getMassFluxes"); + } + + //! Return a vector of Thermal diffusion coefficients [kg/m/sec]. + /*! * The thermal diffusion coefficient \f$ D^T_k \f$ is defined * so that the diffusive mass flux of species k induced by the * local temperature gradient is \f[ M_k J_k = -D^T_k \nabla * \ln T. \f]. The thermal diffusion coefficient can be either * positive or negative. * - * @param dt on return, dt will contain the species thermal - * diffusion coefficients. Dimension dt at least as large as - * the number of species. + * @param dt On return, dt will contain the species thermal + * diffusion coefficients. Dimension dt at least as large as + * the number of species. */ - virtual void getThermalDiffCoeffs(doublereal* const dt) - { err("getThermalDiffCoeffs"); } + virtual void getThermalDiffCoeffs(doublereal* const dt) { + err("getThermalDiffCoeffs"); + } - //! Returns the matrix of binary diffusion coefficients [m^2/s]. + //! Returns the matrix of binary diffusion coefficients [m^2/s]. /*! * @param ld Inner stride for writing the two dimension diffusion * coefficients into a one dimensional vector * @param d Diffusion coefficient matrix (must be at least m_k * m_k * in length. */ - virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d) - { err("getBinaryDiffCoeffs"); } + virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d) { + err("getBinaryDiffCoeffs"); + } - - /** - * Multicomponent diffusion coefficients. Units: [m^2/s]. If - * the transport manager implements a multicomponent diffusion + + //! Return the Multicomponent diffusion coefficients. Units: [m^2/s]. + /*! + * If the transport manager implements a multicomponent diffusion * model, then this method returns the array of multicomponent * diffusion coefficients. Otherwise it throws an exception. + * + * @param ld The dimension of the inner loop of d (usually equal to m_nsp) + * @param d flat vector of diffusion coefficients, fortran ordering. + * d[ld*j+i] is the D_ij diffusion coefficient (the diffusion + * coefficient for species i due to species j). */ virtual void getMultiDiffCoeffs(const int ld, doublereal* const d) { err("getMultiDiffCoeffs"); } From a2a507d779acdd32bf20005ea9cccfd502d8fc6b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 24 Dec 2009 17:11:51 +0000 Subject: [PATCH 090/446] Reverted commit #316# , which added a pointer to a transport object. We are trying to keep the major sections of cantera separate from each other to impose a coarse grained modularity on the code. And, adding a pointer here leads to their linkages at a lower level. Linkages at a higher level are encouraged, however This is the same reason why there isn't a kinetics pointer here as well. --- Cantera/src/thermo/Phase.h | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index 7395d9933..60c5ec06a 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -26,7 +26,6 @@ using namespace ctml; namespace Cantera { - class Transport; //forward declaration /** * @defgroup phases Models of Phases of Matter @@ -222,9 +221,6 @@ namespace Cantera { */ void setName(std::string nm); - //! Attach a Transport object pointer to this Phase - void setTransport( Transport* tr ) { m_trans = tr; } - //! Returns the index of the phase /*! * The index is used in the Python and matlab interfaces to @@ -438,9 +434,6 @@ namespace Cantera { */ void getMoleFractionsByName(compositionMap& x) const; - //! Get a Transport object pointer attached to this Phase - Transport* getTransport( ) { return m_trans; } - //! Return the mole fraction of a single species /*! * @param k String name of the species @@ -522,13 +515,6 @@ namespace Cantera { */ int m_index; - /** - * A Transport object pointer attached to this Phase - */ - Transport *m_trans; - - - private: //! This stores the initial state of the system From 6a3cf226ec10cc19c69d1b08343955ed34565f97 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 24 Dec 2009 22:16:31 +0000 Subject: [PATCH 091/446] Changed the install behavior to be one that a copy occurs --- config/install-sh | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/config/install-sh b/config/install-sh index 7093cc7e5..a992cfcdb 100755 --- a/config/install-sh +++ b/config/install-sh @@ -44,7 +44,7 @@ mkdirprog="${MKDIRPROG-mkdir}" verbose="" transformbasename="" transform_arg="" -instcmd="$mvprog" +instcmd="$cpprog" chmodcmd="$chmodprog 0755" chowncmd="" chgrpcmd="" @@ -57,7 +57,10 @@ dir_arg="" while [ x"$1" != x ]; do case $1 in - -c) instcmd="$cpprog" + -c) shift + continue;; + + -move) instcmd="$mvprog" shift continue;; @@ -138,8 +141,8 @@ else then true else - echo "install: $src does not exist" - exit 1 + echo "install: WARNING $src does not exist" + exit 0 fi if [ x"$dst" = x ] From 93020c91bb72ce08050cca6d9d4b72c3e4bf0f9c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 24 Dec 2009 22:47:00 +0000 Subject: [PATCH 092/446] Some changes for the new cygwin --- Makefile.in | 4 +- configure | 11677 +++++++++++++++++++------------------------------ configure.in | 16 +- 3 files changed, 4410 insertions(+), 7287 deletions(-) diff --git a/Makefile.in b/Makefile.in index 410fee99d..d0b63e050 100755 --- a/Makefile.in +++ b/Makefile.in @@ -192,8 +192,8 @@ endif finish-install: @INSTALL@ -d @ct_docdir@ @INSTALL@ -d @ct_bindir@ - cp -f bin/exp3to2.sh "@ct_bindir@" - cp -f bin/csvdiff "@ct_bindir@" + -( cd bin ; @INSTALL@ -c exp3to2.sh "@ct_bindir@" ) + -( cd bin ; @INSTALL@ -c csvdiff "@ct_bindir@" ) ifeq ($(os_is_win),0) # Commands to be executed for non-win systems cp -f License.rtf "@ct_bindir@" diff --git a/configure b/configure index 9473d7c46..a82defef7 100755 --- a/configure +++ b/configure @@ -1,81 +1,413 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.59 for Cantera 1.7.0. +# Generated by GNU Autoconf 2.64 for Cantera 1.7.0. +# +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software +# Foundation, Inc. # -# Copyright (C) 2003 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## -# Be Bourne compatible -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: - # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' -elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then - set -o posix -fi -DUALCASE=1; export DUALCASE # for MKS sh - -# Support unset when possible. -if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then - as_unset=unset + setopt NO_GLOB_SUBST else - as_unset=false + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac fi -# Work around bugs in pre-3.0 UWIN ksh. -$as_unset ENV MAIL MAILPATH +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. 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Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi -if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. -as_me=`$as_basename "$0" || +as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)$' \| \ - . : '\(.\)' 2>/dev/null || -echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } - /^X\/\(\/\/\)$/{ s//\1/; q; } - /^X\/\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` - -# PATH needs CR, and LINENO needs CR and PATH. # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -83,146 +415,107 @@ as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits -# The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then - echo "#! /bin/sh" >conf$$.sh - echo "exit 0" >>conf$$.sh - chmod +x conf$$.sh - if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then - PATH_SEPARATOR=';' - else - PATH_SEPARATOR=: - fi - rm -f conf$$.sh -fi - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" || { - # Find who we are. Look in the path if we contain no path at all - # relative or not. - case $0 in - *[\\/]* ) as_myself=$0 ;; - *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done - - ;; - esac - # We did not find ourselves, most probably we were run as `sh COMMAND' - # in which case we are not to be found in the path. - if test "x$as_myself" = x; then - as_myself=$0 - fi - if test ! -f "$as_myself"; then - { echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2 - { (exit 1); exit 1; }; } - fi - case $CONFIG_SHELL in - '') - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for as_base in sh bash ksh sh5; do - case $as_dir in - /*) - if ("$as_dir/$as_base" -c ' - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then - $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } - $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } - CONFIG_SHELL=$as_dir/$as_base - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$0" ${1+"$@"} - fi;; - esac - done -done -;; - esac - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. The first 'sed' inserts a - # line-number line before each line; the second 'sed' does the real - # work. The second script uses 'N' to pair each line-number line - # with the numbered line, and appends trailing '-' during - # substitution so that $LINENO is not a special case at line end. - # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the - # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) - sed '=' <$as_myself | + as_lineno_1=$LINENO as_lineno_1a=$LINENO + as_lineno_2=$LINENO as_lineno_2a=$LINENO + eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && + test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { + # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno N - s,$,-, - : loop - s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3, + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ t loop - s,-$,, - s,^['$as_cr_digits']*\n,, + s/-\n.*// ' >$as_me.lineno && - chmod +x $as_me.lineno || - { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 - { (exit 1); exit 1; }; } + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the - # original and so on. Autoconf is especially sensible to this). - . ./$as_me.lineno + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" # Exit status is that of the last command. exit } - -case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in - *c*,-n*) ECHO_N= ECHO_C=' -' ECHO_T=' ' ;; - *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;; - *) ECHO_N= ECHO_C='\c' ECHO_T= ;; +ECHO_C= ECHO_N= ECHO_T= +case `echo -n x` in #((((( +-n*) + case `echo 'xy\c'` in + *c*) ECHO_T=' ';; # ECHO_T is single tab character. + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; + esac;; +*) + ECHO_N='-n';; esac -if expr a : '\(a\)' >/dev/null 2>&1; then - as_expr=expr -else - as_expr=false -fi - rm -f conf$$ conf$$.exe conf$$.file -echo >conf$$.file -if ln -s conf$$.file conf$$ 2>/dev/null; then - # We could just check for DJGPP; but this test a) works b) is more generic - # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04). - if test -f conf$$.exe; then - # Don't use ln at all; we don't have any links - as_ln_s='cp -p' - else +if test -d conf$$.dir; then + rm -f conf$$.dir/conf$$.file +else + rm -f conf$$.dir + mkdir conf$$.dir 2>/dev/null +fi +if (echo >conf$$.file) 2>/dev/null; then + if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' + # ... but there are two gotchas: + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -p'. + ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || + as_ln_s='cp -p' + elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln + else + as_ln_s='cp -p' fi -elif ln conf$$.file conf$$ 2>/dev/null; then - as_ln_s=ln else as_ln_s='cp -p' fi -rm -f conf$$ conf$$.exe conf$$.file +rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file +rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi -as_executable_p="test -f" +if test -x / >/dev/null 2>&1; then + as_test_x='test -x' +else + if ls -dL / >/dev/null 2>&1; then + as_ls_L_option=L + else + as_ls_L_option= + fi + as_test_x=' + eval sh -c '\'' + if test -d "$1"; then + test -d "$1/."; + else + case $1 in #( + -*)set "./$1";; + esac; + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + ???[sx]*):;;*)false;;esac;fi + '\'' sh + ' +fi +as_executable_p=$as_test_x # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" @@ -231,38 +524,24 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -# IFS -# We need space, tab and new line, in precisely that order. -as_nl=' -' -IFS=" $as_nl" - -# CDPATH. -$as_unset CDPATH - +exec 7<&0 &1 # Name of the host. # hostname on some systems (SVR3.2, Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` -exec 6>&1 - # # Initializations. # ac_default_prefix=/usr/local +ac_clean_files= ac_config_libobj_dir=. +LIBOBJS= cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= -SHELL=${CONFIG_SHELL-/bin/sh} - -# Maximum number of lines to put in a shell here document. -# This variable seems obsolete. It should probably be removed, and -# only ac_max_sed_lines should be used. -: ${ac_max_here_lines=38} # Identity of this package. PACKAGE_NAME='Cantera' @@ -270,50 +549,263 @@ PACKAGE_TARNAME='cantera' PACKAGE_VERSION='1.7.0' PACKAGE_STRING='Cantera 1.7.0' PACKAGE_BUGREPORT='' +PACKAGE_URL='' # Factoring default headers for most tests. ac_includes_default="\ #include -#if HAVE_SYS_TYPES_H +#ifdef HAVE_SYS_TYPES_H # include #endif -#if HAVE_SYS_STAT_H +#ifdef HAVE_SYS_STAT_H # include #endif -#if STDC_HEADERS +#ifdef STDC_HEADERS # include # include #else -# if HAVE_STDLIB_H +# ifdef HAVE_STDLIB_H # include # endif #endif -#if HAVE_STRING_H -# if !STDC_HEADERS && HAVE_MEMORY_H +#ifdef HAVE_STRING_H +# if !defined STDC_HEADERS && defined HAVE_MEMORY_H # include # endif # include #endif -#if HAVE_STRINGS_H +#ifdef HAVE_STRINGS_H # include #endif -#if HAVE_INTTYPES_H +#ifdef HAVE_INTTYPES_H # include -#else -# if HAVE_STDINT_H -# include -# endif #endif -#if HAVE_UNISTD_H +#ifdef HAVE_STDINT_H +# include +#endif +#ifdef HAVE_UNISTD_H # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' +ac_subst_vars='LTLIBOBJS +LIBOBJS +INSTALL_VERBOSE +INSTALL_abs +TSCOMPARE_abs +EXTRA_LINK +LDSHARED +SO +math_libs +EXE_EXT +OBJ_EXT +CXX_EXT +F77_EXT +mex_ext +SHARED_CTLIB +OS_IS_CYGWIN +OS_IS_WIN +OS_IS_DARWIN +precompile_headers +LCXX_FLIBS +F90LIBS +F90BUILDFLAGS +F90FLAGS +BUILD_F90 +F90 +FLIBS +ac_ct_F77 +FFLAGS +F77 +HAVE_STRIPSYMBOLS +LCXX_END_LIBS +LCXX_FLAGS +CXX_INCLUDES +SHARED +SOEXT +EGREP +GREP +CXXCPP +ac_ct_CC +CFLAGS +CC +INSTALL_DATA +INSTALL_SCRIPT +INSTALL_PROGRAM +PIC +export_name +BUILD_CLIB +BUILD_MATLAB +MATLAB_CMD +CVSTAG +CANTERA_PYTHON_HOME +NUMARRAY_HOME +NUMARRAY_INC_DIR +NUMPY_HOME +NUMPY_INC_DIR +BUILD_PYTHON +PYTHON_CMD +CT_SHARED_LIB +CANTERA_CORE_LIBS_DEP +CANTERA_CORE_LIBS +RAW_LIBS_DEP +INSTALL_LIBS_DEP +LOCAL_LIBS_DEP +LOCAL_LIBS +LOCAL_LIB_DIRS +BOOST_LIB_DIR +F2C_SYSTEMLIB +build_f2c_lib +build_with_f2c +BLAS_LAPACK_DIR +BLAS_LAPACK_LINK +BLAS_LAPACK_LIBS +build_blas +build_lapack +PURIFY +BOOST_LIB +BOOST_INCLUDE +COMPILE_H298MODIFY_CAPABILITY +COMPILE_VCSNONIDEAL +LIB_DIR +BUILD_CK +KERNEL_OBJ +KERNEL +WITH_REACTORS +COMPILE_RXNPATH +COMPILE_HETEROKIN +COMPILE_KINETICS +NEED_CATHERMO +COMPILE_ELECTROLYTES +COMPILE_IDEAL_SOLUTIONS +phase_header_files +phase_object_files +COMPILE_PURE_FLUIDS +CANTERA_DEBUG_MODE +sundials_lib_dep +sundials_lib +sundials_lib_dir +sundials_include +IDA_LIBS +CVODE_LIBS +use_sundials +OBJEXT +EXEEXT +ac_ct_CXX +CPPFLAGS +LDFLAGS +CXXFLAGS +CXX +INCL_USER_CODE +USERDIR +CXX_DEPENDS +RANLIB +DO_RANLIB +ARCHIVE +GRAPHVIZDIR +MAKE +buildbin +buildlib +buildinc +ctroot +username +target_os +target_vendor +target_cpu +target +host_os +host_vendor +host_cpu +host +build_os +build_vendor +build_cpu +build +ct_mandir +ct_dir +ct_docdir +ct_tutdir +ct_templdir +ct_demodir +ct_datadir +ct_incroot +ct_incdir +ct_bindir +ct_libdir +homedir +ctversion +python_win_prefix +python_prefix +local_python_inst +local_inst +USE_CLIB_DLL +CVF_LIBDIR +ldemulationarg +BITCHANGE +BITHARDWARE +BITCOMPILE +target_alias +host_alias +build_alias +LIBS +ECHO_T +ECHO_N +ECHO_C +DEFS +mandir +localedir +libdir +psdir +pdfdir +dvidir +htmldir +infodir +docdir +oldincludedir +includedir +localstatedir +sharedstatedir +sysconfdir +datadir +datarootdir +libexecdir +sbindir +bindir +program_transform_name +prefix +exec_prefix +PACKAGE_URL +PACKAGE_BUGREPORT +PACKAGE_STRING +PACKAGE_VERSION +PACKAGE_TARNAME +PACKAGE_NAME +PATH_SEPARATOR +SHELL' ac_subst_files='' +ac_user_opts=' +enable_option_checking +' + ac_precious_vars='build_alias +host_alias +target_alias +CXX +CXXFLAGS +LDFLAGS +LIBS +CPPFLAGS +CCC +CC +CFLAGS +CXXCPP +F77 +FFLAGS' + # Initialize some variables set by options. ac_init_help= ac_init_version=false +ac_unrecognized_opts= +ac_unrecognized_sep= # The variables have the same names as the options, with # dashes changed to underlines. cache_file=/dev/null @@ -336,34 +828,48 @@ x_libraries=NONE # and all the variables that are supposed to be based on exec_prefix # by default will actually change. # Use braces instead of parens because sh, perl, etc. also accept them. +# (The list follows the same order as the GNU Coding Standards.) bindir='${exec_prefix}/bin' sbindir='${exec_prefix}/sbin' libexecdir='${exec_prefix}/libexec' -datadir='${prefix}/share' +datarootdir='${prefix}/share' +datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' -libdir='${exec_prefix}/lib' includedir='${prefix}/include' oldincludedir='/usr/include' -infodir='${prefix}/info' -mandir='${prefix}/man' +docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' +infodir='${datarootdir}/info' +htmldir='${docdir}' +dvidir='${docdir}' +pdfdir='${docdir}' +psdir='${docdir}' +libdir='${exec_prefix}/lib' +localedir='${datarootdir}/locale' +mandir='${datarootdir}/man' ac_prev= +ac_dashdash= for ac_option do # If the previous option needs an argument, assign it. if test -n "$ac_prev"; then - eval "$ac_prev=\$ac_option" + eval $ac_prev=\$ac_option ac_prev= continue fi - ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'` + case $ac_option in + *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *) ac_optarg=yes ;; + esac # Accept the important Cygnus configure options, so we can diagnose typos. - case $ac_option in + case $ac_dashdash$ac_option in + --) + ac_dashdash=yes ;; -bindir | --bindir | --bindi | --bind | --bin | --bi) ac_prev=bindir ;; @@ -385,33 +891,59 @@ do --config-cache | -C) cache_file=config.cache ;; - -datadir | --datadir | --datadi | --datad | --data | --dat | --da) + -datadir | --datadir | --datadi | --datad) ac_prev=datadir ;; - -datadir=* | --datadir=* | --datadi=* | --datad=* | --data=* | --dat=* \ - | --da=*) + -datadir=* | --datadir=* | --datadi=* | --datad=*) datadir=$ac_optarg ;; + -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \ + | --dataroo | --dataro | --datar) + ac_prev=datarootdir ;; + -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \ + | --dataroot=* | --dataroo=* | --dataro=* | --datar=*) + datarootdir=$ac_optarg ;; + -disable-* | --disable-*) - ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid feature name: $ac_feature" >&2 - { (exit 1); exit 1; }; } - ac_feature=`echo $ac_feature | sed 's/-/_/g'` - eval "enable_$ac_feature=no" ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval enable_$ac_useropt=no ;; + + -docdir | --docdir | --docdi | --doc | --do) + ac_prev=docdir ;; + -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*) + docdir=$ac_optarg ;; + + -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv) + ac_prev=dvidir ;; + -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*) + dvidir=$ac_optarg ;; -enable-* | --enable-*) - ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid feature name: $ac_feature" >&2 - { (exit 1); exit 1; }; } - ac_feature=`echo $ac_feature | sed 's/-/_/g'` - case $ac_option in - *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;; - *) ac_optarg=yes ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; esac - eval "enable_$ac_feature='$ac_optarg'" ;; + eval enable_$ac_useropt=\$ac_optarg ;; -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \ @@ -438,6 +970,12 @@ do -host=* | --host=* | --hos=* | --ho=*) host_alias=$ac_optarg ;; + -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht) + ac_prev=htmldir ;; + -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \ + | --ht=*) + htmldir=$ac_optarg ;; + -includedir | --includedir | --includedi | --included | --include \ | --includ | --inclu | --incl | --inc) ac_prev=includedir ;; @@ -462,13 +1000,16 @@ do | --libexe=* | --libex=* | --libe=*) libexecdir=$ac_optarg ;; + -localedir | --localedir | --localedi | --localed | --locale) + ac_prev=localedir ;; + -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*) + localedir=$ac_optarg ;; + -localstatedir | --localstatedir | --localstatedi | --localstated \ - | --localstate | --localstat | --localsta | --localst \ - | --locals | --local | --loca | --loc | --lo) + | --localstate | --localstat | --localsta | --localst | --locals) ac_prev=localstatedir ;; -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \ - | --localstate=* | --localstat=* | --localsta=* | --localst=* \ - | --locals=* | --local=* | --loca=* | --loc=* | --lo=*) + | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*) localstatedir=$ac_optarg ;; -mandir | --mandir | --mandi | --mand | --man | --ma | --m) @@ -533,6 +1074,16 @@ do | --progr-tra=* | --program-tr=* | --program-t=*) program_transform_name=$ac_optarg ;; + -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd) + ac_prev=pdfdir ;; + -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*) + pdfdir=$ac_optarg ;; + + -psdir | --psdir | --psdi | --psd | --ps) + ac_prev=psdir ;; + -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*) + psdir=$ac_optarg ;; + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) silent=yes ;; @@ -583,26 +1134,36 @@ do ac_init_version=: ;; -with-* | --with-*) - ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid package name: $ac_package" >&2 - { (exit 1); exit 1; }; } - ac_package=`echo $ac_package| sed 's/-/_/g'` - case $ac_option in - *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;; - *) ac_optarg=yes ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig" + ac_unrecognized_sep=', ';; esac - eval "with_$ac_package='$ac_optarg'" ;; + eval with_$ac_useropt=\$ac_optarg ;; -without-* | --without-*) - ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid package name: $ac_package" >&2 - { (exit 1); exit 1; }; } - ac_package=`echo $ac_package | sed 's/-/_/g'` - eval "with_$ac_package=no" ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval with_$ac_useropt=no ;; --x) # Obsolete; use --with-x. @@ -622,26 +1183,25 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) { echo "$as_me: error: unrecognized option: $ac_option -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; } + -*) as_fn_error "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information." ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid variable name: $ac_envvar" >&2 - { (exit 1); exit 1; }; } - ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` - eval "$ac_envvar='$ac_optarg'" + case $ac_envvar in #( + '' | [0-9]* | *[!_$as_cr_alnum]* ) + as_fn_error "invalid variable name: \`$ac_envvar'" ;; + esac + eval $ac_envvar=\$ac_optarg export $ac_envvar ;; *) # FIXME: should be removed in autoconf 3.0. - echo "$as_me: WARNING: you should use --build, --host, --target" >&2 + $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && - echo "$as_me: WARNING: invalid host type: $ac_option" >&2 + $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option} ;; @@ -650,31 +1210,36 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - { echo "$as_me: error: missing argument to $ac_option" >&2 - { (exit 1); exit 1; }; } + as_fn_error "missing argument to $ac_option" fi -# Be sure to have absolute paths. -for ac_var in exec_prefix prefix -do - eval ac_val=$`echo $ac_var` - case $ac_val in - [\\/$]* | ?:[\\/]* | NONE | '' ) ;; - *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 - { (exit 1); exit 1; }; };; +if test -n "$ac_unrecognized_opts"; then + case $enable_option_checking in + no) ;; + fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;; + *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac -done +fi -# Be sure to have absolute paths. -for ac_var in bindir sbindir libexecdir datadir sysconfdir sharedstatedir \ - localstatedir libdir includedir oldincludedir infodir mandir +# Check all directory arguments for consistency. +for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ + datadir sysconfdir sharedstatedir localstatedir includedir \ + oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ + libdir localedir mandir do - eval ac_val=$`echo $ac_var` + eval ac_val=\$$ac_var + # Remove trailing slashes. case $ac_val in - [\\/$]* | ?:[\\/]* ) ;; - *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 - { (exit 1); exit 1; }; };; + */ ) + ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'` + eval $ac_var=\$ac_val;; esac + # Be sure to have absolute directory names. + case $ac_val in + [\\/$]* | ?:[\\/]* ) continue;; + NONE | '' ) case $ac_var in *prefix ) continue;; esac;; + esac + as_fn_error "expected an absolute directory name for --$ac_var: $ac_val" done # There might be people who depend on the old broken behavior: `$host' @@ -688,7 +1253,7 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. + $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. If a cross compiler is detected then cross compile mode will be used." >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes @@ -701,90 +1266,72 @@ test -n "$host_alias" && ac_tool_prefix=$host_alias- test "$silent" = yes && exec 6>/dev/null +ac_pwd=`pwd` && test -n "$ac_pwd" && +ac_ls_di=`ls -di .` && +ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || + as_fn_error "working directory cannot be determined" +test "X$ac_ls_di" = "X$ac_pwd_ls_di" || + as_fn_error "pwd does not report name of working directory" + + # Find the source files, if location was not specified. if test -z "$srcdir"; then ac_srcdir_defaulted=yes - # Try the directory containing this script, then its parent. - ac_confdir=`(dirname "$0") 2>/dev/null || -$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$0" : 'X\(//\)[^/]' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| \ - . : '\(.\)' 2>/dev/null || -echo X"$0" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } - /^X\(\/\/\)[^/].*/{ s//\1/; q; } - /^X\(\/\/\)$/{ s//\1/; q; } - /^X\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + # Try the directory containing this script, then the parent directory. + ac_confdir=`$as_dirname -- "$as_myself" || +$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_myself" : 'X\(//\)[^/]' \| \ + X"$as_myself" : 'X\(//\)$' \| \ + X"$as_myself" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_myself" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` srcdir=$ac_confdir - if test ! -r $srcdir/$ac_unique_file; then + if test ! -r "$srcdir/$ac_unique_file"; then srcdir=.. fi else ac_srcdir_defaulted=no fi -if test ! -r $srcdir/$ac_unique_file; then - if test "$ac_srcdir_defaulted" = yes; then - { echo "$as_me: error: cannot find sources ($ac_unique_file) in $ac_confdir or .." >&2 - { (exit 1); exit 1; }; } - else - { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 - { (exit 1); exit 1; }; } - fi +if test ! -r "$srcdir/$ac_unique_file"; then + test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." + as_fn_error "cannot find sources ($ac_unique_file) in $srcdir" fi -(cd $srcdir && test -r ./$ac_unique_file) 2>/dev/null || - { echo "$as_me: error: sources are in $srcdir, but \`cd $srcdir' does not work" >&2 - { (exit 1); exit 1; }; } -srcdir=`echo "$srcdir" | sed 's%\([^\\/]\)[\\/]*$%\1%'` -ac_env_build_alias_set=${build_alias+set} -ac_env_build_alias_value=$build_alias -ac_cv_env_build_alias_set=${build_alias+set} -ac_cv_env_build_alias_value=$build_alias -ac_env_host_alias_set=${host_alias+set} -ac_env_host_alias_value=$host_alias -ac_cv_env_host_alias_set=${host_alias+set} -ac_cv_env_host_alias_value=$host_alias -ac_env_target_alias_set=${target_alias+set} -ac_env_target_alias_value=$target_alias -ac_cv_env_target_alias_set=${target_alias+set} -ac_cv_env_target_alias_value=$target_alias -ac_env_CXX_set=${CXX+set} -ac_env_CXX_value=$CXX -ac_cv_env_CXX_set=${CXX+set} -ac_cv_env_CXX_value=$CXX -ac_env_CXXFLAGS_set=${CXXFLAGS+set} -ac_env_CXXFLAGS_value=$CXXFLAGS -ac_cv_env_CXXFLAGS_set=${CXXFLAGS+set} -ac_cv_env_CXXFLAGS_value=$CXXFLAGS -ac_env_LDFLAGS_set=${LDFLAGS+set} -ac_env_LDFLAGS_value=$LDFLAGS -ac_cv_env_LDFLAGS_set=${LDFLAGS+set} -ac_cv_env_LDFLAGS_value=$LDFLAGS -ac_env_CPPFLAGS_set=${CPPFLAGS+set} -ac_env_CPPFLAGS_value=$CPPFLAGS -ac_cv_env_CPPFLAGS_set=${CPPFLAGS+set} -ac_cv_env_CPPFLAGS_value=$CPPFLAGS -ac_env_CC_set=${CC+set} -ac_env_CC_value=$CC -ac_cv_env_CC_set=${CC+set} -ac_cv_env_CC_value=$CC -ac_env_CFLAGS_set=${CFLAGS+set} -ac_env_CFLAGS_value=$CFLAGS -ac_cv_env_CFLAGS_set=${CFLAGS+set} -ac_cv_env_CFLAGS_value=$CFLAGS -ac_env_CXXCPP_set=${CXXCPP+set} -ac_env_CXXCPP_value=$CXXCPP -ac_cv_env_CXXCPP_set=${CXXCPP+set} -ac_cv_env_CXXCPP_value=$CXXCPP -ac_env_F77_set=${F77+set} -ac_env_F77_value=$F77 -ac_cv_env_F77_set=${F77+set} -ac_cv_env_F77_value=$F77 -ac_env_FFLAGS_set=${FFLAGS+set} -ac_env_FFLAGS_value=$FFLAGS -ac_cv_env_FFLAGS_set=${FFLAGS+set} -ac_cv_env_FFLAGS_value=$FFLAGS +ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" +ac_abs_confdir=`( + cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg" + pwd)` +# When building in place, set srcdir=. +if test "$ac_abs_confdir" = "$ac_pwd"; then + srcdir=. +fi +# Remove unnecessary trailing slashes from srcdir. +# Double slashes in file names in object file debugging info +# mess up M-x gdb in Emacs. +case $srcdir in +*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;; +esac +for ac_var in $ac_precious_vars; do + eval ac_env_${ac_var}_set=\${${ac_var}+set} + eval ac_env_${ac_var}_value=\$${ac_var} + eval ac_cv_env_${ac_var}_set=\${${ac_var}+set} + eval ac_cv_env_${ac_var}_value=\$${ac_var} +done # # Report the --help message. @@ -813,14 +1360,11 @@ Configuration: -n, --no-create do not create output files --srcdir=DIR find the sources in DIR [configure dir or \`..'] -_ACEOF - - cat <<_ACEOF Installation directories: --prefix=PREFIX install architecture-independent files in PREFIX - [$ac_default_prefix] + [$ac_default_prefix] --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX - [PREFIX] + [PREFIX] By default, \`make install' will install all the files in \`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify @@ -830,18 +1374,25 @@ for instance \`--prefix=\$HOME'. For better control, use the options below. Fine tuning of the installation directories: - --bindir=DIR user executables [EPREFIX/bin] - --sbindir=DIR system admin executables [EPREFIX/sbin] - --libexecdir=DIR program executables [EPREFIX/libexec] - --datadir=DIR read-only architecture-independent data [PREFIX/share] - --sysconfdir=DIR read-only single-machine data [PREFIX/etc] - --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] - --localstatedir=DIR modifiable single-machine data [PREFIX/var] - --libdir=DIR object code libraries [EPREFIX/lib] - --includedir=DIR C header files [PREFIX/include] - --oldincludedir=DIR C header files for non-gcc [/usr/include] - --infodir=DIR info documentation [PREFIX/info] - --mandir=DIR man documentation [PREFIX/man] + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] + --datadir=DIR read-only architecture-independent data [DATAROOTDIR] + --infodir=DIR info documentation [DATAROOTDIR/info] + --localedir=DIR locale-dependent data [DATAROOTDIR/locale] + --mandir=DIR man documentation [DATAROOTDIR/man] + --docdir=DIR documentation root [DATAROOTDIR/doc/cantera] + --htmldir=DIR html documentation [DOCDIR] + --dvidir=DIR dvi documentation [DOCDIR] + --pdfdir=DIR pdf documentation [DOCDIR] + --psdir=DIR ps documentation [DOCDIR] _ACEOF cat <<\_ACEOF @@ -864,8 +1415,9 @@ Some influential environment variables: CXXFLAGS C++ compiler flags LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory - CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have - headers in a nonstandard directory + LIBS libraries to pass to the linker, e.g. -l + CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I if + you have headers in a nonstandard directory CC C compiler command CFLAGS C compiler flags CXXCPP C++ preprocessor @@ -875,121 +1427,541 @@ Some influential environment variables: Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. +Report bugs to the package provider. _ACEOF +ac_status=$? fi if test "$ac_init_help" = "recursive"; then # If there are subdirs, report their specific --help. - ac_popdir=`pwd` for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue - test -d $ac_dir || continue + test -d "$ac_dir" || + { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } || + continue ac_builddir=. -if test "$ac_dir" != .; then - ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'` - # A "../" for each directory in $ac_dir_suffix. - ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'` -else - ac_dir_suffix= ac_top_builddir= -fi +case "$ac_dir" in +.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; +*) + ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + # A ".." for each directory in $ac_dir_suffix. + ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + case $ac_top_builddir_sub in + "") ac_top_builddir_sub=. ac_top_build_prefix= ;; + *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; + esac ;; +esac +ac_abs_top_builddir=$ac_pwd +ac_abs_builddir=$ac_pwd$ac_dir_suffix +# for backward compatibility: +ac_top_builddir=$ac_top_build_prefix case $srcdir in - .) # No --srcdir option. We are building in place. + .) # We are building in place. ac_srcdir=. - if test -z "$ac_top_builddir"; then - ac_top_srcdir=. - else - ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` - fi ;; - [\\/]* | ?:[\\/]* ) # Absolute path. + ac_top_srcdir=$ac_top_builddir_sub + ac_abs_top_srcdir=$ac_pwd ;; + [\\/]* | ?:[\\/]* ) # Absolute name. ac_srcdir=$srcdir$ac_dir_suffix; - ac_top_srcdir=$srcdir ;; - *) # Relative path. - ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix - ac_top_srcdir=$ac_top_builddir$srcdir ;; + ac_top_srcdir=$srcdir + ac_abs_top_srcdir=$srcdir ;; + *) # Relative name. + ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_build_prefix$srcdir + ac_abs_top_srcdir=$ac_pwd/$srcdir ;; esac +ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix -# Do not use `cd foo && pwd` to compute absolute paths, because -# the directories may not exist. -case `pwd` in -.) ac_abs_builddir="$ac_dir";; -*) - case "$ac_dir" in - .) ac_abs_builddir=`pwd`;; - [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";; - *) ac_abs_builddir=`pwd`/"$ac_dir";; - esac;; -esac -case $ac_abs_builddir in -.) ac_abs_top_builddir=${ac_top_builddir}.;; -*) - case ${ac_top_builddir}. in - .) ac_abs_top_builddir=$ac_abs_builddir;; - [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;; - *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;; - esac;; -esac -case $ac_abs_builddir in -.) ac_abs_srcdir=$ac_srcdir;; -*) - case $ac_srcdir in - .) ac_abs_srcdir=$ac_abs_builddir;; - [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;; - *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;; - esac;; -esac -case $ac_abs_builddir in -.) ac_abs_top_srcdir=$ac_top_srcdir;; -*) - case $ac_top_srcdir in - .) ac_abs_top_srcdir=$ac_abs_builddir;; - [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;; - *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;; - esac;; -esac - - cd $ac_dir - # Check for guested configure; otherwise get Cygnus style configure. - if test -f $ac_srcdir/configure.gnu; then - echo - $SHELL $ac_srcdir/configure.gnu --help=recursive - elif test -f $ac_srcdir/configure; then - echo - $SHELL $ac_srcdir/configure --help=recursive - elif test -f $ac_srcdir/configure.ac || - test -f $ac_srcdir/configure.in; then - echo - $ac_configure --help + cd "$ac_dir" || { ac_status=$?; continue; } + # Check for guested configure. + if test -f "$ac_srcdir/configure.gnu"; then + echo && + $SHELL "$ac_srcdir/configure.gnu" --help=recursive + elif test -f "$ac_srcdir/configure"; then + echo && + $SHELL "$ac_srcdir/configure" --help=recursive else - echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 - fi - cd $ac_popdir + $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 + fi || ac_status=$? + cd "$ac_pwd" || { ac_status=$?; break; } done fi -test -n "$ac_init_help" && exit 0 +test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF Cantera configure 1.7.0 -generated by GNU Autoconf 2.59 +generated by GNU Autoconf 2.64 -Copyright (C) 2003 Free Software Foundation, Inc. +Copyright (C) 2009 Free Software Foundation, Inc. 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Returns whether the value could be +# computed +ac_fn_cxx_compute_int () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_lo=0 ac_mid=0 + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=$ac_mid; break +else + as_fn_arith $ac_mid + 1 && ac_lo=$as_val + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + as_fn_arith 2 '*' $ac_mid + 1 && ac_mid=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=-1 ac_mid=-1 + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_lo=$ac_mid; break +else + as_fn_arith '(' $ac_mid ')' - 1 && ac_hi=$as_val + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + as_fn_arith 2 '*' $ac_mid && ac_mid=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + ac_lo= ac_hi= +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + as_fn_arith '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo && ac_mid=$as_val + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=$ac_mid +else + as_fn_arith '(' $ac_mid ')' + 1 && ac_lo=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in #(( +?*) eval "$3=\$ac_lo"; ac_retval=0 ;; +'') ac_retval=1 ;; +esac + else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +static long int longval () { return $2; } +static unsigned long int ulongval () { return $2; } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (($2) < 0) + { + long int i = longval (); + if (i != ($2)) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ($2)) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_run "$LINENO"; then : + echo >>conftest.val; read $3 &5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + return $ac_retval + +} # ac_fn_cxx_try_cpp + +# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES +# --------------------------------------------------------- +# Tests whether HEADER exists and can be compiled using the include files in +# INCLUDES, setting the cache variable VAR accordingly. +ac_fn_cxx_check_header_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +#include <$2> +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + eval "$3=yes" +else + eval "$3=no" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + +} # ac_fn_cxx_check_header_compile + +# ac_fn_f77_try_compile LINENO +# ---------------------------- +# Try to compile conftest.$ac_ext, and return whether this succeeded. +ac_fn_f77_try_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + rm -f conftest.$ac_objext + if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_f77_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + return $ac_retval + +} # ac_fn_f77_try_compile +cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by Cantera $as_me 1.7.0, which was -generated by GNU Autoconf 2.59. Invocation command line was +generated by GNU Autoconf 2.64. Invocation command line was $ $0 $@ _ACEOF +exec 5>>config.log { cat <<_ASUNAME ## --------- ## @@ -1008,7 +1980,7 @@ uname -v = `(uname -v) 2>/dev/null || echo unknown` /bin/arch = `(/bin/arch) 2>/dev/null || echo unknown` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown` -hostinfo = `(hostinfo) 2>/dev/null || echo unknown` +/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown` /bin/machine = `(/bin/machine) 2>/dev/null || echo unknown` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown` /bin/universe = `(/bin/universe) 2>/dev/null || echo unknown` @@ -1020,8 +1992,9 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - echo "PATH: $as_dir" -done + $as_echo "PATH: $as_dir" + done +IFS=$as_save_IFS } >&5 @@ -1043,7 +2016,6 @@ _ACEOF ac_configure_args= ac_configure_args0= ac_configure_args1= -ac_sep= ac_must_keep_next=false for ac_pass in 1 2 do @@ -1054,13 +2026,13 @@ do -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) continue ;; - *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*) - ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) + ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; + 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; 2) - ac_configure_args1="$ac_configure_args1 '$ac_arg'" + as_fn_append ac_configure_args1 " '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1076,21 +2048,19 @@ do -* ) ac_must_keep_next=true ;; esac fi - ac_configure_args="$ac_configure_args$ac_sep'$ac_arg'" - # Get rid of the leading space. - ac_sep=" " + as_fn_append ac_configure_args " '$ac_arg'" ;; esac done done -$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } -$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } +{ ac_configure_args0=; unset ac_configure_args0;} +{ ac_configure_args1=; unset ac_configure_args1;} # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there # would cause problems or look ugly. -# WARNING: Be sure not to use single quotes in there, as some shells, -# such as our DU 5.0 friend, will then `close' the trap. +# WARNING: Use '\'' to represent an apostrophe within the trap. +# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug. trap 'exit_status=$? # Save into config.log some information that might help in debugging. { @@ -1103,20 +2073,35 @@ trap 'exit_status=$? _ASBOX echo # The following way of writing the cache mishandles newlines in values, -{ +( + for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do + eval ac_val=\$$ac_var + case $ac_val in #( + *${as_nl}*) + case $ac_var in #( + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 +$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + esac + case $ac_var in #( + _ | IFS | as_nl) ;; #( + BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( + *) { eval $ac_var=; unset $ac_var;} ;; + esac ;; + esac + done (set) 2>&1 | - case `(ac_space='"'"' '"'"'; set | grep ac_space) 2>&1` in - *ac_space=\ *) + case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #( + *${as_nl}ac_space=\ *) sed -n \ - "s/'"'"'/'"'"'\\\\'"'"''"'"'/g; - s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='"'"'\\2'"'"'/p" - ;; + "s/'\''/'\''\\\\'\'''\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p" + ;; #( *) - sed -n \ - "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p" + sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; - esac; -} + esac | + sort +) echo cat <<\_ASBOX @@ -1127,22 +2112,28 @@ _ASBOX echo for ac_var in $ac_subst_vars do - eval ac_val=$`echo $ac_var` - echo "$ac_var='"'"'$ac_val'"'"'" + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" done | sort echo if test -n "$ac_subst_files"; then cat <<\_ASBOX -## ------------- ## -## Output files. ## -## ------------- ## +## ------------------- ## +## File substitutions. ## +## ------------------- ## _ASBOX echo for ac_var in $ac_subst_files do - eval ac_val=$`echo $ac_var` - echo "$ac_var='"'"'$ac_val'"'"'" + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" done | sort echo fi @@ -1154,26 +2145,26 @@ _ASBOX ## ----------- ## _ASBOX echo - sed "/^$/d" confdefs.h | sort + cat confdefs.h echo fi test "$ac_signal" != 0 && - echo "$as_me: caught signal $ac_signal" - echo "$as_me: exit $exit_status" + $as_echo "$as_me: caught signal $ac_signal" + $as_echo "$as_me: exit $exit_status" } >&5 - rm -f core *.core && - rm -rf conftest* confdefs* conf$$* $ac_clean_files && + rm -f core *.core core.conftest.* && + rm -f -r conftest* confdefs* conf$$* $ac_clean_files && exit $exit_status - ' 0 +' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal + trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. -rm -rf conftest* confdefs.h -# AIX cpp loses on an empty file, so make sure it contains at least a newline. -echo >confdefs.h +rm -f -r conftest* confdefs.h + +$as_echo "/* confdefs.h */" > confdefs.h # Predefined preprocessor variables. @@ -1181,40 +2172,46 @@ cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF +cat >>confdefs.h <<_ACEOF +#define PACKAGE_URL "$PACKAGE_URL" +_ACEOF + # Let the site file select an alternate cache file if it wants to. -# Prefer explicitly selected file to automatically selected ones. -if test -z "$CONFIG_SITE"; then - if test "x$prefix" != xNONE; then - CONFIG_SITE="$prefix/share/config.site $prefix/etc/config.site" - else - CONFIG_SITE="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site" - fi +# Prefer an explicitly selected file to automatically selected ones. +ac_site_file1=NONE +ac_site_file2=NONE +if test -n "$CONFIG_SITE"; then + ac_site_file1=$CONFIG_SITE +elif test "x$prefix" != xNONE; then + ac_site_file1=$prefix/share/config.site + ac_site_file2=$prefix/etc/config.site +else + ac_site_file1=$ac_default_prefix/share/config.site + ac_site_file2=$ac_default_prefix/etc/config.site fi -for ac_site_file in $CONFIG_SITE; do +for ac_site_file in "$ac_site_file1" "$ac_site_file2" +do + test "x$ac_site_file" = xNONE && continue if test -r "$ac_site_file"; then - { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 -echo "$as_me: loading site script $ac_site_file" >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 +$as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 . "$ac_site_file" fi @@ -1224,53 +2221,63 @@ done # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false -for ac_var in `(set) 2>&1 | - sed -n 's/^ac_env_\([a-zA-Z_0-9]*\)_set=.*/\1/p'`; do +for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set - eval ac_old_val="\$ac_cv_env_${ac_var}_value" - eval ac_new_val="\$ac_env_${ac_var}_value" + eval ac_old_val=\$ac_cv_env_${ac_var}_value + eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 -echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 -echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then - { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 -echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} - { echo "$as_me:$LINENO: former value: $ac_old_val" >&5 -echo "$as_me: former value: $ac_old_val" >&2;} - { echo "$as_me:$LINENO: current value: $ac_new_val" >&5 -echo "$as_me: current value: $ac_new_val" >&2;} - ac_cache_corrupted=: + # differences in whitespace do not lead to failure. + ac_old_val_w=`echo x $ac_old_val` + ac_new_val_w=`echo x $ac_new_val` + if test "$ac_old_val_w" != "$ac_new_val_w"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 +$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} + ac_cache_corrupted=: + else + { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 +$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} + eval $ac_var=\$ac_old_val + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 +$as_echo "$as_me: former value: \`$ac_old_val'" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 +$as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in - *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*) - ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 -echo "$as_me: error: changes in the environment can compromise the build" >&2;} - { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 -echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} - { (exit 1); exit 1; }; } + { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 +$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} + as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi +## -------------------- ## +## Main body of script. ## +## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -1279,59 +2286,32 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu - - - - - - - - - - - - - - - - - - - - - - - - - - ac_config_headers="$ac_config_headers config.h" +ac_config_headers="$ac_config_headers config.h" # AC_CONFIG_AUX_DIR(.) # AC_CONFIG_SRCDIR(./License.txt) ac_aux_dir= -for ac_dir in config $srcdir/config; do - if test -f $ac_dir/install-sh; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/install-sh -c" - break - elif test -f $ac_dir/install.sh; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/install.sh -c" - break - elif test -f $ac_dir/shtool; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/shtool install -c" - break - fi +for ac_dir in config "$srcdir"/config; do + for ac_t in install-sh install.sh shtool; do + if test -f "$ac_dir/$ac_t"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/$ac_t -c" + break 2 + fi + done done if test -z "$ac_aux_dir"; then - { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in config $srcdir/config" >&5 -echo "$as_me: error: cannot find install-sh or install.sh in config $srcdir/config" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5 fi -ac_config_guess="$SHELL $ac_aux_dir/config.guess" -ac_config_sub="$SHELL $ac_aux_dir/config.sub" -ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# These three variables are undocumented and unsupported, +# and are intended to be withdrawn in a future Autoconf release. +# They can cause serious problems if a builder's source tree is in a directory +# whose full name contains unusual characters. +ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var. +ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var. +ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. + if test -z $CANTERA_VERSION ; then @@ -1356,9 +2336,7 @@ echo " " echo "--------------------------------------------------------------" echo " " -cat >>confdefs.h <<\_ACEOF -#define NDEBUG 1 -_ACEOF +$as_echo "#define NDEBUG 1" >>confdefs.h ac_sys_system=`uname -s` @@ -1558,79 +2536,107 @@ ct_mandir=${prefix} # Make sure we can run config.sub. -$ac_config_sub sun4 >/dev/null 2>&1 || - { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5 -echo "$as_me: error: cannot run $ac_config_sub" >&2;} - { (exit 1); exit 1; }; } +$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || + as_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 -echo "$as_me:$LINENO: checking build system type" >&5 -echo $ECHO_N "checking build system type... $ECHO_C" >&6 -if test "${ac_cv_build+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +$as_echo_n "checking build system type... " >&6; } +if test "${ac_cv_build+set}" = set; then : + $as_echo_n "(cached) " >&6 else - ac_cv_build_alias=$build_alias -test -z "$ac_cv_build_alias" && - ac_cv_build_alias=`$ac_config_guess` -test -z "$ac_cv_build_alias" && - { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 -echo "$as_me: error: cannot guess build type; you must specify one" >&2;} - { (exit 1); exit 1; }; } -ac_cv_build=`$ac_config_sub $ac_cv_build_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;} - { (exit 1); exit 1; }; } + ac_build_alias=$build_alias +test "x$ac_build_alias" = x && + ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` +test "x$ac_build_alias" = x && + as_fn_error "cannot guess build type; you must specify one" "$LINENO" 5 +ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || + as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 fi -echo "$as_me:$LINENO: result: $ac_cv_build" >&5 -echo "${ECHO_T}$ac_cv_build" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +$as_echo "$ac_cv_build" >&6; } +case $ac_cv_build in +*-*-*) ;; +*) as_fn_error "invalid value of canonical build" "$LINENO" 5;; +esac build=$ac_cv_build -build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_build +shift +build_cpu=$1 +build_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +build_os=$* +IFS=$ac_save_IFS +case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac -echo "$as_me:$LINENO: checking host system type" >&5 -echo $ECHO_N "checking host system type... $ECHO_C" >&6 -if test "${ac_cv_host+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +$as_echo_n "checking host system type... " >&6; } +if test "${ac_cv_host+set}" = set; then : + $as_echo_n "(cached) " >&6 else - ac_cv_host_alias=$host_alias -test -z "$ac_cv_host_alias" && - ac_cv_host_alias=$ac_cv_build_alias -ac_cv_host=`$ac_config_sub $ac_cv_host_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;} - { (exit 1); exit 1; }; } + if test "x$host_alias" = x; then + ac_cv_host=$ac_cv_build +else + ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || + as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 +fi fi -echo "$as_me:$LINENO: result: $ac_cv_host" >&5 -echo "${ECHO_T}$ac_cv_host" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +$as_echo "$ac_cv_host" >&6; } +case $ac_cv_host in +*-*-*) ;; +*) as_fn_error "invalid value of canonical host" "$LINENO" 5;; +esac host=$ac_cv_host -host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_host +shift +host_cpu=$1 +host_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +host_os=$* +IFS=$ac_save_IFS +case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -echo "$as_me:$LINENO: checking target system type" >&5 -echo $ECHO_N "checking target system type... $ECHO_C" >&6 -if test "${ac_cv_target+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 +$as_echo_n "checking target system type... " >&6; } +if test "${ac_cv_target+set}" = set; then : + $as_echo_n "(cached) " >&6 else - ac_cv_target_alias=$target_alias -test "x$ac_cv_target_alias" = "x" && - ac_cv_target_alias=$ac_cv_host_alias -ac_cv_target=`$ac_config_sub $ac_cv_target_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_target_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_target_alias failed" >&2;} - { (exit 1); exit 1; }; } + if test "x$target_alias" = x; then + ac_cv_target=$ac_cv_host +else + ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || + as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 +fi fi -echo "$as_me:$LINENO: result: $ac_cv_target" >&5 -echo "${ECHO_T}$ac_cv_target" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 +$as_echo "$ac_cv_target" >&6; } +case $ac_cv_target in +*-*-*) ;; +*) as_fn_error "invalid value of canonical target" "$LINENO" 5;; +esac target=$ac_cv_target -target_cpu=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -target_vendor=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -target_os=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_target +shift +target_cpu=$1 +target_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +target_os=$* +IFS=$ac_save_IFS +case $target_os in *\ *) target_os=`echo "$target_os" | sed 's/ /-/g'`;; esac # The aliases save the names the user supplied, while $host etc. @@ -1639,6 +2645,7 @@ test -n "$target_alias" && test "$program_prefix$program_suffix$program_transform_name" = \ NONENONEs,x,x, && program_prefix=${target_alias}- + # the root of the source tree ctroot=`(pwd)` builddir=$target @@ -1749,7 +2756,7 @@ if test -n "$USER_SRC_DIR"; then USERDIR=$USER_SRC_DIR; INCL_USER_CODE=1; fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -1775,20 +2782,24 @@ if test "$USE_SUNDIALS" = "default"; then # SUNDIALS_LIB_DIR had a space in it, despite use of double quotes everywhere #ldsave="$LDFLAGS" #LDFLAGS='-L'"$SUNDIALS_LIB_DIR"' '"$ldsave" -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +if test -z "$CXX"; then + if test -n "$CCC"; then + CXX=$CCC + else + if test -n "$ac_tool_prefix"; then + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then ac_cv_prog_CXX="$CXX" # Let the user override the test. @@ -1798,39 +2809,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - echo "$as_me:$LINENO: result: $CXX" >&5 -echo "${ECHO_T}$CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 +$as_echo "$CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CXX" && break done fi if test -z "$CXX"; then ac_ct_CXX=$CXX - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. @@ -1840,176 +2853,221 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 -echo "${ECHO_T}$ac_ct_CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 +$as_echo "$ac_ct_CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CXX" && break done -test -n "$ac_ct_CXX" || ac_ct_CXX="g++" - CXX=$ac_ct_CXX + if test "x$ac_ct_CXX" = x; then + CXX="g++" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CXX=$ac_ct_CXX + fi fi - + fi +fi # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C++ compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ - +#include int main () { +FILE *f = fopen ("conftest.out", "w"); + return ferror (f) || fclose (f) != 0; ; return 0; } _ACEOF ac_clean_files_save=$ac_clean_files -ac_clean_files="$ac_clean_files a.out a.exe b.out" +ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out conftest.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. -echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5 -echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6 -ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` -if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 - (eval $ac_link_default) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - # Find the output, starting from the most likely. 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If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run C++ compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +See \`config.log' for more details." "$LINENO" 5; } fi fi fi -echo "$as_me:$LINENO: result: yes" >&5 -echo "${ECHO_T}yes" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } -rm -f a.out a.exe conftest$ac_cv_exeext b.out +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out conftest.out ac_clean_files=$ac_clean_files_save -# Check the compiler produces executables we can run. If not, either +# Check that the compiler produces executables we can run. If not, either # the compiler is broken, or we cross compile. -echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 -echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 -echo "$as_me:$LINENO: result: $cross_compiling" >&5 -echo "${ECHO_T}$cross_compiling" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } -echo "$as_me:$LINENO: checking for suffix of executables" >&5 -echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : # If both `conftest.exe' and `conftest' are `present' (well, observable) # catch `conftest.exe'. For instance with Cygwin, `ls conftest' will # work properly (i.e., refer to `conftest.exe'), while it won't with @@ -2017,38 +3075,31 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 for ac_file in conftest.exe conftest conftest.*; do test -f "$ac_file" || continue case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - export ac_cv_exeext break;; * ) break;; esac done else - { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." "$LINENO" 5; } fi - rm -f conftest$ac_cv_exeext -echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 -echo "${ECHO_T}$ac_cv_exeext" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } rm -f conftest.$ac_ext EXEEXT=$ac_cv_exeext ac_exeext=$EXEEXT -echo "$as_me:$LINENO: checking for suffix of object files" >&5 -echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 -if test "${ac_cv_objext+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +$as_echo_n "checking for suffix of object files... " >&6; } +if test "${ac_cv_objext+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2060,45 +3111,46 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>&5 +if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>&5 ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + for ac_file in conftest.o conftest.obj conftest.*; do + test -f "$ac_file" || continue; case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;; *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` break;; esac done else - echo "$as_me: failed program was:" >&5 + $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "cannot compute suffix of object files: cannot compile +See \`config.log' for more details." "$LINENO" 5; } fi - rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 -echo "${ECHO_T}$ac_cv_objext" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +$as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2112,55 +3164,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 -GXX=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +$as_echo "$ac_cv_cxx_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GXX=yes +else + GXX= +fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -CXXFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 -echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cxx_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +$as_echo_n "checking whether $CXX accepts -g... " >&6; } +if test "${ac_cv_prog_cxx_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_cxx_werror_flag=$ac_cxx_werror_flag + ac_cxx_werror_flag=yes + ac_cv_prog_cxx_g=no + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2171,39 +3202,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CXXFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cxx_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + +else + ac_cxx_werror_flag=$ac_save_cxx_werror_flag + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_cv_prog_cxx_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cxx_werror_flag=$ac_save_cxx_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +$as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS elif test $ac_cv_prog_cxx_g = yes; then @@ -2219,185 +3260,51 @@ else CXXFLAGS= fi fi -for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi - -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking for CVodeCreate in -lsundials_cvodes" >&5 -echo $ECHO_N "checking for CVodeCreate in -lsundials_cvodes... $ECHO_C" >&6 -if test "${ac_cv_lib_sundials_cvodes_CVodeCreate+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CVodeCreate in -lsundials_cvodes" >&5 +$as_echo_n "checking for CVodeCreate in -lsundials_cvodes... " >&6; } +if test "${ac_cv_lib_sundials_cvodes_CVodeCreate+set}" = set; then : + $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsundials_cvodes \ -lsundials_cvodes -lsundials_nvecserial -lm $LIBS" -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ -/* Override any gcc2 internal prototype to avoid an error. */ +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif -/* We use char because int might match the return type of a gcc2 - builtin and then its argument prototype would still apply. */ char CVodeCreate (); int main () { -CVodeCreate (); +return CVodeCreate (); ; return 0; } _ACEOF -rm -f conftest.$ac_objext conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_sundials_cvodes_CVodeCreate=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_lib_sundials_cvodes_CVodeCreate=no + ac_cv_lib_sundials_cvodes_CVodeCreate=no fi -rm -f conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -echo "$as_me:$LINENO: result: $ac_cv_lib_sundials_cvodes_CVodeCreate" >&5 -echo "${ECHO_T}$ac_cv_lib_sundials_cvodes_CVodeCreate" >&6 -if test $ac_cv_lib_sundials_cvodes_CVodeCreate = yes; then +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sundials_cvodes_CVodeCreate" >&5 +$as_echo "$ac_cv_lib_sundials_cvodes_CVodeCreate" >&6; } +if test "x$ac_cv_lib_sundials_cvodes_CVodeCreate" = x""yes; then : use_sundials=1 else use_sundials=0 @@ -2434,13 +3341,9 @@ CVODE_LIBS='-lsundials_cvodes -lsundials_nvecserial' IDA_LIBS='-lsundials_ida -lsundials_nvecserial' if test "$SUNDIALS_VERSION" = "2.2"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_22 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_22 1" >>confdefs.h sundials_include='-I'${SUNDIALS_HOME}'/include -I'${SUNDIALS_HOME}'/include/sundials -I'${SUNDIALS_HOME}'/include/cvodes -I'${SUNDIALS_HOME}'/include/ida' echo "sundials include directory: " ${sundials_include} @@ -2449,13 +3352,9 @@ _ACEOF sundials_lib="-L$SUNDIALS_LIB_DIR -lsundials_cvodes -lsundials_ida -lsundials_nvecserial" sundials_lib_dep="$SUNDIALS_LIB_DIR/libsundials_cvodes.a $SUNDIALS_LIB_DIR/libsundials_ida.a $SUNDIALS_LIB_DIR/libsundials_nvecserial.a" elif test "$SUNDIALS_VERSION" = "2.3"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_23 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_23 1" >>confdefs.h sundials_include='-I'${SUNDIALS_INC_DIR} echo "sundials include directory: " ${sundials_include} @@ -2465,13 +3364,9 @@ _ACEOF sundials_lib_dep="$SUNDIALS_LIB_DIR/libsundials_cvodes.a $SUNDIALS_LIB_DIR/libsundials_ida.a $SUNDIALS_LIB_DIR/libsundials_nvecserial.a" # python tools/src/sundials_version.py $SUNDIALS_HOME elif test "$SUNDIALS_VERSION" = "2.4"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_24 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_24 1" >>confdefs.h sundials_include='-I'${SUNDIALS_INC_DIR} echo "sundials include directory: " ${sundials_include} @@ -2513,9 +3408,7 @@ fi DEBUG_MODE=${DEBUG_MODE:="n"} CANTERA_DEBUG_MODE=0 if test "$DEBUG_MODE" = "y" -o "$DEBUG_MODE" = "Y" ; then - cat >>confdefs.h <<\_ACEOF -#define DEBUG_MODE 1 -_ACEOF + $as_echo "#define DEBUG_MODE 1" >>confdefs.h CANTERA_DEBUG_MODE="1" else @@ -2542,32 +3435,24 @@ NEED_ZEROD= #fi if test "$WITH_METAL" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_METAL 1 -_ACEOF + $as_echo "#define WITH_METAL 1" >>confdefs.h hdrs=$hdrs' MetalPhase.h' fi if test "$WITH_SEMICONDUCTOR" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_SEMICONDUCTOR 1 -_ACEOF + $as_echo "#define WITH_SEMICONDUCTOR 1" >>confdefs.h hdrs=$hdrs' SemiconductorPhase.h' objs=$objs' SemiconductorPhase.o' fi if test "$WITH_ADSORBATE" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_ADSORBATE 1 -_ACEOF + $as_echo "#define WITH_ADSORBATE 1" >>confdefs.h hdrs=$hdrs' AdsorbateThermo.h' fi if test "$WITH_STOICH_SUBSTANCE" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_STOICH_SUBSTANCE 1 -_ACEOF + $as_echo "#define WITH_STOICH_SUBSTANCE 1" >>confdefs.h hdrs=$hdrs' StoichSubstance.h' objs=$objs' StoichSubstance.o' @@ -2575,9 +3460,7 @@ fi COMPILE_PURE_FLUIDS= if test "$WITH_PURE_FLUIDS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_PURE_FLUIDS 1 -_ACEOF + $as_echo "#define WITH_PURE_FLUIDS 1" >>confdefs.h COMPILE_PURE_FLUIDS=1 hdrs=$hdrs' PureFluidPhase.h' @@ -2586,9 +3469,7 @@ fi if test "$WITH_LATTICE_SOLID" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_LATTICE_SOLID 1 -_ACEOF + $as_echo "#define WITH_LATTICE_SOLID 1" >>confdefs.h hdrs=$hdrs' LatticeSolidPhase.h' objs=$objs' LatticeSolidPhase.o' @@ -2604,9 +3485,7 @@ phase_header_files=$hdrs NEED_CATHERMO= COMPILE_IDEAL_SOLUTIONS=0 if test "$WITH_IDEAL_SOLUTIONS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_IDEAL_SOLUTIONS 1 -_ACEOF + $as_echo "#define WITH_IDEAL_SOLUTIONS 1" >>confdefs.h NEED_CATHERMO=1 COMPILE_IDEAL_SOLUTIONS=1 @@ -2615,9 +3494,7 @@ fi COMPILE_ELECTROLYTES=0 if test "$WITH_ELECTROLYTES" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_ELECTROLYTES 1 -_ACEOF + $as_echo "#define WITH_ELECTROLYTES 1" >>confdefs.h NEED_CATHERMO=1 COMPILE_ELECTROLYTES=1 @@ -2627,17 +3504,13 @@ fi if test "$WITH_PRIME" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_PRIME 1 -_ACEOF + $as_echo "#define WITH_PRIME 1" >>confdefs.h fi COMPILE_KINETICS=0 if test "$WITH_KINETICS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_KINETICS 1 -_ACEOF + $as_echo "#define WITH_KINETICS 1" >>confdefs.h COMPILE_KINETICS=1 fi @@ -2646,9 +3519,7 @@ fi COMPILE_HETEROKIN=0 if test "$WITH_HETERO_KINETICS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_HETEROKINETICS 1 -_ACEOF + $as_echo "#define WITH_HETEROKINETICS 1" >>confdefs.h COMPILE_HETEROKIN=1 fi @@ -2656,9 +3527,7 @@ fi COMPILE_RXNPATH=0 if test "$WITH_REACTION_PATHS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_REACTIONPATHS 1 -_ACEOF + $as_echo "#define WITH_REACTIONPATHS 1" >>confdefs.h COMPILE_RXNPATH=1 fi @@ -2707,17 +3576,13 @@ fi if test "$ENABLE_TPX" = "y" ; then KERNEL=$KERNEL' 'tpx NEED_TPX=1 - cat >>confdefs.h <<\_ACEOF -#define INCL_PURE_FLUIDS 1 -_ACEOF + $as_echo "#define INCL_PURE_FLUIDS 1" >>confdefs.h fi NEED_SPECTRA=0 if test "$WITH_SPECTRA" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_SPECTRA 1 -_ACEOF + $as_echo "#define WITH_SPECTRA 1" >>confdefs.h KERNEL=$KERNEL' 'spectra NEED_SPECTRA=1 @@ -2730,9 +3595,7 @@ fi COMPILE_VCSNONIDEAL=0 if test "$WITH_VCSNONIDEAL" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_VCSNONIDEAL 1 -_ACEOF + $as_echo "#define WITH_VCSNONIDEAL 1" >>confdefs.h COMPILE_VCSNONIDEAL=1 fi @@ -2740,9 +3603,7 @@ fi COMPILE_H298MODIFY_CAPABILITY=0 if test "$WITH_H298MODIFY_CAPABILITY" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define H298MODIFY_CAPABILITY 1 -_ACEOF + $as_echo "#define H298MODIFY_CAPABILITY 1" >>confdefs.h COMPILE_H298MODIFY_CAPABILITY=1 fi @@ -2750,18 +3611,14 @@ fi if test "$WITH_HTML_LOG_FILES" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_HTML_LOGS 1 -_ACEOF + $as_echo "#define WITH_HTML_LOGS 1" >>confdefs.h fi BOOST_INCLUDE= BOOST_LIB= if test "$BUILD_THREAD_SAFE" = "y" ; then - cat >>confdefs.h <<\_ACEOF -#define THREAD_SAFE_CANTERA 1 -_ACEOF + $as_echo "#define THREAD_SAFE_CANTERA 1" >>confdefs.h BOOST_INCLUDE=-I$BOOST_INC_DIR BOOST_LIB=$BOOST_THREAD_LIB @@ -2901,9 +3758,7 @@ echo " " if test "x$PURIFY" != "x"; then - cat >>confdefs.h <<\_ACEOF -#define PURIFY_MODE 1 -_ACEOF + $as_echo "#define PURIFY_MODE 1" >>confdefs.h fi @@ -3169,9 +4024,7 @@ fi # case $ac_sys_system in SunOS* ) - cat >>confdefs.h <<\_ACEOF -#define NEEDS_GENERIC_TEMPL_STATIC_DECL 1 -_ACEOF + $as_echo "#define NEEDS_GENERIC_TEMPL_STATIC_DECL 1" >>confdefs.h echo 'Turned on special handing of static definitions in templated classes' ;; @@ -3209,9 +4062,7 @@ else exit 1 fi if test $BUILD_PYTHON = 0 ; then -cat >>confdefs.h <<\_ACEOF -#define HAS_NO_PYTHON 1 -_ACEOF +$as_echo "#define HAS_NO_PYTHON 1" >>confdefs.h fi @@ -3221,10 +4072,10 @@ if test "$PYTHON_CMD" = "default" -o \ do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_PYTHON_CMD+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_path_PYTHON_CMD+set}" = set; then : + $as_echo_n "(cached) " >&6 else case $PYTHON_CMD in [\\/]* | ?:[\\/]*) @@ -3236,28 +4087,29 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_PYTHON_CMD="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS ;; esac fi PYTHON_CMD=$ac_cv_path_PYTHON_CMD - if test -n "$PYTHON_CMD"; then - echo "$as_me:$LINENO: result: $PYTHON_CMD" >&5 -echo "${ECHO_T}$PYTHON_CMD" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PYTHON_CMD" >&5 +$as_echo "$PYTHON_CMD" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$PYTHON_CMD" && break done test -n "$PYTHON_CMD" || PYTHON_CMD=""none"" @@ -3285,24 +4137,18 @@ USE_NUMARRAY='y' if test "$USE_NUMERIC" = "y"; then USE_NUMARRAY='n' USE_NUMPY='n' -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMERIC 1 -_ACEOF +$as_echo "#define HAS_NUMERIC 1" >>confdefs.h fi if test "$USE_NUMPY" = "y"; then USE_NUMARRAY='n' -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMPY 1 -_ACEOF +$as_echo "#define HAS_NUMPY 1" >>confdefs.h fi if test "$USE_NUMARRAY" = "y"; then -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMARRAY 1 -_ACEOF +$as_echo "#define HAS_NUMARRAY 1" >>confdefs.h fi @@ -3434,10 +4280,10 @@ if test "$BUILD_MATLAB_TOOLBOX" != "n"; then "$MATLAB_CMD"x = "x"; then # Extract the first word of "matlab", so it can be a program name with args. set dummy matlab; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_MATLAB_CMD+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_path_MATLAB_CMD+set}" = set; then : + $as_echo_n "(cached) " >&6 else case $MATLAB_CMD in [\\/]* | ?:[\\/]*) @@ -3449,29 +4295,30 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_MATLAB_CMD="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS test -z "$ac_cv_path_MATLAB_CMD" && ac_cv_path_MATLAB_CMD=""none"" ;; esac fi MATLAB_CMD=$ac_cv_path_MATLAB_CMD - if test -n "$MATLAB_CMD"; then - echo "$as_me:$LINENO: result: $MATLAB_CMD" >&5 -echo "${ECHO_T}$MATLAB_CMD" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MATLAB_CMD" >&5 +$as_echo "$MATLAB_CMD" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + if test "$MATLAB_CMD" = "none"; then MATLAB_CMD=`find /*/MATLAB*/bin/m* -name matlab` fi @@ -3490,8 +4337,8 @@ fi echo "Windows MATLAB command: ${MATLAB_CMD}" fi - echo "$as_me:$LINENO: checking MATLAB ($MATLAB_CMD)" >&5 -echo $ECHO_N "checking MATLAB ($MATLAB_CMD)... $ECHO_C" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking MATLAB ($MATLAB_CMD)" >&5 +$as_echo_n "checking MATLAB ($MATLAB_CMD)... " >&6; } rm -f diary cat >> testmat.m << EOF diary; @@ -3594,22 +4441,23 @@ echo 'checking for Position independent code command ... ' $PIC # SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" # OS/2's system install, which has a completely different semantic # ./install, which can be erroneously created by make from ./install.sh. -echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 -echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if test "${ac_cv_path_install+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +if test "${ac_cv_path_install+set}" = set; then : + $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - # Account for people who put trailing slashes in PATH elements. -case $as_dir/ in - ./ | .// | /cC/* | \ + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in #(( + ./ | .// | /[cC]/* | \ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ - ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -3617,7 +4465,7 @@ case $as_dir/ in # by default. for ac_prog in ginstall scoinst install; do for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then if test $ac_prog = install && grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then # AIX install. It has an incompatible calling convention. @@ -3627,30 +4475,43 @@ case $as_dir/ in # program-specific install script used by HP pwplus--don't use. : else - ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" - break 3 + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi fi fi done done ;; esac -done + done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir fi if test "${ac_cv_path_install+set}" = set; then INSTALL=$ac_cv_path_install else - # As a last resort, use the slow shell script. We don't cache a - # path for INSTALL within a source directory, because that will + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will # break other packages using the cache if that directory is - # removed, or if the path is relative. + # removed, or if the value is a relative name. INSTALL=$ac_install_sh fi fi -echo "$as_me:$LINENO: result: $INSTALL" >&5 -echo "${ECHO_T}$INSTALL" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. # It thinks the first close brace ends the variable substitution. @@ -3670,11 +4531,19 @@ test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' # doesn't have this problem. So, I changed the default # install program to config/install-sh, which should work # on all platforms since its a bourne shell script +# HKM 12/24/2009 - Ran into another problem with the new cygwin 1.7.1. +# THe install (and even cp -f in some cases) program will fail +# when an existing different file is in place. This occurs sometimes +# and I can not quite nail down when. However replacing +# the install command for cygwin. Note, install no longer +# needs to have a wildcard capability within Cantera. + +case $ac_sys_system in + CYGWIN* ) + INSTALL=${INSTALL_BIN:=config/install-sh} + echo 'INSTALL program has been set to ' $INSTALL;; +esac -# problem: install-sh does not handle wildcards in filename. -# commenting this out (DGG) -# INSTALL=${INSTALL_BIN:=config/install-sh} -echo 'INSTALL program has been set to ' $INSTALL # # precompile_headers still relevant? # @@ -3714,20 +4583,24 @@ if test "x$OS_IS_WIN" = "x1"; then #CXX=cl.exe #CC=cl.exe #export CXX - ac_ext=cc + ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +if test -z "$CXX"; then + if test -n "$CCC"; then + CXX=$CCC + else + if test -n "$ac_tool_prefix"; then + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then ac_cv_prog_CXX="$CXX" # Let the user override the test. @@ -3737,39 +4610,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - echo "$as_me:$LINENO: result: $CXX" >&5 -echo "${ECHO_T}$CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 +$as_echo "$CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CXX" && break done fi if test -z "$CXX"; then ac_ct_CXX=$CXX - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. @@ -3779,64 +4654,77 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 -echo "${ECHO_T}$ac_ct_CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 +$as_echo "$ac_ct_CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CXX" && break done -test -n "$ac_ct_CXX" || ac_ct_CXX="g++" - CXX=$ac_ct_CXX + if test "x$ac_ct_CXX" = x; then + CXX="g++" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CXX=$ac_ct_CXX + fi fi - + fi +fi # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C++ compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3850,55 +4738,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 -GXX=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +$as_echo "$ac_cv_cxx_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GXX=yes +else + GXX= +fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -CXXFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 -echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cxx_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +$as_echo_n "checking whether $CXX accepts -g... " >&6; } +if test "${ac_cv_prog_cxx_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_cxx_werror_flag=$ac_cxx_werror_flag + ac_cxx_werror_flag=yes + ac_cv_prog_cxx_g=no + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3909,39 +4776,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CXXFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cxx_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + +else + ac_cxx_werror_flag=$ac_save_cxx_werror_flag + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_cv_prog_cxx_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cxx_werror_flag=$ac_save_cxx_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +$as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS elif test $ac_cv_prog_cxx_g = yes; then @@ -3957,113 +4834,7 @@ else CXXFLAGS= fi fi -for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi - -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -4077,10 +4848,10 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -4090,35 +4861,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -4128,39 +4901,50 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then - if test -n "$ac_tool_prefix"; then - # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -4170,77 +4954,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi -fi -if test -z "$ac_cv_prog_CC"; then - ac_ct_CC=$CC - # Extract the first word of "cc", so it can be a program name with args. -set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_CC"; then - ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 + fi -done -done - -fi -fi -ac_ct_CC=$ac_cv_prog_ac_ct_CC -if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - CC=$ac_ct_CC -else - CC="$ac_cv_prog_CC" -fi - fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -4251,18 +4995,19 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. @@ -4280,24 +5025,25 @@ fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -4307,39 +5053,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -4349,71 +5097,83 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CC" && break done - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi fi fi -test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&5 -echo "$as_me: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "no acceptable C compiler found in \$PATH +See \`config.log' for more details." "$LINENO" 5; } # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 -if test "${ac_cv_c_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if test "${ac_cv_c_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -4427,55 +5187,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 -GCC=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -CFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 -echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if test "${ac_cv_prog_cc_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -4486,39 +5225,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cc_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS elif test $ac_cv_prog_cc_g = yes; then @@ -4534,18 +5283,14 @@ else CFLAGS= fi fi -echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 -echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if test "${ac_cv_prog_cc_c89+set}" = set; then : + $as_echo_n "(cached) " >&6 else - ac_cv_prog_cc_stdc=no + ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -4573,12 +5318,17 @@ static char *f (char * (*g) (char **, int), char **p, ...) /* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has function prototypes and stuff, but not '\xHH' hex character constants. These don't provoke an error unfortunately, instead are silently treated - as 'x'. The following induces an error, until -std1 is added to get + as 'x'. The following induces an error, until -std is added to get proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an array size at least. It's necessary to write '\x00'==0 to get something - that's true only with -std1. */ + that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; @@ -4593,206 +5343,38 @@ return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; return 0; } _ACEOF -# Don't try gcc -ansi; that turns off useful extensions and -# breaks some systems' header files. -# AIX -qlanglvl=ansi -# Ultrix and OSF/1 -std1 -# HP-UX 10.20 and later -Ae -# HP-UX older versions -Aa -D_HPUX_SOURCE -# SVR4 -Xc -D__EXTENSIONS__ -for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_cc_stdc=$ac_arg -break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg fi -rm -f conftest.err conftest.$ac_objext +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break done -rm -f conftest.$ac_ext conftest.$ac_objext +rm -f conftest.$ac_ext CC=$ac_save_CC fi - -case "x$ac_cv_prog_cc_stdc" in - x|xno) - echo "$as_me:$LINENO: result: none needed" >&5 -echo "${ECHO_T}none needed" >&6 ;; +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; *) - echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 - CC="$CC $ac_cv_prog_cc_stdc" ;; + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac - -# Some people use a C++ compiler to compile C. Since we use `exit', -# in C++ we need to declare it. In case someone uses the same compiler -# for both compiling C and C++ we need to have the C++ compiler decide -# the declaration of exit, since it's the most demanding environment. -cat >conftest.$ac_ext <<_ACEOF -#ifndef __cplusplus - choke me -#endif -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if test "x$ac_cv_prog_cc_c89" != xno; then : fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -4804,20 +5386,24 @@ else # Determines the CXX compiler to use # export CXX -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +if test -z "$CXX"; then + if test -n "$CCC"; then + CXX=$CCC + else + if test -n "$ac_tool_prefix"; then + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then ac_cv_prog_CXX="$CXX" # Let the user override the test. @@ -4827,39 +5413,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - echo "$as_me:$LINENO: result: $CXX" >&5 -echo "${ECHO_T}$CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 +$as_echo "$CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CXX" && break done fi if test -z "$CXX"; then ac_ct_CXX=$CXX - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. @@ -4869,64 +5457,77 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 -echo "${ECHO_T}$ac_ct_CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 +$as_echo "$ac_ct_CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CXX" && break done -test -n "$ac_ct_CXX" || ac_ct_CXX="g++" - CXX=$ac_ct_CXX + if test "x$ac_ct_CXX" = x; then + CXX="g++" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CXX=$ac_ct_CXX + fi fi - + fi +fi # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C++ compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -4940,55 +5541,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 -GXX=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +$as_echo "$ac_cv_cxx_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GXX=yes +else + GXX= +fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -CXXFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 -echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cxx_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +$as_echo_n "checking whether $CXX accepts -g... " >&6; } +if test "${ac_cv_prog_cxx_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_cxx_werror_flag=$ac_cxx_werror_flag + ac_cxx_werror_flag=yes + ac_cv_prog_cxx_g=no + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -4999,39 +5579,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CXXFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cxx_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + +else + ac_cxx_werror_flag=$ac_save_cxx_werror_flag + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_cv_prog_cxx_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cxx_werror_flag=$ac_save_cxx_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +$as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS elif test $ac_cv_prog_cxx_g = yes; then @@ -5047,113 +5637,7 @@ else CXXFLAGS= fi fi -for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi - -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -5167,10 +5651,10 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -5180,35 +5664,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -5218,39 +5704,50 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then - if test -n "$ac_tool_prefix"; then - # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -5260,77 +5757,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi -fi -if test -z "$ac_cv_prog_CC"; then - ac_ct_CC=$CC - # Extract the first word of "cc", so it can be a program name with args. -set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_CC"; then - ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 + fi -done -done - -fi -fi -ac_ct_CC=$ac_cv_prog_ac_ct_CC -if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - CC=$ac_ct_CC -else - CC="$ac_cv_prog_CC" -fi - fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -5341,18 +5798,19 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. @@ -5370,24 +5828,25 @@ fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -5397,39 +5856,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -5439,71 +5900,83 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CC" && break done - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi fi fi -test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&5 -echo "$as_me: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "no acceptable C compiler found in \$PATH +See \`config.log' for more details." "$LINENO" 5; } # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 -if test "${ac_cv_c_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if test "${ac_cv_c_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -5517,55 +5990,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 -GCC=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -CFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 -echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if test "${ac_cv_prog_cc_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -5576,39 +6028,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cc_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS elif test $ac_cv_prog_cc_g = yes; then @@ -5624,18 +6086,14 @@ else CFLAGS= fi fi -echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 -echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if test "${ac_cv_prog_cc_c89+set}" = set; then : + $as_echo_n "(cached) " >&6 else - ac_cv_prog_cc_stdc=no + ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -5663,12 +6121,17 @@ static char *f (char * (*g) (char **, int), char **p, ...) /* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has function prototypes and stuff, but not '\xHH' hex character constants. These don't provoke an error unfortunately, instead are silently treated - as 'x'. The following induces an error, until -std1 is added to get + as 'x'. The following induces an error, until -std is added to get proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an array size at least. It's necessary to write '\x00'==0 to get something - that's true only with -std1. */ + that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; @@ -5683,206 +6146,38 @@ return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; return 0; } _ACEOF -# Don't try gcc -ansi; that turns off useful extensions and -# breaks some systems' header files. -# AIX -qlanglvl=ansi -# Ultrix and OSF/1 -std1 -# HP-UX 10.20 and later -Ae -# HP-UX older versions -Aa -D_HPUX_SOURCE -# SVR4 -Xc -D__EXTENSIONS__ -for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_cc_stdc=$ac_arg -break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg fi -rm -f conftest.err conftest.$ac_objext +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break done -rm -f conftest.$ac_ext conftest.$ac_objext +rm -f conftest.$ac_ext CC=$ac_save_CC fi - -case "x$ac_cv_prog_cc_stdc" in - x|xno) - echo "$as_me:$LINENO: result: none needed" >&5 -echo "${ECHO_T}none needed" >&6 ;; +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; *) - echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 - CC="$CC $ac_cv_prog_cc_stdc" ;; + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac - -# Some people use a C++ compiler to compile C. Since we use `exit', -# in C++ we need to declare it. In case someone uses the same compiler -# for both compiling C and C++ we need to have the C++ compiler decide -# the declaration of exit, since it's the most demanding environment. -cat >conftest.$ac_ext <<_ACEOF -#ifndef __cplusplus - choke me -#endif -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if test "x$ac_cv_prog_cc_c89" != xno; then : fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -5890,35 +6185,33 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking for ability to precompile headers" >&5 -echo $ECHO_N "checking for ability to precompile headers... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ability to precompile headers" >&5 +$as_echo_n "checking for ability to precompile headers... " >&6; } if test -n "$GCC"; then msg=`rm -f *h.gch; $CXX testpch.h &> /dev/null` if test -f testpch.h.gch; then precompile_headers=yes - cat >>confdefs.h <<\_ACEOF -#define USE_PCH 1 -_ACEOF + $as_echo "#define USE_PCH 1" >>confdefs.h fi fi -echo "$as_me:$LINENO: result: ${precompile_headers}" >&5 -echo "${ECHO_T}${precompile_headers}" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${precompile_headers}" >&5 +$as_echo "${precompile_headers}" >&6; } # End of the OS_IS_WIN section fi # Sizes of various common basic types -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5 -echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5 +$as_echo_n "checking how to run the C++ preprocessor... " >&6; } if test -z "$CXXCPP"; then - if test "${ac_cv_prog_CXXCPP+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 + if test "${ac_cv_prog_CXXCPP+set}" = set; then : + $as_echo_n "(cached) " >&6 else # Double quotes because CXXCPP needs to be expanded for CXXCPP in "$CXX -E" "/lib/cpp" @@ -5932,11 +6225,7 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -5945,68 +6234,24 @@ cat >>conftest.$ac_ext <<_ACEOF #endif Syntax error _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext - # OK, works on sane cases. Now check whether non-existent headers + # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then +if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - # Passes both tests. ac_preproc_ok=: break @@ -6016,7 +6261,7 @@ rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext -if $ac_preproc_ok; then +if $ac_preproc_ok; then : break fi @@ -6028,8 +6273,8 @@ fi else ac_cv_prog_CXXCPP=$CXXCPP fi -echo "$as_me:$LINENO: result: $CXXCPP" >&5 -echo "${ECHO_T}$CXXCPP" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5 +$as_echo "$CXXCPP" >&6; } ac_preproc_ok=false for ac_cxx_preproc_warn_flag in '' yes do @@ -6039,11 +6284,7 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -6052,68 +6293,24 @@ cat >>conftest.$ac_ext <<_ACEOF #endif Syntax error _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext - # OK, works on sane cases. Now check whether non-existent headers + # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then +if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - # Passes both tests. ac_preproc_ok=: break @@ -6123,48 +6320,158 @@ rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext -if $ac_preproc_ok; then - : +if $ac_preproc_ok; then : + else - { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check -See \`config.log' for more details." >&5 -echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." "$LINENO" 5; } fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking for egrep" >&5 -echo $ECHO_N "checking for egrep... $ECHO_C" >&6 -if test "${ac_cv_prog_egrep+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +$as_echo_n "checking for grep that handles long lines and -e... " >&6; } +if test "${ac_cv_path_GREP+set}" = set; then : + $as_echo_n "(cached) " >&6 else - if echo a | (grep -E '(a|b)') >/dev/null 2>&1 - then ac_cv_prog_egrep='grep -E' - else ac_cv_prog_egrep='egrep' + if test -z "$GREP"; then + ac_path_GREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in grep ggrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue +# Check for GNU ac_path_GREP and select it if it is found. + # Check for GNU $ac_path_GREP +case `"$ac_path_GREP" --version 2>&1` in +*GNU*) + ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'GREP' >> "conftest.nl" + "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_GREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_GREP="$ac_path_GREP" + ac_path_GREP_max=$ac_count fi -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 -echo "${ECHO_T}$ac_cv_prog_egrep" >&6 - EGREP=$ac_cv_prog_egrep + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac - -echo "$as_me:$LINENO: checking for ANSI C header files" >&5 -echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 -if test "${ac_cv_header_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 + $ac_path_GREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_GREP"; then + as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_cv_path_GREP=$GREP +fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +$as_echo "$ac_cv_path_GREP" >&6; } + GREP="$ac_cv_path_GREP" + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +$as_echo_n "checking for egrep... " >&6; } +if test "${ac_cv_path_EGREP+set}" = set; then : + $as_echo_n "(cached) " >&6 +else + if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 + then ac_cv_path_EGREP="$GREP -E" + else + if test -z "$EGREP"; then + ac_path_EGREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in egrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue +# Check for GNU ac_path_EGREP and select it if it is found. + # Check for GNU $ac_path_EGREP +case `"$ac_path_EGREP" --version 2>&1` in +*GNU*) + ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'EGREP' >> "conftest.nl" + "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_EGREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_EGREP="$ac_path_EGREP" + ac_path_EGREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_EGREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_EGREP"; then + as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi +else + ac_cv_path_EGREP=$EGREP +fi + + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +$as_echo "$ac_cv_path_EGREP" >&6; } + EGREP="$ac_cv_path_EGREP" + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +$as_echo_n "checking for ANSI C header files... " >&6; } +if test "${ac_cv_header_stdc+set}" = set; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -6179,51 +6486,23 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_header_stdc=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_header_stdc=no + ac_cv_header_stdc=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then - : + $EGREP "memchr" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -6233,18 +6512,14 @@ fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then - : + $EGREP "free" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -6254,16 +6529,13 @@ fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. - if test "$cross_compiling" = yes; then + if test "$cross_compiling" = yes; then : : else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include +#include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) @@ -6283,109 +6555,40 @@ main () for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) - exit(2); - exit (0); + return 2; + return 0; } _ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_run "$LINENO"; then : -( exit $ac_status ) -ac_cv_header_stdc=no +else + ac_cv_header_stdc=no fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext +fi + fi fi -fi -echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 -echo "${ECHO_T}$ac_cv_header_stdc" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +$as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -cat >>confdefs.h <<\_ACEOF -#define STDC_HEADERS 1 -_ACEOF +$as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. - - - - - - - - - for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h -do -as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` -echo "$as_me:$LINENO: checking for $ac_header" >&5 -echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 -if eval "test \"\${$as_ac_Header+set}\" = set"; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default - -#include <$ac_header> -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - eval "$as_ac_Header=yes" -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -eval "$as_ac_Header=no" -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 -echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 -if test `eval echo '${'$as_ac_Header'}'` = yes; then +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default +" +eval as_val=\$$as_ac_Header + if test "x$as_val" = x""yes; then : cat >>confdefs.h <<_ACEOF -#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi @@ -6393,3313 +6596,273 @@ fi done -echo "$as_me:$LINENO: checking for int" >&5 -echo $ECHO_N "checking for int... $ECHO_C" >&6 -if test "${ac_cv_type_int+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of int" >&5 +$as_echo_n "checking size of int... " >&6; } +if test "${ac_cv_sizeof_int+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((int *) 0) - return 0; -if (sizeof (int)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_int=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (int))" "ac_cv_sizeof_int" "$ac_includes_default"; then : -ac_cv_type_int=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_int" >&5 -echo "${ECHO_T}$ac_cv_type_int" >&6 - -echo "$as_me:$LINENO: checking size of int" >&5 -echo $ECHO_N "checking size of int... $ECHO_C" >&6 -if test "${ac_cv_sizeof_int+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_int" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (int) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_int=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_int" >&5 +$as_echo "$ac_cv_sizeof_int" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_int=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (int)); } -unsigned long ulongval () { return (long) (sizeof (int)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (int))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (int)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (int)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_int=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_int=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_int" >&5 -echo "${ECHO_T}$ac_cv_sizeof_int" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_INT $ac_cv_sizeof_int _ACEOF -echo "$as_me:$LINENO: checking for long" >&5 -echo $ECHO_N "checking for long... $ECHO_C" >&6 -if test "${ac_cv_type_long+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of long" >&5 +$as_echo_n "checking size of long... " >&6; } +if test "${ac_cv_sizeof_long+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((long *) 0) - return 0; -if (sizeof (long)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_long=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (long))" "ac_cv_sizeof_long" "$ac_includes_default"; then : -ac_cv_type_long=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_long" >&5 -echo "${ECHO_T}$ac_cv_type_long" >&6 - -echo "$as_me:$LINENO: checking size of long" >&5 -echo $ECHO_N "checking size of long... $ECHO_C" >&6 -if test "${ac_cv_sizeof_long+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_long" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (long) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_long=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_long" >&5 +$as_echo "$ac_cv_sizeof_long" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_long=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (long), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (long), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (long)); } -unsigned long ulongval () { return (long) (sizeof (long)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (long))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (long)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (long)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if test "${ac_cv_sizeof_void_p+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((void * *) 0) - return 0; -if (sizeof (void *)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_void_p=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (void *))" "ac_cv_sizeof_void_p" "$ac_includes_default"; then : -ac_cv_type_void_p=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_void_p" >&5 -echo "${ECHO_T}$ac_cv_type_void_p" >&6 - -echo "$as_me:$LINENO: checking size of void *" >&5 -echo $ECHO_N "checking size of void *... $ECHO_C" >&6 -if test "${ac_cv_sizeof_void_p+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_void_p" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (void *) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_void_p=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_void_p" >&5 +$as_echo "$ac_cv_sizeof_void_p" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_void_p=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (void *)); } -unsigned long ulongval () { return (long) (sizeof (void *)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (void *))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (void *)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (void *)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if test "${ac_cv_sizeof_char+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((char *) 0) - return 0; -if (sizeof (char)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_char=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (char))" "ac_cv_sizeof_char" "$ac_includes_default"; then : -ac_cv_type_char=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_char" >&5 -echo "${ECHO_T}$ac_cv_type_char" >&6 - -echo "$as_me:$LINENO: checking size of char" >&5 -echo $ECHO_N "checking size of char... $ECHO_C" >&6 -if test "${ac_cv_sizeof_char+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_char" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (char) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_char=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? 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- echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_char" >&5 +$as_echo "$ac_cv_sizeof_char" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_char=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (char), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (char), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (char)); } -unsigned long ulongval () { return (long) (sizeof (char)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (char))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (char)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (char)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if test "${ac_cv_sizeof_short+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((short *) 0) - return 0; -if (sizeof (short)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_short=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (short))" "ac_cv_sizeof_short" "$ac_includes_default"; then : -ac_cv_type_short=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_short" >&5 -echo "${ECHO_T}$ac_cv_type_short" >&6 - -echo "$as_me:$LINENO: checking size of short" >&5 -echo $ECHO_N "checking size of short... $ECHO_C" >&6 -if test "${ac_cv_sizeof_short+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_short" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (short) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_short=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_short" >&5 +$as_echo "$ac_cv_sizeof_short" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_short=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (short)); } -unsigned long ulongval () { return (long) (sizeof (short)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (short))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (short)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (short)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if test "${ac_cv_sizeof_float+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((float *) 0) - return 0; -if (sizeof (float)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_float=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (float))" "ac_cv_sizeof_float" "$ac_includes_default"; then : -ac_cv_type_float=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_float" >&5 -echo "${ECHO_T}$ac_cv_type_float" >&6 - -echo "$as_me:$LINENO: checking size of float" >&5 -echo $ECHO_N "checking size of float... $ECHO_C" >&6 -if test "${ac_cv_sizeof_float+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_float" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (float) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_float=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? 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- echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_float" >&5 +$as_echo "$ac_cv_sizeof_float" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_float=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (float)); } -unsigned long ulongval () { return (long) (sizeof (float)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (float))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (float)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (float)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if test "${ac_cv_sizeof_double+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((double *) 0) - return 0; -if (sizeof (double)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_double=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (double))" "ac_cv_sizeof_double" "$ac_includes_default"; then : -ac_cv_type_double=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_double" >&5 -echo "${ECHO_T}$ac_cv_type_double" >&6 - -echo "$as_me:$LINENO: checking size of double" >&5 -echo $ECHO_N "checking size of double... $ECHO_C" >&6 -if test "${ac_cv_sizeof_double+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_double" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (double) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_double=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_double" >&5 +$as_echo "$ac_cv_sizeof_double" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_double=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (double)); } -unsigned long ulongval () { return (long) (sizeof (double)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (double))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (double)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (double)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_double=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_double=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_double" >&5 -echo "${ECHO_T}$ac_cv_sizeof_double" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_DOUBLE $ac_cv_sizeof_double _ACEOF -echo "$as_me:$LINENO: checking for fpos_t" >&5 -echo $ECHO_N "checking for fpos_t... $ECHO_C" >&6 -if test "${ac_cv_type_fpos_t+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of fpos_t" >&5 +$as_echo_n "checking size of fpos_t... " >&6; } +if test "${ac_cv_sizeof_fpos_t+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((fpos_t *) 0) - return 0; -if (sizeof (fpos_t)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_fpos_t=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (fpos_t))" "ac_cv_sizeof_fpos_t" "$ac_includes_default"; then : -ac_cv_type_fpos_t=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_fpos_t" >&5 -echo "${ECHO_T}$ac_cv_type_fpos_t" >&6 - -echo "$as_me:$LINENO: checking size of fpos_t" >&5 -echo $ECHO_N "checking size of fpos_t... $ECHO_C" >&6 -if test "${ac_cv_sizeof_fpos_t+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_fpos_t" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ as_fn_set_status 77 +as_fn_error "cannot compute sizeof (fpos_t) +See \`config.log' for more details." "$LINENO" 5; }; } + else + ac_cv_sizeof_fpos_t=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_fpos_t" >&5 +$as_echo "$ac_cv_sizeof_fpos_t" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_fpos_t=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (fpos_t)); } -unsigned long ulongval () { return (long) (sizeof (fpos_t)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (fpos_t))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (fpos_t)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (fpos_t)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_fpos_t=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_fpos_t=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_fpos_t" >&5 -echo "${ECHO_T}$ac_cv_sizeof_fpos_t" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_FPOS_T $ac_cv_sizeof_fpos_t _ACEOF @@ -9751,8 +6914,8 @@ esac has_sstream=no -echo "$as_me:$LINENO: checking for sstream" >&5 -echo $ECHO_N "checking for sstream... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sstream" >&5 +$as_echo_n "checking for sstream... " >&6; } cat >> testsstream.cpp << EOF #include main() {} @@ -9761,14 +6924,12 @@ EOF if test -f testsstream.o; then has_sstream=yes rm testsstream.o - cat >>confdefs.h <<\_ACEOF -#define HAS_SSTREAM 1 -_ACEOF + $as_echo "#define HAS_SSTREAM 1" >>confdefs.h fi rm -f testsstream.cpp -echo "$as_me:$LINENO: result: ${has_sstream}" >&5 -echo "${ECHO_T}${has_sstream}" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${has_sstream}" >&5 +$as_echo "${has_sstream}" >&6; } # # Determine if we have a command to strip symbols from an object file @@ -9793,14 +6954,14 @@ ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_f77_compiler_gnu if test -n "$ac_tool_prefix"; then - for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran + for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgf95 lf95 ftn do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_F77+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_F77+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$F77"; then ac_cv_prog_F77="$F77" # Let the user override the test. @@ -9810,39 +6971,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_F77="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi F77=$ac_cv_prog_F77 if test -n "$F77"; then - echo "$as_me:$LINENO: result: $F77" >&5 -echo "${ECHO_T}$F77" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $F77" >&5 +$as_echo "$F77" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$F77" && break done fi if test -z "$F77"; then ac_ct_F77=$F77 - for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran + for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgf95 lf95 ftn do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_F77+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_F77+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_F77"; then ac_cv_prog_ac_ct_F77="$ac_ct_F77" # Let the user override the test. @@ -9852,64 +7015,81 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_F77="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_F77=$ac_cv_prog_ac_ct_F77 if test -n "$ac_ct_F77"; then - echo "$as_me:$LINENO: result: $ac_ct_F77" >&5 -echo "${ECHO_T}$ac_ct_F77" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_F77" >&5 +$as_echo "$ac_ct_F77" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_F77" && break done - F77=$ac_ct_F77 + if test "x$ac_ct_F77" = x; then + F77="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + F77=$ac_ct_F77 + fi fi # Provide some information about the compiler. -echo "$as_me:9883:" \ - "checking for Fortran 77 compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + rm -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done rm -f a.out # If we don't use `.F' as extension, the preprocessor is not run on the # input file. (Note that this only needs to work for GNU compilers.) ac_save_ext=$ac_ext ac_ext=F -echo "$as_me:$LINENO: checking whether we are using the GNU Fortran 77 compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU Fortran 77 compiler... $ECHO_C" >&6 -if test "${ac_cv_f77_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU Fortran 77 compiler" >&5 +$as_echo_n "checking whether we are using the GNU Fortran 77 compiler... " >&6; } +if test "${ac_cv_f77_compiler_gnu+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main #ifndef __GNUC__ choke me @@ -9917,90 +7097,42 @@ else end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_f77_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_f77_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_f77_compiler_gnu" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_f77_compiler_gnu" >&5 +$as_echo "$ac_cv_f77_compiler_gnu" >&6; } ac_ext=$ac_save_ext ac_test_FFLAGS=${FFLAGS+set} ac_save_FFLAGS=$FFLAGS FFLAGS= -echo "$as_me:$LINENO: checking whether $F77 accepts -g" >&5 -echo $ECHO_N "checking whether $F77 accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_f77_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $F77 accepts -g" >&5 +$as_echo_n "checking whether $F77 accepts -g... " >&6; } +if test "${ac_cv_prog_f77_g+set}" = set; then : + $as_echo_n "(cached) " >&6 else FFLAGS=-g -cat >conftest.$ac_ext <<_ACEOF +cat > conftest.$ac_ext <<_ACEOF program main end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_cv_prog_f77_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_prog_f77_g=no + ac_cv_prog_f77_g=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_g" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_g" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_f77_g" >&5 +$as_echo "$ac_cv_prog_f77_g" >&6; } if test "$ac_test_FFLAGS" = set; then FFLAGS=$ac_save_FFLAGS elif test $ac_cv_prog_f77_g = yes; then @@ -10017,8 +7149,12 @@ else fi fi -G77=`test $ac_compiler_gnu = yes && echo yes` -ac_ext=cc +if test $ac_compiler_gnu = yes; then + G77=yes +else + G77= +fi +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10040,42 +7176,21 @@ ac_ext=f ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_f77_compiler_gnu -echo "$as_me:$LINENO: checking how to get verbose linking output from $F77" >&5 -echo $ECHO_N "checking how to get verbose linking output from $F77... $ECHO_C" >&6 -if test "${ac_cv_prog_f77_v+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $F77" >&5 +$as_echo_n "checking how to get verbose linking output from $F77... " >&6; } +if test "${ac_cv_prog_f77_v+set}" = set; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_cv_prog_f77_v= # Try some options frequently used verbose output for ac_verb in -v -verbose --verbose -V -\#\#\#; do - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main end @@ -10087,20 +7202,28 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10090: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 +eval "set x $ac_link" +shift +$as_echo "$as_me:${as_lineno-$LINENO}: $*" >&5 +# gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH, +# LIBRARY_PATH; skip all such settings. +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | + grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="` +$as_echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS -rm -f conftest* +rm -rf conftest* # On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where # /foo, /bar, and /baz are search directories for the Fortran linker. # Here, we change these into -L/foo -L/bar -L/baz (and put it first): ac_f77_v_output="`echo $ac_f77_v_output | grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + sed 's|.*LPATH is\(: *[^ ]*\).*|\1|;s|: */| -L/|g'` $ac_f77_v_output" +# FIXME: we keep getting bitten by quoted arguments; a more general fix +# that detects unbalanced quotes in FLIBS should be implemented +# and (ugh) tested at some point. case $ac_f77_v_output in # If we are using xlf then replace all the commas with spaces. *xlfentry*) @@ -10109,51 +7232,55 @@ case $ac_f77_v_output in # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted # $LIBS confuse us, and the libraries appear later in the output anyway). *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"-mGLOB[^"]*"/ /g'` ;; + + # Portland Group compiler has singly- or doubly-quoted -cmdline argument + # Singly-quoted arguments were reported for versions 5.2-4 and 6.0-4. + # Doubly-quoted arguments were reported for "PGF90/x86 Linux/x86 5.0-2". + *-cmdline\ * | *-ignore\ * | *-def\ *) + ac_f77_v_output=`echo $ac_f77_v_output | sed "\ + s/-cmdline *'[^']*'/ /g; s/-cmdline *\"[^\"]*\"/ /g + s/-ignore *'[^']*'/ /g; s/-ignore *\"[^\"]*\"/ /g + s/-def *'[^']*'/ /g; s/-def *\"[^\"]*\"/ /g"` ;; # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"//g'` ;; esac # look for -l* and *.a constructs in the output for ac_arg in $ac_f77_v_output; do case $ac_arg in - [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) - ac_cv_prog_f77_v=$ac_verb - break 2 ;; + [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) + ac_cv_prog_f77_v=$ac_verb + break 2 ;; esac done done if test -z "$ac_cv_prog_f77_v"; then - { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $F77" >&5 -echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot determine how to obtain linking information from $F77" >&5 +$as_echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} fi else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 -echo "$as_me: WARNING: compilation failed" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: compilation failed" >&5 +$as_echo "$as_me: WARNING: compilation failed" >&2;} fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_v" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_v" >&6 -echo "$as_me:$LINENO: checking for Fortran libraries of $F77" >&5 -echo $ECHO_N "checking for Fortran libraries of $F77... $ECHO_C" >&6 -if test "${ac_cv_f77_libs+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_f77_v" >&5 +$as_echo "$ac_cv_prog_f77_v" >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 libraries of $F77" >&5 +$as_echo_n "checking for Fortran 77 libraries of $F77... " >&6; } +if test "${ac_cv_f77_libs+set}" = set; then : + $as_echo_n "(cached) " >&6 else if test "x$FLIBS" != "x"; then ac_cv_f77_libs="$FLIBS" # Let the user override the test. else -cat >conftest.$ac_ext <<_ACEOF +cat > conftest.$ac_ext <<_ACEOF program main end @@ -10165,20 +7292,28 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10168: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 +eval "set x $ac_link" +shift +$as_echo "$as_me:${as_lineno-$LINENO}: $*" >&5 +# gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH, +# LIBRARY_PATH; skip all such settings. +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | + grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="` +$as_echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS -rm -f conftest* +rm -rf conftest* # On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where # /foo, /bar, and /baz are search directories for the Fortran linker. # Here, we change these into -L/foo -L/bar -L/baz (and put it first): ac_f77_v_output="`echo $ac_f77_v_output | grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + sed 's|.*LPATH is\(: *[^ ]*\).*|\1|;s|: */| -L/|g'` $ac_f77_v_output" +# FIXME: we keep getting bitten by quoted arguments; a more general fix +# that detects unbalanced quotes in FLIBS should be implemented +# and (ugh) tested at some point. case $ac_f77_v_output in # If we are using xlf then replace all the commas with spaces. *xlfentry*) @@ -10187,13 +7322,20 @@ case $ac_f77_v_output in # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted # $LIBS confuse us, and the libraries appear later in the output anyway). *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"-mGLOB[^"]*"/ /g'` ;; + + # Portland Group compiler has singly- or doubly-quoted -cmdline argument + # Singly-quoted arguments were reported for versions 5.2-4 and 6.0-4. + # Doubly-quoted arguments were reported for "PGF90/x86 Linux/x86 5.0-2". + *-cmdline\ * | *-ignore\ * | *-def\ *) + ac_f77_v_output=`echo $ac_f77_v_output | sed "\ + s/-cmdline *'[^']*'/ /g; s/-cmdline *\"[^\"]*\"/ /g + s/-ignore *'[^']*'/ /g; s/-ignore *\"[^\"]*\"/ /g + s/-def *'[^']*'/ /g; s/-def *\"[^\"]*\"/ /g"` ;; # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"//g'` ;; esac @@ -10208,8 +7350,8 @@ while test $# != 1; do shift ac_arg=$1 case $ac_arg in - [\\/]*.a | ?:[\\/]*.a) - ac_exists=false + [\\/]*.a | ?:[\\/]*.a) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -10217,15 +7359,14 @@ while test $# != 1; do fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi - - ;; - -bI:*) - ac_exists=false + ;; + -bI:*) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -10233,8 +7374,8 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else if test "$ac_compiler_gnu" = yes; then for ac_link_opt in $ac_arg; do @@ -10244,18 +7385,18 @@ else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi fi - - ;; - # Ignore these flags. - -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) - ;; - -lkernel32) - test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" - ;; - -[LRuY]) - # These flags, when seen by themselves, take an argument. - # We remove the space between option and argument and re-iterate - # unless we find an empty arg or a new option (starting with -) + ;; + # Ignore these flags. + -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -little \ + |-LANG:=* | -LIST:* | -LNO:*) + ;; + -lkernel32) + test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" + ;; + -[LRuYz]) + # These flags, when seen by themselves, take an argument. + # We remove the space between option and argument and re-iterate + # unless we find an empty arg or a new option (starting with -) case $2 in "" | -*);; *) @@ -10264,10 +7405,10 @@ fi set X $ac_arg "$@" ;; esac - ;; - -YP,*) - for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do - ac_exists=false + ;; + -YP,*) + for ac_j in `$as_echo "$ac_arg" | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_j" = x"$ac_i"; then ac_exists=true @@ -10275,17 +7416,16 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_arg="$ac_arg $ac_j" - ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" + ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" fi - - done - ;; - -[lLR]*) - ac_exists=false + done + ;; + -[lLR]*) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -10293,14 +7433,16 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi - - ;; - # Ignore everything else. + ;; + -zallextract*| -zdefaultextract) + ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" + ;; + # Ignore everything else. esac done # restore positional arguments @@ -10311,10 +7453,10 @@ set X $ac_save_positional; shift # must begin with a "/"). case `(uname -sr) 2>/dev/null` in "SunOS 5"*) - ac_ld_run_path=`echo $ac_f77_v_output | - sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` + ac_ld_run_path=`$as_echo "$ac_f77_v_output" | + sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` test "x$ac_ld_run_path" != x && - if test "$ac_compiler_gnu" = yes; then + if test "$ac_compiler_gnu" = yes; then for ac_link_opt in $ac_ld_run_path; do ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" done @@ -10326,12 +7468,12 @@ esac fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" fi -echo "$as_me:$LINENO: result: $ac_cv_f77_libs" >&5 -echo "${ECHO_T}$ac_cv_f77_libs" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_f77_libs" >&5 +$as_echo "$ac_cv_f77_libs" >&6; } FLIBS="$ac_cv_f77_libs" -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10372,10 +7514,10 @@ if test "x${BUILD_F90}" != "x0"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_F90+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_path_F90+set}" = set; then : + $as_echo_n "(cached) " >&6 else case $F90 in [\\/]* | ?:[\\/]*) @@ -10387,28 +7529,29 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_F90="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS ;; esac fi F90=$ac_cv_path_F90 - if test -n "$F90"; then - echo "$as_me:$LINENO: result: $F90" >&5 -echo "${ECHO_T}$F90" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $F90" >&5 +$as_echo "$F90" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$F90" && break done test -n "$F90" || F90=""none"" @@ -10429,8 +7572,8 @@ f90_module_dir='-I' f90_opts='' if test "x${BUILD_F90}" != "x0"; then - echo "$as_me:$LINENO: checking Fortran 90 compiler ($F90) type" >&5 -echo $ECHO_N "checking Fortran 90 compiler ($F90) type... $ECHO_C" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking Fortran 90 compiler ($F90) type" >&5 +$as_echo_n "checking Fortran 90 compiler ($F90) type... " >&6; } cat >> testf90.f90 << EOF module mt double precision, parameter :: x = 2.3 @@ -10484,8 +7627,8 @@ F90LIBS= f90buildopts="-p. -s -YEXT_NAMES=LCS -YEXT_SFX=_ -YCFRL=1" fi rm -f testf90.f90 - echo "$as_me:$LINENO: result: ${f90type}" >&5 -echo "${ECHO_T}${f90type}" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${f90type}" >&5 +$as_echo "${f90type}" >&6; } if test "x${BUILD_F90}" != "x0"; then if test "x${has_f90}" = "xno"; then echo " -> cannot build the Fortran 90 interface" @@ -10522,7 +7665,7 @@ if test -z "$F77_EXT"; then F77_EXT=f; fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10547,27 +7690,19 @@ math_libs='-lcvode -lctmath' if test "$LAPACK_FTN_TRAILING_UNDERSCORE" = "y" then - cat >>confdefs.h <<\_ACEOF -#define LAPACK_FTN_TRAILING_UNDERSCORE 1 -_ACEOF + $as_echo "#define LAPACK_FTN_TRAILING_UNDERSCORE 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define FTN_TRAILING_UNDERSCORE 1 -_ACEOF + $as_echo "#define FTN_TRAILING_UNDERSCORE 1" >>confdefs.h fi if test "$LAPACK_FTN_STRING_LEN_AT_END" = "y" -then cat >>confdefs.h <<\_ACEOF -#define LAPACK_FTN_STRING_LEN_AT_END 1 -_ACEOF +then $as_echo "#define LAPACK_FTN_STRING_LEN_AT_END 1" >>confdefs.h fi if test "$LAPACK_NAMES" = "lower" -then cat >>confdefs.h <<\_ACEOF -#define LAPACK_NAMES_LOWERCASE 1 -_ACEOF +then $as_echo "#define LAPACK_NAMES_LOWERCASE 1" >>confdefs.h fi @@ -10581,8 +7716,8 @@ fi # SO is the extension of shared libraries `(including the dot!) # -- usually .so, .sl on HP-UX, .dll on Cygwin -echo "$as_me:$LINENO: checking SO" >&5 -echo $ECHO_N "checking SO... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking SO" >&5 +$as_echo_n "checking SO... " >&6; } if test -z "$SO" then case $ac_sys_system in @@ -10592,12 +7727,12 @@ then *) SO=.so;; esac fi -echo "$as_me:$LINENO: result: $SO" >&5 -echo "${ECHO_T}$SO" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $SO" >&5 +$as_echo "$SO" >&6; } -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10672,39 +7807,26 @@ fi - ac_config_files="$ac_config_files Makefile Cantera/Makefile Cantera/src/Makefile Cantera/src/base/Makefile Cantera/src/zeroD/Makefile Cantera/src/oneD/Makefile Cantera/src/converters/Makefile Cantera/src/transport/Makefile Cantera/src/thermo/Makefile Cantera/src/kinetics/Makefile Cantera/src/numerics/Makefile Cantera/src/spectra/Makefile Cantera/src/equil/Makefile Cantera/clib/src/Makefile Cantera/fortran/src/Makefile Cantera/fortran/f77demos/f77demos.mak Cantera/fortran/f77demos/Makefile Cantera/matlab/Makefile Cantera/matlab/setup_matlab.py Cantera/python/Makefile Cantera/python/setup.py Cantera/cxx/Makefile Cantera/cxx/src/Makefile Cantera/cxx/demos/Makefile Cantera/cxx/demos/combustor/Makefile Cantera/cxx/demos/combustor/Makefile.install Cantera/cxx/demos/flamespeed/Makefile Cantera/cxx/demos/flamespeed/Makefile.install Cantera/cxx/demos/kinetics1/Makefile Cantera/cxx/demos/kinetics1/Makefile.install Cantera/cxx/demos/NASA_coeffs/Makefile Cantera/cxx/demos/NASA_coeffs/Makefile.install Cantera/cxx/demos/rankine/Makefile Cantera/cxx/demos/rankine/Makefile.install Cantera/cxx/include/Cantera.mak Cantera/cxx/include/Cantera_bt.mak Cantera/user/Makefile Cantera/python/src/Makefile Cantera/python/examples/Makefile Cantera/python/examples/equilibrium/Makefile Cantera/python/examples/equilibrium/adiabatic_flame/Makefile Cantera/python/examples/equilibrium/multiphase_plasma/Makefile Cantera/python/examples/equilibrium/simple_test/Makefile Cantera/python/examples/equilibrium/stoich_flame/Makefile Cantera/python/examples/gasdynamics/isentropic/Makefile Cantera/python/examples/gasdynamics/soundSpeed/Makefile Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile Cantera/python/examples/reactors/surf_pfr_sim/Makefile Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile Cantera/python/examples/transport/Makefile Cantera/python/examples/flames/Makefile Cantera/python/examples/gasdynamics/Makefile Cantera/python/examples/liquid_vapor/Makefile Cantera/python/examples/reactors/Makefile Cantera/python/examples/surface_chemistry/Makefile ext/lapack/Makefile ext/blas/Makefile ext/cvode/Makefile ext/math/Makefile ext/recipes/Makefile ext/tpx/Makefile ext/Makefile ext/f2c_libs/Makefile ext/f2c_blas/Makefile ext/f2c_lapack/Makefile ext/f2c_math/Makefile examples/Makefile examples/cxx/Makefile tools/Makefile tools/doc/Cantera.cfg tools/doc/Makefile 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test_problems/ck2cti_test/runtest test_problems/nasa9_reader/Makefile test_problems/nasa9_reader/runtest test_problems/min_python/Makefile test_problems/min_python/minDiamond/Makefile test_problems/min_python/negATest/Makefile test_problems/pureFluidTest/Makefile test_problems/rankine_democxx/Makefile test_problems/python/Makefile test_problems/cathermo/Makefile test_problems/cathermo/issp/Makefile test_problems/cathermo/ims/Makefile test_problems/cathermo/stoichSubSSTP/Makefile test_problems/cathermo/testIAPWS/Makefile test_problems/cathermo/testIAPWSPres/Makefile test_problems/cathermo/testIAPWSTripP/Makefile test_problems/cathermo/testWaterPDSS/Makefile test_problems/cathermo/testWaterTP/Makefile test_problems/cathermo/HMW_test_1/Makefile test_problems/cathermo/HMW_test_3/Makefile test_problems/cathermo/HMW_graph_GvT/Makefile test_problems/cathermo/HMW_graph_GvI/Makefile test_problems/cathermo/HMW_graph_HvT/Makefile test_problems/cathermo/HMW_graph_CpvT/Makefile test_problems/cathermo/HMW_graph_VvT/Makefile test_problems/cathermo/DH_graph_1/Makefile test_problems/cathermo/DH_graph_acommon/Makefile test_problems/cathermo/DH_graph_NM/Makefile test_problems/cathermo/DH_graph_Pitzer/Makefile test_problems/cathermo/DH_graph_bdotak/Makefile test_problems/cathermo/HMW_dupl_test/Makefile test_problems/cathermo/VPissp/Makefile test_problems/cathermo/wtWater/Makefile test_problems/VCSnonideal/Makefile test_problems/VPsilane_test/Makefile test_problems/VPsilane_test/runtest test_problems/VCSnonideal/NaCl_equil/Makefile bin/install_tsc" +ac_config_files="$ac_config_files Makefile Cantera/Makefile Cantera/src/Makefile Cantera/src/base/Makefile Cantera/src/zeroD/Makefile Cantera/src/oneD/Makefile Cantera/src/converters/Makefile Cantera/src/transport/Makefile Cantera/src/thermo/Makefile Cantera/src/kinetics/Makefile Cantera/src/numerics/Makefile Cantera/src/spectra/Makefile Cantera/src/equil/Makefile Cantera/clib/src/Makefile Cantera/fortran/src/Makefile Cantera/fortran/f77demos/f77demos.mak Cantera/fortran/f77demos/Makefile Cantera/matlab/Makefile Cantera/matlab/setup_matlab.py Cantera/python/Makefile Cantera/python/setup.py Cantera/cxx/Makefile Cantera/cxx/src/Makefile Cantera/cxx/demos/Makefile Cantera/cxx/demos/combustor/Makefile Cantera/cxx/demos/combustor/Makefile.install Cantera/cxx/demos/flamespeed/Makefile Cantera/cxx/demos/flamespeed/Makefile.install Cantera/cxx/demos/kinetics1/Makefile Cantera/cxx/demos/kinetics1/Makefile.install Cantera/cxx/demos/NASA_coeffs/Makefile Cantera/cxx/demos/NASA_coeffs/Makefile.install Cantera/cxx/demos/rankine/Makefile Cantera/cxx/demos/rankine/Makefile.install Cantera/cxx/include/Cantera.mak Cantera/cxx/include/Cantera_bt.mak Cantera/user/Makefile Cantera/python/src/Makefile Cantera/python/examples/Makefile Cantera/python/examples/equilibrium/Makefile Cantera/python/examples/equilibrium/adiabatic_flame/Makefile Cantera/python/examples/equilibrium/multiphase_plasma/Makefile Cantera/python/examples/equilibrium/simple_test/Makefile Cantera/python/examples/equilibrium/stoich_flame/Makefile Cantera/python/examples/gasdynamics/isentropic/Makefile Cantera/python/examples/gasdynamics/soundSpeed/Makefile Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile Cantera/python/examples/reactors/surf_pfr_sim/Makefile Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile Cantera/python/examples/transport/Makefile Cantera/python/examples/flames/Makefile Cantera/python/examples/gasdynamics/Makefile Cantera/python/examples/liquid_vapor/Makefile Cantera/python/examples/reactors/Makefile Cantera/python/examples/surface_chemistry/Makefile ext/lapack/Makefile ext/blas/Makefile ext/cvode/Makefile ext/math/Makefile ext/recipes/Makefile ext/tpx/Makefile ext/Makefile ext/f2c_libs/Makefile ext/f2c_blas/Makefile ext/f2c_lapack/Makefile ext/f2c_math/Makefile examples/Makefile examples/cxx/Makefile tools/Makefile tools/doc/Cantera.cfg tools/doc/Makefile tools/src/Makefile tools/src/sample.mak tools/src/finish_install.py tools/src/package4mac tools/templates/f77/demo.mak tools/templates/f90/demo.mak tools/templates/cxx/demo.mak tools/testtools/Makefile data/inputs/Makefile data/inputs/mkxml test_problems/Makefile test_problems/cxx_ex/Makefile test_problems/silane_equil/Makefile test_problems/surfkin/Makefile test_problems/spectroscopy/Makefile test_problems/surfSolverTest/Makefile test_problems/diamondSurf/Makefile test_problems/diamondSurf_dupl/Makefile test_problems/ChemEquil_gri_matrix/Makefile test_problems/ChemEquil_gri_pairs/Makefile test_problems/ChemEquil_ionizedGas/Makefile test_problems/ChemEquil_red1/Makefile test_problems/CpJump/Makefile test_problems/mixGasTransport/Makefile test_problems/multiGasTransport/Makefile test_problems/printUtilUnitTest/Makefile test_problems/fracCoeff/Makefile test_problems/negATest/Makefile test_problems/NASA9poly_test/Makefile test_problems/ck2cti_test/Makefile test_problems/ck2cti_test/runtest test_problems/nasa9_reader/Makefile test_problems/nasa9_reader/runtest test_problems/min_python/Makefile test_problems/min_python/minDiamond/Makefile test_problems/min_python/negATest/Makefile test_problems/pureFluidTest/Makefile test_problems/rankine_democxx/Makefile test_problems/python/Makefile test_problems/cathermo/Makefile test_problems/cathermo/issp/Makefile test_problems/cathermo/ims/Makefile test_problems/cathermo/stoichSubSSTP/Makefile test_problems/cathermo/testIAPWS/Makefile test_problems/cathermo/testIAPWSPres/Makefile test_problems/cathermo/testIAPWSTripP/Makefile test_problems/cathermo/testWaterPDSS/Makefile test_problems/cathermo/testWaterTP/Makefile test_problems/cathermo/HMW_test_1/Makefile test_problems/cathermo/HMW_test_3/Makefile test_problems/cathermo/HMW_graph_GvT/Makefile test_problems/cathermo/HMW_graph_GvI/Makefile test_problems/cathermo/HMW_graph_HvT/Makefile test_problems/cathermo/HMW_graph_CpvT/Makefile test_problems/cathermo/HMW_graph_VvT/Makefile test_problems/cathermo/DH_graph_1/Makefile test_problems/cathermo/DH_graph_acommon/Makefile test_problems/cathermo/DH_graph_NM/Makefile test_problems/cathermo/DH_graph_Pitzer/Makefile test_problems/cathermo/DH_graph_bdotak/Makefile test_problems/cathermo/HMW_dupl_test/Makefile test_problems/cathermo/VPissp/Makefile test_problems/cathermo/wtWater/Makefile test_problems/VCSnonideal/Makefile test_problems/VPsilane_test/Makefile test_problems/VPsilane_test/runtest test_problems/VCSnonideal/NaCl_equil/Makefile bin/install_tsc" + test "x$prefix" = xNONE && prefix=$ac_default_prefix # Let make expand exec_prefix. test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' -# VPATH may cause trouble with some makes, so we remove $(srcdir), -# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and -# trailing colons and then remove the whole line if VPATH becomes empty -# (actually we leave an empty line to preserve line numbers). -if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=/{ -s/:*\$(srcdir):*/:/; -s/:*\${srcdir}:*/:/; -s/:*@srcdir@:*/:/; -s/^\([^=]*=[ ]*\):*/\1/; -s/:*$//; -s/^[^=]*=[ ]*$//; -}' -fi - DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. - ac_i=`echo "$ac_i" | - sed 's/\$U\././;s/\.o$//;s/\.obj$//'` - # 2. Add them. - ac_libobjs="$ac_libobjs $ac_i\$U.$ac_objext" - ac_ltlibobjs="$ac_ltlibobjs $ac_i"'$U.lo' + ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' + ac_i=`$as_echo "$ac_i" | sed "$ac_script"` + # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR + # will be set to the directory where LIBOBJS objects are built. + as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" + as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs @@ -10713,11 +7835,13 @@ LTLIBOBJS=$ac_ltlibobjs : ${CONFIG_STATUS=./config.status} +ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 -echo "$as_me: creating $CONFIG_STATUS" >&6;} -cat >$CONFIG_STATUS <<_ACEOF +{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: creating $CONFIG_STATUS" >&6;} +as_write_fail=0 +cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -10727,81 +7851,252 @@ cat >$CONFIG_STATUS <<_ACEOF debug=false ac_cs_recheck=false ac_cs_silent=false + SHELL=\${CONFIG_SHELL-$SHELL} -_ACEOF +export SHELL +_ASEOF +cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## -cat >>$CONFIG_STATUS <<\_ACEOF -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## - -# Be Bourne compatible -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: - # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' -elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then - set -o posix -fi -DUALCASE=1; export DUALCASE # for MKS sh - -# Support unset when possible. -if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then - as_unset=unset + setopt NO_GLOB_SUBST else - as_unset=false + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac fi -# Work around bugs in pre-3.0 UWIN ksh. -$as_unset ENV MAIL MAILPATH +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent editors from complaining about space-tab. +# (If _AS_PATH_WALK were called with IFS unset, it would disable word +# splitting by setting IFS to empty value.) +IFS=" "" $as_nl" + +# Find who we are. Look in the path if we contain no directory separator. +case $0 in #(( + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done +IFS=$as_save_IFS + + ;; +esac +# We did not find ourselves, most probably we were run as `sh COMMAND' +# in which case we are not to be found in the path. +if test "x$as_myself" = x; then + as_myself=$0 +fi +if test ! -f "$as_myself"; then + $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + exit 1 +fi + +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. -for as_var in \ - LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ - LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ - LC_TELEPHONE LC_TIME -do - if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then - eval $as_var=C; export $as_var - else - $as_unset $as_var - fi -done +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE -# Required to use basename. -if expr a : '\(a\)' >/dev/null 2>&1; then +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + + +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi -if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. -as_me=`$as_basename "$0" || +as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)$' \| \ - . : '\(.\)' 2>/dev/null || -echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } - /^X\/\(\/\/\)$/{ s//\1/; q; } - /^X\/\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` - -# PATH needs CR, and LINENO needs CR and PATH. # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -10809,148 +8104,123 @@ as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits -# The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then - echo "#! /bin/sh" >conf$$.sh - echo "exit 0" >>conf$$.sh - chmod +x conf$$.sh - if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then - PATH_SEPARATOR=';' - else - PATH_SEPARATOR=: - fi - rm -f conf$$.sh -fi - - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" || { - # Find who we are. Look in the path if we contain no path at all - # relative or not. - case $0 in - *[\\/]* ) as_myself=$0 ;; - *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done - - ;; - esac - # We did not find ourselves, most probably we were run as `sh COMMAND' - # in which case we are not to be found in the path. - if test "x$as_myself" = x; then - as_myself=$0 - fi - if test ! -f "$as_myself"; then - { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 -echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} - { (exit 1); exit 1; }; } - fi - case $CONFIG_SHELL in - '') - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for as_base in sh bash ksh sh5; do - case $as_dir in - /*) - if ("$as_dir/$as_base" -c ' - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then - $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } - $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } - CONFIG_SHELL=$as_dir/$as_base - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$0" ${1+"$@"} - fi;; - esac - done -done -;; - esac - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. 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Logging --version etc. is OK. -exec 5>>config.log -{ - echo - sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX -## Running $as_me. ## -_ASBOX -} >&5 -cat >&5 <<_CSEOF - +# values after options handling. +ac_log=" This file was extended by Cantera $as_me 1.7.0, which was -generated by GNU Autoconf 2.59. Invocation command line was +generated by GNU Autoconf 2.64. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -10991,45 +8250,45 @@ generated by GNU Autoconf 2.59. Invocation command line was CONFIG_COMMANDS = $CONFIG_COMMANDS $ $0 $@ -_CSEOF -echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 -echo >&5 +on `(hostname || uname -n) 2>/dev/null | sed 1q` +" + _ACEOF +case $ac_config_files in *" +"*) set x $ac_config_files; shift; ac_config_files=$*;; +esac + +case $ac_config_headers in *" +"*) set x $ac_config_headers; shift; ac_config_headers=$*;; +esac + + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 # Files that config.status was made for. -if test -n "$ac_config_files"; then - echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS -fi +config_files="$ac_config_files" +config_headers="$ac_config_headers" -if test -n "$ac_config_headers"; then - echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS -fi - -if test -n "$ac_config_links"; then - echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS -fi - -if test -n "$ac_config_commands"; then - echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS -fi - -cat >>$CONFIG_STATUS <<\_ACEOF +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files from templates according to the -current configuration. +\`$as_me' instantiates files and other configuration actions +from templates according to the current configuration. Unless the files +and actions are specified as TAGs, all are instantiated by default. -Usage: $0 [OPTIONS] [FILE]... +Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit - -V, --version print version number, then exit - -q, --quiet do not print progress messages + -V, --version print version number and configuration settings, then exit + -q, --quiet, --silent + do not print progress messages -d, --debug don't remove temporary files --recheck update $as_me by reconfiguring in the same conditions - --file=FILE[:TEMPLATE] - instantiate the configuration file FILE - --header=FILE[:TEMPLATE] - instantiate the configuration header FILE + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE Configuration files: $config_files @@ -11037,84 +8296,81 @@ $config_files Configuration headers: $config_headers -Report bugs to ." -_ACEOF +Report bugs to the package provider." -cat >>$CONFIG_STATUS <<_ACEOF +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_version="\\ Cantera config.status 1.7.0 -configured by $0, generated by GNU Autoconf 2.59, - with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" +configured by $0, generated by GNU Autoconf 2.64, + with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" -Copyright (C) 2003 Free Software Foundation, Inc. +Copyright (C) 2009 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." -srcdir=$srcdir -INSTALL="$INSTALL" + +ac_pwd='$ac_pwd' +srcdir='$srcdir' +INSTALL='$INSTALL' +test -n "\$AWK" || AWK=awk _ACEOF -cat >>$CONFIG_STATUS <<\_ACEOF -# If no file are specified by the user, then we need to provide default -# value. By we need to know if files were specified by the user. +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# The default lists apply if the user does not specify any file. ac_need_defaults=: while test $# != 0 do case $1 in --*=*) - ac_option=`expr "x$1" : 'x\([^=]*\)='` - ac_optarg=`expr "x$1" : 'x[^=]*=\(.*\)'` + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; - -*) + *) ac_option=$1 ac_optarg=$2 ac_shift=shift ;; - *) # This is not an option, so the user has probably given explicit - # arguments. - ac_option=$1 - ac_need_defaults=false;; esac case $ac_option in # Handling of the options. -_ACEOF -cat >>$CONFIG_STATUS <<\_ACEOF -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) ac_cs_recheck=: ;; - --version | --vers* | -V ) - echo "$ac_cs_version"; exit 0 ;; - --he | --h) - # Conflict between --help and --header - { { echo "$as_me:$LINENO: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&5 -echo "$as_me: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&2;} - { (exit 1); exit 1; }; };; - --help | --hel | -h ) - echo "$ac_cs_usage"; exit 0 ;; - --debug | --d* | -d ) + --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) + $as_echo "$ac_cs_version"; exit ;; + --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift - CONFIG_FILES="$CONFIG_FILES $ac_optarg" + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + esac + as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift - CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg" + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + esac + as_fn_append CONFIG_HEADERS " '$ac_optarg'" ac_need_defaults=false;; + --he | --h) + # Conflict between --help and --header + as_fn_error "ambiguous option: \`$1' +Try \`$0 --help' for more information.";; + --help | --hel | -h ) + $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil | --si | --s) ac_cs_silent=: ;; # This is an error. - -*) { { echo "$as_me:$LINENO: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&5 -echo "$as_me: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&2;} - { (exit 1); exit 1; }; } ;; + -*) as_fn_error "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; - *) ac_config_targets="$ac_config_targets $1" ;; + *) as_fn_append ac_config_targets " $1" + ac_need_defaults=false ;; esac shift @@ -11128,189 +8384,203 @@ if $ac_cs_silent; then fi _ACEOF -cat >>$CONFIG_STATUS <<_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 if \$ac_cs_recheck; then - echo "running $SHELL $0 " $ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6 - exec $SHELL $0 $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + shift + \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 + CONFIG_SHELL='$SHELL' + export CONFIG_SHELL + exec "\$@" fi _ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX + $as_echo "$ac_log" +} >&5 +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - - -cat >>$CONFIG_STATUS <<\_ACEOF +# Handling of arguments. for ac_config_target in $ac_config_targets do - case "$ac_config_target" in - # Handling of arguments. - "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;; 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- "Cantera/python/examples/kinetics/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/kinetics/Makefile" ;; - "Cantera/python/examples/misc/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/misc/Makefile" ;; - "Cantera/python/examples/reactors/combustor_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/combustor_sim/Makefile" ;; - "Cantera/python/examples/reactors/functors_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/functors_sim/Makefile" ;; - "Cantera/python/examples/reactors/mix1_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix1_sim/Makefile" ;; - "Cantera/python/examples/reactors/mix2_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix2_sim/Makefile" ;; - "Cantera/python/examples/reactors/piston_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/piston_sim/Makefile" ;; - "Cantera/python/examples/reactors/reactor1_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor1_sim/Makefile" ;; - "Cantera/python/examples/reactors/reactor2_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor2_sim/Makefile" ;; - "Cantera/python/examples/reactors/sensitivity_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/sensitivity_sim/Makefile" ;; - "Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ;; - "Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ;; - "Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ;; - "Cantera/python/examples/transport/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/transport/Makefile" ;; - "Cantera/python/examples/flames/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/Makefile" ;; - "Cantera/python/examples/gasdynamics/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/Makefile" ;; - "Cantera/python/examples/liquid_vapor/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/Makefile" ;; - "Cantera/python/examples/reactors/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/Makefile" ;; - "Cantera/python/examples/surface_chemistry/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/Makefile" ;; - "ext/lapack/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/lapack/Makefile" ;; - "ext/blas/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/blas/Makefile" ;; - "ext/cvode/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/cvode/Makefile" ;; - "ext/math/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/math/Makefile" ;; - "ext/recipes/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/recipes/Makefile" ;; - "ext/tpx/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/tpx/Makefile" ;; - "ext/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/Makefile" ;; - "ext/f2c_libs/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_libs/Makefile" ;; - "ext/f2c_blas/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_blas/Makefile" ;; - "ext/f2c_lapack/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_lapack/Makefile" ;; - "ext/f2c_math/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_math/Makefile" ;; - "examples/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;; - "examples/cxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/cxx/Makefile" ;; - "tools/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; - "tools/doc/Cantera.cfg" ) CONFIG_FILES="$CONFIG_FILES tools/doc/Cantera.cfg" ;; - "tools/doc/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/doc/Makefile" ;; - "tools/src/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/src/Makefile" ;; - "tools/src/sample.mak" ) CONFIG_FILES="$CONFIG_FILES tools/src/sample.mak" ;; - "tools/src/finish_install.py" ) CONFIG_FILES="$CONFIG_FILES tools/src/finish_install.py" ;; - "tools/src/package4mac" ) CONFIG_FILES="$CONFIG_FILES tools/src/package4mac" ;; - "tools/templates/f77/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/f77/demo.mak" ;; - "tools/templates/f90/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/f90/demo.mak" ;; - "tools/templates/cxx/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/cxx/demo.mak" ;; - "tools/testtools/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/testtools/Makefile" ;; - "data/inputs/Makefile" ) CONFIG_FILES="$CONFIG_FILES data/inputs/Makefile" ;; - "data/inputs/mkxml" ) CONFIG_FILES="$CONFIG_FILES data/inputs/mkxml" ;; - "test_problems/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/Makefile" ;; - "test_problems/cxx_ex/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cxx_ex/Makefile" ;; - "test_problems/silane_equil/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/silane_equil/Makefile" ;; - "test_problems/surfkin/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/surfkin/Makefile" ;; - "test_problems/spectroscopy/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/spectroscopy/Makefile" ;; - "test_problems/surfSolverTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/surfSolverTest/Makefile" ;; - "test_problems/diamondSurf/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf/Makefile" ;; - "test_problems/diamondSurf_dupl/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf_dupl/Makefile" ;; - "test_problems/ChemEquil_gri_matrix/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_matrix/Makefile" ;; - "test_problems/ChemEquil_gri_pairs/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_pairs/Makefile" ;; - "test_problems/ChemEquil_ionizedGas/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_ionizedGas/Makefile" ;; - "test_problems/ChemEquil_red1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_red1/Makefile" ;; - "test_problems/CpJump/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/CpJump/Makefile" ;; - "test_problems/mixGasTransport/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/mixGasTransport/Makefile" ;; - "test_problems/multiGasTransport/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/multiGasTransport/Makefile" ;; - "test_problems/printUtilUnitTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/printUtilUnitTest/Makefile" ;; - "test_problems/fracCoeff/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/fracCoeff/Makefile" ;; - "test_problems/negATest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/negATest/Makefile" ;; - "test_problems/NASA9poly_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/NASA9poly_test/Makefile" ;; - "test_problems/ck2cti_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/Makefile" ;; - "test_problems/ck2cti_test/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/runtest" ;; - "test_problems/nasa9_reader/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/Makefile" ;; - "test_problems/nasa9_reader/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/runtest" ;; - "test_problems/min_python/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/Makefile" ;; - "test_problems/min_python/minDiamond/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/minDiamond/Makefile" ;; - "test_problems/min_python/negATest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/negATest/Makefile" ;; - "test_problems/pureFluidTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/pureFluidTest/Makefile" ;; - "test_problems/rankine_democxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/rankine_democxx/Makefile" ;; - "test_problems/python/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/python/Makefile" ;; - "test_problems/cathermo/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/Makefile" ;; - "test_problems/cathermo/issp/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/issp/Makefile" ;; - "test_problems/cathermo/ims/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/ims/Makefile" ;; - "test_problems/cathermo/stoichSubSSTP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/stoichSubSSTP/Makefile" ;; - "test_problems/cathermo/testIAPWS/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWS/Makefile" ;; - "test_problems/cathermo/testIAPWSPres/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSPres/Makefile" ;; - "test_problems/cathermo/testIAPWSTripP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSTripP/Makefile" ;; - "test_problems/cathermo/testWaterPDSS/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterPDSS/Makefile" ;; - "test_problems/cathermo/testWaterTP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterTP/Makefile" ;; - "test_problems/cathermo/HMW_test_1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_1/Makefile" ;; - "test_problems/cathermo/HMW_test_3/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_3/Makefile" ;; - "test_problems/cathermo/HMW_graph_GvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_GvI/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvI/Makefile" ;; - "test_problems/cathermo/HMW_graph_HvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_HvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_CpvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_CpvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_VvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_VvT/Makefile" ;; - "test_problems/cathermo/DH_graph_1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_1/Makefile" ;; - "test_problems/cathermo/DH_graph_acommon/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_acommon/Makefile" ;; - "test_problems/cathermo/DH_graph_NM/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_NM/Makefile" ;; - "test_problems/cathermo/DH_graph_Pitzer/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_Pitzer/Makefile" ;; - "test_problems/cathermo/DH_graph_bdotak/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_bdotak/Makefile" ;; - "test_problems/cathermo/HMW_dupl_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_dupl_test/Makefile" ;; - "test_problems/cathermo/VPissp/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/VPissp/Makefile" ;; - "test_problems/cathermo/wtWater/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/wtWater/Makefile" ;; - "test_problems/VCSnonideal/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/Makefile" ;; - "test_problems/VPsilane_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/Makefile" ;; - "test_problems/VPsilane_test/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/runtest" ;; - "test_problems/VCSnonideal/NaCl_equil/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/NaCl_equil/Makefile" ;; - "bin/install_tsc" ) CONFIG_FILES="$CONFIG_FILES bin/install_tsc" ;; - "config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 -echo "$as_me: error: invalid argument: $ac_config_target" >&2;} - { (exit 1); exit 1; }; };; + case $ac_config_target in + "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; + "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; + "Cantera/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/Makefile" ;; + "Cantera/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/Makefile" ;; + "Cantera/src/base/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/base/Makefile" ;; + "Cantera/src/zeroD/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/zeroD/Makefile" ;; + "Cantera/src/oneD/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/oneD/Makefile" ;; + "Cantera/src/converters/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/converters/Makefile" ;; + "Cantera/src/transport/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/transport/Makefile" ;; + "Cantera/src/thermo/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/thermo/Makefile" ;; + "Cantera/src/kinetics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/kinetics/Makefile" ;; + "Cantera/src/numerics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/numerics/Makefile" ;; + "Cantera/src/spectra/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/spectra/Makefile" ;; + "Cantera/src/equil/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/equil/Makefile" ;; + "Cantera/clib/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/clib/src/Makefile" ;; + "Cantera/fortran/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/src/Makefile" ;; + "Cantera/fortran/f77demos/f77demos.mak") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/f77demos/f77demos.mak" ;; + "Cantera/fortran/f77demos/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/f77demos/Makefile" ;; + "Cantera/matlab/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/matlab/Makefile" ;; + "Cantera/matlab/setup_matlab.py") CONFIG_FILES="$CONFIG_FILES Cantera/matlab/setup_matlab.py" ;; + "Cantera/python/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/Makefile" ;; + "Cantera/python/setup.py") CONFIG_FILES="$CONFIG_FILES Cantera/python/setup.py" ;; + "Cantera/cxx/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/Makefile" ;; + "Cantera/cxx/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/src/Makefile" ;; + "Cantera/cxx/demos/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/Makefile" ;; + "Cantera/cxx/demos/combustor/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/combustor/Makefile" ;; + "Cantera/cxx/demos/combustor/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/combustor/Makefile.install" ;; + "Cantera/cxx/demos/flamespeed/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/flamespeed/Makefile" ;; + "Cantera/cxx/demos/flamespeed/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/flamespeed/Makefile.install" ;; + "Cantera/cxx/demos/kinetics1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/kinetics1/Makefile" ;; + "Cantera/cxx/demos/kinetics1/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/kinetics1/Makefile.install" ;; + "Cantera/cxx/demos/NASA_coeffs/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/NASA_coeffs/Makefile" ;; + "Cantera/cxx/demos/NASA_coeffs/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/NASA_coeffs/Makefile.install" ;; + "Cantera/cxx/demos/rankine/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/rankine/Makefile" ;; + "Cantera/cxx/demos/rankine/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/rankine/Makefile.install" ;; + "Cantera/cxx/include/Cantera.mak") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/include/Cantera.mak" ;; + "Cantera/cxx/include/Cantera_bt.mak") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/include/Cantera_bt.mak" ;; + "Cantera/user/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/user/Makefile" ;; + "Cantera/python/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/src/Makefile" ;; + "Cantera/python/examples/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/Makefile" ;; + "Cantera/python/examples/equilibrium/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/Makefile" ;; + "Cantera/python/examples/equilibrium/adiabatic_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/adiabatic_flame/Makefile" ;; + "Cantera/python/examples/equilibrium/multiphase_plasma/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/multiphase_plasma/Makefile" ;; + "Cantera/python/examples/equilibrium/simple_test/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/simple_test/Makefile" ;; + "Cantera/python/examples/equilibrium/stoich_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/stoich_flame/Makefile" ;; + "Cantera/python/examples/gasdynamics/isentropic/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/isentropic/Makefile" ;; + "Cantera/python/examples/gasdynamics/soundSpeed/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/soundSpeed/Makefile" ;; + "Cantera/python/examples/flames/adiabatic_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/adiabatic_flame/Makefile" ;; + "Cantera/python/examples/flames/flame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame1/Makefile" ;; + "Cantera/python/examples/flames/flame2/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame2/Makefile" ;; + "Cantera/python/examples/flames/flame_fixed_T/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame_fixed_T/Makefile" ;; + "Cantera/python/examples/flames/free_h2_air/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/free_h2_air/Makefile" ;; + "Cantera/python/examples/flames/npflame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/npflame1/Makefile" ;; + "Cantera/python/examples/flames/stflame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/stflame1/Makefile" ;; + "Cantera/python/examples/fuel_cells/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/fuel_cells/Makefile" ;; + "Cantera/python/examples/liquid_vapor/critProperties/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/critProperties/Makefile" ;; + "Cantera/python/examples/liquid_vapor/rankine/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/rankine/Makefile" ;; + "Cantera/python/examples/kinetics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/kinetics/Makefile" ;; + "Cantera/python/examples/misc/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/misc/Makefile" ;; + "Cantera/python/examples/reactors/combustor_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/combustor_sim/Makefile" ;; + "Cantera/python/examples/reactors/functors_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/functors_sim/Makefile" ;; + "Cantera/python/examples/reactors/mix1_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix1_sim/Makefile" ;; + "Cantera/python/examples/reactors/mix2_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix2_sim/Makefile" ;; + "Cantera/python/examples/reactors/piston_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/piston_sim/Makefile" ;; + "Cantera/python/examples/reactors/reactor1_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor1_sim/Makefile" ;; + "Cantera/python/examples/reactors/reactor2_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor2_sim/Makefile" ;; + "Cantera/python/examples/reactors/sensitivity_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/sensitivity_sim/Makefile" ;; + "Cantera/python/examples/reactors/surf_pfr_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ;; + "Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ;; + "Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ;; + "Cantera/python/examples/transport/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/transport/Makefile" ;; + "Cantera/python/examples/flames/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/Makefile" ;; + "Cantera/python/examples/gasdynamics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/Makefile" ;; + "Cantera/python/examples/liquid_vapor/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/Makefile" ;; + "Cantera/python/examples/reactors/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/Makefile" ;; + "Cantera/python/examples/surface_chemistry/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/Makefile" ;; + "ext/lapack/Makefile") CONFIG_FILES="$CONFIG_FILES ext/lapack/Makefile" ;; + "ext/blas/Makefile") CONFIG_FILES="$CONFIG_FILES ext/blas/Makefile" ;; + "ext/cvode/Makefile") CONFIG_FILES="$CONFIG_FILES ext/cvode/Makefile" ;; + "ext/math/Makefile") CONFIG_FILES="$CONFIG_FILES ext/math/Makefile" ;; + "ext/recipes/Makefile") CONFIG_FILES="$CONFIG_FILES ext/recipes/Makefile" ;; + "ext/tpx/Makefile") CONFIG_FILES="$CONFIG_FILES ext/tpx/Makefile" ;; + "ext/Makefile") CONFIG_FILES="$CONFIG_FILES ext/Makefile" ;; + "ext/f2c_libs/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_libs/Makefile" ;; + "ext/f2c_blas/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_blas/Makefile" ;; + "ext/f2c_lapack/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_lapack/Makefile" ;; + "ext/f2c_math/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_math/Makefile" ;; + "examples/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;; + "examples/cxx/Makefile") CONFIG_FILES="$CONFIG_FILES examples/cxx/Makefile" ;; + "tools/Makefile") CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; + "tools/doc/Cantera.cfg") CONFIG_FILES="$CONFIG_FILES tools/doc/Cantera.cfg" ;; + "tools/doc/Makefile") CONFIG_FILES="$CONFIG_FILES tools/doc/Makefile" ;; + "tools/src/Makefile") CONFIG_FILES="$CONFIG_FILES tools/src/Makefile" ;; + "tools/src/sample.mak") CONFIG_FILES="$CONFIG_FILES tools/src/sample.mak" ;; + "tools/src/finish_install.py") CONFIG_FILES="$CONFIG_FILES tools/src/finish_install.py" ;; + "tools/src/package4mac") CONFIG_FILES="$CONFIG_FILES tools/src/package4mac" ;; + "tools/templates/f77/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/f77/demo.mak" ;; + "tools/templates/f90/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/f90/demo.mak" ;; + "tools/templates/cxx/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/cxx/demo.mak" ;; + "tools/testtools/Makefile") CONFIG_FILES="$CONFIG_FILES tools/testtools/Makefile" ;; + "data/inputs/Makefile") CONFIG_FILES="$CONFIG_FILES data/inputs/Makefile" ;; + "data/inputs/mkxml") CONFIG_FILES="$CONFIG_FILES data/inputs/mkxml" ;; + "test_problems/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/Makefile" ;; + "test_problems/cxx_ex/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cxx_ex/Makefile" ;; + "test_problems/silane_equil/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/silane_equil/Makefile" ;; + "test_problems/surfkin/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/surfkin/Makefile" ;; + "test_problems/spectroscopy/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/spectroscopy/Makefile" ;; + "test_problems/surfSolverTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/surfSolverTest/Makefile" ;; + "test_problems/diamondSurf/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf/Makefile" ;; + "test_problems/diamondSurf_dupl/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf_dupl/Makefile" ;; + "test_problems/ChemEquil_gri_matrix/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_matrix/Makefile" ;; + "test_problems/ChemEquil_gri_pairs/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_pairs/Makefile" ;; + "test_problems/ChemEquil_ionizedGas/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_ionizedGas/Makefile" ;; + "test_problems/ChemEquil_red1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_red1/Makefile" ;; + "test_problems/CpJump/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/CpJump/Makefile" ;; + "test_problems/mixGasTransport/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/mixGasTransport/Makefile" ;; + "test_problems/multiGasTransport/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/multiGasTransport/Makefile" ;; + "test_problems/printUtilUnitTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/printUtilUnitTest/Makefile" ;; + "test_problems/fracCoeff/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/fracCoeff/Makefile" ;; + "test_problems/negATest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/negATest/Makefile" ;; + "test_problems/NASA9poly_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/NASA9poly_test/Makefile" ;; + "test_problems/ck2cti_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/Makefile" ;; + "test_problems/ck2cti_test/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/runtest" ;; + "test_problems/nasa9_reader/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/Makefile" ;; + "test_problems/nasa9_reader/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/runtest" ;; + "test_problems/min_python/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/Makefile" ;; + "test_problems/min_python/minDiamond/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/minDiamond/Makefile" ;; + "test_problems/min_python/negATest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/negATest/Makefile" ;; + "test_problems/pureFluidTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/pureFluidTest/Makefile" ;; + "test_problems/rankine_democxx/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/rankine_democxx/Makefile" ;; + "test_problems/python/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/python/Makefile" ;; + "test_problems/cathermo/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/Makefile" ;; + "test_problems/cathermo/issp/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/issp/Makefile" ;; + "test_problems/cathermo/ims/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/ims/Makefile" ;; + "test_problems/cathermo/stoichSubSSTP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/stoichSubSSTP/Makefile" ;; + "test_problems/cathermo/testIAPWS/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWS/Makefile" ;; + "test_problems/cathermo/testIAPWSPres/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSPres/Makefile" ;; + "test_problems/cathermo/testIAPWSTripP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSTripP/Makefile" ;; + "test_problems/cathermo/testWaterPDSS/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterPDSS/Makefile" ;; + "test_problems/cathermo/testWaterTP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterTP/Makefile" ;; + "test_problems/cathermo/HMW_test_1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_1/Makefile" ;; + "test_problems/cathermo/HMW_test_3/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_3/Makefile" ;; + "test_problems/cathermo/HMW_graph_GvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_GvI/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvI/Makefile" ;; + "test_problems/cathermo/HMW_graph_HvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_HvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_CpvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_CpvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_VvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_VvT/Makefile" ;; + "test_problems/cathermo/DH_graph_1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_1/Makefile" ;; + "test_problems/cathermo/DH_graph_acommon/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_acommon/Makefile" ;; + "test_problems/cathermo/DH_graph_NM/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_NM/Makefile" ;; + "test_problems/cathermo/DH_graph_Pitzer/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_Pitzer/Makefile" ;; + "test_problems/cathermo/DH_graph_bdotak/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_bdotak/Makefile" ;; + "test_problems/cathermo/HMW_dupl_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_dupl_test/Makefile" ;; + "test_problems/cathermo/VPissp/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/VPissp/Makefile" ;; + "test_problems/cathermo/wtWater/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/wtWater/Makefile" ;; + "test_problems/VCSnonideal/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/Makefile" ;; + "test_problems/VPsilane_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/Makefile" ;; + "test_problems/VPsilane_test/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/runtest" ;; + "test_problems/VCSnonideal/NaCl_equil/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/NaCl_equil/Makefile" ;; + "bin/install_tsc") CONFIG_FILES="$CONFIG_FILES bin/install_tsc" ;; + + *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done + # If the user did not use the arguments to specify the items to instantiate, # then the envvar interface is used. Set only those that are not. # We use the long form for the default assignment because of an extremely @@ -11321,698 +8591,539 @@ if $ac_need_defaults; then fi # Have a temporary directory for convenience. Make it in the build tree -# simply because there is no reason to put it here, and in addition, +# simply because there is no reason against having it here, and in addition, # creating and moving files from /tmp can sometimes cause problems. -# Create a temporary directory, and hook for its removal unless debugging. +# Hook for its removal unless debugging. +# Note that there is a small window in which the directory will not be cleaned: +# after its creation but before its name has been assigned to `$tmp'. $debug || { - trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 - trap '{ (exit 1); exit 1; }' 1 2 13 15 + tmp= + trap 'exit_status=$? + { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status +' 0 + trap 'as_fn_exit 1' 1 2 13 15 } - # Create a (secure) tmp directory for tmp files. { - tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && + tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" } || { - tmp=./confstat$$-$RANDOM - (umask 077 && mkdir $tmp) -} || + tmp=./conf$$-$RANDOM + (umask 077 && mkdir "$tmp") +} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5 + +# Set up the scripts for CONFIG_FILES section. +# No need to generate them if there are no CONFIG_FILES. +# This happens for instance with `./config.status config.h'. +if test -n "$CONFIG_FILES"; then + + +ac_cr=`echo X | tr X '\015'` +# On cygwin, bash can eat \r inside `` if the user requested igncr. +# But we know of no other shell where ac_cr would be empty at this +# point, so we can use a bashism as a fallback. +if test "x$ac_cr" = x; then + eval ac_cr=\$\'\\r\' +fi +ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` +if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then + ac_cs_awk_cr='\r' +else + ac_cs_awk_cr=$ac_cr +fi + +echo 'BEGIN {' >"$tmp/subs1.awk" && +_ACEOF + + { - echo "$me: cannot create a temporary directory in ." >&2 - { (exit 1); exit 1; } + echo "cat >conf$$subs.awk <<_ACEOF" && + echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && + echo "_ACEOF" +} >conf$$subs.sh || + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 +ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` +ac_delim='%!_!# ' +for ac_last_try in false false false false false :; do + . ./conf$$subs.sh || + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 + + ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` + if test $ac_delim_n = $ac_delim_num; then + break + elif $ac_last_try; then + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done +rm -f conf$$subs.sh + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +cat >>"\$tmp/subs1.awk" <<\\_ACAWK && +_ACEOF +sed -n ' +h +s/^/S["/; s/!.*/"]=/ +p +g +s/^[^!]*!// +:repl +t repl +s/'"$ac_delim"'$// +t delim +:nl +h +s/\(.\{148\}\).*/\1/ +t more1 +s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ +p +n +b repl +:more1 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t nl +:delim +h +s/\(.\{148\}\).*/\1/ +t more2 +s/["\\]/\\&/g; s/^/"/; s/$/"/ +p +b +:more2 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t delim +' >$CONFIG_STATUS || ac_write_fail=1 +rm -f conf$$subs.awk +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACAWK +cat >>"\$tmp/subs1.awk" <<_ACAWK && + for (key in S) S_is_set[key] = 1 + FS = "" + +} +{ + line = $ 0 + nfields = split(line, field, "@") + substed = 0 + len = length(field[1]) + for (i = 2; i < nfields; i++) { + key = field[i] + keylen = length(key) + if (S_is_set[key]) { + value = S[key] + line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) + len += length(value) + length(field[++i]) + substed = 1 + } else + len += 1 + keylen + } + + print line } +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then + sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" +else + cat +fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ + || as_fn_error "could not setup config files machinery" "$LINENO" 5 _ACEOF -cat >>$CONFIG_STATUS <<_ACEOF +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/ +s/:*\${srcdir}:*/:/ +s/:*@srcdir@:*/:/ +s/^\([^=]*=[ ]*\):*/\1/ +s/:*$// +s/^[^=]*=[ ]*$// +}' +fi -# -# CONFIG_FILES section. -# - -# No need to generate the scripts if there are 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Generated by configure. */" >$tmp/config.h - fi - cat $tmp/in >>$tmp/config.h - rm -f $tmp/in + -) cat "$tmp/out" && rm -f "$tmp/out";; + *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; + esac \ + || as_fn_error "could not create $ac_file" "$LINENO" 5 + ;; + :H) + # + # CONFIG_HEADER + # if test x"$ac_file" != x-; then - if diff $ac_file $tmp/config.h >/dev/null 2>&1; then - { echo "$as_me:$LINENO: $ac_file is unchanged" >&5 -echo "$as_me: $ac_file is unchanged" >&6;} + { + $as_echo "/* $configure_input */" \ + && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" + } >"$tmp/config.h" \ + || as_fn_error "could not create $ac_file" "$LINENO" 5 + if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then + { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 +$as_echo "$as_me: $ac_file is unchanged" >&6;} else - ac_dir=`(dirname "$ac_file") 2>/dev/null || -$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$ac_file" : 'X\(//\)[^/]' \| \ - X"$ac_file" : 'X\(//\)$' \| \ - X"$ac_file" : 'X\(/\)' \| \ - . : '\(.\)' 2>/dev/null || -echo X"$ac_file" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } - /^X\(\/\/\)[^/].*/{ s//\1/; q; } - /^X\(\/\/\)$/{ s//\1/; q; } - /^X\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` - { if $as_mkdir_p; then - mkdir -p "$ac_dir" - else - as_dir="$ac_dir" - as_dirs= - while test ! -d "$as_dir"; do - as_dirs="$as_dir $as_dirs" - as_dir=`(dirname "$as_dir") 2>/dev/null || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| \ - . : '\(.\)' 2>/dev/null || -echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } - /^X\(\/\/\)[^/].*/{ s//\1/; q; } - /^X\(\/\/\)$/{ s//\1/; q; } - /^X\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` - done - test ! -n "$as_dirs" || mkdir $as_dirs - fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5 -echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;} - { (exit 1); exit 1; }; }; } - - rm -f $ac_file - mv $tmp/config.h $ac_file + rm -f "$ac_file" + mv "$tmp/config.h" "$ac_file" \ + || as_fn_error "could not create $ac_file" "$LINENO" 5 fi else - cat $tmp/config.h - rm -f $tmp/config.h + $as_echo "/* $configure_input */" \ + && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ + || as_fn_error "could not create -" "$LINENO" 5 fi -done -_ACEOF + ;; -cat >>$CONFIG_STATUS <<\_ACEOF -{ (exit 0); exit 0; } + esac + +done # for ac_tag + + +as_fn_exit 0 _ACEOF -chmod +x $CONFIG_STATUS ac_clean_files=$ac_clean_files_save +test $ac_write_fail = 0 || + as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5 + # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. @@ -12032,7 +9143,11 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || { (exit 1); exit 1; } + $ac_cs_success || as_fn_exit $? +fi +if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 +$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi # ) diff --git a/configure.in b/configure.in index 0ffaada6c..8e60bdb77 100755 --- a/configure.in +++ b/configure.in @@ -1350,11 +1350,19 @@ AC_PROG_INSTALL # doesn't have this problem. So, I changed the default # install program to config/install-sh, which should work # on all platforms since its a bourne shell script +# HKM 12/24/2009 - Ran into another problem with the new cygwin 1.7.1. +# THe install (and even cp -f in some cases) program will fail +# when an existing different file is in place. This occurs sometimes +# and I can not quite nail down when. However replacing +# the install command for cygwin. Note, install no longer +# needs to have a wildcard capability within Cantera. + +case $ac_sys_system in + CYGWIN* ) + INSTALL=${INSTALL_BIN:=config/install-sh} + echo 'INSTALL program has been set to ' $INSTALL;; +esac -# problem: install-sh does not handle wildcards in filename. -# commenting this out (DGG) -# INSTALL=${INSTALL_BIN:=config/install-sh} -echo 'INSTALL program has been set to ' $INSTALL # # precompile_headers still relevant? # From f85bf977e41d2fcbd6f85cf5829219ba1d19c908 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 29 Dec 2009 02:37:49 +0000 Subject: [PATCH 093/446] Copied changes from 1.8.0 branch to trunk. Changes in the mechanism to make the solution more numerically stable. --- data/inputs/ptcombust.cti | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/data/inputs/ptcombust.cti b/data/inputs/ptcombust.cti index 43154883c..ef9c6b5ed 100644 --- a/data/inputs/ptcombust.cti +++ b/data/inputs/ptcombust.cti @@ -290,3 +290,11 @@ surface_reaction( "C(S) + O(S) => CO(S) + PT(S)", [3.70000E+21, 0, 62800]) # Reaction 24 surface_reaction( "CO(S) + PT(S) => C(S) + O(S)", [1.00000E+18, 0, 184000]) + +# Reaction 25 (12/28/2009 HKM added: This is a fictious rxn that is added for numerical stability. +# The issue is that if multiple surface species have a negative concentration, the +# Jacobian for the surface problem will go singular due to the way negative concentrations +# are truncated within Cantera. Adding in unimolecular desorption rxns with neglibigle real +# effects alleviates the problem.) +surface_reaction( "C(S) => C + PT(S)", [3.7E7, 0, 62800]) + From 3b8018e5fb9c1a9116201fa43672310ff8b74c85 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 29 Dec 2009 02:45:58 +0000 Subject: [PATCH 094/446] Merged the changes in the 1.8.0_Revision into this branch. --- .../equilibrium/adiabatic_flame/Makefile.in | 2 +- .../equilibrium/adiabatic_flame/Makefile.win | 2 +- .../equilibrium/adiabatic_flame/cleanup | 3 +- .../examples/equilibrium/simple_test/cleanup | 3 +- .../flames/adiabatic_flame/Makefile.in | 2 +- .../flames/adiabatic_flame/Makefile.win | 2 +- .../python/examples/flames/flame1/Makefile.in | 2 +- .../examples/flames/flame1/Makefile.win | 2 +- .../python/examples/flames/flame2/Makefile.in | 2 +- .../examples/flames/flame2/Makefile.win | 2 +- .../examples/flames/flame_fixed_T/Makefile.in | 2 +- .../flames/flame_fixed_T/Makefile.win | 2 +- .../examples/flames/free_h2_air/cleanup | 2 +- .../python/examples/flames/npflame1/cleanup | 2 +- .../examples/flames/npflame1/npflame1.csv | 177 - .../python/examples/flames/stflame1/cleanup | 2 +- .../flames/stflame1/output_blessed_0.txt | 94 +- .../python/examples/fuel_cells/Makefile.in | 2 +- .../python/examples/fuel_cells/Makefile.win | 2 +- Cantera/python/examples/fuel_cells/cleanup | 2 +- .../examples/fuel_cells/output_blessed_0.txt | 4 +- .../examples/gasdynamics/isentropic/cleanup | 2 +- .../examples/gasdynamics/soundSpeed/cleanup | 2 +- .../examples/liquid_vapor/rankine/cleanup | 2 +- .../reactors/combustor_sim/Makefile.in | 2 +- .../reactors/combustor_sim/Makefile.win | 2 +- .../combustor_sim/combustor_blessed_0.csv | 8376 +++++++++-------- .../examples/reactors/combustor_sim/runtest | 2 +- .../python/examples/reactors/mix1_sim/cleanup | 2 +- .../reactors/mix1_sim/output_blessed_0.txt | 98 +- .../examples/reactors/piston_sim/cleanup | 2 +- .../reactors/piston_sim/output_blessed_0.txt | 30 +- .../reactor1_sim/output_blessed_0.txt | 126 +- .../sensitivity_sim/output_blessed_0.txt | 312 +- .../surf_pfr_sim/output_blessed_0.txt | 1504 ++- .../examples/reactors/surf_pfr_sim/runtest | 2 +- .../reactors/surf_pfr_sim/surf_pfr.py | 12 +- .../surf_pfr_sim/surf_pfr_blessed_0.csv | 401 +- .../catcomb_stagflow/catcomb_blessed_0.csv | 94 +- .../catcomb_stagflow/output_blessed_0.txt | 981 +- .../surface_chemistry/diamond_cvd/cleanup | 2 +- 41 files changed, 6669 insertions(+), 5598 deletions(-) delete mode 100644 Cantera/python/examples/flames/npflame1/npflame1.csv diff --git a/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.in b/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.in index c0b8181f6..c60fa97ef 100644 --- a/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.in +++ b/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.in @@ -21,7 +21,7 @@ install: @INSTALL@ -c -m ug+rw,o+r adiabatic_blessed_0.csv $(INST_DIR) clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.win b/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.win index 7d514a44f..262335669 100644 --- a/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.win +++ b/Cantera/python/examples/equilibrium/adiabatic_flame/Makefile.win @@ -11,7 +11,7 @@ test: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/equilibrium/adiabatic_flame/cleanup b/Cantera/python/examples/equilibrium/adiabatic_flame/cleanup index 83f3d4dc6..6325f1780 100755 --- a/Cantera/python/examples/equilibrium/adiabatic_flame/cleanup +++ b/Cantera/python/examples/equilibrium/adiabatic_flame/cleanup @@ -2,4 +2,5 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - equil_koh.csv + equil_koh.csv diff_csv.txt diff_out_0.txt output_0.txt + diff --git a/Cantera/python/examples/equilibrium/simple_test/cleanup b/Cantera/python/examples/equilibrium/simple_test/cleanup index 83f3d4dc6..c48763339 100755 --- a/Cantera/python/examples/equilibrium/simple_test/cleanup +++ b/Cantera/python/examples/equilibrium/simple_test/cleanup @@ -2,4 +2,5 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - equil_koh.csv + equil_koh.csv diff_out_0.txt output_0.txt output_1.txt + diff --git a/Cantera/python/examples/flames/adiabatic_flame/Makefile.in b/Cantera/python/examples/flames/adiabatic_flame/Makefile.in index c0b689433..138ad0963 100644 --- a/Cantera/python/examples/flames/adiabatic_flame/Makefile.in +++ b/Cantera/python/examples/flames/adiabatic_flame/Makefile.in @@ -21,7 +21,7 @@ install: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/adiabatic_flame/Makefile.win b/Cantera/python/examples/flames/adiabatic_flame/Makefile.win index ac6ee9604..cbda2e80e 100644 --- a/Cantera/python/examples/flames/adiabatic_flame/Makefile.win +++ b/Cantera/python/examples/flames/adiabatic_flame/Makefile.win @@ -8,7 +8,7 @@ test: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame1/Makefile.in b/Cantera/python/examples/flames/flame1/Makefile.in index f33110f2d..2830f3830 100644 --- a/Cantera/python/examples/flames/flame1/Makefile.in +++ b/Cantera/python/examples/flames/flame1/Makefile.in @@ -24,7 +24,7 @@ install: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame1/Makefile.win b/Cantera/python/examples/flames/flame1/Makefile.win index f47c64fe8..4f29d36bf 100644 --- a/Cantera/python/examples/flames/flame1/Makefile.win +++ b/Cantera/python/examples/flames/flame1/Makefile.win @@ -7,7 +7,7 @@ test: ./runtest clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame2/Makefile.in b/Cantera/python/examples/flames/flame2/Makefile.in index e87eb3788..c18a27d1e 100644 --- a/Cantera/python/examples/flames/flame2/Makefile.in +++ b/Cantera/python/examples/flames/flame2/Makefile.in @@ -21,7 +21,7 @@ install: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame2/Makefile.win b/Cantera/python/examples/flames/flame2/Makefile.win index 6521abdc7..9a1c75587 100644 --- a/Cantera/python/examples/flames/flame2/Makefile.win +++ b/Cantera/python/examples/flames/flame2/Makefile.win @@ -8,7 +8,7 @@ test: ./runtest clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame_fixed_T/Makefile.in b/Cantera/python/examples/flames/flame_fixed_T/Makefile.in index 087f8c64d..cabc8cd07 100644 --- a/Cantera/python/examples/flames/flame_fixed_T/Makefile.in +++ b/Cantera/python/examples/flames/flame_fixed_T/Makefile.in @@ -22,7 +22,7 @@ install: @INSTALL@ -c -m ug+rw,o+r flame_fixed_T_blessed_0.csv $(INST_DIR) clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/flame_fixed_T/Makefile.win b/Cantera/python/examples/flames/flame_fixed_T/Makefile.win index 378d713e3..b8876ebea 100644 --- a/Cantera/python/examples/flames/flame_fixed_T/Makefile.win +++ b/Cantera/python/examples/flames/flame_fixed_T/Makefile.win @@ -8,7 +8,7 @@ test: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/flames/free_h2_air/cleanup b/Cantera/python/examples/flames/free_h2_air/cleanup index a96d13c43..40adf8340 100755 --- a/Cantera/python/examples/flames/free_h2_air/cleanup +++ b/Cantera/python/examples/flames/free_h2_air/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - freeflame1.csv output_0.txt diff* + freeflame1.csv output_0.txt diff* ohn.xml diff --git a/Cantera/python/examples/flames/npflame1/cleanup b/Cantera/python/examples/flames/npflame1/cleanup index 40e1dbd9e..ba1c6c2c2 100755 --- a/Cantera/python/examples/flames/npflame1/cleanup +++ b/Cantera/python/examples/flames/npflame1/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* npflame1.csv diff --git a/Cantera/python/examples/flames/npflame1/npflame1.csv b/Cantera/python/examples/flames/npflame1/npflame1.csv deleted file mode 100644 index 94b6d1784..000000000 --- a/Cantera/python/examples/flames/npflame1/npflame1.csv +++ /dev/null @@ -1,177 +0,0 @@ -z (m), u (m/s), V (1/s), T (K), H2, H, O, O2, OH, H2O, HO2, H2O2, C, CH, CH2, CH2(S), CH3, CH4, CO, CO2, HCO, CH2O, CH2OH, CH3O, 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3.73480325645e-30, 5.05444379521e-50, 1.9383625579e-46, 6.86304993043e-34, 3.39913881296e-63, 1.14619931762e-36, 6.03563983262e-57, 1.01218091997e-38, 1.06018700458e-47, 2.17116573782e-37, 5.4316955365e-51, 1.55384610762e-35, 6.37528440184e-38, 3.66113997528e-33, 2.00925400122e-38, 6.88365262312e-26, 1.89904695221e-26, 1.93587448444e-40, 1.27615170124e-19, 1.18335134733e-20, 2.78327370517e-23, 2.80775346176e-24, 7.04999370073e-51, 9.26397979874e-26, 1.0249395588e-29, 6.680437115e-57, 2.49952325339e-29, 2.08000443075e-28, 2.75258732441e-26, 2.34464121408e-30, 0.779999999998, 0.00999999999998, 1.0551401184e-42, 2.36017424791e-40, 1.76594467498e-52, 1.2086814988e-37, diff --git a/Cantera/python/examples/flames/stflame1/cleanup b/Cantera/python/examples/flames/stflame1/cleanup index 55b97eb53..057afda5c 100755 --- a/Cantera/python/examples/flames/stflame1/cleanup +++ b/Cantera/python/examples/flames/stflame1/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - stflame1_[1234567].csv output_0.txt diff* + stflame1_[1234567].csv output_0.txt diff* h2o2.xml stflame1.xml diff --git a/Cantera/python/examples/flames/stflame1/output_blessed_0.txt b/Cantera/python/examples/flames/stflame1/output_blessed_0.txt index 65319e422..54f6f4a1b 100644 --- a/Cantera/python/examples/flames/stflame1/output_blessed_0.txt +++ b/Cantera/python/examples/flames/stflame1/output_blessed_0.txt @@ -294,7 +294,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [77] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot1. +Solution saved to file stflame1.xml as solution mdot1_1. solution saved to flame1.csv .............................................................................. @@ -323,7 +323,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [88] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot2. +Solution saved to file stflame1.xml as solution mdot2_1. solution saved to flame1.csv .............................................................................. @@ -506,7 +506,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [116] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot3. +Solution saved to file stflame1.xml as solution mdot3_1. solution saved to flame1.csv .............................................................................. @@ -634,7 +634,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [124] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot4. +Solution saved to file stflame1.xml as solution mdot4_1. solution saved to flame1.csv .............................................................................. @@ -731,7 +731,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [126] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot5. +Solution saved to file stflame1.xml as solution mdot5_1. solution saved to flame1.csv .............................................................................. @@ -814,7 +814,7 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [125] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot6. +Solution saved to file stflame1.xml as solution mdot6_1. solution saved to flame1.csv .............................................................................. @@ -881,55 +881,55 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [128] point grid(s). no new points needed in flow -Solution saved to file stflame1.xml as solution mdot7. +Solution saved to file stflame1.xml as solution mdot7_1. solution saved to flame1.csv Statistics: Grid Functions Time Jacobians Time - 10 401 0.1900 21 0.1600 - 12 16 0.0000 2 0.0300 + 10 401 0.1500 21 0.1600 + 12 16 0.0000 2 0.0200 13 14 0.0000 2 0.0200 15 14 0.0100 2 0.0300 - 16 10 0.0000 1 0.0200 - 16 5353 2.9400 140 1.9000 - 29 35 0.0300 2 0.0400 - 45 23 0.0400 2 0.0900 - 59 14 0.0300 2 0.1100 - 67 14 0.0400 2 0.1400 - 74 8 0.0000 1 0.0800 - 78 4 0.0000 1 0.0900 - 79 4 0.0100 1 0.0900 - 79 53 0.1800 5 0.4100 - 88 10 0.0300 1 0.1000 - 90 12 0.0500 1 0.1000 - 90 1067 3.5200 58 5.6400 + 16 10 0.0100 1 0.0100 + 16 5353 3.1400 140 2.0400 + 29 35 0.0400 2 0.0400 + 45 23 0.0200 2 0.0900 + 59 14 0.0200 2 0.1100 + 67 14 0.0400 2 0.1200 + 74 8 0.0200 1 0.0700 + 78 4 0.0200 1 0.0800 + 79 4 0.0100 1 0.0800 + 79 53 0.1500 5 0.4100 + 88 10 0.0400 1 0.1500 + 90 12 0.0800 1 0.1500 + 90 1067 3.5500 58 5.8100 87 25 0.0900 2 0.1800 - 97 46 0.1500 4 0.4400 - 104 60 0.2300 6 0.7100 - 100 59 0.2100 5 0.5800 + 97 46 0.1500 4 0.4300 + 104 60 0.2300 6 0.6900 + 100 59 0.2000 5 0.5500 115 40 0.2000 4 0.5400 - 117 12 0.0700 1 0.1500 - 118 2 0.0000 1 0.1400 - 118 162 0.6800 21 2.8900 - 98 18 0.0500 2 0.2200 - 109 22 0.0900 2 0.2400 - 118 30 0.1400 3 0.4200 - 123 30 0.1300 3 0.4600 - 126 26 0.1000 3 0.4700 - 126 18 0.0800 2 0.3000 - 126 59 0.3200 8 1.2000 - 112 26 0.1100 3 0.3900 - 120 34 0.1500 3 0.4200 - 126 28 0.1300 3 0.4600 - 128 24 0.1100 2 0.3100 + 117 12 0.0500 1 0.1400 + 118 2 0.0100 1 0.1300 + 118 162 0.7100 21 2.9100 + 98 18 0.0600 2 0.2200 + 109 22 0.1200 2 0.2400 + 118 30 0.1100 3 0.4200 + 123 30 0.1300 3 0.4300 + 126 26 0.1200 3 0.4500 + 126 18 0.0700 2 0.3000 + 126 59 0.2800 8 1.2100 + 112 26 0.0700 3 0.3900 + 120 34 0.1400 3 0.4200 + 126 28 0.1600 3 0.4600 + 128 24 0.1100 2 0.3000 128 18 0.0900 2 0.3100 - 128 59 0.2900 7 1.0700 - 114 38 0.1100 4 0.5400 - 121 18 0.0800 2 0.2900 - 126 14 0.0700 2 0.3000 + 128 59 0.2800 7 1.0700 + 114 38 0.1900 4 0.5200 + 121 18 0.0800 2 0.2800 + 126 14 0.0600 2 0.3000 127 4 0.0200 1 0.1500 - 127 58 0.2600 6 0.9100 - 117 28 0.1100 3 0.4200 - 126 26 0.1300 3 0.4600 - 130 10 0.0400 1 0.1500 + 127 58 0.2600 6 0.9000 + 117 28 0.1300 3 0.4000 + 126 26 0.1200 3 0.4500 + 130 10 0.0500 1 0.1600 diff --git a/Cantera/python/examples/fuel_cells/Makefile.in b/Cantera/python/examples/fuel_cells/Makefile.in index f2395ca43..7ef05807f 100644 --- a/Cantera/python/examples/fuel_cells/Makefile.in +++ b/Cantera/python/examples/fuel_cells/Makefile.in @@ -22,7 +22,7 @@ install: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/fuel_cells/Makefile.win b/Cantera/python/examples/fuel_cells/Makefile.win index 288818e49..6761a80b2 100644 --- a/Cantera/python/examples/fuel_cells/Makefile.win +++ b/Cantera/python/examples/fuel_cells/Makefile.win @@ -9,7 +9,7 @@ test: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/fuel_cells/cleanup b/Cantera/python/examples/fuel_cells/cleanup index 40e1dbd9e..67063f5d3 100755 --- a/Cantera/python/examples/fuel_cells/cleanup +++ b/Cantera/python/examples/fuel_cells/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* *tmp~ diff --git a/Cantera/python/examples/fuel_cells/output_blessed_0.txt b/Cantera/python/examples/fuel_cells/output_blessed_0.txt index 851bc0f97..c4bfe5488 100644 --- a/Cantera/python/examples/fuel_cells/output_blessed_0.txt +++ b/Cantera/python/examples/fuel_cells/output_blessed_0.txt @@ -29,9 +29,9 @@ OH'(ox) 0.0002061 H2O(ox) 1.12e-09 -ocv from zero current is: 1.13757806928 +ocv from zero current is: 1.1375780672 OCV from thermo equil is: 1.1375780672 Ea0 = -0.733444291655 -Ec0 = 0.404133777622 +Ec0 = 0.40413377554 polarization curve data written to file sofc.csv diff --git a/Cantera/python/examples/gasdynamics/isentropic/cleanup b/Cantera/python/examples/gasdynamics/isentropic/cleanup index 40e1dbd9e..e687b3e65 100755 --- a/Cantera/python/examples/gasdynamics/isentropic/cleanup +++ b/Cantera/python/examples/gasdynamics/isentropic/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* gri30.xml diff --git a/Cantera/python/examples/gasdynamics/soundSpeed/cleanup b/Cantera/python/examples/gasdynamics/soundSpeed/cleanup index 40e1dbd9e..e687b3e65 100755 --- a/Cantera/python/examples/gasdynamics/soundSpeed/cleanup +++ b/Cantera/python/examples/gasdynamics/soundSpeed/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* gri30.xml diff --git a/Cantera/python/examples/liquid_vapor/rankine/cleanup b/Cantera/python/examples/liquid_vapor/rankine/cleanup index 40e1dbd9e..b42ab0100 100755 --- a/Cantera/python/examples/liquid_vapor/rankine/cleanup +++ b/Cantera/python/examples/liquid_vapor/rankine/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* liquidvapor.xml diff --git a/Cantera/python/examples/reactors/combustor_sim/Makefile.in b/Cantera/python/examples/reactors/combustor_sim/Makefile.in index 97c365bac..370c3b99f 100644 --- a/Cantera/python/examples/reactors/combustor_sim/Makefile.in +++ b/Cantera/python/examples/reactors/combustor_sim/Makefile.in @@ -22,7 +22,7 @@ install: @INSTALL@ -c -m ug+rw,o+r combustor_blessed_0.csv $(INST_DIR) clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/reactors/combustor_sim/Makefile.win b/Cantera/python/examples/reactors/combustor_sim/Makefile.win index 19890b307..a3b151bbb 100644 --- a/Cantera/python/examples/reactors/combustor_sim/Makefile.win +++ b/Cantera/python/examples/reactors/combustor_sim/Makefile.win @@ -11,7 +11,7 @@ test: clean: - rm -f *.log *.csv *.xml + rm -f *.log ./cleanup # end of file diff --git a/Cantera/python/examples/reactors/combustor_sim/combustor_blessed_0.csv b/Cantera/python/examples/reactors/combustor_sim/combustor_blessed_0.csv index 300314df7..765469158 100644 --- a/Cantera/python/examples/reactors/combustor_sim/combustor_blessed_0.csv +++ b/Cantera/python/examples/reactors/combustor_sim/combustor_blessed_0.csv @@ -274,4162 +274,4220 @@ 0.0045416476174437049, 300.02124970814594, 0.040552190256001507, -5.86345099602e-25, 9.398898539e-31, 6.22953683678e-17, 0.0211410723759, 5.78141418724e-24, 4.20054611934e-24, -1.54677004624e-23, 2.15894055278e-34, -6.22947550452e-17, 4.6454593178e-39, 5.47869068023e-40, 5.79491871464e-43, 1.41816646648e-23, 0.00528738304718, 6.22939177817e-17, 3.02479643664e-27, 2.6861573067e-23, 2.30818421567e-25, 6.90516075598e-45, 3.12719027834e-26, 2.85667778801e-31, 7.22086150038e-47, 2.14964878691e-29, -1.13375407013e-55, 9.67502490209e-34, -4.63087653647e-45, 7.086873929e-36, 2.55369517634e-43, -4.93041344305e-50, 7.04777982456e-58, -1.0475775672e-37, 3.71835813769e-44, -1.35635918067e-56, -7.71932063448e-76, 1.61670833704e-40, -4.49878502853e-29, 5.57826572428e-39, 6.57827068459e-28, 2.47701966118e-46, 2.21188377332e-41, -4.49878504612e-29, 5.98863421755e-51, -1.14721304632e-23, -2.16670340999e-62, -2.97298319571e-57, -2.15529734651e-54, -7.65301649358e-38, 0.972564826845, 0.00100671773218, -5.08040895932e-58, 4.6920522067e-60, 2.06099597668e-46, -1.69337007357e-51, 0.0046511071192309964, 300.02119250585906, 0.040552167713375102, -5.84765275484e-25, 2.50060934214e-30, 1.36719484941e-16, 0.0216219456502, 3.47355517218e-24, 5.0976842103e-24, -3.36923667859e-23, 2.15342769706e-34, -1.36718199034e-16, -2.24056856304e-38, 1.44544348572e-39, 8.52130134458e-43, 1.36681117635e-23, 0.00540764947233, 1.36715641578e-16, 3.11481644427e-27, 5.86778763967e-23, 2.33212614251e-25, 1.96682569479e-44, 2.8169915149e-26, 2.88631851711e-31, 1.58746103914e-46, 2.26765397165e-29, -1.02434295725e-55, 9.58662387307e-34, -5.67239054853e-45, 6.87840978225e-36, 1.02663508993e-42, -3.91412712488e-50, 2.10480335308e-58, -1.00215209964e-37, 2.05733886045e-44, -1.32679424702e-56, -8.99218139516e-76, 4.32874356711e-40, -4.51652673738e-29, 5.38226772567e-39, 6.86539398623e-28, 2.49035825616e-46, 5.29188161809e-41, -4.51652675426e-29, 5.97290009672e-51, -2.50605275475e-23, -2.19502310612e-62, -2.9081818822e-57, -1.98633026317e-54, -7.38813164638e-38, 0.971940788418, 0.00102961645953, -3.67373879071e-58, 4.87136050888e-60, -5.77919237268e-47, -1.75891246775e-51, 0.0047605666210182879, 300.02113546067989, 0.040552194327655652, -5.83189372939e-25, 2.64086842262e-31, 4.28474065942e-17, 0.0221015225004, 6.41678543521e-24, 6.01273687703e-24, -1.06965478205e-23, 2.14780132372e-34, -4.28457537423e-17, 3.86488929189e-39, 2.82239526944e-40, 3.39757919432e-43, 1.84414601836e-23, 0.00552759166176, 4.28422148505e-17, 3.16473109316e-27, 1.85445081686e-23, 2.35359488424e-25, 3.35399231703e-45, 2.5317661426e-26, 2.91289226042e-31, 4.96117351536e-47, 2.33525214257e-29, -1.45634977611e-55, 9.49627136818e-34, -5.95764930157e-45, 6.74640601481e-36, 3.60691405279e-44, -3.33828716243e-50, -1.32120735676e-58, -9.67576921327e-38, 1.15441895017e-44, -1.30890549343e-56, -9.76092767676e-76, 4.39180717273e-41, -4.52206866261e-29, 5.23782148745e-39, 7.07194948072e-28, 2.49454554106e-46, 1.39360450056e-41, -4.52206867897e-29, 5.95778882811e-51, -7.91999169957e-24, -2.21045601784e-62, -2.86897241043e-57, -1.88044043421e-54, -7.18672623114e-38, 0.971318432385, 0.0010524534524, -7.87142859716e-59, 4.99441423172e-60, -9.14826458249e-47, 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0.00551782572521, 0.127400841192, 4.84448137244e-06, 1.64492310068e-07, 1.76191849515e-10, 8.3707080271e-09, 2.72844039377e-07, 3.16764564994e-08, 5.2266973682e-06, 1.93579932625e-05, 0.00249644412426, 0.0462967270191, 1.94981786253e-07, 2.99815845273e-06, 2.8723284033e-08, 3.80309183763e-09, 5.08283431233e-08, 2.66665246289e-12, 4.63670099897e-10, 5.2882293117e-11, 1.11195731896e-09, 4.60208527722e-11, 5.40939930135e-11, 1.90169632183e-10, 1.3140260248e-09, 3.26583641516e-11, 2.5049789675e-09, 1.2903953645e-09, 9.10327609758e-10, 7.04585806335e-10, 9.47686206069e-10, 0.000114566229591, 8.11238338553e-08, 4.89453442926e-07, 3.28912045829e-09, 6.23100338529e-11, 2.4400104744e-08, 9.05204592249e-13, 5.29494212669e-12, 1.93263091643e-08, 6.2451075304e-10, 4.30536489597e-08, 3.74645195813e-09, 0.724999156739, 0.0092956028305, 6.51456679858e-17, 1.87796568292e-16, 5.75018855892e-12, 1.36899198708e-10, -1.07695427611941, 1996.8986959610243, 0.0060513816355109162, 0.00126632004555, 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1996.6902232098282, 0.006052117580102134, 0.00126553426561, 0.000549027379858, 0.00177637203924, 0.0802669451302, 0.00551223019699, 0.127378156442, 4.84672975049e-06, 1.64561544264e-07, 1.75668351917e-10, 8.35768177284e-09, 2.72825547814e-07, 3.1665605846e-08, 5.22955406624e-06, 1.93809933749e-05, 0.00249401142173, 0.046300101745, 1.9498180221e-07, 3.00069185352e-06, 2.87115617102e-08, 3.80475441012e-09, 5.09377127724e-08, 2.66590974976e-12, 4.64328251301e-10, 5.29396590856e-11, 1.11437740056e-09, 4.61173174324e-11, 5.43173167594e-11, 1.9020850341e-10, 1.31624384158e-09, 3.26944113717e-11, 2.49486349726e-09, 1.28770683138e-09, 9.08190647378e-10, 7.03109806789e-10, 9.46200334224e-10, 0.000114189682941, 8.09216330658e-08, 4.89668781886e-07, 3.28089746026e-09, 6.20945556653e-11, 2.43581343379e-08, 9.02421945979e-13, 5.29379421081e-12, 1.92891778978e-08, 6.23225347245e-10, 4.29824494782e-08, 3.73810753241e-09, 0.725013755438, 0.00929578757981, 6.53635163191e-17, 1.88992502486e-16, 5.76043559624e-12, 1.372157821e-10, -1.0770451331244766, 1996.4816904228237, 0.0060528533607568605, 0.00126474870813, 0.000548664882916, 0.00177552366764, 0.0802753952307, 0.00550943260448, 0.127366809217, 4.84785695605e-06, 1.64596247112e-07, 1.75407019517e-10, 8.35117133141e-09, 2.72816271293e-07, 3.16601771393e-08, 5.23098395654e-06, 1.9392511447e-05, 0.0024927957983, 0.0463017884336, 1.94981809982e-07, 3.0019601796e-06, 2.87056986397e-08, 3.80558734296e-09, 5.0992519932e-08, 2.66553784834e-12, 4.64657877659e-10, 5.29683879879e-11, 1.11559022863e-09, 4.61656728757e-11, 5.44293873708e-11, 1.90228040133e-10, 1.31735512009e-09, 3.27124565915e-11, 2.48981833505e-09, 1.28636418549e-09, 9.07123471726e-10, 7.02372584985e-10, 9.45457849062e-10, 0.000114001765748, 8.08206826546e-08, 4.89776582309e-07, 3.27679217408e-09, 6.19870332242e-11, 2.43371677194e-08, 9.01033132422e-13, 5.29321960304e-12, 1.92706257358e-08, 6.22583331391e-10, 4.29468730932e-08, 3.7339399093e-09, 0.725021055721, 0.00929587996872, 6.54728677923e-17, 1.8959376662e-16, 5.76557051821e-12, 1.37374496327e-10, -1.0770905616270099, 1996.2730977169529, 0.0060535908899873323, 0.00126396337351, 0.000548302499882, 0.00177467533099, 0.0802838471521, 0.0055066351287, 0.127355458767, 4.84898617386e-06, 1.64631007144e-07, 1.75145964767e-10, 8.34466268743e-09, 2.72806974154e-07, 3.16547461716e-08, 5.23241487199e-06, 1.94040415266e-05, 0.00249158066152, 0.0463034746709, 1.94981817548e-07, 3.0032295891e-06, 2.86998342922e-08, 3.80642137303e-09, 5.10474087386e-08, 2.66516559641e-12, 4.64987874234e-10, 5.299714775e-11, 1.11680492384e-09, 4.62141106806e-11, 5.45417317528e-11, 1.90247645023e-10, 1.31846798768e-09, 3.27305159995e-11, 2.48478154414e-09, 1.28502261896e-09, 9.06057161548e-10, 7.01635876608e-10, 9.44715665005e-10, 0.000113814085926, 8.07198325662e-08, 4.89884469959e-07, 3.27269103023e-09, 6.18796554135e-11, 2.43162136542e-08, 8.99645992374e-13, 5.29264455981e-12, 1.925208257e-08, 6.21941741146e-10, 4.29113122437e-08, 3.72977534442e-09, 0.725028356621, 0.00929597236705, 6.5582506577e-17, 1.90197248944e-16, 5.77071308406e-12, 1.37533493607e-10, -1.0771359901295432, 1996.0644452118995, 0.0060543280480481873, 0.00126317826223, 0.000547940230944, 0.00177382702964, 0.0802923008895, 0.00550383777213, 0.127344105099, 4.85011740457e-06, 1.64665824298e-07, 1.74885187545e-10, 8.33815584283e-09, 2.72797656324e-07, 3.16493129376e-08, 5.23384681151e-06, 1.94155836265e-05, 0.00249036601254, 0.0463051604554, 1.94981824798e-07, 3.00450008085e-06, 2.86939686633e-08, 3.80725650079e-09, 5.11023793013e-08, 2.66479298513e-12, 4.65318239057e-10, 5.30259381963e-11, 1.11802148337e-09, 4.62626308311e-11, 5.46543499186e-11, 1.90267317844e-10, 1.31958244525e-09, 3.2748589325e-11, 2.47975311991e-09, 1.28368213646e-09, 9.04991726026e-10, 7.00899690131e-10, 9.43973782458e-10, 0.000113626643437, 8.06190826796e-08, 4.89992444814e-07, 3.26859402922e-09, 6.17724225285e-11, 2.42952722628e-08, 8.98260525554e-13, 5.29206907954e-12, 1.92335484407e-08, 6.2130051318e-10, 4.28757672233e-08, 3.72561386839e-09, 0.725035658132, 0.00929606477476, 6.56924324307e-17, 1.90802946555e-16, 5.77586327802e-12, 1.37692773812e-10, -1.0771814186320765, 1995.8557330327694, 0.0060550654294871959, 0.00126239337486, 0.000547578076329, 0.00177297876421, 0.0803007564377, 0.00550104053665, 0.12733274822, 4.85125064959e-06, 1.64700698737e-07, 1.7462468794e-10, 8.33165080751e-09, 2.72788317977e-07, 3.164387746e-08, 5.23527977975e-06, 1.94271377669e-05, 0.00248915185251, 0.0463068457855, 1.94981831899e-07, 3.00577165854e-06, 2.86881017745e-08, 3.80809273089e-09, 5.11574318014e-08, 2.66442001522e-12, 4.65648972997e-10, 5.30547594438e-11, 1.1192399133e-09, 4.63112336552e-11, 5.47672432102e-11, 1.90287058439e-10, 1.32069849171e-09, 3.2766677045e-11, 2.47473305433e-09, 1.28234273666e-09, 9.03927164741e-10, 7.00164026279e-10, 9.43232201894e-10, 0.00011343943825, 8.05184329586e-08, 4.90100506822e-07, 3.264501173e-09, 6.16653341665e-11, 2.4274343404e-08, 8.96876731254e-13, 5.29149316477e-12, 1.92150233783e-08, 6.20659743327e-10, 4.28402380334e-08, 3.72145547221e-09, 0.725042960251, 0.00929615719178, 6.58026467765e-17, 1.91410876843e-16, 5.78102112509e-12, 1.37852337739e-10, -1.0772268471346098, 1995.6469613048689, 0.0060558033812346179, 0.00126160871195, 0.000547216036256, 0.00177213053528, 0.0803092137915, 0.00549824342439, 0.127321388137, 4.85238590975e-06, 1.64735630396e-07, 1.7436446598e-10, 8.32514758734e-09, 2.72778959047e-07, 3.16384397364e-08, 5.23671377507e-06, 1.94387039501e-05, 0.00248793818255, 0.0463085306598, 1.94981838806e-07, 3.00704432164e-06, 2.8682233626e-08, 3.80893006334e-09, 5.12125663085e-08, 2.66404669211e-12, 4.6598007754e-10, 5.30836115718e-11, 1.12046021752e-09, 4.63599192481e-11, 5.48804120966e-11, 1.9030686722e-10, 1.32181613269e-09, 3.27847790617e-11, 2.46972134028e-09, 1.2810044179e-09, 9.02863474334e-10, 6.99428880839e-10, 9.42490923776e-10, 0.000113252470331, 8.04178835322e-08, 4.90208655911e-07, 3.26041245902e-09, 6.1558390133e-11, 2.42534270652e-08, 8.95494610004e-13, 5.29091681465e-12, 1.91965073987e-08, 6.20019410402e-10, 4.2804724584e-08, 3.71730014783e-09, 0.725050262972, 0.00929624961804, 6.59131504935e-17, 1.92021046944e-16, 5.78618664276e-12, 1.38012186146e-10, -1.0772958523653857, 1995.3297264546743, 0.0060569247388791263, 0.00126041725102, 0.000546666322287, 0.00177084215894, 0.0803220638309, 0.0054939948924, 0.127304126223, 4.85411421051e-06, 1.6478880062e-07, 1.7396972378e-10, 8.31527277506e-09, 2.72764703563e-07, 3.16301756214e-08, 5.23889395853e-06, 1.9456295877e-05, 0.00248609557574, 0.046311089084, 1.94981848869e-07, 3.00897955526e-06, 2.86733175905e-08, 3.81020407102e-09, 5.12964719725e-08, 2.66347893971e-12, 4.66483728657e-10, 5.31274965627e-11, 1.12231743065e-09, 4.64340305951e-11, 5.5052842603e-11, 1.90337086847e-10, 1.3235168675e-09, 3.28123029297e-11, 2.4621245829e-09, 1.27897360194e-09, 9.01249414391e-10, 6.98313201767e-10, 9.41365512777e-10, 0.000112968922645, 8.02653422754e-08, 4.9037309927e-07, 3.25420968856e-09, 6.1396220063e-11, 2.42216795698e-08, 8.93398388088e-13, 5.29004051294e-12, 1.9168399323e-08, 6.19047543856e-10, 4.27508104473e-08, 3.710994168e-09, 0.725061356841, 0.00929639002972, 6.60815591066e-17, 1.92952187017e-16, 5.79404767384e-12, 1.38255538524e-10, -1.0773648575961616, 1995.0123549200769, 0.0060580468054042382, 0.00125922631095, 0.000546116873818, 0.00176955386995, 0.0803349180065, 0.00548974665699, 0.127286856957, 4.85584716625e-06, 1.64842103085e-07, 1.73575622148e-10, 8.3054021821e-09, 2.72750400557e-07, 3.16219063416e-08, 5.24107651431e-06, 1.94739156523e-05, 0.00248425410614, 0.0463136464482, 1.9498185843e-07, 3.01091729633e-06, 2.86643986701e-08, 3.81148063066e-09, 5.13805675423e-08, 2.6629103665e-12, 4.66988235117e-10, 5.31714528567e-11, 1.12417898273e-09, 4.65083338053e-11, 5.52259130783e-11, 1.90367463872e-10, 1.32522129293e-09, 3.28398596424e-11, 2.45454705598e-09, 1.27694528501e-09, 8.99637372141e-10, 6.97198727433e-10, 9.40240802183e-10, 0.000112685922194, 8.01130324765e-08, 4.90537743245e-07, 3.24801647888e-09, 6.12343833164e-11, 2.41899612644e-08, 8.91306024859e-13, 5.28916320435e-12, 1.91403123318e-08, 6.1807664895e-10, 4.2696933007e-08, 3.70469531599e-09, 0.725072452071, 0.00929653046239, 6.62506400406e-17, 1.93888545522e-16, 5.80192645777e-12, 1.38499550002e-10, -1.0774338628269375, 1994.6948471309381, 0.0060591695975365373, 0.00125803589356, 0.000545567691577, 0.0017682656702, 0.0803477763004, 0.00548549872537, 0.127269580362, 4.85758478039e-06, 1.64895537875e-07, 1.73182161097e-10, 8.29553582931e-09, 2.7273605005e-07, 3.16136319125e-08, 5.24326144433e-06, 1.94915633121e-05, 0.00248241377764, 0.0463162027474, 1.94981867511e-07, 3.01285754747e-06, 2.86554768838e-08, 3.81275974786e-09, 5.146485343e-08, 2.66234097646e-12, 4.67493598958e-10, 5.32154806132e-11, 1.12604488578e-09, 4.65828294496e-11, 5.53996260613e-11, 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1.91020750791e-05, 0.00253354564456, 0.0462632519183, 1.95138453457e-07, 2.95242612992e-06, 2.81746358978e-08, 3.72334230809e-09, 5.00719818174e-08, 2.44323799122e-12, 4.26464713063e-10, 5.01804307402e-11, 1.04516878045e-09, 4.35679805267e-11, 5.21977817055e-11, 1.80798512771e-10, 1.27179265001e-09, 2.86813512071e-11, 2.32435439421e-09, 1.11548076818e-09, 5.83864894308e-10, 4.43862501934e-10, 9.8661295232e-10, 7.13202913442e-05, 5.01884355685e-08, 4.89361264777e-07, 2.26944042302e-09, 4.63101228182e-11, 1.82880358385e-08, 6.11001802448e-13, 5.35389900125e-12, 1.12480793077e-08, 4.4292930932e-10, 2.70247042246e-08, 2.47775599175e-09, 0.725067590603, 0.0092962025555, 6.02881933996e-17, 1.77471967067e-16, 5.55344839101e-12, 1.31544375045e-10, +0.93438074876579746, 1992.1441851434597, 0.0058822282386973802, 0.0013009925562, 0.000576333095051, 0.00183393908724, 0.0803911578406, 0.00556800822709, 0.12710166631, 4.98921434801e-06, 1.6838140696e-07, 1.84027242787e-10, 8.35154293951e-09, 2.66459585923e-07, 3.10859620469e-08, 5.08582778054e-06, 1.904817287e-05, 0.00253943725236, 0.0462550678809, 1.95136776916e-07, 2.94654351851e-06, 2.8203857174e-08, 3.71955246527e-09, 4.98154797339e-08, 2.44560436384e-12, 4.25128228741e-10, 5.00582674464e-11, 1.03991590144e-09, 4.33548448765e-11, 5.16894742762e-11, 1.80745410436e-10, 1.26684420525e-09, 2.86175920301e-11, 2.34724883167e-09, 1.12104058743e-09, 5.87782267716e-10, 4.46593386743e-10, 9.90220012003e-10, 7.19720490991e-05, 5.0550224837e-08, 4.88838790047e-07, 2.28458747775e-09, 4.67134906692e-11, 1.8369398321e-08, 6.16040553679e-13, 5.35635163257e-12, 1.13158965394e-08, 4.45340863179e-10, 2.71619530454e-08, 2.4932095932e-09, 0.725032240845, 0.00929575352935, 5.98112861331e-17, 1.74805524023e-16, 5.53025281474e-12, 1.30826114203e-10, +0.93459291963677993, 1993.1619355936728, 0.0058791840577879602, 0.00130478037199, 0.000578081973412, 0.001837984655, 0.0803502193037, 0.0055814864531, 0.127157020576, 4.98297684086e-06, 1.68191148636e-07, 1.85321424515e-10, 8.38282127644e-09, 2.66519830066e-07, 3.11134004048e-08, 5.07956938735e-06, 1.89945603949e-05, 0.00254533718181, 0.0462468772585, 1.95135104045e-07, 2.94068730635e-06, 2.82330419586e-08, 3.71578964167e-09, 4.95608955054e-08, 2.44796236947e-12, 4.2379910997e-10, 4.99367657062e-11, 1.03470283405e-09, 4.31435182031e-11, 5.11872070542e-11, 1.80693728454e-10, 1.26193047437e-09, 2.85540695305e-11, 2.37032059418e-09, 1.12662179019e-09, 5.9171861449e-10, 4.4933622376e-10, 9.93832141559e-10, 7.26284118402e-05, 5.09140824932e-08, 4.88318487917e-07, 2.29981814562e-09, 4.71195856833e-11, 1.84510350763e-08, 6.21112230034e-13, 5.3587940682e-12, 1.13839678311e-08, 4.47761611264e-10, 2.72996438291e-08, 2.50873110038e-09, 0.724996919664, 0.00929530489913, 5.93405404722e-17, 1.72186388214e-16, 5.50722986606e-12, 1.3011423219e-10, +0.93480509050776239, 1994.1779339520037, 0.0058761479823996104, 0.00130857149866, 0.000579832496432, 0.0018420288792, 0.0803093383216, 0.00559496173017, 0.127212280702, 4.97679135537e-06, 1.68002387487e-07, 1.86621540609e-10, 8.41413034997e-09, 2.66579603902e-07, 3.11407796206e-08, 5.07333497809e-06, 1.8941235832e-05, 0.00255124534198, 0.0462386801561, 1.95133434876e-07, 2.93485735599e-06, 2.82621901208e-08, 3.71205362204e-09, 4.93082127432e-08, 2.45031202156e-12, 4.22477309812e-10, 4.98159212184e-11, 1.02952921309e-09, 4.29339817461e-11, 5.06908995667e-11, 1.80643459122e-10, 1.25705115292e-09, 2.84907829633e-11, 2.3935705138e-09, 1.13222447521e-09, 5.95674043942e-10, 4.52091086135e-10, 9.97449306919e-10, 7.3289409115e-05, 5.12800227565e-08, 4.87800357733e-07, 2.31513300004e-09, 4.75284223861e-11, 1.85329477986e-08, 6.26217018353e-13, 5.36122635812e-12, 1.1452294845e-08, 4.50191599015e-10, 2.74377800154e-08, 2.52432088332e-09, 0.724961627222, 0.00929485666714, 5.88758619371e-17, 1.69613620529e-16, 5.48437794518e-12, 1.29408659957e-10, +0.93501726137874486, 1995.192178255819, 0.0058731200157983946, 0.00131236589959, 0.000581584647777, 0.00184607172528, 0.0802685150121, 0.00560843393589, 0.127267446561, 4.97065764434e-06, 1.67815117708e-07, 1.87927591263e-10, 8.44546975708e-09, 2.66638909453e-07, 3.1168099673e-08, 5.06712445677e-06, 1.88881973902e-05, 0.0025571616401, 0.0462304766812, 1.95131769444e-07, 2.9290535327e-06, 2.8291301517e-08, 3.70834419367e-09, 4.9057415297e-08, 2.45265333148e-12, 4.2116278192e-10, 4.9695729743e-11, 1.02439467865e-09, 4.27262170276e-11, 5.02004726312e-11, 1.80594594734e-10, 1.25220594119e-09, 2.84277315852e-11, 2.41699941181e-09, 1.13784873861e-09, 5.99648662432e-10, 4.54858044739e-10, 1.00107147282e-09, 7.39550701089e-05, 5.16480595819e-08, 4.8728439896e-07, 2.33053260538e-09, 4.79400151248e-11, 1.86151381231e-08, 6.31355102619e-13, 5.36364855171e-12, 1.15208791757e-08, 4.52630870193e-10, 2.75763649042e-08, 2.53997930045e-09, 0.724926363695, 0.00929440883579, 5.84171577942e-17, 1.67086302087e-16, 5.46169547699e-12, 1.28709329531e-10, +0.93522943224972732, 1996.2046661700006, 0.0058701001900612242, 0.0013161635369, 0.000583338410585, 0.00185011315758, 0.0802277495073, 0.00562190294338, 0.127322518006, 4.96457546547e-06, 1.67629331293e-07, 1.89239576018e-10, 8.47683908263e-09, 2.66697748682e-07, 3.11953605283e-08, 5.06093772933e-06, 1.88354433089e-05, 0.00256308598159, 0.0462222669439, 1.95130107781e-07, 2.92327570438e-06, 2.83203759912e-08, 3.70466114662e-09, 4.88084872543e-08, 2.45498630875e-12, 4.19855480567e-10, 4.95761871004e-11, 1.01929887621e-09, 4.25202058531e-11, 4.97158484042e-11, 1.80547127584e-10, 1.24739454418e-09, 2.8364914655e-11, 2.44060809848e-09, 1.14349467389e-09, 6.03642573389e-10, 4.57637168184e-10, 1.00469860278e-09, 7.46254236425e-05, 5.20182066576e-08, 4.86770611175e-07, 2.34601751691e-09, 4.83543780657e-11, 1.86976076269e-08, 6.36526663929e-13, 5.36606069764e-12, 1.1589722352e-08, 4.55079466918e-10, 2.77154016578e-08, 2.55570669864e-09, 0.724891129271, 0.00929396140768, 5.79643370542e-17, 1.64603535351e-16, 5.43918091064e-12, 1.28016174006e-10, +0.93544160312070979, 1997.215394998972, 0.0058670885217206228, 0.00131996437151, 0.000585093767492, 0.0018541531394, 0.0801870419534, 0.00563536862158, 0.127377494871, 4.95854457938e-06, 1.6744502229e-07, 1.90557493766e-10, 8.50823789967e-09, 2.66756123501e-07, 3.12225621415e-08, 5.05477470351e-06, 1.87829718565e-05, 0.00256901827006, 0.0462140510571, 1.95128449921e-07, 2.91752374147e-06, 2.83494133754e-08, 3.70100427342e-09, 4.85614129297e-08, 2.45731096107e-12, 4.18555360602e-10, 4.94572891695e-11, 1.01424145639e-09, 4.23159302986e-11, 4.92369502928e-11, 1.80501049965e-10, 1.24261667139e-09, 2.83023314342e-11, 2.4643973729e-09, 1.14916237196e-09, 6.07655877314e-10, 4.60428522838e-10, 1.00833065914e-09, 7.53004981667e-05, 5.23904774076e-08, 4.86258994059e-07, 2.36158828084e-09, 4.87715251923e-11, 1.87803578295e-08, 6.4173188048e-13, 5.36846284397e-12, 1.16588258366e-08, 4.57537429667e-10, 2.78548933027e-08, 2.57150341328e-09, 0.724855924148, 0.00929351438554, 5.75173103994e-17, 1.62164442396e-16, 5.41683271869e-12, 1.27329127505e-10, +0.93576858080058412, 1998.7695830872237, 0.0058624632086308149, 0.00132582802511, 0.000587802037326, 0.0018603762495, 0.0801244211687, 0.00565611381758, 0.127462034383, 4.94935023977e-06, 1.67163858869e-07, 1.92600156719e-10, 8.55668351344e-09, 2.66845180178e-07, 3.12643665595e-08, 5.04532303177e-06, 1.8702657294e-05, 0.00257817588492, 0.0462013777357, 1.95125902508e-07, 2.90870971332e-06, 2.83940900009e-08, 3.69541942332e-09, 4.81842393646e-08, 2.46087720764e-12, 4.16565697427e-10, 4.92753079328e-11, 1.00652180031e-09, 4.20044778481e-11, 4.85099560928e-11, 1.80432742438e-10, 1.23531844836e-09, 2.8206340011e-11, 2.50141456827e-09, 1.15793970764e-09, 6.13878998422e-10, 4.64754391214e-10, 1.01393759678e-09, 7.63501678384e-05, 5.29683744415e-08, 4.85474787985e-07, 2.38575381033e-09, 4.94198762661e-11, 1.89084375929e-08, 6.49819970362e-13, 5.37214533437e-12, 1.17658344907e-08, 4.61343837575e-10, 2.80707619616e-08, 2.59598428467e-09, 0.724801727209, 0.00929282627896, 5.68395382087e-17, 1.58489080556e-16, 5.38271409938e-12, 1.2628212861e-10, +0.93609555848045845, 2000.3195733543041, 0.0058578576054188931, 0.00133169902347, 0.000590513982887, 0.00186659568218, 0.0800619390455, 0.00567685027067, 0.127546348061, 4.94027631683e-06, 1.6688616364e-07, 1.9465689685e-10, 8.60519646835e-09, 2.66933144855e-07, 3.13060298841e-08, 5.03592711434e-06, 1.86230038389e-05, 0.00258735177332, 0.0461886905159, 1.95123364325e-07, 2.89995636056e-06, 2.84386774008e-08, 3.68989551187e-09, 4.78113761896e-08, 2.46442370999e-12, 4.14592823986e-10, 4.90948336443e-11, 9.9889125063e-10, 4.16970422829e-11, 4.77961131082e-11, 1.80367688529e-10, 1.22809814142e-09, 2.81108992234e-11, 2.5388653606e-09, 1.16676925019e-09, 6.20148752575e-10, 4.69109684878e-10, 1.01955599477e-09, 7.74112174955e-05, 5.3551393297e-08, 4.8469573637e-07, 2.4101264358e-09, 5.00749221852e-11, 1.90371925604e-08, 6.57989034991e-13, 5.37580435885e-12, 1.18734694898e-08, 4.65172716383e-10, 2.82877277721e-08, 2.62063168193e-09, 0.724747601187, 0.00929213915464, 5.61750059934e-17, 1.54912364234e-16, 5.34898165413e-12, 1.2524925226e-10, +0.93642253616033277, 2001.8653514025987, 0.0058532712352226696, 0.00133757720729, 0.000593229533827, 0.00187281128969, 0.0799995962965, 0.00569757744576, 0.12763043505, 4.93132197887e-06, 1.66611912106e-07, 1.96727700907e-10, 8.65377504416e-09, 2.67020023867e-07, 3.13475518032e-08, 5.02658663636e-06, 1.85440055122e-05, 0.00259654555876, 0.0461759898438, 1.95120835498e-07, 2.89126324029e-06, 2.84831748103e-08, 3.68443181179e-09, 4.7442768814e-08, 2.46795047497e-12, 4.12636582446e-10, 4.89158519622e-11, 9.91348592827e-10, 4.13935614402e-11, 4.70951568731e-11, 1.80305859901e-10, 1.22095474409e-09, 2.80160064162e-11, 2.57675250807e-09, 1.17565129632e-09, 6.26465467885e-10, 4.7349461659e-10, 1.02518569941e-09, 7.84837460817e-05, 5.41395795551e-08, 4.83921839223e-07, 2.43470803423e-09, 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0.00948489065317, 2.77342825503e-13, 1.72686265446e-11, 4.20432596977e-10, 2.29486471609e-08, diff --git a/Cantera/python/examples/reactors/combustor_sim/runtest b/Cantera/python/examples/reactors/combustor_sim/runtest index fa3713ef6..1cce6b71f 100755 --- a/Cantera/python/examples/reactors/combustor_sim/runtest +++ b/Cantera/python/examples/reactors/combustor_sim/runtest @@ -30,7 +30,7 @@ fi diff -w output_blessed_0.txt output_0.txt > diff_out_0.txt retnStat_0=$? -csvdiff -a 1.0E-50 combustor_blessed_0.csv combustor.csv > diff_csv.txt +csvdiff -a 1.0E-15 combustor_blessed_0.csv combustor.csv > diff_csv.txt retnStat_csv_0=$? retnTotal=1 diff --git a/Cantera/python/examples/reactors/mix1_sim/cleanup b/Cantera/python/examples/reactors/mix1_sim/cleanup index 40e1dbd9e..e499c5640 100755 --- a/Cantera/python/examples/reactors/mix1_sim/cleanup +++ b/Cantera/python/examples/reactors/mix1_sim/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* gri30.xml air.xml diff --git a/Cantera/python/examples/reactors/mix1_sim/output_blessed_0.txt b/Cantera/python/examples/reactors/mix1_sim/output_blessed_0.txt index 7b499427c..4238b5211 100644 --- a/Cantera/python/examples/reactors/mix1_sim/output_blessed_0.txt +++ b/Cantera/python/examples/reactors/mix1_sim/output_blessed_0.txt @@ -53,56 +53,56 @@ Maximum time step: 0.0222248 X Y Chem. Pot. / RT ------------- ------------ ------------ - H2 6.27858e-26 4.52548e-27 -73.7472 - H 6.40667e-36 2.3089e-37 -7.43615 - O -7.20447e-26 -4.12139e-26 + H2 -6.67941e-23 -4.81439e-24 + H -1.37394e-29 -4.95155e-31 + O 1.05229e-23 6.01975e-24 27.6163 O2 0.193727 0.221647 -26.3149 - OH -1.11833e-25 -6.80054e-26 - H2O 4.6875e-25 3.0194e-25 -175.68 - HO2 3.44811e-25 4.06932e-25 -78.8495 - H2O2 2.32639e-27 2.82936e-27 -144.007 - C 9.6316e-49 4.13634e-49 157.744 - CH 6.3808e-55 2.97022e-55 92.6731 - CH2 1.06303e-38 5.33147e-39 46.4692 - CH2(S) 5.51354e-40 2.76522e-40 59.1922 - CH3 8.66908e-25 4.66025e-25 -19.8456 + OH 1.53004e-22 9.30419e-23 -56.5557 + H2O 2.91766e-22 1.87938e-22 -169.246 + HO2 -4.26035e-22 -5.02789e-22 + H2O2 6.45082e-23 7.84548e-23 -133.777 + C 1.08367e-41 4.65388e-42 173.98 + CH 9.40568e-44 4.37828e-44 118.39 + CH2 -2.08391e-30 -1.04515e-30 + CH2(S) -1.0823e-31 -5.42809e-32 + CH3 1.11024e-20 5.96834e-21 -10.3878 CH4 0.0774913 0.0444499 -54.8803 - CO -9.56189e-25 -9.57639e-25 - CO2 -1.31922e-27 -2.0759e-27 - HCO -1.31408e-43 -1.36343e-43 - CH2O -4.00569e-27 -4.30049e-27 - CH2OH -6.14779e-43 -6.82179e-43 - CH3O 4.44663e-37 4.93412e-37 -104.647 - CH3OH -4.75169e-26 -5.44388e-26 - C2H 6.03881e-58 5.40443e-58 69.5849 - C2H2 1.52623e-27 1.4209e-27 5.57512 - C2H3 7.75323e-54 7.49758e-54 -30.2547 - C2H4 1.44138e-34 1.4458e-34 -83.253 - C2H5 1.0288e-40 1.06903e-40 -74.2256 - C2H6 1.99966e-26 2.14992e-26 -120.36 - HCCO -3.782e-51 -5.54823e-51 - CH2CO -1.47235e-31 -2.21301e-31 - HCCOH 3.2183e-46 4.83725e-46 -101.685 - N -9.15201e-49 -4.58344e-49 - NH 1.28208e-48 6.88289e-49 11.0188 - NH2 9.73847e-32 5.57908e-32 -17.8651 - NH3 1.39623e-41 8.50208e-42 -135.658 - NNH 7.93639e-46 8.23531e-46 -30.8163 - NO 8.92707e-32 9.57761e-32 -60.2516 - NO2 -4.34793e-41 -7.15205e-41 - N2O -8.42223e-32 -1.3254e-31 - HNO 1.58336e-35 1.75581e-35 -64.1012 - CN -2.48257e-57 -2.30945e-57 - HCN 5.30006e-31 5.12148e-31 -41.5413 - H2CN 8.45525e-46 8.47508e-46 -31.5975 - HCNN 2.5427e-55 3.73044e-55 29.4769 - HCNO 2.27874e-49 3.50554e-49 -72.6234 - HOCN 3.83484e-50 5.8994e-50 -147.636 - HNCO -2.83441e-42 -4.36036e-42 - NCO -9.82455e-32 -1.47597e-31 + CO -3.89709e-22 -3.90299e-22 + CO2 -7.3555e-23 -1.15744e-22 + HCO -2.26268e-34 -2.34765e-34 + CH2O -8.57457e-23 -9.2056e-23 + CH2OH -6.08085e-34 -6.74751e-34 + CH3O 4.49215e-29 4.98463e-29 -86.2166 + CH3OH -1.32408e-21 -1.51696e-21 + C2H -6.63826e-54 -5.9409e-54 + C2H2 2.33532e-29 2.17415e-29 1.39529 + C2H3 -3.50144e-43 -3.38599e-43 + C2H4 1.25986e-28 1.26372e-28 -69.5721 + C2H5 1.97031e-31 2.04735e-31 -52.8525 + C2H6 5.5958e-22 6.01629e-22 -110.12 + HCCO -2.80493e-50 -4.11486e-50 + CH2CO 5.6831e-37 8.54198e-37 -131.674 + HCCOH 3.57889e-45 5.37925e-45 -99.2765 + N -2.72993e-52 -1.36719e-52 + NH -2.63888e-51 -1.41669e-51 + NH2 1.76051e-53 1.00858e-53 -67.9298 + NH3 -2.29731e-60 -1.3989e-60 + NNH -9.14155e-40 -9.48586e-40 + NO -1.51947e-32 -1.63019e-32 + NO2 1.62932e-40 2.68013e-40 -106.793 + N2O -3.67096e-33 -5.77694e-33 + HNO -4.5838e-37 -5.08303e-37 + CN 1.48193e-62 1.37859e-62 9.13145 + HCN 6.66046e-44 6.43605e-44 -71.2464 + H2CN -9.30723e-50 -9.32907e-50 + HCNN 4.10305e-44 6.01967e-44 55.2839 + HCNO 2.43017e-44 3.7385e-44 -61.0461 + HOCN 5.52354e-60 8.49723e-60 -170.297 + HNCO 1.93475e-43 2.97635e-43 -174.643 + NCO -2.38702e-42 -3.58609e-42 N2 0.719557 0.720727 -23.3621 AR 0.00922509 0.0131766 -23.2957 - C3H7 -5.91476e-49 -9.1125e-49 - C3H8 -1.41189e-43 -2.22609e-43 - CH2CHO 2.89798e-52 4.46025e-52 -140.817 - CH3CHO 6.89333e-43 1.08579e-42 -195.453 + C3H7 2.35833e-43 3.63333e-43 -92.6765 + C3H8 -1.98071e-36 -3.12294e-36 + CH2CHO -1.30696e-41 -2.01153e-41 + CH3CHO 3.98305e-42 6.2738e-42 -193.699 diff --git a/Cantera/python/examples/reactors/piston_sim/cleanup b/Cantera/python/examples/reactors/piston_sim/cleanup index 40e1dbd9e..2374f570d 100755 --- a/Cantera/python/examples/reactors/piston_sim/cleanup +++ b/Cantera/python/examples/reactors/piston_sim/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - catcomb.csv output_0.txt diff* + catcomb.csv output_0.txt diff* gri30.xml h2o2.xml diff --git a/Cantera/python/examples/reactors/piston_sim/output_blessed_0.txt b/Cantera/python/examples/reactors/piston_sim/output_blessed_0.txt index e3d4dafe4..f528e19eb 100644 --- a/Cantera/python/examples/reactors/piston_sim/output_blessed_0.txt +++ b/Cantera/python/examples/reactors/piston_sim/output_blessed_0.txt @@ -11,21 +11,21 @@ Maximum time step: 0.002 0.002 900.0 900.0006 0.5 0.1 0.6 0.2853 0.004 900.0 900.0017 0.5 0.1 0.6 0.2853 0.006 900.0 900.0108 0.5 0.1 0.6 0.2853 - 0.008 2094.1 1073.0950 0.5423 0.0577 0.6 0.2853 - 0.010 2232.8 1087.5289 0.5447 0.05533 0.6 0.2853 - 0.012 2245.4 1089.1484 0.5449 0.05514 0.6 0.2853 - 0.014 2248.6 1090.1364 0.5449 0.05512 0.6 0.2852 - 0.016 2249.7 1091.4073 0.5448 0.05515 0.6 0.2851 - 0.018 2250.1 1093.3910 0.5448 0.05523 0.6 0.2849 - 0.020 2250.4 1096.5040 0.5446 0.05536 0.6 0.2845 - 0.022 2250.8 1101.2701 0.5445 0.05555 0.6 0.284 - 0.024 2251.4 1108.4677 0.5442 0.05584 0.6 0.2833 - 0.026 2252.3 1119.5404 0.5437 0.0563 0.6 0.2822 - 0.028 2253.7 1138.1891 0.5429 0.05705 0.6 0.2802 - 0.030 2257.3 1183.3660 0.5411 0.05886 0.6 0.2755 - 0.032 2358.9 2820.1201 0.4913 0.1087 0.6 0.03655 - 0.034 2351.1 2819.4428 0.4911 0.1089 0.6 0.0365 - 0.036 2350.5 2819.3898 0.491 0.109 0.6 0.03649 + 0.008 2094.0 1073.0922 0.5423 0.0577 0.6 0.2853 + 0.010 2232.8 1087.5284 0.5447 0.05533 0.6 0.2853 + 0.012 2245.4 1089.1480 0.5449 0.05514 0.6 0.2853 + 0.014 2248.6 1090.1361 0.5449 0.05512 0.6 0.2852 + 0.016 2249.7 1091.4070 0.5448 0.05515 0.6 0.2851 + 0.018 2250.1 1093.3907 0.5448 0.05523 0.6 0.2849 + 0.020 2250.4 1096.5035 0.5446 0.05536 0.6 0.2845 + 0.022 2250.8 1101.2697 0.5445 0.05555 0.6 0.284 + 0.024 2251.4 1108.4670 0.5442 0.05584 0.6 0.2833 + 0.026 2252.3 1119.5392 0.5437 0.0563 0.6 0.2822 + 0.028 2253.7 1138.1869 0.5429 0.05705 0.6 0.2802 + 0.030 2257.3 1183.3585 0.5411 0.05886 0.6 0.2755 + 0.032 2358.9 2820.1203 0.4913 0.1087 0.6 0.03655 + 0.034 2351.1 2819.4429 0.4911 0.1089 0.6 0.0365 + 0.036 2350.5 2819.3899 0.491 0.109 0.6 0.03649 0.038 2350.4 2819.3860 0.491 0.109 0.6 0.03649 0.040 2350.4 2819.3857 0.491 0.109 0.6 0.03649 0.042 2350.4 2819.3857 0.491 0.109 0.6 0.03649 diff --git a/Cantera/python/examples/reactors/reactor1_sim/output_blessed_0.txt b/Cantera/python/examples/reactors/reactor1_sim/output_blessed_0.txt index d0bda3e88..e01140c44 100644 --- a/Cantera/python/examples/reactors/reactor1_sim/output_blessed_0.txt +++ b/Cantera/python/examples/reactors/reactor1_sim/output_blessed_0.txt @@ -27,77 +27,77 @@ Maximum time step: 1e-05 2.100e-04 1001.121 101325.000 6.207272e+05 2.200e-04 1001.200 101325.000 6.206998e+05 2.300e-04 1001.340 101325.000 6.206504e+05 - 2.400e-04 1001.605 101325.000 6.205559e+05 + 2.400e-04 1001.605 101325.000 6.205558e+05 2.500e-04 1002.143 101325.000 6.203620e+05 - 2.600e-04 1003.306 101325.000 6.199379e+05 - 2.700e-04 1005.922 101325.000 6.189784e+05 - 2.800e-04 1011.831 101325.001 6.168064e+05 - 2.900e-04 1025.563 101325.002 6.117624e+05 - 3.000e-04 1061.248 101325.005 5.986897e+05 - 3.100e-04 1190.850 101325.025 5.516418e+05 - 3.200e-04 1697.308 101325.031 3.765732e+05 - 3.300e-04 1941.711 101325.013 2.989421e+05 - 3.400e-04 2076.003 101325.008 2.577857e+05 - 3.500e-04 2167.606 101325.006 2.303083e+05 - 3.600e-04 2236.248 101325.005 2.100312e+05 - 3.700e-04 2290.516 101325.004 1.941874e+05 - 3.800e-04 2334.935 101325.003 1.813415e+05 - 3.900e-04 2372.179 101325.002 1.706547e+05 - 4.000e-04 2403.959 101325.002 1.615959e+05 - 4.100e-04 2431.436 101325.002 1.538081e+05 - 4.200e-04 2455.435 101325.002 1.470399e+05 - 4.300e-04 2476.559 101325.001 1.411080e+05 - 4.400e-04 2495.269 101325.001 1.358745e+05 - 4.500e-04 2511.920 101325.001 1.312326e+05 - 4.600e-04 2526.797 101325.001 1.270981e+05 - 4.700e-04 2540.128 101325.001 1.234032e+05 - 4.800e-04 2552.104 101325.001 1.200923e+05 - 4.900e-04 2562.882 101325.001 1.171190e+05 - 5.000e-04 2572.598 101325.001 1.144443e+05 - 5.100e-04 2581.366 101325.001 1.120350e+05 - 5.200e-04 2589.287 101325.001 1.098623e+05 - 5.300e-04 2596.446 101325.000 1.079013e+05 - 5.400e-04 2602.922 101325.000 1.061301e+05 - 5.500e-04 2608.782 101325.000 1.045296e+05 - 5.600e-04 2614.085 101325.000 1.030827e+05 - 5.700e-04 2618.887 101325.000 1.017743e+05 + 2.600e-04 1003.307 101325.000 6.199379e+05 + 2.700e-04 1005.923 101325.000 6.189783e+05 + 2.800e-04 1011.832 101325.001 6.168062e+05 + 2.900e-04 1025.564 101325.002 6.117618e+05 + 3.000e-04 1061.252 101325.005 5.986882e+05 + 3.100e-04 1190.870 101325.025 5.516348e+05 + 3.200e-04 1697.335 101325.031 3.765645e+05 + 3.300e-04 1941.724 101325.013 2.989383e+05 + 3.400e-04 2076.010 101325.008 2.577833e+05 + 3.500e-04 2167.611 101325.006 2.303067e+05 + 3.600e-04 2236.252 101325.005 2.100299e+05 + 3.700e-04 2290.520 101325.004 1.941864e+05 + 3.800e-04 2334.938 101325.003 1.813407e+05 + 3.900e-04 2372.181 101325.002 1.706540e+05 + 4.000e-04 2403.961 101325.002 1.615953e+05 + 4.100e-04 2431.438 101325.002 1.538075e+05 + 4.200e-04 2455.436 101325.002 1.470394e+05 + 4.300e-04 2476.561 101325.001 1.411076e+05 + 4.400e-04 2495.270 101325.001 1.358741e+05 + 4.500e-04 2511.921 101325.001 1.312323e+05 + 4.600e-04 2526.798 101325.001 1.270978e+05 + 4.700e-04 2540.129 101325.001 1.234030e+05 + 4.800e-04 2552.105 101325.001 1.200921e+05 + 4.900e-04 2562.883 101325.001 1.171188e+05 + 5.000e-04 2572.599 101325.001 1.144442e+05 + 5.100e-04 2581.367 101325.001 1.120348e+05 + 5.200e-04 2589.287 101325.001 1.098621e+05 + 5.300e-04 2596.447 101325.000 1.079012e+05 + 5.400e-04 2602.923 101325.000 1.061300e+05 + 5.500e-04 2608.782 101325.000 1.045295e+05 + 5.600e-04 2614.086 101325.000 1.030826e+05 + 5.700e-04 2618.887 101325.000 1.017742e+05 5.800e-04 2623.235 101325.000 1.005907e+05 - 5.900e-04 2627.172 101325.000 9.952006e+04 - 6.000e-04 2630.737 101325.000 9.855137e+04 - 6.100e-04 2633.966 101325.000 9.767490e+04 - 6.200e-04 2636.890 101325.000 9.688186e+04 - 6.300e-04 2639.539 101325.000 9.616433e+04 - 6.400e-04 2641.936 101325.000 9.551516e+04 - 6.500e-04 2644.107 101325.000 9.492788e+04 - 6.600e-04 2646.073 101325.000 9.439665e+04 - 6.700e-04 2647.852 101325.000 9.391619e+04 - 6.800e-04 2649.462 101325.000 9.348173e+04 - 6.900e-04 2650.919 101325.000 9.308893e+04 - 7.000e-04 2652.237 101325.000 9.273388e+04 - 7.100e-04 2653.429 101325.000 9.241303e+04 - 7.200e-04 2654.507 101325.000 9.212317e+04 - 7.300e-04 2655.482 101325.000 9.186139e+04 - 7.400e-04 2656.363 101325.000 9.162506e+04 - 7.500e-04 2657.159 101325.000 9.141178e+04 - 7.600e-04 2657.878 101325.000 9.121940e+04 - 7.700e-04 2658.528 101325.000 9.104596e+04 - 7.800e-04 2659.114 101325.000 9.088967e+04 - 7.900e-04 2659.642 101325.000 9.074893e+04 - 8.000e-04 2660.119 101325.000 9.062227e+04 - 8.100e-04 2660.548 101325.000 9.050839e+04 - 8.200e-04 2660.935 101325.000 9.040608e+04 - 8.300e-04 2661.283 101325.000 9.031425e+04 - 8.400e-04 2661.596 101325.000 9.023192e+04 - 8.500e-04 2661.878 101325.000 9.015820e+04 + 5.900e-04 2627.172 101325.000 9.951999e+04 + 6.000e-04 2630.738 101325.000 9.855130e+04 + 6.100e-04 2633.967 101325.000 9.767484e+04 + 6.200e-04 2636.891 101325.000 9.688181e+04 + 6.300e-04 2639.539 101325.000 9.616428e+04 + 6.400e-04 2641.936 101325.000 9.551512e+04 + 6.500e-04 2644.107 101325.000 9.492784e+04 + 6.600e-04 2646.073 101325.000 9.439662e+04 + 6.700e-04 2647.852 101325.000 9.391616e+04 + 6.800e-04 2649.462 101325.000 9.348170e+04 + 6.900e-04 2650.919 101325.000 9.308890e+04 + 7.000e-04 2652.237 101325.000 9.273385e+04 + 7.100e-04 2653.429 101325.000 9.241300e+04 + 7.200e-04 2654.507 101325.000 9.212315e+04 + 7.300e-04 2655.482 101325.000 9.186137e+04 + 7.400e-04 2656.363 101325.000 9.162504e+04 + 7.500e-04 2657.159 101325.000 9.141177e+04 + 7.600e-04 2657.878 101325.000 9.121939e+04 + 7.700e-04 2658.528 101325.000 9.104594e+04 + 7.800e-04 2659.114 101325.000 9.088965e+04 + 7.900e-04 2659.642 101325.000 9.074891e+04 + 8.000e-04 2660.119 101325.000 9.062226e+04 + 8.100e-04 2660.549 101325.000 9.050838e+04 + 8.200e-04 2660.935 101325.000 9.040607e+04 + 8.300e-04 2661.283 101325.000 9.031424e+04 + 8.400e-04 2661.596 101325.000 9.023191e+04 + 8.500e-04 2661.878 101325.000 9.015819e+04 8.600e-04 2662.130 101325.000 9.009228e+04 8.700e-04 2662.356 101325.000 9.003343e+04 8.800e-04 2662.559 101325.000 8.998099e+04 - 8.900e-04 2662.740 101325.000 8.993436e+04 + 8.900e-04 2662.740 101325.000 8.993435e+04 9.000e-04 2662.902 101325.000 8.989298e+04 - 9.100e-04 2663.046 101325.000 8.985637e+04 + 9.100e-04 2663.046 101325.000 8.985636e+04 9.200e-04 2663.174 101325.000 8.982407e+04 9.300e-04 2663.287 101325.000 8.979569e+04 - 9.400e-04 2663.388 101325.000 8.977086e+04 + 9.400e-04 2663.388 101325.000 8.977085e+04 9.500e-04 2663.476 101325.000 8.974923e+04 9.600e-04 2663.554 101325.000 8.973051e+04 9.700e-04 2663.622 101325.000 8.971443e+04 diff --git a/Cantera/python/examples/reactors/sensitivity_sim/output_blessed_0.txt b/Cantera/python/examples/reactors/sensitivity_sim/output_blessed_0.txt index a404e75f9..e01fd4fd6 100644 --- a/Cantera/python/examples/reactors/sensitivity_sim/output_blessed_0.txt +++ b/Cantera/python/examples/reactors/sensitivity_sim/output_blessed_0.txt @@ -111,7 +111,7 @@ Maximum time step: 5e-06 5.250e-04 1500.815 101325.000 9.067002e+05 0.001 -0.013 5.300e-04 1500.873 101325.000 9.066824e+05 0.001 -0.014 5.350e-04 1500.935 101325.000 9.066634e+05 0.001 -0.015 - 5.400e-04 1501.002 101325.000 9.066429e+05 0.001 -0.016 + 5.400e-04 1501.002 101325.000 9.066430e+05 0.001 -0.016 5.450e-04 1501.073 101325.000 9.066210e+05 0.001 -0.016 5.500e-04 1501.150 101325.000 9.065974e+05 0.001 -0.017 5.550e-04 1501.234 101325.000 9.065719e+05 0.001 -0.018 @@ -128,168 +128,168 @@ Maximum time step: 5e-06 6.100e-04 1502.778 101325.000 9.060982e+05 0.004 -0.038 6.150e-04 1503.011 101325.000 9.060267e+05 0.004 -0.041 6.200e-04 1503.268 101325.000 9.059474e+05 0.005 -0.044 - 6.250e-04 1503.555 101324.999 9.058592e+05 0.005 -0.048 - 6.300e-04 1503.874 101325.001 9.057608e+05 0.006 -0.052 - 6.350e-04 1504.232 101324.999 9.056504e+05 0.007 -0.057 + 6.250e-04 1503.555 101325.000 9.058592e+05 0.005 -0.048 + 6.300e-04 1503.874 101325.000 9.057608e+05 0.006 -0.052 + 6.350e-04 1504.232 101325.000 9.056504e+05 0.007 -0.057 6.400e-04 1504.634 101325.000 9.055261e+05 0.007 -0.061 6.450e-04 1505.089 101324.999 9.053855e+05 0.008 -0.067 - 6.500e-04 1505.605 101324.998 9.052256e+05 0.009 -0.073 - 6.550e-04 1506.195 101325.001 9.050429e+05 0.011 -0.079 - 6.600e-04 1506.872 101324.999 9.048330e+05 0.012 -0.086 - 6.650e-04 1507.653 101324.998 9.045905e+05 0.013 -0.094 - 6.700e-04 1508.559 101324.999 9.043090e+05 0.015 -0.102 - 6.750e-04 1509.614 101324.999 9.039807e+05 0.017 -0.110 - 6.800e-04 1510.849 101325.000 9.035961e+05 0.019 -0.118 + 6.500e-04 1505.605 101324.999 9.052256e+05 0.009 -0.073 + 6.550e-04 1506.195 101325.000 9.050429e+05 0.011 -0.079 + 6.600e-04 1506.872 101325.000 9.048330e+05 0.012 -0.086 + 6.650e-04 1507.653 101325.000 9.045905e+05 0.013 -0.094 + 6.700e-04 1508.559 101325.000 9.043090e+05 0.015 -0.102 + 6.750e-04 1509.614 101325.001 9.039807e+05 0.017 -0.110 + 6.800e-04 1510.850 101325.000 9.035962e+05 0.019 -0.118 6.850e-04 1512.299 101325.000 9.031445e+05 0.022 -0.126 - 6.900e-04 1514.003 101325.000 9.026132e+05 0.025 -0.134 + 6.900e-04 1514.004 101325.000 9.026132e+05 0.025 -0.134 6.950e-04 1516.006 101325.000 9.019888e+05 0.028 -0.140 - 7.000e-04 1518.351 101325.000 9.012571e+05 0.031 -0.145 - 7.050e-04 1521.083 101325.000 9.004047e+05 0.035 -0.149 - 7.100e-04 1524.239 101325.000 8.994201e+05 0.040 -0.150 - 7.150e-04 1527.844 101325.001 8.982952e+05 0.045 -0.150 + 7.000e-04 1518.351 101325.000 9.012572e+05 0.031 -0.145 + 7.050e-04 1521.083 101325.000 9.004048e+05 0.035 -0.149 + 7.100e-04 1524.239 101325.000 8.994202e+05 0.040 -0.150 + 7.150e-04 1527.845 101325.001 8.982952e+05 0.045 -0.150 7.200e-04 1531.914 101325.001 8.970259e+05 0.051 -0.149 7.250e-04 1536.446 101325.001 8.956129e+05 0.058 -0.147 7.300e-04 1541.427 101325.001 8.940605e+05 0.067 -0.146 7.350e-04 1546.838 101325.001 8.923750e+05 0.078 -0.146 7.400e-04 1552.656 101325.001 8.905635e+05 0.091 -0.149 - 7.450e-04 1558.863 101325.001 8.886320e+05 0.108 -0.154 + 7.450e-04 1558.864 101325.001 8.886320e+05 0.108 -0.154 7.500e-04 1565.447 101325.001 8.865850e+05 0.129 -0.161 7.550e-04 1572.396 101325.001 8.844257e+05 0.154 -0.170 - 7.600e-04 1579.701 101325.001 8.821579e+05 0.184 -0.181 + 7.600e-04 1579.701 101325.001 8.821580e+05 0.184 -0.181 7.650e-04 1587.335 101325.001 8.797903e+05 0.217 -0.192 7.700e-04 1595.236 101325.001 8.773424e+05 0.253 -0.201 7.750e-04 1603.274 101325.001 8.748553e+05 0.288 -0.205 7.800e-04 1611.217 101325.001 8.724012e+05 0.315 -0.199 7.850e-04 1618.721 101325.001 8.700879e+05 0.326 -0.180 - 7.900e-04 1625.375 101325.001 8.680426e+05 0.314 -0.148 + 7.900e-04 1625.375 101325.001 8.680427e+05 0.314 -0.148 7.950e-04 1630.840 101325.001 8.663710e+05 0.278 -0.108 8.000e-04 1634.989 101325.000 8.651113e+05 0.225 -0.068 8.050e-04 1637.955 101325.000 8.642218e+05 0.167 -0.036 8.100e-04 1640.029 101325.000 8.636112e+05 0.117 -0.017 - 8.150e-04 1641.520 101325.000 8.631828e+05 0.080 -0.008 - 8.200e-04 1642.671 101325.000 8.628609e+05 0.055 -0.005 + 8.150e-04 1641.520 101325.000 8.631829e+05 0.080 -0.008 + 8.200e-04 1642.671 101325.000 8.628610e+05 0.055 -0.005 8.250e-04 1643.643 101325.000 8.625958e+05 0.040 -0.006 8.300e-04 1644.529 101325.000 8.623583e+05 0.031 -0.007 - 8.350e-04 1645.380 101325.000 8.621327e+05 0.026 -0.009 + 8.350e-04 1645.380 101325.000 8.621327e+05 0.026 -0.008 8.400e-04 1646.221 101325.000 8.619110e+05 0.022 -0.009 8.450e-04 1647.065 101325.000 8.616893e+05 0.020 -0.009 8.500e-04 1647.918 101325.000 8.614658e+05 0.019 -0.008 8.550e-04 1648.781 101325.000 8.612398e+05 0.017 -0.008 8.600e-04 1649.655 101325.000 8.610111e+05 0.016 -0.007 8.650e-04 1650.540 101325.000 8.607799e+05 0.015 -0.006 - 8.700e-04 1651.434 101325.000 8.605463e+05 0.014 -0.005 + 8.700e-04 1651.434 101325.000 8.605464e+05 0.014 -0.005 8.750e-04 1652.336 101325.000 8.603108e+05 0.013 -0.004 - 8.800e-04 1653.246 101325.000 8.600734e+05 0.012 -0.003 + 8.800e-04 1653.246 101325.000 8.600735e+05 0.012 -0.003 8.850e-04 1654.161 101325.000 8.598347e+05 0.011 -0.003 8.900e-04 1655.081 101325.000 8.595948e+05 0.010 -0.002 8.950e-04 1656.005 101325.000 8.593541e+05 0.009 -0.001 9.000e-04 1656.931 101325.000 8.591129e+05 0.008 -0.001 9.050e-04 1657.859 101325.000 8.588714e+05 0.008 -0.000 - 9.100e-04 1658.787 101325.000 8.586299e+05 0.007 0.000 + 9.100e-04 1658.787 101325.000 8.586299e+05 0.007 0.001 9.150e-04 1659.714 101325.000 8.583887e+05 0.006 0.001 9.200e-04 1660.640 101325.000 8.581480e+05 0.005 0.002 9.250e-04 1661.563 101325.000 8.579080e+05 0.005 0.002 9.300e-04 1662.483 101325.000 8.576689e+05 0.004 0.002 9.350e-04 1663.399 101325.000 8.574310e+05 0.003 0.003 9.400e-04 1664.311 101325.000 8.571944e+05 0.003 0.003 - 9.450e-04 1665.217 101325.000 8.569592e+05 0.002 0.004 - 9.500e-04 1666.117 101325.000 8.567257e+05 0.002 0.004 - 9.550e-04 1667.010 101325.000 8.564940e+05 0.001 0.004 + 9.450e-04 1665.217 101325.000 8.569593e+05 0.002 0.004 + 9.500e-04 1666.117 101325.000 8.567258e+05 0.002 0.004 + 9.550e-04 1667.010 101325.000 8.564941e+05 0.001 0.004 9.600e-04 1667.896 101325.000 8.562643e+05 0.001 0.005 - 9.650e-04 1668.775 101325.000 8.560365e+05 0.000 0.005 + 9.650e-04 1668.775 101325.000 8.560366e+05 0.000 0.005 9.700e-04 1669.645 101325.000 8.558110e+05 -0.000 0.005 9.750e-04 1670.508 101325.000 8.555877e+05 -0.001 0.005 - 9.800e-04 1671.361 101325.000 8.553667e+05 -0.001 0.005 + 9.800e-04 1671.361 101325.000 8.553667e+05 -0.001 0.006 9.850e-04 1672.205 101325.000 8.551482e+05 -0.002 0.006 - 9.900e-04 1673.040 101325.000 8.549321e+05 -0.002 0.006 + 9.900e-04 1673.040 101325.000 8.549322e+05 -0.002 0.006 9.950e-04 1673.865 101325.000 8.547187e+05 -0.002 0.006 - 1.000e-03 1674.680 101325.000 8.545078e+05 -0.003 0.006 + 1.000e-03 1674.680 101325.000 8.545079e+05 -0.003 0.006 1.005e-03 1675.485 101325.000 8.542997e+05 -0.003 0.006 1.010e-03 1676.279 101325.000 8.540942e+05 -0.003 0.007 1.015e-03 1677.064 101325.000 8.538915e+05 -0.004 0.007 1.020e-03 1677.837 101325.000 8.536916e+05 -0.004 0.007 - 1.025e-03 1678.601 101325.000 8.534944e+05 -0.004 0.007 + 1.025e-03 1678.601 101325.000 8.534945e+05 -0.004 0.007 1.030e-03 1679.353 101325.000 8.533001e+05 -0.004 0.007 1.035e-03 1680.095 101325.000 8.531086e+05 -0.005 0.007 1.040e-03 1680.825 101325.000 8.529199e+05 -0.005 0.007 1.045e-03 1681.545 101325.000 8.527341e+05 -0.005 0.007 - 1.050e-03 1682.254 101325.000 8.525510e+05 -0.005 0.007 - 1.055e-03 1682.953 101325.000 8.523708e+05 -0.006 0.007 - 1.060e-03 1683.640 101325.000 8.521935e+05 -0.006 0.007 + 1.050e-03 1682.255 101325.000 8.525511e+05 -0.005 0.007 + 1.055e-03 1682.953 101325.000 8.523709e+05 -0.006 0.007 + 1.060e-03 1683.641 101325.000 8.521935e+05 -0.006 0.007 1.065e-03 1684.317 101325.000 8.520189e+05 -0.006 0.007 - 1.070e-03 1684.984 101325.000 8.518471e+05 -0.006 0.007 + 1.070e-03 1684.984 101325.000 8.518471e+05 -0.006 0.008 1.075e-03 1685.639 101325.000 8.516781e+05 -0.006 0.008 1.080e-03 1686.284 101325.000 8.515118e+05 -0.007 0.008 1.085e-03 1686.919 101325.000 8.513482e+05 -0.007 0.008 1.090e-03 1687.543 101325.000 8.511874e+05 -0.007 0.008 1.095e-03 1688.157 101325.000 8.510292e+05 -0.007 0.008 - 1.100e-03 1688.761 101325.000 8.508736e+05 -0.007 0.008 - 1.105e-03 1689.354 101325.000 8.507207e+05 -0.007 0.008 + 1.100e-03 1688.761 101325.000 8.508737e+05 -0.007 0.008 + 1.105e-03 1689.354 101325.000 8.507208e+05 -0.007 0.008 1.110e-03 1689.938 101325.000 8.505704e+05 -0.008 0.008 1.115e-03 1690.512 101325.000 8.504226e+05 -0.008 0.008 - 1.120e-03 1691.076 101325.000 8.502773e+05 -0.008 0.008 + 1.120e-03 1691.076 101325.000 8.502774e+05 -0.008 0.008 1.125e-03 1691.631 101325.000 8.501346e+05 -0.008 0.008 - 1.130e-03 1692.176 101325.000 8.499942e+05 -0.008 0.008 - 1.135e-03 1692.712 101325.000 8.498563e+05 -0.008 0.008 - 1.140e-03 1693.239 101325.000 8.497208e+05 -0.008 0.008 + 1.130e-03 1692.176 101325.000 8.499943e+05 -0.008 0.008 + 1.135e-03 1692.712 101325.000 8.498564e+05 -0.008 0.008 + 1.140e-03 1693.239 101325.000 8.497209e+05 -0.008 0.008 1.145e-03 1693.756 101325.000 8.495877e+05 -0.008 0.008 1.150e-03 1694.265 101325.000 8.494568e+05 -0.008 0.007 1.155e-03 1694.765 101325.000 8.493282e+05 -0.009 0.007 1.160e-03 1695.256 101325.000 8.492019e+05 -0.009 0.007 - 1.165e-03 1695.739 101325.000 8.490777e+05 -0.009 0.007 - 1.170e-03 1696.213 101325.000 8.489557e+05 -0.009 0.007 + 1.165e-03 1695.739 101325.000 8.490778e+05 -0.009 0.007 + 1.170e-03 1696.213 101325.000 8.489558e+05 -0.009 0.007 1.175e-03 1696.679 101325.000 8.488359e+05 -0.009 0.007 - 1.180e-03 1697.137 101325.000 8.487181e+05 -0.009 0.007 - 1.185e-03 1697.587 101325.000 8.486024e+05 -0.009 0.007 + 1.180e-03 1697.137 101325.000 8.487182e+05 -0.009 0.007 + 1.185e-03 1697.587 101325.000 8.486025e+05 -0.009 0.007 1.190e-03 1698.029 101325.000 8.484888e+05 -0.009 0.007 1.195e-03 1698.464 101325.000 8.483771e+05 -0.009 0.007 - 1.200e-03 1698.891 101325.000 8.482673e+05 -0.009 0.007 + 1.200e-03 1698.891 101325.000 8.482674e+05 -0.009 0.007 1.205e-03 1699.311 101325.000 8.481595e+05 -0.009 0.007 1.210e-03 1699.723 101325.000 8.480536e+05 -0.009 0.007 1.215e-03 1700.128 101325.000 8.479495e+05 -0.009 0.007 1.220e-03 1700.526 101325.000 8.478472e+05 -0.009 0.007 - 1.225e-03 1700.917 101325.000 8.477466e+05 -0.009 0.007 + 1.225e-03 1700.917 101325.000 8.477467e+05 -0.009 0.007 1.230e-03 1701.302 101325.000 8.476479e+05 -0.009 0.007 - 1.235e-03 1701.680 101325.000 8.475508e+05 -0.009 0.007 - 1.240e-03 1702.051 101325.000 8.474554e+05 -0.009 0.007 + 1.235e-03 1701.680 101325.000 8.475509e+05 -0.009 0.007 + 1.240e-03 1702.051 101325.000 8.474555e+05 -0.009 0.007 1.245e-03 1702.416 101325.000 8.473617e+05 -0.009 0.007 1.250e-03 1702.775 101325.000 8.472696e+05 -0.010 0.007 1.255e-03 1703.127 101325.000 8.471791e+05 -0.010 0.006 1.260e-03 1703.474 101325.000 8.470901e+05 -0.010 0.006 - 1.265e-03 1703.814 101325.000 8.470026e+05 -0.010 0.006 + 1.265e-03 1703.814 101325.000 8.470027e+05 -0.010 0.006 1.270e-03 1704.149 101325.000 8.469167e+05 -0.010 0.006 1.275e-03 1704.478 101325.000 8.468322e+05 -0.010 0.006 - 1.280e-03 1704.802 101325.000 8.467491e+05 -0.010 0.006 + 1.280e-03 1704.802 101325.000 8.467492e+05 -0.010 0.006 1.285e-03 1705.120 101325.000 8.466675e+05 -0.010 0.006 - 1.290e-03 1705.433 101325.000 8.465872e+05 -0.010 0.006 - 1.295e-03 1705.740 101325.000 8.465083e+05 -0.010 0.006 - 1.300e-03 1706.042 101325.000 8.464307e+05 -0.010 0.006 + 1.290e-03 1705.433 101325.000 8.465873e+05 -0.010 0.006 + 1.295e-03 1705.740 101325.000 8.465084e+05 -0.010 0.006 + 1.300e-03 1706.042 101325.000 8.464308e+05 -0.010 0.006 1.305e-03 1706.340 101325.000 8.463545e+05 -0.010 0.006 1.310e-03 1706.632 101325.000 8.462795e+05 -0.010 0.006 1.315e-03 1706.919 101325.000 8.462057e+05 -0.010 0.006 1.320e-03 1707.202 101325.000 8.461332e+05 -0.010 0.006 1.325e-03 1707.480 101325.000 8.460619e+05 -0.010 0.006 - 1.330e-03 1707.753 101325.000 8.459917e+05 -0.010 0.006 - 1.335e-03 1708.022 101325.000 8.459227e+05 -0.010 0.005 + 1.330e-03 1707.753 101325.000 8.459918e+05 -0.010 0.006 + 1.335e-03 1708.022 101325.000 8.459228e+05 -0.010 0.005 1.340e-03 1708.286 101325.000 8.458549e+05 -0.010 0.005 - 1.345e-03 1708.547 101325.000 8.457881e+05 -0.010 0.005 - 1.350e-03 1708.802 101325.000 8.457225e+05 -0.010 0.005 + 1.345e-03 1708.547 101325.000 8.457882e+05 -0.010 0.005 + 1.350e-03 1708.803 101325.000 8.457225e+05 -0.010 0.005 1.355e-03 1709.054 101325.000 8.456579e+05 -0.010 0.005 1.360e-03 1709.302 101325.000 8.455944e+05 -0.010 0.005 - 1.365e-03 1709.546 101325.000 8.455318e+05 -0.010 0.005 - 1.370e-03 1709.785 101325.000 8.454703e+05 -0.010 0.005 - 1.375e-03 1710.021 101325.000 8.454098e+05 -0.010 0.005 + 1.365e-03 1709.546 101325.000 8.455319e+05 -0.010 0.005 + 1.370e-03 1709.785 101325.000 8.454704e+05 -0.010 0.005 + 1.375e-03 1710.021 101325.000 8.454099e+05 -0.010 0.005 1.380e-03 1710.254 101325.000 8.453503e+05 -0.010 0.005 1.385e-03 1710.482 101325.000 8.452917e+05 -0.010 0.005 1.390e-03 1710.707 101325.000 8.452340e+05 -0.010 0.005 - 1.395e-03 1710.928 101325.000 8.451772e+05 -0.010 0.005 - 1.400e-03 1711.146 101325.000 8.451213e+05 -0.010 0.005 + 1.395e-03 1710.928 101325.000 8.451773e+05 -0.010 0.005 + 1.400e-03 1711.146 101325.000 8.451214e+05 -0.010 0.005 1.405e-03 1711.360 101325.000 8.450664e+05 -0.010 0.005 - 1.410e-03 1711.572 101325.000 8.450122e+05 -0.010 0.005 - 1.415e-03 1711.779 101325.000 8.449589e+05 -0.010 0.004 + 1.410e-03 1711.572 101325.000 8.450123e+05 -0.010 0.005 + 1.415e-03 1711.779 101325.000 8.449590e+05 -0.010 0.004 1.420e-03 1711.984 101325.000 8.449065e+05 -0.010 0.004 1.425e-03 1712.185 101325.000 8.448548e+05 -0.010 0.004 - 1.430e-03 1712.384 101325.000 8.448039e+05 -0.010 0.004 + 1.430e-03 1712.384 101325.000 8.448040e+05 -0.010 0.004 1.435e-03 1712.579 101325.000 8.447539e+05 -0.009 0.004 1.440e-03 1712.771 101325.000 8.447046e+05 -0.009 0.004 1.445e-03 1712.961 101325.000 8.446560e+05 -0.009 0.004 @@ -297,111 +297,111 @@ Maximum time step: 5e-06 1.455e-03 1713.331 101325.000 8.445611e+05 -0.009 0.004 1.460e-03 1713.512 101325.000 8.445147e+05 -0.009 0.004 1.465e-03 1713.690 101325.000 8.444690e+05 -0.009 0.004 - 1.470e-03 1713.866 101325.000 8.444239e+05 -0.009 0.004 + 1.470e-03 1713.866 101325.000 8.444240e+05 -0.009 0.004 1.475e-03 1714.039 101325.000 8.443796e+05 -0.009 0.004 1.480e-03 1714.209 101325.000 8.443359e+05 -0.009 0.004 - 1.485e-03 1714.377 101325.000 8.442928e+05 -0.009 0.004 - 1.490e-03 1714.542 101325.000 8.442504e+05 -0.009 0.004 - 1.495e-03 1714.705 101325.000 8.442086e+05 -0.009 0.003 - 1.500e-03 1714.866 101325.000 8.441674e+05 -0.009 0.003 - 1.505e-03 1715.024 101325.000 8.441268e+05 -0.009 0.003 - 1.510e-03 1715.180 101325.000 8.440868e+05 -0.009 0.003 + 1.485e-03 1714.377 101325.000 8.442929e+05 -0.009 0.004 + 1.490e-03 1714.542 101325.000 8.442505e+05 -0.009 0.004 + 1.495e-03 1714.705 101325.000 8.442087e+05 -0.009 0.003 + 1.500e-03 1714.866 101325.000 8.441675e+05 -0.009 0.003 + 1.505e-03 1715.024 101325.000 8.441269e+05 -0.009 0.003 + 1.510e-03 1715.180 101325.000 8.440869e+05 -0.009 0.003 1.515e-03 1715.334 101325.000 8.440474e+05 -0.009 0.003 - 1.520e-03 1715.486 101325.000 8.440085e+05 -0.009 0.003 - 1.525e-03 1715.635 101325.000 8.439702e+05 -0.009 0.003 + 1.520e-03 1715.486 101325.000 8.440086e+05 -0.009 0.003 + 1.525e-03 1715.635 101325.000 8.439703e+05 -0.009 0.003 1.530e-03 1715.782 101325.000 8.439325e+05 -0.009 0.003 - 1.535e-03 1715.928 101325.000 8.438952e+05 -0.009 0.003 - 1.540e-03 1716.071 101325.000 8.438585e+05 -0.009 0.003 - 1.545e-03 1716.212 101325.000 8.438223e+05 -0.009 0.003 - 1.550e-03 1716.351 101325.000 8.437866e+05 -0.009 0.003 + 1.535e-03 1715.928 101325.000 8.438953e+05 -0.009 0.003 + 1.540e-03 1716.071 101325.000 8.438586e+05 -0.009 0.003 + 1.545e-03 1716.212 101325.000 8.438224e+05 -0.009 0.003 + 1.550e-03 1716.351 101325.000 8.437867e+05 -0.009 0.003 1.555e-03 1716.488 101325.000 8.437515e+05 -0.009 0.003 1.560e-03 1716.624 101325.000 8.437168e+05 -0.009 0.003 - 1.565e-03 1716.757 101325.000 8.436825e+05 -0.009 0.003 + 1.565e-03 1716.757 101325.000 8.436826e+05 -0.009 0.003 1.570e-03 1716.889 101325.000 8.436488e+05 -0.009 0.003 1.575e-03 1717.019 101325.000 8.436155e+05 -0.009 0.003 1.580e-03 1717.147 101325.000 8.435827e+05 -0.009 0.003 1.585e-03 1717.273 101325.000 8.435503e+05 -0.009 0.002 - 1.590e-03 1717.398 101325.000 8.435183e+05 -0.009 0.002 - 1.595e-03 1717.521 101325.000 8.434868e+05 -0.009 0.002 - 1.600e-03 1717.642 101325.000 8.434557e+05 -0.009 0.002 - 1.605e-03 1717.762 101325.000 8.434250e+05 -0.009 0.002 + 1.590e-03 1717.398 101325.000 8.435184e+05 -0.009 0.002 + 1.595e-03 1717.521 101325.000 8.434869e+05 -0.009 0.002 + 1.600e-03 1717.642 101325.000 8.434558e+05 -0.009 0.002 + 1.605e-03 1717.762 101325.000 8.434251e+05 -0.009 0.002 1.610e-03 1717.880 101325.000 8.433948e+05 -0.009 0.002 1.615e-03 1717.996 101325.000 8.433649e+05 -0.009 0.002 - 1.620e-03 1718.111 101325.000 8.433354e+05 -0.009 0.002 - 1.625e-03 1718.225 101325.000 8.433063e+05 -0.009 0.002 - 1.630e-03 1718.337 101325.000 8.432776e+05 -0.009 0.002 + 1.620e-03 1718.111 101325.000 8.433355e+05 -0.009 0.002 + 1.625e-03 1718.225 101325.000 8.433064e+05 -0.009 0.002 + 1.630e-03 1718.337 101325.000 8.432777e+05 -0.009 0.002 1.635e-03 1718.447 101325.000 8.432493e+05 -0.009 0.002 - 1.640e-03 1718.556 101325.000 8.432213e+05 -0.009 0.002 - 1.645e-03 1718.664 101325.000 8.431937e+05 -0.009 0.002 + 1.640e-03 1718.556 101325.000 8.432214e+05 -0.009 0.002 + 1.645e-03 1718.664 101325.000 8.431938e+05 -0.009 0.002 1.650e-03 1718.770 101325.000 8.431665e+05 -0.009 0.002 1.655e-03 1718.875 101325.000 8.431396e+05 -0.008 0.002 - 1.660e-03 1718.979 101325.000 8.431130e+05 -0.008 0.002 - 1.665e-03 1719.081 101325.000 8.430868e+05 -0.008 0.002 - 1.670e-03 1719.182 101325.000 8.430609e+05 -0.008 0.002 + 1.660e-03 1718.979 101325.000 8.431131e+05 -0.008 0.002 + 1.665e-03 1719.081 101325.000 8.430869e+05 -0.008 0.002 + 1.670e-03 1719.182 101325.000 8.430610e+05 -0.008 0.002 1.675e-03 1719.282 101325.000 8.430354e+05 -0.008 0.002 1.680e-03 1719.380 101325.000 8.430102e+05 -0.008 0.002 - 1.685e-03 1719.477 101325.000 8.429852e+05 -0.008 0.001 - 1.690e-03 1719.573 101325.000 8.429606e+05 -0.008 0.001 - 1.695e-03 1719.668 101325.000 8.429363e+05 -0.008 0.001 - 1.700e-03 1719.762 101325.000 8.429123e+05 -0.008 0.001 - 1.705e-03 1719.854 101325.000 8.428886e+05 -0.008 0.001 + 1.685e-03 1719.477 101325.000 8.429853e+05 -0.008 0.001 + 1.690e-03 1719.573 101325.000 8.429607e+05 -0.008 0.001 + 1.695e-03 1719.668 101325.000 8.429364e+05 -0.008 0.001 + 1.700e-03 1719.762 101325.000 8.429124e+05 -0.008 0.001 + 1.705e-03 1719.854 101325.000 8.428887e+05 -0.008 0.001 1.710e-03 1719.945 101325.000 8.428652e+05 -0.008 0.001 1.715e-03 1720.035 101325.000 8.428421e+05 -0.008 0.001 - 1.720e-03 1720.125 101325.002 8.428192e+05 -0.008 0.001 - 1.725e-03 1720.212 101325.005 8.427962e+05 -0.008 0.001 - 1.730e-03 1720.297 101325.000 8.427723e+05 -0.008 0.001 - 1.735e-03 1720.383 101325.000 8.427501e+05 -0.008 0.001 - 1.740e-03 1720.468 101325.000 8.427283e+05 -0.008 0.001 - 1.745e-03 1720.552 101325.000 8.427068e+05 -0.008 0.001 - 1.750e-03 1720.635 101325.000 8.426855e+05 -0.008 0.001 - 1.755e-03 1720.717 101325.000 8.426646e+05 -0.008 0.001 - 1.760e-03 1720.798 101325.000 8.426438e+05 -0.008 0.001 - 1.765e-03 1720.878 101325.000 8.426233e+05 -0.008 0.001 - 1.770e-03 1720.957 101325.000 8.426030e+05 -0.008 0.001 - 1.775e-03 1721.035 101325.000 8.425830e+05 -0.008 0.001 - 1.780e-03 1721.112 101325.000 8.425632e+05 -0.008 0.001 - 1.785e-03 1721.188 101325.000 8.425436e+05 -0.008 0.001 - 1.790e-03 1721.264 101325.000 8.425243e+05 -0.008 0.001 - 1.795e-03 1721.338 101325.000 8.425052e+05 -0.008 0.000 - 1.800e-03 1721.412 101325.000 8.424863e+05 -0.008 0.000 - 1.805e-03 1721.485 101325.000 8.424676e+05 -0.008 0.000 - 1.810e-03 1721.557 101325.000 8.424491e+05 -0.008 0.000 - 1.815e-03 1721.628 101325.000 8.424308e+05 -0.008 0.000 - 1.820e-03 1721.698 101325.000 8.424128e+05 -0.008 0.000 - 1.825e-03 1721.768 101325.000 8.423949e+05 -0.008 0.000 - 1.830e-03 1721.837 101325.000 8.423773e+05 -0.008 0.000 - 1.835e-03 1721.905 101325.000 8.423598e+05 -0.008 0.000 - 1.840e-03 1721.972 101325.000 8.423425e+05 -0.008 0.000 - 1.845e-03 1722.039 101325.000 8.423255e+05 -0.008 0.000 - 1.850e-03 1722.105 101325.000 8.423086e+05 -0.008 0.000 - 1.855e-03 1722.170 101325.000 8.422919e+05 -0.008 0.000 - 1.860e-03 1722.234 101325.000 8.422753e+05 -0.007 -0.000 - 1.865e-03 1722.298 101325.000 8.422590e+05 -0.007 -0.000 - 1.870e-03 1722.361 101325.000 8.422428e+05 -0.007 -0.000 - 1.875e-03 1722.423 101325.000 8.422269e+05 -0.007 -0.000 - 1.880e-03 1722.485 101325.000 8.422110e+05 -0.007 -0.000 - 1.885e-03 1722.546 101325.000 8.421954e+05 -0.007 -0.000 - 1.890e-03 1722.607 101325.000 8.421799e+05 -0.007 -0.000 - 1.895e-03 1722.666 101325.000 8.421646e+05 -0.007 -0.000 - 1.900e-03 1722.725 101325.000 8.421494e+05 -0.007 -0.000 - 1.905e-03 1722.784 101325.000 8.421344e+05 -0.007 -0.000 - 1.910e-03 1722.842 101325.000 8.421196e+05 -0.007 -0.000 - 1.915e-03 1722.899 101325.000 8.421049e+05 -0.007 -0.000 - 1.920e-03 1722.956 101325.000 8.420904e+05 -0.007 -0.000 - 1.925e-03 1723.012 101325.000 8.420760e+05 -0.007 -0.000 - 1.930e-03 1723.067 101325.000 8.420618e+05 -0.007 -0.001 - 1.935e-03 1723.122 101325.000 8.420477e+05 -0.007 -0.001 - 1.940e-03 1723.176 101325.000 8.420337e+05 -0.007 -0.001 - 1.945e-03 1723.230 101325.000 8.420199e+05 -0.007 -0.001 - 1.950e-03 1723.283 101325.000 8.420063e+05 -0.007 -0.001 - 1.955e-03 1723.336 101325.000 8.419928e+05 -0.007 -0.001 - 1.960e-03 1723.388 101325.000 8.419794e+05 -0.007 -0.001 - 1.965e-03 1723.440 101325.000 8.419662e+05 -0.007 -0.001 - 1.970e-03 1723.491 101325.000 8.419530e+05 -0.007 -0.001 - 1.975e-03 1723.542 101325.000 8.419401e+05 -0.007 -0.001 - 1.980e-03 1723.592 101325.000 8.419272e+05 -0.007 -0.001 - 1.985e-03 1723.641 101325.000 8.419145e+05 -0.007 -0.001 - 1.990e-03 1723.690 101325.000 8.419019e+05 -0.007 -0.001 - 1.995e-03 1723.739 101325.000 8.418894e+05 -0.007 -0.001 - 2.000e-03 1723.787 101325.000 8.418771e+05 -0.007 -0.001 + 1.720e-03 1720.125 101325.000 8.428193e+05 -0.008 0.001 + 1.725e-03 1720.213 101325.000 8.427967e+05 -0.008 0.001 + 1.730e-03 1720.300 101325.000 8.427744e+05 -0.008 0.001 + 1.735e-03 1720.385 101325.000 8.427524e+05 -0.008 0.001 + 1.740e-03 1720.470 101325.000 8.427306e+05 -0.008 0.001 + 1.745e-03 1720.554 101325.000 8.427091e+05 -0.008 0.001 + 1.750e-03 1720.637 101325.000 8.426879e+05 -0.008 0.001 + 1.755e-03 1720.719 101325.000 8.426669e+05 -0.008 0.001 + 1.760e-03 1720.800 101325.000 8.426461e+05 -0.008 0.001 + 1.765e-03 1720.880 101325.000 8.426256e+05 -0.008 0.001 + 1.770e-03 1720.959 101325.000 8.426053e+05 -0.008 0.001 + 1.775e-03 1721.037 101325.000 8.425853e+05 -0.008 0.001 + 1.780e-03 1721.114 101325.000 8.425655e+05 -0.008 0.001 + 1.785e-03 1721.191 101325.000 8.425460e+05 -0.008 0.001 + 1.790e-03 1721.266 101325.000 8.425266e+05 -0.008 0.001 + 1.795e-03 1721.341 101325.000 8.425075e+05 -0.008 0.000 + 1.800e-03 1721.414 101325.000 8.424886e+05 -0.008 0.000 + 1.805e-03 1721.487 101325.000 8.424699e+05 -0.008 0.000 + 1.810e-03 1721.559 101325.000 8.424514e+05 -0.008 0.000 + 1.815e-03 1721.630 101325.000 8.424332e+05 -0.008 0.000 + 1.820e-03 1721.701 101325.000 8.424151e+05 -0.008 0.000 + 1.825e-03 1721.770 101325.000 8.423972e+05 -0.008 0.000 + 1.830e-03 1721.839 101325.000 8.423796e+05 -0.008 0.000 + 1.835e-03 1721.907 101325.000 8.423621e+05 -0.008 0.000 + 1.840e-03 1721.975 101325.000 8.423449e+05 -0.008 0.000 + 1.845e-03 1722.041 101325.000 8.423278e+05 -0.008 0.000 + 1.850e-03 1722.107 101325.000 8.423109e+05 -0.008 0.000 + 1.855e-03 1722.172 101325.000 8.422942e+05 -0.008 0.000 + 1.860e-03 1722.237 101325.000 8.422777e+05 -0.007 -0.000 + 1.865e-03 1722.300 101325.000 8.422613e+05 -0.007 -0.000 + 1.870e-03 1722.363 101325.000 8.422452e+05 -0.007 -0.000 + 1.875e-03 1722.426 101325.000 8.422292e+05 -0.007 -0.000 + 1.880e-03 1722.487 101325.000 8.422133e+05 -0.007 -0.000 + 1.885e-03 1722.549 101325.000 8.421977e+05 -0.007 -0.000 + 1.890e-03 1722.609 101325.000 8.421822e+05 -0.007 -0.000 + 1.895e-03 1722.669 101325.000 8.421669e+05 -0.007 -0.000 + 1.900e-03 1722.728 101325.000 8.421517e+05 -0.007 -0.000 + 1.905e-03 1722.786 101325.000 8.421367e+05 -0.007 -0.000 + 1.910e-03 1722.844 101325.000 8.421219e+05 -0.007 -0.000 + 1.915e-03 1722.901 101325.000 8.421072e+05 -0.007 -0.000 + 1.920e-03 1722.958 101325.000 8.420927e+05 -0.007 -0.000 + 1.925e-03 1723.014 101325.000 8.420783e+05 -0.007 -0.000 + 1.930e-03 1723.069 101325.000 8.420641e+05 -0.007 -0.001 + 1.935e-03 1723.124 101325.000 8.420500e+05 -0.007 -0.001 + 1.940e-03 1723.179 101325.000 8.420361e+05 -0.007 -0.001 + 1.945e-03 1723.232 101325.000 8.420223e+05 -0.007 -0.001 + 1.950e-03 1723.286 101325.000 8.420086e+05 -0.007 -0.001 + 1.955e-03 1723.338 101325.000 8.419951e+05 -0.007 -0.001 + 1.960e-03 1723.391 101325.000 8.419817e+05 -0.007 -0.001 + 1.965e-03 1723.442 101325.000 8.419685e+05 -0.007 -0.001 + 1.970e-03 1723.493 101325.000 8.419554e+05 -0.007 -0.001 + 1.975e-03 1723.544 101325.000 8.419424e+05 -0.007 -0.001 + 1.980e-03 1723.594 101325.000 8.419295e+05 -0.007 -0.001 + 1.985e-03 1723.644 101325.000 8.419168e+05 -0.007 -0.001 + 1.990e-03 1723.693 101325.000 8.419042e+05 -0.007 -0.001 + 1.995e-03 1723.741 101325.000 8.418917e+05 -0.007 -0.001 + 2.000e-03 1723.789 101325.000 8.418794e+05 -0.007 -0.001 To view a plot of these results, run this script with the option -plot diff --git a/Cantera/python/examples/reactors/surf_pfr_sim/output_blessed_0.txt b/Cantera/python/examples/reactors/surf_pfr_sim/output_blessed_0.txt index 45c01b3aa..adb211555 100644 --- a/Cantera/python/examples/reactors/surf_pfr_sim/output_blessed_0.txt +++ b/Cantera/python/examples/reactors/surf_pfr_sim/output_blessed_0.txt @@ -5,7 +5,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -13,7 +13,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -21,7 +21,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -29,7 +29,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -37,7 +37,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -45,7 +45,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -53,7 +53,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -61,7 +61,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -69,7 +69,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -77,7 +77,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -85,7 +85,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -93,7 +93,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -101,7 +101,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -109,7 +109,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -117,7 +117,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -125,7 +125,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -133,7 +133,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -141,7 +141,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -149,7 +149,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -157,7 +157,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -165,7 +165,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -173,7 +173,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -181,7 +181,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -189,7 +189,7 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 +Maximum time step: 0.01 Not adding reactor (none), since type = 1 Adding reactor (none) Not adding reactor (none), since type = 1 @@ -197,50 +197,1412 @@ Initializing reactor network. Reactor 0: 20 variables. 0 sensitivity params. Number of equations: 20 -Maximum time step: 1 -CVode-- Warning.. internal t=100.345 and step size h=6.74399e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=6.74399e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=4.62885e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=4.62885e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=4.62885e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=2.93127e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=2.93127e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=1.63375e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=1.63375e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- Warning.. internal t=100.345 and step size h=1.63375e-15 -are such that t + h == t on the next step. -The solver will continue anyway. - -CVode-- The above warning has been issued 10 times and will not be -issued again for this problem. - -CVode-- At t=100.345 and step size h=6.85664e-25, the corrector -convergence failed repeatedly or with |h| = hmin. - +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 +Not adding reactor (none), since type = 1 +Adding reactor (none) +Not adding reactor (none), since type = 1 +Initializing reactor network. +Reactor 0: 20 variables. + 0 sensitivity params. +Number of equations: 20 +Maximum time step: 0.01 diff --git a/Cantera/python/examples/reactors/surf_pfr_sim/runtest b/Cantera/python/examples/reactors/surf_pfr_sim/runtest index a7ed28918..5829fea1d 100755 --- a/Cantera/python/examples/reactors/surf_pfr_sim/runtest +++ b/Cantera/python/examples/reactors/surf_pfr_sim/runtest @@ -30,7 +30,7 @@ fi diff -w output_blessed_0.txt output_0.txt > diff_out_0.txt retnStat_0=$? -csvdiff -a 1.0E-50 surf_pfr_blessed_0.csv surf_pfr_output.csv > diff_csv.txt +csvdiff -a 1.0E-20 surf_pfr_blessed_0.csv surf_pfr_output.csv > diff_csv.txt retnStat_csv_0=$? retnTotal=1 diff --git a/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr.py b/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr.py index 9b406ece9..639e227cf 100644 --- a/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr.py +++ b/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr.py @@ -39,9 +39,13 @@ cti_file = 'methane_pox_on_pt.cti' # The PFR will be simulated by a chain of 'NReactors' stirred # reactors. -NReactors = 200 -dt = 1.0 - +NReactors = 201 +# +# Decreased the time step by a factor of 100 to help convergence +# 12/28/2009 HKM +# +# dt = 1.0 +dt = 0.01 ##################################################################### @@ -63,7 +67,7 @@ surf.setTemperature(t) s_names = surf.speciesNames() nsurf = surf.nSpecies() -rlen = length/NReactors +rlen = length/(NReactors-1) rvol = area * rlen * porosity names = gas.speciesNames() diff --git a/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr_blessed_0.csv b/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr_blessed_0.csv index 62c7a15e0..b23e32398 100644 --- a/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr_blessed_0.csv +++ b/Cantera/python/examples/reactors/surf_pfr_sim/surf_pfr_blessed_0.csv @@ -1,201 +1,202 @@ Distance (mm), T (C), P (atm), H2, O2, H2O, CH4, CO, CO2, AR, PT(S), H(S), H2O(S), OH(S), CO(S), 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2.754e-05 OH(S) 0.01437 - CO(S) -1.426e-49 - CO2(S) 1.147e-55 - CH3(S) -3.183e-58 - CH2(S)s -1.999e-58 - CH(S) -3.059e-58 - C(S) -2.748e-52 + CO(S) -2.155e-41 + CO2(S) 1.732e-47 + CH3(S) 3.43e-95 + CH2(S)s 9.212e-94 + CH(S) 2.876e-94 + C(S) -7.83e-51 O(S) 0.4977 .............................................................................. @@ -163,43 +163,13 @@ Attempt Newton solution of steady-state problem... success. Problem solved on [8] point grid(s). -############################################################################## -Refining grid in flow. - New points inserted after grid points 6 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [9] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 7 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [10] point grid(s). - no new points needed in flow Multiplier = 0.01 .............................................................................. Attempt Newton solution of steady-state problem... success. -Problem solved on [10] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 8 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [11] point grid(s). +Problem solved on [8] point grid(s). no new points needed in flow Multiplier = 0.1 @@ -207,17 +177,7 @@ Multiplier = 0.1 Attempt Newton solution of steady-state problem... success. -Problem solved on [11] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 9 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [12] point grid(s). +Problem solved on [8] point grid(s). no new points needed in flow Multiplier = 1.0 @@ -225,7 +185,7 @@ Multiplier = 1.0 Attempt Newton solution of steady-state problem... success. -Problem solved on [12] point grid(s). +Problem solved on [8] point grid(s). no new points needed in flow @@ -249,114 +209,86 @@ no new points needed in flow ------------------------------------------------------------------------------- z u V T lambda H2 ------------------------------------------------------------------------------- - 0 0.05335 3.452e-21 300 -0.4151 0.003467 - 0.02 0.05058 0.1384 300 -0.4151 0.003466 - 0.04 0.04229 0.2768 300.1 -0.4151 0.003451 - 0.06 0.02881 0.4167 303.9 -0.4151 0.003274 - 0.08 0.01396 0.5863 384.2 -0.4151 0.002136 - 0.09 0.006538 0.6222 605 -0.4151 0.001115 - 0.095 0.002168 0.4262 757.2 -0.4151 0.0005624 - 0.0975 0.0006079 0.2414 830.5 -0.4151 0.0002873 - 0.09875 0.0001599 0.1275 865.7 -0.4151 0.0001514 - 0.09938 4.096e-05 0.06544 883 -0.4151 8.389e-05 - 0.09969 1.036e-05 0.03314 891.5 -0.4151 5.027e-05 - 0.1 0 0 900 -0.4151 1.685e-05 + 0 0.05335 -2.486e-22 300 -0.4153 0.003467 + 0.02 0.05058 0.1384 300 -0.4153 0.003466 + 0.04 0.04228 0.2769 300.1 -0.4153 0.003451 + 0.06 0.0288 0.4168 303.9 -0.4153 0.003273 + 0.08 0.01393 0.5862 383.9 -0.4153 0.002125 + 0.09 0.006484 0.6212 604 -0.4153 0.001094 + 0.095 0.002117 0.4235 755.4 -0.4153 0.0005369 + 0.1 0 0 900 -0.4153 1.703e-05 ------------------------------------------------------------------------------- z H O O2 OH H2O ------------------------------------------------------------------------------- - 0 -3.76e-21 -7.809e-21 0.2312 -9.848e-25 7.255e-09 - 0.02 -2.437e-27 -4.819e-21 0.2312 -7.032e-24 3.36e-07 - 0.04 3.448e-28 1.853e-21 0.2311 3.057e-24 1.478e-05 - 0.06 5.551e-26 3.835e-19 0.2308 2.273e-22 0.0005406 - 0.08 1.124e-22 2.091e-17 0.2222 6.409e-20 0.01075 - 0.09 2.902e-17 1.443e-15 0.2017 6.916e-16 0.03155 - 0.095 1.902e-14 7.508e-13 0.1867 2.052e-12 0.04542 - 0.0975 3.863e-13 3.319e-11 0.1788 5.707e-11 0.05244 - 0.09875 1.517e-12 2.397e-10 0.175 3.494e-10 0.05589 - 0.09938 3.587e-12 6.906e-10 0.1731 1.424e-09 0.0576 - 0.09969 7.287e-12 8.814e-10 0.1721 4.998e-09 0.05845 - 0.1 1.976e-13 2.444e-11 0.1712 1.889e-08 0.05929 + 0 -4.851e-22 9.858e-21 0.2312 -1.455e-24 7.281e-09 + 0.02 -1.367e-28 3.289e-22 0.2312 4.812e-25 3.372e-07 + 0.04 7.19e-28 4.034e-21 0.2311 5.365e-24 1.483e-05 + 0.06 6.572e-26 5.247e-19 0.2308 1.725e-22 0.0005425 + 0.08 6.217e-23 1.877e-17 0.2222 4.752e-20 0.01079 + 0.09 8.526e-18 1.228e-15 0.2016 2.278e-16 0.03169 + 0.095 1.917e-14 6.659e-13 0.1866 2.617e-12 0.04559 + 0.1 3.472e-17 1.244e-15 0.1717 1.92e-08 0.05885 ------------------------------------------------------------------------------- z HO2 H2O2 C CH CH2 ------------------------------------------------------------------------------- - 0 1.062e-14 1.242e-13 2.11e-21 -1.588e-20 6.143e-23 - 0.02 5.391e-13 6.344e-12 3.066e-29 -7.217e-29 8.208e-30 - 0.04 2.595e-11 3.079e-10 4.135e-37 -2.639e-37 2.043e-36 - 0.06 1.04e-09 1.243e-08 2.502e-45 1.344e-45 7.21e-38 - 0.08 2.442e-08 2.786e-07 -5.247e-47 -1.64e-44 2.391e-36 - 0.09 1.493e-07 8.902e-07 -1.866e-47 2.441e-45 7.668e-34 - 0.095 4.028e-07 1.264e-06 3.215e-49 5.923e-43 9.263e-32 - 0.0975 7.082e-07 1.364e-06 4.609e-43 8.267e-41 1.651e-30 - 0.09875 9.256e-07 1.37e-06 4.7e-37 -1.715e-36 6.901e-30 - 0.09938 1.029e-06 1.366e-06 1.092e-31 -6.732e-31 1.034e-29 - 0.09969 1.064e-06 1.364e-06 5.905e-27 -6.144e-26 1.137e-25 - 0.1 1.064e-06 1.364e-06 2.015e-22 -3.613e-21 1.034e-21 + 0 5.854e-15 5.646e-15 -4.461e-21 -2.125e-21 -1.344e-23 + 0.02 2.971e-13 2.885e-13 -6.49e-29 -9.646e-30 -5.376e-30 + 0.04 1.303e-11 1.467e-11 -7.922e-37 7.971e-38 -1.353e-36 + 0.06 4.688e-10 6.2e-10 -6.739e-45 8.039e-46 6.664e-39 + 0.08 9.592e-09 1.439e-08 -1.811e-41 -5.115e-45 2.386e-35 + 0.09 4.42e-08 4.136e-08 2.326e-35 -5.738e-36 7.142e-33 + 0.095 8.464e-08 5.375e-08 9.036e-28 -4.385e-28 -9.274e-28 + 0.1 8.487e-08 5.39e-08 1.404e-20 -1.519e-20 -7.853e-28 ------------------------------------------------------------------------------- z CH2(S) CH3 CH4 CO CO2 ------------------------------------------------------------------------------- - 0 7e-39 5.014e-22 -2.102e-22 -2.33e-21 5.559e-25 - 0.02 3.345e-37 -3.042e-20 -7.372e-22 -1.192e-19 3.69e-23 - 0.04 7.556e-40 -6.63e-20 -2.053e-21 -1.192e-19 -7.566e-23 - 0.06 3.582e-39 -5.231e-20 -4.215e-21 -1.185e-19 -5.954e-21 - 0.08 -1.795e-39 -1.336e-21 -1.052e-21 -1.034e-19 -1.746e-19 - 0.09 1.127e-35 -1.192e-23 1.341e-20 -6.558e-20 -6.879e-19 - 0.095 1.551e-35 -3.403e-24 2.423e-20 -3.757e-20 -1.108e-18 - 0.0975 -1.511e-32 -3.626e-23 2.989e-20 -2.314e-20 -1.331e-18 - 0.09875 -2.883e-31 -9.595e-23 3.261e-20 -1.563e-20 -1.442e-18 - 0.09938 7.124e-31 -2.192e-23 3.361e-20 -1.157e-20 -1.497e-18 - 0.09969 1.524e-28 1.442e-22 3.388e-20 -9.552e-21 -1.524e-18 - 0.1 1.517e-28 4.277e-22 3.401e-20 -2.141e-29 -1.554e-18 + 0 -7.866e-40 -1.265e-22 3.502e-24 -7.151e-22 -3.884e-25 + 0.02 -2.217e-37 9.045e-21 1.646e-22 -3.602e-20 -2.578e-23 + 0.04 -2.323e-40 2.792e-20 7.396e-22 -3.602e-20 -5.169e-23 + 0.06 -5.968e-40 3.213e-20 1.596e-21 -3.623e-20 -1.402e-21 + 0.08 -5.219e-38 4.148e-21 -9.869e-21 -4.075e-20 -3.957e-20 + 0.09 -1.005e-37 8.104e-23 -5.11e-20 -5.21e-20 -1.536e-19 + 0.095 -5.316e-31 -9.281e-24 -8.322e-20 -6.074e-20 -2.462e-19 + 0.1 -4.837e-31 -9.077e-24 -1.145e-19 -2.092e-29 -3.356e-19 ------------------------------------------------------------------------------- z HCO CH2O CH2OH CH3O CH3OH ------------------------------------------------------------------------------- - 0 -5.574e-29 1.761e-24 2.191e-42 2.989e-28 -9.39e-23 - 0.02 -3.704e-27 1.18e-22 -1.901e-42 2.018e-26 -9.214e-23 - 0.04 -1.623e-34 2.009e-21 -1.101e-41 6.971e-25 -5.917e-23 - 0.06 5.179e-37 -4.166e-20 2.754e-40 -7.006e-24 -1.067e-21 - 0.08 -4.319e-31 -1.424e-19 5.658e-37 -6.389e-24 -6.945e-21 - 0.09 6.803e-30 -1.675e-19 9.657e-32 -6.151e-26 -4.537e-21 - 0.095 9.522e-29 -1.864e-19 4.442e-30 -3.299e-28 -2.367e-21 - 0.0975 -8.43e-28 -1.961e-19 1.108e-29 -4.956e-26 -1.23e-21 - 0.09875 -3.665e-27 -2.011e-19 -2.734e-29 -3.203e-25 -6.792e-22 - 0.09938 2.148e-29 -2.033e-19 -4.047e-29 -4.367e-25 -4.616e-22 - 0.09969 -7.589e-25 -2.042e-19 -2.925e-29 -1.192e-25 -4.076e-22 - 0.1 -7.642e-25 -2.041e-19 -1.982e-29 -7.86e-25 -4.124e-22 + 0 -1.051e-29 1.529e-25 3.226e-42 1.026e-29 5.35e-27 + 0.02 -6.983e-28 1.019e-23 -3.713e-44 6.927e-28 3.655e-25 + 0.04 -2.968e-35 9.525e-22 -1.561e-43 1.039e-25 2.09e-23 + 0.06 2.281e-36 2.918e-20 -9.526e-41 4.281e-24 7.084e-22 + 0.08 3.382e-33 1.331e-19 2.981e-37 5.227e-24 6.263e-21 + 0.09 4.349e-30 2.124e-19 4.785e-32 6.651e-26 6.559e-21 + 0.095 -1.351e-26 2.732e-19 -5.022e-27 -4.417e-28 6.536e-21 + 0.1 -1.014e-26 3.599e-19 -2.678e-20 -1.037e-27 6.558e-21 ------------------------------------------------------------------------------- z C2H C2H2 C2H3 C2H4 C2H5 ------------------------------------------------------------------------------- - 0 -4.008e-20 1.208e-22 8.884e-24 -1.111e-27 8.853e-34 - 0.02 -3.569e-28 2.586e-23 9.999e-31 2.971e-27 6.211e-32 - 0.04 -2.696e-36 2.58e-23 1.137e-37 2.401e-25 6.393e-32 - 0.06 -1.101e-40 2.26e-23 9.234e-39 1.236e-23 1.561e-32 - 0.08 -5.454e-31 -7.5e-23 4.04e-30 3.478e-22 -1.384e-33 - 0.09 4.673e-38 -3.974e-22 1.369e-32 1.327e-21 -9.078e-32 - 0.095 -7.381e-35 -6.654e-22 3.846e-31 2.113e-21 9.275e-29 - 0.0975 -7.038e-33 -8.082e-22 6.286e-31 2.526e-21 2.969e-27 - 0.09875 -4.01e-32 -8.767e-22 5.158e-30 2.72e-21 1.663e-26 - 0.09938 1.301e-30 -9.067e-22 3.499e-29 2.8e-21 5.137e-26 - 0.09969 5.638e-26 -9.22e-22 9.089e-29 2.827e-21 1.708e-25 - 0.1 1.704e-21 -1.127e-21 9.052e-29 2.828e-21 1.708e-25 + 0 -9.17e-21 -1.308e-23 -1.935e-27 -2.51e-27 -2.701e-34 + 0.02 -8.165e-29 -3.481e-23 -4.23e-34 -1.635e-25 -1.895e-32 + 0.04 -4.405e-37 -3.49e-23 -8.494e-40 -1.013e-23 -3.453e-32 + 0.06 -3.812e-45 -3.925e-23 1.266e-40 -5.264e-22 -2.758e-32 + 0.08 -1.839e-43 -1.993e-22 2.066e-36 -1.637e-20 -2.121e-31 + 0.09 -1.273e-34 -8.15e-22 4.589e-32 -6.849e-20 9.695e-30 + 0.095 -4.245e-27 -1.345e-21 2.207e-28 -1.117e-19 -1.672e-24 + 0.1 -3.676e-20 -8.488e-22 2.215e-28 -1.129e-19 -4.688e-20 ------------------------------------------------------------------------------- z C2H6 HCCO CH2CO HCCOH AR ------------------------------------------------------------------------------- - 0 4.642e-22 2.759e-43 2.138e-22 2.642e-24 0.01374 - 0.02 3.08e-20 -1.894e-41 2.138e-22 2.643e-24 0.01374 - 0.04 6.74e-20 -9.236e-41 2.137e-22 2.673e-24 0.01374 - 0.06 7.845e-20 -1.678e-37 2.066e-22 4.537e-24 0.01374 - 0.08 7.809e-20 -1.316e-29 -2.506e-23 6.672e-23 0.01373 - 0.09 7.708e-20 1.032e-32 -2.65e-23 6.816e-23 0.01375 - 0.095 7.634e-20 1.42e-30 -2.779e-23 6.952e-23 0.01378 - 0.0975 7.598e-20 7.58e-29 -2.85e-23 7.027e-23 0.0138 - 0.09875 7.581e-20 1.343e-28 -2.886e-23 7.066e-23 0.01381 - 0.09938 7.575e-20 -1.164e-28 -2.905e-23 7.085e-23 0.01381 - 0.09969 7.573e-20 -7.588e-28 -2.912e-23 7.09e-23 0.01382 - 0.1 7.574e-20 -7.792e-28 -2.916e-23 7.091e-23 0.01382 + 0 -1.346e-22 2.308e-41 3.487e-30 3.499e-34 0.01374 + 0.02 -9.522e-21 -1.346e-42 4.376e-30 2.717e-32 0.01374 + 0.04 -2.955e-20 3.434e-41 2.89e-29 2.003e-30 0.01374 + 0.06 -4.977e-20 1.435e-37 1.169e-27 1.225e-28 0.01374 + 0.08 -6.984e-20 2.469e-34 3.927e-26 4.101e-27 0.01373 + 0.09 -6.985e-20 1.004e-31 1.876e-25 1.759e-26 0.01375 + 0.095 -6.982e-20 1.874e-29 3.143e-25 2.91e-26 0.01378 + 0.1 -7.001e-20 1.902e-29 3.005e-25 2.926e-26 0.01382 ------------------------------------------------------------------------------- z N2 @@ -367,82 +299,46 @@ no new points needed in flow 0.06 0.7517 0.08 0.7512 0.09 0.7519 - 0.095 0.7536 - 0.0975 0.7546 - 0.09875 0.7552 - 0.09938 0.7554 - 0.09969 0.7556 - 0.1 0.7557 + 0.095 0.7535 + 0.1 0.7556 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Temperature: 900 K Coverages: - PT(S) 0.08847 - H(S) 1.366e-07 - H2O(S) 1.705e-05 - OH(S) 0.005717 - CO(S) -3.982e-22 - CO2(S) -5.012e-27 - CH3(S) 9.995e-28 - CH2(S)s 9.995e-28 - CH(S) 9.995e-28 - C(S) -5.262e-26 - O(S) 0.9058 + PT(S) 0.08838 + H(S) 1.359e-07 + H2O(S) 1.691e-05 + OH(S) 0.005694 + CO(S) -1.057e-22 + CO2(S) -1.317e-27 + CH3(S) 1.476e-26 + CH2(S)s 1.476e-26 + CH(S) 1.476e-26 + C(S) 4.108e-25 + O(S) 0.9059 .............................................................................. -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 1 timesteps 1.5e-05 -0.1099 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 2 timesteps 3.375e-05 -0.8978 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 5 timesteps 0.0001281 -0.8981 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.003695 -0.9064 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.1065 -1.056 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.7679 -0.2309 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 1.845 2.304 -.............................................................................. - Attempt Newton solution of steady-state problem... success. -Problem solved on [12] point grid(s). +Problem solved on [8] point grid(s). ############################################################################## Refining grid in flow. - New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 - to resolve C2H4 C2H6 CH2O CH3 CH3OH CH4 CO CO2 H2 H2O H2O2 HO2 O2 OH T V u + New points inserted after grid points 0 1 2 3 4 5 6 + to resolve C C2H6 CH2O CH3 CH4 CO CO2 H2O O2 OH T V u +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [15] point grid(s). + +############################################################################## +Refining grid in flow. + New points inserted after grid points 6 7 8 9 10 11 12 13 + to resolve C2H6 CH2O CH3 CH4 CO CO2 H2O O2 OH T V u .............................................................................. Attempt Newton solution of steady-state problem... success. @@ -451,8 +347,48 @@ Problem solved on [23] point grid(s). ############################################################################## Refining grid in flow. - New points inserted after grid points 6 7 8 9 10 11 13 21 - to resolve C2H4 C2H6 CH2O CH3OH CH4 CO CO2 H2 H2O H2O2 HO2 O2 OH T V u + New points inserted after grid points 19 20 21 + to resolve CH3 CO OH V +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [26] point grid(s). + +############################################################################## +Refining grid in flow. + New points inserted after grid points 24 + to resolve OH +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [27] point grid(s). + +############################################################################## +Refining grid in flow. + New points inserted after grid points 25 + to resolve OH +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [28] point grid(s). + +############################################################################## +Refining grid in flow. + New points inserted after grid points 23 26 + to resolve CH3 OH +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [30] point grid(s). + +############################################################################## +Refining grid in flow. + New points inserted after grid points 28 + to resolve OH .............................................................................. Attempt Newton solution of steady-state problem... success. @@ -461,54 +397,14 @@ Problem solved on [31] point grid(s). ############################################################################## Refining grid in flow. - New points inserted after grid points 29 - to resolve OH + New points inserted after grid points 25 + to resolve CH3 .............................................................................. Attempt Newton solution of steady-state problem... success. Problem solved on [32] point grid(s). -############################################################################## -Refining grid in flow. - New points inserted after grid points 29 30 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [34] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 13 31 32 - to resolve CO OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [37] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 34 35 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [39] point grid(s). - -############################################################################## -Refining grid in flow. - New points inserted after grid points 37 - to resolve OH -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [40] point grid(s). - no new points needed in flow @@ -531,310 +427,254 @@ no new points needed in flow ------------------------------------------------------------------------------- z u V T lambda H2 ------------------------------------------------------------------------------- - 0 0.05304 -5.437e-23 300 -0.389 -1.444e-16 - 0.01 0.05239 0.06484 300 -0.389 -5.488e-17 - 0.02 0.05045 0.1297 300 -0.389 6.351e-16 - 0.03 0.0472 0.1945 300 -0.389 5.782e-15 - 0.04 0.04266 0.2594 300 -0.389 4.204e-14 - 0.05 0.03683 0.3242 300 -0.389 2.764e-13 - 0.06 0.0297 0.389 300 -0.389 1.616e-12 - 0.065 0.02566 0.4215 300.1 -0.389 4.196e-12 - 0.07 0.02133 0.4542 300.8 -0.389 1.1e-11 - 0.075 0.01687 0.4884 304.7 -0.389 2.687e-11 - 0.08 0.01264 0.528 322.6 -0.389 5.792e-11 - 0.0825 0.01082 0.5514 347.3 -0.389 8.044e-11 - 0.085 0.009225 0.5751 392.3 -0.389 1.064e-10 - 0.0875 0.007653 0.5891 459.8 -0.389 1.336e-10 - 0.08875 0.006792 0.5862 500.5 -0.389 1.477e-10 - 0.09 0.005872 0.5736 544.6 -0.389 1.616e-10 - 0.09125 0.004899 0.5494 590.7 -0.389 1.751e-10 - 0.0925 0.003902 0.5123 637.7 -0.389 1.881e-10 - 0.09375 0.00292 0.4615 684.6 -0.389 2.007e-10 - 0.095 0.002002 0.3966 730.6 -0.389 2.125e-10 - 0.09625 0.001199 0.3176 775.4 -0.389 2.218e-10 - 0.09688 0.0008577 0.2729 797.1 -0.389 2.233e-10 - 0.0975 0.0005646 0.2248 818.5 -0.389 2.207e-10 - 0.09813 0.0003262 0.1734 839.5 -0.389 2.104e-10 - 0.09875 0.0001488 0.1188 860.1 -0.389 1.853e-10 - 0.09906 8.474e-05 0.09025 870.2 -0.389 1.619e-10 - 0.09938 3.813e-05 0.06094 880.2 -0.389 1.28e-10 - 0.09953 2.158e-05 0.04599 885.2 -0.389 1.053e-10 - 0.09969 9.647e-06 0.03085 890.2 -0.389 7.788e-11 - 0.09984 2.427e-06 0.01552 895.1 -0.389 4.473e-11 - 0.09992 6.081e-07 0.007785 897.5 -0.389 2.562e-11 - 0.09994 3.424e-07 0.005843 898.2 -0.389 2.061e-11 - 0.09996 1.523e-07 0.003899 898.8 -0.389 1.552e-11 - 0.09997 8.57e-08 0.002925 899.1 -0.389 1.295e-11 - 0.09998 3.81e-08 0.001951 899.4 -0.389 1.036e-11 - 0.09999 2.144e-08 0.001463 899.5 -0.389 9.059e-12 - 0.09999 9.529e-09 0.0009758 899.7 -0.389 7.757e-12 - 0.1 2.383e-09 0.000488 899.8 -0.389 6.453e-12 - 0.1 5.957e-10 0.000244 899.9 -0.389 5.801e-12 - 0.1 0 0 900 -0.389 5.147e-12 + 0 0.05304 2.982e-23 300 -0.3895 2.625e-18 + 0.01 0.05239 0.06491 300 -0.3895 6.28e-17 + 0.02 0.05044 0.1298 300 -0.3895 5.267e-16 + 0.03 0.0472 0.1947 300 -0.3895 3.987e-15 + 0.04 0.04265 0.2596 300 -0.3895 2.836e-14 + 0.05 0.03681 0.3246 300 -0.3895 1.859e-13 + 0.06 0.02967 0.3895 300 -0.3895 1.086e-12 + 0.065 0.02563 0.422 300.1 -0.3895 2.818e-12 + 0.07 0.0213 0.4547 300.8 -0.3895 7.381e-12 + 0.075 0.01684 0.4889 304.9 -0.3895 1.802e-11 + 0.08 0.01262 0.5286 323.1 -0.3895 3.878e-11 + 0.0825 0.0108 0.5519 348.2 -0.3895 5.379e-11 + 0.085 0.009214 0.575 393.7 -0.3895 7.105e-11 + 0.0875 0.00765 0.5876 461.9 -0.3895 8.912e-11 + 0.09 0.005881 0.5729 547.1 -0.3895 1.069e-10 + 0.09125 0.004906 0.5489 592.9 -0.3895 1.159e-10 + 0.0925 0.003906 0.512 639.5 -0.3895 1.245e-10 + 0.09375 0.002923 0.4613 686 -0.3895 1.329e-10 + 0.095 0.002003 0.3965 731.7 -0.3895 1.407e-10 + 0.09625 0.0012 0.3176 776.1 -0.3895 1.468e-10 + 0.09688 0.0008581 0.2729 797.8 -0.3895 1.478e-10 + 0.0975 0.0005648 0.2249 819 -0.3895 1.462e-10 + 0.09813 0.0003264 0.1735 839.9 -0.3895 1.397e-10 + 0.09875 0.0001489 0.1188 860.3 -0.3895 1.242e-10 + 0.09906 8.478e-05 0.09028 870.4 -0.3895 1.1e-10 + 0.09938 3.815e-05 0.06096 880.3 -0.3895 8.976e-11 + 0.09953 2.159e-05 0.04601 885.3 -0.3895 7.642e-11 + 0.09969 9.651e-06 0.03087 890.2 -0.3895 6.052e-11 + 0.09984 2.427e-06 0.01553 895.1 -0.3895 4.154e-11 + 0.09992 6.086e-07 0.007789 897.6 -0.3895 3.073e-11 + 0.09996 1.524e-07 0.0039 898.8 -0.3895 2.502e-11 + 0.1 0 0 900 -0.3895 1.914e-11 ------------------------------------------------------------------------------- z H O O2 OH H2O ------------------------------------------------------------------------------- - 0 4.378e-19 3.259e-19 0.2204 -1.783e-17 3.469e-14 - 0.01 7.793e-26 5.633e-18 0.2204 -2.897e-21 8.45e-13 - 0.02 -1.472e-31 1.922e-18 0.2204 1.199e-21 2.035e-11 - 0.03 1.143e-33 6.291e-19 0.2204 3.929e-22 4.732e-10 - 0.04 5.621e-33 1.929e-19 0.2204 1.205e-22 1.034e-08 - 0.05 2.771e-32 5.369e-20 0.2204 5.696e-23 2.056e-07 - 0.06 1.53e-31 1.311e-20 0.2204 7.672e-21 3.567e-06 - 0.065 4.567e-30 7.338e-21 0.2203 3.063e-19 2.173e-05 - 0.07 1.112e-27 3.618e-20 0.2202 1.399e-17 0.0001421 - 0.075 2.173e-25 4.379e-19 0.2194 4.616e-16 0.0008161 - 0.08 2.057e-23 4.671e-18 0.2153 7.703e-15 0.003744 - 0.0825 1.851e-22 1.181e-17 0.2094 2.454e-14 0.007561 - 0.085 1.748e-21 1.588e-17 0.1985 5.671e-14 0.01395 - 0.0875 1.42e-19 1.335e-17 0.1822 1.026e-13 0.02271 - 0.08875 1.945e-18 1.895e-17 0.1719 1.415e-13 0.02789 - 0.09 2.151e-17 6.883e-17 0.1606 1.972e-13 0.03337 - 0.09125 1.806e-16 4.343e-16 0.1486 2.873e-13 0.03898 - 0.0925 1.135e-15 2.712e-15 0.1362 4.572e-13 0.04461 - 0.09375 5.383e-15 1.437e-14 0.1236 8.342e-13 0.05018 - 0.095 2.004e-14 6.317e-14 0.1112 1.794e-12 0.05563 - 0.09625 6.326e-14 2.396e-13 0.09893 4.512e-12 0.06091 - 0.09688 1.117e-13 4.633e-13 0.09285 7.725e-12 0.06352 - 0.0975 1.96e-13 8.873e-13 0.08686 1.365e-11 0.06608 - 0.09813 3.485e-13 1.714e-12 0.08096 2.51e-11 0.06859 - 0.09875 6.419e-13 3.406e-12 0.07516 4.865e-11 0.07105 - 0.09906 9.038e-13 4.967e-12 0.07228 7.051e-11 0.07227 - 0.09938 1.297e-12 7.366e-12 0.06943 1.044e-10 0.07348 - 0.09953 1.574e-12 9.07e-12 0.068 1.289e-10 0.07409 - 0.09969 1.906e-12 1.111e-11 0.06659 1.613e-10 0.07469 - 0.09984 2.19e-12 1.271e-11 0.06517 2.387e-10 0.07528 - 0.09992 1.955e-12 1.11e-11 0.06443 7.818e-10 0.07554 - 0.09994 1.737e-12 9.794e-12 0.06427 1.684e-09 0.07563 - 0.09996 1.422e-12 7.962e-12 0.06411 3.383e-09 0.07572 - 0.09997 1.21e-12 6.756e-12 0.06402 4.877e-09 0.07576 - 0.09998 9.527e-13 5.31e-12 0.06394 7.005e-09 0.0758 - 0.09999 8.034e-13 4.477e-12 0.06389 8.415e-09 0.07582 - 0.09999 6.386e-13 3.561e-12 0.06385 1.01e-08 0.07584 - 0.1 4.566e-13 2.553e-12 0.06381 1.213e-08 0.07586 - 0.1 3.585e-13 2.012e-12 0.06379 1.329e-08 0.07587 - 0.1 2.555e-13 1.445e-12 0.06377 1.457e-08 0.07588 + 0 -1.54e-20 1.538e-20 0.2204 1.487e-19 3.596e-14 + 0.01 1.303e-27 2.656e-19 0.2204 2.453e-22 8.759e-13 + 0.02 9.271e-33 9.047e-20 0.2204 5.651e-23 2.109e-11 + 0.03 -3.884e-32 2.955e-20 0.2204 1.845e-23 4.905e-10 + 0.04 -7.897e-31 9.043e-21 0.2204 7.303e-24 1.072e-08 + 0.05 -1.586e-29 2.507e-21 0.2204 5.429e-22 2.13e-07 + 0.06 -2.216e-28 4.419e-22 0.2204 1.151e-19 3.694e-06 + 0.065 -5.905e-28 -2.715e-21 0.2203 2.328e-18 2.248e-05 + 0.07 1.584e-26 -1.645e-20 0.2202 5.002e-17 0.0001469 + 0.075 8.238e-25 2.662e-19 0.2193 7.891e-16 0.0008424 + 0.08 2.541e-23 5.223e-18 0.2151 7.458e-15 0.003854 + 0.0825 1.669e-22 1.137e-17 0.209 2.019e-14 0.007763 + 0.085 1.433e-21 1.314e-17 0.1978 4.363e-14 0.01428 + 0.0875 1.224e-19 1.088e-17 0.1811 7.778e-14 0.02317 + 0.09 1.638e-17 6.28e-17 0.1599 1.354e-13 0.03352 + 0.09125 1.336e-16 4.022e-16 0.148 2.011e-13 0.03912 + 0.0925 8.136e-16 2.384e-15 0.1356 3.288e-13 0.04474 + 0.09375 3.742e-15 1.198e-14 0.123 6.257e-13 0.0503 + 0.095 1.354e-14 5.051e-14 0.1106 1.409e-12 0.05573 + 0.09625 4.153e-14 1.853e-13 0.09838 3.654e-12 0.06101 + 0.09688 7.198e-14 3.514e-13 0.0923 6.276e-12 0.06361 + 0.0975 1.238e-13 6.592e-13 0.08632 1.105e-11 0.06617 + 0.09813 2.148e-13 1.242e-12 0.08042 2.009e-11 0.06868 + 0.09875 3.828e-13 2.389e-12 0.07463 3.806e-11 0.07114 + 0.09906 5.254e-13 3.399e-12 0.07175 5.406e-11 0.07236 + 0.09938 7.315e-13 4.902e-12 0.0689 7.808e-11 0.07357 + 0.09953 8.708e-13 6.032e-12 0.06747 9.492e-11 0.07418 + 0.09969 1.033e-12 8.305e-12 0.06606 1.178e-10 0.07478 + 0.09984 1.161e-12 2.036e-11 0.06465 2.037e-10 0.07537 + 0.09992 1.023e-12 6.399e-11 0.06394 1.014e-09 0.07567 + 0.09996 7.337e-13 1.286e-10 0.06359 4.172e-09 0.07582 + 0.1 9.826e-14 1.764e-11 0.06324 1.594e-08 0.07597 ------------------------------------------------------------------------------- z HO2 H2O2 C CH CH2 ------------------------------------------------------------------------------- - 0 -9.666e-19 -4.493e-18 1.262e-17 -3.088e-33 -4.675e-18 - 0.01 -2.558e-17 -4.485e-18 4.07e-25 -2.507e-41 -3.079e-24 - 0.02 -2.299e-17 -2.646e-18 1.267e-32 3.996e-47 -1.955e-30 - 0.03 3.923e-17 4.568e-17 3.705e-40 8.684e-53 8.405e-37 - 0.04 1.509e-15 1.198e-15 9.858e-48 -4.345e-45 5.232e-36 - 0.05 3.309e-14 2.612e-14 2.288e-55 6.777e-43 2.783e-35 - 0.06 6.232e-13 4.948e-13 4.499e-63 -1.486e-41 6.152e-32 - 0.065 4.073e-12 3.251e-12 4.472e-66 2.145e-40 1.504e-29 - 0.07 2.872e-11 2.304e-11 -6.35e-64 -7.008e-40 4.518e-27 - 0.075 1.774e-10 1.429e-10 -3.373e-59 -1.151e-37 8.646e-25 - 0.08 8.809e-10 7.066e-10 4.099e-57 1.794e-37 6.849e-23 - 0.0825 1.905e-09 1.488e-09 2.113e-56 1.107e-37 4.861e-22 - 0.085 3.822e-09 2.87e-09 9.05e-51 -1.073e-37 2.388e-21 - 0.0875 6.817e-09 4.853e-09 1.487e-43 7.878e-36 8.794e-21 - 0.08875 8.802e-09 6.057e-09 6.521e-37 5.617e-35 1.804e-20 - 0.09 1.106e-08 7.346e-09 1.507e-30 -1.359e-33 3.773e-20 - 0.09125 1.357e-08 8.676e-09 -1.299e-30 1.02e-32 8.435e-20 - 0.0925 1.628e-08 1.001e-08 -1.164e-31 1.076e-31 2.132e-19 - 0.09375 1.919e-08 1.13e-08 -3.33e-31 1.651e-30 6.452e-19 - 0.095 2.228e-08 1.25e-08 -6.332e-31 2.502e-29 2.41e-18 - 0.09625 2.555e-08 1.354e-08 7.553e-31 4.022e-28 1.11e-17 - 0.09688 2.731e-08 1.395e-08 1.079e-30 1.829e-27 2.705e-17 - 0.0975 2.913e-08 1.427e-08 -5.852e-30 8.758e-27 6.963e-17 - 0.09813 3.103e-08 1.447e-08 1.569e-29 4.6e-26 1.933e-16 - 0.09875 3.302e-08 1.455e-08 5.534e-35 2.785e-25 5.954e-16 - 0.09906 3.404e-08 1.456e-08 1.118e-33 7.719e-25 1.133e-15 - 0.09938 3.506e-08 1.455e-08 4.915e-33 2.28e-24 2.251e-15 - 0.09953 3.555e-08 1.454e-08 1.089e-32 4.087e-24 3.268e-15 - 0.09969 3.603e-08 1.452e-08 3.872e-33 7.485e-24 4.849e-15 - 0.09984 3.649e-08 1.451e-08 -8.636e-29 1.562e-23 8.542e-15 - 0.09992 3.671e-08 1.45e-08 -1.308e-25 5.673e-23 2.999e-14 - 0.09994 3.678e-08 1.451e-08 -2.046e-27 1.382e-22 6.567e-14 - 0.09996 3.685e-08 1.451e-08 1.68e-28 3.455e-22 1.34e-13 - 0.09997 3.687e-08 1.451e-08 5.132e-27 5.915e-22 1.939e-13 - 0.09998 3.689e-08 1.451e-08 8.887e-26 1.038e-21 2.768e-13 - 0.09999 3.69e-08 1.451e-08 6.413e-25 1.384e-21 3.272e-13 - 0.09999 3.69e-08 1.451e-08 3.647e-24 1.825e-21 3.801e-13 - 0.1 3.691e-08 1.451e-08 2.059e-23 2.326e-21 4.267e-13 - 0.1 3.691e-08 1.451e-08 5.854e-23 2.513e-21 4.391e-13 - 0.1 3.691e-08 1.451e-08 1.523e-22 2.513e-21 4.391e-13 + 0 2.2e-21 9.48e-21 5.284e-19 -3.28e-37 2.188e-19 + 0.01 5.823e-20 2.526e-19 1.705e-26 -1.006e-45 1.441e-25 + 0.02 1.294e-18 1.869e-18 5.306e-34 9.978e-46 9.149e-32 + 0.03 4.386e-17 3.699e-17 1.551e-41 -8.918e-49 -1.04e-34 + 0.04 1.079e-15 8.593e-16 1.165e-44 -6.501e-45 -2.06e-33 + 0.05 2.374e-14 1.841e-14 6.501e-36 -2.815e-43 -3.308e-32 + 0.06 4.557e-13 3.438e-13 -4.848e-36 2.766e-41 1.836e-29 + 0.065 3.036e-12 2.226e-12 -5.164e-36 4.204e-40 1.162e-27 + 0.07 2.165e-11 1.562e-11 2.044e-35 7.032e-39 7.651e-26 + 0.075 1.35e-10 9.603e-11 3.025e-34 -5.804e-38 3.325e-24 + 0.08 6.741e-10 4.706e-10 1.993e-34 2.318e-37 8.455e-23 + 0.0825 1.455e-09 9.87e-10 -9.65e-35 -5.504e-37 4.363e-22 + 0.085 2.903e-09 1.898e-09 -7.681e-36 3.811e-37 1.893e-21 + 0.0875 5.136e-09 3.205e-09 5.613e-34 1.294e-35 6.828e-21 + 0.09 8.091e-09 4.786e-09 -7.606e-33 2.451e-34 2.466e-20 + 0.09125 9.863e-09 5.653e-09 -9.056e-33 3.404e-33 5.673e-20 + 0.0925 1.177e-08 6.526e-09 -9.722e-33 5.393e-32 1.477e-19 + 0.09375 1.38e-08 7.38e-09 -7.478e-32 8.306e-31 4.639e-19 + 0.095 1.595e-08 8.181e-09 1.057e-31 1.264e-29 1.787e-18 + 0.09625 1.822e-08 8.875e-09 3.107e-31 1.991e-28 8.287e-18 + 0.09688 1.943e-08 9.153e-09 1.161e-30 8.772e-28 1.99e-17 + 0.0975 2.068e-08 9.368e-09 -5.654e-29 4.025e-27 4.999e-17 + 0.09813 2.196e-08 9.509e-09 -1.918e-35 1.99e-26 1.337e-16 + 0.09875 2.326e-08 9.571e-09 6.613e-35 1.104e-25 3.892e-16 + 0.09906 2.39e-08 9.576e-09 8.835e-34 2.858e-25 7.083e-16 + 0.09938 2.45e-08 9.569e-09 1.264e-29 7.774e-25 1.334e-15 + 0.09953 2.478e-08 9.563e-09 8.797e-26 1.322e-24 1.873e-15 + 0.09969 2.504e-08 9.556e-09 3.398e-22 2.31e-24 2.7e-15 + 0.09984 2.526e-08 9.551e-09 1.404e-18 5.448e-24 5.392e-15 + 0.09992 2.537e-08 9.549e-09 2.109e-15 3.54e-23 2.821e-14 + 0.09996 2.541e-08 9.548e-09 7.817e-13 2.601e-22 1.12e-13 + 0.1 2.541e-08 9.548e-09 1.922e-10 -1.426e-21 1.119e-13 ------------------------------------------------------------------------------- z CH2(S) CH3 CH4 CO CO2 ------------------------------------------------------------------------------- - 0 -5.135e-33 9.264e-20 0.04998 6.544e-19 8.54e-16 - 0.01 -1.231e-31 2.27e-18 0.04998 1.735e-17 2.945e-14 - 0.02 -3.24e-38 8.472e-18 0.04998 1.893e-17 1.004e-12 - 0.03 9.38e-38 2.567e-17 0.04998 5.896e-17 3.3e-11 - 0.04 2.565e-37 4.173e-16 0.04998 1.008e-15 1.018e-09 - 0.05 1.434e-36 8.297e-15 0.04998 2.143e-14 2.854e-08 - 0.06 3.197e-33 1.448e-13 0.04998 4.035e-13 6.958e-07 - 0.065 7.814e-31 8.865e-13 0.04997 2.64e-12 5.718e-06 - 0.07 2.351e-28 5.833e-12 0.04992 1.864e-11 5.128e-05 - 0.075 4.532e-26 3.388e-11 0.04964 1.152e-10 0.0003979 - 0.08 3.701e-24 1.622e-10 0.04843 5.694e-10 0.002428 - 0.0825 2.719e-23 3.678e-10 0.04684 1.21e-09 0.005861 - 0.085 1.396e-22 8.143e-10 0.04411 2.367e-09 0.01295 - 0.0875 5.284e-22 1.747e-09 0.0402 4.082e-09 0.02463 - 0.08875 1.076e-21 2.644e-09 0.0378 5.157e-09 0.03244 - 0.09 2.201e-21 3.987e-09 0.0352 6.331e-09 0.04132 - 0.09125 4.729e-21 6.03e-09 0.03247 7.568e-09 0.051 - 0.0925 1.129e-20 9.216e-09 0.02967 8.824e-09 0.0612 - 0.09375 3.173e-20 1.437e-08 0.02685 1.004e-08 0.07169 - 0.095 1.087e-19 2.312e-08 0.02405 1.113e-08 0.08223 - 0.09625 4.55e-19 3.908e-08 0.0213 1.189e-08 0.09267 - 0.09688 1.054e-18 5.337e-08 0.01993 1.199e-08 0.09789 - 0.0975 2.572e-18 7.448e-08 0.01858 1.176e-08 0.103 - 0.09813 6.757e-18 1.075e-07 0.01725 1.103e-08 0.1081 - 0.09875 1.966e-17 1.631e-07 0.01594 9.461e-09 0.1131 - 0.09906 3.632e-17 2.089e-07 0.01528 8.12e-09 0.1156 - 0.09938 7.004e-17 2.733e-07 0.01464 6.282e-09 0.1181 - 0.09953 1.001e-16 3.171e-07 0.01432 5.1e-09 0.1193 - 0.09969 1.463e-16 3.71e-07 0.01399 3.711e-09 0.1206 - 0.09984 2.529e-16 4.383e-07 0.01367 2.074e-09 0.1218 - 0.09992 8.727e-16 4.782e-07 0.01351 1.136e-09 0.1223 - 0.09994 1.9e-15 4.883e-07 0.01347 8.818e-10 0.1225 - 0.09996 3.873e-15 4.977e-07 0.01343 6.157e-10 0.1227 - 0.09997 5.62e-15 5.018e-07 0.01341 4.75e-10 0.1228 - 0.09998 8.112e-15 5.051e-07 0.01339 3.274e-10 0.1228 - 0.09999 9.755e-15 5.064e-07 0.01338 2.501e-10 0.1229 - 0.09999 1.171e-14 5.074e-07 0.01337 1.701e-10 0.1229 - 0.1 1.401e-14 5.081e-07 0.01337 8.69e-11 0.123 - 0.1 1.521e-14 5.082e-07 0.01336 4.393e-11 0.123 - 0.1 1.521e-14 5.082e-07 0.01336 2.424e-14 0.123 + 0 2.403e-34 1.295e-19 0.04998 5.853e-20 9.056e-16 + 0.01 5.762e-33 3.173e-18 0.04998 1.552e-18 3.122e-14 + 0.02 -3.007e-37 5.551e-17 0.04998 2.581e-18 1.064e-12 + 0.03 -4.798e-36 1.003e-15 0.04998 2.859e-17 3.498e-11 + 0.04 -9.503e-35 1.763e-14 0.04998 6.45e-16 1.079e-09 + 0.05 -1.48e-33 2.672e-13 0.04998 1.391e-14 3.024e-08 + 0.06 9.573e-31 2.972e-12 0.04998 2.62e-13 7.37e-07 + 0.065 6.038e-29 9.038e-12 0.04997 1.713e-12 6.052e-06 + 0.07 3.982e-27 2.766e-11 0.04992 1.208e-11 5.422e-05 + 0.075 1.743e-25 7.623e-11 0.04963 7.454e-11 0.00042 + 0.08 4.568e-24 2.067e-10 0.04838 3.675e-10 0.002555 + 0.0825 2.438e-23 4.011e-10 0.04675 7.79e-10 0.00615 + 0.085 1.104e-22 8.38e-10 0.04394 1.519e-09 0.01354 + 0.0875 4.081e-22 1.784e-09 0.03995 2.612e-09 0.02567 + 0.09 1.436e-21 3.783e-09 0.03509 3.979e-09 0.04206 + 0.09125 3.17e-21 5.75e-09 0.03236 4.746e-09 0.05172 + 0.0925 7.774e-21 8.749e-09 0.02957 5.525e-09 0.06191 + 0.09375 2.263e-20 1.35e-08 0.02675 6.281e-09 0.07237 + 0.095 7.99e-20 2.139e-08 0.02395 6.954e-09 0.08291 + 0.09625 3.368e-19 3.538e-08 0.02121 7.426e-09 0.09334 + 0.09688 7.683e-19 4.752e-08 0.01984 7.483e-09 0.09856 + 0.0975 1.831e-18 6.505e-08 0.01849 7.35e-09 0.1037 + 0.09813 4.633e-18 9.165e-08 0.01716 6.914e-09 0.1088 + 0.09875 1.274e-17 1.345e-07 0.01585 5.987e-09 0.1138 + 0.09906 2.252e-17 1.682e-07 0.0152 5.21e-09 0.1163 + 0.09938 4.115e-17 2.139e-07 0.01455 4.16e-09 0.1188 + 0.09953 5.689e-17 2.438e-07 0.01423 3.494e-09 0.12 + 0.09969 8.074e-17 2.796e-07 0.01391 2.719e-09 0.1212 + 0.09984 1.58e-16 3.23e-07 0.01359 1.816e-09 0.1224 + 0.09992 8.158e-16 3.474e-07 0.01343 1.301e-09 0.123 + 0.09996 3.407e-15 3.573e-07 0.01335 1.008e-09 0.1234 + 0.1 3.407e-15 3.573e-07 0.01327 2.418e-14 0.1237 ------------------------------------------------------------------------------- z HCO CH2O CH2OH CH3O CH3OH ------------------------------------------------------------------------------- - 0 -7.124e-26 -1.2e-18 1.174e-40 -7.407e-31 -2.398e-19 - 0.01 -2.466e-24 -4.189e-17 4.125e-39 -2.603e-29 -2.292e-19 - 0.02 -1.073e-30 9.596e-19 7.635e-39 -6.982e-30 1.425e-19 - 0.03 1.373e-34 1.425e-15 6.394e-38 4.275e-28 1.273e-17 - 0.04 1.343e-33 4.581e-14 6.215e-37 2.035e-25 4.124e-16 - 0.05 3.44e-32 1.3e-12 7.357e-36 8.862e-23 1.192e-14 - 0.06 1.218e-29 3.208e-11 3.479e-33 2.902e-20 2.995e-13 - 0.065 1.122e-27 2.665e-10 9.02e-31 1.162e-18 2.529e-12 - 0.07 2.788e-25 2.416e-09 3.623e-28 5.367e-17 2.333e-11 - 0.075 6.551e-23 1.893e-08 9.386e-26 1.889e-15 1.859e-10 - 0.08 6.694e-21 1.163e-07 9.514e-24 4.093e-14 1.16e-09 - 0.0825 5.309e-20 2.809e-07 7.289e-23 1.743e-13 2.832e-09 - 0.085 3.017e-19 6.182e-07 3.835e-22 5.815e-13 6.303e-09 - 0.0875 1.513e-18 1.165e-06 1.633e-21 1.408e-12 1.2e-08 - 0.08875 4.047e-18 1.525e-06 4.133e-21 2.09e-12 1.578e-08 - 0.09 1.204e-17 1.928e-06 1.337e-20 2.946e-12 2.005e-08 - 0.09125 3.815e-17 2.361e-06 5.34e-20 3.975e-12 2.465e-08 - 0.0925 1.225e-16 2.81e-06 2.266e-19 5.108e-12 2.946e-08 - 0.09375 3.893e-16 3.262e-06 9.115e-19 6.194e-12 3.431e-08 - 0.095 1.227e-15 3.707e-06 3.331e-18 7.184e-12 3.908e-08 - 0.09625 3.887e-15 4.133e-06 1.114e-17 8.368e-12 4.362e-08 - 0.09688 7.131e-15 4.335e-06 2.022e-17 9.472e-12 4.58e-08 - 0.0975 1.319e-14 4.526e-06 3.662e-17 1.1e-11 4.786e-08 - 0.09813 2.49e-14 4.7e-06 6.728e-17 1.332e-11 4.978e-08 - 0.09875 4.865e-14 4.851e-06 1.287e-16 1.712e-11 5.152e-08 - 0.09906 7.026e-14 4.913e-06 1.852e-16 2.025e-11 5.23e-08 - 0.09938 1.032e-13 4.963e-06 2.751e-16 2.453e-11 5.3e-08 - 0.09953 1.267e-13 4.982e-06 3.421e-16 2.739e-11 5.331e-08 - 0.09969 1.568e-13 4.997e-06 4.317e-16 3.085e-11 5.359e-08 - 0.09984 2.015e-13 5.006e-06 5.79e-16 3.51e-11 5.383e-08 - 0.09992 3.135e-13 5.005e-06 1.117e-15 3.758e-11 5.391e-08 - 0.09994 4.743e-13 5.006e-06 1.978e-15 3.817e-11 5.394e-08 - 0.09996 7.737e-13 5.007e-06 3.626e-15 3.868e-11 5.397e-08 - 0.09997 1.035e-12 5.008e-06 5.087e-15 3.888e-11 5.398e-08 - 0.09998 1.406e-12 5.008e-06 7.165e-15 3.902e-11 5.399e-08 - 0.09999 1.645e-12 5.008e-06 8.51e-15 3.907e-11 5.399e-08 - 0.09999 1.916e-12 5.008e-06 1.003e-14 3.911e-11 5.399e-08 - 0.1 2.187e-12 5.008e-06 1.155e-14 3.913e-11 5.4e-08 - 0.1 2.272e-12 5.008e-06 1.202e-14 3.913e-11 5.4e-08 - 0.1 2.272e-12 5.008e-06 1.202e-14 3.913e-11 5.4e-08 + 0 7.859e-28 4.445e-20 5.151e-43 1.281e-33 1.58e-21 + 0.01 2.721e-26 1.551e-18 1.81e-41 4.501e-32 7.503e-21 + 0.02 1.343e-32 3.248e-17 1.718e-40 2.406e-29 2.156e-19 + 0.03 6.917e-36 1.06e-15 1.966e-39 1.425e-26 7.261e-18 + 0.04 1.337e-33 3.309e-14 1.035e-37 6.147e-24 2.309e-16 + 0.05 5.599e-31 9.382e-13 4.236e-35 2.047e-21 6.67e-15 + 0.06 1.72e-28 2.314e-11 3.347e-32 4.358e-19 1.675e-13 + 0.065 7.129e-27 1.92e-10 4.003e-30 8.828e-18 1.413e-12 + 0.07 7.451e-25 1.739e-09 7.32e-28 1.919e-16 1.302e-11 + 0.075 8.119e-23 1.36e-08 8.98e-26 3.233e-15 1.036e-10 + 0.08 4.67e-21 8.326e-08 5.132e-24 3.985e-14 6.444e-10 + 0.0825 3.152e-20 2.005e-07 3.335e-23 1.446e-13 1.569e-09 + 0.085 1.706e-19 4.395e-07 1.65e-22 4.511e-13 3.478e-09 + 0.0875 9.137e-19 8.254e-07 7.291e-22 1.072e-12 6.599e-09 + 0.09 7.357e-18 1.335e-06 6.354e-21 2.009e-12 1.077e-08 + 0.09125 2.412e-17 1.629e-06 2.681e-20 2.715e-12 1.32e-08 + 0.0925 7.817e-17 1.934e-06 1.15e-19 3.459e-12 1.572e-08 + 0.09375 2.477e-16 2.242e-06 4.585e-19 4.137e-12 1.826e-08 + 0.095 7.725e-16 2.544e-06 1.65e-18 4.717e-12 2.075e-08 + 0.09625 2.407e-15 2.833e-06 5.421e-18 5.384e-12 2.311e-08 + 0.09688 4.353e-15 2.969e-06 9.73e-18 6.002e-12 2.422e-08 + 0.0975 7.917e-15 3.098e-06 1.74e-17 6.85e-12 2.526e-08 + 0.09813 1.46e-14 3.214e-06 3.146e-17 8.108e-12 2.623e-08 + 0.09875 2.764e-14 3.314e-06 5.897e-17 1.009e-11 2.708e-08 + 0.09906 3.896e-14 3.354e-06 8.358e-17 1.165e-11 2.746e-08 + 0.09938 5.564e-14 3.386e-06 1.219e-16 1.369e-11 2.778e-08 + 0.09953 6.71e-14 3.398e-06 1.497e-16 1.501e-11 2.792e-08 + 0.09969 8.156e-14 3.407e-06 1.87e-16 1.655e-11 2.805e-08 + 0.09984 1.067e-13 3.413e-06 2.693e-16 1.838e-11 2.815e-08 + 0.09992 2.131e-13 3.414e-06 7.935e-16 1.937e-11 2.82e-08 + 0.09996 5.837e-13 3.414e-06 2.769e-15 1.969e-11 2.821e-08 + 0.1 5.836e-13 3.414e-06 2.769e-15 1.969e-11 2.821e-08 ------------------------------------------------------------------------------- z C2H C2H2 C2H3 C2H4 C2H5 ------------------------------------------------------------------------------- - 0 1.227e-17 1.183e-19 -3.634e-17 -1.453e-20 -2.416e-32 - 0.01 2.4e-25 -1.674e-19 -8.314e-24 3.58e-20 -8.808e-31 - 0.02 4.527e-33 -1.672e-19 -1.833e-30 1.732e-18 6.634e-30 - 0.03 8.008e-41 -1.586e-19 -3.789e-37 5.653e-17 1.296e-29 - 0.04 1.287e-48 9.051e-20 1.15e-38 1.716e-15 1.934e-29 - 0.05 1.662e-50 6.692e-18 4.924e-36 4.731e-14 1.313e-29 - 0.06 5.401e-47 1.586e-16 2.165e-33 1.135e-12 5.213e-28 - 0.065 1.709e-44 1.245e-15 1.396e-31 9.189e-12 1.6e-25 - 0.07 7.093e-42 1.063e-14 2.148e-29 8.114e-11 6.398e-23 - 0.075 2.455e-39 7.877e-14 4.523e-27 6.203e-10 1.643e-20 - 0.08 1.053e-36 4.601e-13 6.194e-25 3.73e-09 1.532e-18 - 0.0825 4.827e-35 1.081e-12 7.49e-24 8.914e-09 1.051e-17 - 0.085 3.742e-33 2.326e-12 8.605e-23 1.948e-08 4.643e-17 - 0.0875 3.029e-31 4.328e-12 1.089e-21 3.666e-08 1.535e-16 - 0.08875 2.531e-30 5.647e-12 4.556e-21 4.802e-08 3.093e-16 - 0.09 1.864e-29 7.13e-12 1.976e-20 6.085e-08 6.935e-16 - 0.09125 1.215e-28 8.734e-12 8.447e-20 7.474e-08 1.766e-15 - 0.0925 7.3e-28 1.041e-11 3.443e-19 8.929e-08 4.959e-15 - 0.09375 4.282e-27 1.213e-11 1.329e-18 1.041e-07 1.472e-14 - 0.095 2.565e-26 1.384e-11 4.923e-18 1.19e-07 4.529e-14 - 0.09625 1.584e-25 1.552e-11 1.795e-17 1.336e-07 1.45e-13 - 0.09688 4.08e-25 1.635e-11 3.532e-17 1.407e-07 2.732e-13 - 0.0975 1.058e-24 1.715e-11 7.023e-17 1.477e-07 5.268e-13 - 0.09813 2.785e-24 1.791e-11 1.43e-16 1.544e-07 1.057e-12 - 0.09875 7.552e-24 1.862e-11 3.034e-16 1.607e-07 2.26e-12 - 0.09906 1.284e-23 1.893e-11 4.583e-16 1.635e-07 3.48e-12 - 0.09938 2.215e-23 1.922e-11 7.056e-16 1.661e-07 5.531e-12 - 0.09953 2.945e-23 1.934e-11 8.873e-16 1.673e-07 7.131e-12 - 0.09969 3.963e-23 1.945e-11 1.126e-15 1.683e-07 9.464e-12 - 0.09984 6.302e-23 1.954e-11 1.501e-15 1.691e-07 1.555e-11 - 0.09992 2.149e-22 1.956e-11 2.61e-15 1.694e-07 3.709e-11 - 0.09994 4.677e-22 1.958e-11 4.25e-15 1.695e-07 5.244e-11 - 0.09996 9.482e-22 1.959e-11 7.275e-15 1.696e-07 7.199e-11 - 0.09997 1.373e-21 1.959e-11 9.799e-15 1.696e-07 8.255e-11 - 0.09998 1.98e-21 1.959e-11 1.31e-14 1.696e-07 9.273e-11 - 0.09999 2.381e-21 1.959e-11 1.495e-14 1.696e-07 9.706e-11 - 0.09999 2.851e-21 1.959e-11 1.678e-14 1.696e-07 1.006e-10 - 0.1 3.357e-21 1.959e-11 1.826e-14 1.696e-07 1.029e-10 - 0.1 3.536e-21 1.959e-11 1.864e-14 1.696e-07 1.034e-10 - 0.1 3.537e-21 1.959e-11 1.864e-14 1.696e-07 1.034e-10 + 0 -2.03e-19 2.14e-21 4.747e-19 5.911e-22 3.388e-32 + 0.01 -3.971e-27 5.877e-21 1.086e-25 2.431e-20 1.235e-30 + 0.02 -7.49e-35 6.029e-21 2.395e-32 8.189e-19 -5.103e-29 + 0.03 -1.325e-42 1.076e-20 5.289e-39 2.648e-17 -7.897e-28 + 0.04 -2.126e-50 1.489e-19 1.765e-37 8.037e-16 -1.553e-26 + 0.05 8.874e-50 3.807e-18 7.389e-35 2.215e-14 -3.088e-25 + 0.06 4.488e-46 8.794e-17 2.049e-32 5.31e-13 -4.39e-24 + 0.065 7.425e-44 6.892e-16 6.203e-31 4.297e-12 -1.602e-23 + 0.07 1.455e-41 5.88e-15 3.93e-29 3.79e-11 9.776e-23 + 0.075 2.396e-39 4.348e-14 3.706e-27 2.893e-10 1.762e-20 + 0.08 5.834e-37 2.533e-13 2.856e-25 1.734e-09 9.337e-19 + 0.0825 2.286e-35 5.933e-13 2.968e-24 4.133e-09 5.429e-18 + 0.085 1.668e-33 1.272e-12 3.322e-23 8.999e-09 2.249e-17 + 0.0875 1.329e-31 2.36e-12 4.59e-22 1.688e-08 7.568e-17 + 0.09 7.184e-30 3.801e-12 8.253e-21 2.738e-08 3.395e-16 + 0.09125 4.678e-29 4.642e-12 3.592e-20 3.352e-08 9.27e-16 + 0.0925 2.85e-28 5.521e-12 1.464e-19 3.995e-08 2.719e-15 + 0.09375 1.731e-27 6.419e-12 5.594e-19 4.651e-08 8.24e-15 + 0.095 1.08e-26 7.318e-12 2.037e-18 5.307e-08 2.545e-14 + 0.09625 6.853e-26 8.2e-12 7.256e-18 5.95e-08 8.097e-14 + 0.09688 1.768e-25 8.635e-12 1.403e-17 6.265e-08 1.511e-13 + 0.0975 4.558e-25 9.059e-12 2.732e-17 6.571e-08 2.88e-13 + 0.09813 1.185e-24 9.467e-12 5.422e-17 6.863e-08 5.688e-13 + 0.09875 3.141e-24 9.851e-12 1.111e-16 7.132e-08 1.187e-12 + 0.09906 5.237e-24 1.003e-11 1.637e-16 7.252e-08 1.792e-12 + 0.09938 8.833e-24 1.02e-11 2.447e-16 7.36e-08 2.778e-12 + 0.09953 1.205e-23 1.027e-11 3.022e-16 7.406e-08 3.523e-12 + 0.09969 1.523e-23 1.034e-11 3.764e-16 7.447e-08 4.621e-12 + 0.09984 2.875e-23 1.041e-11 5.15e-16 7.479e-08 7.89e-12 + 0.09992 1.497e-22 1.044e-11 1.184e-15 7.491e-08 1.944e-11 + 0.09996 6.335e-22 1.045e-11 3.323e-15 7.494e-08 3.286e-11 + 0.1 6.335e-22 1.045e-11 3.323e-15 7.494e-08 3.286e-11 ------------------------------------------------------------------------------- z C2H6 HCCO CH2CO HCCOH AR ------------------------------------------------------------------------------- - 0 1.396e-17 2.383e-38 -4.516e-27 -1.964e-27 0.0131 - 0.01 1.551e-17 5.222e-37 -4.494e-27 -1.96e-27 0.0131 - 0.02 7.878e-17 1.787e-37 -3.608e-27 -1.791e-27 0.0131 - 0.03 2.24e-15 6.316e-38 3.039e-26 4.674e-27 0.0131 - 0.04 7.305e-14 6.143e-38 1.254e-24 2.373e-25 0.0131 - 0.05 2.179e-12 3.273e-37 4.116e-23 7.826e-24 0.0131 - 0.06 5.656e-11 1.824e-36 1.17e-21 2.225e-22 0.0131 - 0.065 4.917e-10 8.23e-36 1.105e-20 2.101e-21 0.0131 - 0.07 4.677e-09 3.693e-34 1.145e-19 2.178e-20 0.0131 - 0.075 3.839e-08 3.592e-32 1.021e-18 1.941e-19 0.0131 - 0.08 2.469e-07 2.883e-30 7.082e-18 1.347e-18 0.01311 - 0.0825 6.164e-07 2.322e-29 1.855e-17 3.527e-18 0.01311 - 0.085 1.407e-06 1.118e-28 4.425e-17 8.415e-18 0.01311 - 0.0875 2.747e-06 3.447e-28 8.932e-17 1.699e-17 0.01311 - 0.08875 3.657e-06 8.576e-28 1.205e-16 2.292e-17 0.01311 - 0.09 4.7e-06 4.866e-27 1.566e-16 2.978e-17 0.0131 - 0.09125 5.844e-06 4.916e-26 1.965e-16 3.737e-17 0.01309 - 0.0925 7.053e-06 4.922e-25 2.389e-16 4.543e-17 0.01308 - 0.09375 8.294e-06 4.069e-24 2.826e-16 5.375e-17 0.01306 - 0.095 9.538e-06 2.712e-23 3.266e-16 6.212e-17 0.01305 - 0.09625 1.076e-05 1.522e-22 3.701e-16 7.042e-17 0.01304 - 0.09688 1.136e-05 3.555e-22 3.916e-16 7.454e-17 0.01303 - 0.0975 1.194e-05 8.186e-22 4.128e-16 7.86e-17 0.01303 - 0.09813 1.25e-05 1.894e-21 4.334e-16 8.258e-17 0.01302 - 0.09875 1.301e-05 4.488e-21 4.53e-16 8.643e-17 0.01301 - 0.09906 1.323e-05 7.137e-21 4.624e-16 8.828e-17 0.01301 - 0.09938 1.343e-05 1.152e-20 4.712e-16 9.006e-17 0.01301 - 0.09953 1.351e-05 1.479e-20 4.753e-16 9.09e-17 0.013 - 0.09969 1.358e-05 1.885e-20 4.792e-16 9.172e-17 0.013 - 0.09984 1.362e-05 2.242e-20 4.828e-16 9.248e-17 0.013 - 0.09992 1.363e-05 1.982e-20 4.842e-16 9.278e-17 0.01299 - 0.09994 1.363e-05 1.75e-20 4.847e-16 9.289e-17 0.013 - 0.09996 1.363e-05 1.423e-20 4.851e-16 9.298e-17 0.013 - 0.09997 1.364e-05 1.219e-20 4.852e-16 9.301e-17 0.013 - 0.09998 1.364e-05 9.959e-21 4.854e-16 9.304e-17 0.013 - 0.09999 1.364e-05 8.883e-21 4.854e-16 9.305e-17 0.013 - 0.09999 1.364e-05 7.923e-21 4.854e-16 9.306e-17 0.013 - 0.1 1.364e-05 7.222e-21 4.855e-16 9.306e-17 0.013 - 0.1 1.364e-05 7.057e-21 4.855e-16 9.307e-17 0.013 - 0.1 1.364e-05 7.057e-21 4.855e-16 9.307e-17 0.013 + 0 -6.681e-19 -3.584e-41 -4.368e-28 1.807e-28 0.0131 + 0.01 -3.506e-20 -7.854e-40 -4.281e-28 1.822e-28 0.0131 + 0.02 1.311e-17 -2.769e-40 -8.107e-29 2.431e-28 0.0131 + 0.03 8.793e-16 -1.798e-40 1.324e-26 2.581e-27 0.0131 + 0.04 3.558e-14 -8.536e-40 4.925e-25 8.669e-26 0.0131 + 0.05 1.191e-12 -5.963e-39 1.612e-23 2.829e-24 0.0131 + 0.06 3.347e-11 1.243e-37 4.581e-22 8.039e-23 0.0131 + 0.065 3.047e-10 1.71e-35 4.322e-21 7.585e-22 0.0131 + 0.07 2.943e-09 1.633e-33 4.476e-20 7.855e-21 0.0131 + 0.075 2.424e-08 1.028e-31 3.982e-19 6.987e-20 0.0131 + 0.08 1.557e-07 3.01e-30 2.754e-18 4.833e-19 0.01311 + 0.0825 3.876e-07 1.181e-29 7.19e-18 1.262e-18 0.01311 + 0.085 8.815e-07 4.004e-29 1.709e-17 2.998e-18 0.01311 + 0.0875 1.715e-06 1.232e-28 3.436e-17 6.029e-18 0.01311 + 0.09 2.861e-06 2.269e-27 5.865e-17 1.029e-17 0.0131 + 0.09125 3.541e-06 2.407e-26 7.322e-17 1.285e-17 0.01309 + 0.0925 4.26e-06 2.294e-25 8.871e-17 1.557e-17 0.01307 + 0.09375 4.997e-06 1.798e-24 1.047e-16 1.837e-17 0.01306 + 0.095 5.735e-06 1.148e-23 1.208e-16 2.12e-17 0.01305 + 0.09625 6.456e-06 6.228e-23 1.367e-16 2.4e-17 0.01304 + 0.09688 6.809e-06 1.428e-22 1.446e-16 2.539e-17 0.01303 + 0.0975 7.148e-06 3.224e-22 1.523e-16 2.676e-17 0.01302 + 0.09813 7.469e-06 7.288e-22 1.598e-16 2.81e-17 0.01302 + 0.09875 7.759e-06 1.676e-21 1.669e-16 2.939e-17 0.01301 + 0.09906 7.885e-06 2.607e-21 1.702e-16 3e-17 0.01301 + 0.09938 7.992e-06 4.13e-21 1.734e-16 3.059e-17 0.013 + 0.09953 8.034e-06 5.854e-21 1.748e-16 3.087e-17 0.013 + 0.09969 8.067e-06 7.16e-21 1.762e-16 3.113e-17 0.013 + 0.09984 8.089e-06 1.974e-20 1.775e-16 3.137e-17 0.013 + 0.09992 8.094e-06 6.385e-20 1.78e-16 3.149e-17 0.013 + 0.09996 8.095e-06 1.221e-19 1.782e-16 3.153e-17 0.013 + 0.1 8.095e-06 1.221e-19 1.782e-16 3.153e-17 0.013 ------------------------------------------------------------------------------- z N2 @@ -852,75 +692,64 @@ no new points needed in flow 0.08 0.717 0.0825 0.7172 0.085 0.7173 - 0.0875 0.7171 - 0.08875 0.7168 - 0.09 0.7164 - 0.09125 0.7159 - 0.0925 0.7153 - 0.09375 0.7146 - 0.095 0.7139 - 0.09625 0.7131 - 0.09688 0.7128 - 0.0975 0.7124 - 0.09813 0.712 - 0.09875 0.7117 - 0.09906 0.7115 - 0.09938 0.7113 - 0.09953 0.7112 - 0.09969 0.7111 - 0.09984 0.7111 - 0.09992 0.7106 - 0.09994 0.7108 + 0.0875 0.717 + 0.09 0.7163 + 0.09125 0.7158 + 0.0925 0.7151 + 0.09375 0.7145 + 0.095 0.7137 + 0.09625 0.713 + 0.09688 0.7126 + 0.0975 0.7123 + 0.09813 0.7119 + 0.09875 0.7116 + 0.09906 0.7114 + 0.09938 0.7112 + 0.09953 0.7111 + 0.09969 0.711 + 0.09984 0.7109 + 0.09992 0.7109 0.09996 0.7109 - 0.09997 0.7109 - 0.09998 0.7109 - 0.09999 0.7109 - 0.09999 0.7109 0.1 0.7109 - 0.1 0.711 - 0.1 0.711 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Temperature: 900 K Coverages: - PT(S) 0.1251 - H(S) 2.669e-07 - H2O(S) 3.122e-05 - OH(S) 0.007569 + PT(S) 0.1254 + H(S) 2.681e-07 + H2O(S) 3.134e-05 + OH(S) 0.007582 CO(S) 3.847e-05 - CO2(S) 4.166e-10 - CH3(S) 3.111e-09 - CH2(S)s 3.111e-09 - CH(S) 3.111e-09 - C(S) 1.367e-07 - O(S) 0.8673 + CO2(S) 4.164e-10 + CH3(S) 3.102e-09 + CH2(S)s 3.102e-09 + CH(S) 3.102e-09 + C(S) 1.368e-07 + O(S) 0.867 -Solution saved to file catcomb.xml as solution soln1_3. +Solution saved to file catcomb.xml as solution soln1. solution saved to catcomb.csv Statistics: Grid Functions Time Jacobians Time - 8 38 0.2000 3 0.3900 - 9 16 0.1100 2 0.3200 - 10 8 0.0600 1 0.1900 - 10 16 0.1200 2 0.3900 - 10 10 0.0400 1 0.1600 - 10 14 0.0600 2 0.2700 - 11 6 0.0200 1 0.1500 - 12 4 0.0200 1 0.1700 - 12 16 0.1100 2 0.3500 - 13 2 0.0200 1 0.1900 - 13 14 0.1100 2 0.3800 - 14 4 0.0300 1 0.2200 - 14 8 0.0600 1 0.2100 - 14 1241 9.2600 38 8.0000 - 25 18 0.2700 1 0.4400 - 33 24 0.4900 2 1.2200 - 34 6 0.1200 1 0.6300 - 36 4 0.0900 1 0.6800 - 39 14 0.3800 2 1.4800 - 41 2 0.0800 1 0.8400 - 42 2 0.0800 1 1.2200 + 8 38 0.0400 3 0.2100 + 9 16 0.0300 2 0.1800 + 10 8 0.0300 1 0.1000 + 10 16 0.0500 2 0.2200 + 10 10 0.0200 1 0.1100 + 10 14 0.0300 2 0.2200 + 10 16 0.0500 2 0.2100 + 10 14 0.0300 2 0.2200 + 10 8 0.0300 1 0.1000 + 10 41 0.1200 3 0.3100 + 17 37 0.1100 3 0.4800 + 25 26 0.1500 2 0.4900 + 28 11 0.0700 1 0.2800 + 29 11 0.0600 1 0.2900 + 30 6 0.0300 1 0.3100 + 32 6 0.0500 1 0.3300 + 33 4 0.0200 1 0.3500 + 34 2 0.0000 1 0.3600 diff --git a/Cantera/python/examples/surface_chemistry/diamond_cvd/cleanup b/Cantera/python/examples/surface_chemistry/diamond_cvd/cleanup index a5de3bad0..b49c8f463 100755 --- a/Cantera/python/examples/surface_chemistry/diamond_cvd/cleanup +++ b/Cantera/python/examples/surface_chemistry/diamond_cvd/cleanup @@ -2,4 +2,4 @@ # /bin/rm -rf equilibrate_log*.html /bin/rm -rf .cttmp* ct2ctml.log transport_log.xml vcs_equilibrate_res*.csv \ - diamond.csv output_0.txt diff* + diamond.csv output_0.txt diff* diamond.xml From fabfb44b4ece0df39f719a34c4ec8afa8c24bd39 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 30 Dec 2009 17:58:38 +0000 Subject: [PATCH 095/446] Switched a call in MultiPhase to be public. switched velocityBasis to a typedef. It seemed the better solution. Note the concept is still basically undeveloped. Doxygen changes - supporting 1.6.2 --- Cantera/src/equil/MultiPhase.cpp | 1 + Cantera/src/equil/MultiPhase.h | 3 +- Cantera/src/transport/LiquidTransport.cpp | 2 +- Cantera/src/transport/TransportBase.h | 67 +- Cantera/src/transport/TransportFactory.cpp | 14 +- Cantera/src/transport/TransportParams.h | 29 +- .../linux_64_gcc424_dbg_python252_numpy | 3 + .../linux_64_gcc424_opt_python252_numpy | 3 + tools/doc/Cantera.cfg.in | 1656 +++++++++++++++-- 9 files changed, 1634 insertions(+), 144 deletions(-) diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index 81dcb4865..594e243a4 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -183,6 +183,7 @@ namespace Cantera { updateMoleFractions(); + updatePhases(); } diff --git a/Cantera/src/equil/MultiPhase.h b/Cantera/src/equil/MultiPhase.h index fa96148c3..cedb1f06f 100644 --- a/Cantera/src/equil/MultiPhase.h +++ b/Cantera/src/equil/MultiPhase.h @@ -549,8 +549,6 @@ namespace Cantera { */ void uploadMoleFractionsFromPhases(); - private: - //! Set the states of the phase objects to the locally-stored //! state within this MultiPhase object. /*! @@ -567,6 +565,7 @@ namespace Cantera { */ void updatePhases() const; + private: //! Calculate the element abundance vector void calcElemAbundances() const; diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 779000a66..19048d42e 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -189,7 +189,7 @@ namespace Cantera { int k; // constant substance attributes m_thermo = tr.thermo; - m_velocityBasis = tr.velocityBasis; + m_velocityBasis = tr.velocityBasis_; m_nsp = m_thermo->nSpecies(); m_tmin = m_thermo->minTemp(); m_tmax = m_thermo->maxTemp(); diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 097db665d..4d22ab22a 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -57,17 +57,35 @@ namespace Cantera { // forward reference class XML_Writer; - /** The diffusion velocities can be referenced to a variety of things. - * Most typical is to reference to the mass averaged velocity, but + //! The diffusion fluxes must be referenced to a particular reference + //! fluid velocity. + /*! + * Most typical is to reference the diffusion fluxes to the mass averaged velocity, but * referencing to the mole averaged velocity is suitable for some - * liquid flows and referencing to a single species is suitable for - * some solvent mixtures. This enum should provide a means to identify - * the reference velocity used for the transport model. + * liquid flows, and referencing to a single species is suitable for + * solid phase transport within a lattice. Currently, the identity of the reference + * velocity is coded into each transport object as a typedef named VelocityBasis, which + * is equated to an integer. Negative values of this variable refer to mass or mole-averaged + * velocities. Zero or positive quantities refers to the reference + * velocity being referenced to a particular species. Below are the predefined constants + * for its value. + * + * - VB_MASSAVG Diffusion velocities are based on the mass averaged velocity + * - VB_MOLEAVG Diffusion velocities are based on the mole averaged velocities + * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 + * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 + * */ - enum VelocityBasis { - VB_MOLEAVG = -2, - VB_MASSAVG = -1 - }; + typedef int VelocityBasis; + + //! Diffusion velocities are based on the mass averaged velocity + const VelocityBasis VB_MASSAVG = -1; + //! Diffusion velocities are based on the mole averaged velocities + const VelocityBasis VB_MOLEAVG = -2; + //! Diffusion velocities are based on the relative motion wrt species 0 + const VelocityBasis VB_SPECIES_0 = 0; + //! Diffusion velocities are based on the relative motion wrt species 1 + const VelocityBasis VB_SPECIES_1 = 1; //! Base class for transport property managers. /*! @@ -106,6 +124,33 @@ namespace Cantera { * also implicitly assumed that the underlying state within the ThermoPhase * object has not changed its values. * + * + *
+ *

Diffusion Fluxes and their Relationship to Reference Velocities

+ *
+ * + * The diffusion fluxes must be referenced to a particular reference + * fluid velocity. + * Most typical is to reference the diffusion fluxes to the mass averaged velocity, but + * referencing to the mole averaged velocity is suitable for some + * liquid flows, and referencing to a single species is suitable for + * solid phase transport within a lattice. Currently, the identity of the reference + * velocity is coded into each transport object as a typedef named VelocityBasis, which + * is equated to an integer. Negative values of this variable refer to mass or mole-averaged + * velocities. Zero or positive quantities refers to the reference + * velocity being referenced to a particular species. Below are the predefined constants + * for its value. + * + * - VB_MASSAVG Diffusion velocities are based on the mass averaged velocity + * - VB_MOLEAVG Diffusion velocities are based on the mole averaged velocities + * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 + * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 + * + * All transport managers specify a default reference velocity in their default constructors. + * All gas phase transport managers by default specify the mass-averaged velocity as their + * reference velocities. + * + * * @todo Provide a general mechanism to store the gradients of state variables * within the system. * @@ -587,7 +632,7 @@ namespace Cantera { * * @param ivb Species the velocity basis */ - void setVelocityBasis(int ivb) + void setVelocityBasis(VelocityBasis ivb) { m_velocityBasis = ivb; } @@ -600,7 +645,7 @@ namespace Cantera { * * @return Returns the velocity basis */ - int getVelocityBasis( ) const { + VelocityBasis getVelocityBasis( ) const { return m_velocityBasis; } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 7ae020cda..2c6eb8822 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1111,15 +1111,15 @@ namespace Cantera { * * */ - if ( tranTypeNode.hasChild("velocityBasis")) { + if (tranTypeNode.hasChild("velocityBasis")) { std::string velocityBasis = tranTypeNode.child("velocityBasis").attrib("basis"); - if ( velocityBasis == "mass" ) - trParam.velocityBasis = VB_MASSAVG; - else if ( velocityBasis == "mole" ) - trParam.velocityBasis = VB_MOLEAVG; - else if ( trParam.thermo->speciesIndex( velocityBasis ) > 0 ) - trParam.velocityBasis = trParam.thermo->speciesIndex( velocityBasis ) ; + if (velocityBasis == "mass") + trParam.velocityBasis_ = VB_MASSAVG; + else if (velocityBasis == "mole") + trParam.velocityBasis_ = VB_MOLEAVG; + else if (trParam.thermo->speciesIndex(velocityBasis) > 0) + trParam.velocityBasis_ = trParam.thermo->speciesIndex(velocityBasis) ; else { int linenum; throw TransportDBError( linenum, "Unknown attribute " + velocityBasis + " for node. "); diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 563c6d9ca..648847e14 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -19,11 +19,12 @@ namespace Cantera { public: + //! Default Constructor TransportParams() : nsp_(0), thermo(0), mw(0), - velocityBasis(VB_MASSAVG), + velocityBasis_(VB_MASSAVG), tmax(1000000.), tmin(10.), mode_(0), @@ -32,6 +33,7 @@ namespace Cantera { { } + //! Destructor virtual ~TransportParams() { #ifdef DEBUG_MODE @@ -39,20 +41,37 @@ namespace Cantera { #endif } + //! Local storage of the number of species int nsp_; - // phase_t* mix; + + //! Pointer to the ThermoPhase object thermo_t* thermo; + + //! Local storage of the molecular weights of the species + /*! + * Length is nsp_ and units are kg kmol-1. + */ vector_fp mw; //! A basis for the average velocity can be specified. - //! Valid bases include "mole" "mass" and species names. - int velocityBasis; + /*! + * Valid bases include "mole", "mass", and "species" names. + */ + VelocityBasis velocityBasis_; - //minimum and maximum temperatures for parameter fits + //! Maximum temperatures for parameter fits doublereal tmax; + + //! Minimum temperatures for parameter fits doublereal tmin; + + //! Mode parameter int mode_; + + //! Pointer to the xml tree describing the implementation of transport for this object XML_Writer* xml; + + //! Log level int log_level; }; diff --git a/docs/install_examples/linux_64_gcc424_dbg_python252_numpy b/docs/install_examples/linux_64_gcc424_dbg_python252_numpy index 2da813547..b95d79ce2 100755 --- a/docs/install_examples/linux_64_gcc424_dbg_python252_numpy +++ b/docs/install_examples/linux_64_gcc424_dbg_python252_numpy @@ -31,6 +31,9 @@ export WITH_ELECTROLYTES WITH_VCSNONIDEAL="y" export WITH_VCSNONIDEAL +WITH_H298MODIFY_CAPABILITY="y" +export WITH_H298MODIFY_CAPABILITY + BUILD_MATLAB_TOOLBOX="y" export BUILD_MATLAB_TOOLBOX diff --git a/docs/install_examples/linux_64_gcc424_opt_python252_numpy b/docs/install_examples/linux_64_gcc424_opt_python252_numpy index e0a4a2d57..09d12db05 100755 --- a/docs/install_examples/linux_64_gcc424_opt_python252_numpy +++ b/docs/install_examples/linux_64_gcc424_opt_python252_numpy @@ -29,6 +29,9 @@ export WITH_ELECTROLYTES WITH_VCSNONIDEAL="y" export WITH_VCSNONIDEAL +WITH_H298MODIFY_CAPABILITY="y" +export WITH_H298MODIFY_CAPABILITY + BUILD_MATLAB_TOOLBOX="y" export BUILD_MATLAB_TOOLBOX diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index 72b352910..d3c22ee97 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -1,16 +1,91 @@ -# Doxyfile 1.4.2 +# Doxyfile 1.6.2 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + PROJECT_NAME = Cantera -PROJECT_NUMBER = 1.7 + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = 1.8 + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + OUTPUT_DIRECTORY = @ctroot@/tools/doc + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + OUTPUT_LANGUAGE = English -USE_WINDOWS_ENCODING = NO + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ @@ -22,160 +97,719 @@ ABBREVIATE_BRIEF = "The $name class" \ a \ an \ the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + ALWAYS_DETAILED_SEC = YES + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + INLINE_INHERITED_MEMB = YES + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + FULL_PATH_NAMES = NO -STRIP_FROM_PATH = -STRIP_FROM_INC_PATH = + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + MULTILINE_CPP_IS_BRIEF = NO -DETAILS_AT_TOP = YES + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + INHERIT_DOCS = YES -DISTRIBUTE_GROUP_DOC = NO + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + TAB_SIZE = 8 -ALIASES = + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + HIDE_IN_BODY_DOCS = YES + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + HIDE_SCOPE_NAMES = YES + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + GENERATE_DEPRECATEDLIST= YES -ENABLED_SECTIONS = + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + SHOW_DIRECTORIES = YES -FILE_VERSION_FILTER = + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + WARN_NO_PARAMDOC = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + WARN_FORMAT = "$file:$line: $text" -WARN_LOGFILE = + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- -INPUT = ../../Cantera/src \ - ../../Cantera/src/base \ - ../../Cantera/src/numerics \ + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ../../Cantera/src \ + ../../Cantera/src/base \ + ../../Cantera/src/numerics \ ../../Cantera/src/thermo \ ../../Cantera/src/equil \ ../../Cantera/src/kinetics \ ../../Cantera/src/transport \ ../../Cantera/cxx/include \ doxyinput -FILE_PATTERNS = Kinetics.h Kinetics.cpp \ - FactoryBase.h misc.cpp \ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = Kinetics.h Kinetics.cpp \ + FactoryBase.h \ + misc.cpp \ ct_defs.h \ logger.h \ global.h \ units.h \ ctexceptions.h \ *.txt \ - xml.h xml.cpp \ - ctml.h ctml.cpp ct2ctml.cpp \ - stringUtils.h stringUtils.cpp \ - plots.h plots.cpp \ - PrintCtrl.h PrintCtrl.cpp \ - LogPrintCtrl.h LogPrintCtrl.cpp \ - clockWC.h clockWC.cpp \ - Array.h vec_functions.h \ + xml.h \ + xml.cpp \ + ctml.h \ + ctml.cpp \ + ct2ctml.cpp \ + stringUtils.h \ + stringUtils.cpp \ + plots.h \ + plots.cpp \ + PrintCtrl.h \ + PrintCtrl.cpp \ + LogPrintCtrl.h \ + LogPrintCtrl.cpp \ + clockWC.h \ + clockWC.cpp \ + Array.h \ + vec_functions.h \ equilibrium.h \ - ThermoPhase.h ThermoPhase.cpp \ - Phase.h Phase.cpp \ - State.h State.cpp \ - Constituents.h Constituents.cpp \ - Elements.h Elements.cpp \ - importCTML.cpp importCTML.h \ - ThermoFactory.h ThermoFactory.cpp \ - IdealGasPhase.h IdealGasPhase.cpp \ - SurfPhase.h EdgePhase.h SurfPhase.cpp \ + ThermoPhase.h \ + ThermoPhase.cpp \ + Phase.h \ + Phase.cpp \ + State.h \ + State.cpp \ + Constituents.h \ + Constituents.cpp \ + Elements.h \ + Elements.cpp \ + importCTML.cpp \ + importCTML.h \ + ThermoFactory.h \ + ThermoFactory.cpp \ + IdealGasPhase.h \ + IdealGasPhase.cpp \ + SurfPhase.h \ + EdgePhase.h \ + SurfPhase.cpp \ LatticePhase.h LatticePhase.cpp \ - SpeciesThermoFactory.h SpeciesThermoFactory.cpp \ - speciesThermoTypes.h SpeciesThermoMgr.h SpeciesThermoInterpType.h \ - PDSS.h PDSS.cpp \ + SpeciesThermoFactory.h SpeciesThermoFactory.cpp \ + speciesThermoTypes.h \ + SpeciesThermoMgr.h \ + SpeciesThermoInterpType.h \ + PDSS.h \ + PDSS.cpp \ SpeciesThermo.h \ - NasaThermo.h NasaPoly1.h NasaPoly2.h \ - ShomateThermo.h ShomatePoly.h SimpleThermo.h \ - GeneralSpeciesThermo.h GeneralSpeciesThermo.cpp \ - ConstCpPoly.h ConstCpPoly.cpp Mu0Poly.h Mu0Poly.cpp \ - utilities.h phasereport.cpp \ - VPStandardStateTP.h VPStandardStateTP.cpp \ - SingleSpeciesTP.h SingleSpeciesTP.cpp \ - MolalityVPSSTP.h MolalityVPSSTP.cpp \ - IdealMolalSoln.h IdealMolalSoln.cpp \ - IdealSolidSolnPhase.h IdealSolidSolnPhase.cpp \ - StoichSubstanceSSTP.h StoichSubstanceSSTP.cpp \ - DebyeHuckel.h DebyeHuckel.cpp \ - MineralEQ3.h MineralEQ3.cpp \ - HMWSoln.h HMWSoln.cpp HMWSoln_input.cpp \ - GibbsExcessVPSSTP.h GibbsExcessVPSSTP.cpp \ - MargulesVPSSTP.h MargulesVPSSTP.cpp \ - IonsFromNeutralVPSSTP.h IonsFromNeutralVPSSTP.cpp \ - VPSSMgr.h VPSSMgr.cpp VPSSMgr_types.h \ - VPSSMgr_ConstVol.h VPSSMgr_ConstVol.cpp \ - VPSSMgr_IdealGas.h VPSSMgr_IdealGas.cpp \ - VPSSMgr_Water_ConstVol.h VPSSMgr_Water_ConstVol.cpp \ - VPSSMgr_Water_HKFT.h VPSSMgr_Water_HKFT.cpp \ - VPSSMgr_General.h VPSSMgr_General.cpp \ - VPSSMgrFactory.h VPSSMgrFactory.cpp \ - PDSS_ConstVol.h PDSS_ConstVol.cpp \ - PDSS_SSVol.h PDSS_SSVol.cpp \ - PDSS_IdealGas.h PDSS_IdealGas.cpp \ - PDSS_Water.h PDSS_Water.cpp \ - PDSS_HKFT.h PDSS_HKFT.cpp \ - PDSS_IonsFromNeutral.h PDSS_IonsFromNeutral.cpp \ - IdealSolnGasVPSS.h IdealSolnGasVPSS.cpp \ - ConstDensityThermo.h ConstDensityThermo.cpp \ - WaterPropsIAPWSphi.h WaterPropsIAPWSphi.cpp \ - WaterPropsIAPWS.h WaterPropsIAPWS.cpp \ - WaterSSTP.h WaterSSTP.cpp \ - WaterProps.h WaterProps.cpp \ - PureFluidPhase.h PureFluidPhase.cpp \ - equil.h MultiPhase.h MultiPhase.cpp BasisOptimize.cpp \ - Nasa9Poly1.h Nasa9Poly1.cpp \ - Nasa9PolyMultiTempRegion.h Nasa9PolyMultiTempRegion.cpp \ - vcs_internal.h vcs_defs.h \ - vcs_MultiPhaseEquil.h vcs_MultiPhaseEquil.cpp \ - FalloffFactory.h FalloffFactory.cpp \ - TransportBase.h TransportBase.cpp TransportParams.h \ - MMCollisionInt.h L_matrix.h MMCollisionInt.cpp \ - TransportFactory.h TransportFactory.cpp \ - MultiTransport.h MultiTransport.cpp MixTransport.h MixTransport.cpp \ - DustyGasTransport.h DustyGasTransport.cpp \ - SolidTransport.h SolidTransport.cpp \ - SimpleTransport.h SimpleTransport.cpp \ - LiquidTransport.h LiquidTransportParams.h LiquidTransport.cpp \ - AqueousTransport.h AqueousTransport.cpp WaterTransport.h WaterTransport.cpp + NasaThermo.h \ + NasaPoly1.h \ + NasaPoly2.h \ + ShomateThermo.h \ + ShomatePoly.h \ + SimpleThermo.h \ + GeneralSpeciesThermo.h \ + GeneralSpeciesThermo.cpp \ + ConstCpPoly.h \ + ConstCpPoly.cpp \ + Mu0Poly.h \ + Mu0Poly.cpp \ + utilities.h \ + phasereport.cpp \ + VPStandardStateTP.h \ + VPStandardStateTP.cpp \ + SingleSpeciesTP.h \ + SingleSpeciesTP.cpp \ + MolalityVPSSTP.h \ + MolalityVPSSTP.cpp \ + IdealMolalSoln.h \ + IdealMolalSoln.cpp \ + IdealSolidSolnPhase.h \ + IdealSolidSolnPhase.cpp \ + StoichSubstanceSSTP.h \ + StoichSubstanceSSTP.cpp \ + DebyeHuckel.h \ + DebyeHuckel.cpp \ + MineralEQ3.h \ + MineralEQ3.cpp \ + HMWSoln.h \ + HMWSoln.cpp \ + HMWSoln_input.cpp \ + GibbsExcessVPSSTP.h \ + GibbsExcessVPSSTP.cpp \ + MargulesVPSSTP.h \ + MargulesVPSSTP.cpp \ + IonsFromNeutralVPSSTP.h \ + IonsFromNeutralVPSSTP.cpp \ + VPSSMgr.h \ + VPSSMgr.cpp \ + VPSSMgr_types.h \ + VPSSMgr_ConstVol.h \ + VPSSMgr_ConstVol.cpp \ + VPSSMgr_IdealGas.h \ + VPSSMgr_IdealGas.cpp \ + VPSSMgr_Water_ConstVol.h \ + VPSSMgr_Water_ConstVol.cpp \ + VPSSMgr_Water_HKFT.h \ + VPSSMgr_Water_HKFT.cpp \ + VPSSMgr_General.h \ + VPSSMgr_General.cpp \ + VPSSMgrFactory.h \ + VPSSMgrFactory.cpp \ + PDSS_ConstVol.h \ + PDSS_ConstVol.cpp \ + PDSS_SSVol.h \ + PDSS_SSVol.cpp \ + PDSS_IdealGas.h \ + PDSS_IdealGas.cpp \ + PDSS_Water.h \ + PDSS_Water.cpp \ + PDSS_HKFT.h \ + PDSS_HKFT.cpp \ + PDSS_IonsFromNeutral.h \ + PDSS_IonsFromNeutral.cpp \ + IdealSolnGasVPSS.h \ + IdealSolnGasVPSS.cpp \ + ConstDensityThermo.h \ + ConstDensityThermo.cpp \ + WaterPropsIAPWSphi.h \ + WaterPropsIAPWSphi.cpp \ + WaterPropsIAPWS.h \ + WaterPropsIAPWS.cpp \ + WaterSSTP.h \ + WaterSSTP.cpp \ + WaterProps.h \ + WaterProps.cpp \ + PureFluidPhase.h \ + PureFluidPhase.cpp \ + equil.h \ + MultiPhase.h \ + MultiPhase.cpp \ + BasisOptimize.cpp \ + Nasa9Poly1.h \ + Nasa9Poly1.cpp \ + Nasa9PolyMultiTempRegion.h \ + Nasa9PolyMultiTempRegion.cpp \ + vcs_internal.h \ + vcs_defs.h \ + vcs_MultiPhaseEquil.h \ + vcs_MultiPhaseEquil.cpp \ + FalloffFactory.h \ + FalloffFactory.cpp \ + TransportBase.h \ + TransportBase.cpp \ + TransportParams.h \ + MMCollisionInt.h \ + L_matrix.h \ + MMCollisionInt.cpp \ + TransportFactory.h \ + TransportFactory.cpp \ + MultiTransport.h \ + MultiTransport.cpp \ + MixTransport.h \ + MixTransport.cpp \ + DustyGasTransport.h \ + DustyGasTransport.cpp \ + SolidTransport.h \ + SolidTransport.cpp \ + SimpleTransport.h \ + SimpleTransport.cpp \ + LiquidTransport.h \ + LiquidTransportParams.h \ + LiquidTransport.cpp \ + AqueousTransport.h \ + AqueousTransport.cpp \ + WaterTransport.h \ + WaterTransport.cpp + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + RECURSIVE = NO -EXCLUDE = CVS examples converters zeroD + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = CVS \ + examples \ + converters \ + zeroD + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + EXCLUDE_PATTERNS = *old/* \ *old_src/* \ *stl/* \ @@ -183,154 +817,940 @@ EXCLUDE_PATTERNS = *old/* \ *examples/* \ *test/* \ *tests/* + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + EXAMPLE_PATH = ../../examples \ ../../data/inputs \ ./doxyinput + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + EXAMPLE_PATTERNS = *.cpp \ *.h + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + EXAMPLE_RECURSIVE = NO -IMAGE_PATH = -INPUT_FILTER = -FILTER_PATTERNS = + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + FILTER_SOURCE_FILES = NO + #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + VERBATIM_HEADERS = YES + #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + IGNORE_PREFIX = Cantera:: + #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + HTML_FILE_EXTENSION = .html -HTML_HEADER = -HTML_FOOTER = -HTML_STYLESHEET = + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = NO + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + GENERATE_HTMLHELP = YES -CHM_FILE = -HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + GENERATE_TREEVIEW = NO + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = NO + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_LATEX = YES + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + PAPER_TYPE = letter -EXTRA_PACKAGES = -LATEX_HEADER = + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + RTF_HYPERLINKS = NO -RTF_STYLESHEET_FILE = -RTF_EXTENSIONS_FILE = + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + MAN_LINKS = NO + #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + XML_OUTPUT = xml -XML_SCHEMA = -XML_DTD = + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + XML_PROGRAMLISTING = YES + #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + GENERATE_AUTOGEN_DEF = NO + #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + PERLMOD_PRETTY = YES -PERLMOD_MAKEVAR_PREFIX = + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + #--------------------------------------------------------------------------- -# Configuration options related to the preprocessor +# Configuration options related to the preprocessor #--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + MACRO_EXPANSION = YES + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + EXPAND_ONLY_PREDEF = YES + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + SEARCH_INCLUDES = YES -INCLUDE_PATH = -INCLUDE_FILE_PATTERNS = + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + PREDEFINED = WITH_HTML_LOGS \ WITH_PURE_FLUIDS \ THREAD_SAFE_CANTERA \ WITH_LATTICE_SOLID + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + EXPAND_AS_DEFINED = YES + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + SKIP_FUNCTION_MACROS = YES + #--------------------------------------------------------------------------- -# Configuration::additions related to external references +# Configuration::additions related to external references #--------------------------------------------------------------------------- -TAGFILES = -GENERATE_TAGFILE = + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + PERL_PATH = /usr/bin/perl + #--------------------------------------------------------------------------- -# Configuration options related to the dot tool +# Configuration options related to the dot tool #--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + TEMPLATE_RELATIONS = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + DOT_PATH = @GRAPHVIZDIR@ -DOTFILE_DIRS = -MAX_DOT_GRAPH_WIDTH = 1024 -MAX_DOT_GRAPH_HEIGHT = 1024 + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + DOT_CLEANUP = YES -#--------------------------------------------------------------------------- -# Configuration::additions related to the search engine -#--------------------------------------------------------------------------- -SEARCHENGINE = NO From ea7ae8c5837622745d23b4f294a99a99543a9f44 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 30 Dec 2009 18:20:34 +0000 Subject: [PATCH 096/446] Added a stub for a high level description of transport within Cantera. --- tools/doc/doxyinput/Cantera.txt | 1 + tools/doc/doxyinput/transport.txt | 23 +++++++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 tools/doc/doxyinput/transport.txt diff --git a/tools/doc/doxyinput/Cantera.txt b/tools/doc/doxyinput/Cantera.txt index 696124b8a..63a9fd587 100644 --- a/tools/doc/doxyinput/Cantera.txt +++ b/tools/doc/doxyinput/Cantera.txt @@ -22,5 +22,6 @@ Choose one of the links below for an introduction to %Cantera, or use - Computing Properties of Matter - \subpage thermopage + - \subpage transportpage */ diff --git a/tools/doc/doxyinput/transport.txt b/tools/doc/doxyinput/transport.txt new file mode 100644 index 000000000..ad4c8a94f --- /dev/null +++ b/tools/doc/doxyinput/transport.txt @@ -0,0 +1,23 @@ +/** + +\page transportpage Transport Properties + +%Cantera can be used to compute transport properties + + +\section nest Non-Equilibrium Statistical Thermodynamics + + +\section tbase Base Class for Transport Properties + + +The base class \link Cantera::Transport Transport \endlink is used for all +transport classes within Cantera. + + + +There is a list of classes which handle transport for species (see +\ref tranprops " Transport Properties for Species in Phases"). + + +*/ From 4297e1ce11eaed1b3543557ce8f956242c34638b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 30 Dec 2009 18:40:44 +0000 Subject: [PATCH 097/446] Doxygen commit. Added stuff to the tranprops group. --- Cantera/src/transport/TransportBase.h | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 4d22ab22a..fdf1a24f1 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -17,7 +17,7 @@ /** - * @defgroup tranprops Transport Properties + * @defgroup tranprops Transport Properties for Species in Phases * * @ingroup phases * @@ -36,6 +36,11 @@ namespace Cantera { class GasTransportParams; class LiquidTransportParams; + /*! + * \addtogroup tranprops + */ + //@{ + const int CK_Mode = 10; // types of transport models that can be constructed @@ -53,6 +58,7 @@ namespace Cantera { const int cSimpleTransport = 770; const int cRadiativeTransport = 800; const int cWaterTransport = 721; + //@} // forward reference class XML_Writer; @@ -75,9 +81,14 @@ namespace Cantera { * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 * + * @ingroup tranprops */ typedef int VelocityBasis; + /*! + * \addtogroup tranprops + */ + //@{ //! Diffusion velocities are based on the mass averaged velocity const VelocityBasis VB_MASSAVG = -1; //! Diffusion velocities are based on the mole averaged velocities @@ -86,6 +97,7 @@ namespace Cantera { const VelocityBasis VB_SPECIES_0 = 0; //! Diffusion velocities are based on the relative motion wrt species 1 const VelocityBasis VB_SPECIES_1 = 1; + //@} //! Base class for transport property managers. /*! @@ -759,7 +771,10 @@ namespace Cantera { }; - //! general definition for the transport class + //! General definition for the transport class + /*! + * \ingroups tranprops + */ typedef Transport transport_t; } From 4b676b388cb7fe10bd1898076c85ccbc8a69aa97 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Tue, 12 Jan 2010 00:42:50 +0000 Subject: [PATCH 098/446] Changed the signature of LiquidTranInteraction::getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) so that now it takes a reference to the matrix that needs to be filled, avoiding an extra copy construction. For vector and DenseMatrix resize operations, added 0.0 or 0 as initialization value so that we don't have garbage in these. This is most relevant for vectors of pointers where we need NULL values to test against. --- Cantera/src/transport/LiquidTransport.cpp | 50 +++++++++---------- .../src/transport/LiquidTransportParams.cpp | 38 ++++++-------- Cantera/src/transport/LiquidTransportParams.h | 18 +++---- 3 files changed, 50 insertions(+), 56 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 19048d42e..bb19b56c1 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -195,15 +195,15 @@ namespace Cantera { m_tmax = m_thermo->maxTemp(); // make a local copy of the molecular weights - m_mw.resize(m_nsp); + m_mw.resize(m_nsp, 0.0); copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin()); /* * Get the input Viscosities */ - m_viscSpecies.resize(m_nsp); - m_viscTempDep_Ns.resize(m_nsp); + m_viscSpecies.resize(m_nsp, 0.0); + m_viscTempDep_Ns.resize(m_nsp, 0); //for each species, assign viscosity model and coefficients for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; @@ -213,8 +213,8 @@ namespace Cantera { /* * Get the input Thermal Conductivities */ - m_lambdaSpecies.resize(m_nsp); - m_lambdaTempDep_Ns.resize(m_nsp); + m_lambdaSpecies.resize(m_nsp, 0.0); + m_lambdaTempDep_Ns.resize(m_nsp, 0); //for each species, assign thermal conductivity model for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; @@ -224,8 +224,8 @@ namespace Cantera { /* * Get the input Hydrodynamic Radii */ - m_hydrodynamic_radius.resize(m_nsp); - m_radiusTempDep_Ns.resize(m_nsp); + m_hydrodynamic_radius.resize(m_nsp, 0.0); + m_radiusTempDep_Ns.resize(m_nsp, 0); //for each species, assign model for hydrodynamic radius for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; @@ -239,7 +239,7 @@ namespace Cantera { * needed for the current model. This section may, therefore, * be extraneous. */ - m_diffTempDep_Ns.resize(m_nsp); + m_diffTempDep_Ns.resize(m_nsp, 0); //for each species, assign viscosity model and coefficients for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; @@ -267,25 +267,25 @@ namespace Cantera { m_lambdaMixModel = tr.thermalCond; //m_radiusMixModel = tr.hydroRadius; m_diffMixModel = tr.speciesDiffusivity; - m_bdiff.resize(m_nsp,m_nsp); + m_bdiff.resize(m_nsp,m_nsp, 0.0); //Don't really need to update this here. //It is updated in updateDiff_T() - m_bdiff = m_diffMixModel->getMatrixTransProp(); + m_diffMixModel->getMatrixTransProp( m_bdiff ); m_mode = tr.mode_; - m_massfracs.resize(m_nsp); - m_massfracs_tran.resize(m_nsp); - m_molefracs.resize(m_nsp); - m_molefracs_tran.resize(m_nsp); - m_concentrations.resize(m_nsp); - m_actCoeff.resize(m_nsp); - m_chargeSpecies.resize(m_nsp); + m_massfracs.resize(m_nsp, 0.0); + m_massfracs_tran.resize(m_nsp, 0.0); + m_molefracs.resize(m_nsp, 0.0); + m_molefracs_tran.resize(m_nsp, 0.0); + m_concentrations.resize(m_nsp, 0.0); + m_actCoeff.resize(m_nsp, 0.0); + m_chargeSpecies.resize(m_nsp, 0.0); for ( int i = 0; i < m_nsp; i++ ) m_chargeSpecies[i] = m_thermo->charge( i ); - m_volume_spec.resize(m_nsp); - m_Grad_lnAC.resize(m_nsp); - m_spwork.resize(m_nsp); + m_volume_spec.resize(m_nsp, 0.0); + m_Grad_lnAC.resize(m_nsp, 0.0); + m_spwork.resize(m_nsp, 0.0); // resize the internal gradient variables m_Grad_X.resize(m_nDim * m_nsp, 0.0); @@ -293,8 +293,8 @@ namespace Cantera { m_Grad_V.resize(m_nDim, 0.0); m_Grad_mu.resize(m_nDim * m_nsp, 0.0); - m_flux.resize(m_nsp, m_nDim); - m_Vdiff.resize(m_nsp, m_nDim); + m_flux.resize(m_nsp, m_nDim, 0.0); + m_Vdiff.resize(m_nsp, m_nDim, 0.0); // set all flags to false @@ -1082,7 +1082,7 @@ namespace Cantera { //! wrt T using calls to the appropriate LTPspecies subclass void LiquidTransport::updateDiff_T() { - m_bdiff = m_diffMixModel->getMatrixTransProp(); + m_diffMixModel->getMatrixTransProp( m_bdiff ); m_diff_temp_ok = true; m_diff_mix_ok = false; } @@ -1221,8 +1221,8 @@ namespace Cantera { void LiquidTransport::stefan_maxwell_solve() { int i, j, a; doublereal tmp; - m_B.resize(m_nsp, m_nDim); - m_A.resize(m_nsp, m_nsp); + m_B.resize(m_nsp, m_nDim, 0.0); + m_A.resize(m_nsp, m_nsp, 0.0); //! grab a local copy of the molecular weights const vector_fp& M = m_thermo->molecularWeights(); diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 7aafc4859..49613778b 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -58,10 +58,10 @@ namespace Cantera { m_thermo = thermo; int nsp = thermo->nSpecies(); - m_Aij.resize(nsp,nsp); - m_Dij.resize(nsp,nsp); - m_Eij.resize(nsp,nsp); - m_Sij.resize(nsp,nsp); + m_Aij.resize( nsp, nsp, 0.0 ); + m_Dij.resize( nsp, nsp, 0.0 ); + m_Eij.resize( nsp, nsp, 0.0 ); + m_Sij.resize( nsp, nsp, 0.0 ); std::string speciesA; std::string speciesB; @@ -350,7 +350,7 @@ namespace Cantera { void LTI_Pairwise_Interaction::setParameters( LiquidTransportParams& trParam ) { int nsp = m_thermo->nSpecies(); - m_diagonals.resize(nsp); + m_diagonals.resize(nsp, 0); for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; @@ -386,24 +386,21 @@ namespace Cantera { return value; } - DenseMatrix LTI_Pairwise_Interaction::getMatrixTransProp( doublereal *speciesValues ) { + void LTI_Pairwise_Interaction::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); + m_thermo->getMoleFractions( molefracs ); - DenseMatrix tmp; - tmp.resize(nsp,nsp); + mat.resize( nsp, nsp, 0.0 ); for ( int i = 0; i < nsp; i++ ) for ( int j = 0; j < i; j++ ) - tmp(i,j) = tmp(j,i) = m_Dij(i,j) * exp( - m_Eij(i,j) / temp ); + mat(i,j) = mat(j,i) = m_Dij(i,j) * exp( - m_Eij(i,j) / temp ); for ( int i = 0; i < nsp; i++ ) - if ( tmp(i,i) == 0.0 && m_diagonals[i] ) - tmp(i,i) = m_diagonals[i]->getSpeciesTransProp() ; - - return tmp; + if ( mat(i,i) == 0.0 && m_diagonals[i] ) + mat(i,i) = m_diagonals[i]->getSpeciesTransProp() ; } @@ -438,8 +435,8 @@ namespace Cantera { void LTI_StokesEinstein::setParameters( LiquidTransportParams& trParam ) { int nsp = m_thermo->nSpecies(); - m_viscosity.resize(nsp); - m_hydroRadius.resize(nsp); + m_viscosity.resize( nsp, 0 ); + m_hydroRadius.resize( nsp, 0 ); for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; m_viscosity[k] = ltd.viscosity; @@ -447,7 +444,7 @@ namespace Cantera { } } - DenseMatrix LTI_StokesEinstein::getMatrixTransProp( doublereal *speciesValues ) { + void LTI_StokesEinstein::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); @@ -460,17 +457,14 @@ namespace Cantera { radiusSpec[k] = m_hydroRadius[k]->getSpeciesTransProp() ; } - DenseMatrix tmp; - tmp.resize(nsp,nsp); + mat.resize(nsp,nsp, 0.0); for (int i = 0; i < nsp; i++) for (int j = 0; j < nsp; j++) { - tmp(i,j) = GasConstant * temp + mat(i,j) = GasConstant * temp / ( 6.0 * Pi * radiusSpec[i] * viscSpec[j] ) ; } delete radiusSpec; delete viscSpec; - - return tmp; } diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 9267999c4..1805f1560 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -154,8 +154,8 @@ namespace Cantera { throw NotImplemented("LiquidTranInteraction::getMixTransProp"); } - virtual DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { - //return m_Dij; + virtual void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { + //mat = m_Dij; throw NotImplemented("LiquidTranInteraction::getMixTransProp"); } @@ -276,12 +276,12 @@ namespace Cantera { /** * Takes the separate species transport properties * as input (this method does not know what - * transport property it is at this point. + * transport property it is at this point). */ doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } protected: @@ -323,7 +323,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } protected: @@ -366,7 +366,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } protected: @@ -440,7 +440,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) { return m_Eij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } protected: @@ -499,7 +499,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) ; + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; protected: @@ -536,7 +536,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - DenseMatrix getMatrixTransProp( doublereal* speciesValues = 0 ) ; + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; protected: From 86b5fe7dca9f8d8b114e2f4284a58954bfc3401c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Jan 2010 20:40:39 +0000 Subject: [PATCH 099/446] merging. --- tools/doc/Cantera.cfg.in | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index a7238aad6..a93e74080 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -720,8 +720,6 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ VPSSMgrFactory.cpp \ PDSS_ConstVol.h \ PDSS_ConstVol.cpp \ - PDSS_SSVol.h \ - PDSS_SSVol.cpp \ PDSS_IdealGas.h \ PDSS_IdealGas.cpp \ PDSS_Water.h \ @@ -730,6 +728,8 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ PDSS_HKFT.cpp \ PDSS_IonsFromNeutral.h \ PDSS_IonsFromNeutral.cpp \ + PDSS_SSVol.h \ + PDSS_SSVol.cpp \ IdealSolnGasVPSS.h \ IdealSolnGasVPSS.cpp \ ConstDensityThermo.h \ From 7e39fb0ad05abad8679ec57f89e2a7608502d099 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 16 Jan 2010 17:55:02 +0000 Subject: [PATCH 100/446] Eliminated an error --- tools/doc/Cantera.cfg.in | 1 - 1 file changed, 1 deletion(-) diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index 7631a0397..a4d4c9397 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -669,7 +669,6 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ PDSS.h \ PDSS.cpp \ SpeciesThermo.h \ -<<<<<<< .working NasaThermo.h \ NasaPoly1.h \ NasaPoly2.h \ From 8c9a3bdf4b0cd020cc68469caa55ff8c73e2e706 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 16 Jan 2010 18:09:44 +0000 Subject: [PATCH 101/446] Fixed errors in the formulation of the base class. This left unsatisfied externals in applications. --- Cantera/src/transport/LiquidTransport.cpp | 6 +-- Cantera/src/transport/LiquidTransport.h | 21 ++++---- Cantera/src/transport/TransportBase.h | 64 ++++++++++++++++------- Cantera/src/transport/WaterTransport.h | 4 +- 4 files changed, 61 insertions(+), 34 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index bb19b56c1..e25a4da36 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -616,8 +616,8 @@ namespace Cantera { } - //! Compute the electric current density in A/m^2 - /** + // Compute the electric current density in A/m^2 + /* * The electric current is computed first by computing the * species diffusive fluxes using the Stefan Maxwell solution * and then the current, \f$ \vec{i} \f$ by summing over @@ -649,7 +649,7 @@ namespace Cantera { set_Grad_X(grad_X); set_Grad_V(grad_V); - doublereal *fluxes = new doublereal( m_nsp * m_nDim ); + doublereal *fluxes = new doublereal(m_nsp * m_nDim); getSpeciesFluxesExt(ldf, fluxes); diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 767629bcf..063c37d0b 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -337,7 +337,7 @@ namespace Cantera { //! Compute the mixture electrical conductivity from //! the Stefan-Maxwell equation. - /** + /*! * To compute the mixture electrical conductance, the Stefan * Maxwell equation is solved for zero species gradients and * for unit potential gradient, \f$ \nabla V \f$. @@ -355,10 +355,10 @@ namespace Cantera { * \f] * */ - doublereal getElectricConduct( ); + virtual doublereal getElectricConduct(); //! Compute the electric current density in A/m^2 - /** + /*! * The electric current is computed first by computing the * species diffusive fluxes using the Stefan Maxwell solution * and then the current, \f$ \vec{i} \f$ by summing over @@ -378,14 +378,13 @@ namespace Cantera { * @param grad_V The electrostatic potential gradient. * @param current The electric current in A/m^2. */ - void getElectricCurrent(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_V, - doublereal* current) ; - + virtual void getElectricCurrent(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current); //! Get the species diffusive velocities wrt to diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index fdf1a24f1..24ad9d137 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -368,26 +368,54 @@ namespace Cantera { //@} - //! Compute the mixture electrical conductivity - doublereal getElectricConduct( ); - - //! Compute the electric current + //! Compute the mixture electrical conductivity (S m-1) at the current + //! conditions of the phase (Siemens m-1) /*! - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * @param grad_X The gradient of the mole fraction - * @param ldf Leading dimension of the grad_V and current vectors. - * @param grad_V The electrostatic potential gradient. - * @param current The electric current in A/m^2. + * The electrical conductivity, \f$ \sigma \f$, relates the electric + * current density, J, to the electric field, E. + * + * \f[ + * \vec{J} = \sigma \vec{E} + * \f] + * + * We assume here that the mixture electrical conductivity is an + * isotropic quantity, at this stage. Tensors may be included at a + * later time. + * + * The conductivity is the reciprocal of the resistivity. + * + * The units are Siemens m-1, where 1 S = 1 A / volt = 1 s^3 A^2 /kg /m^2 */ - void getElectricCurrent(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_V, - doublereal* current) ; + virtual doublereal getElectricConductivity() + { + err("getElectricConductivity"); return 0.0; + } + + //! Compute the electric current density in A/m^2 + /*! + * Calculates the electric current density as a vector, given + * the gradients of the field variables. + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_X The gradient of the mole fraction + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. this is a vector + * of length ndim + */ + virtual void getElectricCurrent(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current) + { + err("getElectricCurrent"); + } + //! Get the species diffusive mass fluxes wrt to //! the mass averaged velocity, diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index b4ad85348..6dc61555d 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -27,7 +27,7 @@ using namespace std; #include "LiquidTransportParams.h" namespace Cantera { - + //! @{ const int LVISC_CONSTANT = 0; const int LVISC_WILKES = 1; const int LVISC_MIXTUREAVG = 2; @@ -35,7 +35,7 @@ namespace Cantera { const int LDIFF_MIXDIFF_UNCORRECTED = 0; const int LDIFF_MIXDIFF_FLUXCORRECTED = 1; const int LDIFF_MULTICOMP_STEFANMAXWELL = 2; - + //! @} class TransportParams; From be731888a48da4265707723fda7d73d9a1e22b48 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 19 Jan 2010 18:27:34 +0000 Subject: [PATCH 102/446] Fixed a UMR error, due to a missing initialization list. --- Cantera/src/transport/LiquidTransport.cpp | 2 +- Cantera/src/transport/LiquidTransportData.cpp | 23 ++- Cantera/src/transport/LiquidTransportData.h | 25 +-- .../src/transport/LiquidTransportParams.cpp | 14 +- Cantera/src/transport/LiquidTransportParams.h | 146 +++++++++--------- 5 files changed, 113 insertions(+), 97 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index e25a4da36..bce2d57af 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -243,7 +243,7 @@ namespace Cantera { //for each species, assign viscosity model and coefficients for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; - if ( ltd.speciesDiffusivity >= 0 ) { + if (ltd.speciesDiffusivity != 0) { cout << "Warning: diffusion coefficient data for " << m_thermo->speciesName(k) << endl diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 17ba9f1e0..25dcd3c82 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -44,16 +44,31 @@ namespace Cantera { E /= GasConstant; } + LiquidTransportData::LiquidTransportData() : + speciesName("-"), + hydroRadius(0), + viscosity(0), + thermalCond(0), + electCond(0), + speciesDiffusivity(0) + { + } - //! Copy constructor - LiquidTransportData::LiquidTransportData( const LiquidTransportData &right ) + // Copy constructor + LiquidTransportData::LiquidTransportData(const LiquidTransportData &right) : + speciesName("-"), + hydroRadius(0), + viscosity(0), + thermalCond(0), + electCond(0), + speciesDiffusivity(0) { *this = right; //use assignment operator to do other work } - //! Assignment operator - LiquidTransportData& LiquidTransportData::operator=(const LiquidTransportData& right ) + // Assignment operator + LiquidTransportData& LiquidTransportData::operator=(const LiquidTransportData& right) { if (&right != this) { speciesName = right.speciesName; diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index 29fb0bbc9..89708b92b 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -177,12 +177,11 @@ namespace Cantera { public: - LiquidTransportData() : - speciesName("-") - { - } + //! Default constructor + LiquidTransportData(); + //! Copy constructor - LiquidTransportData( const LiquidTransportData &right ) ; + LiquidTransportData(const LiquidTransportData &right) ; //! Assignment operator LiquidTransportData& operator=(const LiquidTransportData& right ); @@ -213,7 +212,7 @@ namespace Cantera { //! Class LTPspecies_Const holds transport parameters for a //! specific liquid-phase species when the transport property //! is just a constant value. - /** + /*! * As an example of the input required for LTPspecies_Const * consider the following XML fragment * @@ -229,7 +228,7 @@ namespace Cantera { * * \endverbatim */ - class LTPspecies_Const : public LTPspecies{ + class LTPspecies_Const : public LTPspecies { public: @@ -269,7 +268,7 @@ namespace Cantera { //! Class LTPspecies_Arrhenius holds transport parameters for a //! specific liquid-phase species when the transport property //! is expressed in Arrhenius form. - /** + /*! * As an example of the input required for LTPspecies_Arrhenius * consider the following XML fragment * @@ -307,7 +306,7 @@ namespace Cantera { //! Return the pure species value for this transport property evaluated //! from the Arrhenius expression - /** + /*! * In general the Arrhenius expression is * * \f[ @@ -343,7 +342,8 @@ namespace Cantera { doublereal m_logProp; //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take + /*! + * Currently just a place holder, but this method could take * the composition from the thermo object and adjust coefficients * accoding to some unspecified model. */ @@ -355,7 +355,7 @@ namespace Cantera { //! Class LTPspecies_Poly holds transport parameters for a //! specific liquid-phase species when the transport property //! is expressed as a polynomial in temperature. - /** + /*! * As an example of the input required for LTPspecies_Poly * consider the following XML fragment * @@ -405,7 +405,8 @@ namespace Cantera { doublereal m_prop; //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take + /*! + * Currently just a place holder, but this method could take * the composition from the thermo object and adjust coefficients * accoding to some unspecified model. */ diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 49613778b..f7e5466ee 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -321,7 +321,7 @@ namespace Cantera { } - doublereal LTI_Log_MoleFracs::getMixTransProp( std::vector LTPptrs ) { + doublereal LTI_Log_MoleFracs::getMixTransProp(std::vector LTPptrs) { int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); @@ -331,7 +331,7 @@ namespace Cantera { doublereal value = 0; for ( int k = 0; k < nsp; k++) { - value += log( LTPptrs[k]->getSpeciesTransProp() ) * LTPptrs[k]->getMixWeight( ) * molefracs[k]; + value += log( LTPptrs[k]->getSpeciesTransProp() ) * LTPptrs[k]->getMixWeight() * molefracs[k]; } for ( int i = 0; i < nsp; i++ ) @@ -348,18 +348,18 @@ namespace Cantera { - void LTI_Pairwise_Interaction::setParameters( LiquidTransportParams& trParam ) { + void LTI_Pairwise_Interaction::setParameters(LiquidTransportParams& trParam) { int nsp = m_thermo->nSpecies(); m_diagonals.resize(nsp, 0); for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; - if ( ltd.speciesDiffusivity ) + if (ltd.speciesDiffusivity) m_diagonals[k] = ltd.speciesDiffusivity; } } - doublereal LTI_Pairwise_Interaction::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { + doublereal LTI_Pairwise_Interaction::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight) { int nsp = m_thermo->nSpecies(); doublereal molefracs[nsp]; @@ -373,7 +373,7 @@ namespace Cantera { } - doublereal LTI_Pairwise_Interaction::getMixTransProp( std::vector LTPptrs ) { + doublereal LTI_Pairwise_Interaction::getMixTransProp(std::vector LTPptrs) { int nsp = m_thermo->nSpecies(); doublereal molefracs[nsp]; @@ -386,7 +386,7 @@ namespace Cantera { return value; } - void LTI_Pairwise_Interaction::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { + void LTI_Pairwise_Interaction::getMatrixTransProp(DenseMatrix &mat, doublereal *speciesValues) { int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 1805f1560..e1c10e6fe 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -33,57 +33,57 @@ namespace Cantera { }; - //! Composition dependence type for liquid mixture transport properties - /*! - * Types of temperature dependencies: - * - 0 - Mixture calculations with this property are not allowed - * - 1 - Use solvent (species 0) properties - * - 2 - Properties weighted linearly by mole fractions - * - 3 - Properties weighted linearly by mass fractions - * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) - * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) - * - * \verbatim - * - * - * - * - * LiCl(L) - * KCl(L) - * -1.0 - * 1.0E-1 - * - * - * - * - * - * - * Li+ - * K+ - * 1.5 - * - * - * K+ - * Cl- - * 1.0 - * - * - * Li+ - * Cl- - * 1.2 - * - * - * - * - * - * - * - * - * - * - * \endverbatim - * - */ + //! Composition dependence type for liquid mixture transport properties + /*! + * Types of temperature dependencies: + * - 0 - Mixture calculations with this property are not allowed + * - 1 - Use solvent (species 0) properties + * - 2 - Properties weighted linearly by mole fractions + * - 3 - Properties weighted linearly by mass fractions + * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) + * + * \verbatim + * + * + * + * + * LiCl(L) + * KCl(L) + * -1.0 + * 1.0E-1 + * + * + * + * + * + * + * Li+ + * K+ + * 1.5 + * + * + * K+ + * Cl- + * 1.0 + * + * + * Li+ + * Cl- + * 1.2 + * + * + * + * + * + * + * + * + * + * + * \endverbatim + * + */ enum LiquidTranMixingModel { LTI_MODEL_NOTSET=-1, LTI_MODEL_NONE, @@ -120,9 +120,9 @@ namespace Cantera { public: //! Constructor - /** - * @param tp_ind Index indicating transport property type (i.e. viscosity) - */ + /** + * @param tp_ind Index indicating transport property type (i.e. viscosity) + */ LiquidTranInteraction( TransportPropertyList tp_ind = TP_UNKNOWN ); //! Copy constructor @@ -140,7 +140,7 @@ namespace Cantera { * @param thermo Pointer to thermo object */ virtual void init( const XML_Node &compModelNode = 0, - thermo_t* thermo = 0 ); + thermo_t* thermo = 0 ); virtual void setParameters( LiquidTransportParams& trParam ) { ; } @@ -260,9 +260,9 @@ namespace Cantera { public: LTI_Solvent( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_SOLVENT; - } + { + m_model = LTI_MODEL_SOLVENT; + } //! Copy constructor // LTI_Solvent( const LTI_Solvent &right ); @@ -301,9 +301,9 @@ namespace Cantera { public: LTI_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_MOLEFRACS; - } + { + m_model = LTI_MODEL_MOLEFRACS; + } //! Copy constructor @@ -344,9 +344,9 @@ namespace Cantera { public: LTI_MassFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_MASSFRACS; - } + { + m_model = LTI_MODEL_MASSFRACS; + } //! Copy constructor @@ -418,9 +418,9 @@ namespace Cantera { public: LTI_Log_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_LOG_MOLEFRACS; - } + { + m_model = LTI_MODEL_LOG_MOLEFRACS; + } //! Copy constructor @@ -475,9 +475,9 @@ namespace Cantera { public: LTI_Pairwise_Interaction( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_PAIRWISE_INTERACTION; - } + { + m_model = LTI_MODEL_PAIRWISE_INTERACTION; + } //! Copy constructor @@ -512,9 +512,9 @@ namespace Cantera { public: LTI_StokesEinstein( TransportPropertyList tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_STOKES_EINSTEIN; - } + { + m_model = LTI_MODEL_STOKES_EINSTEIN; + } //! Copy constructor From e3789e48e30b85b85f68b6440c9f369e26d2547e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 28 Jan 2010 03:28:45 +0000 Subject: [PATCH 103/446] Fixed an obvious error with the stefan maxwell formulation for liquid transport. --- Cantera/src/transport/LiquidTransport.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index bce2d57af..3c15c9931 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -1271,8 +1271,7 @@ namespace Cantera { m_Grad_mu[a*m_nsp + i] = m_chargeSpecies[i] * Faraday * m_Grad_V[a] //+ (m_volume_spec[i] - M[i]/dens_) * m_Grad_P[a] - + GasConstant * T * m_Grad_X[a*m_nsp+i] - * ( 1.0 * m_Grad_lnAC[i] ) / xi_denom; + + GasConstant * T * m_Grad_X[a*m_nsp+i] * ( 1.0 + m_Grad_lnAC[i] ) / xi_denom; } } From 47ef65b849e7007f70f889828d22ee56f134db0a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 30 Jan 2010 22:46:07 +0000 Subject: [PATCH 104/446] Fixed a memory leak error, due to faulty logic in the destructor. --- Cantera/src/thermo/ThermoPhase.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index eb0e60250..61088dcd2 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -49,11 +49,13 @@ namespace Cantera { ThermoPhase::~ThermoPhase() { for (int k = 0; k < m_kk; k++) { - if (!m_speciesData[k]) { + if (m_speciesData[k]) { delete m_speciesData[k]; + m_speciesData[k] = 0; } } delete m_spthermo; + m_spthermo = 0; } /** @@ -95,8 +97,9 @@ namespace Cantera { * We need to destruct first */ for (int k = 0; k < m_kk; k++) { - if (!m_speciesData[k]) { + if (m_speciesData[k]) { delete m_speciesData[k]; + m_speciesData[k] = 0; } } if (m_spthermo) { From 59c867ebae852ba3fa38d93f657bc64930a6297b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 31 Jan 2010 00:26:54 +0000 Subject: [PATCH 105/446] Fixed some malloc errors that left some memory unfreed. --- Cantera/src/transport/LiquidTransport.cpp | 118 +++++++++--------- .../src/transport/LiquidTransportParams.cpp | 46 ++++++- Cantera/src/transport/LiquidTransportParams.h | 6 +- Cantera/src/transport/TransportFactory.cpp | 26 ++-- 4 files changed, 113 insertions(+), 83 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 3c15c9931..ee4756a03 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -156,22 +156,22 @@ namespace Cantera { return (dynamic_cast(tr)); } - LiquidTransport::~LiquidTransport() { + LiquidTransport::~LiquidTransport() { - //These are constructed in TransportFactory::newLTP - for ( int k = 0; k < m_nsp; k++) { - if ( m_viscTempDep_Ns[k] ) delete m_viscTempDep_Ns[k]; - if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; - if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k]; - if ( m_diffTempDep_Ns[k] ) delete m_diffTempDep_Ns[k]; - } - //These are constructed in TransportFactory::newLTI - if ( m_viscMixModel ) delete m_viscMixModel; - if ( m_lambdaMixModel ) delete m_lambdaMixModel; - if ( m_diffMixModel ) delete m_diffMixModel; - //if ( m_radiusMixModel ) delete m_radiusMixModel; + //These are constructed in TransportFactory::newLTP + for ( int k = 0; k < m_nsp; k++) { + if ( m_viscTempDep_Ns[k] ) delete m_viscTempDep_Ns[k]; + if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; + if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k]; + if ( m_diffTempDep_Ns[k] ) delete m_diffTempDep_Ns[k]; + } + //These are constructed in TransportFactory::newLTI + if ( m_viscMixModel ) delete m_viscMixModel; + if ( m_lambdaMixModel ) delete m_lambdaMixModel; + if ( m_diffMixModel ) delete m_diffMixModel; + //if ( m_radiusMixModel ) delete m_radiusMixModel; - } + } // Initialize the transport object /* @@ -264,13 +264,17 @@ namespace Cantera { * present class). */ m_viscMixModel = tr.viscosity; + tr.viscosity = 0; m_lambdaMixModel = tr.thermalCond; - //m_radiusMixModel = tr.hydroRadius; + tr.thermalCond = 0; + m_diffMixModel = tr.speciesDiffusivity; + tr.speciesDiffusivity = 0; + m_bdiff.resize(m_nsp,m_nsp, 0.0); //Don't really need to update this here. //It is updated in updateDiff_T() - m_diffMixModel->getMatrixTransProp( m_bdiff ); + m_diffMixModel->getMatrixTransProp(m_bdiff); m_mode = tr.mode_; @@ -281,8 +285,9 @@ namespace Cantera { m_concentrations.resize(m_nsp, 0.0); m_actCoeff.resize(m_nsp, 0.0); m_chargeSpecies.resize(m_nsp, 0.0); - for ( int i = 0; i < m_nsp; i++ ) - m_chargeSpecies[i] = m_thermo->charge( i ); + for ( int i = 0; i < m_nsp; i++ ) { + m_chargeSpecies[i] = m_thermo->charge(i); + } m_volume_spec.resize(m_nsp, 0.0); m_Grad_lnAC.resize(m_nsp, 0.0); m_spwork.resize(m_nsp, 0.0); @@ -333,17 +338,6 @@ namespace Cantera { m_viscmix = m_viscMixModel->getMixTransProp( m_viscTempDep_Ns ); return m_viscmix; - - /* - // update m_viscSpecies[] if necessary - if (!m_visc_temp_ok) { - updateViscosity_T(); - } - - if (!m_visc_conc_ok) { - updateViscosities_C(); - } - */ } // Returns the pure species viscosities for all species @@ -382,7 +376,7 @@ namespace Cantera { } - //================================================================ + //================================================================ // Return the thermal conductivity of the solution /* @@ -397,8 +391,8 @@ namespace Cantera { update_C(); if (!m_cond_mix_ok) { - m_lambda = m_lambdaMixModel->getMixTransProp( m_lambdaTempDep_Ns ); - m_cond_mix_ok = true; + m_lambda = m_lambdaMixModel->getMixTransProp( m_lambdaTempDep_Ns ); + m_cond_mix_ok = true; } return m_lambda; @@ -638,12 +632,12 @@ namespace Cantera { * @param current The electric current in A/m^2. */ void LiquidTransport::getElectricCurrent(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_V, - doublereal* current) { + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* current) { set_Grad_T(grad_T); set_Grad_X(grad_X); @@ -690,9 +684,9 @@ namespace Cantera { * length = ldx * ndim */ void LiquidTransport::getSpeciesVdiff(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* Vdiff) { + const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, doublereal* Vdiff) { set_Grad_T(grad_T); set_Grad_X(grad_X); getSpeciesVdiffExt(ldf, Vdiff); @@ -709,12 +703,12 @@ namespace Cantera { * \f] */ void LiquidTransport::getSpeciesVdiffES(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_V, - doublereal* Vdiff) { + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_V, + doublereal* Vdiff) { set_Grad_T(grad_T); set_Grad_X(grad_X); set_Grad_V(grad_V); @@ -1305,9 +1299,9 @@ namespace Cantera { && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "Unknown reference velocity provided."); + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ m_B(i,0) = m_Grad_mu[i] / (GasConstant * T); @@ -1315,8 +1309,8 @@ namespace Cantera { for (j = 0; j < m_nsp; j++){ if (j != i) { if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; @@ -1341,9 +1335,9 @@ namespace Cantera { && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "Unknown reference velocity provided."); + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ m_B(i,0) = m_Grad_mu[i] / (GasConstant * T); @@ -1352,8 +1346,8 @@ namespace Cantera { for (j = 0; j < m_nsp; j++) { if (j != i) { if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; @@ -1381,9 +1375,9 @@ namespace Cantera { && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "Unknown reference velocity provided."); + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ m_B(i,0) = m_Grad_mu[i] / (GasConstant * T); @@ -1393,8 +1387,8 @@ namespace Cantera { for (j = 0; j < m_nsp; j++) { if (j != i) { if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); + throw CanteraError("LiquidTransport::stefan_maxwell_solve", + "m_bdiff has zero entry in non-diagonal."); tmp = m_molefracs_tran[j] / m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index f7e5466ee..0caeabc59 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -128,7 +128,46 @@ namespace Cantera { return *this; } - + //==================================================================================================================== + LiquidTransportParams::LiquidTransportParams() : + viscosity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), + model_speciesDiffusivity(LTI_MODEL_NOTSET), model_hydroradius(LTI_MODEL_NOTSET) + { + + } + //==================================================================================================================== + LiquidTransportParams::~LiquidTransportParams() + { + delete viscosity; + delete thermalCond; + delete speciesDiffusivity; + delete electCond; + delete hydroRadius; + } + + //==================================================================================================================== + LiquidTransportParams::LiquidTransportParams(const LiquidTransportParams &right) : + viscosity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), + model_speciesDiffusivity(LTI_MODEL_NOTSET), model_hydroradius(LTI_MODEL_NOTSET) + { + throw CanteraError("LiquidTransportParams(const LiquidTransportParams &right)","not implemented"); + } + + //==================================================================================================================== + + LiquidTransportParams& LiquidTransportParams::operator=(const LiquidTransportParams & right) + { + if (&right != this) { + return *this; + } + + throw CanteraError("LiquidTransportParams(const LiquidTransportParams &right)","not implemented"); + return *this; + + } + + //==================================================================================================================== + doublereal LTI_Solvent::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { @@ -236,10 +275,7 @@ namespace Cantera { } - - - - doublereal LTI_MassFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { + doublereal LTI_MassFracs::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { int nsp = m_thermo->nSpecies(); doublereal massfracs[nsp]; diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index e1c10e6fe..0757978a7 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -196,8 +196,10 @@ namespace Cantera { public: - LiquidTransportParams() {} - ~LiquidTransportParams() {} + LiquidTransportParams(); + ~LiquidTransportParams(); + LiquidTransportParams(const LiquidTransportParams &right); + LiquidTransportParams & operator=(const LiquidTransportParams &right); //! Species transport parameters std::vector LTData; diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 2c6eb8822..a69ba0d77 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -1047,25 +1047,25 @@ namespace Cantera { * instance of TransportParams containing the transport data for * these species read from the file. */ - void TransportFactory::getLiquidInteractionsTransportData( const XML_Node &transportNode, - XML_Node& log, - const std::vector &names, - LiquidTransportParams& trParam) - { - + void + TransportFactory::getLiquidInteractionsTransportData(const XML_Node &transportNode, + XML_Node& log, + const std::vector &names, + LiquidTransportParams& trParam) + { try { int num = transportNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { //tranTypeNode is a type of transport property like viscosity XML_Node &tranTypeNode = transportNode.child(iChild); - if ( tranTypeNode.hasChild("compositionDependence")) { + if (tranTypeNode.hasChild("compositionDependence")) { //compDepNode contains the interaction model XML_Node &compDepNode = tranTypeNode.child("compositionDependence"); std::string nodeName = tranTypeNode.name(); - switch ( m_tranPropMap[nodeName] ) { + switch (m_tranPropMap[nodeName]) { break; case TP_VISCOSITY: trParam.viscosity = newLTI( compDepNode, @@ -1083,9 +1083,9 @@ namespace Cantera { trParam ); break; case TP_HYDRORADIUS: - trParam.hydroRadius = newLTI( compDepNode, - m_tranPropMap[nodeName], - trParam ); + trParam.hydroRadius = newLTI(compDepNode, + m_tranPropMap[nodeName], + trParam); break; case TP_ELECTCOND: trParam.electCond = newLTI( compDepNode, @@ -1123,9 +1123,7 @@ namespace Cantera { else { int linenum; throw TransportDBError( linenum, "Unknown attribute " + velocityBasis + " for node. "); - } - - + } } } From f9d90adbcf0356ba5688816d3255ab8583033d80 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 8 Feb 2010 15:18:52 +0000 Subject: [PATCH 106/446] Added an example of a successful setup on RHEL5 using python 2.6.4 and matlab 7.9 --- .../linux_rhel5_64_gcc424_dbg_python264_numpy | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100755 docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy diff --git a/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy b/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy new file mode 100755 index 000000000..f257eac04 --- /dev/null +++ b/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy @@ -0,0 +1,112 @@ +#!/bin/sh +# +# This is currently the test base. Meaning that the blessed versions +# of all test problems are created from this configuration. +# +CANTERA_CONFIG_PREFIX=${HOME}/arch/linux64_gcc424/cantera-1.8_liquidTransportDevelop +export CANTERA_CONFIG_PREFIX + +SET_PYTHON_SITE_PACKAGE_TOPDIR=y +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_CMD=/home/hkmoffa/arch/linux64_gcc424/python-2.6.4/bin/python +export PYTHON_CMD + +PYTHON_PACKAGE='full' +#PYTHON_PACKAGE='minimal' +export PYTHON_PACKAGE + +DEBUG_MODE='y' +export DEBUG_MODE + +WITH_IDEAL_SOLUTIONS="y" +export WITH_IDEAL_SOLUTIONS + +WITH_ELECTROLYTES="y" +export WITH_ELECTROLYTES + +WITH_VCSNONIDEAL="y" +export WITH_VCSNONIDEAL + +WITH_H298MODIFY_CAPABILITY='y' +export WITH_H298MODIFY_CAPABILITY + +BUILD_MATLAB_TOOLBOX="y" +export BUILD_MATLAB_TOOLBOX + +INSTALL_BIN=config/install-sh +export INSTALL_BIN + +MATLAB_CMD="/usr/local/matlab/7.9/bin/matlab" +export MATLAB_CMD + +BUILD_F90_INTERFACE="y" +export BUILD_F90_INTERFACE + +NUMARRAY_HOME='' +export NUMARRAY_HOME + +USE_NUMPY='y' +export USE_NUMPY + +NUMPY_INC_DIR="/home/hkmoffa/arch/linux64_gcc424/python-2.6.4/lib/python2.6/site-packages/numpy/core/include" +export NUMPY_INC_DIR + +GRAPHVIZDIR=${HOME}'/arch/linux/bin' +export GRAPHVIZDIR + +# +# +USE_NUMERIC="n" +export USE_NUMERIC + +BUILD_WITH_F2C="n" +export BUILD_WITH_F2C + +BITCOMPILE="64" +export BITCOMPILE + +AFLAGS='DEBUG' + +CXX='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/g++' +export CXX + +CXX_DEPENDS='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/g++ -MM' +export CXX_DEPENDS + +CC='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/gcc' +export CC + +F77='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/gfortran' +export F77 + +CFLAGS="-g -Wall" +export CFLAGS + +CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL" +export CXXFLAGS + +FFLAGS="-g -DDEBUG_HKM -fno-second-underscore" +export FFLAGS + +LDFLAGS=' ' +export LDFLAGS + +LCXX_END_LIBS="-lgfortran -lm -lstdc++" +export LCXX_END_LIBS + +EXTRA_LINK=" " +export EXTRA_LINK + +MAKE=gmake +export MAKE + +USE_SUNDIALS='y' +export USE_SUNDIALS +SUNDIALS_HOME='/home/hkmoffa/arch/linux64_gcc424/sundials-2.4.0_dbg' +export SUNDIALS_HOME + +./preconfig From d9b4031614dfc3d74f33467326215a79f60f135a Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Sat, 27 Feb 2010 00:47:47 +0000 Subject: [PATCH 107/446] Added excess volume capability for GibbsExcessVPSSTP and children Corrected activity coefficients calculation for >2 species --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 11 +- Cantera/src/thermo/GibbsExcessVPSSTP.h | 52 ++- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 324 +++++++++++++++++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 92 +++++- Cantera/src/thermo/MargulesVPSSTP.cpp | 322 +++++++++++++++++- Cantera/src/thermo/MargulesVPSSTP.h | 65 +++- Cantera/src/thermo/PDSS_SSVol.cpp | 4 +- Cantera/src/thermo/State.cpp | 4 + Cantera/src/thermo/State.h | 3 + Cantera/src/thermo/ThermoPhase.h | 47 ++- Cantera/src/thermo/VPSSMgr.cpp | 4 +- Cantera/src/thermo/VPStandardStateTP.h | 32 +- 12 files changed, 895 insertions(+), 65 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index fd7e460c3..13ba5ce75 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -65,7 +65,8 @@ namespace Cantera { moleFractions_ = b.moleFractions_; lnActCoeff_Scaled_ = b.lnActCoeff_Scaled_; dlnActCoeffdT_Scaled_ = b.dlnActCoeffdT_Scaled_; - dlnActCoeffdlnC_Scaled_ = b.dlnActCoeffdlnC_Scaled_; + dlnActCoeffdlnX_Scaled_ = b.dlnActCoeffdlnX_Scaled_; + dlnActCoeffdlnN_Scaled_ = b.dlnActCoeffdlnN_Scaled_; m_pp = b.m_pp; return *this; @@ -156,7 +157,9 @@ namespace Cantera { } void GibbsExcessVPSSTP::calcDensity() { - double *vbar = &m_pp[0]; + doublereal* vbar = NULL; + vbar = new doublereal[m_kk]; + // double *vbar = &m_pp[0]; getPartialMolarVolumes(vbar); doublereal vtotal = 0.0; @@ -165,6 +168,7 @@ namespace Cantera { } doublereal dd = meanMolecularWeight() / vtotal; State::setDensity(dd); + delete [] vbar; } void GibbsExcessVPSSTP::setState_TP(doublereal t, doublereal p) { @@ -320,7 +324,8 @@ namespace Cantera { moleFractions_.resize(m_kk); lnActCoeff_Scaled_.resize(m_kk); dlnActCoeffdT_Scaled_.resize(m_kk); - dlnActCoeffdlnC_Scaled_.resize(m_kk); + dlnActCoeffdlnX_Scaled_.resize(m_kk); + dlnActCoeffdlnN_Scaled_.resize(m_kk); m_pp.resize(m_kk); } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 185c2be27..3e8b7cd10 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -301,6 +301,23 @@ namespace Cantera { virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { err("getdlnActCoeffdT"); } + + //! Get the array of change in the log activity coefficients w.r.t. change in state (change temp, change mole fractions) + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can gradX/X. + * + * @param dT Input of temperature change + * @param dX Input vector of changes in mole fraction. length = m_kk + * @param dlnActCoeff Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { + err("getdlnActCoeff"); + } //! Get the array of log concentration-like derivatives of the //! log activity coefficients @@ -317,11 +334,33 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of derivatives of the + * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const { - err("getdlnActCoeffdlnC"); + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + err("getdlnActCoeffdlnN"); + } + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. number of moles in + * in a unit volume. ) that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + err("getdlnActCoeffdlnX"); } //@} @@ -562,7 +601,12 @@ namespace Cantera { //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the //! log of theactivity coefficients of the species - mutable std::vector dlnActCoeffdlnC_Scaled_; + mutable std::vector dlnActCoeffdlnN_Scaled_; + + //! Storage for the current derivative values of the + //! gradients with respect to logarithm of the mole fraction of the + //! log of theactivity coefficients of the species + mutable std::vector dlnActCoeffdlnX_Scaled_; //! Temporary storage space that is fair game mutable std::vector m_pp; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index df90bac16..4e95c4f30 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -197,7 +197,8 @@ namespace Cantera { muNeutralMolecule_ = b.muNeutralMolecule_; gammaNeutralMolecule_ = b.gammaNeutralMolecule_; dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_; - dlnActCoeffdlnC_NeutralMolecule_ = b.dlnActCoeffdlnC_NeutralMolecule_; + dlnActCoeffdlnX_NeutralMolecule_ = b.dlnActCoeffdlnX_NeutralMolecule_; + dlnActCoeffdlnN_NeutralMolecule_ = b.dlnActCoeffdlnN_NeutralMolecule_; return *this; } @@ -332,6 +333,13 @@ namespace Cantera { void IonsFromNeutralVPSSTP::getActivityConcentrations(doublereal* c) const { getActivities(c); } + + void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs,vector_fp& charges){ + coeffs = fm_neutralMolec_ions_; + charges = m_speciesCharge; + //for ( int k = 0; k < fm_neutralMolec_ions_[k]; k++ ) + // coeffs.push_back(fm_neutralMolec_ions_[k]); + } // Return the standard concentration for the kth species /* @@ -598,22 +606,47 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of log(mole fraction) + * @param dlnActCoeffdlnX Output vector of log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - void IonsFromNeutralVPSSTP::getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const { + void IonsFromNeutralVPSSTP::getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { s_update_lnActCoeff(); - s_update_dlnActCoeff_dlnC(); + s_update_dlnActCoeff_dlnX(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnC[k] = dlnActCoeffdlnC_Scaled_[k]; + dlnActCoeffdlnX[k] = dlnActCoeffdlnX_Scaled_[k]; + } + } + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN Output vector of log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + void IonsFromNeutralVPSSTP::getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + s_update_lnActCoeff(); + s_update_dlnActCoeff_dlnN(); + + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN[k] = dlnActCoeffdlnN_Scaled_[k]; } } - - - // This is temporary. We will get rid of this void IonsFromNeutralVPSSTP::setTemperature(const doublereal temp) { double p = pressure(); @@ -717,7 +750,7 @@ namespace Cantera { for (k = 0; k < m_kk; k++) { sum += moleFractions_[k]; } - if (fabs(sum) > 1.0E-11) { + if (fabs(sum) > 1.0E-11) { throw CanteraError("IonsFromNeutralVPSSTP::calcNeutralMoleculeMoleFractions", "molefracts don't sum to one: " + fp2str(sum)); } @@ -791,7 +824,129 @@ namespace Cantera { sum += NeutralMolecMoleFractions_[k]; } for (k = 0; k < numNeutralMoleculeSpecies_; k++) { - NeutralMolecMoleFractions_[k] /= sum; + NeutralMolecMoleFractions_[k] /= sum; + } + + break; + + case cIonSolnType_SINGLECATION: + + throw CanteraError("eosType", "Unknown type"); + + break; + + case cIonSolnType_MULTICATIONANION: + + throw CanteraError("eosType", "Unknown type"); + break; + + default: + + throw CanteraError("eosType", "Unknown type"); + break; + + } + } + +// Calculate neutral molecule mole fractions + /* + * This routine calculates the neutral molecule mole + * fraction given the vector of ion mole fractions, + * i.e., the mole fractions from this ThermoPhase. + * Note, this routine basically assumes that there + * is charge neutrality. If there isn't, then it wouldn't + * make much sense. + * + * for the case of cIonSolnType_SINGLEANION, some slough + * in the charge neutrality is allowed. The cation number + * is followed, while the difference in charge neutrality + * is dumped into the anion mole number to fix the imbalance. + */ + void IonsFromNeutralVPSSTP::getNeutralMoleculeMoleGrads(const doublereal * const dx, doublereal *dy) const { + int k, icat, jNeut; + doublereal sumCat; + doublereal sumAnion; + doublereal fmij; + vector_fp y; + y.resize(numNeutralMoleculeSpecies_,0.0); + doublereal sumy, sumdy; + + //! Zero the vector we are trying to find. + for (k = 0; k < numNeutralMoleculeSpecies_; k++) { + dy[k] = 0.0; + } + + + // bool fmSimple = true; + + switch (ionSolnType_) { + + case cIonSolnType_PASSTHROUGH: + + for (k = 0; k < m_kk; k++) { + dy[k] = dx[k]; + } + break; + + case cIonSolnType_SINGLEANION: + + sumCat = 0.0; + sumAnion = 0.0; + + for (k = 0; k < (int) cationList_.size(); k++) { + //! Get the id for the next cation + icat = cationList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + if (jNeut >= 0) { + fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; + AssertTrace(fmij != 0.0); + dy[jNeut] += dx[icat] / fmij; + y[jNeut] += moleFractions_[icat] / fmij; + } + } + + for (k = 0; k < numPassThroughSpecies_; k++) { + icat = passThroughList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + fmij = fm_neutralMolec_ions_[ icat + jNeut * m_kk]; + dy[jNeut] += dx[icat] / fmij; + y[jNeut] += moleFractions_[icat] / fmij; + } + +#ifdef DEBUG_MODE + for (k = 0; k < m_kk; k++) { + moleFractionsTmp_[k] = dx[k]; + } + for (jNeut = 0; jNeut < numNeutralMoleculeSpecies_; jNeut++) { + for (k = 0; k < m_kk; k++) { + fmij = fm_neutralMolec_ions_[k + jNeut * m_kk]; + moleFractionsTmp_[k] -= fmij * dy[jNeut]; + } + } + for (k = 0; k < m_kk; k++) { + if (fabs(moleFractionsTmp_[k]) > 1.0E-13) { + //! Check to see if we have in fact found the inverse. + if (anionList_[0] != k) { + throw CanteraError("", "neutral molecule calc error"); + } else { + //! For the single anion case, we will allow some slippage + if (fabs(moleFractionsTmp_[k]) > 1.0E-5) { + throw CanteraError("", "neutral molecule calc error - anion"); + } + } + } + } +#endif + + // Normalize the Neutral Molecule mole fractions + sumy = 0.0; + sumdy = 0.0; + for (k = 0; k < numNeutralMoleculeSpecies_; k++) { + sumy += y[k]; + sumdy += dy[k]; + } + for (k = 0; k < numNeutralMoleculeSpecies_; k++) { + dy[k] = dy[k]/sumy - y[k]*sumdy/sumy/sumy; } break; @@ -815,6 +970,7 @@ namespace Cantera { } } + void IonsFromNeutralVPSSTP::setMassFractions(const doublereal* const y) { GibbsExcessVPSSTP::setMassFractions(y); calcNeutralMoleculeMoleFractions(); @@ -836,7 +992,7 @@ namespace Cantera { void IonsFromNeutralVPSSTP::setMoleFractions_NoNorm(const doublereal* const x) { GibbsExcessVPSSTP::setMoleFractions_NoNorm(x); calcNeutralMoleculeMoleFractions(); - neutralMoleculePhase_->setMoleFractions(DATA_PTR(NeutralMolecMoleFractions_)); + neutralMoleculePhase_->setMoleFractions_NoNorm(DATA_PTR(NeutralMolecMoleFractions_)); } @@ -1030,7 +1186,8 @@ namespace Cantera { muNeutralMolecule_.resize(numNeutralMoleculeSpecies_); gammaNeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); - dlnActCoeffdlnC_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); + dlnActCoeffdlnX_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); + dlnActCoeffdlnN_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); } static double factorOverlap(const std::vector& elnamesVN , @@ -1243,7 +1400,7 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - lnActCoeff_Scaled_[icat] = fmij * log(gammaNeutralMolecule_[jNeut]); + lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut])/fmij; } // Do the anion list @@ -1273,6 +1430,75 @@ namespace Cantera { } + + // get the gradient in the activity coefficients + + void IonsFromNeutralVPSSTP::getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { + int k, icat, jNeut; + doublereal fmij; + int numNeutMolSpec; + /* + * Get the activity coefficients of the neutral molecules + */ + GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); + if (!geThermo) { + for ( k = 0; k < m_kk; k++ ){ + dlnActCoeff[k] = dX[k]/moleFractions_[k]; + } + return; + } + + numNeutMolSpec = geThermo->nSpecies(); + vector_fp dlnActCoeff_NeutralMolecule(numNeutMolSpec); + vector_fp dX_NeutralMolecule(numNeutMolSpec); + + + getNeutralMoleculeMoleGrads(DATA_PTR(dX),DATA_PTR(dX_NeutralMolecule)); + + // All mole fractions returned to normal + + geThermo->getdlnActCoeff(dT, DATA_PTR(dX_NeutralMolecule), DATA_PTR(dlnActCoeff_NeutralMolecule)); + + switch (ionSolnType_) { + case cIonSolnType_PASSTHROUGH: + break; + case cIonSolnType_SINGLEANION: + + // Do the cation list + for (k = 0; k < (int) cationList_.size(); k++) { + //! Get the id for the next cation + icat = cationList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; + dlnActCoeff[icat] = dlnActCoeff_NeutralMolecule[jNeut]/fmij; + } + + // Do the anion list + icat = anionList_[0]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeff[icat]= 0.0; + + // Do the list of neutral molecules + for (k = 0; k < numPassThroughSpecies_; k++) { + icat = passThroughList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeff[icat] = dlnActCoeff_NeutralMolecule[jNeut]; + } + break; + + case cIonSolnType_SINGLECATION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + case cIonSolnType_MULTICATIONANION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + default: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + } + + } + // Update the temperatture derivative of the ln activity coefficients /* * This function will be called to update the internally storred @@ -1303,7 +1529,7 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeffdT_Scaled_[icat] = fmij * dlnActCoeffdT_NeutralMolecule_[jNeut]; + dlnActCoeffdT_Scaled_[icat] = dlnActCoeffdT_NeutralMolecule_[jNeut]/fmij; } // Do the anion list @@ -1336,7 +1562,7 @@ namespace Cantera { * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients */ - void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnC() const { + void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnX() const { int k, icat, jNeut; doublereal fmij; /* @@ -1344,11 +1570,11 @@ namespace Cantera { */ GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); if (!geThermo) { - fvo_zero_dbl_1(dlnActCoeffdlnC_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnX_Scaled_, m_kk); return; } - geThermo->getdlnActCoeffdlnC(DATA_PTR(dlnActCoeffdlnC_NeutralMolecule_)); + geThermo->getdlnActCoeffdlnX(DATA_PTR(dlnActCoeffdlnX_NeutralMolecule_)); switch (ionSolnType_) { case cIonSolnType_PASSTHROUGH: @@ -1361,19 +1587,77 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeffdlnC_Scaled_[icat] = fmij * dlnActCoeffdlnC_NeutralMolecule_[jNeut]; + dlnActCoeffdlnX_Scaled_[icat] = dlnActCoeffdlnX_NeutralMolecule_[jNeut]/fmij; } // Do the anion list icat = anionList_[0]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdT_Scaled_[icat]= 0.0; + dlnActCoeffdlnX_Scaled_[icat]= 0.0; // Do the list of neutral molecules for (k = 0; k < numPassThroughSpecies_; k++) { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnC_Scaled_[icat] = dlnActCoeffdlnC_NeutralMolecule_[jNeut]; + dlnActCoeffdlnX_Scaled_[icat] = dlnActCoeffdlnX_NeutralMolecule_[jNeut]; + } + break; + + case cIonSolnType_SINGLECATION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + case cIonSolnType_MULTICATIONANION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + default: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + } + + } + + /* + * This function will be called to update the internally storred + * temperature derivative of the natural logarithm of the activity coefficients + */ + void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN() const { + int k, icat, jNeut; + doublereal fmij; + /* + * Get the activity coefficients of the neutral molecules + */ + GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); + if (!geThermo) { + fvo_zero_dbl_1(dlnActCoeffdlnN_Scaled_, m_kk); + return; + } + + geThermo->getdlnActCoeffdlnN(DATA_PTR(dlnActCoeffdlnN_NeutralMolecule_)); + + switch (ionSolnType_) { + case cIonSolnType_PASSTHROUGH: + break; + case cIonSolnType_SINGLEANION: + + // Do the cation list + for (k = 0; k < (int) cationList_.size(); k++) { + //! Get the id for the next cation + icat = cationList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; + dlnActCoeffdlnN_Scaled_[icat] = dlnActCoeffdlnN_NeutralMolecule_[jNeut]/fmij; + } + + // Do the anion list + icat = anionList_[0]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeffdlnN_Scaled_[icat]= 0.0; + + // Do the list of neutral molecules + for (k = 0; k < numPassThroughSpecies_; k++) { + icat = passThroughList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeffdlnN_Scaled_[icat] = dlnActCoeffdlnN_NeutralMolecule_[jNeut]; } break; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 88b05e786..712ae622a 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -404,6 +404,21 @@ namespace Cantera { */ virtual void getPartialMolarEntropies(doublereal* sbar) const; + //! Get the array of change in the log activity coefficients w.r.t. change in state (change temp, change mole fractions) + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can gradX/X. + * + * @param dT Input of temperature change + * @param dX Input vector of changes in mole fraction. length = m_kk + * @param dlnActCoeff Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const; + //! Get the array of log concentration-like derivatives of the //! log activity coefficients /*! @@ -411,19 +426,65 @@ namespace Cantera { * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. + * logarithm of the concentration-like variable (i.e. mole fraction) + * that represents the standard state. * This quantity is to be used in conjunction with derivatives of * that concentration-like variable when the derivative of the chemical * potential is taken. * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of log(mole fraction) + * @param dlnActCoeffdlnX Output vector of log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - virtual void getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const; + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. number of moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN Output vector of log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; + + + virtual void getDissociationCoeffs(vector_fp& coeffs, vector_fp& charges); + + virtual void getNeutralMolecMoleFractions(vector_fp& fracs){fracs=NeutralMolecMoleFractions_;} + + //! Calculate neutral molecule mole fractions + /*! + * This routine calculates the neutral molecule mole + * fraction given the vector of ion mole fractions, + * i.e., the mole fractions from this ThermoPhase. + * Note, this routine basically assumes that there + * is charge neutrality. If there isn't, then it wouldn't + * make much sense. + * + * for the case of cIonSolnType_SINGLEANION, some slough + * in the charge neutrality is allowed. The cation number + * is followed, while the difference in charge neutrality + * is dumped into the anion mole number to fix the imbalance. + */ + virtual void getNeutralMoleculeMoleGrads(const doublereal * const x, doublereal *y) const; + + virtual void getCationList(std::vector& cation){cation=cationList_;} + virtual void getAnionList(std::vector& anion){anion=anionList_;} + virtual void getSpeciesNames(std::vector& names){names=m_speciesNames;} //@} @@ -680,6 +741,14 @@ namespace Cantera { */ void s_update_dlnActCoeffdT() const; + //! Update the change in the ln activity coefficients + /*! + * This function will be called to update the internally storred + * change of the natural logarithm of the activity coefficients + * w.r.t a change in state (temp, mole fraction, etc) + */ + void s_update_dlnActCoeff() const; + //! Update the derivative of the log of the activity coefficients //! wrt log(mole fraction) /*! @@ -687,7 +756,16 @@ namespace Cantera { * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the mole fractions. */ - void s_update_dlnActCoeff_dlnC() const; + void s_update_dlnActCoeff_dlnX() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(number of moles) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the number of moles of given species. + */ + void s_update_dlnActCoeff_dlnN() const; private: @@ -818,8 +896,10 @@ namespace Cantera { mutable std::vector muNeutralMolecule_; mutable std::vector gammaNeutralMolecule_; + mutable std::vector dlnActCoeff_NeutralMolecule_; mutable std::vector dlnActCoeffdT_NeutralMolecule_; - mutable std::vector dlnActCoeffdlnC_NeutralMolecule_; + mutable std::vector dlnActCoeffdlnX_NeutralMolecule_; + mutable std::vector dlnActCoeffdlnN_NeutralMolecule_; }; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 2017d8357..a6340b7ae 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -99,6 +99,12 @@ namespace Cantera { m_SE_b_ij = b.m_SE_b_ij; m_SE_c_ij = b.m_SE_c_ij; m_SE_d_ij = b.m_SE_d_ij; + m_VHE_b_ij = b.m_VHE_b_ij; + m_VHE_c_ij = b.m_VHE_c_ij; + m_VHE_d_ij = b.m_VHE_d_ij; + m_VSE_b_ij = b.m_VSE_b_ij; + m_VSE_c_ij = b.m_VSE_c_ij; + m_VSE_d_ij = b.m_VSE_d_ij; m_pSpecies_A_ij = b.m_pSpecies_A_ij; m_pSpecies_B_ij = b.m_pSpecies_B_ij; formMargules_ = b.formMargules_; @@ -154,11 +160,20 @@ namespace Cantera { m_SE_b_ij.resize(1); m_SE_c_ij.resize(1); m_SE_d_ij.resize(1); + + m_VHE_b_ij.resize(1); + m_VHE_c_ij.resize(1); + m_VHE_d_ij.resize(1); + + m_VSE_b_ij.resize(1); + m_VSE_c_ij.resize(1); + m_VSE_d_ij.resize(1); m_pSpecies_A_ij.resize(1); m_pSpecies_B_ij.resize(1); + m_HE_b_ij[0] = -17570E3; m_HE_c_ij[0] = -377.0E3; m_HE_d_ij[0] = 0.0; @@ -166,6 +181,7 @@ namespace Cantera { m_SE_b_ij[0] = -7.627E3; m_SE_c_ij[0] = 4.958E3; m_SE_d_ij[0] = 0.0; + int iLiCl = speciesIndex("LiCl(L)"); if (iLiCl < 0) { @@ -217,7 +233,7 @@ namespace Cantera { */ void MargulesVPSSTP::constructPhaseFile(std::string inputFile, std::string id) { - if (inputFile.size() == 0) { + if ((int) inputFile.size() == 0) { throw CanteraError("MargulesVPSSTP:constructPhaseFile", "input file is null"); } @@ -274,7 +290,7 @@ namespace Cantera { */ void MargulesVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id) { string stemp; - if (id.size() > 0) { + if ((int) id.size() > 0) { string idp = phaseNode.id(); if (idp != id) { throw CanteraError("MargulesVPSSTP::constructPhaseXML", @@ -350,7 +366,7 @@ namespace Cantera { * take the exp of the internally storred coefficients. */ for (int k = 0; k < m_kk; k++) { - ac[k] = exp(lnActCoeff_Scaled_[k]); + ac[k] = exp(lnActCoeff_Scaled_[k]); } } @@ -472,7 +488,56 @@ namespace Cantera { } } - + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + + // Return an array of partial molar volumes for the + // species in the mixture. Units: m^3/kmol. + /* + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void MargulesVPSSTP::getPartialMolarVolumes(doublereal* vbar) const { + + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + + /* + * Get the standard state values in m^3 kmol-1 + */ + getStandardVolumes(vbar); + //cout << "species name(0) = " << speciesName(0) << endl; + //cout << "iA = " << speciesName(m_pSpecies_A_ij[0]) << endl; + //cout << "iB = " << speciesName(m_pSpecies_B_ij[0]) << endl; + + for ( iK = 0; iK < m_kk; iK++ ){ + delAK = 0; + delBK = 0; + XK = moleFractions_[iK]; + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_VHE_b_ij[i] - T * m_VSE_b_ij[i]); + g1 = (m_VHE_c_ij[i] - T * m_VSE_c_ij[i]); + + vbar[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + } + } + } doublereal MargulesVPSSTP::err(std::string msg) const { throw CanteraError("MargulesVPSSTP","Base class method " @@ -583,14 +648,54 @@ namespace Cantera { } + // Update the activity coefficients /* * This function will be called to update the internally storred * natural logarithm of the activity coefficients * - * he = X_A X_B(B + C(X_A - X_B)) + * he = X_A X_B(B + C X_B) */ + void MargulesVPSSTP::s_update_lnActCoeff() const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + double RT = GasConstant*T; + + fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + lnActCoeff_Scaled_[iK] += (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + //lnActCoeff_Scaled_[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + } + } + } + + + /* + // Not Right??? void MargulesVPSSTP::s_update_lnActCoeff() const { + int iA, iB; double XA, XB, g0 , g1; double T = temperature(); @@ -612,15 +717,52 @@ namespace Cantera { lnActCoeff_Scaled_[iB] += XA * XA * g0 + XA * XB * g1 * (2 * XA); } } + */ // Update the derivative of the log of the activity coefficients wrt T /* * This function will be called to update the internally storred * natural logarithm of the activity coefficients * - * he = X_A X_B(B + C(X_A - X_B)) + * he = X_A X_B(B + C X_B) */ void MargulesVPSSTP::s_update_dlnActCoeff_dT() const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + double RTT = GasConstant*T*T; + + fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = -m_HE_b_ij[i] / RTT; + g1 = -m_HE_c_ij[i] / RTT; + + dlnActCoeffdT_Scaled_[iK] += (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + } + } + } + + /* Not Right??? + void MargulesVPSSTP::s_update_dlnActCoeff_dT() const {} + int iA, iB; doublereal XA, XB, h0 , h1; doublereal T = temperature(); @@ -642,6 +784,7 @@ namespace Cantera { dlnActCoeffdT_Scaled_[iB] += -(XA * XA * h0 + XA * XB * h1 * (2 * XA))/RTT; } } + */ void MargulesVPSSTP::getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { s_update_dlnActCoeff_dT(); @@ -650,22 +793,123 @@ namespace Cantera { } } + // calculate the change of the log of the activity coefficients wrt change in state: dT, dX + /* + * This function will be called to calculate gradient of the + * logarithm of the activity coefficients based on gradients in temperature and mole fraction. + * + * he = X_A X_B(B + C X_B) + */ + void MargulesVPSSTP::getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal* dlnActCoeff) const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1, dXA, dXB; + double T = temperature(); + double RT = GasConstant*T; + + //fvo_zero_dbl_1(dlnActCoeff, m_kk); + s_update_dlnActCoeff_dT(); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + dlnActCoeff[iK] = 0.0; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + dXA = dX[iA]; + dXB = dX[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeff[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB + dlnActCoeffdT_Scaled_[iK]*dT; + } + } + } + // Update the derivative of the log of the activity coefficients wrt ln(X) /* * This function will be called to update the internally stored gradients of the * logarithm of the activity coefficients. These are used in the determination * of the diffusion coefficients. * - * he = X_A X_B(B + C(X_A - X_B)) + * he = X_A X_B(B + C X_B) */ - void MargulesVPSSTP::s_update_dlnActCoeff_dlnC() const { + void MargulesVPSSTP::s_update_dlnActCoeff_dlnN() const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + double RT = GasConstant*T; + + fvo_zero_dbl_1(dlnActCoeffdlnN_Scaled_, m_kk); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnN_Scaled_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + } + dlnActCoeffdlnN_Scaled_[iK] = XK*dlnActCoeffdlnN_Scaled_[iK]-XK; + } + } + + void MargulesVPSSTP::s_update_dlnActCoeff_dlnX() const { + int iA, iB; doublereal XA, XB, g0 , g1; doublereal T = temperature(); - fvo_zero_dbl_1(dlnActCoeffdlnC_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnX_Scaled_, m_kk); doublereal RT = GasConstant * T; + + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnX_Scaled_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); + dlnActCoeffdlnX_Scaled_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); + } + + /* + // Wrong!!! for (int i = 0; i < numBinaryInteractions_; i++) { iA = m_pSpecies_A_ij[i]; iB = m_pSpecies_B_ij[i]; @@ -676,17 +920,25 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT ; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - dlnActCoeffdlnC_Scaled_[iA] += XA * ( ( - 2.0 + 2.0 * XA ) * g0 + dlnActCoeffdlnX_Scaled_[iA] += XA * ( ( - 2.0 + 2.0 * XA ) * g0 + ( - 4.0 + 10.0 * XA - 6.0 * XA*XA ) * g1 ) ; - dlnActCoeffdlnC_Scaled_[iB] += XB * ( ( - 2.0 + 2.0 * XB ) * g0 + dlnActCoeffdlnX_Scaled_[iB] += XB * ( ( - 2.0 + 2.0 * XB ) * g0 + ( 2.0 - 8.0 * XB + 6.0 * XB*XB ) * g1 ) ; } + */ } + - void MargulesVPSSTP::getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const { - s_update_dlnActCoeff_dlnC(); + void MargulesVPSSTP::getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + s_update_dlnActCoeff_dlnN(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnC[k] = dlnActCoeffdlnC_Scaled_[k]; + dlnActCoeffdlnN[k] = dlnActCoeffdlnN_Scaled_[k]; + } + } + void MargulesVPSSTP::getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + s_update_dlnActCoeff_dlnX(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnX[k] = dlnActCoeffdlnX_Scaled_[k]; } } @@ -699,6 +951,12 @@ namespace Cantera { m_SE_b_ij.resize(num, 0.0); m_SE_c_ij.resize(num, 0.0); m_SE_d_ij.resize(num, 0.0); + m_VHE_b_ij.resize(num, 0.0); + m_VHE_c_ij.resize(num, 0.0); + m_VHE_d_ij.resize(num, 0.0); + m_VSE_b_ij.resize(num, 0.0); + m_VSE_c_ij.resize(num, 0.0); + m_VSE_d_ij.resize(num, 0.0); m_pSpecies_A_ij.resize(num, -1); m_pSpecies_B_ij.resize(num, -1); @@ -769,7 +1027,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "", "excessEnthalpy"); + getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -785,7 +1043,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "", "excessEntropy"); + getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -797,6 +1055,38 @@ namespace Cantera { m_SE_c_ij[iSpot] = vParams[1]; } + if (nodeName == "excessvolume_enthalpy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VHE_b_ij[iSpot] = vParams[0]; + m_VHE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessvolume_entropy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessVolume_Entropy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VSE_b_ij[iSpot] = vParams[0]; + m_VSE_c_ij[iSpot] = vParams[1]; + } + } diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index e9044b1bb..4d8a40776 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -565,6 +565,18 @@ namespace Cantera { virtual void getPartialMolarEntropies(doublereal* sbar) const; + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + //! Get the species electrochemical potentials. /*! * These are partial molar quantities. @@ -579,6 +591,19 @@ namespace Cantera { void getElectrochemPotentials(doublereal* mu) const; + //! Get the array of change in the log activity coefficients with change in state (change temp, change mole fractions) + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param dlnActCoeff Output vector of temperature derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeffdT) const; + //! Get the array of temperature derivatives of the log activity coefficients /*! * This function is a virtual class, but it first appears in GibbsExcessVPSSTP @@ -608,11 +633,12 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of log(mole fraction) + * @param dlnActCoeffdlnX Output vector of log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - virtual void getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const; + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; //@} @@ -761,7 +787,16 @@ namespace Cantera { * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the mole fractions. */ - void s_update_dlnActCoeff_dlnC() const; + void s_update_dlnActCoeff_dlnX() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(moles) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the moles. + */ + void s_update_dlnActCoeff_dlnN() const; private: @@ -802,6 +837,30 @@ namespace Cantera { //! Entropy term for the quaternary mole fraction interaction of the //! excess gibbs free energy expression mutable vector_fp m_SE_d_ij; + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_b_ij; + + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_c_ij; + + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_d_ij; + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_b_ij; + + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_c_ij; + + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_d_ij; //! vector of species indices representing species A in the interaction /*! diff --git a/Cantera/src/thermo/PDSS_SSVol.cpp b/Cantera/src/thermo/PDSS_SSVol.cpp index 71ae96fd0..4ca9cd46f 100644 --- a/Cantera/src/thermo/PDSS_SSVol.cpp +++ b/Cantera/src/thermo/PDSS_SSVol.cpp @@ -134,14 +134,14 @@ namespace Cantera { m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI"); } else if (model == "temperature_polynomial") { volumeModel_ = cSSVOLUME_TPOLY; - int num = getFloatArray(*ss, TCoeff_, true, "", "volumeTemperaturePolynomial"); + int num = getFloatArray(*ss, TCoeff_, true, "toSI", "volumeTemperaturePolynomial"); if (num != 4) { throw CanteraError("PDSS_SSVol::constructPDSSXML", " Didn't get 4 density polynomial numbers for species " + speciesNode.name()); } } else if (model == "density_temperature_polynomial") { volumeModel_ = cSSVOLUME_DENSITY_TPOLY; - int num = getFloatArray(*ss, TCoeff_, true, "", "densityTemperaturePolynomial"); + int num = getFloatArray(*ss, TCoeff_, true, "toSI", "densityTemperaturePolynomial"); if (num != 4) { throw CanteraError("PDSS_SSVol::constructPDSSXML", " Didn't get 4 density polynomial numbers for species " + speciesNode.name()); diff --git a/Cantera/src/thermo/State.cpp b/Cantera/src/thermo/State.cpp index 6191ce6bd..f8b3dbee9 100644 --- a/Cantera/src/thermo/State.cpp +++ b/Cantera/src/thermo/State.cpp @@ -196,6 +196,10 @@ namespace Cantera { return density()/meanMolecularWeight(); } + doublereal State::molarVolume() const { + return 1.0/molarDensity(); + } + void State::setConcentrations(const doublereal* const conc) { int k; doublereal sum = 0.0, norm = 0.0; diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h index d05941add..ca2826df9 100644 --- a/Cantera/src/thermo/State.h +++ b/Cantera/src/thermo/State.h @@ -318,6 +318,9 @@ namespace Cantera { /// Molar density (kmol/m^3). doublereal molarDensity() const; + /// Molar density (kmol/m^3). + doublereal molarVolume() const; + //! Set the internally storred density (kg/m^3) of the phase /*! * Note the density of a phase is an indepedent variable. diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 3d5ddb577..2df0b8546 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -883,6 +883,21 @@ namespace Cantera { } + //! Get the change in activity coefficients w.r.t. change in state + //! (temp, mole fraction, etc.) + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can gradX/X. + * + * @param dT Input of temperature change + * @param dX Input vector of changes in mole fraction. length = m_kk + * @param dlnActCoeff Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { + err("getdlnActCoeff"); + } + //! Get the array of log concentration-like derivatives of the //! log activity coefficients /*! @@ -890,19 +905,41 @@ namespace Cantera { * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. + * logarithm of the concentration-like variable (i.e. mole fraction) + * that represents the standard state. * This quantity is to be used in conjunction with derivatives of * that concentration-like variable when the derivative of the chemical * potential is taken. * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of derivatives of the + * @param dlnActCoeffdlnX Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const { - err("getdlnActCoeffdlnC"); + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + err("getdlnActCoeffdlnX"); + } + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + err("getdlnActCoeffdlnN"); } diff --git a/Cantera/src/thermo/VPSSMgr.cpp b/Cantera/src/thermo/VPSSMgr.cpp index 64ec7e22c..1204bce2c 100644 --- a/Cantera/src/thermo/VPSSMgr.cpp +++ b/Cantera/src/thermo/VPSSMgr.cpp @@ -280,7 +280,8 @@ namespace Cantera { void VPSSMgr::getStandardVolumes_ref(doublereal *vol) const{ - err("getStandardVolumes_ref"); + getStandardVolumes(vol); + //err("getStandardVolumes_ref"); } /*****************************************************************/ @@ -359,6 +360,7 @@ namespace Cantera { m_sss_R.resize(m_kk, 0.0); m_Vss.resize(m_kk, 0.0); + // Storage used by the PDSS objects to store their // answers. mPDSS_h0_RT.resize(m_kk, 0.0); diff --git a/Cantera/src/thermo/VPStandardStateTP.h b/Cantera/src/thermo/VPStandardStateTP.h index c13412fe4..7990b2cff 100644 --- a/Cantera/src/thermo/VPStandardStateTP.h +++ b/Cantera/src/thermo/VPStandardStateTP.h @@ -127,19 +127,41 @@ namespace Cantera { * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. * This quantity is to be used in conjunction with derivatives of * that concentration-like variable when the derivative of the chemical * potential is taken. * * units = dimensionless * - * @param dlnActCoeffdlnC Output vector of derivatives of the + * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnC(doublereal *dlnActCoeffdlnC) const { - err("getdlnActCoeffdlnC"); + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + err("getdlnActCoeffdlnN"); + } + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + err("getdlnActCoeffdlnX"); } From 0d31b2f7a71ca10914dbd8ec18b9aef50bc792ed Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Sat, 27 Feb 2010 00:49:36 +0000 Subject: [PATCH 108/446] Added a few unit definitions to units.h Overloaded getFloat to allow call to getFloatArray and return a vector --- Cantera/src/base/ctml.cpp | 16 ++++++++++++++++ Cantera/src/base/ctml.h | 38 ++++++++++++++++++++++++++++++++++++++ Cantera/src/base/units.h | 24 ++++++++++++++++++++++-- 3 files changed, 76 insertions(+), 2 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 8de42e90f..09bed275f 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -633,6 +633,22 @@ namespace ctml { return getFloatCurrent(node, type); } + doublereal getFloat(vector_fp& v, const Cantera::XML_Node& parent, + const std::string &name, + const std::string type) { + if (!parent.hasChild(name)) + throw CanteraError("getFloat (called from XML Node \"" + + parent.name() + "\"): ", + "no child XML element named \"" + name + "\" exists"); + const XML_Node& node = parent.child(name); + if (node.hasChild("floatArray")){ + getFloatArray(node, v, "true", type); + return 0; + } + else{ return getFloatCurrent(node, type); + } + } + doublereal getFloatCurrent(const Cantera::XML_Node& node, const std::string type) { doublereal x, x0, x1, fctr = 1.0; diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 85d6f8a3b..5ed0539f1 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -566,6 +566,44 @@ namespace ctml { doublereal getFloat(const Cantera::XML_Node& parent, const std::string &name, const std::string type=""); + //! Get a floating-point value from a child element. + /*! + * Returns a doublereal value for the child named 'name' of element 'parent'. If + * 'type' is supplied and matches a known unit type, unit + * conversion to SI will be done if the child element has an attribute + * 'units'. + * + * Note, it's an error for the child element not to exist. + * + * Example: + * + * Code snipet: + * @verbatim + const XML_Node &State_XMLNode; + doublereal pres = OneAtm; + if (state_XMLNode.hasChild("pressure")) { + pres = getFloat(State_XMLNode, "pressure", "toSI"); + } + @endverbatim + * + * reads the corresponding XML file: + * @verbatim + + 101325.0 + <\state> + @endverbatim + * + * @param v vector to assign with getFloatArray is XML data is in an array form + * @param parent reference to the XML_Node object of the parent XML element + * @param name Name of the XML child element + * @param type String type. Currently known types are "toSI" and "actEnergy", + * and "" , for no conversion. The default value is "", + * which implies that no conversion is allowed. + */ + + doublereal getFloat(Cantera::vector_fp& v,const Cantera::XML_Node& parent, const std::string &name, + const std::string type="toSI"); + //! Get a floating-point value from the current XML element /*! * Returns a doublereal value from the current element. If diff --git a/Cantera/src/base/units.h b/Cantera/src/base/units.h index 9aa3a3355..25009ea12 100644 --- a/Cantera/src/base/units.h +++ b/Cantera/src/base/units.h @@ -182,6 +182,9 @@ namespace Cantera { m_act_u() { + // unity + m_u["1"] = 1.0; + // length m_u["m"] = 1.0; m_u["cm"] = 0.01; @@ -200,6 +203,9 @@ namespace Cantera { m_u["kcal"] = 4184.0; m_u["eV"] = Faraday; //1.60217733e-19; + // resistance + m_u["ohm"] = 1.0; + // quantity m_u["mol"] = 1.0e-3; m_u["gmol"] = 1.0e-3; @@ -213,6 +219,7 @@ namespace Cantera { m_u["C"] = 1.0; // mass + m_u["gm"] = 1.0e-3; m_u["g"] = 1.0e-3; m_u["kg"] = 1.0; @@ -227,17 +234,30 @@ namespace Cantera { m_u["hr"] = 3600.0; m_u["ms"] = 0.001; - // frequency + /*// frequency m_u["hZ"] = 0.01/(lightSpeed); m_u["cm^-1"] = 1.0; m_u["m^-1"] = 0.1; m_u["cm-1"] = m_u["cm^-1"]; m_u["m-1"] = m_u["m^-1"]; - m_u["wavenumbers"] = m_u["cm^-1"]; + m_u["wavenumbers"] = m_u["cm^-1"];*/ // viscosity + m_u["Pa-s"] = 1; m_u["poise"] = 0.1; m_u["centipoise"] = 0.001; + m_u["P"] = 0.1; + m_u["cP"] = 0.001; + + // volume + m_u["kL"] = 1.0; + m_u["liter"] = 0.001; + m_u["L"] = 0.001; + m_u["l"] = 0.001; + m_u["mL"] = 1.0e-6; + m_u["ml"] = 1.0e-6; + m_u["cc"] = 1.0e-6; + m_act_u["eV"] = m_u["eV"]; // /m_u["molec"]; m_act_u["K"] = GasConstant; From 60afcc5d573df8c0d380f2a4736e7017aeb817b9 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Mon, 1 Mar 2010 16:16:15 +0000 Subject: [PATCH 109/446] Implemented stefan maxwell equations with input of conductivity, cation mobility ratio, and self diffusion coefficients. --- Cantera/src/transport/LiquidTransport.cpp | 617 ++++++++++++++-- Cantera/src/transport/LiquidTransport.h | 280 ++++++- Cantera/src/transport/LiquidTransportData.cpp | 100 ++- Cantera/src/transport/LiquidTransportData.h | 78 +- .../src/transport/LiquidTransportParams.cpp | 689 ++++++++++++++---- Cantera/src/transport/LiquidTransportParams.h | 272 +++++-- Cantera/src/transport/TransportBase.h | 70 +- Cantera/src/transport/TransportFactory.cpp | 138 +++- 8 files changed, 1930 insertions(+), 314 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index ee4756a03..262b12f0f 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -34,23 +34,38 @@ namespace Cantera { LiquidTransport::LiquidTransport(thermo_t* thermo, int ndim) : Transport(thermo, ndim), m_nsp(0), + m_nBinInt(0), m_tmin(-1.0), m_tmax(100000.), m_iStateMF(-1), m_temp(-1.0), m_press(-1.0), + m_lambda(-1.0), m_viscmix(-1.0), + m_ionCondmix(-1.0), + m_mobRatMix(-1.0), + m_selfDiffMix(-1.0), + m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), + m_ionCond_mix_ok(false), + m_ionCond_temp_ok(false), + m_ionCond_conc_ok(false), + m_mobRat_mix_ok(false), + m_mobRat_temp_ok(false), + m_mobRat_conc_ok(false), + m_selfDiff_mix_ok(false), + m_selfDiff_temp_ok(false), + m_selfDiff_conc_ok(false), m_radi_mix_ok(false), m_radi_temp_ok(false), m_radi_conc_ok(false), m_diff_mix_ok(false), m_diff_temp_ok(false), - m_cond_temp_ok(false), - m_cond_mix_ok(false), + m_lambda_temp_ok(false), + m_lambda_mix_ok(false), m_mode(-1000), m_debug(false), m_nDim(1) @@ -61,23 +76,38 @@ namespace Cantera { LiquidTransport::LiquidTransport(const LiquidTransport &right) : Transport(), m_nsp(0), + m_nBinInt(0), m_tmin(-1.0), m_tmax(100000.), m_iStateMF(-1), m_temp(-1.0), m_press(-1.0), + m_lambda(-1.0), m_viscmix(-1.0), + m_ionCondmix(-1.0), + m_mobRatMix(-1.0), + m_selfDiffMix(-1.0), + m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), + m_ionCond_mix_ok(false), + m_ionCond_temp_ok(false), + m_ionCond_conc_ok(false), + m_mobRat_mix_ok(false), + m_mobRat_temp_ok(false), + m_mobRat_conc_ok(false), + m_selfDiff_mix_ok(false), + m_selfDiff_temp_ok(false), + m_selfDiff_conc_ok(false), m_radi_mix_ok(false), m_radi_temp_ok(false), m_radi_conc_ok(false), m_diff_mix_ok(false), m_diff_temp_ok(false), - m_cond_temp_ok(false), - m_cond_mix_ok(false), + m_lambda_temp_ok(false), + m_lambda_mix_ok(false), m_mode(-1000), m_debug(false), m_nDim(1) @@ -95,10 +125,16 @@ namespace Cantera { } Transport::operator=(right); m_nsp = right.m_nsp; + m_nBinInt = right.m_nBinInt; m_tmin = right.m_tmin; m_tmax = right.m_tmax; m_mw = right.m_mw; m_viscTempDep_Ns = right.m_viscTempDep_Ns; + m_ionCondTempDep_Ns = right.m_ionCondTempDep_Ns; + m_mobRatTempDep_Ns = right.m_mobRatTempDep_Ns; + m_mobRatTempDepIndex = right.m_mobRatTempDepIndex; + m_selfDiffTempDep_Ns = right.m_selfDiffTempDep_Ns; + m_selfDiffTempDepIndex = right.m_selfDiffTempDepIndex; m_lambdaTempDep_Ns = right.m_lambdaTempDep_Ns; m_diffTempDep_Ns = right.m_diffTempDep_Ns; m_radiusTempDep_Ns = right.m_radiusTempDep_Ns; @@ -109,9 +145,19 @@ namespace Cantera { m_Grad_mu = right.m_Grad_mu; m_bdiff = right.m_bdiff; m_viscSpecies = right.m_viscSpecies; + m_ionCondSpecies = right.m_ionCondSpecies; + m_mobRatSpecies = right.m_mobRatSpecies; + m_mobRatSpeciesIndex = right.m_mobRatSpeciesIndex; + m_selfDiffSpecies = right.m_selfDiffSpecies; + m_selfDiffSpeciesIndex = right.m_selfDiffSpeciesIndex; m_hydrodynamic_radius = right.m_hydrodynamic_radius; m_lambdaSpecies = right.m_lambdaSpecies; m_viscMixModel = right.m_viscMixModel; + m_ionCondMixModel = right.m_ionCondMixModel; + m_mobRatMixModel = right.m_mobRatMixModel; + m_mobRatMixModelIndex = right.m_mobRatMixModelIndex; + m_selfDiffMixModel = right.m_selfDiffMixModel; + m_selfDiffMixModelIndex = right.m_selfDiffMixModelIndex; m_lambdaMixModel = right.m_lambdaMixModel; m_diffMixModel = right.m_diffMixModel; m_iStateMF = -1; @@ -123,7 +169,6 @@ namespace Cantera { m_actCoeff = right.m_actCoeff; m_Grad_lnAC = right.m_Grad_lnAC; m_chargeSpecies = right.m_chargeSpecies; - m_volume_spec = right.m_volume_spec; m_B = right.m_B; m_A = right.m_A; m_temp = right.m_temp; @@ -132,17 +177,31 @@ namespace Cantera { m_Vdiff = right.m_Vdiff; m_lambda = right.m_lambda; m_viscmix = right.m_viscmix; + m_ionCondmix = right.m_ionCondmix; + m_mobRatMix = right.m_mobRatMix; + m_mobRatMixIndex = right.m_mobRatMixIndex; + m_selfDiffMix = right.m_selfDiffMix; + m_selfDiffMixIndex = right.m_selfDiffMixIndex; m_spwork = right.m_spwork; m_visc_mix_ok = false; m_visc_temp_ok = false; m_visc_conc_ok = false; + m_ionCond_mix_ok = false; + m_ionCond_temp_ok = false; + m_ionCond_conc_ok = false; + m_mobRat_mix_ok = false; + m_mobRat_temp_ok = false; + m_mobRat_conc_ok = false; + m_selfDiff_mix_ok = false; + m_selfDiff_temp_ok = false; + m_selfDiff_conc_ok = false; m_radi_mix_ok = false; m_radi_temp_ok = false; m_radi_conc_ok = false; m_diff_mix_ok = false; m_diff_temp_ok = false; - m_cond_temp_ok = false; - m_cond_mix_ok = false; + m_lambda_temp_ok = false; + m_lambda_mix_ok = false; m_mode = right.m_mode; m_debug = right.m_debug; m_nDim = right.m_nDim; @@ -158,18 +217,33 @@ namespace Cantera { LiquidTransport::~LiquidTransport() { - //These are constructed in TransportFactory::newLTP - for ( int k = 0; k < m_nsp; k++) { - if ( m_viscTempDep_Ns[k] ) delete m_viscTempDep_Ns[k]; - if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; - if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k]; - if ( m_diffTempDep_Ns[k] ) delete m_diffTempDep_Ns[k]; - } - //These are constructed in TransportFactory::newLTI - if ( m_viscMixModel ) delete m_viscMixModel; - if ( m_lambdaMixModel ) delete m_lambdaMixModel; - if ( m_diffMixModel ) delete m_diffMixModel; - //if ( m_radiusMixModel ) delete m_radiusMixModel; + //These are constructed in TransportFactory::newLTP + for ( int k = 0; k < m_nsp; k++) { + if ( m_viscTempDep_Ns[k] ) delete m_viscTempDep_Ns[k]; + if ( m_ionCondTempDep_Ns[k] ) delete m_ionCondTempDep_Ns[k]; + for ( int l=0;l < m_nsp; l++ ){ + if ( m_selfDiffTempDep_Ns[l][k] ) delete m_selfDiffTempDep_Ns[l][k]; + } + for ( int l=0;l < m_nBinInt; l++ ){ + if ( m_mobRatTempDep_Ns[l][k] ) delete m_mobRatTempDep_Ns[l][k]; + } + if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; + if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k]; + if ( m_diffTempDep_Ns[k] ) delete m_diffTempDep_Ns[k]; + //These are constructed in TransportFactory::newLTI + + if ( m_selfDiffMixModel[k] ) delete m_selfDiffMixModel[k]; + } + + for ( int k = 0; k < m_nBinInt; k++) { + if ( m_mobRatMixModel[k] ) delete m_mobRatMixModel[k]; + } + + if ( m_viscMixModel ) delete m_viscMixModel; + if ( m_ionCondMixModel ) delete m_ionCondMixModel; + if ( m_lambdaMixModel ) delete m_lambdaMixModel; + if ( m_diffMixModel ) delete m_diffMixModel; + //if ( m_radiusMixModel ) delete m_radiusMixModel; } @@ -191,6 +265,7 @@ namespace Cantera { m_thermo = tr.thermo; m_velocityBasis = tr.velocityBasis_; m_nsp = m_thermo->nSpecies(); + m_nBinInt = m_nsp*(m_nsp-1)/2; m_tmin = m_thermo->minTemp(); m_tmax = m_thermo->maxTemp(); @@ -200,38 +275,77 @@ namespace Cantera { m_thermo->molecularWeights().end(), m_mw.begin()); /* - * Get the input Viscosities + * Get the input Viscosities, and stuff */ m_viscSpecies.resize(m_nsp, 0.0); m_viscTempDep_Ns.resize(m_nsp, 0); + m_ionCondSpecies.resize(m_nsp, 0.0); + m_ionCondTempDep_Ns.resize(m_nsp, 0); + m_mobRatTempDepIndex.resize(m_nBinInt); + m_mobRatTempDep_Ns.resize(m_nBinInt); + m_mobRatMixModel.resize(m_nBinInt); + m_mobRatMixModelIndex.resize(m_nBinInt); + m_mobRatSpeciesIndex.resize(m_nBinInt); + m_mobRatSpecies.resize(m_nBinInt, m_nsp, 0.0); + m_mobRatMix.resize(m_nBinInt,0.0); + m_mobRatMixIndex.resize(m_nBinInt); + m_selfDiffTempDepIndex.resize(m_nsp); + m_selfDiffTempDep_Ns.resize(m_nsp); + m_selfDiffMixModel.resize(m_nsp); + m_selfDiffMixModelIndex.resize(m_nsp); + m_selfDiffSpeciesIndex.resize(m_nsp); + m_selfDiffSpecies.resize(m_nsp, m_nsp, 0.0); + m_selfDiffMix.resize(m_nsp,0.0); + m_selfDiffMixIndex.resize(m_nsp); + for (k=0; k < m_nsp; k++){ + m_selfDiffTempDep_Ns[k].resize(m_nsp, 0); + } + for (k=0; k < m_nBinInt; k++){ + m_mobRatTempDep_Ns[k].resize(m_nsp, 0); + } + m_lambdaSpecies.resize(m_nsp, 0.0); + m_lambdaTempDep_Ns.resize(m_nsp, 0); + m_hydrodynamic_radius.resize(m_nsp, 0.0); + m_radiusTempDep_Ns.resize(m_nsp, 0); + + //first populate mixing rules and indices + for (k = 0; k < m_nsp; k++) { + m_selfDiffMixModel[k] = tr.selfDiffusion[k]; + m_selfDiffMixModelIndex[k] = tr.selfDiffIndex[k]; + } + for (k = 0; k < m_nBinInt; k++) { + m_mobRatMixModel[k] = tr.mobilityRatio[k]; + m_mobRatMixModelIndex[k] = tr.mobRatIndex[k]; + } + //for each species, assign viscosity model and coefficients for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; m_viscTempDep_Ns[k] = ltd.viscosity; - } - - /* - * Get the input Thermal Conductivities - */ - m_lambdaSpecies.resize(m_nsp, 0.0); - m_lambdaTempDep_Ns.resize(m_nsp, 0); - //for each species, assign thermal conductivity model - for (k = 0; k < m_nsp; k++) { - Cantera::LiquidTransportData <d = tr.LTData[k]; + m_ionCondTempDep_Ns[k] = ltd.ionConductivity; + for (int j = 0; j < m_nBinInt; j++){ + for (int l=0; l < m_nBinInt; l++){ + if (m_mobRatMixModelIndex[j] == ltd.mobRatIndex[l]) { + m_mobRatTempDep_Ns[j][k] = ltd.mobilityRatio[l]; + m_mobRatTempDepIndex[j] = ltd.mobRatIndex[l]; + break; + } + } + } + for (int j = 0; j < (int) m_selfDiffMixModelIndex.size(); j++){ + for (int l=0; l < (int) m_selfDiffMixModelIndex.size(); l++){ + if (m_selfDiffMixModelIndex[j] == ltd.selfDiffIndex[l]) { + m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[l]; + m_selfDiffTempDepIndex[j] = ltd.selfDiffIndex[l]; + break; + } + } + } m_lambdaTempDep_Ns[k] = ltd.thermalCond; - } - - /* - * Get the input Hydrodynamic Radii - */ - m_hydrodynamic_radius.resize(m_nsp, 0.0); - m_radiusTempDep_Ns.resize(m_nsp, 0); - //for each species, assign model for hydrodynamic radius - for (k = 0; k < m_nsp; k++) { - Cantera::LiquidTransportData <d = tr.LTData[k]; m_radiusTempDep_Ns[k] = ltd.hydroRadius; } + /* * Get the input Species Diffusivities * Note that species diffusivities are not what is needed. @@ -263,18 +377,28 @@ namespace Cantera { * species diffusivity and hydrodynamics radius (perhaps not needed in the * present class). */ + + m_viscMixModel = tr.viscosity; tr.viscosity = 0; + + m_ionCondMixModel = tr.ionConductivity; + tr.ionConductivity = 0; + //m_mobRatMixModel = tr.mobilityRatio; + m_lambdaMixModel = tr.thermalCond; tr.thermalCond = 0; m_diffMixModel = tr.speciesDiffusivity; tr.speciesDiffusivity = 0; - + + m_bdiff.resize(m_nsp,m_nsp, 0.0); + //Don't really need to update this here. //It is updated in updateDiff_T() - m_diffMixModel->getMatrixTransProp(m_bdiff); + m_diffMixModel->getMatrixTransProp( m_bdiff ); + m_mode = tr.mode_; @@ -306,10 +430,19 @@ namespace Cantera { m_visc_mix_ok = false; m_visc_temp_ok = false; m_visc_conc_ok = false; + m_ionCond_mix_ok = false; + m_ionCond_temp_ok = false; + m_ionCond_conc_ok = false; + m_mobRat_mix_ok = false; + m_mobRat_temp_ok = false; + m_mobRat_conc_ok = false; + m_selfDiff_mix_ok = false; + m_selfDiff_temp_ok = false; + m_selfDiff_conc_ok = false; m_radi_temp_ok = false; m_radi_conc_ok = false; - m_cond_temp_ok = false; - m_cond_mix_ok = false; + m_lambda_temp_ok = false; + m_lambda_mix_ok = false; m_diff_temp_ok = false; m_diff_mix_ok = false; @@ -357,6 +490,215 @@ namespace Cantera { copy(m_viscSpecies.begin(), m_viscSpecies.end(), visc); } + /****************** ionConductivity ******************************/ + + // Returns the ionic conductivity of the solution + /* + * The ionConductivity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species ionic conductivities. + */ + + doublereal LiquidTransport:: ionConductivity() { + + update_T(); + update_C(); + + if (m_ionCond_mix_ok) return m_ionCondmix; + + ////// LiquidTranInteraction method + m_ionCondmix = m_ionCondMixModel->getMixTransProp( m_ionCondTempDep_Ns ); + + return m_ionCondmix; + + /* + // update m_ionCondSpecies[] if necessary + if (!m_ionCond_temp_ok) { + updateIonConductivity_T(); + } + + if (!m_ionCond_conc_ok) { + updateIonConductivity_C(); + } + */ + } + + // Returns the pure species ionic conductivities for all species + /* + * The pure species ionic conductivities are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param ionCond array of length "number of species" + * to hold returned ionic conductivities. + */ + void LiquidTransport::getSpeciesIonConductivity(doublereal* ionCond) { + update_T(); + if (!m_ionCond_temp_ok) { + updateIonConductivity_T(); + } + copy(m_ionCondSpecies.begin(), m_ionCondSpecies.end(), ionCond); + } + + /****************** mobilityRatio ******************************/ + + // Returns the mobility ratios of the solution + /* + * The mobility ratio calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species mobility ratios. + */ + void LiquidTransport:: mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex) { + + update_T(); + update_C(); + + ////// LiquidTranInteraction method + if (!m_mobRat_mix_ok){ + for (int k = 0; k < m_nBinInt; k++){ + if ( m_mobRatMixModelIndex[k] != m_mobRatTempDepIndex[k] ) + throw CanteraError("LiquidTransport::mobilityRation","Mobility Ratio Indices Don't Match: Mixture vs. Species"); + m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); + m_mobRatMixIndex[k] = m_mobRatMixModelIndex[k]; + } + } + for (int k = 0; k < m_nBinInt; k++){ + mobRat[k] = m_mobRatMix[k]; + mobRatIndex[k]= m_mobRatMixIndex[k]; + } + } + void LiquidTransport:: mobilityRatio(doublereal* mobRat, std::vector& mobRatIndex) { + + update_T(); + update_C(); + + ////// LiquidTranInteraction method + if (!m_mobRat_mix_ok){ + for (int k = 0; k < m_nBinInt; k++){ + if ( m_mobRatMixModelIndex[k] != m_mobRatTempDepIndex[k] ) + throw CanteraError("LiquidTransport::mobilityRatio","Mobility Ratio Indices Don't Match: Mixture vs. Species"); + m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); + m_mobRatMixIndex[k] = m_mobRatMixModelIndex[k]; + } + } + for (int k = 0; k < m_nBinInt; k++){ + mobRat[k] = m_mobRatMix[k]; + mobRatIndex[k]= m_mobRatMixIndex[k]; + } + } + + // Returns the pure species mobility ratios for all species + /* + * The pure species mobility ratios are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param mobRat array of length "number of species" + * to hold returned mobility ratio. + */ + void LiquidTransport::getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex) { + update_T(); + if (!m_mobRat_temp_ok) { + updateMobilityRatio_T(); + } + mobRat = m_mobRatSpecies; + for (int k = 0; k < m_nBinInt; k++) + mobRatIndex[k] = m_mobRatSpeciesIndex[k]; + } + void LiquidTransport::getSpeciesMobilityRatio(doublereal** mobRat, std::vector& mobRatIndex) { + update_T(); + if (!m_mobRat_temp_ok) { + updateMobilityRatio_T(); + } + for (int k=0; k& selfDiffIndex) { + + update_T(); + update_C(); + + ////// LiquidTranInteraction method + if (!m_selfDiff_mix_ok){ + for (int k = 0; k < m_nsp; k++){ + if ( m_selfDiffMixModelIndex[k] != m_selfDiffTempDepIndex[k] ) + throw CanteraError("LiquidTransport::selfDiffusion","Self Diffusion Indices Don't Match: Mixture vs. Species"); + m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffTempDep_Ns[k] ); + m_selfDiffMixIndex[k] = m_selfDiffMixModelIndex[k]; + } + } + for (int k = 0; k < m_nsp; k++){ + selfDiff[k] = m_selfDiffMix[k]; + selfDiffIndex[k]= m_selfDiffMixIndex[k]; + } + } + + void LiquidTransport:: selfDiffusion(double* selfDiff, std::vector& selfDiffIndex) { + + update_T(); + update_C(); + + ////// LiquidTranInteraction method + if (!m_selfDiff_mix_ok){ + for (int k = 0; k < m_nsp; k++){ + if ( m_selfDiffMixModelIndex[k] != m_selfDiffTempDepIndex[k] ) + throw CanteraError("LiquidTransport::selfDiffusion","Self Diffusion Indices Don't Match: Mixture vs. Species"); + m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffTempDep_Ns[k] ); + m_selfDiffMixIndex[k] = m_selfDiffMixModelIndex[k]; + } + } + for (int k = 0; k < m_nsp; k++){ + selfDiff[k] = m_selfDiffMix[k]; + selfDiffIndex[k]= m_selfDiffMixIndex[k]; + } + } + + // Returns the pure species self diffusion for all species + /* + * The pure species self diffusion coeffs are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param selfDiff array of size "number of species"^2 + * to hold returned self diffusion. + */ + void LiquidTransport::getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex) { + update_T(); + if (!m_selfDiff_temp_ok) { + updateSelfDiffusion_T(); + } + selfDiff = m_selfDiffSpecies; + for (int k = 0; k < m_nsp; k++) + selfDiffIndex[k] = m_selfDiffSpeciesIndex[k]; + } + void LiquidTransport::getSpeciesSelfDiffusion(doublereal** selfDiff, std::vector& selfDiffIndex) { + update_T(); + if (!m_selfDiff_temp_ok) { + updateSelfDiffusion_T(); + } + for (int k=0; kgetMixTransProp( m_lambdaTempDep_Ns ); m_cond_mix_ok = true; } @@ -846,11 +1188,6 @@ namespace Cantera { void LiquidTransport::getSpeciesVdiffExt(int ldf, doublereal* Vdiff) { int n, k; - update_T(); - update_C(); - - update_Grad_lnAC(); - stefan_maxwell_solve(); for (n = 0; n < m_nDim; n++) { @@ -878,11 +1215,6 @@ namespace Cantera { void LiquidTransport::getSpeciesFluxesExt(int ldf, doublereal* fluxes) { int n, k; - update_T(); - update_C(); - - update_Grad_lnAC(); - stefan_maxwell_solve(); for (n = 0; n < m_nDim; n++) { @@ -926,11 +1258,6 @@ namespace Cantera { */ void LiquidTransport::getMixDiffCoeffs(doublereal* const d) { - update_T(); - update_C(); - - update_Grad_lnAC(); - stefan_maxwell_solve(); for ( int n = 0; n < m_nDim; n++) { @@ -975,19 +1302,28 @@ namespace Cantera { // temperature has changed so temp flags are flipped m_visc_temp_ok = false; + m_ionCond_temp_ok = false; + m_mobRat_temp_ok = false; + m_selfDiff_temp_ok = false; m_radi_temp_ok = false; m_diff_temp_ok = false; + m_lambda_temp_ok = false; // temperature has changed, so polynomial temperature // interpolations will need to be reevaluated. // This means that many concentration m_visc_conc_ok = false; - m_cond_temp_ok = false; + m_ionCond_conc_ok = false; + m_mobRat_conc_ok = false; + m_selfDiff_conc_ok = false; // Mixture stuff needs to be evaluated m_visc_mix_ok = false; + m_ionCond_mix_ok = false; + m_mobRat_mix_ok = false; + m_selfDiff_mix_ok = false; m_diff_mix_ok = false; - // m_cond_mix_ok = false; (don't need it because a lower lvl flag is set + m_lambda_mix_ok = false; //(don't need it because a lower lvl flag is set return true; } @@ -1040,11 +1376,17 @@ namespace Cantera { // be recomputed before use, and update the local mole // fractions. m_visc_conc_ok = false; + m_ionCond_conc_ok = false; + m_mobRat_conc_ok = false; + m_selfDiff_conc_ok = false; // Mixture stuff needs to be evaluated m_visc_mix_ok = false; + m_ionCond_mix_ok = false; + m_mobRat_mix_ok = false; + m_selfDiff_mix_ok = false; m_diff_mix_ok = false; - m_cond_mix_ok = false; + m_lambda_mix_ok = false; return true; } @@ -1067,8 +1409,8 @@ namespace Cantera { for (k = 0; k < m_nsp; k++) { m_lambdaSpecies[k] = m_lambdaTempDep_Ns[k]->getSpeciesTransProp() ; } - m_cond_temp_ok = true; - m_cond_mix_ok = false; + m_lambda_temp_ok = true; + m_lambda_mix_ok = false; } @@ -1112,6 +1454,79 @@ namespace Cantera { } + //! Update the pure-species ionic conductivities functional dependence on concentration. + void LiquidTransport::updateIonConductivity_C() { + m_ionCond_conc_ok = true; + } + + + /** + * Updates the array of pure species ionic conductivities internally + * using calls to the appropriate LTPspecies subclass. + * The flag m_ionCond_ok is set to true. + */ + void LiquidTransport::updateIonConductivity_T() { + int k; + + for (k = 0; k < m_nsp; k++) { + m_ionCondSpecies[k] = m_ionCondTempDep_Ns[k]->getSpeciesTransProp() ; + } + m_ionCond_temp_ok = true; + m_ionCond_mix_ok = false; + } + + + //! Update the pure-species mobility ratios functional dependence on concentration. + void LiquidTransport::updateMobilityRatio_C() { + m_mobRat_conc_ok = true; + } + + + /** + * Updates the array of pure species mobility ratios internally + * using calls to the appropriate LTPspecies subclass. + * The flag m_mobRat_ok is set to true. + */ + void LiquidTransport::updateMobilityRatio_T() { + int k; + int j; + + for (k = 0; k < m_nBinInt; k++) { + for (j = 0; j < m_nsp; j++) { + m_mobRatSpecies(k,j) = m_mobRatTempDep_Ns[k][j]->getSpeciesTransProp() ; + } + m_mobRatSpeciesIndex[k] = m_mobRatTempDepIndex[k]; + } + m_mobRat_temp_ok = true; + m_mobRat_mix_ok = false; + } + + + //! Update the pure-species self diffusion functional dependence on concentration. + void LiquidTransport::updateSelfDiffusion_C() { + m_selfDiff_conc_ok = true; + } + + + /** + * Updates the array of pure species self diffusion internally + * using calls to the appropriate LTPspecies subclass. + * The flag m_selfDiff_ok is set to true. + */ + void LiquidTransport::updateSelfDiffusion_T() { + int k; + int j; + + for (k = 0; k < m_nBinInt; k++) { + for (j = 0; j < m_nsp; j++) { + m_selfDiffSpecies(k,j) = m_selfDiffTempDep_Ns[k][j]->getSpeciesTransProp() ; + } + m_selfDiffSpeciesIndex[k] = m_selfDiffTempDepIndex[k]; + } + m_selfDiff_temp_ok = true; + m_selfDiff_mix_ok = false; + } + //! Update the pure-species viscosities functional dependence on concentration. void LiquidTransport::updateHydrodynamicRadius_C() { m_radi_conc_ok = true; @@ -1164,14 +1579,23 @@ namespace Cantera { int k; - vector_fp grad_lnAC(m_nsp); - m_thermo->getdlnActCoeffdlnC( DATA_PTR(grad_lnAC) ); + doublereal grad_T; + vector_fp grad_lnAC(m_nsp), grad_X(m_nsp); + // IonsFromNeutralVPSSTP * tempIons = dynamic_cast m_thermo; + //MargulesVPSSTP * tempMarg = dynamic_cast (tempIons->neutralMoleculePhase_); + - for (k = 0; k < m_nsp; k++) { - m_Grad_lnAC[k] = grad_lnAC[k]; + //m_thermo->getdlnActCoeffdlnX( DATA_PTR(grad_lnAC) ); + for (k = 0; k < m_nDim; k++ ) { + grad_T = m_Grad_T[k]; + grad_X.assign(m_Grad_X.begin()+m_nsp*k,m_Grad_X.begin()+m_nsp*(k+1)); + m_thermo->getdlnActCoeff( grad_T, DATA_PTR(grad_X), DATA_PTR(grad_lnAC) ); + for ( int i = 0; i < m_nsp; i++ ) + grad_lnAC[i] += grad_X[i]/m_molefracs[i]; + copy(grad_lnAC.begin(),grad_lnAC.end(),m_Grad_lnAC.begin()+m_nsp*k); // std::cout << k << " m_Grad_lnAC = " << m_Grad_lnAC[k] << std::endl; } - + return; } @@ -1220,10 +1644,13 @@ namespace Cantera { //! grab a local copy of the molecular weights const vector_fp& M = m_thermo->molecularWeights(); + //! grad a local copy of the ion molar volume (inverse total ion concentration) + const doublereal vol = m_thermo->molarVolume(); /* - * Update the concentrations and diffusion coefficients in the mixture. + * Update the temperature, concentrations and diffusion coefficients in the mixture. */ + update_T(); update_C(); if ( !m_diff_temp_ok ) updateDiff_T(); @@ -1260,12 +1687,11 @@ namespace Cantera { * */ for (i = 0; i < m_nsp; i++) { - double xi_denom = m_molefracs_tran[i]; for (a = 0; a < m_nDim; a++) { m_Grad_mu[a*m_nsp + i] = m_chargeSpecies[i] * Faraday * m_Grad_V[a] //+ (m_volume_spec[i] - M[i]/dens_) * m_Grad_P[a] - + GasConstant * T * m_Grad_X[a*m_nsp+i] * ( 1.0 + m_Grad_lnAC[i] ) / xi_denom; + + GasConstant * T * m_Grad_lnAC[a*m_nsp+i]; } } @@ -1286,8 +1712,11 @@ namespace Cantera { * Just for Note, m_A(i,j) refers to the ith row and jth column. * They are still fortran ordered, so that i varies fastest. */ + + double condSum1, condSum2; switch (m_nDim) { case 1: /* 1-D approximation */ + m_B(0,0) = 0.0; //equation for the reference velocity for (j = 0; j < m_nsp; j++) { @@ -1298,9 +1727,10 @@ namespace Cantera { else if ( ( m_velocityBasis >= 0 ) && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity - if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", + if ( m_velocityBasis == j ) m_A(0,j) = 1.0; + else m_A(0,j) = 0.0; + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ @@ -1320,7 +1750,30 @@ namespace Cantera { //! invert and solve the system Ax = b. Answer is in m_B solve(m_A, m_B); - + + /* + condSum2 = m_chargeSpecies[1]*m_chargeSpecies[1]*m_molefracs_tran[1]/m_bdiff(2,3) + + m_chargeSpecies[2]*m_chargeSpecies[2]*m_molefracs_tran[2]/m_bdiff(1,3) + + m_chargeSpecies[3]*m_chargeSpecies[3]*m_molefracs_tran[3]/m_bdiff(1,2); + condSum1 = m_molefracs_tran[1]/m_bdiff(1,2)/m_bdiff(1,3) + + m_molefracs_tran[2]/m_bdiff(2,3)/m_bdiff(1,2) + + m_molefracs_tran[3]/m_bdiff(1,3)/m_bdiff(2,3); + condSum2 = condSum2/condSum1*Faraday*Faraday/GasConstant/T/vol; + */ + + condSum1 = 0; + for (i = 0; i < m_nsp; i++){ + condSum1 -= Faraday*m_chargeSpecies[i]*m_B(i,0)*m_molefracs_tran[i]/vol; + } + + /* + Check Mobility Ratio of Cations + cout << "mobility ratio = " << m_chargeSpecies[1]*(m_B(1,0)-m_B(2,0))/m_chargeSpecies[0]/(m_B(0,0)-m_B(2,0)) << endl; + */ + + // cout << condSum1 << " = " << condSum2 << endl; + + break; case 2: /* 2-D approximation */ m_B(0,0) = 0.0; @@ -1335,8 +1788,9 @@ namespace Cantera { && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", + else m_A(0,j) = 0.0; + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ @@ -1375,8 +1829,9 @@ namespace Cantera { && ( m_velocityBasis < m_nsp ) ) // use species number m_velocityBasis as reference velocity if ( m_velocityBasis == j ) m_A(0,j) = 1.0; - else - throw CanteraError("LiquidTransport::stefan_maxwell_solve", + else m_A(0,j) = 0.0; + else + throw CanteraError("LiquidTransport::stefan_maxwell_solve", "Unknown reference velocity provided."); } for (i = 1; i < m_nsp; i++){ diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 063c37d0b..133624ca5 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -68,7 +68,7 @@ namespace Cantera { * \f] * for mass fraction \f$ Y_i \f$. For mole-averaged velocities * \f[ - * \sum_{i} X_i \vec{V_i} = 0 + * \sum_{i} X_i \vec{V_i} = 0 * \f] * for mole fraction \f$ X_i \f$. * @@ -165,7 +165,7 @@ namespace Cantera { * determine the individual species viscosities. */ virtual doublereal viscosity(); - + //! Returns the pure species viscosities for all species /*! * The pure species viscosities are evaluated using the @@ -177,6 +177,70 @@ namespace Cantera { */ virtual void getSpeciesViscosities(doublereal* const visc); + //! Returns the ionic conductivity of the solution + /*! + * The ionic conductivity calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species ionic conductivities. + */ + virtual doublereal ionConductivity(); + + //! Returns the pure species ionic conductivities for all species + /*! + * The pure species ionic conductivities are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param visc array of length "number of species" + * to hold returned ionic conductivities. + */ + virtual void getSpeciesIonConductivity(doublereal* const ionCond); + + //! Returns the mobility ratio of the solution + /*! + * The mobility ratio calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species mobility ratios. + */ + virtual void mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex); + virtual void mobilityRatio(double* mobRat, std::vector& mobRatIndex); + + //! Returns the pure species mobility ratios for all species + /*! + * The pure species mobility ratios are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param mobRat array of length "number of species" + * to hold returned mobility ratios. + */ + virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex); + virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex); + + //! Returns the self diffusion coefficients in the solution + /*! + * The self diffusion calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species self diffusion coeffs. + */ + virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex); + virtual void selfDiffusion(double* selfDiff, std::vector& selfDiffIndex); + + //! Returns the pure species self diffusion in solution of each species + /*! + * The pure species molar volumes are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param selfDiff array of length "number of species" + * to hold returned self diffusion coeffs. + */ + virtual void getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex); + virtual void getSpeciesSelfDiffusion(double** selfDiff, std::vector& selfDiffIndex); + //! Returns the hydrodynamic radius for all species /*! * The species hydrodynamic radii are evaluated using the @@ -711,6 +775,25 @@ namespace Cantera { */ void updateViscosity_T(); + //! Update the temperature-dependent ionic conductivity terms + //! for each species internally + /*! + * The flag m_ionCond_temp_ok is set to true. + */ + void updateIonConductivity_T(); + + //! Updates the array of pure species mobility ratios internally. + /*! + * The flag m_mobRat_ok is set to true. + */ + void updateMobilityRatio_T(); + + //! Updates the array of pure species self diffusion coeffs internally. + /*! + * The flag m_selfDiff_ok is set to true. + */ + void updateSelfDiffusion_T(); + //! Update the temperature-dependent hydrodynamic radius terms //! for each species internally /*! @@ -731,7 +814,37 @@ namespace Cantera { * @internal */ void updateViscosities_C(); + + //! Update the concentration parts of the ionic conductivity + /*! + * Internal routine is run whenever the update_boolean + * m_ionCond_conc_ok is false. Currently there is no concentration + * dependence for the pure species ionic conductivity. + * + * @internal + */ + void updateIonConductivity_C(); + //! Update the concentration parts of the mobility ratio + /*! + * Internal routine is run whenever the update_boolean + * m_mobRat_conc_ok is false. Currently there is no concentration + * dependence for the pure species mobility ratio. + * + * @internal + */ + void updateMobilityRatio_C(); + + //! Update the concentration parts of the self diffusion + /*! + * Internal routine is run whenever the update_boolean + * m_selfDiff_conc_ok is false. Currently there is no concentration + * dependence for the pure species self diffusion. + * + * @internal + */ + void updateSelfDiffusion_C(); + //! Update the concentration dependence of the hydrodynamic radius /*! * Internal routine is run whenever the update_boolean @@ -751,6 +864,7 @@ namespace Cantera { //! Number of species in the mixture int m_nsp; + int m_nBinInt; //! Minimum temperature applicable to the transport property eval doublereal m_tmin; @@ -782,6 +896,65 @@ namespace Cantera { */ LiquidTranInteraction *m_viscMixModel; + //! Ionic conductivity for each species expressed as an appropriate subclass + //! of LTPspecies + /*! + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). + */ + std::vector m_ionCondTempDep_Ns; + + //! Ionic Conductivity of the mixture expressed as a subclass of + //! LiquidTranInteraction + /*! + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). + */ + LiquidTranInteraction *m_ionCondMixModel; + + //! Mobility ratio for each species expressed as an appropriate subclass + //! of LTPspecies + /*! + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). + */ + typedef std::vector LTPvector; + std::vector m_mobRatTempDep_Ns; + std::vector m_mobRatTempDepIndex; + + //! Mobility ratio of the mixture expressed as a subclass of + //! LiquidTranInteraction + /*! + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). + */ + std::vector m_mobRatMixModel; + std::vector m_mobRatMixModelIndex; + + //! Self Diffusion for each species expressed as an appropriate subclass + //! of LTPspecies + /*! + * These subclasses of LTPspecies evaluate the species-specific + * transport properties according to the parameters parsed in + * TransportFactory::getLiquidSpeciesTransportData(). + */ + std::vector m_selfDiffTempDep_Ns; + std::vector m_selfDiffTempDepIndex; + + //! Self Diffusion of the mixture expressed as a subclass of + //! LiquidTranInteraction + /*! + * These subclasses of LiquidTranInteraction evaluate the + * mixture transport properties according to the parameters parsed in + * TransportFactory::getLiquidInteractionsTransportData(). + */ + std::vector m_selfDiffMixModel; + std::vector m_selfDiffMixModelIndex; + //! Thermal conductivity for each species expressed as an //! appropriate subclass of LTPspecies /*! @@ -872,19 +1045,24 @@ namespace Cantera { vector_fp m_Grad_X; //! Gradient of the logarithm of the activity coefficients - //! with respect to the logarithm of the mole fraction, plus one. /*! * This quantity appears in the gradient of the chemical potential. * It multiplies the gradient of the mole fraction, and in this way * serves to "modify" the diffusion coefficient. * - * m_Grad_lnAC[k] = \partial \left[ \ln ( \gamma_i ) \right] - * / \partial \left[ \ln ( \X_i ) \right] + * m_Grad_lnAC[k] = \nabla \ln ( \gamma_i ) + \nabla \ln ( \X_i ) * * Note that where "mole fraction" is used here, whatever * concentration-related variable applies, so that if * molality is the concentration variable, the gradient of the * activity coefficient should be with respect to the molality. + * m_nsp is the number of species in the fluid + * + * k is the species index + * n is the dimensional index (x, y, or z). It has a length + * equal to m_nDimm_ + * + * m_Grad_X[n*m_nsp + k] * */ vector_fp m_Grad_lnAC; @@ -964,6 +1142,41 @@ namespace Cantera { */ vector_fp m_viscSpecies; + //! Internal value of the species ionic conductivities + /*! + * Ionic conductivity of the species evaluated using subclass of LTPspecies + * held in m_ionCondTempDep_Ns. + * + * Length = number of species + * + * controlling update boolean -> m_ionCond_temp_ok + */ + vector_fp m_ionCondSpecies; + + //! Internal value of the species mobility ratios + /*! + * Mobility ratio of the species evaluated using subclass of LTPspecies + * held in m_mobRatTempDep_Ns. + * + * Length = number of species + * + * controlling update boolean -> m_mobRat_temp_ok + */ + DenseMatrix m_mobRatSpecies; + std::vector m_mobRatSpeciesIndex; + + //! Internal value of the species self diffusion coefficients + /*! + * Self diffusion of the species evaluated using subclass of LTPspecies + * held in m_selfDiffTempDep_Ns. + * + * Length = number of species + * + * controlling update boolean -> m_selfDiff_temp_ok + */ + DenseMatrix m_selfDiffSpecies; + std::vector m_selfDiffSpeciesIndex; + //! Internal value of the species individual thermal conductivities /*! * Thermal conductivities of the species evaluated using subclass @@ -1093,6 +1306,19 @@ namespace Cantera { //! Saved value of the mixture viscosity doublereal m_viscmix; + //! Saved value of the mixture ionic conductivity + doublereal m_ionCondmix; + + //! Saved values of the mixture mobility ratios + vector_fp m_mobRatMix; + //! Saved species index of the mixture correlated to mobility ratios + std::vector m_mobRatMixIndex; + + //! Saved values of the mixture self diffusion coefficients + vector_fp m_selfDiffMix; + //! Saved species index of the mixture correlated to self diffusion coefficients + std::vector m_selfDiffMixIndex; + //! work space /*! * Length is equal to m_nsp @@ -1115,6 +1341,46 @@ namespace Cantera { //! are current wrt the concentration bool m_visc_conc_ok; + //! Boolean indicating that the top-level mixture ionic conductivity is current + /*! + * This is turned false for every change in T, P, or C. + */ + bool m_ionCond_mix_ok; + + //! Boolean indicating that weight factors wrt ionic conductivty is current + bool m_ionCond_temp_ok; + + //! Flag to indicate that the pure species ionic conductivities + //! are current wrt the concentration + bool m_ionCond_conc_ok; + bool m_cond_mix_ok; + + //! Boolean indicating that the top-level mixture mobility ratio is current + /*! + * This is turned false for every change in T, P, or C. + */ + bool m_mobRat_mix_ok; + + //! Boolean indicating that weight factors wrt mobility ratio is current + bool m_mobRat_temp_ok; + + //! Flag to indicate that the pure species mobility ratios + //! are current wrt the concentration + bool m_mobRat_conc_ok; + + //! Boolean indicating that the top-level mixture self diffusion is current + /*! + * This is turned false for every change in T, P, or C. + */ + bool m_selfDiff_mix_ok; + + //! Boolean indicating that weight factors wrt self diffusion is current + bool m_selfDiff_temp_ok; + + //! Flag to indicate that the pure species self diffusion + //! are current wrt the concentration + bool m_selfDiff_conc_ok; + //! Boolean indicating that mixture diffusion coeffs are current bool m_radi_mix_ok; @@ -1134,10 +1400,10 @@ namespace Cantera { //! Flag to indicate that the pure species conductivities //! are current wrt the temperature - bool m_cond_temp_ok; + bool m_lambda_temp_ok; //! Boolean indicating that mixture conductivity is current - bool m_cond_mix_ok; + bool m_lambda_mix_ok; //! Mode indicator for transport models -- currently unused. int m_mode; diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 25dcd3c82..496fb7c95 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -10,6 +10,7 @@ */ #include "LiquidTransportData.h" +using namespace std; namespace Cantera { @@ -74,6 +75,11 @@ namespace Cantera { speciesName = right.speciesName; hydroRadius = right.hydroRadius; viscosity = right.viscosity; + ionConductivity = right.ionConductivity; + mobilityRatio = right.mobilityRatio; + mobRatIndex = right.mobRatIndex; + selfDiffusion = right.selfDiffusion; + selfDiffIndex = right.selfDiffIndex; thermalCond = right.thermalCond; electCond = right.electCond; speciesDiffusivity = right.speciesDiffusivity; @@ -167,7 +173,9 @@ namespace Cantera { thermo_t* thermo ) : LTPspecies( propNode, name, tp_ind, thermo) { - m_model = LTR_MODEL_ARRHENIUS; + m_model = LTR_MODEL_ARRHENIUS; + m_temp = 0.0; + m_prop = 0.0; doublereal A_k, n_k, Tact_k; getArrhenius(propNode, A_k, n_k, Tact_k); @@ -268,14 +276,16 @@ namespace Cantera { thermo_t* thermo ) : LTPspecies( propNode, name, tp_ind, thermo) { - m_model = LTR_MODEL_POLY; + m_model = LTR_MODEL_POLY; + m_temp = 0.0; + m_prop = 0.0; - getFloatArray(propNode, m_coeffs, true); // if units labeled, convert Angstroms -> meters + getFloatArray(propNode, m_coeffs, "true", "toSI"); - if (m_coeffs[0] <= 0.0) { + /* if (m_coeffs[0] <= 0.0) { throw LTPError("negative or zero " + propNode.name() ); - } + }*/ } //! Copy constructor @@ -308,13 +318,89 @@ namespace Cantera { doublereal LTPspecies_Poly::getSpeciesTransProp( ) { doublereal t = m_thermo->temperature(); - if (t != m_temp) { - double tempN = 1.0; + if (t != m_temp) { + m_temp=t; + double tempN = 1.0; for (int i = 0; i < (int) m_coeffs.size() ; i++) { m_prop += m_coeffs[i] * tempN; + //cout << "m_coeff = " <temperature(); + if (t != m_temp) { + m_temp=t; + m_prop=m_coeffs[0]; + double tempN = 1.0; + for (int i = 1; i < (int) m_coeffs.size() ; i++) { + tempN *= m_temp; + m_prop *= exp(m_coeffs[i] * tempN); + //cout << "m_coeff = " < + * 0.6, -15.0e-5 + * + * + * + * + * \endverbatim + */ + class LTPspecies_ExpT : public LTPspecies{ + + public: + + LTPspecies_ExpT( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ); + + //! Copy constructor + LTPspecies_ExpT( const LTPspecies_ExpT &right ); + + //! Assignment operator + LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); + + virtual ~LTPspecies_ExpT( ) { } + + //! Returns the pure species tranport property + /*! + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal getSpeciesTransProp( ); + + protected: + + //! temperature from thermo object + doublereal m_temp; + + //! most recent evaluation of transport property + doublereal m_prop; + + //! Internal model to adjust species-specific properties for composition. + /** Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void adjustCoeffsForComposition( ){ } + }; + + } #endif diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 0caeabc59..41cebab6a 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -10,6 +10,11 @@ */ #include "LiquidTransportParams.h" +#include +#include "IonsFromNeutralVPSSTP.h" +#include "MargulesVPSSTP.h" +#include +using namespace std; namespace Cantera { @@ -49,19 +54,44 @@ namespace Cantera { { } - + LiquidTranInteraction::~LiquidTranInteraction(){ + int kmax = m_Aij.size(); + for ( int k = 0; k < kmax; k++) + if ( m_Aij[k] ) delete m_Aij[k]; + kmax = m_Bij.size(); + for ( int k = 0; k < kmax; k++) + if ( m_Bij[k] ) delete m_Bij[k]; + kmax = m_Hij.size(); + for ( int k = 0; k < kmax; k++) + if ( m_Hij[k] ) delete m_Hij[k]; + kmax = m_Sij.size(); + for ( int k = 0; k < kmax; k++) + if ( m_Sij[k] ) delete m_Sij[k]; + } void LiquidTranInteraction::init( const XML_Node &compModelNode, thermo_t* thermo ) { + + doublereal poly0; m_thermo = thermo; int nsp = thermo->nSpecies(); - m_Aij.resize( nsp, nsp, 0.0 ); m_Dij.resize( nsp, nsp, 0.0 ); m_Eij.resize( nsp, nsp, 0.0 ); - m_Sij.resize( nsp, nsp, 0.0 ); + /* + m_Aij.resize( nsp); + m_Bij.resize( nsp); + m_Hij.resize( nsp); + m_Sij.resize( nsp); + for ( int k = 0; k < nsp; k++ ){ + (*m_Aij[k]).resize( nsp, nsp, 0.0); + (*m_Bij[k]).resize( nsp, nsp, 0.0); + (*m_Hij[k]).resize( nsp, nsp, 0.0); + (*m_Sij[k]).resize( nsp, nsp, 0.0); + } + */ std::string speciesA; std::string speciesB; @@ -83,10 +113,10 @@ namespace Cantera { if ( jSpecies < 0 ) throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", "Unknown species " + speciesB ); - if ( xmlChild.hasChild( "Aij" ) ) { + /* if ( xmlChild.hasChild( "Aij" ) ) { m_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); m_Aij(jSpecies,iSpecies) = m_Aij(iSpecies,jSpecies) ; - } + }*/ if ( xmlChild.hasChild( "Eij" ) ) { m_Eij(iSpecies,jSpecies) = getFloat( xmlChild, "Eij", "actEnergy" ); @@ -94,11 +124,73 @@ namespace Cantera { m_Eij(jSpecies,iSpecies) = m_Eij(iSpecies,jSpecies) ; } - if ( xmlChild.hasChild( "Sij" ) ) { + if ( xmlChild.hasChild( "Aij" ) ) { + vector_fp poly; + poly0 = getFloat( poly, xmlChild, "Aij", "toSI" ); + if ( !poly.size() ) poly.push_back(poly0); + while (m_Aij.size()resize( nsp, nsp, 0.0); + m_Aij.push_back(aTemp); + } + for( int i=0; i<(int)poly.size(); i++ ){ + (*m_Aij[i])(iSpecies,jSpecies) = poly[i]; + //(*m_Aij[i])(jSpecies,iSpecies) = (*m_Aij[i])(iSpecies,jSpecies) ; + } + } + + if ( xmlChild.hasChild( "Bij" ) ) { + vector_fp poly; + poly0 = getFloat( poly, xmlChild, "Bij", "toSI" ); + if ( !poly.size() ) poly.push_back(poly0); + while (m_Bij.size()resize( nsp, nsp, 0.0); + m_Bij.push_back(bTemp); + } + for( int i=0; i<(int)poly.size(); i++ ){ + (*m_Bij[i])(iSpecies,jSpecies) = poly[i]; + //(*m_Bij[i])(jSpecies,iSpecies) = (*m_Bij[i])(iSpecies,jSpecies) ; + } + } + + if ( xmlChild.hasChild( "Hij" ) ) { + vector_fp poly; + poly0 = getFloat( poly, xmlChild, "Hij", "actEnergy" ); + if ( !poly.size() ) poly.push_back(poly0); + while (m_Hij.size()resize( nsp, nsp, 0.0); + m_Hij.push_back(hTemp); + } + for( int i=0; i<(int)poly.size(); i++ ){ + (*m_Hij[i])(iSpecies,jSpecies) = poly[i]; + (*m_Hij[i])(iSpecies,jSpecies) /= GasConstant; + //(*m_Hij[i])(jSpecies,iSpecies) = (*m_Hij[i])(iSpecies,jSpecies) ; + } + } + + if ( xmlChild.hasChild( "Sij" ) ) { + vector_fp poly; + poly0 = getFloat( poly, xmlChild, "Sij", "actEnergy" ); + if ( !poly.size() ) poly.push_back(poly0); + while (m_Sij.size()resize( nsp, nsp, 0.0); + m_Sij.push_back(sTemp); + } + for( int i=0; i<(int)poly.size(); i++ ){ + (*m_Sij[i])(iSpecies,jSpecies) = poly[i]; + (*m_Sij[i])(iSpecies,jSpecies) /= GasConstant; + //(*m_Sij[i])(jSpecies,iSpecies) = (*m_Sij[i])(iSpecies,jSpecies) ; + } + } + + /*0 if ( xmlChild.hasChild( "Sij" ) ) { m_Sij(iSpecies,jSpecies) = getFloat( xmlChild, "Sij", "toSI" ); m_Sij(iSpecies,jSpecies) /= GasConstant; - m_Sij(jSpecies,iSpecies) = m_Sij(iSpecies,jSpecies) ; - } + //m_Sij(jSpecies,iSpecies) = m_Sij(iSpecies,jSpecies) ; + }*/ if ( xmlChild.hasChild( "Dij" ) ) { m_Dij(iSpecies,jSpecies) = getFloat( xmlChild, "Dij", "toSI" ); @@ -121,7 +213,9 @@ namespace Cantera { m_thermo = right.m_thermo; //m_trParam = right.m_trParam; m_Aij = right.m_Aij; + m_Bij = right.m_Bij; m_Eij = right.m_Eij; + m_Hij = right.m_Hij; m_Sij = right.m_Sij; m_Dij = right.m_Dij; } @@ -173,6 +267,7 @@ namespace Cantera { doublereal LTI_Solvent::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; m_thermo->getMoleFractions(molefracs); @@ -181,23 +276,32 @@ namespace Cantera { //if weightings are specified, use those if ( speciesWeight ) { for ( int k = 0; k < nsp; k++) { - //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. - value += speciesValues[k] * speciesWeight[k]; + molefracs[k] = molefracs[k]; + // should be: molefracs[k] = molefracs[k]*speciesWeight[k]; for consistency, but weight(solvent)=1? } } else { - //This does not follow directly a solvent model + throw CanteraError("LTI_Solvent::getMixTransProp","You should be specifying the speciesWeight"); + /* //This does not follow directly a solvent model //although if the solvent mole fraction is dominant //and the other species values are given or zero, //it should work. for ( int k = 0; k < nsp; k++) { value += speciesValues[k] * molefracs[k]; - } + }*/ } - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] * m_Aij(i,j) ; + for ( int i = 0; i < nsp; i++ ){ + //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. + value += speciesValues[i] * speciesWeight[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } } + } return value; } @@ -206,19 +310,29 @@ namespace Cantera { doublereal LTI_Solvent::getMixTransProp( std::vector LTPptrs ) { int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; m_thermo->getMoleFractions(molefracs); doublereal value = 0; for ( int k = 0; k < nsp; k++) { - //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. - value += LTPptrs[k]->getSpeciesTransProp() * LTPptrs[k]->getMixWeight( ) ; + molefracs[k] = molefracs[k]; + // should be: molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); for consistency, but weight(solvent)=1? } - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] * m_Aij(i,j) ; + for ( int i = 0; i < nsp; i++ ){ + //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. + value += LTPptrs[i]->getSpeciesTransProp() * LTPptrs[i]->getMixWeight(); + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } return value; } @@ -229,105 +343,6 @@ namespace Cantera { doublereal LTI_MoleFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - value += speciesValues[k] * speciesWeight[k] * molefracs[k]; - } - } - else { - for ( int k = 0; k < nsp; k++) { - value += speciesValues[k] * molefracs[k]; - } - } - - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] * m_Aij(i,j) ; - - return value; - } - - - doublereal LTI_MoleFracs::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - value += LTPptrs[k]->getSpeciesTransProp() * LTPptrs[k]->getMixWeight( ) * molefracs[k]; - } - - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] * m_Aij(i,j) ; - - return value; - } - - - doublereal LTI_MassFracs::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal massfracs[nsp]; - m_thermo->getMassFractions(massfracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - value += speciesValues[k] * speciesWeight[k] * massfracs[k]; - } - } - else { - for ( int k = 0; k < nsp; k++) { - value += speciesValues[k] * massfracs[k]; - } - } - - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += massfracs[i] * massfracs[j] * m_Aij(i,j) ; - - return value; - } - - - doublereal LTI_MassFracs::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal massfracs[nsp]; - m_thermo->getMassFractions(massfracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - value += LTPptrs[k]->getSpeciesTransProp() * LTPptrs[k]->getMixWeight( ) * massfracs[k]; - } - - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += massfracs[i] * massfracs[j] * m_Aij(i,j) ; - - return value; - } - - - - - - doublereal LTI_Log_MoleFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; @@ -338,19 +353,157 @@ namespace Cantera { //if weightings are specified, use those if ( speciesWeight ) { for ( int k = 0; k < nsp; k++) { - value += log( speciesValues[k] ) * speciesWeight[k] * molefracs[k]; + molefracs[k] = molefracs[k]*speciesWeight[k]; } } else { - for ( int k = 0; k < nsp; k++) { - value += log( speciesValues[k] ) * molefracs[k]; + throw CanteraError("LTI_MoleFracs::getMixTransProp","You should be specifying the speciesWeight"); + } + + for ( int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } } } - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] - * ( m_Sij(i,j) + m_Eij(i,j) / temp ); + return value; + } + + + doublereal LTI_MoleFracs::getMixTransProp( std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + for ( int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); + } + + for ( int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } + return value; + } + + + doublereal LTI_MassFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal massfracs[nsp]; + m_thermo->getMassFractions(massfracs); + + doublereal value = 0; + + //if weightings are specified, use those + if ( speciesWeight ) { + for ( int k = 0; k < nsp; k++) { + massfracs[k] = massfracs[k]*speciesWeight[k]; + } + } + else { + throw CanteraError("LTI_MassFracs::getMixTransProp","You should be specifying the speciesWeight"); + } + + for ( int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * massfracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); + } + } + } + + return value; + } + + + doublereal LTI_MassFracs::getMixTransProp( std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal massfracs[nsp]; + m_thermo->getMassFractions(massfracs); + + doublereal value = 0; + + for ( int k = 0; k < nsp; k++) { + massfracs[k] = massfracs[k]*LTPptrs[k]->getMixWeight(); + } + + for ( int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * massfracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); + } + for ( int k = 0; k < (int)m_Bij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); + } + } + } + + return value; + } + + + + + doublereal LTI_Log_MoleFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + + + doublereal value = 0; + + //if weightings are specified, use those + if ( speciesWeight ) { + for ( int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*speciesWeight[k]; + } + } + else{ + throw CanteraError("LTI_Log_MoleFracs::getMixTransProp","You probably should have a speciesWeight when you call getMixTransProp to convert ion mole fractions to molecular mole fractions"); + } + + for ( int i = 0; i < nsp; i++ ){ + value += log( speciesValues[i] ) * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Hij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + for ( int k = 0; k < (int)m_Sij.size(); k++ ){ + value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + } + } value = exp( value ); return value; @@ -363,20 +516,36 @@ namespace Cantera { doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; m_thermo->getMoleFractions(molefracs); + doublereal value = 0; + //if weightings are specified, use those + for ( int k = 0; k < nsp; k++) { - value += log( LTPptrs[k]->getSpeciesTransProp() ) * LTPptrs[k]->getMixWeight() * molefracs[k]; + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight( ); } - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - value += molefracs[i] * molefracs[j] - * ( m_Sij(i,j) + m_Eij(i,j) / temp ); + for ( int i = 0; i < nsp; i++ ){ + value += log( LTPptrs[i]->getSpeciesTransProp() ) * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Hij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); + //cout << "1 = " << molefracs[i]+molefracs[j] << endl; + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + for ( int k = 0; k < (int)m_Sij.size(); k++ ){ + value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); + //cout << "1 = " << molefracs[i]+molefracs[j] << endl; + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + } + } value = exp( value ); - + // cout << ", viscSpeciesA = " << LTPptrs[0]->getSpeciesTransProp() << endl; + //cout << ", viscSpeciesB = " << LTPptrs[1]->getSpeciesTransProp() << endl; + //cout << "value = " << value << " FINAL" << endl; return value; } @@ -422,7 +591,7 @@ namespace Cantera { return value; } - void LTI_Pairwise_Interaction::getMatrixTransProp(DenseMatrix &mat, doublereal *speciesValues) { + void LTI_Pairwise_Interaction::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { int nsp = m_thermo->nSpecies(); doublereal temp = m_thermo->temperature(); @@ -439,6 +608,205 @@ namespace Cantera { mat(i,i) = m_diagonals[i]->getSpeciesTransProp() ; } + + void LTI_StefanMaxwell_PPN::setParameters( LiquidTransportParams& trParam ) { + int nsp = m_thermo->nSpecies(); + int nBinInt = nsp*(nsp-1)/2; + //vectornSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError( "Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); + + return value; + } + + + doublereal LTI_StefanMaxwell_PPN::getMixTransProp( std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError( "Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); + + return value; + } + + void LTI_StefanMaxwell_PPN::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { + //CAL + + IonsFromNeutralVPSSTP * ions_thermo = dynamic_cast(m_thermo); + int i, j, k; + int nsp = m_thermo->nSpecies(); + if (nsp != 3) throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); + int nBinInt = nsp*(nsp-1)/2; + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions( molefracs ); + vector_fp neut_molefracs; + ions_thermo->getNeutralMolecMoleFractions(neut_molefracs); + vector cation; + vector anion; + ions_thermo->getCationList(cation); + ions_thermo->getAnionList(anion); + vector speciesNames; + ions_thermo->getSpeciesNames(speciesNames); + + // Reaction Coeffs and Charges + std::vector viS(6); + std::vector charges(3); + ions_thermo->getDissociationCoeffs(viS,charges); + + if ((int)anion.size() != 1) + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have one anion only for StefanMaxwell_PPN"); + if ((int)cation.size() != 2) + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have two cations of equal charge for StefanMaxwell_PPN"); + if (charges[cation[0]] != charges[cation[1]]) + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN"); + + /* + cout << "cation 0: " << speciesNames[cation[0]] << endl; + cout << "cation 1: " << speciesNames[cation[1]] << endl; + cout << "anion 0: " << speciesNames[anion[0]] << endl; + */ + + doublereal kappa = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); + + MargulesVPSSTP * marg_thermo = dynamic_cast (ions_thermo->neutralMoleculePhase_); + doublereal vol = m_thermo->molarVolume(); + + typedef std::vector intVec; + std::vector mobRatIndexMap; + mobRatIndexMap.resize(nsp); + for ( k = 0; k < nsp; k++ ) + mobRatIndexMap[k].resize(nsp,0); + + for ( k = 0; k < nBinInt; k++ ) { + bool missingIndex = 1; + for ( i = 0; i < nsp; i++ ) { + for ( j = 0; j < i; j++ ) { + if ( (speciesNames[i] + ":" + speciesNames[j]) == m_mobRatIndex[k] ) { + mobRatIndexMap[i][j] = k; + m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); + if ( m_mobRatMix(i,j) > 0 ) m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); + missingIndex = 0; + break; + } + else if ( (speciesNames[j] + ":" + speciesNames[i]) == m_mobRatIndex[k] ) { + m_mobRatMix(j,i) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); + if ( m_mobRatMix(j,i) > 0 ) m_mobRatMix(i,j) = 1.0/m_mobRatMix(j,i); + missingIndex = 0; + break; + } + } + } + if ( missingIndex ) throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Incorrect names for mobility ratio of " + m_mobRatIndex[k] + " rather than i.e. " + speciesNames[0] + ":" + speciesNames[1]); + } + + + for ( k = 0; k < nsp; k++ ){ + j = 0; + while (m_selfDiffIndex[k] != speciesNames[j]) { + j++; + if (j == nsp) throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Incorrect names for self diffusion of " + m_selfDiffIndex[k] + " rather than i.e. " + speciesNames[0]); + } + m_selfDiffMix[j] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); + } + + /* + for ( i = 0; i < nsp; i++ ) { + cout << "D" << i << "* = " << m_selfDiffMix[i] << endl; + for ( j = 0; j < nsp; j++ ) { + cout << "ratio" << i << j << " = " << m_mobRatMix(i,j) << endl; + } + } + */ + + int vP = max(viS[cation[0]],viS[cation[1]]); + int vM = viS[anion[0]]; + int zP = charges[cation[0]]; + int zM = charges[anion[0]]; + doublereal xA, xB, eps; + doublereal inv_vP_vM_MutualDiff; + vector_fp dlnActCoeffdlnN; + dlnActCoeffdlnN.resize(neut_molefracs.size(),0.0); + + std::string cationIndex (4,'0'); + for ( i = 0; i < 2; i++ ) + for ( j = 0; j < 2; j++ ) + if ( viS[i*nsp+cation[j]] > 0 ) + cationIndex[i*2+j] = '1'; + + if ( (cationIndex == "1001") | (cationIndex == "0110") ) { + xA = neut_molefracs[cation[0]]; + xB = neut_molefracs[cation[1]]; + eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); + marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); + inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[cation[1]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[cation[0]])/m_selfDiffMix[cation[0]]); + //marg_thermo->getdlnActCoeffdlnX(&dlnActCoeffdlnN[0]); + //inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[cation[1]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[cation[0]])/m_selfDiffMix[cation[0]]); + } + else + throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Dissociation reactions don't make sense: cationIndex = " + cationIndex); + + mat.resize( nsp, nsp, 0.0 ); + mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/kappa/vol; + mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; +mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; + + + for ( i = 0; i < nsp; i++ ) { + for ( j = 0; j < nsp; j++ ) { + mat(i,j) = 1.0/mat(i,j); + //cout << "D" << i << j << " = " << mat(i,j) << endl; + } + } + } + doublereal LTI_StokesEinstein::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { @@ -503,6 +871,61 @@ namespace Cantera { delete viscSpec; } + doublereal LTI_MoleFracs_ExpT::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + //if weightings are specified, use those + if ( speciesWeight ) { + for ( int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*speciesWeight[k]; + } + } + else { + throw CanteraError("LTI_MoleFracs_ExpT::getMixTransProp","You should be specifying the speciesWeight"); + } + + for ( int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); + } + } + } + + return value; + } + + + doublereal LTI_MoleFracs_ExpT::getMixTransProp( std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + for ( int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); + } + + for ( int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; + for ( int j = 0; j < nsp; j++ ){ + for ( int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); + } + } + } + return value; + } diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 0757978a7..cf9570d97 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -33,57 +33,62 @@ namespace Cantera { }; - //! Composition dependence type for liquid mixture transport properties - /*! - * Types of temperature dependencies: - * - 0 - Mixture calculations with this property are not allowed - * - 1 - Use solvent (species 0) properties - * - 2 - Properties weighted linearly by mole fractions - * - 3 - Properties weighted linearly by mass fractions - * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) - * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) - * - * \verbatim - * - * - * - * - * LiCl(L) - * KCl(L) - * -1.0 - * 1.0E-1 - * - * - * - * - * - * - * Li+ - * K+ - * 1.5 - * - * - * K+ - * Cl- - * 1.0 - * - * - * Li+ - * Cl- - * 1.2 - * - * - * - * - * - * - * - * - * - * - * \endverbatim - * - */ + //! Composition dependence type for liquid mixture transport properties + /*! + * Types of temperature dependencies: + * - 0 - Mixture calculations with this property are not allowed + * - 1 - Use solvent (species 0) properties + * - 2 - Properties weighted linearly by mole fractions + * - 3 - Properties weighted linearly by mass fractions + * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) + * + * \verbatim + * + * + * + * + * LiCl(L) + * KCl(L) + * -1.0 + * 1.0E-1 + * -or- + * 1.0E-1, 0.001 0.01 + * + * -same form for Hij,Aij,Bij- + * + * + * + * + * + * + * Li+ + * K+ + * 1.5 + * + * + * K+ + * Cl- + * 1.0 + * + * + * Li+ + * Cl- + * 1.2 + * + * + * + * + * + * + * + * + * + * + * \endverbatim + * + */ + enum LiquidTranMixingModel { LTI_MODEL_NOTSET=-1, LTI_MODEL_NONE, @@ -92,7 +97,9 @@ namespace Cantera { LTI_MODEL_MASSFRACS, LTI_MODEL_LOG_MOLEFRACS, LTI_MODEL_PAIRWISE_INTERACTION, - LTI_MODEL_STOKES_EINSTEIN + LTI_MODEL_STEFANMAXWELL_PPN, + LTI_MODEL_STOKES_EINSTEIN, + LTI_MODEL_MOLEFRACS_EXPT }; @@ -132,7 +139,7 @@ namespace Cantera { LiquidTranInteraction& operator=( const LiquidTranInteraction &right ); //! destructor - virtual ~LiquidTranInteraction() { ; } + virtual ~LiquidTranInteraction(); //! initialize LiquidTranInteraction objects with thermo and XML node /** @@ -172,14 +179,21 @@ namespace Cantera { //LiquidTransportParams* m_trParam; - //! Matrix of interactions (no temperature dependence, dimensionless) - DenseMatrix m_Aij; + //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (no temperature dependence, dimensionless) + std::vector m_Aij; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (linear temperature dependence, units 1/K) + std::vector m_Bij; //! Matrix of interactions (in energy units, 1/RT temperature dependence) DenseMatrix m_Eij; - //! Matrix of interactions (in entropy units, divided by R) - DenseMatrix m_Sij; + //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (in energy units, 1/RT temperature dependence) + std::vector m_Hij; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (in entropy units, divided by R) + std::vector m_Sij; + //DenseMatrix m_Sij; //! Matrix of interactions DenseMatrix m_Dij; @@ -205,6 +219,11 @@ namespace Cantera { std::vector LTData; LiquidTranInteraction* viscosity; + LiquidTranInteraction* ionConductivity; + std::vector mobilityRatio; + std::vector mobRatIndex; + std::vector selfDiffusion; + std::vector selfDiffIndex; LiquidTranInteraction* thermalCond; LiquidTranInteraction* speciesDiffusivity; LiquidTranInteraction* electCond; @@ -213,7 +232,19 @@ namespace Cantera { //! Model for species interaction effects for viscosity //! Takes enum LiquidTranMixingModel LiquidTranMixingModel model_viscosity; + + //! Model for species interaction effects for ionic conductivity + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel model_ionConductivity; + //! Model for species interaction effects for mobility ratio + //! Takes enum LiquidTranMixingModel + std::vector model_mobilityRatio; + + //! Model for species interaction effects for mobility ratio + //! Takes enum LiquidTranMixingModel + std::vector model_selfDiffusion; + //! Interaction associated with linear weighting of //! thermal conductivity. /** @@ -233,7 +264,7 @@ namespace Cantera { //! Interaction associated with linear weighting of //! thermal conductivity. /** - * This is used for either LTI_MODEL_PAIRWISE_INTERACTION. + * This is used for either LTI_MODEL_PAIRWISE_INTERACTION or LTI_MODEL_STEFANMAXWELL_PPN. * These provide species interaction coefficients associated with * the Stefan-Maxwell formulation. */ @@ -256,7 +287,8 @@ namespace Cantera { class LTI_MassFracs; class LTI_Log_MoleFracs; class LTI_Pairwise_Interaction; - + class LTI_StefanMaxwell_PPN; + class LTI_MoleFracs_ExpT; class LTI_Solvent : public LiquidTranInteraction { public: @@ -283,7 +315,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -325,7 +357,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -368,7 +400,7 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Aij; } + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -502,13 +534,84 @@ namespace Cantera { doublereal getMixTransProp( std::vector LTPptrs ) ; void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - protected: std::vector m_diagonals; }; + //! Stefan Maxwell Diffusion Coefficients can be solved for given + //! ion conductivity, mobility ratios, and self diffusion coeffs. + //! This method is only valid for a common anion mixture of two + //! salts with cations of equal charge. + /** + * This class requres you specify + * 1 - ion conductivity + * 2 - mobility ratio of the two cations + * 3 - mutual diffusion coefficient (can be approximated using + * the self diffusion coefficients of the cations + * + * Sample input for this method is + * \verbatim + * + * + * + * + * + * + * \endverbatim + * + */ + class LTI_StefanMaxwell_PPN : public LiquidTranInteraction { + + public: + LTI_StefanMaxwell_PPN( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_STEFANMAXWELL_PPN; + } + + + //! Copy constructor + // LTI_StefanMaxwell_PPN( const LTI_StefanMaxwell_PPN &right ); + + //! Assignment operator + // LTI_StefanMaxwell_PPN& operator=( const LTI_StefanMaxwell_PPN &right ); + + virtual ~LTI_StefanMaxwell_PPN( ) { } + + void setParameters( LiquidTransportParams& trParam ) ; + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; + //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) ; + + protected: + + doublereal m_ionCondMix; + LiquidTranInteraction * m_ionCondMixModel; + std::vector m_ionCondSpecies; + typedef std::vector LTPvector; + DenseMatrix m_mobRatMix; + std::vector m_mobRatMixModel; + std::vector m_mobRatSpecies; + std::vector m_mobRatIndex; + + std::vector m_selfDiffMixModel; + vector_fp m_selfDiffMix; + std::vector m_selfDiffSpecies; + std::vector m_selfDiffIndex; + }; + + class LTI_StokesEinstein : public LiquidTranInteraction { public: @@ -539,7 +642,6 @@ namespace Cantera { doublereal getMixTransProp( std::vector LTPptrs ) ; void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - protected: std::vector m_viscosity; @@ -547,6 +649,48 @@ namespace Cantera { }; + //! Simple mole fraction weighting of transport properties + /** + * This model weights the transport property by the mole + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ \eta_{mix} = \sum_i X_i \eta_i + * + \sum_i \sum_j X_i X_j A_{i,j} \f]. + */ + class LTI_MoleFracs_ExpT : public LiquidTranInteraction { + + public: + LTI_MoleFracs_ExpT( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_MOLEFRACS_EXPT; + } + + + //! Copy constructor + // LTI_MoleFracs_ExpT( const LTI_MoleFracs_ExpT &right ); + + //! Assignment operator + // LTI_MoleFracs_ExpT& operator=( const LTI_MoleFracs_ExpT &right ); + + virtual ~LTI_MoleFracs_ExpT( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + + protected: + + }; } diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 24ad9d137..7dd194f8c 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -28,7 +28,7 @@ #define CT_TRANSPORTBASE_H #include "ThermoPhase.h" - +#include "DenseMatrix.h" namespace Cantera { @@ -80,6 +80,8 @@ namespace Cantera { * - VB_MOLEAVG Diffusion velocities are based on the mole averaged velocities * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 + * - VB_SPECIES_2 Diffusion velocities are based on the relative motion wrt species 2 + * - VB_SPECIES_3 Diffusion velocities are based on the relative motion wrt species 3 * * @ingroup tranprops */ @@ -97,6 +99,10 @@ namespace Cantera { const VelocityBasis VB_SPECIES_0 = 0; //! Diffusion velocities are based on the relative motion wrt species 1 const VelocityBasis VB_SPECIES_1 = 1; + //! Diffusion velocities are based on the relative motion wrt species 2 + const VelocityBasis VB_SPECIES_2 = 2; + //! Diffusion velocities are based on the relative motion wrt species 3 + const VelocityBasis VB_SPECIES_3 = 3; //@} //! Base class for transport property managers. @@ -308,6 +314,68 @@ namespace Cantera { virtual doublereal bulkViscosity() { return err("bulkViscosity"); } + /** + * The ionic conducitivity in 1/ohm/m. + */ + virtual doublereal ionConductivity() + { return err("ionConductivity"); } + + //! Returns the pure species ionic conducitivity + /*! + * The units are 1/ohm/m and the length is the number of species + * + * @param ionCond Vector of ionic conductivities + */ + virtual void getSpecoesIonConductivity(doublereal* const ionCond) + { err("getSpeciesIonConductivity"); } + + + + /** + * The mobility ratio. + */ + virtual void mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex) + { err("mobilityRatio"); } + virtual void mobilityRatio(double* mobRat, std::vector& mobRatIndex) + { err("mobilityRatio"); } + + //! Returns the pure species limit of the mobility ratios + /*! + * The value is dimensionless and the length is the number of species + * + * @param mobRat Vector of mobility ratios + */ + virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex) + { err("getSpeciesMobilityRatio"); } + virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex) + { err("getSpeciesMobilityRatio"); } + + //! Returns the self diffusion coefficients in the solution + /*! + * The self diffusion calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. + * These in turn employ subclasses of LTPspecies to + * determine the individual species self diffusion coeffs. + */ + virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex) + { err("selfDiffusion"); } + virtual void selfDiffusion(double* selfDiff, std::vector& selfDiffIndex) + { err("selfdiffusion"); } + + //! Returns the pure species self diffusion in solution of each species + /*! + * The pure species molar volumes are evaluated using the + * appropriate subclasses of LTPspecies as specified in the + * input file. + * + * @param selfDiff array of length "number of species" + * to hold returned self diffusion coeffs. + */ + virtual void getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex) + { err("getSpeciesSelfDiffusion"); } + virtual void getSpeciesSelfDiffusion(double** selfDiff, std::vector& selfDiffIndex) + { err("getSpeciesSelfDiffusion"); } + //! Returns the mixture thermal conductivity in W/m/K. /*! * Units are in W / m K or equivalently kg m / s3 K diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index a69ba0d77..f000345e2 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -232,6 +232,9 @@ namespace Cantera { //m_models["Radiative"] = cRadiative; m_tranPropMap["viscostiy"] = TP_VISCOSITY; + m_tranPropMap["ionConductivity"] = TP_IONCONDUCTIVITY; + m_tranPropMap["mobilityRatio"] = TP_MOBILITYRATIO; + m_tranPropMap["selfDiffusion"] = TP_SELFDIFFUSION; m_tranPropMap["thermalConductivity"] = TP_THERMALCOND; m_tranPropMap["speciesDiffusivity"] = TP_DIFFUSIVITY; m_tranPropMap["hydrodynamicRadius"] = TP_HYDRORADIUS; @@ -241,6 +244,7 @@ namespace Cantera { m_LTRmodelMap["constant"] = LTR_MODEL_CONSTANT; m_LTRmodelMap["arrhenius"] = LTR_MODEL_ARRHENIUS; m_LTRmodelMap["coeffs"] = LTR_MODEL_POLY; + m_LTRmodelMap["exptemp"] = LTR_MODEL_EXPT; m_LTImodelMap[""] = LTI_MODEL_NOTSET; m_LTImodelMap["none"] = LTI_MODEL_NONE; @@ -249,6 +253,8 @@ namespace Cantera { m_LTImodelMap["massFractions"] = LTI_MODEL_MASSFRACS; m_LTImodelMap["logMoleFractions"] = LTI_MODEL_LOG_MOLEFRACS; m_LTImodelMap["pairwiseInteraction"] = LTI_MODEL_PAIRWISE_INTERACTION; + m_LTImodelMap["stefanMaxwell_PPN"] = LTI_MODEL_STEFANMAXWELL_PPN; + m_LTImodelMap["moleFractionsExpT"] = LTI_MODEL_MOLEFRACS_EXPT; } /** @@ -312,6 +318,12 @@ namespace Cantera { tp_ind, thermo ); break; + case LTR_MODEL_EXPT: + ltps = new LTPspecies_ExpT( trNode, + name, + tp_ind, + thermo ); + break; default: throw CanteraError("newLTP","unknown transport model: " + model ); ltps = new LTPspecies( trNode, @@ -359,11 +371,20 @@ namespace Cantera { lti->init( trNode, thermo ); lti->setParameters( trParam ); break; + case LTI_MODEL_STEFANMAXWELL_PPN: + lti = new LTI_StefanMaxwell_PPN( tp_ind ); + lti->init( trNode, thermo ); + lti->setParameters( trParam ); + break; case LTI_MODEL_STOKES_EINSTEIN: lti = new LTI_StokesEinstein( tp_ind ); lti->init( trNode, thermo ); lti->setParameters( trParam ); break; + case LTI_MODEL_MOLEFRACS_EXPT: + lti = new LTI_MoleFracs_ExpT( tp_ind ); + lti->init( trNode, thermo ); + break; default: // throw CanteraError("newLTI","unknown transport model: " + model ); lti = new LiquidTranInteraction( tp_ind ); @@ -966,7 +987,7 @@ namespace Cantera { for (int iChild = 0; iChild < num; iChild++) { XML_Node &xmlChild = trNode.child(iChild); std::string nodeName = xmlChild.name(); - + switch ( m_tranPropMap[nodeName] ) { case TP_VISCOSITY: data.viscosity = newLTP( xmlChild, @@ -974,23 +995,63 @@ namespace Cantera { m_tranPropMap[nodeName], trParam.thermo ); break; + case TP_IONCONDUCTIVITY: + data.ionConductivity = newLTP( xmlChild, + name, + m_tranPropMap[nodeName], + trParam.thermo ); + break; + case TP_MOBILITYRATIO: + { + int iSpec; + int numSpec = xmlChild.nChildren(); + data.mobRatIndex.resize(numSpec); + data.mobilityRatio.resize(numSpec); + for (iSpec = 0; iSpec< numSpec; iSpec++){ + XML_Node &propSpecNode = xmlChild.child(iSpec); + std::string specName = propSpecNode.name(); + data.mobRatIndex[iSpec] = specName; + data.mobilityRatio[iSpec] = newLTP( propSpecNode, + name, + m_tranPropMap[nodeName], + trParam.thermo ); + }; + }; + break; + case TP_SELFDIFFUSION: + { + int iSpec; + int numSpec = xmlChild.nChildren(); + data.selfDiffIndex.resize(numSpec); + data.selfDiffusion.resize(numSpec); + for (iSpec = 0; iSpec< numSpec; iSpec++){ + XML_Node &propSpecNode = xmlChild.child(iSpec); + std::string specName = propSpecNode.name(); + data.selfDiffIndex[iSpec] = specName; + data.selfDiffusion[iSpec] = newLTP( propSpecNode, + name, + m_tranPropMap[nodeName], + trParam.thermo ); + }; + }; + break; case TP_THERMALCOND: data.thermalCond = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_DIFFUSIVITY: data.speciesDiffusivity = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_HYDRORADIUS: data.hydroRadius = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_ELECTCOND: data.electCond = newLTP( xmlChild, @@ -1005,8 +1066,8 @@ namespace Cantera { } } - - datatable[name] = data; + datatable.insert(pair(name,data)); + // datatable[name] = data; } } catch(CanteraError) { @@ -1059,12 +1120,10 @@ namespace Cantera { for (int iChild = 0; iChild < num; iChild++) { //tranTypeNode is a type of transport property like viscosity XML_Node &tranTypeNode = transportNode.child(iChild); - if (tranTypeNode.hasChild("compositionDependence")) { + std::string nodeName = tranTypeNode.name(); + if ( tranTypeNode.hasChild("compositionDependence")) { //compDepNode contains the interaction model XML_Node &compDepNode = tranTypeNode.child("compositionDependence"); - - std::string nodeName = tranTypeNode.name(); - switch (m_tranPropMap[nodeName]) { break; case TP_VISCOSITY: @@ -1072,6 +1131,43 @@ namespace Cantera { m_tranPropMap[nodeName], trParam ); break; + case TP_IONCONDUCTIVITY: + trParam.ionConductivity = newLTI( compDepNode, + m_tranPropMap[nodeName], + trParam ); + break; + case TP_MOBILITYRATIO: + { + int iSpec; + int numSpec = compDepNode.nChildren(); + trParam.mobRatIndex.resize(numSpec); + trParam.mobilityRatio.resize(numSpec); + for (iSpec = 0; iSpec< numSpec; iSpec++){ + XML_Node &propSpecNode = compDepNode.child(iSpec); + std::string specName = propSpecNode.name(); + trParam.mobRatIndex[iSpec] = specName; + trParam.mobilityRatio[iSpec] = newLTI( propSpecNode, + m_tranPropMap[nodeName], + trParam ); + }; + }; + break; + case TP_SELFDIFFUSION: + { + int iSpec; + int numSpec = compDepNode.nChildren(); + trParam.selfDiffIndex.resize(numSpec); + trParam.selfDiffusion.resize(numSpec); + for (iSpec = 0; iSpec< numSpec; iSpec++){ + XML_Node &propSpecNode = compDepNode.child(iSpec); + std::string specName = propSpecNode.name(); + trParam.selfDiffIndex[iSpec] = specName; + trParam.selfDiffusion[iSpec] = newLTI( propSpecNode, + m_tranPropMap[nodeName], + trParam ); + }; + }; + break; case TP_THERMALCOND: trParam.thermalCond = newLTI( compDepNode, m_tranPropMap[nodeName], @@ -1122,15 +1218,17 @@ namespace Cantera { trParam.velocityBasis_ = trParam.thermo->speciesIndex(velocityBasis) ; else { int linenum; - throw TransportDBError( linenum, "Unknown attribute " + velocityBasis + " for node. "); + throw TransportDBError( linenum, "Unknown attribute \"" + velocityBasis + "\" for node. "); } - } } } - catch(CanteraError) { - ; + catch (CanteraError) { + showErrors(std::cout); } + //catch(CanteraError) { + // ; + //} return; } From 263aeb6b35dbd87353e84cbfef91760b51f8dc13 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 1 Mar 2010 18:14:07 +0000 Subject: [PATCH 110/446] Added a new way to specify the kinetics reaction rate coefficient when dealing with electron transfer surface reactions. This way specifies an exchange current density reaction rate coefficient in units of amps / m2. This is slightly more informative for electrode reactions. The new also preserves the correct treatment of activity coefficients for these reactions. A memo describing this new capability is in the works. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 185 +++++++--- Cantera/src/kinetics/InterfaceKinetics.h | 140 ++++++-- Cantera/src/kinetics/Kinetics.cpp | 26 +- Cantera/src/kinetics/Kinetics.h | 5 +- Cantera/src/kinetics/ReactionData.h | 14 +- Cantera/src/kinetics/ReactionStoichMgr.h | 1 + Cantera/src/kinetics/RxnRates.h | 397 +++++++++++++-------- Cantera/src/kinetics/importKinetics.cpp | 24 ++ Cantera/src/kinetics/reaction_defs.h | 11 +- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 27 +- Cantera/src/thermo/GibbsExcessVPSSTP.h | 39 +- configure | 165 ++++++++- configure.in | 21 ++ data/thermo/nasathermo.dat | 4 +- tools/src/cti2ctml.cpp | 17 +- 15 files changed, 781 insertions(+), 295 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 090b8585e..338e10014 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -25,9 +25,8 @@ using namespace std; namespace Cantera { - ////////////////////////////////////////////////////////////////// - - /** + //==================================================================================================================== + /* * Construct an empty InterfaceKinetics reaction mechanism. * @param thermo This is an optional parameter that may be * used to initialize the inherited Kinetics class with @@ -35,8 +34,7 @@ namespace Cantera { * useful for initialization of homogeneous kinetics * mechanisms. */ - InterfaceKinetics:: - InterfaceKinetics(thermo_t* thermo) : + InterfaceKinetics::InterfaceKinetics(thermo_t* thermo) : Kinetics(), m_kk(0), m_redo_rates(false), @@ -44,27 +42,33 @@ namespace Cantera { m_nrev(0), m_surf(0), m_integrator(0), + m_beta(0), + m_ctrxn(0), + m_ctrxn_ecdf(0), + m_logStandardConc(0), + m_deltaG0(0), + m_logProdStanConcReac(0), m_finalized(false), m_has_coverage_dependence(false), m_has_electrochem_rxns(false), + m_has_exchange_current_density_formulation(false), m_ioFlag(0) { if (thermo != 0) addPhase(*thermo); m_kdata = new InterfaceKineticsData; m_kdata->m_temp = 0.0; } - - /** + //==================================================================================================================== + /* * Destructor */ - InterfaceKinetics:: - ~InterfaceKinetics(){ + InterfaceKinetics::~InterfaceKinetics(){ delete m_kdata; if (m_integrator) { delete m_integrator; } } - + //==================================================================================================================== // Copy Constructor for the %InterfaceKinetics object. /* * Currently, this is not fully implemented. If called it will @@ -78,9 +82,16 @@ namespace Cantera { m_nrev(0), m_surf(0), m_integrator(0), + m_beta(0), + m_ctrxn(0), + m_ctrxn_ecdf(0), + m_logStandardConc(0), + m_deltaG0(0), + m_logProdStanConcReac(0), m_finalized(false), m_has_coverage_dependence(false), m_has_electrochem_rxns(false), + m_has_exchange_current_density_formulation(false), m_ioFlag(0) { m_kdata = new InterfaceKineticsData; @@ -90,7 +101,7 @@ namespace Cantera { */ *this = operator=(right); } - + //==================================================================================================================== // Assignment operator /* * This is NOT a virtual function. @@ -127,19 +138,23 @@ namespace Cantera { m_E = right.m_E; m_surf = right.m_surf; //DANGER - shallow copy m_integrator = right.m_integrator; //DANGER - shallow copy + m_beta = right.m_beta; m_ctrxn = right.m_ctrxn; + m_ctrxn_ecdf = right.m_ctrxn_ecdf; + m_logStandardConc = right.m_logStandardConc; + m_deltaG0 = right.m_deltaG0; + m_logProdStanConcReac = right.m_logProdStanConcReac; m_finalized = right.m_finalized; m_has_coverage_dependence = right.m_has_coverage_dependence; m_has_electrochem_rxns = right.m_has_electrochem_rxns; + m_has_exchange_current_density_formulation = right.m_has_exchange_current_density_formulation; m_ioFlag = right.m_ioFlag; return *this; } - - - // Duplication routine for objects which inherit from - // Kinetics + //==================================================================================================================== + // Duplication routine for objects which inherit from Kinetics /* * This virtual routine can be used to duplicate %Kinetics objects * inherited from %Kinetics even if the application only has @@ -152,14 +167,18 @@ namespace Cantera { InterfaceKinetics* tp = new InterfaceKinetics(*this); return dynamic_cast(tp); } - - - /** - * Update properties that depend on temperature + //==================================================================================================================== + // Update properties that depend on temperature + /* + * This is called to update all of the properties that depend on temperature * - */ - void InterfaceKinetics:: - _update_rates_T() { + * Current objects that this function updates + * m_kdata->m_logtemp + * m_kdata->m_rfn + * m_rates. + * updateKc(); + */ + void InterfaceKinetics::_update_rates_T() { _update_rates_phi(); if (m_has_coverage_dependence) { m_surf->getCoverages(DATA_PTR(m_conc)); @@ -167,20 +186,24 @@ namespace Cantera { m_redo_rates = true; } doublereal T = thermo(surfacePhaseIndex()).temperature(); + m_redo_rates = true; if (T != m_kdata->m_temp || m_redo_rates) { m_kdata->m_logtemp = log(T); m_rates.update(T, m_kdata->m_logtemp, DATA_PTR(m_kdata->m_rfn)); - if (m_has_electrochem_rxns) + if (m_has_exchange_current_density_formulation) { + applyExchangeCurrentDensityFormulation(DATA_PTR(m_kdata->m_rfn)); + } + if (m_has_electrochem_rxns) { applyButlerVolmerCorrection(DATA_PTR(m_kdata->m_rfn)); + } m_kdata->m_temp = T; updateKc(); m_kdata->m_ROP_ok = false; m_redo_rates = false; } } - - void InterfaceKinetics:: - _update_rates_phi() { + //==================================================================================================================== + void InterfaceKinetics::_update_rates_phi() { int np = nPhases(); for (int n = 0; n < np; n++) { if (thermo(n).electricPotential() != m_phi[n]) { @@ -189,6 +212,7 @@ namespace Cantera { } } } + //==================================================================================================================== /** @@ -198,8 +222,7 @@ namespace Cantera { * representing phases should overload to return the appropriate * quantities. */ - void InterfaceKinetics:: - _update_rates_C() { + void InterfaceKinetics::_update_rates_C() { int n; int np = nPhases(); @@ -263,6 +286,8 @@ namespace Cantera { } } } + //==================================================================================================================== + void InterfaceKinetics::checkPartialEquil() { @@ -338,6 +363,36 @@ namespace Cantera { } } + void InterfaceKinetics::getExchangeCurrentQuantities() { + /* + * First collect vectors of the standard Gibbs free energies of the + * species and the standard concentrations + * - m_mu0 + * - m_logStandardConc + */ + int ik = 0; + int np = nPhases(); + + for (int n = 0; n < np; n++) { + thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]); + int nsp = thermo(n).nSpecies(); + for (int k = 0; k < nsp; k++) { + m_logStandardConc[ik] = thermo(n).logStandardConc(k); + ik++; + } + } + + m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_mu0), DATA_PTR(m_deltaG0)); + + + for (int i = 0; i < m_ii; i++) { + m_logProdStanConcReac[i] = 1.0; + } + + m_rxnstoich.multiplyReactants(DATA_PTR(m_logStandardConc), DATA_PTR(m_logProdStanConcReac)); + + } + // Returns the Species creation rates [kmol/m^2/s]. /* * Return the species @@ -385,12 +440,17 @@ namespace Cantera { net); } - /** + //==================================================================================================================== + // Apply corrections for interfacial charge transfer reactions + /* * For reactions that transfer charge across a potential difference, * the activation energies are modified by the potential difference. * (see, for example, ...). This method applies this correction. + * + * @param kf Vector of forward reaction rate constants on which to have + * the correction applied */ - void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* kf) { + void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* const kf) { int i; int n, nsp, k, ik=0; @@ -410,8 +470,7 @@ namespace Cantera { // Compute the change in electrical potential energy for each // reaction. This will only be non-zero if a potential // difference is present. - m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot), - DATA_PTR(m_rwork)); + m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_pot), DATA_PTR(m_rwork)); // Modify the reaction rates. Only modify those with a // non-zero activation energy. Below we decrease the @@ -432,7 +491,8 @@ namespace Cantera { for (i = 0; i < nct; i++) { irxn = m_ctrxn[i]; eamod = m_beta[i]*m_rwork[irxn]; - if (eamod != 0.0 && m_E[irxn] != 0.0) { + // if (eamod != 0.0 && m_E[irxn] != 0.0) { + if (eamod != 0.0) { #ifdef DEBUG_KIN_MODE ea = GasConstant * m_E[irxn]; if (eamod + ea < 0.0) { @@ -450,18 +510,31 @@ namespace Cantera { } } } + //==================================================================================================================== + void InterfaceKinetics::applyExchangeCurrentDensityFormulation(doublereal* const kfwd) { + getExchangeCurrentQuantities(); + int nct = m_ctrxn.size(); + doublereal rt = GasConstant*thermo(0).temperature(); + doublereal rrt = 1.0/rt; + for (int i = 0; i < nct; i++) { + int irxn = m_ctrxn[i]; + int iECDFormulation = m_ctrxn_ecdf[i]; + if (iECDFormulation) { + double tmp = exp(- m_beta[i] * m_deltaG0[irxn] * rrt); + tmp *= 1.0 / m_logProdStanConcReac[irxn] / Faraday; + kfwd[irxn] *= tmp; + } + } - - + } + //==================================================================================================================== /** * Update the rates of progress of the reactions in the reaciton * mechanism. This routine operates on internal data. */ void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd) { - // _update_rates_T(); - // _update_rates_C(); updateROP(); const vector_fp& rf = m_kdata->m_rfn; @@ -738,7 +811,7 @@ namespace Cantera { m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaS); } - + //==================================================================================================================== /** * Add a single reaction to the mechanism. This routine * must be called after init() and before finalize(). @@ -752,8 +825,7 @@ namespace Cantera { * There is no difference between elementary and surface * reactions. */ - void InterfaceKinetics:: - addReaction(const ReactionData& r) { + void InterfaceKinetics::addReaction(const ReactionData& r) { addElementaryReaction(r); @@ -763,10 +835,8 @@ namespace Cantera { incrementRxnCount(); m_rxneqn.push_back(r.equation); } - - - void InterfaceKinetics:: - addElementaryReaction(const ReactionData& r) { + //==================================================================================================================== + void InterfaceKinetics::addElementaryReaction(const ReactionData& r) { int iloc; // install rate coeff calculator @@ -776,12 +846,11 @@ namespace Cantera { if (ncov > 3) { m_has_coverage_dependence = true; } - for (int m = 0; m < ncov; m++) rp.push_back(r.cov[m]); - - iloc = m_rates.install( reactionNumber(), - r.rateCoeffType, rp.size(), - DATA_PTR(rp) ); - + for (int m = 0; m < ncov; m++) { + rp.push_back(r.cov[m]); + } + // iloc = m_rates.install(reactionNumber(), r.rateCoeffType, rp.size(), DATA_PTR(rp)); + iloc = m_rates.install(reactionNumber(), ARRHENIUS_REACTION_RATECOEFF_TYPE, rp.size(), DATA_PTR(rp)); // store activation energy m_E.push_back(r.rateCoeffParameters[2]); @@ -789,13 +858,19 @@ namespace Cantera { m_has_electrochem_rxns = true; m_beta.push_back(r.beta); m_ctrxn.push_back(reactionNumber()); + if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) { + m_has_exchange_current_density_formulation = true; + m_ctrxn_ecdf.push_back(1); + } else { + m_ctrxn_ecdf.push_back(0); + } } // add constant term to rate coeff value vector m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc); } - + //==================================================================================================================== void InterfaceKinetics::setIOFlag(int ioFlag) { m_ioFlag = ioFlag; @@ -958,6 +1033,7 @@ namespace Cantera { * since we don't know this number up to now. */ void InterfaceKinetics::finalize() { + Kinetics::finalize(); m_rwork.resize(nReactions()); int ks = reactionPhaseIndex(); if (ks < 0) throw CanteraError("InterfaceKinetics::finalize", @@ -967,6 +1043,13 @@ namespace Cantera { throw CanteraError("InterfaceKinetics::finalize", "expected interface dimension = 2, but got dimension = " +int2str(m_surf->nDim())); + + + + m_logStandardConc.resize(m_nTotalSpecies, 0.0); + m_deltaG0.resize(m_ii, 0.0); + m_logProdStanConcReac.resize(m_ii, 0.0); + m_finalized = true; } diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index c1b0343a8..a7bc89582 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -45,11 +45,15 @@ namespace Cantera { class InterfaceKineticsData { public: InterfaceKineticsData() : + m_logp0(0.0), + m_logc0(0.0), m_ROP_ok(false), - m_temp(0.0), m_logtemp(0.0) + m_temp(0.0), + m_logtemp(0.0) {} //! Virtual destructor - virtual ~InterfaceKineticsData(){} + virtual ~InterfaceKineticsData() { + } doublereal m_logp0; doublereal m_logc0; @@ -59,7 +63,9 @@ namespace Cantera { bool m_ROP_ok; + //! Current temperature of the data doublereal m_temp; + //! Current log of the temperature doublereal m_logtemp; vector_fp m_rfn; vector_fp m_rkcn; @@ -76,9 +82,9 @@ namespace Cantera { public: - /** - * Constructor - * + + //! Constructor + /*! * @param thermo The optional parameter may be used to initialize * the object with one ThermoPhase object. * HKM Note -> Since the interface kinetics @@ -125,9 +131,9 @@ namespace Cantera { virtual int ID() const { return cInterfaceKinetics; } virtual int type() const { return cInterfaceKinetics; } - /** - * Set the electric potential in the nth phase - * + + //! Set the electric potential in the nth phase + /*! * @param n phase Index in this kinetics object. * @param V Electric potential (volts) */ @@ -172,8 +178,17 @@ namespace Cantera { std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP); } + + //! Get the equilibrium constants of all reactions, whether + //! the reaction is reversible or not. + /*! + * @param kc Returns the concentration equation constant for the reaction. + * Length is the number of reactions + */ virtual void getEquilibriumConstants(doublereal* kc); + void getExchangeCurrentQuantities(); + virtual void getDeltaGibbs( doublereal* deltaG); @@ -394,8 +409,19 @@ namespace Cantera { void updateROP(); - + + //! Update properties that depend on temperature + /*! + * This is called to update all of the properties that depend on temperature + * + * Current objects that this function updates + * m_kdata->m_logtemp + * m_kdata->m_rfn + * m_rates. + * updateKc(); + */ void _update_rates_T(); + void _update_rates_phi(); void _update_rates_C(); @@ -445,12 +471,50 @@ namespace Cantera { void setIOFlag(int ioFlag); void checkPartialEquil(); - + + + int reactionNumber() const { return m_ii;} + + void addElementaryReaction(const ReactionData& r); + void addGlobalReaction(const ReactionData& r); + void installReagents(const ReactionData& r); + + void updateKc(); + + //! Write values into m_index + /*! + * @param rxnNumber reaction number + * @param type reaction type + * @param loc location ?? + */ + void registerReaction(int rxnNumber, int type, int loc) { + m_index[rxnNumber] = std::pair(type, loc); + } + + //! Apply corrections for interfacial charge transfer reactions + /*! + * For reactions that transfer charge across a potential difference, + * the activation energies are modified by the potential difference. + * (see, for example, ...). This method applies this correction. + * + * @param kf Vector of forward reaction rate constants on which to have + * the correction applied + */ + void applyButlerVolmerCorrection(doublereal* const kf); + + //! When an electrode reaction rate is optionally specified in terms of its + //! exchange current density, extra vectors need to be precalculated + /*! + * + */ + void applyExchangeCurrentDensityFormulation(doublereal* const kfwd); + + + protected: + //! Temporary work vector of length m_kk vector_fp m_grt; - protected: - //! m_kk is the number of species in all of the phases //! that participate in this kinetics mechanism. int m_kk; @@ -489,7 +553,7 @@ namespace Cantera { * production rates and also handles turning thermo * properties into reaction thermo properties. */ - ReactionStoichMgr m_rxnstoich; + ReactionStoichMgr m_rxnstoich; //! Number of irreversible reactions in the mechanism int m_nirrev; @@ -607,42 +671,58 @@ namespace Cantera { ImplicitSurfChem* m_integrator; vector_fp m_beta; + + //! Vector of reaction indexes specifying the id of the current transfer reactions + //! in the mechanism + /*! + * Vector of reaction indecices which involve current transfers. This provides + * an index into the m_beta array. + * + * irxn = m_ctrxn[i] + */ vector_int m_ctrxn; - int reactionNumber(){ return m_ii;} + //! Vector of booleans indicating whether the charge transfer reaction may be + //! described by an exchange current density expression + vector_int m_ctrxn_ecdf; - void addElementaryReaction(const ReactionData& r); - void addGlobalReaction(const ReactionData& r); - void installReagents(const ReactionData& r); + vector_fp m_logStandardConc; + vector_fp m_deltaG0; + vector_fp m_logProdStanConcReac; - void updateKc(); - //! Write values into m_index - /*! - * @param rxnNumber reaction number - * @param type reaction type - * @param loc location ?? - */ - void registerReaction(int rxnNumber, int type, int loc) { - m_index[rxnNumber] = std::pair(type, loc); - } - - void applyButlerVolmerCorrection(doublereal* kf); //! boolean indicating whether mechanism has been finalized bool m_finalized; + + //! Boolean flag indicating whether any reaction in the mechanism + //! has a coverage dependent forward reaction rate + /*! + * If this is true, then the coverage dependence is multiplied into + * the forward reaction rates constant + */ bool m_has_coverage_dependence; //! Boolean flag indicating whether any reaction in the mechanism //! has a beta electrochemical parameter. /*! - * If this is true, the the Butler-Volmer correction is applied + * If this is true, the Butler-Volmer correction is applied * to the forward reaction rate for those reactions. * * fac = exp ( - beta * (delta_phi)) */ bool m_has_electrochem_rxns; + //! Boolean flag indicating whether any reaction in the mechanism + //! is described by an exchange current density expression + /*! + * If this is true, the standard state gibbs free energy of the reaction and + * the product of the reactant standard concentrations must be precalculated + * in order to calculate the rate constant. + */ + bool m_has_exchange_current_density_formulation; + + int m_ioFlag; private: diff --git a/Cantera/src/kinetics/Kinetics.cpp b/Cantera/src/kinetics/Kinetics.cpp index 38ea75fe0..1c45823a2 100644 --- a/Cantera/src/kinetics/Kinetics.cpp +++ b/Cantera/src/kinetics/Kinetics.cpp @@ -29,9 +29,16 @@ using namespace std; namespace Cantera { - Kinetics::Kinetics() : m_ii(0), m_thermo(0), - m_index(-1), m_surfphase(-1), m_rxnphase(-1), - m_mindim(4) {} + Kinetics::Kinetics() : + m_ii(0), + m_nTotalSpecies(0), + m_thermo(0), + m_index(-1), + m_surfphase(-1), + m_rxnphase(-1), + m_mindim(4) + { + } Kinetics::~Kinetics(){} @@ -42,7 +49,8 @@ namespace Cantera { * throw an exception. */ Kinetics::Kinetics(const Kinetics &right) : - m_ii(0), + m_ii(0), + m_nTotalSpecies(0), m_thermo(0), m_index(-1), m_surfphase(-1), @@ -70,6 +78,7 @@ namespace Cantera { if (this == &right) return *this; m_ii = right.m_ii; + m_nTotalSpecies = right.m_nTotalSpecies; m_perturb = right.m_perturb; m_reactants = right.m_reactants; m_products = right.m_products; @@ -285,6 +294,15 @@ namespace Cantera { m_phaseindex[m_thermo.back()->id()] = nPhases(); } + void Kinetics::finalize() { + m_nTotalSpecies = 0; + int np = nPhases(); + for (int n = 0; n < np; n++) { + int nsp = m_thermo[n]->nSpecies(); + m_nTotalSpecies += nsp; + } + } + //! Private function of the class Kinetics, indicating that a function //! inherited from the base class hasn't had a definition assigned to it diff --git a/Cantera/src/kinetics/Kinetics.h b/Cantera/src/kinetics/Kinetics.h index 25ca5305f..33b63263b 100644 --- a/Cantera/src/kinetics/Kinetics.h +++ b/Cantera/src/kinetics/Kinetics.h @@ -811,7 +811,7 @@ namespace Cantera { * any initialization (allocating arrays, etc.) that must be * done after the reactions are entered. */ - virtual void finalize() {} + virtual void finalize(); /** * Add a single reaction to the mechanism. This routine @@ -904,6 +904,9 @@ namespace Cantera { //! Number of reactions in the mechanism int m_ii; + + //! Number of species in the species vector for this kinetics operator + int m_nTotalSpecies; /// Vector of perturbation factors for each reaction's rate of /// progress vector. It is initialized to one. diff --git a/Cantera/src/kinetics/ReactionData.h b/Cantera/src/kinetics/ReactionData.h index a02d25f8e..5c4f8c466 100644 --- a/Cantera/src/kinetics/ReactionData.h +++ b/Cantera/src/kinetics/ReactionData.h @@ -25,7 +25,7 @@ namespace Cantera { number = 0; rxn_number = 0; reversible = true; - rateCoeffType = ARRHENIUS; + rateCoeffType = ARRHENIUS_REACTION_RATECOEFF_TYPE; falloffType = NONE; error = 0; equation = ""; @@ -36,7 +36,12 @@ namespace Cantera { } virtual ~ReactionData(){} + //! type of the reaction + /*! + * The valid types are listed in the file, reaction_defs.h. + */ int reactionType; + int number; int rxn_number; vector_int reactants; @@ -51,7 +56,14 @@ namespace Cantera { //! True if the current reaction is reversible. False otherwise bool reversible; + + //! type of the rate coefficient for the forward rate constant + /*! + * The valid types are listed in the file, reaction_defs.h and they + * all end in RATECOEFF_TYPE + */ int rateCoeffType; + vector_fp rateCoeffParameters; vector_fp auxRateCoeffParameters; int falloffType; diff --git a/Cantera/src/kinetics/ReactionStoichMgr.h b/Cantera/src/kinetics/ReactionStoichMgr.h index 203bfc5e4..eba12e5d5 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.h +++ b/Cantera/src/kinetics/ReactionStoichMgr.h @@ -214,6 +214,7 @@ namespace Cantera { * \f[ * R_i = R_i * \prod_k C_k^{o_{k,i}} * \f] + * * Here \f$ o_{k,i} \f$ is the reaction order of species k in reaction i. */ virtual void multiplyReactants(const doublereal* C, doublereal* R); diff --git a/Cantera/src/kinetics/RxnRates.h b/Cantera/src/kinetics/RxnRates.h index 4e3d495ad..bb9ba6937 100644 --- a/Cantera/src/kinetics/RxnRates.h +++ b/Cantera/src/kinetics/RxnRates.h @@ -19,93 +19,100 @@ namespace Cantera { - /** - * A rate coefficient of the form - * \f[ - * A T^b \exp (-E/RT) - * \f] + //! Arrhenius reaction rate type depends only on temperature + /** + * A reaction rate coefficient of the following form. + * + * \f[ + * k_f = A T^b \exp (-E/RT) + * \f] + * + */ + class Arrhenius { + + public: + + //! return the rate coefficient type. + static int type() { + return ARRHENIUS_REACTION_RATECOEFF_TYPE; + } + + //! Default constructor. + Arrhenius() : + m_logA(-1.0E300), + m_b (0.0), + m_E (0.0), + m_A(0.0) {} + + //! Constructor with Arrhenius parameters specified with an array. + Arrhenius(int csize, const doublereal* c) : + m_b (c[1]), + m_E (c[2]), + m_A (c[0]) + { + if (m_A <= 0.0) { + m_logA = -1.0E300; + } else { + m_logA = log(m_A); + } + } + + /// Constructor. + /// @param A pre-exponential. The unit system is + /// (kmol, m, s). The actual units depend on the reaction + /// order and the dimensionality (surface or bulk). + /// @param b Temperature exponent. Non-dimensional. + /// @param E Activation energy in temperature units. Kelvin. + Arrhenius(doublereal A, doublereal b, doublereal E) : + m_b (b), + m_E (E), + m_A (A) + { + if (m_A <= 0.0) { + m_logA = -1.0E300; + } else { + m_logA = log(m_A); + } + } + + //! Update concentration-dependent parts of the rate coefficient. + /*! + * For this class, there are no + * concentration-dependent parts, so this method does nothing. */ - class Arrhenius { - - public: + void update_C(const doublereal* c) { + } - /// return the rate coefficient type. - static int type(){ return ARRHENIUS; } - - /// Default constructor. - Arrhenius() : - m_logA(-1.0E300), - m_b (0.0), - m_E (0.0), - m_A(0.0) {} - - /// Constructor with Arrhenius parameters specified with an array. - Arrhenius(int csize, const doublereal* c) : - m_b (c[1]), - m_E (c[2]), - m_A (c[0]) - { - if (m_A <= 0.0) { - m_logA = -1.0E300; - } else { - m_logA = log(m_A); - } - } - - /// Constructor. - /// @param A pre-exponential. The unit system is - /// (kmol, m, s). The actual units depend on the reaction - /// order and the dimensionality (surface or bulk). - /// @param b Temperature exponent. Non-dimensional. - /// @param E Activation energy in temperature units. Kelvin. - Arrhenius(doublereal A, doublereal b, doublereal E) : - m_b (b), - m_E (E), - m_A (A) - { - if (m_A <= 0.0) { - m_logA = -1.0E300; - } else { - m_logA = log(m_A); - } - } - - /// Update concentration-dependent parts of the rate - /// coefficient. For this class, there are no - /// concentration-dependent parts, so this method does - /// nothing. - void update_C(const doublereal* c) {} + /** + * Update the value of the logarithm of the rate constant. + * + * Note, this function should never be called for negative A values. + * If it does then it will produce a negative overflow result, and + * a zero net forwards reaction rate, instead of a negative reaction + * rate constant that is the expected result. + */ + doublereal update(doublereal logT, doublereal recipT) const { + return m_logA + m_b*logT - m_E*recipT; + } - /** - * Update the value of the logarithm of the rate constant. - * - * Note, this function should never be called for negative A values. - * If it does then it will produce a negative overflow result, and - * a zero net forwards reaction rate, instead of a negative reaction - * rate constant that is the expected result. - */ - doublereal update(doublereal logT, doublereal recipT) const { - return m_logA + m_b*logT - m_E*recipT; - } - - /** - * Update the value the rate constant. - * - * This function returns the actual value of the rate constant. - * It can be safely called for negative values of the pre-exponential - * factor. - */ - doublereal updateRC(doublereal logT, doublereal recipT) const { - return m_A * exp(m_b*logT - m_E*recipT); - } + /** + * Update the value the rate constant. + * + * This function returns the actual value of the rate constant. + * It can be safely called for negative values of the pre-exponential + * factor. + */ + doublereal updateRC(doublereal logT, doublereal recipT) const { + return m_A * exp(m_b*logT - m_E*recipT); + } - void writeUpdateRHS(std::ostream& s) const { - s << " exp(" << m_logA; - if (m_b != 0.0) s << " + " << m_b << " * tlog"; - if (m_E != 0.0) s << " - " << m_E << " * rt"; - s << ");" << std::endl; - } + void writeUpdateRHS(std::ostream& s) const { + s << " exp(" << m_logA; + if (m_b != 0.0) s << " + " << m_b << " * tlog"; + if (m_E != 0.0) s << " - " << m_E << " * rt"; + s << ");" << std::endl; + } doublereal activationEnergy_R() const { return m_E; @@ -121,19 +128,22 @@ namespace Cantera { class ArrheniusSum { public: - static int type(){ return ARRHENIUS_SUM; } + static int type() { + return ARRHENIUS_SUM_REACTION_RATECOEFF_TYPE; + } + ArrheniusSum() : m_nterms(0) {} void addArrheniusTerm(doublereal A, doublereal b, doublereal E) { - if (A > 0.0) { - m_terms.push_back(Arrhenius(A, b, E)); - m_sign.push_back(1); - } - else if (A < 0.0) { - m_terms.push_back(Arrhenius(-A, b, E)); - m_sign.push_back(-1); - } - m_nterms++; + if (A > 0.0) { + m_terms.push_back(Arrhenius(A, b, E)); + m_sign.push_back(1); + } + else if (A < 0.0) { + m_terms.push_back(Arrhenius(-A, b, E)); + m_sign.push_back(-1); + } + m_nterms++; } void update_C(const doublereal* c) {} @@ -169,38 +179,41 @@ namespace Cantera { return fsum; } - void writeUpdateRHS(std::ostream& s) const { + void writeUpdateRHS(std::ostream& s) const { ; } static bool alwaysComputeRate() { return false;} protected: - std::vector m_terms; - vector_int m_sign; - int m_nterms; + std::vector m_terms; + vector_int m_sign; + int m_nterms; }; - /** - * An Arrhenius rate with coverage-dependent terms. - */ - class SurfaceArrhenius { + /** + * An Arrhenius rate with coverage-dependent terms. + */ + class SurfaceArrhenius { - public: - static int type(){ return ARRHENIUS; } - SurfaceArrhenius() : - m_logA(-1.0E300), - m_b (0.0), - m_E (0.0), - m_A(0.0), - m_acov(0.0), - m_ecov(0.0), - m_mcov(0.0), - m_ncov(0), - m_nmcov(0) - { - } + public: + static int type() { + return ARRHENIUS_REACTION_RATECOEFF_TYPE; + } + + SurfaceArrhenius() : + m_logA(-1.0E300), + m_b (0.0), + m_E (0.0), + m_A(0.0), + m_acov(0.0), + m_ecov(0.0), + m_mcov(0.0), + m_ncov(0), + m_nmcov(0) + { + } SurfaceArrhenius( int csize, const doublereal* c ) : m_b (c[1]), @@ -325,7 +338,7 @@ namespace Cantera { return exp(lres); } - void writeUpdateRHS(std::ostream& s) const {} + void writeUpdateRHS(std::ostream& s) const {} protected: doublereal delta_s0, delta_e0; @@ -335,37 +348,143 @@ namespace Cantera { #endif -} -// class LandauTeller { + //! Arrhenius reaction rate type depends only on temperature + /** + * A reaction rate coefficient of the following form. + * + * \f[ + * k_f = A T^b \exp (-E/RT) + * \f] + * + */ + class ExchangeCurrent { -// public: -// static int type(){ return LANDAUTELLER; } -// LandauTeller(){} -// LandauTeller( const vector_fp& c ) : m_c(c) { m_c[0] = log(c[0]); } + public: -// doublereal update(doublereal logT, doublereal recipT) const { -// return m_c[0] + m_c[1]*tt[1] - m_c[2]*tt[2] -// + m_c[3]*tt[3] + m_c[4]*tt[4]; -// } - -// //void writeUpdateRHS(ostream& s) const { -// // s << exp(m_logA); -// // s << " * exp("; -// // if (m_b != 0.0) s << m_b << " * tlog"; -// // if (m_E != 0.0) s << " - " << m_E << " * rt"; -// // if (m_E != 0.0) s << " - " << m_E << " * rt"; -// // s << ");" << endl; -// // } -// //} + //! return the rate coefficient type. + static int type() { + return EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE; + } -// protected: -// doublereal m_logA, m_b, m_E; -// }; + //! Default constructor. + ExchangeCurrent() : + m_logA(-1.0E300), + m_b (0.0), + m_E (0.0), + m_A(0.0) {} + + //! Constructor with Arrhenius parameters specified with an array. + ExchangeCurrent(int csize, const doublereal* c) : + m_b (c[1]), + m_E (c[2]), + m_A (c[0]) + { + if (m_A <= 0.0) { + m_logA = -1.0E300; + } else { + m_logA = log(m_A); + } + } + + /// Constructor. + /// @param A pre-exponential. The unit system is + /// (kmol, m, s). The actual units depend on the reaction + /// order and the dimensionality (surface or bulk). + /// @param b Temperature exponent. Non-dimensional. + /// @param E Activation energy in temperature units. Kelvin. + ExchangeCurrent(doublereal A, doublereal b, doublereal E) : + m_b (b), + m_E (E), + m_A (A) + { + if (m_A <= 0.0) { + m_logA = -1.0E300; + } else { + m_logA = log(m_A); + } + } + + //! Update concentration-dependent parts of the rate coefficient. + /*! + * For this class, there are no + * concentration-dependent parts, so this method does nothing. + */ + void update_C(const doublereal* c) { + } + + /** + * Update the value of the logarithm of the rate constant. + * + * Note, this function should never be called for negative A values. + * If it does then it will produce a negative overflow result, and + * a zero net forwards reaction rate, instead of a negative reaction + * rate constant that is the expected result. + */ + doublereal update(doublereal logT, doublereal recipT) const { + return m_logA + m_b*logT - m_E*recipT; + } + + /** + * Update the value the rate constant. + * + * This function returns the actual value of the rate constant. + * It can be safely called for negative values of the pre-exponential + * factor. + */ + doublereal updateRC(doublereal logT, doublereal recipT) const { + return m_A * exp(m_b*logT - m_E*recipT); + } + + + void writeUpdateRHS(std::ostream& s) const { + s << " exp(" << m_logA; + if (m_b != 0.0) s << " + " << m_b << " * tlog"; + if (m_E != 0.0) s << " - " << m_E << " * rt"; + s << ");" << std::endl; + } + + doublereal activationEnergy_R() const { + return m_E; + } + + static bool alwaysComputeRate() { return false;} + + protected: + doublereal m_logA, m_b, m_E, m_A; + }; + + + // class LandauTeller { + + // public: + // static int type(){ return LANDAUTELLER; } + // LandauTeller(){} + // LandauTeller( const vector_fp& c ) : m_c(c) { m_c[0] = log(c[0]); } + + // doublereal update(doublereal logT, doublereal recipT) const { + // return m_c[0] + m_c[1]*tt[1] - m_c[2]*tt[2] + // + m_c[3]*tt[3] + m_c[4]*tt[4]; + // } + + // //void writeUpdateRHS(ostream& s) const { + // // s << exp(m_logA); + // // s << " * exp("; + // // if (m_b != 0.0) s << m_b << " * tlog"; + // // if (m_E != 0.0) s << " - " << m_E << " * rt"; + // // if (m_E != 0.0) s << " - " << m_E << " * rt"; + // // s << ");" << endl; + // // } + // //} + + // protected: + // doublereal m_logA, m_b, m_E; + // }; -//} + //} +} #endif diff --git a/Cantera/src/kinetics/importKinetics.cpp b/Cantera/src/kinetics/importKinetics.cpp index e40a1df84..267c1b76c 100644 --- a/Cantera/src/kinetics/importKinetics.cpp +++ b/Cantera/src/kinetics/importKinetics.cpp @@ -521,9 +521,24 @@ namespace Cantera { * kf should point to a XML element named "rateCoeff". * rdata is the partially filled ReactionData object for the reaction. * This function will fill in more fields in the ReactionData object. + * + * @param kf Reference to the XML Node named rateCoeff */ void getRateCoefficient(const node_t& kf, kinetics_t& kin, ReactionData& rdata, int negA) { + string type = kf.attrib("type"); + if (type == "") { + type = "Arrhenius"; + rdata.rateCoeffType = ARRHENIUS_REACTION_RATECOEFF_TYPE; + } + if (type == "ExchangeCurrentDensity") { + rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE; + } else if (type == "Arrhenius") { + + } else { + throw CanteraError("getRateCoefficient", + "Unknown type: " + type); + } int nc = kf.nChildren(); nodeset_t& kf_children = kf.children(); @@ -557,6 +572,12 @@ namespace Cantera { "negative or zero A coefficient for reaction "+int2str(rdata.number)); } } + else if (nm == "Arrhenius_ExchangeCurrentDensity") { + vector_fp coeff(3); + getArrhenius(c, highlow, coeff[0], coeff[1], coeff[2]); + chigh = coeff; + rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE; + } else if (nm == "falloff") { getFalloff(c, rdata); } @@ -580,6 +601,9 @@ namespace Cantera { rdata.auxRateCoeffParameters = clow; else if (rdata.reactionType == CHEMACT_RXN) rdata.auxRateCoeffParameters = chigh; + + + } diff --git a/Cantera/src/kinetics/reaction_defs.h b/Cantera/src/kinetics/reaction_defs.h index eb36dc544..f709d36a7 100644 --- a/Cantera/src/kinetics/reaction_defs.h +++ b/Cantera/src/kinetics/reaction_defs.h @@ -81,11 +81,12 @@ namespace Cantera { */ //@{ - const int ARRHENIUS = 1; - const int LANDAUTELLER = 2; - const int TSTRATE = 3; - const int SURF_ARRHENIUS = 4; - const int ARRHENIUS_SUM = 5; + const int ARRHENIUS_REACTION_RATECOEFF_TYPE = 1; + const int LANDAUTELLER_REACTION_RATECOEFF_TYPE = 2; + const int TSTRATE_REACTION_RATECOEFF_TYPE = 3; + const int SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE = 4; + const int ARRHENIUS_SUM_REACTION_RATECOEFF_TYPE = 5; + const int EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE = 6; //@} diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 13ba5ce75..35bd66136 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -72,7 +72,7 @@ namespace Cantera { return *this; } - /** + /* * * ~GibbsExcessVPSSTP(): (virtual) * @@ -313,7 +313,6 @@ namespace Cantera { void GibbsExcessVPSSTP::initThermo() { initLengths(); VPStandardStateTP::initThermo(); - } @@ -328,34 +327,12 @@ namespace Cantera { dlnActCoeffdlnN_Scaled_.resize(m_kk); m_pp.resize(m_kk); } - - /* - * initThermoXML() (virtual from ThermoPhase) - * Import and initialize a ThermoPhase object - * - * @param phaseNode This object must be the phase node of a - * complete XML tree - * description of the phase, including all of the - * species data. In other words while "phase" must - * point to an XML phase object, it must have - * sibling nodes "speciesData" that describe - * the species in the phase. - * @param id ID of the phase. If nonnull, a check is done - * to see if phaseNode is pointing to the phase - * with the correct id. - */ - void GibbsExcessVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { - - - VPStandardStateTP::initThermoXML(phaseNode, id); - } - /** + /* * Format a summary of the mixture state for output. */ std::string GibbsExcessVPSSTP::report(bool show_thermo) const { - char p[800]; string s = ""; try { diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 3e8b7cd10..0a94de3cb 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -71,13 +71,14 @@ namespace Cantera { * \f$k\f$. * * GibbsExcessVPSSTP contains an internal vector with the current mole - * fraction vector. That's one of its primary usages. + * fraction vector. That's one of its primary usages. In order to keep the mole fraction + * vector constant, all of the setState functions are redesigned at this layer. * *

SetState Strategy

* - * The gibbsExcessVPSSTP object does not have a setState strategy. - * It's strictly an interfacial layer that writes the current mole fractions to the - * State object. + * All setState functions that set the internal state of the ThermoPhase object are + * overloaded at this level, so that a current mole fraction vector is maintained within + * the object. * * */ @@ -172,6 +173,7 @@ namespace Cantera { virtual void setPressure(doublereal p); protected: + /** * Calculate the density of the mixture using the partial * molar volumes and mole fractions as input @@ -531,24 +533,6 @@ namespace Cantera { * @see importCTML.cpp */ virtual void initThermo(); - - - /** - * Import and initialize a ThermoPhase object - * - * @param phaseNode This object must be the phase node of a - * complete XML tree - * description of the phase, including all of the - * species data. In other words while "phase" must - * point to an XML phase object, it must have - * sibling nodes "speciesData" that describe - * the species in the phase. - * @param id ID of the phase. If nonnull, a check is done - * to see if phaseNode is pointing to the phase - * with the correct id. - */ - void initThermoXML(XML_Node& phaseNode, std::string id); - //! returns a summary of the state of the phase as a string /*! @@ -560,14 +544,10 @@ namespace Cantera { private: - //! Initialize lengths of local variables after all species have //! been identified. void initLengths(); - - - private: //! Error function /*! * Print an error string and exit @@ -587,6 +567,13 @@ namespace Cantera { protected: //! Storage for the current values of the mole fractions of the species + /*! + * This vector is kept up-to-date when the setState functions are called. + * Therefore, it may be considered to be an independent variable. + * + * Note in order to do this, the setState functions are redefined to always + * keep this vector current. + */ mutable std::vector moleFractions_; //! Storage for the current values of the activity coefficients of the diff --git a/configure b/configure index b40bf7bcd..dd4dcfc83 100755 --- a/configure +++ b/configure @@ -9740,6 +9740,154 @@ if test "$BUILD_WITH_F2C"="n"; then fi +# +# Check to see if we have a -lm line +# +echo "$as_me:$LINENO: checking for printf in -lm" >&5 +echo $ECHO_N "checking for printf in -lm... $ECHO_C" >&6 +if test "${ac_cv_lib_m_printf+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char printf (); +int +main () +{ +printf (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_m_printf=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_m_printf=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_m_printf" >&5 +echo "${ECHO_T}$ac_cv_lib_m_printf" >&6 +if test $ac_cv_lib_m_printf = yes; then + add_stm=1 +else + add_stm=0 +fi + + +# +# Check to see if we have a -lstdc++ line +# +echo "$as_me:$LINENO: checking for printf in -lstdc++" >&5 +echo $ECHO_N "checking for printf in -lstdc++... $ECHO_C" >&6 +if test "${ac_cv_lib_stdcpp_printf+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lstdc++ $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any gcc2 internal prototype to avoid an error. */ +#ifdef __cplusplus +extern "C" +#endif +/* We use char because int might match the return type of a gcc2 + builtin and then its argument prototype would still apply. */ +char printf (); +int +main () +{ +printf (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest$ac_exeext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_lib_stdcpp_printf=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_lib_stdcpp_printf=no +fi +rm -f conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +echo "$as_me:$LINENO: result: $ac_cv_lib_stdcpp_printf" >&5 +echo "${ECHO_T}$ac_cv_lib_stdcpp_printf" >&6 +if test $ac_cv_lib_stdcpp_printf = yes; then + add_stdc=1 +else + add_stdc=0 +fi + + # # Ending Libs for compiling static applications and # dynamically loaded libraries @@ -9755,6 +9903,17 @@ case $ac_sys_system in LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;; esac ;; esac +if test $add_stm = 1 ; then + echo 'Adding -lm to the end of the LCXX_END_LIBS variable' + LCXX_END_LIBS="$LCXX_END_LIBS"" -lm" + echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS +fi +if test $add_stdc = 1 ; then + echo 'Adding -lstdc++ to the end of the LCXX_END_LIBS variable' + LCXX_END_LIBS="$LCXX_END_LIBS"" -lstdc++ " + echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS +fi + @@ -9888,7 +10047,7 @@ fi # Provide some information about the compiler. -echo "$as_me:9891:" \ +echo "$as_me:10050:" \ "checking for Fortran 77 compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 @@ -10095,7 +10254,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10098: \"$ac_link\") >&5 +(eval echo $as_me:10257: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10173,7 +10332,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10176: \"$ac_link\") >&5 +(eval echo $as_me:10335: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS diff --git a/configure.in b/configure.in index 77744b3e7..29067cd17 100755 --- a/configure.in +++ b/configure.in @@ -1463,6 +1463,16 @@ if test "$BUILD_WITH_F2C"="n"; then fi AC_SUBST(LCXX_FLAGS) +# +# Check to see if we have a -lm line +# +AC_CHECK_LIB(m, printf, [add_stm=1], [add_stm=0], [ ]) + +# +# Check to see if we have a -lstdc++ line +# +AC_CHECK_LIB(stdc++, printf, [add_stdc=1], [add_stdc=0], []) + # # Ending Libs for compiling static applications and # dynamically loaded libraries @@ -1478,6 +1488,17 @@ case $ac_sys_system in LCXX_END_LIBS="$LCXX_END_LIBS"" -lCrun -lCstd -lfsu" ;; esac ;; esac +if test $add_stm = 1 ; then + echo 'Adding -lm to the end of the LCXX_END_LIBS variable' + LCXX_END_LIBS="$LCXX_END_LIBS"" -lm" + echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS +fi +if test $add_stdc = 1 ; then + echo 'Adding -lstdc++ to the end of the LCXX_END_LIBS variable' + LCXX_END_LIBS="$LCXX_END_LIBS"" -lstdc++ " + echo 'LCXX_END_LIBS = ' $LCXX_END_LIBS +fi + AC_SUBST(LCXX_END_LIBS) diff --git a/data/thermo/nasathermo.dat b/data/thermo/nasathermo.dat index d78b570aa..b15f5cb12 100755 --- a/data/thermo/nasathermo.dat +++ b/data/thermo/nasathermo.dat @@ -1849,7 +1849,7 @@ LiO J 3/64LI 1.O 1. 0. 0.G 300.000 5000.000 22.94040 1 LiO- J12/67LI 1.O 1.E 1. 0.G 300.000 5000.000 22.94095 1 4.18102170E+00 4.17850000E-04-1.50248450E-07 2.83977320E-11-1.97891810E-15 2 -9.38497020E+03-1.42392337E-01 2.85158660E+00 5.01698800E-03-5.95474750E-06 3 - 3.03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03 4 + 03994510E-09-4.78729690E-13-9.07780760E+03 6.45947067E+00-8.05144594E+03 4 LiOH J 6/71LI 1.O 1.H 1. 0.G 300.000 5000.000 23.94834 1 5.50969570E+00 1.36854640E-03-3.94414690E-07 5.23321950E-11-2.59586760E-15 2 -2.98992310E+04-6.50701600E+00 3.34623000E+00 1.17872530E-02-1.82526570E-05 3 @@ -4558,4 +4558,4 @@ ZrO2(L) J12/65ZR 1.O 2. 0. 0.C 2950.000 5000.000 123.22280 1 1.05676750E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 -1.28427450E+05-5.45922640E+01 1.05676750E+01 0.00000000E+00 0.00000000E+00 3 0.00000000E+00 0.00000000E+00-1.28427450E+05-5.45922640E+01 0.00000000E+00 4 -END \ No newline at end of file +END diff --git a/tools/src/cti2ctml.cpp b/tools/src/cti2ctml.cpp index ef2facb55..0a0280e2a 100644 --- a/tools/src/cti2ctml.cpp +++ b/tools/src/cti2ctml.cpp @@ -1,8 +1,12 @@ /** - * @file example2.cpp + * @file cti2ctml.cpp * */ +/* + * $Id$ + */ + // Example // // Read a mechanism and a thermodynamics file for the @@ -21,9 +25,6 @@ using namespace Cantera; using namespace std; -#ifdef DEBUG_HKM -int iDebug_HKM = 0; -#endif /*****************************************************************/ /*****************************************************************/ @@ -38,14 +39,14 @@ static void printUsage() - +/*****************************************************************/ int main(int argc, char** argv) { - string infile; + std::string infile; // look for command-line options if (argc > 1) { - string tok; + std::string tok; for (int j = 1; j < argc; j++) { tok = string(argv[j]); if (tok[0] == '-') { @@ -75,7 +76,7 @@ int main(int argc, char** argv) { try { XML_Node *xc = new XML_Node(); - string path = findInputFile(infile); + std::string path = findInputFile(infile); ctml::get_CTML_Tree(xc, path, 0); //XML_Node *xd = new XML_Node(); //xc->copy(xd); From 5f327277b0fcdb391c13efdab9a22f1711246483 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Mon, 1 Mar 2010 23:35:35 +0000 Subject: [PATCH 111/446] Corrected memory allocation for ionConductivity, mobRatio, selfDiffusion, etc. that may not be required as input. --- Cantera/src/transport/LiquidTransport.cpp | 11 ++++- Cantera/src/transport/LiquidTransportData.cpp | 2 + .../src/transport/LiquidTransportParams.cpp | 11 ++++- Cantera/src/transport/TransportFactory.cpp | 40 +++++++++++-------- 4 files changed, 44 insertions(+), 20 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 262b12f0f..8833140b0 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -263,6 +263,7 @@ namespace Cantera { int k; // constant substance attributes m_thermo = tr.thermo; + tr.thermo = 0; m_velocityBasis = tr.velocityBasis_; m_nsp = m_thermo->nSpecies(); m_nBinInt = m_nsp*(m_nsp-1)/2; @@ -310,11 +311,13 @@ namespace Cantera { //first populate mixing rules and indices for (k = 0; k < m_nsp; k++) { - m_selfDiffMixModel[k] = tr.selfDiffusion[k]; + m_selfDiffMixModel[k] = tr.selfDiffusion[k]; + tr.selfDiffusion[k] = 0; m_selfDiffMixModelIndex[k] = tr.selfDiffIndex[k]; } for (k = 0; k < m_nBinInt; k++) { m_mobRatMixModel[k] = tr.mobilityRatio[k]; + tr.mobilityRatio[k] = 0; m_mobRatMixModelIndex[k] = tr.mobRatIndex[k]; } @@ -322,11 +325,14 @@ namespace Cantera { for (k = 0; k < m_nsp; k++) { Cantera::LiquidTransportData <d = tr.LTData[k]; m_viscTempDep_Ns[k] = ltd.viscosity; + ltd.viscosity = 0; m_ionCondTempDep_Ns[k] = ltd.ionConductivity; + ltd.ionConductivity = 0; for (int j = 0; j < m_nBinInt; j++){ for (int l=0; l < m_nBinInt; l++){ if (m_mobRatMixModelIndex[j] == ltd.mobRatIndex[l]) { m_mobRatTempDep_Ns[j][k] = ltd.mobilityRatio[l]; + ltd.mobilityRatio[l] = 0; m_mobRatTempDepIndex[j] = ltd.mobRatIndex[l]; break; } @@ -336,13 +342,16 @@ namespace Cantera { for (int l=0; l < (int) m_selfDiffMixModelIndex.size(); l++){ if (m_selfDiffMixModelIndex[j] == ltd.selfDiffIndex[l]) { m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[l]; + ltd.selfDiffusion[l] = 0; m_selfDiffTempDepIndex[j] = ltd.selfDiffIndex[l]; break; } } } m_lambdaTempDep_Ns[k] = ltd.thermalCond; + ltd.thermalCond = 0; m_radiusTempDep_Ns[k] = ltd.hydroRadius; + ltd.hydroRadius = 0; } diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 496fb7c95..e801adf5b 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -49,6 +49,7 @@ namespace Cantera { speciesName("-"), hydroRadius(0), viscosity(0), + ionConductivity(0), thermalCond(0), electCond(0), speciesDiffusivity(0) @@ -61,6 +62,7 @@ namespace Cantera { speciesName("-"), hydroRadius(0), viscosity(0), + ionConductivity(0), thermalCond(0), electCond(0), speciesDiffusivity(0) diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 41cebab6a..446639def 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -224,7 +224,7 @@ namespace Cantera { //==================================================================================================================== LiquidTransportParams::LiquidTransportParams() : - viscosity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), + viscosity(0), ionConductivity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), model_speciesDiffusivity(LTI_MODEL_NOTSET), model_hydroradius(LTI_MODEL_NOTSET) { @@ -233,6 +233,7 @@ namespace Cantera { LiquidTransportParams::~LiquidTransportParams() { delete viscosity; + delete ionConductivity; delete thermalCond; delete speciesDiffusivity; delete electCond; @@ -616,6 +617,7 @@ namespace Cantera { m_ionCondMix = 0; m_ionCondMixModel = trParam.ionConductivity; + trParam.ionConductivity = 0; m_ionCondSpecies.resize(nsp,0); m_mobRatMix.resize(nsp,nsp,0.0); m_mobRatMixModel.resize(nBinInt); @@ -628,11 +630,13 @@ namespace Cantera { for ( int k = 0; k < nBinInt; k++ ) { m_mobRatMixModel[k] = trParam.mobilityRatio[k]; + trParam.mobilityRatio[k] = 0; m_mobRatSpecies[k].resize(nsp,0); m_mobRatIndex[k] = trParam.mobRatIndex[k]; } for ( int k = 0; k < nsp; k++ ) { m_selfDiffMixModel[k] = trParam.selfDiffusion[k]; + trParam.selfDiffusion[k] = 0; m_selfDiffSpecies[k].resize(nsp,0); m_selfDiffIndex[k] = trParam.selfDiffIndex[k]; } @@ -640,11 +644,14 @@ namespace Cantera { for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; m_ionCondSpecies[k] = ltd.ionConductivity; + ltd.ionConductivity = 0; for ( int j = 0; j < nBinInt; j++ ){ m_mobRatSpecies[j][k] = ltd.mobilityRatio[j]; + ltd.mobilityRatio[j] = 0; } for ( int j = 0; j < nsp; j++ ){ - m_selfDiffSpecies[j][k] = ltd.selfDiffusion[j]; + m_selfDiffSpecies[j][k] = ltd.selfDiffusion[j]; + ltd.selfDiffusion[j] = 0; } } } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index f000345e2..81c0d0bc8 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -958,7 +958,8 @@ namespace Cantera { */ std::map datatable; - int nsp = static_cast(xspecies.size()); + int nsp = trParam.nsp_;//static_cast(xspecies.size()); + int nBinInt = nsp*(nsp-1)/2; // read all entries in database into 'datatable' and check for // errors. Note that this procedure validates all entries, not @@ -982,6 +983,14 @@ namespace Cantera { LiquidTransportData data; data.speciesName = name; + //data.viscosity = 0; + //data.ionConductivity = 0; + + data.mobRatIndex.resize(nBinInt,""); + data.mobilityRatio.resize(nBinInt,0); + data.selfDiffIndex.resize(nsp,""); + data.selfDiffusion.resize(nsp,0); + //////// new stuff int num = trNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { @@ -1004,10 +1013,7 @@ namespace Cantera { case TP_MOBILITYRATIO: { int iSpec; - int numSpec = xmlChild.nChildren(); - data.mobRatIndex.resize(numSpec); - data.mobilityRatio.resize(numSpec); - for (iSpec = 0; iSpec< numSpec; iSpec++){ + for (iSpec = 0; iSpec< nBinInt; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); data.mobRatIndex[iSpec] = specName; @@ -1021,10 +1027,7 @@ namespace Cantera { case TP_SELFDIFFUSION: { int iSpec; - int numSpec = xmlChild.nChildren(); - data.selfDiffIndex.resize(numSpec); - data.selfDiffusion.resize(numSpec); - for (iSpec = 0; iSpec< numSpec; iSpec++){ + for (iSpec = 0; iSpec< nsp; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); data.selfDiffIndex[iSpec] = specName; @@ -1116,11 +1119,20 @@ namespace Cantera { { try { + int nsp = trParam.nsp_; + int nBinInt = nsp*(nsp-1)/2; + int num = transportNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { //tranTypeNode is a type of transport property like viscosity XML_Node &tranTypeNode = transportNode.child(iChild); std::string nodeName = tranTypeNode.name(); + + trParam.mobRatIndex.resize(nBinInt,""); + trParam.mobilityRatio.resize(nBinInt,0); + trParam.selfDiffIndex.resize(nsp,""); + trParam.selfDiffusion.resize(nsp,0); + if ( tranTypeNode.hasChild("compositionDependence")) { //compDepNode contains the interaction model XML_Node &compDepNode = tranTypeNode.child("compositionDependence"); @@ -1139,10 +1151,7 @@ namespace Cantera { case TP_MOBILITYRATIO: { int iSpec; - int numSpec = compDepNode.nChildren(); - trParam.mobRatIndex.resize(numSpec); - trParam.mobilityRatio.resize(numSpec); - for (iSpec = 0; iSpec< numSpec; iSpec++){ + for (iSpec = 0; iSpec< nBinInt; iSpec++){ XML_Node &propSpecNode = compDepNode.child(iSpec); std::string specName = propSpecNode.name(); trParam.mobRatIndex[iSpec] = specName; @@ -1155,10 +1164,7 @@ namespace Cantera { case TP_SELFDIFFUSION: { int iSpec; - int numSpec = compDepNode.nChildren(); - trParam.selfDiffIndex.resize(numSpec); - trParam.selfDiffusion.resize(numSpec); - for (iSpec = 0; iSpec< numSpec; iSpec++){ + for (iSpec = 0; iSpec< nsp; iSpec++){ XML_Node &propSpecNode = compDepNode.child(iSpec); std::string specName = propSpecNode.name(); trParam.selfDiffIndex[iSpec] = specName; From c1879a15e5ee4685ac01348b0a3c41ad09d44586 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 2 Mar 2010 00:59:45 +0000 Subject: [PATCH 112/446] Fixed a warning message in LiquidTransport constructor Added a deprecated message for array_fp. --- Cantera/src/base/ct_defs.h | 3 +++ Cantera/src/transport/LiquidTransport.cpp | 32 ++++++++++++++++------- Cantera/src/transport/LiquidTransport.h | 2 +- 3 files changed, 26 insertions(+), 11 deletions(-) diff --git a/Cantera/src/base/ct_defs.h b/Cantera/src/base/ct_defs.h index c394cadb7..85e5e8334 100644 --- a/Cantera/src/base/ct_defs.h +++ b/Cantera/src/base/ct_defs.h @@ -191,6 +191,9 @@ namespace Cantera { #define USE_STL_VECTOR #ifdef USE_STL_VECTOR //! Vector of doubles. + /*! + * @deprecated array_fp is going away, because vector_fp means the same thing + */ typedef std::vector array_fp; //! Vector of doubles. typedef std::vector vector_fp; diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 8833140b0..d6303dc28 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -37,16 +37,22 @@ namespace Cantera { m_nBinInt(0), m_tmin(-1.0), m_tmax(100000.), + m_viscMixModel(0), + m_ionCondMixModel(0), + m_lambdaMixModel(0), + m_diffMixModel(0), + m_radiusMixModel(0), m_iStateMF(-1), + concTot_(0.0), + concTot_tran_(0.0), + dens_(0.0), m_temp(-1.0), m_press(-1.0), - m_lambda(-1.0), m_viscmix(-1.0), m_ionCondmix(-1.0), - m_mobRatMix(-1.0), - m_selfDiffMix(-1.0), - + m_mobRatMix(0), + m_selfDiffMix(0), m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), @@ -73,22 +79,28 @@ namespace Cantera { } - LiquidTransport::LiquidTransport(const LiquidTransport &right) : - Transport(), + LiquidTransport::LiquidTransport(const LiquidTransport &right) : + Transport(right.m_thermo, right.m_nDim), m_nsp(0), m_nBinInt(0), m_tmin(-1.0), m_tmax(100000.), + m_viscMixModel(0), + m_ionCondMixModel(0), + m_lambdaMixModel(0), + m_diffMixModel(0), + m_radiusMixModel(0), m_iStateMF(-1), + concTot_(0.0), + concTot_tran_(0.0), + dens_(0.0), m_temp(-1.0), m_press(-1.0), - m_lambda(-1.0), m_viscmix(-1.0), m_ionCondmix(-1.0), - m_mobRatMix(-1.0), - m_selfDiffMix(-1.0), - + m_mobRatMix(0), + m_selfDiffMix(0), m_visc_mix_ok(false), m_visc_temp_ok(false), m_visc_conc_ok(false), diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 133624ca5..2feb83ee2 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -1060,7 +1060,7 @@ namespace Cantera { * * k is the species index * n is the dimensional index (x, y, or z). It has a length - * equal to m_nDimm_ + * equal to m_nDim * * m_Grad_X[n*m_nsp + k] * From 4220cb318b54ea81d59f1325d4dc3428862d60a3 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Tue, 2 Mar 2010 16:27:50 +0000 Subject: [PATCH 113/446] commented ifdef block in neutralmolecmolegrads --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 4e95c4f30..87e4ca82d 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -871,6 +871,8 @@ namespace Cantera { y.resize(numNeutralMoleculeSpecies_,0.0); doublereal sumy, sumdy; + //check sum dx = 0 + //! Zero the vector we are trying to find. for (k = 0; k < numNeutralMoleculeSpecies_; k++) { dy[k] = 0.0; @@ -912,8 +914,9 @@ namespace Cantera { dy[jNeut] += dx[icat] / fmij; y[jNeut] += moleFractions_[icat] / fmij; } - + /* #ifdef DEBUG_MODE +//check dy sum to zero for (k = 0; k < m_kk; k++) { moleFractionsTmp_[k] = dx[k]; } @@ -937,7 +940,7 @@ namespace Cantera { } } #endif - + */ // Normalize the Neutral Molecule mole fractions sumy = 0.0; sumdy = 0.0; From 1bcec0aac74137d5e73da25a4399f025045dd425 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 2 Mar 2010 21:39:42 +0000 Subject: [PATCH 114/446] Fixed the exchange current density rate coefficient option. There was an obvious error that caused cathodic reactions to fail. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 25 ++++++++++---------- Cantera/src/kinetics/InterfaceKinetics.h | 4 ++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 4 +--- 3 files changed, 16 insertions(+), 17 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 338e10014..446241019 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -45,9 +45,9 @@ namespace Cantera { m_beta(0), m_ctrxn(0), m_ctrxn_ecdf(0), - m_logStandardConc(0), + m_StandardConc(0), m_deltaG0(0), - m_logProdStanConcReac(0), + m_ProdStanConcReac(0), m_finalized(false), m_has_coverage_dependence(false), m_has_electrochem_rxns(false), @@ -85,9 +85,9 @@ namespace Cantera { m_beta(0), m_ctrxn(0), m_ctrxn_ecdf(0), - m_logStandardConc(0), + m_StandardConc(0), m_deltaG0(0), - m_logProdStanConcReac(0), + m_ProdStanConcReac(0), m_finalized(false), m_has_coverage_dependence(false), m_has_electrochem_rxns(false), @@ -142,9 +142,9 @@ namespace Cantera { m_beta = right.m_beta; m_ctrxn = right.m_ctrxn; m_ctrxn_ecdf = right.m_ctrxn_ecdf; - m_logStandardConc = right.m_logStandardConc; + m_StandardConc = right.m_StandardConc; m_deltaG0 = right.m_deltaG0; - m_logProdStanConcReac = right.m_logProdStanConcReac; + m_ProdStanConcReac = right.m_ProdStanConcReac; m_finalized = right.m_finalized; m_has_coverage_dependence = right.m_has_coverage_dependence; m_has_electrochem_rxns = right.m_has_electrochem_rxns; @@ -377,7 +377,7 @@ namespace Cantera { thermo(n).getStandardChemPotentials(DATA_PTR(m_mu0) + m_start[n]); int nsp = thermo(n).nSpecies(); for (int k = 0; k < nsp; k++) { - m_logStandardConc[ik] = thermo(n).logStandardConc(k); + m_StandardConc[ik] = thermo(n).standardConcentration(k); ik++; } } @@ -386,10 +386,10 @@ namespace Cantera { for (int i = 0; i < m_ii; i++) { - m_logProdStanConcReac[i] = 1.0; + m_ProdStanConcReac[i] = 1.0; } - m_rxnstoich.multiplyReactants(DATA_PTR(m_logStandardConc), DATA_PTR(m_logProdStanConcReac)); + m_rxnstoich.multiplyReactants(DATA_PTR(m_StandardConc), DATA_PTR(m_ProdStanConcReac)); } @@ -521,7 +521,8 @@ namespace Cantera { int iECDFormulation = m_ctrxn_ecdf[i]; if (iECDFormulation) { double tmp = exp(- m_beta[i] * m_deltaG0[irxn] * rrt); - tmp *= 1.0 / m_logProdStanConcReac[irxn] / Faraday; + double tmp2 = m_ProdStanConcReac[irxn]; + tmp *= 1.0 / tmp2 / Faraday; kfwd[irxn] *= tmp; } } @@ -1046,9 +1047,9 @@ namespace Cantera { - m_logStandardConc.resize(m_nTotalSpecies, 0.0); + m_StandardConc.resize(m_nTotalSpecies, 0.0); m_deltaG0.resize(m_ii, 0.0); - m_logProdStanConcReac.resize(m_ii, 0.0); + m_ProdStanConcReac.resize(m_ii, 0.0); m_finalized = true; } diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index a7bc89582..6f327dbfe 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -686,9 +686,9 @@ namespace Cantera { //! described by an exchange current density expression vector_int m_ctrxn_ecdf; - vector_fp m_logStandardConc; + vector_fp m_StandardConc; vector_fp m_deltaG0; - vector_fp m_logProdStanConcReac; + vector_fp m_ProdStanConcReac; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 87e4ca82d..143f047bc 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -914,8 +914,7 @@ namespace Cantera { dy[jNeut] += dx[icat] / fmij; y[jNeut] += moleFractions_[icat] / fmij; } - /* -#ifdef DEBUG_MODE +#ifdef DEBUG_MODE_NOT //check dy sum to zero for (k = 0; k < m_kk; k++) { moleFractionsTmp_[k] = dx[k]; @@ -940,7 +939,6 @@ namespace Cantera { } } #endif - */ // Normalize the Neutral Molecule mole fractions sumy = 0.0; sumdy = 0.0; From 01f915d01a7ad993beb1d4e40bf319f049b75aae Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Thu, 4 Mar 2010 18:02:58 +0000 Subject: [PATCH 115/446] Changed storage of stefan maxwell coefficients from Dij to 1/Dij...to allow for negative and zero values of the friction between species. Corrected some memory issues (LTP.cpp was creating null pointers for ionConductivity that were being used in LT.cpp) --- Cantera/src/transport/LiquidTransport.cpp | 48 ++++++++++--------- .../src/transport/LiquidTransportParams.cpp | 22 ++++----- 2 files changed, 37 insertions(+), 33 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index d6303dc28..499672a64 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -802,11 +802,15 @@ namespace Cantera { // from the polynomial fits if (!m_diff_temp_ok) updateDiff_T(); - for (i = 0; i < m_nsp; i++) - for (j = 0; j < m_nsp; j++) { - d[ld*j + i] = m_bdiff(i,j); - + for (i = 0; i < m_nsp; i++) { + for (j = 0; j < m_nsp; j++){ + //if (!( ( m_bdiff(i,j) > 0.0 ) | ( m_bdiff(i,j) < 0.0 ))){ + // throw CanteraError("LiquidTransport::getBinaryDiffCoeffs ", + // "m_bdiff has zero entry in non-diagonal.");} + d[ld*j + i] = 1.0 / m_bdiff(i,j); + } + } } @@ -1759,10 +1763,10 @@ namespace Cantera { m_A(i,i) = 0.0; for (j = 0; j < m_nsp; j++){ if (j != i) { - if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); - tmp = m_molefracs_tran[j] / m_bdiff(i,j); + //if ( !( m_bdiff(i,j) > 0.0 ) ) + //throw CanteraError("LiquidTransport::stefan_maxwell_solve", + // "m_bdiff has zero entry in non-diagonal."); + tmp = m_molefracs_tran[j] * m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; } @@ -1773,12 +1777,12 @@ namespace Cantera { solve(m_A, m_B); /* - condSum2 = m_chargeSpecies[1]*m_chargeSpecies[1]*m_molefracs_tran[1]/m_bdiff(2,3) + - m_chargeSpecies[2]*m_chargeSpecies[2]*m_molefracs_tran[2]/m_bdiff(1,3) + - m_chargeSpecies[3]*m_chargeSpecies[3]*m_molefracs_tran[3]/m_bdiff(1,2); - condSum1 = m_molefracs_tran[1]/m_bdiff(1,2)/m_bdiff(1,3) + - m_molefracs_tran[2]/m_bdiff(2,3)/m_bdiff(1,2) + - m_molefracs_tran[3]/m_bdiff(1,3)/m_bdiff(2,3); + condSum2 = m_chargeSpecies[1]*m_chargeSpecies[1]*m_molefracs_tran[1]*m_bdiff(2,3) + + m_chargeSpecies[2]*m_chargeSpecies[2]*m_molefracs_tran[2]*m_bdiff(1,3) + + m_chargeSpecies[3]*m_chargeSpecies[3]*m_molefracs_tran[3]*m_bdiff(1,2); + condSum1 = m_molefracs_tran[1]*m_bdiff(1,2)*m_bdiff(1,3) + + m_molefracs_tran[2]*m_bdiff(2,3)*m_bdiff(1,2) + + m_molefracs_tran[3]*m_bdiff(1,3)*m_bdiff(2,3); condSum2 = condSum2/condSum1*Faraday*Faraday/GasConstant/T/vol; */ @@ -1820,10 +1824,10 @@ namespace Cantera { m_A(i,i) = 0.0; for (j = 0; j < m_nsp; j++) { if (j != i) { - if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); - tmp = m_molefracs_tran[j] / m_bdiff(i,j); + //if ( !( m_bdiff(i,j) > 0.0 ) ) + //throw CanteraError("LiquidTransport::stefan_maxwell_solve", + // "m_bdiff has zero entry in non-diagonal."); + tmp = m_molefracs_tran[j] * m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; } @@ -1862,10 +1866,10 @@ namespace Cantera { m_A(i,i) = 0.0; for (j = 0; j < m_nsp; j++) { if (j != i) { - if ( !( m_bdiff(i,j) > 0.0 ) ) - throw CanteraError("LiquidTransport::stefan_maxwell_solve", - "m_bdiff has zero entry in non-diagonal."); - tmp = m_molefracs_tran[j] / m_bdiff(i,j); + //if ( !( m_bdiff(i,j) > 0.0 ) ) + //throw CanteraError("LiquidTransport::stefan_maxwell_solve", + // "m_bdiff has zero entry in non-diagonal."); + tmp = m_molefracs_tran[j] * m_bdiff(i,j); m_A(i,i) -= tmp; m_A(i,j) = + tmp; } diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 446639def..c92e913f5 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -602,11 +602,11 @@ namespace Cantera { mat.resize( nsp, nsp, 0.0 ); for ( int i = 0; i < nsp; i++ ) for ( int j = 0; j < i; j++ ) - mat(i,j) = mat(j,i) = m_Dij(i,j) * exp( - m_Eij(i,j) / temp ); + mat(i,j) = mat(j,i) = exp( m_Eij(i,j) / temp ) / m_Dij(i,j); for ( int i = 0; i < nsp; i++ ) if ( mat(i,i) == 0.0 && m_diagonals[i] ) - mat(i,i) = m_diagonals[i]->getSpeciesTransProp() ; + mat(i,i) = 1.0 / m_diagonals[i]->getSpeciesTransProp() ; } @@ -617,7 +617,7 @@ namespace Cantera { m_ionCondMix = 0; m_ionCondMixModel = trParam.ionConductivity; - trParam.ionConductivity = 0; + //trParam.ionConductivity = 0; m_ionCondSpecies.resize(nsp,0); m_mobRatMix.resize(nsp,nsp,0.0); m_mobRatMixModel.resize(nBinInt); @@ -630,13 +630,13 @@ namespace Cantera { for ( int k = 0; k < nBinInt; k++ ) { m_mobRatMixModel[k] = trParam.mobilityRatio[k]; - trParam.mobilityRatio[k] = 0; + //trParam.mobilityRatio[k] = 0; m_mobRatSpecies[k].resize(nsp,0); m_mobRatIndex[k] = trParam.mobRatIndex[k]; } for ( int k = 0; k < nsp; k++ ) { m_selfDiffMixModel[k] = trParam.selfDiffusion[k]; - trParam.selfDiffusion[k] = 0; + //trParam.selfDiffusion[k] = 0; m_selfDiffSpecies[k].resize(nsp,0); m_selfDiffIndex[k] = trParam.selfDiffIndex[k]; } @@ -644,14 +644,14 @@ namespace Cantera { for (int k = 0; k < nsp; k++) { Cantera::LiquidTransportData <d = trParam.LTData[k]; m_ionCondSpecies[k] = ltd.ionConductivity; - ltd.ionConductivity = 0; + //ltd.ionConductivity = 0; for ( int j = 0; j < nBinInt; j++ ){ m_mobRatSpecies[j][k] = ltd.mobilityRatio[j]; - ltd.mobilityRatio[j] = 0; + //ltd.mobilityRatio[j] = 0; } for ( int j = 0; j < nsp; j++ ){ m_selfDiffSpecies[j][k] = ltd.selfDiffusion[j]; - ltd.selfDiffusion[j] = 0; + //ltd.selfDiffusion[j] = 0; } } } @@ -805,13 +805,14 @@ namespace Cantera { mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; - +/* for ( i = 0; i < nsp; i++ ) { for ( j = 0; j < nsp; j++ ) { mat(i,j) = 1.0/mat(i,j); //cout << "D" << i << j << " = " << mat(i,j) << endl; } } +*/ } @@ -871,8 +872,7 @@ mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB) mat.resize(nsp,nsp, 0.0); for (int i = 0; i < nsp; i++) for (int j = 0; j < nsp; j++) { - mat(i,j) = GasConstant * temp - / ( 6.0 * Pi * radiusSpec[i] * viscSpec[j] ) ; + mat(i,j) = ( 6.0 * Pi * radiusSpec[i] * viscSpec[j] ) / GasConstant / temp; } delete radiusSpec; delete viscSpec; From 7080a151a6929ee4a5435fce7ade3a0954ee05f6 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Wed, 10 Mar 2010 16:37:40 +0000 Subject: [PATCH 116/446] Fixed how IonsFromNeutralVPSSTP.cpp calculates the density...now calculates the neutralmolecule_ density and sets its own. Fixed some issues in liquid transport w/ zeroing m_prop properly --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 5 ++++- Cantera/src/transport/LiquidTransport.cpp | 5 ++++- Cantera/src/transport/LiquidTransportData.cpp | 8 ++++++-- Cantera/src/transport/LiquidTransportParams.cpp | 8 ++++---- 4 files changed, 18 insertions(+), 8 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 143f047bc..aeabd53ee 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -677,7 +677,10 @@ namespace Cantera { /* * Calculate the partial molar volumes, and then the density of the fluid */ - calcDensity(); + + //calcDensity(); + double dd = neutralMoleculePhase_->density(); + State::setDensity(dd); } // Calculate ion mole fractions from neutral molecule diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 499672a64..03490ad1b 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -1616,7 +1616,10 @@ namespace Cantera { grad_X.assign(m_Grad_X.begin()+m_nsp*k,m_Grad_X.begin()+m_nsp*(k+1)); m_thermo->getdlnActCoeff( grad_T, DATA_PTR(grad_X), DATA_PTR(grad_lnAC) ); for ( int i = 0; i < m_nsp; i++ ) - grad_lnAC[i] += grad_X[i]/m_molefracs[i]; + if (m_molefracs[i] < 1.e-15) + grad_lnAC[i] = 0; + else + grad_lnAC[i] += grad_X[i]/m_molefracs[i]; copy(grad_lnAC.begin(),grad_lnAC.end(),m_Grad_lnAC.begin()+m_nsp*k); // std::cout << k << " m_Grad_lnAC = " << m_Grad_lnAC[k] << std::endl; } diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index e801adf5b..d0fa25151 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -239,13 +239,15 @@ namespace Cantera { * adjusted internally according to the information provided. */ doublereal LTPspecies_Arrhenius::getSpeciesTransProp( ) { - + doublereal t = m_thermo->temperature(); //m_coeffs[0] holds A //m_coeffs[1] holds n //m_coeffs[2] holds Tact //m_coeffs[3] holds log(A) - if (t != m_temp) { + if (t != m_temp) { + m_prop = 0; + m_logProp = 0; m_temp = t; m_logt = log(m_temp); //For viscosity the sign convention on positive activation energy is swithced @@ -321,6 +323,7 @@ namespace Cantera { doublereal t = m_thermo->temperature(); if (t != m_temp) { + m_prop = 0; m_temp=t; double tempN = 1.0; for (int i = 0; i < (int) m_coeffs.size() ; i++) { @@ -393,6 +396,7 @@ namespace Cantera { doublereal t = m_thermo->temperature(); if (t != m_temp) { + m_prop = 0; m_temp=t; m_prop=m_coeffs[0]; double tempN = 1.0; diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index c92e913f5..5fbad785a 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -721,7 +721,7 @@ namespace Cantera { cout << "anion 0: " << speciesNames[anion[0]] << endl; */ - doublereal kappa = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); + m_ionCondMix = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); MargulesVPSSTP * marg_thermo = dynamic_cast (ions_thermo->neutralMoleculePhase_); doublereal vol = m_thermo->molarVolume(); @@ -801,9 +801,9 @@ namespace Cantera { throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Dissociation reactions don't make sense: cationIndex = " + cationIndex); mat.resize( nsp, nsp, 0.0 ); - mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/kappa/vol; - mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; -mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/kappa/vol; + mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; +mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; /* for ( i = 0; i < nsp; i++ ) { From 43f7dd2e45d73f80cc11d1a4ed56f97d44ac7646 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 15:24:25 +0000 Subject: [PATCH 117/446] Changed the keywords specifier From bdf3bda124a261d978dd01d2fc31459dda1ecb99 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 15:27:16 +0000 Subject: [PATCH 118/446] Working on understanding keyword substitution. --- Cantera/src/transport/LiquidTransportData.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index d0fa25151..8fb79a3a5 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -3,9 +3,9 @@ * Source code for liquid transport property evaluations. */ /* - * $Author: jchewso $ - * $Date: 2009-11-16 17:34:46 -0700 (Mon, 16 Nov 2009) $ - * $Revision: 261 $ + * $Author$ + * $Date$ + * $Revision$ * */ From 409d407581769552203e8ff84994b2faeb34debc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 15:29:38 +0000 Subject: [PATCH 119/446] Changing prop name from keyword to keywords From fc30b6d4c1d5959c88fa9dd942290277f229e1ae Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 15:32:04 +0000 Subject: [PATCH 120/446] fixed keywords property --- Cantera/src/transport/LiquidTransportParams.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 5fbad785a..d42eeca6a 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -3,10 +3,10 @@ * Source code for liquid mixture transport property evaluations. */ /* - * $Author: jchewso $ - * $Date: 2009-11-22 17:34:46 -0700 (Mon, 16 Nov 2009) $ - * $Revision: 261 $ - * + * Latest Checkin: + * $Author$ + * $Date$ + * $Revision$ */ #include "LiquidTransportParams.h" From cb163c521f3b92205cf116f2b3aa80935ad18d44 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 15:33:32 +0000 Subject: [PATCH 121/446] Deleted an unused property From a20321e5c9211cf9e3e7e38f81cbe6ad05b7c918 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 16:44:17 +0000 Subject: [PATCH 122/446] Worked on documenting using doxygen. --- Cantera/src/transport/L_matrix.h | 372 ++++++++++++----------- Cantera/src/transport/MultiTransport.cpp | 14 +- 2 files changed, 199 insertions(+), 187 deletions(-) diff --git a/Cantera/src/transport/L_matrix.h b/Cantera/src/transport/L_matrix.h index 238d68370..ecf5cfe59 100644 --- a/Cantera/src/transport/L_matrix.h +++ b/Cantera/src/transport/L_matrix.h @@ -25,229 +25,231 @@ namespace Cantera { - // #define CHEMKIN_COMPATIBILITY_MODE + // #define CHEMKIN_COMPATIBILITY_MODE - const doublereal Min_C_Internal = 0.001; + //! Constant to compare dimensionless heat capacities against zero + const doublereal Min_C_Internal = 0.001; - bool MultiTransport::hasInternalModes(int j) { + bool MultiTransport::hasInternalModes(int j) { #ifdef CHEMKIN_COMPATIBILITY_MODE - return (m_crot[j] > Min_C_Internal); + return (m_crot[j] > Min_C_Internal); #else - return (m_cinternal[j] > Min_C_Internal); + return (m_cinternal[j] > Min_C_Internal); #endif + } + + + /** + * Evaluate the upper-left block of the L matrix. + */ + void MultiTransport::eval_L0000(const doublereal* x) { + + doublereal prefactor = 16.0*m_temp/25.0; + doublereal sum; + int i, j, k; + for (i = 0; i < m_nsp; i++) { + // subtract-off the k=i term to account for the first delta + // function in Eq. (12.121) + + sum = -x[i]/m_bdiff(i,i); + for (k = 0; k < m_nsp; k++) sum += x[k]/m_bdiff(i,k); + + sum /= m_mw[i]; + for (j = 0; j != m_nsp; ++j) { + m_Lmatrix(i,j) = prefactor * x[j] + * ( m_mw[j] * sum + x[i]/m_bdiff(i,j) ); + } + // diagonal term is zero + m_Lmatrix(i,i) = 0.0; } + } - /** - * Evaluate the upper-left block of the L matrix. - */ - void MultiTransport::eval_L0000(const doublereal* x) { + //////////////////////////////////////////////////////////////////////////// - doublereal prefactor = 16.0*m_temp/25.0; - doublereal sum; - int i, j, k; - for (i = 0; i < m_nsp; i++) - { - // subtract-off the k=i term to account for the first delta - // function in Eq. (12.121) - sum = -x[i]/m_bdiff(i,i); - for (k = 0; k < m_nsp; k++) sum += x[k]/m_bdiff(i,k); + void MultiTransport::eval_L0010(const doublereal* x) { - sum /= m_mw[i]; - for (j = 0; j != m_nsp; ++j) { - m_Lmatrix(i,j) = prefactor * x[j] - * ( m_mw[j] * sum + x[i]/m_bdiff(i,j) ); - } - // diagonal term is zero - m_Lmatrix(i,i) = 0.0; - } + doublereal prefactor = 1.6*m_temp; + + doublereal sum, wj, xj; + int i, j; + for (j = 0; j < m_nsp; j++) { + //constant = prefactor * x[j]; + xj = x[j]; + wj = m_mw[j]; + sum = 0.0; + for (i = 0; i < m_nsp; i++) { + m_Lmatrix(i,j + m_nsp) = - prefactor * x[i] * xj * m_mw[i] * + (1.2 * m_cstar(j,i) - 1.0) / + ( (wj + m_mw[i]) * m_bdiff(j,i) ); + + // the next term is independent of "j"; + // need to do it for the "j,j" term + sum -= m_Lmatrix(i,j+m_nsp); + } + m_Lmatrix(j,j+m_nsp) += sum; } + } - //////////////////////////////////////////////////////////////////////////// + //////////////////////////////////////////////////////////////////////// - void MultiTransport::eval_L0010(const doublereal* x) { - - doublereal prefactor = 1.6*m_temp; - - doublereal sum, wj, xj; - int i, j; - for (j = 0; j < m_nsp; j++) { - //constant = prefactor * x[j]; - xj = x[j]; - wj = m_mw[j]; - sum = 0.0; - for (i = 0; i < m_nsp; i++) { - m_Lmatrix(i,j + m_nsp) = - prefactor * x[i] * xj * m_mw[i] * - (1.2 * m_cstar(j,i) - 1.0) / - ( (wj + m_mw[i]) * m_bdiff(j,i) ); - - // the next term is independent of "j"; - // need to do it for the "j,j" term - sum -= m_Lmatrix(i,j+m_nsp); - } - m_Lmatrix(j,j+m_nsp) += sum; - } + void MultiTransport::eval_L1000() { + int i, j; + for (j = 0; j < m_nsp; j++) { + for (i = 0; i < m_nsp; i++) { + m_Lmatrix(i+m_nsp,j) = m_Lmatrix(j,i+m_nsp); + } } + } + ////////////////////////////////////////////////////////////////////// - //////////////////////////////////////////////////////////////////////// + void MultiTransport::eval_L1010(const doublereal* x) { - void MultiTransport::eval_L1000() { - int i, j; - for (j = 0; j < m_nsp; j++) - for (i = 0; i < m_nsp; i++) - m_Lmatrix(i+m_nsp,j) = m_Lmatrix(j,i+m_nsp); - } + const doublereal fiveover3pi = 5.0/(3.0*Pi); + doublereal prefactor = (16.0*m_temp)/25.0; + int i, j; + doublereal constant1, wjsq, constant2, constant3, constant4, + fourmj, threemjsq, sum, sumwij;; + doublereal term1, term2; - ////////////////////////////////////////////////////////////////////// + for (j = 0; j < m_nsp; j++) { - void MultiTransport::eval_L1010(const doublereal* x) { + // get constant terms that depend on just species "j" - const doublereal fiveover3pi = 5.0/(3.0*Pi); - doublereal prefactor = (16.0*m_temp)/25.0; + constant1 = prefactor*x[j]; + wjsq = m_mw[j]*m_mw[j]; + constant2 = 13.75*wjsq; + constant3 = m_crot[j]/m_rotrelax[j]; + constant4 = 7.5*wjsq; + fourmj = 4.0*m_mw[j]; + threemjsq = 3.0*m_mw[j]*m_mw[j]; + sum = 0.0; + for (i = 0; i < m_nsp; i++) { - int i, j; - doublereal constant1, wjsq, constant2, constant3, constant4, - fourmj, threemjsq, sum, sumwij;; - doublereal term1, term2; + sumwij = m_mw[i] + m_mw[j]; + term1 = m_bdiff(i,j) * sumwij*sumwij; + term2 = fourmj*m_astar(i,j)*(1.0 + fiveover3pi* + (constant3 + + (m_crot[i]/m_rotrelax[i]))); // see Eq. (12.125) - for (j = 0; j < m_nsp; j++) { + m_Lmatrix(i+m_nsp,j+m_nsp) = constant1*x[i]*m_mw[i] /(m_mw[j]*term1) * + (constant2 - threemjsq*m_bstar(i,j) + - term2*m_mw[j]); - // get constant terms that depend on just species "j" - - constant1 = prefactor*x[j]; - wjsq = m_mw[j]*m_mw[j]; - constant2 = 13.75*wjsq; - constant3 = m_crot[j]/m_rotrelax[j]; - constant4 = 7.5*wjsq; - fourmj = 4.0*m_mw[j]; - threemjsq = 3.0*m_mw[j]*m_mw[j]; - sum = 0.0; - for (i = 0; i < m_nsp; i++) { - - sumwij = m_mw[i] + m_mw[j]; - term1 = m_bdiff(i,j) * sumwij*sumwij; - term2 = fourmj*m_astar(i,j)*(1.0 + fiveover3pi* - (constant3 + - (m_crot[i]/m_rotrelax[i]))); // see Eq. (12.125) - - m_Lmatrix(i+m_nsp,j+m_nsp) = constant1*x[i]*m_mw[i] /(m_mw[j]*term1) * - (constant2 - threemjsq*m_bstar(i,j) - - term2*m_mw[j]); - - sum += x[i] /(term1) * - (constant4 + m_mw[i]*m_mw[i]* - (6.25 - 3.0*m_bstar(i,j)) + term2*m_mw[i]); - } + sum += x[i] /(term1) * + (constant4 + m_mw[i]*m_mw[i]* + (6.25 - 3.0*m_bstar(i,j)) + term2*m_mw[i]); + } - m_Lmatrix(j+m_nsp,j+m_nsp) -= sum*constant1; - } + m_Lmatrix(j+m_nsp,j+m_nsp) -= sum*constant1; } + } - ////////////////////////////////////////////////////////////////////////////////// + ////////////////////////////////////////////////////////////////////////////////// - void MultiTransport::eval_L1001(const doublereal* x) { + void MultiTransport::eval_L1001(const doublereal* x) { - doublereal prefactor = 32.00*m_temp/(5.00*Pi); - int i,j; - doublereal constant, sum; - int n2 = 2*m_nsp; - int npoly = 0; - for (j = 0; j < m_nsp; j++) { - // collect terms that depend only on "j" - if (hasInternalModes(j)) { - constant = prefactor*m_mw[j]*x[j]*m_crot[j]/(m_cinternal[j]*m_rotrelax[j]); - sum = 0.0; - for (i = 0; i < m_nsp; i++) { - // see Eq. (12.127) - m_Lmatrix(i+m_nsp,j+n2) = constant * m_astar(j,i) * x[i] / - ( (m_mw[j] + m_mw[i] ) * m_bdiff(j,i)); - sum += m_Lmatrix(i+m_nsp,j+n2); - } - npoly++; - m_Lmatrix(j+m_nsp,j+n2) += sum; - } - else { - for (i = 0; i < m_nsp; i++) m_Lmatrix(i+m_nsp,j+n2) = 0.0; - } - } + doublereal prefactor = 32.00*m_temp/(5.00*Pi); + int i,j; + doublereal constant, sum; + int n2 = 2*m_nsp; + int npoly = 0; + for (j = 0; j < m_nsp; j++) { + // collect terms that depend only on "j" + if (hasInternalModes(j)) { + constant = prefactor*m_mw[j]*x[j]*m_crot[j]/(m_cinternal[j]*m_rotrelax[j]); + sum = 0.0; + for (i = 0; i < m_nsp; i++) { + // see Eq. (12.127) + m_Lmatrix(i+m_nsp,j+n2) = constant * m_astar(j,i) * x[i] / + ( (m_mw[j] + m_mw[i] ) * m_bdiff(j,i)); + sum += m_Lmatrix(i+m_nsp,j+n2); + } + npoly++; + m_Lmatrix(j+m_nsp,j+n2) += sum; + } + else { + for (i = 0; i < m_nsp; i++) m_Lmatrix(i+m_nsp,j+n2) = 0.0; + } } + } - //////////////////////////////////////////////////////////////////////// + //////////////////////////////////////////////////////////////////////// - void MultiTransport::eval_L0001() { - int i, j; - int n2 = 2*m_nsp; - for (j = 0; j < m_nsp; j++) - for (i = 0; i < m_nsp; i++) - m_Lmatrix(i,j+n2) = 0.0; - } - - //////////////////////////////////////////////////////////////////////// - - void MultiTransport::eval_L0100() { - int i, j; - int n2 = 2*m_nsp; - for (j = 0; j < m_nsp; j++) - for (i = 0; i < m_nsp; i++) - m_Lmatrix(i+n2,j) = 0.0; // see Eq. (12.123) - } - - //////////////////////////////////////////////////////////////////////// - - void MultiTransport::eval_L0110() { - int i, j; - int n2 = 2*m_nsp; - for (j = 0; j < m_nsp; j++) - for (i = 0; i < m_nsp; i++) - m_Lmatrix(i+n2,j+m_nsp) = m_Lmatrix(j+m_nsp,i+n2); // see Eq. (12.123) - } - - //////////////////////////////////////////////////////////////////////// - - - void MultiTransport::eval_L0101(const doublereal* x) { - - const doublereal fivepi = 5.00*Pi; - const doublereal eightoverpi = 8.0 / Pi; - - doublereal prefactor = 4.00*m_temp; - int n2 = 2*m_nsp; - int i,k; - doublereal constant1, constant2, diff_int, sum; - for (i = 0; i < m_nsp; i++) { - if (hasInternalModes(i)) { - // collect terms that depend only on "i" - constant1 = prefactor*x[i]/m_cinternal[i]; - constant2 = 12.00*m_mw[i]*m_crot[i] / - (fivepi*m_cinternal[i]*m_rotrelax[i]); - sum = 0.0; - for (k = 0; k < m_nsp; k++) { - // see Eq. (12.131) - diff_int = m_bdiff(i,k); - m_Lmatrix(k+n2,i+n2) = 0.0; - sum += x[k]/diff_int; - if (k != i) sum += x[k]*m_astar(i,k)*constant2 / - (m_mw[k]*diff_int); - } - // see Eq. (12.130) - m_Lmatrix(i+n2,i+n2) = - - eightoverpi*m_mw[i]*x[i]*x[i]*m_crot[i] / - (m_cinternal[i]*m_cinternal[i]*GasConstant*m_visc[i]*m_rotrelax[i]) - - constant1*sum; - } - else { - for (k = 0; k < m_nsp; k++) - m_Lmatrix(i+n2,i+n2) = 1.0; - } - } + void MultiTransport::eval_L0001() { + int i, j; + int n2 = 2*m_nsp; + for (j = 0; j < m_nsp; j++) + for (i = 0; i < m_nsp; i++) + m_Lmatrix(i,j+n2) = 0.0; + } + + //////////////////////////////////////////////////////////////////////// + + void MultiTransport::eval_L0100() { + int i, j; + int n2 = 2*m_nsp; + for (j = 0; j < m_nsp; j++) + for (i = 0; i < m_nsp; i++) + m_Lmatrix(i+n2,j) = 0.0; // see Eq. (12.123) + } + + //////////////////////////////////////////////////////////////////////// + + void MultiTransport::eval_L0110() { + int i, j; + int n2 = 2*m_nsp; + for (j = 0; j < m_nsp; j++) + for (i = 0; i < m_nsp; i++) + m_Lmatrix(i+n2,j+m_nsp) = m_Lmatrix(j+m_nsp,i+n2); // see Eq. (12.123) + } + + //////////////////////////////////////////////////////////////////////// + + + void MultiTransport::eval_L0101(const doublereal* x) { + + const doublereal fivepi = 5.00*Pi; + const doublereal eightoverpi = 8.0 / Pi; + + doublereal prefactor = 4.00*m_temp; + int n2 = 2*m_nsp; + int i,k; + doublereal constant1, constant2, diff_int, sum; + for (i = 0; i < m_nsp; i++) { + if (hasInternalModes(i)) { + // collect terms that depend only on "i" + constant1 = prefactor*x[i]/m_cinternal[i]; + constant2 = 12.00*m_mw[i]*m_crot[i] / + (fivepi*m_cinternal[i]*m_rotrelax[i]); + sum = 0.0; + for (k = 0; k < m_nsp; k++) { + // see Eq. (12.131) + diff_int = m_bdiff(i,k); + m_Lmatrix(k+n2,i+n2) = 0.0; + sum += x[k]/diff_int; + if (k != i) sum += x[k]*m_astar(i,k)*constant2 / + (m_mw[k]*diff_int); + } + // see Eq. (12.130) + m_Lmatrix(i+n2,i+n2) = + - eightoverpi*m_mw[i]*x[i]*x[i]*m_crot[i] / + (m_cinternal[i]*m_cinternal[i]*GasConstant*m_visc[i]*m_rotrelax[i]) + - constant1*sum; + } + else { + for (k = 0; k < m_nsp; k++) + m_Lmatrix(i+n2,i+n2) = 1.0; + } } + } } #endif diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index 4bc72954c..ebf8b047e 100644 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -1010,9 +1010,19 @@ namespace Cantera { m_bdiff(k,k) = d; } - // internal heat capacities + // Calculate the internal heat capacities by subtracting off the translational contributions + /* + * HKM Exploratory comment: + * The translational component is 1.5 + * The rotational component is 1.0 for a linear molecule and 1.5 for a nonlinear molecule + * and zero for a monotomic. + * Chemkin has traditionally subtracted 1.5 here (SAND86-8246). + * The original Dixon-Lewis paper subtracted 1.5 here. + */ const array_fp& cp = ((IdealGasPhase*)m_thermo)->cp_R_ref(); - for (k = 0; k < m_nsp; k++) m_cinternal[k] = cp[k] - 2.5; + for (k = 0; k < m_nsp; k++) { + m_cinternal[k] = cp[k] - 2.5; + } } /** From 357c7ff4d95ec0c11b161dfbeb0401d22513468c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 19 Mar 2010 23:07:45 +0000 Subject: [PATCH 123/446] Resurrected the SimpleTransport object. The test problem was failing and had been ignored. --- Cantera/src/transport/LiquidTransport.cpp | 41 ++---- Cantera/src/transport/LiquidTransport.h | 12 +- Cantera/src/transport/SimpleTransport.cpp | 19 ++- Cantera/src/transport/TransportBase.h | 3 +- Cantera/src/transport/TransportFactory.cpp | 145 ++++++++------------- Cantera/src/transport/TransportFactory.h | 18 ++- 6 files changed, 102 insertions(+), 136 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 03490ad1b..0ecfa3ee9 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -625,19 +625,21 @@ namespace Cantera { updateMobilityRatio_T(); } mobRat = m_mobRatSpecies; - for (int k = 0; k < m_nBinInt; k++) + for (int k = 0; k < m_nBinInt; k++) { mobRatIndex[k] = m_mobRatSpeciesIndex[k]; + } } void LiquidTransport::getSpeciesMobilityRatio(doublereal** mobRat, std::vector& mobRatIndex) { update_T(); if (!m_mobRat_temp_ok) { updateMobilityRatio_T(); } - for (int k=0; kgetMixTransProp( m_selfDiffTempDep_Ns[k] ); + } + m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp(m_selfDiffTempDep_Ns[k]); m_selfDiffMixIndex[k] = m_selfDiffMixModelIndex[k]; } } - for (int k = 0; k < m_nsp; k++){ - selfDiff[k] = m_selfDiffMix[k]; - selfDiffIndex[k]= m_selfDiffMixIndex[k]; - } - } - - void LiquidTransport:: selfDiffusion(double* selfDiff, std::vector& selfDiffIndex) { - - update_T(); - update_C(); - - ////// LiquidTranInteraction method - if (!m_selfDiff_mix_ok){ - for (int k = 0; k < m_nsp; k++){ - if ( m_selfDiffMixModelIndex[k] != m_selfDiffTempDepIndex[k] ) - throw CanteraError("LiquidTransport::selfDiffusion","Self Diffusion Indices Don't Match: Mixture vs. Species"); - m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffTempDep_Ns[k] ); - m_selfDiffMixIndex[k] = m_selfDiffMixModelIndex[k]; - } - } - for (int k = 0; k < m_nsp; k++){ + for (int k = 0; k < m_nsp; k++) { selfDiff[k] = m_selfDiffMix[k]; selfDiffIndex[k]= m_selfDiffMixIndex[k]; } diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 2feb83ee2..52a474665 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -29,6 +29,7 @@ using namespace std; namespace Cantera { + // Forward references class LiquidTransportParams; @@ -227,7 +228,6 @@ namespace Cantera { * determine the individual species self diffusion coeffs. */ virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex); - virtual void selfDiffusion(double* selfDiff, std::vector& selfDiffIndex); //! Returns the pure species self diffusion in solution of each species /*! @@ -862,8 +862,10 @@ namespace Cantera { private: - //! Number of species in the mixture + //! Number of species in the phase int m_nsp; + + int m_nBinInt; //! Minimum temperature applicable to the transport property eval @@ -872,11 +874,11 @@ namespace Cantera { //! Maximum temperature applicable to the transport property evaluator doublereal m_tmax; - //! Local Copy of the molecular weights of the species + //! Local copy of the molecular weights of the species /*! - * Length is Equal to the number of species in the mechanism. + * Length is equal to the number of species in the phase */ - vector_fp m_mw; + vector_fp m_mw; //! Viscosity for each species expressed as an appropriate subclass //! of LTPspecies diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index ef60f8031..c676b0853 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -709,10 +709,12 @@ namespace Cantera { * thermal conductivity. */ void SimpleTransport::updateCond_T() { - int k; - - for (k = 0; k < m_nsp; k++) { - m_condSpecies[k] = m_coeffLambda_Ns[k]->getSpeciesTransProp() ; + if (compositionDepType_ == 0) { + m_condSpecies[0] = m_coeffLambda_Ns[0]->getSpeciesTransProp(); + } else { + for (int k = 0; k < m_nsp; k++) { + m_condSpecies[k] = m_coeffLambda_Ns[k]->getSpeciesTransProp(); + } } m_cond_temp_ok = true; m_cond_mix_ok = false; @@ -753,9 +755,12 @@ namespace Cantera { * The flag m_visc_ok is set to true. */ void SimpleTransport::updateViscosity_T() { - int k; - for (k = 0; k < m_nsp; k++) { - m_viscSpecies[k] = m_coeffVisc_Ns[k]->getSpeciesTransProp(); + if (compositionDepType_ == 0) { + m_viscSpecies[0] = m_coeffVisc_Ns[0]->getSpeciesTransProp(); + } else { + for (int k = 0; k < m_nsp; k++) { + m_viscSpecies[k] = m_coeffVisc_Ns[k]->getSpeciesTransProp(); + } } m_visc_temp_ok = true; m_visc_mix_ok = false; diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 7dd194f8c..ba327142d 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -359,8 +359,7 @@ namespace Cantera { */ virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex) { err("selfDiffusion"); } - virtual void selfDiffusion(double* selfDiff, std::vector& selfDiffIndex) - { err("selfdiffusion"); } + //! Returns the pure species self diffusion in solution of each species /*! diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 81c0d0bc8..4ffb881a3 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -439,9 +439,9 @@ namespace Cantera { dtr->initialize(phase, gastr); break; case cSimpleTransport: - // tr = new SimpleTransport(); - // initLiquidTransport(tr, phase, log_level); - // tr->setThermo(*phase); + tr = new SimpleTransport(); + initLiquidTransport(tr, phase, log_level); + tr->setThermo(*phase); break; #ifdef WITH_IDEAL_SOLUTIONS case cLiquidTransport: @@ -897,6 +897,7 @@ namespace Cantera { for (i = 0; i < tr.nsp_; i++) { + GasTransportData& trdat = datatable[names[i]]; // 'datatable' returns a default TransportData object if @@ -947,33 +948,34 @@ namespace Cantera { * instance of TransportParams containing the transport data for * these species read from the file. */ - void TransportFactory::getLiquidSpeciesTransportData( const std::vector &xspecies, - XML_Node& log, - const std::vector &names, - LiquidTransportParams& trParam) + void TransportFactory::getLiquidSpeciesTransportData(const std::vector &xspecies, + XML_Node& log, + const std::vector &names, + LiquidTransportParams& trParam) { std::string name; /* * Create a map of species names versus liquid transport data parameters */ std::map datatable; + std::map::iterator it; - int nsp = trParam.nsp_;//static_cast(xspecies.size()); + // Store the number of species in the phase + int nsp = trParam.nsp_; + + // Store the number of off-diagonal symmetric interactions between species in the phase int nBinInt = nsp*(nsp-1)/2; // read all entries in database into 'datatable' and check for // errors. Note that this procedure validates all entries, not // only those for the species listed in 'names'. - - int i; - for (i = 0; i < nsp; i++) { + for (int i = 0; i < nsp; i++) { const XML_Node& sp = *xspecies[i]; name = sp["name"]; vector_fp vCoeff; - // std::cout << "Processing node for " << name << std::endl; - // put in a try block so that species with no 'transport' - // child are skipped, instead of throwing an exception. + // Species with no 'transport' child are skipped. However, if that species is in the list, + // it will throw an exception below. try { if (sp.hasChild("transport")) { XML_Node& trNode = sp.child("transport"); @@ -982,121 +984,96 @@ namespace Cantera { // and then insertion into LiquidTransportData objects below. LiquidTransportData data; data.speciesName = name; - - //data.viscosity = 0; - //data.ionConductivity = 0; - data.mobRatIndex.resize(nBinInt,""); data.mobilityRatio.resize(nBinInt,0); data.selfDiffIndex.resize(nsp,""); data.selfDiffusion.resize(nsp,0); - //////// new stuff int num = trNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { XML_Node &xmlChild = trNode.child(iChild); std::string nodeName = xmlChild.name(); - switch ( m_tranPropMap[nodeName] ) { + switch (m_tranPropMap[nodeName]) { case TP_VISCOSITY: - data.viscosity = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.viscosity = newLTP(xmlChild, name, m_tranPropMap[nodeName], trParam.thermo ); break; case TP_IONCONDUCTIVITY: - data.ionConductivity = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.ionConductivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], trParam.thermo); break; case TP_MOBILITYRATIO: { - int iSpec; - for (iSpec = 0; iSpec< nBinInt; iSpec++){ + for (int iSpec = 0; iSpec< nBinInt; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); data.mobRatIndex[iSpec] = specName; - data.mobilityRatio[iSpec] = newLTP( propSpecNode, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.mobilityRatio[iSpec] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], trParam.thermo); }; }; break; case TP_SELFDIFFUSION: { - int iSpec; - for (iSpec = 0; iSpec< nsp; iSpec++){ + for (int iSpec = 0; iSpec< nsp; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); data.selfDiffIndex[iSpec] = specName; - data.selfDiffusion[iSpec] = newLTP( propSpecNode, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.selfDiffusion[iSpec] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], trParam.thermo); }; }; break; case TP_THERMALCOND: - data.thermalCond = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.thermalCond = newLTP(xmlChild, + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_DIFFUSIVITY: - data.speciesDiffusivity = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.speciesDiffusivity = newLTP(xmlChild, + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_HYDRORADIUS: - data.hydroRadius = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.hydroRadius = newLTP(xmlChild, + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; case TP_ELECTCOND: - data.electCond = newLTP( xmlChild, - name, - m_tranPropMap[nodeName], - trParam.thermo ); + data.electCond = newLTP(xmlChild, + name, + m_tranPropMap[nodeName], + trParam.thermo ); break; default: - throw CanteraError("getLiquidSpeciesTransportData","unknown transport property: " + nodeName ); - + throw CanteraError("getLiquidSpeciesTransportData","unknown transport property: " + nodeName); } } datatable.insert(pair(name,data)); - // datatable[name] = data; } } - catch(CanteraError) { - ; + catch (CanteraError yy) { + throw yy; } } trParam.LTData.clear(); - for (i = 0; i < trParam.nsp_; i++) { - - LiquidTransportData& trdat = datatable[names[i]]; - - // 'datatable' returns a default TransportData object if - // the species name is not one in the transport database. - // This can be detected by examining 'geometry'. - if ( !( (trdat.viscosity)->checkPositive() ) ) { - throw TransportDBError(0,"no viscosity transport data found for species " - + names[i]); - std::cout << "No viscosity seen for " << names[i] - << "but this might not be required depending on what you are trying to do." - << std::endl; - } - + for (int i = 0; i < trParam.nsp_; i++) { /* - * this is a much more general way to handle the transfer - * -> calling the default copy constructor for LiquidTransportData + * Check to see that we have a LiquidTransportData object for all of the + * species in the phase. If not, throw an error. + */ + it = datatable.find(names[i]); + if (it == datatable.end()) { + throw TransportDBError(0,"No transport data found for species " + names[i]); + } + LiquidTransportData& trdat = it->second; + + /* + * Now, transfer these objects into LTData in the correct phase index order by + * calling the default copy constructor for LiquidTransportData. */ trParam.LTData.push_back(trdat); } @@ -1133,15 +1110,13 @@ namespace Cantera { trParam.selfDiffIndex.resize(nsp,""); trParam.selfDiffusion.resize(nsp,0); - if ( tranTypeNode.hasChild("compositionDependence")) { + if (tranTypeNode.hasChild("compositionDependence")) { //compDepNode contains the interaction model XML_Node &compDepNode = tranTypeNode.child("compositionDependence"); switch (m_tranPropMap[nodeName]) { break; case TP_VISCOSITY: - trParam.viscosity = newLTI( compDepNode, - m_tranPropMap[nodeName], - trParam ); + trParam.viscosity = newLTI(compDepNode, m_tranPropMap[nodeName], trParam); break; case TP_IONCONDUCTIVITY: trParam.ionConductivity = newLTI( compDepNode, @@ -1198,12 +1173,6 @@ namespace Cantera { throw CanteraError("getLiquidInteractionsTransportData","unknown transport property: " + nodeName ); } - } - else { - int linenum; - throw TransportDBError( linenum, - "missing node for <" - + tranTypeNode.name() + "> node." ); } /* Allow a switch between mass-averaged, mole-averaged * and solvent specified reference velocities. diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index b570bce2a..ae85d414f 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -202,14 +202,22 @@ namespace Cantera { GasTransportParams& tr); - //! Read transport property data from a file for a list of species. + //! Read transport property data from a file for a list of species that comprise + //! the phase. /*! + * Given the name of a file containing transport property + * parameters and a list of species names, this method constructs the LiquidTransport + * Params object containing the transport data for these species. * - * Given the name of a file containing transport property - * parameters and a list of species names, this method returns an - * instance of TransportParams containing the transport data for - * these species read from the file. + * It is an error to not find a "transport" XML element within each of the species + * XML elements listed in the names vector. * + * @param db Reference to a vector of XML_Node pointers containing the species XML + * nodes. + * @param log Reference to an XML log file. (currently unused) + * @param names Vector of names of species. On output, tr will contain transport data + * for each of of these names in the order determined by this vector. + * @param tr Reference to the LiquidTransportParams object that will contain the results. */ void getLiquidSpeciesTransportData(const std::vector &db, XML_Node& log, const std::vector& names, From ae2bd115d0ee3e323e71f04ec23f2587b720c9a4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 20 Mar 2010 03:09:22 +0000 Subject: [PATCH 124/446] Worked on the interface, and took out some chaff --- Cantera/src/transport/LiquidTransport.cpp | 64 ++++++++++++++--------- Cantera/src/transport/LiquidTransport.h | 31 ++++++++--- Cantera/src/transport/TransportBase.h | 27 ++++++++-- 3 files changed, 85 insertions(+), 37 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 0ecfa3ee9..930094e49 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -193,7 +193,6 @@ namespace Cantera { m_mobRatMix = right.m_mobRatMix; m_mobRatMixIndex = right.m_mobRatMixIndex; m_selfDiffMix = right.m_selfDiffMix; - m_selfDiffMixIndex = right.m_selfDiffMixIndex; m_spwork = right.m_spwork; m_visc_mix_ok = false; m_visc_temp_ok = false; @@ -233,8 +232,10 @@ namespace Cantera { for ( int k = 0; k < m_nsp; k++) { if ( m_viscTempDep_Ns[k] ) delete m_viscTempDep_Ns[k]; if ( m_ionCondTempDep_Ns[k] ) delete m_ionCondTempDep_Ns[k]; - for ( int l=0;l < m_nsp; l++ ){ - if ( m_selfDiffTempDep_Ns[l][k] ) delete m_selfDiffTempDep_Ns[l][k]; + for (int l = 0; l < m_nsp; l++ ) { + if (m_selfDiffTempDep_Ns[l][k]) { + delete m_selfDiffTempDep_Ns[l][k]; + } } for ( int l=0;l < m_nBinInt; l++ ){ if ( m_mobRatTempDep_Ns[l][k] ) delete m_mobRatTempDep_Ns[l][k]; @@ -309,7 +310,6 @@ namespace Cantera { m_selfDiffSpeciesIndex.resize(m_nsp); m_selfDiffSpecies.resize(m_nsp, m_nsp, 0.0); m_selfDiffMix.resize(m_nsp,0.0); - m_selfDiffMixIndex.resize(m_nsp); for (k=0; k < m_nsp; k++){ m_selfDiffTempDep_Ns[k].resize(m_nsp, 0); } @@ -350,19 +350,19 @@ namespace Cantera { } } } - for (int j = 0; j < (int) m_selfDiffMixModelIndex.size(); j++){ - for (int l=0; l < (int) m_selfDiffMixModelIndex.size(); l++){ + for (int j = 0; j < (int) m_selfDiffMixModelIndex.size(); j++) { + for (int l = 0; l < (int) m_selfDiffMixModelIndex.size(); l++) { if (m_selfDiffMixModelIndex[j] == ltd.selfDiffIndex[l]) { - m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[l]; + m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[l]; ltd.selfDiffusion[l] = 0; m_selfDiffTempDepIndex[j] = ltd.selfDiffIndex[l]; break; } } } - m_lambdaTempDep_Ns[k] = ltd.thermalCond; + m_lambdaTempDep_Ns[k] = ltd.thermalCond; ltd.thermalCond = 0; - m_radiusTempDep_Ns[k] = ltd.hydroRadius; + m_radiusTempDep_Ns[k] = ltd.hydroRadius; ltd.hydroRadius = 0; } @@ -641,38 +641,50 @@ namespace Cantera { mobRatIndex[k] = m_mobRatSpeciesIndex[k]; } } - - - /****************** SelfDiffusion ******************************/ - - // Returns the mobility ratios of the solution + //==================================================================================================================== + // Returns the self diffusion coefficients of the species in the phase /* - * The mobility ratio calculation is handled by subclasses of - * LiquidTranInteraction as specified in the input file. + * The self diffusion coefficient is the diffusion coefficient of a tracer species + * at the current temperature and composition of the species. Therefore, + * the dilute limit of transport is assumed for the tracer species. + * The effective formula may be calculated from the stefan-maxwell formulation by + * adding another row for the tracer species, assigning all D's to be equal + * to the respective species D's, and then taking the limit as the + * tracer species mole fraction goes to zero. The corresponding flux equation + * for the tracer species k in units of kmol m-2 s-1 is. + * + * \f[ + * J_k = - D^{sd}_k \frac{C_k}{R T} \nabla \mu_k + * \f] + * + * The derivative is taken at constant T and P. + * + * The self diffusion calculation is handled by subclasses of + * LiquidTranInteraction as specified in the input file. * These in turn employ subclasses of LTPspecies to - * determine the individual species mobility ratios. - */ - void LiquidTransport:: selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex) { - + * determine the individual species self diffusion coeffs. + * + * @param selfDiff Vector of self-diffusion coefficients + * Length = number of species in phase + * units = m**2 s-1 + */ + void LiquidTransport::selfDiffusion(doublereal * const selfDiff) { update_T(); update_C(); - - ////// LiquidTranInteraction method if (!m_selfDiff_mix_ok) { for (int k = 0; k < m_nsp; k++) { if (m_selfDiffMixModelIndex[k] != m_selfDiffTempDepIndex[k]) { - throw CanteraError("LiquidTransport::selfDiffusion","Self Diffusion Indices Don't Match: Mixture vs. Species"); + throw CanteraError("LiquidTransport::selfDiffusion", + "Self Diffusion Indices Don't Match: Mixture vs. Species"); } m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp(m_selfDiffTempDep_Ns[k]); - m_selfDiffMixIndex[k] = m_selfDiffMixModelIndex[k]; } } for (int k = 0; k < m_nsp; k++) { selfDiff[k] = m_selfDiffMix[k]; - selfDiffIndex[k]= m_selfDiffMixIndex[k]; } } - + //==================================================================================================================== // Returns the pure species self diffusion for all species /* * The pure species self diffusion coeffs are evaluated using the diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 52a474665..e84cc3969 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -217,17 +217,36 @@ namespace Cantera { * @param mobRat array of length "number of species" * to hold returned mobility ratios. */ - virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex); + virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex); virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex); - //! Returns the self diffusion coefficients in the solution + //! Returns the self diffusion coefficients of the species in the phase /*! + * The self diffusion coefficient is the diffusion coefficient of a tracer species + * at the current temperature and composition of the species. Therefore, + * the dilute limit of transport is assumed for the tracer species. + * The effective formula may be calculated from the stefan-maxwell formulation by + * adding another row for the tracer species, assigning all D's to be equal + * to the respective species D's, and then taking the limit as the + * tracer species mole fraction goes to zero. The corresponding flux equation + * for the tracer species k in units of kmol m-2 s-1 is. + * + * \f[ + * J_k = - D^{sd}_k \frac{C_k}{R T} \nabla \mu_k + * \f] + * + * The derivative is taken at constant T and P. + * * The self diffusion calculation is handled by subclasses of - * LiquidTranInteraction as specified in the input file. + * LiquidTranInteraction as specified in the input file. * These in turn employ subclasses of LTPspecies to * determine the individual species self diffusion coeffs. - */ - virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex); + * + * @param selfDiff Vector of self-diffusion coefficients + * Length = number of species in phase + * units = m**2 s-1 + */ + virtual void selfDiffusion(doublereal * const selfDiff); //! Returns the pure species self diffusion in solution of each species /*! @@ -1318,8 +1337,6 @@ namespace Cantera { //! Saved values of the mixture self diffusion coefficients vector_fp m_selfDiffMix; - //! Saved species index of the mixture correlated to self diffusion coefficients - std::vector m_selfDiffMixIndex; //! work space /*! diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index ba327142d..9ec0b5d91 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -326,7 +326,7 @@ namespace Cantera { * * @param ionCond Vector of ionic conductivities */ - virtual void getSpecoesIonConductivity(doublereal* const ionCond) + virtual void getSpeciesIonConductivity(doublereal* const ionCond) { err("getSpeciesIonConductivity"); } @@ -350,14 +350,33 @@ namespace Cantera { virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex) { err("getSpeciesMobilityRatio"); } - //! Returns the self diffusion coefficients in the solution + //! Returns the self diffusion coefficients of the species in the phase /*! + * The self diffusion coefficient is the diffusion coefficient of a tracer species + * at the current temperature and composition of the species. Therefore, + * the dilute limit of transport is assumed for the tracer species. + * The effective formula may be calculated from the stefan-maxwell formulation by + * adding another row for the tracer species, assigning all D's to be equal + * to the respective species D's, and then taking the limit as the + * tracer species mole fraction goes to zero. The corresponding flux equation + * for the tracer species k in units of kmol m-2 s-1 is. + * + * \f[ + * J_k = - D^{sd}_k \frac{C_k}{R T} \nabla \mu_k + * \f] + * + * The derivative is taken at constant T and P. + * * The self diffusion calculation is handled by subclasses of - * LiquidTranInteraction as specified in the input file. + * LiquidTranInteraction as specified in the input file. * These in turn employ subclasses of LTPspecies to * determine the individual species self diffusion coeffs. + * + * @param selfDiff Vector of self-diffusion coefficients + * Length = number of species in phase + * units = m**2 s-1 */ - virtual void selfDiffusion(vector_fp& selfDiff, std::vector& selfDiffIndex) + virtual void selfDiffusion(doublereal * const selfDiff) { err("selfDiffusion"); } From 2a6207394841356530a405e07849d5c0071c655f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 23 Mar 2010 15:27:42 +0000 Subject: [PATCH 125/446] Added doxygen comments. --- Cantera/src/transport/TransportParams.h | 32 +++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 648847e14..dd42f2c86 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -115,10 +115,13 @@ namespace Cantera { virtual ~GasTransportParams() {} // polynomial fits - //temperature-fit viscosity - std::vector visccoeffs; + + //! temperature-fit of the viscosity + std::vector visccoeffs; + //temperature-fit heat conduction std::vector condcoeffs; + //temperature-fit diffusivity std::vector diffcoeffs; vector_fp polytempvec; @@ -129,14 +132,39 @@ namespace Cantera { std::vector bstar_poly; std::vector cstar_poly; + //! Rotational relaxation number for the species in the current phase + /*! + * length is the number of species in the phase + * units are dimensionless + */ vector_fp zrot; + + //! Dimensionless rotational heat capacity of the species in the current phase + /*! + * These values are 0, 1 and 1.5 for single-molecule, linear, and nonlinear species respectively + * length is the number of species in the pahse + * units are dimensionless (Cr / R) + */ vector_fp crot; std::vector polar; vector_fp alpha; vector_fp fitlist; + + //! Lennard-Jones well-depth of the species in the current phase + /*! + * length is the number of species in the phase + * Units are Joules (Note this is not Joules/kmol) + */ vector_fp eps; + + //! Lennard-Jones diameter of the species in the current phase + /*! + * length is the number of species in the phase + * units are in meters. + */ vector_fp sigma; + DenseMatrix reducedMass; DenseMatrix diam; DenseMatrix epsilon; From 0bbd0879d56e11ec2c0f11d816977a2aea548c12 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 23 Mar 2010 15:28:06 +0000 Subject: [PATCH 126/446] Added doxygen comments. --- Cantera/src/base/ct_defs.h | 21 +++++++++++++++------ Cantera/src/base/misc.cpp | 6 +++++- 2 files changed, 20 insertions(+), 7 deletions(-) diff --git a/Cantera/src/base/ct_defs.h b/Cantera/src/base/ct_defs.h index 85e5e8334..1930ba377 100644 --- a/Cantera/src/base/ct_defs.h +++ b/Cantera/src/base/ct_defs.h @@ -76,21 +76,30 @@ namespace Cantera { */ //@{ - /// Avogadro's Number - const doublereal Avogadro = 6.02214179e26; // /kmol + //! Avogadro's Number + /*! + * Units are number/kmol + */ + const doublereal Avogadro = 6.02214179e26; /// Universal Gas Constant. 2006 CODATA value. const doublereal GasConstant = 8314.47215; // J/kmol/K const doublereal logGasConstant = 9.025752908; - /// One atmosphere - const doublereal OneAtm = 1.01325e5; // Pa + //! One atmosphere + /*! + * Units are Pa + */ + const doublereal OneAtm = 1.01325e5; - /// Universal gas constant in cal/mol/K + //! Universal gas constant in cal/mol/K const doublereal GasConst_cal_mol_K = 1.987; - /// Boltzmann's constant + //! Boltzmann's constant + /*! + * Units are J/K + */ const doublereal Boltzmann = GasConstant / Avogadro; /// Planck's constant. Units of J-s diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index c116b604d..8750abe59 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -195,8 +195,9 @@ namespace Cantera { //! Copy Constructor for the Messages class /*! - * constructor for the Messages class which is a subclass + * Constructor for the Messages class which is a subclass * of the Application class. + * @param r Message to be copied */ Messages(const Messages &r) : errorMessage(r.errorMessage), @@ -216,6 +217,9 @@ namespace Cantera { } //! Assignment operator + /*! + * @param r Message to be copied + */ Messages & operator=(const Messages &r) { if (this == &r) { From 900f5d1530e9c5f054c37034c0a7459ee843ac95 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 25 Mar 2010 17:23:36 +0000 Subject: [PATCH 127/446] Doxygen updates, and code formatting. No actual changes. --- Cantera/src/transport/TransportFactory.cpp | 178 ++++++++++----------- Cantera/src/transport/TransportParams.h | 159 +++++++++++++++--- 2 files changed, 226 insertions(+), 111 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 4ffb881a3..5bfa039c3 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -761,47 +761,45 @@ namespace Cantera { tr.xml->XML_comment(logfile, "*** polynomial coefficients not printed (log_level < 3) ***"); } #endif - for (i = 0; i < nsp; i++) - { - for (j = i; j < nsp; j++) - { - // Chemkin fits only delta* = 0 - if (mode != CK_Mode) - dstar = tr.delta(i,j); - else - dstar = 0.0; + for (i = 0; i < nsp; i++) { + for (j = i; j < nsp; j++) { + // Chemkin fits only delta* = 0 + if (mode != CK_Mode) { + dstar = tr.delta(i,j); + } else { + dstar = 0.0; + } - // if a fit has already been generated for - // delta* = tr.delta(i,j), then use it. Otherwise, - // make a new fit, and add tr.delta(i,j) to the list - // of delta* values for which fits have been done. + // if a fit has already been generated for + // delta* = tr.delta(i,j), then use it. Otherwise, + // make a new fit, and add tr.delta(i,j) to the list + // of delta* values for which fits have been done. - // 'find' returns a pointer to end() if not found - if (dptr = find(tr.fitlist.begin(), tr.fitlist.end(), - dstar), dptr == tr.fitlist.end()) - { - vector_fp ca(degree+1), cb(degree+1), cc(degree+1); - vector_fp co22(degree+1); - m_integrals->fit(logfile, degree, dstar, - DATA_PTR(ca), DATA_PTR(cb), DATA_PTR(cc)); - m_integrals->fit_omega22(logfile, degree, dstar, - DATA_PTR(co22)); - tr.omega22_poly.push_back(co22); - tr.astar_poly.push_back(ca); - tr.bstar_poly.push_back(cb); - tr.cstar_poly.push_back(cc); - tr.poly[i][j] = static_cast(tr.astar_poly.size()) - 1; - tr.fitlist.push_back(dstar); - } + // 'find' returns a pointer to end() if not found + dptr = find(tr.fitlist.begin(), tr.fitlist.end(), dstar); + if (dptr == tr.fitlist.end()) { + vector_fp ca(degree+1), cb(degree+1), cc(degree+1); + vector_fp co22(degree+1); + m_integrals->fit(logfile, degree, dstar, + DATA_PTR(ca), DATA_PTR(cb), DATA_PTR(cc)); + m_integrals->fit_omega22(logfile, degree, dstar, + DATA_PTR(co22)); + tr.omega22_poly.push_back(co22); + tr.astar_poly.push_back(ca); + tr.bstar_poly.push_back(cb); + tr.cstar_poly.push_back(cc); + tr.poly[i][j] = static_cast(tr.astar_poly.size()) - 1; + tr.fitlist.push_back(dstar); + } - // delta* found in fitlist, so just point to this - // polynomial - else { - tr.poly[i][j] = static_cast((dptr - tr.fitlist.begin())); - } - tr.poly[j][i] = tr.poly[i][j]; - } - } + // delta* found in fitlist, so just point to this + // polynomial + else { + tr.poly[i][j] = static_cast((dptr - tr.fitlist.begin())); + } + tr.poly[j][i] = tr.poly[i][j]; + } + } #ifdef DEBUG_MODE if (m_verbose) { tr.xml->XML_close(logfile, "tstar_fits"); @@ -1462,71 +1460,69 @@ namespace Cantera { mxerr = 0.0, mxrelerr = 0.0; vector_fp diff(np + 1); doublereal eps, sigma; - for (k = 0; k < tr.nsp_; k++) - { - for (j = k; j < tr.nsp_; j++) { + for (k = 0; k < tr.nsp_; k++) { + for (j = k; j < tr.nsp_; j++) { - ipoly = tr.poly[k][j]; - for (n = 0; n < np; n++) { + ipoly = tr.poly[k][j]; + for (n = 0; n < np; n++) { - t = tr.tmin + dt*n; + t = tr.tmin + dt*n; - eps = tr.epsilon(j,k); - tstar = Boltzmann * t/eps; - sigma = tr.diam(j,k); - om11 = m_integrals->omega11(tstar, tr.delta(j,k)); + eps = tr.epsilon(j,k); + tstar = Boltzmann * t/eps; + sigma = tr.diam(j,k); + om11 = m_integrals->omega11(tstar, tr.delta(j,k)); - diffcoeff = ThreeSixteenths * - sqrt( 2.0 * Pi/tr.reducedMass(k,j) ) * - pow((Boltzmann * t), 1.5)/ - (Pi * sigma * sigma * om11); + diffcoeff = ThreeSixteenths * + sqrt( 2.0 * Pi/tr.reducedMass(k,j) ) * + pow((Boltzmann * t), 1.5)/ + (Pi * sigma * sigma * om11); - // 2nd order correction - // NOTE: THIS CORRECTION IS NOT APPLIED - doublereal fkj, fjk; - getBinDiffCorrection(t, tr, k, j, 1.0, 1.0, fkj, fjk); - //diffcoeff *= fkj; + // 2nd order correction + // NOTE: THIS CORRECTION IS NOT APPLIED + doublereal fkj, fjk; + getBinDiffCorrection(t, tr, k, j, 1.0, 1.0, fkj, fjk); + //diffcoeff *= fkj; - if (mode == CK_Mode) { - diff[n] = log(diffcoeff); - w[n] = -1.0; - } - else { - diff[n] = diffcoeff/pow(t, 1.5); - w[n] = 1.0/(diff[n]*diff[n]); - } + if (mode == CK_Mode) { + diff[n] = log(diffcoeff); + w[n] = -1.0; } - polyfit(np, DATA_PTR(tlog), DATA_PTR(diff), - DATA_PTR(w), degree, ndeg, 0.0, DATA_PTR(c)); - - doublereal pre; - for (n = 0; n < np; n++) { - if (mode == CK_Mode) { - val = exp(diff[n]); - fit = exp(poly3(tlog[n], DATA_PTR(c))); - } - else { - t = exp(tlog[n]); - pre = pow(t, 1.5); - val = pre * diff[n]; - fit = pre * poly4(tlog[n], DATA_PTR(c)); - } - err = fit - val; - relerr = err/val; - if (fabs(err) > mxerr) mxerr = fabs(err); - if (fabs(relerr) > mxrelerr) mxrelerr = fabs(relerr); + else { + diff[n] = diffcoeff/pow(t, 1.5); + w[n] = 1.0/(diff[n]*diff[n]); } - tr.diffcoeffs.push_back(c); -#ifdef DEBUG_MODE - if (tr.log_level >= 2 && m_verbose) { - tr.xml->XML_writeVector(logfile, " ", tr.thermo->speciesName(k) - + "__"+tr.thermo->speciesName(j), c.size(), DATA_PTR(c)); - } -#endif } + polyfit(np, DATA_PTR(tlog), DATA_PTR(diff), + DATA_PTR(w), degree, ndeg, 0.0, DATA_PTR(c)); + + doublereal pre; + for (n = 0; n < np; n++) { + if (mode == CK_Mode) { + val = exp(diff[n]); + fit = exp(poly3(tlog[n], DATA_PTR(c))); + } else { + t = exp(tlog[n]); + pre = pow(t, 1.5); + val = pre * diff[n]; + fit = pre * poly4(tlog[n], DATA_PTR(c)); + } + err = fit - val; + relerr = err/val; + if (fabs(err) > mxerr) mxerr = fabs(err); + if (fabs(relerr) > mxrelerr) mxrelerr = fabs(relerr); + } + tr.diffcoeffs.push_back(c); +#ifdef DEBUG_MODE + if (tr.log_level >= 2 && m_verbose) { + tr.xml->XML_writeVector(logfile, " ", tr.thermo->speciesName(k) + + "__"+tr.thermo->speciesName(j), c.size(), DATA_PTR(c)); + } +#endif } + } #ifdef DEBUG_MODE if (m_verbose) { sprintf(s,"Maximum binary diffusion coefficient absolute error:" diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index dd42f2c86..de03f32bd 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -86,12 +86,12 @@ namespace Cantera { public: + //! Constructor GasTransportParams() : TransportParams(), visccoeffs(0), condcoeffs(0), diffcoeffs(0), - polytempvec(0), poly(0), omega22_poly(0), astar_poly(0), @@ -112,32 +112,89 @@ namespace Cantera { { } + //! Destructor virtual ~GasTransportParams() {} // polynomial fits //! temperature-fit of the viscosity + /*! + * The outer loop the number of species, nsp + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ std::vector visccoeffs; - //temperature-fit heat conduction - std::vector condcoeffs; + //! temperature-fits of the heat conduction + /*! + * The outer loop the number of species, nsp + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector condcoeffs; - //temperature-fit diffusivity - std::vector diffcoeffs; - vector_fp polytempvec; + //! temperature-fits of the diffusivity + /*! + * The outer loop the number of species, nsp + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector diffcoeffs; + + //! This is vector of vectors containing the integer ookup value for the (i,j) interaction + /*! + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ std::vector > poly; - std::vector omega22_poly; - std::vector astar_poly; - std::vector bstar_poly; - std::vector cstar_poly; + + //! This is vector of vectors containing the astar fit. + /*! + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector omega22_poly; + + //! This is vector of vectors containing the astar fit. + /*! + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector astar_poly; + + //! This is vector of vectors containing the astar fit. + /*! + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector bstar_poly; + + //! This is vector of vectors containing the astar fit. + /*! + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. + */ + std::vector cstar_poly; //! Rotational relaxation number for the species in the current phase /*! * length is the number of species in the phase * units are dimensionless */ - vector_fp zrot; + vector_fp zrot; //! Dimensionless rotational heat capacity of the species in the current phase /*! @@ -145,31 +202,93 @@ namespace Cantera { * length is the number of species in the pahse * units are dimensionless (Cr / R) */ - vector_fp crot; + vector_fp crot; + //! Vector of booleans indicating whether a species is a polar molecule + /*! + * Length is nsp + */ std::vector polar; + + //! Polarizability of each species in the phase + /*! + * Length = nsp + * Units = m^3 + */ vector_fp alpha; - vector_fp fitlist; + + //! This is vector containing the values of delta(i,j) that are used in the collision integral fits. + /*! + * This is used in astar_poly, bstar_poly, cstar_poly, and omega22_poly. + * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. + * Unique values of delta get their own spot in the array. The values of delta are storred in + * the fitlist vector. + * + */ + vector_fp fitlist; //! Lennard-Jones well-depth of the species in the current phase /*! * length is the number of species in the phase - * Units are Joules (Note this is not Joules/kmol) + * Units are Joules (Note this is not Joules/kmol) (note, no kmol -> this is a per molecule amount) */ - vector_fp eps; + vector_fp eps; //! Lennard-Jones diameter of the species in the current phase /*! * length is the number of species in the phase * units are in meters. */ - vector_fp sigma; + vector_fp sigma; + //! This is the reduced mass of the interaction between species i and j + /*! + * tr.reducedMass(i,j) = tr.mw[i] * tr.mw[j] / (Avogadro * (tr.mw[i] + tr.mw[j])); + * + * Units are kg (note, no kmol -> this is a per molecule amount) + * + * Length nsp * nsp. This is a symmetric matrix + */ DenseMatrix reducedMass; - DenseMatrix diam; - DenseMatrix epsilon; - DenseMatrix dipole; - DenseMatrix delta; + + //! hard-sphere diameter for (i,j) collision + /*! + * diam(i,j) = 0.5*(tr.sigma[i] + tr.sigma[j]); + * Units are m (note, no kmol -> this is a per molecule amount) + * + * Length nsp * nsp. This is a symmetric matrix. + */ + DenseMatrix diam; + + //! The effective well depth for (i,j) collisions + /*! + * epsilon(i,j) = sqrt(tr.eps[i]*tr.eps[j]); + * Units are Joules (note, no kmol -> this is a per molecule amount) + * + * Length nsp * nsp. This is a symmetric matrix. + */ + DenseMatrix epsilon; + + //! The effective dipole moment for (i,j) collisions + /*! + * tr.dipoleMoment has units of Debye's. A Debye is 10-18 cm3/2 erg1/2 + * + * tr.dipole(i,i) = 1.e-25 * SqrtTen * trdat.dipoleMoment; + * tr.dipole(i,j) = sqrt(tr.dipole(i,i)*tr.dipole(j,j)); + * Units are in Debye (note, no kmol -> this is a per molecule amount) + * + * Length nsp * nsp. This is a symmetric matrix. + */ + DenseMatrix dipole; + + //! Matrix containing the reduced dipole moment of the interaction between two species + /*! + * This is the reduced dipole moment of the interaction between two species + * 0.5 * tr.dipole(i,j)*tr.dipole(i,j) (epsilon(i,j) * d * d * d); + * + * Length nsp * nsp .This is a symmetric matrix + */ + DenseMatrix delta; }; From b77a8d74070c7b8e95e2d7196b0f609951405578 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 26 Mar 2010 16:23:37 +0000 Subject: [PATCH 128/446] Added text --- tools/doc/doxyinput/thermo.txt | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/tools/doc/doxyinput/thermo.txt b/tools/doc/doxyinput/thermo.txt index cba0b3e18..8206d9729 100644 --- a/tools/doc/doxyinput/thermo.txt +++ b/tools/doc/doxyinput/thermo.txt @@ -2,12 +2,9 @@ \page thermopage Thermodynamic Properties -%Cantera can be used to compute thermodynamic properties of pure -substances, solutions, and mixtures of various types, including ones -containing multiple phases. The first step is to create an object that -represents each phase. +%Cantera can be used to compute thermodynamic properties of pure substances, solutions, and mixtures of various types, including ones containing multiple phases. The first step is to create an object that +represents each phase. A simple complete program that creates an object representing a gas mixture and prints its temperature is shown below. -A simple complete program that creates an object representing a gas mixture and prints its temperature is shown below. \include ex1.cpp Class \link Cantera::ThermoPhase ThermoPhase \endlink @@ -21,15 +18,26 @@ potentials into array \c mu, and so on. Class ThermoPhase can be used to represent the intensive state of any single-phase solution of multiple species. The phase may be a bulk, -three-dimensional phase (a gas, a liquid, or a solid), or may be a +three-dimensional phase (a gas, a liquid, or a solid), or it may be a two-dimensional surface phase, or even a one-dimensional "edge" phase. The specific attributes of each type of phase are specified by -deriving a class from ThemoPhase and providing implementations for the -virtual methods of ThermoPhase. +deriving a class from %ThemoPhase and providing implementations for the +virtual methods of %ThermoPhase. + +%Cantera has a wide variety of models for bulk phase currently. Special +attention (in terms of the speed of execution) has been paid to an ideal gas phase implementation, where the +species thermodynamic polynomial representations adhere to either the NASA +polynomial form or to the Shomate polynomoial form. This is widely used in +combustion applications, the origin application that %Cantera was +designed for. Recently, a lot of effort has been placed into constructing non-ideal +liquid phase thermodynamics models that are used in electrochemistry and +battery applications. These models include a Pitzer implementation for brines +solutions and a Margules excess Gibbs free energy implementation for molten +salts. \section The Intensive Thermodynamic State -Class ThermoPhase and classes derived from it work only with the +Class %ThermoPhase and classes derived from it work only with the intensive thermodynamic state. That is, all extensive properties (enthalpy, entropy, internal energy, volume, etc.) are computed for a unit quantity (on a mass or mole basis). For example, there is a From 5cfd0514d3781a500103645fb28a6c39cd240cdd Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Fri, 26 Mar 2010 16:45:27 +0000 Subject: [PATCH 129/446] Removed repetative functions from transport: now use only customary pass by pointers (not by references to Densematrix or vector_fp) --- Cantera/src/transport/LiquidTransport.cpp | 135 ++++-------------- Cantera/src/transport/LiquidTransport.h | 19 +-- Cantera/src/transport/LiquidTransportData.cpp | 2 - Cantera/src/transport/LiquidTransportData.h | 2 - .../src/transport/LiquidTransportParams.cpp | 54 ++----- Cantera/src/transport/LiquidTransportParams.h | 4 - Cantera/src/transport/TransportBase.h | 18 +-- Cantera/src/transport/TransportFactory.cpp | 57 ++++---- 8 files changed, 84 insertions(+), 207 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 930094e49..6868d0393 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -34,7 +34,7 @@ namespace Cantera { LiquidTransport::LiquidTransport(thermo_t* thermo, int ndim) : Transport(thermo, ndim), m_nsp(0), - m_nBinInt(0), + m_nsp2(0), m_tmin(-1.0), m_tmax(100000.), m_viscMixModel(0), @@ -82,7 +82,7 @@ namespace Cantera { LiquidTransport::LiquidTransport(const LiquidTransport &right) : Transport(right.m_thermo, right.m_nDim), m_nsp(0), - m_nBinInt(0), + m_nsp2(0), m_tmin(-1.0), m_tmax(100000.), m_viscMixModel(0), @@ -137,16 +137,14 @@ namespace Cantera { } Transport::operator=(right); m_nsp = right.m_nsp; - m_nBinInt = right.m_nBinInt; + m_nsp2 = right.m_nsp2; m_tmin = right.m_tmin; m_tmax = right.m_tmax; m_mw = right.m_mw; m_viscTempDep_Ns = right.m_viscTempDep_Ns; m_ionCondTempDep_Ns = right.m_ionCondTempDep_Ns; m_mobRatTempDep_Ns = right.m_mobRatTempDep_Ns; - m_mobRatTempDepIndex = right.m_mobRatTempDepIndex; m_selfDiffTempDep_Ns = right.m_selfDiffTempDep_Ns; - m_selfDiffTempDepIndex = right.m_selfDiffTempDepIndex; m_lambdaTempDep_Ns = right.m_lambdaTempDep_Ns; m_diffTempDep_Ns = right.m_diffTempDep_Ns; m_radiusTempDep_Ns = right.m_radiusTempDep_Ns; @@ -159,17 +157,13 @@ namespace Cantera { m_viscSpecies = right.m_viscSpecies; m_ionCondSpecies = right.m_ionCondSpecies; m_mobRatSpecies = right.m_mobRatSpecies; - m_mobRatSpeciesIndex = right.m_mobRatSpeciesIndex; m_selfDiffSpecies = right.m_selfDiffSpecies; - m_selfDiffSpeciesIndex = right.m_selfDiffSpeciesIndex; m_hydrodynamic_radius = right.m_hydrodynamic_radius; m_lambdaSpecies = right.m_lambdaSpecies; m_viscMixModel = right.m_viscMixModel; m_ionCondMixModel = right.m_ionCondMixModel; m_mobRatMixModel = right.m_mobRatMixModel; - m_mobRatMixModelIndex = right.m_mobRatMixModelIndex; m_selfDiffMixModel = right.m_selfDiffMixModel; - m_selfDiffMixModelIndex = right.m_selfDiffMixModelIndex; m_lambdaMixModel = right.m_lambdaMixModel; m_diffMixModel = right.m_diffMixModel; m_iStateMF = -1; @@ -191,7 +185,6 @@ namespace Cantera { m_viscmix = right.m_viscmix; m_ionCondmix = right.m_ionCondmix; m_mobRatMix = right.m_mobRatMix; - m_mobRatMixIndex = right.m_mobRatMixIndex; m_selfDiffMix = right.m_selfDiffMix; m_spwork = right.m_spwork; m_visc_mix_ok = false; @@ -237,7 +230,7 @@ namespace Cantera { delete m_selfDiffTempDep_Ns[l][k]; } } - for ( int l=0;l < m_nBinInt; l++ ){ + for ( int l=0;l < m_nsp2; l++ ){ if ( m_mobRatTempDep_Ns[l][k] ) delete m_mobRatTempDep_Ns[l][k]; } if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; @@ -248,7 +241,7 @@ namespace Cantera { if ( m_selfDiffMixModel[k] ) delete m_selfDiffMixModel[k]; } - for ( int k = 0; k < m_nBinInt; k++) { + for ( int k = 0; k < m_nsp2; k++) { if ( m_mobRatMixModel[k] ) delete m_mobRatMixModel[k]; } @@ -279,7 +272,7 @@ namespace Cantera { tr.thermo = 0; m_velocityBasis = tr.velocityBasis_; m_nsp = m_thermo->nSpecies(); - m_nBinInt = m_nsp*(m_nsp-1)/2; + m_nsp2 = m_nsp*m_nsp; m_tmin = m_thermo->minTemp(); m_tmax = m_thermo->maxTemp(); @@ -295,25 +288,18 @@ namespace Cantera { m_viscTempDep_Ns.resize(m_nsp, 0); m_ionCondSpecies.resize(m_nsp, 0.0); m_ionCondTempDep_Ns.resize(m_nsp, 0); - m_mobRatTempDepIndex.resize(m_nBinInt); - m_mobRatTempDep_Ns.resize(m_nBinInt); - m_mobRatMixModel.resize(m_nBinInt); - m_mobRatMixModelIndex.resize(m_nBinInt); - m_mobRatSpeciesIndex.resize(m_nBinInt); - m_mobRatSpecies.resize(m_nBinInt, m_nsp, 0.0); - m_mobRatMix.resize(m_nBinInt,0.0); - m_mobRatMixIndex.resize(m_nBinInt); - m_selfDiffTempDepIndex.resize(m_nsp); + m_mobRatTempDep_Ns.resize(m_nsp2); + m_mobRatMixModel.resize(m_nsp2); + m_mobRatSpecies.resize(m_nsp2, m_nsp, 0.0); + m_mobRatMix.resize(m_nsp2,0.0); m_selfDiffTempDep_Ns.resize(m_nsp); m_selfDiffMixModel.resize(m_nsp); - m_selfDiffMixModelIndex.resize(m_nsp); - m_selfDiffSpeciesIndex.resize(m_nsp); m_selfDiffSpecies.resize(m_nsp, m_nsp, 0.0); m_selfDiffMix.resize(m_nsp,0.0); for (k=0; k < m_nsp; k++){ m_selfDiffTempDep_Ns[k].resize(m_nsp, 0); } - for (k=0; k < m_nBinInt; k++){ + for (k=0; k < m_nsp2; k++){ m_mobRatTempDep_Ns[k].resize(m_nsp, 0); } m_lambdaSpecies.resize(m_nsp, 0.0); @@ -325,12 +311,10 @@ namespace Cantera { for (k = 0; k < m_nsp; k++) { m_selfDiffMixModel[k] = tr.selfDiffusion[k]; tr.selfDiffusion[k] = 0; - m_selfDiffMixModelIndex[k] = tr.selfDiffIndex[k]; } - for (k = 0; k < m_nBinInt; k++) { + for (k = 0; k < m_nsp2; k++) { m_mobRatMixModel[k] = tr.mobilityRatio[k]; tr.mobilityRatio[k] = 0; - m_mobRatMixModelIndex[k] = tr.mobRatIndex[k]; } //for each species, assign viscosity model and coefficients @@ -340,25 +324,13 @@ namespace Cantera { ltd.viscosity = 0; m_ionCondTempDep_Ns[k] = ltd.ionConductivity; ltd.ionConductivity = 0; - for (int j = 0; j < m_nBinInt; j++){ - for (int l=0; l < m_nBinInt; l++){ - if (m_mobRatMixModelIndex[j] == ltd.mobRatIndex[l]) { - m_mobRatTempDep_Ns[j][k] = ltd.mobilityRatio[l]; - ltd.mobilityRatio[l] = 0; - m_mobRatTempDepIndex[j] = ltd.mobRatIndex[l]; - break; - } - } + for (int j = 0; j < m_nsp2; j++){ + m_mobRatTempDep_Ns[j][k] = ltd.mobilityRatio[j]; + ltd.mobilityRatio[j] = 0; } - for (int j = 0; j < (int) m_selfDiffMixModelIndex.size(); j++) { - for (int l = 0; l < (int) m_selfDiffMixModelIndex.size(); l++) { - if (m_selfDiffMixModelIndex[j] == ltd.selfDiffIndex[l]) { - m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[l]; - ltd.selfDiffusion[l] = 0; - m_selfDiffTempDepIndex[j] = ltd.selfDiffIndex[l]; - break; - } - } + for (int j = 0; j < m_nsp; j++){ + m_selfDiffTempDep_Ns[j][k] = ltd.selfDiffusion[j]; + ltd.selfDiffusion[j] = 0; } m_lambdaTempDep_Ns[k] = ltd.thermalCond; ltd.thermalCond = 0; @@ -571,42 +543,22 @@ namespace Cantera { * These in turn employ subclasses of LTPspecies to * determine the individual species mobility ratios. */ - void LiquidTransport:: mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex) { + void LiquidTransport:: mobilityRatio(doublereal* mobRat) { update_T(); update_C(); ////// LiquidTranInteraction method if (!m_mobRat_mix_ok){ - for (int k = 0; k < m_nBinInt; k++){ - if ( m_mobRatMixModelIndex[k] != m_mobRatTempDepIndex[k] ) - throw CanteraError("LiquidTransport::mobilityRation","Mobility Ratio Indices Don't Match: Mixture vs. Species"); - m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); - m_mobRatMixIndex[k] = m_mobRatMixModelIndex[k]; + for (int k = 0; k < m_nsp2; k++){ + if(m_mobRatMixModel[k]){ + m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); + if ( m_mobRatMix[k] > 0 ) m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway + } } } - for (int k = 0; k < m_nBinInt; k++){ + for (int k = 0; k < m_nsp2; k++){ mobRat[k] = m_mobRatMix[k]; - mobRatIndex[k]= m_mobRatMixIndex[k]; - } - } - void LiquidTransport:: mobilityRatio(doublereal* mobRat, std::vector& mobRatIndex) { - - update_T(); - update_C(); - - ////// LiquidTranInteraction method - if (!m_mobRat_mix_ok){ - for (int k = 0; k < m_nBinInt; k++){ - if ( m_mobRatMixModelIndex[k] != m_mobRatTempDepIndex[k] ) - throw CanteraError("LiquidTransport::mobilityRatio","Mobility Ratio Indices Don't Match: Mixture vs. Species"); - m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); - m_mobRatMixIndex[k] = m_mobRatMixModelIndex[k]; - } - } - for (int k = 0; k < m_nBinInt; k++){ - mobRat[k] = m_mobRatMix[k]; - mobRatIndex[k]= m_mobRatMixIndex[k]; } } @@ -619,26 +571,15 @@ namespace Cantera { * @param mobRat array of length "number of species" * to hold returned mobility ratio. */ - void LiquidTransport::getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex) { + void LiquidTransport::getSpeciesMobilityRatio(doublereal** mobRat) { update_T(); if (!m_mobRat_temp_ok) { updateMobilityRatio_T(); } - mobRat = m_mobRatSpecies; - for (int k = 0; k < m_nBinInt; k++) { - mobRatIndex[k] = m_mobRatSpeciesIndex[k]; - } - } - void LiquidTransport::getSpeciesMobilityRatio(doublereal** mobRat, std::vector& mobRatIndex) { - update_T(); - if (!m_mobRat_temp_ok) { - updateMobilityRatio_T(); - } - for (int k=0; kgetMixTransProp(m_selfDiffTempDep_Ns[k]); } } @@ -694,16 +631,7 @@ namespace Cantera { * @param selfDiff array of size "number of species"^2 * to hold returned self diffusion. */ - void LiquidTransport::getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex) { - update_T(); - if (!m_selfDiff_temp_ok) { - updateSelfDiffusion_T(); - } - selfDiff = m_selfDiffSpecies; - for (int k = 0; k < m_nsp; k++) - selfDiffIndex[k] = m_selfDiffSpeciesIndex[k]; - } - void LiquidTransport::getSpeciesSelfDiffusion(doublereal** selfDiff, std::vector& selfDiffIndex) { + void LiquidTransport::getSpeciesSelfDiffusion(doublereal** selfDiff) { update_T(); if (!m_selfDiff_temp_ok) { updateSelfDiffusion_T(); @@ -711,7 +639,6 @@ namespace Cantera { for (int k=0; kgetSpeciesTransProp() ; } - m_mobRatSpeciesIndex[k] = m_mobRatTempDepIndex[k]; } m_mobRat_temp_ok = true; m_mobRat_mix_ok = false; @@ -1537,11 +1463,10 @@ namespace Cantera { int k; int j; - for (k = 0; k < m_nBinInt; k++) { + for (k = 0; k < m_nsp2; k++) { for (j = 0; j < m_nsp; j++) { m_selfDiffSpecies(k,j) = m_selfDiffTempDep_Ns[k][j]->getSpeciesTransProp() ; } - m_selfDiffSpeciesIndex[k] = m_selfDiffTempDepIndex[k]; } m_selfDiff_temp_ok = true; m_selfDiff_mix_ok = false; diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index e84cc3969..7fd7c4a86 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -205,8 +205,7 @@ namespace Cantera { * These in turn employ subclasses of LTPspecies to * determine the individual species mobility ratios. */ - virtual void mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex); - virtual void mobilityRatio(double* mobRat, std::vector& mobRatIndex); + virtual void mobilityRatio(double* mobRat); //! Returns the pure species mobility ratios for all species /*! @@ -217,8 +216,7 @@ namespace Cantera { * @param mobRat array of length "number of species" * to hold returned mobility ratios. */ - virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex); - virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex); + virtual void getSpeciesMobilityRatio(double** mobRat); //! Returns the self diffusion coefficients of the species in the phase /*! @@ -257,8 +255,7 @@ namespace Cantera { * @param selfDiff array of length "number of species" * to hold returned self diffusion coeffs. */ - virtual void getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex); - virtual void getSpeciesSelfDiffusion(double** selfDiff, std::vector& selfDiffIndex); + virtual void getSpeciesSelfDiffusion(double** selfDiff); //! Returns the hydrodynamic radius for all species /*! @@ -885,7 +882,7 @@ namespace Cantera { int m_nsp; - int m_nBinInt; + int m_nsp2; //! Minimum temperature applicable to the transport property eval doublereal m_tmin; @@ -944,7 +941,6 @@ namespace Cantera { */ typedef std::vector LTPvector; std::vector m_mobRatTempDep_Ns; - std::vector m_mobRatTempDepIndex; //! Mobility ratio of the mixture expressed as a subclass of //! LiquidTranInteraction @@ -954,7 +950,6 @@ namespace Cantera { * TransportFactory::getLiquidInteractionsTransportData(). */ std::vector m_mobRatMixModel; - std::vector m_mobRatMixModelIndex; //! Self Diffusion for each species expressed as an appropriate subclass //! of LTPspecies @@ -964,7 +959,6 @@ namespace Cantera { * TransportFactory::getLiquidSpeciesTransportData(). */ std::vector m_selfDiffTempDep_Ns; - std::vector m_selfDiffTempDepIndex; //! Self Diffusion of the mixture expressed as a subclass of //! LiquidTranInteraction @@ -974,7 +968,6 @@ namespace Cantera { * TransportFactory::getLiquidInteractionsTransportData(). */ std::vector m_selfDiffMixModel; - std::vector m_selfDiffMixModelIndex; //! Thermal conductivity for each species expressed as an //! appropriate subclass of LTPspecies @@ -1184,7 +1177,6 @@ namespace Cantera { * controlling update boolean -> m_mobRat_temp_ok */ DenseMatrix m_mobRatSpecies; - std::vector m_mobRatSpeciesIndex; //! Internal value of the species self diffusion coefficients /*! @@ -1196,7 +1188,6 @@ namespace Cantera { * controlling update boolean -> m_selfDiff_temp_ok */ DenseMatrix m_selfDiffSpecies; - std::vector m_selfDiffSpeciesIndex; //! Internal value of the species individual thermal conductivities /*! @@ -1332,8 +1323,6 @@ namespace Cantera { //! Saved values of the mixture mobility ratios vector_fp m_mobRatMix; - //! Saved species index of the mixture correlated to mobility ratios - std::vector m_mobRatMixIndex; //! Saved values of the mixture self diffusion coefficients vector_fp m_selfDiffMix; diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 8fb79a3a5..416072452 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -79,9 +79,7 @@ namespace Cantera { viscosity = right.viscosity; ionConductivity = right.ionConductivity; mobilityRatio = right.mobilityRatio; - mobRatIndex = right.mobRatIndex; selfDiffusion = right.selfDiffusion; - selfDiffIndex = right.selfDiffIndex; thermalCond = right.thermalCond; electCond = right.electCond; speciesDiffusivity = right.speciesDiffusivity; diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index 53ab654f1..78d7a80b8 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -205,11 +205,9 @@ namespace Cantera { //! Model type for the mobility ratio std::vector mobilityRatio; - std::vector mobRatIndex; //! Model type for the self diffusion coefficients std::vector selfDiffusion; - std::vector selfDiffIndex; //! Model type for the thermal conductivity LTPspecies* thermalCond; diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index d42eeca6a..48ee0ca72 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -612,7 +612,7 @@ namespace Cantera { void LTI_StefanMaxwell_PPN::setParameters( LiquidTransportParams& trParam ) { int nsp = m_thermo->nSpecies(); - int nBinInt = nsp*(nsp-1)/2; + int nsp2 = nsp*nsp; //vectornSpecies(); if (nsp != 3) throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); - int nBinInt = nsp*(nsp-1)/2; + int nsp2 = nsp*nsp; doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; m_thermo->getMoleFractions( molefracs ); @@ -726,42 +722,20 @@ namespace Cantera { MargulesVPSSTP * marg_thermo = dynamic_cast (ions_thermo->neutralMoleculePhase_); doublereal vol = m_thermo->molarVolume(); - typedef std::vector intVec; - std::vector mobRatIndexMap; - mobRatIndexMap.resize(nsp); - for ( k = 0; k < nsp; k++ ) - mobRatIndexMap[k].resize(nsp,0); - - for ( k = 0; k < nBinInt; k++ ) { - bool missingIndex = 1; + k = 0; + for ( j = 0; j < nsp; j++ ) { for ( i = 0; i < nsp; i++ ) { - for ( j = 0; j < i; j++ ) { - if ( (speciesNames[i] + ":" + speciesNames[j]) == m_mobRatIndex[k] ) { - mobRatIndexMap[i][j] = k; - m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); - if ( m_mobRatMix(i,j) > 0 ) m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); - missingIndex = 0; - break; - } - else if ( (speciesNames[j] + ":" + speciesNames[i]) == m_mobRatIndex[k] ) { - m_mobRatMix(j,i) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); - if ( m_mobRatMix(j,i) > 0 ) m_mobRatMix(i,j) = 1.0/m_mobRatMix(j,i); - missingIndex = 0; - break; - } + if (m_mobRatMixModel[k]) { + m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); + if ( m_mobRatMix(i,j) > 0 ) m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); } + k++; } - if ( missingIndex ) throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Incorrect names for mobility ratio of " + m_mobRatIndex[k] + " rather than i.e. " + speciesNames[0] + ":" + speciesNames[1]); - } + } for ( k = 0; k < nsp; k++ ){ - j = 0; - while (m_selfDiffIndex[k] != speciesNames[j]) { - j++; - if (j == nsp) throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Incorrect names for self diffusion of " + m_selfDiffIndex[k] + " rather than i.e. " + speciesNames[0]); - } - m_selfDiffMix[j] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); + m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); } /* diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index cf9570d97..860ee96b1 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -221,9 +221,7 @@ namespace Cantera { LiquidTranInteraction* viscosity; LiquidTranInteraction* ionConductivity; std::vector mobilityRatio; - std::vector mobRatIndex; std::vector selfDiffusion; - std::vector selfDiffIndex; LiquidTranInteraction* thermalCond; LiquidTranInteraction* speciesDiffusivity; LiquidTranInteraction* electCond; @@ -603,12 +601,10 @@ namespace Cantera { DenseMatrix m_mobRatMix; std::vector m_mobRatMixModel; std::vector m_mobRatSpecies; - std::vector m_mobRatIndex; std::vector m_selfDiffMixModel; vector_fp m_selfDiffMix; std::vector m_selfDiffSpecies; - std::vector m_selfDiffIndex; }; diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 9ec0b5d91..87d911c95 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -79,8 +79,7 @@ namespace Cantera { * - VB_MASSAVG Diffusion velocities are based on the mass averaged velocity * - VB_MOLEAVG Diffusion velocities are based on the mole averaged velocities * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 - * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 - * - VB_SPECIES_2 Diffusion velocities are based on the relative motion wrt species 2 + * - ... * - VB_SPECIES_3 Diffusion velocities are based on the relative motion wrt species 3 * * @ingroup tranprops @@ -162,7 +161,8 @@ namespace Cantera { * - VB_MASSAVG Diffusion velocities are based on the mass averaged velocity * - VB_MOLEAVG Diffusion velocities are based on the mole averaged velocities * - VB_SPECIES_0 Diffusion velocities are based on the relative motion wrt species 0 - * - VB_SPECIES_1 Diffusion velocities are based on the relative motion wrt species 1 + * - ... + * - VB_SPECIES_3 Diffusion velocities are based on the relative motion wrt species 3 * * All transport managers specify a default reference velocity in their default constructors. * All gas phase transport managers by default specify the mass-averaged velocity as their @@ -334,9 +334,7 @@ namespace Cantera { /** * The mobility ratio. */ - virtual void mobilityRatio(vector_fp& mobRat, std::vector& mobRatIndex) - { err("mobilityRatio"); } - virtual void mobilityRatio(double* mobRat, std::vector& mobRatIndex) + virtual void mobilityRatio(double* mobRat) { err("mobilityRatio"); } //! Returns the pure species limit of the mobility ratios @@ -345,9 +343,7 @@ namespace Cantera { * * @param mobRat Vector of mobility ratios */ - virtual void getSpeciesMobilityRatio(DenseMatrix& mobRat, std::vector& mobRatIndex) - { err("getSpeciesMobilityRatio"); } - virtual void getSpeciesMobilityRatio(double** mobRat, std::vector& mobRatIndex) + virtual void getSpeciesMobilityRatio(double** mobRat) { err("getSpeciesMobilityRatio"); } //! Returns the self diffusion coefficients of the species in the phase @@ -389,9 +385,7 @@ namespace Cantera { * @param selfDiff array of length "number of species" * to hold returned self diffusion coeffs. */ - virtual void getSpeciesSelfDiffusion(DenseMatrix& selfDiff, std::vector& selfDiffIndex) - { err("getSpeciesSelfDiffusion"); } - virtual void getSpeciesSelfDiffusion(double** selfDiff, std::vector& selfDiffIndex) + virtual void getSpeciesSelfDiffusion(double** selfDiff) { err("getSpeciesSelfDiffusion"); } //! Returns the mixture thermal conductivity in W/m/K. diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 5bfa039c3..6e61559a6 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -42,6 +42,7 @@ #include "ctml.h" #include +#include //using namespace std; @@ -982,10 +983,9 @@ namespace Cantera { // and then insertion into LiquidTransportData objects below. LiquidTransportData data; data.speciesName = name; - data.mobRatIndex.resize(nBinInt,""); - data.mobilityRatio.resize(nBinInt,0); - data.selfDiffIndex.resize(nsp,""); + data.mobilityRatio.resize(nsp*nsp,0); data.selfDiffusion.resize(nsp,0); + ThermoPhase *temp_thermo = trParam.thermo; int num = trNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { @@ -994,18 +994,21 @@ namespace Cantera { switch (m_tranPropMap[nodeName]) { case TP_VISCOSITY: - data.viscosity = newLTP(xmlChild, name, m_tranPropMap[nodeName], trParam.thermo ); + data.viscosity = newLTP(xmlChild, name, m_tranPropMap[nodeName], temp_thermo ); break; case TP_IONCONDUCTIVITY: - data.ionConductivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], trParam.thermo); + data.ionConductivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], temp_thermo); break; case TP_MOBILITYRATIO: { for (int iSpec = 0; iSpec< nBinInt; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); - data.mobRatIndex[iSpec] = specName; - data.mobilityRatio[iSpec] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], trParam.thermo); + size_t loc = specName.find(":"); + std::string firstSpec = specName.substr(0,loc); + std::string secondSpec = specName.substr(loc+1); + int index = temp_thermo->speciesIndex(firstSpec.c_str())+nsp*temp_thermo->speciesIndex(secondSpec.c_str()); + data.mobilityRatio[index] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], temp_thermo); }; }; break; @@ -1014,8 +1017,8 @@ namespace Cantera { for (int iSpec = 0; iSpec< nsp; iSpec++){ XML_Node &propSpecNode = xmlChild.child(iSpec); std::string specName = propSpecNode.name(); - data.selfDiffIndex[iSpec] = specName; - data.selfDiffusion[iSpec] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], trParam.thermo); + int index = temp_thermo->speciesIndex(specName.c_str()); + data.selfDiffusion[index] = newLTP(propSpecNode, name, m_tranPropMap[nodeName], temp_thermo); }; }; break; @@ -1023,25 +1026,25 @@ namespace Cantera { data.thermalCond = newLTP(xmlChild, name, m_tranPropMap[nodeName], - trParam.thermo ); + temp_thermo ); break; case TP_DIFFUSIVITY: data.speciesDiffusivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], - trParam.thermo ); + temp_thermo ); break; case TP_HYDRORADIUS: data.hydroRadius = newLTP(xmlChild, name, m_tranPropMap[nodeName], - trParam.thermo ); + temp_thermo ); break; case TP_ELECTCOND: data.electCond = newLTP(xmlChild, name, m_tranPropMap[nodeName], - trParam.thermo ); + temp_thermo ); break; default: @@ -1103,10 +1106,9 @@ namespace Cantera { XML_Node &tranTypeNode = transportNode.child(iChild); std::string nodeName = tranTypeNode.name(); - trParam.mobRatIndex.resize(nBinInt,""); - trParam.mobilityRatio.resize(nBinInt,0); - trParam.selfDiffIndex.resize(nsp,""); + trParam.mobilityRatio.resize(nsp*nsp,0); trParam.selfDiffusion.resize(nsp,0); + ThermoPhase *temp_thermo = trParam.thermo; if (tranTypeNode.hasChild("compositionDependence")) { //compDepNode contains the interaction model @@ -1123,25 +1125,26 @@ namespace Cantera { break; case TP_MOBILITYRATIO: { - int iSpec; - for (iSpec = 0; iSpec< nBinInt; iSpec++){ + for (int iSpec = 0; iSpec< nBinInt; iSpec++){ XML_Node &propSpecNode = compDepNode.child(iSpec); - std::string specName = propSpecNode.name(); - trParam.mobRatIndex[iSpec] = specName; - trParam.mobilityRatio[iSpec] = newLTI( propSpecNode, - m_tranPropMap[nodeName], + string specName = propSpecNode.name(); + size_t loc = specName.find(":"); + string firstSpec = specName.substr(0,loc); + string secondSpec = specName.substr(loc+1); + int index = temp_thermo->speciesIndex(firstSpec.c_str())+nsp*temp_thermo->speciesIndex(secondSpec.c_str()); + trParam.mobilityRatio[index] = newLTI( propSpecNode, + m_tranPropMap[nodeName], trParam ); }; }; break; case TP_SELFDIFFUSION: { - int iSpec; - for (iSpec = 0; iSpec< nsp; iSpec++){ + for (int iSpec = 0; iSpec< nsp; iSpec++){ XML_Node &propSpecNode = compDepNode.child(iSpec); - std::string specName = propSpecNode.name(); - trParam.selfDiffIndex[iSpec] = specName; - trParam.selfDiffusion[iSpec] = newLTI( propSpecNode, + string specName = propSpecNode.name(); + int index = temp_thermo->speciesIndex(specName.c_str()); + trParam.selfDiffusion[index] = newLTI( propSpecNode, m_tranPropMap[nodeName], trParam ); }; From a6042af1e78b5cfdc1084e95f23f92118a0b7f7c Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Tue, 30 Mar 2010 18:30:39 +0000 Subject: [PATCH 130/446] Fixed error in IonsFromNeutral to allow for any order of the salts and ions updated doxygen to explain relationship between LiquidTransport, LiquidTransportData, and LiquidTransportParams --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 18 +- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 12 +- Cantera/src/transport/LiquidTransport.cpp | 77 ++---- Cantera/src/transport/LiquidTransport.h | 119 ++++----- Cantera/src/transport/LiquidTransportData.cpp | 60 ++--- Cantera/src/transport/LiquidTransportData.h | 62 ++++- .../src/transport/LiquidTransportParams.cpp | 58 +---- Cantera/src/transport/LiquidTransportParams.h | 105 +++++++- Cantera/src/transport/TransportBase.cpp | 11 +- Cantera/src/transport/TransportFactory.cpp | 228 +++++++++--------- Cantera/src/transport/TransportFactory.h | 96 ++++++-- 11 files changed, 498 insertions(+), 348 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index aeabd53ee..601a937e8 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -334,9 +334,10 @@ namespace Cantera { getActivities(c); } - void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs,vector_fp& charges){ + void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs,vector_fp& charges, std::vector& neutMolIndex){ coeffs = fm_neutralMolec_ions_; charges = m_speciesCharge; + neutMolIndex = fm_invert_ionForNeutral; //for ( int k = 0; k < fm_neutralMolec_ions_[k]; k++ ) // coeffs.push_back(fm_neutralMolec_ions_[k]); } @@ -1297,9 +1298,12 @@ namespace Cantera { std::vector elemVectorI(nElementsI); vector fm_tmp(m_kk); - for (int jNeut = 0; jNeut < numNeutralMoleculeSpecies_; jNeut++) { - fm_invert_ionForNeutral[jNeut] = -1; + for (int k = 0; k < m_kk; k++) { + fm_invert_ionForNeutral[k] = -1; } + /* for (int jNeut = 0; jNeut < numNeutralMoleculeSpecies_; jNeut++) { + fm_invert_ionForNeutral[jNeut] = -1; + }*/ for (int jNeut = 0; jNeut < numNeutralMoleculeSpecies_; jNeut++) { for (int m = 0; m < nElementsN; m++) { elemVectorN[m] = neutralMoleculePhase_->nAtoms(jNeut, m); @@ -1346,12 +1350,16 @@ namespace Cantera { } bool notTaken = true; for (int iNeut = 0; iNeut < jNeut; iNeut++) { - if (fm_invert_ionForNeutral[iNeut] == k) { + if (fm_invert_ionForNeutral[k] == iNeut) { notTaken = false; } } if (notTaken) { - fm_invert_ionForNeutral[jNeut] = k; + fm_invert_ionForNeutral[k] = jNeut; + } + else{ + throw CanteraError("IonsFromNeutralVPSSTP::initThermoXML", + "Simple formula matrix generation failed, one cation is shared between two salts"); } } fm_neutralMolec_ions_[k + jNeut * m_kk] += fac; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 712ae622a..ffaed580d 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -461,8 +461,9 @@ namespace Cantera { */ virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; - - virtual void getDissociationCoeffs(vector_fp& coeffs, vector_fp& charges); + //! Get the Salt Dissociation Coefficients + //! Returns the vector of dissociation coefficients and vector of charges + virtual void getDissociationCoeffs(vector_fp& coeffs, vector_fp& charges, std::vector& neutMolIndex); virtual void getNeutralMolecMoleFractions(vector_fp& fracs){fracs=NeutralMolecMoleFractions_;} @@ -804,7 +805,7 @@ namespace Cantera { //! Formula Matrix for composition of neutral molecules //! in terms of the molecules in this ThermoPhase /*! - * fm_neutralMolec_ions[ i + jNeut * NumNeut ] + * fm_neutralMolec_ions[ i + jNeut * m_kk ] * * This is the number of ions of type i in the neutral * molecule jNeut. @@ -813,6 +814,11 @@ namespace Cantera { //! Mapping between ion species and neutral molecule for quick invert. /*! + * + * fm_invert_ionForNeutral returns vector of int. Each element represents + * an ionic species and stores the value of the corresponding neutral + * molecule + * * For the case of fm_invert_simple_ = true, we assume that there * is a quick way to invert the formula matrix so that we can * quickly calculate the neutral molecule mole fraction diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 6868d0393..929a23a39 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -686,8 +686,8 @@ namespace Cantera { /****************** thermal diffusion coefficients ************/ - //! Return the thermal diffusion coefficients - /*! + // Return the thermal diffusion coefficients + /* * These are all zero for this simple implementaion * * @param dt thermal diffusion coefficients @@ -813,8 +813,8 @@ namespace Cantera { } } //============================================================== - //! Specify the value of the gradient of the temperature - /*! + // Specify the value of the gradient of the temperature + /* * @param grad_T Gradient of the temperature (length num dimensions); */ void LiquidTransport::set_Grad_T(const doublereal* const grad_T) { @@ -823,8 +823,8 @@ namespace Cantera { } } //============================================================== - //! Specify the value of the gradient of the voltage - /*! + // Specify the value of the gradient of the voltage + /* * * @param grad_V Gradient of the voltage (length num dimensions); */ @@ -834,8 +834,8 @@ namespace Cantera { } } //============================================================== - //! Specify the value of the gradient of the MoleFractions - /*! + // Specify the value of the gradient of the MoleFractions + /* * * @param grad_X Gradient of the mole fractions(length nsp * num dimensions); */ @@ -981,7 +981,7 @@ namespace Cantera { getSpeciesVdiffExt(ldf, Vdiff); } - /** + /* * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). * @param ldx Leading dimension of the grad_X array. @@ -1361,8 +1361,8 @@ namespace Cantera { } - //! Update the binary Stefan-Maxwell diffusion coefficients - //! wrt T using calls to the appropriate LTPspecies subclass + // Update the binary Stefan-Maxwell diffusion coefficients + // wrt T using calls to the appropriate LTPspecies subclass void LiquidTransport::updateDiff_T() { m_diffMixModel->getMatrixTransProp( m_bdiff ); @@ -1371,13 +1371,13 @@ namespace Cantera { } - //! Update the pure-species viscosities functional dependence on concentration. + // Update the pure-species viscosities functional dependence on concentration. void LiquidTransport::updateViscosities_C() { m_visc_conc_ok = true; } - /** + /* * Updates the array of pure species viscosities internally * using calls to the appropriate LTPspecies subclass. * The flag m_visc_ok is set to true. @@ -1401,13 +1401,13 @@ namespace Cantera { } - //! Update the pure-species ionic conductivities functional dependence on concentration. + // Update the pure-species ionic conductivities functional dependence on concentration. void LiquidTransport::updateIonConductivity_C() { m_ionCond_conc_ok = true; } - /** + /* * Updates the array of pure species ionic conductivities internally * using calls to the appropriate LTPspecies subclass. * The flag m_ionCond_ok is set to true. @@ -1423,13 +1423,12 @@ namespace Cantera { } - //! Update the pure-species mobility ratios functional dependence on concentration. + // Update the pure-species mobility ratios functional dependence on concentration. void LiquidTransport::updateMobilityRatio_C() { m_mobRat_conc_ok = true; } - - /** + /* * Updates the array of pure species mobility ratios internally * using calls to the appropriate LTPspecies subclass. * The flag m_mobRat_ok is set to true. @@ -1448,13 +1447,13 @@ namespace Cantera { } - //! Update the pure-species self diffusion functional dependence on concentration. + // Update the pure-species self diffusion functional dependence on concentration. void LiquidTransport::updateSelfDiffusion_C() { m_selfDiff_conc_ok = true; } - /** + /* * Updates the array of pure species self diffusion internally * using calls to the appropriate LTPspecies subclass. * The flag m_selfDiff_ok is set to true. @@ -1472,15 +1471,14 @@ namespace Cantera { m_selfDiff_mix_ok = false; } - //! Update the pure-species viscosities functional dependence on concentration. void LiquidTransport::updateHydrodynamicRadius_C() { m_radi_conc_ok = true; } - //! Update the temperature-dependent hydrodynamic radius terms - //! for each species internally using calls to the - //! appropriate LTPspecies subclass + // Update the temperature-dependent hydrodynamic radius terms + // for each species internally using calls to the + // appropriate LTPspecies subclass void LiquidTransport::updateHydrodynamicRadius_T() { int k; @@ -1491,35 +1489,6 @@ namespace Cantera { m_radi_mix_ok = false; } - //! Updates the internal value of the gradient of the - //! logarithm of the activity coefficients, which is - //! used in the gradient of the chemical potential. - /** - * Evaluate the gradients of the activity coefficients - * as they alter the diffusion coefficient. - * - * The gradient of the chemical potential can be written in terms of - * gradient of the logarithm of the mole fraction times a correction - * associated with the gradient of the activity coefficient relative to - * that of the mole fraction. Specifically, the gradients of the - * logarithms of each are involved according to the formula - - * \f[ - * \nabla \mu_k = RT \nabla ( \ln X_k ) - * \left[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \right] - * \f] - * - * The required quantity is the derivitive of the logarithm of the - * activity coefficient with respect to the derivative of the - * logarithm of the mole fraction (or whatever concentration - * variable we are using to express chemical potential. - * - * Updates the vector over species i: - * \[ - * \partial \left[ \ln ( \gamma_i ) \right] - * / \partial \left[ \ln ( \X_i ) \right] - * \] - */ void LiquidTransport::update_Grad_lnAC() { int k; @@ -1553,7 +1522,7 @@ namespace Cantera { * Solve for the diffusional velocities in the Stefan-Maxwell equations * */ - //! Solve the stefan_maxell equations for the diffusive fluxes. + // Solve the stefan_maxell equations for the diffusive fluxes. /* * The diffusive mass flux of species \e k is computed * using the Stefan-Maxwell equation diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 7fd7c4a86..c2253d2a9 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -50,30 +50,36 @@ namespace Cantera { * The class LiquidTransport has several roles. * -# It brings together the individual species transport * properties, expressed as subclasses of LTPspecies - * (Liquid Transport Properties of Species), with - * models for the composition dependence of liquid - * transport properties expressed as subclasses of - * LiquidTranInteraction. - * + * (Liquid Transport Properties of Species) through + * LiquidTransportData, with models for + * the composition dependence of liquid transport properties + * expressed as subclasses of LiquidTranInteraction + * (mixing rules) through LiquidTransportParams. Calculating + * mixture properties generally consists of calling the + * getMixTansProp member of LiquidTranInteraction by passing + * a vector of LTPSpecies * -# It calculates the bulk velocity \f$ \vec{v} \f$ and * individual species diffusion velocities, \f$ \vec{V_i} \f$ - * using the Stefan-Maxwell equations. It is - * possible to set a flag to calculate relative to a - * mass-averaged bulk velocity, relative to a mole-averaged - * bulk velocity or relative to a single species velocity - * using the keyword. - * Mass-averaged velocities are the default for which the - * diffusion velocities satisfy + * using the Stefan-Maxwell equations. It is possible to set a + * flag to calculate relative to a mass-averaged bulk velocity, + * relative to a mole-averaged bulk velocity or relative to a + * single species velocity using the , + * , or + * keyword. Mass-averaged velocities are the default for which + * the diffusion velocities satisfy * \f[ * \sum_{i} Y_i \vec{V_i} = 0 * \f] * for mass fraction \f$ Y_i \f$. For mole-averaged velocities * \f[ - * \sum_{i} X_i \vec{V_i} = 0 + * \sum_{i} X_i \vec{V_i} = 0 * \f] - * for mole fraction \f$ X_i \f$. - * - * -# It provides acccess to a number of derived quantities + * for mole fraction \f$ X_i \f$. or + * \f[ + * \vec{V_i} = 0 + * \f] + * for reference species \f$ i \f$. + * -# It provides access to a number of derived quantities * related to transport properties as described in the * various methods below. * @@ -198,16 +204,21 @@ namespace Cantera { */ virtual void getSpeciesIonConductivity(doublereal* const ionCond); - //! Returns the mobility ratio of the solution + //! Returns the pointer to the mobility ratios of the binary + //! combinations of the transported species for the solution + //! Has size of the number of binary interactions = nsp*nsp /*! * The mobility ratio calculation is handled by subclasses of * LiquidTranInteraction as specified in the input file. * These in turn employ subclasses of LTPspecies to - * determine the individual species mobility ratios. + * determine the mobility ratios in the pure species. */ virtual void mobilityRatio(double* mobRat); - //! Returns the pure species mobility ratios for all species + //! Returns a double pointer to the mobility ratios of the + //! transported species in each pure species phase. + //! Has size of the number of binary interactions by the number + //! of species (nsp*nsp X nsp) /*! * The pure species mobility ratios are evaluated using the * appropriate subclasses of LTPspecies as specified in the @@ -218,7 +229,8 @@ namespace Cantera { */ virtual void getSpeciesMobilityRatio(double** mobRat); - //! Returns the self diffusion coefficients of the species in the phase + //! Returns the self diffusion coefficients of the species in the phase. + //! Has size of nsp(coeffs) /*! * The self diffusion coefficient is the diffusion coefficient of a tracer species * at the current temperature and composition of the species. Therefore, @@ -246,7 +258,8 @@ namespace Cantera { */ virtual void selfDiffusion(doublereal * const selfDiff); - //! Returns the pure species self diffusion in solution of each species + //! Returns the self diffusion coefficients in the pure species phases. + //! Has size of nsp(coeffs) x nsp(phases) /*! * The pure species molar volumes are evaluated using the * appropriate subclasses of LTPspecies as specified in the @@ -713,10 +726,10 @@ namespace Cantera { //! Updates the internal value of the gradient of the - //! logarithm of the activity coefficients, which is + //! logarithm of the activity, which is //! used in the gradient of the chemical potential. /** - * Evaluate the gradients of the activity coefficients + * Evaluate the gradients of the activity * as they alter the diffusion coefficient. * * The gradient of the chemical potential can be written in terms of @@ -724,22 +737,17 @@ namespace Cantera { * associated with the gradient of the activity coefficient relative to * that of the mole fraction. Specifically, the gradients of the * logarithms of each are involved according to the formula - + * * \f[ - * \nabla \mu_k = RT \nabla ( \ln X_k ) - * \left[ 1 + \nabla ( \ln \gamma_k ) / \nabla ( \ln X_k ) \right] + * \nabla \mu_k = RT \left[ \nabla ( \ln X_k ) + + * \nabla ( \ln \gamma_k ) \right] = RT \left[ + * \nabla ( \ln a_k ) \right] * \f] * - * The required quantity is the derivitive of the logarithm of the - * activity coefficient with respect to the derivative of the - * logarithm of the mole fraction (or whatever concentration - * variable we are using to express chemical potential. - * - * Updates the vector over species i: - * \[ - * \partial \left[ \ln ( \gamma_i ) \right] - * / \partial \left[ \ln ( \X_i ) \right] - * \] + * The gradient in the activity coefficient requires the use of thermophase + * getdlnActCoeff that calculates its change based on a chane in the state + * (i.e. temperature and composition of each species) which was first + * implemented in MargulesVPSSTP.cpp (LiquidTransport.h doxygen) */ virtual void update_Grad_lnAC(); @@ -768,7 +776,11 @@ namespace Cantera { * or mass-weighted basis, or the diffusion velocities may * be specified as relative to a specific species (i.e. a * solvent) all according to the \verbatim - * \endverbatim input parameter. + * \endverbatim input para + * The gradient in the activity coefficient requires the use of thermophase + * getdlnActCoeff that calculates its change based on a change in the state + * i.e. temperature and composition of each species. + * First implemented in MargulesVPSSTP.cppmeter. * * One of the Stefan Maxwell equations is replaced by the appropriate * definition of the mass-averaged velocity, the mole-averaged velocity @@ -932,18 +944,18 @@ namespace Cantera { */ LiquidTranInteraction *m_ionCondMixModel; - //! Mobility ratio for each species expressed as an appropriate subclass - //! of LTPspecies + typedef std::vector LTPvector; + //! Mobility ratio for the binary cominations of each species in each + //! pure phase expressed as an appropriate subclass of LTPspecies /*! * These subclasses of LTPspecies evaluate the species-specific * transport properties according to the parameters parsed in * TransportFactory::getLiquidSpeciesTransportData(). */ - typedef std::vector LTPvector; std::vector m_mobRatTempDep_Ns; - //! Mobility ratio of the mixture expressed as a subclass of - //! LiquidTranInteraction + //! Mobility ratio for each binary combination of mobile species in the mixture + //! expressed as a subclass of LiquidTranInteraction /*! * These subclasses of LiquidTranInteraction evaluate the * mixture transport properties according to the parameters parsed in @@ -951,8 +963,8 @@ namespace Cantera { */ std::vector m_mobRatMixModel; - //! Self Diffusion for each species expressed as an appropriate subclass - //! of LTPspecies + //! Self Diffusion for each species in each pure species phase + //! expressed as an appropriate subclass of LTPspecies /*! * These subclasses of LTPspecies evaluate the species-specific * transport properties according to the parameters parsed in @@ -960,7 +972,7 @@ namespace Cantera { */ std::vector m_selfDiffTempDep_Ns; - //! Self Diffusion of the mixture expressed as a subclass of + //! Self Diffusion for each species in the mixture expressed as a subclass of //! LiquidTranInteraction /*! * These subclasses of LiquidTranInteraction evaluate the @@ -1058,19 +1070,16 @@ namespace Cantera { */ vector_fp m_Grad_X; - //! Gradient of the logarithm of the activity coefficients + //! Gradient of the logarithm of the activity /*! * This quantity appears in the gradient of the chemical potential. - * It multiplies the gradient of the mole fraction, and in this way + * It replaces the gradient of the mole fraction, and in this way * serves to "modify" the diffusion coefficient. * - * m_Grad_lnAC[k] = \nabla \ln ( \gamma_i ) + \nabla \ln ( \X_i ) - * - * Note that where "mole fraction" is used here, whatever - * concentration-related variable applies, so that if - * molality is the concentration variable, the gradient of the - * activity coefficient should be with respect to the molality. - * m_nsp is the number of species in the fluid + * \f[ + * m\_Grad\_lnAC[k] = \nabla ( \ln X_k ) + + * \nabla ( \ln \gamma_k ) + * \f] * * k is the species index * n is the dimensional index (x, y, or z). It has a length @@ -1124,7 +1133,7 @@ namespace Cantera { * n is the dimensional index (x, y, or z) * * \f[ - * m_Grad_mu[n*m_nsp + k] + * m\_Grad\_mu[n*m_nsp + k] * \f] */ vector_fp m_Grad_mu; diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 416072452..1b0625f7b 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -90,13 +90,13 @@ namespace Cantera { - //! Copy constructor + // Copy constructor LTPspecies::LTPspecies( const LTPspecies &right ) { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LTPspecies& LTPspecies::operator=(const LTPspecies& right ) { if (&right != this) { @@ -111,9 +111,9 @@ namespace Cantera { } - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a constant value. - /** The transport property is constructed from the XML node, + // Construct an LTPspecies object for a liquid tranport property + // expressed as a constant value. + /* The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) @@ -131,14 +131,14 @@ namespace Cantera { } else throw LTPError("negative or zero " + propNode.name() ); } - //! Copy constructor + // Copy constructor LTPspecies_Const::LTPspecies_Const( const LTPspecies_Const &right ) : LTPspecies() { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right ) { if (&right != this) { @@ -153,16 +153,16 @@ namespace Cantera { return *this; } - //! Return the (constant) value for this transport property + // Return the (constant) value for this transport property doublereal LTPspecies_Const::getSpeciesTransProp( ) { return m_coeffs[0]; } /////////////////////////////////////////////////////////////// - //! Construct an LTPspecies object for a liquid tranport property - //! expressed in extended Arrhenius form. - /** The transport property is constructed from the XML node, + // Construct an LTPspecies object for a liquid tranport property + // expressed in extended Arrhenius form. + /* The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) @@ -188,14 +188,14 @@ namespace Cantera { m_coeffs.push_back( log( A_k ) ); } - //! Copy constructor + // Copy constructor LTPspecies_Arrhenius::LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ) : LTPspecies() { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right ) { if (&right != this) { @@ -215,9 +215,9 @@ namespace Cantera { return *this; } - //! Return the pure species value for this transport property evaluated - //! from the Arrhenius expression - /** + // Return the pure species value for this transport property evaluated + // from the Arrhenius expression + /* * In general the Arrhenius expression is * * \f[ @@ -265,9 +265,9 @@ namespace Cantera { /////////////////////////////////////////////////////////////// - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a polynomial in temperature. - /** The transport property is constructed from the XML node, + // Construct an LTPspecies object for a liquid tranport property + // expressed as a polynomial in temperature. + /* The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) @@ -290,14 +290,14 @@ namespace Cantera { }*/ } - //! Copy constructor + // Copy constructor LTPspecies_Poly::LTPspecies_Poly( const LTPspecies_Poly &right ) : LTPspecies() { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right ) { if (&right != this) { @@ -315,8 +315,8 @@ namespace Cantera { return *this; } - //! Return the value for this transport property evaluated - //! from the polynomial expression + // Return the value for this transport property evaluated + // from the polynomial expression doublereal LTPspecies_Poly::getSpeciesTransProp( ) { doublereal t = m_thermo->temperature(); @@ -338,9 +338,9 @@ namespace Cantera { /////////////////////////////////////////////////////////////// - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as an exponential in temperature. - /** The transport property is constructed from the XML node, + // Construct an LTPspecies object for a liquid tranport property + // expressed as an exponential in temperature. + /* The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) @@ -363,14 +363,14 @@ namespace Cantera { }*/ } - //! Copy constructor + // Copy constructor LTPspecies_ExpT::LTPspecies_ExpT( const LTPspecies_ExpT &right ) : LTPspecies() { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LTPspecies_ExpT& LTPspecies_ExpT::operator=(const LTPspecies_ExpT& right ) { if (&right != this) { @@ -388,8 +388,8 @@ namespace Cantera { return *this; } - //! Return the value for this transport property evaluated - //! from the exponential in temperature expression + // Return the value for this transport property evaluated + // from the exponential in temperature expression doublereal LTPspecies_ExpT::getSpeciesTransProp( ) { doublereal t = m_thermo->temperature(); diff --git a/Cantera/src/transport/LiquidTransportData.h b/Cantera/src/transport/LiquidTransportData.h index 78d7a80b8..276d32409 100644 --- a/Cantera/src/transport/LiquidTransportData.h +++ b/Cantera/src/transport/LiquidTransportData.h @@ -223,8 +223,8 @@ namespace Cantera { //! Class LTPspecies_Const holds transport parameters for a - //! specific liquid-phase species when the transport property - //! is just a constant value. + //! specific liquid-phase species (LTPspecies) when the + //! transport property is just a constant value. /*! * As an example of the input required for LTPspecies_Const * consider the following XML fragment @@ -245,6 +245,13 @@ namespace Cantera { public: + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as a constant value. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ LTPspecies_Const( const XML_Node &propNode, std::string name, TransportPropertyList tp_ind, @@ -279,9 +286,15 @@ namespace Cantera { //! Class LTPspecies_Arrhenius holds transport parameters for a - //! specific liquid-phase species when the transport property - //! is expressed in Arrhenius form. + //! specific liquid-phase species (LTPspecies) when the + //! transport property is expressed in Arrhenius form. /*! + * Used for pure species properties with equations of the form + * \f[ + * x = A T^b \exp( - E / RT ) + * \f] + * where A, b, and E are passed in the xml input file. + * * As an example of the input required for LTPspecies_Arrhenius * consider the following XML fragment * @@ -304,6 +317,13 @@ namespace Cantera { public: + //! Construct an LTPspecies object for a liquid tranport property + //! expressed in extended Arrhenius form. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ LTPspecies_Arrhenius( const XML_Node &propNode, std::string name, TransportPropertyList tp_ind, @@ -366,9 +386,15 @@ namespace Cantera { //! Class LTPspecies_Poly holds transport parameters for a - //! specific liquid-phase species when the transport property - //! is expressed as a polynomial in temperature. + //! specific liquid-phase species (LTPspecies) when the transport + //! property is expressed as a polynomial in temperature. /*! + * Used for pure species properties with equations of the form + * \f[ + * x = f[0] + f[1] T + ... + f[N] T^N + * \f] + * where f[i] are elements of the float array passed in. + * * As an example of the input required for LTPspecies_Poly * consider the following XML fragment * @@ -388,6 +414,13 @@ namespace Cantera { public: + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as a polynomial in temperature. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ LTPspecies_Poly( const XML_Node &propNode, std::string name, TransportPropertyList tp_ind, @@ -428,9 +461,15 @@ namespace Cantera { //! Class LTPspecies_ExpT holds transport parameters for a - //! specific liquid-phase species when the transport property - //! is expressed as a exponential in temperature. + //! specific liquid-phase species (LTPspecies) when the transport + //! property is expressed as a exponential in temperature. /** + * Used for pure species properties with equations of the form + * \f[ + * x = f[0] \exp( f[1] T + ... + f[N] T ) + * \f] + * where f[i] are elements of the float array passed in. + * * As an example of the input required for LTPspecies_ExpT * consider the following XML fragment * @@ -450,6 +489,13 @@ namespace Cantera { public: + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as an exponential in temperature. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ LTPspecies_ExpT( const XML_Node &propNode, std::string name, TransportPropertyList tp_ind, diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 48ee0ca72..53723e68d 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -44,8 +44,8 @@ namespace Cantera { }; - //!Constructor - /** + // Constructor + /* * @param tp_ind Index indicating transport property type (i.e. viscosity) */ LiquidTranInteraction::LiquidTranInteraction( TransportPropertyList tp_ind ) : @@ -199,12 +199,12 @@ namespace Cantera { } } - //! Copy constructor + // Copy constructor LiquidTranInteraction::LiquidTranInteraction( const LiquidTranInteraction &right ) { *this = right; //use assignment operator to do other work } - //! Assignment operator + // Assignment operator LiquidTranInteraction& LiquidTranInteraction::operator=( const LiquidTranInteraction &right ) { if (&right != this) { @@ -702,20 +702,15 @@ namespace Cantera { // Reaction Coeffs and Charges std::vector viS(6); std::vector charges(3); - ions_thermo->getDissociationCoeffs(viS,charges); + std::vector neutMolIndex(3); + ions_thermo->getDissociationCoeffs(viS,charges,neutMolIndex); if ((int)anion.size() != 1) throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have one anion only for StefanMaxwell_PPN"); if ((int)cation.size() != 2) throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have two cations of equal charge for StefanMaxwell_PPN"); if (charges[cation[0]] != charges[cation[1]]) - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN"); - - /* - cout << "cation 0: " << speciesNames[cation[0]] << endl; - cout << "cation 1: " << speciesNames[cation[1]] << endl; - cout << "anion 0: " << speciesNames[anion[0]] << endl; - */ + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN") m_ionCondMix = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); @@ -738,15 +733,6 @@ namespace Cantera { m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); } - /* - for ( i = 0; i < nsp; i++ ) { - cout << "D" << i << "* = " << m_selfDiffMix[i] << endl; - for ( j = 0; j < nsp; j++ ) { - cout << "ratio" << i << j << " = " << m_mobRatMix(i,j) << endl; - } - } - */ - int vP = max(viS[cation[0]],viS[cation[1]]); int vM = viS[anion[0]]; int zP = charges[cation[0]]; @@ -755,38 +741,18 @@ namespace Cantera { doublereal inv_vP_vM_MutualDiff; vector_fp dlnActCoeffdlnN; dlnActCoeffdlnN.resize(neut_molefracs.size(),0.0); + marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); - std::string cationIndex (4,'0'); - for ( i = 0; i < 2; i++ ) - for ( j = 0; j < 2; j++ ) - if ( viS[i*nsp+cation[j]] > 0 ) - cationIndex[i*2+j] = '1'; - - if ( (cationIndex == "1001") | (cationIndex == "0110") ) { - xA = neut_molefracs[cation[0]]; - xB = neut_molefracs[cation[1]]; - eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); - marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); - inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[cation[1]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[cation[0]])/m_selfDiffMix[cation[0]]); - //marg_thermo->getdlnActCoeffdlnX(&dlnActCoeffdlnN[0]); - //inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[cation[1]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[cation[0]])/m_selfDiffMix[cation[0]]); - } - else - throw CanteraError("LTI_StefanMaxwell_PPN::getMixTransProp","Dissociation reactions don't make sense: cationIndex = " + cationIndex); + xA = neut_molefracs[neutMolIndex[cation[0]]]; + xB = neut_molefracs[neutMolIndex[cation[1]]]; + eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); + inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); mat.resize( nsp, nsp, 0.0 ); mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; -/* - for ( i = 0; i < nsp; i++ ) { - for ( j = 0; j < nsp; j++ ) { - mat(i,j) = 1.0/mat(i,j); - //cout << "D" << i << j << " = " << mat(i,j) << endl; - } - } -*/ } diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index 860ee96b1..ba68fcd2a 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -117,6 +117,7 @@ namespace Cantera { * obtained through some mixing rule. These are obtained using the * method getMixTransProp(). Viscosity is typical of this. * Second there are properties for which a matrix of properties may + * @param tp_ind * exist. This matrix of properties is obtained from the method * getMatrixTransProp(). Diffusion coefficients are of this type. * Subclasses should implement the appropriate one or both of @@ -201,9 +202,8 @@ namespace Cantera { }; /** - * Holds transport model parameters relevant to transport in - * liquids for which activated jump processes limit transport - * (giving Arrhenius type transport properties). + * Class LiquidTransportParams holds transport model parameters + * relevant to transport in mixtures. * Used by TransportFactory. */ class LiquidTransportParams : public TransportParams { @@ -313,6 +313,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -355,6 +360,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not Implemented for this Mixing rule; + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -398,6 +408,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -472,6 +487,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } protected: @@ -531,6 +551,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; protected: @@ -540,14 +565,62 @@ namespace Cantera { //! Stefan Maxwell Diffusion Coefficients can be solved for given //! ion conductivity, mobility ratios, and self diffusion coeffs. - //! This method is only valid for a common anion mixture of two - //! salts with cations of equal charge. + //! This class is only valid for a common anion mixture of two + //! salts with cations of equal charge. Hence the name _PPN. /** + * * This class requres you specify + * * 1 - ion conductivity - * 2 - mobility ratio of the two cations - * 3 - mutual diffusion coefficient (can be approximated using - * the self diffusion coefficients of the cations + * + * 2 - mobility ratio of the two cations (set all other ratios to zero) + * + * 3 - Self diffusion coefficients of the cations (set others to zero) + * is used to calculate the "mutual diffusion coefficient". The + * approximation needed to do so requires the cations have equal charge. + * + * We than calculate the Stefan Maxwell Diffusion Coefficients by + * \f[ + * \frac{1}{D_{12}} = (1-\epsilon X_A)(1+\epsilon X_B) + * \frac{\nu_- + \nu_+}{\nu_-\nu_+^2D} + * + \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * \f[ + * \frac{1}{D_{12}} = -\epsilon X_B(1-\epsilon X_A) + * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} + * - \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * \f[ + * \frac{1}{D_{23}} = \epsilon X_A(1+\epsilon X_B) + * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} + * - \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * where F is Faraday's constant, RT is the gas constant times the + * tempurature, and V is the molar volume (basis is moles of ions) that is + * calculated by the thermophase member. X_A and X_B are the mole fractions + * of the salts composed of cation(1) and cation(2), respectively, that share + * a common anion(3). \f$\nu_{+,-}\f$ are the stoichiometric coefficients in + * the dissociation reaction of the salts to the ions with charges of + * \f$z_{+,-}\f$. Assuming that the cations have equal charge, the "mutual + * diffusion coefficient" is calculated using the cation self diffusion + * coefficients. + * \f[ + * \frac{1}{\nu_-\nu_+D} = \left(1+\frac{\partial \gamma_B}{\partial N_B} + * \right)\frac{X_A}{D_2^*}+\left(1+\frac{\partial \gamma_A}{\partial N_A} + * \right)\frac{X_B}{D_1^*} + * \f] + * where the self diffusion coefficients, \f$D_i^*\f$, are temperature and + * composition parameterized inputs and the derivative of the activity + * coefficient, \f$\frac{\partial \gamma_B}{\partial N_B}\f$, is calculated + * by the thermophase member using the excess enthalpy and entropy upon mixing. + * + * Finally, the deviation of the transferrence numbers from ideality, + * \f$\epsilon\f$, is calculated from the mobility ratio of the cations. + * \f[ + * \epsilon = \frac{1-b_2/b_1}{X_A+X_Bb_2/b_1} + * \f] + * Where \f$b_i\f$ are the mobilities of the two cations. Everywhere, + * cation 1 corresponds with salt A and cation 2 with salt B. * * Sample input for this method is * \verbatim @@ -589,8 +662,12 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) ; protected: @@ -637,6 +714,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; protected: @@ -681,6 +763,11 @@ namespace Cantera { doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); doublereal getMixTransProp( std::vector LTPptrs ) ; + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not Implemented for this mixing rule + */ void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } diff --git a/Cantera/src/transport/TransportBase.cpp b/Cantera/src/transport/TransportBase.cpp index dcd317875..1bb18c2e3 100644 --- a/Cantera/src/transport/TransportBase.cpp +++ b/Cantera/src/transport/TransportBase.cpp @@ -84,17 +84,15 @@ namespace Cantera { return m_index; } - /* - * Set an integer index number. This is for internal use of + /* Set an integer index number. This is for internal use of * Cantera, and may be removed in the future. */ void Transport::setIndex(int i) { m_index = i; } - //! Set the number of dimensions to be expected in flux expressions - /*! - * Internal memory will be set with this value + // Set the number of dimensions to be expected in flux expressions + /* Internal memory will be set with this value */ void Transport::setNDim(const int ndim) { m_nDim = ndim; @@ -103,8 +101,7 @@ namespace Cantera { - /* - * Set transport model parameters. This method may be + /* Set transport model parameters. This method may be * overloaded in subclasses to set model-specific parameters. */ void Transport::setParameters(const int type, const int k, diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 6e61559a6..c34d401d5 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -87,29 +87,30 @@ namespace Cantera { //////////////////// class TransportFactory methods ////////////// - /** - * Calculate second-order corrections to binary diffusion - * coefficient pair (dkj, djk). At first order, the binary - * diffusion coefficients are independent of composition, and - * d(k,j) = d(j,k). But at second order, there is a weak - * dependence on composition, with the result that d(k,j) != - * d(j,k). This method computes the multiplier by which the - * first-order binary diffusion coefficient should be multiplied - * to produce the value correct to second order. The expressions - * here are taken from Marerro and Mason, - * J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). - * - * @param t Temperature (K) - * @param tr Transport parameters - * @param k index of first species - * @param j index of second species - * @param xmk mole fraction of species k - * @param xmj mole fraction of species j - * @param fkj multiplier for d(k,j) - * @param fjk multiplier for d(j,k) - * - * @note This method is not used currently. - */ + // Second-order correction to the binary diffusion coefficients + /* + Calculate second-order corrections to binary diffusion + coefficient pair (dkj, djk). At first order, the binary + diffusion coefficients are independent of composition, and + d(k,j) = d(j,k). But at second order, there is a weak + dependence on composition, with the result that d(k,j) != + d(j,k). This method computes the multiplier by which the + first-order binary diffusion coefficient should be multiplied + to produce the value correct to second order. The expressions + here are taken from Marerro and Mason, + J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). + + @param t Temperature (K) + @param tr Transport parameters + @param k index of first species + @param j index of second species + @param xmk mole fraction of species k + @param xmj mole fraction of species j + @param fkj multiplier for d(k,j) + @param fjk multiplier for d(j,k) + + @note This method is not used currently. + */ void TransportFactory::getBinDiffCorrection(doublereal t, const GasTransportParams& tr, int k, int j, doublereal xk, doublereal xj, doublereal& fkj, doublereal& fjk) { @@ -176,12 +177,13 @@ namespace Cantera { } - /** - * Calculate corrections to the well depth parameter and the - * diamter for use in computing the binary diffusion coefficient - * of polar-nonpolar pairs. For more information about this - * correction, see Dixon-Lewis, Proc. Royal Society (1968). - */ + // Corrections for polar-nonpolar binary diffusion coefficients + /* + Calculate corrections to the well depth parameter and the + diamter for use in computing the binary diffusion coefficient + of polar-nonpolar pairs. For more information about this + correction, see Dixon-Lewis, Proc. Royal Society (1968). + */ void TransportFactory::makePolarCorrections(int i, int j, const GasTransportParams& tr, doublereal& f_eps, doublereal& f_sigma) { @@ -207,13 +209,13 @@ namespace Cantera { f_eps = xi*xi; } - /** - * TransportFactory(): default constructor - * - * The default constructor for this class sets up - * m_models[], a mapping between the string name - * for a transport model and the integer name. - */ + /* + TransportFactory(): default constructor + + The default constructor for this class sets up + m_models[], a mapping between the string name + for a transport model and the integer name. + */ TransportFactory::TransportFactory() : m_verbose(false), m_integrals(0) @@ -258,15 +260,15 @@ namespace Cantera { m_LTImodelMap["moleFractionsExpT"] = LTI_MODEL_MOLEFRACS_EXPT; } - /** - * Destructor - * - * We do not delete statically created single instance of this - * class here, because it would create an infinite loop if - * destructor is called for that single instance. However, we do - * have a pointer to m_integrals that does need to be - * explicitly deleted. - */ + /* + Destructor + + We do not delete statically created single instance of this + class here, because it would create an infinite loop if + destructor is called for that single instance. However, we do + have a pointer to m_integrals that does need to be + explicitly deleted. + */ TransportFactory::~TransportFactory() { if (m_integrals) { delete m_integrals; @@ -274,9 +276,7 @@ namespace Cantera { } } - /** - * This static function deletes the statically allocated instance. - */ + // This static function deletes the statically allocated instance. void TransportFactory::deleteFactory() { #if defined(THREAD_SAFE_CANTERA) boost::mutex::scoped_lock lock(transport_mutex) ; @@ -287,12 +287,12 @@ namespace Cantera { } } - /** - * make one of several transport models, and return a base class - * pointer to it. This method operates at the level of a - * single transport property as a function of temperature - * and possibly composition. - */ + /* + make one of several transport models, and return a base class + pointer to it. This method operates at the level of a + single transport property as a function of temperature + and possibly composition. + */ LTPspecies* TransportFactory::newLTP( const XML_Node &trNode, std::string &name, TransportPropertyList tp_ind, @@ -335,13 +335,13 @@ namespace Cantera { return ltps; } - /** - * make one of several transport models, and return a base class - * pointer to it. This method operates at the level of a - * single mixture transport property. Individual species - * transport properties are addressed by the LTPspecies - * returned by newLTP - */ + /* + make one of several transport models, and return a base class + pointer to it. This method operates at the level of a + single mixture transport property. Individual species + transport properties are addressed by the LTPspecies + returned by newLTP + */ LiquidTranInteraction* TransportFactory::newLTI( const XML_Node &trNode, TransportPropertyList tp_ind, LiquidTransportParams& trParam) { @@ -394,10 +394,10 @@ namespace Cantera { return lti; } - /** - * make one of several transport models, and return a base class - * pointer to it. - */ + /* + make one of several transport models, and return a base class + pointer to it. + */ Transport* TransportFactory::newTransport(std::string transportModel, thermo_t* phase, int log_level) { @@ -465,10 +465,10 @@ namespace Cantera { return tr; } - /** - * make one of several transport models, and return a base class - * pointer to it. - */ + /* + make one of several transport models, and return a base class + pointer to it. + */ Transport* TransportFactory::newTransport(thermo_t* phase, int log_level) { XML_Node &phaseNode=phase->xml(); /* @@ -488,11 +488,11 @@ namespace Cantera { } - /** - * Prepare to build a new kinetic-theory-based transport manager - * for low-density gases. Uses polynomial fits to Monchick & Mason - * collision integrals. - */ + /* + Prepare to build a new kinetic-theory-based transport manager + for low-density gases. Uses polynomial fits to Monchick & Mason + collision integrals. + */ void TransportFactory::setupMM(std::ostream &flog, const std::vector &transport_database, thermo_t* thermo, int mode, int log_level, GasTransportParams& tr) { @@ -619,10 +619,10 @@ namespace Cantera { - /** - * Prepare to build a new transport manager for liquids assuming that - * viscosity transport data is provided in Arhennius form. - */ + /* + Prepare to build a new transport manager for liquids assuming that + viscosity transport data is provided in Arhennius form. + */ void TransportFactory::setupLiquidTransport(std::ostream &flog, thermo_t* thermo, int log_level, LiquidTransportParams& trParam) { @@ -701,9 +701,9 @@ namespace Cantera { } - /** Similar to initTransport except uses LiquidTransportParams - * class and calls setupLiquidTransport(). - */ + /* Similar to initTransport except uses LiquidTransportParams + class and calls setupLiquidTransport(). + */ void TransportFactory::initLiquidTransport(Transport* tran, thermo_t* thermo, int log_level) { @@ -817,13 +817,13 @@ namespace Cantera { * *********************************************************/ - /** - * Read transport property data from a file for a list of species. - * Given the name of a file containing transport property - * parameters and a list of species names, this method returns an - * instance of TransportParams containing the transport data for - * these species read from the file. - */ + /* + Read transport property data from a file for a list of species. + Given the name of a file containing transport property + parameters and a list of species names, this method returns an + instance of TransportParams containing the transport data for + these species read from the file. + */ void TransportFactory::getTransportData(const std::vector &xspecies, XML_Node& log, const std::vector &names, GasTransportParams& tr) { @@ -940,13 +940,13 @@ namespace Cantera { } } - /** - * Read transport property data from a file for a list of species. - * Given the name of a file containing transport property - * parameters and a list of species names, this method returns an - * instance of TransportParams containing the transport data for - * these species read from the file. - */ + /* + Read transport property data from a file for a list of species. + Given the name of a file containing transport property + parameters and a list of species names, this method returns an + instance of TransportParams containing the transport data for + these species read from the file. + */ void TransportFactory::getLiquidSpeciesTransportData(const std::vector &xspecies, XML_Node& log, const std::vector &names, @@ -954,8 +954,8 @@ namespace Cantera { { std::string name; /* - * Create a map of species names versus liquid transport data parameters - */ + Create a map of species names versus liquid transport data parameters + */ std::map datatable; std::map::iterator it; @@ -1063,9 +1063,9 @@ namespace Cantera { trParam.LTData.clear(); for (int i = 0; i < trParam.nsp_; i++) { /* - * Check to see that we have a LiquidTransportData object for all of the - * species in the phase. If not, throw an error. - */ + Check to see that we have a LiquidTransportData object for all of the + species in the phase. If not, throw an error. + */ it = datatable.find(names[i]); if (it == datatable.end()) { throw TransportDBError(0,"No transport data found for species " + names[i]); @@ -1073,24 +1073,23 @@ namespace Cantera { LiquidTransportData& trdat = it->second; /* - * Now, transfer these objects into LTData in the correct phase index order by - * calling the default copy constructor for LiquidTransportData. - */ + Now, transfer these objects into LTData in the correct phase index order by + calling the default copy constructor for LiquidTransportData. + */ trParam.LTData.push_back(trdat); } } - /** - * Read transport property data from a file for interactions - * between species in a liquid. - * Given the name of a file containing transport property - * parameters and a list of species names, this method returns an - * instance of TransportParams containing the transport data for - * these species read from the file. - */ - void - TransportFactory::getLiquidInteractionsTransportData(const XML_Node &transportNode, + /* + Read transport property data from a file for interactions + between species in a liquid. + Given the name of a file containing transport property + parameters and a list of species names, this method returns an + instance of TransportParams containing the transport data for + these species read from the file. + */ + void TransportFactory::getLiquidInteractionsTransportData(const XML_Node &transportNode, XML_Node& log, const std::vector &names, LiquidTransportParams& trParam) @@ -1218,8 +1217,7 @@ namespace Cantera { /***************** fitProperties ***************/ - /** - * Generate polynomial fits for the pure-species viscosities and + /* Generate polynomial fits for the pure-species viscosities and * for the binary diffusion coefficients. If * CK_mode, then the fits are of the * form \f[ diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index ae85d414f..3ff192322 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -112,17 +112,18 @@ namespace Cantera { /** - * Deletes the statically malloced instance. + * This static function deletes the statically malloced instance. */ virtual void deleteFactory(); - /** + /*! * Destructor * - * We do not delete statically - * created single instance of this class here, because it would - * create an infinite loop if destructor is called for that - * single instance. + * We do not delete statically created single instance of this + * class here, because it would create an infinite loop if + * destructor is called for that single instance. However, we do + * have a pointer to m_integrals that does need to be + * explicitly deleted. */ virtual ~TransportFactory(); @@ -152,6 +153,7 @@ namespace Cantera { //! Build a new transport manager using a transport manager //! that may not be the same as in the phase description + //! and return a base class pointer to it /*! * @param model String name for the transport manager * @param thermo ThermoPhase object @@ -161,7 +163,7 @@ namespace Cantera { newTransport(std::string model, thermo_t* thermo, int log_level=0); //! Build a new transport manager using the default transport manager - //! in the phase description + //! in the phase description and return a base class pointer to it /*! * @param thermo ThermoPhase object * @param log_level log level @@ -169,11 +171,14 @@ namespace Cantera { virtual Transport* newTransport(thermo_t* thermo, int log_level=0); - /// Initialize an existing transport manager + //! Initialize an existing transport manager virtual void initTransport(Transport* tr, thermo_t* thermo, int mode=0, int log_level=0); - /// Initialize an existing transport manager for liquid phase + //! Initialize an existing transport manager for liquid phase + /*! Similar to initTransport except uses LiquidTransportParams + * class and calls setupLiquidTransport(). + */ virtual void initLiquidTransport(Transport* tr, thermo_t* thermo, int log_level=0); @@ -197,6 +202,14 @@ namespace Cantera { */ TransportFactory(); + //! Read Transport Database + /*! + * Read transport property data from a file for a list of species. + * Given the name of a file containing transport property + * parameters and a list of species names, this method returns an + * instance of TransportParams containing the transport data for + * these species read from the file. + */ void getTransportData(const std::vector &db, XML_Node& log, const std::vector& names, GasTransportParams& tr); @@ -236,33 +249,84 @@ namespace Cantera { XML_Node& log, const std::vector& names, LiquidTransportParams& tr); - /** Generate polynomial fits to viscosity, conductivity, and - * binary diffusion coefficients */ + //! Generate polynomial fits to viscosity, conductivity, and + //! binary diffusion coefficients */ + /*! If CK_mode, then the fits are of the form + * \f[ + * \log(\eta(i)) = \sum_{n = 0}^3 a_n(i) (\log T)^n + * \f] + * and \f[ + * \log(D(i,j)) = \sum_{n = 0}^3 a_n(i,j) (\log T)^n + * \f] + * Otherwise the fits are of the form + * \f[ + * \eta(i)/sqrt(k_BT) = \sum_{n = 0}^4 a_n(i) (\log T)^n + * \f] + * and \f[ + * D(i,j)/sqrt(k_BT)) = \sum_{n = 0}^4 a_n(i,j) (\log T)^n + * \f] + */ void fitProperties(GasTransportParams& tr, std::ostream & logfile); - /// Generate polynomial fits to collision integrals + //! Generate polynomial fits to collision integrals void fitCollisionIntegrals(std::ostream & logfile, GasTransportParams& tr); - + /** + * Prepare to build a new kinetic-theory-based transport manager + * for low-density gases. Uses polynomial fits to Monchick & Mason + * collision integrals. + */ void setupMM(std::ostream &flog, const std::vector &transport_database, thermo_t* thermo, int mode, int log_level, GasTransportParams& tr); - + /** + * Prepare to build a new transport manager for liquids assuming that + * viscosity transport data is provided in Arhennius form. + */ void setupLiquidTransport(std::ostream &flog, thermo_t* thermo, int log_level, LiquidTransportParams& tr); - /// Second-order correction to the binary diffusion coefficients + //! Second-order correction to the binary diffusion coefficients + /*! + * Calculate second-order corrections to binary diffusion + * coefficient pair (dkj, djk). At first order, the binary + * diffusion coefficients are independent of composition, and + * d(k,j) = d(j,k). But at second order, there is a weak + * dependence on composition, with the result that d(k,j) != + * d(j,k). This method computes the multiplier by which the + * first-order binary diffusion coefficient should be multiplied + * to produce the value correct to second order. The expressions + * here are taken from Marerro and Mason, + * J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). + * + * @param t Temperature (K) + * @param tr Transport parameters + * @param k index of first species + * @param j index of second species + * @param xmk mole fraction of species k + * @param xmj mole fraction of species j + * @param fkj multiplier for d(k,j) + * @param fjk multiplier for d(j,k) + * + * @note This method is not used currently. + */ void getBinDiffCorrection(doublereal t, const GasTransportParams& tr, int k, int j, doublereal xk, doublereal xj, doublereal& fkj, doublereal& fjk); - /// Corrections for polar-nonpolar binary diffusion coefficients + //! Corrections for polar-nonpolar binary diffusion coefficients + /*! + * Calculate corrections to the well depth parameter and the + * diamter for use in computing the binary diffusion coefficient + * of polar-nonpolar pairs. For more information about this + * correction, see Dixon-Lewis, Proc. Royal Society (1968). + */ void makePolarCorrections(int i, int j, const GasTransportParams& tr, doublereal& f_eps, doublereal& f_sigma); From 58719349cb7130dafc5ffdc32275f0ced7488bc7 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Thu, 1 Apr 2010 23:05:39 +0000 Subject: [PATCH 131/446] added reportCSV method to ThermoPhase class and all other derived classes that currently contain the report method. reportCSV will output phase data to a text file and a comma separated file that are passed in. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 96 +++++++++++++++++++ Cantera/src/thermo/GibbsExcessVPSSTP.h | 12 +++ Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 96 +++++++++++++++++++ Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 11 +++ Cantera/src/thermo/MargulesVPSSTP.cpp | 97 +++++++++++++++++++- Cantera/src/thermo/MargulesVPSSTP.h | 11 +++ Cantera/src/thermo/MolalityVPSSTP.cpp | 94 +++++++++++++++++++ Cantera/src/thermo/MolalityVPSSTP.h | 12 +++ Cantera/src/thermo/PureFluidPhase.cpp | 92 ++++++++++++++++++- Cantera/src/thermo/PureFluidPhase.h | 12 +++ Cantera/src/thermo/ThermoPhase.cpp | 84 +++++++++++++++++ Cantera/src/thermo/ThermoPhase.h | 11 +++ 12 files changed, 626 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 35bd66136..fe7a5549d 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -23,6 +23,7 @@ #include "GibbsExcessVPSSTP.h" +#include using namespace std; namespace Cantera { @@ -406,6 +407,101 @@ namespace Cantera { return s; } + /* + * Format a summary of the mixture state for output. + */ + void GibbsExcessVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << electricPotential() << ",\n"; + + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + /* + // NOT USED!!!!! + int kk = nSpecies(); + array_fp x(kk); + array_fp y(kk); + array_fp mu(kk); + getMoleFractions(&x[0]); + getMassFractions(&y[0]); + getChemPotentials(&mu[0]); + doublereal rt = GasConstant * temperature(); + int k; + +// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() +// int kk = nSpecies(); +// array_fp x(kk); +// array_fp molal(kk); +// array_fp mu(kk); +// array_fp muss(kk); +// array_fp acMolal(kk); +// array_fp actMolal(kk); +// getMoleFractions(&x[0]); +// +// getChemPotentials(&mu[0]); +// getStandardChemPotentials(&muss[0]); +// getActivities(&actMolal[0]); + + if (show_thermo) { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + */ + } + catch (CanteraError) { + ; + } + } } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 0a94de3cb..eb0c9b8d6 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -541,6 +541,18 @@ namespace Cantera { */ virtual std::string report(bool show_thermo = true) const; + //! returns a summary of the state of the phase to specified + //! comma separated files + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + private: diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 601a937e8..492c2a8f1 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -28,6 +28,7 @@ #include "mix_defs.h" #include +#include using namespace std; @@ -1765,6 +1766,101 @@ namespace Cantera { return s; } + /* + * Format a summary of the mixture state for output. + */ + void IonsFromNeutralVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << electricPotential() << ",\n"; + + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + /* + // NOT USED!!!!! + int kk = nSpecies(); + array_fp x(kk); + array_fp y(kk); + array_fp mu(kk); + getMoleFractions(&x[0]); + getMassFractions(&y[0]); + getChemPotentials(&mu[0]); + doublereal rt = GasConstant * temperature(); + int k; + +// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() +// int kk = nSpecies(); +// array_fp x(kk); +// array_fp molal(kk); +// array_fp mu(kk); +// array_fp muss(kk); +// array_fp acMolal(kk); +// array_fp actMolal(kk); +// getMoleFractions(&x[0]); +// +// getChemPotentials(&mu[0]); +// getStandardChemPotentials(&muss[0]); +// getActivities(&actMolal[0]); + + if (show_thermo) { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + */ + } + catch (CanteraError) { + ; + } + } } diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index ffaed580d..b0af99f10 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -720,6 +720,17 @@ namespace Cantera { */ virtual std::string report(bool show_thermo = true) const; + //! returns a summary of the state of the phase to specified + //! comma separated files + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; private: diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index a6340b7ae..d9caca8e5 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -19,7 +19,7 @@ #include "MargulesVPSSTP.h" #include "ThermoFactory.h" - +#include using namespace std; @@ -1171,6 +1171,101 @@ namespace Cantera { return s; } + /* + * Format a summary of the mixture state for output. + */ + void MargulesVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << electricPotential() << ",\n"; + + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + /* + // NOT USED!!!!! + int kk = nSpecies(); + array_fp x(kk); + array_fp y(kk); + array_fp mu(kk); + getMoleFractions(&x[0]); + getMassFractions(&y[0]); + getChemPotentials(&mu[0]); + doublereal rt = GasConstant * temperature(); + int k; + +// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() +// int kk = nSpecies(); +// array_fp x(kk); +// array_fp molal(kk); +// array_fp mu(kk); +// array_fp muss(kk); +// array_fp acMolal(kk); +// array_fp actMolal(kk); +// getMoleFractions(&x[0]); +// +// getChemPotentials(&mu[0]); +// getStandardChemPotentials(&muss[0]); +// getActivities(&actMolal[0]); + + if (show_thermo) { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + */ + } + catch (CanteraError) { + ; + } + } } diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 4d8a40776..c3a8e60bd 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -738,6 +738,17 @@ namespace Cantera { */ virtual std::string report(bool show_thermo = true) const; + //! returns a summary of the state of the phase to specified + //! comma separated files + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; private: diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp index 285289a9e..32752036e 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.cpp +++ b/Cantera/src/thermo/MolalityVPSSTP.cpp @@ -24,6 +24,7 @@ #include "MolalityVPSSTP.h" +#include using namespace std; namespace Cantera { @@ -910,6 +911,99 @@ namespace Cantera { return s; } + /* + * Format a summary of the mixture state for output. + */ + void MolalityVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << electricPotential() << ",\n"; + + int kk = nSpecies(); + array_fp x(kk); + array_fp molal(kk); + array_fp mu(kk); + array_fp muss(kk); + array_fp acMolal(kk); + array_fp actMolal(kk); + getMoleFractions(&x[0]); + getMolalities(&molal[0]); + getChemPotentials(&mu[0]); + getStandardChemPotentials(&muss[0]); + getMolalityActivityCoefficients(&acMolal[0]); + getActivities(&actMolal[0]); + + int iHp = speciesIndex("H+"); + if (iHp >= 0) { + double pH = -log(actMolal[iHp]) / log(10.0); + textFile << setw(tabM) << "pH\n"; + csvFile << setw(tabM) << pH << ",\n"; + } + + + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + + int k; + if (show_thermo) { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Molalities" << "," << setw(tabM) << "Chem. Pot. (J/kmol)" << "," << setw(tabM) << "Chem Pot SS (J/kmol)" << "," << setw(tabS) << "ActCoeffMolal\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << "," << setw(tabM) << mu[k] << "," << setw(tabM) << muss[k] << "," << setw(tabM) << acMolal[k] << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << "," << setw(tabM) << 0 << "," << setw(tabM) << muss[k] << "," << setw(tabM) << acMolal[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Molalities\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << ",\n"; + + } + } + } + catch (CanteraError) { + ; + } + } } diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h index f9eb439d9..50d68302c 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.h +++ b/Cantera/src/thermo/MolalityVPSSTP.h @@ -800,6 +800,18 @@ namespace Cantera { */ virtual std::string report(bool show_thermo = true) const; + //! returns a summary of the state of the phase to specified + //! comma separated files + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + protected: //! Get the array of unscaled non-dimensional molality based diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index a0748e18c..14c54ef39 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -17,6 +17,7 @@ #include "../../../ext/tpx/utils.h" #include +#include namespace Cantera { @@ -427,8 +428,97 @@ namespace Cantera { } return s; } + + /* + * Format a summary of the mixture state for output. + */ + void PureFluidPhase::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + + if (eosType() == cPureFluid) { + double xx = ((PureFluidPhase *) (this))->vaporFraction(); + textFile << setw(tabM) << "vapor fraction\n"; + csvFile << setw(tabM) << xx << ",\n"; + } + + doublereal phi = electricPotential(); + if (phi != 0.0) { + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << phi << ",\n"; + } + + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + + int kk = nSpecies(); + array_fp x(kk); + array_fp y(kk); + array_fp mu(kk); + getMoleFractions(&x[0]); + getMassFractions(&y[0]); + getChemPotentials(&mu[0]); + doublereal rt = GasConstant * temperature(); + int k; + + if (show_thermo) { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + catch (CanteraError) { + ; + } + } - } #endif // WITH_PURE_FLUIDS diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index 2e2c626c1..2e1943494 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -303,6 +303,18 @@ namespace Cantera { */ virtual std::string report(bool show_thermo = true) const; + //! returns a summary of the state of the phase to specified + //! comma separated files + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + protected: //! Main call to the tpx level to set the state of the system diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 61088dcd2..74e332d3a 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -21,6 +21,7 @@ #endif #include "ThermoPhase.h" +#include //@{ #ifndef MAX @@ -1135,5 +1136,88 @@ namespace Cantera { return s; } + /* + * Format a summary of the mixture state for output. + */ + void ThermoPhase::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + + csvFile.precision(6); + int tabS = 20; + int tabM = 30; + int tabL = 40; + try { + if (name() != "") { + textFile << "\n"+name()+"\n\n"; + csvFile << "\n\n\n"; + } + textFile << setw(tabM) << "temperature (K)\n"; + csvFile << setw(tabM) << temperature() << ",\n"; + textFile << setw(tabM) << "pressure (Pa)\n"; + csvFile << setw(tabM) << pressure() << ",\n"; + textFile << setw(tabM) << "density (kg/m^3)\n"; + csvFile << setw(tabM) << density() << ",\n"; + textFile << setw(tabM) << "mean mol. weight (amu)\n"; + csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; + + doublereal phi = electricPotential(); + if (phi != 0.0) { + textFile << setw(tabM) << "potential (V)\n"; + csvFile << setw(tabM) << phi << ",\n"; + } + if (show_thermo) { + textFile << endl; + csvFile << endl; + textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; + csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; + textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; + csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; + textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; + csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; + textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; + csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; + csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; + textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; + csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + } + + int kk = nSpecies(); + array_fp x(kk); + array_fp y(kk); + array_fp mu(kk); + getMoleFractions(&x[0]); + getMassFractions(&y[0]); + getChemPotentials(&mu[0]); + doublereal rt = GasConstant * temperature(); + int k; + + if (show_thermo) { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + if (x[k] > SmallNumber) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; + } + else { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + else { + textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y\n"; + csvFile << "\n\n"; + for (k = 0; k < kk; k++) { + textFile << setw(tabS) << speciesName(k) << ",\n"; + csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + } + } + } + catch (CanteraError) { + ; + } + } + } diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 2df0b8546..1fcfeefa1 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2111,6 +2111,17 @@ namespace Cantera { * about the thermodynamic state of the system. */ virtual std::string report(bool show_thermo = true) const; + + //! returns a summary of the state of the phase to a comma separated file + /*! + * @param textFile ofstream file to print textual variable names that + * will correspod to data in comma separated file (csv). + * @param csvFile ofstream file to print comma separated data for + * the phase + * @param show_thermo If true, extra information is printed out + * about the thermodynamic state of the system. + */ + virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; protected: From d906ca5951c1630ff50117a0df86f322e5866726 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 2 Apr 2010 17:40:52 +0000 Subject: [PATCH 132/446] Fixed a compilation error Added doxygen info --- .../src/transport/LiquidTransportParams.cpp | 29 +++-- Cantera/src/transport/TransportFactory.cpp | 112 ++++++++++-------- Cantera/src/transport/TransportFactory.h | 54 +++++---- 3 files changed, 110 insertions(+), 85 deletions(-) diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index 53723e68d..f0c587060 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -685,7 +685,9 @@ namespace Cantera { IonsFromNeutralVPSSTP * ions_thermo = dynamic_cast(m_thermo); int i, j, k; int nsp = m_thermo->nSpecies(); - if (nsp != 3) throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); + if (nsp != 3) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); + } int nsp2 = nsp*nsp; doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; @@ -705,12 +707,15 @@ namespace Cantera { std::vector neutMolIndex(3); ions_thermo->getDissociationCoeffs(viS,charges,neutMolIndex); - if ((int)anion.size() != 1) + if ((int)anion.size() != 1) { throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have one anion only for StefanMaxwell_PPN"); - if ((int)cation.size() != 2) + } + if ((int)cation.size() != 2) { throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have two cations of equal charge for StefanMaxwell_PPN"); - if (charges[cation[0]] != charges[cation[1]]) - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN") + } + if (charges[cation[0]] != charges[cation[1]]) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN"); + } m_ionCondMix = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); @@ -718,18 +723,20 @@ namespace Cantera { doublereal vol = m_thermo->molarVolume(); k = 0; - for ( j = 0; j < nsp; j++ ) { - for ( i = 0; i < nsp; i++ ) { + for (j = 0; j < nsp; j++) { + for (i = 0; i < nsp; i++) { if (m_mobRatMixModel[k]) { m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); - if ( m_mobRatMix(i,j) > 0 ) m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); + if (m_mobRatMix(i,j) > 0) { + m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); + } } k++; } } - for ( k = 0; k < nsp; k++ ){ + for (k = 0; k < nsp; k++) { m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); } @@ -750,8 +757,8 @@ namespace Cantera { mat.resize( nsp, nsp, 0.0 ); mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; - mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; -mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index c34d401d5..aed521510 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -487,14 +487,23 @@ namespace Cantera { return newTransport(transportModel, phase,log_level); } - - /* - Prepare to build a new kinetic-theory-based transport manager - for low-density gases. Uses polynomial fits to Monchick & Mason - collision integrals. - */ - void TransportFactory::setupMM(std::ostream &flog, - const std::vector &transport_database, + //==================================================================================================================== + // Prepare to build a new kinetic-theory-based transport manager for low-density gases + /* + * This class fills up the GastransportParams structure for the current phase + * + * Uses polynomial fits to Monchick & Mason collision integrals. store then in tr + * + * @param flog Reference to the ostream for writing log info + * @param transport_database Reference to a vector of pointers containing the + * transport database for each species + * @param thermo Pointer to the %ThermoPhase object + * @param mode Mode -> Either it's CK_Mode, chemkin compatibility mode, or it is not + * We usually run with chemkin compatibility mode turned off. + * @param log_level log level + * @param tr GasTransportParams structure to be filled up with information + */ + void TransportFactory::setupMM(std::ostream &flog, const std::vector &transport_database, thermo_t* thermo, int mode, int log_level, GasTransportParams& tr) { // constant mixture attributes @@ -507,8 +516,7 @@ namespace Cantera { tr.mw.resize(nsp); tr.log_level = log_level; - copy(tr.thermo->molecularWeights().begin(), - tr.thermo->molecularWeights().end(), tr.mw.begin()); + copy(tr.thermo->molecularWeights().begin(), tr.thermo->molecularWeights().end(), tr.mw.begin()); tr.mode_ = mode; tr.epsilon.resize(nsp, nsp, 0.0); @@ -525,8 +533,7 @@ namespace Cantera { tr.eps.resize(nsp); XML_Node root, log; - getTransportData(transport_database, log, - tr.thermo->speciesNames(), tr); + getTransportData(transport_database, log, tr.thermo->speciesNames(), tr); int i, j; for (i = 0; i < nsp; i++) tr.poly[i].resize(nsp); @@ -537,47 +544,44 @@ namespace Cantera { DenseMatrix& diam = tr.diam; DenseMatrix& epsilon = tr.epsilon; - for (i = 0; i < nsp; i++) - { - for (j = i; j < nsp; j++) - { - // the reduced mass - tr.reducedMass(i,j) = - tr.mw[i] * tr.mw[j] / (Avogadro * (tr.mw[i] + tr.mw[j])); + for (i = 0; i < nsp; i++) { + for (j = i; j < nsp; j++) { + // the reduced mass + tr.reducedMass(i,j) = tr.mw[i] * tr.mw[j] / (Avogadro * (tr.mw[i] + tr.mw[j])); - // hard-sphere diameter for (i,j) collisions - diam(i,j) = 0.5*(tr.sigma[i] + tr.sigma[j]); + // hard-sphere diameter for (i,j) collisions + diam(i,j) = 0.5*(tr.sigma[i] + tr.sigma[j]); - // the effective well depth for (i,j) collisions - epsilon(i,j) = sqrt(tr.eps[i]*tr.eps[j]); + // the effective well depth for (i,j) collisions + epsilon(i,j) = sqrt(tr.eps[i]*tr.eps[j]); - // The polynomial fits of collision integrals vs. T* - // will be done for the T* from tstar_min to tstar_max - ts1 = Boltzmann * tr.tmin/epsilon(i,j); - ts2 = Boltzmann * tr.tmax/epsilon(i,j); - if (ts1 < tstar_min) tstar_min = ts1; - if (ts2 > tstar_max) tstar_max = ts2; + // The polynomial fits of collision integrals vs. T* + // will be done for the T* from tstar_min to tstar_max + ts1 = Boltzmann * tr.tmin/epsilon(i,j); + ts2 = Boltzmann * tr.tmax/epsilon(i,j); + if (ts1 < tstar_min) tstar_min = ts1; + if (ts2 > tstar_max) tstar_max = ts2; - // the effective dipole moment for (i,j) collisions - tr.dipole(i,j) = sqrt(tr.dipole(i,i)*tr.dipole(j,j)); + // the effective dipole moment for (i,j) collisions + tr.dipole(i,j) = sqrt(tr.dipole(i,i)*tr.dipole(j,j)); - // reduced dipole moment delta* (nondimensional) - doublereal d = diam(i,j); - tr.delta(i,j) = 0.5 * tr.dipole(i,j)*tr.dipole(i,j) - / (epsilon(i,j) * d * d * d); + // reduced dipole moment delta* (nondimensional) + doublereal d = diam(i,j); + tr.delta(i,j) = 0.5 * tr.dipole(i,j)*tr.dipole(i,j) + / (epsilon(i,j) * d * d * d); - makePolarCorrections(i, j, tr, f_eps, f_sigma); - tr.diam(i,j) *= f_sigma; - epsilon(i,j) *= f_eps; + makePolarCorrections(i, j, tr, f_eps, f_sigma); + tr.diam(i,j) *= f_sigma; + epsilon(i,j) *= f_eps; - // properties are symmetric - tr.reducedMass(j,i) = tr.reducedMass(i,j); - diam(j,i) = diam(i,j); - epsilon(j,i) = epsilon(i,j); - tr.dipole(j,i) = tr.dipole(i,j); - tr.delta(j,i) = tr.delta(i,j); - } + // properties are symmetric + tr.reducedMass(j,i) = tr.reducedMass(i,j); + diam(j,i) = diam(i,j); + epsilon(j,i) = epsilon(i,j); + tr.dipole(j,i) = tr.dipole(i,j); + tr.delta(j,i) = tr.delta(i,j); } + } // Chemkin fits the entire T* range in the Monchick and Mason tables, // so modify tstar_min and tstar_max if in Chemkin compatibility mode @@ -617,14 +621,17 @@ namespace Cantera { #endif } - - + //==================================================================================================================== + // Prepare to build a new transport manager for liquids assuming that + // viscosity transport data is provided in Arhennius form. /* - Prepare to build a new transport manager for liquids assuming that - viscosity transport data is provided in Arhennius form. - */ - void TransportFactory::setupLiquidTransport(std::ostream &flog, - thermo_t* thermo, int log_level, LiquidTransportParams& trParam) { + * @param flog Reference to the ostream for writing log info + * @param thermo Pointer to the %ThermoPhase object + * @param log_level log level + * @param trParam LiquidTransportParams structure to be filled up with information + */ + void TransportFactory::setupLiquidTransport(std::ostream &flog, thermo_t* thermo, int log_level, + LiquidTransportParams& trParam) { const std::vector & species_database = thermo->speciesData(); const XML_Node* phase_database = &thermo->xml(); @@ -668,6 +675,7 @@ namespace Cantera { trParam.thermo->speciesNames(), trParam); } } + //==================================================================================================================== void TransportFactory::initTransport(Transport* tran, diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 3ff192322..fdb55db59 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -86,10 +86,10 @@ namespace Cantera { class TransportFactory : FactoryBase { public: - - /** - * Return a pointer to a TransportFactory - * instance. TransportFactory is implemented as a 'singleton', + + //! Return a pointer to a TransportFactory instance. + /*! + * TransportFactory is implemented as a 'singleton', * which means that at most one instance may be created. The * constructor is private. When a TransportFactory instance is * required, call static method factory() to return a pointer @@ -111,11 +111,10 @@ namespace Cantera { } - /** - * This static function deletes the statically malloced instance. - */ + //! Deletes the statically malloced instance. virtual void deleteFactory(); + /*! * Destructor * @@ -159,8 +158,7 @@ namespace Cantera { * @param thermo ThermoPhase object * @param log_level log level */ - virtual Transport* - newTransport(std::string model, thermo_t* thermo, int log_level=0); + virtual Transport* newTransport(std::string model, thermo_t* thermo, int log_level=0); //! Build a new transport manager using the default transport manager //! in the phase description and return a base class pointer to it @@ -272,23 +270,35 @@ namespace Cantera { void fitCollisionIntegrals(std::ostream & logfile, GasTransportParams& tr); - - /** - * Prepare to build a new kinetic-theory-based transport manager - * for low-density gases. Uses polynomial fits to Monchick & Mason - * collision integrals. + + //! Prepare to build a new kinetic-theory-based transport manager for low-density gases + /*! + * This class fills up the GastransportParams structure for the current phase + * + * Uses polynomial fits to Monchick & Mason collision integrals. store then in tr + * + * @param flog Reference to the ostream for writing log info + * @param transport_database Reference to a vector of pointers containing the + * transport database for each species + * @param thermo Pointer to the %ThermoPhase object + * @param mode Mode -> Either it's CK_Mode, chemkin compatibility mode, or it is not + * We usually run with chemkin compatibility mode turned off. + * @param log_level log level + * @param tr GasTransportParams structure to be filled up with information */ void setupMM(std::ostream &flog, const std::vector &transport_database, - thermo_t* thermo, int mode, int log_level, - GasTransportParams& tr); + thermo_t* thermo, int mode, int log_level, GasTransportParams& tr); - /** - * Prepare to build a new transport manager for liquids assuming that - * viscosity transport data is provided in Arhennius form. + + //! Prepare to build a new transport manager for liquids assuming that + //! viscosity transport data is provided in Arhennius form. + /*! + * @param flog Reference to the ostream for writing log info + * @param thermo Pointer to the %ThermoPhase object + * @param log_level log level + * @param trParam LiquidTransportParams structure to be filled up with information */ - void setupLiquidTransport(std::ostream &flog, - thermo_t* thermo, int log_level, - LiquidTransportParams& tr); + void setupLiquidTransport(std::ostream &flog, thermo_t* thermo, int log_level, LiquidTransportParams& trParam); //! Second-order correction to the binary diffusion coefficients From 356797655fe20d9d34fde50fc46d1e4ee6d3a0a9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 2 Apr 2010 17:43:36 +0000 Subject: [PATCH 133/446] Added a templated function that carries out deep copies of std vectors of pointers. --- Cantera/src/base/mdp_allo.cpp | 2 +- Cantera/src/base/utilities.h | 26 ++++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/Cantera/src/base/mdp_allo.cpp b/Cantera/src/base/mdp_allo.cpp index 1d9f90e3f..d650ed919 100644 --- a/Cantera/src/base/mdp_allo.cpp +++ b/Cantera/src/base/mdp_allo.cpp @@ -1458,7 +1458,7 @@ namespace mdp { * * mdp_copy_dbl_1: * - * Copies one Double vector into another double vector + * Copies one contiguous double vector into another double vector * * Input * ------------- diff --git a/Cantera/src/base/utilities.h b/Cantera/src/base/utilities.h index e54f87c61..19aead0a4 100644 --- a/Cantera/src/base/utilities.h +++ b/Cantera/src/base/utilities.h @@ -660,6 +660,32 @@ namespace Cantera { return (((c[3]*x + c[2])*x + c[1])*x + c[0]); } + //! Templated deep copy of a std vector of pointers + /*! + * Performs a deep copy of a std vectors of pointers to an object. This template assumes that + * that the templated object has a functioning copy constructor. + * It also assumes that pointers are zero when they are not malloced. + * + * @param fromVec Vector of pointers to a templated class. This will be + * deep-copied to the other vector + * @param toVec Vector of pointers to a templated class. This will be + * overwritten and on return will be a copy of the fromVec + */ + template + void deepStdVectorPointerCopy(const std::vector &fromVec, std::vector &toVec) { + int is = toVec.size(); + for (int i = 0; i < is; is++) { + if (toVec[i]) { + delete(toVec[i]); + } + } + is = fromVec.size(); + toVec.resize(is); + for (int i = 0; i < is; is++) { + toVec[i] = new D(*(fromVec[i])); + } + } + //@} } From 35d5677ab6a9c7256b1b6d02e084c3bbf8a0bfa0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 2 Apr 2010 17:44:55 +0000 Subject: [PATCH 134/446] Changed the csvdiff default to return 0 on a successful test not 1. Then I changed all the test problems to follow the new default. --- Cantera/src/equil/MultiPhase.cpp | 3 +- test_problems/VCSnonideal/NaCl_equil/runtest | 2 +- test_problems/VCSnonideal/NaCl_equil/runtestd | 2 +- .../python/flame1/output_blessed.txt | 150 +++++++++--------- test_problems/python/flame1/runtest | 2 +- tools/testtools/csvdiff.cpp | 45 +++--- 6 files changed, 108 insertions(+), 96 deletions(-) diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index 594e243a4..be7111f2f 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -533,7 +533,8 @@ namespace Cantera { int i; doublereal sum = 0; for (i = 0; i < int(m_np); i++) { - sum += m_moles[i]/m_phase[i]->molarDensity(); + double vol = 1.0/m_phase[i]->molarDensity(); + sum += m_moles[i] * vol; } return sum; } diff --git a/test_problems/VCSnonideal/NaCl_equil/runtest b/test_problems/VCSnonideal/NaCl_equil/runtest index 6397b25f6..489e71163 100755 --- a/test_problems/VCSnonideal/NaCl_equil/runtest +++ b/test_problems/VCSnonideal/NaCl_equil/runtest @@ -31,7 +31,7 @@ retnStat_txt=$? $BINDIR/csvdiff -a 1.0E-50 vcs_equilibrate_blessed.csv vcs_equilibrate_res.csv > diff_csv.txt retnStat_csv=$? -if test $retnStat_csv = "1" +if test $retnStat_csv = "0" then echo "Successful test comparison on "`pwd` if [ $retnStat_txt != "0" ] diff --git a/test_problems/VCSnonideal/NaCl_equil/runtestd b/test_problems/VCSnonideal/NaCl_equil/runtestd index b8b7da443..453ec1d11 100755 --- a/test_problems/VCSnonideal/NaCl_equil/runtestd +++ b/test_problems/VCSnonideal/NaCl_equil/runtestd @@ -42,7 +42,7 @@ retnStat_txt=$? $BINDIR/csvdiff -a 1.0E-50 vcs_equilibrate_blessed.csv vcs_equilibrate_res.csv > diff_csv.txt retnStat_csv=$? -if test $retnStat_csv = "1" +if test $retnStat_csv = "0" then echo "Successful test comparison on "`pwd` if [ $retnStat_txt != "0" ] diff --git a/test_problems/python/flame1/output_blessed.txt b/test_problems/python/flame1/output_blessed.txt index 4980f4802..57e085ca2 100644 --- a/test_problems/python/flame1/output_blessed.txt +++ b/test_problems/python/flame1/output_blessed.txt @@ -116,7 +116,17 @@ Problem solved on [13] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 1 + New points inserted after grid points 0 + to resolve H2O2 HO2 +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [14] point grid(s). + +############################################################################## +Refining grid in flame. + New points inserted after grid points 0 to resolve H2O2 HO2 .............................................................................. @@ -127,7 +137,62 @@ Problem solved on [15] point grid(s). ############################################################################## Refining grid in flame. New points inserted after grid points 0 - to resolve H2O2 HO2 + to resolve HO2 +.............................................................................. + +Attempt Newton solution of steady-state problem... success. + +Problem solved on [16] point grid(s). + +no new points needed in flame +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 1 timesteps 7.5e-06 5.055 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 2 timesteps 8.438e-06 5.05 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 5 timesteps 3.204e-05 5.045 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 10 timesteps 0.0002309 4.993 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 10 timesteps 0.0008323 4.76 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 10 timesteps 0.0007499 4.434 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 10 timesteps 0.002703 4.143 +.............................................................................. + +Attempt Newton solution of steady-state problem... failure. + +.............................................................................. +Take 10 timesteps 0.002435 3.937 .............................................................................. Attempt Newton solution of steady-state problem... success. @@ -136,107 +201,48 @@ Problem solved on [16] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 - to resolve HO2 -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [17] point grid(s). - -no new points needed in flame -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 1 timesteps 7.5e-06 5.054 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 2 timesteps 8.438e-06 5.049 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 5 timesteps 3.204e-05 5.044 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.0002309 4.991 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.0008323 4.751 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.0015 4.747 -.............................................................................. - -Attempt Newton solution of steady-state problem... failure. - -.............................................................................. -Take 10 timesteps 0.001351 4.316 -.............................................................................. - -Attempt Newton solution of steady-state problem... success. - -Problem solved on [17] point grid(s). - -############################################################################## -Refining grid in flame. - New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 13 + New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 to resolve H H2 H2O H2O2 HO2 O O2 OH T u .............................................................................. Attempt Newton solution of steady-state problem... success. -Problem solved on [31] point grid(s). +Problem solved on [29] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 22 23 26 27 + New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 20 21 24 25 to resolve H H2 H2O H2O2 HO2 O O2 OH T u .............................................................................. Attempt Newton solution of steady-state problem... success. -Problem solved on [54] point grid(s). +Problem solved on [50] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 47 + New points inserted after grid points 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 43 to resolve H H2 H2O H2O2 HO2 O O2 OH T u .............................................................................. Attempt Newton solution of steady-state problem... success. -Problem solved on [74] point grid(s). +Problem solved on [71] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 1 2 3 5 6 7 8 9 10 11 12 13 14 16 17 24 25 26 27 28 29 30 31 32 33 - to resolve H H2 H2O H2O2 HO2 O O2 + New points inserted after grid points 0 1 2 3 5 6 7 8 9 10 11 12 13 14 16 17 24 25 26 27 28 29 30 31 32 33 34 + to resolve H H2 H2O H2O2 HO2 O O2 OH .............................................................................. Attempt Newton solution of steady-state problem... success. -Problem solved on [100] point grid(s). +Problem solved on [98] point grid(s). ############################################################################## Refining grid in flame. - New points inserted after grid points 0 1 2 - to resolve H2O2 HO2 + New points inserted after grid points 0 1 2 56 57 + to resolve H2O2 HO2 O .............................................................................. Attempt Newton solution of steady-state problem... success. diff --git a/test_problems/python/flame1/runtest b/test_problems/python/flame1/runtest index 3b635d12d..2b9e597c1 100755 --- a/test_problems/python/flame1/runtest +++ b/test_problems/python/flame1/runtest @@ -67,7 +67,7 @@ retnStat_txt=$? $BINDIR/csvdiff -a 1.0E-10 flame1_blessed.csv flame1.csv > diff_csv.txt retnStat_csv=$? -if test $retnStat_csv = "1" +if test $retnStat_csv = "0" then echo " Successful test comparison on "`pwd` if [ $retnStat_txt != "0" ] diff --git a/tools/testtools/csvdiff.cpp b/tools/testtools/csvdiff.cpp index fd03fb734..3ea8e1183 100644 --- a/tools/testtools/csvdiff.cpp +++ b/tools/testtools/csvdiff.cpp @@ -71,6 +71,11 @@ int Debug_Flag = TRUE; double grtol = 1.0E-3; double gatol = 1.0E-9; +#define RT_PASSED 0 +#define RT_FAILED_COL 1 +#define RT_FAILED_HDR 2 +#define RT_FAILED_OTHER 3 + /* * First iteration towards getting this variable */ @@ -646,7 +651,7 @@ int main(int argc, char *argv[]) int mixed_var = 0; int i, j, ndiff, jmax, i1, i2, k, found; double max_diff, rel_diff; - int testPassed = 1; + int testPassed = RT_PASSED; double atol_j, atol_arg = 0.0, rtol_arg = 0.0; /********************** BEGIN EXECUTION ************************************/ @@ -751,37 +756,37 @@ int main(int argc, char *argv[]) get_sizes(fp1, nTitleLines1, nColTitleLines1, nCol1, nDataRows1, &ColIsFloat1); if (nCol1 == 0) { printf("Number of columns in file %s is zero\n", fileName1); - testPassed = -1; - exit (-1); + testPassed = RT_FAILED_OTHER; + exit(RT_FAILED_OTHER); } if (nDataRows1 == 0) { printf("Number of data rows in file %s is zero\n", fileName1); - testPassed = -1; - exit (-1); + testPassed = RT_FAILED_OTHER; + exit(RT_FAILED_OTHER); } get_sizes(fp2, nTitleLines2, nColTitleLines2, nCol2, nDataRows2, &ColIsFloat2); if (nCol2 == 0) { printf("Number of columns in file %s is zero\n", fileName2); - testPassed = -1; - exit (-1); + testPassed = RT_FAILED_OTHER; + exit(RT_FAILED_OTHER); } if (nDataRows2 == 0) { printf("Number of data rows in file %s is zero\n", fileName2); - testPassed = -1; - exit (-1); + testPassed = RT_FAILED_OTHER; + exit(RT_FAILED_OTHER); } if (nTitleLines1 != nTitleLines2) { - printf("Number o Title Lines differ:, %d %d\n",nTitleLines1, nTitleLines2); - testPassed = 0; + printf("Number of Title Lines differ:, %d %d\n",nTitleLines1, nTitleLines2); + testPassed = RT_FAILED_OTHER; } else if (Debug_Flag) { printf("Number of Title Lines in each file = %d\n", nTitleLines1); } if (nColTitleLines1 != nColTitleLines2) { printf("Number of Column title lines differ:, %d %d\n", nColTitleLines1, nColTitleLines2); - testPassed = 0; + testPassed = RT_FAILED_OTHER; } else if (Debug_Flag) { printf("Number of column title lines in each file = %d\n", nColTitleLines1); } @@ -809,27 +814,27 @@ int main(int argc, char *argv[]) for (i = 0; i < n; i++) { if (strcmp(title1[i], title2[i]) != 0) { printf("Title Line %d differ:\n\t\"%s\"\n\t\"%s\"\n", i, title1[i], title2[i]); - testPassed = 0; + testPassed = RT_FAILED_HDR; } else if (Debug_Flag) { printf("Title Line %d for each file: \"%s\"\n", i, title1[i]); } } if (nTitleLines1 != nTitleLines2) { printf("Number of Title Lines differ: %d %d\n", nTitleLines1, nTitleLines2); - testPassed = -1; + testPassed = RT_FAILED_HDR;; } } else { if (nTitleLines1 != nTitleLines2) { if (nTitleLines1) { printf("Titles differ: title for first file: \"%s\"\n", title1[0]); - testPassed = 0; + testPassed = RT_FAILED_HDR; } if (nTitleLines2) { printf("Titles differ: title for second file: \"%s\"\n", title2[0]); } - testPassed = -1; + testPassed = RT_FAILED_HDR; } } @@ -842,7 +847,7 @@ int main(int argc, char *argv[]) printf("Number of column variables differ:, %d %d\n", nCol1, nCol2); mixed_var = TRUE; - testPassed = 0; + testPassed = RT_FAILED_OTHER; } else if (Debug_Flag) { printf("Number of column variables in both files = %d\n", nCol1); @@ -879,7 +884,7 @@ int main(int argc, char *argv[]) if (!found) { printf("csvdiff WARNING Variable %s (%d) in first file not found" " in second file\n", ColNames1[i], i); - testPassed = 0; + testPassed = RT_FAILED_OTHER; } } for (j = 0; j < nCol2; j++) { @@ -891,7 +896,7 @@ int main(int argc, char *argv[]) printf("csvdiff WARNING Variable %s (%d) in second file " "not found in first file\n", ColNames2[j], j); - testPassed = 0; + testPassed = RT_FAILED_OTHER; } } @@ -1024,7 +1029,7 @@ int main(int argc, char *argv[]) printf(" Largest difference was at data row %d ", jmax + 1); printf(": %g %g\n", curVarValues1[jmax], curVarValues2[jmax]); } - testPassed = 0; + testPassed = RT_FAILED_COL; } else if (Debug_Flag) { printf("Column variable %s passed\n", ColNames1[i1]); } From 1f6fe730768f446184c0a6ce907b5e1aa08dc022 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Fri, 2 Apr 2010 23:11:47 +0000 Subject: [PATCH 135/446] Changed output format of reportCSV...still need to implement it properly in MolalityVPSSTP and PureFluidPhase --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 173 ------------------ Cantera/src/thermo/GibbsExcessVPSSTP.h | 19 -- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 174 ------------------ Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 19 -- Cantera/src/thermo/MargulesVPSSTP.cpp | 175 ------------------- Cantera/src/thermo/MargulesVPSSTP.h | 20 --- Cantera/src/thermo/MolalityVPSSTP.cpp | 4 +- Cantera/src/thermo/MolalityVPSSTP.h | 6 +- Cantera/src/thermo/PureFluidPhase.cpp | 4 +- Cantera/src/thermo/PureFluidPhase.h | 6 +- Cantera/src/thermo/ThermoPhase.cpp | 173 +++++++++++------- Cantera/src/thermo/ThermoPhase.h | 6 +- 12 files changed, 120 insertions(+), 659 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index fe7a5549d..d0b14221f 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -329,179 +329,6 @@ namespace Cantera { m_pp.resize(m_kk); } - /* - * Format a summary of the mixture state for output. - */ - std::string GibbsExcessVPSSTP::report(bool show_thermo) const { - - char p[800]; - string s = ""; - try { - if (name() != "") { - sprintf(p, " \n %s:\n", name().c_str()); - s += p; - } - sprintf(p, " \n temperature %12.6g K\n", temperature()); - s += p; - sprintf(p, " pressure %12.6g Pa\n", pressure()); - s += p; - sprintf(p, " density %12.6g kg/m^3\n", density()); - s += p; - sprintf(p, " mean mol. weight %12.6g amu\n", meanMolecularWeight()); - s += p; - - doublereal phi = electricPotential(); - sprintf(p, " potential %12.6g V\n", phi); - s += p; - - int kk = nSpecies(); - array_fp x(kk); - array_fp molal(kk); - array_fp mu(kk); - array_fp muss(kk); - array_fp acMolal(kk); - array_fp actMolal(kk); - getMoleFractions(&x[0]); - - getChemPotentials(&mu[0]); - getStandardChemPotentials(&muss[0]); - getActivities(&actMolal[0]); - - - if (show_thermo) { - sprintf(p, " \n"); - s += p; - sprintf(p, " 1 kg 1 kmol\n"); - s += p; - sprintf(p, " ----------- ------------\n"); - s += p; - sprintf(p, " enthalpy %12.6g %12.4g J\n", - enthalpy_mass(), enthalpy_mole()); - s += p; - sprintf(p, " internal energy %12.6g %12.4g J\n", - intEnergy_mass(), intEnergy_mole()); - s += p; - sprintf(p, " entropy %12.6g %12.4g J/K\n", - entropy_mass(), entropy_mole()); - s += p; - sprintf(p, " Gibbs function %12.6g %12.4g J\n", - gibbs_mass(), gibbs_mole()); - s += p; - sprintf(p, " heat capacity c_p %12.6g %12.4g J/K\n", - cp_mass(), cp_mole()); - s += p; - try { - sprintf(p, " heat capacity c_v %12.6g %12.4g J/K\n", - cv_mass(), cv_mole()); - s += p; - } - catch(CanteraError) { - sprintf(p, " heat capacity c_v \n"); - s += p; - } - } - - } catch (CanteraError) { - ; - } - return s; - } - - /* - * Format a summary of the mixture state for output. - */ - void GibbsExcessVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { - - csvFile.precision(6); - int tabS = 20; - int tabM = 30; - int tabL = 40; - try { - if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; - } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << electricPotential() << ",\n"; - - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; - } - /* - // NOT USED!!!!! - int kk = nSpecies(); - array_fp x(kk); - array_fp y(kk); - array_fp mu(kk); - getMoleFractions(&x[0]); - getMassFractions(&y[0]); - getChemPotentials(&mu[0]); - doublereal rt = GasConstant * temperature(); - int k; - -// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() -// int kk = nSpecies(); -// array_fp x(kk); -// array_fp molal(kk); -// array_fp mu(kk); -// array_fp muss(kk); -// array_fp acMolal(kk); -// array_fp actMolal(kk); -// getMoleFractions(&x[0]); -// -// getChemPotentials(&mu[0]); -// getStandardChemPotentials(&muss[0]); -// getActivities(&actMolal[0]); - - if (show_thermo) { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - } - else { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - */ - } - catch (CanteraError) { - ; - } - } } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index eb0c9b8d6..a100e5f45 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -534,25 +534,6 @@ namespace Cantera { */ virtual void initThermo(); - //! returns a summary of the state of the phase as a string - /*! - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual std::string report(bool show_thermo = true) const; - - //! returns a summary of the state of the phase to specified - //! comma separated files - /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). - * @param csvFile ofstream file to print comma separated data for - * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; - private: diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 492c2a8f1..5beb7725f 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -1687,180 +1687,6 @@ namespace Cantera { } - /** - * Format a summary of the mixture state for output. - */ - std::string IonsFromNeutralVPSSTP::report(bool show_thermo) const { - - - char p[800]; - string s = ""; - try { - if (name() != "") { - sprintf(p, " \n %s:\n", name().c_str()); - s += p; - } - sprintf(p, " \n temperature %12.6g K\n", temperature()); - s += p; - sprintf(p, " pressure %12.6g Pa\n", pressure()); - s += p; - sprintf(p, " density %12.6g kg/m^3\n", density()); - s += p; - sprintf(p, " mean mol. weight %12.6g amu\n", meanMolecularWeight()); - s += p; - - doublereal phi = electricPotential(); - sprintf(p, " potential %12.6g V\n", phi); - s += p; - - int kk = nSpecies(); - array_fp x(kk); - array_fp molal(kk); - array_fp mu(kk); - array_fp muss(kk); - array_fp acMolal(kk); - array_fp actMolal(kk); - getMoleFractions(&x[0]); - - getChemPotentials(&mu[0]); - getStandardChemPotentials(&muss[0]); - getActivities(&actMolal[0]); - - - if (show_thermo) { - sprintf(p, " \n"); - s += p; - sprintf(p, " 1 kg 1 kmol\n"); - s += p; - sprintf(p, " ----------- ------------\n"); - s += p; - sprintf(p, " enthalpy %12.6g %12.4g J\n", - enthalpy_mass(), enthalpy_mole()); - s += p; - sprintf(p, " internal energy %12.6g %12.4g J\n", - intEnergy_mass(), intEnergy_mole()); - s += p; - sprintf(p, " entropy %12.6g %12.4g J/K\n", - entropy_mass(), entropy_mole()); - s += p; - sprintf(p, " Gibbs function %12.6g %12.4g J\n", - gibbs_mass(), gibbs_mole()); - s += p; - sprintf(p, " heat capacity c_p %12.6g %12.4g J/K\n", - cp_mass(), cp_mole()); - s += p; - try { - sprintf(p, " heat capacity c_v %12.6g %12.4g J/K\n", - cv_mass(), cv_mole()); - s += p; - } - catch(CanteraError) { - sprintf(p, " heat capacity c_v \n"); - s += p; - } - } - - } catch (CanteraError) { - ; - } - return s; - } - - /* - * Format a summary of the mixture state for output. - */ - void IonsFromNeutralVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { - - csvFile.precision(6); - int tabS = 20; - int tabM = 30; - int tabL = 40; - try { - if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; - } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << electricPotential() << ",\n"; - - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; - } - /* - // NOT USED!!!!! - int kk = nSpecies(); - array_fp x(kk); - array_fp y(kk); - array_fp mu(kk); - getMoleFractions(&x[0]); - getMassFractions(&y[0]); - getChemPotentials(&mu[0]); - doublereal rt = GasConstant * temperature(); - int k; - -// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() -// int kk = nSpecies(); -// array_fp x(kk); -// array_fp molal(kk); -// array_fp mu(kk); -// array_fp muss(kk); -// array_fp acMolal(kk); -// array_fp actMolal(kk); -// getMoleFractions(&x[0]); -// -// getChemPotentials(&mu[0]); -// getStandardChemPotentials(&muss[0]); -// getActivities(&actMolal[0]); - - if (show_thermo) { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - } - else { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - */ - } - catch (CanteraError) { - ; - } - } } diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index b0af99f10..2aa23319b 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -712,25 +712,6 @@ namespace Cantera { */ void initThermoXML(XML_Node& phaseNode, std::string id); - - //! returns a summary of the state of the phase as a string - /*! - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual std::string report(bool show_thermo = true) const; - - //! returns a summary of the state of the phase to specified - //! comma separated files - /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). - * @param csvFile ofstream file to print comma separated data for - * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; private: diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index d9caca8e5..039f70460 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -1091,181 +1091,6 @@ namespace Cantera { } } - - /** - * Format a summary of the mixture state for output. - */ - std::string MargulesVPSSTP::report(bool show_thermo) const { - - - char p[800]; - string s = ""; - try { - if (name() != "") { - sprintf(p, " \n %s:\n", name().c_str()); - s += p; - } - sprintf(p, " \n temperature %12.6g K\n", temperature()); - s += p; - sprintf(p, " pressure %12.6g Pa\n", pressure()); - s += p; - sprintf(p, " density %12.6g kg/m^3\n", density()); - s += p; - sprintf(p, " mean mol. weight %12.6g amu\n", meanMolecularWeight()); - s += p; - - doublereal phi = electricPotential(); - sprintf(p, " potential %12.6g V\n", phi); - s += p; - - int kk = nSpecies(); - array_fp x(kk); - array_fp molal(kk); - array_fp mu(kk); - array_fp muss(kk); - array_fp acMolal(kk); - array_fp actMolal(kk); - getMoleFractions(&x[0]); - - getChemPotentials(&mu[0]); - getStandardChemPotentials(&muss[0]); - getActivities(&actMolal[0]); - - - if (show_thermo) { - sprintf(p, " \n"); - s += p; - sprintf(p, " 1 kg 1 kmol\n"); - s += p; - sprintf(p, " ----------- ------------\n"); - s += p; - sprintf(p, " enthalpy %12.6g %12.4g J\n", - enthalpy_mass(), enthalpy_mole()); - s += p; - sprintf(p, " internal energy %12.6g %12.4g J\n", - intEnergy_mass(), intEnergy_mole()); - s += p; - sprintf(p, " entropy %12.6g %12.4g J/K\n", - entropy_mass(), entropy_mole()); - s += p; - sprintf(p, " Gibbs function %12.6g %12.4g J\n", - gibbs_mass(), gibbs_mole()); - s += p; - sprintf(p, " heat capacity c_p %12.6g %12.4g J/K\n", - cp_mass(), cp_mole()); - s += p; - try { - sprintf(p, " heat capacity c_v %12.6g %12.4g J/K\n", - cv_mass(), cv_mole()); - s += p; - } - catch(CanteraError) { - sprintf(p, " heat capacity c_v \n"); - s += p; - } - } - - } catch (CanteraError) { - ; - } - return s; - } - - /* - * Format a summary of the mixture state for output. - */ - void MargulesVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { - - csvFile.precision(6); - int tabS = 20; - int tabM = 30; - int tabL = 40; - try { - if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; - } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << electricPotential() << ",\n"; - - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; - } - /* - // NOT USED!!!!! - int kk = nSpecies(); - array_fp x(kk); - array_fp y(kk); - array_fp mu(kk); - getMoleFractions(&x[0]); - getMassFractions(&y[0]); - getChemPotentials(&mu[0]); - doublereal rt = GasConstant * temperature(); - int k; - -// ThermoPhase original above...changed to below comments in GibbsExcessVPSSTP::report() -// int kk = nSpecies(); -// array_fp x(kk); -// array_fp molal(kk); -// array_fp mu(kk); -// array_fp muss(kk); -// array_fp acMolal(kk); -// array_fp actMolal(kk); -// getMoleFractions(&x[0]); -// -// getChemPotentials(&mu[0]); -// getStandardChemPotentials(&muss[0]); -// getActivities(&actMolal[0]); - - if (show_thermo) { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - } - else { - textFile << "\n" << setw(40) << "X" << "," << setw(tabS) << "Y\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(40) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } - */ - } - catch (CanteraError) { - ; - } - } } diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index c3a8e60bd..4e7df72eb 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -729,26 +729,6 @@ namespace Cantera { */ void initThermoXML(XML_Node& phaseNode, std::string id); - - - //! returns a summary of the state of the phase as a string - /*! - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual std::string report(bool show_thermo = true) const; - - //! returns a summary of the state of the phase to specified - //! comma separated files - /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). - * @param csvFile ofstream file to print comma separated data for - * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. - */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; private: diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp index 32752036e..1d2378cc4 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.cpp +++ b/Cantera/src/thermo/MolalityVPSSTP.cpp @@ -914,8 +914,9 @@ namespace Cantera { /* * Format a summary of the mixture state for output. */ - void MolalityVPSSTP::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + void MolalityVPSSTP::reportCSV(std::ofstream& csvFile) const { + /* csvFile.precision(6); int tabS = 20; int tabM = 30; @@ -1003,6 +1004,7 @@ namespace Cantera { catch (CanteraError) { ; } + */ } } diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h index 50d68302c..60ea18feb 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.h +++ b/Cantera/src/thermo/MolalityVPSSTP.h @@ -803,14 +803,10 @@ namespace Cantera { //! returns a summary of the state of the phase to specified //! comma separated files /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). * @param csvFile ofstream file to print comma separated data for * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + virtual void reportCSV(std::ofstream& csvFile) const; protected: diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 14c54ef39..d1e9fb819 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -432,8 +432,9 @@ namespace Cantera { /* * Format a summary of the mixture state for output. */ - void PureFluidPhase::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + void PureFluidPhase::reportCSV(std::ofstream& csvFile) const { + /* csvFile.precision(6); int tabS = 20; int tabM = 30; @@ -517,6 +518,7 @@ namespace Cantera { catch (CanteraError) { ; } + */ } } diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index 2e1943494..74626fe22 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -306,14 +306,10 @@ namespace Cantera { //! returns a summary of the state of the phase to specified //! comma separated files /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). * @param csvFile ofstream file to print comma separated data for * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + virtual void reportCSV(std::ofstream& csvFile) const; protected: diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 74e332d3a..0a7e4dbb8 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -1139,78 +1139,127 @@ namespace Cantera { /* * Format a summary of the mixture state for output. */ - void ThermoPhase::reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo) const { + void ThermoPhase::reportCSV(std::ofstream& csvFile) const { - csvFile.precision(6); - int tabS = 20; + csvFile.precision(3); + int tabS = 15; int tabM = 30; int tabL = 40; try { if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; - } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - - doublereal phi = electricPotential(); - if (phi != 0.0) { - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << phi << ",\n"; - } - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + csvFile << "\n"+name()+"\n\n"; } + csvFile << setw(tabL) << "temperature (K) =" << setw(tabS) << temperature() << endl; + csvFile << setw(tabL) << "pressure (Pa) =" << setw(tabS) << pressure() << endl; + csvFile << setw(tabL) << "density (kg/m^3) =" << setw(tabS) << density() << endl; + csvFile << setw(tabL) << "mean mol. weight (amu) =" << setw(tabS) << meanMolecularWeight() << endl; + csvFile << setw(tabL) << "potential (V) =" << setw(tabS) << electricPotential() << endl; + csvFile << endl; + + csvFile << setw(tabL) << "enthalpy (J/kg) = " << setw(tabS) << enthalpy_mass() << setw(tabL) << "enthalpy (J/kmol) = " << setw(tabS) << enthalpy_mole() << endl; + csvFile << setw(tabL) << "internal E (J/kg) = " << setw(tabS) << intEnergy_mass() << setw(tabL) << "internal E (J/kmol) = " << setw(tabS) << intEnergy_mole() << endl; + csvFile << setw(tabL) << "entropy (J/kg) = " << setw(tabS) << entropy_mass() << setw(tabL) << "entropy (J/kmol) = " << setw(tabS) << entropy_mole() << endl; + csvFile << setw(tabL) << "Gibbs (J/kg) = " << setw(tabS) << gibbs_mass() << setw(tabL) << "Gibbs (J/kmol) = " << setw(tabS) << gibbs_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_p (J/K/kg) = " << setw(tabS) << cp_mass() << setw(tabL) << "heat capacity c_p (J/K/kmol) = " << setw(tabS) << cp_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_v (J/K/kg) = " << setw(tabS) << cv_mass() << setw(tabL) << "heat capacity c_v (J/K/kmol) = " << setw(tabS) << cv_mole() << endl; + + csvFile.precision(8); int kk = nSpecies(); - array_fp x(kk); - array_fp y(kk); - array_fp mu(kk); - getMoleFractions(&x[0]); - getMassFractions(&y[0]); - getChemPotentials(&mu[0]); - doublereal rt = GasConstant * temperature(); - int k; + double x[kk]; + double y[kk]; + double mu[kk]; + double a[kk]; + double ac[kk]; + double hbar[kk]; + double sbar[kk]; + double ubar[kk]; + double cpbar[kk]; + double vbar[kk]; + vector pNames; + vector data; - if (show_thermo) { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } + getMoleFractions(x); + pNames.push_back("X"); + data.push_back(x); + try{ + getMassFractions(y); + pNames.push_back("Y"); + data.push_back(y); } - else { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + catch (CanteraError) {;} + try{ + getChemPotentials(mu); + pNames.push_back("Chem. Pot (J/kmol)"); + data.push_back(mu); + } + catch (CanteraError) {;} + try{ + getActivities(a); + pNames.push_back("Activity"); + data.push_back(a); + } + catch (CanteraError) {;} + try{ + getActivityCoefficients(ac); + pNames.push_back("Act. Coeff."); + data.push_back(ac); + } + catch (CanteraError) {;} + try{ + getPartialMolarEnthalpies(hbar); + pNames.push_back("Part. Mol Enthalpy (J/kmol)"); + data.push_back(hbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarEntropies(sbar); + pNames.push_back("Part. Mol. Entropy (J/K/kmol)"); + data.push_back(sbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarIntEnergies(ubar); + pNames.push_back("Part. Mol. Energy (J/kmol)"); + data.push_back(ubar); + } + catch (CanteraError) {;} + try{ + getPartialMolarCp(cpbar); + pNames.push_back("Part. Mol. Cp (J/K/kmol"); + data.push_back(cpbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarVolumes(vbar); + pNames.push_back("Part. Mol. Cv (J/K/kmol)"); + data.push_back(vbar); + } + catch (CanteraError) {;} + + csvFile << endl << setw(tabS) << "Species,"; + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << pNames[i] << ","; + } + csvFile << endl; + /* + csvFile.fill('-'); + csvFile << setw(tabS+(tabM+1)*pNames.size()) << "-\n"; + csvFile.fill(' '); + */ + for (int k = 0; k < kk; k++) { + csvFile << setw(tabS) << speciesName(k) + ","; + if (x[k] > SmallNumber) { + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << data[i][k] << ","; + } + csvFile << endl; + } + else{ + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << 0 << ","; + } + csvFile << endl; } } } diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 1fcfeefa1..c52e74e75 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2114,14 +2114,10 @@ namespace Cantera { //! returns a summary of the state of the phase to a comma separated file /*! - * @param textFile ofstream file to print textual variable names that - * will correspod to data in comma separated file (csv). * @param csvFile ofstream file to print comma separated data for * the phase - * @param show_thermo If true, extra information is printed out - * about the thermodynamic state of the system. */ - virtual void reportCSV(std::ofstream& textFile, std::ofstream& csvFile, bool show_thermo = true) const; + virtual void reportCSV(std::ofstream& csvFile) const; protected: From 8f8b83e0a29fc27fb712c9e589e0d5a05f959354 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 5 Apr 2010 16:35:49 +0000 Subject: [PATCH 136/446] Changed the runtest so that a value of 0 returned from csvdiff indicates a successful test. Previously, it had been a 1. These tests in this branch weren't changed in my commit of last week. --- test_problems/ChemEquil_ionizedGas/runtest | 4 ++-- test_problems/cxx_ex/runtest | 10 +++++----- test_problems/python/runtest | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/test_problems/ChemEquil_ionizedGas/runtest b/test_problems/ChemEquil_ionizedGas/runtest index 5ba6f1a8e..59d783243 100755 --- a/test_problems/ChemEquil_ionizedGas/runtest +++ b/test_problems/ChemEquil_ionizedGas/runtest @@ -25,7 +25,7 @@ ${CANTERA_BIN}/csvdiff -a 1.0E-19 table.csv table_blessed.csv > diff_csv.txt retnStat_csv=$? eCode=1 -if test $retnStat_csv = "1" +if test $retnStat_csv = "0" then eCode=0 echo "Successful test comparison on " $testName @@ -35,7 +35,7 @@ then fi else echo "Unsuccessful test comparison on " $testName " test" - if test $retnStat_csv != "1" + if test $retnStat_csv != "0" then echo " csv files are different - see diff_csv.txt" fi diff --git a/test_problems/cxx_ex/runtest b/test_problems/cxx_ex/runtest index 083c7c849..aa2b1f1c3 100755 --- a/test_problems/cxx_ex/runtest +++ b/test_problems/cxx_ex/runtest @@ -36,7 +36,7 @@ machType=`../../bin/get_arch` $CANTERA_BIN/csvdiff eq1.csv eq1_blessed.csv > eq1_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on eq1 test" else @@ -57,7 +57,7 @@ fi $CANTERA_BIN/csvdiff tr1.csv tr1_blessed.csv > tr1_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on tr1 test" if [ $temp_success = "1" ] @@ -82,7 +82,7 @@ fi $CANTERA_BIN/csvdiff tr2.csv tr2_blessed.csv > tr2_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on tr2 test" if [ $temp_success = "1" ] @@ -116,7 +116,7 @@ fi $CANTERA_BIN/csvdiff -r 3.0E-3 kin1.csv kin1_blessed_tmp.csv > kin1_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on kin1 test" if [ $temp_success = "1" ] @@ -150,7 +150,7 @@ fi $CANTERA_BIN/csvdiff kin2.csv kin2_blessed_tmp.csv > kin2_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on kin2 test" if [ $temp_success = "1" ] diff --git a/test_problems/python/runtest b/test_problems/python/runtest index 9d9286ded..c74c618b6 100755 --- a/test_problems/python/runtest +++ b/test_problems/python/runtest @@ -70,7 +70,7 @@ fi $CANTERA_BIN/csvdiff diamond.csv diamond_blessed.csv > diamond_test.out retnStat=$? -if [ $retnStat = "1" ] +if [ $retnStat = "0" ] then echo "successful csv comparison on diamond test" if [ $temp_success = "1" ] From 20bf13dbd72e17765bf14bfcbf0260afa716e55c Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Tue, 6 Apr 2010 16:37:11 +0000 Subject: [PATCH 137/446] implemented reportCSV in MolalityPSSTP and PureFluidPhase --- Cantera/src/thermo/MolalityVPSSTP.cpp | 189 ++++++++++++++++---------- Cantera/src/thermo/PureFluidPhase.cpp | 181 +++++++++++++++--------- 2 files changed, 232 insertions(+), 138 deletions(-) diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp index 1d2378cc4..da2a30e60 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.cpp +++ b/Cantera/src/thermo/MolalityVPSSTP.cpp @@ -916,95 +916,144 @@ namespace Cantera { */ void MolalityVPSSTP::reportCSV(std::ofstream& csvFile) const { - /* - csvFile.precision(6); - int tabS = 20; + + csvFile.precision(3); + int tabS = 15; int tabM = 30; int tabL = 40; try { if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; + csvFile << "\n"+name()+"\n\n"; } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << electricPotential() << ",\n"; + csvFile << setw(tabL) << "temperature (K) =" << setw(tabS) << temperature() << endl; + csvFile << setw(tabL) << "pressure (Pa) =" << setw(tabS) << pressure() << endl; + csvFile << setw(tabL) << "density (kg/m^3) =" << setw(tabS) << density() << endl; + csvFile << setw(tabL) << "mean mol. weight (amu) =" << setw(tabS) << meanMolecularWeight() << endl; + csvFile << setw(tabL) << "potential (V) =" << setw(tabS) << electricPotential() << endl; + csvFile << endl; + + csvFile << setw(tabL) << "enthalpy (J/kg) = " << setw(tabS) << enthalpy_mass() << setw(tabL) << "enthalpy (J/kmol) = " << setw(tabS) << enthalpy_mole() << endl; + csvFile << setw(tabL) << "internal E (J/kg) = " << setw(tabS) << intEnergy_mass() << setw(tabL) << "internal E (J/kmol) = " << setw(tabS) << intEnergy_mole() << endl; + csvFile << setw(tabL) << "entropy (J/kg) = " << setw(tabS) << entropy_mass() << setw(tabL) << "entropy (J/kmol) = " << setw(tabS) << entropy_mole() << endl; + csvFile << setw(tabL) << "Gibbs (J/kg) = " << setw(tabS) << gibbs_mass() << setw(tabL) << "Gibbs (J/kmol) = " << setw(tabS) << gibbs_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_p (J/K/kg) = " << setw(tabS) << cp_mass() << setw(tabL) << "heat capacity c_p (J/K/kmol) = " << setw(tabS) << cp_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_v (J/K/kg) = " << setw(tabS) << cv_mass() << setw(tabL) << "heat capacity c_v (J/K/kmol) = " << setw(tabS) << cv_mole() << endl; + + csvFile.precision(8); int kk = nSpecies(); - array_fp x(kk); - array_fp molal(kk); - array_fp mu(kk); - array_fp muss(kk); - array_fp acMolal(kk); - array_fp actMolal(kk); - getMoleFractions(&x[0]); - getMolalities(&molal[0]); - getChemPotentials(&mu[0]); - getStandardChemPotentials(&muss[0]); - getMolalityActivityCoefficients(&acMolal[0]); - getActivities(&actMolal[0]); + double x[kk]; + double molal[kk]; + double mu[kk]; + double muss[kk]; + double aMolal[kk]; + double acMolal[kk]; + double hbar[kk]; + double sbar[kk]; + double ubar[kk]; + double cpbar[kk]; + double vbar[kk]; + vector pNames; + vector data; - int iHp = speciesIndex("H+"); - if (iHp >= 0) { - double pH = -log(actMolal[iHp]) / log(10.0); - textFile << setw(tabM) << "pH\n"; - csvFile << setw(tabM) << pH << ",\n"; + getMoleFractions(x); + pNames.push_back("X"); + data.push_back(x); + try{ + getMolalities(molal); + pNames.push_back("Molal"); + data.push_back(molal); } - - - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + catch (CanteraError) {;} + try{ + getChemPotentials(mu); + pNames.push_back("Chem. Pot. (J/kmol)"); + data.push_back(mu); } - - int k; - if (show_thermo) { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Molalities" << "," << setw(tabM) << "Chem. Pot. (J/kmol)" << "," << setw(tabM) << "Chem Pot SS (J/kmol)" << "," << setw(tabS) << "ActCoeffMolal\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << "," << setw(tabM) << mu[k] << "," << setw(tabM) << muss[k] << "," << setw(tabM) << acMolal[k] << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << "," << setw(tabM) << 0 << "," << setw(tabM) << muss[k] << "," << setw(tabM) << acMolal[k] << ",\n"; - } + catch (CanteraError) {;} + try{ + getStandardChemPotentials(muss); + pNames.push_back("Chem. Pot. SS (J/kmol)"); + data.push_back(muss); + } + catch (CanteraError) {;} + try{ + getMolalityActivityCoefficients(acMolal); + pNames.push_back("Molal Act. Coeff."); + data.push_back(acMolal); + } + catch (CanteraError) {;} + try{ + getActivities(aMolal); + pNames.push_back("Molal Activity"); + data.push_back(aMolal); + int iHp = speciesIndex("H+"); + if (iHp >= 0) { + double pH = -log(aMolal[iHp]) / log(10.0); + csvFile << setw(tabL) << "pH = " << setw(tabS) << pH << endl; } } - else { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Molalities\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << molal[k] << ",\n"; + catch (CanteraError) {;} + try{ + getPartialMolarEnthalpies(hbar); + pNames.push_back("Part. Mol Enthalpy (J/kmol)"); + data.push_back(hbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarEntropies(sbar); + pNames.push_back("Part. Mol. Entropy (J/K/kmol)"); + data.push_back(sbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarIntEnergies(ubar); + pNames.push_back("Part. Mol. Energy (J/kmol)"); + data.push_back(ubar); + } + catch (CanteraError) {;} + try{ + getPartialMolarCp(cpbar); + pNames.push_back("Part. Mol. Cp (J/K/kmol"); + data.push_back(cpbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarVolumes(vbar); + pNames.push_back("Part. Mol. Cv (J/K/kmol)"); + data.push_back(vbar); + } + catch (CanteraError) {;} + csvFile << endl << setw(tabS) << "Species,"; + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << pNames[i] << ","; + } + csvFile << endl; + /* + csvFile.fill('-'); + csvFile << setw(tabS+(tabM+1)*pNames.size()) << "-\n"; + csvFile.fill(' '); + */ + for (int k = 0; k < kk; k++) { + csvFile << setw(tabS) << speciesName(k) + ","; + if (x[k] > SmallNumber) { + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << data[i][k] << ","; + } + csvFile << endl; + } + else{ + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << 0 << ","; + } + csvFile << endl; } } } catch (CanteraError) { ; } - */ } } diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index d1e9fb819..f67df60d7 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -434,91 +434,136 @@ namespace Cantera { */ void PureFluidPhase::reportCSV(std::ofstream& csvFile) const { - /* - csvFile.precision(6); - int tabS = 20; + + csvFile.precision(3); + int tabS = 15; int tabM = 30; int tabL = 40; try { if (name() != "") { - textFile << "\n"+name()+"\n\n"; - csvFile << "\n\n\n"; + csvFile << "\n"+name()+"\n\n"; } - textFile << setw(tabM) << "temperature (K)\n"; - csvFile << setw(tabM) << temperature() << ",\n"; - textFile << setw(tabM) << "pressure (Pa)\n"; - csvFile << setw(tabM) << pressure() << ",\n"; - textFile << setw(tabM) << "density (kg/m^3)\n"; - csvFile << setw(tabM) << density() << ",\n"; - textFile << setw(tabM) << "mean mol. weight (amu)\n"; - csvFile << setw(tabM) << meanMolecularWeight() << ",\n"; - + csvFile << setw(tabL) << "temperature (K) =" << setw(tabS) << temperature() << endl; + csvFile << setw(tabL) << "pressure (Pa) =" << setw(tabS) << pressure() << endl; + csvFile << setw(tabL) << "density (kg/m^3) =" << setw(tabS) << density() << endl; + csvFile << setw(tabL) << "mean mol. weight (amu) =" << setw(tabS) << meanMolecularWeight() << endl; + csvFile << setw(tabL) << "potential (V) =" << setw(tabS) << electricPotential() << endl; if (eosType() == cPureFluid) { double xx = ((PureFluidPhase *) (this))->vaporFraction(); - textFile << setw(tabM) << "vapor fraction\n"; - csvFile << setw(tabM) << xx << ",\n"; - } - - doublereal phi = electricPotential(); - if (phi != 0.0) { - textFile << setw(tabM) << "potential (V)\n"; - csvFile << setw(tabM) << phi << ",\n"; - } - - if (show_thermo) { - textFile << endl; - csvFile << endl; - textFile << setw(tabM) << "enthalpy (J/kg)" << "," << setw(tabM) << "enthalpy (J/kmol)\n"; - csvFile << setw(tabM) << enthalpy_mass() << "," << setw(tabM) << enthalpy_mole() << ",\n"; - textFile << setw(tabM) << "internal E (J/kg)" << "," << setw(tabM) << "internal E (J/kmol)\n"; - csvFile << setw(tabM) << intEnergy_mass() << "," << setw(tabM) << intEnergy_mole() << ",\n"; - textFile << setw(tabM) << "entropy (J/kg)" << "," << setw(tabM) << "entropy (J/kmol)\n"; - csvFile << setw(tabM) << entropy_mass() << "," << setw(tabM) << entropy_mole() << ",\n"; - textFile << setw(tabM) << "Gibbs (J/kg)" << "," << setw(tabM) << "Gibbs (J/kmol)\n"; - csvFile << setw(tabM) << gibbs_mass() << "," << setw(tabM) << gibbs_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_p (J/K/kg)" << "," << setw(tabL) << "heat capacity c_p (J/K/kmol)\n"; - csvFile << setw(tabL) << cp_mass() << "," << setw(tabL) << cp_mole() << ",\n"; - textFile << setw(tabL) << "heat capacity c_v (J/K/kg)" << "," << setw(tabL) << "heat capacity c_v (J/K/kmol)\n"; - csvFile << setw(tabL) << cv_mass() << "," << setw(tabL) << cv_mole() << ",\n"; + csvFile << setw(tabL) << "vapor fraction = " << setw(tabS) << xx << endl; } + csvFile << endl; + + csvFile << setw(tabL) << "enthalpy (J/kg) = " << setw(tabS) << enthalpy_mass() << setw(tabL) << "enthalpy (J/kmol) = " << setw(tabS) << enthalpy_mole() << endl; + csvFile << setw(tabL) << "internal E (J/kg) = " << setw(tabS) << intEnergy_mass() << setw(tabL) << "internal E (J/kmol) = " << setw(tabS) << intEnergy_mole() << endl; + csvFile << setw(tabL) << "entropy (J/kg) = " << setw(tabS) << entropy_mass() << setw(tabL) << "entropy (J/kmol) = " << setw(tabS) << entropy_mole() << endl; + csvFile << setw(tabL) << "Gibbs (J/kg) = " << setw(tabS) << gibbs_mass() << setw(tabL) << "Gibbs (J/kmol) = " << setw(tabS) << gibbs_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_p (J/K/kg) = " << setw(tabS) << cp_mass() << setw(tabL) << "heat capacity c_p (J/K/kmol) = " << setw(tabS) << cp_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_v (J/K/kg) = " << setw(tabS) << cv_mass() << setw(tabL) << "heat capacity c_v (J/K/kmol) = " << setw(tabS) << cv_mole() << endl; + + csvFile.precision(8); int kk = nSpecies(); - array_fp x(kk); - array_fp y(kk); - array_fp mu(kk); - getMoleFractions(&x[0]); - getMassFractions(&y[0]); - getChemPotentials(&mu[0]); - doublereal rt = GasConstant * temperature(); - int k; + double x[kk]; + double y[kk]; + double mu[kk]; + double a[kk]; + double ac[kk]; + double hbar[kk]; + double sbar[kk]; + double ubar[kk]; + double cpbar[kk]; + double vbar[kk]; + vector pNames; + vector data; - if (show_thermo) { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y" << "," << setw(tabS) << "Chem. Pot. / RT\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - if (x[k] > SmallNumber) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << "," << setw(tabS) << mu[k]/rt << ",\n"; - } - else { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; - } - } + getMoleFractions(x); + pNames.push_back("X"); + data.push_back(x); + try{ + getMassFractions(y); + pNames.push_back("Y"); + data.push_back(y); } - else { - textFile << "\n" << setw(2*tabS) << "X" << "," << setw(tabS) << "Y\n"; - csvFile << "\n\n"; - for (k = 0; k < kk; k++) { - textFile << setw(tabS) << speciesName(k) << ",\n"; - csvFile << setw(2*tabS) << x[k] << "," << setw(tabS) << y[k] << ",\n"; + catch (CanteraError) {;} + try{ + getChemPotentials(mu); + pNames.push_back("Chem. Pot (J/kmol)"); + data.push_back(mu); + } + catch (CanteraError) {;} + try{ + getActivities(a); + pNames.push_back("Activity"); + data.push_back(a); + } + catch (CanteraError) {;} + try{ + getActivityCoefficients(ac); + pNames.push_back("Act. Coeff."); + data.push_back(ac); + } + catch (CanteraError) {;} + try{ + getPartialMolarEnthalpies(hbar); + pNames.push_back("Part. Mol Enthalpy (J/kmol)"); + data.push_back(hbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarEntropies(sbar); + pNames.push_back("Part. Mol. Entropy (J/K/kmol)"); + data.push_back(sbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarIntEnergies(ubar); + pNames.push_back("Part. Mol. Energy (J/kmol)"); + data.push_back(ubar); + } + catch (CanteraError) {;} + try{ + getPartialMolarCp(cpbar); + pNames.push_back("Part. Mol. Cp (J/K/kmol"); + data.push_back(cpbar); + } + catch (CanteraError) {;} + try{ + getPartialMolarVolumes(vbar); + pNames.push_back("Part. Mol. Cv (J/K/kmol)"); + data.push_back(vbar); + } + catch (CanteraError) {;} + + csvFile << endl << setw(tabS) << "Species,"; + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << pNames[i] << ","; + } + csvFile << endl; + /* + csvFile.fill('-'); + csvFile << setw(tabS+(tabM+1)*pNames.size()) << "-\n"; + csvFile.fill(' '); + */ + for (int k = 0; k < kk; k++) { + csvFile << setw(tabS) << speciesName(k) + ","; + if (x[k] > SmallNumber) { + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << data[i][k] << ","; + } + csvFile << endl; + } + else{ + for ( int i = 0; i < (int)pNames.size(); i++ ){ + csvFile << setw(tabM) << 0 << ","; + } + csvFile << endl; } } } catch (CanteraError) { ; - } - */ + } } } From 49ba48e602aa98ae91bab2bdad0b009659772e8b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 10 Apr 2010 01:35:13 +0000 Subject: [PATCH 138/446] Fixed variable array declarations. --- Cantera/src/thermo/ThermoPhase.cpp | 60 +++++++++++++++++++----------- 1 file changed, 38 insertions(+), 22 deletions(-) diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 0a7e4dbb8..afc819617 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -1156,28 +1156,34 @@ namespace Cantera { csvFile << setw(tabL) << "potential (V) =" << setw(tabS) << electricPotential() << endl; csvFile << endl; - csvFile << setw(tabL) << "enthalpy (J/kg) = " << setw(tabS) << enthalpy_mass() << setw(tabL) << "enthalpy (J/kmol) = " << setw(tabS) << enthalpy_mole() << endl; - csvFile << setw(tabL) << "internal E (J/kg) = " << setw(tabS) << intEnergy_mass() << setw(tabL) << "internal E (J/kmol) = " << setw(tabS) << intEnergy_mole() << endl; - csvFile << setw(tabL) << "entropy (J/kg) = " << setw(tabS) << entropy_mass() << setw(tabL) << "entropy (J/kmol) = " << setw(tabS) << entropy_mole() << endl; - csvFile << setw(tabL) << "Gibbs (J/kg) = " << setw(tabS) << gibbs_mass() << setw(tabL) << "Gibbs (J/kmol) = " << setw(tabS) << gibbs_mole() << endl; - csvFile << setw(tabL) << "heat capacity c_p (J/K/kg) = " << setw(tabS) << cp_mass() << setw(tabL) << "heat capacity c_p (J/K/kmol) = " << setw(tabS) << cp_mole() << endl; - csvFile << setw(tabL) << "heat capacity c_v (J/K/kg) = " << setw(tabS) << cv_mass() << setw(tabL) << "heat capacity c_v (J/K/kmol) = " << setw(tabS) << cv_mole() << endl; + csvFile << setw(tabL) << "enthalpy (J/kg) = " << setw(tabS) << enthalpy_mass() << setw(tabL) + << "enthalpy (J/kmol) = " << setw(tabS) << enthalpy_mole() << endl; + csvFile << setw(tabL) << "internal E (J/kg) = " << setw(tabS) << intEnergy_mass() << setw(tabL) + << "internal E (J/kmol) = " << setw(tabS) << intEnergy_mole() << endl; + csvFile << setw(tabL) << "entropy (J/kg) = " << setw(tabS) << entropy_mass() << setw(tabL) + << "entropy (J/kmol) = " << setw(tabS) << entropy_mole() << endl; + csvFile << setw(tabL) << "Gibbs (J/kg) = " << setw(tabS) << gibbs_mass() << setw(tabL) + << "Gibbs (J/kmol) = " << setw(tabS) << gibbs_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_p (J/K/kg) = " << setw(tabS) << cp_mass() + << setw(tabL) << "heat capacity c_p (J/K/kmol) = " << setw(tabS) << cp_mole() << endl; + csvFile << setw(tabL) << "heat capacity c_v (J/K/kg) = " << setw(tabS) << cv_mass() + << setw(tabL) << "heat capacity c_v (J/K/kmol) = " << setw(tabS) << cv_mole() << endl; csvFile.precision(8); int kk = nSpecies(); - double x[kk]; - double y[kk]; - double mu[kk]; - double a[kk]; - double ac[kk]; - double hbar[kk]; - double sbar[kk]; - double ubar[kk]; - double cpbar[kk]; - double vbar[kk]; - vector pNames; - vector data; + doublereal *x = new doublereal[kk]; + doublereal *y = new doublereal[kk]; + doublereal *mu = new doublereal[kk]; + doublereal *a = new doublereal[kk]; + doublereal *ac = new doublereal[kk]; + doublereal *hbar = new doublereal[kk]; + doublereal *sbar = new doublereal[kk]; + doublereal *ubar = new doublereal[kk]; + doublereal *cpbar= new doublereal[kk]; + doublereal *vbar = new doublereal[kk]; + std::vector pNames; + std::vector data; getMoleFractions(x); pNames.push_back("X"); @@ -1250,18 +1256,28 @@ namespace Cantera { for (int k = 0; k < kk; k++) { csvFile << setw(tabS) << speciesName(k) + ","; if (x[k] > SmallNumber) { - for ( int i = 0; i < (int)pNames.size(); i++ ){ + for (int i = 0; i < (int)pNames.size(); i++) { csvFile << setw(tabM) << data[i][k] << ","; } csvFile << endl; - } - else{ - for ( int i = 0; i < (int)pNames.size(); i++ ){ + } else { + for (int i = 0; i < (int)pNames.size(); i++) { csvFile << setw(tabM) << 0 << ","; } csvFile << endl; } } + delete [] x; + delete [] y; + delete [] mu; + delete [] a; + delete [] ac; + delete [] hbar; + delete [] sbar; + delete [] ubar; + delete [] cpbar; + delete [] vbar; + } catch (CanteraError) { ; From 497e69d0d0d69657502cbbad1d895fad4cf5320d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 10 Apr 2010 02:35:18 +0000 Subject: [PATCH 139/446] Worked on doxygen updates Split a file in two in order to make the directory more readable. Started working on standardizing the files. --- .../src/transport/LiquidTranInteraction.cpp | 864 +++++++++++++++++ Cantera/src/transport/LiquidTranInteraction.h | 685 +++++++++++++ .../src/transport/LiquidTransportParams.cpp | 902 ++---------------- Cantera/src/transport/LiquidTransportParams.h | 645 +------------ Cantera/src/transport/Makefile.in | 4 +- Cantera/src/transport/TransportFactory.cpp | 97 +- Cantera/src/transport/TransportFactory.h | 27 +- Cantera/src/transport/TransportParams.h | 7 + 8 files changed, 1724 insertions(+), 1507 deletions(-) create mode 100644 Cantera/src/transport/LiquidTranInteraction.cpp create mode 100644 Cantera/src/transport/LiquidTranInteraction.h diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp new file mode 100644 index 000000000..854b7a7ac --- /dev/null +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -0,0 +1,864 @@ +/** + * @file LiquidTransportParams.cpp + * Source code for liquid mixture transport property evaluations. + */ +/* + * Latest Checkin: + * $Author: hkmoffa $ + * $Date: 2010-04-02 11:40:52 -0600 (Fri, 02 Apr 2010) $ + * $Revision: 429 $ + */ + +#include "LiquidTransportParams.h" +#include +#include "IonsFromNeutralVPSSTP.h" +#include "MargulesVPSSTP.h" +#include +using namespace std; + + +namespace Cantera { + + /** + * Exception thrown if an error is encountered while reading the + * transport database. + */ + class LTPError : public CanteraError { + public: + LTPError(std::string msg ) + : CanteraError("LTPspecies", + "error parsing transport data: " + + msg + "\n") {} + }; + + /** + * Exception thrown if an error is encountered while reading the + * transport database. + */ + class LTPmodelError : public CanteraError { + public: + LTPmodelError(std::string msg ) + : CanteraError("LTPspecies", + "error parsing transport data: " + + msg + "\n") {} + }; + + + // Constructor + /* + * @param tp_ind Index indicating transport property type (i.e. viscosity) + */ + LiquidTranInteraction::LiquidTranInteraction(TransportPropertyList tp_ind ) : + m_model(LTI_MODEL_NOTSET), + m_property(tp_ind) + { + } + + LiquidTranInteraction::~LiquidTranInteraction() { + int kmax = m_Aij.size(); + for (int k = 0; k < kmax; k++) { + if (m_Aij[k] ) delete m_Aij[k]; + } + kmax = m_Bij.size(); + for (int k = 0; k < kmax; k++) { + if (m_Bij[k] ) delete m_Bij[k]; + } + kmax = m_Hij.size(); + for (int k = 0; k < kmax; k++) { + if (m_Hij[k] ) delete m_Hij[k]; + } + kmax = m_Sij.size(); + for (int k = 0; k < kmax; k++) { + if (m_Sij[k] ) delete m_Sij[k]; + } + } + + //==================================================================================================================== + + void LiquidTranInteraction::init(const XML_Node &compModelNode, + thermo_t* thermo ) + { + + doublereal poly0; + m_thermo = thermo; + + int nsp = thermo->nSpecies(); + m_Dij.resize(nsp, nsp, 0.0 ); + m_Eij.resize(nsp, nsp, 0.0 ); + /* + m_Aij.resize(nsp); + m_Bij.resize(nsp); + m_Hij.resize(nsp); + m_Sij.resize(nsp); + for (int k = 0; k < nsp; k++ ){ + (*m_Aij[k]).resize(nsp, nsp, 0.0); + (*m_Bij[k]).resize(nsp, nsp, 0.0); + (*m_Hij[k]).resize(nsp, nsp, 0.0); + (*m_Sij[k]).resize(nsp, nsp, 0.0); + } + */ + + std::string speciesA; + std::string speciesB; + + int num = compModelNode.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = compModelNode.child(iChild); + std::string nodeName = lowercase(xmlChild.name() ); + if (nodeName != "interaction" ) + throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", + "expected element and got <" + nodeName + ">" ); + speciesA = xmlChild.attrib("speciesA"); + speciesB = xmlChild.attrib("speciesB"); + int iSpecies = m_thermo->speciesIndex(speciesA ); + if (iSpecies < 0 ) + throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", + "Unknown species " + speciesA ); + int jSpecies = m_thermo->speciesIndex(speciesB ); + if (jSpecies < 0 ) + throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", + "Unknown species " + speciesB ); + /* if (xmlChild.hasChild("Aij" ) ) { + m_Aij(iSpecies,jSpecies) = getFloat(xmlChild, "Aij", "toSI" ); + m_Aij(jSpecies,iSpecies) = m_Aij(iSpecies,jSpecies) ; + }*/ + + if (xmlChild.hasChild("Eij" ) ) { + m_Eij(iSpecies,jSpecies) = getFloat(xmlChild, "Eij", "actEnergy" ); + m_Eij(iSpecies,jSpecies) /= GasConstant; + m_Eij(jSpecies,iSpecies) = m_Eij(iSpecies,jSpecies) ; + } + + if (xmlChild.hasChild("Aij" ) ) { + vector_fp poly; + poly0 = getFloat(poly, xmlChild, "Aij", "toSI" ); + if (!poly.size() ) poly.push_back(poly0); + while (m_Aij.size()resize(nsp, nsp, 0.0); + m_Aij.push_back(aTemp); + } + for(int i=0; i<(int)poly.size(); i++ ){ + (*m_Aij[i])(iSpecies,jSpecies) = poly[i]; + //(*m_Aij[i])(jSpecies,iSpecies) = (*m_Aij[i])(iSpecies,jSpecies) ; + } + } + + if (xmlChild.hasChild("Bij" ) ) { + vector_fp poly; + poly0 = getFloat(poly, xmlChild, "Bij", "toSI" ); + if (!poly.size() ) poly.push_back(poly0); + while (m_Bij.size()resize(nsp, nsp, 0.0); + m_Bij.push_back(bTemp); + } + for(int i=0; i<(int)poly.size(); i++ ){ + (*m_Bij[i])(iSpecies,jSpecies) = poly[i]; + //(*m_Bij[i])(jSpecies,iSpecies) = (*m_Bij[i])(iSpecies,jSpecies) ; + } + } + + if (xmlChild.hasChild("Hij" ) ) { + vector_fp poly; + poly0 = getFloat(poly, xmlChild, "Hij", "actEnergy" ); + if (!poly.size() ) poly.push_back(poly0); + while (m_Hij.size()resize(nsp, nsp, 0.0); + m_Hij.push_back(hTemp); + } + for(int i=0; i<(int)poly.size(); i++ ){ + (*m_Hij[i])(iSpecies,jSpecies) = poly[i]; + (*m_Hij[i])(iSpecies,jSpecies) /= GasConstant; + //(*m_Hij[i])(jSpecies,iSpecies) = (*m_Hij[i])(iSpecies,jSpecies) ; + } + } + + if (xmlChild.hasChild("Sij" ) ) { + vector_fp poly; + poly0 = getFloat(poly, xmlChild, "Sij", "actEnergy" ); + if (!poly.size() ) poly.push_back(poly0); + while (m_Sij.size()resize(nsp, nsp, 0.0); + m_Sij.push_back(sTemp); + } + for(int i=0; i<(int)poly.size(); i++ ){ + (*m_Sij[i])(iSpecies,jSpecies) = poly[i]; + (*m_Sij[i])(iSpecies,jSpecies) /= GasConstant; + //(*m_Sij[i])(jSpecies,iSpecies) = (*m_Sij[i])(iSpecies,jSpecies) ; + } + } + + /*0 if (xmlChild.hasChild("Sij" ) ) { + m_Sij(iSpecies,jSpecies) = getFloat(xmlChild, "Sij", "toSI" ); + m_Sij(iSpecies,jSpecies) /= GasConstant; + //m_Sij(jSpecies,iSpecies) = m_Sij(iSpecies,jSpecies) ; + }*/ + + if (xmlChild.hasChild("Dij" ) ) { + m_Dij(iSpecies,jSpecies) = getFloat(xmlChild, "Dij", "toSI" ); + m_Dij(jSpecies,iSpecies) = m_Dij(iSpecies,jSpecies) ; + } + } + } + + // Copy constructor + LiquidTranInteraction::LiquidTranInteraction(const LiquidTranInteraction &right ) { + *this = right; //use assignment operator to do other work + } + + // Assignment operator + LiquidTranInteraction& LiquidTranInteraction::operator=(const LiquidTranInteraction &right ) + { + if (&right != this) { + m_model = right.m_model; + m_property = right.m_property; + m_thermo = right.m_thermo; + //m_trParam = right.m_trParam; + m_Aij = right.m_Aij; + m_Bij = right.m_Bij; + m_Eij = right.m_Eij; + m_Hij = right.m_Hij; + m_Sij = right.m_Sij; + m_Dij = right.m_Dij; + } + return *this; + } + + + //==================================================================================================================== + LTI_Solvent::LTI_Solvent(TransportPropertyList tp_ind) : + LiquidTranInteraction(tp_ind) + { + m_model = LTI_MODEL_SOLVENT; + } + //==================================================================================================================== + + doublereal LTI_Solvent::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0.0; + + //if weightings are specified, use those + if (speciesWeight) { + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]; + // should be: molefracs[k] = molefracs[k]*speciesWeight[k]; for consistency, but weight(solvent)=1? + } + } + else { + throw CanteraError("LTI_Solvent::getMixTransProp","You should be specifying the speciesWeight"); + /* //This does not follow directly a solvent model + //although if the solvent mole fraction is dominant + //and the other species values are given or zero, + //it should work. + for (int k = 0; k < nsp; k++) { + value += speciesValues[k] * molefracs[k]; + }*/ + } + + for (int i = 0; i < nsp; i++ ){ + //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. + value += speciesValues[i] * speciesWeight[i]; + if (i == 0) { + AssertTrace(speciesWeight[i] == 1.0); + } else { + AssertTrace(speciesWeight[i] == 0.0); + } + for (int j = 0; j < nsp; j++ ) { + for (int k = 0; k < (int)m_Aij.size(); k++) { + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++) { + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } + + return value; + } + //==================================================================================================================== + doublereal LTI_Solvent::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0.0; + + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]; + // should be: molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); for consistency, but weight(solvent)=1? + } + + for (int i = 0; i < nsp; i++) { + //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. + value += LTPptrs[i]->getSpeciesTransProp() * LTPptrs[i]->getMixWeight(); + for (int j = 0; j < nsp; j++) { + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++) { + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } + + return value; + } + //==================================================================================================================== + void LTI_Solvent::getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues) { + mat = (*m_Aij[0]); + } + //==================================================================================================================== + + + doublereal LTI_MoleFracs::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + //if weightings are specified, use those + if (speciesWeight) { + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*speciesWeight[k]; + } + } + else { + throw CanteraError("LTI_MoleFracs::getMixTransProp","You should be specifying the speciesWeight"); + } + + for (int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } + + return value; + } + + + doublereal LTI_MoleFracs::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); + } + + for (int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); + } + } + } + return value; + } + + + doublereal LTI_MassFracs::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal massfracs[nsp]; + m_thermo->getMassFractions(massfracs); + + doublereal value = 0; + + //if weightings are specified, use those + if (speciesWeight ) { + for (int k = 0; k < nsp; k++) { + massfracs[k] = massfracs[k]*speciesWeight[k]; + } + } + else { + throw CanteraError("LTI_MassFracs::getMixTransProp","You should be specifying the speciesWeight"); + } + + for (int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * massfracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); + } + } + } + + return value; + } + + + doublereal LTI_MassFracs::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal massfracs[nsp]; + m_thermo->getMassFractions(massfracs); + + doublereal value = 0; + + for (int k = 0; k < nsp; k++) { + massfracs[k] = massfracs[k]*LTPptrs[k]->getMixWeight(); + } + + for (int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * massfracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); + } + for (int k = 0; k < (int)m_Bij.size(); k++ ){ + value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); + } + } + } + + return value; + } + + + + + doublereal LTI_Log_MoleFracs::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + + + doublereal value = 0; + + //if weightings are specified, use those + if (speciesWeight ) { + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*speciesWeight[k]; + } + } + else{ + throw CanteraError("LTI_Log_MoleFracs::getMixTransProp","You probably should have a speciesWeight when you call getMixTransProp to convert ion mole fractions to molecular mole fractions"); + } + + for (int i = 0; i < nsp; i++ ){ + value += log(speciesValues[i] ) * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Hij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + for (int k = 0; k < (int)m_Sij.size(); k++ ){ + value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + } + } + + value = exp(value ); + return value; + } + + + doublereal LTI_Log_MoleFracs::getMixTransProp(std::vector LTPptrs) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + + doublereal value = 0; + + //if weightings are specified, use those + + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); + } + + for (int i = 0; i < nsp; i++ ){ + value += log(LTPptrs[i]->getSpeciesTransProp() ) * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Hij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); + //cout << "1 = " << molefracs[i]+molefracs[j] << endl; + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + for (int k = 0; k < (int)m_Sij.size(); k++ ){ + value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); + //cout << "1 = " << molefracs[i]+molefracs[j] << endl; + //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; + } + } + } + + value = exp(value ); + // cout << ", viscSpeciesA = " << LTPptrs[0]->getSpeciesTransProp() << endl; + //cout << ", viscSpeciesB = " << LTPptrs[1]->getSpeciesTransProp() << endl; + //cout << "value = " << value << " FINAL" << endl; + return value; + } + + + + + + void LTI_Pairwise_Interaction::setParameters(LiquidTransportParams& trParam) { + int nsp = m_thermo->nSpecies(); + m_diagonals.resize(nsp, 0); + + for (int k = 0; k < nsp; k++) { + Cantera::LiquidTransportData <d = trParam.LTData[k]; + if (ltd.speciesDiffusivity) + m_diagonals[k] = ltd.speciesDiffusivity; + } + } + + doublereal LTI_Pairwise_Interaction::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_Pairwise_Interaction::getMixTransProp does not make sense." ); + + return value; + } + + + doublereal LTI_Pairwise_Interaction::getMixTransProp(std::vector LTPptrs) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_Pairwise_Interaction::getMixTransProp does not make sense." ); + + return value; + } + + void LTI_Pairwise_Interaction::getMatrixTransProp(DenseMatrix &mat, doublereal *speciesValues ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs ); + + mat.resize(nsp, nsp, 0.0 ); + for (int i = 0; i < nsp; i++ ) + for (int j = 0; j < i; j++ ) + mat(i,j) = mat(j,i) = exp(m_Eij(i,j) / temp ) / m_Dij(i,j); + + for (int i = 0; i < nsp; i++ ) + if (mat(i,i) == 0.0 && m_diagonals[i] ) + mat(i,i) = 1.0 / m_diagonals[i]->getSpeciesTransProp() ; + } + + + void LTI_StefanMaxwell_PPN::setParameters(LiquidTransportParams& trParam ) { + int nsp = m_thermo->nSpecies(); + int nsp2 = nsp*nsp; + //vectornSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); + + return value; + } + + + doublereal LTI_StefanMaxwell_PPN::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); + + return value; + } + + void LTI_StefanMaxwell_PPN::getMatrixTransProp(DenseMatrix &mat, doublereal *speciesValues ) { + //CAL + + IonsFromNeutralVPSSTP * ions_thermo = dynamic_cast(m_thermo); + int i, j, k; + int nsp = m_thermo->nSpecies(); + if (nsp != 3) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); + } + int nsp2 = nsp*nsp; + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs ); + vector_fp neut_molefracs; + ions_thermo->getNeutralMolecMoleFractions(neut_molefracs); + vector cation; + vector anion; + ions_thermo->getCationList(cation); + ions_thermo->getAnionList(anion); + vector speciesNames; + ions_thermo->getSpeciesNames(speciesNames); + + // Reaction Coeffs and Charges + std::vector viS(6); + std::vector charges(3); + std::vector neutMolIndex(3); + ions_thermo->getDissociationCoeffs(viS,charges,neutMolIndex); + + if ((int)anion.size() != 1) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have one anion only for StefanMaxwell_PPN"); + } + if ((int)cation.size() != 2) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have two cations of equal charge for StefanMaxwell_PPN"); + } + if (charges[cation[0]] != charges[cation[1]]) { + throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN"); + } + + m_ionCondMix = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); + + MargulesVPSSTP * marg_thermo = dynamic_cast (ions_thermo->neutralMoleculePhase_); + doublereal vol = m_thermo->molarVolume(); + + k = 0; + for (j = 0; j < nsp; j++) { + for (i = 0; i < nsp; i++) { + if (m_mobRatMixModel[k]) { + m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp(m_mobRatSpecies[k] ); + if (m_mobRatMix(i,j) > 0) { + m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); + } + } + k++; + } + } + + + for (k = 0; k < nsp; k++) { + m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp(m_selfDiffSpecies[k] ); + } + + int vP = max(viS[cation[0]],viS[cation[1]]); + int vM = viS[anion[0]]; + int zP = charges[cation[0]]; + int zM = charges[anion[0]]; + doublereal xA, xB, eps; + doublereal inv_vP_vM_MutualDiff; + vector_fp dlnActCoeffdlnN; + dlnActCoeffdlnN.resize(neut_molefracs.size(),0.0); + marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); + + xA = neut_molefracs[neutMolIndex[cation[0]]]; + xB = neut_molefracs[neutMolIndex[cation[1]]]; + eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); + inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); + + mat.resize(nsp, nsp, 0.0 ); + mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; + + } + + + doublereal LTI_StokesEinstein::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_StokesEinstein::getMixTransProp does not make sense." ); + + return value; + } + + + doublereal LTI_StokesEinstein::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + throw LTPmodelError("Calling LTI_StokesEinstein::getMixTransProp does not make sense." ); + + return value; + } + + + + void LTI_StokesEinstein::setParameters(LiquidTransportParams& trParam ) { + int nsp = m_thermo->nSpecies(); + m_viscosity.resize(nsp, 0 ); + m_hydroRadius.resize(nsp, 0 ); + for (int k = 0; k < nsp; k++) { + Cantera::LiquidTransportData <d = trParam.LTData[k]; + m_viscosity[k] = ltd.viscosity; + m_hydroRadius[k] = ltd.hydroRadius; + } + } + + void LTI_StokesEinstein::getMatrixTransProp(DenseMatrix &mat, doublereal *speciesValues ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + + double *viscSpec = new double(nsp); + double *radiusSpec = new double(nsp); + + for (int k = 0; k < nsp; k++) { + viscSpec[k] = m_viscosity[k]->getSpeciesTransProp() ; + radiusSpec[k] = m_hydroRadius[k]->getSpeciesTransProp() ; + } + + mat.resize(nsp,nsp, 0.0); + for (int i = 0; i < nsp; i++) + for (int j = 0; j < nsp; j++) { + mat(i,j) = (6.0 * Pi * radiusSpec[i] * viscSpec[j] ) / GasConstant / temp; + } + delete radiusSpec; + delete viscSpec; + } + + doublereal LTI_MoleFracs_ExpT::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + //if weightings are specified, use those + if (speciesWeight ) { + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*speciesWeight[k]; + } + } + else { + throw CanteraError("LTI_MoleFracs_ExpT::getMixTransProp","You should be specifying the speciesWeight"); + } + + for (int i = 0; i < nsp; i++ ){ + value += speciesValues[i] * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); + } + } + } + + return value; + } + + + doublereal LTI_MoleFracs_ExpT::getMixTransProp(std::vector LTPptrs ) { + + int nsp = m_thermo->nSpecies(); + doublereal temp = m_thermo->temperature(); + doublereal molefracs[nsp]; + m_thermo->getMoleFractions(molefracs); + + doublereal value = 0; + + for (int k = 0; k < nsp; k++) { + molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); + } + + for (int i = 0; i < nsp; i++ ){ + value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; + for (int j = 0; j < nsp; j++ ){ + for (int k = 0; k < (int)m_Aij.size(); k++ ){ + value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); + } + } + } + return value; + } + + + +} //namespace Cantera diff --git a/Cantera/src/transport/LiquidTranInteraction.h b/Cantera/src/transport/LiquidTranInteraction.h new file mode 100644 index 000000000..f7d434c0d --- /dev/null +++ b/Cantera/src/transport/LiquidTranInteraction.h @@ -0,0 +1,685 @@ +/** + * @file LiquidTranInteraction.h + * Header file defining the class LiquidTranInteraction and classes which + * derive from LiquidTranInteraction. + */ +/* + * $Author: christopher.lueth@gmail.com $ + * $Date: 2010-03-30 12:30:39 -0600 (Tue, 30 Mar 2010) $ + * $Revision: 427 $ + * + */ +#ifndef CT_LIQUIDTRANINTERACTION_H +#define CT_LIQUIDTRANINTERACTION_H + +#include "ct_defs.h" +#include "TransportBase.h" +#include "TransportParams.h" +#include "LiquidTransportData.h" +#include "xml.h" +#include "XML_Writer.h" + +namespace Cantera { + + + //! Composition dependence type for liquid mixture transport properties + /*! + * Types of temperature dependencies: + * - 0 - Mixture calculations with this property are not allowed + * - 1 - Use solvent (species 0) properties + * - 2 - Properties weighted linearly by mole fractions + * - 3 - Properties weighted linearly by mass fractions + * - 4 - Properties weighted logarithmically by mole fractions (interaction energy weighting) + * - 5 - Interactions given pairwise between each possible species (i.e. D_ij) + * + * \verbatim + * + * + * + * + * LiCl(L) + * KCl(L) + * -1.0 + * 1.0E-1 + * -or- + * 1.0E-1, 0.001 0.01 + * + * -same form for Hij,Aij,Bij- + * + * + * + * + * + * + * Li+ + * K+ + * 1.5 + * + * + * K+ + * Cl- + * 1.0 + * + * + * Li+ + * Cl- + * 1.2 + * + * + * + * + * + * + * + * + * + * + * \endverbatim + * + */ + + enum LiquidTranMixingModel { + LTI_MODEL_NOTSET=-1, + LTI_MODEL_NONE, + LTI_MODEL_SOLVENT, + LTI_MODEL_MOLEFRACS, + LTI_MODEL_MASSFRACS, + LTI_MODEL_LOG_MOLEFRACS, + LTI_MODEL_PAIRWISE_INTERACTION, + LTI_MODEL_STEFANMAXWELL_PPN, + LTI_MODEL_STOKES_EINSTEIN, + LTI_MODEL_MOLEFRACS_EXPT + }; + + + //! Base class to handle transport property evaluation in a mixture. + /*! + * In a mixture, the mixture transport properties will generally depend on + * the contributions of each of the pure species transport properties. + * Many composition dependencies are possible. This class, + * LiquidTranInteraction, is designed to be a base class for the + * implementation of various models for the mixing of pure species + * transport properties. + * + * There are two very broad types of transport properties to consider. + * First, there are properties for which a mixture value can be + * obtained through some mixing rule. These are obtained using the + * method getMixTransProp(). Viscosity is typical of this. + * Second there are properties for which a matrix of properties may + * @param tp_ind + * exist. This matrix of properties is obtained from the method + * getMatrixTransProp(). Diffusion coefficients are of this type. + * Subclasses should implement the appropriate one or both of + * these methods. + * + */ + class LiquidTranInteraction { + + public: + //! Constructor + /** + * @param tp_ind Index indicating transport property type (i.e. viscosity) + */ + LiquidTranInteraction(TransportPropertyList tp_ind = TP_UNKNOWN); + + //! Copy constructor + LiquidTranInteraction(const LiquidTranInteraction &right); + + //! Assignment operator + LiquidTranInteraction& operator=(const LiquidTranInteraction &right ); + + //! destructor + virtual ~LiquidTranInteraction(); + + //! initialize LiquidTranInteraction objects with thermo and XML node + /** + * @param compModelNode \verbatim \endverbatim XML node + * @param thermo Pointer to thermo object + */ + virtual void init(const XML_Node &compModelNode = 0, + thermo_t* thermo = 0 ); + + virtual void setParameters( LiquidTransportParams& trParam ) { ; } + + //! Return the mixture transport property value. + //! (Must be implemented in subclasses.) + virtual doublereal getMixTransProp(doublereal* speciesValues, doublereal *weightSpecies = 0 ) { + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } + + virtual doublereal getMixTransProp(std::vector LTPptrs ) { + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } + + virtual void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ) { + //mat = m_Dij; + throw NotImplemented("LiquidTranInteraction::getMixTransProp"); + } + + protected: + //! Model for species interaction effects + //! Takes enum LiquidTranMixingModel + LiquidTranMixingModel m_model; + + //! enum indicating what property this is (i.e viscosity) + TransportPropertyList m_property; + + //! pointer to thermo object to get current temperature + thermo_t* m_thermo; + + //LiquidTransportParams* m_trParam; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of + //! speciesA (no temperature dependence, dimensionless) + std::vector m_Aij; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of + //! speciesA (linear temperature dependence, units 1/K) + std::vector m_Bij; + + //! Matrix of interactions (in energy units, 1/RT temperature dependence) + DenseMatrix m_Eij; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of + //! speciesA (in energy units, 1/RT temperature dependence) + std::vector m_Hij; + + //! Matrix of interaction coefficients for polynomial in molefraction*weight of + //! speciesA (in entropy units, divided by R) + std::vector m_Sij; + + //! Matrix of interactions + DenseMatrix m_Dij; + }; + + class LTI_Solvent : public LiquidTranInteraction { + + public: + LTI_Solvent(TransportPropertyList tp_ind = TP_UNKNOWN); + + //! Copy constructor + // LTI_Solvent( const LTI_Solvent &right ); + + //! Assignment operator + // LTI_Solvent& operator=( const LTI_Solvent &right ); + + virtual ~LTI_Solvent( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point). + */ + doublereal getMixTransProp(doublereal *valueSpecies, doublereal *weightSpecies = 0); + doublereal getMixTransProp(std::vector LTPptrs) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ + void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ); + + protected: + + }; + + //! Simple mole fraction weighting of transport properties + /** + * This model weights the transport property by the mole + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ + * \eta_{mix} = \sum_i X_i \eta_i + \sum_i \sum_j X_i X_j A_{i,j} + * \f] + */ + class LTI_MoleFracs : public LiquidTranInteraction { + + public: + LTI_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_MOLEFRACS; + } + + + //! Copy constructor + // LTI_MoleFracs( const LTI_MoleFracs &right ); + + //! Assignment operator + // LTI_MoleFracs& operator=( const LTI_MoleFracs &right ); + + virtual ~LTI_MoleFracs( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not Implemented for this Mixing rule; + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + + protected: + + }; + + + //! Simple mass fraction weighting of transport properties + /*! + * This model weights the transport property by the mass + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ + * \eta_{mix} = \sum_i Y_i \eta_i + * + \sum_i \sum_j Y_i Y_j A_{i,j} + * \f]. + */ + class LTI_MassFracs : public LiquidTranInteraction { + + public: + + LTI_MassFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_MASSFRACS; + } + + + //! Copy constructor + // LTI_MassFracs( const LTI_MassFracs &right ); + + //! Assignment operator + // LTI_MassFracs& operator=( const LTI_MassFracs &right ); + + virtual ~LTI_MassFracs( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + + protected: + + }; + + + //! Mixing rule using logarithms of the mole fractions + /** + * This model is based on the idea that liquid molecules are + * generally interacting with some energy and entropy of interaction. + * For transport properties that depend on these energies of + * interaction, the mixture transport property can be written + * in terms of its logarithm + * + * \f[ \ln \eta_{mix} = \sum_i X_i \ln \eta_i + * + \sum_i \sum_j X_i X_j ( S_{i,j} + E_{i,j} / T ) + * \f]. + * + * These additional interaction terms multiply the mixture property by + * \f[ \exp( \sum_{i} \sum_{j} X_i X_j ( S_{i,j} + E_{i,j} / T ) ) \f] + * so that the self-interaction terms \f$ S_{i,j} \f$ and + * \f$ E_{i,j} \f$ should be zero. + * + * Note that the energies and entropies of interaction should be + * a function of the composition themselves, but this is not yet + * implemented. (We might follow the input of Margules model + * thermodynamic data for the purpose of implementing this.) + * + * Sample input for this method is + * \verbatim + * + * + * + * + * + * -1.0e3 + * 80.0e-5 + * + * + * + * + * \endverbatim + */ + class LTI_Log_MoleFracs : public LiquidTranInteraction { + + public: + LTI_Log_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_LOG_MOLEFRACS; + } + + + //! Copy constructor + // LTI_Log_MoleFracs( const LTI_Log_MoleFracs &right ); + + //! Assignment operator + // LTI_Log_MoleFracs& operator=( const LTI_Log_MoleFracs &right ); + + virtual ~LTI_Log_MoleFracs( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not implemented for this mixing rule. + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } + + protected: + + }; + + + //! Transport properties that act like pairwise interactions + //! as in binary diffusion coefficients. + /** + * This class holds parameters for transport properties expressed + * as a matrix of pairwise interaction parameters. + * Input can be provided for constant or Arrhenius forms of the + * separate parameters. + * + * Sample input for this method is + * \verbatim + * + * + * + * + * 1.0e-8 + * 24.0e6 + * + * + * + * + * \endverbatim + * + */ + class LTI_Pairwise_Interaction : public LiquidTranInteraction { + + public: + LTI_Pairwise_Interaction( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_PAIRWISE_INTERACTION; + } + + + //! Copy constructor + // LTI_Pairwise_Interaction( const LTI_Pairwise_Interaction &right ); + + //! Assignment operator + // LTI_Pairwise_Interaction& operator=( const LTI_Pairwise_Interaction &right ); + + virtual ~LTI_Pairwise_Interaction( ) { } + + void setParameters( LiquidTransportParams& trParam ) ; + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; + protected: + + std::vector m_diagonals; + }; + + + //! Stefan Maxwell Diffusion Coefficients can be solved for given + //! ion conductivity, mobility ratios, and self diffusion coeffs. + //! This class is only valid for a common anion mixture of two + //! salts with cations of equal charge. Hence the name _PPN. + /** + * + * This class requres you specify + * + * 1 - ion conductivity + * + * 2 - mobility ratio of the two cations (set all other ratios to zero) + * + * 3 - Self diffusion coefficients of the cations (set others to zero) + * is used to calculate the "mutual diffusion coefficient". The + * approximation needed to do so requires the cations have equal charge. + * + * We than calculate the Stefan Maxwell Diffusion Coefficients by + * \f[ + * \frac{1}{D_{12}} = (1-\epsilon X_A)(1+\epsilon X_B) + * \frac{\nu_- + \nu_+}{\nu_-\nu_+^2D} + * + \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * \f[ + * \frac{1}{D_{12}} = -\epsilon X_B(1-\epsilon X_A) + * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} + * - \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * \f[ + * \frac{1}{D_{23}} = \epsilon X_A(1+\epsilon X_B) + * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} + * - \frac{z_-z_+ F^2}{\kappa V R T} + * \f] + * where F is Faraday's constant, RT is the gas constant times the + * tempurature, and V is the molar volume (basis is moles of ions) that is + * calculated by the thermophase member. X_A and X_B are the mole fractions + * of the salts composed of cation(1) and cation(2), respectively, that share + * a common anion(3). \f$\nu_{+,-}\f$ are the stoichiometric coefficients in + * the dissociation reaction of the salts to the ions with charges of + * \f$z_{+,-}\f$. Assuming that the cations have equal charge, the "mutual + * diffusion coefficient" is calculated using the cation self diffusion + * coefficients. + * \f[ + * \frac{1}{\nu_-\nu_+D} = \left(1+\frac{\partial \gamma_B}{\partial N_B} + * \right)\frac{X_A}{D_2^*}+\left(1+\frac{\partial \gamma_A}{\partial N_A} + * \right)\frac{X_B}{D_1^*} + * \f] + * where the self diffusion coefficients, \f$D_i^*\f$, are temperature and + * composition parameterized inputs and the derivative of the activity + * coefficient, \f$\frac{\partial \gamma_B}{\partial N_B}\f$, is calculated + * by the thermophase member using the excess enthalpy and entropy upon mixing. + * + * Finally, the deviation of the transferrence numbers from ideality, + * \f$\epsilon\f$, is calculated from the mobility ratio of the cations. + * \f[ + * \epsilon = \frac{1-b_2/b_1}{X_A+X_Bb_2/b_1} + * \f] + * Where \f$b_i\f$ are the mobilities of the two cations. Everywhere, + * cation 1 corresponds with salt A and cation 2 with salt B. + * + * Sample input for this method is + * \verbatim + * + * + * + * + * + * + * \endverbatim + * + */ + class LTI_StefanMaxwell_PPN : public LiquidTranInteraction { + + public: + LTI_StefanMaxwell_PPN( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_STEFANMAXWELL_PPN; + } + + + //! Copy constructor + // LTI_StefanMaxwell_PPN( const LTI_StefanMaxwell_PPN &right ); + + //! Assignment operator + // LTI_StefanMaxwell_PPN& operator=( const LTI_StefanMaxwell_PPN &right ); + + virtual ~LTI_StefanMaxwell_PPN( ) { } + + void setParameters( LiquidTransportParams& trParam ) ; + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; + + protected: + + doublereal m_ionCondMix; + LiquidTranInteraction * m_ionCondMixModel; + std::vector m_ionCondSpecies; + typedef std::vector LTPvector; + DenseMatrix m_mobRatMix; + std::vector m_mobRatMixModel; + std::vector m_mobRatSpecies; + + std::vector m_selfDiffMixModel; + vector_fp m_selfDiffMix; + std::vector m_selfDiffSpecies; + }; + + + class LTI_StokesEinstein : public LiquidTranInteraction { + + public: + LTI_StokesEinstein( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_STOKES_EINSTEIN; + } + + + //! Copy constructor + // LTI_StokesEinstein( const LTI_StokesEinstein &right ); + + //! Assignment operator + // LTI_StokesEinstein& operator=( const LTI_StokesEinstein &right ); + + virtual ~LTI_StokesEinstein( ) { } + + void setParameters( LiquidTransportParams& trParam ); + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; + protected: + + std::vector m_viscosity; + std::vector m_hydroRadius; + + }; + + //! Simple mole fraction weighting of transport properties + /** + * This model weights the transport property by the mole + * fractions. + * The overall formula for the mixture viscosity is + * + * \f[ \eta_{mix} = \sum_i X_i \eta_i + * + \sum_i \sum_j X_i X_j A_{i,j} \f]. + */ + class LTI_MoleFracs_ExpT : public LiquidTranInteraction { + + public: + LTI_MoleFracs_ExpT( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LiquidTranInteraction( tp_ind ) + { + m_model = LTI_MODEL_MOLEFRACS_EXPT; + } + + + //! Copy constructor + // LTI_MoleFracs_ExpT( const LTI_MoleFracs_ExpT &right ); + + //! Assignment operator + // LTI_MoleFracs_ExpT& operator=( const LTI_MoleFracs_ExpT &right ); + + virtual ~LTI_MoleFracs_ExpT( ) { } + + //! Return the mixture transport property value. + /** + * Takes the separate species transport properties + * as input (this method does not know what + * transport property it is at this point. + */ + doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp( std::vector LTPptrs ) ; + + //! Return the matrix of binary interaction parameters. + /** + * Takes the proper mixing rule for the binary interaction parameters + * and calculates them: Not Implemented for this mixing rule + */ + void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + + protected: + + }; + +} + +#endif diff --git a/Cantera/src/transport/LiquidTransportParams.cpp b/Cantera/src/transport/LiquidTransportParams.cpp index f0c587060..73323b97e 100644 --- a/Cantera/src/transport/LiquidTransportParams.cpp +++ b/Cantera/src/transport/LiquidTransportParams.cpp @@ -19,213 +19,30 @@ using namespace std; namespace Cantera { - /** - * Exception thrown if an error is encountered while reading the - * transport database. - */ - class LTPError : public CanteraError { - public: - LTPError( std::string msg ) - : CanteraError("LTPspecies", - "error parsing transport data: " - + msg + "\n") {} - }; - - /** - * Exception thrown if an error is encountered while reading the - * transport database. - */ + //==================================================================================================================== + //! Exception thrown if an error is encountered while reading the transport database. class LTPmodelError : public CanteraError { public: - LTPmodelError( std::string msg ) - : CanteraError("LTPspecies", - "error parsing transport data: " - + msg + "\n") {} + LTPmodelError(std::string msg) : + CanteraError("LTPspecies", "error parsing transport data: " + msg + "\n") + { + } }; - - - // Constructor - /* - * @param tp_ind Index indicating transport property type (i.e. viscosity) - */ - LiquidTranInteraction::LiquidTranInteraction( TransportPropertyList tp_ind ) : - m_model(LTI_MODEL_NOTSET), - m_property(tp_ind) - { - } - - LiquidTranInteraction::~LiquidTranInteraction(){ - int kmax = m_Aij.size(); - for ( int k = 0; k < kmax; k++) - if ( m_Aij[k] ) delete m_Aij[k]; - kmax = m_Bij.size(); - for ( int k = 0; k < kmax; k++) - if ( m_Bij[k] ) delete m_Bij[k]; - kmax = m_Hij.size(); - for ( int k = 0; k < kmax; k++) - if ( m_Hij[k] ) delete m_Hij[k]; - kmax = m_Sij.size(); - for ( int k = 0; k < kmax; k++) - if ( m_Sij[k] ) delete m_Sij[k]; - } - - - void LiquidTranInteraction::init( const XML_Node &compModelNode, - thermo_t* thermo ) - { - - doublereal poly0; - m_thermo = thermo; - - int nsp = thermo->nSpecies(); - m_Dij.resize( nsp, nsp, 0.0 ); - m_Eij.resize( nsp, nsp, 0.0 ); - /* - m_Aij.resize( nsp); - m_Bij.resize( nsp); - m_Hij.resize( nsp); - m_Sij.resize( nsp); - for ( int k = 0; k < nsp; k++ ){ - (*m_Aij[k]).resize( nsp, nsp, 0.0); - (*m_Bij[k]).resize( nsp, nsp, 0.0); - (*m_Hij[k]).resize( nsp, nsp, 0.0); - (*m_Sij[k]).resize( nsp, nsp, 0.0); - } - */ - - std::string speciesA; - std::string speciesB; - - int num = compModelNode.nChildren(); - for (int iChild = 0; iChild < num; iChild++) { - XML_Node &xmlChild = compModelNode.child(iChild); - std::string nodeName = lowercase( xmlChild.name() ); - if ( nodeName != "interaction" ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "expected element and got <" + nodeName + ">" ); - speciesA = xmlChild.attrib("speciesA"); - speciesB = xmlChild.attrib("speciesB"); - int iSpecies = m_thermo->speciesIndex( speciesA ); - if ( iSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesA ); - int jSpecies = m_thermo->speciesIndex( speciesB ); - if ( jSpecies < 0 ) - throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", - "Unknown species " + speciesB ); - /* if ( xmlChild.hasChild( "Aij" ) ) { - m_Aij(iSpecies,jSpecies) = getFloat( xmlChild, "Aij", "toSI" ); - m_Aij(jSpecies,iSpecies) = m_Aij(iSpecies,jSpecies) ; - }*/ - - if ( xmlChild.hasChild( "Eij" ) ) { - m_Eij(iSpecies,jSpecies) = getFloat( xmlChild, "Eij", "actEnergy" ); - m_Eij(iSpecies,jSpecies) /= GasConstant; - m_Eij(jSpecies,iSpecies) = m_Eij(iSpecies,jSpecies) ; - } - - if ( xmlChild.hasChild( "Aij" ) ) { - vector_fp poly; - poly0 = getFloat( poly, xmlChild, "Aij", "toSI" ); - if ( !poly.size() ) poly.push_back(poly0); - while (m_Aij.size()resize( nsp, nsp, 0.0); - m_Aij.push_back(aTemp); - } - for( int i=0; i<(int)poly.size(); i++ ){ - (*m_Aij[i])(iSpecies,jSpecies) = poly[i]; - //(*m_Aij[i])(jSpecies,iSpecies) = (*m_Aij[i])(iSpecies,jSpecies) ; - } - } - - if ( xmlChild.hasChild( "Bij" ) ) { - vector_fp poly; - poly0 = getFloat( poly, xmlChild, "Bij", "toSI" ); - if ( !poly.size() ) poly.push_back(poly0); - while (m_Bij.size()resize( nsp, nsp, 0.0); - m_Bij.push_back(bTemp); - } - for( int i=0; i<(int)poly.size(); i++ ){ - (*m_Bij[i])(iSpecies,jSpecies) = poly[i]; - //(*m_Bij[i])(jSpecies,iSpecies) = (*m_Bij[i])(iSpecies,jSpecies) ; - } - } - - if ( xmlChild.hasChild( "Hij" ) ) { - vector_fp poly; - poly0 = getFloat( poly, xmlChild, "Hij", "actEnergy" ); - if ( !poly.size() ) poly.push_back(poly0); - while (m_Hij.size()resize( nsp, nsp, 0.0); - m_Hij.push_back(hTemp); - } - for( int i=0; i<(int)poly.size(); i++ ){ - (*m_Hij[i])(iSpecies,jSpecies) = poly[i]; - (*m_Hij[i])(iSpecies,jSpecies) /= GasConstant; - //(*m_Hij[i])(jSpecies,iSpecies) = (*m_Hij[i])(iSpecies,jSpecies) ; - } - } - - if ( xmlChild.hasChild( "Sij" ) ) { - vector_fp poly; - poly0 = getFloat( poly, xmlChild, "Sij", "actEnergy" ); - if ( !poly.size() ) poly.push_back(poly0); - while (m_Sij.size()resize( nsp, nsp, 0.0); - m_Sij.push_back(sTemp); - } - for( int i=0; i<(int)poly.size(); i++ ){ - (*m_Sij[i])(iSpecies,jSpecies) = poly[i]; - (*m_Sij[i])(iSpecies,jSpecies) /= GasConstant; - //(*m_Sij[i])(jSpecies,iSpecies) = (*m_Sij[i])(iSpecies,jSpecies) ; - } - } - - /*0 if ( xmlChild.hasChild( "Sij" ) ) { - m_Sij(iSpecies,jSpecies) = getFloat( xmlChild, "Sij", "toSI" ); - m_Sij(iSpecies,jSpecies) /= GasConstant; - //m_Sij(jSpecies,iSpecies) = m_Sij(iSpecies,jSpecies) ; - }*/ - - if ( xmlChild.hasChild( "Dij" ) ) { - m_Dij(iSpecies,jSpecies) = getFloat( xmlChild, "Dij", "toSI" ); - m_Dij(jSpecies,iSpecies) = m_Dij(iSpecies,jSpecies) ; - } - } - } - - // Copy constructor - LiquidTranInteraction::LiquidTranInteraction( const LiquidTranInteraction &right ) { - *this = right; //use assignment operator to do other work - } - - // Assignment operator - LiquidTranInteraction& LiquidTranInteraction::operator=( const LiquidTranInteraction &right ) - { - if (&right != this) { - m_model = right.m_model; - m_property = right.m_property; - m_thermo = right.m_thermo; - //m_trParam = right.m_trParam; - m_Aij = right.m_Aij; - m_Bij = right.m_Bij; - m_Eij = right.m_Eij; - m_Hij = right.m_Hij; - m_Sij = right.m_Sij; - m_Dij = right.m_Dij; - } - return *this; - } - //==================================================================================================================== LiquidTransportParams::LiquidTransportParams() : - viscosity(0), ionConductivity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), - model_speciesDiffusivity(LTI_MODEL_NOTSET), model_hydroradius(LTI_MODEL_NOTSET) + TransportParams(), + LTData(0), + viscosity(0), + ionConductivity(0), + mobilityRatio(0), + selfDiffusion(0), + thermalCond(0), + speciesDiffusivity(0), + electCond(0), + hydroRadius(0), + model_viscosity(LTI_MODEL_NOTSET), + model_speciesDiffusivity(LTI_MODEL_NOTSET), + model_hydroradius(LTI_MODEL_NOTSET) { } @@ -239,15 +56,21 @@ namespace Cantera { delete electCond; delete hydroRadius; } - //==================================================================================================================== LiquidTransportParams::LiquidTransportParams(const LiquidTransportParams &right) : - viscosity(0), thermalCond(0), speciesDiffusivity(0), electCond(0), hydroRadius(0), model_viscosity(LTI_MODEL_NOTSET), - model_speciesDiffusivity(LTI_MODEL_NOTSET), model_hydroradius(LTI_MODEL_NOTSET) + TransportParams(), + LTData(0), + viscosity(0), + thermalCond(0), + speciesDiffusivity(0), + electCond(0), + hydroRadius(0), + model_viscosity(LTI_MODEL_NOTSET), + model_speciesDiffusivity(LTI_MODEL_NOTSET), + model_hydroradius(LTI_MODEL_NOTSET) { - throw CanteraError("LiquidTransportParams(const LiquidTransportParams &right)","not implemented"); + operator=(right); } - //==================================================================================================================== LiquidTransportParams& LiquidTransportParams::operator=(const LiquidTransportParams & right) @@ -256,631 +79,50 @@ namespace Cantera { return *this; } - throw CanteraError("LiquidTransportParams(const LiquidTransportParams &right)","not implemented"); + LTData = right.LTData; + + delete viscosity; + if (right.viscosity) { + viscosity = new LiquidTranInteraction(*(right.viscosity)); + } + delete ionConductivity; + if (right.ionConductivity) { + ionConductivity = new LiquidTranInteraction(*(right.ionConductivity)); + } + deepStdVectorPointerCopy(right.mobilityRatio, mobilityRatio); + deepStdVectorPointerCopy(right.selfDiffusion, selfDiffusion); + + delete thermalCond; + if (right.thermalCond) { + thermalCond = new LiquidTranInteraction(*(right.thermalCond)); + } + delete speciesDiffusivity; + if (right.speciesDiffusivity) { + speciesDiffusivity = new LiquidTranInteraction(*(right.speciesDiffusivity)); + } + + delete electCond; + if (right.electCond) { + electCond = new LiquidTranInteraction(*(right.electCond)); + } + delete hydroRadius; + if (right.hydroRadius) { + hydroRadius = new LiquidTranInteraction(*(right.hydroRadius)); + } + model_viscosity = right.model_viscosity; + model_ionConductivity = right.model_ionConductivity; + deepStdVectorPointerCopy(right.model_mobilityRatio, model_mobilityRatio); + deepStdVectorPointerCopy(right.model_selfDiffusion, model_selfDiffusion); + thermalCond_Aij = right.thermalCond_Aij; + model_speciesDiffusivity = right.model_speciesDiffusivity; + diff_Dij = right.diff_Dij; + model_hydroradius = right.model_hydroradius; + radius_Aij = right.radius_Aij; + + throw CanteraError("LiquidTransportParams(const LiquidTransportParams &right)", "not tested"); + return *this; - } - //==================================================================================================================== - - - doublereal LTI_Solvent::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]; - // should be: molefracs[k] = molefracs[k]*speciesWeight[k]; for consistency, but weight(solvent)=1? - } - } - else { - throw CanteraError("LTI_Solvent::getMixTransProp","You should be specifying the speciesWeight"); - /* //This does not follow directly a solvent model - //although if the solvent mole fraction is dominant - //and the other species values are given or zero, - //it should work. - for ( int k = 0; k < nsp; k++) { - value += speciesValues[k] * molefracs[k]; - }*/ - } - - for ( int i = 0; i < nsp; i++ ){ - //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. - value += speciesValues[i] * speciesWeight[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); - } } - } - - return value; - } - - - doublereal LTI_Solvent::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]; - // should be: molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); for consistency, but weight(solvent)=1? - } - - for ( int i = 0; i < nsp; i++ ){ - //presume that the weighting is set to 1.0 for solvent and 0.0 for everything else. - value += LTPptrs[i]->getSpeciesTransProp() * LTPptrs[i]->getMixWeight(); - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); - } - } - } - - return value; - } - - - - - - doublereal LTI_MoleFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*speciesWeight[k]; - } - } - else { - throw CanteraError("LTI_MoleFracs::getMixTransProp","You should be specifying the speciesWeight"); - } - - for ( int i = 0; i < nsp; i++ ){ - value += speciesValues[i] * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); - } - } - } - - return value; - } - - - doublereal LTI_MoleFracs::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); - } - - for ( int i = 0; i < nsp; i++ ){ - value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Bij[k])(i,j)*temp*pow(molefracs[i],k); - } - } - } - return value; - } - - - doublereal LTI_MassFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal massfracs[nsp]; - m_thermo->getMassFractions(massfracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - massfracs[k] = massfracs[k]*speciesWeight[k]; - } - } - else { - throw CanteraError("LTI_MassFracs::getMixTransProp","You should be specifying the speciesWeight"); - } - - for ( int i = 0; i < nsp; i++ ){ - value += speciesValues[i] * massfracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); - } - } - } - - return value; - } - - - doublereal LTI_MassFracs::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal massfracs[nsp]; - m_thermo->getMassFractions(massfracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - massfracs[k] = massfracs[k]*LTPptrs[k]->getMixWeight(); - } - - for ( int i = 0; i < nsp; i++ ){ - value += LTPptrs[i]->getSpeciesTransProp() * massfracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += massfracs[i]*massfracs[j]*(*m_Aij[k])(i,j)*pow(massfracs[i],k); - } - for ( int k = 0; k < (int)m_Bij.size(); k++ ){ - value += massfracs[i]*massfracs[j]*(*m_Bij[k])(i,j)*temp*pow(massfracs[i],k); - } - } - } - - return value; - } - - - - - doublereal LTI_Log_MoleFracs::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*speciesWeight[k]; - } - } - else{ - throw CanteraError("LTI_Log_MoleFracs::getMixTransProp","You probably should have a speciesWeight when you call getMixTransProp to convert ion mole fractions to molecular mole fractions"); - } - - for ( int i = 0; i < nsp; i++ ){ - value += log( speciesValues[i] ) * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Hij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); - //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; - } - for ( int k = 0; k < (int)m_Sij.size(); k++ ){ - value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); - //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; - } - } - } - - value = exp( value ); - return value; - } - - - doublereal LTI_Log_MoleFracs::getMixTransProp(std::vector LTPptrs) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - - doublereal value = 0; - - //if weightings are specified, use those - - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight( ); - } - - for ( int i = 0; i < nsp; i++ ){ - value += log( LTPptrs[i]->getSpeciesTransProp() ) * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Hij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Hij[k])(i,j)/temp*pow(molefracs[i],k); - //cout << "1 = " << molefracs[i]+molefracs[j] << endl; - //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; - } - for ( int k = 0; k < (int)m_Sij.size(); k++ ){ - value -= molefracs[i]*molefracs[j]*(*m_Sij[k])(i,j)*pow(molefracs[i],k); - //cout << "1 = " << molefracs[i]+molefracs[j] << endl; - //cout << "value = " << value << ", m_Sij = " << (*m_Sij[k])(i,j) << ", m_Hij = " << (*m_Hij[k])(i,j) << endl; - } - } - } - - value = exp( value ); - // cout << ", viscSpeciesA = " << LTPptrs[0]->getSpeciesTransProp() << endl; - //cout << ", viscSpeciesB = " << LTPptrs[1]->getSpeciesTransProp() << endl; - //cout << "value = " << value << " FINAL" << endl; - return value; - } - - - - - - void LTI_Pairwise_Interaction::setParameters(LiquidTransportParams& trParam) { - int nsp = m_thermo->nSpecies(); - m_diagonals.resize(nsp, 0); - - for (int k = 0; k < nsp; k++) { - Cantera::LiquidTransportData <d = trParam.LTData[k]; - if (ltd.speciesDiffusivity) - m_diagonals[k] = ltd.speciesDiffusivity; - } - } - - doublereal LTI_Pairwise_Interaction::getMixTransProp(doublereal *speciesValues, doublereal *speciesWeight) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_Pairwise_Interaction::getMixTransProp does not make sense." ); - - return value; - } - - - doublereal LTI_Pairwise_Interaction::getMixTransProp(std::vector LTPptrs) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_Pairwise_Interaction::getMixTransProp does not make sense." ); - - return value; - } - - void LTI_Pairwise_Interaction::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions( molefracs ); - - mat.resize( nsp, nsp, 0.0 ); - for ( int i = 0; i < nsp; i++ ) - for ( int j = 0; j < i; j++ ) - mat(i,j) = mat(j,i) = exp( m_Eij(i,j) / temp ) / m_Dij(i,j); - - for ( int i = 0; i < nsp; i++ ) - if ( mat(i,i) == 0.0 && m_diagonals[i] ) - mat(i,i) = 1.0 / m_diagonals[i]->getSpeciesTransProp() ; - } - - - void LTI_StefanMaxwell_PPN::setParameters( LiquidTransportParams& trParam ) { - int nsp = m_thermo->nSpecies(); - int nsp2 = nsp*nsp; - //vectornSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); - - return value; - } - - - doublereal LTI_StefanMaxwell_PPN::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_StefanMaxwell_PPN::getMixTransProp does not make sense." ); - - return value; - } - - void LTI_StefanMaxwell_PPN::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { - //CAL - - IonsFromNeutralVPSSTP * ions_thermo = dynamic_cast(m_thermo); - int i, j, k; - int nsp = m_thermo->nSpecies(); - if (nsp != 3) { - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); - } - int nsp2 = nsp*nsp; - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions( molefracs ); - vector_fp neut_molefracs; - ions_thermo->getNeutralMolecMoleFractions(neut_molefracs); - vector cation; - vector anion; - ions_thermo->getCationList(cation); - ions_thermo->getAnionList(anion); - vector speciesNames; - ions_thermo->getSpeciesNames(speciesNames); - - // Reaction Coeffs and Charges - std::vector viS(6); - std::vector charges(3); - std::vector neutMolIndex(3); - ions_thermo->getDissociationCoeffs(viS,charges,neutMolIndex); - - if ((int)anion.size() != 1) { - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have one anion only for StefanMaxwell_PPN"); - } - if ((int)cation.size() != 2) { - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Must have two cations of equal charge for StefanMaxwell_PPN"); - } - if (charges[cation[0]] != charges[cation[1]]) { - throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Cations must be of equal charge for StefanMaxwell_PPN"); - } - - m_ionCondMix = m_ionCondMixModel->getMixTransProp(m_ionCondSpecies); - - MargulesVPSSTP * marg_thermo = dynamic_cast (ions_thermo->neutralMoleculePhase_); - doublereal vol = m_thermo->molarVolume(); - - k = 0; - for (j = 0; j < nsp; j++) { - for (i = 0; i < nsp; i++) { - if (m_mobRatMixModel[k]) { - m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp( m_mobRatSpecies[k] ); - if (m_mobRatMix(i,j) > 0) { - m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); - } - } - k++; - } - } - - - for (k = 0; k < nsp; k++) { - m_selfDiffMix[k] = m_selfDiffMixModel[k]->getMixTransProp( m_selfDiffSpecies[k] ); - } - - int vP = max(viS[cation[0]],viS[cation[1]]); - int vM = viS[anion[0]]; - int zP = charges[cation[0]]; - int zM = charges[anion[0]]; - doublereal xA, xB, eps; - doublereal inv_vP_vM_MutualDiff; - vector_fp dlnActCoeffdlnN; - dlnActCoeffdlnN.resize(neut_molefracs.size(),0.0); - marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); - - xA = neut_molefracs[neutMolIndex[cation[0]]]; - xB = neut_molefracs[neutMolIndex[cation[1]]]; - eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); - inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); - - mat.resize( nsp, nsp, 0.0 ); - mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; - mat(cation[0],anion[0]) = mat(anion[0],cation[0]) = (1+vP/vM)*(-eps*xB*(1-eps*xA)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; - mat(cation[1],anion[0]) = mat(anion[0],cation[1]) = (1+vP/vM)*(eps*xA*(1+eps*xB)*inv_vP_vM_MutualDiff)-zP*zM*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; - - } - - - doublereal LTI_StokesEinstein::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_StokesEinstein::getMixTransProp does not make sense." ); - - return value; - } - - - doublereal LTI_StokesEinstein::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - throw LTPmodelError( "Calling LTI_StokesEinstein::getMixTransProp does not make sense." ); - - return value; - } - - - - void LTI_StokesEinstein::setParameters( LiquidTransportParams& trParam ) { - int nsp = m_thermo->nSpecies(); - m_viscosity.resize( nsp, 0 ); - m_hydroRadius.resize( nsp, 0 ); - for (int k = 0; k < nsp; k++) { - Cantera::LiquidTransportData <d = trParam.LTData[k]; - m_viscosity[k] = ltd.viscosity; - m_hydroRadius[k] = ltd.hydroRadius; - } - } - - void LTI_StokesEinstein::getMatrixTransProp( DenseMatrix &mat, doublereal *speciesValues ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - - double *viscSpec = new double(nsp); - double *radiusSpec = new double(nsp); - - for (int k = 0; k < nsp; k++) { - viscSpec[k] = m_viscosity[k]->getSpeciesTransProp() ; - radiusSpec[k] = m_hydroRadius[k]->getSpeciesTransProp() ; - } - - mat.resize(nsp,nsp, 0.0); - for (int i = 0; i < nsp; i++) - for (int j = 0; j < nsp; j++) { - mat(i,j) = ( 6.0 * Pi * radiusSpec[i] * viscSpec[j] ) / GasConstant / temp; - } - delete radiusSpec; - delete viscSpec; - } - - doublereal LTI_MoleFracs_ExpT::getMixTransProp( doublereal *speciesValues, doublereal *speciesWeight ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - //if weightings are specified, use those - if ( speciesWeight ) { - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*speciesWeight[k]; - } - } - else { - throw CanteraError("LTI_MoleFracs_ExpT::getMixTransProp","You should be specifying the speciesWeight"); - } - - for ( int i = 0; i < nsp; i++ ){ - value += speciesValues[i] * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); - } - } - } - - return value; - } - - - doublereal LTI_MoleFracs_ExpT::getMixTransProp( std::vector LTPptrs ) { - - int nsp = m_thermo->nSpecies(); - doublereal temp = m_thermo->temperature(); - doublereal molefracs[nsp]; - m_thermo->getMoleFractions(molefracs); - - doublereal value = 0; - - for ( int k = 0; k < nsp; k++) { - molefracs[k] = molefracs[k]*LTPptrs[k]->getMixWeight(); - } - - for ( int i = 0; i < nsp; i++ ){ - value += LTPptrs[i]->getSpeciesTransProp() * molefracs[i]; - for ( int j = 0; j < nsp; j++ ){ - for ( int k = 0; k < (int)m_Aij.size(); k++ ){ - value += molefracs[i]*molefracs[j]*(*m_Aij[k])(i,j)*pow(molefracs[i],k)*exp((*m_Bij[k])(i,j)*temp); - } - } - } - return value; - } - - - } //namespace Cantera diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index ba68fcd2a..eaf1a795d 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -13,25 +13,21 @@ #ifndef CT_LIQUIDTRANSPORTPARAMS_H #define CT_LIQUIDTRANSPORTPARAMS_H -#include - #include "ct_defs.h" #include "TransportBase.h" #include "TransportParams.h" #include "LiquidTransportData.h" +#include "LiquidTranInteraction.h" #include "xml.h" #include "XML_Writer.h" + +#include + + namespace Cantera { - class NotImplemented : public CanteraError { - public: - NotImplemented(std::string method) : CanteraError("Transport", - "\n\n**** Method "+method+" not implemented. ****\n" - "(Did you forget to specify a transport model?)\n\n") {} - }; - //! Composition dependence type for liquid mixture transport properties /*! @@ -89,137 +85,45 @@ namespace Cantera { * */ - enum LiquidTranMixingModel { - LTI_MODEL_NOTSET=-1, - LTI_MODEL_NONE, - LTI_MODEL_SOLVENT, - LTI_MODEL_MOLEFRACS, - LTI_MODEL_MASSFRACS, - LTI_MODEL_LOG_MOLEFRACS, - LTI_MODEL_PAIRWISE_INTERACTION, - LTI_MODEL_STEFANMAXWELL_PPN, - LTI_MODEL_STOKES_EINSTEIN, - LTI_MODEL_MOLEFRACS_EXPT - }; - - //! Base class to handle transport property evaluation in a mixture. - /** - * In a mixture, the mixture transport properties will generally depend on - * the contributions of each of the pure species transport properties. - * Many composition dependencies are possible. This class, - * LiquidTranInteraction, is designed to be a base class for the - * implementation of various models for the mixing of pure species - * transport properties. - * - * There are two very broad types of transport properties to consider. - * First, there are properties for which a mixture value can be - * obtained through some mixing rule. These are obtained using the - * method getMixTransProp(). Viscosity is typical of this. - * Second there are properties for which a matrix of properties may - * @param tp_ind - * exist. This matrix of properties is obtained from the method - * getMatrixTransProp(). Diffusion coefficients are of this type. - * Subclasses should implement the appropriate one or both of - * these methods. - * - */ - class LiquidTranInteraction { - - public: - //! Constructor - /** - * @param tp_ind Index indicating transport property type (i.e. viscosity) - */ - LiquidTranInteraction( TransportPropertyList tp_ind = TP_UNKNOWN ); - - //! Copy constructor - LiquidTranInteraction( const LiquidTranInteraction &right ); - - //! Assignment operator - LiquidTranInteraction& operator=( const LiquidTranInteraction &right ); - - //! destructor - virtual ~LiquidTranInteraction(); - //! initialize LiquidTranInteraction objects with thermo and XML node - /** - * @param compModelNode \verbatim \endverbatim XML node - * @param thermo Pointer to thermo object - */ - virtual void init( const XML_Node &compModelNode = 0, - thermo_t* thermo = 0 ); - - virtual void setParameters( LiquidTransportParams& trParam ) { ; } - - //! Return the mixture transport property value. - //! (Must be implemented in subclasses.) - virtual doublereal getMixTransProp( doublereal* speciesValues, doublereal *weightSpecies = 0 ) { - throw NotImplemented("LiquidTranInteraction::getMixTransProp"); - } - - virtual doublereal getMixTransProp( std::vector LTPptrs ) { - throw NotImplemented("LiquidTranInteraction::getMixTransProp"); - } - - virtual void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { - //mat = m_Dij; - throw NotImplemented("LiquidTranInteraction::getMixTransProp"); - } - - protected: - //! Model for species interaction effects - //! Takes enum LiquidTranMixingModel - LiquidTranMixingModel m_model; - - //! enum indicating what property this is (i.e viscosity) - TransportPropertyList m_property; - - //! pointer to thermo object to get current temperature - thermo_t* m_thermo; - - //LiquidTransportParams* m_trParam; - - //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (no temperature dependence, dimensionless) - std::vector m_Aij; - - //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (linear temperature dependence, units 1/K) - std::vector m_Bij; - - //! Matrix of interactions (in energy units, 1/RT temperature dependence) - DenseMatrix m_Eij; - - //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (in energy units, 1/RT temperature dependence) - std::vector m_Hij; - - //! Matrix of interaction coefficients for polynomial in molefraction*weight of speciesA (in entropy units, divided by R) - std::vector m_Sij; - //DenseMatrix m_Sij; - - //! Matrix of interactions - DenseMatrix m_Dij; - - }; - - /** - * Class LiquidTransportParams holds transport model parameters - * relevant to transport in mixtures. - * Used by TransportFactory. + + //! Class LiquidTransportParams holds transport model parameters + //! relevant to transport in mixtures. + /*! + * This class is used by TransportFactory to initialize transport objects. */ class LiquidTransportParams : public TransportParams { public: + //! Constructor LiquidTransportParams(); + + //! Destructor ~LiquidTransportParams(); + + //! Copy constructor + /*! + * @param right Object to be copied + */ LiquidTransportParams(const LiquidTransportParams &right); + + //! Assignment operator + /*! + * @param right Object to be copied + */ LiquidTransportParams & operator=(const LiquidTransportParams &right); //! Species transport parameters std::vector LTData; + //! Object that specifies the viscosity interaction for the mixture LiquidTranInteraction* viscosity; + + //! Object that specifes the ionic Conductivity of the mixture LiquidTranInteraction* ionConductivity; + std::vector mobilityRatio; std::vector selfDiffusion; LiquidTranInteraction* thermalCond; @@ -279,501 +183,8 @@ namespace Cantera { DenseMatrix radius_Aij; }; - - class LTI_Solvent; - class LTI_MoleFracs; - class LTI_MassFracs; - class LTI_Log_MoleFracs; - class LTI_Pairwise_Interaction; - class LTI_StefanMaxwell_PPN; - class LTI_MoleFracs_ExpT; - class LTI_Solvent : public LiquidTranInteraction { + - public: - LTI_Solvent( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_SOLVENT; - } - - //! Copy constructor - // LTI_Solvent( const LTI_Solvent &right ); - - //! Assignment operator - // LTI_Solvent& operator=( const LTI_Solvent &right ); - - virtual ~LTI_Solvent( ) { } - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point). - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them: Not implemented for this mixing rule. - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } - - protected: - - }; - - //! Simple mole fraction weighting of transport properties - /** - * This model weights the transport property by the mole - * fractions. - * The overall formula for the mixture viscosity is - * - * \f[ \eta_{mix} = \sum_i X_i \eta_i - * + \sum_i \sum_j X_i X_j A_{i,j} \f]. - */ - class LTI_MoleFracs : public LiquidTranInteraction { - - public: - LTI_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_MOLEFRACS; - } - - - //! Copy constructor - // LTI_MoleFracs( const LTI_MoleFracs &right ); - - //! Assignment operator - // LTI_MoleFracs& operator=( const LTI_MoleFracs &right ); - - virtual ~LTI_MoleFracs( ) { } - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them: Not Implemented for this Mixing rule; - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } - - protected: - - }; - - - //! Simple mass fraction weighting of transport properties - /** - * This model weights the transport property by the mass - * fractions. - * The overall formula for the mixture viscosity is - * - * \f[ \eta_{mix} = \sum_i Y_i \eta_i - * + \sum_i \sum_j Y_i Y_j A_{i,j} \f]. - */ - class LTI_MassFracs : public LiquidTranInteraction { - - public: - LTI_MassFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_MASSFRACS; - } - - - //! Copy constructor - // LTI_MassFracs( const LTI_MassFracs &right ); - - //! Assignment operator - // LTI_MassFracs& operator=( const LTI_MassFracs &right ); - - virtual ~LTI_MassFracs( ) { } - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them: Not implemented for this mixing rule. - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } - - protected: - - }; - - - //! Mixing rule using logarithms of the mole fractions - /** - * This model is based on the idea that liquid molecules are - * generally interacting with some energy and entropy of interaction. - * For transport properties that depend on these energies of - * interaction, the mixture transport property can be written - * in terms of its logarithm - * - * \f[ \ln \eta_{mix} = \sum_i X_i \ln \eta_i - * + \sum_i \sum_j X_i X_j ( S_{i,j} + E_{i,j} / T ) - * \f]. - * - * These additional interaction terms multiply the mixture property by - * \f[ \exp( \sum_{i} \sum_{j} X_i X_j ( S_{i,j} + E_{i,j} / T ) ) \f] - * so that the self-interaction terms \f$ S_{i,j} \f$ and - * \f$ E_{i,j} \f$ should be zero. - * - * Note that the energies and entropies of interaction should be - * a function of the composition themselves, but this is not yet - * implemented. (We might follow the input of Margules model - * thermodynamic data for the purpose of implementing this.) - * - * Sample input for this method is - * \verbatim - * - * - * - * - * - * -1.0e3 - * 80.0e-5 - * - * - * - * - * \endverbatim - */ - class LTI_Log_MoleFracs : public LiquidTranInteraction { - - public: - LTI_Log_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_LOG_MOLEFRACS; - } - - - //! Copy constructor - // LTI_Log_MoleFracs( const LTI_Log_MoleFracs &right ); - - //! Assignment operator - // LTI_Log_MoleFracs& operator=( const LTI_Log_MoleFracs &right ); - - virtual ~LTI_Log_MoleFracs( ) { } - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them: Not implemented for this mixing rule. - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } - - protected: - - }; - - - //! Transport properties that act like pairwise interactions - //! as in binary diffusion coefficients. - /** - * This class holds parameters for transport properties expressed - * as a matrix of pairwise interaction parameters. - * Input can be provided for constant or Arrhenius forms of the - * separate parameters. - * - * Sample input for this method is - * \verbatim - * - * - * - * - * 1.0e-8 - * 24.0e6 - * - * - * - * - * \endverbatim - * - */ - class LTI_Pairwise_Interaction : public LiquidTranInteraction { - - public: - LTI_Pairwise_Interaction( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_PAIRWISE_INTERACTION; - } - - - //! Copy constructor - // LTI_Pairwise_Interaction( const LTI_Pairwise_Interaction &right ); - - //! Assignment operator - // LTI_Pairwise_Interaction& operator=( const LTI_Pairwise_Interaction &right ); - - virtual ~LTI_Pairwise_Interaction( ) { } - - void setParameters( LiquidTransportParams& trParam ) ; - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - protected: - - std::vector m_diagonals; - }; - - - //! Stefan Maxwell Diffusion Coefficients can be solved for given - //! ion conductivity, mobility ratios, and self diffusion coeffs. - //! This class is only valid for a common anion mixture of two - //! salts with cations of equal charge. Hence the name _PPN. - /** - * - * This class requres you specify - * - * 1 - ion conductivity - * - * 2 - mobility ratio of the two cations (set all other ratios to zero) - * - * 3 - Self diffusion coefficients of the cations (set others to zero) - * is used to calculate the "mutual diffusion coefficient". The - * approximation needed to do so requires the cations have equal charge. - * - * We than calculate the Stefan Maxwell Diffusion Coefficients by - * \f[ - * \frac{1}{D_{12}} = (1-\epsilon X_A)(1+\epsilon X_B) - * \frac{\nu_- + \nu_+}{\nu_-\nu_+^2D} - * + \frac{z_-z_+ F^2}{\kappa V R T} - * \f] - * \f[ - * \frac{1}{D_{12}} = -\epsilon X_B(1-\epsilon X_A) - * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} - * - \frac{z_-z_+ F^2}{\kappa V R T} - * \f] - * \f[ - * \frac{1}{D_{23}} = \epsilon X_A(1+\epsilon X_B) - * \frac{\nu_- + \nu_+}{\nu_-^2\nu_+D} - * - \frac{z_-z_+ F^2}{\kappa V R T} - * \f] - * where F is Faraday's constant, RT is the gas constant times the - * tempurature, and V is the molar volume (basis is moles of ions) that is - * calculated by the thermophase member. X_A and X_B are the mole fractions - * of the salts composed of cation(1) and cation(2), respectively, that share - * a common anion(3). \f$\nu_{+,-}\f$ are the stoichiometric coefficients in - * the dissociation reaction of the salts to the ions with charges of - * \f$z_{+,-}\f$. Assuming that the cations have equal charge, the "mutual - * diffusion coefficient" is calculated using the cation self diffusion - * coefficients. - * \f[ - * \frac{1}{\nu_-\nu_+D} = \left(1+\frac{\partial \gamma_B}{\partial N_B} - * \right)\frac{X_A}{D_2^*}+\left(1+\frac{\partial \gamma_A}{\partial N_A} - * \right)\frac{X_B}{D_1^*} - * \f] - * where the self diffusion coefficients, \f$D_i^*\f$, are temperature and - * composition parameterized inputs and the derivative of the activity - * coefficient, \f$\frac{\partial \gamma_B}{\partial N_B}\f$, is calculated - * by the thermophase member using the excess enthalpy and entropy upon mixing. - * - * Finally, the deviation of the transferrence numbers from ideality, - * \f$\epsilon\f$, is calculated from the mobility ratio of the cations. - * \f[ - * \epsilon = \frac{1-b_2/b_1}{X_A+X_Bb_2/b_1} - * \f] - * Where \f$b_i\f$ are the mobilities of the two cations. Everywhere, - * cation 1 corresponds with salt A and cation 2 with salt B. - * - * Sample input for this method is - * \verbatim - * - * - * - * - * - * - * \endverbatim - * - */ - class LTI_StefanMaxwell_PPN : public LiquidTranInteraction { - - public: - LTI_StefanMaxwell_PPN( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_STEFANMAXWELL_PPN; - } - - - //! Copy constructor - // LTI_StefanMaxwell_PPN( const LTI_StefanMaxwell_PPN &right ); - - //! Assignment operator - // LTI_StefanMaxwell_PPN& operator=( const LTI_StefanMaxwell_PPN &right ); - - virtual ~LTI_StefanMaxwell_PPN( ) { } - - void setParameters( LiquidTransportParams& trParam ) ; - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - - protected: - - doublereal m_ionCondMix; - LiquidTranInteraction * m_ionCondMixModel; - std::vector m_ionCondSpecies; - typedef std::vector LTPvector; - DenseMatrix m_mobRatMix; - std::vector m_mobRatMixModel; - std::vector m_mobRatSpecies; - - std::vector m_selfDiffMixModel; - vector_fp m_selfDiffMix; - std::vector m_selfDiffSpecies; - }; - - - class LTI_StokesEinstein : public LiquidTranInteraction { - - public: - LTI_StokesEinstein( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_STOKES_EINSTEIN; - } - - - //! Copy constructor - // LTI_StokesEinstein( const LTI_StokesEinstein &right ); - - //! Assignment operator - // LTI_StokesEinstein& operator=( const LTI_StokesEinstein &right ); - - virtual ~LTI_StokesEinstein( ) { } - - void setParameters( LiquidTransportParams& trParam ); - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; - protected: - - std::vector m_viscosity; - std::vector m_hydroRadius; - - }; - - //! Simple mole fraction weighting of transport properties - /** - * This model weights the transport property by the mole - * fractions. - * The overall formula for the mixture viscosity is - * - * \f[ \eta_{mix} = \sum_i X_i \eta_i - * + \sum_i \sum_j X_i X_j A_{i,j} \f]. - */ - class LTI_MoleFracs_ExpT : public LiquidTranInteraction { - - public: - LTI_MoleFracs_ExpT( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) - { - m_model = LTI_MODEL_MOLEFRACS_EXPT; - } - - - //! Copy constructor - // LTI_MoleFracs_ExpT( const LTI_MoleFracs_ExpT &right ); - - //! Assignment operator - // LTI_MoleFracs_ExpT& operator=( const LTI_MoleFracs_ExpT &right ); - - virtual ~LTI_MoleFracs_ExpT( ) { } - - //! Return the mixture transport property value. - /** - * Takes the separate species transport properties - * as input (this method does not know what - * transport property it is at this point. - */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; - - //! Return the matrix of binary interaction parameters. - /** - * Takes the proper mixing rule for the binary interaction parameters - * and calculates them: Not Implemented for this mixing rule - */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } - //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } - - protected: - - }; } diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index 6fa9b4734..e21d70d01 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -36,12 +36,12 @@ CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) # Base Transport Object Files TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt.o \ SolidTransport.o DustyGasTransport.o TransportBase.o WaterTransport.o \ - SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o + SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ TransportBase.h L_matrix.h TransportParams.h WaterTransport.h \ - SimpleTransport.h + SimpleTransport.h LiquidTranInteraction.h ifeq ($(do_electro),1) do_issp = 1 diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index aed521510..3ae2482ee 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -6,6 +6,10 @@ * * */ +/* + * $Revision$ + * $Date$ + */ // turn off warnings under Windows #ifdef WIN32 @@ -37,6 +41,7 @@ #include "XML_Writer.h" #include "TransportParams.h" #include "LiquidTransportParams.h" +#include "LiquidTranInteraction.h" #include "global.h" #include "IdealGasPhase.h" #include "ctml.h" @@ -342,54 +347,54 @@ namespace Cantera { transport properties are addressed by the LTPspecies returned by newLTP */ - LiquidTranInteraction* TransportFactory::newLTI( const XML_Node &trNode, - TransportPropertyList tp_ind, - LiquidTransportParams& trParam) { + LiquidTranInteraction* TransportFactory::newLTI(const XML_Node &trNode, + TransportPropertyList tp_ind, + LiquidTransportParams& trParam) { LiquidTranInteraction* lti = 0; thermo_t* thermo = trParam.thermo; std::string model = trNode["model"]; - switch ( m_LTImodelMap[model] ) { + switch (m_LTImodelMap[model] ) { case LTI_MODEL_SOLVENT: - lti = new LTI_Solvent( tp_ind ); - lti->init( trNode, thermo ); + lti = new LTI_Solvent(tp_ind); + lti->init(trNode, thermo ); break; case LTI_MODEL_MOLEFRACS: - lti = new LTI_MoleFracs( tp_ind ); - lti->init( trNode, thermo ); + lti = new LTI_MoleFracs(tp_ind ); + lti->init(trNode, thermo ); break; case LTI_MODEL_MASSFRACS: - lti = new LTI_MassFracs( tp_ind ); - lti->init( trNode, thermo ); + lti = new LTI_MassFracs(tp_ind ); + lti->init(trNode, thermo ); break; case LTI_MODEL_LOG_MOLEFRACS: - lti = new LTI_Log_MoleFracs( tp_ind ); - lti->init( trNode, thermo ); + lti = new LTI_Log_MoleFracs(tp_ind ); + lti->init(trNode, thermo ); break; case LTI_MODEL_PAIRWISE_INTERACTION: - lti = new LTI_Pairwise_Interaction( tp_ind ); - lti->init( trNode, thermo ); - lti->setParameters( trParam ); + lti = new LTI_Pairwise_Interaction(tp_ind ); + lti->init(trNode, thermo ); + lti->setParameters(trParam ); break; case LTI_MODEL_STEFANMAXWELL_PPN: - lti = new LTI_StefanMaxwell_PPN( tp_ind ); - lti->init( trNode, thermo ); - lti->setParameters( trParam ); + lti = new LTI_StefanMaxwell_PPN(tp_ind ); + lti->init(trNode, thermo ); + lti->setParameters(trParam ); break; case LTI_MODEL_STOKES_EINSTEIN: - lti = new LTI_StokesEinstein( tp_ind ); - lti->init( trNode, thermo ); - lti->setParameters( trParam ); + lti = new LTI_StokesEinstein(tp_ind ); + lti->init(trNode, thermo ); + lti->setParameters(trParam ); break; case LTI_MODEL_MOLEFRACS_EXPT: - lti = new LTI_MoleFracs_ExpT( tp_ind ); - lti->init( trNode, thermo ); + lti = new LTI_MoleFracs_ExpT(tp_ind ); + lti->init(trNode, thermo ); break; default: // throw CanteraError("newLTI","unknown transport model: " + model ); - lti = new LiquidTranInteraction( tp_ind ); - lti->init( trNode, thermo ); + lti = new LiquidTranInteraction(tp_ind ); + lti->init(trNode, thermo ); } return lti; } @@ -1002,7 +1007,7 @@ namespace Cantera { switch (m_tranPropMap[nodeName]) { case TP_VISCOSITY: - data.viscosity = newLTP(xmlChild, name, m_tranPropMap[nodeName], temp_thermo ); + data.viscosity = newLTP(xmlChild, name, m_tranPropMap[nodeName], temp_thermo); break; case TP_IONCONDUCTIVITY: data.ionConductivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], temp_thermo); @@ -1034,25 +1039,25 @@ namespace Cantera { data.thermalCond = newLTP(xmlChild, name, m_tranPropMap[nodeName], - temp_thermo ); + temp_thermo); break; case TP_DIFFUSIVITY: data.speciesDiffusivity = newLTP(xmlChild, name, m_tranPropMap[nodeName], - temp_thermo ); + temp_thermo); break; case TP_HYDRORADIUS: data.hydroRadius = newLTP(xmlChild, name, m_tranPropMap[nodeName], - temp_thermo ); + temp_thermo); break; case TP_ELECTCOND: data.electCond = newLTP(xmlChild, name, m_tranPropMap[nodeName], - temp_thermo ); + temp_thermo); break; default: @@ -1126,9 +1131,9 @@ namespace Cantera { trParam.viscosity = newLTI(compDepNode, m_tranPropMap[nodeName], trParam); break; case TP_IONCONDUCTIVITY: - trParam.ionConductivity = newLTI( compDepNode, + trParam.ionConductivity = newLTI(compDepNode, m_tranPropMap[nodeName], - trParam ); + trParam); break; case TP_MOBILITYRATIO: { @@ -1139,9 +1144,9 @@ namespace Cantera { string firstSpec = specName.substr(0,loc); string secondSpec = specName.substr(loc+1); int index = temp_thermo->speciesIndex(firstSpec.c_str())+nsp*temp_thermo->speciesIndex(secondSpec.c_str()); - trParam.mobilityRatio[index] = newLTI( propSpecNode, + trParam.mobilityRatio[index] = newLTI(propSpecNode, m_tranPropMap[nodeName], - trParam ); + trParam); }; }; break; @@ -1151,21 +1156,21 @@ namespace Cantera { XML_Node &propSpecNode = compDepNode.child(iSpec); string specName = propSpecNode.name(); int index = temp_thermo->speciesIndex(specName.c_str()); - trParam.selfDiffusion[index] = newLTI( propSpecNode, + trParam.selfDiffusion[index] = newLTI(propSpecNode, m_tranPropMap[nodeName], - trParam ); + trParam); }; }; break; case TP_THERMALCOND: - trParam.thermalCond = newLTI( compDepNode, + trParam.thermalCond = newLTI(compDepNode, m_tranPropMap[nodeName], - trParam ); + trParam); break; case TP_DIFFUSIVITY: - trParam.speciesDiffusivity = newLTI( compDepNode, + trParam.speciesDiffusivity = newLTI(compDepNode, m_tranPropMap[nodeName], - trParam ); + trParam); break; case TP_HYDRORADIUS: trParam.hydroRadius = newLTI(compDepNode, @@ -1173,12 +1178,12 @@ namespace Cantera { trParam); break; case TP_ELECTCOND: - trParam.electCond = newLTI( compDepNode, + trParam.electCond = newLTI(compDepNode, m_tranPropMap[nodeName], - trParam ); + trParam); break; default: - throw CanteraError("getLiquidInteractionsTransportData","unknown transport property: " + nodeName ); + throw CanteraError("getLiquidInteractionsTransportData","unknown transport property: " + nodeName); } } @@ -1201,7 +1206,7 @@ namespace Cantera { trParam.velocityBasis_ = trParam.thermo->speciesIndex(velocityBasis) ; else { int linenum; - throw TransportDBError( linenum, "Unknown attribute \"" + velocityBasis + "\" for node. "); + throw TransportDBError(linenum, "Unknown attribute \"" + velocityBasis + "\" for node. "); } } } @@ -1320,7 +1325,7 @@ namespace Cantera { // self-diffusion coefficient, without polar // corrections diffcoeff = ThreeSixteenths * - sqrt( 2.0 * Pi/tr.reducedMass(k,k) ) * + sqrt(2.0 * Pi/tr.reducedMass(k,k)) * pow((Boltzmann * t), 1.5)/ (Pi * tr.sigma[k] * tr.sigma[k] * om11); @@ -1483,7 +1488,7 @@ namespace Cantera { om11 = m_integrals->omega11(tstar, tr.delta(j,k)); diffcoeff = ThreeSixteenths * - sqrt( 2.0 * Pi/tr.reducedMass(k,j) ) * + sqrt(2.0 * Pi/tr.reducedMass(k,j)) * pow((Boltzmann * t), 1.5)/ (Pi * sigma * sigma * om11); diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index fdb55db59..504c727c9 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -12,8 +12,8 @@ * */ -#ifndef CT_TRANFACTORY_H -#define CT_TRANFACTORY_H +#ifndef CT_TRANSPORTFACTORY_H +#define CT_TRANSPORTFACTORY_H // turn off warnings under Windows @@ -137,17 +137,20 @@ namespace Cantera { newLTP( const XML_Node &trNode, std::string &name, TransportPropertyList tp_ind, thermo_t* thermo) ; - - /** - * make one of several transport models, and return a base class - * pointer to it. This method operates at the level of a - * single mixture transport property. Individual species - * transport properties are addressed by the LTPspecies - * returned by newLTP + + //! Factory function for the construction of new LiquidTranInteraction + //! objects, which are transport models. + /*! + * This method operates at the level of a single mixture transport property. Individual species + * transport properties are addressed by the LTPspecies returned by newLTP. + * + * @param trNode XML_Node containing the information for the interaction + * @param tp_ind TransportPropertylist object + * @param trParam reference to the LiquidTransportParams object */ - virtual LiquidTranInteraction* newLTI( const XML_Node &trNode, - TransportPropertyList tp_ind, - LiquidTransportParams& trParam) ; + virtual LiquidTranInteraction* newLTI(const XML_Node &trNode, + TransportPropertyList tp_ind, + LiquidTransportParams& trParam); //! Build a new transport manager using a transport manager diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index de03f32bd..9eb85bd9c 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -11,6 +11,13 @@ namespace Cantera { + class NotImplemented : public CanteraError { + public: + NotImplemented(std::string method) : CanteraError("Transport", + "\n\n**** Method "+method+" not implemented. ****\n" + "(Did you forget to specify a transport model?)\n\n") {} + }; + /** * Base class to hold transport model parameters. * Used by TransportFactory. From d466a63d5110c852baae7ac8378c0242d6f448f2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 15 Apr 2010 19:55:23 +0000 Subject: [PATCH 140/446] Transfered some functions to the cpp file. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 26 +++++++++++++++++++--- Cantera/src/kinetics/InterfaceKinetics.h | 14 +++++------- 2 files changed, 29 insertions(+), 11 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 446241019..db03c7cdc 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -153,6 +153,26 @@ namespace Cantera { return *this; } + //==================================================================================================================== + // Return the ID of the kinetics object + int InterfaceKinetics::ID() const { + return cInterfaceKinetics; + } + //==================================================================================================================== + int InterfaceKinetics::type() const { + return cInterfaceKinetics; + } + //==================================================================================================================== + // Set the electric potential in the nth phase + /* + * @param n phase Index in this kinetics object. + * @param V Electric potential (volts) + */ + void InterfaceKinetics::setElectricPotential(int n, doublereal V) { + thermo(n).setElectricPotential(V); + m_redo_rates = true; + } + //==================================================================================================================== // Duplication routine for objects which inherit from Kinetics /* @@ -547,7 +567,7 @@ namespace Cantera { multiply_each(kfwd, kfwd + nReactions(), m_perturb.begin()); } - + //==================================================================================================================== /** * Update the rates of progress of the reactions in the reaciton @@ -567,12 +587,12 @@ namespace Cantera { multiply_each(krev, krev + nReactions(), rkc.begin()); } } - + //==================================================================================================================== void InterfaceKinetics::getActivationEnergies(doublereal *E) { copy(m_E.begin(), m_E.end(), E); } - + //==================================================================================================================== /** * Update the rates of progress of the reactions in the reaction * mechanism. This routine operates on internal data. diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 6f327dbfe..b569afc7f 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -127,20 +127,18 @@ namespace Cantera { */ virtual Kinetics *duplMyselfAsKinetics() const; + //! Return the ID of the kinetics object + virtual int ID() const; - virtual int ID() const { return cInterfaceKinetics; } - virtual int type() const { return cInterfaceKinetics; } + //! Retunr the type of the kinetics object + virtual int type() const; - //! Set the electric potential in the nth phase - /*! + /*! * @param n phase Index in this kinetics object. * @param V Electric potential (volts) */ - void setElectricPotential(int n, doublereal V) { - thermo(n).setElectricPotential(V); - m_redo_rates = true; - } + void setElectricPotential(int n, doublereal V); /// From ec3e7278a0c414b8ebab33d9e587cf14c08ef8c3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Apr 2010 03:36:07 +0000 Subject: [PATCH 141/446] Eliminated an overloaded function, getFloat() for vectors, that was a bit confusing. getFloatArray() can now handle the functionality of getFloat(). Took getFloat() out of the code base. --- Cantera/src/base/ctml.cpp | 129 ++++++++++++------ Cantera/src/base/ctml.h | 45 +----- Cantera/src/base/utilities.h | 2 + .../src/transport/LiquidTranInteraction.cpp | 38 +++--- 4 files changed, 117 insertions(+), 97 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 09bed275f..fcf263364 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -40,7 +40,7 @@ namespace ctml { static doublereal fpValue(std::string val) { return atof(stripws(val).c_str()); } - + //==================================================================================================================== // This function adds a child node with the name, "bool", with a value // consisting of a single bool /* @@ -79,7 +79,7 @@ namespace ctml { XML_Node& f = node.addChild("bool", v); f.addAttribute("title", title); } - + //==================================================================================================================== // This function adds a child node with the name, "integer", with a value // consisting of a single integer /* @@ -123,7 +123,7 @@ namespace ctml { if (type != "") f.addAttribute("type",type); if (units != "") f.addAttribute("units",units); } - + //==================================================================================================================== // This function adds a child node with the name, "intArray", with a value // consisting of a comma separated list of integers /* @@ -196,7 +196,7 @@ namespace ctml { if (minval != Undef) f.addAttribute("min",minval); if (maxval != Undef) f.addAttribute("max",maxval); } - + //==================================================================================================================== // This function adds a child node with the name, "float", with a value // consisting of a single floating point number /* @@ -255,7 +255,7 @@ namespace ctml { if (minval != Undef) f.addAttribute("min",minval); if (maxval != Undef) f.addAttribute("max",maxval); } - + //==================================================================================================================== // This function adds a child node with the name, "floatArray", with a value // consisting of a comma separated list of floats /* @@ -329,7 +329,7 @@ namespace ctml { if (minval != Undef) f.addAttribute("min",minval); if (maxval != Undef) f.addAttribute("max",maxval); } - + //==================================================================================================================== // This function adds a child node with the name string with a string value // to the current node /* @@ -374,7 +374,7 @@ namespace ctml { } return 0; } - + //==================================================================================================================== // This function reads a child node with the name string and returns // its xml value as the return string /* @@ -407,7 +407,7 @@ namespace ctml { if (!parent.hasChild(nameString)) return ""; return parent(nameString); } - + //==================================================================================================================== // This function reads a child node with the name, "string", with a specific // title attribute named "titleString" /* @@ -449,7 +449,7 @@ namespace ctml { } } - + //==================================================================================================================== // Get a vector of integer values from a child element. /* * Returns a std::map containing a keyed values for child XML_Nodes @@ -510,7 +510,7 @@ namespace ctml { } } - + //==================================================================================================================== // Get a vector of floating-point values from a child element. /* * Returns a std::map containing a keyed values for child XML_Nodes @@ -588,7 +588,7 @@ namespace ctml { } } - + //==================================================================================================================== // Get a floating-point value from a child element. /* * Returns a double value for the child named 'name' of element 'parent'. If @@ -633,22 +633,39 @@ namespace ctml { return getFloatCurrent(node, type); } - doublereal getFloat(vector_fp& v, const Cantera::XML_Node& parent, - const std::string &name, - const std::string type) { - if (!parent.hasChild(name)) - throw CanteraError("getFloat (called from XML Node \"" + - parent.name() + "\"): ", - "no child XML element named \"" + name + "\" exists"); - const XML_Node& node = parent.child(name); - if (node.hasChild("floatArray")){ - getFloatArray(node, v, "true", type); - return 0; - } - else{ return getFloatCurrent(node, type); - } - } - + //==================================================================================================================== + // Get a floating-point value from the current XML element + /* + * Returns a doublereal value from the current element. If + * 'type' is supplied and matches a known unit type, unit + * conversion to SI will be done if the child element has an attribute 'units'. + * + * Note, it's an error for the child element not to exist. + * + * Example: + * + * Code snipet: + * @verbatim + const XML_Node &State_XMLNode; + doublereal pres = OneAtm; + if (state_XMLNode.hasChild("pressure")) { + XML_Node *pres_XMLNode = State_XMLNode.getChild("pressure"); + pres = getFloatCurrent(pres_XMLNode, "toSI"); + } + @endverbatim + * + * Rreads the corresponding XML file: + * @verbatim + + 101325.0 + <\state> + @endverbatim + * + * @param currXML reference to the current XML_Node object + * @param type String type. Currently known types are "toSI" and "actEnergy", + * and "" , for no conversion. The default value is "", + * which implies that no conversion is allowed. + */ doublereal getFloatCurrent(const Cantera::XML_Node& node, const std::string type) { doublereal x, x0, x1, fctr = 1.0; @@ -704,7 +721,7 @@ namespace ctml { return fctr*x; } - + //==================================================================================================================== bool getOptionalFloat(const Cantera::XML_Node& parent, const std::string &name, doublereal &fltRtn, @@ -715,7 +732,7 @@ namespace ctml { } return false; } - + //==================================================================================================================== // Get an optional floating-point value from a child element. /* * Returns a doublereal value for the child named 'name' of element 'parent'. If @@ -778,7 +795,37 @@ namespace ctml { val /= fctr; return val; } - + //==================================================================================================================== + // Get an optional model name from a named child node. + /* + * Returns the model name attribute for the child named 'nodeName' of element 'parent'. + * Note, it's optional for the child node to exist + * + * Example: + * + * Code snipet: + * @verbatim + std::string modelName = ""; + bool exists = getOptionalModel(transportNode, "compositionDependence", + modelName); + @endverbatim + * + * Reads the corresponding XML file: + * + * @verbatim + + + + @endverbatim + * + * On return modelName is set to "Solvent_Only". + * + * @param parent Reference to the XML_Node object of the parent XML element + * @param nodeName Name of the XML child element + * @param modelName On return this contains the contents of the model attribute + * + * @return True if the nodeName XML node exists. False otherwise. + */ bool getOptionalModel(const Cantera::XML_Node& parent, const std::string nodeName, std::string &modelName) { if (parent.hasChild(nodeName)) { @@ -788,7 +835,7 @@ namespace ctml { } return false; } - + //==================================================================================================================== // Get an integer value from a child element. /* * Returns an integer value for the child named 'name' of element 'parent'. @@ -809,7 +856,7 @@ namespace ctml { * reads the corresponding XML file: * @verbatum - 10 + 10 <\numProcs> <\state> @endverbatum * @@ -846,7 +893,7 @@ namespace ctml { } return x; } - + //==================================================================================================================== // This function reads the current node or a child node of the current node // with the default name, "floatArray", with a value field // consisting of a comma separated list of floats @@ -921,6 +968,11 @@ namespace ctml { + nodeName + "but accessed " + node.name()); } else { readNode = ll[0]; + ll.clear(); + readNode->getChildren("floatArray", ll); + if (ll.size() > 0) { + readNode = ll[0]; + } } } @@ -987,7 +1039,7 @@ namespace ctml { } return v.size(); } - + //==================================================================================================================== // This routine is used to interpret the value portions of XML // elements that contain colon separated pairs. /* @@ -1025,7 +1077,7 @@ namespace ctml { m[key] = val; } } - + //==================================================================================================================== // This function interprets the value portion of an XML element // as a series of "Pairs" separated by white space. /* @@ -1075,7 +1127,7 @@ namespace ctml { } return n; } - + //==================================================================================================================== // This function interprets the value portion of an XML element // as a series of "Matrix ids and entries" separated by white space. /* @@ -1206,7 +1258,7 @@ namespace ctml { } } } - + //==================================================================================================================== // This function interprets the value portion of an XML element // as a string. It then separates the string up into tokens // according to the location of white space. @@ -1220,7 +1272,7 @@ namespace ctml { std::string val = node.value(); tokenizeString(val, v); } - + //==================================================================================================================== // This function reads a child node with the default name, "floatArray", with a value // consisting of a comma separated list of floats /* @@ -1285,4 +1337,5 @@ namespace ctml { if (node["max"] != "") xmax = fpValue(node["max"]); type = node["type"]; } + //==================================================================================================================== } diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 5ed0539f1..5d065a96c 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -566,50 +566,11 @@ namespace ctml { doublereal getFloat(const Cantera::XML_Node& parent, const std::string &name, const std::string type=""); - //! Get a floating-point value from a child element. - /*! - * Returns a doublereal value for the child named 'name' of element 'parent'. If - * 'type' is supplied and matches a known unit type, unit - * conversion to SI will be done if the child element has an attribute - * 'units'. - * - * Note, it's an error for the child element not to exist. - * - * Example: - * - * Code snipet: - * @verbatim - const XML_Node &State_XMLNode; - doublereal pres = OneAtm; - if (state_XMLNode.hasChild("pressure")) { - pres = getFloat(State_XMLNode, "pressure", "toSI"); - } - @endverbatim - * - * reads the corresponding XML file: - * @verbatim - - 101325.0 - <\state> - @endverbatim - * - * @param v vector to assign with getFloatArray is XML data is in an array form - * @param parent reference to the XML_Node object of the parent XML element - * @param name Name of the XML child element - * @param type String type. Currently known types are "toSI" and "actEnergy", - * and "" , for no conversion. The default value is "", - * which implies that no conversion is allowed. - */ - - doublereal getFloat(Cantera::vector_fp& v,const Cantera::XML_Node& parent, const std::string &name, - const std::string type="toSI"); - //! Get a floating-point value from the current XML element /*! * Returns a doublereal value from the current element. If * 'type' is supplied and matches a known unit type, unit - * conversion to SI will be done if the child element has an attribute - * 'units'. + * conversion to SI will be done if the child element has an attribute 'units'. * * Note, it's an error for the child element not to exist. * @@ -625,7 +586,7 @@ namespace ctml { } @endverbatim * - * reads the corresponding XML file: + * Rreads the corresponding XML file: * @verbatim 101325.0 @@ -816,7 +777,7 @@ namespace ctml { * @param nodeName Name of the XML child element * @param modelName On return this contains the contents of the model attribute * - * @return True if the nodeName XML node exists. False otherwise + * @return True if the nodeName XML node exists. False otherwise. */ bool getOptionalModel(const Cantera::XML_Node& parent, const std::string nodeName, std::string &modelName); diff --git a/Cantera/src/base/utilities.h b/Cantera/src/base/utilities.h index 19aead0a4..7090bacae 100644 --- a/Cantera/src/base/utilities.h +++ b/Cantera/src/base/utilities.h @@ -686,6 +686,8 @@ namespace Cantera { } } + + //@} } diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index 854b7a7ac..36531da93 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -79,7 +79,6 @@ namespace Cantera { thermo_t* thermo ) { - doublereal poly0; m_thermo = thermo; int nsp = thermo->nSpecies(); @@ -104,20 +103,23 @@ namespace Cantera { int num = compModelNode.nChildren(); for (int iChild = 0; iChild < num; iChild++) { XML_Node &xmlChild = compModelNode.child(iChild); - std::string nodeName = lowercase(xmlChild.name() ); - if (nodeName != "interaction" ) + std::string nodeName = lowercase(xmlChild.name()); + if (nodeName != "interaction") { throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", "expected element and got <" + nodeName + ">" ); + } speciesA = xmlChild.attrib("speciesA"); speciesB = xmlChild.attrib("speciesB"); int iSpecies = m_thermo->speciesIndex(speciesA ); - if (iSpecies < 0 ) + if (iSpecies < 0) { throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", "Unknown species " + speciesA ); + } int jSpecies = m_thermo->speciesIndex(speciesB ); - if (jSpecies < 0 ) + if (jSpecies < 0) { throw CanteraError("TransportFactory::getLiquidInteractionsTransportData", "Unknown species " + speciesB ); + } /* if (xmlChild.hasChild("Aij" ) ) { m_Aij(iSpecies,jSpecies) = getFloat(xmlChild, "Aij", "toSI" ); m_Aij(jSpecies,iSpecies) = m_Aij(iSpecies,jSpecies) ; @@ -129,16 +131,17 @@ namespace Cantera { m_Eij(jSpecies,iSpecies) = m_Eij(iSpecies,jSpecies) ; } - if (xmlChild.hasChild("Aij" ) ) { + if (xmlChild.hasChild("Aij")) { vector_fp poly; - poly0 = getFloat(poly, xmlChild, "Aij", "toSI" ); - if (!poly.size() ) poly.push_back(poly0); + // poly0 = getFloat(poly, xmlChild, "Aij", "toSI" ); + getFloatArray(xmlChild, poly, true, "toSI", "Aij"); + // if (!poly.size() ) poly.push_back(poly0); while (m_Aij.size()resize(nsp, nsp, 0.0); m_Aij.push_back(aTemp); } - for(int i=0; i<(int)poly.size(); i++ ){ + for (int i = 0; i < (int)poly.size(); i++ ) { (*m_Aij[i])(iSpecies,jSpecies) = poly[i]; //(*m_Aij[i])(jSpecies,iSpecies) = (*m_Aij[i])(iSpecies,jSpecies) ; } @@ -146,9 +149,9 @@ namespace Cantera { if (xmlChild.hasChild("Bij" ) ) { vector_fp poly; - poly0 = getFloat(poly, xmlChild, "Bij", "toSI" ); - if (!poly.size() ) poly.push_back(poly0); - while (m_Bij.size()resize(nsp, nsp, 0.0); m_Bij.push_back(bTemp); @@ -161,8 +164,9 @@ namespace Cantera { if (xmlChild.hasChild("Hij" ) ) { vector_fp poly; - poly0 = getFloat(poly, xmlChild, "Hij", "actEnergy" ); - if (!poly.size() ) poly.push_back(poly0); + // poly0 = getFloat(poly, xmlChild, "Hij", "actEnergy" ); + getFloatArray(xmlChild, poly, true, "actEnergy", "Hij"); + // if (!poly.size() ) poly.push_back(poly0); while (m_Hij.size()resize(nsp, nsp, 0.0); @@ -177,8 +181,9 @@ namespace Cantera { if (xmlChild.hasChild("Sij" ) ) { vector_fp poly; - poly0 = getFloat(poly, xmlChild, "Sij", "actEnergy" ); - if (!poly.size() ) poly.push_back(poly0); + // poly0 = getFloat(poly, xmlChild, "Sij", "actEnergy" ); + getFloatArray(xmlChild, poly, true, "actEnergy", "Sij"); + // if (!poly.size() ) poly.push_back(poly0); while (m_Sij.size()resize(nsp, nsp, 0.0); @@ -666,7 +671,6 @@ namespace Cantera { if (nsp != 3) { throw CanteraError("LTI_StefanMaxwell_PPN::getMatrixTransProp","Function may only be called with a 3-ion system"); } - int nsp2 = nsp*nsp; doublereal temp = m_thermo->temperature(); doublereal molefracs[nsp]; m_thermo->getMoleFractions(molefracs ); From 75d434fc317a883c83c9ceffdbea91bedc8710d7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Apr 2010 17:57:22 +0000 Subject: [PATCH 142/446] Changed the HKFT formulation. You now can specify 2 of the 3 parameters DG0, DH0, or S0. It will then internally calculate the third parameter that is consistent with the other two. --- Cantera/src/thermo/PDSS_HKFT.cpp | 74 ++++++++++++++++++++++++-------- 1 file changed, 55 insertions(+), 19 deletions(-) diff --git a/Cantera/src/thermo/PDSS_HKFT.cpp b/Cantera/src/thermo/PDSS_HKFT.cpp index f09c28b51..1ba20f27f 100644 --- a/Cantera/src/thermo/PDSS_HKFT.cpp +++ b/Cantera/src/thermo/PDSS_HKFT.cpp @@ -621,10 +621,10 @@ namespace Cantera { void PDSS_HKFT::constructPDSSXML(VPStandardStateTP *tp, int spindex, const XML_Node& speciesNode, const XML_Node& phaseNode, bool spInstalled) { - //PDSS::initThermo(); - - // m_p0 = OneAtm; - + int hasDGO = 0; + int hasSO = 0; + int hasDHO = 0; + if (!spInstalled) { throw CanteraError("PDSS_HKFT::constructPDSSXML", "spInstalled false not handled"); } @@ -666,22 +666,25 @@ namespace Cantera { if (hh->hasChild("DG0_f_Pr_Tr")) { doublereal val = getFloat(*hh, "DG0_f_Pr_Tr"); m_deltaG_formation_tr_pr = val; + hasDGO = 1; } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing DG0_f_Pr_Tr field"); + // throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing DG0_f_Pr_Tr field"); } if (hh->hasChild("DH0_f_Pr_Tr")) { doublereal val = getFloat(*hh, "DH0_f_Pr_Tr"); m_deltaH_formation_tr_pr = val; + hasDHO = 1; } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing DH0_f_Pr_Tr field"); + // throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing DH0_f_Pr_Tr field"); } if (hh->hasChild("S0_Pr_Tr")) { doublereal val = getFloat(*hh, "S0_Pr_Tr"); m_Entrop_tr_pr= val; + hasSO = 1; } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing S0_Pr_Tr field"); + // throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing S0_Pr_Tr field"); } const XML_Node *ss = speciesNode.findByName("standardState"); @@ -720,24 +723,57 @@ namespace Cantera { throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing a4 field"); } - if (ss->hasChild("c1")) { + if (ss->hasChild("c1")) { doublereal val = getFloat(*ss, "c1"); m_c1 = val; - } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing c1 field"); - } - if (ss->hasChild("c2")) { + } else { + throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing c1 field"); + } + if (ss->hasChild("c2")) { doublereal val = getFloat(*ss, "c2"); m_c2 = val; - } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing c2 field"); - } - if (ss->hasChild("omega_Pr_Tr")) { + } else { + throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing c2 field"); + } + if (ss->hasChild("omega_Pr_Tr")) { doublereal val = getFloat(*ss, "omega_Pr_Tr"); m_omega_pr_tr = val; - } else { - throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing omega_Pr_Tr field"); - } + } else { + throw CanteraError("PDSS_HKFT::constructPDSSXML", " missing omega_Pr_Tr field"); + } + + + int isum = hasDGO + hasDHO + hasSO; + if (isum < 2) { + throw CanteraError("PDSS_HKFT::constructPDSSXML", + "Missing 2 or more of DG0_f_Pr_Tr, DH0_f_Pr_Tr, or S0_f_Pr_Tr fields. " + "Need to supply at least two of these fields"); + } + // Ok, if we are missing one, then we construct its value from the other two. + // This code has been internally verified. + if (hasDHO == 0) { + m_charge_j = m_tp->charge(m_spindex); + convertDGFormation(); + doublereal Hcalc = m_Mu0_tr_pr + 298.15 * (m_Entrop_tr_pr * 1.0E3 * 4.184); + m_deltaH_formation_tr_pr = Hcalc / (1.0E3 * 4.184); + } + if (hasDGO == 0) { + doublereal DHjmol = m_deltaH_formation_tr_pr * 1.0E3 * 4.184; + m_Mu0_tr_pr = DHjmol - 298.15 * (m_Entrop_tr_pr * 1.0E3 * 4.184); + m_deltaG_formation_tr_pr = m_Mu0_tr_pr / (1.0E3 * 4.184); + double tmp = m_Mu0_tr_pr; + m_charge_j = m_tp->charge(m_spindex); + convertDGFormation(); + double totalSum = m_Mu0_tr_pr - tmp; + m_Mu0_tr_pr = tmp; + m_deltaG_formation_tr_pr = (m_Mu0_tr_pr - totalSum)/ (1.0E3 * 4.184); + } + if (hasSO == 0) { + m_charge_j = m_tp->charge(m_spindex); + convertDGFormation(); + doublereal DHjmol = m_deltaH_formation_tr_pr * 1.0E3 * 4.184; + m_Entrop_tr_pr = (DHjmol - m_Mu0_tr_pr) / (298.15 * 1.0E3 * 4.184); + } } From 82e215d73292c31430bfe12bcdaa5ebc1801c431 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 May 2010 23:59:16 +0000 Subject: [PATCH 143/446] Changed the comments on one file. --- Cantera/src/thermo/Constituents.h | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h index a38622906..22028b964 100644 --- a/Cantera/src/thermo/Constituents.h +++ b/Cantera/src/thermo/Constituents.h @@ -280,14 +280,13 @@ namespace Cantera { doublereal charge = 0.0, doublereal size = 1.0); - //! Index of species named 'name' + //! Returns the index of a species named 'name' within the ThermoPhase /*! - * The first species added - * will have index 0, and the last one index nSpecies() - 1. + * The first species added will have index 0, and the last one index nSpecies() - 1. * * @param name String name of the species - * @return - * Returns the index of the species. + * @return Returns the index of the species. If the name is not found + * the value of -1 is returned. */ int speciesIndex(std::string name) const; From e8d545fba9ab022f875acf2135ef0672e96017a3 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 5 May 2010 22:49:34 +0000 Subject: [PATCH 144/446] Added classes to compute effects of porous flow on species transport. There are two primary methods in these classes: McMillan() that computes the ratio of the porous transport rate to the non-porous transport rate. toruosityFactor() that computes the "tortuosity" component of this ratio (the increase in the diffusion length scale). The base class implements a general Bruggemann formulation and subclasses implement a percolation theory models and Maxwell's model. I did not put in copy constructors, etc., for these calsses yet. --- Cantera/src/transport/Makefile.in | 2 +- Cantera/src/transport/Tortuosity.h | 176 +++++++++++++++++++++++++++++ 2 files changed, 177 insertions(+), 1 deletion(-) create mode 100644 Cantera/src/transport/Tortuosity.h diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index e21d70d01..2bab492c7 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -41,7 +41,7 @@ TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt. TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ TransportBase.h L_matrix.h TransportParams.h WaterTransport.h \ - SimpleTransport.h LiquidTranInteraction.h + SimpleTransport.h LiquidTranInteraction.h Tortuosity.h ifeq ($(do_electro),1) do_issp = 1 diff --git a/Cantera/src/transport/Tortuosity.h b/Cantera/src/transport/Tortuosity.h new file mode 100644 index 000000000..b8b34b5d5 --- /dev/null +++ b/Cantera/src/transport/Tortuosity.h @@ -0,0 +1,176 @@ +/** + * @file Tortuosity.h + * Class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +namespace Cantera { + +/** + * Class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + * This base class implementation relates tortuosity to volume fraction + * through a power-law relationship that goes back to Bruggemann. The + * exponent is referred to as the Bruggemann exponent. + * + * Note that the total diffusional flux is generally written as + * + * \f[ + * \frac{ \phi C_T D_i \nabla X_i }{ \tau^2 } + * \f] + * + * where \f$ \phi \f$ is the volume fraction of the transported phase, + * \f$ \tau \f$ is referred to as the tortuosity. (Other variables are + * \f$ C_T \f$, the total concentration, \f$ D_i \f$, the diffusion + * coefficient, and \f$ X_i \f$, the mole fraction with Fickian + * transport assumed.) + * + * The tortuosity comes into play in conjunction the the + + */ + class Tortuosity { + + public: + //! Default constructor uses Bruggemann exponent of 1.5 + Tortuosity( double setPower = 1.5 ) : expBrug_(setPower) { + } + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /** + * This method returns \f$ 1/\tau^2 \f$ in the description of the + * flux \f$ \phi C_T D_i \nabla X_i / \tau^2 \f$. + */ + virtual double toruosityFactor( double porosity ) { + return pow( porosity, expBrug_ - 1.0 ); + } + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + virtual double McMillan( double porosity ) { + return pow( porosity, expBrug_ ); + } + + protected: + //! Bruggemann exponent: power to which the tortuosity depends on the volume fraction + double expBrug_ ; + + }; + + + + /** This class implements transport coefficient corrections + * appropriate for porous media where percollation theory applies. + * It is derived from the Tortuosity class. + */ + class TortuosityPercolation : public Tortuosity { + + public: + //! Default constructor uses Bruggemann exponent of 1.5 + TortuosityPercolation( double percolationThreshold = 0.4, double conductivityExponent = 2.0 ) : percolationThreshold_(percolationThreshold), conductivityExponent_(conductivityExponent) { + } + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /** + * This method returns \f$ 1/\tau^2 \f$ in the description of the + * flux \f$ \phi C_T D_i \nabla X_i / \tau^2 \f$. + */ + double toruosityFactor( double porosity ) { + return McMillan( porosity ) / porosity; + } + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + double McMillan( double porosity ) { + return pow( ( porosity - percolationThreshold_ ) + / ( 1.0 - percolationThreshold_ ), + conductivityExponent_ ); + } + + protected: + //! Critical volume fraction / site density for percolation + double percolationThreshold_; + //! Conductivity exponent + /** + * The McMillan number (ratio of effective conductivity + * to non-porous conductivity) is + * \f[ \kappa/\kappa_0 = ( \phi - \phi_c )^\mu \f] + * where \f$ \mu \f$ is the conductivity exponent (typical + * values range from 1.6 to 2.0) and \f$ \phi_c \f$ + * is the percolation threshold. + */ + double conductivityExponent_; + }; + + + + /** This class implements transport coefficient corrections + * appropriate for porous media with a dispersed phase. + * This model goes back to Maxwell. The formula for the + * conductivity is expressed in terms of the volume fraction + * of the continuous phase, \f$ \phi \f$, and the relative + * conductivities of the dispersed and continuous phases, + * \f$ r = \kappa_d / \kappa_0 \f$. For dilute particle + * suspensions the effective conductivity is + * \f[ + * \kappa / \kappa_0 = 1 + 3 ( 1 - \phi ) ( r - 1 ) / ( r + 2 ) + * + O(\phi^2) + * \f] + * The class is derived from the Tortuosity class. + */ + class TortuosityMaxwell : public Tortuosity { + + public: + //! Default constructor uses Bruggemann exponent of 1.5 + TortuosityMaxwell( double relativeConductivites = 0.0 ) : relativeConductivites_(relativeConductivites) { + } + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /** + * This method returns \f$ 1/\tau^2 \f$ in the description of the + * flux \f$ \phi C_T D_i \nabla X_i / \tau^2 \f$. + */ + double toruosityFactor( double porosity ) { + return McMillan( porosity ) / porosity; + } + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + double McMillan( double porosity ) { + return 1 + 3 * ( 1.0 - porosity ) * ( relativeConductivites_ - 1.0 ) / ( relativeConductivites_ + 2 ); + } + + protected: + //! Relative conductivities of the dispersed and continuous phases, + //! \code{relativeConductivites_}\f$ = \kappa_d / \kappa_0 \f$. + double relativeConductivites_; + + }; + +} From 565e57d814f720ae404cf363720129fe1671fac6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 6 May 2010 20:25:50 +0000 Subject: [PATCH 145/446] Added in routines that modify/fix the kinetics operator for heterogeneous reactions. Now the kinetics operator carries around information that indicates whether a phase exists or not. If the phase exists then the species in it can be consumed by the kinetics heterogeneous operator. If it doesn't exist then species within the phase can only be created by the kinetics operator. Worked on Cantera's version control. In the config.h file, we now write several forms of version control information as preprocessor defines CANTERA_VERSION = double quoted string id'ing the branch number CANTERA_VERSION_MAJORNUMBER major number of Cantera as an int Defines that are specific to the branch and that are assigned a 1. e.g.: #define CANTERA_VERSION_18 1 #define CANTERA_VERSION_18_XXX 1 #define CANTERA_VERSION_18_LTD 1 In the Cantera.mak file, we write CANTERA_VERSION = double quoted string id'ing the branch number CANTERA_DEFINES = -DCANTERA_VERSION=@ctversion@ --- Cantera/cxx/include/Cantera.mak.in | 6 + Cantera/cxx/include/Cantera_bt.mak.in | 6 + Cantera/src/kinetics/InterfaceKinetics.cpp | 164 +++++++++++++++++++-- Cantera/src/kinetics/InterfaceKinetics.h | 53 ++++++- Cantera/src/kinetics/Kinetics.cpp | 3 +- Cantera/src/thermo/IdealGasPhase.h | 1 + config.h.in | 16 +- preconfig | 17 ++- 8 files changed, 245 insertions(+), 21 deletions(-) diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in index 67b6b1885..ffbc46197 100644 --- a/Cantera/cxx/include/Cantera.mak.in +++ b/Cantera/cxx/include/Cantera.mak.in @@ -23,6 +23,8 @@ # in_CanteraBuildTree = 0 +CANTERA_VERSION=@ctversion@ + ############################################################################### # CANTERA CORE ############################################################################### @@ -122,6 +124,10 @@ endif # CANTERA_TOTAL_INCLUDES= $(CANTERA_CORE_INCLUDES) $(CANTERA_BOOST_INCLUDES) $(CANTERA_CVODE_INCLUDE) # +# You can add this into the compilation environment to identify the version number +# +CANTERA_DEFINES = -DCANTERA_VERSION=@ctversion@ +# # LIBS and LIBS should be the same ... # CANTERA_TOTAL_LIBS2 = -L$(CANTERA_LIBSDIR) @LOCAL_LIBS@ diff --git a/Cantera/cxx/include/Cantera_bt.mak.in b/Cantera/cxx/include/Cantera_bt.mak.in index 54c124c6e..88cdc0633 100644 --- a/Cantera/cxx/include/Cantera_bt.mak.in +++ b/Cantera/cxx/include/Cantera_bt.mak.in @@ -23,6 +23,8 @@ # in_CanteraBuildTree = 0 +CANTERA_VERSION=@ctversion@ + ############################################################################### # CANTERA CORE ############################################################################### @@ -117,6 +119,10 @@ endif #################################################################### CANTERA_TOTAL_INCLUDES= $(CANTERA_CORE_INCLUDES) $(CANTERA_BOOST_INCLUDES) $(CANTERA_CVODE_INCLUDE) +# +# You can add this into the compilation environment to identify the version number +# +CANTERA_DEFINES = -DCANTERA_VERSION=@ctversion@ CANTERA_TOTAL_LIBS2 = @LOCAL_LIB_DIRS@ @LOCAL_LIBS@ diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index db03c7cdc..2f5cd0cd7 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -52,6 +52,10 @@ namespace Cantera { m_has_coverage_dependence(false), m_has_electrochem_rxns(false), m_has_exchange_current_density_formulation(false), + m_phaseExistsCheck(false), + m_phaseExists(0), + m_rxnPhaseIsReactant(0), + m_rxnPhaseIsProduct(0), m_ioFlag(0) { if (thermo != 0) addPhase(*thermo); @@ -67,6 +71,10 @@ namespace Cantera { if (m_integrator) { delete m_integrator; } + for (int i = 0; i < m_ii; i++) { + delete m_rxnPhaseIsReactant[i]; + delete m_rxnPhaseIsProduct[i]; + } } //==================================================================================================================== // Copy Constructor for the %InterfaceKinetics object. @@ -92,6 +100,10 @@ namespace Cantera { m_has_coverage_dependence(false), m_has_electrochem_rxns(false), m_has_exchange_current_density_formulation(false), + m_phaseExistsCheck(false), + m_phaseExists(0), + m_rxnPhaseIsReactant(0), + m_rxnPhaseIsProduct(0), m_ioFlag(0) { m_kdata = new InterfaceKineticsData; @@ -111,13 +123,21 @@ namespace Cantera { */ InterfaceKinetics& InterfaceKinetics:: operator=(const InterfaceKinetics &right) { + int i; /* * Check for self assignment. */ if (this == &right) return *this; + for (i = 0; i < m_ii; i++) { + delete (m_rxnPhaseIsReactant[i]); + delete (m_rxnPhaseIsProduct[i]); + } + Kinetics::operator=(right); + + m_kk = right.m_kk; m_revindex = right.m_revindex; m_rates = right.m_rates; @@ -138,7 +158,6 @@ namespace Cantera { m_E = right.m_E; m_surf = right.m_surf; //DANGER - shallow copy m_integrator = right.m_integrator; //DANGER - shallow copy - m_beta = right.m_beta; m_ctrxn = right.m_ctrxn; m_ctrxn_ecdf = right.m_ctrxn_ecdf; @@ -149,6 +168,24 @@ namespace Cantera { m_has_coverage_dependence = right.m_has_coverage_dependence; m_has_electrochem_rxns = right.m_has_electrochem_rxns; m_has_exchange_current_density_formulation = right.m_has_exchange_current_density_formulation; + m_phaseExistsCheck = right.m_phaseExistsCheck; + m_phaseExists = right.m_phaseExists; + + + m_rxnPhaseIsReactant.resize(m_ii, 0); + m_rxnPhaseIsProduct.resize(m_ii, 0); + int np = nPhases(); + for (i = 0; i < m_ii; i++) { + m_rxnPhaseIsReactant[i] = new bool[np]; + m_rxnPhaseIsProduct[i] = new bool[np]; + for (int p = 0; p < np; p++) { + m_rxnPhaseIsReactant[i][p] = right.m_rxnPhaseIsReactant[i][p]; + m_rxnPhaseIsProduct[i][p] = right.m_rxnPhaseIsProduct[i][p]; + } + } + + m_rxnPhaseIsProduct = right.m_rxnPhaseIsProduct; + m_ioFlag = right.m_ioFlag; return *this; @@ -639,7 +676,57 @@ namespace Cantera { for (int j = 0; j != m_ii; ++j) { ropnet[j] = ropf[j] - ropr[j]; - } + } + + + /* + * For reactions involving multiple phases, we must check that the phase + * being consumed actually exists. This is particularly important for + * phases that are stoichiometric phases containing one species with a unity activity + */ + if (m_phaseExistsCheck) { + for (int j = 0; j != m_ii; ++j) { + if ((ropr[j] > ropf[j]) && (ropr[j] > 0.0)) { + for (int p = 0; p < nPhases(); p++) { + if (m_rxnPhaseIsProduct[j][p]) { + if (! m_phaseExists[p]) { + ropnet[j] = 0.0; + ropr[j] = ropf[j]; + if (ropf[j] > 0.0) { + for (int rp = 0; rp < nPhases(); rp++) { + if (m_rxnPhaseIsReactant[j][rp]) { + if (! m_phaseExists[rp]) { + ropnet[j] = 0.0; + ropr[j] = ropf[j] = 0.0;; + } + } + } + } + } + } + } + } else if ((ropf[j] > ropr[j]) && (ropf[j] > 0.0)) { + for (int p = 0; p < nPhases(); p++) { + if (m_rxnPhaseIsReactant[j][p]) { + if (! m_phaseExists[p]) { + ropnet[j] = 0.0; + ropf[j] = ropr[j]; + if (ropf[j] > 0.0) { + for (int rp = 0; rp < nPhases(); rp++) { + if (m_rxnPhaseIsProduct[j][rp]) { + if (! m_phaseExists[rp]) { + ropnet[j] = 0.0; + ropf[j] = ropr[j] = 0.0; + } + } + } + } + } + } + } + } + } + } m_kdata->m_ROP_ok = true; } @@ -851,11 +938,37 @@ namespace Cantera { addElementaryReaction(r); // operations common to all reaction types - installReagents( r ); + installReagents(r); //installGroups(reactionNumber(), r.rgroups, r.pgroups); incrementRxnCount(); m_rxneqn.push_back(r.equation); - } + + m_rxnPhaseIsReactant.resize(m_ii, 0); + m_rxnPhaseIsProduct.resize(m_ii, 0); + + int np = nPhases(); + int i = m_ii -1; + m_rxnPhaseIsReactant[i] = new bool[np]; + m_rxnPhaseIsProduct[i] = new bool[np]; + + for (int p = 0; p < np; p++) { + m_rxnPhaseIsReactant[i][p] = false; + m_rxnPhaseIsProduct[i][p] = false; + } + + const vector_int& vr = reactants(i); + for (int ik = 0; ik < (int) vr.size(); ik++) { + int k = vr[ik]; + int p = speciesPhaseIndex(k); + m_rxnPhaseIsReactant[i][p] = true; + } + const vector_int& vp = products(i); + for (int ik = 0; ik < (int) vp.size(); ik++) { + int k = vp[ik]; + int p = speciesPhaseIndex(k); + m_rxnPhaseIsProduct[i][p] = true; + } + } //==================================================================================================================== void InterfaceKinetics::addElementaryReaction(const ReactionData& r) { int iloc; @@ -1008,7 +1121,7 @@ namespace Cantera { * calculates rates of species production from reaction rates of * progress. */ - m_rxnstoich.add( reactionNumber(), r); + m_rxnstoich.add(reactionNumber(), r); /* * register reaction in lists of reversible and irreversible rxns. */ @@ -1016,11 +1129,16 @@ namespace Cantera { m_revindex.push_back(reactionNumber()); m_nrev++; } else { - m_irrev.push_back( reactionNumber() ); + m_irrev.push_back(reactionNumber()); m_nirrev++; } } - + //=============================================================================================== + void InterfaceKinetics::addPhase(thermo_t &thermo) { + Kinetics::addPhase(thermo); + m_phaseExists.push_back(true); + } + //================================================================================================ /** * Prepare the class for the addition of reactions. This function * must be called after instantiation of the class, but before @@ -1044,7 +1162,7 @@ namespace Cantera { m_pot.resize(m_kk, 0.0); m_phi.resize(np, 0.0); } - + //================================================================================================ /** * Finish adding reactions and prepare for use. This function * must be called after all reactions are entered into the mechanism @@ -1071,10 +1189,13 @@ namespace Cantera { m_deltaG0.resize(m_ii, 0.0); m_ProdStanConcReac.resize(m_ii, 0.0); + if (m_thermo.size() != m_phaseExists.size()) { + throw CanteraError("InterfaceKinetics::finalize", "internal error"); + } + m_finalized = true; } - doublereal InterfaceKinetics::electrochem_beta(int irxn) const{ int n = m_ctrxn.size(); for (int i = 0; i < n; i++) { @@ -1089,7 +1210,7 @@ namespace Cantera { bool InterfaceKinetics::ready() const { return (m_finalized); } - + //================================================================================================ // Advance the surface coverages in time /* * @param tstep Time value to advance the surface coverages @@ -1106,7 +1227,7 @@ namespace Cantera { delete m_integrator; m_integrator = 0; } - + //================================================================================================ // Solve for the pseudo steady-state of the surface problem /* * Solve for the steady state of the surface problem. @@ -1135,7 +1256,25 @@ namespace Cantera { */ m_integrator->solvePseudoSteadyStateProblem(ifuncOverride, timeScaleOverride); } + //================================================================================================ + void InterfaceKinetics::setPhaseExistence(const int iphase, const bool exists) { + if (iphase < 0 || iphase >= (int) m_thermo.size()) { + throw CanteraError("InterfaceKinetics:setPhaseExistence", "out of bounds"); + } + if (exists) { + if (!m_phaseExists[iphase]) { + m_phaseExistsCheck--; + m_phaseExists[iphase] = true; + } + } else { + if (m_phaseExists[iphase]) { + m_phaseExistsCheck++; + m_phaseExists[iphase] = false; + } + } + } + //================================================================================================ void EdgeKinetics::finalize() { m_rwork.resize(nReactions()); int ks = reactionPhaseIndex(); @@ -1147,7 +1286,8 @@ namespace Cantera { "expected interface dimension = 1, but got dimension = " +int2str(m_surf->nDim())); m_finalized = true; - } + } + //================================================================================================ } diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index b569afc7f..05e4bc73f 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -374,6 +374,19 @@ namespace Cantera { */ //@{ + //! Add a phase to the kinetics manager object. + /*! + * This must be done before the function init() is called or + * before any reactions are input. + * + * This function calls the Kinetics operator addPhase. + * It also sets the following functions + * + * m_phaseExists[] + * + * @param thermo Reference to the ThermoPhase to be added. + */ + virtual void addPhase(thermo_t& thermo); //! Prepare the class for the addition of reactions. /*! @@ -403,7 +416,10 @@ namespace Cantera { virtual bool ready() const; - + //! Internal routine that updates the Rates of Progress of the reactions + /*! + * This is actually the guts of the functionality of the object + */ void updateROP(); @@ -507,6 +523,16 @@ namespace Cantera { */ void applyExchangeCurrentDensityFormulation(doublereal* const kfwd); + //! Set the existence of a phase in the reaction object + /*! + * Tell the kinetics object whether a phase in the object exists. + * This is actually an extrinsic specification that must be carried out on top of the + * intrinsic calculation of the reaction rate + * + * @param iphase Index of the phase. This is the order within the internal thermo vector object + * @param exists Boolean indicating whether the phase exists or not + */ + void setPhaseExistence(const int iphase, const bool exists); protected: @@ -515,7 +541,7 @@ namespace Cantera { //! m_kk is the number of species in all of the phases //! that participate in this kinetics mechanism. - int m_kk; + int m_kk; //! List of reactions numbers which are reversible reactions /*! @@ -626,7 +652,7 @@ namespace Cantera { */ vector_fp m_mu0; - //! Vector of phase potentials + //! Vector of phase electric potentials /*! * Temporary vector containing the potential of each phase * in the kinetics object @@ -720,6 +746,27 @@ namespace Cantera { */ bool m_has_exchange_current_density_formulation; + //! Int flag to indicate that some phases in the kinetics mechanism are + //! non-existent. + /*! + * We change the ROP vectors to make sure that non-existent phases are treated + * correctly in the kinetics operator. The value of this is equal to the number + * of phases which don't exist. + */ + int m_phaseExistsCheck; + + //! Vector of booleans indicating whether phases exist or not + /*! + * Vector of booleans indicating whether a phase exists or not. + * We use this to set the ROP's so that unphysical things don't happen + * + * length = number of phases in the object + * By default all phases exist. + */ + std::vector m_phaseExists; + + std::vector m_rxnPhaseIsReactant; + std::vector m_rxnPhaseIsProduct; int m_ioFlag; private: diff --git a/Cantera/src/kinetics/Kinetics.cpp b/Cantera/src/kinetics/Kinetics.cpp index 1c45823a2..225ba887d 100644 --- a/Cantera/src/kinetics/Kinetics.cpp +++ b/Cantera/src/kinetics/Kinetics.cpp @@ -224,7 +224,8 @@ namespace Cantera { throw CanteraError("speciesPhase", "unknown species "+nm); } - /** + //============================================================================================== + /* * This function takes as an argument the kineticsSpecies index * (i.e., the list index in the list of species in the kinetics * manager) and returns the index of the phase owning the diff --git a/Cantera/src/thermo/IdealGasPhase.h b/Cantera/src/thermo/IdealGasPhase.h index b83cec970..915e7bfa0 100644 --- a/Cantera/src/thermo/IdealGasPhase.h +++ b/Cantera/src/thermo/IdealGasPhase.h @@ -330,6 +330,7 @@ namespace Cantera { */ IdealGasPhase(const IdealGasPhase &right); + //! Asignment operator /*! * Assignment operator for the object. Constructed diff --git a/config.h.in b/config.h.in index 9cc487cbe..60a4d8e8b 100755 --- a/config.h.in +++ b/config.h.in @@ -4,6 +4,19 @@ #ifndef CT_CONFIG_H #define CT_CONFIG_H +//---------------------------- Version Flags ------------------// +// Cantera version -> this will be a double-quoted string value +// refering to branch number within svn +#undef CANTERA_VERSION + +// Integer for major number of Cantera +#define CANTERA_VERSION_MAJORNUMBER 18 +// Flag indicating it's part of major version 18 +#define CANTERA_VERSION_18 1 +// Flag indicating it's a development version +#define CANTERA_VERSION_18_XXX 1 +// Flag indictaing that its part of 1.8_LiquidTransportDevelop branch +#define CANTERA_VERSION_18_LTD 1 //------------------------ Development flags ------------------// // @@ -64,9 +77,6 @@ typedef int ftnlen; // Fortran hidden string length type #undef DARWIN #undef HAS_SSTREAM -// Cantera version -#undef CANTERA_VERSION - // Identify whether the operating system is cygwin's overlay of // windows, with gcc being used as the compiler. #undef CYGWIN diff --git a/preconfig b/preconfig index ee7b62fea..b6ef3e80f 100755 --- a/preconfig +++ b/preconfig @@ -488,8 +488,21 @@ CT_SHARED_LIB=${CT_SHARED_LIB:=clib} # lowercase 'helvetica'. RPFONT=${RPFONT:="Helvetica"} -# Don't change this. -CANTERA_VERSION=${CANTERA_VERSION:="1.8.0"} +# +# Version Control: +# +# We define a new string for every branch created in svn. +# +# Currently expected versions: +# "1.7" Old version of Cantera +# "1.8.0" Released version of 1.8 +# "1.8.x" Development version of 1.8 +# "1.8_liquidTransportDevelop" branched version of 1.8 having to deal with liquid transport +# +# This field gets written into config.h and is also an autoconf variable. +# +# +CANTERA_VERSION=${CANTERA_VERSION:="1.8_liquidTransportDevelop"} #----------------------------------------------------------------------- #------------------- don't change anything below!! --------------------- From d2a6042f7f2981e793e2c50f4a69fef408f83bc4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 8 May 2010 02:02:10 +0000 Subject: [PATCH 146/446] Added comments. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 2f5cd0cd7..4fa4ed391 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -935,11 +935,27 @@ namespace Cantera { */ void InterfaceKinetics::addReaction(const ReactionData& r) { + /* + * Install the rate coefficient for the current reaction + * in the appropriate data structure. + */ addElementaryReaction(r); - - // operations common to all reaction types + /* + * Add the reactants and products for m_ropnet;the current reaction + * to the various stoichiometric coefficient arrays. + */ installReagents(r); + /* + * Save the reaction and product groups, which are + * part of the ReactionData class, in this class. + * They aren't used for anything but reaction path + * analysis. + */ //installGroups(reactionNumber(), r.rgroups, r.pgroups); + /* + * Increase the internal number of reactions, m_ii, by one. + * increase the size of m_perturb by one as well. + */ incrementRxnCount(); m_rxneqn.push_back(r.equation); From 1611b8715554a6ed3b4360e73acc31b7bfd2eb46 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 8 May 2010 18:06:27 +0000 Subject: [PATCH 147/446] Added version control information to winconfig.h --- Cantera/cxx/include/Cantera.mak.in | 5 ++--- Cantera/cxx/include/Cantera_bt.mak.in | 11 +++++------ config.h.in | 5 +++-- winconfig.h | 15 ++++++++++++--- 4 files changed, 22 insertions(+), 14 deletions(-) diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in index ffbc46197..23c5114bd 100644 --- a/Cantera/cxx/include/Cantera.mak.in +++ b/Cantera/cxx/include/Cantera.mak.in @@ -22,9 +22,9 @@ # build tree environment or in the install tree environment. # in_CanteraBuildTree = 0 - +# CANTERA_VERSION=@ctversion@ - +# ############################################################################### # CANTERA CORE ############################################################################### @@ -140,7 +140,6 @@ CANTERA_TOTAL_LIBS_DEP= $(CANTERA_CORE_LIBS_DEP) \ $(CANTERA_CVODE_LIBS_DEP) \ $(CANTERA_BLAS_LAPACK_LIBS_DEP) # -# # Dependency Line # CANTERA_LIBS_DEP= @INSTALL_LIBS_DEP@ $(CANTERA_LIBDIR)/libctcxx.a diff --git a/Cantera/cxx/include/Cantera_bt.mak.in b/Cantera/cxx/include/Cantera_bt.mak.in index 88cdc0633..f6aa0aee6 100644 --- a/Cantera/cxx/include/Cantera_bt.mak.in +++ b/Cantera/cxx/include/Cantera_bt.mak.in @@ -22,9 +22,9 @@ # build tree environment or in the install tree environment. # in_CanteraBuildTree = 0 - +# CANTERA_VERSION=@ctversion@ - +# ############################################################################### # CANTERA CORE ############################################################################### @@ -112,18 +112,17 @@ CANTERA_F2C_LIBS= -L$(CANTERA_LIBSDIR) -lctf2c else CANTERA_F2C_LIBS= @F2C_SYSTEMLIB@ endif - - +# ##################################################################### # COMBINATIONS OF INCLUDES AND LIBS #################################################################### - +# CANTERA_TOTAL_INCLUDES= $(CANTERA_CORE_INCLUDES) $(CANTERA_BOOST_INCLUDES) $(CANTERA_CVODE_INCLUDE) # # You can add this into the compilation environment to identify the version number # CANTERA_DEFINES = -DCANTERA_VERSION=@ctversion@ - +# CANTERA_TOTAL_LIBS2 = @LOCAL_LIB_DIRS@ @LOCAL_LIBS@ CANTERA_TOTAL_LIBS= $(CANTERA_CORE_LIBS) $(CANTERA_BOOST_LIBS) \ diff --git a/config.h.in b/config.h.in index 60a4d8e8b..9f4d1b1d7 100755 --- a/config.h.in +++ b/config.h.in @@ -5,10 +5,11 @@ #define CT_CONFIG_H //---------------------------- Version Flags ------------------// +// // Cantera version -> this will be a double-quoted string value // refering to branch number within svn #undef CANTERA_VERSION - +// // Integer for major number of Cantera #define CANTERA_VERSION_MAJORNUMBER 18 // Flag indicating it's part of major version 18 @@ -17,7 +18,7 @@ #define CANTERA_VERSION_18_XXX 1 // Flag indictaing that its part of 1.8_LiquidTransportDevelop branch #define CANTERA_VERSION_18_LTD 1 - +// //------------------------ Development flags ------------------// // // Compile in additional debug printing where available. diff --git a/winconfig.h b/winconfig.h index 02d3b239e..94984e233 100644 --- a/winconfig.h +++ b/winconfig.h @@ -5,6 +5,18 @@ #ifndef CT_CONFIG_H #define CT_CONFIG_H +// Cantera version -> this will be a double-quoted string value +// refering to branch number within svn +#define CANTERA_VERSION "1.8_liquidTransportDevelop" + +// Integer for major number of Cantera +#define CANTERA_VERSION_MAJORNUMBER 18 +// Flag indicating it's part of major version 18 +#define CANTERA_VERSION_18 1 +// Flag indicating it's a development version +#define CANTERA_VERSION_18_XXX 1 +// Flag indictaing that its part of 1.8_LiquidTransportDevelop branch +#define CANTERA_VERSION_18_LTD 1 //------------------------ Development flags ------------------// // @@ -64,9 +76,6 @@ typedef int ftnlen; // Fortran hidden string length type /* #undef DARWIN */ #define HAS_SSTREAM 1 -// Cantera version -#define CANTERA_VERSION "1.8.0" - // Identify whether the operating system is cygwin's overlay of // windows, with gcc being used as the compiler. /* #undef CYGWIN */ From bda6c5aed463fd3ac4883021c90f149d5fde9559 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 12 May 2010 18:51:11 +0000 Subject: [PATCH 148/446] Fixed an error in the destructor. Replaced delete with delete []. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 4fa4ed391..fb910a367 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -72,8 +72,8 @@ namespace Cantera { delete m_integrator; } for (int i = 0; i < m_ii; i++) { - delete m_rxnPhaseIsReactant[i]; - delete m_rxnPhaseIsProduct[i]; + delete [] m_rxnPhaseIsReactant[i]; + delete [] m_rxnPhaseIsProduct[i]; } } //==================================================================================================================== @@ -130,8 +130,8 @@ namespace Cantera { if (this == &right) return *this; for (i = 0; i < m_ii; i++) { - delete (m_rxnPhaseIsReactant[i]); - delete (m_rxnPhaseIsProduct[i]); + delete [] m_rxnPhaseIsReactant[i]; + delete [] m_rxnPhaseIsProduct[i]; } Kinetics::operator=(right); @@ -183,9 +183,7 @@ namespace Cantera { m_rxnPhaseIsProduct[i][p] = right.m_rxnPhaseIsProduct[i][p]; } } - m_rxnPhaseIsProduct = right.m_rxnPhaseIsProduct; - m_ioFlag = right.m_ioFlag; return *this; From 4253221ba7171c7d7457a1f2d28311f2acdcc10a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 15 May 2010 00:09:34 +0000 Subject: [PATCH 149/446] Added a parseSpeciesName function --- Cantera/src/base/stringUtils.cpp | 90 ++++++++++++++++++++++---------- Cantera/src/base/stringUtils.h | 16 ++++++ 2 files changed, 79 insertions(+), 27 deletions(-) diff --git a/Cantera/src/base/stringUtils.cpp b/Cantera/src/base/stringUtils.cpp index 54eb66d32..599b34efa 100644 --- a/Cantera/src/base/stringUtils.cpp +++ b/Cantera/src/base/stringUtils.cpp @@ -35,7 +35,7 @@ namespace Cantera { - + //================================================================================================ // Convert a double into a c++ string /* * This routine doesn't assume a formatting. You @@ -62,7 +62,7 @@ namespace Cantera { } return std::string(" "); } - + //================================================================================================ /* * Convert an integer number to a std::string using sprintf. */ @@ -75,7 +75,7 @@ namespace Cantera { } return std::string(" "); } - + //================================================================================================ // Convert an int to a string /* * @param n int to be converted @@ -89,14 +89,14 @@ namespace Cantera { } return std::string(" "); } - + //================================================================================================ std::string lowercase(const std::string &s) { int n = static_cast(s.size()); std::string lc(s); for (int i = 0; i < n; i++) lc[i] = tolower(s[i]); return lc; } - + //================================================================================================ //! Return the position of the first printable //! character in the string /*! @@ -113,7 +113,7 @@ namespace Cantera { } return i; } - + //================================================================================================ //! Return the position of the last printable //! character in the string /*! @@ -129,7 +129,7 @@ namespace Cantera { if (s[i] != ' ' && isprint(s[i])) break; return i; } - + //================================================================================================ // Strip the leading and trailing white space // from a string /* @@ -145,7 +145,7 @@ namespace Cantera { int ilast = lastChar(s); return s.substr(ifirst, ilast - ifirst + 1); } - + //================================================================================================ // Strip non-printing characters wherever they are /* * @param s Input string @@ -163,8 +163,7 @@ namespace Cantera { } return ss; } - - + //================================================================================================ // Parse a composition string into a map consisting of individual key:composition // pairs. /* @@ -218,7 +217,7 @@ namespace Cantera { } while (s != ""); } - + //================================================================================================ // Parse a composition string into individual key:composition // pairs /* @@ -249,7 +248,7 @@ namespace Cantera { } while (s != ""); } - + //================================================================================================ int fillArrayFromString(const std::string& str, doublereal* const a, const char delim) { std::string::size_type iloc; @@ -271,7 +270,7 @@ namespace Cantera { } return count; } - + //================================================================================================ // Get the file name without the path or extension /* * @param fullPath Input file name consisting @@ -296,20 +295,19 @@ namespace Cantera { } return file; } - - + //================================================================================================ int intValue(std::string val) { return std::atoi(stripws(val).c_str()); } - + //================================================================================================ doublereal fpValue(std::string val) { return std::atof(stripws(val).c_str()); } - + //================================================================================================ doublereal fpValueCheck(std::string val) { return atofCheck(stripws(val).c_str()); } - + //================================================================================================ // Generate a logfile name based on an input file name /* * It tries to find the basename. Then, it appends a .log @@ -324,7 +322,7 @@ namespace Cantera { logfile += ".log"; return logfile; } - + //================================================================================================ // Line wrap a string via a copy operation /* * @param s Input string to be line wrapped @@ -346,8 +344,46 @@ namespace Cantera { } return r; } - - + //================================================================================================ + // Parse a name string, separating out the phase name from the species name + /* + * Name strings must not contain these internal characters "; \n \t ," + * Only one colon is allowed, the one separating the phase name from the + * species name. Therefore, names may not include a colon. + * + * @param nameStr (input) Name string containing the phase name and the species + * name separated by a colon. The phase name is optional. + * example: "silane:SiH4" + * @param phaseName (output) Name of the phase, if specified. If not specified, + * a blank string is returned. + * @return (output) Species name is returned. If nameStr is blank + * an empty string is returned. + */ + std::string parseSpeciesName(const std::string& nameStr, std::string &phaseName) { + std::string s = stripws(nameStr); + std::string::size_type ibegin, iend, icolon; + phaseName = ""; + ibegin = s.find_first_not_of(", ;\n\t"); + if (ibegin != std::string::npos) { + s = s.substr(ibegin,s.size()); + icolon = s.find(':'); + iend = s.find_first_of(", ;\n\t"); + if (icolon != std::string::npos) { + phaseName = s.substr(0, icolon); + s = s.substr(icolon+1, s.size()); + icolon = s.find(':'); + if (icolon != std::string::npos) { + throw CanteraError("parseSpeciesName()", "two colons in name: " + nameStr); + } + } + if (iend != std::string::npos) { + throw CanteraError("parseSpeciesName()", + "Species name has \", ;/\n/\t\" in the middle of it: " + nameStr); + } + } + return s; + } + //================================================================================================ // Routine strips off white space from a c character string /* * This routine strips off blanks and tabs (only leading and trailing @@ -396,7 +432,7 @@ namespace Cantera { str[j] = '\0'; return (j); } - + //================================================================================================ // Translate a char string into a single double /* * atofCheck is a wrapper around the C stdlib routine atof(). @@ -472,7 +508,7 @@ namespace Cantera { free(eptr); return rval; } - + //================================================================================================ // Interpret one or two token string as a single double /* * This is similar to atof(). However, the second token @@ -502,7 +538,7 @@ namespace Cantera { doublereal val = atofCheck(v[0].c_str()); return (val * fp); } - + //================================================================================================ static std::string::size_type findFirstWS(const std::string& val) { std::string::size_type ibegin = std::string::npos; int j = 0; @@ -518,7 +554,7 @@ namespace Cantera { } return ibegin; } - + //================================================================================================ static std::string::size_type findFirstNotOfWS(const std::string& val) { std::string::size_type ibegin = std::string::npos; int j = 0; @@ -534,7 +570,7 @@ namespace Cantera { } return ibegin; } - + //================================================================================================ // This function separates a string up into tokens // according to the location of white space. /* @@ -566,6 +602,6 @@ namespace Cantera { } } } - + //================================================================================================ } diff --git a/Cantera/src/base/stringUtils.h b/Cantera/src/base/stringUtils.h index 4dc6c7dbf..0194dc984 100644 --- a/Cantera/src/base/stringUtils.h +++ b/Cantera/src/base/stringUtils.h @@ -182,6 +182,22 @@ namespace Cantera { */ doublereal fpValueCheck(std::string val); + //! Parse a name string, separating out the phase name from the species name + /*! + * Name strings must not contain these internal characters "; \n \t ," + * Only one colon is allowed, the one separating the phase name from the + * species name. Therefore, names may not include a colon. + * + * @param nameStr (input) Name string containing the phase name and the species + * name separated by a colon. The phase name is optional. + * example: "silane:SiH4" + * @param phaseName (output) Name of the phase, if specified. If not specified, + * a blank string is returned. + * @return (output) Species name is returned. If nameStr is blank + * an empty string is returned. + */ + std::string parseSpeciesName(const std::string& nameStr, std::string &phaseName); + //! Line wrap a string via a copy operation /*! * @param s Input string to be line wrapped From 45a427fe54b38dfe75cbfb6aff8e8c7240eac68a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 22 May 2010 20:32:29 +0000 Subject: [PATCH 150/446] Added a first generation capability for a general nonlinear solver for steady state problems. This is based on the surface solver --- Cantera/src/numerics/Makefile.in | 6 +- Cantera/src/numerics/ResidEval.h | 20 +- Cantera/src/numerics/solveProb.cpp | 968 +++++++++++++++++++++++++++++ Cantera/src/numerics/solveProb.h | 435 +++++++++++++ 4 files changed, 1424 insertions(+), 5 deletions(-) create mode 100644 Cantera/src/numerics/solveProb.cpp create mode 100644 Cantera/src/numerics/solveProb.h diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index bffd2a159..97decc3ae 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -34,13 +34,15 @@ CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ ODE_integrators.o BandMatrix.o DAE_solvers.o \ - funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o + funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o \ + solveProb.o NUMERICS_H = ArrayViewer.h DenseMatrix.h \ funcs.h ctlapack.h Func1.h FuncEval.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ - SquareMatrix.h ResidJacEval.h NonlinearSolver.h + SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ + solveProb.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index ec61bd2d2..06da5043b 100755 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -82,11 +82,25 @@ namespace Cantera { throw CanteraError("ResidEval::eval()", "base class called"); } + virtual int evalSS(const doublereal t, const doublereal * const y, + doublereal * const r) { + return eval(t, y, 0, r); + } + + virtual int evalSimpleTD(const doublereal t, const doublereal * const y, + const doublereal * const yold, doublereal deltaT, + doublereal * const r) { + int nn = nEquations(); + vector_fp ydot(nn); + for (int i = 0; i < nn; i++) { + ydot[i] = (y[i] - yold[i]) / deltaT; + } + return eval(t, y, DATA_PTR(ydot), r); + } + /** * Fill the solution and derivative vectors with the initial - * conditions at initial time t0. If these do not satisfy the - * residual equation, call one of the "corrrectInitial_xxx" - * methods before calling solve. + * conditions at initial time t0. */ virtual void getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot) { diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp new file mode 100644 index 000000000..f707f5042 --- /dev/null +++ b/Cantera/src/numerics/solveProb.cpp @@ -0,0 +1,968 @@ +/* + * @file: solveSP.cpp Implicit solver for nonlinear problems + */ +/* + * $Id: solveSP.cpp 381 2010-01-15 21:20:41Z hkmoffa $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#include "solveProb.h" +#include "clockWC.h" +#include "ctlapack.h" + +/* Standard include files */ + +#include +#include +#include + +#include + +using namespace std; +namespace Cantera { + + /*************************************************************************** + * STATIC ROUTINES DEFINED IN THIS FILE + ***************************************************************************/ + + static doublereal calcWeightedNorm(const doublereal [], const doublereal dx[], int); + + /*************************************************************************** + * LAPACK PROTOTYPES + ***************************************************************************/ + + /***************************************************************************** + * PROTOTYPES and PREPROC DIRECTIVES FOR MISC. ROUTINES + *****************************************************************************/ + +#ifndef MAX +# define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) /* max function */ +#endif + +#ifndef MIN +# define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) /* min function */ +#endif + +#ifndef DAMPING +# define DAMPING true +#endif + + /*************************************************************************** + * solveSP Class Definitinos + ***************************************************************************/ + //================================================================================================ + // Main constructor + solveProb::solveProb(ResidEval* resid) : + m_residFunc(resid), + m_neq(0), + m_atol(1.0E-15), + m_rtol(1.0E-4), + m_maxstep(1000), + m_ioflag(0) + { + m_neq = m_residFunc->nEquations(); + + // Dimension solution vector + int dim1 = MAX(1, m_neq); + m_netProductionRatesSave.resize(dim1, 0.0); + m_numEqn1.resize(dim1, 0.0); + m_numEqn2.resize(dim1, 0.0); + m_CSolnSave.resize(dim1, 0.0); + m_CSolnSP.resize(dim1, 0.0); + m_CSolnSPInit.resize(dim1, 0.0); + m_CSolnSPOld.resize(dim1, 0.0); + m_wtResid.resize(dim1, 0.0); + m_wtSpecies.resize(dim1, 0.0); + m_resid.resize(dim1, 0.0); + m_ipiv.resize(dim1, 0); + + m_Jac.resize(dim1, dim1, 0.0); + m_JacCol.resize(dim1, 0); + for (int k = 0; k < dim1; k++) { + m_JacCol[k] = m_Jac.ptrColumn(k); + } + } + //================================================================================================ + // Empty destructor + solveProb::~solveProb() { + } + //================================================================================================ + /* + * The following calculation is a Newton's method to + * get the surface fractions of the surface and bulk species by + * requiring that the + * surface species production rate = 0 and that the bulk fractions are + * proportional to their production rates. + */ + int solveProb::solve(int ifunc, doublereal time_scale, + doublereal reltol, doublereal abstol) + { + doublereal EXTRA_ACCURACY = 0.001; + if (ifunc == SOLVEPROB_JACOBIAN) { + EXTRA_ACCURACY *= 0.001; + } + int irow; + int jcol, info = 0; + int label_t=-1; /* Species IDs for time control */ + int label_d; /* Species IDs for damping control */ + int label_t_old=-1; + doublereal label_factor = 1.0; + int iter=0; // iteration number on numlinear solver + int iter_max=1000; // maximum number of nonlinear iterations + int nrhs=1; + doublereal deltaT = 1.0E-10; // Delta time step + doublereal damp=1.0, tmp; + // Weighted L2 norm of the residual. Currently, this is only + // used for IO purposes. It doesn't control convergence. + // Therefore, it is turned off when DEBUG_SOLVEPROB isn't defined. + doublereal resid_norm; + doublereal inv_t = 0.0; + doublereal t_real = 0.0, update_norm = 1.0E6; + + bool do_time = false, not_converged = true; + +#ifdef DEBUG_SOLVEPROB +#ifdef DEBUG_SOLVEPROB_TIME + doublereal t1; +#endif +#else + if (m_ioflag > 1) { + m_ioflag = 1; + } +#endif + +#ifdef DEBUG_SOLVEPROB +#ifdef DEBUG_SOLVEPROB_TIME + Cantera::clockWC wc; + if (m_ioflag) t1 = wc.secondsWC(); +#endif +#endif + + /* + * Set the initial value of the do_time parameter + */ + if (ifunc == SOLVEPROB_INITIALIZE || ifunc == SOLVEPROB_TRANSIENT) do_time = true; + + /* + * upload the initial conditions + */ + m_residFunc->getInitialConditions(t_real, DATA_PTR(m_CSolnSP), DATA_PTR(m_numEqn1)); + /* + * Store the initial guess in the soln vector, + * CSoln, and in an separate vector CSolnInit. + */ + for (int n = 0; n < m_neq; n++) { + // m_CSolnSP[loc] = m_numEqn1[k]; + + } + + + std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), m_CSolnSPInit.begin()); + + // Calculate the largest species in each phase + // evalSurfLarge(DATA_PTR(m_CSolnSP)); + /* + * Get the net production rate of all species in the kinetics manager. + */ + // m_kin->getNetProductionRates(DATA_PTR(m_netProductionRatesSave)); + + if (m_ioflag) { + print_header(m_ioflag, ifunc, time_scale, DAMPING, reltol, abstol, + DATA_PTR(m_netProductionRatesSave)); + } + + /* + * Quick return when there isn't a surface problem to solve + */ + if (m_neq == 0) { + not_converged = false; + update_norm = 0.0; + } + + /* ------------------------------------------------------------------ + * Start of Newton's method + * ------------------------------------------------------------------ + */ + while (not_converged && iter < iter_max) { + iter++; + /* + * Store previous iteration's solution in the old solution vector + */ + std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), m_CSolnSPOld.begin()); + + /* + * Evaluate the largest surface species for each surface phase every + * 5 iterations. + */ + // if (iter%5 == 4) { + // evalSurfLarge(DATA_PTR(m_CSolnSP)); + // } + + /* + * Calculate the value of the time step + * - heuristics to stop large oscillations in deltaT + */ + if (do_time) { + /* don't hurry increase in time step at the same time as damping */ + if (damp < 1.0) label_factor = 1.0; + tmp = calc_t(DATA_PTR(m_netProductionRatesSave), DATA_PTR(m_CSolnSP), + &label_t, &label_t_old, &label_factor, m_ioflag); + if (iter < 10) + inv_t = tmp; + else if (tmp > 2.0*inv_t) + inv_t = 2.0*inv_t; + else { + inv_t = tmp; + } + + /* + * Check end condition + */ + + if (ifunc == SOLVEPROB_TRANSIENT) { + tmp = t_real + 1.0/inv_t; + if (tmp > time_scale) inv_t = 1.0/(time_scale - t_real); + } + } + else { + /* make steady state calc a step of 1 million seconds to + prevent singular jacobians for some pathological cases */ + inv_t = 1.0e-6; + } + deltaT = 1.0/inv_t; + + /* + * Call the routine to numerically evaluation the jacobian + * and residual for the current iteration. + */ + resjac_eval(m_JacCol, DATA_PTR(m_resid), DATA_PTR(m_CSolnSP), + DATA_PTR(m_CSolnSPOld), do_time, deltaT); + + /* + * Calculate the weights. Make sure the calculation is carried + * out on the first iteration. + */ + if (iter%4 == 1) { + calcWeights(DATA_PTR(m_wtSpecies), DATA_PTR(m_wtResid), + DATA_PTR(m_CSolnSP)); + } + + /* + * Find the weighted norm of the residual + */ + resid_norm = calcWeightedNorm(DATA_PTR(m_wtResid), DATA_PTR(m_resid), m_neq); + +#ifdef DEBUG_SOLVEPROB + if (m_ioflag > 1) { + printIterationHeader(m_ioflag, damp, inv_t, t_real, iter, do_time); + /* + * Print out the residual and jacobian + */ + printResJac(m_ioflag, m_neq, m_Jac, DATA_PTR(m_resid), + DATA_PTR(m_wtResid), resid_norm); + } +#endif + + /* + * Solve Linear system (with LAPACK). The solution is in resid[] + */ + + ct_dgetrf(m_neq, m_neq, m_JacCol[0], m_neq, DATA_PTR(m_ipiv), info); + if (info==0) { + ct_dgetrs(ctlapack::NoTranspose, m_neq, nrhs, m_JacCol[0], + m_neq, DATA_PTR(m_ipiv), DATA_PTR(m_resid), m_neq, + info); + } + /* + * Force convergence if residual is small to avoid + * "nan" results from the linear solve. + */ + else { + if (m_ioflag) { + printf("solveSurfSS: Zero pivot, assuming converged: %g (%d)\n", + resid_norm, info); + } + for (jcol = 0; jcol < m_neq; jcol++) m_resid[jcol] = 0.0; + + /* print out some helpful info */ + if (m_ioflag > 1) { + printf("-----\n"); + printf("solveSurfProb: iter %d t_real %g delta_t %g\n\n", + iter,t_real, 1.0/inv_t); + printf("solveSurfProb: init guess, current concentration," + "and prod rate:\n"); + + printf("-----\n"); + } + if (do_time) t_real += time_scale; +#ifdef DEBUG_SOLVEPROB + if (m_ioflag) { + printf("\nResidual is small, forcing convergence!\n"); + } +#endif + } + + /* + * Calculate the Damping factor needed to keep all unknowns + * between 0 and 1, and not allow too large a change (factor of 2) + * in any unknown. + */ + +#ifdef DAMPING + damp = calc_damping( DATA_PTR(m_CSolnSP), DATA_PTR(m_resid), m_neq, &label_d); +#endif + + /* + * Calculate the weighted norm of the update vector + * Here, resid is the delta of the solution, in concentration + * units. + */ + update_norm = calcWeightedNorm(DATA_PTR(m_wtSpecies), + DATA_PTR(m_resid), m_neq); + /* + * Update the solution vector and real time + * Crop the concentrations to zero. + */ + for (irow = 0; irow < m_neq; irow++) { + m_CSolnSP[irow] -= damp * m_resid[irow]; + } + for (irow = 0; irow < m_neq; irow++) { + m_CSolnSP[irow] = MAX(0.0, m_CSolnSP[irow]); + } + updateState(DATA_PTR(m_CSolnSP)); + + if (do_time) t_real += damp/inv_t; + + if (m_ioflag) { + printIteration(m_ioflag, damp, label_d, label_t, inv_t, t_real, iter, + update_norm, resid_norm, + DATA_PTR(m_netProductionRatesSave), + DATA_PTR(m_CSolnSP), DATA_PTR(m_resid), + DATA_PTR(m_wtSpecies), m_neq, do_time); + } + + if (ifunc == SOLVEPROB_TRANSIENT) + not_converged = (t_real < time_scale); + else { + if (do_time) { + if (t_real > time_scale || + (resid_norm < 1.0e-7 && + update_norm*time_scale/t_real < EXTRA_ACCURACY) ) { + do_time = false; +#ifdef DEBUG_SOLVEPROB + if (m_ioflag > 1) { + printf("\t\tSwitching to steady solve.\n"); + } +#endif + } + } + else { + not_converged = ((update_norm > EXTRA_ACCURACY) || + (resid_norm > EXTRA_ACCURACY)); + } + } + } /* End of Newton's Method while statement */ + + /* + * End Newton's method. If not converged, print error message and + * recalculate sdot's at equal site fractions. + */ + if (not_converged) { + if (m_ioflag) { + printf("#$#$#$# Error in solveProb $#$#$#$ \n"); + printf("Newton iter on surface species did not converge, " + "update_norm = %e \n", update_norm); + printf("Continuing anyway\n"); + } + } +#ifdef DEBUG_SOLVEPROB +#ifdef DEBUG_SOLVEPROB_TIME + if (m_ioflag) { + printf("\nEnd of solve, time used: %e\n", wc.secondsWC()-t1); + } +#endif +#endif + + /* + * Decide on what to return in the solution vector + * - right now, will always return the last solution + * no matter how bad + */ + if (m_ioflag) { + fun_eval(DATA_PTR(m_resid), DATA_PTR(m_CSolnSP), DATA_PTR(m_CSolnSPOld), + false, deltaT); + resid_norm = calcWeightedNorm(DATA_PTR(m_wtResid), + DATA_PTR(m_resid), m_neq); + printFinal(m_ioflag, damp, label_d, label_t, inv_t, t_real, iter, + update_norm, resid_norm, DATA_PTR(m_netProductionRatesSave), + DATA_PTR(m_CSolnSP), DATA_PTR(m_resid), + DATA_PTR(m_wtSpecies), + DATA_PTR(m_wtResid), m_neq, do_time); + } + + /* + * Return with the appropriate flag + */ + if (update_norm > 1.0) { + return -1; + } + return 1; + } + +#undef DAMPING + + //================================================================================================ + /* + * Update the surface states of the surface phases. + */ + void solveProb::updateState(const doublereal *CSolnSP) { + + } + //================================================================================================ + /* + * This calculates the net production rates of all species + * + * This calculates the function eval. + * (should switch to special_species formulation for sum condition) + * + * @internal + * This routine uses the m_numEqn1 and m_netProductionRatesSave vectors + * as temporary internal storage. + */ + void solveProb::fun_eval(doublereal * resid, const doublereal *CSoln, + const doublereal *CSolnOld, const bool do_time, + const doublereal deltaT) + { + if (do_time) { + m_residFunc->evalSimpleTD(0.0, CSoln, CSolnOld, deltaT, resid); + } else { + m_residFunc->evalSS(0.0, CSoln, resid); + } + } + //================================================================================================ + /* + * Calculate the Jacobian and residual + * + * @internal + * This routine uses the m_numEqn2 vector + * as temporary internal storage. + */ + void solveProb::resjac_eval(std::vector &JacCol, + doublereal resid[], doublereal CSoln[], + const doublereal CSolnOld[], const bool do_time, + const doublereal deltaT) + { + int i, kCol; + doublereal dc, cSave, sd; + doublereal *col_j; + /* + * Calculate the residual + */ + fun_eval(resid, CSoln, CSolnOld, do_time, deltaT); + /* + * Now we will look over the columns perturbing each unknown. + */ + + for (kCol = 0; kCol < m_neq; kCol++) { + cSave = CSoln[kCol]; + sd = fabs(cSave) + fabs(CSoln[kCol]) + m_atol[kCol] * 1.0E6; + if (sd < 1.0E-200) { + sd = 1.0E-4; + } + dc = fmaxx(1.0E-11 * sd, fabs(cSave) * 1.0E-6); + CSoln[kCol] += dc; + fun_eval(DATA_PTR(m_numEqn2), CSoln, CSolnOld, do_time, deltaT); + col_j = JacCol[kCol]; + for (i = 0; i < m_neq; i++) { + col_j[i] = (m_numEqn2[i] - resid[i])/dc; + } + CSoln[kCol] = cSave; + } + + } + //================================================================================================ +#define APPROACH 0.50 + /* This function calculates a damping factor for the Newton iteration update + * vector, dxneg, to insure that all site and bulk fractions, x, remain + * bounded between zero and one. + * + * dxneg[] = negative of the update vector. + * + * The constant "APPROACH" sets the fraction of the distance to the boundary + * that the step can take. If the full step would not force any fraction + * outside of 0-1, then Newton's method is allowed to operate normally. + */ + doublereal solveProb::calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label) + { + int i; + doublereal damp = 1.0, xnew, xtop, xbot; + static doublereal damp_old = 1.0; + + *label = -1; + + for (i = 0; i < dim; i++) { + + /* + * Calculate the new suggested new value of x[i] + */ + // x_raw = x[i] - dxneg[i]; + double delta_x = - dxneg[i]; + xnew = x[i] - damp * dxneg[i]; + + /* + * Calculate the allowed maximum and minimum values of x[i] + * - Only going to allow x[i] to converge to zero by a + * single order of magnitude at a time + */ + + xtop = 1.0 - 0.1*fabs(1.0-x[i]); + xbot = fabs(x[i]*0.1) - 1.0e-16; + if (xnew > xtop) { + damp = - APPROACH * (1.0 - x[i]) / dxneg[i]; + *label = i; + } + else if (xnew < xbot) { + damp = APPROACH * x[i] / dxneg[i]; + *label = i; + } else if (xnew > 3.0*MAX(x[i], 1.0E-10)) { + damp = - 2.0 * MAX(x[i], 1.0E-10) / dxneg[i]; + *label = i; + } + double denom = fabs(x[i]) + m_atol[i]; + if ((fabs(delta_x) / denom) > 0.3) { + double newdamp = 0.3 * denom / delta_x; + damp = MIN(damp, newdamp); + } + + } + + // if (damp < 1.0e-2) damp = 1.0e-2; + /* + * Only allow the damping parameter to increase by a factor of three each + * iteration. Heuristic to avoid oscillations in the value of damp + */ + if (damp > damp_old*3) { + damp = damp_old*3; + *label = -1; + } + + /* + * Save old value of the damping parameter for use + * in subsequent calls. + */ + + damp_old = damp; + return damp; + + } +#undef APPROACH + //================================================================================================ + /* + * This function calculates the norm of an update, dx[], + * based on the weighted values of x. + */ + static doublereal calcWeightedNorm(const doublereal wtX[], const doublereal dx[], int dim) { + doublereal norm = 0.0; + doublereal tmp; + if (dim == 0) return 0.0; + for (int i = 0; i < dim; i++) { + tmp = dx[i] / wtX[i]; + norm += tmp * tmp; + } + return (sqrt(norm/dim)); + } + //================================================================================================ + /* + * Calculate the weighting factors for norms wrt both the species + * concentration unknowns and the residual unknowns. + * + */ + void solveProb::calcWeights(doublereal wtSpecies[], doublereal wtResid[], + const doublereal CSoln[]) + { + int k, jcol; + /* + * First calculate the weighting factor + */ + + for (k = 0; k < m_neq; k++) { + wtSpecies[k] = m_atol[k] + m_rtol * fabs(CSoln[k]); + } + /* + * Now do the residual Weights. Since we have the Jacobian, we + * will use it to generate a number based on the what a significant + * change in a solution variable does to each residual. + * This is a row sum scale operation. + */ + for (k = 0; k < m_neq; k++) { + wtResid[k] = 0.0; + for (jcol = 0; jcol < m_neq; jcol++) { + wtResid[k] += fabs(m_Jac(k,jcol) * wtSpecies[jcol]); + } + } + } + //================================================================================================ + /* + * This routine calculates a pretty conservative 1/del_t based + * on MAX_i(sdot_i/(X_i*SDen0)). This probably guarantees + * diagonal dominance. + * + * Small surface fractions are allowed to intervene in the del_t + * determination, no matter how small. This may be changed. + * Now minimum changed to 1.0e-12, + * + * Maximum time step set to time_scale. + */ + doublereal solveProb:: + calc_t(doublereal netProdRateSolnSP[], doublereal Csoln[], + int *label, int *label_old, doublereal *label_factor, int ioflag) + { + int k, kspSpecial; + doublereal tmp, inv_timeScale=0.0; + for (k = 0; k < m_neq; k++) { + if (Csoln[k] <= 1.0E-10) { + tmp = 1.0E-10; + } else { + tmp = Csoln[k]; + } + tmp = fabs(netProdRateSolnSP[k]/ tmp); + + + if (netProdRateSolnSP[k]> 0.0) tmp /= 100.; + if (tmp > inv_timeScale) { + inv_timeScale = tmp; + *label = k; + + kspSpecial = k; + } + } + + + /* + * Increase time step exponentially as same species repeatedly + * controls time step + */ + if (*label == *label_old) { + *label_factor *= 1.5; + } else { + *label_old = *label; + *label_factor = 1.0; + } + inv_timeScale = inv_timeScale / *label_factor; +#ifdef DEBUG_SOLVEPROB + if (ioflag > 1) { + if (*label_factor > 1.0) { + printf("Delta_t increase due to repeated controlling species = %e\n", + *label_factor); + } + int kkin = m_kinSpecIndex[*label]; + + string sn = " " + printf("calc_t: spec=%d(%s) sf=%e pr=%e dt=%e\n", + *label, sn.c_str(), XMolSolnSP[*label], + netProdRateSolnSP[*label], 1.0/inv_timeScale); + } +#endif + + return (inv_timeScale); + + } + //================================================================================================ + /* + * printResJac(): prints out the residual and Jacobian. + * + */ +#ifdef DEBUG_SOLVEPROB + void solveProb::printResJac(int ioflag, int neq, const Array2D &Jac, + doublereal resid[], doublereal wtRes[], + doublereal norm) + { + + } +#endif + //================================================================================================ + /* + * Optional printing at the start of the solveProb problem + */ + void solveProb::print_header(int ioflag, int ifunc, doublereal time_scale, + int damping, doublereal reltol, doublereal abstol, + doublereal netProdRate[]) { + if (ioflag) { + printf("\n================================ SOLVEPROB CALL SETUP " + "========================================\n"); + if (ifunc == SOLVEPROB_INITIALIZE) { + printf("\n SOLVEPROB Called with Initialization turned on\n"); + printf(" Time scale input = %9.3e\n", time_scale); + } + else if (ifunc == SOLVEPROB_RESIDUAL) { + printf("\n SOLVEPROB Called to calculate steady state residual\n"); + printf( " from a good initial guess\n"); + } + else if (ifunc == SOLVEPROB_JACOBIAN) { + printf("\n SOLVEPROB Called to calculate steady state jacobian\n"); + printf( " from a good initial guess\n"); + } + else if (ifunc == SOLVEPROB_TRANSIENT) { + printf("\n SOLVEPROB Called to integrate surface in time\n"); + printf( " for a total of %9.3e sec\n", time_scale); + } + else { + fprintf(stderr,"Unknown ifunc flag = %d\n", ifunc); + exit(EXIT_FAILURE); + } + + + + if (damping) + printf(" Damping is ON \n"); + else + printf(" Damping is OFF \n"); + + printf(" Reltol = %9.3e, Abstol = %9.3e\n", reltol, abstol); + } + + /* + * Print out the initial guess + */ +#ifdef DEBUG_SOLVEPROB + if (ioflag > 1) { + printf("\n================================ INITIAL GUESS " + "========================================\n"); + int kindexSP = 0; + for (int isp = 0; isp < m_numSurfPhases; isp++) { + InterfaceKinetics *m_kin = m_objects[isp]; + int surfIndex = m_kin->surfacePhaseIndex(); + int nPhases = m_kin->nPhases(); + m_kin->getNetProductionRates(netProdRate); + updateMFKinSpecies(XMolKinSpecies, isp); + + printf("\n IntefaceKinetics Object # %d\n\n", isp); + + printf("\t Number of Phases = %d\n", nPhases); + printf("\t Phase:SpecName Prod_Rate MoleFraction kindexSP\n"); + printf("\t -------------------------------------------------------" + "----------\n"); + + int kspindex = 0; + bool inSurfacePhase = false; + for (int ip = 0; ip < nPhases; ip++) { + if (ip == surfIndex) { + inSurfacePhase = true; + } else { + inSurfacePhase = false; + } + ThermoPhase &THref = m_kin->thermo(ip); + int nsp = THref.nSpecies(); + string pname = THref.id(); + for (int k = 0; k < nsp; k++) { + string sname = THref.speciesName(k); + string cname = pname + ":" + sname; + if (inSurfacePhase) { + printf("\t %-24s %10.3e %10.3e %d\n", cname.c_str(), + netProdRate[kspindex], XMolKinSpecies[kspindex], + kindexSP); + kindexSP++; + } else { + printf("\t %-24s %10.3e %10.3e\n", cname.c_str(), + netProdRate[kspindex], XMolKinSpecies[kspindex]); + } + kspindex++; + } + } + printf("==========================================================" + "=================================\n"); + } + } +#endif + if (ioflag == 1) { + printf("\n\n\t Iter Time Del_t Damp DelX " + " Resid Name-Time Name-Damp\n"); + printf( "\t -----------------------------------------------" + "------------------------------------\n"); + } + } + //================================================================================================ + void solveProb::printIteration(int ioflag, doublereal damp, int label_d, + int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRate[], doublereal CSolnSP[], + doublereal resid[], + doublereal wtSpecies[], int dim, bool do_time) + { + int i, k; + string nm; + if (ioflag == 1) { + + printf("\t%6d ", iter); + if (do_time) + printf("%9.4e %9.4e ", t_real, 1.0/inv_t); + else + for (i = 0; i < 22; i++) printf(" "); + if (damp < 1.0) + printf("%9.4e ", damp); + else + for (i = 0; i < 11; i++) printf(" "); + printf("%9.4e %9.4e", update_norm, resid_norm); + if (do_time) { + k = label_t; + printf(" %d", k); + } else { + for (i = 0; i < 16; i++) printf(" "); + } + if (label_d >= 0) { + k = label_d; + printf(" %d", k); + } + printf("\n"); + } +#ifdef DEBUG_SOLVEPROB + else if (ioflag > 1) { + + updateMFSolnSP(XMolSolnSP); + printf("\n\t Weighted norm of update = %10.4e\n", update_norm); + + printf("\t Name Prod_Rate XMol Conc " + " Conc_Old wtConc"); + if (damp < 1.0) printf(" UnDamped_Conc"); + printf("\n"); + printf("\t---------------------------------------------------------" + "-----------------------------\n"); + int kindexSP = 0; + for (int isp = 0; isp < m_numSurfPhases; isp++) { + int nsp = m_nSpeciesSurfPhase[isp]; + InterfaceKinetics *m_kin = m_objects[isp]; + //int surfPhaseIndex = m_kinObjPhaseIDSurfPhase[isp]; + m_kin->getNetProductionRates(DATA_PTR(m_numEqn1)); + for (int k = 0; k < nsp; k++, kindexSP++) { + int kspIndex = m_kinSpecIndex[kindexSP]; + nm = m_kin->kineticsSpeciesName(kspIndex); + printf("\t%-16s %10.3e %10.3e %10.3e %10.3e %10.3e ", + nm.c_str(), + m_numEqn1[kspIndex], + XMolSolnSP[kindexSP], + CSolnSP[kindexSP], CSolnSP[kindexSP]+damp*resid[kindexSP], + wtSpecies[kindexSP]); + if (damp < 1.0) { + printf("%10.4e ", CSolnSP[kindexSP]+(damp-1.0)*resid[kindexSP]); + if (label_d == kindexSP) printf(" Damp "); + } + if (label_t == kindexSP) printf(" Tctrl"); + printf("\n"); + } + + } + + printf("\t--------------------------------------------------------" + "------------------------------\n"); + } +#endif + } /* printIteration */ + + //================================================================================================ + void solveProb::printFinal(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRateKinSpecies[], const doublereal CSolnSP[], + const doublereal resid[], + const doublereal wtSpecies[], const doublereal wtRes[], + int dim, bool do_time) + { + int i, k; + string nm; + if (ioflag == 1) { + + printf("\tFIN%3d ", iter); + if (do_time) + printf("%9.4e %9.4e ", t_real, 1.0/inv_t); + else + for (i = 0; i < 22; i++) printf(" "); + if (damp < 1.0) + printf("%9.4e ", damp); + else + for (i = 0; i < 11; i++) printf(" "); + printf("%9.4e %9.4e", update_norm, resid_norm); + if (do_time) { + k = label_t; + printf(" %d", k); + } else { + for (i = 0; i < 16; i++) printf(" "); + } + if (label_d >= 0) { + k = label_d; + + printf(" %d", k); + } + printf(" -- success\n"); + } +#ifdef DEBUG_SOLVEPROB + else if (ioflag > 1) { + + + printf("\n================================== FINAL RESULT =========" + "==================================================\n"); + + printf("\n Weighted norm of solution update = %10.4e\n", update_norm); + printf(" Weighted norm of residual update = %10.4e\n\n", resid_norm); + + printf(" Name Prod_Rate XMol Conc " + " wtConc Resid Resid/wtResid wtResid"); + if (damp < 1.0) printf(" UnDamped_Conc"); + printf("\n"); + printf("---------------------------------------------------------------" + "---------------------------------------------\n"); + + for (int k = 0; k < m_neq; k++, k++) { + printf("%-16s %10.3e %10.3e %10.3e %10.3e %10.3e %10.3e %10.3e", + nm.c_str(), + m_numEqn1[k], + XMolSolnSP[k], + CSolnSP[k], + wtSpecies[k], + resid[k], + resid[k]/wtRes[k], wtRes[k]); + if (damp < 1.0) { + printf("%10.4e ", CSolnSP[k]+(damp-1.0)*resid[k]); + if (label_d == k) printf(" Damp "); + } + if (label_t == k) printf(" Tctrl"); + printf("\n"); + } + + printf("\n"); + printf("===============================================================" + "============================================\n\n"); + } +#endif + } + //================================================================================================ +#ifdef DEBUG_SOLVEPROB + void solveProb:: + printIterationHeader(int ioflag, doublereal damp,doublereal inv_t, doublereal t_real, + int iter, bool do_time) + { + if (ioflag > 1) { + printf("\n===============================Iteration %5d " + "=================================\n", iter); + if (do_time) { + printf(" Transient step with: Real Time_n-1 = %10.4e sec,", t_real); + printf(" Time_n = %10.4e sec\n", t_real + 1.0/inv_t); + printf(" Delta t = %10.4e sec", 1.0/inv_t); + } else { + printf(" Steady Solve "); + } + if (damp < 1.0) { + printf(", Damping value = %10.4e\n", damp); + } else { + printf("\n"); + } + } + } +#endif + //================================================================================================ +} diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h new file mode 100644 index 000000000..cf0b9bde6 --- /dev/null +++ b/Cantera/src/numerics/solveProb.h @@ -0,0 +1,435 @@ +/** + * @file solveProb.h + * Header file for implicit nonlinear solver with the option of a pseudotransient + * (see \ref numerics and class \link Cantera::solveProb solveProb\endlink). + */ +/* + * $Id: solveSP.h 381 2010-01-15 21:20:41Z hkmoffa $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#ifndef SOLVEPROB_H +#define SOLVEPROB_H +/** + * @defgroup solverGroup Solvers for Equation Systems + */ + + +#include +#include "Array.h" +#include "ResidEval.h" + +//! Solution Methods +/*! + * Flag to specify the solution method + * + * 1: SOLVEPROB_INITIALIZE = This assumes that the initial guess supplied to the + * routine is far from the correct one. Substantial + * work plus transient time-stepping is to be expected + * to find a solution. + * 2: SOLVEPROB_RESIDUAL = Need to solve the surface problem in order to + * calculate the surface fluxes of gas-phase species. + * (Can expect a moderate change in the solution + * vector -> try to solve the system by direct + * methods + * with no damping first -> then, try time-stepping + * if the first method fails) + * A "time_scale" supplied here is used in the + * algorithm to determine when to shut off + * time-stepping. + * 3: SOLVEPROB_JACOBIAN = Calculation of the surface problem is due to the + * need for a numerical jacobian for the gas-problem. + * The solution is expected to be very close to the + * initial guess, and accuracy is needed. + * 4: SOLVEPROB_TRANSIENT = The transient calculation is performed here for an + * amount of time specified by "time_scale". It is + * not garraunted to be time-accurate - just stable + * and fairly fast. The solution after del_t time is + * returned, whether it's converged to a steady + * state or not. + */ +const int SOLVEPROB_INITIALIZE = 1; +const int SOLVEPROB_RESIDUAL = 2; +const int SOLVEPROB_JACOBIAN = 3; +const int SOLVEPROB_TRANSIENT = 4; + + + + +namespace Cantera { + + + //! Method to solve a pseudo steady state of a nonlinear problem + /*! + * The following class handles solving nonlinear problem.s + * + * + * Note there are a couple of different types of species indecices + * floating around in the formulation of this object. + * + * + * + * Solution Method + * + * This routine is typically used within a residual calculation in a large code. + * It's typically invoked millions of times for large calculations, and it must + * work every time. Therefore, requirements demand that it be robust but also + * efficient. + * + * The solution methodology is largely determined by the ifunc<\TT> parameter, + * that is input to the solution object. This parameter may have the following + * 4 values: + * + * + * 1: SFLUX_INITIALIZE = This assumes that the initial guess supplied to the + * routine is far from the correct one. Substantial + * work plus transient time-stepping is to be expected + * to find a solution. + * + * 2: SFLUX_RESIDUAL = Need to solve the nonlinear problem in order to + * calculate quantities for a residual calculation + * (Can expect a moderate change in the solution + * vector -> try to solve the system by direct methods + * with no damping first -> then, try time-stepping + * if the first method fails) + * A "time_scale" supplied here is used in the + * algorithm to determine when to shut off + * time-stepping. + * + * 3: SFLUX_JACOBIAN = Calculation of the surface problem is due to the + * need for a numerical jacobian for the gas-problem. + * The solution is expected to be very close to the + * initial guess, and extra accuracy is needed because + * solution variables have been delta'd from + * nominal values to create jacobian entries. + * + * 4: SFLUX_TRANSIENT = The transient calculation is performed here for an + * amount of time specified by "time_scale". It is + * not garraunted to be time-accurate - just stable + * and fairly fast. The solution after del_t time is + * returned, whether it's converged to a steady + * state or not. This is a poor man's time stepping + * algorithm. + * + * Psuedo time stepping algorithm: + * The time step is determined from sdot[], so that the time step + * doesn't ever change the value of a variable by more than 100%. + * + * This algorithm does use a damped Newton's method to relax the equations. + * Damping is based on a "delta damping" technique. The solution unknowns + * are not allowed to vary too much between iterations. + * + * + * EXTRA_ACCURACY:A constant that is the ratio of the required update norm in + * this Newton iteration compared to that in the nonlinear solver. + * A value of 0.1 is used so surface species are safely overconverged. + * + * Functions called: + *---------------------------------------------------------------------------- + * + * ct_dgetrf -- First half of LAPACK direct solve of a full Matrix + * + * ct_dgetrs -- Second half of LAPACK direct solve of a full matrix. Returns + * solution vector in the right-hand-side vector, resid. + * + *---------------------------------------------------------------------------- + * + * @ingroup solverGroup + */ + class solveProb { + + public: + + //! Constructor for the object + /*! + * @param surfChemPtr Pointer to the ImplicitSurfChem object that + * defines the surface problem to be solved. + * + * @param bulkFunc Integer representing how the bulk phases + * should be handled. Currently, only the + * default value of BULK_ETCH is supported. + */ + solveProb(ResidEval* resid); + + //! Destructor. Deletes the integrator. + ~solveProb(); + + private: + + //! Unimplemented private copy constructor + solveProb(const solveProb &right); + + //! Unimplemented private assignment operator + solveProb& operator=(const solveProb &right); + + public: + + //! Main routine that actually calculates the pseudo steady state + //! of the surface problem + /*! + * The actual converged solution is returned as part of the + * internal state of the InterfaceKinetics objects. + * + * @param ifunc Determines the type of solution algorithm to be + * used. Possible values are SFLUX_INITIALIZE , + * SFLUX_RESIDUAL SFLUX_JACOBIAN SFLUX_TRANSIENT . + * + * @param time_scale Time over which to integrate the surface equations, + * where applicable + * + * @param reltol Relative tolerance to use + * @param abstol absolute tolerance. + * + * @return Returns 1 if the surface problem is successfully solved. + * Returns -1 if the surface problem wasn't solved successfully. + * Note the actual converged solution is returned as part of the + * internal state of the InterfaceKinetics objects. + */ + int solve(int ifunc, doublereal time_scale, + doublereal reltol, doublereal abstol); + + private: + + //! Printing routine that gets called at the start of every + //! invocation + virtual void print_header(int ioflag, int ifunc, doublereal time_scale, + int damping, doublereal reltol, doublereal abstol, + doublereal netProdRate[]); + +#ifdef DEBUG_SOLVEPROB + + virtual void printResJac(int ioflag, int neq, const Array2D &Jac, + doublereal resid[], doublereal wtResid[], doublereal norm); +#endif + + //! Printing routine that gets called after every iteration + virtual void printIteration(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRate[], doublereal CSolnSP[], + doublereal resid[], + doublereal wtSpecies[], int dim, bool do_time); + + + //! Print a summary of the solution + /*! + * + */ + virtual void printFinal(int ioflag, doublereal damp, int label_d, int label_t, + doublereal inv_t, doublereal t_real, int iter, + doublereal update_norm, doublereal resid_norm, + doublereal netProdRateKinSpecies[], const doublereal CSolnSP[], + const doublereal resid[], + const doublereal wtSpecies[], const doublereal wtRes[], + int dim, bool do_time); + + //! Calculate a conservative delta T to use in a pseudo-steady state + //! algorithm + /*! + * This routine calculates a pretty conservative 1/del_t based + * on MAX_i(sdot_i/(X_i*SDen0)). This probably guarantees + * diagonal dominance. + * + * Small surface fractions are allowed to intervene in the del_t + * determination, no matter how small. This may be changed. + * Now minimum changed to 1.0e-12, + * + * Maximum time step set to time_scale. + * + * @param netProdRateSolnSP Output variable. Net production rate + * of all of the species in the solution vector. + * @param XMolSolnSP output variable. + * Mole fraction of all of the species in the solution vector + * @param label Output variable. Pointer to the value of the + * species index (kindexSP) that is controlling + * the time step + * @param label_old Output variable. Pointer to the value of the + * species index (kindexSP) that controlled + * the time step at the previous iteration + * @param label_factor Output variable. Pointer to the current + * factor that is used to indicate the same species + * is controlling the time step. + * + * @param ioflag Level of the output requested. + * + * @return Returns the 1. / delta T to be used on the next step + */ + virtual doublereal calc_t(doublereal netProdRateSolnSP[], doublereal Csoln[], + int *label, int *label_old, + doublereal *label_factor, int ioflag); + + //! Calculate the solution and residual weights + /*! + * @param wtSpecies Weights to use for the soln unknowns. These + * are in concentration units + * @param wtResid Weights to sue for the residual unknowns. + * + * @param CSolnSP Solution vector for the surface problem + */ + virtual void calcWeights(doublereal wtSpecies[], doublereal wtResid[], + const doublereal CSolnSP[]); + +#ifdef DEBUG_SOLVEPROB + //! Utility routine to print a header for high lvls of debugging + /*! + * @param ioflag Lvl of debugging + * @param damp lvl of damping + * @param inv_t Inverse of the value of delta T + * @param t_real Value of the time + * @param iter Interation number + * @param do_time boolean indicating whether time stepping is taking + * place + */ + virtual void printIterationHeader(int ioflag, doublereal damp, + doublereal inv_t, doublereal t_real, int iter, + bool do_time); +#endif + + /** + * Update the surface states of the surface phases. + */ + virtual void updateState(const doublereal *cSurfSpec); + + + + //! Main Function evalulation + /*! + * + * @param resid output Vector of residuals, length = m_neq + * @param CSolnSP Vector of species concentrations, unknowns in the + * problem, length = m_neq + * @param CSolnSPOld Old Vector of species concentrations, unknowns in the + * problem, length = m_neq + * @param do_time Calculate a time dependent residual + * @param deltaT Delta time for time dependent problem. + */ + virtual void fun_eval(doublereal* resid, const doublereal *CSolnSP, + const doublereal *CSolnOldSP, const bool do_time, const doublereal deltaT); + + //! Main routine that calculates the current residual and Jacobian + /*! + * @param JacCol Vector of pointers to the tops of columns of the + * Jacobian to be evalulated. + * @param resid output Vector of residuals, length = m_neq + * @param CSolnSP Vector of species concentrations, unknowns in the + * problem, length = m_neq. These are tweaked in order + * to derive the columns of the jacobian. + * @param CSolnSPOld Old Vector of species concentrations, unknowns in the + * problem, length = m_neq + * @param do_time Calculate a time dependent residual + * @param deltaT Delta time for time dependent problem. + */ + virtual void resjac_eval(std::vector& JacCol, doublereal * resid, + doublereal *CSolnSP, + const doublereal *CSolnSPOld, const bool do_time, + const doublereal deltaT); + + virtual doublereal calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label); + + ResidEval *m_residFunc; + + //! Total number of equations to solve in the implicit problem. + /*! + * Note, this can be zero, and frequently is + */ + int m_neq; + + //! m_atol is the absolute tolerance in real units. + vector_fp m_atol; + + //! m_rtol is the relative error tolerance. + doublereal m_rtol; + + //! maximum value of the time step + /*! + * units = seconds + */ + doublereal m_maxstep; + + //! Temporary vector with length MAX(1, m_neq) + vector_fp m_netProductionRatesSave; + + //! Temporary vector with length MAX(1, m_neq) + vector_fp m_numEqn1; + + //! Temporary vector with length MAX(1, m_neq) + vector_fp m_numEqn2; + + //! Temporary vector with length MAX(1, m_neq) + vector_fp m_CSolnSave; + + //! Solution vector + /*! + * length MAX(1, m_neq) + */ + vector_fp m_CSolnSP; + + //! Saved inital solution vector + /*! + * length MAX(1, m_neq) + */ + vector_fp m_CSolnSPInit; + + //! Saved solution vector at the old time step + /*! + * length MAX(1, m_neq) + */ + vector_fp m_CSolnSPOld; + + //! Weights for the residual norm calculation + /*! + * length MAX(1, m_neq) + */ + vector_fp m_wtResid; + + //! Weights for the species concentrations norm calculation + /*! + * length MAX(1, m_neq) + */ + vector_fp m_wtSpecies; + + //! Residual for the surface problem + /*! + * The residual vector of length "dim" that, that has the value + * of "sdot" for surface species. The residuals for the bulk + * species are a function of the sdots for all species in the bulk + * phase. The last residual of each phase enforces {Sum(fractions) + * = 1}. After linear solve (dgetrf_ & dgetrs_), resid holds the + * update vector. + * + * length MAX(1, m_neq) + */ + vector_fp m_resid; + + //! pivots + /*! + * length MAX(1, m_neq) + */ + vector_int m_ipiv; + + //! Vector of pointers to the top of the columns of the + //! jacobians + /*! + * The "dim" by "dim" computed Jacobian matrix for the + * local Newton's method. + */ + std::vector m_JacCol; + + //! Jacobian + /*! + * m_neq by m_neq computed Jacobian matrix for the + * local Newton's method. + */ + Array2D m_Jac; + + + public: + int m_ioflag; + }; +} +#endif From d8ae74198d3f889a176587c310d15c3cca96a598 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 22 May 2010 21:50:26 +0000 Subject: [PATCH 151/446] Second iteration for solveProp. Added a routine to get the final answer out. --- Cantera/src/numerics/solveProb.cpp | 48 ++++++++++-------------------- Cantera/src/numerics/solveProb.h | 28 ++++++++--------- 2 files changed, 30 insertions(+), 46 deletions(-) diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index f707f5042..7794860d1 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -48,9 +48,6 @@ namespace Cantera { # define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) /* min function */ #endif -#ifndef DAMPING -# define DAMPING true -#endif /*************************************************************************** * solveSP Class Definitinos @@ -152,27 +149,17 @@ namespace Cantera { * upload the initial conditions */ m_residFunc->getInitialConditions(t_real, DATA_PTR(m_CSolnSP), DATA_PTR(m_numEqn1)); + /* * Store the initial guess in the soln vector, - * CSoln, and in an separate vector CSolnInit. + * CSolnSP, and in an separate vector CSolnSPInit. */ - for (int n = 0; n < m_neq; n++) { - // m_CSolnSP[loc] = m_numEqn1[k]; - - } - - std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), m_CSolnSPInit.begin()); - // Calculate the largest species in each phase - // evalSurfLarge(DATA_PTR(m_CSolnSP)); - /* - * Get the net production rate of all species in the kinetics manager. - */ - // m_kin->getNetProductionRates(DATA_PTR(m_netProductionRatesSave)); + if (m_ioflag) { - print_header(m_ioflag, ifunc, time_scale, DAMPING, reltol, abstol, + print_header(m_ioflag, ifunc, time_scale, reltol, abstol, DATA_PTR(m_netProductionRatesSave)); } @@ -313,9 +300,9 @@ namespace Cantera { * in any unknown. */ -#ifdef DAMPING - damp = calc_damping( DATA_PTR(m_CSolnSP), DATA_PTR(m_resid), m_neq, &label_d); -#endif + + damp = calc_damping(DATA_PTR(m_CSolnSP), DATA_PTR(m_resid), m_neq, &label_d); + /* * Calculate the weighted norm of the update vector @@ -334,7 +321,6 @@ namespace Cantera { for (irow = 0; irow < m_neq; irow++) { m_CSolnSP[irow] = MAX(0.0, m_CSolnSP[irow]); } - updateState(DATA_PTR(m_CSolnSP)); if (do_time) t_real += damp/inv_t; @@ -411,17 +397,14 @@ namespace Cantera { if (update_norm > 1.0) { return -1; } - return 1; + return 0; } - -#undef DAMPING - //================================================================================================ /* * Update the surface states of the surface phases. */ - void solveProb::updateState(const doublereal *CSolnSP) { - + void solveProb::reportState(doublereal * const CSolnSP) const { + std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), CSolnSP); } //================================================================================================ /* @@ -434,8 +417,8 @@ namespace Cantera { * This routine uses the m_numEqn1 and m_netProductionRatesSave vectors * as temporary internal storage. */ - void solveProb::fun_eval(doublereal * resid, const doublereal *CSoln, - const doublereal *CSolnOld, const bool do_time, + void solveProb::fun_eval(doublereal * const resid, const doublereal * const CSoln, + const doublereal * const CSolnOld, const bool do_time, const doublereal deltaT) { if (do_time) { @@ -690,8 +673,9 @@ namespace Cantera { * Optional printing at the start of the solveProb problem */ void solveProb::print_header(int ioflag, int ifunc, doublereal time_scale, - int damping, doublereal reltol, doublereal abstol, - doublereal netProdRate[]) { + doublereal reltol, doublereal abstol, + doublereal netProdRate[]) { + int damping = 1; if (ioflag) { printf("\n================================ SOLVEPROB CALL SETUP " "========================================\n"); @@ -864,7 +848,7 @@ namespace Cantera { #endif } /* printIteration */ - //================================================================================================ + //================================================================================================ void solveProb::printFinal(int ioflag, doublereal damp, int label_d, int label_t, doublereal inv_t, doublereal t_real, int iter, doublereal update_norm, doublereal resid_norm, diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index cf0b9bde6..52f6f6097 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -86,12 +86,12 @@ namespace Cantera { * 4 values: * * - * 1: SFLUX_INITIALIZE = This assumes that the initial guess supplied to the + * 1: SOLVEPROB_INITIALIZE = This assumes that the initial guess supplied to the * routine is far from the correct one. Substantial * work plus transient time-stepping is to be expected * to find a solution. * - * 2: SFLUX_RESIDUAL = Need to solve the nonlinear problem in order to + * 2: SOLVEPROB_RESIDUAL = Need to solve the nonlinear problem in order to * calculate quantities for a residual calculation * (Can expect a moderate change in the solution * vector -> try to solve the system by direct methods @@ -101,14 +101,14 @@ namespace Cantera { * algorithm to determine when to shut off * time-stepping. * - * 3: SFLUX_JACOBIAN = Calculation of the surface problem is due to the + * 3: SOLVEPROB_JACOBIAN = Calculation of the surface problem is due to the * need for a numerical jacobian for the gas-problem. * The solution is expected to be very close to the * initial guess, and extra accuracy is needed because * solution variables have been delta'd from * nominal values to create jacobian entries. * - * 4: SFLUX_TRANSIENT = The transient calculation is performed here for an + * 4: SOLVEPROB_TRANSIENT = The transient calculation is performed here for an * amount of time specified by "time_scale". It is * not garraunted to be time-accurate - just stable * and fairly fast. The solution after del_t time is @@ -193,12 +193,19 @@ namespace Cantera { int solve(int ifunc, doublereal time_scale, doublereal reltol, doublereal abstol); + //! Report the current state of the solution + /*! + * @param Report the solution vector for the nonlinear problem + */ + virtual void reportState(doublereal * const CSoln) const; + + private: //! Printing routine that gets called at the start of every //! invocation virtual void print_header(int ioflag, int ifunc, doublereal time_scale, - int damping, doublereal reltol, doublereal abstol, + doublereal reltol, doublereal abstol, doublereal netProdRate[]); #ifdef DEBUG_SOLVEPROB @@ -289,13 +296,6 @@ namespace Cantera { doublereal inv_t, doublereal t_real, int iter, bool do_time); #endif - - /** - * Update the surface states of the surface phases. - */ - virtual void updateState(const doublereal *cSurfSpec); - - //! Main Function evalulation /*! @@ -308,8 +308,8 @@ namespace Cantera { * @param do_time Calculate a time dependent residual * @param deltaT Delta time for time dependent problem. */ - virtual void fun_eval(doublereal* resid, const doublereal *CSolnSP, - const doublereal *CSolnOldSP, const bool do_time, const doublereal deltaT); + virtual void fun_eval(doublereal* const resid, const doublereal * const CSolnSP, + const doublereal * const CSolnOldSP, const bool do_time, const doublereal deltaT); //! Main routine that calculates the current residual and Jacobian /*! From 4856da5083dad329c6b85452ad2e9f1f8bfd5faa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 23 May 2010 02:46:46 +0000 Subject: [PATCH 152/446] Added a solvers.h file --- Cantera/cxx/Makefile.in | 2 +- Cantera/cxx/include/solvers.h | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 Cantera/cxx/include/solvers.h diff --git a/Cantera/cxx/Makefile.in b/Cantera/cxx/Makefile.in index 9bac968f9..49b15123e 100644 --- a/Cantera/cxx/Makefile.in +++ b/Cantera/cxx/Makefile.in @@ -18,7 +18,7 @@ INSTALL_TSC = ../../../bin/install_tsc CXX_H = Cantera.h equilibrium.h IncompressibleSolid.h \ kinetics.h onedim.h surface.h GRI30.h integrators.h \ Metal.h PureFluid.h transport.h Edge.h \ - IdealGasMix.h Interface.h numerics.h \ + IdealGasMix.h Interface.h numerics.h solvers.h \ reactionpaths.h zerodim.h importPhase.h thermo.h \ radiation.h spectra.h electrolyteThermo.h Cantera.mak Cantera_bt.mak diff --git a/Cantera/cxx/include/solvers.h b/Cantera/cxx/include/solvers.h new file mode 100644 index 000000000..b8c76bf2a --- /dev/null +++ b/Cantera/cxx/include/solvers.h @@ -0,0 +1,12 @@ +/** + * @file solvers.h + * solvers of small embedded problems + */ +#ifndef CT_SOLVERS_H_INCL +#define CT_SOLVERS_H_INCL + +#include "kernel/ResidEval.h" + +#include "kernel/solveProb.h" + +#endif From 3167a96541d9aacf9af24c5353aefc92bf912ab9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 23 May 2010 15:11:55 +0000 Subject: [PATCH 153/446] Initial commits of BEulerInt. This is a backwards euler stepper with lots of hooks. Using this to develop a subgrid electrode object. --- Cantera/src/numerics/BEulerInt.cpp | 2359 ++++++++++++++++++++++++++++ Cantera/src/numerics/BEulerInt.h | 465 ++++++ Cantera/src/numerics/Makefile.in | 4 +- Cantera/src/numerics/ResidEval.h | 27 + 4 files changed, 2853 insertions(+), 2 deletions(-) create mode 100644 Cantera/src/numerics/BEulerInt.cpp create mode 100644 Cantera/src/numerics/BEulerInt.h diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp new file mode 100644 index 000000000..e1a202060 --- /dev/null +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -0,0 +1,2359 @@ +/** + * @file BEulerInt.cpp + * + */ + +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#include "BEulerInt.h" + + +#include "mdp_allo.h" +#include + +using namespace std; +using namespace mdp; + +#define SAFE_DELETE(a) if (a) { delete (a); a = 0; } + +namespace Cantera { + /************************************************************************* + * + * subtractRD(): + * This routine subtracts 2 numbers. If the difference is less + * than 1.0E-14 times the magnitude of the smallest number, + * then diff returns an exact zero. + * It also returns an exact zero if the difference is less than + * 1.0E-300. + * + * returns: a - b + * + * This routine is used in numerical differencing schemes in order + * to avoid roundoff errors resulting in creating Jacobian terms. + * Note: This is a slow routine. However, jacobian errors may cause + * loss of convergence. Therefore, in practice this routine + * has proved cost-effective. + */ + double subtractRD(double a, double b) { + double diff = a - b; + double d = MIN(fabs(a), fabs(b)); + d *= 1.0E-14; + double ad = fabs(diff); + if (ad < 1.0E-300) { + diff = 0.0; + } + if (ad < d) { + diff = 0.0; + } + return diff; + } + + /************************************************************************** + * + * + * Function called by BEuler to evaluate the Jacobian matrix and the + * current residual at the current time step. + * @param N = The size of the equation system + * @param J = Jacobian matrix to be filled in + * @param f = Right hand side. This routine returns the current + * value of the rhs (output), so that it does + * not have to be computed again. + * + */ + void BEulerInt::beuler_jac(SquareMatrix &J, double * const f, + double time_curr, double CJ, + double * const y, + double * const ydot, + int num_newt_its) + { + int i, j; + double* col_j; + double ysave, ydotsave, dy; + /** + * Clear the factor flag + */ + J.clearFactorFlag(); + + + if (m_jacFormMethod & BEULER_JAC_ANAL) { + /******************************************************************** + * Call the function to get a jacobian. + */ + m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); +#ifdef DEBUG_HKM + //double dddd = J(89, 89); + //checkFinite(dddd); +#endif + m_nJacEval++; + m_nfe++; + } else { + /******************************************************************* + * Generic algorithm to calculate a numerical Jacobian + */ + /* + * Calculate the current value of the rhs given the + * current conditions. + */ + + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f); + m_nfe++; + m_nJacEval++; + + + /* + * Malloc a vector and call the function object to return a set of + * deltaY's that are appropriate for calculating the numerical + * derivative. + */ + double *dyVector = mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); + m_func->calcDeltaSolnVariables(time_curr, y, m_y_nm1, dyVector, + m_ewt); +#ifdef DEBUG_HKM + bool print_NumJac = false; + if (print_NumJac) { + FILE *idy = fopen("NumJac.csv", "w"); + fprintf(idy, "Unk m_ewt y " + "dyVector ResN\n"); + for (int iii = 0; iii < m_neq; iii++){ + fprintf(idy, " %4d %16.8e %16.8e %16.8e %16.8e \n", + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + } + fclose(idy); + } +#endif + /* + * Loop over the variables, formulating a numerical derivative + * of the dense matrix. + * For the delta in the variable, we will use a variety of approaches + * The original approach was to use the error tolerance amount. + * This may not be the best approach, as it could be overly large in + * some instances and overly small in others. + * We will first protect from being overly small, by using the usual + * sqrt of machine precision approach, i.e., 1.0E-7, + * to bound the lower limit of the delta. + */ + for (j = 0; j < m_neq; j++) { + + + /* + * Get a pointer into the column of the matrix + */ + + + col_j = (double *) J.ptrColumn(j); + ysave = y[j]; + dy = dyVector[j]; + //dy = fmaxx(1.0E-6 * m_ewt[j], fabs(ysave)*1.0E-7); + + y[j] = ysave + dy; + dy = y[j] - ysave; + ydotsave = ydot[j]; + ydot[j] += dy * CJ; + /* + * Call the functon + */ + + + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, m_wksp, + true, j, dy); + m_nfe++; + double diff; + for (i = 0; i < m_neq; i++) { + diff = subtractRD(m_wksp[i], f[i]); + col_j[i] = diff / dy; + //col_j[i] = (m_wksp[i] - f[i])/dy; + } + + y[j] = ysave; + ydot[j] = ydotsave; + + } + /* + * Release memory + */ + mdp_safe_free((void **) &dyVector); + } + + + } + + /************************************************************************** + * + * Exception thrown when a BEuler error is encountered. We just call the + * Cantera Error handler in the initialization list + */ + BEulerErr::BEulerErr(string msg) : + CanteraError("BEulerInt", msg) + { + } + + /** + * Constructor. Default settings: dense jacobian, no user-supplied + * Jacobian function, Newton iteration. + */ + BEulerInt::BEulerInt() : + m_iter(Newton_Iter), + m_method(BEulerVarStep), + m_jacFormMethod(BEULER_JAC_NUM), + m_rowScaling(true), + m_colScaling(false), + m_matrixConditioning(false), + m_itol(0), + m_reltol(1.e-4), + m_abstols(1.e-10), + m_abstol(0), + m_ewt(0), + m_hmax(0.0), + m_maxord(0), + m_time_step_num(0), + m_time_step_attempts(0), + m_max_time_step_attempts(11000000), + m_numInitialConstantDeltaTSteps(0), + m_failure_counter(0), + m_min_newt_its(0), + m_printSolnStepInterval(1), + m_printSolnNumberToTout(1), + m_printSolnFirstSteps(0), + m_dumpJacobians(false), + m_neq(0), + m_y_n(0), + m_y_nm1(0), + m_y_pred_n(0), + m_ydot_n(0), + m_ydot_nm1(0), + m_t0(0.0), + m_time_final(0.0), + time_n(0.0), + time_nm1(0.0), + time_nm2(0.0), + delta_t_n(0.0), + delta_t_nm1(0.0), + delta_t_nm2(0.0), + delta_t_np1(1.0E-8), + delta_t_max(1.0E300), + m_resid(0), + m_residWts(0), + m_wksp(0), + m_func(0), + m_rowScales(0), + m_colScales(0), + tdjac_ptr(0), + m_print_flag(3), + m_nfe(0), + m_nJacEval(0), + m_numTotalNewtIts(0), + m_numTotalLinearSolves(0), + m_numTotalConvFails(0), + m_numTotalTruncFails(0), + num_failures(0) + { + + } + + + /** + * Destructor + */ + BEulerInt::~BEulerInt() + { + mdp_safe_free((void **) &m_y_n); + mdp_safe_free((void **) &m_y_nm1); + mdp_safe_free((void **) &m_y_pred_n); + mdp_safe_free((void **) &m_ydot_n); + mdp_safe_free((void **) &m_ydot_nm1); + mdp_safe_free((void **) &m_resid); + mdp_safe_free((void **) &m_residWts); + mdp_safe_free((void **) &m_wksp); + mdp_safe_free((void **) &m_ewt); + mdp_safe_free((void **) &m_abstol); + mdp_safe_free((void **) &m_rowScales); + mdp_safe_free((void **) &m_colScales); + SAFE_DELETE(tdjac_ptr); + + } + + void BEulerInt::setTolerances(double reltol, int n, double* abstol) { + m_itol = 1; + if (!m_abstol) { + m_abstol = mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); + } + if (n != m_neq) { + printf("ERROR n is wrong\n"); + exit(-1); + } + for (int i = 0; i < m_neq; i++) { + m_abstol[i] = abstol[i]; + } + m_reltol = reltol; + } + + void BEulerInt::setTolerances(double reltol, double abstol) { + m_itol = 0; + m_reltol = reltol; + m_abstols = abstol; + } + + void BEulerInt::setProblemType(int jacFormMethod) { + m_jacFormMethod = jacFormMethod; + } + + void BEulerInt::setMethodBEMT(BEulerMethodType t) { + m_method = t; + } + + void BEulerInt::setMaxStep(doublereal hmax) { + m_hmax = hmax; + } + + void BEulerInt::setMaxNumTimeSteps(int maxNumTimeSteps) { + m_max_time_step_attempts = maxNumTimeSteps; + } + + void BEulerInt::setNumInitialConstantDeltaTSteps(int num) { + m_numInitialConstantDeltaTSteps = num; + } + + /************************************************************************** + * + * setPrintSolnOptins(): + * + * This routine controls when the solution is printed + * + * @param printStepInterval If greater than 0, then the + * soln is printed every printStepInterval + * steps. + * + * @param printNumberToTout The solution is printed at + * regular invervals a total of + * "printNumberToTout" times. + * + * @param printSolnFirstSteps The solution is printed out + * the first "printSolnFirstSteps" + * steps. After these steps the other + * parameters determine the printing. + * default = 0 + * + * @param dumpJacobians Dump jacobians to disk. + * + * default = false + * + */ + void BEulerInt::setPrintSolnOptions(int printSolnStepInterval, + int printSolnNumberToTout, + int printSolnFirstSteps, + bool dumpJacobians) { + m_printSolnStepInterval = printSolnStepInterval; + m_printSolnNumberToTout = printSolnNumberToTout; + m_printSolnFirstSteps = printSolnFirstSteps; + m_dumpJacobians = dumpJacobians; + } + + void BEulerInt::setIterator(IterType t) { + m_iter = t; + } + + /************************************************************************** + * + * setNonLinOptions() + * + * Set the options for the nonlinear method + * + * Defaults are set in the .h file. These are the defaults: + * min_newt_its = 0 + * matrixConditioning = false + * colScaling = false + * rowScaling = true + */ + void BEulerInt::setNonLinOptions(int min_newt_its, bool matrixConditioning, + bool colScaling, bool rowScaling) { + m_min_newt_its = min_newt_its; + m_matrixConditioning = matrixConditioning; + m_colScaling = colScaling; + m_rowScaling = rowScaling; + if (m_colScaling) { + if (!m_colScales) { + m_colScales = mdp_alloc_dbl_1(m_neq, 1.0); + } + } + if (m_rowScaling) { + if (!m_rowScales) { + m_rowScales = mdp_alloc_dbl_1(m_neq, 1.0); + } + } + } + + /************************************************************************** + * + * setInitialTimeStep(): + * + * Set the initial time step. Right now, we set the + * time step by setting delta_t_np1. + */ + void BEulerInt::setInitialTimeStep(double deltaT) { + delta_t_np1 = deltaT; + } + + /************************************************************************** + * + * setPrintFlag(): + * + */ + void BEulerInt::setPrintFlag(int print_flag) { + m_print_flag = print_flag; + } + + /************************************************************************** + * + * initialize(): + * + * Find the initial conditions for y and ydot. + */ + void BEulerInt::initializeRJE(double t0, ResidJacEval &func) + { + m_neq = func.nEquations(); + m_t0 = t0; + internalMalloc(); + + /* + * Get the initial conditions. + */ + func.getInitialConditionsDot(m_t0, m_neq, m_y_n, m_ydot_n); + + // Store a pointer to the residual routine in the object + m_func = &func; + + /* + * Initialize the various time counters in the object + */ + time_n = t0; + time_nm1 = time_n; + time_nm2 = time_nm1; + delta_t_n = 0.0; + delta_t_nm1 = 0.0; + } + + /************************************************************************** + * + * reinitialize(): + * + */ + void BEulerInt::reinitializeRJE(double t0, ResidJacEval& func) + { + m_neq = func.nEquations(); + m_t0 = t0; + internalMalloc(); + /* + * At the initial time, get the initial conditions and time and store + * them into internal storage in the object, my[]. + */ + m_t0 = t0; + func.getInitialConditions(m_t0, m_y_n, m_ydot_n); + /** + * Set up the internal weights that are used for testing convergence + */ + setSolnWeights(); + + // Store a pointer to the function + m_func = &func; + + } + + /****************************************************************************** + * + * getPrintTime(): + * + */ + double BEulerInt::getPrintTime(double time_current) { + double tnext; + if (m_printSolnNumberToTout > 0) { + double dt = (m_time_final - m_t0) / m_printSolnNumberToTout; + for (int i = 0; i <= m_printSolnNumberToTout; i++) { + tnext = m_t0 + dt * i; + if (tnext >= time_current) return tnext; + } + } + return 1.0E300; + } + + /****************************************************************************** + * + * nEvals(): + * + * Return the total number of function evaluations + */ + int BEulerInt::nEvals() const + { + return m_nfe; + } + + /************************************************************************** + * + * internalMalloc(): + * + * Internal routine that sets up the fixed length storage based on + * the size of the problem to solve. + */ + void BEulerInt::internalMalloc() { + mdp_realloc_dbl_1(&m_ewt, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_nm1, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_pred_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_ydot_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_ydot_nm1, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_resid, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_residWts, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_wksp, m_neq, 0, 0.0); + if (m_rowScaling) { + mdp_realloc_dbl_1(&m_rowScales, m_neq, 0, 1.0); + } + if (m_colScaling) { + mdp_realloc_dbl_1(&m_colScales, m_neq, 0, 1.0); + } + tdjac_ptr = new SquareMatrix(m_neq); + } + + /************************************************************************** + * + * setSolnWeights(): + * + * Set the solution weights + * This is a very important routine as it affects quite a few + * operations involving convergence. + * + */ + void BEulerInt::setSolnWeights() + { + int i; + if (m_itol == 1) { + /* + * Adjust the atol vector if we are using vector + * atol conditions. + */ + // m_func->adjustAtol(m_abstol); + + for (i = 0; i < m_neq; i++) { + m_ewt[i] = m_abstol[i] + m_reltol * 0.5 * + (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + } + } else { + for (i = 0; i < m_neq; i++) { + m_ewt[i] = m_abstols + m_reltol * 0.5 * + (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + } + } + } + + /****************************************************************************** + * + * setColumnScales(): + * + * Set the column scaling vector at the current time + */ + void BEulerInt::setColumnScales() + { + m_func->calcSolnScales(time_n, m_y_n, m_y_nm1, m_colScales); + } + + /****************************************************************************** + * + * computeResidWts(): + * + * We compute residual weights here, which we define as the L_0 norm + * of the Jacobian Matrix, weighted by the solution weights. + * This is the proper way to guage the magnitude of residuals. However, + * it does need the evaluation of the jacobian, and the implementation + * below is slow, but doesn't take up much memory. + * + * Here a small weighting indicates that the change in solution is + * very sensitive to that equation. + */ + void BEulerInt::computeResidWts(SquareMatrix &jac) + { + int i, j; + double *data = &(*(jac.begin())); + double value; + for (i = 0; i < m_neq; i++) { + m_residWts[i] = fabs(data[i] * m_ewt[0]); + for (j = 1; j < m_neq; j++) { + value = fabs(data[j*m_neq + i] * m_ewt[j]); + m_residWts[i] = MAX(m_residWts[i], value); + } + } + } + + /****************************************************************************** + * + * filterNewStep(): + * + * void BEulerInt:: + * + */ + double BEulerInt::filterNewStep(double timeCurrent, double *y_current, + double *ydot_current) { + + return 0.0; + } + + + /******************************************************************************/ +} + + +/* + * Blas routines + */ +extern "C" { + extern void dcopy_(int *, double *, int *, double *, int *); +} + +/*****************************************************************************/ +/*****************************************************************************/ +/*****************************************************************************/ +static void print_line(const char *str, int n) +{ + for (int i = 0; i < n; i++) { + printf("%s", str); + } + printf("\n"); +} + +/*****************************************************************************/ +/*****************************************************************************/ +/*****************************************************************************/ + +static void print_time_step1(int order, int n_time_step, double time, + double delta_t_n, double delta_t_nm1, + bool step_failed, int num_failures) + +/* + * Print out for relevant time step information + */ + +{ + const char *string = 0; + if (order == 0) string = "Backward Euler"; + else if (order == 1) string = "Forward/Backward Euler"; + else if (order == 2) string = "Adams-Bashforth/TR"; + printf("\n"); print_line("=", 80); + printf("\nStart of Time Step: %5d Time_n = %9.5g Time_nm1 = %9.5g\n", + n_time_step, time, time - delta_t_n); + printf("\tIntegration method = %s\n", string); + if (step_failed) + printf("\tPreviously attempted step was a failure\n"); + if (delta_t_n > delta_t_nm1) + string = "(Increased from previous iteration)"; + else if (delta_t_n < delta_t_nm1) + string = "(Decreased from previous iteration)"; + else { + string = "(same as previous iteration)"; + } + printf("\tdelta_t_n = %8.5e %s", delta_t_n, string); + if (num_failures > 0) + printf("\t(Bad_History Failure Counter = %d)", num_failures); + printf("\n\tdelta_t_nm1 = %8.5e\n", delta_t_nm1); +} /*************** END print_time_step1 **************************************/ +/*****************************************************************************/ +/* + * Print out for relevant time step information + */ +static void print_time_step2(int time_step_num, int order, + double time, double time_error_factor, + double delta_t_n, double delta_t_np1) +{ + printf("\tTime Step Number %5d was a success: time = %10g\n", time_step_num, + time); + printf("\t\tEstimated Error\n"); + printf("\t\t-------------------- = %8.5e\n", time_error_factor); + printf("\t\tTolerated Error\n\n"); + printf("\t- Recommended next delta_t (not counting history) = %g\n", + delta_t_np1); + printf("\n"); print_line("=", 80); printf("\n"); +} /************* END of print_time_step2 () **********************************/ +/*****************************************************************************/ +/*****************************************************************************/ +/* + * Print Out descriptive information on why the current step failed + */ +static void print_time_fail(bool convFailure, int time_step_num, + double time, double delta_t_n, + double delta_t_np1, double time_error_factor) +{ + printf("\n"); print_line("=", 80); + if (convFailure) { + printf("\tTime Step Number %5d experienced a convergence " + "failure\n", time_step_num); + printf("\tin the non-linear or linear solver\n"); + printf("\t\tValue of time at failed step = %g\n", time); + printf("\t\tdelta_t of the failed step = %g\n", + delta_t_n); + printf("\t\tSuggested value of delta_t to try next = %g\n", + delta_t_np1); + } else { + printf("\tTime Step Number %5d experienced a truncation error " + "failure!\n", time_step_num); + printf("\t\tValue of time at failed step = %g\n", time); + printf("\t\tdelta_t of the failed step = %g\n", + delta_t_n); + printf("\t\tSuggested value of delta_t to try next = %g\n", + delta_t_np1); + printf("\t\tCalculated truncation error factor = %g\n", + time_error_factor); + } + printf("\n"); print_line("=", 80); +} /*************** END of print_time_fail () *********************************/ +/*****************************************************************************/ +/* + * Print out the final results and counters + */ +static void print_final(double time, int step_failed, + int time_step_num, int num_newt_its, + int total_linear_solves, int numConvFails, + int numTruncFails, int nfe, int nJacEval) +{ + printf("\n"); print_line("=", 80); + printf("TIME INTEGRATION ROUTINE HAS FINISHED: "); + if (step_failed) + printf(" IT WAS A FAILURE\n"); + else + printf(" IT WAS A SUCCESS\n"); + printf("\tEnding time = %g\n", time); + printf("\tNumber of time steps = %d\n", time_step_num); + printf("\tNumber of newt its = %d\n", num_newt_its); + printf("\tNumber of linear solves = %d\n", total_linear_solves); + printf("\tNumber of convergence failures= %d\n", numConvFails); + printf("\tNumber of TimeTruncErr fails = %d\n", numTruncFails); + printf("\tNumber of Function evals = %d\n", nfe); + printf("\tNumber of Jacobian evals/solvs= %d\n", nJacEval); + printf("\n"); print_line("=", 80); +} /************* END of print_final () ***************************************/ +/*****************************************************************************/ +/*****************************************************************************/ +/* + * Header info for one line comment about a time step + */ +static void print_lvl1_Header(int nTimes) { + printf("\n"); + if (nTimes) { + print_line("-", 80); + } + printf("time Time Time Time "); + if (nTimes == 0) { + printf(" START"); + } else { + printf(" (continued)"); + } + printf("\n"); + + printf("step (sec) step Newt Aztc bktr trunc "); + printf("\n"); + + printf(" No. Rslt size Its Its stps error |"); + printf(" comment"); + printf("\n"); + print_line("-", 80); +} +/*****************************************************************************/ +/*****************************************************************************/ +/* + * One line entry about time step + * rslt -> 4 letter code + */ +static void print_lvl1_summary( + int time_step_num, double time, const char *rslt, double delta_t_n, + int newt_its, int aztec_its, int bktr_stps, double time_error_factor, + const char *comment) { + printf("%6d %11.6g %4s %10.4g %4d %4d %4d %11.4g", + time_step_num, time, rslt, delta_t_n, newt_its, aztec_its, + bktr_stps, time_error_factor); + if (comment) printf(" | %s", comment); + printf("\n"); +} +/*****************************************************************************/ +/*****************************************************************************/ +namespace Cantera { + + /* + * Function to calculate the predicted solution vector, m_y_pred_n for the + * (n+1)th time step. This routine can be used by a first order - forward + * Euler / backward Euler predictor / corrector method or for a second order + * Adams-Bashforth / Trapezoidal Rule predictor / corrector method. See Nachos + * documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - 83282 for + * more information. + * + * variables: + * + * on input: + * + * N - number of unknowns + * order - indicates order of method + * = 1 -> first order forward Euler/backward Euler + * predictor/corrector + * = 2 -> second order Adams-Bashforth/Trapezoidal Rule + * predictor/corrector + * + * delta_t_n - magnitude of time step at time n (i.e., = t_n+1 - t_n) + * delta_t_nm1 - magnitude of time step at time n - 1 (i.e., = t_n - t_n-1) + * y_n[] - solution vector at time n + * y_dot_n[] - acceleration vector from the predictor at time n + * y_dot_nm1[] - acceleration vector from the predictor at time n - 1 + * + * on output: + * + * m_y_pred_n[] - predicted solution vector at time n + 1 + */ + void BEulerInt::calc_y_pred(int order) + { + int i; + double c1, c2; + switch (order) { + case 0: + case 1: + c1 = delta_t_n; + for (i = 0; i < m_neq; i++) { + m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i]; + } +#ifdef DEBUG_HKM_JJJJJ + if (m_y_pred_n[0] <= 0.0) { + //iDebug_HKM = 1; + c1 = delta_t_n; + m_y_pred_n[0] = 0.0; + } +#endif + break; + case 2: + c1 = delta_t_n * (2.0 + delta_t_n / delta_t_nm1) / 2.0; + c2 = (delta_t_n * delta_t_n) / (delta_t_nm1 * 2.0); + for (i = 0; i < m_neq; i++) { + m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i] - c2 * m_ydot_nm1[i]; + } + break; + } + + /* + * Filter the predictions. + */ + m_func->filterSolnPrediction(time_n, m_y_pred_n); + + } /* calc_y_pred */ + + + /* Function to calculate the acceleration vector ydot for the first or + * second order predictor/corrector time integrator. This routine can be + * called by a first order - forward Euler / backward Euler predictor / + * corrector or for a second order Adams - Bashforth / Trapezoidal Rule + * predictor / corrector. See Nachos documentation Sand86-1816 and Gresho, + * Lee, Sani LLNL report UCRL - 83282 for more information. + * + * variables: + * + * on input: + * + * N - number of local unknowns on the processor + * This is equal to internal plus border unknowns. + * order - indicates order of method + * = 1 -> first order forward Euler/backward Euler + * predictor/corrector + * = 2 -> second order Adams-Bashforth/Trapezoidal Rule + * predictor/corrector + * + * delta_t_n - Magnitude of the current time step at time n + * (i.e., = t_n - t_n-1) + * y_curr[] - Current Solution vector at time n + * y_nm1[] - Solution vector at time n-1 + * ydot_nm1[] - Acceleration vector at time n-1 + * + * on output: + * + * ydot_curr[] - Current acceleration vector at time n + * + * Note we use the current attribute to denote the possibility that + * y_curr[] may not be equal to m_y_n[] during the nonlinear solve + * because we may be using a look-ahead scheme. + */ + void BEulerInt:: + calc_ydot(int order, double *y_curr, double *ydot_curr) + { + int i; + double c1; + switch (order) { + case 0: + case 1: /* First order forward Euler/backward Euler */ + c1 = 1.0 / delta_t_n; + for (i = 0; i < m_neq; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]); + } + return; + case 2: /* Second order Adams-Bashforth / Trapezoidal Rule */ + c1 = 2.0 / delta_t_n; + for (i = 0; i < m_neq; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]) - m_ydot_nm1[i]; + } + return; + } + } /************* END calc_ydot () ****************************************/ + + /* This function calculates the time step truncation error estimate + * from a very simple formula based on Gresho et al. This routine can be + * called for a + * first order - forward Euler/backward Euler predictor/ corrector and + * for a + * second order Adams- Bashforth/Trapezoidal Rule predictor/corrector. See + * Nachos documentation Sand86-1816 and Gresho, Lee, LLNL report + * UCRL - 83282 + * for more information. + * + * variables: + * + * on input: + * + * abs_error - Generic absolute error tolerance + * rel_error - Generic realtive error tolerance + * x_coor[] - Solution vector from the implicit corrector + * x_pred_n[] - Solution vector from the explicit predictor + * + * on output: + * + * delta_t_n - Magnitude of next time step at time t_n+1 + * delta_t_nm1 - Magnitude of previous time step at time t_n + */ + double BEulerInt::time_error_norm() + { + int i; + double rel_norm, error; +#ifdef DEBUG_HKM +#define NUM_ENTRIES 5 + if (m_print_flag > 2) { + int imax[NUM_ENTRIES], j, jnum; + double dmax; + bool used; + printf("\t\ttime step truncation error contributors:\n"); + printf("\t\t I entry actual predicted " + " weight ydot\n"); + printf("\t\t"); print_line("-", 70); + for (j = 0; j < NUM_ENTRIES; j++) imax[j] = -1; + for (jnum = 0; jnum < NUM_ENTRIES; jnum++) { + dmax = -1.0; + for (i = 0; i < m_neq; i++) { + used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; + } + if (!used) { + error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; + rel_norm = sqrt(error * error); + if (rel_norm > dmax) { + imax[jnum] = i; + dmax = rel_norm; + } + } + } + if (imax[jnum] >= 0) { + i = imax[jnum]; + printf("\t\t%4d %12.4e %12.4e %12.4e %12.4e %12.4e\n", + i, dmax, m_y_n[i], m_y_pred_n[i], m_ewt[i], m_ydot_n[i]); + } + } + printf("\t\t"); print_line("-", 70); + } +#endif + rel_norm = 0.0; + for (i = 0; i < m_neq; i++) { + error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; + rel_norm += (error * error); + } + rel_norm = sqrt(rel_norm / m_neq); + return rel_norm; + } + + /************************************************************************* + * Time step control function for the selection of the time step size based on + * a desired accuracy of time integration and on an estimate of the relative + * error of the time integration process. This routine can be called for a + * first order - forward Euler/backward Euler predictor/ corrector and for a + * second order Adams- Bashforth/Trapezoidal Rule predictor/corrector. See + * Nachos documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - + * 83282 for more information. + * + * variables: + * + * on input: + * + * order - indicates order of method + * = 1 -> first order forward Euler/backward Euler + * predictor/corrector + * = 2 -> second order forward Adams-Bashforth/Trapezoidal + * rule predictor/corrector + * + * delta_t_n - Magnitude of time step at time t_n + * delta_t_nm1 - Magnitude of time step at time t_n-1 + * rel_error - Generic realtive error tolerance + * time_error_factor - Estimated value of the time step truncation error + * factor. This value is a ratio of the computed + * error norms. The premultiplying constants + * and the power are not yet applied to normalize the + * predictor/corrector ratio. (see output value) + * + * on output: + * + * return - delta_t for the next time step + * If delta_t is negative, then the current time step is + * rejected because the time-step truncation error is + * too large. The return value will contain the negative + * of the recommended next time step. + * + * time_error_factor - This output value is normalized so that + * values greater than one indicate the current time + * integration error is greater than the user + * specified magnitude. + */ + double BEulerInt::time_step_control(int order, double time_error_factor) + { + double factor = 0.0, power = 0.0, delta_t; + const char *yo = "time_step_control"; + + /* + * Special case time_error_factor so that zeroes don't cause a problem. + */ + time_error_factor = MAX(1.0E-50, time_error_factor); + + /* + * Calculate the factor for the change in magnitude of time step. + */ + switch (order) { + case 1: + factor = 1.0/(2.0 *(time_error_factor)); + power = 0.5; + break; + case 2: + factor = 1.0/(3.0 * (1.0 + delta_t_nm1 / delta_t_n) + * (time_error_factor)); + power = 0.3333333333333333; + } + factor = pow(factor, power); + if (factor < 0.5) { + if (m_print_flag > 1) { + printf("\t%s: WARNING - Current time step will be chucked\n", yo); + printf("\t\tdue to a time step truncation error failure.\n"); + } + delta_t = - 0.5 * delta_t_n; + } else { + factor = MIN(factor, 1.5); + delta_t = factor * delta_t_n; + } + return delta_t; + } /************ END of time_step_control()********************************/ + + /************************************************************************** + * + * integrate(): + * + * defaults are located in the .h file. They are as follows: + * time_init = 0.0 + */ + double BEulerInt::integrateRJE(double tout, double time_init) + { + double time_current; + bool weAreNotFinished = true; + m_time_final = tout; + int flag = SUCCESS; + /** + * Initialize the time step number to zero. step will increment so that + * the first time step is number 1 + */ + m_time_step_num = 0; + + + /* + * Do the integration a step at a time + */ + int istep = 0; + int printStep = 0; + bool doPrintSoln = false; + time_current = time_init; + time_n = time_init; + time_nm1 = time_init; + time_nm2 = time_init; + m_func->evalTimeTrackingEqns(time_current, 0.0, m_y_n, m_ydot_n); + double print_time = getPrintTime(time_current); + if (print_time == time_current) { + m_func->writeSolution(4, time_current, delta_t_n, + istep, m_y_n, m_ydot_n); + } + /* + * We print out column headers here for the case of + */ + if (m_print_flag == 1) { + print_lvl1_Header(0); + } + /* + * Call a different user routine at the end of each step, + * that will probably print to a file. + */ + m_func->user_out2(0, time_current, 0.0, m_y_n, m_ydot_n); + + do { + + print_time = getPrintTime(time_current); + if (print_time >= tout) print_time = tout; + + /************************************************************ + * Step the solution + */ + time_current = step(tout); + istep++; + printStep++; + /***********************************************************/ + if (time_current < 0.0) { + if (time_current == -1234.) { + time_current = 0.0; + } else { + time_current = -time_current; + } + flag = FAILURE; + } + + if (flag != FAILURE) { + bool retn = + m_func->evalStoppingCritera(time_current, delta_t_n, + m_y_n, m_ydot_n); + if (retn) { + weAreNotFinished = false; + doPrintSoln = true; + } + } + + /* + * determine conditional printing of soln + */ + if (time_current >= print_time) { + doPrintSoln = true; + } + if (m_printSolnStepInterval == printStep) { + doPrintSoln = true; + } + if (m_printSolnFirstSteps > istep) { + doPrintSoln = true; + } + + /* + * Evaluate time integrated quantities that are calculated at the + * end of every successful time step. + */ + if (flag != FAILURE) { + m_func->evalTimeTrackingEqns(time_current, delta_t_n, + m_y_n, m_ydot_n); + } + + /* + * Call the printout routine. + */ + if (doPrintSoln) { + m_func->writeSolution(1, time_current, delta_t_n, + istep, m_y_n, m_ydot_n); + printStep = 0; + doPrintSoln = false; + if (m_print_flag == 1) { + print_lvl1_Header(1); + } + } + /* + * Call a different user routine at the end of each step, + * that will probably print to a file. + */ + if (flag == FAILURE) { + m_func->user_out2(-1, time_current, delta_t_n, m_y_n, m_ydot_n); + } else { + m_func->user_out2(1, time_current, delta_t_n, m_y_n, m_ydot_n); + } + + } while (time_current < tout && + m_time_step_attempts < m_max_time_step_attempts && + flag == SUCCESS && weAreNotFinished); + + /* + * Check current time against the max solution time. + */ + if (time_current >= tout) { + printf("Simulation completed time integration in %d time steps\n", + m_time_step_num); + printf("Final Time: %e\n\n", time_current); + } else if (m_time_step_attempts >= m_max_time_step_attempts) { + printf("Simulation ran into time step attempt limit in" + "%d time steps\n", + m_time_step_num); + printf("Final Time: %e\n\n", time_current); + } else if (flag == FAILURE) { + printf("ERROR: time stepper failed at time = %g\n", time_current); + } + + /* + * Print out the final results and counters. + */ + print_final(time_n, flag, m_time_step_num, m_numTotalNewtIts, + m_numTotalLinearSolves, m_numTotalConvFails, + m_numTotalTruncFails, m_nfe, m_nJacEval); + + /* + * Call a different user routine at the end of each step, + * that will probably print to a file. + */ + m_func->user_out2(2, time_current, delta_t_n, m_y_n, m_ydot_n); + + + if (flag != SUCCESS) + throw BEulerErr(" BEuler error encountered."); + return time_current; + } + + /************************************************************************** + * + * step(): + * + * This routine advances the calculations one step using a predictor + * corrector approach. We use an implicit algorithm here. + * + */ + double BEulerInt::step(double t_max) + { + double CJ; + int one = 1; + bool step_failed = false; + bool giveUp = false; + bool convFailure = false; + const char *rslt; + double time_error_factor = 0.0; + double normFilter = 0.0; + int numTSFailures = 0; + int bktr_stps = 0; + int nonlinearloglevel = m_print_flag; + int num_newt_its = 0; + int aztec_its = 0; + string comment; + /* + * Increment the time counter - May have to be taken back, + * if time step is found to be faulty. + */ + m_time_step_num++; + + /** + * Loop here until we achieve a successful step or we set the giveUp + * flag indicating that repeated errors have occurred. + */ + do { + m_time_step_attempts++; + comment.clear(); + + /* + * Possibly adjust the delta_t_n value for this time step from the + * recommended delta_t_np1 value determined in the previous step + * due to maximum time step constraints or other occurences, + * known to happen at a given time. + */ + if ((time_n + delta_t_np1) >= t_max) { + delta_t_np1 =t_max - time_n; + } + + if (delta_t_np1 >= delta_t_max) { + delta_t_np1 = delta_t_max; + } + + /* + * Increment the delta_t counters and the time for the current + * time step. + */ + + delta_t_nm2 = delta_t_nm1; + delta_t_nm1 = delta_t_n; + delta_t_n = delta_t_np1; + time_n += delta_t_n; + + /* + * Determine the integration order of the current step. + * + * Special case for start-up of time integration procedure + * First time step = Do a predictor step as we + * have recently added an initial + * ydot input option. And, setting ydot=0 + * is equivalent to not doing a + * predictor step. + * Second step = If 2nd order method, do a first order + * step for this time-step, only. + * + * If 2nd order method with a constant time step, the + * first and second steps are 1/10 the specified step, and + * the third step is 8/10 the specified step. This reduces + * the error asociated with using lower order + * integration on the first two steps. (RCS 11-6-97) + * + * If the previous time step failed for one reason or another, + * do a linear step. It's more robust. + */ + if (m_time_step_num == 1) { + m_order = 1; /* Backward Euler */ + } + else if (m_time_step_num == 2) { + m_order = 1; /* Forward/Backward Euler */ + } + else if (step_failed) { + m_order = 1; /* Forward/Backward Euler */ + } + else if (m_time_step_num > 2) { + m_order = 1; /* Specified + Predictor/Corrector + - not implemented */ + } + + /* + * Print out an initial statement about the step. + */ + if (m_print_flag > 1) { + print_time_step1(m_order, m_time_step_num, time_n, delta_t_n, + delta_t_nm1, step_failed, m_failure_counter); + } + + /* + * Calculate the predicted solution, m_y_pred_n, for the current + * time step. + */ + calc_y_pred(m_order); + + /* + * HKM - Commented this out. I may need it for particles later. + * If Solution bounds checking is turned on, we need to crop the + * predicted solution to make sure bounds are enforced + * + * + * cropNorm = 0.0; + * if (Cur_Realm->Realm_Nonlinear.Constraint_Backtracking_Flag == + * Constraint_Backtrack_Enable) { + * cropNorm = cropPredictor(mesh, x_pred_n, abs_time_error, + * m_reltol); + */ + + /* + * Save the old solution, before overwriting with the new solution + * - use + */ + mdp_copy_dbl_1(m_y_nm1, m_y_n, m_neq); + + /* + * Use the predicted value as the initial guess for the corrector + * loop, for + * every step other than the first step. + */ + if (m_order > 0) { + mdp_copy_dbl_1(m_y_n, m_y_pred_n, m_neq); + } + + /* + * Save the old time derivative, if necessary, before it is + * overwritten. + * This overwrites ydot_nm1, losing information from the previous time + * step. + */ + mdp_copy_dbl_1(m_ydot_nm1, m_ydot_n, m_neq); + + /* + * Calculate the new time derivative, ydot_n, that is consistent + * with the + * initial guess for the corrected solution vector. + * + */ + calc_ydot(m_order, m_y_n, m_ydot_n); + + /* + * Calculate CJ, the coefficient for the jacobian corresponding to the + * derivative of the residual wrt to the acceleration vector. + */ + if (m_order < 2) CJ = 1.0 / delta_t_n; + else CJ = 2.0 / delta_t_n; + + /* + * Calculate a new Solution Error Weighting vector + */ + setSolnWeights(); + + /* + * Solve the system of equations at the current time step. + * Note - x_corr_n and x_dot_n are considered to be updated, + * on return from this solution. + */ + int ierror = solve_nonlinear_problem(m_y_n, m_ydot_n, + CJ, time_n, *tdjac_ptr, num_newt_its, + aztec_its, bktr_stps, + nonlinearloglevel); + /* + * Set the appropriate flags if a convergence failure is detected. + */ + if (ierror < 0) { /* Step failed */ + convFailure = true; + step_failed = true; + rslt = "fail"; + m_numTotalConvFails++; + m_failure_counter +=3; + if (m_print_flag > 1) { + printf("\tStep is Rejected, nonlinear problem didn't converge," + "ierror = %d\n", ierror); + } + } + else { /* Step succeeded */ + convFailure = false; + step_failed = false; + rslt = "done"; + + /* + * Apply a filter to a new successful step + */ + normFilter = filterNewStep(time_n, m_y_n, m_ydot_n); + if (normFilter > 1.0) { + convFailure = true; + step_failed = true; + rslt = "filt"; + if (m_print_flag > 1) { + printf("\tStep is Rejected, too large filter adjustment = %g\n", + normFilter); + } + } else if (normFilter > 0.0) { + if (normFilter > 0.3) { + if (m_print_flag > 1) { + printf("\tStep was filtered, norm = %g, next " + "time step adjusted\n", normFilter); + } + } else { + if (m_print_flag > 1) { + printf("\tStep was filtered, norm = %g\n", normFilter); + } + } + } + } + + /* + * Calculate the time step truncation error for the current step. + */ + if (!step_failed) { + time_error_factor = time_error_norm(); + } else { + time_error_factor = 1000.; + } + + /* + * Dynamic time step control- delta_t_n, delta_t_nm1 are set here. + */ + if (step_failed) { + /* + * For convergence failures, decrease the step-size by a factor of + * 4 and try again. + */ + delta_t_np1 = 0.25 * delta_t_n; + } + else if (m_method == BEulerVarStep) { + + /* + * If we are doing a predictor/corrector method, and we are + * past a certain number of time steps given by the input file + * then either correct the DeltaT for the next time step or + * + */ + if ((m_order > 0) && + (m_time_step_num > m_numInitialConstantDeltaTSteps) ) { + delta_t_np1 = time_step_control(m_order, time_error_factor); + if (normFilter > 0.1) { + if (delta_t_np1 > delta_t_n) delta_t_np1 = delta_t_n; + } + + /* + * Check for Current time step failing due to violation of + * time step + * truncation bounds. + */ + if (delta_t_np1 < 0.0) { + m_numTotalTruncFails++; + step_failed = true; + delta_t_np1 = -delta_t_np1; + m_failure_counter += 2; + comment += "TIME TRUNC FAILURE"; + rslt = "TRNC"; + } + + /* + * Prevent churning of the time step by not increasing the + * time step, + * if the recent "History" of the time step behavior is still bad + */ + else if (m_failure_counter > 0) { + delta_t_np1 = MIN(delta_t_np1, delta_t_n); + } + } else { + delta_t_np1 = delta_t_n; + } + + /* Decrease time step if a lot of Newton Iterations are + * taken. + * The idea being if more or less Newton iteration are taken + * than the target number of iterations, then adjust the time + * step downwards so that the target number of iterations or lower + * is achieved. This + * should prevent step failure by too many Newton iterations because + * the time step becomes too large. CCO + * hkm -> put in num_new_its min of 3 because the time step + * was being altered even when num_newt_its == 1 + */ + int max_Newton_steps = 10000; + int target_num_iter = 5; + if (num_newt_its > 3000 && !step_failed) { + if (max_Newton_steps != target_num_iter){ + double iter_diff = num_newt_its - target_num_iter; + double iter_adjust_zone = max_Newton_steps - target_num_iter; + double target_time_step = delta_t_n + *(1.0 - iter_diff*fabs(iter_diff)/ + ((2.0*iter_adjust_zone*iter_adjust_zone))); + target_time_step = MAX(0.5*delta_t_n, target_time_step); + if (target_time_step < delta_t_np1) { + printf("\tNext time step will be decreased from %g to %g" + " because of new its restraint\n", + delta_t_np1, target_time_step); + delta_t_np1 = target_time_step; + } + } + } + + + } + + /* + * The final loop in the time stepping algorithm depends on whether the + * current step was a success or not. + */ + if (step_failed) { + /* + * Increment the counter indicating the number of consecutive + * failures + */ + numTSFailures++; + /* + * Print out a statement about the failure of the time step. + */ + if (m_print_flag > 1) { + print_time_fail(convFailure, m_time_step_num, time_n, delta_t_n, + delta_t_np1, time_error_factor); + } else if (m_print_flag == 1) { + print_lvl1_summary(m_time_step_num, time_n, rslt, delta_t_n, + num_newt_its, aztec_its, bktr_stps, + time_error_factor, + comment.c_str()); + } + + /* + * Change time step counters back to the previous step before + * the failed + * time step occurred. + */ + time_n -= delta_t_n; + delta_t_n = delta_t_nm1; + delta_t_nm1 = delta_t_nm2; + + /* + * Replace old solution vector and time derivative solution vector. + */ + dcopy_(&m_neq, m_y_nm1, &one, m_y_n, &one); + dcopy_(&m_neq, m_ydot_nm1, &one, m_ydot_n, &one); + /* + * Decide whether to bail on the whole loop + */ + if (numTSFailures > 35) giveUp = true; + } + + /* + * Do processing for a successful step. + */ + else { + + /* + * Decrement the number of consequative failure counter. + */ + m_failure_counter = MAX(0, m_failure_counter-1); + + /* + * Print out final results of a successfull time step. + */ + if (m_print_flag > 1) { + print_time_step2(m_time_step_num, m_order, time_n, time_error_factor, + delta_t_n, delta_t_np1); + } + else if (m_print_flag == 1) { + print_lvl1_summary(m_time_step_num, time_n, " ", delta_t_n, + num_newt_its, aztec_its, bktr_stps, time_error_factor, + comment.c_str()); + } + + /* + * Output information at the end of every successful time step, if + * requested. + * + * fill in + */ + + + } + } while (step_failed && !giveUp); + + /* + * Send back the overall result of the time step. + */ + if (step_failed) { + if (time_n == 0.0) return -1234.0; + return -time_n; + } + return time_n; + } + + + + //----------------------------------------------------------- + // Constants + //----------------------------------------------------------- + + const double DampFactor = 4; + const int NDAMP = 10; + + //----------------------------------------------------------- + // Static Functions + //----------------------------------------------------------- + + static void print_line(const char *str, int n) { + for (int i = 0; i < n; i++) { + printf("%s", str); + } + printf("\n"); + } + + //----------------------------------------------------------- + // MultiNewton methods + //----------------------------------------------------------- + /** + * L2 Norm of a delta in the solution + * + * The second argument has a default of false. However, + * if true, then a table of the largest values is printed + * out to standard output. + */ + double BEulerInt::soln_error_norm(const double * const delta_y, + bool printLargest) + { + int i; + double sum_norm = 0.0, error; + for (i = 0; i < m_neq; i++) { + error = delta_y[i] / m_ewt[i]; + sum_norm += (error * error); + } + sum_norm = sqrt(sum_norm / m_neq); + if (printLargest) { + const int num_entries = 8; + double dmax1, normContrib; + int j; + int *imax = mdp_alloc_int_1(num_entries, -1); + printf("\t\tPrintout of Largest Contributors to norm " + "of value (%g)\n", sum_norm); + printf("\t\t I ysoln deltaY weightY " + "Error_Norm**2\n"); + printf("\t\t "); print_line("-", 80); + for (int jnum = 0; jnum < num_entries; jnum++) { + dmax1 = -1.0; + for (i = 0; i < m_neq; i++) { + bool used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; + } + if (!used) { + error = delta_y[i] / m_ewt[i]; + normContrib = sqrt(error * error); + if (normContrib > dmax1) { + imax[jnum] = i; + dmax1 = normContrib; + } + } + } + i = imax[jnum]; + if (i >= 0) { + printf("\t\t %4d %12.4e %12.4e %12.4e %12.4e\n", + i, m_y_n[i], delta_y[i], m_ewt[i], dmax1); + } + } + printf("\t\t "); print_line("-", 80); + mdp_safe_free((void **) &imax); + } + return sum_norm; + } +#ifdef DEBUG_HKM_JAC + SquareMatrix jacBack(); +#endif + /************************************************************************** + * + * doNewtonSolve(): + * + * Compute the undamped Newton step. The residual function is + * evaluated at the current time, t_n, at the current values of the + * solution vector, m_y_n, and the solution time derivative, m_ydot_n, + * but the Jacobian is not recomputed. + */ + void BEulerInt::doNewtonSolve(double time_curr, double *y_curr, + double *ydot_curr, double* delta_y, + SquareMatrix& jac, int loglevel) + { + int irow, jcol; + + m_func->evalResidNJ(time_curr, delta_t_n, y_curr, + ydot_curr, delta_y); + m_nfe++; + int sz = m_func->nEquations(); + for (int n = 0; n < sz; n++) { + delta_y[n] = -delta_y[n]; + } + + + /* + * Column scaling -> We scale the columns of the Jacobian + * by the nominal important change in the solution vector + */ + if (m_colScaling) { + if (!jac.m_factored) { + /* + * Go get new scales + */ + setColumnScales(); + + /* + * Scale the new Jacobian + */ + double *jptr = &(*(jac.begin())); + for (jcol = 0; jcol < m_neq; jcol++) { + for (irow = 0; irow < m_neq; irow++) { + *jptr *= m_colScales[jcol]; + jptr++; + } + } + } + } + + if (m_matrixConditioning) { + if (jac.m_factored) { + m_func->matrixConditioning(0, sz, delta_y); + } else { + double *jptr = &(*(jac.begin())); + m_func->matrixConditioning(jptr, sz, delta_y); + } + } + + /* + * row sum scaling -> Note, this is an unequivical success + * at keeping the small numbers well balanced and + * nonnegative. + */ + if (m_rowScaling) { + if (! jac.m_factored) { + /* + * Ok, this is ugly. jac.begin() returns an vector iterator + * to the first data location. + * Then &(*()) reverts it to a double *. + */ + double *jptr = &(*(jac.begin())); + for (irow = 0; irow < m_neq; irow++) { + m_rowScales[irow] = 0.0; + } + for (jcol = 0; jcol < m_neq; jcol++) { + for (irow = 0; irow < m_neq; irow++) { + m_rowScales[irow] += fabs(*jptr); + jptr++; + } + } + + jptr = &(*(jac.begin())); + for (jcol = 0; jcol < m_neq; jcol++) { + for (irow = 0; irow < m_neq; irow++) { + *jptr /= m_rowScales[irow]; + jptr++; + } + } + } + for (irow = 0; irow < m_neq; irow++) { + delta_y[irow] /= m_rowScales[irow]; + } + } + +#ifdef DEBUG_HKM_JAC + bool printJacContributions = false; + if (m_time_step_num > 304) { + printJacContributions = false; + } + int focusRow = 10; + int numRows = 2; + double RRow[2]; + bool freshJac = true; + RRow[0] = delta_y[focusRow]; + RRow[1] = delta_y[focusRow+1]; + double Pcutoff = 1.0E-70; + if (!jac.m_factored) { + jacBack = jac; + } else { + freshJac = false; + } +#endif + /* + * Solve the system -> This also involves inverting the + * matrix + */ + (void) jac.solve(delta_y); + + + /* + * reverse the column scaling if there was any. + */ + if (m_colScaling) { + for (irow = 0; irow < m_neq; irow++) { + delta_y[irow] *= m_colScales[irow]; + } + } + +#ifdef DEBUG_HKM_JAC + if (printJacContributions) { + for (int iNum = 0; iNum < numRows; iNum++) { + if (iNum > 0) focusRow++; + double dsum = 0.0; + vector_fp& Jdata = jacBack.data(); + double dRow = Jdata[m_neq * focusRow + focusRow]; + printf("\n Details on delta_Y for row %d \n", focusRow); + printf(" Value before = %15.5e, delta = %15.5e," + "value after = %15.5e\n", y_curr[focusRow], + delta_y[focusRow], + y_curr[focusRow] + delta_y[focusRow]); + if (!freshJac) { + printf(" Old Jacobian\n"); + } + printf(" col delta_y aij " + "contrib \n"); + printf("--------------------------------------------------" + "---------------------------------------------\n"); + printf(" Res(%d) %15.5e %15.5e %15.5e (Res = %g)\n", + focusRow, delta_y[focusRow], + dRow, RRow[iNum] / dRow, RRow[iNum]); + dsum += RRow[iNum] / dRow; + for (int ii = 0; ii < m_neq; ii++) { + if (ii != focusRow) { + double aij = Jdata[m_neq * ii + focusRow]; + double contrib = aij * delta_y[ii] * (-1.0) / dRow; + dsum += contrib; + if (fabs(contrib) > Pcutoff) { + printf("%6d %15.5e %15.5e %15.5e\n", ii, + delta_y[ii] , aij, contrib); + } + } + } + printf("--------------------------------------------------" + "---------------------------------------------\n"); + printf(" %15.5e %15.5e\n", + delta_y[focusRow], dsum); + } + } + +#endif + + m_numTotalLinearSolves++; + } + + //================================================================================================ + // Bound the Newton step while relaxing the solution + /* + * Return the factor by which the undamped Newton step 'step0' + * must be multiplied in order to keep all solution components in + * all domains between their specified lower and upper bounds. + * Other bounds may be applied here as well. + * + * Currently the bounds are hard coded into this routine: + * + * Minimum value for all variables: - 0.01 * m_ewt[i] + * Maximum value = none. + * + * Thus, this means that all solution components are expected + * to be numerical greater than zero in the limit of time step + * truncation errors going to zero. + * + * Delta bounds: The idea behind these is that the Jacobian + * couldn't possibly be representative if the + * variable is changed by a lot. (true for + * nonlinear systems, false for linear systems) + * Maximum increase in variable in any one newton iteration: + * factor of 2 + * Maximum decrease in variable in any one newton iteration: + * factor of 5 + * + * @param y Current value of the solution + * @param step0 Current raw step change in y[] + * @param loglevel Log level. This routine produces output if loglevel + * is greater than one + * + * @return Returns the damping coefficient + */ + double BEulerInt::boundStep(const double * const y, + const double * const step0, int loglevel) { + int i, i_lower = -1, i_fbounds, ifbd = 0, i_fbd = 0; + double fbound = 1.0, f_lowbounds = 1.0, f_delta_bounds = 1.0; + double ff, y_new, ff_alt; + for (i = 0; i < m_neq; i++) { + y_new = y[i] + step0[i]; + if ((y_new < (-0.01 * m_ewt[i])) && y[i] >= 0.0) { + ff = 0.9 * (y[i] / (y[i] - y_new)); + if (ff < f_lowbounds) { + f_lowbounds = ff; + i_lower = i; + } + } + /* + * Now do a delta bounds + * Increase variables by a factor of 2 only + * decrease variables by a factor of 5 only + */ + ff = 1.0; + if ((fabs(y_new) > 2.0 * fabs(y[i])) && + (fabs(y_new-y[i]) > m_ewt[i])) { + ff = fabs(y[i]/(y_new - y[i])); + ff_alt = fabs(m_ewt[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + ifbd = 1; + } + if ((fabs(5.0 * y_new) < fabs(y[i])) && + (fabs(y_new - y[i]) > m_ewt[i])) { + ff = y[i]/(y_new-y[i]) * (1.0 - 5.0)/5.0; + ff_alt = fabs(m_ewt[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + ifbd = 0; + } + if (ff < f_delta_bounds) { + f_delta_bounds = ff; + i_fbounds = i; + i_fbd = ifbd; + } + f_delta_bounds = MIN(f_delta_bounds, ff); + } + fbound = MIN(f_lowbounds, f_delta_bounds); + /* + * Report on any corrections + */ + if (loglevel > 1) { + if (fbound != 1.0) { + if (f_lowbounds < f_delta_bounds) { + printf("\t\tboundStep: Variable %d causing lower bounds " + "damping of %g\n", + i_lower, f_lowbounds); + } else { + if (ifbd) { + printf("\t\tboundStep: Decrease of Variable %d causing " + "delta damping of %g\n", + i_fbd, f_delta_bounds); + } else { + printf("\t\tboundStep: Increase of variable %d causing" + "delta damping of %g\n", + i_fbd, f_delta_bounds); + } + } + } + } + return fbound; + } + //================================================================================================ + /************************************************************************** + * + * dampStep(): + * + * On entry, step0 must contain an undamped Newton step for the + * solution x0. This method attempts to find a damping coefficient + * such that the next undamped step would have a norm smaller than + * that of step0. If successful, the new solution after taking the + * damped step is returned in y1, and the undamped step at y1 is + * returned in step1. + */ + int BEulerInt::dampStep(double time_curr, const double * y0, + const double *ydot0, const double* step0, + double* y1, double* ydot1, double* step1, + double& s1, SquareMatrix& jac, + int& loglevel, bool writetitle, + int& num_backtracks) { + + + // Compute the weighted norm of the undamped step size step0 + double s0 = soln_error_norm(step0); + + // Compute the multiplier to keep all components in bounds + // A value of one indicates that there is no limitation + // on the current step size in the nonlinear method due to + // bounds constraints (either negative values of delta + // bounds constraints. + double fbound = boundStep(y0, step0, loglevel); + + // if fbound is very small, then y0 is already close to the + // boundary and step0 points out of the allowed domain. In + // this case, the Newton algorithm fails, so return an error + // condition. + if (fbound < 1.e-10) { + if (loglevel > 1) printf("\t\t\tdampStep: At limits.\n"); + return -3; + } + + //-------------------------------------------- + // Attempt damped step + //-------------------------------------------- + + // damping coefficient starts at 1.0 + double damp = 1.0; + int j, m; + double ff; + num_backtracks = 0; + for (m = 0; m < NDAMP; m++) { + + ff = fbound*damp; + + // step the solution by the damped step size + /* + * Whenever we update the solution, we must also always + * update the time derivative. + */ + for (j = 0; j < m_neq; j++) { + y1[j] = y0[j] + ff*step0[j]; + // HKM setting intermediate y's to zero was a tossup. + // slightly different, equivalent results + //#ifdef DEBUG_HKM + // y1[j] = MAX(0.0, y1[j]); + //#endif + } + calc_ydot(m_order, y1, ydot1); + + // compute the next undamped step, step1[], that would result + // if y1[] were accepted. + + doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); + +#ifdef DEBUG_HKM + for (j = 0; j < m_neq; j++) { + checkFinite(step1[j]); + checkFinite(y1[j]); + } +#endif + // compute the weighted norm of step1 + s1 = soln_error_norm(step1); + + // write log information + if (loglevel > 3) { + print_solnDelta_norm_contrib((const double *) step0, + "DeltaSolnTrial", + (const double *) step1, + "DeltaSolnTrialTest", + "dampNewt: Important Entries for " + "Weighted Soln Updates:", + y0, y1, ff, 5); + } + if (loglevel > 1) { + printf("\t\t\tdampNewt: s0 = %g, s1 = %g, fbound = %g," + "damp = %g\n", s0, s1, fbound, damp); + } +#ifdef DEBUG_HKM + if (loglevel > 2) { + if (s1 > 1.00000001 * s0 && s1 > 1.0E-5) { + printf("WARNING: Possible Jacobian Problem " + "-> turning on more debugging for this step!!!\n"); + print_solnDelta_norm_contrib((const double *) step0, + "DeltaSolnTrial", + (const double *) step1, + "DeltaSolnTrialTest", + "dampNewt: Important Entries for " + "Weighted Soln Updates:", + y0, y1, ff, 5); + loglevel = 4; + } + } +#endif + + // if the norm of s1 is less than the norm of s0, then + // accept this damping coefficient. Also accept it if this + // step would result in a converged solution. Otherwise, + // decrease the damping coefficient and try again. + + if (s1 < 1.0E-5 || s1 < s0) { + if (loglevel > 2) { + if (s1 > s0) { + if (s1 > 1.0) { + printf("\t\t\tdampStep: current trial step and damping" + " coefficient accepted because test step < 1\n"); + printf("\t\t\t s1 = %g, s0 = %g\n", s1, s0); + } + } + } + break; + } else { + if (loglevel > 1) { + printf("\t\t\tdampStep: current step rejected: (s1 = %g > " + "s0 = %g)", s1, s0); + if (m < (NDAMP-1)) { + printf(" Decreasing damping factor and retrying"); + } else { + printf(" Giving up!!!"); + } + printf("\n"); + } + } + num_backtracks++; + damp /= DampFactor; + } + + // If a damping coefficient was found, return 1 if the + // solution after stepping by the damped step would represent + // a converged solution, and return 0 otherwise. If no damping + // coefficient could be found, return -2. + if (m < NDAMP) { + if (s1 > 1.0) return 0; + else return 1; + } else { + if (s1 < 0.5 && (s0 < 0.5)) return 1; + if (s1 < 1.0) return 0; + return -2; + } + } + + /************************************************************************** + * + * solve_nonlinear_problem(): + * + * Find the solution to F(X) = 0 by damped Newton iteration. On + * entry, x0 contains an initial estimate of the solution. On + * successful return, x1 contains the converged solution. + * + + * + */ + int BEulerInt::solve_nonlinear_problem(double* const y_comm, + double* const ydot_comm, double CJ, + double time_curr, + SquareMatrix& jac, + int &num_newt_its, + int &num_linear_solves, + int &num_backtracks, + int loglevelInput) + { + bool m_residCurrent = false; + int m = 0; + bool forceNewJac = false; + double s1=1.e30; + + double* y_curr = mdp_alloc_dbl_1(m_neq, 0.0); + double* ydot_curr = mdp_alloc_dbl_1(m_neq, 0.0); + double* stp = mdp_alloc_dbl_1(m_neq, 0.0); + double* stp1 = mdp_alloc_dbl_1(m_neq, 0.0); + double * y_new = mdp_alloc_dbl_1(m_neq, 0.0); + double * ydot_new = mdp_alloc_dbl_1(m_neq, 0.0); + + mdp_copy_dbl_1(y_curr, y_comm, m_neq); + mdp_copy_dbl_1(ydot_curr, ydot_comm, m_neq); + + bool frst = true; + num_newt_its = 0; + num_linear_solves = - m_numTotalLinearSolves; + num_backtracks = 0; + int i_backtracks; + int loglevel = loglevelInput; + + while (1 > 0) { + + /* + * Increment Newton Solve counter + */ + m_numTotalNewtIts++; + num_newt_its++; + + + if (loglevel > 1) { + printf("\t\tSolve_Nonlinear_Problem: iteration %d:\n", + num_newt_its); + } + + // Check whether the Jacobian should be re-evaluated. + + forceNewJac = true; + + if (forceNewJac) { + if (loglevel > 1) { + printf("\t\t\tGetting a new Jacobian and solving system\n"); + } + beuler_jac(jac, m_resid, time_curr, CJ, y_curr, ydot_curr, + num_newt_its); + m_residCurrent = true; + } else { + if (loglevel > 1) { + printf("\t\t\tSolving system with old jacobian\n"); + } + m_residCurrent = false; + } + + // compute the undamped Newton step + doNewtonSolve(time_curr, y_curr, ydot_curr, stp, jac, loglevel); + + // damp the Newton step + m = dampStep(time_curr, y_curr, ydot_curr, stp, y_new, ydot_new, + stp1, s1, jac, loglevel, frst, i_backtracks); + frst = false; + num_backtracks += i_backtracks; + + /* + * Impose the minimum number of newton iterations critera + */ + if (num_newt_its < m_min_newt_its) { + if (m == 1) m = 0; + } + /* + * Impose max newton iteration + */ + if (num_newt_its > 20) { + m = -1; + if (loglevel > 1) { + printf("\t\t\tDampnewton unsuccessful (max newts exceeded) sfinal = %g\n", s1); + } + } + + if (loglevel > 1) { + if (m == 1) { + printf("\t\t\tDampNewton iteration successful, nonlin " + "converged sfinal = %g\n", s1); + } else if (m == 0) { + printf("\t\t\tDampNewton iteration successful, get new" + "direction, sfinal = %g\n", s1); + } else { + printf("\t\t\tDampnewton unsuccessful sfinal = %g\n", s1); + } + } + + // If we are converged, then let's use the best solution possible + // for an end result. We did a resolve in dampStep(). Let's update + // the solution to reflect that. + // HKM 5/16 -> Took this out, since if the last step was a + // damped step, then adding stp1[j] is undamped, and + // may lead to oscillations. It kind of defeats the + // purpose of dampStep() anyway. + // if (m == 1) { + // for (int j = 0; j < m_neq; j++) { + // y_new[j] += stp1[j]; + // HKM setting intermediate y's to zero was a tossup. + // slightly different, equivalent results + // #ifdef DEBUG_HKM + // y_new[j] = MAX(0.0, y_new[j]); + // #endif + // } + // } + + bool m_filterIntermediate = false; + if (m_filterIntermediate) { + if (m == 0) { + (void) filterNewStep(time_n, y_new, ydot_new); + } + } + // Exchange new for curr solutions + if (m == 0 || m == 1) { + mdp_copy_dbl_1(y_curr, y_new, m_neq); + calc_ydot(m_order, y_curr, ydot_curr); + } + + // convergence + if (m == 1) goto done; + + // If dampStep fails, first try a new Jacobian if an old + // one was being used. If it was a new Jacobian, then + // return -1 to signify failure. + else if (m < 0) { + goto done; + } + } + + done: + mdp_copy_dbl_1(y_comm, y_curr, m_neq); + mdp_copy_dbl_1(ydot_comm, ydot_curr, m_neq); + + num_linear_solves += m_numTotalLinearSolves; + mdp_safe_free((void **) &y_curr); + mdp_safe_free((void **) &ydot_curr); + mdp_safe_free((void **) &stp); + mdp_safe_free((void **) &stp1); + mdp_safe_free((void **) &y_new); + mdp_safe_free((void **) &ydot_new); + + double time_elapsed = 0.0; + if (loglevel > 1) { + if (m == 1) { + printf("\t\tNonlinear problem solved successfully in " + "%d its, time elapsed = %g sec\n", + num_newt_its, time_elapsed); + } + } + return m; + } + + /***************************************************************8 + * + * + */ + void BEulerInt:: + print_solnDelta_norm_contrib(const double * const solnDelta0, + const char * const s0, + const double * const solnDelta1, + const char * const s1, + const char * const title, + const double * const y0, + const double * const y1, + double damp, + int num_entries) { + int i, j, jnum; + bool used; + double dmax0, dmax1, error, rel_norm; + printf("\t\t%s currentDamp = %g\n", title, damp); + printf("\t\t I ysoln %10s ysolnTrial " + "%10s weight relSoln0 relSoln1\n", s0, s1); + int *imax = mdp_alloc_int_1(num_entries, -1); + printf("\t\t "); print_line("-", 90); + for (jnum = 0; jnum < num_entries; jnum++) { + dmax1 = -1.0; + for (i = 0; i < m_neq; i++) { + used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; + } + if (!used) { + error = solnDelta0[i] / m_ewt[i]; + rel_norm = sqrt(error * error); + error = solnDelta1[i] / m_ewt[i]; + rel_norm += sqrt(error * error); + if (rel_norm > dmax1) { + imax[jnum] = i; + dmax1 = rel_norm; + } + } + } + if (imax[jnum] >= 0) { + i = imax[jnum]; + error = solnDelta0[i] / m_ewt[i]; + dmax0 = sqrt(error * error); + error = solnDelta1[i] / m_ewt[i]; + dmax1 = sqrt(error * error); + printf("\t\t %4d %12.4e %12.4e %12.4e %12.4e " + "%12.4e %12.4e %12.4e\n", + i, y0[i], solnDelta0[i], y1[i], + solnDelta1[i], m_ewt[i], dmax0, dmax1); + } + } + printf("\t\t "); print_line("-", 90); + mdp_safe_free((void **) &imax); + } + + + +} + diff --git a/Cantera/src/numerics/BEulerInt.h b/Cantera/src/numerics/BEulerInt.h new file mode 100644 index 000000000..6103c29b6 --- /dev/null +++ b/Cantera/src/numerics/BEulerInt.h @@ -0,0 +1,465 @@ +/** + * @file BEulerInt.h + */ + +/* $Author: hkmoffa $ + * $Date: 2009/01/27 16:50:53 $ + * $Revision: 1.19 $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ +#ifndef CT_BEULERINT_H +#define CT_BEULERINT_H + +#include "ct_defs.h" +#include "ctlapack.h" +#include "utilities.h" +#include "ctexceptions.h" + + +#include "Integrator.h" +#include "ResidJacEval.h" + +#include "SquareMatrix.h" +#include "NonlinearSolver.h" + +#include "mdp_allo.h" +#ifndef MAX +# define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) +#endif +#ifndef MIN +# define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) +#endif +#define OPT_SIZE 10 + +#define SUCCESS 0 +#define FAILURE 1 + +#define STEADY 0 +#define TRANSIENT 1 + +namespace Cantera { + + enum BEulerMethodType { + BEulerFixedStep, + BEulerVarStep + }; + + /** + * Exception class thrown when a BEuler error is encountered. + */ + class BEulerErr : public CanteraError { + public: + BEulerErr(std::string msg); + }; + + +#define BEULER_JAC_ANAL 2 +#define BEULER_JAC_NUM 1 + + /** + * Wrapper class for 'beuler' integrator + * We derive the class from the class Integrator + */ + class BEulerInt : public Integrator { + + public: + /** + * The default constructor doesn't take an argument. + */ + BEulerInt(); + virtual ~BEulerInt(); + virtual void setTolerances(double reltol, int n, double* abstol); + virtual void setTolerances(double reltol, double abstol); + virtual void setProblemType(int probtype); + virtual void initializeRJE(double t0, ResidJacEval& func); + virtual void reinitializeRJE(double t0, ResidJacEval& func); + virtual double integrateRJE(double tout, double tinit = 0.0); + virtual doublereal step(double tout); + virtual void setSolnWeights(); + virtual double& solution(int k){ return m_y_n[k]; } + double* solution(){ return m_y_n; } + int nEquations() const { return m_neq;} + virtual int nEvals() const; + virtual void setMethodBEMT(BEulerMethodType t); + virtual void setIterator(IterType t); + virtual void setMaxStep(double hmax); + virtual void setMaxNumTimeSteps(int); + virtual void setNumInitialConstantDeltaTSteps(int); + + void print_solnDelta_norm_contrib(const double * const soln0, + const char * const s0, + const double * const soln1, + const char * const s1, + const char * const title, + const double * const y0, + const double * const y1, + double damp, + int num_entries); + + virtual void setPrintSolnOptions(int printSolnStepInterval, + int printSolnNumberToTout, + int printSolnFirstSteps = 0, + bool dumpJacobians = false); + void setNonLinOptions(int min_newt_its = 0, + bool matrixConditioning = false, + bool colScaling = false, + bool rowScaling = true); + virtual void setPrintFlag(int print_flag); + virtual void setColumnScales(); + /** + * calculate the solution error norm + */ + virtual double soln_error_norm(const double * const, + bool printLargest = false); + virtual void setInitialTimeStep(double delta_t); + + void beuler_jac(SquareMatrix &, double * const, + double, double, double * const, double * const, int); + + + protected: + + //! Internal routine that sets up the fixed length storage based on + //! the size of the problem to solve. + void internalMalloc(); + /** + * Internal function to calculate the predicted solution + * at a time step. + */ + void calc_y_pred(int); + /** + * Internal function to calculate the time derivative at the + * new step + */ + void calc_ydot(int, double *, double *); + /** + * Internal function to calculate the time step truncation + * error for a predictor corrector time step + */ + double time_error_norm(); + /** + * Internal function to calculate the time step for the + * next step based on the time-truncation error on the + * current time step + */ + double time_step_control(int m_order, double time_error_factor); + + //! Solve a nonlinear system + /*! + * + * Find the solution to F(X, xprime) = 0 by damped Newton iteration. On + * entry, y_comm[] contains an initial estimate of the solution and + * ydot_comm[] contains an estimate of the derivative. + * On successful return, y_comm[] contains the converged solution + * and ydot_comm[] contains the derivative + * + * + * @param y_comm[] Contains the input solution. On output y_comm[] contains + * the converged solution + * @param ydot_comm Contains the input derivative solution. On output y_comm[] contains + * the converged derivative solution + * + * + */ + int solve_nonlinear_problem(double * const y_comm, + double * const ydot_comm, double CJ, + double time_curr, + SquareMatrix& jac, + int &num_newt_its, + int &num_linear_solves, + int &num_backtracks, + int loglevelInput); + + /** + * Compute the undamped Newton step. The residual function is + * evaluated at x, but the Jacobian is not recomputed. + */ + void doNewtonSolve(double, double *, double*, double *, + SquareMatrix&, int); + + + //! Bound the Newton step while relaxing the solution + /*! + * Return the factor by which the undamped Newton step 'step0' + * must be multiplied in order to keep all solution components in + * all domains between their specified lower and upper bounds. + * Other bounds may be applied here as well. + * + * Currently the bounds are hard coded into this routine: + * + * Minimum value for all variables: - 0.01 * m_ewt[i] + * Maximum value = none. + * + * Thus, this means that all solution components are expected + * to be numerical greater than zero in the limit of time step + * truncation errors going to zero. + * + * Delta bounds: The idea behind these is that the Jacobian + * couldn't possibly be representative if the + * variable is changed by a lot. (true for + * nonlinear systems, false for linear systems) + * Maximum increase in variable in any one newton iteration: + * factor of 2 + * Maximum decrease in variable in any one newton iteration: + * factor of 5 + * + * @param y Current value of the solution + * @param step0 Current raw step change in y[] + * @param loglevel Log level. This routine produces output if loglevel + * is greater than one + * + * @return Returns the damping coefficient + */ + double boundStep(const double * const y, const double * const step0, int loglevel); + + /* + * Damp step + */ + int dampStep(double, const double*, const double*, + const double *, double*, double*, + double*, double&, SquareMatrix&, int&, bool, int&); + + /* + * Compute Residual Weights + */ + void computeResidWts(SquareMatrix &jac); + + /* + * Filter a new step + */ + double filterNewStep(double, double *, double *); + + /* + * get the next time to print out + */ + double getPrintTime(double time_current); + + /********************** Member data ***************************/ + /********************* + * METHOD FLAGS + *********************/ + + //! IterType is used to specify how the nonlinear equations are + //! to be relaxed at each time step. + IterType m_iter; + /** + * MethodType is used to specify how the time step is to be + * chosen. Currently, there are two choices, one is a fixed + * step method while the other is based on a predictor-corrector + * algorithm and a time-step truncation error tolerance. + */ + BEulerMethodType m_method; + /** + * m_jacFormMethod determines how a matrix is formed. + */ + int m_jacFormMethod; + /** + * m_rowScaling is a boolean. If true then row sum scaling + * of the Jacobian matrix is carried out when solving the + * linear systems. + */ + bool m_rowScaling; + /** + * m_colScaling is a boolean. If true, then column scaling + * is performed on each solution of the linear system. + */ + bool m_colScaling; + /** + * m_matrixConditioning is a boolean. If true, then the + * Jacobian and every rhs is multiplied by the inverse + * of a matrix that is suppose to reduce the condition + * number of the matrix. This is done before row scaling. + */ + bool m_matrixConditioning; + /** + * If m_itol =1 then each component has an individual + * value of atol. If m_itol = 0, the all atols are equal. + */ + int m_itol; + /** + * Relative time truncation error tolerances + */ + double m_reltol; + /** + * Absolute time truncation error tolerances, when uniform + * for all variables. + */ + double m_abstols; + /** + * Vector of absolute time truncation error tolerance + * when not uniform for all variables. + */ + double *m_abstol; + /** + * Error Weights. This is a surprisingly important quantity. + */ + double *m_ewt; + + //! Maximum step size + double m_hmax; + /** + * Maximum integration order + */ + int m_maxord; + /** + * Current integration order + */ + int m_order; + /** + * Time step number + */ + int m_time_step_num; + int m_time_step_attempts; + /** + * Max time steps allowed + */ + int m_max_time_step_attempts; + /** + * Number of initial time steps to take where the + * time truncation error tolerances are not checked. Instead + * the delta T is uniform + */ + int m_numInitialConstantDeltaTSteps; + /** + * Failure Counter -> keeps track of the number + * of consequetive failures + */ + int m_failure_counter; + /** + * Minimum Number of Newton Iterations per nonlinear step + * default = 0 + */ + int m_min_newt_its; + /************************ + * PRINTING OPTIONS + ************************/ + /** + * Step Interval at which to print out the solution + * default = 1; + * If set to zero, there is no printout + */ + int m_printSolnStepInterval; + /** + * Number of evenly spaced printouts of the solution + * If zero, there is no printout from this option + * default 1 + * If set to zero there is no printout. + */ + int m_printSolnNumberToTout; + + /** + * Number of initial steps that the solution is + * printed out. + * default = 0 + */ + int m_printSolnFirstSteps; + + /** + * Dump Jacobians to disk + * default false + */ + bool m_dumpJacobians; + + /********************* + * INTERNAL SOLUTION VALUES + *********************/ + /** + * Number of equations in the ode integrator + */ + int m_neq; + double *m_y_n; + double *m_y_nm1; + double *m_y_pred_n; + double *m_ydot_n; + double *m_ydot_nm1; + /************************ + * TIME VARIABLES + ************************/ + /** + * Initial time at the start of the integration + */ + double m_t0; + /** + * Final time + */ + double m_time_final; + /** + * + */ + double time_n; + double time_nm1; + double time_nm2; + double delta_t_n; + double delta_t_nm1; + double delta_t_nm2; + double delta_t_np1; + /** + * Maximum permissible time step + */ + double delta_t_max; + + + double *m_resid; + double *m_residWts; + double *m_wksp; + ResidJacEval *m_func; + double *m_rowScales; + double *m_colScales; + + /** + * Pointer to the jacobian representing the + * time dependent problem + */ + SquareMatrix *tdjac_ptr; + /** + * Determines the level of printing for each time + * step. + * 0 -> absolutely nothing is printed for + * a single time step. + * 1 -> One line summary per time step + * 2 -> short description, points of interest + * 3 -> Lots printed per time step (default) + */ + int m_print_flag; + /*************************************************************************** + * COUNTERS OF VARIOUS KINDS + ***************************************************************************/ + /** + * Number of function evaluations + */ + int m_nfe; + /** + * Number of Jacobian Evaluations and + * factorization steps (they are the same) + */ + int m_nJacEval; + /** + * Number of total newton iterations + */ + int m_numTotalNewtIts; + /** + * Total number of linear iterations + */ + int m_numTotalLinearSolves; + /** + * Total number of convergence failures. + */ + int m_numTotalConvFails; + /** + * Total Number of time truncation error failures + */ + int m_numTotalTruncFails; + /* + * + */ + int num_failures; + }; + +} // namespace + +#endif // CT_BEULER diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index 97decc3ae..bebd03f7e 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -35,14 +35,14 @@ CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ ODE_integrators.o BandMatrix.o DAE_solvers.o \ funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o \ - solveProb.o + solveProb.o BEulerInt.o NUMERICS_H = ArrayViewer.h DenseMatrix.h \ funcs.h ctlapack.h Func1.h FuncEval.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ - solveProb.h + solveProb.h BEulerInt.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index 06da5043b..1c24843e7 100755 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -110,6 +110,33 @@ namespace Cantera { //! Return the number of equations in the equation system virtual int nEquations() const = 0; + + //! Write out to a file or to standard output the current solution + /*! + * ievent is a description of the event that caused this + * function to be called. + */ + virtual void writeSolution(int ievent, const double time, + const double deltaT, + const int time_step_num, + const double *y, const double *ydot) { + int k; + printf("ResidEval::writeSolution\n"); + printf(" Time = %g, ievent = %d, deltaT = %g\n", time, ievent, deltaT); + if (ydot) { + printf(" k y[] ydot[]\n"); + for (k = 0; k < nEquations(); k++) { + printf("%d %g %g\n", k, y[k], ydot[k]); + } + } else { + printf(" k y[]\n"); + for (k = 0; k < nEquations(); k++) { + printf("%d %g \n", k, y[k]); + } + } + } + + protected: From 9b5560f4253a2938de28d0acdd6bfed07cbb8ca9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 23 May 2010 15:25:02 +0000 Subject: [PATCH 154/446] Incremental commit, cleaning up object --- Cantera/src/numerics/BEulerInt.cpp | 53 ++++++++++++++++++------------ Cantera/src/numerics/BEulerInt.h | 11 +++++-- 2 files changed, 40 insertions(+), 24 deletions(-) diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp index e1a202060..a96204681 100644 --- a/Cantera/src/numerics/BEulerInt.cpp +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -2121,38 +2121,48 @@ namespace Cantera { return -2; } } - - /************************************************************************** + //================================================================================================ + // Solve a nonlinear system + /* + * Find the solution to F(X, xprime) = 0 by damped Newton iteration. On + * entry, y_comm[] contains an initial estimate of the solution and + * ydot_comm[] contains an estimate of the derivative. + * On successful return, y_comm[] contains the converged solution + * and ydot_comm[] contains the derivative * - * solve_nonlinear_problem(): * - * Find the solution to F(X) = 0 by damped Newton iteration. On - * entry, x0 contains an initial estimate of the solution. On - * successful return, x1 contains the converged solution. - * - - * + * @param y_comm[] Contains the input solution. On output y_comm[] contains + * the converged solution + * @param ydot_comm Contains the input derivative solution. On output y_comm[] contains + * the converged derivative solution + * @param CJ Inverse of the time step + * @param time_curr Current value of the time + * @param jac Jacobian + * @param num_newt_its number of newton iterations + * @param num_linear_solves number of linear solves + * @param num_backtracks number of backtracs + * @param loglevel Log level */ - int BEulerInt::solve_nonlinear_problem(double* const y_comm, - double* const ydot_comm, double CJ, + int BEulerInt::solve_nonlinear_problem(double * const y_comm, + double * const ydot_comm, double CJ, double time_curr, SquareMatrix& jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, - int loglevelInput) + int loglevel) { bool m_residCurrent = false; int m = 0; bool forceNewJac = false; double s1=1.e30; - double* y_curr = mdp_alloc_dbl_1(m_neq, 0.0); - double* ydot_curr = mdp_alloc_dbl_1(m_neq, 0.0); - double* stp = mdp_alloc_dbl_1(m_neq, 0.0); - double* stp1 = mdp_alloc_dbl_1(m_neq, 0.0); - double * y_new = mdp_alloc_dbl_1(m_neq, 0.0); - double * ydot_new = mdp_alloc_dbl_1(m_neq, 0.0); + double * y_curr = mdp_alloc_dbl_1(m_neq, 0.0); + double * ydot_curr = mdp_alloc_dbl_1(m_neq, 0.0); + double * stp = mdp_alloc_dbl_1(m_neq, 0.0); + double * stp1 = mdp_alloc_dbl_1(m_neq, 0.0); + double * y_new = mdp_alloc_dbl_1(m_neq, 0.0); + double * ydot_new = mdp_alloc_dbl_1(m_neq, 0.0); mdp_copy_dbl_1(y_curr, y_comm, m_neq); mdp_copy_dbl_1(ydot_curr, ydot_comm, m_neq); @@ -2162,8 +2172,7 @@ namespace Cantera { num_linear_solves = - m_numTotalLinearSolves; num_backtracks = 0; int i_backtracks; - int loglevel = loglevelInput; - + while (1 > 0) { /* @@ -2275,10 +2284,12 @@ namespace Cantera { } done: + // Copy into the return vectors mdp_copy_dbl_1(y_comm, y_curr, m_neq); mdp_copy_dbl_1(ydot_comm, ydot_curr, m_neq); - + // Increment counters num_linear_solves += m_numTotalLinearSolves; + // Free memory mdp_safe_free((void **) &y_curr); mdp_safe_free((void **) &ydot_curr); mdp_safe_free((void **) &stp); diff --git a/Cantera/src/numerics/BEulerInt.h b/Cantera/src/numerics/BEulerInt.h index 6103c29b6..7c8e24782 100644 --- a/Cantera/src/numerics/BEulerInt.h +++ b/Cantera/src/numerics/BEulerInt.h @@ -163,8 +163,13 @@ namespace Cantera { * the converged solution * @param ydot_comm Contains the input derivative solution. On output y_comm[] contains * the converged derivative solution - * - * + * @param CJ Inverse of the time step + * @param time_curr Current value of the time + * @param jac Jacobian + * @param num_newt_its number of newton iterations + * @param num_linear_solves number of linear solves + * @param num_backtracks number of backtracs + * @param loglevel Log level */ int solve_nonlinear_problem(double * const y_comm, double * const ydot_comm, double CJ, @@ -173,7 +178,7 @@ namespace Cantera { int &num_newt_its, int &num_linear_solves, int &num_backtracks, - int loglevelInput); + int loglevel); /** * Compute the undamped Newton step. The residual function is From fae826750f4cdb6ea6c529f665912d9077a94cc5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 25 May 2010 02:56:38 +0000 Subject: [PATCH 155/446] Fixed a memory overwrite error in solveProb --- Cantera/src/numerics/BEulerInt.cpp | 2584 ++++++++++++++-------------- Cantera/src/numerics/BEulerInt.h | 7 +- Cantera/src/numerics/solveProb.cpp | 9 +- 3 files changed, 1282 insertions(+), 1318 deletions(-) diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp index a96204681..75d503de6 100644 --- a/Cantera/src/numerics/BEulerInt.cpp +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -21,9 +21,582 @@ using namespace mdp; #define SAFE_DELETE(a) if (a) { delete (a); a = 0; } + +/* + * Blas routines + */ +extern "C" { + extern void dcopy_(int *, double *, int *, double *, int *); +} namespace Cantera { - /************************************************************************* + + //================================================================================================ + /* + * Exception thrown when a BEuler error is encountered. We just call the + * Cantera Error handler in the initialization list + */ + BEulerErr::BEulerErr(std::string msg) : + CanteraError("BEulerInt", msg) + { + } + + //================================================================================================ + /* + * Constructor. Default settings: dense jacobian, no user-supplied + * Jacobian function, Newton iteration. + */ + BEulerInt::BEulerInt() : + m_iter(Newton_Iter), + m_method(BEulerVarStep), + m_jacFormMethod(BEULER_JAC_NUM), + m_rowScaling(true), + m_colScaling(false), + m_matrixConditioning(false), + m_itol(0), + m_reltol(1.e-4), + m_abstols(1.e-10), + m_abstol(0), + m_ewt(0), + m_hmax(0.0), + m_maxord(0), + m_time_step_num(0), + m_time_step_attempts(0), + m_max_time_step_attempts(11000000), + m_numInitialConstantDeltaTSteps(0), + m_failure_counter(0), + m_min_newt_its(0), + m_printSolnStepInterval(1), + m_printSolnNumberToTout(1), + m_printSolnFirstSteps(0), + m_dumpJacobians(false), + m_neq(0), + m_y_n(0), + m_y_nm1(0), + m_y_pred_n(0), + m_ydot_n(0), + m_ydot_nm1(0), + m_t0(0.0), + m_time_final(0.0), + time_n(0.0), + time_nm1(0.0), + time_nm2(0.0), + delta_t_n(0.0), + delta_t_nm1(0.0), + delta_t_nm2(0.0), + delta_t_np1(1.0E-8), + delta_t_max(1.0E300), + m_resid(0), + m_residWts(0), + m_wksp(0), + m_func(0), + m_rowScales(0), + m_colScales(0), + tdjac_ptr(0), + m_print_flag(3), + m_nfe(0), + m_nJacEval(0), + m_numTotalNewtIts(0), + m_numTotalLinearSolves(0), + m_numTotalConvFails(0), + m_numTotalTruncFails(0), + num_failures(0) + { + + } + //================================================================================================ + /* + * Destructor + */ + BEulerInt::~BEulerInt() + { + mdp::mdp_safe_free((void **) &m_y_n); + mdp::mdp_safe_free((void **) &m_y_nm1); + mdp::mdp_safe_free((void **) &m_y_pred_n); + mdp::mdp_safe_free((void **) &m_ydot_n); + mdp::mdp_safe_free((void **) &m_ydot_nm1); + mdp::mdp_safe_free((void **) &m_resid); + mdp::mdp_safe_free((void **) &m_residWts); + mdp::mdp_safe_free((void **) &m_wksp); + mdp::mdp_safe_free((void **) &m_ewt); + mdp::mdp_safe_free((void **) &m_abstol); + mdp::mdp_safe_free((void **) &m_rowScales); + mdp::mdp_safe_free((void **) &m_colScales); + SAFE_DELETE(tdjac_ptr); + } + //================================================================================================ + void BEulerInt::setTolerances(double reltol, int n, double* abstol) { + m_itol = 1; + if (!m_abstol) { + m_abstol = mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); + } + if (n != m_neq) { + printf("ERROR n is wrong\n"); + exit(-1); + } + for (int i = 0; i < m_neq; i++) { + m_abstol[i] = abstol[i]; + } + m_reltol = reltol; + } + //================================================================================================ + void BEulerInt::setTolerances(double reltol, double abstol) { + m_itol = 0; + m_reltol = reltol; + m_abstols = abstol; + } + //================================================================================================ + void BEulerInt::setProblemType(int jacFormMethod) { + m_jacFormMethod = jacFormMethod; + } + //================================================================================================ + void BEulerInt::setMethodBEMT(BEulerMethodType t) { + m_method = t; + } + //================================================================================================ + void BEulerInt::setMaxStep(doublereal hmax) { + m_hmax = hmax; + } + //================================================================================================ + void BEulerInt::setMaxNumTimeSteps(int maxNumTimeSteps) { + m_max_time_step_attempts = maxNumTimeSteps; + } + //================================================================================================ + void BEulerInt::setNumInitialConstantDeltaTSteps(int num) { + m_numInitialConstantDeltaTSteps = num; + } + //================================================================================================ + /* * + * setPrintSolnOptins(): + * + * This routine controls when the solution is printed + * + * @param printStepInterval If greater than 0, then the + * soln is printed every printStepInterval + * steps. + * + * @param printNumberToTout The solution is printed at + * regular invervals a total of + * "printNumberToTout" times. + * + * @param printSolnFirstSteps The solution is printed out + * the first "printSolnFirstSteps" + * steps. After these steps the other + * parameters determine the printing. + * default = 0 + * + * @param dumpJacobians Dump jacobians to disk. + * + * default = false + * + */ + void BEulerInt::setPrintSolnOptions(int printSolnStepInterval, + int printSolnNumberToTout, + int printSolnFirstSteps, + bool dumpJacobians) + { + m_printSolnStepInterval = printSolnStepInterval; + m_printSolnNumberToTout = printSolnNumberToTout; + m_printSolnFirstSteps = printSolnFirstSteps; + m_dumpJacobians = dumpJacobians; + } + //================================================================================================ + void BEulerInt::setIterator(IterType t) { + m_iter = t; + } + //================================================================================================ + /* + * + * setNonLinOptions() + * + * Set the options for the nonlinear method + * + * Defaults are set in the .h file. These are the defaults: + * min_newt_its = 0 + * matrixConditioning = false + * colScaling = false + * rowScaling = true + */ + void BEulerInt::setNonLinOptions(int min_newt_its, bool matrixConditioning, + bool colScaling, bool rowScaling) + { + m_min_newt_its = min_newt_its; + m_matrixConditioning = matrixConditioning; + m_colScaling = colScaling; + m_rowScaling = rowScaling; + if (m_colScaling) { + if (!m_colScales) { + m_colScales = mdp_alloc_dbl_1(m_neq, 1.0); + } + } + if (m_rowScaling) { + if (!m_rowScales) { + m_rowScales = mdp_alloc_dbl_1(m_neq, 1.0); + } + } + } + //================================================================================================ + /* + * + * setInitialTimeStep(): + * + * Set the initial time step. Right now, we set the + * time step by setting delta_t_np1. + */ + void BEulerInt::setInitialTimeStep(double deltaT) + { + delta_t_np1 = deltaT; + } + //================================================================================================ + /* + * setPrintFlag(): + * + */ + void BEulerInt::setPrintFlag(int print_flag) + { + m_print_flag = print_flag; + } + //================================================================================================ + /* + * + * initialize(): + * + * Find the initial conditions for y and ydot. + */ + void BEulerInt::initializeRJE(double t0, ResidJacEval &func) + { + m_neq = func.nEquations(); + m_t0 = t0; + internalMalloc(); + + /* + * Get the initial conditions. + */ + func.getInitialConditionsDot(m_t0, m_neq, m_y_n, m_ydot_n); + + // Store a pointer to the residual routine in the object + m_func = &func; + + /* + * Initialize the various time counters in the object + */ + time_n = t0; + time_nm1 = time_n; + time_nm2 = time_nm1; + delta_t_n = 0.0; + delta_t_nm1 = 0.0; + } + //================================================================================================ + /* + * + * reinitialize(): + * + */ + void BEulerInt::reinitializeRJE(double t0, ResidJacEval& func) + { + m_neq = func.nEquations(); + m_t0 = t0; + internalMalloc(); + /* + * At the initial time, get the initial conditions and time and store + * them into internal storage in the object, my[]. + */ + m_t0 = t0; + func.getInitialConditions(m_t0, m_y_n, m_ydot_n); + /** + * Set up the internal weights that are used for testing convergence + */ + setSolnWeights(); + + // Store a pointer to the function + m_func = &func; + + } + //================================================================================================ + /* + * + * getPrintTime(): + * + */ + double BEulerInt::getPrintTime(double time_current) + { + double tnext; + if (m_printSolnNumberToTout > 0) { + double dt = (m_time_final - m_t0) / m_printSolnNumberToTout; + for (int i = 0; i <= m_printSolnNumberToTout; i++) { + tnext = m_t0 + dt * i; + if (tnext >= time_current) return tnext; + } + } + return 1.0E300; + } + //================================================================================================ + /* + * nEvals(): + * + * Return the total number of function evaluations + */ + int BEulerInt::nEvals() const + { + return m_nfe; + } + //================================================================================================ + /* + * + * internalMalloc(): + * + * Internal routine that sets up the fixed length storage based on + * the size of the problem to solve. + */ + void BEulerInt::internalMalloc() + { + mdp_realloc_dbl_1(&m_ewt, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_nm1, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_y_pred_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_ydot_n, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_ydot_nm1, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_resid, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_residWts, m_neq, 0, 0.0); + mdp_realloc_dbl_1(&m_wksp, m_neq, 0, 0.0); + if (m_rowScaling) { + mdp_realloc_dbl_1(&m_rowScales, m_neq, 0, 1.0); + } + if (m_colScaling) { + mdp_realloc_dbl_1(&m_colScales, m_neq, 0, 1.0); + } + tdjac_ptr = new SquareMatrix(m_neq); + } + //================================================================================================ + /* + * setSolnWeights(): + * + * Set the solution weights + * This is a very important routine as it affects quite a few + * operations involving convergence. + * + */ + void BEulerInt::setSolnWeights() + { + int i; + if (m_itol == 1) { + /* + * Adjust the atol vector if we are using vector + * atol conditions. + */ + // m_func->adjustAtol(m_abstol); + + for (i = 0; i < m_neq; i++) { + m_ewt[i] = m_abstol[i] + m_reltol * 0.5 * + (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + } + } else { + for (i = 0; i < m_neq; i++) { + m_ewt[i] = m_abstols + m_reltol * 0.5 * + (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + } + } + } + //================================================================================================ + /* + * + * setColumnScales(): + * + * Set the column scaling vector at the current time + */ + void BEulerInt::setColumnScales() + { + m_func->calcSolnScales(time_n, m_y_n, m_y_nm1, m_colScales); + } + //================================================================================================ + /* + * computeResidWts(): + * + * We compute residual weights here, which we define as the L_0 norm + * of the Jacobian Matrix, weighted by the solution weights. + * This is the proper way to guage the magnitude of residuals. However, + * it does need the evaluation of the jacobian, and the implementation + * below is slow, but doesn't take up much memory. + * + * Here a small weighting indicates that the change in solution is + * very sensitive to that equation. + */ + void BEulerInt::computeResidWts(SquareMatrix &jac) + { + int i, j; + double *data = &(*(jac.begin())); + double value; + for (i = 0; i < m_neq; i++) { + m_residWts[i] = fabs(data[i] * m_ewt[0]); + for (j = 1; j < m_neq; j++) { + value = fabs(data[j*m_neq + i] * m_ewt[j]); + m_residWts[i] = MAX(m_residWts[i], value); + } + } + } + //================================================================================================ + /* + * filterNewStep(): + * + * void BEulerInt:: + * + */ + double BEulerInt::filterNewStep(double timeCurrent, double *y_current, double *ydot_current) { + return 0.0; + } + //================================================================================================== + static void print_line(const char *str, int n) + { + for (int i = 0; i < n; i++) { + printf("%s", str); + } + printf("\n"); + } + //================================================================================================== + /* + * Print out for relevant time step information + */ + static void print_time_step1(int order, int n_time_step, double time, + double delta_t_n, double delta_t_nm1, + bool step_failed, int num_failures) + { + const char *string = 0; + if (order == 0) string = "Backward Euler"; + else if (order == 1) string = "Forward/Backward Euler"; + else if (order == 2) string = "Adams-Bashforth/TR"; + printf("\n"); print_line("=", 80); + printf("\nStart of Time Step: %5d Time_n = %9.5g Time_nm1 = %9.5g\n", + n_time_step, time, time - delta_t_n); + printf("\tIntegration method = %s\n", string); + if (step_failed) + printf("\tPreviously attempted step was a failure\n"); + if (delta_t_n > delta_t_nm1) + string = "(Increased from previous iteration)"; + else if (delta_t_n < delta_t_nm1) + string = "(Decreased from previous iteration)"; + else { + string = "(same as previous iteration)"; + } + printf("\tdelta_t_n = %8.5e %s", delta_t_n, string); + if (num_failures > 0) + printf("\t(Bad_History Failure Counter = %d)", num_failures); + printf("\n\tdelta_t_nm1 = %8.5e\n", delta_t_nm1); + } + //================================================================================================ + /* + * Print out for relevant time step information + */ + static void print_time_step2(int time_step_num, int order, + double time, double time_error_factor, + double delta_t_n, double delta_t_np1) + { + printf("\tTime Step Number %5d was a success: time = %10g\n", time_step_num, + time); + printf("\t\tEstimated Error\n"); + printf("\t\t-------------------- = %8.5e\n", time_error_factor); + printf("\t\tTolerated Error\n\n"); + printf("\t- Recommended next delta_t (not counting history) = %g\n", + delta_t_np1); + printf("\n"); print_line("=", 80); printf("\n"); + } + //================================================================================================ + /* + * Print Out descriptive information on why the current step failed + */ + static void print_time_fail(bool convFailure, int time_step_num, + double time, double delta_t_n, + double delta_t_np1, double time_error_factor) + { + printf("\n"); print_line("=", 80); + if (convFailure) { + printf("\tTime Step Number %5d experienced a convergence " + "failure\n", time_step_num); + printf("\tin the non-linear or linear solver\n"); + printf("\t\tValue of time at failed step = %g\n", time); + printf("\t\tdelta_t of the failed step = %g\n", + delta_t_n); + printf("\t\tSuggested value of delta_t to try next = %g\n", + delta_t_np1); + } else { + printf("\tTime Step Number %5d experienced a truncation error " + "failure!\n", time_step_num); + printf("\t\tValue of time at failed step = %g\n", time); + printf("\t\tdelta_t of the failed step = %g\n", + delta_t_n); + printf("\t\tSuggested value of delta_t to try next = %g\n", + delta_t_np1); + printf("\t\tCalculated truncation error factor = %g\n", + time_error_factor); + } + printf("\n"); print_line("=", 80); + } + //================================================================================================ + /* + * Print out the final results and counters + */ + static void print_final(double time, int step_failed, + int time_step_num, int num_newt_its, + int total_linear_solves, int numConvFails, + int numTruncFails, int nfe, int nJacEval) + { + printf("\n"); print_line("=", 80); + printf("TIME INTEGRATION ROUTINE HAS FINISHED: "); + if (step_failed) + printf(" IT WAS A FAILURE\n"); + else + printf(" IT WAS A SUCCESS\n"); + printf("\tEnding time = %g\n", time); + printf("\tNumber of time steps = %d\n", time_step_num); + printf("\tNumber of newt its = %d\n", num_newt_its); + printf("\tNumber of linear solves = %d\n", total_linear_solves); + printf("\tNumber of convergence failures= %d\n", numConvFails); + printf("\tNumber of TimeTruncErr fails = %d\n", numTruncFails); + printf("\tNumber of Function evals = %d\n", nfe); + printf("\tNumber of Jacobian evals/solvs= %d\n", nJacEval); + printf("\n"); print_line("=", 80); + } + //================================================================================================ + /* + * Header info for one line comment about a time step + */ + static void print_lvl1_Header(int nTimes) { + printf("\n"); + if (nTimes) { + print_line("-", 80); + } + printf("time Time Time Time "); + if (nTimes == 0) { + printf(" START"); + } else { + printf(" (continued)"); + } + printf("\n"); + + printf("step (sec) step Newt Aztc bktr trunc "); + printf("\n"); + + printf(" No. Rslt size Its Its stps error |"); + printf(" comment"); + printf("\n"); + print_line("-", 80); + } + //================================================================================================ + /* + * One line entry about time step + * rslt -> 4 letter code + */ + static void print_lvl1_summary( + int time_step_num, double time, const char *rslt, double delta_t_n, + int newt_its, int aztec_its, int bktr_stps, double time_error_factor, + const char *comment) { + printf("%6d %11.6g %4s %10.4g %4d %4d %4d %11.4g", + time_step_num, time, rslt, delta_t_n, newt_its, aztec_its, + bktr_stps, time_error_factor); + if (comment) printf(" | %s", comment); + printf("\n"); + } + //================================================================================================ + /* * subtractRD(): * This routine subtracts 2 numbers. If the difference is less * than 1.0E-14 times the magnitude of the smallest number, @@ -52,9 +625,8 @@ namespace Cantera { } return diff; } - - /************************************************************************** - * + //================================================================================================ + /* * * Function called by BEuler to evaluate the Jacobian matrix and the * current residual at the current time step. @@ -110,7 +682,7 @@ namespace Cantera { * deltaY's that are appropriate for calculating the numerical * derivative. */ - double *dyVector = mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); + double *dyVector = mdp::mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); m_func->calcDeltaSolnVariables(time_curr, y, m_y_nm1, dyVector, m_ewt); #ifdef DEBUG_HKM @@ -176,670 +748,69 @@ namespace Cantera { /* * Release memory */ - mdp_safe_free((void **) &dyVector); + mdp::mdp_safe_free((void **) &dyVector); } } - /************************************************************************** - * - * Exception thrown when a BEuler error is encountered. We just call the - * Cantera Error handler in the initialization list - */ - BEulerErr::BEulerErr(string msg) : - CanteraError("BEulerInt", msg) - { - } - - /** - * Constructor. Default settings: dense jacobian, no user-supplied - * Jacobian function, Newton iteration. - */ - BEulerInt::BEulerInt() : - m_iter(Newton_Iter), - m_method(BEulerVarStep), - m_jacFormMethod(BEULER_JAC_NUM), - m_rowScaling(true), - m_colScaling(false), - m_matrixConditioning(false), - m_itol(0), - m_reltol(1.e-4), - m_abstols(1.e-10), - m_abstol(0), - m_ewt(0), - m_hmax(0.0), - m_maxord(0), - m_time_step_num(0), - m_time_step_attempts(0), - m_max_time_step_attempts(11000000), - m_numInitialConstantDeltaTSteps(0), - m_failure_counter(0), - m_min_newt_its(0), - m_printSolnStepInterval(1), - m_printSolnNumberToTout(1), - m_printSolnFirstSteps(0), - m_dumpJacobians(false), - m_neq(0), - m_y_n(0), - m_y_nm1(0), - m_y_pred_n(0), - m_ydot_n(0), - m_ydot_nm1(0), - m_t0(0.0), - m_time_final(0.0), - time_n(0.0), - time_nm1(0.0), - time_nm2(0.0), - delta_t_n(0.0), - delta_t_nm1(0.0), - delta_t_nm2(0.0), - delta_t_np1(1.0E-8), - delta_t_max(1.0E300), - m_resid(0), - m_residWts(0), - m_wksp(0), - m_func(0), - m_rowScales(0), - m_colScales(0), - tdjac_ptr(0), - m_print_flag(3), - m_nfe(0), - m_nJacEval(0), - m_numTotalNewtIts(0), - m_numTotalLinearSolves(0), - m_numTotalConvFails(0), - m_numTotalTruncFails(0), - num_failures(0) - { - - } - - - /** - * Destructor - */ - BEulerInt::~BEulerInt() - { - mdp_safe_free((void **) &m_y_n); - mdp_safe_free((void **) &m_y_nm1); - mdp_safe_free((void **) &m_y_pred_n); - mdp_safe_free((void **) &m_ydot_n); - mdp_safe_free((void **) &m_ydot_nm1); - mdp_safe_free((void **) &m_resid); - mdp_safe_free((void **) &m_residWts); - mdp_safe_free((void **) &m_wksp); - mdp_safe_free((void **) &m_ewt); - mdp_safe_free((void **) &m_abstol); - mdp_safe_free((void **) &m_rowScales); - mdp_safe_free((void **) &m_colScales); - SAFE_DELETE(tdjac_ptr); - - } - - void BEulerInt::setTolerances(double reltol, int n, double* abstol) { - m_itol = 1; - if (!m_abstol) { - m_abstol = mdp_alloc_dbl_1(m_neq, MDP_DBL_NOINIT); - } - if (n != m_neq) { - printf("ERROR n is wrong\n"); - exit(-1); - } - for (int i = 0; i < m_neq; i++) { - m_abstol[i] = abstol[i]; - } - m_reltol = reltol; - } - - void BEulerInt::setTolerances(double reltol, double abstol) { - m_itol = 0; - m_reltol = reltol; - m_abstols = abstol; - } - - void BEulerInt::setProblemType(int jacFormMethod) { - m_jacFormMethod = jacFormMethod; - } - - void BEulerInt::setMethodBEMT(BEulerMethodType t) { - m_method = t; - } - - void BEulerInt::setMaxStep(doublereal hmax) { - m_hmax = hmax; - } - - void BEulerInt::setMaxNumTimeSteps(int maxNumTimeSteps) { - m_max_time_step_attempts = maxNumTimeSteps; - } - - void BEulerInt::setNumInitialConstantDeltaTSteps(int num) { - m_numInitialConstantDeltaTSteps = num; - } - - /************************************************************************** - * - * setPrintSolnOptins(): - * - * This routine controls when the solution is printed - * - * @param printStepInterval If greater than 0, then the - * soln is printed every printStepInterval - * steps. - * - * @param printNumberToTout The solution is printed at - * regular invervals a total of - * "printNumberToTout" times. - * - * @param printSolnFirstSteps The solution is printed out - * the first "printSolnFirstSteps" - * steps. After these steps the other - * parameters determine the printing. - * default = 0 - * - * @param dumpJacobians Dump jacobians to disk. - * - * default = false - * - */ - void BEulerInt::setPrintSolnOptions(int printSolnStepInterval, - int printSolnNumberToTout, - int printSolnFirstSteps, - bool dumpJacobians) { - m_printSolnStepInterval = printSolnStepInterval; - m_printSolnNumberToTout = printSolnNumberToTout; - m_printSolnFirstSteps = printSolnFirstSteps; - m_dumpJacobians = dumpJacobians; - } - - void BEulerInt::setIterator(IterType t) { - m_iter = t; - } - - /************************************************************************** - * - * setNonLinOptions() - * - * Set the options for the nonlinear method - * - * Defaults are set in the .h file. These are the defaults: - * min_newt_its = 0 - * matrixConditioning = false - * colScaling = false - * rowScaling = true - */ - void BEulerInt::setNonLinOptions(int min_newt_its, bool matrixConditioning, - bool colScaling, bool rowScaling) { - m_min_newt_its = min_newt_its; - m_matrixConditioning = matrixConditioning; - m_colScaling = colScaling; - m_rowScaling = rowScaling; - if (m_colScaling) { - if (!m_colScales) { - m_colScales = mdp_alloc_dbl_1(m_neq, 1.0); - } - } - if (m_rowScaling) { - if (!m_rowScales) { - m_rowScales = mdp_alloc_dbl_1(m_neq, 1.0); - } - } - } - - /************************************************************************** - * - * setInitialTimeStep(): - * - * Set the initial time step. Right now, we set the - * time step by setting delta_t_np1. - */ - void BEulerInt::setInitialTimeStep(double deltaT) { - delta_t_np1 = deltaT; - } - - /************************************************************************** - * - * setPrintFlag(): - * - */ - void BEulerInt::setPrintFlag(int print_flag) { - m_print_flag = print_flag; - } - - /************************************************************************** - * - * initialize(): - * - * Find the initial conditions for y and ydot. - */ - void BEulerInt::initializeRJE(double t0, ResidJacEval &func) - { - m_neq = func.nEquations(); - m_t0 = t0; - internalMalloc(); - /* - * Get the initial conditions. - */ - func.getInitialConditionsDot(m_t0, m_neq, m_y_n, m_ydot_n); - - // Store a pointer to the residual routine in the object - m_func = &func; - - /* - * Initialize the various time counters in the object - */ - time_n = t0; - time_nm1 = time_n; - time_nm2 = time_nm1; - delta_t_n = 0.0; - delta_t_nm1 = 0.0; - } - - /************************************************************************** + /* + * Function to calculate the predicted solution vector, m_y_pred_n for the + * (n+1)th time step. This routine can be used by a first order - forward + * Euler / backward Euler predictor / corrector method or for a second order + * Adams-Bashforth / Trapezoidal Rule predictor / corrector method. See Nachos + * documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - 83282 for + * more information. * - * reinitialize(): + * variables: * + * on input: + * + * N - number of unknowns + * order - indicates order of method + * = 1 -> first order forward Euler/backward Euler + * predictor/corrector + * = 2 -> second order Adams-Bashforth/Trapezoidal Rule + * predictor/corrector + * + * delta_t_n - magnitude of time step at time n (i.e., = t_n+1 - t_n) + * delta_t_nm1 - magnitude of time step at time n - 1 (i.e., = t_n - t_n-1) + * y_n[] - solution vector at time n + * y_dot_n[] - acceleration vector from the predictor at time n + * y_dot_nm1[] - acceleration vector from the predictor at time n - 1 + * + * on output: + * + * m_y_pred_n[] - predicted solution vector at time n + 1 */ - void BEulerInt::reinitializeRJE(double t0, ResidJacEval& func) - { - m_neq = func.nEquations(); - m_t0 = t0; - internalMalloc(); - /* - * At the initial time, get the initial conditions and time and store - * them into internal storage in the object, my[]. - */ - m_t0 = t0; - func.getInitialConditions(m_t0, m_y_n, m_ydot_n); - /** - * Set up the internal weights that are used for testing convergence - */ - setSolnWeights(); - - // Store a pointer to the function - m_func = &func; - - } - - /****************************************************************************** - * - * getPrintTime(): - * - */ - double BEulerInt::getPrintTime(double time_current) { - double tnext; - if (m_printSolnNumberToTout > 0) { - double dt = (m_time_final - m_t0) / m_printSolnNumberToTout; - for (int i = 0; i <= m_printSolnNumberToTout; i++) { - tnext = m_t0 + dt * i; - if (tnext >= time_current) return tnext; - } - } - return 1.0E300; - } - - /****************************************************************************** - * - * nEvals(): - * - * Return the total number of function evaluations - */ - int BEulerInt::nEvals() const - { - return m_nfe; - } - - /************************************************************************** - * - * internalMalloc(): - * - * Internal routine that sets up the fixed length storage based on - * the size of the problem to solve. - */ - void BEulerInt::internalMalloc() { - mdp_realloc_dbl_1(&m_ewt, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_y_n, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_y_nm1, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_y_pred_n, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_ydot_n, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_ydot_nm1, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_resid, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_residWts, m_neq, 0, 0.0); - mdp_realloc_dbl_1(&m_wksp, m_neq, 0, 0.0); - if (m_rowScaling) { - mdp_realloc_dbl_1(&m_rowScales, m_neq, 0, 1.0); - } - if (m_colScaling) { - mdp_realloc_dbl_1(&m_colScales, m_neq, 0, 1.0); - } - tdjac_ptr = new SquareMatrix(m_neq); - } - - /************************************************************************** - * - * setSolnWeights(): - * - * Set the solution weights - * This is a very important routine as it affects quite a few - * operations involving convergence. - * - */ - void BEulerInt::setSolnWeights() + void BEulerInt::calc_y_pred(int order) { int i; - if (m_itol == 1) { - /* - * Adjust the atol vector if we are using vector - * atol conditions. - */ - // m_func->adjustAtol(m_abstol); - + double c1, c2; + switch (order) { + case 0: + case 1: + c1 = delta_t_n; for (i = 0; i < m_neq; i++) { - m_ewt[i] = m_abstol[i] + m_reltol * 0.5 * - (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i]; } - } else { + break; + case 2: + c1 = delta_t_n * (2.0 + delta_t_n / delta_t_nm1) / 2.0; + c2 = (delta_t_n * delta_t_n) / (delta_t_nm1 * 2.0); for (i = 0; i < m_neq; i++) { - m_ewt[i] = m_abstols + m_reltol * 0.5 * - (fabs(m_y_n[i]) + fabs(m_y_pred_n[i])); + m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i] - c2 * m_ydot_nm1[i]; } + break; } - } - /****************************************************************************** - * - * setColumnScales(): - * - * Set the column scaling vector at the current time - */ - void BEulerInt::setColumnScales() - { - m_func->calcSolnScales(time_n, m_y_n, m_y_nm1, m_colScales); - } - - /****************************************************************************** - * - * computeResidWts(): - * - * We compute residual weights here, which we define as the L_0 norm - * of the Jacobian Matrix, weighted by the solution weights. - * This is the proper way to guage the magnitude of residuals. However, - * it does need the evaluation of the jacobian, and the implementation - * below is slow, but doesn't take up much memory. - * - * Here a small weighting indicates that the change in solution is - * very sensitive to that equation. - */ - void BEulerInt::computeResidWts(SquareMatrix &jac) - { - int i, j; - double *data = &(*(jac.begin())); - double value; - for (i = 0; i < m_neq; i++) { - m_residWts[i] = fabs(data[i] * m_ewt[0]); - for (j = 1; j < m_neq; j++) { - value = fabs(data[j*m_neq + i] * m_ewt[j]); - m_residWts[i] = MAX(m_residWts[i], value); - } - } - } - - /****************************************************************************** - * - * filterNewStep(): - * - * void BEulerInt:: - * - */ - double BEulerInt::filterNewStep(double timeCurrent, double *y_current, - double *ydot_current) { - - return 0.0; - } - - - /******************************************************************************/ -} - - -/* - * Blas routines - */ -extern "C" { - extern void dcopy_(int *, double *, int *, double *, int *); -} - -/*****************************************************************************/ -/*****************************************************************************/ -/*****************************************************************************/ -static void print_line(const char *str, int n) -{ - for (int i = 0; i < n; i++) { - printf("%s", str); - } - printf("\n"); -} - -/*****************************************************************************/ -/*****************************************************************************/ -/*****************************************************************************/ - -static void print_time_step1(int order, int n_time_step, double time, - double delta_t_n, double delta_t_nm1, - bool step_failed, int num_failures) - -/* - * Print out for relevant time step information - */ - -{ - const char *string = 0; - if (order == 0) string = "Backward Euler"; - else if (order == 1) string = "Forward/Backward Euler"; - else if (order == 2) string = "Adams-Bashforth/TR"; - printf("\n"); print_line("=", 80); - printf("\nStart of Time Step: %5d Time_n = %9.5g Time_nm1 = %9.5g\n", - n_time_step, time, time - delta_t_n); - printf("\tIntegration method = %s\n", string); - if (step_failed) - printf("\tPreviously attempted step was a failure\n"); - if (delta_t_n > delta_t_nm1) - string = "(Increased from previous iteration)"; - else if (delta_t_n < delta_t_nm1) - string = "(Decreased from previous iteration)"; - else { - string = "(same as previous iteration)"; - } - printf("\tdelta_t_n = %8.5e %s", delta_t_n, string); - if (num_failures > 0) - printf("\t(Bad_History Failure Counter = %d)", num_failures); - printf("\n\tdelta_t_nm1 = %8.5e\n", delta_t_nm1); -} /*************** END print_time_step1 **************************************/ -/*****************************************************************************/ -/* - * Print out for relevant time step information - */ -static void print_time_step2(int time_step_num, int order, - double time, double time_error_factor, - double delta_t_n, double delta_t_np1) -{ - printf("\tTime Step Number %5d was a success: time = %10g\n", time_step_num, - time); - printf("\t\tEstimated Error\n"); - printf("\t\t-------------------- = %8.5e\n", time_error_factor); - printf("\t\tTolerated Error\n\n"); - printf("\t- Recommended next delta_t (not counting history) = %g\n", - delta_t_np1); - printf("\n"); print_line("=", 80); printf("\n"); -} /************* END of print_time_step2 () **********************************/ -/*****************************************************************************/ -/*****************************************************************************/ -/* - * Print Out descriptive information on why the current step failed - */ -static void print_time_fail(bool convFailure, int time_step_num, - double time, double delta_t_n, - double delta_t_np1, double time_error_factor) -{ - printf("\n"); print_line("=", 80); - if (convFailure) { - printf("\tTime Step Number %5d experienced a convergence " - "failure\n", time_step_num); - printf("\tin the non-linear or linear solver\n"); - printf("\t\tValue of time at failed step = %g\n", time); - printf("\t\tdelta_t of the failed step = %g\n", - delta_t_n); - printf("\t\tSuggested value of delta_t to try next = %g\n", - delta_t_np1); - } else { - printf("\tTime Step Number %5d experienced a truncation error " - "failure!\n", time_step_num); - printf("\t\tValue of time at failed step = %g\n", time); - printf("\t\tdelta_t of the failed step = %g\n", - delta_t_n); - printf("\t\tSuggested value of delta_t to try next = %g\n", - delta_t_np1); - printf("\t\tCalculated truncation error factor = %g\n", - time_error_factor); - } - printf("\n"); print_line("=", 80); -} /*************** END of print_time_fail () *********************************/ -/*****************************************************************************/ -/* - * Print out the final results and counters - */ -static void print_final(double time, int step_failed, - int time_step_num, int num_newt_its, - int total_linear_solves, int numConvFails, - int numTruncFails, int nfe, int nJacEval) -{ - printf("\n"); print_line("=", 80); - printf("TIME INTEGRATION ROUTINE HAS FINISHED: "); - if (step_failed) - printf(" IT WAS A FAILURE\n"); - else - printf(" IT WAS A SUCCESS\n"); - printf("\tEnding time = %g\n", time); - printf("\tNumber of time steps = %d\n", time_step_num); - printf("\tNumber of newt its = %d\n", num_newt_its); - printf("\tNumber of linear solves = %d\n", total_linear_solves); - printf("\tNumber of convergence failures= %d\n", numConvFails); - printf("\tNumber of TimeTruncErr fails = %d\n", numTruncFails); - printf("\tNumber of Function evals = %d\n", nfe); - printf("\tNumber of Jacobian evals/solvs= %d\n", nJacEval); - printf("\n"); print_line("=", 80); -} /************* END of print_final () ***************************************/ -/*****************************************************************************/ -/*****************************************************************************/ -/* - * Header info for one line comment about a time step - */ -static void print_lvl1_Header(int nTimes) { - printf("\n"); - if (nTimes) { - print_line("-", 80); - } - printf("time Time Time Time "); - if (nTimes == 0) { - printf(" START"); - } else { - printf(" (continued)"); - } - printf("\n"); - - printf("step (sec) step Newt Aztc bktr trunc "); - printf("\n"); - - printf(" No. Rslt size Its Its stps error |"); - printf(" comment"); - printf("\n"); - print_line("-", 80); -} -/*****************************************************************************/ -/*****************************************************************************/ -/* - * One line entry about time step - * rslt -> 4 letter code - */ -static void print_lvl1_summary( - int time_step_num, double time, const char *rslt, double delta_t_n, - int newt_its, int aztec_its, int bktr_stps, double time_error_factor, - const char *comment) { - printf("%6d %11.6g %4s %10.4g %4d %4d %4d %11.4g", - time_step_num, time, rslt, delta_t_n, newt_its, aztec_its, - bktr_stps, time_error_factor); - if (comment) printf(" | %s", comment); - printf("\n"); -} -/*****************************************************************************/ -/*****************************************************************************/ -namespace Cantera { - /* - * Function to calculate the predicted solution vector, m_y_pred_n for the - * (n+1)th time step. This routine can be used by a first order - forward - * Euler / backward Euler predictor / corrector method or for a second order - * Adams-Bashforth / Trapezoidal Rule predictor / corrector method. See Nachos - * documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - 83282 for - * more information. - * - * variables: - * - * on input: - * - * N - number of unknowns - * order - indicates order of method - * = 1 -> first order forward Euler/backward Euler - * predictor/corrector - * = 2 -> second order Adams-Bashforth/Trapezoidal Rule - * predictor/corrector - * - * delta_t_n - magnitude of time step at time n (i.e., = t_n+1 - t_n) - * delta_t_nm1 - magnitude of time step at time n - 1 (i.e., = t_n - t_n-1) - * y_n[] - solution vector at time n - * y_dot_n[] - acceleration vector from the predictor at time n - * y_dot_nm1[] - acceleration vector from the predictor at time n - 1 - * - * on output: - * - * m_y_pred_n[] - predicted solution vector at time n + 1 + * Filter the predictions. */ - void BEulerInt::calc_y_pred(int order) - { - int i; - double c1, c2; - switch (order) { - case 0: - case 1: - c1 = delta_t_n; - for (i = 0; i < m_neq; i++) { - m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i]; - } -#ifdef DEBUG_HKM_JJJJJ - if (m_y_pred_n[0] <= 0.0) { - //iDebug_HKM = 1; - c1 = delta_t_n; - m_y_pred_n[0] = 0.0; - } -#endif - break; - case 2: - c1 = delta_t_n * (2.0 + delta_t_n / delta_t_nm1) / 2.0; - c2 = (delta_t_n * delta_t_n) / (delta_t_nm1 * 2.0); - for (i = 0; i < m_neq; i++) { - m_y_pred_n[i] = m_y_n[i] + c1 * m_ydot_n[i] - c2 * m_ydot_nm1[i]; - } - break; - } + m_func->filterSolnPrediction(time_n, m_y_pred_n); - /* - * Filter the predictions. - */ - m_func->filterSolnPrediction(time_n, m_y_pred_n); - - } /* calc_y_pred */ + } /* calc_y_pred */ /* Function to calculate the acceleration vector ydot for the first or @@ -875,27 +846,27 @@ namespace Cantera { * y_curr[] may not be equal to m_y_n[] during the nonlinear solve * because we may be using a look-ahead scheme. */ - void BEulerInt:: - calc_ydot(int order, double *y_curr, double *ydot_curr) - { - int i; - double c1; - switch (order) { - case 0: - case 1: /* First order forward Euler/backward Euler */ - c1 = 1.0 / delta_t_n; - for (i = 0; i < m_neq; i++) { - ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]); - } - return; - case 2: /* Second order Adams-Bashforth / Trapezoidal Rule */ - c1 = 2.0 / delta_t_n; - for (i = 0; i < m_neq; i++) { - ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]) - m_ydot_nm1[i]; - } - return; + void BEulerInt:: + calc_ydot(int order, double *y_curr, double *ydot_curr) + { + int i; + double c1; + switch (order) { + case 0: + case 1: /* First order forward Euler/backward Euler */ + c1 = 1.0 / delta_t_n; + for (i = 0; i < m_neq; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]); } - } /************* END calc_ydot () ****************************************/ + return; + case 2: /* Second order Adams-Bashforth / Trapezoidal Rule */ + c1 = 2.0 / delta_t_n; + for (i = 0; i < m_neq; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]) - m_ydot_nm1[i]; + } + return; + } + } /************* END calc_ydot () ****************************************/ /* This function calculates the time step truncation error estimate * from a very simple formula based on Gresho et al. This routine can be @@ -921,696 +892,696 @@ namespace Cantera { * delta_t_n - Magnitude of next time step at time t_n+1 * delta_t_nm1 - Magnitude of previous time step at time t_n */ - double BEulerInt::time_error_norm() - { - int i; - double rel_norm, error; + double BEulerInt::time_error_norm() + { + int i; + double rel_norm, error; #ifdef DEBUG_HKM #define NUM_ENTRIES 5 - if (m_print_flag > 2) { - int imax[NUM_ENTRIES], j, jnum; - double dmax; - bool used; - printf("\t\ttime step truncation error contributors:\n"); - printf("\t\t I entry actual predicted " - " weight ydot\n"); - printf("\t\t"); print_line("-", 70); - for (j = 0; j < NUM_ENTRIES; j++) imax[j] = -1; - for (jnum = 0; jnum < NUM_ENTRIES; jnum++) { - dmax = -1.0; - for (i = 0; i < m_neq; i++) { - used = false; - for (j = 0; j < jnum; j++) { - if (imax[j] == i) used = true; - } - if (!used) { - error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; - rel_norm = sqrt(error * error); - if (rel_norm > dmax) { - imax[jnum] = i; - dmax = rel_norm; - } - } + if (m_print_flag > 2) { + int imax[NUM_ENTRIES], j, jnum; + double dmax; + bool used; + printf("\t\ttime step truncation error contributors:\n"); + printf("\t\t I entry actual predicted " + " weight ydot\n"); + printf("\t\t"); print_line("-", 70); + for (j = 0; j < NUM_ENTRIES; j++) imax[j] = -1; + for (jnum = 0; jnum < NUM_ENTRIES; jnum++) { + dmax = -1.0; + for (i = 0; i < m_neq; i++) { + used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; } - if (imax[jnum] >= 0) { + if (!used) { + error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; + rel_norm = sqrt(error * error); + if (rel_norm > dmax) { + imax[jnum] = i; + dmax = rel_norm; + } + } + } + if (imax[jnum] >= 0) { i = imax[jnum]; printf("\t\t%4d %12.4e %12.4e %12.4e %12.4e %12.4e\n", i, dmax, m_y_n[i], m_y_pred_n[i], m_ewt[i], m_ydot_n[i]); - } } - printf("\t\t"); print_line("-", 70); } -#endif - rel_norm = 0.0; - for (i = 0; i < m_neq; i++) { - error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; - rel_norm += (error * error); - } - rel_norm = sqrt(rel_norm / m_neq); - return rel_norm; + printf("\t\t"); print_line("-", 70); } +#endif + rel_norm = 0.0; + for (i = 0; i < m_neq; i++) { + error = (m_y_n[i] - m_y_pred_n[i]) / m_ewt[i]; + rel_norm += (error * error); + } + rel_norm = sqrt(rel_norm / m_neq); + return rel_norm; + } - /************************************************************************* - * Time step control function for the selection of the time step size based on - * a desired accuracy of time integration and on an estimate of the relative - * error of the time integration process. This routine can be called for a - * first order - forward Euler/backward Euler predictor/ corrector and for a - * second order Adams- Bashforth/Trapezoidal Rule predictor/corrector. See - * Nachos documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - - * 83282 for more information. - * - * variables: - * - * on input: - * - * order - indicates order of method - * = 1 -> first order forward Euler/backward Euler - * predictor/corrector - * = 2 -> second order forward Adams-Bashforth/Trapezoidal - * rule predictor/corrector - * - * delta_t_n - Magnitude of time step at time t_n - * delta_t_nm1 - Magnitude of time step at time t_n-1 - * rel_error - Generic realtive error tolerance - * time_error_factor - Estimated value of the time step truncation error - * factor. This value is a ratio of the computed - * error norms. The premultiplying constants - * and the power are not yet applied to normalize the - * predictor/corrector ratio. (see output value) - * - * on output: - * - * return - delta_t for the next time step - * If delta_t is negative, then the current time step is - * rejected because the time-step truncation error is - * too large. The return value will contain the negative - * of the recommended next time step. - * - * time_error_factor - This output value is normalized so that - * values greater than one indicate the current time - * integration error is greater than the user - * specified magnitude. - */ - double BEulerInt::time_step_control(int order, double time_error_factor) - { - double factor = 0.0, power = 0.0, delta_t; - const char *yo = "time_step_control"; + /************************************************************************* + * Time step control function for the selection of the time step size based on + * a desired accuracy of time integration and on an estimate of the relative + * error of the time integration process. This routine can be called for a + * first order - forward Euler/backward Euler predictor/ corrector and for a + * second order Adams- Bashforth/Trapezoidal Rule predictor/corrector. See + * Nachos documentation Sand86-1816 and Gresho, Lee, Sani LLNL report UCRL - + * 83282 for more information. + * + * variables: + * + * on input: + * + * order - indicates order of method + * = 1 -> first order forward Euler/backward Euler + * predictor/corrector + * = 2 -> second order forward Adams-Bashforth/Trapezoidal + * rule predictor/corrector + * + * delta_t_n - Magnitude of time step at time t_n + * delta_t_nm1 - Magnitude of time step at time t_n-1 + * rel_error - Generic realtive error tolerance + * time_error_factor - Estimated value of the time step truncation error + * factor. This value is a ratio of the computed + * error norms. The premultiplying constants + * and the power are not yet applied to normalize the + * predictor/corrector ratio. (see output value) + * + * on output: + * + * return - delta_t for the next time step + * If delta_t is negative, then the current time step is + * rejected because the time-step truncation error is + * too large. The return value will contain the negative + * of the recommended next time step. + * + * time_error_factor - This output value is normalized so that + * values greater than one indicate the current time + * integration error is greater than the user + * specified magnitude. + */ + double BEulerInt::time_step_control(int order, double time_error_factor) + { + double factor = 0.0, power = 0.0, delta_t; + const char *yo = "time_step_control"; - /* - * Special case time_error_factor so that zeroes don't cause a problem. - */ - time_error_factor = MAX(1.0E-50, time_error_factor); + /* + * Special case time_error_factor so that zeroes don't cause a problem. + */ + time_error_factor = MAX(1.0E-50, time_error_factor); - /* - * Calculate the factor for the change in magnitude of time step. - */ - switch (order) { - case 1: - factor = 1.0/(2.0 *(time_error_factor)); - power = 0.5; - break; - case 2: - factor = 1.0/(3.0 * (1.0 + delta_t_nm1 / delta_t_n) - * (time_error_factor)); - power = 0.3333333333333333; - } - factor = pow(factor, power); - if (factor < 0.5) { - if (m_print_flag > 1) { - printf("\t%s: WARNING - Current time step will be chucked\n", yo); - printf("\t\tdue to a time step truncation error failure.\n"); - } - delta_t = - 0.5 * delta_t_n; - } else { - factor = MIN(factor, 1.5); - delta_t = factor * delta_t_n; - } - return delta_t; - } /************ END of time_step_control()********************************/ - - /************************************************************************** - * - * integrate(): - * - * defaults are located in the .h file. They are as follows: - * time_init = 0.0 + /* + * Calculate the factor for the change in magnitude of time step. */ - double BEulerInt::integrateRJE(double tout, double time_init) - { - double time_current; - bool weAreNotFinished = true; - m_time_final = tout; - int flag = SUCCESS; - /** - * Initialize the time step number to zero. step will increment so that - * the first time step is number 1 - */ - m_time_step_num = 0; + switch (order) { + case 1: + factor = 1.0/(2.0 *(time_error_factor)); + power = 0.5; + break; + case 2: + factor = 1.0/(3.0 * (1.0 + delta_t_nm1 / delta_t_n) + * (time_error_factor)); + power = 0.3333333333333333; + } + factor = pow(factor, power); + if (factor < 0.5) { + if (m_print_flag > 1) { + printf("\t%s: WARNING - Current time step will be chucked\n", yo); + printf("\t\tdue to a time step truncation error failure.\n"); + } + delta_t = - 0.5 * delta_t_n; + } else { + factor = MIN(factor, 1.5); + delta_t = factor * delta_t_n; + } + return delta_t; + } /************ END of time_step_control()********************************/ + //================================================================================================ + /************************************************************************** + * + * integrate(): + * + * defaults are located in the .h file. They are as follows: + * time_init = 0.0 + */ + double BEulerInt::integrateRJE(double tout, double time_init) + { + double time_current; + bool weAreNotFinished = true; + m_time_final = tout; + int flag = SUCCESS; + /** + * Initialize the time step number to zero. step will increment so that + * the first time step is number 1 + */ + m_time_step_num = 0; - /* - * Do the integration a step at a time - */ - int istep = 0; - int printStep = 0; - bool doPrintSoln = false; - time_current = time_init; - time_n = time_init; - time_nm1 = time_init; - time_nm2 = time_init; - m_func->evalTimeTrackingEqns(time_current, 0.0, m_y_n, m_ydot_n); - double print_time = getPrintTime(time_current); - if (print_time == time_current) { - m_func->writeSolution(4, time_current, delta_t_n, - istep, m_y_n, m_ydot_n); - } - /* - * We print out column headers here for the case of - */ - if (m_print_flag == 1) { - print_lvl1_Header(0); - } - /* - * Call a different user routine at the end of each step, - * that will probably print to a file. - */ - m_func->user_out2(0, time_current, 0.0, m_y_n, m_ydot_n); + /* + * Do the integration a step at a time + */ + int istep = 0; + int printStep = 0; + bool doPrintSoln = false; + time_current = time_init; + time_n = time_init; + time_nm1 = time_init; + time_nm2 = time_init; + m_func->evalTimeTrackingEqns(time_current, 0.0, m_y_n, m_ydot_n); + double print_time = getPrintTime(time_current); + if (print_time == time_current) { + m_func->writeSolution(4, time_current, delta_t_n, + istep, m_y_n, m_ydot_n); + } + /* + * We print out column headers here for the case of + */ + if (m_print_flag == 1) { + print_lvl1_Header(0); + } + /* + * Call a different user routine at the end of each step, + * that will probably print to a file. + */ + m_func->user_out2(0, time_current, 0.0, m_y_n, m_ydot_n); - do { + do { - print_time = getPrintTime(time_current); - if (print_time >= tout) print_time = tout; + print_time = getPrintTime(time_current); + if (print_time >= tout) print_time = tout; - /************************************************************ - * Step the solution - */ - time_current = step(tout); - istep++; - printStep++; - /***********************************************************/ - if (time_current < 0.0) { - if (time_current == -1234.) { - time_current = 0.0; - } else { - time_current = -time_current; - } - flag = FAILURE; - } - - if (flag != FAILURE) { - bool retn = - m_func->evalStoppingCritera(time_current, delta_t_n, - m_y_n, m_ydot_n); - if (retn) { - weAreNotFinished = false; - doPrintSoln = true; - } - } - - /* - * determine conditional printing of soln - */ - if (time_current >= print_time) { - doPrintSoln = true; - } - if (m_printSolnStepInterval == printStep) { - doPrintSoln = true; - } - if (m_printSolnFirstSteps > istep) { - doPrintSoln = true; - } - - /* - * Evaluate time integrated quantities that are calculated at the - * end of every successful time step. - */ - if (flag != FAILURE) { - m_func->evalTimeTrackingEqns(time_current, delta_t_n, - m_y_n, m_ydot_n); - } - - /* - * Call the printout routine. - */ - if (doPrintSoln) { - m_func->writeSolution(1, time_current, delta_t_n, - istep, m_y_n, m_ydot_n); - printStep = 0; - doPrintSoln = false; - if (m_print_flag == 1) { - print_lvl1_Header(1); - } - } - /* - * Call a different user routine at the end of each step, - * that will probably print to a file. - */ - if (flag == FAILURE) { - m_func->user_out2(-1, time_current, delta_t_n, m_y_n, m_ydot_n); + /************************************************************ + * Step the solution + */ + time_current = step(tout); + istep++; + printStep++; + /***********************************************************/ + if (time_current < 0.0) { + if (time_current == -1234.) { + time_current = 0.0; } else { - m_func->user_out2(1, time_current, delta_t_n, m_y_n, m_ydot_n); + time_current = -time_current; } + flag = FAILURE; + } - } while (time_current < tout && - m_time_step_attempts < m_max_time_step_attempts && - flag == SUCCESS && weAreNotFinished); - - /* - * Check current time against the max solution time. - */ - if (time_current >= tout) { - printf("Simulation completed time integration in %d time steps\n", - m_time_step_num); - printf("Final Time: %e\n\n", time_current); - } else if (m_time_step_attempts >= m_max_time_step_attempts) { - printf("Simulation ran into time step attempt limit in" - "%d time steps\n", - m_time_step_num); - printf("Final Time: %e\n\n", time_current); - } else if (flag == FAILURE) { - printf("ERROR: time stepper failed at time = %g\n", time_current); + if (flag != FAILURE) { + bool retn = + m_func->evalStoppingCritera(time_current, delta_t_n, + m_y_n, m_ydot_n); + if (retn) { + weAreNotFinished = false; + doPrintSoln = true; + } } /* - * Print out the final results and counters. + * determine conditional printing of soln */ - print_final(time_n, flag, m_time_step_num, m_numTotalNewtIts, - m_numTotalLinearSolves, m_numTotalConvFails, - m_numTotalTruncFails, m_nfe, m_nJacEval); + if (time_current >= print_time) { + doPrintSoln = true; + } + if (m_printSolnStepInterval == printStep) { + doPrintSoln = true; + } + if (m_printSolnFirstSteps > istep) { + doPrintSoln = true; + } + /* + * Evaluate time integrated quantities that are calculated at the + * end of every successful time step. + */ + if (flag != FAILURE) { + m_func->evalTimeTrackingEqns(time_current, delta_t_n, + m_y_n, m_ydot_n); + } + + /* + * Call the printout routine. + */ + if (doPrintSoln) { + m_func->writeSolution(1, time_current, delta_t_n, + istep, m_y_n, m_ydot_n); + printStep = 0; + doPrintSoln = false; + if (m_print_flag == 1) { + print_lvl1_Header(1); + } + } /* * Call a different user routine at the end of each step, * that will probably print to a file. - */ - m_func->user_out2(2, time_current, delta_t_n, m_y_n, m_ydot_n); + */ + if (flag == FAILURE) { + m_func->user_out2(-1, time_current, delta_t_n, m_y_n, m_ydot_n); + } else { + m_func->user_out2(1, time_current, delta_t_n, m_y_n, m_ydot_n); + } + + } while (time_current < tout && + m_time_step_attempts < m_max_time_step_attempts && + flag == SUCCESS && weAreNotFinished); + + /* + * Check current time against the max solution time. + */ + if (time_current >= tout) { + printf("Simulation completed time integration in %d time steps\n", + m_time_step_num); + printf("Final Time: %e\n\n", time_current); + } else if (m_time_step_attempts >= m_max_time_step_attempts) { + printf("Simulation ran into time step attempt limit in" + "%d time steps\n", + m_time_step_num); + printf("Final Time: %e\n\n", time_current); + } else if (flag == FAILURE) { + printf("ERROR: time stepper failed at time = %g\n", time_current); + } + + /* + * Print out the final results and counters. + */ + print_final(time_n, flag, m_time_step_num, m_numTotalNewtIts, + m_numTotalLinearSolves, m_numTotalConvFails, + m_numTotalTruncFails, m_nfe, m_nJacEval); + + /* + * Call a different user routine at the end of each step, + * that will probably print to a file. + */ + m_func->user_out2(2, time_current, delta_t_n, m_y_n, m_ydot_n); - if (flag != SUCCESS) - throw BEulerErr(" BEuler error encountered."); - return time_current; - } + if (flag != SUCCESS) + throw BEulerErr(" BEuler error encountered."); + return time_current; + } - /************************************************************************** - * - * step(): - * - * This routine advances the calculations one step using a predictor - * corrector approach. We use an implicit algorithm here. - * + /************************************************************************** + * + * step(): + * + * This routine advances the calculations one step using a predictor + * corrector approach. We use an implicit algorithm here. + * + */ + double BEulerInt::step(double t_max) + { + double CJ; + int one = 1; + bool step_failed = false; + bool giveUp = false; + bool convFailure = false; + const char *rslt; + double time_error_factor = 0.0; + double normFilter = 0.0; + int numTSFailures = 0; + int bktr_stps = 0; + int nonlinearloglevel = m_print_flag; + int num_newt_its = 0; + int aztec_its = 0; + string comment; + /* + * Increment the time counter - May have to be taken back, + * if time step is found to be faulty. */ - double BEulerInt::step(double t_max) - { - double CJ; - int one = 1; - bool step_failed = false; - bool giveUp = false; - bool convFailure = false; - const char *rslt; - double time_error_factor = 0.0; - double normFilter = 0.0; - int numTSFailures = 0; - int bktr_stps = 0; - int nonlinearloglevel = m_print_flag; - int num_newt_its = 0; - int aztec_its = 0; - string comment; + m_time_step_num++; + + /** + * Loop here until we achieve a successful step or we set the giveUp + * flag indicating that repeated errors have occurred. + */ + do { + m_time_step_attempts++; + comment.clear(); + /* - * Increment the time counter - May have to be taken back, - * if time step is found to be faulty. + * Possibly adjust the delta_t_n value for this time step from the + * recommended delta_t_np1 value determined in the previous step + * due to maximum time step constraints or other occurences, + * known to happen at a given time. */ - m_time_step_num++; + if ((time_n + delta_t_np1) >= t_max) { + delta_t_np1 =t_max - time_n; + } + + if (delta_t_np1 >= delta_t_max) { + delta_t_np1 = delta_t_max; + } - /** - * Loop here until we achieve a successful step or we set the giveUp - * flag indicating that repeated errors have occurred. + /* + * Increment the delta_t counters and the time for the current + * time step. */ - do { - m_time_step_attempts++; - comment.clear(); - /* - * Possibly adjust the delta_t_n value for this time step from the - * recommended delta_t_np1 value determined in the previous step - * due to maximum time step constraints or other occurences, - * known to happen at a given time. - */ - if ((time_n + delta_t_np1) >= t_max) { - delta_t_np1 =t_max - time_n; - } + delta_t_nm2 = delta_t_nm1; + delta_t_nm1 = delta_t_n; + delta_t_n = delta_t_np1; + time_n += delta_t_n; + + /* + * Determine the integration order of the current step. + * + * Special case for start-up of time integration procedure + * First time step = Do a predictor step as we + * have recently added an initial + * ydot input option. And, setting ydot=0 + * is equivalent to not doing a + * predictor step. + * Second step = If 2nd order method, do a first order + * step for this time-step, only. + * + * If 2nd order method with a constant time step, the + * first and second steps are 1/10 the specified step, and + * the third step is 8/10 the specified step. This reduces + * the error asociated with using lower order + * integration on the first two steps. (RCS 11-6-97) + * + * If the previous time step failed for one reason or another, + * do a linear step. It's more robust. + */ + if (m_time_step_num == 1) { + m_order = 1; /* Backward Euler */ + } + else if (m_time_step_num == 2) { + m_order = 1; /* Forward/Backward Euler */ + } + else if (step_failed) { + m_order = 1; /* Forward/Backward Euler */ + } + else if (m_time_step_num > 2) { + m_order = 1; /* Specified + Predictor/Corrector + - not implemented */ + } - if (delta_t_np1 >= delta_t_max) { - delta_t_np1 = delta_t_max; - } + /* + * Print out an initial statement about the step. + */ + if (m_print_flag > 1) { + print_time_step1(m_order, m_time_step_num, time_n, delta_t_n, + delta_t_nm1, step_failed, m_failure_counter); + } - /* - * Increment the delta_t counters and the time for the current - * time step. - */ + /* + * Calculate the predicted solution, m_y_pred_n, for the current + * time step. + */ + calc_y_pred(m_order); - delta_t_nm2 = delta_t_nm1; - delta_t_nm1 = delta_t_n; - delta_t_n = delta_t_np1; - time_n += delta_t_n; + /* + * HKM - Commented this out. I may need it for particles later. + * If Solution bounds checking is turned on, we need to crop the + * predicted solution to make sure bounds are enforced + * + * + * cropNorm = 0.0; + * if (Cur_Realm->Realm_Nonlinear.Constraint_Backtracking_Flag == + * Constraint_Backtrack_Enable) { + * cropNorm = cropPredictor(mesh, x_pred_n, abs_time_error, + * m_reltol); + */ - /* - * Determine the integration order of the current step. - * - * Special case for start-up of time integration procedure - * First time step = Do a predictor step as we - * have recently added an initial - * ydot input option. And, setting ydot=0 - * is equivalent to not doing a - * predictor step. - * Second step = If 2nd order method, do a first order - * step for this time-step, only. - * - * If 2nd order method with a constant time step, the - * first and second steps are 1/10 the specified step, and - * the third step is 8/10 the specified step. This reduces - * the error asociated with using lower order - * integration on the first two steps. (RCS 11-6-97) - * - * If the previous time step failed for one reason or another, - * do a linear step. It's more robust. - */ - if (m_time_step_num == 1) { - m_order = 1; /* Backward Euler */ - } - else if (m_time_step_num == 2) { - m_order = 1; /* Forward/Backward Euler */ - } - else if (step_failed) { - m_order = 1; /* Forward/Backward Euler */ - } - else if (m_time_step_num > 2) { - m_order = 1; /* Specified - Predictor/Corrector - - not implemented */ - } - - /* - * Print out an initial statement about the step. - */ + /* + * Save the old solution, before overwriting with the new solution + * - use + */ + mdp_copy_dbl_1(m_y_nm1, m_y_n, m_neq); + + /* + * Use the predicted value as the initial guess for the corrector + * loop, for + * every step other than the first step. + */ + if (m_order > 0) { + mdp_copy_dbl_1(m_y_n, m_y_pred_n, m_neq); + } + + /* + * Save the old time derivative, if necessary, before it is + * overwritten. + * This overwrites ydot_nm1, losing information from the previous time + * step. + */ + mdp_copy_dbl_1(m_ydot_nm1, m_ydot_n, m_neq); + + /* + * Calculate the new time derivative, ydot_n, that is consistent + * with the + * initial guess for the corrected solution vector. + * + */ + calc_ydot(m_order, m_y_n, m_ydot_n); + + /* + * Calculate CJ, the coefficient for the jacobian corresponding to the + * derivative of the residual wrt to the acceleration vector. + */ + if (m_order < 2) CJ = 1.0 / delta_t_n; + else CJ = 2.0 / delta_t_n; + + /* + * Calculate a new Solution Error Weighting vector + */ + setSolnWeights(); + + /* + * Solve the system of equations at the current time step. + * Note - x_corr_n and x_dot_n are considered to be updated, + * on return from this solution. + */ + int ierror = solve_nonlinear_problem(m_y_n, m_ydot_n, + CJ, time_n, *tdjac_ptr, num_newt_its, + aztec_its, bktr_stps, + nonlinearloglevel); + /* + * Set the appropriate flags if a convergence failure is detected. + */ + if (ierror < 0) { /* Step failed */ + convFailure = true; + step_failed = true; + rslt = "fail"; + m_numTotalConvFails++; + m_failure_counter +=3; if (m_print_flag > 1) { - print_time_step1(m_order, m_time_step_num, time_n, delta_t_n, - delta_t_nm1, step_failed, m_failure_counter); + printf("\tStep is Rejected, nonlinear problem didn't converge," + "ierror = %d\n", ierror); } + } + else { /* Step succeeded */ + convFailure = false; + step_failed = false; + rslt = "done"; /* - * Calculate the predicted solution, m_y_pred_n, for the current - * time step. - */ - calc_y_pred(m_order); - - /* - * HKM - Commented this out. I may need it for particles later. - * If Solution bounds checking is turned on, we need to crop the - * predicted solution to make sure bounds are enforced - * - * - * cropNorm = 0.0; - * if (Cur_Realm->Realm_Nonlinear.Constraint_Backtracking_Flag == - * Constraint_Backtrack_Enable) { - * cropNorm = cropPredictor(mesh, x_pred_n, abs_time_error, - * m_reltol); - */ - - /* - * Save the old solution, before overwriting with the new solution - * - use - */ - mdp_copy_dbl_1(m_y_nm1, m_y_n, m_neq); - - /* - * Use the predicted value as the initial guess for the corrector - * loop, for - * every step other than the first step. - */ - if (m_order > 0) { - mdp_copy_dbl_1(m_y_n, m_y_pred_n, m_neq); - } - - /* - * Save the old time derivative, if necessary, before it is - * overwritten. - * This overwrites ydot_nm1, losing information from the previous time - * step. - */ - mdp_copy_dbl_1(m_ydot_nm1, m_ydot_n, m_neq); - - /* - * Calculate the new time derivative, ydot_n, that is consistent - * with the - * initial guess for the corrected solution vector. - * - */ - calc_ydot(m_order, m_y_n, m_ydot_n); - - /* - * Calculate CJ, the coefficient for the jacobian corresponding to the - * derivative of the residual wrt to the acceleration vector. - */ - if (m_order < 2) CJ = 1.0 / delta_t_n; - else CJ = 2.0 / delta_t_n; - - /* - * Calculate a new Solution Error Weighting vector - */ - setSolnWeights(); - - /* - * Solve the system of equations at the current time step. - * Note - x_corr_n and x_dot_n are considered to be updated, - * on return from this solution. - */ - int ierror = solve_nonlinear_problem(m_y_n, m_ydot_n, - CJ, time_n, *tdjac_ptr, num_newt_its, - aztec_its, bktr_stps, - nonlinearloglevel); - /* - * Set the appropriate flags if a convergence failure is detected. - */ - if (ierror < 0) { /* Step failed */ + * Apply a filter to a new successful step + */ + normFilter = filterNewStep(time_n, m_y_n, m_ydot_n); + if (normFilter > 1.0) { convFailure = true; step_failed = true; - rslt = "fail"; - m_numTotalConvFails++; - m_failure_counter +=3; + rslt = "filt"; if (m_print_flag > 1) { - printf("\tStep is Rejected, nonlinear problem didn't converge," - "ierror = %d\n", ierror); + printf("\tStep is Rejected, too large filter adjustment = %g\n", + normFilter); } - } - else { /* Step succeeded */ - convFailure = false; - step_failed = false; - rslt = "done"; - - /* - * Apply a filter to a new successful step - */ - normFilter = filterNewStep(time_n, m_y_n, m_ydot_n); - if (normFilter > 1.0) { - convFailure = true; - step_failed = true; - rslt = "filt"; + } else if (normFilter > 0.0) { + if (normFilter > 0.3) { if (m_print_flag > 1) { - printf("\tStep is Rejected, too large filter adjustment = %g\n", - normFilter); - } - } else if (normFilter > 0.0) { - if (normFilter > 0.3) { - if (m_print_flag > 1) { - printf("\tStep was filtered, norm = %g, next " - "time step adjusted\n", normFilter); - } - } else { - if (m_print_flag > 1) { - printf("\tStep was filtered, norm = %g\n", normFilter); - } - } - } - } - - /* - * Calculate the time step truncation error for the current step. - */ - if (!step_failed) { - time_error_factor = time_error_norm(); - } else { - time_error_factor = 1000.; - } - - /* - * Dynamic time step control- delta_t_n, delta_t_nm1 are set here. - */ - if (step_failed) { - /* - * For convergence failures, decrease the step-size by a factor of - * 4 and try again. - */ - delta_t_np1 = 0.25 * delta_t_n; - } - else if (m_method == BEulerVarStep) { - - /* - * If we are doing a predictor/corrector method, and we are - * past a certain number of time steps given by the input file - * then either correct the DeltaT for the next time step or - * - */ - if ((m_order > 0) && - (m_time_step_num > m_numInitialConstantDeltaTSteps) ) { - delta_t_np1 = time_step_control(m_order, time_error_factor); - if (normFilter > 0.1) { - if (delta_t_np1 > delta_t_n) delta_t_np1 = delta_t_n; - } - - /* - * Check for Current time step failing due to violation of - * time step - * truncation bounds. - */ - if (delta_t_np1 < 0.0) { - m_numTotalTruncFails++; - step_failed = true; - delta_t_np1 = -delta_t_np1; - m_failure_counter += 2; - comment += "TIME TRUNC FAILURE"; - rslt = "TRNC"; - } - - /* - * Prevent churning of the time step by not increasing the - * time step, - * if the recent "History" of the time step behavior is still bad - */ - else if (m_failure_counter > 0) { - delta_t_np1 = MIN(delta_t_np1, delta_t_n); + printf("\tStep was filtered, norm = %g, next " + "time step adjusted\n", normFilter); } } else { - delta_t_np1 = delta_t_n; - } - - /* Decrease time step if a lot of Newton Iterations are - * taken. - * The idea being if more or less Newton iteration are taken - * than the target number of iterations, then adjust the time - * step downwards so that the target number of iterations or lower - * is achieved. This - * should prevent step failure by too many Newton iterations because - * the time step becomes too large. CCO - * hkm -> put in num_new_its min of 3 because the time step - * was being altered even when num_newt_its == 1 - */ - int max_Newton_steps = 10000; - int target_num_iter = 5; - if (num_newt_its > 3000 && !step_failed) { - if (max_Newton_steps != target_num_iter){ - double iter_diff = num_newt_its - target_num_iter; - double iter_adjust_zone = max_Newton_steps - target_num_iter; - double target_time_step = delta_t_n - *(1.0 - iter_diff*fabs(iter_diff)/ - ((2.0*iter_adjust_zone*iter_adjust_zone))); - target_time_step = MAX(0.5*delta_t_n, target_time_step); - if (target_time_step < delta_t_np1) { - printf("\tNext time step will be decreased from %g to %g" - " because of new its restraint\n", - delta_t_np1, target_time_step); - delta_t_np1 = target_time_step; - } + if (m_print_flag > 1) { + printf("\tStep was filtered, norm = %g\n", normFilter); } - } - - - } - - /* - * The final loop in the time stepping algorithm depends on whether the - * current step was a success or not. - */ - if (step_failed) { - /* - * Increment the counter indicating the number of consecutive - * failures - */ - numTSFailures++; - /* - * Print out a statement about the failure of the time step. - */ - if (m_print_flag > 1) { - print_time_fail(convFailure, m_time_step_num, time_n, delta_t_n, - delta_t_np1, time_error_factor); - } else if (m_print_flag == 1) { - print_lvl1_summary(m_time_step_num, time_n, rslt, delta_t_n, - num_newt_its, aztec_its, bktr_stps, - time_error_factor, - comment.c_str()); } - - /* - * Change time step counters back to the previous step before - * the failed - * time step occurred. - */ - time_n -= delta_t_n; - delta_t_n = delta_t_nm1; - delta_t_nm1 = delta_t_nm2; - - /* - * Replace old solution vector and time derivative solution vector. - */ - dcopy_(&m_neq, m_y_nm1, &one, m_y_n, &one); - dcopy_(&m_neq, m_ydot_nm1, &one, m_ydot_n, &one); - /* - * Decide whether to bail on the whole loop - */ - if (numTSFailures > 35) giveUp = true; } + } - /* - * Do processing for a successful step. - */ - else { - - /* - * Decrement the number of consequative failure counter. - */ - m_failure_counter = MAX(0, m_failure_counter-1); - - /* - * Print out final results of a successfull time step. - */ - if (m_print_flag > 1) { - print_time_step2(m_time_step_num, m_order, time_n, time_error_factor, - delta_t_n, delta_t_np1); - } - else if (m_print_flag == 1) { - print_lvl1_summary(m_time_step_num, time_n, " ", delta_t_n, - num_newt_its, aztec_its, bktr_stps, time_error_factor, - comment.c_str()); - } - - /* - * Output information at the end of every successful time step, if - * requested. - * - * fill in - */ - - - } - } while (step_failed && !giveUp); - /* - * Send back the overall result of the time step. + * Calculate the time step truncation error for the current step. + */ + if (!step_failed) { + time_error_factor = time_error_norm(); + } else { + time_error_factor = 1000.; + } + + /* + * Dynamic time step control- delta_t_n, delta_t_nm1 are set here. */ if (step_failed) { - if (time_n == 0.0) return -1234.0; - return -time_n; + /* + * For convergence failures, decrease the step-size by a factor of + * 4 and try again. + */ + delta_t_np1 = 0.25 * delta_t_n; } - return time_n; + else if (m_method == BEulerVarStep) { + + /* + * If we are doing a predictor/corrector method, and we are + * past a certain number of time steps given by the input file + * then either correct the DeltaT for the next time step or + * + */ + if ((m_order > 0) && + (m_time_step_num > m_numInitialConstantDeltaTSteps) ) { + delta_t_np1 = time_step_control(m_order, time_error_factor); + if (normFilter > 0.1) { + if (delta_t_np1 > delta_t_n) delta_t_np1 = delta_t_n; + } + + /* + * Check for Current time step failing due to violation of + * time step + * truncation bounds. + */ + if (delta_t_np1 < 0.0) { + m_numTotalTruncFails++; + step_failed = true; + delta_t_np1 = -delta_t_np1; + m_failure_counter += 2; + comment += "TIME TRUNC FAILURE"; + rslt = "TRNC"; + } + + /* + * Prevent churning of the time step by not increasing the + * time step, + * if the recent "History" of the time step behavior is still bad + */ + else if (m_failure_counter > 0) { + delta_t_np1 = MIN(delta_t_np1, delta_t_n); + } + } else { + delta_t_np1 = delta_t_n; + } + + /* Decrease time step if a lot of Newton Iterations are + * taken. + * The idea being if more or less Newton iteration are taken + * than the target number of iterations, then adjust the time + * step downwards so that the target number of iterations or lower + * is achieved. This + * should prevent step failure by too many Newton iterations because + * the time step becomes too large. CCO + * hkm -> put in num_new_its min of 3 because the time step + * was being altered even when num_newt_its == 1 + */ + int max_Newton_steps = 10000; + int target_num_iter = 5; + if (num_newt_its > 3000 && !step_failed) { + if (max_Newton_steps != target_num_iter){ + double iter_diff = num_newt_its - target_num_iter; + double iter_adjust_zone = max_Newton_steps - target_num_iter; + double target_time_step = delta_t_n + *(1.0 - iter_diff*fabs(iter_diff)/ + ((2.0*iter_adjust_zone*iter_adjust_zone))); + target_time_step = MAX(0.5*delta_t_n, target_time_step); + if (target_time_step < delta_t_np1) { + printf("\tNext time step will be decreased from %g to %g" + " because of new its restraint\n", + delta_t_np1, target_time_step); + delta_t_np1 = target_time_step; + } + } + } + + + } + + /* + * The final loop in the time stepping algorithm depends on whether the + * current step was a success or not. + */ + if (step_failed) { + /* + * Increment the counter indicating the number of consecutive + * failures + */ + numTSFailures++; + /* + * Print out a statement about the failure of the time step. + */ + if (m_print_flag > 1) { + print_time_fail(convFailure, m_time_step_num, time_n, delta_t_n, + delta_t_np1, time_error_factor); + } else if (m_print_flag == 1) { + print_lvl1_summary(m_time_step_num, time_n, rslt, delta_t_n, + num_newt_its, aztec_its, bktr_stps, + time_error_factor, + comment.c_str()); + } + + /* + * Change time step counters back to the previous step before + * the failed + * time step occurred. + */ + time_n -= delta_t_n; + delta_t_n = delta_t_nm1; + delta_t_nm1 = delta_t_nm2; + + /* + * Replace old solution vector and time derivative solution vector. + */ + dcopy_(&m_neq, m_y_nm1, &one, m_y_n, &one); + dcopy_(&m_neq, m_ydot_nm1, &one, m_ydot_n, &one); + /* + * Decide whether to bail on the whole loop + */ + if (numTSFailures > 35) giveUp = true; + } + + /* + * Do processing for a successful step. + */ + else { + + /* + * Decrement the number of consequative failure counter. + */ + m_failure_counter = MAX(0, m_failure_counter-1); + + /* + * Print out final results of a successfull time step. + */ + if (m_print_flag > 1) { + print_time_step2(m_time_step_num, m_order, time_n, time_error_factor, + delta_t_n, delta_t_np1); + } + else if (m_print_flag == 1) { + print_lvl1_summary(m_time_step_num, time_n, " ", delta_t_n, + num_newt_its, aztec_its, bktr_stps, time_error_factor, + comment.c_str()); + } + + /* + * Output information at the end of every successful time step, if + * requested. + * + * fill in + */ + + + } + } while (step_failed && !giveUp); + + /* + * Send back the overall result of the time step. + */ + if (step_failed) { + if (time_n == 0.0) return -1234.0; + return -time_n; } + return time_n; + } @@ -1621,16 +1592,6 @@ namespace Cantera { const double DampFactor = 4; const int NDAMP = 10; - //----------------------------------------------------------- - // Static Functions - //----------------------------------------------------------- - - static void print_line(const char *str, int n) { - for (int i = 0; i < n; i++) { - printf("%s", str); - } - printf("\n"); - } //----------------------------------------------------------- // MultiNewton methods @@ -2307,8 +2268,8 @@ namespace Cantera { } return m; } - - /***************************************************************8 + //================================================================================================ + /* * * */ @@ -2363,8 +2324,7 @@ namespace Cantera { printf("\t\t "); print_line("-", 90); mdp_safe_free((void **) &imax); } + //=============================================================================================== - - -} +} // End of namespace Cantera diff --git a/Cantera/src/numerics/BEulerInt.h b/Cantera/src/numerics/BEulerInt.h index 7c8e24782..7481558fc 100644 --- a/Cantera/src/numerics/BEulerInt.h +++ b/Cantera/src/numerics/BEulerInt.h @@ -28,6 +28,7 @@ #include "NonlinearSolver.h" #include "mdp_allo.h" + #ifndef MAX # define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) #endif @@ -68,10 +69,10 @@ namespace Cantera { class BEulerInt : public Integrator { public: - /** - * The default constructor doesn't take an argument. - */ + + //! The default constructor doesn't take an argument. BEulerInt(); + //! Destructor virtual ~BEulerInt(); virtual void setTolerances(double reltol, int n, double* abstol); virtual void setTolerances(double reltol, double abstol); diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index 7794860d1..446b4bc0f 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -66,6 +66,8 @@ namespace Cantera { // Dimension solution vector int dim1 = MAX(1, m_neq); + + m_atol.resize(dim1, 0.0); m_netProductionRatesSave.resize(dim1, 0.0); m_numEqn1.resize(dim1, 0.0); m_numEqn2.resize(dim1, 0.0); @@ -76,13 +78,14 @@ namespace Cantera { m_wtResid.resize(dim1, 0.0); m_wtSpecies.resize(dim1, 0.0); m_resid.resize(dim1, 0.0); - m_ipiv.resize(dim1, 0); - + m_ipiv.resize(dim1, 0); + m_Jac.resize(dim1, dim1, 0.0); m_JacCol.resize(dim1, 0); for (int k = 0; k < dim1; k++) { m_JacCol[k] = m_Jac.ptrColumn(k); - } + } + } //================================================================================================ // Empty destructor From 1644b1c3fe1002efd45bf7f9ec554e308bfdc4b7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 26 May 2010 02:08:04 +0000 Subject: [PATCH 156/446] Added a root finder class. This class solves single equation solvers. It's actually, vcs_rootfd1D.cpp, however, putting it up here rather than in the equil directory makes more sense. --- Cantera/src/numerics/Makefile.in | 4 +- Cantera/src/numerics/RootFind.cpp | 502 ++++++++++++++++++++++++++++++ Cantera/src/numerics/RootFind.h | 71 +++++ 3 files changed, 575 insertions(+), 2 deletions(-) create mode 100644 Cantera/src/numerics/RootFind.cpp create mode 100644 Cantera/src/numerics/RootFind.h diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index bebd03f7e..6f4253daa 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -35,14 +35,14 @@ CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ ODE_integrators.o BandMatrix.o DAE_solvers.o \ funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o \ - solveProb.o BEulerInt.o + solveProb.o BEulerInt.o RootFind.o NUMERICS_H = ArrayViewer.h DenseMatrix.h \ funcs.h ctlapack.h Func1.h FuncEval.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ - solveProb.h BEulerInt.h + solveProb.h BEulerInt.h rootFind.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp new file mode 100644 index 000000000..19f4e185c --- /dev/null +++ b/Cantera/src/numerics/RootFind.cpp @@ -0,0 +1,502 @@ +/* + * @file: RootFind.cpp root finder for 1D problems + */ +/* + * $Id: solveSP.cpp 381 2010-01-15 21:20:41Z hkmoffa $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#include "ct_defs.h" +#include "RootFind.h" + +#include "global.h" + +/* Standard include files */ + +#include +#include +#include + +#include + +using namespace std; +namespace Cantera { + + + +#ifndef MAX +# define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) /* max function */ +#endif + +#ifndef MIN +# define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) /* min function */ +#endif + +#ifndef SQUARE +# define SQUARE(x) ( (x) * (x) ) +#endif + +#ifndef DSIGN +#define DSIGN(x) (( (x) == (0.0) ) ? (0.0) : ( ((x) > 0.0) ? 1.0 : -1.0 )) +#endif + + /*****************************************************************************/ + /*****************************************************************************/ + /*****************************************************************************/ +#ifdef DEBUG_MODE + static void print_funcEval(FILE *fp, double xval, double fval, int its) + { + fprintf(fp,"\n"); + fprintf(fp,"...............................................................\n"); + fprintf(fp,".................. RootFind Function Evaluation ...............\n"); + fprintf(fp,".................. iteration = %5d ........................\n", its); + fprintf(fp,".................. value = %12.5g ......................\n", xval); + fprintf(fp,".................. funct = %12.5g ......................\n", fval); + fprintf(fp,"...............................................................\n"); + fprintf(fp,"\n"); + } +#endif + //================================================================================================ + static int smlequ(double *c, int idem, int n, double *b, int m) { + int i, j, k, l; + double R; + if (n > idem || n <= 0) { + writelogf("smlequ ERROR: badly dimensioned matrix: %d %d\n", n, idem); + return 1; + } + + /* + * Loop over the rows + * -> At the end of each loop, the only nonzero entry in the column + * will be on the diagonal. We can therfore just invert the + * diagonal at the end of the program to solve the equation system. + */ + for (i = 0; i < n; ++i) { + if (c[i + i * idem] == 0.0) { + /* + * Do a simple form of row pivoting to find a non-zero pivot + */ + for (k = i + 1; k < n; ++k) { + if (c[k + i * idem] != 0.0) goto FOUND_PIVOT; + } + writelogf("smlequ ERROR: Encountered a zero column: %d\n", i); + return 1; + FOUND_PIVOT: ; + for (j = 0; j < n; ++j) c[i + j * idem] += c[k + j * idem]; + for (j = 0; j < m; ++j) b[i + j * idem] += b[k + j * idem]; + } + + for (l = 0; l < n; ++l) { + if (l != i && c[l + i * idem] != 0.0) { + R = c[l + i * idem] / c[i + i * idem]; + c[l + i * idem] = 0.0; + for (j = i+1; j < n; ++j) c[l + j * idem] -= c[i + j * idem] * R; + for (j = 0; j < m; ++j) b[l + j * idem] -= b[i + j * idem] * R; + } + } + } + /* + * The negative in the last expression is due to the form of B upon + * input + */ + for (i = 0; i < n; ++i) { + for (j = 0; j < m; ++j) { + b[i + j * idem] = -b[i + j * idem] / c[i + i*idem]; + } + } + return 0; + } + //================================================================================================ + // Main constructor + RootFind::RootFind (ResidEval* resid) : + m_residFunc(resid), + m_funcTargetValue(0.0), + m_atol(1.0E-11), + m_rtol(1.0E-5), + m_maxstep(1000), + printLvl(9) + { + + } + //================================================================================================ + // Empty destructor + RootFind::~RootFind() { + } + //================================================================================================ + /* + * The following calculation is a Newton's method to + * get the surface fractions of the surface and bulk species by + * requiring that the + * surface species production rate = 0 and that the bulk fractions are + * proportional to their production rates. + */ + int RootFind::solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) { + + m_funcTargetValue = funcTargetValue; + static int callNum = 0; + const char *stre = "RootFind ERROR: "; + const char *strw = "RootFind WARNING: "; + int converged = 0; +#ifdef DEBUG_MODE + char fileName[80]; + FILE *fp = 0; +#endif + double x1, x2, xnew, f1, f2, fnew, slope; + int its = 0; + int posStraddle = 0; + int retn = 0; + int foundPosF = 0; + int foundNegF = 0; + int foundStraddle = 0; + double xPosF = 0.0; + double xNegF = 0.0; + double fnorm; /* A valid norm for the making the function value + * dimensionless */ + double c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad; + + callNum++; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + sprintf(fileName, "RootFind_%d.log", callNum); + fp = fopen(fileName, "w"); + fprintf(fp, " Iter TP_its xval Func_val | Reasoning\n"); + fprintf(fp, "-----------------------------------------------------" + "-------------------------------\n"); + } +#else + if (printLvl >= 3) { + writelog("WARNING: RootFind: printlvl >= 3, but debug mode not turned on\n"); + } +#endif + if (xmax <= xmin) { + writelogf("%sxmin and xmax are bad: %g %g\n", stre, xmin, xmax); + return ROOTFIND_BADINPUT; + } + x1 = *xbest; + if (x1 < xmin || x1 > xmax) { + x1 = (xmin + xmax) / 2.0; + } + + f1 = func(x1); + +#ifdef DEBUG_MODE + if (printLvl >= 3) { + print_funcEval(fp, x1, f1, its); + fprintf(fp, "%-5d %-5d %-15.5E %-15.5E\n", -2, 0, x1, f1); + } +#endif + + if (f1 == 0.0) { + *xbest = x1; + return 0; + } else if (f1 > 0.0) { + foundPosF = 1; + xPosF = x1; + } else { + foundNegF = 1; + xNegF = x1; + } + + x2 = x1 * 1.1; + if (x2 > xmax) { + x2 = x1 - (xmax - xmin) / 100.; + } + f2 = func(x2); + +#ifdef DEBUG_MODE + if (printLvl >= 3) { + print_funcEval(fp, x2, f2, its); + fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", -1, 0, x2, f2); + } +#endif + + if (m_funcTargetValue != 0.0) { + fnorm = 1.0E-6 + m_atol / m_rtol; + } else { + fnorm = 0.5*(fabs(f1) + fabs(f2)) + fabs(m_funcTargetValue); + } + + if (f2 == 0.0) + return retn; + else if (f2 > 0.0) { + if (!foundPosF) { + foundPosF = 1; + xPosF = x2; + } + } else { + if (!foundNegF) { + foundNegF = 1; + xNegF = x2; + } + } + foundStraddle = foundPosF && foundNegF; + if (foundStraddle) { + if (xPosF > xNegF) posStraddle = 1; + else posStraddle = 0 ; + } + + do { + /* + * Find an estimate of the next point to try based on + * a linear approximation. + */ + slope = (f2 - f1) / (x2 - x1); + if (slope == 0.0) { + writelogf("%s functions evals produced the same result, %g, at %g and %g\n", + strw, f2, x1, x2); + xnew = 2*x2 - x1 + 1.0E-3; + } else { + xnew = x2 - f2 / slope; + } +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlin = %-9.4g", xnew); + } +#endif + + /* + * Do a quadratic fit -> Note this algorithm seems + * to work OK. The quadratic approximation doesn't kick in until + * the end of the run, when it becomes reliable. + */ + if (its > 0) { + c[0] = 1.; c[1] = 1.; c[2] = 1.; + c[3] = x0; c[4] = x1; c[5] = x2; + c[6] = SQUARE(x0); c[7] = SQUARE(x1); c[8] = SQUARE(x2); + f[0] = - f0; f[1] = - f1; f[2] = - f2; + retn = smlequ(c, 3, 3, f, 1); + if (retn == 1) goto QUAD_BAIL; + root = f[1]* f[1] - 4.0 * f[0] * f[2]; + if (root >= 0.0) { + xn1 = (- f[1] + sqrt(root)) / (2.0 * f[2]); + xn2 = (- f[1] - sqrt(root)) / (2.0 * f[2]); + if (fabs(xn2 - x2) < fabs(xn1 - x2) && xn2 > 0.0 ) xquad = xn2; + else xquad = xn1; + theta = fabs(xquad - xnew) / fabs(xnew - x2); + theta = MIN(1.0, theta); + xnew = theta * xnew + (1.0 - theta) * xquad; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + if (theta != 1.0) { + fprintf(fp, " | xquad = %-9.4g", xnew); + } + } +#endif + } else { + /* + * Pick out situations where the convergence may be + * accelerated. + */ + if ((DSIGN(xnew - x2) == DSIGN(x2 - x1)) && + (DSIGN(x2 - x1) == DSIGN(x1 - x0)) ) { + xnew += xnew - x2; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xquada = %-9.4g", xnew); + } +#endif + } + } + } + QUAD_BAIL: ; + + + /* + * + * Put heuristic bounds on the step jump + */ + if ( (xnew > x1 && xnew < x2) || (xnew < x1 && xnew > x2)) { + /* + * + * If we are doing a jump inbetween two points, make sure + * the new trial is between 10% and 90% of the distance + * between the old points. + */ + slope = fabs(x2 - x1) / 10.; + if (fabs(xnew - x1) < slope) { + xnew = x1 + DSIGN(xnew-x1) * slope; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | x10%% = %-9.4g", xnew); + } +#endif + } + if (fabs(xnew - x2) < slope) { + xnew = x2 + DSIGN(xnew-x2) * slope; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | x10%% = %-9.4g", xnew); + } +#endif + } + } else { + /* + * If we are venturing into new ground, only allow the step jump + * to increase by 100% at each interation + */ + slope = 2.0 * fabs(x2 - x1); + if (fabs(slope) < fabs(xnew - x2)) { + xnew = x2 + DSIGN(xnew-x2) * slope; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlimitsize = %-9.4g", xnew); + } +#endif + } + } + + + if (xnew > xmax) { + xnew = x2 + (xmax - x2) / 2.0; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlimitmax = %-9.4g", xnew); + } +#endif + } + if (xnew < xmin) { + xnew = x2 + (x2 - xmin) / 2.0; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlimitmin = %-9.4g", xnew); + } +#endif + } + if (foundStraddle) { +#ifdef DEBUG_MODE + slope = xnew; +#endif + if (posStraddle) { + if (f2 > 0.0) { + if (xnew > x2) xnew = (xNegF + x2)/2; + if (xnew < xNegF) xnew = (xNegF + x2)/2; + } else { + if (xnew < x2) xnew = (xPosF + x2)/2; + if (xnew > xPosF) xnew = (xPosF + x2)/2; + } + } else { + if (f2 > 0.0) { + if (xnew < x2) xnew = (xNegF + x2)/2; + if (xnew > xNegF) xnew = (xNegF + x2)/2; + } else { + if (xnew > x2) xnew = (xPosF + x2)/2; + if (xnew < xPosF) xnew = (xPosF + x2)/2; + } + } +#ifdef DEBUG_MODE + if (printLvl >= 3) { + if (slope != xnew) { + fprintf(fp, " | xstraddle = %-9.4g", xnew); + } + } +#endif + } + + fnew = func(xnew); +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp,"\n"); + print_funcEval(fp, xnew, fnew, its); + fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", its, 0, xnew, fnew); + } +#endif + + if (foundStraddle) { + if (posStraddle) { + if (fnew > 0.0) { + if (xnew < xPosF) xPosF = xnew; + } else { + if (xnew > xNegF) xNegF = xnew; + } + } else { + if (fnew > 0.0) { + if (xnew > xPosF) xPosF = xnew; + } else { + if (xnew < xNegF) xNegF = xnew; + } + } + } + + if (! foundStraddle) { + if (fnew > 0.0) { + if (!foundPosF) { + foundPosF = 1; + xPosF = xnew; + foundStraddle = 1; + if (xPosF > xNegF) posStraddle = 1; + else posStraddle = 0 ; + } + } else { + if (!foundNegF) { + foundNegF = 1; + xNegF = xnew; + foundStraddle = 1; + if (xPosF > xNegF) posStraddle = 1; + else posStraddle = 0; + } + } + } + + x0 = x1; + f0 = f1; + x1 = x2; + f1 = f2; + x2 = xnew; + f2 = fnew; + if (fabs(fnew / fnorm) < m_rtol) { + converged = 1; + } + its++; + } while (! converged && its < itmax); + if (converged) { + if (printLvl >= 1) { + writelogf("RootFind success: convergence achieved\n"); + } +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | RootFind success in %d its, fnorm = %g\n", its, fnorm); + } +#endif + } else { + retn = ROOTFIND_FAILEDCONVERGENCE; + if (printLvl >= 1) { + writelogf("RootFind ERROR: maximum iterations exceeded without convergence\n"); + } +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, "\nRootFind failure in %d its\n", its); + } +#endif + } + *xbest = x2; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fclose(fp); + } +#endif + return retn; + } + //================================================================================================ + double RootFind::func(double x) { + double r; + m_residFunc->evalSS(0.0, &x, &r); + return (r - m_funcTargetValue); + } + //================================================================================================ + void RootFind::setTol(double rtol, double atol) + { + m_atol = atol; + m_rtol = rtol; + } + //================================================================================================ + void RootFind::setPrintLvl(int printlvl) + { + printLvl = printlvl; + } + //================================================================================================ +} diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h new file mode 100644 index 000000000..8fec96ce4 --- /dev/null +++ b/Cantera/src/numerics/RootFind.h @@ -0,0 +1,71 @@ +/** + * @file RootFind.h + * Header file for implicit nonlinear solver of a one dimensional function + * (see \ref numerics and class \link Cantera::RootFind RootFind\endlink). + */ +/* + * $Id: solveSP.h 381 2010-01-15 21:20:41Z hkmoffa $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#ifndef ROOTFIND_H +#define ROOTFIND_H +/** + * @defgroup solverGroup Solvers for Equation Systems + */ + +#include +#include "ResidEval.h" + +namespace Cantera { + +#define ROOTFIND_SUCCESS 0 +#define ROOTFIND_FAILEDCONVERGENCE -1 +#define ROOTFIND_BADINPUT -2 + + class RootFind { + + public: + + //! Constructor for the object + /*! + */ + RootFind(ResidEval* resid); + + //! Destructor. Deletes the integrator. + ~RootFind(); + + private: + + //! Unimplemented private copy constructor + RootFind(const RootFind &right); + + //! Unimplemented private assignment operator + RootFind& operator=(const RootFind &right); + + public: + + int solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) ; + + double func(double x) ; + + void setTol(double rtol, double atol); + + void setPrintLvl(int printLvl) ; + + public: + ResidEval *m_residFunc; + double m_funcTargetValue; + double m_atol; + double m_rtol; + double m_maxstep; + int printLvl; + + }; +} +#endif From 9bba4579e8ca683e96ef2ad7b254e9e33e42009e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 26 May 2010 18:13:34 +0000 Subject: [PATCH 157/446] Added two new functions productOrder getActivityConcentrations --- Cantera/src/kinetics/InterfaceKinetics.cpp | 11 ++++++++ Cantera/src/kinetics/InterfaceKinetics.h | 7 +++++ Cantera/src/kinetics/Kinetics.h | 30 ++++++++++++++++++++-- Cantera/src/kinetics/ReactionStoichMgr.h | 22 +++++++--------- 4 files changed, 55 insertions(+), 15 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index fb910a367..2ed047f16 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -296,6 +296,17 @@ namespace Cantera { } + // Get the vector of activity concentrations used in the kinetics object + /* + * @param conc (output) Vector of activity concentrations. Length is + * equal to the number of species in the kinetics object + */ + void InterfaceKinetics::getActivityConcentrations(doublereal * const conc) { + _update_rates_C(); + copy(m_conc.begin(), m_conc.end(), conc); + } + + /** * Update the equilibrium constants in molar units for all * reversible reactions. Irreversible reactions have their diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 05e4bc73f..0bb06030c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -324,6 +324,13 @@ namespace Cantera { return m_index[i].first; } + //! Get the vector of activity concentrations used in the kinetics object + /*! + * @param conc (output) Vector of activity concentrations. Length is + * equal to the number of species in the kinetics object + */ + virtual void getActivityConcentrations(doublereal * const conc); + //! Return the charge transfer rxn Beta parameter for the ith reaction /*! * Returns the beta parameter for a charge transfer reaction. This diff --git a/Cantera/src/kinetics/Kinetics.h b/Cantera/src/kinetics/Kinetics.h index 33b63263b..f99b0a186 100644 --- a/Cantera/src/kinetics/Kinetics.h +++ b/Cantera/src/kinetics/Kinetics.h @@ -654,8 +654,10 @@ namespace Cantera { return -1.0; } - /** - * reactant Order of species k in reaction i. + //! Reactant order of species k in reaction i. + /*! + * This is the nominal order of the activity concentration in + * determining the forward rate of progress of the reaction * * @param k kinetic species index * @param i reaction index @@ -665,6 +667,30 @@ namespace Cantera { return -1.0; } + //! product Order of species k in reaction i. + /*! + * This is the nominal order of the activity concentration of species k in + * determining the reverse rate of progress of the reaction i + * + * For irreversible reactions, this will all be zero. + * + * @param k kinetic species index + * @param i reaction index + */ + virtual doublereal productOrder(int k, int i) const { + err("productOrder"); + return -1.0; + } + + //! Get the vector of activity concentrations used in the kinetics object + /*! + * @param conc (output) Vector of activity concentrations. Length is + * equal to the number of species in the kinetics object + */ + virtual void getActivityConcentrations(doublereal * const conc) { + err("getActivityConcentrations"); + } + /** * Returns a read-only reference to the vector of reactant * index numbers for reaction i. diff --git a/Cantera/src/kinetics/ReactionStoichMgr.h b/Cantera/src/kinetics/ReactionStoichMgr.h index eba12e5d5..1ccd6b588 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.h +++ b/Cantera/src/kinetics/ReactionStoichMgr.h @@ -26,8 +26,8 @@ namespace Cantera { * user programs. * * Class ReactionStoichMgr handles the calculation of quantities involving - * the stoichiometry of a set of reactions. The reactions must have integer - * stoichiometric coefficients. Specifically, its methods compute + * the stoichiometry of a set of reactions. The reactions may have integer + * or non-integer stoichiometric coefficients. Specifically, its methods compute * - species creation rates * - species destruction rates * - species net production rates @@ -97,7 +97,7 @@ namespace Cantera { * @param reversible true if the reaction is reversible, false otherwise */ virtual void add(int rxn, const vector_int& reactants, const vector_int& products, - bool reversible); + bool reversible); /** * Add a reaction with specified, possibly non-integral, reaction orders. @@ -112,11 +112,7 @@ namespace Cantera { * species with index in the corresponding location in 'reactants.' * */ - // void add(int rxn, const vector_int& reactants, const vector_int& products, - // bool reversible, const vector_fp& fwdOrder); - - - virtual void add(int rxn, const ReactionData& r); + virtual void add(int rxn, const ReactionData& r); /** * Species creation rates. @@ -144,7 +140,7 @@ namespace Cantera { * Note that the stoichiometric coefficient matrices are very sparse, integer * matrices. */ - virtual void getDestructionRates(int nSpecies, + virtual void getDestructionRates(int nSpecies, const doublereal* fwdRatesOfProgress, const doublereal* revRatesOfProgress, doublereal* destructionRates); @@ -164,7 +160,7 @@ namespace Cantera { * W = (N_r - N_p) Q_{\rm net}, * \f] */ - virtual void getNetProductionRates(int nsp, const doublereal* ropnet, doublereal* w); + virtual void getNetProductionRates(int nsp, const doublereal* ropnet, doublereal* w); @@ -205,7 +201,7 @@ namespace Cantera { * calculating reveerse rate coefficients from thermochemistry * for reversible reactions. */ - virtual void getRevReactionDelta(int nr, const doublereal* g, doublereal* dg); + virtual void getRevReactionDelta(int nr, const doublereal* g, doublereal* dg); /** @@ -217,7 +213,7 @@ namespace Cantera { * * Here \f$ o_{k,i} \f$ is the reaction order of species k in reaction i. */ - virtual void multiplyReactants(const doublereal* C, doublereal* R); + virtual void multiplyReactants(const doublereal* C, doublereal* R); /** @@ -229,7 +225,7 @@ namespace Cantera { * Here \f$ \nu^{(p)}_{k,i} \f$ is the product stoichiometric coefficient * of species k in reaction i. */ - virtual void multiplyRevProducts(const doublereal* c, doublereal* r); + virtual void multiplyRevProducts(const doublereal* c, doublereal* r); virtual void write(std::string filename); From 2820296ac57f2d3c66050d7f27ac5b16e265c93b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 26 May 2010 18:54:49 +0000 Subject: [PATCH 158/446] Fixed a typo in the makefile --- Cantera/src/numerics/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index 6f4253daa..ce443314b 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -42,7 +42,7 @@ NUMERICS_H = ArrayViewer.h DenseMatrix.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ - solveProb.h BEulerInt.h rootFind.h + solveProb.h BEulerInt.h RootFind.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h From 42e2dd0c0b57b29c7d1cb2bed4d3de4c7acd59bf Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Wed, 26 May 2010 23:15:29 +0000 Subject: [PATCH 159/446] added enthalpy_mole(), entropy_mole().... capabilities to MargulesVPSSTP --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 2 + Cantera/src/thermo/GibbsExcessVPSSTP.h | 5 ++ Cantera/src/thermo/MargulesVPSSTP.cpp | 87 ++++++++++++++++++++- Cantera/src/thermo/MargulesVPSSTP.h | 48 +++++++++++- Cantera/src/thermo/SpeciesThermoFactory.cpp | 2 +- Cantera/src/thermo/ThermoPhase.h | 4 +- 6 files changed, 143 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index d0b14221f..fe665941a 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -66,6 +66,7 @@ namespace Cantera { moleFractions_ = b.moleFractions_; lnActCoeff_Scaled_ = b.lnActCoeff_Scaled_; dlnActCoeffdT_Scaled_ = b.dlnActCoeffdT_Scaled_; + d2lnActCoeffdT2_Scaled_ = b.d2lnActCoeffdT2_Scaled_; dlnActCoeffdlnX_Scaled_ = b.dlnActCoeffdlnX_Scaled_; dlnActCoeffdlnN_Scaled_ = b.dlnActCoeffdlnN_Scaled_; m_pp = b.m_pp; @@ -324,6 +325,7 @@ namespace Cantera { moleFractions_.resize(m_kk); lnActCoeff_Scaled_.resize(m_kk); dlnActCoeffdT_Scaled_.resize(m_kk); + d2lnActCoeffdT2_Scaled_.resize(m_kk); dlnActCoeffdlnX_Scaled_.resize(m_kk); dlnActCoeffdlnN_Scaled_.resize(m_kk); m_pp.resize(m_kk); diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index a100e5f45..702e1f3b5 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -578,6 +578,11 @@ namespace Cantera { //! log of theactivity coefficients of the species mutable std::vector dlnActCoeffdT_Scaled_; + //! Storage for the current derivative values of the + //! gradients with respect to temperature of the + //! log of theactivity coefficients of the species + mutable std::vector d2lnActCoeffdT2_Scaled_; + //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the //! log of theactivity coefficients of the species diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 039f70460..216e6a273 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -408,6 +408,43 @@ namespace Cantera { } } + /// Molar enthalpy. Units: J/kmol. + doublereal MargulesVPSSTP::enthalpy_mole() const { + int kk = nSpecies(); + double hbar[kk], h = 0; + getPartialMolarEnthalpies(hbar); + for (int i = 0; i < kk; i++){ + h += moleFractions_[i]*hbar[i]; + } + return h; + } + + /// Molar entropy. Units: J/kmol. + doublereal MargulesVPSSTP::entropy_mole() const { + int kk = nSpecies(); + double sbar[kk], s = 0; + getPartialMolarEntropies(sbar); + for (int i = 0; i < kk; i++){ + s += moleFractions_[i]*sbar[i]; + } + return s; + } + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + doublereal MargulesVPSSTP::cp_mole() const { + int kk = nSpecies(); + double cpbar[kk], cp = 0; + getPartialMolarCp(cpbar); + for (int i = 0; i < kk; i++){ + cp += moleFractions_[i]*cpbar[i]; + } + return cp; + } + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + doublereal MargulesVPSSTP::cv_mole() const { + return cp_mole() - GasConstant; + } // Returns an array of partial molar enthalpies for the species // in the mixture. @@ -448,6 +485,44 @@ namespace Cantera { } } + // Returns an array of partial molar heat capacities for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MargulesVPSSTP::getPartialMolarCp(doublereal* cpbar) const { + /* + * Get the nondimensional standard state entropies + */ + getCp_R(cpbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + // Returns an array of partial molar entropies for the species // in the mixture. /* @@ -733,6 +808,7 @@ namespace Cantera { double RTT = GasConstant*T*T; fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); + fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); for ( iK = 0; iK < m_kk; iK++ ){ @@ -755,7 +831,9 @@ namespace Cantera { g0 = -m_HE_b_ij[i] / RTT; g1 = -m_HE_c_ij[i] / RTT; - dlnActCoeffdT_Scaled_[iK] += (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + double temp = (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + dlnActCoeffdT_Scaled_[iK] += temp; + d2lnActCoeffdT2_Scaled_[iK] -= 2*temp/T; } } } @@ -793,6 +871,13 @@ namespace Cantera { } } + void MargulesVPSSTP::getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k]; + } + } + // calculate the change of the log of the activity coefficients wrt change in state: dT, dX /* * This function will be called to calculate gradient of the diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 4e7df72eb..53a57904a 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -525,7 +525,18 @@ namespace Cantera { */ virtual void getChemPotentials(doublereal* mu) const; - + /// Molar enthalpy. Units: J/kmol. + virtual doublereal enthalpy_mole() const; + + /// Molar entropy. Units: J/kmol. + virtual doublereal entropy_mole() const; + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + virtual doublereal cp_mole() const; + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + virtual doublereal cv_mole() const; + //! Returns an array of partial molar enthalpies for the species //! in the mixture. /*! @@ -564,6 +575,28 @@ namespace Cantera { */ virtual void getPartialMolarEntropies(doublereal* sbar) const; + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????????? + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * ??????????????? + * \f] + * + * @param cpbar Vector of returned partial molar heat capacities + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + //! Return an array of partial molar volumes for the //! species in the mixture. Units: m^3/kmol. @@ -604,6 +637,19 @@ namespace Cantera { */ virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeffdT) const; + //! Get the array of temperature second derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param d2lnActCoeffdT2 Output vector of temperature 2nd derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const; + //! Get the array of temperature derivatives of the log activity coefficients /*! * This function is a virtual class, but it first appears in GibbsExcessVPSSTP diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index 816e26f07..ce0d21007 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -829,7 +829,7 @@ namespace Cantera { f0->name() + " and " + f1->name()); } } - else if (nc >= 2) { + else if (nc > 2) { const XML_Node* f0 = tp[0]; if (f0->name() == "NASA9") { installNasa9ThermoFromXML(speciesNode["name"], spthermo, k, tp); diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index c52e74e75..69b517e9c 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -859,7 +859,7 @@ namespace Cantera { /// Molar internal energy. Units: J/kmol. virtual doublereal intEnergy_mole() const { - return err("intEnergy_mole"); + return enthalpy_mole() - pressure()* molarVolume(); } /// Molar entropy. Units: J/kmol/K. @@ -869,7 +869,7 @@ namespace Cantera { /// Molar Gibbs function. Units: J/kmol. virtual doublereal gibbs_mole() const { - return err("gibbs_mole"); + return enthalpy_mole() - temperature()*entropy_mole(); } /// Molar heat capacity at constant pressure. Units: J/kmol/K. From 60f5f31c3b938986fac3921fa3f03dd4a0f95df5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Jun 2010 02:42:59 +0000 Subject: [PATCH 160/446] Added logic to handle constant current simulations in electrodes, where the function may be level over various regions of x. --- Cantera/src/numerics/RootFind.cpp | 252 +++++++++++++++++++++++------- Cantera/src/numerics/RootFind.h | 11 +- 2 files changed, 202 insertions(+), 61 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index 19f4e185c..d5002be99 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -119,7 +119,10 @@ namespace Cantera { m_atol(1.0E-11), m_rtol(1.0E-5), m_maxstep(1000), - printLvl(9) + printLvl(0), + DeltaXnorm_(0.01), + FuncIsGenerallyIncreasing_(false), + FuncIsGenerallyDecreasing_(false) { } @@ -129,15 +132,24 @@ namespace Cantera { } //================================================================================================ /* - * The following calculation is a Newton's method to - * get the surface fractions of the surface and bulk species by - * requiring that the - * surface species production rate = 0 and that the bulk fractions are - * proportional to their production rates. + * The following calculation is a line search method to find the root of a function + * + * + * xbest Returns the x that satisfies the function + * On input, xbest should contain the best estimate + * + * return: + * 0 Found function */ int RootFind::solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) { + /* + * We store the function target and then actually calculate a modified functional + * + * func = eval(x1) - m_funcTargetValue = 0 + */ m_funcTargetValue = funcTargetValue; + static int callNum = 0; const char *stre = "RootFind ERROR: "; const char *strw = "RootFind WARNING: "; @@ -155,9 +167,9 @@ namespace Cantera { int foundStraddle = 0; double xPosF = 0.0; double xNegF = 0.0; - double fnorm; /* A valid norm for the making the function value - * dimensionless */ - double c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad; + double fnorm; /* A valid norm for the making the function value dimensionless */ + double c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; + double CR0, CR1, CR2, CRnew, CRdenom; callNum++; #ifdef DEBUG_MODE @@ -177,6 +189,10 @@ namespace Cantera { writelogf("%sxmin and xmax are bad: %g %g\n", stre, xmin, xmax); return ROOTFIND_BADINPUT; } + /* + * Find the first function value f1 = func(x1), by using the value entered into xbest. + * Process it + */ x1 = *xbest; if (x1 < xmin || x1 > xmax) { x1 = (xmin + xmax) / 2.0; @@ -202,12 +218,16 @@ namespace Cantera { xNegF = x1; } - x2 = x1 * 1.1; + if (x1 == 0.0) { + x2 = 0.00001 * (xmax - xmin); + } else { + x2 = x1 * 1.01; + } if (x2 > xmax) { x2 = x1 - (xmax - xmin) / 100.; } - f2 = func(x2); + f2 = func(x2); #ifdef DEBUG_MODE if (printLvl >= 3) { print_funcEval(fp, x2, f2, its); @@ -221,9 +241,10 @@ namespace Cantera { fnorm = 0.5*(fabs(f1) + fabs(f2)) + fabs(m_funcTargetValue); } - if (f2 == 0.0) + if (f2 == 0.0) { + *xbest = x2; return retn; - else if (f2 > 0.0) { + } else if (f2 > 0.0) { if (!foundPosF) { foundPosF = 1; xPosF = x2; @@ -234,37 +255,106 @@ namespace Cantera { xNegF = x2; } } + /* + * See if we have already achieved a straddle + */ foundStraddle = foundPosF && foundNegF; if (foundStraddle) { if (xPosF > xNegF) posStraddle = 1; else posStraddle = 0 ; } - + bool doQuad = false; + bool useNextStrat = false; + bool slopePointingToHigher = true; + // --------------------------------------------------------------------------------------------- + // MAIN LOOP + // --------------------------------------------------------------------------------------------- do { /* - * Find an estimate of the next point to try based on - * a linear approximation. + * Find an estimate of the next point, xnew, to try based on + * a linear approximation from the last two points. */ slope = (f2 - f1) / (x2 - x1); - if (slope == 0.0) { - writelogf("%s functions evals produced the same result, %g, at %g and %g\n", - strw, f2, x1, x2); - xnew = 2*x2 - x1 + 1.0E-3; + if (fabs(slope) <= 1.0E-100) { + if (printLvl >= 2) { + writelogf("%s functions evals produced the same result, %g, at %g and %g\n", + strw, f2, x1, x2); + } + xnew = x2 + DeltaXnorm_; + slopePointingToHigher = true; } else { + useNextStrat = false; xnew = x2 - f2 / slope; - } + if (xnew > x2) { + slopePointingToHigher = true; + } else { + slopePointingToHigher = false; + } + } #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | xlin = %-9.4g", xnew); + fprintf(fp, " | xlin = %-11.5E", xnew); } #endif + /* + * If the suggested step size is too big, throw out step + */ + if (!foundStraddle) { + if (fabs(xnew - x2) > 3.0 * DeltaXnorm_) { + useNextStrat = true; + } + } + if (useNextStrat) { + if (f2 < 0.0) { + if (FuncIsGenerallyIncreasing_) { + if (slopePointingToHigher) { + xnew = MIN(x2 + 3.0*DeltaXnorm_, xnew); + } else { + xnew = x2 + DeltaXnorm_; + } + } else if (FuncIsGenerallyDecreasing_) { + if ( !slopePointingToHigher) { + xnew = MAX(x2 - 3.0*DeltaXnorm_, xnew); + } else { + xnew = x2 - DeltaXnorm_; + } + } else { + if (slopePointingToHigher) { + xnew = x2 + DeltaXnorm_; + } else { + xnew = x2 - DeltaXnorm_; + } + } + } else { + if (FuncIsGenerallyDecreasing_) { + if (!slopePointingToHigher) { + xnew = MAX(x2 + 3.0*DeltaXnorm_, xnew); + } else { + xnew = x2 + DeltaXnorm_; + } + } else if (FuncIsGenerallyIncreasing_) { + if (! slopePointingToHigher) { + xnew = MIN(x2 - 3.0*DeltaXnorm_, xnew); + } else { + xnew = x2 - DeltaXnorm_; + } + } else { + if (slopePointingToHigher) { + xnew = x2 + DeltaXnorm_; + } else { + xnew = x2 - DeltaXnorm_; + } + } + } + } + /* * Do a quadratic fit -> Note this algorithm seems * to work OK. The quadratic approximation doesn't kick in until * the end of the run, when it becomes reliable. */ - if (its > 0) { + if (its > 0 && doQuad) { c[0] = 1.; c[1] = 1.; c[2] = 1.; c[3] = x0; c[4] = x1; c[5] = x2; c[6] = SQUARE(x0); c[7] = SQUARE(x1); c[8] = SQUARE(x2); @@ -283,7 +373,7 @@ namespace Cantera { #ifdef DEBUG_MODE if (printLvl >= 3) { if (theta != 1.0) { - fprintf(fp, " | xquad = %-9.4g", xnew); + fprintf(fp, " | xquad = %-11.5E", xnew); } } #endif @@ -297,7 +387,7 @@ namespace Cantera { xnew += xnew - x2; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | xquada = %-9.4g", xnew); + fprintf(fp, " | xquada = %-11.5E", xnew); } #endif } @@ -305,57 +395,58 @@ namespace Cantera { } QUAD_BAIL: ; - - /* + /* + * OK, we have an estimate xnew. + * * * Put heuristic bounds on the step jump */ - if ( (xnew > x1 && xnew < x2) || (xnew < x1 && xnew > x2)) { + if ((xnew > x1 && xnew < x2) || (xnew < x1 && xnew > x2)) { /* - * - * If we are doing a jump inbetween two points, make sure - * the new trial is between 10% and 90% of the distance - * between the old points. + * If we are doing a jump in between the two previous points, make sure + * the new trial is no closer that 10% of the distances between x2-x1 to + * any of the original points. */ - slope = fabs(x2 - x1) / 10.; - if (fabs(xnew - x1) < slope) { - xnew = x1 + DSIGN(xnew-x1) * slope; + xDelMin = fabs(x2 - x1) / 10.; + if (fabs(xnew - x1) < xDelMin) { + xnew = x1 + DSIGN(xnew-x1) * xDelMin; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | x10%% = %-9.4g", xnew); + fprintf(fp, " | x10%% = %-11.5E", xnew); } #endif } - if (fabs(xnew - x2) < slope) { - xnew = x2 + DSIGN(xnew-x2) * slope; + if (fabs(xnew - x2) < 0.1 * xDelMin) { + xnew = x2 + DSIGN(xnew-x2) * 0.1 * xDelMin; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | x10%% = %-9.4g", xnew); + fprintf(fp, " | x10%% = %-11.5E", xnew); } #endif } } else { /* * If we are venturing into new ground, only allow the step jump - * to increase by 100% at each interation + * to increase by 50% at each interation */ - slope = 2.0 * fabs(x2 - x1); - if (fabs(slope) < fabs(xnew - x2)) { - xnew = x2 + DSIGN(xnew-x2) * slope; + double xDelMax = 1.5 * fabs(x2 - x1); + if (fabs(xDelMax) < fabs(xnew - x2)) { + xnew = x2 + DSIGN(xnew-x2) * xDelMax; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | xlimitsize = %-9.4g", xnew); + fprintf(fp, " | xlimitsize = %-11.5E", xnew); } #endif } } - - + /* + * Guard against going above xmax or below xmin + */ if (xnew > xmax) { xnew = x2 + (xmax - x2) / 2.0; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | xlimitmax = %-9.4g", xnew); + fprintf(fp, " | xlimitmax = %-11.5E", xnew); } #endif } @@ -363,41 +454,60 @@ namespace Cantera { xnew = x2 + (x2 - xmin) / 2.0; #ifdef DEBUG_MODE if (printLvl >= 3) { - fprintf(fp, " | xlimitmin = %-9.4g", xnew); + fprintf(fp, " | xlimitmin = %-11.5E", xnew); } #endif } + if (foundStraddle) { #ifdef DEBUG_MODE slope = xnew; #endif if (posStraddle) { if (f2 > 0.0) { - if (xnew > x2) xnew = (xNegF + x2)/2; - if (xnew < xNegF) xnew = (xNegF + x2)/2; + if (xnew > x2) { + xnew = (xNegF + x2)/2; + } + if (xnew < xNegF) { + xnew = (xNegF + x2)/2; + } } else { - if (xnew < x2) xnew = (xPosF + x2)/2; - if (xnew > xPosF) xnew = (xPosF + x2)/2; + if (xnew < x2) { + xnew = (xPosF + x2)/2; + } + if (xnew > xPosF) { + xnew = (xPosF + x2)/2; + } } } else { if (f2 > 0.0) { - if (xnew < x2) xnew = (xNegF + x2)/2; - if (xnew > xNegF) xnew = (xNegF + x2)/2; + if (xnew < x2) { + xnew = (xNegF + x2)/2; + } + if (xnew > xNegF) { + xnew = (xNegF + x2)/2; + } } else { - if (xnew > x2) xnew = (xPosF + x2)/2; - if (xnew < xPosF) xnew = (xPosF + x2)/2; + if (xnew > x2) { + xnew = (xPosF + x2)/2; + } + if (xnew < xPosF) { + xnew = (xPosF + x2)/2; + } } } #ifdef DEBUG_MODE if (printLvl >= 3) { if (slope != xnew) { - fprintf(fp, " | xstraddle = %-9.4g", xnew); + fprintf(fp, " | xstraddle = %-11.5E", xnew); } } #endif } fnew = func(xnew); + CRdenom = MAX(fabs(fnew), MAX(fabs(f2), MAX(fabs(f1), fnorm))); + CRnew = sqrt(fabs(fnew) / CRdenom); #ifdef DEBUG_MODE if (printLvl >= 3) { fprintf(fp,"\n"); @@ -429,7 +539,7 @@ namespace Cantera { xPosF = xnew; foundStraddle = 1; if (xPosF > xNegF) posStraddle = 1; - else posStraddle = 0 ; + else posStraddle = 0; } } else { if (!foundNegF) { @@ -437,17 +547,20 @@ namespace Cantera { xNegF = xnew; foundStraddle = 1; if (xPosF > xNegF) posStraddle = 1; - else posStraddle = 0; + else posStraddle = 0; } } } x0 = x1; f0 = f1; + CR0 = CR1; x1 = x2; f1 = f2; + CR1 = CR2; x2 = xnew; f2 = fnew; + CR2 = CRnew; if (fabs(fnew / fnorm) < m_rtol) { converged = 1; } @@ -499,4 +612,25 @@ namespace Cantera { printLvl = printlvl; } //================================================================================================ + void RootFind::setFuncIsGenerallyIncreasing(bool value) + { + if (value) { + FuncIsGenerallyDecreasing_ = false; + } + FuncIsGenerallyIncreasing_ = value; + } + //================================================================================================ + void RootFind::setFuncIsGenerallyDecreasing(bool value) + { + if (value) { + FuncIsGenerallyIncreasing_ = false; + } + FuncIsGenerallyDecreasing_ = value; + } + //================================================================================================ + void RootFind::setDeltaX(double deltaXNorm) + { + DeltaXnorm_ = deltaXNorm; + } + //================================================================================================ } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 8fec96ce4..69dbd187d 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -52,11 +52,14 @@ namespace Cantera { int solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) ; - double func(double x) ; + double func(double x); void setTol(double rtol, double atol); - void setPrintLvl(int printLvl) ; + void setPrintLvl(int printLvl); + void setFuncIsGenerallyIncreasing(bool value); + void setFuncIsGenerallyDecreasing(bool value); + void setDeltaX(double deltaXNorm); public: ResidEval *m_residFunc; @@ -64,7 +67,11 @@ namespace Cantera { double m_atol; double m_rtol; double m_maxstep; + protected: int printLvl; + double DeltaXnorm_; + bool FuncIsGenerallyIncreasing_; + bool FuncIsGenerallyDecreasing_; }; } From e911aa1309e9bafd8130ff430d5ad5a31e50d73a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 6 Jun 2010 02:57:02 +0000 Subject: [PATCH 161/446] Implementing the expanded species name idea, where we can guarantee a unique name, when dealing with a bunch of phases. Working on the LatticePhase --- Cantera/src/thermo/Constituents.h | 7 ++- Cantera/src/thermo/LatticePhase.cpp | 93 ++++++++++++++++++++++++++++- Cantera/src/thermo/LatticePhase.h | 41 +++++++++++++ Cantera/src/thermo/Phase.cpp | 43 +++++++++++-- Cantera/src/thermo/Phase.h | 74 +++++++++++++++++++++++ Cantera/src/thermo/WaterSSTP.cpp | 6 +- 6 files changed, 253 insertions(+), 11 deletions(-) diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h index 22028b964..be134749f 100644 --- a/Cantera/src/thermo/Constituents.h +++ b/Cantera/src/thermo/Constituents.h @@ -280,12 +280,13 @@ namespace Cantera { doublereal charge = 0.0, doublereal size = 1.0); - //! Returns the index of a species named 'name' within the ThermoPhase + //! Returns the index of a species named 'name' within the Constituents object /*! - * The first species added will have index 0, and the last one index nSpecies() - 1. + * The first species in the phase will have an index 0, and the last one in the + * phase will have an index of nSpecies() - 1. * * @param name String name of the species - * @return Returns the index of the species. If the name is not found + * @return Returns the index of the species. If the name is not found, * the value of -1 is returned. */ int speciesIndex(std::string name) const; diff --git a/Cantera/src/thermo/LatticePhase.cpp b/Cantera/src/thermo/LatticePhase.cpp index 00942edfb..1a93923c4 100644 --- a/Cantera/src/thermo/LatticePhase.cpp +++ b/Cantera/src/thermo/LatticePhase.cpp @@ -23,8 +23,10 @@ #include "mix_defs.h" #include "LatticePhase.h" #include "SpeciesThermo.h" +#include "ThermoFactory.h" #include +#include namespace Cantera { @@ -70,7 +72,27 @@ namespace Cantera { // Destructor LatticePhase::~LatticePhase() { } + + + // Full constructor for a lattice phase + /* + * @param inputFile String name of the input file + * @param id string id of the phase name + */ + LatticePhase::LatticePhase(std::string inputFile, std::string id) { + constructPhaseFile(inputFile, id); + } + // Full constructor for a water phase + /* + * @param phaseRef XML node referencing the lattice phase. + * @param id string id of the phase name + */ + LatticePhase::LatticePhase(XML_Node& phaseRef, std::string id) { + constructPhaseXML(phaseRef, id); + } + + // Duplication function /* * This virtual function is used to create a duplicate of the @@ -84,6 +106,75 @@ namespace Cantera { return (ThermoPhase *) igp; } + /* + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void LatticePhase::constructPhaseXML(XML_Node& phaseNode, std::string idTarget) { + std::string idattrib = phaseNode.id(); + if (idTarget != idattrib) { + throw CanteraError("LatticePhase::constructPhaseXML","ids don't match"); + } + + /* + * Call the Cantera importPhase() function. This will import + * all of the species into the phase. This will also handle + * all of the solvent and solute standard states. + */ + bool m_ok = importPhase(phaseNode, this); + if (!m_ok) { + throw CanteraError("LatticePhase::constructPhaseXML","importPhase failed "); + } + } + + /* + * constructPhaseFile + * + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void LatticePhase::constructPhaseFile(std::string inputFile, std::string id) { + + if (inputFile.size() == 0) { + throw CanteraError("LatticePhase::constructPhaseFile", + "input file is null"); + } + std::string path = findInputFile(inputFile); + std::ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("LatticePhase::constructPhaseFile","could not open " + +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + XML_Node &phaseNode_XML = xml(); + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("LatticePhase::constructPhaseFile", + "ERROR: Can not find phase named " + + id + " in file named " + inputFile); + } + fxml_phase->copy(&phaseNode_XML); + constructPhaseXML(*fxml_phase, id); + delete fxml; + } + doublereal LatticePhase:: enthalpy_mole() const { @@ -247,7 +338,7 @@ namespace Cantera { } void LatticePhase::setParametersFromXML(const XML_Node& eosdata) { - eosdata._require("model","Lattice"); + eosdata._require("model", "Lattice"); m_molar_density = getFloat(eosdata, "site_density", "toSI"); m_vacancy = getChildValue(eosdata, "vacancy_species"); } diff --git a/Cantera/src/thermo/LatticePhase.h b/Cantera/src/thermo/LatticePhase.h index 111848b09..093caece3 100644 --- a/Cantera/src/thermo/LatticePhase.h +++ b/Cantera/src/thermo/LatticePhase.h @@ -274,6 +274,20 @@ namespace Cantera { */ LatticePhase& operator=(const LatticePhase& right); + //! Full constructor for a lattice phase + /*! + * @param inputFile String name of the input file + * @param id string id of the phase name + */ + LatticePhase(std::string inputFile, std::string id = ""); + + //! Full constructor for a water phase + /*! + * @param phaseRef XML node referencing the lattice phase. + * @param id string id of the phase name + */ + LatticePhase(XML_Node& phaseRef, std::string id = ""); + //! Destructor virtual ~LatticePhase(); @@ -287,6 +301,31 @@ namespace Cantera { */ ThermoPhase *duplMyselfAsThermoPhase() const; + /* + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseXML(XML_Node& phaseNode, std::string idTarget); + + /* + * constructPhaseFile + * + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseFile(std::string inputFile, std::string id); //! Equation of state flag. Returns the value cLattice virtual int eosType() const { return cLattice; } @@ -814,6 +853,8 @@ namespace Cantera { //! Molar density of the lattice solid /*! + * Currently, this does not change as a function of T, P or composition + * * units are kmol m-3 */ doublereal m_molar_density; diff --git a/Cantera/src/thermo/Phase.cpp b/Cantera/src/thermo/Phase.cpp index 423aa8c24..8367ceb9d 100644 --- a/Cantera/src/thermo/Phase.cpp +++ b/Cantera/src/thermo/Phase.cpp @@ -137,6 +137,41 @@ namespace Cantera { m_index = m; } + // Returns the index of a species named 'name' within the Phase object + /* + * The first species in the phase will have an index 0, and the last one in the + * phase will have an index of nSpecies() - 1. + * + * + * A species name may be referred to via three methods: + * + * - "speciesName" + * - "PhaseId:speciesName" + * - "phaseName:speciesName" + * . + * + * The first two methods of naming may not yield a unique species within + * complicated assemblies of Cantera Phases. + * + * @param nameStr String name of the species. It may also be the phase name + * species name combination, separated by a colon. + * @return Returns the index of the species. If the name is not found, + * the value of -1 is returned. + */ + int Phase::speciesIndex(std::string nameStr) const { + std::string pn; + std::string sn = parseSpeciesName(nameStr, pn); + if (pn == "" || pn == m_name || pn == m_id) { + return Constituents::speciesIndex(sn); + } + return -1; + } + + std::string Phase::speciesSPName(int k) const { + std::string sn = Constituents::speciesName(k); + return(m_name + ":" + sn); + } + void Phase::saveState(vector_fp& state) const { state.resize(nSpecies() + 2); saveState(state.size(),&(state[0])); @@ -315,8 +350,8 @@ namespace Cantera { return State::moleFraction(k); } - doublereal Phase::moleFraction(std::string name) const { - int iloc = speciesIndex(name); + doublereal Phase::moleFraction(std::string nameSpec) const { + int iloc = speciesIndex(nameSpec); if (iloc >= 0) return State::moleFraction(iloc); else return 0.0; } @@ -325,8 +360,8 @@ namespace Cantera { return State::massFraction(k); } - doublereal Phase::massFraction(std::string name) const { - int iloc = speciesIndex(name); + doublereal Phase::massFraction(std::string nameSpec) const { + int iloc = speciesIndex(nameSpec); if (iloc >= 0) return massFractions()[iloc]; else return 0.0; } diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index 60c5ec06a..d6de40b1a 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -138,6 +138,37 @@ namespace Cantera { * vector, which is in general of length (2 + nSpecies()). The first * two entries of the state vector is temperature and density. * + * The class Phase contains two strings that identify a phase. + * The string id() is the value of the ID attribute of the XML phase node + * that is used to initialize a phase when it is read it. + * The id() field will stay that way even if the name is changed. + * The name field is also set to the value of the ID attribute of + * the XML phase node. + * + * However, the name field may be changed to another value during the course of a calculation. + * For example, if a phase is located in two places, but has the same + * constituitive input, the id's of the two phases will be the same, + * but the names of the two phases may be different. + * + * The name of a phase can be the same as the id of that same phase. + * Actually, this is the default and normal condition to have the name and + * the id for each phase to be the same. However, it is expected that + * it's an error to have two phases in a single problem with the same name. + * or the same id (or the name from one phase being the same as the id + * of another phase). + * Thus, it is expected that there is a 1-1 correspondence between + * names and unique phases within a Cantera problem. + * + * A species name may be referred to via three methods: + * + * - "speciesName" + * - "PhaseId:speciesName" + * - "phaseName:speciesName" + * . + * + * The first two methods of naming may not yield a unique species within + * complicated assemblies of Cantera Phases. + * * * @todo * Make the concept of saving state vectors more general, so that @@ -237,6 +268,39 @@ namespace Cantera { */ void setIndex(int m); + //! Returns the index of a species named 'name' within the Phase object + /*! + * The first species in the phase will have an index 0, and the last one in the + * phase will have an index of nSpecies() - 1. + * + * A species name may be referred to via three methods: + * + * - "speciesName" + * - "PhaseId:speciesName" + * - "phaseName:speciesName" + * . + * + * The first two methods of naming may not yield a unique species within + * complicated assemblies of Cantera phases. The last method is guarranteed + * to be unique within a collection of Cantera phases. + * + * @param name String name of the species. It may also be the phase name + * species name combination, separated by a colon. + * @return Returns the index of the species. If the name is not found, + * the value of -1 is returned. + */ + int speciesIndex(std::string name) const; + + //! Returns the expanded species name of a species, including the phase name + /*! + * Returns the expanded phase name species name string. + * This is guarranteed to be unique within a Cantera problem. + * + * @param k Species index within the phase + * @return Returns the "phaseName:speciesName" string + */ + std::string speciesSPName(int k) const; + //! Save the current internal state of the phase /*! * Write to vector 'state' the current internal state. @@ -530,12 +594,22 @@ namespace Cantera { //! ID of the phase. /*! * This is the value of the ID attribute of the XML phase node. + * The field will stay that way even if the name is changed. */ std::string m_id; //! Name of the phase. /*! * Initially, this is the value of the ID attribute of the XML phase node. + * + * It may be changed to another value during the course of a calculation. + * for example, if a phase is located in two places, but has the same + * constituitive input, the id's of the two phases will be the same, + * but the names of the two phases may be different. + * + * The name can be the same as the id, within a phase. However, besides + * that case, it is expected that there is a 1-1 correspondence between + * names and unique phases within a Cantera problem. */ std::string m_name; }; diff --git a/Cantera/src/thermo/WaterSSTP.cpp b/Cantera/src/thermo/WaterSSTP.cpp index 0d3f0ac93..5727ea3de 100644 --- a/Cantera/src/thermo/WaterSSTP.cpp +++ b/Cantera/src/thermo/WaterSSTP.cpp @@ -162,13 +162,13 @@ namespace Cantera { void WaterSSTP::constructPhaseFile(std::string inputFile, std::string id) { if (inputFile.size() == 0) { - throw CanteraError("WaterTp::initThermo", + throw CanteraError("WaterSSTP::constructPhaseFile", "input file is null"); } std::string path = findInputFile(inputFile); std::ifstream fin(path.c_str()); if (!fin) { - throw CanteraError("WaterSSTP::initThermo","could not open " + throw CanteraError("WaterSSTP::constructPhaseFile","could not open " +path+" for reading."); } /* @@ -180,7 +180,7 @@ namespace Cantera { fxml->build(fin); XML_Node *fxml_phase = findXMLPhase(fxml, id); if (!fxml_phase) { - throw CanteraError("WaterSSTP::initThermo", + throw CanteraError("WaterSSTP::constructPhaseFile", "ERROR: Can not find phase named " + id + " in file named " + inputFile); } From ebcdbf3fa14e90a26dbed4515825b59afe82f56f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 10 Jun 2010 19:55:25 +0000 Subject: [PATCH 162/446] Changed the RootFinder algorithm so that delta_x can't go to zero. --- Cantera/src/numerics/ArrayViewer.h | 0 Cantera/src/numerics/BandMatrix.cpp | 0 Cantera/src/numerics/BandMatrix.h | 0 Cantera/src/numerics/DASPK.cpp | 0 Cantera/src/numerics/DASPK.h | 0 Cantera/src/numerics/DenseMatrix.cpp | 0 Cantera/src/numerics/DenseMatrix.h | 0 Cantera/src/numerics/FuncEval.h | 0 Cantera/src/numerics/ResidEval.h | 0 Cantera/src/numerics/RootFind.cpp | 55 ++++++++++++++++++++-------- Cantera/src/numerics/RootFind.h | 24 ++++++------ Cantera/src/numerics/ctlapack.h | 0 Cantera/src/numerics/funcs.cpp | 0 Cantera/src/numerics/lapack.h | 0 Cantera/src/numerics/polyfit.h | 0 Cantera/src/numerics/solveProb.cpp | 2 +- Cantera/src/numerics/solveProb.h | 2 +- Cantera/src/numerics/sort.cpp | 0 Cantera/src/numerics/sort.h | 0 19 files changed, 53 insertions(+), 30 deletions(-) mode change 100755 => 100644 Cantera/src/numerics/ArrayViewer.h mode change 100755 => 100644 Cantera/src/numerics/BandMatrix.cpp mode change 100755 => 100644 Cantera/src/numerics/BandMatrix.h mode change 100755 => 100644 Cantera/src/numerics/DASPK.cpp mode change 100755 => 100644 Cantera/src/numerics/DASPK.h mode change 100755 => 100644 Cantera/src/numerics/DenseMatrix.cpp mode change 100755 => 100644 Cantera/src/numerics/DenseMatrix.h mode change 100755 => 100644 Cantera/src/numerics/FuncEval.h mode change 100755 => 100644 Cantera/src/numerics/ResidEval.h mode change 100755 => 100644 Cantera/src/numerics/ctlapack.h mode change 100755 => 100644 Cantera/src/numerics/funcs.cpp mode change 100755 => 100644 Cantera/src/numerics/lapack.h mode change 100755 => 100644 Cantera/src/numerics/polyfit.h mode change 100755 => 100644 Cantera/src/numerics/sort.cpp mode change 100755 => 100644 Cantera/src/numerics/sort.h diff --git a/Cantera/src/numerics/ArrayViewer.h b/Cantera/src/numerics/ArrayViewer.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/BandMatrix.cpp b/Cantera/src/numerics/BandMatrix.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/BandMatrix.h b/Cantera/src/numerics/BandMatrix.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/DASPK.cpp b/Cantera/src/numerics/DASPK.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/DASPK.h b/Cantera/src/numerics/DASPK.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/FuncEval.h b/Cantera/src/numerics/FuncEval.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index d5002be99..efbda6b34 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -2,7 +2,7 @@ * @file: RootFind.cpp root finder for 1D problems */ /* - * $Id: solveSP.cpp 381 2010-01-15 21:20:41Z hkmoffa $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract @@ -15,6 +15,9 @@ #include "RootFind.h" #include "global.h" +#ifdef DEBUG_MODE +#include "mdp_allo.h" +#endif /* Standard include files */ @@ -49,7 +52,7 @@ namespace Cantera { /*****************************************************************************/ /*****************************************************************************/ #ifdef DEBUG_MODE - static void print_funcEval(FILE *fp, double xval, double fval, int its) + static void print_funcEval(FILE *fp, doublereal xval, doublereal fval, int its) { fprintf(fp,"\n"); fprintf(fp,"...............................................................\n"); @@ -62,9 +65,9 @@ namespace Cantera { } #endif //================================================================================================ - static int smlequ(double *c, int idem, int n, double *b, int m) { + static int smlequ(doublereal *c, int idem, int n, doublereal *b, int m) { int i, j, k, l; - double R; + doublereal R; if (n > idem || n <= 0) { writelogf("smlequ ERROR: badly dimensioned matrix: %d %d\n", n, idem); return 1; @@ -141,7 +144,7 @@ namespace Cantera { * return: * 0 Found function */ - int RootFind::solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) { + int RootFind::solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest) { /* * We store the function target and then actually calculate a modified functional @@ -158,18 +161,18 @@ namespace Cantera { char fileName[80]; FILE *fp = 0; #endif - double x1, x2, xnew, f1, f2, fnew, slope; + doublereal x1, x2, xnew, f1, f2, fnew, slope; int its = 0; int posStraddle = 0; int retn = 0; int foundPosF = 0; int foundNegF = 0; int foundStraddle = 0; - double xPosF = 0.0; - double xNegF = 0.0; - double fnorm; /* A valid norm for the making the function value dimensionless */ - double c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; - double CR0, CR1, CR2, CRnew, CRdenom; + doublereal xPosF = 0.0; + doublereal xNegF = 0.0; + doublereal fnorm; /* A valid norm for the making the function value dimensionless */ + doublereal c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; + doublereal CR0, CR1, CR2, CRnew, CRdenom; callNum++; #ifdef DEBUG_MODE @@ -429,7 +432,7 @@ namespace Cantera { * If we are venturing into new ground, only allow the step jump * to increase by 50% at each interation */ - double xDelMax = 1.5 * fabs(x2 - x1); + doublereal xDelMax = 1.5 * fabs(x2 - x1); if (fabs(xDelMax) < fabs(xnew - x2)) { xnew = x2 + DSIGN(xnew-x2) * xDelMax; #ifdef DEBUG_MODE @@ -564,6 +567,20 @@ namespace Cantera { if (fabs(fnew / fnorm) < m_rtol) { converged = 1; } + /* + * Check for excess convergence in the x coordinate + */ + if (foundStraddle) { + doublereal denom = fabs(x1) + fabs(x2); + if (denom < 1.0E-200) { + retn = ROOTFIND_FAILEDCONVERGENCE; + converged = true; + } + if (fabs(x2 - x1) / denom < 1.0E-13) { + converged = true; + } + + } its++; } while (! converged && its < itmax); if (converged) { @@ -595,13 +612,19 @@ namespace Cantera { return retn; } //================================================================================================ - double RootFind::func(double x) { - double r; + doublereal RootFind::func(doublereal x) { + doublereal r; +#ifdef DEBUG_MODE + mdp::checkFinite(x); +#endif m_residFunc->evalSS(0.0, &x, &r); +#ifdef DEBUG_MODE + mdp::checkFinite(r); +#endif return (r - m_funcTargetValue); } //================================================================================================ - void RootFind::setTol(double rtol, double atol) + void RootFind::setTol(doublereal rtol, doublereal atol) { m_atol = atol; m_rtol = rtol; @@ -628,7 +651,7 @@ namespace Cantera { FuncIsGenerallyDecreasing_ = value; } //================================================================================================ - void RootFind::setDeltaX(double deltaXNorm) + void RootFind::setDeltaX(doublereal deltaXNorm) { DeltaXnorm_ = deltaXNorm; } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 69dbd187d..c8168ed89 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -4,7 +4,7 @@ * (see \ref numerics and class \link Cantera::RootFind RootFind\endlink). */ /* - * $Id: solveSP.h 381 2010-01-15 21:20:41Z hkmoffa $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract @@ -13,8 +13,8 @@ * See file License.txt for licensing information. */ -#ifndef ROOTFIND_H -#define ROOTFIND_H +#ifndef CT_ROOTFIND_H +#define CT_ROOTFIND_H /** * @defgroup solverGroup Solvers for Equation Systems */ @@ -50,26 +50,26 @@ namespace Cantera { public: - int solve(double xmin, double xmax, int itmax, double funcTargetValue, double *xbest) ; + int solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest) ; - double func(double x); + doublereal func(doublereal x); - void setTol(double rtol, double atol); + void setTol(doublereal rtol, doublereal atol); void setPrintLvl(int printLvl); void setFuncIsGenerallyIncreasing(bool value); void setFuncIsGenerallyDecreasing(bool value); - void setDeltaX(double deltaXNorm); + void setDeltaX(doublereal deltaXNorm); public: ResidEval *m_residFunc; - double m_funcTargetValue; - double m_atol; - double m_rtol; - double m_maxstep; + doublereal m_funcTargetValue; + doublereal m_atol; + doublereal m_rtol; + doublereal m_maxstep; protected: int printLvl; - double DeltaXnorm_; + doublereal DeltaXnorm_; bool FuncIsGenerallyIncreasing_; bool FuncIsGenerallyDecreasing_; diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/funcs.cpp b/Cantera/src/numerics/funcs.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/lapack.h b/Cantera/src/numerics/lapack.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/polyfit.h b/Cantera/src/numerics/polyfit.h old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index 446b4bc0f..5bf2b766b 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -2,7 +2,7 @@ * @file: solveSP.cpp Implicit solver for nonlinear problems */ /* - * $Id: solveSP.cpp 381 2010-01-15 21:20:41Z hkmoffa $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index 52f6f6097..658fff0e3 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -4,7 +4,7 @@ * (see \ref numerics and class \link Cantera::solveProb solveProb\endlink). */ /* - * $Id: solveSP.h 381 2010-01-15 21:20:41Z hkmoffa $ + * $Id$ */ /* * Copywrite 2004 Sandia Corporation. Under the terms of Contract diff --git a/Cantera/src/numerics/sort.cpp b/Cantera/src/numerics/sort.cpp old mode 100755 new mode 100644 diff --git a/Cantera/src/numerics/sort.h b/Cantera/src/numerics/sort.h old mode 100755 new mode 100644 From 7b4aeeb4290b2e28a8e5788c25a1bc790abc67d0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 18 Jun 2010 20:54:59 +0000 Subject: [PATCH 163/446] Doxygen update Beat down a few warnings from doxygen Moved some definitions from .h files to .cpp files. There is no change in functionality in this update --- Cantera/src/transport/Makefile.in | 3 +- Cantera/src/transport/TransportFactory.cpp | 85 +++++++++----- Cantera/src/transport/TransportFactory.h | 104 ++++++++---------- Cantera/src/transport/TransportParams.cpp | 85 ++++++++++++++ Cantera/src/transport/TransportParams.h | 122 +++++++++------------ 5 files changed, 241 insertions(+), 158 deletions(-) create mode 100644 Cantera/src/transport/TransportParams.cpp diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index 2bab492c7..208b7e055 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -36,7 +36,8 @@ CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) # Base Transport Object Files TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt.o \ SolidTransport.o DustyGasTransport.o TransportBase.o WaterTransport.o \ - SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o + SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o \ + TransportParams.o TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 3ae2482ee..3daa32f84 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -298,44 +298,27 @@ namespace Cantera { single transport property as a function of temperature and possibly composition. */ - LTPspecies* TransportFactory::newLTP( const XML_Node &trNode, - std::string &name, - TransportPropertyList tp_ind, - thermo_t* thermo) { + LTPspecies* TransportFactory::newLTP(const XML_Node &trNode, std::string &name, + TransportPropertyList tp_ind, thermo_t* thermo) + { LTPspecies* ltps = 0; - std::string model = lowercase(trNode["model"]); - switch ( m_LTRmodelMap[model] ) { + switch (m_LTRmodelMap[model]) { case LTR_MODEL_CONSTANT: - ltps = new LTPspecies_Const( trNode, - name, - tp_ind, - thermo ); + ltps = new LTPspecies_Const(trNode, name, tp_ind, thermo); break; case LTR_MODEL_ARRHENIUS: - ltps = new LTPspecies_Arrhenius( trNode, - name, - tp_ind, - thermo ); + ltps = new LTPspecies_Arrhenius(trNode, name, tp_ind, thermo); break; case LTR_MODEL_POLY: - ltps = new LTPspecies_Poly( trNode, - name, - tp_ind, - thermo ); + ltps = new LTPspecies_Poly(trNode, name, tp_ind, thermo); break; case LTR_MODEL_EXPT: - ltps = new LTPspecies_ExpT( trNode, - name, - tp_ind, - thermo ); + ltps = new LTPspecies_ExpT(trNode, name, tp_ind, thermo); break; default: - throw CanteraError("newLTP","unknown transport model: " + model ); - ltps = new LTPspecies( trNode, - name, - tp_ind, - thermo ); + throw CanteraError("newLTP","unknown transport model: " + model); + ltps = new LTPspecies(trNode, name, tp_ind, thermo); } return ltps; } @@ -1549,5 +1532,53 @@ namespace Cantera { } #endif } + //==================================================================================================================== + // Create a new transport manager instance. + /* + * @param transportModel String identifying the transport model to be instantiated, defaults to the empty string + * @param thermo ThermoPhase object associated with the phase, defaults to null pointer + * @param loglevel int containing the Loglevel, defaults to zero + * @param f ptr to the TransportFactory object if it's been malloced. + * + * @ingroup transportProps + */ + Transport* newTransportMgr(std::string transportModel, thermo_t* thermo, int loglevel, TransportFactory* f) + { + if (f == 0) { + f = TransportFactory::factory(); + } + Transport* ptr = f->newTransport(transportModel, thermo, loglevel); + /* + * Note: We delete the static s_factory instance here, instead of in + * appdelete() in misc.cpp, to avoid linking problems involving + * the need for multiple cantera and transport library statements + * for applications that don't have transport in them. + */ + return ptr; + } + //==================================================================================================================== + // Create a new transport manager instance. + /* + * @param thermo ThermoPhase object associated with the phase, defaults to null pointer + * @param loglevel int containing the Loglevel, defaults to zero + * @param f ptr to the TransportFactory object if it's been malloced. + * + * @ingroup transportProps + */ + Transport* newDefaultTransportMgr(thermo_t* thermo, int loglevel, TransportFactory* f) + { + if (f == 0) { + f = TransportFactory::factory(); + } + Transport* ptr = f->newTransport(thermo, loglevel); + /* + * Note: We delete the static s_factory instance here, instead of in + * appdelete() in misc.cpp, to avoid linking problems involving + * the need for multiple cantera and transport library statements + * for applications that don't have transport in them. + */ + return ptr; + } + //==================================================================================================================== } diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 504c727c9..1945b6e37 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -40,12 +40,10 @@ #if defined(THREAD_SAFE_CANTERA) #include #endif - +//====================================================================================================================== namespace Cantera { - - /** - * Struct to hold data read from a transport property database file. - */ + //==================================================================================================================== + //! Struct to hold data read from a transport property database file. struct GasTransportData { GasTransportData() : speciesName("-"), geometry(-1), wellDepth(-1.0), @@ -63,27 +61,25 @@ namespace Cantera { doublereal rotRelaxNumber; }; - + //==================================================================================================================== // forward references class MMCollisionInt; class GasTransportParams; class LiquidTransportParams; class XML_Node; - - //! The purpose of TransportFactory is to create new instances of + //==================================================================================================================== + //! The purpose of the TransportFactory class is to create new instances of //! 'transport managers', which are classes that provide transport - //! properties and are derived from base class Transport. + //! properties and which are derived from the base class, %Transport. /*! - * TransportFactory handles all initialization - * required, including evaluation of collision integrals and - * generating polynomial fits. Transport managers can also be - * created in other ways. + * TransportFactory handles all initialization required, including evaluation of collision integrals and + * generating polynomial fits. Transport managers can also be created in other ways. * * @ingroup transportgroup * @ingroup transportProps */ - class TransportFactory : FactoryBase { + class TransportFactory : public FactoryBase { public: @@ -127,15 +123,19 @@ namespace Cantera { virtual ~TransportFactory(); - /** - * make one of several transport models, and return a base class - * pointer to it. This method operates at the level of a - * single transport property as a function of temperature - * and possibly composition. + + //! Make one of several transport models, and return a base class pointer to it. + /*! + * This method operates at the level of a single transport property as a function of temperature + * and possibly composition. It's a factory for LTPspecies classes. + * + * @param trNode XML node + * @param name reference to the name + * @param tp_ind TransportPropertyList class + * @param thermo Pointer to the %ThermoPhase class */ - virtual LTPspecies* - newLTP( const XML_Node &trNode, std::string &name, - TransportPropertyList tp_ind, thermo_t* thermo) ; + virtual LTPspecies* newLTP(const XML_Node &trNode, std::string &name, + TransportPropertyList tp_ind, thermo_t* thermo); //! Factory function for the construction of new LiquidTranInteraction @@ -368,46 +368,32 @@ namespace Cantera { std::map m_LTImodelMap; }; - - /** - * Create a new transport manager instance. + //==================================================================================================================== + //! Create a new transport manager instance. + /*! + * @param transportModel String identifying the transport model to be instantiated, defaults to the empty string + * @param thermo ThermoPhase object associated with the phase, defaults to null pointer + * @param loglevel int containing the Loglevel, defaults to zero + * @param f ptr to the TransportFactory object if it's been malloced. + * * @ingroup transportProps */ - inline Transport* newTransportMgr(std::string transportModel = "", - thermo_t* thermo = 0, int loglevel=0, - TransportFactory* f=0) { - if (f == 0) { - f = TransportFactory::factory(); - } - Transport* ptr = f->newTransport(transportModel, thermo, loglevel); - /* - * Note: We delete the static s_factory instance here, instead of in - * appdelete() in misc.cpp, to avoid linking problems involving - * the need for multiple cantera and transport library statements - * for applications that don't have transport in them. - */ - return ptr; - } - - /** - * Create a new transport manager instance. + Transport* newTransportMgr(std::string transportModel = "", thermo_t* thermo = 0, int loglevel = 0, + TransportFactory* f = 0); + //==================================================================================================================== + //! Create a new transport manager instance. + /*! + * @param thermo ThermoPhase object associated with the phase, defaults to null pointer + * @param loglevel int containing the Loglevel, defaults to zero + * @param f ptr to the TransportFactory object if it's been malloced. + * + * @return Returns a transport manager for the phase + * * @ingroup transportProps */ - inline Transport* newDefaultTransportMgr(thermo_t* thermo, int loglevel=0, - TransportFactory* f=0) { - if (f == 0) { - f = TransportFactory::factory(); - } - Transport* ptr = f->newTransport(thermo, loglevel); - /* - * Note: We delete the static s_factory instance here, instead of in - * appdelete() in misc.cpp, to avoid linking problems involving - * the need for multiple cantera and transport library statements - * for applications that don't have transport in them. - */ - return ptr; - } + Transport* newDefaultTransportMgr(thermo_t* thermo, int loglevel = 0, TransportFactory* f = 0); - -} + //==================================================================================================================== +} // End of namespace Cantera +//====================================================================================================================== #endif diff --git a/Cantera/src/transport/TransportParams.cpp b/Cantera/src/transport/TransportParams.cpp new file mode 100644 index 000000000..330d6266b --- /dev/null +++ b/Cantera/src/transport/TransportParams.cpp @@ -0,0 +1,85 @@ +/** + * @file TransportParams.h + * Class that holds the data that is read in from the xml file, and which is used for + * processing of the transport object + * (see \ref tranprops and \link Cantera::TransportParams TransportParams \endlink). + */ +/* + * Latest Checkin: + * $Author: hkmoffa $ + * $Date: 2010-04-02 11:40:52 -0600 (Fri, 02 Apr 2010) $ + * $Revision: 429 $ + */ + +#include "TransportParams.h" + +#ifdef DEBUG_MODE +#include "XML_Writer.h" +#endif +using namespace std; + + +namespace Cantera { + //==================================================================================================================== + NotImplemented::NotImplemented(std::string method) : + CanteraError("Transport", + "\n\n**** Method " + method + " not implemented. ****\n" + "(Did you forget to specify a transport model?)\n\n") + { + } + //==================================================================================================================== + TransportParams::TransportParams() : + nsp_(0), + thermo(0), + mw(0), + velocityBasis_(VB_MASSAVG), + tmax(1000000.), + tmin(10.), + mode_(0), + xml(0), + log_level(-1) + { + } + //==================================================================================================================== + // Destructor + TransportParams::~TransportParams() + { +#ifdef DEBUG_MODE + delete xml; +#endif + } + //==================================================================================================================== + // Constructor + GasTransportParams::GasTransportParams() : + TransportParams(), + visccoeffs(0), + condcoeffs(0), + diffcoeffs(0), + poly(0), + omega22_poly(0), + astar_poly(0), + bstar_poly(0), + cstar_poly(0), + zrot(0), + crot(0), + polar(0), + alpha(0), + fitlist(0), + eps(0), + sigma(0), + reducedMass(0, 0), + diam(0, 0), + epsilon(0, 0), + dipole(0, 0), + delta(0, 0) + { + } + //==================================================================================================================== + GasTransportParams:: ~GasTransportParams() + { + } + + + //==================================================================================================================== +} // End of namespace Cantera +//====================================================================================================================== diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 9eb85bd9c..786dd099b 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -1,52 +1,57 @@ +/** + * @file TransportParams.h + * Class that holds the data that is read in from the xml file, and which is used for + * processing of the transport object + * (see \ref tranprops and \link Cantera::TransportParams TransportParams \endlink). + */ +/* + * Latest Checkin: + * $Date$ + * $Revision$ + */ + #ifndef CT_TRANSPORTPARAMS_H #define CT_TRANSPORTPARAMS_H #include #include "ct_defs.h" -#include "TransportBase.h" -#include "xml.h" -#include "XML_Writer.h" #include "DenseMatrix.h" +#include "TransportBase.h" namespace Cantera { + class XML_Writer; + + + //==================================================================================================================== + //! Error class to indicate an unimplemented method + /*! + * This class is used by transport objects + */ class NotImplemented : public CanteraError { public: - NotImplemented(std::string method) : CanteraError("Transport", - "\n\n**** Method "+method+" not implemented. ****\n" - "(Did you forget to specify a transport model?)\n\n") {} + + //! Constructor for error class + /*! + * @param method Single string indicating a method that is not implemented + */ + NotImplemented(std::string method); }; - - /** - * Base class to hold transport model parameters. - * Used by TransportFactory. + //==================================================================================================================== + //! Base structure to hold transport model parameters. + /*! + * This structure is used by TransportFactory. */ class TransportParams { public: //! Default Constructor - TransportParams() : - nsp_(0), - thermo(0), - mw(0), - velocityBasis_(VB_MASSAVG), - tmax(1000000.), - tmin(10.), - mode_(0), - xml(0), - log_level(-1) - { - } + TransportParams(); //! Destructor - virtual ~TransportParams() - { -#ifdef DEBUG_MODE - delete xml; -#endif - } + virtual ~TransportParams(); //! Local storage of the number of species int nsp_; @@ -58,7 +63,7 @@ namespace Cantera { /*! * Length is nsp_ and units are kg kmol-1. */ - vector_fp mw; + vector_fp mw; //! A basis for the average velocity can be specified. /*! @@ -80,47 +85,23 @@ namespace Cantera { //! Log level int log_level; - }; - - /** - * Holds transport model parameters relevant to transport in ideal - * gases with a kinetic theory of gases derived transport model. - * Used by TransportFactory. + //==================================================================================================================== + //! This structure holds transport model parameters relevant to transport in ideal + //! gases with a kinetic theory of gases derived transport model. + /*! + * This structure is used by TransportFactory object. */ class GasTransportParams : public TransportParams { public: //! Constructor - GasTransportParams() : - TransportParams(), - visccoeffs(0), - condcoeffs(0), - diffcoeffs(0), - poly(0), - omega22_poly(0), - astar_poly(0), - bstar_poly(0), - cstar_poly(0), - zrot(0), - crot(0), - polar(0), - alpha(0), - fitlist(0), - eps(0), - sigma(0), - reducedMass(0, 0), - diam(0, 0), - epsilon(0, 0), - dipole(0, 0), - delta(0, 0) - { - } + GasTransportParams(); //! Destructor - virtual ~GasTransportParams() {} + virtual ~GasTransportParams(); // polynomial fits @@ -143,8 +124,7 @@ namespace Cantera { * The outer loop the number of species, nsp * The inner loop is over degree + 1, which is the polynomial order of the collision integral fit. */ - std::vector diffcoeffs; - + std::vector diffcoeffs; //! This is vector of vectors containing the integer ookup value for the (i,j) interaction /*! @@ -222,7 +202,7 @@ namespace Cantera { * Length = nsp * Units = m^3 */ - vector_fp alpha; + vector_fp alpha; //! This is vector containing the values of delta(i,j) that are used in the collision integral fits. /*! @@ -256,7 +236,7 @@ namespace Cantera { * * Length nsp * nsp. This is a symmetric matrix */ - DenseMatrix reducedMass; + DenseMatrix reducedMass; //! hard-sphere diameter for (i,j) collision /*! @@ -265,7 +245,7 @@ namespace Cantera { * * Length nsp * nsp. This is a symmetric matrix. */ - DenseMatrix diam; + DenseMatrix diam; //! The effective well depth for (i,j) collisions /*! @@ -274,7 +254,7 @@ namespace Cantera { * * Length nsp * nsp. This is a symmetric matrix. */ - DenseMatrix epsilon; + DenseMatrix epsilon; //! The effective dipole moment for (i,j) collisions /*! @@ -286,7 +266,7 @@ namespace Cantera { * * Length nsp * nsp. This is a symmetric matrix. */ - DenseMatrix dipole; + DenseMatrix dipole; //! Matrix containing the reduced dipole moment of the interaction between two species /*! @@ -295,10 +275,10 @@ namespace Cantera { * * Length nsp * nsp .This is a symmetric matrix */ - DenseMatrix delta; - + DenseMatrix delta; }; - -} + //==================================================================================================================== +} // End of namespace Cantera +//====================================================================================================================== #endif //CT_TRANSPORTPARAMS_H From fba698e8909df263885cbf864bfbda0f63f107de Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 18 Jun 2010 21:11:36 +0000 Subject: [PATCH 164/446] doxygen update changed double to doublereal --- Cantera/src/transport/LiquidTransport.h | 14 +++++++------- Cantera/src/transport/SolidTransport.cpp | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index c2253d2a9..a463792d6 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -213,21 +213,21 @@ namespace Cantera { * These in turn employ subclasses of LTPspecies to * determine the mobility ratios in the pure species. */ - virtual void mobilityRatio(double* mobRat); + virtual void mobilityRatio(doublereal* mobRat); //! Returns a double pointer to the mobility ratios of the //! transported species in each pure species phase. - //! Has size of the number of binary interactions by the number - //! of species (nsp*nsp X nsp) /*! + * Has size of the number of binary interactions by the number + * of species (nsp*nsp X nsp) * The pure species mobility ratios are evaluated using the * appropriate subclasses of LTPspecies as specified in the * input file. * * @param mobRat array of length "number of species" - * to hold returned mobility ratios. + * to hold returned mobility ratios. */ - virtual void getSpeciesMobilityRatio(double** mobRat); + virtual void getSpeciesMobilityRatio(doublereal** mobRat); //! Returns the self diffusion coefficients of the species in the phase. //! Has size of nsp(coeffs) @@ -256,7 +256,7 @@ namespace Cantera { * Length = number of species in phase * units = m**2 s-1 */ - virtual void selfDiffusion(doublereal * const selfDiff); + virtual void selfDiffusion(doublereal* const selfDiff); //! Returns the self diffusion coefficients in the pure species phases. //! Has size of nsp(coeffs) x nsp(phases) @@ -268,7 +268,7 @@ namespace Cantera { * @param selfDiff array of length "number of species" * to hold returned self diffusion coeffs. */ - virtual void getSpeciesSelfDiffusion(double** selfDiff); + virtual void getSpeciesSelfDiffusion(doublereal** selfDiff); //! Returns the hydrodynamic radius for all species /*! diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index 35d12d54e..0d8e5535d 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -89,7 +89,7 @@ namespace Cantera { return (dynamic_cast(tr)); } //==================================================================================================================== - void SolidTransport::setParameters(const int n, const int k, const double* const p) { + void SolidTransport::setParameters(const int n, const int k, const doublereal * const p) { switch (n) { case 0: From 6e9d490dc1b6c9ad51481257a063e0484dbab063 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 21 Jun 2010 23:47:34 +0000 Subject: [PATCH 165/446] Updates to the LatticeSolidPhase object. This object is not ready for primetime. --- Cantera/src/thermo/LatticeSolidPhase.cpp | 494 +++++++++++++---------- Cantera/src/thermo/LatticeSolidPhase.h | 188 ++++++++- Cantera/src/thermo/ThermoFactory.cpp | 2 +- Cantera/src/thermo/ThermoPhase.h | 10 +- 4 files changed, 466 insertions(+), 228 deletions(-) diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index e9671db02..64da30a24 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -1,7 +1,11 @@ /** - * - * @file LatticeSolidPhase.cpp - * + * @file LatticeSolidPhase.h + * Definitions for a simple thermodynamics model of a bulk solid phase + * derived from %ThermoPhase, + * assuming an ideal solution model based on a lattice of solid atoms + * (see \ref thermoprops and class \link Cantera::LatticeSolidPhase LatticeSolidPhase\endlink). + */ +/* * $Id$ */ @@ -10,39 +14,53 @@ #pragma warning(disable:4503) #endif -#include "config.h" -#ifdef WITH_LATTICE_SOLID #include "ct_defs.h" +#ifdef WITH_LATTICE_SOLID + #include "mix_defs.h" #include "LatticeSolidPhase.h" #include "LatticePhase.h" #include "SpeciesThermo.h" #include "ThermoFactory.h" -//#include "importCTML.h" #include -using namespace std; +using namespace std; +//====================================================================================================================== namespace Cantera { - + //==================================================================================================================== // Base empty constructor LatticeSolidPhase::LatticeSolidPhase() : - m_tlast(0.0) + m_mm(0), + m_kk(0), + m_tlast(0.0), + m_press(-1.0), + m_molar_density(0.0), + m_nlattice(0), + m_lattice(0), + m_x(0) { } - + //==================================================================================================================== // Copy Constructor /* * @param right Object to be copied */ LatticeSolidPhase::LatticeSolidPhase(const LatticeSolidPhase &right) : - m_tlast(0.0) + m_mm(0), + m_kk(0), + m_tlast(0.0), + m_press(-1.0), + m_molar_density(0.0), + m_nlattice(0), + m_lattice(0), + m_x(0) { *this = operator=(right); } - + //==================================================================================================================== // Assignment operator /* * @param right Object to be copied @@ -51,21 +69,26 @@ namespace Cantera { LatticeSolidPhase::operator=(const LatticeSolidPhase& right) { if (&right != this) { ThermoPhase::operator=(right); - m_mm = right.m_mm; - m_kk = right.m_kk; - m_tlast = right.m_tlast; - m_press = right.m_press; + m_mm = right.m_mm; + m_kk = right.m_kk; + m_tlast = right.m_tlast; + m_press = right.m_press; m_molar_density = right.m_molar_density; - m_nlattice = right.m_nlattice; - m_x = right.m_x; + m_nlattice = right.m_nlattice; + deepStdVectorPointerCopy(right.m_lattice, m_lattice); + m_x = right.m_x; } return *this; } - - //! Destructor + //==================================================================================================================== + // Destructor LatticeSolidPhase::~LatticeSolidPhase() { + for (int n = 0; n < m_nlattice; n++) { + delete m_lattice[n]; + m_lattice[n] = 0; + } } - + //==================================================================================================================== // Duplication function /* * This virtual function is used to create a duplicate of the @@ -78,7 +101,7 @@ namespace Cantera { LatticeSolidPhase *igp = new LatticeSolidPhase(*this); return (ThermoPhase *) igp; } - + //==================================================================================================================== doublereal LatticeSolidPhase:: enthalpy_mole() const { _updateThermo(); @@ -90,200 +113,249 @@ namespace Cantera { } return sum/molarDensity(); } - - doublereal LatticeSolidPhase::intEnergy_mole() const { - _updateThermo(); - doublereal ndens, sum = 0.0; - int n; - for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->intEnergy_mole(); - } - return sum/molarDensity(); + //==================================================================================================================== + doublereal LatticeSolidPhase::intEnergy_mole() const { + _updateThermo(); + doublereal ndens, sum = 0.0; + int n; + for (n = 0; n < m_nlattice; n++) { + ndens = m_lattice[n]->molarDensity(); + sum += ndens * m_lattice[n]->intEnergy_mole(); } - - doublereal LatticeSolidPhase::entropy_mole() const { - _updateThermo(); - doublereal ndens, sum = 0.0; - int n; - for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->entropy_mole(); - } - return sum/molarDensity(); + return sum/molarDensity(); + } + //==================================================================================================================== + doublereal LatticeSolidPhase::entropy_mole() const { + _updateThermo(); + doublereal ndens, sum = 0.0; + int n; + for (n = 0; n < m_nlattice; n++) { + ndens = m_lattice[n]->molarDensity(); + sum += ndens * m_lattice[n]->entropy_mole(); } - - doublereal LatticeSolidPhase::gibbs_mole() const { - _updateThermo(); - doublereal ndens, sum = 0.0; - int n; - for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->gibbs_mole(); - } - return sum/molarDensity(); + return sum/molarDensity(); + } + //==================================================================================================================== + doublereal LatticeSolidPhase::gibbs_mole() const { + _updateThermo(); + doublereal ndens, sum = 0.0; + for (int n = 0; n < m_nlattice; n++) { + ndens = m_lattice[n]->molarDensity(); + sum += ndens * m_lattice[n]->gibbs_mole(); } - - doublereal LatticeSolidPhase::cp_mole() const { - _updateThermo(); - doublereal ndens, sum = 0.0; - int n; - for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->cp_mole(); - } - return sum/molarDensity(); + return sum/molarDensity(); + } + //==================================================================================================================== + doublereal LatticeSolidPhase::cp_mole() const { + _updateThermo(); + doublereal sum = 0.0; + for (int n = 0; n < m_nlattice; n++) { + doublereal ndens = m_lattice[n]->molarDensity(); + sum += ndens * m_lattice[n]->cp_mole(); } - - void LatticeSolidPhase::getActivityConcentrations(doublereal* c) const { - _updateThermo(); - int n; - int strt = 0; - for (n = 0; n < m_nlattice; n++) { - m_lattice[n]->getMoleFractions(c+strt); - strt += m_lattice[n]->nSpecies(); - } + return sum/molarDensity(); + } + //==================================================================================================================== + void LatticeSolidPhase::getActivityConcentrations(doublereal* c) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + m_lattice[n]->getMoleFractions(c+strt); + strt += m_lattice[n]->nSpecies(); } + } + //==================================================================================================================== + void LatticeSolidPhase::getActivityCoefficients(doublereal* ac) const { + for (int k = 0; k < m_kk; k++) { + ac[k] = 1.0; + } + } + //==================================================================================================================== + doublereal LatticeSolidPhase::standardConcentration(int k) const { + return 1.0; + } + //==================================================================================================================== + doublereal LatticeSolidPhase::logStandardConc(int k) const { + return 0.0; + } - void LatticeSolidPhase::getActivityCoefficients(doublereal* ac) const { - for (int k = 0; k < m_kk; k++) { - ac[k] = 1.0; + //==================================================================================================================== + void LatticeSolidPhase::setMoleFractions(const doublereal* x) { + int nsp, strt = 0; + doublereal sum = 0.0; + for (int n = 0; n < m_nlattice; n++) { + nsp = m_lattice[n]->nSpecies(); + m_lattice[n]->setMoleFractions(x+strt); + for (int k = 0; k < nsp; k++) { + sum += x[strt + k]; + } + strt += nsp; + } + for (int k = 0; k < strt; k++) { + m_x[k] = x[k] / sum; + } + State::setMoleFractions(DATA_PTR(m_x)); + } + //==================================================================================================================== + void LatticeSolidPhase::getMoleFractions(doublereal* x) const { + int nsp, strt = 0; + State::getMoleFractions(x); + doublereal sum; + for (int n = 0; n < m_nlattice; n++) { + nsp = m_lattice[n]->nSpecies(); + sum = 0.0; + for (int k = 0; k < nsp; k++) { + sum += (x + strt)[k]; + } + for (int k = 0; k < nsp; k++) { + (x + strt)[k] /= sum; + } + /* + * At this point we can check against the mole fraction vector of the underlying LatticePhase objects and + * get the same answer. + */ +#ifdef DEBUG_MODE + m_lattice[n]->getMoleFractions(&(m_x[strt])); + for (int k = 0; k < nsp; k++) { + if (fabs((x + strt)[k] - m_x[strt+k]) > 1.0E-14) { + throw CanteraError("LatticeSolidPhase::getMoleFractions()", + "internal error"); } - } - - doublereal LatticeSolidPhase::standardConcentration(int k) const { - return 1.0; - } - - doublereal LatticeSolidPhase::logStandardConc(int k) const { - return 0.0; - } - - void LatticeSolidPhase::getChemPotentials(doublereal* mu) const { - _updateThermo(); - int n; - int strt = 0; - double dratio; - for (n = 0; n < m_nlattice; n++) { - dratio = m_lattice[n]->molarDensity()/molarDensity(); - m_lattice[n]->getChemPotentials(mu+strt); - scale(mu + strt, mu + strt + m_lattice[n]->nSpecies(), mu + strt, dratio); - strt += m_lattice[n]->nSpecies(); - } - } - - void LatticeSolidPhase::getStandardChemPotentials(doublereal* mu0) const { - _updateThermo(); - int n; - int strt = 0; - double dratio; - for (n = 0; n < m_nlattice; n++) { - dratio = m_lattice[n]->molarDensity()/molarDensity(); - m_lattice[n]->getStandardChemPotentials(mu0+strt); - scale(mu0 + strt, mu0 + strt + m_lattice[n]->nSpecies(), mu0 + strt, dratio); - strt += m_lattice[n]->nSpecies(); - } - } - - void LatticeSolidPhase::initThermo() { - m_kk = nSpecies(); - m_mm = nElements(); - m_x.resize(m_kk); - int n, nsp, k, loc = 0; - doublereal ndens; - m_molar_density = 0.0; - for (n = 0; n < m_nlattice; n++) { - nsp = m_lattice[n]->nSpecies(); - ndens = m_lattice[n]->molarDensity(); - for (k = 0; k < nsp; k++) { - m_x[loc] = ndens * m_lattice[n]->moleFraction(k); - loc++; - } - m_molar_density += ndens; - } - setMoleFractions(DATA_PTR(m_x)); - -// const vector& spnames = speciesNames(); -// int n, k, kl, namesize; -// int nl = m_sitedens.size(); -// string s; -// m_lattice.resize(m_kk,-1); -// vector_fp conc(m_kk, 0.0); - -// compositionMap xx; -// for (n = 0; n < nl; n++) { -// for (k = 0; k < m_kk; k++) { -// xx[speciesName(k)] = -1.0; -// } -// parseCompString(m_sp[n], xx); -// for (k = 0; k < m_kk; k++) { -// if (xx[speciesName(k)] != -1.0) { -// conc[k] = m_sitedens[n]*xx[speciesName(k)]; -// m_lattice[k] = n; -// } -// } - -// } -// for (k = 0; k < m_kk; k++) { -// if (m_lattice[k] == -1) { -// throw CanteraError("LatticeSolidPhase::" -// "setParametersFromXML","Species "+speciesName(k) -// +" not a member of any lattice."); -// } -// } -// setMoleFractions(DATA_PTR(conc)); - } - - - void LatticeSolidPhase::_updateThermo() const { - doublereal tnow = temperature(); - // if (fabs(molarDensity() - m_molar_density)/m_molar_density > 0.0001) { - // throw CanteraError("_updateThermo","molar density changed from " - // +fp2str(m_molar_density)+" to "+fp2str(molarDensity())); - //} - if (m_tlast != tnow) { - int n; - getMoleFractions(DATA_PTR(m_x)); - int strt = 0; - for (n = 0; n < m_nlattice; n++) { - m_lattice[n]->setTemperature(tnow); - m_lattice[n]->setMoleFractions(DATA_PTR(m_x) + strt); - m_lattice[n]->setPressure(m_press); - strt += m_lattice[n]->nSpecies(); - } - m_tlast = tnow; - } - } - - void LatticeSolidPhase::setLatticeMoleFractions(int nn, - string x) { - m_lattice[nn]->setMoleFractionsByName(x); - int n, k, loc=0, nsp; - doublereal ndens; - for (n = 0; n < m_nlattice; n++) { - nsp = m_lattice[n]->nSpecies(); - ndens = m_lattice[n]->molarDensity(); - for (k = 0; k < nsp; k++) { - m_x[loc] = ndens * m_lattice[n]->moleFraction(k); - loc++; - } - } - setMoleFractions(DATA_PTR(m_x)); - } - - void LatticeSolidPhase::setParametersFromXML(const XML_Node& eosdata) { - eosdata._require("model","LatticeSolid"); - XML_Node& la = eosdata.child("LatticeArray"); - vector lattices; - la.getChildren("phase",lattices); - int n; - int nl = lattices.size(); - m_nlattice = nl; - for (n = 0; n < nl; n++) { - XML_Node& i = *lattices[n]; - m_lattice.push_back((LatticePhase*)newPhase(i)); - } - } -} - + } #endif + strt += nsp; + } + } + //==================================================================================================================== + void LatticeSolidPhase::getChemPotentials(doublereal* mu) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + doublereal dratio = m_lattice[n]->molarDensity()/molarDensity(); + m_lattice[n]->getChemPotentials(mu+strt); + scale(mu + strt, mu + strt + m_lattice[n]->nSpecies(), mu + strt, dratio); + strt += m_lattice[n]->nSpecies(); + } + } + //==================================================================================================================== + void LatticeSolidPhase::getStandardChemPotentials(doublereal* mu0) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + doublereal dratio = m_lattice[n]->molarDensity()/molarDensity(); + m_lattice[n]->getStandardChemPotentials(mu0+strt); + scale(mu0 + strt, mu0 + strt + m_lattice[n]->nSpecies(), mu0 + strt, dratio); + strt += m_lattice[n]->nSpecies(); + } + } + //==================================================================================================================== + void LatticeSolidPhase::initThermo() { + m_kk = nSpecies(); + m_mm = nElements(); + m_x.resize(m_kk); + int nsp, k, loc = 0; + doublereal ndens; + m_molar_density = 0.0; + for (int n = 0; n < m_nlattice; n++) { + nsp = m_lattice[n]->nSpecies(); + ndens = m_lattice[n]->molarDensity(); + for (k = 0; k < nsp; k++) { + m_x[loc] = ndens * m_lattice[n]->moleFraction(k); + loc++; + } + m_molar_density += ndens; + } + setMoleFractions(DATA_PTR(m_x)); + + // const vector& spnames = speciesNames(); + // int n, k, kl, namesize; + // int nl = m_sitedens.size(); + // string s; + // m_lattice.resize(m_kk,-1); + // vector_fp conc(m_kk, 0.0); + + // compositionMap xx; + // for (n = 0; n < nl; n++) { + // for (k = 0; k < m_kk; k++) { + // xx[speciesName(k)] = -1.0; + // } + // parseCompString(m_sp[n], xx); + // for (k = 0; k < m_kk; k++) { + // if (xx[speciesName(k)] != -1.0) { + // conc[k] = m_sitedens[n]*xx[speciesName(k)]; + // m_lattice[k] = n; + // } + // } + + // } + // for (k = 0; k < m_kk; k++) { + // if (m_lattice[k] == -1) { + // throw CanteraError("LatticeSolidPhase::" + // "setParametersFromXML","Species "+speciesName(k) + // +" not a member of any lattice."); + // } + // } + // setMoleFractions(DATA_PTR(conc)); + } + + //==================================================================================================================== + void LatticeSolidPhase::_updateThermo() const { + doublereal tnow = temperature(); + // if (fabs(molarDensity() - m_molar_density)/m_molar_density > 0.0001) { + // throw CanteraError("_updateThermo","molar density changed from " + // +fp2str(m_molar_density)+" to "+fp2str(molarDensity())); + //} + if (m_tlast != tnow) { + int n; + getMoleFractions(DATA_PTR(m_x)); + int strt = 0; + for (n = 0; n < m_nlattice; n++) { + m_lattice[n]->setTemperature(tnow); + m_lattice[n]->setMoleFractions(DATA_PTR(m_x) + strt); + m_lattice[n]->setPressure(m_press); + strt += m_lattice[n]->nSpecies(); + } + m_tlast = tnow; + } + } + //==================================================================================================================== + void LatticeSolidPhase::setLatticeMoleFractions(int nn, std::string x) { + m_lattice[nn]->setMoleFractionsByName(x); + int n, k, loc=0, nsp; + doublereal ndens; + for (n = 0; n < m_nlattice; n++) { + nsp = m_lattice[n]->nSpecies(); + ndens = m_lattice[n]->molarDensity(); + for (k = 0; k < nsp; k++) { + m_x[loc] = ndens * m_lattice[n]->moleFraction(k); + loc++; + } + } + setMoleFractions(DATA_PTR(m_x)); + } + //==================================================================================================================== + void LatticeSolidPhase::setParametersFromXML(const XML_Node& eosdata) { + eosdata._require("model","LatticeSolid"); + XML_Node& la = eosdata.child("LatticeArray"); + std::vector lattices; + la.getChildren("phase",lattices); + int n; + int nl = lattices.size(); + m_nlattice = nl; + for (n = 0; n < nl; n++) { + XML_Node& i = *lattices[n]; + m_lattice.push_back((LatticePhase*)newPhase(i)); + } + } + //==================================================================================================================== + + + doublereal LatticeSolidPhase::err(std::string msg) const { + throw CanteraError("LatticeSolidPhase","Unimplemented " + msg); + return 0.0; + } + +} // End namespace Cantera +//====================================================================================================================== +#endif // End #define WITH_LATTICE_SOLID +//====================================================================================================================== diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index 16f1bc4a7..c605ae119 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -27,19 +27,44 @@ #include "mix_defs.h" #include "ThermoPhase.h" #include "SpeciesThermo.h" +#include "LatticePhase.h" #include "utilities.h" namespace Cantera { - class LatticePhase; - - //! Additive combination of lattice phases + //! A phase that is comprised of an additive combination of other lattice phases /*! + * This is the main way Cantera describes semiconductors and other solid phases. + * This Thermophase object calculates its properties as a sum over other LatticePhase objects. Each of the %LatticePhase + * objects is a ThermoPhase object by itself. * + * The sum over the LatticePhase objects is carried out by weighting each LatticePhase object + * value with the molarDensity of the LatticePhase. Then the resulting quantity is divided by + * the molar density of the total compound. The LatticeSolidPhase object therefore only contains a + * listing of the number of Lattice Phases + * that comprises the solid and it contains a value for the molar density of the entire mixture. + * + * Let's take FeS2 as an example, which may be thought of as a combination of two lattices: Fe and S lattice. + * The Fe sublattice has a molar density of 1 gmol cm-3. The S sublattice has a molar density of 2 gmol cm-3. + * We then define the LatticeSolidPhase object as having a nominal composition of FeS2, and having a + * molar density of 1 gmol cm-3. All quantities pertaining to the FeS2 compound will be have weights + * associated with the sublattices. The Fe sublattice will have a weight of 1.0 associated with it. The + * S sublattice will have a weight of 2.0 associated with it. + * + * Currently, the molar density is set to a constant. + * + * The results from this LatticeSolidPhase model reduces to the LatticePhase model when there is one + * lattice phase and the molar densities of the sublattice and the molar density within the LatticeSolidPhase + * have the same values. + * + * The mole fraction vector has been redefined within the LatticeSolidPhase object. The mole fractions sum + * to one within each of the individual lattice phases. The routine getMoleFraction() and setMoleFraction() + * have been redefined to use this convention. + * */ - class LatticeSolidPhase : public ThermoPhase { + class LatticeSolidPhase : public ThermoPhase { public: @@ -77,41 +102,166 @@ namespace Cantera { */ virtual int eosType() const { return cLatticeSolid; } + //! This method returns the convention used in specification + //! of the standard state, of which there are currently two, + //! temperature based, and variable pressure based. + /*! + * All of the thermo is determined by slave %ThermoPhase routines. + */ + virtual int standardStateConvention() const { + return cSS_CONVENTION_SLAVE; + } + //! Return the Molar Enthalpy. Units: J/kmol. /*! - * For an ideal solution, - * \f[ - * \hat h(T,P) = \sum_k X_k \hat h^0_k(T), - * \f] - * and is a function only of temperature. - * The standard-state pure-species Enthalpies - * \f$ \hat h^0_k(T) \f$ are computed by the species thermodynamic - * property manager. + * The molar enthalpy is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. * - * \see SpeciesThermo + * \f[ + * \tilde h(T,P) = \frac{\sum_n C_n \tilde h_n(T,P) }{C_T}, + * \f] + * + * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. + * + * units J/kmol */ virtual doublereal enthalpy_mole() const; + + //! Return the Molar Internal Energy. Units: J/kmol. + /*! + * The molar internal energy is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. + * + * \f[ + * \tilde u(T,P) = \frac{\sum_n C_n \tilde u_n(T,P) }{C_T}, + * \f] + * + * \f$ \tilde u_n(T,P) \f$ is the internal energy of the nth lattice. + * + * units J/kmol + */ virtual doublereal intEnergy_mole() const; + //! Return the Molar Entropy. Units: J/kmol/K. + /*! + * The molar entropy is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. + * + * \f[ + * \tilde s(T,P) = \frac{\sum_n C_n \tilde s_n(T,P) }{C_T}, + * \f] + * + * \f$ \tilde s_n(T,P) \f$ is the molar entropy of the nth lattice. + * + * units J/kmol/K + */ virtual doublereal entropy_mole() const; + //! Return the Molar Enthalpy. Units: J/kmol. + /*! + * The molar enthalpy is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. + * + * \f[ + * \tilde h(T,P) = \frac{\sum_n C_n \tilde h_n(T,P) }{C_T}, + * \f] + * + * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. + * + * units J/kmol + */ virtual doublereal gibbs_mole() const; + //! Return the constant pressure heat capacity. Units: J/kmol/K + /*! + * The molar constant pressure heat capacity is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. + * + * \f[ + * \tilde c_{p,n}(T,P) = \frac{\sum_n C_n \tilde c_{p,n}(T,P) }{C_T}, + * \f] + * + * \f$ \tilde c_{p,n}(T,P) \f$ is the heat capacity of the nth lattice. + * + * units J/kmol/K + */ virtual doublereal cp_mole() const; + //! Return the constant volume heat capacity. Units: J/kmol/K + /*! + * The molar constant volume heat capacity is determined by the following formula, where \f$ C_n \f$ is the + * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density + * of the solid compound. + * + * \f[ + * \tilde c_{v,n}(T,P) = \frac{\sum_n C_n \tilde c_{v,n}(T,P) }{C_T}, + * \f] + * + * \f$ \tilde c_{v,n}(T,P) \f$ is the heat capacity of the nth lattice. + * + * units J/kmol/K + */ virtual doublereal cv_mole() const { return cp_mole(); } + //! Report the Pressure. Units: Pa. + /*! + * This method simply returns the storred pressure value. + */ virtual doublereal pressure() const { return m_press; } + //! Set the pressure at constant temperature. Units: Pa. + /*! + * + * @param p Pressure (units - Pa) + */ virtual void setPressure(doublereal p) { m_press = p; setMolarDensity(m_molar_density); } + virtual void setMoleFractions(const doublereal *x); + virtual void getMoleFractions(doublereal *x) const; + + doublereal moleFraction(const int k) const { + return err("not implemented"); + } + + + void getMassFractions(doublereal* const y) const { + err("not implemented"); + } + doublereal massFraction(const int k) const { + return err("not implemented"); + } + + virtual void setMassFractions(const doublereal *y) { + err("not implemented"); + } + virtual void setMassFractions_NoNorm(const doublereal* const y) { + err("not implemented"); + } + + void getConcentrations(doublereal* const c) const { + err("not implemented"); + } + + doublereal concentration(int k) const { + return err("not implemented"); + } + + virtual void setConcentrations(const doublereal* const conc) { + err("not implemented"); + } + virtual void getActivityConcentrations(doublereal* c) const; @@ -145,6 +295,15 @@ namespace Cantera { } #endif + private: + //! error routine + /*! + * @param msg Message + * + * @return nothing + */ + doublereal err(std::string msg) const; + protected: int m_mm; @@ -164,5 +323,6 @@ namespace Cantera { }; } -#endif +#endif // #ifdef WITH_LATTICE_SOLID + #endif diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 7913d50d4..8e3f52035 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -627,7 +627,7 @@ namespace Cantera { // Perform any required subclass-specific initialization // that requires the XML phase object - string id = ""; + std::string id = ""; th->initThermoXML(phase, id); return true; diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 69b517e9c..19887fa1f 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -37,9 +37,11 @@ namespace Cantera { */ //@{ //! Standard state uses the molar convention - const int cSS_CONVENTION_TEMPERATURE = 0; + const int cSS_CONVENTION_TEMPERATURE = 0; //! Standard state uses the molality convention - const int cSS_CONVENTION_VPSS = 1; + const int cSS_CONVENTION_VPSS = 1; + //! Standard state thermodynamics is obtained from slave %ThermoPhase objects + const int cSS_CONVENTION_SLAVE = 2; //@} @@ -1085,6 +1087,10 @@ namespace Cantera { * * - Variable Pressure and Temperature -based activities * cSS_CONVENTION_VPSS 1 + * + * - Thermodynamics is set via slave ThermoPhase objects with + * nothing being carried out at this %ThermoPhase object level + * cSS_CONVENTION_SLAVE 2 */ virtual int standardStateConvention() const; From 1f2afb41e2577c04b0804133dae33d59b5eede86 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 22 Jun 2010 15:52:49 +0000 Subject: [PATCH 166/446] More work with LatticeSolidPhase. Still not ready for prime time. --- Cantera/src/thermo/LatticeSolidPhase.cpp | 32 ++++++++++++++++++++++++ Cantera/src/thermo/LatticeSolidPhase.h | 6 +++++ Cantera/src/thermo/ThermoFactory.cpp | 20 +++++++++++++-- Cantera/src/thermo/ThermoPhase.cpp | 10 +++++--- Cantera/src/thermo/ThermoPhase.h | 6 +++++ 5 files changed, 69 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index 64da30a24..f4f2a911e 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -249,6 +249,38 @@ namespace Cantera { } } //==================================================================================================================== + void LatticeSolidPhase::installSlavePhases(Cantera::XML_Node* phaseNode) + { + int m, k; + for (int n = 0; n < m_nlattice; n++) { + LatticePhase *lp = m_lattice[n]; + int nsp = lp->nSpecies(); + vector constArr(lp->nElements()); + for (k = 0; k < nsp; k++) { + std::string sname = lp->speciesName(k); + std::map comp; + lp->getAtoms(k, DATA_PTR(constArr)); + for (m = 0; m < lp->nElements(); m++) { + if (constArr[m] != 0.0) { + std::string ename = lp->elementName(m); + comp[ename] = constArr[m]; + } + } + int nel = nElements(); + vector_fp ecomp(nel, 0.0); + for (m = 0; m < nel; m++) { + double anum = comp[elementName(m)]; + if (anum != 0.0) { + ecomp[m] = anum; + } + } + double chrg = lp->charge(k); + double sz = lp->size(k); + addUniqueSpecies(sname, &ecomp[0], chrg, sz); + } + } + } + //==================================================================================================================== void LatticeSolidPhase::initThermo() { m_kk = nSpecies(); m_mm = nElements(); diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index c605ae119..e8ee4d510 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -274,6 +274,12 @@ namespace Cantera { virtual void initThermo(); + //! Add in species from Slave phases + /*! + * This hook is used for cSS_CONVENTION_SLAVE phases + */ + virtual void installSlavePhases(Cantera::XML_Node* phaseNode); + virtual void setParametersFromXML(const XML_Node& eosdata); void setLatticeMoleFractions(int n, std::string x); diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 8e3f52035..11741b193 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -561,7 +561,7 @@ namespace Cantera { // file. db = get_XML_Node(speciesArray["datasrc"], &phase.root()); if (db == 0) { - throw CanteraError("importPhase", + throw CanteraError("importPhase()", " Can not find XML node for species database: " + speciesArray["datasrc"]); } @@ -597,17 +597,29 @@ namespace Cantera { // install it in the phase object th->setSpeciesThermo(spth); - } else { + } else if (ssConvention == cSS_CONVENTION_SLAVE) { + /* + * No species thermo manager for this type + */ + } else if (ssConvention == cSS_CONVENTION_VPSS) { vp_spth = newVPSSMgr(vpss_ptr, &phase, spDataNodeList); vpss_ptr->setVPSSMgr(vp_spth); spth = vp_spth->SpeciesThermoMgr(); th->setSpeciesThermo(spth); + } else { + throw CanteraError("importPhase()", "unknown convention"); } int k = 0; int nsp = spDataNodeList.size(); + if (ssConvention == cSS_CONVENTION_SLAVE) { + if (nsp > 0) { + throw CanteraError("importPhase()", "For Slave standard states, number of species must be zero: " + + int2str(nsp)); + } + } for (int i = 0; i < nsp; i++) { XML_Node *s = spDataNodeList[i]; AssertTrace(s != 0); @@ -619,6 +631,10 @@ namespace Cantera { } } + if (ssConvention == cSS_CONVENTION_SLAVE) { + th->installSlavePhases(&phase); + } + // done adding species. th->freezeSpecies(); diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index afc819617..c1d1034a5 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -941,16 +941,20 @@ namespace Cantera { } xMol_Ref.resize(m_kk, 0.0); } + //==================================================================================================================== + void ThermoPhase::installSlavePhases(Cantera::XML_Node* phaseNode) { + } + //==================================================================================================================== void ThermoPhase::saveSpeciesData(const int k, const XML_Node* const data) { if ((int) m_speciesData.size() < (k + 1)) { m_speciesData.resize(k+1, 0); } m_speciesData[k] = new XML_Node(*data); } - - //! Return a pointer to the XML tree containing the species - /// data for this phase. + //==================================================================================================================== + // Return a pointer to the XML tree containing the species + // data for this phase. const std::vector & ThermoPhase::speciesData() const { if ((int) m_speciesData.size() != m_kk) { throw CanteraError("ThermoPhase::speciesData", diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 19887fa1f..1d3f82443 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2016,6 +2016,12 @@ namespace Cantera { */ virtual void initThermo(); + //! Add in species from Slave phases + /*! + * This hook is used for cSS_CONVENTION_SLAVE phases + */ + virtual void installSlavePhases(Cantera::XML_Node* phaseNode); + // The following methods are used by the clib interface // library, and should not be used by application programs. From 63aadd5ab06c8df82344a220efc766992b04fe7f Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Tue, 22 Jun 2010 20:42:49 +0000 Subject: [PATCH 167/446] Added getActivityConcentrations, standardConcentration, logStandarConc to MargulesVPSSTP so it can be used in reactions --- Cantera/src/thermo/MargulesVPSSTP.cpp | 33 +++++++++++++++++++++++---- Cantera/src/thermo/MargulesVPSSTP.h | 19 ++++++++++++++- 2 files changed, 47 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 216e6a273..708d0e130 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -340,15 +340,40 @@ namespace Cantera { * - Activities, Standard States, Activity Concentrations ----------- */ + // This method returns an array of generalized concentrations + /* + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * Here we define the activity concentrations as equal + * to the activities, because the standard concentration is 1. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + void MargulesVPSSTP::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } doublereal MargulesVPSSTP::standardConcentration(int k) const { - err("standardConcentration"); - return -1.0; + //err("standardConcentration"); + //return -1.0; + return 1.0; } doublereal MargulesVPSSTP::logStandardConc(int k) const { - err("logStandardConc"); - return -1.0; + //err("logStandardConc"); + //return -1.0; + return 0.0; } // Get the array of non-dimensional molar-based activity coefficients at diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 53a57904a..7e92c4a6b 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -474,7 +474,24 @@ namespace Cantera { * @{ */ - + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; /** From 7d901ed74f1255a33f26c0c985b7fc0b5f25e71c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Jun 2010 16:04:29 +0000 Subject: [PATCH 168/446] Added in duplication routines. Added in a shallow pointer copy facility. --- Cantera/src/kinetics/GasKinetics.cpp | 1175 +++++++++++--------- Cantera/src/kinetics/GasKinetics.h | 748 +++++++------ Cantera/src/kinetics/InterfaceKinetics.cpp | 10 +- Cantera/src/kinetics/InterfaceKinetics.h | 14 +- Cantera/src/kinetics/Kinetics.cpp | 72 +- Cantera/src/kinetics/Kinetics.h | 60 +- 6 files changed, 1134 insertions(+), 945 deletions(-) diff --git a/Cantera/src/kinetics/GasKinetics.cpp b/Cantera/src/kinetics/GasKinetics.cpp index 4633a08ee..9aeff996e 100644 --- a/Cantera/src/kinetics/GasKinetics.cpp +++ b/Cantera/src/kinetics/GasKinetics.cpp @@ -29,636 +29,711 @@ using namespace std; namespace Cantera { + //==================================================================================================================== + /* + * Construct an empty reaction mechanism. + */ + GasKinetics:: + GasKinetics(thermo_t* thermo) : + Kinetics(), + m_kk(0), + m_nfall(0), + m_nirrev(0), + m_nrev(0), + m_finalized(false) + { + if (thermo != 0) addPhase(*thermo); + m_kdata = new GasKineticsData; + m_kdata->m_temp = 0.0; + m_rxnstoich = new ReactionStoichMgr; + } - /** - * Construct an empty reaction mechanism. - */ - GasKinetics:: - GasKinetics(thermo_t* thermo) : - Kinetics(), - m_kk(0), - m_nfall(0), - m_nirrev(0), - m_nrev(0), - m_finalized(false) - { - if (thermo != 0) addPhase(*thermo); - m_kdata = new GasKineticsData; - m_kdata->m_temp = 0.0; - m_rxnstoich = new ReactionStoichMgr; - } + //==================================================================================================================== + GasKinetics::GasKinetics(const GasKinetics &right) : + Kinetics(), + m_kk(0), + m_nfall(0), + m_nirrev(0), + m_nrev(0), + m_finalized(false) + { + *this = right; + } + //==================================================================================================================== + GasKinetics::~GasKinetics() + { + delete m_kdata; + delete m_rxnstoich; + } + //==================================================================================================================== + GasKinetics& GasKinetics::operator=(const GasKinetics &right) + { + if (this == &right) return *this; - GasKinetics:: - ~GasKinetics() {delete m_kdata; delete m_rxnstoich;} + Kinetics::operator=(right); + + m_kk = right.m_kk; + m_nfall = right.m_nfall; + m_fallindx = right.m_fallindx; + m_falloff_low_rates = right.m_falloff_low_rates; + m_falloff_high_rates = right.m_falloff_high_rates; + m_rates = right.m_rates; + m_index = right.m_index; + m_falloffn = right.m_falloffn; + m_3b_concm = right.m_3b_concm; + m_falloff_concm = right.m_falloff_concm; + m_irrev = right.m_irrev; + m_rxnstoich = right.m_rxnstoich; + m_fwdOrder = right.m_fwdOrder; + m_nirrev = right.m_nirrev; + m_nrev = right.m_nrev; + m_rgroups = right.m_rgroups; + m_pgroups = right.m_pgroups; + m_rxntype = right.m_rxntype; + m_rrxn = right.m_rrxn; + m_prxn = right.m_prxn; + m_dn = right.m_dn; + m_revindex = right.m_revindex; + m_rxneqn = right.m_rxneqn; + m_kdata = right.m_kdata; + m_conc = right.m_conc; + m_grt = right.m_grt; + m_finalized = right.m_finalized; - /** - * Update temperature-dependent portions of reaction rates and - * falloff functions. - */ - void GasKinetics:: - update_T() {} + throw CanteraError("GasKinetics::operator=()", + "Unfinished implementation"); - void GasKinetics:: - update_C() {} + return *this; + } + //==================================================================================================================== + // Duplication routine for objects which inherit from Kinetics + /* + * This virtual routine can be used to duplicate %Kinetics objects + * inherited from %Kinetics even if the application only has + * a pointer to %Kinetics to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object + */ + Kinetics *GasKinetics::duplMyselfAsKinetics(const std::vector & tpVector) const { + GasKinetics* gK = new GasKinetics(*this); + gK->assignShallowPointers(tpVector); + return dynamic_cast(gK); + } + //==================================================================================================================== + /** + * Update temperature-dependent portions of reaction rates and + * falloff functions. + */ + void GasKinetics::update_T() + { + } + //==================================================================================================================== + void GasKinetics:: + update_C() {} + //==================================================================================================================== + void GasKinetics:: + _update_rates_T() { + doublereal T = thermo().temperature(); + m_kdata->m_logStandConc = log(thermo().standardConcentration()); + //if (fabs(T - m_kdata->m_temp) > 0.0) { + doublereal logT = log(T); + m_rates.update(T, logT, &m_kdata->m_rfn[0]); + m_falloff_low_rates.update(T, logT, &m_kdata->m_rfn_low[0]); + m_falloff_high_rates.update(T, logT, &m_kdata->m_rfn_high[0]); + m_falloffn.updateTemp(T, &m_kdata->falloff_work[0]); + m_kdata->m_temp = T; + updateKc(); + m_kdata->m_ROP_ok = false; + //} + }; - void GasKinetics:: - _update_rates_T() { - doublereal T = thermo().temperature(); - m_kdata->m_logStandConc = log(thermo().standardConcentration()); - //if (fabs(T - m_kdata->m_temp) > 0.0) { - doublereal logT = log(T); - m_rates.update(T, logT, &m_kdata->m_rfn[0]); - m_falloff_low_rates.update(T, logT, &m_kdata->m_rfn_low[0]); - m_falloff_high_rates.update(T, logT, &m_kdata->m_rfn_high[0]); - m_falloffn.updateTemp(T, &m_kdata->falloff_work[0]); - m_kdata->m_temp = T; - updateKc(); - m_kdata->m_ROP_ok = false; - //} - }; - - - /** - * Update properties that depend on concentrations. Currently only - * the enhanced collision partner concentrations are updated here. - */ - void GasKinetics:: - _update_rates_C() { - thermo().getActivityConcentrations(&m_conc[0]); - doublereal ctot = thermo().molarDensity(); - m_3b_concm.update(m_conc, ctot, &m_kdata->concm_3b_values[0]); - m_falloff_concm.update(m_conc, ctot, - &m_kdata->concm_falloff_values[0]); - m_kdata->m_ROP_ok = false; - } - - /** - * Update the equilibrium constants in molar units. - */ - void GasKinetics::updateKc() { - int i, irxn; - vector_fp& m_rkc = m_kdata->m_rkcn; + //==================================================================================================================== + /** + * Update properties that depend on concentrations. Currently only + * the enhanced collision partner concentrations are updated here. + */ + void GasKinetics:: + _update_rates_C() { + thermo().getActivityConcentrations(&m_conc[0]); + doublereal ctot = thermo().molarDensity(); + m_3b_concm.update(m_conc, ctot, &m_kdata->concm_3b_values[0]); + m_falloff_concm.update(m_conc, ctot, + &m_kdata->concm_falloff_values[0]); + m_kdata->m_ROP_ok = false; + } + //==================================================================================================================== + /** + * Update the equilibrium constants in molar units. + */ + void GasKinetics::updateKc() { + int i, irxn; + vector_fp& m_rkc = m_kdata->m_rkcn; - thermo().getStandardChemPotentials(&m_grt[0]); - fill(m_rkc.begin(), m_rkc.end(), 0.0); + thermo().getStandardChemPotentials(&m_grt[0]); + fill(m_rkc.begin(), m_rkc.end(), 0.0); - // compute Delta G^0 for all reversible reactions - m_rxnstoich->getRevReactionDelta(m_ii, &m_grt[0], &m_rkc[0]); + // compute Delta G^0 for all reversible reactions + m_rxnstoich->getRevReactionDelta(m_ii, &m_grt[0], &m_rkc[0]); - doublereal logStandConc = m_kdata->m_logStandConc; - doublereal rrt = 1.0/(GasConstant * thermo().temperature()); - for (i = 0; i < m_nrev; i++) { - irxn = m_revindex[i]; - m_rkc[irxn] = exp(m_rkc[irxn]*rrt - m_dn[irxn]*logStandConc); - } - - for(i = 0; i != m_nirrev; ++i) { - m_rkc[ m_irrev[i] ] = 0.0; - } + doublereal logStandConc = m_kdata->m_logStandConc; + doublereal rrt = 1.0/(GasConstant * thermo().temperature()); + for (i = 0; i < m_nrev; i++) { + irxn = m_revindex[i]; + m_rkc[irxn] = exp(m_rkc[irxn]*rrt - m_dn[irxn]*logStandConc); } - /** - * Get the equilibrium constants of all reactions, whether - * reversible or not. - */ - void GasKinetics::getEquilibriumConstants(doublereal* kc) { - int i; - _update_rates_T(); - vector_fp& rkc = m_kdata->m_rkcn; - //thermo().getGibbs_RT(m_grt.begin()); - thermo().getStandardChemPotentials(&m_grt[0]); - fill(rkc.begin(), rkc.end(), 0.0); + for(i = 0; i != m_nirrev; ++i) { + m_rkc[ m_irrev[i] ] = 0.0; + } + } + //==================================================================================================================== + /** + * Get the equilibrium constants of all reactions, whether + * reversible or not. + */ + void GasKinetics::getEquilibriumConstants(doublereal* kc) { + int i; + _update_rates_T(); + vector_fp& rkc = m_kdata->m_rkcn; + //thermo().getGibbs_RT(m_grt.begin()); + thermo().getStandardChemPotentials(&m_grt[0]); + fill(rkc.begin(), rkc.end(), 0.0); - // compute Delta G^0 for all reactions - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], &rkc[0]); + // compute Delta G^0 for all reactions + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], &rkc[0]); - doublereal logStandConc = m_kdata->m_logStandConc; - doublereal rrt = 1.0/(GasConstant * thermo().temperature()); - for (i = 0; i < m_ii; i++) { - kc[i] = exp(-rkc[i]*rrt + m_dn[i]*logStandConc); - } - - // force an update of T-dependent properties, so that m_rkcn will - // be updated before it is used next. - m_kdata->m_temp = 0.0; + doublereal logStandConc = m_kdata->m_logStandConc; + doublereal rrt = 1.0/(GasConstant * thermo().temperature()); + for (i = 0; i < m_ii; i++) { + kc[i] = exp(-rkc[i]*rrt + m_dn[i]*logStandConc); } - /** - * - * getDeltaGibbs(): - * - * Return the vector of values for the reaction gibbs free energy - * change - * These values depend upon the concentration - * of the ideal gas. - * - * units = J kmol-1 + // force an update of T-dependent properties, so that m_rkcn will + // be updated before it is used next. + m_kdata->m_temp = 0.0; + } + //==================================================================================================================== + /** + * + * getDeltaGibbs(): + * + * Return the vector of values for the reaction gibbs free energy + * change + * These values depend upon the concentration + * of the ideal gas. + * + * units = J kmol-1 + */ + void GasKinetics::getDeltaGibbs(doublereal* deltaG) { + /* + * Get the chemical potentials of the species in the + * ideal gas solution. */ - void GasKinetics::getDeltaGibbs(doublereal* deltaG) { - /* - * Get the chemical potentials of the species in the - * ideal gas solution. - */ - thermo().getChemPotentials(&m_grt[0]); - /* - * Use the stoichiometric manager to find deltaG for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaG); - } - - /** - * - * getDeltaEnthalpy(): - * - * Return the vector of values for the reactions change in - * enthalpy. - * These values depend upon the concentration - * of the solution. - * - * units = J kmol-1 + thermo().getChemPotentials(&m_grt[0]); + /* + * Use the stoichiometric manager to find deltaG for each + * reaction. */ - void GasKinetics::getDeltaEnthalpy(doublereal* deltaH) { - /* - * Get the partial molar enthalpy of all species in the - * ideal gas. - */ - thermo().getPartialMolarEnthalpies(&m_grt[0]); - /* - * Use the stoichiometric manager to find deltaG for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaH); - } - - /************************************************************************ - * - * getDeltaEntropy(): - * - * Return the vector of values for the reactions change in - * entropy. - * These values depend upon the concentration - * of the solution. - * - * units = J kmol-1 Kelvin-1 + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaG); + } + //==================================================================================================================== + /** + * + * getDeltaEnthalpy(): + * + * Return the vector of values for the reactions change in + * enthalpy. + * These values depend upon the concentration + * of the solution. + * + * units = J kmol-1 + */ + void GasKinetics::getDeltaEnthalpy(doublereal* deltaH) { + /* + * Get the partial molar enthalpy of all species in the + * ideal gas. */ - void GasKinetics::getDeltaEntropy( doublereal* deltaS) { - /* - * Get the partial molar entropy of all species in the - * solid solution. - */ - thermo().getPartialMolarEntropies(&m_grt[0]); - /* - * Use the stoichiometric manager to find deltaS for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaS); - } - - /** - * - * getDeltaSSGibbs(): - * - * Return the vector of values for the reaction - * standard state gibbs free energy change. - * These values don't depend upon the concentration - * of the solution. - * - * units = J kmol-1 + thermo().getPartialMolarEnthalpies(&m_grt[0]); + /* + * Use the stoichiometric manager to find deltaG for each + * reaction. */ - void GasKinetics::getDeltaSSGibbs(doublereal* deltaG) { - /* - * Get the standard state chemical potentials of the species. - * This is the array of chemical potentials at unit activity - * We define these here as the chemical potentials of the pure - * species at the temperature and pressure of the solution. - */ - thermo().getStandardChemPotentials(&m_grt[0]); - /* - * Use the stoichiometric manager to find deltaG for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaG); - } - - /** - * - * getDeltaSSEnthalpy(): - * - * Return the vector of values for the change in the - * standard state enthalpies of reaction. - * These values don't depend upon the concentration - * of the solution. - * - * units = J kmol-1 + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaH); + } + //==================================================================================================================== + /* + * + * getDeltaEntropy(): + * + * Return the vector of values for the reactions change in + * entropy. + * These values depend upon the concentration + * of the solution. + * + * units = J kmol-1 Kelvin-1 + */ + void GasKinetics::getDeltaEntropy( doublereal* deltaS) { + /* + * Get the partial molar entropy of all species in the + * solid solution. */ - void GasKinetics::getDeltaSSEnthalpy(doublereal* deltaH) { - /* - * Get the standard state enthalpies of the species. - * This is the array of chemical potentials at unit activity - * We define these here as the enthalpies of the pure - * species at the temperature and pressure of the solution. - */ - thermo().getEnthalpy_RT(&m_grt[0]); - doublereal RT = thermo().temperature() * GasConstant; - for (int k = 0; k < m_kk; k++) { - m_grt[k] *= RT; - } - /* - * Use the stoichiometric manager to find deltaG for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaH); - } - - /********************************************************************* - * - * getDeltaSSEntropy(): - * - * Return the vector of values for the change in the - * standard state entropies for each reaction. - * These values don't depend upon the concentration - * of the solution. - * - * units = J kmol-1 Kelvin-1 + thermo().getPartialMolarEntropies(&m_grt[0]); + /* + * Use the stoichiometric manager to find deltaS for each + * reaction. */ - void GasKinetics::getDeltaSSEntropy(doublereal* deltaS) { - /* - * Get the standard state entropy of the species. - * We define these here as the entropies of the pure - * species at the temperature and pressure of the solution. - */ - thermo().getEntropy_R(&m_grt[0]); - doublereal R = GasConstant; - for (int k = 0; k < m_kk; k++) { - m_grt[k] *= R; - } - /* - * Use the stoichiometric manager to find deltaS for each - * reaction. - */ - m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaS); + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaS); + } + //==================================================================================================================== + /** + * + * getDeltaSSGibbs(): + * + * Return the vector of values for the reaction + * standard state gibbs free energy change. + * These values don't depend upon the concentration + * of the solution. + * + * units = J kmol-1 + */ + void GasKinetics::getDeltaSSGibbs(doublereal* deltaG) { + /* + * Get the standard state chemical potentials of the species. + * This is the array of chemical potentials at unit activity + * We define these here as the chemical potentials of the pure + * species at the temperature and pressure of the solution. + */ + thermo().getStandardChemPotentials(&m_grt[0]); + /* + * Use the stoichiometric manager to find deltaG for each + * reaction. + */ + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaG); + } + //==================================================================================================================== + /** + * + * getDeltaSSEnthalpy(): + * + * Return the vector of values for the change in the + * standard state enthalpies of reaction. + * These values don't depend upon the concentration + * of the solution. + * + * units = J kmol-1 + */ + void GasKinetics::getDeltaSSEnthalpy(doublereal* deltaH) { + /* + * Get the standard state enthalpies of the species. + * This is the array of chemical potentials at unit activity + * We define these here as the enthalpies of the pure + * species at the temperature and pressure of the solution. + */ + thermo().getEnthalpy_RT(&m_grt[0]); + doublereal RT = thermo().temperature() * GasConstant; + for (int k = 0; k < m_kk; k++) { + m_grt[k] *= RT; + } + /* + * Use the stoichiometric manager to find deltaG for each + * reaction. + */ + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaH); + } + //==================================================================================================================== + /********************************************************************* + * + * getDeltaSSEntropy(): + * + * Return the vector of values for the change in the + * standard state entropies for each reaction. + * These values don't depend upon the concentration + * of the solution. + * + * units = J kmol-1 Kelvin-1 + */ + void GasKinetics::getDeltaSSEntropy(doublereal* deltaS) { + /* + * Get the standard state entropy of the species. + * We define these here as the entropies of the pure + * species at the temperature and pressure of the solution. + */ + thermo().getEntropy_R(&m_grt[0]); + doublereal R = GasConstant; + for (int k = 0; k < m_kk; k++) { + m_grt[k] *= R; + } + /* + * Use the stoichiometric manager to find deltaS for each + * reaction. + */ + m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaS); + } + + void GasKinetics::processFalloffReactions() { + + int i; + const vector_fp& fc = m_kdata->concm_falloff_values; + const array_fp& m_rf_low = m_kdata->m_rfn_low; + const array_fp& m_rf_high = m_kdata->m_rfn_high; + + // use m_ropr for temporary storage of reduced pressure + array_fp& pr = m_kdata->m_ropr; + + array_fp& ropf = m_kdata->m_ropf; + + for (i = 0; i < m_nfall; i++) { + pr[i] = fc[i] * m_rf_low[i] / m_rf_high[i]; } - void GasKinetics::processFalloffReactions() { - - int i; - const vector_fp& fc = m_kdata->concm_falloff_values; - const array_fp& m_rf_low = m_kdata->m_rfn_low; - const array_fp& m_rf_high = m_kdata->m_rfn_high; - - // use m_ropr for temporary storage of reduced pressure - array_fp& pr = m_kdata->m_ropr; - - array_fp& ropf = m_kdata->m_ropf; - - for (i = 0; i < m_nfall; i++) { - pr[i] = fc[i] * m_rf_low[i] / m_rf_high[i]; - } - - m_falloffn.pr_to_falloff( &pr[0], &m_kdata->falloff_work[0] ); + m_falloffn.pr_to_falloff( &pr[0], &m_kdata->falloff_work[0] ); - for (i = 0; i < m_nfall; i++) { - pr[i] *= m_rf_high[i]; - } - - scatter_copy(pr.begin(), pr.begin() + m_nfall, - ropf.begin(), m_fallindx.begin()); + for (i = 0; i < m_nfall; i++) { + pr[i] *= m_rf_high[i]; } + scatter_copy(pr.begin(), pr.begin() + m_nfall, + ropf.begin(), m_fallindx.begin()); + } - void GasKinetics::updateROP() { + //==================================================================================================================== + void GasKinetics::updateROP() { - _update_rates_T(); - _update_rates_C(); + _update_rates_T(); + _update_rates_C(); - if (m_kdata->m_ROP_ok) return; + if (m_kdata->m_ROP_ok) return; - const vector_fp& rf = m_kdata->m_rfn; - const vector_fp& m_rkc = m_kdata->m_rkcn; - array_fp& ropf = m_kdata->m_ropf; - array_fp& ropr = m_kdata->m_ropr; - array_fp& ropnet = m_kdata->m_ropnet; + const vector_fp& rf = m_kdata->m_rfn; + const vector_fp& m_rkc = m_kdata->m_rkcn; + array_fp& ropf = m_kdata->m_ropf; + array_fp& ropr = m_kdata->m_ropr; + array_fp& ropnet = m_kdata->m_ropnet; - // copy rate coefficients into ropf - copy(rf.begin(), rf.end(), ropf.begin()); + // copy rate coefficients into ropf + copy(rf.begin(), rf.end(), ropf.begin()); - // multiply ropf by enhanced 3b conc for all 3b rxns - m_3b_concm.multiply( &ropf[0], &m_kdata->concm_3b_values[0] ); + // multiply ropf by enhanced 3b conc for all 3b rxns + m_3b_concm.multiply( &ropf[0], &m_kdata->concm_3b_values[0] ); - processFalloffReactions(); + processFalloffReactions(); - // multiply by perturbation factor - multiply_each(ropf.begin(), ropf.end(), m_perturb.begin()); + // multiply by perturbation factor + multiply_each(ropf.begin(), ropf.end(), m_perturb.begin()); - // copy the forward rates to the reverse rates - copy(ropf.begin(), ropf.end(), ropr.begin()); + // copy the forward rates to the reverse rates + copy(ropf.begin(), ropf.end(), ropr.begin()); - // for reverse rates computed from thermochemistry, multiply - // the forward rates copied into m_ropr by the reciprocals of - // the equilibrium constants - multiply_each(ropr.begin(), ropr.end(), m_rkc.begin()); + // for reverse rates computed from thermochemistry, multiply + // the forward rates copied into m_ropr by the reciprocals of + // the equilibrium constants + multiply_each(ropr.begin(), ropr.end(), m_rkc.begin()); - // multiply ropf by concentration products - m_rxnstoich->multiplyReactants(&m_conc[0], &ropf[0]); - //m_reactantStoich.multiply(m_conc.begin(), ropf.begin()); + // multiply ropf by concentration products + m_rxnstoich->multiplyReactants(&m_conc[0], &ropf[0]); + //m_reactantStoich.multiply(m_conc.begin(), ropf.begin()); - // for reversible reactions, multiply ropr by concentration - // products - m_rxnstoich->multiplyRevProducts(&m_conc[0], &ropr[0]); - //m_revProductStoich.multiply(m_conc.begin(), ropr.begin()); + // for reversible reactions, multiply ropr by concentration + // products + m_rxnstoich->multiplyRevProducts(&m_conc[0], &ropr[0]); + //m_revProductStoich.multiply(m_conc.begin(), ropr.begin()); - for (int j = 0; j != m_ii; ++j) { - ropnet[j] = ropf[j] - ropr[j]; - } - - m_kdata->m_ROP_ok = true; + for (int j = 0; j != m_ii; ++j) { + ropnet[j] = ropf[j] - ropr[j]; } - /** - * - * getFwdRateConstants(): - * - * Update the rate of progress for the reactions. - * This key routine makes sure that the rate of progress vectors - * located in the solid kinetics data class are up to date. + m_kdata->m_ROP_ok = true; + } + //==================================================================================================================== + /** + * + * getFwdRateConstants(): + * + * Update the rate of progress for the reactions. + * This key routine makes sure that the rate of progress vectors + * located in the solid kinetics data class are up to date. + */ + void GasKinetics:: + getFwdRateConstants(doublereal *kfwd) { + _update_rates_T(); + _update_rates_C(); + + // copy rate coefficients into ropf + const vector_fp& rf = m_kdata->m_rfn; + array_fp& ropf = m_kdata->m_ropf; + copy(rf.begin(), rf.end(), ropf.begin()); + + // multiply ropf by enhanced 3b conc for all 3b rxns + m_3b_concm.multiply(&ropf[0], &m_kdata->concm_3b_values[0] ); + + /* + * This routine is hardcoded to replace some of the values + * of the ropf vector. */ - void GasKinetics:: - getFwdRateConstants(doublereal *kfwd) { - _update_rates_T(); - _update_rates_C(); + processFalloffReactions(); - // copy rate coefficients into ropf - const vector_fp& rf = m_kdata->m_rfn; - array_fp& ropf = m_kdata->m_ropf; - copy(rf.begin(), rf.end(), ropf.begin()); - - // multiply ropf by enhanced 3b conc for all 3b rxns - m_3b_concm.multiply(&ropf[0], &m_kdata->concm_3b_values[0] ); - - /* - * This routine is hardcoded to replace some of the values - * of the ropf vector. - */ - processFalloffReactions(); - - // multiply by perturbation factor - multiply_each(ropf.begin(), ropf.end(), m_perturb.begin()); + // multiply by perturbation factor + multiply_each(ropf.begin(), ropf.end(), m_perturb.begin()); - for (int i = 0; i < m_ii; i++) { - kfwd[i] = ropf[i]; - } + for (int i = 0; i < m_ii; i++) { + kfwd[i] = ropf[i]; } - - /** - * - * getRevRateConstants(): - * - * Return a vector of the reverse reaction rate constants - * - * Length is the number of reactions. units depends - * on many issues. Note, this routine will return rate constants - * for irreversible reactions if the default for - * doIrreversible is overridden. + } + //==================================================================================================================== + /** + * + * getRevRateConstants(): + * + * Return a vector of the reverse reaction rate constants + * + * Length is the number of reactions. units depends + * on many issues. Note, this routine will return rate constants + * for irreversible reactions if the default for + * doIrreversible is overridden. + */ + void GasKinetics:: + getRevRateConstants(doublereal *krev, bool doIrreversible) { + /* + * go get the forward rate constants. -> note, we don't + * really care about speed or redundancy in these + * informational routines. */ - void GasKinetics:: - getRevRateConstants(doublereal *krev, bool doIrreversible) { - /* - * go get the forward rate constants. -> note, we don't - * really care about speed or redundancy in these - * informational routines. - */ - getFwdRateConstants(krev); + getFwdRateConstants(krev); - if (doIrreversible) { - doublereal *tmpKc = &m_kdata->m_ropnet[0]; - getEquilibriumConstants(tmpKc); - for (int i = 0; i < m_ii; i++) { - krev[i] /= tmpKc[i]; - } - } else { - /* - * m_rkc[] is zero for irreversibly reactions - */ - const vector_fp& m_rkc = m_kdata->m_rkcn; - for (int i = 0; i < m_ii; i++) { - krev[i] *= m_rkc[i]; - } - } + if (doIrreversible) { + doublereal *tmpKc = &m_kdata->m_ropnet[0]; + getEquilibriumConstants(tmpKc); + for (int i = 0; i < m_ii; i++) { + krev[i] /= tmpKc[i]; + } + } else { + /* + * m_rkc[] is zero for irreversibly reactions + */ + const vector_fp& m_rkc = m_kdata->m_rkcn; + for (int i = 0; i < m_ii; i++) { + krev[i] *= m_rkc[i]; + } } + } + //==================================================================================================================== + void GasKinetics:: + addReaction(const ReactionData& r) { - void GasKinetics:: - addReaction(const ReactionData& r) { + if (r.reactionType == ELEMENTARY_RXN) addElementaryReaction(r); + else if (r.reactionType == THREE_BODY_RXN) addThreeBodyReaction(r); + else if (r.reactionType == FALLOFF_RXN) addFalloffReaction(r); - if (r.reactionType == ELEMENTARY_RXN) addElementaryReaction(r); - else if (r.reactionType == THREE_BODY_RXN) addThreeBodyReaction(r); - else if (r.reactionType == FALLOFF_RXN) addFalloffReaction(r); + // operations common to all reaction types + installReagents( r ); + installGroups(reactionNumber(), r.rgroups, r.pgroups); + incrementRxnCount(); + m_rxneqn.push_back(r.equation); + } - // operations common to all reaction types - installReagents( r ); - installGroups(reactionNumber(), r.rgroups, r.pgroups); - incrementRxnCount(); - m_rxneqn.push_back(r.equation); - } + //==================================================================================================================== + void GasKinetics:: + addFalloffReaction(const ReactionData& r) { + // install high and low rate coeff calculators - void GasKinetics:: - addFalloffReaction(const ReactionData& r) { - - // install high and low rate coeff calculators - - int iloc = m_falloff_high_rates.install(m_nfall, - r.rateCoeffType, - r.rateCoeffParameters.size(), - &r.rateCoeffParameters[0] ); + int iloc = m_falloff_high_rates.install(m_nfall, + r.rateCoeffType, + r.rateCoeffParameters.size(), + &r.rateCoeffParameters[0] ); - m_falloff_low_rates.install( m_nfall, - r.rateCoeffType, r.auxRateCoeffParameters.size(), - DATA_PTR(r.auxRateCoeffParameters) ); + m_falloff_low_rates.install( m_nfall, + r.rateCoeffType, r.auxRateCoeffParameters.size(), + DATA_PTR(r.auxRateCoeffParameters) ); - // add constant terms to high and low rate - // coeff value vectors - m_kdata->m_rfn_high.push_back(r.rateCoeffParameters[0]); - m_kdata->m_rfn_low.push_back(r.auxRateCoeffParameters[0]); + // add constant terms to high and low rate + // coeff value vectors + m_kdata->m_rfn_high.push_back(r.rateCoeffParameters[0]); + m_kdata->m_rfn_low.push_back(r.auxRateCoeffParameters[0]); - // add a dummy entry in m_rf, where computed falloff - // rate coeff will be put - m_kdata->m_rfn.push_back(0.0); + // add a dummy entry in m_rf, where computed falloff + // rate coeff will be put + m_kdata->m_rfn.push_back(0.0); - // add this reaction number to the list of - // falloff reactions - m_fallindx.push_back( reactionNumber() ); + // add this reaction number to the list of + // falloff reactions + m_fallindx.push_back( reactionNumber() ); - // install the enhanced third-body concentration - // calculator for this reaction - m_falloff_concm.install( m_nfall, r.thirdBodyEfficiencies, - r.default_3b_eff); + // install the enhanced third-body concentration + // calculator for this reaction + m_falloff_concm.install( m_nfall, r.thirdBodyEfficiencies, + r.default_3b_eff); - // install the falloff function calculator for - // this reaction - m_falloffn.install( m_nfall, r.falloffType, r.falloffParameters ); + // install the falloff function calculator for + // this reaction + m_falloffn.install( m_nfall, r.falloffType, r.falloffParameters ); - // forward rxn order equals number of reactants, since rate - // coeff is defined in terms of the high-pressure limit - m_fwdOrder.push_back(r.reactants.size()); + // forward rxn order equals number of reactants, since rate + // coeff is defined in terms of the high-pressure limit + m_fwdOrder.push_back(r.reactants.size()); - // increment the falloff reaction counter - ++m_nfall; - registerReaction( reactionNumber(), FALLOFF_RXN, iloc); - } + // increment the falloff reaction counter + ++m_nfall; + registerReaction( reactionNumber(), FALLOFF_RXN, iloc); + } + //==================================================================================================================== + void GasKinetics:: + addElementaryReaction(const ReactionData& r) { + int iloc; - void GasKinetics:: - addElementaryReaction(const ReactionData& r) { - int iloc; + // install rate coeff calculator + iloc = m_rates.install( reactionNumber(), + r.rateCoeffType, r.rateCoeffParameters.size(), + DATA_PTR(r.rateCoeffParameters) ); - // install rate coeff calculator - iloc = m_rates.install( reactionNumber(), - r.rateCoeffType, r.rateCoeffParameters.size(), - DATA_PTR(r.rateCoeffParameters) ); + // add constant term to rate coeff value vector + m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); - // add constant term to rate coeff value vector - m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); + // forward rxn order equals number of reactants + m_fwdOrder.push_back(r.reactants.size()); + registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc); + } - // forward rxn order equals number of reactants - m_fwdOrder.push_back(r.reactants.size()); - registerReaction( reactionNumber(), ELEMENTARY_RXN, iloc); - } - - - void GasKinetics:: - addThreeBodyReaction(const ReactionData& r) { + //==================================================================================================================== + void GasKinetics:: + addThreeBodyReaction(const ReactionData& r) { - int iloc; - // install rate coeff calculator - iloc = m_rates.install( reactionNumber(), - r.rateCoeffType, r.rateCoeffParameters.size(), - DATA_PTR(r.rateCoeffParameters) ); + int iloc; + // install rate coeff calculator + iloc = m_rates.install( reactionNumber(), + r.rateCoeffType, r.rateCoeffParameters.size(), + DATA_PTR(r.rateCoeffParameters) ); - // add constant term to rate coeff value vector - m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); + // add constant term to rate coeff value vector + m_kdata->m_rfn.push_back(r.rateCoeffParameters[0]); - // forward rxn order equals number of reactants + 1 - m_fwdOrder.push_back(r.reactants.size() + 1); - - m_3b_concm.install( reactionNumber(), r.thirdBodyEfficiencies, - r.default_3b_eff ); - registerReaction( reactionNumber(), THREE_BODY_RXN, iloc); - } + // forward rxn order equals number of reactants + 1 + m_fwdOrder.push_back(r.reactants.size() + 1); + m_3b_concm.install( reactionNumber(), r.thirdBodyEfficiencies, + r.default_3b_eff ); + registerReaction( reactionNumber(), THREE_BODY_RXN, iloc); + } + //==================================================================================================================== - void GasKinetics::installReagents(const ReactionData& r) { + void GasKinetics::installReagents(const ReactionData& r) { - m_kdata->m_ropf.push_back(0.0); // extend by one for new rxn - m_kdata->m_ropr.push_back(0.0); - m_kdata->m_ropnet.push_back(0.0); - int n, ns, m; - doublereal nsFlt; - doublereal reactantGlobalOrder = 0.0; - doublereal productGlobalOrder = 0.0; - int rnum = reactionNumber(); + m_kdata->m_ropf.push_back(0.0); // extend by one for new rxn + m_kdata->m_ropr.push_back(0.0); + m_kdata->m_ropnet.push_back(0.0); + int n, ns, m; + doublereal nsFlt; + doublereal reactantGlobalOrder = 0.0; + doublereal productGlobalOrder = 0.0; + int rnum = reactionNumber(); - vector_int rk; - int nr = r.reactants.size(); - for (n = 0; n < nr; n++) { - nsFlt = r.rstoich[n]; - reactantGlobalOrder += nsFlt; - ns = (int) nsFlt; - if ((doublereal) ns != nsFlt) { - if (ns < 1) { - ns = 1; - } - } - if (r.rstoich[n] != 0.0) - m_rrxn[r.reactants[n]][rnum] += r.rstoich[n]; - for (m = 0; m < ns; m++) { - rk.push_back(r.reactants[n]); - } - } - m_reactants.push_back(rk); - - vector_int pk; - int np = r.products.size(); - for (n = 0; n < np; n++) { - nsFlt = r.pstoich[n]; - productGlobalOrder += nsFlt; - ns = (int) nsFlt; - if ((double) ns != nsFlt) { - if (ns < 1) { - ns = 1; - } - } - if (r.pstoich[n] != 0.0) - m_prxn[r.products[n]][rnum] += r.pstoich[n]; - for (m = 0; m < ns; m++) { - pk.push_back(r.products[n]); - } - } - m_products.push_back(pk); - - m_kdata->m_rkcn.push_back(0.0); - - m_rxnstoich->add(reactionNumber(), r); - - if (r.reversible) { - m_dn.push_back(productGlobalOrder - reactantGlobalOrder); - m_revindex.push_back(reactionNumber()); - m_nrev++; - } - else { - m_dn.push_back(productGlobalOrder - reactantGlobalOrder); - m_irrev.push_back( reactionNumber() ); - m_nirrev++; - } + vector_int rk; + int nr = r.reactants.size(); + for (n = 0; n < nr; n++) { + nsFlt = r.rstoich[n]; + reactantGlobalOrder += nsFlt; + ns = (int) nsFlt; + if ((doublereal) ns != nsFlt) { + if (ns < 1) { + ns = 1; + } + } + if (r.rstoich[n] != 0.0) + m_rrxn[r.reactants[n]][rnum] += r.rstoich[n]; + for (m = 0; m < ns; m++) { + rk.push_back(r.reactants[n]); + } } + m_reactants.push_back(rk); - - void GasKinetics::installGroups(int irxn, - const vector& r, const vector& p) { - if (!r.empty()) { - writelog("installing groups for reaction "+int2str(reactionNumber())); - m_rgroups[reactionNumber()] = r; - m_pgroups[reactionNumber()] = p; - } + vector_int pk; + int np = r.products.size(); + for (n = 0; n < np; n++) { + nsFlt = r.pstoich[n]; + productGlobalOrder += nsFlt; + ns = (int) nsFlt; + if ((double) ns != nsFlt) { + if (ns < 1) { + ns = 1; + } + } + if (r.pstoich[n] != 0.0) + m_prxn[r.products[n]][rnum] += r.pstoich[n]; + for (m = 0; m < ns; m++) { + pk.push_back(r.products[n]); + } } + m_products.push_back(pk); + m_kdata->m_rkcn.push_back(0.0); - void GasKinetics::init() { - m_kk = thermo().nSpecies(); - m_rrxn.resize(m_kk); - m_prxn.resize(m_kk); - m_conc.resize(m_kk); - m_grt.resize(m_kk); - m_kdata->m_logp_ref = log(thermo().refPressure()) - log(GasConstant); + m_rxnstoich->add(reactionNumber(), r); + + if (r.reversible) { + m_dn.push_back(productGlobalOrder - reactantGlobalOrder); + m_revindex.push_back(reactionNumber()); + m_nrev++; } + else { + m_dn.push_back(productGlobalOrder - reactantGlobalOrder); + m_irrev.push_back( reactionNumber() ); + m_nirrev++; + } + } + //==================================================================================================================== - void GasKinetics::finalize() { - if (!m_finalized) { - // int i, j, nr, np; - m_kdata->falloff_work.resize( - static_cast(m_falloffn.workSize())); - m_kdata->concm_3b_values.resize( - static_cast(m_3b_concm.workSize())); - m_kdata->concm_falloff_values.resize( - static_cast(m_falloff_concm.workSize())); - -// for (i = 0; i < m_ii; i++) { -// nr = m_reactants[i].size(); -// for (j = 0; j < nr; j++) { -// m_rstoich[i][m_reactants[i][j]]++; -// } -// np = m_products[i].size(); -// for (j = 0; j < np; j++) { -// m_pstoich[i][m_products[i][j]]++; -// } -// } - //m_rxnstoich->write("c.cpp"); - m_finalized = true; - } + void GasKinetics::installGroups(int irxn, + const vector& r, const vector& p) { + if (!r.empty()) { + writelog("installing groups for reaction "+int2str(reactionNumber())); + m_rgroups[reactionNumber()] = r; + m_pgroups[reactionNumber()] = p; } + } - bool GasKinetics::ready() const { - return (m_finalized); + //==================================================================================================================== + void GasKinetics::init() { + m_kk = thermo().nSpecies(); + m_rrxn.resize(m_kk); + m_prxn.resize(m_kk); + m_conc.resize(m_kk); + m_grt.resize(m_kk); + m_kdata->m_logp_ref = log(thermo().refPressure()) - log(GasConstant); + } + //==================================================================================================================== + void GasKinetics::finalize() { + if (!m_finalized) { + // int i, j, nr, np; + m_kdata->falloff_work.resize( + static_cast(m_falloffn.workSize())); + m_kdata->concm_3b_values.resize( + static_cast(m_3b_concm.workSize())); + m_kdata->concm_falloff_values.resize( + static_cast(m_falloff_concm.workSize())); + + // for (i = 0; i < m_ii; i++) { + // nr = m_reactants[i].size(); + // for (j = 0; j < nr; j++) { + // m_rstoich[i][m_reactants[i][j]]++; + // } + // np = m_products[i].size(); + // for (j = 0; j < np; j++) { + // m_pstoich[i][m_products[i][j]]++; + // } + // } + //m_rxnstoich->write("c.cpp"); + m_finalized = true; } - + } + //==================================================================================================================== + bool GasKinetics::ready() const { + return (m_finalized); + } + //==================================================================================================================== } +//====================================================================================================================== diff --git a/Cantera/src/kinetics/GasKinetics.h b/Cantera/src/kinetics/GasKinetics.h index 7dee80dcd..f221a76ab 100644 --- a/Cantera/src/kinetics/GasKinetics.h +++ b/Cantera/src/kinetics/GasKinetics.h @@ -34,385 +34,435 @@ void get_wdot(const doublereal* rop, doublereal* wdot); namespace Cantera { - // forward references + // forward references - class Enhanced3BConc; - class ReactionData; - class GasKineticsData; - class Thermo; + class Enhanced3BConc; + class ReactionData; + class GasKineticsData; + class Thermo; + + /** + * Holds mechanism-specific data. + */ + class GasKineticsData { + public: + GasKineticsData() : + m_logp_ref(0.0), + m_logc_ref(0.0), + m_logStandConc(0.0), + m_ROP_ok(false), + m_temp(0.0) + {} + virtual ~GasKineticsData(){} + + doublereal m_logp_ref, m_logc_ref, m_logStandConc; + array_fp m_ropf, m_ropr, m_ropnet; + array_fp m_rfn_low, m_rfn_high; + bool m_ROP_ok; + + doublereal m_temp; + array_fp m_rfn; + array_fp falloff_work; + array_fp concm_3b_values; + array_fp concm_falloff_values; + array_fp m_rkcn; + }; + + + /** + * Kinetics manager for elementary gas-phase chemistry. This + * kinetics manager implements standard mass-action reaction rate + * expressions for low-density gases. + * @ingroup kinetics + */ + class GasKinetics : public Kinetics { + + public: /** - * Holds mechanism-specific data. + * @name Constructors and General Information */ - class GasKineticsData { - public: - GasKineticsData() : - m_logp_ref(0.0), - m_logc_ref(0.0), - m_logStandConc(0.0), - m_ROP_ok(false), - m_temp(0.0) - {} - virtual ~GasKineticsData(){} + //@{ - doublereal m_logp_ref, m_logc_ref, m_logStandConc; - array_fp m_ropf, m_ropr, m_ropnet; - array_fp m_rfn_low, m_rfn_high; - bool m_ROP_ok; + //! Constructor. + /*! + * @param thermo Pointer to the gas ThermoPhase (optional) + */ + GasKinetics(thermo_t* thermo = 0); - doublereal m_temp; - array_fp m_rfn; - array_fp falloff_work; - array_fp concm_3b_values; - array_fp concm_falloff_values; - array_fp m_rkcn; - }; + + //!Copy Constructor for the %GasKinetics object. + /*! + * Currently, this is not fully implemented. If called it will + * throw an exception. + * + * @param right object to be copied + */ + GasKinetics(const GasKinetics &right); + + //! Destructor. + virtual ~GasKinetics(); + + //! Assignment operator + /*! + * This is NOT a virtual function. + * + * @param right Reference to %GasKinetics object to be copied into the + * current one. + */ + GasKinetics& operator=(const GasKinetics &right); + + //! Duplication routine for objects which inherit from Kinetics + /*! + * This virtual routine can be used to duplicate %Kinetics objects + * inherited from %Kinetics even if the application only has + * a pointer to %Kinetics to work with. + * + * These routines are basically wrappers around the derived copy constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object + */ + virtual Kinetics *duplMyselfAsKinetics(const std::vector & tpVector) const; + + + //! Identifies the subclass of the Kinetics manager type. + /*! + * These are listed in mix_defs.h. + */ + virtual int ID() const { return cGasKinetics; } + + //! Identifies the kinetics manager type. + /*! + * Each class derived from Kinetics should overload this method to + * return a unique integer. Standard values are defined in file + * mix_defs.h. + */ + virtual int type() const { return cGasKinetics; } + + virtual doublereal reactantStoichCoeff(int k, int i) const { + return m_rrxn[k][i]; + } + + virtual doublereal productStoichCoeff(int k, int i) const { + return m_prxn[k][i]; + } + + //@} + /** + * @name Reaction Rates Of Progress + */ + //@{ + /** + * Forward rates of progress. + * Return the forward rates of progress in array fwdROP, which + * must be dimensioned at least as large as the total number + * of reactions. + */ + virtual void getFwdRatesOfProgress(doublereal* fwdROP) { + updateROP(); + std::copy(m_kdata->m_ropf.begin(), m_kdata->m_ropf.end(), fwdROP); + } + + /** + * Reverse rates of progress. + * Return the reverse rates of progress in array revROP, which + * must be dimensioned at least as large as the total number + * of reactions. + */ + virtual void getRevRatesOfProgress(doublereal* revROP) { + updateROP(); + std::copy(m_kdata->m_ropr.begin(), m_kdata->m_ropr.end(), revROP); + } + + /** + * Net rates of progress. Return the net (forward - reverse) + * rates of progress in array netROP, which must be + * dimensioned at least as large as the total number of + * reactions. + */ + virtual void getNetRatesOfProgress(doublereal* netROP) { + updateROP(); + std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP); + } /** - * Kinetics manager for elementary gas-phase chemistry. This - * kinetics manager implements standard mass-action reaction rate - * expressions for low-density gases. - * @ingroup kinetics + * Equilibrium constants. Return the equilibrium constants of + * the reactions in concentration units in array kc, which + * must be dimensioned at least as large as the total number + * of reactions. */ - class GasKinetics : public Kinetics { + virtual void getEquilibriumConstants(doublereal* kc); - public: + /** + * Return the array of values for the reaction gibbs free energy + * change. + * These values depend on the species concentrations. + * + * units = J kmol-1 + */ + virtual void getDeltaGibbs( doublereal* deltaG); - /** - * @name Constructors and General Information - */ - //@{ - /// Constructor. - GasKinetics(thermo_t* thermo = 0); + /** + * Return the array of values for the reaction enthalpy change. + * These values depend upon the species concentrations. + * + * units = J kmol-1 + */ + virtual void getDeltaEnthalpy( doublereal* deltaH); - /// Destructor. - virtual ~GasKinetics(); + /** + * Return the array of values for the reactions change in + * entropy. + * These values depend upon the concentration + * of the solution. + * + * units = J kmol-1 Kelvin-1 + */ + virtual void getDeltaEntropy(doublereal* deltaS); - virtual int ID() const { return cGasKinetics; } - virtual int type() const { return cGasKinetics; } + /** + * Return the array of values for the reaction + * standard state Gibbs free energy change. + * These values do not depend on the species + * concentrations. + * + * units = J kmol-1 + */ + virtual void getDeltaSSGibbs(doublereal* deltaG); - virtual doublereal reactantStoichCoeff(int k, int i) const { - return m_rrxn[k][i]; - } + /** + * Return the array of values for the change in the + * standard state enthalpies of reaction. + * These values do not depend upon the concentration + * of the solution. + * + * units = J kmol-1 + */ + virtual void getDeltaSSEnthalpy(doublereal* deltaH); - virtual doublereal productStoichCoeff(int k, int i) const { - return m_prxn[k][i]; - } + /** + * Return the array of values for the change in the + * standard state entropies for each reaction. + * These values do not depend upon the concentration + * of the solution. + * + * units = J kmol-1 Kelvin-1 + */ + virtual void getDeltaSSEntropy(doublereal* deltaS); - //@} - /** - * @name Reaction Rates Of Progress - */ - //@{ - /** - * Forward rates of progress. - * Return the forward rates of progress in array fwdROP, which - * must be dimensioned at least as large as the total number - * of reactions. - */ - virtual void getFwdRatesOfProgress(doublereal* fwdROP) { - updateROP(); - std::copy(m_kdata->m_ropf.begin(), m_kdata->m_ropf.end(), fwdROP); - } + //@} + /** + * @name Species Production Rates + */ + //@{ - /** - * Reverse rates of progress. - * Return the reverse rates of progress in array revROP, which - * must be dimensioned at least as large as the total number - * of reactions. - */ - virtual void getRevRatesOfProgress(doublereal* revROP) { - updateROP(); - std::copy(m_kdata->m_ropr.begin(), m_kdata->m_ropr.end(), revROP); - } + //! Return the species net production rates + /*! + * Species net production rates [kmol/m^3/s]. Return the species + * net production rates (creation - destruction) in array + * wdot, which must be dimensioned at least as large as the + * total number of species. + * + * @param net Array of species production rates. + * units kmol m-3 s-1 + */ + virtual void getNetProductionRates(doublereal* net) { + updateROP(); + //#ifdef HWMECH + //get_wdot(&m_kdata->m_ropnet[0], net); + //#else + m_rxnstoich->getNetProductionRates(m_kk, + &m_kdata->m_ropnet[0], net); + //#endif + } - /** - * Net rates of progress. Return the net (forward - reverse) - * rates of progress in array netROP, which must be - * dimensioned at least as large as the total number of - * reactions. - */ - virtual void getNetRatesOfProgress(doublereal* netROP) { - updateROP(); - std::copy(m_kdata->m_ropnet.begin(), m_kdata->m_ropnet.end(), netROP); - } + /** + * Species creation rates [kmol/m^3]. Return the species + * creation rates in array cdot, which must be + * dimensioned at least as large as the total number of + * species. + * + */ + virtual void getCreationRates(doublereal* cdot) { + updateROP(); + m_rxnstoich->getCreationRates(m_kk, &m_kdata->m_ropf[0], + &m_kdata->m_ropr[0], cdot); + } + + /** + * Species destruction rates [kmol/m^3]. Return the species + * destruction rates in array ddot, which must be + * dimensioned at least as large as the total number of + * species. + * + */ + virtual void getDestructionRates(doublereal* ddot) { + updateROP(); + m_rxnstoich->getDestructionRates(m_kk, &m_kdata->m_ropf[0], + &m_kdata->m_ropr[0], ddot); + // fill(ddot, ddot + m_kk, 0.0); + //m_revProductStoich.incrementSpecies( + // m_kdata->m_ropr.begin(), ddot); + //m_reactantStoich.incrementSpecies( + // m_kdata->m_ropf.begin(), ddot); + } + + //@} + /** + * @name Reaction Mechanism Informational Query Routines + */ + //@{ + + /** + * Flag specifying the type of reaction. The legal values and + * their meaning are specific to the particular kinetics + * manager. + */ + virtual int reactionType(int i) const { + return m_index[i].first; + } + + virtual std::string reactionString(int i) const { + return m_rxneqn[i]; + } + + /** + * True if reaction i has been declared to be reversible. If + * isReversible(i) is false, then the reverse rate of progress + * for reaction i is always zero. + */ + virtual bool isReversible(int i) { + if (std::find(m_revindex.begin(), m_revindex.end(), i) + < m_revindex.end()) return true; + else return false; + } + + /** + * Return the forward rate constants + * + * length is the number of reactions. units depends + * on many issues. + */ + virtual void getFwdRateConstants(doublereal *kfwd); + + /** + * Return the reverse rate constants. + * + * length is the number of reactions. units depends + * on many issues. Note, this routine will return rate constants + * for irreversible reactions if the default for + * doIrreversible is overridden. + */ + virtual void getRevRateConstants(doublereal *krev, + bool doIrreversible = false); + + //@} + /** + * @name Reaction Mechanism Setup Routines + */ + //@{ + + virtual void init(); + + /// Add a reaction to the mechanism. + virtual void addReaction(const ReactionData& r); + + virtual void finalize(); + virtual bool ready() const; + + virtual void update_T(); + virtual void update_C(); + + void updateROP(); - /** - * Equilibrium constants. Return the equilibrium constants of - * the reactions in concentration units in array kc, which - * must be dimensioned at least as large as the total number - * of reactions. - */ - virtual void getEquilibriumConstants(doublereal* kc); - - /** - * Return the array of values for the reaction gibbs free energy - * change. - * These values depend on the species concentrations. - * - * units = J kmol-1 - */ - virtual void getDeltaGibbs( doublereal* deltaG); - - /** - * Return the array of values for the reaction enthalpy change. - * These values depend upon the species concentrations. - * - * units = J kmol-1 - */ - virtual void getDeltaEnthalpy( doublereal* deltaH); - - /** - * Return the array of values for the reactions change in - * entropy. - * These values depend upon the concentration - * of the solution. - * - * units = J kmol-1 Kelvin-1 - */ - virtual void getDeltaEntropy(doublereal* deltaS); - - /** - * Return the array of values for the reaction - * standard state Gibbs free energy change. - * These values do not depend on the species - * concentrations. - * - * units = J kmol-1 - */ - virtual void getDeltaSSGibbs(doublereal* deltaG); - - /** - * Return the array of values for the change in the - * standard state enthalpies of reaction. - * These values do not depend upon the concentration - * of the solution. - * - * units = J kmol-1 - */ - virtual void getDeltaSSEnthalpy(doublereal* deltaH); - - /** - * Return the array of values for the change in the - * standard state entropies for each reaction. - * These values do not depend upon the concentration - * of the solution. - * - * units = J kmol-1 Kelvin-1 - */ - virtual void getDeltaSSEntropy(doublereal* deltaS); - - //@} - /** - * @name Species Production Rates - */ - //@{ - - //! Return the species net production rates - /*! - * Species net production rates [kmol/m^3/s]. Return the species - * net production rates (creation - destruction) in array - * wdot, which must be dimensioned at least as large as the - * total number of species. - * - * @param net Array of species production rates. - * units kmol m-3 s-1 - */ - virtual void getNetProductionRates(doublereal* net) { - updateROP(); - //#ifdef HWMECH - //get_wdot(&m_kdata->m_ropnet[0], net); - //#else - m_rxnstoich->getNetProductionRates(m_kk, - &m_kdata->m_ropnet[0], net); - //#endif - } - - /** - * Species creation rates [kmol/m^3]. Return the species - * creation rates in array cdot, which must be - * dimensioned at least as large as the total number of - * species. - * - */ - virtual void getCreationRates(doublereal* cdot) { - updateROP(); - m_rxnstoich->getCreationRates(m_kk, &m_kdata->m_ropf[0], - &m_kdata->m_ropr[0], cdot); - } - - /** - * Species destruction rates [kmol/m^3]. Return the species - * destruction rates in array ddot, which must be - * dimensioned at least as large as the total number of - * species. - * - */ - virtual void getDestructionRates(doublereal* ddot) { - updateROP(); - m_rxnstoich->getDestructionRates(m_kk, &m_kdata->m_ropf[0], - &m_kdata->m_ropr[0], ddot); - // fill(ddot, ddot + m_kk, 0.0); - //m_revProductStoich.incrementSpecies( - // m_kdata->m_ropr.begin(), ddot); - //m_reactantStoich.incrementSpecies( - // m_kdata->m_ropf.begin(), ddot); - } - - //@} - /** - * @name Reaction Mechanism Informational Query Routines - */ - //@{ - - /** - * Flag specifying the type of reaction. The legal values and - * their meaning are specific to the particular kinetics - * manager. - */ - virtual int reactionType(int i) const { - return m_index[i].first; - } - - virtual std::string reactionString(int i) const { - return m_rxneqn[i]; - } - - /** - * True if reaction i has been declared to be reversible. If - * isReversible(i) is false, then the reverse rate of progress - * for reaction i is always zero. - */ - virtual bool isReversible(int i) { - if (std::find(m_revindex.begin(), m_revindex.end(), i) - < m_revindex.end()) return true; - else return false; - } - - /** - * Return the forward rate constants - * - * length is the number of reactions. units depends - * on many issues. - */ - virtual void getFwdRateConstants(doublereal *kfwd); - - /** - * Return the reverse rate constants. - * - * length is the number of reactions. units depends - * on many issues. Note, this routine will return rate constants - * for irreversible reactions if the default for - * doIrreversible is overridden. - */ - virtual void getRevRateConstants(doublereal *krev, - bool doIrreversible = false); - - //@} - /** - * @name Reaction Mechanism Setup Routines - */ - //@{ - - virtual void init(); - - /// Add a reaction to the mechanism. - virtual void addReaction(const ReactionData& r); - - virtual void finalize(); - virtual bool ready() const; - - virtual void update_T(); - virtual void update_C(); - - void updateROP(); + const std::vector& reactantGroups(int i) + { return m_rgroups[i]; } + const std::vector& productGroups(int i) + { return m_pgroups[i]; } - const std::vector& reactantGroups(int i) - { return m_rgroups[i]; } - const std::vector& productGroups(int i) - { return m_pgroups[i]; } + void _update_rates_T(); + void _update_rates_C(); + + //@} + + protected: + + int m_kk; + + int m_nfall; + + array_int m_fallindx; + + Rate1 m_falloff_low_rates; + Rate1 m_falloff_high_rates; + Rate1 m_rates; + + mutable std::map > m_index; + + FalloffMgr m_falloffn; + + ThirdBodyMgr m_3b_concm; + ThirdBodyMgr m_falloff_concm; + + std::vector m_irrev; + + ReactionStoichMgr* m_rxnstoich; + + std::vector m_fwdOrder; + + int m_nirrev; + int m_nrev; + + std::map > m_rgroups; + std::map > m_pgroups; + + std::vector m_rxntype; + + mutable std::vector > m_rrxn; + mutable std::vector > m_prxn; + + /** + * Difference between the input global reactants order + * and the input global products order. Changed to a double + * to account for the fact that we can have real-valued + * stoichiometries. + */ + array_fp m_dn; + array_int m_revindex; + + std::vector m_rxneqn; + + GasKineticsData* m_kdata; + + array_fp m_conc; + void processFalloffReactions(); + array_fp m_grt; - void _update_rates_T(); - void _update_rates_C(); + private: - //@} + int reactionNumber(){ return m_ii;} + std::vector > m_stoich; - protected: + void addElementaryReaction(const ReactionData& r); + void addThreeBodyReaction(const ReactionData& r); + void addFalloffReaction(const ReactionData& r); - int m_kk, m_nfall; + void installReagents(const ReactionData& r); - array_int m_fallindx; + void installGroups(int irxn, const std::vector& r, + const std::vector& p); + void updateKc(); - Rate1 m_falloff_low_rates; - Rate1 m_falloff_high_rates; - Rate1 m_rates; - - mutable std::map > m_index; - - FalloffMgr m_falloffn; - - ThirdBodyMgr m_3b_concm; - ThirdBodyMgr m_falloff_concm; - - std::vector m_irrev; - - ReactionStoichMgr* m_rxnstoich; - - std::vector m_fwdOrder; - - int m_nirrev; - int m_nrev; - - std::map > m_rgroups; - std::map > m_pgroups; - - std::vector m_rxntype; - - mutable std::vector > m_rrxn; - mutable std::vector > m_prxn; - - /** - * Difference between the input global reactants order - * and the input global products order. Changed to a double - * to account for the fact that we can have real-valued - * stoichiometries. - */ - array_fp m_dn; - array_int m_revindex; - - std::vector m_rxneqn; - - GasKineticsData* m_kdata; - - array_fp m_conc; - void processFalloffReactions(); - array_fp m_grt; - - - private: - - int reactionNumber(){ return m_ii;} - std::vector > m_stoich; - - void addElementaryReaction(const ReactionData& r); - void addThreeBodyReaction(const ReactionData& r); - void addFalloffReaction(const ReactionData& r); - - void installReagents(const ReactionData& r); - - void installGroups(int irxn, const std::vector& r, - const std::vector& p); - void updateKc(); - - void registerReaction(int rxnNumber, int type, int loc) { - m_index[rxnNumber] = std::pair(type, loc); - } - bool m_finalized; - }; + void registerReaction(int rxnNumber, int type, int loc) { + m_index[rxnNumber] = std::pair(type, loc); + } + bool m_finalized; + }; } #endif diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 2ed047f16..451116ada 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -217,10 +217,14 @@ namespace Cantera { * * These routines are basically wrappers around the derived copy * constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object */ - Kinetics *InterfaceKinetics::duplMyselfAsKinetics() const { - InterfaceKinetics* tp = new InterfaceKinetics(*this); - return dynamic_cast(tp); + Kinetics *InterfaceKinetics::duplMyselfAsKinetics(const std::vector & tpVector) const { + InterfaceKinetics* iK = new InterfaceKinetics(*this); + iK->assignShallowPointers(tpVector); + return dynamic_cast(iK); } //==================================================================================================================== // Update properties that depend on temperature diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 0bb06030c..b6b9208d9 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -115,17 +115,19 @@ namespace Cantera { InterfaceKinetics& operator=(const InterfaceKinetics &right); - //! Duplication routine for objects which inherit from - //! Kinetics + + //! Duplication routine for objects which inherit from Kinetics /*! - * This virtual routine can be used to duplicate %InterfaceKinetics objects + * This virtual routine can be used to duplicate %Kinetics objects * inherited from %Kinetics even if the application only has * a pointer to %Kinetics to work with. * - * These routines are basically wrappers around the derived copy - * constructor. + * These routines are basically wrappers around the derived copy constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object */ - virtual Kinetics *duplMyselfAsKinetics() const; + virtual Kinetics *duplMyselfAsKinetics(const std::vector & tpVector) const; //! Return the ID of the kinetics object virtual int ID() const; diff --git a/Cantera/src/kinetics/Kinetics.cpp b/Cantera/src/kinetics/Kinetics.cpp index 225ba887d..e935c0410 100644 --- a/Cantera/src/kinetics/Kinetics.cpp +++ b/Cantera/src/kinetics/Kinetics.cpp @@ -32,11 +32,17 @@ namespace Cantera { Kinetics::Kinetics() : m_ii(0), m_nTotalSpecies(0), + m_perturb(0), + m_reactants(0), + m_products(0), m_thermo(0), + m_start(0), + m_phaseindex(), m_index(-1), m_surfphase(-1), m_rxnphase(-1), - m_mindim(4) + m_mindim(4), + m_dummygroups(0) { } @@ -51,16 +57,22 @@ namespace Cantera { Kinetics::Kinetics(const Kinetics &right) : m_ii(0), m_nTotalSpecies(0), + m_perturb(0), + m_reactants(0), + m_products(0), m_thermo(0), + m_start(0), + m_phaseindex(), m_index(-1), m_surfphase(-1), m_rxnphase(-1), - m_mindim(4) + m_mindim(4), + m_dummygroups(0) { /* * Call the assignment operator */ - *this = operator=(right); + *this = right; } // Assignment operator @@ -96,7 +108,7 @@ namespace Cantera { return *this; } - + //==================================================================================================================== // Duplication routine for objects which inherit from // Kinetics /* @@ -107,22 +119,48 @@ namespace Cantera { * These routines are basically wrappers around the derived copy * constructor. */ - Kinetics *Kinetics::duplMyselfAsKinetics() const { - Kinetics* tp = new Kinetics(*this); - return tp; + Kinetics *Kinetics::duplMyselfAsKinetics(const std::vector & tpVector) const { + Kinetics* ko = new Kinetics(*this); + + ko->assignShallowPointers(tpVector); + return ko; } - - - + //==================================================================================================================== int Kinetics::ID() const { return 0; } - + //==================================================================================================================== int Kinetics::type() const { return 0; } + //==================================================================================================================== + void Kinetics::assignShallowPointers(const std::vector & tpVector) { + size_t ns = tpVector.size(); + if (ns != m_thermo.size()) { + throw CanteraError(" Kinetics::assignShallowPointers", + " Number of ThermoPhase objects arent't the same"); + } + for (size_t i = 0; i < ns; i++) { + ThermoPhase *ntp = tpVector[i]; + ThermoPhase *otp = m_thermo[i]; + if (ntp->id() != otp->id()) { + throw CanteraError(" Kinetics::assignShallowPointers", + " id() of the ThermoPhase objects isn't the same"); + } + if (ntp->eosType() != otp->eosType()) { + throw CanteraError(" Kinetics::assignShallowPointers", + " eosType() of the ThermoPhase objects isn't the same"); + } + if (ntp->nSpecies() != otp->nSpecies()) { + throw CanteraError(" Kinetics::assignShallowPointers", + " Number of ThermoPhase objects isn't the same"); + } + m_thermo[i] = tpVector[i]; + } + } + //==================================================================================================================== /** * Takes as input an array of properties for all species in the * mechanism and copies those values beloning to a particular @@ -284,17 +322,13 @@ namespace Cantera { if (type() == cEdgeKinetics) ptype = cEdge; else if (type() == cInterfaceKinetics) ptype = cSurf; if (thermo.eosType() == ptype) { - // if (m_surfphase >= 0) { - // throw CanteraError("Kinetics::addPhase", - // "cannot add more than one surface phase"); - // } m_surfphase = nPhases(); m_rxnphase = nPhases(); } m_thermo.push_back(&thermo); m_phaseindex[m_thermo.back()->id()] = nPhases(); } - + void Kinetics::finalize() { m_nTotalSpecies = 0; int np = nPhases(); @@ -305,9 +339,9 @@ namespace Cantera { } - //! Private function of the class Kinetics, indicating that a function - //! inherited from the base class hasn't had a definition assigned to it - /*! + // Private function of the class Kinetics, indicating that a function + // inherited from the base class hasn't had a definition assigned to it + /* * @param m String message */ void Kinetics::err(std::string m) const { diff --git a/Cantera/src/kinetics/Kinetics.h b/Cantera/src/kinetics/Kinetics.h index f99b0a186..8559d4137 100644 --- a/Cantera/src/kinetics/Kinetics.h +++ b/Cantera/src/kinetics/Kinetics.h @@ -169,18 +169,35 @@ namespace Cantera { Kinetics& operator=(const Kinetics &right); - //! Duplication routine for objects which inherit from - //! Kinetics + //! Duplication routine for objects which inherit from Kinetics /*! * This virtual routine can be used to duplicate %Kinetics objects * inherited from %Kinetics even if the application only has * a pointer to %Kinetics to work with. * - * These routines are basically wrappers around the derived copy - * constructor. + * These routines are basically wrappers around the derived copy constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object */ - virtual Kinetics *duplMyselfAsKinetics() const; + virtual Kinetics *duplMyselfAsKinetics(const std::vector & tpVector) const; + //! Reassign the shallow pointers within the %FKinetics object + /*! + * This type or routine is absolute necessary because the Kinetics object doesn't + * own the ThermoPhase objects. After a duplication, we need to point to different + * ThermoPhase objects. + * + * We check that the ThermoPhase objects are alligned in the same order and have + * the following identical properties to the ones that they are replacing. + * id() + * eosType() + * nSpecies() + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object + */ + virtual void assignShallowPointers(const std::vector & tpVector); //! Identifies the subclass of the Kinetics manager type. /*! @@ -875,13 +892,13 @@ namespace Cantera { */ //@{ - /// The current value of the multiplier for reaction i. + //! The current value of the multiplier for reaction i. /*! * @param i index of the reaction */ doublereal multiplier(int i) const {return m_perturb[i];} - /// Set the multiplier for reaction i to f. + //! Set the multiplier for reaction i to f. /*! * @param i index of the reaction * @param f value of the multiplier. @@ -965,8 +982,7 @@ namespace Cantera { */ std::vector m_products; - //! m_thermo is a vector of pointers to ThermoPhase - //! objects. + //! m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator /*! * For homogeneous kinetics applications, this vector * will only have one entry. For interfacial reactions, this @@ -999,21 +1015,27 @@ namespace Cantera { * -1. */ std::map m_phaseindex; + //! Index of the Kinetics Manager int m_index; - /** - * Index in the list of phases of the one surface phase. - */ + + //! Index in the list of phases of the one surface phase. + /*! + * + */ int m_surfphase; - /** - * Index in the list of phases of the one phase where the reactions - * occur. + + //! Phase Index where reactions are assumed to be taking place + /*! + * We calculate this by assuming that the phase with the lowest dimensionality is the phase where reactions + * are taking place + * @deprecated */ int m_rxnphase; - /// number of spatial dimensions of lowest-dimensional phase. + //! number of spatial dimensions of lowest-dimensional phase. int m_mindim; private: @@ -1021,9 +1043,11 @@ namespace Cantera { //! Vector of group lists std::vector m_dummygroups; - //! Function for unhandled situations + + //! Private function of the class Kinetics, indicating that a function + //! inherited from the base class hasn't had a definition assigned to it /*! - * @param m String error message + * @param m String message */ void err(std::string m) const; From e98ae73fc1ccc22e35ebc0bf87ae0f83953eb7a0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Jun 2010 16:46:36 +0000 Subject: [PATCH 169/446] Allowed "," to be in names again. This was already being used in some cases. --- Cantera/src/base/stringUtils.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Cantera/src/base/stringUtils.cpp b/Cantera/src/base/stringUtils.cpp index 599b34efa..62bc8e8da 100644 --- a/Cantera/src/base/stringUtils.cpp +++ b/Cantera/src/base/stringUtils.cpp @@ -347,7 +347,7 @@ namespace Cantera { //================================================================================================ // Parse a name string, separating out the phase name from the species name /* - * Name strings must not contain these internal characters "; \n \t ," + * Name strings must not contain these internal characters "; \n \t " * Only one colon is allowed, the one separating the phase name from the * species name. Therefore, names may not include a colon. * @@ -363,11 +363,11 @@ namespace Cantera { std::string s = stripws(nameStr); std::string::size_type ibegin, iend, icolon; phaseName = ""; - ibegin = s.find_first_not_of(", ;\n\t"); + ibegin = s.find_first_not_of(" ;\n\t"); if (ibegin != std::string::npos) { s = s.substr(ibegin,s.size()); icolon = s.find(':'); - iend = s.find_first_of(", ;\n\t"); + iend = s.find_first_of(" ;\n\t"); if (icolon != std::string::npos) { phaseName = s.substr(0, icolon); s = s.substr(icolon+1, s.size()); @@ -378,7 +378,7 @@ namespace Cantera { } if (iend != std::string::npos) { throw CanteraError("parseSpeciesName()", - "Species name has \", ;/\n/\t\" in the middle of it: " + nameStr); + "Species name has \" ;/\n/\t\" in the middle of it: " + nameStr); } } return s; From b7bc8a8eb619d78a3f0f06cf12262ee23701ea87 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Jun 2010 17:16:00 +0000 Subject: [PATCH 170/446] Added assignment operator to GasKineticsData --- Cantera/src/kinetics/GasKinetics.cpp | 59 ++++++++++++++++++++++++++-- Cantera/src/kinetics/GasKinetics.h | 29 ++++++++------ 2 files changed, 72 insertions(+), 16 deletions(-) diff --git a/Cantera/src/kinetics/GasKinetics.cpp b/Cantera/src/kinetics/GasKinetics.cpp index 9aeff996e..c73145991 100644 --- a/Cantera/src/kinetics/GasKinetics.cpp +++ b/Cantera/src/kinetics/GasKinetics.cpp @@ -29,6 +29,52 @@ using namespace std; namespace Cantera { + //==================================================================================================================== + GasKineticsData::GasKineticsData() : + m_logp_ref(0.0), + m_logc_ref(0.0), + m_logStandConc(0.0), + m_ROP_ok(false), + m_temp(0.0) + { + } + //==================================================================================================================== + GasKineticsData::GasKineticsData(const GasKineticsData &right) : + m_logp_ref(0.0), + m_logc_ref(0.0), + m_logStandConc(0.0), + m_ROP_ok(false), + m_temp(0.0) + { + *this = right; + } + //==================================================================================================================== + GasKineticsData::~GasKineticsData() + { + } + //==================================================================================================================== + GasKineticsData& GasKineticsData::operator=(const GasKineticsData &right) + { + if (this == &right) return *this; + + m_logp_ref = right.m_logp_ref; + m_logc_ref = right.m_logc_ref; + m_logStandConc = right.m_logStandConc; + m_ropf = right.m_ropf; + m_ropr = right.m_ropr; + m_ropnet = right.m_ropnet; + m_rfn_low = right.m_rfn_low; + m_rfn_high = right.m_rfn_high; + m_ROP_ok = right.m_ROP_ok; + m_temp = right.m_temp; + m_rfn = right.m_rfn; + falloff_work = right.falloff_work; + concm_3b_values = right.concm_3b_values; + concm_falloff_values = right.concm_falloff_values; + m_rkcn = right.m_rkcn; + + return *this; + } //==================================================================================================================== /* * Construct an empty reaction mechanism. @@ -43,9 +89,9 @@ namespace Cantera { m_finalized(false) { if (thermo != 0) addPhase(*thermo); - m_kdata = new GasKineticsData; + m_kdata = new GasKineticsData(); m_kdata->m_temp = 0.0; - m_rxnstoich = new ReactionStoichMgr; + m_rxnstoich = new ReactionStoichMgr(); } //==================================================================================================================== @@ -83,7 +129,10 @@ namespace Cantera { m_3b_concm = right.m_3b_concm; m_falloff_concm = right.m_falloff_concm; m_irrev = right.m_irrev; - m_rxnstoich = right.m_rxnstoich; + + // needs updating + m_rxnstoich = (right.m_rxnstoich); + m_fwdOrder = right.m_fwdOrder; m_nirrev = right.m_nirrev; m_nrev = right.m_nrev; @@ -95,7 +144,9 @@ namespace Cantera { m_dn = right.m_dn; m_revindex = right.m_revindex; m_rxneqn = right.m_rxneqn; - m_kdata = right.m_kdata; + + *m_kdata = *(right.m_kdata); + m_conc = right.m_conc; m_grt = right.m_grt; m_finalized = right.m_finalized; diff --git a/Cantera/src/kinetics/GasKinetics.h b/Cantera/src/kinetics/GasKinetics.h index f221a76ab..84fc551af 100644 --- a/Cantera/src/kinetics/GasKinetics.h +++ b/Cantera/src/kinetics/GasKinetics.h @@ -46,22 +46,27 @@ namespace Cantera { */ class GasKineticsData { public: - GasKineticsData() : - m_logp_ref(0.0), - m_logc_ref(0.0), - m_logStandConc(0.0), - m_ROP_ok(false), - m_temp(0.0) - {} - virtual ~GasKineticsData(){} - doublereal m_logp_ref, m_logc_ref, m_logStandConc; - array_fp m_ropf, m_ropr, m_ropnet; - array_fp m_rfn_low, m_rfn_high; + GasKineticsData(); + + GasKineticsData(const GasKineticsData &right); + + virtual ~GasKineticsData(); + + GasKineticsData& operator=(const GasKineticsData &right); + + doublereal m_logp_ref; + doublereal m_logc_ref; + doublereal m_logStandConc; + array_fp m_ropf; + array_fp m_ropr; + array_fp m_ropnet; + array_fp m_rfn_low; + array_fp m_rfn_high; bool m_ROP_ok; doublereal m_temp; - array_fp m_rfn; + array_fp m_rfn; array_fp falloff_work; array_fp concm_3b_values; array_fp concm_falloff_values; From 0cbec89c52f2d5bb4c2e766e9e66155092df5897 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Jun 2010 19:59:27 +0000 Subject: [PATCH 171/446] More copy constructors and assignment operators. --- Cantera/src/kinetics/GasKinetics.cpp | 8 +- Cantera/src/kinetics/ReactionStoichMgr.cpp | 55 ++++++- Cantera/src/kinetics/ReactionStoichMgr.h | 7 + Cantera/src/kinetics/StoichManager.h | 164 +++++++++++++++++++-- 4 files changed, 213 insertions(+), 21 deletions(-) diff --git a/Cantera/src/kinetics/GasKinetics.cpp b/Cantera/src/kinetics/GasKinetics.cpp index c73145991..805ddf598 100644 --- a/Cantera/src/kinetics/GasKinetics.cpp +++ b/Cantera/src/kinetics/GasKinetics.cpp @@ -102,7 +102,10 @@ namespace Cantera { m_nirrev(0), m_nrev(0), m_finalized(false) - { + { + m_kdata = new GasKineticsData(); + m_kdata->m_temp = 0.0; + m_rxnstoich = new ReactionStoichMgr(); *this = right; } //==================================================================================================================== @@ -130,8 +133,7 @@ namespace Cantera { m_falloff_concm = right.m_falloff_concm; m_irrev = right.m_irrev; - // needs updating - m_rxnstoich = (right.m_rxnstoich); + *m_rxnstoich = *(right.m_rxnstoich); m_fwdOrder = right.m_fwdOrder; m_nirrev = right.m_nirrev; diff --git a/Cantera/src/kinetics/ReactionStoichMgr.cpp b/Cantera/src/kinetics/ReactionStoichMgr.cpp index 6009a1164..13ff8ece9 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.cpp +++ b/Cantera/src/kinetics/ReactionStoichMgr.cpp @@ -24,12 +24,18 @@ using namespace std; namespace Cantera { - + //==================================================================================================================== // create stoichiometry managers for the reactants of all reactions, // for the products of the reversible reactions, and for the // products of the irreversible reactions. - ReactionStoichMgr:: - ReactionStoichMgr() { + ReactionStoichMgr::ReactionStoichMgr() : + m_reactants(0), + m_revproducts(0), + m_irrevproducts(0) +#ifdef INCL_STOICH_WRITER + , m_rwriter(0) +#endif + { m_reactants = new StoichManagerN; m_revproducts = new StoichManagerN; m_irrevproducts = new StoichManagerN; @@ -38,19 +44,54 @@ namespace Cantera { #endif m_dummy.resize(10,1.0); } - + //==================================================================================================================== // delete the three stoichiometry managers - ReactionStoichMgr::~ReactionStoichMgr() { + ReactionStoichMgr::~ReactionStoichMgr() + { delete m_reactants; delete m_revproducts; delete m_irrevproducts; - // delete m_global; #ifdef INCL_STOICH_WRITER delete m_rwriter; #endif } + //==================================================================================================================== + ReactionStoichMgr::ReactionStoichMgr(const ReactionStoichMgr &right) : + m_reactants(0), + m_revproducts(0), + m_irrevproducts(0) +#ifdef INCL_STOICH_WRITER + , m_rwriter(0) +#endif + { + m_reactants = new StoichManagerN(*right.m_reactants); + m_revproducts = new StoichManagerN(*right.m_revproducts); + m_irrevproducts = new StoichManagerN(*right.m_irrevproducts); + m_dummy = right.m_dummy; +#ifdef INCL_STOICH_WRITER + m_rwriter = new StoichManagerN(right.m_writer); +#endif + } + //==================================================================================================================== + ReactionStoichMgr & ReactionStoichMgr::operator=(const ReactionStoichMgr &right) + { + if (this != &right) { + if (m_reactants) delete(m_reactants); + if (m_revproducts) delete(m_revproducts); + if (m_irrevproducts) delete(m_irrevproducts); - + m_reactants = new StoichManagerN(*right.m_reactants); + m_revproducts = new StoichManagerN(*right.m_revproducts); + m_irrevproducts = new StoichManagerN(*right.m_irrevproducts); + m_dummy = right.m_dummy; +#ifdef INCL_STOICH_WRITER + if(m_writer) delete (m_writer); + m_rwriter = new StoichManagerN(right.m_writer); +#endif + } + return *this; + } + //==================================================================================================================== void ReactionStoichMgr:: add(int rxn, const vector_int& reactants, const vector_int& products, bool reversible) { diff --git a/Cantera/src/kinetics/ReactionStoichMgr.h b/Cantera/src/kinetics/ReactionStoichMgr.h index 1ccd6b588..7824d3916 100644 --- a/Cantera/src/kinetics/ReactionStoichMgr.h +++ b/Cantera/src/kinetics/ReactionStoichMgr.h @@ -70,6 +70,10 @@ namespace Cantera { /// Destructor. virtual ~ReactionStoichMgr(); + ReactionStoichMgr(const ReactionStoichMgr &right); + + ReactionStoichMgr & operator=(const ReactionStoichMgr &right); + /** * Add a reaction with mass-action kinetics. Vectors * 'reactants' and 'products' contain the integer species @@ -236,6 +240,9 @@ namespace Cantera { void writeNetProductionRates(std::ostream& f); void writeMultiplyReactants(std::ostream& f); void writeMultiplyRevProducts(std::ostream& f); + + protected: + StoichManagerN* m_reactants; StoichManagerN* m_revproducts; StoichManagerN* m_irrevproducts; diff --git a/Cantera/src/kinetics/StoichManager.h b/Cantera/src/kinetics/StoichManager.h index 56327d85a..97a9ff4ce 100644 --- a/Cantera/src/kinetics/StoichManager.h +++ b/Cantera/src/kinetics/StoichManager.h @@ -164,8 +164,26 @@ namespace Cantera { public: - C1( int rxn = 0, int ic0 = 0) - : m_rxn (rxn), m_ic0 (ic0) {} + C1(int rxn = 0, int ic0 = 0) : + m_rxn (rxn), + m_ic0 (ic0) + { + } + + C1(const C1 &right) : + m_rxn (right.m_rxn), + m_ic0 (right.m_ic0) + { + } + + C1& operator=(const C1 &right) + { + if (this != &right) { + m_rxn = right.m_rxn; + m_ic0 = right.m_ic0; + } + return *this; + } int data(std::vector& ic) { ic.resize(1); @@ -216,7 +234,9 @@ namespace Cantera { } private: + //! Reaction number int m_rxn; + //! Species number int m_ic0; }; @@ -231,6 +251,23 @@ namespace Cantera { C2( int rxn = 0, int ic0 = 0, int ic1 = 0) : m_rxn (rxn), m_ic0 (ic0), m_ic1 (ic1) {} + C2(const C2 &right) : + m_rxn(right.m_rxn), + m_ic0(right.m_ic0), + m_ic1(right.m_ic1) + { + } + + C2& operator=(const C2 &right) + { + if (this != &right) { + m_rxn = right.m_rxn; + m_ic0 = right.m_ic0; + m_ic1 = right.m_ic1; + } + return *this; + } + int data(std::vector& ic) { ic.resize(2); ic[0] = m_ic0; @@ -296,7 +333,8 @@ namespace Cantera { * Species indecise -> index into the species vector for the * two species. */ - int m_ic0, m_ic1; + int m_ic0; + int m_ic1; }; @@ -309,6 +347,25 @@ namespace Cantera { C3( int rxn = 0, int ic0 = 0, int ic1 = 0, int ic2 = 0) : m_rxn (rxn), m_ic0 (ic0), m_ic1 (ic1), m_ic2 (ic2) {} + C3(const C3 &right) : + m_rxn(right.m_rxn), + m_ic0(right.m_ic0), + m_ic1(right.m_ic1), + m_ic2(right.m_ic2) + { + } + + C3& operator=(const C3 &right) + { + if (this != &right) { + m_rxn = right.m_rxn; + m_ic0 = right.m_ic0; + m_ic1 = right.m_ic1; + m_ic2 = right.m_ic2; + } + return *this; + } + int data(std::vector& ic) { ic.resize(3); ic[0] = m_ic0; @@ -367,7 +424,10 @@ namespace Cantera { out[m_ic2] += s; } private: - int m_rxn, m_ic0, m_ic1, m_ic2; + int m_rxn; + int m_ic0; + int m_ic1; + int m_ic2; }; @@ -378,11 +438,17 @@ namespace Cantera { */ class C_AnyN { public: - C_AnyN() : m_rxn (-1) {} - C_AnyN( int rxn, const vector_int& ic, const vector_fp& order, - const vector_fp& stoich) - : m_rxn (rxn) { + C_AnyN() : + m_n(0), + m_rxn(-1) + { + } + + C_AnyN(int rxn, const vector_int& ic, const vector_fp& order, const vector_fp& stoich) : + m_n(0), + m_rxn(rxn) + { m_n = ic.size(); m_ic.resize(m_n); m_order.resize(m_n); @@ -394,6 +460,27 @@ namespace Cantera { } } + C_AnyN(const C_AnyN &right) : + m_n(right.m_n), + m_rxn(right.m_rxn), + m_ic(right.m_ic), + m_order(right.m_order), + m_stoich(right.m_stoich) + { + } + + C_AnyN& operator=(const C_AnyN &right) + { + if (this != &right) { + m_n = right.m_n; + m_rxn = right.m_rxn; + m_ic = right.m_ic; + m_order = right.m_order; + m_stoich = right.m_stoich; + } + return *this; + } + int data(std::vector& ic) { ic.resize(m_n); int n; @@ -627,7 +714,34 @@ namespace Cantera { * DGG - the problem is that the number of reactions and species * are not known initially. */ - StoichManagerN() {} + StoichManagerN() + { + } + + StoichManagerN(const StoichManagerN &right) : + m_c1_list(right.m_c1_list), + m_c2_list(right.m_c2_list), + m_c3_list(right.m_c3_list), + m_cn_list(right.m_cn_list), + m_n(right.m_n), + m_loc(right.m_loc) + { + + + } + + StoichManagerN& operator=(const StoichManagerN &right) + { + if (this != &right) { + m_c1_list = right.m_c1_list; + m_c2_list = right.m_c2_list; + m_c3_list = right.m_c3_list; + m_cn_list = right.m_cn_list; + m_n = right.m_n; + m_loc = right.m_loc; + } + return *this; + } /** * Add a single reaction to the list of reactions that this @@ -795,7 +909,31 @@ namespace Cantera { class StoichWriter { public: - StoichWriter() {} + StoichWriter() + { + } + + StoichWriter(const StoichWriter &right) : + m_mult(right.m_mult), + m_ir(right.m_ir), + m_dr(right.m_dr), + m_is(right.m_is), + m_ds(right.m_ds) + { + } + + StoichWriter& operator=(const StoichWriter &right) + { + if (this != &right) { + m_mult = right.m_mult; + m_ir = right.m_ir; + m_dr = right.m_dr; + m_is = right.m_is; + m_ds = right.m_ds; + } + return *this; + } + void add(int rxn, const vector_int& k) { int n, nn = k.size(); @@ -841,7 +979,11 @@ namespace Cantera { std::string decrRxn(int rxn) { return m_dr[rxn]; } private: - std::map m_mult, m_ir, m_dr, m_is, m_ds; + std::map m_mult; + std::map m_ir; + std::map m_dr; + std::map m_is; + std::map m_ds; }; #endif From 0766b9469dfd7cc8c7d5a20713b03f48e4f8a9ca Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Jun 2010 20:56:45 +0000 Subject: [PATCH 172/446] Nominally finished the copy constructors/assignment operators for the Kinetics class and friends. However, I have not done any testing on this, none. --- Cantera/src/kinetics/AqueousKinetics.cpp | 105 ++++++++++++++++++++- Cantera/src/kinetics/AqueousKinetics.h | 41 ++++++-- Cantera/src/kinetics/EdgeKinetics.h | 32 +++++++ Cantera/src/kinetics/InterfaceKinetics.cpp | 70 ++++++++++---- Cantera/src/kinetics/InterfaceKinetics.h | 19 ++-- 5 files changed, 229 insertions(+), 38 deletions(-) diff --git a/Cantera/src/kinetics/AqueousKinetics.cpp b/Cantera/src/kinetics/AqueousKinetics.cpp index 0559dec2b..6ab77b9f5 100644 --- a/Cantera/src/kinetics/AqueousKinetics.cpp +++ b/Cantera/src/kinetics/AqueousKinetics.cpp @@ -30,7 +30,50 @@ using namespace std; namespace Cantera { + //==================================================================================================================== + AqueousKineticsData::AqueousKineticsData() : + m_logp_ref(0.0), + m_logc_ref(0.0), + m_ROP_ok(false), + m_temp(0.0) + { + } + //==================================================================================================================== + AqueousKineticsData::~AqueousKineticsData() + { + } + //==================================================================================================================== + AqueousKineticsData::AqueousKineticsData(const AqueousKineticsData &right) : + m_logp_ref(0.0), + m_logc_ref(0.0), + m_ROP_ok(false), + m_temp(0.0) + { + *this=right; + } + //==================================================================================================================== + AqueousKineticsData& AqueousKineticsData::operator=(const AqueousKineticsData &right) + { + if (this != &right) { + m_logp_ref = right.m_logp_ref; + m_logc_ref = right.m_logc_ref; + m_ropf = right.m_ropf; + m_ropr = right.m_ropr; + m_ropnet = right.m_ropnet; + m_rfn_low = right.m_rfn_low; + m_rfn_high = right.m_rfn_high; + m_ROP_ok = right.m_ROP_ok; + m_temp = right.m_temp; + m_rfn = right.m_rfn; + m_rkcn = right.m_rkcn; + } + return *this; + } + //==================================================================================================================== + + + //==================================================================================================================== /** * Construct an empty reaction mechanism. */ @@ -47,12 +90,70 @@ namespace Cantera { m_kdata->m_temp = 0.0; m_rxnstoich = new ReactionStoichMgr; } - + //==================================================================================================================== + AqueousKinetics::AqueousKinetics(const AqueousKinetics &right) : + Kinetics(), + m_kk(0), + m_nfall(0), + m_nirrev(0), + m_nrev(0), + m_finalized(false) + { + *this = right; + } + //==================================================================================================================== AqueousKinetics::~AqueousKinetics() { delete m_kdata; delete m_rxnstoich; - } + } + //==================================================================================================================== + AqueousKinetics& AqueousKinetics::operator=(const AqueousKinetics &right) + { + if (this == &right) return *this; + Kinetics::operator=(right); + + m_kk = right.m_kk; + m_nfall = right.m_nfall; + m_rates = right.m_rates; + m_index = right.m_index; + m_irrev = right.m_irrev; + + *m_rxnstoich = *(right.m_rxnstoich); + + m_fwdOrder = right.m_fwdOrder; + m_nirrev = right.m_nirrev; + m_nrev = right.m_nrev; + m_rgroups = right.m_rgroups; + m_pgroups = right.m_pgroups; + m_rxntype = right.m_rxntype; + m_rrxn = right.m_rrxn; + m_prxn = right.m_prxn; + m_dn = right.m_dn; + m_revindex = right.m_revindex; + m_rxneqn = right.m_rxneqn; + + *m_kdata = *(right.m_kdata); + + m_conc = right.m_conc; + m_grt = right.m_grt; + m_finalized = right.m_finalized; + + throw CanteraError("GasKinetics::operator=()", + "Unfinished implementation"); + + return *this; + + } + //==================================================================================================================== + Kinetics *AqueousKinetics::duplMyselfAsKinetics(const std::vector & tpVector) const + { + AqueousKinetics* gK = new AqueousKinetics(*this); + gK->assignShallowPointers(tpVector); + return dynamic_cast(gK); + } + + //==================================================================================================================== /** * Update temperature-dependent portions of reaction rates and * falloff functions. diff --git a/Cantera/src/kinetics/AqueousKinetics.h b/Cantera/src/kinetics/AqueousKinetics.h index a23bc0626..7036714a9 100644 --- a/Cantera/src/kinetics/AqueousKinetics.h +++ b/Cantera/src/kinetics/AqueousKinetics.h @@ -46,18 +46,21 @@ namespace Cantera { */ class AqueousKineticsData { public: - AqueousKineticsData() : - m_logp_ref(0.0), - m_logc_ref(0.0), - m_ROP_ok(false), - m_temp(0.0) - {} - virtual ~AqueousKineticsData(){} + AqueousKineticsData(); - doublereal m_logp_ref, m_logc_ref; + ~AqueousKineticsData(); + + AqueousKineticsData(const AqueousKineticsData &right); + + AqueousKineticsData& operator=(const AqueousKineticsData &right); + + doublereal m_logp_ref; + doublereal m_logc_ref; array_fp m_ropf; - array_fp m_ropr, m_ropnet; - array_fp m_rfn_low, m_rfn_high; + array_fp m_ropr; + array_fp m_ropnet; + array_fp m_rfn_low; + array_fp m_rfn_high; bool m_ROP_ok; doublereal m_temp; @@ -88,9 +91,27 @@ namespace Cantera { /// Constructor. AqueousKinetics(thermo_t* thermo = 0); + AqueousKinetics(const AqueousKinetics &right); + + AqueousKinetics& operator=(const AqueousKinetics &right); + /// Destructor. virtual ~AqueousKinetics(); + + //! Duplication routine for objects which inherit from Kinetics + /*! + * This virtual routine can be used to duplicate %Kinetics objects + * inherited from %Kinetics even if the application only has + * a pointer to %Kinetics to work with. + * + * These routines are basically wrappers around the derived copy constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object + */ + virtual Kinetics *duplMyselfAsKinetics(const std::vector & tpVector) const; + virtual int ID() const { return cAqueousKinetics; } virtual int type() const { return cAqueousKinetics; } diff --git a/Cantera/src/kinetics/EdgeKinetics.h b/Cantera/src/kinetics/EdgeKinetics.h index b19e7b3e6..6f1b5528b 100644 --- a/Cantera/src/kinetics/EdgeKinetics.h +++ b/Cantera/src/kinetics/EdgeKinetics.h @@ -37,6 +37,38 @@ namespace Cantera { /// Destructor. virtual ~EdgeKinetics() {} + EdgeKinetics(const EdgeKinetics &right) : + InterfaceKinetics(right) + { + *this=right; + } + + EdgeKinetics & operator=(const EdgeKinetics &right) + { + if (this != &right) { + InterfaceKinetics::operator=(right); + } + return *this; + } + + //! Duplication routine for objects which inherit from Kinetics + /*! + * This virtual routine can be used to duplicate %Kinetics objects + * inherited from %Kinetics even if the application only has + * a pointer to %Kinetics to work with. + * + * These routines are basically wrappers around the derived copy constructor. + * + * @param tpVector Vector of shallow pointers to ThermoPhase objects. this is the + * m_thermo vector within this object + */ + virtual Kinetics *duplMyselfAsKinetics(const std::vector & tpVector) const + { + EdgeKinetics* iK = new EdgeKinetics(*this); + iK->assignShallowPointers(tpVector); + return dynamic_cast(iK); + } + /** * Identifies the subclass of the Kinetics manager type. * These are listed in mix_defs.h. diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 451116ada..790ab0796 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -24,7 +24,45 @@ using namespace std; namespace Cantera { - + //==================================================================================================================== + InterfaceKineticsData::InterfaceKineticsData() : + m_logp0(0.0), + m_logc0(0.0), + m_ROP_ok(false), + m_temp(0.0), + m_logtemp(0.0) + { + } + //==================================================================================================================== + InterfaceKineticsData:: InterfaceKineticsData(const InterfaceKineticsData &right) : + m_logp0(0.0), + m_logc0(0.0), + m_ROP_ok(false), + m_temp(0.0), + m_logtemp(0.0) + { + *this = right; + } + //==================================================================================================================== + InterfaceKineticsData::~InterfaceKineticsData() + { + } + //==================================================================================================================== + InterfaceKineticsData & InterfaceKineticsData::operator=(const InterfaceKineticsData &right) + { + if (this == &right) return *this; + m_logp0 = right.m_logp0; + m_logc0 = right.m_logc0; + m_ropf = right.m_ropf; + m_ropr = right.m_ropr; + m_ropnet = right.m_ropnet; + m_ROP_ok = right.m_ROP_ok; + m_temp = right.m_temp; + m_logtemp = right.m_logtemp; + m_rfn = right.m_rfn; + m_rkcn = right.m_rkcn; + return *this; + } //==================================================================================================================== /* * Construct an empty InterfaceKinetics reaction mechanism. @@ -136,8 +174,7 @@ namespace Cantera { Kinetics::operator=(right); - - + m_grt = right.m_grt; m_kk = right.m_kk; m_revindex = right.m_revindex; m_rates = right.m_rates; @@ -150,7 +187,8 @@ namespace Cantera { m_rrxn = right.m_rrxn; m_prxn = right.m_prxn; m_rxneqn = right.m_rxneqn; - *m_kdata = *right.m_kdata; // needs to be developed + *m_kdata = *right.m_kdata; + m_conc = right.m_conc; m_mu0 = right.m_mu0; m_phi = right.m_phi; m_pot = right.m_pot; @@ -171,7 +209,6 @@ namespace Cantera { m_phaseExistsCheck = right.m_phaseExistsCheck; m_phaseExists = right.m_phaseExists; - m_rxnPhaseIsReactant.resize(m_ii, 0); m_rxnPhaseIsProduct.resize(m_ii, 0); int np = nPhases(); @@ -183,7 +220,7 @@ namespace Cantera { m_rxnPhaseIsProduct[i][p] = right.m_rxnPhaseIsProduct[i][p]; } } - m_rxnPhaseIsProduct = right.m_rxnPhaseIsProduct; + m_ioFlag = right.m_ioFlag; return *this; @@ -197,17 +234,6 @@ namespace Cantera { int InterfaceKinetics::type() const { return cInterfaceKinetics; } - //==================================================================================================================== - // Set the electric potential in the nth phase - /* - * @param n phase Index in this kinetics object. - * @param V Electric potential (volts) - */ - void InterfaceKinetics::setElectricPotential(int n, doublereal V) { - thermo(n).setElectricPotential(V); - m_redo_rates = true; - } - //==================================================================================================================== // Duplication routine for objects which inherit from Kinetics /* @@ -227,6 +253,16 @@ namespace Cantera { return dynamic_cast(iK); } //==================================================================================================================== + // Set the electric potential in the nth phase + /* + * @param n phase Index in this kinetics object. + * @param V Electric potential (volts) + */ + void InterfaceKinetics::setElectricPotential(int n, doublereal V) { + thermo(n).setElectricPotential(V); + m_redo_rates = true; + } + //==================================================================================================================== // Update properties that depend on temperature /* * This is called to update all of the properties that depend on temperature diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index b6b9208d9..c14e0b8f2 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -44,16 +44,17 @@ namespace Cantera { */ class InterfaceKineticsData { public: - InterfaceKineticsData() : - m_logp0(0.0), - m_logc0(0.0), - m_ROP_ok(false), - m_temp(0.0), - m_logtemp(0.0) - {} + InterfaceKineticsData(); + + InterfaceKineticsData(const InterfaceKineticsData &right); + + InterfaceKineticsData &operator=(const InterfaceKineticsData &right); + //! Virtual destructor - virtual ~InterfaceKineticsData() { - } + /*! + * todo - why is this virtual + */ + virtual ~InterfaceKineticsData(); doublereal m_logp0; doublereal m_logc0; From 86be28621a1fe3658d6f76064b2e608bd0097e8a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 29 Jun 2010 18:28:08 +0000 Subject: [PATCH 173/446] Added doxygen input. --- .../src/transport/LiquidTranInteraction.cpp | 2 +- Cantera/src/transport/LiquidTransport.cpp | 23 ++++++++++--------- Cantera/src/transport/TransportBase.h | 21 +++++++++++++---- Cantera/src/transport/WaterTransport.h | 7 ++++++ 4 files changed, 37 insertions(+), 16 deletions(-) diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index 36531da93..e4585f832 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -709,7 +709,7 @@ namespace Cantera { for (i = 0; i < nsp; i++) { if (m_mobRatMixModel[k]) { m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp(m_mobRatSpecies[k] ); - if (m_mobRatMix(i,j) > 0) { + if (m_mobRatMix(i,j) > 0.0) { m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j); } } diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 929a23a39..eed8b7c53 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -231,14 +231,13 @@ namespace Cantera { } } for ( int l=0;l < m_nsp2; l++ ){ - if ( m_mobRatTempDep_Ns[l][k] ) delete m_mobRatTempDep_Ns[l][k]; + if (m_mobRatTempDep_Ns[l][k]) delete m_mobRatTempDep_Ns[l][k]; } if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k]; if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k]; if ( m_diffTempDep_Ns[k] ) delete m_diffTempDep_Ns[k]; - //These are constructed in TransportFactory::newLTI - - if ( m_selfDiffMixModel[k] ) delete m_selfDiffMixModel[k]; + //These are constructed in TransportFactory::newLTI + if (m_selfDiffMixModel[k]) delete m_selfDiffMixModel[k]; } for ( int k = 0; k < m_nsp2; k++) { @@ -548,12 +547,14 @@ namespace Cantera { update_T(); update_C(); - ////// LiquidTranInteraction method - if (!m_mobRat_mix_ok){ + // LiquidTranInteraction method + if (!m_mobRat_mix_ok) { for (int k = 0; k < m_nsp2; k++){ if(m_mobRatMixModel[k]){ - m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] ); - if ( m_mobRatMix[k] > 0 ) m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway + m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp(m_mobRatTempDep_Ns[k]); + if (m_mobRatMix[k] > 0) { + m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway + } } } } @@ -576,7 +577,7 @@ namespace Cantera { if (!m_mobRat_temp_ok) { updateMobilityRatio_T(); } - for (int k=0; kgetSpeciesTransProp() ; + m_mobRatSpecies(k,j) = m_mobRatTempDep_Ns[k][j]->getSpeciesTransProp(); } } m_mobRat_temp_ok = true; @@ -1630,7 +1631,7 @@ namespace Cantera { * They are still fortran ordered, so that i varies fastest. */ - double condSum1, condSum2; + double condSum1; switch (m_nDim) { case 1: /* 1-D approximation */ diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 87d911c95..667190ccc 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -329,10 +329,23 @@ namespace Cantera { virtual void getSpeciesIonConductivity(doublereal* const ionCond) { err("getSpeciesIonConductivity"); } - - - /** - * The mobility ratio. + + //! Returns the pointer to the mobility ratios of the species in the phase + /*! + * + * @param mobRat Returns a matrix of mobility ratios for the current problem. + * The mobility ratio mobRat(i,j) is defined as the ratio of the + * mobility of species i to species j. + * + * mobRat(i,j) = mu_i / mu_j + * + * It is returned in fortran-ordering format. ie. it is returned as mobRat[k], where + * + * k = j * nsp + i + * + * The size of mobRat must be at least equal to nsp*nsp + * + * @deprecated This doesn't seem to be the essential input; it should just be the mobility. */ virtual void mobilityRatio(double* mobRat) { err("mobilityRatio"); } diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index 6dc61555d..e95fadcda 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -47,6 +47,13 @@ namespace Cantera { public: //! default constructor + /*! + * @param thermo ThermoPhase object that represents the phase. + * Defaults to zero + * + * @param ndim Number of dimensions of the flux expressions. + * Defaults to a value of one. + */ WaterTransport(thermo_t* thermo = 0, int ndim = 1); //!Copy Constructor for the %LiquidThermo object. From ccb4737040edcb52530ca27ca721799dbd298152 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 6 Jul 2010 14:07:36 +0000 Subject: [PATCH 174/446] Doxygen updates --- Cantera/src/transport/TransportFactory.cpp | 43 ++++++++++++++++------ Cantera/src/transport/TransportFactory.h | 26 +++++++++++-- 2 files changed, 55 insertions(+), 14 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 3daa32f84..7b9c89aa9 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -181,14 +181,20 @@ namespace Cantera { (q2*xk*xk + q1*xj*xj + q12*xk*xj); } - + //============================================================================================================================= // Corrections for polar-nonpolar binary diffusion coefficients /* - Calculate corrections to the well depth parameter and the - diamter for use in computing the binary diffusion coefficient - of polar-nonpolar pairs. For more information about this - correction, see Dixon-Lewis, Proc. Royal Society (1968). - */ + * Calculate corrections to the well depth parameter and the + * diameter for use in computing the binary diffusion coefficient + * of polar-nonpolar pairs. For more information about this + * correction, see Dixon-Lewis, Proc. Royal Society (1968). + * + * @param i Species one - this is a bimolecular correction routine + * @param j species two - this is a bimolecular correction routine + * @param tr Database of species properties read in from the input xml file. + * @param f_eps Multiplicative correction factor to be applied to epsilon(i,j) + * @param f_sigma Multiplicative correction factor to be applied to diam(i,j) + */ void TransportFactory::makePolarCorrections(int i, int j, const GasTransportParams& tr, doublereal& f_eps, doublereal& f_sigma) { @@ -213,7 +219,7 @@ namespace Cantera { f_sigma = pow(xi, -1.0/6.0); f_eps = xi*xi; } - + //============================================================================================================================= /* TransportFactory(): default constructor @@ -224,7 +230,6 @@ namespace Cantera { TransportFactory::TransportFactory() : m_verbose(false), m_integrals(0) - { m_models["Mix"] = cMixtureAveraged; m_models["Multi"] = cMulticomponent; @@ -664,8 +669,21 @@ namespace Cantera { } } //==================================================================================================================== - - + // Initialize an existing transport manager + /* + * This routine sets up an existing gas-phase transport manager. + * It calculates the collision integrals and calls the initGas() function to + * populate the species-dependent data structure. + * + * @param tr Pointer to the Transport manager + * @param thermo Pointer to the ThermoPhase object + * @param mode Chemkin compatible mode or not. This alters the specification of the + * collision integrals. defaults to no. + * @param log_level Defaults to zero, no logging + * + * In DEBUG_MODE, this routine will create the file transport_log.xml + * and write informative information to it. + */ void TransportFactory::initTransport(Transport* tran, thermo_t* thermo, int mode, int log_level) { @@ -673,6 +691,9 @@ namespace Cantera { GasTransportParams trParam; #ifdef DEBUG_MODE + if (log_level == 0) { + m_verbose = 0; + } ofstream flog("transport_log.xml"); trParam.xml = new XML_Writer(flog); if (m_verbose) { @@ -695,7 +716,7 @@ namespace Cantera { #endif return; } - + //==================================================================================================================== /* Similar to initTransport except uses LiquidTransportParams class and calls setupLiquidTransport(). diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 1945b6e37..a7784c17a 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -173,8 +173,22 @@ namespace Cantera { newTransport(thermo_t* thermo, int log_level=0); //! Initialize an existing transport manager - virtual void initTransport(Transport* tr, - thermo_t* thermo, int mode=0, int log_level=0); + /*! + * This routine sets up an existing gas-phase transport manager. + * It calculates the collision integrals and calls the initGas() function to + * populate the species-dependent data structure. + * + * @param tr Pointer to the Transport manager + * @param thermo Pointer to the ThermoPhase object + * @param mode Chemkin compatible mode or not. This alters the specification of the + * collision integrals. defaults to no. + * @param log_level Defaults to zero, no logging + * + * In DEBUG_MODE, this routine will create the file transport_log.xml + * and write informative information to it. + * + */ + virtual void initTransport(Transport* tr, thermo_t* thermo, int mode=0, int log_level=0); //! Initialize an existing transport manager for liquid phase /*! Similar to initTransport except uses LiquidTransportParams @@ -336,9 +350,15 @@ namespace Cantera { //! Corrections for polar-nonpolar binary diffusion coefficients /*! * Calculate corrections to the well depth parameter and the - * diamter for use in computing the binary diffusion coefficient + * diameter for use in computing the binary diffusion coefficient * of polar-nonpolar pairs. For more information about this * correction, see Dixon-Lewis, Proc. Royal Society (1968). + * + * @param i Species one - this is a bimolecular correction routine + * @param j species two - this is a bimolecular correction routine + * @param tr Database of species properties read in from the input xml file. + * @param f_eps Multiplicative correction factor to be applied to epsilon(i,j) + * @param f_sigma Multiplicative correction factor to be applied to diam(i,j) */ void makePolarCorrections(int i, int j, const GasTransportParams& tr, doublereal& f_eps, From 1dd189fefb02581c22e26f2e64e55eda1161e3e1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 8 Jul 2010 17:01:55 +0000 Subject: [PATCH 175/446] Doxygen update --- Cantera/src/transport/TransportFactory.cpp | 5 ++- Cantera/src/transport/TransportFactory.h | 37 +++++++++++++++------- 2 files changed, 28 insertions(+), 14 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 7b9c89aa9..8c05b2688 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -865,7 +865,7 @@ namespace Cantera { for (i = 0; i < nsp; i++) { const XML_Node& sp = *xspecies[i]; name = sp["name"]; - // std::cout << "Processing node for " << name << std::endl; + // std::cout << "Processing node for " << name << std::endl; // put in a try block so that species with no 'transport' // child are skipped, instead of throwing an exception. @@ -905,8 +905,7 @@ namespace Cantera { "negative rotation relaxation number"); datatable[name] = data; - } - catch(CanteraError) { + } catch(CanteraError) { ; } } diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index a7784c17a..620b32836 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -178,10 +178,10 @@ namespace Cantera { * It calculates the collision integrals and calls the initGas() function to * populate the species-dependent data structure. * - * @param tr Pointer to the Transport manager - * @param thermo Pointer to the ThermoPhase object - * @param mode Chemkin compatible mode or not. This alters the specification of the - * collision integrals. defaults to no. + * @param tr Pointer to the Transport manager + * @param thermo Pointer to the ThermoPhase object + * @param mode Chemkin compatible mode or not. This alters the specification of the + * collision integrals. defaults to no. * @param log_level Defaults to zero, no logging * * In DEBUG_MODE, this routine will create the file transport_log.xml @@ -191,12 +191,20 @@ namespace Cantera { virtual void initTransport(Transport* tr, thermo_t* thermo, int mode=0, int log_level=0); //! Initialize an existing transport manager for liquid phase - /*! Similar to initTransport except uses LiquidTransportParams - * class and calls setupLiquidTransport(). + /*! + * This routine sets up an existing liquid-phase transport manager. + * It is similar to initTransport except that it uses the LiquidTransportParams + * class and calls setupLiquidTransport(). + * + * @param tr Pointer to the Transport manager + * @param thermo Pointer to the ThermoPhase object + * @param log_level Defaults to zero, no logging + * + * In DEBUG_MODE, this routine will create the file transport_log.xml + * and write informative information to it. */ - virtual void initLiquidTransport(Transport* tr, - thermo_t* thermo, - int log_level=0); + virtual void initLiquidTransport(Transport* tr, thermo_t* thermo, int log_level=0); + private: @@ -217,15 +225,22 @@ namespace Cantera { */ TransportFactory(); - //! Read Transport Database + //! Read the transport database /*! * Read transport property data from a file for a list of species. * Given the name of a file containing transport property * parameters and a list of species names, this method returns an * instance of TransportParams containing the transport data for * these species read from the file. + * + * @param xspecies Vector of pointers to species XML_Node databases. + * @param log reference to an XML_Node that will contain the log (unused) + * @param names vector of species names that must be filled in with valid transport parameters + * @param tr Output object containing the transport parameters + * for the species listed in names (in the order of their listing + * in names). */ - void getTransportData(const std::vector &db, + void getTransportData(const std::vector &xspecies, XML_Node& log, const std::vector& names, GasTransportParams& tr); From 101d4543fb2011c3940438fe7a5a42425b42a134 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 8 Jul 2010 22:05:17 +0000 Subject: [PATCH 176/446] Cleared up some documentation issues. --- Cantera/src/thermo/LatticeSolidPhase.h | 19 ++++++++++ Cantera/src/thermo/State.h | 50 +++++++++++++------------- 2 files changed, 45 insertions(+), 24 deletions(-) diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index e8ee4d510..f5abcee4b 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -62,6 +62,8 @@ namespace Cantera { * The mole fraction vector has been redefined within the LatticeSolidPhase object. The mole fractions sum * to one within each of the individual lattice phases. The routine getMoleFraction() and setMoleFraction() * have been redefined to use this convention. + * + * (This object is still under construction) * */ class LatticeSolidPhase : public ThermoPhase { @@ -228,7 +230,24 @@ namespace Cantera { m_press = p; setMolarDensity(m_molar_density); } + + //! Set the mole fractions to the specified values, and then + //! normalize them so that they sum to 1.0 for each of the subphases + /*! + * + * @param x Input vector of mole fractions. There is no restriction + * on the sum of the mole fraction vector. Internally, + * this object will normalize this vector before + * storring its contents. + * Length is m_kk. + */ virtual void setMoleFractions(const doublereal *x); + + //! Get the species mole fraction vector. + /*! + * @param x On return, x contains the mole fractions. Must have a + * length greater than or equal to the number of species. + */ virtual void getMoleFractions(doublereal *x) const; doublereal moleFraction(const int k) const { diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h index ca2826df9..faba94ea9 100644 --- a/Cantera/src/thermo/State.h +++ b/Cantera/src/thermo/State.h @@ -122,20 +122,16 @@ namespace Cantera { * @param k species index */ doublereal moleFraction(const int k) const; - //! Set the mole fractions to the specified values, and then //! normalize them so that they sum to 1.0. /*! * @param x Array of unnormalized mole fraction values (input). * Must have a length greater than or equal to the number of - * species. - * - * @param x Input vector of mole fractions. There is no restriction - * on the sum of the mole fraction vector. Internally, - * the State object will normalize this vector before - * storring its contents. - * Length is m_kk. + * species, m_kk. There is no restriction + * on the sum of the mole fraction vector. Internally, + * the State object will normalize this vector before + * storring its contents. */ virtual void setMoleFractions(const doublereal* const x); @@ -151,23 +147,17 @@ namespace Cantera { */ virtual void setMoleFractions_NoNorm(const doublereal* const x); - /** - * Get the species mass fractions. - * @param y On return, y - * contains the mass fractions. Array \a y must have a length - * greater than or equal to the number of species. - * - * @param y Output vector of mass fractions. - * Length is m_kk. + //! Get the species mass fractions. + /*! + * @param y On return, y contains the mass fractions. Array \a y must have a length + * greater than or equal to the number of species. */ void getMassFractions(doublereal* const y) const; //! Mass fraction of species k. /*! - * If k is outside the valid - * range, an exception will be thrown. Note that it is - * somewhat more efficent to call getMassFractions if the - * mass fractions of all species are desired. + * If k is outside the valid range, an exception will be thrown. Note that it is + * somewhat more efficent to call getMassFractions if the mass fractions of all species are desired. * * @param k species index */ @@ -305,20 +295,32 @@ namespace Cantera { /// mass density. //@{ - /// Temperature (K). + //! Temperature (K). + /*! + * @return Returns the temperature of the phase + */ doublereal temperature() const { return m_temp; } - /// Density (kg/m^3). + //! Density (kg/m^3). + /*! + * @return Returns the density of the phase + */ virtual doublereal density() const { return m_dens; } - /// Molar density (kmol/m^3). + //! Molar density (kmol/m^3). + /*! + * @return Returns the molar density of the phase + */ doublereal molarDensity() const; - /// Molar density (kmol/m^3). + //! Molar volume (m^3/kmol). + /*! + * @return Returns the molar volume of the phase + */ doublereal molarVolume() const; //! Set the internally storred density (kg/m^3) of the phase From a066cc0bc7594267d542a21913f6279ed1cdf0bd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 9 Jul 2010 23:05:09 +0000 Subject: [PATCH 177/446] doxgyen update -> no functionality changed. --- Cantera/src/transport/TransportFactory.cpp | 77 ++++++++++--------- Cantera/src/transport/TransportFactory.h | 89 +++++++++++++--------- 2 files changed, 92 insertions(+), 74 deletions(-) diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 8c05b2688..810cfe799 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -61,7 +61,9 @@ namespace Cantera { TransportFactory* TransportFactory::s_factory = 0; + #if defined(THREAD_SAFE_CANTERA) + // declaration of static storage for the mutex boost::mutex TransportFactory::transport_mutex; #endif @@ -656,16 +658,14 @@ namespace Cantera { XML_Node root, log; // Note that getLiquidSpeciesTransportData just populates the pure species transport data. - getLiquidSpeciesTransportData(species_database, log, - trParam.thermo->speciesNames(), trParam); + getLiquidSpeciesTransportData(species_database, log, trParam.thermo->speciesNames(), trParam); // getLiquidInteractionsTransportData() populates the // species-species interaction models parameters // like visc_Eij if (phase_database->hasChild("transport")) { XML_Node& transportNode = phase_database->child("transport"); - getLiquidInteractionsTransportData(transportNode, log, - trParam.thermo->speciesNames(), trParam); + getLiquidInteractionsTransportData(transportNode, log, trParam.thermo->speciesNames(), trParam); } } //==================================================================================================================== @@ -749,18 +749,14 @@ namespace Cantera { return; } - - - - /******************************************************** - * - * Collision Integral Fits - * - ********************************************************/ - - - void TransportFactory::fitCollisionIntegrals(ostream& logfile, - GasTransportParams& tr) { + //==================================================================================================================== + // Generate polynomial fits to collision integrals + /* + * @param logfile Reference to an ostream that will contain log information when in + * DEBUG_MODE + * @param tr Reference to the GasTransportParams object that will contain the results. + */ + void TransportFactory::fitCollisionIntegrals(ostream& logfile, GasTransportParams& tr) { vector_fp::iterator dptr; doublereal dstar; @@ -824,7 +820,7 @@ namespace Cantera { } #endif } - + //==================================================================================================================== @@ -1230,28 +1226,33 @@ namespace Cantera { *********************************************************/ - - /***************** fitProperties ***************/ - - /* Generate polynomial fits for the pure-species viscosities and - * for the binary diffusion coefficients. If - * CK_mode, then the fits are of the - * form \f[ - * \log(\eta(i)) = \sum_{n = 0}^3 a_n(i) (\log T)^n - * \f] - * and \f[ - * \log(D(i,j)) = \sum_{n = 0}^3 a_n(i,j) (\log T)^n - * \f] - * Otherwise the fits are of the form - * \f[ - * \eta(i)/sqrt(k_BT) = \sum_{n = 0}^4 a_n(i) (\log T)^n - * \f] - * and \f[ - * D(i,j)/sqrt(k_BT)) = \sum_{n = 0}^4 a_n(i,j) (\log T)^n - * \f] + //==================================================================================================================== + // Generate polynomial fits to the viscosity, conductivity, and + // the binary diffusion coefficients + /* + * If CK_mode, then the fits are of the form + * \f[ + * \log(\eta(i)) = \sum_{n = 0}^3 a_n(i) (\log T)^n + * \f] + * and + * \f[ + * \log(D(i,j)) = \sum_{n = 0}^3 a_n(i,j) (\log T)^n + * \f] + * Otherwise the fits are of the form + * \f[ + * \eta(i)/sqrt(k_BT) = \sum_{n = 0}^4 a_n(i) (\log T)^n + * \f] + * and + * \f[ + * D(i,j)/sqrt(k_BT)) = \sum_{n = 0}^4 a_n(i,j) (\log T)^n + * \f] + * + * @param tr Reference to the GasTransportParams object that will contain the results. + * @param logfile Reference to an ostream that will contain log information when in + * DEBUG_MODE */ - void TransportFactory::fitProperties(GasTransportParams& tr, - ostream& logfile) { + void TransportFactory::fitProperties(GasTransportParams& tr, std::ostream& logfile) { + doublereal tstar; int k, j, n, ndeg = 0; #ifdef DEBUG_MODE diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 620b32836..ebbbef53b 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -43,7 +43,7 @@ //====================================================================================================================== namespace Cantera { //==================================================================================================================== - //! Struct to hold data read from a transport property database file. + //! Struct to hold data read from a transport property database file for gas-phase species struct GasTransportData { GasTransportData() : speciesName("-"), geometry(-1), wellDepth(-1.0), @@ -211,8 +211,10 @@ namespace Cantera { //! Static instance of the factor -> This is the only instance of this //! object allowed static TransportFactory* s_factory; + #if defined(THREAD_SAFE_CANTERA) - static boost::mutex transport_mutex ; + //! Static instance of the mutex used to ensure the proper reading of the transport database + static boost::mutex transport_mutex; #endif //! The constructor is private; use static method factory() to @@ -248,8 +250,8 @@ namespace Cantera { //! Read transport property data from a file for a list of species that comprise //! the phase. /*! - * Given the name of a file containing transport property - * parameters and a list of species names, this method constructs the LiquidTransport + * Given a vector of pointers to species XML data bases + * and a list of species names, this method constructs the LiquidTransport * Params object containing the transport data for these species. * * It is an error to not find a "transport" XML element within each of the species @@ -266,41 +268,58 @@ namespace Cantera { XML_Node& log, const std::vector& names, LiquidTransportParams& tr); - //! Read transport property data from a file for a list of species. + //! Read transport property data from a file for interactions between species. /*! - * - * Given the name of a file containing transport property - * parameters and a list of species names, this method returns an + * Given the XML_Node database for transport interactions defined within the current phase + * and a list of species names within the phase, this method returns an * instance of TransportParams containing the transport data for * these species read from the file. * + * This routine reads interaction parameters between species within the phase. + * + * @param phaseTran_db Reference to the transport XML field for the phase + * @param log Reference to an XML log file. (currently unused) + * @param names Vector of names of species. On output, tr will contain transport data + * for each of of these names in the order determined by this vector. + * @param tr Reference to the LiquidTransportParams object that will contain the results. */ - void getLiquidInteractionsTransportData(const XML_Node &db, - XML_Node& log, const std::vector& names, - LiquidTransportParams& tr); + void getLiquidInteractionsTransportData(const XML_Node &phaseTran_db, XML_Node& log, + const std::vector& names, LiquidTransportParams& tr); - //! Generate polynomial fits to viscosity, conductivity, and - //! binary diffusion coefficients */ - /*! If CK_mode, then the fits are of the form - * \f[ - * \log(\eta(i)) = \sum_{n = 0}^3 a_n(i) (\log T)^n - * \f] - * and \f[ - * \log(D(i,j)) = \sum_{n = 0}^3 a_n(i,j) (\log T)^n - * \f] - * Otherwise the fits are of the form - * \f[ - * \eta(i)/sqrt(k_BT) = \sum_{n = 0}^4 a_n(i) (\log T)^n - * \f] - * and \f[ - * D(i,j)/sqrt(k_BT)) = \sum_{n = 0}^4 a_n(i,j) (\log T)^n - * \f] + //! Generate polynomial fits to the viscosity, conductivity, and + //! the binary diffusion coefficients + /*! + * If CK_mode, then the fits are of the form + * \f[ + * \log(\eta(i)) = \sum_{n = 0}^3 a_n(i) (\log T)^n + * \f] + * and + * \f[ + * \log(D(i,j)) = \sum_{n = 0}^3 a_n(i,j) (\log T)^n + * \f] + * Otherwise the fits are of the form + * \f[ + * \eta(i)/sqrt(k_BT) = \sum_{n = 0}^4 a_n(i) (\log T)^n + * \f] + * and + * \f[ + * D(i,j)/sqrt(k_BT)) = \sum_{n = 0}^4 a_n(i,j) (\log T)^n + * \f] + * + * @param tr Reference to the GasTransportParams object that will contain the results. + * @param logfile Reference to an ostream that will contain log information when in + * DEBUG_MODE + * */ - void fitProperties(GasTransportParams& tr, std::ostream & logfile); + void fitProperties(GasTransportParams& tr, std::ostream &logfile); //! Generate polynomial fits to collision integrals - void fitCollisionIntegrals(std::ostream & logfile, - GasTransportParams& tr); + /*! + * @param logfile Reference to an ostream that will contain log information when in + * DEBUG_MODE + * @param tr Reference to the GasTransportParams object that will contain the results. + */ + void fitCollisionIntegrals(std::ostream & logfile, GasTransportParams& tr); //! Prepare to build a new kinetic-theory-based transport manager for low-density gases @@ -343,22 +362,20 @@ namespace Cantera { * d(j,k). This method computes the multiplier by which the * first-order binary diffusion coefficient should be multiplied * to produce the value correct to second order. The expressions - * here are taken from Marerro and Mason, - * J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). + * here are taken from Marerro and Mason, J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). * * @param t Temperature (K) * @param tr Transport parameters * @param k index of first species * @param j index of second species - * @param xmk mole fraction of species k - * @param xmj mole fraction of species j + * @param xk Mole fraction of species k + * @param xj Mole fraction of species j * @param fkj multiplier for d(k,j) * @param fjk multiplier for d(j,k) * * @note This method is not used currently. */ - void getBinDiffCorrection(doublereal t, - const GasTransportParams& tr, int k, int j, + void getBinDiffCorrection(doublereal t, const GasTransportParams& tr, int k, int j, doublereal xk, doublereal xj, doublereal& fkj, doublereal& fjk); From 42f96b7dd968f93cb157a63e32d6dedeef2cd0dd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 10 Jul 2010 01:50:32 +0000 Subject: [PATCH 178/446] Made sure memset and memcpy were in the std:: namespace --- Cantera/src/base/vec_functions.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Cantera/src/base/vec_functions.h b/Cantera/src/base/vec_functions.h index c3b14fff1..d3ed6ebd3 100644 --- a/Cantera/src/base/vec_functions.h +++ b/Cantera/src/base/vec_functions.h @@ -181,7 +181,7 @@ namespace Cantera { inline void fbo_copy_dbl_1(doublereal * const copyTo, const doublereal * const copyFrom, const int len) { if (len > 0) { - (void) memcpy((void *)copyTo, (const void *)copyFrom, len * sizeof(doublereal)); + (void) std::memcpy((void *)copyTo, (const void *)copyFrom, len * sizeof(doublereal)); } } @@ -196,7 +196,7 @@ namespace Cantera { inline void fvo_copy_dbl_1(std::vector ©To, const std::vector ©From, const int len) { if (len > 0) { - (void) memcpy((void *)(©To[0]), (const void *)(©From[0]), len * sizeof(doublereal)); + (void) std::memcpy((void *)(©To[0]), (const void *)(©From[0]), len * sizeof(doublereal)); } } @@ -209,7 +209,7 @@ namespace Cantera { */ inline void fbo_zero_dbl_1(doublereal * const v, const int len) { if (len > 0) { - (void) memset((void *)v, 0, len * sizeof(doublereal)); + (void) std::memset((void *)v, 0, len * sizeof(doublereal)); } } @@ -222,7 +222,7 @@ namespace Cantera { */ inline void fvo_zero_dbl_1(std::vector &v, const int len) { if (len > 0) { - (void) memset((void *)(&v[0]), 0, len * sizeof(doublereal)); + (void) std::memset((void *)(&v[0]), 0, len * sizeof(doublereal)); } } From 260c2f75eda4d57e0d2b367d513cd7fb3b2ac7c6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 10 Jul 2010 03:23:21 +0000 Subject: [PATCH 179/446] Updated this file --- docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh b/docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh index 3fe470105..f6df415ab 100755 --- a/docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh +++ b/docs/install_examples/cygwin_gcc434_dbg_f2c_numpy.sh @@ -25,11 +25,11 @@ Cantera_Install_Dir='/cygdrive/c/cygwin_env/arch/cygwin/cantera-1.8.0' # if you don't want to link sundials in # # Sundials_Home='' -Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.3.0_dbg' +Sundials_Home='/cygdrive/c/cygwin_env/arch/cygwin/sundials-2.4.0_dbg' # # Specify the Sundials version number (either 2.2, 2.3, or 2.4) -Sundials_Version='2.3' -# Sundials_Version=2.4' +# Sundials_Version='2.3' +Sundials_Version=2.4' # ----------------------------------------------------------------------------- # CANTERA_CONFIG_PREFIX=$Cantera_Install_Dir From 37b38c7a53f03d4a3eb1b4308e172a5943c6c2e9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 10 Jul 2010 03:28:36 +0000 Subject: [PATCH 180/446] Added ignore files From ed848f6f88c9ac435be1795e071438dbe05c01b7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 12 Jul 2010 21:08:22 +0000 Subject: [PATCH 181/446] doxygen update --- Cantera/src/transport/SolidTransport.h | 43 ++++++++++++- Cantera/src/transport/TransportFactory.cpp | 74 +++++++++++----------- Cantera/src/transport/TransportFactory.h | 49 ++++++++++++-- 3 files changed, 121 insertions(+), 45 deletions(-) diff --git a/Cantera/src/transport/SolidTransport.h b/Cantera/src/transport/SolidTransport.h index 8c6be50d2..3d2833f79 100644 --- a/Cantera/src/transport/SolidTransport.h +++ b/Cantera/src/transport/SolidTransport.h @@ -117,14 +117,55 @@ namespace Cantera { private: - int m_nmobile; // number of mobile species + //! number of mobile species + /*! + * This is equal to the + */ + int m_nmobile; + + //! Coefficient for the diffusivity of species within a solid + /*! + * This is with respect to the lattice + * units = m**2 / s + * vector of length m_nmobile + */ vector_fp m_Adiff; + + //! Temperature power coefficient for the diffusivity of species in a solid + /*! + * vector of length m_nmobile + */ vector_fp m_Ndiff; + + //! Arrhenius factor for the species diffusivities of a solid + /*! + * units = temperature + * vector of length m_nmobile + */ vector_fp m_Ediff; + + //! Index of mobile species to global species + /*! + * vector of length m_nmobile + */ vector_int m_sp; + + //! Coefficient for the thermal conductivity of a solid + /*! + * units = kg m / s3 /K = W/m/K + */ doublereal m_Alam; + + //! Temperature power coefficient for the thermal conductivity of a solid doublereal m_Nlam; + + //! Arrhenius factor for the thermal conductivity of a solid + /*! + * units = temperature + */ doublereal m_Elam; + + //! extra fp array of length nSpecies() vector_fp m_work; }; } diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 810cfe799..3bae891b5 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -49,7 +49,6 @@ #include #include -//using namespace std; /** * polynomial degree used for fitting collision integrals @@ -59,7 +58,7 @@ namespace Cantera { - + //==================================================================================================================== TransportFactory* TransportFactory::s_factory = 0; #if defined(THREAD_SAFE_CANTERA) @@ -70,54 +69,54 @@ namespace Cantera { ////////////////////////// exceptions ///////////////////////// - /** - * Exception thrown if an error is encountered while reading the - * transport database. - */ + //==================================================================================================================== + //! Exception thrown if an error is encountered while reading the transport database class TransportDBError : public CanteraError { public: - TransportDBError(int linenum, std::string msg) - : CanteraError("getTransportData", - "error reading transport data: " - + msg + "\n") {} + //! Default constructor + /*! + * @param linenum inputs the line number + * @param msg String message to be sent to the user + */ + TransportDBError(int linenum, std::string msg) : + CanteraError("getTransportData", "error reading transport data: " + msg + "\n") + { + } }; - - + //==================================================================================================================== /////////////////////////// constants ////////////////////////// const doublereal ThreeSixteenths = 3.0/16.0; const doublereal TwoOverPi = 2.0/Pi; const doublereal FiveThirds = 5.0/3.0; - - //////////////////// class TransportFactory methods ////////////// - + //==================================================================================================================== // Second-order correction to the binary diffusion coefficients /* - Calculate second-order corrections to binary diffusion - coefficient pair (dkj, djk). At first order, the binary - diffusion coefficients are independent of composition, and - d(k,j) = d(j,k). But at second order, there is a weak - dependence on composition, with the result that d(k,j) != - d(j,k). This method computes the multiplier by which the - first-order binary diffusion coefficient should be multiplied - to produce the value correct to second order. The expressions - here are taken from Marerro and Mason, - J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). - - @param t Temperature (K) - @param tr Transport parameters - @param k index of first species - @param j index of second species - @param xmk mole fraction of species k - @param xmj mole fraction of species j - @param fkj multiplier for d(k,j) - @param fjk multiplier for d(j,k) - - @note This method is not used currently. - */ + * Calculate second-order corrections to binary diffusion + * coefficient pair (dkj, djk). At first order, the binary + * diffusion coefficients are independent of composition, and + * d(k,j) = d(j,k). But at second order, there is a weak + * dependence on composition, with the result that d(k,j) != + * d(j,k). This method computes the multiplier by which the + * first-order binary diffusion coefficient should be multiplied + * to produce the value correct to second order. The expressions + * here are taken from Marerro and Mason, + * J. Phys. Chem. Ref. Data, vol. 1, p. 3 (1972). + * + * @param t Temperature (K) + * @param tr Transport parameters + * @param k index of first species + * @param j index of second species + * @param xmk mole fraction of species k + * @param xmj mole fraction of species j + * @param fkj multiplier for d(k,j) + * @param fjk multiplier for d(j,k) + * + * @note This method is not used currently. + */ void TransportFactory::getBinDiffCorrection(doublereal t, const GasTransportParams& tr, int k, int j, doublereal xk, doublereal xj, doublereal& fkj, doublereal& fjk) { @@ -182,7 +181,6 @@ namespace Cantera { (p2*xk*xk + p1*xj*xj + p12*xk*xj)/ (q2*xk*xk + q1*xj*xj + q12*xk*xj); } - //============================================================================================================================= // Corrections for polar-nonpolar binary diffusion coefficients /* diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index ebbbef53b..7154ee5cf 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -45,19 +45,56 @@ namespace Cantera { //==================================================================================================================== //! Struct to hold data read from a transport property database file for gas-phase species struct GasTransportData { - GasTransportData() : speciesName("-"), - geometry(-1), wellDepth(-1.0), - diameter(-1.0), - dipoleMoment(-1.0), - polarizability(-1.0), - rotRelaxNumber(-1.0) {} + //! Default constructor + GasTransportData() : + speciesName("-"), + geometry(-1), + wellDepth(-1.0), + diameter(-1.0), + dipoleMoment(-1.0), + polarizability(-1.0), + rotRelaxNumber(-1.0) + { + } + //! gas phase species name std::string speciesName; + //! Geometry of the molecule + /*! + * 0 - single atom + * 1 - linear atom + * 2 - non-linear geom + */ int geometry; + + //! well-depth parameter + /*! + * units - temperature (CHECK) + */ doublereal wellDepth; + + //! Lennard-Jones diameter of the molecule + /*! + * units - Angstroms + */ doublereal diameter; + + //! dipole Moment of the molecule + /*! + * units = Debye (a debye is 10-18 cm3/2 erg1/2) + */ doublereal dipoleMoment; + + //! Polarizability of the molecule + /*! + * units = A**3 + */ doublereal polarizability; + + //! Rotational relaxation number + /*! + * Number of collisions it takes to equilibrate the rotational dofs with the temperature + */ doublereal rotRelaxNumber; }; From 6d45ecbace81ad6c65e45eb5919015887fbb61d2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 13 Jul 2010 19:22:30 +0000 Subject: [PATCH 182/446] Split LiquidTransportData from LTPspecies into separate files; they are separate concepts. Fixed pointers within LTPspecies and LiquidTransportData so that there aren't any more memory leaks. Everything now is based on deep copies. --- Cantera/src/transport/LTPspecies.cpp | 407 ++++++++++++++ Cantera/src/transport/LTPspecies.h | 513 ++++++++++++++++++ Cantera/src/transport/LiquidTransportData.cpp | 423 ++------------- Cantera/src/transport/LiquidTransportData.h | 499 ++--------------- Cantera/src/transport/Makefile.in | 8 +- Cantera/src/transport/SimpleTransport.cpp | 67 ++- Cantera/src/transport/SimpleTransport.h | 57 +- 7 files changed, 1116 insertions(+), 858 deletions(-) create mode 100644 Cantera/src/transport/LTPspecies.cpp create mode 100644 Cantera/src/transport/LTPspecies.h diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp new file mode 100644 index 000000000..1f0875ee8 --- /dev/null +++ b/Cantera/src/transport/LTPspecies.cpp @@ -0,0 +1,407 @@ +/** + * @file LiquidTransportData.cpp + * Source code for liquid transport property evaluations. + */ +/* + * $Author: christopher.lueth@gmail.com $ + * $Date: 2010-03-30 12:30:39 -0600 (Tue, 30 Mar 2010) $ + * $Revision: 427 $ + * + */ + +#include "LTPspecies.h" +using namespace std; + +namespace Cantera { + + /** + * Exception thrown if an error is encountered while reading the + * transport database. + */ + class LTPError : public CanteraError { + public: + LTPError( std::string msg ) + : CanteraError("LTPspecies", + "error parsing transport data: " + + msg + "\n") {} + }; + + + /** + * getArrhenius() parses the xml element called Arrhenius. + * The Arrhenius expression is + * \f[ k = A T^(b) exp (-E_a / RT). \f] + */ + static void getArrhenius(const XML_Node& node, + doublereal& A, doublereal& b, doublereal& E) { + /* parse the children for the A, b, and E conponents. + */ + A = getFloat(node, "A", "toSI"); + b = getFloat(node, "b"); + E = getFloat(node, "E", "actEnergy"); + E /= GasConstant; + } + + // Copy constructor + LTPspecies::LTPspecies( const LTPspecies &right ) + { + *this = right; //use assignment operator to do other work + } + + // Assignment operator + LTPspecies& LTPspecies::operator=(const LTPspecies& right ) + { + if (&right != this) { + m_speciesName = right.m_speciesName; + m_property = right.m_property; + m_model = right.m_model; + m_coeffs = right.m_coeffs; + m_thermo = right.m_thermo; + m_mixWeight = right.m_mixWeight; + } + return *this; + } + //==================================================================================================================== + // Duplication routine + /* + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + LTPspecies * LTPspecies::duplMyselfAsLTPspecies() const + { + LTPspecies *prp = new LTPspecies(*this); + return prp; + } + //==================================================================================================================== + // Construct an LTPspecies object for a liquid tranport property + // expressed as a constant value. + /* The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Const::LTPspecies_Const( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ) : + LTPspecies( propNode, name, tp_ind, thermo) + { + m_model = LTR_MODEL_CONSTANT; + double A_k = getFloatCurrent(propNode, "toSI"); + if (A_k > 0.0) { + m_coeffs.push_back(A_k); + } else throw LTPError("negative or zero " + propNode.name() ); + } + //==================================================================================================================== + // Copy constructor + LTPspecies_Const::LTPspecies_Const( const LTPspecies_Const &right ) + : LTPspecies() + { + *this = right; //use assignment operator to do other work + } + //==================================================================================================================== + // Assignment operator + LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right ) + { + if (&right != this) { + //LTPspecies::operator=(right); + m_speciesName = right.m_speciesName; + m_property = right.m_property; + m_model = right.m_model; + m_coeffs = right.m_coeffs; + m_thermo = right.m_thermo; + m_mixWeight = right.m_mixWeight; + } + return *this; + } + //==================================================================================================================== + // Duplication routine + /* + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + LTPspecies * LTPspecies_Const::duplMyselfAsLTPspecies() const + { + LTPspecies_Const *prp = new LTPspecies_Const(*this); + return (dynamic_cast(prp)); + } + //==================================================================================================================== + // Return the (constant) value for this transport property + doublereal LTPspecies_Const::getSpeciesTransProp( ) { + return m_coeffs[0]; + } + //==================================================================================================================== + + // Construct an LTPspecies object for a liquid tranport property + // expressed in extended Arrhenius form. + /* The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Arrhenius::LTPspecies_Arrhenius( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ) : + LTPspecies( propNode, name, tp_ind, thermo) + { + m_model = LTR_MODEL_ARRHENIUS; + m_temp = 0.0; + m_prop = 0.0; + + doublereal A_k, n_k, Tact_k; + getArrhenius(propNode, A_k, n_k, Tact_k); + if (A_k <= 0.0) { + throw LTPError("negative or zero " + propNode.name() ); + } + m_coeffs.push_back( A_k ); + m_coeffs.push_back( n_k ); + m_coeffs.push_back( Tact_k ); + m_coeffs.push_back( log( A_k ) ); + } + //==================================================================================================================== + // Copy constructor + LTPspecies_Arrhenius::LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ) + : LTPspecies() + { + *this = right; //use assignment operator to do other work + } + //==================================================================================================================== + // Assignment operator + LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right ) + { + if (&right != this) { + // LTPspecies::operator=(right); + m_speciesName = right.m_speciesName; + m_property = right.m_property; + m_model = right.m_model; + m_coeffs = right.m_coeffs; + m_thermo = right.m_thermo; + m_mixWeight = right.m_mixWeight; + + m_temp = right.m_temp; + m_logt = right.m_logt; + m_prop = right.m_prop; + m_logProp = right.m_logProp; + } + return *this; + } + //==================================================================================================================== + // Duplication routine + /* + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + LTPspecies * LTPspecies_Arrhenius::duplMyselfAsLTPspecies() const + { + LTPspecies_Arrhenius *prp = new LTPspecies_Arrhenius(*this); + return (dynamic_cast(prp)); + } + //=================================================================================================================== + // Return the pure species value for this transport property evaluated + // from the Arrhenius expression + /* + * In general the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( - E / R T ). + * \f] + * + * Note that for viscosity, the convention is such that + * a positive activation energy corresponds to the typical + * case of a positive argument to the exponential so that + * the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( + E / R T ). + * \f] + * + * Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal LTPspecies_Arrhenius::getSpeciesTransProp( ) { + + doublereal t = m_thermo->temperature(); + //m_coeffs[0] holds A + //m_coeffs[1] holds n + //m_coeffs[2] holds Tact + //m_coeffs[3] holds log(A) + if (t != m_temp) { + m_prop = 0; + m_logProp = 0; + m_temp = t; + m_logt = log(m_temp); + //For viscosity the sign convention on positive activation energy is swithced + if ( m_property == TP_VISCOSITY ) + m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt + m_coeffs[2] / m_temp ; + else + m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt - m_coeffs[2] / m_temp ; + m_prop = exp( m_logProp ); + } + return m_prop; + } + + + //==================================================================================================================== + // Construct an LTPspecies object for a liquid tranport property + // expressed as a polynomial in temperature. + /* The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ) : + LTPspecies( propNode, name, tp_ind, thermo) + { + m_model = LTR_MODEL_POLY; + m_temp = 0.0; + m_prop = 0.0; + + + getFloatArray(propNode, m_coeffs, "true", "toSI"); + + /* if (m_coeffs[0] <= 0.0) { + throw LTPError("negative or zero " + propNode.name() ); + }*/ + } + //==================================================================================================================== + // Copy constructor + LTPspecies_Poly::LTPspecies_Poly( const LTPspecies_Poly &right ) + : LTPspecies() + { + *this = right; //use assignment operator to do other work + } + //==================================================================================================================== + // Assignment operator + LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right ) + { + if (&right != this) { + //LTPspecies::operator=(right); + m_speciesName = right.m_speciesName; + m_property = right.m_property; + m_model = right.m_model; + m_coeffs = right.m_coeffs; + m_thermo = right.m_thermo; + m_mixWeight = right.m_mixWeight; + + m_temp = right.m_temp; + m_prop = right.m_prop; + } + return *this; + } + //==================================================================================================================== + // Duplication routine + /* + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + LTPspecies * LTPspecies_Poly::duplMyselfAsLTPspecies() const + { + LTPspecies_Poly *prp = new LTPspecies_Poly(*this); + return (dynamic_cast(prp)); + } + //==================================================================================================================== + // Return the value for this transport property evaluated + // from the polynomial expression + doublereal LTPspecies_Poly::getSpeciesTransProp( ) { + + doublereal t = m_thermo->temperature(); + if (t != m_temp) { + m_prop = 0; + m_temp=t; + double tempN = 1.0; + for (int i = 0; i < (int) m_coeffs.size() ; i++) { + m_prop += m_coeffs[i] * tempN; + //cout << "m_coeff = " <(prp)); + } + //==================================================================================================================== + // Return the value for this transport property evaluated + // from the exponential in temperature expression + doublereal LTPspecies_ExpT::getSpeciesTransProp( ) { + + doublereal t = m_thermo->temperature(); + if (t != m_temp) { + m_prop = 0; + m_temp=t; + m_prop=m_coeffs[0]; + double tempN = 1.0; + for (int i = 1; i < (int) m_coeffs.size() ; i++) { + tempN *= m_temp; + m_prop *= exp(m_coeffs[i] * tempN); + //cout << "m_coeff = " < +#include + + +namespace Cantera { + + + //! Enumeration of the types of transport properties that can be + //! handled by the variables in the various Transport classes. + /*! + * Not all of these are handled by each class and each class + * should handle exceptions where the transport property is not handled. + * + * Tranport properties currently on the list + * 0 - viscosity + * 1 - thermal conductivity + * 2 - species diffusivity + * 3 - hydrodynamic radius + * 4 - thermal conductivity + */ + enum TransportPropertyList { + TP_UNKNOWN = -1, + TP_VISCOSITY = 0, + TP_IONCONDUCTIVITY, + TP_MOBILITYRATIO, + TP_SELFDIFFUSION, + TP_THERMALCOND, + TP_DIFFUSIVITY, + TP_HYDRORADIUS, + TP_ELECTCOND + }; + + //! Temperature dependence type for pure (liquid) species properties + /*! + * Types of temperature dependencies: + * 0 - Independent of temperature + * 1 - extended arrhenius form + * 2 - polynomial in temperature form + */ + enum LiquidTR_Model { + LTR_MODEL_NOTSET=-1, + LTR_MODEL_CONSTANT, + LTR_MODEL_ARRHENIUS, + LTR_MODEL_POLY, + LTR_MODEL_EXPT + }; + + //==================================================================================================================== + //! Class LTPspecies holds transport parameters for a + //! specific liquid-phase species. + /*! + * Subclasses handle different means of specifying transport properties + * like constant, %Arrhenius or polynomial fits. In its current state, + * it is primarily suitable for specifying temperature dependence, but + * the adjustCoeffsForComposition() method can be implemented to + * adjust for composition dependence. + * Mixing rules for computing mixture transport properties are handled + * separately in LiquidTranInteraction subclasses. + */ + class LTPspecies { + + public: + + //! Construct an LTPspecies object for a liquid tranport property. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies(const XML_Node &propNode = 0, + std::string name = "-", + TransportPropertyList tp_ind = TP_UNKNOWN, + thermo_t* thermo = 0 ) : + m_speciesName(name), + m_model(LTR_MODEL_NOTSET), + m_property(tp_ind), + m_thermo(thermo), + m_mixWeight(1.0) + { + if (propNode.hasChild("mixtureWeighting") ) { + m_mixWeight = getFloat(propNode,"mixtureWeighting"); + } + } + + //! Copy constructor + LTPspecies(const LTPspecies &right); + + //! Assignment operator + LTPspecies& operator=(const LTPspecies& right); + + virtual ~LTPspecies( ) { } + + //! duplication routine + /*! + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + virtual LTPspecies * duplMyselfAsLTPspecies() const; + + //! Returns the vector of pure species tranport property + /*! + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided by the + * subclass object. + */ + virtual doublereal getSpeciesTransProp( ) { return 0.0; } + + virtual bool checkPositive( ) { return ( m_coeffs[0] > 0 ); } + + doublereal getMixWeight( ) { + return m_mixWeight; + } + + protected: + //! Species Name + std::string m_speciesName; + + //! Model type for the temperature dependence + LiquidTR_Model m_model; + + //! enum indicating which property this is (i.e viscosity) + TransportPropertyList m_property; + + //! Model temperature-dependence ceofficients + vector_fp m_coeffs; + + //! pointer to thermo object to get current temperature + thermo_t* m_thermo; + + //! Weighting used for mixing. + /** + * This weighting can be employed to allow salt transport + * properties to be represented by specific ions. + * For example, to have Li+ and Ca+ represent the mixing + * transport properties of LiCl and CaCl2, the weightings for + * Li+ would be 2.0, for K+ would be 3.0 and for Cl- would be 0.0. + * The tranport properties for Li+ would be those for LiCl and + * the tranport properties for Ca+ would be those for CaCl2. + * The transport properties for Cl- should be something innoccuous like + * 1.0--note that 0.0 is not innocuous if there are logarithms involved. + */ + doublereal m_mixWeight; + + //! Internal model to adjust species-specific properties for composition. + /** Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + virtual void adjustCoeffsForComposition() { } + }; + + + //==================================================================================================================== + //! Class LTPspecies_Const holds transport parameters for a + //! specific liquid-phase species (LTPspecies) when the + //! transport property is just a constant value. + /*! + * As an example of the input required for LTPspecies_Const + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * 1.000 + * + * + * + * + * \endverbatim + */ + class LTPspecies_Const : public LTPspecies { + + public: + + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as a constant value. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Const(const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo); + + //! Copy constructor + LTPspecies_Const(const LTPspecies_Const &right); + + //! Assignment operator + LTPspecies_Const& operator=(const LTPspecies_Const& right ); + + virtual ~LTPspecies_Const( ) { } + + //! duplication routine + /*! + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + virtual LTPspecies * duplMyselfAsLTPspecies() const; + + //! Returns the pure species tranport property + /*! + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal getSpeciesTransProp( ); + + protected: + + //! Internal model to adjust species-specific properties for composition. + /** Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void adjustCoeffsForComposition( ) { } + }; + + //==================================================================================================================== + //! Class LTPspecies_Arrhenius holds transport parameters for a + //! specific liquid-phase species (LTPspecies) when the + //! transport property is expressed in Arrhenius form. + /*! + * Used for pure species properties with equations of the form + * \f[ + * x = A T^b \exp( - E / RT ) + * \f] + * where A, b, and E are passed in the xml input file. + * + * As an example of the input required for LTPspecies_Arrhenius + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * + * 6.578e-5 + * 0.0 + * 23788.e3 + * + * + * + * + * \endverbatim + */ + class LTPspecies_Arrhenius : public LTPspecies{ + + public: + + //! Construct an LTPspecies object for a liquid tranport property + //! expressed in extended Arrhenius form. + /*! + * The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Arrhenius( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ); + + //! Copy constructor + LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ); + + //! Assignment operator + LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right ); + + virtual ~LTPspecies_Arrhenius( ) { } + + //! duplication routine + /*! + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + virtual LTPspecies * duplMyselfAsLTPspecies() const; + + //! Return the pure species value for this transport property evaluated + //! from the Arrhenius expression + /*! + * In general the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( - E / R T ). + * \f] + * + * Note that for viscosity, the convention is such that + * a positive activation energy corresponds to the typical + * case of a positive argument to the exponential so that + * the Arrhenius expression is + * + * \f[ + * \mu = A T^n \exp( + E / R T ). + * \f] + * + * Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal getSpeciesTransProp( ); + + protected: + + //! temperature from thermo object + doublereal m_temp; + + //! logarithm of current temperature + doublereal m_logt; + + //! most recent evaluation of transport property + doublereal m_prop; + + //! logarithm of most recent evaluation of transport property + doublereal m_logProp; + + //! Internal model to adjust species-specific properties for composition. + /*! + * Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void adjustCoeffsForComposition( ) { } + }; + + //==================================================================================================================== + //! Class LTPspecies_Poly holds transport parameters for a + //! specific liquid-phase species (LTPspecies) when the transport + //! property is expressed as a polynomial in temperature. + /*! + * Used for pure species properties with equations of the form + * \f[ + * x = f[0] + f[1] T + ... + f[N] T^N + * \f] + * where f[i] are elements of the float array passed in. + * + * As an example of the input required for LTPspecies_Poly + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * 0.6, -15.0e-5 + * + * + * + * + * \endverbatim + */ + class LTPspecies_Poly : public LTPspecies { + + public: + + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as a polynomial in temperature. + /** The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_Poly( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ); + + //! Copy constructor + LTPspecies_Poly( const LTPspecies_Poly &right ); + + //! Assignment operator + LTPspecies_Poly& operator=(const LTPspecies_Poly& right ); + + virtual ~LTPspecies_Poly( ) { } + + //! Duplication routine + /*! + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + virtual LTPspecies * duplMyselfAsLTPspecies() const; + + //! Returns the pure species tranport property + /*! + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal getSpeciesTransProp( ); + + protected: + + //! temperature from thermo object + doublereal m_temp; + + //! most recent evaluation of transport property + doublereal m_prop; + + //! Internal model to adjust species-specific properties for composition. + /*! + * Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void adjustCoeffsForComposition( ){ } + }; + + //==================================================================================================================== + //! Class LTPspecies_ExpT holds transport parameters for a + //! specific liquid-phase species (LTPspecies) when the transport + //! property is expressed as a exponential in temperature. + /** + * Used for pure species properties with equations of the form + * \f[ + * x = f[0] \exp( f[1] T + ... + f[N] T ) + * \f] + * where f[i] are elements of the float array passed in. + * + * As an example of the input required for LTPspecies_ExpT + * consider the following XML fragment + * + * \verbatim + * + * + * + * + * 0.6, -15.0e-5 + * + * + * + * + * \endverbatim + */ + class LTPspecies_ExpT : public LTPspecies { + + public: + + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as an exponential in temperature. + /*! + * The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) + */ + LTPspecies_ExpT( const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo ); + + //! Copy constructor + LTPspecies_ExpT( const LTPspecies_ExpT &right ); + + //! Assignment operator + LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); + + virtual ~LTPspecies_ExpT( ) { } + + //! duplication routine + /*! + * @return Returns a copy of this routine as a pointer to LTPspecies + */ + virtual LTPspecies * duplMyselfAsLTPspecies() const; + + //! Returns the pure species tranport property + /*! + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided. + */ + doublereal getSpeciesTransProp( ); + + protected: + + //! temperature from thermo object + doublereal m_temp; + + //! most recent evaluation of transport property + doublereal m_prop; + + //! Internal model to adjust species-specific properties for composition. + /** Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void adjustCoeffsForComposition( ){ } + }; + + //==================================================================================================================== + +} +#endif diff --git a/Cantera/src/transport/LiquidTransportData.cpp b/Cantera/src/transport/LiquidTransportData.cpp index 1b0625f7b..93115ea68 100644 --- a/Cantera/src/transport/LiquidTransportData.cpp +++ b/Cantera/src/transport/LiquidTransportData.cpp @@ -6,413 +6,110 @@ * $Author$ * $Date$ * $Revision$ - * */ #include "LiquidTransportData.h" using namespace std; - +#ifndef SAFE_DELETE +#define SAFE_DELETE(x) if (x) { delete (x); x = 0; } +#endif namespace Cantera { - - - /** - * Exception thrown if an error is encountered while reading the - * transport database. - */ - class LTPError : public CanteraError { - public: - LTPError( std::string msg ) - : CanteraError("LTPspecies", - "error parsing transport data: " - + msg + "\n") {} - }; - - - /** - * getArrhenius() parses the xml element called Arrhenius. - * The Arrhenius expression is - * \f[ k = A T^(b) exp (-E_a / RT). \f] - */ - static void getArrhenius(const XML_Node& node, - doublereal& A, doublereal& b, doublereal& E) { - /* parse the children for the A, b, and E conponents. - */ - A = getFloat(node, "A", "toSI"); - b = getFloat(node, "b"); - E = getFloat(node, "E", "actEnergy"); - E /= GasConstant; - } - + //==================================================================================================================== LiquidTransportData::LiquidTransportData() : speciesName("-"), hydroRadius(0), viscosity(0), ionConductivity(0), + mobilityRatio(0), + selfDiffusion(0), thermalCond(0), electCond(0), speciesDiffusivity(0) { } - + //==================================================================================================================== // Copy constructor LiquidTransportData::LiquidTransportData(const LiquidTransportData &right) : speciesName("-"), hydroRadius(0), viscosity(0), ionConductivity(0), + mobilityRatio(0), + selfDiffusion(0), thermalCond(0), electCond(0), speciesDiffusivity(0) { *this = right; //use assignment operator to do other work } - + //==================================================================================================================== // Assignment operator LiquidTransportData& LiquidTransportData::operator=(const LiquidTransportData& right) { if (&right != this) { + // These are all shallow pointer copies - yes, yes, yes horrible crime. speciesName = right.speciesName; - hydroRadius = right.hydroRadius; - viscosity = right.viscosity; - ionConductivity = right.ionConductivity; - mobilityRatio = right.mobilityRatio; - selfDiffusion = right.selfDiffusion; - thermalCond = right.thermalCond; - electCond = right.electCond; - speciesDiffusivity = right.speciesDiffusivity; - } - return *this; - } + if (right.hydroRadius) { + hydroRadius = (right.hydroRadius)->duplMyselfAsLTPspecies(); + } + if (right.viscosity) { + viscosity = (right.viscosity)->duplMyselfAsLTPspecies(); + } + if (right.ionConductivity) { + ionConductivity = (right.ionConductivity)->duplMyselfAsLTPspecies(); + } + mobilityRatio = right.mobilityRatio; + for (size_t k = 0; k < mobilityRatio.size(); k++) { + if (right.mobilityRatio[k]) { + mobilityRatio[k] = (right.mobilityRatio[k])->duplMyselfAsLTPspecies(); + } + } + selfDiffusion = right.selfDiffusion; + for (size_t k = 0; k < selfDiffusion.size(); k++) { + if (right.selfDiffusion[k]) { + selfDiffusion[k] = (right.selfDiffusion[k])->duplMyselfAsLTPspecies(); + } + } - - // Copy constructor - LTPspecies::LTPspecies( const LTPspecies &right ) - { - *this = right; //use assignment operator to do other work - } - - // Assignment operator - LTPspecies& LTPspecies::operator=(const LTPspecies& right ) - { - if (&right != this) { - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - } - return *this; - } - - - // Construct an LTPspecies object for a liquid tranport property - // expressed as a constant value. - /* The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Const::LTPspecies_Const( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) - { - m_model = LTR_MODEL_CONSTANT; - double A_k = getFloatCurrent(propNode, "toSI"); - if (A_k > 0.0) { - m_coeffs.push_back(A_k); - } else throw LTPError("negative or zero " + propNode.name() ); - } - - // Copy constructor - LTPspecies_Const::LTPspecies_Const( const LTPspecies_Const &right ) - : LTPspecies() - { - *this = right; //use assignment operator to do other work - } - - // Assignment operator - LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right ) - { - if (&right != this) { - //LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - } - return *this; - } - - // Return the (constant) value for this transport property - doublereal LTPspecies_Const::getSpeciesTransProp( ) { - return m_coeffs[0]; - } - - /////////////////////////////////////////////////////////////// - - // Construct an LTPspecies object for a liquid tranport property - // expressed in extended Arrhenius form. - /* The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Arrhenius::LTPspecies_Arrhenius( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) - { - m_model = LTR_MODEL_ARRHENIUS; - m_temp = 0.0; - m_prop = 0.0; - - doublereal A_k, n_k, Tact_k; - getArrhenius(propNode, A_k, n_k, Tact_k); - if (A_k <= 0.0) { - throw LTPError("negative or zero " + propNode.name() ); - } - m_coeffs.push_back( A_k ); - m_coeffs.push_back( n_k ); - m_coeffs.push_back( Tact_k ); - m_coeffs.push_back( log( A_k ) ); - } - - // Copy constructor - LTPspecies_Arrhenius::LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ) - : LTPspecies() - { - *this = right; //use assignment operator to do other work - } - - // Assignment operator - LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right ) - { - if (&right != this) { - // LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - - m_temp = right.m_temp; - m_logt = right.m_logt; - m_prop = right.m_prop; - m_logProp = right.m_logProp; - } - return *this; - } - - // Return the pure species value for this transport property evaluated - // from the Arrhenius expression - /* - * In general the Arrhenius expression is - * - * \f[ - * \mu = A T^n \exp( - E / R T ). - * \f] - * - * Note that for viscosity, the convention is such that - * a positive activation energy corresponds to the typical - * case of a positive argument to the exponential so that - * the Arrhenius expression is - * - * \f[ - * \mu = A T^n \exp( + E / R T ). - * \f] - * - * Any temperature and composition dependence will be - * adjusted internally according to the information provided. - */ - doublereal LTPspecies_Arrhenius::getSpeciesTransProp( ) { - - doublereal t = m_thermo->temperature(); - //m_coeffs[0] holds A - //m_coeffs[1] holds n - //m_coeffs[2] holds Tact - //m_coeffs[3] holds log(A) - if (t != m_temp) { - m_prop = 0; - m_logProp = 0; - m_temp = t; - m_logt = log(m_temp); - //For viscosity the sign convention on positive activation energy is swithced - if ( m_property == TP_VISCOSITY ) - m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt + m_coeffs[2] / m_temp ; - else - m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt - m_coeffs[2] / m_temp ; - m_prop = exp( m_logProp ); - } - return m_prop; - } - - - - - - - /////////////////////////////////////////////////////////////// - - // Construct an LTPspecies object for a liquid tranport property - // expressed as a polynomial in temperature. - /* The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Poly::LTPspecies_Poly( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) - { - m_model = LTR_MODEL_POLY; - m_temp = 0.0; - m_prop = 0.0; - - - getFloatArray(propNode, m_coeffs, "true", "toSI"); - - /* if (m_coeffs[0] <= 0.0) { - throw LTPError("negative or zero " + propNode.name() ); - }*/ - } - - // Copy constructor - LTPspecies_Poly::LTPspecies_Poly( const LTPspecies_Poly &right ) - : LTPspecies() - { - *this = right; //use assignment operator to do other work - } - - // Assignment operator - LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right ) - { - if (&right != this) { - //LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - - m_temp = right.m_temp; - m_prop = right.m_prop; - } - return *this; - } - - // Return the value for this transport property evaluated - // from the polynomial expression - doublereal LTPspecies_Poly::getSpeciesTransProp( ) { - - doublereal t = m_thermo->temperature(); - if (t != m_temp) { - m_prop = 0; - m_temp=t; - double tempN = 1.0; - for (int i = 0; i < (int) m_coeffs.size() ; i++) { - m_prop += m_coeffs[i] * tempN; - //cout << "m_coeff = " <temperature(); - if (t != m_temp) { - m_prop = 0; - m_temp=t; - m_prop=m_coeffs[0]; - double tempN = 1.0; - for (int i = 1; i < (int) m_coeffs.size() ; i++) { - tempN *= m_temp; - m_prop *= exp(m_coeffs[i] * tempN); - //cout << "m_coeff = " <, \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies( const XML_Node &propNode = 0, - std::string name = "-", - TransportPropertyList tp_ind = TP_UNKNOWN, - thermo_t* thermo = 0 ) : - m_speciesName(name), - m_model(LTR_MODEL_NOTSET), - m_property(tp_ind), - m_thermo(thermo), - m_mixWeight(1.0) - { - if ( propNode.hasChild("mixtureWeighting") ) - m_mixWeight = getFloat(propNode,"mixtureWeighting"); - } - - //! Copy constructor - LTPspecies( const LTPspecies &right ); - - //! Assignment operator - LTPspecies& operator=(const LTPspecies& right ); - - virtual ~LTPspecies( ) { } - - //! Returns the vector of pure species tranport property - /*! - * The pure species transport property (i.e. pure species viscosity) - * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided by the - * subclass object. - */ - virtual doublereal getSpeciesTransProp( ) { return 0.0; } - - virtual bool checkPositive( ) { return ( m_coeffs[0] > 0 ); } - - doublereal getMixWeight( ) {return m_mixWeight; } - - protected: - std::string m_speciesName; - - //! Model type for the temperature dependence - LiquidTR_Model m_model; - - //! enum indicating what property this is (i.e viscosity) - TransportPropertyList m_property; - - //! Model temperature-dependence ceofficients - vector_fp m_coeffs; - - //! pointer to thermo object to get current temperature - thermo_t* m_thermo; - - //! Weighting used for mixing. - /** - * This weighting can be employed to allow salt transport - * properties to be represented by specific ions. - * For example, to have Li+ and Ca+ represent the mixing - * transport properties of LiCl and CaCl2, the weightings for - * Li+ would be 2.0, for K+ would be 3.0 and for Cl- would be 0.0. - * The tranport properties for Li+ would be those for LiCl and - * the tranport properties for Ca+ would be those for CaCl2. - * The transport properties for Cl- should be something innoccuous like - * 1.0--note that 0.0 is not innocuous if there are logarithms involved. - */ - doublereal m_mixWeight; - - //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - virtual void adjustCoeffsForComposition() { } - }; - - - //! Class LiquidTransportData holds transport parameters for a //! specific liquid-phase species. - /** + /*! * A LiquidTransportData object is created for each species. * * This class is mainly used to collect transport properties @@ -175,7 +34,11 @@ namespace Cantera { * them to the Transport class. Transport properties are * expressed by subclasses of LTPspecies. * One may need to be careful about deleting pointers to LTPspecies - * objects created in the TransportFactory. + * objects created in the TransportFactory. + * + * All of the pointers in this class are shallow pointers. Therefore, this + * is a passthrough class, which keeps track of pointer ownership by zeroing + * pointers as we go. Yes, Yes, yes, this is not good. */ class LiquidTransportData { @@ -185,355 +48,67 @@ namespace Cantera { LiquidTransportData(); //! Copy constructor - LiquidTransportData(const LiquidTransportData &right) ; + LiquidTransportData(const LiquidTransportData &right); //! Assignment operator - LiquidTransportData& operator=(const LiquidTransportData& right ); + LiquidTransportData& operator=(const LiquidTransportData& right ); + + //! Destructor + ~LiquidTransportData(); //! A LiquidTransportData object is instantiated for each species. //! This is the species name for which this object is instantiated. std::string speciesName; //! Model type for the hydroradius + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* hydroRadius; //! Model type for the viscosity + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* viscosity; //! Model type for the ionic conductivity + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* ionConductivity; //! Model type for the mobility ratio + /*! + * shallow pointers that should be zero during destructor + */ std::vector mobilityRatio; //! Model type for the self diffusion coefficients + /*! + * shallow pointers that should be zero during destructor + */ std::vector selfDiffusion; //! Model type for the thermal conductivity + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* thermalCond; //! Model type for the electrical conductivity + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* electCond; //! Model type for the speciesDiffusivity + /*! + * shallow pointer that should be zero during destructor + */ LTPspecies* speciesDiffusivity; }; - - - - //! Class LTPspecies_Const holds transport parameters for a - //! specific liquid-phase species (LTPspecies) when the - //! transport property is just a constant value. - /*! - * As an example of the input required for LTPspecies_Const - * consider the following XML fragment - * - * \verbatim - * - * - * - * - * 1.000 - * - * - * - * - * \endverbatim - */ - class LTPspecies_Const : public LTPspecies { - - public: - - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a constant value. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Const( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) ; - - //! Copy constructor - LTPspecies_Const( const LTPspecies_Const &right ); - - //! Assignment operator - LTPspecies_Const& operator=(const LTPspecies_Const& right ); - - virtual ~LTPspecies_Const( ) { } - - //! Returns the pure species tranport property - /*! - * The pure species transport property (i.e. pure species viscosity) - * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided. - */ - doublereal getSpeciesTransProp( ); - - protected: - - //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ) { } - }; - - - - //! Class LTPspecies_Arrhenius holds transport parameters for a - //! specific liquid-phase species (LTPspecies) when the - //! transport property is expressed in Arrhenius form. - /*! - * Used for pure species properties with equations of the form - * \f[ - * x = A T^b \exp( - E / RT ) - * \f] - * where A, b, and E are passed in the xml input file. - * - * As an example of the input required for LTPspecies_Arrhenius - * consider the following XML fragment - * - * \verbatim - * - * - * - * - * - * 6.578e-5 - * 0.0 - * 23788.e3 - * - * - * - * - * \endverbatim - */ - class LTPspecies_Arrhenius : public LTPspecies{ - - public: - - //! Construct an LTPspecies object for a liquid tranport property - //! expressed in extended Arrhenius form. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Arrhenius( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ); - - //! Copy constructor - LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ); - - //! Assignment operator - LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right ); - - virtual ~LTPspecies_Arrhenius( ) { } - - //! Return the pure species value for this transport property evaluated - //! from the Arrhenius expression - /*! - * In general the Arrhenius expression is - * - * \f[ - * \mu = A T^n \exp( - E / R T ). - * \f] - * - * Note that for viscosity, the convention is such that - * a positive activation energy corresponds to the typical - * case of a positive argument to the exponential so that - * the Arrhenius expression is - * - * \f[ - * \mu = A T^n \exp( + E / R T ). - * \f] - * - * Any temperature and composition dependence will be - * adjusted internally according to the information provided. - */ - doublereal getSpeciesTransProp( ); - - protected: - - //! temperature from thermo object - doublereal m_temp; - - //! logarithm of current temperature - doublereal m_logt; - - //! most recent evaluation of transport property - doublereal m_prop; - - //! logarithm of most recent evaluation of transport property - doublereal m_logProp; - - //! Internal model to adjust species-specific properties for composition. - /*! - * Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ) { } - }; - - - - //! Class LTPspecies_Poly holds transport parameters for a - //! specific liquid-phase species (LTPspecies) when the transport - //! property is expressed as a polynomial in temperature. - /*! - * Used for pure species properties with equations of the form - * \f[ - * x = f[0] + f[1] T + ... + f[N] T^N - * \f] - * where f[i] are elements of the float array passed in. - * - * As an example of the input required for LTPspecies_Poly - * consider the following XML fragment - * - * \verbatim - * - * - * - * - * 0.6, -15.0e-5 - * - * - * - * - * \endverbatim - */ - class LTPspecies_Poly : public LTPspecies{ - - public: - - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a polynomial in temperature. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Poly( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ); - - //! Copy constructor - LTPspecies_Poly( const LTPspecies_Poly &right ); - - //! Assignment operator - LTPspecies_Poly& operator=(const LTPspecies_Poly& right ); - - virtual ~LTPspecies_Poly( ) { } - - //! Returns the pure species tranport property - /*! - * The pure species transport property (i.e. pure species viscosity) - * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided. - */ - doublereal getSpeciesTransProp( ); - - protected: - - //! temperature from thermo object - doublereal m_temp; - - //! most recent evaluation of transport property - doublereal m_prop; - - //! Internal model to adjust species-specific properties for composition. - /*! - * Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ){ } - }; - - - //! Class LTPspecies_ExpT holds transport parameters for a - //! specific liquid-phase species (LTPspecies) when the transport - //! property is expressed as a exponential in temperature. - /** - * Used for pure species properties with equations of the form - * \f[ - * x = f[0] \exp( f[1] T + ... + f[N] T ) - * \f] - * where f[i] are elements of the float array passed in. - * - * As an example of the input required for LTPspecies_ExpT - * consider the following XML fragment - * - * \verbatim - * - * - * - * - * 0.6, -15.0e-5 - * - * - * - * - * \endverbatim - */ - class LTPspecies_ExpT : public LTPspecies{ - - public: - - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as an exponential in temperature. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_ExpT( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ); - - //! Copy constructor - LTPspecies_ExpT( const LTPspecies_ExpT &right ); - - //! Assignment operator - LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); - - virtual ~LTPspecies_ExpT( ) { } - - //! Returns the pure species tranport property - /*! - * The pure species transport property (i.e. pure species viscosity) - * is returned. Any temperature and composition dependence will be - * adjusted internally according to the information provided. - */ - doublereal getSpeciesTransProp( ); - - protected: - - //! temperature from thermo object - doublereal m_temp; - - //! most recent evaluation of transport property - doublereal m_prop; - - //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ){ } - }; - - - } #endif + diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index 208b7e055..cc1a0bbec 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -37,12 +37,12 @@ CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt.o \ SolidTransport.o DustyGasTransport.o TransportBase.o WaterTransport.o \ SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o \ - TransportParams.o + TransportParams.o LTRspecies.o TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ TransportBase.h L_matrix.h TransportParams.h WaterTransport.h \ - SimpleTransport.h LiquidTranInteraction.h Tortuosity.h + SimpleTransport.h LiquidTranInteraction.h Tortuosity.h ifeq ($(do_electro),1) do_issp = 1 @@ -51,8 +51,8 @@ ELECTRO_H = AqueousTransport.h endif ifeq ($(do_issp),1) -ISSP_OBJ = LiquidTransport.o LiquidTransportData.o -ISSP_H = LiquidTransport.h LiquidTransportParams.h LiquidTransportData.h +ISSP_OBJ = LiquidTransport.o LiquidTransportData.o LTPspecies.o +ISSP_H = LiquidTransport.h LiquidTransportParams.h LiquidTransportData.h LTPspecies.h endif diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index c676b0853..b9121ecb3 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -26,6 +26,10 @@ using namespace std; #define MIN_X 1.e-14 +#ifndef SAFE_DELETE +#define SAFE_DELETE(x) if (x) { delete (x); x = 0; } +#endif + namespace Cantera { //================================================================================================ SimpleTransport::SimpleTransport(thermo_t* thermo, int ndim) : @@ -97,10 +101,34 @@ namespace Cantera { m_tmax = right.m_tmax; m_mw = right.m_mw; - m_coeffVisc_Ns = right.m_coeffVisc_Ns; - m_coeffLambda_Ns = right.m_coeffLambda_Ns; - m_coeffDiff_Ns = right.m_coeffDiff_Ns; - + m_coeffVisc_Ns = right.m_coeffVisc_Ns; + for (size_t k = 0; k duplMyselfAsLTPspecies(); + } + } + + m_coeffLambda_Ns = right.m_coeffLambda_Ns; + for (size_t k = 0; k < right.m_coeffLambda_Ns.size(); k++) { + if (right.m_coeffLambda_Ns[k]) { + m_coeffLambda_Ns[k] = (right.m_coeffLambda_Ns[k])->duplMyselfAsLTPspecies(); + } + } + + m_coeffDiff_Ns = right.m_coeffDiff_Ns; + for (size_t k = 0; k < right.m_coeffDiff_Ns.size(); k++) { + if (right.m_coeffDiff_Ns[k]) { + m_coeffDiff_Ns[k] = (right.m_coeffDiff_Ns[k])->duplMyselfAsLTPspecies(); + } + } + + m_coeffHydroRadius_Ns = right.m_coeffHydroRadius_Ns; + for (size_t k = 0; k < right.m_coeffHydroRadius_Ns.size(); k++) { + if (right.m_coeffHydroRadius_Ns[k]) { + m_coeffHydroRadius_Ns[k] = (right.m_coeffHydroRadius_Ns[k])->duplMyselfAsLTPspecies(); + } + } + m_Grad_X = right.m_Grad_X; m_Grad_T = right.m_Grad_T; m_Grad_P = right.m_Grad_P; @@ -132,13 +160,27 @@ namespace Cantera { return *this; } - //================================================================================================ Transport *SimpleTransport::duplMyselfAsTransport() const { SimpleTransport* tr = new SimpleTransport(*this); return (dynamic_cast(tr)); } //================================================================================================ + SimpleTransport::~SimpleTransport() { + for (size_t k = 0; k < m_coeffVisc_Ns.size() ; k++) { + SAFE_DELETE(m_coeffVisc_Ns[k]); + } + for (size_t k = 0; k < m_coeffLambda_Ns.size(); k++) { + SAFE_DELETE(m_coeffLambda_Ns[k]); + } + for (size_t k = 0; k < m_coeffDiff_Ns.size(); k++) { + SAFE_DELETE(m_coeffDiff_Ns[k]); + } + for (size_t k = 0; k < m_coeffHydroRadius_Ns.size(); k++) { + SAFE_DELETE(m_coeffHydroRadius_Ns[k]); + } + } + //================================================================================================ // Initialize the object /* * This is where we dimension everything. @@ -230,6 +272,7 @@ namespace Cantera { } */ m_coeffVisc_Ns[k] = ltd.viscosity; + ltd.viscosity = 0; } /* @@ -260,6 +303,7 @@ namespace Cantera { } */ m_coeffLambda_Ns[k] = ltd.thermalCond; + ltd.thermalCond = 0; } /* @@ -317,10 +361,13 @@ namespace Cantera { */ m_coeffDiff_Ns[k] = ltd.speciesDiffusivity; + ltd.speciesDiffusivity = 0; - if ( !(m_coeffDiff_Ns[k]) ) { - m_coeffHydroRadius_Ns[k] = ltd.hydroRadius; - if ( !(m_coeffHydroRadius_Ns[k]) ) { + if (!(m_coeffDiff_Ns[k])) { + if (ltd.hydroRadius) { + m_coeffHydroRadius_Ns[k] = (ltd.hydroRadius)->duplMyselfAsLTPspecies(); + } + if (!(m_coeffHydroRadius_Ns[k])) { throw CanteraError("SimpleTransport::initLiquid", "Neither diffusivity nor hydroradius is set for species " + spName); } @@ -345,8 +392,6 @@ namespace Cantera { m_Grad_P.resize(m_nDim, 0.0); m_Grad_V.resize(m_nDim, 0.0); - - // set all flags to false m_visc_mix_ok = false; m_visc_temp_ok = false; @@ -793,7 +838,7 @@ namespace Cantera { return true; } //================================================================================================ - /** + /* * Throw an exception if this method is invoked. * This probably indicates something is not yet implemented. */ diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 2e892b142..2ff007cb8 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -1,10 +1,8 @@ /** - * * @file SimpleTransport.h * Header file for the class SimpleTransport which provides simple * transport properties for liquids and solids * (see \ref tranprops and \link Cantera::SimpleTransport SimpleTransport \endlink) . - */ /* * $Revision$ @@ -176,7 +174,7 @@ namespace Cantera { //! virtual destructor - virtual ~SimpleTransport() {} + virtual ~SimpleTransport(); //! Initialize the transport object /*! @@ -196,7 +194,6 @@ namespace Cantera { return cSimpleTransport; } - //! overloaded base class methods //! Returns the mixture viscosity of the solution /*! @@ -214,6 +211,8 @@ namespace Cantera { * * Here \f$ \mu_k \f$ is the viscosity of pure species \e k. * + * units are Pa s or kg/m/s + * * @see updateViscosity_T(); */ virtual doublereal viscosity(); @@ -221,7 +220,12 @@ namespace Cantera { //! Returns the pure species viscosities /*! * The pure species viscosities are to be given in an Arrhenius - * form in accordance with activated-jump-process dominated transport. + * form in accordance with activated-jump-process dominated transport. + * + * units are Pa s or kg/m/s + * + * @param visc Return the species viscosities as a vector of + * length m_nsp */ virtual void getSpeciesViscosities(doublereal* const visc); @@ -322,8 +326,7 @@ namespace Cantera { //! Specify the value of the gradient of the temperature /*! - * - * @param grad_V Gradient of the temperature (length num dimensions); + * @param grad_T Gradient of the temperature (length num dimensions); */ virtual void set_Grad_T(const doublereal* const grad_T); @@ -335,15 +338,32 @@ namespace Cantera { virtual void set_Grad_X(const doublereal* const grad_X); - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from + //! Return the species fluxes given gradients in temperature and mole fraction + /*! + * units = kg/m2/s + * The diffusive mass flux of species \e k is computed from the following + * formula * * + * \f[ + * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * V_c = - \sum_j {\rho M_j D_j \nabla X_j} + * \f] + * + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_X Gradient of the mole fractions(length nsp * num dimensions); + * @param ldf Leading dimension of the fluxes array. + * @param fluxes Output fluxes of species. */ - virtual void getSpeciesFluxes(int ndim, + virtual void getSpeciesFluxes(int ndim, const doublereal* grad_T, int ldx, const doublereal* grad_X, int ldf, doublereal* fluxes); @@ -493,20 +513,21 @@ namespace Cantera { vector_fp m_mw; //! Pure species viscosities in Arrhenius temperature-dependent form. - std::vector m_coeffVisc_Ns; + std::vector m_coeffVisc_Ns; //! Pure species thermal conductivities in Arrhenius temperature-dependent form. /*! * */ - std::vector m_coeffLambda_Ns; + std::vector m_coeffLambda_Ns; //! Pure species viscosities in Arrhenius temperature-dependent form. - std::vector m_coeffDiff_Ns; + std::vector m_coeffDiff_Ns; - std::vector m_coeffHydroRadius_Ns; + //! Hydrodynamic radius in LTPspecies form + std::vector m_coeffHydroRadius_Ns; //! Internal value of the gradient of the mole fraction vector @@ -706,7 +727,7 @@ namespace Cantera { /*! * This probably indicates something is not yet implemented. * - * @pram msg Indicates the member function which is not implemented + * @param msg Indicates the member function which is not implemented */ doublereal err(std::string msg) const; From ef1370cc5b4349b4593fe49e730b05598cca83a1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 13 Jul 2010 19:27:59 +0000 Subject: [PATCH 183/446] Doxygen updates --- Cantera/src/transport/SimpleTransport.h | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 2ff007cb8..cedcd3180 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -129,10 +129,7 @@ namespace Cantera { */ class SimpleTransport : public Transport { public: - - typedef vector_fp Coeff_T_; - //! Default constructor. /*! * This requires call to initLiquid(LiquidTransportParams& tr) @@ -186,9 +183,6 @@ namespace Cantera { */ virtual bool initLiquid(LiquidTransportParams& tr); - friend class TransportFactory; - - //! Return the model id for this transport parameterization virtual int model() const { return cSimpleTransport; @@ -491,6 +485,11 @@ namespace Cantera { */ int compositionDepType_; + //! Boolean indicating whether to use the hydrodynamic radius formulation + /*! + * If true, then the diffusion coefficient is calculated from the + * hydrodynamic radius. + */ bool useHydroRadius_; //! Boolean indicating whether electro-migration term should be From 16a12766c0b10cc27282fa8f8af627928f8a7c97 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 14 Jul 2010 15:42:59 +0000 Subject: [PATCH 184/446] doxygen update --- Cantera/src/transport/L_matrix.h | 67 +- Cantera/src/transport/MultiTransport.cpp | 1699 +++++++++++----------- Cantera/src/transport/MultiTransport.h | 133 +- 3 files changed, 953 insertions(+), 946 deletions(-) diff --git a/Cantera/src/transport/L_matrix.h b/Cantera/src/transport/L_matrix.h index ecf5cfe59..f5990d238 100644 --- a/Cantera/src/transport/L_matrix.h +++ b/Cantera/src/transport/L_matrix.h @@ -1,10 +1,13 @@ /** * @file L_matrix.h - * - * functions to evaluate portions of the L matrix needed for + * Functions to evaluate portions of the L matrix needed for * multicomponent transport properties. */ +/* + * $Id$ + */ + #ifndef CT_LMATRIX_H #define CT_LMATRIX_H @@ -20,16 +23,15 @@ #include - ///////////////////////////////////////////////////////////////////// namespace Cantera { - + //==================================================================================================================== // #define CHEMKIN_COMPATIBILITY_MODE //! Constant to compare dimensionless heat capacities against zero const doublereal Min_C_Internal = 0.001; - + //==================================================================================================================== bool MultiTransport::hasInternalModes(int j) { #ifdef CHEMKIN_COMPATIBILITY_MODE return (m_crot[j] > Min_C_Internal); @@ -38,11 +40,11 @@ namespace Cantera { #endif } - - /** + //==================================================================================================================== + /* * Evaluate the upper-left block of the L matrix. */ - void MultiTransport::eval_L0000(const doublereal* x) { + void MultiTransport::eval_L0000(const doublereal* const x) { doublereal prefactor = 16.0*m_temp/25.0; doublereal sum; @@ -63,12 +65,8 @@ namespace Cantera { m_Lmatrix(i,i) = 0.0; } } - - - //////////////////////////////////////////////////////////////////////////// - - - void MultiTransport::eval_L0010(const doublereal* x) { + //==================================================================================================================== + void MultiTransport::eval_L0010(const doublereal* const x) { doublereal prefactor = 1.6*m_temp; @@ -91,11 +89,7 @@ namespace Cantera { m_Lmatrix(j,j+m_nsp) += sum; } } - - - - //////////////////////////////////////////////////////////////////////// - + //==================================================================================================================== void MultiTransport::eval_L1000() { int i, j; for (j = 0; j < m_nsp; j++) { @@ -104,10 +98,7 @@ namespace Cantera { } } } - - - ////////////////////////////////////////////////////////////////////// - + //==================================================================================================================== void MultiTransport::eval_L1010(const doublereal* x) { const doublereal fiveover3pi = 5.0/(3.0*Pi); @@ -150,10 +141,7 @@ namespace Cantera { m_Lmatrix(j+m_nsp,j+m_nsp) -= sum*constant1; } } - - - ////////////////////////////////////////////////////////////////////////////////// - + //==================================================================================================================== void MultiTransport::eval_L1001(const doublereal* x) { doublereal prefactor = 32.00*m_temp/(5.00*Pi); @@ -180,18 +168,18 @@ namespace Cantera { } } } - - //////////////////////////////////////////////////////////////////////// + //==================================================================================================================== void MultiTransport::eval_L0001() { int i, j; int n2 = 2*m_nsp; - for (j = 0; j < m_nsp; j++) - for (i = 0; i < m_nsp; i++) + for (j = 0; j < m_nsp; j++) { + for (i = 0; i < m_nsp; i++) { m_Lmatrix(i,j+n2) = 0.0; + } + } } - - //////////////////////////////////////////////////////////////////////// + //==================================================================================================================== void MultiTransport::eval_L0100() { int i, j; @@ -200,8 +188,7 @@ namespace Cantera { for (i = 0; i < m_nsp; i++) m_Lmatrix(i+n2,j) = 0.0; // see Eq. (12.123) } - - //////////////////////////////////////////////////////////////////////// + //==================================================================================================================== void MultiTransport::eval_L0110() { int i, j; @@ -210,10 +197,7 @@ namespace Cantera { for (i = 0; i < m_nsp; i++) m_Lmatrix(i+n2,j+m_nsp) = m_Lmatrix(j+m_nsp,i+n2); // see Eq. (12.123) } - - //////////////////////////////////////////////////////////////////////// - - + //==================================================================================================================== void MultiTransport::eval_L0101(const doublereal* x) { const doublereal fivepi = 5.00*Pi; @@ -245,11 +229,12 @@ namespace Cantera { - constant1*sum; } else { - for (k = 0; k < m_nsp; k++) + for (k = 0; k < m_nsp; k++) { m_Lmatrix(i+n2,i+n2) = 1.0; + } } } } } - +//====================================================================================================================== #endif diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index ebf8b047e..88659cf64 100644 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -49,1005 +49,974 @@ using namespace std; namespace Cantera { -// template -// struct UpdateSpeciesVisc : public Updater { -// UpdateSpeciesVisc(S& s) : Updater(), m_s(s) {} -// void update() { m_s._update_species_visc_T(); } -// S& m_s; -// }; + /////////////////////////// constants ////////////////////////// -// template -// struct UpdateVisc_T : public Updater { -// UpdateVisc_T(S& s) : Updater(), m_s(s) {} -// void update() { m_s._update_visc_T(); } -// S& m_s; -// }; - -// template -// struct UpdateDiff_T : public Updater { -// UpdateDiff_T(S& s) : Updater(), m_s(s) {} -// void update() { m_s._update_diff_T(); } -// S& m_s; -// }; - -// template -// struct UpdateThermal_T : public Updater { -// UpdateThermal_T(S& s) : Updater(), m_s(s) {} -// void update() { m_s._update_thermal_T(); } -// S& m_s; -// }; - - - /////////////////////////// constants ////////////////////////// - - // const doublereal ThreeSixteenths = 3.0/16.0; + // const doublereal ThreeSixteenths = 3.0/16.0; - ///////////////////// helper functions ///////////////////////// + ///////////////////// helper functions ///////////////////////// - /** - * @internal - * - * The Parker temperature correction to the rotational collision - * number. - * - * @param tr Reduced temperature \f$ \epsilon/kT \f$ - * @param sqtr square root of tr. - */ - inline doublereal Frot(doublereal tr, doublereal sqtr) { - const doublereal c1 = 0.5*SqrtPi*Pi; - const doublereal c2 = 0.25*Pi*Pi + 2.0; - const doublereal c3 = SqrtPi*Pi; - return 1.0 + c1*sqtr + c2*tr + c3*sqtr*tr; - } + /** + * @internal + * + * The Parker temperature correction to the rotational collision + * number. + * + * @param tr Reduced temperature \f$ \epsilon/kT \f$ + * @param sqtr square root of tr. + */ + inline doublereal Frot(doublereal tr, doublereal sqtr) { + const doublereal c1 = 0.5*SqrtPi*Pi; + const doublereal c2 = 0.25*Pi*Pi + 2.0; + const doublereal c3 = SqrtPi*Pi; + return 1.0 + c1*sqtr + c2*tr + c3*sqtr*tr; + } - /** - * This method is used by GMRES to multiply the L matrix by a - * vector b. The L matrix has a 3x3 block structure, where each - * block is a K x K matrix. The elements of the upper-right and - * lower-left blocks are all zero. This method is defined so - * that the multiplication only involves the seven non-zero - * blocks. - */ - void L_Matrix::mult(const doublereal* b, doublereal* prod) const { - integer n = static_cast(nRows())/3; - integer n2 = 2*n; - integer n3 = 3*n; - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n2, 1.0, - DATA_PTR(data()), static_cast(nRows()), b, 1, 0.0, prod, 1); - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n3, 1.0, - DATA_PTR(data()) + n, static_cast(nRows()), - b, 1, 0.0, prod+n, 1); - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n, 1.0, - DATA_PTR(data()) + n*n3 + n2, static_cast(nRows()), - b + n, 1, 0.0, prod+n2, 1); - for (int i = 0; i < n; i++) - prod[i + n2] += b[i + n2] * value(i + n2, i + n2); - } + /** + * This method is used by GMRES to multiply the L matrix by a + * vector b. The L matrix has a 3x3 block structure, where each + * block is a K x K matrix. The elements of the upper-right and + * lower-left blocks are all zero. This method is defined so + * that the multiplication only involves the seven non-zero + * blocks. + */ + void L_Matrix::mult(const doublereal* b, doublereal* prod) const { + integer n = static_cast(nRows())/3; + integer n2 = 2*n; + integer n3 = 3*n; + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n2, 1.0, + DATA_PTR(data()), static_cast(nRows()), b, 1, 0.0, prod, 1); + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n3, 1.0, + DATA_PTR(data()) + n, static_cast(nRows()), + b, 1, 0.0, prod+n, 1); + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, n, n, 1.0, + DATA_PTR(data()) + n*n3 + n2, static_cast(nRows()), + b + n, 1, 0.0, prod+n2, 1); + for (int i = 0; i < n; i++) + prod[i + n2] += b[i + n2] * value(i + n2, i + n2); + } - //////////////////// class MultiTransport methods ////////////// + //////////////////// class MultiTransport methods ////////////// - MultiTransport::MultiTransport(thermo_t* thermo) - : Transport(thermo), - m_temp(-1.0) - { - } + MultiTransport::MultiTransport(thermo_t* thermo) + : Transport(thermo), + m_temp(-1.0) + { + } MultiTransport::~MultiTransport() { } - bool MultiTransport::initGas( GasTransportParams& tr ) { + bool MultiTransport::initGas( GasTransportParams& tr ) { - // constant mixture attributes - //m_phase = tr.mix; - m_thermo = tr.thermo; - m_nsp = m_thermo->nSpecies(); - m_tmin = m_thermo->minTemp(); - m_tmax = m_thermo->maxTemp(); + // constant mixture attributes + //m_phase = tr.mix; + m_thermo = tr.thermo; + m_nsp = m_thermo->nSpecies(); + m_tmin = m_thermo->minTemp(); + m_tmax = m_thermo->maxTemp(); - // make a local copy of the molecular weights - m_mw.resize(m_nsp); - copy(m_thermo->molecularWeights().begin(), - m_thermo->molecularWeights().end(), m_mw.begin()); + // make a local copy of the molecular weights + m_mw.resize(m_nsp); + copy(m_thermo->molecularWeights().begin(), + m_thermo->molecularWeights().end(), m_mw.begin()); - // copy polynomials and parameters into local storage - m_poly = tr.poly; - m_visccoeffs = tr.visccoeffs; - m_diffcoeffs = tr.diffcoeffs; - m_astar_poly = tr.astar_poly; - m_bstar_poly = tr.bstar_poly; - m_cstar_poly = tr.cstar_poly; - m_om22_poly = tr.omega22_poly; - m_zrot = tr.zrot; - m_crot = tr.crot; - m_epsilon = tr.epsilon; - m_mode = tr.mode_; - m_diam = tr.diam; - m_eps = tr.eps; - m_alpha = tr.alpha; - m_dipoleDiag.resize(m_nsp); - int i; - for (i = 0; i < m_nsp; i++) { - m_dipoleDiag[i] = tr.dipole(i,i); - } + // copy polynomials and parameters into local storage + m_poly = tr.poly; + m_visccoeffs = tr.visccoeffs; + m_diffcoeffs = tr.diffcoeffs; + m_astar_poly = tr.astar_poly; + m_bstar_poly = tr.bstar_poly; + m_cstar_poly = tr.cstar_poly; + m_om22_poly = tr.omega22_poly; + m_zrot = tr.zrot; + m_crot = tr.crot; + m_epsilon = tr.epsilon; + m_mode = tr.mode_; + m_diam = tr.diam; + m_eps = tr.eps; + m_alpha = tr.alpha; + m_dipoleDiag.resize(m_nsp); + int i; + for (i = 0; i < m_nsp; i++) { + m_dipoleDiag[i] = tr.dipole(i,i); + } - // the L matrix - m_Lmatrix.resize(3*m_nsp, 3*m_nsp); - m_a.resize(3*m_nsp, 1.0); - m_b.resize(3*m_nsp, 0.0); - m_aa.resize(m_nsp, m_nsp, 0.0); + // the L matrix + m_Lmatrix.resize(3*m_nsp, 3*m_nsp); + m_a.resize(3*m_nsp, 1.0); + m_b.resize(3*m_nsp, 0.0); + m_aa.resize(m_nsp, m_nsp, 0.0); - m_frot_298.resize(m_nsp); - m_rotrelax.resize(m_nsp); + m_frot_298.resize(m_nsp); + m_rotrelax.resize(m_nsp); - m_phi.resize(m_nsp, m_nsp, 0.0); - m_wratjk.resize(m_nsp, m_nsp, 0.0); - m_wratkj1.resize(m_nsp, m_nsp, 0.0); - int j, k; - for (j = 0; j < m_nsp; j++) - for (k = j; k < m_nsp; k++) { - m_wratjk(j,k) = sqrt(m_mw[j]/m_mw[k]); - m_wratjk(k,j) = sqrt(m_wratjk(j,k)); - m_wratkj1(j,k) = sqrt(1.0 + m_mw[k]/m_mw[j]); - } + m_phi.resize(m_nsp, m_nsp, 0.0); + m_wratjk.resize(m_nsp, m_nsp, 0.0); + m_wratkj1.resize(m_nsp, m_nsp, 0.0); + int j, k; + for (j = 0; j < m_nsp; j++) + for (k = j; k < m_nsp; k++) { + m_wratjk(j,k) = sqrt(m_mw[j]/m_mw[k]); + m_wratjk(k,j) = sqrt(m_wratjk(j,k)); + m_wratkj1(j,k) = sqrt(1.0 + m_mw[k]/m_mw[j]); + } - m_cinternal.resize(m_nsp); + m_cinternal.resize(m_nsp); - m_polytempvec.resize(5); - m_visc.resize(m_nsp); - m_sqvisc.resize(m_nsp); - m_bdiff.resize(m_nsp, m_nsp); + m_polytempvec.resize(5); + m_visc.resize(m_nsp); + m_sqvisc.resize(m_nsp); + m_bdiff.resize(m_nsp, m_nsp); - //m_poly.resize(m_nsp); - m_om22.resize(m_nsp, m_nsp); - m_astar.resize(m_nsp, m_nsp); - m_bstar.resize(m_nsp, m_nsp); - m_cstar.resize(m_nsp, m_nsp); + //m_poly.resize(m_nsp); + m_om22.resize(m_nsp, m_nsp); + m_astar.resize(m_nsp, m_nsp); + m_bstar.resize(m_nsp, m_nsp); + m_cstar.resize(m_nsp, m_nsp); - m_molefracs.resize(m_nsp); + m_molefracs.resize(m_nsp); - // set flags all false - m_visc_ok = false; - m_spvisc_ok = false; - m_diff_ok = false; - m_abc_ok = false; - m_l0000_ok = false; - m_lmatrix_soln_ok = false; + // set flags all false + m_visc_ok = false; + m_spvisc_ok = false; + m_diff_ok = false; + m_abc_ok = false; + m_l0000_ok = false; + m_lmatrix_soln_ok = false; - m_diff_tlast = 0.0; - m_spvisc_tlast = 0.0; - m_visc_tlast = 0.0; - m_thermal_tlast = 0.0; + m_diff_tlast = 0.0; + m_spvisc_tlast = 0.0; + m_visc_tlast = 0.0; + m_thermal_tlast = 0.0; - // use LU decomposition by default - m_gmres = false; + // use LU decomposition by default + m_gmres = false; - // default GMRES parameters - m_mgmres = 100; - m_eps_gmres = 1.e-4; + // default GMRES parameters + m_mgmres = 100; + m_eps_gmres = 1.e-4; - // some work space - m_spwork.resize(m_nsp); - m_spwork1.resize(m_nsp); - m_spwork2.resize(m_nsp); - m_spwork3.resize(m_nsp); + // some work space + m_spwork.resize(m_nsp); + m_spwork1.resize(m_nsp); + m_spwork2.resize(m_nsp); + m_spwork3.resize(m_nsp); - // precompute and store log(epsilon_ij/k_B) - m_log_eps_k.resize(m_nsp, m_nsp); - // int j; - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - m_log_eps_k(i,j) = log(tr.epsilon(i,j)/Boltzmann); - m_log_eps_k(j,i) = m_log_eps_k(i,j); - } - } - - - // precompute and store constant parts of the Parker rotational - // collision number temperature correction - const doublereal sq298 = sqrt(298.0); - const doublereal kb298 = Boltzmann * 298.0; - m_sqrt_eps_k.resize(m_nsp); - //int k; - for (k = 0; k < m_nsp; k++) { - m_sqrt_eps_k[k] = sqrt(tr.eps[k]/Boltzmann); - m_frot_298[k] = Frot( tr.eps[k]/kb298, - m_sqrt_eps_k[k]/sq298); - } - -// // install updaters -// m_update_transport_T = m_thermo->installUpdater_T( -// new UpdateTransport_T(*this)); -// m_update_transport_C = m_thermo->installUpdater_C( -// new UpdateTransport_C(*this)); -// m_update_spvisc_T = m_thermo->installUpdater_T( -// new UpdateSpeciesVisc(*this)); -// m_update_visc_T = m_thermo->installUpdater_T( -// new UpdateVisc_T(*this)); -// m_update_diff_T = m_thermo->installUpdater_T( -// new UpdateDiff_T(*this)); -// m_update_thermal_T = m_thermo->installUpdater_T( -// new UpdateThermal_T(*this)); - - return true; + // precompute and store log(epsilon_ij/k_B) + m_log_eps_k.resize(m_nsp, m_nsp); + // int j; + for (i = 0; i < m_nsp; i++) { + for (j = i; j < m_nsp; j++) { + m_log_eps_k(i,j) = log(tr.epsilon(i,j)/Boltzmann); + m_log_eps_k(j,i) = m_log_eps_k(i,j); + } } - /****************** viscosity ******************************/ - - doublereal MultiTransport::viscosity() { - doublereal vismix = 0.0, denom; - int k, j; - - // update m_visc if necessary - updateViscosity_T(); - - // update the mole fractions - updateTransport_C(); - - for (k = 0; k < m_nsp; k++) { - denom = 0.0; - for (j = 0; j < m_nsp; j++) { - denom += m_phi(k,j) * m_molefracs[j]; - } - vismix += m_molefracs[k] * m_visc[k]/denom; - } - return vismix; + // precompute and store constant parts of the Parker rotational + // collision number temperature correction + const doublereal sq298 = sqrt(298.0); + const doublereal kb298 = Boltzmann * 298.0; + m_sqrt_eps_k.resize(m_nsp); + //int k; + for (k = 0; k < m_nsp; k++) { + m_sqrt_eps_k[k] = sqrt(tr.eps[k]/Boltzmann); + m_frot_298[k] = Frot( tr.eps[k]/kb298, + m_sqrt_eps_k[k]/sq298); } + // // install updaters + // m_update_transport_T = m_thermo->installUpdater_T( + // new UpdateTransport_T(*this)); + // m_update_transport_C = m_thermo->installUpdater_C( + // new UpdateTransport_C(*this)); + // m_update_spvisc_T = m_thermo->installUpdater_T( + // new UpdateSpeciesVisc(*this)); + // m_update_visc_T = m_thermo->installUpdater_T( + // new UpdateVisc_T(*this)); + // m_update_diff_T = m_thermo->installUpdater_T( + // new UpdateDiff_T(*this)); + // m_update_thermal_T = m_thermo->installUpdater_T( + // new UpdateThermal_T(*this)); + + return true; + } - /******************* binary diffusion coefficients **************/ + /****************** viscosity ******************************/ - void MultiTransport::getBinaryDiffCoeffs(int ld, doublereal* d) { - int i,j; + doublereal MultiTransport::viscosity() { + doublereal vismix = 0.0, denom; + int k, j; - // if necessary, evaluate the binary diffusion coefficents - // from the polynomial fits - updateDiff_T(); + // update m_visc if necessary + updateViscosity_T(); - doublereal p = pressure_ig(); - doublereal rp = 1.0/p; - for (i = 0; i < m_nsp; i++) - for (j = 0; j < m_nsp; j++) { - d[ld*j + i] = rp * m_bdiff(i,j); - } + // update the mole fractions + updateTransport_C(); + + for (k = 0; k < m_nsp; k++) { + denom = 0.0; + for (j = 0; j < m_nsp; j++) { + denom += m_phi(k,j) * m_molefracs[j]; + } + vismix += m_molefracs[k] * m_visc[k]/denom; } + return vismix; + } - /****************** thermal conductivity **********************/ + /******************* binary diffusion coefficients **************/ - /** - * @internal - */ - doublereal MultiTransport::thermalConductivity() { + void MultiTransport::getBinaryDiffCoeffs(int ld, doublereal* d) { + int i,j; + + // if necessary, evaluate the binary diffusion coefficents + // from the polynomial fits + updateDiff_T(); + + doublereal p = pressure_ig(); + doublereal rp = 1.0/p; + for (i = 0; i < m_nsp; i++) + for (j = 0; j < m_nsp; j++) { + d[ld*j + i] = rp * m_bdiff(i,j); + } + } + + + + /****************** thermal conductivity **********************/ + + /** + * @internal + */ + doublereal MultiTransport::thermalConductivity() { - solveLMatrixEquation(); - doublereal sum = 0.0; - int k; - for (k = 0; k < 2*m_nsp; k++) { - sum += m_b[k + m_nsp] * m_a[k + m_nsp]; - } - return -4.0*sum; + solveLMatrixEquation(); + doublereal sum = 0.0; + int k; + for (k = 0; k < 2*m_nsp; k++) { + sum += m_b[k + m_nsp] * m_a[k + m_nsp]; } - - - /****************** thermal diffusion coefficients ************/ - - /** - * @internal - */ - void MultiTransport::getThermalDiffCoeffs(doublereal* const dt) { - - solveLMatrixEquation(); - const doublereal c = 1.6/GasConstant; - int k; - for (k = 0; k < m_nsp; k++) { - dt[k] = c * m_mw[k] * m_molefracs[k] * m_a[k]; - } + return -4.0*sum; + } + //==================================================================================================================== + // Return the thermal diffusion coefficients for the species + /* + * + * @param dt thermal diffusion coefficients + * (length = m_nsp) + */ + void MultiTransport::getThermalDiffCoeffs(doublereal* const dt) { + solveLMatrixEquation(); + const doublereal c = 1.6/GasConstant; + for (int k = 0; k < m_nsp; k++) { + dt[k] = c * m_mw[k] * m_molefracs[k] * m_a[k]; } + } + //==================================================================================================================== + /** + * @internal + */ + void MultiTransport::solveLMatrixEquation() { - /** - * @internal - */ - void MultiTransport::solveLMatrixEquation() { - - // if T has changed, update the temperature-dependent - // properties. + // if T has changed, update the temperature-dependent + // properties. - updateThermal_T(); - updateTransport_C(); + updateThermal_T(); + updateTransport_C(); - // Copy the mole fractions twice into the last two blocks of - // the right-hand-side vector m_b. The first block of m_b was - // set to zero when it was created, and is not modified so - // doesn't need to be reset to zero. - int k; - for (k = 0; k < m_nsp; k++) { - m_b[k] = 0.0; - m_b[k + m_nsp] = m_molefracs[k]; - m_b[k + 2*m_nsp] = m_molefracs[k]; - } - - // Set the right-hand side vector to zero in the 3rd block for - // all species with no internal energy modes. The - // corresponding third-block rows and columns will be set to - // zero, except on the diagonal of L01,01, where they are set - // to 1.0. This has the effect of eliminating these equations - // from the system, since the equation becomes: m_a[2*m_nsp + - // k] = 0.0. - - // Note that this differs from the Chemkin procedure, where - // all *monatomic* species are excluded. Since monatomic - // radicals can have non-zero internal heat capacities due to - // electronic excitation, they should be retained. - // - // But if CHEMKIN_COMPATIBILITY_MODE is defined, then all - // monatomic species are excluded. - - for (k = 0; k < m_nsp; k++) { - if (!hasInternalModes(k)) m_b[2*m_nsp + k] = 0.0; - } - - // evaluate the submatrices of the L matrix - - m_Lmatrix.resize(3*m_nsp, 3*m_nsp, 0.0); - - eval_L0000(DATA_PTR(m_molefracs)); - eval_L0010(DATA_PTR(m_molefracs)); - eval_L0001(); - eval_L1000(); - eval_L1010(DATA_PTR(m_molefracs)); - eval_L1001(DATA_PTR(m_molefracs)); - eval_L0100(); - eval_L0110(); - eval_L0101(DATA_PTR(m_molefracs)); - - - // Solve it using GMRES or LU decomposition. The last solution - // in m_a should provide a good starting guess, so convergence - // should be fast. - - //if (m_gmres) { - // gmres(m_mgmres, 3*m_nsp, m_Lmatrix, m_b.begin(), - // m_a.begin(), m_eps_gmres); - // m_lmatrix_soln_ok = true; - // m_l0000_ok = true; // L matrix not modified by GMRES - //} - //else { - copy(m_b.begin(), m_b.end(), m_a.begin()); - try { - solve(m_Lmatrix, DATA_PTR(m_a)); - } - catch (CanteraError) { - //if (info != 0) { - throw CanteraError("MultiTransport::solveLMatrixEquation", - "error in solving L matrix."); - } - m_lmatrix_soln_ok = true; - m_l0000_ok = false; - // L matrix is overwritten with LU decomposition - //} - m_lmatrix_soln_ok = true; + // Copy the mole fractions twice into the last two blocks of + // the right-hand-side vector m_b. The first block of m_b was + // set to zero when it was created, and is not modified so + // doesn't need to be reset to zero. + int k; + for (k = 0; k < m_nsp; k++) { + m_b[k] = 0.0; + m_b[k + m_nsp] = m_molefracs[k]; + m_b[k + 2*m_nsp] = m_molefracs[k]; } + // Set the right-hand side vector to zero in the 3rd block for + // all species with no internal energy modes. The + // corresponding third-block rows and columns will be set to + // zero, except on the diagonal of L01,01, where they are set + // to 1.0. This has the effect of eliminating these equations + // from the system, since the equation becomes: m_a[2*m_nsp + + // k] = 0.0. - /** - * - */ - void MultiTransport::getSpeciesFluxes(int ndim, - const doublereal* grad_T, int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes) { + // Note that this differs from the Chemkin procedure, where + // all *monatomic* species are excluded. Since monatomic + // radicals can have non-zero internal heat capacities due to + // electronic excitation, they should be retained. + // + // But if CHEMKIN_COMPATIBILITY_MODE is defined, then all + // monatomic species are excluded. - // update the binary diffusion coefficients if necessary - updateDiff_T(); + for (k = 0; k < m_nsp; k++) { + if (!hasInternalModes(k)) m_b[2*m_nsp + k] = 0.0; + } - doublereal sum; - int i, j; + // evaluate the submatrices of the L matrix + + m_Lmatrix.resize(3*m_nsp, 3*m_nsp, 0.0); - // If any component of grad_T is non-zero, then get the - // thermal diffusion coefficients + eval_L0000(DATA_PTR(m_molefracs)); + eval_L0010(DATA_PTR(m_molefracs)); + eval_L0001(); + eval_L1000(); + eval_L1010(DATA_PTR(m_molefracs)); + eval_L1001(DATA_PTR(m_molefracs)); + eval_L0100(); + eval_L0110(); + eval_L0101(DATA_PTR(m_molefracs)); - bool addThermalDiffusion = false; - for (i = 0; i < ndim; i++) { - if (grad_T[i] != 0.0) addThermalDiffusion = true; - } - if (addThermalDiffusion) getThermalDiffCoeffs(DATA_PTR(m_spwork)); - const doublereal* y = m_thermo->massFractions(); - doublereal rho = m_thermo->density(); + // Solve it using GMRES or LU decomposition. The last solution + // in m_a should provide a good starting guess, so convergence + // should be fast. - for (i = 0; i < m_nsp; i++) { - sum = 0.0; - for (j = 0; j < m_nsp; j++) { - m_aa(i,j) = m_molefracs[j]*m_molefracs[i]/m_bdiff(i,j); - sum += m_aa(i,j); - } - m_aa(i,i) -= sum; - } + //if (m_gmres) { + // gmres(m_mgmres, 3*m_nsp, m_Lmatrix, m_b.begin(), + // m_a.begin(), m_eps_gmres); + // m_lmatrix_soln_ok = true; + // m_l0000_ok = true; // L matrix not modified by GMRES + //} + //else { + copy(m_b.begin(), m_b.end(), m_a.begin()); + try { + solve(m_Lmatrix, DATA_PTR(m_a)); + } + catch (CanteraError) { + //if (info != 0) { + throw CanteraError("MultiTransport::solveLMatrixEquation", + "error in solving L matrix."); + } + m_lmatrix_soln_ok = true; + m_l0000_ok = false; + // L matrix is overwritten with LU decomposition + //} + m_lmatrix_soln_ok = true; + } - // enforce the condition \sum Y_k V_k = 0. This is done by replacing - // the flux equation with the largest gradx component in the first - // coordinate direction with the flux balance condition. - int jmax = 0; - doublereal gradmax = -1.0; - for (j = 0; j < m_nsp; j++) { - if (fabs(grad_X[j]) > gradmax) { - gradmax = fabs(grad_X[j]); - jmax = j; - } - } - // set the matrix elements in this row to the mass fractions, - // and set the entry in gradx to zero + /** + * + */ + void MultiTransport::getSpeciesFluxes(int ndim, + const doublereal* grad_T, int ldx, const doublereal* grad_X, + int ldf, doublereal* fluxes) { - for (j = 0; j < m_nsp; j++) { - m_aa(jmax,j) = y[j]; - } - vector_fp gsave(ndim), grx(ldx*m_nsp); - int n; - for (n = 0; n < ldx*ndim; n++) { - grx[n] = grad_X[n]; - } - //for (n = 0; n < ndim; n++) { - // gsave[n] = grad_X[jmax + n*ldx]; // save the input mole frac gradient - //grad_X[jmax + n*ldx] = 0.0; - // grx[jmax + n*ldx] = 0.0; - // } + // update the binary diffusion coefficients if necessary + updateDiff_T(); - // copy grad_X to fluxes - const doublereal* gx; - for (n = 0; n < ndim; n++) { - gx = grad_X + ldx*n; - copy(gx, gx + m_nsp, fluxes + ldf*n); - fluxes[jmax + n*ldf] = 0.0; - } + doublereal sum; + int i, j; - // use LAPACK to solve the equations - int info=0; - ct_dgetrf(static_cast(m_aa.nRows()), - static_cast(m_aa.nColumns()), m_aa.ptrColumn(0), - static_cast(m_aa.nRows()), - &m_aa.ipiv()[0], info); - if (info == 0) { - ct_dgetrs(ctlapack::NoTranspose, - static_cast(m_aa.nRows()), ndim, + // If any component of grad_T is non-zero, then get the + // thermal diffusion coefficients + + bool addThermalDiffusion = false; + for (i = 0; i < ndim; i++) { + if (grad_T[i] != 0.0) addThermalDiffusion = true; + } + if (addThermalDiffusion) getThermalDiffCoeffs(DATA_PTR(m_spwork)); + + const doublereal* y = m_thermo->massFractions(); + doublereal rho = m_thermo->density(); + + for (i = 0; i < m_nsp; i++) { + sum = 0.0; + for (j = 0; j < m_nsp; j++) { + m_aa(i,j) = m_molefracs[j]*m_molefracs[i]/m_bdiff(i,j); + sum += m_aa(i,j); + } + m_aa(i,i) -= sum; + } + + // enforce the condition \sum Y_k V_k = 0. This is done by replacing + // the flux equation with the largest gradx component in the first + // coordinate direction with the flux balance condition. + int jmax = 0; + doublereal gradmax = -1.0; + for (j = 0; j < m_nsp; j++) { + if (fabs(grad_X[j]) > gradmax) { + gradmax = fabs(grad_X[j]); + jmax = j; + } + } + + // set the matrix elements in this row to the mass fractions, + // and set the entry in gradx to zero + + for (j = 0; j < m_nsp; j++) { + m_aa(jmax,j) = y[j]; + } + vector_fp gsave(ndim), grx(ldx*m_nsp); + int n; + for (n = 0; n < ldx*ndim; n++) { + grx[n] = grad_X[n]; + } + //for (n = 0; n < ndim; n++) { + // gsave[n] = grad_X[jmax + n*ldx]; // save the input mole frac gradient + //grad_X[jmax + n*ldx] = 0.0; + // grx[jmax + n*ldx] = 0.0; + // } + + // copy grad_X to fluxes + const doublereal* gx; + for (n = 0; n < ndim; n++) { + gx = grad_X + ldx*n; + copy(gx, gx + m_nsp, fluxes + ldf*n); + fluxes[jmax + n*ldf] = 0.0; + } + + // use LAPACK to solve the equations + int info=0; + ct_dgetrf(static_cast(m_aa.nRows()), + static_cast(m_aa.nColumns()), m_aa.ptrColumn(0), + static_cast(m_aa.nRows()), + &m_aa.ipiv()[0], info); + if (info == 0) { + ct_dgetrs(ctlapack::NoTranspose, + static_cast(m_aa.nRows()), ndim, m_aa.ptrColumn(0), static_cast(m_aa.nRows()), &m_aa.ipiv()[0], fluxes, ldf, info); - if (info != 0) info += 100; - } - else - throw CanteraError("MultiTransport::getSpeciesFluxes", - "Error in DGETRF"); - if (info > 50) - throw CanteraError("MultiTransport::getSpeciesFluxes", - "Error in DGETRS"); + if (info != 0) info += 100; + } + else + throw CanteraError("MultiTransport::getSpeciesFluxes", + "Error in DGETRF"); + if (info > 50) + throw CanteraError("MultiTransport::getSpeciesFluxes", + "Error in DGETRS"); - int offset; - doublereal pp = pressure_ig(); + int offset; + doublereal pp = pressure_ig(); - // multiply diffusion velocities by rho * V to create - // mass fluxes, and restore the gradx elements that were - // modified - for (n = 0; n < ndim; n++) { - offset = n*ldf; - for (i = 0; i < m_nsp; i++) { - fluxes[i + offset] *= rho * y[i] / pp; - } - //grad_X[jmax + n*ldx] = gsave[n]; - } - - // thermal diffusion - if (addThermalDiffusion) { - for (n = 0; n < ndim; n++) { - offset = n*ldf; - doublereal grad_logt = grad_T[n]/m_temp; - for (i = 0; i < m_nsp; i++) - fluxes[i + offset] -= m_spwork[i]*grad_logt; - } - } + // multiply diffusion velocities by rho * V to create + // mass fluxes, and restore the gradx elements that were + // modified + for (n = 0; n < ndim; n++) { + offset = n*ldf; + for (i = 0; i < m_nsp; i++) { + fluxes[i + offset] *= rho * y[i] / pp; + } + //grad_X[jmax + n*ldx] = gsave[n]; } + // thermal diffusion + if (addThermalDiffusion) { + for (n = 0; n < ndim; n++) { + offset = n*ldf; + doublereal grad_logt = grad_T[n]/m_temp; + for (i = 0; i < m_nsp; i++) + fluxes[i + offset] -= m_spwork[i]*grad_logt; + } + } + } + //==================================================================================================================== - void MultiTransport::getMassFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, - doublereal* fluxes) { + void MultiTransport::getMassFluxes(const doublereal* state1, + const doublereal* state2, doublereal delta, + doublereal* fluxes) { - double* x1 = DATA_PTR(m_spwork1); - double* x2 = DATA_PTR(m_spwork2); - double* x3 = DATA_PTR(m_spwork3); - int n, nsp = m_thermo->nSpecies(); - m_thermo->restoreState(nsp+2, state1); - double p1 = m_thermo->pressure(); - double t1 = state1[0]; - m_thermo->getMoleFractions(x1); + double* x1 = DATA_PTR(m_spwork1); + double* x2 = DATA_PTR(m_spwork2); + double* x3 = DATA_PTR(m_spwork3); + int n, nsp = m_thermo->nSpecies(); + m_thermo->restoreState(nsp+2, state1); + double p1 = m_thermo->pressure(); + double t1 = state1[0]; + m_thermo->getMoleFractions(x1); - m_thermo->restoreState(nsp+2, state2); - double p2 = m_thermo->pressure(); - double t2 = state2[0]; - m_thermo->getMoleFractions(x2); + m_thermo->restoreState(nsp+2, state2); + double p2 = m_thermo->pressure(); + double t2 = state2[0]; + m_thermo->getMoleFractions(x2); - // - double p = 0.5*(p1 + p2); - double t = 0.5*(state1[0] + state2[0]); + // + double p = 0.5*(p1 + p2); + double t = 0.5*(state1[0] + state2[0]); - for (n = 0; n < nsp; n++) { - x3[n] = 0.5*(x1[n] + x2[n]); - } - m_thermo->setState_TPX(t, p, x3); - m_thermo->getMoleFractions(DATA_PTR(m_molefracs)); + for (n = 0; n < nsp; n++) { + x3[n] = 0.5*(x1[n] + x2[n]); + } + m_thermo->setState_TPX(t, p, x3); + m_thermo->getMoleFractions(DATA_PTR(m_molefracs)); - // update the binary diffusion coefficients if necessary - updateDiff_T(); + // update the binary diffusion coefficients if necessary + updateDiff_T(); - doublereal sum; - int i, j; + doublereal sum; + int i, j; - // If there is a temperature gadient, then get the - // thermal diffusion coefficients + // If there is a temperature gadient, then get the + // thermal diffusion coefficients - bool addThermalDiffusion = false; - if (state1[0] != state2[0]) { - addThermalDiffusion = true; - getThermalDiffCoeffs(DATA_PTR(m_spwork)); - } + bool addThermalDiffusion = false; + if (state1[0] != state2[0]) { + addThermalDiffusion = true; + getThermalDiffCoeffs(DATA_PTR(m_spwork)); + } - const doublereal* y = m_thermo->massFractions(); - doublereal rho = m_thermo->density(); + const doublereal* y = m_thermo->massFractions(); + doublereal rho = m_thermo->density(); - for (i = 0; i < m_nsp; i++) { - sum = 0.0; - for (j = 0; j < m_nsp; j++) { - m_aa(i,j) = m_molefracs[j]*m_molefracs[i]/m_bdiff(i,j); - sum += m_aa(i,j); - } - m_aa(i,i) -= sum; - } + for (i = 0; i < m_nsp; i++) { + sum = 0.0; + for (j = 0; j < m_nsp; j++) { + m_aa(i,j) = m_molefracs[j]*m_molefracs[i]/m_bdiff(i,j); + sum += m_aa(i,j); + } + m_aa(i,i) -= sum; + } - // enforce the condition \sum Y_k V_k = 0. This is done by - // replacing the flux equation with the largest gradx - // component with the flux balance condition. - int jmax = 0; - doublereal gradmax = -1.0; - for (j = 0; j < m_nsp; j++) { - if (fabs(x2[j] - x1[j]) > gradmax) { - gradmax = fabs(x1[j] - x2[j]); - jmax = j; - } - } + // enforce the condition \sum Y_k V_k = 0. This is done by + // replacing the flux equation with the largest gradx + // component with the flux balance condition. + int jmax = 0; + doublereal gradmax = -1.0; + for (j = 0; j < m_nsp; j++) { + if (fabs(x2[j] - x1[j]) > gradmax) { + gradmax = fabs(x1[j] - x2[j]); + jmax = j; + } + } - // set the matrix elements in this row to the mass fractions, - // and set the entry in gradx to zero + // set the matrix elements in this row to the mass fractions, + // and set the entry in gradx to zero - for (j = 0; j < m_nsp; j++) { - m_aa(jmax,j) = y[j]; - fluxes[j] = x2[j] - x1[j]; - } - fluxes[jmax] = 0.0; + for (j = 0; j < m_nsp; j++) { + m_aa(jmax,j) = y[j]; + fluxes[j] = x2[j] - x1[j]; + } + fluxes[jmax] = 0.0; - // use LAPACK to solve the equations - int info=0; - int nr = m_aa.nRows(); - int nc = m_aa.nColumns(); + // use LAPACK to solve the equations + int info=0; + int nr = m_aa.nRows(); + int nc = m_aa.nColumns(); - ct_dgetrf(nr, nc, m_aa.ptrColumn(0), nr, &m_aa.ipiv()[0], info); - if (info == 0) { - int ndim = 1; - ct_dgetrs(ctlapack::NoTranspose, nr, ndim, + ct_dgetrf(nr, nc, m_aa.ptrColumn(0), nr, &m_aa.ipiv()[0], info); + if (info == 0) { + int ndim = 1; + ct_dgetrs(ctlapack::NoTranspose, nr, ndim, m_aa.ptrColumn(0), nr, &m_aa.ipiv()[0], fluxes, nr, info); - if (info != 0) - throw CanteraError("MultiTransport::getMassFluxes", - "Error in DGETRS. Info = "+int2str(info)); - } - else - throw CanteraError("MultiTransport::getMassFluxes", - "Error in DGETRF. Info = "+int2str(info)); + if (info != 0) + throw CanteraError("MultiTransport::getMassFluxes", + "Error in DGETRS. Info = "+int2str(info)); + } + else + throw CanteraError("MultiTransport::getMassFluxes", + "Error in DGETRF. Info = "+int2str(info)); - doublereal pp = pressure_ig(); + doublereal pp = pressure_ig(); - // multiply diffusion velocities by rho * Y_k to create - // mass fluxes, and divide by pressure - for (i = 0; i < m_nsp; i++) { - fluxes[i] *= rho * y[i] / pp; - } - - // thermal diffusion - if (addThermalDiffusion) { - doublereal grad_logt = (t2 - t1)/m_temp; - for (i = 0; i < m_nsp; i++) { - fluxes[i] -= m_spwork[i]*grad_logt; - } - } + // multiply diffusion velocities by rho * Y_k to create + // mass fluxes, and divide by pressure + for (i = 0; i < m_nsp; i++) { + fluxes[i] *= rho * y[i] / pp; } - void MultiTransport::getMolarFluxes(const doublereal* const state1, - const doublereal * const state2, - const doublereal delta, - doublereal * const fluxes) { - getMassFluxes(state1, state2, delta, fluxes); - int k, nsp = m_thermo->nSpecies(); - for (k = 0; k < nsp; k++) { - fluxes[k] /= m_mw[k]; - } + // thermal diffusion + if (addThermalDiffusion) { + doublereal grad_logt = (t2 - t1)/m_temp; + for (i = 0; i < m_nsp; i++) { + fluxes[i] -= m_spwork[i]*grad_logt; + } } + } + //==================================================================================================================== + void MultiTransport::getMolarFluxes(const doublereal* const state1, + const doublereal * const state2, + const doublereal delta, + doublereal * const fluxes) { + getMassFluxes(state1, state2, delta, fluxes); + int k, nsp = m_thermo->nSpecies(); + for (k = 0; k < nsp; k++) { + fluxes[k] /= m_mw[k]; + } + } + //==================================================================================================================== + void MultiTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { + int i,j; - void MultiTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { - int i,j; + doublereal p = pressure_ig(); - doublereal p = pressure_ig(); + // update the mole fractions + updateTransport_C(); - // update the mole fractions - updateTransport_C(); + // update the binary diffusion coefficients + updateDiff_T(); - // update the binary diffusion coefficients - updateDiff_T(); - - // evaluate L0000 if the temperature or concentrations have - // changed since it was last evaluated. - if (!m_l0000_ok) eval_L0000(DATA_PTR(m_molefracs)); + // evaluate L0000 if the temperature or concentrations have + // changed since it was last evaluated. + if (!m_l0000_ok) eval_L0000(DATA_PTR(m_molefracs)); - // invert L00,00 - int ierr = invert(m_Lmatrix, m_nsp); - if (ierr != 0) { - throw CanteraError("MultiTransport::getMultiDiffCoeffs", - string(" invert returned ierr = ")+int2str(ierr)); - } - m_l0000_ok = false; // matrix is overwritten by inverse - - //doublereal pres = m_thermo->pressure(); - doublereal prefactor = 16.0 * m_temp - * m_thermo->meanMolecularWeight()/(25.0 * p); - doublereal c; - - for (i = 0; i < m_nsp; i++) { - for (j = 0; j < m_nsp; j++) { - c = prefactor/m_mw[j]; - d[ld*j + i] = c*m_molefracs[i]* - (m_Lmatrix(i,j) - m_Lmatrix(i,i)); - } - } + // invert L00,00 + int ierr = invert(m_Lmatrix, m_nsp); + if (ierr != 0) { + throw CanteraError("MultiTransport::getMultiDiffCoeffs", + string(" invert returned ierr = ")+int2str(ierr)); } + m_l0000_ok = false; // matrix is overwritten by inverse + //doublereal pres = m_thermo->pressure(); + doublereal prefactor = 16.0 * m_temp + * m_thermo->meanMolecularWeight()/(25.0 * p); + doublereal c; - void MultiTransport::getMixDiffCoeffs(doublereal* const d) { + for (i = 0; i < m_nsp; i++) { + for (j = 0; j < m_nsp; j++) { + c = prefactor/m_mw[j]; + d[ld*j + i] = c*m_molefracs[i]* + (m_Lmatrix(i,j) - m_Lmatrix(i,i)); + } + } + } + //==================================================================================================================== - // update the mole fractions - updateTransport_C(); + void MultiTransport::getMixDiffCoeffs(doublereal* const d) { - // update the binary diffusion coefficients if necessary - updateDiff_T(); + // update the mole fractions + updateTransport_C(); - int k, j; - doublereal mmw = m_thermo->meanMolecularWeight(); - doublereal sumxw = 0.0, sum2; - doublereal p = pressure_ig(); - if (m_nsp == 1) { - d[0] = m_bdiff(0,0) / p; - } else { - for (k = 0; k < m_nsp; k++) sumxw += m_molefracs[k] * m_mw[k]; - for (k = 0; k < m_nsp; k++) { - sum2 = 0.0; - for (j = 0; j < m_nsp; j++) { - if (j != k) { - sum2 += m_molefracs[j] / m_bdiff(j,k); - } - } - if (sum2 <= 0.0) { - d[k] = m_bdiff(k,k) / p; - } else { - d[k] = (sumxw - m_molefracs[k] * m_mw[k])/(p * mmw * sum2); - } + // update the binary diffusion coefficients if necessary + updateDiff_T(); + + int k, j; + doublereal mmw = m_thermo->meanMolecularWeight(); + doublereal sumxw = 0.0, sum2; + doublereal p = pressure_ig(); + if (m_nsp == 1) { + d[0] = m_bdiff(0,0) / p; + } else { + for (k = 0; k < m_nsp; k++) sumxw += m_molefracs[k] * m_mw[k]; + for (k = 0; k < m_nsp; k++) { + sum2 = 0.0; + for (j = 0; j < m_nsp; j++) { + if (j != k) { + sum2 += m_molefracs[j] / m_bdiff(j,k); } } + if (sum2 <= 0.0) { + d[k] = m_bdiff(k,k) / p; + } else { + d[k] = (sumxw - m_molefracs[k] * m_mw[k])/(p * mmw * sum2); + } + } } + } - void MultiTransport::updateTransport_T() { - //m_thermo->update_T(m_update_transport_T); - _update_transport_T(); - } + void MultiTransport::updateTransport_T() { + //m_thermo->update_T(m_update_transport_T); + _update_transport_T(); + } - void MultiTransport::updateTransport_C() { - // {m_thermo->update_C(m_update_transport_C); - _update_transport_C(); - } + void MultiTransport::updateTransport_C() { + // {m_thermo->update_C(m_update_transport_C); + _update_transport_C(); + } - /** - * Update temperature-dependent quantities. This method is called - * by the temperature property updater. - */ - void MultiTransport::_update_transport_T() - { - if (m_temp == m_thermo->temperature()) return; + /** + * Update temperature-dependent quantities. This method is called + * by the temperature property updater. + */ + void MultiTransport::_update_transport_T() + { + if (m_temp == m_thermo->temperature()) return; - m_temp = m_thermo->temperature(); - m_logt = log(m_temp); - m_kbt = Boltzmann * m_temp; - m_sqrt_t = sqrt(m_temp); - m_t14 = sqrt(m_sqrt_t); - m_t32 = m_temp * m_sqrt_t; - m_sqrt_kbt = sqrt(Boltzmann*m_temp); + m_temp = m_thermo->temperature(); + m_logt = log(m_temp); + m_kbt = Boltzmann * m_temp; + m_sqrt_t = sqrt(m_temp); + m_t14 = sqrt(m_sqrt_t); + m_t32 = m_temp * m_sqrt_t; + m_sqrt_kbt = sqrt(Boltzmann*m_temp); - // compute powers of log(T) - m_polytempvec[0] = 1.0; - m_polytempvec[1] = m_logt; - m_polytempvec[2] = m_logt*m_logt; - m_polytempvec[3] = m_logt*m_logt*m_logt; - m_polytempvec[4] = m_logt*m_logt*m_logt*m_logt; + // compute powers of log(T) + m_polytempvec[0] = 1.0; + m_polytempvec[1] = m_logt; + m_polytempvec[2] = m_logt*m_logt; + m_polytempvec[3] = m_logt*m_logt*m_logt; + m_polytempvec[4] = m_logt*m_logt*m_logt*m_logt; - // temperature has changed, so polynomial fits will need to be - // redone, and the L matrix reevaluated. - m_visc_ok = false; - m_spvisc_ok = false; - m_diff_ok = false; - m_abc_ok = false; - m_lmatrix_soln_ok = false; - m_l0000_ok = false; - } + // temperature has changed, so polynomial fits will need to be + // redone, and the L matrix reevaluated. + m_visc_ok = false; + m_spvisc_ok = false; + m_diff_ok = false; + m_abc_ok = false; + m_lmatrix_soln_ok = false; + m_l0000_ok = false; + } - /** - * This is called the first time any transport property - * is requested from ThermoSubstance after the concentrations - * have changed. - */ - void MultiTransport::_update_transport_C() - { - // signal that concentration-dependent quantities will need to - // be recomputed before use, and update the local mole - // fraction array. - m_l0000_ok = false; - m_lmatrix_soln_ok = false; - m_thermo->getMoleFractions(DATA_PTR(m_molefracs)); + /** + * This is called the first time any transport property + * is requested from ThermoSubstance after the concentrations + * have changed. + */ + void MultiTransport::_update_transport_C() + { + // signal that concentration-dependent quantities will need to + // be recomputed before use, and update the local mole + // fraction array. + m_l0000_ok = false; + m_lmatrix_soln_ok = false; + m_thermo->getMoleFractions(DATA_PTR(m_molefracs)); - // add an offset to avoid a pure species condition - // (check - this may be unnecessary) - int k; - for (k = 0; k < m_nsp; k++) { - m_molefracs[k] = fmaxx(MIN_X, m_molefracs[k]); - } + // add an offset to avoid a pure species condition + // (check - this may be unnecessary) + int k; + for (k = 0; k < m_nsp; k++) { + m_molefracs[k] = fmaxx(MIN_X, m_molefracs[k]); } + } - /************************************************************************* - * - * methods to update temperature-dependent properties - * - *************************************************************************/ + /************************************************************************* + * + * methods to update temperature-dependent properties + * + *************************************************************************/ - /** - * @internal - * Update the binary diffusion coefficients. These are evaluated - * from the polynomial fits at unit pressure (1 Pa). - */ - void MultiTransport::updateDiff_T() { - if (m_diff_tlast == m_thermo->temperature()) return; - _update_diff_T(); - m_diff_tlast = m_thermo->temperature(); - //m_thermo->update_T(m_update_diff_T); - } + /** + * @internal + * Update the binary diffusion coefficients. These are evaluated + * from the polynomial fits at unit pressure (1 Pa). + */ + void MultiTransport::updateDiff_T() { + if (m_diff_tlast == m_thermo->temperature()) return; + _update_diff_T(); + m_diff_tlast = m_thermo->temperature(); + //m_thermo->update_T(m_update_diff_T); + } - void MultiTransport::_update_diff_T() { + void MultiTransport::_update_diff_T() { - updateTransport_T(); + updateTransport_T(); - // evaluate binary diffusion coefficients at unit pressure - int i,j; - int ic = 0; - if (m_mode == CK_Mode) { - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - m_bdiff(i,j) = exp(dot4(m_polytempvec, m_diffcoeffs[ic])); - m_bdiff(j,i) = m_bdiff(i,j); - ic++; - } - } - } - else { - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - m_bdiff(i,j) = m_temp * m_sqrt_t*dot5(m_polytempvec, - m_diffcoeffs[ic]); - m_bdiff(j,i) = m_bdiff(i,j); - ic++; - } - } - } - m_diff_ok = true; - } - - - /** - * @internal - * Update the temperature-dependent viscosity terms. - * Updates the array of pure species viscosities, and the - * weighting functions in the viscosity mixture rule. - * The flag m_visc_ok is set to true. - */ - void MultiTransport::updateSpeciesViscosities_T() { - if (m_spvisc_tlast == m_thermo->temperature()) return; - _update_species_visc_T(); - //m_thermo->update_T(m_update_spvisc_T); - m_spvisc_tlast = m_thermo->temperature(); - } - - - void MultiTransport::_update_species_visc_T() { - - updateTransport_T(); - - int k; - if (m_mode == CK_Mode) { - for (k = 0; k < m_nsp; k++) { - m_visc[k] = exp(dot4(m_polytempvec, m_visccoeffs[k])); - m_sqvisc[k] = sqrt(m_visc[k]); - } - } - else { - for (k = 0; k < m_nsp; k++) { - //m_visc[k] = m_sqrt_t*dot5(m_polytempvec, m_visccoeffs[k]); - // the polynomial fit is done for sqrt(visc/sqrt(T)) - m_sqvisc[k] = m_t14*dot5(m_polytempvec, m_visccoeffs[k]); - m_visc[k] = (m_sqvisc[k]*m_sqvisc[k]); - } - } - m_spvisc_ok = true; - } - - /** - * @internal - */ - void MultiTransport::updateViscosity_T() { - if (m_visc_tlast == m_thermo->temperature()) return; - _update_visc_T(); - m_visc_tlast = m_thermo->temperature(); - } - - void MultiTransport::_update_visc_T() { - doublereal vratiokj, wratiojk, factor1; - - updateSpeciesViscosities_T(); - - // see Eq. (9-5.15) of Reid, Prausnitz, and Poling - int j, k; - for (j = 0; j < m_nsp; j++) { - for (k = j; k < m_nsp; k++) { - vratiokj = m_visc[k]/m_visc[j]; - wratiojk = m_mw[j]/m_mw[k]; - //rootwjk = sqrt(wratiojk); - //factor1 = 1.0 + sqrt(vratiokj * rootwjk); - //m_phi(k,j) = factor1*factor1 / - // (SqrtEight * sqrt(1.0 + m_mw[k]/m_mw[j])); - //m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk); - - // Note that m_wratjk(k,j) holds the square root of - // m_wratjk(j,k)! - factor1 = 1.0 + (m_sqvisc[k]/m_sqvisc[j]) * m_wratjk(k,j); - m_phi(k,j) = factor1*factor1 / - (SqrtEight * m_wratkj1(j,k)); - m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk); - } - } - m_visc_ok = true; - } - - - /** - * @internal - * Update the temperature-dependent terms needed to compute the - * thermal conductivity and thermal diffusion coefficients. - */ - void MultiTransport::updateThermal_T() { - if (m_thermal_tlast == m_thermo->temperature()) return; - _update_thermal_T(); - // m_thermo->update_T(m_update_thermal_T); - m_thermal_tlast = m_thermo->temperature(); - } - - void MultiTransport::_update_thermal_T() { - - // we need species viscosities and binary diffusion - // coefficients - updateSpeciesViscosities_T(); - updateDiff_T(); - - // evaluate polynomial fits for A*, B*, C* - doublereal z; - int ipoly; - int i, j; - for (i = 0; i < m_nsp; i++) { - for (j = i; j < m_nsp; j++) { - z = m_logt - m_log_eps_k(i,j); - ipoly = m_poly[i][j]; - if (m_mode == CK_Mode) { - m_om22(i,j) = poly6(z, DATA_PTR(m_om22_poly[ipoly])); - m_astar(i,j) = poly6(z, DATA_PTR(m_astar_poly[ipoly])); - m_bstar(i,j) = poly6(z, DATA_PTR(m_bstar_poly[ipoly])); - m_cstar(i,j) = poly6(z, DATA_PTR(m_cstar_poly[ipoly])); - } - else { - m_om22(i,j) = poly8(z, DATA_PTR(m_om22_poly[ipoly])); - m_astar(i,j) = poly8(z, DATA_PTR(m_astar_poly[ipoly])); - m_bstar(i,j) = poly8(z, DATA_PTR(m_bstar_poly[ipoly])); - m_cstar(i,j) = poly8(z, DATA_PTR(m_cstar_poly[ipoly])); - } - m_om22(j,i) = m_om22(i,j); - m_astar(j,i) = m_astar(i,j); - m_bstar(j,i) = m_bstar(i,j); - m_cstar(j,i) = m_cstar(i,j); - } - } - m_abc_ok = true; - - // evaluate the temperature-dependent rotational relaxation - // rate - - int k; - doublereal tr, sqtr; - for (k = 0; k < m_nsp; k++) { - tr = m_eps[k]/ m_kbt; - sqtr = m_sqrt_eps_k[k] / m_sqrt_t; - m_rotrelax[k] = fmaxx(1.0,m_zrot[k]) * m_frot_298[k]/Frot(tr, sqtr); - } - - doublereal d; - doublereal c = 1.2*GasConstant*m_temp; - for (k = 0; k < m_nsp; k++) { - d = c * m_visc[k] * m_astar(k,k)/m_mw[k]; - m_bdiff(k,k) = d; - } - - // Calculate the internal heat capacities by subtracting off the translational contributions - /* - * HKM Exploratory comment: - * The translational component is 1.5 - * The rotational component is 1.0 for a linear molecule and 1.5 for a nonlinear molecule - * and zero for a monotomic. - * Chemkin has traditionally subtracted 1.5 here (SAND86-8246). - * The original Dixon-Lewis paper subtracted 1.5 here. - */ - const array_fp& cp = ((IdealGasPhase*)m_thermo)->cp_R_ref(); - for (k = 0; k < m_nsp; k++) { - m_cinternal[k] = cp[k] - 2.5; - } - } - - /** - * This function returns a Transport data object for a given species. - * - */ - struct GasTransportData MultiTransport:: - getGasTransportData(int kSpecies) - { - struct GasTransportData td; - td.speciesName = m_thermo->speciesName(kSpecies); - - td.geometry = 2; - if (m_crot[kSpecies] == 0.0) { - td.geometry = 0; - } else if (m_crot[kSpecies] == 1.0) { - td.geometry = 1; + // evaluate binary diffusion coefficients at unit pressure + int i,j; + int ic = 0; + if (m_mode == CK_Mode) { + for (i = 0; i < m_nsp; i++) { + for (j = i; j < m_nsp; j++) { + m_bdiff(i,j) = exp(dot4(m_polytempvec, m_diffcoeffs[ic])); + m_bdiff(j,i) = m_bdiff(i,j); + ic++; + } } - td.wellDepth = m_eps[kSpecies] / Boltzmann; - td.dipoleMoment = m_dipoleDiag[kSpecies] * 1.0E25 / SqrtTen; - td.diameter = m_diam(kSpecies, kSpecies) * 1.0E10; - td.polarizability = m_alpha[kSpecies] * 1.0E30; - td.rotRelaxNumber = m_zrot[kSpecies]; - - return td; } + else { + for (i = 0; i < m_nsp; i++) { + for (j = i; j < m_nsp; j++) { + m_bdiff(i,j) = m_temp * m_sqrt_t*dot5(m_polytempvec, + m_diffcoeffs[ic]); + m_bdiff(j,i) = m_bdiff(i,j); + ic++; + } + } + } + m_diff_ok = true; + } + + + /** + * @internal + * Update the temperature-dependent viscosity terms. + * Updates the array of pure species viscosities, and the + * weighting functions in the viscosity mixture rule. + * The flag m_visc_ok is set to true. + */ + void MultiTransport::updateSpeciesViscosities_T() { + if (m_spvisc_tlast == m_thermo->temperature()) return; + _update_species_visc_T(); + //m_thermo->update_T(m_update_spvisc_T); + m_spvisc_tlast = m_thermo->temperature(); + } + + + void MultiTransport::_update_species_visc_T() { + + updateTransport_T(); + + int k; + if (m_mode == CK_Mode) { + for (k = 0; k < m_nsp; k++) { + m_visc[k] = exp(dot4(m_polytempvec, m_visccoeffs[k])); + m_sqvisc[k] = sqrt(m_visc[k]); + } + } + else { + for (k = 0; k < m_nsp; k++) { + //m_visc[k] = m_sqrt_t*dot5(m_polytempvec, m_visccoeffs[k]); + // the polynomial fit is done for sqrt(visc/sqrt(T)) + m_sqvisc[k] = m_t14*dot5(m_polytempvec, m_visccoeffs[k]); + m_visc[k] = (m_sqvisc[k]*m_sqvisc[k]); + } + } + m_spvisc_ok = true; + } + + /** + * @internal + */ + void MultiTransport::updateViscosity_T() { + if (m_visc_tlast == m_thermo->temperature()) return; + _update_visc_T(); + m_visc_tlast = m_thermo->temperature(); + } + + void MultiTransport::_update_visc_T() { + doublereal vratiokj, wratiojk, factor1; + + updateSpeciesViscosities_T(); + + // see Eq. (9-5.15) of Reid, Prausnitz, and Poling + int j, k; + for (j = 0; j < m_nsp; j++) { + for (k = j; k < m_nsp; k++) { + vratiokj = m_visc[k]/m_visc[j]; + wratiojk = m_mw[j]/m_mw[k]; + //rootwjk = sqrt(wratiojk); + //factor1 = 1.0 + sqrt(vratiokj * rootwjk); + //m_phi(k,j) = factor1*factor1 / + // (SqrtEight * sqrt(1.0 + m_mw[k]/m_mw[j])); + //m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk); + + // Note that m_wratjk(k,j) holds the square root of + // m_wratjk(j,k)! + factor1 = 1.0 + (m_sqvisc[k]/m_sqvisc[j]) * m_wratjk(k,j); + m_phi(k,j) = factor1*factor1 / + (SqrtEight * m_wratkj1(j,k)); + m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk); + } + } + m_visc_ok = true; + } + + + /** + * @internal + * Update the temperature-dependent terms needed to compute the + * thermal conductivity and thermal diffusion coefficients. + */ + void MultiTransport::updateThermal_T() { + if (m_thermal_tlast == m_thermo->temperature()) return; + _update_thermal_T(); + // m_thermo->update_T(m_update_thermal_T); + m_thermal_tlast = m_thermo->temperature(); + } + + void MultiTransport::_update_thermal_T() { + + // we need species viscosities and binary diffusion + // coefficients + updateSpeciesViscosities_T(); + updateDiff_T(); + + // evaluate polynomial fits for A*, B*, C* + doublereal z; + int ipoly; + int i, j; + for (i = 0; i < m_nsp; i++) { + for (j = i; j < m_nsp; j++) { + z = m_logt - m_log_eps_k(i,j); + ipoly = m_poly[i][j]; + if (m_mode == CK_Mode) { + m_om22(i,j) = poly6(z, DATA_PTR(m_om22_poly[ipoly])); + m_astar(i,j) = poly6(z, DATA_PTR(m_astar_poly[ipoly])); + m_bstar(i,j) = poly6(z, DATA_PTR(m_bstar_poly[ipoly])); + m_cstar(i,j) = poly6(z, DATA_PTR(m_cstar_poly[ipoly])); + } + else { + m_om22(i,j) = poly8(z, DATA_PTR(m_om22_poly[ipoly])); + m_astar(i,j) = poly8(z, DATA_PTR(m_astar_poly[ipoly])); + m_bstar(i,j) = poly8(z, DATA_PTR(m_bstar_poly[ipoly])); + m_cstar(i,j) = poly8(z, DATA_PTR(m_cstar_poly[ipoly])); + } + m_om22(j,i) = m_om22(i,j); + m_astar(j,i) = m_astar(i,j); + m_bstar(j,i) = m_bstar(i,j); + m_cstar(j,i) = m_cstar(i,j); + } + } + m_abc_ok = true; + + // evaluate the temperature-dependent rotational relaxation + // rate + + int k; + doublereal tr, sqtr; + for (k = 0; k < m_nsp; k++) { + tr = m_eps[k]/ m_kbt; + sqtr = m_sqrt_eps_k[k] / m_sqrt_t; + m_rotrelax[k] = fmaxx(1.0,m_zrot[k]) * m_frot_298[k]/Frot(tr, sqtr); + } + + doublereal d; + doublereal c = 1.2*GasConstant*m_temp; + for (k = 0; k < m_nsp; k++) { + d = c * m_visc[k] * m_astar(k,k)/m_mw[k]; + m_bdiff(k,k) = d; + } + + // Calculate the internal heat capacities by subtracting off the translational contributions + /* + * HKM Exploratory comment: + * The translational component is 1.5 + * The rotational component is 1.0 for a linear molecule and 1.5 for a nonlinear molecule + * and zero for a monotomic. + * Chemkin has traditionally subtracted 1.5 here (SAND86-8246). + * The original Dixon-Lewis paper subtracted 1.5 here. + */ + const array_fp& cp = ((IdealGasPhase*)m_thermo)->cp_R_ref(); + for (k = 0; k < m_nsp; k++) { + m_cinternal[k] = cp[k] - 2.5; + } + } + //==================================================================================================================== + /** + * This function returns a Transport data object for a given species. + * + */ + struct GasTransportData MultiTransport:: + getGasTransportData(int kSpecies) + { + struct GasTransportData td; + td.speciesName = m_thermo->speciesName(kSpecies); + + td.geometry = 2; + if (m_crot[kSpecies] == 0.0) { + td.geometry = 0; + } else if (m_crot[kSpecies] == 1.0) { + td.geometry = 1; + } + td.wellDepth = m_eps[kSpecies] / Boltzmann; + td.dipoleMoment = m_dipoleDiag[kSpecies] * 1.0E25 / SqrtTen; + td.diameter = m_diam(kSpecies, kSpecies) * 1.0E10; + td.polarizability = m_alpha[kSpecies] * 1.0E30; + td.rotRelaxNumber = m_zrot[kSpecies]; + + return td; + } } diff --git a/Cantera/src/transport/MultiTransport.h b/Cantera/src/transport/MultiTransport.h index 03bb146ee..a9f878d2d 100644 --- a/Cantera/src/transport/MultiTransport.h +++ b/Cantera/src/transport/MultiTransport.h @@ -1,5 +1,4 @@ /** - * * @file MultiTransport.h * Interface for class MultiTransport * @@ -31,7 +30,7 @@ namespace Cantera { - + //==================================================================================================================== //! Transport solve options enum TRANSOLVE_TYPE { //! Solve the dense matrix via a gmres iteration @@ -39,14 +38,12 @@ namespace Cantera { //! Solve the dense matrix via an LU gauss elimination TRANSOLVE_LU }; - + //==================================================================================================================== class GasTransportParams; - - ///////////////////////////////////////////////////////////// - - /** - * Class L_Matrix is used to represent the "L" matrix. This class - * is used instead of DenseMatrix so that a version of mult can be + //==================================================================================================================== + //! Class L_Matrix is used to represent the "L" matrix. + /*! + * This class is used instead of DenseMatrix so that a version of mult can be * used that knows about the structure of the L matrix, * specifically that the upper-right and lower-left blocks are * zero. @@ -69,19 +66,28 @@ namespace Cantera { }; - - /** - * Class MultiTransport implements multicomponent transport - * properties for ideal gas mixtures. The implementation generally + //==================================================================================================================== + //! Class MultiTransport implements multicomponent transport + //! properties for ideal gas mixtures. + /*! + * + * The implementation generally * follows the procedure outlined in Kee, Coltrin, and Glarborg, * "Theoretical and Practical Aspects of Chemically Reacting Flow - * Modeling," Wiley Interscience. @ingroup transportProps + * Modeling," Wiley Interscience. + * + * @ingroup transportProps */ class MultiTransport : public Transport { + protected: + + //! default constructor + MultiTransport(thermo_t* thermo=0); + public: - + //! Destructor virtual ~MultiTransport(); // overloaded base class methods @@ -97,7 +103,14 @@ namespace Cantera { virtual void getSpeciesViscosities(doublereal* const visc) { updateViscosity_T(); std::copy(m_visc.begin(), m_visc.end(), visc); } + //! Return the thermal diffusion coefficients for the species + /*! + * + * @param dt thermal diffusion coefficients + * (length = m_nsp) + */ virtual void getThermalDiffCoeffs(doublereal* const dt); + virtual doublereal thermalConductivity(); virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d); @@ -118,19 +131,19 @@ namespace Cantera { /*! * Units for the returned fluxes are kg m-2 s-1. * - * @param ndim Number of dimensions in the flux expressions - * @param grad_T Gradient of the temperature - * (length = ndim) - * @param ldx Leading dimension of the grad_X array - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ virtual void getSpeciesFluxes(int ndim, const doublereal* grad_T, @@ -139,20 +152,39 @@ namespace Cantera { int ldf, doublereal* fluxes); - //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic + //! Get the molar diffusional fluxes [kmol/m^2/s] of the species, given the thermodynamic //! state at two nearby points. /*! + * The molar diffusional fluxes are calculated with reference to the mass averaged + * velocity. This is a one-dimensional vector + * * @param state1 Array of temperature, density, and mass * fractions for state 1. * @param state2 Array of temperature, density, and mass * fractions for state 2. * @param delta Distance from state 1 to state 2 (m). + * @param fluxes Output molar fluxes of the species. + * (length = m_nsp) */ virtual void getMolarFluxes(const doublereal* const state1, const doublereal* const state2, const doublereal delta, doublereal* const fluxes); + //! Get the mass diffusional fluxes [kg/m^2/s] of the species, given the thermodynamic + //! state at two nearby points. + /*! + * The specific diffusional fluxes are calculated with reference to the mass averaged + * velocity. This is a one-dimensional vector + * + * @param state1 Array of temperature, density, and mass + * fractions for state 1. + * @param state2 Array of temperature, density, and mass + * fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). + * @param fluxes Output mass fluxes of the species. + * (length = m_nsp) + */ virtual void getMassFluxes(const doublereal* state1, const doublereal* state2, doublereal delta, doublereal* fluxes); @@ -172,7 +204,12 @@ namespace Cantera { /** * @internal */ - virtual bool initGas( GasTransportParams& tr ); + + //! Initialize the transport operator with parameters from GasTransportParams object + /*! + * @param tr input GasTransportParams object + */ + virtual bool initGas(GasTransportParams& tr); /** @@ -214,10 +251,6 @@ namespace Cantera { struct GasTransportData getGasTransportData(int); - protected: - /// default constructor - MultiTransport(thermo_t* thermo=0); - private: // int m_update_transport_T; @@ -249,10 +282,12 @@ namespace Cantera { std::vector > m_poly; - std::vector m_astar_poly; - std::vector m_bstar_poly; - std::vector m_cstar_poly; - std::vector m_om22_poly; + std::vector m_astar_poly; + std::vector m_bstar_poly; + std::vector m_cstar_poly; + std::vector m_om22_poly; + + //! Dense matrix for astar DenseMatrix m_astar; DenseMatrix m_bstar; DenseMatrix m_cstar; @@ -293,6 +328,8 @@ namespace Cantera { vector_fp m_spwork, m_spwork1, m_spwork2, m_spwork3; void correctBinDiffCoeffs(); + + //! Boolean indicating viscosity is up to date bool m_visc_ok; bool m_spvisc_ok; bool m_diff_ok; @@ -301,9 +338,25 @@ namespace Cantera { bool m_lmatrix_soln_ok; int m_mode; - void eval_L0000(const doublereal* x); - void eval_L0010(const doublereal* x); + //! Evalulate the L0000 matrices + /*! + * Evaluate the upper-left block of the L matrix. + * @param x vector of species mole fractions + */ + void eval_L0000(const doublereal* const x); + + //! Evalulate the L0010 matrices + /*! + * @param x vector of species mole fractions + */ + void eval_L0010(const doublereal* const x); + + //! Evalulate the L1000 matrices + /*! + * + */ void eval_L1000(); + void eval_L0100(); void eval_L0001(); void eval_L1010(const doublereal* x); From 6c8835bb84b1757a470d4b35081ac6b8538cfd34 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 15 Jul 2010 15:45:37 +0000 Subject: [PATCH 185/446] doxygen input --- Cantera/src/transport/MultiTransport.cpp | 43 +++++++++++--- Cantera/src/transport/MultiTransport.h | 72 ++++++++++++++---------- 2 files changed, 76 insertions(+), 39 deletions(-) diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index 88659cf64..32076b462 100644 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -1,9 +1,8 @@ /** - * * @file MultiTransport.cpp * Implementation file for class MultiTransport - * - * @ingroup transportProps + */ +/* * * $Author$ * $Date$ @@ -526,10 +525,22 @@ namespace Cantera { } } } - //==================================================================================================================== - - void MultiTransport::getMassFluxes(const doublereal* state1, - const doublereal* state2, doublereal delta, + //==================================================================================================================== + // Get the mass diffusional fluxes [kg/m^2/s] of the species, given the thermodynamic + // state at two nearby points. + /* + * The specific diffusional fluxes are calculated with reference to the mass averaged + * velocity. This is a one-dimensional vector + * + * @param state1 Array of temperature, density, and mass + * fractions for state 1. + * @param state2 Array of temperature, density, and mass + * fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). + * @param fluxes Output mass fluxes of the species. + * (length = m_nsp) + */ + void MultiTransport::getMassFluxes(const doublereal* state1, const doublereal* state2, doublereal delta, doublereal* fluxes) { double* x1 = DATA_PTR(m_spwork1); @@ -652,6 +663,20 @@ namespace Cantera { } } //==================================================================================================================== + // Set the solution method for inverting the L matrix + /* + * @param method enum TRANSOLVE_TYPE Either use direct or TRANSOLVE_GMRES + */ + void MultiTransport::setSolutionMethod(TRANSOLVE_TYPE method) { + if (method == TRANSOLVE_GMRES) m_gmres = true; + else m_gmres = false; + } + //==================================================================================================================== + void MultiTransport::setOptions_GMRES(int m, doublereal eps) { + if (m > 0) m_mgmres = m; + if (eps > 0.0) m_eps_gmres = eps; + } + //==================================================================================================================== void MultiTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { int i,j; @@ -994,7 +1019,7 @@ namespace Cantera { } } //==================================================================================================================== - /** + /* * This function returns a Transport data object for a given species. * */ @@ -1018,5 +1043,5 @@ namespace Cantera { return td; } - + //==================================================================================================================== } diff --git a/Cantera/src/transport/MultiTransport.h b/Cantera/src/transport/MultiTransport.h index a9f878d2d..754c96fcf 100644 --- a/Cantera/src/transport/MultiTransport.h +++ b/Cantera/src/transport/MultiTransport.h @@ -51,16 +51,24 @@ namespace Cantera { */ class L_Matrix : public DenseMatrix { public: + + //! default constructor L_Matrix() {} + + //! destructor virtual ~L_Matrix(){} - /** + //! Conduct a multiply with the Dense matrix + /*! * This method is used by GMRES to multiply the L matrix by a * vector b. The L matrix has a 3x3 block structure, where each * block is a K x K matrix. The elements of the upper-right and * lower-left blocks are all zero. This method is defined so * that the multiplication only involves the seven non-zero * blocks. + * + * @param b + * @param prod */ virtual void mult(const doublereal* b, doublereal* prod) const; }; @@ -83,6 +91,9 @@ namespace Cantera { protected: //! default constructor + /*! + * @param thermo Optional parameter for the pointer to the ThermoPhase object + */ MultiTransport(thermo_t* thermo=0); public: @@ -189,17 +200,18 @@ namespace Cantera { const doublereal* state2, doublereal delta, doublereal* fluxes); - virtual void setSolutionMethod(TRANSOLVE_TYPE method) { - if (method == TRANSOLVE_GMRES) m_gmres = true; - else m_gmres = false; - } + //! Set the solution method for inverting the L matrix + /*! + * @param method enum TRANSOLVE_TYPE Either use direct or TRANSOLVE_GMRES + */ + virtual void setSolutionMethod(TRANSOLVE_TYPE method); - virtual void setOptions_GMRES(int m, doublereal eps) { - if (m > 0) m_mgmres = m; - if (eps > 0.0) m_eps_gmres = eps; - } - - void save(std::string outfile); + //! Set the options for the GMRES solution + /*! + * @param m set the mgmres param + * @param eps Set the eps parameter + */ + virtual void setOptions_GMRES(int m, doublereal eps); /** * @internal @@ -241,31 +253,25 @@ namespace Cantera { friend class TransportFactory; - /** - * Return a structure containing all of the pertinent parameters - * about a species that was used to construct the Transport - * properties in this object. - * - * @param k Species number to obtain the properties from. + + //! Return a structure containing all of the pertinent parameters + //! about a species that was used to construct the Transport properties in this object + /*! + * @param k Species index */ - struct GasTransportData getGasTransportData(int); - + struct GasTransportData getGasTransportData(int k); private: - // int m_update_transport_T; - // int m_update_transport_C; - // int m_update_spvisc_T; - // int m_update_visc_T; - // int m_update_diff_T; - // int m_update_thermal_T; + doublereal m_diff_tlast; + doublereal m_spvisc_tlast; + doublereal m_visc_tlast; + doublereal m_thermal_tlast; - doublereal m_diff_tlast, m_spvisc_tlast, m_visc_tlast, - m_thermal_tlast; - - // mixture attributes + //! Number of species in the phase int m_nsp; - doublereal m_tmin, m_tmax; + doublereal m_tmin; + doublereal m_tmax; vector_fp m_mw; // polynomial fits @@ -289,8 +295,14 @@ namespace Cantera { //! Dense matrix for astar DenseMatrix m_astar; + + //! Dense matrix for bstar DenseMatrix m_bstar; + + //! Dense matrix for cstar DenseMatrix m_cstar; + + //! Dense matrix for omega22 DenseMatrix m_om22; DenseMatrix m_phi; // viscosity weighting functions From e759ea1a4b738218b05f79988a9e5145a9bd3a83 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 16 Jul 2010 16:25:32 +0000 Subject: [PATCH 186/446] Added copy constructor and assignment operator --- Cantera/cxx/include/Interface.h | 173 +++++++++++++++++++++----------- 1 file changed, 112 insertions(+), 61 deletions(-) diff --git a/Cantera/cxx/include/Interface.h b/Cantera/cxx/include/Interface.h index 0734fd233..48fe96479 100644 --- a/Cantera/cxx/include/Interface.h +++ b/Cantera/cxx/include/Interface.h @@ -15,77 +15,128 @@ #include "Cantera.h" #include "thermo.h" #include "kinetics.h" -// #include "kernel/SurfPhase.h" -// #include "kernel/InterfaceKinetics.h" -// #include "kernel/importKinetics.h" + /** * This namespace is used for the Cantera C++ user interface. */ namespace Cantera_CXX { - /** - * An interface between multiple bulk phases. This class is - * defined mostly for convenience. It inherits both from - * Cantera::SurfPhase and Cantera::InterfaceKinetics. It therefore - * represents a surface phase, and also acts as the kinetics - * manager to manage reaction occurring on the surface, possibly - * involving species from other phases. + + //! An interface between multiple bulk phases. + /*! + * This class isdefined mostly for convenience. It inherits both from + * Cantera::SurfPhase and Cantera::InterfaceKinetics. It therefore + * represents a surface phase, and also acts as the kinetics + * manager to manage reactions occurring on the surface, possibly + * involving species from other phases. + */ + class Interface : + public Cantera::SurfPhase, + public Cantera::InterfaceKinetics + { + public: + + + //! Constructor. + /*! + * Construct an Interface instance from a specification in an input file. + * + * @param infile. Cantera input file in CTI or CTML format. + * @param id Identification string to distinguish between + * multiple definitions within one input file. + * @param otherPhases Neighboring phases that may participate in the + * reactions on this interface. Don't include the + * surface phase + * + * @deprecated + * While it's convenient to have the surface phase and the interfacial reaction + * together, this class doesn't satisfy the primary issue, which is one + * of instantiation of all the ThermoPhase classes that accompany a + * surface reaction. This is accomplished by the PhaseList class along with + * the ReactingSurface class. These classes will be migrated into Cantera + * soon. */ - class Interface : - public Cantera::SurfPhase, - public Cantera::InterfaceKinetics + Interface(std::string infile, std::string id, + std::vector otherPhases) : + m_ok(false), + m_r(0) { - public: - - /** - * Constructor. Construct an Interface instance from - * a specification in an input file. - * @param infile. Cantera input file in CTI or CTML format. - * @param id Identification string to distinguish between - * multiple definitions within one input file. - * @param phases Neighboring phases that may participate in the - * reactions on this interface. - */ - Interface(std::string infile, std::string id, - std::vector phases) - : m_ok(false), m_r(0) { - m_r = Cantera::get_XML_File(infile); - if (id == "-") id = ""; - - Cantera::XML_Node* x = Cantera::get_XML_Node("#"+id, m_r); - if (!x) - throw Cantera::CanteraError("Interface","error in get_XML_Node"); - - Cantera::importPhase(*x, this); - phases.push_back(this); - Cantera::importKinetics(*x, phases, this); - m_ok = true; - } - - /// Destructor. Does nothing. - virtual ~Interface() {} - - bool operator!() { return !m_ok;} - bool ready() const { return m_ok; } - - protected: - bool m_ok; - Cantera::XML_Node* m_r; - - private: - }; - - /** - * Import an instance of class Interface from a specification in an - * input file. This is the preferred method to create an Interface - * instance. - */ - inline Interface* importInterface(std::string infile, std::string id, - std::vector phases) { - return new Interface(infile, id, phases); + m_r = Cantera::get_XML_File(infile); + if (id == "-") id = ""; + + Cantera::XML_Node* x = Cantera::get_XML_Node("#"+id, m_r); + if (!x) { + throw Cantera::CanteraError("Interface","error in get_XML_Node"); + } + Cantera::importPhase(*x, this); + otherPhases.push_back(this); + Cantera::importKinetics(*x, otherPhases, this); + m_ok = true; } + //! Copy Constructor + /*! + * @param ii Interface object to be copied. + */ + Interface(const Interface& ii) : + Cantera::SurfPhase(ii), + Cantera::InterfaceKinetics(ii), + m_ok(ii.m_ok), + m_r(ii.m_r) + { + } + + //! Assignment operator + /*! + * @param right Interface object to be copied. + */ + Interface & operator=(const Interface &right) { + if (this == &right) return *this; + Cantera::SurfPhase::operator=(right); + Cantera::InterfaceKinetics::operator=(right); + m_ok = right.m_ok; + m_r = right.m_r; + return *this; + } + + //! Destructor. Does nothing. + virtual ~Interface() { + } + + //! Not operator + bool operator!() { + return !m_ok; + } + + //! return whether the object has been instantiated + /*! + * @return Returns a bool. + */ + bool ready() const { + return m_ok; + } + + protected: + + //! Flag indicating that the object has been instantiated + bool m_ok; + + //! XML_Node pointer to the XML File object that contains the Surface and the Interfacial Reaction object + //! description + Cantera::XML_Node* m_r; + + }; + + + //! Import an instance of class Interface from a specification in an input file. + /*! + * This is the preferred method to create an Interface instance. + */ + Interface* importInterface(std::string infile, std::string id, std::vector phases) { + return new Interface(infile, id, phases); + } + } From 6b3912e1dd05720e4f47bf58dfbb28d49ae5a4ac Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 16 Jul 2010 21:25:27 +0000 Subject: [PATCH 187/446] Moved the CanteraError constructor to a .cpp file. --- Cantera/src/base/ctexceptions.h | 4 ++-- Cantera/src/base/misc.cpp | 9 +++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/Cantera/src/base/ctexceptions.h b/Cantera/src/base/ctexceptions.h index 1c29cbd36..1a7d9c0f4 100644 --- a/Cantera/src/base/ctexceptions.h +++ b/Cantera/src/base/ctexceptions.h @@ -90,14 +90,14 @@ namespace Cantera { CanteraError(std::string procedure, std::string msg); //! Destructor for base class does nothing - virtual ~CanteraError() throw() {} + virtual ~CanteraError() throw(); protected: //! Empty base constructor is made protected so that it may be used only by //! inherited classes. /*! * We want to discourage throwing an error containing no information. */ - CanteraError() {} + CanteraError(); }; //! Array size error. diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index 8750abe59..ef1ef6507 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -1509,6 +1509,15 @@ protected: CanteraError::CanteraError(std::string proc, std::string msg) { app()->addError(proc, msg); } + + CanteraError::CanteraError() + { + } + + CanteraError::~CanteraError() throw() + { + } + ArraySizeError::ArraySizeError(std::string proc, int sz, int reqd) : CanteraError(proc, "Array size ("+int2str(sz)+ From 8eea4732501af74f2880e507659c5e2b0f623d15 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 16 Jul 2010 21:47:21 +0000 Subject: [PATCH 188/446] doxygen update only - got rid of error messages. --- Cantera/src/transport/MMCollisionInt.cpp | 34 ++++--- Cantera/src/transport/MMCollisionInt.h | 110 +++++++++++++++++++++-- 2 files changed, 125 insertions(+), 19 deletions(-) diff --git a/Cantera/src/transport/MMCollisionInt.cpp b/Cantera/src/transport/MMCollisionInt.cpp index 42e6c267a..d4949529a 100644 --- a/Cantera/src/transport/MMCollisionInt.cpp +++ b/Cantera/src/transport/MMCollisionInt.cpp @@ -235,9 +235,17 @@ namespace Cantera { { } //==================================================================================================================== - - void MMCollisionInt::init(XML_Writer* xml, - doublereal tsmin, doublereal tsmax, int log_level) { + // Initialize the object for calculation + /* + * + * @param xml Pointer to the log file that will receive the debug output + * messages + * @param tsmin Minimum value of Tstar to carry out the fitting + * @param tsmax Maximum value of Tstar to carry out the fitting + * @param loglevel Set the loglevel for the object. The default + * loglevel is zero, indicating no output. + */ + void MMCollisionInt::init(XML_Writer* xml, doublereal tsmin, doublereal tsmax, int log_level) { #ifdef DEBUG_MODE if (!xml) { throw CanteraError("MMCollisionInt::init", "pointer to xml file is zero"); @@ -355,11 +363,9 @@ namespace Cantera { #endif } } + //==================================================================================================================== - - - doublereal MMCollisionInt::fitDelta(int table, int ntstar, - int degree, doublereal* c) { + doublereal MMCollisionInt::fitDelta(int table, int ntstar, int degree, doublereal* c) { vector_fp w(8); doublereal* begin = 0; int ndeg=0; @@ -378,6 +384,7 @@ namespace Cantera { w[0] = -1.0; return polyfit(8, delta, begin, DATA_PTR(w), degree, ndeg, 0.0, c); } + //==================================================================================================================== doublereal MMCollisionInt::omega22(double ts, double deltastar) { int i; @@ -398,6 +405,7 @@ namespace Cantera { return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, DATA_PTR(values)); } + //==================================================================================================================== doublereal MMCollisionInt::astar(double ts, double deltastar) { int i; @@ -418,6 +426,7 @@ namespace Cantera { return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, DATA_PTR(values)); } + //==================================================================================================================== doublereal MMCollisionInt::bstar(double ts, double deltastar) { @@ -439,7 +448,7 @@ namespace Cantera { return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, DATA_PTR(values)); } - + //==================================================================================================================== doublereal MMCollisionInt::cstar(double ts, double deltastar) { int i; @@ -458,8 +467,10 @@ namespace Cantera { else values[i-i1] = poly5(deltastar, DATA_PTR(m_cpoly[i])); } return quadInterp(log(ts), DATA_PTR(m_logTemp) + i1, - DATA_PTR(values)); } + DATA_PTR(values)); + } + //==================================================================================================================== void MMCollisionInt::fit_omega22(ostream& logfile, int degree, doublereal deltastar, doublereal* o22) @@ -488,6 +499,7 @@ namespace Cantera { } #endif } + //==================================================================================================================== void MMCollisionInt::fit(ostream& logfile, int degree, doublereal deltastar, doublereal* a, doublereal* b, doublereal* c) @@ -551,9 +563,9 @@ namespace Cantera { } #endif } - + //==================================================================================================================== } // namespace - +//====================================================================================================================== diff --git a/Cantera/src/transport/MMCollisionInt.h b/Cantera/src/transport/MMCollisionInt.h index 4bc0c3e17..0db470d6b 100644 --- a/Cantera/src/transport/MMCollisionInt.h +++ b/Cantera/src/transport/MMCollisionInt.h @@ -28,14 +28,25 @@ namespace Cantera { class XML_Writer; + + //! Error handler class for collision integrals + /*! + * This class doesn't + */ class MMCollisionIntError { public: + + //! Constructor + /*! + * @param logfile ostream reference for writing out errors + * @param msg error message + */ MMCollisionIntError(std::ostream& logfile, std::string msg) { logfile << "#### ERROR ####" << std::endl; logfile << "MMCollisionInt: " << msg << std::endl; std::cerr << "Error in fitting collision integrals. " - << "Execution terminated." << std::endl - << "See transport log file for more information." << std::endl; + << "Execution terminated." << std::endl + << "See transport log file for more information." << std::endl; } }; @@ -70,44 +81,127 @@ namespace Cantera { * @param loglevel Set the loglevel for the object. The default * loglevel is zero, indicating no output. */ - void init(XML_Writer* xml, doublereal tsmin, - doublereal tsmax, int loglevel = 0); + void init(XML_Writer* xml, doublereal tsmin, doublereal tsmax, int loglevel = 0); - + //! omega22 + /*! + * @param ts + * @param deltastar + */ doublereal omega22(double ts, double deltastar); + + //! astar + /*! + * @param ts + * @param deltastar + */ doublereal astar(double ts, double deltastar); + + //! bstar + /*! + * @param ts + * @param deltastar + */ doublereal bstar(double ts, double deltastar); + + //! cstar + /*! + * @param ts + * @param deltastar + */ doublereal cstar(double ts, double deltastar); + //! fit + /*! + * @param logfile + * @param degree + * @param deltastar + * @param astar + * @param bstar + * @param cstar + */ void fit(std::ostream& logfile, int degree, doublereal deltastar, doublereal* astar, doublereal* bstar, doublereal* cstar); + //! fit_omega22 + /*! + * @param logfile + * @param degree + * @param deltastar + * @param om22 + */ void fit_omega22(std::ostream& logfile, int degree, doublereal deltastar, doublereal* om22); + + //! omega11 + /*! + * @param ts + * @param deltastar + */ doublereal omega11(double ts, double deltastar) { return omega22(ts, deltastar)/astar(ts, deltastar); } private: - doublereal fitDelta(int table, int ntstar, - int degree, doublereal* c); + //! Fit delta + /*! + * @param table + * @param ntstar + * @param degree + * @param c C is probable the output vector + * + * @return + */ + doublereal fitDelta(int table, int ntstar, int degree, doublereal* c); + //! m_o22poly std::vector m_o22poly; + + //! m_apoly std::vector m_apoly; + //! m_bpoly std::vector m_bpoly; + + //! m_cpoly std::vector m_cpoly; + //! delta static doublereal delta[8]; + + //! tstar22 static doublereal tstar22[37]; + + //! Table of omega22 values from MM static doublereal omega22_table[37*8]; + + //! tstar + /*! + * table of tstar values + */ static doublereal tstar[39]; + + //! astar table from MM static doublereal astar_table[39*8]; + + //! bstar table from MM static doublereal bstar_table[39*8]; + + //! cstar table from MM static doublereal cstar_table[39*8]; + //! Log temp vector_fp m_logTemp; - int m_nmin, m_nmax; + + //! nmin + int m_nmin; + + //! nmax + int m_nmax; + + //! XML_Writer pointer XML_Writer* m_xml; + + //! loglevel int m_loglevel; }; } From a0263339d91d5dbd6a1b5fa7b558cb588b0d16fa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 18 Jul 2010 19:39:47 +0000 Subject: [PATCH 189/446] doxygen update - Worked on beating down doxygen warnings. --- Cantera/src/transport/MixTransport.cpp | 48 ++++++++++++-------- Cantera/src/transport/MixTransport.h | 61 +++++++++++++++++++++----- 2 files changed, 80 insertions(+), 29 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 4f70664af..56580c50d 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -180,6 +180,7 @@ namespace Cantera { } + //=================================================================================================================== void MixTransport::getMobilities(doublereal* const mobil) { int k; getMixDiffCoeffs(DATA_PTR(m_spwork)); @@ -188,16 +189,25 @@ namespace Cantera { mobil[k] = c1 * m_spwork[k] * m_thermo->charge(k); } } - - - /****************** thermal conductivity **********************/ - - /** + //=================================================================================================================== + // Returns the mixture thermal conductivity (W/m /K) + /* * The thermal conductivity is computed from the following mixture rule: - * \[ - * \lambda = 0.5 \left( \sum_k X_k \lambda_k - * + \frac{1}{\sum_k X_k/\lambda_k}\right) - * \] + * \f[ + * \lambda = 0.5 \left( \sum_k X_k \lambda_k + \frac{1}{\sum_k X_k/\lambda_k} \right) + * \f] + * + * It's used to compute the flux of energy due to a thermal gradient + * + * \f[ + * j_T = - \lambda \nabla T + * \f] + * + * The flux of energy has units of energy (kg m2 /s2) per second per area. + * + * The units of lambda are W / m K which is equivalent to kg m / s^3 K. + * + * @return Returns the mixture thermal conductivity, with units of W/m/K */ doublereal MixTransport::thermalConductivity() { int k; @@ -216,8 +226,7 @@ namespace Cantera { } return m_lambda; } - - + //=================================================================================================================== /****************** thermal diffusion coefficients ************/ /** @@ -270,14 +279,16 @@ namespace Cantera { } } } - - /** - * Mixture-averaged diffusion coefficients [m^2/s]. - * - * For the single species case or the pure fluid case - * the routine returns the self-diffusion coefficient. + //=========================================================================================================== + // Mixture-averaged diffusion coefficients [m^2/s]. + /* + * Returns the mixture averaged diffusion coefficients for a gas. + * Note, for the single species case or the pure fluid case the routine returns the self-diffusion coefficient. * This is need to avoid a Nan result in the formula * below. + * + * @param d Output Vector of diffusion coefficients for each species (m^2/s) + * length m_nsp */ void MixTransport::getMixDiffCoeffs(doublereal* const d) { @@ -310,8 +321,7 @@ namespace Cantera { } } } - - + //=========================================================================================================== /** * @internal This is called whenever a transport property is * requested from ThermoSubstance if the temperature has changed diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 8ef0ef52a..686cc555d 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -66,20 +66,52 @@ namespace Cantera { */ virtual void getThermalDiffCoeffs(doublereal* const dt); - //! returns the mixture thermal conductivity + //! Returns the mixture thermal conductivity (W/m /K) + /*! + * The thermal conductivity is computed from the following mixture rule: + * \f[ + * \lambda = 0.5 \left( \sum_k X_k \lambda_k + \frac{1}{\sum_k X_k/\lambda_k} \right) + * \f] + * + * It's used to compute the flux of energy due to a thermal gradient + * + * \f[ + * j_T = - \lambda \nabla T + * \f] + * + * The flux of energy has units of energy (kg m2 /s2) per second per area. + * + * The units of lambda are W / m K which is equivalent to kg m / s^3 K. + * + * @return Returns the mixture thermal conductivity, with units of W/m/K + */ virtual doublereal thermalConductivity(); virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d); - //! Mixture-averaged diffusion coefficients [m^2/s]. + //! Returns the Mixture-averaged diffusion coefficients [m^2/s]. /*! - * For the single species case or the pure fluid case - * the routine returns the self-diffusion coefficient. - * This is need to avoid a Nan result in the formula - * below. - */ + * Returns the mixture averaged diffusion coefficients for a gas, appropriate for calculating the + * mass averged diffusive flux with respect to the mass averaged velocity using gradients of the + * mole fraction. + * Note, for the single species case or the pure fluid case the routine returns the self-diffusion coefficient. + * This is need to avoid a Nan result in the formula below. + * + * This is Eqn. 12.180 from "Chemicaly Reacting Flow" + * + * \f[ + * D_{km}' = \frac{\left( \bar{M} - X_k M_k \right)}{ \bar{\qquad M \qquad } } {\left( \sum_{j \ne k} \frac{X_j}{D_{kj}} \right) }^{-1} + * \f] + * + * + * + * @param d Output Vector of mixture diffusion coefficients, \f$ D_{km}' \f$ , for each species (m^2/s). + * length m_nsp + */ virtual void getMixDiffCoeffs(doublereal* const d); + + virtual void getMobilities(doublereal* const mobil); virtual void update_T(); virtual void update_C(); @@ -146,7 +178,14 @@ namespace Cantera { // mixture attributes int m_nsp; - doublereal m_tmin, m_tmax; + + //! Minimum value of the temperature that this transport parameterization is valid + doublereal m_tmin; + + //! Maximum value of the temperature that this transport parameterization is valid + doublereal m_tmax; + + //! Local copy of the species molecular weights. vector_fp m_mw; // polynomial fits @@ -173,8 +212,10 @@ namespace Cantera { DenseMatrix m_cstar; DenseMatrix m_om22; - DenseMatrix m_phi; // viscosity weighting functions - DenseMatrix m_wratjk, m_wratkj1; + //! Viscosity Weighting Functions + DenseMatrix m_phi; + DenseMatrix m_wratjk; + DenseMatrix m_wratkj1; vector_fp m_zrot; vector_fp m_crot; From 60678fc85664c5126aad7b61abe2943863150259 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 18 Jul 2010 20:36:47 +0000 Subject: [PATCH 190/446] doxygen updates for LatticePhase It's now complete --- Cantera/src/thermo/LatticePhase.cpp | 67 ++++++++++++++++++---- Cantera/src/thermo/LatticePhase.h | 88 ++++++++++++----------------- 2 files changed, 93 insertions(+), 62 deletions(-) diff --git a/Cantera/src/thermo/LatticePhase.cpp b/Cantera/src/thermo/LatticePhase.cpp index 1a93923c4..f86a26823 100644 --- a/Cantera/src/thermo/LatticePhase.cpp +++ b/Cantera/src/thermo/LatticePhase.cpp @@ -289,7 +289,48 @@ namespace Cantera { vbar[k] = vv; } } - + //======================================================================================================= + // Returns the vector of nondimensional Enthalpies of the reference state at the current temperature + // of the solution and the reference pressure for the phase. + /* + * @return Output vector of nondimensional reference state Enthalpies of the species. + * Length: m_kk + */ + const array_fp& LatticePhase::enthalpy_RT_ref() const { + _updateThermo(); + return m_h0_RT; + } + //======================================================================================================= + // Returns a reference to the dimensionless reference state Gibbs free energy vector. + /* + * This function is part of the layer that checks/recalculates the reference + * state thermo functions. + */ + const array_fp& LatticePhase::gibbs_RT_ref() const { + _updateThermo(); + return m_g0_RT; + } + //======================================================================================================= + // Returns a reference to the dimensionless reference state Entropy vector. + /* + * This function is part of the layer that checks/recalculates the reference + * state thermo functions. + */ + const array_fp& LatticePhase::entropy_R_ref() const { + _updateThermo(); + return m_s0_R; + } + //======================================================================================================= + // Returns a reference to the dimensionless reference state Heat Capacity vector. + /* + * This function is part of the layer that checks/recalculates the reference + * state thermo functions. + */ + const array_fp& LatticePhase::cp_R_ref() const { + _updateThermo(); + return m_cp0_R; + } + //======================================================================================================= void LatticePhase::initThermo() { m_kk = nSpecies(); m_mm = nElements(); @@ -306,8 +347,12 @@ namespace Cantera { m_s0_R.resize(leng); setMolarDensity(m_molar_density); } - - + //===================================================================================================== + // Update the species reference state thermodynamic functions + /* + * The polynomials for the standard state functions are only + * reevalulated if the temperature has changed. + */ void LatticePhase::_updateThermo() const { doublereal tnow = temperature(); if (fabs(molarDensity() - m_molar_density)/m_molar_density > 0.0001) { @@ -315,33 +360,33 @@ namespace Cantera { +fp2str(m_molar_density)+" to "+fp2str(molarDensity())); } if (m_tlast != tnow) { - m_spthermo->update(tnow, &m_cp0_R[0], &m_h0_RT[0], - &m_s0_R[0]); + m_spthermo->update(tnow, &m_cp0_R[0], &m_h0_RT[0], &m_s0_R[0]); m_tlast = tnow; - int k; - for (k = 0; k < m_kk; k++) { + for (int k = 0; k < m_kk; k++) { m_g0_RT[k] = m_h0_RT[k] - m_s0_R[k]; } m_tlast = tnow; } } - + //===================================================================================================== void LatticePhase::setParameters(int n, doublereal* const c) { m_molar_density = c[0]; setMolarDensity(m_molar_density); } - + //===================================================================================================== void LatticePhase::getParameters(int &n, doublereal * const c) const { double d = molarDensity(); c[0] = d; n = 1; } - + //===================================================================================================== void LatticePhase::setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model", "Lattice"); m_molar_density = getFloat(eosdata, "site_density", "toSI"); m_vacancy = getChildValue(eosdata, "vacancy_species"); } + //===================================================================================================== } - +//======================================================================================================= #endif + diff --git a/Cantera/src/thermo/LatticePhase.h b/Cantera/src/thermo/LatticePhase.h index 093caece3..b2622955a 100644 --- a/Cantera/src/thermo/LatticePhase.h +++ b/Cantera/src/thermo/LatticePhase.h @@ -1,7 +1,6 @@ /** * @file LatticePhase.h - * Header for a simple thermodynamics model of a bulk phase - * derived from ThermoPhase, + * Header for a simple thermodynamics model of a bulk phase derived from ThermoPhase, * assuming a lattice of solid atoms * (see \ref thermoprops and class \link Cantera::LatticePhase LatticePhase\endlink). * @@ -255,7 +254,7 @@ namespace Cantera { * @ingroup thermoprops * */ - class LatticePhase : public ThermoPhase { + class LatticePhase : public ThermoPhase { public: @@ -301,34 +300,33 @@ namespace Cantera { */ ThermoPhase *duplMyselfAsThermoPhase() const; - /* - * @param infile XML file containing the description of the - * phase - * - * @param id Optional parameter identifying the name of the - * phase. If none is given, the first XML - * phase element will be used. - */ + //! Import and initialize a %LatticePhase phase specification from an XML tree into the current object. + /*! + * @param phaseNode XML file containing the description of the phase + * + * @param idTarget Optional parameter identifying the name of the + * phase. If none is given, the first XML phase element is used. + */ void constructPhaseXML(XML_Node& phaseNode, std::string idTarget); - /* - * constructPhaseFile - * - * - * This routine is a precursor to constructPhaseXML(XML_Node*) - * routine, which does most of the work. - * - * @param inputFile XML file containing the description of the - * phase - * - * @param id Optional parameter identifying the name of the - * phase. If none is given, the first XML - * phase element will be used. - */ + //! Initialization of a %LatticePhase phase using an xml file + /*! + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ void constructPhaseFile(std::string inputFile, std::string id); //! Equation of state flag. Returns the value cLattice - virtual int eosType() const { return cLattice; } + virtual int eosType() const { + return cLattice; + } /** * @name Molar Thermodynamic Properties of the Solution ------------------------ @@ -695,40 +693,28 @@ namespace Cantera { * Enthalpies of the species. * Length: m_kk */ - const array_fp& enthalpy_RT_ref() const { - _updateThermo(); - return m_h0_RT; - } + const array_fp& enthalpy_RT_ref() const; //! Returns a reference to the dimensionless reference state Gibbs free energy vector. /*! * This function is part of the layer that checks/recalculates the reference * state thermo functions. */ - const array_fp& gibbs_RT_ref() const { - _updateThermo(); - return m_g0_RT; - } + const array_fp& gibbs_RT_ref() const; //! Returns a reference to the dimensionless reference state Entropy vector. /*! * This function is part of the layer that checks/recalculates the reference * state thermo functions. */ - const array_fp& entropy_R_ref() const { - _updateThermo(); - return m_s0_R; - } + const array_fp& entropy_R_ref() const; //! Returns a reference to the dimensionless reference state Heat Capacity vector. /*! * This function is part of the layer that checks/recalculates the reference * state thermo functions. */ - const array_fp& cp_R_ref() const { - _updateThermo(); - return m_cp0_R; - } + const array_fp& cp_R_ref() const; //@} /// @name Utilities for Initialization of the Object @@ -827,29 +813,29 @@ namespace Cantera { doublereal m_p0; //! Current value of the temperature (Kelvin) - mutable doublereal m_tlast; + mutable doublereal m_tlast; //! Reference state enthalpies / RT - mutable array_fp m_h0_RT; + mutable array_fp m_h0_RT; //! Temporary storage for the reference state heat capacities - mutable array_fp m_cp0_R; + mutable array_fp m_cp0_R; //! Temporary storage for the reference state gibbs energies - mutable array_fp m_g0_RT; + mutable array_fp m_g0_RT; - //! Temporary storage for the reference state entropies - mutable array_fp m_s0_R; + //! Temporary storage for the reference state entropies at the current temperature + mutable array_fp m_s0_R; //! Current value of the pressure (Pa) - doublereal m_press; + doublereal m_press; //! String name for the species which represents a vacency //! in the lattice /*! * This string is currently unused */ - std::string m_vacancy; + std::string m_vacancy; //! Molar density of the lattice solid /*! @@ -857,7 +843,7 @@ namespace Cantera { * * units are kmol m-3 */ - doublereal m_molar_density; + doublereal m_molar_density; private: From 942fa9c2ec9820fb3cfe0ade591f017f608a2cbf Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 18 Jul 2010 21:21:38 +0000 Subject: [PATCH 191/446] doxygen updates for LatticeSolidPhase. There is still a lot of work to be done for this object, including validation examples. --- Cantera/src/thermo/IdealSolidSolnPhase.cpp | 8 +-- Cantera/src/thermo/LatticeSolidPhase.cpp | 30 +++++++-- Cantera/src/thermo/LatticeSolidPhase.h | 72 +++++++++++++++++----- Cantera/src/thermo/State.h | 23 +++---- 4 files changed, 96 insertions(+), 37 deletions(-) diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.cpp b/Cantera/src/thermo/IdealSolidSolnPhase.cpp index b8ba0af30..d297ca6f4 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.cpp +++ b/Cantera/src/thermo/IdealSolidSolnPhase.cpp @@ -57,7 +57,7 @@ namespace Cantera { } constructPhaseFile(inputFile, id); } - + //==================================================================================================================== IdealSolidSolnPhase::IdealSolidSolnPhase(XML_Node& root, std::string id, int formGC) : ThermoPhase(), @@ -75,12 +75,12 @@ namespace Cantera { } constructPhaseXML(root, id); } - + //==================================================================================================================== IdealSolidSolnPhase::IdealSolidSolnPhase(const IdealSolidSolnPhase &b) { *this = b; } - + //==================================================================================================================== IdealSolidSolnPhase& IdealSolidSolnPhase:: operator=(const IdealSolidSolnPhase &b) { @@ -117,7 +117,7 @@ namespace Cantera { IdealSolidSolnPhase *ii = new IdealSolidSolnPhase(*this); return (ThermoPhase*) ii; } - +//==================================================================================================================== /** * Equation of state flag. Returns the value cIdealGas, defined * in mix_defs.h. diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index f4f2a911e..378ac3313 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -34,7 +34,6 @@ namespace Cantera { // Base empty constructor LatticeSolidPhase::LatticeSolidPhase() : m_mm(0), - m_kk(0), m_tlast(0.0), m_press(-1.0), m_molar_density(0.0), @@ -50,7 +49,6 @@ namespace Cantera { */ LatticeSolidPhase::LatticeSolidPhase(const LatticeSolidPhase &right) : m_mm(0), - m_kk(0), m_tlast(0.0), m_press(-1.0), m_molar_density(0.0), @@ -70,7 +68,6 @@ namespace Cantera { if (&right != this) { ThermoPhase::operator=(right); m_mm = right.m_mm; - m_kk = right.m_kk; m_tlast = right.m_tlast; m_press = right.m_press; m_molar_density = right.m_molar_density; @@ -180,7 +177,17 @@ namespace Cantera { } //==================================================================================================================== - void LatticeSolidPhase::setMoleFractions(const doublereal* x) { + // Set the mole fractions to the specified values, and then + // normalize them so that they sum to 1.0 for each of the subphases + /* + * + * @param x Input vector of mole fractions. There is no restriction + * on the sum of the mole fraction vector. Internally, + * this object will pass portions of this vector to the sublattices which assume that the portions + * individually sum to one. + * Length is m_kk. + */ + void LatticeSolidPhase::setMoleFractions(const doublereal* const x) { int nsp, strt = 0; doublereal sum = 0.0; for (int n = 0; n < m_nlattice; n++) { @@ -197,7 +204,14 @@ namespace Cantera { State::setMoleFractions(DATA_PTR(m_x)); } //==================================================================================================================== - void LatticeSolidPhase::getMoleFractions(doublereal* x) const { + // Get the species mole fraction vector. + /* + * On output the mole fraction vector will sum to one for each of the subphases which make up this phase. + * + * @param x On return, x contains the mole fractions. Must have a + * length greater than or equal to the number of species. + */ + void LatticeSolidPhase::getMoleFractions(doublereal* const x) const { int nsp, strt = 0; State::getMoleFractions(x); doublereal sum; @@ -249,6 +263,12 @@ namespace Cantera { } } //==================================================================================================================== + // Add in species from Slave phases + /* + * This hook is used for cSS_CONVENTION_SLAVE phases + * + * @param phaseNode XML_Node for the current phase + */ void LatticeSolidPhase::installSlavePhases(Cantera::XML_Node* phaseNode) { int m, k; diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index f5abcee4b..e05c81874 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -37,10 +37,10 @@ namespace Cantera { //! A phase that is comprised of an additive combination of other lattice phases /*! * This is the main way Cantera describes semiconductors and other solid phases. - * This Thermophase object calculates its properties as a sum over other LatticePhase objects. Each of the %LatticePhase + * This %ThermoPhase object calculates its properties as a sum over other LatticePhase objects. Each of the %LatticePhase * objects is a ThermoPhase object by itself. * - * The sum over the LatticePhase objects is carried out by weighting each LatticePhase object + * The sum over the %LatticePhase objects is carried out by weighting each %LatticePhase object * value with the molarDensity of the LatticePhase. Then the resulting quantity is divided by * the molar density of the total compound. The LatticeSolidPhase object therefore only contains a * listing of the number of Lattice Phases @@ -237,18 +237,20 @@ namespace Cantera { * * @param x Input vector of mole fractions. There is no restriction * on the sum of the mole fraction vector. Internally, - * this object will normalize this vector before - * storring its contents. + * this object will pass portions of this vector to the sublattices which assume that the portions + * individually sum to one. * Length is m_kk. */ - virtual void setMoleFractions(const doublereal *x); + virtual void setMoleFractions(const doublereal * const x); //! Get the species mole fraction vector. /*! + * On output the mole fraction vector will sum to one for each of the subphases which make up this phase. + * * @param x On return, x contains the mole fractions. Must have a * length greater than or equal to the number of species. */ - virtual void getMoleFractions(doublereal *x) const; + virtual void getMoleFractions(doublereal * const x) const; doublereal moleFraction(const int k) const { return err("not implemented"); @@ -262,9 +264,32 @@ namespace Cantera { return err("not implemented"); } - virtual void setMassFractions(const doublereal *y) { + + //! Set the mass fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param y Array of unnormalized mass fraction values (input). + * Must have a length greater than or equal to the number of species. + * Input vector of mass fractions. There is no restriction + * on the sum of the mass fraction vector. Internally, + * the State object will normalize this vector before + * storring its contents. + * Length is m_kk. + */ + virtual void setMassFractions(const doublereal * const y) { err("not implemented"); } + + + //! Set the mass fractions to the specified values without normalizing. + /*! + * This is useful when the normalization + * condition is being handled by some other means, for example + * by a constraint equation as part of a larger set of equations. + * + * @param y Input vector of mass fractions. + * Length is m_kk. + */ virtual void setMassFractions_NoNorm(const doublereal* const y) { err("not implemented"); } @@ -296,6 +321,8 @@ namespace Cantera { //! Add in species from Slave phases /*! * This hook is used for cSS_CONVENTION_SLAVE phases + * + * @param phaseNode XML_Node for the current phase */ virtual void installSlavePhases(Cantera::XML_Node* phaseNode); @@ -330,20 +357,35 @@ namespace Cantera { doublereal err(std::string msg) const; protected: - + + //! Number of elements int m_mm; - int m_kk; - mutable doublereal m_tlast; - doublereal m_press; - doublereal m_molar_density; + //! Last temperature at which the reference thermo was calculated + mutable doublereal m_tlast; - int m_nlattice; - std::vector m_lattice; - mutable vector_fp m_x; + //! Current value of the pressure + doublereal m_press; + + //! Current value of the molar density + doublereal m_molar_density; + + //! Number of sublattice phases + int m_nlattice; + + //! Vector of sublattic ThermoPhase objects + std::vector m_lattice; + + //! Vector of mole fractions + /*! + * Note these mole fractions sum to one when summed over all phases. + * However, this is not what's passed down to the lower m_lattice objects. + */ + mutable vector_fp m_x; private: + //! Update the reference thermodynamic functions void _updateThermo() const; }; } diff --git a/Cantera/src/thermo/State.h b/Cantera/src/thermo/State.h index faba94ea9..d9725b33e 100644 --- a/Cantera/src/thermo/State.h +++ b/Cantera/src/thermo/State.h @@ -163,14 +163,12 @@ namespace Cantera { */ doublereal massFraction(const int k) const; - /** - * Set the mass fractions to the specified values, and then - * normalize them so that they sum to 1.0. - * @param y Array of unnormalized mass fraction values (input). - * Must have a length greater than or equal to the number of - * species. - * - * @param y Input vector of mass fractions. There is no restriction + //! Set the mass fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param y Array of unnormalized mass fraction values (input). + * Must have a length greater than or equal to the number of species. + * Input vector of mass fractions. There is no restriction * on the sum of the mass fraction vector. Internally, * the State object will normalize this vector before * storring its contents. @@ -178,12 +176,11 @@ namespace Cantera { */ virtual void setMassFractions(const doublereal* const y); - /** - * Set the mass fractions to the specified values without - * normalizing. This is useful when the normalization + //! Set the mass fractions to the specified values without normalizing. + /*! + * This is useful when the normalization * condition is being handled by some other means, for example - * by a constraint equation as part of a larger set of - * equations. + * by a constraint equation as part of a larger set of equations. * * @param y Input vector of mass fractions. * Length is m_kk. From 4334ec5d8ae32dfda35630de52a81433fee746b6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Jul 2010 16:31:45 +0000 Subject: [PATCH 192/446] Worked on documentation --- Cantera/src/transport/MixTransport.cpp | 19 +++++++++---------- Cantera/src/transport/MixTransport.h | 4 ++++ Cantera/src/transport/MultiTransport.h | 12 ++++++++---- 3 files changed, 21 insertions(+), 14 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 56580c50d..aac11a58c 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -227,21 +227,20 @@ namespace Cantera { return m_lambda; } //=================================================================================================================== - /****************** thermal diffusion coefficients ************/ - - /** - * Thermal diffusion is not considered in this mixture-averaged - * model. To include thermal diffusion, use transport manager - * MultiTransport instead. This methods fills out array dt with - * zeros. + // Return the thermal diffusion coefficients + /* + * For this approximation, these are all zero. + * + * Eqns. (12.168) shows how they are used in an expression for the species flux. + * + * @param dt Vector of thermal diffusion coefficients. Units = kg/m/s */ void MixTransport::getThermalDiffCoeffs(doublereal* const dt) { - int k; - for (k = 0; k < m_nsp; k++) { + for (int k = 0; k < m_nsp; k++) { dt[k] = 0.0; } } - + //=================================================================================================================== /** * @param ndim The number of spatial dimensions (1, 2, or 3). * @param grad_T The temperature gradient (ignored in this model). diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 686cc555d..1e6f01f53 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -63,6 +63,10 @@ namespace Cantera { //! Return the thermal diffusion coefficients /*! * For this approximation, these are all zero. + * + * Eqns. (12.168) shows how they are used in an expression for the species flux. + * + * @param dt Vector of thermal diffusion coefficients. Units = kg/m/s */ virtual void getThermalDiffCoeffs(doublereal* const dt); diff --git a/Cantera/src/transport/MultiTransport.h b/Cantera/src/transport/MultiTransport.h index 754c96fcf..58aca9087 100644 --- a/Cantera/src/transport/MultiTransport.h +++ b/Cantera/src/transport/MultiTransport.h @@ -114,11 +114,15 @@ namespace Cantera { virtual void getSpeciesViscosities(doublereal* const visc) { updateViscosity_T(); std::copy(m_visc.begin(), m_visc.end(), visc); } - //! Return the thermal diffusion coefficients for the species + + //! Return the thermal diffusion coefficients (kg/m/s) /*! - * - * @param dt thermal diffusion coefficients - * (length = m_nsp) + * Eqn. (12.126) displays how they are calculated. The reference work is from + * Dixon-Lewis. + * + * Eqns. (12.168) shows how they are used in an expression for the species flux. + * + * @param dt Vector of thermal diffusion coefficients. Units = kg/m/s */ virtual void getThermalDiffCoeffs(doublereal* const dt); From ec23984da8c48c0acc507b20c1e4e232a14142ff Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Jul 2010 23:24:10 +0000 Subject: [PATCH 193/446] Doxygen update for MixTransport Fleshed out and implemented the copy constructor, assignment operator, and the duplicator for the object. --- Cantera/src/transport/MixTransport.cpp | 294 +++++++++++++++++++++---- Cantera/src/transport/MixTransport.h | 96 ++++++-- 2 files changed, 322 insertions(+), 68 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index aac11a58c..016fec4a9 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -31,25 +31,232 @@ using namespace std; * Mole fractions below MIN_X will be set to MIN_X when computing * transport properties. */ +#ifndef MIN_X #define MIN_X 1.e-20 - +#endif namespace Cantera { - //////////////////// class MixTransport methods ////////////// - + //==================================================================================================================== MixTransport::MixTransport() : m_nsp(0), m_tmin(-1.0), m_tmax(100000.), + m_mw(0), + m_visccoeffs(0), + m_condcoeffs(0), + m_diffcoeffs(0), + m_polytempvec(0), + m_bdiff(0, 0), + m_visc(0), + m_sqvisc(0), + m_cond(0), + m_molefracs(0), + m_poly(0), + m_astar_poly(0), + m_bstar_poly(0), + m_cstar_poly(0), + m_om22_poly(0), + m_astar(0, 0), + m_bstar(0, 0), + m_cstar(0, 0), + m_om22(0, 0), + m_phi(0,0), + m_wratjk(0,0), + m_wratkj1(0,0), + m_zrot(0), + m_crot(0), + m_cinternal(0), + m_eps(0), + m_alpha(0), + m_dipoleDiag(0), m_temp(-1.0), - m_logt(0.0) + m_logt(0.0), + m_kbt(0.0), + m_t14(0.0), + m_t32(0.0), + m_sqrt_kbt(0.0), + m_sqrt_t(0.0), + m_sqrt_eps_k(0), + m_log_eps_k(0, 0), + m_frot_298(0), + m_rotrelax(0), + m_lambda(0.0), + m_viscmix(0.0), + m_spwork(0), + m_viscmix_ok(false), + m_viscwt_ok(false), + m_spvisc_ok(false), + m_diffmix_ok(false), + m_bindiff_ok(false), + m_abc_ok (false), + m_spcond_ok(false), + m_condmix_ok(false), + m_mode(0), + m_epsilon(0, 0), + m_diam(0, 0), + incl(0, 0), + m_debug(false) { - - } + //==================================================================================================================== + MixTransport::MixTransport(const MixTransport &right) : + m_nsp(0), + m_tmin(-1.0), + m_tmax(100000.), + m_mw(0), + m_visccoeffs(0), + m_condcoeffs(0), + m_diffcoeffs(0), + m_polytempvec(0), + m_bdiff(0, 0), + m_visc(0), + m_sqvisc(0), + m_cond(0), + m_molefracs(0), + m_poly(0), + m_astar_poly(0), + m_bstar_poly(0), + m_cstar_poly(0), + m_om22_poly(0), + m_astar(0, 0), + m_bstar(0, 0), + m_cstar(0, 0), + m_om22(0, 0), + m_phi(0,0), + m_wratjk(0,0), + m_wratkj1(0,0), + m_zrot(0), + m_crot(0), + m_cinternal(0), + m_eps(0), + m_alpha(0), + m_dipoleDiag(0), + m_temp(-1.0), + m_logt(0.0), + m_kbt(0.0), + m_t14(0.0), + m_t32(0.0), + m_sqrt_kbt(0.0), + m_sqrt_t(0.0), + m_sqrt_eps_k(0), + m_log_eps_k(0, 0), + m_frot_298(0), + m_rotrelax(0), + m_lambda(0.0), + m_viscmix(0.0), + m_spwork(0), + m_viscmix_ok(false), + m_viscwt_ok(false), + m_spvisc_ok(false), + m_diffmix_ok(false), + m_bindiff_ok(false), + m_abc_ok (false), + m_spcond_ok(false), + m_condmix_ok(false), + m_mode(0), + m_epsilon(0, 0), + m_diam(0, 0), + incl(0, 0), + m_debug(false) + { + *this = right; + } + //==================================================================================================================== + // Assignment operator + /* + * This is NOT a virtual function. + * + * @param right Reference to %LiquidTransport object to be copied + * into the current one. + */ + MixTransport& MixTransport::operator=(const MixTransport& right) { + if (&right == this) { + return *this; + } + Transport::operator=(right); + + m_nsp = right.m_nsp; + m_tmin = right.m_tmin; + m_tmax = right.m_tmax; + m_mw =right.m_mw; + m_visccoeffs = right.m_visccoeffs; + m_condcoeffs = right.m_condcoeffs; + m_diffcoeffs = right.m_diffcoeffs; + m_polytempvec = right.m_polytempvec; + m_bdiff = right.m_bdiff; + m_visc = right.m_visc; + m_sqvisc = right.m_sqvisc; + m_cond = right.m_cond; + m_molefracs = right.m_molefracs; + m_poly = right.m_poly; + m_astar_poly = right.m_astar_poly; + m_bstar_poly = right.m_bstar_poly; + m_cstar_poly = right.m_cstar_poly; + m_om22_poly = right.m_om22_poly; + m_astar = right.m_astar; + m_bstar = right.m_bstar; + m_cstar = right.m_cstar; + m_om22 = right.m_om22; + m_phi = right.m_phi; + m_wratjk = right.m_wratjk; + m_wratkj1 = right.m_wratkj1; + m_zrot = right.m_zrot; + m_crot = right.m_crot; + m_cinternal = right.m_cinternal; + m_eps = right.m_eps; + m_alpha = right.m_alpha; + m_dipoleDiag = right.m_dipoleDiag; + m_temp = right.m_temp; + m_logt = right.m_logt; + m_kbt = right.m_kbt; + m_t14 = right.m_t14; + m_t32 = right.m_t32; + m_sqrt_kbt = right.m_sqrt_kbt; + m_sqrt_t = right.m_sqrt_t; + m_sqrt_eps_k = right.m_sqrt_eps_k; + m_log_eps_k = right.m_log_eps_k; + m_frot_298 = right.m_frot_298; + m_rotrelax = right.m_rotrelax; + m_lambda = right.m_lambda; + m_viscmix = right.m_viscmix; + m_spwork = right.m_spwork; + m_viscmix_ok = right.m_viscmix_ok; + m_viscwt_ok = right.m_viscwt_ok; + m_spvisc_ok = right.m_spvisc_ok; + m_diffmix_ok = right.m_diffmix_ok; + m_bindiff_ok = right.m_bindiff_ok; + m_abc_ok = right.m_abc_ok; + m_spcond_ok = right.m_spcond_ok; + m_condmix_ok = right.m_condmix_ok; + m_mode = right.m_mode; + m_epsilon = right.m_epsilon; + m_diam = right.m_diam; + incl = right.incl; + m_debug = right.m_debug; + return *this; + } + //==================================================================================================================== + // Duplication routine for objects which inherit from %Transport + /* + * This virtual routine can be used to duplicate %Transport objects + * inherited from %Transport even if the application only has + * a pointer to %Transport to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + */ + Transport *MixTransport::duplMyselfAsTransport() const { + MixTransport* tr = new MixTransport(*this); + return (dynamic_cast(tr)); + } + //==================================================================================================================== + MixTransport::~MixTransport() + { + } + //==================================================================================================================== bool MixTransport::initGas( GasTransportParams& tr ) { // constant substance attributes @@ -113,29 +320,24 @@ namespace Cantera { return true; } - - - /********************************************************* + //==================================================================================================================== + // Viscosity of the mixture + /* * - * Public methods - * - *********************************************************/ - - - /****************** viscosity ******************************/ - - /** * The viscosity is computed using the Wilke mixture rule. - * \f[ - * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. - * \f] - * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, - * and - * \f[ - * \Phi_{k,j} = \frac{\left[1 - * + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2} - * {\sqrt{8}\sqrt{1 + M_k/M_j}} - * \f] + * + * \f[ + * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. + * \f] + * + * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, and + * + * \f[ + * \Phi_{k,j} = \frac{\left[1 + * + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2} + * {\sqrt{8}\sqrt{1 + M_k/M_j}} + * \f] + * * @see updateViscosity_T(); */ doublereal MixTransport::viscosity() { @@ -158,7 +360,7 @@ namespace Cantera { m_viscmix = vismix; return vismix; } - + //==================================================================================================================== /******************* binary diffusion coefficients **************/ @@ -321,7 +523,7 @@ namespace Cantera { } } //=========================================================================================================== - /** + /* * @internal This is called whenever a transport property is * requested from ThermoSubstance if the temperature has changed * since the last call to update_T. @@ -360,8 +562,8 @@ namespace Cantera { m_abc_ok = false; m_condmix_ok = false; } - - /** + //==================================================================================================================== + /* * @internal This is called the first time any transport property * is requested from Mixture after the concentrations * have changed. @@ -384,15 +586,15 @@ namespace Cantera { m_molefracs[k] = fmaxx(MIN_X, m_molefracs[k]); } } - + //==================================================================================================================== /************************************************************************* * * methods to update temperature-dependent properties * *************************************************************************/ - - /** + //==================================================================================================================== + /* * Update the temperature-dependent parts of the mixture-averaged * thermal conductivity. */ @@ -413,8 +615,8 @@ namespace Cantera { m_condmix_ok = false; } - - /** + //==================================================================================================================== + /* * Update the binary diffusion coefficients. These are evaluated * from the polynomial fits at unit pressure (1 Pa). */ @@ -446,9 +648,8 @@ namespace Cantera { m_bindiff_ok = true; m_diffmix_ok = false; } - - - /** + //==================================================================================================================== + /* * Update the pure-species viscosities. */ void MixTransport::updateSpeciesViscosities() { @@ -470,8 +671,8 @@ namespace Cantera { m_spvisc_ok = true; } - - /** + //==================================================================================================================== + /* * Update the temperature-dependent viscosity terms. * Updates the array of pure species viscosities, and the * weighting functions in the viscosity mixture rule. @@ -499,14 +700,13 @@ namespace Cantera { } m_viscwt_ok = true; } - - /** + //==================================================================================================================== + /* * This function returns a Transport data object for a given species. * */ - struct GasTransportData MixTransport:: - getGasTransportData(int kSpecies) - { + struct GasTransportData MixTransport::getGasTransportData(int kSpecies) const { + struct GasTransportData td; td.speciesName = m_thermo->speciesName(kSpecies); @@ -524,6 +724,6 @@ namespace Cantera { return td; } - + //==================================================================================================================== } diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 1e6f01f53..3ede840f5 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -45,11 +45,52 @@ namespace Cantera { */ class MixTransport : public Transport { + protected: + //! Default constructor. + /*! + * + */ + MixTransport(); + public: + //!Copy Constructor for the %MixTransport object. + /*! + * @param right %LiquidTransport to be copied + */ + MixTransport(const MixTransport &right); - virtual ~MixTransport() {} + //! Assignment operator + /*! + * This is NOT a virtual function. + * + * @param right Reference to %LiquidTransport object to be copied + * into the current one. + */ + MixTransport& operator=(const MixTransport& right); + + //! Duplication routine for objects which inherit from + //! %Transport + /*! + * This virtual routine can be used to duplicate %Transport objects + * inherited from %Transport even if the application only has + * a pointer to %Transport to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + */ + virtual Transport *duplMyselfAsTransport() const; - virtual int model() const { return cMixtureAveraged; } + + //! Destructor + virtual ~MixTransport(); + + //! Return the model id for transport + /*! + * @return cMixtureAverage + */ + virtual int model() const { + return cMixtureAveraged; + } //! Viscosity of the mixture /*! @@ -158,19 +199,17 @@ namespace Cantera { friend class TransportFactory; - /** - * Return a structure containing all of the pertinent parameters - * about a species that was used to construct the Transport - * properties in this object. + + //! Return a structure containing all of the pertinent parameters about a species that was + //! used to construct the Transport properties in this object. + /*! + * @param kspec Species number to obtain the properties from. * - * @param k Species number to obtain the properties from. + * @return GasTransportData returned structure. */ - struct GasTransportData getGasTransportData(int); + struct GasTransportData getGasTransportData(int kspec) const; - protected: - - /// default constructor - MixTransport(); + private: @@ -179,6 +218,16 @@ namespace Cantera { return (m_thermo->molarDensity() * GasConstant * m_thermo->temperature()); } + void updateThermal_T(); + void updateViscosity_T(); + void updateCond_T(); + void updateSpeciesViscosities(); + void updateDiff_T(); + void correctBinDiffCoeffs(); + + + + // --------- Member Data ------------- // mixture attributes int m_nsp; @@ -200,11 +249,14 @@ namespace Cantera { // property values DenseMatrix m_bdiff; + + //! vector of species viscosities vector_fp m_visc; vector_fp m_sqvisc; vector_fp m_cond; - array_fp m_molefracs; + //! Vector of species molefractions + array_fp m_molefracs; std::vector > m_poly; std::vector m_astar_poly; @@ -228,8 +280,13 @@ namespace Cantera { vector_fp m_alpha; vector_fp m_dipoleDiag; - doublereal m_temp, m_logt, m_kbt, m_t14, m_t32; - doublereal m_sqrt_kbt, m_sqrt_t; + doublereal m_temp; + doublereal m_logt; + doublereal m_kbt; + doublereal m_t14; + doublereal m_t32; + doublereal m_sqrt_kbt; + doublereal m_sqrt_t; vector_fp m_sqrt_eps_k; DenseMatrix m_log_eps_k; @@ -242,12 +299,7 @@ namespace Cantera { // work space vector_fp m_spwork; - void updateThermal_T(); - void updateViscosity_T(); - void updateCond_T(); - void updateSpeciesViscosities(); - void updateDiff_T(); - void correctBinDiffCoeffs(); + bool m_viscmix_ok; bool m_viscwt_ok; bool m_spvisc_ok; @@ -262,6 +314,8 @@ namespace Cantera { DenseMatrix m_epsilon; DenseMatrix m_diam; DenseMatrix incl; + + //! Debug flag - turns on more printing bool m_debug; }; } From a737dd308f154c2f9dcfc4ab39f0b4ab5473b44a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Jul 2010 23:35:42 +0000 Subject: [PATCH 194/446] Doxygen update to DenseMatrix --- Cantera/src/numerics/DenseMatrix.cpp | 279 +++++++++++++++------------ Cantera/src/numerics/DenseMatrix.h | 129 +++++++------ 2 files changed, 222 insertions(+), 186 deletions(-) diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp index 762e4e393..4cc2c46cf 100644 --- a/Cantera/src/numerics/DenseMatrix.cpp +++ b/Cantera/src/numerics/DenseMatrix.cpp @@ -16,134 +16,165 @@ #include "stringUtils.h" namespace Cantera { - - /// assignment. - DenseMatrix& DenseMatrix::operator=(const DenseMatrix& y) { - if (&y == this) return *this; - Array2D::operator=(y); - m_ipiv = y.ipiv(); - return *this; - } - - void DenseMatrix::resize(int n, int m, doublereal v) { - Array2D::resize(n,m,v); - m_ipiv.resize( max(n,m) ); - } - - void DenseMatrix::mult(const double* b, double* prod) const { - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, - static_cast(nRows()), - static_cast(nRows()), 1.0, ptrColumn(0), //begin(), - static_cast(nRows()), b, 1, 0.0, prod, 1); - } - - void DenseMatrix::leftMult(const double* b, double* prod) const { - int nc = static_cast(nColumns()); - int nr = static_cast(nRows()); - int n, i; - double sum = 0.0; - for (n = 0; n < nc; n++) { - sum = 0.0; - for (i = 0; i < nr; i++) { - sum += value(i,n)*b[i]; - } - prod[n] = sum; - } - } - - int solve(DenseMatrix& A, double* b) { - int info=0; - ct_dgetrf(static_cast(A.nRows()), - static_cast(A.nColumns()), A.ptrColumn(0), //begin(), - static_cast(A.nRows()), &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRF returned INFO = "+int2str(info)); - ct_dgetrs(ctlapack::NoTranspose, - static_cast(A.nRows()), 1, A.ptrColumn(0), //begin(), - static_cast(A.nRows()), - &A.ipiv()[0], b, - static_cast(A.nColumns()), info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRS returned INFO = "+int2str(info)); - return 0; + //==================================================================================================================== + // Default Constructor + DenseMatrix::DenseMatrix() + { + } + //==================================================================================================================== + /* + * Constructor. Create an \c n by \c m matrix, and initialize + * all elements to \c v. + */ + DenseMatrix::DenseMatrix(int n, int m, doublereal v) : + Array2D(n, m, v) + { + m_ipiv.resize(max(n, m)); + } + //==================================================================================================================== + // copy constructor + /* + * @param y Object to be copied + */ + DenseMatrix::DenseMatrix(const DenseMatrix& y) : + Array2D(y) + { + m_ipiv = y.ipiv(); + } + //==================================================================================================================== + // assignment + DenseMatrix& DenseMatrix::operator=(const DenseMatrix& y) { + if (&y == this) return *this; + Array2D::operator=(y); + m_ipiv = y.ipiv(); + return *this; + } + //==================================================================================================================== + // Destructor. Does nothing. + DenseMatrix::~DenseMatrix() + { + } + //==================================================================================================================== + void DenseMatrix::resize(int n, int m, doublereal v) { + Array2D::resize(n,m,v); + m_ipiv.resize( max(n,m) ); + } + //==================================================================================================================== + void DenseMatrix::mult(const double* b, double* prod) const { + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, + static_cast(nRows()), + static_cast(nRows()), 1.0, ptrColumn(0), //begin(), + static_cast(nRows()), b, 1, 0.0, prod, 1); + } + //==================================================================================================================== + void DenseMatrix::leftMult(const double* b, double* prod) const { + int nc = static_cast(nColumns()); + int nr = static_cast(nRows()); + int n, i; + double sum = 0.0; + for (n = 0; n < nc; n++) { + sum = 0.0; + for (i = 0; i < nr; i++) { + sum += value(i,n)*b[i]; + } + prod[n] = sum; } - - int solve(DenseMatrix& A, DenseMatrix& b) { - int info=0; - ct_dgetrf(static_cast(A.nRows()), - static_cast(A.nColumns()), A.ptrColumn(0), - static_cast(A.nRows()), &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRF returned INFO = "+int2str(info)); - ct_dgetrs(ctlapack::NoTranspose, static_cast(A.nRows()), - static_cast(b.nColumns()), - A.ptrColumn(0), static_cast(A.nRows()), - &A.ipiv()[0], b.ptrColumn(0), - static_cast(b.nRows()), info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRS returned INFO = "+int2str(info)); - return 0; - } - + } + //==================================================================================================================== + int solve(DenseMatrix& A, double* b) { + int info=0; + ct_dgetrf(static_cast(A.nRows()), + static_cast(A.nColumns()), A.ptrColumn(0), //begin(), + static_cast(A.nRows()), &A.ipiv()[0], info); + if (info != 0) + throw CanteraError("DenseMatrix::solve", + "DGETRF returned INFO = "+int2str(info)); + ct_dgetrs(ctlapack::NoTranspose, + static_cast(A.nRows()), 1, A.ptrColumn(0), //begin(), + static_cast(A.nRows()), + &A.ipiv()[0], b, + static_cast(A.nColumns()), info); + if (info != 0) + throw CanteraError("DenseMatrix::solve", + "DGETRS returned INFO = "+int2str(info)); + return 0; + } + //==================================================================================================================== + int solve(DenseMatrix& A, DenseMatrix& b) { + int info=0; + ct_dgetrf(static_cast(A.nRows()), + static_cast(A.nColumns()), A.ptrColumn(0), + static_cast(A.nRows()), &A.ipiv()[0], info); + if (info != 0) + throw CanteraError("DenseMatrix::solve", + "DGETRF returned INFO = "+int2str(info)); + ct_dgetrs(ctlapack::NoTranspose, static_cast(A.nRows()), + static_cast(b.nColumns()), + A.ptrColumn(0), static_cast(A.nRows()), + &A.ipiv()[0], b.ptrColumn(0), + static_cast(b.nRows()), info); + if (info != 0) + throw CanteraError("DenseMatrix::solve", + "DGETRS returned INFO = "+int2str(info)); + return 0; + } + //==================================================================================================================== #ifdef INCL_LEAST_SQUARES - /** @todo fix lwork */ - int leastSquares(DenseMatrix& A, double* b) { - int info = 0; - int rank = 0; - double rcond = -1.0; - // fix this! - int lwork = 6000; // 2*(3*min(m,n) + max(2*min(m,n), max(m,n))); - vector_fp work(lwork); - vector_fp s(min(static_cast(A.nRows()), - static_cast(A.nColumns()))); - ct_dgelss(static_cast(A.nRows()), - static_cast(A.nColumns()), 1, A.ptrColumn(0), - static_cast(A.nRows()), b, - static_cast(A.nColumns()), &s[0], //.begin(), - rcond, rank, &work[0], work.size(), info); - if (info != 0) - throw CanteraError("DenseMatrix::leaseSquares", - "DGELSS returned INFO = "+int2str(info)); - return 0; - } + /** @todo fix lwork */ + int leastSquares(DenseMatrix& A, double* b) { + int info = 0; + int rank = 0; + double rcond = -1.0; + // fix this! + int lwork = 6000; // 2*(3*min(m,n) + max(2*min(m,n), max(m,n))); + vector_fp work(lwork); + vector_fp s(min(static_cast(A.nRows()), + static_cast(A.nColumns()))); + ct_dgelss(static_cast(A.nRows()), + static_cast(A.nColumns()), 1, A.ptrColumn(0), + static_cast(A.nRows()), b, + static_cast(A.nColumns()), &s[0], //.begin(), + rcond, rank, &work[0], work.size(), info); + if (info != 0) + throw CanteraError("DenseMatrix::leaseSquares", + "DGELSS returned INFO = "+int2str(info)); + return 0; + } #endif + //==================================================================================================================== + void multiply(const DenseMatrix& A, const double* b, double* prod) { + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, + static_cast(A.nRows()), static_cast(A.nColumns()), 1.0, + A.ptrColumn(0), static_cast(A.nRows()), b, 1, 0.0, prod, 1); + } + //==================================================================================================================== + void increment(const DenseMatrix& A, + const double* b, double* prod) { + ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, + static_cast(A.nRows()), static_cast(A.nRows()), 1.0, + A.ptrColumn(0), static_cast(A.nRows()), b, 1, 1.0, prod, 1); + } + //==================================================================================================================== + int invert(DenseMatrix& A, int nn) { + integer n = (nn > 0 ? nn : static_cast(A.nRows())); + int info=0; + ct_dgetrf(n, n, A.ptrColumn(0), static_cast(A.nRows()), + &A.ipiv()[0], info); + if (info != 0) + throw CanteraError("invert", + "DGETRF returned INFO="+int2str(info)); - void multiply(const DenseMatrix& A, const double* b, double* prod) { - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, - static_cast(A.nRows()), static_cast(A.nColumns()), 1.0, - A.ptrColumn(0), static_cast(A.nRows()), b, 1, 0.0, prod, 1); - } - - void increment(const DenseMatrix& A, - const double* b, double* prod) { - ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, - static_cast(A.nRows()), static_cast(A.nRows()), 1.0, - A.ptrColumn(0), static_cast(A.nRows()), b, 1, 1.0, prod, 1); - } - - int invert(DenseMatrix& A, int nn) { - integer n = (nn > 0 ? nn : static_cast(A.nRows())); - int info=0; - ct_dgetrf(n, n, A.ptrColumn(0), static_cast(A.nRows()), - &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("invert", - "DGETRF returned INFO="+int2str(info)); - - vector_fp work(n); - integer lwork = static_cast(work.size()); - ct_dgetri(n, A.ptrColumn(0), static_cast(A.nRows()), - &A.ipiv()[0], - &work[0], lwork, info); - if (info != 0) - throw CanteraError("invert", - "DGETRI returned INFO="+int2str(info)); - return 0; - } + vector_fp work(n); + integer lwork = static_cast(work.size()); + ct_dgetri(n, A.ptrColumn(0), static_cast(A.nRows()), + &A.ipiv()[0], + &work[0], lwork, info); + if (info != 0) + throw CanteraError("invert", + "DGETRI returned INFO="+int2str(info)); + return 0; + } + //==================================================================================================================== } diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index 613bb948b..0686eca25 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -22,83 +22,88 @@ namespace Cantera { - /** - * A class for full (non-sparse) matrices with Fortran-compatible - * data storage. Adds matrix operations to class Array2D. + /** + * A class for full (non-sparse) matrices with Fortran-compatible + * data storage. Adds matrix operations to class Array2D. + */ + class DenseMatrix : public Array2D { + + public: + + //! Default Constructor + DenseMatrix(); + + /** + * Constructor. Create an \c n by \c m matrix, and initialize + * all elements to \c v. */ - class DenseMatrix : public Array2D { + DenseMatrix(int n, int m, doublereal v = 0.0); - public: + //! copy constructor + /*! + * @param y Object to be copied + */ + DenseMatrix(const DenseMatrix& y); - DenseMatrix(){} + //! assignment operator + /*! + * @param y Object to be copied + */ + DenseMatrix& operator=(const DenseMatrix& y); - /** - * Constructor. Create an \c n by \c m matrix, and initialize - * all elements to \c v. - */ - DenseMatrix(int n, int m, doublereal v = 0.0) : Array2D(n,m,v) { - m_ipiv.resize( max(n, m) ); - } + //! Destructor. Does nothing. + virtual ~DenseMatrix(); + - /// copy constructor - DenseMatrix(const DenseMatrix& y) : Array2D(y) { - m_ipiv = y.ipiv(); - } - - /// assignment. - DenseMatrix& operator=(const DenseMatrix& y); - - void resize(int n, int m, doublereal v = 0.0); - - /// Destructor. Does nothing. - virtual ~DenseMatrix(){} - - - /** - * Multiply A*b and write result to \c prod. - */ - virtual void mult(const double* b, double* prod) const; - - /** - * Left-multiply the matrix by transpose(b), and write the - * result to prod. - */ - virtual void leftMult(const double* b, double* prod) const; - - vector_int& ipiv() { return m_ipiv; } - const vector_int& ipiv() const { return m_ipiv; } - - protected: - - vector_int m_ipiv; - }; + void resize(int n, int m, doublereal v = 0.0); + /** - * Solve Ax = b. Array b is overwritten on exit with x. + * Multiply A*b and write result to \c prod. */ - int solve(DenseMatrix& A, double* b); + virtual void mult(const double* b, double* prod) const; - /** Solve Ax = b for multiple right-hand-side vectors. */ - int solve(DenseMatrix& A, DenseMatrix& b); + /** + * Left-multiply the matrix by transpose(b), and write the + * result to prod. + */ + virtual void leftMult(const double* b, double* prod) const; + + vector_int& ipiv() { return m_ipiv; } + const vector_int& ipiv() const { return m_ipiv; } + + protected: + + vector_int m_ipiv; + }; + + + /** + * Solve Ax = b. Array b is overwritten on exit with x. + */ + int solve(DenseMatrix& A, double* b); + + /** Solve Ax = b for multiple right-hand-side vectors. */ + int solve(DenseMatrix& A, DenseMatrix& b); #ifdef INCL_LEAST_SQUARES - /** @todo fix lwork */ - int leastSquares(DenseMatrix& A, double* b); + /** @todo fix lwork */ + int leastSquares(DenseMatrix& A, double* b); #endif - /** - * Multiply \c A*b and return the result in \c prod. Uses BLAS - * routine DGEMV. - */ - void multiply(const DenseMatrix& A, const double* b, double* prod); + /** + * Multiply \c A*b and return the result in \c prod. Uses BLAS + * routine DGEMV. + */ + void multiply(const DenseMatrix& A, const double* b, double* prod); - void increment(const DenseMatrix& A, - const double* b, double* prod); + void increment(const DenseMatrix& A, + const double* b, double* prod); - /** - * invert A. A is overwritten with A^-1. - */ - int invert(DenseMatrix& A, int nn=-1); + /** + * invert A. A is overwritten with A^-1. + */ + int invert(DenseMatrix& A, int nn=-1); } From baed272b2bcc67f40e91cfa8e6702ad2f0ffd499 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 22 Jul 2010 15:22:18 +0000 Subject: [PATCH 195/446] Fixed a makefile error --- Cantera/src/transport/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index cc1a0bbec..df4315d5a 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -37,7 +37,7 @@ CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt.o \ SolidTransport.o DustyGasTransport.o TransportBase.o WaterTransport.o \ SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o \ - TransportParams.o LTRspecies.o + TransportParams.o TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ From 96be2620308eaca3b2aa9ea41d90bc9953df86aa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 22 Jul 2010 16:30:10 +0000 Subject: [PATCH 196/446] Added apps directories in the lib and include dirs. Also added the install install_tsc dir --- Makefile.in | 4 +++- tools/doc/Cantera.cfg.in | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Makefile.in b/Makefile.in index d0b63e050..f1b466967 100755 --- a/Makefile.in +++ b/Makefile.in @@ -81,6 +81,7 @@ kernel-install: ( for ilib in @buildlib@/*.a ; do \ @INSTALL@ -c -m 644 $${ilib} @ct_libdir@ ; \ done ) + @INSTALL@ -d @ct_libdir@/apps ifeq ($(do_ranlib),1) @RANLIB@ @ct_libdir@/*.a endif @@ -116,7 +117,7 @@ hdr-install: @INSTALL@ -d @ct_incdir@ cp -r -f build/include/cantera @ct_incroot@ @(if test -f @ct_incroot@/cantera/Cantera_bt.mak ; then rm -f @ct_incroot@/cantera/Cantera_bt.mak ; fi ) - + @INSTALL@ -d @ct_incroot@/apps f90-modules-install: ifeq ($(build_f90),1) @@ -194,6 +195,7 @@ finish-install: @INSTALL@ -d @ct_bindir@ -( cd bin ; @INSTALL@ -c exp3to2.sh "@ct_bindir@" ) -( cd bin ; @INSTALL@ -c csvdiff "@ct_bindir@" ) + -( cd bin ; @INSTALL@ -c install_tsc "@ct_bindir@" ) ifeq ($(os_is_win),0) # Commands to be executed for non-win systems cp -f License.rtf "@ct_bindir@" diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index a4d4c9397..642a3afa0 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -662,6 +662,7 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ EdgePhase.h \ SurfPhase.cpp \ LatticePhase.h LatticePhase.cpp \ + LatticeSolidPhase.h LatticeSolidPhase.cpp \ SpeciesThermoFactory.h SpeciesThermoFactory.cpp \ speciesThermoTypes.h \ SpeciesThermoMgr.h \ From ea5d8387353c82f47d4cd6e86d50b4d12e4c24c4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 23 Jul 2010 17:51:03 +0000 Subject: [PATCH 197/446] Added a bit more logic into the phaseStability calc. More to come on this. --- Cantera/src/equil/equil.h | 3 +- Cantera/src/equil/vcs_MultiPhaseEquil.h | 18 +++---- Cantera/src/equil/vcs_defs.h | 18 ++++++- Cantera/src/equil/vcs_phaseStability.cpp | 69 +++++++++++++++++++++--- Cantera/src/equil/vcs_solve.h | 25 +++++---- 5 files changed, 102 insertions(+), 31 deletions(-) diff --git a/Cantera/src/equil/equil.h b/Cantera/src/equil/equil.h index 937b70a4a..c8d4498a8 100644 --- a/Cantera/src/equil/equil.h +++ b/Cantera/src/equil/equil.h @@ -19,6 +19,7 @@ //#include "ChemEquil.h" #include "MultiPhase.h" +#include "vcs_defs.h" namespace Cantera { @@ -72,7 +73,7 @@ namespace Cantera { * @ingroup equil */ int equilibrate(thermo_t& s, const char* XY, - int solver = -1, doublereal rtol = 1.0e-9, int maxsteps = 5000, + int solver = -1, doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS, int maxiter = 100, int loglevel = -99); //! Equilibrate a MultiPhase object diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.h b/Cantera/src/equil/vcs_MultiPhaseEquil.h index 3b35973a4..9abff4bb5 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.h +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.h @@ -15,7 +15,7 @@ #include "ct_defs.h" #include "MultiPhase.h" - +#include "vcs_defs.h" namespace Cantera { @@ -81,7 +81,7 @@ namespace Cantera { int vcs_equilibrate(thermo_t& s, const char* XY, int estimateEquil = 0, int printLvl = 0, int solver = -1, doublereal rtol = 1.0e-9, - int maxsteps = 5000, + int maxsteps = VCS_MAXSTEPS, int maxiter = 100, int loglevel = -99); @@ -142,7 +142,7 @@ namespace Cantera { int vcs_equilibrate(MultiPhase& s, const char* XY, int estimateEquil = 0, int printLvl = 0, int solver = 2, - doublereal rtol = 1.0e-9, int maxsteps = 5000, + doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS, int maxiter = 100, int loglevel = -99); //! Set a multi-phase chemical solution to chemical equilibrium. @@ -202,7 +202,7 @@ namespace Cantera { int vcs_equilibrate_1(MultiPhase& s, int ixy, int estimateEquil = 0, int printLvl = 0, int solver = 2, - doublereal rtol = 1.0e-9, int maxsteps = 5000, + doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS, int maxiter = 100, int loglevel = -99); } @@ -355,7 +355,7 @@ namespace VCSnonideal { */ int equilibrate(int XY, int estimateEquil = 0, int printLvl= 0, doublereal err = 1.0e-6, - int maxsteps = 5000, int loglevel=-99); + int maxsteps = VCS_MAXSTEPS, int loglevel=-99); //! Equilibrate the solution using the current element abundances //! storred in the MultiPhase object using constant T and P @@ -385,7 +385,7 @@ namespace VCSnonideal { */ int equilibrate_TP(int estimateEquil = 0, int printLvl= 0, doublereal err = 1.0e-6, - int maxsteps = 5000, int loglevel=-99); + int maxsteps = VCS_MAXSTEPS, int loglevel=-99); //! Equilibrate the solution using the current element abundances //! storred in the MultiPhase object using either constant H and P @@ -439,7 +439,7 @@ namespace VCSnonideal { int equilibrate_HP(doublereal Htarget, int XY, double Tlow, double Thigh, int estimateEquil = 0, int printLvl = 0, doublereal err = 1.0E-6, - int maxsteps = 5000, int loglevel=-99); + int maxsteps = VCS_MAXSTEPS, int loglevel=-99); //! Equilibrate the solution using the current element abundances //! storred in the MultiPhase object using constant S and P. @@ -490,7 +490,7 @@ namespace VCSnonideal { int equilibrate_SP(doublereal Starget, double Tlow, double Thigh, int estimateEquil = 0, int printLvl = 0, doublereal err = 1.0E-6, - int maxsteps = 5000, int loglevel=-99); + int maxsteps = VCS_MAXSTEPS, int loglevel=-99); //! Equilibrate the solution using the current element abundances @@ -538,7 +538,7 @@ namespace VCSnonideal { int equilibrate_TV(int XY, doublereal xtarget, int estimateEquil = 0, int printLvl = 0, doublereal err = 1.0E-6, - int maxsteps = 5000, int loglevel = -99); + int maxsteps = VCS_MAXSTEPS, int loglevel = -99); //! Report the equilibrium answer in a comma separated table format /*! diff --git a/Cantera/src/equil/vcs_defs.h b/Cantera/src/equil/vcs_defs.h index 056859ff6..2ee2b26ca 100644 --- a/Cantera/src/equil/vcs_defs.h +++ b/Cantera/src/equil/vcs_defs.h @@ -78,7 +78,8 @@ namespace VCSnonideal { /*! * @name Sizes of Phases and Cutoff Mole Numbers - * + * + * All size parameters are listed here * @{ */ @@ -103,14 +104,27 @@ namespace VCSnonideal { //! Cutoff relative moles below which a phase is deleted //! from the equilibrium problem. #ifndef VCS_DELETE_PHASE_CUTOFF -#define VCS_DELETE_PHASE_CUTOFF 1.0e-12 +#define VCS_DELETE_PHASE_CUTOFF 1.0e-13 #endif + //! Relative mole number of species in a phase that is created + //! We want this to be comfortably larger than the VCS_DELETE_PHASE_CUTOFF value + //! so that the phase can have a chance to survive. +#ifndef VCS_POP_PHASE_MOLENUM +#define VCS_POP_PHASE_MOLENUM 1.0e-11 +#endif + + //! Cutoff moles below which a phase or species which //! comprises the bulk of an element's total concentration //! is deleted. #ifndef VCS_DELETE_ELEMENTABS_CUTOFF #define VCS_DELETE_ELEMENTABS_CUTOFF 1.0e-280 +#endif + + //! Maximum steps in the inner loop +#ifndef VCS_MAXSTEPS +#define VCS_MAXSTEPS 50000 #endif //@} diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index a0a560abf..e92dd7f54 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -20,13 +20,17 @@ using namespace std; namespace VCSnonideal { - + //==================================================================================================================== // Utility function that evaluates whether a phase can be popped // into existence /* * A phase can be popped iff the stoichiometric coefficients for the * component species, whose concentrations will be lowered during the * process, are positive by at least a small degree. + * + * If one of the phase species is a zeroed component, then the phase can + * be popped if the component increases in mole number as the phase moles + * are increased. * * @param iphasePop id of the phase, which is currently zeroed, * @@ -52,6 +56,13 @@ namespace VCSnonideal { */ for (int k = 0; k < Vphase->nSpecies(); k++) { int kspec = Vphase->spGlobalIndexVCS(k); +#ifdef DEBUG_MODE + if (m_molNumSpecies_old[kspec] > 0.0) { + printf("ERROR vcs_popPhasePossible we shouldn't be here %d %g > 0.0", + kspec, m_molNumSpecies_old[kspec]); + exit(-1); + } +#endif int irxn = kspec - m_numComponents; if (irxn >= 0) { int iPopPossible = true; @@ -62,7 +73,7 @@ namespace VCSnonideal { double negChangeComp = - stoicC * 1.0; if (negChangeComp > 0.0) { // TODO: We may have to come up with a tolerance here - if (m_molNumSpecies_old[j] <= VCS_DELETE_ELEMENTABS_CUTOFF*0.1) { + if (m_molNumSpecies_old[j] <= VCS_DELETE_ELEMENTABS_CUTOFF*0.5) { iPopPossible = false; } } @@ -72,11 +83,56 @@ namespace VCSnonideal { if (iPopPossible == true) { return true; } + } else { + /* + * We are here when the species in the phase is a component. Its mole number is zero. + * We loop through the regular reaction looking for a reaction that can pop the + * component. + */ + printf("WE are here at new logic - CHECK\n"); + for (int jrxn = 0; jrxn < m_numRxnRdc; jrxn++) { + bool foundJrxn = false; + // First, if the component is a product of the reaction + if (m_stoichCoeffRxnMatrix[jrxn][kspec] > 0.0) { + foundJrxn = true; + for (int kcomp = 0; kcomp < m_numComponents; kcomp++) { + if (m_stoichCoeffRxnMatrix[jrxn][kcomp] < 0.0) { + if (m_molNumSpecies_old[kcomp] <= VCS_DELETE_ELEMENTABS_CUTOFF*0.5) { + foundJrxn = false; + } + } + } + if (foundJrxn) { + printf("We have found a component phase pop! CHECK1 \n"); + return true; + } + } + // Second we are here if the component is a reactant in the reaction, and the reaction goes backwards. + else if (m_stoichCoeffRxnMatrix[jrxn][kspec] < 0.0) { + foundJrxn = true; + int jspec = jrxn + m_numComponents; + if (m_molNumSpecies_old[jspec] <= VCS_DELETE_ELEMENTABS_CUTOFF*0.5) { + foundJrxn = false; + continue; + } + for (int kcomp = 0; kcomp < m_numComponents; kcomp++) { + if (m_stoichCoeffRxnMatrix[jrxn][kcomp] > 0.0) { + if (m_molNumSpecies_old[kcomp] <= VCS_DELETE_ELEMENTABS_CUTOFF*0.5) { + foundJrxn = false; + } + } + } + if (foundJrxn) { + printf("We have found a component phase pop! CHECK2 \n"); + return true; + } + } + } } } return false; } - + //==================================================================================================================== // Decision as to whether a phase pops back into existence /* * @return returns the phase id of the phase that pops back into @@ -195,7 +251,7 @@ namespace VCSnonideal { #endif return iphasePop; } - + //==================================================================================================================== // Calculates the deltas of the reactions due to phases popping // into existence /* @@ -415,7 +471,7 @@ namespace VCSnonideal { // - + //==================================================================================================================== double VCS_SOLVE::vcs_phaseStabilityTest(const int iph) { /* @@ -719,6 +775,7 @@ namespace VCSnonideal { #endif return funcPhaseStability; } - + //==================================================================================================================== } +//====================================================================================================================== diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 64acf7ee0..053e681c8 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -200,7 +200,7 @@ public: * m_stoichCoeffRxnMatrix[irxn][jcomp] * Stoichiometric coefficient matrix for the reaction mechanism * expressed in Reduced Canonical Form. - * j refers to the component number, and irxn + * jcomp refers to the component number, and irxn * refers to the irxn_th non-component species. * * m_deltaMolNumPhase[irxn] @@ -1438,7 +1438,7 @@ public: //! Number of components calculated for the problem int m_numComponents; - //! Total number of non-component species in the problem + //! Total number of non-component species in the problem int m_numRxnTot; //! Current number of species in the problems @@ -1448,7 +1448,7 @@ public: */ int m_numSpeciesRdc; - //! Current number of non-component species in the problem + //! Current number of non-component species in the problem /*! * Species can be deleted if they aren't * stable under the current conditions @@ -1470,20 +1470,19 @@ public: */ DoubleStarStar m_formulaMatrix; - //! Stoichiometric coefficient matrix for the reaction mechanism - //! expressed in Reduced Canonical Form. + //! Stoichiometric coefficient matrix for the reaction mechanism expressed in Reduced Canonical Form. /*! * This is the stoichiometric coefficient matrix for the - * reaction which forms species K from the component species. A - * stoichiometric coefficient of one is assumed for the - * species K in this mechanism. + * reaction which forms species kspec from the component species. A + * stoichiometric coefficient of one is assumed for the species kspec in this mechanism. * - * NOTE: kspec = Irxn + m_numComponents + * NOTE: kspec = irxn + m_numComponents * - * sc[irxn][j] : - * j refers to the component number, and irxn - * refers to the irxn_th non-component species. - * + * m_stoichCoeffRxnMatrix[irxn][j] : + * j refers to the component number, and irxn refers to the irxn_th non-component species. + * The stoichiometric coefficents multilpled by the Formula coefficients of the + * component species add up to the negative value of the number of elements in + * the species kspec. * * length = [nspecies0][nelements0] */ From 7d63641f9654d7557f451f12780cd410b836ee4d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 26 Jul 2010 16:16:41 +0000 Subject: [PATCH 198/446] Fixed a comment. --- Cantera/src/equil/vcs_linmaxc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/equil/vcs_linmaxc.cpp b/Cantera/src/equil/vcs_linmaxc.cpp index 813324eb7..fc0dd7688 100644 --- a/Cantera/src/equil/vcs_linmaxc.cpp +++ b/Cantera/src/equil/vcs_linmaxc.cpp @@ -43,7 +43,7 @@ int linprogmax(double *XMOLES, double *CC, double *AX, double *BB, /*----------------------------------------------------------------------- * Find XMOLES(I), i = 1, M such that - * Maximize CC dot W, subject to the NE constraints: + * Maximize CC dot XMOLES, subject to the NE constraints: * * [AX] [XMOLES] = [BB] * and XMOLES(i) > 0 From 74f33b882938880c7e6858df955ed5e5a5fe88d2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 27 Jul 2010 01:10:58 +0000 Subject: [PATCH 199/446] Added a topBounds and botBounds capability --- Cantera/src/numerics/solveProb.cpp | 62 ++++++++++++++++++++---------- Cantera/src/numerics/solveProb.h | 53 +++++++++++++++++++++++-- 2 files changed, 91 insertions(+), 24 deletions(-) diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index 5bf2b766b..2da41b13c 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -79,6 +79,8 @@ namespace Cantera { m_wtSpecies.resize(dim1, 0.0); m_resid.resize(dim1, 0.0); m_ipiv.resize(dim1, 0); + m_topBounds.resize(dim1, 1.0); + m_botBounds.resize(dim1, 0.0); m_Jac.resize(dim1, dim1, 0.0); m_JacCol.resize(dim1, 0); @@ -473,47 +475,55 @@ namespace Cantera { } //================================================================================================ #define APPROACH 0.50 - /* This function calculates a damping factor for the Newton iteration update - * vector, dxneg, to insure that all site and bulk fractions, x, remain - * bounded between zero and one. + // This function calculates a damping factor for the Newton iteration update + // vector, dxneg, to insure that all solution components stay within perscribed bounds + /* + * The default for this class is that all solution components are bounded between zero and one. + * this is because the original unknowns were mole fractions and surface site fractions. * * dxneg[] = negative of the update vector. * * The constant "APPROACH" sets the fraction of the distance to the boundary * that the step can take. If the full step would not force any fraction - * outside of 0-1, then Newton's method is allowed to operate normally. + * outside of the bounds, then Newton's method is mostly allowed to operate normally. + * There is also some solution damping employed. + * + * @param x Vector of the current solution components + * @param dxneg Vector of the negative of the full solution update vector. + * @param dim Size of the solution vector + * @param label return int, stating which solution component caused the most damping. */ doublereal solveProb::calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label) { - int i; - doublereal damp = 1.0, xnew, xtop, xbot; + doublereal damp = 1.0, xnew, xtop, xbot; static doublereal damp_old = 1.0; - *label = -1; - for (i = 0; i < dim; i++) { - + for (int i = 0; i < dim; i++) { + doublereal topBounds = m_topBounds[i]; + doublereal botBounds = m_botBounds[i]; /* * Calculate the new suggested new value of x[i] */ - // x_raw = x[i] - dxneg[i]; double delta_x = - dxneg[i]; xnew = x[i] - damp * dxneg[i]; /* * Calculate the allowed maximum and minimum values of x[i] - * - Only going to allow x[i] to converge to zero by a - * single order of magnitude at a time + * - Only going to allow x[i] to converge to the top and bottom bounds by a + * single order of magnitude at one time */ - xtop = 1.0 - 0.1*fabs(1.0-x[i]); - xbot = fabs(x[i]*0.1) - 1.0e-16; + xtop = topBounds - 0.1 * fabs(topBounds - x[i]); + + xbot = botBounds + 0.1 * fabs(x[i] - botBounds); + if (xnew > xtop) { - damp = - APPROACH * (1.0 - x[i]) / dxneg[i]; + damp = - APPROACH * (xtop - x[i]) / dxneg[i]; *label = i; } else if (xnew < xbot) { - damp = APPROACH * x[i] / dxneg[i]; + damp = APPROACH * (x[i] - xbot) / dxneg[i]; *label = i; } else if (xnew > 3.0*MAX(x[i], 1.0E-10)) { damp = - 2.0 * MAX(x[i], 1.0E-10) / dxneg[i]; @@ -527,7 +537,6 @@ namespace Cantera { } - // if (damp < 1.0e-2) damp = 1.0e-2; /* * Only allow the damping parameter to increase by a factor of three each * iteration. Heuristic to avoid oscillations in the value of damp @@ -541,7 +550,6 @@ namespace Cantera { * Save old value of the damping parameter for use * in subsequent calls. */ - damp_old = damp; return damp; @@ -628,7 +636,6 @@ namespace Cantera { } } - /* * Increase time step exponentially as same species repeatedly * controls time step @@ -658,7 +665,22 @@ namespace Cantera { return (inv_timeScale); } - //================================================================================================ + //==================================================================================================================== + // Set the bottom and top bounds on the solution vector + /* + * The default is for the bottom is 0.0, while the default for the top is 1.0 + * + * @param botBounds Vector of bottom bounds + * @param topBounds vector of top bounds + */ + void solveProb::setBounds(const doublereal botBounds[], const doublereal topBounds[]) + { + for (int k = 0; k < m_neq; k++) { + m_botBounds[k] = botBounds[k]; + m_topBounds[k] = topBounds[k]; + } + } + //==================================================================================================================== /* * printResJac(): prints out the residual and Jacobian. * diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index 658fff0e3..1e7cf479c 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -66,12 +66,17 @@ namespace Cantera { //! Method to solve a pseudo steady state of a nonlinear problem /*! - * The following class handles solving nonlinear problem.s + * The following class handles the solution of a nonlinear problem. + * + * Res_ss(C) = - Res(C) = 0 * + * Optionally a pseudo transient algorithm may be used to relax the residual if + * it is available. * - * Note there are a couple of different types of species indecices - * floating around in the formulation of this object. - * + * Res_td(C) = dC/dt - Res(C) = 0; + * + * Res_ss(C) is the steady state residual to be solved. Res_td(C) is the + * time dependent residual which leads to the steady state residual. * * * Solution Method @@ -329,8 +334,36 @@ namespace Cantera { const doublereal *CSolnSPOld, const bool do_time, const doublereal deltaT); + //! This function calculates a damping factor for the Newton iteration update + //! vector, dxneg, to insure that all solution components stay within perscribed bounds + /*! + * The default for this class is that all solution components are bounded between zero and one. + * this is because the original unknowns were mole fractions and surface site fractions. + * + * dxneg[] = negative of the update vector. + * + * The constant "APPROACH" sets the fraction of the distance to the boundary + * that the step can take. If the full step would not force any fraction + * outside of the bounds, then Newton's method is mostly allowed to operate normally. + * There is also some solution damping employed. + * + * @param x Vector of the current solution components + * @param dxneg Vector of the negative of the full solution update vector. + * @param dim Size of the solution vector + * @param label return int, stating which solution component caused the most damping. + */ virtual doublereal calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label); + //! Set the bottom and top bounds on the solution vector + /*! + * The default is for the bottom is 0.0, while the default for the top is 1.0 + * + * @param botBounds Vector of bottom bounds + * @param topBounds vector of top bounds + */ + virtual void setBounds(const doublereal botBounds[], const doublereal topBounds[]); + + //! residual function pointer to be solved. ResidEval *m_residFunc; //! Total number of equations to solve in the implicit problem. @@ -427,6 +460,18 @@ namespace Cantera { */ Array2D m_Jac; + //! Top bounds for the solution vector + /*! + * This defaults to 1.0 + */ + vector_fp m_topBounds; + + //! Bottom bounds for the solution vector + /*! + * This defaults to 0.0 + */ + vector_fp m_botBounds; + public: int m_ioflag; From 36add9bc08ffd482e81db4185cdd696361565fb7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 27 Jul 2010 01:48:00 +0000 Subject: [PATCH 200/446] Iteration on getting this class to work. There was a member function that wasn't even defined. --- Cantera/src/numerics/NonlinearSolver.cpp | 186 ++++++++++++++++++++++- Cantera/src/numerics/NonlinearSolver.h | 29 +++- Cantera/src/numerics/ResidJacEval.h | 1 - 3 files changed, 210 insertions(+), 6 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index caae05959..0bea4844e 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -79,6 +79,8 @@ namespace Cantera { m_numTotalNewtIts(0), m_min_newt_its(0), filterNewstep(0), + m_jacFormMethod(NSOLN_JAC_NUM), + m_nJacEval(0), time_n(0.0), m_matrixConditioning(0), m_order(1), @@ -104,7 +106,25 @@ namespace Cantera { } } - NonlinearSolver::NonlinearSolver(const NonlinearSolver &right) { + NonlinearSolver::NonlinearSolver(const NonlinearSolver &right) : + m_func(right.m_func), + neq_(0), + delta_t_n(-1.0), + m_nfe(0), + m_colScaling(0), + m_rowScaling(0), + m_numTotalLinearSolves(0), + m_numTotalNewtIts(0), + m_min_newt_its(0), + filterNewstep(0), + m_jacFormMethod(NSOLN_JAC_NUM), + m_nJacEval(0), + time_n(0.0), + m_matrixConditioning(0), + m_order(1), + rtol_(1.0E-3), + atolBase_(1.0E-10) + { *this =operator=(right); } @@ -137,6 +157,8 @@ namespace Cantera { m_numTotalNewtIts = right.m_numTotalNewtIts; m_min_newt_its = right.m_min_newt_its; filterNewstep = right.filterNewstep; + m_jacFormMethod = right.m_jacFormMethod; + m_nJacEval = right.m_nJacEval; time_n = right.time_n; m_matrixConditioning = right.m_matrixConditioning; m_order = right.m_order; @@ -146,7 +168,7 @@ namespace Cantera { return *this; } - + //==================================================================================================================== // Create solution weights for convergence criteria /* * We create soln weights from the following formula @@ -163,7 +185,7 @@ namespace Cantera { m_ewt[i] = rtol_ * fabs(y[i]) + atolk_[i]; } } - + //==================================================================================================================== // set bounds constraints for all variables in the problem /* * @@ -966,6 +988,164 @@ namespace Cantera { mdp::mdp_safe_free((void **) &imax); } + //================================================================================================ + /* + * subtractRD(): + * This routine subtracts 2 numbers. If the difference is less + * than 1.0E-14 times the magnitude of the smallest number, + * then diff returns an exact zero. + * It also returns an exact zero if the difference is less than + * 1.0E-300. + * + * returns: a - b + * + * This routine is used in numerical differencing schemes in order + * to avoid roundoff errors resulting in creating Jacobian terms. + * Note: This is a slow routine. However, jacobian errors may cause + * loss of convergence. Therefore, in practice this routine + * has proved cost-effective. + */ + static inline double subtractRD(double a, double b) { + double diff = a - b; + double d = MIN(fabs(a), fabs(b)); + d *= 1.0E-14; + double ad = fabs(diff); + if (ad < 1.0E-300) { + diff = 0.0; + } + if (ad < d) { + diff = 0.0; + } + return diff; + } + //================================================================================================ + /* + * + * Function called by BEuler to evaluate the Jacobian matrix and the + * current residual at the current time step. + * @param N = The size of the equation system + * @param J = Jacobian matrix to be filled in + * @param f = Right hand side. This routine returns the current + * value of the rhs (output), so that it does + * not have to be computed again. + * + */ + void NonlinearSolver::beuler_jac(SquareMatrix &J, double * const f, + double time_curr, double CJ, + double * const y, + double * const ydot, + int num_newt_its) + { + int i, j; + double* col_j; + double ysave, ydotsave, dy; + /* + * Clear the factor flag + */ + J.clearFactorFlag(); + if (m_jacFormMethod == NSOLN_JAC_ANAL) { + /******************************************************************** + * Call the function to get a jacobian. + */ + m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); +#ifdef DEBUG_HKM + //double dddd = J(89, 89); + //checkFinite(dddd); +#endif + m_nJacEval++; + m_nfe++; + } else { + /******************************************************************* + * Generic algorithm to calculate a numerical Jacobian + */ + /* + * Calculate the current value of the rhs given the + * current conditions. + */ + + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f); + m_nfe++; + m_nJacEval++; + + + /* + * Malloc a vector and call the function object to return a set of + * deltaY's that are appropriate for calculating the numerical + * derivative. + */ + double *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); + + +#ifdef DEBUG_HKM + bool print_NumJac = false; + if (print_NumJac) { + FILE *idy = fopen("NumJac.csv", "w"); + fprintf(idy, "Unk m_ewt y " + "dyVector ResN\n"); + for (int iii = 0; iii < neq_; iii++){ + fprintf(idy, " %4d %16.8e %16.8e %16.8e %16.8e \n", + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + } + fclose(idy); + } +#endif + /* + * Loop over the variables, formulating a numerical derivative + * of the dense matrix. + * For the delta in the variable, we will use a variety of approaches + * The original approach was to use the error tolerance amount. + * This may not be the best approach, as it could be overly large in + * some instances and overly small in others. + * We will first protect from being overly small, by using the usual + * sqrt of machine precision approach, i.e., 1.0E-7, + * to bound the lower limit of the delta. + */ + for (j = 0; j < neq_; j++) { + + + /* + * Get a pointer into the column of the matrix + */ + + + col_j = (double *) J.ptrColumn(j); + ysave = y[j]; + dy = dyVector[j]; + //dy = fmaxx(1.0E-6 * m_ewt[j], fabs(ysave)*1.0E-7); + + y[j] = ysave + dy; + dy = y[j] - ysave; + ydotsave = ydot[j]; + ydot[j] += dy * CJ; + /* + * Call the functon + */ + + + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_y_nm1), + true, j, dy); + m_nfe++; + double diff; + for (i = 0; i < neq_; i++) { + diff = subtractRD(m_y_nm1[i], f[i]); + col_j[i] = diff / dy; + //col_j[i] = (m_wksp[i] - f[i])/dy; + } + + y[j] = ysave; + ydot[j] = ydotsave; + + } + /* + * Release memory + */ + mdp::mdp_safe_free((void **) &dyVector); + } + + + } + } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 420ce23e1..680abf40c 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -23,12 +23,19 @@ namespace Cantera { + // I think steady state is the only option I'm gunning for #define NSOLN_TYPE_PSEUDO_TIME_DEPENDENT 2 #define NSOLN_TYPE_TIME_DEPENDENT 1 #define NSOLN_TYPE_STEADY_STATE 0 +#define NSOLN_JAC_NUM 1 +#define NSOLN_JAC_ANAL 2 + + + //! Class that calculates the solution to a nonlinear system /*! + * UNDER CONSTRUCTION - do not use!!!!!!!!!!!!!!!!!!!!!!!!! * * @ingroup numerics */ @@ -192,8 +199,16 @@ namespace Cantera { */ void calc_ydot(int order, double * const y_curr, double * const ydot_curr); - void beuler_jac(SquareMatrix &, double * const, - double, double, double * const, double * const, int); + + //! Function called to evaluate the jacobian matrix and the curent + //! residual vector. + /*! + * + * + */ + void beuler_jac(SquareMatrix &J, double * const f, + double time_curr, double CJ, double * const y, + double * const ydot, int num_newt_its); double filterNewStep(double, double *, double *); @@ -311,6 +326,16 @@ namespace Cantera { int filterNewstep; + //! Jacobian formation method + /*! + * 1 = numerical (default) + * 2 = analytical + */ + int m_jacFormMethod; + + int m_nJacEval; + + //! Current system time /*! * Note, we assume even for steady state problems that the residual diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index daa3bb6aa..6602f8765 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -158,7 +158,6 @@ namespace Cantera { * Backwards Euler is assumed. */ virtual void evalJacobian(const doublereal t, const doublereal deltaT, - const double* const y, const double* const ydot, SquareMatrix &J, From 71167df80fccdb92270fe59efb6d69a7416284ca Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 27 Jul 2010 18:05:22 +0000 Subject: [PATCH 201/446] Initial test problem is working. --- Cantera/src/numerics/NonlinearSolver.cpp | 125 ++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 21 +++- 2 files changed, 104 insertions(+), 42 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 0bea4844e..49eb577ca 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -45,14 +45,14 @@ using namespace std; namespace Cantera { - + //==================================================================================================================== //----------------------------------------------------------- // Constants //----------------------------------------------------------- const double DampFactor = 4; const int NDAMP = 7; - + //==================================================================================================================== //----------------------------------------------------------- // Static Functions //----------------------------------------------------------- @@ -63,13 +63,14 @@ namespace Cantera { } printf("\n"); } - + //==================================================================================================================== // Default constructor /* * @param func Residual and jacobian evaluator function object */ NonlinearSolver::NonlinearSolver(ResidJacEval *func) : m_func(func), + solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), delta_t_n(-1.0), m_nfe(0), @@ -92,6 +93,7 @@ namespace Cantera { m_ewt.resize(neq_, rtol_); m_y_n.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); + ydot_new.resize(neq_, 0.0); m_colScales.resize(neq_, 1.0); m_rowScales.resize(neq_, 1.0); m_resid.resize(neq_, 0.0); @@ -105,9 +107,10 @@ namespace Cantera { m_ewt[i] = atolk_[i]; } } - + //==================================================================================================================== NonlinearSolver::NonlinearSolver(const NonlinearSolver &right) : - m_func(right.m_func), + m_func(right.m_func), + solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), delta_t_n(-1.0), m_nfe(0), @@ -128,10 +131,10 @@ namespace Cantera { *this =operator=(right); } - + //==================================================================================================================== NonlinearSolver::~NonlinearSolver() { } - + //==================================================================================================================== NonlinearSolver& NonlinearSolver::operator=(const NonlinearSolver &right) { if (this == &right) { return *this; @@ -140,10 +143,12 @@ namespace Cantera { // create a deep copy m_func = right.m_func->duplMyselfAsResidJacEval(); + solnType_ = right.solnType_; neq_ = right.neq_; m_ewt = right.m_ewt; m_y_n = right.m_y_n; m_y_nm1 = right.m_y_nm1; + ydot_new = right.ydot_new; m_colScales = right.m_colScales; m_rowScales = right.m_rowScales; m_resid = right.m_resid; @@ -199,7 +204,7 @@ namespace Cantera { m_y_high_bounds[i] = y_high_bounds[i]; } } - + //==================================================================================================================== /** * L2 Norm of a delta in the solution * @@ -254,8 +259,8 @@ namespace Cantera { } return sum_norm; } - - /** + //==================================================================================================================== + /* * L2 Norm of the residual * * The second argument has a default of false. However, @@ -309,7 +314,7 @@ namespace Cantera { } return sum_norm; } - + //==================================================================================================================== /** * setColumnScales(): @@ -320,7 +325,7 @@ namespace Cantera { m_func->calcSolnScales(time_n, DATA_PTR(m_y_n), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); } - + //==================================================================================================================== void NonlinearSolver::doResidualCalc(const double time_curr, const int typeCalc, const double * const y_curr, @@ -336,7 +341,7 @@ namespace Cantera { m_nfe++; } - + //==================================================================================================================== // Compute the undamped Newton step /* * Compute the undamped Newton step. The residual function is @@ -495,7 +500,7 @@ namespace Cantera { m_numTotalLinearSolves++; } - + //==================================================================================================================== /************************************************************************** * * boundStep(): @@ -535,7 +540,7 @@ namespace Cantera { * Force the step to only take 80% a step towards the lower bounds */ if (step0[i] < 0.0) { - if (y_new < m_y_low_bounds[i]) { + if (y_new < (y[i] + 0.8 * (m_y_low_bounds[i] - y[i]))) { double legalDelta = 0.8*(m_y_low_bounds[i] - y[i]); ff = legalDelta / step0[i]; if (ff < f_bounds) { @@ -548,7 +553,7 @@ namespace Cantera { * Force the step to only take 80% a step towards the high bounds */ if (step0[i] > 0.0) { - if (y_new > m_y_high_bounds[i]) { + if (y_new > (y[i] + 0.8 * (m_y_high_bounds[i] - y[i]))) { double legalDelta = 0.8*(m_y_high_bounds[i] - y[i]); ff = legalDelta / step0[i]; if (ff < f_bounds) { @@ -557,22 +562,22 @@ namespace Cantera { } } } - /** + /* * Now do a delta bounds - * Increase variables by a factor of 2 only - * decrease variables by a factor of 5 only + * Increase variables by a factor of 1.5 only + * decrease variables by a factor of 2 only */ ff = 1.0; - if ((fabs(y_new) > 2.0 * fabs(y[i])) && + if ((fabs(y_new) > 1.5 * fabs(y[i])) && (fabs(y_new-y[i]) > m_ewt[i])) { - ff = fabs(y[i]/(y_new - y[i])); + ff = 0.5 * fabs(y[i]/(y_new - y[i])); ff_alt = fabs(m_ewt[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); ifbd = 1; } - if ((fabs(5.0 * y_new) < fabs(y[i])) && + if ((fabs(2.0 * y_new) < fabs(y[i])) && (fabs(y_new - y[i]) > m_ewt[i])) { - ff = y[i]/(y_new-y[i]) * (1.0 - 5.0)/5.0; + ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; ff_alt = fabs(m_ewt[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); ifbd = 0; @@ -598,11 +603,11 @@ namespace Cantera { if (ifbd) { printf("\t\tboundStep: Decrease of Variable %d causing " "delta damping of %g\n", - i_fbd, f_delta_bounds); + i_fbounds, f_delta_bounds); } else { printf("\t\tboundStep: Increase of variable %d causing" "delta damping of %g\n", - i_fbd, f_delta_bounds); + i_fbounds, f_delta_bounds); } } } @@ -610,7 +615,7 @@ namespace Cantera { //return fbound; return 1.0; } - + //==================================================================================================================== /************************************************************************** * * dampStep(): @@ -670,7 +675,10 @@ namespace Cantera { for (j = 0; j < neq_; j++) { y1[j] = y0[j] + ff * step0[j]; } - calc_ydot(m_order, y1, ydot1); + + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y1, ydot1); + } doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, y1, ydot1, step1, loglevel); @@ -743,8 +751,8 @@ namespace Cantera { return -2; } } - - /** + //==================================================================================================================== + /* * * solve_nonlinear_problem(): * @@ -768,6 +776,8 @@ namespace Cantera { { clockWC wc; + solnType_ = SolnType; + bool m_residCurrent = false; int m = 0; bool forceNewJac = false; @@ -779,13 +789,14 @@ namespace Cantera { std::vector stp1(neq_, 0.0); std::vector y_new(neq_, 0.0); - std::vector ydot_new(neq_, 0.0); + mdp::mdp_copy_dbl_1(DATA_PTR(y_curr), y_comm, neq_); // copyn((size_t)neq_, y_comm, y_curr); - mdp::mdp_copy_dbl_1(DATA_PTR(ydot_curr), ydot_comm, neq_); - - + if (SolnType != NSOLN_TYPE_STEADY_STATE) { + mdp::mdp_copy_dbl_1(DATA_PTR(ydot_curr), ydot_comm, neq_); + } + bool frst = true; num_newt_its = 0; @@ -900,7 +911,10 @@ namespace Cantera { // Exchange new for curr solutions if (m == 0 || m == 1) { mdp::mdp_copy_dbl_1(DATA_PTR(y_curr), DATA_PTR(y_new), neq_); - calc_ydot(m_order, DATA_PTR(y_curr), DATA_PTR(ydot_curr)); + + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, DATA_PTR(y_curr), DATA_PTR(ydot_curr)); + } } // convergence @@ -931,7 +945,7 @@ namespace Cantera { } return m; } - + //==================================================================================================================== /***************************************************************8 * * @@ -987,8 +1001,8 @@ namespace Cantera { printf("\t\t "); print_line("-", 90); mdp::mdp_safe_free((void **) &imax); } + //==================================================================================================================== - //================================================================================================ /* * subtractRD(): * This routine subtracts 2 numbers. If the difference is less @@ -1145,8 +1159,43 @@ namespace Cantera { } + //==================================================================================================================== + void NonlinearSolver:: + calc_ydot(int order, double *y_curr, double *ydot_curr) + { + if (!ydot_curr) { + return; + } + int i; + double c1; + switch (order) { + case 0: + case 1: /* First order forward Euler/backward Euler */ + c1 = 1.0 / delta_t_n; + for (i = 0; i < neq_; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]); + } + return; + case 2: /* Second order Adams-Bashforth / Trapezoidal Rule */ + c1 = 2.0 / delta_t_n; + for (i = 0; i < neq_; i++) { + ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]) - m_ydot_nm1[i]; + } + throw CanteraError("", "not implemented"); + return; + } + } + //================================================================================================ + /* + * filterNewStep(): + * + * void BEulerInt:: + * + */ + double NonlinearSolver::filterNewStep(double timeCurrent, double *y_current, double *ydot_current) { + return 0.0; + } - - + //==================================================================================================================== } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 680abf40c..b23902c6e 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -41,6 +41,7 @@ namespace Cantera { */ class NonlinearSolver { + public: //! Default constructor /*! * @param func Residual and jacobian evaluator function object @@ -192,13 +193,14 @@ namespace Cantera { * at a time step. */ void calc_y_pred(int); - + /** * Internal function to calculate the time derivative at the * new step */ - void calc_ydot(int order, double * const y_curr, double * const ydot_curr); - + void calc_ydot(int, double *, double *); + + //! Function called to evaluate the jacobian matrix and the curent //! residual vector. @@ -276,7 +278,7 @@ namespace Cantera { double damp, int num_entries); - + private: //! Pointer to the residual and jacobian evaluator for the //! function @@ -285,6 +287,9 @@ namespace Cantera { */ ResidJacEval *m_func; + //! Solution type + int solnType_; + //! Local copy of the number of equations int neq_; @@ -293,6 +298,11 @@ namespace Cantera { std::vector m_y_n; std::vector m_y_nm1; + + + std::vector ydot_new; + + std::vector m_colScales; //! Weights for normalizing the values of the residuals @@ -307,6 +317,7 @@ namespace Cantera { //! Lower bounds vector for each species std::vector m_y_low_bounds; + double delta_t_n; //! Counter for the total number of function evaluations @@ -351,6 +362,8 @@ namespace Cantera { doublereal atolBase_; + double * m_ydot_nm1; + std::vector atolk_; }; From 6490892f9536ae5344e2641e748099acf8a442a6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 27 Jul 2010 20:07:24 +0000 Subject: [PATCH 202/446] Modifications to sovleProb to get it to cross the origin --- Cantera/src/numerics/solveProb.cpp | 45 ++++++++++++++++++++---------- Cantera/src/numerics/solveProb.h | 27 +++++++++--------- 2 files changed, 45 insertions(+), 27 deletions(-) diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index 2da41b13c..ec5592c12 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -57,7 +57,7 @@ namespace Cantera { solveProb::solveProb(ResidEval* resid) : m_residFunc(resid), m_neq(0), - m_atol(1.0E-15), + m_atol(0), m_rtol(1.0E-4), m_maxstep(1000), m_ioflag(0) @@ -67,7 +67,7 @@ namespace Cantera { // Dimension solution vector int dim1 = MAX(1, m_neq); - m_atol.resize(dim1, 0.0); + m_atol.resize(dim1, 1.0E-9); m_netProductionRatesSave.resize(dim1, 0.0); m_numEqn1.resize(dim1, 0.0); m_numEqn2.resize(dim1, 0.0); @@ -102,7 +102,7 @@ namespace Cantera { * proportional to their production rates. */ int solveProb::solve(int ifunc, doublereal time_scale, - doublereal reltol, doublereal abstol) + doublereal reltol) { doublereal EXTRA_ACCURACY = 0.001; if (ifunc == SOLVEPROB_JACOBIAN) { @@ -164,7 +164,7 @@ namespace Cantera { if (m_ioflag) { - print_header(m_ioflag, ifunc, time_scale, reltol, abstol, + print_header(m_ioflag, ifunc, time_scale, reltol, DATA_PTR(m_netProductionRatesSave)); } @@ -323,9 +323,7 @@ namespace Cantera { for (irow = 0; irow < m_neq; irow++) { m_CSolnSP[irow] -= damp * m_resid[irow]; } - for (irow = 0; irow < m_neq; irow++) { - m_CSolnSP[irow] = MAX(0.0, m_CSolnSP[irow]); - } + if (do_time) t_real += damp/inv_t; @@ -513,6 +511,10 @@ namespace Cantera { * - Only going to allow x[i] to converge to the top and bottom bounds by a * single order of magnitude at one time */ + bool canCrossOrigin = false; + if (topBounds > 0.0 && botBounds < 0.0) { + canCrossOrigin = true; + } xtop = topBounds - 0.1 * fabs(topBounds - x[i]); @@ -525,13 +527,21 @@ namespace Cantera { else if (xnew < xbot) { damp = APPROACH * (x[i] - xbot) / dxneg[i]; *label = i; - } else if (xnew > 3.0*MAX(x[i], 1.0E-10)) { - damp = - 2.0 * MAX(x[i], 1.0E-10) / dxneg[i]; - *label = i; } - double denom = fabs(x[i]) + m_atol[i]; + // else if (fabs(xnew) > 2.0*MAX(fabs(x[i]), 1.0E-10)) { +// damp = 0.5 * MAX(fabs(x[i]), 1.0E-9)/ fabs(xnew); +// *label = i; + // } + double denom = fabs(x[i]) + 1.0E5 * m_atol[i]; if ((fabs(delta_x) / denom) > 0.3) { - double newdamp = 0.3 * denom / delta_x; + double newdamp = 0.3 * denom / fabs(delta_x); + if (canCrossOrigin) { + if (xnew * x[i] < 0.0) { + if (fabs(x[i]) < 1.0E8 * m_atol[i]) { + newdamp = 2.0 * fabs(x[i]) / fabs(delta_x); + } + } + } damp = MIN(damp, newdamp); } @@ -698,7 +708,7 @@ namespace Cantera { * Optional printing at the start of the solveProb problem */ void solveProb::print_header(int ioflag, int ifunc, doublereal time_scale, - doublereal reltol, doublereal abstol, + doublereal reltol, doublereal netProdRate[]) { int damping = 1; if (ioflag) { @@ -732,7 +742,7 @@ namespace Cantera { else printf(" Damping is OFF \n"); - printf(" Reltol = %9.3e, Abstol = %9.3e\n", reltol, abstol); + printf(" Reltol = %9.3e, Abstol = %9.3e\n", reltol, m_atol[0]); } /* @@ -974,4 +984,11 @@ namespace Cantera { } #endif //================================================================================================ + void solveProb::setAtol(const doublereal atol[]) { + + for (int k = 0; k < m_neq; k++, k++) { + m_atol[k] = atol[k]; + } + } + } diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index 1e7cf479c..c23249c01 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -188,15 +188,13 @@ namespace Cantera { * where applicable * * @param reltol Relative tolerance to use - * @param abstol absolute tolerance. * * @return Returns 1 if the surface problem is successfully solved. * Returns -1 if the surface problem wasn't solved successfully. * Note the actual converged solution is returned as part of the * internal state of the InterfaceKinetics objects. */ - int solve(int ifunc, doublereal time_scale, - doublereal reltol, doublereal abstol); + int solve(int ifunc, doublereal time_scale, doublereal reltol); //! Report the current state of the solution /*! @@ -204,13 +202,25 @@ namespace Cantera { */ virtual void reportState(doublereal * const CSoln) const; + //! Set the bottom and top bounds on the solution vector + /*! + * The default is for the bottom is 0.0, while the default for the top is 1.0 + * + * @param botBounds Vector of bottom bounds + * @param topBounds vector of top bounds + */ + virtual void setBounds(const doublereal botBounds[], const doublereal topBounds[]); + + + void setAtol(const doublereal atol[]); + private: //! Printing routine that gets called at the start of every //! invocation virtual void print_header(int ioflag, int ifunc, doublereal time_scale, - doublereal reltol, doublereal abstol, + doublereal reltol, doublereal netProdRate[]); #ifdef DEBUG_SOLVEPROB @@ -354,15 +364,6 @@ namespace Cantera { */ virtual doublereal calc_damping(doublereal x[], doublereal dxneg[], int dim, int *label); - //! Set the bottom and top bounds on the solution vector - /*! - * The default is for the bottom is 0.0, while the default for the top is 1.0 - * - * @param botBounds Vector of bottom bounds - * @param topBounds vector of top bounds - */ - virtual void setBounds(const doublereal botBounds[], const doublereal topBounds[]); - //! residual function pointer to be solved. ResidEval *m_residFunc; From 14a349a14a5653b332339f593ae33a0652be015c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 28 Jul 2010 18:50:22 +0000 Subject: [PATCH 203/446] Added a setAtolConst routine. --- Cantera/src/numerics/solveProb.cpp | 9 ++++++++- Cantera/src/numerics/solveProb.h | 2 +- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/Cantera/src/numerics/solveProb.cpp b/Cantera/src/numerics/solveProb.cpp index ec5592c12..6fcd09655 100644 --- a/Cantera/src/numerics/solveProb.cpp +++ b/Cantera/src/numerics/solveProb.cpp @@ -985,10 +985,17 @@ namespace Cantera { #endif //================================================================================================ void solveProb::setAtol(const doublereal atol[]) { - for (int k = 0; k < m_neq; k++, k++) { m_atol[k] = atol[k]; } } + //================================================================================================ + void solveProb::setAtolConst(const doublereal atolconst) { + for (int k = 0; k < m_neq; k++, k++) { + m_atol[k] = atolconst; + } + } + //================================================================================================ + } diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index c23249c01..c6fad55c0 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -213,7 +213,7 @@ namespace Cantera { void setAtol(const doublereal atol[]); - + void setAtolConst(const doublereal atolconst); private: From 43798deb6280c477982b260fc97e08eabf227eb8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 30 Jul 2010 18:16:31 +0000 Subject: [PATCH 204/446] Incremental update on solver. Changing some names --- Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 4 +- Cantera/src/equil/vcs_VolPhase.cpp | 18 +++--- Cantera/src/equil/vcs_VolPhase.h | 2 +- Cantera/src/equil/vcs_phaseStability.cpp | 69 ++++++++++++++++++----- Cantera/src/equil/vcs_prob.cpp | 2 +- Cantera/src/equil/vcs_solve.cpp | 4 +- Cantera/src/equil/vcs_solve.h | 9 ++- Cantera/src/equil/vcs_solve_TP.cpp | 4 +- 8 files changed, 79 insertions(+), 33 deletions(-) diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index 9d8863917..b142a3078 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -1280,7 +1280,7 @@ namespace VCSnonideal { vcs_VolPhase *VolPhase = vprob->VPhaseList[iphase]; std::string sEOS = string16_EOSType(VolPhase->m_eqnState); plogf("%16s %5d %5d %8d %16s %8d %16e ", VolPhase->PhaseName.c_str(), - VolPhase->VP_ID, VolPhase->m_singleSpecies, + VolPhase->VP_ID_, VolPhase->m_singleSpecies, VolPhase->m_gasPhase, sEOS.c_str(), VolPhase->nSpecies(), VolPhase->totalMolesInert() ); plogf("%16e\n", VolPhase->totalMoles()); @@ -1402,7 +1402,7 @@ namespace VCSnonideal { vcs_VolPhase *VolPhase = vprob->VPhaseList[iphase]; std::string sEOS = string16_EOSType(VolPhase->m_eqnState); plogf("%16s %5d %5d %8d %16s %8d %16e ", VolPhase->PhaseName.c_str(), - VolPhase->VP_ID, VolPhase->m_singleSpecies, + VolPhase->VP_ID_, VolPhase->m_singleSpecies, VolPhase->m_gasPhase, sEOS.c_str(), VolPhase->nSpecies(), VolPhase->totalMolesInert() ); plogf("%16e\n", VolPhase->totalMoles() ); diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 760f919ff..47a3f1d7c 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -32,7 +32,7 @@ namespace VCSnonideal { */ vcs_VolPhase::vcs_VolPhase(VCS_SOLVE * owningSolverObject) : m_owningSolverObject(0), - VP_ID(-1), + VP_ID_(-1), Domain_ID(-1), m_singleSpecies(true), m_gasPhase(false), @@ -94,7 +94,7 @@ namespace VCSnonideal { */ vcs_VolPhase::vcs_VolPhase(const vcs_VolPhase& b) : m_owningSolverObject(b.m_owningSolverObject), - VP_ID(b.VP_ID), + VP_ID_(b.VP_ID_), Domain_ID(b.Domain_ID), m_singleSpecies(b.m_singleSpecies), m_gasPhase(b.m_gasPhase), @@ -147,7 +147,7 @@ namespace VCSnonideal { // operator but is true for a copy constructor // m_owningSolverObject = b.m_owningSolverObject; - VP_ID = b.VP_ID; + VP_ID_ = b.VP_ID_; Domain_ID = b.Domain_ID; m_singleSpecies = b.m_singleSpecies; m_gasPhase = b.m_gasPhase; @@ -261,17 +261,17 @@ namespace VCSnonideal { m_phi = 0.0; m_phiVarIndex = -1; - if (phaseNum == VP_ID) { + if (phaseNum == VP_ID_) { if (strcmp(PhaseName.c_str(), phaseName)) { plogf("Strings are different: %s %s :unknown situation\n", PhaseName.c_str(), phaseName); exit(EXIT_FAILURE); } } else { - VP_ID = phaseNum; + VP_ID_ = phaseNum; if (!phaseName) { char itmp[40]; - sprintf(itmp, "Phase_%d", VP_ID); + sprintf(itmp, "Phase_%d", VP_ID_); PhaseName = itmp; } else { PhaseName = phaseName; @@ -711,7 +711,7 @@ namespace VCSnonideal { /* * Check for consistency with TPhMoles[] */ - double Tcheck = TPhMoles[VP_ID]; + double Tcheck = TPhMoles[VP_ID_]; if (Tcheck != v_totalMoles) { if (vcs_doubleEqual(Tcheck, v_totalMoles)) { Tcheck = v_totalMoles; @@ -1104,7 +1104,7 @@ namespace VCSnonideal { if (m_numSpecies != 0) { plogf("Warning Nsp != NVolSpeces: %d %d \n", nsp, m_numSpecies); } - resize(VP_ID, nsp, nelem, PhaseName.c_str()); + resize(VP_ID_, nsp, nelem, PhaseName.c_str()); } TP_ptr->getMoleFractions(VCS_DATA_PTR(Xmol)); fractionCreationDelta_ = Xmol; @@ -1567,7 +1567,7 @@ namespace VCSnonideal { std::string pname = tPhase->id(); if (pname == "") { char sss[50]; - sprintf(sss, "phase%d", VP_ID); + sprintf(sss, "phase%d", VP_ID_); pname = sss; } ename = "cn_" + pname; diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 808558a16..2ea6349c2 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -673,7 +673,7 @@ namespace VCSnonideal { * miscibility gap, these numbers will stay the * same after the split. */ - int VP_ID; + int VP_ID_; //! ID of the surface or volume domain in which the //! this phase exists diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index e92dd7f54..3a370809b 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -1,8 +1,17 @@ -/* ======================================================================= */ -/* $RCSfile: vcs_phaseStability.cpp,v $ */ -/* $Date$ */ -/* $Revision$ */ -/* ======================================================================= */ +/** + * @file vcs_phaseStability.cpp + * Implementation class for functions associated with determining the stability of a phase + * (see Class \link Cantera::VCS_SOLVE VCS_SOLVE\endlink and \ref equilfunctions ). + */ + +/* + * $Id$ + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ #include "vcs_solve.h" @@ -138,7 +147,7 @@ namespace VCSnonideal { * @return returns the phase id of the phase that pops back into * existence. Returns -1 if there are no phases */ - int VCS_SOLVE::vcs_popPhaseID() { + int VCS_SOLVE::vcs_popPhaseID(std::vector & phasePopPhaseIDs) { int iphasePop = -1; int iph; int irxn, kspec; @@ -151,8 +160,8 @@ namespace VCSnonideal { char anote[128]; if (m_debug_print_lvl >= 2) { plogf(" --- vcs_popPhaseID() called\n"); - plogf(" --- Phase Status F_e MoleNum\n"); - plogf(" --------------------------------------------------------------\n"); + plogf(" --- Phase Status F_e MoleNum\n"); + plogf(" --------------------------------------------------------------------------\n"); } #endif for (iph = 0; iph < m_numPhases; iph++) { @@ -165,7 +174,7 @@ namespace VCSnonideal { #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - plogf(" --- %18s %5d NA %11.3e\n", + plogf(" --- %18s %5d NA %11.3e\n", Vphase->PhaseName.c_str(), existence, m_tPhaseMoles_old[iph]); @@ -194,10 +203,19 @@ namespace VCSnonideal { #endif } } +#ifdef DEBUG_MODE + if (Fephase < 0.0) { + strcpy(anote," (not stable)"); + if (m_tPhaseMoles_old[iph] > 0.0) { + printf("shouldn't be here\n"); + exit(-1); + } + } +#endif #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - plogf(" --- %18s %5d NA %11.3g %s\n", + plogf(" --- %18s %5d %10.3g %10.3g %s\n", Vphase->PhaseName.c_str(), existence, Fephase, m_tPhaseMoles_old[iph], anote); @@ -242,11 +260,19 @@ namespace VCSnonideal { } } } + phasePopPhaseIDs.resize(0); + if (iphasePop >= 0) { + phasePopPhaseIDs.push_back(iphasePop); + } + /* + * Insert logic here to figure out if phase pops are linked together. Only do one linked + * pop at a time. + */ #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - plogf(" --------------------------------------------------------------\n"); + plogf(" ---------------------------------------------------------------------\n"); } #endif return iphasePop; @@ -280,6 +306,7 @@ namespace VCSnonideal { int kspec = Vphase->spGlobalIndexVCS(0); // Identify the formation reaction for that species int irxn = kspec - m_numComponents; + std::vector creationGlobalRxnNumbers; doublereal s; int j, k; @@ -378,8 +405,10 @@ namespace VCSnonideal { } else { vector fracDelta(Vphase->nSpecies()); vector X_est(Vphase->nSpecies()); + + // fracDelta = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); fracDelta = Vphase->fractionCreationDeltas(); - + double sumFrac = 0.0; for (k = 0; k < Vphase->nSpecies(); k++) { sumFrac += fracDelta[k]; @@ -490,6 +519,8 @@ namespace VCSnonideal { vector fracDelta_new(Vphase->nSpecies(), 0.0); vector fracDelta_old(Vphase->nSpecies(), 0.0); vector fracDelta_raw(Vphase->nSpecies(), 0.0); + vector creationGlobalRxnNumbers(Vphase->nSpecies(), -1); + vector m_feSpecies_Deficient(m_numComponents, 0.0); doublereal damp = 1.0; @@ -505,8 +536,8 @@ namespace VCSnonideal { // Get the storred estimate for the composition of the phase if // it gets created + // fracDelta_new = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); fracDelta_new = Vphase->fractionCreationDeltas(); - bool oneIsComponent = false; std::vector componentList; @@ -539,6 +570,12 @@ namespace VCSnonideal { plogf(" --- vcs_phaseStabilityTest() called for phase %d\n", iph); } #endif + + for (k = 0; k < Vphase->nSpecies(); k++) { + if (fracDelta_new[k] < 1.0E-13) { + fracDelta_new[k] = 1.0E-13; + } + } bool converged = false; for (int its = 0; its < 200 && (!converged); its++) { @@ -547,6 +584,8 @@ namespace VCSnonideal { fracDelta_old = fracDelta_new; dirProdOld = dirProd; + + // Given a set of fracDelta's, we calculate the fracDelta's // for the component species, if any for (i = 0; i < (int) componentList.size(); i++) { @@ -753,7 +792,9 @@ namespace VCSnonideal { if (converged) { Vphase->setMoleFractionsState(0.0, VCS_DATA_PTR(X_est), VCS_STATECALC_PHASESTABILITY); - Vphase->setFractionCreationDeltas( VCS_DATA_PTR(fracDelta_new)); + // Vphase->setCreationMoleNumbers(VCS_DATA_PTR(fracDelta_new), creationGlobalRxnNumbers); + Vphase->setFractionCreationDeltas(VCS_DATA_PTR(fracDelta_new)); + } diff --git a/Cantera/src/equil/vcs_prob.cpp b/Cantera/src/equil/vcs_prob.cpp index 6d1891b4c..7fe4d6542 100644 --- a/Cantera/src/equil/vcs_prob.cpp +++ b/Cantera/src/equil/vcs_prob.cpp @@ -284,7 +284,7 @@ namespace VCSnonideal { Vphase = VPhaseList[iphase]; std::string EOS_cstr = string16_EOSType(Vphase->m_eqnState); plogf("%16s %5d %5d %8d ", Vphase->PhaseName.c_str(), - Vphase->VP_ID, Vphase->m_singleSpecies, Vphase->m_gasPhase); + Vphase->VP_ID_, Vphase->m_singleSpecies, Vphase->m_gasPhase); plogf("%16s %8d %16e ", EOS_cstr.c_str(), Vphase->nSpecies(), Vphase->totalMolesInert()); if (iest >= 0) plogf("%16e\n", Vphase->totalMoles()); diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 108d1dcbc..6331ef942 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -869,9 +869,9 @@ namespace VCSnonideal { vcs_VolPhase *vPhase = m_VolPhaseList[iph]; vcs_VolPhase *pub_phase_ptr = pub->VPhaseList[iph]; - if (vPhase->VP_ID != pub_phase_ptr->VP_ID) { + if (vPhase->VP_ID_ != pub_phase_ptr->VP_ID_) { plogf("%sPhase numbers have changed:%d %d\n", yo.c_str(), - vPhase->VP_ID, pub_phase_ptr->VP_ID); + vPhase->VP_ID_, pub_phase_ptr->VP_ID_); retn = VCS_PUB_BAD; } diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 053e681c8..6100de9e5 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -1,6 +1,7 @@ /** * @file vcs_solve.h - * Header file for the internal object that holds the problem + * Header file for the internal object that holds the vcs equilibrium problem + * (see Class \link Cantera::VCS_SOLVE VCS_SOLVE\endlink and \ref equilfunctions ). */ /* * $Id$ @@ -501,7 +502,6 @@ public: */ void vcs_updateVP(const int stateCalc); - //! Utility function that evaluates whether a phase can be popped //! into existence /*! @@ -514,10 +514,13 @@ public: //! Decision as to whether a phase pops back into existence /*! + * @param phasePopPhaseIDs Vector containing the phase ids of the phases + * that will be popped this step. + * * @return returns the phase id of the phase that pops back into * existence. Returns -1 if there are no phases */ - int vcs_popPhaseID(); + int vcs_popPhaseID(std::vector &phasePopPhaseIDs); //! Calculates the deltas of the reactions due to phases popping //! into existence diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 5d8bae98b..d6de12ad7 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -122,6 +122,7 @@ namespace VCSnonideal { double *dnPhase_irxn; double atomComp; int iphasePop; + std::vector phasePopPhaseIDs(0); #ifdef DEBUG_MODE char ANOTE[128]; /* @@ -399,7 +400,8 @@ namespace VCSnonideal { * First step is a major branch in the algorithm. * We first determine if a phase pops into existence. */ - iphasePop = vcs_popPhaseID(); + phasePopPhaseIDs.clear(); + iphasePop = vcs_popPhaseID(phasePopPhaseIDs); /* * */ From 0085115f0bc5228bb9ed9e243250d9796ba12411 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 30 Jul 2010 18:34:08 +0000 Subject: [PATCH 205/446] Incremental update --- Cantera/src/equil/vcs_VolPhase.cpp | 14 ++++++++++---- Cantera/src/equil/vcs_VolPhase.h | 8 +++++++- Cantera/src/equil/vcs_phaseStability.cpp | 4 ++-- Cantera/src/equil/vcs_util.cpp | 2 +- 4 files changed, 20 insertions(+), 8 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 47a3f1d7c..afd547563 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -1159,11 +1159,17 @@ namespace VCSnonideal { } /***************************************************************************/ - void vcs_VolPhase::setFractionCreationDeltas(const double * const F_k) { - for (int k = 0; k < m_numSpecies; k++) { - fractionCreationDelta_[k] = F_k[k]; - } + void vcs_VolPhase::setCreationMoleNumbers(const double * const n_k, + const std::vector &creationGlobalRxnNumbers) { + vcs_dcopy(VCS_DATA_PTR(fractionCreationDelta_), n_k, m_numSpecies); + // vcs_icopy(VCS_DATA_PTR(creationGlobalRxnNumbers_), VCS_DATA_PTR(creationGlobalRxnNumbers), m_numSpecies); } + + // void vcs_VolPhase::setFractionCreationDeltas(const double * const F_k) { + // for (int k = 0; k < m_numSpecies; k++) { + // fractionCreationDelta_[k] = F_k[k]; + // } + //} /***************************************************************************/ const std::vector & vcs_VolPhase::fractionCreationDeltas() const { diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 2ea6349c2..ce763402f 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -419,11 +419,17 @@ namespace VCSnonideal { //! object. const std::vector & moleFractions() const; + //! Sets the creationMoleNum's within the phase object + /*! + * @param F_k Pointer to a vector of n_k's + */ + void setCreationMoleNumbers(const double * const n_k, const std::vector &creationGlobalRxnNumbers); + //! Sets the fractionCreationDelta's within the phase object /*! * @param F_k Pointer to a vector of F_k's */ - void setFractionCreationDeltas( const double * const F_k); + // void setFractionCreationDeltas( const double * const F_k); //! Return a const reference to the fractionCreationDeltas storred in the //! object. diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index 3a370809b..c055c76e9 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -792,8 +792,8 @@ namespace VCSnonideal { if (converged) { Vphase->setMoleFractionsState(0.0, VCS_DATA_PTR(X_est), VCS_STATECALC_PHASESTABILITY); - // Vphase->setCreationMoleNumbers(VCS_DATA_PTR(fracDelta_new), creationGlobalRxnNumbers); - Vphase->setFractionCreationDeltas(VCS_DATA_PTR(fracDelta_new)); + Vphase->setCreationMoleNumbers(VCS_DATA_PTR(fracDelta_new), creationGlobalRxnNumbers); + //Vphase->setFractionCreationDeltas(VCS_DATA_PTR(fracDelta_new)); } diff --git a/Cantera/src/equil/vcs_util.cpp b/Cantera/src/equil/vcs_util.cpp index ae34e3a12..463c383d0 100644 --- a/Cantera/src/equil/vcs_util.cpp +++ b/Cantera/src/equil/vcs_util.cpp @@ -61,7 +61,7 @@ namespace VCSnonideal { /***************************************************************************/ #ifndef USE_MEMSET - void vcs_dcopy(double *vec_to, double *vec_from, int length) + void vcs_dcopy(double *const vec_to, const double * const vec_from, int length) /************************************************************************** * From 5cf9a9faf99c5b71854df288e1afb8c9e3952241 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 30 Jul 2010 19:04:37 +0000 Subject: [PATCH 206/446] Incremental update --- Cantera/src/equil/vcs_VolPhase.cpp | 39 ++++++++++++++---------- Cantera/src/equil/vcs_VolPhase.h | 28 ++++++++++++++--- Cantera/src/equil/vcs_phaseStability.cpp | 12 +++----- 3 files changed, 51 insertions(+), 28 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index afd547563..19c93a2c4 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -51,6 +51,8 @@ namespace VCSnonideal { m_useCanteraCalls(false), TP_ptr(0), v_totalMoles(0.0), + creationMoleNumbers_(0), + creationGlobalRxnNumbers_(0), m_phiVarIndex(-1), m_totalVol(0.0), m_vcsStateStatus(VCS_STATECALC_OLD), @@ -110,7 +112,9 @@ namespace VCSnonideal { m_MFStartIndex(b.m_MFStartIndex), m_useCanteraCalls(b.m_useCanteraCalls), TP_ptr(b.TP_ptr), - v_totalMoles(b.v_totalMoles), + v_totalMoles(b.v_totalMoles), + creationMoleNumbers_(0), + creationGlobalRxnNumbers_(0), m_phiVarIndex(-1), m_totalVol(b.m_totalVol), m_vcsStateStatus(VCS_STATECALC_OLD), @@ -214,7 +218,9 @@ namespace VCSnonideal { v_totalMoles = b.v_totalMoles; Xmol = b.Xmol; - fractionCreationDelta_ = b.fractionCreationDelta_; + + creationMoleNumbers_ = b.creationMoleNumbers_; + creationGlobalRxnNumbers_ = b.creationGlobalRxnNumbers_; m_phi = b.m_phi; m_phiVarIndex = b.m_phiVarIndex; @@ -309,10 +315,12 @@ namespace VCSnonideal { } Xmol.resize(nspecies, 0.0); - fractionCreationDelta_.resize(nspecies, 0.0); + creationMoleNumbers_.resize(nspecies, 0.0); + creationGlobalRxnNumbers_.resize(nspecies, -1); for (int i = 0; i < nspecies; i++) { Xmol[i] = 1.0/nspecies; - fractionCreationDelta_[i] = 1.0/nspecies; + creationMoleNumbers_[i] = 1.0/nspecies; + creationGlobalRxnNumbers_[i] = IndSpecies[i] - m_numElemConstraints; } SS0ChemicalPotential.resize(nspecies, -1.0); @@ -675,7 +683,7 @@ namespace VCSnonideal { */ if (stateCalc == VCS_STATECALC_OLD) { if (v_totalMoles > 0.0) { - fractionCreationDelta_ = Xmol; + creationMoleNumbers_ = Xmol; } } @@ -1107,7 +1115,7 @@ namespace VCSnonideal { resize(VP_ID_, nsp, nelem, PhaseName.c_str()); } TP_ptr->getMoleFractions(VCS_DATA_PTR(Xmol)); - fractionCreationDelta_ = Xmol; + creationMoleNumbers_ = Xmol; _updateMoleFractionDependencies(); /* @@ -1161,20 +1169,16 @@ namespace VCSnonideal { void vcs_VolPhase::setCreationMoleNumbers(const double * const n_k, const std::vector &creationGlobalRxnNumbers) { - vcs_dcopy(VCS_DATA_PTR(fractionCreationDelta_), n_k, m_numSpecies); - // vcs_icopy(VCS_DATA_PTR(creationGlobalRxnNumbers_), VCS_DATA_PTR(creationGlobalRxnNumbers), m_numSpecies); + vcs_dcopy(VCS_DATA_PTR(creationMoleNumbers_), n_k, m_numSpecies); + vcs_icopy(VCS_DATA_PTR(creationGlobalRxnNumbers_), VCS_DATA_PTR(creationGlobalRxnNumbers), m_numSpecies); } - - // void vcs_VolPhase::setFractionCreationDeltas(const double * const F_k) { - // for (int k = 0; k < m_numSpecies; k++) { - // fractionCreationDelta_[k] = F_k[k]; - // } - //} /***************************************************************************/ - const std::vector & vcs_VolPhase::fractionCreationDeltas() const { - return fractionCreationDelta_; + const std::vector & vcs_VolPhase::creationMoleNumbers(std::vector &creationGlobalRxnNumbers) const { + creationGlobalRxnNumbers = creationGlobalRxnNumbers_; + return creationMoleNumbers_; } + /***************************************************************************/ // Sets the total moles in the phase @@ -1387,6 +1391,9 @@ namespace VCSnonideal { void vcs_VolPhase::setSpGlobalIndexVCS(const int spIndex, const int spGlobalIndex) { IndSpecies[spIndex] = spGlobalIndex; + if (spGlobalIndex >= m_numElemConstraints) { + creationGlobalRxnNumbers_[spIndex] = spGlobalIndex - m_numElemConstraints; + } } /**********************************************************************/ diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index ce763402f..9363a2068 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -425,11 +425,11 @@ namespace VCSnonideal { */ void setCreationMoleNumbers(const double * const n_k, const std::vector &creationGlobalRxnNumbers); - //! Sets the fractionCreationDelta's within the phase object + //! Return a const reference to the creationMoleNumbers storred in the object. /*! - * @param F_k Pointer to a vector of F_k's + * @return Returns a const reference to the vector of creationMoleNumbers */ - // void setFractionCreationDeltas( const double * const F_k); + const std::vector & creationMoleNumbers(std::vector &creationGlobalRxnNumbers) const; //! Return a const reference to the fractionCreationDeltas storred in the //! object. @@ -879,11 +879,31 @@ namespace VCSnonideal { //! in the phase std::vector Xmol; + //! Vector of current creationMoleNumbers_ + /*! + * These are the actual unknowns in the phase stability problem + */ + std::vector creationMoleNumbers_; + + //! Vector of creation global reaction numbers for the phase stability problem + /*! + * The phase stability problem requires a global reaction number for each + * species in the phase. Usually this is the krxn = kglob - M for species + * in the phase that are not components. For component species, the + * choice of the reaction is one which maximimes the chance that the phase + * pops into (or remains in) existence. + * The index here is the local phase species index. + * the value of the variable is the global vcs reaction number. Note, + * that the global reaction number will go out of order when the species positions + * are swapped. So, this number has to be recalculated. + */ + std::vector creationGlobalRxnNumbers_; + //! Vector of current fractionalCreationDeltas /*! * These are the actual unknowns in the problem */ - std::vector fractionCreationDelta_; + // std::vector fractionCreationDelta_; //! If the potential is a solution variable in VCS, it acts as a species. diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index c055c76e9..17cbf9a2c 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -405,10 +405,8 @@ namespace VCSnonideal { } else { vector fracDelta(Vphase->nSpecies()); vector X_est(Vphase->nSpecies()); - - // fracDelta = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); - fracDelta = Vphase->fractionCreationDeltas(); - + fracDelta = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); + double sumFrac = 0.0; for (k = 0; k < Vphase->nSpecies(); k++) { sumFrac += fracDelta[k]; @@ -536,8 +534,8 @@ namespace VCSnonideal { // Get the storred estimate for the composition of the phase if // it gets created - // fracDelta_new = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); - fracDelta_new = Vphase->fractionCreationDeltas(); + fracDelta_new = Vphase->creationMoleNumbers(creationGlobalRxnNumbers); + bool oneIsComponent = false; std::vector componentList; @@ -793,8 +791,6 @@ namespace VCSnonideal { Vphase->setMoleFractionsState(0.0, VCS_DATA_PTR(X_est), VCS_STATECALC_PHASESTABILITY); Vphase->setCreationMoleNumbers(VCS_DATA_PTR(fracDelta_new), creationGlobalRxnNumbers); - //Vphase->setFractionCreationDeltas(VCS_DATA_PTR(fracDelta_new)); - } From 72aa3cff0174cf20c4e0b3f48f77a3d323f53a79 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 30 Jul 2010 19:33:53 +0000 Subject: [PATCH 207/446] Incremental update --- Cantera/src/equil/vcs_VolPhase.cpp | 49 +++++++++++++++--------------- Cantera/src/equil/vcs_VolPhase.h | 20 +++--------- 2 files changed, 28 insertions(+), 41 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 19c93a2c4..49da2fe79 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -63,9 +63,8 @@ namespace VCSnonideal { m_UpToDate_VolPM(false), m_UpToDate_GStar(false), m_UpToDate_G0(false), - Temp(273.15), - Pres(1.01325E5), - RefPres(1.01325E5) + Temp_(273.15), + Pres_(1.01325E5) { m_owningSolverObject = owningSolverObject; } @@ -125,8 +124,8 @@ namespace VCSnonideal { m_UpToDate_VolPM(false), m_UpToDate_GStar(false), m_UpToDate_G0(false), - Temp(b.Temp), - Pres(b.Pres) + Temp_(b.Temp_), + Pres_(b.Pres_) { /* * Call the Assignment operator to do the heavy @@ -241,9 +240,9 @@ namespace VCSnonideal { m_UpToDate_VolPM = false; m_UpToDate_GStar = false; m_UpToDate_G0 = false; - Temp = b.Temp; - Pres = b.Pres; - setState_TP(Temp, Pres); + Temp_ = b.Temp_; + Pres_ = b.Pres_; + setState_TP(Temp_, Pres_); _updateMoleFractionDependencies(); } return *this; @@ -409,7 +408,7 @@ namespace VCSnonideal { vcs_SpeciesProperties *sProp = ListSpeciesPtr[k]; VCS_SPECIES_THERMO *sTherm = sProp->SpeciesThermo; SS0ChemicalPotential[k] = - R * (sTherm->G0_R_calc(kglob, Temp)); + R * (sTherm->G0_R_calc(kglob, Temp_)); } } m_UpToDate_G0 = true; @@ -450,7 +449,7 @@ namespace VCSnonideal { vcs_SpeciesProperties *sProp = ListSpeciesPtr[k]; VCS_SPECIES_THERMO *sTherm = sProp->SpeciesThermo; StarChemicalPotential[k] = - R * (sTherm->GStar_R_calc(kglob, Temp, Pres)); + R * (sTherm->GStar_R_calc(kglob, Temp_, Pres_)); } } m_UpToDate_GStar = true; @@ -508,7 +507,7 @@ namespace VCSnonideal { void vcs_VolPhase::_updateMoleFractionDependencies() { if (m_useCanteraCalls) { if (TP_ptr) { - TP_ptr->setState_PX(Pres, &(Xmol[m_MFStartIndex])); + TP_ptr->setState_PX(Pres_, &(Xmol[m_MFStartIndex])); } } if (!m_isIdealSoln) { @@ -683,7 +682,8 @@ namespace VCSnonideal { */ if (stateCalc == VCS_STATECALC_OLD) { if (v_totalMoles > 0.0) { - creationMoleNumbers_ = Xmol; + vcs_dcopy(VCS_DATA_PTR(creationMoleNumbers_), VCS_DATA_PTR(Xmol), m_numSpecies); + } } @@ -856,8 +856,8 @@ namespace VCSnonideal { */ void vcs_VolPhase::setState_TP(const double temp, const double pres) { - if (Temp == temp) { - if (Pres == pres) { + if (Temp_ == temp) { + if (Pres_ == pres) { return; } } @@ -865,8 +865,8 @@ namespace VCSnonideal { TP_ptr->setElectricPotential(m_phi); TP_ptr->setState_TP(temp, pres); } - Temp = temp; - Pres = pres; + Temp_ = temp; + Pres_ = pres; m_UpToDate_AC = false; m_UpToDate_VolStar = false; m_UpToDate_VolPM = false; @@ -885,7 +885,7 @@ namespace VCSnonideal { * @param temperature_Kelvin (Kelvin) */ void vcs_VolPhase::setState_T(const double temp) { - setState_TP(temp, Pres); + setState_TP(temp, Pres_); } /***************************************************************************/ @@ -907,7 +907,7 @@ namespace VCSnonideal { int kglob = IndSpecies[k]; vcs_SpeciesProperties *sProp = ListSpeciesPtr[k]; VCS_SPECIES_THERMO *sTherm = sProp->SpeciesThermo; - StarMolarVol[k] = (sTherm->VolStar_calc(kglob, Temp, Pres)); + StarMolarVol[k] = (sTherm->VolStar_calc(kglob, Temp_, Pres_)); } } m_UpToDate_VolStar = true; @@ -952,7 +952,7 @@ namespace VCSnonideal { kglob = IndSpecies[k]; vcs_SpeciesProperties *sProp = ListSpeciesPtr[k]; VCS_SPECIES_THERMO *sTherm = sProp->SpeciesThermo; - StarMolarVol[k] = (sTherm->VolStar_calc(kglob, Temp, Pres)); + StarMolarVol[k] = (sTherm->VolStar_calc(kglob, Temp_, Pres_)); } for (k = 0; k < m_numSpecies; k++) { PartialMolarVol[k] = StarMolarVol[k]; @@ -967,7 +967,7 @@ namespace VCSnonideal { if (m_totalMolesInert > 0.0) { if (m_gasPhase) { - double volI = m_totalMolesInert * 8314.47215 * Temp / Pres; + double volI = m_totalMolesInert * 8314.47215 * Temp_ / Pres_; m_totalVol += volI; } else { printf("unknown situation\n"); @@ -1101,9 +1101,9 @@ namespace VCSnonideal { TP_ptr = tp_ptr; if (TP_ptr) { m_useCanteraCalls = true; - Temp = TP_ptr->temperature(); - Pres = TP_ptr->pressure(); - setState_TP(Temp, Pres); + Temp_ = TP_ptr->temperature(); + Pres_ = TP_ptr->pressure(); + setState_TP(Temp_, Pres_); p_VCS_UnitsFormat = VCS_UNITS_MKS; m_phi = TP_ptr->electricPotential(); int nsp = TP_ptr->nSpecies(); @@ -1388,8 +1388,7 @@ namespace VCSnonideal { * @return Returns the VCS_SOLVE species index of the that species * This changes as rearrangements are carried out. */ - void vcs_VolPhase::setSpGlobalIndexVCS(const int spIndex, - const int spGlobalIndex) { + void vcs_VolPhase::setSpGlobalIndexVCS(const int spIndex, const int spGlobalIndex) { IndSpecies[spIndex] = spGlobalIndex; if (spGlobalIndex >= m_numElemConstraints) { creationGlobalRxnNumbers_[spIndex] = spGlobalIndex - m_numElemConstraints; diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 9363a2068..55936c80a 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -431,10 +431,6 @@ namespace VCSnonideal { */ const std::vector & creationMoleNumbers(std::vector &creationGlobalRxnNumbers) const; - //! Return a const reference to the fractionCreationDeltas storred in the - //! object. - const std::vector & fractionCreationDeltas() const; - //! Returns whether the phase is an ideal solution phase bool isIdealSoln() const; @@ -898,14 +894,7 @@ namespace VCSnonideal { * are swapped. So, this number has to be recalculated. */ std::vector creationGlobalRxnNumbers_; - - //! Vector of current fractionalCreationDeltas - /*! - * These are the actual unknowns in the problem - */ - // std::vector fractionCreationDelta_; - - + //! If the potential is a solution variable in VCS, it acts as a species. //! This is the species index in the phase for the potential int m_phiVarIndex; @@ -1024,13 +1013,12 @@ namespace VCSnonideal { mutable bool m_UpToDate_G0; //! Current value of the temperature for this object, and underlying objects - double Temp; + double Temp_; //! Current value of the pressure for this object, and underlying objects - double Pres; + double Pres_; - //! Reference pressure for the phase - double RefPres; + }; From 300862c1e772e9f8bb0eb46519f057d5124e9b75 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 30 Jul 2010 20:08:35 +0000 Subject: [PATCH 208/446] Working to implement a new phase Pop capability. The old one has been shown to have flaws in it. - End of incremental updates. --- Cantera/src/equil/vcs_VolPhase.cpp | 78 ++++++++++++------------------ Cantera/src/equil/vcs_VolPhase.h | 2 +- 2 files changed, 33 insertions(+), 47 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 49da2fe79..a6ca97434 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -155,37 +155,30 @@ namespace VCSnonideal { m_singleSpecies = b.m_singleSpecies; m_gasPhase = b.m_gasPhase; m_eqnState = b.m_eqnState; - - m_numSpecies = b.m_numSpecies; - m_numElemConstraints = b.m_numElemConstraints; ChargeNeutralityElement = b.ChargeNeutralityElement; - - + p_VCS_UnitsFormat = b.p_VCS_UnitsFormat; + p_activityConvention= b.p_activityConvention; + m_numElemConstraints = b.m_numElemConstraints; m_elementNames.resize(b.m_numElemConstraints); for (int e = 0; e < b.m_numElemConstraints; e++) { m_elementNames[e] = b.m_elementNames[e]; } - m_elementActive = b.m_elementActive; m_elementType = b.m_elementType; - m_formulaMatrix.resize(m_numElemConstraints, m_numSpecies, 0.0); for (int e = 0; e < m_numElemConstraints; e++) { for (int k = 0; k < m_numSpecies; k++) { m_formulaMatrix[e][k] = b.m_formulaMatrix[e][k]; } } - m_speciesUnknownType = b.m_speciesUnknownType; m_elemGlobalIndex = b.m_elemGlobalIndex; m_numSpecies = b.m_numSpecies; PhaseName = b.PhaseName; m_totalMolesInert = b.m_totalMolesInert; - p_activityConvention= b.p_activityConvention; m_isIdealSoln = b.m_isIdealSoln; m_existence = b.m_existence; m_MFStartIndex = b.m_MFStartIndex; - /* * Do a shallow copy because we haven' figured this out. */ @@ -203,8 +196,6 @@ namespace VCSnonideal { ListSpeciesPtr[k] = new vcs_SpeciesProperties(*(b.ListSpeciesPtr[k])); } - - p_VCS_UnitsFormat = b.p_VCS_UnitsFormat; m_useCanteraCalls = b.m_useCanteraCalls; /* * Do a shallow copy of the ThermoPhase object pointer. @@ -215,26 +206,20 @@ namespace VCSnonideal { */ TP_ptr = b.TP_ptr; v_totalMoles = b.v_totalMoles; - - Xmol = b.Xmol; - + Xmol_ = b.Xmol_; creationMoleNumbers_ = b.creationMoleNumbers_; creationGlobalRxnNumbers_ = b.creationGlobalRxnNumbers_; - - m_phi = b.m_phi; m_phiVarIndex = b.m_phiVarIndex; - + m_totalVol = b.m_totalVol; SS0ChemicalPotential = b.SS0ChemicalPotential; StarChemicalPotential = b.StarChemicalPotential; - StarMolarVol = b.StarMolarVol; PartialMolarVol = b.PartialMolarVol; ActCoeff = b.ActCoeff; - dLnActCoeffdMolNumber = b.dLnActCoeffdMolNumber; - - m_UpToDate = false; m_vcsStateStatus = b.m_vcsStateStatus; + m_phi = b.m_phi; + m_UpToDate = false; m_UpToDate_AC = false; m_UpToDate_VolStar = false; m_UpToDate_VolPM = false; @@ -242,6 +227,7 @@ namespace VCSnonideal { m_UpToDate_G0 = false; Temp_ = b.Temp_; Pres_ = b.Pres_; + setState_TP(Temp_, Pres_); _updateMoleFractionDependencies(); } @@ -313,11 +299,11 @@ namespace VCSnonideal { ListSpeciesPtr[i] = new vcs_SpeciesProperties(phaseNum, i, this); } - Xmol.resize(nspecies, 0.0); + Xmol_.resize(nspecies, 0.0); creationMoleNumbers_.resize(nspecies, 0.0); creationGlobalRxnNumbers_.resize(nspecies, -1); for (int i = 0; i < nspecies; i++) { - Xmol[i] = 1.0/nspecies; + Xmol_[i] = 1.0/nspecies; creationMoleNumbers_[i] = 1.0/nspecies; creationGlobalRxnNumbers_[i] = IndSpecies[i] - m_numElemConstraints; } @@ -485,12 +471,12 @@ namespace VCSnonideal { void vcs_VolPhase::setMoleFractions(const double * const xmol) { double sum = -1.0; for (int k = 0; k < m_numSpecies; k++) { - Xmol[k] = xmol[k]; + Xmol_[k] = xmol[k]; sum+= xmol[k]; } if (std::fabs(sum) > 1.0E-13) { for (int k = 0; k < m_numSpecies; k++) { - Xmol[k] /= sum; + Xmol_[k] /= sum; } } _updateMoleFractionDependencies(); @@ -507,7 +493,7 @@ namespace VCSnonideal { void vcs_VolPhase::_updateMoleFractionDependencies() { if (m_useCanteraCalls) { if (TP_ptr) { - TP_ptr->setState_PX(Pres_, &(Xmol[m_MFStartIndex])); + TP_ptr->setState_PX(Pres_, &(Xmol_[m_MFStartIndex])); } } if (!m_isIdealSoln) { @@ -519,7 +505,7 @@ namespace VCSnonideal { // Return a const reference to the mole fraction vector in the phase const std::vector & vcs_VolPhase::moleFractions() const { - return Xmol; + return Xmol_; } /***************************************************************************/ @@ -556,7 +542,7 @@ namespace VCSnonideal { v_totalMoles = totalMoles; double sum = 0.0; for (int k = 0; k < m_numSpecies; k++) { - Xmol[k] = moleFractions[k]; + Xmol_[k] = moleFractions[k]; sum += moleFractions[k]; } if (sum == 0.0) { @@ -565,7 +551,7 @@ namespace VCSnonideal { } if (sum != 1.0) { for (int k = 0; k < m_numSpecies; k++) { - Xmol[k] /= sum; + Xmol_[k] /= sum; } } _updateMoleFractionDependencies(); @@ -640,7 +626,7 @@ namespace VCSnonideal { if (m_speciesUnknownType[k] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { kglob = IndSpecies[k]; tmp = MAX(0.0, molesSpeciesVCS[kglob]); - Xmol[k] = tmp / v_totalMoles; + Xmol_[k] = tmp / v_totalMoles; } } m_existence = VCS_PHASE_EXIST_YES; @@ -649,7 +635,7 @@ namespace VCSnonideal { // for the mole fractions, when the phase doesn't exist. // This is currently unimplemented. //for (int k = 0; k < m_numSpecies; k++) { - // Xmol[k] = 1.0 / m_numSpecies; + // Xmol_[k] = 1.0 / m_numSpecies; //} m_existence = VCS_PHASE_EXIST_NO; } @@ -660,9 +646,9 @@ namespace VCSnonideal { if (m_phiVarIndex >= 0) { kglob = IndSpecies[m_phiVarIndex]; if (m_numSpecies == 1) { - Xmol[m_phiVarIndex] = 1.0; + Xmol_[m_phiVarIndex] = 1.0; } else { - Xmol[m_phiVarIndex] = 0.0; + Xmol_[m_phiVarIndex] = 0.0; } double phi = molesSpeciesVCS[kglob]; setElectricPotential(phi); @@ -682,7 +668,7 @@ namespace VCSnonideal { */ if (stateCalc == VCS_STATECALC_OLD) { if (v_totalMoles > 0.0) { - vcs_dcopy(VCS_DATA_PTR(creationMoleNumbers_), VCS_DATA_PTR(Xmol), m_numSpecies); + vcs_dcopy(VCS_DATA_PTR(creationMoleNumbers_), VCS_DATA_PTR(Xmol_), m_numSpecies); } } @@ -961,7 +947,7 @@ namespace VCSnonideal { m_totalVol = 0.0; for (k = 0; k < m_numSpecies; k++) { - m_totalVol += PartialMolarVol[k] * Xmol[k]; + m_totalVol += PartialMolarVol[k] * Xmol_[k]; } m_totalVol *= v_totalMoles; @@ -994,9 +980,9 @@ namespace VCSnonideal { _updateActCoeff(); } - // Make copies of ActCoeff and Xmol for use in taking differences + // Make copies of ActCoeff and Xmol_ for use in taking differences std::vector ActCoeff_Base(ActCoeff); - std::vector Xmol_Base(Xmol); + std::vector Xmol_Base(Xmol_); double TMoles_base = v_totalMoles; /* @@ -1005,7 +991,7 @@ namespace VCSnonideal { for (j = 0; j < m_numSpecies; j++) { /* * Calculate a value for the delta moles of species j - * -> NOte Xmol[] and Tmoles are always positive or zero + * -> NOte Xmol_[] and Tmoles are always positive or zero * quantities. */ double moles_j_base = v_totalMoles * Xmol_Base[j]; @@ -1016,9 +1002,9 @@ namespace VCSnonideal { */ v_totalMoles = TMoles_base + deltaMoles_j; for (k = 0; k < m_numSpecies; k++) { - Xmol[k] = Xmol_Base[k] * TMoles_base / v_totalMoles; + Xmol_[k] = Xmol_Base[k] * TMoles_base / v_totalMoles; } - Xmol[j] = (moles_j_base + deltaMoles_j) / v_totalMoles; + Xmol_[j] = (moles_j_base + deltaMoles_j) / v_totalMoles; /* * Go get new values for the activity coefficients. @@ -1035,10 +1021,10 @@ namespace VCSnonideal { ((ActCoeff[k] + ActCoeff_Base[k]) * 0.5 * deltaMoles_j); } /* - * Revert to the base case Xmol, v_totalMoles + * Revert to the base case Xmol_, v_totalMoles */ v_totalMoles = TMoles_base; - vcs_vdcopy(Xmol, Xmol_Base, m_numSpecies); + vcs_vdcopy(Xmol_, Xmol_Base, m_numSpecies); } /* * Go get base values for the activity coefficients. @@ -1114,8 +1100,8 @@ namespace VCSnonideal { } resize(VP_ID_, nsp, nelem, PhaseName.c_str()); } - TP_ptr->getMoleFractions(VCS_DATA_PTR(Xmol)); - creationMoleNumbers_ = Xmol; + TP_ptr->getMoleFractions(VCS_DATA_PTR(Xmol_)); + vcs_dcopy(VCS_DATA_PTR(creationMoleNumbers_), VCS_DATA_PTR(Xmol_), m_numSpecies); _updateMoleFractionDependencies(); /* @@ -1163,7 +1149,7 @@ namespace VCSnonideal { /***************************************************************************/ double vcs_VolPhase::molefraction(int k) const { - return Xmol[k]; + return Xmol_[k]; } /***************************************************************************/ diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 55936c80a..03715db1e 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -873,7 +873,7 @@ namespace VCSnonideal { //! Vector of the current mole fractions for species //! in the phase - std::vector Xmol; + std::vector Xmol_; //! Vector of current creationMoleNumbers_ /*! From 24d179c6c57aa1d342fae141037cc0d114a27009 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 2 Aug 2010 22:46:14 +0000 Subject: [PATCH 209/446] Changed the name of getdlnActCoeff to getdlnActCoeffds and fixed up the documentation so that it accurately represents what the function does. Changed the doxygen configuration file. More to come on this. --- Cantera/src/base/ctml.cpp | 7 + Cantera/src/numerics/solveProb.h | 4 +- Cantera/src/thermo/GibbsExcessVPSSTP.h | 17 --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 35 +++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 21 ++- Cantera/src/thermo/MargulesVPSSTP.cpp | 150 ++++--------------- Cantera/src/thermo/MargulesVPSSTP.h | 31 ++-- Cantera/src/thermo/ThermoPhase.h | 22 +-- Cantera/src/transport/LiquidTransport.cpp | 3 +- Cantera/src/transport/LiquidTransport.h | 20 +-- tools/doc/Cantera.cfg.in | 13 +- 11 files changed, 120 insertions(+), 203 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index fcf263364..d03ebc5ce 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -37,6 +37,13 @@ using namespace Cantera; namespace ctml { + //==================================================================================================================== + //! Convert a floating point value from a string to a double + /*! + * @param val String value input + * + * @return Returns a double + */ static doublereal fpValue(std::string val) { return atof(stripws(val).c_str()); } diff --git a/Cantera/src/numerics/solveProb.h b/Cantera/src/numerics/solveProb.h index c6fad55c0..999b700ae 100644 --- a/Cantera/src/numerics/solveProb.h +++ b/Cantera/src/numerics/solveProb.h @@ -181,8 +181,8 @@ namespace Cantera { * internal state of the InterfaceKinetics objects. * * @param ifunc Determines the type of solution algorithm to be - * used. Possible values are SFLUX_INITIALIZE , - * SFLUX_RESIDUAL SFLUX_JACOBIAN SFLUX_TRANSIENT . + * used. Possible values are SOLVEPROB_INITIALIZE , + * SOLVEPROB_RESIDUAL SOLVEPROB_JACOBIAN SOLVEPROB_TRANSIENT . * * @param time_scale Time over which to integrate the surface equations, * where applicable diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 702e1f3b5..832c75c45 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -304,23 +304,6 @@ namespace Cantera { err("getdlnActCoeffdT"); } - //! Get the array of change in the log activity coefficients w.r.t. change in state (change temp, change mole fractions) - /*! - * This function is a virtual class, but it first appears in GibbsExcessVPSSTP - * class and derived classes from GibbsExcessVPSSTP. - * - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can gradX/X. - * - * @param dT Input of temperature change - * @param dX Input vector of changes in mole fraction. length = m_kk - * @param dlnActCoeff Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { - err("getdlnActCoeff"); - } - //! Get the array of log concentration-like derivatives of the //! log activity coefficients /*! diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 5beb7725f..c7a1540da 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -1441,12 +1441,19 @@ namespace Cantera { } } - - - - // get the gradient in the activity coefficients - - void IonsFromNeutralVPSSTP::getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { + //==================================================================================================================== + // Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + // a line in parameter space or along a line in physical space + /* + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + */ + void IonsFromNeutralVPSSTP::getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { int k, icat, jNeut; doublereal fmij; int numNeutMolSpec; @@ -1456,7 +1463,7 @@ namespace Cantera { GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); if (!geThermo) { for ( k = 0; k < m_kk; k++ ){ - dlnActCoeff[k] = dX[k]/moleFractions_[k]; + dlnActCoeffds[k] = dXds[k] / moleFractions_[k]; } return; } @@ -1466,11 +1473,11 @@ namespace Cantera { vector_fp dX_NeutralMolecule(numNeutMolSpec); - getNeutralMoleculeMoleGrads(DATA_PTR(dX),DATA_PTR(dX_NeutralMolecule)); + getNeutralMoleculeMoleGrads(DATA_PTR(dXds),DATA_PTR(dX_NeutralMolecule)); // All mole fractions returned to normal - geThermo->getdlnActCoeff(dT, DATA_PTR(dX_NeutralMolecule), DATA_PTR(dlnActCoeff_NeutralMolecule)); + geThermo->getdlnActCoeffds(dTds, DATA_PTR(dX_NeutralMolecule), DATA_PTR(dlnActCoeff_NeutralMolecule)); switch (ionSolnType_) { case cIonSolnType_PASSTHROUGH: @@ -1483,19 +1490,19 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeff[icat] = dlnActCoeff_NeutralMolecule[jNeut]/fmij; + dlnActCoeffds[icat] = dlnActCoeff_NeutralMolecule[jNeut]/fmij; } // Do the anion list icat = anionList_[0]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeff[icat]= 0.0; + dlnActCoeffds[icat]= 0.0; // Do the list of neutral molecules for (k = 0; k < numPassThroughSpecies_; k++) { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeff[icat] = dlnActCoeff_NeutralMolecule[jNeut]; + dlnActCoeffds[icat] = dlnActCoeff_NeutralMolecule[jNeut]; } break; @@ -1511,8 +1518,8 @@ namespace Cantera { } } - - // Update the temperatture derivative of the ln activity coefficients + //==================================================================================================================== + // Update the temperature derivative of the ln activity coefficients /* * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 2aa23319b..5393fa9ff 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -404,20 +404,19 @@ namespace Cantera { */ virtual void getPartialMolarEntropies(doublereal* sbar) const; - //! Get the array of change in the log activity coefficients w.r.t. change in state (change temp, change mole fractions) + + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space /*! - * This function is a virtual class, but it first appears in GibbsExcessVPSSTP - * class and derived classes from GibbsExcessVPSSTP. * - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can gradX/X. - * - * @param dT Input of temperature change - * @param dX Input vector of changes in mole fraction. length = m_kk - * @param dlnActCoeff Output vector of derivatives of the - * log Activity Coefficients. length = m_kk + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk */ - virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const; + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const; //! Get the array of log concentration-like derivatives of the //! log activity coefficients diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 708d0e130..cd28e0497 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -747,8 +747,7 @@ namespace Cantera { } - - + //=================================================================================================================== // Update the activity coefficients /* * This function will be called to update the internally storred @@ -761,64 +760,25 @@ namespace Cantera { double XA, XB, XK, g0 , g1; double T = temperature(); double RT = GasConstant*T; - fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); - for ( iK = 0; iK < m_kk; iK++ ){ - XK = moleFractions_[iK]; - for (int i = 0; i < numBinaryInteractions_; i++) { - iA = m_pSpecies_A_ij[i]; iB = m_pSpecies_B_ij[i]; - delAK = 0; delBK = 0; - - if (iA==iK) delAK = 1; + if (iA==iK) delAK = 1; else if (iB==iK) delBK = 1; - XA = moleFractions_[iA]; XB = moleFractions_[iB]; - g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - - lnActCoeff_Scaled_[iK] += (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; - //lnActCoeff_Scaled_[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + lnActCoeff_Scaled_[iK] += (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; } } } - - - /* - // Not Right??? - void MargulesVPSSTP::s_update_lnActCoeff() const { - - int iA, iB; - double XA, XB, g0 , g1; - double T = temperature(); - - fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); - - double RT = GasConstant * temperature(); - for (int i = 0; i < numBinaryInteractions_; i++) { - iA = m_pSpecies_A_ij[i]; - iB = m_pSpecies_B_ij[i]; - - XA = moleFractions_[iA]; - XB = moleFractions_[iB]; - - g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT ; - g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - - lnActCoeff_Scaled_[iA] += XB * XB * (g0 + g1 * (XB - XA)); - lnActCoeff_Scaled_[iB] += XA * XA * g0 + XA * XB * g1 * (2 * XA); - } - } - */ - + //=================================================================================================================== // Update the derivative of the log of the activity coefficients wrt T /* * This function will be called to update the internally storred @@ -828,89 +788,61 @@ namespace Cantera { */ void MargulesVPSSTP::s_update_dlnActCoeff_dT() const { int iA, iB, iK, delAK, delBK; - double XA, XB, XK, g0 , g1; - double T = temperature(); - double RTT = GasConstant*T*T; - + doublereal XA, XB, XK, g0, g1; + doublereal T = temperature(); + doublereal RTT = GasConstant*T*T; fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); - for ( iK = 0; iK < m_kk; iK++ ){ - XK = moleFractions_[iK]; - for (int i = 0; i < numBinaryInteractions_; i++) { - iA = m_pSpecies_A_ij[i]; iB = m_pSpecies_B_ij[i]; - delAK = 0; delBK = 0; - - if (iA==iK) delAK = 1; + if (iA==iK) delAK = 1; else if (iB==iK) delBK = 1; - XA = moleFractions_[iA]; XB = moleFractions_[iB]; - g0 = -m_HE_b_ij[i] / RTT; g1 = -m_HE_c_ij[i] / RTT; - - double temp = (delAK*XB+XA*delBK-XA*XB)*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + double temp = (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; dlnActCoeffdT_Scaled_[iK] += temp; - d2lnActCoeffdT2_Scaled_[iK] -= 2*temp/T; + d2lnActCoeffdT2_Scaled_[iK] -= 2.0 * temp / T; } } } - - /* Not Right??? - void MargulesVPSSTP::s_update_dlnActCoeff_dT() const {} - - int iA, iB; - doublereal XA, XB, h0 , h1; - doublereal T = temperature(); - - fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); - - doublereal RTT = GasConstant * T * T; - for (int i = 0; i < numBinaryInteractions_; i++) { - iA = m_pSpecies_A_ij[i]; - iB = m_pSpecies_B_ij[i]; - - XA = moleFractions_[iA]; - XB = moleFractions_[iB]; - - h0 = m_HE_b_ij[i]; - h1 = m_HE_c_ij[i]; - - dlnActCoeffdT_Scaled_[iA] += -(XB * XB * (h0 + h1 * (XB - XA))) / RTT; - dlnActCoeffdT_Scaled_[iB] += -(XA * XA * h0 + XA * XB * h1 * (2 * XA))/RTT; - } - } - */ - + //==================================================================================================================== void MargulesVPSSTP::getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { s_update_dlnActCoeff_dT(); for (int k = 0; k < m_kk; k++) { dlnActCoeffdT[k] = dlnActCoeffdT_Scaled_[k]; } } - + //==================================================================================================================== void MargulesVPSSTP::getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const { s_update_dlnActCoeff_dT(); for (int k = 0; k < m_kk; k++) { d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k]; } } + //==================================================================================================================== - // calculate the change of the log of the activity coefficients wrt change in state: dT, dX + // Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + // a line in parameter space or along a line in physical space /* - * This function will be called to calculate gradient of the - * logarithm of the activity coefficients based on gradients in temperature and mole fraction. * - * he = X_A X_B(B + C X_B) + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. */ - void MargulesVPSSTP::getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal* dlnActCoeff) const { + void MargulesVPSSTP::getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + + int iA, iB, iK, delAK, delBK; double XA, XB, XK, g0 , g1, dXA, dXB; double T = temperature(); @@ -922,7 +854,7 @@ namespace Cantera { for ( iK = 0; iK < m_kk; iK++ ){ XK = moleFractions_[iK]; - dlnActCoeff[iK] = 0.0; + dlnActCoeffds[iK] = 0.0; for (int i = 0; i < numBinaryInteractions_; i++) { @@ -938,18 +870,19 @@ namespace Cantera { XA = moleFractions_[iA]; XB = moleFractions_[iB]; - dXA = dX[iA]; - dXB = dX[iB]; + dXA = dXds[iA]; + dXB = dXds[iB]; g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - dlnActCoeff[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB + dlnActCoeffdT_Scaled_[iK]*dT; + dlnActCoeffds[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB + + dlnActCoeffdT_Scaled_[iK]*dTds; } } } - - // Update the derivative of the log of the activity coefficients wrt ln(X) + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt dlnN /* * This function will be called to update the internally stored gradients of the * logarithm of the activity coefficients. These are used in the determination @@ -1017,25 +950,6 @@ namespace Cantera { dlnActCoeffdlnX_Scaled_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); dlnActCoeffdlnX_Scaled_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); } - - /* - // Wrong!!! - for (int i = 0; i < numBinaryInteractions_; i++) { - iA = m_pSpecies_A_ij[i]; - iB = m_pSpecies_B_ij[i]; - - XA = moleFractions_[iA]; - XB = moleFractions_[iB]; - - g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT ; - g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - - dlnActCoeffdlnX_Scaled_[iA] += XA * ( ( - 2.0 + 2.0 * XA ) * g0 - + ( - 4.0 + 10.0 * XA - 6.0 * XA*XA ) * g1 ) ; - dlnActCoeffdlnX_Scaled_[iB] += XB * ( ( - 2.0 + 2.0 * XB ) * g0 - + ( 2.0 - 8.0 * XB + 6.0 * XB*XB ) * g1 ) ; - } - */ } diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 7e92c4a6b..773cb7987 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -78,7 +78,9 @@ namespace Cantera { *

Specification of Solution Thermodynamic Properties

*
* - * The excess Gibbs free energy + * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. + * This is the generalization of the Margules formulation within a phase + * that has more than 2 species. * * \f[ * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) @@ -98,6 +100,12 @@ namespace Cantera { * a_k = \gamma_k X_k * \f] * + * where + * + * \f[ + * R T \log( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} + * \f] + * * where \f$ X_k \f$ is the mole fraction of species k. * The chemical potential for species k is equal to * @@ -107,7 +115,6 @@ namespace Cantera { * * In terms of the reference state, the above can be rewritten * - * * \f[ * \mu_k(T,P) = \mu^{ref}_k(T, P) + R T \log(\frac{P X_k}{P_{ref}}) * \f] @@ -640,19 +647,19 @@ namespace Cantera { */ void getElectrochemPotentials(doublereal* mu) const; - - //! Get the array of change in the log activity coefficients with change in state (change temp, change mole fractions) + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space /*! - * This function is a virtual class, but it first appears in GibbsExcessVPSSTP - * class and derived classes from GibbsExcessVPSSTP. - * - * units = 1/Kelvin - * - * @param dlnActCoeff Output vector of temperature derivatives of the - * log Activity Coefficients. length = m_kk * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. */ - virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeffdT) const; + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; + //! Get the array of temperature second derivatives of the log activity coefficients /*! diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 1d3f82443..a72644b67 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -884,20 +884,20 @@ namespace Cantera { return err("cv_mole"); } - - //! Get the change in activity coefficients w.r.t. change in state - //! (temp, mole fraction, etc.) + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can gradX/X. * - * @param dT Input of temperature change - * @param dX Input vector of changes in mole fraction. length = m_kk - * @param dlnActCoeff Output vector of derivatives of the - * log Activity Coefficients. length = m_kk + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. */ - virtual void getdlnActCoeff(const doublereal dT, const doublereal * const dX, doublereal *dlnActCoeff) const { - err("getdlnActCoeff"); + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + err("getdlnActCoeffds"); } //! Get the array of log concentration-like derivatives of the diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index eed8b7c53..2c1dd2a65 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -1504,7 +1504,7 @@ namespace Cantera { for (k = 0; k < m_nDim; k++ ) { grad_T = m_Grad_T[k]; grad_X.assign(m_Grad_X.begin()+m_nsp*k,m_Grad_X.begin()+m_nsp*(k+1)); - m_thermo->getdlnActCoeff( grad_T, DATA_PTR(grad_X), DATA_PTR(grad_lnAC) ); + m_thermo->getdlnActCoeffds( grad_T, DATA_PTR(grad_X), DATA_PTR(grad_lnAC) ); for ( int i = 0; i < m_nsp; i++ ) if (m_molefracs[i] < 1.e-15) grad_lnAC[i] = 0; @@ -1517,7 +1517,6 @@ namespace Cantera { return; } - /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index a463792d6..6a3009c04 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -552,7 +552,7 @@ namespace Cantera { //! Return the species diffusive mass fluxes wrt to //! the averaged velocity in [kmol/m^2/s]. - /** + /*! * * The diffusive mass flux of species \e k is computed * using the Stefan-Maxwell equation @@ -606,7 +606,7 @@ namespace Cantera { //! Return the species diffusive mass fluxes wrt to //! the averaged velocity in [kmol/m^2/s]. - /** + /*! * * The diffusive mass flux of species \e k is computed * using the Stefan-Maxwell equation @@ -658,7 +658,7 @@ namespace Cantera { //! Return the species diffusive velocities relative to //! the averaged velocity. - /** + /*! * This method acts similarly to getSpeciesVdiffES() but * requires all gradients to be preset using methods * set_Grad_X(), set_Grad_V(), set_Grad_T(). @@ -673,7 +673,7 @@ namespace Cantera { //! Return the species diffusive fluxes relative to //! the averaged velocity. - /** + /*! * This method acts similarly to getSpeciesFluxesES() but * requires all gradients to be preset using methods * set_Grad_X(), set_Grad_V(), set_Grad_T(). @@ -728,7 +728,7 @@ namespace Cantera { //! Updates the internal value of the gradient of the //! logarithm of the activity, which is //! used in the gradient of the chemical potential. - /** + /*! * Evaluate the gradients of the activity * as they alter the diffusion coefficient. * @@ -753,7 +753,7 @@ namespace Cantera { //! Solve the stefan_maxell equations for the diffusive fluxes. - /** + /*! * The diffusive mass flux of species \e k is computed * using the Stefan-Maxwell equation * \f[ @@ -777,10 +777,10 @@ namespace Cantera { * be specified as relative to a specific species (i.e. a * solvent) all according to the \verbatim * \endverbatim input para - * The gradient in the activity coefficient requires the use of thermophase - * getdlnActCoeff that calculates its change based on a change in the state - * i.e. temperature and composition of each species. - * First implemented in MargulesVPSSTP.cppmeter. + * The gradient in the activity coefficient requires the use of thermophase + * getdlnActCoeff that calculates its change based on a change in the state + * i.e. temperature and composition of each species. + * First implemented in MargulesVPSSTP.cppmeter. * * One of the Stefan Maxwell equations is replaced by the appropriate * definition of the mass-averaged velocity, the mole-averaged velocity diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index 642a3afa0..457ae6662 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -323,7 +323,7 @@ EXTRACT_PRIVATE = YES # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. -EXTRACT_STATIC = NO +EXTRACT_STATIC = YES # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. @@ -418,7 +418,7 @@ INLINE_INFO = YES # alphabetically by member name. If set to NO the members will appear in # declaration order. -SORT_MEMBER_DOCS = YES +SORT_MEMBER_DOCS = NO # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically @@ -445,7 +445,7 @@ SORT_GROUP_NAMES = NO # Note: This option applies only to the class list, not to the # alphabetical list. -SORT_BY_SCOPE_NAME = NO +SORT_BY_SCOPE_NAME = YES # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo @@ -1475,7 +1475,7 @@ MACRO_EXPANSION = YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. -EXPAND_ONLY_PREDEF = YES +EXPAND_ONLY_PREDEF = YES # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # in the INCLUDE_PATH (see below) will be search if a #include is found. @@ -1506,14 +1506,15 @@ INCLUDE_FILE_PATTERNS = PREDEFINED = WITH_HTML_LOGS \ WITH_PURE_FLUIDS \ THREAD_SAFE_CANTERA \ - WITH_LATTICE_SOLID + WITH_LATTICE_SOLID \ + HAVE_CONFIG_H # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition. -EXPAND_AS_DEFINED = YES +EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all function-like macros that are alone From f18989a7beff186670bdc70ec68b6f5ccbe1269c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 2 Aug 2010 23:21:31 +0000 Subject: [PATCH 210/446] Roughed in a new derivative routine for activity coefficients that has the proper format. We have yet to implement this format. --- Cantera/src/thermo/ThermoPhase.h | 180 ++++++++++++++++++------------- 1 file changed, 104 insertions(+), 76 deletions(-) diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index a72644b67..d12f1330f 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -847,6 +847,17 @@ namespace Cantera { doublereal maxTemp(int k = -1) const { return m_spthermo->maxTemp(k); } + + //! Returns the chargeNeutralityNecessity boolean + /*! + * Some phases must have zero net charge in order for their thermodynamics functions to be valid. + * If this is so, then the value returned from this function is true. + * If this is not the case, then this is false. Now, ideal gases have this parameter set to false, + * while solution with molality-based activity coefficients have this parameter set to true. + */ + bool chargeNeutralityNecessary() const { + return m_chargeNeutralityNecessary; + } /** * @} @@ -884,66 +895,6 @@ namespace Cantera { return err("cv_mole"); } - //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along - //! a line in parameter space or along a line in physical space - /*! - * - * @param dTds Input of temperature change along the path - * @param dXds Input vector of changes in mole fraction along the path. length = m_kk - * Along the path length it must be the case that the mole fractions sum to one. - * @param dlnActCoeffds Output vector of the directional derivatives of the - * log Activity Coefficients along the path. length = m_kk - * units are 1/units(s). if s is a physical coordinate then the units are 1/m. - */ - virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, - doublereal *dlnActCoeffds) const { - err("getdlnActCoeffds"); - } - - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnX Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { - err("getdlnActCoeffdlnX"); - } - - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. moles) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnN Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { - err("getdlnActCoeffdlnN"); - } - /** * @} @@ -2098,24 +2049,99 @@ namespace Cantera { */ virtual void setStateFromXML(const XML_Node& state); - - //@} - - //! Returns the chargeNeutralityNecessity boolean - /*! - * Some phases must have zero net charge in order for - * their thermodynamics functions to be valid. - * If this is so, then the value returned from this - * function is true. - * If this is not the case, then this is false. - * Now, ideal gases have this parameter set to false, - * while solution with molality-based activity - * coefficients have this parameter set to true. + /** + * @} + * @name Derivatives of Thermodynamic Variables needed for Applications + * @{ */ - bool chargeNeutralityNecessary() const { - return m_chargeNeutralityNecessary; + + //! Get the change in activity coefficients wrt changes in state (temp, mole fraction, etc) along + //! a line in parameter space or along a line in physical space + /*! + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + err("getdlnActCoeffds"); } + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + err("getdlnActCoeffdlnX"); + } + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + err("getdlnActCoeffdlnN"); + } + + //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d n_k }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const { + err("getdlnActCoeffdN"); + } + + /** + * @} + * @name Printing + * @{ + */ //! returns a summary of the state of the phase as a string /*! @@ -2130,7 +2156,9 @@ namespace Cantera { * the phase */ virtual void reportCSV(std::ofstream& csvFile) const; - + + //@} + protected: //! Pointer to the calculation manager for species From 673cf207ed34be2a0d79996d999e87534ee75a9c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Aug 2010 15:55:51 +0000 Subject: [PATCH 211/446] Worked on the Margules Documentation --- Cantera/src/thermo/MargulesVPSSTP.cpp | 4 +- Cantera/src/thermo/MargulesVPSSTP.h | 145 ++++++++++++++++---------- tools/doc/Cantera.cfg.in | 4 +- 3 files changed, 95 insertions(+), 58 deletions(-) diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index cd28e0497..8664a1ba9 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -612,9 +612,7 @@ namespace Cantera { * Get the standard state values in m^3 kmol-1 */ getStandardVolumes(vbar); - //cout << "species name(0) = " << speciesName(0) << endl; - //cout << "iA = " << speciesName(m_pSpecies_A_ij[0]) << endl; - //cout << "iB = " << speciesName(m_pSpecies_B_ij[0]) << endl; + for ( iK = 0; iK < m_kk; iK++ ){ delAK = 0; diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 773cb7987..9ebfd9aa1 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -78,8 +78,10 @@ namespace Cantera { *

Specification of Solution Thermodynamic Properties

*
* - * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. - * This is the generalization of the Margules formulation within a phase + * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. + * Each of the interactions are binary interactions involving two of the species in the phase, denoted, Ai + * and Bi. + * This is the generalization of the Margules formulation for a phase * that has more than 2 species. * * \f[ @@ -103,44 +105,53 @@ namespace Cantera { * where * * \f[ - * R T \log( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} + * R T \ln( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} * \f] * - * where \f$ X_k \f$ is the mole fraction of species k. + * Taking the derivatives results in the following expression + * + * \f[ + * R T \ln( \gamma_k )= \sum_i \left( \left( \delta_{Ai,k} X_{Bi} + \delta_{Bi,k} X_{Ai} - X_{Ai} X_{Bi} \right) + * \left( g^E_{o,i} + g^E_{1,i} X_{Bi} \right) + + * \left( \delta_{Ai,k} - X_{Bi} \right) X_{Ai} X_{Bi} g^E_{1,i} \right) + * \f] + * where + * \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ + * and where \f$ X_k \f$ is the mole fraction of species k. + * + * This object inherits from the class VPStandardStateTP. Therefore, the specification and + * calculation of all standard state and reference state values are handled at that level. Various functional + * forms for the standard state are permissible. * The chemical potential for species k is equal to * * \f[ - * \mu_k(T,P) = \mu^o_k(T, P) + R T \log(\gamma_k X_k) - * \f] - * - * In terms of the reference state, the above can be rewritten - * - * \f[ - * \mu_k(T,P) = \mu^{ref}_k(T, P) + R T \log(\frac{P X_k}{P_{ref}}) + * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) * \f] * * The partial molar entropy for species k is given by the following relation, * * \f[ - * \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(\frac{P X_k}{P_{ref}}) + * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) + * - R T \frac{d \ln(\gamma_k) }{dT} * \f] * - * The partial molar enthalpy for species k is + * The partial molar enthalpy for species k is given by * * \f[ - * \tilde{h}_k(T,P) = h^o_k(T,P) = h^{ref}_k(T) + * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * - * The partial molar Internal Energy for species k is + * The partial molar volume for species k is * * \f[ - * \tilde{u}_k(T,P) = u^o_k(T,P) = u^{ref}_k(T) + * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} * \f] * * The partial molar Heat Capacity for species k is * * \f[ - * \tilde{Cp}_k(T,P) = Cp^o_k(T,P) = Cp^{ref}_k(T) + * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} + * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} * \f] * *
@@ -647,20 +658,6 @@ namespace Cantera { */ void getElectrochemPotentials(doublereal* mu) const; - //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along - //! a line in parameter space or along a line in physical space - /*! - * - * @param dTds Input of temperature change along the path - * @param dXds Input vector of changes in mole fraction along the path. length = m_kk - * Along the path length it must be the case that the mole fractions sum to one. - * @param dlnActCoeffds Output vector of the directional derivatives of the - * log Activity Coefficients along the path. length = m_kk - * units are 1/units(s). if s is a physical coordinate then the units are 1/m. - */ - virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; - - //! Get the array of temperature second derivatives of the log activity coefficients /*! * This function is a virtual class, but it first appears in GibbsExcessVPSSTP @@ -687,28 +684,6 @@ namespace Cantera { */ virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const; - - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnX Output vector of log(mole fraction) - * derivatives of the log Activity Coefficients. - * length = m_kk - */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; //@} @@ -799,6 +774,70 @@ namespace Cantera { */ void initThermoXML(XML_Node& phaseNode, std::string id); + /** + * @} + * @name Derivatives of Thermodynamic Variables needed for Applications + * @{ + */ + + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space + /*! + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction, + * molality, etc.) that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX Output vector of log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; + virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; + + + //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d n_k }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const { + err("getdlnActCoeffdN"); + } + //@} private: diff --git a/tools/doc/Cantera.cfg.in b/tools/doc/Cantera.cfg.in index 457ae6662..e796bec02 100755 --- a/tools/doc/Cantera.cfg.in +++ b/tools/doc/Cantera.cfg.in @@ -1655,7 +1655,7 @@ UML_LOOK = NO # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. -TEMPLATE_RELATIONS = YES +TEMPLATE_RELATIONS = NO # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented @@ -1690,7 +1690,7 @@ CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will graphical hierarchy of all classes instead of a textual one. -GRAPHICAL_HIERARCHY = YES +GRAPHICAL_HIERARCHY = NO # If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories From b6cf6b313996c5c6f8308e3b7dc2945c8833d73e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Aug 2010 21:07:28 +0000 Subject: [PATCH 212/446] Fleshed out the gradient of actcoeff wrt mole number. --- Cantera/src/base/Array.h | 11 +++ Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 22 +++++- Cantera/src/thermo/GibbsExcessVPSSTP.h | 19 +++-- Cantera/src/thermo/MargulesVPSSTP.cpp | 96 +++++++++++++++++++++--- Cantera/src/thermo/MargulesVPSSTP.h | 17 ++++- 5 files changed, 144 insertions(+), 21 deletions(-) diff --git a/Cantera/src/base/Array.h b/Cantera/src/base/Array.h index bde5f28c6..a0c637db5 100644 --- a/Cantera/src/base/Array.h +++ b/Cantera/src/base/Array.h @@ -223,6 +223,17 @@ namespace Cantera { for (; b != end(); ++b, ++xb, ++yb) *b = a*(*xb) + *yb; } + //! Set all of the entries to zero + inline void zero() { + int nn = m_nrows * m_ncols; + if (nn > 0) { + /* + * Using memset is the fastest way to zero a contiguous + * section of memory. + */ + (void) memset((void *) &m_data[0], 0, nn * sizeof(doublereal)); + } + } //! Allows setting elements using the syntax A(i,j) = x. /*! diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index fe665941a..a2cc35383 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -33,7 +33,15 @@ namespace Cantera { * */ GibbsExcessVPSSTP::GibbsExcessVPSSTP() : - VPStandardStateTP() + VPStandardStateTP(), + moleFractions_(0), + lnActCoeff_Scaled_(0), + dlnActCoeffdT_Scaled_(0), + d2lnActCoeffdT2_Scaled_(0), + dlnActCoeffdlnN_Scaled_(0), + dlnActCoeffdlnX_Scaled_(0), + dlnActCoeffdN_Scaled_(0,0), + m_pp(0) { } @@ -44,7 +52,15 @@ namespace Cantera { * has a working copy constructor */ GibbsExcessVPSSTP::GibbsExcessVPSSTP(const GibbsExcessVPSSTP &b) : - VPStandardStateTP() + VPStandardStateTP(), + moleFractions_(0), + lnActCoeff_Scaled_(0), + dlnActCoeffdT_Scaled_(0), + d2lnActCoeffdT2_Scaled_(0), + dlnActCoeffdlnN_Scaled_(0), + dlnActCoeffdlnX_Scaled_(0), + dlnActCoeffdN_Scaled_(0,0), + m_pp(0) { GibbsExcessVPSSTP::operator=(b); } @@ -69,6 +85,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_ = b.d2lnActCoeffdT2_Scaled_; dlnActCoeffdlnX_Scaled_ = b.dlnActCoeffdlnX_Scaled_; dlnActCoeffdlnN_Scaled_ = b.dlnActCoeffdlnN_Scaled_; + dlnActCoeffdN_Scaled_ = b.dlnActCoeffdN_Scaled_; m_pp = b.m_pp; return *this; @@ -328,6 +345,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_.resize(m_kk); dlnActCoeffdlnX_Scaled_.resize(m_kk); dlnActCoeffdlnN_Scaled_.resize(m_kk); + dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); m_pp.resize(m_kk); } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 832c75c45..da716c5fa 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -542,6 +542,8 @@ namespace Cantera { protected: + // HKM get rid of _Scaled_ prefix + //! Storage for the current values of the mole fractions of the species /*! * This vector is kept up-to-date when the setState functions are called. @@ -553,29 +555,36 @@ namespace Cantera { mutable std::vector moleFractions_; //! Storage for the current values of the activity coefficients of the - //! species, divided by RT + //! species mutable std::vector lnActCoeff_Scaled_; //! Storage for the current derivative values of the //! gradients with respect to temperature of the - //! log of theactivity coefficients of the species + //! log of the activity coefficients of the species mutable std::vector dlnActCoeffdT_Scaled_; //! Storage for the current derivative values of the //! gradients with respect to temperature of the - //! log of theactivity coefficients of the species + //! log of the activity coefficients of the species mutable std::vector d2lnActCoeffdT2_Scaled_; //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the - //! log of theactivity coefficients of the species + //! log of the activity coefficients of the species @deprecated mutable std::vector dlnActCoeffdlnN_Scaled_; //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the - //! log of theactivity coefficients of the species + //! log of theactivity coefficients of the species @deprecated mutable std::vector dlnActCoeffdlnX_Scaled_; + //! Storage for the current derivative values of the gradients with respect to logarithm of the species mole number of the + //! log of the activity coefficients of the species + /*! + * dlnActCoeffdN_Scaled_(k, m) is the derivative of ln(gamma_k) wrt ln mole number of species m + */ + mutable Array2D dlnActCoeffdN_Scaled_; + //! Temporary storage space that is fair game mutable std::vector m_pp; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 8664a1ba9..140f71b1f 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -375,7 +375,7 @@ namespace Cantera { //return -1.0; return 0.0; } - + //==================================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. /* @@ -667,7 +667,7 @@ namespace Cantera { // been identified. void MargulesVPSSTP::initLengths() { m_kk = nSpecies(); - + dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); } /* @@ -759,7 +759,7 @@ namespace Cantera { double T = temperature(); double RT = GasConstant*T; fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); - for ( iK = 0; iK < m_kk; iK++ ){ + for (iK = 0; iK < m_kk; iK++) { XK = moleFractions_[iK]; for (int i = 0; i < numBinaryInteractions_; i++) { iA = m_pSpecies_A_ij[i]; @@ -786,13 +786,12 @@ namespace Cantera { */ void MargulesVPSSTP::s_update_dlnActCoeff_dT() const { int iA, iB, iK, delAK, delBK; - doublereal XA, XB, XK, g0, g1; + doublereal XA, XB, g0, g1; doublereal T = temperature(); doublereal RTT = GasConstant*T*T; fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); - for ( iK = 0; iK < m_kk; iK++ ){ - XK = moleFractions_[iK]; + for (iK = 0; iK < m_kk; iK++) { for (int i = 0; i < numBinaryInteractions_; i++) { iA = m_pSpecies_A_ij[i]; iB = m_pSpecies_B_ij[i]; @@ -923,6 +922,73 @@ namespace Cantera { } } + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt dlnN + /* + * This function will be called to update the internally stored gradients of the + * logarithm of the activity coefficients. These are used in the determination + * of the diffusion coefficients. + * + * he = X_A X_B(B + C X_B) + */ + void MargulesVPSSTP::s_update_dlnActCoeff_dN() const { + int iA, iB; + doublereal delAK, delBK; + double XA, XB, g0 , g1; + double T = temperature(); + double RT = GasConstant*T; + + doublereal delAM, delBM; + + dlnActCoeffdN_Scaled_.zero(); + + /* + * Loop over the activity coefficient gamma_k + */ + for (int iK = 0; iK < m_kk; iK++) { + for (int iM = 0; iM < m_kk; iM++) { + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0.0; + delBK = 0.0; + delAM = 0.0; + delBM = 0.0; + if (iA==iK) delAK = 1.0; + else if (iB==iK) delBK = 1.0; + if (iA==iM) delAM = 1.0; + else if (iB==iM) delBM = 1.0; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + double gfac = g0 + g1 * XB; + double gggg = (delBK - XB) * g1; + + // all values of dlnActCoeffdN_Scaled_(iK, iM) hare an additional divisor of n_total + + dlnActCoeffdN_Scaled_(iK, iM) += gfac * delAK * ( - XB + delBM); + + dlnActCoeffdN_Scaled_(iK, iM) += gfac * delBK * ( - XA + delAM); + + dlnActCoeffdN_Scaled_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); + + dlnActCoeffdN_Scaled_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); + + dlnActCoeffdN_Scaled_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); + + dlnActCoeffdN_Scaled_(iK, iM) += - g1 * XA * XB * (- XB + delBM); + } + } + } + } + //==================================================================================================================== void MargulesVPSSTP::s_update_dlnActCoeff_dlnX() const { int iA, iB; @@ -950,21 +1016,31 @@ namespace Cantera { } } - + //==================================================================================================================== void MargulesVPSSTP::getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { s_update_dlnActCoeff_dlnN(); for (int k = 0; k < m_kk; k++) { dlnActCoeffdlnN[k] = dlnActCoeffdlnN_Scaled_[k]; } } + //==================================================================================================================== void MargulesVPSSTP::getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { s_update_dlnActCoeff_dlnX(); for (int k = 0; k < m_kk; k++) { dlnActCoeffdlnX[k] = dlnActCoeffdlnX_Scaled_[k]; } } - - + //==================================================================================================================== + void MargulesVPSSTP::getdlnActCoeffdN(const int ld, doublereal *dlnActCoeffdN) const { + s_update_dlnActCoeff_dN(); + double *data = & dlnActCoeffdN_Scaled_(0,0); + for (int k = 0; k < m_kk; k++) { + for (int m = 0; m < m_kk; m++) { + dlnActCoeffdN[ld * k + m] = data[m_kk * k + m]; + } + } + } + //==================================================================================================================== void MargulesVPSSTP::resizeNumInteractions(const int num) { numBinaryInteractions_ = num; m_HE_b_ij.resize(num, 0.0); @@ -984,7 +1060,7 @@ namespace Cantera { m_pSpecies_B_ij.resize(num, -1); } - + //==================================================================================================================== /* * Process an XML node called "binaryNeutralSpeciesParameters" diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 9ebfd9aa1..b35719d33 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -113,7 +113,7 @@ namespace Cantera { * \f[ * R T \ln( \gamma_k )= \sum_i \left( \left( \delta_{Ai,k} X_{Bi} + \delta_{Bi,k} X_{Ai} - X_{Ai} X_{Bi} \right) * \left( g^E_{o,i} + g^E_{1,i} X_{Bi} \right) + - * \left( \delta_{Ai,k} - X_{Bi} \right) X_{Ai} X_{Bi} g^E_{1,i} \right) + * \left( \delta_{Bi,k} - X_{Bi} \right) X_{Ai} X_{Bi} g^E_{1,i} \right) * \f] * where * \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ @@ -834,9 +834,8 @@ namespace Cantera { * @param dlnActCoeffdN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const { - err("getdlnActCoeffdN"); - } + virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const; + //@} private: @@ -898,6 +897,14 @@ namespace Cantera { */ void s_update_dlnActCoeff_dlnN() const; + //! Update the derivative of the log of the activity coefficients wrt log(moles_m) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the mole number of species + */ + void s_update_dlnActCoeff_dN() const; + private: //! Error function @@ -961,6 +968,8 @@ namespace Cantera { //! Entropy term for the quaternary mole fraction interaction of the //! excess gibbs free energy expression mutable vector_fp m_VSE_d_ij; + + //! vector of species indices representing species A in the interaction /*! From 3b8b18e72d4305d43261e1783a19a5954da9ba76 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 15:50:37 +0000 Subject: [PATCH 213/446] Changed the name of getdactcoeffdlnN to getdactcoeffdlnN_diag to reflect what it's actually doing. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 8 +-- Cantera/src/thermo/GibbsExcessVPSSTP.h | 8 +-- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 62 +++++++++---------- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 18 +++--- Cantera/src/thermo/MargulesVPSSTP.cpp | 14 ++--- Cantera/src/thermo/MargulesVPSSTP.h | 27 ++++++-- Cantera/src/thermo/ThermoPhase.h | 6 +- Cantera/src/thermo/VPStandardStateTP.h | 6 +- .../src/transport/LiquidTranInteraction.cpp | 8 +-- 9 files changed, 86 insertions(+), 71 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index a2cc35383..5dc65a056 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -38,7 +38,7 @@ namespace Cantera { lnActCoeff_Scaled_(0), dlnActCoeffdT_Scaled_(0), d2lnActCoeffdT2_Scaled_(0), - dlnActCoeffdlnN_Scaled_(0), + dlnActCoeffdlnN_diag_(0), dlnActCoeffdlnX_Scaled_(0), dlnActCoeffdN_Scaled_(0,0), m_pp(0) @@ -57,7 +57,7 @@ namespace Cantera { lnActCoeff_Scaled_(0), dlnActCoeffdT_Scaled_(0), d2lnActCoeffdT2_Scaled_(0), - dlnActCoeffdlnN_Scaled_(0), + dlnActCoeffdlnN_diag_(0), dlnActCoeffdlnX_Scaled_(0), dlnActCoeffdN_Scaled_(0,0), m_pp(0) @@ -84,7 +84,7 @@ namespace Cantera { dlnActCoeffdT_Scaled_ = b.dlnActCoeffdT_Scaled_; d2lnActCoeffdT2_Scaled_ = b.d2lnActCoeffdT2_Scaled_; dlnActCoeffdlnX_Scaled_ = b.dlnActCoeffdlnX_Scaled_; - dlnActCoeffdlnN_Scaled_ = b.dlnActCoeffdlnN_Scaled_; + dlnActCoeffdlnN_diag_ = b.dlnActCoeffdlnN_diag_; dlnActCoeffdN_Scaled_ = b.dlnActCoeffdN_Scaled_; m_pp = b.m_pp; @@ -344,7 +344,7 @@ namespace Cantera { dlnActCoeffdT_Scaled_.resize(m_kk); d2lnActCoeffdT2_Scaled_.resize(m_kk); dlnActCoeffdlnX_Scaled_.resize(m_kk); - dlnActCoeffdlnN_Scaled_.resize(m_kk); + dlnActCoeffdlnN_diag_.resize(m_kk); dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); m_pp.resize(m_kk); } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index da716c5fa..da4d91394 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -319,11 +319,11 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnN Output vector of derivatives of the + * @param dlnActCoeffdlnN_diag Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { - err("getdlnActCoeffdlnN"); + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + err("getdlnActCoeffdlnN_diag"); } //! Get the array of log concentration-like derivatives of the @@ -571,7 +571,7 @@ namespace Cantera { //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the //! log of the activity coefficients of the species @deprecated - mutable std::vector dlnActCoeffdlnN_Scaled_; + mutable std::vector dlnActCoeffdlnN_diag_; //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index c7a1540da..96726725b 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -199,7 +199,7 @@ namespace Cantera { gammaNeutralMolecule_ = b.gammaNeutralMolecule_; dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_; dlnActCoeffdlnX_NeutralMolecule_ = b.dlnActCoeffdlnX_NeutralMolecule_; - dlnActCoeffdlnN_NeutralMolecule_ = b.dlnActCoeffdlnN_NeutralMolecule_; + dlnActCoeffdlnN_diag_NeutralMolecule_ = b.dlnActCoeffdlnN_diag_NeutralMolecule_; return *this; } @@ -621,31 +621,31 @@ namespace Cantera { } } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. moles) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnN Output vector of log(mole fraction) - * derivatives of the log Activity Coefficients. - * length = m_kk - */ - void IonsFromNeutralVPSSTP::getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { + // Get the array of log concentration-like derivatives of the + // log activity coefficients + /* + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN_diag Output vector of log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + void IonsFromNeutralVPSSTP::getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { s_update_lnActCoeff(); - s_update_dlnActCoeff_dlnN(); + s_update_dlnActCoeff_dlnN_diag(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnN[k] = dlnActCoeffdlnN_Scaled_[k]; + dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k]; } } @@ -1193,9 +1193,9 @@ namespace Cantera { gammaNeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnX_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); - dlnActCoeffdlnN_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); + dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); } - + //==================================================================================================================== static double factorOverlap(const std::vector& elnamesVN , const std::vector& elemVectorN, const int nElementsN, @@ -1640,7 +1640,7 @@ namespace Cantera { * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients */ - void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN() const { + void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN_diag() const { int k, icat, jNeut; doublereal fmij; /* @@ -1648,11 +1648,11 @@ namespace Cantera { */ GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); if (!geThermo) { - fvo_zero_dbl_1(dlnActCoeffdlnN_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnN_diag_, m_kk); return; } - geThermo->getdlnActCoeffdlnN(DATA_PTR(dlnActCoeffdlnN_NeutralMolecule_)); + geThermo->getdlnActCoeffdlnN_diag(DATA_PTR(dlnActCoeffdlnN_diag_NeutralMolecule_)); switch (ionSolnType_) { case cIonSolnType_PASSTHROUGH: @@ -1665,19 +1665,19 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeffdlnN_Scaled_[icat] = dlnActCoeffdlnN_NeutralMolecule_[jNeut]/fmij; + dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]/fmij; } // Do the anion list icat = anionList_[0]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnN_Scaled_[icat]= 0.0; + dlnActCoeffdlnN_diag_[icat]= 0.0; // Do the list of neutral molecules for (k = 0; k < numPassThroughSpecies_; k++) { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnN_Scaled_[icat] = dlnActCoeffdlnN_NeutralMolecule_[jNeut]; + dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]; } break; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 5393fa9ff..e590366f0 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -440,25 +440,21 @@ namespace Cantera { virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; //! Get the array of log concentration-like derivatives of the - //! log activity coefficients + //! log activity coefficients - diagonal components /*! * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. number of moles) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. + * logarithm of the species mole numbe. This routine just does the diagonal entries. * * units = dimensionless * - * @param dlnActCoeffdlnN Output vector of log(mole fraction) + * @param dlnActCoeffdlnN_diag Output vector of diagonal components of the log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; //! Get the Salt Dissociation Coefficients //! Returns the vector of dissociation coefficients and vector of charges @@ -751,13 +747,13 @@ namespace Cantera { void s_update_dlnActCoeff_dlnX() const; //! Update the derivative of the log of the activity coefficients - //! wrt log(number of moles) + //! wrt log(number of moles) - diagonal components /*! * This function will be called to update the internally storred * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the number of moles of given species. */ - void s_update_dlnActCoeff_dlnN() const; + void s_update_dlnActCoeff_dlnN_diag() const; private: @@ -896,7 +892,7 @@ namespace Cantera { mutable std::vector dlnActCoeff_NeutralMolecule_; mutable std::vector dlnActCoeffdT_NeutralMolecule_; mutable std::vector dlnActCoeffdlnX_NeutralMolecule_; - mutable std::vector dlnActCoeffdlnN_NeutralMolecule_; + mutable std::vector dlnActCoeffdlnN_diag_NeutralMolecule_; }; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 140f71b1f..065be1023 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -887,13 +887,13 @@ namespace Cantera { * * he = X_A X_B(B + C X_B) */ - void MargulesVPSSTP::s_update_dlnActCoeff_dlnN() const { + void MargulesVPSSTP::s_update_dlnActCoeff_dlnN_diag() const { int iA, iB, iK, delAK, delBK; double XA, XB, XK, g0 , g1; double T = temperature(); double RT = GasConstant*T; - fvo_zero_dbl_1(dlnActCoeffdlnN_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnN_diag_, m_kk); for ( iK = 0; iK < m_kk; iK++ ){ @@ -916,9 +916,9 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - dlnActCoeffdlnN_Scaled_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); } - dlnActCoeffdlnN_Scaled_[iK] = XK*dlnActCoeffdlnN_Scaled_[iK]-XK; + dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK]-XK; } } @@ -1017,10 +1017,10 @@ namespace Cantera { } //==================================================================================================================== - void MargulesVPSSTP::getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { - s_update_dlnActCoeff_dlnN(); + void MargulesVPSSTP::getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + s_update_dlnActCoeff_dlnN_diag(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnN[k] = dlnActCoeffdlnN_Scaled_[k]; + dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k]; } } //==================================================================================================================== diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index b35719d33..c607a50e0 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -813,7 +813,26 @@ namespace Cantera { * length = m_kk */ virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const; + + //! Get the array of derivatives of the log activity coefficients wrt mole numbers - diagonal only + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction, + * molality, etc.) that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX Output vector of the diagonal entries for the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers @@ -889,13 +908,13 @@ namespace Cantera { void s_update_dlnActCoeff_dlnX() const; //! Update the derivative of the log of the activity coefficients - //! wrt log(moles) + //! wrt log(moles) - diagonal only /*! - * This function will be called to update the internally storred + * This function will be called to update the internally storred diagonal entries for the * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the moles. */ - void s_update_dlnActCoeff_dlnN() const; + void s_update_dlnActCoeff_dlnN_diag() const; //! Update the derivative of the log of the activity coefficients wrt log(moles_m) /*! diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index d12f1330f..649606e78 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2108,11 +2108,11 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnN Output vector of derivatives of the + * @param dlnActCoeffdlnN_diag Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { - err("getdlnActCoeffdlnN"); + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + err("getdlnActCoeffdlnN_diag"); } //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers diff --git a/Cantera/src/thermo/VPStandardStateTP.h b/Cantera/src/thermo/VPStandardStateTP.h index 7990b2cff..ea6b0eb0f 100644 --- a/Cantera/src/thermo/VPStandardStateTP.h +++ b/Cantera/src/thermo/VPStandardStateTP.h @@ -135,11 +135,11 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnN Output vector of derivatives of the + * @param dlnActCoeffdlnN_diag Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnN(doublereal *dlnActCoeffdlnN) const { - err("getdlnActCoeffdlnN"); + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + err("getdlnActCoeffdlnN_diag"); } //! Get the array of log concentration-like derivatives of the diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index e4585f832..76aa063f2 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -728,14 +728,14 @@ namespace Cantera { int zM = charges[anion[0]]; doublereal xA, xB, eps; doublereal inv_vP_vM_MutualDiff; - vector_fp dlnActCoeffdlnN; - dlnActCoeffdlnN.resize(neut_molefracs.size(),0.0); - marg_thermo->getdlnActCoeffdlnN(&dlnActCoeffdlnN[0]); + vector_fp dlnActCoeffdlnN_diag; + dlnActCoeffdlnN_diag.resize(neut_molefracs.size(),0.0); + marg_thermo->getdlnActCoeffdlnN_diag(&dlnActCoeffdlnN_diag[0]); xA = neut_molefracs[neutMolIndex[cation[0]]]; xB = neut_molefracs[neutMolIndex[cation[1]]]; eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); - inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); + inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN_diag[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN_diag[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); mat.resize(nsp, nsp, 0.0 ); mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; From 7b063f3fc83a0489efdc8a2851e1349e5069af47 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 16:06:14 +0000 Subject: [PATCH 214/446] changed the name of getdlnActcoeffdlnX to getdlnActCoeffdlnX_diag to reflect what it is really doing. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 8 ++-- Cantera/src/thermo/GibbsExcessVPSSTP.h | 46 +------------------- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 28 ++++++------ Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 16 +++---- Cantera/src/thermo/MargulesVPSSTP.cpp | 14 +++--- Cantera/src/thermo/MargulesVPSSTP.h | 19 +++----- Cantera/src/thermo/ThermoPhase.cpp | 3 +- Cantera/src/thermo/ThermoPhase.h | 8 ++-- Cantera/src/thermo/VPStandardStateTP.h | 22 ---------- 9 files changed, 45 insertions(+), 119 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 5dc65a056..5ee5c16e8 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -39,7 +39,7 @@ namespace Cantera { dlnActCoeffdT_Scaled_(0), d2lnActCoeffdT2_Scaled_(0), dlnActCoeffdlnN_diag_(0), - dlnActCoeffdlnX_Scaled_(0), + dlnActCoeffdlnX_diag_(0), dlnActCoeffdN_Scaled_(0,0), m_pp(0) { @@ -58,7 +58,7 @@ namespace Cantera { dlnActCoeffdT_Scaled_(0), d2lnActCoeffdT2_Scaled_(0), dlnActCoeffdlnN_diag_(0), - dlnActCoeffdlnX_Scaled_(0), + dlnActCoeffdlnX_diag_(0), dlnActCoeffdN_Scaled_(0,0), m_pp(0) { @@ -83,7 +83,7 @@ namespace Cantera { lnActCoeff_Scaled_ = b.lnActCoeff_Scaled_; dlnActCoeffdT_Scaled_ = b.dlnActCoeffdT_Scaled_; d2lnActCoeffdT2_Scaled_ = b.d2lnActCoeffdT2_Scaled_; - dlnActCoeffdlnX_Scaled_ = b.dlnActCoeffdlnX_Scaled_; + dlnActCoeffdlnX_diag_ = b.dlnActCoeffdlnX_diag_; dlnActCoeffdlnN_diag_ = b.dlnActCoeffdlnN_diag_; dlnActCoeffdN_Scaled_ = b.dlnActCoeffdN_Scaled_; m_pp = b.m_pp; @@ -343,7 +343,7 @@ namespace Cantera { lnActCoeff_Scaled_.resize(m_kk); dlnActCoeffdT_Scaled_.resize(m_kk); d2lnActCoeffdT2_Scaled_.resize(m_kk); - dlnActCoeffdlnX_Scaled_.resize(m_kk); + dlnActCoeffdlnX_diag_.resize(m_kk); dlnActCoeffdlnN_diag_.resize(m_kk); dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); m_pp.resize(m_kk); diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index da4d91394..63b387da6 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -304,50 +304,8 @@ namespace Cantera { err("getdlnActCoeffdT"); } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnN_diag Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { - err("getdlnActCoeffdlnN_diag"); - } - - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. number of moles in - * in a unit volume. ) that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnX Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { - err("getdlnActCoeffdlnX"); - } + //@} /// @name Partial Molar Properties of the Solution //@{ @@ -576,7 +534,7 @@ namespace Cantera { //! Storage for the current derivative values of the //! gradients with respect to logarithm of the mole fraction of the //! log of theactivity coefficients of the species @deprecated - mutable std::vector dlnActCoeffdlnX_Scaled_; + mutable std::vector dlnActCoeffdlnX_diag_; //! Storage for the current derivative values of the gradients with respect to logarithm of the species mole number of the //! log of the activity coefficients of the species diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 96726725b..8aaeb95da 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -198,7 +198,7 @@ namespace Cantera { muNeutralMolecule_ = b.muNeutralMolecule_; gammaNeutralMolecule_ = b.gammaNeutralMolecule_; dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_; - dlnActCoeffdlnX_NeutralMolecule_ = b.dlnActCoeffdlnX_NeutralMolecule_; + dlnActCoeffdlnX_diag_NeutralMolecule_ = b.dlnActCoeffdlnX_diag_NeutralMolecule_; dlnActCoeffdlnN_diag_NeutralMolecule_ = b.dlnActCoeffdlnN_diag_NeutralMolecule_; return *this; @@ -593,9 +593,9 @@ namespace Cantera { } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! + // Get the array of log concentration-like derivatives of the + // log activity coefficients + /* * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the @@ -612,12 +612,12 @@ namespace Cantera { * derivatives of the log Activity Coefficients. * length = m_kk */ - void IonsFromNeutralVPSSTP::getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { + void IonsFromNeutralVPSSTP::getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { s_update_lnActCoeff(); - s_update_dlnActCoeff_dlnX(); + s_update_dlnActCoeff_dlnX_diag(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnX[k] = dlnActCoeffdlnX_Scaled_[k]; + dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; } } @@ -1192,7 +1192,7 @@ namespace Cantera { muNeutralMolecule_.resize(numNeutralMoleculeSpecies_); gammaNeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); - dlnActCoeffdlnX_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); + dlnActCoeffdlnX_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); } //==================================================================================================================== @@ -1582,7 +1582,7 @@ namespace Cantera { * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients */ - void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnX() const { + void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnX_diag() const { int k, icat, jNeut; doublereal fmij; /* @@ -1590,11 +1590,11 @@ namespace Cantera { */ GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); if (!geThermo) { - fvo_zero_dbl_1(dlnActCoeffdlnX_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnX_diag_, m_kk); return; } - geThermo->getdlnActCoeffdlnX(DATA_PTR(dlnActCoeffdlnX_NeutralMolecule_)); + geThermo->getdlnActCoeffdlnX_diag(DATA_PTR(dlnActCoeffdlnX_diag_NeutralMolecule_)); switch (ionSolnType_) { case cIonSolnType_PASSTHROUGH: @@ -1607,19 +1607,19 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeffdlnX_Scaled_[icat] = dlnActCoeffdlnX_NeutralMolecule_[jNeut]/fmij; + dlnActCoeffdlnX_diag_[icat] = dlnActCoeffdlnX_diag_NeutralMolecule_[jNeut]/fmij; } // Do the anion list icat = anionList_[0]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnX_Scaled_[icat]= 0.0; + dlnActCoeffdlnX_diag_[icat]= 0.0; // Do the list of neutral molecules for (k = 0; k < numPassThroughSpecies_; k++) { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnX_Scaled_[icat] = dlnActCoeffdlnX_NeutralMolecule_[jNeut]; + dlnActCoeffdlnX_diag_[icat] = dlnActCoeffdlnX_diag_NeutralMolecule_[jNeut]; } break; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index e590366f0..f73105263 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -419,25 +419,21 @@ namespace Cantera { doublereal *dlnActCoeffds) const; //! Get the array of log concentration-like derivatives of the - //! log activity coefficients + //! log activity coefficients - diagonal component /*! * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. + * logarithm of the mole fraction. * * units = dimensionless * - * @param dlnActCoeffdlnX Output vector of log(mole fraction) + * @param dlnActCoeffdlnX_diag Output vector of log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const; //! Get the array of log concentration-like derivatives of the //! log activity coefficients - diagonal components @@ -744,7 +740,7 @@ namespace Cantera { * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the mole fractions. */ - void s_update_dlnActCoeff_dlnX() const; + void s_update_dlnActCoeff_dlnX_diag() const; //! Update the derivative of the log of the activity coefficients //! wrt log(number of moles) - diagonal components @@ -891,7 +887,7 @@ namespace Cantera { mutable std::vector gammaNeutralMolecule_; mutable std::vector dlnActCoeff_NeutralMolecule_; mutable std::vector dlnActCoeffdT_NeutralMolecule_; - mutable std::vector dlnActCoeffdlnX_NeutralMolecule_; + mutable std::vector dlnActCoeffdlnX_diag_NeutralMolecule_; mutable std::vector dlnActCoeffdlnN_diag_NeutralMolecule_; }; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 065be1023..bb50b31db 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -989,13 +989,13 @@ namespace Cantera { } } //==================================================================================================================== - void MargulesVPSSTP::s_update_dlnActCoeff_dlnX() const { + void MargulesVPSSTP::s_update_dlnActCoeff_dlnX_diag() const { int iA, iB; doublereal XA, XB, g0 , g1; doublereal T = temperature(); - fvo_zero_dbl_1(dlnActCoeffdlnX_Scaled_, m_kk); + fvo_zero_dbl_1(dlnActCoeffdlnX_diag_, m_kk); doublereal RT = GasConstant * T; @@ -1011,8 +1011,8 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - dlnActCoeffdlnX_Scaled_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); - dlnActCoeffdlnX_Scaled_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); + dlnActCoeffdlnX_diag_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); + dlnActCoeffdlnX_diag_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); } } @@ -1024,10 +1024,10 @@ namespace Cantera { } } //==================================================================================================================== - void MargulesVPSSTP::getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { - s_update_dlnActCoeff_dlnX(); + void MargulesVPSSTP::getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { + s_update_dlnActCoeff_dlnX_diag(); for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnX[k] = dlnActCoeffdlnX_Scaled_[k]; + dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; } } //==================================================================================================================== diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index c607a50e0..8e3f4b198 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -794,25 +794,21 @@ namespace Cantera { virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; //! Get the array of log concentration-like derivatives of the - //! log activity coefficients + //! log activity coefficients - diagonal component /*! * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction, - * molality, etc.) that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. + * logarithm of the mole fraction. * * units = dimensionless * - * @param dlnActCoeffdlnX Output vector of log(mole fraction) + * @param dlnActCoeffdlnX_diag Output vector of the diagonal component of the log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const; + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const; //! Get the array of derivatives of the log activity coefficients wrt mole numbers - diagonal only /*! @@ -822,13 +818,10 @@ namespace Cantera { * logarithm of the activity coefficient with respect to the * logarithm of the concentration-like variable (i.e. mole fraction, * molality, etc.) that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. * * units = dimensionless * - * @param dlnActCoeffdlnX Output vector of the diagonal entries for the log(mole fraction) + * @param dlnActCoeffdlnN_diag Output vector of the diagonal entries for the log(mole fraction) * derivatives of the log Activity Coefficients. * length = m_kk */ @@ -905,7 +898,7 @@ namespace Cantera { * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the mole fractions. */ - void s_update_dlnActCoeff_dlnX() const; + void s_update_dlnActCoeff_dlnX_diag() const; //! Update the derivative of the log of the activity coefficients //! wrt log(moles) - diagonal only diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index c1d1034a5..20e5deff7 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -59,7 +59,8 @@ namespace Cantera { m_spthermo = 0; } - /** + //==================================================================================================================== + /* * Copy Constructor for the ThermoPhase object. * * Currently, this is implemented, but not tested. If called it will diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 649606e78..fc5f868c5 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2072,7 +2072,7 @@ namespace Cantera { } //! Get the array of log concentration-like derivatives of the - //! log activity coefficients + //! log activity coefficients - diagonal component only /*! * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. @@ -2086,11 +2086,11 @@ namespace Cantera { * * units = dimensionless * - * @param dlnActCoeffdlnX Output vector of derivatives of the + * @param dlnActCoeffdln_diag Output vector of derivatives of the * log Activity Coefficients. length = m_kk */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { - err("getdlnActCoeffdlnX"); + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { + err("getdlnActCoeffdlnX_diag"); } //! Get the array of log concentration-like derivatives of the diff --git a/Cantera/src/thermo/VPStandardStateTP.h b/Cantera/src/thermo/VPStandardStateTP.h index ea6b0eb0f..4bf25fb97 100644 --- a/Cantera/src/thermo/VPStandardStateTP.h +++ b/Cantera/src/thermo/VPStandardStateTP.h @@ -142,29 +142,7 @@ namespace Cantera { err("getdlnActCoeffdlnN_diag"); } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. - * - * units = dimensionless - * - * @param dlnActCoeffdlnX Output vector of derivatives of the - * log Activity Coefficients. length = m_kk - */ - virtual void getdlnActCoeffdlnX(doublereal *dlnActCoeffdlnX) const { - err("getdlnActCoeffdlnX"); - } - //@} /// @name Partial Molar Properties of the Solution (VPStandardStateTP) //@{ From ab9ca908c2cfd3440d60a09a0d83c23ef496def8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 17:04:46 +0000 Subject: [PATCH 215/446] Changed the name dlnActCoeffdN to dlnActCoeffdlnN to reflect what its actually doing. Fixed an error in dlnActCoeffdlnN_diag() for MargulesVPSSTP. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 8 +-- Cantera/src/thermo/GibbsExcessVPSSTP.h | 26 ++++++- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 73 ++++++++++++++++++-- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 11 +++ Cantera/src/thermo/MargulesVPSSTP.cpp | 48 ++++++++----- Cantera/src/thermo/MargulesVPSSTP.h | 16 ++--- Cantera/src/thermo/MolalityVPSSTP.h | 23 ++++++ Cantera/src/thermo/ThermoPhase.cpp | 36 ++++++++-- Cantera/src/thermo/ThermoPhase.h | 17 +++-- 9 files changed, 208 insertions(+), 50 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 5ee5c16e8..94b366c79 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -40,7 +40,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_(0), dlnActCoeffdlnN_diag_(0), dlnActCoeffdlnX_diag_(0), - dlnActCoeffdN_Scaled_(0,0), + dlnActCoeffdlnN_(0,0), m_pp(0) { } @@ -59,7 +59,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_(0), dlnActCoeffdlnN_diag_(0), dlnActCoeffdlnX_diag_(0), - dlnActCoeffdN_Scaled_(0,0), + dlnActCoeffdlnN_(0,0), m_pp(0) { GibbsExcessVPSSTP::operator=(b); @@ -85,7 +85,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_ = b.d2lnActCoeffdT2_Scaled_; dlnActCoeffdlnX_diag_ = b.dlnActCoeffdlnX_diag_; dlnActCoeffdlnN_diag_ = b.dlnActCoeffdlnN_diag_; - dlnActCoeffdN_Scaled_ = b.dlnActCoeffdN_Scaled_; + dlnActCoeffdlnN_ = b.dlnActCoeffdlnN_; m_pp = b.m_pp; return *this; @@ -345,7 +345,7 @@ namespace Cantera { d2lnActCoeffdT2_Scaled_.resize(m_kk); dlnActCoeffdlnX_diag_.resize(m_kk); dlnActCoeffdlnN_diag_.resize(m_kk); - dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); + dlnActCoeffdlnN_.resize(m_kk, m_kk); m_pp.resize(m_kk); } diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 63b387da6..d98b95241 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -304,6 +304,28 @@ namespace Cantera { err("getdlnActCoeffdT"); } + //! Get the array of derivatives of the log activity coefficients with respect to the log of the species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * species log mole number (with all other species mole numbers held constant). The default treatment in the + * %ThermoPhase object is to set this vector to zero. + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { + err(" getdlnActCoeffdlnN: nonzero and nonimplemented"); + } //@} @@ -539,9 +561,9 @@ namespace Cantera { //! Storage for the current derivative values of the gradients with respect to logarithm of the species mole number of the //! log of the activity coefficients of the species /*! - * dlnActCoeffdN_Scaled_(k, m) is the derivative of ln(gamma_k) wrt ln mole number of species m + * dlnActCoeffdlnN_(k, m) is the derivative of ln(gamma_k) wrt ln mole number of species m */ - mutable Array2D dlnActCoeffdN_Scaled_; + mutable Array2D dlnActCoeffdlnN_; //! Temporary storage space that is fair game mutable std::vector m_pp; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 8aaeb95da..57acfd7ed 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -1221,7 +1221,7 @@ namespace Cantera { } return fMax; } - + //==================================================================================================================== /* * initThermoXML() (virtual from ThermoPhase) * Import and initialize a ThermoPhase object @@ -1386,7 +1386,7 @@ namespace Cantera { * have charge conservation. */ } - + //==================================================================================================================== // Update the activity coefficients /* * This function will be called to update the internally storred @@ -1577,7 +1577,7 @@ namespace Cantera { } } - + //==================================================================================================================== /* * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients @@ -1635,7 +1635,7 @@ namespace Cantera { } } - + //==================================================================================================================== /* * This function will be called to update the internally storred * temperature derivative of the natural logarithm of the activity coefficients @@ -1693,7 +1693,70 @@ namespace Cantera { } } + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients + // wrt log(number of moles) - diagonal components + /* + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the number of moles of given species. + */ + void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN() const { + int k, icat, jNeut; + doublereal fmij; + dlnActCoeffdlnN_.zero(); + /* + * Get the activity coefficients of the neutral molecules + */ + GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); + + if (!geThermo) { + + return; + } + int nsp_ge = geThermo->nSpecies(); + geThermo->getdlnActCoeffdlnN(nsp_ge, &(dlnActCoeffdlnN_NeutralMolecule_(0,0))); + switch (ionSolnType_) { + case cIonSolnType_PASSTHROUGH: + break; + case cIonSolnType_SINGLEANION: + + // Do the cation list + for (k = 0; k < (int) cationList_.size(); k++) { + //! Get the id for the next cation + icat = cationList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; + dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]/fmij; + } + + // Do the anion list + icat = anionList_[0]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeffdlnN_diag_[icat]= 0.0; + + // Do the list of neutral molecules + for (k = 0; k < numPassThroughSpecies_; k++) { + icat = passThroughList_[k]; + jNeut = fm_invert_ionForNeutral[icat]; + dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]; + } + break; -} + case cIonSolnType_SINGLECATION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + case cIonSolnType_MULTICATIONANION: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + default: + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + break; + } + + } + //==================================================================================================================== +} +//====================================================================================================================== diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index f73105263..964891acd 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -751,6 +751,15 @@ namespace Cantera { */ void s_update_dlnActCoeff_dlnN_diag() const; + //! Update the derivative of the log of the activity coefficients + //! wrt log(number of moles) - diagonal components + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the number of moles of given species. + */ + void s_update_dlnActCoeff_dlnN() const; + private: //! Error function @@ -890,6 +899,8 @@ namespace Cantera { mutable std::vector dlnActCoeffdlnX_diag_NeutralMolecule_; mutable std::vector dlnActCoeffdlnN_diag_NeutralMolecule_; + mutable Array2D dlnActCoeffdlnN_NeutralMolecule_; + }; diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index bb50b31db..bc2a11b7f 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -667,7 +667,7 @@ namespace Cantera { // been identified. void MargulesVPSSTP::initLengths() { m_kk = nSpecies(); - dlnActCoeffdN_Scaled_.resize(m_kk, m_kk); + dlnActCoeffdlnN_.resize(m_kk, m_kk); } /* @@ -916,9 +916,25 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + // dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + + double gfac = g0 + g1 * XB; + double gggg = (delBK - XB) * g1; + + + dlnActCoeffdlnN_diag_[iK] += gfac * delAK * ( - XB + delBK); + + dlnActCoeffdlnN_diag_[iK] += gfac * delBK * ( - XA + delAK); + + dlnActCoeffdlnN_diag_[iK] += gfac * (2.0 * XA * XB - delAK * XB - XA * delBK); + + dlnActCoeffdlnN_diag_[iK] += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBK); + + dlnActCoeffdlnN_diag_[iK] += gggg * ( - 2.0 * XA * XB + delAK * XB + XA * delBK); + + dlnActCoeffdlnN_diag_[iK] += - g1 * XA * XB * (- XB + delBK); } - dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK]-XK; + // dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK]-XK; } } @@ -929,9 +945,8 @@ namespace Cantera { * logarithm of the activity coefficients. These are used in the determination * of the diffusion coefficients. * - * he = X_A X_B(B + C X_B) */ - void MargulesVPSSTP::s_update_dlnActCoeff_dN() const { + void MargulesVPSSTP::s_update_dlnActCoeff_dlnN() const { int iA, iB; doublereal delAK, delBK; double XA, XB, g0 , g1; @@ -940,7 +955,7 @@ namespace Cantera { doublereal delAM, delBM; - dlnActCoeffdN_Scaled_.zero(); + dlnActCoeffdlnN_.zero(); /* * Loop over the activity coefficient gamma_k @@ -971,19 +986,18 @@ namespace Cantera { double gfac = g0 + g1 * XB; double gggg = (delBK - XB) * g1; - // all values of dlnActCoeffdN_Scaled_(iK, iM) hare an additional divisor of n_total - dlnActCoeffdN_Scaled_(iK, iM) += gfac * delAK * ( - XB + delBM); + dlnActCoeffdlnN_(iK, iM) += gfac * delAK * ( - XB + delBM); - dlnActCoeffdN_Scaled_(iK, iM) += gfac * delBK * ( - XA + delAM); + dlnActCoeffdlnN_(iK, iM) += gfac * delBK * ( - XA + delAM); - dlnActCoeffdN_Scaled_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); + dlnActCoeffdlnN_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); - dlnActCoeffdN_Scaled_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); + dlnActCoeffdlnN_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); - dlnActCoeffdN_Scaled_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); + dlnActCoeffdlnN_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); - dlnActCoeffdN_Scaled_(iK, iM) += - g1 * XA * XB * (- XB + delBM); + dlnActCoeffdlnN_(iK, iM) += - g1 * XA * XB * (- XB + delBM); } } } @@ -1031,12 +1045,12 @@ namespace Cantera { } } //==================================================================================================================== - void MargulesVPSSTP::getdlnActCoeffdN(const int ld, doublereal *dlnActCoeffdN) const { - s_update_dlnActCoeff_dN(); - double *data = & dlnActCoeffdN_Scaled_(0,0); + void MargulesVPSSTP::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) const { + s_update_dlnActCoeff_dlnN(); + double *data = & dlnActCoeffdlnN_(0,0); for (int k = 0; k < m_kk; k++) { for (int m = 0; m < m_kk; m++) { - dlnActCoeffdN[ld * k + m] = data[m_kk * k + m]; + dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m]; } } } diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 8e3f4b198..af2edca83 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -828,25 +828,25 @@ namespace Cantera { virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; - //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers + //! Get the array of derivatives of the log activity coefficients with respect to the ln species mole numbers /*! * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a - * species mole number (with all other species mole numbers held constant) + * log of a species mole number (with all other species mole numbers held constant) * * units = 1 / kmol * - * dlnActCoeffdN[ ld * k + m] will contain the derivative of log act_coeff for the mth - * species with respect to the number of moles of the kth species. + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. * * \f[ - * \frac{d \ln(\gamma_m) }{d n_k }\Bigg|_{n_i} + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} * \f] * * @param ld Number of rows in the matrix - * @param dlnActCoeffdN Output vector of derivatives of the + * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const; + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; //@} @@ -915,7 +915,7 @@ namespace Cantera { * derivative of the natural logarithm of the activity coefficients * wrt logarithm of the mole number of species */ - void s_update_dlnActCoeff_dN() const; + void s_update_dlnActCoeff_dlnN() const; private: diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h index 60ea18feb..4bb286c64 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.h +++ b/Cantera/src/thermo/MolalityVPSSTP.h @@ -793,6 +793,29 @@ namespace Cantera { */ void setState_TPM(doublereal t, doublereal p, const std::string& m); + //! Get the array of derivatives of the log activity coefficients with respect to the log of the species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * species log mole number (with all other species mole numbers held constant). The default treatment in the + * %ThermoPhase object is to set this vector to zero. + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { + err(" getdlnActCoeffdlnN: nonzero and nonimplemented"); + } + //! returns a summary of the state of the phase as a string /*! * @param show_thermo If true, extra information is printed out diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 20e5deff7..d7952e724 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -81,7 +81,7 @@ namespace Cantera { */ *this = operator=(right); } - + //==================================================================================================================== /* * operator=() * @@ -135,7 +135,7 @@ namespace Cantera { m_ssConvention = right.m_ssConvention; return *this; } - +//==================================================================================================================== /* * Duplication routine for objects which inherit from * ThermoPhase. @@ -151,7 +151,7 @@ namespace Cantera { ThermoPhase* tp = new ThermoPhase(*this); return tp; } - +//==================================================================================================================== int ThermoPhase::activityConvention() const { return cAC_CONVENTION_MOLAR; } @@ -1031,7 +1031,33 @@ namespace Cantera { } return (m_hasElementPotentials); } - + //==================================================================================================================== + // Get the array of derivatives of the log activity coefficients with respect to the species mole numbers + /* + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d n_k }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + void ThermoPhase::getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { + for (int m = 0; m < m_kk; m++) { + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN[ld * k + m] = 0.0; + } + } + } + //==================================================================================================================== /* * Format a summary of the mixture state for output. */ @@ -1140,7 +1166,7 @@ namespace Cantera { } return s; } - +//==================================================================================================================== /* * Format a summary of the mixture state for output. */ diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index fc5f868c5..274047eed 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2115,27 +2115,26 @@ namespace Cantera { err("getdlnActCoeffdlnN_diag"); } - //! Get the array of derivatives of the log activity coefficients with respect to the species mole numbers + //! Get the array of derivatives of the log activity coefficients with respect to the log of the species mole numbers /*! * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a - * species mole number (with all other species mole numbers held constant) + * species log mole number (with all other species mole numbers held constant). The default treatment in the + * %ThermoPhase object is to set this vector to zero. * * units = 1 / kmol * - * dlnActCoeffdN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth * species with respect to the number of moles of the kth species. * * \f[ - * \frac{d \ln(\gamma_m) }{d n_k }\Bigg|_{n_i} + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} * \f] * * @param ld Number of rows in the matrix - * @param dlnActCoeffdN Output vector of derivatives of the - * log Activity Coefficients. length = m_kk * m_kk + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdN(const int ld, doublereal * const dlnActCoeffdN) const { - err("getdlnActCoeffdN"); - } + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; /** * @} From 8b3f18666f3fcf24e38c9cf1de09fd6279c8ebf5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 17:42:40 +0000 Subject: [PATCH 216/446] Update to s_update_dlnActCoeff_dlnN this has not been checked yet --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 112 +++++++++++++------ 1 file changed, 75 insertions(+), 37 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 57acfd7ed..441df0f86 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -1392,7 +1392,6 @@ namespace Cantera { * This function will be called to update the internally storred * natural logarithm of the activity coefficients * - * he = X_A X_B(B + C(X_A - X_B)) */ void IonsFromNeutralVPSSTP::s_update_lnActCoeff() const { int k, icat, jNeut; @@ -1507,13 +1506,13 @@ namespace Cantera { break; case cIonSolnType_SINGLECATION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffds", "Unimplemented type"); break; case cIonSolnType_MULTICATIONANION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffds", "Unimplemented type"); break; default: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffds", "Unimplemented type"); break; } @@ -1566,13 +1565,13 @@ namespace Cantera { break; case cIonSolnType_SINGLECATION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffdT", "Unimplemented type"); break; case cIonSolnType_MULTICATIONANION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffdT", "Unimplemented type"); break; default: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeffdT", "Unimplemented type"); break; } @@ -1624,13 +1623,13 @@ namespace Cantera { break; case cIonSolnType_SINGLECATION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnX_diag()", "Unimplemented type"); break; case cIonSolnType_MULTICATIONANION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnX_diag()", "Unimplemented type"); break; default: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnX_diag()", "Unimplemented type"); break; } @@ -1682,28 +1681,28 @@ namespace Cantera { break; case cIonSolnType_SINGLECATION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN_diag()", "Unimplemented type"); break; case cIonSolnType_MULTICATIONANION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN_diag()", "Unimplemented type"); break; default: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN_diag()", "Unimplemented type"); break; } } //==================================================================================================================== - // Update the derivative of the log of the activity coefficients - // wrt log(number of moles) - diagonal components - /* - * This function will be called to update the internally storred - * derivative of the natural logarithm of the activity coefficients - * wrt logarithm of the number of moles of given species. - */ + // Update the derivative of the log of the activity coefficients + // wrt log(number of moles) - diagonal components + /* + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the number of moles of given species. + */ void IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN() const { - int k, icat, jNeut; - doublereal fmij; + int k, m, kcat, kNeut, mcat, mNeut; + doublereal fmij, mfmij; dlnActCoeffdlnN_.zero(); /* * Get the activity coefficients of the neutral molecules @@ -1724,34 +1723,73 @@ namespace Cantera { // Do the cation list for (k = 0; k < (int) cationList_.size(); k++) { - //! Get the id for the next cation - icat = cationList_[k]; - jNeut = fm_invert_ionForNeutral[icat]; - fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]/fmij; + for (m = 0; m < (int) cationList_.size(); m++) { + //! Get the id for the next cation + //icat = cationList_[k]; + //jNeut = fm_invert_ionForNeutral[icat]; + //fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; + //lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut])/fmij; + + kcat = cationList_[k]; + + kNeut = fm_invert_ionForNeutral[kcat]; + fmij = fm_neutralMolec_ions_[kcat + kNeut * m_kk]; + dlnActCoeffdlnN_diag_[kcat] = dlnActCoeffdlnN_diag_NeutralMolecule_[kNeut]/fmij; + + mcat = cationList_[m]; + mNeut = fm_invert_ionForNeutral[mcat]; + mfmij = fm_neutralMolec_ions_[mcat + mNeut * m_kk]; + + dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut,mNeut) * mfmij / fmij; + + + for (m = 0; m < numPassThroughSpecies_; m++) { + mcat = passThroughList_[m]; + mNeut = fm_invert_ionForNeutral[mcat]; + dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut, mNeut) / fmij; + } + } } - // Do the anion list - icat = anionList_[0]; - jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnN_diag_[icat]= 0.0; + // Do the anion list -> anion activity coefficient is one + kcat = anionList_[0]; + kNeut = fm_invert_ionForNeutral[kcat]; + for (k = 0; k < m_kk; k++) { + dlnActCoeffdlnN_(kcat, k) = 0.0; + dlnActCoeffdlnN_(k, kcat) = 0.0; + } // Do the list of neutral molecules for (k = 0; k < numPassThroughSpecies_; k++) { - icat = passThroughList_[k]; - jNeut = fm_invert_ionForNeutral[icat]; - dlnActCoeffdlnN_diag_[icat] = dlnActCoeffdlnN_diag_NeutralMolecule_[jNeut]; + kcat = passThroughList_[k]; + kNeut = fm_invert_ionForNeutral[kcat]; + dlnActCoeffdlnN_diag_[kcat] = dlnActCoeffdlnN_diag_NeutralMolecule_[kNeut]; + + for (m = 0; m < m_kk; m++) { + mcat = passThroughList_[m]; + mNeut = fm_invert_ionForNeutral[mcat]; + dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut, mNeut); + } + + + for (m = 0; m < (int) cationList_.size(); m++) { + mcat = cationList_[m]; + mNeut = fm_invert_ionForNeutral[mcat]; + mfmij = fm_neutralMolec_ions_[mcat + mNeut * m_kk]; + dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut,mNeut); + } + } break; case cIonSolnType_SINGLECATION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN", "Unimplemented type"); break; case cIonSolnType_MULTICATIONANION: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN", "Unimplemented type"); break; default: - throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff", "Unimplemented type"); + throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN", "Unimplemented type"); break; } From 3c00f1666c80e3b643021f65e7b5524153655fd4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 23:15:35 +0000 Subject: [PATCH 217/446] Moved the tools/doc directory directly into docs. --- Makefile.in | 6 ++---- configure | 6 +++--- configure.in | 4 ++-- {tools/doc => docs}/Cantera.cfg.in | 18 +++++++++--------- {tools/doc => docs}/Makefile.in | 6 +++--- {tools/doc => docs}/doxyinput/Cantera.txt | 0 {tools/doc => docs}/doxyinput/bindings.txt | 0 {tools/doc => docs}/doxyinput/build.txt | 0 {tools/doc => docs}/doxyinput/buildcygwin.txt | 0 {tools/doc => docs}/doxyinput/configuring.txt | 0 {tools/doc => docs}/doxyinput/ctnew.txt | 0 {tools/doc => docs}/doxyinput/cxx-headers.txt | 0 {tools/doc => docs}/doxyinput/cxx-setup.txt | 0 {tools/doc => docs}/doxyinput/demo.cpp | 0 {tools/doc => docs}/doxyinput/demo1.cpp | 0 {tools/doc => docs}/doxyinput/demo1a.cpp | 0 {tools/doc => docs}/doxyinput/demoequil.cpp | 0 {tools/doc => docs}/doxyinput/edemo.cpp | 0 {tools/doc => docs}/doxyinput/equildemo.txt | 0 {tools/doc => docs}/doxyinput/ex1.cpp | 0 {tools/doc => docs}/doxyinput/except.cpp | 0 {tools/doc => docs}/doxyinput/exceptions.txt | 0 {tools/doc => docs}/doxyinput/initthermo.txt | 0 {tools/doc => docs}/doxyinput/introcxx.txt | 0 {tools/doc => docs}/doxyinput/languages.txt | 0 {tools/doc => docs}/doxyinput/matlab.txt | 0 {tools/doc => docs}/doxyinput/numarray.txt | 0 {tools/doc => docs}/doxyinput/thermo.txt | 0 {tools/doc => docs}/doxyinput/thermodemo.cpp | 0 {tools/doc => docs}/doxyinput/thermodemo.txt | 0 {tools/doc => docs}/doxyinput/transport.txt | 0 {tools/doc => docs}/doxyinput/winbuild.txt | 0 {tools/doc => docs}/html/banner4.jpg | Bin {tools/doc => docs}/python/.cvsignore | 0 {tools/doc => docs}/python/makedoc | 0 {tools/doc => docs}/python/mkmkdoc.py | 0 tools/doc/html/.cvsignore | 11 ----------- 37 files changed, 19 insertions(+), 32 deletions(-) rename {tools/doc => docs}/Cantera.cfg.in (99%) rename {tools/doc => docs}/Makefile.in (75%) rename {tools/doc => docs}/doxyinput/Cantera.txt (100%) rename {tools/doc => docs}/doxyinput/bindings.txt (100%) rename {tools/doc => docs}/doxyinput/build.txt (100%) rename {tools/doc => docs}/doxyinput/buildcygwin.txt (100%) rename {tools/doc => docs}/doxyinput/configuring.txt (100%) rename {tools/doc => docs}/doxyinput/ctnew.txt (100%) rename {tools/doc => docs}/doxyinput/cxx-headers.txt (100%) rename {tools/doc => docs}/doxyinput/cxx-setup.txt (100%) rename {tools/doc => docs}/doxyinput/demo.cpp (100%) rename {tools/doc => docs}/doxyinput/demo1.cpp (100%) rename {tools/doc => docs}/doxyinput/demo1a.cpp (100%) rename {tools/doc => docs}/doxyinput/demoequil.cpp (100%) rename {tools/doc => docs}/doxyinput/edemo.cpp (100%) rename {tools/doc => docs}/doxyinput/equildemo.txt (100%) rename {tools/doc => docs}/doxyinput/ex1.cpp (100%) rename {tools/doc => docs}/doxyinput/except.cpp (100%) rename {tools/doc => docs}/doxyinput/exceptions.txt (100%) rename {tools/doc => docs}/doxyinput/initthermo.txt (100%) rename {tools/doc => docs}/doxyinput/introcxx.txt (100%) rename {tools/doc => docs}/doxyinput/languages.txt (100%) rename {tools/doc => docs}/doxyinput/matlab.txt (100%) rename {tools/doc => docs}/doxyinput/numarray.txt (100%) rename {tools/doc => docs}/doxyinput/thermo.txt (100%) rename {tools/doc => docs}/doxyinput/thermodemo.cpp (100%) rename {tools/doc => docs}/doxyinput/thermodemo.txt (100%) rename {tools/doc => docs}/doxyinput/transport.txt (100%) rename {tools/doc => docs}/doxyinput/winbuild.txt (100%) rename {tools/doc => docs}/html/banner4.jpg (100%) rename {tools/doc => docs}/python/.cvsignore (100%) rename {tools/doc => docs}/python/makedoc (100%) rename {tools/doc => docs}/python/mkmkdoc.py (100%) delete mode 100644 tools/doc/html/.cvsignore diff --git a/Makefile.in b/Makefile.in index f1b466967..ddc1a6679 100755 --- a/Makefile.in +++ b/Makefile.in @@ -249,20 +249,18 @@ clean: -$(RMDIRTREE) *.*~ @buildlib@/*.* build/include/cantera/config.h svn*~ -cd Cantera; @MAKE@ clean -cd tools; @MAKE@ clean + -cd docs; @MAKE@ clean -cd ext; @MAKE@ clean -cd test_problems; @MAKE@ clean -$(RM) mt.mod docs: - cd tools/doxygen/Cantera; doxygen Cantera.cfg + cd docs; doxygen Cantera.cfg depends: cd Cantera; @MAKE@ depends cd tools; @MAKE@ depends cd ext; @MAKE@ depends -ifeq ($(build_particles),1) - cd Cantera/cads; @MAKE@ depends -endif ChangeLog: CVS/Entries tools/bin/cvs2cl.pl --prune diff --git a/configure b/configure index dd4dcfc83..3d376dd60 100755 --- a/configure +++ b/configure @@ -10839,7 +10839,7 @@ fi - ac_config_files="$ac_config_files Makefile Cantera/Makefile Cantera/src/Makefile Cantera/src/base/Makefile Cantera/src/zeroD/Makefile Cantera/src/oneD/Makefile Cantera/src/converters/Makefile Cantera/src/transport/Makefile Cantera/src/thermo/Makefile Cantera/src/kinetics/Makefile Cantera/src/numerics/Makefile Cantera/src/spectra/Makefile Cantera/src/equil/Makefile Cantera/clib/src/Makefile Cantera/fortran/src/Makefile Cantera/fortran/f77demos/f77demos.mak Cantera/fortran/f77demos/Makefile Cantera/matlab/Makefile Cantera/matlab/setup_matlab.py Cantera/python/Makefile Cantera/python/setup.py Cantera/cxx/Makefile Cantera/cxx/src/Makefile Cantera/cxx/demos/Makefile Cantera/cxx/demos/combustor/Makefile Cantera/cxx/demos/combustor/Makefile.install Cantera/cxx/demos/flamespeed/Makefile Cantera/cxx/demos/flamespeed/Makefile.install Cantera/cxx/demos/kinetics1/Makefile Cantera/cxx/demos/kinetics1/Makefile.install Cantera/cxx/demos/NASA_coeffs/Makefile Cantera/cxx/demos/NASA_coeffs/Makefile.install Cantera/cxx/demos/rankine/Makefile Cantera/cxx/demos/rankine/Makefile.install Cantera/cxx/include/Cantera.mak Cantera/cxx/include/Cantera_bt.mak Cantera/user/Makefile Cantera/python/src/Makefile Cantera/python/examples/Makefile Cantera/python/examples/equilibrium/Makefile Cantera/python/examples/equilibrium/adiabatic_flame/Makefile Cantera/python/examples/equilibrium/multiphase_plasma/Makefile Cantera/python/examples/equilibrium/simple_test/Makefile Cantera/python/examples/equilibrium/stoich_flame/Makefile Cantera/python/examples/gasdynamics/isentropic/Makefile Cantera/python/examples/gasdynamics/soundSpeed/Makefile Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile 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Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile Cantera/python/examples/reactors/surf_pfr_sim/Makefile Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile Cantera/python/examples/transport/Makefile Cantera/python/examples/flames/Makefile Cantera/python/examples/gasdynamics/Makefile Cantera/python/examples/liquid_vapor/Makefile Cantera/python/examples/reactors/Makefile Cantera/python/examples/surface_chemistry/Makefile ext/lapack/Makefile ext/blas/Makefile ext/cvode/Makefile ext/math/Makefile ext/recipes/Makefile ext/tpx/Makefile ext/Makefile ext/f2c_libs/Makefile ext/f2c_blas/Makefile ext/f2c_lapack/Makefile ext/f2c_math/Makefile examples/Makefile examples/cxx/Makefile docs/Makefile tools/Makefile docs/Cantera.cfg tools/src/Makefile tools/src/sample.mak tools/src/finish_install.py tools/src/package4mac tools/templates/f77/demo.mak tools/templates/f90/demo.mak tools/templates/cxx/demo.mak tools/testtools/Makefile data/inputs/Makefile data/inputs/mkxml test_problems/Makefile test_problems/cxx_ex/Makefile test_problems/silane_equil/Makefile test_problems/surfkin/Makefile test_problems/spectroscopy/Makefile test_problems/surfSolverTest/Makefile test_problems/diamondSurf/Makefile test_problems/diamondSurf_dupl/Makefile test_problems/ChemEquil_gri_matrix/Makefile test_problems/ChemEquil_gri_pairs/Makefile test_problems/ChemEquil_ionizedGas/Makefile test_problems/ChemEquil_red1/Makefile test_problems/CpJump/Makefile test_problems/mixGasTransport/Makefile test_problems/multiGasTransport/Makefile test_problems/printUtilUnitTest/Makefile test_problems/fracCoeff/Makefile test_problems/negATest/Makefile test_problems/NASA9poly_test/Makefile test_problems/ck2cti_test/Makefile test_problems/ck2cti_test/runtest test_problems/nasa9_reader/Makefile test_problems/nasa9_reader/runtest test_problems/min_python/Makefile test_problems/min_python/minDiamond/Makefile test_problems/min_python/negATest/Makefile test_problems/pureFluidTest/Makefile test_problems/rankine_democxx/Makefile test_problems/python/Makefile test_problems/cathermo/Makefile test_problems/cathermo/issp/Makefile test_problems/cathermo/ims/Makefile test_problems/cathermo/stoichSubSSTP/Makefile test_problems/cathermo/testIAPWS/Makefile test_problems/cathermo/testIAPWSPres/Makefile test_problems/cathermo/testIAPWSTripP/Makefile test_problems/cathermo/testWaterPDSS/Makefile test_problems/cathermo/testWaterTP/Makefile test_problems/cathermo/HMW_test_1/Makefile test_problems/cathermo/HMW_test_3/Makefile test_problems/cathermo/HMW_graph_GvT/Makefile test_problems/cathermo/HMW_graph_GvI/Makefile test_problems/cathermo/HMW_graph_HvT/Makefile test_problems/cathermo/HMW_graph_CpvT/Makefile test_problems/cathermo/HMW_graph_VvT/Makefile test_problems/cathermo/DH_graph_1/Makefile test_problems/cathermo/DH_graph_acommon/Makefile test_problems/cathermo/DH_graph_NM/Makefile test_problems/cathermo/DH_graph_Pitzer/Makefile test_problems/cathermo/DH_graph_bdotak/Makefile test_problems/cathermo/HMW_dupl_test/Makefile test_problems/cathermo/VPissp/Makefile test_problems/cathermo/wtWater/Makefile test_problems/VCSnonideal/Makefile test_problems/VPsilane_test/Makefile test_problems/VPsilane_test/runtest test_problems/VCSnonideal/NaCl_equil/Makefile bin/install_tsc" test "x$prefix" = xNONE && prefix=$ac_default_prefix @@ -11400,9 +11400,9 @@ do "ext/f2c_math/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_math/Makefile" ;; "examples/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;; "examples/cxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/cxx/Makefile" ;; + "docs/Makefile" ) CONFIG_FILES="$CONFIG_FILES docs/Makefile" ;; "tools/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; - "tools/doc/Cantera.cfg" ) CONFIG_FILES="$CONFIG_FILES tools/doc/Cantera.cfg" ;; - "tools/doc/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/doc/Makefile" ;; + "docs/Cantera.cfg" ) CONFIG_FILES="$CONFIG_FILES docs/Cantera.cfg" ;; "tools/src/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/src/Makefile" ;; "tools/src/sample.mak" ) CONFIG_FILES="$CONFIG_FILES tools/src/sample.mak" ;; "tools/src/finish_install.py" ) CONFIG_FILES="$CONFIG_FILES tools/src/finish_install.py" ;; diff --git a/configure.in b/configure.in index 29067cd17..3c2b34d1f 100755 --- a/configure.in +++ b/configure.in @@ -1907,9 +1907,9 @@ AC_OUTPUT(Makefile \ ext/f2c_math/Makefile \ examples/Makefile \ examples/cxx/Makefile \ + docs/Makefile \ tools/Makefile \ - tools/doc/Cantera.cfg \ - tools/doc/Makefile \ + docs/Cantera.cfg \ tools/src/Makefile \ tools/src/sample.mak \ tools/src/finish_install.py \ diff --git a/tools/doc/Cantera.cfg.in b/docs/Cantera.cfg.in similarity index 99% rename from tools/doc/Cantera.cfg.in rename to docs/Cantera.cfg.in index e796bec02..0c2278db3 100755 --- a/tools/doc/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -44,7 +44,7 @@ PROJECT_NUMBER = 1.8 # If a relative path is entered, it will be relative to the location # where doxygen was started. If left blank the current directory will be used. -OUTPUT_DIRECTORY = @ctroot@/tools/doc +OUTPUT_DIRECTORY = @ctroot@/docs # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create # 4096 sub-directories (in 2 levels) under the output directory of each output @@ -590,14 +590,14 @@ WARN_LOGFILE = # directories like "/usr/src/myproject". Separate the files or directories # with spaces. -INPUT = ../../Cantera/src \ - ../../Cantera/src/base \ - ../../Cantera/src/numerics \ - ../../Cantera/src/thermo \ - ../../Cantera/src/equil \ - ../../Cantera/src/kinetics \ - ../../Cantera/src/transport \ - ../../Cantera/cxx/include \ +INPUT = ../Cantera/src \ + ../Cantera/src/base \ + ../Cantera/src/numerics \ + ../Cantera/src/thermo \ + ../Cantera/src/equil \ + ../Cantera/src/kinetics \ + ../Cantera/src/transport \ + ../Cantera/cxx/include \ doxyinput # This tag can be used to specify the character encoding of the source files diff --git a/tools/doc/Makefile.in b/docs/Makefile.in similarity index 75% rename from tools/doc/Makefile.in rename to docs/Makefile.in index 68bcabb1a..562e17866 100644 --- a/tools/doc/Makefile.in +++ b/docs/Makefile.in @@ -1,7 +1,7 @@ # -# $Revision$ -# $Author$ -# $Date$ +# $Revision: 255 $ +# $Author: hkmoffa $ +# $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ # build_ck=@BUILD_CK@ diff --git a/tools/doc/doxyinput/Cantera.txt b/docs/doxyinput/Cantera.txt similarity index 100% rename from tools/doc/doxyinput/Cantera.txt rename to docs/doxyinput/Cantera.txt diff --git a/tools/doc/doxyinput/bindings.txt b/docs/doxyinput/bindings.txt similarity index 100% rename from tools/doc/doxyinput/bindings.txt rename to docs/doxyinput/bindings.txt diff --git a/tools/doc/doxyinput/build.txt b/docs/doxyinput/build.txt similarity index 100% rename from tools/doc/doxyinput/build.txt rename to docs/doxyinput/build.txt diff --git a/tools/doc/doxyinput/buildcygwin.txt b/docs/doxyinput/buildcygwin.txt similarity index 100% rename from tools/doc/doxyinput/buildcygwin.txt rename to docs/doxyinput/buildcygwin.txt diff --git a/tools/doc/doxyinput/configuring.txt b/docs/doxyinput/configuring.txt similarity index 100% rename from tools/doc/doxyinput/configuring.txt rename to docs/doxyinput/configuring.txt diff --git a/tools/doc/doxyinput/ctnew.txt b/docs/doxyinput/ctnew.txt similarity index 100% rename from tools/doc/doxyinput/ctnew.txt rename to docs/doxyinput/ctnew.txt diff --git a/tools/doc/doxyinput/cxx-headers.txt b/docs/doxyinput/cxx-headers.txt similarity index 100% rename from tools/doc/doxyinput/cxx-headers.txt rename to docs/doxyinput/cxx-headers.txt diff --git a/tools/doc/doxyinput/cxx-setup.txt b/docs/doxyinput/cxx-setup.txt similarity index 100% rename from tools/doc/doxyinput/cxx-setup.txt rename to docs/doxyinput/cxx-setup.txt diff --git a/tools/doc/doxyinput/demo.cpp b/docs/doxyinput/demo.cpp similarity index 100% rename from tools/doc/doxyinput/demo.cpp rename to docs/doxyinput/demo.cpp diff --git a/tools/doc/doxyinput/demo1.cpp b/docs/doxyinput/demo1.cpp similarity index 100% rename from tools/doc/doxyinput/demo1.cpp rename to docs/doxyinput/demo1.cpp diff --git a/tools/doc/doxyinput/demo1a.cpp b/docs/doxyinput/demo1a.cpp similarity index 100% rename from tools/doc/doxyinput/demo1a.cpp rename to docs/doxyinput/demo1a.cpp diff --git a/tools/doc/doxyinput/demoequil.cpp b/docs/doxyinput/demoequil.cpp similarity index 100% rename from tools/doc/doxyinput/demoequil.cpp rename to docs/doxyinput/demoequil.cpp diff --git a/tools/doc/doxyinput/edemo.cpp b/docs/doxyinput/edemo.cpp similarity index 100% rename from tools/doc/doxyinput/edemo.cpp rename to docs/doxyinput/edemo.cpp diff --git a/tools/doc/doxyinput/equildemo.txt b/docs/doxyinput/equildemo.txt similarity index 100% rename from tools/doc/doxyinput/equildemo.txt rename to docs/doxyinput/equildemo.txt diff --git a/tools/doc/doxyinput/ex1.cpp b/docs/doxyinput/ex1.cpp similarity index 100% rename from tools/doc/doxyinput/ex1.cpp rename to docs/doxyinput/ex1.cpp diff --git a/tools/doc/doxyinput/except.cpp b/docs/doxyinput/except.cpp similarity index 100% rename from tools/doc/doxyinput/except.cpp rename to docs/doxyinput/except.cpp diff --git a/tools/doc/doxyinput/exceptions.txt b/docs/doxyinput/exceptions.txt similarity index 100% rename from tools/doc/doxyinput/exceptions.txt rename to docs/doxyinput/exceptions.txt diff --git a/tools/doc/doxyinput/initthermo.txt b/docs/doxyinput/initthermo.txt similarity index 100% rename from tools/doc/doxyinput/initthermo.txt rename to docs/doxyinput/initthermo.txt diff --git a/tools/doc/doxyinput/introcxx.txt b/docs/doxyinput/introcxx.txt similarity index 100% rename from tools/doc/doxyinput/introcxx.txt rename to docs/doxyinput/introcxx.txt diff --git a/tools/doc/doxyinput/languages.txt b/docs/doxyinput/languages.txt similarity index 100% rename from tools/doc/doxyinput/languages.txt rename to docs/doxyinput/languages.txt diff --git a/tools/doc/doxyinput/matlab.txt b/docs/doxyinput/matlab.txt similarity index 100% rename from tools/doc/doxyinput/matlab.txt rename to docs/doxyinput/matlab.txt diff --git a/tools/doc/doxyinput/numarray.txt b/docs/doxyinput/numarray.txt similarity index 100% rename from tools/doc/doxyinput/numarray.txt rename to docs/doxyinput/numarray.txt diff --git a/tools/doc/doxyinput/thermo.txt b/docs/doxyinput/thermo.txt similarity index 100% rename from tools/doc/doxyinput/thermo.txt rename to docs/doxyinput/thermo.txt diff --git a/tools/doc/doxyinput/thermodemo.cpp b/docs/doxyinput/thermodemo.cpp similarity index 100% rename from tools/doc/doxyinput/thermodemo.cpp rename to docs/doxyinput/thermodemo.cpp diff --git a/tools/doc/doxyinput/thermodemo.txt b/docs/doxyinput/thermodemo.txt similarity index 100% rename from tools/doc/doxyinput/thermodemo.txt rename to docs/doxyinput/thermodemo.txt diff --git a/tools/doc/doxyinput/transport.txt b/docs/doxyinput/transport.txt similarity index 100% rename from tools/doc/doxyinput/transport.txt rename to docs/doxyinput/transport.txt diff --git a/tools/doc/doxyinput/winbuild.txt b/docs/doxyinput/winbuild.txt similarity index 100% rename from tools/doc/doxyinput/winbuild.txt rename to docs/doxyinput/winbuild.txt diff --git a/tools/doc/html/banner4.jpg b/docs/html/banner4.jpg similarity index 100% rename from tools/doc/html/banner4.jpg rename to docs/html/banner4.jpg diff --git a/tools/doc/python/.cvsignore b/docs/python/.cvsignore similarity index 100% rename from tools/doc/python/.cvsignore rename to docs/python/.cvsignore diff --git a/tools/doc/python/makedoc b/docs/python/makedoc similarity index 100% rename from tools/doc/python/makedoc rename to docs/python/makedoc diff --git a/tools/doc/python/mkmkdoc.py b/docs/python/mkmkdoc.py similarity index 100% rename from tools/doc/python/mkmkdoc.py rename to docs/python/mkmkdoc.py diff --git a/tools/doc/html/.cvsignore b/tools/doc/html/.cvsignore deleted file mode 100644 index 7f8de4b2d..000000000 --- a/tools/doc/html/.cvsignore +++ /dev/null @@ -1,11 +0,0 @@ -*.html -*.md5 -*.png -*.dot -*.gif -*.hhc -*.hhk -*.hhp -*.map -*.css -formula.repository From 2af06f0e795a7eeb64da9590e78b5d2b8635eb7d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 4 Aug 2010 23:34:45 +0000 Subject: [PATCH 218/446] Completed move of doxygen directories. --- docs/{ => install_examples}/README.txt | 0 tools/Makefile.in | 3 -- tools/doc/.cvsignore | 2 - tools/doc/README | 15 -------- tools/doc/ct.css | 52 -------------------------- tools/doc/footer.html | 16 -------- tools/doc/header.html | 25 ------------- 7 files changed, 113 deletions(-) rename docs/{ => install_examples}/README.txt (100%) delete mode 100644 tools/doc/.cvsignore delete mode 100644 tools/doc/README delete mode 100755 tools/doc/ct.css delete mode 100755 tools/doc/footer.html delete mode 100755 tools/doc/header.html diff --git a/docs/README.txt b/docs/install_examples/README.txt similarity index 100% rename from docs/README.txt rename to docs/install_examples/README.txt diff --git a/tools/Makefile.in b/tools/Makefile.in index 287cddbd2..18c8e502d 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -35,9 +35,6 @@ clean: cd src; @MAKE@ clean cd testtools; @MAKE@ clean -docs: - cd doc; doxygen Cantera.cfg - depends: cd src; @MAKE@ depends cd testtools; @MAKE@ depends diff --git a/tools/doc/.cvsignore b/tools/doc/.cvsignore deleted file mode 100644 index ffc15abf8..000000000 --- a/tools/doc/.cvsignore +++ /dev/null @@ -1,2 +0,0 @@ -Makefile -Cantera.cfg diff --git a/tools/doc/README b/tools/doc/README deleted file mode 100644 index 036298805..000000000 --- a/tools/doc/README +++ /dev/null @@ -1,15 +0,0 @@ -Doxygen information: - - -The current version is 1.4.7: -I have version 1.3.9.1 - -Support is provided in the following versions for the following features - -SEPARATE_MEMBER_PAGES = 1.4.2 -FILE_VERSION_FILTER = 1.4.0 -WARN_NO_PARAMDOC = 1.4.0 -GROUP_GRAPHS = 1.4.0 -DIRECTORY_GRAPHS = 1.4.0 -DOT_TRANSPARENT = 1.4.0 -DOT_MULTI_TARGET =1.4.0 diff --git a/tools/doc/ct.css b/tools/doc/ct.css deleted file mode 100755 index ba2a320e5..000000000 --- a/tools/doc/ct.css +++ /dev/null @@ -1,52 +0,0 @@ -A.qindex{ font-family: Verdana, Arial, Helvetica, sans-serif; font-weight: bold; color: #663366; text-decoration: none; font-size: smaller; } -A.qindexRef{ font-family: Verdana, Arial, Helvetica, sans-serif; color: #333366; text-decoration: none; font-size: smaller; } -BODY { font-family: Arial, Helvetica, sans-serif; font-weight: normal; } -H1 { font-family: Arial, Helvetica, sans-serif; font-weight: normal; text-align: center; font-size: large} -H2 { font-family: Arial, Helvetica, sans-serif; font-weight: normal; font-size: large} -H3 { font-family: Arial, Helvetica, sans-serif; font-weight: normal } -A.el { text-decoration: none; font-weight: bold } -A.elRef { font-weight: bold } -A.code { text-decoration: none; font-weight: normal; } -A.codeRef { font-weight: normal;} -a.headerref {color: #ffffff; text-decoration: none } -DL.el { margin-left: -1cm } -DIV.fragment { width: 100%; border: none; background-color: #eeeeee } -DIV.ah { background-color: #663333; margin-bottom: 3 px; margin-top: 3 px } -TD.md { background-color: #f2f2ff; font-weight: bold; } -TD.mdname1 { background-color: #f2f2ff; font-weight: bold; color: #602020; } -TD.mdname { background-color: #f2f2ff; font-weight: bold; color: #602020; width: 600px; } -DIV.groupHeader { margin-left: 16px; margin-top: 12px; margin-bottom: 6px; font-weight: bold } -DIV.groupText { margin-left: 16px; font-style: italic; font-size: smaller } - -TD.indexkey { - background-color: #eeeeff; - font-weight: bold; - padding-right : 10px; - padding-top : 2px; - padding-left : 10px; - padding-bottom : 2px; - margin-left : 0px; - margin-right : 0px; - margin-top : 2px; - margin-bottom : 2px -} -TD.indexvalue { - background-color: #eeeeff; - font-style: italic; - padding-right : 10px; - padding-top : 2px; - padding-left : 10px; - padding-bottom : 2px; - margin-left : 0px; - margin-right : 0px; - margin-top : 2px; - margin-bottom : 2px -} -FONT.keyword { color: #008000 } -FONT.keywordtype { color: #604020 } -FONT.keywordflow { color: #e08000 } -FONT.comment { color: #800000 } -FONT.preprocessor { color: #806020 } -FONT.stringliteral { color: #002080 } -FONT.charliteral { color: #008080 } - diff --git a/tools/doc/footer.html b/tools/doc/footer.html deleted file mode 100755 index 30ddd178a..000000000 --- a/tools/doc/footer.html +++ /dev/null @@ -1,16 +0,0 @@ - -
- - - -
Copyright (c) 2005 California Institute of Technology
- - - - - - - - - - diff --git a/tools/doc/header.html b/tools/doc/header.html deleted file mode 100755 index 17e4b8b0f..000000000 --- a/tools/doc/header.html +++ /dev/null @@ -1,25 +0,0 @@ - - - -Cantera Reference Manual - - - - - - - - - -
- - - - - - - - - From b216c194aa8d0c52deb36584d498a61cfc995e75 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 6 Aug 2010 20:09:58 +0000 Subject: [PATCH 219/446] Changed the name of getLNActivityCoefficient to getLnActivityCoefficient Doxygen updates --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 55 +++++++++++++------- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 31 ++++++++++- Cantera/src/thermo/ThermoPhase.cpp | 47 ++++++++++------- Cantera/src/thermo/ThermoPhase.h | 7 ++- 4 files changed, 99 insertions(+), 41 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 441df0f86..92da2a6b9 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -39,7 +39,7 @@ using namespace std; namespace Cantera { static const double xxSmall = 1.0E-150; - + //==================================================================================================================== /* * Default constructor. * @@ -54,11 +54,14 @@ namespace Cantera { numAnionSpecies_(0), numPassThroughSpecies_(0), neutralMoleculePhase_(0), - IOwnNThermoPhase_(true) + IOwnNThermoPhase_(true), + moleFractionsTmp_(0), + muNeutralMolecule_(0), + lnActCoeff_NeutralMolecule_(0) { } - + //==================================================================================================================== // Construct and initialize an IonsFromNeutralVPSSTP object // directly from an asci input file /* @@ -95,14 +98,17 @@ namespace Cantera { numAnionSpecies_(0), numPassThroughSpecies_(0), neutralMoleculePhase_(neutralPhase), - IOwnNThermoPhase_(true) + IOwnNThermoPhase_(true), + moleFractionsTmp_(0), + muNeutralMolecule_(0), + lnActCoeff_NeutralMolecule_(0) { if (neutralPhase) { IOwnNThermoPhase_ = false; } constructPhaseFile(inputFile, id); } - + //==================================================================================================================== IonsFromNeutralVPSSTP::IonsFromNeutralVPSSTP(XML_Node& phaseRoot, std::string id, ThermoPhase *neutralPhase) : GibbsExcessVPSSTP(), @@ -114,7 +120,11 @@ namespace Cantera { numAnionSpecies_(0), numPassThroughSpecies_(0), neutralMoleculePhase_(neutralPhase), - IOwnNThermoPhase_(true) + IOwnNThermoPhase_(true), + moleFractionsTmp_(0), + muNeutralMolecule_(0), + + lnActCoeff_NeutralMolecule_(0) { if (neutralPhase) { IOwnNThermoPhase_ = false; @@ -122,7 +132,7 @@ namespace Cantera { constructPhaseXML(phaseRoot, id); } - + //==================================================================================================================== /* * Copy Constructor: @@ -140,11 +150,15 @@ namespace Cantera { numAnionSpecies_(0), numPassThroughSpecies_(0), neutralMoleculePhase_(0), - IOwnNThermoPhase_(true) + IOwnNThermoPhase_(true), + moleFractionsTmp_(0), + muNeutralMolecule_(0), + + lnActCoeff_NeutralMolecule_(0) { IonsFromNeutralVPSSTP::operator=(b); } - + //==================================================================================================================== /* * operator=() * @@ -196,10 +210,12 @@ namespace Cantera { IOwnNThermoPhase_ = b.IOwnNThermoPhase_; moleFractionsTmp_ = b.moleFractionsTmp_; muNeutralMolecule_ = b.muNeutralMolecule_; - gammaNeutralMolecule_ = b.gammaNeutralMolecule_; + // gammaNeutralMolecule_ = b.gammaNeutralMolecule_; + lnActCoeff_NeutralMolecule_ = b.lnActCoeff_NeutralMolecule_; dlnActCoeffdT_NeutralMolecule_ = b.dlnActCoeffdT_NeutralMolecule_; dlnActCoeffdlnX_diag_NeutralMolecule_ = b.dlnActCoeffdlnX_diag_NeutralMolecule_; dlnActCoeffdlnN_diag_NeutralMolecule_ = b.dlnActCoeffdlnN_diag_NeutralMolecule_; + dlnActCoeffdlnN_NeutralMolecule_ = b.dlnActCoeffdlnN_NeutralMolecule_; return *this; } @@ -472,7 +488,8 @@ namespace Cantera { neutralMoleculePhase_->getChemPotentials(mu); break; case cIonSolnType_SINGLEANION: - neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_)); + // neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_)); + neutralMoleculePhase_->getLnActivityCoefficients(DATA_PTR(lnActCoeff_NeutralMolecule_)); fact2 = 2.0 * RT_ * log(2.0); @@ -482,7 +499,7 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; xx = fmaxx(SmallNumber, moleFractions_[icat]); - mu[icat] = muNeutralMolecule_[jNeut] + fact2 + RT_ * log(gammaNeutralMolecule_[jNeut] * xx); + mu[icat] = muNeutralMolecule_[jNeut] + fact2 + RT_ * (lnActCoeff_NeutralMolecule_[jNeut] + log(xx)); } // Do the anion list @@ -496,7 +513,7 @@ namespace Cantera { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; xx = fmaxx(SmallNumber, moleFractions_[icat]); - mu[icat] = muNeutralMolecule_[jNeut] + RT_ * log( gammaNeutralMolecule_[jNeut] * xx); + mu[icat] = muNeutralMolecule_[jNeut] + RT_ * (lnActCoeff_NeutralMolecule_[jNeut] + log(xx)); } break; @@ -1156,7 +1173,7 @@ namespace Cantera { } - + //==================================================================================================================== /* * @internal Initialize. This method is provided to allow * subclasses to perform any initialization required after all @@ -1174,7 +1191,7 @@ namespace Cantera { initLengths(); GibbsExcessVPSSTP::initThermo(); } - + //==================================================================================================================== // Initialize lengths of local variables after all species have // been identified. @@ -1190,7 +1207,7 @@ namespace Cantera { passThroughList_.resize(m_kk); moleFractionsTmp_.resize(m_kk); muNeutralMolecule_.resize(numNeutralMoleculeSpecies_); - gammaNeutralMolecule_.resize(numNeutralMoleculeSpecies_); + lnActCoeff_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnX_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); @@ -1399,7 +1416,7 @@ namespace Cantera { /* * Get the activity coefficiens of the neutral molecules */ - neutralMoleculePhase_->getActivityCoefficients(DATA_PTR(gammaNeutralMolecule_)); + neutralMoleculePhase_->getLnActivityCoefficients(DATA_PTR(lnActCoeff_NeutralMolecule_)); switch (ionSolnType_) { case cIonSolnType_PASSTHROUGH: @@ -1412,7 +1429,7 @@ namespace Cantera { icat = cationList_[k]; jNeut = fm_invert_ionForNeutral[icat]; fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut])/fmij; + lnActCoeff_Scaled_[icat] = lnActCoeff_NeutralMolecule_[jNeut] / fmij; } // Do the anion list @@ -1424,7 +1441,7 @@ namespace Cantera { for (k = 0; k < numPassThroughSpecies_; k++) { icat = passThroughList_[k]; jNeut = fm_invert_ionForNeutral[icat]; - lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut]); + lnActCoeff_Scaled_[icat] = lnActCoeff_NeutralMolecule_[jNeut]; } break; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 964891acd..f0d4be062 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -892,9 +892,36 @@ namespace Cantera { //! Temporary mole fraction vector mutable std::vector moleFractionsTmp_; + //! Storage vector for the neutral molecule chemical potentials + /*! + * This vector is used as a temporary storage area when calculating the ion chemical + * potentials. + * + * Units = Joules/kmol + * Length = numNeutralMoleculeSpecies_ + */ mutable std::vector muNeutralMolecule_; - mutable std::vector gammaNeutralMolecule_; - mutable std::vector dlnActCoeff_NeutralMolecule_; + + //! Storage vector for the neutral molecule activity coefficients + /*! + * This vector is used as a temporary storage area when calculating the ion chemical + * potentials and activity coefficients + * + * Units = none + * Length = numNeutralMoleculeSpecies_ + */ + // mutable std::vector gammaNeutralMolecule_; + + //! Storage vector for the neutral molecule ln activity coefficients + /*! + * This vector is used as a temporary storage area when calculating the ion chemical + * potentials and activity coefficients + * + * Units = none + * Length = numNeutralMoleculeSpecies_ + */ + mutable std::vector lnActCoeff_NeutralMolecule_; + mutable std::vector dlnActCoeffdT_NeutralMolecule_; mutable std::vector dlnActCoeffdlnX_diag_NeutralMolecule_; mutable std::vector dlnActCoeffdlnN_diag_NeutralMolecule_; diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index d7952e724..42ec63f7d 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -135,7 +135,7 @@ namespace Cantera { m_ssConvention = right.m_ssConvention; return *this; } -//==================================================================================================================== + //==================================================================================================================== /* * Duplication routine for objects which inherit from * ThermoPhase. @@ -151,45 +151,42 @@ namespace Cantera { ThermoPhase* tp = new ThermoPhase(*this); return tp; } -//==================================================================================================================== + //==================================================================================================================== int ThermoPhase::activityConvention() const { return cAC_CONVENTION_MOLAR; } - + //================================================================================================================= int ThermoPhase::standardStateConvention() const { return m_ssConvention; } - + //================================================================================================================= doublereal ThermoPhase::logStandardConc(int k) const { return log(standardConcentration(k)); } - + //================================================================================================================= void ThermoPhase::getActivities(doublereal* a) const { getActivityConcentrations(a); int nsp = nSpecies(); int k; for (k = 0; k < nsp; k++) a[k] /= standardConcentration(k); } - - void ThermoPhase::getLNActivityCoefficients(doublereal *const lnac) const { + //================================================================================================================= + void ThermoPhase::getLnActivityCoefficients(doublereal *const lnac) const { getActivityCoefficients(lnac); for (int k = 0; k < m_kk; k++) { lnac[k] = std::log(lnac[k]); } } - - void ThermoPhase::setState_TPX(doublereal t, doublereal p, - const doublereal* x) { + //================================================================================================================= + void ThermoPhase::setState_TPX(doublereal t, doublereal p, const doublereal* x) { setMoleFractions(x); setTemperature(t); setPressure(p); } - - void ThermoPhase::setState_TPX(doublereal t, doublereal p, - compositionMap& x) { + //================================================================================================================= + void ThermoPhase::setState_TPX(doublereal t, doublereal p, compositionMap& x) { setMoleFractionsByName(x); setTemperature(t); setPressure(p); } - - void ThermoPhase::setState_TPX(doublereal t, doublereal p, - const std::string& x) { + //================================================================================================================= + void ThermoPhase::setState_TPX(doublereal t, doublereal p, const std::string& x) { compositionMap xx; int kk = nSpecies(); for (int k = 0; k < kk; k++) xx[speciesName(k)] = -1.0; @@ -202,17 +199,17 @@ namespace Cantera { } setMoleFractionsByName(xx); setTemperature(t); setPressure(p); } - + //================================================================================================================= void ThermoPhase::setState_TPY(doublereal t, doublereal p, const doublereal* y) { setMassFractions(y); setTemperature(t); setPressure(p); } - + //================================================================================================================= void ThermoPhase::setState_TPY(doublereal t, doublereal p, compositionMap& y) { setMassFractionsByName(y); setTemperature(t); setPressure(p); } - + //================================================================================================================= void ThermoPhase::setState_TPY(doublereal t, doublereal p, const std::string& y) { compositionMap yy; @@ -227,28 +224,34 @@ namespace Cantera { } setMassFractionsByName(yy); setTemperature(t); setPressure(p); } + //================================================================================================================= void ThermoPhase::setState_TP(doublereal t, doublereal p) { setTemperature(t); setPressure(p); } + //================================================================================================================= void ThermoPhase::setState_PX(doublereal p, doublereal* x) { setMoleFractions(x); setPressure(p); } + //================================================================================================================= void ThermoPhase::setState_PY(doublereal p, doublereal* y) { setMassFractions(y); setPressure(p); } + //================================================================================================================= void ThermoPhase::setState_HP(doublereal Htarget, doublereal p, doublereal dTtol) { setState_HPorUV(Htarget, p, dTtol, false); } + //================================================================================================================= void ThermoPhase::setState_UV(doublereal u, doublereal v, doublereal dTtol) { setState_HPorUV(u, v, dTtol, true); } + //================================================================================================================= // Do the convergence work /* @@ -513,16 +516,19 @@ namespace Cantera { throw CanteraError("setState_HPorUV (HP)", ErrString); } } + //================================================================================================================= void ThermoPhase::setState_SP(doublereal Starget, doublereal p, doublereal dTtol) { setState_SPorSV(Starget, p, dTtol, false); } + //================================================================================================================= void ThermoPhase::setState_SV(doublereal Starget, doublereal v, doublereal dTtol) { setState_SPorSV(Starget, v, dTtol, true); } + //================================================================================================================= // Do the convergence work for fixed entropy situations /* @@ -772,6 +778,7 @@ namespace Cantera { throw CanteraError("setState_SPorSV (SP)", ErrString); } } + //================================================================================================================= doublereal ThermoPhase::err(std::string msg) const { throw CanteraError("ThermoPhase","Base class method " @@ -816,6 +823,7 @@ namespace Cantera { if (i == 5) uA[5] = 0.0; } } + //================================================================================================================= /* * initThermoFile(): @@ -861,6 +869,7 @@ namespace Cantera { initThermoXML(*fxml_phase, id); delete fxml; } + //================================================================================================================= /* * Import and initialize a ThermoPhase object diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 274047eed..21ea9b1eb 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -1153,7 +1153,12 @@ namespace Cantera { } } - virtual void getLNActivityCoefficients(doublereal * const lnac) const; + //! Get the array of non-dimensional molar-based ln activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param ac Output vector of ln activity coefficients. Length: m_kk. + */ + virtual void getLnActivityCoefficients(doublereal * const lnac) const; //@} /// @name Partial Molar Properties of the Solution From 1f5ade84887b25f75fe37c331707b07edc497ea6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 6 Aug 2010 20:33:20 +0000 Subject: [PATCH 220/446] Doxygen update - filling in the missing entries. --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 7 +- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 94 +++++++++++++------ .../src/transport/LiquidTranInteraction.cpp | 2 - 3 files changed, 69 insertions(+), 34 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index 92da2a6b9..d05845830 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -351,12 +351,11 @@ namespace Cantera { getActivities(c); } - void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs,vector_fp& charges, std::vector& neutMolIndex){ + void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs, + vector_fp& charges, std::vector& neutMolIndex) const { coeffs = fm_neutralMolec_ions_; charges = m_speciesCharge; neutMolIndex = fm_invert_ionForNeutral; - //for ( int k = 0; k < fm_neutralMolec_ions_[k]; k++ ) - // coeffs.push_back(fm_neutralMolec_ions_[k]); } // Return the standard concentration for the kth species @@ -884,7 +883,7 @@ namespace Cantera { * is followed, while the difference in charge neutrality * is dumped into the anion mole number to fix the imbalance. */ - void IonsFromNeutralVPSSTP::getNeutralMoleculeMoleGrads(const doublereal * const dx, doublereal *dy) const { + void IonsFromNeutralVPSSTP::getNeutralMoleculeMoleGrads(const doublereal * const dx, doublereal * const dy) const { int k, icat, jNeut; doublereal sumCat; doublereal sumAnion; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index f0d4be062..7f4886b1b 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -454,9 +454,23 @@ namespace Cantera { //! Get the Salt Dissociation Coefficients //! Returns the vector of dissociation coefficients and vector of charges - virtual void getDissociationCoeffs(vector_fp& coeffs, vector_fp& charges, std::vector& neutMolIndex); + /*! + * @param fm_neutralMolec_ions Returns the formula matrix for the composition of neutral molecules + * in terms of the ions. + * @param charges Returns a vector containing the charges of all species in this phase + * @param neutMolIndex Returns the vector fm_invert_ionForNeutral + * This is the mapping between ion species and neutral molecule for quick invert. + */ + void getDissociationCoeffs(vector_fp& fm_neutralMolec_ions, vector_fp& charges, std::vector& neutMolIndex) const; - virtual void getNeutralMolecMoleFractions(vector_fp& fracs){fracs=NeutralMolecMoleFractions_;} + + //! Return the current value of the neutral mole fraction vector + /*! + * @param neutralMoleculeMoleFractions Vector of neutral molecule mole fractions. + */ + void getNeutralMolecMoleFractions(vector_fp& neutralMoleculeMoleFractions) const { + neutralMoleculeMoleFractions = NeutralMolecMoleFractions_; + } //! Calculate neutral molecule mole fractions /*! @@ -471,14 +485,29 @@ namespace Cantera { * in the charge neutrality is allowed. The cation number * is followed, while the difference in charge neutrality * is dumped into the anion mole number to fix the imbalance. + * + * @param dx input vector of ion mole fraction gradients + * @param dy output Vector of neutral molecule mole fraction gradients */ - virtual void getNeutralMoleculeMoleGrads(const doublereal * const x, doublereal *y) const; + void getNeutralMoleculeMoleGrads(const doublereal * const dx, doublereal *const dy) const; - virtual void getCationList(std::vector& cation){cation=cationList_;} - virtual void getAnionList(std::vector& anion){anion=anionList_;} - virtual void getSpeciesNames(std::vector& names){names=m_speciesNames;} + //! Get the list of cations in this object + /*! + * @param cation List of cations + */ + void getCationList(std::vector& cation) const { + cation=cationList_; + } + //! Get the list of anions in this object + /*! + * @param anion List of anions + */ + void getAnionList(std::vector& anion) const { + anion=anionList_; + } + //@} /// @name Properties of the Standard State of the Species in the Solution //@{ @@ -876,18 +905,6 @@ namespace Cantera { * as a shallow pointer. */ bool IOwnNThermoPhase_; - - //! ThermoPhase for the cation lattice - /*! - * Currently this is unimplemented and may be deleted - */ - // ThermoPhase *cationPhase_; - - //! ThermoPhase for the anion lattice - /*! - * Currently this is unimplemented and may be deleted - */ - //ThermoPhase *anionPhase_; //! Temporary mole fraction vector mutable std::vector moleFractionsTmp_; @@ -902,16 +919,6 @@ namespace Cantera { */ mutable std::vector muNeutralMolecule_; - //! Storage vector for the neutral molecule activity coefficients - /*! - * This vector is used as a temporary storage area when calculating the ion chemical - * potentials and activity coefficients - * - * Units = none - * Length = numNeutralMoleculeSpecies_ - */ - // mutable std::vector gammaNeutralMolecule_; - //! Storage vector for the neutral molecule ln activity coefficients /*! * This vector is used as a temporary storage area when calculating the ion chemical @@ -922,10 +929,41 @@ namespace Cantera { */ mutable std::vector lnActCoeff_NeutralMolecule_; + //! Storage vector for the neutral molecule d ln activity coefficients dT + /*! + * This vector is used as a temporary storage area when calculating the ion derivatives + + * + * Units = 1/Kelvin + * Length = numNeutralMoleculeSpecies_ + */ mutable std::vector dlnActCoeffdT_NeutralMolecule_; + + //! Storage vector for the neutral molecule d ln activity coefficients dX - diagonal component + /*! + * This vector is used as a temporary storage area when calculating the ion derivatives + * + * Units = none + * Length = numNeutralMoleculeSpecies_ + */ mutable std::vector dlnActCoeffdlnX_diag_NeutralMolecule_; + + //! Storage vector for the neutral molecule d ln activity coefficients dlnN - diagonal component + /*! + * This vector is used as a temporary storage area when calculating the ion derivatives + * + * Units = none + * Length = numNeutralMoleculeSpecies_ + */ mutable std::vector dlnActCoeffdlnN_diag_NeutralMolecule_; + //! Storage vector for the neutral molecule d ln activity coefficients dlnN + /*! + * This vector is used as a temporary storage area when calculating the ion derivatives + * + * Units = none + * Length = numNeutralMoleculeSpecies_ + */ mutable Array2D dlnActCoeffdlnN_NeutralMolecule_; }; diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index 76aa063f2..7acfb0db0 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -680,8 +680,6 @@ namespace Cantera { vector anion; ions_thermo->getCationList(cation); ions_thermo->getAnionList(anion); - vector speciesNames; - ions_thermo->getSpeciesNames(speciesNames); // Reaction Coeffs and Charges std::vector viS(6); From fc101d40490d590f9ff907c6c5b8fcd8cafc0baa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Aug 2010 15:07:44 +0000 Subject: [PATCH 221/446] Doxygen update --- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 6 + Cantera/src/thermo/PDSS_IonsFromNeutral.cpp | 133 ++++++++++++-------- Cantera/src/thermo/PDSS_IonsFromNeutral.h | 35 +++++- Cantera/src/thermo/ThermoPhase.h | 38 +++--- 4 files changed, 134 insertions(+), 78 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 7f4886b1b..787b305df 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -384,6 +384,8 @@ namespace Cantera { * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * + * @param hbar Output vector of species partial molar enthalpies. + * Length: m_kk. Units: J/kmol */ virtual void getPartialMolarEnthalpies(doublereal* hbar) const; @@ -401,6 +403,10 @@ namespace Cantera { * - R \ln( \gamma_k X_k) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] + * + * + * @param sbar Output vector of species partial molar entropies. + * Length: m_kk. Units: J/kmol/K */ virtual void getPartialMolarEntropies(doublereal* sbar) const; diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp index 28fa361de..2bf67b6a3 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.cpp @@ -24,10 +24,8 @@ using namespace std; namespace Cantera { - /** - * Basic list of constructors and duplicators - */ - + + //==================================================================================================================== PDSS_IonsFromNeutral::PDSS_IonsFromNeutral(VPStandardStateTP *tp, int spindex) : PDSS(tp, spindex), neutralMoleculePhase_(0), @@ -128,15 +126,27 @@ namespace Cantera { neutralMoleculePhase_ = ionPhase->neutralMoleculePhase_; } //==================================================================================================================== - /** - * constructPDSSXML: + // Initialization of a PDSS object using an xml tree + /* + * This routine is a driver for the initialization of the + * object. + * + * basic logic: + * initThermo() (cascade) + * getStuff from species Part of XML file + * initThermoXML(phaseNode) (cascade) + * + * @param vptp_ptr Pointer to the Variable pressure %ThermoPhase object + * This object must have already been malloced. * - * Initialization of a PDSS_IonsFromNeutral object using an - * xml file. - - * @param id Optional parameter identifying the name of the - * phase. If none is given, the first XML - * phase element will be used. + * @param spindex Species index within the phase + * + * @param phaseNode Reference to the phase Information for the phase + * that owns this species. + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. */ void PDSS_IonsFromNeutral::constructPDSSXML(VPStandardStateTP *tp, int spindex, const XML_Node& speciesNode, @@ -195,7 +205,25 @@ namespace Cantera { } //==================================================================================================================== - + // Initialization of a PDSS object using an + // input XML file. + /* + * + * This routine is a precursor to constructPDSSXML(XML_Node*) + * routine, which does most of the work. + * + * @param vptp_ptr Pointer to the Variable pressure %ThermoPhase object + * This object must have already been malloced. + * + * @param spindex Species index within the phase + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ void PDSS_IonsFromNeutral::constructPDSSFile(VPStandardStateTP *tp, int spindex, std::string inputFile, std::string id) { @@ -233,11 +261,11 @@ namespace Cantera { constructPDSSXML(tp, spindex, *s, *fxml_phase, id); delete fxml; } - + //======================================================================================================= void PDSS_IonsFromNeutral::initThermoXML(const XML_Node& phaseNode, std::string &id) { PDSS::initThermoXML(phaseNode, id); } - + //======================================================================================================= void PDSS_IonsFromNeutral::initThermo() { PDSS::initThermo(); SpeciesThermo &sp = m_tp->speciesThermo(); @@ -245,8 +273,8 @@ namespace Cantera { m_minTemp = m_spthermo->minTemp(m_spindex); m_maxTemp = m_spthermo->maxTemp(m_spindex); } - - /** + //======================================================================================================= + /* * Return the molar enthalpy in units of J kmol-1 */ doublereal @@ -255,7 +283,7 @@ namespace Cantera { doublereal RT = GasConstant * m_temp; return (val * RT); } - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::enthalpy_RT() const { neutralMoleculePhase_->getEnthalpy_RT(DATA_PTR(tmpNM)); @@ -266,9 +294,8 @@ namespace Cantera { } return val; } - - - /** + //======================================================================================================= + /* * Calculate the internal energy in mks units of * J kmol-1 */ @@ -278,8 +305,8 @@ namespace Cantera { doublereal RT = GasConstant * m_temp; return (val * RT); } - - /** + //======================================================================================================= + /* * Calculate the entropy in mks units of * J kmol-1 K-1 */ @@ -288,7 +315,7 @@ namespace Cantera { doublereal val = entropy_R(); return (val * GasConstant); } - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::entropy_R() const { neutralMoleculePhase_->getEntropy_R(DATA_PTR(tmpNM)); @@ -302,8 +329,8 @@ namespace Cantera { } return val; } - - /** + //======================================================================================================= + /* * Calculate the Gibbs free energy in mks units of * J kmol-1 K-1. */ @@ -313,7 +340,7 @@ namespace Cantera { doublereal RT = GasConstant * m_temp; return (val * RT); } - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::gibbs_RT() const { neutralMoleculePhase_->getGibbs_RT(DATA_PTR(tmpNM)); @@ -327,8 +354,8 @@ namespace Cantera { } return val; } - - /** + //======================================================================================================= + /* * Calculate the constant pressure heat capacity * in mks units of J kmol-1 K-1 */ @@ -337,7 +364,7 @@ namespace Cantera { doublereal val = cp_R(); return (val * GasConstant); } - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::cp_R() const { neutralMoleculePhase_->getCp_R(DATA_PTR(tmpNM)); @@ -348,7 +375,7 @@ namespace Cantera { } return val; } - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::molarVolume() const { neutralMoleculePhase_->getStandardVolumes(DATA_PTR(tmpNM)); @@ -359,8 +386,7 @@ namespace Cantera { } return val; } - - + //======================================================================================================= doublereal PDSS_IonsFromNeutral::density() const { return (m_pres * m_mw / (GasConstant * m_temp)); @@ -375,7 +401,7 @@ namespace Cantera { throw CanteraError("PDSS_IonsFromNeutral::cv_mole()", "unimplemented"); return 0.0; } - + //==================================================================================================================== doublereal PDSS_IonsFromNeutral::gibbs_RT_ref() const { @@ -390,7 +416,7 @@ namespace Cantera { } return val; } - + //==================================================================================================================== doublereal PDSS_IonsFromNeutral::enthalpy_RT_ref() const { neutralMoleculePhase_->getEnthalpy_RT_ref(DATA_PTR(tmpNM)); doublereal val = 0.0; @@ -400,7 +426,7 @@ namespace Cantera { } return val; } - + //==================================================================================================================== doublereal PDSS_IonsFromNeutral::entropy_R_ref() const { neutralMoleculePhase_->getEntropy_R_ref(DATA_PTR(tmpNM)); doublereal val = 0.0; @@ -413,7 +439,7 @@ namespace Cantera { } return val; } - + //==================================================================================================================== doublereal PDSS_IonsFromNeutral::cp_R_ref() const { neutralMoleculePhase_->getCp_R_ref(DATA_PTR(tmpNM)); doublereal val = 0.0; @@ -423,7 +449,7 @@ namespace Cantera { } return val; } - + //==================================================================================================================== doublereal PDSS_IonsFromNeutral::molarVolume_ref() const { neutralMoleculePhase_->getStandardVolumes_ref(DATA_PTR(tmpNM)); doublereal val = 0.0; @@ -433,7 +459,7 @@ namespace Cantera { } return val; } - + //==================================================================================================================== /* * Calculate the pressure (Pascals), given the temperature and density * Temperature: kelvin @@ -442,31 +468,31 @@ namespace Cantera { doublereal PDSS_IonsFromNeutral::pressure() const { return m_pres; } - + //==================================================================================================================== void PDSS_IonsFromNeutral::setPressure(doublereal p) { m_pres = p; neutralMoleculePhase_->setPressure(p); } - - /// critical temperature + //==================================================================================================================== + // critical temperature doublereal PDSS_IonsFromNeutral::critTemperature() const { throw CanteraError("PDSS_IonsFromNeutral::critTemperature()", "unimplemented"); return (0.0); } - - /// critical pressure + //==================================================================================================================== + // critical pressure doublereal PDSS_IonsFromNeutral::critPressure() const { throw CanteraError("PDSS_IonsFromNeutral::critPressure()", "unimplemented"); return (0.0); } - - /// critical density + //==================================================================================================================== + // critical density doublereal PDSS_IonsFromNeutral::critDensity() const { throw CanteraError("PDSS_IonsFromNeutral::critDensity()", "unimplemented"); return (0.0); } - + //==================================================================================================================== /* * Return the temperature @@ -478,29 +504,30 @@ namespace Cantera { m_temp = m_vpssmgr_ptr->temperature(); return m_temp; } - + //==================================================================================================================== void PDSS_IonsFromNeutral::setTemperature(doublereal temp) { m_temp = temp; neutralMoleculePhase_->setTemperature(temp); } - + //==================================================================================================================== void PDSS_IonsFromNeutral::setState_TP(doublereal temp, doublereal pres) { m_pres = pres; m_temp = temp; neutralMoleculePhase_->setState_TP(temp, pres); } - + //==================================================================================================================== void PDSS_IonsFromNeutral::setState_TR(doublereal temp, doublereal rho) { neutralMoleculePhase_->setState_TR(temp, rho); } - - /// saturation pressure + //==================================================================================================================== + // saturation pressure doublereal PDSS_IonsFromNeutral::satPressure(doublereal t){ throw CanteraError("PDSS_IonsFromNeutral::satPressure()", "unimplemented"); /*NOTREACHED*/ return (0.0); } - + //==================================================================================================================== } +//==================================================================================================================== diff --git a/Cantera/src/thermo/PDSS_IonsFromNeutral.h b/Cantera/src/thermo/PDSS_IonsFromNeutral.h index 4b95fd6c2..06782b254 100644 --- a/Cantera/src/thermo/PDSS_IonsFromNeutral.h +++ b/Cantera/src/thermo/PDSS_IonsFromNeutral.h @@ -183,12 +183,21 @@ namespace Cantera { */ virtual doublereal gibbs_mole() const; - //! Return the molar gibbs free energy divided by RT + //! Return the molar gibbs free energy divided by RT /*! - * Returns the species standard state gibbs free energy divided by RT at the + * Returns the species standard state gibbs free energy divided by RT at the * current temperature and pressure. * - * @return returns the species standard state gibbs free energy divided by RT + * \f[ + * \frac{\mu^o_k}{RT} = \sum_{m}{ \alpha_{m , k} \frac{\mu^o_{m}}{RT}} + ( 1 - \delta_{k,sp}) 2.0 \ln{2.0} + * \f] + * + * m is the neutral molecule species index. \f$ \alpha_{m , k} \f$ is the stoiciometric + * coefficient for the neutral molecule, m, that creates the thermodynamics for the ionic species k. + * A factor \f$ 2.0 \ln{2.0} \f$ is added to all ions except for the species ionic species, which in this + * case is the single anion species, with species index sp. + * + * @return Returns the species standard state gibbs free energy divided by RT */ virtual doublereal gibbs_RT() const; @@ -388,10 +397,9 @@ namespace Cantera { void constructPDSSFile(VPStandardStateTP *vptp_ptr, int spindex, std::string inputFile, std::string id); - //!Initialization of a PDSS object using an xml tree + //! Initialization of a PDSS object using an xml tree /*! - * This routine is a driver for the initialization of the - * object. + * This routine is a driver for the initialization of the object. * * basic logic: * initThermo() (cascade) @@ -403,6 +411,9 @@ namespace Cantera { * * @param spindex Species index within the phase * + * @param speciesNode Reference to the phase Information for the species + * that this standard state refers to + * * @param phaseNode Reference to the phase Information for the phase * that owns this species. * @@ -461,16 +472,28 @@ namespace Cantera { ThermoPhase *neutralMoleculePhase_; public: + + //! Number of neutral molecule species that make up the stoichiometric vector for + //! this species, in terms of calculating thermodynamic functions int numMult_; + //! Vector of species indecises in the neutral molecule ThermoPhase std::vector idNeutralMoleculeVec; + //! Stoichiometric coefficient for this species using the Neutral Molecule Species + //! in the vector idNeutralMoleculeVec std::vector factorVec; + //! Add 2RTln2 to the entropy and Gibbs free energies for this species + /*! + * This is true if this species is not the special species + */ bool add2RTln2_; + //! Vector of length equal to the number of species in the neutral molecule phase mutable std::vector tmpNM; + //! True if this species is the special species int specialSpecies_; }; } diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 21ea9b1eb..8e35524d0 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -1156,7 +1156,7 @@ namespace Cantera { //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! - * @param ac Output vector of ln activity coefficients. Length: m_kk. + * @param lnac Output vector of ln activity coefficients. Length: m_kk. */ virtual void getLnActivityCoefficients(doublereal * const lnac) const; @@ -1975,6 +1975,8 @@ namespace Cantera { //! Add in species from Slave phases /*! * This hook is used for cSS_CONVENTION_SLAVE phases + * + * @param phaseNode XML Element for the phase */ virtual void installSlavePhases(Cantera::XML_Node* phaseNode); @@ -2076,45 +2078,43 @@ namespace Cantera { err("getdlnActCoeffds"); } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients - diagonal component only + //! Get the array of ln mole fraction derivatives of the log activity coefficients - diagonal component only /*! * This function is a virtual method. For ideal mixtures * (unity activity coefficients), this can return zero. * Implementations should take the derivative of the * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. mole fraction) + * logarithm of the mole fraction variable * that represents the standard state. * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical + * that mole fraction variable when the derivative of the chemical * potential is taken. * * units = dimensionless * - * @param dlnActCoeffdln_diag Output vector of derivatives of the - * log Activity Coefficients. length = m_kk + * @param dlnActCoeffdlnX_diag Output vector of derivatives of the + * log Activity Coefficients wrt the mole fractions. length = m_kk */ virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { err("getdlnActCoeffdlnX_diag"); } - //! Get the array of log concentration-like derivatives of the - //! log activity coefficients + //! Get the array of log species mole number derivatives of the log activity coefficients /*! - * This function is a virtual method. For ideal mixtures - * (unity activity coefficients), this can return zero. - * Implementations should take the derivative of the - * logarithm of the activity coefficient with respect to the - * logarithm of the concentration-like variable (i.e. moles) - * that represents the standard state. - * This quantity is to be used in conjunction with derivatives of - * that concentration-like variable when the derivative of the chemical - * potential is taken. + * This function is a virtual method. + * For ideal mixtures (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that species mole number variable when the derivative of the chemical + * potential is taken. * * units = dimensionless * * @param dlnActCoeffdlnN_diag Output vector of derivatives of the - * log Activity Coefficients. length = m_kk + * log Activity Coefficients. length = m_kk */ virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { err("getdlnActCoeffdlnN_diag"); From 09e2a0e71d3db6dc259201524cb37e400967c2ad Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Aug 2010 21:24:21 +0000 Subject: [PATCH 222/446] Doxygen updates --- Cantera/src/thermo/DebyeHuckel.cpp | 8 +- Cantera/src/thermo/SpeciesThermoFactory.cpp | 98 +++++++++++++-------- Cantera/src/thermo/ThermoFactory.cpp | 8 +- Cantera/src/thermo/VPSSMgrFactory.cpp | 22 +++-- 4 files changed, 87 insertions(+), 49 deletions(-) diff --git a/Cantera/src/thermo/DebyeHuckel.cpp b/Cantera/src/thermo/DebyeHuckel.cpp index 91546cf6d..d3dca91f5 100644 --- a/Cantera/src/thermo/DebyeHuckel.cpp +++ b/Cantera/src/thermo/DebyeHuckel.cpp @@ -915,11 +915,9 @@ namespace Cantera { delete fxml; } - /** - * interp_est() (static) - * - * utility function to assign an integer value from a string - * for the ElectrolyteSpeciesType field. + //! Utility function to assign an integer value from a string for the ElectrolyteSpeciesType field. + /*! + * @param estString input string that will be interpreted */ static int interp_est(std::string estString) { const char *cc = estString.c_str(); diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index ce0d21007..0d404873e 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -53,15 +53,18 @@ namespace Cantera { boost::mutex SpeciesThermoFactory::species_thermo_mutex ; #endif - //! Examine the types of species thermo parameterizations, //! and return a flag indicating the type of reference state thermo manager //! that will be needed in order to evaluate them all. /*! * - * @param spDataNodeList, This vector contains a list - * of species XML nodes that will be in the phase + * @param spDataNodeList This vector contains a list + * of species XML nodes that will be in the phase + * @param has_nasa Return int that indicates whether the phase has a NASA polynomial form for one of its species + * @param has_shomate Return int that indicates whether the phase has a SHOMATE polynomial form for one of its species + * @param has_simple Return int that indicates whether the phase has a SIMPLE polynomial form for one of its species + * @param has_other Return int that indicates whether the phase has a form for one of its species that is not one of the ones listed above. * * @todo Make sure that spDadta_node is species Data XML node by checking its name is speciesData */ @@ -294,11 +297,15 @@ namespace Cantera { } - /** - * Install a NASA polynomial thermodynamic property - * parameterization for species k into a SpeciesThermo instance. - * This is called by method installThermoForSpecies if a NASA - * block is found in the XML input. + //! Install a NASA polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a NASA block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param f0ptr Ptr to the first XML_Node for the first NASA polynomial + * @param f1ptr Ptr to the first XML_Node for the first NASA polynomial */ static void installNasaThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, @@ -377,12 +384,17 @@ namespace Cantera { #ifdef INCL_NASA96 - /** - * Install a NASA96 polynomial thermodynamic property - * parameterization for species k into a SpeciesThermo instance. + //! Install a NASA96 polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a NASA block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param f0ptr Ptr to the first XML_Node for the first NASA polynomial + * @param f1ptr Ptr to the first XML_Node for the first NASA polynomial */ - static void installNasa96ThermoFromXML(std::string speciesName, - SpeciesThermo& sp, int k, + static void installNasa96ThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, const XML_Node* f0ptr, const XML_Node* f1ptr) { doublereal tmin0, tmax0, tmin1, tmax1, tmin, tmid, tmax; @@ -570,13 +582,17 @@ namespace Cantera { sp.install(speciesName, k, SHOMATE, &coef[0], tmin0, tmax0, p0); } - - /** - * Install a Shomate polynomial thermodynamic property - * parameterization for species k. + //! Install a Shomate polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a Shomate block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param f0ptr Ptr to the first XML_Node for the first NASA polynomial + * @param f1ptr Ptr to the first XML_Node for the first NASA polynomial */ - static void installShomateThermoFromXML(std::string speciesName, - SpeciesThermo& sp, int k, + static void installShomateThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, const XML_Node* f0ptr, const XML_Node* f1ptr) { doublereal tmin0, tmax0, tmin1, tmax1, tmin, tmid, tmax; @@ -624,11 +640,14 @@ namespace Cantera { sp.install(speciesName, k, SHOMATE, &c[0], tmin, tmax, p0); } - - - /** - * Install a constant-cp thermodynamic property - * parameterization for species k. + //! Install a Simple thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a SimpleThermo block is found + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param f XML_Node for the SimpleThermo block */ static void installSimpleThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, @@ -647,11 +666,15 @@ namespace Cantera { sp.install(speciesName, k, SIMPLE, &c[0], tmin, tmax, p0); } - /** - * Install a NASA9 polynomial thermodynamic property - * parameterization for species k into a SpeciesThermo instance. - * This is called by method installThermoForSpecies if a NASA9 - * block is found in the XML input. + + //! Install a NASA9 polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a NASA9 block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param tp Vector of XML Nodes that make up the parameterization */ static void installNasa9ThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, @@ -705,13 +728,16 @@ namespace Cantera { } - /** - * Install an Adsorbate thermodynamic property - * parameterization for species k into a SpeciesThermo instance. - * This is called by method installThermoForSpecies if a NASA9 - * block is found in the XML input. - */ #ifdef WITH_ADSORBATE + //! Install a Adsorbate polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a Adsorbate block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param tp Vector of XML Nodes that make up the parameterization + */ static void installAdsorbateThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, const XML_Node& f) { @@ -739,8 +765,6 @@ namespace Cantera { coeffs[0] = nfreq; coeffs[1] = getFloat(f, "binding_energy", "toSI"); copy(freqs.begin(), freqs.end(), coeffs.begin() + 2); - //posc = new Adsorbate(k, tmin, tmax, pref, - // DATA_PTR(coeffs)); (&sp)->install(speciesName, k, ADSORBATE, &coeffs[0], tmin, tmax, pref); } #endif diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 11741b193..9fe8a1456 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -87,8 +87,13 @@ namespace Cantera { #if defined(THREAD_SAFE_CANTERA) boost::mutex ThermoFactory::thermo_mutex; #endif - + //! Define the number of %ThermoPhase types for use in this factory routine + /*! + * @deprecated This entire structure could be replaced with a std::map + */ static int ntypes = 18; + + //! Define the string name of the %ThermoPhase types that are handled by this factory routine static string _types[] = {"IdealGas", "Incompressible", "Surface", "Edge", "Metal", "StoichSubstance", "PureFluid", "LatticeSolid", "Lattice", @@ -98,6 +103,7 @@ namespace Cantera { "IonsFromNeutralMolecule" }; + //! Define the integer id of the %ThermoPhase types that are handled by this factory routine static int _itypes[] = {cIdealGas, cIncompressible, cSurf, cEdge, cMetal, cStoichSubstance, cPureFluid, cLatticeSolid, cLattice, diff --git a/Cantera/src/thermo/VPSSMgrFactory.cpp b/Cantera/src/thermo/VPSSMgrFactory.cpp index 6e3962fb6..8b7e4e390 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.cpp +++ b/Cantera/src/thermo/VPSSMgrFactory.cpp @@ -60,13 +60,23 @@ namespace Cantera { boost::mutex VPSSMgrFactory::vpss_species_thermo_mutex; #endif - /* - * Examine the types of species thermo parameterizations, - * and return a flag indicating the type of parameterization - * needed by the species. + + //! Examine the types of species thermo parameterizations, and return a flag indicating the type of parameterization + //! needed by the species. + /*! * - * @param spData_node Species Data XML node. This node contains a list - * of species XML nodes underneath it. + * @param spDataNodeList Species Data XML node. This node contains a list + * of species XML nodes underneath it. + * @param has_nasa_idealGas Boolean indicating that one species has a nasa ideal gas standard state + * @param has_nasa_constVol Boolean indicating that one species has a nasa ideal solution standard state + * @param has_shomate_idealGas Boolean indicating that one species has a shomate ideal gas standard state + * @param has_shomate_constVol Boolean indicating that one species has a shomate ideal solution standard state + * @param has_simple_idealGas Boolean indicating that one species has a simple ideal gas standard state + * @param has_simple_constVol Boolean indicating that one species has a simple ideal solution standard state + * @param has_water Boolean indicating that one species has a water standard state + * @param has_tpx Boolean indicating that one species has a tpx standard state + * @param has_htpx Boolean indicating that one species has a htpx standard state + * @param has_other Boolean indicating that one species has different standard state than the ones listed above * * @todo Make sure that spDadta_node is species Data XML node by checking * its name is speciesData From 38efb3d996f88af6063bfa67fa0beda4e18ca80b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Aug 2010 23:27:33 +0000 Subject: [PATCH 223/446] Doxygen update --- Cantera/src/base/misc.cpp | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index ef1ef6507..feba01606 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -1891,9 +1891,13 @@ protected: #endif // WITH_HTML_LOGS - - /// split a string at a '#' sign. Used to separate a file name - /// from an id string. + //=============================================================================================================== + //! split a string at a '#' sign. Used to separate a file name from an id string. + /*! + * @param src Original string to be split up. This is unchanged. + * @param file Output string representing the first part of the string, which is the filename. + * @param id Output string representing the last part of the string, which is the id. + */ static void split_at_pound(const std::string& src, std::string& file, std::string& id) { string::size_type ipound = src.find('#'); if (ipound != string::npos) { @@ -1905,6 +1909,7 @@ protected: file = src; } } + //=============================================================================================================== /* * This routine will locate an XML node in either the input * XML tree or in another input file specified by the file From ec30757b88c06e923383a9556c212a51a3e17eda Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Aug 2010 23:53:33 +0000 Subject: [PATCH 224/446] Doxygen changes. --- Cantera/src/thermo/IdealMolalSoln.cpp | 5 +++-- Cantera/src/thermo/SpeciesThermoFactory.cpp | 22 ++++++++++++++++++++- Cantera/src/thermo/ThermoFactory.cpp | 20 ++++++++++++++++--- Cantera/src/thermo/VPSSMgrFactory.cpp | 2 +- Cantera/src/thermo/WaterPropsIAPWS.cpp | 2 +- 5 files changed, 43 insertions(+), 8 deletions(-) diff --git a/Cantera/src/thermo/IdealMolalSoln.cpp b/Cantera/src/thermo/IdealMolalSoln.cpp index 0c560636a..3730d60cb 100644 --- a/Cantera/src/thermo/IdealMolalSoln.cpp +++ b/Cantera/src/thermo/IdealMolalSoln.cpp @@ -35,9 +35,10 @@ namespace Cantera { - + //! Small value to be used in cutoff expressions with logs static double xxSmall = 1.0E-150; - /** + + /* * Default constructor */ IdealMolalSoln::IdealMolalSoln() : diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index 0d404873e..2cf31dcc8 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -456,6 +456,11 @@ namespace Cantera { #endif + //! Look up the elemental reference state entropies + /*! + * @param elemName String name of the element + * @param th_ptr Pointer to the thermophase. + */ static doublereal LookupGe(const std::string& elemName, ThermoPhase *th_ptr) { #ifdef OLDWAY int num = sizeof(geDataTable) / sizeof(struct GeData); @@ -483,6 +488,13 @@ namespace Cantera { #endif } + //! Convert delta G formulation + /*! + * Calculates the sum of the elemental reference state entropies + * + * @param k species index + * @param th_ptr Pointer to the ThermoPhase + */ static doublereal convertDGFormation(int k, ThermoPhase *th_ptr) { /* * Ok let's get the element compositions and conversion factors. @@ -505,7 +517,15 @@ namespace Cantera { } - + //! Install a NASA96 polynomial thermodynamic property parameterization for species k into a SpeciesThermo instance. + /*! + * This is called by method installThermoForSpecies if a MinEQ3node block is found in the XML input. + * + * @param speciesName String name of the species + * @param sp SpeciesThermo object that will receive the nasa polynomial object + * @param k Species index within the phase + * @param MinEQ3node Ptr to the first XML_Node for the first MinEQ3 parameterization + */ static void installMinEQ3asShomateThermoFromXML(std::string speciesName, ThermoPhase *th_ptr, SpeciesThermo& sp, int k, diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 9fe8a1456..cf04e5e00 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -297,7 +297,21 @@ namespace Cantera { return (ThermoPhase *) 0; } - + //==================================================================================================================== + //! Gather a vector of pointers to XML_Nodes for a phase + /*! + * + * @param spDataNodeList Output vector of pointer to XML_Nodes which contain the species XML_Nodes for the + * species in the current phase. + * @param spNamesList Output Vector of strings, which contain the names of the species in the phase + * @param spRuleList Output Vector of ints, which contain the value of sprule for each species in the phase + * @param spArray_names Vector of pointers to the XML_Nodes which contains the names of the + * species in the phase + * + * @param spArray_dbases Input vector of pointers to species data bases. + * We search each data base for the required species names + * @param sprule Input vector of sprule values + */ static void formSpeciesXMLNodeList(std::vector &spDataNodeList, std::vector &spNamesList, std::vector &spRuleList, @@ -318,7 +332,7 @@ namespace Cantera { // Get the top XML for the database const XML_Node *db = spArray_dbases[jsp]; - // Get the array of species name strings and the count them + // Get the array of species name strings and then count them std::vector spnames; getStringArray(speciesArray, spnames); int nsp = static_cast(spnames.size()); @@ -408,7 +422,7 @@ namespace Cantera { } } } - + //==================================================================================================================== /* * Import a phase specification. * Here we read an XML description of the phase. diff --git a/Cantera/src/thermo/VPSSMgrFactory.cpp b/Cantera/src/thermo/VPSSMgrFactory.cpp index 8b7e4e390..a237ec5db 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.cpp +++ b/Cantera/src/thermo/VPSSMgrFactory.cpp @@ -75,7 +75,7 @@ namespace Cantera { * @param has_simple_constVol Boolean indicating that one species has a simple ideal solution standard state * @param has_water Boolean indicating that one species has a water standard state * @param has_tpx Boolean indicating that one species has a tpx standard state - * @param has_htpx Boolean indicating that one species has a htpx standard state + * @param has_hptx Boolean indicating that one species has a htpx standard state * @param has_other Boolean indicating that one species has different standard state than the ones listed above * * @todo Make sure that spDadta_node is species Data XML node by checking diff --git a/Cantera/src/thermo/WaterPropsIAPWS.cpp b/Cantera/src/thermo/WaterPropsIAPWS.cpp index 0a7a83f9c..4853e2d09 100644 --- a/Cantera/src/thermo/WaterPropsIAPWS.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWS.cpp @@ -33,13 +33,13 @@ const doublereal Rho_c = 322.; //! Molecular Weight of water that is consistent with the paper (kg kmol-1) static const doublereal M_water = 18.015268; +//! Gas constant that is quoted in the paper /* * Note, this is the Rgas value quoted in the paper. For consistency * we have to use that value and not the updated value * * The Ratio of R/M = 0.46151805 kJ kg-1 K-1 , which is Eqn. (6.3) in the paper. */ -//static const doublereal Rgas = 8.314472E3; // Joules kmol-1 K-1 static const doublereal Rgas = 8.314371E3; // Joules kmol-1 K-1 //@{ #ifndef MAX From cc5e72a2b35f6419d0dfd827cf2812d6f2b243c2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 10 Aug 2010 15:30:53 +0000 Subject: [PATCH 225/446] doxygen update --- Cantera/src/base/ctml.cpp | 17 ++++++++++------- Cantera/src/base/ctml.h | 7 +++++-- Cantera/src/base/misc.cpp | 19 ++++++++++++++----- Cantera/src/base/stringUtils.cpp | 16 ++++++++++++++++ 4 files changed, 45 insertions(+), 14 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index d03ebc5ce..8d20215dc 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -559,7 +559,7 @@ namespace ctml { * @param v Output map of the results. * @param convert Turn on conversion to SI units */ - void getFloats(const Cantera::XML_Node& node, std::map& v, + void getFloats(const Cantera::XML_Node& node, std::map & v, const bool convert) { std::vector f; node.getChildren("float",f); @@ -629,8 +629,7 @@ namespace ctml { * and "" , for no conversion. The default value is "" * which implies that no conversion is allowed. */ - doublereal getFloat(const Cantera::XML_Node& parent, - const std::string &name, + doublereal getFloat(const Cantera::XML_Node& parent, const std::string &name, const std::string type) { if (!parent.hasChild(name)) throw CanteraError("getFloat (called from XML Node \"" + @@ -728,7 +727,7 @@ namespace ctml { return fctr*x; } - //==================================================================================================================== + //==================================================================================================================== bool getOptionalFloat(const Cantera::XML_Node& parent, const std::string &name, doublereal &fltRtn, @@ -957,11 +956,13 @@ namespace ctml { * The default value for the node name is floatArray * * @return Returns the number of floats read + * + * @note change the v to a std::vector to eliminate a doxygen error. No idea why doxygen needs this. */ - int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, + int getFloatArray(const Cantera::XML_Node& node, std::vector &v, const bool convert, const std::string unitsString, const std::string nodeName) { - string::size_type icom; + std::string::size_type icom; string numstr; doublereal dtmp; string nn = node.name(); @@ -1332,9 +1333,11 @@ namespace ctml { * units converter is used. * @param nodeName XML Name of the XML node to read. * The default value for the node name is floatArray + * + * @note change the coeffs to a std::vector to eliminate a doxygen error. No idea why doxygen needs this. */ void getFunction(const Cantera::XML_Node& node, std::string& type, doublereal& xmin, - doublereal& xmax, Cantera::vector_fp& coeffs) { + doublereal& xmax, std::vector< double > & coeffs) { const XML_Node& c = node.child("floatArray"); coeffs.clear(); getFloatArray(c,coeffs); diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 5d065a96c..2febcfa31 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -22,6 +22,9 @@ //! The ctml namespace adds functionality to the XML object, by providing //! standard functions that read, write, and interpret XML files and //! object trees. +/*! + * Standardization of reads and write from Cantera files occur here. + */ namespace ctml { //! const Specifying the CTML version number @@ -367,7 +370,7 @@ namespace ctml { * The default value for the node name is floatArray * @return Returns the number of floats read into v. */ - int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp& v, + int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp & v, const bool convert=true, const std::string unitsString="", const std::string nodeName = "floatArray"); @@ -681,7 +684,7 @@ namespace ctml { * @param v Output map of the results. * @param convert Turn on conversion to SI units */ - void getFloats(const Cantera::XML_Node& node, std::map& v, + void getFloats(const Cantera::XML_Node& node, std::map& v, const bool convert=true); //! Get an integer value from a child element. diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index feba01606..7f493ed82 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -53,11 +53,20 @@ using namespace std; #include #include -static boost::mutex dir_mutex; // For input directory access -static boost::mutex msg_mutex; // For access to string messages -static boost::mutex app_mutex; // Application state including creating singleton -//static boost::mutex log_mutex; // Logger pointer -static boost::mutex xml_mutex; // XML file storage +//! Mutex for input directory access +static boost::mutex dir_mutex; + +//! Mutex for access to string messages +static boost::mutex msg_mutex; + +//! Mutex for creating singeltons within the application object +static boost::mutex app_mutex; + +// Mutex for controlling access to the log file +//static boost::mutex log_mutex; + +//! Mutex for controlling access to XML file storage +static boost::mutex xml_mutex; //! Macro for locking input directory access #define DIR_LOCK() boost::mutex::scoped_lock d_lock(dir_mutex) diff --git a/Cantera/src/base/stringUtils.cpp b/Cantera/src/base/stringUtils.cpp index 62bc8e8da..88d19251c 100644 --- a/Cantera/src/base/stringUtils.cpp +++ b/Cantera/src/base/stringUtils.cpp @@ -539,6 +539,14 @@ namespace Cantera { return (val * fp); } //================================================================================================ + //! Find the first white space in a string + /*! + * Returns the location of the first white space character in a string + * + * @param val Input string to be parsed + * @return In a size_type variable, return the location of the first white space character. + * Return npos if none is found + */ static std::string::size_type findFirstWS(const std::string& val) { std::string::size_type ibegin = std::string::npos; int j = 0; @@ -555,6 +563,14 @@ namespace Cantera { return ibegin; } //================================================================================================ + //! Find the first non-white space in a string + /*! + * Returns the location of the first non-white space character in a string + * + * @param val Input string to be parsed + * @return In a size_type variable, return the location of the first nonwhite space character. + * Return npos if none is found + */ static std::string::size_type findFirstNotOfWS(const std::string& val) { std::string::size_type ibegin = std::string::npos; int j = 0; From b784726e08cc43badeed16aa688e79914ed47074 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 10 Aug 2010 15:34:05 +0000 Subject: [PATCH 226/446] Doxygen update --- Cantera/src/base/xml.cpp | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 927f36a04..8aa6afe53 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -221,10 +221,12 @@ namespace Cantera { else return aline.substr(j+1, i - j - 1); } - /** - * Find the first position of a character, q, in string s, - * which is not immediately preceded by the backslash character - * '\' + + //! Find the first position of a character, q, in string, s, which is not immediately preceded by the backslash character + /*! + * @param s Input string + * @param q Search for this character + * @param istart Defaults to 0 */ static string::size_type findUnbackslashed(std::string s, const char q, std::string::size_type istart = 0) { From 67529bcba068998d9bc6e6991aaf46c5a6b074ef Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 10 Aug 2010 15:34:19 +0000 Subject: [PATCH 227/446] doxygen update --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 11 +++++++++++ Cantera/src/thermo/SpeciesThermoFactory.cpp | 1 + Cantera/src/thermo/WaterProps.cpp | 4 ++-- Cantera/src/thermo/WaterPropsIAPWSphi.cpp | 9 ++++++--- 4 files changed, 20 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index d05845830..e2ed1351a 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -33,6 +33,7 @@ using namespace std; #ifndef MIN +//! standard MIN function # define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) #endif @@ -1212,6 +1213,16 @@ namespace Cantera { dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); } //==================================================================================================================== + //! Return the factor overlap + /*! + * @param elnamesVN + * @param elemVectorN + * @param nElementsN + * @param elnamesVI + * @param elemVectorI + * @param nElementsI + * + */ static double factorOverlap(const std::vector& elnamesVN , const std::vector& elemVectorN, const int nElementsN, diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index 2cf31dcc8..d8e901afc 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -522,6 +522,7 @@ namespace Cantera { * This is called by method installThermoForSpecies if a MinEQ3node block is found in the XML input. * * @param speciesName String name of the species + * @param th_ptr Pointer to the %ThermoPhase object * @param sp SpeciesThermo object that will receive the nasa polynomial object * @param k Species index within the phase * @param MinEQ3node Ptr to the first XML_Node for the first MinEQ3 parameterization diff --git a/Cantera/src/thermo/WaterProps.cpp b/Cantera/src/thermo/WaterProps.cpp index 91f4ca20a..f9e5a236a 100644 --- a/Cantera/src/thermo/WaterProps.cpp +++ b/Cantera/src/thermo/WaterProps.cpp @@ -496,7 +496,7 @@ namespace Cantera { // Parameters for the viscosityWater() function - //@{ + // \cond const doublereal H[4] = {1., 0.978197, 0.579829, @@ -515,7 +515,7 @@ namespace Cantera { const doublereal rhoStar = 317.763; // kg / m3 const doublereal presStar = 22.115E6; // Pa const doublereal muStar = 55.071E-6; //Pa s - //@} + // \endcond // Returns the viscosity of water at the current conditions // (kg/m/s) diff --git a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp index 5f8a382de..51d623e22 100644 --- a/Cantera/src/thermo/WaterPropsIAPWSphi.cpp +++ b/Cantera/src/thermo/WaterPropsIAPWSphi.cpp @@ -29,10 +29,12 @@ using std::fabs; * routine, except for internal checks. All calculations here are done * in dimensionless units. */ +// \cond static const doublereal T_c = 647.096; // Kelvin static const doublereal P_c = 22.064E6; // Pascals static const doublereal Rho_c = 322.; // kg m-3 static const doublereal M_water = 18.015268; // kg kmol-1 +// \endcond /* * The added constants were calculated so that u = s = 0 @@ -42,6 +44,7 @@ static const doublereal M_water = 18.015268; // kg kmol-1 * H didn't turn out to be .611872 J/kg, but .611782 J/kg. * There may be a slight error here somehow. */ +// \cond static const doublereal ni0[9] = { 0.0, -8.32044648201 - 0.000000001739715, @@ -240,7 +243,6 @@ static const int tiR[55] = { 1, 4 // 54 }; - static const doublereal ni[57] = { +0.0, +0.12533547935523E-1, // 1 @@ -360,8 +362,9 @@ static const doublereal Bbetai[2] = { +0.3, +0.3 }; +// \endcond -/** +/* * Constructor for the object. */ WaterPropsIAPWSphi::WaterPropsIAPWSphi() : @@ -1106,7 +1109,7 @@ doublereal WaterPropsIAPWSphi::phiR_dt() const { return val; } -/** +/* * This program computes the reduced density, given the reduced pressure * and the reduced temperature, tau. It takes an initial guess, deltaGuess. * DeltaGuess is important as this is a multivalued function below the From 1c6c9aefeacb1633576199dd4dedbb7331d50fb3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 10 Aug 2010 15:43:26 +0000 Subject: [PATCH 228/446] Doxygen updates --- Cantera/src/equil/BasisOptimize.cpp | 57 +++++++++++++++++++++++ Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 6 ++- 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/Cantera/src/equil/BasisOptimize.cpp b/Cantera/src/equil/BasisOptimize.cpp index b98d36ff4..a6bcc476b 100644 --- a/Cantera/src/equil/BasisOptimize.cpp +++ b/Cantera/src/equil/BasisOptimize.cpp @@ -22,11 +22,68 @@ using namespace std; namespace Cantera { int BasisOptimize_print_lvl = 0; } + +//! Print a string within a given space limit. This routine limits the amount of the string that will be printed to a +//! maximum of "space" characters. +/*! + * + * @param str String -> must be null terminated. + * @param space space limit for the printing. + * @param alignment 0 centered + * 1 right aligned + * 2 left aligned + */ static void print_stringTrunc(const char *str, int space, int alignment); #endif + + //! Finds the location of the maximum component in a double vector INPUT + /*! + * @param x Vector to search + * @param j j <= i < n : i is the range of indecises to search in X(*) + * @param n Length of the vector + * + * @return index of the greatest value on X(*) searched + */ static int amax(double *x, int j, int n); + +//! Switch the position in the vector +/*! + * @param orderVector Vector to be manipulated + * @param jr first position + * @param kspec second species + */ static void switch_pos(vector_int &orderVector, int jr, int kspec); + + + //! Invert an nxn matrix and solve m rhs's + /*! + * + * Solve C X + B = 0; + * + * This routine uses Gauss elimination and is optimized for the solution + * of lots of rhs's. + * A crude form of row pivoting is used here. + * + * @param c C is the matrix to be inverted + * @param idem first dimension in the calling routine + * idem >= n must be true + * @param n number of rows and columns in the matrix + * @param b rhs of the matrix problem + * @param m number of rhs to be solved for + * + * c[i+j*idem] = c_i_j = Matrix to be inverted: i = row number + * j = column number + * b[i+j*idem] = b_i_j = vectors of rhs's: i = row number + * j = column number + * (each column is a new rhs) + * + * @return Retuns the value + * 1 : Matrix is singluar + * 0 : solution is OK + * + * The solution is returned in the matrix b. + */ static int mlequ(double *c, int idem, int n, double *b, int m); //@{ diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index b142a3078..387a83f1e 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -897,7 +897,11 @@ namespace VCSnonideal { fclose(FP); } - + //! print char repeatedly to log file + /*! + * @param letter letter to be repeated + * @param num Number of times repeated + */ static void print_char(const char letter, const int num) { for (int i = 0; i < num; i++) plogf("%c", letter); } From b72581b2227bda9442850d01e39e7f75bae469b2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 10 Aug 2010 21:06:42 +0000 Subject: [PATCH 229/446] Doxygen update --- Cantera/src/transport/MixTransport.cpp | 41 +++++---- Cantera/src/transport/MixTransport.h | 120 ++++++++++++++++++++----- 2 files changed, 123 insertions(+), 38 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 016fec4a9..5eebd68f1 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -54,11 +54,9 @@ namespace Cantera { m_cond(0), m_molefracs(0), m_poly(0), - m_astar_poly(0), m_bstar_poly(0), m_cstar_poly(0), m_om22_poly(0), - m_astar(0, 0), m_bstar(0, 0), m_cstar(0, 0), m_om22(0, 0), @@ -116,11 +114,9 @@ namespace Cantera { m_cond(0), m_molefracs(0), m_poly(0), - m_astar_poly(0), m_bstar_poly(0), m_cstar_poly(0), m_om22_poly(0), - m_astar(0, 0), m_bstar(0, 0), m_cstar(0, 0), m_om22(0, 0), @@ -191,11 +187,9 @@ namespace Cantera { m_cond = right.m_cond; m_molefracs = right.m_molefracs; m_poly = right.m_poly; - m_astar_poly = right.m_astar_poly; m_bstar_poly = right.m_bstar_poly; m_cstar_poly = right.m_cstar_poly; m_om22_poly = right.m_om22_poly; - m_astar = right.m_astar; m_bstar = right.m_bstar; m_cstar = right.m_cstar; m_om22 = right.m_om22; @@ -425,6 +419,7 @@ namespace Cantera { sum2 += m_molefracs[k] / m_cond[k]; } m_lambda = 0.5*(sum1 + 1.0/sum2); + m_condmix_ok = true; } return m_lambda; } @@ -443,14 +438,30 @@ namespace Cantera { } } //=================================================================================================================== - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. + // Get the species diffusive mass fluxes wrt to the mass averaged velocity, + // given the gradients in mole fraction and temperature + /* + * Units for the returned fluxes are kg m-2 s-1. + * + * * The diffusive mass flux of species \e k is computed from * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. + * \vec{j}_k = -n M_k D_k \nabla X_k. * \f] + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ void MixTransport::getSpeciesFluxes(int ndim, const doublereal* grad_T, int ldx, const doublereal* grad_X, @@ -608,7 +619,7 @@ namespace Cantera { } else { for (k = 0; k < m_nsp; k++) { - m_cond[k] = m_sqrt_t*dot5(m_polytempvec, m_condcoeffs[k]); + m_cond[k] = m_sqrt_t * dot5(m_polytempvec, m_condcoeffs[k]); } } m_spcond_ok = true; @@ -653,7 +664,6 @@ namespace Cantera { * Update the pure-species viscosities. */ void MixTransport::updateSpeciesViscosities() { - int k; if (m_mode == CK_Mode) { for (k = 0; k < m_nsp; k++) { @@ -664,13 +674,12 @@ namespace Cantera { else { for (k = 0; k < m_nsp; k++) { // the polynomial fit is done for sqrt(visc/sqrt(T)) - m_sqvisc[k] = m_t14*dot5(m_polytempvec, m_visccoeffs[k]); - m_visc[k] = (m_sqvisc[k]*m_sqvisc[k]); + m_sqvisc[k] = m_t14 * dot5(m_polytempvec, m_visccoeffs[k]); + m_visc[k] = (m_sqvisc[k] * m_sqvisc[k]); } } m_spvisc_ok = true; } - //==================================================================================================================== /* * Update the temperature-dependent viscosity terms. diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 3ede840f5..e901a61eb 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -37,11 +37,44 @@ namespace Cantera { class GasTransportParams; - /** - * Class MixTransport implements mixture-averaged transport - * properties for ideal gas mixtures. The model is based on that - * described by Kee, Coltrin, and Glarborg, "Theoretical and - * Practical Aspects of Chemically Reacting Flow Modeling." + + //! Class MixTransport implements mixture-averaged transport properties for ideal gas mixtures. + /*! + * The model is based on that described by Kee, Coltrin, and Glarborg, "Theoretical and + * Practical Aspects of Chemically Reacting Flow Modeling." + * + * + * The viscosity is computed using the Wilke mixture rule (kg /m /s) + * + * \f[ + * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. + * \f] + * + * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, and + * + * \f[ + * \Phi_{k,j} = \frac{\left[1 + * + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2} + * {\sqrt{8}\sqrt{1 + M_k/M_j}} + * \f] + * + * + * The thermal conductivity is computed from the following mixture rule: + * \f[ + * \lambda = 0.5 \left( \sum_k X_k \lambda_k + \frac{1}{\sum_k X_k/\lambda_k} \right) + * \f] + * + * It's used to compute the flux of energy due to a thermal gradient + * + * \f[ + * j_T = - \lambda \nabla T + * \f] + * + * The flux of energy has units of energy (kg m2 /s2) per second per area. + * + * The units of lambda are W / m K which is equivalent to kg m / s^3 K. + * + * */ class MixTransport : public Transport { @@ -53,6 +86,7 @@ namespace Cantera { MixTransport(); public: + //!Copy Constructor for the %MixTransport object. /*! * @param right %LiquidTransport to be copied @@ -92,9 +126,25 @@ namespace Cantera { return cMixtureAveraged; } - //! Viscosity of the mixture + //! Viscosity of the mixture (kg /m /s) /*! + * The viscosity is computed using the Wilke mixture rule (kg /m /s) * + * \f[ + * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. + * \f] + * + * Here \f$ \mu_k \f$ is the viscosity of pure species \e k, and + * + * \f[ + * \Phi_{k,j} = \frac{\left[1 + * + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2} + * {\sqrt{8}\sqrt{1 + M_k/M_j}} + * \f] + * + * @return Returns the viscosity of the mixture ( units = Pa s = kg /m /s) + * + * @see updateViscosity_T(); */ virtual doublereal viscosity(); @@ -161,20 +211,25 @@ namespace Cantera { virtual void update_T(); virtual void update_C(); - //! Get the species diffusive mass fluxes wrt to - //! the mass averaged velocity, + //! Get the species diffusive mass fluxes wrt to the mass averaged velocity, //! given the gradients in mole fraction and temperature /*! * Units for the returned fluxes are kg m-2 s-1. - * - * @param ndim Number of dimensions in the flux expressions - * @param grad_T Gradient of the temperature - * (length = ndim) - * @param ldx Leading dimension of the grad_X array - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * + * + * The diffusive mass flux of species \e k is computed from + * \f[ + * \vec{j}_k = -n M_k D_k \nabla X_k. + * \f] + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim * @param ldf Leading dimension of the fluxes array * (usually equal to m_nsp but not always) * @param fluxes Output of the diffusive mass fluxes @@ -250,20 +305,41 @@ namespace Cantera { // property values DenseMatrix m_bdiff; - //! vector of species viscosities + //! vector of species viscosities (kg /m /s) + /*! + * These are used in wilke's rule to calculate the viscosity of the solution + * length = m_kk + */ vector_fp m_visc; + + //! vector of square root of species viscosities sqrt(kg /m /s) + /*! + * These are used in wilke's rule to calculate the viscosity of the solution + * length = m_kk + */ vector_fp m_sqvisc; - vector_fp m_cond; + + //! vector of species thermal conductivities (W/m /K) + /*! + * These are used in wilke's rule to calculate the viscosity of the solution + * units = W /m /K = kg m /s^3 /K. + * length = m_kk + */ + vector_fp m_cond; //! Vector of species molefractions - array_fp m_molefracs; + /*! + * These are processed so that all mole fractions are >= MIN_X + * Length = m_kk + */ + vector_fp m_molefracs; std::vector > m_poly; - std::vector m_astar_poly; + std::vector m_bstar_poly; std::vector m_cstar_poly; std::vector m_om22_poly; - DenseMatrix m_astar; + DenseMatrix m_bstar; DenseMatrix m_cstar; DenseMatrix m_om22; From 6766225d8040d436d41c7db50326611818cd8163 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 11 Aug 2010 00:07:03 +0000 Subject: [PATCH 230/446] doxygen update --- Cantera/src/transport/MixTransport.cpp | 22 +-------- Cantera/src/transport/MixTransport.h | 57 +++++++++++++++++------- Cantera/src/transport/MultiTransport.cpp | 2 +- 3 files changed, 42 insertions(+), 39 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 5eebd68f1..b3a54ceb0 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -54,16 +54,9 @@ namespace Cantera { m_cond(0), m_molefracs(0), m_poly(0), - m_bstar_poly(0), - m_cstar_poly(0), - m_om22_poly(0), - m_bstar(0, 0), - m_cstar(0, 0), - m_om22(0, 0), m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), - m_zrot(0), m_crot(0), m_cinternal(0), m_eps(0), @@ -114,16 +107,9 @@ namespace Cantera { m_cond(0), m_molefracs(0), m_poly(0), - m_bstar_poly(0), - m_cstar_poly(0), - m_om22_poly(0), - m_bstar(0, 0), - m_cstar(0, 0), - m_om22(0, 0), m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), - m_zrot(0), m_crot(0), m_cinternal(0), m_eps(0), @@ -187,12 +173,6 @@ namespace Cantera { m_cond = right.m_cond; m_molefracs = right.m_molefracs; m_poly = right.m_poly; - m_bstar_poly = right.m_bstar_poly; - m_cstar_poly = right.m_cstar_poly; - m_om22_poly = right.m_om22_poly; - m_bstar = right.m_bstar; - m_cstar = right.m_cstar; - m_om22 = right.m_om22; m_phi = right.m_phi; m_wratjk = right.m_wratjk; m_wratkj1 = right.m_wratkj1; @@ -251,7 +231,7 @@ namespace Cantera { { } //==================================================================================================================== - bool MixTransport::initGas( GasTransportParams& tr ) { + bool MixTransport::initGas(GasTransportParams& tr) { // constant substance attributes m_thermo = tr.thermo; diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index e901a61eb..13d098606 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -79,6 +79,7 @@ namespace Cantera { class MixTransport : public Transport { protected: + //! Default constructor. /*! * @@ -303,21 +304,21 @@ namespace Cantera { vector_fp m_polytempvec; // property values - DenseMatrix m_bdiff; + DenseMatrix m_bdiff; //! vector of species viscosities (kg /m /s) /*! * These are used in wilke's rule to calculate the viscosity of the solution * length = m_kk */ - vector_fp m_visc; + vector_fp m_visc; //! vector of square root of species viscosities sqrt(kg /m /s) /*! * These are used in wilke's rule to calculate the viscosity of the solution * length = m_kk */ - vector_fp m_sqvisc; + vector_fp m_sqvisc; //! vector of species thermal conductivities (W/m /K) /*! @@ -336,31 +337,53 @@ namespace Cantera { std::vector > m_poly; - std::vector m_bstar_poly; - std::vector m_cstar_poly; - std::vector m_om22_poly; - - DenseMatrix m_bstar; - DenseMatrix m_cstar; - DenseMatrix m_om22; - //! Viscosity Weighting Functions DenseMatrix m_phi; DenseMatrix m_wratjk; DenseMatrix m_wratkj1; - vector_fp m_zrot; - vector_fp m_crot; - vector_fp m_cinternal; - vector_fp m_eps; - vector_fp m_alpha; - vector_fp m_dipoleDiag; + //! Rotational relaxation number for the species in the current phase + /*! + * Not used in this routine -> just a passthrough + * + * length is the number of species in the phase + * units are dimensionless + */ + vector_fp m_zrot; + //! Dimensionless rotational heat capacity of the species in the current phase + /*! + * These values are 0, 1 and 1.5 for single-molecule, linear, and nonlinear species respectively + * length is the number of species in the pahse + * units are dimensionless (Cr / R) + */ + vector_fp m_crot; + vector_fp m_cinternal; + + //! Lennard-Jones well-depth of the species in the current phase + /*! + * length is the number of species in the phase + * Units are Joules (Note this is not Joules/kmol) (note, no kmol -> this is a per molecule amount) + */ + vector_fp m_eps; + vector_fp m_alpha; + vector_fp m_dipoleDiag; + + //! Current value of the temperature at which the properties in this object are calculated (Kelvin) doublereal m_temp; + + //! Current value of the log of the temperature doublereal m_logt; + + //! Current value of Boltzman's constant times the temperature (Joules) doublereal m_kbt; + + //! Current value of temperature to 1/4 power doublereal m_t14; + + //! Current value of temperature to the 3/2 power doublereal m_t32; + doublereal m_sqrt_kbt; doublereal m_sqrt_t; diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index 32076b462..19d21ee7f 100644 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -112,7 +112,7 @@ namespace Cantera { } - bool MultiTransport::initGas( GasTransportParams& tr ) { + bool MultiTransport::initGas(GasTransportParams& tr) { // constant mixture attributes //m_phase = tr.mix; From 7813618357b07742d9e4fdf6a889a500cd7a1c83 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 11 Aug 2010 15:36:27 +0000 Subject: [PATCH 231/446] Doxygen updates Removed deadwood data members and member functions --- Cantera/src/transport/MixTransport.cpp | 72 +++--------- Cantera/src/transport/MixTransport.h | 154 ++++++++++++++++++------- 2 files changed, 130 insertions(+), 96 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index b3a54ceb0..8d37aecaa 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -57,11 +57,6 @@ namespace Cantera { m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), - m_crot(0), - m_cinternal(0), - m_eps(0), - m_alpha(0), - m_dipoleDiag(0), m_temp(-1.0), m_logt(0.0), m_kbt(0.0), @@ -69,25 +64,22 @@ namespace Cantera { m_t32(0.0), m_sqrt_kbt(0.0), m_sqrt_t(0.0), - m_sqrt_eps_k(0), - m_log_eps_k(0, 0), - m_frot_298(0), - m_rotrelax(0), m_lambda(0.0), m_viscmix(0.0), m_spwork(0), m_viscmix_ok(false), m_viscwt_ok(false), m_spvisc_ok(false), - m_diffmix_ok(false), m_bindiff_ok(false), - m_abc_ok (false), m_spcond_ok(false), m_condmix_ok(false), m_mode(0), - m_epsilon(0, 0), + m_eps(0), m_diam(0, 0), - incl(0, 0), + m_dipoleDiag(0), + m_alpha(0), + m_crot(0), + m_zrot(0), m_debug(false) { } @@ -110,11 +102,6 @@ namespace Cantera { m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), - m_crot(0), - m_cinternal(0), - m_eps(0), - m_alpha(0), - m_dipoleDiag(0), m_temp(-1.0), m_logt(0.0), m_kbt(0.0), @@ -122,25 +109,22 @@ namespace Cantera { m_t32(0.0), m_sqrt_kbt(0.0), m_sqrt_t(0.0), - m_sqrt_eps_k(0), - m_log_eps_k(0, 0), - m_frot_298(0), - m_rotrelax(0), m_lambda(0.0), m_viscmix(0.0), m_spwork(0), m_viscmix_ok(false), m_viscwt_ok(false), m_spvisc_ok(false), - m_diffmix_ok(false), m_bindiff_ok(false), - m_abc_ok (false), m_spcond_ok(false), m_condmix_ok(false), m_mode(0), - m_epsilon(0, 0), + m_eps(0), m_diam(0, 0), - incl(0, 0), + m_dipoleDiag(0), + m_alpha(0), + m_crot(0), + m_zrot(0), m_debug(false) { *this = right; @@ -176,12 +160,6 @@ namespace Cantera { m_phi = right.m_phi; m_wratjk = right.m_wratjk; m_wratkj1 = right.m_wratkj1; - m_zrot = right.m_zrot; - m_crot = right.m_crot; - m_cinternal = right.m_cinternal; - m_eps = right.m_eps; - m_alpha = right.m_alpha; - m_dipoleDiag = right.m_dipoleDiag; m_temp = right.m_temp; m_logt = right.m_logt; m_kbt = right.m_kbt; @@ -189,25 +167,22 @@ namespace Cantera { m_t32 = right.m_t32; m_sqrt_kbt = right.m_sqrt_kbt; m_sqrt_t = right.m_sqrt_t; - m_sqrt_eps_k = right.m_sqrt_eps_k; - m_log_eps_k = right.m_log_eps_k; - m_frot_298 = right.m_frot_298; - m_rotrelax = right.m_rotrelax; m_lambda = right.m_lambda; m_viscmix = right.m_viscmix; m_spwork = right.m_spwork; m_viscmix_ok = right.m_viscmix_ok; m_viscwt_ok = right.m_viscwt_ok; m_spvisc_ok = right.m_spvisc_ok; - m_diffmix_ok = right.m_diffmix_ok; m_bindiff_ok = right.m_bindiff_ok; - m_abc_ok = right.m_abc_ok; m_spcond_ok = right.m_spcond_ok; m_condmix_ok = right.m_condmix_ok; m_mode = right.m_mode; - m_epsilon = right.m_epsilon; + m_eps = right.m_eps; m_diam = right.m_diam; - incl = right.incl; + m_dipoleDiag = right.m_dipoleDiag; + m_alpha = right.m_alpha; + m_crot = right.m_crot; + m_zrot = right.m_zrot; m_debug = right.m_debug; return *this; @@ -252,7 +227,6 @@ namespace Cantera { m_zrot = tr.zrot; m_crot = tr.crot; - m_epsilon = tr.epsilon; m_mode = tr.mode_; m_diam = tr.diam; m_eps = tr.eps; @@ -288,9 +262,6 @@ namespace Cantera { m_spvisc_ok = false; m_spcond_ok = false; m_condmix_ok = false; - m_spcond_ok = false; - m_diffmix_ok = false; - m_abc_ok = false; return true; } @@ -548,9 +519,7 @@ namespace Cantera { m_spvisc_ok = false; m_viscwt_ok = false; m_spcond_ok = false; - m_diffmix_ok = false; m_bindiff_ok = false; - m_abc_ok = false; m_condmix_ok = false; } //==================================================================================================================== @@ -566,7 +535,6 @@ namespace Cantera { // fractions. m_viscmix_ok = false; - m_diffmix_ok = false; m_condmix_ok = false; m_thermo->getMoleFractions(DATA_PTR(m_molefracs)); @@ -578,13 +546,6 @@ namespace Cantera { } } //==================================================================================================================== - - /************************************************************************* - * - * methods to update temperature-dependent properties - * - *************************************************************************/ - //==================================================================================================================== /* * Update the temperature-dependent parts of the mixture-averaged * thermal conductivity. @@ -605,7 +566,6 @@ namespace Cantera { m_spcond_ok = true; m_condmix_ok = false; } - //==================================================================================================================== /* * Update the binary diffusion coefficients. These are evaluated @@ -635,9 +595,7 @@ namespace Cantera { } } } - m_bindiff_ok = true; - m_diffmix_ok = false; } //==================================================================================================================== /* diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 13d098606..d5e501495 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -276,16 +276,32 @@ namespace Cantera { } void updateThermal_T(); void updateViscosity_T(); + + //! Update the temperature dependent parts of the species thermal conductivities + /*! + * These are evaluated from the polynomial fits of the temperature and are assumed to be + * independent of pressure + */ void updateCond_T(); + + //! Update the species viscosities + /*! + * These are evaluated from the polynomial fits of the temperature and are assumed to be + * independent of pressure + */ void updateSpeciesViscosities(); + + //! Update the binary diffusion coefficients + /*! + * These are evaluated from the polynomial fits of the temperature at the unit pressure of 1 Pa. + */ void updateDiff_T(); - void correctBinDiffCoeffs(); - - + // --------- Member Data ------------- + private: - // mixture attributes + //! Number of species in the phase int m_nsp; //! Minimum value of the temperature that this transport parameterization is valid @@ -301,6 +317,11 @@ namespace Cantera { std::vector m_visccoeffs; std::vector m_condcoeffs; std::vector m_diffcoeffs; + + //! Powers of the ln temperature + /*! + * up to fourth order + */ vector_fp m_polytempvec; // property values @@ -342,32 +363,11 @@ namespace Cantera { DenseMatrix m_wratjk; DenseMatrix m_wratkj1; - //! Rotational relaxation number for the species in the current phase - /*! - * Not used in this routine -> just a passthrough - * - * length is the number of species in the phase - * units are dimensionless - */ - vector_fp m_zrot; + - //! Dimensionless rotational heat capacity of the species in the current phase - /*! - * These values are 0, 1 and 1.5 for single-molecule, linear, and nonlinear species respectively - * length is the number of species in the pahse - * units are dimensionless (Cr / R) - */ - vector_fp m_crot; - vector_fp m_cinternal; - //! Lennard-Jones well-depth of the species in the current phase - /*! - * length is the number of species in the phase - * Units are Joules (Note this is not Joules/kmol) (note, no kmol -> this is a per molecule amount) - */ - vector_fp m_eps; - vector_fp m_alpha; - vector_fp m_dipoleDiag; + + //! Current value of the temperature at which the properties in this object are calculated (Kelvin) doublereal m_temp; @@ -384,35 +384,111 @@ namespace Cantera { //! Current value of temperature to the 3/2 power doublereal m_t32; + //! current value of Boltzman's constant times the temperature (Joules) to 1/2 power doublereal m_sqrt_kbt; + + //! current value of temperature to 1/2 power doublereal m_sqrt_t; - vector_fp m_sqrt_eps_k; - DenseMatrix m_log_eps_k; - vector_fp m_frot_298; - vector_fp m_rotrelax; - + //! Internal storage for the calculated mixture thermal conductivity + /*! + * Units = W /m /K + */ doublereal m_lambda; + + //! Internal storage for the viscosity of the mixture (kg /m /s) doublereal m_viscmix; - // work space + //! work space length = m_kk vector_fp m_spwork; - + //! Update boolean for mixture rule for the mixture viscosity bool m_viscmix_ok; + + //! Update boolean for the weighting factors for the mixture viscosity bool m_viscwt_ok; + + //! Update boolean for the species viscosities bool m_spvisc_ok; - bool m_diffmix_ok; + + //! Update boolean for the binary diffusivities at unit pressure bool m_bindiff_ok; - bool m_abc_ok; + + //! Update boolean for the species thermal conductivities bool m_spcond_ok; + + //! Update boolean for the mixture rule for the mixture thermal conductivity bool m_condmix_ok; + //! Type of the polynomial fits to temperature + /*! + * CK_Mode means chemkin mode. Currently CA_Mode is used which are different types + * of fits to temperature. + */ int m_mode; - DenseMatrix m_epsilon; + //! Lennard-Jones well-depth of the species in the current phase + /*! + * Not used in this routine -> just a passthrough + * + * length is the number of species in the phase + * Units are Joules (Note this is not Joules/kmol) (note, no kmol -> this is a per molecule amount) + */ + vector_fp m_eps; + + //! hard-sphere diameter for (i,j) collision + /*! + * Not used in this routine -> just a passthrough + * + * diam(i,j) = 0.5*(tr.sigma[i] + tr.sigma[j]); + * Units are m (note, no kmol -> this is a per molecule amount) + * + * Length nsp * nsp. This is a symmetric matrix. + */ DenseMatrix m_diam; - DenseMatrix incl; + + //! The effective dipole moment for (i,j) collisions + /*! + * tr.dipoleMoment has units of Debye's. A Debye is 10-18 cm3/2 erg1/2 + * + * Not used in this routine -> just a passthrough + * + * tr.dipole(i,i) = 1.e-25 * SqrtTen * trdat.dipoleMoment; + * tr.dipole(i,j) = sqrt(tr.dipole(i,i)*tr.dipole(j,j)); + * Units are in Debye (note, no kmol -> this is a per molecule amount) + * + * Length nsp. We store only the diagonal component here. + */ + vector_fp m_dipoleDiag; + + //! Polarizability of each species in the phase + /*! + * Not used in this routine -> just a passthrough + * + * Length = nsp + * Units = m^3 + */ + vector_fp m_alpha; + + //! Dimensionless rotational heat capacity of the species in the current phase + /*! + * Not used in this routine -> just a passthrough + * + * These values are 0, 1 and 1.5 for single-molecule, linear, and nonlinear species respectively + * length is the number of species in the pahse + * units are dimensionless (Cr / R) + */ + vector_fp m_crot; + + //! Rotational relaxation number for the species in the current phase + /*! + * Not used in this routine -> just a passthrough + * + * length is the number of species in the phase + * units are dimensionless + */ + vector_fp m_zrot; + //! Debug flag - turns on more printing bool m_debug; From d92b7817111a130086fb2a6dd08265ca10a91fc1 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Wed, 11 Aug 2010 20:31:59 +0000 Subject: [PATCH 232/446] Must be changed due to modified dlnActCoeffdlnN being fixed --- Cantera/src/transport/LiquidTranInteraction.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index 7acfb0db0..b223608cf 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -733,7 +733,7 @@ namespace Cantera { xA = neut_molefracs[neutMolIndex[cation[0]]]; xB = neut_molefracs[neutMolIndex[cation[1]]]; eps = (1-m_mobRatMix(cation[1],cation[0]))/(xA+xB*m_mobRatMix(cation[1],cation[0])); - inv_vP_vM_MutualDiff = (xA*(1+dlnActCoeffdlnN_diag[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1+dlnActCoeffdlnN_diag[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); + inv_vP_vM_MutualDiff = (xA*(1-xB+dlnActCoeffdlnN_diag[neutMolIndex[cation[1]]])/m_selfDiffMix[cation[1]]+xB*(1-xA+dlnActCoeffdlnN_diag[neutMolIndex[cation[0]]])/m_selfDiffMix[cation[0]]); mat.resize(nsp, nsp, 0.0 ); mat(cation[0],cation[1]) = mat(cation[1],cation[0]) = (1+vM/vP)*(1+eps*xB)*(1-eps*xA)*inv_vP_vM_MutualDiff-zP*zP*Faraday*Faraday/GasConstant/temp/m_ionCondMix/vol; From e3c4a82dc9bf893e09a732ad5c133dbb575ccc19 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 11 Aug 2010 21:09:04 +0000 Subject: [PATCH 233/446] Doxygen updates eliminated m_poly from MixTransport. It wasn't being used --- Cantera/src/transport/MixTransport.cpp | 21 +++++++------ Cantera/src/transport/MixTransport.h | 40 ++++++++++++++++++++----- Cantera/src/transport/TransportParams.h | 2 +- 3 files changed, 46 insertions(+), 17 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index 8d37aecaa..af264c2f7 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -53,7 +53,6 @@ namespace Cantera { m_sqvisc(0), m_cond(0), m_molefracs(0), - m_poly(0), m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), @@ -98,7 +97,6 @@ namespace Cantera { m_sqvisc(0), m_cond(0), m_molefracs(0), - m_poly(0), m_phi(0,0), m_wratjk(0,0), m_wratkj1(0,0), @@ -156,7 +154,6 @@ namespace Cantera { m_sqvisc = right.m_sqvisc; m_cond = right.m_cond; m_molefracs = right.m_molefracs; - m_poly = right.m_poly; m_phi = right.m_phi; m_wratjk = right.m_wratjk; m_wratkj1 = right.m_wratkj1; @@ -220,7 +217,6 @@ namespace Cantera { m_thermo->molecularWeights().end(), m_mw.begin()); // copy polynomials and parameters into local storage - m_poly = tr.poly; m_visccoeffs = tr.visccoeffs; m_condcoeffs = tr.condcoeffs; m_diffcoeffs = tr.diffcoeffs; @@ -619,11 +615,19 @@ namespace Cantera { m_spvisc_ok = true; } //==================================================================================================================== + // Update the temperature-dependent viscosity terms. /* - * Update the temperature-dependent viscosity terms. - * Updates the array of pure species viscosities, and the - * weighting functions in the viscosity mixture rule. + * Updates the array of pure species viscosities, and the weighting functions in the viscosity mixture rule. * The flag m_visc_ok is set to true. + * + * The formula for the weighting function is from Poling and Prausnitz. + * See Eq. (9-5.14) of Poling, Prausnitz, and O'Connell. The equation for the weighting function + * \f$ \phi_{ij} \f$ is reproduced below. + * + * \f[ + * \phi_{ij} = \frac{ \left[ 1 + \left( \mu_i / \mu_j \right)^{1/2} \left( M_j / M_i \right)^{1/4} \right]^2 } + * {\left[ 8 \left( 1 + M_i / M_j \right) \right]^{1/2}} + * \f] */ void MixTransport::updateViscosity_T() { doublereal vratiokj, wratiojk, factor1; @@ -640,8 +644,7 @@ namespace Cantera { // Note that m_wratjk(k,j) holds the square root of // m_wratjk(j,k)! factor1 = 1.0 + (m_sqvisc[k]/m_sqvisc[j]) * m_wratjk(k,j); - m_phi(k,j) = factor1*factor1 / - (SqrtEight * m_wratkj1(j,k)); + m_phi(k,j) = factor1*factor1 / (SqrtEight * m_wratkj1(j,k)); m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk); } } diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index d5e501495..aba28a288 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -275,6 +275,22 @@ namespace Cantera { m_thermo->temperature()); } void updateThermal_T(); + + + //! Update the temperature-dependent viscosity terms. + /*! + * Updates the array of pure species viscosities, and the weighting functions in the viscosity mixture rule. + * The flag m_visc_ok is set to true. + * + * The formula for the weighting function is from Poling and Prausnitz. + * See Eq. (9-5.14) of Poling, Prausnitz, and O'Connell. The equation for the weighting function + * \f$ \phi_{ij} \f$ is reproduced below. + * + * \f[ + * \phi_{ij} = \frac{ \left[ 1 + \left( \mu_i / \mu_j \right)^{1/2} \left( M_j / M_i \right)^{1/4} \right]^2 } + * {\left[ 8 \left( 1 + M_i / M_j \right) \right]^{1/2}} + * \f] + */ void updateViscosity_T(); //! Update the temperature dependent parts of the species thermal conductivities @@ -356,16 +372,26 @@ namespace Cantera { */ vector_fp m_molefracs; - std::vector > m_poly; - - //! Viscosity Weighting Functions - DenseMatrix m_phi; + //! m_phi is a Viscosity Weighting Function + /*! + * size = m_nsp * n_nsp + */ + DenseMatrix m_phi; + + //! Holds square roots or molecular weight ratios + /*! + * m_wratjk(j,k) = sqrt(mw[j]/mw[k]) j < k + * m_wratjk(k,j) = sqrt(sqrt(mw[j]/mw[k])) j < k + */ DenseMatrix m_wratjk; + + //! Holds square roots of molecular weight ratios + /*! + * m_wratjk1(j,k) = sqrt(1.0 + mw[k]/mw[j]) j < k + */ DenseMatrix m_wratkj1; - - - + diff --git a/Cantera/src/transport/TransportParams.h b/Cantera/src/transport/TransportParams.h index 786dd099b..24a81ada5 100644 --- a/Cantera/src/transport/TransportParams.h +++ b/Cantera/src/transport/TransportParams.h @@ -126,7 +126,7 @@ namespace Cantera { */ std::vector diffcoeffs; - //! This is vector of vectors containing the integer ookup value for the (i,j) interaction + //! This is vector of vectors containing the integer lookup value for the (i,j) interaction /*! * The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value. * Unique values of delta get their own spot in the array. The values of delta are storred in From 08a84b83a9bfa3452acdc37bee749a688a2cdfe1 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Wed, 11 Aug 2010 21:22:20 +0000 Subject: [PATCH 234/446] Fixed Calculation of dlnActCoeffdlnN --- Cantera/src/thermo/MargulesVPSSTP.cpp | 45 +++++++++++++++------------ 1 file changed, 25 insertions(+), 20 deletions(-) diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index bc2a11b7f..f2923c44d 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -916,25 +916,25 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - // dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); - double gfac = g0 + g1 * XB; - double gggg = (delBK - XB) * g1; +// double gfac = g0 + g1 * XB; +// double gggg = (delBK - XB) * g1; - dlnActCoeffdlnN_diag_[iK] += gfac * delAK * ( - XB + delBK); +// dlnActCoeffdlnN_diag_[iK] += gfac * delAK * ( - XB + delBK); - dlnActCoeffdlnN_diag_[iK] += gfac * delBK * ( - XA + delAK); +// dlnActCoeffdlnN_diag_[iK] += gfac * delBK * ( - XA + delAK); - dlnActCoeffdlnN_diag_[iK] += gfac * (2.0 * XA * XB - delAK * XB - XA * delBK); +// dlnActCoeffdlnN_diag_[iK] += gfac * (2.0 * XA * XB - delAK * XB - XA * delBK); - dlnActCoeffdlnN_diag_[iK] += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBK); +// dlnActCoeffdlnN_diag_[iK] += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBK); - dlnActCoeffdlnN_diag_[iK] += gggg * ( - 2.0 * XA * XB + delAK * XB + XA * delBK); +// dlnActCoeffdlnN_diag_[iK] += gggg * ( - 2.0 * XA * XB + delAK * XB + XA * delBK); - dlnActCoeffdlnN_diag_[iK] += - g1 * XA * XB * (- XB + delBK); +// dlnActCoeffdlnN_diag_[iK] += - g1 * XA * XB * (- XB + delBK); } - // dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK]-XK; + dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK];//-XK; } } @@ -949,7 +949,7 @@ namespace Cantera { void MargulesVPSSTP::s_update_dlnActCoeff_dlnN() const { int iA, iB; doublereal delAK, delBK; - double XA, XB, g0 , g1; + double XA, XB, g0 , g1, XK,XM; double T = temperature(); double RT = GasConstant*T; @@ -961,8 +961,9 @@ namespace Cantera { * Loop over the activity coefficient gamma_k */ for (int iK = 0; iK < m_kk; iK++) { + XK = moleFractions_[iK]; for (int iM = 0; iM < m_kk; iM++) { - + XM = moleFractions_[iM]; for (int i = 0; i < numBinaryInteractions_; i++) { iA = m_pSpecies_A_ij[i]; @@ -983,22 +984,26 @@ namespace Cantera { g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; - double gfac = g0 + g1 * XB; - double gggg = (delBK - XB) * g1; + dlnActCoeffdlnN_(iK,iM) += g0*((delAM-XA)*(delBK-XB)+(delAK-XA)*(delBM-XB)); + dlnActCoeffdlnN_(iK,iM) += 2*g1*((delAM-XA)*(delBK-XB)*XB+(delAK-XA)*(delBM-XB)*XB+(delBM-XB)*(delBK-XB)*XA); + +// double gfac = g0 + g1 * XB; +// double gggg = (delBK - XB) * g1; - dlnActCoeffdlnN_(iK, iM) += gfac * delAK * ( - XB + delBM); +// dlnActCoeffdlnN_(iK, iM) += gfac * delAK * ( - XB + delBM); - dlnActCoeffdlnN_(iK, iM) += gfac * delBK * ( - XA + delAM); +// dlnActCoeffdlnN_(iK, iM) += gfac * delBK * ( - XA + delAM); - dlnActCoeffdlnN_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); +// dlnActCoeffdlnN_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); - dlnActCoeffdlnN_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); +// dlnActCoeffdlnN_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); - dlnActCoeffdlnN_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); +// dlnActCoeffdlnN_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); - dlnActCoeffdlnN_(iK, iM) += - g1 * XA * XB * (- XB + delBM); +// dlnActCoeffdlnN_(iK, iM) += - g1 * XA * XB * (- XB + delBM); } + dlnActCoeffdlnN_(iK,iM) = XM*dlnActCoeffdlnN_(iK,iM); } } } From 41a6d58d18c355175c10eb5a11c22de083d37ca1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 12 Aug 2010 22:51:53 +0000 Subject: [PATCH 235/446] Doxygen update Changed the getMobilities routine in MixTransport and SolidTransport so that the charge does not appear in the mobility formulation. --- Cantera/src/transport/MixTransport.cpp | 32 +++++----- Cantera/src/transport/MixTransport.h | 78 ++++++++++++++++++++++-- Cantera/src/transport/SolidTransport.cpp | 2 +- 3 files changed, 90 insertions(+), 22 deletions(-) diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp index af264c2f7..1f1d88a70 100644 --- a/Cantera/src/transport/MixTransport.cpp +++ b/Cantera/src/transport/MixTransport.cpp @@ -302,34 +302,36 @@ namespace Cantera { return vismix; } //==================================================================================================================== - - /******************* binary diffusion coefficients **************/ - - + // Returns the matrix of binary diffusion coefficients. + /* + * + * d[ld*j + i] = rp * m_bdiff(i,j); + * + * units of m**2 / s + * + * @param ld offset of rows in the storage + * @param d output vector of diffusion coefficients + */ void MixTransport::getBinaryDiffCoeffs(const int ld, doublereal* const d) { - int i,j; - update_T(); - - // if necessary, evaluate the binary diffusion coefficents - // from the polynomial fits + // if necessary, evaluate the binary diffusion coefficents from the polynomial fits if (!m_bindiff_ok) updateDiff_T(); - + if (ld < m_nsp) { + throw CanteraError(" MixTransport::getBinaryDiffCoeffs()", "ld is too small"); + } doublereal rp = 1.0/pressure_ig(); - for (i = 0; i < m_nsp; i++) - for (j = 0; j < m_nsp; j++) { + for (int i = 0; i < m_nsp; i++) + for (int j = 0; j < m_nsp; j++) { d[ld*j + i] = rp * m_bdiff(i,j); } } - - //=================================================================================================================== void MixTransport::getMobilities(doublereal* const mobil) { int k; getMixDiffCoeffs(DATA_PTR(m_spwork)); doublereal c1 = ElectronCharge / (Boltzmann * m_temp); for (k = 0; k < m_nsp; k++) { - mobil[k] = c1 * m_spwork[k] * m_thermo->charge(k); + mobil[k] = c1 * m_spwork[k]; } } //=================================================================================================================== diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index aba28a288..568156504 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -149,6 +149,10 @@ namespace Cantera { */ virtual doublereal viscosity(); + //! returns the vector of species viscosities + /*! + * @param visc Vector of species viscosities + */ virtual void getSpeciesViscosities(doublereal* visc) { update_T(); updateViscosity_T(); copy(m_visc.begin(), m_visc.end(), visc); } @@ -183,8 +187,17 @@ namespace Cantera { */ virtual doublereal thermalConductivity(); + //! Returns the matrix of binary diffusion coefficients. + /*! + * + * d[ld*j + i] = rp * m_bdiff(i,j); + * + * units of m**2 / s + * + * @param ld offset of rows in the storage + * @param d output vector of diffusion coefficients + */ virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d); - //! Returns the Mixture-averaged diffusion coefficients [m^2/s]. /*! @@ -207,9 +220,36 @@ namespace Cantera { */ virtual void getMixDiffCoeffs(doublereal* const d); - + //! Get the Electrical mobilities (m^2/V/s). + /*! + * This function returns the mobilities. In some formulations + * this is equal to the normal mobility multiplied by Faraday's constant. + * + * Here, the mobility is calculated from the diffusion coefficient using the Einstein relation + * + * \f[ + * \mu^e_k = \frac{F D_k}{R T} + * \f] + * + * @param mobil Returns the mobilities of the species in array \c mobil. The array must be + * dimensioned at least as large as the number of species. + */ virtual void getMobilities(doublereal* const mobil); + + //! Update the internal parameters whenever the temperature has changed + /*! + * @internal + * This is called whenever a transport property is requested if the temperature has changed + * since the last call to update_T(). + */ virtual void update_T(); + + //! Update the internal parameters whenever the concentrations have changed + /*! + * @internal + * This is called whenever a transport property is requested if the concentrations have changed + * since the last call to update_C(). + */ virtual void update_C(); //! Get the species diffusive mass fluxes wrt to the mass averaged velocity, @@ -274,9 +314,7 @@ namespace Cantera { return (m_thermo->molarDensity() * GasConstant * m_thermo->temperature()); } - void updateThermal_T(); - //! Update the temperature-dependent viscosity terms. /*! * Updates the array of pure species viscosities, and the weighting functions in the viscosity mixture rule. @@ -329,9 +367,34 @@ namespace Cantera { //! Local copy of the species molecular weights. vector_fp m_mw; - // polynomial fits + //! Polynomial fits to the viscosity of each species + /*! + * m_visccoeffs[k] is vector of polynomial coefficients for species k + * that fits the viscosity as a function of temperature + */ std::vector m_visccoeffs; + + //! Polynomial fits to the thermal conductivity of each species + /*! + * m_condcoeffs[k] is vector of polynomial coefficients for species k + * that fits the thermal conductivity + */ std::vector m_condcoeffs; + + //! Polynomial fits to the binary diffusivity of each species + /*! + * m_diffcoeff[ic] is vector of polynomial coefficients for species i species j + * that fits the binary diffusion coefficient. The relationship between i + * j and ic is determined from the following algorithm: + * + * int ic = 0; + * for (i = 0; i < m_nsp; i++) { + * for (j = i; j < m_nsp; j++) { + * ic++; + * } + * } + * + */ std::vector m_diffcoeffs; //! Powers of the ln temperature @@ -340,7 +403,10 @@ namespace Cantera { */ vector_fp m_polytempvec; - // property values + //! Matrix of binary diffusion coefficients at the reference pressure and the current temperature + /*! + * Size is nsp x nsp + */ DenseMatrix m_bdiff; //! vector of species viscosities (kg /m /s) diff --git a/Cantera/src/transport/SolidTransport.cpp b/Cantera/src/transport/SolidTransport.cpp index 0d8e5535d..4f27ed757 100644 --- a/Cantera/src/transport/SolidTransport.cpp +++ b/Cantera/src/transport/SolidTransport.cpp @@ -127,7 +127,7 @@ namespace Cantera { int nsp = m_thermo->nSpecies(); doublereal c1 = ElectronCharge / (Boltzmann * t); for (k = 0; k < nsp; k++) { - mobil[k] *= c1 * fabs(m_thermo->charge(k)); + mobil[k] *= c1; } } //==================================================================================================================== From 61efb6ec90ad88b1735bea1578fe90772c975316 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 13 Aug 2010 19:19:50 +0000 Subject: [PATCH 236/446] Doxygen update --- Cantera/src/transport/LiquidTransport.cpp | 3 --- Cantera/src/transport/LiquidTransportParams.h | 10 ++++++++++ 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 2c1dd2a65..70f163397 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -735,8 +735,6 @@ namespace Cantera { } } } - - //================================================================================================ // Get the Electrical mobilities (m^2/V/s). /* @@ -775,7 +773,6 @@ namespace Cantera { mobil[k] = c1 * m_spwork[k]; } } - //================================================================================================ // Get the fluid mobilities (s kmol/kg). /* diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index eaf1a795d..b51af65f7 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -128,7 +128,17 @@ namespace Cantera { std::vector selfDiffusion; LiquidTranInteraction* thermalCond; LiquidTranInteraction* speciesDiffusivity; + + //! Pointer to the LiquidTranInteraction object which handles the calculation of the + //! electrical conductivity for the phase LiquidTranInteraction* electCond; + + //! Pointer to the LiquidTranInteraction object which handles the calculation of the hydrodynamic + //! radius for the phase + /*! + * @note I don't understand at the moment how one can define a hydrodynamic + * radius for the phase + */ LiquidTranInteraction* hydroRadius; //! Model for species interaction effects for viscosity From 15608ed25d497c8acc9a95e8e4a283014fb3450e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 01:44:28 +0000 Subject: [PATCH 237/446] Doxygen update --- Cantera/src/transport/LiquidTransport.cpp | 29 +++++++++---------- Cantera/src/transport/LiquidTransport.h | 2 +- Cantera/src/transport/LiquidTransportParams.h | 24 +++++++++++++-- 3 files changed, 35 insertions(+), 20 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index 70f163397..b28bd408f 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -491,7 +491,6 @@ namespace Cantera { * These in turn employ subclasses of LTPspecies to * determine the individual species ionic conductivities. */ - doublereal LiquidTransport:: ionConductivity() { update_T(); @@ -550,10 +549,10 @@ namespace Cantera { // LiquidTranInteraction method if (!m_mobRat_mix_ok) { for (int k = 0; k < m_nsp2; k++){ - if(m_mobRatMixModel[k]){ + if (m_mobRatMixModel[k]) { m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp(m_mobRatTempDep_Ns[k]); - if (m_mobRatMix[k] > 0) { - m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway + if (m_mobRatMix[k] > 0.0) { + m_mobRatMix[k / m_nsp + m_nsp * (k % m_nsp)] = 1.0 / m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway } } } @@ -577,8 +576,8 @@ namespace Cantera { if (!m_mobRat_temp_ok) { updateMobilityRatio_T(); } - for (int k=0; k < m_nsp2; k++) { - for (int j=0; j < m_nsp; j++) { + for (int k = 0; k < m_nsp2; k++) { + for (int j = 0; j < m_nsp; j++) { mobRat[k][j] = m_mobRatSpecies(k,j); } } @@ -1513,7 +1512,7 @@ namespace Cantera { return; } - + //==================================================================================================================== /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations @@ -1782,20 +1781,18 @@ namespace Cantera { } } } - - - /** - * Throw an exception if this method is invoked. - * This probably indicates something is not yet implemented. + //==================================================================================================================== + // Throw an exception indicating something is not yet implemented. + /* + * @param msg String with an informative message */ doublereal LiquidTransport::err(std::string msg) const { - throw CanteraError("Liquid Transport Class", + throw CanteraError("LiquidTransport::err()", "\n\n\n**** Method "+ msg +" not implemented in model " + int2str(model()) + " ****\n" "(Did you forget to specify a transport model?)\n\n\n"); - return 0.0; } - - + //==================================================================================================================== } +//====================================================================================================================== diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 6a3009c04..a2808f643 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -1441,7 +1441,7 @@ namespace Cantera { /*! * This probably indicates something is not yet implemented. * - * @pram msg Indicates the member function which is not implemented + * @param msg Indicates the member function which is not implemented */ doublereal err(std::string msg) const; diff --git a/Cantera/src/transport/LiquidTransportParams.h b/Cantera/src/transport/LiquidTransportParams.h index b51af65f7..a459ea212 100644 --- a/Cantera/src/transport/LiquidTransportParams.h +++ b/Cantera/src/transport/LiquidTransportParams.h @@ -72,7 +72,7 @@ namespace Cantera { * Cl- * 1.2 * - * + * * * * @@ -124,9 +124,27 @@ namespace Cantera { //! Object that specifes the ionic Conductivity of the mixture LiquidTranInteraction* ionConductivity; - std::vector mobilityRatio; - std::vector selfDiffusion; + //! Vector of pointer to the LiquidTranInteraction object which handles the calculation of + //! each species' mobility ratios for the phase + /*! + * mobRat(i,j) = mu_i / mu_j + * + * It is returned in fortran-ordering format. ie. it is returned as mobRat[k], where + * + * k = j * nsp + i + */ + std::vector mobilityRatio; + + //! Vector of pointer to the LiquidTranInteraction object which handles the calculation of + //! each species' self diffusion coefficient for the phase + std::vector selfDiffusion; + + //! Pointer to the LiquidTranInteraction object which handles the calculation of the + //! mixture thermal conductivity for the phase LiquidTranInteraction* thermalCond; + + //! Pointer to the LiquidTranInteraction object which handles the calculation of the + //! species diffusivity for the phase LiquidTranInteraction* speciesDiffusivity; //! Pointer to the LiquidTranInteraction object which handles the calculation of the From 8af154e295173f0c82b0b840187cb1dd8b5a23f2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 02:05:25 +0000 Subject: [PATCH 238/446] Doxgyen update --- Cantera/src/transport/LiquidTransport.h | 212 ++++++++++++------------ 1 file changed, 106 insertions(+), 106 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index a2808f643..96b7ef40f 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -63,8 +63,8 @@ namespace Cantera { * using the Stefan-Maxwell equations. It is possible to set a * flag to calculate relative to a mass-averaged bulk velocity, * relative to a mole-averaged bulk velocity or relative to a - * single species velocity using the , - * , or + * single species velocity using the \, + * \, or \ * keyword. Mass-averaged velocities are the default for which * the diffusion velocities satisfy * \f[ @@ -96,6 +96,7 @@ namespace Cantera { class LiquidTransport : public Transport { public: + //! Typedef equating vector_fp with Coeff_T_ typedef vector_fp Coeff_T_; @@ -199,8 +200,7 @@ namespace Cantera { * appropriate subclasses of LTPspecies as specified in the * input file. * - * @param visc array of length "number of species" - * to hold returned ionic conductivities. + * @param ionCond Array of length "number of species" to hold returned ionic conductivities. */ virtual void getSpeciesIonConductivity(doublereal* const ionCond); @@ -212,6 +212,8 @@ namespace Cantera { * LiquidTranInteraction as specified in the input file. * These in turn employ subclasses of LTPspecies to * determine the mobility ratios in the pure species. + * + * @param mobRat Vector of mobility ratios */ virtual void mobilityRatio(doublereal* mobRat); @@ -461,15 +463,17 @@ namespace Cantera { * \f] * where \f$ z_i \f$ is the charge on species i, * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, - * \f$ W_i \f$ is the molecular mass of species i. + * \f$ W_i \f$ is the molecular mass of species \c i. * - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * @param grad_T The temperature gradient (ignored in this model). - * @param ldf Leading dimension of the grad_V and current vectors. - * @param grad_V The electrostatic potential gradient. - * @param current The electric current in A/m^2. + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. */ virtual void getElectricCurrent(int ndim, const doublereal* grad_T, @@ -489,7 +493,7 @@ namespace Cantera { * be specified as relative to a specific species (i.e. a * solvent) all according to the velocityBasis input parameter. * - * Units for the returned fluxes are kg m-2 s-1. + * Units for the returned velocities are m s-1. * * @param ndim Number of dimensions in the flux expressions * @param grad_T Gradient of the temperature @@ -512,94 +516,85 @@ namespace Cantera { int ldf, doublereal* Vdiff); - //! Get the species diffusive mass fluxes wrt to - //! the averaged velocity, - //! given the gradients in mole fraction, temperature - //! and electrostatic potential. + //! Get the species diffusive velocities wrt to the averaged velocity, + //! given the gradients in mole fraction, temperature and electrostatic potential. /*! * The average velocity can be computed on a mole-weighted * or mass-weighted basis, or the diffusion velocities may * be specified as relative to a specific species (i.e. a * solvent) all according to the velocityBasis input parameter. * - * Units for the returned fluxes are kg m-2 s-1. + * Units for the returned velocities are m s-1. * - * @param ndim Number of dimensions in the flux expressions - * @param grad_T Gradient of the temperature - * (length = ndim) - * @param ldx Leading dimension of the grad_X array - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param grad_Phi Gradients of the electrostatic potential - * (length = ndim) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * (length = ndim) + * @param Vdiff Output of the species diffusion velocities + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - virtual void getSpeciesVdiffES(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_Phi, + virtual void getSpeciesVdiffES(int ndim, const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, const doublereal* grad_Phi, doublereal* Vdiff) ; - - //! Return the species diffusive mass fluxes wrt to - //! the averaged velocity in [kmol/m^2/s]. - /*! - * - * The diffusive mass flux of species \e k is computed - * using the Stefan-Maxwell equation - * \f[ - * X_i \nabla \mu_i - * = RT \sum_i \frac{X_i X_j}{D_{ij}} - * ( \vec{V}_j - \vec{V}_i ) - * \f] - * to determine the diffusion velocity and - * \f[ - * \vec{N}_i = C_T X_i \vec{V}_i - * \f] - * to determine the diffusion flux. Here \f$ C_T \f$ is the - * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ - * are the Stefa-Maxwell interaction parameters in [m^2/s], - * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, - * \f$ \mu_i \f$ is the electrochemical potential of species \e i. - * - * Note that for this method, there is no argument for the - * gradient of the electric potential (voltage). Electric - * potential gradients can be set with set_Grad_V() or - * method getSpeciesFluxesES() can be called.x - * - * The diffusion velocity is relative to an average velocity - * that can be computed on a mole-weighted - * or mass-weighted basis, or the diffusion velocities may - * be specified as relative to a specific species (i.e. a - * solvent) all according to the \verbatim - * \endverbatim input parameter. - - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * (length = ndim) - * @param ldx Leading dimension of the grad_X array. - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param grad_Phi Gradients of the electrostatic potential - * length = ndim - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - */ - virtual void getSpeciesFluxes(int ndim, + //! Return the species diffusive mass fluxes wrt to + //! the averaged velocity in [kmol/m^2/s]. + /*! + * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * Note that for this method, there is no argument for the + * gradient of the electric potential (voltage). Electric + * potential gradients can be set with set_Grad_V() or + * method getSpeciesFluxesES() can be called.x + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim \endverbatim input parameter. + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) + * @param ldx Leading dimension of the grad_X array. + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + virtual void getSpeciesFluxes(int ndim, const doublereal* grad_T, int ldx, const doublereal* grad_X, int ldf, doublereal* fluxes); @@ -632,21 +627,21 @@ namespace Cantera { * solvent) all according to the \verbatim * \endverbatim input parameter. - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * (length = ndim) - * @param ldx Leading dimension of the grad_X array. - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param grad_Phi Gradients of the electrostatic potential - * length = ndim - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) + * @param ldx Leading dimension of the grad_X array. + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * length = ndim + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ virtual void getSpeciesFluxesES(int ndim, const doublereal* grad_T, @@ -893,7 +888,7 @@ namespace Cantera { //! Number of species in the phase int m_nsp; - + //! Number of species squared int m_nsp2; //! Minimum temperature applicable to the transport property eval @@ -944,7 +939,9 @@ namespace Cantera { */ LiquidTranInteraction *m_ionCondMixModel; + //! Type def for LTPvector equating it with a vector of pointers to LTPspecies typedef std::vector LTPvector; + //! Mobility ratio for the binary cominations of each species in each //! pure phase expressed as an appropriate subclass of LTPspecies /*! @@ -1289,6 +1286,7 @@ namespace Cantera { //! Specific volume for each species. Local copy from thermo object. vector_fp m_volume_spec; + //! Vector of activity coefficients vector_fp m_actCoeff; //! RHS to the stefan-maxwell equation @@ -1370,6 +1368,8 @@ namespace Cantera { //! Flag to indicate that the pure species ionic conductivities //! are current wrt the concentration bool m_ionCond_conc_ok; + + //! Flag to indicate that the mixture conductivity is current bool m_cond_mix_ok; //! Boolean indicating that the top-level mixture mobility ratio is current From 4a1b09fd5801b807d8a8030f48af0f043e0a54eb Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 02:21:57 +0000 Subject: [PATCH 239/446] Doxygen update --- Cantera/src/transport/LTPspecies.cpp | 38 +++++++++++------------ Cantera/src/transport/LiquidTransport.cpp | 5 ++- Cantera/src/transport/LiquidTransport.h | 8 ++--- 3 files changed, 24 insertions(+), 27 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index 1f0875ee8..c9d37f4c4 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -14,9 +14,9 @@ using namespace std; namespace Cantera { + //==================================================================================================================== /** - * Exception thrown if an error is encountered while reading the - * transport database. + * Exception thrown if an error is encountered while reading the transport database. */ class LTPError : public CanteraError { public: @@ -25,12 +25,18 @@ namespace Cantera { "error parsing transport data: " + msg + "\n") {} }; - - - /** - * getArrhenius() parses the xml element called Arrhenius. + //==================================================================================================================== + //! getArrhenius() parses the xml element called Arrhenius. + /*! * The Arrhenius expression is - * \f[ k = A T^(b) exp (-E_a / RT). \f] + * \f[ + * k = A T^(b) exp (-E_a / RT) + * \f] + * + * @param node XML_Node to be read + * @param A Output pre-exponential factor. The units are variable. + * @param b output temperature power + * @param E Output activation energy in units of Kelvin */ static void getArrhenius(const XML_Node& node, doublereal& A, doublereal& b, doublereal& E) { @@ -41,15 +47,15 @@ namespace Cantera { E = getFloat(node, "E", "actEnergy"); E /= GasConstant; } - + //==================================================================================================================== // Copy constructor - LTPspecies::LTPspecies( const LTPspecies &right ) + LTPspecies::LTPspecies(const LTPspecies &right) { *this = right; //use assignment operator to do other work } - + //==================================================================================================================== // Assignment operator - LTPspecies& LTPspecies::operator=(const LTPspecies& right ) + LTPspecies& LTPspecies::operator=(const LTPspecies& right) { if (&right != this) { m_speciesName = right.m_speciesName; @@ -98,7 +104,7 @@ namespace Cantera { { *this = right; //use assignment operator to do other work } - //==================================================================================================================== + //==================================================================================================================== // Assignment operator LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right ) { @@ -129,7 +135,6 @@ namespace Cantera { return m_coeffs[0]; } //==================================================================================================================== - // Construct an LTPspecies object for a liquid tranport property // expressed in extended Arrhenius form. /* The transport property is constructed from the XML node, @@ -318,11 +323,7 @@ namespace Cantera { //cout << "m_prop = " << m_prop << endl; return m_prop; } - //==================================================================================================================== - -/////////////////////////////////////////////////////////////// - // Construct an LTPspecies object for a liquid tranport property // expressed as an exponential in temperature. /* The transport property is constructed from the XML node, @@ -339,8 +340,6 @@ namespace Cantera { m_model = LTR_MODEL_EXPT; m_temp = 0.0; m_prop = 0.0; - - getFloatArray(propNode, m_coeffs, "true", "toSI"); /* if (m_coeffs[0] <= 0.0) { @@ -402,6 +401,5 @@ namespace Cantera { //cout << "m_prop = " << m_prop << endl; return m_prop; } - //==================================================================================================================== } diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp index b28bd408f..92cbd8651 100644 --- a/Cantera/src/transport/LiquidTransport.cpp +++ b/Cantera/src/transport/LiquidTransport.cpp @@ -1467,12 +1467,11 @@ namespace Cantera { m_selfDiff_temp_ok = true; m_selfDiff_mix_ok = false; } - + //============================================================================================================= void LiquidTransport::updateHydrodynamicRadius_C() { m_radi_conc_ok = true; } - - + //============================================================================================================= // Update the temperature-dependent hydrodynamic radius terms // for each species internally using calls to the // appropriate LTPspecies subclass diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 96b7ef40f..1848367d7 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -877,7 +877,7 @@ namespace Cantera { * @internal */ void updateHydrodynamicRadius_C(); - + //! Update the binary Stefan-Maxwell diffusion coefficients //! wrt T using calls to the appropriate LTPspecies subclass void updateDiff_T(); @@ -1025,14 +1025,14 @@ namespace Cantera { DenseMatrix m_diff_Dij; - //!Hydrodynamic radius for each species expressed as an - //! appropriate subclass of LTPspecies + //! Hydrodynamic radius for each species expressed as an appropriate subclass of LTPspecies /*! * These subclasses of LTPspecies evaluate the species-specific * transport properties according to the parameters parsed in * TransportFactory::getLiquidSpeciesTransportData(). + * length = nsp */ - std::vector m_radiusTempDep_Ns; + std::vector m_radiusTempDep_Ns; //! (Not used in LiquidTransport) //! Hydrodynamic radius of the mixture expressed as a subclass of From 57a2ca965ddaa3bbb77b8d7506f3bfc640584f88 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 18:02:39 +0000 Subject: [PATCH 240/446] doxygen update --- Cantera/src/transport/LTPspecies.cpp | 12 +++--- Cantera/src/transport/LTPspecies.h | 58 +++++++++++++++------------ Cantera/src/transport/TransportBase.h | 18 +++++---- 3 files changed, 49 insertions(+), 39 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index c9d37f4c4..de0325347 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -331,11 +331,11 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_ExpT::LTPspecies_ExpT( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) + LTPspecies_ExpT::LTPspecies_ExpT(const XML_Node &propNode, + std::string name, + TransportPropertyList tp_ind, + thermo_t* thermo) : + LTPspecies(propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_EXPT; m_temp = 0.0; @@ -388,7 +388,7 @@ namespace Cantera { doublereal t = m_thermo->temperature(); if (t != m_temp) { - m_prop = 0; + m_prop = 0.0; m_temp=t; m_prop=m_coeffs[0]; double tempN = 1.0; diff --git a/Cantera/src/transport/LTPspecies.h b/Cantera/src/transport/LTPspecies.h index 00a1b9507..72d033623 100644 --- a/Cantera/src/transport/LTPspecies.h +++ b/Cantera/src/transport/LTPspecies.h @@ -67,14 +67,14 @@ namespace Cantera { }; //==================================================================================================================== - //! Class LTPspecies holds transport parameters for a - //! specific liquid-phase species. + //! Class LTPspecies holds transport parameters for a specific liquid-phase species. /*! * Subclasses handle different means of specifying transport properties * like constant, %Arrhenius or polynomial fits. In its current state, * it is primarily suitable for specifying temperature dependence, but * the adjustCoeffsForComposition() method can be implemented to * adjust for composition dependence. + * * Mixing rules for computing mixture transport properties are handled * separately in LiquidTranInteraction subclasses. */ @@ -83,15 +83,16 @@ namespace Cantera { public: //! Construct an LTPspecies object for a liquid tranport property. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + /*! + * The transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of + * transport property (like viscosity) */ LTPspecies(const XML_Node &propNode = 0, std::string name = "-", TransportPropertyList tp_ind = TP_UNKNOWN, - thermo_t* thermo = 0 ) : + const thermo_t* const thermo = 0) : m_speciesName(name), m_model(LTR_MODEL_NOTSET), m_property(tp_ind), @@ -99,7 +100,7 @@ namespace Cantera { m_mixWeight(1.0) { if (propNode.hasChild("mixtureWeighting") ) { - m_mixWeight = getFloat(propNode,"mixtureWeighting"); + m_mixWeight = getFloat(propNode, "mixtureWeighting"); } } @@ -145,11 +146,11 @@ namespace Cantera { //! Model temperature-dependence ceofficients vector_fp m_coeffs; - //! pointer to thermo object to get current temperature - thermo_t* m_thermo; + //! Pointer to a const thermo object to get current temperature + const thermo_t * m_thermo; //! Weighting used for mixing. - /** + /*! * This weighting can be employed to allow salt transport * properties to be represented by specific ions. * For example, to have Li+ and Ca+ represent the mixing @@ -163,9 +164,10 @@ namespace Cantera { doublereal m_mixWeight; //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. + /*! + * Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. */ virtual void adjustCoeffsForComposition() { } }; @@ -427,14 +429,15 @@ namespace Cantera { }; //==================================================================================================================== - //! Class LTPspecies_ExpT holds transport parameters for a - //! specific liquid-phase species (LTPspecies) when the transport - //! property is expressed as a exponential in temperature. + //! Class LTPspecies_ExpT holds transport parameters for a specific liquid-phase species (LTPspecies) + //! when the transport property is expressed as a exponential in temperature. /** * Used for pure species properties with equations of the form - * \f[ - * x = f[0] \exp( f[1] T + ... + f[N] T ) - * \f] + * + * \f[ + * x = f[0] \exp( f[1] T + ... + f[N] T^{N} ) + * \f] + * * where f[i] are elements of the float array passed in. * * As an example of the input required for LTPspecies_ExpT @@ -459,18 +462,21 @@ namespace Cantera { //! Construct an LTPspecies object for a liquid tranport property //! expressed as an exponential in temperature. /*! - * The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + * The transport property is constructed from the XML node, \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity). + * + * @param propNode */ - LTPspecies_ExpT( const XML_Node &propNode, + LTPspecies_ExpT(const XML_Node &propNode, std::string name, TransportPropertyList tp_ind, thermo_t* thermo ); //! Copy constructor - LTPspecies_ExpT( const LTPspecies_ExpT &right ); + /*! + * @param right Object to be copied + */ + LTPspecies_ExpT(const LTPspecies_ExpT &right); //! Assignment operator LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 667190ccc..4e42258ff 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -222,13 +222,16 @@ namespace Cantera { // Note ->need working copy constructors and operator=() functions for all first virtual Transport *duplMyselfAsTransport() const; - /** - * Transport model. The transport model is the set of - * equations used to compute the transport properties. This + + //! Transport model. + /*! + * The transport model is the set of equations used to compute the transport properties. This * virtual method returns an integer flag that identifies the * transport model implemented. The base class returns 0. */ - virtual int model() const {return 0;} + virtual int model() const { + return 0; + } /** * Phase object. Every transport manager is designed to compute @@ -237,7 +240,9 @@ namespace Cantera { * returns a reference to the object representing the phase * itself. */ - thermo_t& thermo() { return *m_thermo; } + thermo_t& thermo() { + return *m_thermo; + } /** @@ -495,8 +500,7 @@ namespace Cantera { * @param grad_X The gradient of the mole fraction * @param ldf Leading dimension of the grad_V and current vectors. * @param grad_V The electrostatic potential gradient. - * @param current The electric current in A/m^2. this is a vector - * of length ndim + * @param current The electric current in A/m^2. This is a vector of length ndim */ virtual void getElectricCurrent(int ndim, const doublereal* grad_T, From 741d0940655a6097befc32289972756bc58ba95b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 18:29:39 +0000 Subject: [PATCH 241/446] Updated the test --- .../mixGasTransport/output_blessed.txt | 106 +++++++++--------- test_problems/mixGasTransport/runtest | 2 +- 2 files changed, 54 insertions(+), 54 deletions(-) diff --git a/test_problems/mixGasTransport/output_blessed.txt b/test_problems/mixGasTransport/output_blessed.txt index 610c3a9a0..3b3084806 100644 --- a/test_problems/mixGasTransport/output_blessed.txt +++ b/test_problems/mixGasTransport/output_blessed.txt @@ -226,59 +226,59 @@ Binary Diffusion Coefficients H2 vs species H2 - CH2CHO 0.00072342 0.00072342 H2 - CH3CHO 0.00072305 0.00072305 Dump of the species mobilities: - H2 0 - H 0 - O 0 - O2 0 - OH 0 - H2O 0 - HO2 0 - H2O2 0 - C 0 - CH 0 - CH2 0 - CH2(S) 0 - CH3 0 - CH4 0 - CO 0 - CO2 0 - HCO 0 - CH2O 0 - CH2OH 0 - CH3O 0 - CH3OH 0 - C2H 0 - C2H2 0 - C2H3 0 - C2H4 0 - C2H5 0 - C2H6 0 - HCCO 0 - CH2CO 0 - HCCOH 0 - N 0 - NH 0 - NH2 0 - NH3 0 - NNH 0 - NO 0 - NO2 0 - N2O 0 - HNO 0 - CN 0 - HCN 0 - H2CN 0 - HCNN 0 - HCNO 0 - HOCN 0 - HNCO 0 - NCO 0 - N2 0 - AR 0 - C3H7 0 - C3H8 0 - CH2CHO 0 - CH3CHO 0 + H2 0.011345 + H 0.015874 + O 0.0045049 + O2 0.0029711 + OH 0.0044285 + H2O 0.0038855 + HO2 0.0029546 + H2O2 0.0029366 + C 0.0041647 + CH 0.0047859 + CH2 0.003238 + CH2(S) 0.003238 + CH3 0.003173 + CH4 0.0031601 + CO 0.0028304 + CO2 0.0023276 + HCO 0.0025297 + CH2O 0.002511 + CH2OH 0.0024471 + CH3O 0.0024471 + CH3OH 0.0024573 + C2H 0.0024734 + C2H2 0.0024509 + C2H3 0.0024298 + C2H4 0.0024281 + C2H5 0.0022284 + C2H6 0.002212 + HCCO 0.0037298 + CH2CO 0.0021429 + HCCOH 0.0021429 + N 0.0039749 + NH 0.0047421 + NH2 0.0046426 + NH3 0.0035032 + NNH 0.0028493 + NO 0.0028987 + NO2 0.0025993 + N2O 0.0023511 + HNO 0.0029459 + CN 0.0028599 + HCN 0.0025036 + H2CN 0.0024832 + HCNN 0.0037297 + HCNO 0.0023604 + HOCN 0.0023604 + HNCO 0.0023604 + NCO 0.0023703 + N2 0.0027544 + AR 0.0028988 + C3H7 0.0017303 + C3H8 0.0017234 + CH2CHO 0.0021339 + CH3CHO 0.0021254 Dump of the species fluxes: H2 4.9545e-06 4.7567e-07 H 1.7837e-08 1.789e-08 diff --git a/test_problems/mixGasTransport/runtest b/test_problems/mixGasTransport/runtest index f914fa775..ab4d9e6b9 100755 --- a/test_problems/mixGasTransport/runtest +++ b/test_problems/mixGasTransport/runtest @@ -21,7 +21,7 @@ then fi ../../bin/exp3to2.sh output.txt > outputa.txt -diff -w outputa.txt output_blessed.txt > diff_test.out +diff -w output_blessed.txt outputa.txt > diff_test.out retnStat=$? if [ $retnStat = "0" ] then From 6ab225ebdf4e7dd6a8e211fef1acbe2e97717a11 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 18:33:37 +0000 Subject: [PATCH 242/446] Changed the enum name from TransportPropertyList to TransportPropertyType --- Cantera/src/transport/LTPspecies.cpp | 81 +++++++++---------- Cantera/src/transport/LTPspecies.h | 26 +++--- .../src/transport/LiquidTranInteraction.cpp | 4 +- Cantera/src/transport/LiquidTranInteraction.h | 54 ++++++------- Cantera/src/transport/TransportFactory.cpp | 4 +- Cantera/src/transport/TransportFactory.h | 12 ++- 6 files changed, 87 insertions(+), 94 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index de0325347..ba9bb020e 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -20,7 +20,7 @@ namespace Cantera { */ class LTPError : public CanteraError { public: - LTPError( std::string msg ) + LTPError(std::string msg) : CanteraError("LTPspecies", "error parsing transport data: " + msg + "\n") {} @@ -85,28 +85,28 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_Const::LTPspecies_Const( const XML_Node &propNode, + LTPspecies_Const::LTPspecies_Const(const XML_Node &propNode, std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) + TransportPropertyType tp_ind, + thermo_t* thermo) : + LTPspecies(propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_CONSTANT; double A_k = getFloatCurrent(propNode, "toSI"); if (A_k > 0.0) { m_coeffs.push_back(A_k); - } else throw LTPError("negative or zero " + propNode.name() ); + } else throw LTPError("negative or zero " + propNode.name()); } //==================================================================================================================== // Copy constructor - LTPspecies_Const::LTPspecies_Const( const LTPspecies_Const &right ) + LTPspecies_Const::LTPspecies_Const(const LTPspecies_Const &right) : LTPspecies() { *this = right; //use assignment operator to do other work } //==================================================================================================================== // Assignment operator - LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right ) + LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right) { if (&right != this) { //LTPspecies::operator=(right); @@ -131,7 +131,7 @@ namespace Cantera { } //==================================================================================================================== // Return the (constant) value for this transport property - doublereal LTPspecies_Const::getSpeciesTransProp( ) { + doublereal LTPspecies_Const::getSpeciesTransProp() { return m_coeffs[0]; } //==================================================================================================================== @@ -142,11 +142,9 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_Arrhenius::LTPspecies_Arrhenius( const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) + LTPspecies_Arrhenius::LTPspecies_Arrhenius(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, thermo_t* thermo) : + LTPspecies(propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_ARRHENIUS; m_temp = 0.0; @@ -155,23 +153,23 @@ namespace Cantera { doublereal A_k, n_k, Tact_k; getArrhenius(propNode, A_k, n_k, Tact_k); if (A_k <= 0.0) { - throw LTPError("negative or zero " + propNode.name() ); + throw LTPError("negative or zero " + propNode.name()); } - m_coeffs.push_back( A_k ); - m_coeffs.push_back( n_k ); - m_coeffs.push_back( Tact_k ); - m_coeffs.push_back( log( A_k ) ); + m_coeffs.push_back(A_k); + m_coeffs.push_back(n_k); + m_coeffs.push_back(Tact_k); + m_coeffs.push_back(log(A_k)); } //==================================================================================================================== // Copy constructor - LTPspecies_Arrhenius::LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ) + LTPspecies_Arrhenius::LTPspecies_Arrhenius(const LTPspecies_Arrhenius &right) : LTPspecies() { *this = right; //use assignment operator to do other work } //==================================================================================================================== // Assignment operator - LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right ) + LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right) { if (&right != this) { // LTPspecies::operator=(right); @@ -206,7 +204,7 @@ namespace Cantera { * In general the Arrhenius expression is * * \f[ - * \mu = A T^n \exp( - E / R T ). + * \mu = A T^n \exp(- E / R T). * \f] * * Note that for viscosity, the convention is such that @@ -215,13 +213,13 @@ namespace Cantera { * the Arrhenius expression is * * \f[ - * \mu = A T^n \exp( + E / R T ). + * \mu = A T^n \exp(+ E / R T). * \f] * * Any temperature and composition dependence will be * adjusted internally according to the information provided. */ - doublereal LTPspecies_Arrhenius::getSpeciesTransProp( ) { + doublereal LTPspecies_Arrhenius::getSpeciesTransProp() { doublereal t = m_thermo->temperature(); //m_coeffs[0] holds A @@ -234,16 +232,14 @@ namespace Cantera { m_temp = t; m_logt = log(m_temp); //For viscosity the sign convention on positive activation energy is swithced - if ( m_property == TP_VISCOSITY ) + if (m_property == TP_VISCOSITY) m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt + m_coeffs[2] / m_temp ; else m_logProp = m_coeffs[3] + m_coeffs[1] * m_logt - m_coeffs[2] / m_temp ; - m_prop = exp( m_logProp ); + m_prop = exp(m_logProp); } return m_prop; } - - //==================================================================================================================== // Construct an LTPspecies object for a liquid tranport property // expressed as a polynomial in temperature. @@ -252,11 +248,9 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, - thermo_t* thermo ) : - LTPspecies( propNode, name, tp_ind, thermo) + LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, thermo_t* thermo) : + LTPspecies(propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_POLY; m_temp = 0.0; @@ -266,19 +260,19 @@ namespace Cantera { getFloatArray(propNode, m_coeffs, "true", "toSI"); /* if (m_coeffs[0] <= 0.0) { - throw LTPError("negative or zero " + propNode.name() ); + throw LTPError("negative or zero " + propNode.name()); }*/ } //==================================================================================================================== // Copy constructor - LTPspecies_Poly::LTPspecies_Poly( const LTPspecies_Poly &right ) + LTPspecies_Poly::LTPspecies_Poly(const LTPspecies_Poly &right) : LTPspecies() { *this = right; //use assignment operator to do other work } //==================================================================================================================== // Assignment operator - LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right ) + LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right) { if (&right != this) { //LTPspecies::operator=(right); @@ -307,7 +301,7 @@ namespace Cantera { //==================================================================================================================== // Return the value for this transport property evaluated // from the polynomial expression - doublereal LTPspecies_Poly::getSpeciesTransProp( ) { + doublereal LTPspecies_Poly::getSpeciesTransProp() { doublereal t = m_thermo->temperature(); if (t != m_temp) { @@ -331,9 +325,7 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_ExpT::LTPspecies_ExpT(const XML_Node &propNode, - std::string name, - TransportPropertyList tp_ind, + LTPspecies_ExpT::LTPspecies_ExpT(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, thermo_t* thermo) : LTPspecies(propNode, name, tp_ind, thermo) { @@ -343,19 +335,19 @@ namespace Cantera { getFloatArray(propNode, m_coeffs, "true", "toSI"); /* if (m_coeffs[0] <= 0.0) { - throw LTPError("negative or zero " + propNode.name() ); + throw LTPError("negative or zero " + propNode.name()); }*/ } //==================================================================================================================== // Copy constructor - LTPspecies_ExpT::LTPspecies_ExpT( const LTPspecies_ExpT &right ) + LTPspecies_ExpT::LTPspecies_ExpT(const LTPspecies_ExpT &right) : LTPspecies() { *this = right; //use assignment operator to do other work } //==================================================================================================================== // Assignment operator - LTPspecies_ExpT& LTPspecies_ExpT::operator=(const LTPspecies_ExpT& right ) + LTPspecies_ExpT& LTPspecies_ExpT::operator=(const LTPspecies_ExpT& right) { if (&right != this) { //LTPspecies::operator=(right); @@ -384,7 +376,7 @@ namespace Cantera { //==================================================================================================================== // Return the value for this transport property evaluated // from the exponential in temperature expression - doublereal LTPspecies_ExpT::getSpeciesTransProp( ) { + doublereal LTPspecies_ExpT::getSpeciesTransProp() { doublereal t = m_thermo->temperature(); if (t != m_temp) { @@ -395,7 +387,6 @@ namespace Cantera { for (int i = 1; i < (int) m_coeffs.size() ; i++) { tempN *= m_temp; m_prop *= exp(m_coeffs[i] * tempN); - //cout << "m_coeff = " < LTPptrs ) ; + doublereal getMixTransProp(doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp(std::vector LTPptrs) ; //! Return the matrix of binary interaction parameters. /** * Takes the proper mixing rule for the binary interaction parameters * and calculates them: Not implemented for this mixing rule. */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: @@ -368,7 +368,7 @@ namespace Cantera { class LTI_Log_MoleFracs : public LiquidTranInteraction { public: - LTI_Log_MoleFracs( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LTI_Log_MoleFracs( TransportPropertyType tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) { m_model = LTI_MODEL_LOG_MOLEFRACS; @@ -389,15 +389,15 @@ namespace Cantera { * as input (this method does not know what * transport property it is at this point. */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; + doublereal getMixTransProp(doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp(std::vector LTPptrs ) ; //! Return the matrix of binary interaction parameters. /** * Takes the proper mixing rule for the binary interaction parameters * and calculates them: Not implemented for this mixing rule. */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } + void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = m_Eij; } protected: @@ -430,7 +430,7 @@ namespace Cantera { class LTI_Pairwise_Interaction : public LiquidTranInteraction { public: - LTI_Pairwise_Interaction( TransportPropertyList tp_ind = TP_UNKNOWN ) : + LTI_Pairwise_Interaction( TransportPropertyType tp_ind = TP_UNKNOWN ) : LiquidTranInteraction( tp_ind ) { m_model = LTI_MODEL_PAIRWISE_INTERACTION; @@ -541,8 +541,8 @@ namespace Cantera { class LTI_StefanMaxwell_PPN : public LiquidTranInteraction { public: - LTI_StefanMaxwell_PPN( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) + LTI_StefanMaxwell_PPN(TransportPropertyType tp_ind = TP_UNKNOWN) : + LiquidTranInteraction(tp_ind) { m_model = LTI_MODEL_STEFANMAXWELL_PPN; } @@ -556,7 +556,7 @@ namespace Cantera { virtual ~LTI_StefanMaxwell_PPN( ) { } - void setParameters( LiquidTransportParams& trParam ) ; + void setParameters(LiquidTransportParams& trParam ) ; //! Return the mixture transport property value. /** @@ -593,8 +593,8 @@ namespace Cantera { class LTI_StokesEinstein : public LiquidTranInteraction { public: - LTI_StokesEinstein( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) + LTI_StokesEinstein(TransportPropertyType tp_ind = TP_UNKNOWN) : + LiquidTranInteraction(tp_ind) { m_model = LTI_MODEL_STOKES_EINSTEIN; } @@ -608,7 +608,7 @@ namespace Cantera { virtual ~LTI_StokesEinstein( ) { } - void setParameters( LiquidTransportParams& trParam ); + void setParameters(LiquidTransportParams& trParam); //! Return the mixture transport property value. /** @@ -616,15 +616,15 @@ namespace Cantera { * as input (this method does not know what * transport property it is at this point. */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; + doublereal getMixTransProp(doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp(std::vector LTPptrs ) ; //! Return the matrix of binary interaction parameters. /** * Takes the proper mixing rule for the binary interaction parameters * and calculates them */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) ; + void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ) ; protected: std::vector m_viscosity; @@ -644,8 +644,8 @@ namespace Cantera { class LTI_MoleFracs_ExpT : public LiquidTranInteraction { public: - LTI_MoleFracs_ExpT( TransportPropertyList tp_ind = TP_UNKNOWN ) : - LiquidTranInteraction( tp_ind ) + LTI_MoleFracs_ExpT(TransportPropertyType tp_ind = TP_UNKNOWN) : + LiquidTranInteraction(tp_ind) { m_model = LTI_MODEL_MOLEFRACS_EXPT; } @@ -665,15 +665,15 @@ namespace Cantera { * as input (this method does not know what * transport property it is at this point. */ - doublereal getMixTransProp( doublereal *valueSpecies, doublereal *weightSpecies = 0 ); - doublereal getMixTransProp( std::vector LTPptrs ) ; + doublereal getMixTransProp(doublereal *valueSpecies, doublereal *weightSpecies = 0 ); + doublereal getMixTransProp(std::vector LTPptrs ) ; //! Return the matrix of binary interaction parameters. /** * Takes the proper mixing rule for the binary interaction parameters * and calculates them: Not Implemented for this mixing rule */ - void getMatrixTransProp( DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } + void getMatrixTransProp(DenseMatrix &mat, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } //CAL void getMatrixTransProp( DenseMatrix &mat, LiquidTransport* lt, doublereal* speciesValues = 0 ) { mat = (*m_Aij[0]); } protected: diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 3bae891b5..b87cdad0c 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -304,7 +304,7 @@ namespace Cantera { and possibly composition. */ LTPspecies* TransportFactory::newLTP(const XML_Node &trNode, std::string &name, - TransportPropertyList tp_ind, thermo_t* thermo) + TransportPropertyType tp_ind, thermo_t* thermo) { LTPspecies* ltps = 0; std::string model = lowercase(trNode["model"]); @@ -336,7 +336,7 @@ namespace Cantera { returned by newLTP */ LiquidTranInteraction* TransportFactory::newLTI(const XML_Node &trNode, - TransportPropertyList tp_ind, + TransportPropertyType tp_ind, LiquidTransportParams& trParam) { LiquidTranInteraction* lti = 0; diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index 7154ee5cf..ec6ccd973 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -147,7 +147,6 @@ namespace Cantera { //! Deletes the statically malloced instance. virtual void deleteFactory(); - /*! * Destructor * @@ -160,7 +159,6 @@ namespace Cantera { virtual ~TransportFactory(); - //! Make one of several transport models, and return a base class pointer to it. /*! * This method operates at the level of a single transport property as a function of temperature @@ -168,11 +166,11 @@ namespace Cantera { * * @param trNode XML node * @param name reference to the name - * @param tp_ind TransportPropertyList class + * @param tp_ind TransportPropertyType class * @param thermo Pointer to the %ThermoPhase class */ virtual LTPspecies* newLTP(const XML_Node &trNode, std::string &name, - TransportPropertyList tp_ind, thermo_t* thermo); + TransportPropertyType tp_ind, thermo_t* thermo); //! Factory function for the construction of new LiquidTranInteraction @@ -182,11 +180,11 @@ namespace Cantera { * transport properties are addressed by the LTPspecies returned by newLTP. * * @param trNode XML_Node containing the information for the interaction - * @param tp_ind TransportPropertylist object + * @param tp_ind TransportPropertyType object * @param trParam reference to the LiquidTransportParams object */ virtual LiquidTranInteraction* newLTI(const XML_Node &trNode, - TransportPropertyList tp_ind, + TransportPropertyType tp_ind, LiquidTransportParams& trParam); @@ -446,7 +444,7 @@ namespace Cantera { //! Mapping between between the string name //! for a transport property and the integer name. - std::map m_tranPropMap; + std::map m_tranPropMap; //! Mapping between between the string name for a //! species-specific transport property model and the integer name. From 95fd7f0b760de12c896607d39eaa6d790e5b6d21 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 19:19:43 +0000 Subject: [PATCH 243/446] Doxygen update Rearrangement of LTPspecies to put more routines in .cpp files --- Cantera/src/transport/LTPspecies.cpp | 97 ++++++++++--- Cantera/src/transport/LTPspecies.h | 161 ++++++++++----------- Cantera/src/transport/TransportFactory.cpp | 2 +- 3 files changed, 160 insertions(+), 100 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index ba9bb020e..2b61d35a7 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -15,7 +15,7 @@ using namespace std; namespace Cantera { //==================================================================================================================== - /** + /* * Exception thrown if an error is encountered while reading the transport database. */ class LTPError : public CanteraError { @@ -48,6 +48,34 @@ namespace Cantera { E /= GasConstant; } //==================================================================================================================== + // Construct an LTPspecies object for a liquid tranport property. + /* + * The species transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node in the species block and specifies a type of transport + * property (like viscosity) + * + * @param propNode Pointer to the XML node that contains the property information + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + */ + LTPspecies::LTPspecies(const XML_Node * const propNode, std::string name, + TransportPropertyType tp_ind, const thermo_t* const thermo) : + m_speciesName(name), + m_model(LTR_MODEL_NOTSET), + m_property(tp_ind), + m_thermo(thermo), + m_mixWeight(1.0) + { + if (propNode) { + if (propNode->hasChild("mixtureWeighting") ) { + m_mixWeight = getFloat(*propNode, "mixtureWeighting"); + } + } + } + //==================================================================================================================== // Copy constructor LTPspecies::LTPspecies(const LTPspecies &right) { @@ -78,6 +106,43 @@ namespace Cantera { return prp; } //==================================================================================================================== + LTPspecies::~LTPspecies() + { + } + //==================================================================================================================== + // Returns the vector of pure species tranport property + /* + * The pure species transport property (i.e. pure species viscosity) + * is returned. Any temperature and composition dependence will be + * adjusted internally according to the information provided by the + * subclass object. + */ + doublereal LTPspecies::getSpeciesTransProp() + { + return 0.0; + } + //==================================================================================================================== + // Check to see if the property evaluation will be positive + bool LTPspecies::checkPositive() const + { + return (m_coeffs[0] > 0); + } + //==================================================================================================================== + doublereal LTPspecies::getMixWeight() const + { + return m_mixWeight; + } + //==================================================================================================================== + // Internal model to adjust species-specific properties for composition. + /* + * Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + void LTPspecies::adjustCoeffsForComposition() + { + } + //==================================================================================================================== // Construct an LTPspecies object for a liquid tranport property // expressed as a constant value. /* The transport property is constructed from the XML node, @@ -85,17 +150,17 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_Const::LTPspecies_Const(const XML_Node &propNode, - std::string name, - TransportPropertyType tp_ind, - thermo_t* thermo) : - LTPspecies(propNode, name, tp_ind, thermo) + LTPspecies_Const::LTPspecies_Const(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, const thermo_t * const thermo) : + LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_CONSTANT; double A_k = getFloatCurrent(propNode, "toSI"); if (A_k > 0.0) { m_coeffs.push_back(A_k); - } else throw LTPError("negative or zero " + propNode.name()); + } else { + throw LTPError("negative or zero " + propNode.name()); + } } //==================================================================================================================== // Copy constructor @@ -109,17 +174,15 @@ namespace Cantera { LTPspecies_Const& LTPspecies_Const::operator=(const LTPspecies_Const& right) { if (&right != this) { - //LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; + LTPspecies::operator=(right); } return *this; } //==================================================================================================================== + LTPspecies_Const::~LTPspecies_Const() + { + } + //==================================================================================================================== // Duplication routine /* * @return Returns a copy of this routine as a pointer to LTPspecies @@ -144,7 +207,7 @@ namespace Cantera { */ LTPspecies_Arrhenius::LTPspecies_Arrhenius(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, thermo_t* thermo) : - LTPspecies(propNode, name, tp_ind, thermo) + LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_ARRHENIUS; m_temp = 0.0; @@ -250,7 +313,7 @@ namespace Cantera { */ LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, thermo_t* thermo) : - LTPspecies(propNode, name, tp_ind, thermo) + LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_POLY; m_temp = 0.0; @@ -327,7 +390,7 @@ namespace Cantera { */ LTPspecies_ExpT::LTPspecies_ExpT(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, thermo_t* thermo) : - LTPspecies(propNode, name, tp_ind, thermo) + LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_EXPT; m_temp = 0.0; diff --git a/Cantera/src/transport/LTPspecies.h b/Cantera/src/transport/LTPspecies.h index bca630a48..9c128f165 100644 --- a/Cantera/src/transport/LTPspecies.h +++ b/Cantera/src/transport/LTPspecies.h @@ -12,7 +12,6 @@ #ifndef CT_LTPSPECIES_H #define CT_LTPSPECIES_H - // Cantera includes #include "ct_defs.h" #include "TransportBase.h" @@ -25,7 +24,7 @@ namespace Cantera { - + //==================================================================================================================== //! Enumeration of the types of transport properties that can be //! handled by the variables in the various Transport classes. /*! @@ -53,8 +52,9 @@ namespace Cantera { TP_DIFFUSIVITY, TP_HYDRORADIUS, TP_ELECTCOND - }; + }; + //==================================================================================================================== //! Temperature dependence type for pure (liquid) species properties /*! * Types of temperature dependencies: @@ -88,35 +88,38 @@ namespace Cantera { //! Construct an LTPspecies object for a liquid tranport property. /*! - * The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + * The species transport property is constructed from the XML node, + * \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node in the species block and specifies a type of transport + * property (like viscosity) + * + * @param propNode Pointer to the XML node that contains the property information. A default + * value of 0 is allowed for the base class, but not for classes which + * are assumed to be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. */ - LTPspecies(const XML_Node &propNode = 0, - std::string name = "-", - TransportPropertyType tp_ind = TP_UNKNOWN, - const thermo_t* const thermo = 0) : - m_speciesName(name), - m_model(LTR_MODEL_NOTSET), - m_property(tp_ind), - m_thermo(thermo), - m_mixWeight(1.0) - { - if (propNode.hasChild("mixtureWeighting") ) { - m_mixWeight = getFloat(propNode, "mixtureWeighting"); - } - } + LTPspecies(const XML_Node * const propNode = 0, std::string name = "-", + TransportPropertyType tp_ind = TP_UNKNOWN, const thermo_t* const thermo = 0); //! Copy constructor + /*! + * @param right Object to be copied + */ LTPspecies(const LTPspecies &right); //! Assignment operator - LTPspecies& operator=(const LTPspecies& right); + /*! + * @param right Object to be copied + */ + LTPspecies& operator=(const LTPspecies& right); - virtual ~LTPspecies( ) { } + //! Destructor + virtual ~LTPspecies(); - //! duplication routine + //! Duplication routine /*! * @return Returns a copy of this routine as a pointer to LTPspecies */ @@ -127,17 +130,36 @@ namespace Cantera { * The pure species transport property (i.e. pure species viscosity) * is returned. Any temperature and composition dependence will be * adjusted internally according to the information provided by the - * subclass object. + * subclass object. + * + * @return Returns a single double containing the property evaluation + * at the current ThermoPhase temperature. */ - virtual doublereal getSpeciesTransProp( ) { return 0.0; } + virtual doublereal getSpeciesTransProp(); - virtual bool checkPositive( ) { return ( m_coeffs[0] > 0 ); } + //! Check to see if the property evaluation will be positive + /*! + * @return returns a boolean + */ + virtual bool checkPositive() const; - doublereal getMixWeight( ) { - return m_mixWeight; - } + //! return the weight mixture + /*! + * @return returns a single double which is used as a weight + */ + doublereal getMixWeight() const; + + private: + //! Internal model to adjust species-specific properties for composition. + /*! + * Currently just a place holder, but this method could take + * the composition from the thermo object and adjust coefficients + * accoding to some unspecified model. + */ + virtual void adjustCoeffsForComposition(); protected: + //! Species Name std::string m_speciesName; @@ -166,17 +188,8 @@ namespace Cantera { * 1.0--note that 0.0 is not innocuous if there are logarithms involved. */ doublereal m_mixWeight; - - //! Internal model to adjust species-specific properties for composition. - /*! - * Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - virtual void adjustCoeffsForComposition() { } }; - //==================================================================================================================== //! Class LTPspecies_Const holds transport parameters for a //! specific liquid-phase species (LTPspecies) when the @@ -206,20 +219,32 @@ namespace Cantera { /** The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + * transport property (like viscosity). + * + * + * @param propNode Reference to the XML node that contains the property information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. */ - LTPspecies_Const(const XML_Node &propNode, - std::string name, - TransportPropertyType tp_ind, - thermo_t* thermo); + LTPspecies_Const(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, const thermo_t * const thermo); //! Copy constructor + /*! + * @param right Object to be copied + */ LTPspecies_Const(const LTPspecies_Const &right); //! Assignment operator - LTPspecies_Const& operator=(const LTPspecies_Const& right ); + /*! + * @param right Object to be copied + */ + LTPspecies_Const& operator=(const LTPspecies_Const& right); - virtual ~LTPspecies_Const( ) { } + //! Destructor + virtual ~LTPspecies_Const(); //! duplication routine /*! @@ -233,16 +258,8 @@ namespace Cantera { * is returned. Any temperature and composition dependence will be * adjusted internally according to the information provided. */ - doublereal getSpeciesTransProp( ); + doublereal getSpeciesTransProp(); - protected: - - //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ) { } }; //==================================================================================================================== @@ -295,7 +312,7 @@ namespace Cantera { LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ); //! Assignment operator - LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right ); + LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right); virtual ~LTPspecies_Arrhenius( ) { } @@ -326,7 +343,7 @@ namespace Cantera { * Any temperature and composition dependence will be * adjusted internally according to the information provided. */ - doublereal getSpeciesTransProp( ); + doublereal getSpeciesTransProp(); protected: @@ -341,14 +358,6 @@ namespace Cantera { //! logarithm of most recent evaluation of transport property doublereal m_logProp; - - //! Internal model to adjust species-specific properties for composition. - /*! - * Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ) { } }; //==================================================================================================================== @@ -399,7 +408,8 @@ namespace Cantera { //! Assignment operator LTPspecies_Poly& operator=(const LTPspecies_Poly& right ); - virtual ~LTPspecies_Poly( ) { } + //! Destructor + virtual ~LTPspecies_Poly() { } //! Duplication routine /*! @@ -413,7 +423,7 @@ namespace Cantera { * is returned. Any temperature and composition dependence will be * adjusted internally according to the information provided. */ - doublereal getSpeciesTransProp( ); + doublereal getSpeciesTransProp(); protected: @@ -423,13 +433,6 @@ namespace Cantera { //! most recent evaluation of transport property doublereal m_prop; - //! Internal model to adjust species-specific properties for composition. - /*! - * Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ){ } }; //==================================================================================================================== @@ -485,7 +488,7 @@ namespace Cantera { //! Assignment operator LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); - virtual ~LTPspecies_ExpT( ) { } + virtual ~LTPspecies_ExpT() { } //! duplication routine /*! @@ -499,7 +502,7 @@ namespace Cantera { * is returned. Any temperature and composition dependence will be * adjusted internally according to the information provided. */ - doublereal getSpeciesTransProp( ); + doublereal getSpeciesTransProp(); protected: @@ -509,12 +512,6 @@ namespace Cantera { //! most recent evaluation of transport property doublereal m_prop; - //! Internal model to adjust species-specific properties for composition. - /** Currently just a place holder, but this method could take - * the composition from the thermo object and adjust coefficients - * accoding to some unspecified model. - */ - void adjustCoeffsForComposition( ){ } }; //==================================================================================================================== diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index b87cdad0c..79b07a415 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -323,7 +323,7 @@ namespace Cantera { break; default: throw CanteraError("newLTP","unknown transport model: " + model); - ltps = new LTPspecies(trNode, name, tp_ind, thermo); + ltps = new LTPspecies(&trNode, name, tp_ind, thermo); } return ltps; } From 83d0bbf7c7505deca38bf0051af74488fbe30da1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 19:25:53 +0000 Subject: [PATCH 244/446] doxygen update --- Cantera/src/base/ctml.cpp | 31 +++++++++++++------------------ Cantera/src/base/ctml.h | 6 ++---- 2 files changed, 15 insertions(+), 22 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 8d20215dc..0ed75a220 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -959,7 +959,7 @@ namespace ctml { * * @note change the v to a std::vector to eliminate a doxygen error. No idea why doxygen needs this. */ - int getFloatArray(const Cantera::XML_Node& node, std::vector &v, + int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp & v, const bool convert, const std::string unitsString, const std::string nodeName) { std::string::size_type icom; @@ -1294,26 +1294,27 @@ namespace ctml { * separating each field. * If the node array has an units attribute field, then * the units are used to convert the floats, iff convert is true. + * This function is a wrapper around the function getFloatArray(). * * Example: * * Code snipet: - * @verbatum + * @verbatim const XML_Node &State_XMLNode; vector_fp v; bool convert = true; unitsString = ""; nodeName="floatArray"; getFloatArray(State_XMLNode, v, convert, unitsString, nodeName); - @endverbatum + @endverbatim * * reads the corresponding XML file: * - * @verbatum + * @verbatim 32.4, 1, 100. <\floatArray> <\state> - @endverbatum + @endverbatim * * Will produce the vector * @@ -1323,21 +1324,15 @@ namespace ctml { * * * @param node XML parent node of the floatArray - * @param v Output vector of floats containing the floatArray information. - * @param convert Conversion to SI is carried out if this boolean is - * True. The default is true. - * @param typeString String name of the type attribute. This is an optional - * parameter. The default is to have an empty string. - * The only string that is recognized is actEnergy. - * Anything else has no effect. This affects what - * units converter is used. - * @param nodeName XML Name of the XML node to read. - * The default value for the node name is floatArray - * - * @note change the coeffs to a std::vector to eliminate a doxygen error. No idea why doxygen needs this. + * @param typeString Returns the type attribute of the current node. + * @param xmin Returns the minimum value attribute of the + * current node. + * @param xmax Returns the maximum value attribute of the + * current node. + * @param coeffs Output vector of floats containing the floatArray information. */ void getFunction(const Cantera::XML_Node& node, std::string& type, doublereal& xmin, - doublereal& xmax, std::vector< double > & coeffs) { + doublereal& xmax, Cantera::vector_fp & coeffs) { const XML_Node& c = node.child("floatArray"); coeffs.clear(); getFloatArray(c,coeffs); diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 2febcfa31..de39776a6 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -833,12 +833,10 @@ namespace ctml { * current node. * @param xmax Returns the maximum value attribute of the * current node. - * @param v Output vector of floats containing the floatArray - * information. + * @param coeffs Output vector of floats containing the floatArray information. */ void getFunction(const Cantera::XML_Node& node, std::string& typeString, - doublereal& xmin, doublereal& xmax, Cantera::vector_fp& v); - + doublereal& xmin, doublereal& xmax, Cantera::vector_fp & coeffs); //! Search the child nodes of the current node for an XML Node with a Title //! attribute of a given name. From cd9262501acfae87a0a8cb8e65326e7e7e56684a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 19:30:17 +0000 Subject: [PATCH 245/446] Added some files. --- docs/Cantera.cfg.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index 0c2278db3..44d5e82fc 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -772,6 +772,8 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ MMCollisionInt.cpp \ TransportFactory.h \ TransportFactory.cpp \ + LTPspecies.h \ + LTPspecies.cpp \ MultiTransport.h \ MultiTransport.cpp \ MixTransport.h \ From afd51b53e3bdec4edb05919f5a43539a7b4fa021 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 20:53:35 +0000 Subject: [PATCH 246/446] Added an include for 4.4.4 support --- Cantera/src/base/Array.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Cantera/src/base/Array.h b/Cantera/src/base/Array.h index a0c637db5..a81864175 100644 --- a/Cantera/src/base/Array.h +++ b/Cantera/src/base/Array.h @@ -19,6 +19,8 @@ #include "ctexceptions.h" #include "utilities.h" +#include + namespace Cantera { From d6fbf98862f80c26f6e1be66a409acedfde7806d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Aug 2010 22:15:17 +0000 Subject: [PATCH 247/446] Added a gcc4.4.4. compile example --- .../linux.64_sierra_gcc444_python264_numpy | 112 ++++++++++++++++++ .../linux_rhel5_64_gcc424_dbg_python264_numpy | 6 +- .../mac_gcc401_python251_numpy | 4 +- 3 files changed, 117 insertions(+), 5 deletions(-) create mode 100755 docs/install_examples/linux.64_sierra_gcc444_python264_numpy diff --git a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy new file mode 100755 index 000000000..dc66fcce8 --- /dev/null +++ b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy @@ -0,0 +1,112 @@ +#!/bin/sh +# +# This is currently the test base. Meaning that the blessed versions +# of all test problems are created from this configuration. +# +CANTERA_CONFIG_PREFIX=${HOME}/arch/linux64_gcc444/cantera-1.8_liquidTransportDevelop +export CANTERA_CONFIG_PREFIX + +SET_PYTHON_SITE_PACKAGE_TOPDIR=y +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_CMD=${HOME}/arch/linux64_gcc444/python-2.6.4/bin/python +export PYTHON_CMD + +PYTHON_PACKAGE='full' +#PYTHON_PACKAGE='minimal' +export PYTHON_PACKAGE + +DEBUG_MODE='y' +export DEBUG_MODE + +WITH_IDEAL_SOLUTIONS="y" +export WITH_IDEAL_SOLUTIONS + +WITH_ELECTROLYTES="y" +export WITH_ELECTROLYTES + +WITH_VCSNONIDEAL="y" +export WITH_VCSNONIDEAL + +WITH_H298MODIFY_CAPABILITY='y' +export WITH_H298MODIFY_CAPABILITY + +BUILD_MATLAB_TOOLBOX="y" +export BUILD_MATLAB_TOOLBOX + +INSTALL_BIN=config/install-sh +export INSTALL_BIN + +MATLAB_CMD="/usr/local/matlab/7.9/bin/matlab" +export MATLAB_CMD + +BUILD_F90_INTERFACE="y" +export BUILD_F90_INTERFACE + +NUMARRAY_HOME='' +export NUMARRAY_HOME + +USE_NUMPY='y' +export USE_NUMPY + +NUMPY_INC_DIR="${HOME}/arch/linux64_gcc444/python-2.6.4/lib/python2.6/site-packages/numpy/core/include" +export NUMPY_INC_DIR + +GRAPHVIZDIR=/usr/netpub/graphviz-2.26.3/bin +export GRAPHVIZDIR + +# +# +USE_NUMERIC="n" +export USE_NUMERIC + +BUILD_WITH_F2C="n" +export BUILD_WITH_F2C + +BITCOMPILE="64" +export BITCOMPILE + +AFLAGS='DEBUG' + +CXX='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/g++' +export CXX + +CXX_DEPENDS='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/g++ -MM' +export CXX_DEPENDS + +CC='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/gcc' +export CC + +F77='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/gfortran' +export F77 + +CFLAGS="-g -Wall" +export CFLAGS + +CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL" +export CXXFLAGS + +FFLAGS="-g -DDEBUG_HKM -fno-second-underscore" +export FFLAGS + +LDFLAGS=' ' +export LDFLAGS + +LCXX_END_LIBS="-lgfortran " +export LCXX_END_LIBS + +EXTRA_LINK=" " +export EXTRA_LINK + +MAKE=gmake +export MAKE + +USE_SUNDIALS='y' +export USE_SUNDIALS +SUNDIALS_HOME="${HOME}/arch/linux64_gcc444/sundials-2.4.0_dbg" +export SUNDIALS_HOME + +./preconfig diff --git a/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy b/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy index f257eac04..a7608e776 100755 --- a/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy +++ b/docs/install_examples/linux_rhel5_64_gcc424_dbg_python264_numpy @@ -12,7 +12,7 @@ export SET_PYTHON_SITE_PACKAGE_TOPDIR PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX export PYTHON_SITE_PACKAGE_TOPDIR -PYTHON_CMD=/home/hkmoffa/arch/linux64_gcc424/python-2.6.4/bin/python +PYTHON_CMD=${HOME}/arch/linux64_gcc424/python-2.6.4/bin/python export PYTHON_CMD PYTHON_PACKAGE='full' @@ -52,7 +52,7 @@ export NUMARRAY_HOME USE_NUMPY='y' export USE_NUMPY -NUMPY_INC_DIR="/home/hkmoffa/arch/linux64_gcc424/python-2.6.4/lib/python2.6/site-packages/numpy/core/include" +NUMPY_INC_DIR="${HOME}/arch/linux64_gcc424/python-2.6.4/lib/python2.6/site-packages/numpy/core/include" export NUMPY_INC_DIR GRAPHVIZDIR=${HOME}'/arch/linux/bin' @@ -106,7 +106,7 @@ export MAKE USE_SUNDIALS='y' export USE_SUNDIALS -SUNDIALS_HOME='/home/hkmoffa/arch/linux64_gcc424/sundials-2.4.0_dbg' +SUNDIALS_HOME="${HOME}/arch/linux64_gcc424/sundials-2.4.0_dbg" export SUNDIALS_HOME ./preconfig diff --git a/docs/install_examples/mac_gcc401_python251_numpy b/docs/install_examples/mac_gcc401_python251_numpy index 3940a8e50..3317d1a4d 100755 --- a/docs/install_examples/mac_gcc401_python251_numpy +++ b/docs/install_examples/mac_gcc401_python251_numpy @@ -46,7 +46,7 @@ export BUILD_F90_INTERFACE USE_NUMPY='y' export USE_NUMPY -NUMPY_INC_DIR="/home/hkmoffa/arch/mac/lib/python2.5/site-packages/numpy/core/include" +NUMPY_INC_DIR="${HOME}/arch/mac/lib/python2.5/site-packages/numpy/core/include" export NUMPY_INC_DIR #GRAPHVIZDIR=${HOME}'/arch/linux/bin' @@ -100,7 +100,7 @@ export MAKE USE_SUNDIALS='n' export USE_SUNDIALS -SUNDIALS_HOME='/home/hkmoffa/arch/linux64/sundials' +SUNDIALS_HOME="${HOME}/arch/linux64/sundials" export SUNDIALS_HOME ./preconfig From 438fea4660566f03a7da816ee83c22b0f6650aed Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 16 Aug 2010 20:01:30 +0000 Subject: [PATCH 248/446] Doxygen update --- Cantera/src/transport/LTPspecies.cpp | 28 ++++++++++++----- Cantera/src/transport/LTPspecies.h | 45 ++++++++++++++++++---------- 2 files changed, 50 insertions(+), 23 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index 2b61d35a7..17c74db7e 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -62,7 +62,7 @@ namespace Cantera { * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. */ LTPspecies::LTPspecies(const XML_Node * const propNode, std::string name, - TransportPropertyType tp_ind, const thermo_t* const thermo) : + TransportPropertyType tp_ind, const thermo_t * thermo) : m_speciesName(name), m_model(LTR_MODEL_NOTSET), m_property(tp_ind), @@ -200,13 +200,22 @@ namespace Cantera { //==================================================================================================================== // Construct an LTPspecies object for a liquid tranport property // expressed in extended Arrhenius form. - /* The transport property is constructed from the XML node, + /* + * The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity) + * + * + * @param propNode Referenc to the XML node that contains the property information.This class + * is assumed to be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + * */ LTPspecies_Arrhenius::LTPspecies_Arrhenius(const XML_Node &propNode, std::string name, - TransportPropertyType tp_ind, thermo_t* thermo) : + TransportPropertyType tp_ind, const thermo_t* thermo) : LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_ARRHENIUS; @@ -251,6 +260,11 @@ namespace Cantera { return *this; } //==================================================================================================================== + // Destructor + LTPspecies_Arrhenius::~LTPspecies_Arrhenius() + { + } + //==================================================================================================================== // Duplication routine /* * @return Returns a copy of this routine as a pointer to LTPspecies @@ -312,7 +326,7 @@ namespace Cantera { * transport property (like viscosity) */ LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, std::string name, - TransportPropertyType tp_ind, thermo_t* thermo) : + TransportPropertyType tp_ind, const thermo_t* thermo) : LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_POLY; @@ -389,7 +403,7 @@ namespace Cantera { * transport property (like viscosity) */ LTPspecies_ExpT::LTPspecies_ExpT(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, - thermo_t* thermo) : + const thermo_t* thermo) : LTPspecies(&propNode, name, tp_ind, thermo) { m_model = LTR_MODEL_EXPT; diff --git a/Cantera/src/transport/LTPspecies.h b/Cantera/src/transport/LTPspecies.h index 9c128f165..b0be5b6f1 100644 --- a/Cantera/src/transport/LTPspecies.h +++ b/Cantera/src/transport/LTPspecies.h @@ -102,7 +102,7 @@ namespace Cantera { * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. */ LTPspecies(const XML_Node * const propNode = 0, std::string name = "-", - TransportPropertyType tp_ind = TP_UNKNOWN, const thermo_t* const thermo = 0); + TransportPropertyType tp_ind = TP_UNKNOWN, const thermo_t* thermo = 0); //! Copy constructor /*! @@ -300,21 +300,34 @@ namespace Cantera { /*! * The transport property is constructed from the XML node, * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity) + * + * + * @param propNode Referenc to the XML node that contains the property information.This class + * is assumed to be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + * */ - LTPspecies_Arrhenius( const XML_Node &propNode, - std::string name, - TransportPropertyType tp_ind, - thermo_t* thermo ); + LTPspecies_Arrhenius(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, const thermo_t * thermo); //! Copy constructor - LTPspecies_Arrhenius( const LTPspecies_Arrhenius &right ); + /*! + * @param Object to be copied + */ + LTPspecies_Arrhenius(const LTPspecies_Arrhenius &right); //! Assignment operator - LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right); + /*! + * @param Object to be copied + */ + LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right); - virtual ~LTPspecies_Arrhenius( ) { } + //! Destructor + virtual ~LTPspecies_Arrhenius(); //! duplication routine /*! @@ -397,16 +410,16 @@ namespace Cantera { * \verbatim \endverbatim node and specifies a type of * transport property (like viscosity) */ - LTPspecies_Poly( const XML_Node &propNode, + LTPspecies_Poly(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, - thermo_t* thermo ); + const thermo_t * thermo); //! Copy constructor - LTPspecies_Poly( const LTPspecies_Poly &right ); + LTPspecies_Poly(const LTPspecies_Poly &right); //! Assignment operator - LTPspecies_Poly& operator=(const LTPspecies_Poly& right ); + LTPspecies_Poly& operator=(const LTPspecies_Poly& right); //! Destructor virtual ~LTPspecies_Poly() { } @@ -477,7 +490,7 @@ namespace Cantera { LTPspecies_ExpT(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, - thermo_t* thermo ); + const thermo_t* thermo); //! Copy constructor /*! @@ -486,7 +499,7 @@ namespace Cantera { LTPspecies_ExpT(const LTPspecies_ExpT &right); //! Assignment operator - LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right ); + LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right); virtual ~LTPspecies_ExpT() { } From 36e90d5df59edb398657af2f8e3b28c7f7a4c2e4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 17 Aug 2010 00:58:23 +0000 Subject: [PATCH 249/446] Changed the enum name Liquid_TR_Model to LTPTemperatureDepencenceType doxygen update --- Cantera/src/transport/LTPspecies.cpp | 148 ++++++++++----------- Cantera/src/transport/LTPspecies.h | 104 +++++++++------ Cantera/src/transport/TransportFactory.cpp | 20 +-- Cantera/src/transport/TransportFactory.h | 2 +- 4 files changed, 141 insertions(+), 133 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index 17c74db7e..7ca7704b5 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -8,22 +8,23 @@ * $Revision: 427 $ * */ - #include "LTPspecies.h" using namespace std; namespace Cantera { - //==================================================================================================================== - /* - * Exception thrown if an error is encountered while reading the transport database. - */ + //! Exception thrown if an error is encountered while reading the transport database. class LTPError : public CanteraError { public: - LTPError(std::string msg) - : CanteraError("LTPspecies", - "error parsing transport data: " - + msg + "\n") {} + + //! Constructor is a wrapper around CanteraError + /*! + * @param msg Informative message + */ + LTPError(std::string msg) : + CanteraError("LTPspecies", "error parsing transport data: " + msg + "\n") + { + } }; //==================================================================================================================== //! getArrhenius() parses the xml element called Arrhenius. @@ -64,7 +65,7 @@ namespace Cantera { LTPspecies::LTPspecies(const XML_Node * const propNode, std::string name, TransportPropertyType tp_ind, const thermo_t * thermo) : m_speciesName(name), - m_model(LTR_MODEL_NOTSET), + m_model(LTP_TD_NOTSET), m_property(tp_ind), m_thermo(thermo), m_mixWeight(1.0) @@ -79,7 +80,7 @@ namespace Cantera { // Copy constructor LTPspecies::LTPspecies(const LTPspecies &right) { - *this = right; //use assignment operator to do other work + *this = right; } //==================================================================================================================== // Assignment operator @@ -154,7 +155,7 @@ namespace Cantera { TransportPropertyType tp_ind, const thermo_t * const thermo) : LTPspecies(&propNode, name, tp_ind, thermo) { - m_model = LTR_MODEL_CONSTANT; + m_model = LTP_TD_CONSTANT; double A_k = getFloatCurrent(propNode, "toSI"); if (A_k > 0.0) { m_coeffs.push_back(A_k); @@ -218,7 +219,7 @@ namespace Cantera { TransportPropertyType tp_ind, const thermo_t* thermo) : LTPspecies(&propNode, name, tp_ind, thermo) { - m_model = LTR_MODEL_ARRHENIUS; + m_model = LTP_TD_ARRHENIUS; m_temp = 0.0; m_prop = 0.0; @@ -237,21 +238,14 @@ namespace Cantera { LTPspecies_Arrhenius::LTPspecies_Arrhenius(const LTPspecies_Arrhenius &right) : LTPspecies() { - *this = right; //use assignment operator to do other work + *this = right; } //==================================================================================================================== // Assignment operator LTPspecies_Arrhenius& LTPspecies_Arrhenius::operator=(const LTPspecies_Arrhenius& right) { if (&right != this) { - // LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - + LTPspecies::operator=(right); m_temp = right.m_temp; m_logt = right.m_logt; m_prop = right.m_prop; @@ -318,54 +312,52 @@ namespace Cantera { return m_prop; } //==================================================================================================================== - // Construct an LTPspecies object for a liquid tranport property - // expressed as a polynomial in temperature. - /* The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) + // Construct an LTPspecies object for a liquid tranport property expressed as a polynomial in temperature. + /* + * The transport property is constructed from the XML node, \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity). + * + * + * @param propNode Referenc to the XML node that contains the property information. This class + * must be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + * */ LTPspecies_Poly::LTPspecies_Poly(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, const thermo_t* thermo) : - LTPspecies(&propNode, name, tp_ind, thermo) + LTPspecies(&propNode, name, tp_ind, thermo), + m_temp(-1.0), + m_prop(0.0) { - m_model = LTR_MODEL_POLY; - m_temp = 0.0; - m_prop = 0.0; - - + m_model = LTP_TD_POLY; getFloatArray(propNode, m_coeffs, "true", "toSI"); - - /* if (m_coeffs[0] <= 0.0) { - throw LTPError("negative or zero " + propNode.name()); - }*/ } //==================================================================================================================== // Copy constructor LTPspecies_Poly::LTPspecies_Poly(const LTPspecies_Poly &right) : LTPspecies() { - *this = right; //use assignment operator to do other work + *this = right; } //==================================================================================================================== // Assignment operator LTPspecies_Poly& LTPspecies_Poly::operator=(const LTPspecies_Poly& right) { if (&right != this) { - //LTPspecies::operator=(right); - m_speciesName = right.m_speciesName; - m_property = right.m_property; - m_model = right.m_model; - m_coeffs = right.m_coeffs; - m_thermo = right.m_thermo; - m_mixWeight = right.m_mixWeight; - + LTPspecies::operator=(right); m_temp = right.m_temp; m_prop = right.m_prop; } return *this; } //==================================================================================================================== + LTPspecies_Poly::~LTPspecies_Poly() + { + } + //==================================================================================================================== // Duplication routine /* * @return Returns a copy of this routine as a pointer to LTPspecies @@ -376,44 +368,44 @@ namespace Cantera { return (dynamic_cast(prp)); } //==================================================================================================================== - // Return the value for this transport property evaluated - // from the polynomial expression + // Return the value for this transport property evaluated from the polynomial expression doublereal LTPspecies_Poly::getSpeciesTransProp() { - doublereal t = m_thermo->temperature(); if (t != m_temp) { - m_prop = 0; - m_temp=t; + m_prop = 0.0; + m_temp = t; double tempN = 1.0; for (int i = 0; i < (int) m_coeffs.size() ; i++) { m_prop += m_coeffs[i] * tempN; - //cout << "m_coeff = " <temperature(); if (t != m_temp) { - m_prop = 0.0; m_temp=t; - m_prop=m_coeffs[0]; - double tempN = 1.0; + m_prop = m_coeffs[0]; + doublereal tempN = 1.0; + doublereal tmp = 0.0; for (int i = 1; i < (int) m_coeffs.size() ; i++) { tempN *= m_temp; - m_prop *= exp(m_coeffs[i] * tempN); + tmp += m_coeffs[i] * tempN; } + m_prop *= exp(tmp); } - //cout << "m_prop = " << m_prop << endl; return m_prop; } //==================================================================================================================== diff --git a/Cantera/src/transport/LTPspecies.h b/Cantera/src/transport/LTPspecies.h index b0be5b6f1..d8945af6d 100644 --- a/Cantera/src/transport/LTPspecies.h +++ b/Cantera/src/transport/LTPspecies.h @@ -61,13 +61,14 @@ namespace Cantera { * 0 - Independent of temperature * 1 - extended arrhenius form * 2 - polynomial in temperature form + * 3 - exponential temperature polynomial */ - enum LiquidTR_Model { - LTR_MODEL_NOTSET=-1, - LTR_MODEL_CONSTANT, - LTR_MODEL_ARRHENIUS, - LTR_MODEL_POLY, - LTR_MODEL_EXPT + enum LTPTemperatureDependenceType { + LTP_TD_NOTSET=-1, + LTP_TD_CONSTANT, + LTP_TD_ARRHENIUS, + LTP_TD_POLY, + LTP_TD_EXPT }; //==================================================================================================================== @@ -139,13 +140,13 @@ namespace Cantera { //! Check to see if the property evaluation will be positive /*! - * @return returns a boolean + * @return Returns a boolean */ virtual bool checkPositive() const; - //! return the weight mixture + //! Return the weight mixture /*! - * @return returns a single double which is used as a weight + * @return Returns a single double which is used as a weight */ doublereal getMixWeight() const; @@ -164,7 +165,7 @@ namespace Cantera { std::string m_speciesName; //! Model type for the temperature dependence - LiquidTR_Model m_model; + LTPTemperatureDependenceType m_model; //! enum indicating which property this is (i.e viscosity) TransportPropertyType m_property; @@ -291,7 +292,7 @@ namespace Cantera { * * \endverbatim */ - class LTPspecies_Arrhenius : public LTPspecies{ + class LTPspecies_Arrhenius : public LTPspecies { public: @@ -316,13 +317,13 @@ namespace Cantera { //! Copy constructor /*! - * @param Object to be copied + * @param right Object to be copied */ LTPspecies_Arrhenius(const LTPspecies_Arrhenius &right); //! Assignment operator /*! - * @param Object to be copied + * @param right Object to be copied */ LTPspecies_Arrhenius& operator=(const LTPspecies_Arrhenius& right); @@ -403,26 +404,36 @@ namespace Cantera { public: - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as a polynomial in temperature. - /** The transport property is constructed from the XML node, - * \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of - * transport property (like viscosity) - */ - LTPspecies_Poly(const XML_Node &propNode, - std::string name, - TransportPropertyType tp_ind, - const thermo_t * thermo); + //! Construct an LTPspecies object for a liquid tranport property expressed as a polynomial in temperature. + /*! + * The transport property is constructed from the XML node, \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity). + * + * + * @param propNode Referenc to the XML node that contains the property information. This class + * must be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + * + */ + LTPspecies_Poly(const XML_Node &propNode, std::string name, TransportPropertyType tp_ind, const thermo_t * thermo); //! Copy constructor + /*! + * @param right Object to be copied + */ LTPspecies_Poly(const LTPspecies_Poly &right); //! Assignment operator - LTPspecies_Poly& operator=(const LTPspecies_Poly& right); + /*! + * @param right Object to be copied + */ + LTPspecies_Poly& operator=(const LTPspecies_Poly& right); //! Destructor - virtual ~LTPspecies_Poly() { } + virtual ~LTPspecies_Poly(); //! Duplication routine /*! @@ -450,8 +461,8 @@ namespace Cantera { //==================================================================================================================== //! Class LTPspecies_ExpT holds transport parameters for a specific liquid-phase species (LTPspecies) - //! when the transport property is expressed as a exponential in temperature. - /** + //! when the transport property is expressed as an exponential in temperature. + /*! * Used for pure species properties with equations of the form * * \f[ @@ -479,18 +490,23 @@ namespace Cantera { public: - //! Construct an LTPspecies object for a liquid tranport property - //! expressed as an exponential in temperature. - /*! - * The transport property is constructed from the XML node, \verbatim , \endverbatim that is a child of the - * \verbatim \endverbatim node and specifies a type of transport property (like viscosity). - * - * @param propNode - */ - LTPspecies_ExpT(const XML_Node &propNode, - std::string name, - TransportPropertyType tp_ind, - const thermo_t* thermo); + //! Construct an LTPspecies object for a liquid tranport property + //! expressed as an exponential in temperature. + /*! + * The transport property is constructed from the XML node, \verbatim , \endverbatim that is a child of the + * \verbatim \endverbatim node and specifies a type of transport property (like viscosity). + * + * + * @param propNode Referenc to the XML node that contains the property information. This class + * must be parameterized by reading XML_Node information. + * @param name String containing the species name + * @param tp_ind enum TransportPropertyType containing the property id that this object + * is creating a parameterization for (e.g., viscosity) + * @param thermo const pointer to the ThermoPhase object, which is used to find the temperature. + * + */ + LTPspecies_ExpT(const XML_Node &propNode, std::string name, + TransportPropertyType tp_ind, const thermo_t* thermo); //! Copy constructor /*! @@ -499,11 +515,15 @@ namespace Cantera { LTPspecies_ExpT(const LTPspecies_ExpT &right); //! Assignment operator + /*! + * @param right Object to be copied + */ LTPspecies_ExpT& operator=(const LTPspecies_ExpT& right); - virtual ~LTPspecies_ExpT() { } + //! Destructor + virtual ~LTPspecies_ExpT(); - //! duplication routine + //! Duplication routine /*! * @return Returns a copy of this routine as a pointer to LTPspecies */ diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 79b07a415..4ddb1ce7a 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -253,11 +253,11 @@ namespace Cantera { m_tranPropMap["hydrodynamicRadius"] = TP_HYDRORADIUS; m_tranPropMap["electricalConductivity"] = TP_ELECTCOND; - m_LTRmodelMap[""] = LTR_MODEL_CONSTANT; - m_LTRmodelMap["constant"] = LTR_MODEL_CONSTANT; - m_LTRmodelMap["arrhenius"] = LTR_MODEL_ARRHENIUS; - m_LTRmodelMap["coeffs"] = LTR_MODEL_POLY; - m_LTRmodelMap["exptemp"] = LTR_MODEL_EXPT; + m_LTRmodelMap[""] = LTP_TD_CONSTANT; + m_LTRmodelMap["constant"] = LTP_TD_CONSTANT; + m_LTRmodelMap["arrhenius"] = LTP_TD_ARRHENIUS; + m_LTRmodelMap["coeffs"] = LTP_TD_POLY; + m_LTRmodelMap["exptemp"] = LTP_TD_EXPT; m_LTImodelMap[""] = LTI_MODEL_NOTSET; m_LTImodelMap["none"] = LTI_MODEL_NONE; @@ -309,16 +309,16 @@ namespace Cantera { LTPspecies* ltps = 0; std::string model = lowercase(trNode["model"]); switch (m_LTRmodelMap[model]) { - case LTR_MODEL_CONSTANT: + case LTP_TD_CONSTANT: ltps = new LTPspecies_Const(trNode, name, tp_ind, thermo); break; - case LTR_MODEL_ARRHENIUS: + case LTP_TD_ARRHENIUS: ltps = new LTPspecies_Arrhenius(trNode, name, tp_ind, thermo); break; - case LTR_MODEL_POLY: + case LTP_TD_POLY: ltps = new LTPspecies_Poly(trNode, name, tp_ind, thermo); break; - case LTR_MODEL_EXPT: + case LTP_TD_EXPT: ltps = new LTPspecies_ExpT(trNode, name, tp_ind, thermo); break; default: @@ -1202,7 +1202,7 @@ namespace Cantera { else if (trParam.thermo->speciesIndex(velocityBasis) > 0) trParam.velocityBasis_ = trParam.thermo->speciesIndex(velocityBasis) ; else { - int linenum; + int linenum = __LINE__; throw TransportDBError(linenum, "Unknown attribute \"" + velocityBasis + "\" for node. "); } } diff --git a/Cantera/src/transport/TransportFactory.h b/Cantera/src/transport/TransportFactory.h index ec6ccd973..d69e9519a 100644 --- a/Cantera/src/transport/TransportFactory.h +++ b/Cantera/src/transport/TransportFactory.h @@ -448,7 +448,7 @@ namespace Cantera { //! Mapping between between the string name for a //! species-specific transport property model and the integer name. - std::map m_LTRmodelMap; + std::map m_LTRmodelMap; //! Mapping between between the string name for a //! liquid mixture transport property model and the integer name. From f525d742f3c12f900a4703cd6b38ad0ced0a053f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 17 Aug 2010 01:04:55 +0000 Subject: [PATCH 250/446] Added keywords control --- Cantera/src/transport/LTPspecies.cpp | 6 +++--- Cantera/src/transport/LTPspecies.h | 6 +++--- Cantera/src/transport/LiquidTranInteraction.cpp | 6 +++--- Cantera/src/transport/TransportParams.cpp | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index 7ca7704b5..aa8f8dbb2 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -3,9 +3,9 @@ * Source code for liquid transport property evaluations. */ /* - * $Author: christopher.lueth@gmail.com $ - * $Date: 2010-03-30 12:30:39 -0600 (Tue, 30 Mar 2010) $ - * $Revision: 427 $ + * $Author$ + * $Date$ + * $Revision$ * */ #include "LTPspecies.h" diff --git a/Cantera/src/transport/LTPspecies.h b/Cantera/src/transport/LTPspecies.h index d8945af6d..008a07263 100644 --- a/Cantera/src/transport/LTPspecies.h +++ b/Cantera/src/transport/LTPspecies.h @@ -3,9 +3,9 @@ * Header file defining class LTPspecies and its child classes */ /* - * $Author: christopher.lueth@gmail.com $ - * $Date: 2010-03-30 12:30:39 -0600 (Tue, 30 Mar 2010) $ - * $Revision: 427 $ + * $Author$ + * $Date$ + * $Revision$ */ diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index 282e8edeb..f6c0ae203 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -4,9 +4,9 @@ */ /* * Latest Checkin: - * $Author: hkmoffa $ - * $Date: 2010-04-02 11:40:52 -0600 (Fri, 02 Apr 2010) $ - * $Revision: 429 $ + * $Author$ + * $Date$ + * $Revision$ */ #include "LiquidTransportParams.h" diff --git a/Cantera/src/transport/TransportParams.cpp b/Cantera/src/transport/TransportParams.cpp index 330d6266b..a3e57b86d 100644 --- a/Cantera/src/transport/TransportParams.cpp +++ b/Cantera/src/transport/TransportParams.cpp @@ -6,9 +6,9 @@ */ /* * Latest Checkin: - * $Author: hkmoffa $ - * $Date: 2010-04-02 11:40:52 -0600 (Fri, 02 Apr 2010) $ - * $Revision: 429 $ + * $Author$ + * $Date$ + * $Revision$ */ #include "TransportParams.h" From 6d766926bdd1e1feb1dc7e5ef5dd42704976765e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 17 Aug 2010 22:48:59 +0000 Subject: [PATCH 251/446] Updated this object Put in the standard copy constructors and assignment operators Started documenting it. --- Cantera/src/transport/DustyGasTransport.cpp | 511 ++++++++++++-------- Cantera/src/transport/DustyGasTransport.h | 161 ++++-- 2 files changed, 432 insertions(+), 240 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index fee667dde..bca1e6de3 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -38,221 +38,332 @@ using namespace std; namespace Cantera { - - //////////////////// class DustyGasTransport methods ////////////// - - - DustyGasTransport::DustyGasTransport(thermo_t* thermo) - : Transport(thermo), - m_temp(-1.0), - m_porosity(0.0), - m_tortuosity(1.0), - m_pore_radius(0.0), - m_diam(0.0), - m_perm(-1.0), - m_gastran(0) - {} - - void DustyGasTransport::setParameters(const int type, const int k, const doublereal* const p) { - switch(type) { - case 0: - setPorosity(p[0]); break; - case 1: - setTortuosity(p[0]); break; - case 2: - setMeanPoreRadius(p[0]); break; - case 3: - setMeanParticleDiameter(p[0]); break; - case 4: - setPermeability(p[0]); break; - default: - throw CanteraError("DustyGasTransport::init", - "unknown parameter"); - } - } - - void DustyGasTransport::initialize(ThermoPhase* phase, Transport* gastr) { - - // constant mixture attributes - m_thermo = phase; - m_nsp = m_thermo->nSpecies(); - m_tmin = m_thermo->minTemp(); - m_tmax = m_thermo->maxTemp(); - - m_gastran = gastr; - - // make a local copy of the molecular weights - m_mw.resize(m_nsp); - copy(m_thermo->molecularWeights().begin(), - m_thermo->molecularWeights().end(), m_mw.begin()); - - m_multidiff.resize(m_nsp, m_nsp); - m_d.resize(m_nsp, m_nsp); - m_dk.resize(m_nsp, 0.0); - m_x.resize(m_nsp); - //m_gradConc.resize(m_nsp); - //m_conc.resize(m_nsp); - - // set flags all false - m_knudsen_ok = false; - m_bulk_ok = false; - - // some work space - m_spwork.resize(m_nsp); - m_spwork2.resize(m_nsp); + //==================================================================================================================== + DustyGasTransport::DustyGasTransport(thermo_t* thermo) : + Transport(thermo), + m_nsp(0), + m_tmin(0.0), + m_tmax(1.0E300), + m_mw(0), + m_dk(0), + m_temp(-1.0), + m_multidiff(0,0), + m_spwork(0), + m_spwork2(0), + m_gradP(0.0), + m_knudsen_ok(false), + m_bulk_ok(false), + m_conc_set(false), + m_gradConc_set(false), + m_gradP_set(false), + m_porosity(0.0), + m_tortuosity(1.0), + m_pore_radius(0.0), + m_diam(0.0), + m_perm(-1.0), + m_gastran(0) + { + } + //==================================================================================================================== + DustyGasTransport::DustyGasTransport(const DustyGasTransport &right) : + Transport(), + m_nsp(0), + m_tmin(0.0), + m_tmax(1.0E300), + m_mw(0), + m_dk(0), + m_temp(-1.0), + m_multidiff(0,0), + m_spwork(0), + m_spwork2(0), + m_gradP(0.0), + m_knudsen_ok(false), + m_bulk_ok(false), + m_conc_set(false), + m_gradConc_set(false), + m_gradP_set(false), + m_porosity(0.0), + m_tortuosity(1.0), + m_pore_radius(0.0), + m_diam(0.0), + m_perm(-1.0), + m_gastran(0) + { + *this = right; + } + //==================================================================================================================== + // Assignment operator + /* + * This is NOT a virtual function. + * + * @param right Reference to %DustyGasTransport object to be copied + * into the current one. + */ + DustyGasTransport& DustyGasTransport::operator=(const DustyGasTransport& right) + { + if (&right == this) { + return *this; } + Transport::operator=(right); + m_nsp = right.m_nsp; + m_tmin = right.m_tmin; + m_tmax = right.m_tmax; + m_mw = right.m_mw; + m_d = right.m_d; + m_x = right.m_x; + m_dk = right.m_dk; + m_temp = m_temp; + m_multidiff = right.m_multidiff; + m_spwork = right.m_spwork; + m_spwork2 = right.m_spwork2; + m_gradP = right.m_gradP; + m_knudsen_ok = right.m_knudsen_ok; + m_bulk_ok= right.m_bulk_ok; + m_conc_set = right.m_conc_set; + m_gradConc_set = right.m_gradConc_set; + m_gradP_set = right.m_gradP_set; + m_porosity = right.m_porosity; + m_tortuosity = right.m_tortuosity; + m_pore_radius = right.m_pore_radius; + m_diam = right.m_diam; + m_perm = right.m_perm; - /******************* binary diffusion coefficients **************/ + // Warning -> This is a shallow pointer copy. gastran may not point to the correct object + // after this copy. The routine initialize() must be called + m_gastran = right.m_gastran; - - void DustyGasTransport::updateBinaryDiffCoeffs() { - if (m_bulk_ok) return; - int n,m; - - // get the gaseous binary diffusion coefficients - m_gastran->getBinaryDiffCoeffs(m_nsp, m_d.ptrColumn(0)); - doublereal por2tort = m_porosity / m_tortuosity; - for (n = 0; n < m_nsp; n++) - for (m = 0; m < m_nsp; m++) - m_d(n,m) *= por2tort; - m_bulk_ok = true; + return *this; + } + //==================================================================================================================== + DustyGasTransport::~DustyGasTransport() { + } + //==================================================================================================================== + // Duplication routine for objects which inherit from %Transport + /* + * This virtual routine can be used to duplicate %Transport objects + * inherited from %Transport even if the application only has + * a pointer to %Transport to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + */ + Transport *DustyGasTransport::duplMyselfAsTransport() const { + DustyGasTransport* tr = new DustyGasTransport(*this); + return (dynamic_cast(tr)); + } + //==================================================================================================================== + void DustyGasTransport::setParameters(const int type, const int k, const doublereal* const p) { + switch(type) { + case 0: + setPorosity(p[0]); break; + case 1: + setTortuosity(p[0]); break; + case 2: + setMeanPoreRadius(p[0]); break; + case 3: + setMeanParticleDiameter(p[0]); break; + case 4: + setPermeability(p[0]); break; + default: + throw CanteraError("DustyGasTransport::init", + "unknown parameter"); } + } + //==================================================================================================================== + // Initialization routine called by TransportFactory + /* + * The DustyGas model is a subordinate model to the gas phase transport model. Here we + * set the gas phase models. + * + * This is a protected routine, so that initialiation of the Model must occur within Cantera's setup + * + * @param phase Pointer to the underlying ThermoPhase model for the gas phase + * @param gastr Pointer to the underlying Transport model for transport in the gas phse. + */ + void DustyGasTransport::initialize(ThermoPhase* phase, Transport* gastr) { - void DustyGasTransport::updateKnudsenDiffCoeffs() { - if (m_knudsen_ok) return; - doublereal K_g = m_pore_radius * m_porosity / m_tortuosity; - const doublereal TwoThirds = 2.0/3.0; - for (int k = 0; k < m_nsp; k++) { - m_dk[k] = TwoThirds * K_g * sqrt((8.0 * GasConstant * m_temp)/ - (Pi * m_mw[k])); - } - m_knudsen_ok = true; + // constant mixture attributes + m_thermo = phase; + m_nsp = m_thermo->nSpecies(); + m_tmin = m_thermo->minTemp(); + m_tmax = m_thermo->maxTemp(); + m_gastran = gastr; + + // make a local copy of the molecular weights + m_mw.resize(m_nsp); + copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin()); + + m_multidiff.resize(m_nsp, m_nsp); + m_d.resize(m_nsp, m_nsp); + m_dk.resize(m_nsp, 0.0); + + m_x.resize(m_nsp, 0.0); + m_thermo->getMoleFractions(DATA_PTR(m_x)); + + // set flags all false + m_knudsen_ok = false; + m_bulk_ok = false; + m_conc_set = false; + m_gradConc_set = false; + m_gradP_set = false; + + m_spwork.resize(m_nsp); + m_spwork2.resize(m_nsp); + } + //==================================================================================================================== + + void DustyGasTransport::updateBinaryDiffCoeffs() { + if (m_bulk_ok) return; + int n,m; + + // get the gaseous binary diffusion coefficients + m_gastran->getBinaryDiffCoeffs(m_nsp, m_d.ptrColumn(0)); + doublereal por2tort = m_porosity / m_tortuosity; + for (n = 0; n < m_nsp; n++) { + for (m = 0; m < m_nsp; m++) { + m_d(n,m) *= por2tort; + } } - - - void DustyGasTransport::eval_H_matrix() { - updateBinaryDiffCoeffs(); - updateKnudsenDiffCoeffs(); - int k,l,j; - doublereal sum; - for (k = 0; k < m_nsp; k++) { - - // evaluate off-diagonal terms - for (l = 0; l < m_nsp; l++) m_multidiff(k,l) = -m_x[k]/m_d(k,l); - - // evaluate diagonal term - sum = 0.0; - for (j = 0; j < m_nsp; j++) if (j != k) sum += m_x[j]/m_d(k,j); - m_multidiff(k,k) = 1.0/m_dk[k] + sum; - } + m_bulk_ok = true; + } + //==================================================================================================================== + void DustyGasTransport::updateKnudsenDiffCoeffs() { + if (m_knudsen_ok) return; + doublereal K_g = m_pore_radius * m_porosity / m_tortuosity; + const doublereal TwoThirds = 2.0/3.0; + for (int k = 0; k < m_nsp; k++) { + m_dk[k] = TwoThirds * K_g * sqrt((8.0 * GasConstant * m_temp)/ + (Pi * m_mw[k])); } + m_knudsen_ok = true; + } - void DustyGasTransport::getMolarFluxes(const doublereal* const state1, - const doublereal * const state2, - const doublereal delta, - doublereal * const fluxes) { + //==================================================================================================================== + void DustyGasTransport::eval_H_matrix() { + updateBinaryDiffCoeffs(); + updateKnudsenDiffCoeffs(); + int k,l,j; + doublereal sum; + for (k = 0; k < m_nsp; k++) { - int k; - doublereal conc1, conc2; - doublereal* cbar = DATA_PTR(m_spwork); - doublereal* gradc = DATA_PTR(m_spwork2); - doublereal t1 = state1[0]; - doublereal t2 = state2[0]; - doublereal rho1 = state1[1]; - doublereal rho2 = state2[1]; - const doublereal* y1 = state1 + 2; - const doublereal* y2 = state2 + 2; - doublereal c1sum = 0.0, c2sum = 0.0; - for (k = 0; k < m_nsp; k++) { - conc1 = rho1*y1[k]/m_mw[k]; - conc2 = rho2*y2[k]/m_mw[k]; - cbar[k] = 0.5*(conc1 + conc2); - gradc[k] = (conc2 - conc1)/delta; - c1sum += conc1; - c2sum += conc2; - } - doublereal p1 = c1sum * GasConstant * state1[0]; - doublereal p2 = c2sum * GasConstant * state2[0]; - doublereal pbar = 0.5*(p1 + p2); - doublereal gradp = (p2 - p1)/delta; - doublereal tbar = 0.5*(t1 + t2); + // evaluate off-diagonal terms + for (l = 0; l < m_nsp; l++) m_multidiff(k,l) = -m_x[k]/m_d(k,l); - m_thermo->setState_TPX(tbar, pbar, cbar); - - updateMultiDiffCoeffs(); - - multiply(m_multidiff, gradc, fluxes); - divide_each(cbar, cbar + m_nsp, m_dk.begin()); - - // if no permeability has been specified, use result for - // close-packed spheres - double b = 0.0; - if (m_perm < 0.0) { - double p = m_porosity; - double d = m_diam; - double t = m_tortuosity; - b = p*p*p*d*d/(72.0*t*(1.0-p)*(1.0-p)); - } - else { - b = m_perm; - } - b *= gradp / m_gastran->viscosity(); - scale(cbar, cbar + m_nsp, cbar, b); - increment(m_multidiff, cbar, fluxes); - scale(fluxes, fluxes + m_nsp, fluxes, -1.0); + // evaluate diagonal term + sum = 0.0; + for (j = 0; j < m_nsp; j++) if (j != k) sum += m_x[j]/m_d(k,j); + m_multidiff(k,k) = 1.0/m_dk[k] + sum; } + } + //==================================================================================================================== + void DustyGasTransport::getMolarFluxes(const doublereal* const state1, + const doublereal * const state2, + const doublereal delta, + doublereal * const fluxes) { - - void DustyGasTransport::updateMultiDiffCoeffs() { - // see if temperature has changed - updateTransport_T(); - - // update the mole fractions - updateTransport_C(); - - eval_H_matrix(); - - // invert H - int ierr = invert(m_multidiff); - - if (ierr != 0) { - throw CanteraError("DustyGasTransport::updateMultiDiffCoeffs", - "invert returned ierr = "+int2str(ierr)); - } + int k; + doublereal conc1, conc2; + doublereal* cbar = DATA_PTR(m_spwork); + doublereal* gradc = DATA_PTR(m_spwork2); + doublereal t1 = state1[0]; + doublereal t2 = state2[0]; + doublereal rho1 = state1[1]; + doublereal rho2 = state2[1]; + const doublereal* y1 = state1 + 2; + const doublereal* y2 = state2 + 2; + doublereal c1sum = 0.0, c2sum = 0.0; + for (k = 0; k < m_nsp; k++) { + conc1 = rho1*y1[k]/m_mw[k]; + conc2 = rho2*y2[k]/m_mw[k]; + cbar[k] = 0.5*(conc1 + conc2); + gradc[k] = (conc2 - conc1)/delta; + c1sum += conc1; + c2sum += conc2; } + doublereal p1 = c1sum * GasConstant * state1[0]; + doublereal p2 = c2sum * GasConstant * state2[0]; + doublereal pbar = 0.5*(p1 + p2); + doublereal gradp = (p2 - p1)/delta; + doublereal tbar = 0.5*(t1 + t2); - void DustyGasTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { - int i,j; - updateMultiDiffCoeffs(); - for (i = 0; i < m_nsp; i++) { - for (j = 0; j < m_nsp; j++) { - d[ld*j + i] = m_multidiff(i,j); - } - } + m_thermo->setState_TPX(tbar, pbar, cbar); + + updateMultiDiffCoeffs(); + + multiply(m_multidiff, gradc, fluxes); + divide_each(cbar, cbar + m_nsp, m_dk.begin()); + + // if no permeability has been specified, use result for + // close-packed spheres + double b = 0.0; + if (m_perm < 0.0) { + double p = m_porosity; + double d = m_diam; + double t = m_tortuosity; + b = p*p*p*d*d/(72.0*t*(1.0-p)*(1.0-p)); } - - - /** - * Update temperature-dependent quantities. - */ - void DustyGasTransport::updateTransport_T() - { - if (m_temp == m_thermo->temperature()) return; - m_temp = m_thermo->temperature(); - m_knudsen_ok = false; - m_bulk_ok = false; - } - - void DustyGasTransport::updateTransport_C() - { - m_thermo->getMoleFractions(DATA_PTR(m_x)); - - // add an offset to avoid a pure species condition - // (check - this may be unnecessary) - int k; - for (k = 0; k < m_nsp; k++) { - m_x[k] = fmaxx(MIN_X, m_x[k]); - } + else { + b = m_perm; } + b *= gradp / m_gastran->viscosity(); + scale(cbar, cbar + m_nsp, cbar, b); + increment(m_multidiff, cbar, fluxes); + scale(fluxes, fluxes + m_nsp, fluxes, -1.0); + } + //==================================================================================================================== + + void DustyGasTransport::updateMultiDiffCoeffs() { + // see if temperature has changed + updateTransport_T(); + + // update the mole fractions + updateTransport_C(); + + eval_H_matrix(); + + // invert H + int ierr = invert(m_multidiff); + + if (ierr != 0) { + throw CanteraError("DustyGasTransport::updateMultiDiffCoeffs", + "invert returned ierr = "+int2str(ierr)); + } + } + //==================================================================================================================== + void DustyGasTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { + int i,j; + updateMultiDiffCoeffs(); + for (i = 0; i < m_nsp; i++) { + for (j = 0; j < m_nsp; j++) { + d[ld*j + i] = m_multidiff(i,j); + } + } + } + + //==================================================================================================================== + /** + * Update temperature-dependent quantities. + */ + void DustyGasTransport::updateTransport_T() + { + if (m_temp == m_thermo->temperature()) return; + m_temp = m_thermo->temperature(); + m_knudsen_ok = false; + m_bulk_ok = false; + } + //==================================================================================================================== + void DustyGasTransport::updateTransport_C() + { + m_thermo->getMoleFractions(DATA_PTR(m_x)); + + // add an offset to avoid a pure species condition + // (check - this may be unnecessary) + for (int k = 0; k < m_nsp; k++) { + m_x[k] = fmaxx(MIN_X, m_x[k]); + } + // diffusion coeffs depend on Pressure + m_bulk_ok = false; + } + //==================================================================================================================== } diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index bad14bc4f..4dea75558 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -1,10 +1,14 @@ -/// -/// -/// @file DustyGasTransport.h -/// Interface for class DustyGasTransport -/// -/// - +/** + * @file DustyGasTransport.h + * Headers for the DustyGasTransport object, which models transport properties + * in porous media using the dusty gas approximation + * (see \ref tranprops and \link Cantera::DustyGasTransport DustyGasTransport \endlink) . + * + */ +/* + * $Revision$ + * $Date$ + */ // Copyright 2003 California Institute of Technology @@ -19,23 +23,52 @@ namespace Cantera { - /// - /// Class DustyGasTransport implements the Dusty Gas model for - /// transport in porous media. As implemented here, only species - /// transport is handled. The viscosity, thermal conductivity, and - /// thermal diffusion coefficients are not implemented. - /// + //! Class DustyGasTransport implements the Dusty Gas model for transport in porous media. + /*! + * As implemented here, only species transport is handled. The viscosity, thermal conductivity, and thermal + * diffusion coefficients are not implemented. + */ class DustyGasTransport : public Transport { public: - /// default constructor + //! default constructor + /*! + * @param thermo Pointer to the %ThermoPhase object for this phase. Defaults to zero. + */ DustyGasTransport(thermo_t* thermo=0); + + //! Copy Constructor for the %DustyGasTransport object. + /*! + * @param right %LiquidTransport to be copied + */ + DustyGasTransport(const DustyGasTransport &right); + + //! Assignment operator + /*! + * + * Warning -> Shallow pointer copies are made of m_thermo and m_gastran.. gastran may not point to the correct + * object after this copy. The routine initialize() must be called after this + * routine to complete the copy. + * + * @param right Reference to %DustyGasTransport object to be copied + * into the current one. + */ + DustyGasTransport& operator=(const DustyGasTransport& right); - /// Destructor. Does nothing, since class allocates no memory - /// on the heap. - virtual ~DustyGasTransport() {} - + //! Destructor. + virtual ~DustyGasTransport(); + + //! Duplication routine for objects which inherit from %Transport + /*! + * This virtual routine can be used to duplicate %Transport objects + * inherited from %Transport even if the application only has + * a pointer to %Transport to work with. + * + * These routines are basically wrappers around the derived copy + * constructor. + */ + virtual Transport *duplMyselfAsTransport() const; //--------------------------------------------------------- // overloaded base class methods @@ -87,14 +120,25 @@ namespace Cantera { m_diam = dbar; } - /// Set the permeability. If not set, the value for - /// close-packed spheres will be used by default. + //! Set the permeability of the media + /*! + * If not set, the value for close-packed spheres will be used by default. + * + * The value for close-packed spheres is given below, where p is the porosity, + * t is the tortuosity, and d is the diameter of the sphere + * + * \f[ + * \kappa = \frac{p^3 d^2}{72 t (1 - p)^2} + * \f] + * + * @param B set the permeability of the media (units = m^2) + */ void setPermeability(doublereal B) { m_perm = B; } - /// Return a reference to the transport manager used to compute the gas - /// binary diffusion coefficients and the visdcosity. + //! Return a reference to the transport manager used to compute the gas + //! binary diffusion coefficients and the visdcosity. Transport& gasTransport() { return *m_gastran; } @@ -103,12 +147,26 @@ namespace Cantera { protected: - // called by TransportFactory + //! Initialization routine called by TransportFactory + /*! + * The DustyGas model is a subordinate model to the gas phase transport model. Here we + * set the gas phase models. + * + * This is a protected routine, so that initialiation of the Model must occur within Cantera's setup + * + * @param phase Pointer to the underlying ThermoPhase model for the gas phase + * @param gastr Pointer to the underlying Transport model for transport in the gas phse. + */ void initialize(ThermoPhase* phase, Transport* gastr); private: + //! Update temperature-dependent quantities within the object + /*! + * The object keeps a value m_temp, which is the temperature at which quantities were last evaluated + * at. If the temperature is changed, update Booleans are set false, triggering recomputation. + */ void updateTransport_T(); void updateTransport_C(); @@ -123,32 +181,31 @@ namespace Cantera { doublereal m_tmin, m_tmax; vector_fp m_mw; - // property values - - /// binary diffusion coefficients + + //! binary diffusion coefficients DenseMatrix m_d; - /// mole fractions + //! mole fractions vector_fp m_x; - /// Knudsen diffusion coefficients + //! Knudsen diffusion coefficients vector_fp m_dk; - /// temperature + //! temperature doublereal m_temp; - /// multicomponent diffusion coefficients + //! multicomponent diffusion coefficients DenseMatrix m_multidiff; - // work space + //! work space of size m_nsp; vector_fp m_spwork; + + //! work space of size m_nsp; vector_fp m_spwork2; - // concentration gradients - //vector_fp m_gradConc; - //vector_fp m_conc; - - doublereal m_gradP; /// pressure gradient + + //! Pressure Gradient + doublereal m_gradP; bool m_knudsen_ok; bool m_bulk_ok; @@ -156,11 +213,35 @@ namespace Cantera { bool m_gradConc_set; bool m_gradP_set; - doublereal m_porosity; /// porosity - doublereal m_tortuosity; /// tortuosity + //! Porosity + doublereal m_porosity; + + //! Tortuosity + doublereal m_tortuosity; doublereal m_pore_radius; /// pore radius (m) - doublereal m_diam; /// particle diameter (m) - doublereal m_perm; /// permeability + + //! Particle diameter + /*! + * The medium is assumed to consist of particles of size m_diam + * units = m + */ + doublereal m_diam; + + //! Permeability of the media + /*! + * The permeability is the proportionality constant for Darcy's + * law which relates discharge rate and viscosity to the applied + * pressure gradient. + * + * Below is Darcy's law, where \f$ \kappa \f$ is the permeability + * + * \f[ + * v = \frac{\kappa}{\mu} \frac{\delta P}{\delta x} + * \f] + * + * units are m2 + */ + doublereal m_perm; Transport* m_gastran; /// pointer to gas transport manager From 4ec5327086d6803b9c78d910b988b6a72919f071 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 19 Aug 2010 00:30:18 +0000 Subject: [PATCH 252/446] Doxygen update --- Cantera/src/transport/DustyGasTransport.cpp | 14 ++++++----- Cantera/src/transport/DustyGasTransport.h | 26 +++++++++++++++++++-- 2 files changed, 32 insertions(+), 8 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index bca1e6de3..dc0cead8d 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -53,7 +53,6 @@ namespace Cantera { m_gradP(0.0), m_knudsen_ok(false), m_bulk_ok(false), - m_conc_set(false), m_gradConc_set(false), m_gradP_set(false), m_porosity(0.0), @@ -79,7 +78,6 @@ namespace Cantera { m_gradP(0.0), m_knudsen_ok(false), m_bulk_ok(false), - m_conc_set(false), m_gradConc_set(false), m_gradP_set(false), m_porosity(0.0), @@ -120,7 +118,6 @@ namespace Cantera { m_gradP = right.m_gradP; m_knudsen_ok = right.m_knudsen_ok; m_bulk_ok= right.m_bulk_ok; - m_conc_set = right.m_conc_set; m_gradConc_set = right.m_gradConc_set; m_gradP_set = right.m_gradP_set; m_porosity = right.m_porosity; @@ -204,7 +201,6 @@ namespace Cantera { // set flags all false m_knudsen_ok = false; m_bulk_ok = false; - m_conc_set = false; m_gradConc_set = false; m_gradP_set = false; @@ -248,11 +244,17 @@ namespace Cantera { for (k = 0; k < m_nsp; k++) { // evaluate off-diagonal terms - for (l = 0; l < m_nsp; l++) m_multidiff(k,l) = -m_x[k]/m_d(k,l); + for (l = 0; l < m_nsp; l++) { + m_multidiff(k,l) = -m_x[k]/m_d(k,l); + } // evaluate diagonal term sum = 0.0; - for (j = 0; j < m_nsp; j++) if (j != k) sum += m_x[j]/m_d(k,j); + for (j = 0; j < m_nsp; j++) { + if (j != k) { + sum += m_x[j]/m_d(k,j); + } + } m_multidiff(k,k) = 1.0/m_dk[k] + sum; } } diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index 4dea75558..dee73bdd3 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -189,12 +189,30 @@ namespace Cantera { vector_fp m_x; //! Knudsen diffusion coefficients + /*! + * The Knudsen diffusion coefficients are given by the following form + * + * \f[ + * \mathcal{D}^{knud}_k = \frac{2}{3} \frac{r_{pore} \phi}{\tau} \left( \frac{8 R T}{\pi W_k} \right)^{1/2} + * \f] + * + */ vector_fp m_dk; //! temperature doublereal m_temp; - //! multicomponent diffusion coefficients + //! Multicomponent diffusion coefficients + /*! + * The multicomponent diffusion matrix \f$ H_{k,l} \f$ is given by the following form + * + * \f[ + * H_{k,l} = - \frac{X_k}{D_{k,l}} + * \f] + * \f[ + * H_{k,k} = \frac{1}{\mathcal(D)^{knud}_{k}} + \sum_{j \ne k}^N{ \frac{X_j}{D_{k,j}} } + * \f] + */ DenseMatrix m_multidiff; //! work space of size m_nsp; @@ -207,10 +225,14 @@ namespace Cantera { //! Pressure Gradient doublereal m_gradP; + //! Update-to-date variable for Knudsen diffusion coefficients bool m_knudsen_ok; + + //! Update-to-date variable for Binary diffusion coefficients bool m_bulk_ok; - bool m_conc_set; + bool m_gradConc_set; + bool m_gradP_set; //! Porosity From fc7c88ab9141c22ac974717d0457194a7d19ce3d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 19 Aug 2010 15:27:15 +0000 Subject: [PATCH 253/446] Doxygen update --- Cantera/src/transport/DustyGasTransport.cpp | 30 +++++++++++---------- Cantera/src/transport/DustyGasTransport.h | 26 +++++++++++++++--- 2 files changed, 39 insertions(+), 17 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index dc0cead8d..9f1a50c25 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -42,8 +42,6 @@ namespace Cantera { DustyGasTransport::DustyGasTransport(thermo_t* thermo) : Transport(thermo), m_nsp(0), - m_tmin(0.0), - m_tmax(1.0E300), m_mw(0), m_dk(0), m_temp(-1.0), @@ -67,8 +65,6 @@ namespace Cantera { DustyGasTransport::DustyGasTransport(const DustyGasTransport &right) : Transport(), m_nsp(0), - m_tmin(0.0), - m_tmax(1.0E300), m_mw(0), m_dk(0), m_temp(-1.0), @@ -105,8 +101,6 @@ namespace Cantera { Transport::operator=(right); m_nsp = right.m_nsp; - m_tmin = right.m_tmin; - m_tmax = right.m_tmax; m_mw = right.m_mw; m_d = right.m_d; m_x = right.m_x; @@ -183,8 +177,6 @@ namespace Cantera { // constant mixture attributes m_thermo = phase; m_nsp = m_thermo->nSpecies(); - m_tmin = m_thermo->minTemp(); - m_tmax = m_thermo->maxTemp(); m_gastran = gastr; // make a local copy of the molecular weights @@ -332,21 +324,31 @@ namespace Cantera { "invert returned ierr = "+int2str(ierr)); } } - //==================================================================================================================== + //==================================================================================================================== + // Return the Multicomponent diffusion coefficients. Units: [m^2/s]. + /* + * Returns the array of multicomponent diffusion coefficients. + * + * @param ld The dimension of the inner loop of d (usually equal to m_nsp) + * @param d flat vector of diffusion coefficients, fortran ordering. + * d[ld*j+i] is the D_ij diffusion coefficient (the diffusion + * coefficient for species i due to species j). + */ void DustyGasTransport::getMultiDiffCoeffs(const int ld, doublereal* const d) { int i,j; updateMultiDiffCoeffs(); for (i = 0; i < m_nsp; i++) { - for (j = 0; j < m_nsp; j++) { + for (j = 0; j < m_nsp; j++) { d[ld*j + i] = m_multidiff(i,j); } } } - //==================================================================================================================== - /** - * Update temperature-dependent quantities. - */ + // Update temperature-dependent quantities within the object + /* + * The object keeps a value m_temp, which is the temperature at which quantities were last evaluated + * at. If the temperature is changed, update Booleans are set false, triggering recomputation. + */ void DustyGasTransport::updateTransport_T() { if (m_temp == m_thermo->temperature()) return; diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index dee73bdd3..36129948f 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -77,6 +77,16 @@ namespace Cantera { virtual void setParameters(const int type, const int k, const doublereal* const p); + + //! Return the Multicomponent diffusion coefficients. Units: [m^2/s]. + /*! + * Returns the array of multicomponent diffusion coefficients. + * + * @param ld The dimension of the inner loop of d (usually equal to m_nsp) + * @param d flat vector of diffusion coefficients, fortran ordering. + * d[ld*j+i] is the D_ij diffusion coefficient (the diffusion + * coefficient for species i due to species j). + */ virtual void getMultiDiffCoeffs(const int ld, doublereal* const d); //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic @@ -168,6 +178,12 @@ namespace Cantera { * at. If the temperature is changed, update Booleans are set false, triggering recomputation. */ void updateTransport_T(); + + //! Update concentration-dependent quantities within the object + /*! + * The object keeps a value m_temp, which is the temperature at which quantities were last evaluated + * at. If the temperature is changed, update Booleans are set false, triggering recomputation. + */ void updateTransport_C(); void updateBinaryDiffCoeffs(); @@ -176,12 +192,16 @@ namespace Cantera { void eval_H_matrix(); - // gas attributes + //! Number of species in the gas phase int m_nsp; - doublereal m_tmin, m_tmax; + + //! Local copy of the species molecular weights + /*! + * units kg /kmol + * length = m_nsp; + */ vector_fp m_mw; - //! binary diffusion coefficients DenseMatrix m_d; From 039b01cbe38ff8ddab6059761460b5e7dd924fb9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 20 Aug 2010 15:40:08 +0000 Subject: [PATCH 254/446] Doxygen update --- Cantera/src/transport/DustyGasTransport.cpp | 151 ++++++++++++++--- Cantera/src/transport/DustyGasTransport.h | 170 ++++++++++++++------ 2 files changed, 251 insertions(+), 70 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index 9f1a50c25..95c185e7c 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -51,8 +51,6 @@ namespace Cantera { m_gradP(0.0), m_knudsen_ok(false), m_bulk_ok(false), - m_gradConc_set(false), - m_gradP_set(false), m_porosity(0.0), m_tortuosity(1.0), m_pore_radius(0.0), @@ -74,8 +72,6 @@ namespace Cantera { m_gradP(0.0), m_knudsen_ok(false), m_bulk_ok(false), - m_gradConc_set(false), - m_gradP_set(false), m_porosity(0.0), m_tortuosity(1.0), m_pore_radius(0.0), @@ -112,8 +108,6 @@ namespace Cantera { m_gradP = right.m_gradP; m_knudsen_ok = right.m_knudsen_ok; m_bulk_ok= right.m_bulk_ok; - m_gradConc_set = right.m_gradConc_set; - m_gradP_set = right.m_gradP_set; m_porosity = right.m_porosity; m_tortuosity = right.m_tortuosity; m_pore_radius = right.m_pore_radius; @@ -193,18 +187,26 @@ namespace Cantera { // set flags all false m_knudsen_ok = false; m_bulk_ok = false; - m_gradConc_set = false; - m_gradP_set = false; m_spwork.resize(m_nsp); m_spwork2.resize(m_nsp); } //==================================================================================================================== - + // Private routine to update the dusty gas binary diffusion coefficients + /* + * The dusty gas binary diffusion coefficients \f$ D^{dg}_{i,j} \f$ are evaluated from the binary + * gas-phase diffusion coefficients \f$ D^{bin}_{i,j} \f$ using the following formula + * + * \f[ + * D^{dg}_{i,j} = \frac{\phi}{\tau} D^{bin}_{i,j} + * \f] + * + * where \f$ \phi \f$ is the porosity of the media and \f$ \tau \f$ is the tortuosity of the media. + * + */ void DustyGasTransport::updateBinaryDiffCoeffs() { if (m_bulk_ok) return; int n,m; - // get the gaseous binary diffusion coefficients m_gastran->getBinaryDiffCoeffs(m_nsp, m_d.ptrColumn(0)); doublereal por2tort = m_porosity / m_tortuosity; @@ -216,6 +218,15 @@ namespace Cantera { m_bulk_ok = true; } //==================================================================================================================== + // Private routine to update the Knudsen diffusion coefficients + /* + * The Knudsen diffusion coefficients are given by the following form + * + * \f[ + * \mathcal{D}^{knud}_k = \frac{2}{3} \frac{r_{pore} \phi}{\tau} \left( \frac{8 R T}{\pi W_k} \right)^{1/2} + * \f] + * + */ void DustyGasTransport::updateKnudsenDiffCoeffs() { if (m_knudsen_ok) return; doublereal K_g = m_pore_radius * m_porosity / m_tortuosity; @@ -227,7 +238,21 @@ namespace Cantera { m_knudsen_ok = true; } - //==================================================================================================================== + //==================================================================================================================== + // Private routine to calculate the H matrix + /* + * The H matrix is the term we have given to the matrix of coefficients in the equation for the molar + * fluxes. The matrix must be inverted in order to calculate the molar fluxes. + * + * The multicomponent diffusion H matrix \f$ H_{k,l} \f$ is given by the following formulas + * + * \f[ + * H_{k,l} = - \frac{X_k}{D^e_{k,l}} + * \f] + * \f[ + * H_{k,k} = \frac{1}{\mathcal(D)^{e}_{k, knud}} + \sum_{j \ne k}^N{ \frac{X_j}{D^e_{k,j}} } + * \f] + */ void DustyGasTransport::eval_H_matrix() { updateBinaryDiffCoeffs(); updateKnudsenDiffCoeffs(); @@ -258,25 +283,30 @@ namespace Cantera { int k; doublereal conc1, conc2; - doublereal* cbar = DATA_PTR(m_spwork); - doublereal* gradc = DATA_PTR(m_spwork2); - doublereal t1 = state1[0]; - doublereal t2 = state2[0]; - doublereal rho1 = state1[1]; - doublereal rho2 = state2[1]; - const doublereal* y1 = state1 + 2; - const doublereal* y2 = state2 + 2; + + // cbar will be the average concentration between the two points + doublereal * const cbar = DATA_PTR(m_spwork); + doublereal * const gradc = DATA_PTR(m_spwork2); + const doublereal t1 = state1[0]; + const doublereal t2 = state2[0]; + const doublereal rho1 = state1[1]; + const doublereal rho2 = state2[1]; + const doublereal* const y1 = state1 + 2; + const doublereal* const y2 = state2 + 2; doublereal c1sum = 0.0, c2sum = 0.0; + for (k = 0; k < m_nsp; k++) { - conc1 = rho1*y1[k]/m_mw[k]; - conc2 = rho2*y2[k]/m_mw[k]; + conc1 = rho1 * y1[k] / m_mw[k]; + conc2 = rho2 * y2[k] / m_mw[k]; cbar[k] = 0.5*(conc1 + conc2); - gradc[k] = (conc2 - conc1)/delta; + gradc[k] = (conc2 - conc1) / delta; c1sum += conc1; c2sum += conc2; } - doublereal p1 = c1sum * GasConstant * state1[0]; - doublereal p2 = c2sum * GasConstant * state2[0]; + + // Calculate the pressures at p1 p2 and pbar + doublereal p1 = c1sum * GasConstant * t1; + doublereal p2 = c2sum * GasConstant * t2; doublereal pbar = 0.5*(p1 + p2); doublereal gradp = (p2 - p1)/delta; doublereal tbar = 0.5*(t1 + t2); @@ -285,7 +315,9 @@ namespace Cantera { updateMultiDiffCoeffs(); + // Multiply m_multidiff and gradc together and store the result in fluxes[] multiply(m_multidiff, gradc, fluxes); + divide_each(cbar, cbar + m_nsp, m_dk.begin()); // if no permeability has been specified, use result for @@ -302,11 +334,16 @@ namespace Cantera { } b *= gradp / m_gastran->viscosity(); scale(cbar, cbar + m_nsp, cbar, b); + + // Multiply m_multidiff with cbar and add it to fluxes increment(m_multidiff, cbar, fluxes); scale(fluxes, fluxes + m_nsp, fluxes, -1.0); } //==================================================================================================================== - + // Private routine to update the Multicomponent diffusion coefficients that are used in the approximation + /* + * This routine updates the H matrix and then inverts it. + */ void DustyGasTransport::updateMultiDiffCoeffs() { // see if temperature has changed updateTransport_T(); @@ -370,4 +407,68 @@ namespace Cantera { m_bulk_ok = false; } //==================================================================================================================== + // Set the porosity (dimensionless) + /* + * @param porosity Set the value of the porosity + */ + void DustyGasTransport::setPorosity(doublereal porosity) { + m_porosity = porosity; + m_knudsen_ok = false; + m_bulk_ok = false; + } + //==================================================================================================================== + // Set the tortuosity (dimensionless) + /* + * @param tort Value of the tortuosity + */ + void DustyGasTransport::setTortuosity(doublereal tort) { + m_tortuosity = tort; + m_knudsen_ok = false; + m_bulk_ok = false; + } + //==================================================================================================================== + // Set the mean pore radius (m) + /* + * @param rbar Value of the pore radius ( m) + */ + void DustyGasTransport::setMeanPoreRadius(doublereal rbar) { + m_pore_radius = rbar; + m_knudsen_ok = false; + } + //==================================================================================================================== + // Set the mean particle diameter + /* + * @param dbar Set the mean particle diameter (m) + */ + void DustyGasTransport::setMeanParticleDiameter(doublereal dbar) { + m_diam = dbar; + } + //==================================================================================================================== + // Set the permeability of the media + /* + * If not set, the value for close-packed spheres will be used by default. + * + * The value for close-packed spheres is given below, where p is the porosity, + * t is the tortuosity, and d is the diameter of the sphere + * + * \f[ + * \kappa = \frac{p^3 d^2}{72 t (1 - p)^2} + * \f] + * + * @param B set the permeability of the media (units = m^2) + */ + void DustyGasTransport::setPermeability(doublereal B) { + m_perm = B; + } + //==================================================================================================================== + // Return a reference to the transport manager used to compute the gas + // binary diffusion coefficients and the visdcosity. + /* + * @return Returns a reference to the gas transport object + */ + Transport& DustyGasTransport::gasTransport() { + return *m_gastran; + } + + //==================================================================================================================== } diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index 36129948f..89315d4e3 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -27,6 +27,41 @@ namespace Cantera { /*! * As implemented here, only species transport is handled. The viscosity, thermal conductivity, and thermal * diffusion coefficients are not implemented. + * + * The dusty gas model includes the effects of Darcy's law. There is a net flux of species due to a pressure gradient + * that is part of Darcy's law. + * + * The dusty gas model expresses the value of the molar flux of species \f$ k \f$, \f$ J_k \f$ by the following formula. + * + * \f[ + * \sum_{j \ne k}{\frac{X_j J_k - X_k J_j}{D^e_{kj}}} + \frac{J_k}{\mathcal{D}^{e}_{k,knud}} = + * - \nabla C_k - \frac{C_k}{\mathcal{D}^{e}_{k,knud}} \frac{\kappa}{\mu} \nabla p + * \f] + * + * \f$ j \f$ is a sum over all species in the gas. + * + * The effective Knudsen diffusion coefficients are given by the following form + * + * \f[ + * \mathcal{D}^e_{k,knud} = \frac{2}{3} \frac{r_{pore} \phi}{\tau} \left( \frac{8 R T}{\pi W_k} \right)^{1/2} + * \f] + * + * The effective knudsen diffusion coefficients take into account the effects of collisions of gas-phase + * molecules with the wall. + * + * References for the Dusty Gas Model + * + * (1) H. Zhu, R. J. Kee, "Modeling Electrochemical Impedance Spectra in SOFC Button Cells with + * Internal Methane Reforming," J. Electrochem. Soc., 153(9) A1765-1772 (2006). + * + * (2) H. Zhu, R. J. Kee, V. M. Janardhanan, O. Deutschmann, D. G. Goodwin, J. Electrochem. Soc., 152, A2427 (2005). + * + * (3) E. A. Mason, A. P. Malinauskas," Gas Transport in Porous Media: the Dusty-Gas Model", + * American Elsevier, New York (1983). + * + * (4) J. W. Veldsink, R. M. J. van Damme, G. F. Versteeg, W. P. M. van Swaaij, + * "The use of the dusty gas model for the description of mass transport with chemical reaction in porous media," + * Chemical Engineering Journal, 57, 115 - 125 (1995). */ class DustyGasTransport : public Transport { @@ -89,14 +124,18 @@ namespace Cantera { */ virtual void getMultiDiffCoeffs(const int ld, doublereal* const d); - //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic - //! state at two nearby points. + //! Get the molar fluxes [kmol/m^2/s], given the thermodynamic state at two nearby points. /*! - * @param state1 Array of temperature, density, and mass - * fractions for state 1. - * @param state2 Array of temperature, density, and mass - * fractions for state 2. - * @param delta Distance from state 1 to state 2 (m). + * + * \f[ + * J_k = - \sum_{j = 1, N} \left[D^{multi}_{kj}\right]^{-1} \left( \nabla C_j + \frac{C_j}{\mathcal{D}^{knud}_j} \frac{\kappa}{\mu} \nabla p \right) + * \f] + * + * @param state1 Array of temperature, density, and mass fractions for state 1. + * @param state2 Array of temperature, density, and mass fractions for state 2. + * @param delta Distance from state 1 to state 2 (m). + * + * @param fluxes Vector of species molar fluxes due to diffusional driving force */ virtual void getMolarFluxes(const doublereal * const state1, const doublereal* const state2, const doublereal delta, @@ -105,30 +144,31 @@ namespace Cantera { //----------------------------------------------------------- // new methods added in this class - /// Set the porosity (dimensionless) - void setPorosity(doublereal porosity) { - m_porosity = porosity; - m_knudsen_ok = false; - m_bulk_ok = false; - } + //! Set the porosity (dimensionless) + /*! + * @param porosity Set the value of the porosity + */ + void setPorosity(doublereal porosity); - /// Set the tortuosity (dimensionless) - void setTortuosity(doublereal tort) { - m_tortuosity = tort; - m_knudsen_ok = false; - m_bulk_ok = false; - } + //! Set the tortuosity (dimensionless) + /*! + * Tortuosity is considered to be constant within the object + * + * @param tort Value of the tortuosity + */ + void setTortuosity(doublereal tort); - /// Set the mean pore radius (m) - void setMeanPoreRadius(doublereal rbar) { - m_pore_radius = rbar; - m_knudsen_ok = false; - } + //! Set the mean pore radius (m) + /*! + * @param rbar Value of the pore radius ( m) + */ + void setMeanPoreRadius(doublereal rbar); - /// Set the mean particle diameter - void setMeanParticleDiameter(doublereal dbar) { - m_diam = dbar; - } + //! Set the mean particle diameter + /*! + * @param dbar Set the mean particle diameter (m) + */ + void setMeanParticleDiameter(doublereal dbar); //! Set the permeability of the media /*! @@ -143,15 +183,18 @@ namespace Cantera { * * @param B set the permeability of the media (units = m^2) */ - void setPermeability(doublereal B) { - m_perm = B; - } + void setPermeability(doublereal B); //! Return a reference to the transport manager used to compute the gas //! binary diffusion coefficients and the visdcosity. - Transport& gasTransport() { return *m_gastran; } + /*! + * @return Returns a reference to the gas transport object + */ + Transport& gasTransport(); + //! Make the TransportFactory object a friend, because this object has restricted its + //! instantiation to classes which are friends. friend class TransportFactory; @@ -186,9 +229,48 @@ namespace Cantera { */ void updateTransport_C(); + //! Private routine to update the dusty gas binary diffusion coefficients + /*! + * The dusty gas binary diffusion coefficients \f$ D^{dg}_{i,j} \f$ are evaluated from the binary + * gas-phase diffusion coefficients \f$ D^{bin}_{i,j} \f$ using the following formula + * + * \f[ + * D^{dg}_{i,j} = \frac{\phi}{\tau} D^{bin}_{i,j} + * \f] + * + * where \f$ \phi \f$ is the porosity of the media and \f$ \tau \f$ is the tortuosity of the media. + * + */ void updateBinaryDiffCoeffs(); + + //! Private routine to update the Multicomponent diffusion coefficients that are used in the approximation + /*! + * This routine updates the H matrix and then inverts it. + */ void updateMultiDiffCoeffs(); + + //! Private routine to update the Knudsen diffusion coefficients + /*! + * The Knudsen diffusion coefficients are given by the following form + * + * \f[ + * \mathcal{D}^{knud}_k = \frac{2}{3} \frac{r_{pore} \phi}{\tau} \left( \frac{8 R T}{\pi W_k} \right)^{1/2} + * \f] + * + */ void updateKnudsenDiffCoeffs(); + + //! Private routine to calculate the H matrix + /*! + * The multicomponent diffusion H matrix \f$ H_{k,l} \f$ is given by the following form + * + * \f[ + * H_{k,l} = - \frac{X_k}{D_{k,l}} + * \f] + * \f[ + * H_{k,k} = \frac{1}{\mathcal(D)^{knud}_{k}} + \sum_{j \ne k}^N{ \frac{X_j}{D_{k,j}} } + * \f] + */ void eval_H_matrix(); @@ -203,10 +285,10 @@ namespace Cantera { vector_fp m_mw; //! binary diffusion coefficients - DenseMatrix m_d; + DenseMatrix m_d; //! mole fractions - vector_fp m_x; + vector_fp m_x; //! Knudsen diffusion coefficients /*! @@ -217,10 +299,10 @@ namespace Cantera { * \f] * */ - vector_fp m_dk; + vector_fp m_dk; //! temperature - doublereal m_temp; + doublereal m_temp; //! Multicomponent diffusion coefficients /*! @@ -233,14 +315,13 @@ namespace Cantera { * H_{k,k} = \frac{1}{\mathcal(D)^{knud}_{k}} + \sum_{j \ne k}^N{ \frac{X_j}{D_{k,j}} } * \f] */ - DenseMatrix m_multidiff; + DenseMatrix m_multidiff; //! work space of size m_nsp; vector_fp m_spwork; //! work space of size m_nsp; vector_fp m_spwork2; - //! Pressure Gradient doublereal m_gradP; @@ -248,19 +329,17 @@ namespace Cantera { //! Update-to-date variable for Knudsen diffusion coefficients bool m_knudsen_ok; - //! Update-to-date variable for Binary diffusion coefficients + //! Update-to-date variable for Binary diffusion coefficients bool m_bulk_ok; - bool m_gradConc_set; - - bool m_gradP_set; - //! Porosity doublereal m_porosity; //! Tortuosity doublereal m_tortuosity; - doublereal m_pore_radius; /// pore radius (m) + + //! Pore radius (meter) + doublereal m_pore_radius; //! Particle diameter /*! @@ -285,7 +364,8 @@ namespace Cantera { */ doublereal m_perm; - Transport* m_gastran; /// pointer to gas transport manager + //! Pointer to the transport object for the gas phase + Transport* m_gastran; }; } From d1e27613c36d35c390ef32651d780d7a7f9e81cc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 20 Aug 2010 15:47:29 +0000 Subject: [PATCH 255/446] doxygen update --- Cantera/src/transport/DustyGasTransport.cpp | 15 +++++++++++++-- Cantera/src/transport/DustyGasTransport.h | 13 +++++++++++++ 2 files changed, 26 insertions(+), 2 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index 95c185e7c..a6d3cd404 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -138,6 +138,18 @@ namespace Cantera { return (dynamic_cast(tr)); } //==================================================================================================================== + // Set the Parameters in the model + /* + * @param type Type of the parameter to set + * 0 - porosity + * 1 - tortuosity + * 2 - mean pore radius + * 3 - mean particle radius + * 4 - permeability + * @param k Unused int + * @param p pointer to double for the input list of parameters + * + */ void DustyGasTransport::setParameters(const int type, const int k, const doublereal* const p) { switch(type) { case 0: @@ -151,8 +163,7 @@ namespace Cantera { case 4: setPermeability(p[0]); break; default: - throw CanteraError("DustyGasTransport::init", - "unknown parameter"); + throw CanteraError("DustyGasTransport::init", "unknown parameter"); } } //==================================================================================================================== diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index 89315d4e3..2a9e96813 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -110,6 +110,19 @@ namespace Cantera { virtual int model() const { return cDustyGasTransport; } + + //! Set the Parameters in the model + /*! + * @param type Type of the parameter to set + * 0 - porosity + * 1 - tortuosity + * 2 - mean pore radius + * 3 - mean particle radius + * 4 - permeability + * @param k Unused int + * @param p pointer to double for the input list of parameters + * + */ virtual void setParameters(const int type, const int k, const doublereal* const p); From 1baff10c032296d87ea1f716cd6294fa7d95b2be Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 21 Aug 2010 16:41:46 +0000 Subject: [PATCH 256/446] Doxygen update --- Cantera/src/transport/AqueousTransport.cpp | 112 +++++---- Cantera/src/transport/AqueousTransport.h | 73 ++++-- Cantera/src/transport/LiquidTransport.h | 268 +++++++++++---------- Cantera/src/transport/MixTransport.h | 24 +- Cantera/src/transport/MultiTransport.cpp | 30 ++- Cantera/src/transport/MultiTransport.h | 12 +- Cantera/src/transport/SimpleTransport.cpp | 44 +++- Cantera/src/transport/SimpleTransport.h | 24 +- Cantera/src/transport/TransportBase.cpp | 7 + Cantera/src/transport/TransportBase.h | 43 ++-- Cantera/src/transport/TransportFactory.cpp | 21 +- 11 files changed, 379 insertions(+), 279 deletions(-) diff --git a/Cantera/src/transport/AqueousTransport.cpp b/Cantera/src/transport/AqueousTransport.cpp index df6fdf188..228bb2cd5 100644 --- a/Cantera/src/transport/AqueousTransport.cpp +++ b/Cantera/src/transport/AqueousTransport.cpp @@ -247,13 +247,13 @@ namespace Cantera { } } //================================================================================================ - void AqueousTransport::set_Grad_X(const doublereal* const grad_X) { - int itop = m_nDim * m_nsp; - for (int i = 0; i < itop; i++) { - m_Grad_X[i] = grad_X[i]; - } - } - + void AqueousTransport::set_Grad_X(const doublereal* const grad_X) { + int itop = m_nDim * m_nsp; + for (int i = 0; i < itop; i++) { + m_Grad_X[i] = grad_X[i]; + } + } + //==================================================================================================================== /****************** thermal conductivity **********************/ @@ -284,7 +284,7 @@ namespace Cantera { /****************** thermal diffusion coefficients ************/ - + //==================================================================================================================== /** * Thermal diffusion is not considered in this mixture-averaged * model. To include thermal diffusion, use transport manager @@ -298,42 +298,71 @@ namespace Cantera { } } - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from + + //==================================================================================================================== + // Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, + // given the gradients in mole fraction and temperature + /* + * Units for the returned fluxes are kg m-2 s-1. * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - void AqueousTransport::getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes) { + void AqueousTransport::getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes) { set_Grad_T(grad_T); set_Grad_X(grad_X); getSpeciesFluxesExt(ldf, fluxes); } - - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from + //==================================================================================================================== + // Return the species diffusive mass fluxes wrt to the specified averaged velocity, + /* + * This method acts similarly to getSpeciesFluxesES() but + * requires all gradients to be preset using methods set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesFluxesES() for details. * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * units = kg/m2/s + * + * Internally, gradients in the in mole fraction, temperature + * and electrostatic potential contribute to the diffusive flux + * + * The diffusive mass flux of species \e k is computed from the following formula + * + * \f[ + * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * V_c = - \sum_j {\rho M_j D_j \nabla X_j} + * \f] + * + * @param ldf Stride of the fluxes array. Must be equal to or greater than the number of species. + * @param fluxes Output of the diffusive fluxes. Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - void AqueousTransport::getSpeciesFluxesExt(int ldf, doublereal* fluxes) { + void AqueousTransport::getSpeciesFluxesExt(int ldf, doublereal * const fluxes) { int n, k; update_T(); update_C(); - getMixDiffCoeffs(DATA_PTR(m_spwork)); @@ -355,7 +384,7 @@ namespace Cantera { } } } - + //==================================================================================================================== /** * Mixture-averaged diffusion coefficients [m^2/s]. * @@ -396,7 +425,7 @@ namespace Cantera { } } - + //==================================================================================================================== // Handles the effects of changes in the Temperature, internally // within the object. /* @@ -447,7 +476,7 @@ namespace Cantera { // For now, for a concentration redo also m_iStateMF = -1; } - + //==================================================================================================================== /** * @internal This is called the first time any transport property * is requested from Mixture after the concentrations @@ -486,7 +515,7 @@ namespace Cantera { m_molefracs[k] = fmaxx(MIN_X, m_molefracs[k]); } } - + //==================================================================================================================== /************************************************************************* * @@ -514,7 +543,7 @@ namespace Cantera { m_spcond_ok = true; m_condmix_ok = false; } - + //==================================================================================================================== /** * Update the binary diffusion coefficients. These are evaluated @@ -548,7 +577,7 @@ namespace Cantera { m_bindiff_ok = true; m_diffmix_ok = false; } - + //==================================================================================================================== /** * Update the pure-species viscosities. @@ -572,7 +601,7 @@ namespace Cantera { m_spvisc_ok = true; } - + //==================================================================================================================== /** * Update the temperature-dependent viscosity terms. * Updates the array of pure species viscosities, and the @@ -601,7 +630,7 @@ namespace Cantera { } m_viscwt_ok = true; } - + //==================================================================================================================== /** * This function returns a Transport data object for a given species. * @@ -619,7 +648,7 @@ namespace Cantera { return td; } - + //==================================================================================================================== /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations @@ -750,5 +779,6 @@ namespace Cantera { } - } + } + //==================================================================================================================== } diff --git a/Cantera/src/transport/AqueousTransport.h b/Cantera/src/transport/AqueousTransport.h index f5bfc3d8f..07429be73 100644 --- a/Cantera/src/transport/AqueousTransport.h +++ b/Cantera/src/transport/AqueousTransport.h @@ -35,7 +35,7 @@ namespace Cantera { //! Class AqueousTransport implements mixture-averaged transport - //! properties for liquid phases. + //! properties for brine phases. /*! * The model is based on that * described by Newman, Electrochemical Systems @@ -276,28 +276,61 @@ namespace Cantera { */ virtual void update_C(); - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * - * - */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes); - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from - * + //! Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, + //! given the gradients in mole fraction and temperature + /*! + * Units for the returned fluxes are kg m-2 s-1. * + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - virtual void getSpeciesFluxesExt(int ldf, doublereal* fluxes); + virtual void getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes); + + //! Return the species diffusive mass fluxes wrt to the specified averaged velocity, + /*! + * This method acts similarly to getSpeciesFluxesES() but + * requires all gradients to be preset using methods set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesFluxesES() for details. + * + * units = kg/m2/s + * + * Internally, gradients in the in mole fraction, temperature + * and electrostatic potential contribute to the diffusive flux + * + * The diffusive mass flux of species \e k is computed from the following formula + * + * \f[ + * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * V_c = - \sum_j {\rho M_j D_j \nabla X_j} + * \f] + * + * @param ldf Stride of the fluxes array. Must be equal to or greater than the number of species. + * @param fluxes Output of the diffusive fluxes. Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + virtual void getSpeciesFluxesExt(int ldf, doublereal* const fluxes); //! Initialize the transport object diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 1848367d7..4c056475c 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -430,51 +430,51 @@ namespace Cantera { */ virtual void set_Grad_X(const doublereal* const grad_X); - //! Compute the mixture electrical conductivity from - //! the Stefan-Maxwell equation. - /*! - * To compute the mixture electrical conductance, the Stefan - * Maxwell equation is solved for zero species gradients and - * for unit potential gradient, \f$ \nabla V \f$. - * The species fluxes are converted to current by summing over - * the charge-weighted fluxes according to - * \f[ - * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i - * \f] - * where \f$ z_i \f$ is the charge on species i, - * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, - * \f$ W_i \f$ is the molecular mass of species i. - * The conductance, \f$ \kappa \f$ is obtained from - * \f[ - * \kappa = \vec{i} / \nabla V. - * \f] - * - */ + //! Compute the mixture electrical conductivity from + //! the Stefan-Maxwell equation. + /*! + * To compute the mixture electrical conductance, the Stefan + * Maxwell equation is solved for zero species gradients and + * for unit potential gradient, \f$ \nabla V \f$. + * The species fluxes are converted to current by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species i. + * The conductance, \f$ \kappa \f$ is obtained from + * \f[ + * \kappa = \vec{i} / \nabla V. + * \f] + * + */ virtual doublereal getElectricConduct(); - //! Compute the electric current density in A/m^2 - /*! - * The electric current is computed first by computing the - * species diffusive fluxes using the Stefan Maxwell solution - * and then the current, \f$ \vec{i} \f$ by summing over - * the charge-weighted fluxes according to - * \f[ - * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i - * \f] - * where \f$ z_i \f$ is the charge on species i, - * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, - * \f$ W_i \f$ is the molecular mass of species \c i. - * - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the grad_V and current vectors. - * @param grad_V The electrostatic potential gradient. - * @param current The electric current in A/m^2. - */ + //! Compute the electric current density in A/m^2 + /*! + * The electric current is computed first by computing the + * species diffusive fluxes using the Stefan Maxwell solution + * and then the current, \f$ \vec{i} \f$ by summing over + * the charge-weighted fluxes according to + * \f[ + * \vec{i} = \sum_{i} z_i F \rho \vec{V_i} / W_i + * \f] + * where \f$ z_i \f$ is the charge on species i, + * \f$ F \f$ is Faradays constant, \f$ \rho \f$ is the density, + * \f$ W_i \f$ is the molecular mass of species \c i. + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the grad_V and current vectors. + * @param grad_V The electrostatic potential gradient. + * @param current The electric current in A/m^2. + */ virtual void getElectricCurrent(int ndim, const doublereal* grad_T, int ldx, @@ -543,26 +543,29 @@ namespace Cantera { * length = ldx * ndim */ virtual void getSpeciesVdiffES(int ndim, const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, const doublereal* grad_Phi, - doublereal* Vdiff) ; + int ldx, const doublereal* grad_X, + int ldf, const doublereal* grad_Phi, + doublereal* Vdiff) ; //! Return the species diffusive mass fluxes wrt to //! the averaged velocity in [kmol/m^2/s]. /*! * - * The diffusive mass flux of species \e k is computed + * The diffusive mass flux of species \e k [kmol/m^2/s] is computed * using the Stefan-Maxwell equation + * * \f[ - * X_i \nabla \mu_i - * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * X_i \nabla \mu_i = RT \sum_i \frac{X_i X_j}{D_{ij}} * ( \vec{V}_j - \vec{V}_i ) * \f] + * * to determine the diffusion velocity and + * * \f[ * \vec{N}_i = C_T X_i \vec{V}_i * \f] + * * to determine the diffusion flux. Here \f$ C_T \f$ is the * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ * are the Stefa-Maxwell interaction parameters in [m^2/s], @@ -594,93 +597,92 @@ namespace Cantera { * Flat vector with the m_nsp in the inner loop. * length = ldx * ndim */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes); + virtual void getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes); - //! Return the species diffusive mass fluxes wrt to - //! the averaged velocity in [kmol/m^2/s]. - /*! - * - * The diffusive mass flux of species \e k is computed - * using the Stefan-Maxwell equation - * \f[ - * X_i \nabla \mu_i - * = RT \sum_i \frac{X_i X_j}{D_{ij}} - * ( \vec{V}_j - \vec{V}_i ) - * \f] - * to determine the diffusion velocity and - * \f[ - * \vec{N}_i = C_T X_i \vec{V}_i - * \f] - * to determine the diffusion flux. Here \f$ C_T \f$ is the - * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ - * are the Stefa-Maxwell interaction parameters in [m^2/s], - * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, - * \f$ \mu_i \f$ is the electrochemical potential of species \e i. - * - * The diffusion velocity is relative to an average velocity - * that can be computed on a mole-weighted - * or mass-weighted basis, or the diffusion velocities may - * be specified as relative to a specific species (i.e. a - * solvent) all according to the \verbatim - * \endverbatim input parameter. + //! Return the species diffusive mass fluxes wrt to + //! the averaged velocity in [kmol/m^2/s]. + /*! + * + * The diffusive mass flux of species \e k is computed + * using the Stefan-Maxwell equation + * \f[ + * X_i \nabla \mu_i + * = RT \sum_i \frac{X_i X_j}{D_{ij}} + * ( \vec{V}_j - \vec{V}_i ) + * \f] + * to determine the diffusion velocity and + * \f[ + * \vec{N}_i = C_T X_i \vec{V}_i + * \f] + * to determine the diffusion flux. Here \f$ C_T \f$ is the + * total concentration of the mixture [kmol/m^3], \f$ D_{ij} \f$ + * are the Stefa-Maxwell interaction parameters in [m^2/s], + * \f$ \vec{V}_{i} \f$ is the diffusion velocity of species \e i, + * \f$ \mu_i \f$ is the electrochemical potential of species \e i. + * + * The diffusion velocity is relative to an average velocity + * that can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the \verbatim + * \endverbatim input parameter. - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * (length = ndim) - * @param ldx Leading dimension of the grad_X array. - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param grad_Phi Gradients of the electrostatic potential - * length = ndim - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - */ - virtual void getSpeciesFluxesES(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - const doublereal* grad_Phi, - doublereal* fluxes); + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * (length = ndim) + * @param ldx Leading dimension of the grad_X array. + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * length = ndim + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + virtual void getSpeciesFluxesES(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + const doublereal* grad_Phi, + doublereal* fluxes); - //! Return the species diffusive velocities relative to - //! the averaged velocity. - /*! - * This method acts similarly to getSpeciesVdiffES() but - * requires all gradients to be preset using methods - * set_Grad_X(), set_Grad_V(), set_Grad_T(). - * See the documentation of getSpeciesVdiffES() for details. - * - * @param ldf Leading dimension of the Vdiff array. - * @param Vdiff Output of the diffusive velocities. - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - */ + //! Return the species diffusive velocities relative to + //! the averaged velocity. + /*! + * This method acts similarly to getSpeciesVdiffES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesVdiffES() for details. + * + * @param ldf Leading dimension of the Vdiff array. + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ virtual void getSpeciesVdiffExt(int ldf, doublereal* Vdiff); - //! Return the species diffusive fluxes relative to - //! the averaged velocity. - /*! - * This method acts similarly to getSpeciesFluxesES() but - * requires all gradients to be preset using methods - * set_Grad_X(), set_Grad_V(), set_Grad_T(). - * See the documentation of getSpeciesFluxesES() for details. - * - * units = kg/m2/s - * - * @param ldf Leading dimension of the Vdiff array. - * @param fluxes Output of the diffusive fluxes. - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - */ + //! Return the species diffusive fluxes relative to + //! the averaged velocity. + /*! + * This method acts similarly to getSpeciesFluxesES() but + * requires all gradients to be preset using methods + * set_Grad_X(), set_Grad_V(), set_Grad_T(). + * See the documentation of getSpeciesFluxesES() for details. + * + * units = kg/m2/s + * + * @param ldf Leading dimension of the Vdiff array. + * @param fluxes Output of the diffusive fluxes. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ virtual void getSpeciesFluxesExt(int ldf, doublereal* fluxes); protected: @@ -744,7 +746,7 @@ namespace Cantera { * (i.e. temperature and composition of each species) which was first * implemented in MargulesVPSSTP.cpp (LiquidTransport.h doxygen) */ - virtual void update_Grad_lnAC(); + virtual void update_Grad_lnAC(); //! Solve the stefan_maxell equations for the diffusive fluxes. @@ -924,7 +926,7 @@ namespace Cantera { //! Ionic conductivity for each species expressed as an appropriate subclass //! of LTPspecies /*! - * These subclasses of LTPspecies evaluate the species-specific + * These subclasses of LTPspecies evaluate the species-specific * transport properties according to the parameters parsed in * TransportFactory::getLiquidSpeciesTransportData(). */ diff --git a/Cantera/src/transport/MixTransport.h b/Cantera/src/transport/MixTransport.h index 568156504..0d0209a49 100644 --- a/Cantera/src/transport/MixTransport.h +++ b/Cantera/src/transport/MixTransport.h @@ -266,21 +266,19 @@ namespace Cantera { * @param ndim Number of dimensions in the flux expressions * @param grad_T Gradient of the temperature * (length = ndim) - * @param ldx Leading dimension of the grad_X array + * @param ldx Leading dimension of the grad_X array * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, + virtual void getSpeciesFluxes(int ndim, const doublereal* grad_T, + int ldx, const doublereal* grad_X, int ldf, doublereal* fluxes); //! Initialize the transport object diff --git a/Cantera/src/transport/MultiTransport.cpp b/Cantera/src/transport/MultiTransport.cpp index 19d21ee7f..12d0242e3 100644 --- a/Cantera/src/transport/MultiTransport.cpp +++ b/Cantera/src/transport/MultiTransport.cpp @@ -111,7 +111,7 @@ namespace Cantera { MultiTransport::~MultiTransport() { } - + //==================================================================================================================== bool MultiTransport::initGas(GasTransportParams& tr) { // constant mixture attributes @@ -272,7 +272,7 @@ namespace Cantera { return vismix; } - + //==================================================================================================================== /******************* binary diffusion coefficients **************/ @@ -408,13 +408,29 @@ namespace Cantera { m_lmatrix_soln_ok = true; } - - /** + //==================================================================================================================== + // Get the species diffusive mass fluxes wrt to the mass averaged velocity, + // given the gradients in mole fraction and temperature + /* + * Units for the returned fluxes are kg m-2 s-1. * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - void MultiTransport::getSpeciesFluxes(int ndim, - const doublereal* grad_T, int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes) { + void MultiTransport::getSpeciesFluxes(int ndim, const doublereal * const grad_T, int ldx, + const doublereal * const grad_X, + int ldf, doublereal * const fluxes) { // update the binary diffusion coefficients if necessary updateDiff_T(); diff --git a/Cantera/src/transport/MultiTransport.h b/Cantera/src/transport/MultiTransport.h index 58aca9087..792099292 100644 --- a/Cantera/src/transport/MultiTransport.h +++ b/Cantera/src/transport/MultiTransport.h @@ -140,8 +140,7 @@ namespace Cantera { */ virtual void getMixDiffCoeffs(doublereal* const d); - //! Get the species diffusive mass fluxes wrt to - //! the mass averaged velocity, + //! Get the species diffusive mass fluxes wrt to the mass averaged velocity, //! given the gradients in mole fraction and temperature /*! * Units for the returned fluxes are kg m-2 s-1. @@ -160,12 +159,9 @@ namespace Cantera { * Flat vector with the m_nsp in the inner loop. * length = ldx * ndim */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - doublereal* fluxes); + virtual void getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes); //! Get the molar diffusional fluxes [kmol/m^2/s] of the species, given the thermodynamic //! state at two nearby points. diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index b9121ecb3..680f77805 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -596,21 +596,39 @@ namespace Cantera { dt[k] = 0.0; } } -//================================================================================================ - /** - * @param ndim The number of spatial dimensions (1, 2, or 3). - * @param grad_T The temperature gradient (ignored in this model). - * @param ldx Leading dimension of the grad_X array. - * The diffusive mass flux of species \e k is computed from + //================================================================================================ + // Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, + // given the gradients in mole fraction and temperature + /* + * units = kg/m2/s * - * \f[ - * \vec{j}_k = -n M_k D_k \nabla X_k. - * \f] + * The diffusive mass flux of species \e k is computed from the following + * formula + * + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. + * + * \f[ + * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * V_c = - \sum_j {\rho M_j D_j \nabla X_j} + * \f] + * + * + * @param ndim The number of spatial dimensions (1, 2, or 3). + * @param grad_T The temperature gradient (ignored in this model). + * @param ldx Leading dimension of the grad_X array. + * @param grad_X Gradient of the mole fractions(length nsp * num dimensions); + * @param ldf Leading dimension of the fluxes array. + * @param fluxes Output fluxes of species. */ - void SimpleTransport::getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes) { + void SimpleTransport::getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes) { set_Grad_T(grad_T); set_Grad_X(grad_X); getSpeciesFluxesExt(ldf, fluxes); diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index cedcd3180..d7c4c9f26 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -316,29 +316,32 @@ namespace Cantera { * * @param grad_V Gradient of the voltage (length num dimensions); */ - virtual void set_Grad_V(const doublereal* const grad_V); + virtual void set_Grad_V(const doublereal * const grad_V); //! Specify the value of the gradient of the temperature /*! * @param grad_T Gradient of the temperature (length num dimensions); */ - virtual void set_Grad_T(const doublereal* const grad_T); + virtual void set_Grad_T(const doublereal * const grad_T); //! Specify the value of the gradient of the MoleFractions /*! * * @param grad_X Gradient of the mole fractions(length nsp * num dimensions); */ - virtual void set_Grad_X(const doublereal* const grad_X); + virtual void set_Grad_X(const doublereal * const grad_X); - - //! Return the species fluxes given gradients in temperature and mole fraction + //! Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, + //! given the gradients in mole fraction and temperature /*! * units = kg/m2/s + * * The diffusive mass flux of species \e k is computed from the following * formula - * - * + * + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. + * * \f[ * j_k = - \rho M_k D_k \nabla X_k - Y_k V_c * \f] @@ -357,10 +360,9 @@ namespace Cantera { * @param ldf Leading dimension of the fluxes array. * @param fluxes Output fluxes of species. */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, const doublereal* grad_X, - int ldf, doublereal* fluxes); + virtual void getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes); //! Return the species diffusive mass fluxes wrt to //! the mass averaged velocity, diff --git a/Cantera/src/transport/TransportBase.cpp b/Cantera/src/transport/TransportBase.cpp index 1bb18c2e3..f7a9a6fed 100644 --- a/Cantera/src/transport/TransportBase.cpp +++ b/Cantera/src/transport/TransportBase.cpp @@ -142,4 +142,11 @@ namespace Cantera { "finalize has already been called."); } + //==================================================================================================================== + void Transport::getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes) { + err("getSpeciesFluxes"); + } + //==================================================================================================================== } diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 4e42258ff..47dd4207e 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -514,34 +514,31 @@ namespace Cantera { } - //! Get the species diffusive mass fluxes wrt to - //! the mass averaged velocity, + //! Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, //! given the gradients in mole fraction and temperature /*! * Units for the returned fluxes are kg m-2 s-1. + * + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. * - * @param ndim Number of dimensions in the flux expressions - * @param grad_T Gradient of the temperature - * (length = ndim) - * @param ldx Leading dimension of the grad_X array - * (usually equal to m_nsp but not always) - * @param grad_X Gradients of the mole fraction - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim - * @param ldf Leading dimension of the fluxes array - * (usually equal to m_nsp but not always) - * @param fluxes Output of the diffusive mass fluxes - * Flat vector with the m_nsp in the inner loop. - * length = ldx * ndim + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param fluxes Output of the diffusive mass fluxes + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim */ - virtual void getSpeciesFluxes(int ndim, - const doublereal* grad_T, - int ldx, - const doublereal* grad_X, - int ldf, - doublereal* fluxes) { - err("getSpeciesFluxes"); - } + virtual void getSpeciesFluxes(int ndim, const doublereal * const grad_T, + int ldx, const doublereal * const grad_X, + int ldf, doublereal * const fluxes); //! Get the species diffusive mass fluxes wrt to //! the mass averaged velocity, diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 4ddb1ce7a..555e56c2d 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -50,14 +50,20 @@ #include -/** - * polynomial degree used for fitting collision integrals - * except in CK mode, where the degree is 6. - */ + +//! polynomial degree used for fitting collision integrals +//! except in CK mode, where the degree is 6. #define COLL_INT_POLY_DEGREE 8 - namespace Cantera { + /////////////////////////// constants ////////////////////////// + //@ \cond + const doublereal ThreeSixteenths = 3.0/16.0; + const doublereal TwoOverPi = 2.0/Pi; + const doublereal FiveThirds = 5.0/3.0; + //@ \endcond + + //==================================================================================================================== TransportFactory* TransportFactory::s_factory = 0; @@ -84,11 +90,6 @@ namespace Cantera { } }; //==================================================================================================================== - /////////////////////////// constants ////////////////////////// - - const doublereal ThreeSixteenths = 3.0/16.0; - const doublereal TwoOverPi = 2.0/Pi; - const doublereal FiveThirds = 5.0/3.0; //////////////////// class TransportFactory methods ////////////// From 21ebf8876672f812695e86ce56c9857363b37703 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 22 Aug 2010 17:46:08 +0000 Subject: [PATCH 257/446] Doxygen update --- Cantera/src/transport/AqueousTransport.cpp | 120 +++++++++------------ Cantera/src/transport/AqueousTransport.h | 40 ++++--- Cantera/src/transport/TransportBase.h | 14 ++- 3 files changed, 89 insertions(+), 85 deletions(-) diff --git a/Cantera/src/transport/AqueousTransport.cpp b/Cantera/src/transport/AqueousTransport.cpp index 228bb2cd5..96adb885f 100644 --- a/Cantera/src/transport/AqueousTransport.cpp +++ b/Cantera/src/transport/AqueousTransport.cpp @@ -36,9 +36,8 @@ using namespace std; namespace Cantera { - //////////////////// class AqueousTransport methods ////////////// - + //==================================================================================================================== AqueousTransport::AqueousTransport() : m_nsp(0), m_tmin(-1.0), @@ -68,7 +67,7 @@ namespace Cantera { } - + //==================================================================================================================== // Initialize the object /* * This is where we dimension everything. @@ -136,17 +135,7 @@ namespace Cantera { return true; } - - - /********************************************************* - * - * Public methods - * - *********************************************************/ - - - /****************** viscosity ******************************/ - + //==================================================================================================================== /* * The viscosity is computed using the Wilke mixture rule. * \f[ @@ -179,12 +168,19 @@ namespace Cantera { } return m_viscmix; } - - - /******************* binary diffusion coefficients **************/ - - - //================================================================================================ + //==================================================================================================================== + // Returns the pure species viscosities + /* + * + * Controlling update boolean = m_viscwt_ok + * + * @param visc Vector of species viscosities + */ + void AqueousTransport::getSpeciesViscosities(doublereal * const visc) { + updateViscosity_T(); + copy(m_visc.begin(), m_visc.end(), visc); + } + //==================================================================================================================== void AqueousTransport::getBinaryDiffCoeffs(const int ld, doublereal* const d) { int i,j; @@ -201,7 +197,7 @@ namespace Cantera { d[ld*j + i] = rp * m_bdiff(i,j); } } - //================================================================================================ + //==================================================================================================================== // Get the electrical Mobilities (m^2/V/s). /* * This function returns the mobilities. In some formulations @@ -226,7 +222,7 @@ namespace Cantera { mobil[k] = c1 * m_spwork[k]; } } - //================================================================================================ + //==================================================================================================================== void AqueousTransport::getFluidMobilities(doublereal* const mobil) { getMixDiffCoeffs(DATA_PTR(m_spwork)); doublereal c1 = 1.0 / (GasConstant * m_temp); @@ -234,19 +230,19 @@ namespace Cantera { mobil[k] = c1 * m_spwork[k]; } } - //================================================================================================ + //==================================================================================================================== void AqueousTransport::set_Grad_V(const doublereal* const grad_V) { for (int a = 0; a < m_nDim; a++) { m_Grad_V[a] = grad_V[a]; } } - //================================================================================================ + //==================================================================================================================== void AqueousTransport::set_Grad_T(const doublereal* const grad_T) { for (int a = 0; a < m_nDim; a++) { m_Grad_T[a] = grad_T[a]; } } - //================================================================================================ + //==================================================================================================================== void AqueousTransport::set_Grad_X(const doublereal* const grad_X) { int itop = m_nDim * m_nsp; for (int i = 0; i < itop; i++) { @@ -254,9 +250,6 @@ namespace Cantera { } } //==================================================================================================================== - - /****************** thermal conductivity **********************/ - /* * The thermal conductivity is computed from the following mixture rule: * \[ @@ -281,15 +274,24 @@ namespace Cantera { } return m_lambda; } - - - /****************** thermal diffusion coefficients ************/ //==================================================================================================================== - /** - * Thermal diffusion is not considered in this mixture-averaged - * model. To include thermal diffusion, use transport manager - * MultiTransport instead. This methods fills out array dt with - * zeros. + // Return a vector of Thermal diffusion coefficients [kg/m/sec]. + /* + * The thermal diffusion coefficient \f$ D^T_k \f$ is defined + * so that the diffusive mass flux of species k<\I> induced by the + * local temperature gradient is given by the following formula + * + * \f[ + * M_k J_k = -D^T_k \nabla \ln T. + * \f] + * + * The thermal diffusion coefficient can be either positive or negative. + * + * In this method we set it to zero. + * + * @param dt On return, dt will contain the species thermal + * diffusion coefficients. Dimension dt at least as large as + * the number of species. Units are kg/m/s. */ void AqueousTransport::getThermalDiffCoeffs(doublereal* const dt) { int k; @@ -297,8 +299,6 @@ namespace Cantera { dt[k] = 0.0; } } - - //==================================================================================================================== // Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, // given the gradients in mole fraction and temperature @@ -515,15 +515,8 @@ namespace Cantera { m_molefracs[k] = fmaxx(MIN_X, m_molefracs[k]); } } - //==================================================================================================================== - - /************************************************************************* - * - * methods to update temperature-dependent properties - * - *************************************************************************/ - - /** + //==================================================================================================================== + /* * Update the temperature-dependent parts of the mixture-averaged * thermal conductivity. */ @@ -544,8 +537,7 @@ namespace Cantera { m_condmix_ok = false; } //==================================================================================================================== - - /** + /* * Update the binary diffusion coefficients. These are evaluated * from the polynomial fits at unit pressure (1 Pa). */ @@ -577,9 +569,8 @@ namespace Cantera { m_bindiff_ok = true; m_diffmix_ok = false; } - //==================================================================================================================== - - /** + //==================================================================================================================== + /* * Update the pure-species viscosities. */ void AqueousTransport::updateSpeciesViscosities() { @@ -600,9 +591,8 @@ namespace Cantera { } m_spvisc_ok = true; } - //==================================================================================================================== - /** + /* * Update the temperature-dependent viscosity terms. * Updates the array of pure species viscosities, and the * weighting functions in the viscosity mixture rule. @@ -630,25 +620,20 @@ namespace Cantera { } m_viscwt_ok = true; } - //==================================================================================================================== - /** + //==================================================================================================================== + /* * This function returns a Transport data object for a given species. * */ - struct LiquidTransportData AqueousTransport:: - getLiquidTransportData(int kSpecies) + struct LiquidTransportData AqueousTransport::getLiquidTransportData(int kSpecies) { struct LiquidTransportData td; td.speciesName = m_thermo->speciesName(kSpecies); - /* NEEDS WORK - td.hydroradius = ???; - */ return td; } - - //==================================================================================================================== + //==================================================================================================================== /* * * Solve for the diffusional velocities in the Stefan-Maxwell equations @@ -659,15 +644,15 @@ namespace Cantera { int VIM = 2; m_B.resize(m_nsp, VIM); - //! grab a local copy of the molecular weights + // grab a local copy of the molecular weights const vector_fp& M = m_thermo->molecularWeights(); - //! get the mean molecular weight of the mixture + // get the mean molecular weight of the mixture //double M_mix = m_thermo->meanMolecularWeight(); - //! get the concentration of the mixture + // get the concentration of the mixture //double rho = m_thermo->density(); //double c = rho/M_mix; @@ -779,6 +764,7 @@ namespace Cantera { } - } + } //==================================================================================================================== } +//====================================================================================================================== diff --git a/Cantera/src/transport/AqueousTransport.h b/Cantera/src/transport/AqueousTransport.h index 07429be73..efe4d0f7c 100644 --- a/Cantera/src/transport/AqueousTransport.h +++ b/Cantera/src/transport/AqueousTransport.h @@ -135,9 +135,9 @@ namespace Cantera { virtual ~AqueousTransport() {} //! Return the model id for this transport parameterization - virtual int model() const { return cAqueousTransport; } - - //! overloaded base class methods + virtual int model() const { + return cAqueousTransport; + } //! Returns the viscosity of the solution /*! @@ -162,11 +162,30 @@ namespace Cantera { /*! * * Controlling update boolean = m_viscwt_ok + * + * @param visc Vector of species viscosities */ - virtual void getSpeciesViscosities(doublereal* visc) - { updateViscosity_T(); copy(m_visc.begin(), m_visc.end(), visc); } + virtual void getSpeciesViscosities(doublereal * const visc); - virtual void getThermalDiffCoeffs(doublereal* const dt); + //! Return a vector of Thermal diffusion coefficients [kg/m/sec]. + /*! + * The thermal diffusion coefficient \f$ D^T_k \f$ is defined + * so that the diffusive mass flux of species k induced by the + * local temperature gradient is given by the following formula + * + * \f[ + * M_k J_k = -D^T_k \nabla \ln T. + * \f] + * + * The thermal diffusion coefficient can be either positive or negative. + * + * In this method we set it to zero. + * + * @param dt On return, dt will contain the species thermal + * diffusion coefficients. Dimension dt at least as large as + * the number of species. Units are kg/m/s. + */ + virtual void getThermalDiffCoeffs(doublereal* const dt); //! Return the thermal conductivity of the solution /*! @@ -242,7 +261,7 @@ namespace Cantera { //! Specify the value of the gradient of the temperature /*! * - * @param grad_V Gradient of the temperature (length num dimensions); + * @param grad_T Gradient of the temperature (length num dimensions); */ virtual void set_Grad_T(const doublereal* const grad_T); @@ -379,9 +398,6 @@ namespace Cantera { */ vector_fp m_mw; - // polynomial fits - vector > m_poly; - //! Polynomial coefficients of the viscosity /*! * These express the temperature dependendence of the pures @@ -597,11 +613,9 @@ namespace Cantera { //! Saved value of the mixture viscosity doublereal m_viscmix; - // work space + //! work space of size m_nsp vector_fp m_spwork; - //! Internal Function - //! Update the temperature-dependent viscosity terms. //! Updates the array of pure species viscosities, and the //! weighting functions in the viscosity mixture rule. diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 47dd4207e..1b2650fe8 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -683,14 +683,18 @@ namespace Cantera { //! Return a vector of Thermal diffusion coefficients [kg/m/sec]. /*! * The thermal diffusion coefficient \f$ D^T_k \f$ is defined - * so that the diffusive mass flux of species k induced by the - * local temperature gradient is \f[ M_k J_k = -D^T_k \nabla - * \ln T. \f]. The thermal diffusion coefficient can be either - * positive or negative. + * so that the diffusive mass flux of species k induced by the + * local temperature gradient is given by the following formula + * + * \f[ + * M_k J_k = -D^T_k \nabla \ln T. + * \f] + * + * The thermal diffusion coefficient can be either positive or negative. * * @param dt On return, dt will contain the species thermal * diffusion coefficients. Dimension dt at least as large as - * the number of species. + * the number of species. Units are kg/m/s. */ virtual void getThermalDiffCoeffs(doublereal* const dt) { err("getThermalDiffCoeffs"); From 92e460ca1703fc644691ce407691c32d2676ed2b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 23 Aug 2010 17:43:43 +0000 Subject: [PATCH 258/446] doxygen updates Changed the hame of setLatticeMoleFraction to setLatticeMoleFractionByName --- Cantera/src/thermo/LatticeSolidPhase.cpp | 2 +- Cantera/src/thermo/LatticeSolidPhase.h | 134 ++++++++++++++++++++++- 2 files changed, 130 insertions(+), 6 deletions(-) diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index 378ac3313..7e1aac142 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -371,7 +371,7 @@ namespace Cantera { } } //==================================================================================================================== - void LatticeSolidPhase::setLatticeMoleFractions(int nn, std::string x) { + void LatticeSolidPhase::setLatticeMoleFractionsByName(int nn, std::string x) { m_lattice[nn]->setMoleFractionsByName(x); int n, k, loc=0, nsp; doublereal ndens; diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index e05c81874..f7acfd2e0 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -252,14 +252,34 @@ namespace Cantera { */ virtual void getMoleFractions(doublereal * const x) const; + //! The mole fraction of species k. + /*! + * If k is ouside the valid + * range, an exception will be thrown. Note that it is + * somewhat more efficent to call getMoleFractions if the + * mole fractions of all species are desired. + * @param k species index + */ doublereal moleFraction(const int k) const { return err("not implemented"); } - + //! Get the species mass fractions. + /*! + * @param y On return, y contains the mass fractions. Array \a y must have a length + * greater than or equal to the number of species. + */ void getMassFractions(doublereal* const y) const { err("not implemented"); - } + } + + //! Mass fraction of species k. + /*! + * If k is outside the valid range, an exception will be thrown. Note that it is + * somewhat more efficent to call getMassFractions if the mass fractions of all species are desired. + * + * @param k species index + */ doublereal massFraction(const int k) const { return err("not implemented"); } @@ -306,16 +326,98 @@ namespace Cantera { err("not implemented"); } - + //! This method returns an array of generalized activity concentrations + /*! + * The generalized activity concentrations, + * \f$ C^a_k \f$, are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ virtual void getActivityConcentrations(doublereal* c) const; + //! Get the array of non-dimensional molar-based activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param ac Output vector of activity coefficients. Length: m_kk. + */ virtual void getActivityCoefficients(doublereal* ac) const; + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ virtual void getChemPotentials(doublereal* mu) const; + + //! Get the array of standard state chemical potentials at unit activity for the species + //! at their standard states at the current T and P of the solution. + /*! + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution + * + * @param mu0 Output vector of chemical potentials. + * Length: m_kk. + */ virtual void getStandardChemPotentials(doublereal* mu0) const; + + //! Return the standard concentration for the kth species + /*! + * The standard concentration \f$ C^0_k \f$ used to normalize + * the activity (i.e., generalized) concentration. In many cases, this quantity + * will be the same for all species in a phase - for example, + * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this + * reason, this method returns a single value, instead of an + * array. However, for phases in which the standard + * concentration is species-specific (e.g. surface species of + * different sizes), this method may be called with an + * optional parameter indicating the species. + * + * @param k Optional parameter indicating the species. The default + * is to assume this refers to species 0. + * @return + * Returns the standard concentration. The units are by definition + * dependent on the ThermoPhase and kinetics manager representation. + */ virtual doublereal standardConcentration(int k=0) const; + + //! Natural logarithm of the standard concentration of the kth species. + /*! + * @param k index of the species (defaults to zero) + */ virtual doublereal logStandardConc(int k=0) const; + //! Initialize the ThermoPhase object after all species have been set up + /*! + * @internal Initialize. + * + * This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called from ThermoPhase::initThermoXML(), + * which is called from importPhase(), + * just prior to returning from function importPhase(). + * + * @see importCTML.cpp + */ virtual void initThermo(); //! Add in species from Slave phases @@ -326,9 +428,31 @@ namespace Cantera { */ virtual void installSlavePhases(Cantera::XML_Node* phaseNode); + + //! Set equation of state parameter values from XML entries. + /*! + * + * This method is called by function importPhase() in + * file importCTML.cpp when processing a phase definition in + * an input file. It should be overloaded in subclasses to set + * any parameters that are specific to that particular phase + * model. Note, this method is called before the phase is + * initialzed with elements and/or species. + * + * @param eosdata An XML_Node object corresponding to + * the "thermo" entry for this phase in the input file. + */ virtual void setParametersFromXML(const XML_Node& eosdata); - void setLatticeMoleFractions(int n, std::string x); + + //! Set the Lattice mole fractions using a string + /*! + * + * @param n Integer value of the lattice whose mole fractions are being set + * @param x string comtaining Name:value pairs that will specify the mole fractions + * of species on a particular lattice + */ + void setLatticeMoleFractionsByName(int n, std::string x); #ifdef H298MODIFY_CAPABILITY @@ -339,7 +463,7 @@ namespace Cantera { * of the species from its constituent elements in their standard states at 298 K and 1 bar. * * @param k Species k - * @param HF298New Specify the new value of the Heat of Formation at 298K and 1 bar + * @param Hf298New Specify the new value of the Heat of Formation at 298K and 1 bar */ virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) { m_spthermo->modifyOneHf298(k, Hf298New); From 9a8fe5b47e6c14b8e2219d36d7e9644e7b80dd5a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 23 Aug 2010 17:59:37 +0000 Subject: [PATCH 259/446] doxygen changes doxygen has troubles differentiating between Cantera::vector_fp and std::vector. I don't know what to do. --- Cantera/src/base/ctml.cpp | 4 ++-- Cantera/src/base/ctml.h | 4 ++-- Cantera/src/base/mdp_allo.h | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 0ed75a220..45172dd54 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -959,7 +959,7 @@ namespace ctml { * * @note change the v to a std::vector to eliminate a doxygen error. No idea why doxygen needs this. */ - int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp & v, + int getFloatArray(const Cantera::XML_Node& node, std::vector & v, const bool convert, const std::string unitsString, const std::string nodeName) { std::string::size_type icom; @@ -1332,7 +1332,7 @@ namespace ctml { * @param coeffs Output vector of floats containing the floatArray information. */ void getFunction(const Cantera::XML_Node& node, std::string& type, doublereal& xmin, - doublereal& xmax, Cantera::vector_fp & coeffs) { + doublereal& xmax, std::vector & coeffs) { const XML_Node& c = node.child("floatArray"); coeffs.clear(); getFloatArray(c,coeffs); diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index de39776a6..6c57abdee 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -370,7 +370,7 @@ namespace ctml { * The default value for the node name is floatArray * @return Returns the number of floats read into v. */ - int getFloatArray(const Cantera::XML_Node& node, Cantera::vector_fp & v, + int getFloatArray(const Cantera::XML_Node& node, std::vector & v, const bool convert=true, const std::string unitsString="", const std::string nodeName = "floatArray"); @@ -836,7 +836,7 @@ namespace ctml { * @param coeffs Output vector of floats containing the floatArray information. */ void getFunction(const Cantera::XML_Node& node, std::string& typeString, - doublereal& xmin, doublereal& xmax, Cantera::vector_fp & coeffs); + doublereal& xmin, doublereal& xmax, std::vector & coeffs); //! Search the child nodes of the current node for an XML Node with a Title //! attribute of a given name. diff --git a/Cantera/src/base/mdp_allo.h b/Cantera/src/base/mdp_allo.h index ef41f9b95..756b6dce4 100644 --- a/Cantera/src/base/mdp_allo.h +++ b/Cantera/src/base/mdp_allo.h @@ -45,7 +45,7 @@ * then it may be freed, always (and vica-versa). * * Where possible, the low leve routines - * memcopy and memset are used to copy or zero memory. + * memcpy and memset are used to copy or zero memory. * * No array bounds checking is ever done within these routines. buyer beware. * The bounds of arrays are not carried with the array object, ever. From d8caa353a06f88dfd790c598efaff192d61e2312 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 23 Aug 2010 18:00:01 +0000 Subject: [PATCH 260/446] Doxygen updates --- Cantera/src/transport/LTPspecies.cpp | 7 +++++-- Cantera/src/transport/MMCollisionInt.cpp | 4 ++++ Cantera/src/transport/SimpleTransport.cpp | 6 ++++-- Cantera/src/transport/TransportBase.h | 6 +++--- Cantera/src/transport/WaterTransport.h | 5 ++++- 5 files changed, 20 insertions(+), 8 deletions(-) diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index aa8f8dbb2..74ce83edb 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -1,6 +1,9 @@ /** - * @file LiquidTransportData.cpp - * Source code for liquid transport property evaluations. + * @file LTPspecies.cpp \ + * definitions for the LTPspecies objects and its children, which is the virtual base class + * for describing temperature dependence of submodels for transport parameters + * (see \ref tranprops and \link Cantera::LTPspecies LTPspecies \endlink) . + * */ /* * $Author$ diff --git a/Cantera/src/transport/MMCollisionInt.cpp b/Cantera/src/transport/MMCollisionInt.cpp index d4949529a..a1b7d5750 100644 --- a/Cantera/src/transport/MMCollisionInt.cpp +++ b/Cantera/src/transport/MMCollisionInt.cpp @@ -27,6 +27,8 @@ using namespace std; namespace Cantera { + + //! \cond const int DeltaDegree = 6; double MMCollisionInt::delta[8] = {0.0, 0.25, 0.50, 0.75, 1.0, @@ -226,6 +228,8 @@ namespace Cantera { 0.94863, 0.9487,0.9489,0.9491,0.9493,0.9491,0.9483,0.9476, 0.94444, 0.94444,0.94444,0.94444,0.94444,0.94444,0.94444,0.94444}; + //! \endcond + //==================================================================================================================== MMCollisionInt::MMCollisionInt() { diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index 680f77805..405baedee 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -27,7 +27,9 @@ using namespace std; #ifndef SAFE_DELETE +//! \cond #define SAFE_DELETE(x) if (x) { delete (x); x = 0; } +//! \endcond #endif namespace Cantera { @@ -868,7 +870,7 @@ namespace Cantera { return 0.0; } - //================================================================================================ + //=================================================================================================================== } -//================================================================================================ +//====================================================================================================================== diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 1b2650fe8..d9f3d10d6 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -39,7 +39,7 @@ namespace Cantera { /*! * \addtogroup tranprops */ - //@{ + //! \cond const int CK_Mode = 10; @@ -58,7 +58,7 @@ namespace Cantera { const int cSimpleTransport = 770; const int cRadiativeTransport = 800; const int cWaterTransport = 721; - //@} + //! \endcond // forward reference class XML_Writer; @@ -899,7 +899,7 @@ namespace Cantera { //! General definition for the transport class /*! - * \ingroups tranprops + * \ingroup tranprops */ typedef Transport transport_t; diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index e95fadcda..c8ad75a67 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -42,7 +42,10 @@ namespace Cantera { class WaterProps; class PDSS_Water; - + //! Transport Parameters for pure water + /*! + * + */ class WaterTransport : public Transport { public: From 0950fbe256bb93298196d8d2fbc6272df34dfb96 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Mon, 30 Aug 2010 21:23:17 +0000 Subject: [PATCH 261/446] in gibbs() added if (moles>0) statement --- Cantera/src/equil/MultiPhase.cpp | 35 +++++++++++++++++++++++--------- 1 file changed, 25 insertions(+), 10 deletions(-) diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index be7111f2f..b1e29ace4 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -327,8 +327,11 @@ namespace Cantera { index_t i; doublereal sum = 0.0; updatePhases(); - for (i = 0; i < m_np; i++) - sum += m_phase[i]->gibbs_mole() * m_moles[i]; + for (i = 0; i < m_np; i++) { + if (m_moles[i] > 0.0) { + sum += m_phase[i]->gibbs_mole() * m_moles[i]; + } + } return sum; } @@ -337,8 +340,11 @@ namespace Cantera { index_t i; doublereal sum = 0.0; updatePhases(); - for (i = 0; i < m_np; i++) - sum += m_phase[i]->enthalpy_mole() * m_moles[i]; + for (i = 0; i < m_np; i++) { + if (m_moles[i] > 0.0) { + sum += m_phase[i]->enthalpy_mole() * m_moles[i]; + } + } return sum; } @@ -347,8 +353,11 @@ namespace Cantera { index_t i; doublereal sum = 0.0; updatePhases(); - for (i = 0; i < m_np; i++) - sum += m_phase[i]->intEnergy_mole() * m_moles[i]; + for (i = 0; i < m_np; i++) { + if (m_moles[i] > 0.0) { + sum += m_phase[i]->intEnergy_mole() * m_moles[i]; + } + } return sum; } @@ -357,8 +366,11 @@ namespace Cantera { index_t i; doublereal sum = 0.0; updatePhases(); - for (i = 0; i < m_np; i++) - sum += m_phase[i]->entropy_mole() * m_moles[i]; + for (i = 0; i < m_np; i++) { + if (m_moles[i] > 0.0) { + sum += m_phase[i]->entropy_mole() * m_moles[i]; + } + } return sum; } @@ -369,8 +381,11 @@ namespace Cantera { index_t i; doublereal sum = 0.0; updatePhases(); - for (i = 0; i < m_np; i++) - sum += m_phase[i]->cp_mole() * m_moles[i]; + for (i = 0; i < m_np; i++) { + if (m_moles[i] > 0.0) { + sum += m_phase[i]->cp_mole() * m_moles[i]; + } + } return sum; } From 4ccbaed86234d261fad3b3c890f46e4b82a4a768 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 16 Sep 2010 20:23:56 +0000 Subject: [PATCH 262/446] Doxygen update for DenseMatrix --- Cantera/src/numerics/DAE_Solver.h | 5 - Cantera/src/numerics/DenseMatrix.cpp | 32 ++++-- Cantera/src/numerics/DenseMatrix.h | 151 +++++++++++++++++++++------ 3 files changed, 142 insertions(+), 46 deletions(-) diff --git a/Cantera/src/numerics/DAE_Solver.h b/Cantera/src/numerics/DAE_Solver.h index 4d570cca7..f57d28bbe 100644 --- a/Cantera/src/numerics/DAE_Solver.h +++ b/Cantera/src/numerics/DAE_Solver.h @@ -27,11 +27,6 @@ namespace Cantera { #ifdef DAE_DEVEL - /** - * @defgroup numerics Numerical Utilities within Cantera - * - * - */ class Jacobian { public: diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp index 4cc2c46cf..ae5376a77 100644 --- a/Cantera/src/numerics/DenseMatrix.cpp +++ b/Cantera/src/numerics/DenseMatrix.cpp @@ -67,7 +67,7 @@ namespace Cantera { static_cast(nRows()), b, 1, 0.0, prod, 1); } //==================================================================================================================== - void DenseMatrix::leftMult(const double* b, double* prod) const { + void DenseMatrix::leftMult(const double* const b, double* const prod) const { int nc = static_cast(nColumns()); int nr = static_cast(nRows()); int n, i; @@ -81,14 +81,30 @@ namespace Cantera { } } //==================================================================================================================== + vector_int& DenseMatrix::ipiv() { + return m_ipiv; + } + //==================================================================================================================== int solve(DenseMatrix& A, double* b) { + if (A.nColumns() != A.nRows()) { + throw CanteraError("DenseMatrix::solve", "Can only solve a square matrix"); + } int info=0; ct_dgetrf(static_cast(A.nRows()), static_cast(A.nColumns()), A.ptrColumn(0), //begin(), static_cast(A.nRows()), &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRF returned INFO = "+int2str(info)); + if (info != 0) { + if (info > 0) { + throw CanteraError("DenseMatrix::solve", + "DGETRF returned INFO = "+int2str(info) + ". U(i,i) is exactly zero. The factorization has" + " been completed, but the factor U is exactly singular, and division by zero will occur if " + "it is used to solve a system of equations."); + + } else { + throw CanteraError("DenseMatrix::solve", + "DGETRF returned INFO = "+int2str(info) + ". The argument i has an illegal value"); + } + } ct_dgetrs(ctlapack::NoTranspose, static_cast(A.nRows()), 1, A.ptrColumn(0), //begin(), static_cast(A.nRows()), @@ -101,6 +117,9 @@ namespace Cantera { } //==================================================================================================================== int solve(DenseMatrix& A, DenseMatrix& b) { + if (A.nColumns() != A.nRows()) { + throw CanteraError("DenseMatrix::solve", "Can only solve a square matrix"); + } int info=0; ct_dgetrf(static_cast(A.nRows()), static_cast(A.nColumns()), A.ptrColumn(0), @@ -143,14 +162,13 @@ namespace Cantera { } #endif //==================================================================================================================== - void multiply(const DenseMatrix& A, const double* b, double* prod) { + void multiply(const DenseMatrix& A, const double * const b, double * const prod) { ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, static_cast(A.nRows()), static_cast(A.nColumns()), 1.0, A.ptrColumn(0), static_cast(A.nRows()), b, 1, 0.0, prod, 1); } //==================================================================================================================== - void increment(const DenseMatrix& A, - const double* b, double* prod) { + void increment(const DenseMatrix& A, const double* b, double* prod) { ct_dgemv(ctlapack::ColMajor, ctlapack::NoTranspose, static_cast(A.nRows()), static_cast(A.nRows()), 1.0, A.ptrColumn(0), static_cast(A.nRows()), b, 1, 1.0, prod, 1); diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index 0686eca25..6d43eaef4 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -1,7 +1,8 @@ /** * @file DenseMatrix.h - * - * Dense (not sparse) matrices. + * Headers for the %DenseMatrix object, which deals with dense rectangular matrices and + * description of the numerics groupings of objects + * (see \ref numerics and \link Cantera::DenseMatrix DenseMatrix \endlink) . */ /* @@ -21,10 +22,23 @@ #include "Array.h" namespace Cantera { - /** - * A class for full (non-sparse) matrices with Fortran-compatible - * data storage. Adds matrix operations to class Array2D. + * @defgroup numerics Numerical Utilities within Cantera + * + * Cantera contains some capabilities for solving nonlinear equations and + * integrating both ODE and DAE equation systems in time. This section describes these + * capabilities. + * + */ + + + //! A class for full (non-sparse) matrices with Fortran-compatible + //! data storage, which adds matrix operations to class Array2D. + /*! + * The dense matrix class adds matrix operations onto the Array2D class. + * These matrix operations are carried out by the appropriate BLAS and LAPACK routines + * + * @ingroup numerics */ class DenseMatrix : public Array2D { @@ -32,20 +46,24 @@ namespace Cantera { //! Default Constructor DenseMatrix(); - - /** - * Constructor. Create an \c n by \c m matrix, and initialize - * all elements to \c v. + + //! Constructor. + /*! + * Create an \c n by \c m matrix, and initialize all elements to \c v. + * + * @param n New number of rows + * @param m New number of columns + * @param v Default fill value. defaults to zero. */ DenseMatrix(int n, int m, doublereal v = 0.0); - //! copy constructor + //! Copy constructor /*! * @param y Object to be copied */ DenseMatrix(const DenseMatrix& y); - //! assignment operator + //! Assignment operator /*! * @param y Object to be copied */ @@ -53,55 +71,120 @@ namespace Cantera { //! Destructor. Does nothing. virtual ~DenseMatrix(); - + //! Resize the matrix + /*! + * Resize the matrix to n rows by m cols. + * + * @param n New number of rows + * @param m New number of columns + * @param v Default fill value. defaults to zero. + */ void resize(int n, int m, doublereal v = 0.0); - - - /** - * Multiply A*b and write result to \c prod. + //! Multiply A*b and write result to \c prod. + /*! + * + * @param b input vector b with length N + * @param prod output output vector prod length = M */ virtual void mult(const double* b, double* prod) const; - /** - * Left-multiply the matrix by transpose(b), and write the - * result to prod. + //! Left-multiply the matrix by transpose(b), and write the result to prod. + /*! + * @param b left multiply by this vector. The length must be equal to n + * the number of rows in the matrix. + * + * @param prod Resulting vector. This is of length m, the number of columns + * in the matrix */ - virtual void leftMult(const double* b, double* prod) const; + virtual void leftMult(const double * const b, double* const prod) const; - vector_int& ipiv() { return m_ipiv; } + //! Return a changeable value of the pivot vector + /*! + * @return Returns a reference to the pivot vector as a vector_int + */ + vector_int& ipiv(); + + //! Return a changeable value of the pivot vector + /*! + * @return Returns a reference to the pivot vector as a vector_int + */ const vector_int& ipiv() const { return m_ipiv; } protected: + //! Vector of pivots. Length is equal to the max of m and n. vector_int m_ipiv; }; + //================================================================================================================== - /** - * Solve Ax = b. Array b is overwritten on exit with x. + + //! Solve Ax = b. Array b is overwritten on exit with x. + /*! + * The solve class uses the LAPACK routine dgetrf to invert the m xy n matrix. + * + * The factorization has the form + * A = P * L * U + * where P is a permutation matrix, L is lower triangular with unit + * diagonal elements (lower trapezoidal if m > n), and U is upper + * triangular (upper trapezoidal if m < n). + * + * The system is then solved using the LAPACK routine dgetrs + * + * @param A Dense matrix to be factored + * @param b rhs to be solved. */ int solve(DenseMatrix& A, double* b); - /** Solve Ax = b for multiple right-hand-side vectors. */ + //! Solve Ax = b for multiple right-hand-side vectors. + /*! + * @param A Dense matrix to be factored + * @param b Dense matrix of rhs's. Each column is a rhs + */ int solve(DenseMatrix& A, DenseMatrix& b); #ifdef INCL_LEAST_SQUARES - /** @todo fix lwork */ + //! Solve Ax = b in the least squares sense + /*! + * @param A Matrix to be inverted in the least squares sense + * @param b Vector b to be solved for + * @todo fix lwork + */ int leastSquares(DenseMatrix& A, double* b); #endif - /** - * Multiply \c A*b and return the result in \c prod. Uses BLAS - * routine DGEMV. - */ - void multiply(const DenseMatrix& A, const double* b, double* prod); + + //! Multiply \c A*b and return the result in \c prod. Uses BLAS routine DGEMV. + /*! + * \f[ + * prod_i = sum^N_{j = 1}{A_{ij} b_j} + * \f] + * + * @param A input Dense Matrix A with M rows and N columns + * @param b input vector b with length N + * @param prod output output vector prod length = M + */ + void multiply(const DenseMatrix& A, const double * const b, double * const prod); - void increment(const DenseMatrix& A, - const double* b, double* prod); + //! Multiply \c A*b and add it to the result in \c prod. Uses BLAS routine DGEMV. + /*! + * \f[ + * prod_i += sum^N_{j = 1}{A_{ij} b_j} + * \f] + * + * @param A input Dense Matrix A with M rows and N columns + * @param b input vector b with length N + * @param prod output output vector prod length = M + */ + void increment(const DenseMatrix& A, const double * const b, double * const prod); - /** - * invert A. A is overwritten with A^-1. + //! invert A. A is overwritten with A^-1. + /*! + * @param A Invert the matrix A and store it back in place + * + * @param nn Size of A. This defaults to -1, which means that the number + * of rows is used as the default size of n */ int invert(DenseMatrix& A, int nn=-1); From 3446c335201cd65bffadf3d99d95c3b0066baf68 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 21 Sep 2010 15:52:27 +0000 Subject: [PATCH 263/446] fixed an error in the reading of the XML file. Comments in the node of a file would create error conditions. Now, you can add comments anywhere and there shouldn't be any runtime differences. --- Cantera/src/thermo/SpeciesThermoFactory.cpp | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index d8e901afc..100a77b29 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -816,7 +816,17 @@ namespace Cantera { speciesNode["name"], ""); } const XML_Node& thermo = speciesNode.child("thermo"); - const std::vector& tp = thermo.children(); + + // Get the children of the thermo XML node. In the next bit of code we take out the comments that + // may have been childrent of the thermo XML node by doing a selective copy. + // These shouldn't interfere with the algorithm at any point. + const std::vector& tpWC = thermo.children(); + std::vector tp; + for (int i = 0; i < static_cast(tpWC.size()); i++) { + if (! (tpWC[i])->isComment()) { + tp.push_back(tpWC[i]); + } + } int nc = static_cast(tp.size()); string mname = thermo["model"]; @@ -845,9 +855,6 @@ namespace Cantera { else if (f->name() == "NASA9") { installNasa9ThermoFromXML(speciesNode["name"], spthermo, k, tp); } - // else if (f->name() == "HKFT") { - // installHKFTThermoFromXML(s["name"], spthermo, k, tp); - //} #ifdef WITH_ADSORBATE else if (f->name() == "adsorbate") { installAdsorbateThermoFromXML(speciesNode["name"], spthermo, k, *f); From fd62251e6fa2b20226490ed6d747d39965df8643 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 21 Sep 2010 16:03:45 +0000 Subject: [PATCH 264/446] Added a capability to expose the comment field. nChildren now takes an argument (has a default) to ignore comments. --- Cantera/src/base/xml.cpp | 24 +++++++++++++++++++----- Cantera/src/base/xml.h | 10 +++++++--- 2 files changed, 26 insertions(+), 8 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 8aa6afe53..2ea75093c 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -835,15 +835,29 @@ namespace Cantera { const std::vector& XML_Node::children() const { return m_children; } - - // return the number of children + //===================================================================================================================== + // Return the number of children /* - * + * @param discardComments Bool indicating whether we should ignore comments in the count. defaults to false */ - int XML_Node::nChildren() const { + int XML_Node::nChildren(const bool discardComments) const { + if (discardComments) { + int count = 0; + for (int i = 0; i < m_nchildren; i++) { + XML_Node *xc = m_children[i]; + if (!(xc->isComment())) { + count++; + } + } + return count; + } return m_nchildren; } - + //===================================================================================================================== + bool XML_Node::isComment() const { + return m_iscomment; + } + //===================================================================================================================== // Require that the current xml node have an attribute named // by the first argument, a, and that this attribute have the // the string value listed in the second argument, v. diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index f3063ba9f..3be1378a3 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -472,12 +472,16 @@ namespace Cantera { */ const std::vector& children() const; - //! return the number of children + //! Return the number of children /*! - * + * @param discardComments If true comments are discarded when adding up the number of children. + * Defaults to false. */ - int nChildren() const; + int nChildren(bool discardComments = false) const; + //! Boolean function indicating whether a comment + bool isComment() const; + //! Require that the current xml node have an attribute named //! by the first argument, a, and that this attribute have the //! the string value listed in the second argument, v. From 1522cded0aa73fe9c15ea3ece82da1ae028e8d73 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 29 Sep 2010 23:01:05 +0000 Subject: [PATCH 265/446] Modest improvements to the routine. Still has a long way to go --- Cantera/src/numerics/NonlinearSolver.cpp | 317 ++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 81 +++++- 2 files changed, 290 insertions(+), 108 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 49eb577ca..1ef7dcf75 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -72,6 +72,9 @@ namespace Cantera { m_func(func), solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), + m_ewt(0), + m_manualDeltaBoundsSet(0), + m_deltaBoundsMagnitudes(0), delta_t_n(-1.0), m_nfe(0), m_colScaling(0), @@ -91,6 +94,7 @@ namespace Cantera { neq_ = m_func->nEquations(); m_ewt.resize(neq_, rtol_); + m_deltaBoundsMagnitudes.resize(neq_, 0.001); m_y_n.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); ydot_new.resize(neq_, 0.0); @@ -112,6 +116,9 @@ namespace Cantera { m_func(right.m_func), solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), + m_ewt(0), + m_manualDeltaBoundsSet(0), + m_deltaBoundsMagnitudes(0), delta_t_n(-1.0), m_nfe(0), m_colScaling(0), @@ -146,6 +153,8 @@ namespace Cantera { solnType_ = right.solnType_; neq_ = right.neq_; m_ewt = right.m_ewt; + m_manualDeltaBoundsSet = right.m_manualDeltaBoundsSet; + m_deltaBoundsMagnitudes = right.m_deltaBoundsMagnitudes; m_y_n = right.m_y_n; m_y_nm1 = right.m_y_nm1; ydot_new = right.ydot_new; @@ -335,13 +344,13 @@ namespace Cantera { // Calculate the current residual - // Put the current residual into the vector, delta_y[] + // Put the current residual into the vector, residual // We need to pull this out of this function and carry it in. m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, residual); m_nfe++; } - //==================================================================================================================== + //==================================================================================================================== // Compute the undamped Newton step /* * Compute the undamped Newton step. The residual function is @@ -356,7 +365,7 @@ namespace Cantera { * scaling has been implemented. */ void NonlinearSolver::doNewtonSolve(const double time_curr, const double * const y_curr, - const double * const ydot_curr, double* const delta_y, + const double * const ydot_curr, double * const delta_y, SquareMatrix& jac, int loglevel) { int irow, jcol; @@ -393,15 +402,7 @@ namespace Cantera { } } - // if (m_matrixConditioning) { - // if (jac.m_factored) { - // m_func->matrixConditioning(0, neq_, delta_y); - // } else { - //double *jptr = &(*(jac.begin())); - // m_func->matrixConditioning(jptr, neq_, delta_y); - // } - //} - + /* * row sum scaling -> Note, this is an unequivical success * at keeping the small numbers well balanced and @@ -501,7 +502,138 @@ namespace Cantera { m_numTotalLinearSolves++; } //==================================================================================================================== - /************************************************************************** + void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() + { + for (int i = 0; i < neq_; i++) { + m_deltaBoundsMagnitudes[i] = MAX(m_deltaBoundsMagnitudes[i], 1000. * atolk_[i]); + m_deltaBoundsMagnitudes[i] = MAX(m_deltaBoundsMagnitudes[i], 0.1 * fabs(m_y_n[i])); + } + } + //==================================================================================================================== + void NonlinearSolver::setDeltaBoundsMagnitudes(const double * const deltaBoundsMagnitudes) + { + + for (int i = 0; i < neq_; i++) { + m_deltaBoundsMagnitudes[i] = deltaBoundsMagnitudes[i]; + } + m_manualDeltaBoundsSet = 1; + } + //==================================================================================================================== + /* + * + * Return the factor by which the undamped Newton step 'step0' + * must be multiplied in order to keep the update within the bounds of an accurate jacobian. + * + * The idea behind these is that the Jacobian couldn't possibly be representative, if the + * variable is changed by a lot. (true for nonlinear systems, false for linear systems) + * Maximum increase in variable in any one newton iteration: + * factor of 1.5 + * Maximum decrease in variable in any one newton iteration: + * factor of 2 + * + * @param y Initial value of the solution vector + * @param step0 initial proposed step size + * @param loglevel log level + * + * @return returns the damping factor + */ + double + NonlinearSolver::deltaBoundStep(const double * const y, const double * const step0, const int loglevel) { + + int i_fbounds = 0; + int ifbd = 0; + int i_fbd = 0; + + double sameSign = 0.0; + double ff; + double f_delta_bounds = 1.0; + double ff_alt; + for (int i = 0; i < neq_; i++) { + double y_new = y[i] + step0[i]; + sameSign = y_new * y[i]; + + /* + * Now do a delta bounds + * Increase variables by a factor of 1.5 only + * decrease variables by a factor of 2 only + */ + ff = 1.0; + + + if (sameSign >= 0.0) { + if ((fabs(y_new) > 1.5 * fabs(y[i])) && + (fabs(y_new - y[i]) > m_deltaBoundsMagnitudes[i])) { + ff = 0.5 * fabs(y[i]/(y_new - y[i])); + ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + ifbd = 1; + } + if ((fabs(2.0 * y_new) < fabs(y[i])) && + (fabs(y_new - y[i]) > m_deltaBoundsMagnitudes[i])) { + ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; + ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + ifbd = 0; + } + } else { + /* + * This handles the case where the value crosses the origin. + * - First we don't let it cross the origin until its shrunk to the size of m_deltaBoundsMagnitudes[i] + */ + if (fabs(y[i]) > m_deltaBoundsMagnitudes[i]) { + ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; + ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + if (y[i] >= 0.0) { + ifbd = 0; + } else { + ifbd = 1; + } + } + /* + * Second when it does cross the origin, we make sure that its magnitude is only 50% of the previous value. + */ + else if (fabs(y_new) > 0.5 * fabs(y[i])) { + ff = y[i]/(y_new - y[i]) * (-1.5); + ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff = MAX(ff, ff_alt); + ifbd = 0; + } + } + + if (ff < f_delta_bounds) { + f_delta_bounds = ff; + i_fbounds = i; + i_fbd = ifbd; + } + + + } + + + /* + * Report on any corrections + */ + if (loglevel > 1) { + if (f_delta_bounds < 1.0) { + if (i_fbd) { + printf("\t\tdeltaBoundStep: Increase of Variable %d causing " + "delta damping of %g\n", + i_fbounds, f_delta_bounds); + } else { + printf("\t\tdeltaBoundStep: Decrease of variable %d causing" + "delta damping of %g\n", + i_fbounds, f_delta_bounds); + } + } + } + + + return f_delta_bounds; + } + //==================================================================================================================== + + /* * * boundStep(): * @@ -528,11 +660,10 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - double NonlinearSolver::boundStep(const double* const y, - const double* const step0, const int loglevel) { - int i, i_lower = -1, i_fbounds, ifbd = 0, i_fbd = 0; - double fbound = 1.0, f_bounds = 1.0, f_delta_bounds = 1.0; - double ff, y_new, ff_alt; + double NonlinearSolver::boundStep(const double * const y, const double * const step0, const int loglevel) { + int i, i_lower = -1; + double fbound = 1.0, f_bounds = 1.0; + double ff, y_new; for (i = 0; i < neq_; i++) { y_new = y[i] + step0[i]; @@ -562,61 +693,26 @@ namespace Cantera { } } } - /* - * Now do a delta bounds - * Increase variables by a factor of 1.5 only - * decrease variables by a factor of 2 only - */ - ff = 1.0; - if ((fabs(y_new) > 1.5 * fabs(y[i])) && - (fabs(y_new-y[i]) > m_ewt[i])) { - ff = 0.5 * fabs(y[i]/(y_new - y[i])); - ff_alt = fabs(m_ewt[i] / (y_new - y[i])); - ff = MAX(ff, ff_alt); - ifbd = 1; - } - if ((fabs(2.0 * y_new) < fabs(y[i])) && - (fabs(y_new - y[i]) > m_ewt[i])) { - ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; - ff_alt = fabs(m_ewt[i] / (y_new - y[i])); - ff = MAX(ff, ff_alt); - ifbd = 0; - } - if (ff < f_delta_bounds) { - f_delta_bounds = ff; - i_fbounds = i; - i_fbd = ifbd; - } - f_delta_bounds = MIN(f_delta_bounds, ff); + } - fbound = MIN(f_bounds, f_delta_bounds); + + /* * Report on any corrections */ if (loglevel > 1) { - if (fbound != 1.0) { - if (f_bounds < f_delta_bounds) { - printf("\t\tboundStep: Variable %d causing bounds " - "damping of %g\n", - i_lower, f_bounds); - } else { - if (ifbd) { - printf("\t\tboundStep: Decrease of Variable %d causing " - "delta damping of %g\n", - i_fbounds, f_delta_bounds); - } else { - printf("\t\tboundStep: Increase of variable %d causing" - "delta damping of %g\n", - i_fbounds, f_delta_bounds); - } - } + if (f_bounds != 1.0) { + printf("\t\tboundStep: Variable %d causing bounds damping of %g\n", i_lower, f_bounds); } } - //return fbound; - return 1.0; + + double f_delta_bounds = deltaBoundStep(y, step0, loglevel); + fbound = MIN(f_bounds, f_delta_bounds); + + return fbound; } //==================================================================================================================== - /************************************************************************** + /* * * dampStep(): * @@ -678,14 +774,22 @@ namespace Cantera { if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, y1, ydot1); - } + } else { - doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, y1, ydot1, step1, loglevel); + } + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + doResidualCalc(time_curr, solnType_, y1, ydot1, step1, loglevel); + } else { + doResidualCalc(time_curr, solnType_, y1, ydot0, step1, loglevel); + } // compute the next undamped step, step1[], that would result // if y1[] were accepted. - - doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); + } else { + doNewtonSolve(time_curr, y1, ydot0, step1, jac, loglevel); + } // compute the weighted norm of step1 s1 = solnErrorNorm(step1); @@ -693,9 +797,9 @@ namespace Cantera { // write log information if (loglevel > 3) { print_solnDelta_norm_contrib((const double *) step0, - "DeltaSolnTrial", + "DeltaSoln", (const double *) step1, - "DeltaSolnTrialTest", + "DeltaSolnTrial", "dampNewt: Important Entries for " "Weighted Soln Updates:", y0, y1, ff, 5); @@ -793,8 +897,9 @@ namespace Cantera { mdp::mdp_copy_dbl_1(DATA_PTR(y_curr), y_comm, neq_); // copyn((size_t)neq_, y_comm, y_curr); - if (SolnType != NSOLN_TYPE_STEADY_STATE) { + if (SolnType != NSOLN_TYPE_STEADY_STATE || ydot_comm) { mdp::mdp_copy_dbl_1(DATA_PTR(ydot_curr), ydot_comm, neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(ydot_new), ydot_comm, neq_); } @@ -805,6 +910,9 @@ namespace Cantera { int i_backtracks; int loglevel = loglevelInput; + + + while (1 > 0) { /* @@ -813,6 +921,13 @@ namespace Cantera { m_numTotalNewtIts++; num_newt_its++; + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_curr), neq_); + /* + * Set default values of Delta bounds constraints + */ + if (!m_manualDeltaBoundsSet) { + setDefaultDeltaBoundsMagnitudes(); + } if (loglevel > 1) { printf("\t\tSolve_Nonlinear_Problem: iteration %d:\n", @@ -930,8 +1045,9 @@ namespace Cantera { done: mdp::mdp_copy_dbl_1(y_comm, DATA_PTR(y_curr), neq_); - mdp::mdp_copy_dbl_1(ydot_comm, DATA_PTR(ydot_curr), neq_); - + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + mdp::mdp_copy_dbl_1(ydot_comm, DATA_PTR(ydot_curr), neq_); + } num_linear_solves += m_numTotalLinearSolves; @@ -945,8 +1061,8 @@ namespace Cantera { } return m; } - //==================================================================================================================== - /***************************************************************8 + //==================================================================================================================== + /* * * */ @@ -964,10 +1080,10 @@ namespace Cantera { bool used; double dmax0, dmax1, error, rel_norm; printf("\t\t%s currentDamp = %g\n", title, damp); - printf("\t\t I ysoln %10s ysolnTrial " - "%10s weight relSoln0 relSoln1\n", s0, s1); + printf("\t\t I ysolnOld %10s ysolnNewRaw ysolnNewTrial " + "%10s ysolnNewTrialRaw solnWeight wtDelSoln wtDelSolnTrial\n", s0, s1); int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - printf("\t\t "); print_line("-", 90); + printf("\t\t "); print_line("-", 120); for (jnum = 0; jnum < num_entries; jnum++) { dmax1 = -1.0; for (i = 0; i < neq_; i++) { @@ -992,13 +1108,12 @@ namespace Cantera { dmax0 = sqrt(error * error); error = solnDelta1[i] / m_ewt[i]; dmax1 = sqrt(error * error); - printf("\t\t %4d %12.4e %12.4e %12.4e %12.4e " - "%12.4e %12.4e %12.4e\n", - i, y0[i], solnDelta0[i], y1[i], - solnDelta1[i], m_ewt[i], dmax0, dmax1); + printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e\n", + i, y0[i], solnDelta0[i], y0[i] + solnDelta0[i], y1[i], + solnDelta1[i], y1[i]+ solnDelta1[i], m_ewt[i], dmax0, dmax1); } } - printf("\t\t "); print_line("-", 90); + printf("\t\t "); print_line("-", 120); mdp::mdp_safe_free((void **) &imax); } //==================================================================================================================== @@ -1032,7 +1147,7 @@ namespace Cantera { } return diff; } - //================================================================================================ + //==================================================================================================================== /* * * Function called by BEuler to evaluate the Jacobian matrix and the @@ -1130,8 +1245,10 @@ namespace Cantera { y[j] = ysave + dy; dy = y[j] - ysave; - ydotsave = ydot[j]; - ydot[j] += dy * CJ; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydotsave = ydot[j]; + ydot[j] += dy * CJ; + } /* * Call the functon */ @@ -1146,9 +1263,10 @@ namespace Cantera { col_j[i] = diff / dy; //col_j[i] = (m_wksp[i] - f[i])/dy; } - - y[j] = ysave; - ydot[j] = ydotsave; + y[j] = ysave; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydot[j] = ydotsave; + } } /* @@ -1160,8 +1278,14 @@ namespace Cantera { } //==================================================================================================================== + // Internal function to calculate the time derivative at the new step + /* + * @param order of the BDF method + * @param y_curr current value of the solution + * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr + */ void NonlinearSolver:: - calc_ydot(int order, double *y_curr, double *ydot_curr) + calc_ydot(const int order, const double * const y_curr, double * const ydot_curr) { if (!ydot_curr) { return; @@ -1185,17 +1309,18 @@ namespace Cantera { return; } } - //================================================================================================ + //==================================================================================================================== + // Apply a filtering step /* - * filterNewStep(): - * - * void BEulerInt:: + * @param timeCurrent Current value of the time + * @param y_current current value of the solution + * @param ydot_current Current value of the solution derivative. * + * @return Returns the norm of the value of the amount filtered */ - double NonlinearSolver::filterNewStep(double timeCurrent, double *y_current, double *ydot_current) { + double NonlinearSolver::filterNewStep(const double timeCurrent, double * const y_current, double *const ydot_current) { return 0.0; } - //==================================================================================================================== } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index b23902c6e..123ca9bce 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -144,12 +144,33 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. * + * @param timeCurrent Current value of the time + * @param y_current Current value of the solution + * @param ydot_current Current value of the solution derivative. + * */ void doNewtonSolve(const double time_curr, const double * const y_curr, const double * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel); + + + //! Set default deulta bounds amounts + /*! + * Delta bounds are set to 0.01 for all unknowns arbitrarily and capriciously + * Then, for each call to the nonlinear solver + * Then, they are increased to 1000 x atol + * then, they are increased to 0.1 fab(y[i]) + */ + void setDefaultDeltaBoundsMagnitudes(); + + //! Set the delta Bounds magnitudes by hand + /*! + * @param deltaboundsMagnitudes + */ + void setDeltaBoundsMagnitudes(const double * const deltaBoundsMagnitudes); + - //! + //! Bound the step /*! * * Return the factor by which the undamped Newton step 'step0' @@ -194,13 +215,14 @@ namespace Cantera { */ void calc_y_pred(int); - /** - * Internal function to calculate the time derivative at the - * new step - */ - void calc_ydot(int, double *, double *); - - + + //! Internal function to calculate the time derivative at the new step + /*! + * @param order of the BDF method + * @param y_curr current value of the solution + * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr + */ + void calc_ydot(const int order, const double * const y_curr, double * const ydot_curr); //! Function called to evaluate the jacobian matrix and the curent //! residual vector. @@ -213,8 +235,36 @@ namespace Cantera { double * const ydot, int num_newt_its); - double filterNewStep(double, double *, double *); - + //! Apply a filtering step + /*! + * @param timeCurrent Current value of the time + * @param y_current current value of the solution + * @param ydot_current Current value of the solution derivative. + * + * @return Returns the norm of the value of the amount filtered + */ + double filterNewStep(const double timeCurrent, double * const y_current, double * const ydot_current); + + + //! Return the factor by which the undamped Newton step 'step0' + //! must be multiplied in order to keep the update within the bounds of an accurate jacobian. + /*! + * + * The idea behind these is that the Jacobian couldn't possibly be representative, if the + * variable is changed by a lot. (true for nonlinear systems, false for linear systems) + * Maximum increase in variable in any one newton iteration: + * factor of 1.5 + * Maximum decrease in variable in any one newton iteration: + * factor of 2 + * + * @param y Initial value of the solution vector + * @param step0 initial proposed step size + * @param loglevel log level + * + * @return returns the damping factor + */ + double deltaBoundStep(const double * const y, const double * const step0, const int loglevel); + //! Find a damping coefficient through a look-ahead mechanism /*! * On entry, step0 must contain an undamped Newton step for the @@ -242,8 +292,6 @@ namespace Cantera { - // Compute the weighted norm of the undamped step size step0 - //! Find the solution to F(X) = 0 by damped Newton iteration. /*! * On @@ -265,8 +313,11 @@ namespace Cantera { int loglevelInput); + //! Set the column scales void setColumnScales(); + + //! Print solution norm contribution void print_solnDelta_norm_contrib(const double * const solnDelta0, const char * const s0, @@ -296,6 +347,12 @@ namespace Cantera { //! Soln error weights std::vector m_ewt; + //! Boolean indicating whether a manual delta bounds has been input. + + int m_manualDeltaBoundsSet; + //! Soln Delta bounds magnitudes + std::vector m_deltaBoundsMagnitudes; + std::vector m_y_n; std::vector m_y_nm1; From 6baf8238b620f1d4cbc56e4210dd49fc39efb9b6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 2 Oct 2010 04:47:22 +0000 Subject: [PATCH 266/446] Added functions to PureFluidPhase. Added a read of p0 for shomate. Note, we still are not honoring that value. This will change most computed results when we change this. --- Cantera/src/thermo/PureFluidPhase.cpp | 484 ++++++++++++-------- Cantera/src/thermo/PureFluidPhase.h | 109 ++++- Cantera/src/thermo/SpeciesThermoFactory.cpp | 12 +- 3 files changed, 389 insertions(+), 216 deletions(-) diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index f67df60d7..41dcc6bcc 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -76,239 +76,323 @@ namespace Cantera { - PureFluidPhase::~PureFluidPhase() { - delete m_sub; - } + PureFluidPhase::~PureFluidPhase() { + delete m_sub; + } - void PureFluidPhase:: - initThermo() { - if (m_sub) delete m_sub; - m_sub = tpx::GetSub(m_subflag); - if (m_sub == 0) { - throw CanteraError("PureFluidPhase::initThermo", - "could not create new substance object."); - } - m_mw = m_sub->MolWt(); - m_weight[0] = m_mw; - setMolecularWeight(0,m_mw); - double one = 1.0; - setMoleFractions(&one); - double cp0_R, h0_RT, s0_R, T0, p; - T0 = 298.15; - if (T0 < m_sub->Tcrit()) { - m_sub->Set(tpx::TX, T0, 1.0); - p = 0.01*m_sub->P(); - } - else { - p = 0.001*m_sub->Pcrit(); - } - m_sub->Set(tpx::TP, T0, p); + void PureFluidPhase:: + initThermo() { + if (m_sub) delete m_sub; + m_sub = tpx::GetSub(m_subflag); + if (m_sub == 0) { + throw CanteraError("PureFluidPhase::initThermo", + "could not create new substance object."); + } + m_mw = m_sub->MolWt(); + m_weight[0] = m_mw; + setMolecularWeight(0,m_mw); + double one = 1.0; + setMoleFractions(&one); + double cp0_R, h0_RT, s0_R, T0, p; + T0 = 298.15; + if (T0 < m_sub->Tcrit()) { + m_sub->Set(tpx::TX, T0, 1.0); + p = 0.01*m_sub->P(); + } + else { + p = 0.001*m_sub->Pcrit(); + } + p = 0.001 * p; + m_sub->Set(tpx::TP, T0, p); - m_spthermo->update_one(0, T0, &cp0_R, &h0_RT, &s0_R); - double s_R = s0_R - log(p/refPressure()); - m_sub->setStdState(h0_RT*GasConstant*298.15/m_mw, - s_R*GasConstant/m_mw, T0, p); - if (m_verbose) { - writelog("PureFluidPhase::initThermo: initialized phase " - +id()+"\n"); - } + m_spthermo->update_one(0, T0, &cp0_R, &h0_RT, &s0_R); + double s_R = s0_R - log(p/refPressure()); + m_sub->setStdState(h0_RT*GasConstant*298.15/m_mw, + s_R*GasConstant/m_mw, T0, p); + if (m_verbose) { + writelog("PureFluidPhase::initThermo: initialized phase " + +id()+"\n"); } + } - void PureFluidPhase:: - setParametersFromXML(const XML_Node& eosdata) { - eosdata._require("model","PureFluid"); - m_subflag = atoi(eosdata["fluid_type"].c_str()); - if (m_subflag < 0) - throw CanteraError("PureFluidPhase::setParametersFromXML", - "missing or negative substance flag"); - } + void PureFluidPhase:: + setParametersFromXML(const XML_Node& eosdata) { + eosdata._require("model","PureFluid"); + m_subflag = atoi(eosdata["fluid_type"].c_str()); + if (m_subflag < 0) + throw CanteraError("PureFluidPhase::setParametersFromXML", + "missing or negative substance flag"); + } - doublereal PureFluidPhase:: - enthalpy_mole() const { - setTPXState(); - doublereal h = m_sub->h() * m_mw; - check(h); - return h; - } + doublereal PureFluidPhase:: + enthalpy_mole() const { + setTPXState(); + doublereal h = m_sub->h() * m_mw; + check(h); + return h; + } - doublereal PureFluidPhase:: - intEnergy_mole() const { - setTPXState(); - doublereal u = m_sub->u() * m_mw; - check(u); - return u; - } + doublereal PureFluidPhase:: + intEnergy_mole() const { + setTPXState(); + doublereal u = m_sub->u() * m_mw; + check(u); + return u; + } - doublereal PureFluidPhase:: - entropy_mole() const { - setTPXState(); - doublereal s = m_sub->s() * m_mw; - check(s); - return s; - } + doublereal PureFluidPhase:: + entropy_mole() const { + setTPXState(); + doublereal s = m_sub->s() * m_mw; + check(s); + return s; + } - doublereal PureFluidPhase:: - gibbs_mole() const { - setTPXState(); - doublereal g = m_sub->g() * m_mw; - check(g); - return g; - } + doublereal PureFluidPhase:: + gibbs_mole() const { + setTPXState(); + doublereal g = m_sub->g() * m_mw; + check(g); + return g; + } - doublereal PureFluidPhase:: - cp_mole() const { - setTPXState(); - doublereal cp = m_sub->cp() * m_mw; - check(cp); - return cp; - } + doublereal PureFluidPhase:: + cp_mole() const { + setTPXState(); + doublereal cp = m_sub->cp() * m_mw; + check(cp); + return cp; + } - doublereal PureFluidPhase:: - cv_mole() const { - setTPXState(); - doublereal cv = m_sub->cv() * m_mw; - check(cv); - return cv; - } + doublereal PureFluidPhase:: + cv_mole() const { + setTPXState(); + doublereal cv = m_sub->cv() * m_mw; + check(cv); + return cv; + } - doublereal PureFluidPhase:: - pressure() const { - setTPXState(); - doublereal p = m_sub->P(); - check(p); - return p; - } + doublereal PureFluidPhase:: + pressure() const { + setTPXState(); + doublereal p = m_sub->P(); + check(p); + return p; + } - void PureFluidPhase:: - setPressure(doublereal p) { - Set(tpx::TP, temperature(), p); - setDensity(1.0/m_sub->v()); - check(); - } + void PureFluidPhase:: + setPressure(doublereal p) { + Set(tpx::TP, temperature(), p); + setDensity(1.0/m_sub->v()); + check(); + } - void PureFluidPhase::Set(int n, double x, double y) const { - try { - m_sub->Set(n, x, y); - } - catch(tpx::TPX_Error) { - reportTPXError(); - } + void PureFluidPhase::Set(int n, double x, double y) const { + try { + m_sub->Set(n, x, y); } + catch(tpx::TPX_Error) { + reportTPXError(); + } + } - void PureFluidPhase::setTPXState() const { - Set(tpx::TV, temperature(), 1.0/density()); - } + void PureFluidPhase::setTPXState() const { + Set(tpx::TV, temperature(), 1.0/density()); + } - void PureFluidPhase::check(doublereal v) const { - if (m_sub->Error() || v == tpx::Undef) { - throw CanteraError("PureFluidPhase",string(tpx::errorMsg( - m_sub->Error()))); - } + void PureFluidPhase::check(doublereal v) const { + if (m_sub->Error() || v == tpx::Undef) { + throw CanteraError("PureFluidPhase",string(tpx::errorMsg( + m_sub->Error()))); } + } - void PureFluidPhase::reportTPXError() const { - string msg = tpx::TPX_Error::ErrorMessage; - string proc = "tpx::"+tpx::TPX_Error::ErrorProcedure; - throw CanteraError(proc,msg); - } + void PureFluidPhase::reportTPXError() const { + string msg = tpx::TPX_Error::ErrorMessage; + string proc = "tpx::"+tpx::TPX_Error::ErrorProcedure; + throw CanteraError(proc,msg); + } - doublereal PureFluidPhase::isothermalCompressibility() const { - return m_sub->isothermalCompressibility(); - } + doublereal PureFluidPhase::isothermalCompressibility() const { + return m_sub->isothermalCompressibility(); + } - doublereal PureFluidPhase::thermalExpansionCoeff() const { - return m_sub->thermalExpansionCoeff(); - } + doublereal PureFluidPhase::thermalExpansionCoeff() const { + return m_sub->thermalExpansionCoeff(); + } - tpx::Substance& PureFluidPhase::TPX_Substance() { return *m_sub; } + tpx::Substance& PureFluidPhase::TPX_Substance() { return *m_sub; } - /// critical temperature - doublereal PureFluidPhase::critTemperature() const { return m_sub->Tcrit(); } + + //==================================================================================================================== + // Get the nondimensional Enthalpy functions for the species + // at their standard states at the current T and P of the solution. + /* + * @param hrt Output vector of nondimensional standard state enthalpies. + * Length: m_kk. + */ + void PureFluidPhase::getEnthalpy_RT(doublereal* hrt) const { + doublereal rt = _RT(); + doublereal h = enthalpy_mole(); + hrt[0] = h / rt; + } + + //==================================================================================================================== + // Get the array of nondimensional Entropy functions for the + // standard state species at the current T and P of the solution. + /* + * @param sr Output vector of nondimensional standard state entropies. + * Length: m_kk. + */ + void PureFluidPhase::getEntropy_R(doublereal* sr) const { + doublereal s = entropy_mole(); + sr[0] = s / GasConstant; + } + //==================================================================================================================== + // Get the nondimensional Gibbs functions for the species + // in their standard states at the current T and P of the solution. + /* + * @param grt Output vector of nondimensional standard state gibbs free energies + * Length: m_kk. + */ + void PureFluidPhase::getGibbs_RT(doublereal* grt) const { + doublereal rt = _RT(); + doublereal g = gibbs_mole(); + grt[0] = g / rt; + } + //==================================================================================================================== + // Returns the vector of nondimensional enthalpies of the reference state at the current temperature + // of the solution and the reference pressure for the species. + /* + * This base function will throw a CanteraException unless + * it is overwritten in a derived class. + * + * @param hrt Output vector containing the nondimensional reference state enthalpies + * Length: m_kk. + */ + void PureFluidPhase::getEnthalpy_RT_ref(doublereal *hrt) const { + double psave = pressure(); + double t = temperature(); + double pref = m_spthermo->refPressure(); + Set(tpx::TP, t, pref); + getEnthalpy_RT(hrt); + Set(tpx::TP, t, psave); + + } + //==================================================================================================================== + // Returns the vector of nondimensional Gibbs Free Energies of the reference state at the current temperature + // of the solution and the reference pressure for the species. + /* + * @param grt Output vector containing the nondimensional reference state + * Gibbs Free energies. Length: m_kk. + */ + void PureFluidPhase::getGibbs_RT_ref(doublereal *grt) const { + double psave = pressure(); + double t = temperature(); + double pref = m_spthermo->refPressure(); + Set(tpx::TP, t, pref); + getGibbs_RT(grt); + Set(tpx::TP, t, psave); + } + //==================================================================================================================== + // Returns the vector of nondimensional entropies of the reference state at the current temperature + // of the solution and the reference pressure for each species. + /*! + * @param er Output vector containing the nondimensional reference state + * entropies. Length: m_kk. + */ + void PureFluidPhase::getEntropy_R_ref(doublereal *er) const { + + } + //==================================================================================================================== + + /// critical temperature + doublereal PureFluidPhase::critTemperature() const { return m_sub->Tcrit(); } - /// critical pressure - doublereal PureFluidPhase::critPressure() const { return m_sub->Pcrit(); } + /// critical pressure + doublereal PureFluidPhase::critPressure() const { return m_sub->Pcrit(); } - /// critical density - doublereal PureFluidPhase::critDensity() const { return 1.0/m_sub->Vcrit(); } + /// critical density + doublereal PureFluidPhase::critDensity() const { return 1.0/m_sub->Vcrit(); } - /// saturation temperature - doublereal PureFluidPhase::satTemperature(doublereal p) const { - try { - doublereal ts = m_sub->Tsat(p); - return ts; - } - catch(tpx::TPX_Error) { - reportTPXError(); - return -1.0; - } + /// saturation temperature + doublereal PureFluidPhase::satTemperature(doublereal p) const { + try { + doublereal ts = m_sub->Tsat(p); + return ts; } + catch(tpx::TPX_Error) { + reportTPXError(); + return -1.0; + } + } - void PureFluidPhase::setState_HP(doublereal h, doublereal p, - doublereal tol) { - Set(tpx::HP, h, p); - setState_TR(m_sub->Temp(), 1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_HP(doublereal h, doublereal p, + doublereal tol) { + Set(tpx::HP, h, p); + setState_TR(m_sub->Temp(), 1.0/m_sub->v()); + check(); + } - void PureFluidPhase::setState_UV(doublereal u, doublereal v, - doublereal tol) { - Set(tpx::UV, u, v); - setState_TR(m_sub->Temp(), 1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_UV(doublereal u, doublereal v, + doublereal tol) { + Set(tpx::UV, u, v); + setState_TR(m_sub->Temp(), 1.0/m_sub->v()); + check(); + } - void PureFluidPhase::setState_SV(doublereal s, doublereal v, - doublereal tol) { - Set(tpx::SV, s, v); - setState_TR(m_sub->Temp(), 1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_SV(doublereal s, doublereal v, + doublereal tol) { + Set(tpx::SV, s, v); + setState_TR(m_sub->Temp(), 1.0/m_sub->v()); + check(); + } - void PureFluidPhase::setState_SP(doublereal s, doublereal p, - doublereal tol) { - Set(tpx::SP, s, p); - setState_TR(m_sub->Temp(), 1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_SP(doublereal s, doublereal p, + doublereal tol) { + Set(tpx::SP, s, p); + setState_TR(m_sub->Temp(), 1.0/m_sub->v()); + check(); + } - /// saturation pressure - doublereal PureFluidPhase::satPressure(doublereal t) const { - doublereal vsv = m_sub->v(); - try { - Set(tpx::TV,t,vsv); - doublereal ps = m_sub->Ps(); - return ps; - } - catch(tpx::TPX_Error) { - reportTPXError(); - return -1.0; - } + // saturation pressure + doublereal PureFluidPhase::satPressure(doublereal t) const { + doublereal vsv = m_sub->v(); + try { + Set(tpx::TV,t,vsv); + doublereal ps = m_sub->Ps(); + return ps; } + catch(tpx::TPX_Error) { + reportTPXError(); + return -1.0; + } + } - doublereal PureFluidPhase::vaporFraction() const { - setTPXState(); - doublereal x = m_sub->x(); - check(x); - return x; - } + doublereal PureFluidPhase::vaporFraction() const { + setTPXState(); + doublereal x = m_sub->x(); + check(x); + return x; + } - void PureFluidPhase::setState_Tsat(doublereal t, doublereal x) { - setTemperature(t); - setTPXState(); - Set(tpx::TX, t, x); - setDensity(1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_Tsat(doublereal t, doublereal x) { + setTemperature(t); + setTPXState(); + Set(tpx::TX, t, x); + setDensity(1.0/m_sub->v()); + check(); + } - void PureFluidPhase::setState_Psat(doublereal p, doublereal x) { - setTPXState(); - Set(tpx::PX, p, x); - setTemperature(m_sub->Temp()); - setDensity(1.0/m_sub->v()); - check(); - } + void PureFluidPhase::setState_Psat(doublereal p, doublereal x) { + setTPXState(); + Set(tpx::PX, p, x); + setTemperature(m_sub->Temp()); + setDensity(1.0/m_sub->v()); + check(); + } /** @@ -435,7 +519,7 @@ namespace Cantera { void PureFluidPhase::reportCSV(std::ofstream& csvFile) const { - csvFile.precision(3); + csvFile.precision(3); int tabS = 15; int tabM = 30; int tabL = 40; @@ -541,9 +625,9 @@ namespace Cantera { } csvFile << endl; /* - csvFile.fill('-'); - csvFile << setw(tabS+(tabM+1)*pNames.size()) << "-\n"; - csvFile.fill(' '); + csvFile.fill('-'); + csvFile << setw(tabS+(tabM+1)*pNames.size()) << "-\n"; + csvFile.fill(' '); */ for (int k = 0; k < kk; k++) { csvFile << setw(tabS) << speciesName(k) + ","; diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index 74626fe22..e08b0e2b3 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -34,7 +34,7 @@ #include "mix_defs.h" namespace tpx { - class Substance; + class Substance; } namespace Cantera { @@ -107,7 +107,7 @@ namespace Cantera { /// Molar Gibbs function. Units: J/kmol. virtual doublereal gibbs_mole() const; - /// Molar heat capacity at constant pressure. Units: J/kmol/K. + /// Molar heat capacity at constant pressure. Units: J/kmol/K. virtual doublereal cp_mole() const; /// Molar heat capacity at constant volume. Units: J/kmol/K. @@ -163,20 +163,77 @@ namespace Cantera { //! Returns a reference to the substance object tpx::Substance& TPX_Substance(); - /// critical temperature - virtual doublereal critTemperature() const; - - /// critical pressure - virtual doublereal critPressure() const; - - /// critical density - virtual doublereal critDensity() const; - - /// saturation temperature + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + + //! Get the nondimensional Enthalpy functions for the species + //! at their standard states at the current T and P of the solution. /*! - * @param p Pressure (Pa) + * @param hrt Output vector of nondimensional standard state enthalpies. + * Length: m_kk. */ - virtual doublereal satTemperature(doublereal p) const; + virtual void getEnthalpy_RT(doublereal* hrt) const; + + //! Get the array of nondimensional Entropy functions for the + //! standard state species at the current T and P of the solution. + /*! + * @param sr Output vector of nondimensional standard state entropies. + * Length: m_kk. + */ + virtual void getEntropy_R(doublereal* sr) const; + + //! Get the nondimensional Gibbs functions for the species + //! in their standard states at the current T and P of the solution. + /*! + * @param grt Output vector of nondimensional standard state gibbs free energies + * Length: m_kk. + */ + virtual void getGibbs_RT(doublereal* grt) const; + + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + //! Returns the vector of nondimensional enthalpies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * This base function will throw a CanteraException unless + * it is overwritten in a derived class. + * + * @param hrt Output vector containing the nondimensional reference state enthalpies + * Length: m_kk. + */ + virtual void getEnthalpy_RT_ref(doublereal *hrt) const; + + //! Returns the vector of nondimensional + //! Gibbs Free Energies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * @param grt Output vector containing the nondimensional reference state + * Gibbs Free energies. Length: m_kk. + */ + virtual void getGibbs_RT_ref(doublereal *grt) const; + + //! Returns the vector of nondimensional + //! entropies of the reference state at the current temperature + //! of the solution and the reference pressure for each species. + /*! + * @param er Output vector containing the nondimensional reference state + * entropies. Length: m_kk. + */ + virtual void getEntropy_R_ref(doublereal *er) const; + + + /** + * @name Setting the State + * + * These methods set all or part of the thermodynamic state. + * @{ + */ + //! Set the internally storred specific enthalpy (J/kg) and pressure (Pa) of the phase. /*! @@ -227,8 +284,25 @@ namespace Cantera { virtual void setState_SP(doublereal s, doublereal p, doublereal tol = 1.e-8); + //@} + //! @name Critical State Properties + /*! + * Critical properties for the pure fluid + */ + //@{ + + //! critical temperature + virtual doublereal critTemperature() const; + + //! critical pressure + virtual doublereal critPressure() const; + + //! critical density + virtual doublereal critDensity() const; + //@} + //! @name Saturation properties. /*! * These methods are only implemented by subclasses that @@ -237,6 +311,13 @@ namespace Cantera { */ //@{ + + //! saturation temperature + /*! + * @param p Pressure (Pa) + */ + virtual doublereal satTemperature(doublereal p) const; + //! Return the saturation pressure given the temperatur /*! * @param t Temperature (Kelvin) diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp index 100a77b29..a26a53c8e 100644 --- a/Cantera/src/thermo/SpeciesThermoFactory.cpp +++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp @@ -616,12 +616,21 @@ namespace Cantera { static void installShomateThermoFromXML(std::string speciesName, SpeciesThermo& sp, int k, const XML_Node* f0ptr, const XML_Node* f1ptr) { doublereal tmin0, tmax0, tmin1, tmax1, tmin, tmid, tmax; - const XML_Node& f0 = *f0ptr; bool dualRange = false; if (f1ptr) {dualRange = true;} tmin0 = fpValue(f0["Tmin"]); tmax0 = fpValue(f0["Tmax"]); + + doublereal p0 = OneAtm; + if (f0.hasAttrib("P0")) { + p0 = fpValue(f0["P0"]); + } + if (f0.hasAttrib("Pref")) { + p0 = fpValue(f0["Pref"]); + } + p0 = OneAtm; + tmin1 = tmax0; tmax1 = tmin1 + 0.0001; if (dualRange) { @@ -655,7 +664,6 @@ namespace Cantera { } array_fp c(15); c[0] = tmid; - doublereal p0 = OneAtm; copy(c0.begin(), c0.begin()+7, c.begin() + 1); copy(c1.begin(), c1.begin()+7, c.begin() + 8); sp.install(speciesName, k, SHOMATE, &c[0], tmin, tmax, p0); From 367d1f90b019fa75403ba687bcc5667dbf042ab4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 2 Oct 2010 04:51:00 +0000 Subject: [PATCH 267/446] Small changes that I found improved things --- ext/tpx/CarbonDioxide.cpp | 3 ++- ext/tpx/CarbonDioxide.h | 4 +++- ext/tpx/Sub.cpp | 6 ++++++ ext/tpx/Sub.h | 10 ++++++---- 4 files changed, 17 insertions(+), 6 deletions(-) diff --git a/ext/tpx/CarbonDioxide.cpp b/ext/tpx/CarbonDioxide.cpp index d0859aa06..5e717b53b 100755 --- a/ext/tpx/CarbonDioxide.cpp +++ b/ext/tpx/CarbonDioxide.cpp @@ -26,7 +26,8 @@ static const double Gamma=5.0E-6; // [??] static const double u0=3.217405E5; // [] internal energy at To static const double s0=2.1396056E3; // [] entropy at To static const double Tp=250; // [K] ?? -static const double Pc=7.38350E6; // [Pa] critical pressure +//static const double Pc=7.38350E6; // [Pa] critical pressure +static const double Pc=7.3817589E6; // Adjusted to fit the actual functional form static const double M=44.01; // [kg/kmol] molar density /* diff --git a/ext/tpx/CarbonDioxide.h b/ext/tpx/CarbonDioxide.h index ed3467616..945acf24a 100755 --- a/ext/tpx/CarbonDioxide.h +++ b/ext/tpx/CarbonDioxide.h @@ -17,7 +17,9 @@ namespace tpx { class CarbonDioxide : public Substance{ public: - CarbonDioxide() { + CarbonDioxide() : + Substance() + { m_name="CarbonDioxide"; m_formula="CO2"; } diff --git a/ext/tpx/Sub.cpp b/ext/tpx/Sub.cpp index dda02e7ab..e1c91d172 100755 --- a/ext/tpx/Sub.cpp +++ b/ext/tpx/Sub.cpp @@ -398,6 +398,12 @@ namespace tpx { if (sat >= Pcrit()) return 0; psat = sat; T = Tsat(psat); + if (T == Undef) { + Err = 0; + T = Tsave; + Rho = Rhosave; + return 0; + } } else { throw TPX_Error("Substance::Lever","general error"); diff --git a/ext/tpx/Sub.h b/ext/tpx/Sub.h index 3fd40eef8..e15106209 100755 --- a/ext/tpx/Sub.h +++ b/ext/tpx/Sub.h @@ -90,10 +90,12 @@ namespace tpx { void setStdState(double h0 = 0.0, double s0 = 0.0, double t0 = 298.15, double p0 = 1.01325e5) { Set(TP, t0, p0); - double hoff = h0 - h(); - double soff = s0 - s(); - m_entropy_offset = soff; - m_energy_offset = hoff; + double hh = h(); + double ss = s(); + double hoff = h0 - hh; + double soff = s0 - ss; + m_entropy_offset += soff; + m_energy_offset += hoff; } // information about a substance: From 452e8a495727a77148b228b651408f13b2565e2c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 4 Oct 2010 22:57:34 +0000 Subject: [PATCH 268/446] Added DenseMatrix --- docs/Cantera.cfg.in | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index 44d5e82fc..e73623793 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -790,7 +790,9 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ AqueousTransport.h \ AqueousTransport.cpp \ WaterTransport.h \ - WaterTransport.cpp + WaterTransport.cpp \ + DenseMatrix.h \ + DenseMatrix.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. From 7905ea977f327c991cb1a84cd1fe038dba2b8f5f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 4 Oct 2010 23:00:26 +0000 Subject: [PATCH 269/446] Rebaselined some test problems. --- .../min_python/negATest/negATest_blessed.out | 4 +- .../pureFluidTest/output_blessed.txt | 56 +++++++++---------- .../rankine_democxx/output_blessed.txt | 8 +-- 3 files changed, 34 insertions(+), 34 deletions(-) diff --git a/test_problems/min_python/negATest/negATest_blessed.out b/test_problems/min_python/negATest/negATest_blessed.out index d170960c3..e63158035 100644 --- a/test_problems/min_python/negATest/negATest_blessed.out +++ b/test_problems/min_python/negATest/negATest_blessed.out @@ -1,7 +1,7 @@ Number of species = 12 Number of reactions = 12 rop [ 0:O ] = 0.447058 -rop [ 1:O2 ] = -0.0021443 +rop [ 1:O2 ] = -0.00214428 rop [ 2:N ] = 0 rop [ 3:NO ] = -279.361 rop [ 4:NO2 ] = 0.00214319 @@ -17,7 +17,7 @@ fwd_rop[ 0] = 479.304 rev_rop[ 0] = 97.94 fwd_rop[ 1] = -128.201 rev_rop[ 1] = -26.1964 fwd_rop[ 2] = 0 rev_rop[ 2] = 0 fwd_rop[ 3] = -0 rev_rop[ 3] = -0 -fwd_rop[ 4] = 0 rev_rop[ 4] = 1.10334e-06 +fwd_rop[ 4] = 0 rev_rop[ 4] = 1.08891e-06 fwd_rop[ 5] = 0 rev_rop[ 5] = 0 fwd_rop[ 6] = 0 rev_rop[ 6] = 0 fwd_rop[ 7] = 0 rev_rop[ 7] = 0 diff --git a/test_problems/pureFluidTest/output_blessed.txt b/test_problems/pureFluidTest/output_blessed.txt index eef045f2e..bab40b901 100644 --- a/test_problems/pureFluidTest/output_blessed.txt +++ b/test_problems/pureFluidTest/output_blessed.txt @@ -2,29 +2,29 @@ psat(273.16) = 610.157 Comparisons to NIST: (see http://webbook.nist.gov): H0(298.15) = -2.41825e+08 J/kmol -S0(298.15) = 188939 J/kmolK +S0(298.15) = 188938 J/kmolK Ideal Gas Standard State: T Cp0 S0 -(G0-H298)/T H0-H298 (K) (J/molK) (J/molK) (J/molK) (kJ/mol) - 298.15 33.5708 188.939 188.939 0 - 500 35.2032 206.633 192.788 6.92212 - 600 36.2894 213.145 195.652 10.4959 - 1000 41.2083 232.81 206.832 25.9778 + 298.15 33.5708 188.938 188.938 0 + 500 35.2032 206.631 192.787 6.92212 + 600 36.2894 213.144 195.651 10.4959 + 1000 41.2083 232.809 206.831 25.9778 H_liq(298.15, onebar) = -2.85839e+08 J/kmol -S_liq(298.15, onebar) = 70035.2 J/kmolK +S_liq(298.15, onebar) = 70034.1 J/kmolK Liquid 1bar or psat Standard State T press psat Cp0 S0 -(G0-H298)/T H0-H298 (K) (bar) (bar) (J/molK) (J/molK) (J/molK) (kJ/mol) - 273.19 1 0.00611488 75.6592 63.4258 70.3324 -1.88682 - 298.15 1 0.0316222 75.3497 70.0352 70.0352 0 - 300 1 0.0352821 75.3212 70.5012 70.0366 0.13937 - 373.15 1.01429 1.01227 75.9509 86.9605 71.7971 5.65822 - 400 2.45845 2.45354 76.7271 92.2602 72.9877 7.70899 - 500 26.4023 26.3496 83.779 109.915 78.552 15.6817 + 273.19 1 0.00611488 75.6592 63.4248 70.3314 -1.88682 + 298.15 1 0.0316222 75.3497 70.0341 70.0341 0 + 300 1 0.0352821 75.3212 70.5001 70.0356 0.13937 + 373.15 1.01429 1.01227 75.9509 86.9595 71.7961 5.65822 + 400 2.45845 2.45354 76.7271 92.2592 72.9867 7.70899 + 500 26.4023 26.3496 83.779 109.914 78.551 15.6817 Liquid Densities: T press psat Density molarVol @@ -40,30 +40,30 @@ Liquid Densities: Table of increasing Enthalpy at 1 atm Enthalpy, Temperature, x_Vapor, Density, Entropy_mass, Gibbs_mass - -1.58665e+07, 298, 0, 997.16, 3885.3, -1.7024e+07 - -1.58665e+07, 298, 0, 997.16, 3885.3, -1.7024e+07 - -1.57665e+07, 321.939, 0, 988.59, 4208.1, -1.7121e+07 - -1.56665e+07, 345.851, 0, 976.14, 4507.7, -1.7225e+07 - -1.55665e+07, 369.663, 0, 960.78, 4787.3, -1.7336e+07 + -1.58665e+07, 298, 0, 997.16, 3885.2, -1.7024e+07 + -1.58665e+07, 298, 0, 997.16, 3885.2, -1.7024e+07 + -1.57665e+07, 321.939, 0, 988.59, 4208, -1.7121e+07 + -1.56665e+07, 345.851, 0, 976.14, 4507.6, -1.7225e+07 + -1.55665e+07, 369.663, 0, 960.78, 4787.2, -1.7336e+07 -1.54665e+07, 373.177, 0.0377465, 15.583, 5055.4, -1.7353e+07 -1.53665e+07, 373.177, 0.0820536, 7.2323, 5323.4, -1.7353e+07 - -1.52665e+07, 373.177, 0.126361, 4.7088, 5591.4, -1.7353e+07 - -1.51665e+07, 373.177, 0.170668, 3.4908, 5859.4, -1.7353e+07 + -1.52665e+07, 373.177, 0.126361, 4.7088, 5591.3, -1.7353e+07 + -1.51665e+07, 373.177, 0.170668, 3.4908, 5859.3, -1.7353e+07 -1.50665e+07, 373.177, 0.214975, 2.7734, 6127.3, -1.7353e+07 - -1.49665e+07, 373.177, 0.259282, 2.3006, 6395.3, -1.7353e+07 - -1.48665e+07, 373.177, 0.303589, 1.9655, 6663.3, -1.7353e+07 + -1.49665e+07, 373.177, 0.259282, 2.3006, 6395.2, -1.7353e+07 + -1.48665e+07, 373.177, 0.303589, 1.9655, 6663.2, -1.7353e+07 -1.47665e+07, 373.177, 0.347897, 1.7157, 6931.2, -1.7353e+07 - -1.46665e+07, 373.177, 0.392204, 1.5222, 7199.2, -1.7353e+07 - -1.45665e+07, 373.177, 0.436511, 1.3679, 7467.2, -1.7353e+07 + -1.46665e+07, 373.177, 0.392204, 1.5222, 7199.1, -1.7353e+07 + -1.45665e+07, 373.177, 0.436511, 1.3679, 7467.1, -1.7353e+07 -1.44665e+07, 373.177, 0.480818, 1.242, 7735.1, -1.7353e+07 -1.43665e+07, 373.177, 0.525125, 1.1373, 8003.1, -1.7353e+07 - -1.42665e+07, 373.177, 0.569432, 1.0489, 8271.1, -1.7353e+07 + -1.42665e+07, 373.177, 0.569432, 1.0489, 8271, -1.7353e+07 -1.41665e+07, 373.177, 0.613739, 0.97328, 8539, -1.7353e+07 -1.40665e+07, 373.177, 0.658047, 0.90781, 8807, -1.7353e+07 - -1.39665e+07, 373.177, 0.702354, 0.85059, 9075, -1.7353e+07 - -1.38665e+07, 373.177, 0.746661, 0.80016, 9343, -1.7353e+07 + -1.39665e+07, 373.177, 0.702354, 0.85059, 9074.9, -1.7353e+07 + -1.38665e+07, 373.177, 0.746661, 0.80016, 9342.9, -1.7353e+07 -1.37665e+07, 373.177, 0.790968, 0.75537, 9610.9, -1.7353e+07 - -1.36665e+07, 373.177, 0.835275, 0.71533, 9878.9, -1.7353e+07 + -1.36665e+07, 373.177, 0.835275, 0.71533, 9878.8, -1.7353e+07 -1.35665e+07, 373.177, 0.879582, 0.67932, 10147, -1.7353e+07 -1.34665e+07, 373.177, 0.923889, 0.64677, 10415, -1.7353e+07 -1.33665e+07, 373.177, 0.968197, 0.61719, 10683, -1.7353e+07 @@ -81,7 +81,7 @@ Table of increasing Enthalpy at 1 atm -1.21665e+07, 918.101, 1, 0.23923, 12723, -2.3847e+07 -1.20665e+07, 962.603, 1, 0.22815, 12829, -2.4416e+07 -1.19665e+07, 1006.5, 1, 0.21819, 12931, -2.4981e+07 - -1.18665e+07, 1049.82, 1, 0.20918, 13028, -2.5544e+07 + -1.18665e+07, 1049.82, 1, 0.20918, 13028, -2.5543e+07 Critical Temp = 647 K Critical Pressure = 218 atm Critical Dens = 317 kg/m3 diff --git a/test_problems/rankine_democxx/output_blessed.txt b/test_problems/rankine_democxx/output_blessed.txt index 1aec97b1a..4503b6b4b 100644 --- a/test_problems/rankine_democxx/output_blessed.txt +++ b/test_problems/rankine_democxx/output_blessed.txt @@ -1,7 +1,7 @@ - 1 300 101325 -1.58581e+07 3913.25 0 - 2s 300.014 800000 -1.58574e+07 3913.25 0 - 2 300.126 800000 -1.58569e+07 3914.81 0 + 1 300 101325 -1.58581e+07 3913.2 0 + 2s 300.014 800000 -1.58574e+07 3913.2 0 + 2 300.126 800000 -1.5857e+07 3914.75 0 3 443.624 800000 -1.32016e+07 10183 1 4s 373.177 101325 -1.3553e+07 10183 0.89 - 4 373.177 101325 -1.34827e+07 10371.4 0.92 + 4 373.177 101325 -1.34827e+07 10371.3 0.92 efficiency = 0.105873 From 1d0ba2d3b8fe2484fa4352d9c4b79d62353be93b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 8 Oct 2010 17:16:25 +0000 Subject: [PATCH 270/446] Changed the interface for ResidJacEval. Updated NonlinearSolver with a lot of heuristic algorithm changes. --- Cantera/src/numerics/BEulerInt.cpp | 8 +- Cantera/src/numerics/NonlinearSolver.cpp | 794 +++++++++++++++++------ Cantera/src/numerics/NonlinearSolver.h | 164 ++++- Cantera/src/numerics/ResidJacEval.cpp | 281 ++++---- Cantera/src/numerics/ResidJacEval.h | 244 +++++-- 5 files changed, 1067 insertions(+), 424 deletions(-) diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp index 75d503de6..154a89d7f 100644 --- a/Cantera/src/numerics/BEulerInt.cpp +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -272,7 +272,7 @@ namespace Cantera { /* * Get the initial conditions. */ - func.getInitialConditionsDot(m_t0, m_neq, m_y_n, m_ydot_n); + func.getInitialConditions(m_t0, m_y_n, m_ydot_n); // Store a pointer to the residual routine in the object m_func = &func; @@ -672,7 +672,7 @@ namespace Cantera { * current conditions. */ - m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f); + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); m_nfe++; m_nJacEval++; @@ -732,7 +732,7 @@ namespace Cantera { m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, m_wksp, - true, j, dy); + JacDelta_ResidEval, j, dy); m_nfe++; double diff; for (i = 0; i < m_neq; i++) { @@ -1669,7 +1669,7 @@ namespace Cantera { int irow, jcol; m_func->evalResidNJ(time_curr, delta_t_n, y_curr, - ydot_curr, delta_y); + ydot_curr, delta_y, Base_ResidEval); m_nfe++; int sz = m_func->nEquations(); for (int n = 0; n < sz; n++) { diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 1ef7dcf75..e9ac2c248 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -75,6 +75,23 @@ namespace Cantera { m_ewt(0), m_manualDeltaBoundsSet(0), m_deltaBoundsMagnitudes(0), + m_y_n(0), + m_y_nm1(0), + ydot_new(0), + m_colScales(0), + m_rowScales(0), + m_resid(0), + m_wksp(0), + m_residWts(0), + m_normResid0(0.0), + m_normResidFRaw(0.0), + m_normSolnFRaw(0.0), + m_normResidTrial(0.0), + m_resid_scaled(false), + m_y_high_bounds(0), + m_y_low_bounds(0), + m_dampBound(1.0), + m_dampRes(1.0), delta_t_n(-1.0), m_nfe(0), m_colScaling(0), @@ -89,7 +106,10 @@ namespace Cantera { m_matrixConditioning(0), m_order(1), rtol_(1.0E-3), - atolBase_(1.0E-10) + atolBase_(1.0E-10), + m_ydot_nm1(0), + atolk_(0), + m_print_flag(0) { neq_ = m_func->nEquations(); @@ -101,6 +121,8 @@ namespace Cantera { m_colScales.resize(neq_, 1.0); m_rowScales.resize(neq_, 1.0); m_resid.resize(neq_, 0.0); + m_wksp.resize(neq_, 0.0); + m_residWts.resize(neq_, 0.0); atolk_.resize(neq_, atolBase_); doublereal hb = std::numeric_limits::max(); m_y_high_bounds.resize(neq_, hb); @@ -119,6 +141,23 @@ namespace Cantera { m_ewt(0), m_manualDeltaBoundsSet(0), m_deltaBoundsMagnitudes(0), + m_y_n(0), + m_y_nm1(0), + ydot_new(0), + m_colScales(0), + m_rowScales(0), + m_resid(0), + m_wksp(0), + m_residWts(0), + m_normResid0(0.0), + m_normResidFRaw(0.0), + m_normSolnFRaw(0.0), + m_normResidTrial(0.0), + m_resid_scaled(false), + m_y_high_bounds(0), + m_y_low_bounds(0), + m_dampBound(1.0), + m_dampRes(1.0), delta_t_n(-1.0), m_nfe(0), m_colScaling(0), @@ -133,7 +172,10 @@ namespace Cantera { m_matrixConditioning(0), m_order(1), rtol_(1.0E-3), - atolBase_(1.0E-10) + atolBase_(1.0E-10), + m_ydot_nm1(0), + atolk_(0), + m_print_flag(0) { *this =operator=(right); } @@ -161,8 +203,17 @@ namespace Cantera { m_colScales = right.m_colScales; m_rowScales = right.m_rowScales; m_resid = right.m_resid; + m_wksp = right.m_wksp; + m_residWts = right.m_residWts; + m_normResid0 = right.m_normResid0; + m_normResidFRaw = right.m_normResidFRaw; + m_normSolnFRaw = right.m_normSolnFRaw; + m_normResidTrial = right.m_normResidTrial; + m_resid_scaled = right.m_resid_scaled; m_y_high_bounds = right.m_y_high_bounds; m_y_low_bounds = right.m_y_low_bounds; + m_dampBound = right.m_dampBound; + m_dampRes = right.m_dampRes; delta_t_n = right.delta_t_n; m_nfe = right.m_nfe; m_colScaling = right.m_colScaling; @@ -179,6 +230,7 @@ namespace Cantera { rtol_ = right.rtol_; atolBase_ = right.atolBase_; atolk_ = right.atolk_; + m_print_flag = right.m_print_flag; return *this; } @@ -213,58 +265,96 @@ namespace Cantera { m_y_high_bounds[i] = y_high_bounds[i]; } } - //==================================================================================================================== - /** - * L2 Norm of a delta in the solution + //==================================================================================================================== + // L2 norm of the delta of the solution vector + /* + * calculate the norm of the solution vector. This will + * involve the column scaling of the matrix * - * The second argument has a default of false. However, - * if true, then a table of the largest values is printed - * out to standard output. + * The third argument has a default of false. However, + * if true, then a table of the largest values is printed + * out to standard output. + * + * @param delta_y Vector to take the norm of + * @param title Optional title to be printed out + * @param printLargest int indicating how many specific lines should be printed out + * @param dampFactor Current value of the damping factor. Defaults to 1. + * only used for printout out a table. */ - double NonlinearSolver::solnErrorNorm(const double * const delta_y, - bool printLargest) + double NonlinearSolver::solnErrorNorm(const double * const delta_y, const char * title, int printLargest, + const double dampFactor) { - int i; + int i; double sum_norm = 0.0, error; for (i = 0; i < neq_; i++) { error = delta_y[i] / m_ewt[i]; sum_norm += (error * error); } sum_norm = sqrt(sum_norm / neq_); - if (printLargest) { - const int num_entries = 8; - double dmax1, normContrib; - int j; - int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - printf("\t\tPrintout of Largest Contributors to norm " - "of value (%g)\n", sum_norm); - printf("\t\t I ysoln deltaY weightY " - "Error_Norm**2\n"); - printf("\t\t "); print_line("-", 80); - for (int jnum = 0; jnum < num_entries; jnum++) { - dmax1 = -1.0; - for (i = 0; i < neq_; i++) { - bool used = false; - for (j = 0; j < jnum; j++) { - if (imax[j] == i) used = true; - } - if (!used) { - error = delta_y[i] / m_ewt[i]; - normContrib = sqrt(error * error); - if (normContrib > dmax1) { - imax[jnum] = i; - dmax1 = normContrib; + if (printLargest) { + if (m_print_flag >= 4 && m_print_flag <= 5) { + + printf("\t\t solnErrorNorm(): "); + if (title) { + printf("%s", title); + } else { + printf(" Delta soln norm "); + } + printf(" = %-11.4E\n", sum_norm); + } else if (m_print_flag >= 6) { + + + + const int num_entries = printLargest; + printf("\t\t "); + print_line("-", 90); + printf("\t\t solnErrorNorm(): "); + if (title) { + printf("%s", title); + } else { + printf(" Delta soln norm "); + } + printf(" = %-11.4E\n", sum_norm); + + double dmax1, normContrib; + int j; + int *imax = mdp::mdp_alloc_int_1(num_entries, -1); + printf("\t\t Printout of Largest Contributors:\n"); + printf("\t\t (damp = %g)\n", dampFactor); + printf("\t\t I weightdeltaY/sqtN| deltaY " + "ysolnOld ysolnNew Soln_Weights\n"); + printf("\t\t "); + print_line("-", 90); + + for (int jnum = 0; jnum < num_entries; jnum++) { + dmax1 = -1.0; + for (i = 0; i < neq_; i++) { + bool used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; + } + if (!used) { + error = delta_y[i] / m_ewt[i]; + normContrib = sqrt(error * error); + if (normContrib > dmax1) { + imax[jnum] = i; + dmax1 = normContrib; + } } } + i = imax[jnum]; + if (i >= 0) { + error = delta_y[i] / m_ewt[i]; + normContrib = sqrt(error * error); + printf("\t\t %4d %12.4e | %12.4e %12.4e %12.4e %12.4e\n", i, normContrib/sqrt((double)neq_), + delta_y[i], m_y_n[i], m_y_n[i] + dampFactor * delta_y[i], m_ewt[i]); + + } } - i = imax[jnum]; - if (i >= 0) { - printf("\t\t %4d %12.4e %12.4e %12.4e %12.4e\n", - i, m_y_n[i], delta_y[i], m_ewt[i], dmax1); - } + printf("\t\t "); + print_line("-", 90); + mdp::mdp_safe_free((void **) &imax); } - printf("\t\t "); print_line("-", 80); - mdp::mdp_safe_free((void **) &imax); } return sum_norm; } @@ -276,81 +366,103 @@ namespace Cantera { * if true, then a table of the largest values is printed * out to standard output. */ - double NonlinearSolver::residErrorNorm(const double * const resid, - bool printLargest) + double NonlinearSolver::residErrorNorm(const double * const resid, const char * title, const int printLargest, + const double * const y) { int i; double sum_norm = 0.0, error; for (i = 0; i < neq_; i++) { - error = resid[i] / m_rowScales[i]; + error = resid[i] / m_residWts[i]; sum_norm += (error * error); } sum_norm = sqrt(sum_norm / neq_); if (printLargest) { - const int num_entries = 8; + const int num_entries = printLargest; double dmax1, normContrib; int j; int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - printf("\t\tPrintout of Largest Contributors to norm " - "of Residual (%g)\n", sum_norm); - printf("\t\t I resid rowScale weightN " - "Error_Norm**2\n"); - printf("\t\t "); print_line("-", 80); - for (int jnum = 0; jnum < num_entries; jnum++) { - dmax1 = -1.0; - for (i = 0; i < neq_; i++) { - bool used = false; - for (j = 0; j < jnum; j++) { - if (imax[j] == i) used = true; - } - if (!used) { - error = resid[i] / m_rowScales[i]; - normContrib = sqrt(error * error); - if (normContrib > dmax1) { - imax[jnum] = i; - dmax1 = normContrib; + + + printf("\t "); + print_line("-", 90); + printf("\t\t residErrorNorm():"); + if (title) { + printf(" %s ", title); + } else { + printf(" residual L2 norm "); + } + printf("= %12.4E\n", sum_norm); + + if (m_print_flag >= 6) { + printf("\t\t Printout of Largest Contributors to norm:\n"); + printf("\t\t I |Resid/ResWt| UnsclRes ResWt | y_curr\n"); + printf("\t\t "); + print_line("-", 80); + for (int jnum = 0; jnum < num_entries; jnum++) { + dmax1 = -1.0; + for (i = 0; i < neq_; i++) { + bool used = false; + for (j = 0; j < jnum; j++) { + if (imax[j] == i) used = true; + } + if (!used) { + error = resid[i] / m_residWts[i]; + normContrib = sqrt(error * error); + if (normContrib > dmax1) { + imax[jnum] = i; + dmax1 = normContrib; + } } } + i = imax[jnum]; + if (i >= 0) { + error = resid[i] / m_residWts[i]; + normContrib = sqrt(error * error); + printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e\n", i, normContrib, resid[i], m_residWts[i], y[i]); + } } - i = imax[jnum]; - if (i >= 0) { - printf("\t\t %4d %12.4e %12.4e %12.4e \n", - i, resid[i], m_rowScales[i], normContrib); - } + + printf("\t\t "); + print_line("-", 80); } - printf("\t\t "); print_line("-", 80); mdp::mdp_safe_free((void **) &imax); } return sum_norm; } //==================================================================================================================== - - /** + /* * setColumnScales(): * * Set the column scaling vector at the current time */ void NonlinearSolver::setColumnScales() { - m_func->calcSolnScales(time_n, DATA_PTR(m_y_n), DATA_PTR(m_y_nm1), - DATA_PTR(m_colScales)); + if (m_colScaling) { + for (int i = 0; i < neq_; i++) { + m_colScales[i] = m_ewt[i]; + } + } else { + for (int i = 0; i < neq_; i++) { + m_colScales[i] = 1.0; + } + } + m_func->calcSolnScales(time_n, DATA_PTR(m_y_n), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); } //==================================================================================================================== - - void NonlinearSolver::doResidualCalc(const double time_curr, const int typeCalc, - const double * const y_curr, - const double * const ydot_curr, double* const residual, - int loglevel) + // Compute the current residual + /* + * @param time_curr Value of the time + * @param typeCalc Type of the calculation + * @param y_curr Current value of the solution vector + * @param ydot_curr Current value of the time derivative of the solution vector + */ + void NonlinearSolver::doResidualCalc(const double time_curr, const int typeCalc, const double * const y_curr, + const double * const ydot_curr) { - - - // Calculate the current residual - // Put the current residual into the vector, residual - // We need to pull this out of this function and carry it in. - m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, residual); + m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), Base_ResidEval); m_nfe++; + m_resid_scaled = false; } - - //==================================================================================================================== + //==================================================================================================================== // Compute the undamped Newton step /* * Compute the undamped Newton step. The residual function is @@ -364,18 +476,11 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. */ - void NonlinearSolver::doNewtonSolve(const double time_curr, const double * const y_curr, - const double * const ydot_curr, double * const delta_y, - SquareMatrix& jac, int loglevel) + void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, double time_curr) { int irow, jcol; - //! multiply the residual by -1 - for (int n = 0; n < neq_; n++) { - delta_y[n] = -delta_y[n]; - } - /* * Column scaling -> We scale the columns of the Jacobian @@ -405,46 +510,86 @@ namespace Cantera { /* * row sum scaling -> Note, this is an unequivical success - * at keeping the small numbers well balanced and - * nonnegative. + * at keeping the small numbers well balanced and nonnegative. */ - if (m_rowScaling) { - if (! jac.m_factored) { - /* - * Ok, this is ugly. jac.begin() returns an vector iterator - * to the first data location. - * Then &(*()) reverts it to a double *. - */ - double *jptr = &(*(jac.begin())); + + if (! jac.m_factored) { + /* + * Ok, this is ugly. jac.begin() returns an vector iterator + * to the first data location. + * Then &(*()) reverts it to a double *. + */ + double *jptr = &(*(jac.begin())); + for (irow = 0; irow < neq_; irow++) { + m_rowScales[irow] = 0.0; + } + for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { - m_rowScales[irow] = 0.0; - } - for (jcol = 0; jcol < neq_; jcol++) { - for (irow = 0; irow < neq_; irow++) { - m_rowScales[irow] += fabs(*jptr); - jptr++; - } + m_rowScales[irow] += fabs(*jptr); + jptr++; } + } + + for (irow = 0; irow < neq_; irow++) { + m_rowScales[irow] = 1.0/m_rowScales[irow]; + } + + if (m_rowScaling) { jptr = &(*(jac.begin())); for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { - *jptr /= m_rowScales[irow]; + *jptr *= m_rowScales[irow]; jptr++; } } } - for (irow = 0; irow < neq_; irow++) { - delta_y[irow] /= m_rowScales[irow]; + + + computeResidWts(); + + } + + } + //==================================================================================================================== + // Compute the undamped Newton step + /* + * Compute the undamped Newton step. The residual function is + * evaluated at the current time, t_n, at the current values of the + * solution vector, m_y_n, and the solution time derivative, m_ydot_n. + * The Jacobian is not recomputed. + * + * A factored jacobian is reused, if available. If a factored jacobian + * is not available, then the jacobian is factored. Before factoring, + * the jacobian is row and column-scaled. Column scaling is not + * recomputed. The row scales are recomputed here, after column + * scaling has been implemented. + */ + void NonlinearSolver::doNewtonSolve(const double time_curr, const double * const y_curr, + const double * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) + { + int irow; + + + // multiply the residual by -1 + if (m_rowScaling && !m_resid_scaled) { + for (int n = 0; n < neq_; n++) { + delta_y[n] = -m_rowScales[n] * m_resid[n]; + } + m_resid_scaled = true; + } else { + for (int n = 0; n < neq_; n++) { + delta_y[n] = -m_resid[n]; } } + /* * Solve the system -> This also involves inverting the * matrix */ - (void) jac.solve(delta_y); + (void) jac.solve(DATA_PTR(delta_y)); /* @@ -452,7 +597,7 @@ namespace Cantera { */ if (m_colScaling) { for (irow = 0; irow < neq_; irow++) { - delta_y[irow] *= m_colScales[irow]; + delta_y[irow] = delta_y[irow] * m_colScales[irow]; } } @@ -722,6 +867,18 @@ namespace Cantera { * that of step0. If successful, the new solution after taking the * damped step is returned in y1, and the undamped step at y1 is * returned in step1. + * + * + * @return 1 Successful step was taken: Next step was less than previous step. + * s1 is calculated + * 2 Successful step: Next step's norm is less than 0.8 + * 3 Success: The final residual is less than 1.0 + * A predicted deltaSoln is not produced however. s1 is estimated. + * 4 Success: The final residual is less than the residual + * from the previous step. + * A predicted deltaSoln is not produced however. s1 is estimated. + * 0 Uncertain Success: s1 is about the same as s0 + * -2 Unsuccessful step. */ int NonlinearSolver::dampStep(const double time_curr, const double* y0, const double *ydot0, const double* step0, @@ -730,7 +887,7 @@ namespace Cantera { int& loglevel, bool writetitle, int& num_backtracks) { - + int retnTrial = -2; // Compute the weighted norm of the undamped step size step0 double s0 = solnErrorNorm(step0); @@ -739,13 +896,13 @@ namespace Cantera { // on the current step size in the nonlinear method due to // bounds constraints (either negative values of delta // bounds constraints. - double fbound = boundStep(y0, step0, loglevel); + m_dampBound = boundStep(y0, step0, loglevel); // if fbound is very small, then y0 is already close to the // boundary and step0 points out of the allowed domain. In // this case, the Newton algorithm fails, so return an error // condition. - if (fbound < 1.e-10) { + if (m_dampBound < 1.e-10) { if (loglevel > 1) printf("\t\t\tdampStep: At limits.\n"); return -3; } @@ -755,13 +912,13 @@ namespace Cantera { //-------------------------------------------- // damping coefficient starts at 1.0 - double damp = 1.0; + m_dampRes = 1.0; int j, m; - double ff; + double ff = m_dampBound; num_backtracks = 0; for (m = 0; m < NDAMP; m++) { - ff = fbound*damp; + ff = m_dampBound * m_dampRes; // step the solution by the damped step size /* @@ -778,11 +935,41 @@ namespace Cantera { } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - doResidualCalc(time_curr, solnType_, y1, ydot1, step1, loglevel); + doResidualCalc(time_curr, solnType_, y1, ydot1); } else { - doResidualCalc(time_curr, solnType_, y1, ydot0, step1, loglevel); + doResidualCalc(time_curr, solnType_, y1, ydot0); } - + m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); + + if (m_normResidTrial < 1.0 || m_normResidTrial < m_normResid0) { + if (loglevel >= 5) { + if (m_normResidTrial < 1.0) { + printf("\t dampStep(): Current trial step and damping" + " coefficient accepted because residTrial test step < 1:\n"); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + } else if (m_normResidTrial < m_normResid0) { + printf("\t dampStep(): Current trial step and damping" + " coefficient accepted because resid0 > residTrial:\n"); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + } else { + printf("\t dampStep(): Current trial step and damping" + " coefficient accepted because residual solution damping is turned off:\n"); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + } + } + /* + * We aren't going to solve the system if we don't need to. Therefore, return an estimate + * of the next solution update based on the ratio of the residual reduction. + */ + s1 = s0 * m_normResidTrial / m_normResid0; + if (m_normResidTrial < 1.0) { + retnTrial = 3; + } else { + retnTrial = 4; + } + break; + } + // compute the next undamped step, step1[], that would result // if y1[] were accepted. if (solnType_ != NSOLN_TYPE_STEADY_STATE) { @@ -805,8 +992,8 @@ namespace Cantera { y0, y1, ff, 5); } if (loglevel > 1) { - printf("\t\t\tdampNewt: s0 = %g, s1 = %g, fbound = %g," - "damp = %g\n", s0, s1, fbound, damp); + printf("\t\t\tdampStep(): s0 = %g, s1 = %g, dampBound = %g," + "dampRes = %g\n", s0, s1, m_dampBound, m_dampRes); } @@ -815,15 +1002,18 @@ namespace Cantera { // step would result in a converged solution. Otherwise, // decrease the damping coefficient and try again. - if (s1 < 1.0E-5 || s1 < s0) { - if (loglevel > 2) { - if (s1 > s0) { - if (s1 > 1.0) { + if (s1 < 0.8 || s1 < s0) { + if (s1 < 1.0) { + if (loglevel > 2) { + if (s1 < 1.0) { printf("\t\t\tdampStep: current trial step and damping" " coefficient accepted because test step < 1\n"); printf("\t\t\t s1 = %g, s0 = %g\n", s1, s0); } - } + } + retnTrial = 2; + } else { + retnTrial = 1; } break; } else { @@ -839,7 +1029,7 @@ namespace Cantera { } } num_backtracks++; - damp /= DampFactor; + m_dampRes /= DampFactor; } // If a damping coefficient was found, return 1 if the @@ -847,13 +1037,28 @@ namespace Cantera { // a converged solution, and return 0 otherwise. If no damping // coefficient could be found, return -2. if (m < NDAMP) { - if (s1 > 1.0) return 0; - else return 1; + if (loglevel >= 4 ) { + printf("\t dampStep(): current trial step accepted retnTrial = %d, its = %d, damp = %g\n", retnTrial, m+1, ff); + } + return retnTrial; } else { - if (s1 < 0.5 && (s0 < 0.5)) return 1; - if (s1 < 1.0) return 0; - return -2; + if (s1 < 0.5 && (s0 < 0.5)) { + if (loglevel >= 4 ) { + printf("\t dampStep(): current trial step accepted kindof retnTrial = %d, its = %d, damp = %g\n", 2, m+1, ff); + } + return 2; + } + if (s1 < 1.0) { + if (loglevel >= 4 ) { + printf("\t dampStep(): current trial step accepted and soln converged retnTrial = %d, its = %d, damp = %g\n", 0, m+1, ff); + } + return 0; + } } + if (loglevel >= 4 ) { + printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", -2, m+1, ff); + } + return -2; } //==================================================================================================================== /* @@ -879,7 +1084,7 @@ namespace Cantera { int loglevelInput) { clockWC wc; - + int convRes = 0; solnType_ = SolnType; bool m_residCurrent = false; @@ -887,30 +1092,38 @@ namespace Cantera { bool forceNewJac = false; double s1=1.e30; - std::vector y_curr(neq_, 0.0); + // std::vector y_curr(neq_, 0.0); std::vector ydot_curr(neq_, 0.0); std::vector stp(neq_, 0.0); std::vector stp1(neq_, 0.0); std::vector y_new(neq_, 0.0); - - mdp::mdp_copy_dbl_1(DATA_PTR(y_curr), y_comm, neq_); - // copyn((size_t)neq_, y_comm, y_curr); + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_comm), neq_); + if (SolnType != NSOLN_TYPE_STEADY_STATE || ydot_comm) { mdp::mdp_copy_dbl_1(DATA_PTR(ydot_curr), ydot_comm, neq_); mdp::mdp_copy_dbl_1(DATA_PTR(ydot_new), ydot_comm, neq_); } - - + // Redo the solution weights every time we enter the function + createSolnWeights(DATA_PTR(m_y_n)); + m_normSolnFRaw = 1.0E1; bool frst = true; num_newt_its = 0; num_linear_solves = - m_numTotalLinearSolves; num_backtracks = 0; int i_backtracks; - int loglevel = loglevelInput; + m_print_flag = loglevelInput; + if (m_print_flag == 2 || m_print_flag == 3) { + + printf("\tsolve_nonlinear_problem():\n\n"); + printf("\t Iter Resid NewJac | LinearIts Ax-b | Fbound Fdamp DampIts | DeltaSolnF ResidF\n"); + printf("\t-------------------------------------------------------------------------------------------------\n"); + + } + while (1 > 0) { @@ -921,7 +1134,14 @@ namespace Cantera { m_numTotalNewtIts++; num_newt_its++; - mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_curr), neq_); + /* + * If we are far enough away from the solution, redo the solution weights. + */ + if (m_normSolnFRaw > 1.0E2) { + createSolnWeights(DATA_PTR(m_y_n)); + } + + //mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_curr), neq_); /* * Set default values of Delta bounds constraints */ @@ -929,8 +1149,8 @@ namespace Cantera { setDefaultDeltaBoundsMagnitudes(); } - if (loglevel > 1) { - printf("\t\tSolve_Nonlinear_Problem: iteration %d:\n", + if (m_print_flag > 1) { + printf("\tsolve_nonlinear_problem(): iteration %d:\n", num_newt_its); } @@ -939,15 +1159,15 @@ namespace Cantera { forceNewJac = true; if (forceNewJac) { - if (loglevel > 1) { - printf("\t\t\tGetting a new Jacobian and solving system\n"); + if (m_print_flag > 3) { + printf("\tsolve_nonlinear_problem(): Getting a new Jacobian and solving system\n"); } - beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(y_curr), DATA_PTR(ydot_curr), + beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), num_newt_its); m_residCurrent = true; } else { - if (loglevel > 1) { - printf("\t\t\tSolving system with old jacobian\n"); + if (m_print_flag > 1) { + printf("\tsolve_nonlinear_problem(): Solving system with old jacobian\n"); } m_residCurrent = false; } @@ -957,17 +1177,50 @@ namespace Cantera { setColumnScales(); - doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, - DATA_PTR(y_curr), DATA_PTR(ydot_curr), DATA_PTR(stp), loglevel); + doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); + + + /* + * Scale the matrix and the rhs, if they aren't already scaled + * Figure out and store the residual scaling factors. + */ + scaleMatrix(jac, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), time_curr); + + + /* + * Optional print out the initial residual + */ + if (m_print_flag >= 6) { + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n)); + } else if (m_print_flag == 4 || m_print_flag == 5) { + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n)); + } else { + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n)); + } + // compute the undamped Newton step - doNewtonSolve(time_curr, DATA_PTR(y_curr), DATA_PTR(ydot_curr), DATA_PTR(stp), - jac, loglevel); + doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), jac, m_print_flag); + + + if (m_print_flag > 3) { + m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); + } else { + m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); + } + - // damp the Newton step - m = dampStep(time_curr, DATA_PTR(y_curr), DATA_PTR(ydot_curr), + // Damp the Newton step + /* + * On return the recommended new solution and derivative is located in: + * m_y_new + * m_y_dot_new + * The estimate of the solution update norm for the next step is located in + * s1 + */ + m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), - DATA_PTR(stp1), s1, jac, loglevel, frst, i_backtracks); + DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); frst = false; num_backtracks += i_backtracks; @@ -975,65 +1228,82 @@ namespace Cantera { * Impose the minimum number of newton iterations critera */ if (num_newt_its < m_min_newt_its) { - if (m == 1) m = 0; + if (m > 0) { + if (m_print_flag > 2) { + printf("\t Damped Newton successful (m=%d) but minimum newton iterations not attained. Resolving ...\n", m); + } + m = 0; + } } + /* * Impose max newton iteration */ if (num_newt_its > 20) { m = -1; - if (loglevel > 1) { - printf("\t\t\tDampnewton unsuccessful (max newts exceeded) sfinal = %g\n", s1); + if (m_print_flag > 1) { + printf("\t\tDampnewton unsuccessful (max newts exceeded) sfinal = %g\n", s1); } } - if (loglevel > 1) { - if (m == 1) { - printf("\t\t\tDampNewton iteration successful, nonlin " - "converged sfinal = %g\n", s1); - } else if (m == 0) { - printf("\t\t\tDampNewton iteration successful, get new" - "direction, sfinal = %g\n", s1); + if (m_print_flag > 3) { + residErrorNorm(DATA_PTR(m_resid), "Resulting Residual Norm", 10, DATA_PTR(y_new)); + } + + convRes = 0; + if (m > 0) { + convRes = convergenceCheck(m, s1); + } + + if (m_print_flag >= 4) { + if (convRes > 0) { + printf("\t Damped Newton iteration successful, nonlin " + "converged, final estimate of the next solution update norm = %-12.4E\n", s1); + } else if (m >= 0) { + printf("\t Damped Newton iteration successful, " + "final estimate of the next solution update norm = %-12.4E\n", s1); } else { - printf("\t\t\tDampnewton unsuccessful sfinal = %g\n", s1); + printf("\t Damped Newton unsuccessful, final estimate of the next solution update norm = %-12.4E\n", s1); } } - // If we are converged, then let's use the best solution possible - // for an end result. We did a resolve in dampStep(). Let's update - // the solution to reflect that. - // HKM 5/16 -> Took this out, since if the last step was a - // damped step, then adding stp1[j] is undamped, and - // may lead to oscillations. It kind of defeats the - // purpose of dampStep() anyway. - // if (m == 1) { - // for (int j = 0; j < neq_; j++) { - // y_new[j] += stp1[j]; - // HKM setting intermediate y's to zero was a tossup. - // slightly different, equivalent results - // #ifdef DEBUG_HKM - // y_new[j] = MAX(0.0, y_new[j]); - // #endif - // } - // } - + + bool m_filterIntermediate = false; if (m_filterIntermediate) { if (m == 0) { (void) filterNewStep(time_n, DATA_PTR(y_new), DATA_PTR(ydot_new)); } } + // Exchange new for curr solutions - if (m == 0 || m == 1) { - mdp::mdp_copy_dbl_1(DATA_PTR(y_curr), DATA_PTR(y_new), neq_); + if (m >= 0) { + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_new), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - calc_ydot(m_order, DATA_PTR(y_curr), DATA_PTR(ydot_curr)); + calc_ydot(m_order, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); } } + if (m_print_flag == 2 || m_print_flag == 3) { + // printf("\t Iter Resid NewJac | LinearIts Ax-b | Fbound Fdamp DampIts | DeltaSolnF ResidF\n"); + + printf("\t%4d %11.3E", num_newt_its, m_normResid0); + bool m_jacAge = false; + if (!m_jacAge) { + printf(" Y |"); + } else { + printf(" N |"); + } + printf("%5d %11.3E | %10.2E %10.2E %2d | %11.3E %11.3E ", m_numTotalLinearSolves, 0.0, m_dampBound, m_dampRes, + i_backtracks, m_normSolnFRaw, m_normResidFRaw); + printf("\n"); + + } // convergence - if (m == 1) goto done; + if (convRes) { + goto done; + } // If dampStep fails, first try a new Jacobian if an old // one was being used. If it was a new Jacobian, then @@ -1044,7 +1314,24 @@ namespace Cantera { } done: - mdp::mdp_copy_dbl_1(y_comm, DATA_PTR(y_curr), neq_); + + + if (m_print_flag == 2 || m_print_flag == 3) { + if (convRes > 0) { + if (convRes == 3) { + printf("\t | | converged = 3 |(%11.3E) \n", s1); + } else { + printf("\t | | converged = %1d | %11.3E %11.3E \n", convRes, + s1, m_normResidTrial); + } + } + + printf("\t --------------------------------------------------------------------------------------------\n"); + + } + + + mdp::mdp_copy_dbl_1(y_comm, DATA_PTR(m_y_n), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { mdp::mdp_copy_dbl_1(ydot_comm, DATA_PTR(ydot_curr), neq_); } @@ -1052,8 +1339,8 @@ namespace Cantera { num_linear_solves += m_numTotalLinearSolves; double time_elapsed = wc.secondsWC(); - if (loglevel > 1) { - if (m == 1) { + if (m_print_flag > 1) { + if (m > 0) { printf("\t\tNonlinear problem solved successfully in " "%d its, time elapsed = %g sec\n", num_newt_its, time_elapsed); @@ -1080,10 +1367,10 @@ namespace Cantera { bool used; double dmax0, dmax1, error, rel_norm; printf("\t\t%s currentDamp = %g\n", title, damp); - printf("\t\t I ysolnOld %10s ysolnNewRaw ysolnNewTrial " - "%10s ysolnNewTrialRaw solnWeight wtDelSoln wtDelSolnTrial\n", s0, s1); + printf("\t\t I ysolnOld %13s ysolnNewRaw | ysolnNewTrial " + "%10s ysolnNewTrialRaw | solnWeight wtDelSoln wtDelSolnTrial\n", s0, s1); int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - printf("\t\t "); print_line("-", 120); + printf("\t\t "); print_line("-", 125); for (jnum = 0; jnum < num_entries; jnum++) { dmax1 = -1.0; for (i = 0; i < neq_; i++) { @@ -1108,12 +1395,12 @@ namespace Cantera { dmax0 = sqrt(error * error); error = solnDelta1[i] / m_ewt[i]; dmax1 = sqrt(error * error); - printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e\n", + printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e |%12.4e %12.4e %12.4e\n", i, y0[i], solnDelta0[i], y0[i] + solnDelta0[i], y1[i], solnDelta1[i], y1[i]+ solnDelta1[i], m_ewt[i], dmax0, dmax1); } } - printf("\t\t "); print_line("-", 120); + printf("\t\t "); print_line("-", 125); mdp::mdp_safe_free((void **) &imax); } //==================================================================================================================== @@ -1172,7 +1459,7 @@ namespace Cantera { * Clear the factor flag */ J.clearFactorFlag(); - if (m_jacFormMethod == NSOLN_JAC_ANAL) { + if (m_jacFormMethod == NSOLN_JAC_ANAL) { /******************************************************************** * Call the function to get a jacobian. */ @@ -1192,7 +1479,7 @@ namespace Cantera { * current conditions. */ - m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f); + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); m_nfe++; m_nJacEval++; @@ -1254,12 +1541,12 @@ namespace Cantera { */ - m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_y_nm1), - true, j, dy); + m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), + JacDelta_ResidEval, j, dy); m_nfe++; double diff; for (i = 0; i < neq_; i++) { - diff = subtractRD(m_y_nm1[i], f[i]); + diff = subtractRD(m_wksp[i], f[i]); col_j[i] = diff / dy; //col_j[i] = (m_wksp[i] - f[i])/dy; } @@ -1322,5 +1609,98 @@ namespace Cantera { return 0.0; } //==================================================================================================================== + // Compute the Residual Weights + /* + * The residual weights are defined here to be equal to the inverse of the row scaling factors used to + * row scale the matrix, after column scaling is used. They are multiplied by rtol and an atol factor + * is added as well so that if the residual is less than 1, then the calculation is deemed to be comverged. + * + * The basic idea is that a change in the solution vector on the order of the convergence tolerance + * multiplied by [RJC] which is of order one after row scaling should give you the relative weight + * of the row. Values of the residual for that row can then be normalized by the value of this weight. + * When the tolerance in delta x is achieved, the tolerance in the residual should also be achieved + * and should be checked + */ + void + NonlinearSolver::computeResidWts() + { + doublereal sum = 0.0; + for (int i = 0; i < neq_; i++) { + m_residWts[i] = 1.0 / m_rowScales[i]; + sum += m_residWts[i]; + } + sum /= neq_; + for (int i = 0; i < neq_; i++) { + m_residWts[i] = rtol_ * m_residWts[i] + atolBase_ * sum; + } + } + //===================================================================================================================== + // return the residual weights + /* + * @param residWts Vector of length neq_ + */ + void + NonlinearSolver::getResidWts(double * const residWts) const + { + for (int i = 0; i < neq_; i++) { + residWts[i] = (m_residWts)[i]; + } + } + + //===================================================================================================================== + + // Check to see if the nonlinear problem has converged + /* + * + * @return integer is returned. If positive, then the problem has converged + * 1 Successful step was taken: Next step's norm is less than 1.0. + * The final residual norm is less than 1.0. + * 2 Successful step: Next step's norm is less than 0.8. + * This step's norm is less than 1.0. + * The residual norm can be anything. + * 3 Success: The final residual is less than 1.0 + * The predicted deltaSoln is below 1.0. + * 0 Not converged yet + */ + int + NonlinearSolver::convergenceCheck(int dampCode, double s1) + { + int retn = 0; + if (m_dampBound < 0.9999) { + return retn; + } + if (m_dampRes < 0.9999) { + return retn; + } + if (dampCode <= 0) { + return retn; + } + if (dampCode == 3) { + if (s1 < 1.0) { + if (m_normResidTrial < 1.0) { + return 3; + } + } + } + if (dampCode == 4) { + if (s1 < 1.0) { + if (m_normResidTrial < 1.0) { + return 3; + } + } + } + if (s1 < 0.8) { + if (m_normSolnFRaw < 1.0) { + return 2; + } + } + if (s1 < 1.0) { + if (m_normSolnFRaw < 1.0) { + return 1; + } + } + return retn; + } + //===================================================================================================================== } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 123ca9bce..f7ff48f58 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -87,12 +87,18 @@ namespace Cantera { * calculate the norm of the solution vector. This will * involve the column scaling of the matrix * - * The second argument has a default of false. However, + * The third argument has a default of false. However, * if true, then a table of the largest values is printed * out to standard output. + * + * @param delta_y Vector to take the norm of + * @param title Optional title to be printed out + * @param printLargest int indicating how many specific lines should be printed out + * @param dampFactor Current value of the damping factor. Defaults to 1. + * only used for printout out a table. */ - double solnErrorNorm(const double * const delta_y, - bool printLargest = false); + double solnErrorNorm(const double * const delta_y, const char * title = 0, int printLargest = 0, + const double dampFactor = 1.0); //! L2 norm of the residual of the equation system /*! @@ -102,33 +108,42 @@ namespace Cantera { * The second argument has a default of false. However, * if true, then a table of the largest values is printed * out to standard output. + * + * @param resid Vector of the residuals + * @param title Optional title to be printed out + * @param printLargest Number of specific entries to be printed + * @param y Current value of y - only used for printouts */ - double residErrorNorm(const double * const resid, - bool printLargest = false); + double residErrorNorm(const double * const resid, const char * title = 0, const int printLargest = 0, + const double * const y = 0); //! Compute the current Residual /*! * Compute the time dependent residual of * the set of equations. */ - void doTDResidualCalc(const double time_curr, const int typeCalc, - const double * const y_curr, - const double * const ydot_curr, double* const residual, - int loglevel); + // void doTDResidualCalc(const double time_curr, const int typeCalc, + // const double * const y_curr, const double * const ydot_curr, int loglevel); //! Compute the current Residual /*! * Compute the steady state residual of * the set of equations. */ - void doSteadyResidualCalc(const double time_curr, const int typeCalc, - const double * const y_curr, - double* const residual, int loglevel); + // void doSteadyResidualCalc(const double time_curr, const int typeCalc, + // const double * const y_curr, int loglevel); - void doResidualCalc(const double time_curr, const int typeCalc, - const double * const y_curr, - const double * const ydot_curr, double* const residual, - int loglevel); + //! Compute the current residual + /*! + * The current value of the residual is storred in the internal work array m_resid. + * + * @param time_curr Value of the time + * @param typeCalc Type of the calculation + * @param y_curr Current value of the solution vector + * @param ydot_curr Current value of the time derivative of the solution vector + */ + void doResidualCalc(const double time_curr, const int typeCalc, const double * const y_curr, + const double * const ydot_curr); //! Compute the undamped Newton step /*! @@ -316,6 +331,12 @@ namespace Cantera { //! Set the column scales void setColumnScales(); + //! Scale the matrix + /*! + * + */ + void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, double time_curr); + //! Print solution norm contribution void @@ -329,6 +350,41 @@ namespace Cantera { double damp, int num_entries); + //! Compute the Residual Weights + /*! + * The residual weights are defined here to be equal to the inverse of the row scaling factors used to + * row scale the matrix, after column scaling is used. They are multiplied by 10-3 because the column + * weights are also multiplied by that same quantity. + * + * The basic idea is that a change in the solution vector on the order of the convergence tolerance + * multiplied by [RJC] which is of order one after row scaling should give you the relative weight + * of the row. Values of the residual for that row can then be normalized by the value of this weight. + * When the tolerance in delta x is achieved, the tolerance in the residual is also achieved. + */ + void computeResidWts(); + + //! Return the residual weights + /*! + * @param residWts Vector of length neq_ + */ + void getResidWts(double * const residWts) const; + + + //! Check to see if the nonlinear problem has converged + /*! + * + * @return integer is returned. If positive, then the problem has converged + * 1 Successful step was taken: Next step's norm is less than 1.0. + * The final residual norm is less than 1.0. + * 2 Successful step: Next step's norm is less than 0.8. + * This step's norm is less than 1.0. + * The residual norm can be anything. + * 3 Success: The final residual is less than 1.0 + * The predicted deltaSoln is below 1.0. + * 0 Not converged yet + */ + int convergenceCheck(int dampCode, double s1); + private: //! Pointer to the residual and jacobian evaluator for the @@ -347,9 +403,13 @@ namespace Cantera { //! Soln error weights std::vector m_ewt; - //! Boolean indicating whether a manual delta bounds has been input. + + + + //! Boolean indicating whether a manual delta bounds has been input. int m_manualDeltaBoundsSet; + //! Soln Delta bounds magnitudes std::vector m_deltaBoundsMagnitudes; @@ -359,28 +419,79 @@ namespace Cantera { std::vector ydot_new; - + //! Vector of column scaling factors std::vector m_colScales; //! Weights for normalizing the values of the residuals - + /*! + * These are computed if row scaling, m_rowScaling, is turned on. They are calculated currently as the + * sum of the absolute values of the rows of the jacobian. + */ std::vector m_rowScales; + + //! Value of the residual for the nonlinear problem std::vector m_resid; + //! Workspace of length neq_ + std::vector m_wksp; + + /***************************************************************************************** + * INTERNAL WEIGHTS FOR TAKING SOLUTION NORMS + ******************************************************************************************/ + //! Vector of residual weights + /*! + * These are used to establish useful and informative weighted norms of the residual vector. + */ + std::vector m_residWts; + + //! Norm of the residual at the start of each nonlinear iteration + double m_normResid0; + + //! Norm of the residual before damping + double m_normResidFRaw; + + //! Norm of the solution update created by the iteration in its raw, undamped form. + double m_normSolnFRaw; + + //! Norm of the residual for a trial calculation which may or may not be used + double m_normResidTrial; + + //! Vector of the norm + double m_normResidPoints[15]; + + bool m_resid_scaled; + + + /***************************************************************************************** + * INTERNAL BOUNDARY INFO FOR SOLUTIONS + *****************************************************************************************/ + + //! Bounds vector for each species std::vector m_y_high_bounds; //! Lower bounds vector for each species std::vector m_y_low_bounds; + //! Damping factor imposed by hard bounds and by delta bounds + double m_dampBound; + //! Additional damping factor due to bounds on the residual and solution norms + double m_dampRes; + + //! Delta t for the current step double delta_t_n; //! Counter for the total number of function evaluations int m_nfe; //! The type of column scaled used in the solution of the problem + /*! + * If true then colScaling = m_ewt[] + * if false then colScaling = 1.0 + * Currently, this is not part of the interface + */ bool m_colScaling; //! int indicating whether row scaling is turned on (1) or not (0) @@ -417,11 +528,26 @@ namespace Cantera { doublereal rtol_; + //! Base value of the absolute tolerance doublereal atolBase_; double * m_ydot_nm1; std::vector atolk_; + + //! Determines the level of printing for each time step. + /*! + * 0 -> absolutely nothing is printed for a single time step. + * 1 -> One line summary per solve_nonlinear call + * 2 -> short description, points of interest: Table of nonlinear solve - one line per iteration + * 3 -> Table is included -> More printing per nonlinear iteration (default) that occurs during the table + * 4 -> Summaries of the nonlinear solve iteration as they are occurring -> table no longer printed + * 5 -> Algorithm information on the nonlinear iterates are printed out + * 6 -> Additional info on the nonlinear iterates are printed out + * 7 -> Additional info on the linear solve is printed out. + * 8 -> Info on a per iterate of the linear solve is printed out. + */ + int m_print_flag; }; } diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 18168c055..97acf51e5 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -23,21 +23,14 @@ using namespace std; namespace Cantera { - - /************************************************************************* - * - * ResidJacEval(): - * - * Default constructor for the ResidJacEval class. - * - * atol has a default of 1.0E-13. - */ + //==================================================================================================================== + ResidJacEval::ResidJacEval(doublereal atol) : ResidEval(), m_atol(atol) { } - + //==================================================================================================================== // Copy Constructor for the %ResidJacEval object /* */ @@ -46,14 +39,11 @@ namespace Cantera { { *this = operator=(right); } - - /* - * - */ + //==================================================================================================================== ResidJacEval::~ResidJacEval() { } - + //==================================================================================================================== ResidJacEval& ResidJacEval::operator=(const ResidJacEval &right) { if (this == &right) { return *this; @@ -66,9 +56,8 @@ namespace Cantera { return *this; } - - // Duplication routine for objects which inherit from - // %ResidJacEval + //==================================================================================================================== + // Duplication routine for objects which inherit from %ResidJacEval /* * This virtual routine can be used to duplicate %ResidJacEval objects * inherited from %ResidJacEval even if the application only has @@ -81,16 +70,14 @@ namespace Cantera { ResidJacEval *ff = new ResidJacEval(*this); return ff; } - + //==================================================================================================================== int ResidJacEval::nEquations() const { return neq_; } - + //==================================================================================================================== + // Set a global value of the absolute tolerance /* - * - * setAtol(): - * - * Set the absolute tolerance value + * @param atol Value of atol */ void ResidJacEval::setAtol(doublereal atol) { @@ -100,17 +87,17 @@ namespace Cantera { "atol must be greater than zero"); } } - - /************************************************************************** + //==================================================================================================================== + //! Fill in the initial conditions + /*! + * Values for both the solution and the value of ydot may be provided. * - * - * - * Fill the solution vector with the initial conditions - * at initial time t0. + * @param t0 Time (input) + * @param y Solution vector (output) + * @param ydot Rate of change of solution vector. (output) */ void ResidJacEval:: - getInitialConditionsDot(const doublereal t0, const size_t leny, - doublereal * const y, doublereal * const ydot) { + getInitialConditions(doublereal t0, doublereal * const y, doublereal * const ydot) { for (int i = 0; i < neq_; i++) { y[i] = 0.0; } @@ -120,65 +107,75 @@ namespace Cantera { } } } - - /************************************************************************** + //==================================================================================================================== + // This function may be used to create output at various points in the execution of an application. + /* * + * @param ifunc identity of the call + * 0 Initial call + * 1 Called at the end of every successful time step + * -1 Called at the end of every unsuccessful time step + * 2 Called at the end of every call to integrateRJE() * - * - * Fill the solution vector with the initial conditions - * at initial time t0. - * - */ - void ResidJacEval:: - getInitialConditions(doublereal t0, - doublereal * const y, doublereal * const ydot) { - size_t leny = neq_; - getInitialConditionsDot(t0, leny, y, 0); - } - - /************************************************************************** - * - * user_out(): - * - * This function may be used to create output at various points in the - * execution of an application. - * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input) */ void ResidJacEval:: user_out2(const int ifunc, const doublereal t, const doublereal deltaT, const doublereal *y, const doublereal *ydot) { - } + //==================================================================================================================== + // This function may be used to create output at various points in the execution of an application. + /* + * This routine calls user_out2(). + * + * @param ifunc identity of the call + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input) + */ void ResidJacEval:: user_out(const int ifunc, const doublereal t, const doublereal *y, const doublereal *ydot) { user_out2(ifunc, t, 0.0, y, ydot); } - - /************************************************************************** - * + //==================================================================================================================== + //! Evaluate the time tracking equations, if any + /*! + * Evaluate time integrated quantities that are calculated at the + * end of every successful time step. This call is made once at the end of every successful + * time step that advances the time. It's also made once at the start of the time stepping. * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) */ void ResidJacEval:: - evalTimeTrackingEqns(const doublereal t, const doublereal deltaT, - const doublereal *y, - const doublereal *ydot) { - + evalTimeTrackingEqns(const doublereal t, const doublereal delta_t, const doublereal *y, + const doublereal *ydot) + { } - - /******************************************************************** + //==================================================================================================================== + // Return a vector of delta y's for calculation of the numerical Jacobian + /* + * There is a default algorithm provided. * + * delta_y[i] = atol[i] + 1.0E-6 ysoln[i] + * delta_y[i] = atol[i] + MAX(1.0E-6 ysoln[i] * 0.01 * solnWeights[i]) * - * - * Return a vector of delta y's for calculation of the - * numerical Jacobian + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param delta_y Value of the delta to be used in calculating the numerical jacobian + * @param solnWeights Value of the solution weights that are used in determining convergence (default = 0) */ void ResidJacEval:: - calcDeltaSolnVariables(const doublereal t, - const doublereal * const ySoln, - const doublereal * const ySolnDot, - doublereal * const deltaYSoln, + calcDeltaSolnVariables(const doublereal t, const doublereal * const ySoln, + const doublereal * const ySolnDot, doublereal * const deltaYSoln, const doublereal *const solnWeights) { if (!solnWeights) { @@ -192,95 +189,123 @@ namespace Cantera { } } } - - /****************************************************************** + //==================================================================================================================== + // Returns a vector of column scale factors that can be used to column scale Jacobians. + /* + * Default to yScales[] = 1.0 * - * calcSolnScales(): - * - * Returns a vector of ysolnScales[] that can be used to column scale - * Jacobians. + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param y_old Old Solution vector (input, do not modify) + * @param yScales Value of the column scales */ void ResidJacEval:: - calcSolnScales(const doublereal t, - const doublereal * const ysoln, - const doublereal * const ysolnOld, + calcSolnScales(const doublereal t, const doublereal * const ysoln, const doublereal * const ysolnOld, doublereal * const ysolnScales) { - for (int i = 0; i < neq_; i++) { - ysolnScales[i] = 1.0; + if (ysolnScales[0] == 0.0) { + for (int i = 0; i < neq_; i++) { + ysolnScales[i] = 1.0; + } } } - - void ResidJacEval::filterSolnPrediction(doublereal t, - doublereal * const y) { - + //==================================================================================================================== + // Filter the solution predictions + /* + * Codes might provide a predicted solution vector. This routine filters the predicted + * solution vector. + * + * @param t Time (input) + * @param y Solution vector (input, output) + */ + void ResidJacEval::filterSolnPrediction(doublereal t, doublereal * const y) + { } - - /************************************************************************** + //==================================================================================================================== + // Evalulate any stopping criteria other than a final time limit + /* + * If we are to stop the time integration for any reason other than reaching a final time limit, tout, + * provide a test here. This call is made at the end of every succesful time step iteration * - * evalStoppingCriteria() - * - * If there is a stopping critera other than time set it here. + * @return If true, the the time stepping is stopped. If false, then time stepping is stopped if t >= tout + * Defaults to false. * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) */ bool ResidJacEval:: - evalStoppingCritera(doublereal &time_current, - doublereal &delta_t_n, - doublereal *y_n, - doublereal *ydot_n) + evalStoppingCritera(const doublereal t, + const doublereal delta_t, + const doublereal * const y, + const doublereal * const ydot) { return false; } - - /************************************************************************** + //==================================================================================================================== + // Multiply the matrix by another matrix that leads to better conditioning + /* + * Provide a left sided matrix that will multiply the current jacobian, after scaling + * and lead to a better conditioned system. + * This routine is called just before the matrix is factored. + * + * Original Problem: + * J delta_x = - Resid * - * matrixConditioning() + * New problem: + * M (J delta_x) = - M Resid * - * Multiply the matrix by the inverse of a matrix which lead to a - * better conditioned system. The default, specified here, is to - * do nothing. + * @param matrix Pointer to the current jacobian (if zero, it's already been factored) + * @param nrows offsets for the matrix + * @param rhs residual vector. This also needs to be lhs multiplied by M */ void ResidJacEval:: - matrixConditioning(doublereal * const matrix, const int nrows, - doublereal * const rhs) + matrixConditioning(doublereal * const matrix, const int nrows, doublereal * const rhs) { } - - /************************************************************************** - * - */ + //==================================================================================================================== + // Evaluate the residual function + /* + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param resid Value of the residual that is computed (output) + * @param evalType Type of the residual being computed (defaults to Base_ResidEval) + * @param id_x Index of the variable that is being numerically differenced to find + * the jacobian (defaults to -1, which indicates that no variable is being + * differenced or that the residual doesn't take this issue into account) + * @param delta_x Value of the delta used in the numerical differencing + */ void ResidJacEval:: - evalResidNJ(doublereal t, const doublereal deltaT, - const doublereal * y, - const doublereal * ydot, - doublereal * resid, - bool NJevaluation, - int id_x, - doublereal delta_x) - { - printf("Not implemented\n"); - std::exit(-1); + evalResidNJ(const doublereal t, const doublereal deltaT, const doublereal * y, + const doublereal * ydot, doublereal * const resid, const ResidEval_Type_Enum evalType, + const int id_x, const doublereal delta_x) + { + throw CanteraError("ResidJacEval::evalResidNJ()", "Not implemented\n"); } - - /************************************************************************** + //==================================================================================================================== + // Calculate an analytical jacobian and the residual at the current time and values. + /* + * Only called if the jacFormation method is set to analytical * - * evalJacobian() - * - * Calculate the jacobian and the residual at the current - * time and values. - * Backwards Euler is assumed. + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param J Reference to the SquareMatrix object to be calculated (output) + * @param resid Value of the residual that is computed (output) */ void ResidJacEval:: - evalJacobian(const doublereal t, const doublereal deltaT, + evalJacobian(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot, SquareMatrix &J, doublereal * const resid) { - printf("Not implemented\n"); - std::exit(-1); + throw CanteraError("ResidJacEval::evalJacobian()", "Not implemented\n"); } - + //==================================================================================================================== } - diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 6602f8765..085c7fe02 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -25,16 +25,38 @@ namespace Cantera { - /** - * A class for full (non-sparse) matrices with Fortran-compatible - * data storage. Adds matrix operations to class Array2D. +//! Differentiates the type of residual evaluations according to functionality + enum ResidEval_Type_Enum + { + //! Base residual calculation for the time-stepping function + Base_ResidEval = 0, + //! Base residual calculation for the Jacobian calculation + JacBase_ResidEval, + //! Delta residual calculation for the Jacbobian calculation + JacDelta_ResidEval, + //! Base residual calculation for the showSolution routine + /*! + * We calculate this when we want to display a solution + */ + Base_ShowSolution + }; + + //! Wrappers for the function evaluators for Nonlinear solvers and Time steppers + /*! + * A class for full (non-sparse dense matrices with Fortran-compatible data storage. + * The class adds support for identifying what types of calls are made to the residual + * evaluator by adding the ResidEval_Type_Enum class. + * + * */ class ResidJacEval : public ResidEval { public: - /** - * Default constructor + + //!Default constructor + /*! + * @param atol Initial value of the global tolerance (defaults to 1.0E-13) */ ResidJacEval(doublereal atol = 1.0e-13); @@ -71,106 +93,196 @@ namespace Cantera { //! Return the number of equations in the equation system virtual int nEquations() const; - /** - * Evaluate the residual function. - * @param t time (input, do not modify) - * @param y solution vector (input, do not modify) - * @param ydot rate of change of solution vector. (input, do - * not modify) + //! Evaluate the residual function + /*! + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param resid Value of the residual that is computed (output) + * @param evalType Type of the residual being computed (defaults to Base_ResidEval) + * @param id_x Index of the variable that is being numerically differenced to find + * the jacobian (defaults to -1, which indicates that no variable is being + * differenced or that the residual doesn't take this issue into account) + * @param delta_x Value of the delta used in the numerical differencing */ - virtual void evalResidNJ(doublereal t, const doublereal deltaT, + virtual void evalResidNJ(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot, doublereal * const resid, - bool NJevaluation = false, - int id_x = 0, - doublereal delta_x = 0.0); + const ResidEval_Type_Enum evalType = Base_ResidEval, + const int id_x = -1, + const doublereal delta_x = 0.0); - /** - * Fill the solution vector with the initial conditions - * at initial time t0. + + //! Fill in the initial conditions + /*! + * Values for both the solution and the value of ydot may be provided. + * + * @param t0 Time (input) + * @param y Solution vector (output) + * @param ydot Rate of change of solution vector. (output) */ - virtual void getInitialConditionsDot(const doublereal t0, size_t leny, - doublereal * const y, - doublereal * const ydot); - - virtual void getInitialConditions(const doublereal t0, - doublereal * const y, - doublereal * const ydot); + virtual void getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot); - virtual void filterSolnPrediction(doublereal t, - doublereal * const y); + //! Filter the solution predictions + /*! + * Codes might provide a predicted solution vector. This routine filters the predicted + * solution vector. + * + * @param t Time (input) + * @param y Solution vector (input, output) + */ + virtual void filterSolnPrediction(const doublereal t, doublereal * const y); + //! Set a global value of the absolute tolerance + /*! + * @param atol Value of atol + */ void setAtol(doublereal atol); - virtual void evalTimeTrackingEqns(const doublereal t, const doublereal deltaT, - const doublereal * const y, + //! Evaluate the time tracking equations, if any + /*! + * Evaluate time integrated quantities that are calculated at the + * end of every successful time step. This call is made once at the end of every successful + * time step that advances the time. It's also made once at the start of the time stepping. + * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + */ + virtual void evalTimeTrackingEqns(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot); - virtual bool evalStoppingCritera(doublereal &time_current, - doublereal &delta_t_n, - doublereal *y_n, - doublereal *ydot_n); - /** - * Return a vector of delta y's for calculation of the - * numerical Jacobian + //! Evalulate any stopping criteria other than a final time limit + /*! + * If we are to stop the time integration for any reason other than reaching a final time limit, tout, + * provide a test here. This call is made at the end of every succesful time step iteration + * + * @return If true, the the time stepping is stopped. If false, then time stepping is stopped if t >= tout + * Defaults to false. + * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + */ + virtual bool evalStoppingCritera(const doublereal t, + const doublereal delta_t, + const doublereal * const y, + const doublereal * const ydot); + + + //! Return a vector of delta y's for calculation of the numerical Jacobian + /*! + * There is a default algorithm provided. + * + * delta_y[i] = atol[i] + 1.0E-6 ysoln[i] + * delta_y[i] = atol[i] + MAX(1.0E-6 ysoln[i] * 0.01 * solnWeights[i]) + * + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param delta_y Value of the delta to be used in calculating the numerical jacobian + * @param solnWeights Value of the solution weights that are used in determining convergence (default = 0) */ virtual void - calcDeltaSolnVariables(const doublereal t, - const doublereal * const ysoln, - const doublereal * const ysolnDot, - doublereal * const deltaYsoln, - const doublereal * const solnWeights=0); + calcDeltaSolnVariables(const doublereal t, + const doublereal * const y, + const doublereal * const ydot, + doublereal * const delta_y, + const doublereal * const solnWeights = 0); - /** - * Returns a vector of ysolnScales[] that can be used to column - * scale Jacobians. - */ - virtual void calcSolnScales(const doublereal t, - const doublereal * const ysoln, - const doublereal * const ysolnOld, - doublereal * const ysolnScales); - - /** - * This function may be used to create output at various points in the - * execution of an application. + + //! Returns a vector of column scale factors that can be used to column scale Jacobians. + /*! + * Default to yScales[] = 1.0 * + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param y_old Old Solution vector (input, do not modify) + * @param yScales Value of the column scales + */ + virtual void calcSolnScales(const doublereal t, const doublereal * const y, + const doublereal * const y_old, doublereal * const yScales); + + //! This function may be used to create output at various points in the execution of an application. + /*! + * + * @param ifunc identity of the call + * 0 Initial call + * 1 Called at the end of every successful time step + * -1 Called at the end of every unsuccessful time step + * 2 Called at the end of every call to integrateRJE() + * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input) */ virtual void user_out2(const int ifunc, const doublereal t, - const doublereal deltaT, + const doublereal delta_t, const doublereal * const y, const doublereal * const ydot); + //! This function may be used to create output at various points in the execution of an application. + /*! + * This routine calls user_out2(). + * + * @param ifunc identity of the call + * @param t Time (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input) + */ virtual void user_out(const int ifunc, const doublereal t, const doublereal *y, const doublereal *ydot); - + //! Multiply the matrix by another matrix that leads to better conditioning + /*! + * Provide a left sided matrix that will multiply the current jacobian, after scaling + * and lead to a better conditioned system. + * This routine is called just before the matrix is factored. + * + * Original Problem: + * J delta_x = - Resid + * + * New problem: + * M (J delta_x) = - M Resid + * + * @param matrix Pointer to the current jacobian (if zero, it's already been factored) + * @param nrows offsets for the matrix + * @param rhs residual vector. This also needs to be lhs multiplied by M + */ virtual void matrixConditioning(doublereal * const matrix, const int nrows, doublereal * const rhs); - /********************************************************************* + //! Calculate an analytical jacobian and the residual at the current time and values. + /*! + * Only called if the jacFormation method is set to analytical * - * evalJacobian() - * - * Calculate the jacobian and the residual at the current - * time and values. - * Backwards Euler is assumed. + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param J Reference to the SquareMatrix object to be calculated (output) + * @param resid Value of the residual that is computed (output) */ - virtual void evalJacobian(const doublereal t, const doublereal deltaT, - const double* const y, - const double* const ydot, + virtual void evalJacobian(const doublereal t, const doublereal delta_t, + const doublereal* const y, + const doublereal* const ydot, SquareMatrix &J, doublereal * const resid); - protected: + //! constant value of atol doublereal m_atol; + //! Number of equations int neq_; - }; } From ae989985eb98e376213e9325bb29c6be38b30f57 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 13 Oct 2010 16:58:34 +0000 Subject: [PATCH 271/446] Added a hook for specifying atol --- Cantera/src/numerics/NonlinearSolver.cpp | 14 ++++++++++++++ Cantera/src/numerics/NonlinearSolver.h | 15 ++++++++++++++- 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index e9ac2c248..19faf2def 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1702,5 +1702,19 @@ namespace Cantera { return retn; } //===================================================================================================================== + // Set the absolute tolerances for the solution variables + /* + * Set the absolute tolerances used in the calculation + * + * @param atol Vector of length neq_ that contains the tolerances to be used for the solution variables + */ + void NonlinearSolver::setAtol(const doublereal * const atol) + { + for (int i = 0; i < neq_; i++) { + atolk_[i]= atol[i]; + } + } + //===================================================================================================================== + } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index f7ff48f58..43ef2daea 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -385,6 +385,15 @@ namespace Cantera { */ int convergenceCheck(int dampCode, double s1); + + //! Set the absolute tolerances for the solution variables + /*! + * Set the absolute tolerances used in the calculation + * + * @param atol Vector of length neq_ that contains the tolerances to be used for the solution variables + */ + void setAtol(const doublereal * const atol); + private: //! Pointer to the residual and jacobian evaluator for the @@ -497,12 +506,16 @@ namespace Cantera { //! int indicating whether row scaling is turned on (1) or not (0) int m_rowScaling; + //! Total number of linear solves int m_numTotalLinearSolves; + //! Total number of newton iterations int m_numTotalNewtIts; + //! Minimum number of newton iterations to use int m_min_newt_its; + //! Boolean that turns on solution filtering int filterNewstep; //! Jacobian formation method @@ -512,8 +525,8 @@ namespace Cantera { */ int m_jacFormMethod; + //! Number of Jacobian evaluations int m_nJacEval; - //! Current system time /*! From 9630216f3e659575988ebe052af53c50424b2c53 Mon Sep 17 00:00:00 2001 From: Christopher Lueth Date: Wed, 13 Oct 2010 22:06:03 +0000 Subject: [PATCH 272/446] Fixed nan problem if m_normResid0 = 0.0 at line 965 --- Cantera/src/numerics/NonlinearSolver.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 19faf2def..c816d3f2a 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -961,7 +961,12 @@ namespace Cantera { * We aren't going to solve the system if we don't need to. Therefore, return an estimate * of the next solution update based on the ratio of the residual reduction. */ - s1 = s0 * m_normResidTrial / m_normResid0; + if (m_normResid0 > 0.0) { + s1 = s0 * m_normResidTrial / m_normResid0; + } + else { + s1 = 0; + } if (m_normResidTrial < 1.0) { retnTrial = 3; } else { From 97f326a6288fe233f0e3b94a7ceaf720159a6b91 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 14 Oct 2010 02:44:23 +0000 Subject: [PATCH 273/446] Tightened the convergence tolerances --- Cantera/src/numerics/NonlinearSolver.cpp | 60 +++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 30 ++++++++---- 2 files changed, 64 insertions(+), 26 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index c816d3f2a..ce29aef16 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -63,6 +63,8 @@ namespace Cantera { } printf("\n"); } + + bool NonlinearSolver::m_TurnOffTiming(false); //==================================================================================================================== // Default constructor /* @@ -80,6 +82,7 @@ namespace Cantera { ydot_new(0), m_colScales(0), m_rowScales(0), + m_rowWtScales(0), m_resid(0), m_wksp(0), m_residWts(0), @@ -120,6 +123,7 @@ namespace Cantera { ydot_new.resize(neq_, 0.0); m_colScales.resize(neq_, 1.0); m_rowScales.resize(neq_, 1.0); + m_rowWtScales.resize(neq_, 1.0); m_resid.resize(neq_, 0.0); m_wksp.resize(neq_, 0.0); m_residWts.resize(neq_, 0.0); @@ -146,6 +150,7 @@ namespace Cantera { ydot_new(0), m_colScales(0), m_rowScales(0), + m_rowWtScales(0), m_resid(0), m_wksp(0), m_residWts(0), @@ -202,6 +207,7 @@ namespace Cantera { ydot_new = right.ydot_new; m_colScales = right.m_colScales; m_rowScales = right.m_rowScales; + m_rowWtScales = right.m_rowWtScales; m_resid = right.m_resid; m_wksp = right.m_wksp; m_residWts = right.m_residWts; @@ -231,7 +237,7 @@ namespace Cantera { atolBase_ = right.atolBase_; atolk_ = right.atolk_; m_print_flag = right.m_print_flag; - + return *this; } //==================================================================================================================== @@ -522,16 +528,23 @@ namespace Cantera { double *jptr = &(*(jac.begin())); for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 0.0; + m_rowWtScales[irow] = 0.0; } for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] += fabs(*jptr); + if (m_colScaling) { + m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol] / m_colScales[jcol]; + } else { + m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol]; + } jptr++; } } for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 1.0/m_rowScales[irow]; + m_rowWtScales[irow] = 1.0/m_rowWtScales[irow]; } if (m_rowScaling) { @@ -1212,8 +1225,7 @@ namespace Cantera { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); } else { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); - } - + } // Damp the Newton step /* @@ -1247,7 +1259,7 @@ namespace Cantera { if (num_newt_its > 20) { m = -1; if (m_print_flag > 1) { - printf("\t\tDampnewton unsuccessful (max newts exceeded) sfinal = %g\n", s1); + printf("\t\tsolve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); } } @@ -1346,9 +1358,13 @@ namespace Cantera { double time_elapsed = wc.secondsWC(); if (m_print_flag > 1) { if (m > 0) { - printf("\t\tNonlinear problem solved successfully in " - "%d its, time elapsed = %g sec\n", - num_newt_its, time_elapsed); + if (NonlinearSolver::m_TurnOffTiming) { + printf("\t\tNonlinear problem solved successfully in %d its\n", + num_newt_its); + } else { + printf("\t\tNonlinear problem solved successfully in %d its, time elapsed = %g sec\n", + num_newt_its, time_elapsed); + } } } return m; @@ -1631,12 +1647,12 @@ namespace Cantera { { doublereal sum = 0.0; for (int i = 0; i < neq_; i++) { - m_residWts[i] = 1.0 / m_rowScales[i]; + m_residWts[i] = 1.0 / m_rowWtScales[i]; sum += m_residWts[i]; } sum /= neq_; for (int i = 0; i < neq_; i++) { - m_residWts[i] = rtol_ * m_residWts[i] + atolBase_ * sum; + m_residWts[i] = m_residWts[i] + atolBase_ * sum; } } //===================================================================================================================== @@ -1663,8 +1679,8 @@ namespace Cantera { * 2 Successful step: Next step's norm is less than 0.8. * This step's norm is less than 1.0. * The residual norm can be anything. - * 3 Success: The final residual is less than 1.0 - * The predicted deltaSoln is below 1.0. + * 3 Success: The final residual is less than 1.0E-2 + * The predicted deltaSoln is below 1.0E-2. * 0 Not converged yet */ int @@ -1681,27 +1697,35 @@ namespace Cantera { return retn; } if (dampCode == 3) { - if (s1 < 1.0) { - if (m_normResidTrial < 1.0) { + if (s1 < 1.0E-2) { + if (m_normResidTrial < 1.0E-2) { return 3; } } + if (s1 < 0.8) { + if (m_normSolnFRaw < 1.0) { + return 2; + } + } } if (dampCode == 4) { - if (s1 < 1.0) { - if (m_normResidTrial < 1.0) { + if (s1 < 1.0E-2) { + if (m_normResidTrial < 1.0E-2) { return 3; } } } + if (s1 < 0.8) { if (m_normSolnFRaw < 1.0) { return 2; } } - if (s1 < 1.0) { - if (m_normSolnFRaw < 1.0) { - return 1; + if (dampCode == 1 || dampCode == 2) { + if (s1 < 1.0) { + if (m_normResidTrial < 1.0) { + return 1; + } } } return retn; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 43ef2daea..91d814d85 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -215,7 +215,7 @@ namespace Cantera { const double* const step0, const int loglevel); - //! set bounds constraints for all variables in the problem + //! Set bounds constraints for all variables in the problem /*! * * @param y_low_bounds Vector of lower bounds @@ -224,12 +224,6 @@ namespace Cantera { void setBoundsConstraints(const double * const y_low_bounds, const double * const y_high_bounds); - /** - * Internal function to calculate the predicted solution - * at a time step. - */ - void calc_y_pred(int); - //! Internal function to calculate the time derivative at the new step /*! @@ -316,7 +310,11 @@ namespace Cantera { * SolnType = TRANSIENT -> we will assume we are relaxing a transient * equation system for now. Will make it more general later, * if an application comes up. - * + * + * + * + * @return A positive value indicates a successful convergence + * -1 Failed convergence */ int solve_nonlinear_problem(int SolnType, double* y_comm, double* ydot_comm, double CJ, @@ -438,6 +436,15 @@ namespace Cantera { */ std::vector m_rowScales; + //! Weights for normalizing the values of the residuals + /*! + * These are computed if row scaling, m_rowScaling, is turned on. They are calculated currently as the + * sum of the absolute values jacobian multiplied by the solution weight function + */ + std::vector m_rowWtScales; + + + //! Value of the residual for the nonlinear problem std::vector m_resid; @@ -561,6 +568,13 @@ namespace Cantera { * 8 -> Info on a per iterate of the linear solve is printed out. */ int m_print_flag; + + public: + //! Turn off printing of time + /*! + * Necessary to do for test suites + */ + static bool m_TurnOffTiming; }; } From fad1f9f7ffc3a7be96c5ee7553cbc7d98c8621e1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 14 Oct 2010 22:34:59 +0000 Subject: [PATCH 274/446] Added hooks for rtol and max newton iterations --- Cantera/src/numerics/NonlinearSolver.cpp | 177 +++++++++++++---------- Cantera/src/numerics/NonlinearSolver.h | 104 +++++++------ 2 files changed, 157 insertions(+), 124 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index ce29aef16..ef8aa8e88 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -50,7 +50,7 @@ namespace Cantera { // Constants //----------------------------------------------------------- - const double DampFactor = 4; + const doublereal DampFactor = 4; const int NDAMP = 7; //==================================================================================================================== //----------------------------------------------------------- @@ -103,6 +103,7 @@ namespace Cantera { m_numTotalNewtIts(0), m_min_newt_its(0), filterNewstep(0), + maxNewtIts_(50), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), time_n(0.0), @@ -171,6 +172,7 @@ namespace Cantera { m_numTotalNewtIts(0), m_min_newt_its(0), filterNewstep(0), + maxNewtIts_(50), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), time_n(0.0), @@ -228,6 +230,7 @@ namespace Cantera { m_numTotalNewtIts = right.m_numTotalNewtIts; m_min_newt_its = right.m_min_newt_its; filterNewstep = right.filterNewstep; + maxNewtIts_ = right.maxNewtIts_; m_jacFormMethod = right.m_jacFormMethod; m_nJacEval = right.m_nJacEval; time_n = right.time_n; @@ -252,7 +255,7 @@ namespace Cantera { * * param y vector of the current solution values */ - void NonlinearSolver::createSolnWeights(const double * const y) { + void NonlinearSolver::createSolnWeights(const doublereal * const y) { for (int i = 0; i < neq_; i++) { m_ewt[i] = rtol_ * fabs(y[i]) + atolk_[i]; } @@ -264,8 +267,8 @@ namespace Cantera { * @param y_low_bounds Vector of lower bounds * @param y_high_bounds Vector of high bounds */ - void NonlinearSolver::setBoundsConstraints(const double * const y_low_bounds, - const double * const y_high_bounds) { + void NonlinearSolver::setBoundsConstraints(const doublereal * const y_low_bounds, + const doublereal * const y_high_bounds) { for (int i = 0; i < neq_; i++) { m_y_low_bounds[i] = y_low_bounds[i]; m_y_high_bounds[i] = y_high_bounds[i]; @@ -287,11 +290,11 @@ namespace Cantera { * @param dampFactor Current value of the damping factor. Defaults to 1. * only used for printout out a table. */ - double NonlinearSolver::solnErrorNorm(const double * const delta_y, const char * title, int printLargest, - const double dampFactor) + doublereal NonlinearSolver::solnErrorNorm(const doublereal * const delta_y, const char * title, int printLargest, + const doublereal dampFactor) { int i; - double sum_norm = 0.0, error; + doublereal sum_norm = 0.0, error; for (i = 0; i < neq_; i++) { error = delta_y[i] / m_ewt[i]; sum_norm += (error * error); @@ -322,7 +325,7 @@ namespace Cantera { } printf(" = %-11.4E\n", sum_norm); - double dmax1, normContrib; + doublereal dmax1, normContrib; int j; int *imax = mdp::mdp_alloc_int_1(num_entries, -1); printf("\t\t Printout of Largest Contributors:\n"); @@ -372,11 +375,11 @@ namespace Cantera { * if true, then a table of the largest values is printed * out to standard output. */ - double NonlinearSolver::residErrorNorm(const double * const resid, const char * title, const int printLargest, - const double * const y) + doublereal NonlinearSolver::residErrorNorm(const doublereal * const resid, const char * title, const int printLargest, + const doublereal * const y) { int i; - double sum_norm = 0.0, error; + doublereal sum_norm = 0.0, error; for (i = 0; i < neq_; i++) { error = resid[i] / m_residWts[i]; sum_norm += (error * error); @@ -384,7 +387,7 @@ namespace Cantera { sum_norm = sqrt(sum_norm / neq_); if (printLargest) { const int num_entries = printLargest; - double dmax1, normContrib; + doublereal dmax1, normContrib; int j; int *imax = mdp::mdp_alloc_int_1(num_entries, -1); @@ -461,8 +464,8 @@ namespace Cantera { * @param y_curr Current value of the solution vector * @param ydot_curr Current value of the time derivative of the solution vector */ - void NonlinearSolver::doResidualCalc(const double time_curr, const int typeCalc, const double * const y_curr, - const double * const ydot_curr) + void NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, + const doublereal * const ydot_curr) { m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), Base_ResidEval); m_nfe++; @@ -482,7 +485,7 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. */ - void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, double time_curr) + void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr) { int irow, jcol; @@ -503,7 +506,7 @@ namespace Cantera { /* * Scale the new Jacobian */ - double *jptr = &(*(jac.begin())); + doublereal *jptr = &(*(jac.begin())); for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { *jptr *= m_colScales[jcol]; @@ -523,9 +526,9 @@ namespace Cantera { /* * Ok, this is ugly. jac.begin() returns an vector iterator * to the first data location. - * Then &(*()) reverts it to a double *. + * Then &(*()) reverts it to a doublereal *. */ - double *jptr = &(*(jac.begin())); + doublereal *jptr = &(*(jac.begin())); for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 0.0; m_rowWtScales[irow] = 0.0; @@ -578,8 +581,8 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. */ - void NonlinearSolver::doNewtonSolve(const double time_curr, const double * const y_curr, - const double * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) + void NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, + const doublereal * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) { int irow; @@ -618,9 +621,9 @@ namespace Cantera { if (printJacContributions) { for (int iNum = 0; iNum < numRows; iNum++) { if (iNum > 0) focusRow++; - double dsum = 0.0; + doublereal dsum = 0.0; vector_fp& Jdata = jacBack.data(); - double dRow = Jdata[neq_ * focusRow + focusRow]; + doublereal dRow = Jdata[neq_ * focusRow + focusRow]; printf("\n Details on delta_Y for row %d \n", focusRow); printf(" Value before = %15.5e, delta = %15.5e," "value after = %15.5e\n", y_curr[focusRow], @@ -639,8 +642,8 @@ namespace Cantera { dsum += RRow[iNum] / dRow; for (int ii = 0; ii < neq_; ii++) { if (ii != focusRow) { - double aij = Jdata[neq_ * ii + focusRow]; - double contrib = aij * delta_y[ii] * (-1.0) / dRow; + doublereal aij = Jdata[neq_ * ii + focusRow]; + doublereal contrib = aij * delta_y[ii] * (-1.0) / dRow; dsum += contrib; if (fabs(contrib) > Pcutoff) { printf("%6d %15.5e %15.5e %15.5e\n", ii, @@ -668,7 +671,7 @@ namespace Cantera { } } //==================================================================================================================== - void NonlinearSolver::setDeltaBoundsMagnitudes(const double * const deltaBoundsMagnitudes) + void NonlinearSolver::setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes) { for (int i = 0; i < neq_; i++) { @@ -696,18 +699,18 @@ namespace Cantera { * @return returns the damping factor */ double - NonlinearSolver::deltaBoundStep(const double * const y, const double * const step0, const int loglevel) { + NonlinearSolver::deltaBoundStep(const doublereal * const y, const doublereal * const step0, const int loglevel) { int i_fbounds = 0; int ifbd = 0; int i_fbd = 0; - double sameSign = 0.0; - double ff; - double f_delta_bounds = 1.0; - double ff_alt; + doublereal sameSign = 0.0; + doublereal ff; + doublereal f_delta_bounds = 1.0; + doublereal ff_alt; for (int i = 0; i < neq_; i++) { - double y_new = y[i] + step0[i]; + doublereal y_new = y[i] + step0[i]; sameSign = y_new * y[i]; /* @@ -818,10 +821,10 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - double NonlinearSolver::boundStep(const double * const y, const double * const step0, const int loglevel) { + doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0, const int loglevel) { int i, i_lower = -1; - double fbound = 1.0, f_bounds = 1.0; - double ff, y_new; + doublereal fbound = 1.0, f_bounds = 1.0; + doublereal ff, y_new; for (i = 0; i < neq_; i++) { y_new = y[i] + step0[i]; @@ -830,7 +833,7 @@ namespace Cantera { */ if (step0[i] < 0.0) { if (y_new < (y[i] + 0.8 * (m_y_low_bounds[i] - y[i]))) { - double legalDelta = 0.8*(m_y_low_bounds[i] - y[i]); + doublereal legalDelta = 0.8*(m_y_low_bounds[i] - y[i]); ff = legalDelta / step0[i]; if (ff < f_bounds) { f_bounds = ff; @@ -843,7 +846,7 @@ namespace Cantera { */ if (step0[i] > 0.0) { if (y_new > (y[i] + 0.8 * (m_y_high_bounds[i] - y[i]))) { - double legalDelta = 0.8*(m_y_high_bounds[i] - y[i]); + doublereal legalDelta = 0.8*(m_y_high_bounds[i] - y[i]); ff = legalDelta / step0[i]; if (ff < f_bounds) { f_bounds = ff; @@ -864,7 +867,7 @@ namespace Cantera { } } - double f_delta_bounds = deltaBoundStep(y, step0, loglevel); + doublereal f_delta_bounds = deltaBoundStep(y, step0, loglevel); fbound = MIN(f_bounds, f_delta_bounds); return fbound; @@ -886,23 +889,23 @@ namespace Cantera { * s1 is calculated * 2 Successful step: Next step's norm is less than 0.8 * 3 Success: The final residual is less than 1.0 - * A predicted deltaSoln is not produced however. s1 is estimated. + * A predicted deltaSoln1 is not produced however. s1 is estimated. * 4 Success: The final residual is less than the residual * from the previous step. - * A predicted deltaSoln is not produced however. s1 is estimated. + * A predicted deltaSoln1 is not produced however. s1 is estimated. * 0 Uncertain Success: s1 is about the same as s0 * -2 Unsuccessful step. */ - int NonlinearSolver::dampStep(const double time_curr, const double* y0, - const double *ydot0, const double* step0, + int NonlinearSolver::dampStep(const doublereal time_curr, const double* y0, + const doublereal *ydot0, const double* step0, double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, - int& loglevel, bool writetitle, - int& num_backtracks) { + double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + int& num_backtracks) + { int retnTrial = -2; // Compute the weighted norm of the undamped step size step0 - double s0 = solnErrorNorm(step0); + doublereal s0 = solnErrorNorm(step0); // Compute the multiplier to keep all components in bounds // A value of one indicates that there is no limitation @@ -927,7 +930,7 @@ namespace Cantera { // damping coefficient starts at 1.0 m_dampRes = 1.0; int j, m; - double ff = m_dampBound; + doublereal ff = m_dampBound; num_backtracks = 0; for (m = 0; m < NDAMP; m++) { @@ -947,6 +950,10 @@ namespace Cantera { } else { } + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { doResidualCalc(time_curr, solnType_, y1, ydot1); } else { @@ -988,8 +995,8 @@ namespace Cantera { break; } - // compute the next undamped step, step1[], that would result - // if y1[] were accepted. + // Compute the next undamped step, step1[], that would result if y1[] were accepted. + // We now have two steps that we have calculated step0[] and step1[] if (solnType_ != NSOLN_TYPE_STEADY_STATE) { doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); } else { @@ -1001,9 +1008,9 @@ namespace Cantera { // write log information if (loglevel > 3) { - print_solnDelta_norm_contrib((const double *) step0, + print_solnDelta_norm_contrib((const doublereal *) step0, "DeltaSoln", - (const double *) step1, + (const doublereal *) step1, "DeltaSolnTrial", "dampNewt: Important Entries for " "Weighted Soln Updates:", @@ -1093,8 +1100,8 @@ namespace Cantera { * */ int NonlinearSolver::solve_nonlinear_problem(int SolnType, double* y_comm, - double* ydot_comm, double CJ, - double time_curr, + double* ydot_comm, doublereal CJ, + doublereal time_curr, SquareMatrix& jac, int &num_newt_its, int &num_linear_solves, @@ -1108,7 +1115,7 @@ namespace Cantera { bool m_residCurrent = false; int m = 0; bool forceNewJac = false; - double s1=1.e30; + doublereal s1=1.e30; // std::vector y_curr(neq_, 0.0); std::vector ydot_curr(neq_, 0.0); @@ -1256,7 +1263,7 @@ namespace Cantera { /* * Impose max newton iteration */ - if (num_newt_its > 20) { + if (num_newt_its > maxNewtIts_) { m = -1; if (m_print_flag > 1) { printf("\t\tsolve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); @@ -1355,7 +1362,7 @@ namespace Cantera { num_linear_solves += m_numTotalLinearSolves; - double time_elapsed = wc.secondsWC(); + doublereal time_elapsed = wc.secondsWC(); if (m_print_flag > 1) { if (m > 0) { if (NonlinearSolver::m_TurnOffTiming) { @@ -1375,18 +1382,18 @@ namespace Cantera { * */ void NonlinearSolver:: - print_solnDelta_norm_contrib(const double * const solnDelta0, + print_solnDelta_norm_contrib(const doublereal * const solnDelta0, const char * const s0, - const double * const solnDelta1, + const doublereal * const solnDelta1, const char * const s1, const char * const title, - const double * const y0, - const double * const y1, - double damp, + const doublereal * const y0, + const doublereal * const y1, + doublereal damp, int num_entries) { int i, j, jnum; bool used; - double dmax0, dmax1, error, rel_norm; + doublereal dmax0, dmax1, error, rel_norm; printf("\t\t%s currentDamp = %g\n", title, damp); printf("\t\t I ysolnOld %13s ysolnNewRaw | ysolnNewTrial " "%10s ysolnNewTrialRaw | solnWeight wtDelSoln wtDelSolnTrial\n", s0, s1); @@ -1442,11 +1449,11 @@ namespace Cantera { * loss of convergence. Therefore, in practice this routine * has proved cost-effective. */ - static inline double subtractRD(double a, double b) { - double diff = a - b; - double d = MIN(fabs(a), fabs(b)); + static inline doublereal subtractRD(doublereal a, doublereal b) { + doublereal diff = a - b; + doublereal d = MIN(fabs(a), fabs(b)); d *= 1.0E-14; - double ad = fabs(diff); + doublereal ad = fabs(diff); if (ad < 1.0E-300) { diff = 0.0; } @@ -1467,15 +1474,15 @@ namespace Cantera { * not have to be computed again. * */ - void NonlinearSolver::beuler_jac(SquareMatrix &J, double * const f, - double time_curr, double CJ, - double * const y, - double * const ydot, + void NonlinearSolver::beuler_jac(SquareMatrix &J, doublereal * const f, + doublereal time_curr, doublereal CJ, + doublereal * const y, + doublereal * const ydot, int num_newt_its) { int i, j; double* col_j; - double ysave, ydotsave, dy; + doublereal ysave, ydotsave, dy; /* * Clear the factor flag */ @@ -1486,7 +1493,7 @@ namespace Cantera { */ m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); #ifdef DEBUG_HKM - //double dddd = J(89, 89); + //doublereal dddd = J(89, 89); //checkFinite(dddd); #endif m_nJacEval++; @@ -1510,7 +1517,7 @@ namespace Cantera { * deltaY's that are appropriate for calculating the numerical * derivative. */ - double *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); @@ -1546,7 +1553,7 @@ namespace Cantera { */ - col_j = (double *) J.ptrColumn(j); + col_j = (doublereal *) J.ptrColumn(j); ysave = y[j]; dy = dyVector[j]; //dy = fmaxx(1.0E-6 * m_ewt[j], fabs(ysave)*1.0E-7); @@ -1565,7 +1572,7 @@ namespace Cantera { m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), JacDelta_ResidEval, j, dy); m_nfe++; - double diff; + doublereal diff; for (i = 0; i < neq_; i++) { diff = subtractRD(m_wksp[i], f[i]); col_j[i] = diff / dy; @@ -1593,13 +1600,13 @@ namespace Cantera { * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr */ void NonlinearSolver:: - calc_ydot(const int order, const double * const y_curr, double * const ydot_curr) + calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr) { if (!ydot_curr) { return; } int i; - double c1; + doublereal c1; switch (order) { case 0: case 1: /* First order forward Euler/backward Euler */ @@ -1626,7 +1633,7 @@ namespace Cantera { * * @return Returns the norm of the value of the amount filtered */ - double NonlinearSolver::filterNewStep(const double timeCurrent, double * const y_current, double *const ydot_current) { + doublereal NonlinearSolver::filterNewStep(const doublereal timeCurrent, doublereal * const y_current, doublereal *const ydot_current) { return 0.0; } //==================================================================================================================== @@ -1661,7 +1668,7 @@ namespace Cantera { * @param residWts Vector of length neq_ */ void - NonlinearSolver::getResidWts(double * const residWts) const + NonlinearSolver::getResidWts(doublereal * const residWts) const { for (int i = 0; i < neq_; i++) { residWts[i] = (m_residWts)[i]; @@ -1684,7 +1691,7 @@ namespace Cantera { * 0 Not converged yet */ int - NonlinearSolver::convergenceCheck(int dampCode, double s1) + NonlinearSolver::convergenceCheck(int dampCode, doublereal s1) { int retn = 0; if (m_dampBound < 0.9999) { @@ -1743,6 +1750,18 @@ namespace Cantera { atolk_[i]= atol[i]; } } + + //===================================================================================================================== + // Set the relative tolerances for the solution variables + /* + * Set the relative tolerances used in the calculation + * + * @param rtol single double + */ + void NonlinearSolver::setRtol(const doublereal rtol) + { + rtol_ = rtol; + } //===================================================================================================================== } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 91d814d85..32aefe367 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -79,7 +79,7 @@ namespace Cantera { * * param y vector of the current solution values */ - void createSolnWeights(const double * const y); + void createSolnWeights(const doublereal * const y); //! L2 norm of the delta of the solution vector @@ -97,8 +97,8 @@ namespace Cantera { * @param dampFactor Current value of the damping factor. Defaults to 1. * only used for printout out a table. */ - double solnErrorNorm(const double * const delta_y, const char * title = 0, int printLargest = 0, - const double dampFactor = 1.0); + doublereal solnErrorNorm(const doublereal * const delta_y, const char * title = 0, int printLargest = 0, + const doublereal dampFactor = 1.0); //! L2 norm of the residual of the equation system /*! @@ -114,8 +114,8 @@ namespace Cantera { * @param printLargest Number of specific entries to be printed * @param y Current value of y - only used for printouts */ - double residErrorNorm(const double * const resid, const char * title = 0, const int printLargest = 0, - const double * const y = 0); + doublereal residErrorNorm(const doublereal * const resid, const char * title = 0, const int printLargest = 0, + const doublereal * const y = 0); //! Compute the current Residual /*! @@ -142,8 +142,8 @@ namespace Cantera { * @param y_curr Current value of the solution vector * @param ydot_curr Current value of the time derivative of the solution vector */ - void doResidualCalc(const double time_curr, const int typeCalc, const double * const y_curr, - const double * const ydot_curr); + void doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, + const doublereal * const ydot_curr); //! Compute the undamped Newton step /*! @@ -164,8 +164,8 @@ namespace Cantera { * @param ydot_current Current value of the solution derivative. * */ - void doNewtonSolve(const double time_curr, const double * const y_curr, - const double * const ydot_curr, double* const delta_y, + void doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, + const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac, int loglevel); @@ -182,7 +182,7 @@ namespace Cantera { /*! * @param deltaboundsMagnitudes */ - void setDeltaBoundsMagnitudes(const double * const deltaBoundsMagnitudes); + void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); //! Bound the step @@ -211,7 +211,7 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - double boundStep(const double* const y, + doublereal boundStep(const double* const y, const double* const step0, const int loglevel); @@ -221,8 +221,8 @@ namespace Cantera { * @param y_low_bounds Vector of lower bounds * @param y_high_bounds Vector of high bounds */ - void setBoundsConstraints(const double * const y_low_bounds, - const double * const y_high_bounds); + void setBoundsConstraints(const doublereal * const y_low_bounds, + const doublereal * const y_high_bounds); //! Internal function to calculate the time derivative at the new step @@ -231,7 +231,7 @@ namespace Cantera { * @param y_curr current value of the solution * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr */ - void calc_ydot(const int order, const double * const y_curr, double * const ydot_curr); + void calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr); //! Function called to evaluate the jacobian matrix and the curent //! residual vector. @@ -239,9 +239,9 @@ namespace Cantera { * * */ - void beuler_jac(SquareMatrix &J, double * const f, - double time_curr, double CJ, double * const y, - double * const ydot, int num_newt_its); + void beuler_jac(SquareMatrix &J, doublereal * const f, + doublereal time_curr, doublereal CJ, doublereal * const y, + doublereal * const ydot, int num_newt_its); //! Apply a filtering step @@ -252,7 +252,7 @@ namespace Cantera { * * @return Returns the norm of the value of the amount filtered */ - double filterNewStep(const double timeCurrent, double * const y_current, double * const ydot_current); + doublereal filterNewStep(const doublereal timeCurrent, doublereal * const y_current, doublereal * const ydot_current); //! Return the factor by which the undamped Newton step 'step0' @@ -272,7 +272,7 @@ namespace Cantera { * * @return returns the damping factor */ - double deltaBoundStep(const double * const y, const double * const step0, const int loglevel); + doublereal deltaBoundStep(const doublereal * const y, const doublereal * const step0, const int loglevel); //! Find a damping coefficient through a look-ahead mechanism /*! @@ -292,8 +292,8 @@ namespace Cantera { * @param step0 Initial step suggested. * @param y1 */ - int dampStep(const double time_curr, const double* y0, - const double *ydot0, const double* step0, + int dampStep(const doublereal time_curr, const double* y0, + const doublereal *ydot0, const double* step0, double* const y1, double* const ydot1, double* step1, double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, @@ -317,8 +317,8 @@ namespace Cantera { * -1 Failed convergence */ int solve_nonlinear_problem(int SolnType, double* y_comm, - double* ydot_comm, double CJ, - double time_curr, + double* ydot_comm, doublereal CJ, + doublereal time_curr, SquareMatrix& jac, int &num_newt_its, int &num_linear_solves, @@ -333,19 +333,19 @@ namespace Cantera { /*! * */ - void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, double time_curr); + void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr); //! Print solution norm contribution void - print_solnDelta_norm_contrib(const double * const solnDelta0, + print_solnDelta_norm_contrib(const doublereal * const solnDelta0, const char * const s0, - const double * const solnDelta1, + const doublereal * const solnDelta1, const char * const s1, const char * const title, - const double * const y0, - const double * const y1, - double damp, + const doublereal * const y0, + const doublereal * const y1, + doublereal damp, int num_entries); //! Compute the Residual Weights @@ -365,7 +365,7 @@ namespace Cantera { /*! * @param residWts Vector of length neq_ */ - void getResidWts(double * const residWts) const; + void getResidWts(doublereal * const residWts) const; //! Check to see if the nonlinear problem has converged @@ -381,7 +381,7 @@ namespace Cantera { * The predicted deltaSoln is below 1.0. * 0 Not converged yet */ - int convergenceCheck(int dampCode, double s1); + int convergenceCheck(int dampCode, doublereal s1); //! Set the absolute tolerances for the solution variables @@ -392,6 +392,20 @@ namespace Cantera { */ void setAtol(const doublereal * const atol); + //! Set the relative tolerances for the solution variables + /*! + * Set the relative tolerances used in the calculation + * + * @param rtol single double + */ + void setRtol(const doublereal rtol); + + //! Set the value of the maximum # of newton iterations + /*! + * @param maxNewtIts Maximum number of newton iterations + */ + void setMaxNewtIts(const int maxNewtIts); + private: //! Pointer to the residual and jacobian evaluator for the @@ -410,10 +424,6 @@ namespace Cantera { //! Soln error weights std::vector m_ewt; - - - - //! Boolean indicating whether a manual delta bounds has been input. int m_manualDeltaBoundsSet; @@ -462,19 +472,19 @@ namespace Cantera { std::vector m_residWts; //! Norm of the residual at the start of each nonlinear iteration - double m_normResid0; + doublereal m_normResid0; //! Norm of the residual before damping - double m_normResidFRaw; + doublereal m_normResidFRaw; //! Norm of the solution update created by the iteration in its raw, undamped form. - double m_normSolnFRaw; + doublereal m_normSolnFRaw; //! Norm of the residual for a trial calculation which may or may not be used - double m_normResidTrial; + doublereal m_normResidTrial; //! Vector of the norm - double m_normResidPoints[15]; + doublereal m_normResidPoints[15]; bool m_resid_scaled; @@ -491,13 +501,13 @@ namespace Cantera { std::vector m_y_low_bounds; //! Damping factor imposed by hard bounds and by delta bounds - double m_dampBound; + doublereal m_dampBound; //! Additional damping factor due to bounds on the residual and solution norms - double m_dampRes; + doublereal m_dampRes; //! Delta t for the current step - double delta_t_n; + doublereal delta_t_n; //! Counter for the total number of function evaluations int m_nfe; @@ -525,6 +535,9 @@ namespace Cantera { //! Boolean that turns on solution filtering int filterNewstep; + //! Maximum number of newton iterations + int maxNewtIts_; + //! Jacobian formation method /*! * 1 = numerical (default) @@ -540,18 +553,19 @@ namespace Cantera { * Note, we assume even for steady state problems that the residual * is a function of a system time. */ - double time_n; + doublereal time_n; int m_matrixConditioning; int m_order; + //! value of the relative tolerance to use in solving the equation set doublereal rtol_; //! Base value of the absolute tolerance doublereal atolBase_; - double * m_ydot_nm1; + doublereal * m_ydot_nm1; std::vector atolk_; From 43c4d1215c8adca658ffd47f24e161a6590df3ad Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Oct 2010 18:33:57 +0000 Subject: [PATCH 275/446] Fixed a printLvl error --- Cantera/src/numerics/NonlinearSolver.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index ef8aa8e88..f79d9e093 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1174,7 +1174,7 @@ namespace Cantera { setDefaultDeltaBoundsMagnitudes(); } - if (m_print_flag > 1) { + if (m_print_flag > 3) { printf("\tsolve_nonlinear_problem(): iteration %d:\n", num_newt_its); } From 78b2d5689c594defb02594751ce091d4ed4009c0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Oct 2010 21:02:19 +0000 Subject: [PATCH 276/446] Took out an unneeded m_atol call that wasn't necessary and caused problems with numerical deltas. --- Cantera/src/numerics/ResidJacEval.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 97acf51e5..220a64560 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -184,8 +184,7 @@ namespace Cantera { } } else { for (int i = 0; i < neq_; i++) { - deltaYSoln[i] = m_atol + - fmaxx(1.0E-2 * solnWeights[i], 1.0E-6 * fabs(ySoln[i])); + deltaYSoln[i] = fmaxx(1.0E-2 * solnWeights[i], 1.0E-6 * fabs(ySoln[i])); } } } From 550c33c6285b7ccd4a8001ab6692baa249ff14b0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 18 Oct 2010 19:27:06 +0000 Subject: [PATCH 277/446] Added a getDeltaElectrochemPotentials() member function --- Cantera/src/kinetics/InterfaceKinetics.cpp | 35 +++++++++++++++++++--- Cantera/src/kinetics/InterfaceKinetics.h | 24 +++++++++++++-- Cantera/src/kinetics/Kinetics.h | 33 +++++++++++++------- 3 files changed, 76 insertions(+), 16 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 790ab0796..6b6f60c9d 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -780,8 +780,8 @@ namespace Cantera { m_kdata->m_ROP_ok = true; } - - /** + //================================================================================================= + /* * * getDeltaGibbs(): * @@ -812,8 +812,35 @@ namespace Cantera { */ m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaG); } - - /** + //================================================================================================= + // Return the vector of values for the reaction electrochemical free energy change. + /* + * These values depend upon the concentration of the solution and + * the voltage of the phases + * + * units = J kmol-1 + * + * @param deltaM Output vector of deltaM's for reactions + * Length: m_ii. + */ + void InterfaceKinetics::getDeltaElectrochemPotentials(doublereal* deltaM) { + /* + * Get the chemical potentials of the species in the + * ideal gas solution. + */ + int np = nPhases(); + int n; + for (n = 0; n < np; n++) { + thermo(n).getElectrochemPotentials(DATA_PTR(m_grt) + m_start[n]); + } + /* + * Use the stoichiometric manager to find deltaG for each + * reaction. + */ + m_rxnstoich.getReactionDelta(m_ii, DATA_PTR(m_grt), deltaM); + } + //================================================================================================= + /* * * getDeltaEnthalpy(): * diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index c14e0b8f2..9c8c4ac5c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -190,8 +190,28 @@ namespace Cantera { void getExchangeCurrentQuantities(); + //! Return the vector of values for the reaction gibbs free energy change. + /*! + * These values depend upon the concentration of the solution. + * + * units = J kmol-1 + * + * @param deltaG Output vector of deltaG's for reactions + * Length: m_ii. + */ + virtual void getDeltaGibbs(doublereal* deltaG); - virtual void getDeltaGibbs( doublereal* deltaG); + //! Return the vector of values for the reaction electrochemical free energy change. + /*! + * These values depend upon the concentration of the solution and + * the voltage of the phases + * + * units = J kmol-1 + * + * @param deltaM Output vector of deltaM's for reactions + * Length: m_ii. + */ + virtual void getDeltaElectrochemPotentials(doublereal* deltaM); /** * Return the vector of values for the reactions change in @@ -201,7 +221,7 @@ namespace Cantera { * * units = J kmol-1 */ - virtual void getDeltaEnthalpy( doublereal* deltaH); + virtual void getDeltaEnthalpy(doublereal* deltaH); //! Return the vector of values for the change in //! entropy due to each reaction diff --git a/Cantera/src/kinetics/Kinetics.h b/Cantera/src/kinetics/Kinetics.h index 8559d4137..ea8bc6ab2 100644 --- a/Cantera/src/kinetics/Kinetics.h +++ b/Cantera/src/kinetics/Kinetics.h @@ -509,20 +509,33 @@ namespace Cantera { err("getReactionDelta"); } - /** - * Return the vector of values for the reaction gibbs free - * energy change. These values depend upon the concentration - * of the solution. + //! Return the vector of values for the reaction gibbs free energy change. + /*! + * These values depend upon the concentration of the solution. * * units = J kmol-1 * * @param deltaG Output vector of deltaG's for reactions * Length: m_ii. */ - virtual void getDeltaGibbs( doublereal* deltaG) { + virtual void getDeltaGibbs(doublereal* deltaG) { err("getDeltaGibbs"); } + //! Return the vector of values for the reaction electrochemical free energy change. + /*! + * These values depend upon the concentration of the solution and + * the voltage of the phases + * + * units = J kmol-1 + * + * @param deltaM Output vector of deltaM's for reactions + * Length: m_ii. + */ + virtual void getDeltaElectrochemPotentials(doublereal* deltaM) { + err("getDeltaElectrochemPotentials"); + } + /** * Return the vector of values for the reactions change in * enthalpy. These values depend upon the concentration of @@ -533,7 +546,7 @@ namespace Cantera { * @param deltaH Output vector of deltaH's for reactions * Length: m_ii. */ - virtual void getDeltaEnthalpy( doublereal* deltaH) { + virtual void getDeltaEnthalpy(doublereal* deltaH) { err("getDeltaEnthalpy"); } @@ -547,7 +560,7 @@ namespace Cantera { * @param deltaS Output vector of deltaS's for reactions * Length: m_ii. */ - virtual void getDeltaEntropy( doublereal* deltaS) { + virtual void getDeltaEntropy(doublereal* deltaS) { err("getDeltaEntropy"); } @@ -561,7 +574,7 @@ namespace Cantera { * @param deltaG Output vector of ss deltaG's for reactions * Length: m_ii. */ - virtual void getDeltaSSGibbs( doublereal* deltaG) { + virtual void getDeltaSSGibbs(doublereal* deltaG) { err("getDeltaSSGibbs"); } @@ -575,7 +588,7 @@ namespace Cantera { * @param deltaH Output vector of ss deltaH's for reactions * Length: m_ii. */ - virtual void getDeltaSSEnthalpy( doublereal* deltaH) { + virtual void getDeltaSSEnthalpy(doublereal* deltaH) { err("getDeltaSSEnthalpy"); } @@ -589,7 +602,7 @@ namespace Cantera { * @param deltaS Output vector of ss deltaS's for reactions * Length: m_ii. */ - virtual void getDeltaSSEntropy( doublereal* deltaS) { + virtual void getDeltaSSEntropy(doublereal* deltaS) { err("getDeltaSSEntropy"); } From e23a78062909ed4ab136979c0ffa20b20ee4fb9a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 20 Oct 2010 18:18:05 +0000 Subject: [PATCH 278/446] Added missing functions from PureFluidPhase --- Cantera/src/thermo/PureFluidPhase.cpp | 152 +++++++++++++++++++----- Cantera/src/thermo/PureFluidPhase.h | 162 ++++++++++++++++++++++++++ 2 files changed, 286 insertions(+), 28 deletions(-) diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 41dcc6bcc..f753bc8cd 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -179,14 +179,14 @@ namespace Cantera { check(p); return p; } - + //==================================================================================================================== void PureFluidPhase:: setPressure(doublereal p) { Set(tpx::TP, temperature(), p); setDensity(1.0/m_sub->v()); check(); } - + //==================================================================================================================== void PureFluidPhase::Set(int n, double x, double y) const { try { m_sub->Set(n, x, y); @@ -195,36 +195,115 @@ namespace Cantera { reportTPXError(); } } - + //==================================================================================================================== void PureFluidPhase::setTPXState() const { Set(tpx::TV, temperature(), 1.0/density()); } - + //==================================================================================================================== void PureFluidPhase::check(doublereal v) const { if (m_sub->Error() || v == tpx::Undef) { throw CanteraError("PureFluidPhase",string(tpx::errorMsg( m_sub->Error()))); } } - + //==================================================================================================================== void PureFluidPhase::reportTPXError() const { string msg = tpx::TPX_Error::ErrorMessage; string proc = "tpx::"+tpx::TPX_Error::ErrorProcedure; throw CanteraError(proc,msg); } - + //==================================================================================================================== doublereal PureFluidPhase::isothermalCompressibility() const { return m_sub->isothermalCompressibility(); } - + //==================================================================================================================== doublereal PureFluidPhase::thermalExpansionCoeff() const { return m_sub->thermalExpansionCoeff(); } - + //==================================================================================================================== tpx::Substance& PureFluidPhase::TPX_Substance() { return *m_sub; } - - + //==================================================================================================================== + // Returns an array of partial molar enthalpies for the species + // in the mixture. Units (J/kmol) + /* + * @param hbar Output vector of species partial molar enthalpies. + * Length: m_kk. units are J/kmol. + */ + void PureFluidPhase::getPartialMolarEnthalpies(doublereal* hbar) const { + hbar[0] = enthalpy_mole(); + } + //==================================================================================================================== + // Returns an array of partial molar entropies of the species in the + // solution. Units: J/kmol/K. + /* + * @param sbar Output vector of species partial molar entropies. + * Length = m_kk. units are J/kmol/K. + */ + void PureFluidPhase::getPartialMolarEntropies(doublereal* sbar) const { + sbar[0] = entropy_mole(); + } + //==================================================================================================================== + // Return an array of partial molar internal energies for the + // species in the mixture. Units: J/kmol. + /* + * @param ubar Output vector of speciar partial molar internal energies. + * Length = m_kk. units are J/kmol. + */ + void PureFluidPhase::getPartialMolarIntEnergies(doublereal* ubar) const { + ubar[0] = intEnergy_mole(); + } + //==================================================================================================================== + // Return an array of partial molar heat capacities for the + // species in the mixture. Units: J/kmol/K + /* + * @param cpbar Output vector of species partial molar heat + * capacities at constant pressure. + * Length = m_kk. units are J/kmol/K. + */ + void PureFluidPhase::getPartialMolarCp(doublereal* cpbar) const { + cpbar[0] = cp_mole(); + } + //==================================================================================================================== + // Return an array of partial molar volumes for the + // species in the mixture. Units: m^3/kmol. + /* + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void PureFluidPhase::getPartialMolarVolumes(doublereal* vbar) const { + vbar[0] = 1.0 / molarDensity(); + } + //==================================================================================================================== + int PureFluidPhase::standardStateConvention() const { + return cSS_CONVENTION_TEMPERATURE; + } + //==================================================================================================================== + void PureFluidPhase::getActivityConcentrations(doublereal* c) const { + c[0] = 1.0; + } + //==================================================================================================================== + doublereal PureFluidPhase::standardConcentration(int k) const { + return 1.0; + } + //==================================================================================================================== + void PureFluidPhase::getActivities(doublereal *a) const { + a[0] = 1.0; + } + //==================================================================================================================== + // Get the array of chemical potentials at unit activity for the species + // at their standard states at the current T and P of the solution. + /* + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution + * + * @param mu Output vector of chemical potentials. + * Length: m_kk. + */ + void PureFluidPhase::getStandardChemPotentials(doublereal* mu) const { + mu[0] = gibbs_mole(); + } //==================================================================================================================== // Get the nondimensional Enthalpy functions for the species // at their standard states at the current T and P of the solution. @@ -237,7 +316,6 @@ namespace Cantera { doublereal h = enthalpy_mole(); hrt[0] = h / rt; } - //==================================================================================================================== // Get the array of nondimensional Entropy functions for the // standard state species at the current T and P of the solution. @@ -296,26 +374,43 @@ namespace Cantera { Set(tpx::TP, t, psave); } //==================================================================================================================== + // Returns the vector of the gibbs function of the reference state at the current temperature + // of the solution and the reference pressure for the species. + /* + * units = J/kmol + * + * @param g Output vector containing the reference state + * Gibbs Free energies. Length: m_kk. Units: J/kmol. + */ + void PureFluidPhase::getGibbs_ref(doublereal *g) const { + getGibbs_RT_ref(g); + g[0] *= (GasConstant * temperature()); + } + //==================================================================================================================== // Returns the vector of nondimensional entropies of the reference state at the current temperature // of the solution and the reference pressure for each species. - /*! + /* * @param er Output vector containing the nondimensional reference state * entropies. Length: m_kk. */ void PureFluidPhase::getEntropy_R_ref(doublereal *er) const { - + double psave = pressure(); + double t = temperature(); + double pref = m_spthermo->refPressure(); + Set(tpx::TP, t, pref); + getEntropy_R(er); + Set(tpx::TP, t, psave); } //==================================================================================================================== - - /// critical temperature + // critical temperature doublereal PureFluidPhase::critTemperature() const { return m_sub->Tcrit(); } - + //==================================================================================================================== /// critical pressure doublereal PureFluidPhase::critPressure() const { return m_sub->Pcrit(); } - + //==================================================================================================================== /// critical density doublereal PureFluidPhase::critDensity() const { return 1.0/m_sub->Vcrit(); } - + //==================================================================================================================== /// saturation temperature doublereal PureFluidPhase::satTemperature(doublereal p) const { @@ -328,35 +423,35 @@ namespace Cantera { return -1.0; } } - + //==================================================================================================================== void PureFluidPhase::setState_HP(doublereal h, doublereal p, doublereal tol) { Set(tpx::HP, h, p); setState_TR(m_sub->Temp(), 1.0/m_sub->v()); check(); } - + //==================================================================================================================== void PureFluidPhase::setState_UV(doublereal u, doublereal v, doublereal tol) { Set(tpx::UV, u, v); setState_TR(m_sub->Temp(), 1.0/m_sub->v()); check(); } - + //==================================================================================================================== void PureFluidPhase::setState_SV(doublereal s, doublereal v, doublereal tol) { Set(tpx::SV, s, v); setState_TR(m_sub->Temp(), 1.0/m_sub->v()); check(); } - + //==================================================================================================================== void PureFluidPhase::setState_SP(doublereal s, doublereal p, doublereal tol) { Set(tpx::SP, s, p); setState_TR(m_sub->Temp(), 1.0/m_sub->v()); check(); } - + //==================================================================================================================== // saturation pressure doublereal PureFluidPhase::satPressure(doublereal t) const { doublereal vsv = m_sub->v(); @@ -370,14 +465,14 @@ namespace Cantera { return -1.0; } } - + //==================================================================================================================== doublereal PureFluidPhase::vaporFraction() const { setTPXState(); doublereal x = m_sub->x(); check(x); return x; } - + //==================================================================================================================== void PureFluidPhase::setState_Tsat(doublereal t, doublereal x) { setTemperature(t); setTPXState(); @@ -385,7 +480,7 @@ namespace Cantera { setDensity(1.0/m_sub->v()); check(); } - + //==================================================================================================================== void PureFluidPhase::setState_Psat(doublereal p, doublereal x) { setTPXState(); Set(tpx::PX, p, x); @@ -394,7 +489,7 @@ namespace Cantera { check(); } - + //==================================================================================================================== /** * Format a summary of the mixture state for output. */ @@ -512,7 +607,7 @@ namespace Cantera { } return s; } - + //==================================================================================================================== /* * Format a summary of the mixture state for output. */ @@ -650,6 +745,7 @@ namespace Cantera { } } + } #endif // WITH_PURE_FLUIDS diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index e08b0e2b3..f692bad1d 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -142,6 +142,145 @@ namespace Cantera { mu[0] = gibbs_mole(); } + + + //! Get the species electrochemical potentials. + /*! + * These are partial molar quantities. This method adds a term \f$ F z_k + * \phi_p \f$ to each chemical potential. + * The electrochemical potential of species k in a phase p, \f$ \zeta_k \f$, + * is related to the chemical potential via + * the following equation, + * + * \f[ + * \zeta_{k}(T,P) = \mu_{k}(T,P) + F z_k \phi_p + * \f] + * + * @param mu Output vector of species electrochemical + * potentials. Length: m_kk. Units: J/kmol + */ + void getElectrochemPotentials(doublereal* mu) const { + getChemPotentials(mu); + double ve = Faraday * electricPotential(); + for (int k = 0; k < m_kk; k++) { + mu[k] += ve*charge(k); + } + } + + //! Returns an array of partial molar enthalpies for the species + //! in the mixture. Units (J/kmol) + /*! + * @param hbar Output vector of species partial molar enthalpies. + * Length: m_kk. units are J/kmol. + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + + //! Returns an array of partial molar entropies of the species in the + //! solution. Units: J/kmol/K. + /*! + * @param sbar Output vector of species partial molar entropies. + * Length = m_kk. units are J/kmol/K. + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Return an array of partial molar internal energies for the + //! species in the mixture. Units: J/kmol. + /*! + * @param ubar Output vector of speciar partial molar internal energies. + * Length = m_kk. units are J/kmol. + */ + virtual void getPartialMolarIntEnergies(doublereal* ubar) const; + + //! Return an array of partial molar heat capacities for the + //! species in the mixture. Units: J/kmol/K + /*! + * @param cpbar Output vector of species partial molar heat + * capacities at constant pressure. + * Length = m_kk. units are J/kmol/K. + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //! This method returns the convention used in specification + //! of the standard state, of which there are currently two, + //! temperature based, and variable pressure based. + /*! + * Currently, there are two standard state conventions: + * - Temperature-based activities + * cSS_CONVENTION_TEMPERATURE 0 + * - default + * + * - Variable Pressure and Temperature -based activities + * cSS_CONVENTION_VPSS 1 + * + * - Thermodynamics is set via slave ThermoPhase objects with + * nothing being carried out at this %ThermoPhase object level + * cSS_CONVENTION_SLAVE 2 + */ + virtual int standardStateConvention() const; + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + //! Return the standard concentration for the kth species + /*! + * The standard concentration \f$ C^0_k \f$ used to normalize + * the activity (i.e., generalized) concentration. In many cases, this quantity + * will be the same for all species in a phase - for example, + * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this + * reason, this method returns a single value, instead of an + * array. However, for phases in which the standard + * concentration is species-specific (e.g. surface species of + * different sizes), this method may be called with an + * optional parameter indicating the species. + * + * @param k Optional parameter indicating the species. The default + * is to assume this refers to species 0. + * @return + * Returns the standard concentration. The units are by definition + * dependent on the ThermoPhase and kinetics manager representation. + */ + virtual doublereal standardConcentration(int k=0) const; + + //! Get the array of non-dimensional activities at + //! the current solution temperature, pressure, and solution concentration. + /*! + * Note, for molality based formulations, this returns the + * molality based activities. + * + * We resolve this function at this level by calling + * on the activityConcentration function. However, + * derived classes may want to override this default + * implementation. + * + * @param a Output vector of activities. Length: m_kk. + */ + virtual void getActivities(doublereal* a) const; + //! Returns the isothermal compressibility. Units: 1/Pa. /*! * The isothermal compressibility is defined as @@ -167,6 +306,17 @@ namespace Cantera { /// @name Properties of the Standard State of the Species in the Solution //@{ + //! Get the array of chemical potentials at unit activity for the species + //! at their standard states at the current T and P of the solution. + /*! + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution + * + * @param mu Output vector of chemical potentials. + * Length: m_kk. + */ + virtual void getStandardChemPotentials(doublereal* mu) const; //! Get the nondimensional Enthalpy functions for the species //! at their standard states at the current T and P of the solution. @@ -217,6 +367,18 @@ namespace Cantera { */ virtual void getGibbs_RT_ref(doublereal *grt) const; + //! Returns the vector of the gibbs function of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * units = J/kmol + * + * @param g Output vector containing the reference state + * Gibbs Free energies. Length: m_kk. Units: J/kmol. + */ + virtual void getGibbs_ref(doublereal *g) const; + + + //! Returns the vector of nondimensional //! entropies of the reference state at the current temperature //! of the solution and the reference pressure for each species. From 76322811977e9c0372182a18fa9e74c96f989c8d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 22 Oct 2010 20:18:10 +0000 Subject: [PATCH 279/446] Changed table at the start of debug printing --- Cantera/src/equil/vcs_MultiPhaseEquil.h | 13 +++++++++++-- Cantera/src/equil/vcs_solve_TP.cpp | 20 ++++++++++---------- 2 files changed, 21 insertions(+), 12 deletions(-) diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.h b/Cantera/src/equil/vcs_MultiPhaseEquil.h index 9abff4bb5..c090c5a7c 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.h +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.h @@ -642,9 +642,18 @@ namespace VCSnonideal { * This object owns the pointer. */ VCSnonideal::VCS_SOLVE *m_vsolvePtr; + }; + //! Global hook for turning on and off time printing. + /*! + * Default is to allow printing. But, you can assign this to zero + * globally to turn off all time printing. + * This is helpful for test suite purposes where you are interested + * in differences in text files. + */ + extern int vcs_timing_print_lvl; + } - - #endif + diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index d6de12ad7..8348a9ebb 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -216,20 +216,20 @@ namespace VCSnonideal { if (m_VCS_UnitsFormat == VCS_UNITS_MKS) { plogf(" Stan. Chem. Pot. in J/kmol\n"); } - plogf("\n SPECIES FORMULA VECTOR"); - print_space(29); - plogf(" STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type\n\n"); - print_space(14); - for (i = 0; i < m_numElemConstraints; ++i) plogf(" %-2.2s", m_elementName[i].c_str()); - plogf(" SI(I)\n"); + plogf("\n SPECIES FORMULA VECTOR "); + print_space(41); + plogf(" STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type\n\n"); + print_space(20); + for (i = 0; i < m_numElemConstraints; ++i) plogf("%-4.4s ", m_elementName[i].c_str()); + plogf(" PhaseID\n"); RT = vcs_nondimMult_TP(m_VCS_UnitsFormat, m_temperature); for (i = 0; i < m_numSpeciesTot; ++i) { - plogf(" %-12s", m_speciesName[i].c_str()); + plogf(" %-18.18s", m_speciesName[i].c_str()); for (j = 0; j < m_numElemConstraints; ++j) { - plogf("%3g", m_formulaMatrix[j][i]); + plogf("% -7.3g ", m_formulaMatrix[j][i]); } - plogf("%3d", m_phaseID[i]); - print_space(47-m_numElemConstraints*3); + plogf(" %3d ", m_phaseID[i]); + print_space(55-m_numElemConstraints*8); plogf("%12.5E %12.5E", RT * m_SSfeSpecies[i], m_molNumSpecies_old[i]); if (m_speciesUnknownType[i] == VCS_SPECIES_TYPE_MOLNUM) { plogf(" Mol_Num"); From f26ff9452534c5294b173fe4daa35e208adf787b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 22 Oct 2010 22:30:24 +0000 Subject: [PATCH 280/446] Changed NaCl_equil printouts due to rebaseline. Fixed Makefile error --- .../VCSnonideal/NaCl_equil/good_dout.txt | 584 +++++++++--------- .../VCSnonideal/NaCl_equil/good_out.txt | 30 +- .../min_python/minDiamond/Makefile.in | 4 + 3 files changed, 311 insertions(+), 307 deletions(-) diff --git a/test_problems/VCSnonideal/NaCl_equil/good_dout.txt b/test_problems/VCSnonideal/NaCl_equil/good_dout.txt index 5b996bb1a..6499cd319 100644 --- a/test_problems/VCSnonideal/NaCl_equil/good_dout.txt +++ b/test_problems/VCSnonideal/NaCl_equil/good_dout.txt @@ -206,22 +206,22 @@ VCS CALCULATION METHOD USER ESTIMATE OF EQUILIBRIUM Stan. Chem. Pot. in J/kmol - SPECIES FORMULA VECTOR STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type + SPECIES FORMULA VECTOR STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type - O H C N Na Cl cn Fe E Si Ca SI(I) - NaCl(S) 0 0 0 0 1 1 0 0 0 0 0 2 -4.32620E+08 5.00000E+00 Mol_Num - N2 0 0 0 2 0 0 0 0 0 0 0 1 -5.71282E+07 4.00000E+00 Mol_Num - H2O(L) 1 2 0 0 0 0 0 0 -0 0 0 0 -3.06686E+08 2.00000E+00 Mol_Num - H+ 0 1 0 0 0 0 1 0 -1 0 0 0 0.00000E+00 0.00000E+00 Mol_Num - Na+ 0 0 0 0 1 0 1 0 -1 0 0 0 -2.57752E+08 0.00000E+00 Mol_Num - OH 1 1 0 0 0 0 0 0 0 0 0 1 -2.26793E+08 0.00000E+00 Mol_Num - CO2 2 0 1 0 0 0 0 0 0 0 0 1 -4.57249E+08 0.00000E+00 Mol_Num - H2 0 2 0 0 0 0 0 0 0 0 0 1 -3.89624E+07 0.00000E+00 Mol_Num - H2O 1 2 0 0 0 0 0 0 0 0 0 1 -2.98124E+08 0.00000E+00 Mol_Num - NaCl 0 0 0 0 1 1 0 0 0 0 0 1 -2.49904E+08 0.00000E+00 Mol_Num - Cl- 0 0 0 0 0 1 -1 0 1 0 0 0 -1.83974E+08 0.00000E+00 Mol_Num - O2 2 0 0 0 0 0 0 0 0 0 0 1 -6.11650E+07 0.00000E+00 Mol_Num - OH- 1 1 0 0 0 0 -1 0 1 0 0 0 -2.26784E+08 0.00000E+00 Mol_Num + O H C N Na Cl cn_N Fe E Si Ca PhaseID + NaCl(S) 0 0 0 0 1 1 0 0 0 0 0 2 -4.32620E+08 5.00000E+00 Mol_Num + N2 0 0 0 2 0 0 0 0 0 0 0 1 -5.71282E+07 4.00000E+00 Mol_Num + H2O(L) 1 2 0 0 0 0 0 0 -0 0 0 0 -3.06686E+08 2.00000E+00 Mol_Num + H+ 0 1 0 0 0 0 1 0 -1 0 0 0 0.00000E+00 0.00000E+00 Mol_Num + Na+ 0 0 0 0 1 0 1 0 -1 0 0 0 -2.57752E+08 0.00000E+00 Mol_Num + OH 1 1 0 0 0 0 0 0 0 0 0 1 -2.26793E+08 0.00000E+00 Mol_Num + CO2 2 0 1 0 0 0 0 0 0 0 0 1 -4.57249E+08 0.00000E+00 Mol_Num + H2 0 2 0 0 0 0 0 0 0 0 0 1 -3.89624E+07 0.00000E+00 Mol_Num + H2O 1 2 0 0 0 0 0 0 0 0 0 1 -2.98124E+08 0.00000E+00 Mol_Num + NaCl 0 0 0 0 1 1 0 0 0 0 0 1 -2.49904E+08 0.00000E+00 Mol_Num + Cl- 0 0 0 0 0 1 -1 0 1 0 0 0 -1.83974E+08 0.00000E+00 Mol_Num + O2 2 0 0 0 0 0 0 0 0 0 0 1 -6.11650E+07 0.00000E+00 Mol_Num + OH- 1 1 0 0 0 0 -1 0 1 0 0 0 -2.26784E+08 0.00000E+00 Mol_Num --- Subroutine vcs_dfe called for all species ----------------------------------------------------------------------------- --- Subroutine BASOPT called to reevaluate the components @@ -284,12 +284,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 0, Iterations since last evaluation of optimal basis = 0 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.000e+00 - --- air 2 NA 4.000e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.000e+00 + --- air 2 NA 4.000e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -416,12 +416,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 1, Iterations since last evaluation of optimal basis = 0 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.000e+00 - --- air 2 NA 4.000e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.000e+00 + --- air 2 NA 4.000e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -544,12 +544,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 2, Iterations since last evaluation of optimal basis = 0 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.000e+00 - --- air 2 NA 4.000e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.000e+00 + --- air 2 NA 4.000e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -621,12 +621,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 3, Iterations since last evaluation of optimal basis = 1 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.960e+00 - --- air 2 NA 4.040e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.960e+00 + --- air 2 NA 4.040e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -695,12 +695,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 4, Iterations since last evaluation of optimal basis = 2 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.913e+00 - --- air 2 NA 4.087e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.913e+00 + --- air 2 NA 4.087e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -771,12 +771,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 5, Iterations since last evaluation of optimal basis = 3 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.878e+00 - --- air 2 NA 4.122e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.878e+00 + --- air 2 NA 4.122e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -846,12 +846,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 6, Iterations since last evaluation of optimal basis = 4 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.870e+00 - --- air 2 NA 4.130e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.870e+00 + --- air 2 NA 4.130e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -920,12 +920,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 7, Iterations since last evaluation of optimal basis = 5 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -972,7 +972,7 @@ VCS CALCULATION METHOD --- OH 9.579955E-19 2.672075E-17 -1.343949E+02 -1.310666E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 1.128556E-17 2.315351E-16 -3.563207E+01 -3.261086E+01 -3.903212E+01 -3.298970E+01 - --- H2O 1 1.306372E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -2.456850E-06 -3.211653E-12 + --- H2O 1 1.306372E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -2.456850E-06 -3.225864E-12 --- NaCl 0 4.024024E-32 4.024024E-32 -1.745188E+02 -1.745188E+02 -2.054692E-03 -2.054772E-03 --- Cl- 1 1.491328E-16 5.351979E-15 -1.072648E+02 -1.036844E+02 -6.977469E+01 -6.261392E+01 --- H2 1 4.789978E-19 1.336038E-17 -5.931825E+01 -5.598989E+01 -8.067707E+01 -7.069201E+01 @@ -994,18 +994,18 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 8, Iterations since last evaluation of optimal basis = 6 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 2.3154E-16 3.8191E-15 -3.2990E+01 | Normal calc: diag adjusted from 8.638e+15 to 8.638e+15 due to act coeff - --- H2O 1.3064E-01 0.0000E+00 -3.2117E-12 | Skipped: superconverged DG = -3.212E-12 + --- H2O 1.3064E-01 0.0000E+00 -3.2259E-12 | Skipped: superconverged DG = -3.226E-12 --- NaCl 4.0240E-32 8.2685E-35 -2.0548E-03 | Normal Calc --- Cl- 5.3520E-15 1.6755E-13 -6.2614E+01 | Normal calc: diag adjusted from 3.73694e+14 to 3.73693e+14 due to act coeff --- H2 1.3360E-17 3.1482E-16 -7.0692E+01 | Normal Calc @@ -1046,7 +1046,7 @@ VCS CALCULATION METHOD --- OH 2.672075E-17 6.563687E-16 -1.310666E+02 -1.278653E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 2.315351E-16 4.050672E-15 -3.261086E+01 -2.974896E+01 -3.298970E+01 -2.726589E+01 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.211653E-12 -3.026912E-12 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.225864E-12 -3.026912E-12 --- NaCl 0 4.024024E-32 4.024024E-32 -1.745188E+02 -1.745188E+02 -2.054772E-03 -2.054772E-03 --- Cl- 1 5.351979E-15 1.729062E-13 -1.036844E+02 -1.002091E+02 -6.261392E+01 -5.566336E+01 --- H2 1 1.336038E-17 3.281844E-16 -5.598989E+01 -5.278861E+01 -7.069201E+01 -6.108817E+01 @@ -1070,12 +1070,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 9, Iterations since last evaluation of optimal basis = 7 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1122,8 +1122,8 @@ VCS CALCULATION METHOD --- OH 6.563687E-16 1.402182E-14 -1.278653E+02 -1.248036E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 4.050672E-15 5.927327E-14 -2.974896E+01 -2.706569E+01 -2.726589E+01 -2.189936E+01 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.026912E-12 2.188472E-12 - --- NaCl 0 4.024024E-32 4.032301E-32 -1.745188E+02 -1.745168E+02 -2.054772E-03 -2.842171E-14 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.026912E-12 2.174261E-12 + --- NaCl 0 4.024024E-32 4.032301E-32 -1.745188E+02 -1.745168E+02 -2.054772E-03 0.000000E+00 --- Cl- 1 1.729062E-13 4.985182E-12 -1.002091E+02 -9.684768E+01 -5.566336E+01 -4.894043E+01 --- H2 1 3.281844E-16 7.010911E-15 -5.278861E+01 -4.972696E+01 -6.108817E+01 -5.190322E+01 --- O2 0 5.499996E-39 5.499996E-49 -1.141882E+02 -1.372140E+02 1.498420E+02 1.145695E+02 @@ -1145,19 +1145,19 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 10, Iterations since last evaluation of optimal basis = 8 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 5.9273E-14 6.4902E-13 -2.1899E+01 | Normal calc: diag adjusted from 3.3742e+13 to 3.3742e+13 due to act coeff - --- H2O 1.3064E-01 0.0000E+00 2.1885E-12 | Skipped: superconverged DG = 2.188E-12 - --- NaCl 4.0323E-32 0.0000E+00 -2.8422E-14 | Skipped: superconverged DG = -2.842E-14 + --- H2O 1.3064E-01 0.0000E+00 2.1743E-12 | Skipped: superconverged DG = 2.174E-12 + --- NaCl 4.0323E-32 0.0000E+00 0.0000E+00 | Skipped: superconverged DG = 0.000E+00 --- Cl- 4.9852E-12 1.2199E-10 -4.8940E+01 | Normal calc: diag adjusted from 4.01189e+11 to 4.01186e+11 due to act coeff --- H2 7.0109E-15 1.2130E-13 -5.1903E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 1.1457E+02 | Skipped: IC = 0 and DG >0: 1.146E+02 @@ -1197,8 +1197,8 @@ VCS CALCULATION METHOD --- OH 1.402182E-14 2.566144E-13 -1.248036E+02 -1.218967E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 5.927327E-14 7.082968E-13 -2.706569E+01 -2.458505E+01 -2.189936E+01 -1.693807E+01 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.188472E-12 1.332978E-10 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 -2.842171E-14 -1.136868E-13 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.174261E-12 1.332836E-10 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 0.000000E+00 -8.526513E-14 --- Cl- 1 4.985182E-12 1.269745E-10 -9.684768E+01 -9.361022E+01 -4.894043E+01 -4.246551E+01 --- H2 1 7.010911E-15 1.283072E-13 -4.972696E+01 -4.682000E+01 -5.190322E+01 -4.318234E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 1.145695E+02 1.029417E+02 @@ -1219,19 +1219,19 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 11, Iterations since last evaluation of optimal basis = 9 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 7.0830E-13 5.9986E-12 -1.6938E+01 | Normal calc: diag adjusted from 2.82368e+12 to 2.82367e+12 due to act coeff - --- H2O 1.3064E-01 -1.7982E-11 1.3330E-10 | Normal Calc - --- NaCl 4.0323E-32 0.0000E+00 -1.1369E-13 | Skipped: superconverged DG = -1.137E-13 + --- H2O 1.3064E-01 -1.7981E-11 1.3328E-10 | Normal Calc + --- NaCl 4.0323E-32 0.0000E+00 -8.5265E-14 | Skipped: superconverged DG = -8.527E-14 --- Cl- 1.2697E-10 2.6961E-09 -4.2466E+01 | Normal calc: diag adjusted from 1.57512e+10 to 1.57506e+10 due to act coeff --- H2 1.2831E-13 1.8469E-12 -4.3182E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 1.0294E+02 | Skipped: IC = 0 and DG >0: 1.029E+02 @@ -1239,14 +1239,14 @@ VCS CALCULATION METHOD --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment --- H+ 1 7.0830E-13 6.7069E-12 5.9986E-12 | Normal Major Calc - --- H2O 1 1.3064E-01 1.3064E-01-1.7982E-11 | Normal Major Calc + --- H2O 1 1.3064E-01 1.3064E-01-1.7981E-11 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered --- Cl- 1 1.2697E-10 2.8231E-09 2.6961E-09 | Normal Major Calc --- H2 1 1.2831E-13 1.9752E-12 1.8469E-12 | Normal Major Calc --- O2 0 5.5000E-49 5.5000E-49 0.0000E+00 | minor species not considered --- NaCl(S) c 5.0000E+00 5.0000E+00-2.6961E-09 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.8694E+00 1.8694E+00 8.2901E-12 | + --- H2O(L) c 1.8694E+00 1.8694E+00 8.2882E-12 | --- Na+ c 1.2697E-10 2.8231E-09 2.6961E-09 | --- OH- c 7.0830E-13 6.7069E-12 5.9986E-12 | --- OH c 2.5661E-13 3.9504E-12 3.6937E-12 | @@ -1271,8 +1271,8 @@ VCS CALCULATION METHOD --- OH 2.566144E-13 3.950352E-12 -1.218967E+02 -1.191627E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 7.082968E-13 6.706888E-12 -2.458505E+01 -2.233729E+01 -1.693807E+01 -1.244255E+01 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 1.332978E-10 2.889266E-09 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 -1.136868E-13 2.899014E-12 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 1.332836E-10 2.889266E-09 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 -8.526513E-14 2.927436E-12 --- Cl- 1 1.269745E-10 2.823091E-09 -9.361022E+01 -9.050889E+01 -4.246551E+01 -3.626285E+01 --- H2 1 1.283072E-13 1.975176E-12 -4.682000E+01 -4.408602E+01 -4.318234E+01 -3.498039E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 1.029417E+02 9.200573E+01 @@ -1293,19 +1293,19 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 12, Iterations since last evaluation of optimal basis = 10 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 6.7069E-12 4.1725E-11 -1.2443E+01 | Normal calc: diag adjusted from 2.98201e+11 to 2.98201e+11 due to act coeff - --- H2O 1.3064E-01 -3.8977E-10 2.8893E-09 | Normal calc: diag adjusted from 7.41267 to 7.41267 due to act coeff - --- NaCl 4.0323E-32 0.0000E+00 2.8990E-12 | Skipped: superconverged DG = 2.899E-12 + --- H2O 1.3064E-01 -3.8977E-10 2.8893E-09 | Normal Calc + --- NaCl 4.0323E-32 0.0000E+00 2.9274E-12 | Skipped: superconverged DG = 2.927E-12 --- Cl- 2.8231E-09 5.1195E-08 -3.6263E+01 | Normal calc: diag adjusted from 7.08443e+08 to 7.08323e+08 due to act coeff --- H2 1.9752E-12 2.3031E-11 -3.4980E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 9.2006E+01 | Skipped: IC = 0 and DG >0: 9.201E+01 @@ -1345,8 +1345,8 @@ VCS CALCULATION METHOD --- OH 3.950352E-12 5.001197E-11 -1.191627E+02 -1.166242E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 6.706888E-12 4.843231E-11 -2.233729E+01 -2.036140E+01 -1.244255E+01 -8.490778E+00 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.889266E-09 5.477268E-08 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.899014E-12 8.051870E-11 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.889266E-09 5.477270E-08 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.927436E-12 8.054712E-11 --- Cl- 1 2.823091E-09 5.401842E-08 -9.050889E+01 -8.755854E+01 -3.626285E+01 -3.036215E+01 --- H2 1 1.975176E-12 2.500598E-11 -4.408602E+01 -4.154756E+01 -3.498039E+01 -2.736502E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 9.200573E+01 8.185190E+01 @@ -1369,19 +1369,19 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 13, Iterations since last evaluation of optimal basis = 11 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 4.8432E-11 2.0561E-10 -8.4908E+00 | Normal calc: diag adjusted from 4.12947e+10 to 4.12947e+10 due to act coeff --- H2O 1.3064E-01 -7.3891E-09 5.4773E-08 | Normal Calc - --- NaCl 4.0323E-32 0.0000E+00 8.0519E-11 | Skipped: superconverged DG = 8.052E-11 + --- NaCl 4.0323E-32 0.0000E+00 8.0547E-11 | Skipped: superconverged DG = 8.055E-11 --- Cl- 5.4018E-08 8.2067E-07 -3.0362E+01 | Normal calc: diag adjusted from 3.70244e+07 to 3.6997e+07 due to act coeff --- H2 2.5006E-11 2.2810E-10 -2.7365E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 8.1852E+01 | Skipped: IC = 0 and DG >0: 8.185E+01 @@ -1421,8 +1421,8 @@ VCS CALCULATION METHOD --- OH 5.001197E-11 5.062047E-10 -1.166242E+02 -1.143096E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 4.843231E-11 2.540464E-10 -2.036140E+01 -1.870850E+01 -8.490778E+00 -5.184988E+00 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 5.477268E-08 8.762514E-07 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 8.051870E-11 1.703711E-09 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 5.477270E-08 8.762514E-07 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 8.054712E-11 1.703739E-09 --- Cl- 1 5.401842E-08 8.746840E-07 -8.755854E+01 -8.477846E+01 -3.036215E+01 -2.480199E+01 --- H2 1 2.500598E-11 2.531024E-10 -4.154756E+01 -3.923288E+01 -2.736502E+01 -2.042098E+01 --- O2 0 5.499996E-49 5.500000E-59 -1.372140E+02 -1.602399E+02 8.185190E+01 4.956734E+01 @@ -1444,12 +1444,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 14, Iterations since last evaluation of optimal basis = 12 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1497,7 +1497,7 @@ VCS CALCULATION METHOD --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 2.540464E-10 9.126609E-10 -1.870850E+01 -1.744499E+01 -5.184988E+00 -2.658091E+00 --- H2O 1 1.306375E-01 1.306374E-01 -1.237155E+02 -1.237155E+02 8.762514E-07 1.155212E-05 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 1.703711E-09 2.907026E-08 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 1.703739E-09 2.907029E-08 --- Cl- 1 8.746840E-07 1.175373E-05 -8.477846E+01 -8.219584E+01 -2.480199E+01 -1.963675E+01 --- H2 1 2.531024E-10 1.975968E-09 -3.923288E+01 -3.717786E+01 -2.042098E+01 -1.425589E+01 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 4.956734E+01 4.134723E+01 @@ -1518,12 +1518,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 15, Iterations since last evaluation of optimal basis = 13 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.869e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.869e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1555,7 +1555,7 @@ VCS CALCULATION METHOD --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474310E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123265632836E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123265632837E+03 --- subroutine FORCE: Beginning Slope = -0.00229013 --- subroutine FORCE: End Slope = -0.00174304 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1571,7 +1571,7 @@ VCS CALCULATION METHOD --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 9.126609E-10 2.125630E-09 -1.744499E+01 -1.664373E+01 -2.658091E+00 -1.056949E+00 --- H2O 1 1.306374E-01 1.306359E-01 -1.237155E+02 -1.237155E+02 1.155212E-05 1.219229E-04 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.907026E-08 3.995352E-07 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.907029E-08 3.995353E-07 --- Cl- 1 1.175373E-05 1.283713E-04 -8.219584E+01 -7.985041E+01 -1.963675E+01 -1.494589E+01 --- H2 1 1.975968E-09 1.136570E-08 -3.717786E+01 -3.542832E+01 -1.425589E+01 -9.007025E+00 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 4.134723E+01 3.434882E+01 @@ -1583,7 +1583,7 @@ VCS CALCULATION METHOD --- NaCl(S) = 4.9998716E+00 ------------------------------------------------------------------------------------------------------- --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474310E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123265632836E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123265632837E+03 --- Increment counter increased, step is accepted: 16 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1592,12 +1592,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 16, Iterations since last evaluation of optimal basis = 14 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.870e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 5.000e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.870e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 5.000e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1628,8 +1628,8 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632836E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123386178417E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632837E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123386178418E+03 --- subroutine FORCE: Beginning Slope = -0.0147915 --- subroutine FORCE: End Slope = -0.0107105 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1645,7 +1645,7 @@ VCS CALCULATION METHOD --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 --- H+ 1 2.125630E-09 3.248971E-09 -1.664373E+01 -1.631279E+01 -1.056949E+00 -4.063358E-01 --- H2O 1 1.306359E-01 1.306194E-01 -1.237155E+02 -1.237156E+02 1.219229E-04 1.002074E-03 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 3.995352E-07 4.356599E-06 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 3.995353E-07 4.356599E-06 --- Cl- 1 1.283713E-04 1.118018E-03 -7.985041E+01 -7.778867E+01 -1.494589E+01 -1.082240E+01 --- H2 1 1.136570E-08 4.548942E-08 -3.542832E+01 -3.404144E+01 -9.007025E+00 -4.844370E+00 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 3.434882E+01 2.879929E+01 @@ -1656,8 +1656,8 @@ VCS CALCULATION METHOD --- air = 4.1306196E+00 --- NaCl(S) = 4.9988820E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632836E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123386178417E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632837E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123386178418E+03 --- Increment counter increased, step is accepted: 17 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1668,12 +1668,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 17, Iterations since last evaluation of optimal basis = 15 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.872e+00 - --- air 2 NA 4.131e+00 - --- NaCl(S) 2 NA 4.999e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.872e+00 + --- air 2 NA 4.131e+00 + --- NaCl(S) 2 NA 4.999e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1704,7 +1704,7 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178417E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178418E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123938322437E+03 --- subroutine FORCE: Beginning Slope = -0.0701224 --- subroutine FORCE: End Slope = -0.0472713 @@ -1732,7 +1732,7 @@ VCS CALCULATION METHOD --- air = 4.1304846E+00 --- NaCl(S) = 4.9924027E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178417E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178418E+03 --- Total New Dimensionless Gibbs Free Energy = -1.2123938322437E+03 --- Increment counter increased, step is accepted: 18 --- Normal element abundance check - passed @@ -1743,12 +1743,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 18, Iterations since last evaluation of optimal basis = 16 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.885e+00 - --- air 2 NA 4.130e+00 - --- NaCl(S) 2 NA 4.992e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.885e+00 + --- air 2 NA 4.130e+00 + --- NaCl(S) 2 NA 4.992e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1780,7 +1780,7 @@ VCS CALCULATION METHOD --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123938322437E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2125582635496E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2125582635489E+03 --- subroutine FORCE: Beginning Slope = -0.221211 --- subroutine FORCE: End Slope = -0.129981 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1808,7 +1808,7 @@ VCS CALCULATION METHOD --- NaCl(S) = 4.9620821E+00 ------------------------------------------------------------------------------------------------------- --- Total Old Dimensionless Gibbs Free Energy = -1.2123938322437E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2125582635496E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2125582635489E+03 --- Increment counter increased, step is accepted: 19 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1817,12 +1817,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 19, Iterations since last evaluation of optimal basis = 17 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 1.946e+00 - --- air 2 NA 4.130e+00 - --- NaCl(S) 2 NA 4.962e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 1.946e+00 + --- air 2 NA 4.130e+00 + --- NaCl(S) 2 NA 4.962e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1853,8 +1853,8 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635496E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2127905822680E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635489E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2127905822678E+03 --- subroutine FORCE: Beginning Slope = -0.352682 --- subroutine FORCE: End Slope = -0.141262 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1881,8 +1881,8 @@ VCS CALCULATION METHOD --- air = 4.1255402E+00 --- NaCl(S) = 4.8798249E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635496E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2127905822680E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635489E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2127905822678E+03 --- Increment counter increased, step is accepted: 20 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1891,12 +1891,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 20, Iterations since last evaluation of optimal basis = 18 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.115e+00 - --- air 2 NA 4.126e+00 - --- NaCl(S) 2 NA 4.880e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.115e+00 + --- air 2 NA 4.126e+00 + --- NaCl(S) 2 NA 4.880e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -1927,8 +1927,8 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822680E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2128646676327E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822678E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2128646676326E+03 --- subroutine FORCE: Beginning Slope = -0.133331 --- subroutine FORCE: End Slope = -0.0193693 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1946,7 +1946,7 @@ VCS CALCULATION METHOD --- H2O 1 1.255396E-01 1.126909E-01 -1.237541E+02 -1.238589E+02 1.004058E-01 1.193288E-01 --- NaCl 0 4.032284E-32 4.032284E-32 -1.745156E+02 -1.745124E+02 1.230431E-03 4.349718E-03 --- Cl- 1 1.201751E-01 1.972869E-01 -7.323363E+01 -7.249312E+01 -1.712334E+00 -2.313017E-01 - --- H2 1 2.213541E-07 2.079361E-07 -3.245792E+01 -3.251734E+01 1.818533E-01 2.511647E-01 + --- H2 1 2.213541E-07 2.079361E-07 -3.245792E+01 -3.251734E+01 1.818533E-01 2.511646E-01 --- O2 0 5.499999E-69 5.499999E-69 -1.832645E+02 -1.832614E+02 -8.350718E-01 -8.418503E-01 --- Norms of Delta G(): 8.415159E-01 4.705939E-01 --- Phase_Name KMoles(after update) @@ -1955,8 +1955,8 @@ VCS CALCULATION METHOD --- air = 4.1126915E+00 --- NaCl(S) = 4.8027131E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822680E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2128646676327E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822678E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2128646676326E+03 --- Increment counter increased, step is accepted: 21 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1967,12 +1967,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 21, Iterations since last evaluation of optimal basis = 19 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.282e+00 - --- air 2 NA 4.113e+00 - --- NaCl(S) 2 NA 4.803e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.282e+00 + --- air 2 NA 4.113e+00 + --- NaCl(S) 2 NA 4.803e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2003,7 +2003,7 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676327E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676326E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673025651E+03 --- subroutine FORCE: Beginning Slope = -0.00465137 --- subroutine FORCE: End Slope = -0.000598004 @@ -2018,11 +2018,11 @@ VCS CALCULATION METHOD --- OH- 2.817521E-09 1.832197E-09 -1.084016E+02 -1.088342E+02 --- OH 4.158722E-07 3.810548E-07 -1.075940E+02 -1.076782E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082278E+02 -5.082245E+02 - --- H+ 1 2.817521E-09 1.832197E-09 -1.487722E+01 -1.519494E+01 6.994265E-01 -2.906329E-02 + --- H+ 1 2.817521E-09 1.832197E-09 -1.487722E+01 -1.519494E+01 6.994265E-01 -2.906328E-02 --- H2O 1 1.126909E-01 9.916639E-02 -1.238589E+02 -1.239835E+02 1.193288E-01 1.660229E-02 --- NaCl 0 4.032284E-32 4.014783E-32 -1.745124E+02 -1.745135E+02 4.349718E-03 3.293917E-03 --- Cl- 1 1.972869E-01 2.104191E-01 -7.249312E+01 -7.239168E+01 -2.313017E-01 -2.843889E-02 - --- H2 1 2.079361E-07 1.905274E-07 -3.251734E+01 -3.260148E+01 2.511647E-01 4.239981E-02 + --- H2 1 2.079361E-07 1.905274E-07 -3.251734E+01 -3.260148E+01 2.511646E-01 4.239982E-02 --- O2 0 5.499999E-69 1.276361E-68 -1.832614E+02 -1.824162E+02 -8.418503E-01 2.961998E-01 --- Norms of Delta G(): 4.705939E-01 1.234720E-01 --- Phase_Name KMoles(after update) @@ -2031,7 +2031,7 @@ VCS CALCULATION METHOD --- air = 4.0991670E+00 --- NaCl(S) = 4.7895809E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676327E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676326E+03 --- Total New Dimensionless Gibbs Free Energy = -1.2128673025651E+03 --- Increment counter increased, step is accepted: 22 --- Normal element abundance check - passed @@ -2042,12 +2042,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 22, Iterations since last evaluation of optimal basis = 20 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.322e+00 - --- air 2 NA 4.099e+00 - --- NaCl(S) 2 NA 4.790e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.322e+00 + --- air 2 NA 4.099e+00 + --- NaCl(S) 2 NA 4.790e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2093,11 +2093,11 @@ VCS CALCULATION METHOD --- OH- 1.832197E-09 1.858822E-09 -1.088342E+02 -1.088200E+02 --- OH 3.810548E-07 3.756692E-07 -1.076782E+02 -1.076920E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082245E+02 -5.082241E+02 - --- H+ 1 1.832197E-09 1.858822E-09 -1.519494E+01 -1.516629E+01 -2.906329E-02 1.659943E-02 + --- H+ 1 1.832197E-09 1.858822E-09 -1.519494E+01 -1.516629E+01 -2.906328E-02 1.659943E-02 --- H2O 1 9.916639E-02 9.751445E-02 -1.239835E+02 -1.239999E+02 1.660229E-02 3.012001E-03 --- NaCl 0 4.014783E-32 4.014783E-32 -1.745135E+02 -1.745131E+02 3.293917E-03 3.696994E-03 --- Cl- 1 2.104191E-01 2.120780E-01 -7.239168E+01 -7.237906E+01 -2.843889E-02 -3.186461E-03 - --- H2 1 1.905274E-07 1.878346E-07 -3.260148E+01 -3.261531E+01 4.239981E-02 6.517138E-03 + --- H2 1 1.905274E-07 1.878346E-07 -3.260148E+01 -3.261531E+01 4.239982E-02 6.517138E-03 --- O2 0 1.276361E-68 1.276361E-68 -1.824162E+02 -1.824158E+02 2.961998E-01 3.463166E-01 --- Norms of Delta G(): 1.234720E-01 1.415898E-01 --- Phase_Name KMoles(after update) @@ -2116,12 +2116,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 23, Iterations since last evaluation of optimal basis = 21 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.098e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.098e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2168,10 +2168,10 @@ VCS CALCULATION METHOD --- OH 3.756692E-07 3.748531E-07 -1.076920E+02 -1.076941E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082241E+02 -5.082240E+02 --- H+ 1 1.858822E-09 1.843394E-09 -1.516629E+01 -1.517321E+01 1.659943E-02 1.552390E-03 - --- H2O 1 9.751445E-02 9.721983E-02 -1.239999E+02 -1.240028E+02 3.012001E-03 3.506627E-04 + --- H2O 1 9.751445E-02 9.721983E-02 -1.239999E+02 -1.240028E+02 3.012001E-03 3.506628E-04 --- NaCl 0 4.014783E-32 4.014783E-32 -1.745131E+02 -1.745130E+02 3.696994E-03 3.768900E-03 --- Cl- 1 2.120780E-01 2.122644E-01 -7.237906E+01 -7.237775E+01 -3.186461E-03 -5.619620E-04 - --- H2 1 1.878346E-07 1.874266E-07 -3.261531E+01 -3.261741E+01 6.517138E-03 7.939681E-04 + --- H2 1 1.878346E-07 1.874266E-07 -3.261531E+01 -3.261741E+01 6.517138E-03 7.939682E-04 --- O2 0 1.276361E-68 1.276361E-68 -1.824158E+02 -1.824158E+02 3.463166E-01 3.542145E-01 --- Norms of Delta G(): 1.415898E-01 1.446177E-01 --- Phase_Name KMoles(after update) @@ -2190,12 +2190,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 24, Iterations since last evaluation of optimal basis = 22 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2241,11 +2241,11 @@ VCS CALCULATION METHOD --- OH- 1.843394E-09 1.841963E-09 -1.088284E+02 -1.088292E+02 --- OH 3.748531E-07 3.747539E-07 -1.076941E+02 -1.076943E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.843394E-09 1.841963E-09 -1.517321E+01 -1.517371E+01 1.552390E-03 3.291143E-04 - --- H2O 1 9.721983E-02 9.718563E-02 -1.240028E+02 -1.240032E+02 3.506627E-04 6.262934E-05 + --- H+ 1 1.843394E-09 1.841963E-09 -1.517321E+01 -1.517371E+01 1.552390E-03 3.291142E-04 + --- H2O 1 9.721983E-02 9.718563E-02 -1.240028E+02 -1.240032E+02 3.506628E-04 6.262933E-05 --- NaCl 0 4.014783E-32 4.014783E-32 -1.745130E+02 -1.745130E+02 3.768900E-03 3.777246E-03 - --- Cl- 1 2.122644E-01 2.122973E-01 -7.237775E+01 -7.237750E+01 -5.619620E-04 -6.518287E-05 - --- H2 1 1.874266E-07 1.873770E-07 -3.261741E+01 -3.261767E+01 7.939681E-04 1.357775E-04 + --- Cl- 1 2.122644E-01 2.122973E-01 -7.237775E+01 -7.237750E+01 -5.619620E-04 -6.518288E-05 + --- H2 1 1.874266E-07 1.873770E-07 -3.261741E+01 -3.261767E+01 7.939682E-04 1.357774E-04 --- O2 0 1.276361E-68 1.276361E-68 -1.824158E+02 -1.824157E+02 3.542145E-01 3.551374E-01 --- Norms of Delta G(): 1.446177E-01 1.449925E-01 --- Phase_Name KMoles(after update) @@ -2266,12 +2266,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 25, Iterations since last evaluation of optimal basis = 23 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2317,11 +2317,11 @@ VCS CALCULATION METHOD --- OH- 1.841963E-09 1.841660E-09 -1.088292E+02 -1.088294E+02 --- OH 3.747539E-07 3.747369E-07 -1.076943E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841963E-09 1.841660E-09 -1.517371E+01 -1.517384E+01 3.291143E-04 3.297167E-05 - --- H2O 1 9.718563E-02 9.717953E-02 -1.240032E+02 -1.240032E+02 6.262934E-05 7.270506E-06 + --- H+ 1 1.841963E-09 1.841660E-09 -1.517371E+01 -1.517384E+01 3.291142E-04 3.297168E-05 + --- H2O 1 9.718563E-02 9.717953E-02 -1.240032E+02 -1.240032E+02 6.262933E-05 7.270507E-06 --- NaCl 0 4.014783E-32 3.999646E-32 -1.745130E+02 -1.745168E+02 3.777246E-03 1.490136E-06 - --- Cl- 1 2.122973E-01 2.123012E-01 -7.237750E+01 -7.237747E+01 -6.518287E-05 -1.163523E-05 - --- H2 1 1.873770E-07 1.873685E-07 -3.261767E+01 -3.261771E+01 1.357775E-04 1.641605E-05 + --- Cl- 1 2.122973E-01 2.123012E-01 -7.237750E+01 -7.237747E+01 -6.518288E-05 -1.163523E-05 + --- H2 1 1.873770E-07 1.873685E-07 -3.261767E+01 -3.261771E+01 1.357774E-04 1.641605E-05 --- O2 0 1.276361E-68 8.948274E-69 -1.824157E+02 -1.827709E+02 3.551374E-01 1.646216E-04 --- Norms of Delta G(): 1.449925E-01 6.909817E-05 --- Phase_Name KMoles(after update) @@ -2341,12 +2341,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 26, Iterations since last evaluation of optimal basis = 24 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2392,13 +2392,13 @@ VCS CALCULATION METHOD --- OH- 1.841660E-09 1.841630E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747369E-07 3.747349E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841660E-09 1.841630E-09 -1.517384E+01 -1.517385E+01 3.297167E-05 6.825273E-06 - --- H2O 1 9.717953E-02 9.717882E-02 -1.240032E+02 -1.240032E+02 7.270506E-06 1.298138E-06 - --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.490136E-06 1.663112E-06 + --- H+ 1 1.841660E-09 1.841630E-09 -1.517384E+01 -1.517385E+01 3.297168E-05 6.825272E-06 + --- H2O 1 9.717953E-02 9.717882E-02 -1.240032E+02 -1.240032E+02 7.270507E-06 1.298138E-06 + --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.490136E-06 1.663111E-06 --- Cl- 1 2.123012E-01 2.123018E-01 -7.237747E+01 -7.237747E+01 -1.163523E-05 -1.350606E-06 - --- H2 1 1.873685E-07 1.873674E-07 -3.261771E+01 -3.261772E+01 1.641605E-05 2.813834E-06 + --- H2 1 1.873685E-07 1.873674E-07 -3.261771E+01 -3.261772E+01 1.641605E-05 2.813833E-06 --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.646216E-04 1.836958E-04 - --- Norms of Delta G(): 6.909817E-05 7.506102E-05 + --- Norms of Delta G(): 6.909817E-05 7.506101E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274245E+00 @@ -2415,12 +2415,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 27, Iterations since last evaluation of optimal basis = 25 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2466,13 +2466,13 @@ VCS CALCULATION METHOD --- OH- 1.841630E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747349E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841630E-09 1.841623E-09 -1.517385E+01 -1.517386E+01 6.825273E-06 6.836550E-07 + --- H+ 1 1.841630E-09 1.841623E-09 -1.517385E+01 -1.517386E+01 6.825272E-06 6.836552E-07 --- H2O 1 9.717882E-02 9.717869E-02 -1.240032E+02 -1.240033E+02 1.298138E-06 1.506892E-07 - --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.663112E-06 1.693996E-06 + --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.663111E-06 1.693996E-06 --- Cl- 1 2.123018E-01 2.123019E-01 -7.237747E+01 -7.237746E+01 -1.350606E-06 -2.411459E-07 - --- H2 1 1.873674E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 2.813834E-06 3.402212E-07 + --- H2 1 1.873674E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 2.813833E-06 3.402213E-07 --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.836958E-04 1.871074E-04 - --- Norms of Delta G(): 7.506102E-05 7.639013E-05 + --- Norms of Delta G(): 7.506101E-05 7.639012E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2489,12 +2489,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 28, Iterations since last evaluation of optimal basis = 26 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2540,13 +2540,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 6.836550E-07 1.414622E-07 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 6.836552E-07 1.414622E-07 --- H2O 1 9.717869E-02 9.717868E-02 -1.240033E+02 -1.240033E+02 1.506892E-07 2.690517E-08 --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.693996E-06 1.697581E-06 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.411459E-07 -2.799241E-08 - --- H2 1 1.873673E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 3.402212E-07 5.831922E-08 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.411459E-07 -2.799244E-08 + --- H2 1 1.873673E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 3.402213E-07 5.831919E-08 --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.871074E-04 1.875027E-04 - --- Norms of Delta G(): 7.639013E-05 7.655082E-05 + --- Norms of Delta G(): 7.639012E-05 7.655082E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2565,12 +2565,12 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 29, Iterations since last evaluation of optimal basis = 27 (all species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- @@ -2616,13 +2616,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.414622E-07 1.416953E-08 - --- H2O 1 9.717868E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 2.690517E-08 3.123176E-09 - --- NaCl 0 3.999646E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 1.697581E-06 6.401422E-10 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.799241E-08 -4.998000E-09 - --- H2 1 1.873673E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 5.831922E-08 7.051398E-09 - --- O2 0 8.948274E-69 8.946597E-69 -1.827709E+02 -1.827711E+02 1.875027E-04 7.070759E-08 - --- Norms of Delta G(): 7.655082E-05 2.967941E-08 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.414622E-07 1.416954E-08 + --- H2O 1 9.717868E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 2.690517E-08 3.123191E-09 + --- NaCl 0 3.999646E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 1.697581E-06 6.401137E-10 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.799244E-08 -4.997958E-09 + --- H2 1 1.873673E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 5.831919E-08 7.051426E-09 + --- O2 0 8.948274E-69 8.946597E-69 -1.827709E+02 -1.827711E+02 1.875027E-04 7.070747E-08 + --- Norms of Delta G(): 7.655082E-05 2.967937E-08 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2640,22 +2640,22 @@ VCS CALCULATION METHOD ============================================================================================================== Iteration = 30, Iterations since last evaluation of optimal basis = 28 (only major species) --- vcs_popPhaseID() called - --- Phase Status F_e MoleNum - -------------------------------------------------------------- - --- NaCl_electrolyte 2 NA 2.327e+00 - --- air 2 NA 4.097e+00 - --- NaCl(S) 2 NA 4.788e+00 - -------------------------------------------------------------- + --- Phase Status F_e MoleNum + -------------------------------------------------------------------------- + --- NaCl_electrolyte 2 NA 2.327e+00 + --- air 2 NA 4.097e+00 + --- NaCl(S) 2 NA 4.788e+00 + --------------------------------------------------------------------- ---------------------------------------------------------------------------------- --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 1.8416E-09 -1.3047E-17 1.4170E-08 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff --- H2O 9.7179E-02 -3.0444E-10 3.1232E-09 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff - --- NaCl 3.9996E-32 0.0000E+00 6.4014E-10 | Skipped: IC = 0 and DG >0: 6.401E-10 + --- NaCl 3.9996E-32 0.0000E+00 6.4011E-10 | Skipped: IC = 0 and DG >0: 6.401E-10 --- Cl- 2.1230E-01 2.9261E-10 -4.9980E-09 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff --- H2 1.8737E-07 -4.4040E-16 7.0514E-09 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff - --- O2 8.9466E-69 0.0000E+00 7.0708E-08 | Skipped: IC = 0 and DG >0: 7.071E-08 + --- O2 8.9466E-69 0.0000E+00 7.0707E-08 | Skipped: IC = 0 and DG >0: 7.071E-08 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment @@ -2678,8 +2678,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -2.4133e-18 - --- subroutine FORCE: End Slope = -3.39523e-19 + --- subroutine FORCE: Beginning Slope = -2.41328e-18 + --- subroutine FORCE: End Slope = -3.39535e-19 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2691,13 +2691,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.416953E-08 2.931955E-09 - --- H2O 1 9.717867E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 3.123176E-09 5.576481E-10 - --- NaCl 0 3.999640E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 6.401422E-10 7.144649E-10 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -4.998000E-09 -5.801297E-10 - --- H2 1 1.873672E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 7.051398E-09 1.208747E-09 - --- O2 0 8.946597E-69 8.946597E-69 -1.827711E+02 -1.827711E+02 7.070759E-08 7.890071E-08 - --- Norms of Delta G(): 2.967941E-08 3.224008E-08 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.416954E-08 2.931912E-09 + --- H2O 1 9.717867E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 3.123191E-09 5.576339E-10 + --- NaCl 0 3.999640E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 6.401137E-10 7.144081E-10 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -4.997958E-09 -5.801866E-10 + --- H2 1 1.873672E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 7.051426E-09 1.208718E-09 + --- O2 0 8.946597E-69 8.946597E-69 -1.827711E+02 -1.827711E+02 7.070747E-08 7.890060E-08 + --- Norms of Delta G(): 2.967937E-08 3.224004E-08 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 diff --git a/test_problems/VCSnonideal/NaCl_equil/good_out.txt b/test_problems/VCSnonideal/NaCl_equil/good_out.txt index c9c8d1085..565135025 100644 --- a/test_problems/VCSnonideal/NaCl_equil/good_out.txt +++ b/test_problems/VCSnonideal/NaCl_equil/good_out.txt @@ -158,22 +158,22 @@ VCS CALCULATION METHOD USER ESTIMATE OF EQUILIBRIUM Stan. Chem. Pot. in J/kmol - SPECIES FORMULA VECTOR STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type + SPECIES FORMULA VECTOR STAN_CHEM_POT EQUILIBRIUM_EST. Species_Type - O H C N Na Cl cn Fe E Si Ca SI(I) - NaCl(S) 0 0 0 0 1 1 0 0 0 0 0 2 -4.32620E+08 5.00000E+00 Mol_Num - N2 0 0 0 2 0 0 0 0 0 0 0 1 -5.71282E+07 4.00000E+00 Mol_Num - H2O(L) 1 2 0 0 0 0 0 0 -0 0 0 0 -3.06686E+08 2.00000E+00 Mol_Num - H+ 0 1 0 0 0 0 1 0 -1 0 0 0 0.00000E+00 0.00000E+00 Mol_Num - Na+ 0 0 0 0 1 0 1 0 -1 0 0 0 -2.57752E+08 0.00000E+00 Mol_Num - OH 1 1 0 0 0 0 0 0 0 0 0 1 -2.26793E+08 0.00000E+00 Mol_Num - CO2 2 0 1 0 0 0 0 0 0 0 0 1 -4.57249E+08 0.00000E+00 Mol_Num - H2 0 2 0 0 0 0 0 0 0 0 0 1 -3.89624E+07 0.00000E+00 Mol_Num - H2O 1 2 0 0 0 0 0 0 0 0 0 1 -2.98124E+08 0.00000E+00 Mol_Num - NaCl 0 0 0 0 1 1 0 0 0 0 0 1 -2.49904E+08 0.00000E+00 Mol_Num - Cl- 0 0 0 0 0 1 -1 0 1 0 0 0 -1.83974E+08 0.00000E+00 Mol_Num - O2 2 0 0 0 0 0 0 0 0 0 0 1 -6.11650E+07 0.00000E+00 Mol_Num - OH- 1 1 0 0 0 0 -1 0 1 0 0 0 -2.26784E+08 0.00000E+00 Mol_Num + O H C N Na Cl cn_N Fe E Si Ca PhaseID + NaCl(S) 0 0 0 0 1 1 0 0 0 0 0 2 -4.32620E+08 5.00000E+00 Mol_Num + N2 0 0 0 2 0 0 0 0 0 0 0 1 -5.71282E+07 4.00000E+00 Mol_Num + H2O(L) 1 2 0 0 0 0 0 0 -0 0 0 0 -3.06686E+08 2.00000E+00 Mol_Num + H+ 0 1 0 0 0 0 1 0 -1 0 0 0 0.00000E+00 0.00000E+00 Mol_Num + Na+ 0 0 0 0 1 0 1 0 -1 0 0 0 -2.57752E+08 0.00000E+00 Mol_Num + OH 1 1 0 0 0 0 0 0 0 0 0 1 -2.26793E+08 0.00000E+00 Mol_Num + CO2 2 0 1 0 0 0 0 0 0 0 0 1 -4.57249E+08 0.00000E+00 Mol_Num + H2 0 2 0 0 0 0 0 0 0 0 0 1 -3.89624E+07 0.00000E+00 Mol_Num + H2O 1 2 0 0 0 0 0 0 0 0 0 1 -2.98124E+08 0.00000E+00 Mol_Num + NaCl 0 0 0 0 1 1 0 0 0 0 0 1 -2.49904E+08 0.00000E+00 Mol_Num + Cl- 0 0 0 0 0 1 -1 0 1 0 0 0 -1.83974E+08 0.00000E+00 Mol_Num + O2 2 0 0 0 0 0 0 0 0 0 0 1 -6.11650E+07 0.00000E+00 Mol_Num + OH- 1 1 0 0 0 0 -1 0 1 0 0 0 -2.26784E+08 0.00000E+00 Mol_Num diff --git a/test_problems/min_python/minDiamond/Makefile.in b/test_problems/min_python/minDiamond/Makefile.in index 2eef7041f..a1015041b 100644 --- a/test_problems/min_python/minDiamond/Makefile.in +++ b/test_problems/min_python/minDiamond/Makefile.in @@ -106,3 +106,7 @@ clean: $(RM) -rf SunWS_cache ; \ fi ) +ifeq ($(wildcard .depends), .depends) +include .depends +endif + From 1bdee902891535902fa2a1d6bc8ab1923912e310 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 23 Oct 2010 01:35:10 +0000 Subject: [PATCH 281/446] Fixed an error that occured when components of multispecies phases were zeroed because other phases were being zeroed. Then the noncomponents of that same multispecies phase could comprise the entire phase and the Hessian diagonal would then be zero. The fix to zero the species seems to work. --- Cantera/src/equil/vcs_rxnadj.cpp | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/Cantera/src/equil/vcs_rxnadj.cpp b/Cantera/src/equil/vcs_rxnadj.cpp index 0a4983045..7e68813a4 100644 --- a/Cantera/src/equil/vcs_rxnadj.cpp +++ b/Cantera/src/equil/vcs_rxnadj.cpp @@ -306,6 +306,33 @@ namespace VCSnonideal { * added back into the component species. */ if (dss != 0.0) { + + if ((k == kspec) && (m_SSPhase[kspec] != 1)) { + /* + * Found out that we can be in this spot, when components of multispecies phases + * are zeroed, leaving noncomponent species of the same phase having all of the + * mole numbers of that phases. it seems that we can suggest a zero of the species + * and the code will recover. + */ +#ifdef DEBUG_MODE + sprintf(ANOTE, "Delta damped from %g to %g due to delete %s", + m_deltaMolNumSpecies[kspec], + -m_molNumSpecies_old[kspec], m_speciesName[kspec].c_str()); +#endif + m_deltaMolNumSpecies[kspec] = -m_molNumSpecies_old[kspec]; +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); + plogf(" %12.4E %12.4E %12.4E | %s\n", + m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec], + m_deltaGRxn_new[irxn], ANOTE); + } +#endif + continue; + } + /* + * Delete the single species phase + */ m_molNumSpecies_old[kspec] += dss; m_tPhaseMoles_old[m_phaseID[kspec]] += dss; for (j = 0; j < m_numComponents; ++j) { From 13f151a3586671f136a4f5cd0d8906cf275c7aa8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 25 Oct 2010 22:12:55 +0000 Subject: [PATCH 282/446] Modification to the structure of solve_TP() Took the special case of SS species deletion in RxnStep and moved it into the main routine. It now counts as an interation step. I'm trying to simplify the structure of the program. --- Cantera/src/equil/vcs_VolPhase.cpp | 13 +- Cantera/src/equil/vcs_rxnadj.cpp | 90 +- Cantera/src/equil/vcs_solve.h | 12 +- Cantera/src/equil/vcs_solve_TP.cpp | 1302 +++++++++++++++------------- 4 files changed, 756 insertions(+), 661 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index a6ca97434..51d4515a0 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -539,7 +539,16 @@ namespace VCSnonideal { m_existence = VCS_PHASE_EXIST_NO; } } + double fractotal = 1.0; v_totalMoles = totalMoles; + if (m_totalMolesInert > 0.0) { + if (m_totalMolesInert > v_totalMoles) { + printf("vcs_VolPhase::setMolesFractionsState: inerts greater than total: %g %g\n", + v_totalMoles, m_totalMolesInert); + exit(EXIT_FAILURE); + } + fractotal = 1.0 - m_totalMolesInert/v_totalMoles; + } double sum = 0.0; for (int k = 0; k < m_numSpecies; k++) { Xmol_[k] = moleFractions[k]; @@ -549,9 +558,9 @@ namespace VCSnonideal { printf("vcs_VolPhase::setMolesFractionsState: inappropriate usage\n"); exit(EXIT_FAILURE); } - if (sum != 1.0) { + if (sum != fractotal) { for (int k = 0; k < m_numSpecies; k++) { - Xmol_[k] /= sum; + Xmol_[k] *= (fractotal /sum); } } _updateMoleFractionDependencies(); diff --git a/Cantera/src/equil/vcs_rxnadj.cpp b/Cantera/src/equil/vcs_rxnadj.cpp index 7e68813a4..da1bd9bba 100644 --- a/Cantera/src/equil/vcs_rxnadj.cpp +++ b/Cantera/src/equil/vcs_rxnadj.cpp @@ -43,8 +43,9 @@ namespace VCSnonideal { * in this routine. The species is a noncomponent * - 2 : Same as one but, the zeroed species is a component. */ - int VCS_SOLVE::vcs_RxnStepSizes() { - int j, irxn, kspec, soldel = 0, iph; + int VCS_SOLVE::vcs_RxnStepSizes(int & forceComponentCalc, int &kSpecial) { + int j, irxn, kspec, iph; + int iphDel = -1; double s, xx, dss; int k = 0; vcs_VolPhase *Vphase = 0; @@ -315,24 +316,25 @@ namespace VCSnonideal { * and the code will recover. */ #ifdef DEBUG_MODE - sprintf(ANOTE, "Delta damped from %g to %g due to delete %s", - m_deltaMolNumSpecies[kspec], - -m_molNumSpecies_old[kspec], m_speciesName[kspec].c_str()); + sprintf(ANOTE, "Delta damped from %g to %g due to delete %s", + m_deltaMolNumSpecies[kspec], + -m_molNumSpecies_old[kspec], m_speciesName[kspec].c_str()); #endif - m_deltaMolNumSpecies[kspec] = -m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = -m_molNumSpecies_old[kspec]; #ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); - plogf(" %12.4E %12.4E %12.4E | %s\n", - m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec], - m_deltaGRxn_new[irxn], ANOTE); - } + if (m_debug_print_lvl >= 2) { + plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); + plogf(" %12.4E %12.4E %12.4E | %s\n", + m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec], + m_deltaGRxn_new[irxn], ANOTE); + } #endif - continue; + continue; } /* * Delete the single species phase */ +#ifdef OLDSTUFF m_molNumSpecies_old[kspec] += dss; m_tPhaseMoles_old[m_phaseID[kspec]] += dss; for (j = 0; j < m_numComponents; ++j) { @@ -351,29 +353,53 @@ namespace VCSnonideal { exit(EXIT_FAILURE); } } +#else + + for (j = 0; j < m_numSpeciesTot; j++) { + m_deltaMolNumSpecies[j] = 0.0; + } + m_deltaMolNumSpecies[kspec] = dss; + for (j = 0; j < m_numComponents; ++j) { + m_deltaMolNumSpecies[j] = dss * m_stoichCoeffRxnMatrix[irxn][j]; + } + + iphDel = m_phaseID[k]; + kSpecial = k; + #ifdef DEBUG_MODE + if (k != kspec) { + sprintf(ANOTE, "Delete component SS phase %d named %s - SS phases only", + iphDel, m_speciesName[k].c_str()); + } else { + sprintf(ANOTE, "Delete this SS phase %d - SS components only", iphDel); + } if (m_debug_print_lvl >= 2) { - plogf(" --- vcs_RxnStepSizes Special section to delete %s", + plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); + plogf(" %12.4E %12.4E %12.4E | %s\n", + m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec], + m_deltaGRxn_new[irxn], ANOTE); + plogf(" --- vcs_RxnStepSizes Special section to set up to delete %s", m_speciesName[k].c_str()); plogendl(); } + #endif - /* - * We need to immediately recompute the - * component basis, because we just zeroed - * it out. - */ - soldel = 1; if (k != kspec) { - soldel = 2; + forceComponentCalc = 1; #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - plogf(" --- Immediate return to get new basis - Restart iteration\n"); + plogf(" --- Force a component recalculation \n"); plogendl(); } #endif - return soldel; } +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" "); vcs_print_line("-", 82); + } +#endif + return iphDel; +#endif } } } /* End of regular processing */ @@ -392,13 +418,12 @@ namespace VCSnonideal { plogf(" "); vcs_print_line("-", 82); } #endif - return soldel; + return iphDel; } - /*****************************************************************************/ - - - //! Calculates reaction adjustments using a full Hessian approximation - /*! + + //==================================================================================================================== + // Calculates reaction adjustments using a full Hessian approximation + /* * Calculates reaction adjustments. This does what equation 6.4-16, p. 143 * in Smith and Missen is suppose to do. However, a full matrix is * formed and then solved via a conjugate gradient algorithm. No @@ -613,8 +638,8 @@ namespace VCSnonideal { #endif return soldel; } - /*****************************************************************************/ + //==================================================================================================================== // Calculates the diagonal contribution to the Hessian due to // the dependence of the activity coefficients on the mole numbers. /* @@ -642,8 +667,8 @@ namespace VCSnonideal { } return diag; } - /*****************************************************************************/ + //==================================================================================================================== //! Calculates the diagonal contribution to the Hessian due to //! the dependence of the activity coefficients on the mole numbers. /*! @@ -680,8 +705,7 @@ namespace VCSnonideal { } return s; } - /*****************************************************************************/ - + //==================================================================================================================== // Recalculate all of the activity coefficients in all of the phases // based on input mole numbers /* diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 6100de9e5..2b43c55a6 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -549,13 +549,13 @@ public: * Special branching occurs sometimes. This causes the component basis * to be reevaluated * - * @return Returns an int representing the status of the step - * - 0 : normal return - * - 1 : A single species phase species has been zeroed out - * in this routine. The species is a noncomponent - * - 2 : Same as one but, the zeroed species is a component. + * @param forceComponentRecalc integer flagging whether a component recalculation needs + * to be carried out. + * @param kSpecial species number of phase being zeroed. + * + * @return Returns an int representing which phase may need to be zeroed */ - int vcs_RxnStepSizes(); + int vcs_RxnStepSizes(int & forceComponentCalc, int & kSpecial); //! Calculates the total number of moles of species in all phases. /*! diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 8348a9ebb..556cd0b93 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -122,6 +122,8 @@ namespace VCSnonideal { double *dnPhase_irxn; double atomComp; int iphasePop; + int forceComponentCalc = 1; + int iphaseDelete; /* integer that determines which phase is being deleted */ std::vector phasePopPhaseIDs(0); #ifdef DEBUG_MODE char ANOTE[128]; @@ -285,6 +287,8 @@ namespace VCSnonideal { // Update the phase objects with the contents of the soln vector vcs_updateVP(VCS_STATECALC_OLD); vcs_deltag(0, false, VCS_STATECALC_OLD); + // Turn off the force componentCalc flag + forceComponentCalc = 0; if (conv) { goto L_RETURN_BLOCK; @@ -377,6 +381,9 @@ namespace VCSnonideal { check_tmoles(); #endif vcs_tmoles(); + /*************************************************************************/ + /************** COPY OLD into NEW and ZERO VECTORS ***********************/ + /*************************************************************************/ /* * Copy the old solution into the new solution as an initial guess */ @@ -387,15 +394,16 @@ namespace VCSnonideal { vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_new), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_Deficient), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); - /* Go find a new reaction adjustment -> - * i.e., change in extent of reaction for each reaction. - * + /* * Zero out the entire vector of updates. We sometimes would * query these values below, and we want to be sure that no * information is left from previous iterations. */ vcs_dzero(VCS_DATA_PTR(m_deltaMolNumSpecies), m_numSpeciesTot); + /*************************************************************************/ + /************** DETERMINE IF DEAD PHASES POP INTO EXISTENCE **************/ + /*************************************************************************/ /* * First step is a major branch in the algorithm. * We first determine if a phase pops into existence. @@ -418,18 +426,21 @@ namespace VCSnonideal { #endif } } + + /*************************************************************************/ + /* DETERMINE THE REACTION STEP SIZES FOR MAIN STEP AND IF PHASES DIE *****/ + /*************************************************************************/ + /* + * Don't do this step if there is a phase pop + */ + iphaseDelete = -1; if (iphasePop < 0) { /* * Figure out the new reaction step sizes * for the major species (do minor species in the future too) */ - - soldel = vcs_RxnStepSizes(); - - if (soldel == 2) { - goto L_COMPONENT_CALC; - } - + kspec = -1; + iphaseDelete = vcs_RxnStepSizes(forceComponentCalc, kspec); } #ifdef DEBUG_MODE else { @@ -478,657 +489,702 @@ namespace VCSnonideal { * * * - */ + */ + if (iphaseDelete >= 0) { #ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- Main Loop Treatment of each non-component species "); - if (iti == 0) plogf("- Full Calculation:\n"); - else plogf("- Major Components Calculation:\n"); - plogf(" --- Species IC "); - plogf(" KMoles Tent_KMoles Rxn_Adj | Comment \n"); - } + if (m_debug_print_lvl >= 2) { + plogf(" --- Main Loop Treatment -> Circumvented due to Phase Deletion "); + plogendl(); + } #endif - - for (irxn = 0; irxn < m_numRxnRdc; irxn++) { - kspec = m_indexRxnToSpecies[irxn]; - sc_irxn = m_stoichCoeffRxnMatrix[irxn]; - iph = m_phaseID[kspec]; - Vphase = m_VolPhaseList[iph]; -#ifdef DEBUG_MODE - ANOTE[0] = '\0'; -#endif - if (iphasePop >= 0) { - if (iph == iphasePop) { - dx = m_deltaMolNumSpecies[kspec]; - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; -#ifdef DEBUG_MODE - sprintf(ANOTE, "Phase pop"); -#endif - } else { - dx = 0.0; - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + + for (k = 0; k < m_numSpeciesTot; k++) { + m_molNumSpecies_new[k] = m_molNumSpecies_old[k] + m_deltaMolNumSpecies[k]; + iph = m_phaseID[k]; + m_tPhaseMoles_new[iph] += m_deltaMolNumSpecies[k]; + } + if (kspec >= m_numComponents) { + if (m_molNumSpecies_new[k] != 0.0) { + printf("vcs_solve_tp:: we shouldn't be here!\n"); + exit(EXIT_FAILURE); } - } else { + if (m_SSPhase[kspec] == 1) { + m_speciesStatus[kspec] = VCS_SPECIES_ZEROEDSS; + } else { + printf("vcs_solve_tp:: we shouldn't be here!\n"); + exit(EXIT_FAILURE); + } + ++m_numRxnMinorZeroed; + allMinorZeroedSpecies = (m_numRxnMinorZeroed == m_numRxnRdc); + } + /* + * Set the flags indicating the mole numbers in the vcs_VolPhase + * objects are out of date. + */ + vcs_setFlagsVolPhases(false, VCS_STATECALC_NEW); + + /* + * Calculate the new chemical potentials using the tentative + * solution values. We only calculate a subset of these, because + * we have only updated a subset of the W(). + */ + vcs_dfe(VCS_STATECALC_NEW, 0, 0, m_numSpeciesTot); + + /* + * Evaluate DeltaG for all components if ITI=0, and for + * major components only if ITI NE 0 + */ + vcs_deltag(0, false, VCS_STATECALC_NEW); + } else { +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- Main Loop Treatment of each non-component species "); + if (iti == 0) plogf("- Full Calculation:\n"); + else plogf("- Major Components Calculation:\n"); + plogf(" --- Species IC "); + plogf(" KMoles Tent_KMoles Rxn_Adj | Comment \n"); + } +#endif + for (irxn = 0; irxn < m_numRxnRdc; irxn++) { + kspec = m_indexRxnToSpecies[irxn]; + sc_irxn = m_stoichCoeffRxnMatrix[irxn]; + iph = m_phaseID[kspec]; + Vphase = m_VolPhaseList[iph]; +#ifdef DEBUG_MODE + ANOTE[0] = '\0'; +#endif + if (iphasePop >= 0) { + if (iph == iphasePop) { + dx = m_deltaMolNumSpecies[kspec]; + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; +#ifdef DEBUG_MODE + sprintf(ANOTE, "Phase pop"); +#endif + } else { + dx = 0.0; + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + } + } else { - if (m_speciesStatus[kspec] == VCS_SPECIES_INTERFACIALVOLTAGE) { - /********************************************************************/ - /************************ VOLTAGE SPECIES ***************************/ - /********************************************************************/ + if (m_speciesStatus[kspec] == VCS_SPECIES_INTERFACIALVOLTAGE) { + /********************************************************************/ + /************************ VOLTAGE SPECIES ***************************/ + /********************************************************************/ #ifdef DEBUG_MODE - dx = vcs_minor_alt_calc(kspec, irxn, &soldel, ANOTE); + dx = vcs_minor_alt_calc(kspec, irxn, &soldel, ANOTE); #else - dx = vcs_minor_alt_calc(kspec, irxn, &soldel); + dx = vcs_minor_alt_calc(kspec, irxn, &soldel); #endif - m_deltaMolNumSpecies[kspec] = dx; - } - else if (m_speciesStatus[kspec] < VCS_SPECIES_MINOR) { - /********************************************************************/ - /********************** ZEROED OUT SPECIES **************************/ - /********************************************************************/ - bool resurrect = (m_deltaMolNumSpecies[kspec] > 0.0); -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 3) { - plogf(" --- %s currently zeroed (SpStatus=%-2d):", - m_speciesName[kspec].c_str(), m_speciesStatus[kspec]); - plogf("%3d DG = %11.4E WT = %11.4E W = %11.4E DS = %11.4E\n", - irxn, m_deltaGRxn_new[irxn], m_molNumSpecies_new[kspec], - m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec]); + m_deltaMolNumSpecies[kspec] = dx; } + else if (m_speciesStatus[kspec] < VCS_SPECIES_MINOR) { + /********************************************************************/ + /********************** ZEROED OUT SPECIES **************************/ + /********************************************************************/ + bool resurrect = (m_deltaMolNumSpecies[kspec] > 0.0); +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 3) { + plogf(" --- %s currently zeroed (SpStatus=%-2d):", + m_speciesName[kspec].c_str(), m_speciesStatus[kspec]); + plogf("%3d DG = %11.4E WT = %11.4E W = %11.4E DS = %11.4E\n", + irxn, m_deltaGRxn_new[irxn], m_molNumSpecies_new[kspec], + m_molNumSpecies_old[kspec], m_deltaMolNumSpecies[kspec]); + } #endif - if (m_deltaGRxn_new[irxn] >= 0.0 || !resurrect) { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; - m_deltaMolNumSpecies[kspec] = 0.0; - resurrect = false; + if (m_deltaGRxn_new[irxn] >= 0.0 || !resurrect) { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = 0.0; + resurrect = false; #ifdef DEBUG_MODE - sprintf(ANOTE, "Species stays zeroed: DG = %11.4E", m_deltaGRxn_new[irxn]); - if (m_deltaGRxn_new[irxn] < 0.0) { - if (m_speciesStatus[kspec] == VCS_SPECIES_STOICHZERO) { - sprintf(ANOTE, "Species stays zeroed even though dg neg due to " - "STOICH/PHASEPOP constraint: DG = %11.4E", - m_deltaGRxn_new[irxn]); - } else { - sprintf(ANOTE, "Species stays zeroed even though dg neg: DG = %11.4E, ds zeroed", - m_deltaGRxn_new[irxn]); - } - } -#endif - } else { - for (int j = 0; j < m_numElemConstraints; ++j) { - int elType = m_elType[j]; - if (elType == VCS_ELEM_TYPE_ABSPOS) { - atomComp = m_formulaMatrix[j][kspec]; - if (atomComp > 0.0) { - double maxPermissible = m_elemAbundancesGoal[j] / atomComp; - if (maxPermissible < VCS_DELETE_MINORSPECIES_CUTOFF) { -#ifdef DEBUG_MODE - sprintf(ANOTE, "Species stays zeroed even though dG " - "neg, because of %s elemAbund", - m_elementName[j].c_str()); -#endif - resurrect = false; - break; - } - } - } - } - } - /* - * Resurrect the species - */ - if (resurrect) { - bool phaseResurrected = false; - if (Vphase->exists() == VCS_PHASE_EXIST_NO) { - //Vphase->setExistence(1); - phaseResurrected = true; - } - - if (phaseResurrected) { -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- Zeroed species changed to major: "); - plogf("%-12s\n", m_speciesName[kspec].c_str()); - } -#endif - m_speciesStatus[kspec] = VCS_SPECIES_MAJOR; - MajorSpeciesHaveConverged = false; - allMinorZeroedSpecies = false; - } else { -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- Zeroed species changed to minor: "); - plogf("%-12s\n", m_speciesName[kspec].c_str()); - } -#endif - m_speciesStatus[kspec] = VCS_SPECIES_MINOR; - } - if (m_deltaMolNumSpecies[kspec] > 0.0) { - dx = m_deltaMolNumSpecies[kspec] * 0.01; - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; - } else { - m_molNumSpecies_new[kspec] = m_totalMolNum * VCS_DELETE_PHASE_CUTOFF * 10.; - dx = m_molNumSpecies_new[kspec] - m_molNumSpecies_old[kspec]; - } - m_deltaMolNumSpecies[kspec] = dx; -#ifdef DEBUG_MODE - sprintf(ANOTE, "Born:IC=-1 to IC=1:DG=%11.4E", m_deltaGRxn_new[irxn]); -#endif - } else { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; - m_deltaMolNumSpecies[kspec] = 0.0; - dx = 0.0; - } - } else if (m_speciesStatus[kspec] == VCS_SPECIES_MINOR) { - /********************************************************************/ - /***************************** MINOR SPECIES ************************/ - /********************************************************************/ - /* - * Unless ITI isn't equal to zero we zero out changes - * to minor species. - */ - if (iti != 0) { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; - m_deltaMolNumSpecies[kspec] = 0.0; - dx = 0.0; -#ifdef DEBUG_MODE - sprintf(ANOTE,"minor species not considered"); - if (m_debug_print_lvl >= 2) { - plogf(" --- "); plogf("%-12s", m_speciesName[kspec].c_str()); - plogf("%3d%11.4E%11.4E%11.4E | %s", - m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec], - m_deltaMolNumSpecies[kspec], ANOTE); - plogendl(); - } -#endif - continue; - } - /* - * Minor species alternative calculation - * --------------------------------------- - * This is based upon the following approximation: - * The mole fraction changes due to these reactions don't affect - * the mole numbers of the component species. Therefore the - * following approximation is valid for an ideal solution - * 0 = DG(I) + log(WT(I)/W(I)) - * (DG contains the contribution from FF(I) + log(W(I)/TL) ) - * Thus, - * WT(I) = W(I) EXP(-DG(I)) - * If soldel is true on return, then we branch to the section - * that deletes a species from the current set of active species. - */ -#ifdef DEBUG_MODE - dx = vcs_minor_alt_calc(kspec, irxn, &soldel, ANOTE); -#else - dx = vcs_minor_alt_calc(kspec, irxn, &soldel); -#endif - m_deltaMolNumSpecies[kspec] = dx; - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; - - if (soldel) { - /*******************************************************************/ - /***** DELETE MINOR SPECIES LESS THAN VCS_DELETE_SPECIES_CUTOFF */ - /***** MOLE NUMBER */ - /*******************************************************************/ -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- Delete minor species in multispec phase: %-12s", - m_speciesName[kspec].c_str()); - plogendl(); - } -#endif - m_deltaMolNumSpecies[kspec] = 0.0; - /* - * Delete species, kspec. The alternate return is for the case - * where all species become deleted. Then, we need to - * branch to the code where we reevaluate the deletion - * of all species. - */ - lnospec = vcs_delete_species(kspec); - if (lnospec) goto L_RECHECK_DELETED; - /* - * Go back to consider the next species in the list. - * Note, however, that the next species in the list is now - * in slot l. In deleting the previous species L, We have - * exchanged slot MR with slot l, and then have - * decremented MR. - * Therefore, we will decrement the species counter, here. - */ - --irxn; -#ifdef DEBUG_MODE - goto L_MAIN_LOOP_END_NO_PRINT; -#else - goto L_MAIN_LOOP_END; -#endif - } - } else { - /********************************************************************/ - /*********************** MAJOR SPECIES ******************************/ - /********************************************************************/ -#ifdef DEBUG_MODE - sprintf(ANOTE, "Normal Major Calc"); -#endif - /* - * Check for superconvergence of the formation reaction. Do - * nothing if it is superconverged. Skip to the end of the - * irxn loop if it is superconverged. - */ - if (fabs(m_deltaGRxn_new[irxn]) <= m_tolmaj2) { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; - m_deltaMolNumSpecies[kspec] = 0.0; - dx = 0.0; -#ifdef DEBUG_MODE - sprintf(ANOTE, "major species is converged"); - if (m_debug_print_lvl >= 2) { - plogf(" --- "); plogf("%-12s", m_speciesName[kspec].c_str()); - plogf("%3d%11.4E%11.4E%11.4E | %s", - m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec], - m_deltaMolNumSpecies[kspec], ANOTE); - plogendl(); - } -#endif - continue; - } - /* - * Set the initial step size, dx, equal to the value produced - * by the routine, vcs_RxnStepSize(). - * - * Note the multiplition logic is to make sure that - * dg[] didn't change sign due to w[] changing in the - * middle of the iteration. (it can if a single species - * phase goes out of existence). - */ - if ((m_deltaGRxn_new[irxn] * m_deltaMolNumSpecies[kspec]) <= 0.0) { - dx = m_deltaMolNumSpecies[kspec]; - } else { - dx = 0.0; - m_deltaMolNumSpecies[kspec] = 0.0; -#ifdef DEBUG_MODE - sprintf(ANOTE, "dx set to 0, DG flipped sign due to " - "changed initial point"); -#endif - } - /* - * Form a tentative value of the new species moles - */ - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; - - /* - * Check for non-positive mole fraction of major species. - * If we find one, we branch to a section below. Then, - * depending upon the outcome, we branch to sections below, - * or we restart the entire iteration. - */ - if (m_molNumSpecies_new[kspec] <= 0.0) { -#ifdef DEBUG_MODE - sprintf(ANOTE, "initial nonpos kmoles= %11.3E", - m_molNumSpecies_new[kspec]); -#endif - /* ************************************************* */ - /* *** NON-POSITIVE MOLES OF MAJOR SPECIES ********* */ - /* ************************************************* */ - /* - * We are here when a tentative value of a mole fraction - * created by a tentative value of M_DELTAMOLNUMSPECIES(*) is negative. - * We branch from here depending upon whether this - * species is in a single species phase or in - * a multispecies phase. - */ - if (! (m_SSPhase[kspec])) { - /* - * Section for multispecies phases: - * - Cut reaction adjustment for positive kmoles of - * major species in multispecies phases. - * Decrease its concentration by a factor of 10. - */ - dx = -0.9 * m_molNumSpecies_old[kspec]; - m_deltaMolNumSpecies[kspec] = dx; - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; - } else { - /* - * Section for single species phases: - * Calculate a dx that will wipe out the - * moles in the phase. - */ - dx = -m_molNumSpecies_old[kspec]; - /* - * Calculate an update that doesn't create a negative mole - * number for a component species. Actually, restrict this - * a little more so that the component values can only be - * reduced by two 99%, - */ - for (j = 0; j < m_numComponents; ++j) { - if (sc_irxn[j] != 0.0) { - wx[j] = m_molNumSpecies_old[j] + sc_irxn[j] * dx; - if (wx[j] <= m_molNumSpecies_old[j] * 0.01 - 1.0E-150) { - dx = MAX(dx, m_molNumSpecies_old[j] * -0.99 / sc_irxn[j]); - } + sprintf(ANOTE, "Species stays zeroed: DG = %11.4E", m_deltaGRxn_new[irxn]); + if (m_deltaGRxn_new[irxn] < 0.0) { + if (m_speciesStatus[kspec] == VCS_SPECIES_STOICHZERO) { + sprintf(ANOTE, "Species stays zeroed even though dg neg due to " + "STOICH/PHASEPOP constraint: DG = %11.4E", + m_deltaGRxn_new[irxn]); } else { - wx[j] = m_molNumSpecies_old[j]; + sprintf(ANOTE, "Species stays zeroed even though dg neg: DG = %11.4E, ds zeroed", + m_deltaGRxn_new[irxn]); } } - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; - if (m_molNumSpecies_new[kspec] > 0.0) { - m_deltaMolNumSpecies[kspec] = dx; -#ifdef DEBUG_MODE - sprintf(ANOTE, - "zeroing SS phase created a neg component species " - "-> reducing step size instead"); -#endif - } else { - /* - * We are going to zero the single species phase. - * Set the existence flag - */ - iph = m_phaseID[kspec]; - Vphase = m_VolPhaseList[iph]; - //Vphase->setExistence(0); -#ifdef DEBUG_MODE - sprintf(ANOTE, "zeroing out SS phase: "); #endif - /* - * Change the base mole numbers for the iteration. - * We need to do this here, because we have decided - * to eliminate the phase in this special section - * outside the main loop. - */ - m_molNumSpecies_new[kspec] = 0.0; - doPhaseDeleteIph = iph; - doPhaseDeleteKspec = kspec; + } else { + for (int j = 0; j < m_numElemConstraints; ++j) { + int elType = m_elType[j]; + if (elType == VCS_ELEM_TYPE_ABSPOS) { + atomComp = m_formulaMatrix[j][kspec]; + if (atomComp > 0.0) { + double maxPermissible = m_elemAbundancesGoal[j] / atomComp; + if (maxPermissible < VCS_DELETE_MINORSPECIES_CUTOFF) { +#ifdef DEBUG_MODE + sprintf(ANOTE, "Species stays zeroed even though dG " + "neg, because of %s elemAbund", + m_elementName[j].c_str()); +#endif + resurrect = false; + break; + } + } + } + } + } + /* + * Resurrect the species + */ + if (resurrect) { + bool phaseResurrected = false; + if (Vphase->exists() == VCS_PHASE_EXIST_NO) { + //Vphase->setExistence(1); + phaseResurrected = true; + } + if (phaseResurrected) { #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - if (m_speciesStatus[kspec] >= 0) { - plogf(" --- SS species changed to zeroedss: "); - plogf("%-12s", m_speciesName[kspec].c_str()); - plogendl(); + plogf(" --- Zeroed species changed to major: "); + plogf("%-12s\n", m_speciesName[kspec].c_str()); + } +#endif + m_speciesStatus[kspec] = VCS_SPECIES_MAJOR; + MajorSpeciesHaveConverged = false; + allMinorZeroedSpecies = false; + } else { +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- Zeroed species changed to minor: "); + plogf("%-12s\n", m_speciesName[kspec].c_str()); + } +#endif + m_speciesStatus[kspec] = VCS_SPECIES_MINOR; + } + if (m_deltaMolNumSpecies[kspec] > 0.0) { + dx = m_deltaMolNumSpecies[kspec] * 0.01; + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; + } else { + m_molNumSpecies_new[kspec] = m_totalMolNum * VCS_DELETE_PHASE_CUTOFF * 10.; + dx = m_molNumSpecies_new[kspec] - m_molNumSpecies_old[kspec]; + } + m_deltaMolNumSpecies[kspec] = dx; +#ifdef DEBUG_MODE + sprintf(ANOTE, "Born:IC=-1 to IC=1:DG=%11.4E", m_deltaGRxn_new[irxn]); +#endif + } else { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = 0.0; + dx = 0.0; + } + } else if (m_speciesStatus[kspec] == VCS_SPECIES_MINOR) { + /********************************************************************/ + /***************************** MINOR SPECIES ************************/ + /********************************************************************/ + /* + * Unless ITI isn't equal to zero we zero out changes + * to minor species. + */ + if (iti != 0) { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = 0.0; + dx = 0.0; +#ifdef DEBUG_MODE + sprintf(ANOTE,"minor species not considered"); + if (m_debug_print_lvl >= 2) { + plogf(" --- "); plogf("%-12s", m_speciesName[kspec].c_str()); + plogf("%3d%11.4E%11.4E%11.4E | %s", + m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec], + m_deltaMolNumSpecies[kspec], ANOTE); + plogendl(); + } +#endif + continue; + } + /* + * Minor species alternative calculation + * --------------------------------------- + * This is based upon the following approximation: + * The mole fraction changes due to these reactions don't affect + * the mole numbers of the component species. Therefore the + * following approximation is valid for an ideal solution + * 0 = DG(I) + log(WT(I)/W(I)) + * (DG contains the contribution from FF(I) + log(W(I)/TL) ) + * Thus, + * WT(I) = W(I) EXP(-DG(I)) + * If soldel is true on return, then we branch to the section + * that deletes a species from the current set of active species. + */ +#ifdef DEBUG_MODE + dx = vcs_minor_alt_calc(kspec, irxn, &soldel, ANOTE); +#else + dx = vcs_minor_alt_calc(kspec, irxn, &soldel); +#endif + m_deltaMolNumSpecies[kspec] = dx; + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; + + if (soldel) { + /*******************************************************************/ + /***** DELETE MINOR SPECIES LESS THAN VCS_DELETE_SPECIES_CUTOFF */ + /***** MOLE NUMBER */ + /*******************************************************************/ +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- Delete minor species in multispec phase: %-12s", + m_speciesName[kspec].c_str()); + plogendl(); + } +#endif + m_deltaMolNumSpecies[kspec] = 0.0; + /* + * Delete species, kspec. The alternate return is for the case + * where all species become deleted. Then, we need to + * branch to the code where we reevaluate the deletion + * of all species. + */ + lnospec = vcs_delete_species(kspec); + if (lnospec) goto L_RECHECK_DELETED; + /* + * Go back to consider the next species in the list. + * Note, however, that the next species in the list is now + * in slot l. In deleting the previous species L, We have + * exchanged slot MR with slot l, and then have + * decremented MR. + * Therefore, we will decrement the species counter, here. + */ + --irxn; +#ifdef DEBUG_MODE + goto L_MAIN_LOOP_END_NO_PRINT; +#else + goto L_MAIN_LOOP_END; +#endif + } + } else { + /********************************************************************/ + /*********************** MAJOR SPECIES ******************************/ + /********************************************************************/ +#ifdef DEBUG_MODE + sprintf(ANOTE, "Normal Major Calc"); +#endif + /* + * Check for superconvergence of the formation reaction. Do + * nothing if it is superconverged. Skip to the end of the + * irxn loop if it is superconverged. + */ + if (fabs(m_deltaGRxn_new[irxn]) <= m_tolmaj2) { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = 0.0; + dx = 0.0; +#ifdef DEBUG_MODE + sprintf(ANOTE, "major species is converged"); + if (m_debug_print_lvl >= 2) { + plogf(" --- "); plogf("%-12s", m_speciesName[kspec].c_str()); + plogf("%3d%11.4E%11.4E%11.4E | %s", + m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec], + m_deltaMolNumSpecies[kspec], ANOTE); + plogendl(); + } +#endif + continue; + } + /* + * Set the initial step size, dx, equal to the value produced + * by the routine, vcs_RxnStepSize(). + * + * Note the multiplition logic is to make sure that + * dg[] didn't change sign due to w[] changing in the + * middle of the iteration. (it can if a single species + * phase goes out of existence). + */ + if ((m_deltaGRxn_new[irxn] * m_deltaMolNumSpecies[kspec]) <= 0.0) { + dx = m_deltaMolNumSpecies[kspec]; + } else { + dx = 0.0; + m_deltaMolNumSpecies[kspec] = 0.0; +#ifdef DEBUG_MODE + sprintf(ANOTE, "dx set to 0, DG flipped sign due to " + "changed initial point"); +#endif + } + /* + * Form a tentative value of the new species moles + */ + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; + + /* + * Check for non-positive mole fraction of major species. + * If we find one, we branch to a section below. Then, + * depending upon the outcome, we branch to sections below, + * or we restart the entire iteration. + */ + if (m_molNumSpecies_new[kspec] <= 0.0) { +#ifdef DEBUG_MODE + sprintf(ANOTE, "initial nonpos kmoles= %11.3E", + m_molNumSpecies_new[kspec]); +#endif + /* ************************************************* */ + /* *** NON-POSITIVE MOLES OF MAJOR SPECIES ********* */ + /* ************************************************* */ + /* + * We are here when a tentative value of a mole fraction + * created by a tentative value of M_DELTAMOLNUMSPECIES(*) is negative. + * We branch from here depending upon whether this + * species is in a single species phase or in + * a multispecies phase. + */ + if (! (m_SSPhase[kspec])) { + /* + * Section for multispecies phases: + * - Cut reaction adjustment for positive kmoles of + * major species in multispecies phases. + * Decrease its concentration by a factor of 10. + */ + dx = -0.9 * m_molNumSpecies_old[kspec]; + m_deltaMolNumSpecies[kspec] = dx; + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; + } else { + /* + * Section for single species phases: + * Calculate a dx that will wipe out the + * moles in the phase. + */ + dx = -m_molNumSpecies_old[kspec]; + /* + * Calculate an update that doesn't create a negative mole + * number for a component species. Actually, restrict this + * a little more so that the component values can only be + * reduced by two 99%, + */ + for (j = 0; j < m_numComponents; ++j) { + if (sc_irxn[j] != 0.0) { + wx[j] = m_molNumSpecies_old[j] + sc_irxn[j] * dx; + if (wx[j] <= m_molNumSpecies_old[j] * 0.01 - 1.0E-150) { + dx = MAX(dx, m_molNumSpecies_old[j] * -0.99 / sc_irxn[j]); + } + } else { + wx[j] = m_molNumSpecies_old[j]; } } + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx; + if (m_molNumSpecies_new[kspec] > 0.0) { + m_deltaMolNumSpecies[kspec] = dx; +#ifdef DEBUG_MODE + sprintf(ANOTE, + "zeroing SS phase created a neg component species " + "-> reducing step size instead"); +#endif + } else { + /* + * We are going to zero the single species phase. + * Set the existence flag + */ + iph = m_phaseID[kspec]; + Vphase = m_VolPhaseList[iph]; + //Vphase->setExistence(0); +#ifdef DEBUG_MODE + sprintf(ANOTE, "zeroing out SS phase: "); #endif - m_speciesStatus[kspec] = VCS_SPECIES_ZEROEDSS; - ++m_numRxnMinorZeroed; - allMinorZeroedSpecies = (m_numRxnMinorZeroed == m_numRxnRdc); + /* + * Change the base mole numbers for the iteration. + * We need to do this here, because we have decided + * to eliminate the phase in this special section + * outside the main loop. + */ + m_molNumSpecies_new[kspec] = 0.0; + doPhaseDeleteIph = iph; + doPhaseDeleteKspec = kspec; - for (int kk = 0; kk < m_numSpeciesTot; kk++) { - m_deltaMolNumSpecies[kk] = 0.0; - m_molNumSpecies_new[kk] = m_molNumSpecies_old[kk]; - } - m_deltaMolNumSpecies[kspec] = dx; - m_molNumSpecies_new[kspec] = 0.0; +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + if (m_speciesStatus[kspec] >= 0) { + plogf(" --- SS species changed to zeroedss: "); + plogf("%-12s", m_speciesName[kspec].c_str()); + plogendl(); + } + } +#endif + m_speciesStatus[kspec] = VCS_SPECIES_ZEROEDSS; + ++m_numRxnMinorZeroed; + allMinorZeroedSpecies = (m_numRxnMinorZeroed == m_numRxnRdc); - for (k = 0; k < m_numComponents; ++k) { - m_deltaMolNumSpecies[k] = 0.0; - } - for (iph = 0; iph < m_numPhases; iph++) { - m_deltaPhaseMoles[iph] = 0.0; - } + for (int kk = 0; kk < m_numSpeciesTot; kk++) { + m_deltaMolNumSpecies[kk] = 0.0; + m_molNumSpecies_new[kk] = m_molNumSpecies_old[kk]; + } + m_deltaMolNumSpecies[kspec] = dx; + m_molNumSpecies_new[kspec] = 0.0; + for (k = 0; k < m_numComponents; ++k) { + m_deltaMolNumSpecies[k] = 0.0; + } + for (iph = 0; iph < m_numPhases; iph++) { + m_deltaPhaseMoles[iph] = 0.0; + } + + } } - } - } + } #ifdef VCS_LINE_SEARCH - /*********************************************************************/ - /*** LINE SEARCH ALGORITHM FOR MAJOR SPECIES IN NON-IDEAL PHASES *****/ - /*********************************************************************/ - /* - * Skip the line search if we are birthing a species - */ - if ((dx != 0.0) && - (m_molNumSpecies_old[kspec] > 0.0) && - (doPhaseDeleteIph == -1) && - (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { - double dx_old = dx; + /*********************************************************************/ + /*** LINE SEARCH ALGORITHM FOR MAJOR SPECIES IN NON-IDEAL PHASES *****/ + /*********************************************************************/ + /* + * Skip the line search if we are birthing a species + */ + if ((dx != 0.0) && + (m_molNumSpecies_old[kspec] > 0.0) && + (doPhaseDeleteIph == -1) && + (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { + double dx_old = dx; #ifdef DEBUG_MODE - dx = vcs_line_search(irxn, dx_old, ANOTE); + dx = vcs_line_search(irxn, dx_old, ANOTE); #else - dx = vcs_line_search(irxn, dx_old); + dx = vcs_line_search(irxn, dx_old); #endif - vcs_setFlagsVolPhases(false, VCS_STATECALC_NEW); - } - m_deltaMolNumSpecies[kspec] = dx; + vcs_setFlagsVolPhases(false, VCS_STATECALC_NEW); + } + m_deltaMolNumSpecies[kspec] = dx; #endif - }/* End of Loop on ic[irxn] -> the type of species */ - } - /***********************************************************************/ - /****** CALCULATE KMOLE NUMBER CHANGE FOR THE COMPONENT BASIS **********/ - /***********************************************************************/ - if (dx != 0.0 && (m_speciesUnknownType[kspec] != - VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { - /* - * Change the amount of the component compounds according - * to the reaction delta that we just computed. - * This should keep the amount of material constant. - */ + }/* End of Loop on ic[irxn] -> the type of species */ + } + /***********************************************************************/ + /****** CALCULATE KMOLE NUMBER CHANGE FOR THE COMPONENT BASIS **********/ + /***********************************************************************/ + if (dx != 0.0 && (m_speciesUnknownType[kspec] != + VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { + /* + * Change the amount of the component compounds according + * to the reaction delta that we just computed. + * This should keep the amount of material constant. + */ #ifdef DEBUG_MODE - if (fabs(m_deltaMolNumSpecies[kspec] -dx) > - 1.0E-14*(fabs(m_deltaMolNumSpecies[kspec]) + fabs(dx) + 1.0E-32)) { - plogf(" ds[kspec] = %20.16g dx = %20.16g , kspec = %d\n", - m_deltaMolNumSpecies[kspec], dx, kspec); - plogf("we have a problem!"); + if (fabs(m_deltaMolNumSpecies[kspec] -dx) > + 1.0E-14*(fabs(m_deltaMolNumSpecies[kspec]) + fabs(dx) + 1.0E-32)) { + plogf(" ds[kspec] = %20.16g dx = %20.16g , kspec = %d\n", + m_deltaMolNumSpecies[kspec], dx, kspec); + plogf("we have a problem!"); + plogendl(); + exit(EXIT_FAILURE); + } +#endif + for (k = 0; k < m_numComponents; ++k) { + m_deltaMolNumSpecies[k] += sc_irxn[k] * dx; + } + /* + * Calculate the tentative change in the total number of + * moles in all of the phases + */ + dnPhase_irxn = m_deltaMolNumPhase[irxn]; + for (iph = 0; iph < m_numPhases; iph++) { + m_deltaPhaseMoles[iph] += dx * dnPhase_irxn[iph]; + } + } + +#ifdef DEBUG_MODE + checkDelta1(VCS_DATA_PTR(m_deltaMolNumSpecies), + VCS_DATA_PTR(m_deltaPhaseMoles), kspec+1); +#endif + /* + * Branch point for returning - + */ +#ifndef DEBUG_MODE + L_MAIN_LOOP_END: ; +#endif +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; + plogf(" --- "); plogf("%-12.12s", m_speciesName[kspec].c_str()); + plogf("%3d%11.4E%11.4E%11.4E | %s", + m_speciesStatus[kspec], m_molNumSpecies_old[kspec], + m_molNumSpecies_new[kspec], + m_deltaMolNumSpecies[kspec], ANOTE); + plogendl(); + } + L_MAIN_LOOP_END_NO_PRINT: ; +#endif + if (doPhaseDeleteIph != -1) { +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- "); + plogf("%-12.12s Main Loop Special Case deleting phase with species: ", + m_speciesName[doPhaseDeleteKspec].c_str()); + plogendl(); + } +#endif + break; + } + } /**************** END OF MAIN LOOP OVER FORMATION REACTIONS ************/ + +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + for (k = 0; k < m_numComponents; k++) { + plogf(" --- "); plogf("%-12.12s", m_speciesName[k].c_str()); + plogf(" c%11.4E%11.4E%11.4E |\n", + m_molNumSpecies_old[k], + m_molNumSpecies_old[k]+m_deltaMolNumSpecies[k], m_deltaMolNumSpecies[k]); + } + plogf(" "); vcs_print_line("-", 80); + plogf(" --- Finished Main Loop"); + plogendl(); + } +#endif + + /*************************************************************************/ + /*********** LIMIT REDUCTION OF BASIS SPECIES TO 99% *********************/ + /*************************************************************************/ + /* + * We have a tentative m_deltaMolNumSpecies[]. Now apply other criteria + * to limit it's magnitude. + * + * + */ + par = 0.5; + for (k = 0; k < m_numComponents; ++k) { + if (m_molNumSpecies_old[k] > 0.0) { + xx = -m_deltaMolNumSpecies[k] / m_molNumSpecies_old[k]; + if (par < xx) { + par = xx; +#ifdef DEBUG_MODE + ll = k; +#endif + } + } else { + if (m_deltaMolNumSpecies[k] < 0.0) { + /* + * If we are here, we then do a step which violates element + * conservation. + */ + iph = m_phaseID[k]; + m_deltaPhaseMoles[iph] -= m_deltaMolNumSpecies[k]; + m_deltaMolNumSpecies[k] = 0.0; + } + } + } + par = 1.0 / par; + if (par <= 1.01 && par > 0.0) { + /* Reduce the size of the step by the multiplicative factor, par */ + par *= 0.99; +#ifdef DEBUG_MODE + if (m_debug_print_lvl >= 2) { + plogf(" --- Reduction in step size due to component "); + plogf("%s", m_speciesName[ll].c_str()); + plogf(" going negative = %11.3E", par); + plogendl(); + } +#endif + for (i = 0; i < m_numSpeciesTot; ++i) { + m_deltaMolNumSpecies[i] *= par; + } + for (iph = 0; iph < m_numPhases; iph++) { + m_deltaPhaseMoles[iph] *= par; + } + } else { + par = 1.0; + } +#ifdef DEBUG_MODE + checkDelta1(VCS_DATA_PTR(m_deltaMolNumSpecies), + VCS_DATA_PTR(m_deltaPhaseMoles), m_numSpeciesTot); +#endif + + /* + * Now adjust the wt[kspec]'s so that the reflect the decrease in + * the overall length of m_deltaMolNumSpecies[kspec] just calculated. At the end + * of this section wt[], m_deltaMolNumSpecies[], tPhMoles, and tPhMoles1 should all be + * consistent with a new estimate of the state of the system. + */ + for (kspec = 0; kspec < m_numSpeciesTot; ++kspec) { + m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; + if (m_molNumSpecies_new[kspec] < 0.0 && (m_speciesUnknownType[kspec] + != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { + plogf("vcs_solve_TP: ERROR on step change wt[%d:%s]: %g < 0.0", + kspec, m_speciesName[kspec].c_str(), m_molNumSpecies_new[kspec]); plogendl(); exit(EXIT_FAILURE); } -#endif - for (k = 0; k < m_numComponents; ++k) { - m_deltaMolNumSpecies[k] += sc_irxn[k] * dx; - } - /* - * Calculate the tentative change in the total number of - * moles in all of the phases - */ - dnPhase_irxn = m_deltaMolNumPhase[irxn]; - for (iph = 0; iph < m_numPhases; iph++) { - m_deltaPhaseMoles[iph] += dx * dnPhase_irxn[iph]; - } } - -#ifdef DEBUG_MODE - checkDelta1(VCS_DATA_PTR(m_deltaMolNumSpecies), - VCS_DATA_PTR(m_deltaPhaseMoles), kspec+1); -#endif + /* - * Branch point for returning - + * Calculate the tentative total mole numbers for each phase */ -#ifndef DEBUG_MODE - L_MAIN_LOOP_END: ; -#endif -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; - plogf(" --- "); plogf("%-12.12s", m_speciesName[kspec].c_str()); - plogf("%3d%11.4E%11.4E%11.4E | %s", - m_speciesStatus[kspec], m_molNumSpecies_old[kspec], - m_molNumSpecies_new[kspec], - m_deltaMolNumSpecies[kspec], ANOTE); - plogendl(); - } - L_MAIN_LOOP_END_NO_PRINT: ; -#endif - if (doPhaseDeleteIph != -1) { -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- "); - plogf("%-12.12s Main Loop Special Case deleting phase with species: ", - m_speciesName[doPhaseDeleteKspec].c_str()); - plogendl(); - } -#endif - break; - } - } /**************** END OF MAIN LOOP OVER FORMATION REACTIONS ************/ - -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - for (k = 0; k < m_numComponents; k++) { - plogf(" --- "); plogf("%-12.12s", m_speciesName[k].c_str()); - plogf(" c%11.4E%11.4E%11.4E |\n", - m_molNumSpecies_old[k], - m_molNumSpecies_old[k]+m_deltaMolNumSpecies[k], m_deltaMolNumSpecies[k]); - } - plogf(" "); vcs_print_line("-", 80); - plogf(" --- Finished Main Loop"); - plogendl(); - } -#endif - - /*************************************************************************/ - /*********** LIMIT REDUCTION OF BASIS SPECIES TO 99% *********************/ - /*************************************************************************/ - /* - * We have a tentative m_deltaMolNumSpecies[]. Now apply other criteria - * to limit it's magnitude. - * - * - */ - par = 0.5; - for (k = 0; k < m_numComponents; ++k) { - if (m_molNumSpecies_old[k] > 0.0) { - xx = -m_deltaMolNumSpecies[k] / m_molNumSpecies_old[k]; - if (par < xx) { - par = xx; -#ifdef DEBUG_MODE - ll = k; -#endif - } - } else { - if (m_deltaMolNumSpecies[k] < 0.0) { - /* - * If we are here, we then do a step which violates element - * conservation. - */ - iph = m_phaseID[k]; - m_deltaPhaseMoles[iph] -= m_deltaMolNumSpecies[k]; - m_deltaMolNumSpecies[k] = 0.0; - } - } - } - par = 1.0 / par; - if (par <= 1.01 && par > 0.0) { - /* Reduce the size of the step by the multiplicative factor, par */ - par *= 0.99; -#ifdef DEBUG_MODE - if (m_debug_print_lvl >= 2) { - plogf(" --- Reduction in step size due to component "); - plogf("%s", m_speciesName[ll].c_str()); - plogf(" going negative = %11.3E", par); - plogendl(); - } -#endif - for (i = 0; i < m_numSpeciesTot; ++i) { - m_deltaMolNumSpecies[i] *= par; - } for (iph = 0; iph < m_numPhases; iph++) { - m_deltaPhaseMoles[iph] *= par; + m_tPhaseMoles_new[iph] = m_tPhaseMoles_old[iph] + m_deltaPhaseMoles[iph]; } - } else { - par = 1.0; - } -#ifdef DEBUG_MODE - checkDelta1(VCS_DATA_PTR(m_deltaMolNumSpecies), - VCS_DATA_PTR(m_deltaPhaseMoles), m_numSpeciesTot); -#endif - - /* - * Now adjust the wt[kspec]'s so that the reflect the decrease in - * the overall length of m_deltaMolNumSpecies[kspec] just calculated. At the end - * of this section wt[], m_deltaMolNumSpecies[], tPhMoles, and tPhMoles1 should all be - * consistent with a new estimate of the state of the system. - */ - for (kspec = 0; kspec < m_numSpeciesTot; ++kspec) { - m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec]; - if (m_molNumSpecies_new[kspec] < 0.0 && (m_speciesUnknownType[kspec] - != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) { - plogf("vcs_solve_TP: ERROR on step change wt[%d:%s]: %g < 0.0", - kspec, m_speciesName[kspec].c_str(), m_molNumSpecies_new[kspec]); + + /* + * Set the flags indicating the mole numbers in the vcs_VolPhase + * objects are out of date. + */ + vcs_setFlagsVolPhases(false, VCS_STATECALC_NEW); + + /* + * Calculate the new chemical potentials using the tentative + * solution values. We only calculate a subset of these, because + * we have only updated a subset of the W(). + */ + vcs_dfe(VCS_STATECALC_NEW, 0, 0, m_numSpeciesTot); + + /* + * Evaluate DeltaG for all components if ITI=0, and for + * major components only if ITI NE 0 + */ + vcs_deltag(0, false, VCS_STATECALC_NEW); + + /* *************************************************************** */ + /* **** CONVERGENCE FORCER SECTION ******************************* */ + /* *************************************************************** */ + if (printDetails) { + plogf(" --- Total Old Dimensionless Gibbs Free Energy = %20.13E\n", + vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_old), VCS_DATA_PTR(m_feSpecies_old), + VCS_DATA_PTR(m_tPhaseMoles_old))); + plogf(" --- Total tentative Dimensionless Gibbs Free Energy = %20.13E", + vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_feSpecies_new), + VCS_DATA_PTR(m_tPhaseMoles_new))); plogendl(); - exit(EXIT_FAILURE); } - } - - /* - * Calculate the tentative total mole numbers for each phase - */ - for (iph = 0; iph < m_numPhases; iph++) { - m_tPhaseMoles_new[iph] = m_tPhaseMoles_old[iph] + m_deltaPhaseMoles[iph]; - } - /* - * Set the flags indicating the mole numbers in the vcs_VolPhase - * objects are out of date. - */ - vcs_setFlagsVolPhases(false, VCS_STATECALC_NEW); + forced = vcs_globStepDamp(); - /* - * Calculate the new chemical potentials using the tentative - * solution values. We only calculate a subset of these, because - * we have only updated a subset of the W(). - */ - vcs_dfe(VCS_STATECALC_NEW, 0, 0, m_numSpeciesTot); - - /* - * Evaluate DeltaG for all components if ITI=0, and for - * major components only if ITI NE 0 - */ - vcs_deltag(0, false, VCS_STATECALC_NEW); - - /* *************************************************************** */ - /* **** CONVERGENCE FORCER SECTION ******************************* */ - /* *************************************************************** */ - if (printDetails) { - plogf(" --- Total Old Dimensionless Gibbs Free Energy = %20.13E\n", - vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_old), VCS_DATA_PTR(m_feSpecies_old), - VCS_DATA_PTR(m_tPhaseMoles_old))); - plogf(" --- Total tentative Dimensionless Gibbs Free Energy = %20.13E", - vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_feSpecies_new), - VCS_DATA_PTR(m_tPhaseMoles_new))); - plogendl(); - } - - forced = vcs_globStepDamp(); - - /* - * Print out the changes to the solution that FORCER produced - */ - if (printDetails && forced) { + /* + * Print out the changes to the solution that FORCER produced + */ + if (printDetails && forced) { - plogf(" -----------------------------------------------------\n"); - plogf(" --- FORCER SUBROUTINE changed the solution:\n"); - plogf(" --- SPECIES Status INIT MOLES TENT_MOLES"); - plogf(" FINAL KMOLES INIT_DEL_G/RT TENT_DEL_G/RT FINAL_DELTA_G/RT\n"); - for (i = 0; i < m_numComponents; ++i) { - plogf(" --- %-12.12s", m_speciesName[i].c_str()); - plogf(" %14.6E %14.6E %14.6E\n", m_molNumSpecies_old[i], - m_molNumSpecies_old[i] + m_deltaMolNumSpecies[i], m_molNumSpecies_new[i]); + plogf(" -----------------------------------------------------\n"); + plogf(" --- FORCER SUBROUTINE changed the solution:\n"); + plogf(" --- SPECIES Status INIT MOLES TENT_MOLES"); + plogf(" FINAL KMOLES INIT_DEL_G/RT TENT_DEL_G/RT FINAL_DELTA_G/RT\n"); + for (i = 0; i < m_numComponents; ++i) { + plogf(" --- %-12.12s", m_speciesName[i].c_str()); + plogf(" %14.6E %14.6E %14.6E\n", m_molNumSpecies_old[i], + m_molNumSpecies_old[i] + m_deltaMolNumSpecies[i], m_molNumSpecies_new[i]); + } + for (kspec = m_numComponents; kspec < m_numSpeciesRdc; ++kspec) { + irxn = kspec - m_numComponents; + plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); + plogf(" %2d %14.6E%14.6E%14.6E%14.6E%14.6E%14.6E\n", m_speciesStatus[kspec], + m_molNumSpecies_old[kspec], + m_molNumSpecies_old[kspec]+m_deltaMolNumSpecies[kspec], + m_molNumSpecies_new[kspec], m_deltaGRxn_old[irxn], + m_deltaGRxn_tmp[irxn], m_deltaGRxn_new[irxn]); + } + print_space(26); + plogf("Norms of Delta G():%14.6E%14.6E\n", + l2normdg(VCS_DATA_PTR(m_deltaGRxn_old)), + l2normdg(VCS_DATA_PTR(m_deltaGRxn_new))); + plogf(" Total kmoles of gas = %15.7E\n", m_tPhaseMoles_old[0]); + if ((m_numPhases > 1) && (! (m_VolPhaseList[1])->m_singleSpecies)) { + plogf(" Total kmoles of liquid = %15.7E\n", m_tPhaseMoles_old[1]); + } else { + plogf(" Total kmoles of liquid = %15.7E\n", 0.0); + } + plogf(" Total New Dimensionless Gibbs Free Energy = %20.13E\n", + vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_feSpecies_new), + VCS_DATA_PTR(m_tPhaseMoles_new))); + plogf(" -----------------------------------------------------"); + plogendl(); } - for (kspec = m_numComponents; kspec < m_numSpeciesRdc; ++kspec) { - irxn = kspec - m_numComponents; - plogf(" --- %-12.12s", m_speciesName[kspec].c_str()); - plogf(" %2d %14.6E%14.6E%14.6E%14.6E%14.6E%14.6E\n", m_speciesStatus[kspec], - m_molNumSpecies_old[kspec], - m_molNumSpecies_old[kspec]+m_deltaMolNumSpecies[kspec], - m_molNumSpecies_new[kspec], m_deltaGRxn_old[irxn], - m_deltaGRxn_tmp[irxn], m_deltaGRxn_new[irxn]); - } - print_space(26); - plogf("Norms of Delta G():%14.6E%14.6E\n", - l2normdg(VCS_DATA_PTR(m_deltaGRxn_old)), - l2normdg(VCS_DATA_PTR(m_deltaGRxn_new))); - plogf(" Total kmoles of gas = %15.7E\n", m_tPhaseMoles_old[0]); - if ((m_numPhases > 1) && (! (m_VolPhaseList[1])->m_singleSpecies)) { - plogf(" Total kmoles of liquid = %15.7E\n", m_tPhaseMoles_old[1]); - } else { - plogf(" Total kmoles of liquid = %15.7E\n", 0.0); - } - plogf(" Total New Dimensionless Gibbs Free Energy = %20.13E\n", - vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_feSpecies_new), - VCS_DATA_PTR(m_tPhaseMoles_new))); - plogf(" -----------------------------------------------------"); - plogendl(); } - /* *************************************************************** */ /* **** ITERATION SUMMARY PRINTOUT SECTION *********************** */ /* *************************************************************** */ @@ -1595,7 +1651,10 @@ namespace VCSnonideal { MajorSpeciesHaveConverged = false; /* * Go back and do another iteration with variable ITI - */ + */ + if (forceComponentCalc) { + goto L_COMPONENT_CALC; + } goto L_MAINLOOP_MM4_SPECIES; } } @@ -1661,6 +1720,9 @@ namespace VCSnonideal { * to the main loop to do another iteration. */ iti = 0; + if (forceComponentCalc) { + goto L_COMPONENT_CALC; + } goto L_MAINLOOP_ALL_SPECIES; } } @@ -2098,9 +2160,9 @@ namespace VCSnonideal { double delta = *delta_ptr; #ifdef DEBUG_MODE if (irxn < 0) { - plogf(" --- delete_species() ERROR: called for a component %d", kspec); - plogendl(); - exit(EXIT_FAILURE); + plogf(" --- delete_species() ERROR: called for a component %d", kspec); + plogendl(); + exit(EXIT_FAILURE); } #endif if (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { @@ -2585,8 +2647,8 @@ namespace VCSnonideal { for (kspec = m_numSpeciesRdc; kspec < m_numSpeciesTot; ++kspec) { iph = m_phaseID[kspec]; m_feSpecies_new[kspec] = (m_SSfeSpecies[kspec] + log(m_actCoeffSpecies_old[kspec]) - - m_lnMnaughtSpecies[kspec] - + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); + - m_lnMnaughtSpecies[kspec] + + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); } /* @@ -2747,8 +2809,8 @@ namespace VCSnonideal { for (kspec = m_numSpeciesRdc; kspec < m_numSpeciesTot; ++kspec) { iph = m_phaseID[kspec]; m_feSpecies_new[kspec] = (m_SSfeSpecies[kspec] + log(m_actCoeffSpecies_old[kspec]) - - m_lnMnaughtSpecies[kspec] - + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); + - m_lnMnaughtSpecies[kspec] + + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); } /* * Recalculate the DeltaG's of the formation reactions for the @@ -2769,7 +2831,7 @@ namespace VCSnonideal { if (m_debug_print_lvl) { plogf(" --- add_deleted(): delta_species() failed for " "species %s (%d) with mol number %g\n", - m_speciesName[kspec].c_str(), kspec, dx); + m_speciesName[kspec].c_str(), kspec, dx); } #endif if (dx > 1.0E-50) { From a96f86540381cb693dd91a22e725d29303ca1dcd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 27 Oct 2010 17:00:46 +0000 Subject: [PATCH 283/446] Added FixedChemPotSSTP object. This is a utility object that will provide a bath species at a certain chemical potential to the equilibrium solver. --- Cantera/src/thermo/FixedChemPotSSTP.cpp | 492 ++++++++++++++++++ Cantera/src/thermo/FixedChemPotSSTP.h | 630 ++++++++++++++++++++++++ Cantera/src/thermo/Makefile.in | 4 +- Cantera/src/thermo/SingleSpeciesTP.cpp | 14 +- Cantera/src/thermo/ThermoFactory.cpp | 14 +- Cantera/src/thermo/mix_defs.h | 3 + 6 files changed, 1148 insertions(+), 9 deletions(-) create mode 100644 Cantera/src/thermo/FixedChemPotSSTP.cpp create mode 100644 Cantera/src/thermo/FixedChemPotSSTP.h diff --git a/Cantera/src/thermo/FixedChemPotSSTP.cpp b/Cantera/src/thermo/FixedChemPotSSTP.cpp new file mode 100644 index 000000000..38aabe132 --- /dev/null +++ b/Cantera/src/thermo/FixedChemPotSSTP.cpp @@ -0,0 +1,492 @@ +/** + * @file FixedChemPotSSTP.cpp + * Definition file for the FixedChemPotSSTP class, which represents a fixed-composition + * incompressible substance with a constant chemical potential (see \ref thermoprops and + * class \link Cantera::FixedChemPotSSTP FixedChemPotSSTP\endlink) + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + * + */ + +/* + * $Id: FixedChemPotSSTP.cpp 255 2009-11-09 23:36:49Z hkmoffa $ + */ + +#include "ct_defs.h" +#include "mix_defs.h" +#include "FixedChemPotSSTP.h" +#include "SpeciesThermo.h" +#include "ThermoFactory.h" + +#include + +namespace Cantera { + //==================================================================================================================== + /* + * ---- Constructors ------- + */ + //==================================================================================================================== + /* + * Default Constructor for the FixedChemPotSSTP class + */ + FixedChemPotSSTP::FixedChemPotSSTP() : + SingleSpeciesTP(), + chemPot_(0.0) + { + } + //==================================================================================================================== + // Create and initialize a FixedChemPotSSTP ThermoPhase object + // from an asci input file + /* + * @param infile name of the input file + * @param id name of the phase id in the file. + * If this is blank, the first phase in the file is used. + */ + FixedChemPotSSTP::FixedChemPotSSTP(std::string infile, std::string id) : + SingleSpeciesTP(), + chemPot_(0.0) + { + XML_Node* root = get_XML_File(infile); + if (id == "-") id = ""; + XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, root); + if (!xphase) { + throw CanteraError("FixedChemPotSSTP::FixedChemPotSSTP", + "Couldn't find phase name in file:" + id); + } + // Check the model name to ensure we have compatibility + const XML_Node& th = xphase->child("thermo"); + std::string model = th["model"]; + if (model != "StoichSubstance" && model != "StoichSubstanceSSTP" && model != "FixedChemPot") { + throw CanteraError("FixedChemPotSSTP::FixedChemPotSSTP", + "thermo model attribute must be FixedChemPot or StoichSubstance"); + } + importPhase(*xphase, this); + } + //==================================================================================================================== + // Full Constructor. + /* + * @param phaseRef XML node pointing to a FixedChemPotSSTP description + * @param id Id of the phase. + */ + FixedChemPotSSTP::FixedChemPotSSTP(XML_Node& xmlphase, std::string id) : + SingleSpeciesTP(), + chemPot_(0.0) + { + if (id != "") { + std::string idxml = xmlphase["id"]; + if (id != idxml) { + throw CanteraError("FixedChemPotSSTP::FixedChemPotSSTP", + "id's don't match"); + } + } + const XML_Node& th = xmlphase.child("thermo"); + std::string model = th["model"]; + if (model != "StoichSubstance" && model != "StoichSubstanceSSTP" && model != "FixedChemPotSSTP") { + throw CanteraError("FixedChemPotSSTP::FixedChemPotSSTP", + "thermo model attribute must be StoichSubstance or FixedChemPot"); + } + importPhase(xmlphase, this); + + if (model == "StoichSubstance" || model == "StoichSubstanceSSTP") { + _updateThermo(); + chemPot_ = (m_h0_RT[0] - m_s0_R[0]) * GasConstant * temperature(); + } + } + //==================================================================================================================== + // Copy constructor + /* + * @param right Object to be copied + */ + FixedChemPotSSTP::FixedChemPotSSTP(const FixedChemPotSSTP &right) : + SingleSpeciesTP() + { + *this = operator=(right); + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + FixedChemPotSSTP & + FixedChemPotSSTP::operator=(const FixedChemPotSSTP & right) { + if (&right != this) { + SingleSpeciesTP::operator=(right); + + chemPot_ = right.chemPot_; + } + return *this; + } + //==================================================================================================================== + /* + * Destructor for the routine (virtual) + * + */ + FixedChemPotSSTP::~FixedChemPotSSTP() + { + } + //==================================================================================================================== + // Duplication function + /* + * This virtual function is used to create a duplicate of the + * current phase. It's used to duplicate the phase when given + * a ThermoPhase pointer to the phase. + * + * @return It returns a ThermoPhase pointer. + */ + ThermoPhase *FixedChemPotSSTP::duplMyselfAsThermoPhase() const { + FixedChemPotSSTP *stp = new FixedChemPotSSTP(*this); + return (ThermoPhase *) stp; + } + //==================================================================================================================== + + /* + * ---- Utilities ----- + */ + + /* + * Equation of state flag. Returns the value cStoichSubstance, + * defined in mix_defs.h. + */ + int FixedChemPotSSTP::eosType() const { + return cFixedChemPot; + } + + /* + * ---- Molar Thermodynamic properties of the solution ---- + */ + + /* + * ----- Mechanical Equation of State ------ + */ + //==================================================================================================================== + /* + * Pressure. Units: Pa. + * For an incompressible substance, the density is independent + * of pressure. This method simply returns the stored + * pressure value. + */ + doublereal FixedChemPotSSTP::pressure() const { + return m_press; + } + //==================================================================================================================== + /* + * Set the pressure at constant temperature. Units: Pa. + * For an incompressible substance, the density is + * independent of pressure. Therefore, this method only + * stores the specified pressure value. It does not + * modify the density. + */ + void FixedChemPotSSTP::setPressure(doublereal p) { + m_press = p; + } + //==================================================================================================================== + /* + * The isothermal compressibility. Units: 1/Pa. + * The isothermal compressibility is defined as + * \f[ + * \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T + * \f] + * + * It's equal to zero for this model, since the molar volume + * doesn't change with pressure or temperature. + */ + doublereal FixedChemPotSSTP::isothermalCompressibility() const { + return 0.0; + } + //==================================================================================================================== + /* + * The thermal expansion coefficient. Units: 1/K. + * The thermal expansion coefficient is defined as + * + * \f[ + * \beta = \frac{1}{v}\left(\frac{\partial v}{\partial T}\right)_P + * \f] + * + * It's equal to zero for this model, since the molar volume + * doesn't change with pressure or temperature. + */ + doublereal FixedChemPotSSTP::thermalExpansionCoeff() const { + return 0.0; + } + //==================================================================================================================== + /* + * ---- Chemical Potentials and Activities ---- + */ + //==================================================================================================================== + /* + * This method returns the array of generalized + * concentrations. For a stoichiometric substance, there is + * only one species, and the generalized concentration is 1.0. + */ + void FixedChemPotSSTP:: + getActivityConcentrations(doublereal* c) const { + c[0] = 1.0; + } + //==================================================================================================================== + /* + * The standard concentration. This is defined as the concentration + * by which the generalized concentration is normalized to produce + * the activity. + */ + doublereal FixedChemPotSSTP::standardConcentration(int k) const { + return 1.0; + } + //==================================================================================================================== + /* + * Returns the natural logarithm of the standard + * concentration of the kth species + */ + doublereal FixedChemPotSSTP::logStandardConc(int k) const { + return 0.0; + } + //==================================================================================================================== + /* + * Returns the units of the standard and generalized + * concentrations Note they have the same units, as their + * ratio is defined to be equal to the activity of the kth + * species in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + */ + void FixedChemPotSSTP:: + getUnitsStandardConc(doublereal *uA, int k, int sizeUA) const { + for (int i = 0; i < 6; i++) { + uA[i] = 0; + } + } + //==================================================================================================================== + /* + * ---- Partial Molar Properties of the Solution ---- + */ + void FixedChemPotSSTP::getPartialMolarVolumes(doublereal* vbar) const { + vbar[0] = 0.0; + } + //==================================================================================================================== + /* + * ---- Properties of the Standard State of the Species in the Solution + * ---- + */ + //==================================================================================================================== + /* + * Get the array of chemical potentials at unit activity + * \f$ \mu^0_k \f$. + * + * For a stoichiometric substance, there is no activity term in + * the chemical potential expression, and therefore the + * standard chemical potential and the chemical potential + * are both equal to the molar Gibbs function. + */ + void FixedChemPotSSTP:: + getStandardChemPotentials(doublereal* mu0) const { + mu0[0] = chemPot_; + } + //==================================================================================================================== + /* + * Get the nondimensional Enthalpy functions for the species + * at their standard states at the current + * T and P of the solution. + * Molar enthalpy. Units: J/kmol. For an incompressible, + * stoichiometric substance, the internal energy is + * independent of pressure, and therefore the molar enthalpy + * is \f[ \hat h(T, P) = \hat u(T) + P \hat v \f], where the + * molar specific volume is constant. + */ + void FixedChemPotSSTP::getEnthalpy_RT(doublereal* hrt) const { + double rt = _RT(); + hrt[0] = chemPot_ / rt; + } + //==================================================================================================================== + /* + * Get the array of nondimensional Entropy functions for the + * standard state species + * at the current T and P of the solution. + */ + void FixedChemPotSSTP::getEntropy_R(doublereal* sr) const { + sr[0] = 0.0; + } + //==================================================================================================================== + /* + * Get the nondimensional Gibbs functions for the species + * at their standard states of solution at the current T and P + * of the solution + */ + void FixedChemPotSSTP::getGibbs_RT(doublereal* grt) const { + double rt = _RT(); + grt[0] = chemPot_ / rt; + } + //==================================================================================================================== + /* + * Get the nondimensional Gibbs functions for the standard + * state of the species at the current T and P. + */ + void FixedChemPotSSTP::getCp_R(doublereal* cpr) const { + cpr[0] = 0.0; + } + //==================================================================================================================== + /* + * Molar internal energy (J/kmol). + * For an incompressible, + * stoichiometric substance, the molar internal energy is + * independent of pressure. Since the thermodynamic properties + * are specified by giving the standard-state enthalpy, the + * term \f$ P_0 \hat v\f$ is subtracted from the specified molar + * enthalpy to compute the molar internal energy. + */ + void FixedChemPotSSTP::getIntEnergy_RT(doublereal* urt) const { + urt[0] = chemPot_; + } + //==================================================================================================================== + // Get the molar volumes of each species in their standard + // states at the current T and P of the solution. + /* + * units = m^3 / kmol + * + * We set this to zero + * + * @param vbar On output this contains the standard volume of the species + * and phase (m^3/kmol). Vector of length 1 + */ + void FixedChemPotSSTP::getStandardVolumes(doublereal* vbar) const { + vbar[0] = 0.0; + } + //==================================================================================================================== + /* + * ---- Thermodynamic Values for the Species Reference States ---- + */ + //==================================================================================================================== + void FixedChemPotSSTP::getIntEnergy_RT_ref(doublereal* urt) const { + urt[0] = chemPot_; + } + //==================================================================================================================== + void FixedChemPotSSTP::getEnthalpy_RT_ref(doublereal* hrt) const { + double rt = _RT(); + hrt[0] = chemPot_ / rt; + } + //==================================================================================================================== + void FixedChemPotSSTP::getEntropy_R_ref(doublereal* sr) const { + sr[0] = 0.0; + } + //==================================================================================================================== + void FixedChemPotSSTP::getGibbs_RT_ref(doublereal* grt) const { + double rt = _RT(); + grt[0] = chemPot_ / rt; + } + //==================================================================================================================== + void FixedChemPotSSTP::getGibbs_ref(doublereal* g) const { + g[0] = chemPot_; + } + //==================================================================================================================== + void FixedChemPotSSTP::getCp_R_ref(doublereal* cpr) const { + cpr[0] = 0.0; + } + //==================================================================================================================== + /* + * ---- Saturation Properties + */ + //==================================================================================================================== + /* + * ---- Initialization and Internal functions + */ + //==================================================================================================================== + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + void FixedChemPotSSTP::initThermo() { + /* + * Call the base class thermo initializer + */ + SingleSpeciesTP::initThermo(); + } + //==================================================================================================================== + + void FixedChemPotSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("FixedChemPotSSTP::initThermoXML", "no thermo XML node"); + } + XML_Node &tnode = phaseNode.child("thermo"); + std::string model = tnode["model"]; + if (model != "StoichSubstance" && model != "FixedChemPot" && model != "StoichSubstanceSSTP") { + throw CanteraError("FixedChemPotSSTP::initThermoXML()", + "thermo model attribute must be FixedChemPot or StoichSubstance or StoichSubstanceSSTP"); + } + if (model == "FixedChemPot") { + double val = getFloatDefaultUnits(tnode, "chemicalPotential", "J/kmol"); + chemPot_ = val; + } + SingleSpeciesTP::initThermoXML(phaseNode, id); + + + } + //==================================================================================================================== + /* + * setParameters: + * + * Generic routine that is used to set the parameters used + * by this model. + * C[0] = density of phase [ kg/m3 ] + */ + void FixedChemPotSSTP::setParameters(int n, doublereal * const c) { + chemPot_ = c[0]; + } + //==================================================================================================================== + /* + * getParameters: + * + * Generic routine that is used to get the parameters used + * by this model. + * n = 1 + * C[0] = density of phase [ kg/m3 ] + */ + void FixedChemPotSSTP::getParameters(int &n, doublereal * const c) const { + n = 1; + c[0] = chemPot_; + } + //==================================================================================================================== + void FixedChemPotSSTP::setParametersFromXML(const XML_Node& eosdata) { + std::string model = eosdata["model"]; + if (model != "StoichSubstance" && model != "FixedChemPot" && model != "StoichSubstanceSSTP") { + throw CanteraError("FixedChemPotSSTP::setParametersFromXML", + "thermo model attribute must be FixedChemPot or StoichSubstance or StoichSubstanceSSTP"); + } + if (model == "FixedChemPotSSTP") { + doublereal val = getFloatDefaultUnits(eosdata, "chemicalPotential", "J/kmol"); + chemPot_ = val; + } + } + //==================================================================================================================== + // Function to set the chemical potential directly + /* + * @param chemPot Value of the chemical potential (units J/kmol) + */ + void FixedChemPotSSTP::setChemicalPotential(doublereal chemPot) { + chemPot_ = chemPot; + } + //==================================================================================================================== +} diff --git a/Cantera/src/thermo/FixedChemPotSSTP.h b/Cantera/src/thermo/FixedChemPotSSTP.h new file mode 100644 index 000000000..1df7ec613 --- /dev/null +++ b/Cantera/src/thermo/FixedChemPotSSTP.h @@ -0,0 +1,630 @@ +/** + * @file FixedChemPotSSTP.h + * Header file for the FixedChemPotSSTP class, which represents a fixed-composition + * incompressible substance with a constant chemical potential (see \ref thermoprops and + * class \link Cantera::FixedChemPotSSTP FixedChemPotSSTP\endlink) + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ + * $Revision: 255 $ + */ + +#ifndef CT_FIXEDCHEMPOTSSTP_H +#define CT_FIXEDCHEMPOTSSTP_H + +#include "mix_defs.h" +#include "SingleSpeciesTP.h" +#include "SpeciesThermo.h" + +namespace Cantera { + + //! Class %FixedChemPotSSTP represents a stoichiometric (fixed + //! composition) incompressible substance. + /*! + * This class internally changes the independent degree of freedom from + * density to pressure. This is necessary because the phase is + * incompressible. It uses a zero volume approximation. + * + * + * Specification of Species Standard %State Properties + * + * This class inherits from SingleSpeciesTP. + * It uses a single value for the chemical potential which is assumed to be constant + * with respect to temperature and pressure. + * + * The reference state thermodynamics is inherited from SingleSpeciesTP. However, + * it's only used to set the initial chemical potential to the value + * of the chemical potential at the starting conditions. Thereafter, + * it is ignored. + * + * For a zero volume material, the internal energy and the enthalpy are + * equal to the chemical potential. The entropy, the heat capacity, and the molar volume + * are equal to zero. + * + * + * Specification of Solution Thermodynamic Properties + * + * All solution properties are obtained from the standard state + * species functions, since there is only one species in the phase. + * + * Application within %Kinetics Managers + * + * The standard concentration is equal to 1.0. This means that the + * kinetics operator works on an (activities basis). Since this + * is a stoichiometric substance, this means that the concentration + * of this phase drops out of kinetics expressions. + * + * An example of a reaction using this is a sticking coefficient + * reaction of a substance in an ideal gas phase on a surface with a bulk phase + * species in this phase. In this case, the rate of progress for this + * reaction, \f$ R_s \f$, may be expressed via the following equation: + * \f[ + * R_s = k_s C_{gas} + * \f] + * where the units for \f$ R_s \f$ are kmol m-2 s-1. \f$ C_{gas} \f$ has units + * of kmol m-3. Therefore, the kinetic rate constant, \f$ k_s \f$, has + * units of m s-1. Nowhere does the concentration of the bulk phase + * appear in the rate constant expression, since it's a stoichiometric + * phase, and the activity is always equal to 1.0. + * + * Instanteation of the Class + * + * The constructor for this phase is located in the default ThermoFactory + * for %Cantera. A new %FixedChemPotSSTP may be created by a standalone xml file + * which is given below. + * + * It may also be created by the following code snippets. The code + * includes the special member function setChemicalPotential( chempot), which + * sets the chemical potential to a specific value in J / kmol. + * + * @code + * sprintf(file_ID,"%s#Li(Fixed)", iFile); + * XML_Node *xm = get_XML_NameID("phase", file_ID, 0); + * FixedChemPotSSTP *LiFixed = new FixedChemPotSSTP(*xm); + // Set the chemical potential to -2.3E7 J/kmol + * LiFixed->setChemicalPotential(-2.3E7.) + * @endcode + * + * or by the following call to importPhase(): + * + * @code + * sprintf(file_ID,"%s#NaCl(S)", iFile); + * XML_Node *xm = get_XML_NameID("phase", file_ID, 0); + * FixedChemPotSSTP solid; + * importPhase(*xm, &solid); + * @endcode + * + * XML Example + * + * The phase model name for this is called StoichSubstance. It must be supplied + * as the model attribute of the thermo XML element entry. + * Within the phase XML block, + * the density of the phase must be specified. An example of an XML file + * this phase is given below. + * + * @verbatim + + + + + + + + Li + + + LiFixed + + + -2.3E7 + + + + + + + + + + Li:1 + + + + 50.72389, 6.672267, -2.517167, + 10.15934, -0.200675, -427.2115, + 130.3973 + + + + + + + @endverbatim + * + * The model attribute, "FixedChemPot", on the thermo element + * identifies the phase as being a FixedChemPotSSTP object. + * + * @ingroup thermoprops + */ + class FixedChemPotSSTP : public SingleSpeciesTP { + + public: + + //! Default constructor for the FixedChemPotSSTP class + FixedChemPotSSTP(); + + //! Construct and initialize a FixedChemPotSSTP ThermoPhase object + //! directly from an asci input file + /*! + * @param infile name of the input file + * @param id name of the phase id in the file. + * If this is blank, the first phase in the file is used. + */ + FixedChemPotSSTP(std::string infile, std::string id = ""); + + //! Construct and initialize a FixedChemPotSSTP ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML node pointing to a FixedChemPotSSTP description + * @param id Id of the phase. + */ + FixedChemPotSSTP(XML_Node& phaseRef, std::string id = ""); + + //! Copy constructor + /*! + * @param right Object to be copied + */ + FixedChemPotSSTP(const FixedChemPotSSTP &right); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + FixedChemPotSSTP & operator=(const FixedChemPotSSTP & right); + + //! Destructor for the routine (virtual) + virtual ~FixedChemPotSSTP(); + + //! Duplication function + /*! + * This virtual function is used to create a duplicate of the + * current phase. It's used to duplicate the phase when given + * a ThermoPhase pointer to the phase. + * + * @return It returns a ThermoPhase pointer. + */ + ThermoPhase *duplMyselfAsThermoPhase() const; + + /** + * + * @name Utilities + * @{ + */ + + /** + * Equation of state flag. + * + * Returns the value cStoichSubstance, defined in mix_defs.h. + */ + virtual int eosType() const; + + /** + * @} + * @name Molar Thermodynamic Properties of the Solution + * @{ + */ + + /** + * @} + * @name Mechanical Equation of State + * @{ + */ + + + //! Report the Pressure. Units: Pa. + /*! + * For an incompressible substance, the density is independent + * of pressure. This method simply returns the storred + * pressure value. + */ + virtual doublereal pressure() const; + + //! Set the pressure at constant temperature. Units: Pa. + /*! + * For an incompressible substance, the density is + * independent of pressure. Therefore, this method only + * stores the specified pressure value. It does not + * modify the density. + * + * @param p Pressure (units - Pa) + */ + virtual void setPressure(doublereal p); + + //! Returns the isothermal compressibility. Units: 1/Pa. + /*! + * The isothermal compressibility is defined as + * \f[ + * \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T + * \f] + */ + virtual doublereal isothermalCompressibility() const; + + //! Return the volumetric thermal expansion coefficient. Units: 1/K. + /*! + * The thermal expansion coefficient is defined as + * \f[ + * \beta = \frac{1}{v}\left(\frac{\partial v}{\partial T}\right)_P + * \f] + */ + virtual doublereal thermalExpansionCoeff() const ; + + /** + * @} + * @name Activities, Standard States, and Activity Concentrations + * + * This section is largely handled by parent classes, since there + * is only one species. Therefore, the activity is equal to one. + * @{ + */ + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. + * + * For a stoichiomeetric substance, there is + * only one species, and the generalized concentration is 1.0. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + //! Return the standard concentration for the kth species + /*! + * The standard concentration \f$ C^0_k \f$ used to normalize + * the activity (i.e., generalized) concentration. + * This phase assumes that the kinetics operator works on an + * dimensionless basis. Thus, the standard concentration is + * equal to 1.0. + * + * @param k Optional parameter indicating the species. The default + * is to assume this refers to species 0. + * @return + * Returns The standard Concentration as 1.0 + */ + virtual doublereal standardConcentration(int k=0) const; + + //! Natural logarithm of the standard concentration of the kth species. + /*! + * @param k index of the species (defaults to zero) + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Get the array of chemical potentials at unit activity for the species + //! at their standard states at the current T and P of the solution. + /*! + * For a stoichiometric substance, there is no activity term in + * the chemical potential expression, and therefore the + * standard chemical potential and the chemical potential + * are both equal to the molar Gibbs function. + * + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution + * + * @param mu0 Output vector of chemical potentials. + * Length: m_kk. + */ + virtual void getStandardChemPotentials(doublereal* mu0) const; + + //! Returns the units of the standard and generalized concentrations. + /*! + * Note they have the same units, as their + * ratio is defined to be equal to the activity of the kth + * species in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * The base %ThermoPhase class assigns thedefault quantities + * of (kmol/m3) for all species. + * Inherited classes are responsible for overriding the default + * values if necessary. + * + * @param uA Output vector containing the units + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + * @param k species index. Defaults to 0. + * @param sizeUA output int containing the size of the vector. + * Currently, this is equal to 6. + */ + virtual void getUnitsStandardConc(doublereal *uA, int k = 0, + int sizeUA = 6) const; + + //@} + /// @name Partial Molar Properties of the Solution + /// + /// These properties are handled by the parent class, + /// SingleSpeciesTP + //@{ + + //! Get the species partial molar volumes. Units: m^3/kmol. + /*! + * This is the phase molar volume. \f$ V(T,P) = V_o(T,P) \f$. + * + * set to zero. + * + * @param vbar On return, contains the molar volume of the single species + * and the phase. Units are m^3 / kmol. Length = 1 + */ + void getPartialMolarVolumes(doublereal* vbar) const; + + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + //! Get the nondimensional Enthalpy functions for the species + //! at their standard states at the current T and P of the solution. + /*! + * @param hrt Output vector of nondimensional standard state enthalpies. + * Length: m_kk. + */ + virtual void getEnthalpy_RT(doublereal* hrt) const; + + //! Get the array of nondimensional Entropy functions for the + //! standard state species at the current T and P of the solution. + /*! + * @param sr Output vector of nondimensional standard state entropies. + * Length: m_kk. + */ + virtual void getEntropy_R(doublereal* sr) const; + + //! Get the nondimensional Gibbs functions for the species + //! in their standard states at the current T and P of the solution. + /*! + * @param grt Output vector of nondimensional standard state gibbs free energies + * Length: m_kk. + */ + virtual void getGibbs_RT(doublereal* grt) const; + + //! Get the nondimensional Heat Capacities at constant + //! pressure for the species standard states + //! at the current T and P of the solution + /*! + * @param cpr Output vector of nondimensional standard state heat capacities + * Length: m_kk. + */ + virtual void getCp_R(doublereal* cpr) const; + + //! Returns the vector of nondimensional Internal Energies of the standard + //! state species at the current T and P of the solution + /*! + * For an incompressible, + * stoichiometric substance, the molar internal energy is + * independent of pressure. Since the thermodynamic properties + * are specified by giving the standard-state enthalpy, the + * term \f$ P_{ref} \hat v\f$ is subtracted from the specified reference molar + * enthalpy to compute the standard state molar internal energy. + * + * @param urt output vector of nondimensional standard state + * internal energies of the species. Length: m_kk. + */ + virtual void getIntEnergy_RT(doublereal* urt) const; + + //! Get the molar volumes of each species in their standard + //! states at the current T and P of the solution. + /* + * units = m^3 / kmol + * + * We set this to zero + * + * @param vbar On output this contains the standard volume of the species + * and phase (m^3/kmol). Vector of length 1 + */ + virtual void getStandardVolumes(doublereal* vbar) const; + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + //! Returns the vector of nondimensional + //! internal Energies of the reference state at the current temperature + //! of the solution and the reference pressure for each species. + /*! + * @param urt Output vector of nondimensional reference state + * internal energies of the species. + * Length: m_kk + */ + virtual void getIntEnergy_RT_ref(doublereal *urt) const; + + //@} + /// @name Thermodynamic Values for the Species Reference State + /// + + /*! + * Returns the vector of nondimensional + * enthalpies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * + * This function is resolved in this class. It is assumed that the m_spthermo species thermo + * pointer is populated and yields the reference state. + * + * @param hrt Output vector containing the nondimensional reference state enthalpies + * Length: m_kk. + */ + virtual void getEnthalpy_RT_ref(doublereal *hrt) const; + + /*! + * Returns the vector of nondimensional + * enthalpies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * + * This function is resolved in this class. It is assumed that the m_spthermo species thermo + * pointer is populated and yields the reference state. + * + * @param grt Output vector containing the nondimensional reference state + * Gibbs Free energies. Length: m_kk. + */ + virtual void getGibbs_RT_ref(doublereal *grt) const; + + + /*! + * Returns the vector of the + * gibbs function of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * units = J/kmol + * + * This function is resolved in this class. It is assumed that the m_spthermo species thermo + * pointer is populated and yields the reference state. + * + * @param g Output vector containing the reference state + * Gibbs Free energies. Length: m_kk. Units: J/kmol. + */ + virtual void getGibbs_ref(doublereal *g) const; + + /*! + * Returns the vector of nondimensional + * entropies of the reference state at the current temperature + * of the solution and the reference pressure for each species. + * + * This function is resolved in this class. It is assumed that the m_spthermo species thermo + * pointer is populated and yields the reference state. + * + * @param er Output vector containing the nondimensional reference state + * entropies. Length: m_kk. + */ + virtual void getEntropy_R_ref(doublereal *er) const; + + /*! + * Returns the vector of nondimensional + * constant pressure heat capacities of the reference state + * at the current temperature of the solution + * and reference pressure for each species. + * + * This function is resolved in this class. It is assumed that the m_spthermo species thermo + * pointer is populated and yields the reference state. + * + * @param cprt Output vector of nondimensional reference state + * heat capacities at constant pressure for the species. + * Length: m_kk + */ + virtual void getCp_R_ref(doublereal *cprt) const; + + + + + /* + * ---- Critical State Properties + */ + + + /* + * ---- Saturation Properties + */ + + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + virtual void initThermoXML(XML_Node& phaseNode, std::string id); + + //! Set the equation of state parameters + /*! + * @internal + * The number and meaning of these depends on the subclass. + * + * @param n number of parameters + * @param c array of \a n coefficients + * c[0] = density of phase [ kg/m3 ] + */ + virtual void setParameters(int n, doublereal * const c); + + //! Get the equation of state parameters in a vector + /*! + * @internal + * + * @param n number of parameters + * @param c array of \a n coefficients + * + * For this phase: + * - n = 1 + * - c[0] = density of phase [ kg/m3 ] + */ + virtual void getParameters(int &n, doublereal * const c) const; + + //! Set equation of state parameter values from XML entries. + /*! + * This method is called by function importPhase() in + * file importCTML.cpp when processing a phase definition in + * an input file. It should be overloaded in subclasses to set + * any parameters that are specific to that particular phase + * model. Note, this method is called before the phase is + * initialzed with elements and/or species. + * + * For this phase, the chemical potential is set + * + * @param eosdata An XML_Node object corresponding to + * the "thermo" entry for this phase in the input file. + * + * eosdata points to the thermo block, and looks like this: + * + * @verbatim + + + -2.7E7 + + @endverbatim + * + */ + virtual void setParametersFromXML(const XML_Node& eosdata); + + + //! Function to set the chemical potential directly + /*! + * @param chemPot Value of the chemical potential (units J/kmol) + */ + void setChemicalPotential(doublereal chemPot); + + protected: + + + double chemPot_; + + }; + + +} + +#endif diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index 73669357e..b359d5579 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -80,10 +80,10 @@ endif ifeq ($(do_issp),1) ISSP_OBJ = IdealSolidSolnPhase.o StoichSubstanceSSTP.o SingleSpeciesTP.o MineralEQ3.o \ GibbsExcessVPSSTP.o PseudoBinaryVPSSTP.o MargulesVPSSTP.o \ - IonsFromNeutralVPSSTP.o PDSS_IonsFromNeutral.o + IonsFromNeutralVPSSTP.o PDSS_IonsFromNeutral.o FixedChemPotSSTP.o ISSP_H = IdealSolidSolnPhase.h StoichSubstanceSSTP.h SingleSpeciesTP.h MineralEQ3.h \ GibbsExcessVPSSTP.h PseudoBinaryVPSSTP.h MargulesVPSSTP.h \ - IonsFromNeutralVPSSTP.h PDSS_IonsFromNeutral.h + IonsFromNeutralVPSSTP.h PDSS_IonsFromNeutral.h FixedChemPotSSTP.h endif CATHERMO_OBJ = $(THERMO_OBJ) $(ELECTRO_OBJ) $(ISSP_OBJ) diff --git a/Cantera/src/thermo/SingleSpeciesTP.cpp b/Cantera/src/thermo/SingleSpeciesTP.cpp index 8e8372c47..7860bb859 100644 --- a/Cantera/src/thermo/SingleSpeciesTP.cpp +++ b/Cantera/src/thermo/SingleSpeciesTP.cpp @@ -346,7 +346,7 @@ namespace Cantera { * This member function is resolved here. A single species phase obtains its * thermo from the standard state function. * - * @param cpbar On return, Contains the molar volume of the single species + * @param vbar On return, Contains the molar volume of the single species * and the phase. Units are m^3 / kmol. Length = 1 */ void SingleSpeciesTP::getPartialMolarVolumes(doublereal* vbar) const { @@ -514,7 +514,11 @@ namespace Cantera { void SingleSpeciesTP::setState_UV(doublereal u, doublereal v, doublereal tol) { doublereal dt; - setDensity(1.0/v); + if (v == 0.0) { + setDensity(1.0E100); + } else { + setDensity(1.0/v); + } for (int n = 0; n < 50; n++) { dt = (u - intEnergy_mass())/cv_mass(); if (dt > 100.0) dt = 100.0; @@ -548,7 +552,11 @@ namespace Cantera { void SingleSpeciesTP::setState_SV(doublereal s, doublereal v, doublereal tol) { doublereal dt; - setDensity(1.0/v); + if (v == 0.0) { + setDensity(1.0E100); + } else { + setDensity(1.0/v); + } for (int n = 0; n < 50; n++) { dt = (s - entropy_mass())*temperature()/cv_mass(); if (dt > 100.0) dt = 100.0; diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index cf04e5e00..ea91a0cd7 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -51,7 +51,6 @@ #ifdef WITH_STOICH_SUBSTANCE #ifdef USE_SSTP #include "StoichSubstanceSSTP.h" - #else #include "StoichSubstance.h" #endif @@ -60,6 +59,7 @@ #ifdef WITH_STOICH_SUBSTANCE #include "MineralEQ3.h" #include "MetalSHEelectrons.h" +#include "FixedChemPotSSTP.h" #endif //#include "importCTML.h" @@ -91,7 +91,7 @@ namespace Cantera { /*! * @deprecated This entire structure could be replaced with a std::map */ - static int ntypes = 18; + static int ntypes = 19; //! Define the string name of the %ThermoPhase types that are handled by this factory routine static string _types[] = {"IdealGas", "Incompressible", @@ -100,7 +100,7 @@ namespace Cantera { "HMW", "IdealSolidSolution", "DebyeHuckel", "IdealMolalSolution", "IdealGasVPSS", "MineralEQ3", "MetalSHEelectrons", "Margules", - "IonsFromNeutralMolecule" + "IonsFromNeutralMolecule", "FixedChemPot" }; //! Define the integer id of the %ThermoPhase types that are handled by this factory routine @@ -110,7 +110,7 @@ namespace Cantera { cHMW, cIdealSolidSolnPhase, cDebyeHuckel, cIdealMolalSoln, cVPSS_IdealGas, cMineralEQ3, cMetalSHEelectrons, - cMargulesVPSSTP, cIonsFromNeutral + cMargulesVPSSTP, cIonsFromNeutral, cFixedChemPot }; /* @@ -173,6 +173,12 @@ namespace Cantera { break; #endif +#ifdef WITH_STOICH_SUBSTANCE + case cFixedChemPot: + th = new FixedChemPotSSTP; + break; +#endif + #ifdef WITH_STOICH_SUBSTANCE case cMineralEQ3: th = new MineralEQ3(); diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index 50482d169..02ab93eb9 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -55,6 +55,9 @@ namespace Cantera { /// An edge between two 2D surfaces const int cEdge = 6; + //! Stoichiometric compound with a constant chemical potential + const int cFixedChemPot = 70; + /// Constant partial molar volume solution IdealSolidSolnPhase.h const int cIdealSolidSolnPhase = 5009; From 9373fe02f73390416ea4a6ed45b936f89c555f48 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 27 Oct 2010 21:07:15 +0000 Subject: [PATCH 284/446] These routines needed std:: added to the arguments and function bodies of std c++ library calls. --- Cantera/src/thermo/NasaThermo.h | 40 +++++++++++++++--------------- Cantera/src/thermo/ShomateThermo.h | 38 ++++++++++++++-------------- Cantera/src/thermo/SimpleThermo.h | 10 ++++---- 3 files changed, 44 insertions(+), 44 deletions(-) diff --git a/Cantera/src/thermo/NasaThermo.h b/Cantera/src/thermo/NasaThermo.h index 46cf02a71..7d4d81fbd 100644 --- a/Cantera/src/thermo/NasaThermo.h +++ b/Cantera/src/thermo/NasaThermo.h @@ -155,7 +155,7 @@ namespace Cantera { * parameterization. * @see speciesThermoTypes.h */ - virtual void install(string name, int index, int type, + virtual void install(std::string name, int index, int type, const doublereal* c, doublereal minTemp, doublereal maxTemp, doublereal refPressure) { @@ -164,7 +164,7 @@ namespace Cantera { int imid = int(c[0]); // midpoint temp converted to integer int igrp = m_index[imid]; // has this value been seen before? if (igrp == 0) { // if not, prepare new group - vector v; + std::vector v; m_high.push_back(v); m_low.push_back(v); m_tmid.push_back(c[0]); @@ -209,7 +209,7 @@ namespace Cantera { if (m_p0 < 0.0) { m_p0 = refPressure; } else if (fabs(m_p0 - refPressure) > 0.1) { - string logmsg = " WARNING NasaThermo: New Species, " + name + ", has a different reference pressure, " + std::string logmsg = " WARNING NasaThermo: New Species, " + name + ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); logmsg = " This may become a fatal error in the future \n"; @@ -253,14 +253,14 @@ namespace Cantera { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - const vector &mlg = m_low[grp-1]; + const std::vector &mlg = m_low[grp-1]; const NasaPoly1 *nlow = &(mlg[pos]); doublereal tmid = nlow->maxTemp(); if (t < tmid) { nlow->updateProperties(&m_t[0], cp_R, h_RT, s_R); } else { - const vector &mhg = m_high[grp-1]; + const std::vector &mhg = m_high[grp-1]; const NasaPoly1 *nhigh = &(mhg[pos]); nhigh->updateProperties(&m_t[0], cp_R, h_RT, s_R); } @@ -294,7 +294,7 @@ namespace Cantera { m_t[5] = log(t); // iterate over the groups - vector::const_iterator _begin, _end; + std::vector::const_iterator _begin, _end; for (i = 0; i != m_ngroups; i++) { if (t > m_tmid[i]) { _begin = m_high[i].begin(); @@ -391,8 +391,8 @@ namespace Cantera { if (type == NASA) { int grp = m_group_map[index]; int pos = m_posInGroup_map[index]; - const vector &mlg = m_low[grp-1]; - const vector &mhg = m_high[grp-1]; + const std::vector &mlg = m_low[grp-1]; + const std::vector &mhg = m_high[grp-1]; const NasaPoly1 *lowPoly = &(mlg[pos]); const NasaPoly1 *highPoly = &(mhg[pos]); int itype = NASA; @@ -439,8 +439,8 @@ namespace Cantera { if (type == NASA) { int grp = m_group_map[index]; int pos = m_posInGroup_map[index]; - vector &mlg = m_low[grp-1]; - vector &mhg = m_high[grp-1]; + std::vector &mlg = m_low[grp-1]; + std::vector &mhg = m_high[grp-1]; NasaPoly1 *lowPoly = &(mlg[pos]); NasaPoly1 *highPoly = &(mhg[pos]); doublereal tmid = lowPoly->maxTemp(); @@ -460,14 +460,14 @@ namespace Cantera { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - const vector &mlg = m_low[grp-1]; + const std::vector &mlg = m_low[grp-1]; const NasaPoly1 *nlow = &(mlg[pos]); doublereal tmid = nlow->maxTemp(); double h; if (298.15 <= tmid) { h = nlow->reportHf298(0); } else { - const vector &mhg = m_high[grp-1]; + const std::vector &mhg = m_high[grp-1]; const NasaPoly1 *nhigh = &(mhg[pos]); h = nhigh->reportHf298(0); } @@ -477,9 +477,9 @@ namespace Cantera { virtual void modifyOneHf298(const int k, const doublereal Hf298New) { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - vector &mlg = m_low[grp-1]; + std::vector &mlg = m_low[grp-1]; NasaPoly1 *nlow = &(mlg[pos]); - vector &mhg = m_high[grp-1]; + std::vector &mhg = m_high[grp-1]; NasaPoly1 *nhigh = &(mhg[pos]); doublereal tmid = nlow->maxTemp(); @@ -508,7 +508,7 @@ namespace Cantera { * The second vector is equal to the number of species * in that particular group. */ - vector > m_high; + std::vector > m_high; //! Vector of vector of NasaPoly1's for the low temp region. /*! @@ -517,13 +517,13 @@ namespace Cantera { * The second vector is equal to the number of species * in that particular group. */ - vector > m_low; + std::vector > m_low; //! Map between the midpoint temperature, as an int, to the group number /*! * Length is equal to the number of groups. Only used in the setup. */ - map m_index; + std::map m_index; //! Vector of log temperature limits /*! @@ -567,17 +567,17 @@ namespace Cantera { * for that species are stored. group indecises start at 1, * so a decrement is always performed to access vectors. */ - mutable map m_group_map; + mutable std::map m_group_map; /*! * This map takes as its index, the species index in the phase. * It returns the position index within the group, where the * temperature polynomials for that species are storred. */ - mutable map m_posInGroup_map; + mutable std::map m_posInGroup_map; //! Species name as a function of the species index - mutable map m_name; + mutable std::map m_name; private: diff --git a/Cantera/src/thermo/ShomateThermo.h b/Cantera/src/thermo/ShomateThermo.h index c37822801..06ef0bf2a 100644 --- a/Cantera/src/thermo/ShomateThermo.h +++ b/Cantera/src/thermo/ShomateThermo.h @@ -162,14 +162,14 @@ namespace Cantera { * @see ShomatePoly * @see ShomatePoly2 */ - virtual void install(string name, int index, int type, + virtual void install(std::string name, int index, int type, const doublereal* c, doublereal minTemp, doublereal maxTemp, doublereal refPressure) { int imid = int(c[0]); // midpoint temp converted to integer int igrp = m_index[imid]; // has this value been seen before? if (igrp == 0) { // if not, prepare new group - vector v; + std::vector v; m_high.push_back(v); m_low.push_back(v); m_tmid.push_back(c[0]); @@ -201,7 +201,7 @@ namespace Cantera { if (m_p0 < 0.0) { m_p0 = refPressure; } else if (fabs(m_p0 - refPressure) > 0.1) { - string logmsg = " WARNING ShomateThermo: New Species, " + name + std::string logmsg = " WARNING ShomateThermo: New Species, " + name + ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); @@ -247,14 +247,14 @@ namespace Cantera { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - const vector &mlg = m_low[grp-1]; + const std::vector &mlg = m_low[grp-1]; const ShomatePoly *nlow = &(mlg[pos]); doublereal tmid = nlow->maxTemp(); if (t < tmid) { nlow->updateProperties(&m_t[0], cp_R, h_RT, s_R); } else { - const vector &mhg = m_high[grp-1]; + const std::vector &mhg = m_high[grp-1]; const ShomatePoly *nhigh = &(mhg[pos]); nhigh->updateProperties(&m_t[0], cp_R, h_RT, s_R); } @@ -288,7 +288,7 @@ namespace Cantera { m_t[5] = 1.0/GasConstant; m_t[6] = 1.0/(GasConstant * t); - vector::const_iterator _begin, _end; + std::vector::const_iterator _begin, _end; for (i = 0; i != m_ngroups; i++) { if (t > m_tmid[i]) { _begin = m_high[i].begin(); @@ -387,8 +387,8 @@ namespace Cantera { int grp = m_group_map[index]; int pos = m_posInGroup_map[index]; int itype = SHOMATE; - const vector &mlg = m_low[grp-1]; - const vector &mhg = m_high[grp-1]; + const std::vector &mlg = m_low[grp-1]; + const std::vector &mhg = m_high[grp-1]; const ShomatePoly *lowPoly = &(mlg[pos]); const ShomatePoly *highPoly = &(mhg[pos]); doublereal tmid = lowPoly->maxTemp(); @@ -427,8 +427,8 @@ namespace Cantera { if (type == SHOMATE) { int grp = m_group_map[index]; int pos = m_posInGroup_map[index]; - vector &mlg = m_low[grp-1]; - vector &mhg = m_high[grp-1]; + std::vector &mlg = m_low[grp-1]; + std::vector &mhg = m_high[grp-1]; ShomatePoly *lowPoly = &(mlg[pos]); ShomatePoly *highPoly = &(mhg[pos]); doublereal tmid = lowPoly->maxTemp(); @@ -453,14 +453,14 @@ namespace Cantera { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - const vector &mlg = m_low[grp-1]; + const std::vector &mlg = m_low[grp-1]; const ShomatePoly *nlow = &(mlg[pos]); doublereal tmid = nlow->maxTemp(); if (t <= tmid) { h = nlow->reportHf298(); } else { - const vector &mhg = m_high[grp-1]; + const std::vector &mhg = m_high[grp-1]; const ShomatePoly *nhigh = &(mhg[pos]); h = nhigh->reportHf298(); } @@ -471,9 +471,9 @@ namespace Cantera { int grp = m_group_map[k]; int pos = m_posInGroup_map[k]; - vector &mlg = m_low[grp-1]; + std::vector &mlg = m_low[grp-1]; ShomatePoly *nlow = &(mlg[pos]); - vector &mhg = m_high[grp-1]; + std::vector &mhg = m_high[grp-1]; ShomatePoly *nhigh = &(mhg[pos]); doublereal tmid = nlow->maxTemp(); @@ -504,7 +504,7 @@ namespace Cantera { * The second vector is equal to the number of species * in that particular group. */ - vector > m_high; + std::vector > m_high; //! Vector of vector of NasaPoly1's for the low temp region. /*! @@ -513,13 +513,13 @@ namespace Cantera { * The second vector is equal to the number of species * in that particular group. */ - vector > m_low; + std::vector > m_low; //! Map between the midpoint temperature, as an int, to the group number /*! * Length is equal to the number of groups. Only used in the setup. */ - map m_index; + std::map m_index; //! Vector of log temperature limits /*! @@ -563,14 +563,14 @@ namespace Cantera { * for that species are stored. group indecises start at 1, * so a decrement is always performed to access vectors. */ - mutable map m_group_map; + mutable std::map m_group_map; /*! * This map takes as its index, the species index in the phase. * It returns the position index within the group, where the * temperature polynomials for that species are storred. */ - mutable map m_posInGroup_map; + mutable std::map m_posInGroup_map; }; } diff --git a/Cantera/src/thermo/SimpleThermo.h b/Cantera/src/thermo/SimpleThermo.h index e0536259f..cced50e0c 100644 --- a/Cantera/src/thermo/SimpleThermo.h +++ b/Cantera/src/thermo/SimpleThermo.h @@ -13,6 +13,7 @@ #define CT_SIMPLETHERMO_H #include "SpeciesThermoMgr.h" +#include "speciesThermoTypes.h" namespace Cantera { @@ -150,10 +151,9 @@ namespace Cantera { * * @see ConstCpPoly */ - virtual void install(string name, int index, int type, - const doublereal* c, + virtual void install(std::string name, int index, int type, const doublereal* c, doublereal minTemp, doublereal maxTemp, doublereal refPressure) { - //writelog("installing const_cp for species "+name+"\n"); + m_logt0.push_back(log(c[0])); m_t0.push_back(c[0]); m_h0_R.push_back(c[1]/GasConstant); @@ -178,7 +178,7 @@ namespace Cantera { if (m_p0 < 0.0) { m_p0 = refPressure; } else if (fabs(m_p0 - refPressure) > 0.1) { - string logmsg = " WARNING SimpleThermo: New Species, " + name + + std::string logmsg = " WARNING SimpleThermo: New Species, " + name + ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); @@ -382,7 +382,7 @@ namespace Cantera { * This index keeps track of it. * indexData = m_loc[kspec] */ - mutable map m_loc; + mutable std::map m_loc; //! Map between the vector index where the coefficients are kept and the species index /*! From c7ce446b32ac81d90910a9b86f0b4e2d9ae57118 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 27 Oct 2010 21:07:51 +0000 Subject: [PATCH 285/446] Added a special constructor for setting the element potential directly. --- Cantera/src/thermo/FixedChemPotSSTP.cpp | 35 ++++++++++++++++++++- Cantera/src/thermo/FixedChemPotSSTP.h | 41 +++++++++++++++++++------ 2 files changed, 66 insertions(+), 10 deletions(-) diff --git a/Cantera/src/thermo/FixedChemPotSSTP.cpp b/Cantera/src/thermo/FixedChemPotSSTP.cpp index 38aabe132..e9d565e82 100644 --- a/Cantera/src/thermo/FixedChemPotSSTP.cpp +++ b/Cantera/src/thermo/FixedChemPotSSTP.cpp @@ -22,8 +22,9 @@ #include "SpeciesThermo.h" #include "ThermoFactory.h" -#include +#include +#include "SimpleThermo.h" namespace Cantera { //==================================================================================================================== /* @@ -96,6 +97,38 @@ namespace Cantera { chemPot_ = (m_h0_RT[0] - m_s0_R[0]) * GasConstant * temperature(); } } + //==================================================================================================================== + FixedChemPotSSTP::FixedChemPotSSTP(std::string Ename, doublereal val) : + SingleSpeciesTP(), + chemPot_(0.0) + { + + std::string pname = Ename + "Fixed"; + setID(pname); + setName(pname); + setNDim(3); + addUniqueElement(Ename, -12345.); + freezeElements(); + int nel = nElements(); + vector_fp ecomp(nel, 0.0); + ecomp[0] = 1.0; + double chrg = 0.0; + SpeciesThermo* spth = new SimpleThermo(); + setSpeciesThermo(spth); + addUniqueSpecies(pname, &ecomp[0], chrg, 0.0); + double c[4]; + c[0] = 298.15; + c[1] = val; + c[2] = 0.0; + c[3] = 0.0; + m_spthermo->install(pname, 0, SIMPLE, c, 0.0, 1.0E30, OneAtm); + freezeSpecies(); + initThermo(); + m_p0 = OneAtm; + m_tlast = 298.15; + setChemicalPotential(val); + } + //==================================================================================================================== // Copy constructor /* diff --git a/Cantera/src/thermo/FixedChemPotSSTP.h b/Cantera/src/thermo/FixedChemPotSSTP.h index 1df7ec613..8090aac8a 100644 --- a/Cantera/src/thermo/FixedChemPotSSTP.h +++ b/Cantera/src/thermo/FixedChemPotSSTP.h @@ -76,9 +76,11 @@ namespace Cantera { * * Instanteation of the Class * - * The constructor for this phase is located in the default ThermoFactory - * for %Cantera. A new %FixedChemPotSSTP may be created by a standalone xml file - * which is given below. + * This phase may be instanteated by calling the default ThermoFactory routine + * for %Cantera. This new %FixedChemPotSSTP object must then have a standalone xml file + * description an example of which is given below. + * + * * * It may also be created by the following code snippets. The code * includes the special member function setChemicalPotential( chempot), which @@ -101,13 +103,19 @@ namespace Cantera { * importPhase(*xm, &solid); * @endcode * + * The phase may also be created by a special constructor so that element + * potentials may be set. The constructor takes the name of the element and + * the value of the element chemical potential. An example is given below. + * + * @code + * FixedChemPotSSTP *LiFixed = new FixedChemPotSSTP("Li", -2.3E7); + * @endcode + * * XML Example * - * The phase model name for this is called StoichSubstance. It must be supplied + * The phase model name for this is called FixedChemPot. It must be supplied * as the model attribute of the thermo XML element entry. - * Within the phase XML block, - * the density of the phase must be specified. An example of an XML file - * this phase is given below. + * * * @verbatim @@ -182,6 +190,18 @@ namespace Cantera { * @param right Object to be copied */ FixedChemPotSSTP(const FixedChemPotSSTP &right); + + //! Special constructor for the FixecChemPotSSTP class setting an element chemical + //! potential directly + /*! + * This will create a %FixedChemPotSSTP consisting of a single species with the + * stoichiometry of one of the specified atom. It will have a chemical potential + * that is given by the second argument. + * + * @param Ename String name of the element + * @param chemPot Value of the chemical potential of that element (J/kmol) + */ + FixedChemPotSSTP(std::string Ename, doublereal chemPot); //! Assignment operator /*! @@ -619,8 +639,11 @@ namespace Cantera { protected: - - double chemPot_; + //! Value of the chemical potential of the bath species + /*! + * units are J/kmol + */ + doublereal chemPot_; }; From 7fc2841f85f0eca39649a2a85594a24c7135066c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 28 Oct 2010 01:33:54 +0000 Subject: [PATCH 286/446] Fixed an error in vcs_solve_TP. m_tPhaseMoles_new wasn't set before being used. --- Cantera/src/equil/vcs_defs.h | 20 ++- Cantera/src/equil/vcs_phaseStability.cpp | 159 ++++++++++++++++++++++- Cantera/src/equil/vcs_solve.h | 17 +++ Cantera/src/equil/vcs_solve_TP.cpp | 7 +- 4 files changed, 191 insertions(+), 12 deletions(-) diff --git a/Cantera/src/equil/vcs_defs.h b/Cantera/src/equil/vcs_defs.h index 2ee2b26ca..534d5ca54 100644 --- a/Cantera/src/equil/vcs_defs.h +++ b/Cantera/src/equil/vcs_defs.h @@ -146,7 +146,16 @@ namespace VCSnonideal { * These defines are valid values for spStatus() */ //@{ - //! Species is a component + + //! Species is a component which can never be nonzero because of a + //! stoichiometric constraint + /*! + * An example of this would be a species that contains Ni. But, + * the amount of Ni elements is exactly zero. + */ +#define VCS_SPECIES_COMPONENT_STOICHZERO 3 + + //! Species is a component which can be nonzero #define VCS_SPECIES_COMPONENT 2 //! Species is a major species @@ -223,10 +232,11 @@ namespace VCSnonideal { //! Species lies in a multicomponent phase that is active, //! but species concentration is zero due to stoich constraint /*! - * The species lies in a multicomponent phase which - * currently does exist. Its concentration is currently - * identically zero, though the phase exists. This is - * a permament condition due to stoich constraints + * The species lies in a multicomponent phase which currently does exist. Its concentration is currently + * identically zero, though the phase exists. This is a permament condition due to stoich constraints. + * + * An example of this would be a species that contains Ni. But, + * the amount of Ni elements in the current problem statement is exactly zero. */ #define VCS_SPECIES_STOICHZERO -8 diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index 17cbf9a2c..997bbf830 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -30,8 +30,7 @@ using namespace std; namespace VCSnonideal { //==================================================================================================================== - // Utility function that evaluates whether a phase can be popped - // into existence + // Utility function that evaluates whether a phase can be popped into existence /* * A phase can be popped iff the stoichiometric coefficients for the * component species, whose concentrations will be lowered during the @@ -141,10 +140,164 @@ namespace VCSnonideal { } return false; } + //==================================================================================================================== + + int inList(const std::vector &list, int val) + { + for (int i = 0; i < (int) list.size(); i++) { + if (val == list[i]) { + return i; + } + } + return -1; + } + + //==================================================================================================================== + // Determine the list of problems that need to be checked to see if there are any phases pops + /* + * This routine evaluates and fills in the following quantities + * phasePopProblemLists_ + * + * Need to work in species that are zeroed by element constraints + * + * @return Returns the number of problems that must be checked. + */ + int VCS_SOLVE::vcs_phasePopDeterminePossibleList() { + + int nfound = 0; + int irxn, kspec; + vcs_VolPhase *Vphase = 0; + int iph, j, k; + int nsp; + double stoicC; + double molComp; + std::vector linkedPhases; + phasePopProblemLists_.clear(); + + /* + * This is a vector over each component. + * For zeroed components it lists the phases, which are currently zeroed, + * which have a species with a positive stoichiometric value wrt the component. + * Therefore, we could pop the component species and pop that phase at the same time + * if we considered no other factors than keeping the component mole number positve. + * + * It does not count species with positive stoichiometric values if that species + * already has a positive mole number. The phase is already popped. + */ + std::vector< std::vector > zeroedComponentLinkedPhasePops(m_numComponents); + /* + * The logic below calculates zeroedComponentLinkedPhasePops + */ + for (j = 0; j < m_numComponents; j++) { + if (m_elType[j] == VCS_ELEM_TYPE_ABSPOS) { + molComp = m_molNumSpecies_old[j]; + if (molComp <= 0.0) { + std::vector &jList = zeroedComponentLinkedPhasePops[j]; + iph = m_phaseID[j]; + jList.push_back(iph); + for (irxn = 0; irxn < m_numRxnTot; irxn++) { + kspec = irxn + m_numComponents; + iph = m_phaseID[kspec]; + Vphase = m_VolPhaseList[iph]; + int existence = Vphase->exists(); + if (existence < 0) { + stoicC = m_stoichCoeffRxnMatrix[irxn][j]; + if (stoicC > 0.0) { + if (inList(jList, iph) != -1) { + jList.push_back(iph); + } + } + } + } + } + } + } + /* + * This is a vector over each zeroed phase + * For zeroed phases, it lists the components, which are currently zereoed, + * which have a species with a negative stoichiometric value wrt one or more species in the phase. + * Cut out components which have a pos stoichiometric value with another species in the phase. + */ + std::vector< std::vector > zeroedPhaseLinkedZeroComponents(m_numPhases); + /* + * The logic below calculates zeroedPhaseLinkedZeroComponents + */ + for (iph = 0; iph < m_numPhases; iph++) { + std::vector &iphList = zeroedPhaseLinkedZeroComponents[iph]; + iphList.clear(); + Vphase = m_VolPhaseList[iph]; + int existence = Vphase->exists(); + if (existence < 0) { + + linkedPhases.clear(); + nsp = Vphase->nSpecies(); + for (k = 0; k < nsp; k++) { + + kspec = Vphase->spGlobalIndexVCS(k); + irxn = kspec - m_numComponents; + + for (j = 0; j < m_numComponents; j++) { + if (m_elType[j] == VCS_ELEM_TYPE_ABSPOS) { + molComp = m_molNumSpecies_old[j]; + if (molComp <= 0.0) { + stoicC = m_stoichCoeffRxnMatrix[irxn][j]; + if (stoicC < 0.0) { + bool foundPos = false; + for (int kk = 0; kk < nsp; kk++) { + int kkspec = Vphase->spGlobalIndexVCS(kk); + int iirxn = kkspec - m_numComponents; + if (iirxn >= 0) { + if (m_stoichCoeffRxnMatrix[iirxn][j] > 0.0) { + foundPos = true; + } + } + } + if (!foundPos) { + if (inList(iphList, j) != -1) { + iphList.push_back(j); + } + } + } + } + } + } + } + } + } + + /* + * Now fill in the phasePopProblemLists_ list. + * + */ + for (iph = 0; iph < m_numPhases; iph++) { + Vphase = m_VolPhaseList[iph]; + int existence = Vphase->exists(); + if (existence < 0) { + std::vector &iphList = zeroedPhaseLinkedZeroComponents[iph]; + std::vector popProblem(0); + popProblem.push_back(iph); + for (int i = 0; i < (int) iphList.size(); i++) { + j = iphList[i]; + std::vector &jList = zeroedComponentLinkedPhasePops[j]; + for (int jjl = 0; jjl < (int) jList.size(); jjl++) { + int jph = jList[jjl]; + if (inList(popProblem, jph) != -1) { + popProblem.push_back(jph); + } + } + } + phasePopProblemLists_.push_back(popProblem); + } + } + + return nfound; + } + + //==================================================================================================================== // Decision as to whether a phase pops back into existence /* - * @return returns the phase id of the phase that pops back into + * @return returns the phase id of the phases that pops back into * existence. Returns -1 if there are no phases */ int VCS_SOLVE::vcs_popPhaseID(std::vector & phasePopPhaseIDs) { diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 2b43c55a6..6da5b2358 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -512,6 +512,21 @@ public: */ bool vcs_popPhasePossible(const int iphasePop) const; + + //! Determine the list of problems that need to be checked to see if there are any phases pops + /*! + * This routine evaluates and fills in the following quantities + * phasePopProblemLists_ + * + * @return Returns the number of problems that must be checked. + */ + int vcs_phasePopDeterminePossibleList(); + + + + + + //! Decision as to whether a phase pops back into existence /*! * @param phasePopPhaseIDs Vector containing the phase ids of the phases @@ -1960,6 +1975,8 @@ public: */ std::vector m_chargeSpecies; + std::vector > phasePopProblemLists_; + //! Vector of pointers to thermostructures which identify the model //! and parameters for evaluating the thermodynamic functions for that //! particular species. diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 556cd0b93..2772202f7 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -387,12 +387,11 @@ namespace VCSnonideal { /* * Copy the old solution into the new solution as an initial guess */ - vcs_dcopy(VCS_DATA_PTR(m_feSpecies_new), - VCS_DATA_PTR(m_feSpecies_old), m_numSpeciesRdc); - vcs_dcopy(VCS_DATA_PTR(m_actCoeffSpecies_new), - VCS_DATA_PTR(m_actCoeffSpecies_old), m_numSpeciesRdc); + vcs_dcopy(VCS_DATA_PTR(m_feSpecies_new), VCS_DATA_PTR(m_feSpecies_old), m_numSpeciesRdc); + vcs_dcopy(VCS_DATA_PTR(m_actCoeffSpecies_new), VCS_DATA_PTR(m_actCoeffSpecies_old), m_numSpeciesRdc); vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_new), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_Deficient), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); + vcs_dcopy(VCS_DATA_PTR(m_tPhaseMoles_new), VCS_DATA_PTR(m_tPhaseMoles_old), m_numPhases); /* * Zero out the entire vector of updates. We sometimes would From c44b477285e2f39f6784816c21082c73be2192e6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 2 Nov 2010 15:44:09 +0000 Subject: [PATCH 287/446] Fixed an error in the specification of m_deltaBoundsMagnitudes Made the residual check in dampStep a lot harder to satisfy. --- Cantera/src/numerics/NonlinearSolver.cpp | 22 +++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 5 +++++ 2 files changed, 20 insertions(+), 7 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index f79d9e093..b02e910e7 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -103,7 +103,7 @@ namespace Cantera { m_numTotalNewtIts(0), m_min_newt_its(0), filterNewstep(0), - maxNewtIts_(50), + maxNewtIts_(100), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), time_n(0.0), @@ -172,7 +172,7 @@ namespace Cantera { m_numTotalNewtIts(0), m_min_newt_its(0), filterNewstep(0), - maxNewtIts_(50), + maxNewtIts_(100), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), time_n(0.0), @@ -666,7 +666,7 @@ namespace Cantera { void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { for (int i = 0; i < neq_; i++) { - m_deltaBoundsMagnitudes[i] = MAX(m_deltaBoundsMagnitudes[i], 1000. * atolk_[i]); + m_deltaBoundsMagnitudes[i] = 1000. * atolk_[i]; m_deltaBoundsMagnitudes[i] = MAX(m_deltaBoundsMagnitudes[i], 0.1 * fabs(m_y_n[i])); } } @@ -918,7 +918,7 @@ namespace Cantera { // boundary and step0 points out of the allowed domain. In // this case, the Newton algorithm fails, so return an error // condition. - if (m_dampBound < 1.e-10) { + if (m_dampBound < 1.e-30) { if (loglevel > 1) printf("\t\t\tdampStep: At limits.\n"); return -3; } @@ -961,15 +961,17 @@ namespace Cantera { } m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); - if (m_normResidTrial < 1.0 || m_normResidTrial < m_normResid0) { + bool steepEnough = (m_normResidTrial < m_normResid0 * (0.9 * (1.0 - ff) * (1.0 - ff)* (1.0 - ff) + 0.1)); + + if (m_normResidTrial < 1.0 || steepEnough) { if (loglevel >= 5) { if (m_normResidTrial < 1.0) { printf("\t dampStep(): Current trial step and damping" " coefficient accepted because residTrial test step < 1:\n"); printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); - } else if (m_normResidTrial < m_normResid0) { + } else if (steepEnough) { printf("\t dampStep(): Current trial step and damping" - " coefficient accepted because resid0 > residTrial:\n"); + " coefficient accepted because resid0 > residTrial and steep enough:\n"); printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); } else { printf("\t dampStep(): Current trial step and damping" @@ -1179,6 +1181,11 @@ namespace Cantera { num_newt_its); } +#ifdef DEBUG_HKM + if (num_newt_its > 2) { + // printf("we are > 2\n"); + } +#endif // Check whether the Jacobian should be re-evaluated. forceNewJac = true; @@ -1202,6 +1209,7 @@ namespace Cantera { setColumnScales(); + doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 32aefe367..d3120195c 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -430,6 +430,11 @@ namespace Cantera { //! Soln Delta bounds magnitudes std::vector m_deltaBoundsMagnitudes; + //! Boolean indicating whether a manual delta steps have been input. + int m_manualDeltaStepSet; + + std::vector m_deltaStepMagnitudes; + std::vector m_y_n; std::vector m_y_nm1; From 154b234da902373e2b8a315fc67af91777bfa53e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 5 Nov 2010 19:44:05 +0000 Subject: [PATCH 288/446] Added a printout of the jacobian, when an ifdef block is turned on. --- Cantera/src/numerics/NonlinearSolver.cpp | 62 +++++++++++++++++------- 1 file changed, 45 insertions(+), 17 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index b02e910e7..a0eadc77e 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1491,6 +1491,11 @@ namespace Cantera { int i, j; double* col_j; doublereal ysave, ydotsave, dy; +#ifdef DEBUG_NUMJAC + bool print_NumJac = true; +#else + bool print_NumJac = false; +#endif /* * Clear the factor flag */ @@ -1500,10 +1505,6 @@ namespace Cantera { * Call the function to get a jacobian. */ m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); -#ifdef DEBUG_HKM - //doublereal dddd = J(89, 89); - //checkFinite(dddd); -#endif m_nJacEval++; m_nfe++; } else { @@ -1519,7 +1520,6 @@ namespace Cantera { m_nfe++; m_nJacEval++; - /* * Malloc a vector and call the function object to return a set of * deltaY's that are appropriate for calculating the numerical @@ -1528,18 +1528,17 @@ namespace Cantera { doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); - -#ifdef DEBUG_HKM - bool print_NumJac = false; + #ifdef DEBUG_NUMJAC if (print_NumJac) { - FILE *idy = fopen("NumJac.csv", "w"); - fprintf(idy, "Unk m_ewt y " - "dyVector ResN\n"); - for (int iii = 0; iii < neq_; iii++){ - fprintf(idy, " %4d %16.8e %16.8e %16.8e %16.8e \n", - iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); - } - fclose(idy); + if (m_print_flag >= 7 && print_NumJac ) { + if (neq_ < 20) { + printf("\t\tUnk m_ewt y dyVector ResN\n"); + for (int iii = 0; iii < neq_; iii++){ + printf("\t\t %4d %16.8e %16.8e %16.8e %16.8e \n", + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + } + } + } } #endif /* @@ -1584,7 +1583,6 @@ namespace Cantera { for (i = 0; i < neq_; i++) { diff = subtractRD(m_wksp[i], f[i]); col_j[i] = diff / dy; - //col_j[i] = (m_wksp[i] - f[i])/dy; } y[j] = ysave; if (solnType_ != NSOLN_TYPE_STEADY_STATE) { @@ -1597,8 +1595,38 @@ namespace Cantera { */ mdp::mdp_safe_free((void **) &dyVector); } +#ifdef DEBUG_NUMJAC + if (m_print_flag >= 7 && print_NumJac) { + if (neq_ < 30) { + printf("\t\tCurrent Matrix:\n"); + printf("\t\t I,J | "); + for (j = 0; j < neq_; j++) { + printf(" %5d ", j); + } + printf("\n"); + printf("\t\t --"); + for (j = 0; j < neq_; j++) { + printf("------------"); + } + printf("\n"); + for (i = 0; i < neq_; i++) { + printf("\t\t %4d |", i); + for (j = 0; j < neq_; j++) { + printf(" % 11.4E", J(i,j) ); + } + printf("\n"); + } + + printf("\t\t --"); + for (j = 0; j < neq_; j++) { + printf("------------"); + } + printf("\n"); + } + } +#endif } //==================================================================================================================== // Internal function to calculate the time derivative at the new step From 12b6f572e69678e1bc2a8bf6dd8d2a614affdfd2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 8 Nov 2010 22:22:13 +0000 Subject: [PATCH 289/446] Added in a new Residual evaluation type, Base_LaggedSolutionComponents, to properly handle Picard iterations within the damping algorithm. --- Cantera/src/numerics/NonlinearSolver.cpp | 8 ++++---- Cantera/src/numerics/NonlinearSolver.h | 5 ++++- Cantera/src/numerics/ResidJacEval.h | 9 ++++++++- 3 files changed, 16 insertions(+), 6 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index a0eadc77e..5595564f2 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -465,9 +465,9 @@ namespace Cantera { * @param ydot_curr Current value of the time derivative of the solution vector */ void NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, - const doublereal * const ydot_curr) + const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) { - m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), Base_ResidEval); + m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), evalType); m_nfe++; m_resid_scaled = false; } @@ -955,9 +955,9 @@ namespace Cantera { * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - doResidualCalc(time_curr, solnType_, y1, ydot1); + doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); } else { - doResidualCalc(time_curr, solnType_, y1, ydot0); + doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); } m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index d3120195c..6232f9c67 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -141,9 +141,12 @@ namespace Cantera { * @param typeCalc Type of the calculation * @param y_curr Current value of the solution vector * @param ydot_curr Current value of the time derivative of the solution vector + * @param evalType Base evalulation type + * Defaults to Base_ResidEval */ void doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, - const doublereal * const ydot_curr); + const doublereal * const ydot_curr, + const ResidEval_Type_Enum evalType = Base_ResidEval); //! Compute the undamped Newton step /*! diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 085c7fe02..ee4c2a7d0 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -38,7 +38,14 @@ namespace Cantera { /*! * We calculate this when we want to display a solution */ - Base_ShowSolution + Base_ShowSolution, + //! Base residual calculation containing any lagged components + /*! + * We use this to calculate residuals when doing line searches along + * directions determined by Jacobians that are missing contributions + * from lagged entries. + */ + Base_LaggedSolutionComponents }; //! Wrappers for the function evaluators for Nonlinear solvers and Time steppers From 813a98ddf17f0704b4a06c8ee31f96390506bb6e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 10 Nov 2010 01:39:48 +0000 Subject: [PATCH 290/446] Fixed the residual norm calculation. What was in there before was necessary but not sufficient. Since there is no good theory in tying the residual calculation to convergence short of calculating the condition number, I've made its magnitude a slave to the solution update magnitude. --- Cantera/src/numerics/NonlinearSolver.cpp | 75 +++++++++++++++--------- Cantera/src/numerics/NonlinearSolver.h | 16 ++++- 2 files changed, 62 insertions(+), 29 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 5595564f2..2c9ff4cd9 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -65,6 +65,12 @@ namespace Cantera { } bool NonlinearSolver::m_TurnOffTiming(false); + +#ifdef DEBUG_NUMJAC + bool NonlinearSolver::s_print_NumJac(true); +#else + bool NonlinearSolver::s_print_NumJac(false); +#endif //==================================================================================================================== // Default constructor /* @@ -113,7 +119,8 @@ namespace Cantera { atolBase_(1.0E-10), m_ydot_nm1(0), atolk_(0), - m_print_flag(0) + m_print_flag(0), + m_ScaleSolnNormToResNorm(0.001) { neq_ = m_func->nEquations(); @@ -182,7 +189,8 @@ namespace Cantera { atolBase_(1.0E-10), m_ydot_nm1(0), atolk_(0), - m_print_flag(0) + m_print_flag(0), + m_ScaleSolnNormToResNorm(0.001) { *this =operator=(right); } @@ -240,6 +248,7 @@ namespace Cantera { atolBase_ = right.atolBase_; atolk_ = right.atolk_; m_print_flag = right.m_print_flag; + m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; return *this; } @@ -547,8 +556,10 @@ namespace Cantera { for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 1.0/m_rowScales[irow]; - m_rowWtScales[irow] = 1.0/m_rowWtScales[irow]; + m_rowWtScales[irow] = m_rowWtScales[irow]; } + // What we have defined is a maximum value that the residual can be and still pass. + // This isn't sufficient. if (m_rowScaling) { @@ -568,6 +579,18 @@ namespace Cantera { } //==================================================================================================================== + void NonlinearSolver::calcSolnToResNormVector() + { + double oldVal = m_ScaleSolnNormToResNorm; + if (m_normSolnFRaw > 1.0E-13) { + m_ScaleSolnNormToResNorm = m_normResid0 / m_normSolnFRaw * oldVal; + } + m_normResid0 = m_normSolnFRaw; + computeResidWts(); + + //double tmp = residErrorNorm(DATA_PTR(m_resid)); + } + //==================================================================================================================== // Compute the undamped Newton step /* * Compute the undamped Newton step. The residual function is @@ -583,7 +606,7 @@ namespace Cantera { */ void NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) - { + { int irow; @@ -1181,11 +1204,7 @@ namespace Cantera { num_newt_its); } -#ifdef DEBUG_HKM - if (num_newt_its > 2) { - // printf("we are > 2\n"); - } -#endif + // Check whether the Jacobian should be re-evaluated. forceNewJac = true; @@ -1241,10 +1260,11 @@ namespace Cantera { } else { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); } - + calcSolnToResNormVector(); + // Damp the Newton step /* - * On return the recommended new solution and derivative is located in: + * On return the recommended new solution and derivatisve is located in: * m_y_new * m_y_dot_new * The estimate of the solution update norm for the next step is located in @@ -1278,6 +1298,10 @@ namespace Cantera { } } + + doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(ydot_new)); + + if (m_print_flag > 3) { residErrorNorm(DATA_PTR(m_resid), "Resulting Residual Norm", 10, DATA_PTR(y_new)); } @@ -1491,11 +1515,7 @@ namespace Cantera { int i, j; double* col_j; doublereal ysave, ydotsave, dy; -#ifdef DEBUG_NUMJAC - bool print_NumJac = true; -#else - bool print_NumJac = false; -#endif + /* * Clear the factor flag */ @@ -1528,9 +1548,9 @@ namespace Cantera { doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); - #ifdef DEBUG_NUMJAC - if (print_NumJac) { - if (m_print_flag >= 7 && print_NumJac ) { + + if (s_print_NumJac) { + if (m_print_flag >= 7) { if (neq_ < 20) { printf("\t\tUnk m_ewt y dyVector ResN\n"); for (int iii = 0; iii < neq_; iii++){ @@ -1540,7 +1560,7 @@ namespace Cantera { } } } -#endif + /* * Loop over the variables, formulating a numerical derivative * of the dense matrix. @@ -1595,8 +1615,8 @@ namespace Cantera { */ mdp::mdp_safe_free((void **) &dyVector); } -#ifdef DEBUG_NUMJAC - if (m_print_flag >= 7 && print_NumJac) { + + if (m_print_flag >= 7 && s_print_NumJac) { if (neq_ < 30) { printf("\t\tCurrent Matrix:\n"); printf("\t\t I,J | "); @@ -1626,7 +1646,7 @@ namespace Cantera { printf("\n"); } } -#endif + } //==================================================================================================================== // Internal function to calculate the time derivative at the new step @@ -1690,12 +1710,13 @@ namespace Cantera { { doublereal sum = 0.0; for (int i = 0; i < neq_; i++) { - m_residWts[i] = 1.0 / m_rowWtScales[i]; + m_residWts[i] =m_rowWtScales[i]; + sum += m_residWts[i]; } sum /= neq_; for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_residWts[i] + atolBase_ * sum; + m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * sum); } } //===================================================================================================================== @@ -1741,7 +1762,7 @@ namespace Cantera { } if (dampCode == 3) { if (s1 < 1.0E-2) { - if (m_normResidTrial < 1.0E-2) { + if (m_normResidTrial < 1.0E-6) { return 3; } } @@ -1753,7 +1774,7 @@ namespace Cantera { } if (dampCode == 4) { if (s1 < 1.0E-2) { - if (m_normResidTrial < 1.0E-2) { + if (m_normResidTrial < 1.0E-6) { return 3; } } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 6232f9c67..a09245728 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -370,7 +370,6 @@ namespace Cantera { */ void getResidWts(doublereal * const residWts) const; - //! Check to see if the nonlinear problem has converged /*! * @@ -408,7 +407,11 @@ namespace Cantera { * @param maxNewtIts Maximum number of newton iterations */ void setMaxNewtIts(const int maxNewtIts); - + + //! Calculate the scaling factor for translating residual norms into + //! solution norms. + void calcSolnToResNormVector(); + private: //! Pointer to the residual and jacobian evaluator for the @@ -591,12 +594,21 @@ namespace Cantera { */ int m_print_flag; + //! Scale factor for turning residual norms into solution norms + double m_ScaleSolnNormToResNorm; + public: //! Turn off printing of time /*! * Necessary to do for test suites */ static bool m_TurnOffTiming; + + // Turn on or off printing of the Jacobian + /*! + * + */ + static bool s_print_NumJac; }; } From 54e1280e08e596afa35d4044f3797dc965e859a6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 10 Nov 2010 05:01:22 +0000 Subject: [PATCH 291/446] Added hooks in for filters for New step directions and for new solutions. --- Cantera/src/numerics/NonlinearSolver.cpp | 45 +++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 18 ++++++---- Cantera/src/numerics/ResidJacEval.cpp | 17 ++++++++- Cantera/src/numerics/ResidJacEval.h | 14 +++++++- 4 files changed, 73 insertions(+), 21 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 2c9ff4cd9..9cc67f1ee 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -108,7 +108,6 @@ namespace Cantera { m_numTotalLinearSolves(0), m_numTotalNewtIts(0), m_min_newt_its(0), - filterNewstep(0), maxNewtIts_(100), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), @@ -178,7 +177,6 @@ namespace Cantera { m_numTotalLinearSolves(0), m_numTotalNewtIts(0), m_min_newt_its(0), - filterNewstep(0), maxNewtIts_(100), m_jacFormMethod(NSOLN_JAC_NUM), m_nJacEval(0), @@ -237,7 +235,6 @@ namespace Cantera { m_numTotalLinearSolves = right.m_numTotalLinearSolves; m_numTotalNewtIts = right.m_numTotalNewtIts; m_min_newt_its = right.m_min_newt_its; - filterNewstep = right.filterNewstep; maxNewtIts_ = right.maxNewtIts_; m_jacFormMethod = right.m_jacFormMethod; m_nJacEval = right.m_nJacEval; @@ -1261,6 +1258,12 @@ namespace Cantera { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); } calcSolnToResNormVector(); + + /* + * Filter out bad directions + */ + doublereal normFilter = filterNewStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(stp)); + // Damp the Newton step /* @@ -1328,7 +1331,7 @@ namespace Cantera { bool m_filterIntermediate = false; if (m_filterIntermediate) { if (m == 0) { - (void) filterNewStep(time_n, DATA_PTR(y_new), DATA_PTR(ydot_new)); + (void) filterNewSolution(time_n, DATA_PTR(y_new), DATA_PTR(ydot_new)); } } @@ -1592,7 +1595,7 @@ namespace Cantera { ydot[j] += dy * CJ; } /* - * Call the functon + * Call the function */ @@ -1618,17 +1621,17 @@ namespace Cantera { if (m_print_flag >= 7 && s_print_NumJac) { if (neq_ < 30) { - printf("\t\tCurrent Matrix:\n"); + printf("\t\tCurrent Matrix and Residual:\n"); printf("\t\t I,J | "); for (j = 0; j < neq_; j++) { printf(" %5d ", j); } - printf("\n"); + printf("| Residual \n"); printf("\t\t --"); for (j = 0; j < neq_; j++) { printf("------------"); } - printf("\n"); + printf("| -----------\n"); for (i = 0; i < neq_; i++) { @@ -1636,14 +1639,14 @@ namespace Cantera { for (j = 0; j < neq_; j++) { printf(" % 11.4E", J(i,j) ); } - printf("\n"); + printf(" | % 11.4E\n", f[i]); } printf("\t\t --"); for (j = 0; j < neq_; j++) { printf("------------"); } - printf("\n"); + printf("--------------\n"); } } @@ -1681,7 +1684,7 @@ namespace Cantera { } } //==================================================================================================================== - // Apply a filtering step + // Apply a filtering process to the new step /* * @param timeCurrent Current value of the time * @param y_current current value of the solution @@ -1689,8 +1692,24 @@ namespace Cantera { * * @return Returns the norm of the value of the amount filtered */ - doublereal NonlinearSolver::filterNewStep(const doublereal timeCurrent, doublereal * const y_current, doublereal *const ydot_current) { - return 0.0; + doublereal NonlinearSolver::filterNewStep(const doublereal timeCurrent, + const doublereal * const ybase, doublereal * const step0) { + doublereal tmp = m_func->filterNewStep(timeCurrent, ybase, step0); + return tmp; + } + //==================================================================================================================== + // Apply a filtering process to the new solution + /* + * @param timeCurrent Current value of the time + * @param y_current current value of the solution + * @param ydot_current Current value of the solution derivative. + * + * @return Returns the norm of the value of the amount filtered + */ + doublereal NonlinearSolver::filterNewSolution(const doublereal timeCurrent, + doublereal * const y_current, doublereal *const ydot_current) { + doublereal tmp = m_func->filterSolnPrediction(timeCurrent, y_current); + return tmp; } //==================================================================================================================== // Compute the Residual Weights diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index a09245728..65136e4c7 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -247,7 +247,16 @@ namespace Cantera { doublereal * const ydot, int num_newt_its); - //! Apply a filtering step + //! Apply a filtering process to the step + /*! + * @param timeCurrent Current value of the time + * @param ybase current value of the solution + * + * @return Returns the norm of the value of the amount filtered + */ + doublereal filterNewStep(const doublereal timeCurrent, const doublereal * const ybase, doublereal * const step0); + + //! Apply a filter to the solution /*! * @param timeCurrent Current value of the time * @param y_current current value of the solution @@ -255,8 +264,8 @@ namespace Cantera { * * @return Returns the norm of the value of the amount filtered */ - doublereal filterNewStep(const doublereal timeCurrent, doublereal * const y_current, doublereal * const ydot_current); - + doublereal filterNewSolution(const doublereal timeCurrent, doublereal * const y_current, doublereal * const ydot_current); + //! Return the factor by which the undamped Newton step 'step0' //! must be multiplied in order to keep the update within the bounds of an accurate jacobian. @@ -543,9 +552,6 @@ namespace Cantera { //! Minimum number of newton iterations to use int m_min_newt_its; - //! Boolean that turns on solution filtering - int filterNewstep; - //! Maximum number of newton iterations int maxNewtIts_; diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 220a64560..e27aa8db9 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -210,6 +210,20 @@ namespace Cantera { } //==================================================================================================================== // Filter the solution predictions + /* + * Codes might provide a predicted step change. This routine filters the predicted + * solution vector eliminating illegal directions. + * + * @param t Time (input) + * @param y Solution vector (input, output) + * @param step Proposed step in the solution that will be cropped + */ + doublereal ResidJacEval::filterNewStep(doublereal t, const doublereal * const ybase, doublereal * const step) + { + return 0.0; + } + //==================================================================================================================== + // Filter the solution predictions /* * Codes might provide a predicted solution vector. This routine filters the predicted * solution vector. @@ -217,8 +231,9 @@ namespace Cantera { * @param t Time (input) * @param y Solution vector (input, output) */ - void ResidJacEval::filterSolnPrediction(doublereal t, doublereal * const y) + doublereal ResidJacEval::filterSolnPrediction(doublereal t, doublereal * const y) { + return 0.0; } //==================================================================================================================== // Evalulate any stopping criteria other than a final time limit diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index ee4c2a7d0..7ddb4e0a9 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -132,6 +132,18 @@ namespace Cantera { */ virtual void getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot); + //! Filter the solution predictions + /*! + * Codes might provide a predicted step change. This routine filters the predicted + * solution vector eliminating illegal directions. + * + * @param t Time (input) + * @param y Solution vector (input, output) + * @param step Proposed step in the solution that will be cropped + */ + virtual doublereal filterNewStep(const doublereal t, const doublereal * const ybase, + doublereal * const step); + //! Filter the solution predictions /*! * Codes might provide a predicted solution vector. This routine filters the predicted @@ -140,7 +152,7 @@ namespace Cantera { * @param t Time (input) * @param y Solution vector (input, output) */ - virtual void filterSolnPrediction(const doublereal t, doublereal * const y); + virtual doublereal filterSolnPrediction(const doublereal t, doublereal * const y); //! Set a global value of the absolute tolerance /*! From 4942cf30aaf0bba719fe67fa9499aded69ebdfda Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 11 Nov 2010 00:17:45 +0000 Subject: [PATCH 292/446] Fixed issue #17. There was an obvious error in the THREAD_SAFE_CANTERA ifdef block compile. --- Cantera/src/thermo/VPSSMgrFactory.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/thermo/VPSSMgrFactory.cpp b/Cantera/src/thermo/VPSSMgrFactory.cpp index a237ec5db..3e2265e0d 100644 --- a/Cantera/src/thermo/VPSSMgrFactory.cpp +++ b/Cantera/src/thermo/VPSSMgrFactory.cpp @@ -210,7 +210,7 @@ namespace Cantera { void VPSSMgrFactory::deleteFactory() { #if defined(THREAD_SAFE_CANTERA) - boost::mutex::scoped_lock lock(species_thermo_mutex); + boost::mutex::scoped_lock lock(vpss_species_thermo_mutex); #endif if (s_factory) { delete s_factory; From 4eb6e622be8f7608a09ac4b66b34e37b9b5763bc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 12 Nov 2010 18:08:51 +0000 Subject: [PATCH 293/446] Fixed a compiler error on the THREAD_SAFE ifdef --- Cantera/src/base/misc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/base/misc.cpp b/Cantera/src/base/misc.cpp index 7f493ed82..5a6e48d0e 100644 --- a/Cantera/src/base/misc.cpp +++ b/Cantera/src/base/misc.cpp @@ -553,7 +553,7 @@ namespace Cantera { tmp_dir("."), xmlfiles(), m_sleep("1"), - pMessenger(0) + pMessenger() { #if !defined( THREAD_SAFE_CANTERA ) pMessenger = std::auto_ptr(new Messages()); From b6e1b14216460af027705a5ba51ca471e8c85ebe Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 12 Nov 2010 20:00:56 +0000 Subject: [PATCH 294/446] Deleted a file --- tools/testtools/.cvsignore | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 tools/testtools/.cvsignore diff --git a/tools/testtools/.cvsignore b/tools/testtools/.cvsignore deleted file mode 100644 index 96db0f094..000000000 --- a/tools/testtools/.cvsignore +++ /dev/null @@ -1,4 +0,0 @@ -*.csv -.depends -Makefile -csvdiff From c3405dad333c45c156e9f2f07ade6e4d804b3fd0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 12 Nov 2010 20:06:53 +0000 Subject: [PATCH 295/446] Added a file --- .../linux_64_gcc424_dbg_python264_numpy | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100755 docs/install_examples/linux_64_gcc424_dbg_python264_numpy diff --git a/docs/install_examples/linux_64_gcc424_dbg_python264_numpy b/docs/install_examples/linux_64_gcc424_dbg_python264_numpy new file mode 100755 index 000000000..d5e2effa5 --- /dev/null +++ b/docs/install_examples/linux_64_gcc424_dbg_python264_numpy @@ -0,0 +1,112 @@ +#!/bin/sh +# +# This is currently the test base. Meaning that the blessed versions +# of all test problems are created from this configuration. +# +CANTERA_CONFIG_PREFIX=${HOME}/arch/linux64_gcc424/cantera-1.8_Develop +export CANTERA_CONFIG_PREFIX + +SET_PYTHON_SITE_PACKAGE_TOPDIR=y +export SET_PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_SITE_PACKAGE_TOPDIR=$CANTERA_CONFIG_PREFIX +export PYTHON_SITE_PACKAGE_TOPDIR + +PYTHON_CMD=${HOME}/arch/linux64_gcc424/python-2.6.4/bin/python +export PYTHON_CMD + +PYTHON_PACKAGE='full' +#PYTHON_PACKAGE='minimal' +export PYTHON_PACKAGE + +DEBUG_MODE='y' +export DEBUG_MODE + +WITH_IDEAL_SOLUTIONS="y" +export WITH_IDEAL_SOLUTIONS + +WITH_ELECTROLYTES="y" +export WITH_ELECTROLYTES + +WITH_VCSNONIDEAL="y" +export WITH_VCSNONIDEAL + +WITH_H298MODIFY_CAPABILITY='y' +export WITH_H298MODIFY_CAPABILITY + +BUILD_MATLAB_TOOLBOX="y" +export BUILD_MATLAB_TOOLBOX + +INSTALL_BIN=config/install-sh +export INSTALL_BIN + +MATLAB_CMD="/usr/local/matlab/7.9/bin/matlab" +export MATLAB_CMD + +BUILD_F90_INTERFACE="y" +export BUILD_F90_INTERFACE + +NUMARRAY_HOME='' +export NUMARRAY_HOME + +USE_NUMPY='y' +export USE_NUMPY + +NUMPY_INC_DIR="${HOME}/arch/linux64_gcc424/python-2.6.4/lib/python2.6/site-packages/numpy/core/include" +export NUMPY_INC_DIR + +GRAPHVIZDIR=${HOME}'/arch/linux/bin' +export GRAPHVIZDIR + +# +# +USE_NUMERIC="n" +export USE_NUMERIC + +BUILD_WITH_F2C="n" +export BUILD_WITH_F2C + +BITCOMPILE="64" +export BITCOMPILE + +AFLAGS='DEBUG' + +CXX='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/g++' +export CXX + +CXX_DEPENDS='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/g++ -MM' +export CXX_DEPENDS + +CC='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/gcc' +export CC + +F77='/sierra/Sntools/extras/compilers/gcc-4.2.4/bin/gfortran' +export F77 + +CFLAGS="-g -Wall" +export CFLAGS + +CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL" +export CXXFLAGS + +FFLAGS="-g -DDEBUG_HKM -fno-second-underscore" +export FFLAGS + +LDFLAGS=' ' +export LDFLAGS + +LCXX_END_LIBS="-lgfortran " +export LCXX_END_LIBS + +EXTRA_LINK=" " +export EXTRA_LINK + +MAKE=gmake +export MAKE + +USE_SUNDIALS='y' +export USE_SUNDIALS +SUNDIALS_HOME='${HOME}/arch/linux64_gcc424/sundials-2.4.0_dbg' +export SUNDIALS_HOME + +./preconfig From 3e0d9cef21ccf854696baf58eefb95491d6d8821 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 12 Nov 2010 22:06:23 +0000 Subject: [PATCH 296/446] Fixed an error that crept in from the recent merge --- Cantera/cxx/include/Cantera.mak.in | 4 ---- 1 file changed, 4 deletions(-) diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in index c59840454..23c5114bd 100644 --- a/Cantera/cxx/include/Cantera.mak.in +++ b/Cantera/cxx/include/Cantera.mak.in @@ -25,10 +25,6 @@ in_CanteraBuildTree = 0 # CANTERA_VERSION=@ctversion@ # -CANTERA_VERSION=@ctversion@ - -CANTERA_VERSION=@ctversion@ - ############################################################################### # CANTERA CORE ############################################################################### From 1f53f7db72a4eac422e774dea68e8d59d7db75ad Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 15 Nov 2010 22:34:21 +0000 Subject: [PATCH 297/446] Fixed minimal python build. --- Makefile.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Makefile.in b/Makefile.in index ddc1a6679..623726454 100755 --- a/Makefile.in +++ b/Makefile.in @@ -206,8 +206,10 @@ ifneq ($(build_python),0) cp -f "@homedir@/setup_cantera" "@ct_bindir@" chmod +x @ct_bindir@/setup_cantera chmod +x @ct_bindir@/ctnew +ifeq ($(build_python),2) chmod +x @ct_bindir@/mixmaster endif +endif else # Commands to be executed for win systems cd Cantera/fortran/f77demos; sed s'/isentropic/ctlib/g' isentropic.dsp > ctlib.dsp From 2e50b8a929eeb43c8399cfb9748ad9935b2daa07 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 18 Nov 2010 03:09:45 +0000 Subject: [PATCH 298/446] Fixed an error. The m_speciesData XML tree wasn't being created. I created one in the constructor. --- Cantera/src/thermo/FixedChemPotSSTP.cpp | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/Cantera/src/thermo/FixedChemPotSSTP.cpp b/Cantera/src/thermo/FixedChemPotSSTP.cpp index e9d565e82..0f845b1f6 100644 --- a/Cantera/src/thermo/FixedChemPotSSTP.cpp +++ b/Cantera/src/thermo/FixedChemPotSSTP.cpp @@ -127,6 +127,23 @@ namespace Cantera { m_p0 = OneAtm; m_tlast = 298.15; setChemicalPotential(val); + + // Create an XML_Node entry for this species + XML_Node *s = new XML_Node("species", 0); + s->addAttribute("name", pname); + std::string aaS = Ename + ":1"; + s->addChild("atomArray", aaS); + XML_Node &tt = s->addChild("thermo"); + XML_Node &ss = tt.addChild("Simple"); + ss.addAttribute("Pref", "1 bar"); + ss.addAttribute("Tmax", "5000."); + ss.addAttribute("Tmin", "100."); + ss.addChild("t0", "298.15"); + ss.addChild("cp0", "0.0"); + std::string sval = fp2str(val); + ss.addChild("h", sval); + ss.addChild("s", "0.0"); + saveSpeciesData(0, s); } //==================================================================================================================== From 44e03fcf795f42587052b2c924ca97c24abea43b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 30 Nov 2010 15:33:50 +0000 Subject: [PATCH 299/446] Basic upgrade to the DenseMatrix Class. We've added a capability to change the handling of singular matrix conditions. Options exist to either throw an exception or return an error code. Options exist to print out a warning or to not print out anything. --- Cantera/src/numerics/DenseMatrix.cpp | 155 ++++++++++++++++++----- Cantera/src/numerics/DenseMatrix.h | 34 +++++ Cantera/src/numerics/NonlinearSolver.cpp | 37 ++++-- Cantera/src/numerics/NonlinearSolver.h | 8 +- Cantera/src/numerics/SquareMatrix.cpp | 30 +++-- 5 files changed, 208 insertions(+), 56 deletions(-) diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp index ae5376a77..89f6d7519 100644 --- a/Cantera/src/numerics/DenseMatrix.cpp +++ b/Cantera/src/numerics/DenseMatrix.cpp @@ -14,11 +14,16 @@ #include "utilities.h" #include "DenseMatrix.h" #include "stringUtils.h" +#include "global.h" namespace Cantera { //==================================================================================================================== // Default Constructor - DenseMatrix::DenseMatrix() + DenseMatrix::DenseMatrix() : + Array2D(0,0,0.0), + m_ipiv(0), + m_useReturnErrorCode(0), + m_printLevel(0) { } //==================================================================================================================== @@ -27,17 +32,23 @@ namespace Cantera { * all elements to \c v. */ DenseMatrix::DenseMatrix(int n, int m, doublereal v) : - Array2D(n, m, v) + Array2D(n, m, v), + m_ipiv(0), + m_useReturnErrorCode(0), + m_printLevel(0) { m_ipiv.resize(max(n, m)); } //==================================================================================================================== - // copy constructor + // Copy constructor /* * @param y Object to be copied */ DenseMatrix::DenseMatrix(const DenseMatrix& y) : - Array2D(y) + Array2D(y), + m_ipiv(0), + m_useReturnErrorCode(0), + m_printLevel(0) { m_ipiv = y.ipiv(); } @@ -47,6 +58,8 @@ namespace Cantera { if (&y == this) return *this; Array2D::operator=(y); m_ipiv = y.ipiv(); + m_useReturnErrorCode = y.m_useReturnErrorCode; + m_printLevel = y.m_printLevel; return *this; } //==================================================================================================================== @@ -86,56 +99,113 @@ namespace Cantera { } //==================================================================================================================== int solve(DenseMatrix& A, double* b) { + int info = 0; if (A.nColumns() != A.nRows()) { - throw CanteraError("DenseMatrix::solve", "Can only solve a square matrix"); + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, double* b): Can only solve a square matrix\n"); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, double* b)", "Can only solve a square matrix"); + } + return -1; } - int info=0; ct_dgetrf(static_cast(A.nRows()), static_cast(A.nColumns()), A.ptrColumn(0), //begin(), static_cast(A.nRows()), &A.ipiv()[0], info); if (info != 0) { if (info > 0) { - throw CanteraError("DenseMatrix::solve", + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, double* b): DGETRF returned INFO = %d U(i,i) is exactly zero. The factorization has" + " been completed, but the factor U is exactly singular, and division by zero will occur if " + "it is used to solve a system of equations.\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, double* b)", "DGETRF returned INFO = "+int2str(info) + ". U(i,i) is exactly zero. The factorization has" " been completed, but the factor U is exactly singular, and division by zero will occur if " "it is used to solve a system of equations."); - + } } else { - throw CanteraError("DenseMatrix::solve", + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, double* b): DGETRF returned INFO = %d. The argument i has an illegal value\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, double* b)", "DGETRF returned INFO = "+int2str(info) + ". The argument i has an illegal value"); + } } + return info; } ct_dgetrs(ctlapack::NoTranspose, static_cast(A.nRows()), 1, A.ptrColumn(0), //begin(), static_cast(A.nRows()), &A.ipiv()[0], b, static_cast(A.nColumns()), info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRS returned INFO = "+int2str(info)); - return 0; + if (info != 0) { + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, double* b): DGETRS returned INFO = %d\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, double* b)", "DGETRS returned INFO = "+int2str(info)); + } + } + return info; } //==================================================================================================================== int solve(DenseMatrix& A, DenseMatrix& b) { + int info = 0; if (A.nColumns() != A.nRows()) { - throw CanteraError("DenseMatrix::solve", "Can only solve a square matrix"); + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, DenseMatrix& b): Can only solve a square matrix\n"); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, DenseMatrix& b)", "Can only solve a square matrix"); + } + return -1; } - int info=0; ct_dgetrf(static_cast(A.nRows()), static_cast(A.nColumns()), A.ptrColumn(0), static_cast(A.nRows()), &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRF returned INFO = "+int2str(info)); + if (info != 0) { + if (info > 0) { + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, DenseMatrix& b): DGETRF returned INFO = %d U(i,i) is exactly zero. The factorization has" + " been completed, but the factor U is exactly singular, and division by zero will occur if " + "it is used to solve a system of equations.\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, DenseMatrix& b)", + "DGETRF returned INFO = "+int2str(info) + ". U(i,i) is exactly zero. The factorization has" + " been completed, but the factor U is exactly singular, and division by zero will occur if " + "it is used to solve a system of equations."); + } + } else { + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, DenseMatrix& b): DGETRF returned INFO = %d. The argument i has an illegal value\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, DenseMatrix& b)", + "DGETRF returned INFO = "+int2str(info) + ". The argument i has an illegal value"); + } + } + return info; + } + ct_dgetrs(ctlapack::NoTranspose, static_cast(A.nRows()), static_cast(b.nColumns()), A.ptrColumn(0), static_cast(A.nRows()), &A.ipiv()[0], b.ptrColumn(0), static_cast(b.nRows()), info); - if (info != 0) - throw CanteraError("DenseMatrix::solve", - "DGETRS returned INFO = "+int2str(info)); - return 0; + if (info != 0) { + if (A.m_printLevel) { + writelogf("solve(DenseMatrix& A, DenseMatrix& b): DGETRS returned INFO = %d\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("solve(DenseMatrix& A, DenseMatrix& b)", "DGETRS returned INFO = "+int2str(info)); + } + } + + return info; } //==================================================================================================================== @@ -155,10 +225,15 @@ namespace Cantera { static_cast(A.nRows()), b, static_cast(A.nColumns()), &s[0], //.begin(), rcond, rank, &work[0], work.size(), info); - if (info != 0) - throw CanteraError("DenseMatrix::leaseSquares", - "DGELSS returned INFO = "+int2str(info)); - return 0; + if (info != 0) { + if (A.m_printLevel) { + writelogf("leastSquares(): DGELSS returned INFO = %d\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("leastSquares()", "DGELSS returned INFO = " + int2str(info)); + } + } + return info; } #endif //==================================================================================================================== @@ -179,19 +254,29 @@ namespace Cantera { int info=0; ct_dgetrf(n, n, A.ptrColumn(0), static_cast(A.nRows()), &A.ipiv()[0], info); - if (info != 0) - throw CanteraError("invert", - "DGETRF returned INFO="+int2str(info)); + if (info != 0) { + if (A.m_printLevel) { + writelogf("invert(DenseMatrix& A, int nn): DGETRS returned INFO = %d\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("invert(DenseMatrix& A, int nn)", "DGETRS returned INFO = "+int2str(info)); + } + return info; + } vector_fp work(n); integer lwork = static_cast(work.size()); ct_dgetri(n, A.ptrColumn(0), static_cast(A.nRows()), - &A.ipiv()[0], - &work[0], lwork, info); - if (info != 0) - throw CanteraError("invert", - "DGETRI returned INFO="+int2str(info)); - return 0; + &A.ipiv()[0], &work[0], lwork, info); + if (info != 0) { + if (A.m_printLevel) { + writelogf("invert(DenseMatrix& A, int nn): DGETRS returned INFO = %d\n", info); + } + if (! A.m_useReturnErrorCode) { + throw CELapackError("invert(DenseMatrix& A, int nn)", "DGETRI returned INFO="+int2str(info)); + } + } + return info; } //==================================================================================================================== } diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index 6d43eaef4..c9d38af47 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -31,6 +31,22 @@ namespace Cantera { * */ + + //! Exception thrown when an LAPACK error is encountered associated with inverting or solving a matrix + class CELapackError : public CanteraError { + public: + + //! Constructor passes through to main Cantera error handler + /*! + * @param routine Name of calling routine + * @param msg Informative message + */ + CELapackError(std::string routine, std::string msg) : + CanteraError(routine + " LAPACK ERROR", msg) + { + } + + }; //! A class for full (non-sparse) matrices with Fortran-compatible //! data storage, which adds matrix operations to class Array2D. @@ -116,6 +132,24 @@ namespace Cantera { //! Vector of pivots. Length is equal to the max of m and n. vector_int m_ipiv; + + public: + //! Error Handling Flag + /*! + * The default is to set this to 0. In this case, if a factorization is requested and can't be achieved, + * a CESingularMatrix exception is triggered. No return code is used, because an exception is thrown. + * If this is set to 1, then an exception is not thrown. Routines return with an error code, that is up + * to the calling routine to handle correctly + */ + int m_useReturnErrorCode; + + //! Print Level + /*! + * Printing is done to the log file using the routine writelogf(). + * + * Level of printing that is carried out. Only error conditions are printed out, if this value is nonzero. + */ + int m_printLevel; }; //================================================================================================================== diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 9cc67f1ee..c0e65774c 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -601,8 +601,8 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. */ - void NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, - const doublereal * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) + int NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, + const doublereal * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) { int irow; @@ -625,7 +625,7 @@ namespace Cantera { * Solve the system -> This also involves inverting the * matrix */ - (void) jac.solve(DATA_PTR(delta_y)); + int info = jac.solve(DATA_PTR(delta_y)); /* @@ -681,6 +681,7 @@ namespace Cantera { #endif m_numTotalLinearSolves++; + return info; } //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() @@ -922,7 +923,7 @@ namespace Cantera { double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, int& num_backtracks) { - + int info = 0; int retnTrial = -2; // Compute the weighted norm of the undamped step size step0 doublereal s0 = solnErrorNorm(step0); @@ -1020,9 +1021,15 @@ namespace Cantera { // Compute the next undamped step, step1[], that would result if y1[] were accepted. // We now have two steps that we have calculated step0[] and step1[] if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); + info = doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); } else { - doNewtonSolve(time_curr, y1, ydot0, step1, jac, loglevel); + info = doNewtonSolve(time_curr, y1, ydot0, step1, jac, loglevel); + } + if (info) { + if (loglevel > 0) { + printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); + } + return -1; } // compute the weighted norm of step1 @@ -1133,11 +1140,13 @@ namespace Cantera { clockWC wc; int convRes = 0; solnType_ = SolnType; + int info = 0; bool m_residCurrent = false; int m = 0; bool forceNewJac = false; doublereal s1=1.e30; + // std::vector y_curr(neq_, 0.0); std::vector ydot_curr(neq_, 0.0); @@ -1161,6 +1170,11 @@ namespace Cantera { num_backtracks = 0; int i_backtracks; m_print_flag = loglevelInput; + if (m_print_flag > 1) { + jac.m_printLevel = 1; + } else { + jac.m_printLevel = 0; + } if (m_print_flag == 2 || m_print_flag == 3) { @@ -1249,8 +1263,11 @@ namespace Cantera { // compute the undamped Newton step - doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), jac, m_print_flag); - + info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), jac, m_print_flag); + if (info) { + m = -1; + goto done; + } if (m_print_flag > 3) { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); @@ -1262,7 +1279,7 @@ namespace Cantera { /* * Filter out bad directions */ - doublereal normFilter = filterNewStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(stp)); + filterNewStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(stp)); // Damp the Newton step @@ -1407,6 +1424,8 @@ namespace Cantera { printf("\t\tNonlinear problem solved successfully in %d its, time elapsed = %g sec\n", num_newt_its, time_elapsed); } + } else { + printf("\t\tNonlinear problem failed to solve after %d its\n", num_newt_its); } } return m; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 65136e4c7..21062cc8e 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -166,10 +166,12 @@ namespace Cantera { * @param y_current Current value of the solution * @param ydot_current Current value of the solution derivative. * + * @return returns the result code from lapack. A zero means success. Anything + * else indicates a failure. */ - void doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, - const doublereal * const ydot_curr, doublereal * const delta_y, - SquareMatrix& jac, int loglevel); + int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, + const doublereal * const ydot_curr, doublereal * const delta_y, + SquareMatrix& jac, int loglevel); //! Set default deulta bounds amounts diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 8b34c083f..41c7857cc 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -17,6 +17,7 @@ #include "stringUtils.h" #include "ctlapack.h" #include "SquareMatrix.h" +#include "global.h" #include #include @@ -56,7 +57,10 @@ namespace Cantera { * Check to see whether the matrix has been factored. */ if (!m_factored) { - factor(); + int retn = factor(); + if (retn) { + return retn; + } } /* * Solve the factored system @@ -64,10 +68,15 @@ namespace Cantera { ct_dgetrs(ctlapack::NoTranspose, static_cast(nRows()), 1, &(*(begin())), static_cast(nRows()), DATA_PTR(ipiv()), b, static_cast(nColumns()), info); - if (info != 0) - throw CanteraError("SquareMatrix::solve", - "DGETRS returned INFO = "+int2str(info)); - return 0; + if (info != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::solve(): DGETRS returned INFO = %d\n", info); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::solve()", "DGETRS returned INFO = " + int2str(info)); + } + } + return info; } /** @@ -96,11 +105,14 @@ namespace Cantera { ct_dgetrf(n, n, &(*(begin())), static_cast(nRows()), DATA_PTR(ipiv()), info); if (info != 0) { - cout << "Singular matrix, info = " << info << endl; - throw CanteraError("invert", - "DGETRF returned INFO="+int2str(info)); + if (m_printLevel) { + writelogf("SquareMatrix::factor(): DGETRS returned INFO = %d\n", info); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::factor()", "DGETRS returned INFO = "+int2str(info)); + } } - return 0; + return info; } /* * clear the factored flag From d5f44a5e6b959dc8a20effb07cb252e115b3a7fd Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 7 Dec 2010 18:05:25 +0000 Subject: [PATCH 300/446] ResidJacEval: Added in support for returning a failure condition from calcDeltaSolnVariables() NonLinearSolver: Added in support for returning a failure condition from bueler_jac(). Added in a call to return an editable bounds constraint vector. DenseMatrix: Added in comments about error handling from LAPACK routines. mdp_allo: Added in a new routine, mdp_zero_int_1 thermo.h electrolyteThermo.h Started to add in ifdef blocks. These are not handled correctly currently. --- Cantera/cxx/include/electrolyteThermo.h | 4 ++- Cantera/cxx/include/thermo.h | 29 +++++++++++++++++ Cantera/src/base/mdp_allo.cpp | 24 ++++++++++++++ Cantera/src/base/mdp_allo.h | 7 +++++ Cantera/src/numerics/DenseMatrix.h | 31 ++++++++++++++++++- Cantera/src/numerics/NonlinearSolver.cpp | 29 ++++++++++++----- Cantera/src/numerics/NonlinearSolver.h | 20 ++++++++++-- Cantera/src/numerics/ResidJacEval.cpp | 7 ++++- Cantera/src/numerics/ResidJacEval.h | 12 +++++-- docs/Cantera.cfg.in | 4 ++- .../linux.64_sierra_gcc444_python264_numpy | 3 +- 11 files changed, 153 insertions(+), 17 deletions(-) diff --git a/Cantera/cxx/include/electrolyteThermo.h b/Cantera/cxx/include/electrolyteThermo.h index cdd1db33c..aef557f24 100644 --- a/Cantera/cxx/include/electrolyteThermo.h +++ b/Cantera/cxx/include/electrolyteThermo.h @@ -9,8 +9,8 @@ #ifndef CT_ELECTROLYTETHERMO_INCL #define CT_ELECTROLYTETHERMO_INCL -#include "thermo.h" +#ifdef WITH_ELECTROLYTES #include "kernel/electrolytes.h" #include "kernel/MolalityVPSSTP.h" #include "kernel/VPStandardStateTP.h" @@ -26,3 +26,5 @@ #include "kernel/VPSSMgr_Water_HKFT.h" #include "kernel/VPSSMgr_Water_ConstVol.h" #endif + +#endif diff --git a/Cantera/cxx/include/thermo.h b/Cantera/cxx/include/thermo.h index a27b23336..5eff5eaea 100755 --- a/Cantera/cxx/include/thermo.h +++ b/Cantera/cxx/include/thermo.h @@ -14,4 +14,33 @@ #include "kernel/SurfPhase.h" #include "kernel/EdgePhase.h" + +#ifdef WITH_IDEAL_SOLUTIONS + +#include "kernel/GibbsExcessVPSSTP.h" +#include "kernel/MargulesVPSSTP.h" + +#endif + +#ifdef WITH_ELECTROLYTES + +#include "electrolyteThermo.h" + +#endif + + +#ifdef WITH_LATTICE_SOLID + +#include "kernel/LatticePhase.h" +#include "kernel/LatticeSolidPhase.h" + +#endif + +#ifdef WITH_PURE_FLUIDS + + +#endif + + + #endif diff --git a/Cantera/src/base/mdp_allo.cpp b/Cantera/src/base/mdp_allo.cpp index d650ed919..c1308049a 100644 --- a/Cantera/src/base/mdp_allo.cpp +++ b/Cantera/src/base/mdp_allo.cpp @@ -1697,6 +1697,30 @@ namespace mdp { (void) memset((void *)v, 0, len * sizeof(double)); } } + + /****************************************************************************/ + /****************************************************************************/ + /****************************************************************************/ + + void mdp_zero_int_1(int * const v, const int len) + + /************************************************************************** + * + * mdp_zero_int_1: + * + * Zeroes out an int vector + * + * Input + * ------------- + * v = Vector of values to be set to zero + * len = Length of the vector + **************************************************************************/ + { + if (len > 0) { + (void) memset((void *)v, 0, len * sizeof(int)); + } + } + /****************************************************************************/ /****************************************************************************/ /****************************************************************************/ diff --git a/Cantera/src/base/mdp_allo.h b/Cantera/src/base/mdp_allo.h index 756b6dce4..1b196bf3f 100644 --- a/Cantera/src/base/mdp_allo.h +++ b/Cantera/src/base/mdp_allo.h @@ -674,6 +674,13 @@ namespace mdp { */ extern void mdp_zero_dbl_1(double * const v , const int len); + //! Zeroes an int vector + /*! + * @param v = Vector of values to be assigned + * @param len = Length of the vector + */ + extern void mdp_zero_int_1(int * const v , const int len); + //! Assigns a single value to a double matrix. Contiguous data for the //! matrix is assumed. /*! diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index c9d38af47..04aac8f48 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -33,6 +33,10 @@ namespace Cantera { //! Exception thrown when an LAPACK error is encountered associated with inverting or solving a matrix + /*! + * A named error condition is used so that the calling code may differentiate this type of error + * from other error conditions. + */ class CELapackError : public CanteraError { public: @@ -48,12 +52,25 @@ namespace Cantera { }; - //! A class for full (non-sparse) matrices with Fortran-compatible + //! A class for full (non-sparse) matrices with Fortran-compatible //! data storage, which adds matrix operations to class Array2D. /*! * The dense matrix class adds matrix operations onto the Array2D class. * These matrix operations are carried out by the appropriate BLAS and LAPACK routines * + * Error handling from BLAS and LAPACK are handled via the following formulation. + * Depending on a variable, a singular matrix or other terminal error condition from + * LAPACK is handled by either throwing an exception of type, CELapackError, or by + * returning the error code condition to the calling routine. + * + * The int variable, m_useReturnErrorCode, determines which method is used. + * The default value of zero means that an exception is thrown. A value of 1 + * means that a return code is used. + * + * Reporting of these LAPACK error conditions is handled by the class variable + * m_printLevel. The default is for no reporting. If m_printLevel is nonzero, + * the error condition is reported to Cantera's log file. + * * @ingroup numerics */ class DenseMatrix : public Array2D { @@ -134,6 +151,7 @@ namespace Cantera { vector_int m_ipiv; public: + //! Error Handling Flag /*! * The default is to set this to 0. In this case, if a factorization is requested and can't be achieved, @@ -150,6 +168,17 @@ namespace Cantera { * Level of printing that is carried out. Only error conditions are printed out, if this value is nonzero. */ int m_printLevel; + + + // Listing of friend functions which are defined below + + friend int solve(DenseMatrix& A, double* b); + friend int solve(DenseMatrix& A, DenseMatrix& b); + friend int invert(DenseMatrix& A, int nn); +#ifdef INCL_LEAST_SQUARES + friend int leastSquares(DenseMatrix& A, double* b); +#endif + }; //================================================================================================================== diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index c0e65774c..b8df9939d 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -281,6 +281,14 @@ namespace Cantera { } } //==================================================================================================================== + std::vector & NonlinearSolver::lowBoundsConstraintVector() { + return m_y_low_bounds; + } + //==================================================================================================================== + std::vector & NonlinearSolver::highBoundsConstraintVector() { + return m_y_high_bounds; + } + //==================================================================================================================== // L2 norm of the delta of the solution vector /* * calculate the norm of the solution vector. This will @@ -1224,8 +1232,11 @@ namespace Cantera { if (m_print_flag > 3) { printf("\tsolve_nonlinear_problem(): Getting a new Jacobian and solving system\n"); } - beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), - num_newt_its); + info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), num_newt_its); + if (info == 0) { + m = -1; + goto done; + } m_residCurrent = true; } else { if (m_print_flag > 1) { @@ -1526,9 +1537,12 @@ namespace Cantera { * @param f = Right hand side. This routine returns the current * value of the rhs (output), so that it does * not have to be computed again. - * + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * 0 Means an unsuccessful operation */ - void NonlinearSolver::beuler_jac(SquareMatrix &J, doublereal * const f, + int NonlinearSolver::beuler_jac(SquareMatrix &J, doublereal * const f, doublereal time_curr, doublereal CJ, doublereal * const y, doublereal * const ydot, @@ -1537,7 +1551,7 @@ namespace Cantera { int i, j; double* col_j; doublereal ysave, ydotsave, dy; - + int retn = 1; /* * Clear the factor flag */ @@ -1568,7 +1582,8 @@ namespace Cantera { * derivative. */ doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); - m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); + retn = m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); + if (s_print_NumJac) { @@ -1668,7 +1683,7 @@ namespace Cantera { printf("--------------\n"); } } - + return retn; } //==================================================================================================================== // Internal function to calculate the time derivative at the new step diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 21062cc8e..08699226e 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -229,6 +229,11 @@ namespace Cantera { void setBoundsConstraints(const doublereal * const y_low_bounds, const doublereal * const y_high_bounds); + //! return an editable vector of the low bounds constraints + std::vector & lowBoundsConstraintVector(); + + //! return an editable vector of the high bounds constraints + std::vector & highBoundsConstraintVector(); //! Internal function to calculate the time derivative at the new step /*! @@ -238,13 +243,22 @@ namespace Cantera { */ void calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr); - //! Function called to evaluate the jacobian matrix and the curent - //! residual vector. + //! Function called to evaluate the jacobian matrix and the current + //! residual vector at the current time step /*! + * * + * @param J = Jacobian matrix to be filled in + * @param f = Right hand side. This routine returns the current + * value of the rhs (output), so that it does + * not have to be computed again. + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * 0 Means an unsuccessful operation * */ - void beuler_jac(SquareMatrix &J, doublereal * const f, + int beuler_jac(SquareMatrix &J, doublereal * const f, doublereal time_curr, doublereal CJ, doublereal * const y, doublereal * const ydot, int num_newt_its); diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index e27aa8db9..b1ae4edf1 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -172,8 +172,12 @@ namespace Cantera { * @param ydot Rate of change of solution vector. (input, do not modify) * @param delta_y Value of the delta to be used in calculating the numerical jacobian * @param solnWeights Value of the solution weights that are used in determining convergence (default = 0) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * 0 Means an unsuccessful operation */ - void ResidJacEval:: + int ResidJacEval:: calcDeltaSolnVariables(const doublereal t, const doublereal * const ySoln, const doublereal * const ySolnDot, doublereal * const deltaYSoln, const doublereal *const solnWeights) @@ -187,6 +191,7 @@ namespace Cantera { deltaYSoln[i] = fmaxx(1.0E-2 * solnWeights[i], 1.0E-6 * fabs(ySoln[i])); } } + return 1; } //==================================================================================================================== // Returns a vector of column scale factors that can be used to column scale Jacobians. diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 7ddb4e0a9..e1b1fc069 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -138,8 +138,10 @@ namespace Cantera { * solution vector eliminating illegal directions. * * @param t Time (input) - * @param y Solution vector (input, output) + * @param ybase Solution vector (input, output) * @param step Proposed step in the solution that will be cropped + * + * @return Return the norm of the amount of filtering */ virtual doublereal filterNewStep(const doublereal t, const doublereal * const ybase, doublereal * const step); @@ -151,6 +153,8 @@ namespace Cantera { * * @param t Time (input) * @param y Solution vector (input, output) + * + * @return Return the norm of the amount of filtering */ virtual doublereal filterSolnPrediction(const doublereal t, doublereal * const y); @@ -205,8 +209,12 @@ namespace Cantera { * @param ydot Rate of change of solution vector. (input, do not modify) * @param delta_y Value of the delta to be used in calculating the numerical jacobian * @param solnWeights Value of the solution weights that are used in determining convergence (default = 0) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void + virtual int calcDeltaSolnVariables(const doublereal t, const doublereal * const y, const doublereal * const ydot, diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index e73623793..a732ce226 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -792,7 +792,9 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ WaterTransport.h \ WaterTransport.cpp \ DenseMatrix.h \ - DenseMatrix.cpp + DenseMatrix.cpp \ + ResidJacEval.h \ + ResidJacEval.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. diff --git a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy index dc66fcce8..30e9e8181 100755 --- a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy +++ b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy @@ -86,7 +86,8 @@ export F77 CFLAGS="-g -Wall" export CFLAGS -CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL" +#CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL -DDEBUG_NUMJAC" +CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL " export CXXFLAGS FFLAGS="-g -DDEBUG_HKM -fno-second-underscore" From ec8bbc5be23ff189a96997d258023d4056e24cb9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 14 Dec 2010 23:56:12 +0000 Subject: [PATCH 301/446] Fixed the help section to be in line with what the code actually does. --- tools/testtools/csvdiff.cpp | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/tools/testtools/csvdiff.cpp b/tools/testtools/csvdiff.cpp index 3ea8e1183..9d6df04a2 100644 --- a/tools/testtools/csvdiff.cpp +++ b/tools/testtools/csvdiff.cpp @@ -9,7 +9,6 @@ * $Name: $ *====================================================================*/ /* - * * csvdiff File1.csv File2.csv * * Compares the variable values in two Excel formatted @@ -24,9 +23,10 @@ * -h = prints this usage information * * Shell Return Values - * 1 = Comparison was successful - * 0 = One or more nodal values failed the comparison - * -1 = Apples to oranges, the files can not even be compared against + * 0 = Comparison was successful + * 1 = One or more nodal values failed the comparison + * 2 = One or more of the header values failed the comparison + * 3 = Apples to oranges, the files can not even be compared against * one another. */ @@ -616,9 +616,10 @@ static void print_usage() { printf("\t -r rtol = Set relative tolerance parameter - default = 1.0E-3\n"); printf("\t\n"); printf("\t Shell Return Values:\n"); - printf("\t 1 = Comparison was successful\n"); - printf("\t 0 = One or more nodal values failed the comparison\n"); - printf("\t -1 = Apples to oranges, the files can not even be compared against\n"); + printf("\t 0 = Comparison was successful\n"); + printf("\t 1 = One or more nodal values failed the comparison\n"); + printf("\t 2 = One or more header values failed the comparison\n"); + printf("\t 3 = Apples to oranges, the files can not even be compared against\n"); printf("\t one another.\n"); printf("\t\n"); } From 73d8df7f4c8bfdc3bc4d780af31d78e5485bda1c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 15 Dec 2010 02:15:27 +0000 Subject: [PATCH 302/446] Tightend up the tolerances on the nonlinear solvers. --- Cantera/src/numerics/NonlinearSolver.cpp | 14 ++++++++++++-- Cantera/src/numerics/RootFind.cpp | 2 +- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index b8df9939d..596d44cda 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -394,11 +394,21 @@ namespace Cantera { { int i; doublereal sum_norm = 0.0, error; + for (i = 0; i < neq_; i++) { +#ifdef DEBUG_HKM + mdp::checkFinite(resid[i]); +#endif error = resid[i] / m_residWts[i]; +#ifdef DEBUG_HKM + mdp::checkFinite(error); +#endif sum_norm += (error * error); } sum_norm = sqrt(sum_norm / neq_); +#ifdef DEBUG_HKM + mdp::checkFinite(sum_norm); +#endif if (printLargest) { const int num_entries = printLargest; doublereal dmax1, normContrib; @@ -588,7 +598,7 @@ namespace Cantera { { double oldVal = m_ScaleSolnNormToResNorm; if (m_normSolnFRaw > 1.0E-13) { - m_ScaleSolnNormToResNorm = m_normResid0 / m_normSolnFRaw * oldVal; + m_ScaleSolnNormToResNorm = 1.0E-2 * m_normResid0 / m_normSolnFRaw * oldVal; } m_normResid0 = m_normSolnFRaw; computeResidWts(); @@ -1769,7 +1779,7 @@ namespace Cantera { } sum /= neq_; for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * sum); + m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * atolBase_ * sum); } } //===================================================================================================================== diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index efbda6b34..0bc16bd9d 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -224,7 +224,7 @@ namespace Cantera { if (x1 == 0.0) { x2 = 0.00001 * (xmax - xmin); } else { - x2 = x1 * 1.01; + x2 = x1 * 1.0001; } if (x2 > xmax) { x2 = x1 - (xmax - xmin) / 100.; From e10fa97af025eb6371f575a067388cc512152e71 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 15 Dec 2010 02:54:08 +0000 Subject: [PATCH 303/446] Added the phaseIsStable idea --- Cantera/src/kinetics/InterfaceKinetics.cpp | 30 ++++++++ Cantera/src/kinetics/InterfaceKinetics.h | 85 ++++++++++++++++++++-- 2 files changed, 108 insertions(+), 7 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 6b6f60c9d..3ad664d24 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -92,6 +92,7 @@ namespace Cantera { m_has_exchange_current_density_formulation(false), m_phaseExistsCheck(false), m_phaseExists(0), + m_phaseIsStable(0), m_rxnPhaseIsReactant(0), m_rxnPhaseIsProduct(0), m_ioFlag(0) @@ -140,6 +141,7 @@ namespace Cantera { m_has_exchange_current_density_formulation(false), m_phaseExistsCheck(false), m_phaseExists(0), + m_phaseIsStable(0), m_rxnPhaseIsReactant(0), m_rxnPhaseIsProduct(0), m_ioFlag(0) @@ -208,6 +210,7 @@ namespace Cantera { m_has_exchange_current_density_formulation = right.m_has_exchange_current_density_formulation; m_phaseExistsCheck = right.m_phaseExistsCheck; m_phaseExists = right.m_phaseExists; + m_phaseIsStable = right.m_phaseIsStable; m_rxnPhaseIsReactant.resize(m_ii, 0); m_rxnPhaseIsProduct.resize(m_ii, 0); @@ -753,6 +756,12 @@ namespace Cantera { } } } + if (m_rxnPhaseIsReactant[j][p]) { + if (! m_phaseIsStable[p]) { + ropnet[j] = 0.0; + ropr[j] = ropf[j]; + } + } } } else if ((ropf[j] > ropr[j]) && (ropf[j] > 0.0)) { for (int p = 0; p < nPhases(); p++) { @@ -772,6 +781,12 @@ namespace Cantera { } } } + if (m_rxnPhaseIsProduct[j][p]) { + if (! m_phaseIsStable[p]) { + ropnet[j] = 0.0; + ropf[j] = ropr[j]; + } + } } } } @@ -1229,6 +1244,7 @@ namespace Cantera { void InterfaceKinetics::addPhase(thermo_t &thermo) { Kinetics::addPhase(thermo); m_phaseExists.push_back(true); + m_phaseIsStable.push_back(true); } //================================================================================================ /** @@ -1358,14 +1374,28 @@ namespace Cantera { if (!m_phaseExists[iphase]) { m_phaseExistsCheck--; m_phaseExists[iphase] = true; + m_phaseIsStable[iphase] = true; } } else { if (m_phaseExists[iphase]) { m_phaseExistsCheck++; m_phaseExists[iphase] = false; + m_phaseIsStable[iphase] = false; } } } + //================================================================================================ + + void InterfaceKinetics::setPhaseStability(const int iphase, const bool isStable) { + if (iphase < 0 || iphase >= (int) m_thermo.size()) { + throw CanteraError("InterfaceKinetics:setPhaseStability", "out of bounds"); + } + if (isStable) { + m_phaseIsStable[iphase] = true; + } else { + m_phaseIsStable[iphase] = false; + } + } //================================================================================================ void EdgeKinetics::finalize() { m_rwork.resize(nReactions()); diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 9c8c4ac5c..82f30bd4c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -73,12 +73,38 @@ namespace Cantera { }; - /// - /// A kinetics manager for heterogeneous reaction mechanisms. The - /// reactions are assumed to occur at a 2D interface between two - /// 3D phases. - /// - /// @ingroup chemkinetics + + //! A kinetics manager for heterogeneous reaction mechanisms. The + //! reactions are assumed to occur at a 2D interface between two 3D phases. + /*! + * + * There are some important additions to the behavior of the kinetics class due to the + * presence of multiple phases and a heterogeneous interface. If a reactant phase + * doesn't exists, i.e., has a mole number of zero, a heterogeneous reaction can not + * proceed from reactants to products. Note it could perhaps proceed from products to + * reactants if all of the product phases exist. + * + * In order to make the determination of whether a phase exists or not actually involves + * the specification of additional information to the kinetics object., which heretofore + * has only had access to intrinsic field information about the phases (i.e., temperature + * pressure, and mole fraction). + * + * The extrinsic specification of whether a phase exists or not must be specified on top of the + * intrinsic calculation of the reaction rate. This routine carries a set of + * booleans indicating whether a phase in the heterogeneous mechanism exists or not. + * + * Additionally, the routine carries a set of booleans around indicating whether a product + * phase is stable or not. If a phase is not thermodynamically stable, it may be the case that + * a particular reaction in a heterogeneous mechanism will create a product species in the + * unstable phase. However, other reactions in the mechanism will destruct that species. + * This may cause oscillations in the formation of the unstable phase from time step to time + * step within a ODE solver, in practice. In order to avoid this situation, a set of + * booleans is tracked which sets the stability of a phase. If a phase is deemed to be unstable, + * then species in that phase will not be allowed to be birthed by the kinetics operator. + * Nonexistent phases are deemed to be unstable by default, but this can be changed. + * + * @ingroup chemkinetics + */ class InterfaceKinetics : public Kinetics { public: @@ -557,13 +583,34 @@ namespace Cantera { /*! * Tell the kinetics object whether a phase in the object exists. * This is actually an extrinsic specification that must be carried out on top of the - * intrinsic calculation of the reaction rate + * intrinsic calculation of the reaction rate. + * The routine will also flip the IsStable boolean within the kinetics object as well. * * @param iphase Index of the phase. This is the order within the internal thermo vector object * @param exists Boolean indicating whether the phase exists or not */ void setPhaseExistence(const int iphase, const bool exists); + + //! Set the stability of a phase in the reaction object + /*! + * Tell the kinetics object whether a phase in the object is stable. Species in an unstable phase + * will not be allowed to have a positive rate of formation from this kinetics object. + * This is actually an extrinsic specification that must be carried out on top of the + * intrinsic calculation of the reaction rate. + * + * While conceptually not needed since kinetics is consistent with thermo when taken as a whole, + * in practice it has found to be very useful to turn off the creation of phases which shouldn't + * be forming. Typically thais can reduce the oscillations in phase formation and destruction + * which are observed. + * + * @param iphase Index of the phase. This is the order within the internal thermo vector object + * @param exists Boolean indicating whether the phase exists or not + */ + void setPhaseStability(const int iphase, const bool isStable); + + + protected: //! Temporary work vector of length m_kk @@ -795,7 +842,31 @@ namespace Cantera { */ std::vector m_phaseExists; + //! Vector of booleans indicating whether phases are stable or not + /*! + * Vector of booleans indicating whether a phase is stable or not + * under the current conditions. + * We use this to set the ROP's so that unphysical things don't happen + * + * length = number of phases in the object + * By default all phases are stable + */ + std::vector m_phaseIsStable; + + //! Vector of vector of booleans indicating whether a phase participates in a + //! reaction as a reactant + /*! + * m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p + * participates in reaction j as a reactant. + */ std::vector m_rxnPhaseIsReactant; + + //! Vector of vector of booleans indicating whether a phase participates in a + //! reaction as a product + /*! + * m_rxnPhaseIsReactant[j][p] indicates whether a species in phase p + * participates in reaction j as a product. + */ std::vector m_rxnPhaseIsProduct; int m_ioFlag; From 32816b1fa79044f8ad6b19408f66096dda897d6e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 15 Dec 2010 20:20:13 +0000 Subject: [PATCH 304/446] Incremental commit of new ability to determine phase stability without actually solving the equilibrium equations. --- Cantera/src/equil/Makefile.in | 2 +- Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 202 +++++++++++++++-- Cantera/src/equil/vcs_MultiPhaseEquil.h | 47 +++- Cantera/src/equil/vcs_equilibrate.cpp | 72 +++++- Cantera/src/equil/vcs_solve.cpp | 2 - Cantera/src/equil/vcs_solve.h | 7 +- .../src/equil/vcs_solve_phaseStability.cpp | 212 ++++++++++++++++++ 7 files changed, 519 insertions(+), 25 deletions(-) create mode 100644 Cantera/src/equil/vcs_solve_phaseStability.cpp diff --git a/Cantera/src/equil/Makefile.in b/Cantera/src/equil/Makefile.in index 363c44348..0cdec0ecd 100644 --- a/Cantera/src/equil/Makefile.in +++ b/Cantera/src/equil/Makefile.in @@ -74,7 +74,7 @@ VCSNONIDEAL_OBJ = vcs_solve_TP.o vcs_VolPhase.o vcs_solve.o vcs_prob.o \ vcs_root1d.o vcs_rxnadj.o \ vcs_SpeciesProperties.o vcs_equilibrate.o \ vcs_prep.o vcs_species_thermo.o vcs_Gibbs.o vcs_phaseStability.o \ - $(DALT_OBJ) + vcs_solve_phaseStability.o $(DALT_OBJ) VCSNONIDEAL_H = vcs_internal.h vcs_VolPhase.h vcs_solve.h vcs_prob.h \ vcs_IntStarStar.h vcs_DoubleStarStar.h vcs_defs.h \ diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index 387a83f1e..f4b0a3b7c 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -42,7 +42,7 @@ using namespace std; //using namespace VCSnonideal; namespace VCSnonideal { - + //==================================================================================================================== vcs_MultiPhaseEquil::vcs_MultiPhaseEquil() : m_vprob(0), @@ -51,7 +51,7 @@ namespace VCSnonideal { m_vsolvePtr(0) { } - + //==================================================================================================================== vcs_MultiPhaseEquil::vcs_MultiPhaseEquil(mix_t* mix, int printLvl) : m_vprob(0), m_mix(0), @@ -89,7 +89,7 @@ namespace VCSnonideal { m_vsolvePtr = 0; } } - + //==================================================================================================================== int vcs_MultiPhaseEquil::equilibrate_TV(int XY, doublereal xtarget, int estimateEquil, int printLvl, doublereal err, @@ -209,7 +209,7 @@ namespace VCSnonideal { return iSuccess; } - + //==================================================================================================================== int vcs_MultiPhaseEquil::equilibrate_HP(doublereal Htarget, int XY, double Tlow, double Thigh, int estimateEquil, @@ -359,7 +359,7 @@ namespace VCSnonideal { done:; return iSuccess; } - + //==================================================================================================================== int vcs_MultiPhaseEquil::equilibrate_SP(doublereal Starget, double Tlow, double Thigh, int estimateEquil, @@ -515,7 +515,7 @@ namespace VCSnonideal { done:; return iSuccess; } - + //==================================================================================================================== /* * Equilibrate the solution using the current element abundances @@ -566,7 +566,7 @@ namespace VCSnonideal { } return iSuccess; } - + //==================================================================================================================== /* * Equilibrate the solution using the current element abundances */ @@ -733,7 +733,7 @@ namespace VCSnonideal { } - + //==================================================================================================================== /************************************************************************** * * @@ -905,7 +905,7 @@ namespace VCSnonideal { static void print_char(const char letter, const int num) { for (int i = 0; i < num; i++) plogf("%c", letter); } - + //==================================================================================================================== /* * * @@ -1299,7 +1299,7 @@ namespace VCSnonideal { return VCS_SUCCESS; } - + //==================================================================================================================== // Transfer the current state of mphase into the VCS_PROB object /* * The basic problem has already been set up. @@ -1421,7 +1421,7 @@ namespace VCSnonideal { return VCS_SUCCESS; } - + //==================================================================================================================== // This routine hasn't been checked yet void vcs_MultiPhaseEquil::getStoichVector(index_t rxn, Cantera::vector_fp& nu) { int nsp = m_vsolvePtr->m_numSpeciesTot; @@ -1442,7 +1442,7 @@ namespace VCSnonideal { } } - + //==================================================================================================================== int vcs_MultiPhaseEquil::numComponents() const { int nc = -1; if (m_vsolvePtr) { @@ -1450,7 +1450,7 @@ namespace VCSnonideal { } return nc; } - + //==================================================================================================================== int vcs_MultiPhaseEquil::numElemConstraints() const { int nec = -1; if (m_vsolvePtr) { @@ -1459,11 +1459,185 @@ namespace VCSnonideal { return nec; } - + //==================================================================================================================== int vcs_MultiPhaseEquil::component(int m) const { int nc = numComponents(); if (m < nc) return m_vsolvePtr->m_speciesMapIndex[m]; else return -1; } + //==================================================================================================================== + // Determine the phase stability of a phase at the current conditions + /* + * Equilibration of the solution is not done before the determination is made. + * + * @param iph Phase number to determine the equilibrium. If the phase + * has a non-zero mole number.... + * + * @param funcStab Value of the phase pop function + * + * @param printLvl Determines the amount of printing that + * gets sent to stdout from the vcs package + * (Note, you may have to compile with debug + * flags to get some printing). + * + * @param loglevel Determines the amount of printing to the HTML + * output file. + */ + int vcs_MultiPhaseEquil::determine_PhaseStability(int iph, double &funcStab, int printLvl, int loglevel) { + + + clockWC tickTock; + int nsp = m_mix->nSpecies(); + int nel = m_mix->nElements(); + int nph = m_mix->nPhases(); + if (m_vprob == 0) { + m_vprob = new VCS_PROB(nsp, nel, nph); + } + m_printLvl = printLvl; + m_vprob->m_printLvl = printLvl; + + /* + * Extract the current state information + * from the MultiPhase object and + * Transfer it to VCS_PROB object. + */ + int res = vcs_Cantera_update_vprob(m_mix, m_vprob); + if (res != 0) { + plogf("problems\n"); + } + + + + // Check obvious bounds on the temperature and pressure + // NOTE, we may want to do more here with the real bounds + // given by the ThermoPhase objects. + double T = m_mix->temperature(); + if (T <= 0.0) { + throw CanteraError("vcs_MultiPhaseEquil::determine_PhaseStability", + "Temperature less than zero on input"); + } + double pres = m_mix->pressure(); + if (pres <= 0.0) { + throw CanteraError("vcs_MultiPhaseEquil::determine_PhaseStability", + "Pressure less than zero on input"); + } + + beginLogGroup("vcs_MultiPhaseEquil::determine_PhaseStability", loglevel); + addLogEntry("problem type", "fixed T,P"); + addLogEntry("Temperature", T); + addLogEntry("Pressure", pres); + + + /* + * Print out the problem specification from the point of + * view of the vprob object. + */ + m_vprob->prob_report(m_printLvl); + + /* + * Call the thermo Program + */ + int ip1 = m_printLvl; + if (m_printLvl >= 3) { + ip1 = m_printLvl - 2; + } else { + ip1 = 0; + } + if (!m_vsolvePtr) { + m_vsolvePtr = new VCS_SOLVE(); + } + double feStable; + int iStable = m_vsolvePtr->vcs_PS(m_vprob, iph, printLvl, feStable); + + /* + * Transfer the information back to the MultiPhase object. + * Note we don't just call setMoles, because some multispecies + * solution phases may be zeroed out, and that would cause a problem + * for that routine. Also, the mole fractions of such zereod out + * phases actually contain information about likely reemergent + * states. + */ + m_mix->uploadMoleFractionsFromPhases(); + int kGlob = 0; + for (int ip = 0; ip < m_vprob->NPhase; ip++) { + double phaseMole = 0.0; + Cantera::ThermoPhase &tref = m_mix->phase(ip); + int nspPhase = tref.nSpecies(); + for (int k = 0; k < nspPhase; k++, kGlob++) { + phaseMole += m_vprob->w[kGlob]; + } + //phaseMole *= 1.0E-3; + m_mix->setPhaseMoles(ip, phaseMole); + } + + double te = tickTock.secondsWC(); + if (printLvl > 0) { + plogf("\n Results from vcs_PS:\n"); + + plogf("\n"); + plogf("Temperature = %g Kelvin\n", m_vprob->T); + plogf("Pressure = %g Pa\n", m_vprob->PresPA); + std::string sss = m_mix->phaseName(iph); + if (iStable) { + plogf("Phase %d named %s is stable, function value = %g > 0\n", iph, sss.c_str(), feStable); + } else { + plogf("Phase %d named %s is not stable + function value = %g < 0\n", iph, sss.c_str(), feStable); + } + plogf("\n"); + plogf("----------------------------------------" + "---------------------\n"); + plogf(" Name Mole_Number"); + if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_MKS) { + plogf("(kmol)"); + } else { + plogf("(gmol)"); + } + plogf(" Mole_Fraction Chem_Potential"); + if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_KCALMOL) + plogf(" (kcal/mol)\n"); + else if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_UNITLESS) + plogf(" (Dimensionless)\n"); + else if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_KJMOL) + plogf(" (kJ/mol)\n"); + else if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_KELVIN) + plogf(" (Kelvin)\n"); + else if (m_vprob->m_VCS_UnitsFormat == VCS_UNITS_MKS) + plogf(" (J/kmol)\n"); + plogf("-------------------------------------------------------------\n"); + for (int i = 0; i < m_vprob->nspecies; i++) { + plogf("%-12s", m_vprob->SpName[i].c_str()); + if (m_vprob->SpeciesUnknownType[i] == VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { + plogf(" %15.3e %15.3e ", 0.0, m_vprob->mf[i]); + plogf("%15.3e\n", m_vprob->m_gibbsSpecies[i]); + } else { + plogf(" %15.3e %15.3e ", m_vprob->w[i], m_vprob->mf[i]); + if (m_vprob->w[i] <= 0.0) { + int iph = m_vprob->PhaseID[i]; + vcs_VolPhase *VPhase = m_vprob->VPhaseList[iph]; + if (VPhase->nSpecies() > 1) { + plogf(" -1.000e+300\n"); + } else { + plogf("%15.3e\n", m_vprob->m_gibbsSpecies[i]); + } + } else { + plogf("%15.3e\n", m_vprob->m_gibbsSpecies[i]); + } + } + } + plogf("------------------------------------------" + "-------------------\n"); + if (printLvl > 2) { + if (m_vsolvePtr->m_timing_print_lvl > 0) { + plogf("Total time = %12.6e seconds\n", te); + } + } + } + if (loglevel > 0) { + endLogGroup(); + } + return iStable; + } +//==================================================================================================================== + } diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.h b/Cantera/src/equil/vcs_MultiPhaseEquil.h index c090c5a7c..699b6e46a 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.h +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.h @@ -154,7 +154,7 @@ namespace Cantera { * themselves. Two other thermodynamic quantities, determined by the * XY string, are held constant during the equilibration. * - * @param s The object to set to an equilibrium state + * @param s The MultiPhase object to be set to an equilibrium state * * @param ixy An integer specifying the two properties to be held * constant. @@ -205,6 +205,30 @@ namespace Cantera { doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS, int maxiter = 100, int loglevel = -99); + //! Determine the phase stability of a single phase given the current conditions + //! in a MultiPhase object + /*! + * + * @param s The MultiPhase object to be set to an equilibrium state + * @param iphase Phase index within the multiphase object to be + * tested for stability. + * @param funcStab Function value that tests equilibrium. > 0 indicates stable + * < 0 indicates unstable + * + * @param printLvl Determines the amount of printing that + * gets sent to stdout from the vcs package + * (Note, you may have to compile with debug + * flags to get some printing). + * + * @param loglevel Controls amount of diagnostic output. loglevel + * = 0 suppresses diagnostics, and increasingly-verbose + * messages are written as loglevel increases. The + * messages are written to a file in HTML format for viewing + * in a web browser. @see HTML_logs + */ + int vcs_determine_PhaseStability(MultiPhase& s, int iphase, + double &funcStab, int printLvl, int loglevel); + } namespace VCSnonideal { @@ -540,6 +564,22 @@ namespace VCSnonideal { int printLvl = 0, doublereal err = 1.0E-6, int maxsteps = VCS_MAXSTEPS, int loglevel = -99); + //! Determine the phase stability of a phase at the current conditions + /*! + * Equilibration of the solution is not done before the determination is made. + * + * @param iph Phase number to determine the equilibrium. If the phase + * has a non-zero mole number.... + * @param funcStab Value of the phase pop function + * @param printLvl Determines the amount of printing that + * gets sent to stdout from the vcs package + * (Note, you may have to compile with debug + * flags to get some printing). + * @param loglevel Determines the amount of printing to the HTML + * output file. + */ + int determine_PhaseStability(int iph, double &funcStab, int printLvl= 0, int logLevel = -99); + //! Report the equilibrium answer in a comma separated table format /*! * This routine is used for in the test suite. @@ -563,6 +603,8 @@ namespace VCSnonideal { */ int numElemConstraints() const; + + // Friend functions friend int vcs_Cantera_to_vprob(Cantera::MultiPhase *mphase, @@ -638,8 +680,7 @@ namespace VCSnonideal { //! Pointer to the object that does all of the equilibration work. /*! * VCS_SOLVE will have different ordering for species and element constraints - * than this object or the VCS_PROB object. - * This object owns the pointer. + * than this object or the VCS_PROB object. This object owns the pointer. */ VCSnonideal::VCS_SOLVE *m_vsolvePtr; diff --git a/Cantera/src/equil/vcs_equilibrate.cpp b/Cantera/src/equil/vcs_equilibrate.cpp index ed46e6c14..03692c6b5 100644 --- a/Cantera/src/equil/vcs_equilibrate.cpp +++ b/Cantera/src/equil/vcs_equilibrate.cpp @@ -327,10 +327,8 @@ namespace Cantera { if (solver == 2) { try { - VCSnonideal::vcs_MultiPhaseEquil *eqsolve = - new VCSnonideal::vcs_MultiPhaseEquil(&s, printLvlSub); - int err = eqsolve->equilibrate(ixy, estimateEquil, printLvlSub, - tol, maxsteps, loglevel); + VCSnonideal::vcs_MultiPhaseEquil *eqsolve = new VCSnonideal::vcs_MultiPhaseEquil(&s, printLvlSub); + int err = eqsolve->equilibrate(ixy, estimateEquil, printLvlSub, tol, maxsteps, loglevel); if (err != 0) { retn = -1; addLogEntry("vcs_equilibrate Error - ", err); @@ -386,4 +384,70 @@ namespace Cantera { } return retn; } + + //==================================================================================================================== + // Determine the phase stability of a single phase given the current conditions + // in a MultiPhase object + /* + * + * @param s The MultiPhase object to be set to an equilibrium state + * @param iphase Phase index within the multiphase object to be + * tested for stability. + * @param funcStab Function value that tests equilibrium. > 0 indicates stable + * < 0 indicates unstable + * + * @param printLvl Determines the amount of printing that + * gets sent to stdout from the vcs package + * (Note, you may have to compile with debug + * flags to get some printing). + * + * @param loglevel Controls amount of diagnostic output. loglevel + * = 0 suppresses diagnostics, and increasingly-verbose + * messages are written as loglevel increases. The + * messages are written to a file in HTML format for viewing + * in a web browser. @see HTML_logs + */ + int vcs_determine_PhaseStability(MultiPhase& s, int iphase, + double &funcStab, int printLvl, int loglevel) + { + int iStab = 0; + static int counter = 0; + beginLogGroup("PhaseStability",loglevel); + addLogEntry("multiphase phase stability function"); + beginLogGroup("arguments"); + addLogEntry("iphase",iphase); + addLogEntry("loglevel",loglevel); + endLogGroup("arguments"); + + int printLvlSub = MAX(0, printLvl-1); + + s.init(); + try { + VCSnonideal::vcs_MultiPhaseEquil *eqsolve = new VCSnonideal::vcs_MultiPhaseEquil(&s, printLvlSub); + iStab = eqsolve->determine_PhaseStability(iphase, funcStab, printLvlSub, loglevel); + if (iStab != 0) { + addLogEntry("Phase is stable - ", iphase); + } else { + addLogEntry("Phase is not stable - ", iphase); + } + endLogGroup("PhaseStability"); + // hard code a csv output file. + if (printLvl > 0) { + string reportFile = "vcs_phaseStability.csv"; + if (counter > 0) { + reportFile = "vcs_phaseStability_" + int2str(counter) + ".csv"; + } + eqsolve->reportCSV(reportFile); + counter++; + } + delete eqsolve; + } + catch (CanteraError &e) { + addLogEntry("Failure.", lastErrorMessage()); + endLogGroup("equilibrate"); + throw e; + } + return iStab; + } + //==================================================================================================================== } diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 6331ef942..dc790bb28 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -411,9 +411,7 @@ namespace VCSnonideal { * a 2x2 Newton's method, using loops over vcs_TP() to * calculate the residual and Jacobian) */ - iconv = vcs_TP(ipr, ip1, maxit, vprob->T, vprob->PresPA); - /* * If requested to print anything out, go ahead and do so; diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 6da5b2358..cc47b2061 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -147,6 +147,9 @@ public: */ int vcs_solve_TP(int print_lvl, int printDetails, int maxit); + + int vcs_PS(VCS_PROB *vprob, int iph, int printLvl, double &feStable); + void vcs_reinsert_deleted(int kspec); //! Choose the optimum species basis for the calculations @@ -550,6 +553,7 @@ public: */ int vcs_popPhaseRxnStepSizes(const int iphasePop); + //! Calculates formation reaction step sizes. /*! * This is equation 6.4-16, p. 143 in Smith and Missen. @@ -681,7 +685,8 @@ public: * have. */ double vcs_birthGuess(const int kspec); - + + int vcs_solve_phaseStability(const int iphase, int ifunc, double &funcval, int print_lvl); //! Main program to test whether a deleted phase should be brought //! back into existence diff --git a/Cantera/src/equil/vcs_solve_phaseStability.cpp b/Cantera/src/equil/vcs_solve_phaseStability.cpp new file mode 100644 index 000000000..5244414c8 --- /dev/null +++ b/Cantera/src/equil/vcs_solve_phaseStability.cpp @@ -0,0 +1,212 @@ +/** + * @file vcs_solve_TP.cpp Implementation file that contains the + * main algorithm for finding an equilibrium + */ +/* + * $Id: vcs_solve_TP.cpp 626 2010-10-28 01:33:54Z hkmoffa $ + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +#include +#include +#include +#include + +#include "vcs_solve.h" +#include "vcs_internal.h" +#include "vcs_VolPhase.h" +#include "vcs_species_thermo.h" +#include "vcs_prob.h" + +#include "clockWC.h" + +#ifdef WIN32 +#pragma warning(disable:4996) +#endif + +using namespace std; + +namespace VCSnonideal { + + + int VCS_SOLVE::vcs_PS(VCS_PROB *vprob, int iphase, int printLvl, double &feStable) { + + /* + * ifunc determines the problem type + */ + int ifunc = 0; + int iStab = 0; + + + + if (ifunc < 0 || ifunc > 2) { + plogf("vcs: Unrecognized value of ifunc, %d: bailing!\n", + ifunc); + return VCS_PUB_BAD; + } + + /* + * This function is called to copy the public data + * and the current problem specification + * into the current object's data structure. + */ + int retn = vcs_prob_specifyFully(vprob); + if (retn != 0) { + plogf("vcs_pub_to_priv returned a bad status, %d: bailing!\n", + retn); + return retn; + } + /* + * Prep the problem data + * - adjust the identity of any phases + * - determine the number of components in the problem + */ + retn = vcs_prep_oneTime(printLvl); + if (retn != 0) { + plogf("vcs_prep_oneTime returned a bad status, %d: bailing!\n", + retn); + return retn; + } + + + /* + * This function is called to copy the current problem + * into the current object's data structure. + */ + retn = vcs_prob_specify(vprob); + if (retn != 0) { + plogf("vcs_prob_specify returned a bad status, %d: bailing!\n", + retn); + return retn; + } + + + /* + * Prep the problem data for this particular instantiation of + * the problem + */ + retn = vcs_prep(); + if (retn != VCS_SUCCESS) { + plogf("vcs_prep returned a bad status, %d: bailing!\n", retn); + return retn; + } + /* + * Check to see if the current problem is well posed. + */ + if (!vcs_wellPosed(vprob)) { + plogf("vcs has determined the problem is not well posed: Bailing\n"); + return VCS_PUB_BAD; + } + + + int iconv; + /* + * Store the temperature and pressure in the private global variables + */ + m_temperature = vprob->T; + m_pressurePA = vprob->PresPA; + /* + * Evaluate the standard state free energies + * at the current temperatures and pressures. + */ + iconv = vcs_evalSS_TP(printLvl, printLvl, m_temperature, m_pressurePA); + + /* + * Prepare the problem data: + * ->nondimensionalize the free energies using + * the divisor, R * T + */ + vcs_nondim_TP(); + /* + * Prep the fe field + */ + vcs_fePrep_TP(); + + /* + * Solve the problem at a fixed Temperature and Pressure + * (all information concerning Temperature and Pressure has already + * been derived. The free energies are now in dimensionless form.) + */ + double funcVal; + iStab = vcs_solve_phaseStability(iphase, ifunc, funcVal, printLvl); + + + /* + * Redimensionalize the free energies using + * the reverse of vcs_nondim to add back units. + */ + vcs_redim_TP(); + /* + * Return the convergence success flag. + */ + return iStab; + + + } + //==================================================================================================================== + // Routine that independently determines whether a phase should be popped + // under the current conditions. + /* + * This is the main routine that solves for equilibrium at constant T and P + * using a variant of the VCS method. Nonideal phases can be accommodated + * as well. + * + * Any number of single-species phases and multi-species phases + * can be handled by the present version. + * + * Input + * ------------ + * @param print_lvl 1 -> Print results to standard output + * 0 -> don't report on anything + * + * @param printDetails 1 -> Print intermediate results. + * + * @param maxit Maximum number of iterations for the algorithm + * + * @return 0 = Equilibrium Achieved + * 1 = Range space error encountered. The element abundance criteria are + * only partially satisfied. Specifically, the first NC= (number of + * components) conditions are satisfied. However, the full NE + * (number of elements) conditions are not satisfied. The equilibrirum + * condition is returned. + * -1 = Maximum number of iterations is exceeded. Convergence was not + * found. + */ + int VCS_SOLVE::vcs_solve_phaseStability(const int iph, const int ifunc, + double &funcVal, + int printLv) { + int retn = 0; + double test = -1.0E-10; + int usedZeroedSpecies; + std::vector phasePopPhaseIDs(0); + int iphasePop; + int iStab = 0; + + std::vector sm(m_numElemConstraints*m_numElemConstraints, 0.0); + std::vector ss(m_numElemConstraints, 0.0); + std::vector sa(m_numElemConstraints, 0.0); + + std::vector aw(m_numSpeciesTot, 0.0); + std::vector wx(m_numElemConstraints, 0.0); + + + retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa), + VCS_DATA_PTR(sm), VCS_DATA_PTR(ss), + test, &usedZeroedSpecies); + phasePopPhaseIDs.clear(); + iphasePop = vcs_popPhaseID(phasePopPhaseIDs); + funcVal = vcs_phaseStabilityTest(iph); + if (funcVal > 0.0) { + iStab = 1; + } else { + iStab = 0; + } + + return iStab; + } + +} From fc7b7e8dc6a9400d04ad62bc08a515b3eb1d315b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 16 Dec 2010 22:44:29 +0000 Subject: [PATCH 305/446] Initial attempt at exposing the phase stability routine to the outside without actually doing an equilibrium solution. --- Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 28 +++++++-------- Cantera/src/equil/vcs_solve.cpp | 2 +- Cantera/src/equil/vcs_solve.h | 6 ++-- Cantera/src/equil/vcs_solve_TP.cpp | 6 ++-- .../src/equil/vcs_solve_phaseStability.cpp | 36 +++++++++++++++++-- 5 files changed, 52 insertions(+), 26 deletions(-) diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index f4b0a3b7c..aa7eac6e6 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -1559,18 +1559,14 @@ namespace VCSnonideal { * states. */ m_mix->uploadMoleFractionsFromPhases(); - int kGlob = 0; - for (int ip = 0; ip < m_vprob->NPhase; ip++) { - double phaseMole = 0.0; - Cantera::ThermoPhase &tref = m_mix->phase(ip); - int nspPhase = tref.nSpecies(); - for (int k = 0; k < nspPhase; k++, kGlob++) { - phaseMole += m_vprob->w[kGlob]; - } - //phaseMole *= 1.0E-3; - m_mix->setPhaseMoles(ip, phaseMole); - } - + for (int i = 0; i < m_vprob->nspecies; i++) { + plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); + } + m_mix->getChemPotentials(DATA_PTR(m_vprob->m_gibbsSpecies)); + for (int i = 0; i < m_vprob->nspecies; i++) { + plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); + } + double te = tickTock.secondsWC(); if (printLvl > 0) { plogf("\n Results from vcs_PS:\n"); @@ -1615,11 +1611,11 @@ namespace VCSnonideal { if (m_vprob->w[i] <= 0.0) { int iph = m_vprob->PhaseID[i]; vcs_VolPhase *VPhase = m_vprob->VPhaseList[iph]; - if (VPhase->nSpecies() > 1) { - plogf(" -1.000e+300\n"); - } else { + //if (VPhase->nSpecies() > 1) { + // plogf(" -1.000e+300\n"); + //} else { plogf("%15.3e\n", m_vprob->m_gibbsSpecies[i]); - } + //} } else { plogf("%15.3e\n", m_vprob->m_gibbsSpecies[i]); } diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index dc790bb28..3f52c273c 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -896,7 +896,7 @@ namespace VCSnonideal { retn = VCS_PUB_BAD; } - if (vPhase->PhaseName == pub_phase_ptr->PhaseName) { + if (vPhase->PhaseName != pub_phase_ptr->PhaseName) { plogf("%sPhaseName value have changed:%s %s\n", yo.c_str(), vPhase->PhaseName.c_str(), pub_phase_ptr->PhaseName.c_str()); diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index cc47b2061..954bfebda 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -1257,16 +1257,16 @@ private: * the mole numbers of the component species. Therefore the following * approximation is valid for a small component of an ideal phase: * - * 0 = m_deltaGrxn_old(I) + log(molNum_new(I)/molNum_old(I)) + * 0 = m_deltaGRxn_old(I) + log(molNum_new(I)/molNum_old(I)) * - * m_deltaGrxn_old contains the contribution from + * m_deltaGRxn_old contains the contribution from * * m_feSpecies_old(I) = * m_SSfeSpecies(I) + * log(ActCoeff[i] * molNum_old(I) / m_tPhaseMoles_old(iph)) * Thus, * - * molNum_new(I)= molNum_old(I) * EXP(-m_deltaGrxn_old(I)) + * molNum_new(I)= molNum_old(I) * EXP(-m_deltaGRxn_old(I)) * * Most of this section is mainly restricting the update to reasonable * values. diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 2772202f7..1f4eaf3e3 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -2015,16 +2015,16 @@ namespace VCSnonideal { * the mole numbers of the component species. Therefore the following * approximation is valid for a small component of an ideal phase: * - * 0 = m_deltaGrxn_old(I) + log(molNum_new(I)/molNum_old(I)) + * 0 = m_deltaGRxn_old(I) + log(molNum_new(I)/molNum_old(I)) * - * m_deltaGrxn_old contains the contribution from + * m_deltaGRxn_old contains the contribution from * * m_feSpecies_old(I) = * m_SSfeSpecies(I) + * log(ActCoeff[i] * molNum_old(I) / m_tPhaseMoles_old(iph)) * Thus, * - * molNum_new(I)= molNum_old(I) * EXP(-m_deltaGrxn_old(I)) + * molNum_new(I)= molNum_old(I) * EXP(-m_deltaGRxn_old(I)) * * Most of this section is mainly restricting the update to reasonable * values. diff --git a/Cantera/src/equil/vcs_solve_phaseStability.cpp b/Cantera/src/equil/vcs_solve_phaseStability.cpp index 5244414c8..f3e6b35de 100644 --- a/Cantera/src/equil/vcs_solve_phaseStability.cpp +++ b/Cantera/src/equil/vcs_solve_phaseStability.cpp @@ -41,7 +41,16 @@ namespace VCSnonideal { int ifunc = 0; int iStab = 0; - + /* + * This function is called to create the private data + * using the public data. + */ + int nspecies0 = vprob->nspecies + 10; + int nelements0 = vprob->ne; + int nphase0 = vprob->NPhase; + + vcs_initSizes(nspecies0, nelements0, nphase0); + if (ifunc < 0 || ifunc > 2) { plogf("vcs: Unrecognized value of ifunc, %d: bailing!\n", @@ -131,8 +140,7 @@ namespace VCSnonideal { * (all information concerning Temperature and Pressure has already * been derived. The free energies are now in dimensionless form.) */ - double funcVal; - iStab = vcs_solve_phaseStability(iphase, ifunc, funcVal, printLvl); + iStab = vcs_solve_phaseStability(iphase, ifunc, feStable, printLvl); /* @@ -140,6 +148,23 @@ namespace VCSnonideal { * the reverse of vcs_nondim to add back units. */ vcs_redim_TP(); + + /* + vcs_VolPhase *Vphase = m_VolPhaseList[iphase]; + + std::vector mfPop = Vphase->moleFractions(); + int nsp = Vphase->nSpecies(); + + vcs_VolPhase *VPphase = vprob->VPhaseList[iphase]; + int kstart = Vphase->spGlobalIndexVCS(0); + for (int k = 0; k < nsp; k++) { + vprob->mf[kstart + k] = mfPop[k]; + } + VPphase->setMoleFractionsState(Vphase->totalMoles(), + VCS_DATA_PTR(Vphase->moleFractions()), + VCS_STATECALC_TMP); + */ + vcs_prob_update(vprob); /* * Return the convergence success flag. */ @@ -197,6 +222,11 @@ namespace VCSnonideal { retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa), VCS_DATA_PTR(sm), VCS_DATA_PTR(ss), test, &usedZeroedSpecies); + + + vcs_dfe(VCS_STATECALC_OLD, 0, 0, m_numSpeciesRdc); + vcs_deltag(0, true, VCS_STATECALC_OLD); + phasePopPhaseIDs.clear(); iphasePop = vcs_popPhaseID(phasePopPhaseIDs); funcVal = vcs_phaseStabilityTest(iph); From 8c4d47f59cefb20fab2d99b25674fc295aad9ac3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 18 Dec 2010 18:26:16 +0000 Subject: [PATCH 306/446] Fixed an error in the phase stability calculation --- Cantera/src/equil/vcs_VolPhase.cpp | 4 + Cantera/src/equil/vcs_VolPhase.h | 2 + Cantera/src/equil/vcs_phaseStability.cpp | 13 +- Cantera/src/equil/vcs_solve.h | 21 +- Cantera/src/equil/vcs_solve_TP.cpp | 209 +++++++++++++++++- .../src/equil/vcs_solve_phaseStability.cpp | 11 +- 6 files changed, 242 insertions(+), 18 deletions(-) diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 51d4515a0..664544779 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -507,6 +507,10 @@ namespace VCSnonideal { const std::vector & vcs_VolPhase::moleFractions() const { return Xmol_; } + + double vcs_VolPhase::moleFraction(int k) const { + return Xmol_[k]; + } /***************************************************************************/ // Set the moles and/or mole fractions within the phase diff --git a/Cantera/src/equil/vcs_VolPhase.h b/Cantera/src/equil/vcs_VolPhase.h index 03715db1e..15cd25d3c 100644 --- a/Cantera/src/equil/vcs_VolPhase.h +++ b/Cantera/src/equil/vcs_VolPhase.h @@ -419,6 +419,8 @@ namespace VCSnonideal { //! object. const std::vector & moleFractions() const; + double moleFraction(int klocal) const; + //! Sets the creationMoleNum's within the phase object /*! * @param F_k Pointer to a vector of n_k's diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index 997bbf830..6d323da8c 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -671,7 +671,7 @@ namespace VCSnonideal { vector fracDelta_old(Vphase->nSpecies(), 0.0); vector fracDelta_raw(Vphase->nSpecies(), 0.0); vector creationGlobalRxnNumbers(Vphase->nSpecies(), -1); - + vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_Deficient), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); vector m_feSpecies_Deficient(m_numComponents, 0.0); doublereal damp = 1.0; @@ -779,18 +779,16 @@ namespace VCSnonideal { Vphase->sendToVCS_ActCoeff(VCS_STATECALC_OLD, VCS_DATA_PTR(m_actCoeffSpecies_new)); /* - * first Calculate altered chemical potentials for component species + * First calculate altered chemical potentials for component species * belonging to this phase. */ for (i = 0; i < (int) componentList.size(); i++) { kc = componentList[i]; kc_spec = Vphase->spGlobalIndexVCS(kc); if ( X_est[kc] > VCS_DELETE_MINORSPECIES_CUTOFF) { - m_feSpecies_Deficient[kc_spec] = m_feSpecies_old[kc_spec] - + log(m_actCoeffSpecies_new[kc_spec] * X_est[kc]); + m_feSpecies_Deficient[kc_spec] = m_feSpecies_old[kc_spec] + log(m_actCoeffSpecies_new[kc_spec] * X_est[kc]); } else { - m_feSpecies_Deficient[kc_spec] = m_feSpecies_old[kc_spec] - + log(m_actCoeffSpecies_new[kc_spec] * VCS_DELETE_MINORSPECIES_CUTOFF); + m_feSpecies_Deficient[kc_spec] = m_feSpecies_old[kc_spec] + log(m_actCoeffSpecies_new[kc_spec] * VCS_DELETE_MINORSPECIES_CUTOFF); } } @@ -807,8 +805,7 @@ namespace VCSnonideal { } double *dtmp_ptr = m_stoichCoeffRxnMatrix[irxn]; if (dtmp_ptr[kc_spec] != 0.0) { - m_deltaGRxn_Deficient[irxn] += - dtmp_ptr[kc_spec] * (m_feSpecies_Deficient[kc_spec]- m_feSpecies_old[kc_spec]); + m_deltaGRxn_Deficient[irxn] += dtmp_ptr[kc_spec] * (m_feSpecies_Deficient[kc_spec]- m_feSpecies_old[kc_spec]); } } diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index 954bfebda..daf952d26 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -495,13 +495,20 @@ public: */ void vcs_dfe(const int stateCalc, const int ll, const int lbot, const int ltop); + //! Print out a table of chemical potentials + /*! + * @param vcsState Determines where to get the mole numbers from. + * - VCS_STATECALC_OLD -> from m_molNumSpecies_old + * - VCS_STATECALC_NEW -> from m_molNumSpecies_new + */ + void vcs_printSpeciesChemPot(const int stateCalc) const; + //! This routine uploads the state of the system into all of the //! vcs_VolumePhase objects in the current problem. /*! * @param vcsState Determines where to get the mole numbers from. * - VCS_STATECALC_OLD -> from m_molNumSpecies_old * - VCS_STATECALC_NEW -> from m_molNumSpecies_new - * */ void vcs_updateVP(const int stateCalc); @@ -621,6 +628,8 @@ public: void vcs_deltag(const int l, const bool doDeleted, const int vcsState, const bool alterZeroedPhases = true); + void vcs_printDeltaG(const int stateCalc); + //! Calculate deltag of formation for all species in a single phase. /*! * Calculate deltag of formation for all species in a single @@ -1618,8 +1627,10 @@ public: //! Last deltag[irxn] from the previous step std::vector m_deltaGRxn_old; - //! Last deltag[irxn] from the previous step with additions for - //! possible births of zeroed phases. + //! Last deltag[irxn] from the previous step with additions for possible births of zeroed phases for component species + /*! + * + */ std::vector m_deltaGRxn_Deficient; //! Temporary vector of Rxn DeltaG's @@ -1684,10 +1695,10 @@ public: std::vector m_tPhaseMoles_new; //! Temporary vector of length NPhase - std::vector m_TmpPhase; + mutable std::vector m_TmpPhase; //! Temporary vector of length NPhase - std::vector m_TmpPhase2; + mutable std::vector m_TmpPhase2; //! Change in the total moles in each phase /*! diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 1f4eaf3e3..7dfc0d821 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -4371,10 +4371,10 @@ namespace VCSnonideal { feSpecies[kspec] = m_SSfeSpecies[kspec] + log(actCoeff_ptr[kspec] * VCS_DELETE_MINORSPECIES_CUTOFF) - tlogMoles[m_phaseID[kspec]] - m_lnMnaughtSpecies[kspec] - + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iphase]; ; + + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iphase]; } else { feSpecies[kspec] = m_SSfeSpecies[kspec] - m_lnMnaughtSpecies[kspec] - + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iphase]; ; + + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iphase]; } } else { feSpecies[kspec] = m_SSfeSpecies[kspec] @@ -4438,7 +4438,93 @@ namespace VCSnonideal { } } } + + } + //==================================================================================================================== + // Print out a table of chemical potentials + /* + * @param vcsState Determines where to get the mole numbers from. + * - VCS_STATECALC_OLD -> from m_molNumSpecies_old + * - VCS_STATECALC_NEW -> from m_molNumSpecies_new + */ + void VCS_SOLVE::vcs_printSpeciesChemPot(const int stateCalc) const { + double mfValue = 1.0; + bool zeroedPhase = false; + int kspec; + + const double * molNum = VCS_DATA_PTR(m_molNumSpecies_old); + const double * tPhMoles_ptr = VCS_DATA_PTR(m_tPhaseMoles_old); + const double * actCoeff_ptr = VCS_DATA_PTR(m_actCoeffSpecies_old); + if (stateCalc == VCS_STATECALC_NEW) { + tPhMoles_ptr = VCS_DATA_PTR(m_tPhaseMoles_new); + actCoeff_ptr = VCS_DATA_PTR(m_actCoeffSpecies_new); + molNum = VCS_DATA_PTR(m_molNumSpecies_new); + } + + double * tMoles = VCS_DATA_PTR(m_TmpPhase); + const double *tPhInertMoles = VCS_DATA_PTR(TPhInertMoles); + for (int iph = 0; iph < m_numPhases; iph++) { + tMoles[iph] = tPhInertMoles[iph]; + } + for (kspec = 0; kspec < m_numSpeciesTot; kspec++) { + if(m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { + int iph = m_phaseID[kspec]; + tMoles[iph] += molNum[kspec]; + } + } + + double RT = m_temperature * Cantera::GasConstant; + printf(" --- CHEMICAL POT TABLE (J/kmol) Name PhID MolFR ChemoSS " + " logMF Gamma Elect extra ElectrChem\n"); + printf(" "); + vcs_print_line("-", 132); + + for (kspec = 0; kspec < m_numSpeciesTot; ++kspec) { + mfValue = 1.0; + int iphase = m_phaseID[kspec]; + const vcs_VolPhase * Vphase = m_VolPhaseList[iphase]; + if ((m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDMS) || + (m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDPHASE) || + (m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDSS) ) { + zeroedPhase = true; + } else { + zeroedPhase = false; + } + if (tMoles[iphase] > 0.0) { + if (molNum[kspec] <= VCS_DELETE_MINORSPECIES_CUTOFF) { + mfValue = VCS_DELETE_MINORSPECIES_CUTOFF / tMoles[iphase]; + } else { + mfValue = molNum[kspec]/tMoles[iphase]; + } + } else { + int klocal = m_speciesLocalPhaseIndex[kspec]; + mfValue = Vphase->moleFraction(klocal); + } + double volts = Vphase->electricPotential(); + double elect = m_chargeSpecies[kspec] * m_Faraday_dim * volts; + double comb = - m_lnMnaughtSpecies[kspec]; + double total = (m_SSfeSpecies[kspec] + log(mfValue) + elect + log(actCoeff_ptr[kspec]) + comb); + + if (zeroedPhase) { + printf(" --- ** zp *** "); + } else { + printf(" --- "); + } + printf("%-24.24s", m_speciesName[kspec].c_str()); + printf(" %-3d", iphase); + printf(" % -12.4e", mfValue); + printf(" % -12.4e", m_SSfeSpecies[kspec] * RT); + printf(" % -12.4e", log(mfValue) * RT); + printf(" % -12.4e", log(actCoeff_ptr[kspec]) * RT); + printf(" % -12.4e", elect * RT); + printf(" % -12.4e", comb * RT); + printf(" % -12.4e\n", total *RT); + } + printf(" "); + vcs_print_line("-", 132); + } + /*****************************************************************************/ #ifdef DEBUG_MODE @@ -4990,8 +5076,125 @@ namespace VCSnonideal { } #endif } - /*****************************************************************************/ + //==================================================================================================================== + void VCS_SOLVE::vcs_printDeltaG( const int stateCalc) { + int j; + double * deltaGRxn = VCS_DATA_PTR(m_deltaGRxn_old); + double * feSpecies = VCS_DATA_PTR(m_feSpecies_old); + double * molNumSpecies = VCS_DATA_PTR(m_molNumSpecies_old); + const double * tPhMoles_ptr = VCS_DATA_PTR(m_tPhaseMoles_old); + const double * actCoeff_ptr = VCS_DATA_PTR(m_actCoeffSpecies_old); + if (stateCalc == VCS_STATECALC_NEW) { + deltaGRxn = VCS_DATA_PTR(m_deltaGRxn_new); + feSpecies = VCS_DATA_PTR(m_feSpecies_new); + molNumSpecies = VCS_DATA_PTR(m_molNumSpecies_new); + actCoeff_ptr = VCS_DATA_PTR(m_actCoeffSpecies_new); + tPhMoles_ptr = VCS_DATA_PTR(m_tPhaseMoles_new); + } + double RT = m_temperature * Cantera::GasConstant; + bool zeroedPhase = false; + if (m_debug_print_lvl >= 2) { + plogf(" --- DELTA_G TABLE Components:"); + for (j = 0; j < m_numComponents; j++) { + plogf(" %3d ", j); + } + plogf("\n --- Components Moles:"); + for (j = 0; j < m_numComponents; j++) { + plogf("%10.3g", m_molNumSpecies_old[j]); + } + plogf("\n --- NonComponent| Moles | "); + for (j = 0; j < m_numComponents; j++) { + plogf("%-10.10s", m_speciesName[j].c_str()); + } + //plogf("| m_scSize"); + plogf("\n"); + for (int i = 0; i < m_numRxnTot; i++) { + plogf(" --- %3d ", m_indexRxnToSpecies[i]); + plogf("%-10.10s", m_speciesName[m_indexRxnToSpecies[i]].c_str()); + plogf("|%10.3g|", m_molNumSpecies_old[m_indexRxnToSpecies[i]]); + for (j = 0; j < m_numComponents; j++) { + plogf(" %6.2f", m_stoichCoeffRxnMatrix[i][j]); + } + //plogf(" | %6.2f", m_scSize[i]); + plogf("\n"); + } + plogf(" "); for(int i=0; i<77; i++) plogf("-"); plogf("\n"); + } + printf(" --- DeltaG Table (J/kmol) Name PhID MoleNum MolFR " + " ElectrChemStar ElectrChem DeltaGStar DeltaG(Pred) Stability\n"); + printf(" "); + vcs_print_line("-", 132); + + for (int kspec = 0; kspec < m_numSpeciesTot; kspec++) { + + int irxn = kspec - m_numComponents; + + double mfValue = 1.0; + int iphase = m_phaseID[kspec]; + const vcs_VolPhase * Vphase = m_VolPhaseList[iphase]; + if ((m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDMS) || + (m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDPHASE) || + (m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDSS) ) { + zeroedPhase = true; + } else { + zeroedPhase = false; + } + if (tPhMoles_ptr[iphase] > 0.0) { + if (molNumSpecies[kspec] <= VCS_DELETE_MINORSPECIES_CUTOFF) { + mfValue = VCS_DELETE_MINORSPECIES_CUTOFF / tPhMoles_ptr[iphase]; + } else { + mfValue = molNumSpecies[kspec] / tPhMoles_ptr[iphase]; + } + } else { + int klocal = m_speciesLocalPhaseIndex[kspec]; + mfValue = Vphase->moleFraction(klocal); + } + if (zeroedPhase) { + printf(" --- ** zp *** "); + } else { + printf(" --- "); + } + double feFull = feSpecies[kspec]; + if ((m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDMS) || + (m_speciesStatus[kspec] == VCS_SPECIES_ZEROEDPHASE) ) { + feFull += log(actCoeff_ptr[kspec]) + log(mfValue); + } + printf("%-24.24s", m_speciesName[kspec].c_str()); + printf(" %-3d", iphase); + printf(" % -12.4e", molNumSpecies[kspec]); + printf(" % -12.4e", mfValue); + printf(" % -12.4e", feSpecies[kspec] * RT); + printf(" % -12.4e", feFull * RT); + if (irxn >= 0) { + printf(" % -12.4e", deltaGRxn[irxn] * RT); + printf(" % -12.4e", (deltaGRxn[irxn] + feFull - feSpecies[kspec]) * RT); + + if (deltaGRxn[irxn] < 0.0) { + if ( molNumSpecies[kspec] > 0.0) { + printf(" growing"); + } else { + printf(" stable"); + } + } else if (deltaGRxn[irxn] > 0.0) { + if ( molNumSpecies[kspec] > 0.0) { + printf(" shrinking"); + } else { + printf(" unstable"); + } + } else { + printf(" balanced"); + } + } + + printf(" \n"); + } + + printf(" "); + vcs_print_line("-", 132); + + } + //==================================================================================================================== // Calculate deltag of formation for all species in a single phase. /* * Calculate deltag of formation for all species in a single diff --git a/Cantera/src/equil/vcs_solve_phaseStability.cpp b/Cantera/src/equil/vcs_solve_phaseStability.cpp index f3e6b35de..73e851416 100644 --- a/Cantera/src/equil/vcs_solve_phaseStability.cpp +++ b/Cantera/src/equil/vcs_solve_phaseStability.cpp @@ -203,7 +203,7 @@ namespace VCSnonideal { */ int VCS_SOLVE::vcs_solve_phaseStability(const int iph, const int ifunc, double &funcVal, - int printLv) { + int printLvl) { int retn = 0; double test = -1.0E-10; int usedZeroedSpecies; @@ -222,11 +222,18 @@ namespace VCSnonideal { retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa), VCS_DATA_PTR(sm), VCS_DATA_PTR(ss), test, &usedZeroedSpecies); - + vcs_evaluate_speciesType(); vcs_dfe(VCS_STATECALC_OLD, 0, 0, m_numSpeciesRdc); + if (printLvl > 3) { + vcs_printSpeciesChemPot(VCS_STATECALC_OLD); + } vcs_deltag(0, true, VCS_STATECALC_OLD); + if (printLvl > 3) { + vcs_printDeltaG(VCS_STATECALC_OLD); + } + vcs_dcopy(VCS_DATA_PTR(m_deltaGRxn_Deficient), VCS_DATA_PTR(m_deltaGRxn_old), m_numRxnRdc); phasePopPhaseIDs.clear(); iphasePop = vcs_popPhaseID(phasePopPhaseIDs); funcVal = vcs_phaseStabilityTest(iph); From eb35f9e2532769e1f356f5400bce5cbad1256ed4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 31 Dec 2010 23:20:55 +0000 Subject: [PATCH 307/446] Some changes to reduce extra printing Some changes due to a bad algorithm - Known - need to fix this. --- Cantera/src/equil/vcs_MultiPhaseEquil.cpp | 19 +++++++++---------- Cantera/src/equil/vcs_phaseStability.cpp | 12 ++++++++---- 2 files changed, 17 insertions(+), 14 deletions(-) diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp index aa7eac6e6..5446bb00c 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp @@ -1547,8 +1547,7 @@ namespace VCSnonideal { if (!m_vsolvePtr) { m_vsolvePtr = new VCS_SOLVE(); } - double feStable; - int iStable = m_vsolvePtr->vcs_PS(m_vprob, iph, printLvl, feStable); + int iStable = m_vsolvePtr->vcs_PS(m_vprob, iph, printLvl, funcStab); /* * Transfer the information back to the MultiPhase object. @@ -1559,13 +1558,13 @@ namespace VCSnonideal { * states. */ m_mix->uploadMoleFractionsFromPhases(); - for (int i = 0; i < m_vprob->nspecies; i++) { - plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); - } + // for (int i = 0; i < m_vprob->nspecies; i++) { + // plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); + //} m_mix->getChemPotentials(DATA_PTR(m_vprob->m_gibbsSpecies)); - for (int i = 0; i < m_vprob->nspecies; i++) { - plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); - } + //for (int i = 0; i < m_vprob->nspecies; i++) { + // plogf("%d %15.3e\n", m_vprob->m_gibbsSpecies[i]); + //} double te = tickTock.secondsWC(); if (printLvl > 0) { @@ -1576,9 +1575,9 @@ namespace VCSnonideal { plogf("Pressure = %g Pa\n", m_vprob->PresPA); std::string sss = m_mix->phaseName(iph); if (iStable) { - plogf("Phase %d named %s is stable, function value = %g > 0\n", iph, sss.c_str(), feStable); + plogf("Phase %d named %s is stable, function value = %g > 0\n", iph, sss.c_str(), funcStab); } else { - plogf("Phase %d named %s is not stable + function value = %g < 0\n", iph, sss.c_str(), feStable); + plogf("Phase %d named %s is not stable + function value = %g < 0\n", iph, sss.c_str(), funcStab); } plogf("\n"); plogf("----------------------------------------" diff --git a/Cantera/src/equil/vcs_phaseStability.cpp b/Cantera/src/equil/vcs_phaseStability.cpp index 6d323da8c..3307f6954 100644 --- a/Cantera/src/equil/vcs_phaseStability.cpp +++ b/Cantera/src/equil/vcs_phaseStability.cpp @@ -97,7 +97,7 @@ namespace VCSnonideal { * We loop through the regular reaction looking for a reaction that can pop the * component. */ - printf("WE are here at new logic - CHECK\n"); + //printf("WE are here at new logic - CHECK\n"); for (int jrxn = 0; jrxn < m_numRxnRdc; jrxn++) { bool foundJrxn = false; // First, if the component is a product of the reaction @@ -111,7 +111,7 @@ namespace VCSnonideal { } } if (foundJrxn) { - printf("We have found a component phase pop! CHECK1 \n"); + //printf("We have found a component phase pop! CHECK1 \n"); return true; } } @@ -131,7 +131,7 @@ namespace VCSnonideal { } } if (foundJrxn) { - printf("We have found a component phase pop! CHECK2 \n"); + //printf("We have found a component phase pop! CHECK2 \n"); return true; } } @@ -717,7 +717,7 @@ namespace VCSnonideal { " normUpdate damp FuncPhaseStability\n", KP, KP, KP, KP); plogf(" --------------------------------------------------------------" "--------------------------------------------------------\n"); - } else { + } else if (m_debug_print_lvl == 1) { plogf(" --- vcs_phaseStabilityTest() called for phase %d\n", iph); } #endif @@ -757,6 +757,10 @@ namespace VCSnonideal { for (k = 0; k < Vphase->nSpecies(); k++) { sumFrac += fracDelta_old[k]; } + // Necessary because this can be identically zero. -> we need to fix this algorithm! + if (sumFrac <= 0.0) { + sumFrac = 1.0; + } double sum_Xcomp = 0.0; for (k = 0; k < Vphase->nSpecies(); k++) { X_est[k] = fracDelta_old[k] / sumFrac; From 5395e214b8072d224caa659ead1b6bdf740e5557 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 31 Dec 2010 23:54:29 +0000 Subject: [PATCH 308/446] Fixed a doxygen error. --- Cantera/src/equil/vcs_MultiPhaseEquil.h | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.h b/Cantera/src/equil/vcs_MultiPhaseEquil.h index 699b6e46a..bba5f4d1e 100644 --- a/Cantera/src/equil/vcs_MultiPhaseEquil.h +++ b/Cantera/src/equil/vcs_MultiPhaseEquil.h @@ -556,13 +556,13 @@ namespace VCSnonideal { * * @param maxsteps max steps allowed. * - * @param loglevel Determines the amount of printing to the HTML + * @param logLevel Determines the amount of printing to the HTML * output file. */ int equilibrate_TV(int XY, doublereal xtarget, int estimateEquil = 0, int printLvl = 0, doublereal err = 1.0E-6, - int maxsteps = VCS_MAXSTEPS, int loglevel = -99); + int maxsteps = VCS_MAXSTEPS, int logLevel = -99); //! Determine the phase stability of a phase at the current conditions /*! @@ -575,8 +575,7 @@ namespace VCSnonideal { * gets sent to stdout from the vcs package * (Note, you may have to compile with debug * flags to get some printing). - * @param loglevel Determines the amount of printing to the HTML - * output file. + * @param logLevel Determines the amount of printing to the HTML output file. */ int determine_PhaseStability(int iph, double &funcStab, int printLvl= 0, int logLevel = -99); From b1750d579ae7c3c5937b8a06474330ea8c9a14cf Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 Jan 2011 22:04:59 +0000 Subject: [PATCH 309/446] Added return variables to a lot of Residual evaluation functions. These are now used by the nonlinear solver to bail if the residual says to bail. --- Cantera/src/numerics/NonlinearSolver.cpp | 50 +++++++-- Cantera/src/numerics/NonlinearSolver.h | 52 +++++----- Cantera/src/numerics/ResidEval.h | 5 +- Cantera/src/numerics/ResidJacEval.cpp | 15 ++- Cantera/src/numerics/ResidJacEval.h | 38 +++++-- Cantera/src/numerics/RootFind.cpp | 125 ++++++++++++++++++----- Cantera/src/numerics/RootFind.h | 54 +++++++++- 7 files changed, 258 insertions(+), 81 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 596d44cda..1d7df013a 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -487,13 +487,18 @@ namespace Cantera { * @param typeCalc Type of the calculation * @param y_curr Current value of the solution vector * @param ydot_curr Current value of the time derivative of the solution vector + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - void NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, + int NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) { - m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), evalType); + int retn = m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), evalType); m_nfe++; m_resid_scaled = false; + return retn; } //==================================================================================================================== // Compute the undamped Newton step @@ -994,9 +999,15 @@ namespace Cantera { * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); } else { - doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + if (info != 1) { + if (loglevel > 0) { + printf("\t\t\tdampStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + } + return -1; } m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); @@ -1143,8 +1154,10 @@ namespace Cantera { * * SolnType = TRANSIENT -> we will assume we are relaxing a transient * equation system for now. Will make it more general later, - * if an application comes up. - * + * if an application comes up. + * + * @return A positive value indicates a successful convergence + * -1 Failed convergence */ int NonlinearSolver::solve_nonlinear_problem(int SolnType, double* y_comm, double* ydot_comm, doublereal CJ, @@ -1261,8 +1274,14 @@ namespace Cantera { - doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); - + info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); + if (info != 1) { + if (m_print_flag > 0) { + printf("\t\t\tsolve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); + } + m = -1; + goto done; + } /* * Scale the matrix and the rhs, if they aren't already scaled @@ -1340,8 +1359,14 @@ namespace Cantera { } - doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(ydot_new)); - + info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(ydot_new)); + if (info != 1) { + if (m_print_flag > 0) { + printf("\t\t\tdampStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + } + m = -1; + goto done; + } if (m_print_flag > 3) { residErrorNorm(DATA_PTR(m_resid), "Resulting Residual Norm", 10, DATA_PTR(y_new)); @@ -1884,5 +1909,10 @@ namespace Cantera { } //===================================================================================================================== + void NonlinearSolver::setPrintLvl( int printLvl) + { + m_print_flag = printLvl; + } + //===================================================================================================================== } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 08699226e..96dd0e08a 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -96,6 +96,8 @@ namespace Cantera { * @param printLargest int indicating how many specific lines should be printed out * @param dampFactor Current value of the damping factor. Defaults to 1. * only used for printout out a table. + * + * @return Returns the L2 norm of the delta */ doublereal solnErrorNorm(const doublereal * const delta_y, const char * title = 0, int printLargest = 0, const doublereal dampFactor = 1.0); @@ -113,26 +115,13 @@ namespace Cantera { * @param title Optional title to be printed out * @param printLargest Number of specific entries to be printed * @param y Current value of y - only used for printouts + * + * + * @return Returns the L2 norm of the delta */ doublereal residErrorNorm(const doublereal * const resid, const char * title = 0, const int printLargest = 0, const doublereal * const y = 0); - //! Compute the current Residual - /*! - * Compute the time dependent residual of - * the set of equations. - */ - // void doTDResidualCalc(const double time_curr, const int typeCalc, - // const double * const y_curr, const double * const ydot_curr, int loglevel); - - //! Compute the current Residual - /*! - * Compute the steady state residual of - * the set of equations. - */ - // void doSteadyResidualCalc(const double time_curr, const int typeCalc, - // const double * const y_curr, int loglevel); - //! Compute the current residual /*! * The current value of the residual is storred in the internal work array m_resid. @@ -143,10 +132,14 @@ namespace Cantera { * @param ydot_curr Current value of the time derivative of the solution vector * @param evalType Base evalulation type * Defaults to Base_ResidEval + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - void doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, - const doublereal * const ydot_curr, - const ResidEval_Type_Enum evalType = Base_ResidEval); + int doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, + const doublereal * const ydot_curr, + const ResidEval_Type_Enum evalType = Base_ResidEval); //! Compute the undamped Newton step /*! @@ -166,7 +159,7 @@ namespace Cantera { * @param y_current Current value of the solution * @param ydot_current Current value of the solution derivative. * - * @return returns the result code from lapack. A zero means success. Anything + * @return Returns the result code from lapack. A zero means success. Anything * else indicates a failure. */ int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, @@ -215,9 +208,10 @@ namespace Cantera { * factor of 2 * Maximum decrease in variable in any one newton iteration: * factor of 5 + * + * @return Returns the damping factor determined by the bounds calculation */ - doublereal boundStep(const double* const y, - const double* const step0, const int loglevel); + doublereal boundStep(const double* const y, const double* const step0, const int loglevel); //! Set bounds constraints for all variables in the problem @@ -229,13 +223,13 @@ namespace Cantera { void setBoundsConstraints(const doublereal * const y_low_bounds, const doublereal * const y_high_bounds); - //! return an editable vector of the low bounds constraints + //! Return an editable vector of the low bounds constraints std::vector & lowBoundsConstraintVector(); - //! return an editable vector of the high bounds constraints + //! Return an editable vector of the high bounds constraints std::vector & highBoundsConstraintVector(); - //! Internal function to calculate the time derivative at the new step + //! Internal function to calculate the time derivative at the new step /*! * @param order of the BDF method * @param y_curr current value of the solution @@ -256,13 +250,11 @@ namespace Cantera { * @return Returns a flag to indicate that operation is successful. * 1 Means a successful operation * 0 Means an unsuccessful operation - * */ int beuler_jac(SquareMatrix &J, doublereal * const f, doublereal time_curr, doublereal CJ, doublereal * const y, doublereal * const ydot, int num_newt_its); - //! Apply a filtering process to the step /*! * @param timeCurrent Current value of the time @@ -290,9 +282,9 @@ namespace Cantera { * The idea behind these is that the Jacobian couldn't possibly be representative, if the * variable is changed by a lot. (true for nonlinear systems, false for linear systems) * Maximum increase in variable in any one newton iteration: - * factor of 1.5 + * factor of 1.5 * Maximum decrease in variable in any one newton iteration: - * factor of 2 + * factor of 2 * * @param y Initial value of the solution vector * @param step0 initial proposed step size @@ -437,6 +429,8 @@ namespace Cantera { //! solution norms. void calcSolnToResNormVector(); + void setPrintLvl(int printLvl); + private: //! Pointer to the residual and jacobian evaluator for the diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index 1c24843e7..da65c4cfa 100644 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -101,10 +101,13 @@ namespace Cantera { /** * Fill the solution and derivative vectors with the initial * conditions at initial time t0. + * @return 1 Everything is fine + * 0 or neg Something went wrong */ - virtual void getInitialConditions(const doublereal t0, doublereal * const y, + virtual int getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot) { throw CanteraError("ResidEval::GetInitialConditions()", "base class called"); + return 1; } //! Return the number of equations in the equation system diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index b1ae4edf1..cb6d08988 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -96,7 +96,7 @@ namespace Cantera { * @param y Solution vector (output) * @param ydot Rate of change of solution vector. (output) */ - void ResidJacEval:: + int ResidJacEval:: getInitialConditions(doublereal t0, doublereal * const y, doublereal * const ydot) { for (int i = 0; i < neq_; i++) { y[i] = 0.0; @@ -106,6 +106,7 @@ namespace Cantera { ydot[i] = 0.0; } } + return 1; } //==================================================================================================================== // This function may be used to create output at various points in the execution of an application. @@ -154,10 +155,11 @@ namespace Cantera { * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) */ - void ResidJacEval:: + int ResidJacEval:: evalTimeTrackingEqns(const doublereal t, const doublereal delta_t, const doublereal *y, const doublereal *ydot) { + return 1; } //==================================================================================================================== // Return a vector of delta y's for calculation of the numerical Jacobian @@ -279,9 +281,10 @@ namespace Cantera { * @param nrows offsets for the matrix * @param rhs residual vector. This also needs to be lhs multiplied by M */ - void ResidJacEval:: + int ResidJacEval:: matrixConditioning(doublereal * const matrix, const int nrows, doublereal * const rhs) { + return 1; } //==================================================================================================================== // Evaluate the residual function @@ -297,12 +300,13 @@ namespace Cantera { * differenced or that the residual doesn't take this issue into account) * @param delta_x Value of the delta used in the numerical differencing */ - void ResidJacEval:: + int ResidJacEval:: evalResidNJ(const doublereal t, const doublereal deltaT, const doublereal * y, const doublereal * ydot, doublereal * const resid, const ResidEval_Type_Enum evalType, const int id_x, const doublereal delta_x) { throw CanteraError("ResidJacEval::evalResidNJ()", "Not implemented\n"); + return 1; } //==================================================================================================================== // Calculate an analytical jacobian and the residual at the current time and values. @@ -316,7 +320,7 @@ namespace Cantera { * @param J Reference to the SquareMatrix object to be calculated (output) * @param resid Value of the residual that is computed (output) */ - void ResidJacEval:: + int ResidJacEval:: evalJacobian(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot, @@ -324,6 +328,7 @@ namespace Cantera { doublereal * const resid) { throw CanteraError("ResidJacEval::evalJacobian()", "Not implemented\n"); + return 1; } //==================================================================================================================== diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index e1b1fc069..08a23fc35 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -112,8 +112,12 @@ namespace Cantera { * the jacobian (defaults to -1, which indicates that no variable is being * differenced or that the residual doesn't take this issue into account) * @param delta_x Value of the delta used in the numerical differencing + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void evalResidNJ(const doublereal t, const doublereal delta_t, + virtual int evalResidNJ(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot, doublereal * const resid, @@ -129,8 +133,12 @@ namespace Cantera { * @param t0 Time (input) * @param y Solution vector (output) * @param ydot Rate of change of solution vector. (output) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot); + virtual int getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot); //! Filter the solution predictions /*! @@ -174,8 +182,12 @@ namespace Cantera { * @param delta_t The current value of the time step (input) * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void evalTimeTrackingEqns(const doublereal t, const doublereal delta_t, const doublereal * const y, + virtual int evalTimeTrackingEqns(const doublereal t, const doublereal delta_t, const doublereal * const y, const doublereal * const ydot); //! Evalulate any stopping criteria other than a final time limit @@ -281,8 +293,12 @@ namespace Cantera { * @param matrix Pointer to the current jacobian (if zero, it's already been factored) * @param nrows offsets for the matrix * @param rhs residual vector. This also needs to be lhs multiplied by M + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void matrixConditioning(doublereal * const matrix, const int nrows, + virtual int matrixConditioning(doublereal * const matrix, const int nrows, doublereal * const rhs); //! Calculate an analytical jacobian and the residual at the current time and values. @@ -295,12 +311,16 @@ namespace Cantera { * @param ydot Rate of change of solution vector. (input, do not modify) * @param J Reference to the SquareMatrix object to be calculated (output) * @param resid Value of the residual that is computed (output) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation */ - virtual void evalJacobian(const doublereal t, const doublereal delta_t, - const doublereal* const y, - const doublereal* const ydot, - SquareMatrix &J, - doublereal * const resid); + virtual int evalJacobian(const doublereal t, const doublereal delta_t, + const doublereal* const y, + const doublereal* const ydot, + SquareMatrix &J, + doublereal * const resid); protected: diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index 0bc16bd9d..b72ffefff 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -125,7 +125,8 @@ namespace Cantera { printLvl(0), DeltaXnorm_(0.01), FuncIsGenerallyIncreasing_(false), - FuncIsGenerallyDecreasing_(false) + FuncIsGenerallyDecreasing_(false), + deltaXConverged_(0.0) { } @@ -133,6 +134,49 @@ namespace Cantera { // Empty destructor RootFind::~RootFind() { } + //================================================================================================ + double RootFind::delXNonzero(double x1) const { + double deltaX = 1.0E-14 * fabs(x1); + double delmin = DeltaXnorm_ * 1.0E-14; + if (delmin > deltaX) { + return delmin; + } + return deltaX; + } + //================================================================================================ + double RootFind::delXMeaningful(double x1) const { + double del = delXNonzero(x1); + if (deltaXConverged_ > del) { + return deltaXConverged_; + } + return del; + } + //================================================================================================ + double RootFind::deltaXControlled(double x2, double x1) const { + double sgnn = 1.0; + if (x1 > x2) { + sgnn = -1.0; + } + double deltaX = x2 - x1; + double x = fabs(x2) + fabs(x1); + double deltaXm = delXMeaningful(x); + if (fabs(deltaX) < deltaXm) { + deltaX = sgnn * deltaXm; + } + return deltaX; + } + //================================================================================================ + bool RootFind::theSame(double x2, double x1) const { + double x = fabs(x2) + fabs(x1); + double deltaX = delXMeaningful(x); + if (fabs(x2 - x1) < deltaX) { + return true; + } + return false; + } + + + //================================================================================================ /* * The following calculation is a line search method to find the root of a function @@ -162,6 +206,7 @@ namespace Cantera { FILE *fp = 0; #endif doublereal x1, x2, xnew, f1, f2, fnew, slope; + doublereal deltaX1 = 0.0, deltaX2 = 0.0, deltaXnew = 0.0; int its = 0; int posStraddle = 0; int retn = 0; @@ -173,6 +218,7 @@ namespace Cantera { doublereal fnorm; /* A valid norm for the making the function value dimensionless */ doublereal c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; doublereal CR0, CR1, CR2, CRnew, CRdenom; + doublereal sgn; callNum++; #ifdef DEBUG_MODE @@ -230,6 +276,7 @@ namespace Cantera { x2 = x1 - (xmax - xmin) / 100.; } + deltaX2 = x2 - x1; f2 = func(x2); #ifdef DEBUG_MODE if (printLvl >= 3) { @@ -277,7 +324,13 @@ namespace Cantera { * Find an estimate of the next point, xnew, to try based on * a linear approximation from the last two points. */ - slope = (f2 - f1) / (x2 - x1); +#ifdef DEBUG_HKM + if (fabs(x2 - x1) < 1.0E-14) { + printf(" RootFind: we are here x2 = %g x1 = %g\n", x2, x1); + } +#endif + double delXtmp = deltaXControlled(x2, x1); + slope = (f2 - f1) / delXtmp; if (fabs(slope) <= 1.0E-100) { if (printLvl >= 2) { writelogf("%s functions evals produced the same result, %g, at %g and %g\n", @@ -299,6 +352,7 @@ namespace Cantera { fprintf(fp, " | xlin = %-11.5E", xnew); } #endif + deltaXnew = xnew - x2; /* * If the suggested step size is too big, throw out step */ @@ -306,6 +360,10 @@ namespace Cantera { if (fabs(xnew - x2) > 3.0 * DeltaXnorm_) { useNextStrat = true; } + if (fabs(deltaXnew) < fabs(deltaX2)) { + deltaXnew = DSIGN(deltaXnew) * 1.1 * fabs(deltaX2); + xnew = deltaXnew + x2; + } } if (useNextStrat) { if (f2 < 0.0) { @@ -442,26 +500,7 @@ namespace Cantera { #endif } } - /* - * Guard against going above xmax or below xmin - */ - if (xnew > xmax) { - xnew = x2 + (xmax - x2) / 2.0; -#ifdef DEBUG_MODE - if (printLvl >= 3) { - fprintf(fp, " | xlimitmax = %-11.5E", xnew); - } -#endif - } - if (xnew < xmin) { - xnew = x2 + (x2 - xmin) / 2.0; -#ifdef DEBUG_MODE - if (printLvl >= 3) { - fprintf(fp, " | xlimitmin = %-11.5E", xnew); - } -#endif - } - + if (foundStraddle) { #ifdef DEBUG_MODE slope = xnew; @@ -507,7 +546,42 @@ namespace Cantera { } #endif } - + + /* + * Enforce a minimum stepsize if we haven't found a straddle. + */ + deltaXnew = xnew - x2; + if (fabs(deltaXnew) < 1.2 * delXMeaningful(xnew)) { + if (!foundStraddle) { + sgn = 1.0; + if (x2 < xnew) { + sgn = -1.0; + } + deltaXnew = 1.2 * delXMeaningful(xnew) * sgn; + xnew = x2 + deltaXnew; + } + } + + /* + * Guard against going above xmax or below xmin + */ + if (xnew > xmax) { + xnew = x2 + (xmax - x2) / 2.0; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlimitmax = %-11.5E", xnew); + } +#endif + } + if (xnew < xmin) { + xnew = x2 + (x2 - xmin) / 2.0; +#ifdef DEBUG_MODE + if (printLvl >= 3) { + fprintf(fp, " | xlimitmin = %-11.5E", xnew); + } +#endif + } + fnew = func(xnew); CRdenom = MAX(fabs(fnew), MAX(fabs(f2), MAX(fabs(f1), fnorm))); CRnew = sqrt(fabs(fnew) / CRdenom); @@ -563,6 +637,8 @@ namespace Cantera { CR1 = CR2; x2 = xnew; f2 = fnew; + deltaX1 = deltaX2; + deltaX2 = deltaXnew; CR2 = CRnew; if (fabs(fnew / fnorm) < m_rtol) { converged = 1; @@ -576,10 +652,9 @@ namespace Cantera { retn = ROOTFIND_FAILEDCONVERGENCE; converged = true; } - if (fabs(x2 - x1) / denom < 1.0E-13) { + if (theSame(x2, x1)) { converged = true; } - } its++; } while (! converged && its < itmax); diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index c8168ed89..98e3a3ede 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -28,6 +28,12 @@ namespace Cantera { #define ROOTFIND_FAILEDCONVERGENCE -1 #define ROOTFIND_BADINPUT -2 + //! Root finder for 1D problems + /*! + * + * + * + */ class RootFind { public: @@ -48,10 +54,53 @@ namespace Cantera { //! Unimplemented private assignment operator RootFind& operator=(const RootFind &right); - public: - int solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest) ; + double delXNonzero(double x1) const; + + double delXMeaningful(double x1) const; + + double deltaXControlled(double x2, double x1) const; + + bool theSame(double x2, double x1) const; + public: + + //! Using a line search method, find the root of a 1D function + /*! + * This routine solves the following equation. + * + * \f[ + * R(x) = f(x) - f_o = 0 + * \f] + * + * @param xmin Minimum value of x to be used. + * @param xmax Maximum value of x to be used + * @param itmax maximum number of iterations. Usually, it can be less than 50. + * @param funcTargetValue Value of \f$ f_o \f$ in the equation. + * @param xbest Returns the x that satisfies the function + * On input, xbest should contain the best estimate of the solution. + * An attempt to find the solution near xbest is made. + * + * @return: + * 0 = ROOTFIND_SUCCESS Found function + * -1 = ROOTFIND_FAILEDCONVERGENCE Failed to find the answer + * -2 = ROOTFIND_BADINPUT Bad input was detected + */ + int solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest); + + + //! Return the function value + /*! + * This routine evaluates the following equation. + * + * \f[ + * R(x) = f(x) - f_o = 0 + * \f] + * + * @param x Value of the independent variable + * + * @return The routine returns the value of \f$ R(x) \f$ + */ doublereal func(doublereal x); void setTol(doublereal rtol, doublereal atol); @@ -72,6 +121,7 @@ namespace Cantera { doublereal DeltaXnorm_; bool FuncIsGenerallyIncreasing_; bool FuncIsGenerallyDecreasing_; + doublereal deltaXConverged_; }; } From a36864543a711e2b36de19ebd3b0140b4dcd93e3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 Jan 2011 23:02:07 +0000 Subject: [PATCH 310/446] Got rid of a print statement. --- Cantera/src/equil/vcs_solve.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 3f52c273c..75444a566 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -966,7 +966,7 @@ namespace VCSnonideal { pub->w[i] = m_molNumSpecies_old[k1]; } else { pub->w[i] = 0.0; - plogf("voltage species = %g\n", m_molNumSpecies_old[k1]); + // plogf("voltage species = %g\n", m_molNumSpecies_old[k1]); } //pub->mf[i] = m_molNumSpecies_new[k1]; pub->m_gibbsSpecies[i] = m_feSpecies_old[k1]; From f727cd44af203f74348afcc179f835a963804690 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 5 Jan 2011 03:55:13 +0000 Subject: [PATCH 311/446] Added in a more robust treatment of handling limits --- Cantera/src/numerics/NonlinearSolver.cpp | 20 +++++++++++--- Cantera/src/numerics/RootFind.cpp | 35 ++++++++++++++++++++++-- Cantera/src/numerics/RootFind.h | 6 ++-- 3 files changed, 52 insertions(+), 9 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 1d7df013a..602892d68 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1585,6 +1585,7 @@ namespace Cantera { { int i, j; double* col_j; + int info; doublereal ysave, ydotsave, dy; int retn = 1; /* @@ -1595,9 +1596,12 @@ namespace Cantera { /******************************************************************** * Call the function to get a jacobian. */ - m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); + info = m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); m_nJacEval++; m_nfe++; + if (info != 1) { + return info; + } } else { /******************************************************************* * Generic algorithm to calculate a numerical Jacobian @@ -1607,8 +1611,11 @@ namespace Cantera { * current conditions. */ - m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); m_nfe++; + if (info != 1) { + return info; + } m_nJacEval++; /* @@ -1668,9 +1675,14 @@ namespace Cantera { */ - m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), - JacDelta_ResidEval, j, dy); + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), + JacDelta_ResidEval, j, dy); m_nfe++; + if (info != 1) { + mdp::mdp_safe_free((void **) &dyVector); + return info; + } + doublereal diff; for (i = 0; i < neq_; i++) { diff = subtractRD(m_wksp[i], f[i]); diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index b72ffefff..e6e703ede 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -188,7 +188,7 @@ namespace Cantera { * return: * 0 Found function */ - int RootFind::solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest) { + int RootFind::solve(doublereal xmin, doublereal xmax, int itmax, doublereal &funcTargetValue, doublereal *xbest) { /* * We store the function target and then actually calculate a modified functional @@ -201,6 +201,8 @@ namespace Cantera { const char *stre = "RootFind ERROR: "; const char *strw = "RootFind WARNING: "; int converged = 0; + int bottomBump = 0; + int topBump = 0; #ifdef DEBUG_MODE char fileName[80]; FILE *fp = 0; @@ -236,6 +238,7 @@ namespace Cantera { #endif if (xmax <= xmin) { writelogf("%sxmin and xmax are bad: %g %g\n", stre, xmin, xmax); + funcTargetValue = func(*xbest); return ROOTFIND_BADINPUT; } /* @@ -566,7 +569,18 @@ namespace Cantera { * Guard against going above xmax or below xmin */ if (xnew > xmax) { - xnew = x2 + (xmax - x2) / 2.0; + topBump++; + if (topBump < 5) { + xnew = x2 + (xmax - x2) / 2.0; + } else { + if (x2 == xmax || x1 == xmax) { + // we are here when we are bumping against the top limit. + // No further action is possible + goto done; + } else { + xnew = xmax; + } + } #ifdef DEBUG_MODE if (printLvl >= 3) { fprintf(fp, " | xlimitmax = %-11.5E", xnew); @@ -574,7 +588,18 @@ namespace Cantera { #endif } if (xnew < xmin) { - xnew = x2 + (x2 - xmin) / 2.0; + bottomBump++; + if (bottomBump < 5) { + xnew = x2 + (x2 - xmin) / 2.0; + } else { + if (x2 == xmin || x1 == xmin) { + // we are here when we are bumping against the bottom limit. + // No further action is possible + goto done; + } else { + xnew = xmin; + } + } #ifdef DEBUG_MODE if (printLvl >= 3) { fprintf(fp, " | xlimitmin = %-11.5E", xnew); @@ -658,6 +683,8 @@ namespace Cantera { } its++; } while (! converged && its < itmax); + + done: if (converged) { if (printLvl >= 1) { writelogf("RootFind success: convergence achieved\n"); @@ -679,11 +706,13 @@ namespace Cantera { #endif } *xbest = x2; + funcTargetValue = f2 + m_funcTargetValue; #ifdef DEBUG_MODE if (printLvl >= 3) { fclose(fp); } #endif + return retn; } //================================================================================================ diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 98e3a3ede..5e6dd6429 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -76,7 +76,9 @@ namespace Cantera { * @param xmin Minimum value of x to be used. * @param xmax Maximum value of x to be used * @param itmax maximum number of iterations. Usually, it can be less than 50. - * @param funcTargetValue Value of \f$ f_o \f$ in the equation. + * @param funcTargetValue + * Value of \f$ f_o \f$ in the equation. + * On return, it contains the value of the function actually obtained. * @param xbest Returns the x that satisfies the function * On input, xbest should contain the best estimate of the solution. * An attempt to find the solution near xbest is made. @@ -86,7 +88,7 @@ namespace Cantera { * -1 = ROOTFIND_FAILEDCONVERGENCE Failed to find the answer * -2 = ROOTFIND_BADINPUT Bad input was detected */ - int solve(doublereal xmin, doublereal xmax, int itmax, doublereal funcTargetValue, doublereal *xbest); + int solve(doublereal xmin, doublereal xmax, int itmax, doublereal &funcTargetValue, doublereal *xbest); //! Return the function value From 14bf2b1ee22509273618b5406a79cd612d0ed08b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 10 Jan 2011 23:22:19 +0000 Subject: [PATCH 312/446] Started putting these files into the standard form. Started eliminating doxygen errors. --- Cantera/src/kinetics/GasKinetics.cpp | 48 ++++++++++++++++++++++++++++ Cantera/src/kinetics/GasKinetics.h | 39 ++++++++-------------- 2 files changed, 61 insertions(+), 26 deletions(-) diff --git a/Cantera/src/kinetics/GasKinetics.cpp b/Cantera/src/kinetics/GasKinetics.cpp index 805ddf598..8e976f096 100644 --- a/Cantera/src/kinetics/GasKinetics.cpp +++ b/Cantera/src/kinetics/GasKinetics.cpp @@ -427,6 +427,54 @@ namespace Cantera { m_rxnstoich->getReactionDelta(m_ii, &m_grt[0], deltaS); } + //==================================================================================================================== + // Return the species net production rates + /* + * Species net production rates [kmol/m^3/s]. Return the species + * net production rates (creation - destruction) in array + * wdot, which must be dimensioned at least as large as the + * total number of species. + * + * @param net Array of species production rates. + * units kmol m-3 s-1 + */ + void GasKinetics::getNetProductionRates(doublereal* net) { + updateROP(); + m_rxnstoich->getNetProductionRates(m_kk, &m_kdata->m_ropnet[0], net); + } + //==================================================================================================================== + // Return the species creation rates + /* + * Species creation rates [kmol/m^3]. Return the species + * creation rates in array cdot, which must be + * dimensioned at least as large as the total number of + * species. + * + * @param cdot Array of species production rates. + * units kmol m-3 s-1 + */ + void GasKinetics::getCreationRates(doublereal* cdot) { + updateROP(); + m_rxnstoich->getCreationRates(m_kk, &m_kdata->m_ropf[0], &m_kdata->m_ropr[0], cdot); + } + //==================================================================================================================== + // Return a vector of the species destruction rates + /* + * Species destruction rates [kmol/m^3]. Return the species + * destruction rates in array ddot, which must be + * dimensioned at least as large as the total number of + * species. + * + * + * @param ddot Array of species destruction rates. + * units kmol m-3 s-1 + * + */ + void GasKinetics::getDestructionRates(doublereal* ddot) { + updateROP(); + m_rxnstoich->getDestructionRates(m_kk, &m_kdata->m_ropf[0], &m_kdata->m_ropr[0], ddot); + } + //==================================================================================================================== void GasKinetics::processFalloffReactions() { int i; diff --git a/Cantera/src/kinetics/GasKinetics.h b/Cantera/src/kinetics/GasKinetics.h index 84fc551af..ce81edd0f 100644 --- a/Cantera/src/kinetics/GasKinetics.h +++ b/Cantera/src/kinetics/GasKinetics.h @@ -273,46 +273,33 @@ namespace Cantera { * @param net Array of species production rates. * units kmol m-3 s-1 */ - virtual void getNetProductionRates(doublereal* net) { - updateROP(); - //#ifdef HWMECH - //get_wdot(&m_kdata->m_ropnet[0], net); - //#else - m_rxnstoich->getNetProductionRates(m_kk, - &m_kdata->m_ropnet[0], net); - //#endif - } + virtual void getNetProductionRates(doublereal* net); - /** + //! Return the species creation rates + /*! * Species creation rates [kmol/m^3]. Return the species * creation rates in array cdot, which must be * dimensioned at least as large as the total number of * species. * + * @param cdot Array of species creation rates. + * units kmol m-3 s-1 */ - virtual void getCreationRates(doublereal* cdot) { - updateROP(); - m_rxnstoich->getCreationRates(m_kk, &m_kdata->m_ropf[0], - &m_kdata->m_ropr[0], cdot); - } + virtual void getCreationRates(doublereal* cdot); - /** + //! Return a vector of the species destruction rates + /*! * Species destruction rates [kmol/m^3]. Return the species * destruction rates in array ddot, which must be * dimensioned at least as large as the total number of * species. * + * + * @param ddot Array of species destruction rates. + * units kmol m-3 s-1 + * */ - virtual void getDestructionRates(doublereal* ddot) { - updateROP(); - m_rxnstoich->getDestructionRates(m_kk, &m_kdata->m_ropf[0], - &m_kdata->m_ropr[0], ddot); - // fill(ddot, ddot + m_kk, 0.0); - //m_revProductStoich.incrementSpecies( - // m_kdata->m_ropr.begin(), ddot); - //m_reactantStoich.incrementSpecies( - // m_kdata->m_ropf.begin(), ddot); - } + virtual void getDestructionRates(doublereal* ddot); //@} /** From 3a63c938ea87c34f9b5978dcaa12442024e8280c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 11 Jan 2011 15:27:59 +0000 Subject: [PATCH 313/446] Added a few more files --- docs/Cantera.cfg.in | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index a732ce226..789deaf44 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -794,7 +794,11 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ DenseMatrix.h \ DenseMatrix.cpp \ ResidJacEval.h \ - ResidJacEval.cpp + ResidJacEval.cpp \ + RootFind.h \ + RootFind.cpp \ + NonlinearSolver.h \ + NonlinearSolver.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. From f493f8f39aa649e662f6e451911f271ab12ed65d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 11 Jan 2011 17:34:31 +0000 Subject: [PATCH 314/446] Doxygen update --- Cantera/src/numerics/Integrator.h | 5 +- Cantera/src/numerics/NonlinearSolver.cpp | 47 ++++---- Cantera/src/numerics/NonlinearSolver.h | 140 +++++++++++++++++++---- Cantera/src/numerics/RootFind.cpp | 139 +++++++++++++++++----- Cantera/src/numerics/RootFind.h | 135 +++++++++++++++++++++- 5 files changed, 385 insertions(+), 81 deletions(-) diff --git a/Cantera/src/numerics/Integrator.h b/Cantera/src/numerics/Integrator.h index 6b498dc0a..55e8185c3 100644 --- a/Cantera/src/numerics/Integrator.h +++ b/Cantera/src/numerics/Integrator.h @@ -1,7 +1,8 @@ /** * @file Integrator.h - * - * $Author$ + */ + +/* $Author$ * $Date$ * $Revision$ * diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 602892d68..f1115589c 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -28,35 +28,37 @@ #include "mdp_allo.h" #include -extern void print_line(const char *, int); - #include #include #include +//@{ +extern void print_line(const char *, int); #ifndef MAX #define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) #define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) #endif - +//@} using namespace std; namespace Cantera { - //==================================================================================================================== + //==================================================================================================================== //----------------------------------------------------------- // Constants //----------------------------------------------------------- - - const doublereal DampFactor = 4; + //! Dampfactor is the factor by which the damping factor is reduced by when a reduction in step length is warranted + const doublereal DampFactor = 4.0; + //! Number of damping steps that are carried out before the solution is deemed a failure const int NDAMP = 7; - //==================================================================================================================== - //----------------------------------------------------------- - // Static Functions - //----------------------------------------------------------- - + //==================================================================================================================== + //! Print a line of a single repeated character string + /*! + * @param str Character string + * @param n Iteration length + */ static void print_line(const char *str, int n) { for (int i = 0; i < n; i++) { printf("%s", str); @@ -625,7 +627,8 @@ namespace Cantera { * scaling has been implemented. */ int NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, - const doublereal * const ydot_curr, double* const delta_y, SquareMatrix& jac, int loglevel) + const doublereal * const ydot_curr, doublereal * const delta_y, + SquareMatrix& jac, int loglevel) { int irow; @@ -837,7 +840,6 @@ namespace Cantera { return f_delta_bounds; } //==================================================================================================================== - /* * * boundStep(): @@ -865,7 +867,8 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0, const int loglevel) { + doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0, + const int loglevel) { int i, i_lower = -1; doublereal fbound = 1.0, f_bounds = 1.0; doublereal ff, y_new; @@ -1532,12 +1535,10 @@ namespace Cantera { mdp::mdp_safe_free((void **) &imax); } //==================================================================================================================== - - /* - * subtractRD(): + //! This routine subtracts two numbers for one another + /*! * This routine subtracts 2 numbers. If the difference is less - * than 1.0E-14 times the magnitude of the smallest number, - * then diff returns an exact zero. + * than 1.0E-14 times the magnitude of the smallest number, then diff returns an exact zero. * It also returns an exact zero if the difference is less than * 1.0E-300. * @@ -1546,8 +1547,12 @@ namespace Cantera { * This routine is used in numerical differencing schemes in order * to avoid roundoff errors resulting in creating Jacobian terms. * Note: This is a slow routine. However, jacobian errors may cause - * loss of convergence. Therefore, in practice this routine - * has proved cost-effective. + * loss of convergence. Therefore, in practice this routine has proved cost-effective. + * + * @param a Value of a + * @param b value of b + * + * @return returns the difference between a and b */ static inline doublereal subtractRD(doublereal a, doublereal b) { doublereal diff = a - b; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 96dd0e08a..918e2f50c 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -1,5 +1,5 @@ /** - * @file NonlinearSolve.h + * @file NonlinearSolver.h * Class that calculates the solution to a nonlinear, dense, set * of equations (see \ref numerics * and class \link Cantera::NonlinearSolver NonlinearSolver\endlink). @@ -22,20 +22,55 @@ #include "ResidJacEval.h" namespace Cantera { - - // I think steady state is the only option I'm gunning for + + //@{ + /// @name Constant which determines the type of the nonlinear solve + /*! + * I think steady state is the only option I'm gunning for + */ + //! The nonlinear problem is part of a pseudo time dependent calculation (NOT TESTED) #define NSOLN_TYPE_PSEUDO_TIME_DEPENDENT 2 + //! The nonlinear problem is part of a time dependent calculation #define NSOLN_TYPE_TIME_DEPENDENT 1 + //! The nonlinear problem is part of a steady state calculation #define NSOLN_TYPE_STEADY_STATE 0 + //@} + //@{ + /// @name Constant which determines the type of the Jacobian + //! The jacobian will be calculated from a numerical method #define NSOLN_JAC_NUM 1 + //! The jacobian is calculated from an analytical function #define NSOLN_JAC_ANAL 2 - + //@} //! Class that calculates the solution to a nonlinear system /*! - * UNDER CONSTRUCTION - do not use!!!!!!!!!!!!!!!!!!!!!!!!! + * This is a small nonlinear solver that can solve highly nonlinear problems that + * must use a dense matrix to relax the system. + * + * Newton's method is used. + * + * Damping is used extensively when relaxing the system + * + * + * + * @code + * + * + * NonlinearSolver *nls = new NonlinearSolver(&r1); + * + * int solnType = NSOLN_TYPE_STEADY_STATE ; + * + * nls->setDeltaBoundsMagnitudes(deltaBounds); + * + * nls->solve_nonlinear_problem(solnType, y_comm, ydot_comm, CJ, time_curr, jac, + * num_newt_its, num_linear_solves, numBacktracks, + * loglevelInput); + * + * @endcode + * * * @ingroup numerics */ @@ -77,7 +112,7 @@ namespace Cantera { * The program always assumes that atol is specific * to the solution component * - * param y vector of the current solution values + * @param y vector of the current solution values */ void createSolnWeights(const doublereal * const y); @@ -155,9 +190,12 @@ namespace Cantera { * recomputed. The row scales are recomputed here, after column * scaling has been implemented. * - * @param timeCurrent Current value of the time - * @param y_current Current value of the solution - * @param ydot_current Current value of the solution derivative. + * @param time_curr Current value of the time + * @param y_curr Current value of the solution + * @param ydot_curr Current value of the solution derivative. + * @param delta_y return value of the raw change in y + * @param jac Jacobian + * @param loglevel Log level * * @return Returns the result code from lapack. A zero means success. Anything * else indicates a failure. @@ -178,7 +216,7 @@ namespace Cantera { //! Set the delta Bounds magnitudes by hand /*! - * @param deltaboundsMagnitudes + * @param deltaBoundsMagnitudes set the deltaBoundsMagnitude vector */ void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); @@ -209,9 +247,13 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 * + * @param y Current solution value of the old step + * @param step0 Proposed step change in the solution + * @param loglevel Log level + * * @return Returns the damping factor determined by the bounds calculation */ - doublereal boundStep(const double* const y, const double* const step0, const int loglevel); + doublereal boundStep(const doublereal * const y, const doublereal * const step0, const int loglevel); //! Set bounds constraints for all variables in the problem @@ -242,10 +284,15 @@ namespace Cantera { /*! * * - * @param J = Jacobian matrix to be filled in - * @param f = Right hand side. This routine returns the current + * @param J Jacobian matrix to be filled in + * @param f Right hand side. This routine returns the current * value of the rhs (output), so that it does * not have to be computed again. + * @param time_curr Current time + * @param CJ inverse of the value of deltaT + * @param y value of the solution vector + * @param ydot value of the time derivative of the solution vector + * @param num_newt_its Number of newton iterations * * @return Returns a flag to indicate that operation is successful. * 1 Means a successful operation @@ -259,6 +306,7 @@ namespace Cantera { /*! * @param timeCurrent Current value of the time * @param ybase current value of the solution + * @param step0 Proposed step change in the solution * * @return Returns the norm of the value of the amount filtered */ @@ -310,7 +358,16 @@ namespace Cantera { * @param ydot0 Base value of the time derivative of teh * solution * @param step0 Initial step suggested. - * @param y1 + * @param y1 Value of y1, the suggested solution after damping + * @param ydot1 Value of the time derivative of the solution at y1 + * @param step1 Value of the step change from y0 to y1 + * @param s1 norm of the step change in going from y0 to y1 + * @param jac Jacobian + * @param loglevel Log level to be used + * @param writetitle Write a title line + * @param num_backtracks Number of backtracks taken + * + * @return returns an integer indicating what happened. */ int dampStep(const doublereal time_curr, const double* y0, const doublereal *ydot0, const double* step0, @@ -331,6 +388,18 @@ namespace Cantera { * equation system for now. Will make it more general later, * if an application comes up. * + * @param SolnType Solution type + * @param y_comm Initial value of the solution. On return this is the converged + * value of the solution + * @param ydot_comm Initial value of the solution derivative. On return this is the + * converged value of the solution derivative. + * @param CJ Inverse of the value of deltaT + * @param time_curr Current value of the time + * @param jac Matrix that will be used to store the jacobian + * @param num_newt_its Number of newton iterations taken + * @param num_linear_solves Number of linear solves taken + * @param num_backtracks Number of backtracking steps taken + * @param loglevelInput Input log level determines the amount of printing. * * * @return A positive value indicates a successful convergence @@ -389,6 +458,9 @@ namespace Cantera { //! Check to see if the nonlinear problem has converged /*! + * + * @param dampCode Code from the damping routine + * @param s1 Value of the norm of the step change * * @return integer is returned. If positive, then the problem has converged * 1 Successful step was taken: Next step's norm is less than 1.0. @@ -429,6 +501,21 @@ namespace Cantera { //! solution norms. void calcSolnToResNormVector(); + //! Set the print level from the rootfinder + /*! + * + * 0 -> absolutely nothing is printed for a single time step. + * 1 -> One line summary per solve_nonlinear call + * 2 -> short description, points of interest: Table of nonlinear solve - one line per iteration + * 3 -> Table is included -> More printing per nonlinear iteration (default) that occurs during the table + * 4 -> Summaries of the nonlinear solve iteration as they are occurring -> table no longer printed + * 5 -> Algorithm information on the nonlinear iterates are printed out + * 6 -> Additional info on the nonlinear iterates are printed out + * 7 -> Additional info on the linear solve is printed out. + * 8 -> Info on a per iterate of the linear solve is printed out. + * + * @param printLvl integer value + */ void setPrintLvl(int printLvl); private: @@ -457,13 +544,17 @@ namespace Cantera { //! Boolean indicating whether a manual delta steps have been input. int m_manualDeltaStepSet; - + + //! Value of the delta step magnitudes std::vector m_deltaStepMagnitudes; + //! Vector containing the current solution of the nonlinear solver std::vector m_y_n; + + //! Vector containing the solution at the previous time step std::vector m_y_nm1; - + //! New value of the solution time derivative std::vector ydot_new; //! Vector of column scaling factors @@ -483,9 +574,6 @@ namespace Cantera { */ std::vector m_rowWtScales; - - - //! Value of the residual for the nonlinear problem std::vector m_resid; @@ -516,6 +604,7 @@ namespace Cantera { //! Vector of the norm doublereal m_normResidPoints[15]; + //! Boolean indicating whether we should scale the residual bool m_resid_scaled; @@ -523,7 +612,6 @@ namespace Cantera { * INTERNAL BOUNDARY INFO FOR SOLUTIONS *****************************************************************************************/ - //! Bounds vector for each species std::vector m_y_high_bounds; @@ -582,8 +670,10 @@ namespace Cantera { */ doublereal time_n; + //! Boolean indicating matrix conditioning int m_matrixConditioning; + //! Order of the time step method = 1 int m_order; //! value of the relative tolerance to use in solving the equation set @@ -592,8 +682,13 @@ namespace Cantera { //! Base value of the absolute tolerance doublereal atolBase_; + //! Vector containing the solution derivative at the previous time step doublereal * m_ydot_nm1; + //! absolute tolerance in the solution unknown + /*! + * This is used to evaluating the weighting factor + */ std::vector atolk_; //! Determines the level of printing for each time step. @@ -620,10 +715,7 @@ namespace Cantera { */ static bool m_TurnOffTiming; - // Turn on or off printing of the Jacobian - /*! - * - */ + //! Turn on or off printing of the Jacobian static bool s_print_NumJac; }; diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index e6e703ede..c209026cb 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -134,50 +134,80 @@ namespace Cantera { // Empty destructor RootFind::~RootFind() { } - //================================================================================================ - double RootFind::delXNonzero(double x1) const { - double deltaX = 1.0E-14 * fabs(x1); - double delmin = DeltaXnorm_ * 1.0E-14; + //================================================================================================ + // Calculate a deltaX from an input value of x + /* + * This routine ensure that the deltaX will be greater or equal to DeltaXNorm_ + * or 1.0E-14 x + * + * @param x1 input value of x + */ + doublereal RootFind::delXNonzero(doublereal x1) const { + doublereal deltaX = 1.0E-14 * fabs(x1); + doublereal delmin = DeltaXnorm_ * 1.0E-14; if (delmin > deltaX) { return delmin; } return deltaX; } //================================================================================================ - double RootFind::delXMeaningful(double x1) const { - double del = delXNonzero(x1); + // Calculate a deltaX from an input value of x + /* + * This routine ensure that the deltaX will be greater or equal to DeltaXNorm_ + * or 1.0E-14 x or deltaXConverged_. + * + * @param x1 input value of x + */ + doublereal RootFind::delXMeaningful(doublereal x1) const { + doublereal del = delXNonzero(x1); if (deltaXConverged_ > del) { return deltaXConverged_; } return del; } //================================================================================================ - double RootFind::deltaXControlled(double x2, double x1) const { - double sgnn = 1.0; + // Calcuated a controlled, nonzero delta between two numbers + /* + * The delta is designed to be greater than or equal to delXMeaningful(x) defined above + * with the same sign as the original delta. Therefore if you subtract it from either + * of the two original numbers, you get a different number. + * + * @param x2 first number + * @param x2 second number + */ + double RootFind::deltaXControlled(doublereal x2, doublereal x1) const { + doublereal sgnn = 1.0; if (x1 > x2) { sgnn = -1.0; } - double deltaX = x2 - x1; - double x = fabs(x2) + fabs(x1); - double deltaXm = delXMeaningful(x); + doublereal deltaX = x2 - x1; + doublereal x = fabs(x2) + fabs(x1); + doublereal deltaXm = delXMeaningful(x); if (fabs(deltaX) < deltaXm) { deltaX = sgnn * deltaXm; } return deltaX; } - //================================================================================================ - bool RootFind::theSame(double x2, double x1) const { - double x = fabs(x2) + fabs(x1); - double deltaX = delXMeaningful(x); + //==================================================================================================================== + // Function to decide whether two real numbers are the same or not + /* + * A comparison is made between the two numbers to decide whether they + * are close to one another. This is defined as being within delXMeaningful() of each other + * + * @param x2 First number + * @param x2 second number + * + * @return Returns a boolean indicating whether the two numbers are the same or not. + */ + bool RootFind::theSame(doublereal x2, doublereal x1) const { + doublereal x = fabs(x2) + fabs(x1); + doublereal deltaX = delXMeaningful(x); if (fabs(x2 - x1) < deltaX) { return true; } return false; } - - - - //================================================================================================ + //==================================================================================================================== /* * The following calculation is a line search method to find the root of a function * @@ -313,8 +343,8 @@ namespace Cantera { */ foundStraddle = foundPosF && foundNegF; if (foundStraddle) { - if (xPosF > xNegF) posStraddle = 1; - else posStraddle = 0 ; + if (xPosF > xNegF) posStraddle = 1; + else posStraddle = 0 ; } bool doQuad = false; bool useNextStrat = false; @@ -332,7 +362,7 @@ namespace Cantera { printf(" RootFind: we are here x2 = %g x1 = %g\n", x2, x1); } #endif - double delXtmp = deltaXControlled(x2, x1); + doublereal delXtmp = deltaXControlled(x2, x1); slope = (f2 - f1) / delXtmp; if (fabs(slope) <= 1.0E-100) { if (printLvl >= 2) { @@ -715,7 +745,7 @@ namespace Cantera { return retn; } - //================================================================================================ + //==================================================================================================================== doublereal RootFind::func(doublereal x) { doublereal r; #ifdef DEBUG_MODE @@ -727,18 +757,52 @@ namespace Cantera { #endif return (r - m_funcTargetValue); } - //================================================================================================ + //==================================================================================================================== + // Set the tolerance parameters for the rootfinder + /* + * These tolerance parameters are used on the function value to determine convergence + * + * + * @param rtol Relative tolerance. The default is 10^-5 + * @param atol absolute tolerance. The default is 10^-11 + */ void RootFind::setTol(doublereal rtol, doublereal atol) { m_atol = atol; m_rtol = rtol; } - //================================================================================================ + //==================================================================================================================== + // Set the print level from the rootfinder + /* + * + * 0 -> absolutely nothing is printed for a single time step. + * 1 -> One line summary per solve_nonlinear call + * 2 -> short description, points of interest: Table of nonlinear solve - one line per iteration + * 3 -> Table is included -> More printing per nonlinear iteration (default) that occurs during the table + * 4 -> Summaries of the nonlinear solve iteration as they are occurring -> table no longer printed + * 5 -> Algorithm information on the nonlinear iterates are printed out + * 6 -> Additional info on the nonlinear iterates are printed out + * 7 -> Additional info on the linear solve is printed out. + * 8 -> Info on a per iterate of the linear solve is printed out. + * + * @param printLvl integer value + */ void RootFind::setPrintLvl(int printlvl) { printLvl = printlvl; } - //================================================================================================ + //==================================================================================================================== + // Set the function behavior flag + /* + * If this is true, the function is generally an increasing function of x. + * In particular, if the algorithm is seeking a higher value of f, it will look + * in the positive x direction. + * + * This type of function is needed because this algorithm must deal with regions of f(x) where + * f is not changing with x. + * + * @param value boolean value + */ void RootFind::setFuncIsGenerallyIncreasing(bool value) { if (value) { @@ -746,7 +810,18 @@ namespace Cantera { } FuncIsGenerallyIncreasing_ = value; } - //================================================================================================ + //==================================================================================================================== + // Set the function behavior flag + /* + * If this is true, the function is generally a decreasing function of x. + * In particular, if the algorithm is seeking a higher value of f, it will look + * in the negative x direction. + * + * This type of function is needed because this algorithm must deal with regions of f(x) where + * f is not changing with x. + * + * @param value boolean value + */ void RootFind::setFuncIsGenerallyDecreasing(bool value) { if (value) { @@ -754,10 +829,16 @@ namespace Cantera { } FuncIsGenerallyDecreasing_ = value; } - //================================================================================================ + //==================================================================================================================== + // Set the minimum value of deltaX + /* + * This sets the value of deltaXNorm_ + * + * @param deltaXNorm + */ void RootFind::setDeltaX(doublereal deltaXNorm) { DeltaXnorm_ = deltaXNorm; } - //================================================================================================ + //==================================================================================================================== } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 5e6dd6429..7a50aaaf9 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -24,9 +24,16 @@ namespace Cantera { + //@{ + /// @name Constant which determines the return integer from the routine + + //! This means that the root solver was a success #define ROOTFIND_SUCCESS 0 + //! This means that the root solver failed to achieve convergence #define ROOTFIND_FAILEDCONVERGENCE -1 + //! This means that the input to the root solver was defective #define ROOTFIND_BADINPUT -2 + //@{ //! Root finder for 1D problems /*! @@ -40,6 +47,8 @@ namespace Cantera { //! Constructor for the object /*! + * + * @param resid Pointer to the residual function to be used to calculate f(x) */ RootFind(ResidEval* resid); @@ -49,19 +58,57 @@ namespace Cantera { private: //! Unimplemented private copy constructor + /*! + * @param right object to be copied + */ RootFind(const RootFind &right); //! Unimplemented private assignment operator + /*! + * @param right object to be copied + */ RootFind& operator=(const RootFind &right); + //! Calculate a deltaX from an input value of x + /*! + * This routine ensure that the deltaX will be greater or equal to DeltaXNorm_ + * or 1.0E-14 x + * + * @param x1 input value of x + */ + doublereal delXNonzero(doublereal x1) const; - double delXNonzero(double x1) const; - - double delXMeaningful(double x1) const; + //! Calculate a deltaX from an input value of x + /*! + * This routine ensure that the deltaX will be greater or equal to DeltaXNorm_ + * or 1.0E-14 x or deltaXConverged_. + * + * @param x1 input value of x + */ + doublereal delXMeaningful(doublereal x1) const; - double deltaXControlled(double x2, double x1) const; + //! Calcuated a controlled, nonzero delta between two numbers + /*! + * The delta is designed to be greater than or equal to delXMeaningful(x) defined above + * with the same sign as the original delta. Therefore if you subtract it from either + * of the two original numbers, you get a different number. + * + * @param x2 first number + * @param x1 second number + */ + doublereal deltaXControlled(doublereal x2, doublereal x1) const; - bool theSame(double x2, double x1) const; + //! Function to decide whether two real numbers are the same or not + /*! + * A comparison is made between the two numbers to decide whether they + * are close to one another. This is defined as being within delXMeaningful() of each other + * + * @param x1 First number + * @param x2 second number + * + * @return Returns a boolean indicating whether the two numbers are the same or not. + */ + bool theSame(doublereal x2, doublereal x1) const; public: @@ -105,24 +152,102 @@ namespace Cantera { */ doublereal func(doublereal x); + //! Set the tolerance parameters for the rootfinder + /*! + * These tolerance parameters are used on the function value to determine convergence + * + * + * @param rtol Relative tolerance. The default is 10^-5 + * @param atol absolute tolerance. The default is 10^-11 + */ void setTol(doublereal rtol, doublereal atol); + //! Set the print level from the rootfinder + /*! + * + * 0 -> absolutely nothing is printed for a single time step. + * 1 -> One line summary per solve_nonlinear call + * 2 -> short description, points of interest: Table of nonlinear solve - one line per iteration + * 3 -> Table is included -> More printing per nonlinear iteration (default) that occurs during the table + * 4 -> Summaries of the nonlinear solve iteration as they are occurring -> table no longer printed + * 5 -> Algorithm information on the nonlinear iterates are printed out + * 6 -> Additional info on the nonlinear iterates are printed out + * 7 -> Additional info on the linear solve is printed out. + * 8 -> Info on a per iterate of the linear solve is printed out. + * + * @param printLvl integer value + */ void setPrintLvl(int printLvl); + + //! Set the function behavior flag + /*! + * If this is true, the function is generally an increasing function of x. + * In particular, if the algorithm is seeking a higher value of f, it will look + * in the positive x direction. + * + * This type of function is needed because this algorithm must deal with regions of f(x) where + * f is not changing with x. + * + * @param value boolean value + */ void setFuncIsGenerallyIncreasing(bool value); + + //! Set the function behavior flag + /*! + * If this is true, the function is generally a decreasing function of x. + * In particular, if the algorithm is seeking a higher value of f, it will look + * in the negative x direction. + * + * This type of function is needed because this algorithm must deal with regions of f(x) where + * f is not changing with x. + * + * @param value boolean value + */ void setFuncIsGenerallyDecreasing(bool value); + + //! Set the minimum value of deltaX + /*! + * This sets the value of deltaXNorm_ + * + * @param deltaXNorm + */ void setDeltaX(doublereal deltaXNorm); public: + + //! Pointer to the residual function evaluator ResidEval *m_residFunc; + + //! Target value for the function. We seek the value of f that is equal to this value doublereal m_funcTargetValue; + + //! Absolute tolerance for the value of f doublereal m_atol; + + //! Relative tolerance for the value of f doublereal m_rtol; + + //! Maximum number of step sizes doublereal m_maxstep; protected: + + //! Print level int printLvl; + + //! Delta X norm. This is the minimum value of deltaX that will be used by the program doublereal DeltaXnorm_; + + //! Boolean indicating whether the function is an increasing with x bool FuncIsGenerallyIncreasing_; + + //! Boolean indicating whether the function is decreasing with x bool FuncIsGenerallyDecreasing_; + + //! Value of delta X that is needed for convergence + /*! + * X will be considered as converged if we are within deltaXConverged_ of the solution + * The default is zero. + */ doublereal deltaXConverged_; }; From bab66a8b892cf233c36a9eb6e90fa1c641e90255 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 12 Jan 2011 00:52:01 +0000 Subject: [PATCH 315/446] Doxygen update --- Cantera/src/numerics/NonlinearSolver.cpp | 32 +++++++------ Cantera/src/numerics/NonlinearSolver.h | 60 +++++++++++------------- Cantera/src/numerics/RootFind.cpp | 15 ++++++ 3 files changed, 60 insertions(+), 47 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index f1115589c..b632f72d1 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -502,20 +502,14 @@ namespace Cantera { m_resid_scaled = false; return retn; } - //==================================================================================================================== - // Compute the undamped Newton step + //==================================================================================================================== + // Scale the matrix /* - * Compute the undamped Newton step. The residual function is - * evaluated at the current time, t_n, at the current values of the - * solution vector, m_y_n, and the solution time derivative, m_ydot_n. - * The Jacobian is not recomputed. - * - * A factored jacobian is reused, if available. If a factored jacobian - * is not available, then the jacobian is factored. Before factoring, - * the jacobian is row and column-scaled. Column scaling is not - * recomputed. The row scales are recomputed here, after column - * scaling has been implemented. - */ + * @param jac Jacobian + * @param y_comm Current value of the solution vector + * @param ydot_comm Current value of the time derivative of the solution vector + * @param time_curr current value of the time + */ void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr) { int irow, jcol; @@ -1480,9 +1474,19 @@ namespace Cantera { return m; } //==================================================================================================================== + // Print solution norm contribution /* + * Prints out the most important entries to the update to the solution vector for the current step * - * + * @param solnDelta0 Raw update vector for the current nonlinear step + * @param s0 Norm of the vector solnDelta0 + * @param solnDelta1 Raw update vector for the next solution value based on the old matrix + * @param s1 Norm of the vector solnDelta1 + * @param title title of the printout + * @param y0 Old value of the solution + * @param y1 New value of the solution after damping corrections + * @param damp Value of the damping factor + * @param num_entries Number of entries to print out */ void NonlinearSolver:: print_solnDelta_norm_contrib(const doublereal * const solnDelta0, diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 918e2f50c..aeec870e5 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -102,7 +102,6 @@ namespace Cantera { */ NonlinearSolver& operator=(const NonlinearSolver &right); - //! Create solution weights for convergence criteria /*! * We create soln weights from the following formula @@ -116,7 +115,6 @@ namespace Cantera { */ void createSolnWeights(const doublereal * const y); - //! L2 norm of the delta of the solution vector /*! * calculate the norm of the solution vector. This will @@ -204,7 +202,6 @@ namespace Cantera { const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac, int loglevel); - //! Set default deulta bounds amounts /*! * Delta bounds are set to 0.01 for all unknowns arbitrarily and capriciously @@ -219,7 +216,6 @@ namespace Cantera { * @param deltaBoundsMagnitudes set the deltaBoundsMagnitude vector */ void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); - //! Bound the step /*! @@ -255,7 +251,6 @@ namespace Cantera { */ doublereal boundStep(const doublereal * const y, const doublereal * const step0, const int loglevel); - //! Set bounds constraints for all variables in the problem /*! * @@ -320,9 +315,9 @@ namespace Cantera { * * @return Returns the norm of the value of the amount filtered */ - doublereal filterNewSolution(const doublereal timeCurrent, doublereal * const y_current, doublereal * const ydot_current); + doublereal filterNewSolution(const doublereal timeCurrent, doublereal * const y_current, + doublereal * const ydot_current); - //! Return the factor by which the undamped Newton step 'step0' //! must be multiplied in order to keep the update within the bounds of an accurate jacobian. /*! @@ -372,12 +367,9 @@ namespace Cantera { int dampStep(const doublereal time_curr, const double* y0, const doublereal *ydot0, const double* step0, double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, - int& loglevel, bool writetitle, + double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, int& num_backtracks); - - //! Find the solution to F(X) = 0 by damped Newton iteration. /*! * On @@ -405,37 +397,41 @@ namespace Cantera { * @return A positive value indicates a successful convergence * -1 Failed convergence */ - int solve_nonlinear_problem(int SolnType, double* y_comm, - double* ydot_comm, doublereal CJ, - doublereal time_curr, - SquareMatrix& jac, - int &num_newt_its, - int &num_linear_solves, - int &num_backtracks, - int loglevelInput); - + int solve_nonlinear_problem(int SolnType, double* y_comm,double* ydot_comm, doublereal CJ, + doublereal time_curr, SquareMatrix& jac,int &num_newt_its, + int &num_linear_solves, int &num_backtracks, int loglevelInput); //! Set the column scales void setColumnScales(); //! Scale the matrix /*! - * + * @param jac Jacobian + * @param y_comm Current value of the solution vector + * @param ydot_comm Current value of the time derivative of the solution vector + * @param time_curr current value of the time */ void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr); - //! Print solution norm contribution + /*! + * Prints out the most important entries to the update to the solution vector for the current step + * + * @param solnDelta0 Raw update vector for the current nonlinear step + * @param s0 Norm of the vector solnDelta0 + * @param solnDelta1 Raw update vector for the next solution value based on the old matrix + * @param s1 Norm of the vector solnDelta1 + * @param title title of the printout + * @param y0 Old value of the solution + * @param y1 New value of the solution after damping corrections + * @param damp Value of the damping factor + * @param num_entries Number of entries to print out + */ void - print_solnDelta_norm_contrib(const doublereal * const solnDelta0, - const char * const s0, - const doublereal * const solnDelta1, - const char * const s1, - const char * const title, - const doublereal * const y0, - const doublereal * const y1, - doublereal damp, - int num_entries); + print_solnDelta_norm_contrib(const doublereal * const solnDelta0, const char * const s0, + const doublereal * const solnDelta1, const char * const s1, + const char * const title, const doublereal * const y0, const doublereal * const y1, + doublereal damp, int num_entries); //! Compute the Residual Weights /*! @@ -474,7 +470,6 @@ namespace Cantera { */ int convergenceCheck(int dampCode, doublereal s1); - //! Set the absolute tolerances for the solution variables /*! * Set the absolute tolerances used in the calculation @@ -607,7 +602,6 @@ namespace Cantera { //! Boolean indicating whether we should scale the residual bool m_resid_scaled; - /***************************************************************************************** * INTERNAL BOUNDARY INFO FOR SOLUTIONS *****************************************************************************************/ diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index c209026cb..cc1b2c103 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -52,6 +52,13 @@ namespace Cantera { /*****************************************************************************/ /*****************************************************************************/ #ifdef DEBUG_MODE + //! Print out a form for the current function evaluation + /*! + * @param fp Pointer to the FILE object + * @param xval Current value of x + * @param fval Current value of f + * @param its Current iteration value + */ static void print_funcEval(FILE *fp, doublereal xval, doublereal fval, int its) { fprintf(fp,"\n"); @@ -65,6 +72,14 @@ namespace Cantera { } #endif //================================================================================================ + //! Solve Ax = b using gauss's method + /*! + * @param c Matrix + * @param idem Assumed number of rows in the matrix + * @param n Number of rows and columns + * @param b right hand side + * @param m Number of right hand sides + */ static int smlequ(doublereal *c, int idem, int n, doublereal *b, int m) { int i, j, k, l; doublereal R; From 60194831c1d5d519432d651152baeab3fe7d6afc Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 12 Jan 2011 20:55:07 +0000 Subject: [PATCH 316/446] Added a copy constructor and an assignment operator --- Cantera/src/equil/MultiPhase.cpp | 162 +++++++++++++++++++++---------- Cantera/src/equil/MultiPhase.h | 18 +++- 2 files changed, 127 insertions(+), 53 deletions(-) diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index b1e29ace4..96e49176c 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -21,7 +21,8 @@ using namespace std; namespace Cantera { - /// Constructor. + //==================================================================================================================== + // Constructor. MultiPhase::MultiPhase() : m_np(0), m_temp(0.0), @@ -33,8 +34,67 @@ namespace Cantera { m_Tmin(1.0), m_Tmax(100000.0) { + } + //==================================================================================================================== + // Copy Constructor + /* + * @param right Object to be copied + */ + MultiPhase::MultiPhase(const MultiPhase &right) : + m_np(0), + m_temp(0.0), + m_press(0.0), + m_nel(0), + m_nsp(0), + m_init(false), + m_eloc(-1), + m_Tmin(1.0), + m_Tmax(100000.0) + { + operator=(right); } - + //==================================================================================================================== + // Destructor. + /* + * Does nothing. Class MultiPhase does not take + * "ownership" (i.e. responsibility for destroying) the + * phase objects. + */ + MultiPhase::~MultiPhase() + { + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + MultiPhase& MultiPhase::operator=(const MultiPhase& right) + { + if (&right != this) { + m_moles = right.m_moles; + // shallow copy of phase pointers + m_phase = right.m_phase; + m_atoms = right.m_atoms; + m_moleFractions = right.m_moleFractions; + m_spphase = right.m_spphase; + m_spstart = right.m_spstart; + m_enames = right.m_enames; + m_enamemap = right.m_enamemap; + m_np = right.m_np; + m_temp = right.m_temp; + m_press = right.m_press; + m_nel = right.m_nel; + m_nsp = right.m_nsp; + m_init = right.m_init; + m_eloc = right.m_eloc; + m_temp_OK = right.m_temp_OK; + m_Tmin = right.m_Tmin; + m_Tmax = right.m_Tmax; + m_elemAbundances = right.m_elemAbundances; + } + return *this; + } + //==================================================================================================================== void MultiPhase:: addPhases(MultiPhase& mix) { index_t n; @@ -42,7 +102,7 @@ namespace Cantera { addPhase(mix.m_phase[n], mix.m_moles[n]); } } - + //==================================================================================================================== void MultiPhase:: addPhases(phase_list& phases, const vector_fp& phaseMoles) { index_t np = phases.size(); @@ -52,7 +112,7 @@ namespace Cantera { } init(); } - + //==================================================================================================================== void MultiPhase:: addPhase(phase_t* p, doublereal moles) { if (m_init) { @@ -121,8 +181,7 @@ namespace Cantera { if (t < m_Tmax) m_Tmax = t; } } - - + //==================================================================================================================== // Process phases and build atomic composition array. This method // must be called after all phases are added, before doing // anything else with the mixture. After init() has been called, @@ -186,7 +245,7 @@ namespace Cantera { updatePhases(); } - + //==================================================================================================================== // Return a reference to phase n. The state of phase n is // also updated to match the state stored locally in the // mixture object. @@ -197,15 +256,17 @@ namespace Cantera { m_phase[n]->setPressure(m_press); return *m_phase[n]; } - + //==================================================================================================================== /// Moles of species \c k. doublereal MultiPhase::speciesMoles(index_t k) const { index_t ip = m_spphase[k]; return m_moles[ip]*m_moleFractions[k]; } - - /// Total moles of element m, summed over all - /// phases + //==================================================================================================================== + // Total moles of global element \a m, summed over all phases. + /* + * @param m Index of the global element + */ doublereal MultiPhase::elementMoles(index_t m) const { doublereal sum = 0.0, phasesum; index_t i, k = 0, ik, nsp; @@ -220,8 +281,8 @@ namespace Cantera { } return sum; } - - /// Total charge, summed over all phases + //==================================================================================================================== + // Total charge, summed over all phases doublereal MultiPhase::charge() const { doublereal sum = 0.0; index_t i; @@ -230,7 +291,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== int MultiPhase::speciesIndex(std::string speciesName, std::string phaseName) { int p = phaseIndex(phaseName); if (p < 0) { @@ -242,7 +303,7 @@ namespace Cantera { } return m_spstart[p] + k; } - + //==================================================================================================================== /// Net charge of one phase (Coulombs). The net charge is computed as /// \f[ Q_p = N_p \sum_k F z_k X_k \f] /// where the sum runs only over species in phase \a p. @@ -256,7 +317,7 @@ namespace Cantera { } return Faraday*phasesum*m_moles[p]; } - + //==================================================================================================================== /// Get the chemical potentials of all species in all phases. void MultiPhase::getChemPotentials(doublereal* mu) const { @@ -267,7 +328,7 @@ namespace Cantera { loc += m_phase[i]->nSpecies(); } } - + //==================================================================================================================== // Get chemical potentials of species with valid thermo // data. This method is designed for use in computing chemical // equilibrium by Gibbs minimization. For solution phases (more @@ -313,7 +374,7 @@ namespace Cantera { loc += m_phase[i]->nSpecies(); } } - + //==================================================================================================================== /// True if species \a k belongs to a solution phase. bool MultiPhase::solutionSpecies(index_t k) const { if (m_phase[m_spphase[k]]->nSpecies() > 1) @@ -334,7 +395,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== /// The enthalpy of the mixture (J). doublereal MultiPhase::enthalpy() const { index_t i; @@ -347,7 +408,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== /// The internal energy of the mixture (J). doublereal MultiPhase::IntEnergy() const { index_t i; @@ -360,7 +421,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== /// The entropy of the mixture (J/K). doublereal MultiPhase::entropy() const { index_t i; @@ -373,7 +434,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== /// The specific heat at constant pressure and composition (J/K). /// Note that this does not account for changes in composition of /// the mixture with temperature. @@ -389,7 +450,7 @@ namespace Cantera { return sum; } - + //==================================================================================================================== /// Set the mole fractions of phase \a n to the values in /// array \a x. @@ -402,7 +463,7 @@ namespace Cantera { m_moleFractions[istart+k] = x[k]; } } - + //==================================================================================================================== // Set the species moles using a map. The map \a xMap maps // species name strings to mole numbers. Mole numbers that are // less than or equal to zero will be set to zero. @@ -416,7 +477,7 @@ namespace Cantera { } setMoles(DATA_PTR(moles)); } - + //==================================================================================================================== // Set the species moles using a string. Unspecified species are // set to zero. void MultiPhase::setMolesByName(const std::string& x) { @@ -435,7 +496,7 @@ namespace Cantera { parseCompString(x, xx); setMolesByName(xx); } - + //==================================================================================================================== // Get the mole numbers of all species in the multiphase // object void MultiPhase::getMoles(doublereal * molNum) const { @@ -454,7 +515,7 @@ namespace Cantera { } } } - + //==================================================================================================================== /// Set the species moles to the values in array \a n. The state /// of each phase object is also updated to have the specified /// composition and the mixture temperature and pressure. @@ -486,7 +547,7 @@ namespace Cantera { loc += nsp; } } - + //==================================================================================================================== void MultiPhase::addSpeciesMoles(const int indexS, const doublereal addedMoles) { vector_fp tmpMoles(m_nsp, 0.0); getMoles(DATA_PTR(tmpMoles)); @@ -496,21 +557,21 @@ namespace Cantera { } setMoles(DATA_PTR(tmpMoles)); } - + //==================================================================================================================== void MultiPhase::setState_TP(const doublereal T, const doublereal Pres) { if (!m_init) init(); m_temp = T; m_press = Pres; updatePhases(); } - + //==================================================================================================================== void MultiPhase::setState_TPMoles(const doublereal T, const doublereal Pres, const doublereal *n) { m_temp = T; m_press = Pres; setMoles(n); } - + //==================================================================================================================== void MultiPhase::getElemAbundances(doublereal *elemAbundances) const { index_t eGlobal; calcElemAbundances(); @@ -518,7 +579,7 @@ namespace Cantera { elemAbundances[eGlobal] = m_elemAbundances[eGlobal]; } } - + //==================================================================================================================== // Internal routine to calculate the element abundance vector void MultiPhase::calcElemAbundances() const { index_t loc = 0; @@ -542,7 +603,7 @@ namespace Cantera { loc += nspPhase; } } - + //==================================================================================================================== /// The total mixture volume [m^3]. doublereal MultiPhase::volume() const { int i; @@ -553,7 +614,7 @@ namespace Cantera { } return sum; } - + //==================================================================================================================== doublereal MultiPhase::equilibrate(int XY, doublereal err, int maxsteps, int maxiter, int loglevel) { doublereal error; @@ -867,18 +928,18 @@ namespace Cantera { } } #endif - + //==================================================================================================================== void MultiPhase::setTemperature(const doublereal T) { if (!m_init) init(); m_temp = T; updatePhases(); } - + //==================================================================================================================== // Name of element \a m. std::string MultiPhase::elementName(int m) const { return m_enames[m]; } - + //==================================================================================================================== // Index of element with name \a name. int MultiPhase::elementIndex(std::string name) const { for (size_t e = 0; e < m_nel; e++) { @@ -888,25 +949,25 @@ namespace Cantera { } return -1; } - + //==================================================================================================================== // Name of species with global index \a k. std::string MultiPhase::speciesName(const int k) const { return m_snames[k]; } - + //==================================================================================================================== doublereal MultiPhase::nAtoms(const int kGlob, const int mGlob) const { return m_atoms(mGlob, kGlob); } - + //==================================================================================================================== void MultiPhase::getMoleFractions(doublereal* const x) const { std::copy(m_moleFractions.begin(), m_moleFractions.end(), x); } - + //==================================================================================================================== std::string MultiPhase::phaseName(const index_t iph) const { const phase_t *tptr = m_phase[iph]; return tptr->id(); } - + //==================================================================================================================== int MultiPhase::phaseIndex(const std::string &pName) const { std::string tmp; for (int iph = 0; iph < (int) m_np; iph++) { @@ -918,32 +979,33 @@ namespace Cantera { } return -1; } - + //==================================================================================================================== doublereal MultiPhase::phaseMoles(const index_t n) const { return m_moles[n]; } - + //==================================================================================================================== void MultiPhase::setPhaseMoles(const index_t n, const doublereal moles) { m_moles[n] = moles; } - + //==================================================================================================================== int MultiPhase::speciesPhaseIndex(const index_t kGlob) const { return m_spphase[kGlob]; } - + //==================================================================================================================== doublereal MultiPhase::moleFraction(const index_t kGlob) const{ return m_moleFractions[kGlob]; } - + //==================================================================================================================== bool MultiPhase::tempOK(const index_t p) const { return m_temp_OK[p]; } - + //==================================================================================================================== /// Update the locally-stored species mole fractions. void MultiPhase::updateMoleFractions() { uploadMoleFractionsFromPhases(); } + //==================================================================================================================== /// Update the locally-stored species mole fractions. void MultiPhase::uploadMoleFractionsFromPhases() { index_t ip, loc = 0; @@ -954,7 +1016,7 @@ namespace Cantera { } calcElemAbundances(); } - + //==================================================================================================================== //------------------------------------------------------------- // // protected methods @@ -981,6 +1043,6 @@ namespace Cantera { } } } - + //==================================================================================================================== } diff --git a/Cantera/src/equil/MultiPhase.h b/Cantera/src/equil/MultiPhase.h index 85ad8a6ae..233602012 100644 --- a/Cantera/src/equil/MultiPhase.h +++ b/Cantera/src/equil/MultiPhase.h @@ -85,13 +85,25 @@ namespace Cantera { */ MultiPhase(); + //! Copy Constructor + /*! + * @param right Object to be copied + */ + MultiPhase(const MultiPhase &right); + //! Destructor. /*! * Does nothing. Class MultiPhase does not take * "ownership" (i.e. responsibility for destroying) the * phase objects. */ - virtual ~MultiPhase() {} + virtual ~MultiPhase(); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + MultiPhase& operator=(const MultiPhase& right); //! Add a vector of phases to the mixture /*! @@ -258,7 +270,7 @@ namespace Cantera { /// conditions for which they are stable. doublereal maxTemp() const { return m_Tmax; } - /// Total charge (Coulombs). + //! Total charge summed over all phases (Coulombs). doublereal charge() const; /// Charge (Coulombs) of phase with index \a p. @@ -267,7 +279,7 @@ namespace Cantera { */ doublereal phaseCharge(index_t p) const; - /// Total moles of global element \a m, summed over all phases. + //! Total moles of global element \a m, summed over all phases. /*! * @param m Index of the global element */ From 8dc95dfbc1e10cf9a9d17ccc1e91b353b02ff115 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 1 Feb 2011 19:08:28 +0000 Subject: [PATCH 317/446] Added accessor functions for phaseStability and phaseExistence() --- Cantera/src/kinetics/InterfaceKinetics.cpp | 38 ++++++++++++++++++--- Cantera/src/kinetics/InterfaceKinetics.h | 39 ++++++++++++++++++---- 2 files changed, 67 insertions(+), 10 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 3ad664d24..00cf51f0c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -1349,8 +1349,7 @@ namespace Cantera { * reduce the computational cost of repeated calls. */ void InterfaceKinetics:: - solvePseudoSteadyStateProblem(int ifuncOverride, - doublereal timeScaleOverride) { + solvePseudoSteadyStateProblem(int ifuncOverride, doublereal timeScaleOverride) { // create our own solver object if (m_integrator == 0) { vector k; @@ -1366,7 +1365,7 @@ namespace Cantera { } //================================================================================================ - void InterfaceKinetics::setPhaseExistence(const int iphase, const bool exists) { + void InterfaceKinetics::setPhaseExistence(const int iphase, const int exists) { if (iphase < 0 || iphase >= (int) m_thermo.size()) { throw CanteraError("InterfaceKinetics:setPhaseExistence", "out of bounds"); } @@ -1384,9 +1383,39 @@ namespace Cantera { } } } + //================================================================================================ + // Gets the phase existence int for the ith phase + /* + * @param iphase Phase Id + * + * @return Returns the int specifying whether the kinetics object thinks the phase exists + * or not. If it exists, then species in that phase can be a reactant in reactions. + */ + int InterfaceKinetics::phaseExistence(const int iphase) const { + if (iphase < 0 || iphase >= (int) m_thermo.size()) { + throw CanteraError("InterfaceKinetics:phaseExistence()", "out of bounds"); + } + return m_phaseExists[iphase]; + } + //================================================================================================ + // Gets the phase stability int for the ith phase + /* + * @param iphase Phase Id + * + * @return Returns the int specifying whether the kinetics object thinks the phase is stable + * with nonzero mole numbers. + * If it stable, then the kinetics object will allow for rates of production of + * of species in that phase that are positive. + */ + int InterfaceKinetics::phaseStability(const int iphase) const { + if (iphase < 0 || iphase >= (int) m_thermo.size()) { + throw CanteraError("InterfaceKinetics:phaseStability()", "out of bounds"); + } + return m_phaseIsStable[iphase]; + } //================================================================================================ - void InterfaceKinetics::setPhaseStability(const int iphase, const bool isStable) { + void InterfaceKinetics::setPhaseStability(const int iphase, const int isStable) { if (iphase < 0 || iphase >= (int) m_thermo.size()) { throw CanteraError("InterfaceKinetics:setPhaseStability", "out of bounds"); } @@ -1396,6 +1425,7 @@ namespace Cantera { m_phaseIsStable[iphase] = false; } } + //================================================================================================ void EdgeKinetics::finalize() { m_rwork.resize(nReactions()); diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 82f30bd4c..23a62928c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -492,7 +492,16 @@ namespace Cantera { */ void _update_rates_T(); + //! Update properties that depend on the electric potential + /*! + * This is called to update all of the properties that depend on potential + */ void _update_rates_phi(); + + //! Update properties that depend on the species mole fractions and/or concentration + /*! + * This is called to update all of the properties that depend on concentration + */ void _update_rates_C(); //! Advance the surface coverages in time @@ -589,8 +598,7 @@ namespace Cantera { * @param iphase Index of the phase. This is the order within the internal thermo vector object * @param exists Boolean indicating whether the phase exists or not */ - void setPhaseExistence(const int iphase, const bool exists); - + void setPhaseExistence(const int iphase, const int exists); //! Set the stability of a phase in the reaction object /*! @@ -607,8 +615,27 @@ namespace Cantera { * @param iphase Index of the phase. This is the order within the internal thermo vector object * @param exists Boolean indicating whether the phase exists or not */ - void setPhaseStability(const int iphase, const bool isStable); + void setPhaseStability(const int iphase, const int isStable); + //! Gets the phase existence int for the ith phase + /*! + * @param iphase Phase Id + * + * @return Returns the int specifying whether the kinetics object thinks the phase exists + * or not. If it exists, then species in that phase can be a reactant in reactions. + */ + int phaseExistence(const int iphase) const; + + //! Gets the phase stability int for the ith phase + /*! + * @param iphase Phase Id + * + * @return Returns the int specifying whether the kinetics object thinks the phase is stable + * with nonzero mole numbers. + * If it stable, then the kinetics object will allow for rates of production of + * of species in that phase that are positive. + */ + int phaseStability(const int iphase) const; protected: @@ -840,9 +867,9 @@ namespace Cantera { * length = number of phases in the object * By default all phases exist. */ - std::vector m_phaseExists; + std::vector m_phaseExists; - //! Vector of booleans indicating whether phases are stable or not + //! Vector of int indicating whether phases are stable or not /*! * Vector of booleans indicating whether a phase is stable or not * under the current conditions. @@ -851,7 +878,7 @@ namespace Cantera { * length = number of phases in the object * By default all phases are stable */ - std::vector m_phaseIsStable; + std::vector m_phaseIsStable; //! Vector of vector of booleans indicating whether a phase participates in a //! reaction as a reactant From 3dbe5d658f4bdf0b3e0fc129ccabfe3fd36f96f9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 2 Feb 2011 05:33:29 +0000 Subject: [PATCH 318/446] Fixed an error in the rootsolver --- Cantera/src/numerics/RootFind.cpp | 29 ++++++++++++++++++++++++++--- Cantera/src/numerics/RootFind.h | 6 ++++++ 2 files changed, 32 insertions(+), 3 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index cc1b2c103..97c42eff1 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -46,6 +46,11 @@ namespace Cantera { #ifndef DSIGN #define DSIGN(x) (( (x) == (0.0) ) ? (0.0) : ( ((x) > 0.0) ? 1.0 : -1.0 )) +#endif + +// turn on debugging for now +#ifndef DEBUG_MODE +#define DEBUG_MODE #endif /*****************************************************************************/ @@ -141,7 +146,11 @@ namespace Cantera { DeltaXnorm_(0.01), FuncIsGenerallyIncreasing_(false), FuncIsGenerallyDecreasing_(false), - deltaXConverged_(0.0) + deltaXConverged_(0.0), + x_maxTried_(-1.0E300), + fx_maxTried_(0.0), + x_minTried_(1.0E300), + fx_minTried_(0.0) { } @@ -239,6 +248,8 @@ namespace Cantera { * We store the function target and then actually calculate a modified functional * * func = eval(x1) - m_funcTargetValue = 0 + * + * */ m_funcTargetValue = funcTargetValue; @@ -295,6 +306,8 @@ namespace Cantera { x1 = (xmin + xmax) / 2.0; } + x_maxTried_ = x1; + x_minTried_ = x1; f1 = func(x1); #ifdef DEBUG_MODE @@ -372,7 +385,7 @@ namespace Cantera { * Find an estimate of the next point, xnew, to try based on * a linear approximation from the last two points. */ -#ifdef DEBUG_HKM +#ifdef DEBUG_MODE if (fabs(x2 - x1) < 1.0E-14) { printf(" RootFind: we are here x2 = %g x1 = %g\n", x2, x1); } @@ -386,6 +399,7 @@ namespace Cantera { } xnew = x2 + DeltaXnorm_; slopePointingToHigher = true; + useNextStrat = true; } else { useNextStrat = false; xnew = x2 - f2 / slope; @@ -770,7 +784,16 @@ namespace Cantera { #ifdef DEBUG_MODE mdp::checkFinite(r); #endif - return (r - m_funcTargetValue); + doublereal ff = r - m_funcTargetValue; + if (x >= x_maxTried_) { + x_maxTried_ = x; + fx_maxTried_ = ff; + } + if (x <= x_minTried_) { + x_minTried_ = x; + fx_minTried_ = ff; + } + return ff; } //==================================================================================================================== // Set the tolerance parameters for the rootfinder diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 7a50aaaf9..bc5b6e3fc 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -250,6 +250,12 @@ namespace Cantera { */ doublereal deltaXConverged_; + doublereal x_maxTried_; + doublereal fx_maxTried_; + + doublereal x_minTried_; + doublereal fx_minTried_; + }; } #endif From 0c178dbdd8576d65ced462c917a4e36d47d1e404 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 10 Feb 2011 20:59:53 +0000 Subject: [PATCH 319/446] Prototyping a Dogleg method. Added in the calcualtion of the steepest descent and the Cauchy point --- Cantera/src/numerics/NonlinearSolver.cpp | 98 +++++++++++++++++++++++- Cantera/src/numerics/NonlinearSolver.h | 21 +++++ 2 files changed, 118 insertions(+), 1 deletion(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index b632f72d1..b57c7cb36 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -122,6 +122,11 @@ namespace Cantera { atolk_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001) +#ifdef DEBUG_DOGLEG + ,descentDir_(0), + residNorm2Cauchy_(0.0), + Jd_(0) +#endif { neq_ = m_func->nEquations(); @@ -145,6 +150,13 @@ namespace Cantera { atolk_[i] = atolBase_; m_ewt[i] = atolk_[i]; } + +#ifdef DEBUG_DOGLEG + jacCopy_.resize(neq_, neq_, 0.0); + descentDir_.resize(neq_, 0.0); + Jd_.resize(neq_, 0.0); +#endif + } //==================================================================================================================== NonlinearSolver::NonlinearSolver(const NonlinearSolver &right) : @@ -191,6 +203,11 @@ namespace Cantera { atolk_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001) +#ifdef DEBUG_DOGLEG + ,descentDir_(0), + residNorm2Cauchy_(0.0), + Jd_(0) +#endif { *this =operator=(right); } @@ -248,6 +265,11 @@ namespace Cantera { atolk_ = right.atolk_; m_print_flag = right.m_print_flag; m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; +#ifdef DEBUG_DOGLEG + jacCopy_ = right.jacCopy_; + descentDir_ = right.descentDir_; + Jd_ = right.Jd_; +#endif return *this; } @@ -704,6 +726,75 @@ namespace Cantera { return info; } //==================================================================================================================== + #ifdef DEBUG_DOGLEG + // Do a steepest descent calculation + /* + * This call must be made on the unfactored jacobian! + */ + int NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) + { + double rowFac = 1.0; + // Calculate desDir = -0.5 * R dot J + /* + * this would be faster:: + * vector_fp &dd = jac.data(); + * descentDir[j] -= 0.5 * resid[i] * dd[i*neq_ * j[; + */ + for (int j = 0; j < neq_; j++) { + descentDir_[j] = 0.0; + double colFac = 1.0; + if (m_colScaling) { + colFac = 1.0/m_colScales[j]; + } + for (int i = 0; i < neq_; i++) { + if (m_rowScaling) { + rowFac = 1.0/m_rowScales[i]; + } + descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / (m_residWts[i] * m_residWts[i]); + } + } + for (int j = 0; j < neq_; j++) { + Jd_[j] = 0.0; + double colFac = 1.0; + if (m_colScaling) { + colFac = 1.0/m_colScales[j]; + } + for (int i = 0; i < neq_; i++) { + if (m_rowScaling) { + rowFac = 1.0/m_rowScales[i]; + } + Jd_[j] += descentDir_[j] * jac.value(i,j) *rowFac * colFac/ m_residWts[i]; + } + } + double RJd_norm = 0.0; + double JdJd_norm = 0.0; + for (int i = 0; i < neq_; i++) { + RJd_norm += m_resid[i] * Jd_[i] / m_residWts[i]; + JdJd_norm += Jd_[i] * Jd_[i]; + } + double lambda = - RJd_norm / (JdJd_norm); + + for (int i = 0; i < neq_; i++) { + descentDir_[i] *= lambda; + } + + residNorm2Cauchy_ = m_normResidFRaw * m_normResidFRaw - RJd_norm * RJd_norm / (JdJd_norm*JdJd_norm); + + // Compute the weighted norm of the undamped step size descentDir_[] + doublereal sDD = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); + + + if (m_print_flag > 2) { + printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); + printf("\t\t\t Rraw = %g Rpred = %g, deltaX = %g\n", m_normResidFRaw, residNorm2Cauchy_, sDD); + } + + + + return 0; + } +#endif + //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { for (int i = 0; i < neq_; i++) { @@ -1174,7 +1265,9 @@ namespace Cantera { int m = 0; bool forceNewJac = false; doublereal s1=1.e30; - +#ifdef DEBUG_DOGLEG + jacCopy_ = jac; +#endif // std::vector y_curr(neq_, 0.0); std::vector ydot_curr(neq_, 0.0); @@ -1298,6 +1391,9 @@ namespace Cantera { m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n)); } +#ifdef DEBUG_DOGLEG + doCauchyPointSolve(jac); +#endif // compute the undamped Newton step info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), jac, m_print_flag); diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index aeec870e5..5f93f5aab 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -496,6 +496,11 @@ namespace Cantera { //! solution norms. void calcSolnToResNormVector(); +#ifdef DEBUG_DOGLEG + int doCauchyPointSolve(SquareMatrix& jac); + +#endif + //! Set the print level from the rootfinder /*! * @@ -702,6 +707,22 @@ namespace Cantera { //! Scale factor for turning residual norms into solution norms double m_ScaleSolnNormToResNorm; + +#ifdef DEBUG_DOGLEG + //! Copy of the jacobian that doesn't get overwritten when the inverse is determined + SquareMatrix jacCopy_; + + //! Steepest descent direction. This is also the distance to the Cauchy Point + std::vector descentDir_; + + //! Expected value of the residual norm at the Cauchy point + doublereal residNorm2Cauchy_; + + //! Jacobian times the Steepest descent direction. + std::vector Jd_; + +#endif + public: //! Turn off printing of time /*! From ecc2d271c967019e82d0a305d619c00fc1c05be5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 12 Feb 2011 03:36:24 +0000 Subject: [PATCH 320/446] Worked on verifying the steepest descent calculation --- Cantera/src/numerics/NonlinearSolver.cpp | 119 +++++++++++++++-------- Cantera/src/numerics/NonlinearSolver.h | 33 ++++--- Cantera/src/numerics/SquareMatrix.cpp | 31 +++++- Cantera/src/numerics/SquareMatrix.h | 29 +++--- 4 files changed, 144 insertions(+), 68 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index b57c7cb36..63a56a7c1 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -83,8 +83,8 @@ namespace Cantera { solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), m_ewt(0), - m_manualDeltaBoundsSet(0), - m_deltaBoundsMagnitudes(0), + m_manualDeltaStepSet(0), + m_deltaStepMinimum(0), m_y_n(0), m_y_nm1(0), ydot_new(0), @@ -121,17 +121,19 @@ namespace Cantera { m_ydot_nm1(0), atolk_(0), m_print_flag(0), - m_ScaleSolnNormToResNorm(0.001) -#ifdef DEBUG_DOGLEG - ,descentDir_(0), + m_ScaleSolnNormToResNorm(0.001), + jacCopy_(0), + descentDir_(0), residNorm2Cauchy_(0.0), - Jd_(0) -#endif + Jd_(0), + trustDeltaX_(0) + { neq_ = m_func->nEquations(); m_ewt.resize(neq_, rtol_); - m_deltaBoundsMagnitudes.resize(neq_, 0.001); + m_deltaStepMinimum.resize(neq_, 0.001); + m_deltaStepMaximum.resize(neq_, 1.0E10); m_y_n.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); ydot_new.resize(neq_, 0.0); @@ -142,7 +144,7 @@ namespace Cantera { m_wksp.resize(neq_, 0.0); m_residWts.resize(neq_, 0.0); atolk_.resize(neq_, atolBase_); - doublereal hb = std::numeric_limits::max(); + doublereal hb = std::numeric_limits::max(); m_y_high_bounds.resize(neq_, hb); m_y_low_bounds.resize(neq_, -hb); @@ -155,6 +157,7 @@ namespace Cantera { jacCopy_.resize(neq_, neq_, 0.0); descentDir_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); + trustDeltaX_.resize(neq_, 0.0); #endif } @@ -164,8 +167,8 @@ namespace Cantera { solnType_(NSOLN_TYPE_STEADY_STATE), neq_(0), m_ewt(0), - m_manualDeltaBoundsSet(0), - m_deltaBoundsMagnitudes(0), + m_manualDeltaStepSet(0), + m_deltaStepMinimum(0), m_y_n(0), m_y_nm1(0), ydot_new(0), @@ -202,12 +205,12 @@ namespace Cantera { m_ydot_nm1(0), atolk_(0), m_print_flag(0), - m_ScaleSolnNormToResNorm(0.001) -#ifdef DEBUG_DOGLEG - ,descentDir_(0), + m_ScaleSolnNormToResNorm(0.001), + jacCopy_(0), + descentDir_(0), residNorm2Cauchy_(0.0), - Jd_(0) -#endif + Jd_(0), + trustDeltaX_(0) { *this =operator=(right); } @@ -227,8 +230,8 @@ namespace Cantera { solnType_ = right.solnType_; neq_ = right.neq_; m_ewt = right.m_ewt; - m_manualDeltaBoundsSet = right.m_manualDeltaBoundsSet; - m_deltaBoundsMagnitudes = right.m_deltaBoundsMagnitudes; + m_manualDeltaStepSet = right.m_manualDeltaStepSet; + m_deltaStepMinimum = right.m_deltaStepMinimum; m_y_n = right.m_y_n; m_y_nm1 = right.m_y_nm1; ydot_new = right.ydot_new; @@ -265,11 +268,12 @@ namespace Cantera { atolk_ = right.atolk_; m_print_flag = right.m_print_flag; m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; -#ifdef DEBUG_DOGLEG + jacCopy_ = right.jacCopy_; descentDir_ = right.descentDir_; Jd_ = right.Jd_; -#endif + trustDeltaX_ = right.trustDeltaX_; + return *this; } @@ -726,7 +730,7 @@ namespace Cantera { return info; } //==================================================================================================================== - #ifdef DEBUG_DOGLEG + // Do a steepest descent calculation /* * This call must be made on the unfactored jacobian! @@ -750,7 +754,9 @@ namespace Cantera { if (m_rowScaling) { rowFac = 1.0/m_rowScales[i]; } - descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / (m_residWts[i] * m_residWts[i]); + descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / (m_residWts[i] * m_residWts[i]); + // descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / ( m_residWts[i]); + //descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac; } } for (int j = 0; j < neq_; j++) { @@ -763,7 +769,8 @@ namespace Cantera { if (m_rowScaling) { rowFac = 1.0/m_rowScales[i]; } - Jd_[j] += descentDir_[j] * jac.value(i,j) *rowFac * colFac/ m_residWts[i]; + Jd_[j] += descentDir_[j] * jac.value(i,j) * rowFac * colFac/ m_residWts[i]; + //Jd_[j] += descentDir_[j] * jac.value(i,j) *rowFac * colFac; } } double RJd_norm = 0.0; @@ -778,7 +785,13 @@ namespace Cantera { descentDir_[i] *= lambda; } - residNorm2Cauchy_ = m_normResidFRaw * m_normResidFRaw - RJd_norm * RJd_norm / (JdJd_norm*JdJd_norm); + residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm * RJd_norm / (JdJd_norm); + double residCauchy = 0.0; + if (residNorm2Cauchy_ > 0.0) { + residCauchy = sqrt(residNorm2Cauchy_); + } else { + residCauchy = m_normResid0 - sqrt(RJd_norm * RJd_norm / (JdJd_norm)); + } // Compute the weighted norm of the undamped step size descentDir_[] doublereal sDD = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); @@ -786,30 +799,34 @@ namespace Cantera { if (m_print_flag > 2) { printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); - printf("\t\t\t Rraw = %g Rpred = %g, deltaX = %g\n", m_normResidFRaw, residNorm2Cauchy_, sDD); + printf("\t\t\t R0 = %g \n", m_normResid0); + printf("\t\t\t Rpred = %g\n", residCauchy); + printf("\t\t\t Rjd = %g\n", RJd_norm); + printf("\t\t\t JdJd = %g\n", JdJd_norm); + printf("\t\t\t deltaX = %g\n", sDD); } return 0; } -#endif + //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { for (int i = 0; i < neq_; i++) { - m_deltaBoundsMagnitudes[i] = 1000. * atolk_[i]; - m_deltaBoundsMagnitudes[i] = MAX(m_deltaBoundsMagnitudes[i], 0.1 * fabs(m_y_n[i])); + m_deltaStepMinimum[i] = 1000. * atolk_[i]; + m_deltaStepMinimum[i] = MAX(m_deltaStepMinimum[i], 0.1 * fabs(m_y_n[i])); } } //==================================================================================================================== - void NonlinearSolver::setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes) + void NonlinearSolver::setDeltaBoundsMagnitudes(const doublereal * const deltaStepMinimum) { for (int i = 0; i < neq_; i++) { - m_deltaBoundsMagnitudes[i] = deltaBoundsMagnitudes[i]; + m_deltaStepMinimum[i] = deltaStepMinimum[i]; } - m_manualDeltaBoundsSet = 1; + m_manualDeltaStepSet = 1; } //==================================================================================================================== /* @@ -855,16 +872,16 @@ namespace Cantera { if (sameSign >= 0.0) { if ((fabs(y_new) > 1.5 * fabs(y[i])) && - (fabs(y_new - y[i]) > m_deltaBoundsMagnitudes[i])) { + (fabs(y_new - y[i]) > m_deltaStepMinimum[i])) { ff = 0.5 * fabs(y[i]/(y_new - y[i])); - ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); ifbd = 1; } if ((fabs(2.0 * y_new) < fabs(y[i])) && - (fabs(y_new - y[i]) > m_deltaBoundsMagnitudes[i])) { + (fabs(y_new - y[i]) > m_deltaStepMinimum[i])) { ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; - ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); ifbd = 0; } @@ -873,9 +890,9 @@ namespace Cantera { * This handles the case where the value crosses the origin. * - First we don't let it cross the origin until its shrunk to the size of m_deltaBoundsMagnitudes[i] */ - if (fabs(y[i]) > m_deltaBoundsMagnitudes[i]) { + if (fabs(y[i]) > m_deltaStepMinimum[i]) { ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; - ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); if (y[i] >= 0.0) { ifbd = 0; @@ -888,7 +905,7 @@ namespace Cantera { */ else if (fabs(y_new) > 0.5 * fabs(y[i])) { ff = y[i]/(y_new - y[i]) * (-1.5); - ff_alt = fabs(m_deltaBoundsMagnitudes[i] / (y_new - y[i])); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); ff = MAX(ff, ff_alt); ifbd = 0; } @@ -924,6 +941,28 @@ namespace Cantera { return f_delta_bounds; } + //==================================================================================================================== + + void NonlinearSolver::calcTrustVector(const doublereal * const y, const int loglevel) + { + double oldVal; + double fabsy; + for (int i = 0; i < neq_; i++) { + oldVal = trustDeltaX_[i]; + fabsy = fabs(y[i]); + if (oldVal > 0.5 * fabsy) { + if (fabsy > m_deltaStepMinimum[i]) { + trustDeltaX_[i] = 0.5 * fabsy; + } else { + trustDeltaX_[i] = m_deltaStepMinimum[i]; + } + } + + } + + + } + //==================================================================================================================== /* * @@ -1266,7 +1305,7 @@ namespace Cantera { bool forceNewJac = false; doublereal s1=1.e30; #ifdef DEBUG_DOGLEG - jacCopy_ = jac; + //jacCopy_ = jac; #endif // std::vector y_curr(neq_, 0.0); @@ -1327,7 +1366,7 @@ namespace Cantera { /* * Set default values of Delta bounds constraints */ - if (!m_manualDeltaBoundsSet) { + if (!m_manualDeltaStepSet) { setDefaultDeltaBoundsMagnitudes(); } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 5f93f5aab..2b8a7e7c2 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -20,6 +20,7 @@ #define CT_NONLINEARSOLVER_H #include "ResidJacEval.h" +#include "SquareMatrix.h" namespace Cantera { @@ -217,6 +218,10 @@ namespace Cantera { */ void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); + + void calcTrustVector(const doublereal * const y, const int loglevel); + + //! Bound the step /*! * @@ -496,10 +501,16 @@ namespace Cantera { //! solution norms. void calcSolnToResNormVector(); -#ifdef DEBUG_DOGLEG + //! Calculate the Steepest descent direction and the Cauchy Point where the quadratic formulation + //! of the nonlinear problem expects a minimum along the descent direction. + /*! + * @param jac Jacobian matrix: must be unfactored. + * + * @return Returns 0 for success. + */ int doCauchyPointSolve(SquareMatrix& jac); -#endif + //! Set the print level from the rootfinder /*! @@ -537,16 +548,13 @@ namespace Cantera { std::vector m_ewt; //! Boolean indicating whether a manual delta bounds has been input. - int m_manualDeltaBoundsSet; - - //! Soln Delta bounds magnitudes - std::vector m_deltaBoundsMagnitudes; - - //! Boolean indicating whether a manual delta steps have been input. int m_manualDeltaStepSet; + //! Soln Delta bounds magnitudes + std::vector m_deltaStepMinimum; + //! Value of the delta step magnitudes - std::vector m_deltaStepMagnitudes; + std::vector m_deltaStepMaximum; //! Vector containing the current solution of the nonlinear solver std::vector m_y_n; @@ -707,10 +715,8 @@ namespace Cantera { //! Scale factor for turning residual norms into solution norms double m_ScaleSolnNormToResNorm; - -#ifdef DEBUG_DOGLEG //! Copy of the jacobian that doesn't get overwritten when the inverse is determined - SquareMatrix jacCopy_; + Cantera::SquareMatrix jacCopy_; //! Steepest descent direction. This is also the distance to the Cauchy Point std::vector descentDir_; @@ -721,7 +727,8 @@ namespace Cantera { //! Jacobian times the Steepest descent direction. std::vector Jd_; -#endif + std::vector trustDeltaX_; + public: //! Turn off printing of time diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 41c7857cc..2dc7fc274 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -27,7 +27,30 @@ using namespace std; namespace Cantera { - /** + + + //==================================================================================================================== + SquareMatrix::SquareMatrix() : + DenseMatrix(), + m_factored(false) + { + } + + // Constructor. + /* + * Create an \c n by \c n matrix, and initialize + * all elements to \c v. + * + * @param n size of the square matrix + * @param v intial value of all matrix components. + */ + SquareMatrix::SquareMatrix(int n, doublereal v) : + DenseMatrix(n, n, v), + m_factored(false) + { + } + + /* * * copy constructor */ @@ -94,7 +117,11 @@ namespace Cantera { (void) memset((void *) sm, 0, nn * sizeof(double)); } } - + //==================================================================================================================== + void SquareMatrix::resize(int n, int m, doublereal v) { + DenseMatrix::resize(n, m, v); + } + //==================================================================================================================== /** * Factor A. A is overwritten with the LU decomposition of A. */ diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index d6c767952..a110e6a77 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -29,21 +29,21 @@ namespace Cantera { public: - SquareMatrix(): - DenseMatrix(), - m_factored(false) - { - } - /** - * Constructor. Create an \c n by \c n matrix, and initialize - * all elements to \c v. + //! Base Constructor. + /*! + * Create an \c 0 by \c 0 matrix, and initialize all elements to \c 0. */ - SquareMatrix(int n, doublereal v = 0.0) : - DenseMatrix(n, n, v), - m_factored(false) - { - } + SquareMatrix(); + + //! Constructor. + /*! + * Create an \c n by \c n matrix, and initialize all elements to \c v. + * + * @param n size of the square matrix + * @param v intial value of all matrix components. + */ + SquareMatrix(int n, doublereal v = 0.0); /** * Copy Constructor @@ -64,6 +64,9 @@ namespace Cantera { */ int solve(double *b); + void resize(int n, int m, doublereal v = 0.0); + + /** * Zero the matrix */ From 6a902abd2424c6f982e9243024ea967ae4c16953 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 15 Feb 2011 02:57:34 +0000 Subject: [PATCH 321/446] More work on the dogleg option. Figured out and verified the calculation of the steepest direction when there are scaled residuals and scaled solution variables. --- Cantera/src/numerics/NonlinearSolver.cpp | 172 +++++++++++++++-------- Cantera/src/numerics/NonlinearSolver.h | 27 +++- 2 files changed, 142 insertions(+), 57 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 63a56a7c1..a4f7e3618 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -125,6 +125,8 @@ namespace Cantera { jacCopy_(0), descentDir_(0), residNorm2Cauchy_(0.0), + RJd_norm_(0.0), + lambda_(0.0), Jd_(0), trustDeltaX_(0) @@ -209,6 +211,8 @@ namespace Cantera { jacCopy_(0), descentDir_(0), residNorm2Cauchy_(0.0), + RJd_norm_(0.0), + lambda_(0.0), Jd_(0), trustDeltaX_(0) { @@ -271,6 +275,8 @@ namespace Cantera { jacCopy_ = right.jacCopy_; descentDir_ = right.descentDir_; + RJd_norm_ = right.RJd_norm_; + lambda_ = right.lambda_; Jd_ = right.Jd_; trustDeltaX_ = right.trustDeltaX_; @@ -293,6 +299,11 @@ namespace Cantera { for (int i = 0; i < neq_; i++) { m_ewt[i] = rtol_ * fabs(y[i]) + atolk_[i]; } +#ifdef DEBUG_DOGLEG + // for (int i = 0; i < neq_; i++) { + // m_ewt[i] = 1.0E-4; + // } +#endif } //==================================================================================================================== // set bounds constraints for all variables in the problem @@ -333,7 +344,7 @@ namespace Cantera { * only used for printout out a table. */ doublereal NonlinearSolver::solnErrorNorm(const doublereal * const delta_y, const char * title, int printLargest, - const doublereal dampFactor) + const doublereal dampFactor) { int i; doublereal sum_norm = 0.0, error; @@ -598,7 +609,6 @@ namespace Cantera { for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 1.0/m_rowScales[irow]; - m_rowWtScales[irow] = m_rowWtScales[irow]; } // What we have defined is a maximum value that the residual can be and still pass. // This isn't sufficient. @@ -623,13 +633,13 @@ namespace Cantera { //==================================================================================================================== void NonlinearSolver::calcSolnToResNormVector() { - double oldVal = m_ScaleSolnNormToResNorm; - if (m_normSolnFRaw > 1.0E-13) { - m_ScaleSolnNormToResNorm = 1.0E-2 * m_normResid0 / m_normSolnFRaw * oldVal; - } - m_normResid0 = m_normSolnFRaw; - computeResidWts(); - + // double oldVal = m_ScaleSolnNormToResNorm; + // if (m_normSolnFRaw > 1.0E-13) { + // m_ScaleSolnNormToResNorm = 1.0E-2 * m_normResid0 / m_normSolnFRaw * oldVal; + //} + // m_normResid0 = m_normSolnFRaw; + //computeResidWts(); + m_ScaleSolnNormToResNorm = 1.0; //double tmp = residErrorNorm(DATA_PTR(m_resid)); } //==================================================================================================================== @@ -730,7 +740,6 @@ namespace Cantera { return info; } //==================================================================================================================== - // Do a steepest descent calculation /* * This call must be made on the unfactored jacobian! @@ -740,77 +749,122 @@ namespace Cantera { double rowFac = 1.0; // Calculate desDir = -0.5 * R dot J /* - * this would be faster:: - * vector_fp &dd = jac.data(); - * descentDir[j] -= 0.5 * resid[i] * dd[i*neq_ * j[; - */ + * For confirmation of the scaling factors, see Dennis and Schnabel p, 152, p, 156 and my notes + * + */ for (int j = 0; j < neq_; j++) { descentDir_[j] = 0.0; double colFac = 1.0; if (m_colScaling) { - colFac = 1.0/m_colScales[j]; + colFac = 1.0 / m_colScales[j]; } for (int i = 0; i < neq_; i++) { if (m_rowScaling) { - rowFac = 1.0/m_rowScales[i]; + rowFac = 1.0 / m_rowScales[i]; } - descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / (m_residWts[i] * m_residWts[i]); - // descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac / ( m_residWts[i]); - //descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) *colFac; + descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] + / (m_residWts[i] * m_residWts[i]); } } - for (int j = 0; j < neq_; j++) { - Jd_[j] = 0.0; - double colFac = 1.0; - if (m_colScaling) { - colFac = 1.0/m_colScales[j]; + for (int i = 0; i < neq_; i++) { + Jd_[i] = 0.0; + if (m_rowScaling) { + rowFac = 1.0 / m_rowScales[i]; + } else { + rowFac = 1.0; } - for (int i = 0; i < neq_; i++) { - if (m_rowScaling) { - rowFac = 1.0/m_rowScales[i]; - } - Jd_[j] += descentDir_[j] * jac.value(i,j) * rowFac * colFac/ m_residWts[i]; - //Jd_[j] += descentDir_[j] * jac.value(i,j) *rowFac * colFac; + for (int j = 0; j < neq_; j++) { + Jd_[i] += descentDir_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; } } - double RJd_norm = 0.0; + + RJd_norm_ = 0.0; double JdJd_norm = 0.0; for (int i = 0; i < neq_; i++) { - RJd_norm += m_resid[i] * Jd_[i] / m_residWts[i]; + RJd_norm_ += m_resid[i] * Jd_[i] / m_residWts[i]; JdJd_norm += Jd_[i] * Jd_[i]; } - double lambda = - RJd_norm / (JdJd_norm); + lambda_ = - RJd_norm_ / (JdJd_norm); for (int i = 0; i < neq_; i++) { - descentDir_[i] *= lambda; + descentDir_[i] *= lambda_; } - residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm * RJd_norm / (JdJd_norm); - double residCauchy = 0.0; - if (residNorm2Cauchy_ > 0.0) { - residCauchy = sqrt(residNorm2Cauchy_); - } else { - residCauchy = m_normResid0 - sqrt(RJd_norm * RJd_norm / (JdJd_norm)); - } - - // Compute the weighted norm of the undamped step size descentDir_[] - doublereal sDD = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); - + residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm_ * RJd_norm_ / (JdJd_norm); if (m_print_flag > 2) { + + double residCauchy = 0.0; + if (residNorm2Cauchy_ > 0.0) { + residCauchy = sqrt(residNorm2Cauchy_); + } else { + residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm)); + } + + // Compute the weighted norm of the undamped step size descentDir_[] + doublereal sDD = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); + printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid0); printf("\t\t\t Rpred = %g\n", residCauchy); - printf("\t\t\t Rjd = %g\n", RJd_norm); + printf("\t\t\t Rjd = %g\n", RJd_norm_); printf("\t\t\t JdJd = %g\n", JdJd_norm); printf("\t\t\t deltaX = %g\n", sDD); + printf("\t\t\t lambda = %g\n", lambda_); } - - - return 0; } + //=================================================================================================================== + void NonlinearSolver::descentComparison(double time_curr, double *ydot0, double *ydot1, const double *newtDir) + { + int info; + double ff = 1.0E-5; + double *y1 = DATA_PTR(m_wksp); + double s1 = solnErrorNorm(DATA_PTR(descentDir_)); + for (int i = 0; i < neq_; i++) { + y1[i] = m_y_n[i] + ff * descentDir_[i]; + } + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + double normResid02 = m_normResid0 * m_normResid0 * neq_; + double residSteep = residErrorNorm(DATA_PTR(m_resid)); + double residSteep2 = residSteep * residSteep * neq_; + double residDecrease2 = (residSteep2 - normResid02) / ( ff * s1); + double sNewt = solnErrorNorm(DATA_PTR(newtDir)); + for (int i = 0; i < neq_; i++) { + y1[i] = m_y_n[i] + ff * newtDir[i]; + } + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + double residNewt = residErrorNorm(DATA_PTR(m_resid)); + double residNewt2 = residNewt * residNewt * neq_; + + double residDecreaseNewt2 = (residNewt2 - normResid02) / ( ff * sNewt); + + double residDL = 2.0 * RJd_norm_ / s1 * lambda_; + /* + * HKM These have been shown to exactly match up. + * The steepest direction is always largest even when there are variable solution weights + */ + printf("descentComparison: rate of decrease in linearized cauchy dir = %g\n", residDL); + printf("descentComparison: rate of decrease in cauchy dir = %g\n", residDecrease2); + printf("descentComparison: rate of decrease in newtondir = %g\n", residDecreaseNewt2); + } //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { @@ -1446,13 +1500,22 @@ namespace Cantera { } else { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); } - calcSolnToResNormVector(); + // calcSolnToResNormVector(); + + + + /* * Filter out bad directions */ filterNewStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(stp)); - + + + +#ifdef DEBUG_DOGLEG + descentComparison(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); +#endif // Damp the Newton step /* @@ -1954,13 +2017,12 @@ namespace Cantera { { doublereal sum = 0.0; for (int i = 0; i < neq_; i++) { - m_residWts[i] =m_rowWtScales[i]; - + m_residWts[i] = m_rowWtScales[i]; sum += m_residWts[i]; } sum /= neq_; for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * atolBase_ * sum); + m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * atolBase_ * sum); } } //===================================================================================================================== @@ -1975,9 +2037,7 @@ namespace Cantera { residWts[i] = (m_residWts)[i]; } } - //===================================================================================================================== - // Check to see if the nonlinear problem has converged /* * diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 2b8a7e7c2..c3f5c8ffb 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -501,7 +501,7 @@ namespace Cantera { //! solution norms. void calcSolnToResNormVector(); - //! Calculate the Steepest descent direction and the Cauchy Point where the quadratic formulation + //! Calculate the steepest descent direction and the Cauchy Point where the quadratic formulation //! of the nonlinear problem expects a minimum along the descent direction. /*! * @param jac Jacobian matrix: must be unfactored. @@ -510,6 +510,24 @@ namespace Cantera { */ int doCauchyPointSolve(SquareMatrix& jac); + //! This is a utility routine that can be used to print out the rates of the initial residual decline + /*! + * The residual**2 decline for various directions is printed out. The rate of decline of the + * square of the residuals multiplied by the number of equations along each direction is printed out + * This quantity can be directly related to the theory, and may be calculated from derivatives at the + * original point. + * + * ( (r)**2 * neq - (r0)**2 * neq ) / distance + * + * What's printed out: + * + * The theoretical linearized residual decline + * The actual residual decline in the steepest descent direction determined by numerical differencing + * The actual residual decline in the newton direction determined by numerical differencing + * + * This routine doesn't need to be called for the solution of the nonlinear problem. + */ + void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); //! Set the print level from the rootfinder @@ -724,9 +742,16 @@ namespace Cantera { //! Expected value of the residual norm at the Cauchy point doublereal residNorm2Cauchy_; + //! Residual dot Jd norm + doublereal RJd_norm_; + + //! Value of lambda_ which is used to calculate the Cauchy point + doublereal lambda_; + //! Jacobian times the Steepest descent direction. std::vector Jd_; + //! Vector of trust region values. std::vector trustDeltaX_; From 96880bae269799dcd6f611eac7e50b847f99b5c0 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 15 Feb 2011 17:09:03 +0000 Subject: [PATCH 322/446] Worked on trust region calculcations --- Cantera/src/numerics/NonlinearSolver.cpp | 101 ++++++++++++++++++----- Cantera/src/numerics/NonlinearSolver.h | 38 ++++++++- 2 files changed, 116 insertions(+), 23 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index a4f7e3618..c1d9868c4 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -128,7 +128,8 @@ namespace Cantera { RJd_norm_(0.0), lambda_(0.0), Jd_(0), - trustDeltaX_(0) + trustDeltaX_(0), + trustDelta_(1.0) { neq_ = m_func->nEquations(); @@ -159,7 +160,7 @@ namespace Cantera { jacCopy_.resize(neq_, neq_, 0.0); descentDir_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); - trustDeltaX_.resize(neq_, 0.0); + trustDeltaX_.resize(neq_, 1.0); #endif } @@ -214,7 +215,8 @@ namespace Cantera { RJd_norm_(0.0), lambda_(0.0), Jd_(0), - trustDeltaX_(0) + trustDeltaX_(0), + trustDelta_(1.0) { *this =operator=(right); } @@ -279,7 +281,7 @@ namespace Cantera { lambda_ = right.lambda_; Jd_ = right.Jd_; trustDeltaX_ = right.trustDeltaX_; - + trustDelta_ = right.trustDelta_; return *this; } @@ -429,7 +431,7 @@ namespace Cantera { * out to standard output. */ doublereal NonlinearSolver::residErrorNorm(const doublereal * const resid, const char * title, const int printLargest, - const doublereal * const y) + const doublereal * const y) { int i; doublereal sum_norm = 0.0, error; @@ -996,27 +998,73 @@ namespace Cantera { return f_delta_bounds; } //==================================================================================================================== - - void NonlinearSolver::calcTrustVector(const doublereal * const y, const int loglevel) + //! Calculate the trust region vectors + /*! + * The trust region is made up of the trust region vector calculation and the trustDelta_ value + * We periodically recalculate the trustVector_ values so that they renormalize to the + * correct length. + */ + void NonlinearSolver::calcTrustVector() { + double wtSum = 0.0; + for (int i = 0; i < neq_; i++) { + wtSum += m_ewt[i]; + } + + // This is the size of each component. + double trustDeltaEach = trustDelta_ / neq_; double oldVal; double fabsy; + // we use the old value of the trust region as an indicator for (int i = 0; i < neq_; i++) { oldVal = trustDeltaX_[i]; - fabsy = fabs(y[i]); + fabsy = fabs(m_y_n[i]); + // First off make sure that each trust region vector is 1/2 the size of each variable or smaller + // unless overridden by the deltaStepMininum value. if (oldVal > 0.5 * fabsy) { if (fabsy > m_deltaStepMinimum[i]) { trustDeltaX_[i] = 0.5 * fabsy; } else { trustDeltaX_[i] = m_deltaStepMinimum[i]; } + } else { + double newValue = trustDeltaEach * m_ewt[i] / wtSum; + if (newValue > 2.0 * oldVal) { + newValue = 2.0 * oldVal; + } else if (newValue < 0.5 * oldVal) { + newValue = 0.5 * oldVal; + } + trustDeltaX_[i] = newValue; + if (trustDeltaX_[i] > 0.75 * m_deltaStepMaximum[i]) { + trustDeltaX_[i] = m_deltaStepMaximum[i]; + } } - - } + } + // Final renormalization. + double sum = 0.0; + for (int i = 0; i < neq_; i++) { + sum += trustDeltaX_[i]; + } + for (int i = 0; i < neq_; i++) { + trustDeltaX_[i] = trustDelta_ / sum; + } + trustDelta_ = 1.0; + + } + //==================================================================================================================== + doublereal NonlinearSolver::calcTrustDistance(std::vector const & deltaX) const + { + doublereal sum = 0.0; + doublereal tmp = 0.0; + for (int i = 0; i < neq_; i++) { + tmp = deltaX[i] / trustDeltaX_[i]; + sum += tmp * tmp; + } + sum = sqrt(sum / neq_); + return sum; } - //==================================================================================================================== /* * @@ -1344,10 +1392,8 @@ namespace Cantera { double* ydot_comm, doublereal CJ, doublereal time_curr, SquareMatrix& jac, - int &num_newt_its, - int &num_linear_solves, - int &num_backtracks, - int loglevelInput) + int &num_newt_its, int &num_linear_solves, + int &num_backtracks, int loglevelInput) { clockWC wc; int convRes = 0; @@ -1410,10 +1456,21 @@ namespace Cantera { num_newt_its++; /* - * If we are far enough away from the solution, redo the solution weights. + * If we are far enough away from the solution, redo the solution weights and the trust vectors. */ if (m_normSolnFRaw > 1.0E2) { createSolnWeights(DATA_PTR(m_y_n)); +#ifdef DEBUG_DOGLEG + calcTrustVector(); +#endif + } else { + // Do this stuff every 5 iterations + if ( (num_newt_its % 5) == 1) { + createSolnWeights(DATA_PTR(m_y_n)); +#ifdef DEBUG_DOGLEG + calcTrustVector(); +#endif + } } //mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_curr), neq_); @@ -1500,10 +1557,16 @@ namespace Cantera { } else { m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); } - // calcSolnToResNormVector(); - - + +#ifdef DEBUG_DOGLEG + double trustD = calcTrustDistance(stp); + if (trustD > trustDelta_) { + printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); + } else { + printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); + } +#endif /* diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index c3f5c8ffb..339a11059 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -53,7 +53,12 @@ namespace Cantera { * * Newton's method is used. * - * Damping is used extensively when relaxing the system + * Damping is used extensively when relaxing the system. + * + * + * The basic idea is that we predict a direction that is parameterized by an overall coordinate + * value, beta, from zero to one, This may or may not be the same as the value, damp, + * depending upon whether the direction is straight. * * * @@ -218,10 +223,31 @@ namespace Cantera { */ void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); + protected: + //! Calculate the trust region vectors + /*! + * The trust region is made up of the trust region vector calculation and the trustDelta_ value + * We periodically recalculate the trustVector_ values so that they renormalize to the + * correct length. We change the trustDelta_ values regularly + * + * The trust region calculate is based on + * + * || delta_x dot 1/trustDeltaX_ || <= trustDelta_ + * + * @param y current value of the solution + */ + void calcTrustVector(); - void calcTrustVector(const doublereal * const y, const int loglevel); - - + //! Calculate the trust distance + /*! + * We calculate the trust distance by the following method + * + * trustDist = || delta_x dot 1/trustDeltaX_ || + * + * @param deltaX Current value of deltaX + */ + doublereal calcTrustDistance(std::vector const & deltaX) const; + public: //! Bound the step /*! * @@ -754,6 +780,10 @@ namespace Cantera { //! Vector of trust region values. std::vector trustDeltaX_; + //! Current value of trust radius. This is used with trustDeltaX_ to + //! calculate the max step size. + doublereal trustDelta_; + public: //! Turn off printing of time From 80227d3314b7fd2b6533fd40b93b802340df77ef Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 16 Feb 2011 16:40:02 +0000 Subject: [PATCH 323/446] More work on dogleg algorithm --- Cantera/src/numerics/Makefile.in | 2 + Cantera/src/numerics/NonlinearSolver.cpp | 90 ++++++++++++++++++------ Cantera/src/numerics/NonlinearSolver.h | 25 +++++-- 3 files changed, 92 insertions(+), 25 deletions(-) diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index ce443314b..bfd885d08 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -30,6 +30,8 @@ PURIFY=@PURIFY@ PIC_FLAG=@PIC@ +#LOCAL_DEFS=-DDEBUG_DOGLEG + CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index c1d9868c4..0e0f5f52b 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -96,7 +96,8 @@ namespace Cantera { m_residWts(0), m_normResid0(0.0), m_normResidFRaw(0.0), - m_normSolnFRaw(0.0), + m_normDeltaSoln_Newton(0.0), + m_normDeltaSoln_CP(0.0), m_normResidTrial(0.0), m_resid_scaled(false), m_y_high_bounds(0), @@ -183,7 +184,8 @@ namespace Cantera { m_residWts(0), m_normResid0(0.0), m_normResidFRaw(0.0), - m_normSolnFRaw(0.0), + m_normDeltaSoln_Newton(0.0), + m_normDeltaSoln_CP(0.0), m_normResidTrial(0.0), m_resid_scaled(false), m_y_high_bounds(0), @@ -249,7 +251,8 @@ namespace Cantera { m_residWts = right.m_residWts; m_normResid0 = right.m_normResid0; m_normResidFRaw = right.m_normResidFRaw; - m_normSolnFRaw = right.m_normSolnFRaw; + m_normDeltaSoln_Newton = right.m_normDeltaSoln_Newton; + m_normDeltaSoln_CP = right.m_normDeltaSoln_CP; m_normResidTrial = right.m_normResidTrial; m_resid_scaled = right.m_resid_scaled; m_y_high_bounds = right.m_y_high_bounds; @@ -645,7 +648,7 @@ namespace Cantera { //double tmp = residErrorNorm(DATA_PTR(m_resid)); } //==================================================================================================================== - // Compute the undamped Newton step + // Compute the undamped Newton step based on the current jacobian and an input rhs /* * Compute the undamped Newton step. The residual function is * evaluated at the current time, t_n, at the current values of the @@ -705,8 +708,7 @@ namespace Cantera { printf("\n Details on delta_Y for row %d \n", focusRow); printf(" Value before = %15.5e, delta = %15.5e," "value after = %15.5e\n", y_curr[focusRow], - delta_y[focusRow], - y_curr[focusRow] + delta_y[focusRow]); + delta_y[focusRow], y_curr[focusRow] + delta_y[focusRow]); if (!freshJac) { printf(" Old Jacobian\n"); } @@ -746,9 +748,10 @@ namespace Cantera { /* * This call must be made on the unfactored jacobian! */ - int NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) + doublereal NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) { double rowFac = 1.0; + double normSoln; // Calculate desDir = -0.5 * R dot J /* * For confirmation of the scaling factors, see Dennis and Schnabel p, 152, p, 156 and my notes @@ -804,17 +807,17 @@ namespace Cantera { } // Compute the weighted norm of the undamped step size descentDir_[] - doublereal sDD = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); + normSoln = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid0); printf("\t\t\t Rpred = %g\n", residCauchy); printf("\t\t\t Rjd = %g\n", RJd_norm_); printf("\t\t\t JdJd = %g\n", JdJd_norm); - printf("\t\t\t deltaX = %g\n", sDD); + printf("\t\t\t deltaX = %g\n", normSoln); printf("\t\t\t lambda = %g\n", lambda_); } - return 0; + return normSoln; } //=================================================================================================================== void NonlinearSolver::descentComparison(double time_curr, double *ydot0, double *ydot1, const double *newtDir) @@ -859,14 +862,59 @@ namespace Cantera { double residDecreaseNewt2 = (residNewt2 - normResid02) / ( ff * sNewt); double residDL = 2.0 * RJd_norm_ / s1 * lambda_; + + double residDecreaseNewtExp2 = - 2.0 * normResid02 / sNewt; + /* * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights */ printf("descentComparison: rate of decrease in linearized cauchy dir = %g\n", residDL); printf("descentComparison: rate of decrease in cauchy dir = %g\n", residDecrease2); + printf("\n"); + printf("descentComparison: rate of decrease in newtondir (expected) = %g\n", residDecreaseNewtExp2); printf("descentComparison: rate of decrease in newtondir = %g\n", residDecreaseNewt2); } + + //==================================================================================================================== + // Setup the line search along the double dog leg + /* + * the calls the doCauchySolve() and doNewtonSolve() are done at the main level + */ + void NonlinearSolver::setupDoubleDogleg() + { + + for (int i = 0; i < neq_; i++) { + // m_wksp[i] = Nuu_ * stepNewton_[i] - descentCauchy_[i]; + } + + + double gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; + + + Nuu_ = 0.8 * gamma + 0.2; + + dist_R0_ = m_normDeltaSoln_CP; + dist_R1_ = solnErrorNorm( DATA_PTR(m_wksp)); + dist_R2_ = (1.0 - Nuu_) * m_normDeltaSoln_Newton; + dist_Total_ = dist_R0_ + dist_R1_ + dist_R2_; + + + } + //==================================================================================================================== + double NonlinearSolver::expectedResid(double lambda) { + if (lambda < dist_R0_ / dist_Total_) { + + } else if (lambda < ((dist_R0_ + dist_R1_)/ dist_Total_)) { + + } else { + + } + + return 0.0; + + } + //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { @@ -1423,7 +1471,7 @@ namespace Cantera { } // Redo the solution weights every time we enter the function createSolnWeights(DATA_PTR(m_y_n)); - m_normSolnFRaw = 1.0E1; + m_normDeltaSoln_Newton = 1.0E1; bool frst = true; num_newt_its = 0; num_linear_solves = - m_numTotalLinearSolves; @@ -1458,7 +1506,7 @@ namespace Cantera { /* * If we are far enough away from the solution, redo the solution weights and the trust vectors. */ - if (m_normSolnFRaw > 1.0E2) { + if (m_normDeltaSoln_Newton > 1.0E2) { createSolnWeights(DATA_PTR(m_y_n)); #ifdef DEBUG_DOGLEG calcTrustVector(); @@ -1542,7 +1590,7 @@ namespace Cantera { } #ifdef DEBUG_DOGLEG - doCauchyPointSolve(jac); + m_normSolnCP = doCauchyPointSolve(jac); #endif // compute the undamped Newton step @@ -1553,9 +1601,9 @@ namespace Cantera { } if (m_print_flag > 3) { - m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); } else { - m_normSolnFRaw = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); } @@ -1583,8 +1631,10 @@ namespace Cantera { // Damp the Newton step /* * On return the recommended new solution and derivatisve is located in: - * m_y_new - * m_y_dot_new + * y_new + * y_dot_new + * The update delta vector is located in + * stp1 * The estimate of the solution update norm for the next step is located in * s1 */ @@ -1676,7 +1726,7 @@ namespace Cantera { printf(" N |"); } printf("%5d %11.3E | %10.2E %10.2E %2d | %11.3E %11.3E ", m_numTotalLinearSolves, 0.0, m_dampBound, m_dampRes, - i_backtracks, m_normSolnFRaw, m_normResidFRaw); + i_backtracks, m_normDeltaSoln_Newton, m_normResidFRaw); printf("\n"); } @@ -2134,7 +2184,7 @@ namespace Cantera { } } if (s1 < 0.8) { - if (m_normSolnFRaw < 1.0) { + if (m_normDeltaSoln_Newton < 1.0) { return 2; } } @@ -2148,7 +2198,7 @@ namespace Cantera { } if (s1 < 0.8) { - if (m_normSolnFRaw < 1.0) { + if (m_normDeltaSoln_Newton < 1.0) { return 2; } } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 339a11059..5ec4cc34c 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -204,7 +204,7 @@ namespace Cantera { * @return Returns the result code from lapack. A zero means success. Anything * else indicates a failure. */ - int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, + int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac, int loglevel); @@ -532,9 +532,9 @@ namespace Cantera { /*! * @param jac Jacobian matrix: must be unfactored. * - * @return Returns 0 for success. + * @return Returns the norm of the solution update */ - int doCauchyPointSolve(SquareMatrix& jac); + doublereal doCauchyPointSolve(SquareMatrix& jac); //! This is a utility routine that can be used to print out the rates of the initial residual decline /*! @@ -555,6 +555,8 @@ namespace Cantera { */ void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); + void setupDoubleDogleg(); + double expectedResid(double lambda); //! Set the print level from the rootfinder /*! @@ -600,7 +602,7 @@ namespace Cantera { //! Value of the delta step magnitudes std::vector m_deltaStepMaximum; - //! Vector containing the current solution of the nonlinear solver + //! Vector containing the current solution vector within the nonlinear solver std::vector m_y_n; //! Vector containing the solution at the previous time step @@ -648,7 +650,11 @@ namespace Cantera { doublereal m_normResidFRaw; //! Norm of the solution update created by the iteration in its raw, undamped form. - doublereal m_normSolnFRaw; + doublereal m_normDeltaSoln_Newton; + + + //! Norm of the solution update created by the iteration in its raw, undamped form. + doublereal m_normDeltaSoln_CP; //! Norm of the residual for a trial calculation which may or may not be used doublereal m_normResidTrial; @@ -784,6 +790,15 @@ namespace Cantera { //! calculate the max step size. doublereal trustDelta_; + doublereal Nuu_; + + doublereal dist_R0_; + doublereal dist_R1_; + doublereal dist_R2_; + doublereal dist_Total_; + doublereal m_normSolnCP; + + public: //! Turn off printing of time From 3996c38b3c0045cde2a1096747cc1ca28f8acbb8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 16 Feb 2011 17:46:28 +0000 Subject: [PATCH 324/446] Changed the residual weights formula --- Cantera/src/numerics/NonlinearSolver.cpp | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 0e0f5f52b..cfc16b8a0 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -869,11 +869,10 @@ namespace Cantera { * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights */ - printf("descentComparison: rate of decrease in linearized cauchy dir = %g\n", residDL); - printf("descentComparison: rate of decrease in cauchy dir = %g\n", residDecrease2); - printf("\n"); - printf("descentComparison: rate of decrease in newtondir (expected) = %g\n", residDecreaseNewtExp2); - printf("descentComparison: rate of decrease in newtondir = %g\n", residDecreaseNewt2); + printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", residDL); + printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", residDecrease2); + printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", residDecreaseNewtExp2); + printf("descentComparison: initial rate of decrease in newton dir = %g\n", residDecreaseNewt2); } //==================================================================================================================== @@ -904,6 +903,10 @@ namespace Cantera { //==================================================================================================================== double NonlinearSolver::expectedResid(double lambda) { if (lambda < dist_R0_ / dist_Total_) { + /* + * We are on the steepest descent line + */ + } else if (lambda < ((dist_R0_ + dist_R1_)/ dist_Total_)) { @@ -2130,7 +2133,7 @@ namespace Cantera { { doublereal sum = 0.0; for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_rowWtScales[i]; + m_residWts[i] = m_rowWtScales[i] / neq_; sum += m_residWts[i]; } sum /= neq_; From 6dd143640c2bc1724d5854f194f46f8373260f93 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 18 Feb 2011 20:25:53 +0000 Subject: [PATCH 325/446] Incremental progress on dogleg --- Cantera/src/numerics/NonlinearSolver.cpp | 300 +++++++++++++++++++---- Cantera/src/numerics/NonlinearSolver.h | 62 ++++- 2 files changed, 305 insertions(+), 57 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index cfc16b8a0..3f878ea6f 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -39,6 +39,9 @@ extern void print_line(const char *, int); #define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) #define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) #endif +#ifndef CONSTD_DATA_PTR +#define CONSTD_DATA_PTR(x) (( const double *) (&x[0])) +#endif //@} using namespace std; @@ -124,7 +127,8 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), - descentDir_(0), + deltax_cp_(0), + deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), lambda_(0.0), @@ -148,6 +152,7 @@ namespace Cantera { m_wksp.resize(neq_, 0.0); m_residWts.resize(neq_, 0.0); atolk_.resize(neq_, atolBase_); + deltaX_Newton_.resize(neq_, 0.0); doublereal hb = std::numeric_limits::max(); m_y_high_bounds.resize(neq_, hb); m_y_low_bounds.resize(neq_, -hb); @@ -159,7 +164,7 @@ namespace Cantera { #ifdef DEBUG_DOGLEG jacCopy_.resize(neq_, neq_, 0.0); - descentDir_.resize(neq_, 0.0); + deltax_cp_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); trustDeltaX_.resize(neq_, 1.0); #endif @@ -212,7 +217,8 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), - descentDir_(0), + deltax_cp_(0), + deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), lambda_(0.0), @@ -279,7 +285,8 @@ namespace Cantera { m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; jacCopy_ = right.jacCopy_; - descentDir_ = right.descentDir_; + deltax_cp_ = right.deltax_cp_; + deltaX_Newton_ = right.deltaX_Newton_; RJd_norm_ = right.RJd_norm_; lambda_ = right.lambda_; Jd_ = right.Jd_; @@ -349,7 +356,7 @@ namespace Cantera { * only used for printout out a table. */ doublereal NonlinearSolver::solnErrorNorm(const doublereal * const delta_y, const char * title, int printLargest, - const doublereal dampFactor) + const doublereal dampFactor) const { int i; doublereal sum_norm = 0.0, error; @@ -758,7 +765,7 @@ namespace Cantera { * */ for (int j = 0; j < neq_; j++) { - descentDir_[j] = 0.0; + deltax_cp_[j] = 0.0; double colFac = 1.0; if (m_colScaling) { colFac = 1.0 / m_colScales[j]; @@ -767,8 +774,8 @@ namespace Cantera { if (m_rowScaling) { rowFac = 1.0 / m_rowScales[i]; } - descentDir_[j] -= 0.5 * m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] - / (m_residWts[i] * m_residWts[i]); + deltax_cp_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] + / (m_residWts[i] * m_residWts[i]); } } for (int i = 0; i < neq_; i++) { @@ -779,23 +786,23 @@ namespace Cantera { rowFac = 1.0; } for (int j = 0; j < neq_; j++) { - Jd_[i] += descentDir_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; + Jd_[i] += deltax_cp_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; } } RJd_norm_ = 0.0; - double JdJd_norm = 0.0; + JdJd_norm_ = 0.0; for (int i = 0; i < neq_; i++) { RJd_norm_ += m_resid[i] * Jd_[i] / m_residWts[i]; - JdJd_norm += Jd_[i] * Jd_[i]; + JdJd_norm_ += Jd_[i] * Jd_[i]; } - lambda_ = - RJd_norm_ / (JdJd_norm); + lambda_ = - RJd_norm_ / (JdJd_norm_); for (int i = 0; i < neq_; i++) { - descentDir_[i] *= lambda_; + deltax_cp_[i] *= lambda_; } - residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm_ * RJd_norm_ / (JdJd_norm); + residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); if (m_print_flag > 2) { @@ -803,17 +810,17 @@ namespace Cantera { if (residNorm2Cauchy_ > 0.0) { residCauchy = sqrt(residNorm2Cauchy_); } else { - residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm)); + residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); } // Compute the weighted norm of the undamped step size descentDir_[] - normSoln = solnErrorNorm(DATA_PTR(descentDir_), "SteepestDescentDir", 10); + normSoln = solnErrorNorm(DATA_PTR(deltax_cp_), "SteepestDescentDir", 10); printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid0); - printf("\t\t\t Rpred = %g\n", residCauchy); + printf("\t\t\t Rpred = %g\n", residCauchy); printf("\t\t\t Rjd = %g\n", RJd_norm_); - printf("\t\t\t JdJd = %g\n", JdJd_norm); + printf("\t\t\t JdJd = %g\n", JdJd_norm_); printf("\t\t\t deltaX = %g\n", normSoln); printf("\t\t\t lambda = %g\n", lambda_); } @@ -825,9 +832,9 @@ namespace Cantera { int info; double ff = 1.0E-5; double *y1 = DATA_PTR(m_wksp); - double s1 = solnErrorNorm(DATA_PTR(descentDir_)); + double s1 = solnErrorNorm(DATA_PTR(deltax_cp_)); for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + ff * descentDir_[i]; + y1[i] = m_y_n[i] + ff * deltax_cp_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -842,7 +849,8 @@ namespace Cantera { double normResid02 = m_normResid0 * m_normResid0 * neq_; double residSteep = residErrorNorm(DATA_PTR(m_resid)); double residSteep2 = residSteep * residSteep * neq_; - double residDecrease2 = (residSteep2 - normResid02) / ( ff * s1); + double funcDecrease2 = 0.5 * (residSteep2 - normResid02) / ( ff * s1); + double sNewt = solnErrorNorm(DATA_PTR(newtDir)); for (int i = 0; i < neq_; i++) { y1[i] = m_y_n[i] + ff * newtDir[i]; @@ -859,20 +867,20 @@ namespace Cantera { double residNewt = residErrorNorm(DATA_PTR(m_resid)); double residNewt2 = residNewt * residNewt * neq_; - double residDecreaseNewt2 = (residNewt2 - normResid02) / ( ff * sNewt); + double funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); - double residDL = 2.0 * RJd_norm_ / s1 * lambda_; + double funcDecreaseSDExp = RJd_norm_ / s1 * lambda_; - double residDecreaseNewtExp2 = - 2.0 * normResid02 / sNewt; + double funcDecreaseNewtExp2 = - normResid02 / sNewt; /* * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights */ - printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", residDL); - printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", residDecrease2); - printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", residDecreaseNewtExp2); - printf("descentComparison: initial rate of decrease in newton dir = %g\n", residDecreaseNewt2); + printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); + printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); + printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); + printf("descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); } //==================================================================================================================== @@ -880,41 +888,235 @@ namespace Cantera { /* * the calls the doCauchySolve() and doNewtonSolve() are done at the main level */ - void NonlinearSolver::setupDoubleDogleg() + void NonlinearSolver::setupDoubleDogleg(double * newtDir) { - - for (int i = 0; i < neq_; i++) { - // m_wksp[i] = Nuu_ * stepNewton_[i] - descentCauchy_[i]; - } - + /* + * Gamma = ||grad f ||**4 + * --------------------------------------------- + * (grad f)T H (grad f) (grad f)T H-1 (grad f) + */ + // doublereal sumG = 0.0; + // doublereal sumH = 0.0; + // for (int i = 0; i < neq_; i++) { + // sumG = deltax_cp_[i] * deltax_cp_[i]; + // sumH = deltax_cp_[i] * newtDir[i]; + // } + // double fac1 = sumG / lambda_; + // double fac2 = sumH / lambda_; + // double gamma = fac1 / fac2; + // double gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; + /* + * This hasn't worked. so will do it heuristically. One issue is that the newton + * direction is not the inverse of the Hessian times the gradient. The Hession + * is the matrix squared. Until I have the inverse of the Hessian from QR factorization + * I may not be able to do it this way. + */ - double gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; + /* + * Heuristic algorithm - Find out where on the Newton line the residual is the same + * as the residual at the cauchy point. Then, go halfway to + * the newton point and call that Nuu. + * Maybe we need to check that the linearized residual is + * monotonic along that line. However, we haven't needed to yet. + */ + double residSteepLin = expectedResidLeg(0, 1.0); + double Nres2CP = residSteepLin * residSteepLin * neq_; + double Nres2_o = m_normResid0 * m_normResid0 * neq_; + double a = Nres2CP / Nres2_o; + double betaEqual = (2.0 - sqrt(4.0 - 4 * (1.0 - a))) / 2.0; + double beta = (1.0 + betaEqual) / 2.0; + + + Nuu_ = beta; + + // put in a loop here to test derivative. - - Nuu_ = 0.8 * gamma + 0.2; dist_R0_ = m_normDeltaSoln_CP; dist_R1_ = solnErrorNorm( DATA_PTR(m_wksp)); dist_R2_ = (1.0 - Nuu_) * m_normDeltaSoln_Newton; dist_Total_ = dist_R0_ + dist_R1_ + dist_R2_; + /* + * Calculate the trust distances + */ + } //==================================================================================================================== - double NonlinearSolver::expectedResid(double lambda) { + int NonlinearSolver::lambdaToLeg(const double lambda, double &alpha) const { + if (lambda < dist_R0_ / dist_Total_) { + alpha = lambda * dist_Total_ / dist_R0_; + return 0; + } else if (lambda < ((dist_R0_ + dist_R1_)/ dist_Total_)) { + alpha = (lambda * dist_Total_ - dist_R0_) / dist_R1_; + return 1; + } + alpha = (lambda * dist_Total_ - dist_R0_ - dist_R1_) / dist_R2_; + return 2; + } + //==================================================================================================================== + double NonlinearSolver::expectedResidLeg(int leg, double alpha) const { + + double resD2, res2, resNorm; + double normResid02 = m_normResid0 * m_normResid0 * neq_; + + if (leg == 0) { /* * We are on the steepest descent line + * along that line + * R2 = R2 + 2 lambda R dot Jd + lambda**2 Jd dot Jd */ - - } else if (lambda < ((dist_R0_ + dist_R1_)/ dist_Total_)) { + double tmp = - 2.0 * alpha + alpha * alpha; + double tmp2 = - RJd_norm_ * lambda_; + resD2 = tmp2 * tmp; + + } else if (leg == 1) { + + + double tmp2 = - RJd_norm_ * lambda_; + resD2 =- tmp2; + + double res2 = m_normResid0 * m_normResid0 * neq_ + resD2; + double resCP; + if (res2 < 0.0) { + resCP = m_normResid0 - sqrt(resD2/neq_); + } else { + resCP = sqrt(res2 / neq_); + } + + double beta = Nuu_; + double tmpN2 = normResid02; + double tmpN = 1.0 - 2.0 * beta + 1.0 * beta * beta - 1.0; + double resNu2 = tmpN * tmpN2; + res2 = m_normResid0 * m_normResid0 * neq_ + resNu2; + double resNuu; + if (res2 < 0.0) { + resNuu = m_normResid0 - sqrt(res2/neq_); + } else { + resNuu = sqrt(res2 / neq_); + } + resNorm = resCP + alpha * (resNuu - resCP); + return resNorm; + } else { - + double beta = Nuu_ + alpha * (1.0 - Nuu_); + double tmp2 = normResid02; + double tmp = 1.0 - 2.0 * beta + 1.0 * beta * beta - 1.0; + resD2 = tmp * tmp2; + } + + res2 = m_normResid0 * m_normResid0 * neq_ + resD2; + if (res2 < 0.0) { + resNorm = m_normResid0 - sqrt(resD2/neq_); + } else { + resNorm = sqrt(res2 / neq_); + } + + return resNorm; + + } + //==================================================================================================================== + // Here we print out the residual at various points along the double dogleg, comparing against the quadratic model + + void NonlinearSolver::residualComparisonLeg(const double time_curr, const double *ydot0, + const double *ydot1, const double *newtDir) { + double *y1 = DATA_PTR(m_wksp); + double sLen; + printf(" residualComparisonLeg() \n"); + printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); + // First compare at 1/4 along SD curve + std::vector alphaT; + alphaT.push_back(0.00); + alphaT.push_back(0.01); + alphaT.push_back(0.1); + alphaT.push_back(0.25); + alphaT.push_back(0.50); + alphaT.push_back(0.75); + alphaT.push_back(1.0); + for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { + double alpha = alphaT[iteration]; + for (int i = 0; i < neq_; i++) { + y1[i] = m_y_n[i] + alpha * deltax_cp_[i]; + } + sLen = alpha * solnErrorNorm(DATA_PTR(deltax_cp_)); + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + + + double residSteep = residErrorNorm(DATA_PTR(m_resid)); + double residSteepLin = expectedResidLeg(0, alpha); + + double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); + } + + for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { + double alpha = alphaT[iteration]; + for (int i = 0; i < neq_; i++) { + y1[i] = m_y_n[i] + (1.0 - alpha) * deltax_cp_[i]; + y1[i] += alpha * Nuu_ * newtDir[i]; + } + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + + for (int i = 0; i < neq_; i++) { + y1[i] -= m_y_n[i]; + } + sLen = solnErrorNorm(DATA_PTR(y1)); + + double residSteep = residErrorNorm(DATA_PTR(m_resid)); + double residSteepLin = expectedResidLeg(1, alpha); + + double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); + } + + for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { + double alpha = alphaT[iteration]; + for (int i = 0; i < neq_; i++) { + y1[i] = m_y_n[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* newtDir[i]; + } + sLen = ( Nuu_ + alpha * (1.0 - Nuu_)) * solnErrorNorm(DATA_PTR(newtDir)); + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + + + + double residSteep = residErrorNorm(DATA_PTR(m_resid)); + double residSteepLin = expectedResidLeg(2, alpha); + + double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); } - return 0.0; } @@ -1593,15 +1795,16 @@ namespace Cantera { } #ifdef DEBUG_DOGLEG - m_normSolnCP = doCauchyPointSolve(jac); + m_normDeltaSoln_CP = doCauchyPointSolve(jac); #endif // compute the undamped Newton step - info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), jac, m_print_flag); + info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac, m_print_flag); if (info) { m = -1; goto done; } + mdp::mdp_copy_dbl_1(DATA_PTR(stp), CONSTD_DATA_PTR(deltaX_Newton_), neq_); if (m_print_flag > 3) { m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); @@ -1629,6 +1832,9 @@ namespace Cantera { #ifdef DEBUG_DOGLEG descentComparison(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + setupDoubleDogleg(DATA_PTR(stp)); + residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + #endif // Damp the Newton step @@ -1711,7 +1917,7 @@ namespace Cantera { // Exchange new for curr solutions if (m >= 0) { - mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_new), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), CONSTD_DATA_PTR(y_new), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); @@ -1764,9 +1970,9 @@ namespace Cantera { } - mdp::mdp_copy_dbl_1(y_comm, DATA_PTR(m_y_n), neq_); + mdp::mdp_copy_dbl_1(y_comm, CONSTD_DATA_PTR(m_y_n), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - mdp::mdp_copy_dbl_1(ydot_comm, DATA_PTR(ydot_curr), neq_); + mdp::mdp_copy_dbl_1(ydot_comm, CONSTD_DATA_PTR(ydot_curr), neq_); } num_linear_solves += m_numTotalLinearSolves; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 5ec4cc34c..ccda92128 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -139,7 +139,7 @@ namespace Cantera { * @return Returns the L2 norm of the delta */ doublereal solnErrorNorm(const doublereal * const delta_y, const char * title = 0, int printLargest = 0, - const doublereal dampFactor = 1.0); + const doublereal dampFactor = 1.0) const; //! L2 norm of the residual of the equation system /*! @@ -247,6 +247,7 @@ namespace Cantera { * @param deltaX Current value of deltaX */ doublereal calcTrustDistance(std::vector const & deltaX) const; + public: //! Bound the step /*! @@ -555,8 +556,28 @@ namespace Cantera { */ void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); - void setupDoubleDogleg(); - double expectedResid(double lambda); + void setupDoubleDogleg(double *newtDir); + + //! Change the global lambda coordinate into the (leg,alpha) coordinate for the double dogleg + /*! + * @param lambda Global value of the distance along the double dogleg + * @param alpha relative value along the particular leg + * + * @return Returns the leg number ( 0, 1, or 2). + */ + int lambdaToLeg(const double lambda, double &alpha) const; + + //! Calculated the expected residual along the double dogleg curve. + /*! + * @param leg 0, 1, or 2 representing the curves of the dogleg + * @param alpha Relative distance along the particular curve. + * + * @return Returns the expected value of the residual at that point according to the quadratic model. + * The residual at the newton point will always be zero. + */ + double expectedResidLeg(int leg, doublereal alpha) const; + + void residualComparisonLeg(const double time_curr, const double *ydot0, const double *ydot1, const double *newtDir); //! Set the print level from the rootfinder /*! @@ -575,6 +596,11 @@ namespace Cantera { */ void setPrintLvl(int printLvl); + /* + * ----------------------------------------------------------------------------------------------------------------- + * MEMBER DATA + * ------------------------------------------------------------------------------------------------ + */ private: //! Pointer to the residual and jacobian evaluator for the @@ -632,7 +658,7 @@ namespace Cantera { std::vector m_resid; //! Workspace of length neq_ - std::vector m_wksp; + mutable std::vector m_wksp; /***************************************************************************************** * INTERNAL WEIGHTS FOR TAKING SOLUTION NORMS @@ -652,8 +678,6 @@ namespace Cantera { //! Norm of the solution update created by the iteration in its raw, undamped form. doublereal m_normDeltaSoln_Newton; - - //! Norm of the solution update created by the iteration in its raw, undamped form. doublereal m_normDeltaSoln_CP; //! Norm of the residual for a trial calculation which may or may not be used @@ -687,6 +711,10 @@ namespace Cantera { //! Counter for the total number of function evaluations int m_nfe; + /*********************************************************************************************** + * MATRIX INFORMATION + **************************************************************************************/ + //! The type of column scaled used in the solution of the problem /*! * If true then colScaling = m_ewt[] @@ -739,8 +767,8 @@ namespace Cantera { //! Base value of the absolute tolerance doublereal atolBase_; - //! Vector containing the solution derivative at the previous time step - doublereal * m_ydot_nm1; + //! Pointer containing the solution derivative at the previous time step + doublereal *m_ydot_nm1; //! absolute tolerance in the solution unknown /*! @@ -768,8 +796,18 @@ namespace Cantera { //! Copy of the jacobian that doesn't get overwritten when the inverse is determined Cantera::SquareMatrix jacCopy_; + /********************************************************************************************* + * VARIABLES ASSOCIATED WITH STEPS AND ASSOCIATED DOUBLE DOGLEG PARAMETERS + *********************************************************************************************/ + //! Steepest descent direction. This is also the distance to the Cauchy Point - std::vector descentDir_; + std::vector deltax_cp_; + + //! Newton Step - This is the newton step determined from the straight Jacobian + /* + * Newton step for the current step only + */ + std::vector deltaX_Newton_; //! Expected value of the residual norm at the Cauchy point doublereal residNorm2Cauchy_; @@ -790,14 +828,18 @@ namespace Cantera { //! calculate the max step size. doublereal trustDelta_; + //! Relative distance down the Newton step that the second dogleg starts doublereal Nuu_; doublereal dist_R0_; doublereal dist_R1_; doublereal dist_R2_; doublereal dist_Total_; - doublereal m_normSolnCP; + doublereal JdJd_norm_; + /******************************************************************************************* + * OTHER COUNTERS + *****************************************************************************************/ public: From 08716fa3f155f73408141266c2aab0d245f81cdf Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 18 Feb 2011 23:04:50 +0000 Subject: [PATCH 326/446] Make sure that phaseIsStable flag is set correctly --- Cantera/src/kinetics/InterfaceKinetics.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 00cf51f0c..775839fc0 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -1373,14 +1373,14 @@ namespace Cantera { if (!m_phaseExists[iphase]) { m_phaseExistsCheck--; m_phaseExists[iphase] = true; - m_phaseIsStable[iphase] = true; } + m_phaseIsStable[iphase] = true; } else { if (m_phaseExists[iphase]) { m_phaseExistsCheck++; m_phaseExists[iphase] = false; - m_phaseIsStable[iphase] = false; } + m_phaseIsStable[iphase] = false; } } //================================================================================================ From 144c6b23bde22d84756f75f5a367a3a85363b3ae Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 19 Feb 2011 00:08:29 +0000 Subject: [PATCH 327/446] Another delta on the dogleg implementation of the nonlinear solver. Added lapack routines for calculation of condition number and to fill out the QR factorization capability. --- Cantera/src/base/Array.h | 10 + Cantera/src/equil/vcs_solve.h | 4 +- Cantera/src/numerics/NonlinearSolver.cpp | 173 ++++++++-- Cantera/src/numerics/NonlinearSolver.h | 21 +- ext/f2c_lapack/Makefile.in | 4 + ext/f2c_lapack/dgecon.c | 228 ++++++++++++ ext/f2c_lapack/dgeequ.c | 297 ++++++++++++++++ ext/f2c_lapack/dgerfs.c | 420 +++++++++++++++++++++++ ext/f2c_lapack/dtrtrs.c | 187 ++++++++++ ext/lapack/Makefile.in | 4 + ext/lapack/dgecon.f | 181 ++++++++++ ext/lapack/dgeequ.f | 226 ++++++++++++ ext/lapack/dgerfs.f | 332 ++++++++++++++++++ ext/lapack/dtrtrs.f | 148 ++++++++ 14 files changed, 2200 insertions(+), 35 deletions(-) create mode 100644 ext/f2c_lapack/dgecon.c create mode 100644 ext/f2c_lapack/dgeequ.c create mode 100644 ext/f2c_lapack/dgerfs.c create mode 100644 ext/f2c_lapack/dtrtrs.c create mode 100644 ext/lapack/dgecon.f create mode 100644 ext/lapack/dgeequ.f create mode 100644 ext/lapack/dgerfs.f create mode 100644 ext/lapack/dtrtrs.f diff --git a/Cantera/src/base/Array.h b/Cantera/src/base/Array.h index a81864175..ae5e472df 100644 --- a/Cantera/src/base/Array.h +++ b/Cantera/src/base/Array.h @@ -120,6 +120,16 @@ namespace Cantera { m_data.resize(n*m, v); } + //! Copy the data from one array into another without doing any checking + /*! + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + void copyData(const Array2D& y) { + size_t n = sizeof(doublereal) * m_nrows * m_ncols; + (void) memcpy(DATA_PTR(m_data), y.ptrColumn(0), n); + } + //! Append a column to the existing matrix using a std vector /*! * This operation will add a column onto the existing matrix. diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h index daf952d26..e0c52b12a 100644 --- a/Cantera/src/equil/vcs_solve.h +++ b/Cantera/src/equil/vcs_solve.h @@ -7,7 +7,7 @@ * $Id$ */ /* - * Copywrite (2005) Sandia Corporation. Under the terms of + *_ Copywrite (2005) Sandia Corporation. Under the terms of * Contract DE-AC04-94AL85000 with Sandia Corporation, the * U.S. Government retains certain rights in this software. */ @@ -2073,6 +2073,8 @@ public: */ int m_VCS_UnitsFormat; + friend class vcs_phaseStabilitySolve; + }; #ifdef ALTLINPROG diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 3f878ea6f..06a6b1bfe 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -127,15 +127,22 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), - deltax_cp_(0), + deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), lambda_(0.0), Jd_(0), - trustDeltaX_(0), - trustDelta_(1.0) - + deltaX_trust_(0), + trustDelta_(1.0), + Nuu_(0.0), + dist_R0_(0.0), + dist_R1_(0.0), + dist_R2_(0.0), + dist_Total_(0.0), + JdJd_norm_(0.0), + normTrust_Newton_(0.0), + normTrust_CP_(0.0) { neq_ = m_func->nEquations(); @@ -164,9 +171,9 @@ namespace Cantera { #ifdef DEBUG_DOGLEG jacCopy_.resize(neq_, neq_, 0.0); - deltax_cp_.resize(neq_, 0.0); + deltaX_CP_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); - trustDeltaX_.resize(neq_, 1.0); + deltaX_trust_.resize(neq_, 1.0); #endif } @@ -217,14 +224,22 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), - deltax_cp_(0), + deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), lambda_(0.0), Jd_(0), - trustDeltaX_(0), - trustDelta_(1.0) + deltaX_trust_(0), + trustDelta_(1.0), + Nuu_(0.0), + dist_R0_(0.0), + dist_R1_(0.0), + dist_R2_(0.0), + dist_Total_(0.0), + JdJd_norm_(0.0), + normTrust_Newton_(0.0), + normTrust_CP_(0.0) { *this =operator=(right); } @@ -285,14 +300,23 @@ namespace Cantera { m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; jacCopy_ = right.jacCopy_; - deltax_cp_ = right.deltax_cp_; + deltaX_CP_ = right.deltaX_CP_; deltaX_Newton_ = right.deltaX_Newton_; RJd_norm_ = right.RJd_norm_; lambda_ = right.lambda_; Jd_ = right.Jd_; - trustDeltaX_ = right.trustDeltaX_; + deltaX_trust_ = right.deltaX_trust_; trustDelta_ = right.trustDelta_; - + + Nuu_ = right.Nuu_; + dist_R0_ = right.dist_R0_; + dist_R1_ = right.dist_R1_; + dist_R2_ = right.dist_R2_; + dist_Total_ = right.dist_Total_; + JdJd_norm_ = right.JdJd_norm_; + normTrust_Newton_ = right.normTrust_Newton_; + normTrust_CP_ = right.normTrust_CP_; + return *this; } //==================================================================================================================== @@ -765,7 +789,7 @@ namespace Cantera { * */ for (int j = 0; j < neq_; j++) { - deltax_cp_[j] = 0.0; + deltaX_CP_[j] = 0.0; double colFac = 1.0; if (m_colScaling) { colFac = 1.0 / m_colScales[j]; @@ -774,7 +798,7 @@ namespace Cantera { if (m_rowScaling) { rowFac = 1.0 / m_rowScales[i]; } - deltax_cp_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] + deltaX_CP_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] / (m_residWts[i] * m_residWts[i]); } } @@ -786,7 +810,7 @@ namespace Cantera { rowFac = 1.0; } for (int j = 0; j < neq_; j++) { - Jd_[i] += deltax_cp_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; + Jd_[i] += deltaX_CP_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; } } @@ -799,7 +823,7 @@ namespace Cantera { lambda_ = - RJd_norm_ / (JdJd_norm_); for (int i = 0; i < neq_; i++) { - deltax_cp_[i] *= lambda_; + deltaX_CP_[i] *= lambda_; } residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); @@ -814,7 +838,7 @@ namespace Cantera { } // Compute the weighted norm of the undamped step size descentDir_[] - normSoln = solnErrorNorm(DATA_PTR(deltax_cp_), "SteepestDescentDir", 10); + normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 10); printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid0); @@ -832,9 +856,9 @@ namespace Cantera { int info; double ff = 1.0E-5; double *y1 = DATA_PTR(m_wksp); - double s1 = solnErrorNorm(DATA_PTR(deltax_cp_)); + double s1 = solnErrorNorm(DATA_PTR(deltaX_CP_)); for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + ff * deltax_cp_[i]; + y1[i] = m_y_n[i] + ff * deltaX_CP_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -940,7 +964,9 @@ namespace Cantera { /* * Calculate the trust distances */ - + normTrust_Newton_ = calcTrustDistance(deltaX_Newton_); + + normTrust_CP_ = calcTrustDistance(deltaX_CP_); } //==================================================================================================================== @@ -1040,9 +1066,9 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + alpha * deltax_cp_[i]; + y1[i] = m_y_n[i] + alpha * deltaX_CP_[i]; } - sLen = alpha * solnErrorNorm(DATA_PTR(deltax_cp_)); + sLen = alpha * solnErrorNorm(DATA_PTR(deltaX_CP_)); /* * Calculate the residual that would result if y1[] were the new solution vector * -> m_resid[] contains the result of the residual calculation @@ -1065,7 +1091,7 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + (1.0 - alpha) * deltax_cp_[i]; + y1[i] = m_y_n[i] + (1.0 - alpha) * deltaX_CP_[i]; y1[i] += alpha * Nuu_ * newtDir[i]; } /* @@ -1270,15 +1296,15 @@ namespace Cantera { double fabsy; // we use the old value of the trust region as an indicator for (int i = 0; i < neq_; i++) { - oldVal = trustDeltaX_[i]; + oldVal = deltaX_trust_[i]; fabsy = fabs(m_y_n[i]); // First off make sure that each trust region vector is 1/2 the size of each variable or smaller // unless overridden by the deltaStepMininum value. if (oldVal > 0.5 * fabsy) { if (fabsy > m_deltaStepMinimum[i]) { - trustDeltaX_[i] = 0.5 * fabsy; + deltaX_trust_[i] = 0.5 * fabsy; } else { - trustDeltaX_[i] = m_deltaStepMinimum[i]; + deltaX_trust_[i] = m_deltaStepMinimum[i]; } } else { double newValue = trustDeltaEach * m_ewt[i] / wtSum; @@ -1287,9 +1313,9 @@ namespace Cantera { } else if (newValue < 0.5 * oldVal) { newValue = 0.5 * oldVal; } - trustDeltaX_[i] = newValue; - if (trustDeltaX_[i] > 0.75 * m_deltaStepMaximum[i]) { - trustDeltaX_[i] = m_deltaStepMaximum[i]; + deltaX_trust_[i] = newValue; + if (deltaX_trust_[i] > 0.75 * m_deltaStepMaximum[i]) { + deltaX_trust_[i] = m_deltaStepMaximum[i]; } } } @@ -1298,10 +1324,10 @@ namespace Cantera { // Final renormalization. double sum = 0.0; for (int i = 0; i < neq_; i++) { - sum += trustDeltaX_[i]; + sum += deltaX_trust_[i]; } for (int i = 0; i < neq_; i++) { - trustDeltaX_[i] = trustDelta_ / sum; + deltaX_trust_[i] = deltaX_trust_[i] / sum; } trustDelta_ = 1.0; @@ -1312,12 +1338,51 @@ namespace Cantera { doublereal sum = 0.0; doublereal tmp = 0.0; for (int i = 0; i < neq_; i++) { - tmp = deltaX[i] / trustDeltaX_[i]; + tmp = deltaX[i] / deltaX_trust_[i]; sum += tmp * tmp; } sum = sqrt(sum / neq_); return sum; } + //==================================================================================================================== + int NonlinearSolver::calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const + { + double dist; + if (normTrust_Newton_ < trustDelta) { + lambda = 1.0; + alpha = 1.0; + return 2; + } + + if (normTrust_Newton_ * Nuu_ > trustDelta) { + alpha = (trustDelta - normTrust_Newton_ * Nuu_) / (normTrust_Newton_ - normTrust_Newton_ * Nuu_); + dist = dist_R0_ + dist_R1_ + alpha * dist_R2_; + lambda = dist / dist_Total_; + return 2; + } + if (normTrust_CP_ > trustDelta) { + lambda = 1.0; + dist = dist_R0_ * trustDelta / normTrust_CP_; + lambda = dist / dist_Total_; + alpha = trustDelta / normTrust_CP_; + return 0; + } + double sumv = 0.0; + for (int i = 0; i < neq_; i++) { + sumv += (deltaX_Newton_[i] / deltaX_trust_[i]) * (deltaX_CP_[i] / deltaX_trust_[i]); + } + + double a = normTrust_Newton_ * normTrust_Newton_ * Nuu_ * Nuu_; + double b = 2.0 * Nuu_ * sumv; + double c = normTrust_CP_ * normTrust_CP_ - trustDelta * trustDelta; + + alpha =( -b + sqrt( b * b - 4.0 * a * c)) / (2.0 * a); + // alpha = (trustDelta - normTrust_CP_) / (normTrust_Newton_ * Nuu_ - normTrust_CP_); + + dist = dist_R0_ + alpha * dist_R1_; + lambda = dist / dist_Total_; + return 1; + } //==================================================================================================================== /* * @@ -1625,6 +1690,50 @@ namespace Cantera { } return -2; } + + //==================================================================================================================== + + int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y0, + const doublereal *ydot0, const double* step0, + double* const y1, double* const ydot1, double* step1, + double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + int& num_backtracks) + { + double lambda; + double alpha; + + //-------------------------------------------- + // Attempt damped step + //-------------------------------------------- + + // damping coefficient starts at 1.0 + m_dampRes = 1.0; + int j, m; + doublereal ff = m_dampBound; + num_backtracks = 0; + + /* + * Find the initial value of lambda that satisfies the trust distance + */ + int leg = calcTrustIntersection(trustDelta_, lambda, alpha); + + for (m = 0; m < NDAMP; m++) { + + + + + + + + + + + + + + } + + } //==================================================================================================================== /* * diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index ccda92128..47df6ab86 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -248,6 +248,7 @@ namespace Cantera { */ doublereal calcTrustDistance(std::vector const & deltaX) const; + int calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const; public: //! Bound the step /*! @@ -567,6 +568,14 @@ namespace Cantera { */ int lambdaToLeg(const double lambda, double &alpha) const; + int calcTrustIntersection(double trustVal, const double &lambda, double &alpha) const; + + int dampDogLeg(const doublereal time_curr, const double* y0, + const doublereal *ydot0, const double* step0, + double* const y1, double* const ydot1, double* step1, + double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + int& num_backtracks); + //! Calculated the expected residual along the double dogleg curve. /*! * @param leg 0, 1, or 2 representing the curves of the dogleg @@ -801,7 +810,7 @@ namespace Cantera { *********************************************************************************************/ //! Steepest descent direction. This is also the distance to the Cauchy Point - std::vector deltax_cp_; + std::vector deltaX_CP_; //! Newton Step - This is the newton step determined from the straight Jacobian /* @@ -822,7 +831,7 @@ namespace Cantera { std::vector Jd_; //! Vector of trust region values. - std::vector trustDeltaX_; + std::vector deltaX_trust_; //! Current value of trust radius. This is used with trustDeltaX_ to //! calculate the max step size. @@ -837,6 +846,14 @@ namespace Cantera { doublereal dist_Total_; doublereal JdJd_norm_; + //! Norm of the Newton Step wrt trust region + doublereal normTrust_Newton_; + + //! Norm of the Cauchy Step direction wrt trust region + doublereal normTrust_CP_; + + + /******************************************************************************************* * OTHER COUNTERS *****************************************************************************************/ diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index f85c8c20a..68dff0ce8 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -100,6 +100,10 @@ dormqr.o \ drscl.o \ dtrtri.o \ dtrti2.o \ +dtrtrs.o \ +dgecon.o \ +dgeequ.o \ +dgerfs.o \ ieeeck.o \ ilaenv.o diff --git a/ext/f2c_lapack/dgecon.c b/ext/f2c_lapack/dgecon.c new file mode 100644 index 000000000..277e922af --- /dev/null +++ b/ext/f2c_lapack/dgecon.c @@ -0,0 +1,228 @@ +/* dgecon.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; + +/* Subroutine */ int dgecon_(char *norm, integer *n, doublereal *a, integer * + lda, doublereal *anorm, doublereal *rcond, doublereal *work, integer * + iwork, integer *info, ftnlen norm_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1; + doublereal d__1; + + /* Local variables */ + static doublereal sl; + static integer ix; + static doublereal su; + static integer kase, kase1; + static doublereal scale; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int drscl_(integer *, doublereal *, doublereal *, + integer *); + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int dlacon_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + extern integer idamax_(integer *, doublereal *, integer *); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + static doublereal ainvnm; + extern /* Subroutine */ int dlatrs_(char *, char *, char *, char *, + integer *, doublereal *, integer *, doublereal *, doublereal *, + doublereal *, integer *, ftnlen, ftnlen, ftnlen, ftnlen); + static logical onenrm; + static char normin[1]; + static doublereal smlnum; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* February 29, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DGECON estimates the reciprocal of the condition number of a general */ +/* real matrix A, in either the 1-norm or the infinity-norm, using */ +/* the LU factorization computed by DGETRF. */ + +/* An estimate is obtained for norm(inv(A)), and the reciprocal of the */ +/* condition number is computed as */ +/* RCOND = 1 / ( norm(A) * norm(inv(A)) ). */ + +/* Arguments */ +/* ========= */ + +/* NORM (input) CHARACTER*1 */ +/* Specifies whether the 1-norm condition number or the */ +/* infinity-norm condition number is required: */ +/* = '1' or 'O': 1-norm; */ +/* = 'I': Infinity-norm. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The factors L and U from the factorization A = P*L*U */ +/* as computed by DGETRF. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* ANORM (input) DOUBLE PRECISION */ +/* If NORM = '1' or 'O', the 1-norm of the original matrix A. */ +/* If NORM = 'I', the infinity-norm of the original matrix A. */ + +/* RCOND (output) DOUBLE PRECISION */ +/* The reciprocal of the condition number of the matrix A, */ +/* computed as RCOND = 1/(norm(A) * norm(inv(A))). */ + +/* WORK (workspace) DOUBLE PRECISION array, dimension (4*N) */ + +/* IWORK (workspace) INTEGER array, dimension (N) */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + --work; + --iwork; + + /* Function Body */ + *info = 0; + onenrm = *(unsigned char *)norm == '1' || lsame_(norm, "O", (ftnlen)1, ( + ftnlen)1); + if (! onenrm && ! lsame_(norm, "I", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*lda < max(1,*n)) { + *info = -4; + } else if (*anorm < 0.) { + *info = -5; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DGECON", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + *rcond = 0.; + if (*n == 0) { + *rcond = 1.; + return 0; + } else if (*anorm == 0.) { + return 0; + } + + smlnum = dlamch_("Safe minimum", (ftnlen)12); + +/* Estimate the norm of inv(A). */ + + ainvnm = 0.; + *(unsigned char *)normin = 'N'; + if (onenrm) { + kase1 = 1; + } else { + kase1 = 2; + } + kase = 0; +L10: + dlacon_(n, &work[*n + 1], &work[1], &iwork[1], &ainvnm, &kase); + if (kase != 0) { + if (kase == kase1) { + +/* Multiply by inv(L). */ + + dlatrs_("Lower", "No transpose", "Unit", normin, n, &a[a_offset], + lda, &work[1], &sl, &work[(*n << 1) + 1], info, (ftnlen)5, + (ftnlen)12, (ftnlen)4, (ftnlen)1); + +/* Multiply by inv(U). */ + + dlatrs_("Upper", "No transpose", "Non-unit", normin, n, &a[ + a_offset], lda, &work[1], &su, &work[*n * 3 + 1], info, ( + ftnlen)5, (ftnlen)12, (ftnlen)8, (ftnlen)1); + } else { + +/* Multiply by inv(U'). */ + + dlatrs_("Upper", "Transpose", "Non-unit", normin, n, &a[a_offset], + lda, &work[1], &su, &work[*n * 3 + 1], info, (ftnlen)5, ( + ftnlen)9, (ftnlen)8, (ftnlen)1); + +/* Multiply by inv(L'). */ + + dlatrs_("Lower", "Transpose", "Unit", normin, n, &a[a_offset], + lda, &work[1], &sl, &work[(*n << 1) + 1], info, (ftnlen)5, + (ftnlen)9, (ftnlen)4, (ftnlen)1); + } + +/* Divide X by 1/(SL*SU) if doing so will not cause overflow. */ + + scale = sl * su; + *(unsigned char *)normin = 'Y'; + if (scale != 1.) { + ix = idamax_(n, &work[1], &c__1); + if (scale < (d__1 = work[ix], abs(d__1)) * smlnum || scale == 0.) + { + goto L20; + } + drscl_(n, &scale, &work[1], &c__1); + } + goto L10; + } + +/* Compute the estimate of the reciprocal condition number. */ + + if (ainvnm != 0.) { + *rcond = 1. / ainvnm / *anorm; + } + +L20: + return 0; + +/* End of DGECON */ + +} /* dgecon_ */ + diff --git a/ext/f2c_lapack/dgeequ.c b/ext/f2c_lapack/dgeequ.c new file mode 100644 index 000000000..125849ce7 --- /dev/null +++ b/ext/f2c_lapack/dgeequ.c @@ -0,0 +1,297 @@ +/* dgeequ.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Subroutine */ int dgeequ_(integer *m, integer *n, doublereal *a, integer * + lda, doublereal *r__, doublereal *c__, doublereal *rowcnd, doublereal + *colcnd, doublereal *amax, integer *info) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1, i__2; + doublereal d__1, d__2, d__3; + + /* Local variables */ + static integer i__, j; + static doublereal rcmin, rcmax; + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + static doublereal bignum, smlnum; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DGEEQU computes row and column scalings intended to equilibrate an */ +/* M-by-N matrix A and reduce its condition number. R returns the row */ +/* scale factors and C the column scale factors, chosen to try to make */ +/* the largest element in each row and column of the matrix B with */ +/* elements B(i,j)=R(i)*A(i,j)*C(j) have absolute value 1. */ + +/* R(i) and C(j) are restricted to be between SMLNUM = smallest safe */ +/* number and BIGNUM = largest safe number. Use of these scaling */ +/* factors is not guaranteed to reduce the condition number of A but */ +/* works well in practice. */ + +/* Arguments */ +/* ========= */ + +/* M (input) INTEGER */ +/* The number of rows of the matrix A. M >= 0. */ + +/* N (input) INTEGER */ +/* The number of columns of the matrix A. N >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The M-by-N matrix whose equilibration factors are */ +/* to be computed. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,M). */ + +/* R (output) DOUBLE PRECISION array, dimension (M) */ +/* If INFO = 0 or INFO > M, R contains the row scale factors */ +/* for A. */ + +/* C (output) DOUBLE PRECISION array, dimension (N) */ +/* If INFO = 0, C contains the column scale factors for A. */ + +/* ROWCND (output) DOUBLE PRECISION */ +/* If INFO = 0 or INFO > M, ROWCND contains the ratio of the */ +/* smallest R(i) to the largest R(i). If ROWCND >= 0.1 and */ +/* AMAX is neither too large nor too small, it is not worth */ +/* scaling by R. */ + +/* COLCND (output) DOUBLE PRECISION */ +/* If INFO = 0, COLCND contains the ratio of the smallest */ +/* C(i) to the largest C(i). If COLCND >= 0.1, it is not */ +/* worth scaling by C. */ + +/* AMAX (output) DOUBLE PRECISION */ +/* Absolute value of largest matrix element. If AMAX is very */ +/* close to overflow or very close to underflow, the matrix */ +/* should be scaled. */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ +/* > 0: if INFO = i, and i is */ +/* <= M: the i-th row of A is exactly zero */ +/* > M: the (i-M)-th column of A is exactly zero */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + --r__; + --c__; + + /* Function Body */ + *info = 0; + if (*m < 0) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*lda < max(1,*m)) { + *info = -4; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DGEEQU", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*m == 0 || *n == 0) { + *rowcnd = 1.; + *colcnd = 1.; + *amax = 0.; + return 0; + } + +/* Get machine constants. */ + + smlnum = dlamch_("S", (ftnlen)1); + bignum = 1. / smlnum; + +/* Compute row scale factors. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + r__[i__] = 0.; +/* L10: */ + } + +/* Find the maximum element in each row. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = r__[i__], d__3 = (d__1 = a[i__ + j * a_dim1], abs(d__1)); + r__[i__] = max(d__2,d__3); +/* L20: */ + } +/* L30: */ + } + +/* Find the maximum and minimum scale factors. */ + + rcmin = bignum; + rcmax = 0.; + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { +/* Computing MAX */ + d__1 = rcmax, d__2 = r__[i__]; + rcmax = max(d__1,d__2); +/* Computing MIN */ + d__1 = rcmin, d__2 = r__[i__]; + rcmin = min(d__1,d__2); +/* L40: */ + } + *amax = rcmax; + + if (rcmin == 0.) { + +/* Find the first zero scale factor and return an error code. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + if (r__[i__] == 0.) { + *info = i__; + return 0; + } +/* L50: */ + } + } else { + +/* Invert the scale factors. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { +/* Computing MIN */ +/* Computing MAX */ + d__2 = r__[i__]; + d__1 = max(d__2,smlnum); + r__[i__] = 1. / min(d__1,bignum); +/* L60: */ + } + +/* Compute ROWCND = min(R(I)) / max(R(I)) */ + + *rowcnd = max(rcmin,smlnum) / min(rcmax,bignum); + } + +/* Compute column scale factors */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + c__[j] = 0.; +/* L70: */ + } + +/* Find the maximum element in each column, */ +/* assuming the row scaling computed above. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = c__[j], d__3 = (d__1 = a[i__ + j * a_dim1], abs(d__1)) * + r__[i__]; + c__[j] = max(d__2,d__3); +/* L80: */ + } +/* L90: */ + } + +/* Find the maximum and minimum scale factors. */ + + rcmin = bignum; + rcmax = 0.; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + d__1 = rcmin, d__2 = c__[j]; + rcmin = min(d__1,d__2); +/* Computing MAX */ + d__1 = rcmax, d__2 = c__[j]; + rcmax = max(d__1,d__2); +/* L100: */ + } + + if (rcmin == 0.) { + +/* Find the first zero scale factor and return an error code. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + if (c__[j] == 0.) { + *info = *m + j; + return 0; + } +/* L110: */ + } + } else { + +/* Invert the scale factors. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ +/* Computing MAX */ + d__2 = c__[j]; + d__1 = max(d__2,smlnum); + c__[j] = 1. / min(d__1,bignum); +/* L120: */ + } + +/* Compute COLCND = min(C(J)) / max(C(J)) */ + + *colcnd = max(rcmin,smlnum) / min(rcmax,bignum); + } + + return 0; + +/* End of DGEEQU */ + +} /* dgeequ_ */ + diff --git a/ext/f2c_lapack/dgerfs.c b/ext/f2c_lapack/dgerfs.c new file mode 100644 index 000000000..5dcebe627 --- /dev/null +++ b/ext/f2c_lapack/dgerfs.c @@ -0,0 +1,420 @@ +/* dgerfs.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static doublereal c_b15 = -1.; +static doublereal c_b17 = 1.; + +/* Subroutine */ int dgerfs_(char *trans, integer *n, integer *nrhs, + doublereal *a, integer *lda, doublereal *af, integer *ldaf, integer * + ipiv, doublereal *b, integer *ldb, doublereal *x, integer *ldx, + doublereal *ferr, doublereal *berr, doublereal *work, integer *iwork, + integer *info, ftnlen trans_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, af_dim1, af_offset, b_dim1, b_offset, x_dim1, + x_offset, i__1, i__2, i__3; + doublereal d__1, d__2, d__3; + + /* Local variables */ + static integer i__, j, k; + static doublereal s, xk; + static integer nz; + static doublereal eps; + static integer kase; + static doublereal safe1, safe2; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int dgemv_(char *, integer *, integer *, + doublereal *, doublereal *, integer *, doublereal *, integer *, + doublereal *, doublereal *, integer *, ftnlen), dcopy_(integer *, + doublereal *, integer *, doublereal *, integer *), daxpy_(integer + *, doublereal *, doublereal *, integer *, doublereal *, integer *) + ; + static integer count; + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int dlacon_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + static doublereal safmin; + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen), dgetrs_( + char *, integer *, integer *, doublereal *, integer *, integer *, + doublereal *, integer *, integer *, ftnlen); + static logical notran; + static char transt[1]; + static doublereal lstres; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* September 30, 1994 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DGERFS improves the computed solution to a system of linear */ +/* equations and provides error bounds and backward error estimates for */ +/* the solution. */ + +/* Arguments */ +/* ========= */ + +/* TRANS (input) CHARACTER*1 */ +/* Specifies the form of the system of equations: */ +/* = 'N': A * X = B (No transpose) */ +/* = 'T': A**T * X = B (Transpose) */ +/* = 'C': A**H * X = B (Conjugate transpose = Transpose) */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* NRHS (input) INTEGER */ +/* The number of right hand sides, i.e., the number of columns */ +/* of the matrices B and X. NRHS >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The original N-by-N matrix A. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* AF (input) DOUBLE PRECISION array, dimension (LDAF,N) */ +/* The factors L and U from the factorization A = P*L*U */ +/* as computed by DGETRF. */ + +/* LDAF (input) INTEGER */ +/* The leading dimension of the array AF. LDAF >= max(1,N). */ + +/* IPIV (input) INTEGER array, dimension (N) */ +/* The pivot indices from DGETRF; for 1<=i<=N, row i of the */ +/* matrix was interchanged with row IPIV(i). */ + +/* B (input) DOUBLE PRECISION array, dimension (LDB,NRHS) */ +/* The right hand side matrix B. */ + +/* LDB (input) INTEGER */ +/* The leading dimension of the array B. LDB >= max(1,N). */ + +/* X (input/output) DOUBLE PRECISION array, dimension (LDX,NRHS) */ +/* On entry, the solution matrix X, as computed by DGETRS. */ +/* On exit, the improved solution matrix X. */ + +/* LDX (input) INTEGER */ +/* The leading dimension of the array X. LDX >= max(1,N). */ + +/* FERR (output) DOUBLE PRECISION array, dimension (NRHS) */ +/* The estimated forward error bound for each solution vector */ +/* X(j) (the j-th column of the solution matrix X). */ +/* If XTRUE is the true solution corresponding to X(j), FERR(j) */ +/* is an estimated upper bound for the magnitude of the largest */ +/* element in (X(j) - XTRUE) divided by the magnitude of the */ +/* largest element in X(j). The estimate is as reliable as */ +/* the estimate for RCOND, and is almost always a slight */ +/* overestimate of the true error. */ + +/* BERR (output) DOUBLE PRECISION array, dimension (NRHS) */ +/* The componentwise relative backward error of each solution */ +/* vector X(j) (i.e., the smallest relative change in */ +/* any element of A or B that makes X(j) an exact solution). */ + +/* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) */ + +/* IWORK (workspace) INTEGER array, dimension (N) */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ + +/* Internal Parameters */ +/* =================== */ + +/* ITMAX is the maximum number of steps of iterative refinement. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + af_dim1 = *ldaf; + af_offset = 1 + af_dim1; + af -= af_offset; + --ipiv; + b_dim1 = *ldb; + b_offset = 1 + b_dim1; + b -= b_offset; + x_dim1 = *ldx; + x_offset = 1 + x_dim1; + x -= x_offset; + --ferr; + --berr; + --work; + --iwork; + + /* Function Body */ + *info = 0; + notran = lsame_(trans, "N", (ftnlen)1, (ftnlen)1); + if (! notran && ! lsame_(trans, "T", (ftnlen)1, (ftnlen)1) && ! lsame_( + trans, "C", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*nrhs < 0) { + *info = -3; + } else if (*lda < max(1,*n)) { + *info = -5; + } else if (*ldaf < max(1,*n)) { + *info = -7; + } else if (*ldb < max(1,*n)) { + *info = -10; + } else if (*ldx < max(1,*n)) { + *info = -12; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DGERFS", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0 || *nrhs == 0) { + i__1 = *nrhs; + for (j = 1; j <= i__1; ++j) { + ferr[j] = 0.; + berr[j] = 0.; +/* L10: */ + } + return 0; + } + + if (notran) { + *(unsigned char *)transt = 'T'; + } else { + *(unsigned char *)transt = 'N'; + } + +/* NZ = maximum number of nonzero elements in each row of A, plus 1 */ + + nz = *n + 1; + eps = dlamch_("Epsilon", (ftnlen)7); + safmin = dlamch_("Safe minimum", (ftnlen)12); + safe1 = nz * safmin; + safe2 = safe1 / eps; + +/* Do for each right hand side */ + + i__1 = *nrhs; + for (j = 1; j <= i__1; ++j) { + + count = 1; + lstres = 3.; +L20: + +/* Loop until stopping criterion is satisfied. */ + +/* Compute residual R = B - op(A) * X, */ +/* where op(A) = A, A**T, or A**H, depending on TRANS. */ + + dcopy_(n, &b[j * b_dim1 + 1], &c__1, &work[*n + 1], &c__1); + dgemv_(trans, n, n, &c_b15, &a[a_offset], lda, &x[j * x_dim1 + 1], & + c__1, &c_b17, &work[*n + 1], &c__1, (ftnlen)1); + +/* Compute componentwise relative backward error from formula */ + +/* max(i) ( abs(R(i)) / ( abs(op(A))*abs(X) + abs(B) )(i) ) */ + +/* where abs(Z) is the componentwise absolute value of the matrix */ +/* or vector Z. If the i-th component of the denominator is less */ +/* than SAFE2, then SAFE1 is added to the i-th components of the */ +/* numerator and denominator before dividing. */ + + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { + work[i__] = (d__1 = b[i__ + j * b_dim1], abs(d__1)); +/* L30: */ + } + +/* Compute abs(op(A))*abs(X) + abs(B). */ + + if (notran) { + i__2 = *n; + for (k = 1; k <= i__2; ++k) { + xk = (d__1 = x[k + j * x_dim1], abs(d__1)); + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + work[i__] += (d__1 = a[i__ + k * a_dim1], abs(d__1)) * xk; +/* L40: */ + } +/* L50: */ + } + } else { + i__2 = *n; + for (k = 1; k <= i__2; ++k) { + s = 0.; + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + s += (d__1 = a[i__ + k * a_dim1], abs(d__1)) * (d__2 = x[ + i__ + j * x_dim1], abs(d__2)); +/* L60: */ + } + work[k] += s; +/* L70: */ + } + } + s = 0.; + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { + if (work[i__] > safe2) { +/* Computing MAX */ + d__2 = s, d__3 = (d__1 = work[*n + i__], abs(d__1)) / work[ + i__]; + s = max(d__2,d__3); + } else { +/* Computing MAX */ + d__2 = s, d__3 = ((d__1 = work[*n + i__], abs(d__1)) + safe1) + / (work[i__] + safe1); + s = max(d__2,d__3); + } +/* L80: */ + } + berr[j] = s; + +/* Test stopping criterion. Continue iterating if */ +/* 1) The residual BERR(J) is larger than machine epsilon, and */ +/* 2) BERR(J) decreased by at least a factor of 2 during the */ +/* last iteration, and */ +/* 3) At most ITMAX iterations tried. */ + + if (berr[j] > eps && berr[j] * 2. <= lstres && count <= 5) { + +/* Update solution and try again. */ + + dgetrs_(trans, n, &c__1, &af[af_offset], ldaf, &ipiv[1], &work[*n + + 1], n, info, (ftnlen)1); + daxpy_(n, &c_b17, &work[*n + 1], &c__1, &x[j * x_dim1 + 1], &c__1) + ; + lstres = berr[j]; + ++count; + goto L20; + } + +/* Bound error from formula */ + +/* norm(X - XTRUE) / norm(X) .le. FERR = */ +/* norm( abs(inv(op(A)))* */ +/* ( abs(R) + NZ*EPS*( abs(op(A))*abs(X)+abs(B) ))) / norm(X) */ + +/* where */ +/* norm(Z) is the magnitude of the largest component of Z */ +/* inv(op(A)) is the inverse of op(A) */ +/* abs(Z) is the componentwise absolute value of the matrix or */ +/* vector Z */ +/* NZ is the maximum number of nonzeros in any row of A, plus 1 */ +/* EPS is machine epsilon */ + +/* The i-th component of abs(R)+NZ*EPS*(abs(op(A))*abs(X)+abs(B)) */ +/* is incremented by SAFE1 if the i-th component of */ +/* abs(op(A))*abs(X) + abs(B) is less than SAFE2. */ + +/* Use DLACON to estimate the infinity-norm of the matrix */ +/* inv(op(A)) * diag(W), */ +/* where W = abs(R) + NZ*EPS*( abs(op(A))*abs(X)+abs(B) ))) */ + + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { + if (work[i__] > safe2) { + work[i__] = (d__1 = work[*n + i__], abs(d__1)) + nz * eps * + work[i__]; + } else { + work[i__] = (d__1 = work[*n + i__], abs(d__1)) + nz * eps * + work[i__] + safe1; + } +/* L90: */ + } + + kase = 0; +L100: + dlacon_(n, &work[(*n << 1) + 1], &work[*n + 1], &iwork[1], &ferr[j], & + kase); + if (kase != 0) { + if (kase == 1) { + +/* Multiply by diag(W)*inv(op(A)**T). */ + + dgetrs_(transt, n, &c__1, &af[af_offset], ldaf, &ipiv[1], & + work[*n + 1], n, info, (ftnlen)1); + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { + work[*n + i__] = work[i__] * work[*n + i__]; +/* L110: */ + } + } else { + +/* Multiply by inv(op(A))*diag(W). */ + + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { + work[*n + i__] = work[i__] * work[*n + i__]; +/* L120: */ + } + dgetrs_(trans, n, &c__1, &af[af_offset], ldaf, &ipiv[1], & + work[*n + 1], n, info, (ftnlen)1); + } + goto L100; + } + +/* Normalize error. */ + + lstres = 0.; + i__2 = *n; + for (i__ = 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = lstres, d__3 = (d__1 = x[i__ + j * x_dim1], abs(d__1)); + lstres = max(d__2,d__3); +/* L130: */ + } + if (lstres != 0.) { + ferr[j] /= lstres; + } + +/* L140: */ + } + + return 0; + +/* End of DGERFS */ + +} /* dgerfs_ */ + diff --git a/ext/f2c_lapack/dtrtrs.c b/ext/f2c_lapack/dtrtrs.c new file mode 100644 index 000000000..4c4035d8e --- /dev/null +++ b/ext/f2c_lapack/dtrtrs.c @@ -0,0 +1,187 @@ +/* dtrtrs.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static doublereal c_b12 = 1.; + +/* Subroutine */ int dtrtrs_(char *uplo, char *trans, char *diag, integer *n, + integer *nrhs, doublereal *a, integer *lda, doublereal *b, integer * + ldb, integer *info, ftnlen uplo_len, ftnlen trans_len, ftnlen + diag_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, b_dim1, b_offset, i__1; + + /* Local variables */ + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int dtrsm_(char *, char *, char *, char *, + integer *, integer *, doublereal *, doublereal *, integer *, + doublereal *, integer *, ftnlen, ftnlen, ftnlen, ftnlen), xerbla_( + char *, integer *, ftnlen); + static logical nounit; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DTRTRS solves a triangular system of the form */ + +/* A * X = B or A**T * X = B, */ + +/* where A is a triangular matrix of order N, and B is an N-by-NRHS */ +/* matrix. A check is made to verify that A is nonsingular. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* = 'U': A is upper triangular; */ +/* = 'L': A is lower triangular. */ + +/* TRANS (input) CHARACTER*1 */ +/* Specifies the form of the system of equations: */ +/* = 'N': A * X = B (No transpose) */ +/* = 'T': A**T * X = B (Transpose) */ +/* = 'C': A**H * X = B (Conjugate transpose = Transpose) */ + +/* DIAG (input) CHARACTER*1 */ +/* = 'N': A is non-unit triangular; */ +/* = 'U': A is unit triangular. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* NRHS (input) INTEGER */ +/* The number of right hand sides, i.e., the number of columns */ +/* of the matrix B. NRHS >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The triangular matrix A. If UPLO = 'U', the leading N-by-N */ +/* upper triangular part of the array A contains the upper */ +/* triangular matrix, and the strictly lower triangular part of */ +/* A is not referenced. If UPLO = 'L', the leading N-by-N lower */ +/* triangular part of the array A contains the lower triangular */ +/* matrix, and the strictly upper triangular part of A is not */ +/* referenced. If DIAG = 'U', the diagonal elements of A are */ +/* also not referenced and are assumed to be 1. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* B (input/output) DOUBLE PRECISION array, dimension (LDB,NRHS) */ +/* On entry, the right hand side matrix B. */ +/* On exit, if INFO = 0, the solution matrix X. */ + +/* LDB (input) INTEGER */ +/* The leading dimension of the array B. LDB >= max(1,N). */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ +/* > 0: if INFO = i, the i-th diagonal element of A is zero, */ +/* indicating that the matrix is singular and the solutions */ +/* X have not been computed. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + b_dim1 = *ldb; + b_offset = 1 + b_dim1; + b -= b_offset; + + /* Function Body */ + *info = 0; + nounit = lsame_(diag, "N", (ftnlen)1, (ftnlen)1); + if (! lsame_(uplo, "U", (ftnlen)1, (ftnlen)1) && ! lsame_(uplo, "L", ( + ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (! lsame_(trans, "N", (ftnlen)1, (ftnlen)1) && ! lsame_(trans, + "T", (ftnlen)1, (ftnlen)1) && ! lsame_(trans, "C", (ftnlen)1, ( + ftnlen)1)) { + *info = -2; + } else if (! nounit && ! lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + *info = -3; + } else if (*n < 0) { + *info = -4; + } else if (*nrhs < 0) { + *info = -5; + } else if (*lda < max(1,*n)) { + *info = -7; + } else if (*ldb < max(1,*n)) { + *info = -9; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DTRTRS", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + return 0; + } + +/* Check for singularity. */ + + if (nounit) { + i__1 = *n; + for (*info = 1; *info <= i__1; ++(*info)) { + if (a[*info + *info * a_dim1] == 0.) { + return 0; + } +/* L10: */ + } + } + *info = 0; + +/* Solve A * x = b or A' * x = b. */ + + dtrsm_("Left", uplo, trans, diag, n, nrhs, &c_b12, &a[a_offset], lda, &b[ + b_offset], ldb, (ftnlen)4, (ftnlen)1, (ftnlen)1, (ftnlen)1); + + return 0; + +/* End of DTRTRS */ + +} /* dtrtrs_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index 48b38590c..50a478cca 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -67,6 +67,10 @@ dorml2.o \ dormlq.o \ dormqr.o \ drscl.o \ +dtrtrs.o \ +dgerfs.o \ +dgecon.o \ +dgeequ.o \ ilaenv.o #SRCS = $(OBJS:.o=.cpp) diff --git a/ext/lapack/dgecon.f b/ext/lapack/dgecon.f new file mode 100644 index 000000000..f6bd485f4 --- /dev/null +++ b/ext/lapack/dgecon.f @@ -0,0 +1,181 @@ + SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK, + $ INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* February 29, 1992 +* +* .. Scalar Arguments .. + CHARACTER NORM + INTEGER INFO, LDA, N + DOUBLE PRECISION ANORM, RCOND +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION A( LDA, * ), WORK( * ) +* .. +* +* Purpose +* ======= +* +* DGECON estimates the reciprocal of the condition number of a general +* real matrix A, in either the 1-norm or the infinity-norm, using +* the LU factorization computed by DGETRF. +* +* An estimate is obtained for norm(inv(A)), and the reciprocal of the +* condition number is computed as +* RCOND = 1 / ( norm(A) * norm(inv(A)) ). +* +* Arguments +* ========= +* +* NORM (input) CHARACTER*1 +* Specifies whether the 1-norm condition number or the +* infinity-norm condition number is required: +* = '1' or 'O': 1-norm; +* = 'I': Infinity-norm. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The factors L and U from the factorization A = P*L*U +* as computed by DGETRF. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* ANORM (input) DOUBLE PRECISION +* If NORM = '1' or 'O', the 1-norm of the original matrix A. +* If NORM = 'I', the infinity-norm of the original matrix A. +* +* RCOND (output) DOUBLE PRECISION +* The reciprocal of the condition number of the matrix A, +* computed as RCOND = 1/(norm(A) * norm(inv(A))). +* +* WORK (workspace) DOUBLE PRECISION array, dimension (4*N) +* +* IWORK (workspace) INTEGER array, dimension (N) +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL ONENRM + CHARACTER NORMIN + INTEGER IX, KASE, KASE1 + DOUBLE PRECISION AINVNM, SCALE, SL, SMLNUM, SU +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER IDAMAX + DOUBLE PRECISION DLAMCH + EXTERNAL LSAME, IDAMAX, DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL DLACON, DLATRS, DRSCL, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + ONENRM = NORM.EQ.'1' .OR. LSAME( NORM, 'O' ) + IF( .NOT.ONENRM .AND. .NOT.LSAME( NORM, 'I' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -4 + ELSE IF( ANORM.LT.ZERO ) THEN + INFO = -5 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGECON', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + RCOND = ZERO + IF( N.EQ.0 ) THEN + RCOND = ONE + RETURN + ELSE IF( ANORM.EQ.ZERO ) THEN + RETURN + END IF +* + SMLNUM = DLAMCH( 'Safe minimum' ) +* +* Estimate the norm of inv(A). +* + AINVNM = ZERO + NORMIN = 'N' + IF( ONENRM ) THEN + KASE1 = 1 + ELSE + KASE1 = 2 + END IF + KASE = 0 + 10 CONTINUE + CALL DLACON( N, WORK( N+1 ), WORK, IWORK, AINVNM, KASE ) + IF( KASE.NE.0 ) THEN + IF( KASE.EQ.KASE1 ) THEN +* +* Multiply by inv(L). +* + CALL DLATRS( 'Lower', 'No transpose', 'Unit', NORMIN, N, A, + $ LDA, WORK, SL, WORK( 2*N+1 ), INFO ) +* +* Multiply by inv(U). +* + CALL DLATRS( 'Upper', 'No transpose', 'Non-unit', NORMIN, N, + $ A, LDA, WORK, SU, WORK( 3*N+1 ), INFO ) + ELSE +* +* Multiply by inv(U'). +* + CALL DLATRS( 'Upper', 'Transpose', 'Non-unit', NORMIN, N, A, + $ LDA, WORK, SU, WORK( 3*N+1 ), INFO ) +* +* Multiply by inv(L'). +* + CALL DLATRS( 'Lower', 'Transpose', 'Unit', NORMIN, N, A, + $ LDA, WORK, SL, WORK( 2*N+1 ), INFO ) + END IF +* +* Divide X by 1/(SL*SU) if doing so will not cause overflow. +* + SCALE = SL*SU + NORMIN = 'Y' + IF( SCALE.NE.ONE ) THEN + IX = IDAMAX( N, WORK, 1 ) + IF( SCALE.LT.ABS( WORK( IX ) )*SMLNUM .OR. SCALE.EQ.ZERO ) + $ GO TO 20 + CALL DRSCL( N, SCALE, WORK, 1 ) + END IF + GO TO 10 + END IF +* +* Compute the estimate of the reciprocal condition number. +* + IF( AINVNM.NE.ZERO ) + $ RCOND = ( ONE / AINVNM ) / ANORM +* + 20 CONTINUE + RETURN +* +* End of DGECON +* + END diff --git a/ext/lapack/dgeequ.f b/ext/lapack/dgeequ.f new file mode 100644 index 000000000..a1be3c169 --- /dev/null +++ b/ext/lapack/dgeequ.f @@ -0,0 +1,226 @@ + SUBROUTINE DGEEQU( M, N, A, LDA, R, C, ROWCND, COLCND, AMAX, + $ INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + INTEGER INFO, LDA, M, N + DOUBLE PRECISION AMAX, COLCND, ROWCND +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), C( * ), R( * ) +* .. +* +* Purpose +* ======= +* +* DGEEQU computes row and column scalings intended to equilibrate an +* M-by-N matrix A and reduce its condition number. R returns the row +* scale factors and C the column scale factors, chosen to try to make +* the largest element in each row and column of the matrix B with +* elements B(i,j)=R(i)*A(i,j)*C(j) have absolute value 1. +* +* R(i) and C(j) are restricted to be between SMLNUM = smallest safe +* number and BIGNUM = largest safe number. Use of these scaling +* factors is not guaranteed to reduce the condition number of A but +* works well in practice. +* +* Arguments +* ========= +* +* M (input) INTEGER +* The number of rows of the matrix A. M >= 0. +* +* N (input) INTEGER +* The number of columns of the matrix A. N >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The M-by-N matrix whose equilibration factors are +* to be computed. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,M). +* +* R (output) DOUBLE PRECISION array, dimension (M) +* If INFO = 0 or INFO > M, R contains the row scale factors +* for A. +* +* C (output) DOUBLE PRECISION array, dimension (N) +* If INFO = 0, C contains the column scale factors for A. +* +* ROWCND (output) DOUBLE PRECISION +* If INFO = 0 or INFO > M, ROWCND contains the ratio of the +* smallest R(i) to the largest R(i). If ROWCND >= 0.1 and +* AMAX is neither too large nor too small, it is not worth +* scaling by R. +* +* COLCND (output) DOUBLE PRECISION +* If INFO = 0, COLCND contains the ratio of the smallest +* C(i) to the largest C(i). If COLCND >= 0.1, it is not +* worth scaling by C. +* +* AMAX (output) DOUBLE PRECISION +* Absolute value of largest matrix element. If AMAX is very +* close to overflow or very close to underflow, the matrix +* should be scaled. +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* > 0: if INFO = i, and i is +* <= M: the i-th row of A is exactly zero +* > M: the (i-M)-th column of A is exactly zero +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, J + DOUBLE PRECISION BIGNUM, RCMAX, RCMIN, SMLNUM +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH + EXTERNAL DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + IF( M.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, M ) ) THEN + INFO = -4 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGEEQU', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + ROWCND = ONE + COLCND = ONE + AMAX = ZERO + RETURN + END IF +* +* Get machine constants. +* + SMLNUM = DLAMCH( 'S' ) + BIGNUM = ONE / SMLNUM +* +* Compute row scale factors. +* + DO 10 I = 1, M + R( I ) = ZERO + 10 CONTINUE +* +* Find the maximum element in each row. +* + DO 30 J = 1, N + DO 20 I = 1, M + R( I ) = MAX( R( I ), ABS( A( I, J ) ) ) + 20 CONTINUE + 30 CONTINUE +* +* Find the maximum and minimum scale factors. +* + RCMIN = BIGNUM + RCMAX = ZERO + DO 40 I = 1, M + RCMAX = MAX( RCMAX, R( I ) ) + RCMIN = MIN( RCMIN, R( I ) ) + 40 CONTINUE + AMAX = RCMAX +* + IF( RCMIN.EQ.ZERO ) THEN +* +* Find the first zero scale factor and return an error code. +* + DO 50 I = 1, M + IF( R( I ).EQ.ZERO ) THEN + INFO = I + RETURN + END IF + 50 CONTINUE + ELSE +* +* Invert the scale factors. +* + DO 60 I = 1, M + R( I ) = ONE / MIN( MAX( R( I ), SMLNUM ), BIGNUM ) + 60 CONTINUE +* +* Compute ROWCND = min(R(I)) / max(R(I)) +* + ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) + END IF +* +* Compute column scale factors +* + DO 70 J = 1, N + C( J ) = ZERO + 70 CONTINUE +* +* Find the maximum element in each column, +* assuming the row scaling computed above. +* + DO 90 J = 1, N + DO 80 I = 1, M + C( J ) = MAX( C( J ), ABS( A( I, J ) )*R( I ) ) + 80 CONTINUE + 90 CONTINUE +* +* Find the maximum and minimum scale factors. +* + RCMIN = BIGNUM + RCMAX = ZERO + DO 100 J = 1, N + RCMIN = MIN( RCMIN, C( J ) ) + RCMAX = MAX( RCMAX, C( J ) ) + 100 CONTINUE +* + IF( RCMIN.EQ.ZERO ) THEN +* +* Find the first zero scale factor and return an error code. +* + DO 110 J = 1, N + IF( C( J ).EQ.ZERO ) THEN + INFO = M + J + RETURN + END IF + 110 CONTINUE + ELSE +* +* Invert the scale factors. +* + DO 120 J = 1, N + C( J ) = ONE / MIN( MAX( C( J ), SMLNUM ), BIGNUM ) + 120 CONTINUE +* +* Compute COLCND = min(C(J)) / max(C(J)) +* + COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) + END IF +* + RETURN +* +* End of DGEEQU +* + END diff --git a/ext/lapack/dgerfs.f b/ext/lapack/dgerfs.f new file mode 100644 index 000000000..aa6c13415 --- /dev/null +++ b/ext/lapack/dgerfs.f @@ -0,0 +1,332 @@ + SUBROUTINE DGERFS( TRANS, N, NRHS, A, LDA, AF, LDAF, IPIV, B, LDB, + $ X, LDX, FERR, BERR, WORK, IWORK, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* September 30, 1994 +* +* .. Scalar Arguments .. + CHARACTER TRANS + INTEGER INFO, LDA, LDAF, LDB, LDX, N, NRHS +* .. +* .. Array Arguments .. + INTEGER IPIV( * ), IWORK( * ) + DOUBLE PRECISION A( LDA, * ), AF( LDAF, * ), B( LDB, * ), + $ BERR( * ), FERR( * ), WORK( * ), X( LDX, * ) +* .. +* +* Purpose +* ======= +* +* DGERFS improves the computed solution to a system of linear +* equations and provides error bounds and backward error estimates for +* the solution. +* +* Arguments +* ========= +* +* TRANS (input) CHARACTER*1 +* Specifies the form of the system of equations: +* = 'N': A * X = B (No transpose) +* = 'T': A**T * X = B (Transpose) +* = 'C': A**H * X = B (Conjugate transpose = Transpose) +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* NRHS (input) INTEGER +* The number of right hand sides, i.e., the number of columns +* of the matrices B and X. NRHS >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The original N-by-N matrix A. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* AF (input) DOUBLE PRECISION array, dimension (LDAF,N) +* The factors L and U from the factorization A = P*L*U +* as computed by DGETRF. +* +* LDAF (input) INTEGER +* The leading dimension of the array AF. LDAF >= max(1,N). +* +* IPIV (input) INTEGER array, dimension (N) +* The pivot indices from DGETRF; for 1<=i<=N, row i of the +* matrix was interchanged with row IPIV(i). +* +* B (input) DOUBLE PRECISION array, dimension (LDB,NRHS) +* The right hand side matrix B. +* +* LDB (input) INTEGER +* The leading dimension of the array B. LDB >= max(1,N). +* +* X (input/output) DOUBLE PRECISION array, dimension (LDX,NRHS) +* On entry, the solution matrix X, as computed by DGETRS. +* On exit, the improved solution matrix X. +* +* LDX (input) INTEGER +* The leading dimension of the array X. LDX >= max(1,N). +* +* FERR (output) DOUBLE PRECISION array, dimension (NRHS) +* The estimated forward error bound for each solution vector +* X(j) (the j-th column of the solution matrix X). +* If XTRUE is the true solution corresponding to X(j), FERR(j) +* is an estimated upper bound for the magnitude of the largest +* element in (X(j) - XTRUE) divided by the magnitude of the +* largest element in X(j). The estimate is as reliable as +* the estimate for RCOND, and is almost always a slight +* overestimate of the true error. +* +* BERR (output) DOUBLE PRECISION array, dimension (NRHS) +* The componentwise relative backward error of each solution +* vector X(j) (i.e., the smallest relative change in +* any element of A or B that makes X(j) an exact solution). +* +* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) +* +* IWORK (workspace) INTEGER array, dimension (N) +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* +* Internal Parameters +* =================== +* +* ITMAX is the maximum number of steps of iterative refinement. +* +* ===================================================================== +* +* .. Parameters .. + INTEGER ITMAX + PARAMETER ( ITMAX = 5 ) + DOUBLE PRECISION ZERO + PARAMETER ( ZERO = 0.0D+0 ) + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D+0 ) + DOUBLE PRECISION TWO + PARAMETER ( TWO = 2.0D+0 ) + DOUBLE PRECISION THREE + PARAMETER ( THREE = 3.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL NOTRAN + CHARACTER TRANST + INTEGER COUNT, I, J, K, KASE, NZ + DOUBLE PRECISION EPS, LSTRES, S, SAFE1, SAFE2, SAFMIN, XK +* .. +* .. External Subroutines .. + EXTERNAL DAXPY, DCOPY, DGEMV, DGETRS, DLACON, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX +* .. +* .. External Functions .. + LOGICAL LSAME + DOUBLE PRECISION DLAMCH + EXTERNAL LSAME, DLAMCH +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + NOTRAN = LSAME( TRANS, 'N' ) + IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'T' ) .AND. .NOT. + $ LSAME( TRANS, 'C' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -5 + ELSE IF( LDAF.LT.MAX( 1, N ) ) THEN + INFO = -7 + ELSE IF( LDB.LT.MAX( 1, N ) ) THEN + INFO = -10 + ELSE IF( LDX.LT.MAX( 1, N ) ) THEN + INFO = -12 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGERFS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 .OR. NRHS.EQ.0 ) THEN + DO 10 J = 1, NRHS + FERR( J ) = ZERO + BERR( J ) = ZERO + 10 CONTINUE + RETURN + END IF +* + IF( NOTRAN ) THEN + TRANST = 'T' + ELSE + TRANST = 'N' + END IF +* +* NZ = maximum number of nonzero elements in each row of A, plus 1 +* + NZ = N + 1 + EPS = DLAMCH( 'Epsilon' ) + SAFMIN = DLAMCH( 'Safe minimum' ) + SAFE1 = NZ*SAFMIN + SAFE2 = SAFE1 / EPS +* +* Do for each right hand side +* + DO 140 J = 1, NRHS +* + COUNT = 1 + LSTRES = THREE + 20 CONTINUE +* +* Loop until stopping criterion is satisfied. +* +* Compute residual R = B - op(A) * X, +* where op(A) = A, A**T, or A**H, depending on TRANS. +* + CALL DCOPY( N, B( 1, J ), 1, WORK( N+1 ), 1 ) + CALL DGEMV( TRANS, N, N, -ONE, A, LDA, X( 1, J ), 1, ONE, + $ WORK( N+1 ), 1 ) +* +* Compute componentwise relative backward error from formula +* +* max(i) ( abs(R(i)) / ( abs(op(A))*abs(X) + abs(B) )(i) ) +* +* where abs(Z) is the componentwise absolute value of the matrix +* or vector Z. If the i-th component of the denominator is less +* than SAFE2, then SAFE1 is added to the i-th components of the +* numerator and denominator before dividing. +* + DO 30 I = 1, N + WORK( I ) = ABS( B( I, J ) ) + 30 CONTINUE +* +* Compute abs(op(A))*abs(X) + abs(B). +* + IF( NOTRAN ) THEN + DO 50 K = 1, N + XK = ABS( X( K, J ) ) + DO 40 I = 1, N + WORK( I ) = WORK( I ) + ABS( A( I, K ) )*XK + 40 CONTINUE + 50 CONTINUE + ELSE + DO 70 K = 1, N + S = ZERO + DO 60 I = 1, N + S = S + ABS( A( I, K ) )*ABS( X( I, J ) ) + 60 CONTINUE + WORK( K ) = WORK( K ) + S + 70 CONTINUE + END IF + S = ZERO + DO 80 I = 1, N + IF( WORK( I ).GT.SAFE2 ) THEN + S = MAX( S, ABS( WORK( N+I ) ) / WORK( I ) ) + ELSE + S = MAX( S, ( ABS( WORK( N+I ) )+SAFE1 ) / + $ ( WORK( I )+SAFE1 ) ) + END IF + 80 CONTINUE + BERR( J ) = S +* +* Test stopping criterion. Continue iterating if +* 1) The residual BERR(J) is larger than machine epsilon, and +* 2) BERR(J) decreased by at least a factor of 2 during the +* last iteration, and +* 3) At most ITMAX iterations tried. +* + IF( BERR( J ).GT.EPS .AND. TWO*BERR( J ).LE.LSTRES .AND. + $ COUNT.LE.ITMAX ) THEN +* +* Update solution and try again. +* + CALL DGETRS( TRANS, N, 1, AF, LDAF, IPIV, WORK( N+1 ), N, + $ INFO ) + CALL DAXPY( N, ONE, WORK( N+1 ), 1, X( 1, J ), 1 ) + LSTRES = BERR( J ) + COUNT = COUNT + 1 + GO TO 20 + END IF +* +* Bound error from formula +* +* norm(X - XTRUE) / norm(X) .le. FERR = +* norm( abs(inv(op(A)))* +* ( abs(R) + NZ*EPS*( abs(op(A))*abs(X)+abs(B) ))) / norm(X) +* +* where +* norm(Z) is the magnitude of the largest component of Z +* inv(op(A)) is the inverse of op(A) +* abs(Z) is the componentwise absolute value of the matrix or +* vector Z +* NZ is the maximum number of nonzeros in any row of A, plus 1 +* EPS is machine epsilon +* +* The i-th component of abs(R)+NZ*EPS*(abs(op(A))*abs(X)+abs(B)) +* is incremented by SAFE1 if the i-th component of +* abs(op(A))*abs(X) + abs(B) is less than SAFE2. +* +* Use DLACON to estimate the infinity-norm of the matrix +* inv(op(A)) * diag(W), +* where W = abs(R) + NZ*EPS*( abs(op(A))*abs(X)+abs(B) ))) +* + DO 90 I = 1, N + IF( WORK( I ).GT.SAFE2 ) THEN + WORK( I ) = ABS( WORK( N+I ) ) + NZ*EPS*WORK( I ) + ELSE + WORK( I ) = ABS( WORK( N+I ) ) + NZ*EPS*WORK( I ) + SAFE1 + END IF + 90 CONTINUE +* + KASE = 0 + 100 CONTINUE + CALL DLACON( N, WORK( 2*N+1 ), WORK( N+1 ), IWORK, FERR( J ), + $ KASE ) + IF( KASE.NE.0 ) THEN + IF( KASE.EQ.1 ) THEN +* +* Multiply by diag(W)*inv(op(A)**T). +* + CALL DGETRS( TRANST, N, 1, AF, LDAF, IPIV, WORK( N+1 ), + $ N, INFO ) + DO 110 I = 1, N + WORK( N+I ) = WORK( I )*WORK( N+I ) + 110 CONTINUE + ELSE +* +* Multiply by inv(op(A))*diag(W). +* + DO 120 I = 1, N + WORK( N+I ) = WORK( I )*WORK( N+I ) + 120 CONTINUE + CALL DGETRS( TRANS, N, 1, AF, LDAF, IPIV, WORK( N+1 ), N, + $ INFO ) + END IF + GO TO 100 + END IF +* +* Normalize error. +* + LSTRES = ZERO + DO 130 I = 1, N + LSTRES = MAX( LSTRES, ABS( X( I, J ) ) ) + 130 CONTINUE + IF( LSTRES.NE.ZERO ) + $ FERR( J ) = FERR( J ) / LSTRES +* + 140 CONTINUE +* + RETURN +* +* End of DGERFS +* + END diff --git a/ext/lapack/dtrtrs.f b/ext/lapack/dtrtrs.f new file mode 100644 index 000000000..c1b4c5c4c --- /dev/null +++ b/ext/lapack/dtrtrs.f @@ -0,0 +1,148 @@ + SUBROUTINE DTRTRS( UPLO, TRANS, DIAG, N, NRHS, A, LDA, B, LDB, + $ INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + CHARACTER DIAG, TRANS, UPLO + INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* Purpose +* ======= +* +* DTRTRS solves a triangular system of the form +* +* A * X = B or A**T * X = B, +* +* where A is a triangular matrix of order N, and B is an N-by-NRHS +* matrix. A check is made to verify that A is nonsingular. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* = 'U': A is upper triangular; +* = 'L': A is lower triangular. +* +* TRANS (input) CHARACTER*1 +* Specifies the form of the system of equations: +* = 'N': A * X = B (No transpose) +* = 'T': A**T * X = B (Transpose) +* = 'C': A**H * X = B (Conjugate transpose = Transpose) +* +* DIAG (input) CHARACTER*1 +* = 'N': A is non-unit triangular; +* = 'U': A is unit triangular. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* NRHS (input) INTEGER +* The number of right hand sides, i.e., the number of columns +* of the matrix B. NRHS >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The triangular matrix A. If UPLO = 'U', the leading N-by-N +* upper triangular part of the array A contains the upper +* triangular matrix, and the strictly lower triangular part of +* A is not referenced. If UPLO = 'L', the leading N-by-N lower +* triangular part of the array A contains the lower triangular +* matrix, and the strictly upper triangular part of A is not +* referenced. If DIAG = 'U', the diagonal elements of A are +* also not referenced and are assumed to be 1. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* B (input/output) DOUBLE PRECISION array, dimension (LDB,NRHS) +* On entry, the right hand side matrix B. +* On exit, if INFO = 0, the solution matrix X. +* +* LDB (input) INTEGER +* The leading dimension of the array B. LDB >= max(1,N). +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* > 0: if INFO = i, the i-th diagonal element of A is zero, +* indicating that the matrix is singular and the solutions +* X have not been computed. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL NOUNIT +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + NOUNIT = LSAME( DIAG, 'N' ) + IF( .NOT.LSAME( UPLO, 'U' ) .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( .NOT.LSAME( TRANS, 'N' ) .AND. .NOT. + $ LSAME( TRANS, 'T' ) .AND. .NOT.LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( .NOT.NOUNIT .AND. .NOT.LSAME( DIAG, 'U' ) ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -7 + ELSE IF( LDB.LT.MAX( 1, N ) ) THEN + INFO = -9 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DTRTRS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* Check for singularity. +* + IF( NOUNIT ) THEN + DO 10 INFO = 1, N + IF( A( INFO, INFO ).EQ.ZERO ) + $ RETURN + 10 CONTINUE + END IF + INFO = 0 +* +* Solve A * x = b or A' * x = b. +* + CALL DTRSM( 'Left', UPLO, TRANS, DIAG, N, NRHS, ONE, A, LDA, B, + $ LDB ) +* + RETURN +* +* End of DTRTRS +* + END From af4b40d9c3eebafdd6ead03d57ae5cc14d34ae7e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 22 Feb 2011 00:21:17 +0000 Subject: [PATCH 328/446] Fixed the expectedResidLeg() routine. There was an error in there --- Cantera/src/numerics/NonlinearSolver.cpp | 282 ++++++++++++++++++----- Cantera/src/numerics/NonlinearSolver.h | 24 +- 2 files changed, 251 insertions(+), 55 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 06a6b1bfe..a014d99db 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -983,6 +983,7 @@ namespace Cantera { return 2; } //==================================================================================================================== + double NonlinearSolver::expectedResidLeg(int leg, double alpha) const { double resD2, res2, resNorm; @@ -1001,33 +1002,24 @@ namespace Cantera { } else if (leg == 1) { - + /* + * Same formula as above for lambda=1. + */ double tmp2 = - RJd_norm_ * lambda_; - resD2 =- tmp2; + double RdotJS = - tmp2; + double JsJs = tmp2; - double res2 = m_normResid0 * m_normResid0 * neq_ + resD2; - double resCP; - if (res2 < 0.0) { - resCP = m_normResid0 - sqrt(resD2/neq_); - } else { - resCP = sqrt(res2 / neq_); - } - - double beta = Nuu_; - double tmpN2 = normResid02; - double tmpN = 1.0 - 2.0 * beta + 1.0 * beta * beta - 1.0; - double resNu2 = tmpN * tmpN2; - res2 = m_normResid0 * m_normResid0 * neq_ + resNu2; - double resNuu; - if (res2 < 0.0) { - resNuu = m_normResid0 - sqrt(res2/neq_); - } else { - resNuu = sqrt(res2 / neq_); - } - resNorm = resCP + alpha * (resNuu - resCP); + + double res0_2 = m_normResid0 * m_normResid0 * neq_; + + res2 = res0_2 + (1.0 - alpha) * 2 * RdotJS - 2 * alpha * Nuu_ * res0_2 + + (1.0 - alpha) * (1.0 - alpha) * JsJs + + alpha * alpha * Nuu_ * Nuu_ * res0_2 + - 2 * alpha * Nuu_ * (1.0 - alpha) * RdotJS; + + resNorm = sqrt(res2 / neq_); return resNorm; - } else { double beta = Nuu_ + alpha * (1.0 - Nuu_); double tmp2 = normResid02; @@ -1053,7 +1045,7 @@ namespace Cantera { double *y1 = DATA_PTR(m_wksp); double sLen; printf(" residualComparisonLeg() \n"); - printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); + printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); // First compare at 1/4 along SD curve std::vector alphaT; alphaT.push_back(0.00); @@ -1333,6 +1325,40 @@ namespace Cantera { } //==================================================================================================================== + // Fill a dogleg solution step vector + /* + * Previously, we have filled up deltaX_Newton_[], deltaX_CP_[], and Nuu_, so that + * this routine is straightforward. + * + * @param leg Leg of the dog leg you are on (0, 1, or 2) + * @param alpha Relative length along the dog length that you are on. + * @param deltaX Vector to be filled up + */ + void NonlinearSolver::fillDogLegStep(int leg, double alpha, std::vector & deltaX) const { + if (leg == 0) { + for (int i = 0; i < neq_; i++) { + deltaX[i] = alpha * deltaX_CP_[i]; + } + } else if (leg == 2) { + for (int i = 0; i < neq_; i++) { + deltaX[i] = (alpha + (1.0 - alpha) * Nuu_) * deltaX_Newton_[i]; + } + } else { + for (int i = 0; i < neq_; i++) { + deltaX[i] = deltaX_CP_[i] * (1.0 - alpha) + alpha * Nuu_ * deltaX_Newton_[i]; + } + } + } + //==================================================================================================================== + // Calculate the trust distance of a step in the solution variables + /* + * The trust distance is defined as the length of the step according to the norm wrt to the trust region. + * We calculate the trust distance by the following method + * + * trustDist = || delta_x dot 1/trustDeltaX_ || + * + * @param deltaX Current value of deltaX + */ doublereal NonlinearSolver::calcTrustDistance(std::vector const & deltaX) const { doublereal sum = 0.0; @@ -1354,7 +1380,7 @@ namespace Cantera { return 2; } - if (normTrust_Newton_ * Nuu_ > trustDelta) { + if (normTrust_Newton_ * Nuu_ < trustDelta) { alpha = (trustDelta - normTrust_Newton_ * Nuu_) / (normTrust_Newton_ - normTrust_Newton_ * Nuu_); dist = dist_R0_ + dist_R1_ + alpha * dist_R2_; lambda = dist / dist_Total_; @@ -1538,8 +1564,6 @@ namespace Cantera { if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, y1, ydot1); - } else { - } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -1694,14 +1718,20 @@ namespace Cantera { //==================================================================================================================== int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y0, - const doublereal *ydot0, const double* step0, - double* const y1, double* const ydot1, double* step1, + const doublereal *ydot0, std::vector & step0, + double* const y_new, double* const ydot_new, double* step1, double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, int& num_backtracks) { double lambda; double alpha; - + int info; + int leg = 2; + bool success = false; + int retn = 0; + bool haveASuccess = false; + double normResid02 = m_normResid0 * m_normResid0 * neq_; + double trustDeltaOld = trustDelta_; //-------------------------------------------- // Attempt damped step //-------------------------------------------- @@ -1711,28 +1741,170 @@ namespace Cantera { int j, m; doublereal ff = m_dampBound; num_backtracks = 0; + double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; + bool goodStep = false; - /* - * Find the initial value of lambda that satisfies the trust distance - */ - int leg = calcTrustIntersection(trustDelta_, lambda, alpha); + for (m = 0; m < NDAMP; m++) { + /* + * Find the initial value of lambda that satisfies the trust distance, trustDelta_ + */ + leg = calcTrustIntersection(trustDelta_, lambda, alpha); + /* + * Figure out the new step vector, step0, based on (leg, alpha) + */ + fillDogLegStep(leg, alpha, step0); + + /* + * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria + * as a good step. Also, make sure that it stays within bounds. + */ + info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, loglevel, trustDeltaOld); + /* + * The algorithm failed to find a solution vector sufficiently different than the current point + */ + if (info == -1) { + if (loglevel >= 1) { + double stepNorm = solnErrorNorm(DATA_PTR(step0)); + printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); + success = false; + retn = -1; + break; + } + } + if (info == -2) { + if (loglevel >= 1) { + printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); + success = false; + retn = -1; + break; + } + } + if (info == 0) { + success = true; + break; + } + if (info == 3) { + haveASuccess = true; + // Store the good results in step1 + mdp::mdp_copy_dbl_1(DATA_PTR(step1), CONSTD_DATA_PTR(step0), neq_); - - - - - - - - - + } + if (info == 2) { + if (haveASuccess) { + mdp::mdp_copy_dbl_1(DATA_PTR(step0), CONSTD_DATA_PTR(step1), neq_); + for (j = 0; j < neq_; j++) { + y_new[j] = y0[j] + step0[j]; + } + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y_new, ydot_new); + } + success = true; + break; + } + } } + if (success) { + if (m_normResidTrial < 1.0) { + return 1; + } + return 0; + } + return -1; + } + //==================================================================================================================== + int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, const doublereal *ydot0, + std::vector & step0, + double* const y1, double* const ydot1, int& loglevel, double trustDeltaOld) + + { + int retn = 2; + bool goodStep = false; + int j; + int info; + double stepNorm = solnErrorNorm(DATA_PTR(step0)); + double normResid02 = m_normResid0 * m_normResid0 * neq_; + double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; + // Compute the multiplier to keep all components in bounds + // A value of one indicates that there is no limitation + // on the current step size in the nonlinear method due to + // bounds constraints (either negative values of delta + // bounds constraints. + m_dampBound = boundStep(y0, DATA_PTR(step0), loglevel); + + double ff = m_dampBound; + + for (j = 0; j < neq_; j++) { + y1[j] = y0[j] + ff * step0[j]; + } + + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y1, ydot1); + } + + + /* + * Calculate the residual that would result if y1[] were the new solution vector + * -> m_resid[] contains the result of the residual calculation + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + } else { + info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + } + if (info != 1) { + if (loglevel > 0) { + printf("\t\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + } + return -2; + } + m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); + + double funcDecrease = 0.5 * (m_normResidTrial - normResid02) / (ff * stepNorm); + if (funcDecrease < 1.0E-4 * funcDecreaseSDExp) { + goodStep = true; + retn = 0; + } else { + trustDelta_ *= 0.33; + retn = 2; + // error condition if step is getting too small + if (stepNorm * .5 < 0.2) { + retn = -1; + } + return retn; + } + /* + * Figure out the next trust region + * + * If we had to bounds delta the update, decrease the trust region + */ + if (m_dampBound < 1.0) { + trustDelta_ *= 0.5; + } else { + retn = 0; + double expectedNormRes = expectedResidLeg(leg, alpha); + if (m_normResidTrial > 1.1 * expectedNormRes) { + trustDelta_ *= 0.5; + } else { + + if (trustDelta_ <= trustDeltaOld) { + trustDelta_ *= 2.0; + retn = 3; + } else { + if (m_normResidTrial < 0.75 * expectedNormRes) { + trustDelta_ *= 2.0; + } + } + } + } + return retn; } //==================================================================================================================== /* @@ -1939,13 +2111,18 @@ namespace Cantera { + int doDogLeg = 0; #ifdef DEBUG_DOGLEG + doDogLeg = 0; descentComparison(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); setupDoubleDogleg(DATA_PTR(stp)); residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); - -#endif - + if (doDogLeg) { + m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), + stp, DATA_PTR(y_new), DATA_PTR(ydot_new), + DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); + } +#endif // Damp the Newton step /* * On return the recommended new solution and derivatisve is located in: @@ -1956,12 +2133,13 @@ namespace Cantera { * The estimate of the solution update norm for the next step is located in * s1 */ - m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), - DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), - DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); - frst = false; - num_backtracks += i_backtracks; - + if (!doDogLeg) { + m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), + DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), + DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); + frst = false; + num_backtracks += i_backtracks; + } /* * Impose the minimum number of newton iterations critera */ diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 47df6ab86..8c3b20fb8 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -238,9 +238,21 @@ namespace Cantera { */ void calcTrustVector(); - //! Calculate the trust distance + //! Fill a dogleg solution step vector /*! - * We calculate the trust distance by the following method + * Previously, we have filled up deltaX_Newton_[], deltaX_CP_[], and Nuu_, so that + * this routine is straightforward. + * + * @param leg Leg of the dog leg you are on (0, 1, or 2) + * @param alpha Relative length along the dog length that you are on. + * @param deltaX Vector to be filled up + */ + void fillDogLegStep(int leg, double alpha, std::vector & deltaX) const; + + //! Calculate the trust distance of a step in the solution variables + /*! + * The trust distance is defined as the length of the step according to the norm wrt to the trust region. + * We calculate the trust distance by the following method. * * trustDist = || delta_x dot 1/trustDeltaX_ || * @@ -248,6 +260,8 @@ namespace Cantera { */ doublereal calcTrustDistance(std::vector const & deltaX) const; + + int calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const; public: //! Bound the step @@ -571,11 +585,15 @@ namespace Cantera { int calcTrustIntersection(double trustVal, const double &lambda, double &alpha) const; int dampDogLeg(const doublereal time_curr, const double* y0, - const doublereal *ydot0, const double* step0, + const doublereal *ydot0, std::vector & step0, double* const y1, double* const ydot1, double* step1, double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, int& num_backtracks); + int decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, const doublereal *ydot0, + std::vector & step0, + double* const y1, double* const ydot1, int& loglevel, double trustDeltaOld); + //! Calculated the expected residual along the double dogleg curve. /*! * @param leg 0, 1, or 2 representing the curves of the dogleg From f1669ba3e2c36c972f47ccf1430fb5ceebaa8137 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 22 Feb 2011 18:50:54 +0000 Subject: [PATCH 329/446] Got the dog leg algorithm into a working state, at least on one problem. --- Cantera/src/numerics/NonlinearSolver.cpp | 190 +++++++++++++++++------ Cantera/src/numerics/NonlinearSolver.h | 25 ++- 2 files changed, 166 insertions(+), 49 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index a014d99db..99d96bd3d 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -142,7 +142,8 @@ namespace Cantera { dist_Total_(0.0), JdJd_norm_(0.0), normTrust_Newton_(0.0), - normTrust_CP_(0.0) + normTrust_CP_(0.0), + doDogLeg_(0) { neq_ = m_func->nEquations(); @@ -239,7 +240,8 @@ namespace Cantera { dist_Total_(0.0), JdJd_norm_(0.0), normTrust_Newton_(0.0), - normTrust_CP_(0.0) + normTrust_CP_(0.0), + doDogLeg_(0) { *this =operator=(right); } @@ -316,6 +318,7 @@ namespace Cantera { JdJd_norm_ = right.JdJd_norm_; normTrust_Newton_ = right.normTrust_Newton_; normTrust_CP_ = right.normTrust_CP_; + doDogLeg_ = right.doDogLeg_; return *this; } @@ -356,6 +359,10 @@ namespace Cantera { } } //==================================================================================================================== + void NonlinearSolver::setSolverScheme(int doDogLeg) { + doDogLeg_ = doDogLeg; + } + //==================================================================================================================== std::vector & NonlinearSolver::lowBoundsConstraintVector() { return m_y_low_bounds; } @@ -1137,7 +1144,12 @@ namespace Cantera { } - + //==================================================================================================================== + double NonlinearSolver::trustRegionLength() const + { + double dlen = solnErrorNorm(DATA_PTR(deltaX_trust_)); + return (trustDelta_ * dlen); + } //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() { @@ -1281,9 +1293,12 @@ namespace Cantera { for (int i = 0; i < neq_; i++) { wtSum += m_ewt[i]; } + wtSum /= neq_; + double trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); + double trustNormGoal = trustNorm * trustDelta_; // This is the size of each component. - double trustDeltaEach = trustDelta_ / neq_; + double trustDeltaEach = trustDelta_ * trustNorm / neq_; double oldVal; double fabsy; // we use the old value of the trust region as an indicator @@ -1300,30 +1315,47 @@ namespace Cantera { } } else { double newValue = trustDeltaEach * m_ewt[i] / wtSum; - if (newValue > 2.0 * oldVal) { - newValue = 2.0 * oldVal; - } else if (newValue < 0.5 * oldVal) { - newValue = 0.5 * oldVal; + if (newValue > 4.0 * oldVal) { + newValue = 4.0 * oldVal; + } else if (newValue < 0.25 * oldVal) { + newValue = 0.25 * oldVal; + if (deltaX_trust_[i] < m_deltaStepMinimum[i]) { + newValue = m_deltaStepMinimum[i]; + } } deltaX_trust_[i] = newValue; if (deltaX_trust_[i] > 0.75 * m_deltaStepMaximum[i]) { - deltaX_trust_[i] = m_deltaStepMaximum[i]; + deltaX_trust_[i] = 0.75 * m_deltaStepMaximum[i]; } } } // Final renormalization. - double sum = 0.0; + trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); + double sum = trustNormGoal / trustNorm; for (int i = 0; i < neq_; i++) { - sum += deltaX_trust_[i]; - } - for (int i = 0; i < neq_; i++) { - deltaX_trust_[i] = deltaX_trust_[i] / sum; + deltaX_trust_[i] = deltaX_trust_[i] * sum; } trustDelta_ = 1.0; - + printf("calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", + trustNorm, trustNormGoal); + } + //==================================================================================================================== + void NonlinearSolver::initializeTrustRegion() + { + double cpd = calcTrustDistance(deltaX_CP_); + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + trustDelta_ = trustDelta_ * cpd; + calcTrustVector(); + cpd = calcTrustDistance(deltaX_CP_); + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + trustDelta_ = trustDelta_ * cpd; + calcTrustVector(); + cpd = calcTrustDistance(deltaX_CP_); + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } + //==================================================================================================================== // Fill a dogleg solution step vector /* @@ -1355,7 +1387,7 @@ namespace Cantera { * The trust distance is defined as the length of the step according to the norm wrt to the trust region. * We calculate the trust distance by the following method * - * trustDist = || delta_x dot 1/trustDeltaX_ || + * trustDist = || delta_x dot 1/trustDeltaX_ || / trustDelta_ * * @param deltaX Current value of deltaX */ @@ -1367,7 +1399,7 @@ namespace Cantera { tmp = deltaX[i] / deltaX_trust_[i]; sum += tmp * tmp; } - sum = sqrt(sum / neq_); + sum = sqrt(sum / neq_) / trustDelta_; return sum; } //==================================================================================================================== @@ -1744,7 +1776,7 @@ namespace Cantera { double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; bool goodStep = false; - + double tlen; for (m = 0; m < NDAMP; m++) { @@ -1752,10 +1784,29 @@ namespace Cantera { * Find the initial value of lambda that satisfies the trust distance, trustDelta_ */ leg = calcTrustIntersection(trustDelta_, lambda, alpha); + + if (loglevel > 5) { + tlen = trustRegionLength(); + printf("\tdampDogLeg: trust region with length %13.5E has intersection at leg = %d, alpha = %g\n", + tlen, leg, alpha); + } /* * Figure out the new step vector, step0, based on (leg, alpha) */ fillDogLegStep(leg, alpha, step0); + + /* + * Bound the step + */ + m_dampBound = boundStep(y0, DATA_PTR(step0), loglevel); + /* + * Decrease the step length if we are bound + */ + if (m_dampBound < 1.0) { + for (j = 0; j < neq_; j++) { + step0[j] = step0[j] * m_dampBound; + } + } /* * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria @@ -1810,6 +1861,16 @@ namespace Cantera { } + /* + * Estimate s1, the norm after the next step + */ + double stepNorm = solnErrorNorm(DATA_PTR(step1)); + if ( m_dampBound < 1.0) { + stepNorm /= m_dampBound; + } + stepNorm *= m_normResidTrial / m_normResid0; + s1 = stepNorm; + if (success) { if (m_normResidTrial < 1.0) { return 1; @@ -1828,21 +1889,15 @@ namespace Cantera { bool goodStep = false; int j; int info; + double ll; double stepNorm = solnErrorNorm(DATA_PTR(step0)); double normResid02 = m_normResid0 * m_normResid0 * neq_; double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; - // Compute the multiplier to keep all components in bounds - // A value of one indicates that there is no limitation - // on the current step size in the nonlinear method due to - // bounds constraints (either negative values of delta - // bounds constraints. - m_dampBound = boundStep(y0, DATA_PTR(step0), loglevel); - - double ff = m_dampBound; + for (j = 0; j < neq_; j++) { - y1[j] = y0[j] + ff * step0[j]; + y1[j] = y0[j] + step0[j]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { @@ -1867,7 +1922,7 @@ namespace Cantera { } m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); - double funcDecrease = 0.5 * (m_normResidTrial - normResid02) / (ff * stepNorm); + double funcDecrease = 0.5 * (m_normResidTrial - normResid02) / (stepNorm); if (funcDecrease < 1.0E-4 * funcDecreaseSDExp) { goodStep = true; retn = 0; @@ -1887,19 +1942,33 @@ namespace Cantera { */ if (m_dampBound < 1.0) { trustDelta_ *= 0.5; + ll = trustRegionLength(); + printf("decideStep(): Trust region decreased from %g to %g due to bounds constraint\n", + ll*2, ll); } else { retn = 0; double expectedNormRes = expectedResidLeg(leg, alpha); if (m_normResidTrial > 1.1 * expectedNormRes) { - trustDelta_ *= 0.5; + if ((m_normResidTrial > 0.2 * m_normResid0) && (m_normResidTrial > 0.1)) { + trustDelta_ *= 0.5; + ll = trustRegionLength(); + printf("decideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", + ll*2, ll); + } } else { if (trustDelta_ <= trustDeltaOld) { trustDelta_ *= 2.0; + ll = trustRegionLength(); + printf("decideStep(): Trust region increased from %g to %g due to good quad approximation\n", + ll*0.5, ll); retn = 3; } else { if (m_normResidTrial < 0.75 * expectedNormRes) { trustDelta_ *= 2.0; + ll = trustRegionLength(); + printf("decideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + ll*0.5, ll); } } } @@ -1938,9 +2007,7 @@ namespace Cantera { int m = 0; bool forceNewJac = false; doublereal s1=1.e30; -#ifdef DEBUG_DOGLEG - //jacCopy_ = jac; -#endif + // std::vector y_curr(neq_, 0.0); std::vector ydot_curr(neq_, 0.0); @@ -1996,6 +2063,10 @@ namespace Cantera { createSolnWeights(DATA_PTR(m_y_n)); #ifdef DEBUG_DOGLEG calcTrustVector(); +#else + if (doDogLeg_) { + calcTrustVector(); + } #endif } else { // Do this stuff every 5 iterations @@ -2003,6 +2074,10 @@ namespace Cantera { createSolnWeights(DATA_PTR(m_y_n)); #ifdef DEBUG_DOGLEG calcTrustVector(); +#else + if (doDogLeg_) { + calcTrustVector(); + } #endif } } @@ -2077,6 +2152,16 @@ namespace Cantera { #ifdef DEBUG_DOGLEG m_normDeltaSoln_CP = doCauchyPointSolve(jac); + if (m_numTotalNewtIts == 1) { + initializeTrustRegion(); + } +#else + if (doDogLeg_) { + m_normDeltaSoln_CP = doCauchyPointSolve(jac); + if (m_numTotalNewtIts == 1) { + initializeTrustRegion(); + } + } #endif // compute the undamped Newton step @@ -2094,15 +2179,17 @@ namespace Cantera { } -#ifdef DEBUG_DOGLEG - double trustD = calcTrustDistance(stp); - if (trustD > trustDelta_) { - printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); - } else { - printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); - } -#endif + if (doDogLeg_) { + double trustD = calcTrustDistance(stp); +#ifdef DEBUG_DOGLEG + if (trustD > trustDelta_) { + printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); + } else { + printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); + } +#endif + } /* * Filter out bad directions @@ -2111,18 +2198,27 @@ namespace Cantera { - int doDogLeg = 0; + #ifdef DEBUG_DOGLEG - doDogLeg = 0; descentComparison(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); - setupDoubleDogleg(DATA_PTR(stp)); - residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); - if (doDogLeg) { +#endif + + + if (doDogLeg_) { + setupDoubleDogleg(DATA_PTR(stp)); +#ifdef DEBUG_DOGLEG + residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); +#endif m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), stp, DATA_PTR(y_new), DATA_PTR(ydot_new), DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); } -#endif +#ifdef DEBUG_DOGLEG + else { + residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + } +#endif + // Damp the Newton step /* * On return the recommended new solution and derivatisve is located in: @@ -2133,7 +2229,7 @@ namespace Cantera { * The estimate of the solution update norm for the next step is located in * s1 */ - if (!doDogLeg) { + if (!doDogLeg_) { m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 8c3b20fb8..43b6c6e4b 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -208,6 +208,13 @@ namespace Cantera { const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac, int loglevel); + //! Calculate the size of the current trust region + /*! + * We carry out a norm of deltaX_trust_ first. Then, we multiply that value + * by trustDelta_ + */ + double trustRegionLength() const; + //! Set default deulta bounds amounts /*! * Delta bounds are set to 0.01 for all unknowns arbitrarily and capriciously @@ -262,7 +269,6 @@ namespace Cantera { - int calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const; public: //! Bound the step /*! @@ -582,7 +588,9 @@ namespace Cantera { */ int lambdaToLeg(const double lambda, double &alpha) const; - int calcTrustIntersection(double trustVal, const double &lambda, double &alpha) const; + int calcTrustIntersection(double trustVal, double &lambda, double &alpha) const; + + void initializeTrustRegion(); int dampDogLeg(const doublereal time_curr, const double* y0, const doublereal *ydot0, std::vector & step0, @@ -623,6 +631,15 @@ namespace Cantera { */ void setPrintLvl(int printLvl); + //! Parameter to turn on solution solver schemes + /*! + * @param doDogLeg Parameter to turn on the double dog leg scheme + * Default is to always use a damping scheme in the Newton Direction. + * When this is nonzero, a model trust region approach is used using a double dog leg + * with the steepest descent direction used for small step sizes. + */ + void setSolverScheme(int doDogLeg = 0); + /* * ----------------------------------------------------------------------------------------------------------------- * MEMBER DATA @@ -871,6 +888,10 @@ namespace Cantera { doublereal normTrust_CP_; + //! General toggle for turning on dog leg damping. + int doDogLeg_; + + /******************************************************************************************* * OTHER COUNTERS From c3847347e8e065c79657cd3ff3985408c2ff3a4b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 11 Mar 2011 00:04:38 +0000 Subject: [PATCH 330/446] Updated to reflect the renewal of the copywrite --- License.rtf | 4 ++-- License.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/License.rtf b/License.rtf index 1adaa3d95..9142e3da8 100755 --- a/License.rtf +++ b/License.rtf @@ -43,7 +43,7 @@ \par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid12135870 Copyright (c) 2001-2009}{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid2033138\charrsid602915 , California Institute of Technology}{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid602915 . }{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid2033138\charrsid602915 All rights reserved.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid2033138 \par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid602915 -\par }\pard \ltrpar\ql \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12135870 {\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid12135870 Copyright (c) 2009, Sandia Corporation. Under the terms of +\par }\pard \ltrpar\ql \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12135870 {\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid12135870 Copyright (c) 2009, 2011, Sandia Corporation. Under the terms of Contract AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights to certain parts of this software. \par All rights reserved. \par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid12135870\charrsid602915 @@ -173,4 +173,4 @@ ffffffffffffffffffffffffffffffff52006f006f007400200045006e0074007200790000000000 98404912ca01feffffff00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff00000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff0000000000000000000000000000000000000000000000000000 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffffffffffffffffff000000000000000000000000000000000000000000000000 -0000000000000000000000000000000000000000000000000105000000000000}} \ No newline at end of file +0000000000000000000000000000000000000000000000000105000000000000}} diff --git a/License.txt b/License.txt index 9c39fa167..215387e61 100755 --- a/License.txt +++ b/License.txt @@ -2,7 +2,7 @@ Copyright (c) 2001-2009, California Institute of Technology All rights reserved. -Copyright (c) 2009, Sandia Corporation. Under the terms of +Copyright (c) 2009, 2011, Sandia Corporation. Under the terms of Contract AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights to certain parts of this software. All rights reserved. From f3bec02808c375979091f0bf98c2381b1848214c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 11 Mar 2011 00:10:50 +0000 Subject: [PATCH 331/446] A reworking of the LatticePhase and LatticeSolidPhase classes. --- Cantera/src/base/xml.cpp | 3 +- Cantera/src/equil/vcs_VolPhase.cpp | 1 + Cantera/src/equil/vcs_defs.h | 33 +- Cantera/src/equil/vcs_solve.cpp | 25 +- Cantera/src/numerics/ResidEval.h | 29 +- Cantera/src/numerics/ResidJacEval.h | 6 - Cantera/src/thermo/Constituents.cpp | 71 +++- Cantera/src/thermo/Constituents.h | 22 +- Cantera/src/thermo/DebyeHuckel.h | 7 - Cantera/src/thermo/Elements.cpp | 74 +++- Cantera/src/thermo/Elements.h | 106 ++++- Cantera/src/thermo/FixedChemPotSSTP.cpp | 2 + Cantera/src/thermo/HMWSoln.h | 8 - Cantera/src/thermo/IdealMolalSoln.h | 8 - Cantera/src/thermo/IdealSolidSolnPhase.cpp | 11 +- Cantera/src/thermo/IdealSolidSolnPhase.h | 9 +- Cantera/src/thermo/LatticePhase.cpp | 263 +++++++++--- Cantera/src/thermo/LatticePhase.h | 213 +++++++++- Cantera/src/thermo/LatticeSolidPhase.cpp | 467 +++++++++++++++++---- Cantera/src/thermo/LatticeSolidPhase.h | 299 +++++++++++-- Cantera/src/thermo/ThermoFactory.cpp | 14 +- Cantera/src/thermo/ThermoPhase.cpp | 40 +- Cantera/src/thermo/ThermoPhase.h | 14 +- Cantera/src/thermo/mix_defs.h | 2 +- 24 files changed, 1436 insertions(+), 291 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 2ea75093c..1484c1b6f 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -52,9 +52,8 @@ namespace Cantera { */ XML_Error(int line=0) : m_line(line), - m_msg(0) + m_msg("Error in XML file") { - m_msg = "Error in XML file"; if (line > 0) { m_msg += " at line " + int2str(line+1); } diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 664544779..5683e640c 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -1571,6 +1571,7 @@ namespace VCSnonideal { for (eT = 0; eT < nebase; eT++) { ename = tPhase->elementName(eT); m_elementNames[e] = ename; + m_elementType[e] = tPhase->elementType(eT); e++; } diff --git a/Cantera/src/equil/vcs_defs.h b/Cantera/src/equil/vcs_defs.h index 534d5ca54..2c50ffaa1 100644 --- a/Cantera/src/equil/vcs_defs.h +++ b/Cantera/src/equil/vcs_defs.h @@ -314,6 +314,11 @@ namespace VCSnonideal { * constraint to one category. * @{ */ + + + //! An element constraint that is current turned off +#define VCS_ELEM_TYPE_TURNEDOFF -1 + //! Normal element constraint consisting of positive coefficients for the //! formula matrix. /*! @@ -335,11 +340,37 @@ namespace VCSnonideal { */ #define VCS_ELEM_TYPE_CHARGENEUTRALITY 2 + //! Constraint associated with maintaing a fixed lattice stoichiometry int eh + //! solids + /*! + * The constraint may have positive or negative values. The lattice 0 species will + * have negative values while higher lattices will have positive values + */ +#define VCS_ELEM_TYPE_LATTICERATIO 3 + + //! Constraint associated with maintaining frozen kinetic equilibria in + //! some functional groups within molecules + /*! + * We seek here to say that some functional groups or ionic states should be + * treated as if they are separate elements given the time scale of the problem. + * This will be abs positive constraint. We have not implemented any examples yet. + * A requirement will be that we must be able to add and subtract these contraints. + */ +#define VCS_ELEM_TYPE_KINETICFROZEN 4 + + //! Constraint associated with the maintenance of a surface phase + /*! + * We don't have any examples of this yet either. However, surfaces only exist + * because they are interfaces between bulk layers. If we want to treat surfaces + * within thermodynamic systems we must come up with a way to constrain their total + * number. + */ +#define VCS_ELEM_TYPE_SURFACECONSTRAINT 5 //! Other constraint equations /*! * currently there are none */ -#define VCS_ELEM_TYPE_OTHERCONSTRAINT 3 +#define VCS_ELEM_TYPE_OTHERCONSTRAINT 6 //@} /*! diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 75444a566..251b1496d 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -518,9 +518,18 @@ namespace VCSnonideal { * FormulaMatrix[] -> Copy the formula matrix over */ for (i = 0; i < nspecies; i++) { + bool nonzero = false; for (j = 0; j < nelements; j++) { + if (pub->FormulaMatrix[j][i] != 0.0) { + nonzero = true; + } m_formulaMatrix[j][i] = pub->FormulaMatrix[j][i]; } + if (!nonzero) { + plogf("vcs_prob_specifyFully:: species %d %s has a zero formula matrix!\n", i, + pub->SpName[i].c_str()); + return VCS_PUB_BAD; + } } /* @@ -573,17 +582,31 @@ namespace VCSnonideal { /* * Formulate the Goal Element Abundance Vector */ + double sum; if (pub->gai.size() != 0) { - for (i = 0; i < nelements; i++) m_elemAbundancesGoal[i] = pub->gai[i]; + for (i = 0; i < nelements; i++) { + m_elemAbundancesGoal[i] = pub->gai[i]; + if (pub->m_elType[i] == VCS_ELEM_TYPE_LATTICERATIO) { + if (m_elemAbundancesGoal[i] < 1.0E-10) { + m_elemAbundancesGoal[i] = 0.0; + } + } + } } else { if (m_doEstimateEquil == 0) { for (j = 0; j < nelements; j++) { m_elemAbundancesGoal[j] = 0.0; for (kspec = 0; kspec < nspecies; kspec++) { if (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { + sum += m_molNumSpecies_old[kspec]; m_elemAbundancesGoal[j] += m_formulaMatrix[j][kspec] * m_molNumSpecies_old[kspec]; } } + if (pub->m_elType[j] == VCS_ELEM_TYPE_LATTICERATIO) { + if (m_elemAbundancesGoal[j] < 1.0E-10 * sum) { + m_elemAbundancesGoal[j] = 0.0; + } + } } } else { plogf("%sElement Abundances, m_elemAbundancesGoal[], not specified\n", ser); diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index da65c4cfa..3e25f8129 100644 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -31,7 +31,7 @@ namespace Cantera { * Virtual base class for DAE residual function evaluators. * Classes derived from ResidEval evaluate the residual function * \f[ - \vec{F}(t,\vec{y}, \vec{y^\prime}) + * \vec{F}(t,\vec{y}, \vec{y^\prime}) * \f] * The DAE solver attempts to find a solution y(t) such that F = 0. * @ingroup DAE_Group @@ -59,13 +59,28 @@ namespace Cantera { return c_NONE; } + //! Initialization function + virtual void initSizes() + { + int neq = nEquations(); + m_alg.resize(neq, 0); + } + /** * Specify that solution component k is purely algebraic - * that is, the derivative of this component does not appear * in the residual function. */ - virtual void setAlgebraic(const int k) { m_alg[k] = 1; } - virtual bool isAlgebraic(const int k) {return (m_alg[k] == 1); } + virtual void setAlgebraic(const int k) { + if ((int) m_alg.size() < (k+1)) { + initSizes(); + } + m_alg[k] = 1; + } + + virtual bool isAlgebraic(const int k) { + return (m_alg[k] == 1); + } /** @@ -106,6 +121,7 @@ namespace Cantera { */ virtual int getInitialConditions(const doublereal t0, doublereal * const y, doublereal * const ydot) { + initSizes(); throw CanteraError("ResidEval::GetInitialConditions()", "base class called"); return 1; } @@ -143,7 +159,12 @@ namespace Cantera { protected: - std::map m_alg; + //! Mapping vector that stores whether a degree of freedom is a DAE or not + /*! + * The first index is the equation number. The second index is 1 if it is a DAE, + * and zero if it is not. + */ + std::vector m_alg; std::map m_constrain; private: diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 08a23fc35..a1799253e 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -60,7 +60,6 @@ namespace Cantera { public: - //!Default constructor /*! * @param atol Initial value of the global tolerance (defaults to 1.0E-13) @@ -208,7 +207,6 @@ namespace Cantera { const doublereal * const y, const doublereal * const ydot); - //! Return a vector of delta y's for calculation of the numerical Jacobian /*! * There is a default algorithm provided. @@ -233,7 +231,6 @@ namespace Cantera { doublereal * const delta_y, const doublereal * const solnWeights = 0); - //! Returns a vector of column scale factors that can be used to column scale Jacobians. /*! * Default to yScales[] = 1.0 @@ -322,7 +319,6 @@ namespace Cantera { SquareMatrix &J, doublereal * const resid); - protected: //! constant value of atol @@ -335,5 +331,3 @@ namespace Cantera { #endif - - diff --git a/Cantera/src/thermo/Constituents.cpp b/Cantera/src/thermo/Constituents.cpp index 2d42d9564..ff7446d80 100644 --- a/Cantera/src/thermo/Constituents.cpp +++ b/Cantera/src/thermo/Constituents.cpp @@ -118,6 +118,9 @@ namespace Cantera { return m_Elements->atomicNumber(m); } + int Constituents::elementType(int m) const{ + return m_Elements->elementType(m); + } /* * Add an element to the set. @@ -155,9 +158,9 @@ namespace Cantera { */ void Constituents:: addUniqueElement(const std::string& symbol, doublereal weight, - int atomicNumber, doublereal entropy298) + int atomicNumber, doublereal entropy298, int elem_type) { - m_Elements->addUniqueElement(symbol, weight, atomicNumber, entropy298); + m_Elements->addUniqueElement(symbol, weight, atomicNumber, entropy298, elem_type); } void Constituents:: @@ -291,10 +294,10 @@ namespace Cantera { m_speciesNames.push_back(name); m_speciesCharge.push_back(charge); m_speciesSize.push_back(size); - int m_mm = m_Elements->nElements(); + int ne = m_Elements->nElements(); // Create a changeable copy of the element composition. We now change the charge potentially - vector_fp compNew(m_mm); - for (int m = 0; m < m_mm; m++) { + vector_fp compNew(ne); + for (int m = 0; m < ne; m++) { compNew[m] = comp[m]; } double wt = 0.0; @@ -313,30 +316,17 @@ namespace Cantera { } } } else { - m_Elements->m_elementsFrozen = false; - addUniqueElement("E", 0.000545, 0, 0.0); - m_Elements->m_elementsFrozen = true; - m_mm = m_Elements->nElements(); - if (m_kk > 0) { - vector_fp old(m_speciesComp); - m_speciesComp.resize(m_kk*m_mm, 0.0); - for (int k = 0; k < m_kk; k++) { - int m_old = m_mm - 1; - for (int m = 0; m < m_old; m++) { - m_speciesComp[k * m_mm + m] = old[k * (m_old) + m]; - } - m_speciesComp[k * (m_mm) + (m_mm-1)] = 0.0; - } - } + addUniqueElementAfterFreeze("E", 0.000545, 0, 0.0, CT_ELEM_TYPE_ELECTRONCHARGE); + ne = m_Elements->nElements(); eindex = m_Elements->elementIndex("E"); - compNew.resize(m_mm); - compNew[m_mm-1] = - charge; + compNew.resize(ne); + compNew[ne - 1] = - charge; //comp[eindex] = -charge; // throw CanteraError("Constituents::addSpecies", // "Element List doesn't include E, yet this species has charge:" + name); } } - for (int m = 0; m < m_mm; m++) { + for (int m = 0; m < ne; m++) { m_speciesComp.push_back(compNew[m]); wt += compNew[m] * aw[m]; } @@ -470,6 +460,8 @@ namespace Cantera { return m_speciesComp[m_mm * k + m]; } + + //==================================================================================================================== /* * * getAtoms() @@ -485,6 +477,39 @@ namespace Cantera { } } + + + //==================================================================================================================== + int Constituents::addUniqueElementAfterFreeze(const std::string& symbol, doublereal weight, int atomicNumber, + doublereal entropy298, int elem_type) + { + int ii = elementIndex(symbol); + if (ii != -1) { + return ii; + } + // Check to see that the element isn't really in the list + m_Elements->m_elementsFrozen = false; + addUniqueElement(symbol, weight, atomicNumber, entropy298, elem_type); + m_Elements->m_elementsFrozen = true; + int m_mm = m_Elements->nElements(); + ii = elementIndex(symbol); + if (ii != m_mm-1) { + throw CanteraError("Constituents::addElementAfterFreeze()", "confused"); + } + if (m_kk > 0) { + vector_fp old(m_speciesComp); + m_speciesComp.resize(m_kk*m_mm, 0.0); + for (int k = 0; k < m_kk; k++) { + int m_old = m_mm - 1; + for (int m = 0; m < m_old; m++) { + m_speciesComp[k * m_mm + m] = old[k * (m_old) + m]; + } + m_speciesComp[k * (m_mm) + (m_mm-1)] = 0.0; + } + } + return ii; + } + //==================================================================================================================== /* * This copy constructor just calls the assignment operator * for this class. diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h index be134749f..3a31522c3 100644 --- a/Cantera/src/thermo/Constituents.h +++ b/Cantera/src/thermo/Constituents.h @@ -110,7 +110,6 @@ namespace Cantera { /// exception, ElementRangeError, is thrown. std::string elementName(int m) const; - /// Index of element named 'name'. /// The index is an integer /// assigned to each element in the order it was added, @@ -141,6 +140,8 @@ namespace Cantera { */ int atomicNumber(int m) const; + int elementType(int m) const; + /// Return a read-only reference to the vector of element names. const std::vector& elementNames() const; @@ -193,7 +194,7 @@ namespace Cantera { */ void addUniqueElement(const std::string& symbol, doublereal weight, int atomicNumber = 0, - doublereal entropy298 = ENTROPY298_UNKNOWN); + doublereal entropy298 = ENTROPY298_UNKNOWN, int elem_type = CT_ELEM_TYPE_ABSPOS); //! Adde an element, checking for uniqueness /*! @@ -216,6 +217,23 @@ namespace Cantera { /// True if freezeElements has been called. bool elementsFrozen(); + //! Add an element after the elements have been frozen, checking for uniqueness + /*! + * The uniqueness is checked by comparing the string symbol. If + * not unique, nothing is done. + * + * @param symbol String symbol of the element + * @param weight Atomic weight of the element (kg kmol-1). + * @param atomicNumber Atomic number of the element (unitless) + * @param entropy298 Entropy of the element at 298 K and 1 bar + * in its most stable form. The default is + * the value ENTROPY298_UNKNOWN, which is + * interpreted as an unknown, and if used + * will cause Cantera to throw an error. + */ + int addUniqueElementAfterFreeze(const std::string& symbol, doublereal weight, int atomicNumber, + doublereal entropy298 = ENTROPY298_UNKNOWN, int elem_type = CT_ELEM_TYPE_ABSPOS); + //@} /// Returns the number of species in the phase diff --git a/Cantera/src/thermo/DebyeHuckel.h b/Cantera/src/thermo/DebyeHuckel.h index 16e3b5dc8..f2ce3d375 100644 --- a/Cantera/src/thermo/DebyeHuckel.h +++ b/Cantera/src/thermo/DebyeHuckel.h @@ -1255,13 +1255,6 @@ namespace Cantera { * -------------- Utilities ------------------------------- */ - - /** - * Return a reference to the species thermodynamic property - * manager. @todo This method will fail if no species thermo - * manager has been installed. - */ - SpeciesThermo& speciesThermo() { return *m_spthermo; } //! Initialize the object's internal lengths after species are set /** diff --git a/Cantera/src/thermo/Elements.cpp b/Cantera/src/thermo/Elements.cpp index 2c9e61bdc..7641a2365 100644 --- a/Cantera/src/thermo/Elements.cpp +++ b/Cantera/src/thermo/Elements.cpp @@ -222,6 +222,7 @@ namespace Cantera { Elements::Elements() : m_mm(0), m_elementsFrozen(false), + m_elem_type(0), numSubscribers(0) { } @@ -256,7 +257,7 @@ namespace Cantera { m_atomicNumbers = right.m_atomicNumbers; m_elementNames = right.m_elementNames; m_entropy298 = right.m_entropy298; - + m_elem_type = right.m_elem_type; numSubscribers = 0; return *this; @@ -335,7 +336,43 @@ namespace Cantera { AssertTrace(m >= 0 && m < m_mm); return (m_entropy298[m]); } - + //==================================================================================================================== + //! Return the element constraint type + /*! + * Possible types include: + * + * CT_ELEM_TYPE_TURNEDOFF -1 + * CT_ELEM_TYPE_ABSPOS 0 + * CT_ELEM_TYPE_ELECTRONCHARGE 1 + * CT_ELEM_TYPE_CHARGENEUTRALITY 2 + * CT_ELEM_TYPE_LATTICERATIO 3 + * CT_ELEM_TYPE_KINETICFROZEN 4 + * CT_ELEM_TYPE_SURFACECONSTRAINT 5 + * CT_ELEM_TYPE_OTHERCONSTRAINT 6 + * + * The default is CT_ELEM_TYPE_ABSPOS + */ + int Elements::elementType(int m) const + { + return m_elem_type[m]; + } + //==================================================================================================================== + // Change the element type of the mth constraint + /* + * Reassigns an element type + * + * @param m Element index + * @param elem_type New elem type to be assigned + * + * @return Returns the old element type + */ + int Elements::changeElementType(int m, int elem_type) + { + int old = m_elem_type[m]; + m_elem_type[m] = elem_type; + return old; + } + //==================================================================================================================== /* * * Add an element to the current set of elements in the current object. @@ -367,16 +404,22 @@ namespace Cantera { #ifdef USE_DGG_CODE m_definedElements[symbol] = nElements() + 1; #endif + if (symbol == "E") { + m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE); + } else { + m_elem_type.push_back(CT_ELEM_TYPE_ABSPOS); + } + m_mm++; } - + //=========================================================================================================== void Elements:: addElement(const XML_Node& e) { doublereal weight = atof(e["atomicWt"].c_str()); string symbol = e["name"]; addElement(symbol, weight); } - + //=========================================================================================================== /* * addUniqueElement(): * @@ -393,7 +436,7 @@ namespace Cantera { #ifdef USE_DGG_CODE void Elements:: addUniqueElement(const std::string& symbol, doublereal weight, int atomicNumber, - doublereal entropy298) + doublereal entropy298, int elem_type) { if (m_elementsFrozen) throw ElementsFrozen("addElement"); @@ -413,13 +456,17 @@ namespace Cantera { m_elementNames.push_back(symbol); m_atomicNumbers.push_back(atomicNumber); m_entropy298.push_back(entropy298); + if (symbol == "E") { + m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE); + } else { + m_elem_type.push_back(elem_type); + } m_mm++; } else { if (m_atomicWeights[i] != weight) { throw CanteraError("AddUniqueElement", - "Duplicate Elements (" + symbol + - ") have different weights"); + "Duplicate Elements (" + symbol + ") have different weights"); } } } @@ -427,7 +474,8 @@ namespace Cantera { #else void Elements:: addUniqueElement(const std::string& symbol, - doublereal weight, int atomicNumber, doublereal entropy298) + doublereal weight, int atomicNumber, doublereal entropy298, + int elem_type) { if (weight == -12345.0) { weight = LookupWtElements(symbol); @@ -458,12 +506,16 @@ namespace Cantera { m_elementNames.push_back(symbol); m_atomicNumbers.push_back(atomicNumber); m_entropy298.push_back(entropy298); + if (symbol == "E") { + m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE); + } else { + m_elem_type.push_back(elem_type); + } m_mm++; } else { if (m_atomicWeights[i] != weight) { throw CanteraError("AddUniqueElement", - "Duplicate Elements (" + symbol + - ") have different weights"); + "Duplicate Elements (" + symbol + ") have different weights"); } } } @@ -506,6 +558,8 @@ namespace Cantera { m_mm = 0; m_atomicWeights.resize(0); m_elementNames.resize(0); + m_entropy298.resize(0); + m_elem_type.resize(0); m_elementsFrozen = false; } diff --git a/Cantera/src/thermo/Elements.h b/Cantera/src/thermo/Elements.h index fa0e5dc2b..8f738acad 100644 --- a/Cantera/src/thermo/Elements.h +++ b/Cantera/src/thermo/Elements.h @@ -26,6 +26,74 @@ namespace Cantera { class XML_Node; class ElementRangeError; + /*! + * @name Types of Element Constraint Equations + * + * There may be several different types of element constraints handled + * by the equilibrium program and by Cantera in other contexts. + * These defines are used to assign each constraint to one category. + * @{ + */ + + //! An element constraint that is current turned off +#define CT_ELEM_TYPE_TURNEDOFF -1 + + //! Normal element constraint consisting of positive coefficients for the + //! formula matrix. + /*! + * All species have positive coefficients within the formula matrix. + * With this constraint, we may employ various strategies to handle + * small values of the element number successfully. + */ +#define CT_ELEM_TYPE_ABSPOS 0 + + //! This refers to conservation of electrons + /*! + * Electrons may have positive or negative values in the Formula matrix. + */ +#define CT_ELEM_TYPE_ELECTRONCHARGE 1 + + //! This refers to a charge neutrality of a single phase + /*! + * Charge neutrality may have positive or negative values in the Formula matrix. + */ +#define CT_ELEM_TYPE_CHARGENEUTRALITY 2 + + //! Constraint associated with maintaing a fixed lattice stoichiometry int eh + //! solids + /*! + * The constraint may have positive or negative values. The lattice 0 species will + * have negative values while higher lattices will have positive values + */ +#define CT_ELEM_TYPE_LATTICERATIO 3 + + //! Constraint associated with maintaining frozen kinetic equilibria in + //! some functional groups within molecules + /*! + * We seek here to say that some functional groups or ionic states should be + * treated as if they are separate elements given the time scale of the problem. + * This will be abs positive constraint. We have not implemented any examples yet. + * A requirement will be that we must be able to add and subtract these contraints. + */ +#define CT_ELEM_TYPE_KINETICFROZEN 4 + + //! Constraint associated with the maintenance of a surface phase + /*! + * We don't have any examples of this yet either. However, surfaces only exist + * because they are interfaces between bulk layers. If we want to treat surfaces + * within thermodynamic systems we must come up with a way to constrain their total + * number. + */ +#define CT_ELEM_TYPE_SURFACECONSTRAINT 5 + + //! Other constraint equations + /*! + * currently there are none + */ +#define CT_ELEM_TYPE_OTHERCONSTRAINT 6 + //@} + + //! Positive number indicating we don't know the gibbs free energy //! of the element in its most stable state at 298.15 K and 1 bar. //#define GIBSSFE298_UNKNOWN 123456789. @@ -120,6 +188,37 @@ namespace Cantera { */ doublereal entropyElement298(int m) const; + //! Return the element constraint type + /*! + * Possible types include: + * + * CT_ELEM_TYPE_ABSPOS 0 + * CT_ELEM_TYPE_ELECTRONCHARGE 1 + * CT_ELEM_TYPE_CHARGENEUTRALITY 2 + * CT_ELEM_TYPE_LATTICERATIO 3 + * CT_ELEM_TYPE_KINETICFROZEN 4 + * CT_ELEM_TYPE_SURFACECONSTRAINT 5 + * CT_ELEM_TYPE_OTHERCONSTRAINT 6 + * + * The default is CT_ELEM_TYPE_ABSPOS + * + * @param m Element index + * + * @return Returns the element type + */ + int elementType(int m) const; + + //! Change the element type of the mth constraint + /*! + * Reassigns an element type + * + * @param m Element index + * @param elem_type New elem type to be assigned + * + * @return Returns the old element type + */ + int changeElementType(int m, int elem_type); + /// vector of element atomic weights const vector_fp& atomicWeights() const { return m_atomicWeights; } @@ -199,7 +298,7 @@ namespace Cantera { */ void addUniqueElement(const std::string& symbol, doublereal weight = -12345.0, int atomicNumber = 0, - doublereal entropy298 = ENTROPY298_UNKNOWN); + doublereal entropy298 = ENTROPY298_UNKNOWN, int elem_type = CT_ELEM_TYPE_ABSPOS); //! Add an element to the current set of elements in the current object. /*! @@ -258,7 +357,7 @@ namespace Cantera { * If this is true, then no elements may be added to the * object. */ - bool m_elementsFrozen; + bool m_elementsFrozen; /** * Vector of element atomic weights: @@ -285,6 +384,9 @@ namespace Cantera { */ vector_fp m_entropy298; + //! Vector of element types + vector_int m_elem_type; + /** * Number of Constituents Objects that use this object * diff --git a/Cantera/src/thermo/FixedChemPotSSTP.cpp b/Cantera/src/thermo/FixedChemPotSSTP.cpp index 0f845b1f6..42a99d96e 100644 --- a/Cantera/src/thermo/FixedChemPotSSTP.cpp +++ b/Cantera/src/thermo/FixedChemPotSSTP.cpp @@ -144,6 +144,8 @@ namespace Cantera { ss.addChild("h", sval); ss.addChild("s", "0.0"); saveSpeciesData(0, s); + delete s; + s = 0; } //==================================================================================================================== diff --git a/Cantera/src/thermo/HMWSoln.h b/Cantera/src/thermo/HMWSoln.h index 17339386b..2526b9ff9 100644 --- a/Cantera/src/thermo/HMWSoln.h +++ b/Cantera/src/thermo/HMWSoln.h @@ -2053,14 +2053,6 @@ namespace Cantera { * -------------- Utilities ------------------------------- */ - /** - * Return a reference to the species thermodynamic property - * manager. - * - * @todo This method will fail if no species thermo - * manager has been installed. - */ - SpeciesThermo& speciesThermo() { return *m_spthermo; } //! Initialization of a HMWSoln phase using an xml file /*! diff --git a/Cantera/src/thermo/IdealMolalSoln.h b/Cantera/src/thermo/IdealMolalSoln.h index 737fe349a..151eb3083 100644 --- a/Cantera/src/thermo/IdealMolalSoln.h +++ b/Cantera/src/thermo/IdealMolalSoln.h @@ -777,14 +777,6 @@ namespace Cantera { /* * -------------- Utilities ------------------------------- */ - - /*! - * Return a reference to the species thermodynamic property - * manager. @todo This method will fail if no species thermo - * manager has been installed. - */ - SpeciesThermo& speciesThermo() { return *m_spthermo; } - //! Initialization routine for an IdealMolalSoln phase. /*! diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.cpp b/Cantera/src/thermo/IdealSolidSolnPhase.cpp index 6fd4107e6..8841712eb 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.cpp +++ b/Cantera/src/thermo/IdealSolidSolnPhase.cpp @@ -117,7 +117,7 @@ namespace Cantera { IdealSolidSolnPhase *ii = new IdealSolidSolnPhase(*this); return (ThermoPhase*) ii; } -//==================================================================================================================== + //==================================================================================================================== /** * Equation of state flag. Returns the value cIdealGas, defined * in mix_defs.h. @@ -679,8 +679,7 @@ namespace Cantera { * property manager. They are polynomial functions of temperature. * @see SpeciesThermo */ - void IdealSolidSolnPhase:: - getPartialMolarEnthalpies(doublereal* hbar) const { + void IdealSolidSolnPhase::getPartialMolarEnthalpies(doublereal* hbar) const { const array_fp& _h = enthalpy_RT_ref(); doublereal rt = GasConstant * temperature(); scale(_h.begin(), _h.end(), hbar, rt); @@ -892,8 +891,7 @@ namespace Cantera { * units = m^3 / kmol */ void IdealSolidSolnPhase::getStandardVolumes(doublereal *vol) const { - copy(m_speciesMolarVolume.begin(), - m_speciesMolarVolume.end(), vol); + copy(m_speciesMolarVolume.begin(), m_speciesMolarVolume.end(), vol); } @@ -1227,8 +1225,7 @@ namespace Cantera { "Unknown standardConc model: " + formStringa); } } else { - throw CanteraError(subname.c_str(), - "Unspecified standardConc model"); + throw CanteraError(subname.c_str(), "Unspecified standardConc model"); } /* diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.h b/Cantera/src/thermo/IdealSolidSolnPhase.h index a9f87b29c..279463915 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.h +++ b/Cantera/src/thermo/IdealSolidSolnPhase.h @@ -579,9 +579,9 @@ namespace Cantera { /// @name Partial Molar Properties of the Solution ----------------------------- //@{ - /** - * Returns an array of partial molar enthalpies for the species - * in the mixture. + + //! Returns an array of partial molar enthalpies for the species in the mixture. + /*! * Units (J/kmol) * For this phase, the partial molar enthalpies are equal to the * pure species enthalpies @@ -1057,8 +1057,9 @@ namespace Cantera { */ doublereal m_Pcurrent; + //! Vector of molar volumes for each species in the solution /** - * Species molar volume \f$ m^3 kmol^-1 \f$ + * Species molar volumes \f$ m^3 kmol^-1 \f$ */ array_fp m_speciesMolarVolume; diff --git a/Cantera/src/thermo/LatticePhase.cpp b/Cantera/src/thermo/LatticePhase.cpp index f86a26823..a0c900464 100644 --- a/Cantera/src/thermo/LatticePhase.cpp +++ b/Cantera/src/thermo/LatticePhase.cpp @@ -28,11 +28,20 @@ #include #include +using namespace std; + namespace Cantera { // Base Empty constructor LatticePhase::LatticePhase() : - m_tlast(0.0) + m_mm(0), + m_tmin(0.0), + m_tmax(0.0), + m_Pref(OneAtm), + m_Pcurrent(OneAtm), + m_tlast(0.0), + m_speciesMolarVolume(0), + m_site_density(0.0) { } @@ -41,7 +50,14 @@ namespace Cantera { * @param right Object to be copied */ LatticePhase::LatticePhase(const LatticePhase &right) : - m_tlast(0.0) + m_mm(0), + m_tmin(0.0), + m_tmax(0.0), + m_Pref(OneAtm), + m_Pcurrent(OneAtm), + m_tlast(0.0), + m_speciesMolarVolume(0), + m_site_density(0.0) { *this = operator=(right); } @@ -56,15 +72,16 @@ namespace Cantera { m_mm = right.m_mm; m_tmin = right.m_tmin; m_tmax = right.m_tmax; - m_p0 = right.m_p0; + m_Pref = right.m_Pref; + m_Pcurrent = right.m_Pcurrent; m_tlast = right.m_tlast; m_h0_RT = right.m_h0_RT; m_cp0_R = right.m_cp0_R; m_g0_RT = right.m_g0_RT; m_s0_R = right.m_s0_R; - m_press = right.m_press; m_vacancy = right.m_vacancy; - m_molar_density = right.m_molar_density; + m_speciesMolarVolume = right.m_speciesMolarVolume; + m_site_density = right.m_site_density; } return *this; } @@ -195,99 +212,176 @@ namespace Cantera { return GasConstant * (mean_X(&entropy_R_ref()[0]) - sum_xlogx()); } - + //==================================================================================================================== doublereal LatticePhase::gibbs_mole() const { return enthalpy_mole() - temperature() * entropy_mole(); } - + //==================================================================================================================== doublereal LatticePhase::cp_mole() const { return GasConstant * mean_X(&cp_R_ref()[0]); } - + //==================================================================================================================== doublereal LatticePhase::cv_mole() const { return cp_mole(); } - - - - void LatticePhase::setPressure(doublereal p) { - m_press = p; - setMolarDensity(m_molar_density); + //==================================================================================================================== + doublereal LatticePhase::calcDensity() { + setMolarDensity(m_site_density); + doublereal mw = meanMolecularWeight(); + doublereal dens = mw * m_site_density; + /* + * Calculate the molarVolume of the solution (m**3 kmol-1) + */ + // const doublereal * const dtmp = moleFractdivMMW(); + // doublereal invDens = dot(m_speciesMolarVolume.begin(), m_speciesMolarVolume.end(), dtmp); + /* + * Set the density in the parent State object directly, + * by calling the State::setDensity() function. + */ + // doublereal dens = 1.0/invDens; + // State::setDensity(dens); + return dens; } - + //==================================================================================================================== + void LatticePhase::setPressure(doublereal p) { + m_Pcurrent = p; + calcDensity(); + } + //==================================================================================================================== + void LatticePhase::setMoleFractions(const doublereal * const x) { + State::setMoleFractions(x); + calcDensity(); + } + //==================================================================================================================== + void LatticePhase::setMoleFractions_NoNorm(const doublereal * const x) { + State::setMoleFractions(x); + calcDensity(); + } + //==================================================================================================================== + void LatticePhase::setMassFractions(const doublereal * const y) { + State::setMassFractions(y); + calcDensity(); + } + //==================================================================================================================== + void LatticePhase::setMassFractions_NoNorm(const doublereal * const y) { + State::setMassFractions_NoNorm(y); + calcDensity(); + } + //==================================================================================================================== + void LatticePhase::setConcentrations(const doublereal * const c) { + State::setConcentrations(c); + calcDensity(); + } + //==================================================================================================================== void LatticePhase::getActivityConcentrations(doublereal* c) const { getMoleFractions(c); } - + //==================================================================================================================== void LatticePhase::getActivityCoefficients(doublereal* ac) const { for (int k = 0; k < m_kk; k++) { ac[k] = 1.0; } } - + //==================================================================================================================== doublereal LatticePhase::standardConcentration(int k) const { return 1.0; } - + //==================================================================================================================== doublereal LatticePhase::logStandardConc(int k) const { return 0.0; } - + //==================================================================================================================== void LatticePhase::getChemPotentials(doublereal* mu) const { - doublereal vdp = ((pressure() - m_spthermo->refPressure())/ - molarDensity()); + doublereal delta_p = m_Pcurrent - m_Pref; doublereal xx; - doublereal rt = temperature() * GasConstant; + doublereal RT = temperature() * GasConstant; const array_fp& g_RT = gibbs_RT_ref(); for (int k = 0; k < m_kk; k++) { xx = fmaxx(SmallNumber, moleFraction(k)); - mu[k] = rt*(g_RT[k] + log(xx)) + vdp; + mu[k] = RT * (g_RT[k] + log(xx)) + + delta_p * m_speciesMolarVolume[k]; + } + + } + //==================================================================================================================== + void LatticePhase::getPartialMolarEnthalpies(doublereal* hbar) const { + const array_fp& _h = enthalpy_RT_ref(); + doublereal rt = GasConstant * temperature(); + scale(_h.begin(), _h.end(), hbar, rt); + } + //==================================================================================================================== + void LatticePhase::getPartialMolarEntropies(doublereal* sbar) const { + const array_fp& _s = entropy_R_ref(); + doublereal r = GasConstant; + doublereal xx; + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(SmallNumber, moleFraction(k)); + sbar[k] = r * (_s[k] - log(xx)); } } - + //==================================================================================================================== + void LatticePhase::getPartialMolarCp(doublereal* cpbar) const { + getCp_R(cpbar); + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + //==================================================================================================================== void LatticePhase::getPartialMolarVolumes(doublereal* vbar) const { getStandardVolumes(vbar); } - + //==================================================================================================================== void LatticePhase::getStandardChemPotentials(doublereal* mu0) const { const array_fp& gibbsrt = gibbs_RT_ref(); scale(gibbsrt.begin(), gibbsrt.end(), mu0, _RT()); } - + //==================================================================================================================== void LatticePhase::getPureGibbs(doublereal* gpure) const { const array_fp& gibbsrt = gibbs_RT_ref(); - scale(gibbsrt.begin(), gibbsrt.end(), gpure, _RT()); - } - - void LatticePhase::getEnthalpy_RT(doublereal* hrt) const { - const array_fp& _h = enthalpy_RT_ref(); - std::copy(_h.begin(), _h.end(), hrt); - doublereal tmp = (pressure() - m_p0) / (molarDensity() * GasConstant * temperature()); + doublereal delta_p = (m_Pcurrent - m_Pref); + double RT = GasConstant * temperature(); for (int k = 0; k < m_kk; k++) { - hrt[k] += tmp; + gpure[k] = RT * gibbsrt[k] + delta_p * m_speciesMolarVolume[k]; } } - + //==================================================================================================================== + void LatticePhase::getEnthalpy_RT(doublereal* hrt) const { + const array_fp& _h = enthalpy_RT_ref(); + doublereal delta_prt = ((m_Pcurrent - m_Pref) / (GasConstant * temperature())); + for (int k = 0; k < m_kk; k++) { + hrt[k] = _h[k] + delta_prt * m_speciesMolarVolume[k]; + } + } + //==================================================================================================================== void LatticePhase::getEntropy_R(doublereal* sr) const { const array_fp& _s = entropy_R_ref(); std::copy(_s.begin(), _s.end(), sr); } - + //==================================================================================================================== void LatticePhase::getGibbs_RT(doublereal* grt) const { const array_fp& gibbsrt = gibbs_RT_ref(); - std::copy(gibbsrt.begin(), gibbsrt.end(), grt); + doublereal RT = _RT(); + doublereal delta_prt = (m_Pcurrent - m_Pref)/ RT; + for (int k = 0; k < m_kk; k++) { + grt[k] = gibbsrt[k] + delta_prt * m_speciesMolarVolume[k]; + } } + //==================================================================================================================== + void LatticePhase::getGibbs_ref(doublereal *g) const { + getGibbs_RT_ref(g); + for (int k = 0; k < m_kk; k++) { + g[k] *= GasConstant * temperature(); + } + } + //=================================================================================================================== void LatticePhase::getCp_R(doublereal* cpr) const { const array_fp& _cpr = cp_R_ref(); std::copy(_cpr.begin(), _cpr.end(), cpr); } - + //=================================================================================================================== void LatticePhase::getStandardVolumes(doublereal* vbar) const { - doublereal vv = 1.0/m_molar_density; - for (int k = 0; k < m_kk; k++) { - vbar[k] = vv; - } + copy(m_speciesMolarVolume.begin(), m_speciesMolarVolume.end(), vbar); } //======================================================================================================= // Returns the vector of nondimensional Enthalpies of the reference state at the current temperature @@ -310,6 +404,13 @@ namespace Cantera { _updateThermo(); return m_g0_RT; } + //==================================================================================================================== + void LatticePhase::getGibbs_RT_ref(doublereal *grt) const { + _updateThermo(); + for (int k = 0; k < m_kk; k++) { + grt[k] = m_g0_RT[k]; + } + } //======================================================================================================= // Returns a reference to the dimensionless reference state Entropy vector. /* @@ -330,7 +431,21 @@ namespace Cantera { _updateThermo(); return m_cp0_R; } - //======================================================================================================= + //==================================================================================================================== + // Initialize the ThermoPhase object after all species have been set up + /* + * @internal Initialize. + * + * This method performs any initialization required after all + * species have been added. For example, it is used to + * resize internal work arrays that must have an entry for + * each species. + * This method is called from ThermoPhase::initThermoXML(), + * which is called from importPhase(), + * just prior to returning from the function, importPhase(). + * + * @see importCTML.cpp + */ void LatticePhase::initThermo() { m_kk = nSpecies(); m_mm = nElements(); @@ -338,14 +453,62 @@ namespace Cantera { doublereal tmax = m_spthermo->maxTemp(); if (tmin > 0.0) m_tmin = tmin; if (tmax > 0.0) m_tmax = tmax; - m_p0 = refPressure(); + m_Pref = refPressure(); int leng = m_kk; m_h0_RT.resize(leng); m_g0_RT.resize(leng); m_cp0_R.resize(leng); m_s0_R.resize(leng); - setMolarDensity(m_molar_density); + m_speciesMolarVolume.resize(leng, 0.0); + + ThermoPhase::initThermo(); + } + //==================================================================================================================== + void LatticePhase::initThermoXML(XML_Node& phaseNode, std::string id) { + std::string subname = "LatticePhase::initThermoXML"; + /* + * Check on the thermo field. Must have: + * + */ + if (phaseNode.hasChild("thermo")) { + XML_Node& thNode = phaseNode.child("thermo"); + std::string mStringa = thNode.attrib("model"); + std::string mString = lowercase(mStringa); + if (mString != "lattice") { + throw CanteraError(subname.c_str(), + "Unknown thermo model: " + mStringa); + } + } else { + throw CanteraError(subname.c_str(), + "Unspecified thermo model"); + } + /* + * Now go get the molar volumes. use the default if not found + */ + XML_Node& speciesList = phaseNode.child("speciesArray"); + XML_Node* speciesDB = get_XML_NameID("speciesData", speciesList["datasrc"], &phaseNode.root()); + const std::vector &sss = speciesNames(); + + for (int k = 0; k < m_kk; k++) { + m_speciesMolarVolume[k] = m_site_density; + XML_Node* s = speciesDB->findByAttr("name", sss[k]); + if (!s) { + throw CanteraError(" LatticePhase::initThermoXML", "database problems"); + } + XML_Node *ss = s->findByName("standardState"); + if (ss) { + if (ss->findByName("molarVolume")) { + m_speciesMolarVolume[k] = getFloat(*ss, "molarVolume", "toSI"); + } + } + } + + /* + * Call the base initThermo, which handles setting the initial + * state. + */ + ThermoPhase::initThermoXML(phaseNode, id); } //===================================================================================================== // Update the species reference state thermodynamic functions @@ -355,10 +518,6 @@ namespace Cantera { */ void LatticePhase::_updateThermo() const { doublereal tnow = temperature(); - if (fabs(molarDensity() - m_molar_density)/m_molar_density > 0.0001) { - throw CanteraError("_updateThermo","molar density changed from " - +fp2str(m_molar_density)+" to "+fp2str(molarDensity())); - } if (m_tlast != tnow) { m_spthermo->update(tnow, &m_cp0_R[0], &m_h0_RT[0], &m_s0_R[0]); m_tlast = tnow; @@ -370,8 +529,8 @@ namespace Cantera { } //===================================================================================================== void LatticePhase::setParameters(int n, doublereal* const c) { - m_molar_density = c[0]; - setMolarDensity(m_molar_density); + m_site_density = c[0]; + setMolarDensity(m_site_density); } //===================================================================================================== void LatticePhase::getParameters(int &n, doublereal * const c) const { @@ -382,7 +541,7 @@ namespace Cantera { //===================================================================================================== void LatticePhase::setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model", "Lattice"); - m_molar_density = getFloat(eosdata, "site_density", "toSI"); + m_site_density = getFloat(eosdata, "site_density", "toSI"); m_vacancy = getChildValue(eosdata, "vacancy_species"); } //===================================================================================================== diff --git a/Cantera/src/thermo/LatticePhase.h b/Cantera/src/thermo/LatticePhase.h index b2622955a..eabde4c25 100644 --- a/Cantera/src/thermo/LatticePhase.h +++ b/Cantera/src/thermo/LatticePhase.h @@ -453,7 +453,7 @@ namespace Cantera { * independent value of the pressure. */ virtual doublereal pressure() const { - return m_press; + return m_Pcurrent; } //! Set the internally storred pressure (Pa) at constant @@ -465,7 +465,67 @@ namespace Cantera { * @param p Input Pressure (Pa) */ virtual void setPressure(doublereal p); - + + //! Calculate the density of the mixture using the partial + //! molar volumes and mole fractions as input + /*! + * The formula for this is + * + * \f[ + * \rho = \frac{\sum_k{X_k W_k}}{\sum_k{X_k V_k}} + * \f] + * + * where \f$X_k\f$ are the mole fractions, \f$W_k\f$ are + * the molecular weights, and \f$V_k\f$ are the pure species + * molar volumes. + * + * Note, the basis behind this formula is that in an ideal + * solution the partial molar volumes are equal to the pure + * species molar volumes. We have additionally specified + * in this class that the pure species molar volumes are + * independent of temperature and pressure. + * + * NOTE: This is a non-virtual function, which is not a + * member of the ThermoPhase base class. + */ + doublereal calcDensity(); + + //! Set the mole fractions + /*! + * @param x Input vector of mole fractions. + * Length: m_kk. + */ + virtual void setMoleFractions(const doublereal * const x); + + //! Set the mole fractions, but don't normalize them to one. + /*! + * @param x Input vector of mole fractions. + * Length: m_kk. + */ + virtual void setMoleFractions_NoNorm(const doublereal * const x); + + //! Set the mass fractions, and normalize them to one. + /*! + * @param y Input vector of mass fractions. + * Length: m_kk. + */ + virtual void setMassFractions(const doublereal * const y); + + //! Set the mass fractions, but don't normalize them to one + /*! + * @param y Input vector of mass fractions. + * Length: m_kk. + */ + virtual void setMassFractions_NoNorm(const doublereal * const y); + + //! Set the concentration, + /*! + * @param c Input vector of concentrations. + * Length: m_kk. + */ + virtual void setConcentrations(const doublereal * const c); + + //@} /// @name Activities, Standard States, and Activity Concentrations /** @@ -547,6 +607,71 @@ namespace Cantera { */ virtual void getChemPotentials(doublereal* mu) const; + + //@} + /// @name Partial Molar Properties of the Solution ----------------------------- + //@{ + + + /** + * Returns an array of partial molar enthalpies for the species + * in the mixture. + * Units (J/kmol) + * For this phase, the partial molar enthalpies are equal to the + * pure species enthalpies + * \f[ + * \bar h_k(T,P) = \hat h^{ref}_k(T) + (P - P_{ref}) \hat V^0_k + * \f] + * The reference-state pure-species enthalpies, \f$ \hat h^{ref}_k(T) \f$, + * at the reference pressure,\f$ P_{ref} \f$, + * are computed by the species thermodynamic + * property manager. They are polynomial functions of temperature. + * @see SpeciesThermo + * + * @param hbar Output vector containing partial molar enthalpies. + * Length: m_kk. + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + /** + * Returns an array of partial molar entropies of the species in the + * solution. Units: J/kmol/K. + * For this phase, the partial molar entropies are equal to the + * pure species entropies plus the ideal solution contribution. + * \f[ + * \bar s_k(T,P) = \hat s^0_k(T) - R log(X_k) + * \f] + * The reference-state pure-species entropies,\f$ \hat s^{ref}_k(T) \f$, + * at the reference pressure, \f$ P_{ref} \f$, are computed by the + * species thermodynamic + * property manager. They are polynomial functions of temperature. + * @see SpeciesThermo + * + * @param sbar Output vector containing partial molar entropies. + * Length: m_kk. + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + /** + * Returns an array of partial molar Heat Capacities at constant + * pressure of the species in the + * solution. Units: J/kmol/K. + * For this phase, the partial molar heat capacities are equal + * to the standard state heat capacities. + * + * @param cpbar Output vector of partial heat capacities. Length: m_kk. + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //! Get the array of chemical potentials at unit activity for the //! species standard states at the current T and P of the solution. /*! @@ -568,14 +693,7 @@ namespace Cantera { */ virtual void getPureGibbs(doublereal* gpure) const; - //! Return an array of partial molar volumes for the - //! species in the mixture. Units: m^3/kmol. - /*! - * @param vbar Output vector of speciar partial molar volumes. - * Length = m_kk. units are m^3/kmol. - */ - virtual void getPartialMolarVolumes(doublereal* vbar) const; - + //@} /// @name Properties of the Standard State of the Species in the Solution //@{ @@ -702,6 +820,25 @@ namespace Cantera { */ const array_fp& gibbs_RT_ref() const; + //! Returns the vector of nondimensional + //! Gibbs Free Energies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * @param grt Output vector containing the nondimensional reference state + * Gibbs Free energies. Length: m_kk. + */ + virtual void getGibbs_RT_ref(doublereal *grt) const; + + //! Returns the vector of the gibbs function of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * units = J/kmol + * + * @param g Output vector containing the reference state + * Gibbs Free energies. Length: m_kk. Units: J/kmol. + */ + virtual void getGibbs_ref(doublereal *g) const; + //! Returns a reference to the dimensionless reference state Entropy vector. /*! * This function is part of the layer that checks/recalculates the reference @@ -736,6 +873,33 @@ namespace Cantera { */ virtual void initThermo(); + + //! Import and initialize a ThermoPhase object using an XML tree. + /*! + * Here we read extra information about the XML description + * of a phase. Regular information about elements and species + * and their reference state thermodynamic information + * have already been read at this point. + * For example, we do not need to call this function for + * ideal gas equations of state. + * This function is called from importPhase() + * after the elements and the + * species are initialized with default ideal solution + * level data. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + virtual void initThermoXML(XML_Node& phaseNode, std::string id); + //! Set the equation of state parameters from the argument list /*! * @internal @@ -792,6 +956,7 @@ namespace Cantera { protected: + //! Number of elements int m_mm; @@ -810,7 +975,17 @@ namespace Cantera { doublereal m_tmax; //! Reference state pressure - doublereal m_p0; + doublereal m_Pref; + + + //! The current pressure + /*! + * Since the density isn't a function of pressure, but only of the + * mole fractions, we need to independently specify the pressure. + * The density variable which is inherited as part of the State class, + * m_dens, is always kept current whenever T, P, or X[] change. + */ + doublereal m_Pcurrent; //! Current value of the temperature (Kelvin) mutable doublereal m_tlast; @@ -827,8 +1002,6 @@ namespace Cantera { //! Temporary storage for the reference state entropies at the current temperature mutable array_fp m_s0_R; - //! Current value of the pressure (Pa) - doublereal m_press; //! String name for the species which represents a vacency //! in the lattice @@ -837,13 +1010,21 @@ namespace Cantera { */ std::string m_vacancy; - //! Molar density of the lattice solid + //! Vector of molar volumes for each species in the solution + /** + * Species molar volumes \f$ m^3 kmol^-1 \f$ + */ + array_fp m_speciesMolarVolume; + + //! Site Density of the lattice solid /*! - * Currently, this does not change as a function of T, P or composition + * Currently, this is imposed as a function of T, P or composition * * units are kmol m-3 */ - doublereal m_molar_density; + doublereal m_site_density; + + // doublereal m_molar_lattice_volume; private: diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index 7e1aac142..6b0d04385 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -23,8 +23,16 @@ #include "LatticePhase.h" #include "SpeciesThermo.h" #include "ThermoFactory.h" +#include "SpeciesThermoFactory.h" +#include "GeneralSpeciesThermo.h" #include +#ifndef MIN +# define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) +#endif +#ifndef MAX +# define MAX(x,y) (( (x) > (y) ) ? (x) : (y)) +#endif using namespace std; //====================================================================================================================== @@ -39,7 +47,9 @@ namespace Cantera { m_molar_density(0.0), m_nlattice(0), m_lattice(0), - m_x(0) + m_x(0), + theta_(0), + tmpV_(0) { } //==================================================================================================================== @@ -54,7 +64,9 @@ namespace Cantera { m_molar_density(0.0), m_nlattice(0), m_lattice(0), - m_x(0) + m_x(0), + theta_(0), + tmpV_(0) { *this = operator=(right); } @@ -74,12 +86,15 @@ namespace Cantera { m_nlattice = right.m_nlattice; deepStdVectorPointerCopy(right.m_lattice, m_lattice); m_x = right.m_x; + theta_ = right.theta_; + tmpV_ = right.tmpV_; } return *this; } //==================================================================================================================== // Destructor LatticeSolidPhase::~LatticeSolidPhase() { + // We own the sublattices. So we have to delete the sublattices for (int n = 0; n < m_nlattice; n++) { delete m_lattice[n]; m_lattice[n] = 0; @@ -98,59 +113,121 @@ namespace Cantera { LatticeSolidPhase *igp = new LatticeSolidPhase(*this); return (ThermoPhase *) igp; } + + //==================================================================================================================== + // Minimum temperature for which the thermodynamic data for the species + // or phase are valid. + /* + * If no argument is supplied, the + * value returned will be the lowest temperature at which the + * data for \e all species are valid. Otherwise, the value + * will be only for species \a k. This function is a wrapper + * that calls the species thermo minTemp function. + * + * @param k index of the species. Default is -1, which will return the max of the min value + * over all species. + */ + doublereal LatticeSolidPhase::minTemp(int k) const { + if (k >= 0) { + for (int n = 0; n < m_nlattice; n++) { + if (lkstart_[n+1] < k) { + double ml = (m_lattice[n])->minTemp(k-lkstart_[n]); + return ml; + } + } + } + doublereal mm = 1.0E300; + for (int n = 0; n < m_nlattice; n++) { + double ml = (m_lattice[n])->minTemp(-1); + mm = MIN(mm, ml); + } + return mm; + } + //==================================================================================================================== + // Maximum temperature for which the thermodynamic data for the species + // or phase are valid. + /* + * If no argument is supplied, the + * value returned will be the lowest temperature at which the + * data for \e all species are valid. Otherwise, the value + * will be only for species \a k. This function is a wrapper + * that calls the species thermo minTemp function. + * + * @param k index of the species. Default is -1, which will return the max of the min value + * over all species. + */ + doublereal LatticeSolidPhase::maxTemp(int k) const { + if (k >= 0) { + for (int n = 0; n < m_nlattice; n++) { + if (lkstart_[n+1] < k) { + double ml = (m_lattice[n])->maxTemp(k - lkstart_[n]); + return ml; + } + } + } + doublereal mm = -1.0E300; + for (int n = 0; n < m_nlattice; n++) { + double ml = (m_lattice[n])->maxTemp(-1); + mm = MAX(mm, ml); + } + return mm; + } + //==================================================================================================================== + /* + * Returns the reference pressure in Pa. This function is a wrapper + * that calls the species thermo refPressure function. + */ + doublereal LatticeSolidPhase::refPressure() const { + return m_lattice[0]->refPressure(); + } //==================================================================================================================== doublereal LatticeSolidPhase:: enthalpy_mole() const { _updateThermo(); - doublereal ndens, sum = 0.0; + doublereal sum = 0.0; int n; for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->enthalpy_mole(); + sum += theta_[n] * m_lattice[n]->enthalpy_mole(); } - return sum/molarDensity(); + return sum; } //==================================================================================================================== doublereal LatticeSolidPhase::intEnergy_mole() const { _updateThermo(); - doublereal ndens, sum = 0.0; + doublereal sum = 0.0; int n; for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->intEnergy_mole(); + sum += theta_[n] * m_lattice[n]->intEnergy_mole(); } - return sum/molarDensity(); + return sum; } //==================================================================================================================== doublereal LatticeSolidPhase::entropy_mole() const { _updateThermo(); - doublereal ndens, sum = 0.0; + doublereal sum = 0.0; int n; for (n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->entropy_mole(); + sum += theta_[n] * m_lattice[n]->entropy_mole(); } - return sum/molarDensity(); + return sum; } //==================================================================================================================== doublereal LatticeSolidPhase::gibbs_mole() const { _updateThermo(); - doublereal ndens, sum = 0.0; + doublereal sum = 0.0; for (int n = 0; n < m_nlattice; n++) { - ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->gibbs_mole(); + sum += theta_[n] * m_lattice[n]->gibbs_mole(); } - return sum/molarDensity(); + return sum; } //==================================================================================================================== doublereal LatticeSolidPhase::cp_mole() const { _updateThermo(); doublereal sum = 0.0; for (int n = 0; n < m_nlattice; n++) { - doublereal ndens = m_lattice[n]->molarDensity(); - sum += ndens * m_lattice[n]->cp_mole(); + sum += theta_[n] * m_lattice[n]->cp_mole(); } - return sum/molarDensity(); + return sum; } //==================================================================================================================== void LatticeSolidPhase::getActivityConcentrations(doublereal* c) const { @@ -176,12 +253,49 @@ namespace Cantera { return 0.0; } + //==================================================================================================================== + // Set the pressure at constant temperature. Units: Pa. + /* + * + * @param p Pressure (units - Pa) + */ + void LatticeSolidPhase::setPressure(doublereal p) { + m_press = p; + for (int n = 0; n < m_nlattice; n++) { + m_lattice[n]->setPressure(m_press); + } + calcDensity(); + } + //==================================================================================================================== + // Calculate the density of the solid mixture + /* + * The formula for this is + * + * \f[ + * \rho = \sum_n{ \rho_n \theta_n } + * \f] + * + * where \f$ \rho_n \f$ is the density of the nth sublattice + * + * Note this is a nonvirtual function. + */ + doublereal LatticeSolidPhase::calcDensity() { + double sum = 0.0; + for (int n = 0; n < m_nlattice; n++) { + sum += theta_[n] * m_lattice[n]->density(); + } + State::setDensity(sum); + return sum; + } //==================================================================================================================== // Set the mole fractions to the specified values, and then // normalize them so that they sum to 1.0 for each of the subphases /* + * On input, the mole fraction vector is assumed to sum to one for each of the sublattices. The sublattices + * are updated with this mole fraction vector. The mole fractions are also storred within this object, after + * they are normalized to one by dividing by the number of sublattices. * - * @param x Input vector of mole fractions. There is no restriction + * @param x Input vector of mole fractions. There is no restriction * on the sum of the mole fraction vector. Internally, * this object will pass portions of this vector to the sublattices which assume that the portions * individually sum to one. @@ -189,19 +303,16 @@ namespace Cantera { */ void LatticeSolidPhase::setMoleFractions(const doublereal* const x) { int nsp, strt = 0; - doublereal sum = 0.0; for (int n = 0; n < m_nlattice; n++) { nsp = m_lattice[n]->nSpecies(); - m_lattice[n]->setMoleFractions(x+strt); - for (int k = 0; k < nsp; k++) { - sum += x[strt + k]; - } + m_lattice[n]->setMoleFractions(x + strt); strt += nsp; } for (int k = 0; k < strt; k++) { - m_x[k] = x[k] / sum; + m_x[k] = x[k] / m_nlattice; } State::setMoleFractions(DATA_PTR(m_x)); + calcDensity(); } //==================================================================================================================== // Get the species mole fraction vector. @@ -213,6 +324,7 @@ namespace Cantera { */ void LatticeSolidPhase::getMoleFractions(doublereal* const x) const { int nsp, strt = 0; + // the ifdef block should be the way we calculate this.!!!!! State::getMoleFractions(x); doublereal sum; for (int n = 0; n < m_nlattice; n++) { @@ -241,28 +353,103 @@ namespace Cantera { } } //==================================================================================================================== + // Get the species chemical potentials. Units: J/kmol. + /* + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * This returns the underlying lattice chemical potentials + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ void LatticeSolidPhase::getChemPotentials(doublereal* mu) const { _updateThermo(); int strt = 0; for (int n = 0; n < m_nlattice; n++) { - doublereal dratio = m_lattice[n]->molarDensity()/molarDensity(); + int nlsp = m_lattice[n]->nSpecies(); m_lattice[n]->getChemPotentials(mu+strt); - scale(mu + strt, mu + strt + m_lattice[n]->nSpecies(), mu + strt, dratio); - strt += m_lattice[n]->nSpecies(); + strt += nlsp; } } //==================================================================================================================== + void LatticeSolidPhase::getPartialMolarEnthalpies(doublereal* hbar) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + int nlsp = m_lattice[n]->nSpecies(); + m_lattice[n]->getPartialMolarEnthalpies(hbar + strt); + strt += nlsp; + } + } + //==================================================================================================================== + void LatticeSolidPhase::getPartialMolarEntropies(doublereal* sbar) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + int nlsp = m_lattice[n]->nSpecies(); + m_lattice[n]->getPartialMolarEntropies(sbar + strt); + strt += nlsp; + } + } + //==================================================================================================================== + void LatticeSolidPhase::getPartialMolarCp(doublereal* cpbar) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + int nlsp = m_lattice[n]->nSpecies(); + m_lattice[n]->getPartialMolarCp(cpbar + strt); + strt += nlsp; + } + } + //==================================================================================================================== + void LatticeSolidPhase::getPartialMolarVolumes(doublereal* vbar) const { + _updateThermo(); + int strt = 0; + for (int n = 0; n < m_nlattice; n++) { + int nlsp = m_lattice[n]->nSpecies(); + m_lattice[n]->getPartialMolarVolumes(vbar + strt); + strt += nlsp; + } + } + //==================================================================================================================== + // Get the array of standard state chemical potentials at unit activity for the species + // at their standard states at the current T and P of the solution. + /* + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current + * temperature and pressure of the solution. + * + * This returns the underlying lattice standard chemical potentials, as the units are kmol-1 of + * the sublattice species. + * + * @param mu0 Output vector of chemical potentials. + * Length: m_kk. Units: J/kmol + */ void LatticeSolidPhase::getStandardChemPotentials(doublereal* mu0) const { _updateThermo(); int strt = 0; for (int n = 0; n < m_nlattice; n++) { - doublereal dratio = m_lattice[n]->molarDensity()/molarDensity(); m_lattice[n]->getStandardChemPotentials(mu0+strt); - scale(mu0 + strt, mu0 + strt + m_lattice[n]->nSpecies(), mu0 + strt, dratio); strt += m_lattice[n]->nSpecies(); } } //==================================================================================================================== + void LatticeSolidPhase::getGibbs_RT_ref(doublereal *grt) const { + _updateThermo(); + for (int n = 0; n < m_nlattice; n++) { + m_lattice[n]->getGibbs_RT_ref(grt + lkstart_[n]); + } + } + //==================================================================================================================== + void LatticeSolidPhase::getGibbs_ref(doublereal *g) const { + getGibbs_RT_ref(g); + for (int k = 0; k < m_kk; k++) { + g[k] *= GasConstant * temperature(); + } + } + //==================================================================================================================== // Add in species from Slave phases /* * This hook is used for cSS_CONVENTION_SLAVE phases @@ -272,84 +459,127 @@ namespace Cantera { void LatticeSolidPhase::installSlavePhases(Cantera::XML_Node* phaseNode) { int m, k; + int kk = 0; + int kstart = 0; + SpeciesThermoFactory* spFactory = SpeciesThermoFactory::factory(); + SpeciesThermo * spthermo_ptr = new GeneralSpeciesThermo(); + setSpeciesThermo(spthermo_ptr); + m_speciesData.clear(); + + XML_Node& eosdata = phaseNode->child("thermo"); + XML_Node& la = eosdata.child("LatticeArray"); + std::vector lattices; + la.getChildren("phase",lattices); for (int n = 0; n < m_nlattice; n++) { LatticePhase *lp = m_lattice[n]; + XML_Node* phaseNode_ptr = lattices[n]; int nsp = lp->nSpecies(); vector constArr(lp->nElements()); + const vector_fp& aws = lp->atomicWeights(); + for (int es = 0; es < lp->nElements(); es++) { + string esName = lp->elementName(es); + double wt = aws[es]; + int an = lp->atomicNumber(es); + int e298 = lp->entropyElement298(es); + int et = lp->elementType(es); + addUniqueElementAfterFreeze(esName, wt, an, e298, et); + } + const std::vector & spNode = lp->speciesData(); + kstart = kk; + + for (k = 0; k < nsp; k++) { std::string sname = lp->speciesName(k); std::map comp; lp->getAtoms(k, DATA_PTR(constArr)); + int nel = nElements(); + vector_fp ecomp(nel, 0.0); for (m = 0; m < lp->nElements(); m++) { if (constArr[m] != 0.0) { - std::string ename = lp->elementName(m); - comp[ename] = constArr[m]; - } - } - int nel = nElements(); - vector_fp ecomp(nel, 0.0); - for (m = 0; m < nel; m++) { - double anum = comp[elementName(m)]; - if (anum != 0.0) { - ecomp[m] = anum; + std::string oldEname = lp->elementName(m); + int newIndex = elementIndex(oldEname); + if (newIndex < 0) { + throw CanteraError("LatticeSolidPhase::installSlavePhases", "confused"); + } + ecomp[newIndex] = constArr[m]; } } double chrg = lp->charge(k); double sz = lp->size(k); addUniqueSpecies(sname, &ecomp[0], chrg, sz); + spFactory->installThermoForSpecies(kk, *(spNode[k]), this, *m_spthermo, phaseNode_ptr); + + m_speciesData.push_back(new XML_Node(*(spNode[k]))); + kk++; + } + /* + * Add in the lattice stoichiometry constraint + */ + if (n > 0) { + string econ = "LC_"; + econ += int2str(n); + econ += "_" + id(); + int m = addUniqueElementAfterFreeze(econ, 0.0, 0, 0.0, CT_ELEM_TYPE_LATTICERATIO); + m_mm = nElements(); + LatticePhase *lp0 = m_lattice[0]; + int nsp0 = lp0->nSpecies(); + for (k = 0; k < nsp0; k++) { + m_speciesComp[k * m_mm + m] = -theta_[0]; + } + for (k = 0; k < nsp; k++) { + int ks = kstart + k; + m_speciesComp[ks * m_mm + m] = theta_[n]; + } } } } + //==================================================================================================================== + // Initialize the ThermoPhase object after all species have been set up + /* + * @internal Initialize. + * + * This method is provided to allow subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called from ThermoPhase::initThermoXML(), + * which is called from importPhase(), just prior to returning from function importPhase(). + * + * @see importCTML.cpp + */ void LatticeSolidPhase::initThermo() { m_kk = nSpecies(); m_mm = nElements(); - m_x.resize(m_kk); + initLengths(); int nsp, k, loc = 0; - doublereal ndens; - m_molar_density = 0.0; for (int n = 0; n < m_nlattice; n++) { nsp = m_lattice[n]->nSpecies(); - ndens = m_lattice[n]->molarDensity(); + lkstart_[n] = loc; + nspLattice_[n] = nsp; for (k = 0; k < nsp; k++) { - m_x[loc] = ndens * m_lattice[n]->moleFraction(k); + m_x[loc] =m_lattice[n]->moleFraction(k) / (double) m_nlattice; loc++; } - m_molar_density += ndens; + lkstart_[n+1] = loc; } setMoleFractions(DATA_PTR(m_x)); - - // const vector& spnames = speciesNames(); - // int n, k, kl, namesize; - // int nl = m_sitedens.size(); - // string s; - // m_lattice.resize(m_kk,-1); - // vector_fp conc(m_kk, 0.0); - - // compositionMap xx; - // for (n = 0; n < nl; n++) { - // for (k = 0; k < m_kk; k++) { - // xx[speciesName(k)] = -1.0; - // } - // parseCompString(m_sp[n], xx); - // for (k = 0; k < m_kk; k++) { - // if (xx[speciesName(k)] != -1.0) { - // conc[k] = m_sitedens[n]*xx[speciesName(k)]; - // m_lattice[k] = n; - // } - // } - - // } - // for (k = 0; k < m_kk; k++) { - // if (m_lattice[k] == -1) { - // throw CanteraError("LatticeSolidPhase::" - // "setParametersFromXML","Species "+speciesName(k) - // +" not a member of any lattice."); - // } - // } - // setMoleFractions(DATA_PTR(conc)); + ThermoPhase::initThermo(); + } + //==================================================================================================================== + // Initialize vectors that depend on the number of species and sublattices + /* + * + */ + void LatticeSolidPhase::initLengths() { + theta_.resize(m_nlattice,0); + nspLattice_.resize(m_nlattice); + lkstart_.resize(m_nlattice+1); + m_x.resize(m_kk, 0.0); + tmpV_.resize(m_kk, 0.0); } - //==================================================================================================================== void LatticeSolidPhase::_updateThermo() const { doublereal tnow = temperature(); @@ -386,6 +616,14 @@ namespace Cantera { setMoleFractions(DATA_PTR(m_x)); } //==================================================================================================================== + + + //==================================================================================================================== + // Set the parameters from the XML file + /*! + * Currently, this is the spot that we read in all of the sublattice phases. + * The SetParametersFromXML() call is carried out at + */ void LatticeSolidPhase::setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model","LatticeSolid"); XML_Node& la = eosdata.child("LatticeArray"); @@ -398,9 +636,78 @@ namespace Cantera { XML_Node& i = *lattices[n]; m_lattice.push_back((LatticePhase*)newPhase(i)); } + std::vector pnam; + std::vector pval; + XML_Node& ls = eosdata.child("LatticeStoichiometry"); + int np = getPairs(ls, pnam, pval); + theta_.resize(nl); + for (int i = 0; i < np; i++) { + double val = fpValueCheck(pval[i]); + bool found = false; + for (int j = 0; j < nl; j++) { + ThermoPhase &tp = *(m_lattice[j]); + string idj = tp.id(); + if (idj == pnam[i]) { + theta_[j] = val; + found = true; + break; + } + } + if (!found) { + throw CanteraError("", "not found"); + } + } + + } + //==================================================================================================================== + // Return a changeable reference to the calculation manager + // for species reference-state thermodynamic properties + /* + * + * @param k Speices id. The default is -1, meaning return the default + * + * @internal + */ + SpeciesThermo& LatticeSolidPhase::speciesThermo(int k) { + return *m_spthermo; + /* + int kk; + if (k >= 0) { + for (int n = 0; n < m_nlattice; n++) { + if (lkstart_[n+1] < k) { + kk = k - lkstart_[n]; + return m_lattice[n]->speciesThermo(kk); + } + } + } + return m_lattice[0]->speciesThermo(-1); + */ } //==================================================================================================================== +#ifdef H298MODIFY_CAPABILITY + + //! Modify the value of the 298 K Heat of Formation of one species in the phase (J kmol-1) + /*! + * The 298K heat of formation is defined as the enthalpy change to create the standard state + * of the species from its constituent elements in their standard states at 298 K and 1 bar. + * + * @param k Species k + * @param Hf298New Specify the new value of the Heat of Formation at 298K and 1 bar + */ + void LatticeSolidPhase::modifyOneHf298SS(const int k, const doublereal Hf298New) { + for (int n = 0; n < m_nlattice; n++) { + if (lkstart_[n+1] < k) { + int kk = k-lkstart_[n]; + SpeciesThermo& l_spthermo = m_lattice[n]->speciesThermo(); + l_spthermo.modifyOneHf298(kk, Hf298New); + } + } + m_tlast += 0.0001234; + _updateThermo(); + } +#endif + //==================================================================================================================== doublereal LatticeSolidPhase::err(std::string msg) const { throw CanteraError("LatticeSolidPhase","Unimplemented " + msg); diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index f7acfd2e0..961c42316 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -34,17 +34,49 @@ namespace Cantera { - //! A phase that is comprised of an additive combination of other lattice phases + //! A phase that is comprised of a fixed additive combination of other lattice phases /*! - * This is the main way Cantera describes semiconductors and other solid phases. - * This %ThermoPhase object calculates its properties as a sum over other LatticePhase objects. Each of the %LatticePhase - * objects is a ThermoPhase object by itself. + * This is the main way %Cantera describes semiconductors and other solid phases. + * This %ThermoPhase object calculates its properties as a sum over other %LatticePhase objects. Each of the %LatticePhase + * objects is a %ThermoPhase object by itself. + * + * The results from this LatticeSolidPhase model reduces to the LatticePhase model when there is one + * lattice phase and the molar densities of the sublattice and the molar density within the LatticeSolidPhase + * have the same values. * + * + * The mole fraction vector is redefined witin the the LatticeSolidPhase object. Each of the mole + * fractions sum to one on each of the sublattices. The routine getMoleFraction() and setMoleFraction() + * have been redefined to use this convention. + * + *
+ *

Specification of Species Standard %State Properties

+ *
+ * + * The standard state properties are calculated in the normal way for each of the sublattices. The normal way + * here means that a thermodynamic polynomial in temperature is developed. Also, a constant volume approximation + * for the pressure dependence is assumed. All of these properties are on a Joules per kmol of sublattice + * constituent basis. + * + *
+ *

Specification of Solution Thermodynamic Properties

+ *
+ * The sum over the %LatticePhase objects is carried out by weighting each %LatticePhase object - * value with the molarDensity of the LatticePhase. Then the resulting quantity is divided by + * value with the molar density (kmol m-3) of its %LatticePhase. Then the resulting quantity is divided by * the molar density of the total compound. The LatticeSolidPhase object therefore only contains a - * listing of the number of Lattice Phases - * that comprises the solid and it contains a value for the molar density of the entire mixture. + * listing of the number of %LatticePhase object + * that comprises the solid, and it contains a value for the molar density of the entire mixture. + * This is the same thing as saying that + * + * \f[ + * L_i = L^{solid} \theta_i + * \f] + * + * \f$ L_i \f$ is the molar volume of the ith lattice. \f$ L^{solid} \f$ is the molar volume of the entire + * solid. \f$ \theta_i \f$ is a fixed weighting factor for the ith lattice representing the lattice + * stoichiometric coefficient. For this object the \f$ \theta_i \f$ values are fixed. + * * * Let's take FeS2 as an example, which may be thought of as a combination of two lattices: Fe and S lattice. * The Fe sublattice has a molar density of 1 gmol cm-3. The S sublattice has a molar density of 2 gmol cm-3. @@ -53,14 +85,34 @@ namespace Cantera { * associated with the sublattices. The Fe sublattice will have a weight of 1.0 associated with it. The * S sublattice will have a weight of 2.0 associated with it. * - * Currently, the molar density is set to a constant. + * + *
+ *

Specification of Solution Density Properties

+ *
* - * The results from this LatticeSolidPhase model reduces to the LatticePhase model when there is one - * lattice phase and the molar densities of the sublattice and the molar density within the LatticeSolidPhase - * have the same values. + * Currently, molar density is not a constant within the object, even though the species molar volumes are a + * constant. The basic idea is that a swelling of one of the sublattices will result in a swelling of + * of all of the lattices. Therefore, the molar volumes of the individual lattices are not independent of + * one another. * - * The mole fraction vector has been redefined within the LatticeSolidPhase object. The mole fractions sum - * to one within each of the individual lattice phases. The routine getMoleFraction() and setMoleFraction() + * The molar volume of the Lattice solid is calculated from the following formula + * + * \f[ + * V = \sum_i{ \theta_i V_i^{lattice}} + * \f] + * + * where \f$ V_i^{lattice} \f$ is the molar volume of the ith sublattice. This is calculated from the + * following standard formula. + * + * + * \f[ + * V_i = \sum_k{ \X_k V_k} + * \f] + * + * where k is a species in the ith sublattice. + * + * The mole fraction vector is redefined witin the the LatticeSolidPhase object. Each of the mole + * fractions sum to one on each of the sublattices. The routine getMoleFraction() and setMoleFraction() * have been redefined to use this convention. * * (This object is still under construction) @@ -104,6 +156,39 @@ namespace Cantera { */ virtual int eosType() const { return cLatticeSolid; } + //! Minimum temperature for which the thermodynamic data for the species + //! or phase are valid. + /*! + * If no argument is supplied, the + * value returned will be the lowest temperature at which the + * data for \e all species are valid. Otherwise, the value + * will be only for species \a k. This function is a wrapper + * that calls the species thermo minTemp function. + * + * @param k index of the species. Default is -1, which will return the max of the min value + * over all species. + */ + virtual doublereal minTemp(int k = -1) const; + + //! Maximum temperature for which the thermodynamic data for the species + //! are valid. + /*! + * If no argument is supplied, the + * value returned will be the highest temperature at which the + * data for \e all species are valid. Otherwise, the value + * will be only for species \a k. This function is a wrapper + * that calls the species thermo maxTemp function. + * + * @param k index of the species. Default is -1, which will return the min of the max value + * over all species. + */ + virtual doublereal maxTemp(int k = -1) const; + + + //! Returns the reference pressure in Pa. This function is a wrapper + //! that calls the species thermo refPressure function. + virtual doublereal refPressure() const ; + //! This method returns the convention used in specification //! of the standard state, of which there are currently two, //! temperature based, and variable pressure based. @@ -116,12 +201,11 @@ namespace Cantera { //! Return the Molar Enthalpy. Units: J/kmol. /*! - * The molar enthalpy is determined by the following formula, where \f$ C_n \f$ is the - * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density - * of the solid compound. + * The molar enthalpy is determined by the following formula, where \f$ \theta_n \f$ is the + * lattice stoichiometric coefficient of the nth lattice * * \f[ - * \tilde h(T,P) = \frac{\sum_n C_n \tilde h_n(T,P) }{C_T}, + * \tilde h(T,P) = {\sum_n \theta_n \tilde h_n(T,P) } * \f] * * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. @@ -133,12 +217,11 @@ namespace Cantera { //! Return the Molar Internal Energy. Units: J/kmol. /*! - * The molar internal energy is determined by the following formula, where \f$ C_n \f$ is the - * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density - * of the solid compound. + * The molar enthalpy is determined by the following formula, where \f$ \theta_n \f$ is the + * lattice stoichiometric coefficient of the nth lattice * * \f[ - * \tilde u(T,P) = \frac{\sum_n C_n \tilde u_n(T,P) }{C_T}, + * \tilde u(T,P) = {\sum_n \theta_n \tilde u_n(T,P) } * \f] * * \f$ \tilde u_n(T,P) \f$ is the internal energy of the nth lattice. @@ -148,13 +231,12 @@ namespace Cantera { virtual doublereal intEnergy_mole() const; //! Return the Molar Entropy. Units: J/kmol/K. - /*! - * The molar entropy is determined by the following formula, where \f$ C_n \f$ is the - * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density - * of the solid compound. + /*! + * The molar enthalpy is determined by the following formula, where \f$ \theta_n \f$ is the + * lattice stoichiometric coefficient of the nth lattice * * \f[ - * \tilde s(T,P) = \frac{\sum_n C_n \tilde s_n(T,P) }{C_T}, + * \tilde s(T,P) = \sum_n \theta_n \tilde s_n(T,P) * \f] * * \f$ \tilde s_n(T,P) \f$ is the molar entropy of the nth lattice. @@ -163,14 +245,13 @@ namespace Cantera { */ virtual doublereal entropy_mole() const; - //! Return the Molar Enthalpy. Units: J/kmol. + //! Return the Molar Gibbs energy. Units: J/kmol. /*! - * The molar enthalpy is determined by the following formula, where \f$ C_n \f$ is the - * lattice molar density of the nth lattice, and \f$ C_T \f$ is the molar density - * of the solid compound. + * The molar gibbs free energy is determined by the following formula, where \f$ \theta_n \f$ is the + * lattice stoichiometric coefficient of the nth lattice * * \f[ - * \tilde h(T,P) = \frac{\sum_n C_n \tilde h_n(T,P) }{C_T}, + * \tilde h(T,P) = {\sum_n \theta_n \tilde h_n(T,P) } * \f] * * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. @@ -226,16 +307,30 @@ namespace Cantera { * * @param p Pressure (units - Pa) */ - virtual void setPressure(doublereal p) { - m_press = p; - setMolarDensity(m_molar_density); - } + virtual void setPressure(doublereal p); + + //! Calculate the density of the solid mixture + /*! + * The formula for this is + * + * \f[ + * \rho = \sum_n{ \rho_n \theta_n } + * \f] + * + * where \f$ \rho_n \f$ is the density of the nth sublattice + * + * Note this is a nonvirtual function. + */ + doublereal calcDensity(); //! Set the mole fractions to the specified values, and then //! normalize them so that they sum to 1.0 for each of the subphases - /*! + /* + * On input, the mole fraction vector is assumed to sum to one for each of the sublattices. The sublattices + * are updated with this mole fraction vector. The mole fractions are also storred within this object, after + * they are normalized to one by dividing by the number of sublattices. * - * @param x Input vector of mole fractions. There is no restriction + * @param x Input vector of mole fractions. There is no restriction * on the sum of the mole fraction vector. Internally, * this object will pass portions of this vector to the sublattices which assume that the portions * individually sum to one. @@ -358,20 +453,88 @@ namespace Cantera { * species in solution at the current temperature, pressure * and mole fraction of the solution. * + * This returns the underlying lattice chemical potentials, as the units are kmol-1 of + * the sublattice species. + * * @param mu Output vector of species chemical * potentials. Length: m_kk. Units: J/kmol */ virtual void getChemPotentials(doublereal* mu) const; + + //! Returns an array of partial molar enthalpies for the species in the mixture. + /*! + * Units (J/kmol) + * For this phase, the partial molar enthalpies are equal to the + * pure species enthalpies + * \f[ + * \bar h_k(T,P) = \hat h^{ref}_k(T) + (P - P_{ref}) \hat V^0_k + * \f] + * The reference-state pure-species enthalpies, \f$ \hat h^{ref}_k(T) \f$, + * at the reference pressure,\f$ P_{ref} \f$, + * are computed by the species thermodynamic + * property manager. They are polynomial functions of temperature. + * @see SpeciesThermo + * + * @param hbar Output vector containing partial molar enthalpies. + * Length: m_kk. + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + /** + * Returns an array of partial molar entropies of the species in the + * solution. Units: J/kmol/K. + * For this phase, the partial molar entropies are equal to the + * pure species entropies plus the ideal solution contribution. + * \f[ + * \bar s_k(T,P) = \hat s^0_k(T) - R log(X_k) + * \f] + * The reference-state pure-species entropies,\f$ \hat s^{ref}_k(T) \f$, + * at the reference pressure, \f$ P_{ref} \f$, are computed by the + * species thermodynamic + * property manager. They are polynomial functions of temperature. + * @see SpeciesThermo + * + * @param sbar Output vector containing partial molar entropies. + * Length: m_kk. + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + /** + * Returns an array of partial molar Heat Capacities at constant + * pressure of the species in the + * solution. Units: J/kmol/K. + * For this phase, the partial molar heat capacities are equal + * to the standard state heat capacities. + * + * @param cpbar Output vector of partial heat capacities. Length: m_kk. + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + /** + * returns an array of partial molar volumes of the species + * in the solution. Units: m^3 kmol-1. + * + * For this solution, thepartial molar volumes are equal to the + * constant species molar volumes. + * + * @param vbar Output vector of partial molar volumes. Length: m_kk. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + //! Get the array of standard state chemical potentials at unit activity for the species //! at their standard states at the current T and P of the solution. /*! * These are the standard state chemical potentials \f$ \mu^0_k(T,P) * \f$. The values are evaluated at the current - * temperature and pressure of the solution + * temperature and pressure of the solution. + * + * + * This returns the underlying lattice standard chemical potentials, as the units are kmol-1 of + * the sublattice species. * * @param mu0 Output vector of chemical potentials. - * Length: m_kk. + * Length: m_kk. Units: J/kmol */ virtual void getStandardChemPotentials(doublereal* mu0) const; @@ -400,6 +563,36 @@ namespace Cantera { * @param k index of the species (defaults to zero) */ virtual doublereal logStandardConc(int k=0) const; + //@} + /// @name Thermodynamic Values for the Species Reference States -------------------- + //@{ + + /** + * Returns the vector of nondimensional + * enthalpies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * + * This function fills in its one entry in hrt[] by calling + * the underlying species thermo function for the + * dimensionless gibbs free energy, calculated from the + * dimensionless enthalpy and entropy. + */ + virtual void getGibbs_RT_ref(doublereal *grt) const; + + + /** + * Returns the vector of the + * gibbs function of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * units = J/kmol + * + * This function fills in its one entry in g[] by calling + * the underlying species thermo functions for the + * gibbs free energy, calculated from enthalpy and the + * entropy, and the multiplying by RT. + */ + virtual void getGibbs_ref(doublereal *g) const; + //! Initialize the ThermoPhase object after all species have been set up /*! @@ -420,6 +613,9 @@ namespace Cantera { */ virtual void initThermo(); + //! Initialize vectors that depend on the number of species and sublattices + void initLengths(); + //! Add in species from Slave phases /*! * This hook is used for cSS_CONVENTION_SLAVE phases @@ -454,6 +650,16 @@ namespace Cantera { */ void setLatticeMoleFractionsByName(int n, std::string x); + //! Return a changeable reference to the calculation manager + //! for species reference-state thermodynamic properties + /*! + * This routine returns the calculation manager for the sublattice + * + * @param k Speices id. The default is -1, meaning return the default + * + * @internal + */ + virtual SpeciesThermo& speciesThermo(int k = -1); #ifdef H298MODIFY_CAPABILITY @@ -465,10 +671,7 @@ namespace Cantera { * @param k Species k * @param Hf298New Specify the new value of the Heat of Formation at 298K and 1 bar */ - virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) { - m_spthermo->modifyOneHf298(k, Hf298New); - m_tlast += 0.0001234; - } + virtual void modifyOneHf298SS(const int k, const doublereal Hf298New); #endif private: @@ -507,6 +710,16 @@ namespace Cantera { */ mutable vector_fp m_x; + //! Lattice stoichiometric coefficients + std::vector theta_; + + //! Temporary vector + mutable vector_fp tmpV_; + + std::vector nspLattice_; + + std::vector lkstart_; + private: //! Update the reference thermodynamic functions diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index ea91a0cd7..d6d2dc451 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -525,7 +525,9 @@ namespace Cantera { /*************************************************************** * Add the elements. ***************************************************************/ - th->addElementsFromXML(phase); + if (ssConvention != cSS_CONVENTION_SLAVE) { + th->addElementsFromXML(phase); + } /*************************************************************** * Add the species. @@ -538,11 +540,13 @@ namespace Cantera { vector sparrays; phase.getChildren("speciesArray", sparrays); int jsp, nspa = static_cast(sparrays.size()); - if (nspa == 0) { - throw CanteraError("importPhase", - "phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n" + if (ssConvention != cSS_CONVENTION_SLAVE) { + if (nspa == 0) { + throw CanteraError("importPhase", + "phase, " + th->id() + ", has zero \"speciesArray\" XML nodes.\n" + " There must be at least one speciesArray nodes " "with one or more species"); + } } vector dbases; vector_int sprule(nspa,0); @@ -608,7 +612,7 @@ namespace Cantera { // If the phase has a species thermo manager already installed, // delete it since we are adding new species. - delete &th->speciesThermo(); + //delete &th->speciesThermo(); // Decide whether the the phase has a variable pressure ss or not SpeciesThermo* spth = 0; diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 42ec63f7d..0d8a11618 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -822,9 +822,47 @@ namespace Cantera { if (i == 4) uA[4] = 0.0; if (i == 5) uA[5] = 0.0; } + } + //================================================================================================================= + // Install a species thermodynamic property manager. + /* + * The species thermodynamic property manager + * computes properties of the pure species for use in + * constructing solution properties. It is meant for internal + * use, and some classes derived from ThermoPhase may not use + * any species thermodynamic property manager. This method is + * called by function importPhase() in importCTML.cpp. + * + * @param spthermo input pointer to the species thermodynamic property + * manager. + * + * @internal + */ + void ThermoPhase::setSpeciesThermo(SpeciesThermo* spthermo) { + if (m_spthermo) { + if (m_spthermo != spthermo) { + delete m_spthermo; + } + } + m_spthermo = spthermo; + } + //================================================================================================================= + // Return a changeable reference to the calculation manager + // for species reference-state thermodynamic properties + /* + * + * @param k Speices id. The default is -1, meaning return the default + * + * @internal + */ + SpeciesThermo& ThermoPhase::speciesThermo(int k) { + if (!m_spthermo) { + throw CanteraError("ThermoPhase::speciesThermo()", + "species reference state thermo manager was not set"); + } + return *m_spthermo; } //================================================================================================================= - /* * initThermoFile(): * diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 8e35524d0..a27d999b8 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -758,7 +758,7 @@ namespace Cantera { * Returns the reference pressure in Pa. This function is a wrapper * that calls the species thermo refPressure function. */ - doublereal refPressure() const { + virtual doublereal refPressure() const { return m_spthermo->refPressure(); } @@ -775,7 +775,7 @@ namespace Cantera { * @param k index of the species. Default is -1, which will return the max of the min value * over all species. */ - doublereal minTemp(int k = -1) const { + virtual doublereal minTemp(int k = -1) const { return m_spthermo->minTemp(k); } @@ -844,7 +844,7 @@ namespace Cantera { * @param k index of the species. Default is -1, which will return the min of the max value * over all species. */ - doublereal maxTemp(int k = -1) const { + virtual doublereal maxTemp(int k = -1) const { return m_spthermo->maxTemp(k); } @@ -1883,19 +1883,17 @@ namespace Cantera { * * @internal */ - void setSpeciesThermo(SpeciesThermo* spthermo) - { m_spthermo = spthermo; } + void setSpeciesThermo(SpeciesThermo* spthermo); //! Return a changeable reference to the calculation manager //! for species reference-state thermodynamic properties /*! * - * @todo This method will fail if no species thermo - * manager has been installed. + * @param k Speices id. The default is -1, meaning return the default * * @internal */ - SpeciesThermo& speciesThermo() { return *m_spthermo; } + virtual SpeciesThermo& speciesThermo(int k = -1); /** * @internal diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index 02ab93eb9..b104d12dc 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -47,7 +47,7 @@ namespace Cantera { const int cMetalSHEelectrons = 9; // SHE electrode electrons const int cLatticeSolid = 20; // LatticeSolidPhase.h - const int cLattice = 21; + const int cLattice = 21; //LatticePhase.h // pure fluids with liquid/vapor eqs of state const int cPureFluid = 10; From 30d59b8c4922a05c79b0a44dcbbf6286d19ce7a8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 24 Mar 2011 18:43:36 +0000 Subject: [PATCH 332/446] Added a new ThermoPhase object. This one, PhaseCombo_Interaction, is based on the Margules object. However, it eliminates the ideal solution mixing term. Therefore, zero mole fractions are possible. Needed for the thermal battery program. It may have some semblance of physical meaning or it may not. This has yet to be worked out. --- Cantera/src/thermo/Makefile.in | 4 +- Cantera/src/thermo/MargulesVPSSTP.cpp | 2 +- Cantera/src/thermo/PhaseCombo_Interaction.cpp | 1276 +++++++++++++++++ Cantera/src/thermo/PhaseCombo_Interaction.h | 705 +++++++++ Cantera/src/thermo/ThermoFactory.cpp | 9 +- Cantera/src/thermo/mix_defs.h | 1 + 6 files changed, 1992 insertions(+), 5 deletions(-) create mode 100644 Cantera/src/thermo/PhaseCombo_Interaction.cpp create mode 100644 Cantera/src/thermo/PhaseCombo_Interaction.h diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index b359d5579..690877d38 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -67,7 +67,7 @@ ELECTRO_OBJ = MolalityVPSSTP.o VPStandardStateTP.o \ PDSS.o PDSS_Water.o PDSS_HKFT.o \ HMWSoln.o HMWSoln_input.o DebyeHuckel.o \ WaterSSTP.o MetalSHEelectrons.o \ - VPSSMgr_Water_ConstVol.o VPSSMgr_Water_HKFT.o + VPSSMgr_Water_ConstVol.o VPSSMgr_Water_HKFT.o PhaseCombo_Interaction.o ELECTRO_H = MolalityVPSSTP.h VPStandardStateTP.h \ IdealMolalSoln.h \ @@ -75,7 +75,7 @@ ELECTRO_H = MolalityVPSSTP.h VPStandardStateTP.h \ PDSS.h PDSS_Water.h PDSS_HKFT.h \ HMWSoln.h electrolytes.h \ DebyeHuckel.h WaterSSTP.h MetalSHEelectrons.h VPSSMgr_Water_HKFT.h \ - VPSSMgr_Water_ConstVol.h + VPSSMgr_Water_ConstVol.h PhaseCombo_Interaction.h endif ifeq ($(do_issp),1) ISSP_OBJ = IdealSolidSolnPhase.o StoichSubstanceSSTP.o SingleSpeciesTP.o MineralEQ3.o \ diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index f039c561d..b3e85eda7 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -715,7 +715,7 @@ namespace Cantera { if (thermoNode.hasChild("activityCoefficients")) { XML_Node& acNode = thermoNode.child("activityCoefficients"); acNodePtr = &acNode; - string mStringa = thermoNode.attrib("model"); + string mStringa = acNode.attrib("model"); string mString = lowercase(mStringa); if (mString != "margules") { throw CanteraError(subname.c_str(), diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.cpp b/Cantera/src/thermo/PhaseCombo_Interaction.cpp new file mode 100644 index 000000000..f3ac98ab1 --- /dev/null +++ b/Cantera/src/thermo/PhaseCombo_Interaction.cpp @@ -0,0 +1,1276 @@ +/** + * @file + * + */ +/* + * Copywrite (2009) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Date: 2010-11-12 14:37:41 -0700 (Fri, 12 Nov 2010) $ + * $Revision: 641 $ + */ + + +#include "PhaseCombo_Interaction.h" +#include "ThermoFactory.h" +#include + +using namespace std; + +namespace Cantera { + + static const double xxSmall = 1.0E-150; + //==================================================================================================================== + /* + * Default constructor. + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction::PhaseCombo_Interaction() : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + } + //==================================================================================================================== + /* + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call\ + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction::PhaseCombo_Interaction(std::string inputFile, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + constructPhaseFile(inputFile, id); + } + //==================================================================================================================== + // + /* + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction::PhaseCombo_Interaction(XML_Node& phaseRoot, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + constructPhaseXML(phaseRoot, id); + } + + //==================================================================================================================== + /* + * Copy Constructor: + * + * Note this stuff will not work until the underlying phase + * has a working copy constructor + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction::PhaseCombo_Interaction(const PhaseCombo_Interaction &b) : + GibbsExcessVPSSTP() + { + PhaseCombo_Interaction::operator=(b); + } + //==================================================================================================================== + /* + * operator=() + * + * Note this stuff will not work until the underlying phase + * has a working assignment operator + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction& PhaseCombo_Interaction:: + operator=(const PhaseCombo_Interaction &b) { + if (&b == this) { + return *this; + } + + GibbsExcessVPSSTP::operator=(b); + + numBinaryInteractions_ = b.numBinaryInteractions_ ; + m_HE_b_ij = b.m_HE_b_ij; + m_HE_c_ij = b.m_HE_c_ij; + m_HE_d_ij = b.m_HE_d_ij; + m_SE_b_ij = b.m_SE_b_ij; + m_SE_c_ij = b.m_SE_c_ij; + m_SE_d_ij = b.m_SE_d_ij; + m_VHE_b_ij = b.m_VHE_b_ij; + m_VHE_c_ij = b.m_VHE_c_ij; + m_VHE_d_ij = b.m_VHE_d_ij; + m_VSE_b_ij = b.m_VSE_b_ij; + m_VSE_c_ij = b.m_VSE_c_ij; + m_VSE_d_ij = b.m_VSE_d_ij; + m_pSpecies_A_ij = b.m_pSpecies_A_ij; + m_pSpecies_B_ij = b.m_pSpecies_B_ij; + formMargules_ = b.formMargules_; + formTempModel_ = b.formTempModel_; + + return *this; + } + //==================================================================================================================== + /** + * + * ~PhaseCombo_Interaction(): (virtual) + * + * Destructor: does nothing: + * + * HKM - Checked for Transition + */ + PhaseCombo_Interaction::~PhaseCombo_Interaction() { + } + //==================================================================================================================== + /* + * This routine duplicates the current object and returnsa pointer to ThermoPhase. + * + * HKM - Checked for Transition + */ + ThermoPhase* + PhaseCombo_Interaction::duplMyselfAsThermoPhase() const { + PhaseCombo_Interaction* mtp = new PhaseCombo_Interaction(*this); + return (ThermoPhase *) mtp; + } + //==================================================================================================================== + // Special constructor for a hard-coded problem + /* + * + * LiKCl treating the PseudoBinary layer as passthrough. + * -> test to predict the eutectic and liquidus correctly. + * + */ + PhaseCombo_Interaction::PhaseCombo_Interaction(int testProb) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + + + constructPhaseFile("PhaseCombo_Interaction.xml", ""); + + + numBinaryInteractions_ = 1; + + m_HE_b_ij.resize(1); + m_HE_c_ij.resize(1); + m_HE_d_ij.resize(1); + + m_SE_b_ij.resize(1); + m_SE_c_ij.resize(1); + m_SE_d_ij.resize(1); + + m_VHE_b_ij.resize(1); + m_VHE_c_ij.resize(1); + m_VHE_d_ij.resize(1); + + m_VSE_b_ij.resize(1); + m_VSE_c_ij.resize(1); + m_VSE_d_ij.resize(1); + + m_pSpecies_A_ij.resize(1); + m_pSpecies_B_ij.resize(1); + + + + m_HE_b_ij[0] = -17570E3; + m_HE_c_ij[0] = -377.0E3; + m_HE_d_ij[0] = 0.0; + + m_SE_b_ij[0] = -7.627E3; + m_SE_c_ij[0] = 4.958E3; + m_SE_d_ij[0] = 0.0; + + + int iLiT = speciesIndex("LiTFe1S2(S)"); + if (iLiT < 0) { + throw CanteraError("PhaseCombo_Interaction test1 constructor", + "Unable to find LiTFe1S2(S)"); + } + m_pSpecies_A_ij[0] = iLiT; + + + int iLi2 = speciesIndex("Li2Fe1S2(S)"); + if (iLi2 < 0) { + throw CanteraError("PhaseCombo_Interaction test1 constructor", + "Unable to find Li2Fe1S2(S)"); + } + m_pSpecies_B_ij[0] = iLi2; + throw CanteraError("", "unimplemented"); + } + //==================================================================================================================== + + /* + * -------------- Utilities ------------------------------- + */ + + + // Equation of state type flag. + /* + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The PhaseCombo_Interaction class also returns + * zero, as it is a non-complete class. + */ + int PhaseCombo_Interaction::eosType() const { + return cPhaseCombo_Interaction; + } + //==================================================================================================================== + /* + * Import, construct, and initialize a phase + * specification from an XML tree into the current object. + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::constructPhaseFile(std::string inputFile, std::string id) { + + if ((int) inputFile.size() == 0) { + throw CanteraError("PhaseCombo_Interaction:constructPhaseFile", + "input file is null"); + } + string path = findInputFile(inputFile); + std::ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("PhaseCombo_Interaction:constructPhaseFile", + "Could not open " +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + XML_Node &phaseNode_XML = xml(); + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("PhaseCombo_Interaction:constructPhaseFile", + "ERROR: Can not find phase named " + id + " in file named " + inputFile); + } + fxml_phase->copy(&phaseNode_XML); + constructPhaseXML(*fxml_phase, id); + delete fxml; + } + //==================================================================================================================== + /* + * Import, construct, and initialize a HMWSoln phase + * specification from an XML tree into the current object. + * + * Most of the work is carried out by the cantera base + * routine, importPhase(). That routine imports all of the + * species and element data, including the standard states + * of the species. + * + * Then, In this routine, we read the information + * particular to the specification of the activity + * coefficient model for the Pitzer parameterization. + * + * We also read information about the molar volumes of the + * standard states if present in the XML file. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::constructPhaseXML(XML_Node& phaseNode, std::string id) { + string stemp; + if ((int) id.size() > 0) { + string idp = phaseNode.id(); + if (idp != id) { + throw CanteraError("PhaseCombo_Interaction::constructPhaseXML", + "phasenode and Id are incompatible"); + } + } + + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("PhaseCombo_Interaction::constructPhaseXML", + "no thermo XML node"); + } + XML_Node& thermoNode = phaseNode.child("thermo"); + + /* + * Make sure that the thermo model is PhaseCombo_Interaction + */ + stemp = thermoNode.attrib("model"); + string formString = lowercase(stemp); + if (formString != "phasecombo_interaction") { + throw CanteraError("PhaseCombo_Interaction::constructPhaseXML", + "model name isn't PhaseCombo_Interaction: " + formString); + } + + /* + * Call the Cantera importPhase() function. This will import + * all of the species into the phase. This will also handle + * all of the species standard states + */ + bool m_ok = importPhase(phaseNode, this); + if (!m_ok) { + throw CanteraError("PhaseCombo_Interaction::constructPhaseXML","importPhase failed "); + } + } + //==================================================================================================================== + + /* + * ------------ Molar Thermodynamic Properties ---------------------- + */ + + + /* + * - Activities, Standard States, Activity Concentrations ----------- + */ + + // This method returns an array of generalized concentrations + /* + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * Here we define the activity concentrations as equal + * to the activities, because the standard concentration is 1. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + void PhaseCombo_Interaction::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } + //==================================================================================================================== + doublereal PhaseCombo_Interaction::standardConcentration(int k) const { + //err("standardConcentration"); + //return -1.0; + return 1.0; + } + //==================================================================================================================== + doublereal PhaseCombo_Interaction::logStandardConc(int k) const { + //err("logStandardConc"); + //return -1.0; + return 0.0; + } + //==================================================================================================================== + // Get the array of non-dimensional molar-based activity coefficients at + // the current solution temperature, pressure, and solution concentration. + /* + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void PhaseCombo_Interaction::getActivityCoefficients(doublereal* ac) const { + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + + /* + * take the exp of the internally storred coefficients. + */ + for (int k = 0; k < m_kk; k++) { + ac[k] = exp(lnActCoeff_Scaled_[k]); + } + } + + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + + //==================================================================================================================== + + void PhaseCombo_Interaction::getElectrochemPotentials(doublereal* mu) const { + getChemPotentials(mu); + double ve = Faraday * electricPotential(); + for (int k = 0; k < m_kk; k++) { + mu[k] += ve*charge(k); + } + } + + //==================================================================================================================== + void PhaseCombo_Interaction::getChemPotentials(doublereal* mu) const { + doublereal xx; + /* + * First get the standard chemical potentials in + * molar form. + * -> this requires updates of standard state as a function + * of T and P + */ + getStandardChemPotentials(mu); + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + /* + * + */ + doublereal RT = GasConstant * temperature(); + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + mu[k] += RT * (log(xx) + lnActCoeff_Scaled_[k]); + } + } + //==================================================================================================================== + // Molar enthalpy. Units: J/kmol. + doublereal PhaseCombo_Interaction::enthalpy_mole() const { + int kk = nSpecies(); + double hbar[kk], h = 0; + getPartialMolarEnthalpies(hbar); + for (int i = 0; i < kk; i++){ + h += moleFractions_[i]*hbar[i]; + } + return h; + } + //==================================================================================================================== + // Molar entropy. Units: J/kmol. + doublereal PhaseCombo_Interaction::entropy_mole() const { + int kk = nSpecies(); + double sbar[kk], s = 0; + getPartialMolarEntropies(sbar); + for (int i = 0; i < kk; i++){ + s += moleFractions_[i]*sbar[i]; + } + return s; + } + //==================================================================================================================== + // Molar heat capacity at constant pressure. Units: J/kmol/K. + doublereal PhaseCombo_Interaction::cp_mole() const { + int kk = nSpecies(); + double cpbar[kk], cp = 0; + getPartialMolarCp(cpbar); + for (int i = 0; i < kk; i++){ + cp += moleFractions_[i]*cpbar[i]; + } + return cp; + } + //==================================================================================================================== + // Molar heat capacity at constant volume. Units: J/kmol/K. + doublereal PhaseCombo_Interaction::cv_mole() const { + return cp_mole() - GasConstant; + } + //==================================================================================================================== + // Returns an array of partial molar enthalpies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void PhaseCombo_Interaction::getPartialMolarEnthalpies(doublereal* hbar) const { + /* + * Get the nondimensional standard state enthalpies + */ + getEnthalpy_RT(hbar); + /* + * dimensionalize it. + */ + double T = temperature(); + double RT = GasConstant * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] *= RT; + } + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + double RTT = RT * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] -= RTT * dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + // Returns an array of partial molar heat capacities for the species in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void PhaseCombo_Interaction::getPartialMolarCp(doublereal* cpbar) const { + /* + * Get the nondimensional standard state entropies + */ + getCp_R(cpbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + //==================================================================================================================== + // Returns an array of partial molar entropies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void PhaseCombo_Interaction::getPartialMolarEntropies(doublereal* sbar) const { + double xx; + /* + * Get the nondimensional standard state entropies + */ + getEntropy_R(sbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + sbar[k] += - lnActCoeff_Scaled_[k] - log(xx) - T * dlnActCoeffdT_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + sbar[k] *= GasConstant; + } + } + //==================================================================================================================== + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + + // Return an array of partial molar volumes for the species in the mixture. Units: m^3/kmol. + /* + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void PhaseCombo_Interaction::getPartialMolarVolumes(doublereal* vbar) const { + + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + + /* + * Get the standard state values in m^3 kmol-1 + */ + getStandardVolumes(vbar); + + for ( iK = 0; iK < m_kk; iK++ ){ + delAK = 0; + delBK = 0; + XK = moleFractions_[iK]; + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_VHE_b_ij[i] - T * m_VSE_b_ij[i]); + g1 = (m_VHE_c_ij[i] - T * m_VSE_c_ij[i]); + + vbar[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + } + } + } + //==================================================================================================================== + doublereal PhaseCombo_Interaction::err(std::string msg) const { + throw CanteraError("PhaseCombo_Interaction","Base class method " + +msg+" called. Equation of state type: "+int2str(eosType())); + return 0; + } + + //==================================================================================================================== + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + void PhaseCombo_Interaction::initThermo() { + initLengths(); + GibbsExcessVPSSTP::initThermo(); + } + + //==================================================================================================================== + // Initialize lengths of local variables after all species have + // been identified. + void PhaseCombo_Interaction::initLengths() { + m_kk = nSpecies(); + dlnActCoeffdlnN_.resize(m_kk, m_kk); + } + //==================================================================================================================== + /* + * initThermoXML() (virtual from ThermoPhase) + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void PhaseCombo_Interaction::initThermoXML(XML_Node& phaseNode, std::string id) { + string subname = "PhaseCombo_Interaction::initThermoXML"; + string stemp; + + /* + * Check on the thermo field. Must have: + * + */ + + XML_Node& thermoNode = phaseNode.child("thermo"); + string mStringa = thermoNode.attrib("model"); + string mString = lowercase(mStringa); + if (mString != "phasecombo_interaction") { + throw CanteraError(subname.c_str(), "Unknown thermo model: " + mStringa); + } + + + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + XML_Node *acNodePtr = 0; + if (thermoNode.hasChild("activityCoefficients")) { + XML_Node& acNode = thermoNode.child("activityCoefficients"); + acNodePtr = &acNode; + string mStringa = acNode.attrib("model"); + string mString = lowercase(mStringa); + if (mString != "margules") { + throw CanteraError(subname.c_str(), + "Unknown activity coefficient model: " + mStringa); + } + int n = acNodePtr->nChildren(); + for (int i = 0; i < n; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + stemp = xmlACChild.name(); + string nodeName = lowercase(stemp); + /* + * Process a binary salt field, or any of the other XML fields + * that make up the Pitzer Database. Entries will be ignored + * if any of the species in the entry isn't in the solution. + */ + if (nodeName == "binaryneutralspeciesparameters") { + readXMLBinarySpecies(xmlACChild); + + } + } + } + + /* + * Go down the chain + */ + GibbsExcessVPSSTP::initThermoXML(phaseNode, id); + + + } + //=================================================================================================================== + // Update the activity coefficients + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + * he = X_A X_B(B + C X_B) + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::s_update_lnActCoeff() const { + int iA, iB, iK, delAK, delBK; + doublereal XA, XB, g0 , g1; + doublereal xx; + doublereal T = temperature(); + doublereal RT = GasConstant*T; + fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + + for (iK = 0; iK < m_kk; iK++) { + /* + * We never sample the end of the mole fraction domains + */ + xx = fmaxx(moleFractions_[iK], xxSmall); + /* + * First wipe out the ideal solution mixing term + */ + lnActCoeff_Scaled_[iK] = - log(xx); + + /* + * Then add in the Margules interaction terms. that's it! + */ + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + delAK = 0; + delBK = 0; + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + lnActCoeff_Scaled_[iK] += (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; + } + } + } + //=================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt T + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + * he = X_A X_B(B + C X_B) + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::s_update_dlnActCoeff_dT() const { + int iA, iB, iK, delAK, delBK; + doublereal XA, XB, g0, g1; + doublereal T = temperature(); + doublereal RTT = GasConstant*T*T; + fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); + fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); + for (iK = 0; iK < m_kk; iK++) { + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + delAK = 0; + delBK = 0; + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + g0 = -m_HE_b_ij[i] / RTT; + g1 = -m_HE_c_ij[i] / RTT; + double temp = (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; + dlnActCoeffdT_Scaled_[iK] += temp; + d2lnActCoeffdT2_Scaled_[iK] -= 2.0 * temp / T; + } + } + } + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdT[k] = dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k]; + } + } + //==================================================================================================================== + + // Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + // a line in parameter space or along a line in physical space + /* + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + + + int iA, iB, iK, delAK, delBK; + doublereal XA, XB, XK, g0 , g1, dXA, dXB; + doublereal T = temperature(); + doublereal RT = GasConstant*T; + doublereal xx; + + //fvo_zero_dbl_1(dlnActCoeff, m_kk); + s_update_dlnActCoeff_dT(); + + for (iK = 0; iK < m_kk; iK++) { + + XK = moleFractions_[iK]; + + /* + * We never sample the end of the mole fraction domains + */ + xx = fmaxx(moleFractions_[iK], xxSmall); + /* + * First wipe out the ideal solution mixing term + */ + if (xx > xxSmall) { + dlnActCoeffds[iK] += - 1.0 / xx; + } + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + dXA = dXds[iA]; + dXB = dXds[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffds[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB + + dlnActCoeffdT_Scaled_[iK]*dTds; + } + } + } + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt the log of the corresponding species number density + /* + * This function will be called to update the internally stored gradients of the + * logarithm of the activity coefficients. These are used in the determination + * of the diffusion coefficients. + * + * he = X_A X_B(B + C X_B) + * + * This function only carries out the diagonal calculation + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnN_diag() const { + int iA, iB, iK, delAK, delBK; + doublereal XA, XB, XK, g0 , g1; + doublereal T = temperature(); + doublereal RT = GasConstant*T; + doublereal xx; + + fvo_zero_dbl_1(dlnActCoeffdlnN_diag_, m_kk); + + for (iK = 0; iK < m_kk; iK++) { + + XK = moleFractions_[iK]; + /* + * We never sample the end of the mole fraction domains + */ + xx = fmaxx(moleFractions_[iK], xxSmall); + /* + * First wipe out the ideal solution mixing term + */ + // lnActCoeff_Scaled_[iK] = - log(xx); + if (xx > xxSmall) { + dlnActCoeffdlnN_diag_[iK] = - 1.0 + xx; + } + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + } + dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK]; + } + + } + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt ln N_k + /* + * This function will be called to update the internally storred gradients of the + * logarithm of the activity coefficients. These are used in the determination + * of the diffusion coefficients. + * + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnN() const { + int iA, iB; + doublereal delAK, delBK; + double XA, XB, g0 , g1, XK, XM; + double xx , delKM; + double T = temperature(); + double RT = GasConstant*T; + + doublereal delAM, delBM; + + dlnActCoeffdlnN_.zero(); + + /* + * Loop over the activity coefficient gamma_k + */ + for (int iK = 0; iK < m_kk; iK++) { + XK = moleFractions_[iK]; + /* + * We never sample the end of the mole fraction domains + */ + xx = fmaxx(moleFractions_[iK], xxSmall); + + for (int iM = 0; iM < m_kk; iM++) { + XM = moleFractions_[iM]; + + if (xx > xxSmall) { + delKM = 0.0; + if (iK == iM) delKM = 1.0; + // this gets multiplied by XM at the bottom + dlnActCoeffdlnN_(iK,iM) += - delKM/XM + 1.0; + } + + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0.0; + delBK = 0.0; + delAM = 0.0; + delBM = 0.0; + if (iA==iK) delAK = 1.0; + else if (iB==iK) delBK = 1.0; + if (iA==iM) delAM = 1.0; + else if (iB==iM) delBM = 1.0; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnN_(iK,iM) += g0*((delAM-XA)*(delBK-XB)+(delAK-XA)*(delBM-XB)); + dlnActCoeffdlnN_(iK,iM) += 2*g1*((delAM-XA)*(delBK-XB)*XB+(delAK-XA)*(delBM-XB)*XB+(delBM-XB)*(delBK-XB)*XA); + + } + dlnActCoeffdlnN_(iK,iM) = XM * dlnActCoeffdlnN_(iK,iM); + } + } + } + //==================================================================================================================== + void PhaseCombo_Interaction::s_update_dlnActCoeff_dlnX_diag() const { + + int iA, iB; + doublereal XA, XB, g0 , g1; + doublereal T = temperature(); + + fvo_zero_dbl_1(dlnActCoeffdlnX_diag_, m_kk); + + doublereal RT = GasConstant * T; + + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnX_diag_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); + dlnActCoeffdlnX_diag_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); + } + throw CanteraError("", "unimplemented"); + } + + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + s_update_dlnActCoeff_dlnN_diag(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k]; + } + } + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { + s_update_dlnActCoeff_dlnX_diag(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; + } + } + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) const { + s_update_dlnActCoeff_dlnN(); + double *data = & dlnActCoeffdlnN_(0,0); + for (int k = 0; k < m_kk; k++) { + for (int m = 0; m < m_kk; m++) { + dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m]; + } + } + } + //==================================================================================================================== + // + /* + * HKM - Checked for Transition + */ + void PhaseCombo_Interaction::resizeNumInteractions(const int num) { + numBinaryInteractions_ = num; + m_HE_b_ij.resize(num, 0.0); + m_HE_c_ij.resize(num, 0.0); + m_HE_d_ij.resize(num, 0.0); + m_SE_b_ij.resize(num, 0.0); + m_SE_c_ij.resize(num, 0.0); + m_SE_d_ij.resize(num, 0.0); + m_VHE_b_ij.resize(num, 0.0); + m_VHE_c_ij.resize(num, 0.0); + m_VHE_d_ij.resize(num, 0.0); + m_VSE_b_ij.resize(num, 0.0); + m_VSE_c_ij.resize(num, 0.0); + m_VSE_d_ij.resize(num, 0.0); + + m_pSpecies_A_ij.resize(num, -1); + m_pSpecies_B_ij.resize(num, -1); + throw CanteraError("", "unimplemented"); + } + //==================================================================================================================== + + /* + * Process an XML node called "binaryNeutralSpeciesParameters" + * This node contains all of the parameters necessary to describe + * the Margules Interaction for a single binary interaction + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + */ + void PhaseCombo_Interaction::readXMLBinarySpecies(XML_Node &xmLBinarySpecies) { + string xname = xmLBinarySpecies.name(); + if (xname != "binaryNeutralSpeciesParameters") { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", + "Incorrect name for processing this routine: " + xname); + } + double *charge = DATA_PTR(m_speciesCharge); + string stemp; + int nParamsFound; + vector_fp vParams; + string iName = xmLBinarySpecies.attrib("speciesA"); + if (iName == "") { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "no speciesA attrib"); + } + string jName = xmLBinarySpecies.attrib("speciesB"); + if (jName == "") { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "no speciesB attrib"); + } + /* + * Find the index of the species in the current phase. It's not + * an error to not find the species + */ + int iSpecies = speciesIndex(iName); + if (iSpecies < 0) { + return; + } + string ispName = speciesName(iSpecies); + if (charge[iSpecies] != 0) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "speciesA charge problem"); + } + int jSpecies = speciesIndex(jName); + if (jSpecies < 0) { + return; + } + string jspName = speciesName(jSpecies); + if (charge[jSpecies] != 0) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies", "speciesB charge problem"); + } + + resizeNumInteractions(numBinaryInteractions_ + 1); + int iSpot = numBinaryInteractions_ - 1; + m_pSpecies_A_ij[iSpot] = iSpecies; + m_pSpecies_B_ij[iSpot] = jSpecies; + + int num = xmLBinarySpecies.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = xmLBinarySpecies.child(iChild); + stemp = xmlChild.name(); + string nodeName = lowercase(stemp); + /* + * Process the binary species interaction child elements + */ + if (nodeName == "excessenthalpy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessEnthalpy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_HE_b_ij[iSpot] = vParams[0]; + m_HE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessentropy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessEntropy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_SE_b_ij[iSpot] = vParams[0]; + m_SE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessvolume_enthalpy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VHE_b_ij[iSpot] = vParams[0]; + m_VHE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessvolume_entropy") { + /* + * Get the string containing all of the values + */ + getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("PhaseCombo_Interaction::readXMLBinarySpecies::excessVolume_Entropy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VSE_b_ij[iSpot] = vParams[0]; + m_VSE_c_ij[iSpot] = vParams[1]; + } + + + } + } + //==================================================================================================================== +} +//====================================================================================================================== diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.h b/Cantera/src/thermo/PhaseCombo_Interaction.h new file mode 100644 index 000000000..c5dacb318 --- /dev/null +++ b/Cantera/src/thermo/PhaseCombo_Interaction.h @@ -0,0 +1,705 @@ +/** + * @file + */ +/* + * Copywrite (2006) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Id: MargulesVPSSTP.h 641 2010-11-12 21:37:41Z hkmoffa $ + */ + +#ifndef CT_LIFES_X_ONEPHASE_VPSSTP_H +#define CT_LIFES_X_ONEPHASE_VPSSTP_H + +#include "PseudoBinaryVPSSTP.h" +#include "GibbsExcessVPSSTP.h" + +namespace Cantera { + + /** + * @ingroup thermoprops + */ + + + //! MargulesVPSSTP is a derived class of GibbsExcessVPSSTP that employs + //! the Margules approximation for the excess gibbs free energy + + class PhaseCombo_Interaction : public GibbsExcessVPSSTP { + + public: + + //! Constructor + /*! + * This doesn't do much more than initialize constants with + * default values for water at 25C. Water molecular weight + * comes from the default elements.xml file. It actually + * differs slightly from the IAPWS95 value of 18.015268. However, + * density conservation and therefore element conservation + * is the more important principle to follow. + */ + PhaseCombo_Interaction(); + + //! Construct and initialize a PhaseCombo_Interaction ThermoPhase object + //! directly from an xml input file + /*! + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + * + * @param inputFile Name of the input file containing the phase XML data + * to set up the object + * @param id ID of the phase in the input file. Defaults to the + * empty string. + */ + PhaseCombo_Interaction(std::string inputFile, std::string id = ""); + + //! Construct and initialize a PhaseCombo_Interaction ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML phase node containing the description of the phase + * @param id id attribute containing the name of the phase. + * (default is the empty string) + */ + PhaseCombo_Interaction(XML_Node& phaseRef, std::string id = ""); + + + //! Special constructor for a hard-coded problem + /*! + * + * @param testProb Hard-coded value. Only the value of 1 is + * used. It's for + * a LiKCl system + * -> test to predict the eutectic and liquidus correctly. + */ + PhaseCombo_Interaction(int testProb); + + //! Copy constructor + /*! + * Note this stuff will not work until the underlying phase + * has a working copy constructor + * + * @param b class to be copied + */ + PhaseCombo_Interaction(const PhaseCombo_Interaction& b); + + //! Assignment operator + /*! + * + * @param b class to be copied. + */ + PhaseCombo_Interaction& operator=(const PhaseCombo_Interaction &b); + + //! Destructor + virtual ~PhaseCombo_Interaction(); + + //! Duplication routine for objects which inherit from ThermoPhase. + /*! + * This virtual routine can be used to duplicate thermophase objects + * inherited from ThermoPhase even if the application only has + * a pointer to ThermoPhase to work with. + */ + virtual ThermoPhase *duplMyselfAsThermoPhase() const; + + /** + * + * @name Utilities + * @{ + */ + + + //! Equation of state type flag. + /*! + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The MolalityVPSSTP class also returns + * zero, as it is a non-complete class. + */ + virtual int eosType() const; + + //! Initialization of a phase using an xml file + /*! + * This routine is a precursor to + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseFile(std::string inputFile, std::string id); + + //! Import and initialize a phase + //! specification in an XML tree into the current object. + /*! + * Here we read an XML description of the phase. + * We import descriptions of the elements that make up the + * species in a phase. + * We import information about the species, including their + * reference state thermodynamic polynomials. We then freeze + * the state of the species. + * + * Then, we read the species molar volumes from the xml + * tree to finish the initialization. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void constructPhaseXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Molar Thermodynamic Properties + * @{ + */ + + + /** + * @} + * @name Utilities for Solvent ID and Molality + * @{ + */ + + + + + /** + * @} + * @name Mechanical Properties + * @{ + */ + + /** + * @} + * @name Potential Energy + * + * Species may have an additional potential energy due to the + * presence of external gravitation or electric fields. These + * methods allow specifying a potential energy for individual + * species. + * @{ + */ + + /** + * @} + * @name Activities, Standard States, and Activity Concentrations + * + * The activity \f$a_k\f$ of a species in solution is + * related to the chemical potential by \f[ \mu_k = \mu_k^0(T) + * + \hat R T \log a_k. \f] The quantity \f$\mu_k^0(T,P)\f$ is + * the chemical potential at unit activity, which depends only + * on temperature and pressure. + * @{ + */ + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + + /** + * The standard concentration \f$ C^0_k \f$ used to normalize + * the generalized concentration. In many cases, this quantity + * will be the same for all species in a phase - for example, + * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this + * reason, this method returns a single value, instead of an + * array. However, for phases in which the standard + * concentration is species-specific (e.g. surface species of + * different sizes), this method may be called with an + * optional parameter indicating the species. + * + * @param k species index. Defaults to zero. + */ + virtual doublereal standardConcentration(int k=0) const; + + /** + * Returns the natural logarithm of the standard + * concentration of the kth species + * + * @param k species index + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Get the array of non-dimensional molar-based activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + virtual void getActivityCoefficients(doublereal* ac) const; + + + + + //@} + /// @name Partial Molar Properties of the Solution + //@{ + + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ + virtual void getChemPotentials(doublereal* mu) const; + + /// Molar enthalpy. Units: J/kmol. + virtual doublereal enthalpy_mole() const; + + /// Molar entropy. Units: J/kmol. + virtual doublereal entropy_mole() const; + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + virtual doublereal cp_mole() const; + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + virtual doublereal cv_mole() const; + + //! Returns an array of partial molar enthalpies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * @param hbar Vector of returned partial molar enthalpies + * (length m_kk, units = J/kmol) + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * @param sbar Vector of returned partial molar entropies + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????????? + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * ??????????????? + * \f] + * + * @param cpbar Vector of returned partial molar heat capacities + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //! Get the species electrochemical potentials. + /*! + * These are partial molar quantities. + * This method adds a term \f$ Fz_k \phi_k \f$ to the + * to each chemical potential. + * + * Units: J/kmol + * + * @param mu output vector containing the species electrochemical potentials. + * Length: m_kk., units = J/kmol + */ + void getElectrochemPotentials(doublereal* mu) const; + + //! Get the array of temperature second derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param d2lnActCoeffdT2 Output vector of temperature 2nd derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const; + + //! Get the array of temperature derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param dlnActCoeffdT Output vector of temperature derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const; + + + + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + + + + + /// The following methods are used in the process of constructing + /// the phase and setting its parameters from a specification in an + /// input file. They are not normally used in application programs. + /// To see how they are used, see files importCTML.cpp and + /// ThermoFactory.cpp. + + + /*! + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + /** + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void initThermoXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Derivatives of Thermodynamic Variables needed for Applications + * @{ + */ + + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space + /*! + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients - diagonal component + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the mole fraction. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX_diag Output vector of the diagonal component of the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const; + + //! Get the array of derivatives of the log activity coefficients wrt mole numbers - diagonal only + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction, + * molality, etc.) that represents the standard state. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN_diag Output vector of the diagonal entries for the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; + + + //! Get the array of derivatives of the log activity coefficients with respect to the ln species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * log of a species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; + + //@} + + private: + + //! Process an XML node called "binaryNeutralSpeciesParameters" + /*! + * This node contains all of the parameters necessary to describe + * the Margules model for a particular binary interaction. + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + * + * @param xmlBinarySpecies Reference to the XML_Node named "binaryNeutralSpeciesParameters" + * containing the binary interaction + */ + void readXMLBinarySpecies(XML_Node &xmlBinarySpecies); + + //! Resize internal arrays within the object that depend upon the number + //! of binary Margules interaction terms + /*! + * @param num Number of binary Margules interaction terms + */ + void resizeNumInteractions(const int num); + + + //! Initialize lengths of local variables after all species have + //! been identified. + void initLengths(); + + //! Update the activity coefficients + /*! + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + */ + void s_update_lnActCoeff() const; + + //! Update the derivative of the log of the activity coefficients wrt T + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt temperature. + */ + void s_update_dlnActCoeff_dT() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(mole fraction) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the mole fractions. + */ + void s_update_dlnActCoeff_dlnX_diag() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(moles) - diagonal only + /*! + * This function will be called to update the internally storred diagonal entries for the + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the moles. + */ + void s_update_dlnActCoeff_dlnN_diag() const; + + //! Update the derivative of the log of the activity coefficients wrt log(moles_m) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the mole number of species + */ + void s_update_dlnActCoeff_dlnN() const; + + + private: + //! Error function + /*! + * Print an error string and exit + * + * @param msg Message to be printed + */ + doublereal err(std::string msg) const; + + protected: + + + //! number of binary interaction expressions + int numBinaryInteractions_; + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_b_ij; + + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_c_ij; + + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_d_ij; + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_b_ij; + + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_c_ij; + + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_d_ij; + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_b_ij; + + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_c_ij; + + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_d_ij; + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_b_ij; + + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_c_ij; + + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_d_ij; + + + + //! vector of species indices representing species A in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species A. + */ + vector_int m_pSpecies_A_ij; + + //! vector of species indices representing species B in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species B. + */ + vector_int m_pSpecies_B_ij; + + //! form of the Margules interaction expression + /*! + * Currently there is only one form. + */ + int formMargules_; + + //! form of the temperatuer dependence of the Margules interaction expression + /*! + * Currently there is only one form -> constant wrt temperature. + */ + int formTempModel_; + + + }; + + + +} + +#endif + + + + + diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index d6d2dc451..18454b841 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -29,6 +29,7 @@ #include "IdealSolidSolnPhase.h" #include "MargulesVPSSTP.h" #include "IonsFromNeutralVPSSTP.h" +#include "PhaseCombo_Interaction.h" #endif #ifdef WITH_PURE_FLUIDS @@ -99,7 +100,7 @@ namespace Cantera { "PureFluid", "LatticeSolid", "Lattice", "HMW", "IdealSolidSolution", "DebyeHuckel", "IdealMolalSolution", "IdealGasVPSS", - "MineralEQ3", "MetalSHEelectrons", "Margules", + "MineralEQ3", "MetalSHEelectrons", "Margules", "PhaseCombo_Interaction", "IonsFromNeutralMolecule", "FixedChemPot" }; @@ -110,7 +111,7 @@ namespace Cantera { cHMW, cIdealSolidSolnPhase, cDebyeHuckel, cIdealMolalSoln, cVPSS_IdealGas, cMineralEQ3, cMetalSHEelectrons, - cMargulesVPSSTP, cIonsFromNeutral, cFixedChemPot + cMargulesVPSSTP, cPhaseCombo_Interaction, cIonsFromNeutral, cFixedChemPot }; /* @@ -152,6 +153,10 @@ namespace Cantera { th = new MargulesVPSSTP(); break; + case cPhaseCombo_Interaction: + th = new PhaseCombo_Interaction(); + break; + case cIonsFromNeutral: th = new IonsFromNeutralVPSSTP(); break; diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index b104d12dc..b81981de7 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -75,6 +75,7 @@ namespace Cantera { const int cMargulesVPSSTP = 301; + const int cPhaseCombo_Interaction = 305; const int cIonsFromNeutral = 2000; From 0b4c221f1484f98dd73af70c4994483d51f86c26 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 25 Mar 2011 18:46:04 +0000 Subject: [PATCH 333/446] Added documentation for the class --- Cantera/src/thermo/PhaseCombo_Interaction.h | 331 +++++++++++++++++++- 1 file changed, 325 insertions(+), 6 deletions(-) diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.h b/Cantera/src/thermo/PhaseCombo_Interaction.h index c5dacb318..56603aeae 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.h +++ b/Cantera/src/thermo/PhaseCombo_Interaction.h @@ -1,19 +1,26 @@ /** - * @file + * @file PhaseCombo_Interaction.h + * Header for intermediate ThermoPhase object for phases which + * employ the Margules gibbs free energy formulation and eliminates the ideal mixing term. + * (see \ref thermoprops + * and class \link Cantera::PhaseCombo_Interaction PhaseCombo_Interaction\endlink). */ /* - * Copywrite (2006) Sandia Corporation. Under the terms of + * Copywrite (2011) Sandia Corporation. Under the terms of * Contract DE-AC04-94AL85000 with Sandia Corporation, the * U.S. Government retains certain rights in this software. */ + /* - * $Id: MargulesVPSSTP.h 641 2010-11-12 21:37:41Z hkmoffa $ + * $Author: hkmoffa $ + * $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ + * $Revision: 255 $ */ #ifndef CT_LIFES_X_ONEPHASE_VPSSTP_H #define CT_LIFES_X_ONEPHASE_VPSSTP_H -#include "PseudoBinaryVPSSTP.h" + #include "GibbsExcessVPSSTP.h" namespace Cantera { @@ -23,9 +30,321 @@ namespace Cantera { */ - //! MargulesVPSSTP is a derived class of GibbsExcessVPSSTP that employs - //! the Margules approximation for the excess gibbs free energy + //! PhaseCombo_Interaction is a derived class of GibbsExcessVPSSTP that employs + //! the Margules approximation for the excess gibbs free energy while eliminating + //! the entropy of mixing term. + /*! + * + * %PhaseCombo_Interaction derives from class GibbsExcessVPSSTP which is derived from VPStandardStateTP, + * and overloads the virtual methods defined there with ones that + * use expressions appropriate for the Margules Excess gibbs free energy approximation. + * The reader should refer to the MargulesVPSSTP class for information on that class. + * This class in addition adds a term to the activity coefficient that eliminates the + * ideal solution mixing term within the chemical potential. This is a very radical thing + * to do, but it is supported by experimental evidence under some conditions. + * + * The independent unknowns are pressure, temperature, and mass fraction. + * + * Several concepts are introduced. The first concept is that there are temporary + * variables for holding the species standard state values of Cp, H, S, G, and V at the + * last temperature and pressure called. These functions are not recalculated + * if a new call is made using the previous temperature and pressure. Currently, + * these variables and the calculation method are handled by the VPSSMgr class, + * for which VPStandardStateTP owns a pointer to. + * + * To support the above functionality, pressure and temperature variables, + * m_plast_ss and m_tlast_ss, are kept which store the last pressure and temperature + * used in the evaluation of standard state properties. + * + * This class is introduced to represent specific conditions observed in thermal batteries. + * HOwever, it may be physically motivated to represent conditions where there may + * be a mixture of componds that are not "mixed" at the molecular level. Therefore, there + * is no mixing term. + * + * The lack of a mixing term has profound effects. First, the mole fraction of a species + * can now be identically zero due to thermodynamic considerations. The phase behaves more + * like a series of phases. That's why we named it PhaseCombo. + * + * + * + *
+ *

Specification of Species Standard %State Properties

+ *
+ * + * All species are defined to have standard states that depend upon both + * the temperature and the pressure. The Margules approximation assumes + * symmetric standard states, where all of the standard state assume + * that the species are in pure component states at the temperatue + * and pressure of the solution. I don't think it prevents, however, + * some species from being dilute in the solution. + * + * + *
+ *

Specification of Solution Thermodynamic Properties

+ *
+ * + * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. + * Each of the interactions are binary interactions involving two of the species in the phase, denoted, Ai + * and Bi. + * This is the generalization of the Margules formulation for a phase + * that has more than 2 species. The second term in the excess gibbs free energy is a negation of the + * ideal solution's mixing term. + * + * \f[ + * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) - \sum_i \left( n_i R T \ln{X_i} \right) + * \f] + * \f[ + * H^E_i = n X_{Ai} X_{Bi} \left( h_{o,i} + h_{1,i} X_{Bi} \right) + * \f] + * \f[ + * S^E_i = n X_{Ai} X_{Bi} \left( s_{o,i} + s_{1,i} X_{Bi} \right) + * \f] + * + * where n is the total moles in the solution. + * + * The activity of a species defined in the phase is given by an excess Gibbs free energy formulation. + * + * \f[ + * a_k = \gamma_k X_k + * \f] + * + * where + * + * \f[ + * R T \ln( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} + * \f] + * + * Taking the derivatives results in the following expression + * + * \f[ + * R T \ln( \gamma_k )= \sum_i \left( \left( \delta_{Ai,k} X_{Bi} + \delta_{Bi,k} X_{Ai} - X_{Ai} X_{Bi} \right) + * \left( g^E_{o,i} + g^E_{1,i} X_{Bi} \right) + + * \left( \delta_{Bi,k} - X_{Bi} \right) X_{Ai} X_{Bi} g^E_{1,i} \right) - RT \ln{X_k} + * \f] + * + * where + * \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ + * and where \f$ X_k \f$ is the mole fraction of species k. + * + * This object inherits from the class VPStandardStateTP. Therefore, the specification and + * calculation of all standard state and reference state values are handled at that level. Various functional + * forms for the standard state are permissible. + * The chemical potential for species k is equal to + * + * \f[ + * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) + * \f] + * + * The partial molar entropy for species k is given by the following relation, + * + * \f[ + * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * The partial molar enthalpy for species k is given by + * + * \f[ + * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * The partial molar volume for species k is + * + * \f[ + * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} + * \f] + * + * The partial molar Heat Capacity for species k is + * + * \f[ + * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} + * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} + * \f] + * + * + *
+ *

%Application within %Kinetics Managers

+ *
+ * + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^s_k, \f$ where \f$ C^s_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) concentrations are used + * by kinetics manager classes to compute the forward and reverse rates of elementary reactions. + * The activity concentration,\f$ C^a_k \f$,is given by the following expression. + * + * \f[ + * C^a_k = C^s_k X_k = \frac{P}{R T} X_k + * \f] + * + * The standard concentration for species k is independent of k and equal to + * + * \f[ + * C^s_k = C^s = \frac{P}{R T} + * \f] + * + * For example, a bulk-phase binary gas reaction between species j and k, producing + * a new gas species l would have the + * following equation for its rate of progress variable, \f$ R^1 \f$, which has + * units of kmol m-3 s-1. + * + * \f[ + * R^1 = k^1 C_j^a C_k^a = k^1 (C^s a_j) (C^s a_k) + * \f] + * + * where + * + * \f[ + * C_j^a = C^s a_j \mbox{\quad and \quad} C_k^a = C^s a_k + * \f] + * + * \f$ C_j^a \f$ is the activity concentration of species j, and + * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^s \f$ + * is the standard concentration. \f$ a_j \f$ is + * the activity of species j which is equal to the mole fraction of j. + * + * The reverse rate constant can then be obtained from the law of microscopic reversibility + * and the equilibrium expression for the system. + * + * \f[ + * \frac{a_j a_k}{ a_l} = K_a^{o,1} = \exp(\frac{\mu^o_l - \mu^o_j - \mu^o_k}{R T} ) + * \f] + * + * \f$ K_a^{o,1} \f$ is the dimensionless form of the equilibrium constant, associated with + * the pressure dependent standard states \f$ \mu^o_l(T,P) \f$ and their associated activities, + * \f$ a_l \f$, repeated here: + * + * \f[ + * \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l) + * \f] + * + * We can switch over to expressing the equilibrium constant in terms of the reference + * state chemical potentials + * + * \f[ + * K_a^{o,1} = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{P} + * \f] + * + * The concentration equilibrium constant, \f$ K_c \f$, may be obtained by changing over + * to activity concentrations. When this is done: + * + * \f[ + * \frac{C^a_j C^a_k}{ C^a_l} = C^o K_a^{o,1} = K_c^1 = + * \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{RT} + * \f] + * + * %Kinetics managers will calculate the concentration equilibrium constant, \f$ K_c \f$, + * using the second and third part of the above expression as a definition for the concentration + * equilibrium constant. + * + * For completeness, the pressure equilibrium constant may be obtained as well + * + * \f[ + * \frac{P_j P_k}{ P_l P_{ref}} = K_p^1 = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) + * \f] + * + * \f$ K_p \f$ is the simplest form of the equilibrium constant for ideal gases. However, it isn't + * necessarily the simplest form of the equilibrium constant for other types of phases; \f$ K_c \f$ is + * used instead because it is completely general. + * + * The reverse rate of progress may be written down as + * \f[ + * R^{-1} = k^{-1} C_l^a = k^{-1} (C^o a_l) + * \f] + * + * where we can use the concept of microscopic reversibility to + * write the reverse rate constant in terms of the + * forward reate constant and the concentration equilibrium + * constant, \f$ K_c \f$. + * + * \f[ + * k^{-1} = k^1 K^1_c + * \f] + * + * \f$k^{-1} \f$ has units of s-1. + * + * + *
+ *

Instantiation of the Class

+ *
+ * + * + * The constructor for this phase is located in the default ThermoFactory + * for %Cantera. A new %PhaseCombo_Interaction object may be created by the following code + * snippet: + * + * @code + * XML_Node *xc = get_XML_File("LiFeS_X_combo.xml"); + * XML_Node * const xs = xc->findNameID("phase", "LiFeS_X"); + * ThermoPhase *l_tp = newPhase(*xs); + * PhaseCombo_Interaction *LiFeS_X_solid = dynamic_cast (l_tp); + * @endcode + * + * or by the following code + * + * @code + * std::string id = "LiFeS_X"; + * Cantera::ThermoPhase *LiFeS_X_Phase = Cantera::newPhase("LiFeS_X_combo.xml", id); + * PhaseCombo_Interaction *LiFeS_X_solid = dynamic_cast (l_tp); + * @endcode + * + * + * or by the following constructor: + * + * @code + * XML_Node *xc = get_XML_File("LiFeS_X_combo.xml"); + * XML_Node * const xs = xc->findNameID("phase", "LiFeS_X"); + * PhaseCombo_Interaction *LiFeS_X_solid = new PhaseCombo_Interaction(*xs); + * @endcode + * + * + *
+ *

XML Example

+ *
+ * An example of an XML Element named phase setting up a PhaseCombo_Interaction + * object named LiFeS_X is given below. + * + * + * @verbatim + + + + Li Fe S + + + LiTFe1S2(S) Li2Fe1S2(S) + + + + + + 84.67069219, -269.1959421 + + + 100.7511565, -361.4222659 + + + 0, 0 + + + 0, 0 + + + + + + + + + @endverbatim + * + * The model attribute "PhaseCombo_Interaction" of the thermo XML element identifies the phase as + * being of the type handled by the PhaseCombo_Interaction object. + * + * @ingroup thermoprops + * + */ class PhaseCombo_Interaction : public GibbsExcessVPSSTP { public: From d1bc1e273c5b795da3aee779715db4b19c55546d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 19:51:35 +0000 Subject: [PATCH 334/446] Took out namespaces in headers. --- ext/tpx/CarbonDioxide.cpp | 4 +++- ext/tpx/Sub.cpp | 2 ++ ext/tpx/Sub.h | 13 ++++++------- ext/tpx/utils.cpp | 2 ++ 4 files changed, 13 insertions(+), 8 deletions(-) diff --git a/ext/tpx/CarbonDioxide.cpp b/ext/tpx/CarbonDioxide.cpp index 5e717b53b..24774a51f 100755 --- a/ext/tpx/CarbonDioxide.cpp +++ b/ext/tpx/CarbonDioxide.cpp @@ -11,6 +11,8 @@ #include #include +using namespace std; + namespace tpx { /* @@ -312,7 +314,7 @@ double CarbonDioxide::Psat(){ double log, sum=0,P; if ((T < Tmn) || (T > Tc)) { - cout << " error in Psat " << TempError << endl; + std::cout << " error in Psat " << TempError << endl; set_Err(TempError); // Error("CarbonDioxide::Psat",TempError,T); } for (int i=1;i<=8;i++) diff --git a/ext/tpx/Sub.cpp b/ext/tpx/Sub.cpp index e1c91d172..7b9d66179 100755 --- a/ext/tpx/Sub.cpp +++ b/ext/tpx/Sub.cpp @@ -7,6 +7,8 @@ #include #include +using namespace std; + namespace tpx { static string fp2str(double x, string fmt="%g") { diff --git a/ext/tpx/Sub.h b/ext/tpx/Sub.h index e15106209..3f3767bbf 100755 --- a/ext/tpx/Sub.h +++ b/ext/tpx/Sub.h @@ -21,19 +21,18 @@ #include #include -using namespace std; namespace tpx { class TPX_Error { public: - TPX_Error(string p, string e) { + TPX_Error(std::string p, std::string e) { ErrorMessage = e; ErrorProcedure = p; } virtual ~TPX_Error(){} - static string ErrorMessage; - static string ErrorProcedure; + static std::string ErrorMessage; + static std::string ErrorProcedure; }; @@ -70,7 +69,7 @@ namespace tpx { const double Undef = 999.1234; - string errorMsg(int flag); + std::string errorMsg(int flag); class Substance { public: @@ -202,8 +201,8 @@ namespace tpx { int Err; double m_energy_offset; double m_entropy_offset; - string m_name; - string m_formula; + std::string m_name; + std::string m_formula; // virtual double Xm(int k) { return 1.0;} //virtual int Species() { return 1;} diff --git a/ext/tpx/utils.cpp b/ext/tpx/utils.cpp index be81b09ac..c050af3f0 100755 --- a/ext/tpx/utils.cpp +++ b/ext/tpx/utils.cpp @@ -1,6 +1,8 @@ #include "subs.h" #include "utils.h" +using namespace std; + namespace tpx { static string lowercase(string s) { From 2d5f8c4a453b8076104c5cce6e8a86bf584557e4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:08:31 +0000 Subject: [PATCH 335/446] took out namespaces from headers --- Cantera/src/converters/CKParser.cpp | 1 - Cantera/src/converters/CKParser.h | 11 +++++------ Cantera/src/converters/CKReader.h | 1 - Cantera/src/converters/Constituent.h | 3 +-- Cantera/src/converters/Element.h | 22 +++++++--------------- Cantera/src/converters/Reaction.cpp | 2 ++ Cantera/src/converters/Reaction.h | 24 ++++++++++++------------ Cantera/src/converters/RxnSpecies.h | 10 +++------- Cantera/src/converters/Species.h | 16 ++++++++-------- Cantera/src/converters/ckr_defs.h | 3 --- Cantera/src/converters/ckr_utils.h | 23 +++++++++++------------ Cantera/src/converters/writelog.h | 4 +--- 12 files changed, 50 insertions(+), 70 deletions(-) diff --git a/Cantera/src/converters/CKParser.cpp b/Cantera/src/converters/CKParser.cpp index b51b408ea..03d5336e6 100755 --- a/Cantera/src/converters/CKParser.cpp +++ b/Cantera/src/converters/CKParser.cpp @@ -22,7 +22,6 @@ #include "ckr_utils.h" #include "writelog.h" #include -//#include "../stringUtils.h" #include using namespace std; diff --git a/Cantera/src/converters/CKParser.h b/Cantera/src/converters/CKParser.h index f8da04605..90ab2a3f5 100755 --- a/Cantera/src/converters/CKParser.h +++ b/Cantera/src/converters/CKParser.h @@ -16,7 +16,6 @@ #include #include #include -//using namespace std; #include "ckr_defs.h" #include "Element.h" @@ -58,17 +57,17 @@ namespace ckr { bool readElementSection(elementList& elements); bool readSpeciesSection(speciesList& species); - bool readThermoSection(vector& names, + bool readThermoSection(std::vector& names, speciesTable& speciesData, vector_fp& temp, - int& optionFlag, ostream& log); - bool readReactionSection(const vector& speciesNames, - vector& elementNames, + int& optionFlag, std::ostream& log); + bool readReactionSection(const std::vector& speciesNames, + std::vector& elementNames, reactionList& reactions, ReactionUnits& units); bool advanceToKeyword(const std::string& kw, const std::string& stop); bool verbose; bool debug; - bool readNASA9ThermoSection(std::vector& names, + bool readNASA9ThermoSection(std::vector& names, speciesTable& species, vector_fp& temp, int& optionFlag, std::ostream& log); diff --git a/Cantera/src/converters/CKReader.h b/Cantera/src/converters/CKReader.h index 4c4274c7a..61b02b217 100755 --- a/Cantera/src/converters/CKReader.h +++ b/Cantera/src/converters/CKReader.h @@ -23,7 +23,6 @@ #include #include -using namespace std; namespace ckr { diff --git a/Cantera/src/converters/Constituent.h b/Cantera/src/converters/Constituent.h index d8daf5d06..c81773045 100755 --- a/Cantera/src/converters/Constituent.h +++ b/Cantera/src/converters/Constituent.h @@ -11,7 +11,6 @@ #include #include -using namespace std; namespace ckr { @@ -22,7 +21,7 @@ namespace ckr { */ class Constituent { public: - string name; //!< The name of the object. + std::string name; //!< The name of the object. double number; //!< The number of units (molecules, etc.). }; diff --git a/Cantera/src/converters/Element.h b/Cantera/src/converters/Element.h index 5ba352502..30c6b9070 100755 --- a/Cantera/src/converters/Element.h +++ b/Cantera/src/converters/Element.h @@ -11,8 +11,8 @@ #include #include +#include -using namespace std; namespace ckr { @@ -41,7 +41,7 @@ public: /// Construct a new empty Element object - Element(const string& nm, double wt) : + Element(const std::string& nm, double wt) : name(nm), atomicWeight(wt), valid(0), @@ -54,12 +54,12 @@ public: /// Destructor ~Element() {} - string name; //!< Element name + std::string name; //!< Element name double atomicWeight; //!< Atomic weight in amu int valid; //!< flag returned by validation routines int index; //!< index number bool weightFromDB; //!< true if atomic weight is not specified - string comment; //!< comment in input file + std::string comment; //!< comment in input file /** @@ -72,11 +72,11 @@ public: bool operator!=(const Element& e) const { return !(*this == e); } - friend ostream& operator<<(ostream& s, const Element& e) { + friend std::ostream& operator<<(std::ostream& s, const Element& e) { s << e.name; if (!e.weightFromDB) s << "/" << e.atomicWeight << "/"; if (e.comment != "") - s << " !" << e.comment << endl; + s << " !" << e.comment << std::endl; else s << " "; return s; @@ -84,18 +84,10 @@ public: }; /// a list (vector) of Elements -typedef vector elementList; +typedef std::vector elementList; } #endif - - - - - - - - diff --git a/Cantera/src/converters/Reaction.cpp b/Cantera/src/converters/Reaction.cpp index fd4b57d2d..bce59d0ee 100755 --- a/Cantera/src/converters/Reaction.cpp +++ b/Cantera/src/converters/Reaction.cpp @@ -14,6 +14,8 @@ #include #include +using namespace std; + namespace ckr { Reaction forwardReaction(const Reaction& rxn) { diff --git a/Cantera/src/converters/Reaction.h b/Cantera/src/converters/Reaction.h index c626ea87e..52c3c4948 100755 --- a/Cantera/src/converters/Reaction.h +++ b/Cantera/src/converters/Reaction.h @@ -12,7 +12,7 @@ #include #include #include -using namespace std; +#include #include "ckr_defs.h" #include "ckr_utils.h" @@ -183,7 +183,7 @@ namespace ckr { * third body collision partners, or a species name if only * one species does. */ - string thirdBody; + std::string thirdBody; /// Reaction number. int number; @@ -192,21 +192,21 @@ namespace ckr { * list of species that participate as reactants, * and their stoichiometric coefficients */ - vector reactants; + std::vector reactants; - mutable map fwdOrder; + mutable std::map fwdOrder; /** * list of species that participate as products, * and their stoichiometric coefficients */ - vector products; + std::vector products; /** * map from species names to enhanced third-body collision efficiencies */ - mutable map e3b; + mutable std::map e3b; /** * Forward rate coefficient. For falloff reactions, this is the @@ -231,28 +231,28 @@ namespace ckr { /** * auxiliary data not handled elsewhere. */ - mutable map otherAuxData; + mutable std::map otherAuxData; /** * input file lines */ - vector lines; + std::vector lines; /** * comments */ - vector comment; + std::vector comment; // methods - double stoichCoefficient(const string& s) const; + double stoichCoefficient(const std::string& s) const; bool operator==(const Reaction& r) const; - void write(ostream& s) const; + void write(std::ostream& s) const; }; /// a list of Reaction objects - typedef vector reactionList; + typedef std::vector reactionList; Reaction forwardReaction(const Reaction& rxn); Reaction reverseReaction(const Reaction& rxn); diff --git a/Cantera/src/converters/RxnSpecies.h b/Cantera/src/converters/RxnSpecies.h index e49b46a79..7565fafbe 100755 --- a/Cantera/src/converters/RxnSpecies.h +++ b/Cantera/src/converters/RxnSpecies.h @@ -11,15 +11,11 @@ #include #include -//#include "Cantera.h" - -using namespace std; namespace ckr { - typedef vector_int group_t; - typedef vector grouplist_t; - + typedef vector_int group_t; + typedef std::vector grouplist_t; /** * A class for species in a reaction. @@ -29,7 +25,7 @@ class RxnSpecies { public: RxnSpecies() : number(0) {} - string name; //!< The name of the object. + std::string name; //!< The name of the object. double number; //!< The number of units (molecules, etc.). grouplist_t groups; }; diff --git a/Cantera/src/converters/Species.h b/Cantera/src/converters/Species.h index 9b82c7d3a..37afde930 100755 --- a/Cantera/src/converters/Species.h +++ b/Cantera/src/converters/Species.h @@ -58,19 +58,19 @@ namespace ckr { int thermoFormatType; //! Species Name - string name; - string id; //!< ID tag from 'date' field in input - string phase; //!< Phase string. Usually "G", "L", or "S". + std::string name; + std::string id; //!< ID tag from 'date' field in input + std::string phase; //!< Phase string. Usually "G", "L", or "S". double tlow; //!< Min temperature for thermo data fit double tmid; //!< Mid temperature for thermo data fit double thigh; //!< Max temperature for thermo data fit /// list of Constituent objects defining elemental composition - vector elements; + std::vector elements; /// map from element symbols to atom numbers - mutable map comp; + mutable std::map comp; /// polynomial coefficients for the lower temperature range vector_fp lowCoeffs; @@ -91,7 +91,7 @@ namespace ckr { /// position in the list of species in the input file int index; - string m_commentsRef; + std::string m_commentsRef; private: //! Delete private data @@ -99,10 +99,10 @@ namespace ckr { }; //! Shorthand for a list of Species - typedef vector speciesList; + typedef std::vector speciesList; //! A map from species names to Species objects - typedef map speciesTable; + typedef std::map speciesTable; } #endif diff --git a/Cantera/src/converters/ckr_defs.h b/Cantera/src/converters/ckr_defs.h index 8138974f7..52ffb68d5 100755 --- a/Cantera/src/converters/ckr_defs.h +++ b/Cantera/src/converters/ckr_defs.h @@ -14,9 +14,6 @@ #include #include #include -//using namespace std; - -//#include "../ctvector.h" /// the namespace for the CKReader packaage namespace ckr { diff --git a/Cantera/src/converters/ckr_utils.h b/Cantera/src/converters/ckr_utils.h index 634a6ace4..04c6f5260 100755 --- a/Cantera/src/converters/ckr_utils.h +++ b/Cantera/src/converters/ckr_utils.h @@ -17,7 +17,6 @@ #include #include -using namespace std; #ifdef WIN32 #define TYPENAME_KEYWORD @@ -35,9 +34,9 @@ namespace ckr { */ template -void getMapKeys(const map& mp, vector& keys) { +void getMapKeys(const std::map& mp, std::vector& keys) { keys.clear(); - TYPENAME_KEYWORD map::const_iterator i = mp.begin(); + TYPENAME_KEYWORD std::map::const_iterator i = mp.begin(); for (; i != mp.end(); ++i) keys.push_back(i->first); } @@ -49,9 +48,9 @@ void getMapKeys(const map& mp, vector& keys) { */ template -void getMapValues(const map& mp, vector& values) { +void getMapValues(const std::map& mp, std::vector& values) { values.clear(); - TYPENAME_KEYWORD map::const_iterator i = mp.begin(); + TYPENAME_KEYWORD std::map::const_iterator i = mp.begin(); for (; i != mp.end(); ++i) values.push_back(i->second); } @@ -120,10 +119,10 @@ inline bool valid(L& list) { /// Remove all white space from string s. -void removeWhiteSpace(string& s); +void removeWhiteSpace(std::string& s); -void getTokens(string& begin, - int n, vector& toks, char delim=' '); +void getTokens(std::string& begin, + int n, std::vector& toks, char delim=' '); /** @@ -137,12 +136,12 @@ void getTokens(string& begin, * */ -bool match(const string& s1, const string& s2); +bool match(const std::string& s1, const std::string& s2); /** * Check whether string 'word' begins with a Chemkin keyword. */ -inline bool isKeyword(string word) +inline bool isKeyword(std::string word) { return (match(word, "ELEM") || match(word, "SPEC") || @@ -152,8 +151,8 @@ inline bool isKeyword(string word) } -bool extractSlashData(string& s, string& name, string& data); -string capitalize(const string& word); +bool extractSlashData(std::string& s, std::string& name, std::string& data); +std::string capitalize(const std::string& word); } diff --git a/Cantera/src/converters/writelog.h b/Cantera/src/converters/writelog.h index b079d90bf..906fc57d9 100755 --- a/Cantera/src/converters/writelog.h +++ b/Cantera/src/converters/writelog.h @@ -12,15 +12,13 @@ #include #include #include -//using namespace std; #include "Species.h" #include "Reaction.h" -//#include "Cantera.h" namespace ckr { - std::string newTask(string msg); + std::string newTask(std::string msg); bool writeFalloff(int type, const vector_fp& c, std::ostream& log); bool writeRateCoeff(const RateCoeff& k, std::ostream& log); void printReactionEquation(std::ostream& f, const Reaction& r); From 905abc99afe2877da57f11d0612682909b37f2c8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:09:51 +0000 Subject: [PATCH 336/446] put in namespace line --- Cantera/src/thermo/PureFluidPhase.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 70336dbd7..9c07788a7 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -19,6 +19,8 @@ #include #include +using namespace std; + namespace Cantera { // Base Constructor From 5de392c0a6b28b70ffc49abb66fc346a1dc3152d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:18:37 +0000 Subject: [PATCH 337/446] Took out namespaces from headers. --- Cantera/src/transport/AqueousTransport.h | 7 +++---- Cantera/src/transport/LiquidTransport.h | 2 -- Cantera/src/transport/SimpleTransport.h | 5 ----- Cantera/src/transport/TransportFactory.cpp | 1 + Cantera/src/transport/WaterTransport.h | 1 - 5 files changed, 4 insertions(+), 12 deletions(-) diff --git a/Cantera/src/transport/AqueousTransport.h b/Cantera/src/transport/AqueousTransport.h index efe4d0f7c..c2d9b47d5 100644 --- a/Cantera/src/transport/AqueousTransport.h +++ b/Cantera/src/transport/AqueousTransport.h @@ -13,7 +13,6 @@ #ifndef CT_AQUEOUSTRAN_H #define CT_AQUEOUSTRAN_H -using namespace std; // Cantera includes #include "TransportBase.h" @@ -403,14 +402,14 @@ namespace Cantera { * These express the temperature dependendence of the pures * species viscosities. */ - vector m_visccoeffs; + std::vector m_visccoeffs; //! Polynomial coefficients of the conductivities /*! * These express the temperature dependendence of the pures * species conductivities */ - vector m_condcoeffs; + std::vector m_condcoeffs; //! Polynomial coefficients of the binary diffusion coefficients /*! @@ -418,7 +417,7 @@ namespace Cantera { * binary diffusivities. An overall pressure dependence is then * added. */ - vector m_diffcoeffs; + std::vector m_diffcoeffs; //! Internal value of the gradient of the mole fraction vector diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 4c056475c..352687c47 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -19,8 +19,6 @@ #include #include -using namespace std; - // Cantera includes #include "TransportBase.h" #include "DenseMatrix.h" diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index d7c4c9f26..b82d6120b 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -21,8 +21,6 @@ #include #include -using namespace std; - // Cantera includes #include "TransportBase.h" #include "DenseMatrix.h" @@ -31,9 +29,6 @@ using namespace std; namespace Cantera { - - - class LiquidTransportParams; diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 555e56c2d..8162bdec5 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -49,6 +49,7 @@ #include #include +using namespace std; //! polynomial degree used for fitting collision integrals diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h index c8ad75a67..f4e626bbe 100644 --- a/Cantera/src/transport/WaterTransport.h +++ b/Cantera/src/transport/WaterTransport.h @@ -19,7 +19,6 @@ #include #include -using namespace std; // Cantera includes #include "TransportBase.h" From 361c8f655b6e83270e3b398dafdb266ae3a76747 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:29:33 +0000 Subject: [PATCH 338/446] Took out namespaces from headers --- Cantera/src/thermo/ConstDensityThermo.cpp | 2 ++ Cantera/src/thermo/DebyeHuckel.cpp | 1 + Cantera/src/thermo/FixedChemPotSSTP.cpp | 4 ++-- Cantera/src/thermo/HMWSoln_input.cpp | 1 + Cantera/src/thermo/IdealMolalSoln.cpp | 2 ++ Cantera/src/thermo/IdealSolidSolnPhase.cpp | 2 +- Cantera/src/thermo/LatticePhase.cpp | 6 +++--- Cantera/src/thermo/LatticeSolidPhase.cpp | 2 +- Cantera/src/thermo/MargulesVPSSTP.cpp | 8 ++++---- Cantera/src/thermo/MetalPhase.h | 2 +- Cantera/src/thermo/MetalSHEelectrons.cpp | 4 ++-- Cantera/src/thermo/MineralEQ3.cpp | 14 +++++++------- Cantera/src/thermo/MolalityVPSSTP.cpp | 4 ++-- Cantera/src/thermo/PDSS_ConstVol.cpp | 2 +- Cantera/src/thermo/PDSS_HKFT.cpp | 1 + Cantera/src/thermo/PDSS_SSVol.cpp | 6 +++--- Cantera/src/thermo/Phase.h | 1 - Cantera/src/thermo/PhaseCombo_Interaction.cpp | 8 ++++---- Cantera/src/thermo/PhaseCombo_Interaction.h | 4 ++-- Cantera/src/thermo/SemiconductorPhase.h | 16 ++++++++-------- Cantera/src/thermo/StoichSubstance.cpp | 2 +- Cantera/src/thermo/StoichSubstanceSSTP.cpp | 4 ++-- Cantera/src/thermo/SurfPhase.cpp | 2 ++ Cantera/src/thermo/ThermoFactory.cpp | 1 + Cantera/src/thermo/ThermoPhase.cpp | 1 + Cantera/src/thermo/VPSSMgr_ConstVol.cpp | 4 ++-- Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp | 4 ++-- 27 files changed, 59 insertions(+), 49 deletions(-) diff --git a/Cantera/src/thermo/ConstDensityThermo.cpp b/Cantera/src/thermo/ConstDensityThermo.cpp index b0adfaca1..f4129d143 100644 --- a/Cantera/src/thermo/ConstDensityThermo.cpp +++ b/Cantera/src/thermo/ConstDensityThermo.cpp @@ -22,6 +22,8 @@ #include +using namespace ctml; + namespace Cantera { ConstDensityThermo::ConstDensityThermo() : m_tlast(0.0) { diff --git a/Cantera/src/thermo/DebyeHuckel.cpp b/Cantera/src/thermo/DebyeHuckel.cpp index d3dca91f5..b2b1f9c81 100644 --- a/Cantera/src/thermo/DebyeHuckel.cpp +++ b/Cantera/src/thermo/DebyeHuckel.cpp @@ -28,6 +28,7 @@ #include using namespace std; +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/FixedChemPotSSTP.cpp b/Cantera/src/thermo/FixedChemPotSSTP.cpp index 42a99d96e..0e7f87f4f 100644 --- a/Cantera/src/thermo/FixedChemPotSSTP.cpp +++ b/Cantera/src/thermo/FixedChemPotSSTP.cpp @@ -489,7 +489,7 @@ namespace Cantera { "thermo model attribute must be FixedChemPot or StoichSubstance or StoichSubstanceSSTP"); } if (model == "FixedChemPot") { - double val = getFloatDefaultUnits(tnode, "chemicalPotential", "J/kmol"); + double val = ctml::getFloatDefaultUnits(tnode, "chemicalPotential", "J/kmol"); chemPot_ = val; } SingleSpeciesTP::initThermoXML(phaseNode, id); @@ -528,7 +528,7 @@ namespace Cantera { "thermo model attribute must be FixedChemPot or StoichSubstance or StoichSubstanceSSTP"); } if (model == "FixedChemPotSSTP") { - doublereal val = getFloatDefaultUnits(eosdata, "chemicalPotential", "J/kmol"); + doublereal val = ctml::getFloatDefaultUnits(eosdata, "chemicalPotential", "J/kmol"); chemPot_ = val; } } diff --git a/Cantera/src/thermo/HMWSoln_input.cpp b/Cantera/src/thermo/HMWSoln_input.cpp index bca1ae93f..f4380c784 100644 --- a/Cantera/src/thermo/HMWSoln_input.cpp +++ b/Cantera/src/thermo/HMWSoln_input.cpp @@ -24,6 +24,7 @@ #include using namespace std; +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/IdealMolalSoln.cpp b/Cantera/src/thermo/IdealMolalSoln.cpp index 3730d60cb..9a60d5da1 100644 --- a/Cantera/src/thermo/IdealMolalSoln.cpp +++ b/Cantera/src/thermo/IdealMolalSoln.cpp @@ -33,6 +33,8 @@ #endif //@} +using namespace ctml; + namespace Cantera { //! Small value to be used in cutoff expressions with logs diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.cpp b/Cantera/src/thermo/IdealSolidSolnPhase.cpp index 8841712eb..4425531a7 100644 --- a/Cantera/src/thermo/IdealSolidSolnPhase.cpp +++ b/Cantera/src/thermo/IdealSolidSolnPhase.cpp @@ -1244,7 +1244,7 @@ namespace Cantera { for (int k = 0; k < m_kk; k++) { XML_Node* s = speciesDB->findByAttr("name", sss[k]); XML_Node *ss = s->findByName("standardState"); - m_speciesMolarVolume[k] = getFloat(*ss, "molarVolume", "toSI"); + m_speciesMolarVolume[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); } /* diff --git a/Cantera/src/thermo/LatticePhase.cpp b/Cantera/src/thermo/LatticePhase.cpp index a0c900464..f23b5b009 100644 --- a/Cantera/src/thermo/LatticePhase.cpp +++ b/Cantera/src/thermo/LatticePhase.cpp @@ -499,7 +499,7 @@ namespace Cantera { XML_Node *ss = s->findByName("standardState"); if (ss) { if (ss->findByName("molarVolume")) { - m_speciesMolarVolume[k] = getFloat(*ss, "molarVolume", "toSI"); + m_speciesMolarVolume[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); } } } @@ -541,8 +541,8 @@ namespace Cantera { //===================================================================================================== void LatticePhase::setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model", "Lattice"); - m_site_density = getFloat(eosdata, "site_density", "toSI"); - m_vacancy = getChildValue(eosdata, "vacancy_species"); + m_site_density = ctml::getFloat(eosdata, "site_density", "toSI"); + m_vacancy = ctml::getChildValue(eosdata, "vacancy_species"); } //===================================================================================================== } diff --git a/Cantera/src/thermo/LatticeSolidPhase.cpp b/Cantera/src/thermo/LatticeSolidPhase.cpp index 6b0d04385..4a024cfc9 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.cpp +++ b/Cantera/src/thermo/LatticeSolidPhase.cpp @@ -639,7 +639,7 @@ namespace Cantera { std::vector pnam; std::vector pval; XML_Node& ls = eosdata.child("LatticeStoichiometry"); - int np = getPairs(ls, pnam, pval); + int np = ctml::getPairs(ls, pnam, pval); theta_.resize(nl); for (int i = 0; i < np; i++) { double val = fpValueCheck(pval[i]); diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index b3e85eda7..b2c57cde8 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -1145,7 +1145,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1161,7 +1161,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1177,7 +1177,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1193,7 +1193,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { diff --git a/Cantera/src/thermo/MetalPhase.h b/Cantera/src/thermo/MetalPhase.h index 32ad3431d..315e4c344 100644 --- a/Cantera/src/thermo/MetalPhase.h +++ b/Cantera/src/thermo/MetalPhase.h @@ -104,7 +104,7 @@ namespace Cantera { virtual void setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model","Metal"); - doublereal rho = getFloat(eosdata, "density", "density"); + doublereal rho = ctml::getFloat(eosdata, "density", "density"); setDensity(rho); } diff --git a/Cantera/src/thermo/MetalSHEelectrons.cpp b/Cantera/src/thermo/MetalSHEelectrons.cpp index 221fa5ae9..d9ef37ec5 100644 --- a/Cantera/src/thermo/MetalSHEelectrons.cpp +++ b/Cantera/src/thermo/MetalSHEelectrons.cpp @@ -433,7 +433,7 @@ namespace Cantera { XML_Node &tnode = phaseNode.child("thermo"); doublereal dens = 2.65E3; if (tnode.hasChild("density")) { - dens = getFloatDefaultUnits(tnode, "density", "kg/m3"); + dens = ctml::getFloatDefaultUnits(tnode, "density", "kg/m3"); } setDensity(dens); SingleSpeciesTP::initThermoXML(phaseNode, id); @@ -537,7 +537,7 @@ namespace Cantera { } doublereal rho = 2.65E3; if (eosdata.hasChild("density")) { - rho = getFloat(eosdata, "density", "toSI"); + rho = ctml::getFloat(eosdata, "density", "toSI"); } setDensity(rho); } diff --git a/Cantera/src/thermo/MineralEQ3.cpp b/Cantera/src/thermo/MineralEQ3.cpp index 1758f95de..e97c8f9e2 100644 --- a/Cantera/src/thermo/MineralEQ3.cpp +++ b/Cantera/src/thermo/MineralEQ3.cpp @@ -493,7 +493,7 @@ namespace Cantera { Aunits = aV.attrib("units"); Afactor = toSI(Aunits); } - volVal = getFloat(*aStandardState, "V0_Pr_Tr"); + volVal = ctml::getFloat(*aStandardState, "V0_Pr_Tr"); m_V0_pr_tr= volVal; volVal *= Afactor; m_speciesSize[0] = volVal; @@ -509,13 +509,13 @@ namespace Cantera { m_deltaG_formation_pr_tr = - getFloatDefaultUnits(MinEQ3node, "DG0_f_Pr_Tr", "cal/gmol", "actEnergy"); + ctml::getFloatDefaultUnits(MinEQ3node, "DG0_f_Pr_Tr", "cal/gmol", "actEnergy"); m_deltaH_formation_pr_tr = - getFloatDefaultUnits(MinEQ3node, "DH0_f_Pr_Tr", "cal/gmol", "actEnergy"); - m_Entrop_pr_tr = getFloatDefaultUnits(MinEQ3node, "S0_Pr_Tr", "cal/gmol/K"); - m_a = getFloatDefaultUnits(MinEQ3node, "a", "cal/gmol/K"); - m_b = getFloatDefaultUnits(MinEQ3node, "b", "cal/gmol/K2"); - m_c = getFloatDefaultUnits(MinEQ3node, "c", "cal-K/gmol"); + ctml::getFloatDefaultUnits(MinEQ3node, "DH0_f_Pr_Tr", "cal/gmol", "actEnergy"); + m_Entrop_pr_tr = ctml::getFloatDefaultUnits(MinEQ3node, "S0_Pr_Tr", "cal/gmol/K"); + m_a = ctml::getFloatDefaultUnits(MinEQ3node, "a", "cal/gmol/K"); + m_b = ctml::getFloatDefaultUnits(MinEQ3node, "b", "cal/gmol/K2"); + m_c = ctml::getFloatDefaultUnits(MinEQ3node, "c", "cal-K/gmol"); convertDGFormation(); diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp index da2a30e60..617f0224b 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.cpp +++ b/Cantera/src/thermo/MolalityVPSSTP.cpp @@ -590,12 +590,12 @@ namespace Cantera { */ void MolalityVPSSTP::setStateFromXML(const XML_Node& state) { VPStandardStateTP::setStateFromXML(state); - string comp = getChildValue(state,"soluteMolalities"); + string comp = ctml::getChildValue(state,"soluteMolalities"); if (comp != "") { setMolalitiesByName(comp); } if (state.hasChild("pressure")) { - double p = getFloat(state, "pressure", "pressure"); + double p = ctml::getFloat(state, "pressure", "pressure"); setPressure(p); } } diff --git a/Cantera/src/thermo/PDSS_ConstVol.cpp b/Cantera/src/thermo/PDSS_ConstVol.cpp index 6bd07eac0..c5e33b749 100644 --- a/Cantera/src/thermo/PDSS_ConstVol.cpp +++ b/Cantera/src/thermo/PDSS_ConstVol.cpp @@ -119,7 +119,7 @@ namespace Cantera { "standardState model for species isn't constant_incompressible: " + speciesNode.name()); } - m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI"); + m_constMolarVolume = ctml::getFloat(*ss, "molarVolume", "toSI"); std::string id = ""; // initThermoXML(phaseNode, id); diff --git a/Cantera/src/thermo/PDSS_HKFT.cpp b/Cantera/src/thermo/PDSS_HKFT.cpp index 1ba20f27f..224c08d0a 100644 --- a/Cantera/src/thermo/PDSS_HKFT.cpp +++ b/Cantera/src/thermo/PDSS_HKFT.cpp @@ -24,6 +24,7 @@ #include using namespace std; +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/PDSS_SSVol.cpp b/Cantera/src/thermo/PDSS_SSVol.cpp index 4ca9cd46f..78cd4f3e5 100644 --- a/Cantera/src/thermo/PDSS_SSVol.cpp +++ b/Cantera/src/thermo/PDSS_SSVol.cpp @@ -131,17 +131,17 @@ namespace Cantera { std::string model = (*ss)["model"]; if (model == "constant_incompressible" || model == "constant") { volumeModel_ = cSSVOLUME_CONSTANT; - m_constMolarVolume = getFloat(*ss, "molarVolume", "toSI"); + m_constMolarVolume = ctml::getFloat(*ss, "molarVolume", "toSI"); } else if (model == "temperature_polynomial") { volumeModel_ = cSSVOLUME_TPOLY; - int num = getFloatArray(*ss, TCoeff_, true, "toSI", "volumeTemperaturePolynomial"); + int num = ctml::getFloatArray(*ss, TCoeff_, true, "toSI", "volumeTemperaturePolynomial"); if (num != 4) { throw CanteraError("PDSS_SSVol::constructPDSSXML", " Didn't get 4 density polynomial numbers for species " + speciesNode.name()); } } else if (model == "density_temperature_polynomial") { volumeModel_ = cSSVOLUME_DENSITY_TPOLY; - int num = getFloatArray(*ss, TCoeff_, true, "toSI", "densityTemperaturePolynomial"); + int num = ctml::getFloatArray(*ss, TCoeff_, true, "toSI", "densityTemperaturePolynomial"); if (num != 4) { throw CanteraError("PDSS_SSVol::constructPDSSXML", " Didn't get 4 density polynomial numbers for species " + speciesNode.name()); diff --git a/Cantera/src/thermo/Phase.h b/Cantera/src/thermo/Phase.h index d6de40b1a..5163d6d42 100644 --- a/Cantera/src/thermo/Phase.h +++ b/Cantera/src/thermo/Phase.h @@ -22,7 +22,6 @@ #include "vec_functions.h" #include "ctml.h" -using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.cpp b/Cantera/src/thermo/PhaseCombo_Interaction.cpp index f3ac98ab1..ae891ec49 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.cpp +++ b/Cantera/src/thermo/PhaseCombo_Interaction.cpp @@ -1208,7 +1208,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1224,7 +1224,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1240,7 +1240,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { @@ -1256,7 +1256,7 @@ namespace Cantera { /* * Get the string containing all of the values */ - getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); nParamsFound = vParams.size(); if (nParamsFound != 2) { diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.h b/Cantera/src/thermo/PhaseCombo_Interaction.h index 56603aeae..59ffb72e0 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.h +++ b/Cantera/src/thermo/PhaseCombo_Interaction.h @@ -17,8 +17,8 @@ * $Revision: 255 $ */ -#ifndef CT_LIFES_X_ONEPHASE_VPSSTP_H -#define CT_LIFES_X_ONEPHASE_VPSSTP_H +#ifndef CT_PHASECOMBO_INTERACTION_H +#define CT_PHASECOMBO_INTERACTION_H #include "GibbsExcessVPSSTP.h" diff --git a/Cantera/src/thermo/SemiconductorPhase.h b/Cantera/src/thermo/SemiconductorPhase.h index 561d7df0b..a6e121f02 100644 --- a/Cantera/src/thermo/SemiconductorPhase.h +++ b/Cantera/src/thermo/SemiconductorPhase.h @@ -70,15 +70,15 @@ namespace Cantera { virtual void setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model","Semiconductor"); - doublereal rho = getFloat(eosdata, "density", "-"); + doublereal rho = ctml::getFloat(eosdata, "density", "-"); setDensity(rho); - doublereal bandgap = getFloat(eosdata, "bandgap", "-"); - doublereal e_mass = getFloat(eosdata, "electron_mass", "-"); - doublereal h_mass = getFloat(eosdata, "hole_mass", "-"); - doublereal e_donor = getFloat(eosdata, "donor_energy", "-"); - doublereal n_donor = getFloat(eosdata, "donor_concentration", "-"); - doublereal e_acceptor = getFloat(eosdata, "acceptor_energy", "-"); - doublereal n_acceptor = getFloat(eosdata, "acceptor_concentration", "-"); + doublereal bandgap = ctml::getFloat(eosdata, "bandgap", "-"); + doublereal e_mass = ctml::getFloat(eosdata, "electron_mass", "-"); + doublereal h_mass = ctml::getFloat(eosdata, "hole_mass", "-"); + doublereal e_donor = ctml::getFloat(eosdata, "donor_energy", "-"); + doublereal n_donor = ctml::getFloat(eosdata, "donor_concentration", "-"); + doublereal e_acceptor = ctml::getFloat(eosdata, "acceptor_energy", "-"); + doublereal n_acceptor = ctml::getFloat(eosdata, "acceptor_concentration", "-"); setEffectiveMasses(e_mass, h_mass); setDonorDoping(n_donor, e_donor); setAcceptorDoping(n_acceptor, e_acceptor); diff --git a/Cantera/src/thermo/StoichSubstance.cpp b/Cantera/src/thermo/StoichSubstance.cpp index 7770c149a..995333aa9 100644 --- a/Cantera/src/thermo/StoichSubstance.cpp +++ b/Cantera/src/thermo/StoichSubstance.cpp @@ -293,7 +293,7 @@ namespace Cantera { void StoichSubstance::setParametersFromXML(const XML_Node& eosdata) { eosdata._require("model","StoichSubstance"); - doublereal rho = getFloat(eosdata, "density", "toSI"); + doublereal rho = ctml::getFloat(eosdata, "density", "toSI"); setDensity(rho); } diff --git a/Cantera/src/thermo/StoichSubstanceSSTP.cpp b/Cantera/src/thermo/StoichSubstanceSSTP.cpp index 565e7cfc5..84345f861 100644 --- a/Cantera/src/thermo/StoichSubstanceSSTP.cpp +++ b/Cantera/src/thermo/StoichSubstanceSSTP.cpp @@ -434,7 +434,7 @@ namespace Cantera { "no thermo XML node"); } XML_Node &tnode = phaseNode.child("thermo"); - double dens = getFloatDefaultUnits(tnode, "density", "kg/m3"); + double dens = ctml::getFloatDefaultUnits(tnode, "density", "kg/m3"); setDensity(dens); SingleSpeciesTP::initThermoXML(phaseNode, id); } @@ -482,7 +482,7 @@ namespace Cantera { throw CanteraError("StoichSubstanceSSTP::setParametersFromXML", "thermo model attribute must be StoichSubstance"); } - doublereal rho = getFloat(eosdata, "density", "toSI"); + doublereal rho = ctml::getFloat(eosdata, "density", "toSI"); setDensity(rho); } diff --git a/Cantera/src/thermo/SurfPhase.cpp b/Cantera/src/thermo/SurfPhase.cpp index 44fea43fd..acd506062 100644 --- a/Cantera/src/thermo/SurfPhase.cpp +++ b/Cantera/src/thermo/SurfPhase.cpp @@ -23,6 +23,8 @@ #include "EdgePhase.h" #include "ThermoFactory.h" +using namespace ctml; + using namespace std; /////////////////////////////////////////////////////////// diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 18454b841..a7181554c 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -81,6 +81,7 @@ #include using namespace std; +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 0d8a11618..0acf3a7ca 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -30,6 +30,7 @@ //@} using namespace std; +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/thermo/VPSSMgr_ConstVol.cpp b/Cantera/src/thermo/VPSSMgr_ConstVol.cpp index 12bc083be..1734384ca 100644 --- a/Cantera/src/thermo/VPSSMgr_ConstVol.cpp +++ b/Cantera/src/thermo/VPSSMgr_ConstVol.cpp @@ -154,7 +154,7 @@ namespace Cantera { throw CanteraError("VPSSMgr_ConstVol::initThermoXML", "standardState model for species isn't constant_incompressible: " + s->name()); } - m_Vss[k] = getFloat(*ss, "molarVolume", "toSI"); + m_Vss[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); } } @@ -181,7 +181,7 @@ namespace Cantera { if ((int) m_Vss.size() < k+1) { m_Vss.resize(k+1, 0.0); } - m_Vss[k] = getFloat(*ss, "molarVolume", "toSI"); + m_Vss[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); installSTSpecies(k, speciesNode, phaseNode_ptr); diff --git a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp index 40a65a8eb..c9d803cff 100644 --- a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp +++ b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp @@ -249,7 +249,7 @@ namespace Cantera { "standardState model for species isn't " "constant_incompressible: " + sName); } - m_Vss[k] = getFloat(*ss, "molarVolume", "toSI"); + m_Vss[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); } } @@ -300,7 +300,7 @@ namespace Cantera { if ((int) m_Vss.size() < k+1) { m_Vss.resize(k+1, 0.0); } - m_Vss[k] = getFloat(*ss, "molarVolume", "toSI"); + m_Vss[k] = ctml::getFloat(*ss, "molarVolume", "toSI"); // instantiate a new kPDSS object kPDSS = new PDSS_ConstVol(m_vptp_ptr, k, speciesNode, *phaseNode_ptr, true); From d7a00c9126c8ab99daebd52adae4ece7797034d4 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:39:34 +0000 Subject: [PATCH 339/446] Took out namespaces from headers. --- Cantera/src/spectra/rotor.cpp | 1 + Cantera/src/spectra/rotor.h | 11 +++++------ 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Cantera/src/spectra/rotor.cpp b/Cantera/src/spectra/rotor.cpp index ea9d7a31a..9b4770e20 100644 --- a/Cantera/src/spectra/rotor.cpp +++ b/Cantera/src/spectra/rotor.cpp @@ -11,6 +11,7 @@ #include "rotor.h" using namespace std; +using namespace Cantera; namespace CanteraSpectra { diff --git a/Cantera/src/spectra/rotor.h b/Cantera/src/spectra/rotor.h index 70e2ba6ab..b8d6aab18 100644 --- a/Cantera/src/spectra/rotor.h +++ b/Cantera/src/spectra/rotor.h @@ -14,7 +14,6 @@ */ #include "ct_defs.h" -using namespace Cantera; /** * Namespace for spectroscopic functions and classes. @@ -63,24 +62,24 @@ namespace CanteraSpectra { /** convert from Hz to wavenmbers */ inline doublereal hz_to_wnum(doublereal freq) { - return freq/(100.0*lightSpeed); + return freq/(100.0*Cantera::lightSpeed); } /** Convert from wavenumbers to Joules. */ inline doublereal wnum_to_J(doublereal w) { - return Planck * w * 100.0 * lightSpeed; + return Cantera::Planck * w * 100.0 * Cantera::lightSpeed; } inline doublereal J_to_wnum(doublereal e) { - return e /(Planck * 100.0 * lightSpeed); + return e /(Cantera::Planck * 100.0 * Cantera::lightSpeed); } inline doublereal wnum_to_eV(doublereal w) { - return Planck * w * 100.0 * lightSpeed / ElectronCharge; + return Cantera::Planck * w * 100.0 * Cantera::lightSpeed / Cantera::ElectronCharge; } inline doublereal eV_to_wnum(doublereal e) { - return e * ElectronCharge / (Planck * 100.0 * lightSpeed); + return e * Cantera::ElectronCharge / (Cantera::Planck * 100.0 * Cantera::lightSpeed); } } From 566fcdea0c77c0536a550204f778cc7a1c124c97 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:41:51 +0000 Subject: [PATCH 340/446] Took out namespaces from headers. --- Cantera/src/spectra/LineBroadener.cpp | 5 +++-- Cantera/src/spectra/LineBroadener.h | 5 ++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Cantera/src/spectra/LineBroadener.cpp b/Cantera/src/spectra/LineBroadener.cpp index 167261e3d..5daa0ae4c 100644 --- a/Cantera/src/spectra/LineBroadener.cpp +++ b/Cantera/src/spectra/LineBroadener.cpp @@ -3,6 +3,7 @@ #include "LineBroadener.h" using namespace std; +using namespace Cantera; namespace CanteraSpectra { @@ -20,7 +21,7 @@ namespace CanteraSpectra { * Units: 1/wavenumber (or cm). */ doublereal Lorentzian::profile(doublereal deltaFreq) { - return (1.0/Pi) *m_hwhm/(deltaFreq*deltaFreq + m_hwhm2); + return (1.0/Cantera::Pi) *m_hwhm/(deltaFreq*deltaFreq + m_hwhm2); } /** @@ -47,7 +48,7 @@ namespace CanteraSpectra { //cout << "entered Gaussian::profile" << endl; //cout << "deltaFreq = " << deltaFreq << endl; //cout << "m_sigma = " << m_sigma << endl; - return 1.0/(m_sigma*SqrtTwo*SqrtPi) * + return 1.0/(m_sigma * Cantera::SqrtTwo *Cantera::SqrtPi) * exp(-deltaFreq*deltaFreq/(2.0*m_sigma2)); } diff --git a/Cantera/src/spectra/LineBroadener.h b/Cantera/src/spectra/LineBroadener.h index 30560d19d..ac7828939 100644 --- a/Cantera/src/spectra/LineBroadener.h +++ b/Cantera/src/spectra/LineBroadener.h @@ -7,7 +7,6 @@ #include "ct_defs.h" #include "ctexceptions.h" -using namespace Cantera; namespace CanteraSpectra { /** @@ -38,7 +37,7 @@ namespace CanteraSpectra { * an exception will be thrown. */ virtual doublereal profile(doublereal deltaFreq) { - throw CanteraError("LineBroadener::profile", + throw Cantera::CanteraError("LineBroadener::profile", "base class method called!"); } @@ -53,7 +52,7 @@ namespace CanteraSpectra { * \f] */ virtual doublereal cumulative(doublereal deltaFreq) { - throw CanteraError("LineBroadener::cumulative", + throw Cantera::CanteraError("LineBroadener::cumulative", "base class method called!"); } From 368cdc8167c11523f351ef6d07481e1eb23e4b35 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:49:24 +0000 Subject: [PATCH 341/446] Took namespaces out of headers --- Cantera/src/zeroD/FlowDevice.cpp | 1 + Cantera/src/zeroD/FlowDevice.h | 7 +++---- Cantera/src/zeroD/Reactor.h | 16 ++++++++-------- Cantera/src/zeroD/ReactorBase.cpp | 2 ++ Cantera/src/zeroD/ReactorBase.h | 18 ++++++++---------- Cantera/src/zeroD/ReactorFactory.cpp | 2 +- Cantera/src/zeroD/ReactorFactory.h | 2 +- Cantera/src/zeroD/ReactorNet.cpp | 1 + Cantera/src/zeroD/ReactorNet.h | 16 ++++++++-------- Cantera/src/zeroD/Reservoir.h | 4 ++-- Cantera/src/zeroD/Wall.cpp | 1 + Cantera/src/zeroD/Wall.h | 1 - 12 files changed, 36 insertions(+), 35 deletions(-) diff --git a/Cantera/src/zeroD/FlowDevice.cpp b/Cantera/src/zeroD/FlowDevice.cpp index 60d9fdeef..85a39aa70 100644 --- a/Cantera/src/zeroD/FlowDevice.cpp +++ b/Cantera/src/zeroD/FlowDevice.cpp @@ -4,6 +4,7 @@ #include "Func1.h" using namespace std; +using namespace Cantera; namespace CanteraZeroD { diff --git a/Cantera/src/zeroD/FlowDevice.h b/Cantera/src/zeroD/FlowDevice.h index 3273f5c5e..efd59b13d 100644 --- a/Cantera/src/zeroD/FlowDevice.h +++ b/Cantera/src/zeroD/FlowDevice.h @@ -23,7 +23,6 @@ namespace Cantera { class Func1; } -using namespace Cantera; namespace CanteraZeroD { @@ -166,7 +165,7 @@ namespace CanteraZeroD { doublereal m_mdot; Cantera::Func1* m_func; - vector_fp m_coeffs; + Cantera::vector_fp m_coeffs; int m_type; private: @@ -174,10 +173,10 @@ namespace CanteraZeroD { int m_nspin, m_nspout; ReactorBase* m_in; ReactorBase* m_out; - vector_int m_in2out, m_out2in; + Cantera::vector_int m_in2out, m_out2in; void warn(std::string meth) { - writelog(std::string("Warning: method ") + meth + " of base class " + Cantera::writelog(std::string("Warning: method ") + meth + " of base class " + " FlowDevice called. Nothing done.\n"); } }; diff --git a/Cantera/src/zeroD/Reactor.h b/Cantera/src/zeroD/Reactor.h index aca2506ce..d43760f08 100644 --- a/Cantera/src/zeroD/Reactor.h +++ b/Cantera/src/zeroD/Reactor.h @@ -82,7 +82,7 @@ namespace CanteraZeroD { setKineticsMgr(contents); } - void setKineticsMgr(Kinetics& kin) { + void setKineticsMgr(Cantera::Kinetics& kin) { m_kin = &kin; if (m_kin->nReactions() == 0) disableChemistry(); } @@ -122,24 +122,24 @@ namespace CanteraZeroD { protected: - Kinetics* m_kin; + Cantera::Kinetics* m_kin; doublereal m_temp_atol; // tolerance on T doublereal m_maxstep; // max step size doublereal m_vdot, m_Q; - vector_fp m_atol; + Cantera::vector_fp m_atol; doublereal m_rtol; - vector_fp m_work; - vector_fp m_sdot; // surface production rates + Cantera::vector_fp m_work; + Cantera::vector_fp m_sdot; // surface production rates bool m_chem; bool m_energy; int m_nv; int m_nsens; - vector_int m_pnum; + Cantera::vector_int m_pnum; std::vector m_pname; - vector_int m_nsens_wall; - vector_fp m_mult_save; + Cantera::vector_int m_nsens_wall; + Cantera::vector_fp m_mult_save; private: }; diff --git a/Cantera/src/zeroD/ReactorBase.cpp b/Cantera/src/zeroD/ReactorBase.cpp index 9348e6d66..dc7693a31 100644 --- a/Cantera/src/zeroD/ReactorBase.cpp +++ b/Cantera/src/zeroD/ReactorBase.cpp @@ -19,6 +19,8 @@ #include "Wall.h" using namespace std; +using namespace Cantera; + namespace CanteraZeroD { ReactorBase::ReactorBase(string name) : m_nsp(0), diff --git a/Cantera/src/zeroD/ReactorBase.h b/Cantera/src/zeroD/ReactorBase.h index 047265478..008050bdb 100644 --- a/Cantera/src/zeroD/ReactorBase.h +++ b/Cantera/src/zeroD/ReactorBase.h @@ -20,8 +20,6 @@ #include "ThermoPhase.h" -using namespace Cantera; - /// Namespace for classes implementing zero-dimensional reactor networks. namespace CanteraZeroD { @@ -82,7 +80,7 @@ namespace CanteraZeroD { * a pointer to this substance is stored, and as the integration * proceeds, the state of the substance is modified. */ - void setThermoMgr(thermo_t& thermo); + void setThermoMgr(Cantera::thermo_t& thermo); void addInlet(FlowDevice& inlet); void addOutlet(FlowDevice& outlet); @@ -118,9 +116,9 @@ namespace CanteraZeroD { void resetState(); /// return a reference to the contents. - thermo_t& contents() { return *m_thermo; } + Cantera::thermo_t& contents() { return *m_thermo; } - const thermo_t& contents() const { return *m_thermo; } + const Cantera::thermo_t& contents() const { return *m_thermo; } doublereal residenceTime(); @@ -148,14 +146,14 @@ namespace CanteraZeroD { //@} int error(std::string msg) const { - writelog("Error: "+msg); + Cantera::writelog("Error: "+msg); return 1; } protected: int m_nsp; - thermo_t* m_thermo; + Cantera::thermo_t* m_thermo; doublereal m_time; doublereal m_vol, m_vol0; bool m_init; @@ -164,10 +162,10 @@ namespace CanteraZeroD { doublereal m_enthalpy; doublereal m_intEnergy; doublereal m_pressure; - vector_fp m_state; + Cantera::vector_fp m_state; std::vector m_inlet, m_outlet; std::vector m_wall; - vector_int m_lr; + Cantera::vector_int m_lr; int m_nwalls; std::string m_name; double m_rho0; @@ -175,7 +173,7 @@ namespace CanteraZeroD { private: void tilt(std::string method="") const { - throw CanteraError("ReactorBase::"+method, + throw Cantera::CanteraError("ReactorBase::"+method, "ReactorBase method called!"); } }; } diff --git a/Cantera/src/zeroD/ReactorFactory.cpp b/Cantera/src/zeroD/ReactorFactory.cpp index 3a07c12fa..541e5d0ad 100644 --- a/Cantera/src/zeroD/ReactorFactory.cpp +++ b/Cantera/src/zeroD/ReactorFactory.cpp @@ -64,7 +64,7 @@ namespace CanteraZeroD { case ConstPressureReactorType: return new ConstPressureReactor(); default: - throw CanteraError("ReactorFactory::newReactor", + throw Cantera::CanteraError("ReactorFactory::newReactor", "unknown reactor type!"); } return 0; diff --git a/Cantera/src/zeroD/ReactorFactory.h b/Cantera/src/zeroD/ReactorFactory.h index d1da8024f..e54d07380 100644 --- a/Cantera/src/zeroD/ReactorFactory.h +++ b/Cantera/src/zeroD/ReactorFactory.h @@ -24,7 +24,7 @@ namespace CanteraZeroD { - class ReactorFactory : FactoryBase { + class ReactorFactory : Cantera::FactoryBase { public: diff --git a/Cantera/src/zeroD/ReactorNet.cpp b/Cantera/src/zeroD/ReactorNet.cpp index 48a02776b..e1a9d3693 100644 --- a/Cantera/src/zeroD/ReactorNet.cpp +++ b/Cantera/src/zeroD/ReactorNet.cpp @@ -4,6 +4,7 @@ #include "Wall.h" using namespace std; +using namespace Cantera; namespace CanteraZeroD { diff --git a/Cantera/src/zeroD/ReactorNet.h b/Cantera/src/zeroD/ReactorNet.h index 021610a23..b4d33b847 100644 --- a/Cantera/src/zeroD/ReactorNet.h +++ b/Cantera/src/zeroD/ReactorNet.h @@ -101,7 +101,7 @@ namespace CanteraZeroD { void setVerbose(bool v = true) { m_verbose = v; } /// Return a reference to the integrator. - Integrator& integrator() { return *m_integ; } + Cantera::Integrator& integrator() { return *m_integ; } void updateState(doublereal* y); @@ -115,7 +115,7 @@ namespace CanteraZeroD { } void evalJacobian(doublereal t, doublereal* y, - doublereal* ydot, doublereal* p, Array2D* j); + doublereal* ydot, doublereal* p, Cantera::Array2D* j); //----------------------------------------------------- @@ -144,20 +144,20 @@ namespace CanteraZeroD { std::vector m_reactors; int m_nr; int m_nreactors; - Integrator* m_integ; + Cantera::Integrator* m_integ; doublereal m_time; bool m_init; int m_nv; - vector_int m_size; - vector_fp m_atol; + Cantera::vector_int m_size; + Cantera::vector_fp m_atol; doublereal m_rtol, m_rtolsens; doublereal m_atols, m_atolsens; doublereal m_maxstep; bool m_verbose; int m_ntotpar; - vector_int m_nparams; - vector_int m_connect; - vector_fp m_ydot; + Cantera::vector_int m_nparams; + Cantera::vector_int m_connect; + Cantera::vector_fp m_ydot; std::vector m_iown; diff --git a/Cantera/src/zeroD/Reservoir.h b/Cantera/src/zeroD/Reservoir.h index d60539df3..e7ec546fa 100644 --- a/Cantera/src/zeroD/Reservoir.h +++ b/Cantera/src/zeroD/Reservoir.h @@ -33,8 +33,8 @@ namespace CanteraZeroD { virtual void initialize(doublereal t0 = 0.0) {} virtual void advance(doublereal time) {m_time = time;} - void insert(ThermoPhase& contents) { - setThermoMgr(contents); + void insert(Cantera::ThermoPhase& contents) { + setThermoMgr(contents); } private: diff --git a/Cantera/src/zeroD/Wall.cpp b/Cantera/src/zeroD/Wall.cpp index 2cfd91e46..30cbf5bf4 100644 --- a/Cantera/src/zeroD/Wall.cpp +++ b/Cantera/src/zeroD/Wall.cpp @@ -9,6 +9,7 @@ using Cantera::Func1; using Cantera::Kinetics; using namespace std; +using namespace Cantera; namespace CanteraZeroD { diff --git a/Cantera/src/zeroD/Wall.h b/Cantera/src/zeroD/Wall.h index 4afeb4b3f..8a9c7e351 100644 --- a/Cantera/src/zeroD/Wall.h +++ b/Cantera/src/zeroD/Wall.h @@ -28,7 +28,6 @@ namespace Cantera { class Func1; class SurfPhase; } -//using namespace Cantera; namespace CanteraZeroD { From fc168e47ab796c6950391123f7322a0c1ecce556 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 20:52:35 +0000 Subject: [PATCH 342/446] Fixes due to namespace isues. --- Cantera/clib/src/ctfunc.cpp | 3 ++- Cantera/clib/src/ctreactor.cpp | 2 ++ Cantera/clib/src/ctxml.cpp | 1 + 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/Cantera/clib/src/ctfunc.cpp b/Cantera/clib/src/ctfunc.cpp index 8e7fd442a..646c4ba9e 100755 --- a/Cantera/clib/src/ctfunc.cpp +++ b/Cantera/clib/src/ctfunc.cpp @@ -17,10 +17,11 @@ #include "Func1.h" #include "ctexceptions.h" -using namespace Cantera; #include "Cabinet.h" +using namespace Cantera; +using namespace std; typedef Func1 func_t; diff --git a/Cantera/clib/src/ctreactor.cpp b/Cantera/clib/src/ctreactor.cpp index 0e8fff638..8b12ae5c2 100755 --- a/Cantera/clib/src/ctreactor.cpp +++ b/Cantera/clib/src/ctreactor.cpp @@ -27,6 +27,8 @@ #include "Storage.h" using namespace CanteraZeroD; +using namespace Cantera; +using namespace std; typedef ReactorBase reactor_t; typedef ReactorNet reactornet_t; diff --git a/Cantera/clib/src/ctxml.cpp b/Cantera/clib/src/ctxml.cpp index 57b237293..7c1049ebf 100644 --- a/Cantera/clib/src/ctxml.cpp +++ b/Cantera/clib/src/ctxml.cpp @@ -24,6 +24,7 @@ using namespace std; using namespace Cantera; +using namespace ctml; // Assign storage for the static member of the Templated Cabinet class From fc816aefb64017cfc2e9fb93f97c589136b5f65e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 21:00:26 +0000 Subject: [PATCH 343/446] Fixed namespace issues. --- Cantera/cxx/demos/kinetics1/example_utils.h | 19 ++++++++----------- Cantera/cxx/demos/kinetics1/kinetics1.cpp | 4 ++++ 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/Cantera/cxx/demos/kinetics1/example_utils.h b/Cantera/cxx/demos/kinetics1/example_utils.h index 59e62ef7d..a4697ae38 100644 --- a/Cantera/cxx/demos/kinetics1/example_utils.h +++ b/Cantera/cxx/demos/kinetics1/example_utils.h @@ -5,11 +5,8 @@ #include namespace Cantera{} -using namespace Cantera; namespace std{} -using namespace std; namespace CanteraZeroD{} -using namespace CanteraZeroD; // Save the temperature, density, pressure, and mole fractions at one // time @@ -48,18 +45,18 @@ void makeDataLabels(const G& gas, V& names) { } template -void plotSoln(string fname, string fmt, string title, const G& gas, const A& soln) { - vector names; +void plotSoln(std::string fname, std::string fmt, std::string title, const G& gas, const A& soln) { + std::vector names; makeDataLabels(gas, names); writePlotFile(fname, fmt, title, names, soln); } -inline void writeCanteraHeader(ostream& s) { - s << endl; - s << " Cantera version " << "CANTERA_VERSION" << endl; - s << " Copyright California Institute of Technology, 2002." << endl; - s << " http://www.cantera.org" << endl; - s << endl; +inline void writeCanteraHeader(std::ostream& s) { + s << std::endl; + s << " Cantera version " << "CANTERA_VERSION" << std::endl; + s << " Copyright California Institute of Technology, 2002." << std::endl; + s << " http://www.cantera.org" << std::endl; + s << std::endl; } #endif diff --git a/Cantera/cxx/demos/kinetics1/kinetics1.cpp b/Cantera/cxx/demos/kinetics1/kinetics1.cpp index b8e440838..08ad2e152 100644 --- a/Cantera/cxx/demos/kinetics1/kinetics1.cpp +++ b/Cantera/cxx/demos/kinetics1/kinetics1.cpp @@ -24,6 +24,10 @@ #include #include "example_utils.h" +using namespace std; +using namespace Cantera; +using namespace CanteraZeroD; +using namespace Cantera_CXX; int kinetics1(int np, void* p) { From 5d5138c677ec1239232f2bec52eae3bbd712face Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 21:05:22 +0000 Subject: [PATCH 344/446] Fixed namespace issues. --- examples/cxx/equil_example1.cpp | 2 ++ examples/cxx/example_utils.h | 20 +++++++++----------- examples/cxx/kinetics_example2.cpp | 2 ++ examples/cxx/kinetics_example3.cpp | 2 ++ examples/cxx/rxnpath_example1.cpp | 3 ++- examples/cxx/transport_example1.cpp | 2 ++ examples/cxx/transport_example2.cpp | 2 ++ 7 files changed, 21 insertions(+), 12 deletions(-) diff --git a/examples/cxx/equil_example1.cpp b/examples/cxx/equil_example1.cpp index d188be7f0..a3a414161 100755 --- a/examples/cxx/equil_example1.cpp +++ b/examples/cxx/equil_example1.cpp @@ -25,6 +25,8 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace CanteraZeroD; +using namespace std; //------------------------------------------------------------------- // utility functions for plotting diff --git a/examples/cxx/example_utils.h b/examples/cxx/example_utils.h index 2439816e1..9211aa94d 100755 --- a/examples/cxx/example_utils.h +++ b/examples/cxx/example_utils.h @@ -5,9 +5,7 @@ #include using namespace Cantera; -using namespace std; namespace CanteraZeroD{} -using namespace CanteraZeroD; // Save the temperature, density, pressure, and mole fractions at one // time @@ -47,22 +45,22 @@ void makeDataLabels(const G& gas, V& names) { } template -void plotSoln(string fname, string fmt, string title, const G& gas, const A& soln) { - vector names; +void plotSoln(std::string fname, std::string fmt, std::string title, const G& gas, const A& soln) { + std::vector names; makeDataLabels(gas, names); writePlotFile(fname, fmt, title, names, soln); } -inline void writeCanteraHeader(ostream& s) { - s << endl; +inline void writeCanteraHeader(std::ostream& s) { + s << std::endl; #ifdef CANTERA_VERSION - s << " Cantera version " << CANTERA_VERSION << endl; + s << " Cantera version " << CANTERA_VERSION << std::endl; #else - s << " ???" << endl; + s << " ???" << std::endl; #endif - s << " Copyright California Institute of Technology, 2002." << endl; - s << " http://www.cantera.org" << endl; - s << endl; + s << " Copyright California Institute of Technology, 2002." << std::endl; + s << " http://www.cantera.org" << std::endl; + s << std::endl; } #endif diff --git a/examples/cxx/kinetics_example2.cpp b/examples/cxx/kinetics_example2.cpp index 2aa5ee684..5e1c74770 100755 --- a/examples/cxx/kinetics_example2.cpp +++ b/examples/cxx/kinetics_example2.cpp @@ -24,6 +24,8 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace CanteraZeroD; +using namespace std; /** * Same as kinetics_example1, except that it uses class GRI30 instead * of class IdealGasMix. diff --git a/examples/cxx/kinetics_example3.cpp b/examples/cxx/kinetics_example3.cpp index ab2932cfb..f21973376 100644 --- a/examples/cxx/kinetics_example3.cpp +++ b/examples/cxx/kinetics_example3.cpp @@ -24,6 +24,8 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace std; +using namespace CanteraZeroD; // Kinetics example. This is written as a function so that one // driver program can run multiple examples. diff --git a/examples/cxx/rxnpath_example1.cpp b/examples/cxx/rxnpath_example1.cpp index 5ad7690ae..19cdc5777 100755 --- a/examples/cxx/rxnpath_example1.cpp +++ b/examples/cxx/rxnpath_example1.cpp @@ -24,9 +24,10 @@ #include // #include -// using namespace std; +using namespace std; using namespace Cantera; using namespace Cantera_CXX; +using namespace CanteraZeroD; void writeRxnPathDiagram(double time, ReactionPathBuilder& b, IdealGasMix& gas, ostream& logfile, ostream& outfile) { diff --git a/examples/cxx/transport_example1.cpp b/examples/cxx/transport_example1.cpp index d483c70b0..a349396e6 100755 --- a/examples/cxx/transport_example1.cpp +++ b/examples/cxx/transport_example1.cpp @@ -24,6 +24,8 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace CanteraZeroD; +using namespace std; template void makeTransportDataLabels(const G& gas, V& names) { diff --git a/examples/cxx/transport_example2.cpp b/examples/cxx/transport_example2.cpp index e5ac40030..da18303cb 100755 --- a/examples/cxx/transport_example2.cpp +++ b/examples/cxx/transport_example2.cpp @@ -25,6 +25,8 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace CanteraZeroD; +using namespace std; template void makeTransportDataLabels(const G& gas, V& names) { From 2abd551d7129ce02a4f880226cb90d7e8af39e6a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 28 Mar 2011 21:12:25 +0000 Subject: [PATCH 345/446] Took out all using namespace calls from headers. --- Cantera/clib/src/clib_defs.h | 2 -- Cantera/cxx/include/Cantera.h | 2 -- Cantera/cxx/include/Edge.h | 1 - Cantera/cxx/include/GRI30.h | 1 + Cantera/cxx/include/zerodim.h | 1 - Cantera/fortran/src/fct.cpp | 5 ++++- Cantera/fortran/src/fctxml.cpp | 1 + Cantera/fortran/src/flib_defs.h | 2 -- Cantera/matlab/cantera/private/ctmatutils.h | 5 ++--- Cantera/matlab/cantera/private/mllogger.h | 1 - Cantera/python/src/pylogger.h | 5 ++--- Cantera/src/equil/vcs_internal.h | 2 -- Cantera/src/kinetics/Group.h | 1 - Cantera/src/numerics/Func1.h | 1 - Cantera/src/oneD/boundaries1D.cpp | 8 ++++---- Cantera/src/transport/LTPspecies.cpp | 1 + Cantera/src/transport/LiquidTranInteraction.cpp | 2 +- Cantera/src/transport/SimpleTransport.cpp | 4 ++-- Cantera/src/transport/TransportFactory.cpp | 12 ++++++------ apps/bvp/BoundaryValueProblem.h | 2 -- examples/cxx/example_utils.h | 1 - ext/f2c_math/gmres.h | 1 - ext/math/gmres.h | 1 - 23 files changed, 24 insertions(+), 38 deletions(-) diff --git a/Cantera/clib/src/clib_defs.h b/Cantera/clib/src/clib_defs.h index f3fa601f7..7e89e7dc2 100755 --- a/Cantera/clib/src/clib_defs.h +++ b/Cantera/clib/src/clib_defs.h @@ -48,8 +48,6 @@ #endif namespace Cantera {} -//using namespace Cantera; namespace std {} -//using namespace std; #endif diff --git a/Cantera/cxx/include/Cantera.h b/Cantera/cxx/include/Cantera.h index 0093fe998..08dad4bb9 100755 --- a/Cantera/cxx/include/Cantera.h +++ b/Cantera/cxx/include/Cantera.h @@ -21,8 +21,6 @@ namespace Cantera_CXX{ } -using namespace Cantera_CXX; - #include "kernel/ct_defs.h" // some useful functions diff --git a/Cantera/cxx/include/Edge.h b/Cantera/cxx/include/Edge.h index 0ae5f8ba6..40eaa25e7 100644 --- a/Cantera/cxx/include/Edge.h +++ b/Cantera/cxx/include/Edge.h @@ -7,7 +7,6 @@ #include "kernel/EdgeKinetics.h" #include "kernel/importKinetics.h" -using namespace Cantera; namespace Cantera_CXX { class Edge : diff --git a/Cantera/cxx/include/GRI30.h b/Cantera/cxx/include/GRI30.h index 6bc28cb26..d11afede0 100644 --- a/Cantera/cxx/include/GRI30.h +++ b/Cantera/cxx/include/GRI30.h @@ -11,6 +11,7 @@ #include "kernel/importKinetics.h" #include "kernel/stringUtils.h" + namespace Cantera_CXX { /** diff --git a/Cantera/cxx/include/zerodim.h b/Cantera/cxx/include/zerodim.h index 168039815..fb32b807d 100644 --- a/Cantera/cxx/include/zerodim.h +++ b/Cantera/cxx/include/zerodim.h @@ -11,7 +11,6 @@ #include "kernel/FlowReactor.h" #include "kernel/ConstPressureReactor.h" -using namespace CanteraZeroD; #endif diff --git a/Cantera/fortran/src/fct.cpp b/Cantera/fortran/src/fct.cpp index cbfb0c84d..29f7a812a 100644 --- a/Cantera/fortran/src/fct.cpp +++ b/Cantera/fortran/src/fct.cpp @@ -30,6 +30,9 @@ #include "flib_defs.h" +using namespace Cantera; +using namespace std; + // Assert that there is storage // for the templated classes' static member // (needed to compile on solaris) @@ -39,7 +42,7 @@ inline XML_Node* _xml(const integer* n) { return Cabinet::cabinet()->item(*n); } -inline ThermoPhase* _fph(const integer* n) { +inline Cantera::ThermoPhase* _fph(const integer* n) { return th(*n); } diff --git a/Cantera/fortran/src/fctxml.cpp b/Cantera/fortran/src/fctxml.cpp index 93efbc8a3..246c187da 100644 --- a/Cantera/fortran/src/fctxml.cpp +++ b/Cantera/fortran/src/fctxml.cpp @@ -19,6 +19,7 @@ using namespace ctml; using namespace std; +using namespace Cantera; #include "../../clib/src/Cabinet.h" diff --git a/Cantera/fortran/src/flib_defs.h b/Cantera/fortran/src/flib_defs.h index 3da47e4a9..e879a2479 100644 --- a/Cantera/fortran/src/flib_defs.h +++ b/Cantera/fortran/src/flib_defs.h @@ -21,8 +21,6 @@ typedef integer status_t; namespace Cantera {} -using namespace Cantera; namespace std{} -using namespace std; #endif diff --git a/Cantera/matlab/cantera/private/ctmatutils.h b/Cantera/matlab/cantera/private/ctmatutils.h index ffabe9d40..17e4f3369 100755 --- a/Cantera/matlab/cantera/private/ctmatutils.h +++ b/Cantera/matlab/cantera/private/ctmatutils.h @@ -2,7 +2,6 @@ const double Undef = -999.123; //const double DERR = -999.999; #include -using namespace std; void reportError(); @@ -24,13 +23,13 @@ inline char* getString(const mxArray* p) { int m = mxGetM(p); int n = mxGetN(p); int buflen = m*n + 1; - string msg; + std::string msg; if (m == 1) { input_buf = (char*)mxCalloc(buflen, sizeof(char)); status = mxGetString(p, input_buf, buflen); if(status != 0) { - msg = string(input_buf) + msg = std::string(input_buf) + "\nNot enough space. String is truncated."; mexWarnMsgTxt(msg.c_str()); } diff --git a/Cantera/matlab/cantera/private/mllogger.h b/Cantera/matlab/cantera/private/mllogger.h index 30d0e2dd3..94844c42a 100644 --- a/Cantera/matlab/cantera/private/mllogger.h +++ b/Cantera/matlab/cantera/private/mllogger.h @@ -13,7 +13,6 @@ #include "cantera/kernel/logger.h" #include -//using namespace std; static std::string ss = "disp(' "; diff --git a/Cantera/python/src/pylogger.h b/Cantera/python/src/pylogger.h index 9a84139cb..a60ac2447 100644 --- a/Cantera/python/src/pylogger.h +++ b/Cantera/python/src/pylogger.h @@ -5,7 +5,6 @@ #include #include "cantera/kernel/logger.h" -using namespace std; static std::string ss = "print \"\"\" "; @@ -18,7 +17,7 @@ namespace Cantera { Py_Logger() {} virtual ~Py_Logger() {} - virtual void write(const string& s) { + virtual void write(const std::string& s) { char ch = s[0]; int n = 0; while (ch != '\0') { @@ -35,7 +34,7 @@ namespace Cantera { } virtual void error(const std::string& msg) { - string err = "raise \""+msg+"\""; + std::string err = "raise \""+msg+"\""; PyRun_SimpleString((char *)err.c_str()); } diff --git a/Cantera/src/equil/vcs_internal.h b/Cantera/src/equil/vcs_internal.h index b816240e2..b3d87bbf7 100644 --- a/Cantera/src/equil/vcs_internal.h +++ b/Cantera/src/equil/vcs_internal.h @@ -249,8 +249,6 @@ namespace VCSnonideal { #include "Cantera.h" #include "kernel/vcs_internal.h" - using namespace Cantera; - using namespace VCSnonideal; const double g_cgs = 980.; const double mass_cyl = 0.066; diff --git a/Cantera/src/kinetics/Group.h b/Cantera/src/kinetics/Group.h index 82e13b74f..cf44e475c 100644 --- a/Cantera/src/kinetics/Group.h +++ b/Cantera/src/kinetics/Group.h @@ -14,7 +14,6 @@ #include "ct_defs.h" -//using namespace std; namespace Cantera { /** diff --git a/Cantera/src/numerics/Func1.h b/Cantera/src/numerics/Func1.h index fa3e6b23f..e91263101 100644 --- a/Cantera/src/numerics/Func1.h +++ b/Cantera/src/numerics/Func1.h @@ -23,7 +23,6 @@ #include #include -using namespace std; namespace Cantera { diff --git a/Cantera/src/oneD/boundaries1D.cpp b/Cantera/src/oneD/boundaries1D.cpp index cfe591a33..b87ab2e79 100644 --- a/Cantera/src/oneD/boundaries1D.cpp +++ b/Cantera/src/oneD/boundaries1D.cpp @@ -262,8 +262,8 @@ namespace Cantera { restore(const XML_Node& dom, doublereal* soln) { //map x; //getFloats(dom, x); - soln[0] = getFloat(dom, "mdot", "massflowrate"); // x["mdot"]; - soln[1] = getFloat(dom, "temperature", "temperature"); // x["temperature"]; + soln[0] = ctml::getFloat(dom, "mdot", "massflowrate"); // x["mdot"]; + soln[1] = ctml::getFloat(dom, "temperature", "temperature"); // x["temperature"]; resize(2,1); } @@ -726,7 +726,7 @@ namespace Cantera { void Surf1D:: restore(const XML_Node& dom, doublereal* soln) { map x; - getFloats(dom, x); + ctml::getFloats(dom, x); soln[0] = x["temperature"]; resize(1,1); } @@ -886,7 +886,7 @@ namespace Cantera { void ReactingSurf1D:: restore(const XML_Node& dom, doublereal* soln) { map x; - getFloats(dom, x); + ctml::getFloats(dom, x); soln[0] = x["temperature"]; resize(1,1); } diff --git a/Cantera/src/transport/LTPspecies.cpp b/Cantera/src/transport/LTPspecies.cpp index 74ce83edb..7fa8b4cb7 100644 --- a/Cantera/src/transport/LTPspecies.cpp +++ b/Cantera/src/transport/LTPspecies.cpp @@ -13,6 +13,7 @@ */ #include "LTPspecies.h" using namespace std; +using namespace ctml; namespace Cantera { //==================================================================================================================== diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp index f6c0ae203..7d52b2127 100644 --- a/Cantera/src/transport/LiquidTranInteraction.cpp +++ b/Cantera/src/transport/LiquidTranInteraction.cpp @@ -15,7 +15,7 @@ #include "MargulesVPSSTP.h" #include using namespace std; - +using namespace ctml; namespace Cantera { diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index 405baedee..6c9b62c64 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -210,8 +210,8 @@ namespace Cantera { * */ std::string modelName = ""; - if (getOptionalModel(transportNode, "compositionDependence", - modelName)) { + if (ctml::getOptionalModel(transportNode, "compositionDependence", + modelName)) { modelName = lowercase(modelName); if (modelName == "solvent_only") { compositionDepType_ = 0; diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp index 8162bdec5..0b82466a8 100644 --- a/Cantera/src/transport/TransportFactory.cpp +++ b/Cantera/src/transport/TransportFactory.cpp @@ -867,15 +867,15 @@ namespace Cantera { // child are skipped, instead of throwing an exception. try { XML_Node& tr = sp.child("transport"); - getString(tr, "geometry", val, type); + ctml::getString(tr, "geometry", val, type); geom = gindx[val] - 100; map fv; - welldepth = getFloat(tr, "LJ_welldepth"); - diam = getFloat(tr, "LJ_diameter"); - dipole = getFloat(tr, "dipoleMoment"); - polar = getFloat(tr, "polarizability"); - rot = getFloat(tr, "rotRelax"); + welldepth = ctml::getFloat(tr, "LJ_welldepth"); + diam = ctml::getFloat(tr, "LJ_diameter"); + dipole = ctml::getFloat(tr, "dipoleMoment"); + polar = ctml::getFloat(tr, "polarizability"); + rot = ctml::getFloat(tr, "rotRelax"); GasTransportData data; data.speciesName = name; diff --git a/apps/bvp/BoundaryValueProblem.h b/apps/bvp/BoundaryValueProblem.h index 106aabc4b..dc000fb91 100644 --- a/apps/bvp/BoundaryValueProblem.h +++ b/apps/bvp/BoundaryValueProblem.h @@ -7,8 +7,6 @@ #include #include -using namespace Cantera; -using namespace std; /// Namespace for the boundary value problem package. namespace BVP { diff --git a/examples/cxx/example_utils.h b/examples/cxx/example_utils.h index 9211aa94d..f9b529c43 100755 --- a/examples/cxx/example_utils.h +++ b/examples/cxx/example_utils.h @@ -4,7 +4,6 @@ #include #include -using namespace Cantera; namespace CanteraZeroD{} // Save the temperature, density, pressure, and mole fractions at one diff --git a/ext/f2c_math/gmres.h b/ext/f2c_math/gmres.h index 1f6a044d5..8bde197c2 100644 --- a/ext/f2c_math/gmres.h +++ b/ext/f2c_math/gmres.h @@ -33,7 +33,6 @@ gmres( int m, int N, const Matrix &A, const doublereal *b, doublereal *x, double #include "cblas.h" #include "../../Cantera/src/ctlapack.h" -using namespace Cantera; template< class Matrix > inline int diff --git a/ext/math/gmres.h b/ext/math/gmres.h index 1f6a044d5..8bde197c2 100755 --- a/ext/math/gmres.h +++ b/ext/math/gmres.h @@ -33,7 +33,6 @@ gmres( int m, int N, const Matrix &A, const doublereal *b, doublereal *x, double #include "cblas.h" #include "../../Cantera/src/ctlapack.h" -using namespace Cantera; template< class Matrix > inline int From 0d33823d9ea838df9e6d908ad018e1fd01168d72 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 29 Mar 2011 15:17:42 +0000 Subject: [PATCH 346/446] Reblessed this test --- test_problems/min_python/negATest/negATest_blessed.out | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test_problems/min_python/negATest/negATest_blessed.out b/test_problems/min_python/negATest/negATest_blessed.out index e63158035..d170960c3 100644 --- a/test_problems/min_python/negATest/negATest_blessed.out +++ b/test_problems/min_python/negATest/negATest_blessed.out @@ -1,7 +1,7 @@ Number of species = 12 Number of reactions = 12 rop [ 0:O ] = 0.447058 -rop [ 1:O2 ] = -0.00214428 +rop [ 1:O2 ] = -0.0021443 rop [ 2:N ] = 0 rop [ 3:NO ] = -279.361 rop [ 4:NO2 ] = 0.00214319 @@ -17,7 +17,7 @@ fwd_rop[ 0] = 479.304 rev_rop[ 0] = 97.94 fwd_rop[ 1] = -128.201 rev_rop[ 1] = -26.1964 fwd_rop[ 2] = 0 rev_rop[ 2] = 0 fwd_rop[ 3] = -0 rev_rop[ 3] = -0 -fwd_rop[ 4] = 0 rev_rop[ 4] = 1.08891e-06 +fwd_rop[ 4] = 0 rev_rop[ 4] = 1.10334e-06 fwd_rop[ 5] = 0 rev_rop[ 5] = 0 fwd_rop[ 6] = 0 rev_rop[ 6] = 0 fwd_rop[ 7] = 0 rev_rop[ 7] = 0 From 3994bb9438b503bb5d83032ca748ff9d9e32760e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 4 Apr 2011 23:01:42 +0000 Subject: [PATCH 347/446] Started an ifdef block for intermediate zeroed phases in kinetics objects. --- Cantera/src/kinetics/InterfaceKinetics.cpp | 34 ++++++++++++++++++++-- Cantera/src/kinetics/InterfaceKinetics.h | 31 ++++++++++++++++++++ config.h.in | 4 +++ configure | 20 ++++++++++--- configure.in | 8 +++++ preconfig | 5 ++++ 6 files changed, 96 insertions(+), 6 deletions(-) diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp index 775839fc0..63325fae7 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.cpp +++ b/Cantera/src/kinetics/InterfaceKinetics.cpp @@ -795,6 +795,36 @@ namespace Cantera { m_kdata->m_ROP_ok = true; } +#ifdef KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES + //================================================================================================= + InterfaceKinetics::adjustRatesForIntermediatePhases() { + doublereal sFac = 1.0; + + array_fp& ropf = m_kdata->m_ropf; + array_fp& ropr = m_kdata->m_ropr; + array_fp& ropnet = m_kdata->m_ropnet; + + getCreatingRates(DATA_PTR(m_speciestmpP)); + getDestructionRates(DATA_PTR(m_speciestmpD)); + + for (iphase = 0; iphase < nphases; iphase++) { + if (m_intermediatePhases(iphase)) { + for (isp = 0; isp < nspecies; isp++) { + if (m_speciesTmpD[ispI] > m_speciesTmpP[I]) { + sFac = m_speciesTmpD[ispI]/ m_speciesTmpP[I]; + } + // Loop over reactions that are reactants for the species in the phase + // reducing their rates. + + + } + } + + } + + } +#endif + //================================================================================================= //================================================================================================= /* * @@ -1303,7 +1333,7 @@ namespace Cantera { m_finalized = true; } - + //================================================================================================ doublereal InterfaceKinetics::electrochem_beta(int irxn) const{ int n = m_ctrxn.size(); for (int i = 0; i < n; i++) { @@ -1314,7 +1344,7 @@ namespace Cantera { return 0.0; } - + //================================================================================================ bool InterfaceKinetics::ready() const { return (m_finalized); } diff --git a/Cantera/src/kinetics/InterfaceKinetics.h b/Cantera/src/kinetics/InterfaceKinetics.h index 23a62928c..a7011237c 100644 --- a/Cantera/src/kinetics/InterfaceKinetics.h +++ b/Cantera/src/kinetics/InterfaceKinetics.h @@ -783,6 +783,7 @@ namespace Cantera { //! Vector of raw activation energies for the reactions /*! * units are in Kelvin + * Length is number of reactions. */ vector_fp m_E; @@ -896,6 +897,36 @@ namespace Cantera { */ std::vector m_rxnPhaseIsProduct; +#ifdef KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES + //! Vector of ints indicating whether zeroed phase is an intermediate for + //! the formation of another phase + /*! + * If a phase is zeroed out but it is an intermediate, then the phase + * can be formed whether it is stable or not, but the destruction rate of + * species in that phase can't exceed the formation rate for species in that + * phase. + * + * length = number of phases in the object + * By default all phases are not intermediates + */ + std::vector m_phaseIsIntermediate; + int m_numIntermediatePhases; + + //! Reaction rate reduction factor for intermediates + /*! + * Individual reaction rates are reduced to accommodate the requirements of intermediate + * zero phases. + * + * length = number of reactions in the object + * By default all phases are not intermediates + */ + std::vector m_rxnRateFactorPhaseIntermediates; + + //! Work vector having length number of species + std::vector m_speciesTmpP; + std::vector m_speciesTmpD; +#endif + int m_ioFlag; private: diff --git a/config.h.in b/config.h.in index c7a867245..767d95361 100755 --- a/config.h.in +++ b/config.h.in @@ -189,6 +189,10 @@ typedef int ftnlen; // Fortran hidden string length type // accessed by specifying the solver=2 option #undef WITH_VCSNONIDEAL +// Enable intermediate zeroed phases to be included in the +// interfacial kinetics operator +#undef KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES + //-------------- Optional Cantera Capabilities ---------------------- // Enable sensitivity analysis via changing H298 directly diff --git a/configure b/configure index 3d376dd60..c746849d0 100755 --- a/configure +++ b/configure @@ -308,7 +308,7 @@ ac_includes_default="\ # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' +ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' ac_subst_files='' # Initialize some variables set by options. @@ -2749,6 +2749,17 @@ fi +COMPILE_INTERMEDIATE_ZEROED_KINETICS=0 +if test "$KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS" = "y"; then + cat >>confdefs.h <<\_ACEOF +#define KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS 1 +_ACEOF + + COMPILE_INTERMEDIATE_ZEROED_KINETICS=1 +fi + + + if test "$WITH_HTML_LOG_FILES" = "y"; then cat >>confdefs.h <<\_ACEOF #define WITH_HTML_LOGS 1 @@ -10047,7 +10058,7 @@ fi # Provide some information about the compiler. -echo "$as_me:10050:" \ +echo "$as_me:10061:" \ "checking for Fortran 77 compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 @@ -10254,7 +10265,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10257: \"$ac_link\") >&5 +(eval echo $as_me:10268: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10332,7 +10343,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10335: \"$ac_link\") >&5 +(eval echo $as_me:10346: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -11635,6 +11646,7 @@ s,@BUILD_CK@,$BUILD_CK,;t t s,@LIB_DIR@,$LIB_DIR,;t t s,@COMPILE_VCSNONIDEAL@,$COMPILE_VCSNONIDEAL,;t t s,@COMPILE_H298MODIFY_CAPABILITY@,$COMPILE_H298MODIFY_CAPABILITY,;t t +s,@COMPILE_INTERMEDIATE_ZEROED_KINETICS@,$COMPILE_INTERMEDIATE_ZEROED_KINETICS,;t t s,@BOOST_INCLUDE@,$BOOST_INCLUDE,;t t s,@BOOST_LIB@,$BOOST_LIB,;t t s,@PURIFY@,$PURIFY,;t t diff --git a/configure.in b/configure.in index 3c2b34d1f..5afbb896b 100755 --- a/configure.in +++ b/configure.in @@ -617,6 +617,14 @@ fi AC_SUBST(COMPILE_H298MODIFY_CAPABILITY) +COMPILE_INTERMEDIATE_ZEROED_KINETICS=0 +if test "$KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS" = "y"; then + AC_DEFINE(KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS) + COMPILE_INTERMEDIATE_ZEROED_KINETICS=1 +fi +AC_SUBST(COMPILE_INTERMEDIATE_ZEROED_KINETICS) + + if test "$WITH_HTML_LOG_FILES" = "y"; then AC_DEFINE(WITH_HTML_LOGS) fi diff --git a/preconfig b/preconfig index b6ef3e80f..98b6f9f3a 100755 --- a/preconfig +++ b/preconfig @@ -238,6 +238,11 @@ WITH_PRIME=${WITH_PRIME:="n"} # to have a value of "y" WITH_H298MODIFY_CAPABILITY=${WITH_H298MODIFY_CAPABILITY:="n"} +# Capability in the planning and implementation stage +# Phases may be intermediates but actually have zero mole numbers +# in the InterfacialKinetics object +KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES=${KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES:="n'} + ###################################################################### # if set to 'y', the ck2cti program that converts Chemkin input files # to Cantera format will be built. If you don't use Chemkin format From fa30f630569631b6c3005ff9d5b3a3ab0e261c88 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 6 Apr 2011 15:40:04 +0000 Subject: [PATCH 348/446] Added QR factorization algorithms to Cantera's fortran interface within the numerics directory. --- Cantera/src/numerics/SquareMatrix.cpp | 42 ++++++++-- Cantera/src/numerics/SquareMatrix.h | 14 +++- Cantera/src/numerics/ctlapack.h | 112 ++++++++++++++++++++++++-- 3 files changed, 153 insertions(+), 15 deletions(-) diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 2dc7fc274..d93f55cd7 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -32,7 +32,7 @@ namespace Cantera { //==================================================================================================================== SquareMatrix::SquareMatrix() : DenseMatrix(), - m_factored(false) + m_factored(0) { } @@ -46,7 +46,7 @@ namespace Cantera { */ SquareMatrix::SquareMatrix(int n, doublereal v) : DenseMatrix(n, n, v), - m_factored(false) + m_factored(0) { } @@ -128,7 +128,7 @@ namespace Cantera { int SquareMatrix::factor() { integer n = static_cast(nRows()); int info=0; - m_factored = true; + m_factored = 1; ct_dgetrf(n, n, &(*(begin())), static_cast(nRows()), DATA_PTR(ipiv()), info); if (info != 0) { @@ -141,17 +141,47 @@ namespace Cantera { } return info; } + //===================================================================================================================== /* * clear the factored flag */ void SquareMatrix::clearFactorFlag() { - m_factored = false; + m_factored = 0; } - /** + //===================================================================================================================== + /* * set the factored flag */ void SquareMatrix::setFactorFlag() { - m_factored = true; + m_factored = 1; } + //===================================================================================================================== + int SquareMatrix::factorQR() { + if ((int) tau.size() < m_nrows) { + tau.resize(m_nrows, 0.0); + work.resize(9 * m_nrows, 0.0); + } + int info; + int lwork = work.size(); + ct_dgeqrf(m_nrows, m_nrows, &(*(begin())), m_nrows, DATA_PTR(tau), DATA_PTR(work), lwork, info); + if (info != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::factorQR(): DGEQRF returned INFO = %d\n", info); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::factorQR()", "DGEQRF returned INFO = " + int2str(info)); + } + } + int lworkOpt = work[0]; + if (lworkOpt != lwork) { + work.resize(lworkOpt); + } + return info; + } + //===================================================================================================================== + + + + } diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index a110e6a77..79f77ec08 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -77,6 +77,15 @@ namespace Cantera { * boolean to indicate that the matrix is now A-1. */ int factor(); + + //! Factors the A matrix using the QR algorithm, overwriting A + /*! + * we set m_factored to 2 to indicate the matrix is now QR factored + * + * @return Returns the info variable from lapack + */ + int factorQR(); + /** * clear the factored flag */ @@ -89,7 +98,10 @@ namespace Cantera { /* * the factor flag */ - bool m_factored; + int m_factored; + + vector_fp tau; + vector_fp work; }; } diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index 0b5a6da3a..fc50dfcab 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -35,6 +35,9 @@ #define _DSCAL_ dscal +#define _DGEQRF_ dgeqrf +#define _DORMQR_ dormqr + #else #define _DGEMV_ dgemv_ @@ -48,14 +51,21 @@ #define _DSCAL_ dscal_ +#define _DGEQRF_ dgreqrf_ +#define _DORMQR_ dormqr_ + #endif namespace ctlapack { typedef enum {Transpose = 1, NoTranspose = 0} transpose_t; typedef enum {ColMajor = 1, RowMajor = 0} storage_t; + typedef enum {UpperTriangular = 0, LowerTriangular = 1} upperlower_t; + typedef enum {Left = 0, Right = 1} side_t; } const char no_yes[2] = {'N', 'T'}; +const char upper_lower[2] = {'U', 'L'}; +const char left_right[2] = {'L', 'R'}; #ifdef USE_CBLAS #include @@ -129,7 +139,36 @@ extern "C" { #endif int _DSCAL_(integer *n, doublereal *da, doublereal *dx, integer *incx); -void cblas_dscal(const int N, const double alpha, double *X, const int incX); + void cblas_dscal(const int N, const double alpha, double *X, const int incX); + + + int _DGEQRF_(const integer* m, const integer* n, doublereal* a, const integer* lda, + doublereal* tau, doublereal* work, const integer *lwork, integer *info); + +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DORMQR_(const char* side, const char* trans, const integer* m, const integer* n, + const integer * k, doublereal* a, const integer* lda, + doublereal* tau, doublereal* c, const integer* ldc, + doublereal* work, const integer *lwork, integer *info, ftnlen sisize, ftnlen trsize); +#else + int _DORMQR_(const char* side, ftnlen sisize, const char* trans, ftnlen trsize, const integer* m, + const integer* n, const integer * k, doublereal* a, const integer* lda, + doublereal* tau,doublereal* c, const integer* ldc, + doublereal* work, const integer *lwork, integer *info); +#endif + +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DTRTRS_(const char* uplo, const char* trans, const char *diag, const integer* n, + const integer * nrhs, doublereal* a, const integer* lda, + doublereal* b, const integer* ldb, integer *info, + ftnlen upsize, ftnlen trsize, ftnlen disize); +#else + int _DTRTRS_(const char* uplo, ftnlen upsize, const char* trans, ftnlen trsize, const char *diag, + ftnlen disize, const integer* n, const integer * nrhs, doublereal* a, const integer* lda, + doublereal* b, const integer* ldb, integer *info); +#endif + + } //#endif @@ -230,11 +269,9 @@ namespace Cantera { #else ftnlen trsize = 1; #ifdef LAPACK_FTN_STRING_LEN_AT_END - _DGETRS_(&tr, &f_n, &f_nrhs, a, &f_lda, ipiv, b, &f_ldb, - &f_info, trsize); + _DGETRS_(&tr, &f_n, &f_nrhs, a, &f_lda, ipiv, b, &f_ldb, &f_info, trsize); #else - _DGETRS_(&tr, trsize, &f_n, &f_nrhs, a, &f_lda, ipiv, b, &f_ldb, - &f_info); + _DGETRS_(&tr, trsize, &f_n, &f_nrhs, a, &f_lda, ipiv, b, &f_ldb, &f_info); #endif #endif info = f_info; @@ -260,13 +297,72 @@ namespace Cantera { rank = f_rank; } - inline void ct_dscal(int n, doublereal da, doublereal* dx, int incx) { + inline void ct_dscal(int n, doublereal da, doublereal* dx, int incx) { //integer f_n = n, f_incx = incx; //_DSCAL_(&f_n, &da, dx, &f_incx); - cblas_dscal(n, da, dx, incx); + cblas_dscal(n, da, dx, incx); + } + inline void ct_dgeqrf(int m, int n, doublereal* a, int lda, doublereal *tau, + doublereal* work, int lwork, int &info) { + integer f_m = m; + integer f_n = n; + integer f_lda = lda; + integer f_lwork = lwork; + integer f_info = info; + _DGEQRF_(&f_m, &f_n, a, &f_lda, tau, work, &f_lwork, &f_info); + info = f_info; + } + + inline void ct_dormqr(ctlapack::side_t rlside, ctlapack::transpose_t trans, int m, + int n, int k, doublereal* a, int lda, doublereal *tau, doublereal *c, int ldc, + doublereal *work, const integer *lwork, int &info) { + char side = left_right[rlside]; + char tr = no_yes[trans]; + integer f_m = m; + integer f_n = n; + integer f_k = k; + integer f_lda = lda; + integer f_ldc = ldc; + integer f_info = info; +#ifdef NO_FTN_STRING_LEN_AT_END + _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info, trsize, trsize); +#else + _DORMQR_(&side, trsize, &tr, trsize, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info); +#endif +#endif + info = f_info; + } + + inline void ct_dtrtrs(ctlapack::upperlower_t uplot, ctlapack::transpose_t trans, const char *diag, + int n, int nrhs, doublereal* a, int lda, doublereal *b, int ldb, int &info) { + char uplo = upper_lower[uplot]; + char tr = no_yes[trans]; + char dd = 'N'; + if (diag) { + dd = diag[0]; } - + integer f_n = n; + integer f_nrhs = nrhs; + integer f_lda = lda; + integer f_ldb = ldb; + integer f_info = info; +#ifdef NO_FTN_STRING_LEN_AT_END + _DTRTRS_(&uplo, &tr, &dd, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DTRTRS_(&uplo, &tr, &dd, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info, trsize, trsize, trsize); +#else + _DTRTRS_(&uplo, trsize, &tr, trsize, &dd, trsize, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info); +#endif +#endif + info = f_info; + } } From 68768e56e7834e6eb552a35026045d3ed35415b2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 6 Apr 2011 16:26:32 +0000 Subject: [PATCH 349/446] Another iteration to get the QR solve up to speed --- Cantera/src/numerics/SquareMatrix.cpp | 56 +++++++++++++++++++++++++++ Cantera/src/numerics/SquareMatrix.h | 7 ++++ Cantera/src/numerics/ctlapack.h | 9 +++-- 3 files changed, 68 insertions(+), 4 deletions(-) diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index d93f55cd7..8ecc08972 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -179,6 +179,62 @@ namespace Cantera { return info; } //===================================================================================================================== + /* + * Solve Ax = b. Vector b is overwritten on exit with x. + */ + int SquareMatrix::solveQR(double* b) + { + int info=0; + /* + * Check to see whether the matrix has been factored. + */ + if (!m_factored) { + int retn = factorQR(); + if (retn) { + return retn; + } + } + + int lwork = work.size(); + if (lwork < m_nrows) { + work.resize(8 * m_nrows, 0.0); + lwork = 8 * m_nrows; + } + + /* + * Solve the factored system + */ + ct_dormqr(ctlapack::Left, ctlapack::Transpose, m_nrows, 1, m_nrows, &(*(begin())), m_nrows, DATA_PTR(tau), b, m_nrows, + DATA_PTR(work), lwork, info); + if (info != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::solveQR(): DORMQR returned INFO = %d\n", info); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::solveQR()", "DORMQR returned INFO = " + int2str(info)); + } + } + int lworkOpt = work[0]; + if (lworkOpt <= lwork) { + work.resize(lworkOpt); + } + + char dd = 'N'; + + ct_dtrtrs(ctlapack::UpperTriangular, ctlapack::NoTranspose, &dd, m_nrows, 1, &(*(begin())), m_nrows, b, + m_nrows, info); + if (info != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::solveQR(): DTRTRS returned INFO = %d\n", info); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::solveQR()", "DTRTRS returned INFO = " + int2str(info)); + } + } + + return info; + } + //===================================================================================================================== diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index 79f77ec08..c8dac8895 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -86,6 +86,13 @@ namespace Cantera { */ int factorQR(); + //! Solves the linear problem Ax=b using the QR algorithm + //! returning x in the b spot + /*! + * @param b RHS to be solved. + */ + int solveQR(doublereal *b); + /** * clear the factored flag */ diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index fc50dfcab..28afaa25d 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -316,23 +316,24 @@ namespace Cantera { inline void ct_dormqr(ctlapack::side_t rlside, ctlapack::transpose_t trans, int m, int n, int k, doublereal* a, int lda, doublereal *tau, doublereal *c, int ldc, - doublereal *work, const integer *lwork, int &info) { + doublereal *work, int lwork, int &info) { char side = left_right[rlside]; char tr = no_yes[trans]; integer f_m = m; integer f_n = n; integer f_k = k; + integer f_lwork = lwork; integer f_lda = lda; integer f_ldc = ldc; integer f_info = info; #ifdef NO_FTN_STRING_LEN_AT_END - _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info); + _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, &f_lwork, &f_info); #else ftnlen trsize = 1; #ifdef LAPACK_FTN_STRING_LEN_AT_END - _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info, trsize, trsize); + _DORMQR_(&side, &tr, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, &f_lwork, &f_info, trsize, trsize); #else - _DORMQR_(&side, trsize, &tr, trsize, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, lwork, &f_info); + _DORMQR_(&side, trsize, &tr, trsize, &f_m, &f_n, &f_k, a, &f_lda, tau, c, &f_ldc, work, &f_lwork, &f_info); #endif #endif info = f_info; From 7d4222eedf4c2f5f3ce9d110019ce36a321c0b04 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 6 Apr 2011 23:38:14 +0000 Subject: [PATCH 350/446] Fixed errors that were preventing linking. --- Cantera/src/numerics/ctlapack.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index 28afaa25d..3b160184b 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -37,6 +37,7 @@ #define _DGEQRF_ dgeqrf #define _DORMQR_ dormqr +#define _DTRTRS_ dtrtrs #else @@ -51,8 +52,9 @@ #define _DSCAL_ dscal_ -#define _DGEQRF_ dgreqrf_ +#define _DGEQRF_ dgeqrf_ #define _DORMQR_ dormqr_ +#define _DTRTRS_ dtrtrs_ #endif From 62af5826eac61e30146b6df13fb56868c8c1517f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 7 Apr 2011 15:58:01 +0000 Subject: [PATCH 351/446] Added a lapack routine --- ext/f2c_lapack/Makefile.in | 1 + ext/f2c_lapack/dlantr.c | 401 +++++++++++++++++++++++++++++++++++++ ext/lapack/Makefile.in | 1 + ext/lapack/dlantr.f | 277 +++++++++++++++++++++++++ 4 files changed, 680 insertions(+) create mode 100644 ext/f2c_lapack/dlantr.c create mode 100644 ext/lapack/dlantr.f diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 68dff0ce8..16b3add23 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -67,6 +67,7 @@ dlabrd.o \ dlacpy.o \ dlamch.o \ dlange.o \ +dlangtr.o \ dlapy2.o \ dlarf.o \ dlarfb.o \ diff --git a/ext/f2c_lapack/dlantr.c b/ext/f2c_lapack/dlantr.c new file mode 100644 index 000000000..17a0e0724 --- /dev/null +++ b/ext/f2c_lapack/dlantr.c @@ -0,0 +1,401 @@ +/* dlantr.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; + +doublereal dlantr_(char *norm, char *uplo, char *diag, integer *m, integer *n, + doublereal *a, integer *lda, doublereal *work, ftnlen norm_len, + ftnlen uplo_len, ftnlen diag_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1, i__2, i__3, i__4; + doublereal ret_val, d__1, d__2, d__3; + + /* Builtin functions */ + double sqrt(doublereal); + + /* Local variables */ + static integer i__, j; + static doublereal sum, scale; + static logical udiag; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + static doublereal value; + extern /* Subroutine */ int dlassq_(integer *, doublereal *, integer *, + doublereal *, doublereal *); + + +/* -- LAPACK auxiliary routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* October 31, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DLANTR returns the value of the one norm, or the Frobenius norm, or */ +/* the infinity norm, or the element of largest absolute value of a */ +/* trapezoidal or triangular matrix A. */ + +/* Description */ +/* =========== */ + +/* DLANTR returns the value */ + +/* DLANTR = ( max(abs(A(i,j))), NORM = 'M' or 'm' */ +/* ( */ +/* ( norm1(A), NORM = '1', 'O' or 'o' */ +/* ( */ +/* ( normI(A), NORM = 'I' or 'i' */ +/* ( */ +/* ( normF(A), NORM = 'F', 'f', 'E' or 'e' */ + +/* where norm1 denotes the one norm of a matrix (maximum column sum), */ +/* normI denotes the infinity norm of a matrix (maximum row sum) and */ +/* normF denotes the Frobenius norm of a matrix (square root of sum of */ +/* squares). Note that max(abs(A(i,j))) is not a matrix norm. */ + +/* Arguments */ +/* ========= */ + +/* NORM (input) CHARACTER*1 */ +/* Specifies the value to be returned in DLANTR as described */ +/* above. */ + +/* UPLO (input) CHARACTER*1 */ +/* Specifies whether the matrix A is upper or lower trapezoidal. */ +/* = 'U': Upper trapezoidal */ +/* = 'L': Lower trapezoidal */ +/* Note that A is triangular instead of trapezoidal if M = N. */ + +/* DIAG (input) CHARACTER*1 */ +/* Specifies whether or not the matrix A has unit diagonal. */ +/* = 'N': Non-unit diagonal */ +/* = 'U': Unit diagonal */ + +/* M (input) INTEGER */ +/* The number of rows of the matrix A. M >= 0, and if */ +/* UPLO = 'U', M <= N. When M = 0, DLANTR is set to zero. */ + +/* N (input) INTEGER */ +/* The number of columns of the matrix A. N >= 0, and if */ +/* UPLO = 'L', N <= M. When N = 0, DLANTR is set to zero. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The trapezoidal matrix A (A is triangular if M = N). */ +/* If UPLO = 'U', the leading m by n upper trapezoidal part of */ +/* the array A contains the upper trapezoidal matrix, and the */ +/* strictly lower triangular part of A is not referenced. */ +/* If UPLO = 'L', the leading m by n lower trapezoidal part of */ +/* the array A contains the lower trapezoidal matrix, and the */ +/* strictly upper triangular part of A is not referenced. Note */ +/* that when DIAG = 'U', the diagonal elements of A are not */ +/* referenced and are assumed to be one. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(M,1). */ + +/* WORK (workspace) DOUBLE PRECISION array, dimension (LWORK), */ +/* where LWORK >= M when NORM = 'I'; otherwise, WORK is not */ +/* referenced. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + --work; + + /* Function Body */ + if (min(*m,*n) == 0) { + value = 0.; + } else if (lsame_(norm, "M", (ftnlen)1, (ftnlen)1)) { + +/* Find max(abs(A(i,j))). */ + + if (lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + value = 1.; + if (lsame_(uplo, "U", (ftnlen)1, (ftnlen)1)) { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + i__3 = *m, i__4 = j - 1; + i__2 = min(i__3,i__4); + for (i__ = 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = value, d__3 = (d__1 = a[i__ + j * a_dim1], abs( + d__1)); + value = max(d__2,d__3); +/* L10: */ + } +/* L20: */ + } + } else { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = j + 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = value, d__3 = (d__1 = a[i__ + j * a_dim1], abs( + d__1)); + value = max(d__2,d__3); +/* L30: */ + } +/* L40: */ + } + } + } else { + value = 0.; + if (lsame_(uplo, "U", (ftnlen)1, (ftnlen)1)) { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = min(*m,j); + for (i__ = 1; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = value, d__3 = (d__1 = a[i__ + j * a_dim1], abs( + d__1)); + value = max(d__2,d__3); +/* L50: */ + } +/* L60: */ + } + } else { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = j; i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = value, d__3 = (d__1 = a[i__ + j * a_dim1], abs( + d__1)); + value = max(d__2,d__3); +/* L70: */ + } +/* L80: */ + } + } + } + } else if (lsame_(norm, "O", (ftnlen)1, (ftnlen)1) || *(unsigned char *) + norm == '1') { + +/* Find norm1(A). */ + + value = 0.; + udiag = lsame_(diag, "U", (ftnlen)1, (ftnlen)1); + if (lsame_(uplo, "U", (ftnlen)1, (ftnlen)1)) { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + if (udiag && j <= *m) { + sum = 1.; + i__2 = j - 1; + for (i__ = 1; i__ <= i__2; ++i__) { + sum += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L90: */ + } + } else { + sum = 0.; + i__2 = min(*m,j); + for (i__ = 1; i__ <= i__2; ++i__) { + sum += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L100: */ + } + } + value = max(value,sum); +/* L110: */ + } + } else { + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + if (udiag) { + sum = 1.; + i__2 = *m; + for (i__ = j + 1; i__ <= i__2; ++i__) { + sum += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L120: */ + } + } else { + sum = 0.; + i__2 = *m; + for (i__ = j; i__ <= i__2; ++i__) { + sum += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L130: */ + } + } + value = max(value,sum); +/* L140: */ + } + } + } else if (lsame_(norm, "I", (ftnlen)1, (ftnlen)1)) { + +/* Find normI(A). */ + + if (lsame_(uplo, "U", (ftnlen)1, (ftnlen)1)) { + if (lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + work[i__] = 1.; +/* L150: */ + } + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + i__3 = *m, i__4 = j - 1; + i__2 = min(i__3,i__4); + for (i__ = 1; i__ <= i__2; ++i__) { + work[i__] += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L160: */ + } +/* L170: */ + } + } else { + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + work[i__] = 0.; +/* L180: */ + } + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = min(*m,j); + for (i__ = 1; i__ <= i__2; ++i__) { + work[i__] += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L190: */ + } +/* L200: */ + } + } + } else { + if (lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + work[i__] = 1.; +/* L210: */ + } + i__1 = *m; + for (i__ = *n + 1; i__ <= i__1; ++i__) { + work[i__] = 0.; +/* L220: */ + } + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = j + 1; i__ <= i__2; ++i__) { + work[i__] += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L230: */ + } +/* L240: */ + } + } else { + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + work[i__] = 0.; +/* L250: */ + } + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m; + for (i__ = j; i__ <= i__2; ++i__) { + work[i__] += (d__1 = a[i__ + j * a_dim1], abs(d__1)); +/* L260: */ + } +/* L270: */ + } + } + } + value = 0.; + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { +/* Computing MAX */ + d__1 = value, d__2 = work[i__]; + value = max(d__1,d__2); +/* L280: */ + } + } else if (lsame_(norm, "F", (ftnlen)1, (ftnlen)1) || lsame_(norm, "E", ( + ftnlen)1, (ftnlen)1)) { + +/* Find normF(A). */ + + if (lsame_(uplo, "U", (ftnlen)1, (ftnlen)1)) { + if (lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + scale = 1.; + sum = (doublereal) min(*m,*n); + i__1 = *n; + for (j = 2; j <= i__1; ++j) { +/* Computing MIN */ + i__3 = *m, i__4 = j - 1; + i__2 = min(i__3,i__4); + dlassq_(&i__2, &a[j * a_dim1 + 1], &c__1, &scale, &sum); +/* L290: */ + } + } else { + scale = 0.; + sum = 1.; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = min(*m,j); + dlassq_(&i__2, &a[j * a_dim1 + 1], &c__1, &scale, &sum); +/* L300: */ + } + } + } else { + if (lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + scale = 1.; + sum = (doublereal) min(*m,*n); + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m - j; +/* Computing MIN */ + i__3 = *m, i__4 = j + 1; + dlassq_(&i__2, &a[min(i__3,i__4) + j * a_dim1], &c__1, & + scale, &sum); +/* L310: */ + } + } else { + scale = 0.; + sum = 1.; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = *m - j + 1; + dlassq_(&i__2, &a[j + j * a_dim1], &c__1, &scale, &sum); +/* L320: */ + } + } + } + value = scale * sqrt(sum); + } + + ret_val = value; + return ret_val; + +/* End of DLANTR */ + +} /* dlantr_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index 50a478cca..4dd38ef02 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -38,6 +38,7 @@ dlabrd.o \ dlacpy.o \ dlamch.o \ dlange.o \ +dlangtr.o \ dlapy2.o \ dlarf.o \ dlarfb.o \ diff --git a/ext/lapack/dlantr.f b/ext/lapack/dlantr.f new file mode 100644 index 000000000..19e9b5d92 --- /dev/null +++ b/ext/lapack/dlantr.f @@ -0,0 +1,277 @@ + DOUBLE PRECISION FUNCTION DLANTR( NORM, UPLO, DIAG, M, N, A, LDA, + $ WORK ) +* +* -- LAPACK auxiliary routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* October 31, 1992 +* +* .. Scalar Arguments .. + CHARACTER DIAG, NORM, UPLO + INTEGER LDA, M, N +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), WORK( * ) +* .. +* +* Purpose +* ======= +* +* DLANTR returns the value of the one norm, or the Frobenius norm, or +* the infinity norm, or the element of largest absolute value of a +* trapezoidal or triangular matrix A. +* +* Description +* =========== +* +* DLANTR returns the value +* +* DLANTR = ( max(abs(A(i,j))), NORM = 'M' or 'm' +* ( +* ( norm1(A), NORM = '1', 'O' or 'o' +* ( +* ( normI(A), NORM = 'I' or 'i' +* ( +* ( normF(A), NORM = 'F', 'f', 'E' or 'e' +* +* where norm1 denotes the one norm of a matrix (maximum column sum), +* normI denotes the infinity norm of a matrix (maximum row sum) and +* normF denotes the Frobenius norm of a matrix (square root of sum of +* squares). Note that max(abs(A(i,j))) is not a matrix norm. +* +* Arguments +* ========= +* +* NORM (input) CHARACTER*1 +* Specifies the value to be returned in DLANTR as described +* above. +* +* UPLO (input) CHARACTER*1 +* Specifies whether the matrix A is upper or lower trapezoidal. +* = 'U': Upper trapezoidal +* = 'L': Lower trapezoidal +* Note that A is triangular instead of trapezoidal if M = N. +* +* DIAG (input) CHARACTER*1 +* Specifies whether or not the matrix A has unit diagonal. +* = 'N': Non-unit diagonal +* = 'U': Unit diagonal +* +* M (input) INTEGER +* The number of rows of the matrix A. M >= 0, and if +* UPLO = 'U', M <= N. When M = 0, DLANTR is set to zero. +* +* N (input) INTEGER +* The number of columns of the matrix A. N >= 0, and if +* UPLO = 'L', N <= M. When N = 0, DLANTR is set to zero. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The trapezoidal matrix A (A is triangular if M = N). +* If UPLO = 'U', the leading m by n upper trapezoidal part of +* the array A contains the upper trapezoidal matrix, and the +* strictly lower triangular part of A is not referenced. +* If UPLO = 'L', the leading m by n lower trapezoidal part of +* the array A contains the lower trapezoidal matrix, and the +* strictly upper triangular part of A is not referenced. Note +* that when DIAG = 'U', the diagonal elements of A are not +* referenced and are assumed to be one. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(M,1). +* +* WORK (workspace) DOUBLE PRECISION array, dimension (LWORK), +* where LWORK >= M when NORM = 'I'; otherwise, WORK is not +* referenced. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UDIAG + INTEGER I, J + DOUBLE PRECISION SCALE, SUM, VALUE +* .. +* .. External Subroutines .. + EXTERNAL DLASSQ +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN, SQRT +* .. +* .. Executable Statements .. +* + IF( MIN( M, N ).EQ.0 ) THEN + VALUE = ZERO + ELSE IF( LSAME( NORM, 'M' ) ) THEN +* +* Find max(abs(A(i,j))). +* + IF( LSAME( DIAG, 'U' ) ) THEN + VALUE = ONE + IF( LSAME( UPLO, 'U' ) ) THEN + DO 20 J = 1, N + DO 10 I = 1, MIN( M, J-1 ) + VALUE = MAX( VALUE, ABS( A( I, J ) ) ) + 10 CONTINUE + 20 CONTINUE + ELSE + DO 40 J = 1, N + DO 30 I = J + 1, M + VALUE = MAX( VALUE, ABS( A( I, J ) ) ) + 30 CONTINUE + 40 CONTINUE + END IF + ELSE + VALUE = ZERO + IF( LSAME( UPLO, 'U' ) ) THEN + DO 60 J = 1, N + DO 50 I = 1, MIN( M, J ) + VALUE = MAX( VALUE, ABS( A( I, J ) ) ) + 50 CONTINUE + 60 CONTINUE + ELSE + DO 80 J = 1, N + DO 70 I = J, M + VALUE = MAX( VALUE, ABS( A( I, J ) ) ) + 70 CONTINUE + 80 CONTINUE + END IF + END IF + ELSE IF( ( LSAME( NORM, 'O' ) ) .OR. ( NORM.EQ.'1' ) ) THEN +* +* Find norm1(A). +* + VALUE = ZERO + UDIAG = LSAME( DIAG, 'U' ) + IF( LSAME( UPLO, 'U' ) ) THEN + DO 110 J = 1, N + IF( ( UDIAG ) .AND. ( J.LE.M ) ) THEN + SUM = ONE + DO 90 I = 1, J - 1 + SUM = SUM + ABS( A( I, J ) ) + 90 CONTINUE + ELSE + SUM = ZERO + DO 100 I = 1, MIN( M, J ) + SUM = SUM + ABS( A( I, J ) ) + 100 CONTINUE + END IF + VALUE = MAX( VALUE, SUM ) + 110 CONTINUE + ELSE + DO 140 J = 1, N + IF( UDIAG ) THEN + SUM = ONE + DO 120 I = J + 1, M + SUM = SUM + ABS( A( I, J ) ) + 120 CONTINUE + ELSE + SUM = ZERO + DO 130 I = J, M + SUM = SUM + ABS( A( I, J ) ) + 130 CONTINUE + END IF + VALUE = MAX( VALUE, SUM ) + 140 CONTINUE + END IF + ELSE IF( LSAME( NORM, 'I' ) ) THEN +* +* Find normI(A). +* + IF( LSAME( UPLO, 'U' ) ) THEN + IF( LSAME( DIAG, 'U' ) ) THEN + DO 150 I = 1, M + WORK( I ) = ONE + 150 CONTINUE + DO 170 J = 1, N + DO 160 I = 1, MIN( M, J-1 ) + WORK( I ) = WORK( I ) + ABS( A( I, J ) ) + 160 CONTINUE + 170 CONTINUE + ELSE + DO 180 I = 1, M + WORK( I ) = ZERO + 180 CONTINUE + DO 200 J = 1, N + DO 190 I = 1, MIN( M, J ) + WORK( I ) = WORK( I ) + ABS( A( I, J ) ) + 190 CONTINUE + 200 CONTINUE + END IF + ELSE + IF( LSAME( DIAG, 'U' ) ) THEN + DO 210 I = 1, N + WORK( I ) = ONE + 210 CONTINUE + DO 220 I = N + 1, M + WORK( I ) = ZERO + 220 CONTINUE + DO 240 J = 1, N + DO 230 I = J + 1, M + WORK( I ) = WORK( I ) + ABS( A( I, J ) ) + 230 CONTINUE + 240 CONTINUE + ELSE + DO 250 I = 1, M + WORK( I ) = ZERO + 250 CONTINUE + DO 270 J = 1, N + DO 260 I = J, M + WORK( I ) = WORK( I ) + ABS( A( I, J ) ) + 260 CONTINUE + 270 CONTINUE + END IF + END IF + VALUE = ZERO + DO 280 I = 1, M + VALUE = MAX( VALUE, WORK( I ) ) + 280 CONTINUE + ELSE IF( ( LSAME( NORM, 'F' ) ) .OR. ( LSAME( NORM, 'E' ) ) ) THEN +* +* Find normF(A). +* + IF( LSAME( UPLO, 'U' ) ) THEN + IF( LSAME( DIAG, 'U' ) ) THEN + SCALE = ONE + SUM = MIN( M, N ) + DO 290 J = 2, N + CALL DLASSQ( MIN( M, J-1 ), A( 1, J ), 1, SCALE, SUM ) + 290 CONTINUE + ELSE + SCALE = ZERO + SUM = ONE + DO 300 J = 1, N + CALL DLASSQ( MIN( M, J ), A( 1, J ), 1, SCALE, SUM ) + 300 CONTINUE + END IF + ELSE + IF( LSAME( DIAG, 'U' ) ) THEN + SCALE = ONE + SUM = MIN( M, N ) + DO 310 J = 1, N + CALL DLASSQ( M-J, A( MIN( M, J+1 ), J ), 1, SCALE, + $ SUM ) + 310 CONTINUE + ELSE + SCALE = ZERO + SUM = ONE + DO 320 J = 1, N + CALL DLASSQ( M-J+1, A( J, J ), 1, SCALE, SUM ) + 320 CONTINUE + END IF + END IF + VALUE = SCALE*SQRT( SUM ) + END IF +* + DLANTR = VALUE + RETURN +* +* End of DLANTR +* + END From 155d7604b5976f92d92fdc852eec3e66122a4ff3 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 7 Apr 2011 16:14:00 +0000 Subject: [PATCH 352/446] Verified that the QR factorization works on one problem. --- Cantera/src/numerics/SquareMatrix.cpp | 37 ++++++++++++++------ Cantera/src/numerics/SquareMatrix.h | 49 +++++++++++++++++---------- 2 files changed, 58 insertions(+), 28 deletions(-) diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 8ecc08972..c8371d889 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -32,10 +32,12 @@ namespace Cantera { //==================================================================================================================== SquareMatrix::SquareMatrix() : DenseMatrix(), - m_factored(0) + m_factored(0), + useQR_(0) { } + //==================================================================================================================== // Constructor. /* * Create an \c n by \c n matrix, and initialize @@ -46,21 +48,24 @@ namespace Cantera { */ SquareMatrix::SquareMatrix(int n, doublereal v) : DenseMatrix(n, n, v), - m_factored(0) + m_factored(0), + useQR_(0) { } - + //==================================================================================================================== /* * * copy constructor */ SquareMatrix::SquareMatrix(const SquareMatrix& y) : DenseMatrix(y), - m_factored(y.m_factored) + m_factored(y.m_factored), + useQR_(y.useQR_) { } - /** + //==================================================================================================================== + /* * Assignment operator */ SquareMatrix& SquareMatrix::operator=(const SquareMatrix& y) { @@ -69,12 +74,18 @@ namespace Cantera { m_factored = y.m_factored; return *this; } - - /** + //==================================================================================================================== + SquareMatrix::~SquareMatrix() { + } + //==================================================================================================================== + /* * Solve Ax = b. Vector b is overwritten on exit with x. */ int SquareMatrix::solve(double* b) { + if (useQR_) { + return solveQR(b); + } int info=0; /* * Check to see whether the matrix has been factored. @@ -122,10 +133,13 @@ namespace Cantera { DenseMatrix::resize(n, m, v); } //==================================================================================================================== - /** + /* * Factor A. A is overwritten with the LU decomposition of A. */ int SquareMatrix::factor() { + if (useQR_) { + return factorQR(); + } integer n = static_cast(nRows()); int info=0; m_factored = 1; @@ -159,9 +173,10 @@ namespace Cantera { int SquareMatrix::factorQR() { if ((int) tau.size() < m_nrows) { tau.resize(m_nrows, 0.0); - work.resize(9 * m_nrows, 0.0); + work.resize(8 * m_nrows, 0.0); } int info; + m_factored = 2; int lwork = work.size(); ct_dgeqrf(m_nrows, m_nrows, &(*(begin())), m_nrows, DATA_PTR(tau), DATA_PTR(work), lwork, info); if (info != 0) { @@ -173,7 +188,7 @@ namespace Cantera { } } int lworkOpt = work[0]; - if (lworkOpt != lwork) { + if (lworkOpt > lwork) { work.resize(lworkOpt); } return info; @@ -215,7 +230,7 @@ namespace Cantera { } } int lworkOpt = work[0]; - if (lworkOpt <= lwork) { + if (lworkOpt > lwork) { work.resize(lworkOpt); } diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index c8dac8895..1be99b62e 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -45,25 +45,35 @@ namespace Cantera { */ SquareMatrix(int n, doublereal v = 0.0); - /** - * Copy Constructor + //! Copy Constructor + /*! + * @param right Object to be copied */ - SquareMatrix(const SquareMatrix&); - - /** - * Assignment operator + SquareMatrix(const SquareMatrix& right); + + //! Assignment operator + /*! + * @param right Object to be copied */ - SquareMatrix& operator=(const SquareMatrix&); + SquareMatrix& operator=(const SquareMatrix& right); - /// Destructor. Does nothing. - virtual ~SquareMatrix(){} + //! Destructor. Does nothing. + virtual ~SquareMatrix(); - /** - * Solves the Ax = b system returning x in the b spot. + + //! Solves the Ax = b system returning x in the b spot. + /*! + * @param b Vector for the rhs of the equation system */ - int solve(double *b); + int solve(doublereal *b); + //! Resize the matrix + /*! + * @param n Number of rows + * @param m Number of columns + * @param v double to fill the new space (defaults to zero) + */ void resize(int n, int m, doublereal v = 0.0); @@ -86,16 +96,14 @@ namespace Cantera { */ int factorQR(); - //! Solves the linear problem Ax=b using the QR algorithm - //! returning x in the b spot + //! Solves the linear problem Ax=b using the QR algorithm returning x in the b spot /*! * @param b RHS to be solved. */ int solveQR(doublereal *b); - /** - * clear the factored flag - */ + + //! clear the factored flag void clearFactorFlag(); /** * set the factored flag @@ -107,8 +115,15 @@ namespace Cantera { */ int m_factored; + //! Work vector for QR algorithm vector_fp tau; + + //! Work vector for QR algorithm vector_fp work; + + public: + //! Use the QR algorithm to factor and invert the matrix + int useQR_; }; } From b20a73b92abb589676763e2ddb659b92d5dc608b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 11 Apr 2011 20:52:00 +0000 Subject: [PATCH 353/446] Fixed an error with unbalanced quotes --- preconfig | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/preconfig b/preconfig index 98b6f9f3a..22259a98c 100755 --- a/preconfig +++ b/preconfig @@ -241,7 +241,7 @@ WITH_H298MODIFY_CAPABILITY=${WITH_H298MODIFY_CAPABILITY:="n"} # Capability in the planning and implementation stage # Phases may be intermediates but actually have zero mole numbers # in the InterfacialKinetics object -KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES=${KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES:="n'} +KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES=${KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES:="n"} ###################################################################### # if set to 'y', the ck2cti program that converts Chemkin input files From 4b2b215da95a63a11618f5c481a57fb01b6789af Mon Sep 17 00:00:00 2001 From: John Hewson Date: Mon, 11 Apr 2011 21:08:08 +0000 Subject: [PATCH 354/446] File named dlantr.o was misnamed in Makefile.in --This line, and those dlantrbelow, will be ignored-- M Makefile.in --- ext/lapack/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index 4dd38ef02..a0db0ac4c 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -38,7 +38,7 @@ dlabrd.o \ dlacpy.o \ dlamch.o \ dlange.o \ -dlangtr.o \ +dlantr.o \ dlapy2.o \ dlarf.o \ dlarfb.o \ From 59a800218f5b52cebf6ca5ae4b548737adf100be Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 14 Apr 2011 18:24:13 +0000 Subject: [PATCH 355/446] Changed getdlnActCoeffdlnN to be nonconst. added getdlnActCoeffdlnN_numderiv() function --- Cantera/src/thermo/GibbsExcessVPSSTP.h | 2 +- Cantera/src/thermo/MargulesVPSSTP.cpp | 2 +- Cantera/src/thermo/MargulesVPSSTP.h | 2 +- Cantera/src/thermo/MolalityVPSSTP.h | 4 +- Cantera/src/thermo/PhaseCombo_Interaction.cpp | 3 +- Cantera/src/thermo/PhaseCombo_Interaction.h | 2 +- Cantera/src/thermo/ThermoPhase.cpp | 85 ++++++++++++++++++- Cantera/src/thermo/ThermoPhase.h | 4 +- 8 files changed, 91 insertions(+), 13 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 68a4f3ad5..521f7f344 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -323,7 +323,7 @@ namespace Cantera { * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) { err(" getdlnActCoeffdlnN: nonzero and nonimplemented"); } diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index b2c57cde8..15fc3edb2 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -1051,7 +1051,7 @@ namespace Cantera { } } //==================================================================================================================== - void MargulesVPSSTP::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) const { + void MargulesVPSSTP::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) { s_update_dlnActCoeff_dlnN(); double *data = & dlnActCoeffdlnN_(0,0); for (int k = 0; k < m_kk; k++) { diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 8913c53c2..b80b2aa4c 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -847,7 +847,7 @@ namespace Cantera { * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) ; //@} diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h index 4bb286c64..5999b0add 100644 --- a/Cantera/src/thermo/MolalityVPSSTP.h +++ b/Cantera/src/thermo/MolalityVPSSTP.h @@ -812,8 +812,8 @@ namespace Cantera { * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { - err(" getdlnActCoeffdlnN: nonzero and nonimplemented"); + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) { + getdlnActCoeffdlnN_numderiv(ld, dlnActCoeffdlnN); } //! returns a summary of the state of the phase as a string diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.cpp b/Cantera/src/thermo/PhaseCombo_Interaction.cpp index ae891ec49..574d3477e 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.cpp +++ b/Cantera/src/thermo/PhaseCombo_Interaction.cpp @@ -1110,7 +1110,7 @@ namespace Cantera { /* * HKM - Checked for Transition */ - void PhaseCombo_Interaction::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) const { + void PhaseCombo_Interaction::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) { s_update_dlnActCoeff_dlnN(); double *data = & dlnActCoeffdlnN_(0,0); for (int k = 0; k < m_kk; k++) { @@ -1141,7 +1141,6 @@ namespace Cantera { m_pSpecies_A_ij.resize(num, -1); m_pSpecies_B_ij.resize(num, -1); - throw CanteraError("", "unimplemented"); } //==================================================================================================================== diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.h b/Cantera/src/thermo/PhaseCombo_Interaction.h index 59ffb72e0..a14049990 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.h +++ b/Cantera/src/thermo/PhaseCombo_Interaction.h @@ -846,7 +846,7 @@ namespace Cantera { * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN); //@} diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index 0acf3a7ca..b014eaf89 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -21,6 +21,7 @@ #endif #include "ThermoPhase.h" +#include "mdp_allo.h" #include //@{ @@ -1098,12 +1099,88 @@ namespace Cantera { * @param dlnActCoeffdN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - void ThermoPhase::getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const { - for (int m = 0; m < m_kk; m++) { - for (int k = 0; k < m_kk; k++) { - dlnActCoeffdlnN[ld * k + m] = 0.0; + void ThermoPhase::getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) { + + + for (int m = 0; m < m_kk; m++) { + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN[ld * k + m] = 0.0; + } } + return; + } + //==================================================================================================================== + void ThermoPhase::getdlnActCoeffdlnN_numderiv(const int ld, doublereal * const dlnActCoeffdlnN) { + + int k, j; + double deltaMoles_j = 0.0; + double pres = pressure(); + + /* + * Evaluate the current base activity coefficients if necessary + */ + std::vector ActCoeff_Base(m_kk); + getActivityCoefficients(DATA_PTR(ActCoeff_Base)); + std::vector Xmol_Base(m_kk); + getMoleFractions(DATA_PTR(Xmol_Base)); + + // Make copies of ActCoeff and Xmol_ for use in taking differences + std::vector ActCoeff(m_kk); + std::vector Xmol(m_kk); + double v_totalMoles = 1.0; + double TMoles_base = v_totalMoles; + + /* + * Loop over the columns species to be deltad + */ + for (j = 0; j < m_kk; j++) { + /* + * Calculate a value for the delta moles of species j + * -> NOte Xmol_[] and Tmoles are always positive or zero + * quantities. + * -> experience has shown that you always need to make the deltas greater than needed to + * change the other mole fractions in order to capture some effects. + */ + double moles_j_base = v_totalMoles * Xmol_Base[j]; + deltaMoles_j = 1.0E-7 * moles_j_base + v_totalMoles * 1.0E-13 + 1.0E-150; + /* + * Now, update the total moles in the phase and all of the + * mole fractions based on this. + */ + v_totalMoles = TMoles_base + deltaMoles_j; + for (k = 0; k < m_kk; k++) { + Xmol[k] = Xmol_Base[k] * TMoles_base / v_totalMoles; + } + Xmol[j] = (moles_j_base + deltaMoles_j) / v_totalMoles; + + /* + * Go get new values for the activity coefficients. + * -> Note this calls setState_PX(); + */ + setState_PX(pres, DATA_PTR(Xmol)); + getActivityCoefficients(DATA_PTR(ActCoeff)); + + /* + * Calculate the column of the matrix + */ + double * const lnActCoeffCol = dlnActCoeffdlnN + ld * j; + for (k = 0; k < m_kk; k++) { + lnActCoeffCol[k] = (2*moles_j_base + deltaMoles_j) *(ActCoeff[k] - ActCoeff_Base[k]) / + ((ActCoeff[k] + ActCoeff_Base[k]) * deltaMoles_j); + } + /* + * Revert to the base case Xmol_, v_totalMoles + */ + v_totalMoles = TMoles_base; + mdp::mdp_copy_dbl_1(DATA_PTR(Xmol), DATA_PTR(Xmol_Base), m_kk); } + /* + * Go get base values for the activity coefficients. + * -> Note this calls setState_TPX() again; + * -> Just wanted to make sure that cantera is in sync + * with VolPhase after this call. + */ + setState_PX(pres, DATA_PTR(Xmol_Base)); } //==================================================================================================================== /* diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index a27d999b8..d1b15ebbf 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -2137,7 +2137,9 @@ namespace Cantera { * @param dlnActCoeffdlnN Output vector of derivatives of the * log Activity Coefficients. length = m_kk * m_kk */ - virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) const; + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN); + + virtual void getdlnActCoeffdlnN_numderiv(const int ld, doublereal * const dlnActCoeffdlnN); /** * @} From 5f73e33c9ea1497ac36f3e716736b2d2f6e10a72 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 14 Apr 2011 18:25:24 +0000 Subject: [PATCH 356/446] Changed the algorithms a little bit to accomodate PhaseCombo, which doesn't have an ideal mixing term. This caused problems in places. --- Cantera/src/equil/MultiPhase.h | 2 +- Cantera/src/equil/vcs_VolPhase.cpp | 31 ++++++-- Cantera/src/equil/vcs_solve_TP.cpp | 109 ++++++++++++++++++++--------- 3 files changed, 104 insertions(+), 38 deletions(-) diff --git a/Cantera/src/equil/MultiPhase.h b/Cantera/src/equil/MultiPhase.h index 233602012..5b56e7bee 100644 --- a/Cantera/src/equil/MultiPhase.h +++ b/Cantera/src/equil/MultiPhase.h @@ -123,7 +123,7 @@ namespace Cantera { //! Add a phase to the mixture. /*! - * This function must be called befure the init() function is called, + * This function must be called before the init() function is called, * which serves to freeze the MultiPhase. * * @param p pointer to the phase object diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp index 5683e640c..87ca0124c 100644 --- a/Cantera/src/equil/vcs_VolPhase.cpp +++ b/Cantera/src/equil/vcs_VolPhase.cpp @@ -984,15 +984,30 @@ namespace VCSnonideal { */ void vcs_VolPhase::_updateLnActCoeffJac() { int k, j; - double deltaMoles_j = 0.0; - + /* * Evaluate the current base activity coefficients if necessary */ if (!m_UpToDate_AC) { _updateActCoeff(); } +#ifndef NOOLD + if (!TP_ptr) return; + TP_ptr->getdlnActCoeffdlnN(m_numSpecies, &dLnActCoeffdMolNumber[0][0]); + for (j = 0; j < m_numSpecies; j++) { + double moles_j_base = v_totalMoles * Xmol_[j]; + double * const lnActCoeffCol = dLnActCoeffdMolNumber[j]; + if (moles_j_base < 1.0E-200) { + moles_j_base = 1.0E-7 * moles_j_base + 1.0E-20 * v_totalMoles + 1.0E-150; + } + for (k = 0; k < m_numSpecies; k++) { + lnActCoeffCol[k] /= moles_j_base; + } + } +#endif + + double deltaMoles_j = 0.0; // Make copies of ActCoeff and Xmol_ for use in taking differences std::vector ActCoeff_Base(ActCoeff); std::vector Xmol_Base(Xmol_); @@ -1008,7 +1023,7 @@ namespace VCSnonideal { * quantities. */ double moles_j_base = v_totalMoles * Xmol_Base[j]; - deltaMoles_j = 1.0E-7 * moles_j_base + 1.0E-20 * v_totalMoles + 1.0E-150; + deltaMoles_j = 1.0E-7 * moles_j_base + 1.0E-13 * v_totalMoles + 1.0E-150; /* * Now, update the total moles in the phase and all of the * mole fractions based on this. @@ -1030,8 +1045,15 @@ namespace VCSnonideal { */ double * const lnActCoeffCol = dLnActCoeffdMolNumber[j]; for (k = 0; k < m_numSpecies; k++) { - lnActCoeffCol[k] = (ActCoeff[k] - ActCoeff_Base[k]) / + double tmp; + tmp = (ActCoeff[k] - ActCoeff_Base[k]) / ((ActCoeff[k] + ActCoeff_Base[k]) * 0.5 * deltaMoles_j); + if (fabs(tmp - lnActCoeffCol[k]) > 1.0E-4 * fabs(tmp) + fabs(lnActCoeffCol[k])) { + // printf(" we have an error\n"); + + } + //tmp = lnActCoeffCol[k]; + } /* * Revert to the base case Xmol_, v_totalMoles @@ -1048,6 +1070,7 @@ namespace VCSnonideal { setMoleFractions(VCS_DATA_PTR(Xmol_Base)); _updateMoleFractionDependencies(); _updateActCoeff(); + } /***************************************************************************/ diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 7dfc0d821..721a87278 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -1243,11 +1243,12 @@ namespace VCSnonideal { vcs_Total_Gibbs(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_feSpecies_new), VCS_DATA_PTR(m_tPhaseMoles_new))); plogendl(); +#ifdef DEBUG_MODE if (m_VCount->Its > 550) { plogf(" --- Troublesome solve"); plogendl(); } - +#endif } /*************************************************************************/ @@ -2056,12 +2057,15 @@ namespace VCSnonideal { , char *ANOTE #endif ) const { - double dx = 0.0; + double dx = 0.0, a; double w_kspec = m_molNumSpecies_old[kspec]; double molNum_kspec_new; double wTrial; - double dg_irxn = m_deltaGRxn_old[irxn]; + double dg_irxn = m_deltaGRxn_old[irxn]; + doublereal s; + vcs_VolPhase * Vphase = 0; int iph = m_phaseID[kspec]; + *do_delete = FALSE; if (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) { if (w_kspec <= 0.0) { @@ -2086,8 +2090,36 @@ namespace VCSnonideal { return 0.0; } } - - wTrial = w_kspec * exp(-dg_irxn); + + /* + * get the diagonal of the activity coefficent jacobian + */ + Vphase = m_VolPhaseList[iph]; + s = m_dLnActCoeffdMolNum[kspec][kspec]; + // s *= (m_tPhaseMoles_old[iph]); + /* + * We fit it to a power law approximation of the activity coefficient + * + * gamma = gamma_0 * ( x / x0)**a + * + * where a is forced to be a little bit greater than -1. + * We do this so that the resulting expression is always nonnegative + * + * We then solve the resulting calculation: + * + * gamma * x = gamma_0 * x0 exp (-deltaG/RT); + * + * + */ + a = w_kspec * s; + if (a < (-1.0 + 0.01)) { + a = -1.0 + 0.01; + } else if (a > 1.0) { + a = 1.0; + } + wTrial = w_kspec * (exp( -dg_irxn / (1.0 + a))); + // wTrial = w_kspec * exp(-dg_irxn); + molNum_kspec_new = wTrial; if (wTrial > 100. * w_kspec) { @@ -2785,10 +2817,8 @@ namespace VCSnonideal { } return false; } - /*************************************************************************************/ - - // Provide an estimate for the deleted species in phases that - // are not zeroed out + //==================================================================================================================== + // Provide an estimate for the deleted species in phases that are not zeroed out /* * Try to add back in all deleted species. An estimate of the kmol numbers * are obtained and the species is added back into the equation system, @@ -2798,38 +2828,53 @@ namespace VCSnonideal { int iph, kspec, retn; if (m_numSpeciesRdc == m_numSpeciesTot) return 0; /* - * Use the standard chemical potentials for the chemical potentials - * of deleted species. Then, calculate Delta G for + * Use the standard chemical potentials for the chemical potentials of deleted species. Then, calculate Delta G for * for formation reactions. * We are relying here on a old saved value of m_actCoeffSpecies_old[kspec] - * being sufficiently good. Note, we will recalculate everything at the - * end of the routine. + * being sufficiently good. Note, we will recalculate everything at the end of the routine. */ - for (kspec = m_numSpeciesRdc; kspec < m_numSpeciesTot; ++kspec) { - iph = m_phaseID[kspec]; - m_feSpecies_new[kspec] = (m_SSfeSpecies[kspec] + log(m_actCoeffSpecies_old[kspec]) - - m_lnMnaughtSpecies[kspec] - + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); + vcs_dcopy(VCS_DATA_PTR(m_molNumSpecies_new), VCS_DATA_PTR(m_molNumSpecies_old), m_numSpeciesTot); + + for (int cits = 0; cits < 3; cits++) { + for (kspec = m_numSpeciesRdc; kspec < m_numSpeciesTot; ++kspec) { + iph = m_phaseID[kspec]; + vcs_VolPhase *Vphase = m_VolPhaseList[iph]; + if (m_molNumSpecies_new[kspec] == 0.0) { + m_molNumSpecies_new[kspec] = VCS_DELETE_MINORSPECIES_CUTOFF * 1.0E-10; + } + if (!Vphase->m_singleSpecies) { + Vphase->sendToVCS_ActCoeff(VCS_STATECALC_NEW, VCS_DATA_PTR(m_actCoeffSpecies_new)); + } + m_feSpecies_new[kspec] = (m_SSfeSpecies[kspec] + log(m_actCoeffSpecies_new[kspec]) - m_lnMnaughtSpecies[kspec] + + m_chargeSpecies[kspec] * m_Faraday_dim * m_phasePhi[iph]); + } + /* + * Recalculate the DeltaG's of the formation reactions for the deleted species in the mechanism + */ + vcs_deltag(0, true, VCS_STATECALC_NEW); + for (int irxn = m_numRxnRdc; irxn < m_numRxnTot; ++irxn) { + kspec = m_indexRxnToSpecies[irxn]; + iph = m_phaseID[kspec]; + if (m_tPhaseMoles_old[iph] > 0.0) { + double maxDG = MIN(m_deltaGRxn_new[irxn], 690.0); + double dx = m_tPhaseMoles_old[iph] * exp(- maxDG); + m_molNumSpecies_new[kspec] = dx; + if (m_molNumSpecies_new[kspec] > 2 *VCS_DELETE_MINORSPECIES_CUTOFF) { + m_molNumSpecies_new[kspec] = 2 * VCS_DELETE_MINORSPECIES_CUTOFF; + } + } + } } - /* - * Recalculate the DeltaG's of the formation reactions for the - * deleted species in the mechanism - */ - vcs_deltag(0, true, VCS_STATECALC_NEW); - for (int irxn = m_numRxnRdc; irxn < m_numRxnTot; ++irxn) { kspec = m_indexRxnToSpecies[irxn]; iph = m_phaseID[kspec]; if (m_tPhaseMoles_old[iph] > 0.0) { - double maxDG = MIN(m_deltaGRxn_new[irxn], 690.0); - - double dx = m_tPhaseMoles_old[iph] * exp(- maxDG); + double dx = m_molNumSpecies_new[kspec]; retn = delta_species(kspec, &dx); if (retn == 0) { #ifdef DEBUG_MODE if (m_debug_print_lvl) { - plogf(" --- add_deleted(): delta_species() failed for " - "species %s (%d) with mol number %g\n", + plogf(" --- add_deleted(): delta_species() failed for species %s (%d) with mol number %g\n", m_speciesName[kspec].c_str(), kspec, dx); } #endif @@ -2839,8 +2884,7 @@ namespace VCSnonideal { #ifdef DEBUG_MODE if (retn == 0) { if (m_debug_print_lvl) { - plogf(" --- add_deleted(): delta_species() failed for " - "species %s (%d) with mol number %g\n", + plogf(" --- add_deleted(): delta_species() failed for species %s (%d) with mol number %g\n", m_speciesName[kspec].c_str(), kspec, dx); } } @@ -2877,8 +2921,7 @@ namespace VCSnonideal { retn++; #ifdef DEBUG_MODE if (m_debug_print_lvl >= 2) { - plogf(" --- add_deleted(): species %s " - "with mol number %g not converged: DG = %g", + plogf(" --- add_deleted(): species %s with mol number %g not converged: DG = %g", m_speciesName[kspec].c_str(), m_molNumSpecies_old[kspec], m_deltaGRxn_old[irxn]); plogendl(); From 1207d95824707cd7b28448b20eb4a05d7ec27b6f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 15 Apr 2011 14:53:07 +0000 Subject: [PATCH 357/446] Changed the algorithm slightly --- Cantera/src/equil/vcs_solve_TP.cpp | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 721a87278..dc77b016f 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -2060,7 +2060,7 @@ namespace VCSnonideal { double dx = 0.0, a; double w_kspec = m_molNumSpecies_old[kspec]; double molNum_kspec_new; - double wTrial; + double wTrial, tmp; double dg_irxn = m_deltaGRxn_old[irxn]; doublereal s; vcs_VolPhase * Vphase = 0; @@ -2112,12 +2112,18 @@ namespace VCSnonideal { * */ a = w_kspec * s; - if (a < (-1.0 + 0.01)) { - a = -1.0 + 0.01; - } else if (a > 1.0) { - a = 1.0; + if (a < (-1.0 + 1.0E-8)) { + a = -1.0 + 1.0E-8; + } else if (a > 100.0) { + a = 100.0; } - wTrial = w_kspec * (exp( -dg_irxn / (1.0 + a))); + tmp = -dg_irxn / (1.0 + a); + if (tmp < 200.) { + tmp = -200.; + } else if ( tmp > 200.) { + tmp = 200.; + } + wTrial = w_kspec * exp(tmp); // wTrial = w_kspec * exp(-dg_irxn); molNum_kspec_new = wTrial; From 36b44fd27858b49146b376810668f62ef0e82939 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 18 Apr 2011 16:46:40 +0000 Subject: [PATCH 358/446] Fixed a Makefile error. --- ext/f2c_lapack/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 16b3add23..7dd08bca1 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -67,7 +67,7 @@ dlabrd.o \ dlacpy.o \ dlamch.o \ dlange.o \ -dlangtr.o \ +dlantr.o \ dlapy2.o \ dlarf.o \ dlarfb.o \ From d60d189843d3a4620ddbd312bc6bc703a030d294 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 19 Apr 2011 16:41:45 +0000 Subject: [PATCH 359/446] Fixed a bad error that crept into the solver from a recent commit --- Cantera/src/equil/vcs_solve_TP.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index dc77b016f..bc660e603 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -2118,7 +2118,7 @@ namespace VCSnonideal { a = 100.0; } tmp = -dg_irxn / (1.0 + a); - if (tmp < 200.) { + if (tmp < -200.) { tmp = -200.; } else if ( tmp > 200.) { tmp = 200.; From 60ae1d2c11204d8b051efe0345cd5d4e0324e575 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 19 Apr 2011 16:45:04 +0000 Subject: [PATCH 360/446] Small rebaseline for roundoff error --- .../VCSnonideal/NaCl_equil/good_dout.txt | 880 +++++++++--------- 1 file changed, 440 insertions(+), 440 deletions(-) diff --git a/test_problems/VCSnonideal/NaCl_equil/good_dout.txt b/test_problems/VCSnonideal/NaCl_equil/good_dout.txt index 6499cd319..cd46016da 100644 --- a/test_problems/VCSnonideal/NaCl_equil/good_dout.txt +++ b/test_problems/VCSnonideal/NaCl_equil/good_dout.txt @@ -464,17 +464,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.304522E+01 -2.304532E+01 --- H2O(L) 2.000000E+00 1.999600E+00 -1.237155E+02 -1.237155E+02 - --- OH- 1.100000E-26 4.546575E-25 -1.479320E+02 -1.442101E+02 - --- Na+ 1.100000E-26 6.521361E-25 -1.604244E+02 -1.563419E+02 + --- OH- 1.100000E-26 4.546584E-25 -1.479320E+02 -1.442101E+02 + --- Na+ 1.100000E-26 6.521374E-25 -1.604244E+02 -1.563419E+02 --- H2 1.100000E-26 6.600000E-27 -7.687542E+01 -7.738635E+01 --- CO2 0.000000E+00 0.000000E+00 -5.082000E+02 -5.082001E+02 - --- H+ 1 1.100000E-26 4.546575E-25 -5.644851E+01 -5.272667E+01 -8.066500E+01 -7.322130E+01 + --- H+ 1 1.100000E-26 4.546584E-25 -5.644851E+01 -5.272666E+01 -8.066500E+01 -7.322130E+01 --- H2O 0 1.100000E-26 4.000000E-04 -1.814199E+02 -1.294722E+02 -5.770444E+01 -5.756680E+00 --- NaCl 0 1.100000E-26 3.904774E-32 -1.619682E+02 -1.745169E+02 1.254862E+01 -9.999499E-05 - --- Cl- 1 1.100000E-26 6.521361E-25 -1.306626E+02 -1.265800E+02 -1.165702E+02 -1.084051E+02 + --- Cl- 1 1.100000E-26 6.521374E-25 -1.306626E+02 -1.265800E+02 -1.165702E+02 -1.084051E+02 --- OH 0 0.000000E+00 1.100000E-26 -4.152353E+02 -1.526453E+02 -3.299575E+02 -6.762301E+01 --- O2 1 5.500000E-27 5.500000E-28 -8.652501E+01 -8.882770E+01 7.155163E+00 3.830627E+00 - --- Norms of Delta G(): 1.486079E+02 6.018542E+01 + --- Norms of Delta G(): 1.486079E+02 6.018541E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.9996000E+00 @@ -554,10 +554,10 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 4.5466E-25 1.6645E-23 -7.3221E+01 | Normal calc: diag adjusted from 4.39892e+24 to 4.39892e+24 due to act coeff + --- H+ 4.5466E-25 1.6645E-23 -7.3221E+01 | Normal calc: diag adjusted from 4.39891e+24 to 4.3989e+24 due to act coeff --- H2O 4.0000E-04 2.3029E-03 -5.7567E+00 | Normal Calc --- NaCl 3.9048E-32 3.9046E-36 -9.9995E-05 | Normal Calc - --- Cl- 6.5214E-25 3.5347E-23 -1.0841E+02 | Normal calc: diag adjusted from 3.06684e+24 to 3.06684e+24 due to act coeff + --- Cl- 6.5214E-25 3.5348E-23 -1.0841E+02 | Normal calc: diag adjusted from 3.06684e+24 to 3.06683e+24 due to act coeff --- H2 6.6000E-27 2.6254E-25 -1.3525E+02 | Normal Calc --- O2 5.5000E-28 -5.5000E-28 2.7432E+02 | Delta damped from -8.38208e-26 to -5.5e-28 due to O2 going negative ---------------------------------------------------------------------------------- @@ -566,13 +566,13 @@ VCS CALCULATION METHOD --- H+ 1 4.5466E-25 1.7100E-23 1.6645E-23 | Normal Major Calc --- H2O 0 4.0000E-04 4.0000E-02 3.9600E-02 | minor species alternative calc --- NaCl 0 3.9048E-32 3.9052E-32 3.9048E-36 | minor species alternative calc - --- Cl- 1 6.5214E-25 3.6000E-23 3.5347E-23 | Normal Major Calc + --- Cl- 1 6.5214E-25 3.6000E-23 3.5348E-23 | Normal Major Calc --- H2 1 6.6000E-27 2.6914E-25 2.6254E-25 | Normal Major Calc --- O2 1 5.5000E-28 5.5000E-29-4.9500E-28 | initial nonpos kmoles= 0.000E+00 - --- NaCl(S) c 5.0000E+00 5.0000E+00-3.5347E-23 | + --- NaCl(S) c 5.0000E+00 5.0000E+00-3.5348E-23 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9996E+00 1.9600E+00-3.9600E-02 | - --- Na+ c 6.5214E-25 3.6000E-23 3.5347E-23 | + --- Na+ c 6.5214E-25 3.6000E-23 3.5348E-23 | --- OH- c 4.5466E-25 1.7100E-23 1.6645E-23 | --- OH c 1.1000E-26 5.3805E-25 5.2705E-25 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -591,14 +591,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.304532E+01 -2.305517E+01 --- H2O(L) 1.999600E+00 1.960000E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 6.521361E-25 3.599957E-23 -1.563419E+02 -1.523109E+02 - --- OH- 4.546575E-25 1.709997E-23 -1.442101E+02 -1.405629E+02 + --- Na+ 6.521374E-25 3.599971E-23 -1.563419E+02 -1.523108E+02 + --- OH- 4.546584E-25 1.710003E-23 -1.442101E+02 -1.405629E+02 --- OH 1.100000E-26 5.380528E-25 -1.526453E+02 -1.487651E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082001E+02 -5.082100E+02 - --- H+ 1 4.546575E-25 1.709997E-23 -5.272667E+01 -4.907938E+01 -7.322130E+01 -6.592672E+01 + --- H+ 1 4.546584E-25 1.710003E-23 -5.272666E+01 -4.907937E+01 -7.322130E+01 -6.592672E+01 --- H2O 0 4.000000E-04 4.000000E-02 -1.294722E+02 -1.248769E+02 -5.756680E+00 -1.161360E+00 --- NaCl 0 3.904774E-32 3.905164E-32 -1.745169E+02 -1.745266E+02 -9.999499E-05 -9.850336E-03 - --- Cl- 1 6.521361E-25 3.599957E-23 -1.265800E+02 -1.225490E+02 -1.084051E+02 -1.003431E+02 + --- Cl- 1 6.521374E-25 3.599971E-23 -1.265800E+02 -1.225490E+02 -1.084051E+02 -1.003431E+02 --- H2 1 6.600000E-27 2.691364E-25 -7.738635E+01 -7.368805E+01 -1.352460E+02 -1.237873E+02 --- O2 1 5.500000E-28 5.500000E-29 -8.882770E+01 -9.114013E+01 2.743227E+02 2.564894E+02 --- Norms of Delta G(): 1.358250E+02 1.261788E+02 @@ -631,16 +631,16 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.7100E-23 5.6367E-22 -6.5927E+01 | Normal calc: diag adjusted from 1.16959e+23 to 1.16959e+23 due to act coeff + --- H+ 1.7100E-23 5.6368E-22 -6.5927E+01 | Normal calc: diag adjusted from 1.16959e+23 to 1.16959e+23 due to act coeff --- H2O 4.0000E-02 4.6919E-02 -1.1614E+00 | Normal Calc --- NaCl 3.9052E-32 3.8467E-34 -9.8503E-03 | Normal Calc - --- Cl- 3.6000E-23 1.8062E-21 -1.0034E+02 | Normal calc: diag adjusted from 5.55562e+22 to 5.55562e+22 due to act coeff + --- Cl- 3.6000E-23 1.8062E-21 -1.0034E+02 | Normal calc: diag adjusted from 5.5556e+22 to 5.55559e+22 due to act coeff --- H2 2.6914E-25 1.1102E-23 -1.2379E+02 | Normal Calc --- O2 5.5000E-29 0.0000E+00 2.5649E+02 | Skipped: IC = 0 and DG >0: 2.565E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 1.7100E-23 5.8077E-22 5.6367E-22 | Normal Major Calc + --- H+ 1 1.7100E-23 5.8078E-22 5.6368E-22 | Normal Major Calc --- H2O 1 4.0000E-02 8.6919E-02 4.6919E-02 | Normal Major Calc --- NaCl 0 3.9052E-32 3.9052E-32 0.0000E+00 | minor species not considered --- Cl- 1 3.6000E-23 1.8422E-21 1.8062E-21 | Normal Major Calc @@ -650,7 +650,7 @@ VCS CALCULATION METHOD --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9600E+00 1.9131E+00-4.6919E-02 | --- Na+ c 3.6000E-23 1.8422E-21 1.8062E-21 | - --- OH- c 1.7100E-23 5.8077E-22 5.6367E-22 | + --- OH- c 1.7100E-23 5.8078E-22 5.6368E-22 | --- OH c 5.3805E-25 2.2742E-23 2.2204E-23 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -668,14 +668,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.305517E+01 -2.306672E+01 --- H2O(L) 1.960000E+00 1.913081E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 3.599957E-23 1.842153E-21 -1.523109E+02 -1.483514E+02 - --- OH- 1.709997E-23 5.807723E-22 -1.405629E+02 -1.370133E+02 + --- Na+ 3.599971E-23 1.842164E-21 -1.523108E+02 -1.483514E+02 + --- OH- 1.710003E-23 5.807756E-22 -1.405629E+02 -1.370133E+02 --- OH 5.380528E-25 2.274244E-23 -1.487651E+02 -1.450326E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082100E+02 -5.082215E+02 - --- H+ 1 1.709997E-23 5.807723E-22 -4.907938E+01 -4.552986E+01 -6.592672E+01 -5.882770E+01 + --- H+ 1 1.710003E-23 5.807756E-22 -4.907937E+01 -4.552986E+01 -6.592672E+01 -5.882769E+01 --- H2O 1 4.000000E-02 8.691895E-02 -1.248769E+02 -1.241123E+02 -1.161360E+00 -3.968102E-01 --- NaCl 0 3.905164E-32 3.905164E-32 -1.745266E+02 -1.745382E+02 -9.850336E-03 -2.139702E-02 - --- Cl- 1 3.599957E-23 1.842153E-21 -1.225490E+02 -1.185896E+02 -1.003431E+02 -9.242424E+01 + --- Cl- 1 3.599971E-23 1.842164E-21 -1.225490E+02 -1.185896E+02 -1.003431E+02 -9.242423E+01 --- H2 1 2.691364E-25 1.137133E-23 -7.368805E+01 -6.995596E+01 -1.237873E+02 -1.125902E+02 --- O2 0 5.500000E-29 5.500000E-29 -9.114013E+01 -9.115168E+01 2.564894E+02 2.415479E+02 --- Norms of Delta G(): 1.261788E+02 1.176329E+02 @@ -705,26 +705,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 5.8077E-22 1.7083E-20 -5.8828E+01 | Normal calc: diag adjusted from 3.44369e+21 to 3.44369e+21 due to act coeff + --- H+ 5.8078E-22 1.7083E-20 -5.8828E+01 | Normal calc: diag adjusted from 3.44367e+21 to 3.44366e+21 due to act coeff --- H2O 8.6919E-02 3.5240E-02 -3.9681E-01 | Normal Calc --- NaCl 3.9052E-32 8.3559E-34 -2.1397E-02 | Normal Calc - --- Cl- 1.8422E-21 8.5130E-20 -9.2424E+01 | Normal calc: diag adjusted from 1.08569e+21 to 1.08569e+21 due to act coeff + --- Cl- 1.8422E-21 8.5130E-20 -9.2424E+01 | Normal calc: diag adjusted from 1.08568e+21 to 1.08568e+21 due to act coeff --- H2 1.1371E-23 4.2676E-22 -1.1259E+02 | Normal Calc --- O2 5.5000E-29 0.0000E+00 2.4155E+02 | Skipped: IC = 0 and DG >0: 2.415E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 5.8077E-22 1.7664E-20 1.7083E-20 | Normal Major Calc + --- H+ 1 5.8078E-22 1.7664E-20 1.7083E-20 | Normal Major Calc --- H2O 1 8.6919E-02 1.2216E-01 3.5240E-02 | Normal Major Calc --- NaCl 0 3.9052E-32 3.9052E-32 0.0000E+00 | minor species not considered - --- Cl- 1 1.8422E-21 8.6972E-20 8.5130E-20 | Normal Major Calc + --- Cl- 1 1.8422E-21 8.6973E-20 8.5130E-20 | Normal Major Calc --- H2 1 1.1371E-23 4.3814E-22 4.2676E-22 | Normal Major Calc --- O2 0 5.5000E-29 5.5000E-29 0.0000E+00 | minor species not considered --- NaCl(S) c 5.0000E+00 5.0000E+00-8.5130E-20 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9131E+00 1.8778E+00-3.5240E-02 | - --- Na+ c 1.8422E-21 8.6972E-20 8.5130E-20 | - --- OH- c 5.8077E-22 1.7664E-20 1.7083E-20 | + --- Na+ c 1.8422E-21 8.6973E-20 8.5130E-20 | + --- OH- c 5.8078E-22 1.7664E-20 1.7083E-20 | --- OH c 2.2742E-23 8.7627E-22 8.5353E-22 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -742,14 +742,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.306672E+01 -2.307531E+01 --- H2O(L) 1.913081E+00 1.877841E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 1.842153E-21 8.697195E-20 -1.483514E+02 -1.444782E+02 - --- OH- 5.807723E-22 1.766352E-20 -1.370133E+02 -1.335799E+02 + --- Na+ 1.842164E-21 8.697260E-20 -1.483514E+02 -1.444782E+02 + --- OH- 5.807756E-22 1.766365E-20 -1.370133E+02 -1.335798E+02 --- OH 2.274244E-23 8.762709E-22 -1.450326E+02 -1.413898E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082215E+02 -5.082301E+02 - --- H+ 1 5.807723E-22 1.766352E-20 -4.552986E+01 -4.209637E+01 -5.882770E+01 -5.196072E+01 + --- H+ 1 5.807756E-22 1.766365E-20 -4.552986E+01 -4.209637E+01 -5.882769E+01 -5.196071E+01 --- H2O 1 8.691895E-02 1.221587E-01 -1.241123E+02 -1.237806E+02 -3.968102E-01 -6.505054E-02 --- NaCl 0 3.905164E-32 3.905164E-32 -1.745382E+02 -1.745468E+02 -2.139702E-02 -2.998264E-02 - --- Cl- 1 1.842153E-21 8.697195E-20 -1.185896E+02 -1.147163E+02 -9.242424E+01 -8.467775E+01 + --- Cl- 1 1.842164E-21 8.697260E-20 -1.185896E+02 -1.147163E+02 -9.242423E+01 -8.467774E+01 --- H2 1 1.137133E-23 4.381355E-22 -6.995596E+01 -6.631312E+01 -1.125902E+02 -1.016617E+02 --- O2 0 5.500000E-29 5.500000E-29 -9.115168E+01 -9.116027E+01 2.415479E+02 2.269679E+02 --- Norms of Delta G(): 1.176329E+02 1.093311E+02 @@ -781,26 +781,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.7664E-20 4.5890E-19 -5.1961E+01 | Normal calc: diag adjusted from 1.13228e+20 to 1.13228e+20 due to act coeff + --- H+ 1.7664E-20 4.5891E-19 -5.1961E+01 | Normal calc: diag adjusted from 1.13227e+20 to 1.13227e+20 due to act coeff --- H2O 1.2216E-01 8.1892E-03 -6.5051E-02 | Normal Calc --- NaCl 3.9052E-32 1.1709E-33 -2.9983E-02 | Normal Calc - --- Cl- 8.6972E-20 3.6823E-18 -8.4678E+01 | Normal calc: diag adjusted from 2.29959e+19 to 2.29959e+19 due to act coeff + --- Cl- 8.6973E-20 3.6823E-18 -8.4678E+01 | Normal calc: diag adjusted from 2.29957e+19 to 2.29957e+19 due to act coeff --- H2 4.3814E-22 1.4847E-20 -1.0166E+02 | Normal Calc --- O2 5.5000E-29 0.0000E+00 2.2697E+02 | Skipped: IC = 0 and DG >0: 2.270E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Full Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 1.7664E-20 4.7657E-19 4.5890E-19 | Normal Major Calc + --- H+ 1 1.7664E-20 4.7657E-19 4.5891E-19 | Normal Major Calc --- H2O 1 1.2216E-01 1.3035E-01 8.1892E-03 | Normal Major Calc --- NaCl 0 3.9052E-32 4.0240E-32 1.1886E-33 | minor species alternative calc - --- Cl- 1 8.6972E-20 3.7693E-18 3.6823E-18 | Normal Major Calc + --- Cl- 1 8.6973E-20 3.7693E-18 3.6823E-18 | Normal Major Calc --- H2 1 4.3814E-22 1.5285E-20 1.4847E-20 | Normal Major Calc --- O2 0 5.5000E-29 5.5000E-39-5.5000E-29 | minor species alternative calc --- NaCl(S) c 5.0000E+00 5.0000E+00-3.6823E-18 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8778E+00 1.8697E+00-8.1892E-03 | - --- Na+ c 8.6972E-20 3.7693E-18 3.6823E-18 | - --- OH- c 1.7664E-20 4.7657E-19 4.5890E-19 | + --- Na+ c 8.6973E-20 3.7693E-18 3.6823E-18 | + --- OH- c 1.7664E-20 4.7657E-19 4.5891E-19 | --- OH c 8.7627E-22 3.0571E-20 2.9694E-20 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -818,14 +818,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307531E+01 -2.307729E+01 --- H2O(L) 1.877841E+00 1.869652E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 8.697195E-20 3.769267E-18 -1.444782E+02 -1.407048E+02 - --- OH- 1.766352E-20 4.765682E-19 -1.335799E+02 -1.302804E+02 + --- Na+ 8.697260E-20 3.769301E-18 -1.444782E+02 -1.407048E+02 + --- OH- 1.766365E-20 4.765725E-19 -1.335798E+02 -1.302804E+02 --- OH 8.762709E-22 3.057066E-20 -1.413898E+02 -1.378397E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082301E+02 -5.082321E+02 - --- H+ 1 1.766352E-20 4.765682E-19 -4.209637E+01 -3.879689E+01 -5.196072E+01 -4.536176E+01 + --- H+ 1 1.766365E-20 4.765725E-19 -4.209637E+01 -3.879688E+01 -5.196071E+01 -4.536174E+01 --- H2O 1 1.221587E-01 1.303479E-01 -1.237806E+02 -1.237177E+02 -6.505054E-02 -2.149391E-03 --- NaCl 0 3.905164E-32 4.024024E-32 -1.745468E+02 -1.745188E+02 -2.998264E-02 -1.984652E-03 - --- Cl- 1 8.697195E-20 3.769267E-18 -1.147163E+02 -1.109429E+02 -8.467775E+01 -7.713091E+01 + --- Cl- 1 8.697260E-20 3.769301E-18 -1.147163E+02 -1.109429E+02 -8.467774E+01 -7.713089E+01 --- H2 1 4.381355E-22 1.528533E-20 -6.631312E+01 -6.276298E+01 -1.016617E+02 -9.101127E+01 --- O2 0 5.500000E-29 5.499996E-39 -9.116027E+01 -1.141881E+02 2.269679E+02 1.897395E+02 --- Norms of Delta G(): 1.093311E+02 9.335505E+01 @@ -856,10 +856,10 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 4.7657E-19 1.0809E-17 -4.5362E+01 | Normal calc: diag adjusted from 4.19667e+18 to 4.19667e+18 due to act coeff + --- H+ 4.7657E-19 1.0809E-17 -4.5362E+01 | Normal calc: diag adjusted from 4.19663e+18 to 4.19663e+18 due to act coeff --- H2O 1.3035E-01 2.8930E-04 -2.1494E-03 | Normal Calc --- NaCl 4.0240E-32 7.9863E-35 -1.9847E-03 | Normal Calc - --- Cl- 3.7693E-18 1.4536E-16 -7.7131E+01 | Normal calc: diag adjusted from 5.30607e+17 to 5.30607e+17 due to act coeff + --- Cl- 3.7693E-18 1.4537E-16 -7.7131E+01 | Normal calc: diag adjusted from 5.30602e+17 to 5.30601e+17 due to act coeff --- H2 1.5285E-20 4.6371E-19 -9.1011E+01 | Normal Calc --- O2 5.5000E-39 0.0000E+00 1.8974E+02 | Skipped: IC = 0 and DG >0: 1.897E+02 ---------------------------------------------------------------------------------- @@ -868,13 +868,13 @@ VCS CALCULATION METHOD --- H+ 1 4.7657E-19 1.1286E-17 1.0809E-17 | Normal Major Calc --- H2O 1 1.3035E-01 1.3064E-01 2.8930E-04 | Normal Major Calc --- NaCl 0 4.0240E-32 4.0240E-32 0.0000E+00 | minor species not considered - --- Cl- 1 3.7693E-18 1.4913E-16 1.4536E-16 | Normal Major Calc + --- Cl- 1 3.7693E-18 1.4913E-16 1.4537E-16 | Normal Major Calc --- H2 1 1.5285E-20 4.7900E-19 4.6371E-19 | Normal Major Calc --- O2 0 5.5000E-39 5.5000E-39 0.0000E+00 | minor species not considered - --- NaCl(S) c 5.0000E+00 5.0000E+00-1.4536E-16 | + --- NaCl(S) c 5.0000E+00 5.0000E+00-1.4537E-16 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8697E+00 1.8694E+00-2.8930E-04 | - --- Na+ c 3.7693E-18 1.4913E-16 1.4536E-16 | + --- Na+ c 3.7693E-18 1.4913E-16 1.4537E-16 | --- OH- c 4.7657E-19 1.1286E-17 1.0809E-17 | --- OH c 3.0571E-20 9.5800E-19 9.2742E-19 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -893,14 +893,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307729E+01 -2.307736E+01 --- H2O(L) 1.869652E+00 1.869363E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 3.769267E-18 1.491328E-16 -1.407048E+02 -1.370267E+02 - --- OH- 4.765682E-19 1.128556E-17 -1.302804E+02 -1.271156E+02 + --- Na+ 3.769301E-18 1.491344E-16 -1.407048E+02 -1.370267E+02 + --- OH- 4.765725E-19 1.128567E-17 -1.302804E+02 -1.271155E+02 --- OH 3.057066E-20 9.579955E-19 -1.378397E+02 -1.343949E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082321E+02 -5.082322E+02 - --- H+ 1 4.765682E-19 1.128556E-17 -3.879689E+01 -3.563207E+01 -4.536176E+01 -3.903212E+01 + --- H+ 1 4.765725E-19 1.128567E-17 -3.879688E+01 -3.563206E+01 -4.536174E+01 -3.903210E+01 --- H2O 1 1.303479E-01 1.306372E-01 -1.237177E+02 -1.237155E+02 -2.149391E-03 -2.456850E-06 --- NaCl 0 4.024024E-32 4.024024E-32 -1.745188E+02 -1.745188E+02 -1.984652E-03 -2.054692E-03 - --- Cl- 1 3.769267E-18 1.491328E-16 -1.109429E+02 -1.072648E+02 -7.713091E+01 -6.977469E+01 + --- Cl- 1 3.769301E-18 1.491344E-16 -1.109429E+02 -1.072648E+02 -7.713089E+01 -6.977467E+01 --- H2 1 1.528533E-20 4.789978E-19 -6.276298E+01 -5.931825E+01 -9.101127E+01 -8.067707E+01 --- O2 0 5.499996E-39 5.499996E-39 -1.141881E+02 -1.141882E+02 1.897395E+02 1.759605E+02 --- Norms of Delta G(): 9.335505E+01 8.550136E+01 @@ -930,10 +930,10 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.1286E-17 2.2025E-16 -3.9032E+01 | Normal calc: diag adjusted from 1.77218e+17 to 1.77218e+17 due to act coeff + --- H+ 1.1286E-17 2.2025E-16 -3.9032E+01 | Normal calc: diag adjusted from 1.77216e+17 to 1.77216e+17 due to act coeff --- H2O 1.3064E-01 3.3144E-07 -2.4569E-06 | Normal Calc --- NaCl 4.0240E-32 8.2681E-35 -2.0547E-03 | Normal Calc - --- Cl- 1.4913E-16 5.2028E-15 -6.9775E+01 | Normal calc: diag adjusted from 1.34109e+16 to 1.34109e+16 due to act coeff + --- Cl- 1.4913E-16 5.2029E-15 -6.9775E+01 | Normal calc: diag adjusted from 1.34107e+16 to 1.34107e+16 due to act coeff --- H2 4.7900E-19 1.2881E-17 -8.0677E+01 | Normal Calc --- O2 5.5000E-39 0.0000E+00 1.7596E+02 | Skipped: IC = 0 and DG >0: 1.760E+02 ---------------------------------------------------------------------------------- @@ -942,13 +942,13 @@ VCS CALCULATION METHOD --- H+ 1 1.1286E-17 2.3154E-16 2.2025E-16 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01 3.3144E-07 | Normal Major Calc --- NaCl 0 4.0240E-32 4.0240E-32 0.0000E+00 | minor species not considered - --- Cl- 1 1.4913E-16 5.3520E-15 5.2028E-15 | Normal Major Calc + --- Cl- 1 1.4913E-16 5.3520E-15 5.2029E-15 | Normal Major Calc --- H2 1 4.7900E-19 1.3360E-17 1.2881E-17 | Normal Major Calc --- O2 0 5.5000E-39 5.5000E-39 0.0000E+00 | minor species not considered - --- NaCl(S) c 5.0000E+00 5.0000E+00-5.2028E-15 | + --- NaCl(S) c 5.0000E+00 5.0000E+00-5.2029E-15 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00-3.3144E-07 | - --- Na+ c 1.4913E-16 5.3520E-15 5.2028E-15 | + --- Na+ c 1.4913E-16 5.3520E-15 5.2029E-15 | --- OH- c 1.1286E-17 2.3154E-16 2.2025E-16 | --- OH c 9.5800E-19 2.6721E-17 2.5763E-17 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -959,7 +959,7 @@ VCS CALCULATION METHOD --- Total Old Dimensionless Gibbs Free Energy = -1.2123243932456E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243932456E+03 --- subroutine FORCE: Beginning Slope = -1.18696e-12 - --- subroutine FORCE: End Slope = -3.33948e-13 + --- subroutine FORCE: End Slope = -3.33952e-13 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -967,14 +967,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869363E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 1.491328E-16 5.351979E-15 -1.370267E+02 -1.334463E+02 - --- OH- 1.128556E-17 2.315351E-16 -1.271156E+02 -1.240943E+02 + --- Na+ 1.491344E-16 5.352045E-15 -1.370267E+02 -1.334463E+02 + --- OH- 1.128567E-17 2.315378E-16 -1.271155E+02 -1.240943E+02 --- OH 9.579955E-19 2.672075E-17 -1.343949E+02 -1.310666E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 1.128556E-17 2.315351E-16 -3.563207E+01 -3.261086E+01 -3.903212E+01 -3.298970E+01 + --- H+ 1 1.128567E-17 2.315378E-16 -3.563206E+01 -3.261085E+01 -3.903210E+01 -3.298968E+01 --- H2O 1 1.306372E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -2.456850E-06 -3.225864E-12 --- NaCl 0 4.024024E-32 4.024024E-32 -1.745188E+02 -1.745188E+02 -2.054692E-03 -2.054772E-03 - --- Cl- 1 1.491328E-16 5.351979E-15 -1.072648E+02 -1.036844E+02 -6.977469E+01 -6.261392E+01 + --- Cl- 1 1.491344E-16 5.352045E-15 -1.072648E+02 -1.036844E+02 -6.977467E+01 -6.261389E+01 --- H2 1 4.789978E-19 1.336038E-17 -5.931825E+01 -5.598989E+01 -8.067707E+01 -7.069201E+01 --- O2 0 5.499996E-39 5.499996E-39 -1.141882E+02 -1.141882E+02 1.759605E+02 1.626471E+02 --- Norms of Delta G(): 8.550136E+01 7.795325E+01 @@ -1004,26 +1004,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 2.3154E-16 3.8191E-15 -3.2990E+01 | Normal calc: diag adjusted from 8.638e+15 to 8.638e+15 due to act coeff + --- H+ 2.3154E-16 3.8192E-15 -3.2990E+01 | Normal calc: diag adjusted from 8.6379e+15 to 8.63789e+15 due to act coeff --- H2O 1.3064E-01 0.0000E+00 -3.2259E-12 | Skipped: superconverged DG = -3.226E-12 --- NaCl 4.0240E-32 8.2685E-35 -2.0548E-03 | Normal Calc - --- Cl- 5.3520E-15 1.6755E-13 -6.2614E+01 | Normal calc: diag adjusted from 3.73694e+14 to 3.73693e+14 due to act coeff + --- Cl- 5.3520E-15 1.6756E-13 -6.2614E+01 | Normal calc: diag adjusted from 3.73689e+14 to 3.73688e+14 due to act coeff --- H2 1.3360E-17 3.1482E-16 -7.0692E+01 | Normal Calc --- O2 5.5000E-39 0.0000E+00 1.6265E+02 | Skipped: IC = 0 and DG >0: 1.626E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 2.3154E-16 4.0507E-15 3.8191E-15 | Normal Major Calc + --- H+ 1 2.3154E-16 4.0507E-15 3.8192E-15 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01 0.0000E+00 | major species is converged --- NaCl 0 4.0240E-32 4.0240E-32 0.0000E+00 | minor species not considered - --- Cl- 1 5.3520E-15 1.7291E-13 1.6755E-13 | Normal Major Calc + --- Cl- 1 5.3520E-15 1.7291E-13 1.6756E-13 | Normal Major Calc --- H2 1 1.3360E-17 3.2818E-16 3.1482E-16 | Normal Major Calc --- O2 0 5.5000E-39 5.5000E-39 0.0000E+00 | minor species not considered - --- NaCl(S) c 5.0000E+00 5.0000E+00-1.6755E-13 | + --- NaCl(S) c 5.0000E+00 5.0000E+00-1.6756E-13 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00-4.4488E-15 | - --- Na+ c 5.3520E-15 1.7291E-13 1.6755E-13 | - --- OH- c 2.3154E-16 4.0507E-15 3.8191E-15 | + --- Na+ c 5.3520E-15 1.7291E-13 1.6756E-13 | + --- OH- c 2.3154E-16 4.0507E-15 3.8192E-15 | --- OH c 2.6721E-17 6.5637E-16 6.2965E-16 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1032,8 +1032,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243932456E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243932456E+03 - --- subroutine FORCE: Beginning Slope = -1.06395e-11 - --- subroutine FORCE: End Slope = -9.44999e-12 + --- subroutine FORCE: Beginning Slope = -1.06396e-11 + --- subroutine FORCE: End Slope = -9.45012e-12 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1041,14 +1041,14 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 5.351979E-15 1.729062E-13 -1.334463E+02 -1.299710E+02 - --- OH- 2.315351E-16 4.050672E-15 -1.240943E+02 -1.212324E+02 + --- Na+ 5.352045E-15 1.729085E-13 -1.334463E+02 -1.299710E+02 + --- OH- 2.315378E-16 4.050722E-15 -1.240943E+02 -1.212324E+02 --- OH 2.672075E-17 6.563687E-16 -1.310666E+02 -1.278653E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 2.315351E-16 4.050672E-15 -3.261086E+01 -2.974896E+01 -3.298970E+01 -2.726589E+01 + --- H+ 1 2.315378E-16 4.050722E-15 -3.261085E+01 -2.974895E+01 -3.298968E+01 -2.726587E+01 --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.225864E-12 -3.026912E-12 --- NaCl 0 4.024024E-32 4.024024E-32 -1.745188E+02 -1.745188E+02 -2.054772E-03 -2.054772E-03 - --- Cl- 1 5.351979E-15 1.729062E-13 -1.036844E+02 -1.002091E+02 -6.261392E+01 -5.566336E+01 + --- Cl- 1 5.352045E-15 1.729085E-13 -1.036844E+02 -1.002091E+02 -6.261389E+01 -5.566333E+01 --- H2 1 1.336038E-17 3.281844E-16 -5.598989E+01 -5.278861E+01 -7.069201E+01 -6.108817E+01 --- O2 0 5.499996E-39 5.499996E-39 -1.141882E+02 -1.141882E+02 1.626471E+02 1.498420E+02 --- Norms of Delta G(): 7.795325E+01 7.074156E+01 @@ -1080,16 +1080,16 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 4.0507E-15 5.5223E-14 -2.7266E+01 | Normal calc: diag adjusted from 4.93745e+14 to 4.93745e+14 due to act coeff + --- H+ 4.0507E-15 5.5223E-14 -2.7266E+01 | Normal calc: diag adjusted from 4.93739e+14 to 4.93739e+14 due to act coeff --- H2O 1.3064E-01 0.0000E+00 -3.0269E-12 | Skipped: superconverged DG = -3.027E-12 --- NaCl 4.0240E-32 8.2685E-35 -2.0548E-03 | Normal Calc - --- Cl- 1.7291E-13 4.8123E-12 -5.5663E+01 | Normal calc: diag adjusted from 1.1567e+13 to 1.1567e+13 due to act coeff + --- Cl- 1.7291E-13 4.8123E-12 -5.5663E+01 | Normal calc: diag adjusted from 1.15668e+13 to 1.15668e+13 due to act coeff --- H2 3.2818E-16 6.6827E-15 -6.1088E+01 | Normal Calc --- O2 5.5000E-39 0.0000E+00 1.4984E+02 | Skipped: IC = 0 and DG >0: 1.498E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Full Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 4.0507E-15 5.9273E-14 5.5223E-14 | Normal Major Calc + --- H+ 1 4.0507E-15 5.9274E-14 5.5223E-14 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01 0.0000E+00 | major species is converged --- NaCl 0 4.0240E-32 4.0323E-32 8.2770E-35 | minor species alternative calc --- Cl- 1 1.7291E-13 4.9852E-12 4.8123E-12 | Normal Major Calc @@ -1097,9 +1097,9 @@ VCS CALCULATION METHOD --- O2 0 5.5000E-39 5.5000E-49-5.5000E-39 | minor species alternative calc --- NaCl(S) c 5.0000E+00 5.0000E+00-4.8123E-12 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.8694E+00 1.8694E+00-6.8588E-14 | + --- H2O(L) c 1.8694E+00 1.8694E+00-6.8589E-14 | --- Na+ c 1.7291E-13 4.9852E-12 4.8123E-12 | - --- OH- c 4.0507E-15 5.9273E-14 5.5223E-14 | + --- OH- c 4.0507E-15 5.9274E-14 5.5223E-14 | --- OH c 6.5637E-16 1.4022E-14 1.3365E-14 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1108,8 +1108,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243932456E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243932459E+03 - --- subroutine FORCE: Beginning Slope = -2.69781e-10 - --- subroutine FORCE: End Slope = -2.37071e-10 + --- subroutine FORCE: Beginning Slope = -2.69785e-10 + --- subroutine FORCE: End Slope = -2.37074e-10 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -1117,17 +1117,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 1.729062E-13 4.985182E-12 -1.299710E+02 -1.266095E+02 - --- OH- 4.050672E-15 5.927327E-14 -1.212324E+02 -1.185492E+02 + --- Na+ 1.729085E-13 4.985249E-12 -1.299710E+02 -1.266095E+02 + --- OH- 4.050722E-15 5.927399E-14 -1.212324E+02 -1.185492E+02 --- OH 6.563687E-16 1.402182E-14 -1.278653E+02 -1.248036E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 4.050672E-15 5.927327E-14 -2.974896E+01 -2.706569E+01 -2.726589E+01 -2.189936E+01 + --- H+ 1 4.050722E-15 5.927399E-14 -2.974895E+01 -2.706568E+01 -2.726587E+01 -2.189934E+01 --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 -3.026912E-12 2.174261E-12 --- NaCl 0 4.024024E-32 4.032301E-32 -1.745188E+02 -1.745168E+02 -2.054772E-03 0.000000E+00 - --- Cl- 1 1.729062E-13 4.985182E-12 -1.002091E+02 -9.684768E+01 -5.566336E+01 -4.894043E+01 + --- Cl- 1 1.729085E-13 4.985249E-12 -1.002091E+02 -9.684767E+01 -5.566333E+01 -4.894040E+01 --- H2 1 3.281844E-16 7.010911E-15 -5.278861E+01 -4.972696E+01 -6.108817E+01 -5.190322E+01 --- O2 0 5.499996E-39 5.499996E-49 -1.141882E+02 -1.372140E+02 1.498420E+02 1.145695E+02 - --- Norms of Delta G(): 7.074156E+01 5.581945E+01 + --- Norms of Delta G(): 7.074156E+01 5.581944E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693625E+00 @@ -1155,26 +1155,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 5.9273E-14 6.4902E-13 -2.1899E+01 | Normal calc: diag adjusted from 3.3742e+13 to 3.3742e+13 due to act coeff + --- H+ 5.9274E-14 6.4903E-13 -2.1899E+01 | Normal calc: diag adjusted from 3.37416e+13 to 3.37416e+13 due to act coeff --- H2O 1.3064E-01 0.0000E+00 2.1743E-12 | Skipped: superconverged DG = 2.174E-12 --- NaCl 4.0323E-32 0.0000E+00 0.0000E+00 | Skipped: superconverged DG = 0.000E+00 - --- Cl- 4.9852E-12 1.2199E-10 -4.8940E+01 | Normal calc: diag adjusted from 4.01189e+11 to 4.01186e+11 due to act coeff + --- Cl- 4.9852E-12 1.2199E-10 -4.8940E+01 | Normal calc: diag adjusted from 4.01184e+11 to 4.01181e+11 due to act coeff --- H2 7.0109E-15 1.2130E-13 -5.1903E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 1.1457E+02 | Skipped: IC = 0 and DG >0: 1.146E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 5.9273E-14 7.0830E-13 6.4902E-13 | Normal Major Calc + --- H+ 1 5.9274E-14 7.0830E-13 6.4903E-13 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01 0.0000E+00 | major species is converged --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 4.9852E-12 1.2697E-10 1.2199E-10 | Normal Major Calc + --- Cl- 1 4.9852E-12 1.2698E-10 1.2199E-10 | Normal Major Calc --- H2 1 7.0109E-15 1.2831E-13 1.2130E-13 | Normal Major Calc --- O2 0 5.5000E-49 5.5000E-49 0.0000E+00 | minor species not considered --- NaCl(S) c 5.0000E+00 5.0000E+00-1.2199E-10 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00-8.9162E-13 | - --- Na+ c 4.9852E-12 1.2697E-10 1.2199E-10 | - --- OH- c 5.9273E-14 7.0830E-13 6.4902E-13 | + --- Na+ c 4.9852E-12 1.2698E-10 1.2199E-10 | + --- OH- c 5.9274E-14 7.0830E-13 6.4903E-13 | --- OH c 1.4022E-14 2.5661E-13 2.4259E-13 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1183,8 +1183,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243932459E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243932513E+03 - --- subroutine FORCE: Beginning Slope = -5.99072e-09 - --- subroutine FORCE: End Slope = -5.19657e-09 + --- subroutine FORCE: Beginning Slope = -5.99079e-09 + --- subroutine FORCE: End Slope = -5.19663e-09 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1192,17 +1192,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 4.985182E-12 1.269745E-10 -1.266095E+02 -1.233721E+02 - --- OH- 5.927327E-14 7.082968E-13 -1.185492E+02 -1.160685E+02 + --- Na+ 4.985249E-12 1.269762E-10 -1.266095E+02 -1.233721E+02 + --- OH- 5.927399E-14 7.083047E-13 -1.185492E+02 -1.160685E+02 --- OH 1.402182E-14 2.566144E-13 -1.248036E+02 -1.218967E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 5.927327E-14 7.082968E-13 -2.706569E+01 -2.458505E+01 -2.189936E+01 -1.693807E+01 + --- H+ 1 5.927399E-14 7.083047E-13 -2.706568E+01 -2.458504E+01 -2.189934E+01 -1.693805E+01 --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.174261E-12 1.332836E-10 --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 0.000000E+00 -8.526513E-14 - --- Cl- 1 4.985182E-12 1.269745E-10 -9.684768E+01 -9.361022E+01 -4.894043E+01 -4.246551E+01 + --- Cl- 1 4.985249E-12 1.269762E-10 -9.684767E+01 -9.361021E+01 -4.894040E+01 -4.246549E+01 --- H2 1 7.010911E-15 1.283072E-13 -4.972696E+01 -4.682000E+01 -5.190322E+01 -4.318234E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 1.145695E+02 1.029417E+02 - --- Norms of Delta G(): 5.581945E+01 4.924754E+01 + --- Norms of Delta G(): 5.581944E+01 4.924754E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693625E+00 @@ -1229,26 +1229,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 7.0830E-13 5.9986E-12 -1.6938E+01 | Normal calc: diag adjusted from 2.82368e+12 to 2.82367e+12 due to act coeff + --- H+ 7.0830E-13 5.9987E-12 -1.6938E+01 | Normal calc: diag adjusted from 2.82364e+12 to 2.82364e+12 due to act coeff --- H2O 1.3064E-01 -1.7981E-11 1.3328E-10 | Normal Calc --- NaCl 4.0323E-32 0.0000E+00 -8.5265E-14 | Skipped: superconverged DG = -8.527E-14 - --- Cl- 1.2697E-10 2.6961E-09 -4.2466E+01 | Normal calc: diag adjusted from 1.57512e+10 to 1.57506e+10 due to act coeff + --- Cl- 1.2698E-10 2.6961E-09 -4.2465E+01 | Normal calc: diag adjusted from 1.5751e+10 to 1.57504e+10 due to act coeff --- H2 1.2831E-13 1.8469E-12 -4.3182E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 1.0294E+02 | Skipped: IC = 0 and DG >0: 1.029E+02 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 7.0830E-13 6.7069E-12 5.9986E-12 | Normal Major Calc + --- H+ 1 7.0830E-13 6.7070E-12 5.9987E-12 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01-1.7981E-11 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 1.2697E-10 2.8231E-09 2.6961E-09 | Normal Major Calc + --- Cl- 1 1.2698E-10 2.8231E-09 2.6961E-09 | Normal Major Calc --- H2 1 1.2831E-13 1.9752E-12 1.8469E-12 | Normal Major Calc --- O2 0 5.5000E-49 5.5000E-49 0.0000E+00 | minor species not considered --- NaCl(S) c 5.0000E+00 5.0000E+00-2.6961E-09 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.8694E+00 1.8694E+00 8.2882E-12 | - --- Na+ c 1.2697E-10 2.8231E-09 2.6961E-09 | - --- OH- c 7.0830E-13 6.7069E-12 5.9986E-12 | + --- H2O(L) c 1.8694E+00 1.8694E+00 8.2881E-12 | + --- Na+ c 1.2698E-10 2.8231E-09 2.6961E-09 | + --- OH- c 7.0830E-13 6.7070E-12 5.9987E-12 | --- OH c 2.5661E-13 3.9504E-12 3.6937E-12 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1257,8 +1257,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243932513E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243933538E+03 - --- subroutine FORCE: Beginning Slope = -1.14673e-07 - --- subroutine FORCE: End Slope = -9.79081e-08 + --- subroutine FORCE: Beginning Slope = -1.14675e-07 + --- subroutine FORCE: End Slope = -9.79092e-08 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1266,17 +1266,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 1.269745E-10 2.823091E-09 -1.233721E+02 -1.202707E+02 - --- OH- 7.082968E-13 6.706888E-12 -1.160685E+02 -1.138208E+02 + --- Na+ 1.269762E-10 2.823125E-09 -1.233721E+02 -1.202707E+02 + --- OH- 7.083047E-13 6.706956E-12 -1.160685E+02 -1.138208E+02 --- OH 2.566144E-13 3.950352E-12 -1.218967E+02 -1.191627E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 7.082968E-13 6.706888E-12 -2.458505E+01 -2.233729E+01 -1.693807E+01 -1.244255E+01 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 1.332836E-10 2.889266E-09 + --- H+ 1 7.083047E-13 6.706956E-12 -2.458504E+01 -2.233728E+01 -1.693805E+01 -1.244253E+01 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 1.332836E-10 2.889323E-09 --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 -8.526513E-14 2.927436E-12 - --- Cl- 1 1.269745E-10 2.823091E-09 -9.361022E+01 -9.050889E+01 -4.246551E+01 -3.626285E+01 + --- Cl- 1 1.269762E-10 2.823125E-09 -9.361021E+01 -9.050888E+01 -4.246549E+01 -3.626282E+01 --- H2 1 1.283072E-13 1.975176E-12 -4.682000E+01 -4.408602E+01 -4.318234E+01 -3.498039E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 1.029417E+02 9.200573E+01 - --- Norms of Delta G(): 4.924754E+01 4.312481E+01 + --- Norms of Delta G(): 4.924754E+01 4.312480E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693625E+00 @@ -1303,26 +1303,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 6.7069E-12 4.1725E-11 -1.2443E+01 | Normal calc: diag adjusted from 2.98201e+11 to 2.98201e+11 due to act coeff - --- H2O 1.3064E-01 -3.8977E-10 2.8893E-09 | Normal Calc + --- H+ 6.7070E-12 4.1726E-11 -1.2443E+01 | Normal calc: diag adjusted from 2.98198e+11 to 2.98198e+11 due to act coeff + --- H2O 1.3064E-01 -3.8978E-10 2.8893E-09 | Normal calc: diag adjusted from 7.41267 to 7.41267 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 2.9274E-12 | Skipped: superconverged DG = 2.927E-12 - --- Cl- 2.8231E-09 5.1195E-08 -3.6263E+01 | Normal calc: diag adjusted from 7.08443e+08 to 7.08323e+08 due to act coeff + --- Cl- 2.8231E-09 5.1196E-08 -3.6263E+01 | Normal calc: diag adjusted from 7.08435e+08 to 7.08315e+08 due to act coeff --- H2 1.9752E-12 2.3031E-11 -3.4980E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 9.2006E+01 | Skipped: IC = 0 and DG >0: 9.201E+01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 6.7069E-12 4.8432E-11 4.1725E-11 | Normal Major Calc - --- H2O 1 1.3064E-01 1.3064E-01-3.8977E-10 | Normal Major Calc + --- H+ 1 6.7070E-12 4.8433E-11 4.1726E-11 | Normal Major Calc + --- H2O 1 1.3064E-01 1.3064E-01-3.8978E-10 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 2.8231E-09 5.4018E-08 5.1195E-08 | Normal Major Calc + --- Cl- 1 2.8231E-09 5.4019E-08 5.1196E-08 | Normal Major Calc --- H2 1 1.9752E-12 2.5006E-11 2.3031E-11 | Normal Major Calc --- O2 0 5.5000E-49 5.5000E-49 0.0000E+00 | minor species not considered - --- NaCl(S) c 5.0000E+00 5.0000E+00-5.1195E-08 | + --- NaCl(S) c 5.0000E+00 5.0000E+00-5.1196E-08 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00 3.0199E-10 | - --- Na+ c 2.8231E-09 5.4018E-08 5.1195E-08 | - --- OH- c 6.7069E-12 4.8432E-11 4.1725E-11 | + --- Na+ c 2.8231E-09 5.4019E-08 5.1196E-08 | + --- OH- c 6.7070E-12 4.8433E-11 4.1726E-11 | --- OH c 3.9504E-12 5.0012E-11 4.6062E-11 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1331,8 +1331,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243933538E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2123243949950E+03 - --- subroutine FORCE: Beginning Slope = -1.85781e-06 - --- subroutine FORCE: End Slope = -1.55538e-06 + --- subroutine FORCE: Beginning Slope = -1.85783e-06 + --- subroutine FORCE: End Slope = -1.5554e-06 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1340,17 +1340,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 5.000000E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 2.823091E-09 5.401842E-08 -1.202707E+02 -1.173204E+02 - --- OH- 6.706888E-12 4.843231E-11 -1.138208E+02 -1.118449E+02 + --- Na+ 2.823125E-09 5.401906E-08 -1.202707E+02 -1.173204E+02 + --- OH- 6.706956E-12 4.843273E-11 -1.138208E+02 -1.118449E+02 --- OH 3.950352E-12 5.001197E-11 -1.191627E+02 -1.166242E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 6.706888E-12 4.843231E-11 -2.233729E+01 -2.036140E+01 -1.244255E+01 -8.490778E+00 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.889266E-09 5.477270E-08 + --- H+ 1 6.706956E-12 4.843273E-11 -2.233728E+01 -2.036139E+01 -1.244253E+01 -8.490760E+00 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 2.889323E-09 5.477331E-08 --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.927436E-12 8.054712E-11 - --- Cl- 1 2.823091E-09 5.401842E-08 -9.050889E+01 -8.755854E+01 -3.626285E+01 -3.036215E+01 + --- Cl- 1 2.823125E-09 5.401906E-08 -9.050888E+01 -8.755853E+01 -3.626282E+01 -3.036213E+01 --- H2 1 1.975176E-12 2.500598E-11 -4.408602E+01 -4.154756E+01 -3.498039E+01 -2.736502E+01 --- O2 0 5.499996E-49 5.499996E-49 -1.372140E+02 -1.372140E+02 9.200573E+01 8.185190E+01 - --- Norms of Delta G(): 4.312481E+01 3.751118E+01 + --- Norms of Delta G(): 4.312480E+01 3.751118E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693626E+00 @@ -1379,26 +1379,26 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 4.8432E-11 2.0561E-10 -8.4908E+00 | Normal calc: diag adjusted from 4.12947e+10 to 4.12947e+10 due to act coeff + --- H+ 4.8433E-11 2.0562E-10 -8.4908E+00 | Normal calc: diag adjusted from 4.12944e+10 to 4.12944e+10 due to act coeff --- H2O 1.3064E-01 -7.3891E-09 5.4773E-08 | Normal Calc --- NaCl 4.0323E-32 0.0000E+00 8.0547E-11 | Skipped: superconverged DG = 8.055E-11 - --- Cl- 5.4018E-08 8.2067E-07 -3.0362E+01 | Normal calc: diag adjusted from 3.70244e+07 to 3.6997e+07 due to act coeff + --- Cl- 5.4019E-08 8.2067E-07 -3.0362E+01 | Normal calc: diag adjusted from 3.7024e+07 to 3.69965e+07 due to act coeff --- H2 2.5006E-11 2.2810E-10 -2.7365E+01 | Normal Calc --- O2 5.5000E-49 0.0000E+00 8.1852E+01 | Skipped: IC = 0 and DG >0: 8.185E+01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Full Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 4.8432E-11 2.5405E-10 2.0561E-10 | Normal Major Calc + --- H+ 1 4.8433E-11 2.5405E-10 2.0562E-10 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01-7.3891E-09 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species alternative calc - --- Cl- 1 5.4018E-08 8.7468E-07 8.2067E-07 | Normal Major Calc + --- Cl- 1 5.4019E-08 8.7469E-07 8.2067E-07 | Normal Major Calc --- H2 1 2.5006E-11 2.5310E-10 2.2810E-10 | Normal Major Calc --- O2 0 5.5000E-49 5.5000E-59-5.5000E-49 | minor species alternative calc --- NaCl(S) c 5.0000E+00 5.0000E+00-8.2067E-07 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00 6.7273E-09 | - --- Na+ c 5.4018E-08 8.7468E-07 8.2067E-07 | - --- OH- c 4.8432E-11 2.5405E-10 2.0561E-10 | + --- Na+ c 5.4019E-08 8.7469E-07 8.2067E-07 | + --- OH- c 4.8433E-11 2.5405E-10 2.0562E-10 | --- OH c 5.0012E-11 5.0620E-10 4.5619E-10 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- @@ -1406,9 +1406,9 @@ VCS CALCULATION METHOD --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2123243949950E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123244166932E+03 - --- subroutine FORCE: Beginning Slope = -2.49252e-05 - --- subroutine FORCE: End Slope = -2.03599e-05 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123244166934E+03 + --- subroutine FORCE: Beginning Slope = -2.49254e-05 + --- subroutine FORCE: End Slope = -2.03601e-05 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -1416,17 +1416,17 @@ VCS CALCULATION METHOD --- NaCl(S) 5.000000E+00 4.999999E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869362E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 5.401842E-08 8.746840E-07 -1.173204E+02 -1.145403E+02 - --- OH- 4.843231E-11 2.540464E-10 -1.118449E+02 -1.101920E+02 + --- Na+ 5.401906E-08 8.746936E-07 -1.173204E+02 -1.145403E+02 + --- OH- 4.843273E-11 2.540482E-10 -1.118449E+02 -1.101920E+02 --- OH 5.001197E-11 5.062047E-10 -1.166242E+02 -1.143096E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 4.843231E-11 2.540464E-10 -2.036140E+01 -1.870850E+01 -8.490778E+00 -5.184988E+00 - --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 5.477270E-08 8.762514E-07 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 8.054712E-11 1.703739E-09 - --- Cl- 1 5.401842E-08 8.746840E-07 -8.755854E+01 -8.477846E+01 -3.036215E+01 -2.480199E+01 + --- H+ 1 4.843273E-11 2.540482E-10 -2.036139E+01 -1.870849E+01 -8.490760E+00 -5.184974E+00 + --- H2O 1 1.306375E-01 1.306375E-01 -1.237155E+02 -1.237155E+02 5.477331E-08 8.762610E-07 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 8.054712E-11 1.703768E-09 + --- Cl- 1 5.401906E-08 8.746936E-07 -8.755853E+01 -8.477845E+01 -3.036213E+01 -2.480197E+01 --- H2 1 2.500598E-11 2.531024E-10 -4.154756E+01 -3.923288E+01 -2.736502E+01 -2.042098E+01 --- O2 0 5.499996E-49 5.500000E-59 -1.372140E+02 -1.602399E+02 8.185190E+01 4.956734E+01 - --- Norms of Delta G(): 3.751118E+01 2.420730E+01 + --- Norms of Delta G(): 3.751118E+01 2.420729E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693642E+00 @@ -1434,7 +1434,7 @@ VCS CALCULATION METHOD --- NaCl(S) = 4.9999991E+00 ------------------------------------------------------------------------------------------------------- --- Total Old Dimensionless Gibbs Free Energy = -1.2123243949950E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123244166932E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123244166934E+03 --- Increment counter increased, step is accepted: 14 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1454,36 +1454,36 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 2.5405E-10 6.5861E-10 -5.1850E+00 | Normal calc: diag adjusted from 7.87258e+09 to 7.87257e+09 due to act coeff - --- H2O 1.3064E-01 -1.1821E-07 8.7625E-07 | Normal calc: diag adjusted from 7.41267 to 7.41267 due to act coeff - --- NaCl 4.0323E-32 0.0000E+00 1.7037E-09 | Skipped: IC = 0 and DG >0: 1.704E-09 - --- Cl- 8.7468E-07 1.0879E-05 -2.4802E+01 | Normal calc: diag adjusted from 2.28654e+06 to 2.27979e+06 due to act coeff + --- H+ 2.5405E-10 6.5862E-10 -5.1850E+00 | Normal calc: diag adjusted from 7.87252e+09 to 7.87251e+09 due to act coeff + --- H2O 1.3064E-01 -1.1821E-07 8.7626E-07 | Normal calc: diag adjusted from 7.41267 to 7.41267 due to act coeff + --- NaCl 4.0323E-32 0.0000E+00 1.7038E-09 | Skipped: IC = 0 and DG >0: 1.704E-09 + --- Cl- 8.7469E-07 1.0879E-05 -2.4802E+01 | Normal calc: diag adjusted from 2.28651e+06 to 2.27977e+06 due to act coeff --- H2 2.5310E-10 1.7229E-09 -2.0421E+01 | Normal Calc --- O2 5.5000E-59 0.0000E+00 4.9567E+01 | Skipped: IC = 0 and DG >0: 4.957E+01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 2.5405E-10 9.1266E-10 6.5861E-10 | Normal Major Calc + --- H+ 1 2.5405E-10 9.1267E-10 6.5862E-10 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01-1.1821E-07 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 8.7468E-07 1.1754E-05 1.0879E-05 | Normal Major Calc + --- Cl- 1 8.7469E-07 1.1754E-05 1.0879E-05 | Normal Major Calc --- H2 1 2.5310E-10 1.9760E-09 1.7229E-09 | Normal Major Calc --- O2 0 5.5000E-59 5.5000E-59 0.0000E+00 | minor species not considered --- NaCl(S) c 5.0000E+00 5.0000E+00-1.0879E-05 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00 1.1411E-07 | - --- Na+ c 8.7468E-07 1.1754E-05 1.0879E-05 | - --- OH- c 2.5405E-10 9.1266E-10 6.5861E-10 | + --- Na+ c 8.7469E-07 1.1754E-05 1.0879E-05 | + --- OH- c 2.5405E-10 9.1267E-10 6.5862E-10 | --- OH c 5.0620E-10 3.9519E-09 3.4457E-09 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123244166932E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123246474310E+03 - --- subroutine FORCE: Beginning Slope = -0.000269861 - --- subroutine FORCE: End Slope = -0.000213655 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123244166934E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123246474334E+03 + --- subroutine FORCE: Beginning Slope = -0.000269863 + --- subroutine FORCE: End Slope = -0.000213657 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1491,25 +1491,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.999999E+00 4.999988E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869362E+00 1.869363E+00 -1.237155E+02 -1.237155E+02 - --- Na+ 8.746840E-07 1.175373E-05 -1.145403E+02 -1.119577E+02 - --- OH- 2.540464E-10 9.126609E-10 -1.101920E+02 -1.089286E+02 + --- Na+ 8.746936E-07 1.175385E-05 -1.145403E+02 -1.119577E+02 + --- OH- 2.540482E-10 9.126655E-10 -1.101920E+02 -1.089286E+02 --- OH 5.062047E-10 3.951936E-09 -1.143096E+02 -1.122545E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 2.540464E-10 9.126609E-10 -1.870850E+01 -1.744499E+01 -5.184988E+00 -2.658091E+00 - --- H2O 1 1.306375E-01 1.306374E-01 -1.237155E+02 -1.237155E+02 8.762514E-07 1.155212E-05 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 1.703739E-09 2.907029E-08 - --- Cl- 1 8.746840E-07 1.175373E-05 -8.477846E+01 -8.219584E+01 -2.480199E+01 -1.963675E+01 + --- H+ 1 2.540482E-10 9.126655E-10 -1.870849E+01 -1.744498E+01 -5.184974E+00 -2.658081E+00 + --- H2O 1 1.306375E-01 1.306374E-01 -1.237155E+02 -1.237155E+02 8.762610E-07 1.155224E-05 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 1.703768E-09 2.907063E-08 + --- Cl- 1 8.746936E-07 1.175385E-05 -8.477845E+01 -8.219583E+01 -2.480197E+01 -1.963673E+01 --- H2 1 2.531024E-10 1.975968E-09 -3.923288E+01 -3.717786E+01 -2.042098E+01 -1.425589E+01 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 4.956734E+01 4.134723E+01 - --- Norms of Delta G(): 2.420730E+01 1.960226E+01 + --- Norms of Delta G(): 2.420729E+01 1.960226E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8693861E+00 --- air = 4.1306374E+00 --- NaCl(S) = 4.9999882E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123244166932E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123246474310E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123244166934E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123246474334E+03 --- Increment counter increased, step is accepted: 15 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1528,16 +1528,16 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 9.1266E-10 1.2130E-09 -2.6581E+00 | Normal calc: diag adjusted from 2.19139e+09 to 2.19139e+09 due to act coeff + --- H+ 9.1267E-10 1.2130E-09 -2.6581E+00 | Normal calc: diag adjusted from 2.19138e+09 to 2.19138e+09 due to act coeff --- H2O 1.3064E-01 -1.5584E-06 1.1552E-05 | Normal calc: diag adjusted from 7.41269 to 7.41269 due to act coeff - --- NaCl 4.0323E-32 0.0000E+00 2.9070E-08 | Skipped: IC = 0 and DG >0: 2.907E-08 - --- Cl- 1.1754E-05 1.1662E-04 -1.9637E+01 | Normal calc: diag adjusted from 170157 to 168386 due to act coeff + --- NaCl 4.0323E-32 0.0000E+00 2.9071E-08 | Skipped: IC = 0 and DG >0: 2.907E-08 + --- Cl- 1.1754E-05 1.1662E-04 -1.9637E+01 | Normal calc: diag adjusted from 170155 to 168384 due to act coeff --- H2 1.9760E-09 9.3897E-09 -1.4256E+01 | Normal calc: diag adjusted from 1.51824e+09 to 1.51824e+09 due to act coeff --- O2 5.5000E-59 0.0000E+00 4.1347E+01 | Skipped: IC = 0 and DG >0: 4.135E+01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 9.1266E-10 2.1256E-09 1.2130E-09 | Normal Major Calc + --- H+ 1 9.1267E-10 2.1256E-09 1.2130E-09 | Normal Major Calc --- H2O 1 1.3064E-01 1.3064E-01-1.5584E-06 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered --- Cl- 1 1.1754E-05 1.2837E-04 1.1662E-04 | Normal Major Calc @@ -1547,17 +1547,17 @@ VCS CALCULATION METHOD --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00 1.5384E-06 | --- Na+ c 1.1754E-05 1.2837E-04 1.1662E-04 | - --- OH- c 9.1266E-10 2.1256E-09 1.2130E-09 | + --- OH- c 9.1267E-10 2.1256E-09 1.2130E-09 | --- OH c 3.9519E-09 2.2731E-08 1.8779E-08 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474310E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123265632837E+03 - --- subroutine FORCE: Beginning Slope = -0.00229013 - --- subroutine FORCE: End Slope = -0.00174304 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474334E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123265633015E+03 + --- subroutine FORCE: Beginning Slope = -0.00229015 + --- subroutine FORCE: End Slope = -0.00174305 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1565,25 +1565,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.999988E+00 4.999872E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869363E+00 1.869364E+00 -1.237155E+02 -1.237156E+02 - --- Na+ 1.175373E-05 1.283713E-04 -1.119577E+02 -1.096123E+02 - --- OH- 9.126609E-10 2.125630E-09 -1.089286E+02 -1.081289E+02 + --- Na+ 1.175385E-05 1.283725E-04 -1.119577E+02 -1.096123E+02 + --- OH- 9.126655E-10 2.125636E-09 -1.089286E+02 -1.081289E+02 --- OH 3.951936E-09 2.273140E-08 -1.122545E+02 -1.105050E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 9.126609E-10 2.125630E-09 -1.744499E+01 -1.664373E+01 -2.658091E+00 -1.056949E+00 - --- H2O 1 1.306374E-01 1.306359E-01 -1.237155E+02 -1.237155E+02 1.155212E-05 1.219229E-04 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.907029E-08 3.995353E-07 - --- Cl- 1 1.175373E-05 1.283713E-04 -8.219584E+01 -7.985041E+01 -1.963675E+01 -1.494589E+01 + --- H+ 1 9.126655E-10 2.125636E-09 -1.744498E+01 -1.664373E+01 -2.658081E+00 -1.056943E+00 + --- H2O 1 1.306374E-01 1.306359E-01 -1.237155E+02 -1.237155E+02 1.155224E-05 1.219241E-04 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 2.907063E-08 3.995394E-07 + --- Cl- 1 1.175385E-05 1.283725E-04 -8.219583E+01 -7.985040E+01 -1.963673E+01 -1.494588E+01 --- H2 1 1.975968E-09 1.136570E-08 -3.717786E+01 -3.542832E+01 -1.425589E+01 -9.007025E+00 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 4.134723E+01 3.434882E+01 - --- Norms of Delta G(): 1.960226E+01 1.573460E+01 + --- Norms of Delta G(): 1.960226E+01 1.573459E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 1.8696209E+00 --- air = 4.1306359E+00 --- NaCl(S) = 4.9998716E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474310E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123265632837E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123246474334E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123265633015E+03 --- Increment counter increased, step is accepted: 16 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1602,10 +1602,10 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 2.1256E-09 1.1233E-09 -1.0569E+00 | Normal calc: diag adjusted from 9.40898e+08 to 9.40897e+08 due to act coeff + --- H+ 2.1256E-09 1.1233E-09 -1.0569E+00 | Normal calc: diag adjusted from 9.40895e+08 to 9.40894e+08 due to act coeff --- H2O 1.3064E-01 -1.6448E-05 1.2192E-04 | Normal calc: diag adjusted from 7.41285 to 7.41284 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 3.9954E-07 | Skipped: IC = 0 and DG >0: 3.995E-07 - --- Cl- 1.2837E-04 9.8965E-04 -1.4946E+01 | Normal calc: diag adjusted from 15577.7 to 15102.3 due to act coeff + --- Cl- 1.2837E-04 9.8966E-04 -1.4946E+01 | Normal calc: diag adjusted from 15577.5 to 15102.1 due to act coeff --- H2 1.1366E-08 3.4124E-08 -9.0070E+00 | Normal calc: diag adjusted from 2.63952e+08 to 2.63952e+08 due to act coeff --- O2 5.5000E-59 0.0000E+00 3.4349E+01 | Skipped: IC = 0 and DG >0: 3.435E+01 ---------------------------------------------------------------------------------- @@ -1614,13 +1614,13 @@ VCS CALCULATION METHOD --- H+ 1 2.1256E-09 3.2490E-09 1.1233E-09 | Normal Major Calc --- H2O 1 1.3064E-01 1.3062E-01-1.6448E-05 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 1.2837E-04 1.1180E-03 9.8965E-04 | Normal Major Calc + --- Cl- 1 1.2837E-04 1.1180E-03 9.8966E-04 | Normal Major Calc --- H2 1 1.1366E-08 4.5489E-08 3.4124E-08 | Normal Major Calc --- O2 0 5.5000E-59 5.5000E-59 0.0000E+00 | minor species not considered - --- NaCl(S) c 4.9999E+00 4.9989E+00-9.8965E-04 | + --- NaCl(S) c 4.9999E+00 4.9989E+00-9.8966E-04 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8694E+00 1.6378E-05 | - --- Na+ c 1.2837E-04 1.1180E-03 9.8965E-04 | + --- Na+ c 1.2837E-04 1.1180E-03 9.8966E-04 | --- OH- c 2.1256E-09 3.2490E-09 1.1233E-09 | --- OH c 2.2731E-08 9.0979E-08 6.8247E-08 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -1628,10 +1628,10 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632837E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123386178418E+03 - --- subroutine FORCE: Beginning Slope = -0.0147915 - --- subroutine FORCE: End Slope = -0.0107105 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123265633015E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123386179426E+03 + --- subroutine FORCE: Beginning Slope = -0.0147916 + --- subroutine FORCE: End Slope = -0.0107106 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1639,25 +1639,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.999872E+00 4.998882E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307736E+01 --- H2O(L) 1.869364E+00 1.869380E+00 -1.237156E+02 -1.237166E+02 - --- Na+ 1.283713E-04 1.118018E-03 -1.096123E+02 -1.075505E+02 - --- OH- 2.125630E-09 3.248971E-09 -1.081289E+02 -1.078102E+02 + --- Na+ 1.283725E-04 1.118028E-03 -1.096123E+02 -1.075505E+02 + --- OH- 2.125636E-09 3.248975E-09 -1.081289E+02 -1.078102E+02 --- OH 2.273140E-08 9.097883E-08 -1.105050E+02 -1.091181E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082322E+02 - --- H+ 1 2.125630E-09 3.248971E-09 -1.664373E+01 -1.631279E+01 -1.056949E+00 -4.063358E-01 - --- H2O 1 1.306359E-01 1.306194E-01 -1.237155E+02 -1.237156E+02 1.219229E-04 1.002074E-03 - --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 3.995353E-07 4.356599E-06 - --- Cl- 1 1.283713E-04 1.118018E-03 -7.985041E+01 -7.778867E+01 -1.494589E+01 -1.082240E+01 + --- H+ 1 2.125636E-09 3.248975E-09 -1.664373E+01 -1.631279E+01 -1.056943E+00 -4.063344E-01 + --- H2O 1 1.306359E-01 1.306194E-01 -1.237155E+02 -1.237156E+02 1.219241E-04 1.002082E-03 + --- NaCl 0 4.032301E-32 4.032301E-32 -1.745168E+02 -1.745168E+02 3.995394E-07 4.356639E-06 + --- Cl- 1 1.283725E-04 1.118028E-03 -7.985040E+01 -7.778866E+01 -1.494588E+01 -1.082239E+01 --- H2 1 1.136570E-08 4.548942E-08 -3.542832E+01 -3.404144E+01 -9.007025E+00 -4.844370E+00 --- O2 0 5.500000E-59 5.500000E-59 -1.602399E+02 -1.602399E+02 3.434882E+01 2.879929E+01 - --- Norms of Delta G(): 1.573460E+01 1.271585E+01 + --- Norms of Delta G(): 1.573459E+01 1.271584E+01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- - --- NaCl_electrolyte = 1.8716165E+00 + --- NaCl_electrolyte = 1.8716166E+00 --- air = 4.1306196E+00 --- NaCl(S) = 4.9988820E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123265632837E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123386178418E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123265633015E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123386179426E+03 --- Increment counter increased, step is accepted: 17 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1678,10 +1678,10 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 3.2490E-09 6.6009E-10 -4.0634E-01 | Normal calc: diag adjusted from 6.15579e+08 to 6.15579e+08 due to act coeff + --- H+ 3.2490E-09 6.6009E-10 -4.0633E-01 | Normal calc: diag adjusted from 6.15579e+08 to 6.15579e+08 due to act coeff --- H2O 1.3062E-01 -1.3515E-04 1.0021E-03 | Normal calc: diag adjusted from 7.41437 to 7.41433 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 4.3566E-06 | Skipped: IC = 0 and DG >0: 4.357E-06 - --- Cl- 1.1180E-03 6.4793E-03 -1.0822E+01 | Normal calc: diag adjusted from 1786.74 to 1670.3 due to act coeff + --- Cl- 1.1180E-03 6.4794E-03 -1.0822E+01 | Normal calc: diag adjusted from 1786.73 to 1670.28 due to act coeff --- H2 4.5489E-08 7.3456E-08 -4.8444E+00 | Normal calc: diag adjusted from 6.59494e+07 to 6.59494e+07 due to act coeff --- O2 5.5000E-59 0.0000E+00 2.8799E+01 | Skipped: IC = 0 and DG >0: 2.880E+01 ---------------------------------------------------------------------------------- @@ -1690,13 +1690,13 @@ VCS CALCULATION METHOD --- H+ 1 3.2490E-09 3.9091E-09 6.6009E-10 | Normal Major Calc --- H2O 1 1.3062E-01 1.3048E-01-1.3515E-04 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32-1.7567E-37 | minor species alternative calc - --- Cl- 1 1.1180E-03 7.5973E-03 6.4793E-03 | Normal Major Calc + --- Cl- 1 1.1180E-03 7.5974E-03 6.4794E-03 | Normal Major Calc --- H2 1 4.5489E-08 1.1895E-07 7.3456E-08 | Normal Major Calc --- O2 0 5.5000E-59 5.5000E-69-5.5000E-59 | minor species alternative calc - --- NaCl(S) c 4.9989E+00 4.9924E+00-6.4793E-03 | + --- NaCl(S) c 4.9989E+00 4.9924E+00-6.4794E-03 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8694E+00 1.8695E+00 1.3501E-04 | - --- Na+ c 1.1180E-03 7.5973E-03 6.4793E-03 | + --- Na+ c 1.1180E-03 7.5974E-03 6.4794E-03 | --- OH- c 3.2490E-09 3.9091E-09 6.6009E-10 | --- OH c 9.0979E-08 2.3789E-07 1.4691E-07 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -1704,10 +1704,10 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178418E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2123938322437E+03 - --- subroutine FORCE: Beginning Slope = -0.0701224 - --- subroutine FORCE: End Slope = -0.0472713 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123386179426E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2123938326457E+03 + --- subroutine FORCE: Beginning Slope = -0.0701228 + --- subroutine FORCE: End Slope = -0.0472715 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -1715,25 +1715,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.998882E+00 4.992403E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307736E+01 -2.307733E+01 --- H2O(L) 1.869380E+00 1.869515E+00 -1.237166E+02 -1.237230E+02 - --- Na+ 1.118018E-03 7.597348E-03 -1.075505E+02 -1.057871E+02 - --- OH- 3.248971E-09 3.909058E-09 -1.078102E+02 -1.077962E+02 + --- Na+ 1.118028E-03 7.597403E-03 -1.075505E+02 -1.057871E+02 + --- OH- 3.248975E-09 3.909060E-09 -1.078102E+02 -1.077962E+02 --- OH 9.097883E-08 2.378906E-07 -1.091181E+02 -1.081569E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082322E+02 -5.082321E+02 - --- H+ 1 3.248971E-09 3.909058E-09 -1.631279E+01 -1.622271E+01 -4.063358E-01 -2.959275E-01 - --- H2O 1 1.306194E-01 1.304843E-01 -1.237156E+02 -1.237166E+02 1.002074E-03 6.357777E-03 - --- NaCl 0 4.032301E-32 4.032284E-32 -1.745168E+02 -1.745168E+02 4.356599E-06 3.266712E-05 - --- Cl- 1 1.118018E-03 7.597348E-03 -7.778867E+01 -7.602524E+01 -1.082240E+01 -7.295550E+00 + --- H+ 1 3.248975E-09 3.909060E-09 -1.631279E+01 -1.622271E+01 -4.063344E-01 -2.959271E-01 + --- H2O 1 1.306194E-01 1.304843E-01 -1.237156E+02 -1.237166E+02 1.002082E-03 6.357822E-03 + --- NaCl 0 4.032301E-32 4.032284E-32 -1.745168E+02 -1.745168E+02 4.356639E-06 3.266738E-05 + --- Cl- 1 1.118028E-03 7.597403E-03 -7.778866E+01 -7.602523E+01 -1.082239E+01 -7.295537E+00 --- H2 1 4.548942E-08 1.189453E-07 -3.404144E+01 -3.308022E+01 -4.844370E+00 -1.948004E+00 --- O2 0 5.500000E-59 5.499999E-69 -1.602399E+02 -1.832657E+02 2.879929E+01 1.915886E+00 - --- Norms of Delta G(): 1.271585E+01 3.182714E+00 + --- Norms of Delta G(): 1.271584E+01 3.182709E+00 --- Phase_Name KMoles(after update) --- -------------------------------------------------- - --- NaCl_electrolyte = 1.8847102E+00 + --- NaCl_electrolyte = 1.8847103E+00 --- air = 4.1304846E+00 - --- NaCl(S) = 4.9924027E+00 + --- NaCl(S) = 4.9924026E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123386178418E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2123938322437E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123386179426E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2123938326457E+03 --- Increment counter increased, step is accepted: 18 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1754,24 +1754,24 @@ VCS CALCULATION METHOD ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 3.9091E-09 5.7840E-10 -2.9593E-01 | Normal calc: diag adjusted from 5.11632e+08 to 5.11632e+08 due to act coeff - --- H2O 1.3048E-01 -8.5619E-04 6.3578E-03 | Normal calc: diag adjusted from 7.42597 to 7.42563 due to act coeff + --- H2O 1.3048E-01 -8.5620E-04 6.3578E-03 | Normal calc: diag adjusted from 7.42597 to 7.42563 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 3.2667E-05 | Skipped: IC = 0 and DG >0: 3.267E-05 - --- Cl- 7.5973E-03 3.0321E-02 -7.2956E+00 | Normal calc: diag adjusted from 261.127 to 240.614 due to act coeff + --- Cl- 7.5974E-03 3.0321E-02 -7.2955E+00 | Normal calc: diag adjusted from 261.126 to 240.612 due to act coeff --- H2 1.1895E-07 7.7235E-08 -1.9480E+00 | Normal calc: diag adjusted from 2.52217e+07 to 2.52217e+07 due to act coeff --- O2 5.5000E-69 0.0000E+00 1.9159E+00 | Skipped: IC = 0 and DG >0: 1.916E+00 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment --- H+ 1 3.9091E-09 4.4875E-09 5.7840E-10 | Normal Major Calc - --- H2O 1 1.3048E-01 1.2963E-01-8.5619E-04 | Normal Major Calc + --- H2O 1 1.3048E-01 1.2963E-01-8.5620E-04 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered - --- Cl- 1 7.5973E-03 3.7918E-02 3.0321E-02 | Normal Major Calc + --- Cl- 1 7.5974E-03 3.7918E-02 3.0321E-02 | Normal Major Calc --- H2 1 1.1895E-07 1.9618E-07 7.7235E-08 | Normal Major Calc --- O2 0 5.5000E-69 5.5000E-69 0.0000E+00 | minor species not considered --- NaCl(S) c 4.9924E+00 4.9621E+00-3.0321E-02 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8695E+00 1.8704E+00 8.5604E-04 | - --- Na+ c 7.5973E-03 3.7918E-02 3.0321E-02 | + --- Na+ c 7.5974E-03 3.7918E-02 3.0321E-02 | --- OH- c 3.9091E-09 4.4875E-09 5.7840E-10 | --- OH c 2.3789E-07 3.9236E-07 1.5447E-07 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -1779,8 +1779,8 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2123938322437E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2125582635489E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123938326457E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2125582644873E+03 --- subroutine FORCE: Beginning Slope = -0.221211 --- subroutine FORCE: End Slope = -0.129981 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1790,25 +1790,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.992403E+00 4.962082E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307733E+01 -2.307712E+01 --- H2O(L) 1.869515E+00 1.870372E+00 -1.237230E+02 -1.237537E+02 - --- Na+ 7.597348E-03 3.791789E-02 -1.057871E+02 -1.042823E+02 - --- OH- 3.909058E-09 4.487457E-09 -1.077962E+02 -1.078418E+02 + --- Na+ 7.597403E-03 3.791810E-02 -1.057871E+02 -1.042823E+02 + --- OH- 3.909060E-09 4.487459E-09 -1.077962E+02 -1.078418E+02 --- OH 2.378906E-07 3.923612E-07 -1.081569E+02 -1.076563E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082321E+02 -5.082319E+02 - --- H+ 1 3.909058E-09 4.487457E-09 -1.622271E+01 -1.593581E+01 -2.959275E-01 -2.398498E-02 - --- H2O 1 1.304843E-01 1.296281E-01 -1.237166E+02 -1.237230E+02 6.357777E-03 3.063772E-02 - --- NaCl 0 4.032284E-32 4.032284E-32 -1.745168E+02 -1.745165E+02 3.266712E-05 2.399190E-04 - --- Cl- 1 7.597348E-03 3.791789E-02 -7.602524E+01 -7.452048E+01 -7.295550E+00 -4.286032E+00 - --- H2 1 1.189453E-07 1.961806E-07 -3.308022E+01 -3.257964E+01 -1.948004E+00 -3.849543E-01 - --- O2 0 5.499999E-69 5.499999E-69 -1.832657E+02 -1.832655E+02 1.915886E+00 -1.475360E-01 - --- Norms of Delta G(): 3.182714E+00 1.757913E+00 + --- H+ 1 3.909060E-09 4.487459E-09 -1.622271E+01 -1.593581E+01 -2.959271E-01 -2.398281E-02 + --- H2O 1 1.304843E-01 1.296281E-01 -1.237166E+02 -1.237230E+02 6.357822E-03 3.063790E-02 + --- NaCl 0 4.032284E-32 4.032284E-32 -1.745168E+02 -1.745165E+02 3.266738E-05 2.399207E-04 + --- Cl- 1 7.597403E-03 3.791810E-02 -7.602523E+01 -7.452047E+01 -7.295537E+00 -4.286021E+00 + --- H2 1 1.189453E-07 1.961806E-07 -3.308022E+01 -3.257964E+01 -1.948004E+00 -3.849539E-01 + --- O2 0 5.499999E-69 5.499999E-69 -1.832657E+02 -1.832655E+02 1.915886E+00 -1.475363E-01 + --- Norms of Delta G(): 3.182709E+00 1.757908E+00 --- Phase_Name KMoles(after update) --- -------------------------------------------------- - --- NaCl_electrolyte = 1.9462073E+00 - --- air = 4.1296287E+00 - --- NaCl(S) = 4.9620821E+00 + --- NaCl_electrolyte = 1.9462078E+00 + --- air = 4.1296286E+00 + --- NaCl(S) = 4.9620819E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2123938322437E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2125582635489E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2123938326457E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2125582644873E+03 --- Increment counter increased, step is accepted: 19 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1827,34 +1827,34 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 4.4875E-09 5.3816E-11 -2.3985E-02 | Normal calc: diag adjusted from 4.45687e+08 to 4.45687e+08 due to act coeff + --- H+ 4.4875E-09 5.3811E-11 -2.3983E-02 | Normal calc: diag adjusted from 4.45687e+08 to 4.45687e+08 due to act coeff --- H2O 1.2963E-01 -4.0885E-03 3.0638E-02 | Normal calc: diag adjusted from 7.49306 to 7.49364 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 2.3992E-04 | Skipped: IC = 0 and DG >0: 2.399E-04 - --- Cl- 3.7918E-02 8.2257E-02 -4.2860E+00 | Normal calc: diag adjusted from 50.6903 to 52.1053 due to act coeff - --- H2 1.9618E-07 2.5174E-08 -3.8495E-01 | Normal calc: diag adjusted from 1.5292e+07 to 1.5292e+07 due to act coeff + --- Cl- 3.7918E-02 8.2257E-02 -4.2860E+00 | Normal calc: diag adjusted from 50.69 to 52.105 due to act coeff + --- H2 1.9618E-07 2.5173E-08 -3.8495E-01 | Normal calc: diag adjusted from 1.5292e+07 to 1.5292e+07 due to act coeff --- O2 5.5000E-69 8.1145E-70 -1.4754E-01 | Normal Calc ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 4.4875E-09 4.5413E-09 5.3816E-11 | Normal Major Calc + --- H+ 1 4.4875E-09 4.5413E-09 5.3811E-11 | Normal Major Calc --- H2O 1 1.2963E-01 1.2554E-01-4.0885E-03 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0323E-32 0.0000E+00 | minor species not considered --- Cl- 1 3.7918E-02 1.2018E-01 8.2257E-02 | Normal Major Calc - --- H2 1 1.9618E-07 2.2135E-07 2.5174E-08 | Normal Major Calc + --- H2 1 1.9618E-07 2.2135E-07 2.5173E-08 | Normal Major Calc --- O2 0 5.5000E-69 5.5000E-69 0.0000E+00 | minor species not considered --- NaCl(S) c 4.9621E+00 4.8798E+00-8.2257E-02 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.8704E+00 1.8745E+00 4.0884E-03 | + --- H2O(L) c 1.8704E+00 1.8745E+00 4.0885E-03 | --- Na+ c 3.7918E-02 1.2018E-01 8.2257E-02 | - --- OH- c 4.4875E-09 4.5413E-09 5.3816E-11 | + --- OH- c 4.4875E-09 4.5413E-09 5.3811E-11 | --- OH c 3.9236E-07 4.4271E-07 5.0347E-08 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635489E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2127905822678E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2125582644873E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2127905829823E+03 --- subroutine FORCE: Beginning Slope = -0.352682 --- subroutine FORCE: End Slope = -0.141262 --- subroutine FORCE produced no adjustments, s2 < 0 @@ -1864,25 +1864,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.962082E+00 4.879825E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307712E+01 -2.307613E+01 --- H2O(L) 1.870372E+00 1.874460E+00 -1.237537E+02 -1.238545E+02 - --- Na+ 3.791789E-02 1.201751E-01 -1.042823E+02 -1.029955E+02 - --- OH- 4.487457E-09 4.541273E-09 -1.078418E+02 -1.079280E+02 + --- Na+ 3.791810E-02 1.201755E-01 -1.042823E+02 -1.029955E+02 + --- OH- 4.487459E-09 4.541270E-09 -1.078418E+02 -1.079280E+02 --- OH 3.923612E-07 4.427082E-07 -1.076563E+02 -1.075346E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082319E+02 -5.082309E+02 - --- H+ 1 4.487457E-09 4.541273E-09 -1.593581E+01 -1.516733E+01 -2.398498E-02 7.591490E-01 - --- H2O 1 1.296281E-01 1.255396E-01 -1.237230E+02 -1.237541E+02 3.063772E-02 1.004058E-01 - --- NaCl 0 4.032284E-32 4.032284E-32 -1.745165E+02 -1.745156E+02 2.399190E-04 1.230431E-03 - --- Cl- 1 3.791789E-02 1.201751E-01 -7.452048E+01 -7.323363E+01 -4.286032E+00 -1.712334E+00 - --- H2 1 1.961806E-07 2.213541E-07 -3.257964E+01 -3.245792E+01 -3.849543E-01 1.818533E-01 - --- O2 0 5.499999E-69 5.499999E-69 -1.832655E+02 -1.832645E+02 -1.475360E-01 -8.350718E-01 - --- Norms of Delta G(): 1.757913E+00 8.415159E-01 + --- H+ 1 4.487459E-09 4.541270E-09 -1.593581E+01 -1.516733E+01 -2.398281E-02 7.591524E-01 + --- H2O 1 1.296281E-01 1.255395E-01 -1.237230E+02 -1.237541E+02 3.063790E-02 1.004061E-01 + --- NaCl 0 4.032284E-32 4.032284E-32 -1.745165E+02 -1.745156E+02 2.399207E-04 1.230438E-03 + --- Cl- 1 3.791810E-02 1.201755E-01 -7.452047E+01 -7.323363E+01 -4.286021E+00 -1.712325E+00 + --- H2 1 1.961806E-07 2.213541E-07 -3.257964E+01 -3.245792E+01 -3.849539E-01 1.818541E-01 + --- O2 0 5.499999E-69 5.499999E-69 -1.832655E+02 -1.832645E+02 -1.475363E-01 -8.350724E-01 + --- Norms of Delta G(): 1.757908E+00 8.415134E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- - --- NaCl_electrolyte = 2.1148101E+00 + --- NaCl_electrolyte = 2.1148110E+00 --- air = 4.1255402E+00 - --- NaCl(S) = 4.8798249E+00 + --- NaCl(S) = 4.8798245E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2125582635489E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2127905822678E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2125582644873E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2127905829823E+03 --- Increment counter increased, step is accepted: 20 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1902,9 +1902,9 @@ VCS CALCULATION METHOD ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment --- H+ 4.5413E-09 -1.7238E-09 7.5915E-01 | Normal calc: diag adjusted from 4.40405e+08 to 4.40405e+08 due to act coeff - --- H2O 1.2554E-01 -1.2849E-02 1.0041E-01 | Normal calc: diag adjusted from 7.78385 to 7.8145 due to act coeff + --- H2O 1.2554E-01 -1.2849E-02 1.0041E-01 | Normal calc: diag adjusted from 7.78386 to 7.8145 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 1.2304E-03 | Skipped: IC = 0 and DG >0: 1.230E-03 - --- Cl- 1.2018E-01 7.7112E-02 -1.7123E+00 | Normal calc: diag adjusted from 14.751 to 22.2059 due to act coeff + --- Cl- 1.2018E-01 7.7112E-02 -1.7123E+00 | Normal calc: diag adjusted from 14.7509 to 22.2058 due to act coeff --- H2 2.2135E-07 -1.3418E-08 1.8185E-01 | Normal calc: diag adjusted from 1.35529e+07 to 1.35529e+07 due to act coeff --- O2 5.5000E-69 4.5929E-69 -8.3507E-01 | Normal Calc ---------------------------------------------------------------------------------- @@ -1927,10 +1927,10 @@ VCS CALCULATION METHOD --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822678E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2128646676326E+03 - --- subroutine FORCE: Beginning Slope = -0.133331 - --- subroutine FORCE: End Slope = -0.0193693 + --- Total Old Dimensionless Gibbs Free Energy = -1.2127905829823E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2128646676759E+03 + --- subroutine FORCE: Beginning Slope = -0.13333 + --- subroutine FORCE: End Slope = -0.0193691 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -1938,25 +1938,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.879825E+00 4.802713E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307613E+01 -2.307301E+01 --- H2O(L) 1.874460E+00 1.887309E+00 -1.238545E+02 -1.239783E+02 - --- Na+ 1.201751E-01 1.972869E-01 -1.029955E+02 -1.022550E+02 - --- OH- 4.541273E-09 2.817521E-09 -1.079280E+02 -1.084016E+02 - --- OH 4.427082E-07 4.158722E-07 -1.075346E+02 -1.075940E+02 + --- Na+ 1.201755E-01 1.972870E-01 -1.029955E+02 -1.022550E+02 + --- OH- 4.541270E-09 2.817512E-09 -1.079280E+02 -1.084016E+02 + --- OH 4.427082E-07 4.158721E-07 -1.075346E+02 -1.075940E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082309E+02 -5.082278E+02 - --- H+ 1 4.541273E-09 2.817521E-09 -1.516733E+01 -1.487722E+01 7.591490E-01 6.994265E-01 - --- H2O 1 1.255396E-01 1.126909E-01 -1.237541E+02 -1.238589E+02 1.004058E-01 1.193288E-01 - --- NaCl 0 4.032284E-32 4.032284E-32 -1.745156E+02 -1.745124E+02 1.230431E-03 4.349718E-03 - --- Cl- 1 1.201751E-01 1.972869E-01 -7.323363E+01 -7.249312E+01 -1.712334E+00 -2.313017E-01 - --- H2 1 2.213541E-07 2.079361E-07 -3.245792E+01 -3.251734E+01 1.818533E-01 2.511646E-01 - --- O2 0 5.499999E-69 5.499999E-69 -1.832645E+02 -1.832614E+02 -8.350718E-01 -8.418503E-01 - --- Norms of Delta G(): 8.415159E-01 4.705939E-01 + --- H+ 1 4.541270E-09 2.817512E-09 -1.516733E+01 -1.487722E+01 7.591524E-01 6.994215E-01 + --- H2O 1 1.255395E-01 1.126908E-01 -1.237541E+02 -1.238589E+02 1.004061E-01 1.193285E-01 + --- NaCl 0 4.032284E-32 4.032284E-32 -1.745156E+02 -1.745124E+02 1.230438E-03 4.349735E-03 + --- Cl- 1 1.201755E-01 1.972870E-01 -7.323363E+01 -7.249311E+01 -1.712325E+00 -2.312992E-01 + --- H2 1 2.213541E-07 2.079360E-07 -3.245792E+01 -3.251734E+01 1.818541E-01 2.511640E-01 + --- O2 0 5.499999E-69 5.499999E-69 -1.832645E+02 -1.832614E+02 -8.350724E-01 -8.418492E-01 + --- Norms of Delta G(): 8.415134E-01 4.705921E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- - --- NaCl_electrolyte = 2.2818825E+00 + --- NaCl_electrolyte = 2.2818828E+00 --- air = 4.1126915E+00 - --- NaCl(S) = 4.8027131E+00 + --- NaCl(S) = 4.8027130E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2127905822678E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2128646676326E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2127905829823E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2128646676759E+03 --- Increment counter increased, step is accepted: 21 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -1977,17 +1977,17 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 2.8175E-09 -9.8532E-10 6.9943E-01 | Normal calc: diag adjusted from 7.09844e+08 to 7.09844e+08 due to act coeff - --- H2O 1.1269E-01 -1.3525E-02 1.1933E-01 | Normal calc: diag adjusted from 8.7223 to 8.82315 due to act coeff + --- H+ 2.8175E-09 -9.8531E-10 6.9942E-01 | Normal calc: diag adjusted from 7.09846e+08 to 7.09846e+08 due to act coeff + --- H2O 1.1269E-01 -1.3524E-02 1.1933E-01 | Normal calc: diag adjusted from 8.72231 to 8.82315 due to act coeff --- NaCl 4.0323E-32 0.0000E+00 4.3497E-03 | Skipped: IC = 0 and DG >0: 4.350E-03 - --- Cl- 1.9729E-01 1.3132E-02 -2.3130E-01 | Normal calc: diag adjusted from 8.38458 to 17.6133 due to act coeff + --- Cl- 1.9729E-01 1.3132E-02 -2.3130E-01 | Normal calc: diag adjusted from 8.38457 to 17.6133 due to act coeff --- H2 2.0794E-07 -1.7409E-08 2.5116E-01 | Normal calc: diag adjusted from 1.44275e+07 to 1.44275e+07 due to act coeff --- O2 5.5000E-69 4.6302E-69 -8.4185E-01 | Normal Calc ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Full Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 2.8175E-09 1.8322E-09-9.8532E-10 | Normal Major Calc - --- H2O 1 1.1269E-01 9.9166E-02-1.3525E-02 | Normal Major Calc + --- H+ 1 2.8175E-09 1.8322E-09-9.8531E-10 | Normal Major Calc + --- H2O 1 1.1269E-01 9.9166E-02-1.3524E-02 | Normal Major Calc --- NaCl 0 4.0323E-32 4.0148E-32-1.7501E-34 | minor species alternative calc --- Cl- 1 1.9729E-01 2.1042E-01 1.3132E-02 | Normal Major Calc --- H2 1 2.0794E-07 1.9053E-07-1.7409E-08 | Normal Major Calc @@ -1996,17 +1996,17 @@ VCS CALCULATION METHOD --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.8873E+00 1.9008E+00 1.3525E-02 | --- Na+ c 1.9729E-01 2.1042E-01 1.3132E-02 | - --- OH- c 2.8175E-09 1.8322E-09-9.8532E-10 | + --- OH- c 2.8175E-09 1.8322E-09-9.8531E-10 | --- OH c 4.1587E-07 3.8105E-07-3.4817E-08 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676326E+03 - --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673025651E+03 - --- subroutine FORCE: Beginning Slope = -0.00465137 - --- subroutine FORCE: End Slope = -0.000598004 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676759E+03 + --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673025658E+03 + --- subroutine FORCE: Beginning Slope = -0.00465129 + --- subroutine FORCE: End Slope = -0.000597994 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -2014,25 +2014,25 @@ VCS CALCULATION METHOD --- NaCl(S) 4.802713E+00 4.789581E+00 -1.745168E+02 -1.745168E+02 --- N2 4.000000E+00 4.000000E+00 -2.307301E+01 -2.306971E+01 --- H2O(L) 1.887309E+00 1.900833E+00 -1.239783E+02 -1.240001E+02 - --- Na+ 1.972869E-01 2.104191E-01 -1.022550E+02 -1.021535E+02 - --- OH- 2.817521E-09 1.832197E-09 -1.084016E+02 -1.088342E+02 - --- OH 4.158722E-07 3.810548E-07 -1.075940E+02 -1.076782E+02 + --- Na+ 1.972870E-01 2.104191E-01 -1.022550E+02 -1.021535E+02 + --- OH- 2.817512E-09 1.832198E-09 -1.084016E+02 -1.088342E+02 + --- OH 4.158721E-07 3.810547E-07 -1.075940E+02 -1.076782E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082278E+02 -5.082245E+02 - --- H+ 1 2.817521E-09 1.832197E-09 -1.487722E+01 -1.519494E+01 6.994265E-01 -2.906328E-02 - --- H2O 1 1.126909E-01 9.916639E-02 -1.238589E+02 -1.239835E+02 1.193288E-01 1.660229E-02 - --- NaCl 0 4.032284E-32 4.014783E-32 -1.745124E+02 -1.745135E+02 4.349718E-03 3.293917E-03 - --- Cl- 1 1.972869E-01 2.104191E-01 -7.249312E+01 -7.239168E+01 -2.313017E-01 -2.843889E-02 - --- H2 1 2.079361E-07 1.905274E-07 -3.251734E+01 -3.260148E+01 2.511646E-01 4.239982E-02 - --- O2 0 5.499999E-69 1.276361E-68 -1.832614E+02 -1.824162E+02 -8.418503E-01 2.961998E-01 - --- Norms of Delta G(): 4.705939E-01 1.234720E-01 + --- H+ 1 2.817512E-09 1.832198E-09 -1.487722E+01 -1.519493E+01 6.994215E-01 -2.906224E-02 + --- H2O 1 1.126908E-01 9.916637E-02 -1.238589E+02 -1.239835E+02 1.193285E-01 1.660209E-02 + --- NaCl 0 4.032284E-32 4.014782E-32 -1.745124E+02 -1.745135E+02 4.349735E-03 3.293905E-03 + --- Cl- 1 1.972870E-01 2.104191E-01 -7.249311E+01 -7.239168E+01 -2.312992E-01 -2.843874E-02 + --- H2 1 2.079360E-07 1.905273E-07 -3.251734E+01 -3.260148E+01 2.511640E-01 4.239935E-02 + --- O2 0 5.499999E-69 1.276360E-68 -1.832614E+02 -1.824162E+02 -8.418492E-01 2.961994E-01 + --- Norms of Delta G(): 4.705921E-01 1.234717E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3216714E+00 - --- air = 4.0991670E+00 + --- air = 4.0991669E+00 --- NaCl(S) = 4.7895809E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676326E+03 - --- Total New Dimensionless Gibbs Free Energy = -1.2128673025651E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128646676759E+03 + --- Total New Dimensionless Gibbs Free Energy = -1.2128673025658E+03 --- Increment counter increased, step is accepted: 22 --- Normal element abundance check - passed --- Check for an optimum basis passed @@ -2052,36 +2052,36 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.8322E-09 2.6625E-11 -2.9063E-02 | Normal calc: diag adjusted from 1.09159e+09 to 1.09159e+09 due to act coeff + --- H+ 1.8322E-09 2.6624E-11 -2.9062E-02 | Normal calc: diag adjusted from 1.09159e+09 to 1.09159e+09 due to act coeff --- H2O 9.9166E-02 -1.6519E-03 1.6602E-02 | Normal calc: diag adjusted from 9.93547 to 10.0502 due to act coeff --- NaCl 4.0148E-32 0.0000E+00 3.2939E-03 | Skipped: IC = 0 and DG >0: 3.294E-03 --- Cl- 2.1042E-01 1.6589E-03 -2.8439E-02 | Normal calc: diag adjusted from 7.78194 to 17.1433 due to act coeff - --- H2 1.9053E-07 -2.6928E-09 4.2400E-02 | Normal calc: diag adjusted from 1.57458e+07 to 1.57458e+07 due to act coeff + --- H2 1.9053E-07 -2.6927E-09 4.2399E-02 | Normal calc: diag adjusted from 1.57458e+07 to 1.57458e+07 due to act coeff --- O2 1.2764E-68 0.0000E+00 2.9620E-01 | Skipped: IC = 0 and DG >0: 2.962E-01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 1.8322E-09 1.8588E-09 2.6625E-11 | Normal Major Calc + --- H+ 1 1.8322E-09 1.8588E-09 2.6624E-11 | Normal Major Calc --- H2O 1 9.9166E-02 9.7514E-02-1.6519E-03 | Normal Major Calc --- NaCl 0 4.0148E-32 4.0148E-32 0.0000E+00 | minor species not considered --- Cl- 1 2.1042E-01 2.1208E-01 1.6589E-03 | Normal Major Calc - --- H2 1 1.9053E-07 1.8783E-07-2.6928E-09 | Normal Major Calc + --- H2 1 1.9053E-07 1.8783E-07-2.6927E-09 | Normal Major Calc --- O2 0 1.2764E-68 1.2764E-68 0.0000E+00 | minor species not considered --- NaCl(S) c 4.7896E+00 4.7879E+00-1.6589E-03 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9008E+00 1.9025E+00 1.6519E-03 | --- Na+ c 2.1042E-01 2.1208E-01 1.6589E-03 | - --- OH- c 1.8322E-09 1.8588E-09 2.6625E-11 | - --- OH c 3.8105E-07 3.7567E-07-5.3856E-09 | + --- OH- c 1.8322E-09 1.8588E-09 2.6624E-11 | + --- OH c 3.8105E-07 3.7567E-07-5.3855E-09 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop --- Subroutine vcs_dfe called for all species using tentative solution --- Subroutine vcs_deltag called for all noncomponents - --- Total Old Dimensionless Gibbs Free Energy = -1.2128673025651E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128673025658E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673450210E+03 - --- subroutine FORCE: Beginning Slope = -7.46032e-05 - --- subroutine FORCE: End Slope = -1.02617e-05 + --- subroutine FORCE: Beginning Slope = -7.4602e-05 + --- subroutine FORCE: End Slope = -1.02615e-05 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2090,23 +2090,23 @@ VCS CALCULATION METHOD --- N2 4.000000E+00 4.000000E+00 -2.306971E+01 -2.306931E+01 --- H2O(L) 1.900833E+00 1.902485E+00 -1.240001E+02 -1.240029E+02 --- Na+ 2.104191E-01 2.120780E-01 -1.021535E+02 -1.021409E+02 - --- OH- 1.832197E-09 1.858822E-09 -1.088342E+02 -1.088200E+02 - --- OH 3.810548E-07 3.756692E-07 -1.076782E+02 -1.076920E+02 + --- OH- 1.832198E-09 1.858822E-09 -1.088342E+02 -1.088200E+02 + --- OH 3.810547E-07 3.756692E-07 -1.076782E+02 -1.076920E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082245E+02 -5.082241E+02 - --- H+ 1 1.832197E-09 1.858822E-09 -1.519494E+01 -1.516629E+01 -2.906328E-02 1.659943E-02 - --- H2O 1 9.916639E-02 9.751445E-02 -1.239835E+02 -1.239999E+02 1.660229E-02 3.012001E-03 - --- NaCl 0 4.014783E-32 4.014783E-32 -1.745135E+02 -1.745131E+02 3.293917E-03 3.696994E-03 - --- Cl- 1 2.104191E-01 2.120780E-01 -7.239168E+01 -7.237906E+01 -2.843889E-02 -3.186461E-03 - --- H2 1 1.905274E-07 1.878346E-07 -3.260148E+01 -3.261531E+01 4.239982E-02 6.517138E-03 - --- O2 0 1.276361E-68 1.276361E-68 -1.824162E+02 -1.824158E+02 2.961998E-01 3.463166E-01 - --- Norms of Delta G(): 1.234720E-01 1.415898E-01 + --- H+ 1 1.832198E-09 1.858822E-09 -1.519493E+01 -1.516629E+01 -2.906224E-02 1.659939E-02 + --- H2O 1 9.916637E-02 9.751445E-02 -1.239835E+02 -1.239999E+02 1.660209E-02 3.011988E-03 + --- NaCl 0 4.014782E-32 4.014782E-32 -1.745135E+02 -1.745131E+02 3.293905E-03 3.696977E-03 + --- Cl- 1 2.104191E-01 2.120780E-01 -7.239168E+01 -7.237906E+01 -2.843874E-02 -3.186422E-03 + --- H2 1 1.905273E-07 1.878346E-07 -3.260148E+01 -3.261531E+01 4.239935E-02 6.517106E-03 + --- O2 0 1.276360E-68 1.276360E-68 -1.824162E+02 -1.824158E+02 2.961994E-01 3.463156E-01 + --- Norms of Delta G(): 1.234717E-01 1.415894E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3266411E+00 --- air = 4.0975150E+00 --- NaCl(S) = 4.7879220E+00 ------------------------------------------------------------------------------------------------------- - --- Total Old Dimensionless Gibbs Free Energy = -1.2128673025651E+03 + --- Total Old Dimensionless Gibbs Free Energy = -1.2128673025658E+03 --- Total New Dimensionless Gibbs Free Energy = -1.2128673450210E+03 --- Increment counter increased, step is accepted: 23 --- Normal element abundance check - passed @@ -2129,7 +2129,7 @@ VCS CALCULATION METHOD --- H+ 1.8588E-09 -1.5428E-11 1.6599E-02 | Normal calc: diag adjusted from 1.07595e+09 to 1.07595e+09 due to act coeff --- H2O 9.7514E-02 -2.9462E-04 3.0120E-03 | Normal calc: diag adjusted from 10.1067 to 10.2232 due to act coeff --- NaCl 4.0148E-32 0.0000E+00 3.6970E-03 | Skipped: IC = 0 and DG >0: 3.697E-03 - --- Cl- 2.1208E-01 1.8647E-04 -3.1865E-03 | Normal calc: diag adjusted from 7.71128 to 17.0885 due to act coeff + --- Cl- 2.1208E-01 1.8647E-04 -3.1864E-03 | Normal calc: diag adjusted from 7.71128 to 17.0885 due to act coeff --- H2 1.8783E-07 -4.0805E-10 6.5171E-03 | Normal calc: diag adjusted from 1.59715e+07 to 1.59715e+07 due to act coeff --- O2 1.2764E-68 0.0000E+00 3.4632E-01 | Skipped: IC = 0 and DG >0: 3.463E-01 ---------------------------------------------------------------------------------- @@ -2143,10 +2143,10 @@ VCS CALCULATION METHOD --- O2 0 1.2764E-68 1.2764E-68 0.0000E+00 | minor species not considered --- NaCl(S) c 4.7879E+00 4.7877E+00-1.8647E-04 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.9025E+00 1.9028E+00 2.9463E-04 | + --- H2O(L) c 1.9025E+00 1.9028E+00 2.9462E-04 | --- Na+ c 2.1208E-01 2.1226E-01 1.8647E-04 | --- OH- c 1.8588E-09 1.8434E-09-1.5428E-11 | - --- OH c 3.7567E-07 3.7485E-07-8.1610E-10 | + --- OH c 3.7567E-07 3.7485E-07-8.1609E-10 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop @@ -2154,8 +2154,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673450210E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458660E+03 - --- subroutine FORCE: Beginning Slope = -1.48159e-06 - --- subroutine FORCE: End Slope = -2.08102e-07 + --- subroutine FORCE: Beginning Slope = -1.48156e-06 + --- subroutine FORCE: End Slope = -2.08099e-07 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2167,13 +2167,13 @@ VCS CALCULATION METHOD --- OH- 1.858822E-09 1.843394E-09 -1.088200E+02 -1.088284E+02 --- OH 3.756692E-07 3.748531E-07 -1.076920E+02 -1.076941E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082241E+02 -5.082240E+02 - --- H+ 1 1.858822E-09 1.843394E-09 -1.516629E+01 -1.517321E+01 1.659943E-02 1.552390E-03 - --- H2O 1 9.751445E-02 9.721983E-02 -1.239999E+02 -1.240028E+02 3.012001E-03 3.506628E-04 - --- NaCl 0 4.014783E-32 4.014783E-32 -1.745131E+02 -1.745130E+02 3.696994E-03 3.768900E-03 - --- Cl- 1 2.120780E-01 2.122644E-01 -7.237906E+01 -7.237775E+01 -3.186461E-03 -5.619620E-04 - --- H2 1 1.878346E-07 1.874266E-07 -3.261531E+01 -3.261741E+01 6.517138E-03 7.939682E-04 - --- O2 0 1.276361E-68 1.276361E-68 -1.824158E+02 -1.824158E+02 3.463166E-01 3.542145E-01 - --- Norms of Delta G(): 1.415898E-01 1.446177E-01 + --- H+ 1 1.858822E-09 1.843394E-09 -1.516629E+01 -1.517321E+01 1.659939E-02 1.552365E-03 + --- H2O 1 9.751445E-02 9.721983E-02 -1.239999E+02 -1.240028E+02 3.011988E-03 3.506584E-04 + --- NaCl 0 4.014782E-32 4.014782E-32 -1.745131E+02 -1.745130E+02 3.696977E-03 3.768882E-03 + --- Cl- 1 2.120780E-01 2.122644E-01 -7.237906E+01 -7.237775E+01 -3.186422E-03 -5.619597E-04 + --- H2 1 1.878346E-07 1.874266E-07 -3.261531E+01 -3.261741E+01 6.517106E-03 7.939591E-04 + --- O2 0 1.276360E-68 1.276360E-68 -1.824158E+02 -1.824158E+02 3.463156E-01 3.542134E-01 + --- Norms of Delta G(): 1.415894E-01 1.446172E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3273087E+00 @@ -2204,7 +2204,7 @@ VCS CALCULATION METHOD --- H2O 9.7220E-02 -3.4196E-05 3.5066E-04 | Normal calc: diag adjusted from 10.1378 to 10.2545 due to act coeff --- NaCl 4.0148E-32 0.0000E+00 3.7689E-03 | Skipped: IC = 0 and DG >0: 3.769E-03 --- Cl- 2.1226E-01 3.2898E-05 -5.6196E-04 | Normal calc: diag adjusted from 7.70349 to 17.0817 due to act coeff - --- H2 1.8743E-07 -4.9604E-11 7.9397E-04 | Normal calc: diag adjusted from 1.60063e+07 to 1.60063e+07 due to act coeff + --- H2 1.8743E-07 -4.9603E-11 7.9396E-04 | Normal calc: diag adjusted from 1.60063e+07 to 1.60063e+07 due to act coeff --- O2 1.2764E-68 0.0000E+00 3.5421E-01 | Skipped: IC = 0 and DG >0: 3.542E-01 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: @@ -2213,14 +2213,14 @@ VCS CALCULATION METHOD --- H2O 1 9.7220E-02 9.7186E-02-3.4196E-05 | Normal Major Calc --- NaCl 0 4.0148E-32 4.0148E-32 0.0000E+00 | minor species not considered --- Cl- 1 2.1226E-01 2.1230E-01 3.2898E-05 | Normal Major Calc - --- H2 1 1.8743E-07 1.8738E-07-4.9604E-11 | Normal Major Calc + --- H2 1 1.8743E-07 1.8738E-07-4.9603E-11 | Normal Major Calc --- O2 0 1.2764E-68 1.2764E-68 0.0000E+00 | minor species not considered --- NaCl(S) c 4.7877E+00 4.7877E+00-3.2898E-05 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9028E+00 1.9028E+00 3.4196E-05 | --- Na+ c 2.1226E-01 2.1230E-01 3.2898E-05 | --- OH- c 1.8434E-09 1.8420E-09-1.4308E-12 | - --- OH c 3.7485E-07 3.7475E-07-9.9207E-11 | + --- OH c 3.7485E-07 3.7475E-07-9.9206E-11 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop @@ -2228,8 +2228,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458660E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458834E+03 - --- subroutine FORCE: Beginning Slope = -3.0479e-08 - --- subroutine FORCE: End Slope = -4.2861e-09 + --- subroutine FORCE: Beginning Slope = -3.04785e-08 + --- subroutine FORCE: End Slope = -4.28603e-09 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2241,13 +2241,13 @@ VCS CALCULATION METHOD --- OH- 1.843394E-09 1.841963E-09 -1.088284E+02 -1.088292E+02 --- OH 3.748531E-07 3.747539E-07 -1.076941E+02 -1.076943E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.843394E-09 1.841963E-09 -1.517321E+01 -1.517371E+01 1.552390E-03 3.291142E-04 - --- H2O 1 9.721983E-02 9.718563E-02 -1.240028E+02 -1.240032E+02 3.506628E-04 6.262933E-05 - --- NaCl 0 4.014783E-32 4.014783E-32 -1.745130E+02 -1.745130E+02 3.768900E-03 3.777246E-03 - --- Cl- 1 2.122644E-01 2.122973E-01 -7.237775E+01 -7.237750E+01 -5.619620E-04 -6.518288E-05 - --- H2 1 1.874266E-07 1.873770E-07 -3.261741E+01 -3.261767E+01 7.939682E-04 1.357774E-04 - --- O2 0 1.276361E-68 1.276361E-68 -1.824158E+02 -1.824157E+02 3.542145E-01 3.551374E-01 - --- Norms of Delta G(): 1.446177E-01 1.449925E-01 + --- H+ 1 1.843394E-09 1.841963E-09 -1.517321E+01 -1.517371E+01 1.552365E-03 3.291136E-04 + --- H2O 1 9.721983E-02 9.718563E-02 -1.240028E+02 -1.240032E+02 3.506584E-04 6.262908E-05 + --- NaCl 0 4.014782E-32 4.014782E-32 -1.745130E+02 -1.745130E+02 3.768882E-03 3.777229E-03 + --- Cl- 1 2.122644E-01 2.122973E-01 -7.237775E+01 -7.237750E+01 -5.619597E-04 -6.518209E-05 + --- H2 1 1.874266E-07 1.873770E-07 -3.261741E+01 -3.261767E+01 7.939591E-04 1.357768E-04 + --- O2 0 1.276360E-68 1.276360E-68 -1.824158E+02 -1.824157E+02 3.542134E-01 3.551363E-01 + --- Norms of Delta G(): 1.446172E-01 1.449921E-01 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274087E+00 @@ -2279,7 +2279,7 @@ VCS CALCULATION METHOD --- H+ 1.8420E-09 -3.0311E-13 3.2911E-04 | Normal calc: diag adjusted from 1.0858e+09 to 1.0858e+09 due to act coeff --- H2O 9.7186E-02 -6.1053E-06 6.2629E-05 | Normal calc: diag adjusted from 10.1414 to 10.2581 due to act coeff --- NaCl 4.0148E-32 0.0000E+00 3.7772E-03 | Skipped: IC = 0 and DG >0: 3.777E-03 - --- Cl- 2.1230E-01 3.8162E-06 -6.5183E-05 | Normal calc: diag adjusted from 7.7021 to 17.0807 due to act coeff + --- Cl- 2.1230E-01 3.8161E-06 -6.5182E-05 | Normal calc: diag adjusted from 7.7021 to 17.0807 due to act coeff --- H2 1.8738E-07 -8.4805E-12 1.3578E-04 | Normal calc: diag adjusted from 1.60105e+07 to 1.60105e+07 due to act coeff --- O2 1.2764E-68 0.0000E+00 3.5514E-01 | Skipped: IC = 0 and DG >0: 3.551E-01 ---------------------------------------------------------------------------------- @@ -2288,13 +2288,13 @@ VCS CALCULATION METHOD --- H+ 1 1.8420E-09 1.8417E-09-3.0311E-13 | Normal Major Calc --- H2O 1 9.7186E-02 9.7180E-02-6.1053E-06 | Normal Major Calc --- NaCl 0 4.0148E-32 3.9996E-32-1.5136E-34 | minor species alternative calc - --- Cl- 1 2.1230E-01 2.1230E-01 3.8162E-06 | Normal Major Calc + --- Cl- 1 2.1230E-01 2.1230E-01 3.8161E-06 | Normal Major Calc --- H2 1 1.8738E-07 1.8737E-07-8.4805E-12 | Normal Major Calc --- O2 0 1.2764E-68 8.9483E-69-3.8153E-69 | minor species alternative calc - --- NaCl(S) c 4.7877E+00 4.7877E+00-3.8162E-06 | + --- NaCl(S) c 4.7877E+00 4.7877E+00-3.8161E-06 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.9028E+00 1.9028E+00 6.1054E-06 | - --- Na+ c 2.1230E-01 2.1230E-01 3.8162E-06 | + --- H2O(L) c 1.9028E+00 1.9028E+00 6.1053E-06 | + --- Na+ c 2.1230E-01 2.1230E-01 3.8161E-06 | --- OH- c 1.8420E-09 1.8417E-09-3.0311E-13 | --- OH c 3.7475E-07 3.7474E-07-1.6961E-11 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -2304,8 +2304,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458834E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -6.31124e-10 - --- subroutine FORCE: End Slope = -8.87911e-11 + --- subroutine FORCE: Beginning Slope = -6.31115e-10 + --- subroutine FORCE: End Slope = -8.87897e-11 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -2317,13 +2317,13 @@ VCS CALCULATION METHOD --- OH- 1.841963E-09 1.841660E-09 -1.088292E+02 -1.088294E+02 --- OH 3.747539E-07 3.747369E-07 -1.076943E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841963E-09 1.841660E-09 -1.517371E+01 -1.517384E+01 3.291142E-04 3.297168E-05 - --- H2O 1 9.718563E-02 9.717953E-02 -1.240032E+02 -1.240032E+02 6.262933E-05 7.270507E-06 - --- NaCl 0 4.014783E-32 3.999646E-32 -1.745130E+02 -1.745168E+02 3.777246E-03 1.490136E-06 - --- Cl- 1 2.122973E-01 2.123012E-01 -7.237750E+01 -7.237747E+01 -6.518288E-05 -1.163523E-05 - --- H2 1 1.873770E-07 1.873685E-07 -3.261767E+01 -3.261771E+01 1.357774E-04 1.641605E-05 - --- O2 0 1.276361E-68 8.948274E-69 -1.824157E+02 -1.827709E+02 3.551374E-01 1.646216E-04 - --- Norms of Delta G(): 1.449925E-01 6.909817E-05 + --- H+ 1 1.841963E-09 1.841660E-09 -1.517371E+01 -1.517384E+01 3.291136E-04 3.297116E-05 + --- H2O 1 9.718563E-02 9.717953E-02 -1.240032E+02 -1.240032E+02 6.262908E-05 7.270418E-06 + --- NaCl 0 4.014782E-32 3.999646E-32 -1.745130E+02 -1.745168E+02 3.777229E-03 1.490130E-06 + --- Cl- 1 2.122973E-01 2.123012E-01 -7.237750E+01 -7.237747E+01 -6.518209E-05 -1.163518E-05 + --- H2 1 1.873770E-07 1.873685E-07 -3.261767E+01 -3.261771E+01 1.357768E-04 1.641587E-05 + --- O2 0 1.276360E-68 8.948274E-69 -1.824157E+02 -1.827709E+02 3.551363E-01 1.646209E-04 + --- Norms of Delta G(): 1.449921E-01 6.909785E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274224E+00 @@ -2351,8 +2351,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.8417E-09 -3.0361E-14 3.2972E-05 | Normal calc: diag adjusted from 1.08598e+09 to 1.08598e+09 due to act coeff - --- H2O 9.7180E-02 -7.0871E-07 7.2705E-06 | Normal calc: diag adjusted from 10.142 to 10.2588 due to act coeff + --- H+ 1.8417E-09 -3.0361E-14 3.2971E-05 | Normal calc: diag adjusted from 1.08598e+09 to 1.08598e+09 due to act coeff + --- H2O 9.7180E-02 -7.0870E-07 7.2704E-06 | Normal calc: diag adjusted from 10.142 to 10.2588 due to act coeff --- NaCl 3.9996E-32 0.0000E+00 1.4901E-06 | Skipped: IC = 0 and DG >0: 1.490E-06 --- Cl- 2.1230E-01 6.8120E-07 -1.1635E-05 | Normal calc: diag adjusted from 7.70194 to 17.0805 due to act coeff --- H2 1.8737E-07 -1.0253E-12 1.6416E-05 | Normal calc: diag adjusted from 1.60112e+07 to 1.60112e+07 due to act coeff @@ -2361,17 +2361,17 @@ VCS CALCULATION METHOD --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment --- H+ 1 1.8417E-09 1.8416E-09-3.0361E-14 | Normal Major Calc - --- H2O 1 9.7180E-02 9.7179E-02-7.0871E-07 | Normal Major Calc + --- H2O 1 9.7180E-02 9.7179E-02-7.0870E-07 | Normal Major Calc --- NaCl 0 3.9996E-32 3.9996E-32 0.0000E+00 | minor species not considered --- Cl- 1 2.1230E-01 2.1230E-01 6.8120E-07 | Normal Major Calc --- H2 1 1.8737E-07 1.8737E-07-1.0253E-12 | Normal Major Calc --- O2 0 8.9483E-69 8.9483E-69 0.0000E+00 | minor species not considered --- NaCl(S) c 4.7877E+00 4.7877E+00-6.8120E-07 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.9028E+00 1.9028E+00 7.0871E-07 | + --- H2O(L) c 1.9028E+00 1.9028E+00 7.0870E-07 | --- Na+ c 2.1230E-01 2.1230E-01 6.8120E-07 | --- OH- c 1.8417E-09 1.8416E-09-3.0361E-14 | - --- OH c 3.7474E-07 3.7473E-07-2.0506E-12 | + --- OH c 3.7474E-07 3.7473E-07-2.0505E-12 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop @@ -2379,8 +2379,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -1.30786e-11 - --- subroutine FORCE: End Slope = -1.84004e-12 + --- subroutine FORCE: Beginning Slope = -1.30784e-11 + --- subroutine FORCE: End Slope = -1.84001e-12 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2392,13 +2392,13 @@ VCS CALCULATION METHOD --- OH- 1.841660E-09 1.841630E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747369E-07 3.747349E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841660E-09 1.841630E-09 -1.517384E+01 -1.517385E+01 3.297168E-05 6.825272E-06 - --- H2O 1 9.717953E-02 9.717882E-02 -1.240032E+02 -1.240032E+02 7.270507E-06 1.298138E-06 - --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.490136E-06 1.663111E-06 - --- Cl- 1 2.123012E-01 2.123018E-01 -7.237747E+01 -7.237747E+01 -1.163523E-05 -1.350606E-06 - --- H2 1 1.873685E-07 1.873674E-07 -3.261771E+01 -3.261772E+01 1.641605E-05 2.813833E-06 - --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.646216E-04 1.836958E-04 - --- Norms of Delta G(): 6.909817E-05 7.506101E-05 + --- H+ 1 1.841660E-09 1.841630E-09 -1.517384E+01 -1.517385E+01 3.297116E-05 6.825259E-06 + --- H2O 1 9.717953E-02 9.717882E-02 -1.240032E+02 -1.240032E+02 7.270418E-06 1.298133E-06 + --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.490130E-06 1.663103E-06 + --- Cl- 1 2.123012E-01 2.123018E-01 -7.237747E+01 -7.237747E+01 -1.163518E-05 -1.350590E-06 + --- H2 1 1.873685E-07 1.873674E-07 -3.261771E+01 -3.261772E+01 1.641587E-05 2.813821E-06 + --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.646209E-04 1.836949E-04 + --- Norms of Delta G(): 6.909785E-05 7.506065E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274245E+00 @@ -2428,22 +2428,22 @@ VCS CALCULATION METHOD --- H+ 1.8416E-09 -6.2848E-15 6.8253E-06 | Normal calc: diag adjusted from 1.08599e+09 to 1.08599e+09 due to act coeff --- H2O 9.7179E-02 -1.2654E-07 1.2981E-06 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff --- NaCl 3.9996E-32 0.0000E+00 1.6631E-06 | Skipped: IC = 0 and DG >0: 1.663E-06 - --- Cl- 2.1230E-01 7.9073E-08 -1.3506E-06 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff + --- Cl- 2.1230E-01 7.9072E-08 -1.3506E-06 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff --- H2 1.8737E-07 -1.7574E-13 2.8138E-06 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff - --- O2 8.9483E-69 0.0000E+00 1.8370E-04 | Skipped: IC = 0 and DG >0: 1.837E-04 + --- O2 8.9483E-69 0.0000E+00 1.8369E-04 | Skipped: IC = 0 and DG >0: 1.837E-04 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment --- H+ 1 1.8416E-09 1.8416E-09-6.2848E-15 | Normal Major Calc --- H2O 1 9.7179E-02 9.7179E-02-1.2654E-07 | Normal Major Calc --- NaCl 0 3.9996E-32 3.9996E-32 0.0000E+00 | minor species not considered - --- Cl- 1 2.1230E-01 2.1230E-01 7.9073E-08 | Normal Major Calc + --- Cl- 1 2.1230E-01 2.1230E-01 7.9072E-08 | Normal Major Calc --- H2 1 1.8737E-07 1.8737E-07-1.7574E-13 | Normal Major Calc --- O2 0 8.9483E-69 8.9483E-69 0.0000E+00 | minor species not considered - --- NaCl(S) c 4.7877E+00 4.7877E+00-7.9073E-08 | + --- NaCl(S) c 4.7877E+00 4.7877E+00-7.9072E-08 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9028E+00 1.9028E+00 1.2654E-07 | - --- Na+ c 2.1230E-01 2.1230E-01 7.9073E-08 | + --- Na+ c 2.1230E-01 2.1230E-01 7.9072E-08 | --- OH- c 1.8416E-09 1.8416E-09-6.2848E-15 | --- OH c 3.7473E-07 3.7473E-07-3.5148E-13 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -2453,8 +2453,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -2.71061e-13 - --- subroutine FORCE: End Slope = -3.81361e-14 + --- subroutine FORCE: Beginning Slope = -2.71057e-13 + --- subroutine FORCE: End Slope = -3.81355e-14 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2466,13 +2466,13 @@ VCS CALCULATION METHOD --- OH- 1.841630E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747349E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841630E-09 1.841623E-09 -1.517385E+01 -1.517386E+01 6.825272E-06 6.836552E-07 - --- H2O 1 9.717882E-02 9.717869E-02 -1.240032E+02 -1.240033E+02 1.298138E-06 1.506892E-07 - --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.663111E-06 1.693996E-06 - --- Cl- 1 2.123018E-01 2.123019E-01 -7.237747E+01 -7.237746E+01 -1.350606E-06 -2.411459E-07 - --- H2 1 1.873674E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 2.813833E-06 3.402213E-07 - --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.836958E-04 1.871074E-04 - --- Norms of Delta G(): 7.506101E-05 7.639012E-05 + --- H+ 1 1.841630E-09 1.841623E-09 -1.517385E+01 -1.517386E+01 6.825259E-06 6.836445E-07 + --- H2O 1 9.717882E-02 9.717869E-02 -1.240032E+02 -1.240033E+02 1.298133E-06 1.506874E-07 + --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.663103E-06 1.693988E-06 + --- Cl- 1 2.123018E-01 2.123019E-01 -7.237747E+01 -7.237746E+01 -1.350590E-06 -2.411450E-07 + --- H2 1 1.873674E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 2.813821E-06 3.402176E-07 + --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.836949E-04 1.871065E-04 + --- Norms of Delta G(): 7.506065E-05 7.638975E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2499,17 +2499,17 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.8416E-09 -6.2952E-16 6.8366E-07 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff - --- H2O 9.7179E-02 -1.4689E-08 1.5069E-07 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff + --- H+ 1.8416E-09 -6.2951E-16 6.8364E-07 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff + --- H2O 9.7179E-02 -1.4688E-08 1.5069E-07 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff --- NaCl 3.9996E-32 0.0000E+00 1.6940E-06 | Skipped: IC = 0 and DG >0: 1.694E-06 - --- Cl- 2.1230E-01 1.4118E-08 -2.4115E-07 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff + --- Cl- 2.1230E-01 1.4118E-08 -2.4114E-07 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff --- H2 1.8737E-07 -2.1249E-14 3.4022E-07 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff --- O2 8.9483E-69 0.0000E+00 1.8711E-04 | Skipped: IC = 0 and DG >0: 1.871E-04 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment - --- H+ 1 1.8416E-09 1.8416E-09-6.2952E-16 | Normal Major Calc - --- H2O 1 9.7179E-02 9.7179E-02-1.4689E-08 | Normal Major Calc + --- H+ 1 1.8416E-09 1.8416E-09-6.2951E-16 | Normal Major Calc + --- H2O 1 9.7179E-02 9.7179E-02-1.4688E-08 | Normal Major Calc --- NaCl 0 3.9996E-32 3.9996E-32 0.0000E+00 | minor species not considered --- Cl- 1 2.1230E-01 2.1230E-01 1.4118E-08 | Normal Major Calc --- H2 1 1.8737E-07 1.8737E-07-2.1249E-14 | Normal Major Calc @@ -2518,8 +2518,8 @@ VCS CALCULATION METHOD --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9028E+00 1.9028E+00 1.4689E-08 | --- Na+ c 2.1230E-01 2.1230E-01 1.4118E-08 | - --- OH- c 1.8416E-09 1.8416E-09-6.2952E-16 | - --- OH c 3.7473E-07 3.7473E-07-4.2498E-14 | + --- OH- c 1.8416E-09 1.8416E-09-6.2951E-16 | + --- OH c 3.7473E-07 3.7473E-07-4.2497E-14 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop @@ -2527,8 +2527,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -5.61798e-15 - --- subroutine FORCE: End Slope = -7.90405e-16 + --- subroutine FORCE: Beginning Slope = -5.6179e-15 + --- subroutine FORCE: End Slope = -7.90393e-16 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (only major species): @@ -2540,13 +2540,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 6.836552E-07 1.414622E-07 - --- H2O 1 9.717869E-02 9.717868E-02 -1.240033E+02 -1.240033E+02 1.506892E-07 2.690517E-08 - --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.693996E-06 1.697581E-06 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.411459E-07 -2.799244E-08 - --- H2 1 1.873673E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 3.402213E-07 5.831919E-08 - --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.871074E-04 1.875027E-04 - --- Norms of Delta G(): 7.639012E-05 7.655082E-05 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 6.836445E-07 1.414619E-07 + --- H2O 1 9.717869E-02 9.717868E-02 -1.240033E+02 -1.240033E+02 1.506874E-07 2.690507E-08 + --- NaCl 0 3.999646E-32 3.999646E-32 -1.745168E+02 -1.745168E+02 1.693988E-06 1.697573E-06 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.411450E-07 -2.799210E-08 + --- H2 1 1.873673E-07 1.873673E-07 -3.261772E+01 -3.261772E+01 3.402176E-07 5.831896E-08 + --- O2 0 8.948274E-69 8.948274E-69 -1.827709E+02 -1.827709E+02 1.871065E-04 1.875018E-04 + --- Norms of Delta G(): 7.638975E-05 7.655044E-05 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2578,7 +2578,7 @@ VCS CALCULATION METHOD --- H+ 1.8416E-09 -1.3026E-16 1.4146E-07 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff --- H2O 9.7179E-02 -2.6226E-09 2.6905E-08 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff --- NaCl 3.9996E-32 0.0000E+00 1.6976E-06 | Skipped: IC = 0 and DG >0: 1.698E-06 - --- Cl- 2.1230E-01 1.6389E-09 -2.7992E-08 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff + --- Cl- 2.1230E-01 1.6388E-09 -2.7992E-08 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff --- H2 1.8737E-07 -3.6424E-15 5.8319E-08 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff --- O2 8.9483E-69 0.0000E+00 1.8750E-04 | Skipped: IC = 0 and DG >0: 1.875E-04 ---------------------------------------------------------------------------------- @@ -2587,13 +2587,13 @@ VCS CALCULATION METHOD --- H+ 1 1.8416E-09 1.8416E-09-1.3026E-16 | Normal Major Calc --- H2O 1 9.7179E-02 9.7179E-02-2.6226E-09 | Normal Major Calc --- NaCl 0 3.9996E-32 3.9996E-32-6.7897E-38 | minor species alternative calc - --- Cl- 1 2.1230E-01 2.1230E-01 1.6389E-09 | Normal Major Calc + --- Cl- 1 2.1230E-01 2.1230E-01 1.6388E-09 | Normal Major Calc --- H2 1 1.8737E-07 1.8737E-07-3.6424E-15 | Normal Major Calc --- O2 0 8.9483E-69 8.9466E-69-1.6777E-72 | minor species alternative calc - --- NaCl(S) c 4.7877E+00 4.7877E+00-1.6389E-09 | + --- NaCl(S) c 4.7877E+00 4.7877E+00-1.6388E-09 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | --- H2O(L) c 1.9028E+00 1.9028E+00 2.6226E-09 | - --- Na+ c 2.1230E-01 2.1230E-01 1.6389E-09 | + --- Na+ c 2.1230E-01 2.1230E-01 1.6388E-09 | --- OH- c 1.8416E-09 1.8416E-09-1.3026E-16 | --- OH c 3.7473E-07 3.7473E-07-7.2847E-15 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | @@ -2603,8 +2603,8 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -1.16438e-16 - --- subroutine FORCE: End Slope = -1.63819e-17 + --- subroutine FORCE: Beginning Slope = -1.16436e-16 + --- subroutine FORCE: End Slope = -1.63816e-17 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- --- Summary of the Update (all species): @@ -2616,13 +2616,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.414622E-07 1.416954E-08 - --- H2O 1 9.717868E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 2.690517E-08 3.123191E-09 - --- NaCl 0 3.999646E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 1.697581E-06 6.401137E-10 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.799244E-08 -4.997958E-09 - --- H2 1 1.873673E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 5.831919E-08 7.051426E-09 - --- O2 0 8.948274E-69 8.946597E-69 -1.827709E+02 -1.827711E+02 1.875027E-04 7.070747E-08 - --- Norms of Delta G(): 7.655082E-05 2.967937E-08 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.414619E-07 1.416932E-08 + --- H2O 1 9.717868E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 2.690507E-08 3.123120E-09 + --- NaCl 0 3.999646E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 1.697573E-06 6.401137E-10 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -2.799210E-08 -4.997943E-09 + --- H2 1 1.873673E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 5.831896E-08 7.051312E-09 + --- O2 0 8.948274E-69 8.946597E-69 -1.827709E+02 -1.827711E+02 1.875018E-04 7.070736E-08 + --- Norms of Delta G(): 7.655044E-05 2.967930E-08 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 @@ -2650,27 +2650,27 @@ VCS CALCULATION METHOD --- Subroutine vcs_RxnStepSizes called - Details: ---------------------------------------------------------------------------------- --- Species KMoles Rxn_Adjustment DeltaG | Comment - --- H+ 1.8416E-09 -1.3047E-17 1.4170E-08 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff - --- H2O 9.7179E-02 -3.0444E-10 3.1232E-09 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff + --- H+ 1.8416E-09 -1.3047E-17 1.4169E-08 | Normal calc: diag adjusted from 1.086e+09 to 1.086e+09 due to act coeff + --- H2O 9.7179E-02 -3.0443E-10 3.1231E-09 | Normal calc: diag adjusted from 10.1421 to 10.2589 due to act coeff --- NaCl 3.9996E-32 0.0000E+00 6.4011E-10 | Skipped: IC = 0 and DG >0: 6.401E-10 - --- Cl- 2.1230E-01 2.9261E-10 -4.9980E-09 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff - --- H2 1.8737E-07 -4.4040E-16 7.0514E-09 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff + --- Cl- 2.1230E-01 2.9261E-10 -4.9979E-09 | Normal calc: diag adjusted from 7.70191 to 17.0805 due to act coeff + --- H2 1.8737E-07 -4.4040E-16 7.0513E-09 | Normal calc: diag adjusted from 1.60113e+07 to 1.60113e+07 due to act coeff --- O2 8.9466E-69 0.0000E+00 7.0707E-08 | Skipped: IC = 0 and DG >0: 7.071E-08 ---------------------------------------------------------------------------------- --- Main Loop Treatment of each non-component species - Major Components Calculation: --- Species IC KMoles Tent_KMoles Rxn_Adj | Comment --- H+ 1 1.8416E-09 1.8416E-09-1.3047E-17 | Normal Major Calc - --- H2O 1 9.7179E-02 9.7179E-02-3.0444E-10 | Normal Major Calc + --- H2O 1 9.7179E-02 9.7179E-02-3.0443E-10 | Normal Major Calc --- NaCl 0 3.9996E-32 3.9996E-32 0.0000E+00 | minor species not considered --- Cl- 1 2.1230E-01 2.1230E-01 2.9261E-10 | Normal Major Calc --- H2 1 1.8737E-07 1.8737E-07-4.4040E-16 | Normal Major Calc --- O2 0 8.9466E-69 8.9466E-69 0.0000E+00 | minor species not considered --- NaCl(S) c 4.7877E+00 4.7877E+00-2.9261E-10 | --- N2 c 4.0000E+00 4.0000E+00 0.0000E+00 | - --- H2O(L) c 1.9028E+00 1.9028E+00 3.0444E-10 | + --- H2O(L) c 1.9028E+00 1.9028E+00 3.0443E-10 | --- Na+ c 2.1230E-01 2.1230E-01 2.9261E-10 | --- OH- c 1.8416E-09 1.8416E-09-1.3047E-17 | - --- OH c 3.7473E-07 3.7473E-07-8.8080E-16 | + --- OH c 3.7473E-07 3.7473E-07-8.8079E-16 | --- CO2 c 0.0000E+00 0.0000E+00 0.0000E+00 | -------------------------------------------------------------------------------- --- Finished Main Loop @@ -2678,7 +2678,7 @@ VCS CALCULATION METHOD --- Subroutine vcs_deltag called for all noncomponents --- Total Old Dimensionless Gibbs Free Energy = -1.2128673458838E+03 --- Total tentative Dimensionless Gibbs Free Energy = -1.2128673458838E+03 - --- subroutine FORCE: Beginning Slope = -2.41328e-18 + --- subroutine FORCE: Beginning Slope = -2.41323e-18 --- subroutine FORCE: End Slope = -3.39535e-19 --- subroutine FORCE produced no adjustments, s2 < 0 ------------------------------------------------------------------------------------------------------- @@ -2691,13 +2691,13 @@ VCS CALCULATION METHOD --- OH- 1.841623E-09 1.841623E-09 -1.088294E+02 -1.088294E+02 --- OH 3.747345E-07 3.747345E-07 -1.076944E+02 -1.076944E+02 --- CO2 0.000000E+00 0.000000E+00 -5.082240E+02 -5.082240E+02 - --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.416954E-08 2.931912E-09 - --- H2O 1 9.717867E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 3.123191E-09 5.576339E-10 + --- H+ 1 1.841623E-09 1.841623E-09 -1.517386E+01 -1.517386E+01 1.416932E-08 2.931927E-09 + --- H2O 1 9.717867E-02 9.717867E-02 -1.240033E+02 -1.240033E+02 3.123120E-09 5.576624E-10 --- NaCl 0 3.999640E-32 3.999640E-32 -1.745168E+02 -1.745168E+02 6.401137E-10 7.144081E-10 - --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -4.997958E-09 -5.801866E-10 - --- H2 1 1.873672E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 7.051426E-09 1.208718E-09 - --- O2 0 8.946597E-69 8.946597E-69 -1.827711E+02 -1.827711E+02 7.070747E-08 7.890060E-08 - --- Norms of Delta G(): 2.967937E-08 3.224004E-08 + --- Cl- 1 2.123019E-01 2.123019E-01 -7.237746E+01 -7.237746E+01 -4.997943E-09 -5.801724E-10 + --- H2 1 1.873672E-07 1.873672E-07 -3.261772E+01 -3.261772E+01 7.051312E-09 1.208747E-09 + --- O2 0 8.946597E-69 8.946597E-69 -1.827711E+02 -1.827711E+02 7.070736E-08 7.890037E-08 + --- Norms of Delta G(): 2.967930E-08 3.223994E-08 --- Phase_Name KMoles(after update) --- -------------------------------------------------- --- NaCl_electrolyte = 2.3274248E+00 From 7f485a0ba338f14717ef98c26e03beaa2792ba94 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 28 Apr 2011 17:10:32 +0000 Subject: [PATCH 361/446] Worked on reducing the Print outs for DEBUG_DOGLEG option --- Cantera/src/numerics/NonlinearSolver.cpp | 90 +++++++++++++++--------- Cantera/src/numerics/NonlinearSolver.h | 3 + 2 files changed, 59 insertions(+), 34 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 99d96bd3d..1ace7e722 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -76,6 +76,9 @@ namespace Cantera { #else bool NonlinearSolver::s_print_NumJac(false); #endif + + // Turn off printing of dogleg information + bool NonlinearSolver::s_print_DogLeg(false); //==================================================================================================================== // Default constructor /* @@ -845,15 +848,20 @@ namespace Cantera { } // Compute the weighted norm of the undamped step size descentDir_[] - normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 10); - - printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); - printf("\t\t\t R0 = %g \n", m_normResid0); - printf("\t\t\t Rpred = %g\n", residCauchy); - printf("\t\t\t Rjd = %g\n", RJd_norm_); - printf("\t\t\t JdJd = %g\n", JdJd_norm_); - printf("\t\t\t deltaX = %g\n", normSoln); - printf("\t\t\t lambda = %g\n", lambda_); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 10); + } else { + normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 0); + } + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); + printf("\t\t\t R0 = %g \n", m_normResid0); + printf("\t\t\t Rpred = %g\n", residCauchy); + printf("\t\t\t Rjd = %g\n", RJd_norm_); + printf("\t\t\t JdJd = %g\n", JdJd_norm_); + printf("\t\t\t deltaX = %g\n", normSoln); + printf("\t\t\t lambda = %g\n", lambda_); + } } return normSoln; } @@ -908,10 +916,12 @@ namespace Cantera { * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights */ - printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); - printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); - printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); - printf("descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); + printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); + printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); + printf("descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); + } } //==================================================================================================================== @@ -1051,8 +1061,10 @@ namespace Cantera { const double *ydot1, const double *newtDir) { double *y1 = DATA_PTR(m_wksp); double sLen; - printf(" residualComparisonLeg() \n"); - printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + printf(" residualComparisonLeg() \n"); + printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); + } // First compare at 1/4 along SD curve std::vector alphaT; alphaT.push_back(0.00); @@ -1083,8 +1095,9 @@ namespace Cantera { double residSteepLin = expectedResidLeg(0, alpha); double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); - - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); + } } for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { @@ -1112,8 +1125,9 @@ namespace Cantera { double residSteepLin = expectedResidLeg(1, alpha); double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); - - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); + } } for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { @@ -1138,8 +1152,9 @@ namespace Cantera { double residSteepLin = expectedResidLeg(2, alpha); double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); - - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); + } } @@ -1338,22 +1353,30 @@ namespace Cantera { deltaX_trust_[i] = deltaX_trust_[i] * sum; } trustDelta_ = 1.0; - printf("calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", - trustNorm, trustNormGoal); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", + trustNorm, trustNormGoal); + } } //==================================================================================================================== void NonlinearSolver::initializeTrustRegion() { double cpd = calcTrustDistance(deltaX_CP_); - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + } trustDelta_ = trustDelta_ * cpd; calcTrustVector(); cpd = calcTrustDistance(deltaX_CP_); - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + } trustDelta_ = trustDelta_ * cpd; calcTrustVector(); cpd = calcTrustDistance(deltaX_CP_); - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + } } //==================================================================================================================== @@ -1435,7 +1458,7 @@ namespace Cantera { double c = normTrust_CP_ * normTrust_CP_ - trustDelta * trustDelta; alpha =( -b + sqrt( b * b - 4.0 * a * c)) / (2.0 * a); - // alpha = (trustDelta - normTrust_CP_) / (normTrust_Newton_ * Nuu_ - normTrust_CP_); + dist = dist_R0_ + alpha * dist_R1_; lambda = dist / dist_Total_; @@ -1762,7 +1785,6 @@ namespace Cantera { bool success = false; int retn = 0; bool haveASuccess = false; - double normResid02 = m_normResid0 * m_normResid0 * neq_; double trustDeltaOld = trustDelta_; //-------------------------------------------- // Attempt damped step @@ -1771,11 +1793,9 @@ namespace Cantera { // damping coefficient starts at 1.0 m_dampRes = 1.0; int j, m; - doublereal ff = m_dampBound; num_backtracks = 0; double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; - bool goodStep = false; double tlen; @@ -2183,10 +2203,12 @@ namespace Cantera { if (doDogLeg_) { double trustD = calcTrustDistance(stp); #ifdef DEBUG_DOGLEG - if (trustD > trustDelta_) { - printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); - } else { - printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); + if (s_print_DogLeg || m_print_flag > 3) { + if (trustD > trustDelta_) { + printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); + } else { + printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); + } } #endif } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 43b6c6e4b..e586e8cfe 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -907,6 +907,9 @@ namespace Cantera { //! Turn on or off printing of the Jacobian static bool s_print_NumJac; + + //! Turn on all printing of dogleg information + static bool s_print_DogLeg; }; } From 24ac9bd133a9e83bc77c0330ce9a8d4023560a9c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 28 Apr 2011 20:56:02 +0000 Subject: [PATCH 362/446] Added in condition number routines for triangular matrices --- ext/f2c_lapack/Makefile.in | 3 + ext/f2c_lapack/dlacon.c | 257 ++++++++++++ ext/f2c_lapack/dlatrs.c | 820 +++++++++++++++++++++++++++++++++++++ ext/f2c_lapack/dtrcon.c | 242 +++++++++++ ext/lapack/Makefile.in | 3 + ext/lapack/dlacon.f | 204 +++++++++ ext/lapack/dlatrs.f | 702 +++++++++++++++++++++++++++++++ ext/lapack/dtrcon.f | 193 +++++++++ 8 files changed, 2424 insertions(+) create mode 100644 ext/f2c_lapack/dlacon.c create mode 100644 ext/f2c_lapack/dlatrs.c create mode 100644 ext/f2c_lapack/dtrcon.c create mode 100644 ext/lapack/dlacon.f create mode 100644 ext/lapack/dlatrs.f create mode 100644 ext/lapack/dtrcon.f diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 7dd08bca1..bb6764363 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -64,6 +64,7 @@ dgetri.o \ dgetrs.o \ dlabad.o \ dlabrd.o \ +dlacon.o \ dlacpy.o \ dlamch.o \ dlange.o \ @@ -88,6 +89,7 @@ dlasrt.o \ dlassq.o \ dlasv2.o \ dlaswp.o \ +dlatrs.o \ dorg2r.o \ dorgbr.o \ dorgl2.o \ @@ -99,6 +101,7 @@ dorml2.o \ dormlq.o \ dormqr.o \ drscl.o \ +dtrcon.o \ dtrtri.o \ dtrti2.o \ dtrtrs.o \ diff --git a/ext/f2c_lapack/dlacon.c b/ext/f2c_lapack/dlacon.c new file mode 100644 index 000000000..2bc7054ab --- /dev/null +++ b/ext/f2c_lapack/dlacon.c @@ -0,0 +1,257 @@ +/* dlacon.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static doublereal c_b11 = 1.; + +/* Subroutine */ int dlacon_(integer *n, doublereal *v, doublereal *x, + integer *isgn, doublereal *est, integer *kase) +{ + /* System generated locals */ + integer i__1; + doublereal d__1; + + /* Builtin functions */ + double d_sign(doublereal *, doublereal *); + integer i_dnnt(doublereal *); + + /* Local variables */ + static integer i__, j, iter; + static doublereal temp; + static integer jump; + extern doublereal dasum_(integer *, doublereal *, integer *); + static integer jlast; + extern /* Subroutine */ int dcopy_(integer *, doublereal *, integer *, + doublereal *, integer *); + extern integer idamax_(integer *, doublereal *, integer *); + static doublereal altsgn, estold; + + +/* -- LAPACK auxiliary routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* February 29, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DLACON estimates the 1-norm of a square, real matrix A. */ +/* Reverse communication is used for evaluating matrix-vector products. */ + +/* Arguments */ +/* ========= */ + +/* N (input) INTEGER */ +/* The order of the matrix. N >= 1. */ + +/* V (workspace) DOUBLE PRECISION array, dimension (N) */ +/* On the final return, V = A*W, where EST = norm(V)/norm(W) */ +/* (W is not returned). */ + +/* X (input/output) DOUBLE PRECISION array, dimension (N) */ +/* On an intermediate return, X should be overwritten by */ +/* A * X, if KASE=1, */ +/* A' * X, if KASE=2, */ +/* and DLACON must be re-called with all the other parameters */ +/* unchanged. */ + +/* ISGN (workspace) INTEGER array, dimension (N) */ + +/* EST (output) DOUBLE PRECISION */ +/* An estimate (a lower bound) for norm(A). */ + +/* KASE (input/output) INTEGER */ +/* On the initial call to DLACON, KASE should be 0. */ +/* On an intermediate return, KASE will be 1 or 2, indicating */ +/* whether X should be overwritten by A * X or A' * X. */ +/* On the final return from DLACON, KASE will again be 0. */ + +/* Further Details */ +/* ======= ======= */ + +/* Contributed by Nick Higham, University of Manchester. */ +/* Originally named SONEST, dated March 16, 1988. */ + +/* Reference: N.J. Higham, "FORTRAN codes for estimating the one-norm of */ +/* a real or complex matrix, with applications to condition estimation", */ +/* ACM Trans. Math. Soft., vol. 14, no. 4, pp. 381-396, December 1988. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Save statement .. */ +/* .. */ +/* .. Executable Statements .. */ + + /* Parameter adjustments */ + --isgn; + --x; + --v; + + /* Function Body */ + if (*kase == 0) { + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + x[i__] = 1. / (doublereal) (*n); +/* L10: */ + } + *kase = 1; + jump = 1; + return 0; + } + + switch (jump) { + case 1: goto L20; + case 2: goto L40; + case 3: goto L70; + case 4: goto L110; + case 5: goto L140; + } + +/* ................ ENTRY (JUMP = 1) */ +/* FIRST ITERATION. X HAS BEEN OVERWRITTEN BY A*X. */ + +L20: + if (*n == 1) { + v[1] = x[1]; + *est = abs(v[1]); +/* ... QUIT */ + goto L150; + } + *est = dasum_(n, &x[1], &c__1); + + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + x[i__] = d_sign(&c_b11, &x[i__]); + isgn[i__] = i_dnnt(&x[i__]); +/* L30: */ + } + *kase = 2; + jump = 2; + return 0; + +/* ................ ENTRY (JUMP = 2) */ +/* FIRST ITERATION. X HAS BEEN OVERWRITTEN BY TRANDPOSE(A)*X. */ + +L40: + j = idamax_(n, &x[1], &c__1); + iter = 2; + +/* MAIN LOOP - ITERATIONS 2,3,...,ITMAX. */ + +L50: + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + x[i__] = 0.; +/* L60: */ + } + x[j] = 1.; + *kase = 1; + jump = 3; + return 0; + +/* ................ ENTRY (JUMP = 3) */ +/* X HAS BEEN OVERWRITTEN BY A*X. */ + +L70: + dcopy_(n, &x[1], &c__1, &v[1], &c__1); + estold = *est; + *est = dasum_(n, &v[1], &c__1); + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + d__1 = d_sign(&c_b11, &x[i__]); + if (i_dnnt(&d__1) != isgn[i__]) { + goto L90; + } +/* L80: */ + } +/* REPEATED SIGN VECTOR DETECTED, HENCE ALGORITHM HAS CONVERGED. */ + goto L120; + +L90: +/* TEST FOR CYCLING. */ + if (*est <= estold) { + goto L120; + } + + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + x[i__] = d_sign(&c_b11, &x[i__]); + isgn[i__] = i_dnnt(&x[i__]); +/* L100: */ + } + *kase = 2; + jump = 4; + return 0; + +/* ................ ENTRY (JUMP = 4) */ +/* X HAS BEEN OVERWRITTEN BY TRANDPOSE(A)*X. */ + +L110: + jlast = j; + j = idamax_(n, &x[1], &c__1); + if (x[jlast] != (d__1 = x[j], abs(d__1)) && iter < 5) { + ++iter; + goto L50; + } + +/* ITERATION COMPLETE. FINAL STAGE. */ + +L120: + altsgn = 1.; + i__1 = *n; + for (i__ = 1; i__ <= i__1; ++i__) { + x[i__] = altsgn * ((doublereal) (i__ - 1) / (doublereal) (*n - 1) + + 1.); + altsgn = -altsgn; +/* L130: */ + } + *kase = 1; + jump = 5; + return 0; + +/* ................ ENTRY (JUMP = 5) */ +/* X HAS BEEN OVERWRITTEN BY A*X. */ + +L140: + temp = dasum_(n, &x[1], &c__1) / (doublereal) (*n * 3) * 2.; + if (temp > *est) { + dcopy_(n, &x[1], &c__1, &v[1], &c__1); + *est = temp; + } + +L150: + *kase = 0; + return 0; + +/* End of DLACON */ + +} /* dlacon_ */ + diff --git a/ext/f2c_lapack/dlatrs.c b/ext/f2c_lapack/dlatrs.c new file mode 100644 index 000000000..a08a0f09f --- /dev/null +++ b/ext/f2c_lapack/dlatrs.c @@ -0,0 +1,820 @@ +/* dlatrs.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static doublereal c_b36 = .5; + +/* Subroutine */ int dlatrs_(char *uplo, char *trans, char *diag, char * + normin, integer *n, doublereal *a, integer *lda, doublereal *x, + doublereal *scale, doublereal *cnorm, integer *info, ftnlen uplo_len, + ftnlen trans_len, ftnlen diag_len, ftnlen normin_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1, i__2, i__3; + doublereal d__1, d__2, d__3; + + /* Local variables */ + static integer i__, j; + static doublereal xj, rec, tjj; + static integer jinc; + extern doublereal ddot_(integer *, doublereal *, integer *, doublereal *, + integer *); + static doublereal xbnd; + static integer imax; + static doublereal tmax, tjjs, xmax, grow, sumj; + extern /* Subroutine */ int dscal_(integer *, doublereal *, doublereal *, + integer *); + extern logical lsame_(char *, char *, ftnlen, ftnlen); + static doublereal tscal, uscal; + extern doublereal dasum_(integer *, doublereal *, integer *); + static integer jlast; + extern /* Subroutine */ int daxpy_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + static logical upper; + extern /* Subroutine */ int dtrsv_(char *, char *, char *, integer *, + doublereal *, integer *, doublereal *, integer *, ftnlen, ftnlen, + ftnlen); + extern doublereal dlamch_(char *, ftnlen); + extern integer idamax_(integer *, doublereal *, integer *); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + static doublereal bignum; + static logical notran; + static integer jfirst; + static doublereal smlnum; + static logical nounit; + + +/* -- LAPACK auxiliary routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* June 30, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DLATRS solves one of the triangular systems */ + +/* A *x = s*b or A'*x = s*b */ + +/* with scaling to prevent overflow. Here A is an upper or lower */ +/* triangular matrix, A' denotes the transpose of A, x and b are */ +/* n-element vectors, and s is a scaling factor, usually less than */ +/* or equal to 1, chosen so that the components of x will be less than */ +/* the overflow threshold. If the unscaled problem will not cause */ +/* overflow, the Level 2 BLAS routine DTRSV is called. If the matrix A */ +/* is singular (A(j,j) = 0 for some j), then s is set to 0 and a */ +/* non-trivial solution to A*x = 0 is returned. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* Specifies whether the matrix A is upper or lower triangular. */ +/* = 'U': Upper triangular */ +/* = 'L': Lower triangular */ + +/* TRANS (input) CHARACTER*1 */ +/* Specifies the operation applied to A. */ +/* = 'N': Solve A * x = s*b (No transpose) */ +/* = 'T': Solve A'* x = s*b (Transpose) */ +/* = 'C': Solve A'* x = s*b (Conjugate transpose = Transpose) */ + +/* DIAG (input) CHARACTER*1 */ +/* Specifies whether or not the matrix A is unit triangular. */ +/* = 'N': Non-unit triangular */ +/* = 'U': Unit triangular */ + +/* NORMIN (input) CHARACTER*1 */ +/* Specifies whether CNORM has been set or not. */ +/* = 'Y': CNORM contains the column norms on entry */ +/* = 'N': CNORM is not set on entry. On exit, the norms will */ +/* be computed and stored in CNORM. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The triangular matrix A. If UPLO = 'U', the leading n by n */ +/* upper triangular part of the array A contains the upper */ +/* triangular matrix, and the strictly lower triangular part of */ +/* A is not referenced. If UPLO = 'L', the leading n by n lower */ +/* triangular part of the array A contains the lower triangular */ +/* matrix, and the strictly upper triangular part of A is not */ +/* referenced. If DIAG = 'U', the diagonal elements of A are */ +/* also not referenced and are assumed to be 1. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max (1,N). */ + +/* X (input/output) DOUBLE PRECISION array, dimension (N) */ +/* On entry, the right hand side b of the triangular system. */ +/* On exit, X is overwritten by the solution vector x. */ + +/* SCALE (output) DOUBLE PRECISION */ +/* The scaling factor s for the triangular system */ +/* A * x = s*b or A'* x = s*b. */ +/* If SCALE = 0, the matrix A is singular or badly scaled, and */ +/* the vector x is an exact or approximate solution to A*x = 0. */ + +/* CNORM (input or output) DOUBLE PRECISION array, dimension (N) */ + +/* If NORMIN = 'Y', CNORM is an input argument and CNORM(j) */ +/* contains the norm of the off-diagonal part of the j-th column */ +/* of A. If TRANS = 'N', CNORM(j) must be greater than or equal */ +/* to the infinity-norm, and if TRANS = 'T' or 'C', CNORM(j) */ +/* must be greater than or equal to the 1-norm. */ + +/* If NORMIN = 'N', CNORM is an output argument and CNORM(j) */ +/* returns the 1-norm of the offdiagonal part of the j-th column */ +/* of A. */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -k, the k-th argument had an illegal value */ + +/* Further Details */ +/* ======= ======= */ + +/* A rough bound on x is computed; if that is less than overflow, DTRSV */ +/* is called, otherwise, specific code is used which checks for possible */ +/* overflow or divide-by-zero at every operation. */ + +/* A columnwise scheme is used for solving A*x = b. The basic algorithm */ +/* if A is lower triangular is */ + +/* x[1:n] := b[1:n] */ +/* for j = 1, ..., n */ +/* x(j) := x(j) / A(j,j) */ +/* x[j+1:n] := x[j+1:n] - x(j) * A[j+1:n,j] */ +/* end */ + +/* Define bounds on the components of x after j iterations of the loop: */ +/* M(j) = bound on x[1:j] */ +/* G(j) = bound on x[j+1:n] */ +/* Initially, let M(0) = 0 and G(0) = max{x(i), i=1,...,n}. */ + +/* Then for iteration j+1 we have */ +/* M(j+1) <= G(j) / | A(j+1,j+1) | */ +/* G(j+1) <= G(j) + M(j+1) * | A[j+2:n,j+1] | */ +/* <= G(j) ( 1 + CNORM(j+1) / | A(j+1,j+1) | ) */ + +/* where CNORM(j+1) is greater than or equal to the infinity-norm of */ +/* column j+1 of A, not counting the diagonal. Hence */ + +/* G(j) <= G(0) product ( 1 + CNORM(i) / | A(i,i) | ) */ +/* 1<=i<=j */ +/* and */ + +/* |x(j)| <= ( G(0) / |A(j,j)| ) product ( 1 + CNORM(i) / |A(i,i)| ) */ +/* 1<=i< j */ + +/* Since |x(j)| <= M(j), we use the Level 2 BLAS routine DTRSV if the */ +/* reciprocal of the largest M(j), j=1,..,n, is larger than */ +/* max(underflow, 1/overflow). */ + +/* The bound on x(j) is also used to determine when a step in the */ +/* columnwise method can be performed without fear of overflow. If */ +/* the computed bound is greater than a large constant, x is scaled to */ +/* prevent overflow, but if the bound overflows, x is set to 0, x(j) to */ +/* 1, and scale to 0, and a non-trivial solution to A*x = 0 is found. */ + +/* Similarly, a row-wise scheme is used to solve A'*x = b. The basic */ +/* algorithm for A upper triangular is */ + +/* for j = 1, ..., n */ +/* x(j) := ( b(j) - A[1:j-1,j]' * x[1:j-1] ) / A(j,j) */ +/* end */ + +/* We simultaneously compute two bounds */ +/* G(j) = bound on ( b(i) - A[1:i-1,i]' * x[1:i-1] ), 1<=i<=j */ +/* M(j) = bound on x(i), 1<=i<=j */ + +/* The initial values are G(0) = 0, M(0) = max{b(i), i=1,..,n}, and we */ +/* add the constraint G(j) >= G(j-1) and M(j) >= M(j-1) for j >= 1. */ +/* Then the bound on x(j) is */ + +/* M(j) <= M(j-1) * ( 1 + CNORM(j) ) / | A(j,j) | */ + +/* <= M(0) * product ( ( 1 + CNORM(i) ) / |A(i,i)| ) */ +/* 1<=i<=j */ + +/* and we can safely call DTRSV if 1/M(n) and 1/G(n) are both greater */ +/* than max(underflow, 1/overflow). */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + --x; + --cnorm; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + notran = lsame_(trans, "N", (ftnlen)1, (ftnlen)1); + nounit = lsame_(diag, "N", (ftnlen)1, (ftnlen)1); + +/* Test the input parameters. */ + + if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (! notran && ! lsame_(trans, "T", (ftnlen)1, (ftnlen)1) && ! + lsame_(trans, "C", (ftnlen)1, (ftnlen)1)) { + *info = -2; + } else if (! nounit && ! lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + *info = -3; + } else if (! lsame_(normin, "Y", (ftnlen)1, (ftnlen)1) && ! lsame_(normin, + "N", (ftnlen)1, (ftnlen)1)) { + *info = -4; + } else if (*n < 0) { + *info = -5; + } else if (*lda < max(1,*n)) { + *info = -7; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DLATRS", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + return 0; + } + +/* Determine machine dependent parameters to control overflow. */ + + smlnum = dlamch_("Safe minimum", (ftnlen)12) / dlamch_("Precision", ( + ftnlen)9); + bignum = 1. / smlnum; + *scale = 1.; + + if (lsame_(normin, "N", (ftnlen)1, (ftnlen)1)) { + +/* Compute the 1-norm of each column, not including the diagonal. */ + + if (upper) { + +/* A is upper triangular. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + i__2 = j - 1; + cnorm[j] = dasum_(&i__2, &a[j * a_dim1 + 1], &c__1); +/* L10: */ + } + } else { + +/* A is lower triangular. */ + + i__1 = *n - 1; + for (j = 1; j <= i__1; ++j) { + i__2 = *n - j; + cnorm[j] = dasum_(&i__2, &a[j + 1 + j * a_dim1], &c__1); +/* L20: */ + } + cnorm[*n] = 0.; + } + } + +/* Scale the column norms by TSCAL if the maximum element in CNORM is */ +/* greater than BIGNUM. */ + + imax = idamax_(n, &cnorm[1], &c__1); + tmax = cnorm[imax]; + if (tmax <= bignum) { + tscal = 1.; + } else { + tscal = 1. / (smlnum * tmax); + dscal_(n, &tscal, &cnorm[1], &c__1); + } + +/* Compute a bound on the computed solution vector to see if the */ +/* Level 2 BLAS routine DTRSV can be used. */ + + j = idamax_(n, &x[1], &c__1); + xmax = (d__1 = x[j], abs(d__1)); + xbnd = xmax; + if (notran) { + +/* Compute the growth in A * x = b. */ + + if (upper) { + jfirst = *n; + jlast = 1; + jinc = -1; + } else { + jfirst = 1; + jlast = *n; + jinc = 1; + } + + if (tscal != 1.) { + grow = 0.; + goto L50; + } + + if (nounit) { + +/* A is non-unit triangular. */ + +/* Compute GROW = 1/G(j) and XBND = 1/M(j). */ +/* Initially, G(0) = max{x(i), i=1,...,n}. */ + + grow = 1. / max(xbnd,smlnum); + xbnd = grow; + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L50; + } + +/* M(j) = G(j-1) / abs(A(j,j)) */ + + tjj = (d__1 = a[j + j * a_dim1], abs(d__1)); +/* Computing MIN */ + d__1 = xbnd, d__2 = min(1.,tjj) * grow; + xbnd = min(d__1,d__2); + if (tjj + cnorm[j] >= smlnum) { + +/* G(j) = G(j-1)*( 1 + CNORM(j) / abs(A(j,j)) ) */ + + grow *= tjj / (tjj + cnorm[j]); + } else { + +/* G(j) could overflow, set GROW to 0. */ + + grow = 0.; + } +/* L30: */ + } + grow = xbnd; + } else { + +/* A is unit triangular. */ + +/* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. */ + +/* Computing MIN */ + d__1 = 1., d__2 = 1. / max(xbnd,smlnum); + grow = min(d__1,d__2); + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L50; + } + +/* G(j) = G(j-1)*( 1 + CNORM(j) ) */ + + grow *= 1. / (cnorm[j] + 1.); +/* L40: */ + } + } +L50: + + ; + } else { + +/* Compute the growth in A' * x = b. */ + + if (upper) { + jfirst = 1; + jlast = *n; + jinc = 1; + } else { + jfirst = *n; + jlast = 1; + jinc = -1; + } + + if (tscal != 1.) { + grow = 0.; + goto L80; + } + + if (nounit) { + +/* A is non-unit triangular. */ + +/* Compute GROW = 1/G(j) and XBND = 1/M(j). */ +/* Initially, M(0) = max{x(i), i=1,...,n}. */ + + grow = 1. / max(xbnd,smlnum); + xbnd = grow; + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L80; + } + +/* G(j) = max( G(j-1), M(j-1)*( 1 + CNORM(j) ) ) */ + + xj = cnorm[j] + 1.; +/* Computing MIN */ + d__1 = grow, d__2 = xbnd / xj; + grow = min(d__1,d__2); + +/* M(j) = M(j-1)*( 1 + CNORM(j) ) / abs(A(j,j)) */ + + tjj = (d__1 = a[j + j * a_dim1], abs(d__1)); + if (xj > tjj) { + xbnd *= tjj / xj; + } +/* L60: */ + } + grow = min(grow,xbnd); + } else { + +/* A is unit triangular. */ + +/* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. */ + +/* Computing MIN */ + d__1 = 1., d__2 = 1. / max(xbnd,smlnum); + grow = min(d__1,d__2); + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L80; + } + +/* G(j) = ( 1 + CNORM(j) )*G(j-1) */ + + xj = cnorm[j] + 1.; + grow /= xj; +/* L70: */ + } + } +L80: + ; + } + + if (grow * tscal > smlnum) { + +/* Use the Level 2 BLAS solve if the reciprocal of the bound on */ +/* elements of X is not too small. */ + + dtrsv_(uplo, trans, diag, n, &a[a_offset], lda, &x[1], &c__1, (ftnlen) + 1, (ftnlen)1, (ftnlen)1); + } else { + +/* Use a Level 1 BLAS solve, scaling intermediate results. */ + + if (xmax > bignum) { + +/* Scale X so that its components are less than or equal to */ +/* BIGNUM in absolute value. */ + + *scale = bignum / xmax; + dscal_(n, scale, &x[1], &c__1); + xmax = bignum; + } + + if (notran) { + +/* Solve A * x = b */ + + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Compute x(j) = b(j) / A(j,j), scaling x if necessary. */ + + xj = (d__1 = x[j], abs(d__1)); + if (nounit) { + tjjs = a[j + j * a_dim1] * tscal; + } else { + tjjs = tscal; + if (tscal == 1.) { + goto L100; + } + } + tjj = abs(tjjs); + if (tjj > smlnum) { + +/* abs(A(j,j)) > SMLNUM: */ + + if (tjj < 1.) { + if (xj > tjj * bignum) { + +/* Scale x by 1/b(j). */ + + rec = 1. / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + x[j] /= tjjs; + xj = (d__1 = x[j], abs(d__1)); + } else if (tjj > 0.) { + +/* 0 < abs(A(j,j)) <= SMLNUM: */ + + if (xj > tjj * bignum) { + +/* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM */ +/* to avoid overflow when dividing by A(j,j). */ + + rec = tjj * bignum / xj; + if (cnorm[j] > 1.) { + +/* Scale by 1/CNORM(j) to avoid overflow when */ +/* multiplying x(j) times column j. */ + + rec /= cnorm[j]; + } + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + x[j] /= tjjs; + xj = (d__1 = x[j], abs(d__1)); + } else { + +/* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and */ +/* scale = 0, and compute a solution to A*x = 0. */ + + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + x[i__] = 0.; +/* L90: */ + } + x[j] = 1.; + xj = 1.; + *scale = 0.; + xmax = 0.; + } +L100: + +/* Scale x if necessary to avoid overflow when adding a */ +/* multiple of column j of A. */ + + if (xj > 1.) { + rec = 1. / xj; + if (cnorm[j] > (bignum - xmax) * rec) { + +/* Scale x by 1/(2*abs(x(j))). */ + + rec *= .5; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + } + } else if (xj * cnorm[j] > bignum - xmax) { + +/* Scale x by 1/2. */ + + dscal_(n, &c_b36, &x[1], &c__1); + *scale *= .5; + } + + if (upper) { + if (j > 1) { + +/* Compute the update */ +/* x(1:j-1) := x(1:j-1) - x(j) * A(1:j-1,j) */ + + i__3 = j - 1; + d__1 = -x[j] * tscal; + daxpy_(&i__3, &d__1, &a[j * a_dim1 + 1], &c__1, &x[1], + &c__1); + i__3 = j - 1; + i__ = idamax_(&i__3, &x[1], &c__1); + xmax = (d__1 = x[i__], abs(d__1)); + } + } else { + if (j < *n) { + +/* Compute the update */ +/* x(j+1:n) := x(j+1:n) - x(j) * A(j+1:n,j) */ + + i__3 = *n - j; + d__1 = -x[j] * tscal; + daxpy_(&i__3, &d__1, &a[j + 1 + j * a_dim1], &c__1, & + x[j + 1], &c__1); + i__3 = *n - j; + i__ = j + idamax_(&i__3, &x[j + 1], &c__1); + xmax = (d__1 = x[i__], abs(d__1)); + } + } +/* L110: */ + } + + } else { + +/* Solve A' * x = b */ + + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Compute x(j) = b(j) - sum A(k,j)*x(k). */ +/* k<>j */ + + xj = (d__1 = x[j], abs(d__1)); + uscal = tscal; + rec = 1. / max(xmax,1.); + if (cnorm[j] > (bignum - xj) * rec) { + +/* If x(j) could overflow, scale x by 1/(2*XMAX). */ + + rec *= .5; + if (nounit) { + tjjs = a[j + j * a_dim1] * tscal; + } else { + tjjs = tscal; + } + tjj = abs(tjjs); + if (tjj > 1.) { + +/* Divide by A(j,j) when scaling x if A(j,j) > 1. */ + +/* Computing MIN */ + d__1 = 1., d__2 = rec * tjj; + rec = min(d__1,d__2); + uscal /= tjjs; + } + if (rec < 1.) { + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + + sumj = 0.; + if (uscal == 1.) { + +/* If the scaling needed for A in the dot product is 1, */ +/* call DDOT to perform the dot product. */ + + if (upper) { + i__3 = j - 1; + sumj = ddot_(&i__3, &a[j * a_dim1 + 1], &c__1, &x[1], + &c__1); + } else if (j < *n) { + i__3 = *n - j; + sumj = ddot_(&i__3, &a[j + 1 + j * a_dim1], &c__1, &x[ + j + 1], &c__1); + } + } else { + +/* Otherwise, use in-line code for the dot product. */ + + if (upper) { + i__3 = j - 1; + for (i__ = 1; i__ <= i__3; ++i__) { + sumj += a[i__ + j * a_dim1] * uscal * x[i__]; +/* L120: */ + } + } else if (j < *n) { + i__3 = *n; + for (i__ = j + 1; i__ <= i__3; ++i__) { + sumj += a[i__ + j * a_dim1] * uscal * x[i__]; +/* L130: */ + } + } + } + + if (uscal == tscal) { + +/* Compute x(j) := ( x(j) - sumj ) / A(j,j) if 1/A(j,j) */ +/* was not used to scale the dotproduct. */ + + x[j] -= sumj; + xj = (d__1 = x[j], abs(d__1)); + if (nounit) { + tjjs = a[j + j * a_dim1] * tscal; + } else { + tjjs = tscal; + if (tscal == 1.) { + goto L150; + } + } + +/* Compute x(j) = x(j) / A(j,j), scaling if necessary. */ + + tjj = abs(tjjs); + if (tjj > smlnum) { + +/* abs(A(j,j)) > SMLNUM: */ + + if (tjj < 1.) { + if (xj > tjj * bignum) { + +/* Scale X by 1/abs(x(j)). */ + + rec = 1. / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + x[j] /= tjjs; + } else if (tjj > 0.) { + +/* 0 < abs(A(j,j)) <= SMLNUM: */ + + if (xj > tjj * bignum) { + +/* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM. */ + + rec = tjj * bignum / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + x[j] /= tjjs; + } else { + +/* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and */ +/* scale = 0, and compute a solution to A'*x = 0. */ + + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + x[i__] = 0.; +/* L140: */ + } + x[j] = 1.; + *scale = 0.; + xmax = 0.; + } +L150: + ; + } else { + +/* Compute x(j) := x(j) / A(j,j) - sumj if the dot */ +/* product has already been divided by 1/A(j,j). */ + + x[j] = x[j] / tjjs - sumj; + } +/* Computing MAX */ + d__2 = xmax, d__3 = (d__1 = x[j], abs(d__1)); + xmax = max(d__2,d__3); +/* L160: */ + } + } + *scale /= tscal; + } + +/* Scale the column norms by 1/TSCAL for return. */ + + if (tscal != 1.) { + d__1 = 1. / tscal; + dscal_(n, &d__1, &cnorm[1], &c__1); + } + + return 0; + +/* End of DLATRS */ + +} /* dlatrs_ */ + diff --git a/ext/f2c_lapack/dtrcon.c b/ext/f2c_lapack/dtrcon.c new file mode 100644 index 000000000..6323a364e --- /dev/null +++ b/ext/f2c_lapack/dtrcon.c @@ -0,0 +1,242 @@ +/* dtrcon.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; + +/* Subroutine */ int dtrcon_(char *norm, char *uplo, char *diag, integer *n, + doublereal *a, integer *lda, doublereal *rcond, doublereal *work, + integer *iwork, integer *info, ftnlen norm_len, ftnlen uplo_len, + ftnlen diag_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1; + doublereal d__1; + + /* Local variables */ + static integer ix, kase, kase1; + static doublereal scale; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int drscl_(integer *, doublereal *, doublereal *, + integer *); + static doublereal anorm; + static logical upper; + static doublereal xnorm; + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int dlacon_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + extern integer idamax_(integer *, doublereal *, integer *); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + extern doublereal dlantr_(char *, char *, char *, integer *, integer *, + doublereal *, integer *, doublereal *, ftnlen, ftnlen, ftnlen); + static doublereal ainvnm; + extern /* Subroutine */ int dlatrs_(char *, char *, char *, char *, + integer *, doublereal *, integer *, doublereal *, doublereal *, + doublereal *, integer *, ftnlen, ftnlen, ftnlen, ftnlen); + static logical onenrm; + static char normin[1]; + static doublereal smlnum; + static logical nounit; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DTRCON estimates the reciprocal of the condition number of a */ +/* triangular matrix A, in either the 1-norm or the infinity-norm. */ + +/* The norm of A is computed and an estimate is obtained for */ +/* norm(inv(A)), then the reciprocal of the condition number is */ +/* computed as */ +/* RCOND = 1 / ( norm(A) * norm(inv(A)) ). */ + +/* Arguments */ +/* ========= */ + +/* NORM (input) CHARACTER*1 */ +/* Specifies whether the 1-norm condition number or the */ +/* infinity-norm condition number is required: */ +/* = '1' or 'O': 1-norm; */ +/* = 'I': Infinity-norm. */ + +/* UPLO (input) CHARACTER*1 */ +/* = 'U': A is upper triangular; */ +/* = 'L': A is lower triangular. */ + +/* DIAG (input) CHARACTER*1 */ +/* = 'N': A is non-unit triangular; */ +/* = 'U': A is unit triangular. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The triangular matrix A. If UPLO = 'U', the leading N-by-N */ +/* upper triangular part of the array A contains the upper */ +/* triangular matrix, and the strictly lower triangular part of */ +/* A is not referenced. If UPLO = 'L', the leading N-by-N lower */ +/* triangular part of the array A contains the lower triangular */ +/* matrix, and the strictly upper triangular part of A is not */ +/* referenced. If DIAG = 'U', the diagonal elements of A are */ +/* also not referenced and are assumed to be 1. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* RCOND (output) DOUBLE PRECISION */ +/* The reciprocal of the condition number of the matrix A, */ +/* computed as RCOND = 1/(norm(A) * norm(inv(A))). */ + +/* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) */ + +/* IWORK (workspace) INTEGER array, dimension (N) */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + --work; + --iwork; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + onenrm = *(unsigned char *)norm == '1' || lsame_(norm, "O", (ftnlen)1, ( + ftnlen)1); + nounit = lsame_(diag, "N", (ftnlen)1, (ftnlen)1); + + if (! onenrm && ! lsame_(norm, "I", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -2; + } else if (! nounit && ! lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + *info = -3; + } else if (*n < 0) { + *info = -4; + } else if (*lda < max(1,*n)) { + *info = -6; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DTRCON", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + *rcond = 1.; + return 0; + } + + *rcond = 0.; + smlnum = dlamch_("Safe minimum", (ftnlen)12) * (doublereal) max(1,*n); + +/* Compute the norm of the triangular matrix A. */ + + anorm = dlantr_(norm, uplo, diag, n, n, &a[a_offset], lda, &work[1], ( + ftnlen)1, (ftnlen)1, (ftnlen)1); + +/* Continue only if ANORM > 0. */ + + if (anorm > 0.) { + +/* Estimate the norm of the inverse of A. */ + + ainvnm = 0.; + *(unsigned char *)normin = 'N'; + if (onenrm) { + kase1 = 1; + } else { + kase1 = 2; + } + kase = 0; +L10: + dlacon_(n, &work[*n + 1], &work[1], &iwork[1], &ainvnm, &kase); + if (kase != 0) { + if (kase == kase1) { + +/* Multiply by inv(A). */ + + dlatrs_(uplo, "No transpose", diag, normin, n, &a[a_offset], + lda, &work[1], &scale, &work[(*n << 1) + 1], info, ( + ftnlen)1, (ftnlen)12, (ftnlen)1, (ftnlen)1); + } else { + +/* Multiply by inv(A'). */ + + dlatrs_(uplo, "Transpose", diag, normin, n, &a[a_offset], lda, + &work[1], &scale, &work[(*n << 1) + 1], info, ( + ftnlen)1, (ftnlen)9, (ftnlen)1, (ftnlen)1); + } + *(unsigned char *)normin = 'Y'; + +/* Multiply by 1/SCALE if doing so will not cause overflow. */ + + if (scale != 1.) { + ix = idamax_(n, &work[1], &c__1); + xnorm = (d__1 = work[ix], abs(d__1)); + if (scale < xnorm * smlnum || scale == 0.) { + goto L20; + } + drscl_(n, &scale, &work[1], &c__1); + } + goto L10; + } + +/* Compute the estimate of the reciprocal condition number. */ + + if (ainvnm != 0.) { + *rcond = 1. / anorm / ainvnm; + } + } + +L20: + return 0; + +/* End of DTRCON */ + +} /* dtrcon_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index a0db0ac4c..c936ba49f 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -35,6 +35,7 @@ dgetri.o \ dgetrs.o \ dlabad.o \ dlabrd.o \ +dlacon.o \ dlacpy.o \ dlamch.o \ dlange.o \ @@ -45,6 +46,7 @@ dlarfb.o \ dlarfg.o \ dlarft.o \ dlartg.o \ +dlatrs.o \ dlas2.o \ dlascl.o \ dlaset.o \ @@ -68,6 +70,7 @@ dorml2.o \ dormlq.o \ dormqr.o \ drscl.o \ +dtrcon.o \ dtrtrs.o \ dgerfs.o \ dgecon.o \ diff --git a/ext/lapack/dlacon.f b/ext/lapack/dlacon.f new file mode 100644 index 000000000..4efa0e816 --- /dev/null +++ b/ext/lapack/dlacon.f @@ -0,0 +1,204 @@ + SUBROUTINE DLACON( N, V, X, ISGN, EST, KASE ) +* +* -- LAPACK auxiliary routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* February 29, 1992 +* +* .. Scalar Arguments .. + INTEGER KASE, N + DOUBLE PRECISION EST +* .. +* .. Array Arguments .. + INTEGER ISGN( * ) + DOUBLE PRECISION V( * ), X( * ) +* .. +* +* Purpose +* ======= +* +* DLACON estimates the 1-norm of a square, real matrix A. +* Reverse communication is used for evaluating matrix-vector products. +* +* Arguments +* ========= +* +* N (input) INTEGER +* The order of the matrix. N >= 1. +* +* V (workspace) DOUBLE PRECISION array, dimension (N) +* On the final return, V = A*W, where EST = norm(V)/norm(W) +* (W is not returned). +* +* X (input/output) DOUBLE PRECISION array, dimension (N) +* On an intermediate return, X should be overwritten by +* A * X, if KASE=1, +* A' * X, if KASE=2, +* and DLACON must be re-called with all the other parameters +* unchanged. +* +* ISGN (workspace) INTEGER array, dimension (N) +* +* EST (output) DOUBLE PRECISION +* An estimate (a lower bound) for norm(A). +* +* KASE (input/output) INTEGER +* On the initial call to DLACON, KASE should be 0. +* On an intermediate return, KASE will be 1 or 2, indicating +* whether X should be overwritten by A * X or A' * X. +* On the final return from DLACON, KASE will again be 0. +* +* Further Details +* ======= ======= +* +* Contributed by Nick Higham, University of Manchester. +* Originally named SONEST, dated March 16, 1988. +* +* Reference: N.J. Higham, "FORTRAN codes for estimating the one-norm of +* a real or complex matrix, with applications to condition estimation", +* ACM Trans. Math. Soft., vol. 14, no. 4, pp. 381-396, December 1988. +* +* ===================================================================== +* +* .. Parameters .. + INTEGER ITMAX + PARAMETER ( ITMAX = 5 ) + DOUBLE PRECISION ZERO, ONE, TWO + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0, TWO = 2.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, ITER, J, JLAST, JUMP + DOUBLE PRECISION ALTSGN, ESTOLD, TEMP +* .. +* .. External Functions .. + INTEGER IDAMAX + DOUBLE PRECISION DASUM + EXTERNAL IDAMAX, DASUM +* .. +* .. External Subroutines .. + EXTERNAL DCOPY +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, DBLE, NINT, SIGN +* .. +* .. Save statement .. + SAVE +* .. +* .. Executable Statements .. +* + IF( KASE.EQ.0 ) THEN + DO 10 I = 1, N + X( I ) = ONE / DBLE( N ) + 10 CONTINUE + KASE = 1 + JUMP = 1 + RETURN + END IF +* + GO TO ( 20, 40, 70, 110, 140 )JUMP +* +* ................ ENTRY (JUMP = 1) +* FIRST ITERATION. X HAS BEEN OVERWRITTEN BY A*X. +* + 20 CONTINUE + IF( N.EQ.1 ) THEN + V( 1 ) = X( 1 ) + EST = ABS( V( 1 ) ) +* ... QUIT + GO TO 150 + END IF + EST = DASUM( N, X, 1 ) +* + DO 30 I = 1, N + X( I ) = SIGN( ONE, X( I ) ) + ISGN( I ) = NINT( X( I ) ) + 30 CONTINUE + KASE = 2 + JUMP = 2 + RETURN +* +* ................ ENTRY (JUMP = 2) +* FIRST ITERATION. X HAS BEEN OVERWRITTEN BY TRANDPOSE(A)*X. +* + 40 CONTINUE + J = IDAMAX( N, X, 1 ) + ITER = 2 +* +* MAIN LOOP - ITERATIONS 2,3,...,ITMAX. +* + 50 CONTINUE + DO 60 I = 1, N + X( I ) = ZERO + 60 CONTINUE + X( J ) = ONE + KASE = 1 + JUMP = 3 + RETURN +* +* ................ ENTRY (JUMP = 3) +* X HAS BEEN OVERWRITTEN BY A*X. +* + 70 CONTINUE + CALL DCOPY( N, X, 1, V, 1 ) + ESTOLD = EST + EST = DASUM( N, V, 1 ) + DO 80 I = 1, N + IF( NINT( SIGN( ONE, X( I ) ) ).NE.ISGN( I ) ) + $ GO TO 90 + 80 CONTINUE +* REPEATED SIGN VECTOR DETECTED, HENCE ALGORITHM HAS CONVERGED. + GO TO 120 +* + 90 CONTINUE +* TEST FOR CYCLING. + IF( EST.LE.ESTOLD ) + $ GO TO 120 +* + DO 100 I = 1, N + X( I ) = SIGN( ONE, X( I ) ) + ISGN( I ) = NINT( X( I ) ) + 100 CONTINUE + KASE = 2 + JUMP = 4 + RETURN +* +* ................ ENTRY (JUMP = 4) +* X HAS BEEN OVERWRITTEN BY TRANDPOSE(A)*X. +* + 110 CONTINUE + JLAST = J + J = IDAMAX( N, X, 1 ) + IF( ( X( JLAST ).NE.ABS( X( J ) ) ) .AND. ( ITER.LT.ITMAX ) ) THEN + ITER = ITER + 1 + GO TO 50 + END IF +* +* ITERATION COMPLETE. FINAL STAGE. +* + 120 CONTINUE + ALTSGN = ONE + DO 130 I = 1, N + X( I ) = ALTSGN*( ONE+DBLE( I-1 ) / DBLE( N-1 ) ) + ALTSGN = -ALTSGN + 130 CONTINUE + KASE = 1 + JUMP = 5 + RETURN +* +* ................ ENTRY (JUMP = 5) +* X HAS BEEN OVERWRITTEN BY A*X. +* + 140 CONTINUE + TEMP = TWO*( DASUM( N, X, 1 ) / DBLE( 3*N ) ) + IF( TEMP.GT.EST ) THEN + CALL DCOPY( N, X, 1, V, 1 ) + EST = TEMP + END IF +* + 150 CONTINUE + KASE = 0 + RETURN +* +* End of DLACON +* + END diff --git a/ext/lapack/dlatrs.f b/ext/lapack/dlatrs.f new file mode 100644 index 000000000..591c966d2 --- /dev/null +++ b/ext/lapack/dlatrs.f @@ -0,0 +1,702 @@ + SUBROUTINE DLATRS( UPLO, TRANS, DIAG, NORMIN, N, A, LDA, X, SCALE, + $ CNORM, INFO ) +* +* -- LAPACK auxiliary routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* June 30, 1992 +* +* .. Scalar Arguments .. + CHARACTER DIAG, NORMIN, TRANS, UPLO + INTEGER INFO, LDA, N + DOUBLE PRECISION SCALE +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), CNORM( * ), X( * ) +* .. +* +* Purpose +* ======= +* +* DLATRS solves one of the triangular systems +* +* A *x = s*b or A'*x = s*b +* +* with scaling to prevent overflow. Here A is an upper or lower +* triangular matrix, A' denotes the transpose of A, x and b are +* n-element vectors, and s is a scaling factor, usually less than +* or equal to 1, chosen so that the components of x will be less than +* the overflow threshold. If the unscaled problem will not cause +* overflow, the Level 2 BLAS routine DTRSV is called. If the matrix A +* is singular (A(j,j) = 0 for some j), then s is set to 0 and a +* non-trivial solution to A*x = 0 is returned. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* Specifies whether the matrix A is upper or lower triangular. +* = 'U': Upper triangular +* = 'L': Lower triangular +* +* TRANS (input) CHARACTER*1 +* Specifies the operation applied to A. +* = 'N': Solve A * x = s*b (No transpose) +* = 'T': Solve A'* x = s*b (Transpose) +* = 'C': Solve A'* x = s*b (Conjugate transpose = Transpose) +* +* DIAG (input) CHARACTER*1 +* Specifies whether or not the matrix A is unit triangular. +* = 'N': Non-unit triangular +* = 'U': Unit triangular +* +* NORMIN (input) CHARACTER*1 +* Specifies whether CNORM has been set or not. +* = 'Y': CNORM contains the column norms on entry +* = 'N': CNORM is not set on entry. On exit, the norms will +* be computed and stored in CNORM. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The triangular matrix A. If UPLO = 'U', the leading n by n +* upper triangular part of the array A contains the upper +* triangular matrix, and the strictly lower triangular part of +* A is not referenced. If UPLO = 'L', the leading n by n lower +* triangular part of the array A contains the lower triangular +* matrix, and the strictly upper triangular part of A is not +* referenced. If DIAG = 'U', the diagonal elements of A are +* also not referenced and are assumed to be 1. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max (1,N). +* +* X (input/output) DOUBLE PRECISION array, dimension (N) +* On entry, the right hand side b of the triangular system. +* On exit, X is overwritten by the solution vector x. +* +* SCALE (output) DOUBLE PRECISION +* The scaling factor s for the triangular system +* A * x = s*b or A'* x = s*b. +* If SCALE = 0, the matrix A is singular or badly scaled, and +* the vector x is an exact or approximate solution to A*x = 0. +* +* CNORM (input or output) DOUBLE PRECISION array, dimension (N) +* +* If NORMIN = 'Y', CNORM is an input argument and CNORM(j) +* contains the norm of the off-diagonal part of the j-th column +* of A. If TRANS = 'N', CNORM(j) must be greater than or equal +* to the infinity-norm, and if TRANS = 'T' or 'C', CNORM(j) +* must be greater than or equal to the 1-norm. +* +* If NORMIN = 'N', CNORM is an output argument and CNORM(j) +* returns the 1-norm of the offdiagonal part of the j-th column +* of A. +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -k, the k-th argument had an illegal value +* +* Further Details +* ======= ======= +* +* A rough bound on x is computed; if that is less than overflow, DTRSV +* is called, otherwise, specific code is used which checks for possible +* overflow or divide-by-zero at every operation. +* +* A columnwise scheme is used for solving A*x = b. The basic algorithm +* if A is lower triangular is +* +* x[1:n] := b[1:n] +* for j = 1, ..., n +* x(j) := x(j) / A(j,j) +* x[j+1:n] := x[j+1:n] - x(j) * A[j+1:n,j] +* end +* +* Define bounds on the components of x after j iterations of the loop: +* M(j) = bound on x[1:j] +* G(j) = bound on x[j+1:n] +* Initially, let M(0) = 0 and G(0) = max{x(i), i=1,...,n}. +* +* Then for iteration j+1 we have +* M(j+1) <= G(j) / | A(j+1,j+1) | +* G(j+1) <= G(j) + M(j+1) * | A[j+2:n,j+1] | +* <= G(j) ( 1 + CNORM(j+1) / | A(j+1,j+1) | ) +* +* where CNORM(j+1) is greater than or equal to the infinity-norm of +* column j+1 of A, not counting the diagonal. Hence +* +* G(j) <= G(0) product ( 1 + CNORM(i) / | A(i,i) | ) +* 1<=i<=j +* and +* +* |x(j)| <= ( G(0) / |A(j,j)| ) product ( 1 + CNORM(i) / |A(i,i)| ) +* 1<=i< j +* +* Since |x(j)| <= M(j), we use the Level 2 BLAS routine DTRSV if the +* reciprocal of the largest M(j), j=1,..,n, is larger than +* max(underflow, 1/overflow). +* +* The bound on x(j) is also used to determine when a step in the +* columnwise method can be performed without fear of overflow. If +* the computed bound is greater than a large constant, x is scaled to +* prevent overflow, but if the bound overflows, x is set to 0, x(j) to +* 1, and scale to 0, and a non-trivial solution to A*x = 0 is found. +* +* Similarly, a row-wise scheme is used to solve A'*x = b. The basic +* algorithm for A upper triangular is +* +* for j = 1, ..., n +* x(j) := ( b(j) - A[1:j-1,j]' * x[1:j-1] ) / A(j,j) +* end +* +* We simultaneously compute two bounds +* G(j) = bound on ( b(i) - A[1:i-1,i]' * x[1:i-1] ), 1<=i<=j +* M(j) = bound on x(i), 1<=i<=j +* +* The initial values are G(0) = 0, M(0) = max{b(i), i=1,..,n}, and we +* add the constraint G(j) >= G(j-1) and M(j) >= M(j-1) for j >= 1. +* Then the bound on x(j) is +* +* M(j) <= M(j-1) * ( 1 + CNORM(j) ) / | A(j,j) | +* +* <= M(0) * product ( ( 1 + CNORM(i) ) / |A(i,i)| ) +* 1<=i<=j +* +* and we can safely call DTRSV if 1/M(n) and 1/G(n) are both greater +* than max(underflow, 1/overflow). +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, HALF, ONE + PARAMETER ( ZERO = 0.0D+0, HALF = 0.5D+0, ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL NOTRAN, NOUNIT, UPPER + INTEGER I, IMAX, J, JFIRST, JINC, JLAST + DOUBLE PRECISION BIGNUM, GROW, REC, SMLNUM, SUMJ, TJJ, TJJS, + $ TMAX, TSCAL, USCAL, XBND, XJ, XMAX +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER IDAMAX + DOUBLE PRECISION DASUM, DDOT, DLAMCH + EXTERNAL LSAME, IDAMAX, DASUM, DDOT, DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL DAXPY, DSCAL, DTRSV, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN +* .. +* .. Executable Statements .. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + NOTRAN = LSAME( TRANS, 'N' ) + NOUNIT = LSAME( DIAG, 'N' ) +* +* Test the input parameters. +* + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'T' ) .AND. .NOT. + $ LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( .NOT.NOUNIT .AND. .NOT.LSAME( DIAG, 'U' ) ) THEN + INFO = -3 + ELSE IF( .NOT.LSAME( NORMIN, 'Y' ) .AND. .NOT. + $ LSAME( NORMIN, 'N' ) ) THEN + INFO = -4 + ELSE IF( N.LT.0 ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -7 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLATRS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* Determine machine dependent parameters to control overflow. +* + SMLNUM = DLAMCH( 'Safe minimum' ) / DLAMCH( 'Precision' ) + BIGNUM = ONE / SMLNUM + SCALE = ONE +* + IF( LSAME( NORMIN, 'N' ) ) THEN +* +* Compute the 1-norm of each column, not including the diagonal. +* + IF( UPPER ) THEN +* +* A is upper triangular. +* + DO 10 J = 1, N + CNORM( J ) = DASUM( J-1, A( 1, J ), 1 ) + 10 CONTINUE + ELSE +* +* A is lower triangular. +* + DO 20 J = 1, N - 1 + CNORM( J ) = DASUM( N-J, A( J+1, J ), 1 ) + 20 CONTINUE + CNORM( N ) = ZERO + END IF + END IF +* +* Scale the column norms by TSCAL if the maximum element in CNORM is +* greater than BIGNUM. +* + IMAX = IDAMAX( N, CNORM, 1 ) + TMAX = CNORM( IMAX ) + IF( TMAX.LE.BIGNUM ) THEN + TSCAL = ONE + ELSE + TSCAL = ONE / ( SMLNUM*TMAX ) + CALL DSCAL( N, TSCAL, CNORM, 1 ) + END IF +* +* Compute a bound on the computed solution vector to see if the +* Level 2 BLAS routine DTRSV can be used. +* + J = IDAMAX( N, X, 1 ) + XMAX = ABS( X( J ) ) + XBND = XMAX + IF( NOTRAN ) THEN +* +* Compute the growth in A * x = b. +* + IF( UPPER ) THEN + JFIRST = N + JLAST = 1 + JINC = -1 + ELSE + JFIRST = 1 + JLAST = N + JINC = 1 + END IF +* + IF( TSCAL.NE.ONE ) THEN + GROW = ZERO + GO TO 50 + END IF +* + IF( NOUNIT ) THEN +* +* A is non-unit triangular. +* +* Compute GROW = 1/G(j) and XBND = 1/M(j). +* Initially, G(0) = max{x(i), i=1,...,n}. +* + GROW = ONE / MAX( XBND, SMLNUM ) + XBND = GROW + DO 30 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 50 +* +* M(j) = G(j-1) / abs(A(j,j)) +* + TJJ = ABS( A( J, J ) ) + XBND = MIN( XBND, MIN( ONE, TJJ )*GROW ) + IF( TJJ+CNORM( J ).GE.SMLNUM ) THEN +* +* G(j) = G(j-1)*( 1 + CNORM(j) / abs(A(j,j)) ) +* + GROW = GROW*( TJJ / ( TJJ+CNORM( J ) ) ) + ELSE +* +* G(j) could overflow, set GROW to 0. +* + GROW = ZERO + END IF + 30 CONTINUE + GROW = XBND + ELSE +* +* A is unit triangular. +* +* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. +* + GROW = MIN( ONE, ONE / MAX( XBND, SMLNUM ) ) + DO 40 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 50 +* +* G(j) = G(j-1)*( 1 + CNORM(j) ) +* + GROW = GROW*( ONE / ( ONE+CNORM( J ) ) ) + 40 CONTINUE + END IF + 50 CONTINUE +* + ELSE +* +* Compute the growth in A' * x = b. +* + IF( UPPER ) THEN + JFIRST = 1 + JLAST = N + JINC = 1 + ELSE + JFIRST = N + JLAST = 1 + JINC = -1 + END IF +* + IF( TSCAL.NE.ONE ) THEN + GROW = ZERO + GO TO 80 + END IF +* + IF( NOUNIT ) THEN +* +* A is non-unit triangular. +* +* Compute GROW = 1/G(j) and XBND = 1/M(j). +* Initially, M(0) = max{x(i), i=1,...,n}. +* + GROW = ONE / MAX( XBND, SMLNUM ) + XBND = GROW + DO 60 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 80 +* +* G(j) = max( G(j-1), M(j-1)*( 1 + CNORM(j) ) ) +* + XJ = ONE + CNORM( J ) + GROW = MIN( GROW, XBND / XJ ) +* +* M(j) = M(j-1)*( 1 + CNORM(j) ) / abs(A(j,j)) +* + TJJ = ABS( A( J, J ) ) + IF( XJ.GT.TJJ ) + $ XBND = XBND*( TJJ / XJ ) + 60 CONTINUE + GROW = MIN( GROW, XBND ) + ELSE +* +* A is unit triangular. +* +* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. +* + GROW = MIN( ONE, ONE / MAX( XBND, SMLNUM ) ) + DO 70 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 80 +* +* G(j) = ( 1 + CNORM(j) )*G(j-1) +* + XJ = ONE + CNORM( J ) + GROW = GROW / XJ + 70 CONTINUE + END IF + 80 CONTINUE + END IF +* + IF( ( GROW*TSCAL ).GT.SMLNUM ) THEN +* +* Use the Level 2 BLAS solve if the reciprocal of the bound on +* elements of X is not too small. +* + CALL DTRSV( UPLO, TRANS, DIAG, N, A, LDA, X, 1 ) + ELSE +* +* Use a Level 1 BLAS solve, scaling intermediate results. +* + IF( XMAX.GT.BIGNUM ) THEN +* +* Scale X so that its components are less than or equal to +* BIGNUM in absolute value. +* + SCALE = BIGNUM / XMAX + CALL DSCAL( N, SCALE, X, 1 ) + XMAX = BIGNUM + END IF +* + IF( NOTRAN ) THEN +* +* Solve A * x = b +* + DO 110 J = JFIRST, JLAST, JINC +* +* Compute x(j) = b(j) / A(j,j), scaling x if necessary. +* + XJ = ABS( X( J ) ) + IF( NOUNIT ) THEN + TJJS = A( J, J )*TSCAL + ELSE + TJJS = TSCAL + IF( TSCAL.EQ.ONE ) + $ GO TO 100 + END IF + TJJ = ABS( TJJS ) + IF( TJJ.GT.SMLNUM ) THEN +* +* abs(A(j,j)) > SMLNUM: +* + IF( TJJ.LT.ONE ) THEN + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by 1/b(j). +* + REC = ONE / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF + X( J ) = X( J ) / TJJS + XJ = ABS( X( J ) ) + ELSE IF( TJJ.GT.ZERO ) THEN +* +* 0 < abs(A(j,j)) <= SMLNUM: +* + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM +* to avoid overflow when dividing by A(j,j). +* + REC = ( TJJ*BIGNUM ) / XJ + IF( CNORM( J ).GT.ONE ) THEN +* +* Scale by 1/CNORM(j) to avoid overflow when +* multiplying x(j) times column j. +* + REC = REC / CNORM( J ) + END IF + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + X( J ) = X( J ) / TJJS + XJ = ABS( X( J ) ) + ELSE +* +* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and +* scale = 0, and compute a solution to A*x = 0. +* + DO 90 I = 1, N + X( I ) = ZERO + 90 CONTINUE + X( J ) = ONE + XJ = ONE + SCALE = ZERO + XMAX = ZERO + END IF + 100 CONTINUE +* +* Scale x if necessary to avoid overflow when adding a +* multiple of column j of A. +* + IF( XJ.GT.ONE ) THEN + REC = ONE / XJ + IF( CNORM( J ).GT.( BIGNUM-XMAX )*REC ) THEN +* +* Scale x by 1/(2*abs(x(j))). +* + REC = REC*HALF + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + END IF + ELSE IF( XJ*CNORM( J ).GT.( BIGNUM-XMAX ) ) THEN +* +* Scale x by 1/2. +* + CALL DSCAL( N, HALF, X, 1 ) + SCALE = SCALE*HALF + END IF +* + IF( UPPER ) THEN + IF( J.GT.1 ) THEN +* +* Compute the update +* x(1:j-1) := x(1:j-1) - x(j) * A(1:j-1,j) +* + CALL DAXPY( J-1, -X( J )*TSCAL, A( 1, J ), 1, X, + $ 1 ) + I = IDAMAX( J-1, X, 1 ) + XMAX = ABS( X( I ) ) + END IF + ELSE + IF( J.LT.N ) THEN +* +* Compute the update +* x(j+1:n) := x(j+1:n) - x(j) * A(j+1:n,j) +* + CALL DAXPY( N-J, -X( J )*TSCAL, A( J+1, J ), 1, + $ X( J+1 ), 1 ) + I = J + IDAMAX( N-J, X( J+1 ), 1 ) + XMAX = ABS( X( I ) ) + END IF + END IF + 110 CONTINUE +* + ELSE +* +* Solve A' * x = b +* + DO 160 J = JFIRST, JLAST, JINC +* +* Compute x(j) = b(j) - sum A(k,j)*x(k). +* k<>j +* + XJ = ABS( X( J ) ) + USCAL = TSCAL + REC = ONE / MAX( XMAX, ONE ) + IF( CNORM( J ).GT.( BIGNUM-XJ )*REC ) THEN +* +* If x(j) could overflow, scale x by 1/(2*XMAX). +* + REC = REC*HALF + IF( NOUNIT ) THEN + TJJS = A( J, J )*TSCAL + ELSE + TJJS = TSCAL + END IF + TJJ = ABS( TJJS ) + IF( TJJ.GT.ONE ) THEN +* +* Divide by A(j,j) when scaling x if A(j,j) > 1. +* + REC = MIN( ONE, REC*TJJ ) + USCAL = USCAL / TJJS + END IF + IF( REC.LT.ONE ) THEN + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF +* + SUMJ = ZERO + IF( USCAL.EQ.ONE ) THEN +* +* If the scaling needed for A in the dot product is 1, +* call DDOT to perform the dot product. +* + IF( UPPER ) THEN + SUMJ = DDOT( J-1, A( 1, J ), 1, X, 1 ) + ELSE IF( J.LT.N ) THEN + SUMJ = DDOT( N-J, A( J+1, J ), 1, X( J+1 ), 1 ) + END IF + ELSE +* +* Otherwise, use in-line code for the dot product. +* + IF( UPPER ) THEN + DO 120 I = 1, J - 1 + SUMJ = SUMJ + ( A( I, J )*USCAL )*X( I ) + 120 CONTINUE + ELSE IF( J.LT.N ) THEN + DO 130 I = J + 1, N + SUMJ = SUMJ + ( A( I, J )*USCAL )*X( I ) + 130 CONTINUE + END IF + END IF +* + IF( USCAL.EQ.TSCAL ) THEN +* +* Compute x(j) := ( x(j) - sumj ) / A(j,j) if 1/A(j,j) +* was not used to scale the dotproduct. +* + X( J ) = X( J ) - SUMJ + XJ = ABS( X( J ) ) + IF( NOUNIT ) THEN + TJJS = A( J, J )*TSCAL + ELSE + TJJS = TSCAL + IF( TSCAL.EQ.ONE ) + $ GO TO 150 + END IF +* +* Compute x(j) = x(j) / A(j,j), scaling if necessary. +* + TJJ = ABS( TJJS ) + IF( TJJ.GT.SMLNUM ) THEN +* +* abs(A(j,j)) > SMLNUM: +* + IF( TJJ.LT.ONE ) THEN + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale X by 1/abs(x(j)). +* + REC = ONE / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF + X( J ) = X( J ) / TJJS + ELSE IF( TJJ.GT.ZERO ) THEN +* +* 0 < abs(A(j,j)) <= SMLNUM: +* + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM. +* + REC = ( TJJ*BIGNUM ) / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + X( J ) = X( J ) / TJJS + ELSE +* +* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and +* scale = 0, and compute a solution to A'*x = 0. +* + DO 140 I = 1, N + X( I ) = ZERO + 140 CONTINUE + X( J ) = ONE + SCALE = ZERO + XMAX = ZERO + END IF + 150 CONTINUE + ELSE +* +* Compute x(j) := x(j) / A(j,j) - sumj if the dot +* product has already been divided by 1/A(j,j). +* + X( J ) = X( J ) / TJJS - SUMJ + END IF + XMAX = MAX( XMAX, ABS( X( J ) ) ) + 160 CONTINUE + END IF + SCALE = SCALE / TSCAL + END IF +* +* Scale the column norms by 1/TSCAL for return. +* + IF( TSCAL.NE.ONE ) THEN + CALL DSCAL( N, ONE / TSCAL, CNORM, 1 ) + END IF +* + RETURN +* +* End of DLATRS +* + END diff --git a/ext/lapack/dtrcon.f b/ext/lapack/dtrcon.f new file mode 100644 index 000000000..8da58c760 --- /dev/null +++ b/ext/lapack/dtrcon.f @@ -0,0 +1,193 @@ + SUBROUTINE DTRCON( NORM, UPLO, DIAG, N, A, LDA, RCOND, WORK, + $ IWORK, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + CHARACTER DIAG, NORM, UPLO + INTEGER INFO, LDA, N + DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION A( LDA, * ), WORK( * ) +* .. +* +* Purpose +* ======= +* +* DTRCON estimates the reciprocal of the condition number of a +* triangular matrix A, in either the 1-norm or the infinity-norm. +* +* The norm of A is computed and an estimate is obtained for +* norm(inv(A)), then the reciprocal of the condition number is +* computed as +* RCOND = 1 / ( norm(A) * norm(inv(A)) ). +* +* Arguments +* ========= +* +* NORM (input) CHARACTER*1 +* Specifies whether the 1-norm condition number or the +* infinity-norm condition number is required: +* = '1' or 'O': 1-norm; +* = 'I': Infinity-norm. +* +* UPLO (input) CHARACTER*1 +* = 'U': A is upper triangular; +* = 'L': A is lower triangular. +* +* DIAG (input) CHARACTER*1 +* = 'N': A is non-unit triangular; +* = 'U': A is unit triangular. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The triangular matrix A. If UPLO = 'U', the leading N-by-N +* upper triangular part of the array A contains the upper +* triangular matrix, and the strictly lower triangular part of +* A is not referenced. If UPLO = 'L', the leading N-by-N lower +* triangular part of the array A contains the lower triangular +* matrix, and the strictly upper triangular part of A is not +* referenced. If DIAG = 'U', the diagonal elements of A are +* also not referenced and are assumed to be 1. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* RCOND (output) DOUBLE PRECISION +* The reciprocal of the condition number of the matrix A, +* computed as RCOND = 1/(norm(A) * norm(inv(A))). +* +* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) +* +* IWORK (workspace) INTEGER array, dimension (N) +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL NOUNIT, ONENRM, UPPER + CHARACTER NORMIN + INTEGER IX, KASE, KASE1 + DOUBLE PRECISION AINVNM, ANORM, SCALE, SMLNUM, XNORM +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER IDAMAX + DOUBLE PRECISION DLAMCH, DLANTR + EXTERNAL LSAME, IDAMAX, DLAMCH, DLANTR +* .. +* .. External Subroutines .. + EXTERNAL DLACON, DLATRS, DRSCL, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, DBLE, MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + ONENRM = NORM.EQ.'1' .OR. LSAME( NORM, 'O' ) + NOUNIT = LSAME( DIAG, 'N' ) +* + IF( .NOT.ONENRM .AND. .NOT.LSAME( NORM, 'I' ) ) THEN + INFO = -1 + ELSE IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -2 + ELSE IF( .NOT.NOUNIT .AND. .NOT.LSAME( DIAG, 'U' ) ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -6 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DTRCON', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) THEN + RCOND = ONE + RETURN + END IF +* + RCOND = ZERO + SMLNUM = DLAMCH( 'Safe minimum' )*DBLE( MAX( 1, N ) ) +* +* Compute the norm of the triangular matrix A. +* + ANORM = DLANTR( NORM, UPLO, DIAG, N, N, A, LDA, WORK ) +* +* Continue only if ANORM > 0. +* + IF( ANORM.GT.ZERO ) THEN +* +* Estimate the norm of the inverse of A. +* + AINVNM = ZERO + NORMIN = 'N' + IF( ONENRM ) THEN + KASE1 = 1 + ELSE + KASE1 = 2 + END IF + KASE = 0 + 10 CONTINUE + CALL DLACON( N, WORK( N+1 ), WORK, IWORK, AINVNM, KASE ) + IF( KASE.NE.0 ) THEN + IF( KASE.EQ.KASE1 ) THEN +* +* Multiply by inv(A). +* + CALL DLATRS( UPLO, 'No transpose', DIAG, NORMIN, N, A, + $ LDA, WORK, SCALE, WORK( 2*N+1 ), INFO ) + ELSE +* +* Multiply by inv(A'). +* + CALL DLATRS( UPLO, 'Transpose', DIAG, NORMIN, N, A, LDA, + $ WORK, SCALE, WORK( 2*N+1 ), INFO ) + END IF + NORMIN = 'Y' +* +* Multiply by 1/SCALE if doing so will not cause overflow. +* + IF( SCALE.NE.ONE ) THEN + IX = IDAMAX( N, WORK, 1 ) + XNORM = ABS( WORK( IX ) ) + IF( SCALE.LT.XNORM*SMLNUM .OR. SCALE.EQ.ZERO ) + $ GO TO 20 + CALL DRSCL( N, SCALE, WORK, 1 ) + END IF + GO TO 10 + END IF +* +* Compute the estimate of the reciprocal condition number. +* + IF( AINVNM.NE.ZERO ) + $ RCOND = ( ONE / ANORM ) / AINVNM + END IF +* + 20 CONTINUE + RETURN +* +* End of DTRCON +* + END From 701dd1e1cd0a3eeb5678059d309b332edca48f0d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 28 Apr 2011 20:56:41 +0000 Subject: [PATCH 363/446] Added in the estimation of condition numbers for QR factored matrices. --- Cantera/src/numerics/SquareMatrix.cpp | 36 ++++++++++++++--- Cantera/src/numerics/SquareMatrix.h | 11 ++++++ Cantera/src/numerics/ctlapack.h | 56 +++++++++++++++++++++++++-- 3 files changed, 95 insertions(+), 8 deletions(-) diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index c8371d889..9d9d56861 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -112,8 +112,8 @@ namespace Cantera { } return info; } - - /** + //==================================================================================================================== + /* * Set all entries to zero */ void SquareMatrix::zero() { @@ -191,6 +191,8 @@ namespace Cantera { if (lworkOpt > lwork) { work.resize(lworkOpt); } + + return info; } //===================================================================================================================== @@ -250,9 +252,33 @@ namespace Cantera { return info; } //===================================================================================================================== - - - + doublereal SquareMatrix::rcondQR() { + + if ((int) iwork_.size() < m_nrows) { + iwork_.resize(m_nrows); + } + if ((int) work.size() <3 * m_nrows) { + work.resize(3 * m_nrows); + } + doublereal rcond = 0.0; + if (m_factored != 2) { + throw CELapackError("SquareMatrix::rcondQR()", "matrix isn't factored correctly"); + } + + int rinfo; + rcond = ct_dtrcon(0, ctlapack::UpperTriangular, 0, m_nrows, &(*(begin())), m_nrows, DATA_PTR(work), + DATA_PTR(iwork_), rinfo); + if (rinfo != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::rcondQR(): DTRCON returned INFO = %d\n", rinfo); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::rcondQR()", "DTRCON returned INFO = " + int2str(rinfo)); + } + } + return rcond; + } + //===================================================================================================================== } diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index 1be99b62e..1445bc60d 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -96,6 +96,14 @@ namespace Cantera { */ int factorQR(); + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the QR algorithm + * + * @return returns the inverse of the condition number + */ + doublereal rcondQR(); + //! Solves the linear problem Ax=b using the QR algorithm returning x in the b spot /*! * @param b RHS to be solved. @@ -121,6 +129,9 @@ namespace Cantera { //! Work vector for QR algorithm vector_fp work; + //! Integer work vector for QR algorithms + std::vector iwork_; + public: //! Use the QR algorithm to factor and invert the matrix int useQR_; diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index 3b160184b..40d8b1754 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -38,6 +38,7 @@ #define _DGEQRF_ dgeqrf #define _DORMQR_ dormqr #define _DTRTRS_ dtrtrs +#define _DTRCON_ dtrcon #else @@ -55,6 +56,7 @@ #define _DGEQRF_ dgeqrf_ #define _DORMQR_ dormqr_ #define _DTRTRS_ dtrtrs_ +#define _DTRCON_ dtrcon_ #endif @@ -171,6 +173,19 @@ extern "C" { #endif +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DTRCON_(const char* norm, const char* uplo, const char *diag, const integer* n, + doublereal* a, const integer* lda, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info, ftnlen nosize, + ftnlen upsize, ftnlen disize); +#else + int _DTRCON_(const char* norm, ftnlen nosize, const char* uplo, ftnlen upsize, const char *diag, + ftnlen disize, const integer* n, doublereal* a, const integer* lda, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info); +#endif + + + } //#endif @@ -304,7 +319,7 @@ namespace Cantera { //_DSCAL_(&f_n, &da, dx, &f_incx); cblas_dscal(n, da, dx, incx); } - + //==================================================================================================================== inline void ct_dgeqrf(int m, int n, doublereal* a, int lda, doublereal *tau, doublereal* work, int lwork, int &info) { integer f_m = m; @@ -315,7 +330,7 @@ namespace Cantera { _DGEQRF_(&f_m, &f_n, a, &f_lda, tau, work, &f_lwork, &f_info); info = f_info; } - + //==================================================================================================================== inline void ct_dormqr(ctlapack::side_t rlside, ctlapack::transpose_t trans, int m, int n, int k, doublereal* a, int lda, doublereal *tau, doublereal *c, int ldc, doublereal *work, int lwork, int &info) { @@ -340,7 +355,7 @@ namespace Cantera { #endif info = f_info; } - + //==================================================================================================================== inline void ct_dtrtrs(ctlapack::upperlower_t uplot, ctlapack::transpose_t trans, const char *diag, int n, int nrhs, doublereal* a, int lda, doublereal *b, int ldb, int &info) { char uplo = upper_lower[uplot]; @@ -366,7 +381,42 @@ namespace Cantera { #endif info = f_info; } + //==================================================================================================================== + //! + /*! + * @param work Must be dimensioned equal to greater than 3N + * @param iwork Must be dimensioned equal to or greater than N + */ + inline doublereal ct_dtrcon(const char *norm, ctlapack::upperlower_t uplot, const char *diag, + int n, doublereal* a, int lda, doublereal *work, int *iwork, int &info) { + char uplo = upper_lower[uplot]; + char dd = 'N'; + if (diag) { + dd = diag[0]; + } + char nn = '1'; + if (norm) { + nn = norm[0]; + } + integer f_n = n; + integer f_lda = lda; + integer f_info = info; + doublereal rcond; +#ifdef NO_FTN_STRING_LEN_AT_END + _DTRCON_(&nn, &uplo, &dd, &f_n, a, &f_lda, &rcond, work, iwork, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DTRCON_(&nn, &uplo, &dd, &f_n, a, &f_lda, &rcond, work, iwork, &f_info, trsize, trsize, trsize); +#else + _DTRCON_(&nn, trsize, &uplo, trsize, &dd, trsize, &f_n, a, &f_lda, &rcond work, iwork, &f_info); +#endif +#endif + info = f_info; + return rcond; + } + //==================================================================================================================== } #endif From ac660e53c02591a62ff3bac9ae1e8c7fd6d1b197 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 29 Apr 2011 23:07:27 +0000 Subject: [PATCH 364/446] Added cholesky decomp routines. --- ext/f2c_lapack/Makefile.in | 2 + ext/f2c_lapack/dpotrf.c | 254 +++++++++++++++++++++++++++++++++++++ ext/f2c_lapack/dpotrs.c | 171 +++++++++++++++++++++++++ ext/lapack/Makefile.in | 2 + ext/lapack/dpotrf.f | 184 +++++++++++++++++++++++++++ ext/lapack/dpotrs.f | 133 +++++++++++++++++++ 6 files changed, 746 insertions(+) create mode 100644 ext/f2c_lapack/dpotrf.c create mode 100644 ext/f2c_lapack/dpotrs.c create mode 100644 ext/lapack/dpotrf.f create mode 100644 ext/lapack/dpotrs.f diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index bb6764363..1a3d00461 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -100,6 +100,8 @@ dormbr.o \ dorml2.o \ dormlq.o \ dormqr.o \ +dpotrf.o \ +dpotrs.o \ drscl.o \ dtrcon.o \ dtrtri.o \ diff --git a/ext/f2c_lapack/dpotrf.c b/ext/f2c_lapack/dpotrf.c new file mode 100644 index 000000000..4f55fb75b --- /dev/null +++ b/ext/f2c_lapack/dpotrf.c @@ -0,0 +1,254 @@ +/* dpotrf.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static integer c_n1 = -1; +static doublereal c_b13 = -1.; +static doublereal c_b14 = 1.; + +/* Subroutine */ int dpotrf_(char *uplo, integer *n, doublereal *a, integer * + lda, integer *info, ftnlen uplo_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1, i__2, i__3, i__4; + + /* Local variables */ + static integer j, jb, nb; + extern /* Subroutine */ int dgemm_(char *, char *, integer *, integer *, + integer *, doublereal *, doublereal *, integer *, doublereal *, + integer *, doublereal *, doublereal *, integer *, ftnlen, ftnlen); + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int dtrsm_(char *, char *, char *, char *, + integer *, integer *, doublereal *, doublereal *, integer *, + doublereal *, integer *, ftnlen, ftnlen, ftnlen, ftnlen); + static logical upper; + extern /* Subroutine */ int dsyrk_(char *, char *, integer *, integer *, + doublereal *, doublereal *, integer *, doublereal *, doublereal *, + integer *, ftnlen, ftnlen), dpotf2_(char *, integer *, + doublereal *, integer *, integer *, ftnlen), xerbla_(char *, + integer *, ftnlen); + extern integer ilaenv_(integer *, char *, char *, integer *, integer *, + integer *, integer *, ftnlen, ftnlen); + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DPOTRF computes the Cholesky factorization of a real symmetric */ +/* positive definite matrix A. */ + +/* The factorization has the form */ +/* A = U**T * U, if UPLO = 'U', or */ +/* A = L * L**T, if UPLO = 'L', */ +/* where U is an upper triangular matrix and L is lower triangular. */ + +/* This is the block version of the algorithm, calling Level 3 BLAS. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* = 'U': Upper triangle of A is stored; */ +/* = 'L': Lower triangle of A is stored. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* A (input/output) DOUBLE PRECISION array, dimension (LDA,N) */ +/* On entry, the symmetric matrix A. If UPLO = 'U', the leading */ +/* N-by-N upper triangular part of A contains the upper */ +/* triangular part of the matrix A, and the strictly lower */ +/* triangular part of A is not referenced. If UPLO = 'L', the */ +/* leading N-by-N lower triangular part of A contains the lower */ +/* triangular part of the matrix A, and the strictly upper */ +/* triangular part of A is not referenced. */ + +/* On exit, if INFO = 0, the factor U or L from the Cholesky */ +/* factorization A = U**T*U or A = L*L**T. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ +/* > 0: if INFO = i, the leading minor of order i is not */ +/* positive definite, and the factorization could not be */ +/* completed. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*lda < max(1,*n)) { + *info = -4; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DPOTRF", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + return 0; + } + +/* Determine the block size for this environment. */ + + nb = ilaenv_(&c__1, "DPOTRF", uplo, n, &c_n1, &c_n1, &c_n1, (ftnlen)6, ( + ftnlen)1); + if (nb <= 1 || nb >= *n) { + +/* Use unblocked code. */ + + dpotf2_(uplo, n, &a[a_offset], lda, info, (ftnlen)1); + } else { + +/* Use blocked code. */ + + if (upper) { + +/* Compute the Cholesky factorization A = U'*U. */ + + i__1 = *n; + i__2 = nb; + for (j = 1; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Update and factorize the current diagonal block and test */ +/* for non-positive-definiteness. */ + +/* Computing MIN */ + i__3 = nb, i__4 = *n - j + 1; + jb = min(i__3,i__4); + i__3 = j - 1; + dsyrk_("Upper", "Transpose", &jb, &i__3, &c_b13, &a[j * + a_dim1 + 1], lda, &c_b14, &a[j + j * a_dim1], lda, ( + ftnlen)5, (ftnlen)9); + dpotf2_("Upper", &jb, &a[j + j * a_dim1], lda, info, (ftnlen) + 5); + if (*info != 0) { + goto L30; + } + if (j + jb <= *n) { + +/* Compute the current block row. */ + + i__3 = *n - j - jb + 1; + i__4 = j - 1; + dgemm_("Transpose", "No transpose", &jb, &i__3, &i__4, & + c_b13, &a[j * a_dim1 + 1], lda, &a[(j + jb) * + a_dim1 + 1], lda, &c_b14, &a[j + (j + jb) * + a_dim1], lda, (ftnlen)9, (ftnlen)12); + i__3 = *n - j - jb + 1; + dtrsm_("Left", "Upper", "Transpose", "Non-unit", &jb, & + i__3, &c_b14, &a[j + j * a_dim1], lda, &a[j + (j + + jb) * a_dim1], lda, (ftnlen)4, (ftnlen)5, ( + ftnlen)9, (ftnlen)8); + } +/* L10: */ + } + + } else { + +/* Compute the Cholesky factorization A = L*L'. */ + + i__2 = *n; + i__1 = nb; + for (j = 1; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Update and factorize the current diagonal block and test */ +/* for non-positive-definiteness. */ + +/* Computing MIN */ + i__3 = nb, i__4 = *n - j + 1; + jb = min(i__3,i__4); + i__3 = j - 1; + dsyrk_("Lower", "No transpose", &jb, &i__3, &c_b13, &a[j + + a_dim1], lda, &c_b14, &a[j + j * a_dim1], lda, ( + ftnlen)5, (ftnlen)12); + dpotf2_("Lower", &jb, &a[j + j * a_dim1], lda, info, (ftnlen) + 5); + if (*info != 0) { + goto L30; + } + if (j + jb <= *n) { + +/* Compute the current block column. */ + + i__3 = *n - j - jb + 1; + i__4 = j - 1; + dgemm_("No transpose", "Transpose", &i__3, &jb, &i__4, & + c_b13, &a[j + jb + a_dim1], lda, &a[j + a_dim1], + lda, &c_b14, &a[j + jb + j * a_dim1], lda, ( + ftnlen)12, (ftnlen)9); + i__3 = *n - j - jb + 1; + dtrsm_("Right", "Lower", "Transpose", "Non-unit", &i__3, & + jb, &c_b14, &a[j + j * a_dim1], lda, &a[j + jb + + j * a_dim1], lda, (ftnlen)5, (ftnlen)5, (ftnlen)9, + (ftnlen)8); + } +/* L20: */ + } + } + } + goto L40; + +L30: + *info = *info + j - 1; + +L40: + return 0; + +/* End of DPOTRF */ + +} /* dpotrf_ */ + diff --git a/ext/f2c_lapack/dpotrs.c b/ext/f2c_lapack/dpotrs.c new file mode 100644 index 000000000..e5d632002 --- /dev/null +++ b/ext/f2c_lapack/dpotrs.c @@ -0,0 +1,171 @@ +/* dpotrs.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static doublereal c_b9 = 1.; + +/* Subroutine */ int dpotrs_(char *uplo, integer *n, integer *nrhs, + doublereal *a, integer *lda, doublereal *b, integer *ldb, integer * + info, ftnlen uplo_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, b_dim1, b_offset, i__1; + + /* Local variables */ + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int dtrsm_(char *, char *, char *, char *, + integer *, integer *, doublereal *, doublereal *, integer *, + doublereal *, integer *, ftnlen, ftnlen, ftnlen, ftnlen); + static logical upper; + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DPOTRS solves a system of linear equations A*X = B with a symmetric */ +/* positive definite matrix A using the Cholesky factorization */ +/* A = U**T*U or A = L*L**T computed by DPOTRF. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* = 'U': Upper triangle of A is stored; */ +/* = 'L': Lower triangle of A is stored. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* NRHS (input) INTEGER */ +/* The number of right hand sides, i.e., the number of columns */ +/* of the matrix B. NRHS >= 0. */ + +/* A (input) DOUBLE PRECISION array, dimension (LDA,N) */ +/* The triangular factor U or L from the Cholesky factorization */ +/* A = U**T*U or A = L*L**T, as computed by DPOTRF. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* B (input/output) DOUBLE PRECISION array, dimension (LDB,NRHS) */ +/* On entry, the right hand side matrix B. */ +/* On exit, the solution matrix X. */ + +/* LDB (input) INTEGER */ +/* The leading dimension of the array B. LDB >= max(1,N). */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + b_dim1 = *ldb; + b_offset = 1 + b_dim1; + b -= b_offset; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*nrhs < 0) { + *info = -3; + } else if (*lda < max(1,*n)) { + *info = -5; + } else if (*ldb < max(1,*n)) { + *info = -7; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DPOTRS", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0 || *nrhs == 0) { + return 0; + } + + if (upper) { + +/* Solve A*X = B where A = U'*U. */ + +/* Solve U'*X = B, overwriting B with X. */ + + dtrsm_("Left", "Upper", "Transpose", "Non-unit", n, nrhs, &c_b9, &a[ + a_offset], lda, &b[b_offset], ldb, (ftnlen)4, (ftnlen)5, ( + ftnlen)9, (ftnlen)8); + +/* Solve U*X = B, overwriting B with X. */ + + dtrsm_("Left", "Upper", "No transpose", "Non-unit", n, nrhs, &c_b9, & + a[a_offset], lda, &b[b_offset], ldb, (ftnlen)4, (ftnlen)5, ( + ftnlen)12, (ftnlen)8); + } else { + +/* Solve A*X = B where A = L*L'. */ + +/* Solve L*X = B, overwriting B with X. */ + + dtrsm_("Left", "Lower", "No transpose", "Non-unit", n, nrhs, &c_b9, & + a[a_offset], lda, &b[b_offset], ldb, (ftnlen)4, (ftnlen)5, ( + ftnlen)12, (ftnlen)8); + +/* Solve L'*X = B, overwriting B with X. */ + + dtrsm_("Left", "Lower", "Transpose", "Non-unit", n, nrhs, &c_b9, &a[ + a_offset], lda, &b[b_offset], ldb, (ftnlen)4, (ftnlen)5, ( + ftnlen)9, (ftnlen)8); + } + + return 0; + +/* End of DPOTRS */ + +} /* dpotrs_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index c936ba49f..ca09a36b4 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -69,6 +69,8 @@ dormbr.o \ dorml2.o \ dormlq.o \ dormqr.o \ +dpotrf.o \ +dpotrs.o \ drscl.o \ dtrcon.o \ dtrtrs.o \ diff --git a/ext/lapack/dpotrf.f b/ext/lapack/dpotrf.f new file mode 100644 index 000000000..c4b0cb459 --- /dev/null +++ b/ext/lapack/dpotrf.f @@ -0,0 +1,184 @@ + SUBROUTINE DPOTRF( UPLO, N, A, LDA, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, N +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ) +* .. +* +* Purpose +* ======= +* +* DPOTRF computes the Cholesky factorization of a real symmetric +* positive definite matrix A. +* +* The factorization has the form +* A = U**T * U, if UPLO = 'U', or +* A = L * L**T, if UPLO = 'L', +* where U is an upper triangular matrix and L is lower triangular. +* +* This is the block version of the algorithm, calling Level 3 BLAS. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* = 'U': Upper triangle of A is stored; +* = 'L': Lower triangle of A is stored. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* A (input/output) DOUBLE PRECISION array, dimension (LDA,N) +* On entry, the symmetric matrix A. If UPLO = 'U', the leading +* N-by-N upper triangular part of A contains the upper +* triangular part of the matrix A, and the strictly lower +* triangular part of A is not referenced. If UPLO = 'L', the +* leading N-by-N lower triangular part of A contains the lower +* triangular part of the matrix A, and the strictly upper +* triangular part of A is not referenced. +* +* On exit, if INFO = 0, the factor U or L from the Cholesky +* factorization A = U**T*U or A = L*L**T. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* > 0: if INFO = i, the leading minor of order i is not +* positive definite, and the factorization could not be +* completed. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UPPER + INTEGER J, JB, NB +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + EXTERNAL LSAME, ILAENV +* .. +* .. External Subroutines .. + EXTERNAL DGEMM, DPOTF2, DSYRK, DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -4 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOTRF', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* Determine the block size for this environment. +* + NB = ILAENV( 1, 'DPOTRF', UPLO, N, -1, -1, -1 ) + IF( NB.LE.1 .OR. NB.GE.N ) THEN +* +* Use unblocked code. +* + CALL DPOTF2( UPLO, N, A, LDA, INFO ) + ELSE +* +* Use blocked code. +* + IF( UPPER ) THEN +* +* Compute the Cholesky factorization A = U'*U. +* + DO 10 J = 1, N, NB +* +* Update and factorize the current diagonal block and test +* for non-positive-definiteness. +* + JB = MIN( NB, N-J+1 ) + CALL DSYRK( 'Upper', 'Transpose', JB, J-1, -ONE, + $ A( 1, J ), LDA, ONE, A( J, J ), LDA ) + CALL DPOTF2( 'Upper', JB, A( J, J ), LDA, INFO ) + IF( INFO.NE.0 ) + $ GO TO 30 + IF( J+JB.LE.N ) THEN +* +* Compute the current block row. +* + CALL DGEMM( 'Transpose', 'No transpose', JB, N-J-JB+1, + $ J-1, -ONE, A( 1, J ), LDA, A( 1, J+JB ), + $ LDA, ONE, A( J, J+JB ), LDA ) + CALL DTRSM( 'Left', 'Upper', 'Transpose', 'Non-unit', + $ JB, N-J-JB+1, ONE, A( J, J ), LDA, + $ A( J, J+JB ), LDA ) + END IF + 10 CONTINUE +* + ELSE +* +* Compute the Cholesky factorization A = L*L'. +* + DO 20 J = 1, N, NB +* +* Update and factorize the current diagonal block and test +* for non-positive-definiteness. +* + JB = MIN( NB, N-J+1 ) + CALL DSYRK( 'Lower', 'No transpose', JB, J-1, -ONE, + $ A( J, 1 ), LDA, ONE, A( J, J ), LDA ) + CALL DPOTF2( 'Lower', JB, A( J, J ), LDA, INFO ) + IF( INFO.NE.0 ) + $ GO TO 30 + IF( J+JB.LE.N ) THEN +* +* Compute the current block column. +* + CALL DGEMM( 'No transpose', 'Transpose', N-J-JB+1, JB, + $ J-1, -ONE, A( J+JB, 1 ), LDA, A( J, 1 ), + $ LDA, ONE, A( J+JB, J ), LDA ) + CALL DTRSM( 'Right', 'Lower', 'Transpose', 'Non-unit', + $ N-J-JB+1, JB, ONE, A( J, J ), LDA, + $ A( J+JB, J ), LDA ) + END IF + 20 CONTINUE + END IF + END IF + GO TO 40 +* + 30 CONTINUE + INFO = INFO + J - 1 +* + 40 CONTINUE + RETURN +* +* End of DPOTRF +* + END diff --git a/ext/lapack/dpotrs.f b/ext/lapack/dpotrs.f new file mode 100644 index 000000000..ae3ab2f31 --- /dev/null +++ b/ext/lapack/dpotrs.f @@ -0,0 +1,133 @@ + SUBROUTINE DPOTRS( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* Purpose +* ======= +* +* DPOTRS solves a system of linear equations A*X = B with a symmetric +* positive definite matrix A using the Cholesky factorization +* A = U**T*U or A = L*L**T computed by DPOTRF. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* = 'U': Upper triangle of A is stored; +* = 'L': Lower triangle of A is stored. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* NRHS (input) INTEGER +* The number of right hand sides, i.e., the number of columns +* of the matrix B. NRHS >= 0. +* +* A (input) DOUBLE PRECISION array, dimension (LDA,N) +* The triangular factor U or L from the Cholesky factorization +* A = U**T*U or A = L*L**T, as computed by DPOTRF. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* B (input/output) DOUBLE PRECISION array, dimension (LDB,NRHS) +* On entry, the right hand side matrix B. +* On exit, the solution matrix X. +* +* LDB (input) INTEGER +* The leading dimension of the array B. LDB >= max(1,N). +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UPPER +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -5 + ELSE IF( LDB.LT.MAX( 1, N ) ) THEN + INFO = -7 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOTRS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 .OR. NRHS.EQ.0 ) + $ RETURN +* + IF( UPPER ) THEN +* +* Solve A*X = B where A = U'*U. +* +* Solve U'*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Upper', 'Transpose', 'Non-unit', N, NRHS, + $ ONE, A, LDA, B, LDB ) +* +* Solve U*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Upper', 'No transpose', 'Non-unit', N, + $ NRHS, ONE, A, LDA, B, LDB ) + ELSE +* +* Solve A*X = B where A = L*L'. +* +* Solve L*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Lower', 'No transpose', 'Non-unit', N, + $ NRHS, ONE, A, LDA, B, LDB ) +* +* Solve L'*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Lower', 'Transpose', 'Non-unit', N, NRHS, + $ ONE, A, LDA, B, LDB ) + END IF +* + RETURN +* +* End of DPOTRS +* + END From 198ab1864032dedfdb09a3e7e4b1a62c2dbc7a1f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 2 May 2011 16:13:03 +0000 Subject: [PATCH 365/446] Added a needed function --- ext/f2c_lapack/Makefile.in | 1 + ext/f2c_lapack/dpotf2.c | 224 +++++++++++++++++++++++++++++++++++++ ext/lapack/Makefile.in | 1 + ext/lapack/dpotf2.f | 168 ++++++++++++++++++++++++++++ 4 files changed, 394 insertions(+) create mode 100644 ext/f2c_lapack/dpotf2.c create mode 100644 ext/lapack/dpotf2.f diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 1a3d00461..16c2f1a14 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -100,6 +100,7 @@ dormbr.o \ dorml2.o \ dormlq.o \ dormqr.o \ +dpotf2.o \ dpotrf.o \ dpotrs.o \ drscl.o \ diff --git a/ext/f2c_lapack/dpotf2.c b/ext/f2c_lapack/dpotf2.c new file mode 100644 index 000000000..4ceff060e --- /dev/null +++ b/ext/f2c_lapack/dpotf2.c @@ -0,0 +1,224 @@ +/* dpotf2.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static doublereal c_b10 = -1.; +static doublereal c_b12 = 1.; + +/* Subroutine */ int dpotf2_(char *uplo, integer *n, doublereal *a, integer * + lda, integer *info, ftnlen uplo_len) +{ + /* System generated locals */ + integer a_dim1, a_offset, i__1, i__2, i__3; + doublereal d__1; + + /* Builtin functions */ + double sqrt(doublereal); + + /* Local variables */ + static integer j; + static doublereal ajj; + extern doublereal ddot_(integer *, doublereal *, integer *, doublereal *, + integer *); + extern /* Subroutine */ int dscal_(integer *, doublereal *, doublereal *, + integer *); + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int dgemv_(char *, integer *, integer *, + doublereal *, doublereal *, integer *, doublereal *, integer *, + doublereal *, doublereal *, integer *, ftnlen); + static logical upper; + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* February 29, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DPOTF2 computes the Cholesky factorization of a real symmetric */ +/* positive definite matrix A. */ + +/* The factorization has the form */ +/* A = U' * U , if UPLO = 'U', or */ +/* A = L * L', if UPLO = 'L', */ +/* where U is an upper triangular matrix and L is lower triangular. */ + +/* This is the unblocked version of the algorithm, calling Level 2 BLAS. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* Specifies whether the upper or lower triangular part of the */ +/* symmetric matrix A is stored. */ +/* = 'U': Upper triangular */ +/* = 'L': Lower triangular */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* A (input/output) DOUBLE PRECISION array, dimension (LDA,N) */ +/* On entry, the symmetric matrix A. If UPLO = 'U', the leading */ +/* n by n upper triangular part of A contains the upper */ +/* triangular part of the matrix A, and the strictly lower */ +/* triangular part of A is not referenced. If UPLO = 'L', the */ +/* leading n by n lower triangular part of A contains the lower */ +/* triangular part of the matrix A, and the strictly upper */ +/* triangular part of A is not referenced. */ + +/* On exit, if INFO = 0, the factor U or L from the Cholesky */ +/* factorization A = U'*U or A = L*L'. */ + +/* LDA (input) INTEGER */ +/* The leading dimension of the array A. LDA >= max(1,N). */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -k, the k-th argument had an illegal value */ +/* > 0: if INFO = k, the leading minor of order k is not */ +/* positive definite, and the factorization could not be */ +/* completed. */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + a_dim1 = *lda; + a_offset = 1 + a_dim1; + a -= a_offset; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*lda < max(1,*n)) { + *info = -4; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DPOTF2", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + return 0; + } + + if (upper) { + +/* Compute the Cholesky factorization A = U'*U. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + +/* Compute U(J,J) and test for non-positive-definiteness. */ + + i__2 = j - 1; + ajj = a[j + j * a_dim1] - ddot_(&i__2, &a[j * a_dim1 + 1], &c__1, + &a[j * a_dim1 + 1], &c__1); + if (ajj <= 0.) { + a[j + j * a_dim1] = ajj; + goto L30; + } + ajj = sqrt(ajj); + a[j + j * a_dim1] = ajj; + +/* Compute elements J+1:N of row J. */ + + if (j < *n) { + i__2 = j - 1; + i__3 = *n - j; + dgemv_("Transpose", &i__2, &i__3, &c_b10, &a[(j + 1) * a_dim1 + + 1], lda, &a[j * a_dim1 + 1], &c__1, &c_b12, &a[j + ( + j + 1) * a_dim1], lda, (ftnlen)9); + i__2 = *n - j; + d__1 = 1. / ajj; + dscal_(&i__2, &d__1, &a[j + (j + 1) * a_dim1], lda); + } +/* L10: */ + } + } else { + +/* Compute the Cholesky factorization A = L*L'. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + +/* Compute L(J,J) and test for non-positive-definiteness. */ + + i__2 = j - 1; + ajj = a[j + j * a_dim1] - ddot_(&i__2, &a[j + a_dim1], lda, &a[j + + a_dim1], lda); + if (ajj <= 0.) { + a[j + j * a_dim1] = ajj; + goto L30; + } + ajj = sqrt(ajj); + a[j + j * a_dim1] = ajj; + +/* Compute elements J+1:N of column J. */ + + if (j < *n) { + i__2 = *n - j; + i__3 = j - 1; + dgemv_("No transpose", &i__2, &i__3, &c_b10, &a[j + 1 + + a_dim1], lda, &a[j + a_dim1], lda, &c_b12, &a[j + 1 + + j * a_dim1], &c__1, (ftnlen)12); + i__2 = *n - j; + d__1 = 1. / ajj; + dscal_(&i__2, &d__1, &a[j + 1 + j * a_dim1], &c__1); + } +/* L20: */ + } + } + goto L40; + +L30: + *info = j; + +L40: + return 0; + +/* End of DPOTF2 */ + +} /* dpotf2_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index ca09a36b4..e0f242113 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -71,6 +71,7 @@ dormlq.o \ dormqr.o \ dpotrf.o \ dpotrs.o \ +dpotf2.o \ drscl.o \ dtrcon.o \ dtrtrs.o \ diff --git a/ext/lapack/dpotf2.f b/ext/lapack/dpotf2.f new file mode 100644 index 000000000..f9e0de06e --- /dev/null +++ b/ext/lapack/dpotf2.f @@ -0,0 +1,168 @@ + SUBROUTINE DPOTF2( UPLO, N, A, LDA, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* February 29, 1992 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, N +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ) +* .. +* +* Purpose +* ======= +* +* DPOTF2 computes the Cholesky factorization of a real symmetric +* positive definite matrix A. +* +* The factorization has the form +* A = U' * U , if UPLO = 'U', or +* A = L * L', if UPLO = 'L', +* where U is an upper triangular matrix and L is lower triangular. +* +* This is the unblocked version of the algorithm, calling Level 2 BLAS. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* Specifies whether the upper or lower triangular part of the +* symmetric matrix A is stored. +* = 'U': Upper triangular +* = 'L': Lower triangular +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* A (input/output) DOUBLE PRECISION array, dimension (LDA,N) +* On entry, the symmetric matrix A. If UPLO = 'U', the leading +* n by n upper triangular part of A contains the upper +* triangular part of the matrix A, and the strictly lower +* triangular part of A is not referenced. If UPLO = 'L', the +* leading n by n lower triangular part of A contains the lower +* triangular part of the matrix A, and the strictly upper +* triangular part of A is not referenced. +* +* On exit, if INFO = 0, the factor U or L from the Cholesky +* factorization A = U'*U or A = L*L'. +* +* LDA (input) INTEGER +* The leading dimension of the array A. LDA >= max(1,N). +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -k, the k-th argument had an illegal value +* > 0: if INFO = k, the leading minor of order k is not +* positive definite, and the factorization could not be +* completed. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UPPER + INTEGER J + DOUBLE PRECISION AJJ +* .. +* .. External Functions .. + LOGICAL LSAME + DOUBLE PRECISION DDOT + EXTERNAL LSAME, DDOT +* .. +* .. External Subroutines .. + EXTERNAL DGEMV, DSCAL, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -4 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOTF2', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* + IF( UPPER ) THEN +* +* Compute the Cholesky factorization A = U'*U. +* + DO 10 J = 1, N +* +* Compute U(J,J) and test for non-positive-definiteness. +* + AJJ = A( J, J ) - DDOT( J-1, A( 1, J ), 1, A( 1, J ), 1 ) + IF( AJJ.LE.ZERO ) THEN + A( J, J ) = AJJ + GO TO 30 + END IF + AJJ = SQRT( AJJ ) + A( J, J ) = AJJ +* +* Compute elements J+1:N of row J. +* + IF( J.LT.N ) THEN + CALL DGEMV( 'Transpose', J-1, N-J, -ONE, A( 1, J+1 ), + $ LDA, A( 1, J ), 1, ONE, A( J, J+1 ), LDA ) + CALL DSCAL( N-J, ONE / AJJ, A( J, J+1 ), LDA ) + END IF + 10 CONTINUE + ELSE +* +* Compute the Cholesky factorization A = L*L'. +* + DO 20 J = 1, N +* +* Compute L(J,J) and test for non-positive-definiteness. +* + AJJ = A( J, J ) - DDOT( J-1, A( J, 1 ), LDA, A( J, 1 ), + $ LDA ) + IF( AJJ.LE.ZERO ) THEN + A( J, J ) = AJJ + GO TO 30 + END IF + AJJ = SQRT( AJJ ) + A( J, J ) = AJJ +* +* Compute elements J+1:N of column J. +* + IF( J.LT.N ) THEN + CALL DGEMV( 'No transpose', N-J, J-1, -ONE, A( J+1, 1 ), + $ LDA, A( J, 1 ), LDA, ONE, A( J+1, J ), 1 ) + CALL DSCAL( N-J, ONE / AJJ, A( J+1, J ), 1 ) + END IF + 20 CONTINUE + END IF + GO TO 40 +* + 30 CONTINUE + INFO = J +* + 40 CONTINUE + RETURN +* +* End of DPOTF2 +* + END From e110f91a12dcd8eea614bbf92249992d56cf18aa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 2 May 2011 16:13:59 +0000 Subject: [PATCH 366/446] Added hooks for cholesky factorization --- Cantera/src/numerics/ctlapack.h | 92 +++++++++++++++++++++++++++++---- 1 file changed, 82 insertions(+), 10 deletions(-) diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index 40d8b1754..d79c68391 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -39,6 +39,8 @@ #define _DORMQR_ dormqr #define _DTRTRS_ dtrtrs #define _DTRCON_ dtrcon +#define _DPOTRF_ dpotrf +#define _DPOTRS_ dpotrs #else @@ -58,6 +60,9 @@ #define _DTRTRS_ dtrtrs_ #define _DTRCON_ dtrcon_ +#define _DPOTRF_ dpotrf_ +#define _DPOTRS_ dpotrs_ + #endif @@ -185,13 +190,28 @@ extern "C" { #endif +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DPOTRF_(const char* uplo, const integer* n, doublereal* a, const integer* lda, integer *info, + ftnlen upsize); +#else + int _DPOTRF_(const char* uplo, ftnlen upsize, const integer* n, doublereal* a, const integer* lda, + integer *info ); +#endif + +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DPOTRS_(const char* uplo, const integer* n, const integer* nrhs, doublereal* a, const integer* lda, + doublereal* b, const integer* ldb, integer *info, ftnlen upsize); +#else + int _DPOTRS_(const char* uplo, ftnlen upsize, const integer* n, const integer* nrhs, doublereal* a, const integer* lda, + doublereal* b, const integer* ldb, integer *info); +#endif } //#endif namespace Cantera { - + //==================================================================================================================== inline void ct_dgemv(ctlapack::storage_t storage, ctlapack::transpose_t trans, int m, int n, doublereal alpha, const doublereal* a, int lda, @@ -221,7 +241,7 @@ namespace Cantera { } - + //==================================================================================================================== inline void ct_dgbsv(int n, int kl, int ku, int nrhs, doublereal* a, int lda, integer* ipiv, doublereal* b, int ldb, int& info) { @@ -231,7 +251,7 @@ namespace Cantera { b, &f_ldb, &f_info); info = f_info; } - + //==================================================================================================================== inline void ct_dgbtrf(int m, int n, int kl, int ku, doublereal* a, int lda, integer* ipiv, int& info) { integer f_m = m, f_n = n, f_kl = kl, f_ku = ku, @@ -239,7 +259,7 @@ namespace Cantera { _DGBTRF_(&f_m, &f_n, &f_kl, &f_ku, a, &f_lda, ipiv, &f_info); info = f_info; } - + //==================================================================================================================== inline void ct_dgbtrs(ctlapack::transpose_t trans, int n, int kl, int ku, int nrhs, doublereal* a, int lda, integer* ipiv, doublereal* b, int ldb, int& info) { @@ -261,7 +281,7 @@ namespace Cantera { #endif info = f_info; } - + //==================================================================================================================== inline void ct_dgetrf(int m, int n, doublereal* a, int lda, integer* ipiv, int& info) { integer mm = m; @@ -271,7 +291,7 @@ namespace Cantera { _DGETRF_(&mm, &nn, a, &ldaa, ipiv, &infoo); info = infoo; } - + //==================================================================================================================== inline void ct_dgetrs(ctlapack::transpose_t trans, int n, int nrhs, doublereal* a, int lda, integer* ipiv, doublereal* b, int ldb, int& info) @@ -293,13 +313,13 @@ namespace Cantera { #endif info = f_info; } - + //==================================================================================================================== inline void ct_dgetri(int n, doublereal* a, int lda, integer* ipiv, doublereal* work, int lwork, int& info) { integer f_n = n, f_lda = lda, f_lwork = lwork, f_info = info; _DGETRI_(&f_n, a, &f_lda, ipiv, work, &f_lwork, &f_info); } - + //==================================================================================================================== inline void ct_dgelss(int m, int n, int nrhs, doublereal* a, int lda, doublereal* b, int ldb, doublereal* s, doublereal rcond, int& rank, doublereal* work, int lwork, @@ -382,7 +402,6 @@ namespace Cantera { info = f_info; } //==================================================================================================================== - //! /*! * @param work Must be dimensioned equal to greater than 3N @@ -410,13 +429,66 @@ namespace Cantera { #ifdef LAPACK_FTN_STRING_LEN_AT_END _DTRCON_(&nn, &uplo, &dd, &f_n, a, &f_lda, &rcond, work, iwork, &f_info, trsize, trsize, trsize); #else - _DTRCON_(&nn, trsize, &uplo, trsize, &dd, trsize, &f_n, a, &f_lda, &rcond work, iwork, &f_info); + _DTRCON_(&nn, trsize, &uplo, trsize, &dd, trsize, &f_n, a, &f_lda, &rcond, work, iwork, &f_info); #endif #endif info = f_info; return rcond; } //==================================================================================================================== + //! + /*! + * @param work Must be dimensioned equal to greater than 3N + * @param iwork Must be dimensioned equal to or greater than N + */ + inline void ct_dpotrf(ctlapack::upperlower_t uplot, int n, doublereal* a, int lda, int &info) { + char uplo = upper_lower[uplot]; + integer f_n = n; + integer f_lda = lda; + integer f_info = info; + +#ifdef NO_FTN_STRING_LEN_AT_END + _DPOTRF_(&uplo, &f_n, a, &f_lda, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DPOTRF_(&uplo, &f_n, a, &f_lda, &f_info, trsize); +#else + _DPOTRF_(&uplo, trsize, &f_n, a, &f_lda, &f_info); +#endif +#endif + info = f_info; + return; + } + //==================================================================================================================== + //! + /*! + */ + inline void ct_dpotrs(ctlapack::upperlower_t uplot, int n, int nrhs, doublereal* a, int lda, + doublereal* b, int ldb, int &info) { + char uplo = upper_lower[uplot]; + integer f_n = n; + integer f_nrhs = nrhs; + integer f_lda = lda; + integer f_ldb = ldb; + integer f_info = info; + +#ifdef NO_FTN_STRING_LEN_AT_END + _DPOTRS_(&uplo, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DPOTRS_(&uplo, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info, trsize); +#else + _DPOTRS_(&uplo, trsize, &f_n, &f_nrhs, a, &f_lda, b, &f_ldb, &f_info); +#endif +#endif + info = f_info; + return; + } + //==================================================================================================================== + + } #endif From 6eccfa16ed26f069f9738930c511ff16b1731794 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 17 May 2011 00:45:08 +0000 Subject: [PATCH 367/446] Worked on getting the Affine solve capability working. This is now working, so that we can switch to a Hessian with junk on the diagonal when there is a condition number problem. --- Cantera/src/numerics/NonlinearSolver.cpp | 350 ++++++++++++++++++++++- Cantera/src/numerics/NonlinearSolver.h | 55 +++- Cantera/src/numerics/SquareMatrix.cpp | 49 +++- Cantera/src/numerics/SquareMatrix.h | 13 + Cantera/src/numerics/ctlapack.h | 83 +++++- 5 files changed, 532 insertions(+), 18 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 1ace7e722..4d24c605e 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -20,6 +20,7 @@ #include "SquareMatrix.h" #include "NonlinearSolver.h" +#include "ctlapack.h" #include "clockWC.h" #include "vec_functions.h" @@ -79,6 +80,12 @@ namespace Cantera { // Turn off printing of dogleg information bool NonlinearSolver::s_print_DogLeg(false); + + // Turn off solving the system twice and comparing the answer. + /* + * Turn this on if you want to compare the Hessian and Newton solve results. + */ + bool NonlinearSolver::s_doBothSolvesAndCompare(false); //==================================================================================================================== // Default constructor /* @@ -130,6 +137,7 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), + Hessian_(0), deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), @@ -146,7 +154,8 @@ namespace Cantera { JdJd_norm_(0.0), normTrust_Newton_(0.0), normTrust_CP_(0.0), - doDogLeg_(0) + doDogLeg_(0), + doAffineSolve_(0) { neq_ = m_func->nEquations(); @@ -173,12 +182,12 @@ namespace Cantera { m_ewt[i] = atolk_[i]; } -#ifdef DEBUG_DOGLEG + jacCopy_.resize(neq_, neq_, 0.0); deltaX_CP_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); deltaX_trust_.resize(neq_, 1.0); -#endif + } //==================================================================================================================== @@ -228,6 +237,7 @@ namespace Cantera { m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopy_(0), + Hessian_(0), deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), @@ -244,7 +254,8 @@ namespace Cantera { JdJd_norm_(0.0), normTrust_Newton_(0.0), normTrust_CP_(0.0), - doDogLeg_(0) + doDogLeg_(0), + doAffineSolve_(0) { *this =operator=(right); } @@ -305,6 +316,7 @@ namespace Cantera { m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; jacCopy_ = right.jacCopy_; + Hessian_ = right.Hessian_; deltaX_CP_ = right.deltaX_CP_; deltaX_Newton_ = right.deltaX_Newton_; RJd_norm_ = right.RJd_norm_; @@ -322,6 +334,7 @@ namespace Cantera { normTrust_Newton_ = right.normTrust_Newton_; normTrust_CP_ = right.normTrust_CP_; doDogLeg_ = right.doDogLeg_; + doAffineSolve_ = right.doAffineSolve_; return *this; } @@ -362,8 +375,17 @@ namespace Cantera { } } //==================================================================================================================== - void NonlinearSolver::setSolverScheme(int doDogLeg) { + void NonlinearSolver::setSolverScheme(int doDogLeg, int doAffineSolve) { doDogLeg_ = doDogLeg; + doAffineSolve_ = doAffineSolve; +#ifdef DEBUG_DOGLEG + +#else + if (doDogLeg_) { + throw CanteraError("NonlinearSolver::setSolverScheme", + "ifdef block not on"); + } +#endif } //==================================================================================================================== std::vector & NonlinearSolver::lowBoundsConstraintVector() { @@ -785,6 +807,305 @@ namespace Cantera { return info; } //==================================================================================================================== + // Compute the newton step, either by direct newton's or by solving a close problem that is represented + // by a Hessian ( + /* + * This is algorith A.6.5.1 in Dennis / Schnabel + * + * Compute the QR decomposition + */ + int NonlinearSolver::doAffineNewtonSolve(const doublereal * const y_curr, const doublereal * const ydot_curr, + doublereal * const delta_y, SquareMatrix& jac) + { + bool newtonGood = true; + int irow; + doublereal *delyNewton = 0; + // We can default to QR here ( or not ) + jac.useQR_ = true; + // multiply the residual by -1 + // Scale the residual if there is row scaling. Note, the matrix has already been scaled + if (m_rowScaling && !m_resid_scaled) { + for (int n = 0; n < neq_; n++) { + delta_y[n] = -m_rowScales[n] * m_resid[n]; + } + m_resid_scaled = true; + } else { + for (int n = 0; n < neq_; n++) { + delta_y[n] = -m_resid[n]; + } + } + + // Factor the matrix + double cond = 1.0E300; + int info = 0; + if (!jac.m_factored) { + if (jac.useQR_) { + info = jac.factorQR(); + } else { + info = jac.factor(); + } + } + /* + * Find the condition number of the matrix + * If we have failed to factor, we will fall back to calculating and factoring a modified Hessian + */ + if (info == 0) { + double rcond = 0.0; + if (jac.useQR_) { + rcond = jac.rcondQR(); + } else { + rcond = jac.rcond(jac.a1norm_); + } + if (rcond > 0.0) { + cond = 1.0 / rcond; + } + } + bool doHessian = false; + if (s_doBothSolvesAndCompare) { + doHessian = true; + } + bool doNewton = false; + if (cond < 1.0E7) { + doNewton = true; + if (m_print_flag >= 3) { + printf("\t\t\tdoAffineNewtonSolve: Condition number = %g during regular solve\n", cond); + } + + /* + * Solve the system -> This also involves inverting the matrix + */ + int info = jac.solve(DATA_PTR(delta_y)); + if (info) { + if (m_print_flag >= 2) { + printf("\t\t\tNonlinearSolver::doAffineSolve QRSolve returned INFO = %d. Switching to Hessian solve\n", info); + } + doHessian = true; + newtonGood = false; + } + /* + * reverse the column scaling if there was any on a successful solve + */ + if (m_colScaling) { + for (irow = 0; irow < neq_; irow++) { + delta_y[irow] = delta_y[irow] * m_colScales[irow]; + } + } + + } else { + doHessian = true; + newtonGood = false; + if (m_print_flag >= 3) { + printf("\t\t\tdoAffineNewtonSolve: Condition number too large, %g. Doing a Hessian solve \n", cond); + } + } + + if (doHessian) { + // Store the old value for later comparison + if (doNewton) { + delyNewton = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + for (irow = 0; irow < neq_; irow++) { + delyNewton[irow] = delta_y[irow]; + } + } + // Get memory if not done before + if (Hessian_.nRows() == 0) { + Hessian_.resize(neq_, neq_); + } + + /* + * Calculate the symmetric Hessian + */ + Hessian_.zero(); + if (m_rowScaling) { + for (int i = 0; i < neq_; i++) { + for (int j = i; j < neq_; j++) { + for (int k = 0; k < neq_; k++) { + Hessian_(i,j) += jacCopy_(k,i) * jacCopy_(k,j) * m_rowScales[k] * m_rowScales[k]; + } + Hessian_(j,i) = Hessian_(i,j); + } + } + } else { + for (int i = 0; i < neq_; i++) { + for (int j = i; j < neq_; j++) { + for (int k = 0; k < neq_; k++) { + Hessian_(i,j) += jacCopy_(k,i) * jacCopy_(k,j); + } + Hessian_(j,i) = Hessian_(i,j); + } + } + } + + /* + * Calculate the matrix norm of the Hessian + */ + doublereal hnorm = 0.0; + doublereal hcol = 0.0; + if (m_colScaling) { + for (int i = 0; i < neq_; i++) { + for (int j = i; j < neq_; j++) { + hcol += fabs(Hessian_(j,i)) * m_colScales[j]; + } + for (int j = i+1; j < neq_; j++) { + hcol += fabs(Hessian_(i,j)) * m_colScales[j]; + } + hcol *= m_colScales[i]; + if (hcol > hnorm) { + hnorm = hcol; + } + } + } else { + for (int i = 0; i < neq_; i++) { + for (int j = i; j < neq_; j++) { + hcol += fabs(Hessian_(j,i)); + } + for (int j = i+1; j < neq_; j++) { + hcol += fabs(Hessian_(i,j)); + } + if (hcol > hnorm) { + hnorm = hcol; + } + } + } + /* + * Add junk to the Hessian diagonal + */ + hcol = sqrt(neq_) * 1.0E-7 * hnorm; + if (m_colScaling) { + for (int i = 0; i < neq_; i++) { + Hessian_(i,i) += hcol / (m_colScales[i] * m_colScales[i]); + } + } else { + for (int i = 0; i < neq_; i++) { + Hessian_(i,i) += hcol; + } + } + + /* + * Factor the Hessian + */ + int info; + ct_dpotrf(ctlapack::UpperTriangular, neq_, &(*(Hessian_.begin())), neq_, info); + if (info) { + if (m_print_flag >= 2) { + printf("\t\t\tNonlinearSolver::doAffineSolve DPOTRF returned INFO = %d\n", info); + } + return info; + } + + // doublereal *JTF = delta_y; + doublereal *delyH = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + // First recalculate the scaled residual. It got wiped out doing the newton solve + if (m_rowScaling) { + for (int n = 0; n < neq_; n++) { + delyH[n] = -m_rowScales[n] * m_resid[n]; + } + } else { + for (int n = 0; n < neq_; n++) { + delyH[n] = -m_resid[n]; + } + } + + if (m_rowScaling) { + for (int j = 0; j < neq_; j++) { + delta_y[j] = 0.0; + for (int i = 0; i < neq_; i++) { + delta_y[j] += delyH[i] * jacCopy_.value(i,j) * m_rowScales[i]; + } + } + } else { + for (int j = 0; j < neq_; j++) { + delta_y[j] = 0.0; + for (int i = 0; i < neq_; i++) { + delta_y[j] += delyH[i] * jacCopy_.value(i,j); + } + } + } + + + /* + * Solve the factored Hessian System + */ + ct_dpotrs(ctlapack::UpperTriangular, neq_, 1,&(*(Hessian_.begin())), neq_, delta_y, neq_, info); + if (info) { + if (m_print_flag >= 2) { + printf("\t\t\tNonlinearSolver::doAffineSolve DPOTRS returned INFO = %d\n", info); + } + return info; + } + /* + * reverse the column scaling if there was any. + */ + if (m_colScaling) { + for (irow = 0; irow < neq_; irow++) { + delta_y[irow] = delta_y[irow] * m_colScales[irow]; + } + } + + + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + printf("\t\t\t Comparison between Hessian deltaX and newton deltaX\n"); + printf("\t\t\t i Hessian+Junk Newton \n"); + printf("\t\t\t--------------------------------------------------------\n"); + for (int i =0; i < neq_; i++) { + printf("\t\t\t%3d %12.5g %12.5g\n", i, delta_y[i], delyNewton[i]); + } + printf("\t\t\t--------------------------------------------------------\n"); + + } + + if (newtonGood) { + mdp::mdp_copy_dbl_1(DATA_PTR(delta_y), CONSTD_DATA_PTR(delyNewton), neq_); + } + mdp::mdp_safe_free((void **) &delyH); + mdp::mdp_safe_free((void **) &delyNewton); + } + +#ifdef DEBUG_JAC + if (printJacContributions) { + for (int iNum = 0; iNum < numRows; iNum++) { + if (iNum > 0) focusRow++; + doublereal dsum = 0.0; + vector_fp& Jdata = jacBack.data(); + doublereal dRow = Jdata[neq_ * focusRow + focusRow]; + printf("\n Details on delta_Y for row %d \n", focusRow); + printf(" Value before = %15.5e, delta = %15.5e," + "value after = %15.5e\n", y_curr[focusRow], + delta_y[focusRow], y_curr[focusRow] + delta_y[focusRow]); + if (!freshJac) { + printf(" Old Jacobian\n"); + } + printf(" col delta_y aij " + "contrib \n"); + printf("-----------------------------------------------------------------------------------------------\n"); + printf(" Res(%d) %15.5e %15.5e %15.5e (Res = %g)\n", + focusRow, delta_y[focusRow], + dRow, RRow[iNum] / dRow, RRow[iNum]); + dsum += RRow[iNum] / dRow; + for (int ii = 0; ii < neq_; ii++) { + if (ii != focusRow) { + doublereal aij = Jdata[neq_ * ii + focusRow]; + doublereal contrib = aij * delta_y[ii] * (-1.0) / dRow; + dsum += contrib; + if (fabs(contrib) > Pcutoff) { + printf("%6d %15.5e %15.5e %15.5e\n", ii, + delta_y[ii] , aij, contrib); + } + } + } + printf("-----------------------------------------------------------------------------------------------\n"); + printf(" %15.5e %15.5e\n", + delta_y[focusRow], dsum); + } + } + +#endif + + m_numTotalLinearSolves++; + return info; + + } + //==================================================================================================================== // Do a steepest descent calculation /* * This call must be made on the unfactored jacobian! @@ -1794,8 +2115,8 @@ namespace Cantera { m_dampRes = 1.0; int j, m; num_backtracks = 0; - double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); - double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; + //double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + //double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; double tlen; @@ -2185,7 +2506,12 @@ namespace Cantera { #endif // compute the undamped Newton step - info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac, m_print_flag); + if (doAffineSolve_) { + info = doAffineNewtonSolve(DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac); + } else { + info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac, m_print_flag); + } + if (info) { m = -1; goto done; @@ -2201,8 +2527,8 @@ namespace Cantera { if (doDogLeg_) { - double trustD = calcTrustDistance(stp); #ifdef DEBUG_DOGLEG + double trustD = calcTrustDistance(stp); if (s_print_DogLeg || m_print_flag > 3) { if (trustD > trustDelta_) { printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); @@ -2664,6 +2990,12 @@ namespace Cantera { printf("--------------\n"); } } + /* + * Make a copy of the data. Note, this jacobian copy occurs before any matrix scaling operations. + * It's the raw matrix producted by this routine. + */ + jacCopy_.copyData(J); + return retn; } //==================================================================================================================== diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index e586e8cfe..de8aa9a64 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -208,6 +208,40 @@ namespace Cantera { const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac, int loglevel); + //! Compute the newton step, either by direct newton's or by solving a close problem that is represented + //! by a Hessian ( + /*! + * This is algorith A.6.5.1 in Dennis / Schnabel + * + * Compute the QR decomposition + * + * Compute the undamped Newton step. The residual function is + * evaluated at the current time, t_n, at the current values of the + * solution vector, m_y_n, and the solution time derivative, m_ydot_n. + * The Jacobian is not recomputed. + * + * A factored jacobian is reused, if available. If a factored jacobian + * is not available, then the jacobian is factored. Before factoring, + * the jacobian is row and column-scaled. Column scaling is not + * recomputed. The row scales are recomputed here, after column + * scaling has been implemented. + * + * @param y_curr Current value of the solution + * @param ydot_curr Current value of the solution derivative. + * @param delta_y return value of the raw change in y + * @param jac Jacobian + * + * Internal input + * --------------- + * internal m_resid Storred residual is used as input + * + * + * @return Returns the result code from lapack. A zero means success. Anything + * else indicates a failure. + */ + int doAffineNewtonSolve(const doublereal * const y_curr, const doublereal * const ydot_curr, + doublereal * const delta_y, SquareMatrix& jac); + //! Calculate the size of the current trust region /*! * We carry out a norm of deltaX_trust_ first. Then, we multiply that value @@ -637,8 +671,11 @@ namespace Cantera { * Default is to always use a damping scheme in the Newton Direction. * When this is nonzero, a model trust region approach is used using a double dog leg * with the steepest descent direction used for small step sizes. + * + * @param doAffineSolve Parameter to turn on or off the solution of the system using a Hessian + * if the matrix has a bad condition number. */ - void setSolverScheme(int doDogLeg = 0); + void setSolverScheme(int doDogLeg, int doAffineSolve); /* * ----------------------------------------------------------------------------------------------------------------- @@ -838,8 +875,14 @@ namespace Cantera { double m_ScaleSolnNormToResNorm; //! Copy of the jacobian that doesn't get overwritten when the inverse is determined + /*! + * The jacobian storred here is the raw matrix, before any row or column scaling is carried out + */ Cantera::SquareMatrix jacCopy_; + //! Hessian + Cantera::SquareMatrix Hessian_; + /********************************************************************************************* * VARIABLES ASSOCIATED WITH STEPS AND ASSOCIATED DOUBLE DOGLEG PARAMETERS *********************************************************************************************/ @@ -891,6 +934,9 @@ namespace Cantera { //! General toggle for turning on dog leg damping. int doDogLeg_; + //! General toggle for turning on Affine solve with Hessian + int doAffineSolve_; + /******************************************************************************************* @@ -910,6 +956,13 @@ namespace Cantera { //! Turn on all printing of dogleg information static bool s_print_DogLeg; + + //! Turn on solving both the Newton and Hessian systems and comparing the results + /*! + * This is off by default + */ + static bool s_doBothSolvesAndCompare; + }; } diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 9d9d56861..1724f8c93 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -32,7 +32,8 @@ namespace Cantera { //==================================================================================================================== SquareMatrix::SquareMatrix() : DenseMatrix(), - m_factored(0), + m_factored(0), + a1norm_(0.0), useQR_(0) { } @@ -48,8 +49,10 @@ namespace Cantera { */ SquareMatrix::SquareMatrix(int n, doublereal v) : DenseMatrix(n, n, v), - m_factored(0), + m_factored(0), + a1norm_(0.0), useQR_(0) + { } //==================================================================================================================== @@ -60,6 +63,7 @@ namespace Cantera { SquareMatrix::SquareMatrix(const SquareMatrix& y) : DenseMatrix(y), m_factored(y.m_factored), + a1norm_(y.a1norm_), useQR_(y.useQR_) { } @@ -71,7 +75,9 @@ namespace Cantera { SquareMatrix& SquareMatrix::operator=(const SquareMatrix& y) { if (&y == this) return *this; DenseMatrix::operator=(y); - m_factored = y.m_factored; + m_factored = y.m_factored; + a1norm_ = y.a1norm_; + useQR_ = y.useQR_; return *this; } //==================================================================================================================== @@ -140,11 +146,11 @@ namespace Cantera { if (useQR_) { return factorQR(); } + a1norm_ = ct_dlange('1', m_nrows, m_nrows, &(*(begin())), m_nrows, DATA_PTR(work)); integer n = static_cast(nRows()); int info=0; m_factored = 1; - ct_dgetrf(n, n, &(*(begin())), static_cast(nRows()), - DATA_PTR(ipiv()), info); + ct_dgetrf(n, n, &(*(begin())), static_cast(nRows()), DATA_PTR(ipiv()), info); if (info != 0) { if (m_printLevel) { writelogf("SquareMatrix::factor(): DGETRS returned INFO = %d\n", info); @@ -174,7 +180,8 @@ namespace Cantera { if ((int) tau.size() < m_nrows) { tau.resize(m_nrows, 0.0); work.resize(8 * m_nrows, 0.0); - } + } + a1norm_ = ct_dlange('1', m_nrows, m_nrows, &(*(begin())), m_nrows, DATA_PTR(work)); int info; m_factored = 2; int lwork = work.size(); @@ -252,6 +259,36 @@ namespace Cantera { return info; } //===================================================================================================================== + doublereal SquareMatrix::rcond(doublereal anorm) { + + if ((int) iwork_.size() < m_nrows) { + iwork_.resize(m_nrows); + } + if ((int) work.size() <4 * m_nrows) { + work.resize(4 * m_nrows); + } + doublereal rcond = 0.0; + if (m_factored != 1) { + throw CELapackError("SquareMatrix::rcond()", "matrix isn't factored correctly"); + } + + // doublereal anorm = ct_dlange('1', m_nrows, m_nrows, &(*(begin())), m_nrows, DATA_PTR(work)); + + + int rinfo; + rcond = ct_dgecon('1', m_nrows, &(*(begin())), m_nrows, anorm, DATA_PTR(work), + DATA_PTR(iwork_), rinfo); + if (rinfo != 0) { + if (m_printLevel) { + writelogf("SquareMatrix::rcond(): DGECON returned INFO = %d\n", rinfo); + } + if (! m_useReturnErrorCode) { + throw CELapackError("SquareMatrix::rcond()", "DGECON returned INFO = " + int2str(rinfo)); + } + } + return rcond; + } + //===================================================================================================================== doublereal SquareMatrix::rcondQR() { if ((int) iwork_.size() < m_nrows) { diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index 1445bc60d..b95d3b35b 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -104,6 +104,16 @@ namespace Cantera { */ doublereal rcondQR(); + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the LU algorithm + * + * @param a1norm Norm of the matrix + * + * @return returns the inverse of the condition number + */ + doublereal rcond(doublereal a1norm); + //! Solves the linear problem Ax=b using the QR algorithm returning x in the b spot /*! * @param b RHS to be solved. @@ -131,6 +141,9 @@ namespace Cantera { //! Integer work vector for QR algorithms std::vector iwork_; + + //! 1-norm of the matrix. This is determined immediately before every factorization + doublereal a1norm_; public: //! Use the QR algorithm to factor and invert the matrix diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index d79c68391..ea7083c1f 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -32,6 +32,8 @@ #define _DGBSV_ dgbsv #define _DGBTRF_ dgbtrf #define _DGBTRS_ dgbtrs +#define _DGECON_ dgecon +#define _DLANGE_ dlange #define _DSCAL_ dscal @@ -52,6 +54,8 @@ #define _DGBSV_ dgbsv_ #define _DGBTRF_ dgbtrf_ #define _DGBTRS_ dgbtrs_ +#define _DGECON_ dgecon_ +#define _DLANGE_ dlange_ #define _DSCAL_ dscal_ @@ -147,7 +151,7 @@ extern "C" { doublereal *b, integer *ldb, integer *info); #endif - int _DSCAL_(integer *n, doublereal *da, doublereal *dx, integer *incx); + int _DSCAL_(integer *n, doublereal *da, doublereal *dx, integer *incx); void cblas_dscal(const int N, const double alpha, double *X, const int incX); @@ -207,6 +211,26 @@ extern "C" { #endif +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DGECON_(const char *norm, const integer* n, doublereal* a, const integer* lda, + const doublereal *rnorm, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info, ftnlen nosize); +#else + int _DGECON_(const char *norm, ftnlen nosize, const integer* n, doublereal* a, const integer* lda, + const doublereal *rnorm, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info); +#endif + + +#ifdef LAPACK_FTN_STRING_LEN_AT_END + doublereal _DLANGE_(const char *norm, const integer* m, const integer* n, doublereal* a, const integer* lda, + doublereal* work, ftnlen nosize); +#else + doublereal _DLANGE_(const char *norm, ftnlen nosize, const integer* m, const integer* n, doublereal* a, const integer* lda, + doublereal* work); +#endif + + } //#endif @@ -315,7 +339,7 @@ namespace Cantera { } //==================================================================================================================== inline void ct_dgetri(int n, doublereal* a, int lda, integer* ipiv, - doublereal* work, int lwork, int& info) { + doublereal* work, int lwork, int& info) { integer f_n = n, f_lda = lda, f_lwork = lwork, f_info = info; _DGETRI_(&f_n, a, &f_lda, ipiv, work, &f_lwork, &f_info); } @@ -486,9 +510,64 @@ namespace Cantera { info = f_info; return; } + //==================================================================================================================== + //! + /*! + */ + inline doublereal ct_dgecon(const char norm, int n, doublereal* a, int lda, doublereal anorm, + doublereal* work, int *iwork, int &info) { + char cnorm = '1'; + if (norm) { + cnorm = norm; + } + integer f_n = n; + integer f_lda = lda; + integer f_info = info; + doublereal rcond; +#ifdef NO_FTN_STRING_LEN_AT_END + _DGECON_(&cnorm, &f_n a, &f_lda, &anorm, &rcond, work, iwork, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DGECON_(&cnorm, &f_n, a, &f_lda, &anorm, &rcond, work, iwork, &f_info, trsize); +#else + _DGECON_(&cnorm, trsize, &f_n, a, &f_lda, &anorm, &rcond, work, iwork, &f_info); +#endif +#endif + info = f_info; + return rcond; + } + //==================================================================================================================== + //! + /*! + */ + inline doublereal ct_dlange(const char norm, int m, int n, doublereal* a, int lda, + doublereal* work) { + char cnorm = '1'; + if (norm) { + cnorm = norm; + } + integer f_m = m; + integer f_n = n; + integer f_lda = lda; + doublereal anorm; + +#ifdef NO_FTN_STRING_LEN_AT_END + anorm = _DLANGE_(&cnorm, &f_m, &f_n a, &f_lda, work); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + anorm = _DLANGE_(&cnorm, &f_m, &f_n, a, &f_lda, work, trsize); +#else + anorm = _DLANGE_(&cnorm, trsize, &f_m, &f_n, a, &f_lda, work); +#endif +#endif + return anorm; + } + //==================================================================================================================== } #endif From 425085627b9800f8a617ad9d2bfe1b5efdcf32f2 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 28 May 2011 00:18:33 +0000 Subject: [PATCH 368/446] Incremental work. Fixed one error in an output variable. --- Cantera/src/numerics/NonlinearSolver.cpp | 84 +++++++++++++++++++----- Cantera/src/numerics/NonlinearSolver.h | 3 +- 2 files changed, 71 insertions(+), 16 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 4d24c605e..2bb3adfe1 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1118,6 +1118,11 @@ namespace Cantera { /* * For confirmation of the scaling factors, see Dennis and Schnabel p, 152, p, 156 and my notes * + * The colFac and rowFac values are used to eliminate the scaling of the matrix from the + * actual equation + * + * Here we calculate the steepest direction. this is equation (10) in the notes. It is + * storred in deltaX_CP_[].The value corresponds to d_descent[]. */ for (int j = 0; j < neq_; j++) { deltaX_CP_[j] = 0.0; @@ -1133,6 +1138,10 @@ namespace Cantera { / (m_residWts[i] * m_residWts[i]); } } + + /* + * Calculate J_hat d_y_descent. This is formula 17 in the notes. + */ for (int i = 0; i < neq_; i++) { Jd_[i] = 0.0; if (m_rowScaling) { @@ -1145,6 +1154,10 @@ namespace Cantera { } } + /* + * Calculate the distance along the steepest descent until the Cauchy point + * This is Eqn. 16 in the notes. + */ RJd_norm_ = 0.0; JdJd_norm_ = 0.0; for (int i = 0; i < neq_; i++) { @@ -1153,17 +1166,23 @@ namespace Cantera { } lambda_ = - RJd_norm_ / (JdJd_norm_); + /* + * Now we modify the steepest descent vector such that its length is equal to the + * Cauchy distance. From now on, if we want to recreate the descent vector, we have + * to unnormalize it by dividing by lambda_. + */ for (int i = 0; i < neq_; i++) { deltaX_CP_[i] *= lambda_; } + double normResid02 = m_normResid0 * m_normResid0 * neq_; - residNorm2Cauchy_ = m_normResid0 * m_normResid0 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); + residNorm2Cauchy_ = normResid02 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); if (m_print_flag > 2) { double residCauchy = 0.0; if (residNorm2Cauchy_ > 0.0) { - residCauchy = sqrt(residNorm2Cauchy_); + residCauchy = sqrt(residNorm2Cauchy_ / neq_); } else { residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); } @@ -1192,7 +1211,7 @@ namespace Cantera { int info; double ff = 1.0E-5; double *y1 = DATA_PTR(m_wksp); - double s1 = solnErrorNorm(DATA_PTR(deltaX_CP_)); + double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); for (int i = 0; i < neq_; i++) { y1[i] = m_y_n[i] + ff * deltaX_CP_[i]; } @@ -1209,7 +1228,7 @@ namespace Cantera { double normResid02 = m_normResid0 * m_normResid0 * neq_; double residSteep = residErrorNorm(DATA_PTR(m_resid)); double residSteep2 = residSteep * residSteep * neq_; - double funcDecrease2 = 0.5 * (residSteep2 - normResid02) / ( ff * s1); + double funcDecrease2 = 0.5 * (residSteep2 - normResid02) / ( ff * cauchyDistanceNorm); double sNewt = solnErrorNorm(DATA_PTR(newtDir)); for (int i = 0; i < neq_; i++) { @@ -1229,7 +1248,7 @@ namespace Cantera { double funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); - double funcDecreaseSDExp = RJd_norm_ / s1 * lambda_; + double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; double funcDecreaseNewtExp2 = - normResid02 / sNewt; @@ -2221,9 +2240,27 @@ namespace Cantera { return -1; } //==================================================================================================================== - int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, const doublereal *ydot0, - std::vector & step0, - double* const y1, double* const ydot1, int& loglevel, double trustDeltaOld) + // Decide whether the current step is acceptable + /* + * This is an extension of algorithm 6.4.5 of Dennis and Schnabel. + * + * Here we decide whether to accept the current step + * + * @param time_curr INPUT Current value of the time + * @param step0 INPUT Trial step + * @param y1 OUTPUT Solution values at the conditions which are evalulated for success + * + * + * @return This function returns a code which indicates whether the step will be accepted or not. + * + * 2 Step is successful + * + * -2 Current value fo the solution vector caused a residual error in its evaluation. + * Step is a failure, and the step size must be reduced in order to proceed further. + */ + int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, + const doublereal *ydot0, std::vector & step0, + double * const y1, double* const ydot1, int& loglevel, double trustDeltaOld) { int retn = 2; @@ -2231,21 +2268,31 @@ namespace Cantera { int j; int info; double ll; + // Calculate the solution step length double stepNorm = solnErrorNorm(DATA_PTR(step0)); - double normResid02 = m_normResid0 * m_normResid0 * neq_; - double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); - double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; - + // Calculate the initial (R**2 * neq) value for the old function + double normResid02 = m_normResid0 * m_normResid0 * neq_; + + // Calculate the distance to the cauchy point + double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + + // This is the expected inital rate of decrease in the cauchy direction. + double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; + + /* + * Calculate the newsolution value y1[] given the step size + */ for (j = 0; j < neq_; j++) { y1[j] = y0[j] + step0[j]; } - + /* + * Calculate the new solution time derivative given the step size + */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, y1, ydot1); } - - + /* * Calculate the residual that would result if y1[] were the new solution vector * -> m_resid[] contains the result of the residual calculation @@ -2255,14 +2302,21 @@ namespace Cantera { } else { info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); } + if (info != 1) { if (loglevel > 0) { printf("\t\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } return -2; } + /* + * Ok we have a successful new residual. Calculate the normalized residual value and store it in + * m_normResidTrial + */ m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); + + double funcDecrease = 0.5 * (m_normResidTrial - normResid02) / (stepNorm); if (funcDecrease < 1.0E-4 * funcDecreaseSDExp) { goodStep = true; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index de8aa9a64..43556ca39 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -896,7 +896,8 @@ namespace Cantera { */ std::vector deltaX_Newton_; - //! Expected value of the residual norm at the Cauchy point + //! Expected value of the residual norm at the Cauchy point if the quadratic model + //! were valid doublereal residNorm2Cauchy_; //! Residual dot Jd norm From 8710440a1f78613ca471625381e8588788eb1e7f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 28 May 2011 02:51:49 +0000 Subject: [PATCH 369/446] Another incremental update - decideStep() has been documented and checked out --- Cantera/src/numerics/NonlinearSolver.cpp | 87 ++++++++++++++++-------- Cantera/src/numerics/NonlinearSolver.h | 28 ++++++++ 2 files changed, 88 insertions(+), 27 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 2bb3adfe1..9190e9911 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1248,6 +1248,8 @@ namespace Cantera { double funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); + // This is the expected inital rate of decrease in the cauchy direction. + // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; double funcDecreaseNewtExp2 = - normResid02 / sNewt; @@ -2240,22 +2242,32 @@ namespace Cantera { return -1; } //==================================================================================================================== - // Decide whether the current step is acceptable + // Decide whether the current step is acceptable and adjust the trust region size /* * This is an extension of algorithm 6.4.5 of Dennis and Schnabel. * * Here we decide whether to accept the current step + * At the end of the calculation a new estimate of the trust region is calculated * * @param time_curr INPUT Current value of the time + * @param leg INPUT Leg of the dogleg that we are on + * @param alpha INPUT Distance down that leg that we are on + * @param y0 INPUT Current value of the solution vector + * @param ydot0 INPUT Current value of the derivative of the solution vector * @param step0 INPUT Trial step * @param y1 OUTPUT Solution values at the conditions which are evalulated for success + * @param ydot1 OUTPUT Time derivates of solution at the conditions which are evalulated for success + * @param loglevel INPUT Current loglevel + * @param trustDeltaOld INPUT Value of the trust length at the old conditions * * * @return This function returns a code which indicates whether the step will be accepted or not. - * - * 2 Step is successful - * - * -2 Current value fo the solution vector caused a residual error in its evaluation. + * 3 Step passed with flying colors. Try redoing the calculation with a bigger trust region. + * 2 Step didn't pass deltaF requirement. Decrease the size of the next trust region for a retry and return + * 0 The step passed. + * -1 The step size is now too small (||d || < 0.1). A really small step isn't decreasing the function. + * This is an error condition. + * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, @@ -2272,13 +2284,19 @@ namespace Cantera { double stepNorm = solnErrorNorm(DATA_PTR(step0)); // Calculate the initial (R**2 * neq) value for the old function - double normResid02 = m_normResid0 * m_normResid0 * neq_; + double normResid0_2 = m_normResid0 * m_normResid0 * neq_; // Calculate the distance to the cauchy point double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); // This is the expected inital rate of decrease in the cauchy direction. + // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; + if (funcDecreaseSDExp > 0.0) { + if (loglevel > 0) { + printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); + } + } /* * Calculate the newsolution value y1[] given the step size @@ -2305,7 +2323,7 @@ namespace Cantera { if (info != 1) { if (loglevel > 0) { - printf("\t\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + printf("\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } return -2; } @@ -2314,11 +2332,15 @@ namespace Cantera { * m_normResidTrial */ m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); + double normResidTrial_2 = neq_ * m_normResidTrial * m_normResidTrial; - - - double funcDecrease = 0.5 * (m_normResidTrial - normResid02) / (stepNorm); - if (funcDecrease < 1.0E-4 * funcDecreaseSDExp) { + /* + * We have a minimal acceptance test for passage. deltaf < 1.0E-4 (CauchySlope) (deltS) + * This is the condition that D&S use in 6.4.5 + */ + double funcDecrease = 0.5 * (normResidTrial_2 - normResid0_2); + double acceptableDelF = funcDecreaseSDExp * stepNorm * 1.0E-4; + if (funcDecrease < acceptableDelF) { goodStep = true; retn = 0; } else { @@ -2331,39 +2353,50 @@ namespace Cantera { return retn; } /* - * Figure out the next trust region + * Figure out the next trust region. We are here iff retn = 0 * * If we had to bounds delta the update, decrease the trust region */ if (m_dampBound < 1.0) { trustDelta_ *= 0.5; ll = trustRegionLength(); - printf("decideStep(): Trust region decreased from %g to %g due to bounds constraint\n", + printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bounds constraint\n", ll*2, ll); } else { retn = 0; + /* + * Calculate the expected residual from the quadratic model + */ double expectedNormRes = expectedResidLeg(leg, alpha); - if (m_normResidTrial > 1.1 * expectedNormRes) { - if ((m_normResidTrial > 0.2 * m_normResid0) && (m_normResidTrial > 0.1)) { + double expectedFuncDecrease = 0.5 * (neq_ * expectedNormRes * expectedNormRes - normResid0_2); + if (funcDecrease > 0.1 * expectedFuncDecrease) { + if ((m_normResidTrial > 0.5 * m_normResid0) && (m_normResidTrial > 0.1)) { trustDelta_ *= 0.5; ll = trustRegionLength(); - printf("decideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", + printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", ll*2, ll); } } else { - - if (trustDelta_ <= trustDeltaOld) { - trustDelta_ *= 2.0; - ll = trustRegionLength(); - printf("decideStep(): Trust region increased from %g to %g due to good quad approximation\n", - ll*0.5, ll); - retn = 3; - } else { - if (m_normResidTrial < 0.75 * expectedNormRes) { + /* + * If we are doing well, consider increasing the trust region and recalculating + */ + if (funcDecrease < 0.8 * expectedFuncDecrease || (m_normResidTrial < 0.33 * m_normResid0)) { + if (trustDelta_ <= trustDeltaOld) { trustDelta_ *= 2.0; ll = trustRegionLength(); - printf("decideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", - ll*0.5, ll); + printf("\td\tecideStep(): Trust region increased from %g to %g due to good quad approximation\n", + ll*0.5, ll); + retn = 3; + } else { + /* + * Increase the size of the trust region for the next calculation + */ + if (m_normResidTrial < 0.75 * expectedNormRes) { + trustDelta_ *= 2.0; + ll = trustRegionLength(); + printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + ll*0.5, ll); + } } } } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 43556ca39..5ea6ddb6d 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -632,6 +632,34 @@ namespace Cantera { double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, int& num_backtracks); + //! Decide whether the current step is acceptable and adjust the trust region size + /*! + * This is an extension of algorithm 6.4.5 of Dennis and Schnabel. + * + * Here we decide whether to accept the current step + * At the end of the calculation a new estimate of the trust region is calculated + * + * @param time_curr INPUT Current value of the time + * @param leg INPUT Leg of the dogleg that we are on + * @param alpha INPUT Distance down that leg that we are on + * @param y0 INPUT Current value of the solution vector + * @param ydot0 INPUT Current value of the derivative of the solution vector + * @param step0 INPUT Trial step + * @param y1 OUTPUT Solution values at the conditions which are evalulated for success + * @param ydot1 OUTPUT Time derivates of solution at the conditions which are evalulated for success + * @param loglevel INPUT Current loglevel + * @param trustDeltaOld INPUT Value of the trust length at the old conditions + * + * + * @return This function returns a code which indicates whether the step will be accepted or not. + * 3 Step passed with flying colors. Try redoing the calculation with a bigger trust region. + * 2 Step didn't pass deltaF requirement. Decrease the size of the next trust region for a retry and return + * 0 The step passed. + * -1 The step size is now too small (||d || < 0.1). A really small step isn't decreasing the function. + * This is an error condition. + * -2 Current value of the solution vector caused a residual error in its evaluation. + * Step is a failure, and the step size must be reduced in order to proceed further. + */ int decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, const doublereal *ydot0, std::vector & step0, double* const y1, double* const ydot1, int& loglevel, double trustDeltaOld); From 4d245501cf8dffb35a92882f22f62ffde681fd43 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 30 May 2011 17:57:53 +0000 Subject: [PATCH 370/446] Update on the NonlinearSolver: Update to :calcSolnToResNormVector() to align it with documentation. --- Cantera/src/numerics/NonlinearSolver.cpp | 51 +++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 14 +++++-- 2 files changed, 46 insertions(+), 19 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 9190e9911..467d82138 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -348,17 +348,12 @@ namespace Cantera { * The program always assumes that atol is specific * to the solution component * - * param y vector of the current solution values + * @param y vector of the current solution values */ void NonlinearSolver::createSolnWeights(const doublereal * const y) { for (int i = 0; i < neq_; i++) { m_ewt[i] = rtol_ * fabs(y[i]) + atolk_[i]; } -#ifdef DEBUG_DOGLEG - // for (int i = 0; i < neq_; i++) { - // m_ewt[i] = 1.0E-4; - // } -#endif } //==================================================================================================================== // set bounds constraints for all variables in the problem @@ -665,8 +660,10 @@ namespace Cantera { } for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { - m_rowScales[irow] += fabs(*jptr); + //m_rowScales[irow] += fabs(*jptr); if (m_colScaling) { + // This is needed in order to mitgate the change in J_ij carried out just above this loop. + // Alternatively, we could move this loop up to the top m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol] / m_colScales[jcol]; } else { m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol]; @@ -699,16 +696,40 @@ namespace Cantera { } //==================================================================================================================== + // Calculate the scaling factor for translating residual norms into solution norms. + /* + * This routine calls computeResidWts() a couple of times in the calculation of m_ScaleSolnNormToResNorm. + * A more sophisticated routine may do more with signs to get a better value. Perhaps, a series of calculations + * with different signs attached may be in order. Then, m_ScaleSolnNormToResNorm would be calculated + * as the minimum of a series of calculations. + */ void NonlinearSolver::calcSolnToResNormVector() { - // double oldVal = m_ScaleSolnNormToResNorm; - // if (m_normSolnFRaw > 1.0E-13) { - // m_ScaleSolnNormToResNorm = 1.0E-2 * m_normResid0 / m_normSolnFRaw * oldVal; - //} - // m_normResid0 = m_normSolnFRaw; - //computeResidWts(); - m_ScaleSolnNormToResNorm = 1.0; - //double tmp = residErrorNorm(DATA_PTR(m_resid)); + if (! jacCopy_.m_factored) { + m_ScaleSolnNormToResNorm = 1.0; + computeResidWts(); + for (int n = 0; n < neq_; n++) { + m_wksp[n] = 0.0; + } + doublereal *jptr = &(*(jacCopy_.begin())); + for (int jcol = 0; jcol < neq_; jcol++) { + for (int irow = 0; irow < neq_; irow++) { + m_wksp[irow] += (*jptr) * m_ewt[jcol]; + jptr++; + } + } + double resNormOld = residErrorNorm(DATA_PTR(m_wksp)); + if (resNormOld > 0.0) { + m_ScaleSolnNormToResNorm = m_ScaleSolnNormToResNorm * resNormOld; + } + if (m_ScaleSolnNormToResNorm < 1.0E-8) { + m_ScaleSolnNormToResNorm = 1.0E-8; + } + // Recalculate the residual weights now that we know the value of m_ScaleSolnNormToResNorm + computeResidWts(); + } else { + throw CanteraError("NonlinearSolver::calcSolnToResNormVector()" , "Logic error"); + } } //==================================================================================================================== // Compute the undamped Newton step based on the current jacobian and an input rhs diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 5ea6ddb6d..454286edf 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -579,8 +579,13 @@ namespace Cantera { */ void setMaxNewtIts(const int maxNewtIts); - //! Calculate the scaling factor for translating residual norms into - //! solution norms. + //! Calculate the scaling factor for translating residual norms into solution norms. + /*! + * This routine calls computeResidWts() a couple of times in the calculation of m_ScaleSolnNormToResNorm. + * A more sophisticated routine may do more with signs to get a better value. Perhaps, a series of calculations + * with different signs attached may be in order. Then, m_ScaleSolnNormToResNorm would be calculated + * as the minimum of a series of calculations. + */ void calcSolnToResNormVector(); //! Calculate the steepest descent direction and the Cauchy Point where the quadratic formulation @@ -758,8 +763,9 @@ namespace Cantera { //! Weights for normalizing the values of the residuals /*! - * These are computed if row scaling, m_rowScaling, is turned on. They are calculated currently as the - * sum of the absolute values jacobian multiplied by the solution weight function + * They are calculated as the sum of the absolute values of the jacobian + * multiplied by the solution weight function. + * This is carried out in scaleMatrix(). */ std::vector m_rowWtScales; From 68ed8ad5480b031880c51180322a2120337e228a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 30 May 2011 22:19:39 +0000 Subject: [PATCH 371/446] Guarded against a divide by zero that occurred when the cauchy step size and residual were exactly zero. --- Cantera/src/numerics/NonlinearSolver.cpp | 29 +++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 467d82138..2120df2c5 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -1157,6 +1157,9 @@ namespace Cantera { } deltaX_CP_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] / (m_residWts[i] * m_residWts[i]); +#ifdef DEBUG_DOGLEG + mdp::checkFinite(deltaX_CP_[j]); +#endif } } @@ -1185,7 +1188,18 @@ namespace Cantera { RJd_norm_ += m_resid[i] * Jd_[i] / m_residWts[i]; JdJd_norm_ += Jd_[i] * Jd_[i]; } - lambda_ = - RJd_norm_ / (JdJd_norm_); + //if (RJd_norm_ > -1.0E-300) { + // printf("we are here: zero residual\n"); + //} + if (fabs(JdJd_norm_) < 1.0E-290) { + if (fabs(RJd_norm_) < 1.0E-300) { + lambda_ = 0.0; + } else { + throw CanteraError("NonlinearSolver::doCauchyPointSolve()", "Unexpected condition: norms are zero"); + } + } else { + lambda_ = - RJd_norm_ / (JdJd_norm_); + } /* * Now we modify the steepest descent vector such that its length is equal to the @@ -1197,7 +1211,11 @@ namespace Cantera { } double normResid02 = m_normResid0 * m_normResid0 * neq_; - residNorm2Cauchy_ = normResid02 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); + if (fabs(JdJd_norm_) < 1.0E-290) { + residNorm2Cauchy_ = normResid02; + } else { + residNorm2Cauchy_ = normResid02 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); + } if (m_print_flag > 2) { @@ -1205,7 +1223,11 @@ namespace Cantera { if (residNorm2Cauchy_ > 0.0) { residCauchy = sqrt(residNorm2Cauchy_ / neq_); } else { - residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); + if (fabs(JdJd_norm_) < 1.0E-290) { + residCauchy = m_normResid0; + } else { + residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); + } } // Compute the weighted norm of the undamped step size descentDir_[] @@ -1234,6 +1256,7 @@ namespace Cantera { double *y1 = DATA_PTR(m_wksp); double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); for (int i = 0; i < neq_; i++) { + mdp::checkFinite(deltaX_CP_[i]); y1[i] = m_y_n[i] + ff * deltaX_CP_[i]; } /* From 1982d0c9289769b2da114f383a353210a5798d8d Mon Sep 17 00:00:00 2001 From: John Hewson Date: Fri, 15 Jul 2011 23:27:45 +0000 Subject: [PATCH 372/446] Changed return flags for errors to be unique to each return condition. Hopefully this will help track down convergence problems. --- Cantera/src/numerics/NonlinearSolver.cpp | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 2120df2c5..64394870f 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -2150,9 +2150,9 @@ namespace Cantera { return 0; } } - if (loglevel >= 4 ) { + //if (loglevel >= 4 ) { printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", -2, m+1, ff); - } + //} return -2; } @@ -2578,7 +2578,7 @@ namespace Cantera { } info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), num_newt_its); if (info == 0) { - m = -1; + m = -4; goto done; } m_residCurrent = true; @@ -2600,7 +2600,7 @@ namespace Cantera { if (m_print_flag > 0) { printf("\t\t\tsolve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); } - m = -1; + m = -5; goto done; } @@ -2644,7 +2644,7 @@ namespace Cantera { } if (info) { - m = -1; + m = -6; goto done; } mdp::mdp_copy_dbl_1(DATA_PTR(stp), CONSTD_DATA_PTR(deltaX_Newton_), neq_); @@ -2731,7 +2731,7 @@ namespace Cantera { * Impose max newton iteration */ if (num_newt_its > maxNewtIts_) { - m = -1; + m = -7; if (m_print_flag > 1) { printf("\t\tsolve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); } @@ -2743,7 +2743,7 @@ namespace Cantera { if (m_print_flag > 0) { printf("\t\t\tdampStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } - m = -1; + m = -8; goto done; } From ff7e66e5a34e05dff7d678eb255fcf1966090b4e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 23 Jul 2011 00:30:35 +0000 Subject: [PATCH 373/446] This update adds in a Multicomponent Real Gas capability to Cantera. The Object is called RedlichKwongMFTP, and it implements a multicomponent real gas approximation. Most of the functionality has been verified against sample problems involving the CO2-H2O system. --- Cantera/src/base/checkFinite.cpp | 34 +- Cantera/src/numerics/RootFind.h | 1 - Cantera/src/thermo/Makefile.in | 6 +- .../src/thermo/MixedSolventElectrolyte.cpp | 1214 +++++++++++ Cantera/src/thermo/MixedSolventElectrolyte.h | 1025 +++++++++ Cantera/src/thermo/MixtureFugacityTP.cpp | 1367 ++++++++++++ Cantera/src/thermo/MixtureFugacityTP.h | 968 +++++++++ Cantera/src/thermo/NasaThermo.h | 5 +- Cantera/src/thermo/RedlichKwongMFTP.cpp | 1895 +++++++++++++++++ Cantera/src/thermo/RedlichKwongMFTP.h | 843 ++++++++ Cantera/src/thermo/ShomateThermo.h | 5 +- Cantera/src/thermo/SimpleThermo.h | 3 +- Cantera/src/thermo/ThermoFactory.cpp | 11 + Cantera/src/thermo/ThermoPhase.cpp | 4 +- Cantera/src/thermo/ThermoPhase.h | 2 +- Cantera/src/thermo/mix_defs.h | 4 + config.h.in | 3 + configure | 16 +- configure.in | 7 + .../linux.64_sierra_gcc444_python264_numpy | 3 + preconfig | 4 + .../min_python/negATest/negATest_blessed.out | 4 +- 22 files changed, 7390 insertions(+), 34 deletions(-) create mode 100644 Cantera/src/thermo/MixedSolventElectrolyte.cpp create mode 100644 Cantera/src/thermo/MixedSolventElectrolyte.h create mode 100644 Cantera/src/thermo/MixtureFugacityTP.cpp create mode 100644 Cantera/src/thermo/MixtureFugacityTP.h create mode 100644 Cantera/src/thermo/RedlichKwongMFTP.cpp create mode 100644 Cantera/src/thermo/RedlichKwongMFTP.h diff --git a/Cantera/src/base/checkFinite.cpp b/Cantera/src/base/checkFinite.cpp index be4fa224d..443d3d8a7 100644 --- a/Cantera/src/base/checkFinite.cpp +++ b/Cantera/src/base/checkFinite.cpp @@ -50,11 +50,11 @@ namespace mdp { void checkFinite(const double tmp) throw(std::range_error) { if (_finite(tmp)) { if(_isnan(tmp)) { - printf("ERROR: we have encountered a nan!\n"); + printf("checkFinite() ERROR: we have encountered a nan!\n"); } else if (_fpclass(tmp) == _FPCLASS_PINF) { - printf("ERROR: we have encountered a pos inf!\n"); + printf("checkFinite() ERROR: we have encountered a pos inf!\n"); } else { - printf("ERROR: we have encountered a neg inf!\n"); + printf("checkFinite() ERROR: we have encountered a neg inf!\n"); } const std::string s = "checkFinite()"; throw std::range_error(s); @@ -64,11 +64,11 @@ namespace mdp { void checkFinite(const double tmp) throw(std::range_error) { if (! finite(tmp)) { if(isnan(tmp)) { - printf("ERROR: we have encountered a nan!\n"); + printf("checkFinite() ERROR: we have encountered a nan!\n"); } else if (isinf(tmp) == 1) { - printf("ERROR: we have encountered a pos inf!\n"); + printf("checkFinite() ERROR: we have encountered a pos inf!\n"); } else { - printf("ERROR: we have encountered a neg inf!\n"); + printf("checkFinite() ERROR: we have encountered a neg inf!\n"); } const std::string s = "checkFinite()"; throw std::range_error(s); @@ -102,7 +102,7 @@ namespace mdp { checkFinite(tmp); if (fabs(tmp) >= trigger) { char sbuf[64]; - sprintf(sbuf, "checkMagnitude: Trigger %g exceeded: %g\n", trigger, + sprintf(sbuf, "checkMagnitude() ERROR: Trigger %g exceeded: %g\n", trigger, tmp); throw std::range_error(sbuf); } @@ -119,16 +119,16 @@ namespace mdp { void checkZeroFinite(const double tmp) throw(std::range_error) { if ((tmp == 0.0) || (! _finite(tmp))) { if (tmp == 0.0) { - printf("ERROR: we have encountered a zero!\n"); + printf("checkZeroFinite() ERROR: we have encountered a zero!\n"); } else if(_isnan(tmp)) { - printf("ERROR: we have encountered a nan!\n"); + printf("checkZeroFinite() ERROR: we have encountered a nan!\n"); } else if (_fpclass(tmp) == _FPCLASS_PINF) { - printf("ERROR: we have encountered a pos inf!\n"); + printf("checkZeroFinite() ERROR: we have encountered a pos inf!\n"); } else { - printf("ERROR: we have encountered a neg inf!\n"); + printf("checkZeroFinite() ERROR: we have encountered a neg inf!\n"); } char sbuf[64]; - sprintf(sbuf, "checkZeroFinite: zero or indef exceeded: %g\n", + sprintf(sbuf, "checkZeroFinite() ERROR: zero or indef exceeded: %g\n", tmp); throw std::range_error(sbuf); } @@ -137,16 +137,16 @@ void checkZeroFinite(const double tmp) throw(std::range_error) { void checkZeroFinite(const double tmp) throw(std::range_error) { if ((tmp == 0.0) || (! finite(tmp))) { if (tmp == 0.0) { - printf("ERROR: we have encountered a zero!\n"); + printf("checkZeroFinite() ERROR: we have encountered a zero!\n"); } else if(isnan(tmp)) { - printf("ERROR: we have encountered a nan!\n"); + printf("checkZeroFinite() ERROR: we have encountered a nan!\n"); } else if (isinf(tmp) == 1) { - printf("ERROR: we have encountered a pos inf!\n"); + printf("checkZeroFinite() ERROR: we have encountered a pos inf!\n"); } else { - printf("ERROR: we have encountered a neg inf!\n"); + printf("checkZeroFinite() ERROR: we have encountered a neg inf!\n"); } char sbuf[64]; - sprintf(sbuf, "checkZeroFinite: zero or indef exceeded: %g\n", + sprintf(sbuf, "checkZeroFinite() ERROR: zero or indef exceeded: %g\n", tmp); throw std::range_error(sbuf); } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index bc5b6e3fc..0392a8799 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -137,7 +137,6 @@ namespace Cantera { */ int solve(doublereal xmin, doublereal xmax, int itmax, doublereal &funcTargetValue, doublereal *xbest); - //! Return the function value /*! * This routine evaluates the following equation. diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index 690877d38..9a933701f 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -40,7 +40,7 @@ THERMO_OBJ = State.o Elements.o Constituents.o Phase.o \ ThermoFactory.o phasereport.o SpeciesThermoInterpType.o \ VPSSMgr.o VPSSMgrFactory.o VPSSMgr_General.o IdealSolnGasVPSS.o \ VPSSMgr_IdealGas.o VPSSMgr_ConstVol.o PDSS_ConstVol.o PDSS_IdealGas.o \ - PDSS_SSVol.o @phase_object_files@ + PDSS_SSVol.o MixtureFugacityTP.o RedlichKwongMFTP.o @phase_object_files@ THERMO_H = State.h Elements.h Constituents.h Phase.h mix_defs.h \ ThermoPhase.h IdealGasPhase.h ConstDensityThermo.h \ @@ -54,7 +54,7 @@ THERMO_H = State.h Elements.h Constituents.h Phase.h mix_defs.h \ EdgePhase.h \ VPSSMgr.h VPSSMgrFactory.h VPSSMgr_General.h IdealSolnGasVPSS.h \ VPSSMgr_IdealGas.h VPSSMgr_ConstVol.h PDSS_ConstVol.h PDSS_IdealGas.h \ - PDSS_SSVol.h @phase_header_files@ + PDSS_SSVol.h MixtureFugacityTP.h RedlichKwongMFTP.h @phase_header_files@ # Extended Cantera Thermodynamics Object Files @@ -91,7 +91,7 @@ CATHERMO_OBJ = $(THERMO_OBJ) $(ELECTRO_OBJ) $(ISSP_OBJ) CATHERMO_H = $(THERMO_H) $(ELECTRO_H) $(ISSP_H) -CXX_INCLUDES = -I../base @CXX_INCLUDES@ +CXX_INCLUDES = -I../base -I../numerics @CXX_INCLUDES@ LIB = @buildlib@/libthermo.a DEPENDS = $(CATHERMO_OBJ:.o=.d) diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.cpp b/Cantera/src/thermo/MixedSolventElectrolyte.cpp new file mode 100644 index 000000000..64d4b9bd1 --- /dev/null +++ b/Cantera/src/thermo/MixedSolventElectrolyte.cpp @@ -0,0 +1,1214 @@ +/** + * @file MargulesVPSSTP.cpp + * Definitions for ThermoPhase object for phases which + * employ excess gibbs free energy formulations related to Margules + * expansions (see \ref thermoprops + * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). + * + */ +/* + * Copywrite (2009) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Date: 2011-04-14 12:24:13 -0600 (Thu, 14 Apr 2011) $ + * $Revision: 713 $ + */ + + +#include "MixedSolventElectrolyte.h" +#include "ThermoFactory.h" +#include + +using namespace std; + +namespace Cantera { + + static const double xxSmall = 1.0E-150; + /* + * Default constructor. + * + */ + MixedSolventElectrolyte::MixedSolventElectrolyte() : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + } + + /* + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + + */ + MixedSolventElectrolyte::MixedSolventElectrolyte(std::string inputFile, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + constructPhaseFile(inputFile, id); + } + + MixedSolventElectrolyte::MixedSolventElectrolyte(XML_Node& phaseRoot, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + constructPhaseXML(phaseRoot, id); + } + + + /* + * Copy Constructor: + * + * Note this stuff will not work until the underlying phase + * has a working copy constructor + */ + MixedSolventElectrolyte::MixedSolventElectrolyte(const MixedSolventElectrolyte &b) : + GibbsExcessVPSSTP() + { + MixedSolventElectrolyte::operator=(b); + } + + /* + * operator=() + * + * Note this stuff will not work until the underlying phase + * has a working assignment operator + */ + MixedSolventElectrolyte& MixedSolventElectrolyte:: + operator=(const MixedSolventElectrolyte &b) { + if (&b == this) { + return *this; + } + + GibbsExcessVPSSTP::operator=(b); + + numBinaryInteractions_ = b.numBinaryInteractions_ ; + m_HE_b_ij = b.m_HE_b_ij; + m_HE_c_ij = b.m_HE_c_ij; + m_HE_d_ij = b.m_HE_d_ij; + m_SE_b_ij = b.m_SE_b_ij; + m_SE_c_ij = b.m_SE_c_ij; + m_SE_d_ij = b.m_SE_d_ij; + m_VHE_b_ij = b.m_VHE_b_ij; + m_VHE_c_ij = b.m_VHE_c_ij; + m_VHE_d_ij = b.m_VHE_d_ij; + m_VSE_b_ij = b.m_VSE_b_ij; + m_VSE_c_ij = b.m_VSE_c_ij; + m_VSE_d_ij = b.m_VSE_d_ij; + m_pSpecies_A_ij = b.m_pSpecies_A_ij; + m_pSpecies_B_ij = b.m_pSpecies_B_ij; + formMargules_ = b.formMargules_; + formTempModel_ = b.formTempModel_; + + return *this; + } + + /** + * + * ~MixedSolventElectrolyte(): (virtual) + * + * Destructor: does nothing: + * + */ + MixedSolventElectrolyte::~MixedSolventElectrolyte() { + } + + /* + * This routine duplicates the current object and returns + * a pointer to ThermoPhase. + */ + ThermoPhase* + MixedSolventElectrolyte::duplMyselfAsThermoPhase() const { + MixedSolventElectrolyte* mtp = new MixedSolventElectrolyte(*this); + return (ThermoPhase *) mtp; + } + + // Special constructor for a hard-coded problem + /* + * + * LiKCl treating the PseudoBinary layer as passthrough. + * -> test to predict the eutectic and liquidus correctly. + * + */ + MixedSolventElectrolyte::MixedSolventElectrolyte(int testProb) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + formMargules_(0), + formTempModel_(0) + { + + + constructPhaseFile("LiKCl_liquid.xml", ""); + + + numBinaryInteractions_ = 1; + + m_HE_b_ij.resize(1); + m_HE_c_ij.resize(1); + m_HE_d_ij.resize(1); + + m_SE_b_ij.resize(1); + m_SE_c_ij.resize(1); + m_SE_d_ij.resize(1); + + m_VHE_b_ij.resize(1); + m_VHE_c_ij.resize(1); + m_VHE_d_ij.resize(1); + + m_VSE_b_ij.resize(1); + m_VSE_c_ij.resize(1); + m_VSE_d_ij.resize(1); + + m_pSpecies_A_ij.resize(1); + m_pSpecies_B_ij.resize(1); + + + + m_HE_b_ij[0] = -17570E3; + m_HE_c_ij[0] = -377.0E3; + m_HE_d_ij[0] = 0.0; + + m_SE_b_ij[0] = -7.627E3; + m_SE_c_ij[0] = 4.958E3; + m_SE_d_ij[0] = 0.0; + + + int iLiCl = speciesIndex("LiCl(L)"); + if (iLiCl < 0) { + throw CanteraError("MixedSolventElectrolyte test1 constructor", + "Unable to find LiCl(L)"); + } + m_pSpecies_B_ij[0] = iLiCl; + + + int iKCl = speciesIndex("KCl(L)"); + if (iKCl < 0) { + throw CanteraError("MixedSolventElectrolyte test1 constructor", + "Unable to find KCl(L)"); + } + m_pSpecies_A_ij[0] = iKCl; + } + + + /* + * -------------- Utilities ------------------------------- + */ + + + // Equation of state type flag. + /* + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The MixedSolventElectrolyte class also returns + * zero, as it is a non-complete class. + */ + int MixedSolventElectrolyte::eosType() const { + return 0; + } + + /* + * Import, construct, and initialize a phase + * specification from an XML tree into the current object. + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void MixedSolventElectrolyte::constructPhaseFile(std::string inputFile, std::string id) { + + if ((int) inputFile.size() == 0) { + throw CanteraError("MixedSolventElectrolyte:constructPhaseFile", + "input file is null"); + } + string path = findInputFile(inputFile); + std::ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("MixedSolventElectrolyte:constructPhaseFile","could not open " + +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + XML_Node &phaseNode_XML = xml(); + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("MixedSolventElectrolyte:constructPhaseFile", + "ERROR: Can not find phase named " + + id + " in file named " + inputFile); + } + fxml_phase->copy(&phaseNode_XML); + constructPhaseXML(*fxml_phase, id); + delete fxml; + } + + /* + * Import, construct, and initialize a HMWSoln phase + * specification from an XML tree into the current object. + * + * Most of the work is carried out by the cantera base + * routine, importPhase(). That routine imports all of the + * species and element data, including the standard states + * of the species. + * + * Then, In this routine, we read the information + * particular to the specification of the activity + * coefficient model for the Pitzer parameterization. + * + * We also read information about the molar volumes of the + * standard states if present in the XML file. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void MixedSolventElectrolyte::constructPhaseXML(XML_Node& phaseNode, std::string id) { + string stemp; + if ((int) id.size() > 0) { + string idp = phaseNode.id(); + if (idp != id) { + throw CanteraError("MixedSolventElectrolyte::constructPhaseXML", + "phasenode and Id are incompatible"); + } + } + + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("MixedSolventElectrolyte::constructPhaseXML", + "no thermo XML node"); + } + XML_Node& thermoNode = phaseNode.child("thermo"); + + /* + * Make sure that the thermo model is Margules + */ + stemp = thermoNode.attrib("model"); + string formString = lowercase(stemp); + if (formString != "margules") { + throw CanteraError("MixedSolventElectrolyte::constructPhaseXML", + "model name isn't Margules: " + formString); + + } + + /* + * Call the Cantera importPhase() function. This will import + * all of the species into the phase. This will also handle + * all of the solvent and solute standard states + */ + bool m_ok = importPhase(phaseNode, this); + if (!m_ok) { + throw CanteraError("MixedSolventElectrolyte::constructPhaseXML","importPhase failed "); + } + + } + + + /* + * ------------ Molar Thermodynamic Properties ---------------------- + */ + + + /* + * - Activities, Standard States, Activity Concentrations ----------- + */ + + // This method returns an array of generalized concentrations + /* + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * Here we define the activity concentrations as equal + * to the activities, because the standard concentration is 1. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + void MixedSolventElectrolyte::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } + + doublereal MixedSolventElectrolyte::standardConcentration(int k) const { + //err("standardConcentration"); + //return -1.0; + return 1.0; + } + + doublereal MixedSolventElectrolyte::logStandardConc(int k) const { + //err("logStandardConc"); + //return -1.0; + return 0.0; + } + //==================================================================================================================== + // Get the array of non-dimensional molar-based activity coefficients at + // the current solution temperature, pressure, and solution concentration. + /* + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void MixedSolventElectrolyte::getActivityCoefficients(doublereal* ac) const { + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + + /* + * take the exp of the internally storred coefficients. + */ + for (int k = 0; k < m_kk; k++) { + ac[k] = exp(lnActCoeff_Scaled_[k]); + } + } + + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + + + + void MixedSolventElectrolyte::getElectrochemPotentials(doublereal* mu) const { + getChemPotentials(mu); + double ve = Faraday * electricPotential(); + for (int k = 0; k < m_kk; k++) { + mu[k] += ve*charge(k); + } + } + + + void MixedSolventElectrolyte::getChemPotentials(doublereal* mu) const { + doublereal xx; + /* + * First get the standard chemical potentials in + * molar form. + * -> this requires updates of standard state as a function + * of T and P + */ + getStandardChemPotentials(mu); + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + /* + * + */ + doublereal RT = GasConstant * temperature(); + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + mu[k] += RT * (log(xx) + lnActCoeff_Scaled_[k]); + } + } + + /// Molar enthalpy. Units: J/kmol. + doublereal MixedSolventElectrolyte::enthalpy_mole() const { + int kk = nSpecies(); + double hbar[kk], h = 0; + getPartialMolarEnthalpies(hbar); + for (int i = 0; i < kk; i++){ + h += moleFractions_[i]*hbar[i]; + } + return h; + } + + /// Molar entropy. Units: J/kmol. + doublereal MixedSolventElectrolyte::entropy_mole() const { + int kk = nSpecies(); + double sbar[kk], s = 0; + getPartialMolarEntropies(sbar); + for (int i = 0; i < kk; i++){ + s += moleFractions_[i]*sbar[i]; + } + return s; + } + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + doublereal MixedSolventElectrolyte::cp_mole() const { + int kk = nSpecies(); + double cpbar[kk], cp = 0; + getPartialMolarCp(cpbar); + for (int i = 0; i < kk; i++){ + cp += moleFractions_[i]*cpbar[i]; + } + return cp; + } + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + doublereal MixedSolventElectrolyte::cv_mole() const { + return cp_mole() - GasConstant; + } + + // Returns an array of partial molar enthalpies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MixedSolventElectrolyte::getPartialMolarEnthalpies(doublereal* hbar) const { + /* + * Get the nondimensional standard state enthalpies + */ + getEnthalpy_RT(hbar); + /* + * dimensionalize it. + */ + double T = temperature(); + double RT = GasConstant * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] *= RT; + } + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + double RTT = RT * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] -= RTT * dlnActCoeffdT_Scaled_[k]; + } + } + + // Returns an array of partial molar heat capacities for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MixedSolventElectrolyte::getPartialMolarCp(doublereal* cpbar) const { + /* + * Get the nondimensional standard state entropies + */ + getCp_R(cpbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + + // Returns an array of partial molar entropies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MixedSolventElectrolyte::getPartialMolarEntropies(doublereal* sbar) const { + double xx; + /* + * Get the nondimensional standard state entropies + */ + getEntropy_R(sbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + sbar[k] += - lnActCoeff_Scaled_[k] -log(xx) - T * dlnActCoeffdT_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + sbar[k] *= GasConstant; + } + } + + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + + // Return an array of partial molar volumes for the + // species in the mixture. Units: m^3/kmol. + /* + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void MixedSolventElectrolyte::getPartialMolarVolumes(doublereal* vbar) const { + + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + + /* + * Get the standard state values in m^3 kmol-1 + */ + getStandardVolumes(vbar); + + + for ( iK = 0; iK < m_kk; iK++ ){ + delAK = 0; + delBK = 0; + XK = moleFractions_[iK]; + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_VHE_b_ij[i] - T * m_VSE_b_ij[i]); + g1 = (m_VHE_c_ij[i] - T * m_VSE_c_ij[i]); + + vbar[iK] += XA*XB*(g0+g1*XB)+((delAK-XA)*XB+XA*(delBK-XB))*(g0+g1*XB)+XA*XB*(delBK-XB)*g1; + } + } + } + + doublereal MixedSolventElectrolyte::err(std::string msg) const { + throw CanteraError("MixedSolventElectrolyte","Base class method " + +msg+" called. Equation of state type: "+int2str(eosType())); + return 0; + } + + + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + void MixedSolventElectrolyte::initThermo() { + initLengths(); + GibbsExcessVPSSTP::initThermo(); + } + + + // Initialize lengths of local variables after all species have + // been identified. + void MixedSolventElectrolyte::initLengths() { + m_kk = nSpecies(); + dlnActCoeffdlnN_.resize(m_kk, m_kk); + } + + /* + * initThermoXML() (virtual from ThermoPhase) + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void MixedSolventElectrolyte::initThermoXML(XML_Node& phaseNode, std::string id) { + string subname = "MixedSolventElectrolyte::initThermoXML"; + string stemp; + + /* + * Check on the thermo field. Must have: + * + */ + + XML_Node& thermoNode = phaseNode.child("thermo"); + string mStringa = thermoNode.attrib("model"); + string mString = lowercase(mStringa); + if (mString != "margules") { + throw CanteraError(subname.c_str(), + "Unknown thermo model: " + mStringa); + } + + + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + XML_Node *acNodePtr = 0; + if (thermoNode.hasChild("activityCoefficients")) { + XML_Node& acNode = thermoNode.child("activityCoefficients"); + acNodePtr = &acNode; + string mStringa = acNode.attrib("model"); + string mString = lowercase(mStringa); + if (mString != "margules") { + throw CanteraError(subname.c_str(), + "Unknown activity coefficient model: " + mStringa); + } + int n = acNodePtr->nChildren(); + for (int i = 0; i < n; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + stemp = xmlACChild.name(); + string nodeName = lowercase(stemp); + /* + * Process a binary salt field, or any of the other XML fields + * that make up the Pitzer Database. Entries will be ignored + * if any of the species in the entry isn't in the solution. + */ + if (nodeName == "binaryneutralspeciesparameters") { + readXMLBinarySpecies(xmlACChild); + + } + } + } + + /* + * Go down the chain + */ + GibbsExcessVPSSTP::initThermoXML(phaseNode, id); + + + } + //=================================================================================================================== + + // Update the activity coefficients + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + * he = X_A X_B(B + C X_B) + */ + void MixedSolventElectrolyte::s_update_lnActCoeff() const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + double RT = GasConstant*T; + fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + for (iK = 0; iK < m_kk; iK++) { + XK = moleFractions_[iK]; + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + delAK = 0; + delBK = 0; + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + lnActCoeff_Scaled_[iK] += (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; + } + } + } + //=================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt T + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + * he = X_A X_B(B + C X_B) + */ + void MixedSolventElectrolyte::s_update_dlnActCoeff_dT() const { + int iA, iB, iK, delAK, delBK; + doublereal XA, XB, g0, g1; + doublereal T = temperature(); + doublereal RTT = GasConstant*T*T; + fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); + fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); + for (iK = 0; iK < m_kk; iK++) { + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + delAK = 0; + delBK = 0; + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + g0 = -m_HE_b_ij[i] / RTT; + g1 = -m_HE_c_ij[i] / RTT; + double temp = (delAK * XB + XA * delBK - XA * XB) * (g0 + g1 * XB) + XA * XB * (delBK - XB) * g1; + dlnActCoeffdT_Scaled_[iK] += temp; + d2lnActCoeffdT2_Scaled_[iK] -= 2.0 * temp / T; + } + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdT[k] = dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k]; + } + } + //==================================================================================================================== + + // Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + // a line in parameter space or along a line in physical space + /* + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + void MixedSolventElectrolyte::getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + + + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1, dXA, dXB; + double T = temperature(); + double RT = GasConstant*T; + + //fvo_zero_dbl_1(dlnActCoeff, m_kk); + s_update_dlnActCoeff_dT(); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + dlnActCoeffds[iK] = 0.0; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + dXA = dXds[iA]; + dXB = dXds[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffds[iK] += ((delBK-XB)*dXA + (delAK-XA)*dXB)*(g0+2*g1*XB) + (delBK-XB)*2*g1*XA*dXB + + dlnActCoeffdT_Scaled_[iK]*dTds; + } + } + } + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt dlnN + /* + * This function will be called to update the internally stored gradients of the + * logarithm of the activity coefficients. These are used in the determination + * of the diffusion coefficients. + * + * he = X_A X_B(B + C X_B) + */ + void MixedSolventElectrolyte::s_update_dlnActCoeff_dlnN_diag() const { + int iA, iB, iK, delAK, delBK; + double XA, XB, XK, g0 , g1; + double T = temperature(); + double RT = GasConstant*T; + + fvo_zero_dbl_1(dlnActCoeffdlnN_diag_, m_kk); + + for ( iK = 0; iK < m_kk; iK++ ){ + + XK = moleFractions_[iK]; + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0; + delBK = 0; + + if (iA==iK) delAK = 1; + else if (iB==iK) delBK = 1; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnN_diag_[iK] += 2*(delBK-XB)*(g0*(delAK-XA)+g1*(2*(delAK-XA)*XB+XA*(delBK-XB))); + +// double gfac = g0 + g1 * XB; +// double gggg = (delBK - XB) * g1; + + +// dlnActCoeffdlnN_diag_[iK] += gfac * delAK * ( - XB + delBK); + +// dlnActCoeffdlnN_diag_[iK] += gfac * delBK * ( - XA + delAK); + +// dlnActCoeffdlnN_diag_[iK] += gfac * (2.0 * XA * XB - delAK * XB - XA * delBK); + +// dlnActCoeffdlnN_diag_[iK] += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBK); + +// dlnActCoeffdlnN_diag_[iK] += gggg * ( - 2.0 * XA * XB + delAK * XB + XA * delBK); + +// dlnActCoeffdlnN_diag_[iK] += - g1 * XA * XB * (- XB + delBK); + } + dlnActCoeffdlnN_diag_[iK] = XK*dlnActCoeffdlnN_diag_[iK];//-XK; + } + } + + //==================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt dlnN + /* + * This function will be called to update the internally stored gradients of the + * logarithm of the activity coefficients. These are used in the determination + * of the diffusion coefficients. + * + */ + void MixedSolventElectrolyte::s_update_dlnActCoeff_dlnN() const { + int iA, iB; + doublereal delAK, delBK; + double XA, XB, g0 , g1, XK,XM; + double T = temperature(); + double RT = GasConstant*T; + + doublereal delAM, delBM; + + dlnActCoeffdlnN_.zero(); + + /* + * Loop over the activity coefficient gamma_k + */ + for (int iK = 0; iK < m_kk; iK++) { + XK = moleFractions_[iK]; + for (int iM = 0; iM < m_kk; iM++) { + XM = moleFractions_[iM]; + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + delAK = 0.0; + delBK = 0.0; + delAM = 0.0; + delBM = 0.0; + if (iA==iK) delAK = 1.0; + else if (iB==iK) delBK = 1.0; + if (iA==iM) delAM = 1.0; + else if (iB==iM) delBM = 1.0; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnN_(iK,iM) += g0*((delAM-XA)*(delBK-XB)+(delAK-XA)*(delBM-XB)); + dlnActCoeffdlnN_(iK,iM) += 2*g1*((delAM-XA)*(delBK-XB)*XB+(delAK-XA)*(delBM-XB)*XB+(delBM-XB)*(delBK-XB)*XA); + +// double gfac = g0 + g1 * XB; +// double gggg = (delBK - XB) * g1; + + +// dlnActCoeffdlnN_(iK, iM) += gfac * delAK * ( - XB + delBM); + +// dlnActCoeffdlnN_(iK, iM) += gfac * delBK * ( - XA + delAM); + +// dlnActCoeffdlnN_(iK, iM) += gfac * (2.0 * XA * XB - delAM * XB - XA * delBM); + +// dlnActCoeffdlnN_(iK, iM) += (delAK * XB + XA * delBK - XA * XB) * g1 * (-XB + delBM); + +// dlnActCoeffdlnN_(iK, iM) += gggg * ( - 2.0 * XA * XB + delAM * XB + XA * delBM); + +// dlnActCoeffdlnN_(iK, iM) += - g1 * XA * XB * (- XB + delBM); + } + dlnActCoeffdlnN_(iK,iM) = XM*dlnActCoeffdlnN_(iK,iM); + } + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::s_update_dlnActCoeff_dlnX_diag() const { + + int iA, iB; + doublereal XA, XB, g0 , g1; + doublereal T = temperature(); + + fvo_zero_dbl_1(dlnActCoeffdlnX_diag_, m_kk); + + doublereal RT = GasConstant * T; + + + for (int i = 0; i < numBinaryInteractions_; i++) { + + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + + g0 = (m_HE_b_ij[i] - T * m_SE_b_ij[i]) / RT; + g1 = (m_HE_c_ij[i] - T * m_SE_c_ij[i]) / RT; + + dlnActCoeffdlnX_diag_[iA] += XA*XB*(2*g1*-2*g0-6*g1*XB); + dlnActCoeffdlnX_diag_[iB] += XA*XB*(2*g1*-2*g0-6*g1*XB); + } + } + + //==================================================================================================================== + void MixedSolventElectrolyte::getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + s_update_dlnActCoeff_dlnN_diag(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k]; + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { + s_update_dlnActCoeff_dlnX_diag(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) { + s_update_dlnActCoeff_dlnN(); + double *data = & dlnActCoeffdlnN_(0,0); + for (int k = 0; k < m_kk; k++) { + for (int m = 0; m < m_kk; m++) { + dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m]; + } + } + } + //==================================================================================================================== + void MixedSolventElectrolyte::resizeNumInteractions(const int num) { + numBinaryInteractions_ = num; + m_HE_b_ij.resize(num, 0.0); + m_HE_c_ij.resize(num, 0.0); + m_HE_d_ij.resize(num, 0.0); + m_SE_b_ij.resize(num, 0.0); + m_SE_c_ij.resize(num, 0.0); + m_SE_d_ij.resize(num, 0.0); + m_VHE_b_ij.resize(num, 0.0); + m_VHE_c_ij.resize(num, 0.0); + m_VHE_d_ij.resize(num, 0.0); + m_VSE_b_ij.resize(num, 0.0); + m_VSE_c_ij.resize(num, 0.0); + m_VSE_d_ij.resize(num, 0.0); + + m_pSpecies_A_ij.resize(num, -1); + m_pSpecies_B_ij.resize(num, -1); + + } + //==================================================================================================================== + + /* + * Process an XML node called "binaryNeutralSpeciesParameters" + * This node contains all of the parameters necessary to describe + * the Margules Interaction for a single binary interaction + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + */ + void MixedSolventElectrolyte::readXMLBinarySpecies(XML_Node &xmLBinarySpecies) { + string xname = xmLBinarySpecies.name(); + if (xname != "binaryNeutralSpeciesParameters") { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", + "Incorrect name for processing this routine: " + xname); + } + double *charge = DATA_PTR(m_speciesCharge); + string stemp; + int nParamsFound; + vector_fp vParams; + string iName = xmLBinarySpecies.attrib("speciesA"); + if (iName == "") { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "no speciesA attrib"); + } + string jName = xmLBinarySpecies.attrib("speciesB"); + if (jName == "") { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "no speciesB attrib"); + } + /* + * Find the index of the species in the current phase. It's not + * an error to not find the species + */ + int iSpecies = speciesIndex(iName); + if (iSpecies < 0) { + return; + } + string ispName = speciesName(iSpecies); + if (charge[iSpecies] != 0) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "speciesA charge problem"); + } + int jSpecies = speciesIndex(jName); + if (jSpecies < 0) { + return; + } + string jspName = speciesName(jSpecies); + if (charge[jSpecies] != 0) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies", "speciesB charge problem"); + } + + resizeNumInteractions(numBinaryInteractions_ + 1); + int iSpot = numBinaryInteractions_ - 1; + m_pSpecies_A_ij[iSpot] = iSpecies; + m_pSpecies_B_ij[iSpot] = jSpecies; + + int num = xmLBinarySpecies.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = xmLBinarySpecies.child(iChild); + stemp = xmlChild.name(); + string nodeName = lowercase(stemp); + /* + * Process the binary species interaction child elements + */ + if (nodeName == "excessenthalpy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEnthalpy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessEnthalpy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_HE_b_ij[iSpot] = vParams[0]; + m_HE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessentropy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessEntropy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessEntropy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_SE_b_ij[iSpot] = vParams[0]; + m_SE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessvolume_enthalpy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Enthalpy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VHE_b_ij[iSpot] = vParams[0]; + m_VHE_c_ij[iSpot] = vParams[1]; + } + + if (nodeName == "excessvolume_entropy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, vParams, true, "toSI", "excessVolume_Entropy"); + nParamsFound = vParams.size(); + + if (nParamsFound != 2) { + throw CanteraError("MixedSolventElectrolyte::readXMLBinarySpecies::excessVolume_Entropy for " + ispName + + "::" + jspName, + "wrong number of params found"); + } + m_VSE_b_ij[iSpot] = vParams[0]; + m_VSE_c_ij[iSpot] = vParams[1]; + } + + + } + + } + +} + diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.h b/Cantera/src/thermo/MixedSolventElectrolyte.h new file mode 100644 index 000000000..e91caaca2 --- /dev/null +++ b/Cantera/src/thermo/MixedSolventElectrolyte.h @@ -0,0 +1,1025 @@ +/** + * @file MargulesVPSSTP.h + * Header for intermediate ThermoPhase object for phases which + * employ gibbs excess free energy based formulations + * (see \ref thermoprops + * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). + * + * Header file for a derived class of ThermoPhase that handles + * variable pressure standard state methods for calculating + * thermodynamic properties that are further based upon activities + * based on the molality scale. These include most of the methods for + * calculating liquid electrolyte thermodynamics. + */ +/* + * Copywrite (2006) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Id: MargulesVPSSTP.h 713 2011-04-14 18:24:13Z hkmoffa $ + */ + +#ifndef CT_MIXEDSOLVENTELECTROLYTEVPSSTP_H +#define CT_MIXEDSOLVENTELECTROLYTEVPSSTP_H + +#include "PseudoBinaryVPSSTP.h" + +namespace Cantera { + + /** + * @ingroup thermoprops + */ + + + //! MixedSolventElectrolyte is a derived class of GibbsExcessVPSSTP that employs + //! the DH and local Marguless approximations for the excess gibbs free energy + /*! + * + * %MargulesVPSSTP derives from class GibbsExcessVPSSTP which is derived + * from VPStandardStateTP, + * and overloads the virtual methods defined there with ones that + * use expressions appropriate for the Margules Excess gibbs free energy + * approximation. + * + * The independent unknowns are pressure, temperature, and mass fraction. + * + * Several concepts are introduced. The first concept is there are temporary + * variables for holding the species standard state values + * of Cp, H, S, G, and V at the + * last temperature and pressure called. These functions are not recalculated + * if a new call is made using the previous temperature and pressure. Currently, + * these variables and the calculation method are handled by the VPSSMgr class, + * for which VPStandardStateTP owns a pointer to. + * + * To support the above functionality, pressure and temperature variables, + * m_plast_ss and m_tlast_ss, are kept which store the last pressure and temperature + * used in the evaluation of standard state properties. + * + * This class is usually used for nearly incompressible phases. For those phases, it + * makes sense to change the equation of state independent variable from + * density to pressure. The variable m_Pcurrent contains the current value of the + * pressure within the phase. + * + * + *
+ *

Specification of Species Standard %State Properties

+ *
+ * + * All species are defined to have standard states that depend upon both + * the temperature and the pressure. The Margules approximation assumes + * symmetric standard states, where all of the standard state assume + * that the species are in pure component states at the temperatue + * and pressure of the solution. I don't think it prevents, however, + * some species from being dilute in the solution. + * + * + *
+ *

Specification of Solution Thermodynamic Properties

+ *
+ * + * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. + * Each of the interactions are binary interactions involving two of the species in the phase, denoted, Ai + * and Bi. + * This is the generalization of the Margules formulation for a phase + * that has more than 2 species. + * + * \f[ + * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) + * \f] + * \f[ + * H^E_i = n X_{Ai} X_{Bi} \left( h_{o,i} + h_{1,i} X_{Bi} \right) + * \f] + * \f[ + * S^E_i = n X_{Ai} X_{Bi} \left( s_{o,i} + s_{1,i} X_{Bi} \right) + * \f] + * + * where n is the total moles in the solution. + * + * The activity of a species defined in the phase is given by an excess + * Gibbs free energy formulation. + * + * \f[ + * a_k = \gamma_k X_k + * \f] + * + * where + * + * \f[ + * R T \ln( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} + * \f] + * + * Taking the derivatives results in the following expression + * + * \f[ + * R T \ln( \gamma_k )= \sum_i \left( \left( \delta_{Ai,k} X_{Bi} + \delta_{Bi,k} X_{Ai} - X_{Ai} X_{Bi} \right) + * \left( g^E_{o,i} + g^E_{1,i} X_{Bi} \right) + + * \left( \delta_{Bi,k} - X_{Bi} \right) X_{Ai} X_{Bi} g^E_{1,i} \right) + * \f] + * where + * \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ + * and where \f$ X_k \f$ is the mole fraction of species k. + * + * This object inherits from the class VPStandardStateTP. Therefore, the specification and + * calculation of all standard state and reference state values are handled at that level. Various functional + * forms for the standard state are permissible. + * The chemical potential for species k is equal to + * + * \f[ + * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) + * \f] + * + * The partial molar entropy for species k is given by the following relation, + * + * \f[ + * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * The partial molar enthalpy for species k is given by + * + * \f[ + * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * The partial molar volume for species k is + * + * \f[ + * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} + * \f] + * + * The partial molar Heat Capacity for species k is + * + * \f[ + * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} + * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} + * \f] + * + *
+ *

%Application within %Kinetics Managers

+ *
+ * + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^s_k, \f$ where \f$ C^s_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. + * The activity concentration,\f$ C^a_k \f$,is given by the following expression. + * + * \f[ + * C^a_k = C^s_k X_k = \frac{P}{R T} X_k + * \f] + * + * The standard concentration for species k is independent of k and equal to + * + * \f[ + * C^s_k = C^s = \frac{P}{R T} + * \f] + * + * For example, a bulk-phase binary gas reaction between species j and k, producing + * a new gas species l would have the + * following equation for its rate of progress variable, \f$ R^1 \f$, which has + * units of kmol m-3 s-1. + * + * \f[ + * R^1 = k^1 C_j^a C_k^a = k^1 (C^s a_j) (C^s a_k) + * \f] + * where + * \f[ + * C_j^a = C^s a_j \mbox{\quad and \quad} C_k^a = C^s a_k + * \f] + * + * + * \f$ C_j^a \f$ is the activity concentration of species j, and + * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^s \f$ + * is the standard concentration. \f$ a_j \f$ is + * the activity of species j which is equal to the mole fraction of j. + * + * The reverse rate constant can then be obtained from the law of microscopic reversibility + * and the equilibrium expression for the system. + * + * \f[ + * \frac{a_j a_k}{ a_l} = K_a^{o,1} = \exp(\frac{\mu^o_l - \mu^o_j - \mu^o_k}{R T} ) + * \f] + * + * \f$ K_a^{o,1} \f$ is the dimensionless form of the equilibrium constant, associated with + * the pressure dependent standard states \f$ \mu^o_l(T,P) \f$ and their associated activities, + * \f$ a_l \f$, repeated here: + * + * \f[ + * \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l) + * \f] + * + * We can switch over to expressing the equilibrium constant in terms of the reference + * state chemical potentials + * + * \f[ + * K_a^{o,1} = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{P} + * \f] + * + * The concentration equilibrium constant, \f$ K_c \f$, may be obtained by changing over + * to activity concentrations. When this is done: + * + * \f[ + * \frac{C^a_j C^a_k}{ C^a_l} = C^o K_a^{o,1} = K_c^1 = + * \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{RT} + * \f] + * + * %Kinetics managers will calculate the concentration equilibrium constant, \f$ K_c \f$, + * using the second and third part of the above expression as a definition for the concentration + * equilibrium constant. + * + * For completeness, the pressure equilibrium constant may be obtained as well + * + * \f[ + * \frac{P_j P_k}{ P_l P_{ref}} = K_p^1 = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) + * \f] + * + * \f$ K_p \f$ is the simplest form of the equilibrium constant for ideal gases. However, it isn't + * necessarily the simplest form of the equilibrium constant for other types of phases; \f$ K_c \f$ is + * used instead because it is completely general. + * + * The reverse rate of progress may be written down as + * \f[ + * R^{-1} = k^{-1} C_l^a = k^{-1} (C^o a_l) + * \f] + * + * where we can use the concept of microscopic reversibility to + * write the reverse rate constant in terms of the + * forward reate constant and the concentration equilibrium + * constant, \f$ K_c \f$. + * + * \f[ + * k^{-1} = k^1 K^1_c + * \f] + * + * \f$k^{-1} \f$ has units of s-1. + * + * + *
+ *

Instantiation of the Class

+ *
+ * + * + * The constructor for this phase is located in the default ThermoFactory + * for %Cantera. A new %IdealGasPhase may be created by the following code + * snippet: + * + * @code + * XML_Node *xc = get_XML_File("silane.xml"); + * XML_Node * const xs = xc->findNameID("phase", "silane"); + * ThermoPhase *silane_tp = newPhase(*xs); + * IdealGasPhase *silaneGas = dynamic_cast (silane_tp); + * @endcode + * + * or by the following constructor: + * + * @code + * XML_Node *xc = get_XML_File("silane.xml"); + * XML_Node * const xs = xc->findNameID("phase", "silane"); + * IdealGasPhase *silaneGas = new IdealGasPhase(*xs); + * @endcode + * + *
+ *

XML Example

+ *
+ * An example of an XML Element named phase setting up a IdealGasPhase + * object named silane is given below. + * + * + * @verbatim + + + Si H He + + H2 H HE SIH4 SI SIH SIH2 SIH3 H3SISIH SI2H6 + H2SISIH2 SI3H8 SI2 SI3 + + + + + + + @endverbatim + * + * The model attribute "IdealGas" of the thermo XML element identifies the phase as + * being of the type handled by the IdealGasPhase object. + * + * @ingroup thermoprops + * + + */ + class MixedSolventElectrolyte : public GibbsExcessVPSSTP { + + public: + + //! Constructor + /*! + * This doesn't do much more than initialize constants with + * default values for water at 25C. Water molecular weight + * comes from the default elements.xml file. It actually + * differs slightly from the IAPWS95 value of 18.015268. However, + * density conservation and therefore element conservation + * is the more important principle to follow. + */ + MixedSolventElectrolyte(); + + //! Construct and initialize a MixedSolventElectrolyte ThermoPhase object + //! directly from an xml input file + /*! + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + * + * @param inputFile Name of the input file containing the phase XML data + * to set up the object + * @param id ID of the phase in the input file. Defaults to the + * empty string. + */ + MixedSolventElectrolyte(std::string inputFile, std::string id = ""); + + //! Construct and initialize a MixedSolventElectrolyte ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML phase node containing the description of the phase + * @param id id attribute containing the name of the phase. + * (default is the empty string) + */ + MixedSolventElectrolyte(XML_Node& phaseRef, std::string id = ""); + + + //! Special constructor for a hard-coded problem + /*! + * + * @param testProb Hard-coded value. Only the value of 1 is + * used. It's for + * a LiKCl system + * -> test to predict the eutectic and liquidus correctly. + */ + MixedSolventElectrolyte(int testProb); + + //! Copy constructor + /*! + * Note this stuff will not work until the underlying phase + * has a working copy constructor + * + * @param b class to be copied + */ + MixedSolventElectrolyte(const MixedSolventElectrolyte& b); + + //! Assignment operator + /*! + * + * @param b class to be copied. + */ + MixedSolventElectrolyte& operator=(const MixedSolventElectrolyte &b); + + //! Destructor + virtual ~MixedSolventElectrolyte(); + + //! Duplication routine for objects which inherit from ThermoPhase. + /*! + * This virtual routine can be used to duplicate thermophase objects + * inherited from ThermoPhase even if the application only has + * a pointer to ThermoPhase to work with. + */ + virtual ThermoPhase *duplMyselfAsThermoPhase() const; + + /** + * + * @name Utilities + * @{ + */ + + + //! Equation of state type flag. + /*! + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The MolalityVPSSTP class also returns + * zero, as it is a non-complete class. + */ + virtual int eosType() const; + + //! Initialization of a phase using an xml file + /*! + * This routine is a precursor to + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseFile(std::string inputFile, std::string id); + + //! Import and initialize a phase + //! specification in an XML tree into the current object. + /*! + * Here we read an XML description of the phase. + * We import descriptions of the elements that make up the + * species in a phase. + * We import information about the species, including their + * reference state thermodynamic polynomials. We then freeze + * the state of the species. + * + * Then, we read the species molar volumes from the xml + * tree to finish the initialization. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void constructPhaseXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Molar Thermodynamic Properties + * @{ + */ + + + /** + * @} + * @name Utilities for Solvent ID and Molality + * @{ + */ + + + + + /** + * @} + * @name Mechanical Properties + * @{ + */ + + /** + * @} + * @name Potential Energy + * + * Species may have an additional potential energy due to the + * presence of external gravitation or electric fields. These + * methods allow specifying a potential energy for individual + * species. + * @{ + */ + + /** + * @} + * @name Activities, Standard States, and Activity Concentrations + * + * The activity \f$a_k\f$ of a species in solution is + * related to the chemical potential by \f[ \mu_k = \mu_k^0(T) + * + \hat R T \log a_k. \f] The quantity \f$\mu_k^0(T,P)\f$ is + * the chemical potential at unit activity, which depends only + * on temperature and pressure. + * @{ + */ + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + + /** + * The standard concentration \f$ C^0_k \f$ used to normalize + * the generalized concentration. In many cases, this quantity + * will be the same for all species in a phase - for example, + * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this + * reason, this method returns a single value, instead of an + * array. However, for phases in which the standard + * concentration is species-specific (e.g. surface species of + * different sizes), this method may be called with an + * optional parameter indicating the species. + * + * @param k species index. Defaults to zero. + */ + virtual doublereal standardConcentration(int k=0) const; + + /** + * Returns the natural logarithm of the standard + * concentration of the kth species + * + * @param k species index + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Get the array of non-dimensional molar-based activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + virtual void getActivityCoefficients(doublereal* ac) const; + + + + + //@} + /// @name Partial Molar Properties of the Solution + //@{ + + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ + virtual void getChemPotentials(doublereal* mu) const; + + /// Molar enthalpy. Units: J/kmol. + virtual doublereal enthalpy_mole() const; + + /// Molar entropy. Units: J/kmol. + virtual doublereal entropy_mole() const; + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + virtual doublereal cp_mole() const; + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + virtual doublereal cv_mole() const; + + //! Returns an array of partial molar enthalpies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * @param hbar Vector of returned partial molar enthalpies + * (length m_kk, units = J/kmol) + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * @param sbar Vector of returned partial molar entropies + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????????? + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * ??????????????? + * \f] + * + * @param cpbar Vector of returned partial molar heat capacities + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //! Get the species electrochemical potentials. + /*! + * These are partial molar quantities. + * This method adds a term \f$ Fz_k \phi_k \f$ to the + * to each chemical potential. + * + * Units: J/kmol + * + * @param mu output vector containing the species electrochemical potentials. + * Length: m_kk., units = J/kmol + */ + void getElectrochemPotentials(doublereal* mu) const; + + //! Get the array of temperature second derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param d2lnActCoeffdT2 Output vector of temperature 2nd derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const; + + //! Get the array of temperature derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param dlnActCoeffdT Output vector of temperature derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const; + + + + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + + /////////////////////////////////////////////////////// + // + // The methods below are not virtual, and should not + // be overloaded. + // + ////////////////////////////////////////////////////// + + /** + * @name Specific Properties + * @{ + */ + + + /** + * @name Setting the State + * + * These methods set all or part of the thermodynamic + * state. + * @{ + */ + + + + //@} + + /** + * @name Chemical Equilibrium + * Routines that implement the Chemical equilibrium capability + * for a single phase, based on the element-potential method. + * @{ + */ + + + + //@} + + + + /// The following methods are used in the process of constructing + /// the phase and setting its parameters from a specification in an + /// input file. They are not normally used in application programs. + /// To see how they are used, see files importCTML.cpp and + /// ThermoFactory.cpp. + + + /*! + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + /** + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void initThermoXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Derivatives of Thermodynamic Variables needed for Applications + * @{ + */ + + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space + /*! + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients - diagonal component + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the mole fraction. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX_diag Output vector of the diagonal component of the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const; + + //! Get the array of derivatives of the log activity coefficients wrt mole numbers - diagonal only + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction, + * molality, etc.) that represents the standard state. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN_diag Output vector of the diagonal entries for the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; + + + //! Get the array of derivatives of the log activity coefficients with respect to the ln species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * log of a species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) ; + + //@} + + private: + + //! Process an XML node called "binaryNeutralSpeciesParameters" + /*! + * This node contains all of the parameters necessary to describe + * the Margules model for a particular binary interaction. + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + * + * @param xmlBinarySpecies Reference to the XML_Node named "binaryNeutralSpeciesParameters" + * containing the binary interaction + */ + void readXMLBinarySpecies(XML_Node &xmlBinarySpecies); + + //! Resize internal arrays within the object that depend upon the number + //! of binary Margules interaction terms + /*! + * @param num Number of binary Margules interaction terms + */ + void resizeNumInteractions(const int num); + + + //! Initialize lengths of local variables after all species have + //! been identified. + void initLengths(); + + //! Update the activity coefficients + /*! + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + */ + void s_update_lnActCoeff() const; + + //! Update the derivative of the log of the activity coefficients wrt T + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt temperature. + */ + void s_update_dlnActCoeff_dT() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(mole fraction) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the mole fractions. + */ + void s_update_dlnActCoeff_dlnX_diag() const; + + //! Update the derivative of the log of the activity coefficients + //! wrt log(moles) - diagonal only + /*! + * This function will be called to update the internally storred diagonal entries for the + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the moles. + */ + void s_update_dlnActCoeff_dlnN_diag() const; + + //! Update the derivative of the log of the activity coefficients wrt log(moles_m) + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt logarithm of the mole number of species + */ + void s_update_dlnActCoeff_dlnN() const; + + + private: + //! Error function + /*! + * Print an error string and exit + * + * @param msg Message to be printed + */ + doublereal err(std::string msg) const; + + protected: + + + //! number of binary interaction expressions + int numBinaryInteractions_; + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_b_ij; + + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_c_ij; + + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_HE_d_ij; + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_b_ij; + + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_c_ij; + + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_SE_d_ij; + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_b_ij; + + //! Enthalpy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_c_ij; + + //! Enthalpy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VHE_d_ij; + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_b_ij; + + //! Entropy term for the ternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_c_ij; + + //! Entropy term for the quaternary mole fraction interaction of the + //! excess gibbs free energy expression + mutable vector_fp m_VSE_d_ij; + + + + //! vector of species indices representing species A in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species A. + */ + vector_int m_pSpecies_A_ij; + + //! vector of species indices representing species B in the interaction + /*! + * Each Margules excess Gibbs free energy term involves two species, A and B. + * This vector identifies species B. + */ + vector_int m_pSpecies_B_ij; + + //! form of the Margules interaction expression + /*! + * Currently there is only one form. + */ + int formMargules_; + + //! form of the temperatuer dependence of the Margules interaction expression + /*! + * Currently there is only one form -> constant wrt temperature. + */ + int formTempModel_; + + + }; + + + +} + +#endif + + + + + diff --git a/Cantera/src/thermo/MixtureFugacityTP.cpp b/Cantera/src/thermo/MixtureFugacityTP.cpp new file mode 100644 index 000000000..21e032fa6 --- /dev/null +++ b/Cantera/src/thermo/MixtureFugacityTP.cpp @@ -0,0 +1,1367 @@ +/** + * @file MixtureFugacityTP.cpp + * Methods file for a derived class of ThermoPhase that handles + * non-ideal mixtures based on the fugacity models (see \ref thermoprops and + * class \link Cantera::MixtureFugacityTP MixtureFugacityTP\endlink). + * + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Author: hkmoffa $ + * $Date: 2010-01-17 12:08:00 -0700 (Sun, 17 Jan 2010) $ + * $Revision: 388 $ + */ + +// turn off warnings under Windows +#ifdef WIN32 +#pragma warning(disable:4786) +#pragma warning(disable:4503) +#endif + +#include "MixtureFugacityTP.h" +#include "VPSSMgr.h" +#include "PDSS.h" + + +#ifndef MIN +# define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) +#endif +using namespace std; + +namespace Cantera { + + + + //==================================================================================================================== + /* + * Default constructor + */ + MixtureFugacityTP::MixtureFugacityTP() : + ThermoPhase(), + m_Pcurrent(-1.0), + moleFractions_(0), + iState_(FLUID_GAS), + forcedState_(FLUID_UNDEFINED), + m_Tlast_ref(-1.0), + m_logc0(0.0), + m_h0_RT(0), + m_cp0_R(0), + m_g0_RT(0), + m_s0_R(0) + { + } + //==================================================================================================================== + /* + * Copy Constructor: + * + * Note this stuff will not work until the underlying phase + * has a working copy constructor. + * + * The copy constructor just calls the assignment operator + * to do the heavy lifting. + */ + MixtureFugacityTP::MixtureFugacityTP(const MixtureFugacityTP &b) : + ThermoPhase(), + m_Pcurrent(-1.0), + moleFractions_(0), + iState_(FLUID_GAS), + forcedState_(FLUID_UNDEFINED), + m_Tlast_ref(-1.0), + m_logc0(0.0), + m_h0_RT(0), + m_cp0_R(0), + m_g0_RT(0), + m_s0_R(0) + { + MixtureFugacityTP::operator=(b); + } + //==================================================================================================================== + /* + * operator=() + * + * Note this stuff will not work until the underlying phase + * has a working assignment operator + */ + MixtureFugacityTP& + MixtureFugacityTP::operator=(const MixtureFugacityTP &b) { + if (&b != this) { + /* + * Mostly, this is a passthrough to the underlying + * assignment operator for the ThermoPhase parent object. + */ + ThermoPhase::operator=(b); + /* + * However, we have to handle data that we own. + */ + m_Pcurrent = b.m_Pcurrent; + moleFractions_ = b.moleFractions_; + iState_ = b.iState_; + forcedState_ = b.forcedState_; + m_Tlast_ref = b.m_Tlast_ref; + m_logc0 = b.m_logc0; + m_h0_RT = b.m_h0_RT; + m_cp0_R = b.m_cp0_R; + m_g0_RT = b.m_g0_RT; + m_s0_R = b.m_s0_R; + /* + * The VPSSMgr object contains shallow pointers. Whenever you have shallow + * pointers, they have to be fixed up to point to the correct objects refering + * back to this ThermoPhase's properties. + */ + //m_VPSS_ptr->initAllPtrs(this, m_spthermo); + /* + * The PDSS objects contains shallow pointers. Whenever you have shallow + * pointers, they have to be fixed up to point to the correct objects refering + * back to this ThermoPhase's properties. This function also sets m_VPSS_ptr + * so it occurs after m_VPSS_ptr is set. + */ + + /* + * Ok, the VPSSMgr object is ready for business. + * We need to resync the temperature and the pressure of the new standard states + * with what is storred in this object. + */ + // m_VPSS_ptr->setState_TP(m_Tlast_ss, m_Plast_ss); + } + return *this; + } + //==================================================================================================================== + /* + * ~MixtureFugacityTP(): (virtual) + * + */ + MixtureFugacityTP::~MixtureFugacityTP() { + + } + + /* + * Duplication function. + * This calls the copy constructor for this object. + */ + ThermoPhase* MixtureFugacityTP::duplMyselfAsThermoPhase() const { + MixtureFugacityTP* vptp = new MixtureFugacityTP(*this); + return (ThermoPhase *) vptp; + } + //==================================================================================================================== + // This method returns the convention used in specification + // of the standard state, of which there are currently two, + // temperature based, and variable pressure based. + /* + * Currently, there are two standard state conventions: + * - Temperature-based activities + * cSS_CONVENTION_TEMPERATURE 0 + * - default + * + * - Variable Pressure and Temperature -based activities + * cSS_CONVENTION_VPSS 1 + */ + int MixtureFugacityTP::standardStateConvention() const { + return cSS_CONVENTION_TEMPERATURE; + } + //==================================================================================================================== + // Set the solution branch to force the ThermoPhase to exist on one branch or another + /* + * @param solnBranch Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means unrestricted. + * Values of zero or greater refer to species dominated condensed phases. + */ + void MixtureFugacityTP::setForcedSolutionBranch(int solnBranch) { + forcedState_ = solnBranch; + } + //==================================================================================================================== + // Report the solution branch which the solution is restricted to + /* + * @return Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means unrestricted. + * Values of zero or greater refer to species dominated condensed phases. + */ + int MixtureFugacityTP::forcedSolutionBranch() const { + return forcedState_; + } + //==================================================================================================================== + // Report the solution branch which the solution is actually on + /* + * @return Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means superfluid.. + * Values of zero or greater refer to species dominated condensed phases. + */ + int MixtureFugacityTP::reportSolnBranchActual() const { + return iState_; + } + //==================================================================================================================== + + /* + * ------------Molar Thermodynamic Properties ------------------------- + */ + //==================================================================================================================== + + doublereal MixtureFugacityTP::err(std::string msg) const { + throw CanteraError("MixtureFugacityTP","Base class method " + +msg+" called. Equation of state type: "+int2str(eosType())); + return 0; + } + //==================================================================================================================== + /* + * ---- Partial Molar Properties of the Solution ----------------- + */ + //==================================================================================================================== + /* + * Get the array of non-dimensional species chemical potentials + * These are partial molar Gibbs free energies. + * \f$ \mu_k / \hat R T \f$. + * Units: unitless + * + * We close the loop on this function, here, calling + * getChemPotentials() and then dividing by RT. + */ + void MixtureFugacityTP::getChemPotentials_RT(doublereal* muRT) const{ + getChemPotentials(muRT); + doublereal invRT = 1.0 / _RT(); + for (int k = 0; k < m_kk; k++) { + muRT[k] *= invRT; + } + } + //==================================================================================================================== + /* + * ----- Thermodynamic Values for the Species Standard States States ---- + */ + void MixtureFugacityTP::getStandardChemPotentials(doublereal* g) const { + _updateReferenceStateThermo(); + copy(m_g0_RT.begin(), m_g0_RT.end(), g); + doublereal RT = _RT(); + double tmp = log (pressure() /m_spthermo->refPressure()); + for (int k = 0; k < m_kk; k++) { + g[k] = RT * (g[k] + tmp); + } + } + //==================================================================================================================== + void MixtureFugacityTP::getEnthalpy_RT(doublereal* hrt) const { + getEnthalpy_RT_ref(hrt); + } + //================================================================================================ +#ifdef H298MODIFY_CAPABILITY + // Modify the value of the 298 K Heat of Formation of one species in the phase (J kmol-1) + /* + * The 298K heat of formation is defined as the enthalpy change to create the standard state + * of the species from its constituent elements in their standard states at 298 K and 1 bar. + * + * @param k Species k + * @param Hf298New Specify the new value of the Heat of Formation at 298K and 1 bar + */ + void MixtureFugacityTP::modifyOneHf298SS(const int k, const doublereal Hf298New) { + m_spthermo->modifyOneHf298(k, Hf298New); + m_Tlast_ref += 0.0001234; + } +#endif + //==================================================================================================================== + /* + * Get the array of nondimensional entropy functions for the + * standard state species + * at the current T and P of the solution. + */ + void MixtureFugacityTP::getEntropy_R(doublereal* sr) const { + _updateReferenceStateThermo(); + copy(m_s0_R.begin(), m_s0_R.end(), sr); + double tmp = log (pressure() /m_spthermo->refPressure()); + for (int k = 0; k < m_kk; k++) { + sr[k] -= tmp; + } + } + //==================================================================================================================== + /* + * Get the nondimensional gibbs function for the species + * standard states at the current T and P of the solution. + */ + void MixtureFugacityTP::getGibbs_RT(doublereal* grt) const { + _updateReferenceStateThermo(); + copy(m_g0_RT.begin(), m_g0_RT.end(), grt); + double tmp = log (pressure() /m_spthermo->refPressure()); + for (int k = 0; k < m_kk; k++) { + grt[k] += tmp; + } + } + //==================================================================================================================== + /* + * get the pure Gibbs free energies of each species assuming + * it is in its standard state. This is the same as + * getStandardChemPotentials(). + */ + void MixtureFugacityTP::getPureGibbs(doublereal* g) const { + _updateReferenceStateThermo(); + scale(m_g0_RT.begin(), m_g0_RT.end(), g, _RT()); + double tmp = log (pressure() /m_spthermo->refPressure()); + tmp *= _RT(); + for (int k = 0; k < m_kk; k++) { + g[k] += tmp; + } + } + //==================================================================================================================== + /* + * Returns the vector of nondimensional + * internal Energies of the standard state at the current temperature + * and pressure of the solution for each species. + */ + void MixtureFugacityTP::getIntEnergy_RT(doublereal* urt) const { + _updateReferenceStateThermo(); + copy(m_h0_RT.begin(), m_h0_RT.end(), urt); + doublereal p = pressure(); + doublereal tmp = p / _RT(); + doublereal v0 = _RT() / p; + for (int i = 0; i < m_kk; i++) { + urt[i] -= tmp * v0; + } + } + //==================================================================================================================== + /* + * Get the nondimensional heat capacity at constant pressure + * function for the species + * standard states at the current T and P of the solution. + */ + void MixtureFugacityTP::getCp_R(doublereal* cpr) const { + _updateReferenceStateThermo(); + copy(m_cp0_R.begin(), m_cp0_R.end(), cpr); + } + //==================================================================================================================== + /* + * Get the molar volumes of the species standard states at the current + * T and P of the solution. + * units = m^3 / kmol + * + * @param vol Output vector containing the standard state volumes. + * Length: m_kk. + */ + void MixtureFugacityTP::getStandardVolumes(doublereal *vol) const { + _updateReferenceStateThermo(); + doublereal v0 = _RT() / pressure(); + for (int i = 0; i < m_kk; i++) { + vol[i]= v0; + } + } + //==================================================================================================================== + /* + * ----- Thermodynamic Values for the Species Reference States ---- + */ + + /* + * Returns the vector of nondimensional enthalpies of the + * reference state at the current temperature of the solution and + * the reference pressure for the species. + */ + void MixtureFugacityTP::getEnthalpy_RT_ref(doublereal *hrt) const { + _updateReferenceStateThermo(); + copy(m_h0_RT.begin(), m_h0_RT.end(), hrt); + } + //==================================================================================================================== + /* + * Returns the vector of nondimensional + * enthalpies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + */ + void MixtureFugacityTP::getGibbs_RT_ref(doublereal *grt) const { + _updateReferenceStateThermo(); + copy(m_g0_RT.begin(), m_g0_RT.end(), grt); + } + //==================================================================================================================== + /* + * Returns the vector of the + * gibbs function of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * units = J/kmol + * + * This is filled in here so that derived classes don't have to + * take care of it. + */ + void MixtureFugacityTP::getGibbs_ref(doublereal *g) const { + const array_fp& gibbsrt = gibbs_RT_ref(); + scale(gibbsrt.begin(), gibbsrt.end(), g, _RT()); + } + //==================================================================================================================== + const vector_fp & MixtureFugacityTP::gibbs_RT_ref() const { + _updateReferenceStateThermo(); + return m_g0_RT; + } + //==================================================================================================================== + /* + * Returns the vector of nondimensional + * entropies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + */ + void MixtureFugacityTP::getEntropy_R_ref(doublereal *er) const { + _updateReferenceStateThermo(); + copy(m_s0_R.begin(), m_s0_R.end(), er); + return; + } + //==================================================================================================================== + /* + * Returns the vector of nondimensional + * constant pressure heat capacities of the reference state + * at the current temperature of the solution + * and reference pressure for the species. + */ + void MixtureFugacityTP::getCp_R_ref(doublereal *cpr) const { + _updateReferenceStateThermo(); + copy(m_cp0_R.begin(), m_cp0_R.end(), cpr); + } + //==================================================================================================================== + /* + * Get the molar volumes of the species reference states at the current + * T and reference pressure of the solution. + * + * units = m^3 / kmol + */ + void MixtureFugacityTP::getStandardVolumes_ref(doublereal *vol) const { + _updateReferenceStateThermo(); + double pp = refPressure(); + doublereal v0 = _RT() / pp; + for (int i = 0; i < m_kk; i++) { + vol[i]= v0; + } + } + //==================================================================================================================== + // Set the initial state of the phase to the conditions specified in the state XML element. + /* + * + * This method sets the temperature, pressure, and mole fraction vector to a set default value. + * We modify the default behavior here so that TP is evaluated at the same time. + * + * @param state AN XML_Node object corresponding to + * the "state" entry for this phase in the + * input file. + */ + void MixtureFugacityTP::setStateFromXML(const XML_Node& state) { + int doTP = 0; + string comp = ctml::getChildValue(state,"moleFractions"); + if (comp != "") { + // not overloaded in current object -> phase state is not calculated. + setMoleFractionsByName(comp); + doTP = 1; + } else { + comp = ctml::getChildValue(state,"massFractions"); + if (comp != "") { + // not overloaded in current object -> phase state is not calculated. + setMassFractionsByName(comp); + doTP = 1; + } + } + double t = temperature(); + if (state.hasChild("temperature")) { + t = ctml::getFloat(state, "temperature", "temperature"); + doTP = 1; + } + if (state.hasChild("pressure")) { + double p = ctml::getFloat(state, "pressure", "pressure"); + setState_TP(t, p); + } else if (state.hasChild("density")) { + double rho = ctml::getFloat(state, "density", "density"); + setState_TR(t, rho); + } else if (doTP) { + double rho = State::density(); + setState_TR(t, rho); + } + } + //==================================================================================================================== + /* + * Perform initializations after all species have been + * added. + */ + void MixtureFugacityTP::initThermo() { + initLengths(); + ThermoPhase::initThermo(); + } + //==================================================================================================================== + /* + * Initialize the internal lengths. + * (this is not a virtual function) + */ + void MixtureFugacityTP::initLengths() { + m_kk = nSpecies(); + moleFractions_.resize(m_kk, 0.0); + moleFractions_[0] = 1.0; + m_h0_RT.resize(m_kk, 0.0); + m_cp0_R.resize(m_kk, 0.0); + m_g0_RT.resize(m_kk, 0.0); + m_s0_R.resize(m_kk, 0.0); + } + //==================================================================================================================== + void MixtureFugacityTP::setTemperature(const doublereal temp) { + _updateReferenceStateThermo(); + setState_TR(temperature(), density()); + } + //==================================================================================================================== + void MixtureFugacityTP::setPressure(doublereal p) { + setState_TP(temperature(), p); + // double chemPot[5], mf[5]; + // getMoleFractions(mf); + // getChemPotentials(chemPot); + // for (int i = 0; i < m_kk; i++) { + // printf(" MixFug:setPres: mu(%d = %g) = %18.8g\n", i, mf[i], chemPot[i]); + // } + } + //==================================================================================================================== + void MixtureFugacityTP::setMassFractions(const doublereal* const y) { + State::setMassFractions(y); + getMoleFractions(DATA_PTR(moleFractions_)); + } + //==================================================================================================================== + void MixtureFugacityTP::setMassFractions_NoNorm(const doublereal* const y) { + State::setMassFractions_NoNorm(y); + getMoleFractions(DATA_PTR(moleFractions_)); + } + //==================================================================================================================== + void MixtureFugacityTP::setMoleFractions(const doublereal* const x) { + State::setMoleFractions(x); + getMoleFractions(DATA_PTR(moleFractions_)); + } + //==================================================================================================================== + void MixtureFugacityTP::setMoleFractions_NoNorm(const doublereal* const x) { + State::setMoleFractions_NoNorm(x); + getMoleFractions(DATA_PTR(moleFractions_)); + } + //==================================================================================================================== + void MixtureFugacityTP::setConcentrations(const doublereal* const c) { + State::setConcentrations(c); + getMoleFractions(DATA_PTR(moleFractions_)); + } + //==================================================================================================================== + void MixtureFugacityTP::setMoleFractions_NoState(const doublereal* const x) { + State::setMoleFractions(x); + getMoleFractions(DATA_PTR(moleFractions_)); + updateMixingExpressions(); + } + //==================================================================================================================== + void MixtureFugacityTP::calcDensity() { + err("MixtureFugacityTP::calcDensity() called, but EOS for phase is not known"); + } + //==================================================================================================================== + + void MixtureFugacityTP::setState_TP(doublereal t, doublereal pres) { + /* + * A pretty tricky algorithm is needed here, due to problems involving + * standard states of real fluids. For those cases you need + * to combine the T and P specification for the standard state, or else + * you may venture into the forbidden zone, especially when nearing the + * triple point. + * Therefore, we need to do the standard state thermo calc with the + * (t, pres) combo. + */ + getMoleFractions(DATA_PTR(moleFractions_)); + + + State::setTemperature(t); + _updateReferenceStateThermo(); + // Depends on the mole fractions and the temperature + updateMixingExpressions(); + // setPressure(pres); + m_Pcurrent = pres; + // double mmw = meanMolecularWeight(); + + if (forcedState_ == FLUID_UNDEFINED) { + double rhoNow = State::density(); + double rho = densityCalc(t, pres, iState_, rhoNow); + if (rho > 0.0) { + State::setDensity(rho); + m_Pcurrent = pres; + iState_ = phaseState(true); + } else { + if (rho < -1.5) { + rho = densityCalc(t, pres, FLUID_UNDEFINED , rhoNow); + if (rho > 0.0) { + State::setDensity(rho); + m_Pcurrent = pres; + iState_ = phaseState(true); + } else { + throw CanteraError("MixtureFugacityTP::setState_TP()", "neg rho"); + } + } else { + throw CanteraError("MixtureFugacityTP::setState_TP()", "neg rho"); + } + } + + + + } else if (forcedState_ == FLUID_GAS) { + // Normal density calculation + if (iState_ < FLUID_LIQUID_0) { + double rhoNow = State::density(); + double rho = densityCalc(t, pres, iState_, rhoNow); + if (rho > 0.0) { + State::setDensity(rho); + m_Pcurrent = pres; + iState_ = phaseState(true); + if (iState_ >= FLUID_LIQUID_0) { + throw CanteraError("MixtureFugacityTP::setState_TP()", "wrong state"); + } + } else { + throw CanteraError("MixtureFugacityTP::setState_TP()", "neg rho"); + } + + } + + + } else if (forcedState_ > FLUID_LIQUID_0) { + if (iState_ >= FLUID_LIQUID_0) { + double rhoNow = State::density(); + double rho = densityCalc(t, pres, iState_, rhoNow); + if (rho > 0.0) { + State::setDensity(rho); + m_Pcurrent = pres; + iState_ = phaseState(true); + if (iState_ == FLUID_GAS) { + throw CanteraError("MixtureFugacityTP::setState_TP()", "wrong state"); + } + } else { + throw CanteraError("MixtureFugacityTP::setState_TP()", "neg rho"); + } + + } + } + + + + //setTemperature(t); + //setPressure(pres); + //calcDensity(); + } + //==================================================================================================================== + // Set the internally storred temperature (K) and density (kg/m^3) + /* + * This overrides the default behavior. In addition to just storring the state in the object, we need to do + * an equation of state calculation and figure out what phase state we are in. + * + * @param t Temperature in kelvin + * @param rho Density (kg/m^3) + */ + void MixtureFugacityTP::setState_TR(doublereal T, doublereal rho) { + getMoleFractions(DATA_PTR(moleFractions_)); + State::setTemperature(T); + _updateReferenceStateThermo(); + State::setDensity(rho); + doublereal mv = molarVolume(); + // depends on mole fraction and temperature + updateMixingExpressions(); + + m_Pcurrent = pressureCalc(T, mv); + iState_ = phaseState(true); + + // printf("setState_TR: state at T = %g, rho = %g, mv = %g, P = %20.13g, iState = %d\n", T, rho, mv, m_Pcurrent, iState_); + } + + //==================================================================================================================== + // Set the temperature (K), pressure (Pa), and mole fractions. + /* + * Note, the mole fractions are set first before the pressure is set. + * Setting the pressure may involve the solution of a nonlinear equation. + * + * @param t Temperature (K) + * @param p Pressure (Pa) + * @param x Vector of mole fractions. + * Length is equal to m_kk. + */ + void MixtureFugacityTP::setState_TPX(doublereal t, doublereal p, const doublereal* x) { + setMoleFractions_NoState(x); + setState_TP(t,p); + } + //==================================================================================================================== + /* + * Import and initialize a ThermoPhase object + * + * param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + * + * This routine initializes the lengths in the current object and + * then calls the parent routine. + */ + void MixtureFugacityTP::initThermoXML(XML_Node& phaseNode, std::string id) { + MixtureFugacityTP::initLengths(); + + //m_VPSS_ptr->initThermo(); + + // m_VPSS_ptr->initThermoXML(phaseNode, id); + ThermoPhase::initThermoXML(phaseNode, id); + } + //==================================================================================================================== + doublereal MixtureFugacityTP::z() const { + doublereal p = pressure(); + doublereal rho = density(); + doublereal mmw = meanMolecularWeight(); + doublereal molarV = mmw / rho; + doublereal rt = _RT(); + doublereal zz = p * molarV / rt; + return zz; + } + //==================================================================================================================== + doublereal MixtureFugacityTP::sresid() const { + throw CanteraError("MixtureFugacityTP::sresid()", "Base Class: not implemented"); + return 0.0; + } + //==================================================================================================================== + doublereal MixtureFugacityTP::hresid() const { + throw CanteraError("MixtureFugacityTP::hresid()", "Base Class: not implemented"); + return 0.0; + } + //==================================================================================================================== + doublereal MixtureFugacityTP::psatEst(doublereal TKelvin) const { + doublereal tcrit = critTemperature(); + doublereal pcrit = critPressure(); + doublereal tt = tcrit/TKelvin; + if (tt < 1.0) { + return pcrit; + } + doublereal lpr = -0.8734*tt*tt - 3.4522*tt + 4.2918; + return pcrit*exp(lpr); + } + //==================================================================================================================== + doublereal MixtureFugacityTP::liquidVolEst(doublereal TKelvin, doublereal &pres) const { + throw CanteraError("MixtureFugacityTP::liquidVolEst()", "unimplemented"); + return 0.0; + } + //==================================================================================================================== + /* + * Calculates the density given the temperature and the pressure, + * and a guess at the density. Note, below T_c, this is a + * multivalued function. This function assumes that the phase is on one side of the vapor dome + * or the other. It does not allow for crosses of the vapor dome. + * + * parameters: + * temperature: Kelvin + * pressure : Pressure in Pascals (Newton/m**2) + * phase : guessed phase of water + * : -1: no guessed phase + * rhoguess : guessed density of the water + * + * -1.0 no guessed density + * + * If a problem is encountered, a negative 1 is returned. + * + * @TODO make this a const function + */ + doublereal MixtureFugacityTP::densityCalc(doublereal TKelvin, doublereal presPa, + int phase, doublereal rhoguess) { + double tcrit = critTemperature(); + doublereal mmw = meanMolecularWeight(); + // double pcrit = critPressure(); + // doublereal deltaGuess = 0.0; + if (rhoguess == -1.0) { + if (phase != -1) { + if (TKelvin > tcrit) { + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } else { + if (phase == FLUID_GAS || phase == FLUID_SUPERCRIT) { + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } else if (phase >= FLUID_LIQUID_0) { + double lqvol = liquidVolEst(TKelvin, presPa); + rhoguess = mmw / lqvol; + } + } + } else { + /* + * Assume the Gas phase initial guess, if nothing is + * specified to the routine + */ + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } + + } + + double molarVolBase = mmw / rhoguess; + double molarVolLast = molarVolBase; + double vc = mmw / critDensity(); + /* + * molar volume of the spinodal at the current temperature and mole fractions. this will + * be updated as we go. + */ + double molarVolSpinodal = vc; + doublereal pcheck = 1.0E-30 + 1.0E-8 * presPa; + doublereal presBase, dpdVBase, delMV; + bool conv = false; + /* + * We start on one side of the vc and stick with that side + */ + bool gasSide = molarVolBase > vc; + if (gasSide) { + molarVolLast = (GasConstant * TKelvin)/presPa; + } else { + molarVolLast = liquidVolEst(TKelvin, presPa); + } + + /* + * OK, now we do a small solve to calculate the molar volume given the T,P value. + * The algorithm is taken from dfind() + */ + for (int n = 0; n < 200; n++) { + + /* + * Calculate the predicted reduced pressure, pred0, based on the + * current tau and dd. + */ + + /* + * Calculate the derivative of the predicted pressure + * wrt the molar volume. + * This routine also returns the pressure, presBase + */ + dpdVBase = dpdVCalc(TKelvin, molarVolBase, presBase); + + /* + * If dpdV is positve, then we are in the middle of the + * 2 phase region and beyond the spinodal stability curve. We need to adjust + * the initial guess outwards and start a new iteration. + */ + if (dpdVBase >= 0.0) { + if (TKelvin > tcrit) { + throw CanteraError("", "confused"); + } + /* + * TODO Spawn a calculation for the value of the spinodal point that is + * very accurate. Answer the question as to wethera solution is + * possible on the current side of the vapor dome. + */ + if (gasSide) { + if (molarVolBase >= vc) { + molarVolSpinodal = molarVolBase; + molarVolBase = 0.5 * (molarVolLast + molarVolSpinodal); + } else { + molarVolBase = 0.5 * (molarVolLast + molarVolSpinodal); + } + } else { + if (molarVolBase <= vc) { + molarVolSpinodal = molarVolBase; + molarVolBase = 0.5 * (molarVolLast + molarVolSpinodal); + } else { + molarVolBase = 0.5 * (molarVolLast + molarVolSpinodal); + } + } + continue; + } + + /* + * Check for convergence + */ + if (fabs(presBase-presPa) < pcheck) { + conv = true; + break; + } + + /* + * Dampen and crop the update + */ + doublereal dpdV = dpdVBase; + if (n < 10) { + dpdV = dpdVBase * 1.5; + } + // if (dpdV > -0.001) dpdV = -0.001; + + /* + * Formulate the update to the molar volume by + * Newton's method. Then, crop it to a max value + * of 0.1 times the current volume + */ + delMV = - (presBase - presPa) / dpdV; + if (!gasSide || delMV < 0.0) { + if (fabs(delMV) > 0.2 * molarVolBase) { + delMV = delMV / fabs(delMV) * 0.2 * molarVolBase; + } + } + /* + * Only go 1/10 the way towards the spinodal at any one time. + */ + if (TKelvin < tcrit) { + if (gasSide) { + if (delMV < 0.0) { + if (-delMV > 0.5 * (molarVolBase - molarVolSpinodal)) { + delMV = - 0.5 * (molarVolBase - molarVolSpinodal); + } + } + } else { + if (delMV > 0.0) { + if (delMV > 0.5 * (molarVolSpinodal - molarVolBase)) { + delMV = 0.5 * (molarVolSpinodal - molarVolBase); + } + } + } + } + /* + * updated the molar volume value + */ + molarVolLast = molarVolBase; + molarVolBase += delMV; + + + if (fabs(delMV/molarVolBase) < 1.0E-14) { + conv = true; + break; + } + + /* + * Check for negative molar volumes + */ + if (molarVolBase <= 0.0) { + molarVolBase = MIN(1.0E-30, fabs(delMV*1.0E-4)); + } + + } + + + /* + * Check for convergence, and return 0.0 if it wasn't achieved. + */ + double densBase = 0.0; + if (! conv) { + molarVolBase = 0.0; + throw CanteraError("MixtureFugacityTP::densityCalc()", "Process didnot converge"); + } else { + densBase = mmw / molarVolBase; + } + return densBase; + } + //==================================================================================================================== + void MixtureFugacityTP::updateMixingExpressions() { + + } + //==================================================================================================================== + MixtureFugacityTP::spinodalFunc::spinodalFunc(MixtureFugacityTP *tp) : + ResidEval(), + m_tp(tp) + { + } + //==================================================================================================================== + int MixtureFugacityTP::spinodalFunc::evalSS(const doublereal t, const doublereal * const y, + doublereal * const r) { + int status = 0; + doublereal molarVol = y[0]; + doublereal tt = m_tp->temperature(); + doublereal pp; + doublereal val = m_tp->dpdVCalc(tt, molarVol, pp); + r[0] = val; + return status; + } + //==================================================================================================================== + // Utility routine in the calculation of the saturation pressure + /* + * Private routine + * + * @param TKelvin temperature (kelvin) + * @param pres pressure (Pascal) + * @param densLiq Output density of liquid + * @param densGas output density of gas + * @param delGRT output delGRT + * + * @return Returns zero if both the gas and the liquid states are found for a given pressure. + + */ + int MixtureFugacityTP::corr0(doublereal TKelvin, doublereal pres, doublereal &densLiqGuess, + doublereal &densGasGuess, doublereal &liqGRT, doublereal &gasGRT) { + + int retn = 0; + doublereal densLiq = densityCalc(TKelvin, pres, FLUID_LIQUID_0, densLiqGuess); + if (densLiq <= 0.0) { + // throw Cantera::CanteraError("MixtureFugacityTP::corr0", + // "Error occurred trying to find liquid density at (T,P) = " + // + Cantera::fp2str(TKelvin) + " " + Cantera::fp2str(pres)); + retn = -1; + } else { + densLiqGuess = densLiq; + setState_TR(TKelvin, densLiq); + liqGRT = gibbs_mole() / _RT(); + } + + doublereal densGas = densityCalc(TKelvin, pres, FLUID_GAS, densGasGuess); + if (densGas <= 0.0) { + //throw Cantera::CanteraError("MixtureFugacityTP::corr0", + // "Error occurred trying to find gas density at (T,P) = " + // + Cantera::fp2str(TKelvin) + " " + Cantera::fp2str(pres)); + if (retn == -1) { + throw Cantera::CanteraError("MixtureFugacityTP::corr0", + "Error occurred trying to find gas density at (T,P) = " + + Cantera::fp2str(TKelvin) + " " + Cantera::fp2str(pres)); + } + retn = -2; + } else { + densGasGuess = densGas; + setState_TR(TKelvin, densGas); + gasGRT = gibbs_mole() / _RT(); + } + // delGRT = gibbsLiqRT - gibbsGasRT; + return retn; + } + //==================================================================================================================== + // Returns the Phase State flag for the current state of the object + /* + * @param checkState If true, this function does a complete check to see where + * in paramters space we are + * + * There are three values: + * WATER_GAS below the critical temperature but below the critical density + * WATER_LIQUID below the critical temperature but above the critical density + * WATER_SUPERCRIT above the critical temperature + */ + int MixtureFugacityTP::phaseState(bool checkState) const { + int state; + if (checkState) { + double t = temperature(); + double tcrit = critTemperature(); + double rhocrit = critDensity(); + if (t >= tcrit) { + state = FLUID_SUPERCRIT; + return state; + } + double tmid = tcrit - 100.; + if (tmid < 0.0) { + tmid = tcrit / 2.0; + } + double pp = psatEst(tmid); + double mmw = meanMolecularWeight(); + double molVolLiqTmid = liquidVolEst(tmid, pp); + double molVolGasTmid = GasConstant * tmid / (pp); + double densLiqTmid = mmw / molVolLiqTmid; + double densGasTmid = mmw / molVolGasTmid; + double densMidTmid = 0.5 * (densLiqTmid + densGasTmid); + doublereal rhoMid = rhocrit + (t - tcrit) * (rhocrit - densMidTmid) / (tcrit - tmid); + + double rho = density(); + int iStateGuess = FLUID_LIQUID_0; + if (rho < rhoMid) { + iStateGuess = FLUID_GAS; + } + double molarVol = mmw / rho; + double presCalc; + + double dpdv = dpdVCalc(t, molarVol, presCalc); + if (dpdv < 0.0) { + state = iStateGuess; + } else { + state = FLUID_UNSTABLE; + } + + } + return state; + } + //==================================================================================================================== + // Return the value of the density at the liquid spinodal point (on the liquid side) + // for the current temperature. + /* + * @return returns the density with units of kg m-3 + */ + doublereal MixtureFugacityTP::densSpinodalLiquid() const { + throw CanteraError("", "unimplmented"); + return 0.0; + } + //==================================================================================================================== + // Return the value of the density at the gas spinodal point (on the gas side) + // for the current temperature. + /* + * @return returns the density with units of kg m-3 + */ + doublereal MixtureFugacityTP::densSpinodalGas() const { + throw CanteraError("", "unimplmented"); + return 0.0; + } + //==================================================================================================================== + // Calculate the saturation pressure at the current mixture content for the given temperature + /* + * This is a non-const routine that is public. + * + * The algorithm for this routine has undergone quite a bit of work. It probably needs more work. + * However, it seems now to be fairly robust. + * The key requirement is to find an initial pressure where both the liquid and the gas exist. This + * is not as easy as it sounds, and it gets exceedingly hard as the critical temperature is approached + * from below. + * Once we have this initial state, then we seek to equilibrate the gibbs free energies of the + * gas and liquid and use the formula + * + * dp = VdG + * + * to create an update condition for deltaP using + * + * - (Gliq - Ggas) = (Vliq - Vgas) (deltaP) + * + * + * + * @param TKelvin (input) Temperature (Kelvin) + * @param molarVolGas (return) Molar volume of the gas + * @param molarVolLiquid (return) Molar volume of the liquid + * + * @return Returns the saturation pressure at the given temperature + * + * @TODO Suggestions for the future would be to switch it to an algorithm that uses the gas molar volume + * and the liquid molar volumes as the fundamental unknowns. + * + */ + doublereal MixtureFugacityTP::calculatePsat(doublereal TKelvin, doublereal &molarVolGas, + doublereal &molarVolLiquid) { + // we need this because this is a non-const routine that is public + setTemperature(TKelvin); + double tcrit = critTemperature(); + double RhoLiquid, RhoGas; + double RhoLiquidGood, RhoGasGood; + double densSave = density(); + double tempSave = temperature(); + double pres; + doublereal mw = meanMolecularWeight(); + bool conv = false; + if (TKelvin < tcrit) { + + pres = psatEst(TKelvin); + // trial value = Psat from correlation + int i; + doublereal volLiquid = liquidVolEst(TKelvin, pres); + RhoLiquidGood = mw / volLiquid; + RhoGasGood = pres * mw / (GasConstant * TKelvin); + doublereal delGRT, liqGRT, gasGRT; + int stab; + doublereal presLast = pres; + + +#ifdef DDDD + double pVec[100]; + int n = 0; + for (int i = 0; i < 50; i++) { + pVec[n++] = 3.40E6 + 0.01E5 * i; + } + + for (int i = 0; i < 50; i++) { + stab = corr0(TKelvin, pVec[i], RhoLiquid, RhoGas, liqGRT, gasGRT); + printf ("p = %g, T = %g, stab = %d, Rl = %g Rg = %g, Gl = %g, Gg = %g\n", + pVec[i], TKelvin, stab, RhoLiquid, RhoGas,liqGRT, gasGRT); + } +#endif + + /* + * First part of the calculation involves finding a pressure at which the + * gas and the liquid state coexists. + */ + doublereal presLiquid; + doublereal presGas; + doublereal presBase = pres; + bool foundLiquid = false; + bool foundGas = false; + + doublereal densLiquid = densityCalc(TKelvin, presBase, FLUID_LIQUID_0, RhoLiquidGood); + if (densLiquid > 0.0) { + foundLiquid = true; + presLiquid = pres; + RhoLiquidGood = densLiquid; + } + if (!foundLiquid) { + for (int i = 0; i < 50; i++) { + pres = 1.1 * pres; + densLiquid = densityCalc(TKelvin, pres, FLUID_LIQUID_0, RhoLiquidGood); + if (densLiquid > 0.0) { + foundLiquid = true; + presLiquid = pres; + RhoLiquidGood = densLiquid; + break; + } + } + } + + pres = presBase; + doublereal densGas = densityCalc(TKelvin, pres, FLUID_GAS, RhoGasGood); + if (densGas <= 0.0) { + foundGas = false; + } else { + foundGas = true; + presGas = pres; + RhoGasGood = densGas; + } + if (!foundGas) { + for (int i = 0; i < 50; i++) { + pres = 0.9 * pres; + densGas = densityCalc(TKelvin, pres, FLUID_GAS, RhoGasGood); + if (densGas > 0.0) { + foundGas = true; + presGas = pres; + RhoGasGood = densGas; + break; + } + } + } + + if (foundGas && foundLiquid) { + if (presGas == presLiquid) { + pres = presGas; + goto startIteration; + } + pres = 0.5 * (presLiquid + presGas); + bool goodLiq; + bool goodGas; + for (int i = 0; i < 50; i++) { + + doublereal densLiquid = densityCalc(TKelvin, pres, FLUID_LIQUID_0, RhoLiquidGood); + if (densLiquid <= 0.0) { + goodLiq = false; + } else { + goodLiq = true; + RhoLiquidGood = densLiquid; + presLiquid = pres; + } + doublereal densGas = densityCalc(TKelvin, pres, FLUID_GAS, RhoGasGood); + if (densGas <= 0.0) { + goodGas = false; + } else { + goodGas = true; + RhoGasGood = densGas; + presGas = pres; + } + if (goodGas && goodLiq) { + break; + } + if (!goodLiq && !goodGas) { + pres = 0.5 * (pres + presLiquid); + } + if (goodLiq || goodGas) { + pres = 0.5 * (presLiquid + presGas); + } + + } + } + if (!foundGas || !foundLiquid) { + printf("error coundn't find a starting pressure\n"); + return (0.0); + } + if (presGas != presLiquid) { + printf("error coundn't find a starting pressure\n"); + return (0.0); + } + + startIteration: + pres = presGas; + presLast = pres; + RhoGas = RhoGasGood; + RhoLiquid = RhoLiquidGood; + + + /* + * Now that we have found a good pressure we can proceed with the algorithm. + */ + + for (i = 0; i < 20; i++) { + + stab = corr0(TKelvin, pres, RhoLiquid, RhoGas, liqGRT, gasGRT); + if (stab == 0) { + presLast = pres; + delGRT = liqGRT - gasGRT; + doublereal delV = mw * (1.0/RhoLiquid - 1.0/RhoGas); + doublereal dp = - delGRT * GasConstant * TKelvin / delV; + + if (fabs(dp) > 0.1 * pres) { + if (dp > 0.0) { + dp = 0.1 * pres; + } else { + dp = -0.1 * pres; + } + } + pres += dp; + + } else if (stab == -1) { + delGRT = 1.0E6; + if (presLast > pres) { + pres = 0.5 * (presLast + pres); + } else { + // we are stuck here - try this + pres = 1.1 * pres; + } + } else if (stab == -2) { + if (presLast < pres) { + pres = 0.5 * (presLast + pres); + } else { + // we are stuck here - try this + pres = 0.9 * pres; + } + } + molarVolGas = mw / RhoGas; + molarVolLiquid = mw / RhoLiquid; + + + if (fabs(delGRT) < 1.0E-8) { + conv = true; + break; + } + } + + molarVolGas = mw / RhoGas; + molarVolLiquid = mw / RhoLiquid; + // Put the fluid in the desired end condition + setState_TR(tempSave, densSave); + + return pres; + + + } else { + pres = critPressure(); + setState_TP(TKelvin, pres); + RhoGas = density(); + molarVolGas = mw / RhoGas; + molarVolLiquid = molarVolGas; + setState_TR(tempSave, densSave); + } + return pres; + } + + //==================================================================================================================== + // Calculate the pressure given the temperature and the molar volume + doublereal MixtureFugacityTP::pressureCalc(doublereal TKelvin, doublereal molarVol) const { + throw CanteraError("MixtureFugacityTP::pressureCalc", "unimplemented"); + return 0.0; + } + //==================================================================================================================== + // Calculate the pressure given the temperature and the molar volume + doublereal MixtureFugacityTP::dpdVCalc(doublereal TKelvin, doublereal molarVol, doublereal &presCalc) const { + throw CanteraError("MixtureFugacityTP::dpdVCalc", "unimplemented"); + return 0.0; + } + //==================================================================================================================== + + /* + * void _updateStandardStateThermo() (protected, virtual, const) + * + * If m_useTmpStandardStateStorage is true, + * This function must be called for every call to functions in this + * class that need standard state properties. + * Child classes may require that it be called even if m_useTmpStandardStateStorage + * is not true. + * It checks to see whether the temperature has changed and + * thus the ss thermodynamics functions for all of the species + * must be recalculated. + * + * This + */ + void MixtureFugacityTP::_updateReferenceStateThermo() const { + double Tnow = temperature(); + + // If the temperature has changed since the last time these + // properties were computed, recompute them. + if (m_Tlast_ref != Tnow) { + m_spthermo->update(Tnow, &m_cp0_R[0], &m_h0_RT[0], &m_s0_R[0]); + m_Tlast_ref = Tnow; + + // update the species Gibbs functions + int k; + for (k = 0; k < m_kk; k++) { + m_g0_RT[k] = m_h0_RT[k] - m_s0_R[k]; + } + doublereal pref = refPressure(); + if (pref <= 0.0) { + throw CanteraError("MixtureFugacityTP::_updateReferenceStateThermo()", "neg ref pressure"); + } + m_logc0 = log(pref/(GasConstant * Tnow)); + } + } + //==================================================================================================================== + + +} + + diff --git a/Cantera/src/thermo/MixtureFugacityTP.h b/Cantera/src/thermo/MixtureFugacityTP.h new file mode 100644 index 000000000..77e88b061 --- /dev/null +++ b/Cantera/src/thermo/MixtureFugacityTP.h @@ -0,0 +1,968 @@ +/** + * @file MixtureFugacityTP.h + * Header file for a derived class of ThermoPhase that handles + * non-ideal mixtures based on the fugacity models (see \ref thermoprops and + * class \link Cantera::MixtureFugacityTP MixtureFugacityTP\endlink). + * + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Date: 2010-08-04 10:06:14 -0600 (Wed, 04 Aug 2010) $ + * $Revision: 547 $ + */ + +#ifndef CT_MIXTUREFUGACITYTP_H +#define CT_MIXTUREFUGACITYTP_H + +#include "ThermoPhase.h" +#include "VPSSMgr.h" +#include "ResidEval.h" + +namespace Cantera { + + class XML_Node; + class PDSS; + + + //! Various states of the Fugacity object. In general there can be multiple liquid + //! objects for a single phase identified with each species. + +#define FLUID_UNSTABLE -4 +#define FLUID_UNDEFINED -3 +#define FLUID_SUPERCRIT -2 +#define FLUID_GAS -1 +#define FLUID_LIQUID_0 0 +#define FLUID_LIQUID_1 1 +#define FLUID_LIQUID_2 2 +#define FLUID_LIQUID_3 3 +#define FLUID_LIQUID_4 4 +#define FLUID_LIQUID_5 5 +#define FLUID_LIQUID_6 6 +#define FLUID_LIQUID_7 7 +#define FLUID_LIQUID_8 8 +#define FLUID_LIQUID_9 9 + + + + /** + * @ingroup thermoprops + * + * This is a filter class for ThermoPhase that implements some prepatory + * steps for efficiently handling mixture of gases that whose standard states + * are defined as ideal gases, but which describe also non-ideal solutions. + * In addition a multicomponent liquid phase below the critical temperature of the + * mixture is also allowed. The main subclass will be a mixture Redlich-kwong class. + * + * Several concepts are introduced. The first concept is there are temporary + * variables for holding the species standard state values + * of Cp, H, S, G, and V at the last temperature and pressure called. These functions are not recalculated + * if a new call is made using the previous temperature and pressure. + * + * The other concept is that the current state of the mixture is tracked. + * The state variable is either GAS, LIQUID, or SUPERCRIT fluid. Additionally, + * the variable LiquidContent is used and may vary between 0 and 1. + * + * To support the above functionality, pressure and temperature variables, + * m_Plast_ss and m_Tlast_ss, are kept which store the last pressure and temperature + * used in the evaluation of standard state properties. + * + * Typically, only one liquid phase is allowed to be formed within these classes. + * Additionally, there is an inherent contradiction between three phase models and + * the ThermoPhase class. The ThermoPhase class is really only meant to represent a + * single instanteation of a phase. The three phase models may be in equilibrium with + * multiple phases of the fluid in equilibrium with each other. This has yet to be resolved. + * + * This class is usually used for non-ideal gases. + * + * + * @nosubgrouping + */ + class MixtureFugacityTP : public ThermoPhase { + + public: + + /*! + * + * @name Constructors and Duplicators for %MixtureFugacityTP + * + */ + //! Constructor. + MixtureFugacityTP(); + + //! Copy Constructor. + /*! + * @param b Object to be copied + */ + MixtureFugacityTP(const MixtureFugacityTP &b); + + //! Assignment operator + /*! + * @param b Object to be copied + */ + MixtureFugacityTP& operator=(const MixtureFugacityTP &b); + + //! Destructor. + virtual ~MixtureFugacityTP(); + + + //! Duplication routine + /*! + * @return Returns a duplication + */ + virtual ThermoPhase *duplMyselfAsThermoPhase() const; + + //@} + + /** + * @name Utilities (MixtureFugacityTP) + */ + //@{ + /** + * Equation of state type flag. The base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Constants defined for this purpose are + * listed in mix_defs.h. + */ + virtual int eosType() const { return 0; } + + //! This method returns the convention used in specification + //! of the standard state, of which there are currently two, + //! temperature based, and variable pressure based. + /*! + * Currently, there are two standard state conventions: + * - Temperature-based activities + * cSS_CONVENTION_TEMPERATURE 0 + * - default + * + * - Variable Pressure and Temperature -based activities + * cSS_CONVENTION_VPSS 1 + */ + virtual int standardStateConvention() const; + + //! Set the solution branch to force the ThermoPhase to exist on one branch or another + /*! + * @param solnBranch Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means unrestricted. + * Values of zero or greater refer to species dominated condensed phases. + */ + virtual void setForcedSolutionBranch(int solnBranch); + + //! Report the solution branch which the solution is restricted to + /*! + * @return Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means unrestricted. + * Values of zero or greater refer to species dominated condensed phases. + */ + virtual int forcedSolutionBranch() const; + + //! Report the solution branch which the solution is actually on + /*! + * @return Branch that the solution is restricted to. + * the value -1 means gas. The value -2 means superfluid.. + * Values of zero or greater refer to species dominated condensed phases. + */ + virtual int reportSolnBranchActual() const; + + + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. moles) + * that represents the standard state. + * This quantity is to be used in conjunction with derivatives of + * that concentration-like variable when the derivative of the chemical + * potential is taken. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN_diag Output vector of derivatives of the + * log Activity Coefficients. length = m_kk + */ + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + err("getdlnActCoeffdlnN_diag"); + } + + + //@} + /// @name Partial Molar Properties of the Solution (MixtureFugacityTP) + //@{ + + + //! Get the array of non-dimensional species chemical potentials + //! These are partial molar Gibbs free energies. + /*! + * \f$ \mu_k / \hat R T \f$. + * Units: unitless + * + * We close the loop on this function, here, calling + * getChemPotentials() and then dividing by RT. No need for child + * classes to handle. + * + * @param mu Output vector of non-dimensional species chemical potentials + * Length: m_kk. + */ + void getChemPotentials_RT(doublereal* mu) const; + + //@} + + /*! + * @name Properties of the Standard State of the Species in the Solution + * (MixtureFugacityTP) + * + * Within MixtureFugacityTP, these properties are calculated via a common routine, + * _updateStandardStateThermo(), + * which must be overloaded in inherited objects. + * The values are cached within this object, and are not recalculated unless + * the temperature or pressure changes. + */ + //@{ + + //! Get the array of chemical potentials at unit activity. + /*! + * These are the standard state chemical potentials \f$ \mu^0_k(T,P) + * \f$. The values are evaluated at the current temperature and pressure. + * + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * @param mu Output vector of standard state chemical potentials. + * length = m_kk. units are J / kmol. + */ + virtual void getStandardChemPotentials(doublereal* mu) const; + + //! Get the nondimensional Enthalpy functions for the species + //! at their standard states at the current T and P of the solution. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * @param hrt Output vector of standard state enthalpies. + * length = m_kk. units are unitless. + */ + virtual void getEnthalpy_RT(doublereal* hrt) const; + + + //! Get the array of nondimensional Enthalpy functions for the standard state species + /*! + * at the current T and P of the solution. + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * @param sr Output vector of nondimensional standard state + * entropies. length = m_kk. + */ + virtual void getEntropy_R(doublereal* sr) const; + + //! Get the nondimensional Gibbs functions for the species + //! at their standard states of solution at the current T and P of the solution. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * @param grt Output vector of nondimensional standard state + * Gibbs free energies. length = m_kk. + */ + virtual void getGibbs_RT(doublereal* grt) const; + + + //! Get the nondimensional Gibbs functions for the standard + //! state of the species at the current T and P. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * @param gpure Output vector of standard state + * Gibbs free energies. length = m_kk. + * units are J/kmol. + * + * @todo This could be eliminated. It doesn't fit into the current + * naming convention. + */ + void getPureGibbs(doublereal* gpure) const; + + //! Returns the vector of nondimensional internal Energies of the standard state at the current temperature + //! and pressure of the solution for each species. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. + * + * \f[ + * u^{ss}_k(T,P) = h^{ss}_k(T) - P * V^{ss}_k + * \f] + * + * @param urt Output vector of nondimensional standard state + * internal energies. length = m_kk. + */ + virtual void getIntEnergy_RT(doublereal *urt) const; + + + //! Get the nondimensional Heat Capacities at constant + //! pressure for the standard state of the species at the current T and P. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure of the solution. + * + * @param cpr Output vector containing the + * the nondimensional Heat Capacities at constant + * pressure for the standard state of the species. + * Length: m_kk. + */ + virtual void getCp_R(doublereal* cpr) const; + + + //! Get the molar volumes of each species in their standard + //! states at the current T and P of the solution. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure of the solution. + * + * units = m^3 / kmol + * + * @param vol Output vector of species volumes. length = m_kk. + * units = m^3 / kmol + */ + virtual void getStandardVolumes(doublereal *vol) const; + + + //! Set the temperature of the phase + /*! + * Currently this passes down to setState_TP(). It does not + * make sense to calculate the standard state without first + * setting T and P. + * + * @param temp Temperature (kelvin) + */ + virtual void setTemperature(const doublereal temp); + + + //! Set the internally storred pressure (Pa) at constant + //! temperature and composition + /*! + * Currently this passes down to setState_TP(). It does not + * make sense to calculate the standard state without first + * setting T and P. + * + * @param p input Pressure (Pa) + */ + virtual void setPressure(doublereal p); + + + +protected: + /** + * Calculate the density of the mixture using the partial + * molar volumes and mole fractions as input + * + * The formula for this is + * + * \f[ + * \rho = \frac{\sum_k{X_k W_k}}{\sum_k{X_k V_k}} + * \f] + * + * where \f$X_k\f$ are the mole fractions, \f$W_k\f$ are + * the molecular weights, and \f$V_k\f$ are the pure species + * molar volumes. + * + * Note, the basis behind this formula is that in an ideal + * solution the partial molar volumes are equal to the pure + * species molar volumes. We have additionally specified + * in this class that the pure species molar volumes are + * independent of temperature and pressure. + * + * NOTE: This is a non-virtual function, which is not a + * member of the ThermoPhase base class. + */ + virtual void calcDensity(); + + public: + //! Set the temperature and pressure at the same time + /*! + * Note this function triggers a reevalulation of the standard + * state quantities. + * + * @param T temperature (kelvin) + * @param pres pressure (pascal) + */ + virtual void setState_TP(doublereal T, doublereal pres); + + //! Set the internally storred temperature (K) and density (kg/m^3) + /*! + * @param t Temperature in kelvin + * @param rho Density (kg/m^3) + */ + virtual void setState_TR(doublereal T, doublereal rho); + + //! Set the temperature (K), pressure (Pa), and mole fractions. + /*! + * Note, the mole fractions are set first before the pressure is set. + * Setting the pressure may involve the solution of a nonlinear equation. + * + * @param t Temperature (K) + * @param p Pressure (Pa) + * @param x Vector of mole fractions. + * Length is equal to m_kk. + */ + virtual void setState_TPX(doublereal t, doublereal p, const doublereal* x); + + + //! Set the mass fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param y Array of unnormalized mass fraction values (input). + * Must have a length greater than or equal to the number of species. + */ + virtual void setMassFractions(const doublereal* const y); + + + //!Set the mass fractions to the specified values without normalizing. + /*! + * This is useful when the normalization + * condition is being handled by some other means, for example + * by a constraint equation as part of a larger set of + * equations. + * + * @param y Input vector of mass fractions. + * Length is m_kk. + */ + virtual void setMassFractions_NoNorm(const doublereal* const y); + + + + //! Set the mole fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param x Array of unnormalized mole fraction values (input). + * Must have a length greater than or equal to the number of species. + */ + virtual void setMoleFractions(const doublereal* const x); + + + //! Set the mole fractions to the specified values without normalizing. + /*! + * This is useful when the normalization + * condition is being handled by some other means, for example + * by a constraint equation as part of a larger set ofequations. + * + * @param x Input vector of mole fractions. + * Length is m_kk. + */ + virtual void setMoleFractions_NoNorm(const doublereal* const x); + + + //! Set the concentrations to the specified values within the phase. + /*! + * @param c The input vector to this routine is in dimensional + * units. For volumetric phases c[k] is the + * concentration of the kth species in kmol/m3. + * For surface phases, c[k] is the concentration + * in kmol/m2. The length of the vector is the number + * of species in the phase. + */ + virtual void setConcentrations(const doublereal* const c); + + protected: + void setMoleFractions_NoState(const doublereal* const x); + + + public: + //! Returns the current pressure of the phase + /*! + * The pressure is an independent variable in this phase. Its current value + * is storred in the object MixtureFugacityTP. + * + * @return return the pressure in pascals. + */ + doublereal pressure() const { + return m_Pcurrent; + } + + + + + + protected: + + //! Updates the reference state thermodynamic functions at the current T of the solution. + /*! + * + * If m_useTmpStandardStateStorage is true, + * this function must be called for every call to functions in this + * class. It checks to see whether the temperature or pressure has changed and + * thus the ss thermodynamics functions for all of the species + * must be recalculated. + * + * This function is responsible for updating the following internal members, + * when m_useTmpStandardStateStorage is true. + * + * - m_hss_RT; + * - m_cpss_R; + * - m_gss_RT; + * - m_sss_R; + * - m_Vss + * + * If m_useTmpStandardStateStorage is not true, this function may be + * required to be called by child classes to update internal member data. + * + */ + virtual void _updateReferenceStateThermo() const; + public: + + //@} + /// @name Thermodynamic Values for the Species Reference States (MixtureFugacityTP) + /*! + * There are also temporary + * variables for holding the species reference-state values of Cp, H, S, and V at the + * last temperature and reference pressure called. These functions are not recalculated + * if a new call is made using the previous temperature. + * All calculations are done within the routine _updateRefStateThermo(). + */ + //@{ + + + //! Returns the vector of nondimensional + //! enthalpies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * @param hrt Output vector contains the nondimensional enthalpies + * of the reference state of the species + * length = m_kk, units = dimensionless. + */ + virtual void getEnthalpy_RT_ref(doublereal *hrt) const; + +#ifdef H298MODIFY_CAPABILITY + //! Modify the value of the 298 K Heat of Formation of the standard state of + //! one species in the phase (J kmol-1) + /*! + * The 298K heat of formation is defined as the enthalpy change to create the standard state + * of the species from its constituent elements in their standard states at 298 K and 1 bar. + * + * @param k Index of the species + * @param Hf298New Specify the new value of the Heat of Formation at 298K and 1 bar. + * units = J/kmol. + */ + void modifyOneHf298SS(const int k, const doublereal Hf298New); +#endif + + //! Returns the vector of nondimensional + //! Gibbs free energies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * + * @param grt Output vector contains the nondimensional Gibbs free energies + * of the reference state of the species + * length = m_kk, units = dimensionless. + */ + virtual void getGibbs_RT_ref(doublereal *grt) const; + + protected: + //! Returns the vector of nondimensional + //! Gibbs free energies of the reference state at the current temperature + //! of the solution and the reference pressure for the species. + /*! + * @return Output vector contains the nondimensional Gibbs free energies + * of the reference state of the species + * length = m_kk, units = dimensionless. + */ + const vector_fp & gibbs_RT_ref() const; + + public: + /*! + * Returns the vector of the + * gibbs function of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * units = J/kmol + * + * @param g Output vector contain the Gibbs free energies + * of the reference state of the species + * length = m_kk, units = J/kmol. + */ + virtual void getGibbs_ref(doublereal *g) const; + + /*! + * Returns the vector of nondimensional + * entropies of the reference state at the current temperature + * of the solution and the reference pressure for the species. + * + * @param er Output vector contain the nondimensional entropies + * of the species in their reference states + * length: m_kk, units: dimensionless. + */ + virtual void getEntropy_R_ref(doublereal *er) const; + + /*! + * Returns the vector of nondimensional + * constant pressure heat capacities of the reference state + * at the current temperature of the solution + * and reference pressure for the species. + * + * @param cprt Output vector contains the nondimensional heat capacities + * of the species in their reference states + * length: m_kk, units: dimensionless. + */ + virtual void getCp_R_ref(doublereal *cprt) const; + + //! Get the molar volumes of the species reference states at the current + //! T and reference pressure of the solution. + /*! + * units = m^3 / kmol + * + * @param vol Output vector containing the standard state volumes. + * Length: m_kk. + */ + virtual void getStandardVolumes_ref(doublereal *vol) const; + + protected: + + + + //@} + + + public: + + //! @name Initialization Methods - For Internal use (VPStandardState) + /*! + * The following methods are used in the process of constructing + * the phase and setting its parameters from a specification in an + * input file. They are not normally used in application programs. + * To see how they are used, see files importCTML.cpp and + * ThermoFactory.cpp. + */ + //@{ + + + //! Set the initial state of the phase to the conditions specified in the state XML element. + /*! + * + * This method sets the temperature, pressure, and mole fraction vector to a set default value. + * + * @param state AN XML_Node object corresponding to + * the "state" entry for this phase in the input file. + */ + virtual void setStateFromXML(const XML_Node& state); + + //! @internal Initialize the object + /*! + * This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called after calling installSpecies() + * for each species in the phase. It's called before calling + * initThermoXML() for the phase. Therefore, it's the correct + * place for initializing vectors which have lengths equal to the + * number of species. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + //! Initialize a ThermoPhase object, potentially reading activity + //! coefficient information from an XML database. + /*! + * This routine initializes the lengths in the current object and + * then calls the parent routine. + * This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase(). + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + virtual void initThermoXML(XML_Node& phaseNode, std::string id); + + + private: + //! @internal Initialize the internal lengths in this object. + /*! + * Note this is not a virtual function. + */ + void initLengths(); + + protected: + // Special Functions for fugacity classes + + + //! Calculate the value of z + /*! + * \f[ + * z = \frac{P v}{ R T} + * \f] + * + * returns the value of z + */ + doublereal z() const; + + //! Calculate the deviation terms for the total entropy of the mixture from the + //! ideal gas mixture + /* + * Here we use the current state conditions + * + * @return Returns the change in entropy in units of J kmol-1 K-1. + */ + virtual doublereal sresid() const; + + //! Calculate the deviation terms for the total enthalpy of the mixture from the ideal gas mixture + /* + * Here we use the current state conditions + * + * @return Returns the change in entropy in units of J kmol-1. + */ + virtual doublereal hresid() const; + + + //! Estimate for the saturation pressure + /*! + * Note: this is only used as a starting guess for later routines that actually calculate an + * accurate value for the saturation pressure. + * + * @param TKelvin temperature in kelvin + * + * @return returns the estimated saturation pressure at the given temperature + */ + virtual doublereal psatEst(doublereal TKelvin) const; + + //! Estimate for the molar volume of the liquid + /*! + * Note: this is only used as a starting guess for later routines that actually calculate an + * accurate value for the liquid molar volume. + * This routine doesn't change the state of the system. + * + * @param TKelvin temperature in kelvin + * @param pres Pressure in Pa. This is used as an initial guess. If the routine + * needs to change the pressure to find a stable liquid state, the + * new pressure is returned in this variable. + * + * @return Returns the estimate of the liquid volume. If the liquid can't be found, this + * routine returns -1. + */ + virtual doublereal liquidVolEst(doublereal TKelvin, doublereal &pres) const; + + protected: + //! Calculates the density given the temperature and the pressure and a guess at the density. + /*! + * Note, below T_c, this is a multivalued function. We do not cross the vapor dome in this. + * This is protected because it is called during setState_TP() routines. Infinite loops would result + * if it were not protected. + * + * -> why is this not const? + * + * parameters: + * @param TKelvin Temperature in Kelvin + * @param pressure Pressure in Pascals (Newton/m**2) + * @param phaseRequested int representing the phase whose density we are requesting. If we put + * a gas or liquid phase here, we will attempt to find a volume in that + * part of the volume space, only, in this routine. A value of FLUID_UNDEFINED + * means that we will accept anything. + * + * @param rhoguess Guessed density of the fluid. A value of -1.0 indicates that there + * is no guessed density + * + * + * @return We return the density of the fluid at the requested phase. If we have not found any + * acceptable density we return a -1. If we have found an accectable density at a + * different phase, we return a -2. + */ + virtual doublereal densityCalc(doublereal TKelvin, doublereal pressure, int phaseRequested, + doublereal rhoguess); + + //! Utility routine in the calculation of the saturation pressure + /*! + * Private routine + * + * @param TKelvin temperature (kelvin) + * @param pres pressure (Pascal) + * @param densLiq Output density of liquid + * @param densGas output density of gas + * @param delGRT output delGRT + */ + int corr0(doublereal TKelvin, doublereal pre, doublereal &densLiq, + doublereal &densGas, doublereal &liqGRT, doublereal &gasGRT); + public: + //! Returns the Phase State flag for the current state of the object + /*! + * @param checkState If true, this function does a complete check to see where + * in paramters space we are + * + * There are three values: + * WATER_GAS below the critical temperature but below the critical density + * WATER_LIQUID below the critical temperature but above the critical density + * WATER_SUPERCRIT above the critical temperature + */ + int phaseState(bool checkState = false) const ; + + //! Return the value of the density at the liquid spinodal point (on the liquid side) + //! for the current temperature. + /*! + * @return returns the density with units of kg m-3 + */ + virtual doublereal densSpinodalLiquid() const; + + + //! Return the value of the density at the gas spinodal point (on the gas side) + //! for the current temperature. + /*! + * @return returns the density with units of kg m-3 + */ + virtual doublereal densSpinodalGas() const; + + + + + public: + //! Calculate the saturation pressure at the current mixture content for the given temperature + /*! + * @param TKelvin (input) Temperature (Kelvin) + * @param molarVolGas (return) Molar volume of the gas + * @param molarVolLiquid (return) Molar volume of the liquid + * + * @return Returns the saturation pressure at the given temperature + */ + doublereal calculatePsat(doublereal TKelvin, doublereal &molarVolGas, + doublereal &molarVolLiquid); + protected: + //! Calculate the pressure given the temperature and the molar volume + /*! + * Calculate the pressure given the temperature and the molar volume + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @return Returns the pressure. + */ + virtual doublereal pressureCalc(doublereal TKelvin, doublereal molarVol) const; + + + //! Calculate the pressure and the pressure derivative given the temperature and the molar volume + /*! + * Temperature and mole number are held constant + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @param presCalc Returns the pressure. + * + * @return Returns the derivative of the pressure wrt the molar volume + */ + virtual doublereal dpdVCalc(doublereal TKelvin, doublereal molarVol, doublereal &presCalc) const; + + + + virtual void updateMixingExpressions(); + + + //@} + + + class spinodalFunc : public Cantera::ResidEval + { + public: + + spinodalFunc(MixtureFugacityTP *tp); + + virtual int evalSS(const doublereal t, const doublereal * const y, doublereal * const r); + + MixtureFugacityTP *m_tp; + }; + + + protected: + + //! Current value of the pressurees + /*! + * Because the pressure is now a calculation, we store the result of the calculation whenever + * it is recalculated. + * + * units = Pascals + */ + doublereal m_Pcurrent; + + + //! Storage for the current values of the mole fractions of the species + /*! + * This vector is kept up-to-date when some the setState functions are called. + * + * The State object is allowed to com + * + * Therefore, it may be considered to be an independent variable. + * + + */ + std::vector moleFractions_; + + //! Current state of the fluid + /*! + * There are three possible states of the fluid + * FLUID_GAS + * FLUID_LIQUID + * FLUID_SUPERCRIT + */ + int iState_; + + + //! Force the system to be on a particular side of the spinodal curve + int forcedState_; + + //! The last temperature at which the reference state thermodynamic properties were calculated at. + mutable doublereal m_Tlast_ref; + + //! Temporary storage for log of p/rt + mutable doublereal m_logc0; + + //! Temporary storage for dimensionless reference state enthalpies + mutable array_fp m_h0_RT; + + //! Temporary storage for dimensionless reference state heat capacities + mutable array_fp m_cp0_R; + + //! Temporary storage for dimensionless reference state gibbs energies + mutable array_fp m_g0_RT; + + //! Temporary storage for dimensionless reference state entropies + mutable array_fp m_s0_R; + + spinodalFunc *fdpdv_; + private: + + //! MixtureFugacityTP has its own err routine + /*! + * @param msg Error message string + */ + doublereal err(std::string msg) const; + + }; +} + +#endif diff --git a/Cantera/src/thermo/NasaThermo.h b/Cantera/src/thermo/NasaThermo.h index 7d4d81fbd..95bbe4777 100644 --- a/Cantera/src/thermo/NasaThermo.h +++ b/Cantera/src/thermo/NasaThermo.h @@ -209,11 +209,12 @@ namespace Cantera { if (m_p0 < 0.0) { m_p0 = refPressure; } else if (fabs(m_p0 - refPressure) > 0.1) { - std::string logmsg = " WARNING NasaThermo: New Species, " + name + ", has a different reference pressure, " + std::string logmsg = " ERROR NasaThermo: New Species, " + name + ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); - logmsg = " This may become a fatal error in the future \n"; + logmsg = " This is now a fatal error\n"; writelog(logmsg); + throw CanteraError("install()", "species have different reference pressures"); } m_p0 = refPressure; } diff --git a/Cantera/src/thermo/RedlichKwongMFTP.cpp b/Cantera/src/thermo/RedlichKwongMFTP.cpp new file mode 100644 index 000000000..ec1627ba7 --- /dev/null +++ b/Cantera/src/thermo/RedlichKwongMFTP.cpp @@ -0,0 +1,1895 @@ +/** + * @file RedlichKwongMFTP.cpp + * Definition file for a derived class of ThermoPhase that assumes either + * an ideal gas or ideal solution approximation and handles + * variable pressure standard state methods for calculating + * thermodynamic properties (see \ref thermoprops and + * class \link Cantera::RedlichKwongMFTP RedlichKwongMFTP\endlink). + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Author: hkmoffa $ + * $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ + * $Revision: 255 $ + */ + +// turn off warnings under Windows +#ifdef WIN32 +#pragma warning(disable:4786) +#pragma warning(disable:4503) +#endif + +#include "RedlichKwongMFTP.h" + + +#include "mix_defs.h" +#include "ThermoFactory.h" +#include "RootFind.h" + +using namespace std; + +namespace Cantera { +#ifdef WITH_REAL_GASSES + //==================================================================================================================== + /* + * Default constructor + */ + RedlichKwongMFTP::RedlichKwongMFTP() : + MixtureFugacityTP(), + m_standardMixingRules(0), + m_formTempParam(0), + m_b_current(0.0), + m_a_current(0.0), + a_vec_Curr_(0), + b_vec_Curr_(0), + a_coeff_vec(0,0), + m_pc_Species(0), + m_tc_Species(0), + m_vc_Species(0), + NSolns_(0), + m_pp(0), + m_tmpV(0), + m_partialMolarVolumes(0), + dpdV_(0.0), + dpdT_(0.0), + dpdni_(0) + { + Vroot_[0] = 0.0; + Vroot_[1] = 0.0; + Vroot_[2] = 0.0; + } + //==================================================================================================================== + RedlichKwongMFTP::RedlichKwongMFTP(std::string infile, std::string id) : + MixtureFugacityTP(), + m_standardMixingRules(0), + m_formTempParam(0), + m_b_current(0.0), + m_a_current(0.0), + a_vec_Curr_(0), + b_vec_Curr_(0), + a_coeff_vec(0,0), + m_pc_Species(0), + m_tc_Species(0), + m_vc_Species(0), + NSolns_(0), + m_pp(0), + m_tmpV(0), + m_partialMolarVolumes(0), + dpdV_(0.0), + dpdT_(0.0), + dpdni_(0) + { + Vroot_[0] = 0.0; + Vroot_[1] = 0.0; + Vroot_[2] = 0.0; + XML_Node* root = get_XML_File(infile); + if (id == "-") id = ""; + XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, root); + if (!xphase) { + throw CanteraError("newPhase", + "Couldn't find phase named \"" + id + "\" in file, " + infile); + } + importPhase(*xphase, this); + } + //==================================================================================================================== + RedlichKwongMFTP::RedlichKwongMFTP(XML_Node& phaseRefRoot, std::string id) : + MixtureFugacityTP(), + m_standardMixingRules(0), + m_formTempParam(0), + m_b_current(0.0), + m_a_current(0.0), + a_vec_Curr_(0), + b_vec_Curr_(0), + a_coeff_vec(0,0), + m_pc_Species(0), + m_tc_Species(0), + m_vc_Species(0), + NSolns_(0), + m_pp(0), + m_tmpV(0), + m_partialMolarVolumes(0), + dpdV_(0.0), + dpdT_(0.0), + dpdni_(0) + { + Vroot_[0] = 0.0; + Vroot_[1] = 0.0; + Vroot_[2] = 0.0; + XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, &phaseRefRoot); + if (!xphase) { + throw CanteraError("RedlichKwongMFTP::RedlichKwongMFTP()","Couldn't find phase named \"" + id + "\" in XML node"); + } + importPhase(*xphase, this); + } + + //==================================================================================================================== + RedlichKwongMFTP::RedlichKwongMFTP(int testProb) : + MixtureFugacityTP(), + m_standardMixingRules(0), + m_formTempParam(0), + m_b_current(0.0), + m_a_current(0.0), + a_vec_Curr_(0), + b_vec_Curr_(0), + a_coeff_vec(0,0), + m_pc_Species(0), + m_tc_Species(0), + m_vc_Species(0), + NSolns_(0), + m_pp(0), + m_tmpV(0), + m_partialMolarVolumes(0), + dpdV_(0.0), + dpdT_(0.0), + dpdni_(0) + { + std::string infile = "co2_redlichkwong.xml"; + std::string id; + if (testProb == 1) { + infile = "co2_redlichkwong.xml"; + id = "carbondioxide"; + } else { + throw CanteraError("", "test prob = 1 only"); + } + XML_Node* root = get_XML_File(infile); + if (id == "-") id = ""; + XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id, root); + if (!xphase) { + throw CanteraError("newPhase", "Couldn't find phase named \"" + id + "\" in file, " + infile); + } + importPhase(*xphase, this); + } + //==================================================================================================================== + /* + * Copy Constructor: + * + * Note this stuff will not work until the underlying phase + * has a working copy constructor. + * + * The copy constructor just calls the assignment operator + * to do the heavy lifting. + */ + RedlichKwongMFTP::RedlichKwongMFTP(const RedlichKwongMFTP &b) : + MixtureFugacityTP(), + m_standardMixingRules(0), + m_formTempParam(0), + m_b_current(0.0), + m_a_current(0.0), + a_vec_Curr_(0), + b_vec_Curr_(0), + a_coeff_vec(0,0), + m_pc_Species(0), + m_tc_Species(0), + m_vc_Species(0), + NSolns_(0), + m_pp(0), + m_tmpV(0), + m_partialMolarVolumes(0), + dpdV_(0.0), + dpdT_(0.0), + dpdni_(0) + { + *this = b; + } + + //==================================================================================================================== + /* + * operator=() + * + * Note this stuff will not work until the underlying phase + * has a working assignment operator + */ + RedlichKwongMFTP& RedlichKwongMFTP:: + operator=(const RedlichKwongMFTP &b) { + if (&b != this) { + /* + * Mostly, this is a passthrough to the underlying + * assignment operator for the ThermoPhae parent object. + */ + MixtureFugacityTP::operator=(b); + /* + * However, we have to handle data that we own. + */ + m_standardMixingRules = b.m_standardMixingRules; + m_formTempParam = b.m_formTempParam; + m_b_current = b.m_b_current; + m_a_current = b.m_a_current; + a_vec_Curr_ = b.a_vec_Curr_; + b_vec_Curr_ = b.b_vec_Curr_; + a_coeff_vec = b.a_coeff_vec; + + m_pc_Species = b.m_pc_Species; + m_tc_Species = b.m_tc_Species; + m_vc_Species = b.m_vc_Species; + NSolns_ = b.NSolns_; + Vroot_[0] = b.Vroot_[0]; + Vroot_[1] = b.Vroot_[1]; + Vroot_[2] = b.Vroot_[2]; + m_pp = b.m_pp; + m_tmpV = b.m_tmpV; + m_partialMolarVolumes = b.m_partialMolarVolumes; + dpdV_ = b.dpdV_; + dpdT_ = b.dpdT_; + dpdni_ = b.dpdni_; + } + return *this; + } + //==================================================================================================================== + /* + * ~RedlichKwongMFTP(): (virtual) + * + */ + RedlichKwongMFTP::~RedlichKwongMFTP() { + } + //==================================================================================================================== + /* + * Duplication function. + * This calls the copy constructor for this object. + */ + ThermoPhase* RedlichKwongMFTP::duplMyselfAsThermoPhase() const { + RedlichKwongMFTP* vptp = new RedlichKwongMFTP(*this); + return (ThermoPhase *) vptp; + } + //==================================================================================================================== + int RedlichKwongMFTP::eosType() const { + return cRedlichKwongMFTP; + } + + //==================================================================================================================== + /* + * ------------Molar Thermodynamic Properties ------------------------- + */ + //==================================================================================================================== + // Molar enthalpy. Units: J/kmol. + doublereal RedlichKwongMFTP::enthalpy_mole() const { + _updateReferenceStateThermo(); + doublereal rt = _RT(); + doublereal h_ideal = rt * mean_X(DATA_PTR(m_h0_RT)); + doublereal h_nonideal = hresid(); + return (h_ideal + h_nonideal); + } + //==================================================================================================================== + // Molar internal energy. Units: J/kmol. + doublereal RedlichKwongMFTP::intEnergy_mole() const { + doublereal p0 = pressure(); + doublereal md = molarDensity(); + return (enthalpy_mole() - p0 / md); + } + //==================================================================================================================== + // Molar entropy. Units: J/kmol/K. + doublereal RedlichKwongMFTP::entropy_mole() const { + _updateReferenceStateThermo(); + doublereal sr_ideal = GasConstant * (mean_X(DATA_PTR(m_s0_R)) + - sum_xlogx() - std::log(pressure()/m_spthermo->refPressure())); + doublereal sr_nonideal = sresid(); + return (sr_ideal + sr_nonideal); + } + //==================================================================================================================== + // Molar Gibbs function. Units: J/kmol. + doublereal RedlichKwongMFTP::gibbs_mole() const { + return enthalpy_mole() - temperature() * entropy_mole(); + } + //==================================================================================================================== + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + doublereal RedlichKwongMFTP::cp_mole() const { + _updateReferenceStateThermo(); + doublereal TKelvin = temperature(); + doublereal sqt = sqrt(TKelvin); + doublereal mv = molarVolume(); + doublereal vpb = mv + m_b_current; + pressureDerivatives(); + doublereal cpref = GasConstant * mean_X(DATA_PTR(m_cp0_R)); + doublereal dadt = da_dt(); + doublereal fac = TKelvin * dadt - 3.0 * m_a_current / 2.0; + doublereal dHdT_V = (cpref + mv * dpdT_ - GasConstant - 1.0 / (2.0 * m_b_current * TKelvin * sqt) * log(vpb/mv) * fac + +1.0/(m_b_current * sqt) * log(vpb/mv) * (-0.5 * dadt)); + double cp = dHdT_V - (mv + TKelvin * dpdT_ / dpdV_) * dpdT_; + return cp; + } + //==================================================================================================================== + /// Molar heat capacity at constant volume. Units: J/kmol/K. + doublereal RedlichKwongMFTP::cv_mole() const { + throw CanteraError("", "unimplemented"); + return cp_mole() - GasConstant; + } + //==================================================================================================================== + // Return the thermodynamic pressure (Pa). + /* + * Since the mass density, temperature, and mass fractions are stored, + * this method uses these values to implement the + * mechanical equation of state \f$ P(T, \rho, Y_1, \dots, Y_K) \f$. + * + * \f[ + * P = \frac{RT}{v-b_{mix}} - \frac{a_{mix}}{T^{0.5} v \left( v + b_{mix} \right) } + * \f] + * + */ + doublereal RedlichKwongMFTP::pressure() const { + + +#ifdef DEBUG_MODE + _updateReferenceStateThermo(); + + // Get a copy of the private variables stored in the State object + double rho = density(); + doublereal T = temperature(); + doublereal mmw = meanMolecularWeight(); + double molarV = mmw / rho; + + double pp = GasConstant * T/(molarV - m_b_current) - m_a_current/(sqrt(T) * molarV * (molarV + m_b_current)); + + if (fabs(pp -m_Pcurrent) > 1.0E-5 * m_Pcurrent) { + throw CanteraError(" RedlichKwongMFTP::pressure()", "setState broken down, maybe"); + } +#endif + + return m_Pcurrent; + } + //==================================================================================================================== + void RedlichKwongMFTP::calcDensity() { + /* + * Calculate the molarVolume of the solution (m**3 kmol-1) + */ + + const doublereal * const dtmp = moleFractdivMMW(); + getPartialMolarVolumes(DATA_PTR(m_tmpV)); + double invDens = dot(m_tmpV.begin(), m_tmpV.end(), dtmp); + /* + * Set the density in the parent State object directly, + * by calling the State::setDensity() function. + */ + double dens = 1.0/invDens; + State::setDensity(dens); + + } + + //==================================================================================================================== + void RedlichKwongMFTP::setTemperature(const doublereal temp) { + State::setTemperature(temp); + _updateReferenceStateThermo(); + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::setMassFractions(const doublereal * const x) { + MixtureFugacityTP::setMassFractions(x); + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::setMassFractions_NoNorm(const doublereal * const x) { + MixtureFugacityTP::setMassFractions_NoNorm(x); + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::setMoleFractions(const doublereal * const x) { + MixtureFugacityTP::setMoleFractions(x); + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::setMoleFractions_NoNorm(const doublereal * const x) { + MixtureFugacityTP::setMoleFractions(x); + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::setConcentrations(const doublereal * const c) { + MixtureFugacityTP::setConcentrations(c); + updateAB(); + } + + //==================================================================================================================== + doublereal RedlichKwongMFTP::isothermalCompressibility() const { + + + throw CanteraError("RedlichKwongMFTP::isothermalCompressibility() ", + "not implemented"); + + return 0.0; + } + //==================================================================================================================== + void RedlichKwongMFTP::getActivityConcentrations(doublereal* c) const { + + int k; + getPartialMolarVolumes(DATA_PTR(m_partialMolarVolumes)); + + for (k = 0; k < m_kk; k++) { + c[k] = moleFraction(k) / m_partialMolarVolumes[k]; + } + } + //==================================================================================================================== + /* + * Returns the standard concentration \f$ C^0_k \f$, which is used to normalize + * the generalized concentration. + */ + doublereal RedlichKwongMFTP::standardConcentration(int k) const { + + getStandardVolumes(DATA_PTR(m_tmpV)); + + return 1.0 / m_tmpV[k]; + + + + } + //==================================================================================================================== + /* + * Returns the natural logarithm of the standard + * concentration of the kth species + */ + doublereal RedlichKwongMFTP::logStandardConc(int k) const { + double c = standardConcentration(k); + double lc = std::log(c); + return lc; + } + //==================================================================================================================== + /* + * + * getUnitsStandardConcentration() + * + * Returns the units of the standard and general concentrations + * Note they have the same units, as their divisor is + * defined to be equal to the activity of the kth species + * in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + * + * For EOS types other than cIdealSolidSolnPhase1, the default + * kmol/m3 holds for standard concentration units. For + * cIdealSolidSolnPhase0 type, the standard concentrtion is + * unitless. + */ + void RedlichKwongMFTP::getUnitsStandardConc(double *uA, int, int sizeUA) const { + //int eos = eosType(); + + for (int i = 0; i < sizeUA; i++) { + if (i == 0) uA[0] = 1.0; + if (i == 1) uA[1] = -nDim(); + if (i == 2) uA[2] = 0.0; + if (i == 3) uA[3] = 0.0; + if (i == 4) uA[4] = 0.0; + if (i == 5) uA[5] = 0.0; + } + + } + + //==================================================================================================================== + //! Get the array of non-dimensional activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * For ideal gases, the activity coefficients are all equal to one. + * + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void RedlichKwongMFTP::getActivityCoefficients(doublereal *ac) const { + doublereal TKelvin = temperature(); + doublereal rt = TKelvin * GasConstant; + doublereal mv = molarVolume(); + doublereal sqt = sqrt(TKelvin); + doublereal vpb = mv + m_b_current; + doublereal vmb = mv - m_b_current; + + for (int k = 0; k < m_kk; k++) { + m_pp[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_pp[k] += moleFractions_[i] * a_vec_Curr_[counter]; + } + } + doublereal pres = pressure(); + + for (int k = 0; k < m_kk; k++) { + ac[k] = ( - rt * log(pres * mv / rt) + + rt * log(mv / vmb) + + rt * b_vec_Curr_[k] / vmb + - 2.0 * m_pp[k] / (m_b_current * sqt) * log(vpb/mv) + + m_a_current * b_vec_Curr_[k] / (m_b_current * m_b_current * sqt) * log(vpb/mv) + - m_a_current / (m_b_current * sqt) * ( b_vec_Curr_[k]/vpb) + ); + } + for (int k = 0; k < m_kk; k++) { + ac[k] = exp(ac[k]/rt); + } + } + //==================================================================================================================== + /* + * ---- Partial Molar Properties of the Solution ----------------- + */ + //==================================================================================================================== + /* + * Get the array of non-dimensional species chemical potentials + * These are partial molar Gibbs free energies. + * \f$ \mu_k / \hat R T \f$. + * Units: unitless + * + * We close the loop on this function, here, calling + * getChemPotentials() and then dividing by RT. + */ + void RedlichKwongMFTP::getChemPotentials_RT(doublereal* muRT) const{ + getChemPotentials(muRT); + doublereal invRT = 1.0 / _RT(); + for (int k = 0; k < m_kk; k++) { + muRT[k] *= invRT; + } + } + //==================================================================================================================== + void RedlichKwongMFTP::getChemPotentials(doublereal* mu) const { + getGibbs_ref(mu); + doublereal xx; + doublereal rt = temperature() * GasConstant; + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(SmallNumber, moleFraction(k)); + mu[k] += rt*(log(xx)); + } + + doublereal TKelvin = temperature(); + doublereal mv = molarVolume(); + doublereal sqt = sqrt(TKelvin); + doublereal vpb = mv + m_b_current; + doublereal vmb = mv - m_b_current; + + for (int k = 0; k < m_kk; k++) { + m_pp[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_pp[k] += moleFractions_[i] * a_vec_Curr_[counter]; + } + } + doublereal pres = pressure(); + doublereal refP = refPressure(); + + for (int k = 0; k < m_kk; k++) { + mu[k] += (rt * log(pres/refP) - rt * log(pres * mv / rt) + + rt * log(mv / vmb) + + rt * b_vec_Curr_[k] / vmb + - 2.0 * m_pp[k] / (m_b_current * sqt) * log(vpb/mv) + + m_a_current * b_vec_Curr_[k] / (m_b_current * m_b_current * sqt) * log(vpb/mv) + - m_a_current / (m_b_current * sqt) * ( b_vec_Curr_[k]/vpb) + ); + } + } + //==================================================================================================================== + void RedlichKwongMFTP::getPartialMolarEnthalpies(doublereal* hbar) const { + /* + * First we get the reference state contributions + */ + getEnthalpy_RT_ref(hbar); + doublereal rt = GasConstant * temperature(); + scale(hbar, hbar+m_kk, hbar, rt); + + /* + * We calculate dpdni_ + */ + doublereal TKelvin = temperature(); + doublereal mv = molarVolume(); + doublereal sqt = sqrt(TKelvin); + + doublereal vpb = mv + m_b_current; + doublereal vmb = mv - m_b_current; + + for (int k = 0; k < m_kk; k++) { + m_pp[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_pp[k] += moleFractions_[i] * a_vec_Curr_[counter]; + } + } + + + + for (int k = 0; k < m_kk; k++) { + dpdni_[k] = rt/vmb + rt * b_vec_Curr_[k] / (vmb * vmb) - 2.0 * m_pp[k] / (sqt * mv * vpb) + + m_a_current * b_vec_Curr_[k]/(sqt * mv * vpb * vpb); + } + doublereal dadt = da_dt(); + doublereal fac = TKelvin * dadt - 3.0 * m_a_current / 2.0; + + for (int k = 0; k < m_kk; k++) { + m_tmpV[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_tmpV[k] += 2.0 * moleFractions_[i] * TKelvin * a_coeff_vec(1,counter) - 3.0 * moleFractions_[i] * a_vec_Curr_[counter]; + } + } + + pressureDerivatives(); + doublereal fac2 = mv + TKelvin * dpdT_ / dpdV_; + + for (int k = 0; k < m_kk; k++) { + double hE_v = (mv * dpdni_[k] - rt - b_vec_Curr_[k]/ (m_b_current * m_b_current * sqt) * log(vpb/mv)*fac + + 1.0 / (m_b_current * sqt) * log(vpb/mv) * m_tmpV[k] + + b_vec_Curr_[k] / vpb / (m_b_current * sqt) * fac); + hbar[k] = hbar[k] + hE_v; + + + hbar[k] -= fac2 * dpdni_[k]; + } + + } + //==================================================================================================================== + void RedlichKwongMFTP::getPartialMolarEntropies(doublereal* sbar) const { + getEntropy_R_ref(sbar); + doublereal r = GasConstant; + scale(sbar, sbar+m_kk, sbar, r); + doublereal TKelvin = temperature(); + doublereal sqt = sqrt(TKelvin); + doublereal mv = molarVolume(); + doublereal refP = refPressure(); + + for (int k = 0; k < m_kk; k++) { + doublereal xx = fmaxx(SmallNumber, moleFraction(k)); + sbar[k] += r * ( - log(xx)); + } + + for (int k = 0; k < m_kk; k++) { + m_pp[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_pp[k] += moleFractions_[i] * a_vec_Curr_[counter]; + } + } + + for (int k = 0; k < m_kk; k++) { + m_tmpV[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_tmpV[k] += moleFractions_[i] * a_coeff_vec(1,counter); + } + } + + + doublereal dadt = da_dt(); + doublereal fac = dadt - m_a_current / (2.0 * TKelvin); + doublereal vmb = mv - m_b_current; + doublereal vpb = mv + m_b_current; + + + for (int k = 0; k < m_kk; k++) { + sbar[k] -=( GasConstant * log(GasConstant * TKelvin / (refP * mv)) + + GasConstant + + GasConstant * log(mv/vmb) + + GasConstant * b_vec_Curr_[k]/vmb + + m_pp[k]/(m_b_current * TKelvin * sqt) * log(vpb/mv) + - 2.0 * m_tmpV[k]/(m_b_current * sqt) * log(vpb/mv) + + b_vec_Curr_[k] / (m_b_current * m_b_current * sqt) * log(vpb/mv) * fac + - 1.0 / (m_b_current * sqt) * b_vec_Curr_[k] / vpb * fac + ) ; + } + + pressureDerivatives(); + getPartialMolarVolumes(DATA_PTR(m_partialMolarVolumes)); + for (int k = 0; k < m_kk; k++) { + sbar[k] -= -m_partialMolarVolumes[k] * dpdT_; + } + } + //==================================================================================================================== + void RedlichKwongMFTP::getPartialMolarIntEnergies(doublereal* ubar) const { + getIntEnergy_RT(ubar); + doublereal rt = GasConstant * temperature(); + scale(ubar, ubar+m_kk, ubar, rt); + } + //==================================================================================================================== + void RedlichKwongMFTP::getPartialMolarCp(doublereal* cpbar) const { + getCp_R(cpbar); + doublereal r = GasConstant; + scale(cpbar, cpbar+m_kk, cpbar, r); + } + //==================================================================================================================== + void RedlichKwongMFTP::getPartialMolarVolumes(doublereal* vbar) const { + // getStandardVolumes(vbar); + + + for (int k = 0; k < m_kk; k++) { + m_pp[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_pp[k] += moleFractions_[i] * a_vec_Curr_[counter]; + } + } + + for (int k = 0; k < m_kk; k++) { + m_tmpV[k] = 0.0; + for (int i = 0; i < m_kk; i++) { + int counter = k + m_kk*i; + m_tmpV[k] += moleFractions_[i] * a_coeff_vec(1,counter); + } + } + + doublereal TKelvin = temperature(); + doublereal sqt = sqrt(TKelvin); + doublereal mv = molarVolume(); + + doublereal rt = GasConstant * TKelvin; + + doublereal vmb = mv - m_b_current; + doublereal vpb = mv + m_b_current; + + for (int k = 0; k < m_kk; k++) { + + doublereal num = (rt + rt * m_b_current/ vmb + rt * b_vec_Curr_[k] / vmb + + rt * m_b_current * b_vec_Curr_[k] /(vmb * vmb) + - 2.0 * m_pp[k] / (sqt * vpb) + + m_a_current * b_vec_Curr_[k] / (sqt * vpb * vpb) + ); + + doublereal denom = (m_Pcurrent + rt * m_b_current/(vmb * vmb) - m_a_current / (sqt * vpb * vpb) + ); + + vbar[k] = num / denom; + } + + } + //==================================================================================================================== + doublereal RedlichKwongMFTP::critTemperature() const { + double pc, tc, vc; + double a0 = 0.0; + double aT = 0.0; + for (int i = 0; i < m_kk; i++) { + for (int j = 0; j 500.0) { + tmp2 = tmp / 500.; + tmp2 *= tmp2; + m_pp[k] = m_p0 * exp(500.) * tmp2; + } else { + m_pp[k] = m_p0 * exp(tmp); + } + pres += m_pp[k]; + } + // set state + setState_PX(pres, &m_pp[0]); + } + //==================================================================================================================== + /* + * Initialize the internal lengths. + * (this is not a virtual function) + */ + void RedlichKwongMFTP::initLengths() { + + + a_vec_Curr_.resize(m_kk * m_kk, 0.0); + b_vec_Curr_.resize(m_kk, 0.0); + + a_coeff_vec.resize(2, m_kk * m_kk, 0.0); + + + m_pc_Species.resize(m_kk, 0.0); + m_tc_Species.resize(m_kk, 0.0); + m_vc_Species.resize(m_kk, 0.0); + + + m_pp.resize(m_kk, 0.0); + m_tmpV.resize(m_kk, 0.0); + m_partialMolarVolumes.resize(m_kk, 0.0); + dpdni_.resize(m_kk, 0.0); + } + //==================================================================================================================== + /* + * Import and initialize a ThermoPhase object + * + * param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + * + * This routine initializes the lengths in the current object and + * then calls the parent routine. + */ + void RedlichKwongMFTP::initThermoXML(XML_Node& phaseNode, std::string id) { + RedlichKwongMFTP::initLengths(); + + /* + * Check the model parameter for the Redlich-Kwong equation of state + * two are allowed + * RedlichKwong mixture of species, each of which are RK fluids + * RedlichKwongMFTP mixture of species with cross term coefficients + */ + if (phaseNode.hasChild("thermo")) { + XML_Node& thermoNode = phaseNode.child("thermo"); + std::string model = thermoNode["model"]; + if (model == "RedlichKwong" ) { + m_standardMixingRules = 1; + } else if (model == "RedlichKwongMFTP") { + m_standardMixingRules = 0; + } else { + throw CanteraError("RedlichKwongMFTP::initThermoXML", + "Unknown thermo model : " + model); + } + + + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + XML_Node *acNodePtr = 0; + if (thermoNode.hasChild("activityCoefficients")) { + XML_Node& acNode = thermoNode.child("activityCoefficients"); + acNodePtr = &acNode; + int nC = acNode.nChildren(); + + /* + * Loop through the children getting multiple instances of + * parameters + */ + for (int i = 0; i < nC; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + string stemp = xmlACChild.name(); + string nodeName = lowercase(stemp); + /* + * Process a binary salt field, or any of the other XML fields + * that make up the Pitzer Database. Entries will be ignored + * if any of the species in the entry isn't in the solution. + */ + if (nodeName == "purefluidparameters") { + readXMLPureFluid(xmlACChild); + } + } + if (m_standardMixingRules == 1) { + applyStandardMixingRules(); + } + /* + * Loop through the children getting multiple instances of + * parameters + */ + for (int i = 0; i < nC; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + string stemp = xmlACChild.name(); + string nodeName = lowercase(stemp); + /* + * Process a binary salt field, or any of the other XML fields + * that make up the Pitzer Database. Entries will be ignored + * if any of the species in the entry isn't in the solution. + */ + if (nodeName == "crossfluidparameters") { + readXMLCrossFluid(xmlACChild); + } + } + + } + } + + for (int i = 0; i < m_kk; i++) { + double a0coeff = a_coeff_vec(0, i*m_kk + i); + double aTcoeff = a_coeff_vec(1, i*m_kk + i); + double ai = a0coeff + aTcoeff * 500.; + double bi = b_vec_Curr_[i]; + calcCriticalConditions(ai, bi, a0coeff, aTcoeff, m_pc_Species[i], m_tc_Species[i], m_vc_Species[i]); + } + + MixtureFugacityTP::initThermoXML(phaseNode, id); + } + //==================================================================================================================== + + void RedlichKwongMFTP::readXMLPureFluid(XML_Node &PureFluidParam) { + vector_fp vParams; + string xname = PureFluidParam.name(); + if (xname != "pureFluidParameters") { + throw CanteraError("RedlichKwongMFTP::readXMLPureFluid", + "Incorrect name for processing this routine: " + xname); + } + + /* + * Read the species + * Find the index of the species in the current phase. It's not an error to not find the species + */ + string iName = PureFluidParam.attrib("species"); + if (iName == "") { + throw CanteraError("RedlichKwongMFTP::readXMLPureFluid", "no species attribute"); + } + int iSpecies = speciesIndex(iName); + if (iSpecies < 0) { + return; + } + int counter = iSpecies + m_kk * iSpecies; + int nParamsExpected, nParamsFound; + int num = PureFluidParam.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = PureFluidParam.child(iChild); + string stemp = xmlChild.name(); + string nodeName = lowercase(stemp); + + if (nodeName == "a_coeff") { + string iModel = lowercase(xmlChild.attrib("model")); + if (iModel == "constant") { + nParamsExpected = 1; + } else if (iModel == "linear_a") { + nParamsExpected = 2; + if (m_formTempParam == 0) { + m_formTempParam = 1; + } + } else { + throw CanteraError("", "unknown model"); + } + + ctml::getFloatArray(xmlChild, vParams, true, "Pascal-m6/kmol2", "a_coeff"); + nParamsFound = vParams.size(); + if (nParamsFound != nParamsExpected) { + throw CanteraError("RedlichKwongMFTP::readXMLPureFluid(for a_coeff" + iName + ")", + "wrong number of params found"); + } + + for (int i = 0; i < nParamsFound; i++) { + a_coeff_vec(i, counter) = vParams[i]; + } + } else if (nodeName == "b_coeff") { + ctml::getFloatArray(xmlChild, vParams, true, "m3/kmol", "b_coeff"); + nParamsFound = vParams.size(); + if (nParamsFound != 1) { + throw CanteraError("RedlichKwongMFTP::readXMLPureFluid(for b_coeff" + iName + ")", + "wrong number of params found"); + } + b_vec_Curr_[iSpecies] = vParams[0]; + } + } + } + //==================================================================================================================== + void RedlichKwongMFTP::applyStandardMixingRules() { + int nParam = 2; + for (int i = 0; i < m_kk; i++) { + int icounter = i + m_kk * i; + for (int j = 0; j < m_kk; j++) { + if (i != j) { + int counter = i + m_kk * j; + int jcounter = j + m_kk * j; + for (int n = 0; n < nParam; n++) { + a_coeff_vec(n, counter) = sqrt(a_coeff_vec(n, icounter) * a_coeff_vec(n, jcounter)); + } + } + } + } + } + //==================================================================================================================== + + void RedlichKwongMFTP::readXMLCrossFluid(XML_Node &CrossFluidParam) { + vector_fp vParams; + string xname = CrossFluidParam.name(); + if (xname != "crossFluidParameters") { + throw CanteraError("RedlichKwongMFTP::readXMLCrossFluid", + "Incorrect name for processing this routine: " + xname); + } + + /* + * Read the species + * Find the index of the species in the current phase. It's not an error to not find the species + */ + string iName = CrossFluidParam.attrib("species1"); + if (iName == "") { + throw CanteraError("RedlichKwongMFTP::readXMLCrossFluid", "no species1 attribute"); + } + int iSpecies = speciesIndex(iName); + if (iSpecies < 0) { + return; + } + string jName = CrossFluidParam.attrib("species2"); + if (iName == "") { + throw CanteraError("RedlichKwongMFTP::readXMLCrossFluid", "no species2 attribute"); + } + int jSpecies = speciesIndex(jName); + if (jSpecies < 0) { + return; + } + + int counter = iSpecies + m_kk * jSpecies; + int counter0 = jSpecies + m_kk * iSpecies; + int nParamsExpected, nParamsFound; + int num = CrossFluidParam.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = CrossFluidParam.child(iChild); + string stemp = xmlChild.name(); + string nodeName = lowercase(stemp); + + if (nodeName == "a_coeff") { + string iModel = lowercase(xmlChild.attrib("model")); + if (iModel == "constant") { + nParamsExpected = 1; + } else if (iModel == "linear_a") { + nParamsExpected = 2; + if (m_formTempParam == 0) { + m_formTempParam = 1; + } + } else { + throw CanteraError("", "unknown model"); + } + + ctml::getFloatArray(xmlChild, vParams, true, "Pascal-m6/kmol2", "a_coeff"); + nParamsFound = vParams.size(); + if (nParamsFound != nParamsExpected) { + throw CanteraError("RedlichKwongMFTP::readXMLCrossFluid(for a_coeff" + iName + ")", + "wrong number of params found"); + } + + for (int i = 0; i < nParamsFound; i++) { + a_coeff_vec(i, counter) = vParams[i]; + a_coeff_vec(i, counter0) = vParams[i]; + } + } + } + } + //==================================================================================================================== + void RedlichKwongMFTP::setParametersFromXML(const XML_Node& thermoNode) { + MixtureFugacityTP::setParametersFromXML(thermoNode); + std::string model = thermoNode["model"]; + + + } + //==================================================================================================================== + // Calculate the deviation terms for the total entropy of the mixture from the + // ideal gas mixture + /* + * Here we use the current state conditions + * + * @return Returns the change in entropy in units of J kmol-1 K-1. + */ + doublereal RedlichKwongMFTP::sresid() const{ + // note this agrees with tpx + doublereal rho = density(); + doublereal mmw = meanMolecularWeight(); + doublereal molarV = mmw / rho; + double hh = m_b_current / molarV; + doublereal zz = z(); + doublereal dadt = da_dt(); + doublereal T = temperature(); + doublereal sqT = sqrt(T); + doublereal fac = dadt - m_a_current / (2.0 * T); + double sresid_mol_R = log(zz*(1.0 - hh)) + log(1.0 + hh) * fac / (sqT * GasConstant * m_b_current); + double sp = GasConstant * sresid_mol_R; + return sp; + } + //==================================================================================================================== + // Calculate the deviation terms for the total enthalpy of the mixture from the + // ideal gas mixture + /* + * Here we use the current state conditions + * + * @return Returns the change in entropy in units of J kmol-1. + */ + doublereal RedlichKwongMFTP::hresid() const{ + // note this agrees with tpx + doublereal rho = density(); + doublereal mmw = meanMolecularWeight(); + doublereal molarV = mmw / rho; + double hh = m_b_current / molarV; + doublereal zz = z(); + doublereal dadt = da_dt(); + doublereal T = temperature(); + doublereal sqT = sqrt(T); + doublereal fac = T * dadt - 3.0 *m_a_current / (2.0); + double hresid_mol = GasConstant * T * (zz - 1.0) + fac * log(1.0 + hh) / (sqT * m_b_current); + return hresid_mol; + } + //==================================================================================================================== + // Estimate for the molar volume of the liquid + /* + * Note: this is only used as a starting guess for later routines that actually calculate an + * accurate value for the liquid molar volume. + * This routine doesn't change the state of the system. + * + * @param TKelvin temperature in kelvin + * @param pres Pressure in Pa. This is used as an initial guess. If the routine + * needs to change the pressure to find a stable liquid state, the + * new pressure is returned in this variable. + * + * @return Returns the estimate of the liquid volume. If the liquid can't be found, this + * routine returns -1. + */ + doublereal RedlichKwongMFTP::liquidVolEst(doublereal TKelvin, doublereal &presGuess) const + { + + double v = m_b_current * 1.1; + double atmp; + double btmp; + calculateAB(TKelvin, atmp, btmp); + + doublereal pres = presGuess; + double pp = psatEst(TKelvin); + if (pres < pp) { + pres = pp; + } + double Vroot[3]; + +#ifdef NNN + if (TKelvin == 308.) { + double pVec[100]; + int n = 0; + for (int i = 0; i < 100; i++) { + pVec[n++] = 6.8E6 + 2.0E5 * i; + } + + for (int i = 0; i < 100; i++) { + int nsol = NicholsSolve(TKelvin, pVec[i], atmp, btmp, Vroot); + printf ("nsol = %d, p = %g, T = %g, v[0] = %g, v[1] %g, v[2] = %g\n", nsol, pVec[i], TKelvin, Vroot[0], Vroot[1], Vroot[2]); + } + } +#endif + + bool foundLiq = false; + int m = 0; + do { + + int nsol = NicholsSolve(TKelvin, pres, atmp, btmp, Vroot); + + // printf("nsol = %d\n", nsol); + // printf("liquidVolEst start: T = %g , p = %g, a = %g, b = %g\n", TKelvin, pres, m_a_current, m_b_current); + + if (nsol == 1 || nsol == 2) { + double pc = critPressure(); + if (pres > pc) { + foundLiq = true; + } + pres *= 1.04; + + } else { + foundLiq = true; + } + } while ((m < 100) && (!foundLiq)); + +#ifdef DONTUSE + int i; + double c; + double vnew; + double deltav; + double sqt = sqrt(TKelvin); + for (i = 0; i < 200; i++) { + c = bCalc * bCalc + bCalc * GasConstant * TKelvin / pres - atmp / (pres * sqt); + vnew = (1.0/c)*(v*v*v - GasConstant * TKelvin *v*v/pp - atmp * bCalc / (pres * sqt)); + deltav = vnew - v; + if (deltav > v*0.2) { + deltav = v * 0.2; + } else if (deltav < - (v * 0.2)) { + deltav = - v * 0.2; + } + v += deltav; + if (fabs(deltav) < 1.0E-6 * v) { + break; + } + } + if (i > 30) { + printf("liquidVolEst problem solve: T = %g , p = %g, a = %g, b = %g\n", TKelvin, pres, atmp, bCalc); + printf(" v final = %g\n", v); + } + if (fabs(deltav) > 1.0E-5 * v) { + throw CanteraError("RedlichKwongMFTP::liquidVolEst(T = " + fp2str(TKelvin) + ", " + fp2str(pres) + ")", + "failed to converge"); + } +#else + if (foundLiq) { + v = Vroot[0]; + presGuess = pres; + } else { + v = -1.0; + } +#endif + //printf (" RedlichKwongMFTP::liquidVolEst %g %g converged in %d its\n", TKelvin, pres, i); + return v; + } + //==================================================================================================================== + // Calculates the density given the temperature and the pressure and a guess at the density. + /* + * Note, below T_c, this is a multivalued function. We do not cross the vapor dome in this. + * This is protected because it is called during setState_TP() routines. Infinite loops would result + * if it were not protected. + * + * -> why is this not const? + * + * parameters: + * @param TKelvin Temperature in Kelvin + * @param pressure Pressure in Pascals (Newton/m**2) + * @param phaseReqested int representing the phase whose density we are requesting. If we put + * a gas or liquid phase here, we will attempt to find a volume in that + * part of the volume space, only, in this routine. A value of FLUID_UNDEFINED + * means that we will accept anything. + * + * @param rhoguess Guessed density of the fluid. A value of -1.0 indicates that there + * is no guessed density + * + * + * @return We return the density of the fluid at the requested phase. If we have not found any + * acceptable density we return a -1. If we have found an accectable density at a + * different phase, we return a -2. + */ + doublereal RedlichKwongMFTP::densityCalc(doublereal TKelvin, doublereal presPa, int phaseRequested, doublereal rhoguess) { + + //setTemperature(TKelvin); + double tcrit = critTemperature(); + doublereal mmw = meanMolecularWeight(); + double densBase = 0.0; + if (rhoguess == -1.0) { + if (phaseRequested != FLUID_GAS) { + if (TKelvin > tcrit) { + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } else { + if (phaseRequested == FLUID_GAS || phaseRequested == FLUID_SUPERCRIT) { + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } else if (phaseRequested >= FLUID_LIQUID_0) { + double lqvol = liquidVolEst(TKelvin, presPa); + rhoguess = mmw / lqvol; + } + } + } else { + /* + * Assume the Gas phase initial guess, if nothing is + * specified to the routine + */ + rhoguess = presPa * mmw / (GasConstant * TKelvin); + } + + } + + + doublereal volguess = mmw / rhoguess; + NSolns_ = NicholsSolve(TKelvin, presPa, m_a_current, m_b_current, Vroot_); + + doublereal molarVolLast = Vroot_[0]; + if (NSolns_ >= 2) { + if (phaseRequested >= FLUID_LIQUID_0) { + molarVolLast = Vroot_[0]; + } else if (phaseRequested == FLUID_GAS || phaseRequested == FLUID_SUPERCRIT) { + molarVolLast = Vroot_[2]; + } else { + if (volguess > Vroot_[1]) { + molarVolLast = Vroot_[2]; + } else { + molarVolLast = Vroot_[0]; + } + } + } else if (NSolns_ == 1) { + if (phaseRequested == FLUID_GAS || phaseRequested == FLUID_SUPERCRIT || phaseRequested == FLUID_UNDEFINED) { + molarVolLast = Vroot_[0]; + } else { + //molarVolLast = Vroot_[0]; + //printf("DensityCalc(): Possible problem encountered\n"); + return -2.0; + } + } else if (NSolns_ == -1) { + if (phaseRequested >= FLUID_LIQUID_0 || phaseRequested == FLUID_UNDEFINED || phaseRequested == FLUID_SUPERCRIT) { + molarVolLast = Vroot_[0]; + } else if (TKelvin > tcrit) { + molarVolLast = Vroot_[0]; + } else { + // molarVolLast = Vroot_[0]; + //printf("DensityCalc(): Possible problem encountered\n"); + return -2.0; + } + } else { + molarVolLast = Vroot_[0]; + //printf("DensityCalc(): Possible problem encountered\n"); + return -1.0; + } + densBase = mmw / molarVolLast; + return densBase; + } + //==================================================================================================================== + // Return the value of the density at the liquid spinodal point (on the liquid side) + // for the current temperature. + /* + * @return returns the density with units of kg m-3 + */ + doublereal RedlichKwongMFTP::densSpinodalLiquid() const { + if (NSolns_ != 3) { + double dens = critDensity(); + return dens; + } + double vmax = Vroot_[1]; + double vmin = Vroot_[0]; + RootFind rf(fdpdv_); + rf.setPrintLvl(10); + rf.setTol(1.0E-5, 1.0E-10); + rf.setFuncIsGenerallyDecreasing(true); + + double vbest = 0.5 * (Vroot_[0]+Vroot_[1]); + double funcNeeded = 0.0; + + int status = rf.solve(vmin, vmax, 100, funcNeeded, &vbest); + if (status != ROOTFIND_SUCCESS) { + throw CanteraError(" RedlichKwongMFTP::densSpinodalLiquid() ", "didn't converge"); + } + doublereal mmw = meanMolecularWeight(); + doublereal rho = mmw / vbest; + return rho; + } + //==================================================================================================================== + // Return the value of the density at the gas spinodal point (on the gas side) + // for the current temperature. + /* + * @return returns the density with units of kg m-3 + */ + doublereal RedlichKwongMFTP::densSpinodalGas() const { + if (NSolns_ != 3) { + double dens = critDensity(); + return dens; + } + double vmax = Vroot_[2]; + double vmin = Vroot_[1]; + RootFind rf(fdpdv_); + rf.setPrintLvl(10); + rf.setTol(1.0E-5, 1.0E-10); + rf.setFuncIsGenerallyIncreasing(true); + + double vbest = 0.5 * (Vroot_[1]+Vroot_[2]); + double funcNeeded = 0.0; + + int status = rf.solve(vmin, vmax, 100, funcNeeded, &vbest); + if (status != ROOTFIND_SUCCESS) { + throw CanteraError(" RedlichKwongMFTP::densSpinodalGas() ", "didn't converge"); + } + doublereal mmw = meanMolecularWeight(); + doublereal rho = mmw / vbest; + return rho; + } + //==================================================================================================================== + // Calculate the pressure given the temperature and the molar volume + /* + * Calculate the pressure given the temperature and the molar volume + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @return Returns the pressure. + */ + doublereal RedlichKwongMFTP::pressureCalc(doublereal TKelvin, doublereal molarVol) const { + doublereal sqt = sqrt(TKelvin); + double pres = GasConstant * TKelvin / (molarVol - m_b_current) + - m_a_current / (sqt * molarVol * (molarVol + m_b_current)); + return pres; + } + //==================================================================================================================== + // Calculate the pressure and the pressure derivative given the temperature and the molar volume + /* + * Temperature and mole number are held constant + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @param presCalc Returns the pressure. + * + * @return Returns the derivative of the pressure wrt the molar volume + */ + doublereal RedlichKwongMFTP::dpdVCalc(doublereal TKelvin, doublereal molarVol, doublereal &presCalc) const { + doublereal sqt = sqrt(TKelvin); + presCalc = GasConstant * TKelvin / (molarVol - m_b_current) + - m_a_current / (sqt * molarVol * (molarVol + m_b_current)); + + doublereal vpb = molarVol + m_b_current; + doublereal vmb = molarVol - m_b_current; + doublereal dpdv = (- GasConstant * TKelvin / (vmb * vmb) + + m_a_current * (2 * molarVol + m_b_current) / (sqt * molarVol * molarVol * vpb * vpb)); + return dpdv; + } + //==================================================================================================================== + + void RedlichKwongMFTP::pressureDerivatives() const { + doublereal TKelvin = temperature(); + doublereal mv = molarVolume(); + doublereal pres; + + dpdV_ = dpdVCalc(TKelvin, mv, pres); + + doublereal sqt = sqrt(TKelvin); + doublereal vpb = mv + m_b_current; + doublereal vmb = mv - m_b_current; + doublereal dadt = da_dt(); + doublereal fac = dadt - m_a_current/(2.0 * TKelvin); + + dpdT_ = (GasConstant / (vmb) - fac / (sqt * mv * vpb)); + } + //==================================================================================================================== + void RedlichKwongMFTP::updateMixingExpressions() { + updateAB(); + } + //==================================================================================================================== + void RedlichKwongMFTP::updateAB() { + double temp = temperature(); + int counter; + if (m_formTempParam == 1) { + for (int i = 0; i < m_kk; i++) { + for (int j = 0; j < m_kk; j++) { + counter = i * m_kk + j; + a_vec_Curr_[counter] = a_coeff_vec(0,counter) + a_coeff_vec(1,counter) * temp; + } + } + } + + m_b_current = 0.0; + m_a_current = 0.0; + for (int i = 0; i < m_kk; i++) { + m_b_current += moleFractions_[i] * b_vec_Curr_[i]; + for (int j = 0; j < m_kk; j++) { + m_a_current += a_vec_Curr_[i * m_kk + j] * moleFractions_[i] * moleFractions_[j]; + } + } + } + //==================================================================================================================== + void RedlichKwongMFTP::calculateAB(doublereal temp, doublereal &aCalc, doublereal &bCalc) const { + int counter; + bCalc = 0.0; + aCalc = 0.0; + if (m_formTempParam == 1) { + for (int i = 0; i < m_kk; i++) { + bCalc += moleFractions_[i] * b_vec_Curr_[i]; + for (int j = 0; j < m_kk; j++) { + counter = i * m_kk + j; + doublereal a_vec_Curr = a_coeff_vec(0,counter) + a_coeff_vec(1,counter) * temp; + aCalc += a_vec_Curr * moleFractions_[i] * moleFractions_[j]; + } + } + } else { + for (int i = 0; i < m_kk; i++) { + bCalc += moleFractions_[i] * b_vec_Curr_[i]; + for (int j = 0; j < m_kk; j++) { + counter = i * m_kk + j; + doublereal a_vec_Curr = a_coeff_vec(0,counter); + aCalc += a_vec_Curr * moleFractions_[i] * moleFractions_[j]; + } + } + } + } + //==================================================================================================================== + doublereal RedlichKwongMFTP::da_dt() const { + + doublereal dadT = 0.0; + if (m_formTempParam == 1) { + for (int i = 0; i < m_kk; i++) { + for (int j = 0; j < m_kk; j++) { + int counter = i * m_kk + j; + dadT+= a_coeff_vec(1,counter) * moleFractions_[i] * moleFractions_[j]; + } + } + } + return dadT; + } + //==================================================================================================================== + void RedlichKwongMFTP::calcCriticalConditions(doublereal a, doublereal b, doublereal a0_coeff, doublereal aT_coeff, + doublereal &pc, doublereal &tc, doublereal &vc) const { + if (m_formTempParam != 0) { + a = a0_coeff; + } + if (b <= 0.0) { + tc = 1000000.; + pc = 1.0E13; + vc = omega_vc * GasConstant * tc / pc; + return; + } + if (a <= 0.0) { + tc = 0.0; + pc = 0.0; + vc = 2.0 * b; + return; + } + double tmp = a * omega_b / (b * omega_a * GasConstant); + double pp = 2./3.; + doublereal sqrttc, f, dfdt, deltatc; + + if (m_formTempParam == 0) { + + tc = pow(tmp, pp); + } else { + tc = pow(tmp, pp); + for (int j = 0; j < 10; j++) { + sqrttc = sqrt(tc); + f = omega_a * b * GasConstant * tc * sqrttc / omega_b - aT_coeff * tc - a0_coeff; + dfdt = 1.5 * omega_a * b * GasConstant * sqrttc / omega_b - aT_coeff; + deltatc = - f / dfdt; + tc += deltatc; + } + if (deltatc > 0.1) { + throw CanteraError("RedlichKwongMFTP::calcCriticalConditions", "didn't converge"); + } + } + + pc = omega_b * GasConstant * tc / b; + vc = omega_vc * GasConstant * tc / pc; + } + + //==================================================================================================================== + // Solve the cubic equation of state + /* + * The R-K equation of state may be solved via the following formula + * + * V**3 - V**2(RT/P) - V(RTb/P - a/(P T**.5) + b*b) - (a b / (P T**.5)) = 0 + * + + * Returns the number of solutions found. If it only finds the liquid branch solution, it will return a -1 or a -2 + * instead of 1 or 2. If it returns 0, then there is an error. + * + */ + int RedlichKwongMFTP::NicholsSolve(double TKelvin, double pres, doublereal a, doublereal b, + doublereal Vroot[3]) const { + Vroot[0] = 0.0; + Vroot[1] = 0.0; + Vroot[2] = 0.0; + int nTurningPoints; + bool lotsOfNumError = false; + doublereal Vturn[2]; + if (TKelvin <= 0.0) { + throw CanteraError("RedlichKwongMFTP::NicholsSolve()", "neg temperature"); + } + /* + * Derive the coefficients of the cubic polynomial to solve. + */ + doublereal an = 1.0; + doublereal bn = - GasConstant * TKelvin / pres; + doublereal sqt = sqrt(TKelvin); + doublereal cn = - (GasConstant * TKelvin * b / pres - a/(pres * sqt) + b * b); + doublereal dn = - (a * b / (pres * sqt)); + + double tmp = a * omega_b / (b * omega_a * GasConstant); + double pp = 2./3.; + double tc = pow(tmp, pp); + double pc = omega_b * GasConstant * tc / b; + double vc = omega_vc * GasConstant * tc / pc; + // Derive the center of the cubic, x_N + doublereal xN = - bn /(3 * an); + + + // Derive the value of delta**2. This is a key quantity that determines the number of turning points + doublereal delta2 = (bn * bn - 3 * an * cn) / (9 * an * an); + doublereal delta = 0.0; + + // Calculate a couple of ratios + doublereal ratio1 = 3.0 * an * cn / (bn * bn); + doublereal ratio2 = pres * b / (GasConstant * TKelvin); + if (fabs(ratio1) < 1.0E-7) { + //printf("NicholsSolve(): Alternative solution (p = %g T = %g)\n", pres, TKelvin); + doublereal ratio3 = a / (GasConstant * sqt) * pres / (GasConstant * TKelvin); + if (fabs(ratio2) < 1.0E-5 && fabs(ratio3) < 1.0E-5) { + doublereal z = 1.0; + for (int i = 0; i < 10; i++) { + doublereal znew = z / (z - ratio2) - ratio3 / (z + ratio1); + doublereal deltaz = znew - z; + z = znew; + if (fabs(deltaz) < 1.0E-14) { + break; + } + } + doublereal v = z * GasConstant * TKelvin / pres; + Vroot[0] = v; + return 1; + } + } + + + int nSolnValues; + nTurningPoints = 2; + +#ifdef PRINTPV + double V[100]; + int n = 0; + for (int i = 0; i < 90; i++) { + V[n++] = 0.030 + 0.005 * i; + } + double p1, presCalc; + for (int i = 0; i < n; i++) { + p1 = dpdVCalc(TKelvin, V[i], presCalc); + printf(" %13.5g %13.5g %13.5g \n", V[i], presCalc , p1); + } +#endif + + double h2 = 4. * an * an * delta2 * delta2 * delta2; + if (delta2 == 0.0) { + nTurningPoints = 1; + Vturn[0] = xN; + Vturn[1] = xN; + } else if (delta2 < 0.0) { + nTurningPoints = 0; + Vturn[0] = xN; + Vturn[1] = xN; + } else { + delta = sqrt(delta2); + Vturn[0] = xN - delta; + Vturn[1] = xN + delta; +#ifdef PRINTPV + double presCalc; + double p1 = dpdVCalc(TKelvin, Vturn[0], presCalc); + + double p2 = dpdVCalc(TKelvin, Vturn[1], presCalc); + + printf("p1 = %g p2 = %g \n", p1, p2); + p1 = dpdVCalc(TKelvin, 0.9*Vturn[0], presCalc); + printf("0.9 p1 = %g \n", p1); +#endif + } + + doublereal h = 2.0 * an * delta * delta2; + + doublereal yN = 2.0 * bn * bn * bn / (27.0 * an * an) - bn * cn / (3.0 * an) + dn; + + doublereal desc = yN * yN - h2; + + if (fabs(fabs(h) - fabs(yN)) < 1.0E-10) { + if (desc != 0.0) { + // this is for getting to other cases + printf("NicholsSolve(): numerical issues\n"); + throw CanteraError("NicholsSolve()", "numerical issues"); + } + desc = 0.0; + } + + if (desc < 0.0) { + nSolnValues = 3; + } else if (desc == 0.0) { + nSolnValues = 2; + // We are here as p goes to zero. + // double hleft = 3.0 * an * cn / (bn * bn); + //double ynleft = 9.0 * an * cn / (2.0 * bn * bn) - 27.0 * an * an * dn / (2.0 * bn * bn * bn); + //printf("hleft = %g , ynleft = %g\n", -3. / 2. * hleft, -ynleft); + //double h2left = - 3 * hleft + 3 * hleft * hleft - hleft * hleft * hleft; + //double y2left = - 2.0 * ynleft + ynleft * ynleft; + //printf("h2left = %g , yn2left = %g\n", h2left, y2left); + + } else if (desc > 0.0) { + nSolnValues = 1; + } + + /* + * One real root -> have to determine whether gas or liquid is the root + */ + if (desc > 0.0) { + doublereal tmpD = sqrt(desc); + doublereal tmp1 = (- yN + tmpD) / (2.0 * an); + doublereal sgn1 = 1.0; + if (tmp1 < 0.0) { + sgn1 = -1.0; + tmp1 = -tmp1; + } + doublereal tmp2 = (- yN - tmpD) / (2.0 * an); + doublereal sgn2 = 1.0; + if (tmp2 < 0.0) { + sgn2 = -1.0; + tmp2 = -tmp2; + } + doublereal p1 = pow(tmp1, 1./3.); + doublereal p2 = pow(tmp2, 1./3.); + + doublereal alpha = xN + sgn1 * p1 + sgn2 * p2; + Vroot[0] = alpha; + Vroot[1] = 0.0; + Vroot[2] = 0.0; + + double tmp = an * Vroot[0] * Vroot[0] * Vroot[0] + bn * Vroot[0] * Vroot[0] + cn * Vroot[0] + dn; + if (fabs (tmp) > 1.0E-4) { + lotsOfNumError = true; + } + + } else if (desc < 0.0) { + doublereal tmp = - yN/h; + + doublereal val = acos(tmp); + doublereal theta = val / 3.0; + + doublereal oo = 2. * Cantera::Pi / 3.; + doublereal alpha = xN + 2. * delta * cos(theta); + + doublereal beta = xN + 2. * delta * cos(theta + oo); + + doublereal gamma = xN + 2. * delta * cos(theta + 2.0 * oo); + + + Vroot[0] = beta; + Vroot[1] = gamma; + Vroot[2] = alpha; + + for (int i = 0; i < 3; i++) { + double tmp = an * Vroot[i] * Vroot[i] * Vroot[i] + bn * Vroot[i] * Vroot[i] + cn * Vroot[i] + dn; + if (fabs (tmp) > 1.0E-4) { + lotsOfNumError = true; + for (int j = 0; j < 3; j++) { + if (j != i) { + if (fabs(Vroot[i] - Vroot[j]) < 1.0E-4 * (fabs(Vroot[i]) + fabs(Vroot[j]))) { + writelog("RedlichKwongMFTP::NicholsSolve(T = " + fp2str(TKelvin) + ", p = " + + fp2str(pres) + "): WARNING roots have merged: " + + fp2str(Vroot[i]) + ", " + fp2str(Vroot[j])); + writelogendl(); + } + } + } + } + } + } else if (desc == 0.0) { + if (yN == 0.0 && h == 0.0) { + Vroot[0] = xN; + Vroot[1] = xN; + Vroot[2] = xN; + } else { + // need to figure out whether delta is pos or neg + if (yN > 0.0) { + double tmp = pow(yN/(2*an), 1./3.); + if (fabs(tmp - delta) > 1.0E-9) { + throw CanteraError("RedlichKwongMFTP::NicholsSolve()", "unexpected"); + } + Vroot[1] = xN + delta; + Vroot[0] = xN - 2.0*delta; // liquid phase root + } else { + double tmp = pow(yN/(2*an), 1./3.); + if (fabs(tmp - delta) > 1.0E-9) { + throw CanteraError("RedlichKwongMFTP::NicholsSolve()", "unexpected"); + } + delta = -delta; + Vroot[0] = xN + delta; + Vroot[1] = xN - 2.0*delta; // gas phase root + } + } + for (int i = 0; i < 2; i++) { + double tmp = an * Vroot[i] * Vroot[i] * Vroot[i] + bn * Vroot[i] * Vroot[i] + cn * Vroot[i] + dn; + if (fabs (tmp) > 1.0E-4) { + lotsOfNumError = true; + } + } + } + + /* + * Unfortunately, there is a heavy amount of roundoff error due to bad conditioning in this + */ + double res, dresdV;; + for (int i = 0; i < nSolnValues; i++) { + for (int n = 0; n < 20; n++) { + res = an * Vroot[i] * Vroot[i] * Vroot[i] + bn * Vroot[i] * Vroot[i] + cn * Vroot[i] + dn; + if (fabs(res) < 1.0E-14) { + break; + } + dresdV = 3.0 * an * Vroot[i] * Vroot[i] + 2.0 * bn * Vroot[i] + cn; + double del = - res / dresdV; + + Vroot[i] += del; + if (fabs(del) / (fabs(Vroot[i]) + fabs(del)) < 1.0E-14) { + break; + } + double res2 = an * Vroot[i] * Vroot[i] * Vroot[i] + bn * Vroot[i] * Vroot[i] + cn * Vroot[i] + dn; + if (fabs(res2) < fabs(res)) { + continue; + } else { + Vroot[i] -= del; + Vroot[i] += 0.1 * del; + } + } + if ((fabs(res) > 1.0E-14) && (fabs(res) > 1.0E-14 * fabs(dresdV) * fabs(Vroot[i])) ) { + writelog("RedlichKwongMFTP::NicholsSolve(T = " + fp2str(TKelvin) + ", p = " + + fp2str(pres) + "): WARNING root didn't converge V = " + fp2str(Vroot[i]) ); + writelogendl(); + } + } + + if (nSolnValues == 1) { + if (TKelvin > tc) { + if (Vroot[0] < vc) { + nSolnValues = -1; + } + } else { + if (Vroot[0] < xN) { + nSolnValues = -1; + } + } + + } else { + if (nSolnValues == 2) { + if (delta > 0.0) { + nSolnValues = -2; + } + } + } + // writelog("RedlichKwongMFTP::NicholsSolve(T = " + fp2str(TKelvin) + ", p = " + fp2str(pres) + "): finished"); + // writelogendl(); + return nSolnValues; + } + + +#endif +} + + diff --git a/Cantera/src/thermo/RedlichKwongMFTP.h b/Cantera/src/thermo/RedlichKwongMFTP.h new file mode 100644 index 000000000..8728fad52 --- /dev/null +++ b/Cantera/src/thermo/RedlichKwongMFTP.h @@ -0,0 +1,843 @@ +/** + * @file RedlichKwongMFTP.h + * Definition file for a derived class of ThermoPhase that assumes either + * an ideal gas or ideal solution approximation and handles + * variable pressure standard state methods for calculating + * thermodynamic properties (see \ref thermoprops and + * class \link Cantera::RedlichKwongMFTP RedlichKwongMFTP\endlink). + */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Author: hkmoffa $ + * $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ + * $Revision: 255 $ + */ + +#ifndef CT_REDLICHKWONGMFTP_H +#define CT_REDLICHKWONGMFTP_H + +#include "MixtureFugacityTP.h" + +namespace Cantera { + + class XML_Node; + class PDSS; + + /*! + * @name CONSTANTS - Models for the Standard State of IdealSolnPhase's + */ + //@{ + +#ifdef WITH_REAL_GASSES + + /** + * @ingroup thermoprops + * + * This class can handle either an ideal solution or an ideal gas approximation + * of a phase. + * + * + * @nosubgrouping + */ + class RedlichKwongMFTP : public MixtureFugacityTP { + + public: + + /*! + * + * @name Constructors and Duplicators for %RedlichKwongMFTP + * + */ + //! Base constructor. + RedlichKwongMFTP(); + + //! Construct and initialize a RedlichKwongMFTP ThermoPhase object + //! directly from an asci input file + /*! + * Working constructors + * + * The two constructors below are the normal way the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + * + * @param inputFile Name of the input file containing the phase XML data + * to set up the object + * @param id ID of the phase in the input file. Defaults to the empty string. + */ + RedlichKwongMFTP(std::string infile, std::string id=""); + + //! Construct and initialize a RedlichKwongMFTP ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML phase node containing the description of the phase + * @param id id attribute containing the name of the phase. (default is the empty string) + */ + RedlichKwongMFTP(XML_Node& phaseRef, std::string id = ""); + + //! This is a special constructor, used to replicate test problems + //! during the initial verification of the object + /*! + * + * test problems: + * 1: Pure CO2 problem + * input file = CO2_RedlickKwongMFTP.xml + * + * @param testProb Hard -coded test problem to instantiate. + * Current valid values are 1. + */ + RedlichKwongMFTP(int testProb); + + //! Copy Constructor + /*! + * Copy constructor for the object. Constructed object will be a clone of this object, but will + * also own all of its data. This is a wrapper around the assignment operator + * + * @param right Object to be copied. + */ + RedlichKwongMFTP(const RedlichKwongMFTP &right); + + //! Asignment operator + /*! + * Assignment operator for the object. Constructed object will be a clone of this object, but will + * also own all of its data. + * + * @param right Object to be copied. + */ + RedlichKwongMFTP& operator=(const RedlichKwongMFTP &right); + + //! Destructor. + virtual ~RedlichKwongMFTP(); + + + //! Duplicator from the ThermoPhase parent class + /*! + * Given a pointer to a ThermoPhase object, this function will + * duplicate the ThermoPhase object and all underlying structures. + * This is basically a wrapper around the copy constructor. + * + * @return returns a pointer to a ThermoPhase + */ + virtual ThermoPhase *duplMyselfAsThermoPhase() const; + + //@} + + /** + * @name Utilities (RedlichKwongMFTP) + */ + //@{ + /** + * Equation of state type flag. The base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Constants defined for this purpose are + * listed in mix_defs.h. + */ + virtual int eosType() const; + + //@} + + /// Molar enthalpy. Units: J/kmol. + virtual doublereal enthalpy_mole() const; + + /// Molar internal energy. Units: J/kmol. + virtual doublereal intEnergy_mole() const; + + /// Molar entropy. Units: J/kmol/K. + virtual doublereal entropy_mole() const; + + /// Molar Gibbs function. Units: J/kmol. + virtual doublereal gibbs_mole() const; + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + virtual doublereal cp_mole() const; + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + virtual doublereal cv_mole() const; + + /** + * @} + * @name Mechanical Properties + * @{ + */ + + //! Return the thermodynamic pressure (Pa). + /*! + * Since the mass density, temperature, and mass fractions are stored, + * this method uses these values to implement the + * mechanical equation of state \f$ P(T, \rho, Y_1, \dots, Y_K) \f$. + * + * \f[ + * P = \frac{RT}{v-b_{mix}} - \frac{a_{mix}}{T^{0.5} v \left( v + b_{mix} \right) } + * \f] + * + */ + virtual doublereal pressure() const; + + //! Returns the isothermal compressibility. Units: 1/Pa. + /*! + * The isothermal compressibility is defined as + * \f[ + * \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T + * \f] + */ + virtual doublereal isothermalCompressibility() const; + + protected: + /** + * Calculate the density of the mixture using the partial + * molar volumes and mole fractions as input + * + * The formula for this is + * + * \f[ + * \rho = \frac{\sum_k{X_k W_k}}{\sum_k{X_k V_k}} + * \f] + * + * where \f$X_k\f$ are the mole fractions, \f$W_k\f$ are + * the molecular weights, and \f$V_k\f$ are the pure species + * molar volumes. + * + * Note, the basis behind this formula is that in an ideal + * solution the partial molar volumes are equal to the + * species standard state molar volumes. + * The species molar volumes may be functions + * of temperature and pressure. + * + * NOTE: This is a non-virtual function, which is not a + * member of the ThermoPhase base class. + */ + virtual void calcDensity(); + + //! Set the temperature (K) + /*! + * Overwritten setTemperature(double) from State.h. This + * function sets the temperature, and makes sure that + * the value propagates to underlying objects + * + * @todo Make State::setTemperature a virtual function + * + * @param temp Temperature in kelvin + */ + virtual void setTemperature(const doublereal temp); + + //! Set the mass fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param y Array of unnormalized mass fraction values (input). + * Must have a length greater than or equal to the number of species. + */ + virtual void setMassFractions(const doublereal* const y); + + //!Set the mass fractions to the specified values without normalizing. + /*! + * This is useful when the normalization + * condition is being handled by some other means, for example + * by a constraint equation as part of a larger set of + * equations. + * + * @param y Input vector of mass fractions. + * Length is m_kk. + */ + virtual void setMassFractions_NoNorm(const doublereal* const y); + + //! Set the mole fractions to the specified values, and then + //! normalize them so that they sum to 1.0. + /*! + * @param x Array of unnormalized mole fraction values (input). + * Must have a length greater than or equal to the number of species. + */ + virtual void setMoleFractions(const doublereal* const x); + + //! Set the mole fractions to the specified values without normalizing. + /*! + * This is useful when the normalization + * condition is being handled by some other means, for example + * by a constraint equation as part of a larger set ofequations. + * + * @param x Input vector of mole fractions. + * Length is m_kk. + */ + virtual void setMoleFractions_NoNorm(const doublereal* const x); + + + //! Set the concentrations to the specified values within the phase. + /*! + * @param c The input vector to this routine is in dimensional + * units. For volumetric phases c[k] is the + * concentration of the kth species in kmol/m3. + * For surface phases, c[k] is the concentration + * in kmol/m2. The length of the vector is the number + * of species in the phase. + */ + virtual void setConcentrations(const doublereal* const c); + + + public: + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + //! Returns the standard concentration \f$ C^0_k \f$, which is used to normalize + //! the generalized concentration. + /*! + * This is defined as the concentration by which the generalized + * concentration is normalized to produce the activity. + * In many cases, this quantity will be the same for all species in a phase. + * Since the activity for an ideal gas mixture is + * simply the mole fraction, for an ideal gas \f$ C^0_k = P/\hat R T \f$. + * + * @param k Optional parameter indicating the species. The default + * is to assume this refers to species 0. + * @return + * Returns the standard Concentration in units of m3 kmol-1. + */ + virtual doublereal standardConcentration(int k=0) const; + + //! Returns the natural logarithm of the standard + //! concentration of the kth species + /*! + * @param k index of the species. (defaults to zero) + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Returns the units of the standard and generalized concentrations. + /*! + * Note they have the same units, as their + * ratio is defined to be equal to the activity of the kth + * species in the solution, which is unitless. + * + * This routine is used in print out applications where the + * units are needed. Usually, MKS units are assumed throughout + * the program and in the XML input files. + * + * The base %ThermoPhase class assigns the default quantities + * of (kmol/m3) for all species. + * Inherited classes are responsible for overriding the default + * values if necessary. + * + * @param uA Output vector containing the units + * uA[0] = kmol units - default = 1 + * uA[1] = m units - default = -nDim(), the number of spatial + * dimensions in the Phase class. + * uA[2] = kg units - default = 0; + * uA[3] = Pa(pressure) units - default = 0; + * uA[4] = Temperature units - default = 0; + * uA[5] = time units - default = 0 + * @param k species index. Defaults to 0. + * @param sizeUA output int containing the size of the vector. + * Currently, this is equal to 6. + */ + virtual void getUnitsStandardConc(double *uA, int k = 0, int sizeUA = 6) const; + + //! Get the array of non-dimensional activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * For all objects with the Mixture Fugacity approximation, we define the + * standard state as an ideal gas at the current temperature and pressure + * of the solution. The activities are based on this standard state. + * + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + virtual void getActivityCoefficients(doublereal* ac) const; + + + /// @name Partial Molar Properties of the Solution (RedlichKwongMFTP) + //@{ + + //! Get the array of non-dimensional species chemical potentials. + //! These are partial molar Gibbs free energies. + /*! + * \f$ \mu_k / \hat R T \f$. + * Units: unitless + * + * We close the loop on this function, here, calling + * getChemPotentials() and then dividing by RT. No need for child + * classes to handle. + * + * @param mu Output vector of non-dimensional species chemical potentials + * Length: m_kk. + */ + void getChemPotentials_RT(doublereal* mu) const; + + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ + virtual void getChemPotentials(doublereal* mu) const; + + //! Get the species partial molar enthalpies. Units: J/kmol. + /*! + * @param hbar Output vector of species partial molar enthalpies. + * Length: m_kk. units are J/kmol. + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + //! Get the species partial molar entropies. Units: J/kmol/K. + /*! + * @param sbar Output vector of species partial molar entropies. + * Length = m_kk. units are J/kmol/K. + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Get the species partial molar enthalpies. Units: J/kmol. + /*! + * @param ubar Output vector of speciar partial molar internal energies. + * Length = m_kk. units are J/kmol. + */ + virtual void getPartialMolarIntEnergies(doublereal* ubar) const; + + //! Get the partial molar heat capacities Units: J/kmol/K + /*! + * @param cpbar Output vector of species partial molar heat capacities + * at constant pressure. + * Length = m_kk. units are J/kmol/K. + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + //! Get the species partial molar volumes. Units: m^3/kmol. + /*! + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //@} + + /*! + * @name Properties of the Standard State of the Species in the Solution + * + * Properties of the standard states are delegated to the VPSSMgr object. + * The values are cached within this object, and are not recalculated unless + * the temperature or pressure changes. + */ + //@{ + + //@} + + /// @name Thermodynamic Values for the Species Reference States (RedlichKwongMFTP) + /*! + * Properties of the reference states are delegated to the VPSSMgr object. + * The values are cached within this object, and are not recalculated unless + * the temperature or pressure changes. + */ + //@{ + + //@} + + + + //--------------------------------------------------------- + /// @name Critical State Properties. + /// These methods are only implemented by some subclasses, and may + /// be moved out of ThermoPhase at a later date. + + //@{ + + /// Critical temperature (K). + virtual doublereal critTemperature() const; + + /// Critical pressure (Pa). + virtual doublereal critPressure() const; + + /// Critical density (kg/m3). + virtual doublereal critDensity() const; + //@} + + + + + public: + + //! @name Initialization Methods - For Internal use (VPStandardState) + /*! + * The following methods are used in the process of constructing + * the phase and setting its parameters from a specification in an + * input file. They are not normally used in application programs. + * To see how they are used, see files importCTML.cpp and + * ThermoFactory.cpp. + */ + //@{ + + + //! Set equation of state parameter values from XML + //! entries. + /*! + * This method is called by function importPhase in + * file importCTML.cpp when processing a phase definition in + * an input file. It should be overloaded in subclasses to set + * any parameters that are specific to that particular phase + * model. + * + * @param thermoNode An XML_Node object corresponding to + * the "thermo" entry for this phase in the input file. + */ + virtual void setParametersFromXML(const XML_Node& thermoNode); + + //! @internal Initialize the object + /*! + * This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase(). + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + //!This method is used by the ChemEquil equilibrium solver. + /*! + * It sets the state such that the chemical potentials satisfy + * \f[ \frac{\mu_k}{\hat R T} = \sum_m A_{k,m} + * \left(\frac{\lambda_m} {\hat R T}\right) \f] where + * \f$ \lambda_m \f$ is the element potential of element m. The + * temperature is unchanged. Any phase (ideal or not) that + * implements this method can be equilibrated by ChemEquil. + * + * @param lambda_RT Input vector of dimensionless element potentials + * The length is equal to nElements(). + */ + void setToEquilState(const doublereal* lambda_RT); + + //! Initialize a ThermoPhase object, potentially reading activity + //! coefficient information from an XML database. + /*! + * + * This routine initializes the lengths in the current object and + * then calls the parent routine. + * This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase(). + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + virtual void initThermoXML(XML_Node& phaseNode, std::string id); + + private: + //! Read the pure species RedlichKwong input parameters + /*! + * @param pureFluidParam XML_Node for the pure fluid parameters + */ + void readXMLPureFluid(XML_Node &PureFluidParam); + + + //! Apply mixing rules for a coefficients + void applyStandardMixingRules(); + + + //! Read the cross species RedlichKwong input parameters + /*! + * @param pureFluidParam XML_Node for the cross fluid parameters + */ + void readXMLCrossFluid(XML_Node &PureFluidParam); + + + + //============================================================================== + private: + //! @internal Initialize the internal lengths in this object. + /*! + * Note this is not a virtual function and only handles + * this object + */ + void initLengths(); + + //============================================================================== + // Special functions inherited from MixtureFugacityTP + + protected: + + //! Calculate the deviation terms for the total entropy of the mixture from the + //! ideal gas mixture + /*! + * Here we use the current state conditions + * + * @return Returns the change in entropy in units of J kmol-1 K-1. + */ + virtual doublereal sresid() const; + + // Calculate the deviation terms for the total enthalpy of the mixture from the + // ideal gas mixture + /* + * Here we use the current state conditions + * + * @return Returns the change in enthalpy in units of J kmol-1. + */ + virtual doublereal hresid() const; + + //! Estimate for the molar volume of the liquid + /*! + * Note: this is only used as a starting guess for later routines that actually calculate an + * accurate value for the liquid molar volume. + * This routine doesn't change the state of the system. + * + * @param TKelvin temperature in kelvin + * @param pres Pressure in Pa. This is used as an initial guess. If the routine + * needs to change the pressure to find a stable liquid state, the + * new pressure is returned in this variable. + * + * @return Returns the estimate of the liquid volume. + */ + virtual doublereal liquidVolEst(doublereal TKelvin, doublereal &pres) const; + + protected: + //! Calculates the density given the temperature and the pressure and a guess at the density. + /*! + * Note, below T_c, this is a multivalued function. We do not cross the vapor dome in this. + * This is protected because it is called during setState_TP() routines. Infinite loops would result + * if it were not protected. + * + * -> why is this not const? + * + * parameters: + * @param TKelvin Temperature in Kelvin + * @param pressure Pressure in Pascals (Newton/m**2) + * @param phase int representing the phase whose density we are requesting. If we put + * a gas or liquid phase here, we will attempt to find a volume in that + * part of the volume space, only, in this routine. A value of FLUID_UNDEFINED + * means that we will accept anything. + * + * @param rhoguess Guessed density of the fluid. A value of -1.0 indicates that there + * is no guessed density + * + * + * @return We return the density of the fluid at the requested phase. If we have not found any + * acceptable density we return a -1. If we have found an accectable density at a + * different phase, we return a -2. + */ + virtual doublereal densityCalc(doublereal TKelvin, doublereal pressure, int phase, doublereal rhoguess); + + public: + //! Return the value of the density at the liquid spinodal point (on the liquid side) + //! for the current temperature. + /*! + * @return returns the density with units of kg m-3 + */ + virtual doublereal densSpinodalLiquid() const; + + + //! Return the value of the density at the gas spinodal point (on the gas side) + //! for the current temperature. + /*! + * @return returns the density with units of kg m-3 + */ + virtual doublereal densSpinodalGas() const; + + + + //! Calculate the pressure given the temperature and the molar volume + /*! + * Calculate the pressure given the temperature and the molar volume + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @return Returns the pressure. + */ + virtual doublereal pressureCalc(doublereal TKelvin, doublereal molarVol) const; + + + //! Calculate the pressure and the pressure derivative given the temperature and the molar volume + /*! + * Temperature and mole number are held constant + * + * @param TKelvin temperature in kelvin + * @param molarVol molar volume ( m3/kmol) + * + * @param presCalc Returns the pressure. + * + * @return Returns the derivative of the pressure wrt the molar volume + */ + virtual doublereal dpdVCalc(doublereal TKelvin, doublereal molarVol, doublereal &presCalc) const; + + + //! Calculate dpdV and dpdT at the current conditions + /*! + * These are storred internally. + */ + void pressureDerivatives() const; + + + virtual void updateMixingExpressions(); + + + //! Update the a and b parameters + /*! + * The a and the b parameters depend on the mole fraction and the temperature. + * This function updates the internal numbers based on the state of the object. + */ + void updateAB(); + + + //! Calculate the a and the b parameters given the temperature + /*! + * + * This function doesn't change the internal state of the object, so it is a const + * function. It does use the storred mole fractions in the object. + * + * @param temp Temperature (TKelvin) + * + * @param aCalc (output) Returns the a value + * @param bCalc (output) Returns the b value. + */ + void calculateAB(doublereal temp, doublereal &aCalc, doublereal &bCalc) const; + + + //========================================================================================= + // Special functions not inherited from MixtureFugacityTP + + doublereal da_dt() const; + + void calcCriticalConditions(doublereal a, doublereal b, doublereal a0_coeff, doublereal aT_coeff, + doublereal &pc, doublereal &tc, doublereal &vc) const; + + + + int NicholsSolve(double TKelvin, double pres, doublereal a, doublereal b, + doublereal Vroot[3]) const; + + //@} + //============================================================================== + protected: + + //! boolean indicating whether standard mixing rules are applied + /*! + * - 1 = Yes, there are standard cross terms in the a coefficient matrices. + * - 0 = No, there are nonstaandard cross terms in the a coefficient matrices. + */ + int m_standardMixingRules; + + //! Form of the temperature parameterization + /*! + * - 0 = There is no temperature parameterization of a or b + * - 1 = The a_ij parameter is a linear function of the temperature + */ + int m_formTempParam; + + + //! Value of b in the equation of state + /*! + * m_b is a function of the temperature and the mole fraction. + */ + doublereal m_b_current; + + //! Value of a in the equation of state + /*! + * a_b is a function of the temperature and the mole fraction. + */ + doublereal m_a_current; + + + vector_fp a_vec_Curr_; + vector_fp b_vec_Curr_; + + Array2D a_coeff_vec; + + + vector_fp m_pc_Species; + vector_fp m_tc_Species; + vector_fp m_vc_Species; + + int NSolns_; + + doublereal Vroot_[3]; + + + + //! Temporary storage - length = m_kk. + mutable vector_fp m_pp; + + //! Temporary storage - length = m_kk. + mutable vector_fp m_tmpV; + + // mutable vector_fp m_tmpV2; + + // Partial molar volumes of the species + mutable vector_fp m_partialMolarVolumes; + + + + //! The derivative of the pressure wrt the volume + /*! + * Calcualted at the current conditions + * temperature and mole number kept constant + */ + mutable doublereal dpdV_; + + //! The derivative of the pressure wrt the temperature + /*! + * Calcualted at the current conditions + * Total volume and mole number kept constant + */ + mutable doublereal dpdT_; + + //! Vector of derivatives of pressure wrt mole number + /*! + * Calcualted at the current conditions + * Total volume, temperature and other mole number kept constant + */ + mutable vector_fp dpdni_; + + public: + //! Omega constant for a -> value of a in terms of critical properties + /*! + * this was calculated from a small nonlinear solve + */ + static const doublereal omega_a = 4.27480233540E-01; + + //! Omega constant for b + static const doublereal omega_b = 8.66403499650E-02; + + //! Omega constant for the critical molar volume + static const doublereal omega_vc = 3.33333333333333E-01; + + + }; +#endif +} + +#endif diff --git a/Cantera/src/thermo/ShomateThermo.h b/Cantera/src/thermo/ShomateThermo.h index 06ef0bf2a..e82bbf8a4 100644 --- a/Cantera/src/thermo/ShomateThermo.h +++ b/Cantera/src/thermo/ShomateThermo.h @@ -201,12 +201,13 @@ namespace Cantera { if (m_p0 < 0.0) { m_p0 = refPressure; } else if (fabs(m_p0 - refPressure) > 0.1) { - std::string logmsg = " WARNING ShomateThermo: New Species, " + name + std::string logmsg = " ERROR ShomateThermo: New Species, " + name + ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); - logmsg = " This may become a fatal error in the future \n"; + logmsg = " This is now a fatal error\n"; writelog(logmsg); + throw CanteraError("install()", "Species have different reference pressures"); } m_p0 = refPressure; diff --git a/Cantera/src/thermo/SimpleThermo.h b/Cantera/src/thermo/SimpleThermo.h index cced50e0c..83bcb99e1 100644 --- a/Cantera/src/thermo/SimpleThermo.h +++ b/Cantera/src/thermo/SimpleThermo.h @@ -182,8 +182,9 @@ namespace Cantera { ", has a different reference pressure, " + fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n"; writelog(logmsg); - logmsg = " This may become a fatal error in the future \n"; + logmsg = " This is now a fatal error\n"; writelog(logmsg); + throw CanteraError("install()", "Species have different reference pressures"); } m_p0 = refPressure; } diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index a7181554c..9704cae20 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -36,6 +36,10 @@ #include "PureFluidPhase.h" #endif +#ifdef WITH_REAL_GASSES +#include "RedlichKwongMFTP.h" +#endif + #include "ConstDensityThermo.h" #include "SurfPhase.h" #include "EdgePhase.h" @@ -212,6 +216,13 @@ namespace Cantera { th = new PureFluidPhase; break; #endif + +#ifdef WITH_REAL_GASSES + case cRedlichKwongMFTP: + th = new RedlichKwongMFTP; + break; +#endif + #ifdef WITH_ELECTROLYTES case cHMW: th = new HMWSoln; diff --git a/Cantera/src/thermo/ThermoPhase.cpp b/Cantera/src/thermo/ThermoPhase.cpp index b014eaf89..746203f18 100644 --- a/Cantera/src/thermo/ThermoPhase.cpp +++ b/Cantera/src/thermo/ThermoPhase.cpp @@ -1012,7 +1012,7 @@ namespace Cantera { } return m_speciesData; } - + //==================================================================================================================== /* * Set the thermodynamic state. */ @@ -1038,7 +1038,7 @@ namespace Cantera { setDensity(rho); } } - + //==================================================================================================================== /* * Called by function 'equilibrate' in ChemEquil.h to transfer * the element potentials to this object after every successful diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index d1b15ebbf..758919b3e 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -1544,7 +1544,7 @@ namespace Cantera { * @param x Vector of mole fractions. * Length is equal to m_kk. */ - void setState_TPX(doublereal t, doublereal p, const doublereal* x); + virtual void setState_TPX(doublereal t, doublereal p, const doublereal* x); //! Set the temperature (K), pressure (Pa), and mole fractions. /*! diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index b81981de7..3a4dec238 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -73,6 +73,10 @@ namespace Cantera { const int cIdealSolnGasVPSS = 500; const int cIdealSolnGasVPSS_iscv = 501; + //! Fugacity Models + const int cMixtureFugacityTP = 700; + const int cRedlichKwongMFTP = 701; + const int cMargulesVPSSTP = 301; const int cPhaseCombo_Interaction = 305; diff --git a/config.h.in b/config.h.in index 767d95361..c13ec878b 100755 --- a/config.h.in +++ b/config.h.in @@ -183,6 +183,9 @@ typedef int ftnlen; // Fortran hidden string length type // models for electrolyte solutions. #undef WITH_ELECTROLYTES +// Enable Real Gasses +#undef WITH_REAL_GASSES + #undef WITH_PRIME // Enable the VCS NonIdeal equilibrium solver. This is diff --git a/configure b/configure index c746849d0..ed3d01168 100755 --- a/configure +++ b/configure @@ -2585,6 +2585,16 @@ _ACEOF fi +if test "$WITH_REAL_GASSES" = "y"; then + cat >>confdefs.h <<\_ACEOF +#define WITH_REAL_GASSES 1 +_ACEOF + + hdrs=$hdrs' RedlichKwongMFTP.h' + objs=$objs' RedlichKwongMFTP.o' +fi + + if test "$WITH_LATTICE_SOLID" = "y"; then cat >>confdefs.h <<\_ACEOF #define WITH_LATTICE_SOLID 1 @@ -10058,7 +10068,7 @@ fi # Provide some information about the compiler. -echo "$as_me:10061:" \ +echo "$as_me:10071:" \ "checking for Fortran 77 compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 @@ -10265,7 +10275,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10268: \"$ac_link\") >&5 +(eval echo $as_me:10278: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10343,7 +10353,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10346: \"$ac_link\") >&5 +(eval echo $as_me:10356: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS diff --git a/configure.in b/configure.in index 5afbb896b..c58010bc6 100755 --- a/configure.in +++ b/configure.in @@ -486,6 +486,13 @@ if test "$WITH_PURE_FLUIDS" = "y"; then fi AC_SUBST(COMPILE_PURE_FLUIDS) +if test "$WITH_REAL_GASSES" = "y"; then + AC_DEFINE(WITH_REAL_GASSES) + hdrs=$hdrs' RedlichKwongMFTP.h' + objs=$objs' RedlichKwongMFTP.o' +fi + + if test "$WITH_LATTICE_SOLID" = "y"; then AC_DEFINE(WITH_LATTICE_SOLID) hdrs=$hdrs' LatticeSolidPhase.h' diff --git a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy index 30e9e8181..32760d503 100755 --- a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy +++ b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy @@ -34,6 +34,9 @@ export WITH_VCSNONIDEAL WITH_H298MODIFY_CAPABILITY='y' export WITH_H298MODIFY_CAPABILITY +WITH_REAL_GASSES='y' +export WITH_REAL_GASSES + BUILD_MATLAB_TOOLBOX="y" export BUILD_MATLAB_TOOLBOX diff --git a/preconfig b/preconfig index 22259a98c..ebe22275d 100755 --- a/preconfig +++ b/preconfig @@ -228,6 +228,10 @@ WITH_IDEAL_SOLUTIONS=${WITH_IDEAL_SOLUTIONS:="y"} # models for electrolyte solutions WITH_ELECTROLYTES=${WITH_ELECTROLYTES:="y"} +# Enable Real Gas Equations of State +# This supports the multicomponent Redlich-Kwong equation of state. +WITH_REAL_GASSES=${WITH_REAL_GASSES:="n"} + # Enable generating phase models from PrIMe models. For more # information about PrIME, see http://www.primekinetics.org # WARNING: Support for PrIMe is experimental! diff --git a/test_problems/min_python/negATest/negATest_blessed.out b/test_problems/min_python/negATest/negATest_blessed.out index d170960c3..e63158035 100644 --- a/test_problems/min_python/negATest/negATest_blessed.out +++ b/test_problems/min_python/negATest/negATest_blessed.out @@ -1,7 +1,7 @@ Number of species = 12 Number of reactions = 12 rop [ 0:O ] = 0.447058 -rop [ 1:O2 ] = -0.0021443 +rop [ 1:O2 ] = -0.00214428 rop [ 2:N ] = 0 rop [ 3:NO ] = -279.361 rop [ 4:NO2 ] = 0.00214319 @@ -17,7 +17,7 @@ fwd_rop[ 0] = 479.304 rev_rop[ 0] = 97.94 fwd_rop[ 1] = -128.201 rev_rop[ 1] = -26.1964 fwd_rop[ 2] = 0 rev_rop[ 2] = 0 fwd_rop[ 3] = -0 rev_rop[ 3] = -0 -fwd_rop[ 4] = 0 rev_rop[ 4] = 1.10334e-06 +fwd_rop[ 4] = 0 rev_rop[ 4] = 1.08891e-06 fwd_rop[ 5] = 0 rev_rop[ 5] = 0 fwd_rop[ 6] = 0 rev_rop[ 6] = 0 fwd_rop[ 7] = 0 rev_rop[ 7] = 0 From f7d87724aea4b697c3ffcbabce7ed06d42b5134c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 23 Jul 2011 19:39:08 +0000 Subject: [PATCH 374/446] Changed the definition of the reference state of pure fluids. The reference state for pure fluids is defined as an ideal gas at the current temperature of the fluid at the reference pressure. It was defined as the real fluid properties at the current temperature and the reference pressure. However, this definition doesn't allow for the easy calculation of fugacities. Added some documentation, also, concerning the standard state definition. --- Cantera/src/thermo/PureFluidPhase.cpp | 11 ++++++++--- Cantera/src/thermo/PureFluidPhase.h | 24 +++++++++++++++--------- 2 files changed, 23 insertions(+), 12 deletions(-) diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 9c07788a7..7f1266f9e 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -355,7 +355,8 @@ namespace Cantera { double psave = pressure(); double t = temperature(); double pref = m_spthermo->refPressure(); - Set(tpx::TP, t, pref); + double plow = 1.0E-8; + Set(tpx::TP, t, plow); getEnthalpy_RT(hrt); Set(tpx::TP, t, psave); @@ -371,8 +372,10 @@ namespace Cantera { double psave = pressure(); double t = temperature(); double pref = m_spthermo->refPressure(); - Set(tpx::TP, t, pref); + double plow = 1.0E-8; + Set(tpx::TP, t, plow); getGibbs_RT(grt); + grt[0] += log(pref/plow); Set(tpx::TP, t, psave); } //==================================================================================================================== @@ -399,8 +402,10 @@ namespace Cantera { double psave = pressure(); double t = temperature(); double pref = m_spthermo->refPressure(); - Set(tpx::TP, t, pref); + double plow = 1.0E-8; + Set(tpx::TP, t, plow); getEntropy_R(er); + er[0] -= log(pref/plow); Set(tpx::TP, t, psave); } //==================================================================================================================== diff --git a/Cantera/src/thermo/PureFluidPhase.h b/Cantera/src/thermo/PureFluidPhase.h index f692bad1d..d548fc6f4 100644 --- a/Cantera/src/thermo/PureFluidPhase.h +++ b/Cantera/src/thermo/PureFluidPhase.h @@ -304,6 +304,12 @@ namespace Cantera { //@} /// @name Properties of the Standard State of the Species in the Solution + /*! + * The standard state of the pure fluid is defined as the real properties + * of the pure fluid at the most stable state of the fluid at the current + * temperature and pressure of the solution. With this definition, the + * activity of the fluid is always then defined to be equal to one. + */ //@{ //! Get the array of chemical potentials at unit activity for the species @@ -342,15 +348,19 @@ namespace Cantera { */ virtual void getGibbs_RT(doublereal* grt) const; - //@} + /// @name Thermodynamic Values for the Species Reference States + /*! + * The species reference state for pure fluids is defined as an ideal gas at the + * reference pressure and current temperature of the fluid. + */ //@{ //! Returns the vector of nondimensional enthalpies of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! - * This base function will throw a CanteraException unless + * This base function will throw a Cantera exception unless * it is overwritten in a derived class. * * @param hrt Output vector containing the nondimensional reference state enthalpies @@ -358,8 +368,7 @@ namespace Cantera { */ virtual void getEnthalpy_RT_ref(doublereal *hrt) const; - //! Returns the vector of nondimensional - //! Gibbs Free Energies of the reference state at the current temperature + //! Returns the vector of nondimensional Gibbs Free Energies of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! * @param grt Output vector containing the nondimensional reference state @@ -372,15 +381,14 @@ namespace Cantera { /*! * units = J/kmol * - * @param g Output vector containing the reference state + * @param g Output vector containing the reference state * Gibbs Free energies. Length: m_kk. Units: J/kmol. */ virtual void getGibbs_ref(doublereal *g) const; - //! Returns the vector of nondimensional - //! entropies of the reference state at the current temperature + //! Returns the vector of nondimensional entropies of the reference state at the current temperature //! of the solution and the reference pressure for each species. /*! * @param er Output vector containing the nondimensional reference state @@ -388,7 +396,6 @@ namespace Cantera { */ virtual void getEntropy_R_ref(doublereal *er) const; - /** * @name Setting the State * @@ -396,7 +403,6 @@ namespace Cantera { * @{ */ - //! Set the internally storred specific enthalpy (J/kg) and pressure (Pa) of the phase. /*! * @param h Specific enthalpy (J/kg) From 9d46965e7d4d41b30bc6c80ba8886b5903c2400c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 25 Jul 2011 14:44:41 +0000 Subject: [PATCH 375/446] Added a print_lvl check to an output statement. --- Cantera/src/equil/vcs_solve.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Cantera/src/equil/vcs_solve.cpp b/Cantera/src/equil/vcs_solve.cpp index 251b1496d..7ba67cf3c 100644 --- a/Cantera/src/equil/vcs_solve.cpp +++ b/Cantera/src/equil/vcs_solve.cpp @@ -740,8 +740,10 @@ namespace VCSnonideal { m_elementName[i].c_str(), m_elemAbundancesGoal[i]); exit(EXIT_FAILURE); } else { - plogf("Charge neutrality condition %s not zero, %g. Setting it zero\n", - m_elementName[i].c_str(), m_elemAbundancesGoal[i]); + if (m_debug_print_lvl >= 2) { + plogf("Charge neutrality condition %s not zero, %g. Setting it zero\n", + m_elementName[i].c_str(), m_elemAbundancesGoal[i]); + } m_elemAbundancesGoal[i] = 0.0; } From 2082b576994b36e7c6211d693b7a8bdc70290ced Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 30 Jul 2011 03:08:10 +0000 Subject: [PATCH 376/446] Worked on getting the IDA_Solver interface operable. Previously, it hadn't been. It now works on one test problem. --- Cantera/src/numerics/DAE_Solver.h | 361 +++++++------- Cantera/src/numerics/DAE_solvers.cpp | 9 +- Cantera/src/numerics/FuncEval.h | 2 +- Cantera/src/numerics/IDA_Solver.cpp | 689 ++++++++++++++++++-------- Cantera/src/numerics/IDA_Solver.h | 361 ++++++++++---- Cantera/src/numerics/Integrator.h | 45 +- Cantera/src/numerics/Makefile.in | 4 +- Cantera/src/numerics/ResidEval.h | 9 +- Cantera/src/numerics/ResidJacEval.cpp | 7 + Cantera/src/numerics/ResidJacEval.h | 14 + 10 files changed, 1009 insertions(+), 492 deletions(-) diff --git a/Cantera/src/numerics/DAE_Solver.h b/Cantera/src/numerics/DAE_Solver.h index f57d28bbe..cbc4d4b03 100644 --- a/Cantera/src/numerics/DAE_Solver.h +++ b/Cantera/src/numerics/DAE_Solver.h @@ -12,207 +12,236 @@ * Copyright 2006 California Institute of Technology * */ - -#undef DAE_DEVEL - #ifndef CT_DAE_Solver_H #define CT_DAE_Solver_H #include #include "ct_defs.h" -#include "ResidEval.h" +#include "ResidJacEval.h" #include "global.h" namespace Cantera { +#define DAE_DEVEL #ifdef DAE_DEVEL - class Jacobian { - public: - Jacobian(){} - virtual ~Jacobian(){} - virtual bool supplied() { return false; } - virtual bool isBanded() { return false; } - virtual int lowerBandWidth() { return 0; } - virtual int upperBandWidth() { return 0; } - }; + class Jacobian { + public: + Jacobian(){} + virtual ~Jacobian(){} + virtual bool supplied() { return false; } + virtual bool isBanded() { return false; } + virtual int lowerBandWidth() { return 0; } + virtual int upperBandWidth() { return 0; } + }; - class BandedJacobian : public Jacobian { - public: - BandedJacobian(int ml, int mu) { - m_ml = ml; m_mu = mu; - } - virtual bool supplied() { return false; } - virtual bool isBanded() { return true; } - virtual int lowerBandWidth() { return m_ml; } - virtual int upperBandWidth() { return m_mu; } - protected: - int m_ml, m_mu; - }; + class BandedJacobian : public Jacobian { + public: + BandedJacobian(int ml, int mu) { + m_ml = ml; m_mu = mu; + } + virtual bool supplied() { return false; } + virtual bool isBanded() { return true; } + virtual int lowerBandWidth() { return m_ml; } + virtual int upperBandWidth() { return m_mu; } + protected: + int m_ml, m_mu; + }; - const int cDirect = 0; - const int cKrylov = 1; + const int cDirect = 0; + const int cKrylov = 1; + /** + * Wrapper for DAE solvers + */ + class DAE_Solver { + public: + + DAE_Solver(ResidJacEval& f) : + m_resid(f), + m_neq(f.nEquations()), + m_time(0.0) + { + } + + virtual ~DAE_Solver(){} + + /** + * Set error tolerances. This version specifies a scalar + * relative tolerance, and a vector absolute tolerance. + */ + virtual void setTolerances(doublereal reltol, + doublereal* abstol) { + warn("setTolerances"); + } + + /** + * Set error tolerances. This version specifies a scalar + * relative tolerance, and a scalar absolute tolerance. + */ + virtual void setTolerances(doublereal reltol, doublereal abstol) { + warn("setTolerances"); + } + + /** + * Specify a Jacobian evaluator. If this method is not called, + * the Jacobian will be computed by finite difference. + */ + void setJacobian(Jacobian& jac) { + warn("setJacobian"); + } + + virtual void setLinearSolverType(int solverType) { + warn("setLinearSolverType"); + } + + virtual void setDenseLinearSolver() { + warn("setDenseLinearSolver"); + } + + virtual void setBandedLinearSolver(int m_upper, int m_lower) { + warn("setBandedLinearSolver"); + } + virtual void setMaxStepSize(doublereal dtmax) { + warn("setMaxStepSize"); + } + virtual void setMaxOrder(int n) { + warn("setMaxOrder"); + } + virtual void setMaxNumSteps(int n) { + warn("setMaxNumSteps"); + } + virtual void setInitialStepSize(doublereal h0) { + warn("setInitialStepSize"); + } + virtual void setStopTime(doublereal tstop) { + warn("setStopTime"); + } + virtual void setMaxErrTestFailures(int n) { + warn("setMaxErrTestFailures"); + } + virtual void setMaxNonlinIterations(int n) { + warn("setMaxNonlinIterations"); + } + virtual void setMaxNonlinConvFailures(int n) { + warn("setMaxNonlinConvFailures"); + } + virtual void inclAlgebraicInErrorTest(bool yesno) { + warn("inclAlgebraicInErrorTest"); + } + /** - * Wrapper for DAE solvers + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the derivatives + * of all variables, this method computes the initial y + * values. */ - class DAE_Solver { - public: + virtual void correctInitial_Y_given_Yp(doublereal* y, doublereal* yp, + doublereal tout) { + warn("correctInitial_Y_given_Yp"); + } + + /** + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the initial + * values of all differential variables, it computes the + * initial values of all algebraic variables and the initial + * derivatives of all differential variables. + */ + virtual void correctInitial_YaYp_given_Yd(doublereal* y, doublereal* yp, + doublereal tout) + { + warn("correctInitial_YaYp_given_Yd"); + } - DAE_Solver(ResidEval& f) : m_resid(f), - m_neq(f.nEquations()), - m_time(0.0) {} + /** + * Solve the system of equations up to time tout. + */ + virtual int solve(doublereal tout) { + warn("solve"); return 0; + } - virtual ~DAE_Solver(){} + /** + * Take one internal step. + */ + virtual doublereal step(doublereal tout) { + warn("step"); return 0; + } - /** - * Set error tolerances. This version specifies a scalar - * relative tolerance, and a vector absolute tolerance. - */ - virtual void setTolerances(doublereal reltol, - doublereal* abstol) { - warn("setTolerances"); - } + /// Number of equations. + int nEquations() const { + return m_resid.nEquations(); + } - /** - * Set error tolerances. This version specifies a scalar - * relative tolerance, and a scalar absolute tolerance. - */ - virtual void setTolerances(doublereal reltol, doublereal abstol) { - warn("setTolerances"); - } + /** + * initialize. Base class method does nothing. + */ + virtual void init(doublereal t0) {} - /** - * Specify a Jacobian evaluator. If this method is not called, - * the Jacobian will be computed by finite difference. - */ - void setJacobian(Jacobian& jac) { - warn("setJacobian"); - } + /** + * Set a solver-specific input parameter. + */ + virtual void setInputParameter(int flag, doublereal value) { + warn("setInputParameter"); + } - virtual void setLinearSolverType(int solverType) { - warn("setLinearSolverType"); - } + /** + * Get the value of a solver-specific output parameter. + */ + virtual doublereal getOutputParameter(int flag) const { + warn("getOutputParameter"); return 0.0; + } - virtual void setDenseLinearSolver() { - warn("setDenseLinearSolver"); - } + /// the current value of solution component k. + virtual doublereal solution(int k) const { + warn("solution"); return 0.0; + } - virtual void setBandedLinearSolver(int m_upper, int m_lower) { - warn("setBandedLinearSolver"); - } - virtual void setMaxTime(doublereal tmax) { - warn("setMaxTime"); - } - virtual void setMaxStepSize(doublereal dtmax) { - warn("setMaxStepSize"); - } - virtual void setMaxOrder(int n) { - warn("setMaxOrder"); - } - virtual void setMaxNumSteps(int n) { - warn("setMaxNumSteps"); - } - virtual void setInitialStepSize(doublereal h0) { - warn("setInitialStepSize"); - } - virtual void setStopTime(doublereal tstop) { - warn("setStopTime"); - } - virtual void setMaxErrTestFailures(int n) { - warn("setMaxErrTestFailures"); - } - virtual void setMaxNonlinIterations(int n) { - warn("setMaxNonlinIterations"); - } - virtual void setMaxNonlinConvFailures(int n) { - warn("setMaxNonlinConvFailures"); - } - virtual void inclAlgebraicInErrorTest(bool yesno) { - warn("inclAlgebraicInErrorTest"); - } + virtual const doublereal* solutionVector() const { + warn("solutionVector"); return &m_dummy; + } - virtual void correctInitial_Y_given_Yp() { - warn("correctInitial_Y_given_Yp"); - } + /// the current value of the derivative of solution component k. + virtual doublereal derivative(int k) const { + warn("derivative"); return 0.0; + } - virtual void correctInitial_YaYp_given_Yd() { - warn("correctInitial_YaYp_given_Yd"); - } + virtual const doublereal* derivativeVector() const { + warn("derivativeVector"); return &m_dummy; + } - /** - * Solve the system of equations up to time tout. - */ - virtual int solve(doublereal tout) { - warn("solve"); return 0; - } + protected: - /** - * Take one internal step. - */ - virtual doublereal step(doublereal tout) { - warn("step"); return 0; - } + doublereal m_dummy; - /// Number of equations. - int nEquations() const { return m_resid.nEquations(); } + ResidJacEval& m_resid; - /** - * initialize. Base class method does nothing. - */ - virtual void init(doublereal t0) {} - - /** - * Set a solver-specific input parameter. - */ - virtual void setInputParameter(int flag, doublereal value) { - warn("setInputParameter"); - } - - /** - * Get the value of a solver-specific output parameter. - */ - virtual doublereal getOutputParameter(int flag) const { - warn("getOutputParameter"); return 0.0; - } - - /// the current value of solution component k. - virtual doublereal solution(int k) const { - warn("solution"); return 0.0; - } - - virtual const doublereal* solutionVector() const { - warn("solutionVector"); return &m_dummy; - } - - /// the current value of the derivative of solution component k. - virtual doublereal derivative(int k) const { - warn("derivative"); return 0.0; - } - - virtual const doublereal* derivativeVector() const { - warn("derivativeVector"); return &m_dummy; - } - - protected: - - doublereal m_dummy; - - ResidEval& m_resid; - - integer m_neq; - doublereal m_time; + //! Number of total equations in the system + integer m_neq; + doublereal m_time; - private: - void warn(std::string msg) const { - writelog(">>>> Warning: method "+msg+" of base class " - +"DAE_Solver called. Nothing done.\n"); - } - }; + private: + void warn(std::string msg) const { + writelog(">>>> Warning: method "+msg+" of base class " + +"DAE_Solver called. Nothing done.\n"); + } + }; + + + //! Factor method for choosing a DAE solver + /*! + * + * @param itype String identifying the type + * (IDA is the only option) + * @param f Residual function to be solved by the DAE algorithm + * + * @return Returns a point to the instantiated DAE_Solver object + */ + DAE_Solver* newDAE_Solver(std::string itype, ResidJacEval& f); #endif diff --git a/Cantera/src/numerics/DAE_solvers.cpp b/Cantera/src/numerics/DAE_solvers.cpp index 4e0c2d7c7..db3b8b339 100644 --- a/Cantera/src/numerics/DAE_solvers.cpp +++ b/Cantera/src/numerics/DAE_solvers.cpp @@ -3,6 +3,7 @@ #include "DAE_Solver.h" // DAE_DEVEL is turned off at the current time +#define DAE_DEVEL #ifdef DAE_DEVEL #ifdef HAS_SUNDIALS @@ -11,18 +12,18 @@ namespace Cantera { - DAE_Solver* newDAE_Solver(string itype) { + DAE_Solver* newDAE_Solver(string itype, ResidJacEval& f) { if (itype == "IDA") { #ifdef HAS_SUNDIALS - return new IDA_Solver(); + return new IDA_Solver(f); #else raise CanteraError("newDAE_Solver","IDA solver requires sundials" - " package, but Cantera was not built with sundials."); + " package, but Cantera was not built with sundials."); #endif } else { throw CanteraError("newDAE_Solver", - "unknown DAE solver: "+itype); + "unknown DAE solver: "+itype); } } } diff --git a/Cantera/src/numerics/FuncEval.h b/Cantera/src/numerics/FuncEval.h index d88181533..e835eb9ab 100644 --- a/Cantera/src/numerics/FuncEval.h +++ b/Cantera/src/numerics/FuncEval.h @@ -55,7 +55,7 @@ namespace Cantera { */ virtual int neq()=0; - /// Number of parameters. + //! Number of parameters. virtual int nparams() { return 0; } protected: diff --git a/Cantera/src/numerics/IDA_Solver.cpp b/Cantera/src/numerics/IDA_Solver.cpp index eec7f9226..6f2575138 100644 --- a/Cantera/src/numerics/IDA_Solver.cpp +++ b/Cantera/src/numerics/IDA_Solver.cpp @@ -1,4 +1,3 @@ - /** * @file IDA_Solver.cpp * @@ -10,8 +9,8 @@ #include "stringUtils.h" #include -using namespace std; +#ifdef SUNDIALS_VERSION_22 #include #include #include @@ -19,238 +18,506 @@ using namespace std; #include #include #include +#else +#include +#include +#include +#include +#include +#include +#include +#endif + +using namespace std; inline static N_Vector nv(void* x) { - return reinterpret_cast(x); + return reinterpret_cast(x); } namespace Cantera { - /** - * A simple class to hold an array of parameter values and a pointer to - * an instance of a subclass of ResidEval. - */ - class ResidData { + /** + * A simple class to hold an array of parameter values and a pointer to + * an instance of a subclass of ResidEval. + */ + class ResidData { + + public: + ResidData(ResidJacEval* f, int npar = 0) { + m_func = f; + } + virtual ~ResidData() { + } - - public: - ResidData(ResidEval* f, int npar = 0) { - m_func = f; - } - virtual ~ResidData() {} - ResidEval* m_func; - }; + ResidJacEval* m_func; + }; } - +//====================================================================================================================== extern "C" { - - /** - * Function called by IDA to evaluate the residual, given y and - * ydot. IDA allows passing in a void* pointer to access - * external data. Instead of requiring the user to provide a - * residual function directly to IDA (which would require using - * the sundials data types N_Vector, etc.), we define this - * function as the single function that IDA always calls. The - * real evaluation of the residual is done by an instance of a - * subclass of ResidEval, passed in to this function as a pointer - * in the parameters. - */ - static int ida_resid(realtype t, N_Vector y, N_Vector ydot, - N_Vector r, void *f_data) { - double* ydata = NV_DATA_S(y); - double* ydotdata = NV_DATA_S(ydot); - double* rdata = NV_DATA_S(r); - Cantera::ResidData* d = (Cantera::ResidData*)f_data; - Cantera::ResidEval* f = d->m_func; - f->eval(t, ydata, ydotdata, rdata); - return 0; - } - + //! Function called by IDA to evaluate the residual, given y and ydot. + /*! + * IDA allows passing in a void* pointer to access external data. Instead of requiring the user to provide a + * residual function directly to IDA (which would require using + * the sundials data types N_Vector, etc.), we define this function as the single function that IDA always calls. The + * real evaluation of the residual is done by an instance of a subclass of ResidEval, passed in to this + * function as a pointer in the parameters. + */ + static int ida_resid(realtype t, N_Vector y, N_Vector ydot, N_Vector r, void *f_data) { + double* ydata = NV_DATA_S(y); + double* ydotdata = NV_DATA_S(ydot); + double* rdata = NV_DATA_S(r); + Cantera::ResidData* d = (Cantera::ResidData*) f_data; + Cantera::ResidJacEval* f = d->m_func; + f->eval(t, ydata, ydotdata, rdata); + return 0; + } } namespace Cantera { - - /** - * Constructor. Default settings: dense jacobian, no user-supplied - * Jacobian function, Newton iteration. - */ - IDA_Solver::IDA_Solver(ResidEval& f) : DAE_Solver(f), - m_neq(0), - m_ida_mem(0), - m_t0(0.0), - m_y(0), - m_ydot(0), - m_abstol(0), - m_type(0), - m_itol(IDA_SS), - m_iter(0), - m_maxord(0), - m_reltol(1.e-9), - m_abstols(1.e-15), - m_nabs(0), - m_hmax(0.0), - m_maxsteps(20000), - m_mupper(0), - m_mlower(0) {} - - - /// Destructor. - IDA_Solver::~IDA_Solver() - { - if (m_ida_mem) { - IDAFree(&m_ida_mem); - } - if (m_y) N_VDestroy_Serial(nv(m_y)); - if (m_ydot) N_VDestroy_Serial(nv(m_ydot)); - if (m_abstol) N_VDestroy_Serial(nv(m_abstol)); - delete m_fdata; + //==================================================================================================================== + /* + * Constructor. Default settings: dense jacobian, no user-supplied + * Jacobian function, Newton iteration. + */ + IDA_Solver::IDA_Solver(ResidJacEval& f) : + DAE_Solver(f), + m_ida_mem(0), + m_t0(0.0), + m_y(0), + m_ydot(0), + m_id(0), + m_constraints(0), + m_abstol(0), + m_type(0), + m_itol(IDA_SS), + m_iter(0), + m_reltol(1.e-9), + m_abstols(1.e-15), + m_nabs(0), + m_hmax(0.0), + m_hmin(0.0), + m_h0(0.0), + m_maxsteps(20000), + m_maxord(0), + m_tstop(0.0), + m_maxErrTestFails(-1), + m_maxNonlinIters(0), + m_maxNonlinConvFails(-1), + m_setSuppressAlg(0), + m_fdata(0), + m_mupper(0), + m_mlower(0) + { + } + //==================================================================================================================== + IDA_Solver::~IDA_Solver() + { + if (m_ida_mem) { + IDAFree(&m_ida_mem); } - - doublereal IDA_Solver::solution(int k) const { - return NV_Ith_S(nv(m_y),k); + if (m_y) N_VDestroy_Serial(nv(m_y)); + if (m_ydot) N_VDestroy_Serial(nv(m_ydot)); + if (m_abstol) N_VDestroy_Serial(nv(m_abstol)); + if (m_constraints) N_VDestroy_Serial(nv(m_constraints)); + delete m_fdata; + } + //==================================================================================================================== + doublereal IDA_Solver::solution(int k) const { + return NV_Ith_S(nv(m_y),k); + } + //==================================================================================================================== + const doublereal* IDA_Solver::solutionVector() const { + return NV_DATA_S(nv(m_y)); + } + //==================================================================================================================== + doublereal IDA_Solver::derivative(int k) const { + return NV_Ith_S(nv(m_ydot),k); + } + //==================================================================================================================== + const doublereal* IDA_Solver::derivativeVector() const { + return NV_DATA_S(nv(m_ydot)); + } + //==================================================================================================================== + + void IDA_Solver::setTolerances(double reltol, double* abstol) { + m_itol = IDA_SV; + if (!m_abstol) { + m_abstol = reinterpret_cast(N_VNew_Serial(m_neq)); } - - const doublereal* IDA_Solver::solutionVector() const { return NV_DATA_S(nv(m_y));} - - doublereal IDA_Solver::derivative(int k) const { - return NV_Ith_S(nv(m_ydot),k); + for (int i = 0; i < m_neq; i++) { + NV_Ith_S(nv(m_abstol), i) = abstol[i]; } - - const doublereal* IDA_Solver::derivativeVector() const { return NV_DATA_S(nv(m_ydot));} + m_reltol = reltol; + int flag = IDASVtolerances(m_ida_mem, m_reltol, nv(m_abstol)); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } + } + //==================================================================================================================== + void IDA_Solver::setTolerances(doublereal reltol, doublereal abstol) { + m_itol = IDA_SS; + m_reltol = reltol; + m_abstols = abstol; + int flag = IDASStolerances(m_ida_mem, m_reltol, m_abstols); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } + } + //==================================================================================================================== + void IDA_Solver::setLinearSolverType(int solverType) { + m_type = solverType; + } + //==================================================================================================================== + void IDA_Solver::setDenseLinearSolver() { + setLinearSolverType(0); + } + //==================================================================================================================== + void IDA_Solver::setBandedLinearSolver(int m_upper, int m_lower) { + m_type = 2; + m_upper = m_mupper; + m_mlower = m_lower; + } + //==================================================================================================================== + void IDA_Solver::setMaxOrder(int n) { + m_maxord = n; + } + //==================================================================================================================== + void IDA_Solver::setMaxNumSteps(int n) { + m_maxsteps = n; + } + //==================================================================================================================== + void IDA_Solver::setInitialStepSize(doublereal h0) { + m_h0 = h0; + } + //==================================================================================================================== + void IDA_Solver::setStopTime(doublereal tstop) { + m_tstop = tstop; + } + //==================================================================================================================== + void IDA_Solver::setMaxErrTestFailures(int maxErrTestFails) { + m_maxErrTestFails = maxErrTestFails; + } + //==================================================================================================================== + void IDA_Solver::setMaxNonlinIterations(int n) { + m_maxNonlinIters = n; + } + //==================================================================================================================== + void IDA_Solver::setMaxNonlinConvFailures(int n) { + m_maxNonlinConvFails = n; + } + //==================================================================================================================== + void IDA_Solver::inclAlgebraicInErrorTest(bool yesno) { + if (yesno) { + m_setSuppressAlg = 0; + } else { + m_setSuppressAlg = 1; + } + } + //==================================================================================================================== + void IDA_Solver::init(doublereal t0) { - void IDA_Solver::setTolerances(double reltol, double* abstol) { - m_itol = IDA_SV; - if (m_abstol) N_VDestroy_Serial(nv(m_abstol)); - m_abstol = reinterpret_cast(N_VNew_Serial(m_neq)); - for (int i=0; i < m_neq; i++) { - NV_Ith_S(nv(m_abstol), i) = abstol[i]; - } - m_reltol = reltol; + m_t0 = t0; + if (m_y) { + N_VDestroy_Serial(nv(m_y)); + } + if (m_ydot) N_VDestroy_Serial(nv(m_ydot)); + if (m_id) N_VDestroy_Serial(nv(m_id)); + if (m_constraints) N_VDestroy_Serial(nv(m_constraints)); + + m_y = reinterpret_cast(N_VNew_Serial(m_neq)); + m_ydot = reinterpret_cast(N_VNew_Serial(m_neq)); + m_constraints = reinterpret_cast(N_VNew_Serial(m_neq)); + + for (int i=0; i(N_VNew_Serial(m_neq)); - m_ydot = reinterpret_cast(N_VNew_Serial(m_neq)); - m_constraints = reinterpret_cast(N_VNew_Serial(m_neq)); - - for (int i=0; i 0) - // flag = CVodeSetMaxOrd(m_cvode_mem, m_maxord); - //if (m_maxsteps > 0) - // flag = CVodeSetMaxNumSteps(m_cvode_mem, m_maxsteps); - //if (m_hmax > 0) - // flag = CVodeSetMaxStep(m_cvode_mem, m_hmax); - } - - void IDA_Solver::solve(double tout) - { - double t; - int flag; - flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_NORMAL); - if (flag != IDA_SUCCESS) - throw IDA_Err(" IDA error encountered."); - } - - double IDA_Solver::step(double tout) - { - double t; - int flag; - flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_ONE_STEP); - if (flag != IDA_SUCCESS) - throw IDA_Err(" IDA error encountered."); - return t; + /* Call IDACreate */ + m_ida_mem = IDACreate(); + + int flag = 0; + + + + if (m_itol == IDA_SV) { +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) + // vector atol + flag = IDAMalloc(m_ida_mem, ida_resid, m_t0, nv(m_y), nv(m_ydot), + m_itol, m_reltol, nv(m_abstol)); + if (flag != IDA_SUCCESS) { + if (flag == IDA_MEM_FAIL) { + throw IDA_Err("Memory allocation failed."); + } else if (flag == IDA_ILL_INPUT) { + throw IDA_Err("Illegal value for IDAMalloc input argument."); + } else + throw IDA_Err("IDAMalloc failed."); } - doublereal IDA_Solver::getOutputParameter(int flag) { - switch (flag) { - case REAL_WORKSPACE_SIZE: - flag = IDAGetWorkSpace(m_ida_mem, &lenrw, &leniw); - return doublereal(lenrw); - } - +#elif defined(SUNDIALS_VERSION_24) + flag = IDAInit(m_ida_mem, ida_resid, m_t0, nv(m_y), nv(m_ydot)); + if (flag != IDA_SUCCESS) { + if (flag == IDA_MEM_FAIL) { + throw IDA_Err("Memory allocation failed."); + } else if (flag == IDA_ILL_INPUT) { + throw IDA_Err("Illegal value for IDAMalloc input argument."); + } + else + throw IDA_Err("IDAMalloc failed."); + } + flag = IDASVtolerances(m_ida_mem, m_reltol, nv(m_abstol)); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } +#endif + } + else { +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) + // scalar atol + flag = IDAMalloc(m_ida_mem, ida_resid, m_t0, nv(m_y), nv(m_ydot), + m_itol, m_reltol, &m_abstols); + if (flag != IDA_SUCCESS) { + if (flag == IDA_MEM_FAIL) { + throw IDA_Err("Memory allocation failed."); } + else if (flag == IDA_ILL_INPUT) { + throw IDA_Err("Illegal value for IDAMalloc input argument."); + } + else + throw IDA_Err("IDAMalloc failed."); + } + +#elif defined(SUNDIALS_VERSION_24) + flag = IDAInit(m_ida_mem, ida_resid, m_t0, nv(m_y), nv(m_ydot)); + if (flag != IDA_SUCCESS) { + if (flag == IDA_MEM_FAIL) { + throw IDA_Err("Memory allocation failed."); } + else if (flag == IDA_ILL_INPUT) { + throw IDA_Err("Illegal value for IDAMalloc input argument."); + } + else + throw IDA_Err("IDAMalloc failed."); + } + flag = IDASStolerances(m_ida_mem, m_reltol, m_abstols); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } +#endif + } + + //----------------------------------- + // set the linear solver type + //----------------------------------- + + if (m_type == 1 || m_type == 0) { + long int N = m_neq; + flag = IDADense(m_ida_mem, N); + if (flag) { + throw IDA_Err("IDADense failed"); + } + } + else if (m_type == 2) { + long int N = m_neq; + long int nu = m_mupper; + long int nl = m_mlower; + IDABand(m_ida_mem, N, nu, nl); + } + else { + throw IDA_Err("unsupported linear solver type"); + } + + + // pass a pointer to func in m_data + m_fdata = new ResidData(&m_resid, m_resid.nparams()); +#if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) + flag = IDASetRdata(m_ida_mem, (void*)m_fdata); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetRdata failed."); + } +#elif defined(SUNDIALS_VERSION_24) + flag = IDASetUserData(m_ida_mem, (void*)m_fdata); + if (flag != IDA_SUCCESS) + throw IDA_Err("IDASetUserData failed."); +#endif + + // set options + if (m_maxord > 0) { + flag = IDASetMaxOrd(m_ida_mem, m_maxord); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetMaxOrd failed."); + } + } + if (m_maxsteps > 0) { + flag = IDASetMaxNumSteps(m_ida_mem, m_maxsteps); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetMaxNumSteps failed."); + } + } + if (m_h0 > 0.0) { + flag = IDASetInitStep(m_ida_mem, m_h0); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetInitStep failed."); + } + } + if (m_tstop > 0.0) { + flag = IDASetStopTime(m_ida_mem, m_tstop); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetStopTime failed."); + } + } + if (m_maxErrTestFails >= 0) { + flag = IDASetMaxErrTestFails(m_ida_mem, m_maxErrTestFails); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetMaxErrTestFails failed."); + } + } + if (m_maxNonlinIters >= 0) { + flag = IDASetMaxNonlinIters(m_ida_mem, m_maxNonlinIters); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetmaxNonlinIters failed."); + } + } + if (m_maxNonlinConvFails >= 0) { + flag = IDASetMaxConvFails(m_ida_mem, m_maxNonlinConvFails); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetMaxConvFails failed."); + } + } + if (m_setSuppressAlg != 0) { + flag = IDASetSuppressAlg(m_ida_mem, m_setSuppressAlg); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDASetSuppressAlg failed."); + } + } + + + + } + //==================================================================================================================== + // Calculate consistent value of the starting solution given the starting solution derivatives + /* + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the derivatives + * of all variables, this method computes the initial y + * values. + */ + void IDA_Solver::correctInitial_Y_given_Yp(doublereal* y, doublereal* yp, doublereal tout) { + int icopt = IDA_Y_INIT; + doublereal tout1 = tout; + if (tout == 0.0) { + double h0 = 1.0E-5; + if (m_h0 > 0.0) { + h0 = m_h0; + } + tout1 = m_t0 + h0; + } + + int flag = IDACalcIC(m_ida_mem, icopt, tout1); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDACalcIC failed: error = " + int2str(flag)); + } + + + flag = IDAGetSolution(m_ida_mem, tout1, nv(m_y), nv(m_ydot)); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDAGetSolution failed: error = " + int2str(flag)); + } + doublereal *yy = NV_DATA_S(nv(m_y)); + doublereal *yyp = NV_DATA_S(nv(m_ydot)); + + for (int i = 0; i < m_neq; i++) { + y[i] = yy[i]; + yp[i] = yyp[i]; + } + } + //==================================================================================================================== + /* + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the initial + * values of all differential variables, it computes the + * initial values of all algebraic variables and the initial + * derivatives of all differential variables. + * + * @param y Calculated value of the solution vector after the procedure ends + * @param yp Calculated value of the solution derivative after the procedure + * @param The first value of t at which a soluton will be + * requested (from IDASolve). (This is needed here to + * determine the direction of integration and rough scale + * in the independent variable t. + */ + void IDA_Solver::correctInitial_YaYp_given_Yd(doublereal* y, doublereal* yp, doublereal tout) { + + int icopt = IDA_YA_YDP_INIT; + doublereal tout1 = tout; + if (tout == 0.0) { + double h0 = 1.0E-5; + if (m_h0 > 0.0) { + h0 = m_h0; + } + tout1 = m_t0 + h0; + } + + int flag = IDACalcIC(m_ida_mem, icopt, tout1); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDACalcIC failed: error = " + int2str(flag)); + } + + + flag = IDAGetSolution(m_ida_mem, tout1, nv(m_y), nv(m_ydot)); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDAGetSolution failed: error = " + int2str(flag)); + } + doublereal *yy = NV_DATA_S(nv(m_y)); + doublereal *yyp = NV_DATA_S(nv(m_ydot)); + + for (int i = 0; i < m_neq; i++) { + y[i] = yy[i]; + yp[i] = yyp[i]; + } + } + //==================================================================================================================== + int IDA_Solver::solve(double tout) + { + double t; + int flag; + flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_NORMAL); + if (flag != IDA_SUCCESS) + throw IDA_Err(" IDA error encountered."); + return flag; + } + //==================================================================================================================== + double IDA_Solver::step(double tout) + { + double t; + int flag; + flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_ONE_STEP); + if (flag != IDA_SUCCESS) + throw IDA_Err(" IDA error encountered."); + return t; + } + //==================================================================================================================== + doublereal IDA_Solver::getOutputParameter(int flag) const { + long int lenrw, leniw; + switch (flag) { + case REAL_WORKSPACE_SIZE: + flag = IDAGetWorkSpace(m_ida_mem, &lenrw, &leniw); + return doublereal(lenrw); + break; + } + return 0.0; + } + //==================================================================================================================== + } - - diff --git a/Cantera/src/numerics/IDA_Solver.h b/Cantera/src/numerics/IDA_Solver.h index 59546d991..03d60c904 100644 --- a/Cantera/src/numerics/IDA_Solver.h +++ b/Cantera/src/numerics/IDA_Solver.h @@ -13,121 +13,304 @@ * */ -#ifndef CT_IDA_Solver_H -#define CT_IDA_Solver_H +#ifndef CT_IDA_SOLVER_H +#define CT_IDA_SOLVER_H #include #include "DAE_Solver.h" #include "ctexceptions.h" + +#ifdef SUNDIALS_VERSION_22 +#include +#else +#include + +// These constants are defined internally in the ida package, ida.c +#define IDA_NN 0 +#define IDA_SS 1 +#define IDA_SV 2 +#define IDA_WF 3 + +#endif +#if defined(SUNDIALS_VERSION_24) +#define REAL_WORKSPACE_SIZE 0 +#endif + namespace Cantera { - /** - * Exception thrown when a IDA error is encountered. + /** + * Exception thrown when a IDA error is encountered. + */ + class IDA_Err : public CanteraError { + public: + IDA_Err(std::string msg) : CanteraError("IDA_Solver", msg){} + }; + + + class ResidData; // forward reference + + class IDA_Solver : public DAE_Solver { + public: + + //! Constructor. + /*! + * Default settings: dense jacobian, no user-supplied Jacobian function, Newton iteration. + * + * @param f Function that will supply the time dependent residual to be solved */ - class IDA_Err : public CanteraError { - public: - IDA_Err(std::string msg) : CanteraError("IDA_Solver", msg){} - }; + IDA_Solver(ResidJacEval& f); + + virtual ~IDA_Solver(); + + /** + * Set error tolerances. This version specifies a scalar + * relative tolerance, and a vector absolute tolerance. + */ + virtual void setTolerances(doublereal reltol, + doublereal* abstol); + + /** + * Set error tolerances. This version specifies a scalar + * relative tolerance, and a scalar absolute tolerance. + */ + virtual void setTolerances(doublereal reltol, doublereal abstol); + + virtual void setLinearSolverType(int solverType); + + //! Set up the problem to use a dense linear direct solver + virtual void setDenseLinearSolver(); + + //! Set up the problem to use a band solver + /*! + * @param m_upper upper band width of the matrix + * @param m_lower lower band width of the matrix + */ + virtual void setBandedLinearSolver(int m_upper, int m_lower); + + virtual void setMaxOrder(int n); + + //! Set the maximum number of time steps + /*! + * @param n input of maximum number of time steps + */ + virtual void setMaxNumSteps(int n); + + //! Sset the initial step size + /*! + * @param h0 initial step size value + */ + virtual void setInitialStepSize(doublereal h0); + + //! Set the stop time + /*! + * @param tstop the independent variable value past which the solution is not to proceed. + */ + virtual void setStopTime(doublereal tstop); - class ResidData; // forward reference + virtual void setMaxErrTestFailures(int n); - class IDA_Solver : public DAE_Solver { - public: + //! Set the maximum number of nonlinear iterations on a timestep + /*! + * @param n Set the max iterations. The default is 4, which seems awefully low to me. + */ + virtual void setMaxNonlinIterations(int n); - IDA_Solver(ResidEval& f); - - virtual ~IDA_Solver(); - - /** - * Set error tolerances. This version specifies a scalar - * relative tolerance, and a vector absolute tolerance. - */ - virtual void setTolerances(doublereal reltol, - doublereal* abstol); - - /** - * Set error tolerances. This version specifies a scalar - * relative tolerance, and a scalar absolute tolerance. - */ - virtual void setTolerances(doublereal reltol, doublereal abstol); - - virtual void setLinearSolverType(int solverType); - - virtual void setDenseLinearSolver(); - virtual void setBandedLinearSolver(int m_upper, int m_lower); - - virtual void setMaxTime(doublereal tmax); - - virtual void setMaxOrder(int n); - - virtual void setMaxNumSteps(int n); - virtual void setInitialStepSize(doublereal h0); - virtual void setStopTime(doublereal tstop); - virtual void setMaxErrTestFailures(int n); - virtual void setMaxNonlinIterations(int n); - virtual void setMaxNonlinConvFailures(int n); - virtual void inclAlgebraicInErrorTest(bool yesno); - - virtual void setInputParameter(int flag, doublereal value); - virtual doublereal getOutputParameter(int flag); + //! Set the maximum number of nonlinear solver convergence failures + /*! + * @param n Value of nonlin failures. If value is exceeded, the calculation terminates. + */ + virtual void setMaxNonlinConvFailures(int n); - /** - * This method may be called if the initial conditions do not - * satisfy the residual equation F = 0. Given the derivatives - * of all variables, this method computes the initial y - * values. - */ - virtual void correctInitial_Y_given_Yp(doublereal* y, doublereal* yp, - doublereal tout); + virtual void inclAlgebraicInErrorTest(bool yesno); - /** - * This method may be called if the initial conditions do not - * satisfy the residual equation F = 0. Given the initial - * values of all differential variables, it computes the - * initial values of all algebraic variables and the initial - * derivatives of all differential variables. - */ - virtual void correctInitial_YaYp_given_Yd(doublereal* y, doublereal* yp, - doublereal tout); + /** + * Get the value of a solver-specific output parameter. + */ + virtual doublereal getOutputParameter(int flag) const; + + //! Calculate consistent value of the starting solution given the starting solution derivatives + /*! + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the derivatives + * of all variables, this method computes the initial y + * values. + */ + virtual void correctInitial_Y_given_Yp(doublereal* y, doublereal* yp, + doublereal tout); + + //! Calculate consistent value of the algebraic constraints and derivatives at the start of the problem + /*! + * This method may be called if the initial conditions do not + * satisfy the residual equation F = 0. Given the initial + * values of all differential variables, it computes the + * initial values of all algebraic variables and the initial + * derivatives of all differential variables. + */ + virtual void correctInitial_YaYp_given_Yd(doublereal* y, doublereal* yp, doublereal tout); + + //! Step the system to a final value of the time + /*! + * @param tout Final value of the time + * + * @return Returns the IDASolve() return flag + * + * The return values for IDASolve are described below. + * (The numerical return values are defined above in this file.) + * All unsuccessful returns give a negative return value. + * + * IDA_SUCCESS + * IDASolve succeeded and no roots were found. + * + * IDA_ROOT_RETURN: IDASolve succeeded, and found one or more roots. + * If nrtfn > 1, call IDAGetRootInfo to see which g_i were found + * to have a root at (*tret). + * + * IDA_TSTOP_RETURN: + * IDASolve returns computed results for the independent variable + * value tstop. That is, tstop was reached. + * + * IDA_MEM_NULL: + * The IDA_mem argument was NULL. + * + * IDA_ILL_INPUT: + * One of the inputs to IDASolve is illegal. This includes the + * situation when a component of the error weight vectors + * becomes < 0 during internal stepping. It also includes the + * situation where a root of one of the root functions was found + * both at t0 and very near t0. The ILL_INPUT flag + * will also be returned if the linear solver function IDA--- + * (called by the user after calling IDACreate) failed to set one + * of the linear solver-related fields in ida_mem or if the linear + * solver's init routine failed. In any case, the user should see + * the printed error message for more details. + * + * + * IDA_TOO_MUCH_WORK: + * The solver took mxstep internal steps but could not reach tout. + * The default value for mxstep is MXSTEP_DEFAULT = 500. + * + * IDA_TOO_MUCH_ACC: + * The solver could not satisfy the accuracy demanded by the user + * for some internal step. + * + * IDA_ERR_FAIL: + * Error test failures occurred too many times (=MXETF = 10) during + * one internal step. + * + * IDA_CONV_FAIL: + * Convergence test failures occurred too many times (= MXNCF = 10) + * during one internal step. + * + * IDA_LSETUP_FAIL: + * The linear solver's setup routine failed + * in an unrecoverable manner. + * + * IDA_LSOLVE_FAIL: + * The linear solver's solve routine failed + * in an unrecoverable manner. + * + * IDA_CONSTR_FAIL: + * The inequality constraints were violated, + * and the solver was unable to recover. + * + * IDA_REP_RES_ERR: + * The user's residual function repeatedly returned a recoverable + * error flag, but the solver was unable to recover. + * + * IDA_RES_FAIL: + * The user's residual function returned a nonrecoverable error + * flag. + * + */ + virtual int solve(doublereal tout); + + virtual doublereal step(doublereal tout); + + virtual void init(doublereal t0); + + //! the current value of solution component k. + /*! + * @param k index of the solution + */ + virtual doublereal solution(int k) const; + + virtual const doublereal* solutionVector() const; + + //! the current value of the derivative of solution component k. + virtual doublereal derivative(int k) const; + + virtual const doublereal* derivativeVector() const; + + void *IDAMemory() { + return m_ida_mem; + } + + protected: + + //! Pointer to the IDA memory for the problem + void* m_ida_mem; + + //! Initial value of the time + doublereal m_t0; + + //! Current value of the solution vector + void *m_y; + + //! Current value of the derivative of the solution vector + void *m_ydot; + void *m_id; + void *m_constraints; + void *m_abstol; + int m_type; - virtual int solve(doublereal tout); + int m_itol; + int m_iter; + doublereal m_reltol; + doublereal m_abstols; + int m_nabs; - virtual doublereal step(doublereal tout); + //! Maximum value of the timestep allowed + doublereal m_hmax; - virtual void init(doublereal t0); + //! Minimum value of the timestep allowd + doublereal m_hmin; - /// the current value of solution component k. - virtual doublereal solution(int k) const; + //! Value of the initial time step + doublereal m_h0; - virtual const doublereal* solutionVector() const; + //! Maximum number of time steps allowed + int m_maxsteps; - /// the current value of the derivative of solution component k. - virtual doublereal derivative(int k) const; + //! maximum time step order of the method + int m_maxord; - virtual const doublereal* derivativeVector() const; + //! maximum time + doublereal m_tstop; - protected: + //! maximum number of error test failures + int m_maxErrTestFails; - int m_neq; - void* m_ida_mem; - doublereal m_t0; - void *m_y, *m_ydot, *m_id, *m_constraints, *m_abstol; - int m_type; - int m_itol; - int m_iter; - doublereal m_reltol; - doublereal m_abstols; - int m_nabs; - doublereal m_hmax, m_hmin; - int m_maxsteps, m_maxord; - ResidData* m_fdata; - int m_mupper, m_mlower; - }; + //! Maximum number of nonlinear solver iterations at one solution + /*! + * If zero, this is the default of 4. + */ + int m_maxNonlinIters; + + //! Maximum number of nonlinear convergence failures + int m_maxNonlinConvFails; + + //! If true, the algebraic variables don't contribute to error tolerances + int m_setSuppressAlg; + + ResidData* m_fdata; + int m_mupper; + int m_mlower; + }; } diff --git a/Cantera/src/numerics/Integrator.h b/Cantera/src/numerics/Integrator.h index 55e8185c3..be04bc2d4 100644 --- a/Cantera/src/numerics/Integrator.h +++ b/Cantera/src/numerics/Integrator.h @@ -47,18 +47,20 @@ namespace Cantera { Adams_Method /**< Adams */ }; - /** - * Specifies the method used for iteration. + //! Specifies the method used for iteration. + /*! * Not all methods are supported by all integrators. */ enum IterType { - Newton_Iter, /**< Newton iteration */ - Functional_Iter /**< Functional iteration */ + //! Newton Iteration + Newton_Iter, + //! Functional Iteration + Functional_Iter }; - /** - * Abstract base class for ODE system integrators. + //! Abstract base class for ODE system integrators. + /*! * @ingroup odeGroup */ class Integrator { @@ -77,8 +79,8 @@ namespace Cantera { /** Set or reset the number of equations. */ //virtual void resize(int n)=0; - /** - * Set error tolerances. + //! Set error tolerances. + /*! * @param reltol scalar relative tolerance * @param number of equations * @param abstol array of N absolute tolerance values @@ -96,13 +98,20 @@ namespace Cantera { virtual void setTolerances(doublereal reltol, doublereal abstol) { warn("setTolerances"); } - virtual void setSensitivityTolerances(doublereal reltol, doublereal abstol) - {}// { warn("setSensitivityTolerances"); } - - /** - * Set problem type. + //! Set the sensitvity error tolerances + /*! + * @param reltol scalar relative tolerance + * @param abstol scalar absolute tolerance */ - virtual void setProblemType(int probtype) { warn("setProblemType"); } + virtual void setSensitivityTolerances(doublereal reltol, doublereal abstol) + { } + + //! Set the problem type. + /*! + * @param probtype Type of the problem + */ + virtual void setProblemType(int probtype) + { warn("setProblemType"); } /** * Initialize the integrator for a new problem. Call after @@ -116,10 +125,10 @@ namespace Cantera { virtual void reinitialize(doublereal t0, FuncEval& func) { warn("reinitialize"); } - /** - * Integrate the system of equations. - * @param tout integrate to this time. Note that this is the - * absolute time value, not a time interval. + //! Integrate the system of equations. + /*! + * @param tout Integrate to this time. Note that this is the + * absolute time value, not a time interval. */ virtual void integrate(doublereal tout) { warn("integrate"); } diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index bfd885d08..8787bb236 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -37,14 +37,14 @@ CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ ODE_integrators.o BandMatrix.o DAE_solvers.o \ funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o \ - solveProb.o BEulerInt.o RootFind.o + solveProb.o BEulerInt.o RootFind.o IDA_Solver.o NUMERICS_H = ArrayViewer.h DenseMatrix.h \ funcs.h ctlapack.h Func1.h FuncEval.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ - solveProb.h BEulerInt.h RootFind.h + solveProb.h BEulerInt.h RootFind.h IDA_Solver.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h diff --git a/Cantera/src/numerics/ResidEval.h b/Cantera/src/numerics/ResidEval.h index 3e25f8129..4f1eb5e61 100644 --- a/Cantera/src/numerics/ResidEval.h +++ b/Cantera/src/numerics/ResidEval.h @@ -155,7 +155,14 @@ namespace Cantera { } } - + //! Return the number of parameters in the calculation + /*! + * This is the number of parameters in the sensitivity calculation. We have + * set this to zero and have included it for later expansion + */ + int nparams () const { + return 0; + } protected: diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index cb6d08988..ea5ad953d 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -309,6 +309,13 @@ namespace Cantera { return 1; } //==================================================================================================================== + int ResidJacEval::eval(const doublereal t, const doublereal * const y, const doublereal * const ydot, + doublereal * const r) { + double deltaT = -1.0; + int flag = evalResidNJ(t, deltaT, y, ydot, r); + return flag; + } + //==================================================================================================================== // Calculate an analytical jacobian and the residual at the current time and values. /* * Only called if the jacFormation method is set to analytical diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index a1799253e..5277388fb 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -125,6 +125,20 @@ namespace Cantera { const doublereal delta_x = 0.0); + /** + * Evaluate the residual function. Called by the + * integrator. + * @param t time. (input) + * @param y solution vector. (input) + * @param ydot rate of change of solution vector. (input) + * @param r residual vector (output) + */ + virtual int eval(const doublereal t, const doublereal * const y, + const doublereal * const ydot, + doublereal * const r); + + + //! Fill in the initial conditions /*! * Values for both the solution and the value of ydot may be provided. From d2f885acd5570d21818c63c149be153e85a1f243 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 30 Jul 2011 03:17:00 +0000 Subject: [PATCH 377/446] added the ida solver --- Cantera/cxx/include/Cantera.mak.in | 8 ++++++-- Cantera/cxx/include/integrators.h | 2 ++ Cantera/cxx/include/numerics.h | 1 + 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in index 23c5114bd..b45e9bd32 100644 --- a/Cantera/cxx/include/Cantera.mak.in +++ b/Cantera/cxx/include/Cantera.mak.in @@ -88,9 +88,13 @@ CANTERA_SUNDIALS_LIB_DIR=@sundials_lib_dir@ ifeq ($(CANTERA_use_sundials), 1) CANTERA_CVODE_LIBS=-L$(CANTERA_SUNDIALS_LIB_DIR) @CVODE_LIBS@ CANTERA_CVODE_LIBS_DEP=@sundials_lib_dep@ +CANTERA_SUNDIALS_LIBS=-L$(CANTERA_SUNDIALS_LIB_DIR) @sundials_lib@ +CANTERA_SUNDIALS_LIBS_DEP=@sundials_lib_dep@ else CANTERA_CVODE_LIBS= -L$(CANTERA_LIBSDIR) -lcvode CANTERA_CVODE_LIBS_DEP=$(CANTERA_LIBSDIR)/libcvode.a +CANTERA_SUNDIALS_LIBS=-L$(CANTERA_LIBSDIR) -lcvode +CANTERA_SUNDIALS_LIBS_DEP=-L$(CANTERA_LIBSDIR)/libcvode.a endif # ####################################################################### @@ -133,11 +137,11 @@ CANTERA_DEFINES = -DCANTERA_VERSION=@ctversion@ CANTERA_TOTAL_LIBS2 = -L$(CANTERA_LIBSDIR) @LOCAL_LIBS@ # CANTERA_TOTAL_LIBS= $(CANTERA_CORE_LIBS) $(CANTERA_BOOST_LIBS) \ - $(CANTERA_CVODE_LIBS) $(CANTERA_BLAS_LAPACK_LIBS) \ + $(CANTERA_SUNDIALS_LIBS) $(CANTERA_BLAS_LAPACK_LIBS) \ $(CANTERA_F2C_LIBS) # CANTERA_TOTAL_LIBS_DEP= $(CANTERA_CORE_LIBS_DEP) \ - $(CANTERA_CVODE_LIBS_DEP) \ + $(CANTERA_SUNDIALS_LIBS_DEP) \ $(CANTERA_BLAS_LAPACK_LIBS_DEP) # # Dependency Line diff --git a/Cantera/cxx/include/integrators.h b/Cantera/cxx/include/integrators.h index 69a603dae..de9d23719 100755 --- a/Cantera/cxx/include/integrators.h +++ b/Cantera/cxx/include/integrators.h @@ -6,5 +6,7 @@ #define CT_INTEG_H_INCL #include "kernel/Integrator.h" +#include "kernel/DAE_Solver.h" +#include "kernel/IDA_Solver.h" #endif diff --git a/Cantera/cxx/include/numerics.h b/Cantera/cxx/include/numerics.h index ea143c3dd..0aa803eac 100755 --- a/Cantera/cxx/include/numerics.h +++ b/Cantera/cxx/include/numerics.h @@ -4,5 +4,6 @@ #include "kernel/DenseMatrix.h" #include "kernel/BandMatrix.h" #include "kernel/SquareMatrix.h" +#include "kernel/NonlinearSolver.h" #endif From 82e194a2b00298daf231798db0abb572eeba327c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 31 Jul 2011 18:58:19 +0000 Subject: [PATCH 378/446] Added column pointers as a member to this object. This is needed for linking in sundance more closely. --- Cantera/src/numerics/DenseMatrix.cpp | 24 ++++++++++++++++++++++++ Cantera/src/numerics/DenseMatrix.h | 25 ++++++++++++++++++++++++- 2 files changed, 48 insertions(+), 1 deletion(-) diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp index 89f6d7519..c56f242fb 100644 --- a/Cantera/src/numerics/DenseMatrix.cpp +++ b/Cantera/src/numerics/DenseMatrix.cpp @@ -38,6 +38,10 @@ namespace Cantera { m_printLevel(0) { m_ipiv.resize(max(n, m)); + m_colPts.resize(m); + for (int j = 0; j < m; j++) { + m_colPts[j] = &(m_data[m_nrows*j]); + } } //==================================================================================================================== // Copy constructor @@ -51,6 +55,10 @@ namespace Cantera { m_printLevel(0) { m_ipiv = y.ipiv(); + m_colPts.resize(m_ncols); + for (int j = 0; j < m_ncols; j++) { + m_colPts[j] = &(m_data[m_nrows*j]); + } } //==================================================================================================================== // assignment @@ -58,6 +66,10 @@ namespace Cantera { if (&y == this) return *this; Array2D::operator=(y); m_ipiv = y.ipiv(); + m_colPts.resize(m_ncols); + for (int j = 0; j < m_ncols; j++) { + m_colPts[j] = &(m_data[m_nrows*j]); + } m_useReturnErrorCode = y.m_useReturnErrorCode; m_printLevel = y.m_printLevel; return *this; @@ -71,6 +83,18 @@ namespace Cantera { void DenseMatrix::resize(int n, int m, doublereal v) { Array2D::resize(n,m,v); m_ipiv.resize( max(n,m) ); + m_colPts.resize(m_ncols); + for (int j = 0; j < m_ncols; j++) { + m_colPts[j] = &(m_data[m_nrows*j]); + } + } + //==================================================================================================================== + doublereal * const * DenseMatrix::colPts() { + return &(m_colPts[0]); + } + //==================================================================================================================== + const doublereal * const * DenseMatrix::const_colPts() const { + return &(m_colPts[0]); } //==================================================================================================================== void DenseMatrix::mult(const double* b, double* prod) const { diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index 04aac8f48..f635e17bb 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -113,7 +113,27 @@ namespace Cantera { * @param m New number of columns * @param v Default fill value. defaults to zero. */ - void resize(int n, int m, doublereal v = 0.0); + void resize(int n, int m, doublereal v); + + //! Return a vector of const pointers to the columns + /*! + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + doublereal * const * colPts(); + + //! Return a const vector of const pointers to the columns + /*! + * Note, the jacobian can not be altered by this routine, and + * therefore the member function is const. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + const doublereal * const * const_colPts() const; //! Multiply A*b and write result to \c prod. /*! @@ -150,6 +170,9 @@ namespace Cantera { //! Vector of pivots. Length is equal to the max of m and n. vector_int m_ipiv; + //! Vector of column pointers + std::vector m_colPts; + public: //! Error Handling Flag From 2f971807535f55e63221c0d57a4e8fa7a7a7c865 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sun, 31 Jul 2011 23:44:45 +0000 Subject: [PATCH 379/446] Fixed an error in the IDA_Solver class. Added an analytical jacobian capability to IDA_Solver. Added column pointers as a member to DenseMatrix --- Cantera/src/numerics/DenseMatrix.h | 2 +- Cantera/src/numerics/IDA_Solver.cpp | 130 ++++++++++++++++++++++--- Cantera/src/numerics/IDA_Solver.h | 32 ++++++ Cantera/src/numerics/ResidJacEval.cpp | 30 +++++- Cantera/src/numerics/ResidJacEval.h | 21 ++++ Cantera/src/thermo/MixtureFugacityTP.h | 2 +- 6 files changed, 200 insertions(+), 17 deletions(-) diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index f635e17bb..b6d37af1c 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -113,7 +113,7 @@ namespace Cantera { * @param m New number of columns * @param v Default fill value. defaults to zero. */ - void resize(int n, int m, doublereal v); + void resize(int n, int m, doublereal v = 0.0); //! Return a vector of const pointers to the columns /*! diff --git a/Cantera/src/numerics/IDA_Solver.cpp b/Cantera/src/numerics/IDA_Solver.cpp index 6f2575138..91a5532a1 100644 --- a/Cantera/src/numerics/IDA_Solver.cpp +++ b/Cantera/src/numerics/IDA_Solver.cpp @@ -44,14 +44,16 @@ namespace Cantera { public: - ResidData(ResidJacEval* f, int npar = 0) { + ResidData(ResidJacEval* f, IDA_Solver *s, int npar = 0) { m_func = f; + m_solver = s; } virtual ~ResidData() { } ResidJacEval* m_func; + IDA_Solver * m_solver; }; } @@ -71,9 +73,41 @@ extern "C" { double* rdata = NV_DATA_S(r); Cantera::ResidData* d = (Cantera::ResidData*) f_data; Cantera::ResidJacEval* f = d->m_func; + Cantera::IDA_Solver *s = d->m_solver; f->eval(t, ydata, ydotdata, rdata); return 0; } + + //! Function called by by IDA to evaluate the Jacobian, given y and ydot. + /*! + * + * + * typedef int (*IDADlsDenseJacFn)(int N, realtype t, realtype c_j, + * N_Vector y, N_Vector yp, N_Vector r, + * DlsMat Jac, void *user_data, + * N_Vector tmp1, N_Vector tmp2, N_Vector tmp3); + * + * A IDADlsDenseJacFn should return + * 0 if successful, + * a positive int if a recoverable error occurred, or + * a negative int if a nonrecoverable error occurred. + * In the case of a recoverable error return, the integrator will + * attempt to recover by reducing the stepsize (which changes cj). + */ + static int ida_jacobian(int nrows, realtype t, realtype c_j, N_Vector y, N_Vector ydot, N_Vector r, + DlsMat Jac, void *f_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) { + doublereal * ydata = NV_DATA_S(y); + doublereal * ydotdata = NV_DATA_S(ydot); + doublereal * rdata = NV_DATA_S(r); + Cantera::ResidData* d = (Cantera::ResidData*) f_data; + Cantera::ResidJacEval* f = d->m_func; + doublereal * const * colPts = Jac->cols; + doublereal delta_t = 0.0; + f->evalJacobianDP(t, delta_t, c_j, ydata, ydotdata, colPts, rdata); + return 0; + } + + } namespace Cantera { @@ -103,7 +137,12 @@ namespace Cantera { m_h0(0.0), m_maxsteps(20000), m_maxord(0), + m_formJac(0), m_tstop(0.0), + m_told_old(0.0), + m_told(0.0), + m_tcurrent(0.0), + m_deltat(0.0), m_maxErrTestFails(-1), m_maxNonlinIters(0), m_maxNonlinConvFails(-1), @@ -151,10 +190,12 @@ namespace Cantera { for (int i = 0; i < m_neq; i++) { NV_Ith_S(nv(m_abstol), i) = abstol[i]; } - m_reltol = reltol; - int flag = IDASVtolerances(m_ida_mem, m_reltol, nv(m_abstol)); - if (flag != IDA_SUCCESS) { - throw IDA_Err("Memory allocation failed."); + m_reltol = reltol; + if (m_ida_mem) { + int flag = IDASVtolerances(m_ida_mem, m_reltol, nv(m_abstol)); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } } } //==================================================================================================================== @@ -162,9 +203,11 @@ namespace Cantera { m_itol = IDA_SS; m_reltol = reltol; m_abstols = abstol; - int flag = IDASStolerances(m_ida_mem, m_reltol, m_abstols); - if (flag != IDA_SUCCESS) { - throw IDA_Err("Memory allocation failed."); + if (m_ida_mem) { + int flag = IDASStolerances(m_ida_mem, m_reltol, m_abstols); + if (flag != IDA_SUCCESS) { + throw IDA_Err("Memory allocation failed."); + } } } //==================================================================================================================== @@ -198,6 +241,18 @@ namespace Cantera { m_tstop = tstop; } //==================================================================================================================== + void IDA_Solver::setJacobianType(int formJac) { + m_formJac = formJac; + if (m_ida_mem) { + if (m_formJac == 1) { + int flag = IDADlsSetDenseJacFn(m_ida_mem, ida_jacobian); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDADlsSetDenseJacFn failed."); + } + } + } + } + //==================================================================================================================== void IDA_Solver::setMaxErrTestFailures(int maxErrTestFails) { m_maxErrTestFails = maxErrTestFails; } @@ -222,6 +277,9 @@ namespace Cantera { void IDA_Solver::init(doublereal t0) { m_t0 = t0; + m_told = t0; + m_told_old = t0; + m_tcurrent = t0; if (m_y) { N_VDestroy_Serial(nv(m_y)); } @@ -338,9 +396,15 @@ namespace Cantera { throw IDA_Err("unsupported linear solver type"); } + if (m_formJac == 1) { + flag = IDADlsSetDenseJacFn(m_ida_mem, ida_jacobian); + if (flag != IDA_SUCCESS) { + throw IDA_Err("IDADlsSetDenseJacFn failed."); + } + } // pass a pointer to func in m_data - m_fdata = new ResidData(&m_resid, m_resid.nparams()); + m_fdata = new ResidData(&m_resid, this, m_resid.nparams()); #if defined(SUNDIALS_VERSION_22) || defined(SUNDIALS_VERSION_23) flag = IDASetRdata(m_ida_mem, (void*)m_fdata); if (flag != IDA_SUCCESS) { @@ -383,7 +447,7 @@ namespace Cantera { throw IDA_Err("IDASetMaxErrTestFails failed."); } } - if (m_maxNonlinIters >= 0) { + if (m_maxNonlinIters > 0) { flag = IDASetMaxNonlinIters(m_ida_mem, m_maxNonlinIters); if (flag != IDA_SUCCESS) { throw IDA_Err("IDASetmaxNonlinIters failed."); @@ -490,11 +554,35 @@ namespace Cantera { //==================================================================================================================== int IDA_Solver::solve(double tout) { - double t; + double tretn; int flag; - flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_NORMAL); - if (flag != IDA_SUCCESS) + flag = IDASetStopTime(m_ida_mem, tout); + if (flag != IDA_SUCCESS) { throw IDA_Err(" IDA error encountered."); + } + do { + if (tout <= m_tcurrent) { + throw IDA_Err(" tout <= tcurrent"); + } + m_told_old = m_told; + m_told = m_tcurrent; + flag = IDASolve(m_ida_mem, tout, &tretn, nv(m_y), nv(m_ydot), IDA_ONE_STEP); + if (flag < 0) { + throw IDA_Err(" IDA error encountered."); + } else if (flag == IDA_TSTOP_RETURN) { + // we've reached our goal, and have actually integrated past it + } else if (flag == IDA_ROOT_RETURN) { + // not sure what to do with this yet + } else if (flag == IDA_WARNING) { + throw IDA_Err(" IDA Warning encountered."); + } + m_tcurrent = tretn; + m_deltat = m_tcurrent - m_told; + } while (tretn < tout); + + if (flag != IDA_SUCCESS && flag != IDA_TSTOP_RETURN) { + throw IDA_Err(" IDA error encountered."); + } return flag; } //==================================================================================================================== @@ -502,9 +590,23 @@ namespace Cantera { { double t; int flag; + if (tout <= m_tcurrent) { + throw IDA_Err(" tout <= tcurrent"); + } + m_told_old = m_told; + m_told = m_tcurrent; flag = IDASolve(m_ida_mem, tout, &t, nv(m_y), nv(m_ydot), IDA_ONE_STEP); - if (flag != IDA_SUCCESS) + if (flag < 0) { throw IDA_Err(" IDA error encountered."); + } else if (flag == IDA_TSTOP_RETURN) { + // we've reached our goal, and have actually integrated past it + } else if (flag == IDA_ROOT_RETURN) { + // not sure what to do with this yet + } else if (flag == IDA_WARNING) { + throw IDA_Err(" IDA Warning encountered."); + } + m_tcurrent = t; + m_deltat = m_tcurrent - m_told; return t; } //==================================================================================================================== diff --git a/Cantera/src/numerics/IDA_Solver.h b/Cantera/src/numerics/IDA_Solver.h index 03d60c904..4bf250161 100644 --- a/Cantera/src/numerics/IDA_Solver.h +++ b/Cantera/src/numerics/IDA_Solver.h @@ -110,6 +110,17 @@ namespace Cantera { virtual void setStopTime(doublereal tstop); + //! Set the form of the jacobian + /*! + * + * @param formJac Form of the jacobian + * + * 0 numerical jacobian + * 1 analytical jacobian given by the evalJacobianDP() function + */ + virtual void setJacobianType(int formJac); + + virtual void setMaxErrTestFailures(int n); //! Set the maximum number of nonlinear iterations on a timestep @@ -289,9 +300,30 @@ namespace Cantera { //! maximum time step order of the method int m_maxord; + //! Form of the jacobian + /*! + * 0 numerical jacobian created by ida + * 1 analytical jacobian. Must have populated the evalJacobianDP() + * function in the ResidJacEval class. + * 2 numerical jacobian formed by the ResidJacEval class (unimplemented) + */ + int m_formJac; + //! maximum time doublereal m_tstop; + //! Value of the previous, previous time + doublereal m_told_old; + + //! Value of the previous time + doublereal m_told; + + //! Value of the current time + doublereal m_tcurrent; + + //! Value of deltaT for the current step + doublereal m_deltat; + //! maximum number of error test failures int m_maxErrTestFails; diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index ea5ad953d..247f46e5c 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -334,7 +334,35 @@ namespace Cantera { SquareMatrix &J, doublereal * const resid) { - throw CanteraError("ResidJacEval::evalJacobian()", "Not implemented\n"); + doublereal * const * jac_colPts = J.colPts(); + doublereal cj = 0.0; + if (delta_t > 0.0) { + cj = 1.0/delta_t; + } + return evalJacobianDP(t, delta_t, cj, y, ydot, jac_colPts, resid); + } + //==================================================================================================================== + // Calculate an analytical jacobian and the residual at the current time and values. + /* + * Only called if the jacFormation method is set to analytical + * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param c_j The current value of the coefficient of the time derivative + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param jac_colPts Reference to the SquareMatrix object to be calculated (output) + * @param resid Value of the residual that is computed (output) + */ + int ResidJacEval:: + evalJacobianDP(const doublereal t, const doublereal delta_t, + const doublereal c_j, + const doublereal * const y, + const doublereal * const ydot, + doublereal * const * jac_colPts, + doublereal * const resid) + { + throw CanteraError("ResidJacEval::evalJacobianDP()", "Not implemented\n"); return 1; } //==================================================================================================================== diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 5277388fb..b44707ec9 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -333,6 +333,27 @@ namespace Cantera { SquareMatrix &J, doublereal * const resid); + //! Calculate an analytical jacobian and the residual at the current time and values. + /*! + * Only called if the jacFormation method is set to analytical + * + * @param t Time (input) + * @param delta_t The current value of the time step (input) + * @param y Solution vector (input, do not modify) + * @param ydot Rate of change of solution vector. (input, do not modify) + * @param J Reference to the SquareMatrix object to be calculated (output) + * @param resid Value of the residual that is computed (output) + * + * @return Returns a flag to indicate that operation is successful. + * 1 Means a successful operation + * -0 or neg value Means an unsuccessful operation + */ + virtual int evalJacobianDP(const doublereal t, const doublereal delta_t, doublereal cj, + const doublereal* const y, + const doublereal* const ydot, + doublereal * const *jacobianColPts, + doublereal * const resid); + protected: //! constant value of atol diff --git a/Cantera/src/thermo/MixtureFugacityTP.h b/Cantera/src/thermo/MixtureFugacityTP.h index 77e88b061..f5d603334 100644 --- a/Cantera/src/thermo/MixtureFugacityTP.h +++ b/Cantera/src/thermo/MixtureFugacityTP.h @@ -55,7 +55,7 @@ namespace Cantera { * steps for efficiently handling mixture of gases that whose standard states * are defined as ideal gases, but which describe also non-ideal solutions. * In addition a multicomponent liquid phase below the critical temperature of the - * mixture is also allowed. The main subclass will be a mixture Redlich-kwong class. + * mixture is also allowed. The main subclass is currently a mixture Redlich-Kwong class. * * Several concepts are introduced. The first concept is there are temporary * variables for holding the species standard state values From 78eb7b41277328d4b11c4994b0ff8839b49f0a90 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 1 Aug 2011 15:26:20 +0000 Subject: [PATCH 380/446] More integration of IDA into Cantera. added cj parameter to some existing routines. Added correct delta_t to the parameter list of ResidJacEval object --- Cantera/src/numerics/BEulerInt.cpp | 2 +- Cantera/src/numerics/IDA_Solver.cpp | 28 +++++++++++++++++++++--- Cantera/src/numerics/IDA_Solver.h | 6 +++++ Cantera/src/numerics/NonlinearSolver.cpp | 3 ++- Cantera/src/numerics/ResidJacEval.cpp | 6 +---- Cantera/src/numerics/ResidJacEval.h | 10 ++++----- 6 files changed, 40 insertions(+), 15 deletions(-) diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp index 154a89d7f..78753267d 100644 --- a/Cantera/src/numerics/BEulerInt.cpp +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -656,7 +656,7 @@ namespace Cantera { /******************************************************************** * Call the function to get a jacobian. */ - m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); + m_func->evalJacobian(time_curr, delta_t_n, CJ, y, ydot, J, f); #ifdef DEBUG_HKM //double dddd = J(89, 89); //checkFinite(dddd); diff --git a/Cantera/src/numerics/IDA_Solver.cpp b/Cantera/src/numerics/IDA_Solver.cpp index 91a5532a1..7c269b040 100644 --- a/Cantera/src/numerics/IDA_Solver.cpp +++ b/Cantera/src/numerics/IDA_Solver.cpp @@ -66,6 +66,13 @@ extern "C" { * the sundials data types N_Vector, etc.), we define this function as the single function that IDA always calls. The * real evaluation of the residual is done by an instance of a subclass of ResidEval, passed in to this * function as a pointer in the parameters. + * + * FROM IDA WRITEUP -> What the IDA solver expects as a return flag from its residual routines ------ + * A IDAResFn res should return a value of 0 if successful, a positive + * value if a recoverable error occured (e.g. yy has an illegal value), + * or a negative value if a nonrecoverable error occured. In the latter + * case, the program halts. If a recoverable error occured, the integrator + * will attempt to correct and retry. */ static int ida_resid(realtype t, N_Vector y, N_Vector ydot, N_Vector r, void *f_data) { double* ydata = NV_DATA_S(y); @@ -74,8 +81,15 @@ extern "C" { Cantera::ResidData* d = (Cantera::ResidData*) f_data; Cantera::ResidJacEval* f = d->m_func; Cantera::IDA_Solver *s = d->m_solver; - f->eval(t, ydata, ydotdata, rdata); - return 0; + double delta_t = s->getCurrentStepFromIDA(); + // TODO evaluate evalType. Assumed to be Base_ResidEval + int retn = 0; + int flag = f->evalResidNJ(t, delta_t, ydata, ydotdata, rdata); + if (flag < 0) { + // This signals to IDA that a nonrecoverable error has occurred. + retn = flag; + } + return retn; } //! Function called by by IDA to evaluate the Jacobian, given y and ydot. @@ -102,7 +116,9 @@ extern "C" { Cantera::ResidData* d = (Cantera::ResidData*) f_data; Cantera::ResidJacEval* f = d->m_func; doublereal * const * colPts = Jac->cols; - doublereal delta_t = 0.0; + Cantera::IDA_Solver *s = d->m_solver; + double delta_t = s->getCurrentStepFromIDA(); + // printf(" delta_t = %g 1/cj = %g\n", delta_t, 1.0/c_j); f->evalJacobianDP(t, delta_t, c_j, ydata, ydotdata, colPts, rdata); return 0; } @@ -241,6 +257,12 @@ namespace Cantera { m_tstop = tstop; } //==================================================================================================================== + doublereal IDA_Solver::getCurrentStepFromIDA() { + doublereal hcur; + IDAGetCurrentStep(m_ida_mem, &hcur); + return hcur; + } + //==================================================================================================================== void IDA_Solver::setJacobianType(int formJac) { m_formJac = formJac; if (m_ida_mem) { diff --git a/Cantera/src/numerics/IDA_Solver.h b/Cantera/src/numerics/IDA_Solver.h index 4bf250161..928728969 100644 --- a/Cantera/src/numerics/IDA_Solver.h +++ b/Cantera/src/numerics/IDA_Solver.h @@ -109,6 +109,12 @@ namespace Cantera { */ virtual void setStopTime(doublereal tstop); + //! Get the current step size from IDA via a call + /*! + * @return Returns the current step size. + */ + virtual double getCurrentStepFromIDA(); + //! Set the form of the jacobian /*! diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 64394870f..89a2904a0 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -2979,6 +2979,7 @@ namespace Cantera { int info; doublereal ysave, ydotsave, dy; int retn = 1; + /* * Clear the factor flag */ @@ -2987,7 +2988,7 @@ namespace Cantera { /******************************************************************** * Call the function to get a jacobian. */ - info = m_func->evalJacobian(time_curr, delta_t_n, y, ydot, J, f); + info = m_func->evalJacobian(time_curr, delta_t_n, CJ, y, ydot, J, f); m_nJacEval++; m_nfe++; if (info != 1) { diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 247f46e5c..a0261c9f3 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -328,17 +328,13 @@ namespace Cantera { * @param resid Value of the residual that is computed (output) */ int ResidJacEval:: - evalJacobian(const doublereal t, const doublereal delta_t, + evalJacobian(const doublereal t, const doublereal delta_t, doublereal cj, const doublereal * const y, const doublereal * const ydot, SquareMatrix &J, doublereal * const resid) { doublereal * const * jac_colPts = J.colPts(); - doublereal cj = 0.0; - if (delta_t > 0.0) { - cj = 1.0/delta_t; - } return evalJacobianDP(t, delta_t, cj, y, ydot, jac_colPts, resid); } //==================================================================================================================== diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index b44707ec9..678d3fe7b 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -318,6 +318,7 @@ namespace Cantera { * * @param t Time (input) * @param delta_t The current value of the time step (input) + * @param cj Coefficient of yprime used in the evalulation of the jacobian * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) * @param J Reference to the SquareMatrix object to be calculated (output) @@ -327,11 +328,9 @@ namespace Cantera { * 1 Means a successful operation * -0 or neg value Means an unsuccessful operation */ - virtual int evalJacobian(const doublereal t, const doublereal delta_t, - const doublereal* const y, - const doublereal* const ydot, - SquareMatrix &J, - doublereal * const resid); + virtual int evalJacobian(const doublereal t, const doublereal delta_t, doublereal cj, + const doublereal* const y, const doublereal* const ydot, + SquareMatrix &J, doublereal * const resid); //! Calculate an analytical jacobian and the residual at the current time and values. /*! @@ -339,6 +338,7 @@ namespace Cantera { * * @param t Time (input) * @param delta_t The current value of the time step (input) + * @param cj Coefficient of yprime used in the evalulation of the jacobian * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) * @param J Reference to the SquareMatrix object to be calculated (output) From d6604150670ba49bae332f87ef3e8448add5697b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 1 Aug 2011 22:07:28 +0000 Subject: [PATCH 381/446] Rebaselined. --- test_problems/min_python/negATest/negATest_blessed.out | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test_problems/min_python/negATest/negATest_blessed.out b/test_problems/min_python/negATest/negATest_blessed.out index e63158035..d170960c3 100644 --- a/test_problems/min_python/negATest/negATest_blessed.out +++ b/test_problems/min_python/negATest/negATest_blessed.out @@ -1,7 +1,7 @@ Number of species = 12 Number of reactions = 12 rop [ 0:O ] = 0.447058 -rop [ 1:O2 ] = -0.00214428 +rop [ 1:O2 ] = -0.0021443 rop [ 2:N ] = 0 rop [ 3:NO ] = -279.361 rop [ 4:NO2 ] = 0.00214319 @@ -17,7 +17,7 @@ fwd_rop[ 0] = 479.304 rev_rop[ 0] = 97.94 fwd_rop[ 1] = -128.201 rev_rop[ 1] = -26.1964 fwd_rop[ 2] = 0 rev_rop[ 2] = 0 fwd_rop[ 3] = -0 rev_rop[ 3] = -0 -fwd_rop[ 4] = 0 rev_rop[ 4] = 1.08891e-06 +fwd_rop[ 4] = 0 rev_rop[ 4] = 1.10334e-06 fwd_rop[ 5] = 0 rev_rop[ 5] = 0 fwd_rop[ 6] = 0 rev_rop[ 6] = 0 fwd_rop[ 7] = 0 rev_rop[ 7] = 0 From db3f16b6c79881327de9d791d919e5d44c74e572 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 10 Aug 2011 01:37:12 +0000 Subject: [PATCH 382/446] Made a few member functions in MixtureFugacityTP public fixed an error in IonsFromNeutralVPSSTP. a member function used by the equilibrium sovler was missing. --- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 57 ++++++++++---------- Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 21 ++++++++ Cantera/src/thermo/MargulesVPSSTP.h | 2 +- Cantera/src/thermo/MixtureFugacityTP.cpp | 2 +- Cantera/src/thermo/MixtureFugacityTP.h | 6 +-- Cantera/src/thermo/RedlichKwongMFTP.cpp | 9 ++-- Cantera/src/thermo/RedlichKwongMFTP.h | 7 +-- 7 files changed, 64 insertions(+), 40 deletions(-) diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index e2ed1351a..f7c9a79f6 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -637,7 +637,7 @@ namespace Cantera { dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; } } - + //==================================================================================================================== // Get the array of log concentration-like derivatives of the // log activity coefficients /* @@ -665,19 +665,28 @@ namespace Cantera { dlnActCoeffdlnN_diag[k] = dlnActCoeffdlnN_diag_[k]; } } - - // This is temporary. We will get rid of this + //==================================================================================================================== + void IonsFromNeutralVPSSTP::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) { + s_update_lnActCoeff(); + s_update_dlnActCoeff_dlnN(); + double *data = & dlnActCoeffdlnN_(0,0); + for (int k = 0; k < m_kk; k++) { + for (int m = 0; m < m_kk; m++) { + dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m]; + } + } + } + //==================================================================================================================== void IonsFromNeutralVPSSTP::setTemperature(const doublereal temp) { double p = pressure(); IonsFromNeutralVPSSTP::setState_TP(temp, p); } - - // This is temporary. We will get rid of this + //==================================================================================================================== void IonsFromNeutralVPSSTP::setPressure(doublereal p) { double t = temperature(); IonsFromNeutralVPSSTP::setState_TP(t, p); } - + //==================================================================================================================== // Set the temperature (K) and pressure (Pa) /* * Setting the pressure may involve the solution of a nonlinear equation. @@ -741,7 +750,7 @@ namespace Cantera { } } - + //==================================================================================================================== // Calculate neutral molecule mole fractions /* * This routine calculates the neutral molecule mole @@ -869,8 +878,8 @@ namespace Cantera { } } - -// Calculate neutral molecule mole fractions + //==================================================================================================================== + // Calculate neutral molecule mole fractions /* * This routine calculates the neutral molecule mole * fraction given the vector of ion mole fractions, @@ -1211,6 +1220,7 @@ namespace Cantera { dlnActCoeffdT_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnX_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); dlnActCoeffdlnN_diag_NeutralMolecule_.resize(numNeutralMoleculeSpecies_); + dlnActCoeffdlnN_NeutralMolecule_.resize(numNeutralMoleculeSpecies_, numNeutralMoleculeSpecies_, 0.0); } //==================================================================================================================== //! Return the factor overlap @@ -1734,11 +1744,9 @@ namespace Cantera { /* * Get the activity coefficients of the neutral molecules */ - GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); - + GibbsExcessVPSSTP *geThermo = dynamic_cast(neutralMoleculePhase_); if (!geThermo) { - - return; + throw CanteraError("IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN()", "dynamic cast failed"); } int nsp_ge = geThermo->nSpecies(); geThermo->getdlnActCoeffdlnN(nsp_ge, &(dlnActCoeffdlnN_NeutralMolecule_(0,0))); @@ -1750,13 +1758,7 @@ namespace Cantera { // Do the cation list for (k = 0; k < (int) cationList_.size(); k++) { - for (m = 0; m < (int) cationList_.size(); m++) { - //! Get the id for the next cation - //icat = cationList_[k]; - //jNeut = fm_invert_ionForNeutral[icat]; - //fmij = fm_neutralMolec_ions_[icat + jNeut * m_kk]; - //lnActCoeff_Scaled_[icat] = log(gammaNeutralMolecule_[jNeut])/fmij; - + for (m = 0; m < (int) cationList_.size(); m++) { kcat = cationList_[k]; kNeut = fm_invert_ionForNeutral[kcat]; @@ -1767,14 +1769,13 @@ namespace Cantera { mNeut = fm_invert_ionForNeutral[mcat]; mfmij = fm_neutralMolec_ions_[mcat + mNeut * m_kk]; - dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut,mNeut) * mfmij / fmij; + dlnActCoeffdlnN_(kcat,mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut,mNeut) * mfmij / fmij; - - for (m = 0; m < numPassThroughSpecies_; m++) { - mcat = passThroughList_[m]; - mNeut = fm_invert_ionForNeutral[mcat]; - dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut, mNeut) / fmij; - } + } + for (m = 0; m < numPassThroughSpecies_; m++) { + mcat = passThroughList_[m]; + mNeut = fm_invert_ionForNeutral[mcat]; + dlnActCoeffdlnN_(kcat, mcat) = dlnActCoeffdlnN_NeutralMolecule_(kNeut, mNeut) / fmij; } } @@ -1819,8 +1820,6 @@ namespace Cantera { throw CanteraError("IonsFromNeutralVPSSTP::s_update_lnActCoeff_dlnN", "Unimplemented type"); break; } - - } //==================================================================================================================== } diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index 787b305df..d0c62c20a 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -458,6 +458,27 @@ namespace Cantera { */ virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; + //! Get the array of derivatives of the ln activity coefficients with respect to the ln species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * log of a species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) ; + + //! Get the Salt Dissociation Coefficients //! Returns the vector of dissociation coefficients and vector of charges /*! diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index b80b2aa4c..93adb082c 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -829,7 +829,7 @@ namespace Cantera { virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; - //! Get the array of derivatives of the log activity coefficients with respect to the ln species mole numbers + //! Get the array of derivatives of the ln activity coefficients with respect to the ln species mole numbers /*! * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a * log of a species mole number (with all other species mole numbers held constant) diff --git a/Cantera/src/thermo/MixtureFugacityTP.cpp b/Cantera/src/thermo/MixtureFugacityTP.cpp index 21e032fa6..901daa9c9 100644 --- a/Cantera/src/thermo/MixtureFugacityTP.cpp +++ b/Cantera/src/thermo/MixtureFugacityTP.cpp @@ -1008,7 +1008,7 @@ namespace Cantera { * WATER_SUPERCRIT above the critical temperature */ int MixtureFugacityTP::phaseState(bool checkState) const { - int state; + int state = iState_; if (checkState) { double t = temperature(); double tcrit = critTemperature(); diff --git a/Cantera/src/thermo/MixtureFugacityTP.h b/Cantera/src/thermo/MixtureFugacityTP.h index f5d603334..5aa9f7c3a 100644 --- a/Cantera/src/thermo/MixtureFugacityTP.h +++ b/Cantera/src/thermo/MixtureFugacityTP.h @@ -753,7 +753,7 @@ protected: * @return returns the estimated saturation pressure at the given temperature */ virtual doublereal psatEst(doublereal TKelvin) const; - + public: //! Estimate for the molar volume of the liquid /*! * Note: this is only used as a starting guess for later routines that actually calculate an @@ -770,7 +770,7 @@ protected: */ virtual doublereal liquidVolEst(doublereal TKelvin, doublereal &pres) const; - protected: + public: //! Calculates the density given the temperature and the pressure and a guess at the density. /*! * Note, below T_c, this is a multivalued function. We do not cross the vapor dome in this. @@ -797,7 +797,7 @@ protected: */ virtual doublereal densityCalc(doublereal TKelvin, doublereal pressure, int phaseRequested, doublereal rhoguess); - + protected: //! Utility routine in the calculation of the saturation pressure /*! * Private routine diff --git a/Cantera/src/thermo/RedlichKwongMFTP.cpp b/Cantera/src/thermo/RedlichKwongMFTP.cpp index ec1627ba7..4b225585a 100644 --- a/Cantera/src/thermo/RedlichKwongMFTP.cpp +++ b/Cantera/src/thermo/RedlichKwongMFTP.cpp @@ -342,7 +342,7 @@ namespace Cantera { double pp = GasConstant * T/(molarV - m_b_current) - m_a_current/(sqrt(T) * molarV * (molarV + m_b_current)); - if (fabs(pp -m_Pcurrent) > 1.0E-5 * m_Pcurrent) { + if (fabs(pp -m_Pcurrent) > 1.0E-5 * fabs(m_Pcurrent)) { throw CanteraError(" RedlichKwongMFTP::pressure()", "setState broken down, maybe"); } #endif @@ -1306,7 +1306,10 @@ namespace Cantera { */ doublereal RedlichKwongMFTP::densityCalc(doublereal TKelvin, doublereal presPa, int phaseRequested, doublereal rhoguess) { - //setTemperature(TKelvin); + /* + * It's necessary to set the temperature so that m_a_current is set correctly. + */ + setTemperature(TKelvin); double tcrit = critTemperature(); doublereal mmw = meanMolecularWeight(); double densBase = 0.0; @@ -1331,7 +1334,7 @@ namespace Cantera { } } - + doublereal volguess = mmw / rhoguess; NSolns_ = NicholsSolve(TKelvin, presPa, m_a_current, m_b_current, Vroot_); diff --git a/Cantera/src/thermo/RedlichKwongMFTP.h b/Cantera/src/thermo/RedlichKwongMFTP.h index 8728fad52..979957d96 100644 --- a/Cantera/src/thermo/RedlichKwongMFTP.h +++ b/Cantera/src/thermo/RedlichKwongMFTP.h @@ -185,7 +185,7 @@ namespace Cantera { */ virtual doublereal isothermalCompressibility() const; - protected: + protected: /** * Calculate the density of the mixture using the partial * molar volumes and mole fractions as input @@ -211,6 +211,7 @@ namespace Cantera { */ virtual void calcDensity(); + protected: //! Set the temperature (K) /*! * Overwritten setTemperature(double) from State.h. This @@ -608,7 +609,7 @@ namespace Cantera { * @return Returns the change in enthalpy in units of J kmol-1. */ virtual doublereal hresid() const; - + public: //! Estimate for the molar volume of the liquid /*! * Note: this is only used as a starting guess for later routines that actually calculate an @@ -624,7 +625,7 @@ namespace Cantera { */ virtual doublereal liquidVolEst(doublereal TKelvin, doublereal &pres) const; - protected: + public: //! Calculates the density given the temperature and the pressure and a guess at the density. /*! * Note, below T_c, this is a multivalued function. We do not cross the vapor dome in this. From efd58ec5b79194ead4fd550e35a72feb05f42ab5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 15 Aug 2011 00:45:16 +0000 Subject: [PATCH 383/446] Tweaked the algorithm in several ways. The amount of unusual behavior should be reduced. --- Cantera/src/numerics/RootFind.cpp | 359 +++++++++++++++++++++++++++--- Cantera/src/numerics/RootFind.h | 88 ++++++-- 2 files changed, 390 insertions(+), 57 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index 97c42eff1..dce165cc8 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -139,11 +139,16 @@ namespace Cantera { RootFind::RootFind (ResidEval* resid) : m_residFunc(resid), m_funcTargetValue(0.0), - m_atol(1.0E-11), - m_rtol(1.0E-5), + m_atolf(1.0E-11), + m_atolx(1.0E-11), + m_rtolf(1.0E-5), + m_rtolx(1.0E-5), m_maxstep(1000), printLvl(0), DeltaXnorm_(0.01), + specifiedDeltaXnorm_(0), + DeltaXMax_(1.0E6), + specifiedDeltaXMax_(0), FuncIsGenerallyIncreasing_(false), FuncIsGenerallyDecreasing_(false), deltaXConverged_(0.0), @@ -153,11 +158,62 @@ namespace Cantera { fx_minTried_(0.0) { + } + //================================================================================================ + RootFind::RootFind(const RootFind &r) : + m_residFunc(r.m_residFunc), + m_funcTargetValue(0.0), + m_atolf(1.0E-11), + m_atolx(1.0E-11), + m_rtolf(1.0E-5), + m_rtolx(1.0E-5), + m_maxstep(1000), + printLvl(0), + DeltaXnorm_(0.01), + specifiedDeltaXnorm_(0), + DeltaXMax_(1.0E6), + specifiedDeltaXMax_(0), + FuncIsGenerallyIncreasing_(false), + FuncIsGenerallyDecreasing_(false), + deltaXConverged_(0.0), + x_maxTried_(-1.0E300), + fx_maxTried_(0.0), + x_minTried_(1.0E300), + fx_minTried_(0.0) + { + *this = r; } //================================================================================================ // Empty destructor RootFind::~RootFind() { } + //==================================================================================================================== + RootFind & RootFind::operator=(const RootFind &right) { + if (this == &right) { + return *this; + } + m_residFunc = right.m_residFunc; + m_funcTargetValue = right.m_funcTargetValue; + m_atolf = right.m_atolf; + m_atolx = right.m_atolx; + m_rtolf = right.m_rtolf; + m_rtolx = right.m_rtolx; + m_maxstep = right.m_maxstep; + printLvl = right.printLvl; + DeltaXnorm_ = right.DeltaXnorm_; + specifiedDeltaXnorm_ = right.specifiedDeltaXnorm_; + DeltaXMax_ = right.DeltaXMax_; + specifiedDeltaXMax_ = right.specifiedDeltaXMax_; + FuncIsGenerallyIncreasing_ = right.FuncIsGenerallyIncreasing_; + FuncIsGenerallyDecreasing_ = right.FuncIsGenerallyDecreasing_; + deltaXConverged_ = right.deltaXConverged_; + x_maxTried_ = right.x_maxTried_; + fx_maxTried_ = right.fx_maxTried_; + x_minTried_ = right.x_minTried_; + fx_minTried_ = right.fx_minTried_; + + return *this; + } //================================================================================================ // Calculate a deltaX from an input value of x /* @@ -192,11 +248,11 @@ namespace Cantera { //================================================================================================ // Calcuated a controlled, nonzero delta between two numbers /* - * The delta is designed to be greater than or equal to delXMeaningful(x) defined above + * The delta is designed to be greater than or equal to delXNonzero(x) defined above * with the same sign as the original delta. Therefore if you subtract it from either * of the two original numbers, you get a different number. * - * @param x2 first number + * @param x1 first number * @param x2 second number */ double RootFind::deltaXControlled(doublereal x2, doublereal x1) const { @@ -206,7 +262,7 @@ namespace Cantera { } doublereal deltaX = x2 - x1; doublereal x = fabs(x2) + fabs(x1); - doublereal deltaXm = delXMeaningful(x); + doublereal deltaXm = delXNonzero(x); if (fabs(deltaX) < deltaXm) { deltaX = sgnn * deltaXm; } @@ -267,17 +323,20 @@ namespace Cantera { doublereal deltaX1 = 0.0, deltaX2 = 0.0, deltaXnew = 0.0; int its = 0; int posStraddle = 0; - int retn = 0; + int retn = ROOTFIND_FAILEDCONVERGENCE; int foundPosF = 0; int foundNegF = 0; int foundStraddle = 0; doublereal xPosF = 0.0; + doublereal fPosF = 1.0E300; doublereal xNegF = 0.0; + doublereal fNegF = -1.0E300; doublereal fnorm; /* A valid norm for the making the function value dimensionless */ doublereal c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; doublereal CR0, CR1, CR2, CRnew, CRdenom; doublereal sgn; + callNum++; #ifdef DEBUG_MODE if (printLvl >= 3) { @@ -297,6 +356,37 @@ namespace Cantera { funcTargetValue = func(*xbest); return ROOTFIND_BADINPUT; } + + /* + * If the maximum step size has not been specified, set it here to 1/5 of the + * domain range of x. + */ + if (!specifiedDeltaXMax_) { + DeltaXMax_ = 0.2 *(xmax - xmin); + } + + if (!specifiedDeltaXnorm_) { + DeltaXnorm_ = 0.2 * DeltaXMax_; + } else { + if (DeltaXnorm_ > DeltaXMax_ ) { + if (specifiedDeltaXnorm_) { + DeltaXMax_ = DeltaXnorm_; + } else { + DeltaXnorm_ = 0.5 * DeltaXMax_; + } + } + } + + /* + * Calculate an initial value of deltaXConverged_ + */ + deltaXConverged_ = m_rtolx * (*xbest) + m_atolx; + if (DeltaXnorm_ < deltaXConverged_ ) { + writelogf("%s DeltaXnorm_, %g, is too small compared to tols, increasing to %g\n", + stre, DeltaXnorm_, deltaXConverged_); + DeltaXnorm_ = deltaXConverged_; + } + /* * Find the first function value f1 = func(x1), by using the value entered into xbest. * Process it @@ -323,20 +413,30 @@ namespace Cantera { } else if (f1 > 0.0) { foundPosF = 1; xPosF = x1; + fPosF = f1; } else { foundNegF = 1; xNegF = x1; + fNegF = x1; } + /* + * Now, this is actually a tricky part of the algorithm - Find the x value for + * the second point. It's tricky because we don't have a valid idea of the scale of x yet + * + */ if (x1 == 0.0) { - x2 = 0.00001 * (xmax - xmin); + x2 = x1 + 0.01 * DeltaXnorm_; } else { x2 = x1 * 1.0001; } if (x2 > xmax) { - x2 = x1 - (xmax - xmin) / 100.; + x2 = x1 - 0.01 * DeltaXnorm_; } + /* + * Find the second function value f2 = func(x2), Process it + */ deltaX2 = x2 - x1; f2 = func(x2); #ifdef DEBUG_MODE @@ -346,24 +446,30 @@ namespace Cantera { } #endif + /* + * Calculate the norm of the function, this is the nominal value of f. We try + * to reduce the nominal value of f by rtolf, this is the main convergence requirement. + */ if (m_funcTargetValue != 0.0) { - fnorm = 1.0E-6 + m_atol / m_rtol; + fnorm = m_atolf + fabs(m_funcTargetValue); } else { - fnorm = 0.5*(fabs(f1) + fabs(f2)) + fabs(m_funcTargetValue); + fnorm = 0.5*(fabs(f1) + fabs(f2)) + fabs(m_funcTargetValue) + m_atolf; } if (f2 == 0.0) { *xbest = x2; - return retn; + return ROOTFIND_SUCCESS; } else if (f2 > 0.0) { if (!foundPosF) { foundPosF = 1; xPosF = x2; + fPosF = x2; } } else { if (!foundNegF) { foundNegF = 1; xNegF = x2; + fNegF = f2; } } /* @@ -372,7 +478,7 @@ namespace Cantera { foundStraddle = foundPosF && foundNegF; if (foundStraddle) { if (xPosF > xNegF) posStraddle = 1; - else posStraddle = 0 ; + else posStraddle = 0; } bool doQuad = false; bool useNextStrat = false; @@ -419,12 +525,12 @@ namespace Cantera { * If the suggested step size is too big, throw out step */ if (!foundStraddle) { - if (fabs(xnew - x2) > 3.0 * DeltaXnorm_) { + if (fabs(xnew - x2) > DeltaXMax_) { useNextStrat = true; } if (fabs(deltaXnew) < fabs(deltaX2)) { - deltaXnew = DSIGN(deltaXnew) * 1.1 * fabs(deltaX2); - xnew = deltaXnew + x2; + deltaXnew = 1.2 * deltaXnew; + xnew = x2 + deltaXnew; } } if (useNextStrat) { @@ -482,8 +588,8 @@ namespace Cantera { c[3] = x0; c[4] = x1; c[5] = x2; c[6] = SQUARE(x0); c[7] = SQUARE(x1); c[8] = SQUARE(x2); f[0] = - f0; f[1] = - f1; f[2] = - f2; - retn = smlequ(c, 3, 3, f, 1); - if (retn == 1) goto QUAD_BAIL; + int rrr = smlequ(c, 3, 3, f, 1); + if (rrr == 1) goto QUAD_BAIL; root = f[1]* f[1] - 4.0 * f[0] * f[2]; if (root >= 0.0) { xn1 = (- f[1] + sqrt(root)) / (2.0 * f[2]); @@ -550,9 +656,15 @@ namespace Cantera { } else { /* * If we are venturing into new ground, only allow the step jump - * to increase by 50% at each interation + * to increase by 50% at each interation, unless the step jump is less than + * the user has said that it is ok to take */ doublereal xDelMax = 1.5 * fabs(x2 - x1); + if (specifiedDeltaXnorm_) { + if (0.5 * DeltaXnorm_ > xDelMax) { + xDelMax = 0.5 *DeltaXnorm_ ; + } + } if (fabs(xDelMax) < fabs(xnew - x2)) { xnew = x2 + DSIGN(xnew-x2) * xDelMax; #ifdef DEBUG_MODE @@ -616,7 +728,7 @@ namespace Cantera { if (fabs(deltaXnew) < 1.2 * delXMeaningful(xnew)) { if (!foundStraddle) { sgn = 1.0; - if (x2 < xnew) { + if (x2 > xnew) { sgn = -1.0; } deltaXnew = 1.2 * delXMeaningful(xnew) * sgn; @@ -629,12 +741,20 @@ namespace Cantera { */ if (xnew > xmax) { topBump++; - if (topBump < 5) { + if (topBump < 3) { xnew = x2 + (xmax - x2) / 2.0; } else { if (x2 == xmax || x1 == xmax) { // we are here when we are bumping against the top limit. // No further action is possible + if (xnew > xmax) { + slope = (f2 - f1) / delXtmp; + xnew = x2 - f2 / slope; + if (xnew > xmax) { + retn = ROOTFIND_SOLNHIGHERTHANXMAX; + *xbest = xnew; + } + } goto done; } else { xnew = xmax; @@ -648,12 +768,20 @@ namespace Cantera { } if (xnew < xmin) { bottomBump++; - if (bottomBump < 5) { + if (bottomBump < 3) { xnew = x2 + (x2 - xmin) / 2.0; } else { if (x2 == xmin || x1 == xmin) { // we are here when we are bumping against the bottom limit. // No further action is possible + if (xnew < xmin) { + slope = (f2 - f1) / delXtmp; + xmin = x2 - f2 / slope; + if (xnew < xmin) { + retn = ROOTFIND_SOLNLOWERTHANXMIN; + *xbest = xnew; + } + } goto done; } else { xnew = xmin; @@ -680,15 +808,27 @@ namespace Cantera { if (foundStraddle) { if (posStraddle) { if (fnew > 0.0) { - if (xnew < xPosF) xPosF = xnew; + if (xnew < xPosF) { + xPosF = xnew; + fPosF = fnew; + } } else { - if (xnew > xNegF) xNegF = xnew; + if (xnew > xNegF) { + xNegF = xnew; + fNegF = fnew; + } } } else { if (fnew > 0.0) { - if (xnew > xPosF) xPosF = xnew; + if (xnew > xPosF) { + xPosF = xnew; + fPosF = fnew; + } } else { - if (xnew < xNegF) xNegF = xnew; + if (xnew < xNegF) { + xNegF = xnew; + fNegF = fnew; + } } } } @@ -698,6 +838,7 @@ namespace Cantera { if (!foundPosF) { foundPosF = 1; xPosF = xnew; + fPosF = fnew; foundStraddle = 1; if (xPosF > xNegF) posStraddle = 1; else posStraddle = 0; @@ -706,6 +847,7 @@ namespace Cantera { if (!foundNegF) { foundNegF = 1; xNegF = xnew; + fNegF = fnew; foundStraddle = 1; if (xPosF > xNegF) posStraddle = 1; else posStraddle = 0; @@ -721,11 +863,105 @@ namespace Cantera { CR1 = CR2; x2 = xnew; f2 = fnew; + + /* + * As we go on to new data points, we make sure that + * we have the best straddle of the solution with the choice of F1 and F2 when + * we do have a straddle to work with. + */ + if (foundStraddle) { + bool foundBetterPos = false; + bool foundBetterNeg = false; + if (posStraddle) { + if (f2 > 0.0) { + if (xPosF < x2) { + foundBetterPos = false; + x2 = xPosF; + f2 = fPosF; + } + if (f1 > 0.0) { + if (foundBetterPos) { + x1 = xNegF; + f1 = fNegF; + } else { + if (x1 >= x2) { + x1 = xNegF; + f1 = fNegF; + } + } + } + } else { + if (xNegF > x2) { + foundBetterNeg = false; + x2 = xNegF; + f2 = fNegF; + } + if (f1 < 0.0) { + if (foundBetterNeg) { + x1 = xPosF; + f1 = fPosF; + } else { + if (x1 <= x2) { + x1 = xPosF; + f1 = fPosF; + } + } + } + } + } else { + if (f2 < 0.0) { + if (xNegF < x2) { + foundBetterNeg = false; + x2 = xNegF; + f2 = fNegF; + } + if (f1 < 0.0) { + if (foundBetterNeg) { + x1 = xPosF; + f1 = fPosF; + } else { + if (x1 >= x2) { + x1 = xPosF; + f1 = fPosF; + } + } + } + } else { + if (xPosF > x2) { + foundBetterPos = true; + x2 = xPosF; + f2 = fPosF; + } + if (f1 > 0.0) { + if (foundBetterNeg) { + x1 = xNegF; + f1 = fNegF; + } else { + if (x1 <= x2) { + x1 = xNegF; + f1 = fNegF; + } + } + } + } + } + } + deltaX1 = deltaX2; deltaX2 = deltaXnew; CR2 = CRnew; - if (fabs(fnew / fnorm) < m_rtol) { - converged = 1; + deltaXConverged_ = 0.5 * deltaXConverged_ + 0.5 * (m_rtolx * 0.5 * (fabs(x2) + fabs(x1)) + m_atolx); + if (fabs(fnew / fnorm) < m_rtolf) { + if (deltaX2 < deltaXConverged_ && deltaXnew < deltaXConverged_) { + converged = 1; + } + if (fabs(slope) > 1.0E-100) { + double xdels = fabs(fnew / slope); + if (xdels < deltaXConverged_ * 0.5) { + converged = 1; + } + } + } /* * Check for excess convergence in the x coordinate @@ -745,6 +981,28 @@ namespace Cantera { done: if (converged) { + retn = ROOTFIND_SUCCESS; + if (fabs(f1) < 2.0 * fabs(f2)) { + slope = (f2 - f1) / (x2 - x1); + xnew = x2 - f2 / slope; + + fnew = func(xnew); + if (fabs(fnew) < fabs(f2)) { + x2 = xnew; + f2 = fnew; + *xbest = x2; + } + if (fabs(f1) < fabs(f2)) { + x2 = x1; + f2 = f1; + *xbest = x1; + fnew = func(x2); + } + } + + + + if (printLvl >= 1) { writelogf("RootFind success: convergence achieved\n"); } @@ -754,9 +1012,19 @@ namespace Cantera { } #endif } else { - retn = ROOTFIND_FAILEDCONVERGENCE; - if (printLvl >= 1) { - writelogf("RootFind ERROR: maximum iterations exceeded without convergence\n"); + if (retn == ROOTFIND_SOLNHIGHERTHANXMAX) { + if (printLvl >= 1) { + writelogf("RootFind ERROR: Soln probably lies higher than xmax, %g: best guess = %g\n", xmax, *xbest); + } + } else if (retn == ROOTFIND_SOLNLOWERTHANXMIN) { + if (printLvl >= 1) { + writelogf("RootFind ERROR: Soln probably lies lower than xmin, %g: best guess = %g\n", xmin, *xbest); + } + } else { + retn = ROOTFIND_FAILEDCONVERGENCE; + if (printLvl >= 1) { + writelogf("RootFind ERROR: maximum iterations exceeded without convergence, cause unknown\n"); + } } #ifdef DEBUG_MODE if (printLvl >= 3) { @@ -804,10 +1072,20 @@ namespace Cantera { * @param rtol Relative tolerance. The default is 10^-5 * @param atol absolute tolerance. The default is 10^-11 */ - void RootFind::setTol(doublereal rtol, doublereal atol) + void RootFind::setTol(doublereal rtolf, doublereal atolf, doublereal rtolx, doublereal atolx) { - m_atol = atol; - m_rtol = rtol; + m_atolf = atolf; + m_rtolf = rtolf; + if (rtolx <= 0.0) { + m_rtolx = atolf; + } else { + m_rtolx = rtolx; + } + if (atolx <= 0.0) { + m_atolx = atolf; + } else { + m_atolx = atolx; + } } //==================================================================================================================== // Set the print level from the rootfinder @@ -868,7 +1146,7 @@ namespace Cantera { FuncIsGenerallyDecreasing_ = value; } //==================================================================================================================== - // Set the minimum value of deltaX + // Set the nominal value of deltaX /* * This sets the value of deltaXNorm_ * @@ -877,6 +1155,19 @@ namespace Cantera { void RootFind::setDeltaX(doublereal deltaXNorm) { DeltaXnorm_ = deltaXNorm; + specifiedDeltaXnorm_ = 1; + } + //==================================================================================================================== + // Set the maximum value of deltaX + /* + * This sets the value of deltaXMax_ + * + * @param deltaX + */ + void RootFind::setDeltaXMax(doublereal deltaX) + { + DeltaXMax_ = deltaX; + specifiedDeltaXMax_ = 1; } //==================================================================================================================== } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 0392a8799..9f43027ec 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -33,6 +33,13 @@ namespace Cantera { #define ROOTFIND_FAILEDCONVERGENCE -1 //! This means that the input to the root solver was defective #define ROOTFIND_BADINPUT -2 + //! This means that the rootfinder believes the solution is lower than xmin +#define ROOTFIND_SOLNLOWERTHANXMIN -3 + //! This means that the rootfinder believes the solution is higher than xmax + /*! + * + */ +#define ROOTFIND_SOLNHIGHERTHANXMAX -4 //@{ //! Root finder for 1D problems @@ -51,24 +58,26 @@ namespace Cantera { * @param resid Pointer to the residual function to be used to calculate f(x) */ RootFind(ResidEval* resid); + + //! Copy constructor + /*! + * @param r object to be copied + */ + RootFind(const RootFind &r); //! Destructor. Deletes the integrator. ~RootFind(); + //! Assignment operator + /*! + * @param right object to be copied + * + * @return returns a reference to the current object + */ + RootFind & operator=(const RootFind &right); + + private: - - //! Unimplemented private copy constructor - /*! - * @param right object to be copied - */ - RootFind(const RootFind &right); - - //! Unimplemented private assignment operator - /*! - * @param right object to be copied - */ - RootFind& operator=(const RootFind &right); - //! Calculate a deltaX from an input value of x /*! * This routine ensure that the deltaX will be greater or equal to DeltaXNorm_ @@ -153,13 +162,17 @@ namespace Cantera { //! Set the tolerance parameters for the rootfinder /*! - * These tolerance parameters are used on the function value to determine convergence + * These tolerance parameters are used on the function value and the independent value + * to determine convergence * - * - * @param rtol Relative tolerance. The default is 10^-5 - * @param atol absolute tolerance. The default is 10^-11 + * @param rtolf Relative tolerance. The default is 10^-5 + * @param atolf absolute tolerance. The default is 10^-11 + * @param rtolx Relative tolerance. The default is 10^-5 + * Default parameter is 0.0, in which case rtolx is set equal to rtolf + * @param atolx absolute tolerance. The default is 10^-11 + * Default parameter is 0.0, in which case atolx is set equal to atolf */ - void setTol(doublereal rtol, doublereal atol); + void setTol(doublereal rtolf, doublereal atolf, doublereal rtolx = 0.0, doublereal atolx = 0.0); //! Set the print level from the rootfinder /*! @@ -212,6 +225,14 @@ namespace Cantera { */ void setDeltaX(doublereal deltaXNorm); + //! Set the maximum value of deltaX + /*! + * This sets the value of deltaXMax_ + * + * @param deltaX + */ + void setDeltaXMax(doublereal deltaX); + public: //! Pointer to the residual function evaluator @@ -221,21 +242,36 @@ namespace Cantera { doublereal m_funcTargetValue; //! Absolute tolerance for the value of f - doublereal m_atol; + doublereal m_atolf; - //! Relative tolerance for the value of f - doublereal m_rtol; + //! Absolute tolerance for the value of x + doublereal m_atolx; + + //! Relative tolerance for the value of f and x + doublereal m_rtolf; + //! Relative tolerance for the value of x + doublereal m_rtolx; //! Maximum number of step sizes doublereal m_maxstep; protected: //! Print level - int printLvl; + int printLvl; - //! Delta X norm. This is the minimum value of deltaX that will be used by the program + //! Delta X norm. This is the nominal value of deltaX that will be used by the program doublereal DeltaXnorm_; + int specifiedDeltaXnorm_; + + //! Delta X Max. This is the maximum value of deltaX that will be used by the program + /*! + * Sometimes a large change in x causes problems. + */ + doublereal DeltaXMax_; + + int specifiedDeltaXMax_; + //! Boolean indicating whether the function is an increasing with x bool FuncIsGenerallyIncreasing_; @@ -249,10 +285,16 @@ namespace Cantera { */ doublereal deltaXConverged_; + //! Internal variable tracking largest x tried. doublereal x_maxTried_; + + //! Internal variable tracking f(x) of largest x tried. doublereal fx_maxTried_; + //! Internal variable tracking smallest x tried. doublereal x_minTried_; + + //! Internal variable tracking f(x) of smallest x tried. doublereal fx_minTried_; }; From d617f4301347f63266054a98ddeb4a75bc96701f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 15 Aug 2011 00:54:18 +0000 Subject: [PATCH 384/446] Added a capability to turn off writing separate log files --- Cantera/src/numerics/RootFind.cpp | 35 +++++++++++++++++-------------- Cantera/src/numerics/RootFind.h | 7 ++++++- 2 files changed, 25 insertions(+), 17 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index dce165cc8..622a158cf 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -145,6 +145,7 @@ namespace Cantera { m_rtolx(1.0E-5), m_maxstep(1000), printLvl(0), + writeLogAllowed_(false), DeltaXnorm_(0.01), specifiedDeltaXnorm_(0), DeltaXMax_(1.0E6), @@ -169,6 +170,7 @@ namespace Cantera { m_rtolx(1.0E-5), m_maxstep(1000), printLvl(0), + writeLogAllowed_(false), DeltaXnorm_(0.01), specifiedDeltaXnorm_(0), DeltaXMax_(1.0E6), @@ -200,6 +202,7 @@ namespace Cantera { m_rtolx = right.m_rtolx; m_maxstep = right.m_maxstep; printLvl = right.printLvl; + writeLogAllowed_ = right.writeLogAllowed_; DeltaXnorm_ = right.DeltaXnorm_; specifiedDeltaXnorm_ = right.specifiedDeltaXnorm_; DeltaXMax_ = right.DeltaXMax_; @@ -339,7 +342,7 @@ namespace Cantera { callNum++; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { sprintf(fileName, "RootFind_%d.log", callNum); fp = fopen(fileName, "w"); fprintf(fp, " Iter TP_its xval Func_val | Reasoning\n"); @@ -401,7 +404,7 @@ namespace Cantera { f1 = func(x1); #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { print_funcEval(fp, x1, f1, its); fprintf(fp, "%-5d %-5d %-15.5E %-15.5E\n", -2, 0, x1, f1); } @@ -440,7 +443,7 @@ namespace Cantera { deltaX2 = x2 - x1; f2 = func(x2); #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { print_funcEval(fp, x2, f2, its); fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", -1, 0, x2, f2); } @@ -516,7 +519,7 @@ namespace Cantera { } } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xlin = %-11.5E", xnew); } #endif @@ -600,7 +603,7 @@ namespace Cantera { theta = MIN(1.0, theta); xnew = theta * xnew + (1.0 - theta) * xquad; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { if (theta != 1.0) { fprintf(fp, " | xquad = %-11.5E", xnew); } @@ -615,7 +618,7 @@ namespace Cantera { (DSIGN(x2 - x1) == DSIGN(x1 - x0)) ) { xnew += xnew - x2; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xquada = %-11.5E", xnew); } #endif @@ -640,7 +643,7 @@ namespace Cantera { if (fabs(xnew - x1) < xDelMin) { xnew = x1 + DSIGN(xnew-x1) * xDelMin; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | x10%% = %-11.5E", xnew); } #endif @@ -648,7 +651,7 @@ namespace Cantera { if (fabs(xnew - x2) < 0.1 * xDelMin) { xnew = x2 + DSIGN(xnew-x2) * 0.1 * xDelMin; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | x10%% = %-11.5E", xnew); } #endif @@ -668,7 +671,7 @@ namespace Cantera { if (fabs(xDelMax) < fabs(xnew - x2)) { xnew = x2 + DSIGN(xnew-x2) * xDelMax; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xlimitsize = %-11.5E", xnew); } #endif @@ -713,7 +716,7 @@ namespace Cantera { } } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { if (slope != xnew) { fprintf(fp, " | xstraddle = %-11.5E", xnew); } @@ -761,7 +764,7 @@ namespace Cantera { } } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xlimitmax = %-11.5E", xnew); } #endif @@ -788,7 +791,7 @@ namespace Cantera { } } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xlimitmin = %-11.5E", xnew); } #endif @@ -798,7 +801,7 @@ namespace Cantera { CRdenom = MAX(fabs(fnew), MAX(fabs(f2), MAX(fabs(f1), fnorm))); CRnew = sqrt(fabs(fnew) / CRdenom); #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp,"\n"); print_funcEval(fp, xnew, fnew, its); fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", its, 0, xnew, fnew); @@ -1007,7 +1010,7 @@ namespace Cantera { writelogf("RootFind success: convergence achieved\n"); } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | RootFind success in %d its, fnorm = %g\n", its, fnorm); } #endif @@ -1027,7 +1030,7 @@ namespace Cantera { } } #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, "\nRootFind failure in %d its\n", its); } #endif @@ -1035,7 +1038,7 @@ namespace Cantera { *xbest = x2; funcTargetValue = f2 + m_funcTargetValue; #ifdef DEBUG_MODE - if (printLvl >= 3) { + if (printLvl >= 3 && writeLogAllowed_) { fclose(fp); } #endif diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 9f43027ec..17b2eff9a 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -254,11 +254,16 @@ namespace Cantera { //! Maximum number of step sizes doublereal m_maxstep; - protected: + protected: //! Print level int printLvl; + public: + //! Boolean to turn on the possibility of writing a log file. + bool writeLogAllowed_; + + protected: //! Delta X norm. This is the nominal value of deltaX that will be used by the program doublereal DeltaXnorm_; From 36a56093d13bd039767db1a628986815253400ac Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 15 Aug 2011 03:57:40 +0000 Subject: [PATCH 385/446] Buf fixes for handling boundaries. --- Cantera/src/numerics/RootFind.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index 622a158cf..1b61f1779 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -772,14 +772,14 @@ namespace Cantera { if (xnew < xmin) { bottomBump++; if (bottomBump < 3) { - xnew = x2 + (x2 - xmin) / 2.0; + xnew = x2 - (x2 - xmin) / 2.0; } else { if (x2 == xmin || x1 == xmin) { // we are here when we are bumping against the bottom limit. // No further action is possible if (xnew < xmin) { slope = (f2 - f1) / delXtmp; - xmin = x2 - f2 / slope; + xnew = x2 - f2 / slope; if (xnew < xmin) { retn = ROOTFIND_SOLNLOWERTHANXMIN; *xbest = xnew; From 58a0f42ef0cc62dffa2261c5b3e7af4a5f352561 Mon Sep 17 00:00:00 2001 From: John Hewson Date: Wed, 24 Aug 2011 18:50:45 +0000 Subject: [PATCH 386/446] Added "export WITH_REAL_GASSES" and set default to 'y' --- preconfig | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/preconfig b/preconfig index ebe22275d..5dbdadd95 100755 --- a/preconfig +++ b/preconfig @@ -230,7 +230,7 @@ WITH_ELECTROLYTES=${WITH_ELECTROLYTES:="y"} # Enable Real Gas Equations of State # This supports the multicomponent Redlich-Kwong equation of state. -WITH_REAL_GASSES=${WITH_REAL_GASSES:="n"} +WITH_REAL_GASSES=${WITH_REAL_GASSES:="y"} # Enable generating phase models from PrIMe models. For more # information about PrIME, see http://www.primekinetics.org @@ -592,7 +592,8 @@ export WITH_ADSORBATE export WITH_SPECTRA export WITH_STOICH_SUBSTANCE export WITH_PURE_FLUIDS -export WITH_IDEAL_SOLUTIONS +export WITH_IDEAL_SOLUTION +export WITH_REAL_GASSES export WITH_ELECTROLYTES export WITH_PRIME export WITH_H298MODIFY_CAPABILITY From 6fca9189dad380987cee77beda48ff6577dfaa33 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 30 Aug 2011 15:56:00 +0000 Subject: [PATCH 387/446] Added back conditional printing --- Cantera/src/numerics/NonlinearSolver.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 89a2904a0..375a4343f 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -2150,9 +2150,9 @@ namespace Cantera { return 0; } } - //if (loglevel >= 4 ) { + if (loglevel >= 4 ) { printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", -2, m+1, ff); - //} + } return -2; } From 8de54e200d0b543fafc48b4a6a27073a17b7a31b Mon Sep 17 00:00:00 2001 From: John Hewson Date: Sat, 3 Sep 2011 01:00:25 +0000 Subject: [PATCH 388/446] There was a disagreement between the name of getElectricConduct between the base and LiquidTransport class. Since the LiquidTransport class uses it, the base is now compatible with it. --- Cantera/src/transport/TransportBase.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index d9f3d10d6..1e1d07e55 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -484,9 +484,9 @@ namespace Cantera { * * The units are Siemens m-1, where 1 S = 1 A / volt = 1 s^3 A^2 /kg /m^2 */ - virtual doublereal getElectricConductivity() + virtual doublereal getElectricConduct() { - err("getElectricConductivity"); return 0.0; + err("getElectricConduct"); return 0.0; } //! Compute the electric current density in A/m^2 From 2703130a7add528d2a376004c6aed58520154f1e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 8 Sep 2011 02:07:02 +0000 Subject: [PATCH 389/446] Started working on the documentation and cleanup of the dogleg method. Now possible to run the algorithm without the DEBUG_DOGLEG block on. --- Cantera/src/numerics/NonlinearSolver.cpp | 149 ++++++++++++++--------- Cantera/src/numerics/NonlinearSolver.h | 21 +++- 2 files changed, 110 insertions(+), 60 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 375a4343f..d3f8a8ebe 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -142,7 +142,7 @@ namespace Cantera { deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), - lambda_(0.0), + lambdaStar_(0.0), Jd_(0), deltaX_trust_(0), trustDelta_(1.0), @@ -242,7 +242,7 @@ namespace Cantera { deltaX_Newton_(0), residNorm2Cauchy_(0.0), RJd_norm_(0.0), - lambda_(0.0), + lambdaStar_(0.0), Jd_(0), deltaX_trust_(0), trustDelta_(1.0), @@ -320,7 +320,7 @@ namespace Cantera { deltaX_CP_ = right.deltaX_CP_; deltaX_Newton_ = right.deltaX_Newton_; RJd_norm_ = right.RJd_norm_; - lambda_ = right.lambda_; + lambdaStar_ = right.lambdaStar_; Jd_ = right.Jd_; deltaX_trust_ = right.deltaX_trust_; trustDelta_ = right.trustDelta_; @@ -376,10 +376,10 @@ namespace Cantera { #ifdef DEBUG_DOGLEG #else - if (doDogLeg_) { - throw CanteraError("NonlinearSolver::setSolverScheme", - "ifdef block not on"); - } + // if (doDogLeg_) { + //throw CanteraError("NonlinearSolver::setSolverScheme", + // "ifdef block not on"); + //} #endif } //==================================================================================================================== @@ -706,10 +706,21 @@ namespace Cantera { void NonlinearSolver::calcSolnToResNormVector() { if (! jacCopy_.m_factored) { - m_ScaleSolnNormToResNorm = 1.0; - computeResidWts(); - for (int n = 0; n < neq_; n++) { - m_wksp[n] = 0.0; + + + double sum = 0.0; + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = m_rowWtScales[irow] / neq_; + sum += m_residWts[irow]; + } + sum /= neq_; + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = (m_residWts[irow] + atolBase_ * atolBase_ * sum); + } + + + for (int irow = 0; irow < neq_; irow++) { + m_wksp[irow] = 0.0; } doublereal *jptr = &(*(jacCopy_.begin())); for (int jcol = 0; jcol < neq_; jcol++) { @@ -718,9 +729,17 @@ namespace Cantera { jptr++; } } - double resNormOld = residErrorNorm(DATA_PTR(m_wksp)); + double resNormOld = 0.0; + double error; + + for (int irow = 0; irow < neq_; irow++) { + error = m_wksp[irow] / m_residWts[irow]; + resNormOld += error * error; + } + resNormOld = sqrt(resNormOld / neq_); + if (resNormOld > 0.0) { - m_ScaleSolnNormToResNorm = m_ScaleSolnNormToResNorm * resNormOld; + m_ScaleSolnNormToResNorm = resNormOld; } if (m_ScaleSolnNormToResNorm < 1.0E-8) { m_ScaleSolnNormToResNorm = 1.0E-8; @@ -1135,14 +1154,14 @@ namespace Cantera { { double rowFac = 1.0; double normSoln; - // Calculate desDir = -0.5 * R dot J + // Calculate the descent direction /* * For confirmation of the scaling factors, see Dennis and Schnabel p, 152, p, 156 and my notes * * The colFac and rowFac values are used to eliminate the scaling of the matrix from the * actual equation * - * Here we calculate the steepest direction. this is equation (10) in the notes. It is + * Here we calculate the steepest descent direction. This is equation (11) in the notes. It is * storred in deltaX_CP_[].The value corresponds to d_descent[]. */ for (int j = 0; j < neq_; j++) { @@ -1164,7 +1183,7 @@ namespace Cantera { } /* - * Calculate J_hat d_y_descent. This is formula 17 in the notes. + * Calculate J_hat d_y_descent. This is formula 18 in the notes. */ for (int i = 0; i < neq_; i++) { Jd_[i] = 0.0; @@ -1180,7 +1199,7 @@ namespace Cantera { /* * Calculate the distance along the steepest descent until the Cauchy point - * This is Eqn. 16 in the notes. + * This is Eqn. 17 in the notes. */ RJd_norm_ = 0.0; JdJd_norm_ = 0.0; @@ -1193,21 +1212,21 @@ namespace Cantera { //} if (fabs(JdJd_norm_) < 1.0E-290) { if (fabs(RJd_norm_) < 1.0E-300) { - lambda_ = 0.0; + lambdaStar_ = 0.0; } else { throw CanteraError("NonlinearSolver::doCauchyPointSolve()", "Unexpected condition: norms are zero"); } } else { - lambda_ = - RJd_norm_ / (JdJd_norm_); + lambdaStar_ = - RJd_norm_ / (JdJd_norm_); } /* * Now we modify the steepest descent vector such that its length is equal to the * Cauchy distance. From now on, if we want to recreate the descent vector, we have - * to unnormalize it by dividing by lambda_. + * to unnormalize it by dividing by lambdaStar_. */ for (int i = 0; i < neq_; i++) { - deltaX_CP_[i] *= lambda_; + deltaX_CP_[i] *= lambdaStar_; } double normResid02 = m_normResid0 * m_normResid0 * neq_; @@ -1243,7 +1262,7 @@ namespace Cantera { printf("\t\t\t Rjd = %g\n", RJd_norm_); printf("\t\t\t JdJd = %g\n", JdJd_norm_); printf("\t\t\t deltaX = %g\n", normSoln); - printf("\t\t\t lambda = %g\n", lambda_); + printf("\t\t\t lambda = %g\n", lambdaStar_); } } return normSoln; @@ -1294,7 +1313,7 @@ namespace Cantera { // This is the expected inital rate of decrease in the cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || - double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; + double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; double funcDecreaseNewtExp2 = - normResid02 / sNewt; @@ -1311,11 +1330,12 @@ namespace Cantera { } //==================================================================================================================== - // Setup the line search along the double dog leg + // Setup the parameters for the double dog leg /* - * the calls the doCauchySolve() and doNewtonSolve() are done at the main level + * The calls to the doCauchySolve() and doNewtonSolve() routines are done at the main level. This routine comes + * after those calls. */ - void NonlinearSolver::setupDoubleDogleg(double * newtDir) + void NonlinearSolver::setupDoubleDogleg() { /* * Gamma = ||grad f ||**4 @@ -1328,8 +1348,8 @@ namespace Cantera { // sumG = deltax_cp_[i] * deltax_cp_[i]; // sumH = deltax_cp_[i] * newtDir[i]; // } - // double fac1 = sumG / lambda_; - // double fac2 = sumH / lambda_; + // double fac1 = sumG / lambdaStar_; + // double fac2 = sumH / lambdaStar_; // double gamma = fac1 / fac2; // double gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; /* @@ -1400,7 +1420,7 @@ namespace Cantera { */ double tmp = - 2.0 * alpha + alpha * alpha; - double tmp2 = - RJd_norm_ * lambda_; + double tmp2 = - RJd_norm_ * lambdaStar_; resD2 = tmp2 * tmp; } else if (leg == 1) { @@ -1408,7 +1428,7 @@ namespace Cantera { /* * Same formula as above for lambda=1. */ - double tmp2 = - RJd_norm_ * lambda_; + double tmp2 = - RJd_norm_ * lambdaStar_; double RdotJS = - tmp2; double JsJs = tmp2; @@ -1628,7 +1648,7 @@ namespace Cantera { } else { /* * This handles the case where the value crosses the origin. - * - First we don't let it cross the origin until its shrunk to the size of m_deltaBoundsMagnitudes[i] + * - First we don't let it cross the origin until its shrunk to the size of m_deltaStepMinimum[i] */ if (fabs(y[i]) > m_deltaStepMinimum[i]) { ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; @@ -1688,7 +1708,7 @@ namespace Cantera { * We periodically recalculate the trustVector_ values so that they renormalize to the * correct length. */ - void NonlinearSolver::calcTrustVector() + void NonlinearSolver::calcTrustVector() { double wtSum = 0.0; for (int i = 0; i < neq_; i++) { @@ -1708,14 +1728,14 @@ namespace Cantera { fabsy = fabs(m_y_n[i]); // First off make sure that each trust region vector is 1/2 the size of each variable or smaller // unless overridden by the deltaStepMininum value. - if (oldVal > 0.5 * fabsy) { - if (fabsy > m_deltaStepMinimum[i]) { + double newValue = trustDeltaEach * m_ewt[i] / wtSum; + if (newValue > 0.5 * fabsy) { + if (fabsy * 0.5 > m_deltaStepMinimum[i]) { deltaX_trust_[i] = 0.5 * fabsy; } else { deltaX_trust_[i] = m_deltaStepMinimum[i]; } } else { - double newValue = trustDeltaEach * m_ewt[i] / wtSum; if (newValue > 4.0 * oldVal) { newValue = 4.0 * oldVal; } else if (newValue < 0.25 * oldVal) { @@ -1739,6 +1759,7 @@ namespace Cantera { deltaX_trust_[i] = deltaX_trust_[i] * sum; } trustDelta_ = 1.0; + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { printf("calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", trustNorm, trustNormGoal); @@ -1965,17 +1986,13 @@ namespace Cantera { // Compute the weighted norm of the undamped step size step0 doublereal s0 = solnErrorNorm(step0); - // Compute the multiplier to keep all components in bounds - // A value of one indicates that there is no limitation - // on the current step size in the nonlinear method due to - // bounds constraints (either negative values of delta + // Compute the multiplier to keep all components in bounds.A value of one indicates that there is no limitation + // on the current step size in the nonlinear method due to bounds constraints (either negative values of delta // bounds constraints. m_dampBound = boundStep(y0, step0, loglevel); - // if fbound is very small, then y0 is already close to the - // boundary and step0 points out of the allowed domain. In - // this case, the Newton algorithm fails, so return an error - // condition. + // If fbound is very small, then y0 is already close to the boundary and step0 points out of the allowed domain. In + // this case, the Newton algorithm fails, so return an error condition. if (m_dampBound < 1.e-30) { if (loglevel > 1) printf("\t\t\tdampStep: At limits.\n"); return -3; @@ -2158,6 +2175,14 @@ namespace Cantera { //==================================================================================================================== + + // Using Damping along a dog leg to calculate the next step + /*! + * + * + * @param step0 (output) On return this contains the suggested step vector for the current iteration + * + */ int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y0, const doublereal *ydot0, std::vector & step0, double* const y_new, double* const ydot_new, double* step1, @@ -2181,7 +2206,7 @@ namespace Cantera { int j, m; num_backtracks = 0; //double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); - //double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambda_; + //double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambdaStar_; double tlen; @@ -2197,7 +2222,8 @@ namespace Cantera { tlen, leg, alpha); } /* - * Figure out the new step vector, step0, based on (leg, alpha) + * Figure out the new step vector, step0, based on (leg, alpha). Here we are using the + * inter */ fillDogLegStep(leg, alpha, step0); @@ -2210,20 +2236,21 @@ namespace Cantera { */ if (m_dampBound < 1.0) { for (j = 0; j < neq_; j++) { - step0[j] = step0[j] * m_dampBound; + step0[j] = step0[j] * m_dampBound; } } /* * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria - * as a good step. Also, make sure that it stays within bounds. + * as a good step. */ - info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, loglevel, trustDeltaOld); + info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, loglevel, trustDeltaOld); /* * The algorithm failed to find a solution vector sufficiently different than the current point */ if (info == -1) { + num_backtracks++; if (loglevel >= 1) { double stepNorm = solnErrorNorm(DATA_PTR(step0)); printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); @@ -2233,6 +2260,7 @@ namespace Cantera { } } if (info == -2) { + num_backtracks++; if (loglevel >= 1) { printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); success = false; @@ -2248,9 +2276,15 @@ namespace Cantera { haveASuccess = true; // Store the good results in step1 mdp::mdp_copy_dbl_1(DATA_PTR(step1), CONSTD_DATA_PTR(step0), neq_); - + // Within the program decideStep(), we have already increased the value of trustDelta_. We store the + // value of step0 in step1, recalculate a larger step0 in the next fillDogLegStep(), + // and then attempt to see if the larger step works in the next iteration } if (info == 2) { + // Step was a failure. If we had a previous success with a smaller stepsize, haveASuccess is true + // and we execute the next block and break. If we didn't have a previous success, trustDelta_ has + // already been decreased in the decideStep() routine. We go back and try another iteration with + // a smaller trust region. if (haveASuccess) { mdp::mdp_copy_dbl_1(DATA_PTR(step0), CONSTD_DATA_PTR(step1), neq_); for (j = 0; j < neq_; j++) { @@ -2261,6 +2295,8 @@ namespace Cantera { } success = true; break; + } else { + num_backtracks++; } } @@ -2335,7 +2371,7 @@ namespace Cantera { // This is the expected inital rate of decrease in the cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || - double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambda_; + double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; if (funcDecreaseSDExp > 0.0) { if (loglevel > 0) { printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); @@ -2594,7 +2630,9 @@ namespace Cantera { setColumnScales(); - + /* + * Calculate the base residual + */ info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); if (info != 1) { if (m_print_flag > 0) { @@ -2684,13 +2722,13 @@ namespace Cantera { if (doDogLeg_) { - setupDoubleDogleg(DATA_PTR(stp)); + setupDoubleDogleg(); #ifdef DEBUG_DOGLEG residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); #endif - m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), - stp, DATA_PTR(y_new), DATA_PTR(ydot_new), - DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); + m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), + stp, DATA_PTR(y_new), DATA_PTR(ydot_new), + DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); } #ifdef DEBUG_DOGLEG else { @@ -3302,7 +3340,6 @@ namespace Cantera { atolk_[i]= atol[i]; } } - //===================================================================================================================== // Set the relative tolerances for the solution variables /* diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 454286edf..8dc6ad562 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -616,7 +616,12 @@ namespace Cantera { */ void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); - void setupDoubleDogleg(double *newtDir); + //! Setup the parameters for the double dog leg + /*! + * The calls to the doCauchySolve() and doNewtonSolve() routines are done at the main level. This routine comes + * after those calls. + */ + void setupDoubleDogleg(); //! Change the global lambda coordinate into the (leg,alpha) coordinate for the double dogleg /*! @@ -935,12 +940,18 @@ namespace Cantera { doublereal residNorm2Cauchy_; //! Residual dot Jd norm + /*! + * This is equal to R_hat dot J_hat d_y_descent + */ doublereal RJd_norm_; - //! Value of lambda_ which is used to calculate the Cauchy point - doublereal lambda_; + //! Value of lambdaStar_ which is used to calculate the Cauchy point + doublereal lambdaStar_; - //! Jacobian times the Steepest descent direction. + //! Jacobian times the steepest descent direction in the normalized coordinates. + /*! + * This is equal to [ Jhat d^y_{descent} ] in the notes, Eqn. 18. + */ std::vector Jd_; //! Vector of trust region values. @@ -957,6 +968,8 @@ namespace Cantera { doublereal dist_R1_; doublereal dist_R2_; doublereal dist_Total_; + + //! Dot product of the Jd_ variable defined above with itself. doublereal JdJd_norm_; //! Norm of the Newton Step wrt trust region From 4d2e6b65bbc9921410586f619dbf2fda8f063ed1 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 9 Sep 2011 19:16:36 +0000 Subject: [PATCH 390/446] Updates to the internals, trying to simplify --- Cantera/src/numerics/NonlinearSolver.cpp | 175 ++++++++++++++--------- Cantera/src/numerics/NonlinearSolver.h | 24 ++-- 2 files changed, 120 insertions(+), 79 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index d3f8a8ebe..70f44cf7d 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -766,7 +766,7 @@ namespace Cantera { */ int NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, - SquareMatrix& jac, int loglevel) + SquareMatrix& jac) { int irow; @@ -1333,7 +1333,8 @@ namespace Cantera { // Setup the parameters for the double dog leg /* * The calls to the doCauchySolve() and doNewtonSolve() routines are done at the main level. This routine comes - * after those calls. + * after those calls. We calculate the point Nuu_ here, the distances of the dog-legs, + * and the norms of the CP and Newton points in terms of the trust vectors. */ void NonlinearSolver::setupDoubleDogleg() { @@ -1376,11 +1377,11 @@ namespace Cantera { Nuu_ = beta; - // put in a loop here to test derivative. - - dist_R0_ = m_normDeltaSoln_CP; - dist_R1_ = solnErrorNorm( DATA_PTR(m_wksp)); + for (int i = 0; i < neq_; i++) { + m_wksp[i] = Nuu_ * deltaX_Newton_[i] - deltaX_CP_[i]; + } + dist_R1_ = solnErrorNorm(DATA_PTR(m_wksp)); dist_R2_ = (1.0 - Nuu_) * m_normDeltaSoln_Newton; dist_Total_ = dist_R0_ + dist_R1_ + dist_R2_; @@ -1388,11 +1389,17 @@ namespace Cantera { * Calculate the trust distances */ normTrust_Newton_ = calcTrustDistance(deltaX_Newton_); - normTrust_CP_ = calcTrustDistance(deltaX_CP_); } //==================================================================================================================== + // Change the global lambda coordinate into the (leg,alpha) coordinate for the double dogleg + /* + * @param lambda Global value of the distance along the double dogleg + * @param alpha relative value along the particular leg + * + * @return Returns the leg number ( 0, 1, or 2). + */ int NonlinearSolver::lambdaToLeg(const double lambda, double &alpha) const { if (lambda < dist_R0_ / dist_Total_) { @@ -1406,7 +1413,14 @@ namespace Cantera { return 2; } //==================================================================================================================== - + // Calculated the expected residual along the double dogleg curve. + /* + * @param leg 0, 1, or 2 representing the curves of the dogleg + * @param alpha Relative distance along the particular curve. + * + * @return Returns the expected value of the residual at that point according to the quadratic model. + * The residual at the newton point will always be zero. + */ double NonlinearSolver::expectedResidLeg(int leg, double alpha) const { double resD2, res2, resNorm; @@ -1462,9 +1476,15 @@ namespace Cantera { } //==================================================================================================================== // Here we print out the residual at various points along the double dogleg, comparing against the quadratic model - - void NonlinearSolver::residualComparisonLeg(const double time_curr, const double *ydot0, - const double *ydot1, const double *newtDir) { + // in a table format + /*! + * @param time_curr INPUT current time + * @param ydot0 INPUT Current value of the derivative of the solution vector for non-time dependent + * determinations + * @param ydot1 INPUT Time derivate of solution at the conditions which are evalulated + */ + void NonlinearSolver::residualComparisonLeg(const double time_curr, const double * const ydot0, + double * const ydot1) { double *y1 = DATA_PTR(m_wksp); double sLen; if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { @@ -1485,6 +1505,9 @@ namespace Cantera { for (int i = 0; i < neq_; i++) { y1[i] = m_y_n[i] + alpha * deltaX_CP_[i]; } + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y1, ydot1); + } sLen = alpha * solnErrorNorm(DATA_PTR(deltaX_CP_)); /* * Calculate the residual that would result if y1[] were the new solution vector @@ -1510,7 +1533,10 @@ namespace Cantera { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { y1[i] = m_y_n[i] + (1.0 - alpha) * deltaX_CP_[i]; - y1[i] += alpha * Nuu_ * newtDir[i]; + y1[i] += alpha * Nuu_ * deltaX_Newton_[i]; + } + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y1, ydot1); } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -1539,9 +1565,12 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* newtDir[i]; + y1[i] = m_y_n[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* deltaX_Newton_[i]; } - sLen = ( Nuu_ + alpha * (1.0 - Nuu_)) * solnErrorNorm(DATA_PTR(newtDir)); + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y1, ydot1); + } + sLen = ( Nuu_ + alpha * (1.0 - Nuu_)) * solnErrorNorm(DATA_PTR(deltaX_Newton_)); /* * Calculate the residual that would result if y1[] were the new solution vector * -> m_resid[] contains the result of the residual calculation @@ -1603,12 +1632,11 @@ namespace Cantera { * * @param y Initial value of the solution vector * @param step0 initial proposed step size - * @param loglevel log level * * @return returns the damping factor */ double - NonlinearSolver::deltaBoundStep(const doublereal * const y, const doublereal * const step0, const int loglevel) { + NonlinearSolver::deltaBoundStep(const doublereal * const y, const doublereal * const step0) { int i_fbounds = 0; int ifbd = 0; @@ -1684,7 +1712,7 @@ namespace Cantera { /* * Report on any corrections */ - if (loglevel > 1) { + if (m_print_flag > 1) { if (f_delta_bounds < 1.0) { if (i_fbd) { printf("\t\tdeltaBoundStep: Increase of Variable %d causing " @@ -1766,6 +1794,10 @@ namespace Cantera { } } //==================================================================================================================== + //! Initialize the size of the trust vector. + /*! + * The algorithm we use is to set it equal to the length of the Distance to the Cauchy point. + */ void NonlinearSolver::initializeTrustRegion() { double cpd = calcTrustDistance(deltaX_CP_); @@ -1778,12 +1810,6 @@ namespace Cantera { if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } - trustDelta_ = trustDelta_ * cpd; - calcTrustVector(); - cpd = calcTrustDistance(deltaX_CP_); - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); - } } //==================================================================================================================== @@ -1899,8 +1925,7 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0, - const int loglevel) { + doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0) { int i, i_lower = -1; doublereal fbound = 1.0, f_bounds = 1.0; doublereal ff, y_new; @@ -1940,13 +1965,13 @@ namespace Cantera { /* * Report on any corrections */ - if (loglevel > 1) { + if (m_print_flag > 1) { if (f_bounds != 1.0) { printf("\t\tboundStep: Variable %d causing bounds damping of %g\n", i_lower, f_bounds); } } - doublereal f_delta_bounds = deltaBoundStep(y, step0, loglevel); + doublereal f_delta_bounds = deltaBoundStep(y, step0); fbound = MIN(f_bounds, f_delta_bounds); return fbound; @@ -1978,7 +2003,7 @@ namespace Cantera { int NonlinearSolver::dampStep(const doublereal time_curr, const double* y0, const doublereal *ydot0, const double* step0, double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + double& s1, SquareMatrix& jac, bool writetitle, int& num_backtracks) { int info = 0; @@ -1989,12 +2014,12 @@ namespace Cantera { // Compute the multiplier to keep all components in bounds.A value of one indicates that there is no limitation // on the current step size in the nonlinear method due to bounds constraints (either negative values of delta // bounds constraints. - m_dampBound = boundStep(y0, step0, loglevel); + m_dampBound = boundStep(y0, step0); // If fbound is very small, then y0 is already close to the boundary and step0 points out of the allowed domain. In // this case, the Newton algorithm fails, so return an error condition. if (m_dampBound < 1.e-30) { - if (loglevel > 1) printf("\t\t\tdampStep: At limits.\n"); + if (m_print_flag > 1) printf("\t\t\tdampStep(): At limits.\n"); return -3; } @@ -2033,8 +2058,8 @@ namespace Cantera { info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); } if (info != 1) { - if (loglevel > 0) { - printf("\t\t\tdampStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + if (m_print_flag > 0) { + printf("\t\t\tdampStep(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } return -1; } @@ -2043,7 +2068,7 @@ namespace Cantera { bool steepEnough = (m_normResidTrial < m_normResid0 * (0.9 * (1.0 - ff) * (1.0 - ff)* (1.0 - ff) + 0.1)); if (m_normResidTrial < 1.0 || steepEnough) { - if (loglevel >= 5) { + if (m_print_flag >= 5) { if (m_normResidTrial < 1.0) { printf("\t dampStep(): Current trial step and damping" " coefficient accepted because residTrial test step < 1:\n"); @@ -2079,12 +2104,12 @@ namespace Cantera { // Compute the next undamped step, step1[], that would result if y1[] were accepted. // We now have two steps that we have calculated step0[] and step1[] if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doNewtonSolve(time_curr, y1, ydot1, step1, jac, loglevel); + info = doNewtonSolve(time_curr, y1, ydot1, step1, jac); } else { - info = doNewtonSolve(time_curr, y1, ydot0, step1, jac, loglevel); + info = doNewtonSolve(time_curr, y1, ydot0, step1, jac); } if (info) { - if (loglevel > 0) { + if (m_print_flag > 0) { printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); } return -1; @@ -2094,7 +2119,7 @@ namespace Cantera { s1 = solnErrorNorm(step1); // write log information - if (loglevel > 3) { + if (m_print_flag > 3) { print_solnDelta_norm_contrib((const doublereal *) step0, "DeltaSoln", (const doublereal *) step1, @@ -2103,7 +2128,7 @@ namespace Cantera { "Weighted Soln Updates:", y0, y1, ff, 5); } - if (loglevel > 1) { + if (m_print_flag > 1) { printf("\t\t\tdampStep(): s0 = %g, s1 = %g, dampBound = %g," "dampRes = %g\n", s0, s1, m_dampBound, m_dampRes); } @@ -2116,7 +2141,7 @@ namespace Cantera { if (s1 < 0.8 || s1 < s0) { if (s1 < 1.0) { - if (loglevel > 2) { + if (m_print_flag > 2) { if (s1 < 1.0) { printf("\t\t\tdampStep: current trial step and damping" " coefficient accepted because test step < 1\n"); @@ -2129,7 +2154,7 @@ namespace Cantera { } break; } else { - if (loglevel > 1) { + if (m_print_flag > 1) { printf("\t\t\tdampStep: current step rejected: (s1 = %g > " "s0 = %g)", s1, s0); if (m < (NDAMP-1)) { @@ -2149,25 +2174,25 @@ namespace Cantera { // a converged solution, and return 0 otherwise. If no damping // coefficient could be found, return -2. if (m < NDAMP) { - if (loglevel >= 4 ) { + if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted retnTrial = %d, its = %d, damp = %g\n", retnTrial, m+1, ff); } return retnTrial; } else { if (s1 < 0.5 && (s0 < 0.5)) { - if (loglevel >= 4 ) { + if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted kindof retnTrial = %d, its = %d, damp = %g\n", 2, m+1, ff); } return 2; } if (s1 < 1.0) { - if (loglevel >= 4 ) { + if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted and soln converged retnTrial = %d, its = %d, damp = %g\n", 0, m+1, ff); } return 0; } } - if (loglevel >= 4 ) { + if (m_print_flag >= 4 ) { printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", -2, m+1, ff); } return -2; @@ -2182,11 +2207,20 @@ namespace Cantera { * * @param step0 (output) On return this contains the suggested step vector for the current iteration * + * @return 1 Successful step was taken. The predicted residual norm is less than one + * 2 Successful step: Next step's norm is less than 0.8 + * 3 Success: The final residual is less than 1.0 + * A predicted deltaSoln1 is not produced however. s1 is estimated. + * 4 Success: The final residual is less than the residual + * from the previous step. + * A predicted deltaSoln1 is not produced however. s1 is estimated. + * 0 Uncertain Success: s1 is about the same as s0 + * -2 Unsuccessful step. */ int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y0, const doublereal *ydot0, std::vector & step0, - double* const y_new, double* const ydot_new, double* step1, - double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + double* const y_new, double* const ydot_new, double* stepLastGood, + double& s1, SquareMatrix& jac, bool writetitle, int& num_backtracks) { double lambda; @@ -2216,7 +2250,7 @@ namespace Cantera { */ leg = calcTrustIntersection(trustDelta_, lambda, alpha); - if (loglevel > 5) { + if (m_print_flag > 5) { tlen = trustRegionLength(); printf("\tdampDogLeg: trust region with length %13.5E has intersection at leg = %d, alpha = %g\n", tlen, leg, alpha); @@ -2228,9 +2262,9 @@ namespace Cantera { fillDogLegStep(leg, alpha, step0); /* - * Bound the step + * OK, now that we have step0, Bound the step */ - m_dampBound = boundStep(y0, DATA_PTR(step0), loglevel); + m_dampBound = boundStep(y0, DATA_PTR(step0)); /* * Decrease the step length if we are bound */ @@ -2244,14 +2278,14 @@ namespace Cantera { * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria * as a good step. */ - info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, loglevel, trustDeltaOld); + info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, m_print_flag, trustDeltaOld); /* * The algorithm failed to find a solution vector sufficiently different than the current point */ if (info == -1) { num_backtracks++; - if (loglevel >= 1) { + if (m_print_flag >= 1) { double stepNorm = solnErrorNorm(DATA_PTR(step0)); printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); success = false; @@ -2261,7 +2295,7 @@ namespace Cantera { } if (info == -2) { num_backtracks++; - if (loglevel >= 1) { + if (m_print_flag >= 1) { printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); success = false; retn = -1; @@ -2274,8 +2308,8 @@ namespace Cantera { } if (info == 3) { haveASuccess = true; - // Store the good results in step1 - mdp::mdp_copy_dbl_1(DATA_PTR(step1), CONSTD_DATA_PTR(step0), neq_); + // Store the good results in stepLastGood + mdp::mdp_copy_dbl_1(DATA_PTR(stepLastGood), CONSTD_DATA_PTR(step0), neq_); // Within the program decideStep(), we have already increased the value of trustDelta_. We store the // value of step0 in step1, recalculate a larger step0 in the next fillDogLegStep(), // and then attempt to see if the larger step works in the next iteration @@ -2286,7 +2320,7 @@ namespace Cantera { // already been decreased in the decideStep() routine. We go back and try another iteration with // a smaller trust region. if (haveASuccess) { - mdp::mdp_copy_dbl_1(DATA_PTR(step0), CONSTD_DATA_PTR(step1), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(step0), CONSTD_DATA_PTR(stepLastGood), neq_); for (j = 0; j < neq_; j++) { y_new[j] = y0[j] + step0[j]; } @@ -2306,16 +2340,21 @@ namespace Cantera { /* * Estimate s1, the norm after the next step */ - double stepNorm = solnErrorNorm(DATA_PTR(step1)); - if ( m_dampBound < 1.0) { + double stepNorm = solnErrorNorm(DATA_PTR(step0)); + if (m_dampBound < 1.0) { stepNorm /= m_dampBound; } + stepNorm /= lambda; stepNorm *= m_normResidTrial / m_normResid0; s1 = stepNorm; if (success) { if (m_normResidTrial < 1.0) { - return 1; + if (normTrust_Newton_ < trustDelta_ && m_dampBound == 1.0) { + return 1; + } else { + return 0; + } } return 0; } @@ -2373,13 +2412,13 @@ namespace Cantera { // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; if (funcDecreaseSDExp > 0.0) { - if (loglevel > 0) { + if (m_print_flag > 0) { printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); } } /* - * Calculate the newsolution value y1[] given the step size + * Calculate the new solution value y1[] given the step size */ for (j = 0; j < neq_; j++) { y1[j] = y0[j] + step0[j]; @@ -2402,7 +2441,7 @@ namespace Cantera { } if (info != 1) { - if (loglevel > 0) { + if (m_print_flag > 0) { printf("\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } return -2; @@ -2427,7 +2466,7 @@ namespace Cantera { trustDelta_ *= 0.33; retn = 2; // error condition if step is getting too small - if (stepNorm * .5 < 0.2) { + if (rtol_ * stepNorm < 1.0E-6) { retn = -1; } return retn; @@ -2678,7 +2717,7 @@ namespace Cantera { if (doAffineSolve_) { info = doAffineNewtonSolve(DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac); } else { - info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac, m_print_flag); + info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac); } if (info) { @@ -2724,15 +2763,15 @@ namespace Cantera { if (doDogLeg_) { setupDoubleDogleg(); #ifdef DEBUG_DOGLEG - residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new)); #endif m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), stp, DATA_PTR(y_new), DATA_PTR(ydot_new), - DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); + DATA_PTR(stp1), s1, jac, frst, i_backtracks); } #ifdef DEBUG_DOGLEG else { - residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new)); } #endif @@ -2749,7 +2788,7 @@ namespace Cantera { if (!doDogLeg_) { m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), - DATA_PTR(stp1), s1, jac, m_print_flag, frst, i_backtracks); + DATA_PTR(stp1), s1, jac, frst, i_backtracks); frst = false; num_backtracks += i_backtracks; } @@ -2779,7 +2818,7 @@ namespace Cantera { info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(ydot_new)); if (info != 1) { if (m_print_flag > 0) { - printf("\t\t\tdampStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + printf("\t\t\tsolve_nonlinear_problem(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } m = -8; goto done; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 8dc6ad562..4a4047430 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -199,14 +199,13 @@ namespace Cantera { * @param ydot_curr Current value of the solution derivative. * @param delta_y return value of the raw change in y * @param jac Jacobian - * @param loglevel Log level * * @return Returns the result code from lapack. A zero means success. Anything * else indicates a failure. */ int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, - SquareMatrix& jac, int loglevel); + SquareMatrix& jac); //! Compute the newton step, either by direct newton's or by solving a close problem that is represented //! by a Hessian ( @@ -332,11 +331,10 @@ namespace Cantera { * * @param y Current solution value of the old step * @param step0 Proposed step change in the solution - * @param loglevel Log level * * @return Returns the damping factor determined by the bounds calculation */ - doublereal boundStep(const doublereal * const y, const doublereal * const step0, const int loglevel); + doublereal boundStep(const doublereal * const y, const doublereal * const step0); //! Set bounds constraints for all variables in the problem /*! @@ -418,11 +416,10 @@ namespace Cantera { * * @param y Initial value of the solution vector * @param step0 initial proposed step size - * @param loglevel log level * * @return returns the damping factor */ - doublereal deltaBoundStep(const doublereal * const y, const doublereal * const step0, const int loglevel); + doublereal deltaBoundStep(const doublereal * const y, const doublereal * const step0); //! Find a damping coefficient through a look-ahead mechanism /*! @@ -445,7 +442,6 @@ namespace Cantera { * @param step1 Value of the step change from y0 to y1 * @param s1 norm of the step change in going from y0 to y1 * @param jac Jacobian - * @param loglevel Log level to be used * @param writetitle Write a title line * @param num_backtracks Number of backtracks taken * @@ -454,7 +450,7 @@ namespace Cantera { int dampStep(const doublereal time_curr, const double* y0, const doublereal *ydot0, const double* step0, double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + double& s1, SquareMatrix& jac, bool writetitle, int& num_backtracks); //! Find the solution to F(X) = 0 by damped Newton iteration. @@ -616,10 +612,12 @@ namespace Cantera { */ void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); + //! Setup the parameters for the double dog leg /*! * The calls to the doCauchySolve() and doNewtonSolve() routines are done at the main level. This routine comes - * after those calls. + * after those calls. We calculate the point Nuu_ here, the distances of the dog-legs, + * and the norms of the CP and Newton points in terms of the trust vectors. */ void setupDoubleDogleg(); @@ -634,12 +632,16 @@ namespace Cantera { int calcTrustIntersection(double trustVal, double &lambda, double &alpha) const; + //! Initialize the size of the trust vector. + /*! + * The algorithm we use is to set it equal to the length of the Distance to the Cauchy point. + */ void initializeTrustRegion(); int dampDogLeg(const doublereal time_curr, const double* y0, const doublereal *ydot0, std::vector & step0, double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, int& loglevel, bool writetitle, + double& s1, SquareMatrix& jac, bool writetitle, int& num_backtracks); //! Decide whether the current step is acceptable and adjust the trust region size @@ -684,7 +686,7 @@ namespace Cantera { */ double expectedResidLeg(int leg, doublereal alpha) const; - void residualComparisonLeg(const double time_curr, const double *ydot0, const double *ydot1, const double *newtDir); + void residualComparisonLeg(const double time_curr, const double * const ydot0, double * const ydot1); //! Set the print level from the rootfinder /*! From 93d5d43a19a2d04bc2aee4c52eff1846da5b76aa Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 9 Sep 2011 21:32:50 +0000 Subject: [PATCH 391/446] More cleanup --- Cantera/src/numerics/NonlinearSolver.cpp | 133 +++++++++++++---------- Cantera/src/numerics/NonlinearSolver.h | 75 ++++++++++--- 2 files changed, 139 insertions(+), 69 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 70f44cf7d..36181d161 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -70,7 +70,7 @@ namespace Cantera { printf("\n"); } - bool NonlinearSolver::m_TurnOffTiming(false); + bool NonlinearSolver::s_TurnOffTiming(false); #ifdef DEBUG_NUMJAC bool NonlinearSolver::s_print_NumJac(true); @@ -98,7 +98,8 @@ namespace Cantera { m_ewt(0), m_manualDeltaStepSet(0), m_deltaStepMinimum(0), - m_y_n(0), + m_y_n_curr(0), + m_ydot_n_curr(0), m_y_nm1(0), ydot_new(0), m_colScales(0), @@ -106,6 +107,7 @@ namespace Cantera { m_rowWtScales(0), m_resid(0), m_wksp(0), + m_wksp_2(0), m_residWts(0), m_normResid0(0.0), m_normResidFRaw(0.0), @@ -162,7 +164,8 @@ namespace Cantera { m_ewt.resize(neq_, rtol_); m_deltaStepMinimum.resize(neq_, 0.001); m_deltaStepMaximum.resize(neq_, 1.0E10); - m_y_n.resize(neq_, 0.0); + m_y_n_curr.resize(neq_, 0.0); + m_ydot_n_curr.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); ydot_new.resize(neq_, 0.0); m_colScales.resize(neq_, 1.0); @@ -170,6 +173,7 @@ namespace Cantera { m_rowWtScales.resize(neq_, 1.0); m_resid.resize(neq_, 0.0); m_wksp.resize(neq_, 0.0); + m_wksp_2.resize(neq_, 0.0); m_residWts.resize(neq_, 0.0); atolk_.resize(neq_, atolBase_); deltaX_Newton_.resize(neq_, 0.0); @@ -198,7 +202,8 @@ namespace Cantera { m_ewt(0), m_manualDeltaStepSet(0), m_deltaStepMinimum(0), - m_y_n(0), + m_y_n_curr(0), + m_ydot_n_curr(0), m_y_nm1(0), ydot_new(0), m_colScales(0), @@ -206,6 +211,7 @@ namespace Cantera { m_rowWtScales(0), m_resid(0), m_wksp(0), + m_wksp_2(0), m_residWts(0), m_normResid0(0.0), m_normResidFRaw(0.0), @@ -277,7 +283,8 @@ namespace Cantera { m_ewt = right.m_ewt; m_manualDeltaStepSet = right.m_manualDeltaStepSet; m_deltaStepMinimum = right.m_deltaStepMinimum; - m_y_n = right.m_y_n; + m_y_n_curr = right.m_y_n_curr; + m_ydot_n_curr = right.m_ydot_n_curr; m_y_nm1 = right.m_y_nm1; ydot_new = right.ydot_new; m_colScales = right.m_colScales; @@ -285,6 +292,7 @@ namespace Cantera { m_rowWtScales = right.m_rowWtScales; m_resid = right.m_resid; m_wksp = right.m_wksp; + m_wksp_2 = right.m_wksp_2; m_residWts = right.m_residWts; m_normResid0 = right.m_normResid0; m_normResidFRaw = right.m_normResidFRaw; @@ -472,7 +480,7 @@ namespace Cantera { error = delta_y[i] / m_ewt[i]; normContrib = sqrt(error * error); printf("\t\t %4d %12.4e | %12.4e %12.4e %12.4e %12.4e\n", i, normContrib/sqrt((double)neq_), - delta_y[i], m_y_n[i], m_y_n[i] + dampFactor * delta_y[i], m_ewt[i]); + delta_y[i], m_y_n_curr[i], m_y_n_curr[i] + dampFactor * delta_y[i], m_ewt[i]); } } @@ -492,7 +500,7 @@ namespace Cantera { * out to standard output. */ doublereal NonlinearSolver::residErrorNorm(const doublereal * const resid, const char * title, const int printLargest, - const doublereal * const y) + const doublereal * const y) const { int i; doublereal sum_norm = 0.0, error; @@ -580,7 +588,7 @@ namespace Cantera { m_colScales[i] = 1.0; } } - m_func->calcSolnScales(time_n, DATA_PTR(m_y_n), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); + m_func->calcSolnScales(time_n, DATA_PTR(m_y_n_curr), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); } //==================================================================================================================== // Compute the current residual @@ -595,7 +603,7 @@ namespace Cantera { * -0 or neg value Means an unsuccessful operation */ int NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, - const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) + const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) const { int retn = m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), evalType); m_nfe++; @@ -755,7 +763,7 @@ namespace Cantera { /* * Compute the undamped Newton step. The residual function is * evaluated at the current time, t_n, at the current values of the - * solution vector, m_y_n, and the solution time derivative, m_ydot_n. + * solution vector, m_y_n_curr, and the solution time derivative, m_ydot_n. * The Jacobian is not recomputed. * * A factored jacobian is reused, if available. If a factored jacobian @@ -1276,7 +1284,7 @@ namespace Cantera { double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); for (int i = 0; i < neq_; i++) { mdp::checkFinite(deltaX_CP_[i]); - y1[i] = m_y_n[i] + ff * deltaX_CP_[i]; + y1[i] = m_y_n_curr[i] + ff * deltaX_CP_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -1295,7 +1303,7 @@ namespace Cantera { double sNewt = solnErrorNorm(DATA_PTR(newtDir)); for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + ff * newtDir[i]; + y1[i] = m_y_n_curr[i] + ff * newtDir[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -1477,15 +1485,15 @@ namespace Cantera { //==================================================================================================================== // Here we print out the residual at various points along the double dogleg, comparing against the quadratic model // in a table format - /*! + /* * @param time_curr INPUT current time * @param ydot0 INPUT Current value of the derivative of the solution vector for non-time dependent * determinations * @param ydot1 INPUT Time derivate of solution at the conditions which are evalulated */ - void NonlinearSolver::residualComparisonLeg(const double time_curr, const double * const ydot0, - double * const ydot1) { + void NonlinearSolver::residualComparisonLeg(const double time_curr, const double * const ydot0) const { double *y1 = DATA_PTR(m_wksp); + double *ydot1 = DATA_PTR(m_wksp_2); double sLen; if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf(" residualComparisonLeg() \n"); @@ -1503,7 +1511,7 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + alpha * deltaX_CP_[i]; + y1[i] = m_y_n_curr[i] + alpha * deltaX_CP_[i]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, y1, ydot1); @@ -1532,7 +1540,7 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + (1.0 - alpha) * deltaX_CP_[i]; + y1[i] = m_y_n_curr[i] + (1.0 - alpha) * deltaX_CP_[i]; y1[i] += alpha * Nuu_ * deltaX_Newton_[i]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { @@ -1549,7 +1557,7 @@ namespace Cantera { } for (int i = 0; i < neq_; i++) { - y1[i] -= m_y_n[i]; + y1[i] -= m_y_n_curr[i]; } sLen = solnErrorNorm(DATA_PTR(y1)); @@ -1565,7 +1573,7 @@ namespace Cantera { for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { double alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* deltaX_Newton_[i]; + y1[i] = m_y_n_curr[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* deltaX_Newton_[i]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, y1, ydot1); @@ -1605,7 +1613,7 @@ namespace Cantera { { for (int i = 0; i < neq_; i++) { m_deltaStepMinimum[i] = 1000. * atolk_[i]; - m_deltaStepMinimum[i] = MAX(m_deltaStepMinimum[i], 0.1 * fabs(m_y_n[i])); + m_deltaStepMinimum[i] = MAX(m_deltaStepMinimum[i], 0.1 * fabs(m_y_n_curr[i])); } } //==================================================================================================================== @@ -1729,9 +1737,9 @@ namespace Cantera { return f_delta_bounds; } - //==================================================================================================================== - //! Calculate the trust region vectors - /*! + //==================================================================================================================== + // Calculate the trust region vectors + /* * The trust region is made up of the trust region vector calculation and the trustDelta_ value * We periodically recalculate the trustVector_ values so that they renormalize to the * correct length. @@ -1753,7 +1761,7 @@ namespace Cantera { // we use the old value of the trust region as an indicator for (int i = 0; i < neq_; i++) { oldVal = deltaX_trust_[i]; - fabsy = fabs(m_y_n[i]); + fabsy = fabs(m_y_n_curr[i]); // First off make sure that each trust region vector is 1/2 the size of each variable or smaller // unless overridden by the deltaStepMininum value. double newValue = trustDeltaEach * m_ewt[i] / wtSum; @@ -1859,7 +1867,15 @@ namespace Cantera { return sum; } //==================================================================================================================== - int NonlinearSolver::calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const + // Given a trust distance, this routine calculates the intersection of the this distance with the + // double dogleg curve + /* + * @param trustDelta (INPUT) Value of the trust distance + * @param lambda (OUTPUT) Returns the internal coordinate of the double dogleg + * @param alpha (OUTPUT) Returns the relative distance along the appropriate leg + * @return leg (OUTPUT) Returns the leg ID (0, 1, or 2) + */ + int NonlinearSolver::calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const { double dist; if (normTrust_Newton_ < trustDelta) { @@ -2557,20 +2573,20 @@ namespace Cantera { // std::vector y_curr(neq_, 0.0); - std::vector ydot_curr(neq_, 0.0); + // std::vector ydot_curr(neq_, 0.0); std::vector stp(neq_, 0.0); std::vector stp1(neq_, 0.0); std::vector y_new(neq_, 0.0); - mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_comm), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), DATA_PTR(y_comm), neq_); if (SolnType != NSOLN_TYPE_STEADY_STATE || ydot_comm) { - mdp::mdp_copy_dbl_1(DATA_PTR(ydot_curr), ydot_comm, neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_ydot_n_curr), ydot_comm, neq_); mdp::mdp_copy_dbl_1(DATA_PTR(ydot_new), ydot_comm, neq_); } // Redo the solution weights every time we enter the function - createSolnWeights(DATA_PTR(m_y_n)); + createSolnWeights(DATA_PTR(m_y_n_curr)); m_normDeltaSoln_Newton = 1.0E1; bool frst = true; num_newt_its = 0; @@ -2607,7 +2623,7 @@ namespace Cantera { * If we are far enough away from the solution, redo the solution weights and the trust vectors. */ if (m_normDeltaSoln_Newton > 1.0E2) { - createSolnWeights(DATA_PTR(m_y_n)); + createSolnWeights(DATA_PTR(m_y_n_curr)); #ifdef DEBUG_DOGLEG calcTrustVector(); #else @@ -2618,7 +2634,7 @@ namespace Cantera { } else { // Do this stuff every 5 iterations if ( (num_newt_its % 5) == 1) { - createSolnWeights(DATA_PTR(m_y_n)); + createSolnWeights(DATA_PTR(m_y_n_curr)); #ifdef DEBUG_DOGLEG calcTrustVector(); #else @@ -2629,7 +2645,7 @@ namespace Cantera { } } - //mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), DATA_PTR(y_curr), neq_); + //mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), DATA_PTR(y_curr), neq_); /* * Set default values of Delta bounds constraints */ @@ -2651,7 +2667,8 @@ namespace Cantera { if (m_print_flag > 3) { printf("\tsolve_nonlinear_problem(): Getting a new Jacobian and solving system\n"); } - info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), num_newt_its); + info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n_curr), + DATA_PTR(m_ydot_n_curr), num_newt_its); if (info == 0) { m = -4; goto done; @@ -2672,7 +2689,7 @@ namespace Cantera { /* * Calculate the base residual */ - info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); + info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr)); if (info != 1) { if (m_print_flag > 0) { printf("\t\t\tsolve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); @@ -2685,18 +2702,18 @@ namespace Cantera { * Scale the matrix and the rhs, if they aren't already scaled * Figure out and store the residual scaling factors. */ - scaleMatrix(jac, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), time_curr); + scaleMatrix(jac, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), time_curr); /* * Optional print out the initial residual */ if (m_print_flag >= 6) { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n)); + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n_curr)); } else if (m_print_flag == 4 || m_print_flag == 5) { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n)); + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); } else { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n)); + m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); } #ifdef DEBUG_DOGLEG @@ -2715,9 +2732,9 @@ namespace Cantera { // compute the undamped Newton step if (doAffineSolve_) { - info = doAffineNewtonSolve(DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac); + info = doAffineNewtonSolve(DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); } else { - info = doNewtonSolve(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), DATA_PTR(deltaX_Newton_), jac); + info = doNewtonSolve(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); } if (info) { @@ -2750,28 +2767,28 @@ namespace Cantera { /* * Filter out bad directions */ - filterNewStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(stp)); + filterNewStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(stp)); #ifdef DEBUG_DOGLEG - descentComparison(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); #endif if (doDogLeg_) { setupDoubleDogleg(); #ifdef DEBUG_DOGLEG - residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new)); + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr)); #endif - m = dampDogLeg(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), + m = dampDogLeg(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), stp, DATA_PTR(y_new), DATA_PTR(ydot_new), DATA_PTR(stp1), s1, jac, frst, i_backtracks); } #ifdef DEBUG_DOGLEG else { - residualComparisonLeg(time_curr, DATA_PTR(ydot_curr), DATA_PTR(ydot_new)); + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr)); } #endif @@ -2786,7 +2803,7 @@ namespace Cantera { * s1 */ if (!doDogLeg_) { - m = dampStep(time_curr, DATA_PTR(m_y_n), DATA_PTR(ydot_curr), + m = dampStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), DATA_PTR(stp1), s1, jac, frst, i_backtracks); frst = false; @@ -2856,10 +2873,10 @@ namespace Cantera { // Exchange new for curr solutions if (m >= 0) { - mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n), CONSTD_DATA_PTR(y_new), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), CONSTD_DATA_PTR(y_new), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - calc_ydot(m_order, DATA_PTR(m_y_n), DATA_PTR(ydot_curr)); + calc_ydot(m_order, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr)); } } @@ -2909,9 +2926,9 @@ namespace Cantera { } - mdp::mdp_copy_dbl_1(y_comm, CONSTD_DATA_PTR(m_y_n), neq_); + mdp::mdp_copy_dbl_1(y_comm, CONSTD_DATA_PTR(m_y_n_curr), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - mdp::mdp_copy_dbl_1(ydot_comm, CONSTD_DATA_PTR(ydot_curr), neq_); + mdp::mdp_copy_dbl_1(ydot_comm, CONSTD_DATA_PTR(m_ydot_n_curr), neq_); } num_linear_solves += m_numTotalLinearSolves; @@ -2919,7 +2936,7 @@ namespace Cantera { doublereal time_elapsed = wc.secondsWC(); if (m_print_flag > 1) { if (m > 0) { - if (NonlinearSolver::m_TurnOffTiming) { + if (NonlinearSolver::s_TurnOffTiming) { printf("\t\tNonlinear problem solved successfully in %d its\n", num_newt_its); } else { @@ -3208,14 +3225,17 @@ namespace Cantera { return retn; } //==================================================================================================================== - // Internal function to calculate the time derivative at the new step + // Internal function to calculate the time derivative of the solution at the new step /* + * Previously, the user must have supplied information about the previous time step for this routine to + * work as intended. + * * @param order of the BDF method * @param y_curr current value of the solution * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr */ void NonlinearSolver:: - calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr) + calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr) const { if (!ydot_curr) { return; @@ -3235,8 +3255,10 @@ namespace Cantera { for (i = 0; i < neq_; i++) { ydot_curr[i] = c1 * (y_curr[i] - m_y_nm1[i]) - m_ydot_nm1[i]; } - throw CanteraError("", "not implemented"); + return; + default: + throw CanteraError("calc_ydot()", "Case not covered"); } } //==================================================================================================================== @@ -3391,8 +3413,7 @@ namespace Cantera { rtol_ = rtol; } //===================================================================================================================== - - void NonlinearSolver::setPrintLvl( int printLvl) + void NonlinearSolver::setPrintLvl(int printLvl) { m_print_flag = printLvl; } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 4a4047430..adaa51369 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -60,6 +60,29 @@ namespace Cantera { * value, beta, from zero to one, This may or may not be the same as the value, damp, * depending upon whether the direction is straight. * + * + * TIME STEP TYPE + * + * The code solves a nonlinear problem. Frequently the nonlinear problem is created from time-dependent + * residual. Whenever you change the solution vector, you are also changing the derivative of the + * solution vector. Therefore, the code has the option of altering ydot, a vector of time derivatives + * of the solution in tandem with the solution vector and then feeding a residual and Jacobian routine + * with the time derivatives as well as the solution. The code has support for a backwards euler method + * and a second order Adams-Bashforth or Trapezoidal Rule. + * + * In order to use these methods, the solver must be initialized with delta_t and m_y_nm1[i] to specify + * the conditions at the previous time step. For second order methods, the time derivative at t_nm1 must + * also be supplied, m_ydot_nm1[i]. Then the solution type NSOLN_TYPE_TIME_DEPENDENT may be used to + * solve the problem. + * + * For steady state problem whose residual doesn't have a solution time derivative in it, you should + * use the NSOLN_TYPE_STEADY_STATE problem type. + * + * We have a NSOLN_TYPE_PSEUDO_TIME_DEPENDENT defined. However, this is not implemented yet. This would + * be a pseudo time dependent calculation, where an optional time derivative could be added in order to + * help equilibrate a nonlinear steady state system. The time transient is not important in and of + * itself. Many physical systems have a time dependence to them that provides a natural way to relax + * the nonlinear system. * * * @code @@ -159,11 +182,12 @@ namespace Cantera { * @return Returns the L2 norm of the delta */ doublereal residErrorNorm(const doublereal * const resid, const char * title = 0, const int printLargest = 0, - const doublereal * const y = 0); + const doublereal * const y = 0) const; //! Compute the current residual /*! - * The current value of the residual is storred in the internal work array m_resid. + * The current value of the residual is storred in the internal work array m_resid, which is defined + * as mutable * * @param time_curr Value of the time * @param typeCalc Type of the calculation @@ -178,7 +202,7 @@ namespace Cantera { */ int doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, const doublereal * const ydot_curr, - const ResidEval_Type_Enum evalType = Base_ResidEval); + const ResidEval_Type_Enum evalType = Base_ResidEval) const; //! Compute the undamped Newton step /*! @@ -350,14 +374,17 @@ namespace Cantera { //! Return an editable vector of the high bounds constraints std::vector & highBoundsConstraintVector(); - - //! Internal function to calculate the time derivative at the new step + + //! Internal function to calculate the time derivative of the solution at the new step /*! + * Previously, the user must have supplied information about the previous time step for this routine to + * work as intended. + * * @param order of the BDF method * @param y_curr current value of the solution * @param ydot_curr Calculated value of the solution derivative that is consistent with y_curr - */ - void calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr); + */ + void calc_ydot(const int order, const doublereal * const y_curr, doublereal * const ydot_curr) const; //! Function called to evaluate the jacobian matrix and the current //! residual vector at the current time step @@ -630,6 +657,14 @@ namespace Cantera { */ int lambdaToLeg(const double lambda, double &alpha) const; + //! Given a trust distance, this routine calculates the intersection of the this distance with the + //! double dogleg curve + /*! + * @param trustDelta (INPUT) Value of the trust distance + * @param lambda (OUTPUT) Returns the internal coordinate of the double dogleg + * @param alpha (OUTPUT) Returns the relative distance along the appropriate leg + * @return leg (OUTPUT) Returns the leg ID (0, 1, or 2) + */ int calcTrustIntersection(double trustVal, double &lambda, double &alpha) const; //! Initialize the size of the trust vector. @@ -686,7 +721,14 @@ namespace Cantera { */ double expectedResidLeg(int leg, doublereal alpha) const; - void residualComparisonLeg(const double time_curr, const double * const ydot0, double * const ydot1); + //! Here we print out the residual at various points along the double dogleg, comparing against the quadratic model + //! in a table format + /* + * @param time_curr INPUT current time + * @param ydot0 INPUT Current value of the derivative of the solution vector for non-time dependent + * determinations + */ + void residualComparisonLeg(const double time_curr, const double * const ydot0) const; //! Set the print level from the rootfinder /*! @@ -750,7 +792,11 @@ namespace Cantera { std::vector m_deltaStepMaximum; //! Vector containing the current solution vector within the nonlinear solver - std::vector m_y_n; + std::vector m_y_n_curr; + + //! Vector containing the time derivative of the current solution vector within the nonlinear solver + //! (where applicable) + std::vector m_ydot_n_curr; //! Vector containing the solution at the previous time step std::vector m_y_nm1; @@ -777,11 +823,14 @@ namespace Cantera { std::vector m_rowWtScales; //! Value of the residual for the nonlinear problem - std::vector m_resid; + mutable std::vector m_resid; //! Workspace of length neq_ mutable std::vector m_wksp; + //! Workspace of length neq_ + mutable std::vector m_wksp_2; + /***************************************************************************************** * INTERNAL WEIGHTS FOR TAKING SOLUTION NORMS ******************************************************************************************/ @@ -809,7 +858,7 @@ namespace Cantera { doublereal m_normResidPoints[15]; //! Boolean indicating whether we should scale the residual - bool m_resid_scaled; + mutable bool m_resid_scaled; /***************************************************************************************** * INTERNAL BOUNDARY INFO FOR SOLUTIONS @@ -831,7 +880,7 @@ namespace Cantera { doublereal delta_t_n; //! Counter for the total number of function evaluations - int m_nfe; + mutable int m_nfe; /*********************************************************************************************** * MATRIX INFORMATION @@ -999,7 +1048,7 @@ namespace Cantera { /*! * Necessary to do for test suites */ - static bool m_TurnOffTiming; + static bool s_TurnOffTiming; //! Turn on or off printing of the Jacobian static bool s_print_NumJac; From 492a814e9da674ee1d73b23008229c1df2aa2f3c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 12 Sep 2011 15:26:28 +0000 Subject: [PATCH 392/446] Fixed an error in mdp_init_ functions --- Cantera/src/base/mdp_allo.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Cantera/src/base/mdp_allo.cpp b/Cantera/src/base/mdp_allo.cpp index c1308049a..d5673d454 100644 --- a/Cantera/src/base/mdp_allo.cpp +++ b/Cantera/src/base/mdp_allo.cpp @@ -1658,7 +1658,7 @@ namespace mdp { } else { int m = len % 7; if (m != 0) { - for (int i = 0; i < m; m++) { + for (int i = 0; i < m; i++) { v[i] = value; } if (len < 7) return; @@ -1751,7 +1751,7 @@ namespace mdp { } else { int m = len % 7; if (m != 0) { - for (int i = 0; i < m; m++) { + for (int i = 0; i < m; i++) { dstart[i] = value; } if (len < 7) return; @@ -1795,7 +1795,7 @@ namespace mdp { } else { int m = len % 7; if (m != 0) { - for (int i = 0; i < m; m++) { + for (int i = 0; i < m; i++) { v[i] = value; } if (len < 7) return; From d2272b370776b3ac1c5bc82bec98607facb8cc55 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 12 Sep 2011 15:59:52 +0000 Subject: [PATCH 393/446] Initialization for trust regions firmed up. Same results for the second time into the function as the first. --- Cantera/src/numerics/NonlinearSolver.cpp | 98 +++++++++++------------- Cantera/src/numerics/NonlinearSolver.h | 13 ++-- 2 files changed, 52 insertions(+), 59 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 36181d161..4826270dd 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -101,7 +101,7 @@ namespace Cantera { m_y_n_curr(0), m_ydot_n_curr(0), m_y_nm1(0), - ydot_new(0), + m_ydot_n_1(0), m_colScales(0), m_rowScales(0), m_rowWtScales(0), @@ -167,7 +167,7 @@ namespace Cantera { m_y_n_curr.resize(neq_, 0.0); m_ydot_n_curr.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); - ydot_new.resize(neq_, 0.0); + m_ydot_n_1.resize(neq_, 0.0); m_colScales.resize(neq_, 1.0); m_rowScales.resize(neq_, 1.0); m_rowWtScales.resize(neq_, 1.0); @@ -205,7 +205,7 @@ namespace Cantera { m_y_n_curr(0), m_ydot_n_curr(0), m_y_nm1(0), - ydot_new(0), + m_ydot_n_1(0), m_colScales(0), m_rowScales(0), m_rowWtScales(0), @@ -286,7 +286,7 @@ namespace Cantera { m_y_n_curr = right.m_y_n_curr; m_ydot_n_curr = right.m_ydot_n_curr; m_y_nm1 = right.m_y_nm1; - ydot_new = right.ydot_new; + m_ydot_n_1 = right.m_ydot_n_1; m_colScales = right.m_colScales; m_rowScales = right.m_rowScales; m_rowWtScales = right.m_rowWtScales; @@ -1276,7 +1276,7 @@ namespace Cantera { return normSoln; } //=================================================================================================================== - void NonlinearSolver::descentComparison(double time_curr, double *ydot0, double *ydot1, const double *newtDir) + void NonlinearSolver::descentComparison(double time_curr, double *ydot0, double *ydot1) { int info; double ff = 1.0E-5; @@ -1301,9 +1301,9 @@ namespace Cantera { double residSteep2 = residSteep * residSteep * neq_; double funcDecrease2 = 0.5 * (residSteep2 - normResid02) / ( ff * cauchyDistanceNorm); - double sNewt = solnErrorNorm(DATA_PTR(newtDir)); + double sNewt = solnErrorNorm(DATA_PTR(deltaX_Newton_)); for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n_curr[i] + ff * newtDir[i]; + y1[i] = m_y_n_curr[i] + ff * deltaX_Newton_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -2233,9 +2233,9 @@ namespace Cantera { * 0 Uncertain Success: s1 is about the same as s0 * -2 Unsuccessful step. */ - int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y0, - const doublereal *ydot0, std::vector & step0, - double* const y_new, double* const ydot_new, double* stepLastGood, + int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y_n_curr, + const doublereal *ydot_n_curr, std::vector & step_1, + double* const y_n_1, double* const ydot_n_1, double* stepLastGood, double& s1, SquareMatrix& jac, bool writetitle, int& num_backtracks) { @@ -2255,8 +2255,6 @@ namespace Cantera { m_dampRes = 1.0; int j, m; num_backtracks = 0; - //double deltaSolnNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); - //double funcDecreaseSDExp = RJd_norm_ / deltaSolnNorm * lambdaStar_; double tlen; @@ -2275,26 +2273,37 @@ namespace Cantera { * Figure out the new step vector, step0, based on (leg, alpha). Here we are using the * inter */ - fillDogLegStep(leg, alpha, step0); + fillDogLegStep(leg, alpha, step_1); /* * OK, now that we have step0, Bound the step */ - m_dampBound = boundStep(y0, DATA_PTR(step0)); + m_dampBound = boundStep(y_n_curr, DATA_PTR(step_1)); /* * Decrease the step length if we are bound */ if (m_dampBound < 1.0) { for (j = 0; j < neq_; j++) { - step0[j] = step0[j] * m_dampBound; + step_1[j] = step_1[j] * m_dampBound; } } - + /* + * Calculate the new solution value y1[] given the step size + */ + for (j = 0; j < neq_; j++) { + y_n_1[j] = y_n_curr[j] + step_1[j]; + } + /* + * Calculate the new solution time derivative given the step size + */ + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + calc_ydot(m_order, y_n_1, ydot_n_1); + } /* * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria * as a good step. */ - info = decideStep(time_curr, leg, alpha, y0, ydot0, step0, y_new, ydot_new, m_print_flag, trustDeltaOld); + info = decideStep(time_curr, leg, alpha, y_n_curr, ydot_n_curr, step_1, y_n_1, ydot_n_1, trustDeltaOld); /* * The algorithm failed to find a solution vector sufficiently different than the current point @@ -2302,7 +2311,7 @@ namespace Cantera { if (info == -1) { num_backtracks++; if (m_print_flag >= 1) { - double stepNorm = solnErrorNorm(DATA_PTR(step0)); + double stepNorm = solnErrorNorm(DATA_PTR(step_1)); printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); success = false; retn = -1; @@ -2325,7 +2334,7 @@ namespace Cantera { if (info == 3) { haveASuccess = true; // Store the good results in stepLastGood - mdp::mdp_copy_dbl_1(DATA_PTR(stepLastGood), CONSTD_DATA_PTR(step0), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(stepLastGood), CONSTD_DATA_PTR(step_1), neq_); // Within the program decideStep(), we have already increased the value of trustDelta_. We store the // value of step0 in step1, recalculate a larger step0 in the next fillDogLegStep(), // and then attempt to see if the larger step works in the next iteration @@ -2336,12 +2345,12 @@ namespace Cantera { // already been decreased in the decideStep() routine. We go back and try another iteration with // a smaller trust region. if (haveASuccess) { - mdp::mdp_copy_dbl_1(DATA_PTR(step0), CONSTD_DATA_PTR(stepLastGood), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(step_1), CONSTD_DATA_PTR(stepLastGood), neq_); for (j = 0; j < neq_; j++) { - y_new[j] = y0[j] + step0[j]; + y_n_1[j] = y_n_curr[j] + step_1[j]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - calc_ydot(m_order, y_new, ydot_new); + calc_ydot(m_order, y_n_1, ydot_n_1); } success = true; break; @@ -2356,7 +2365,7 @@ namespace Cantera { /* * Estimate s1, the norm after the next step */ - double stepNorm = solnErrorNorm(DATA_PTR(step0)); + double stepNorm = solnErrorNorm(DATA_PTR(step_1)); if (m_dampBound < 1.0) { stepNorm /= m_dampBound; } @@ -2392,7 +2401,6 @@ namespace Cantera { * @param step0 INPUT Trial step * @param y1 OUTPUT Solution values at the conditions which are evalulated for success * @param ydot1 OUTPUT Time derivates of solution at the conditions which are evalulated for success - * @param loglevel INPUT Current loglevel * @param trustDeltaOld INPUT Value of the trust length at the old conditions * * @@ -2405,18 +2413,16 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, - const doublereal *ydot0, std::vector & step0, - double * const y1, double* const ydot1, int& loglevel, double trustDeltaOld) - + int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double * const y0, + const doublereal * const ydot0, const std::vector & step0, + const double * const y1, const double* const ydot1, double trustDeltaOld) { int retn = 2; bool goodStep = false; - int j; int info; double ll; // Calculate the solution step length - double stepNorm = solnErrorNorm(DATA_PTR(step0)); + double stepNorm = solnErrorNorm(DATA_PTR(step0)); // Calculate the initial (R**2 * neq) value for the old function double normResid0_2 = m_normResid0 * m_normResid0 * neq_; @@ -2432,19 +2438,6 @@ namespace Cantera { printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); } } - - /* - * Calculate the new solution value y1[] given the step size - */ - for (j = 0; j < neq_; j++) { - y1[j] = y0[j] + step0[j]; - } - /* - * Calculate the new solution time derivative given the step size - */ - if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - calc_ydot(m_order, y1, ydot1); - } /* * Calculate the residual that would result if y1[] were the new solution vector @@ -2583,7 +2576,7 @@ namespace Cantera { if (SolnType != NSOLN_TYPE_STEADY_STATE || ydot_comm) { mdp::mdp_copy_dbl_1(DATA_PTR(m_ydot_n_curr), ydot_comm, neq_); - mdp::mdp_copy_dbl_1(DATA_PTR(ydot_new), ydot_comm, neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_ydot_n_1), ydot_comm, neq_); } // Redo the solution weights every time we enter the function createSolnWeights(DATA_PTR(m_y_n_curr)); @@ -2599,7 +2592,8 @@ namespace Cantera { } else { jac.m_printLevel = 0; } - + mdp::mdp_init_dbl_1(DATA_PTR(deltaX_trust_), 1.0, neq_); + trustDelta_ = 1.0; if (m_print_flag == 2 || m_print_flag == 3) { @@ -2645,7 +2639,7 @@ namespace Cantera { } } - //mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), DATA_PTR(y_curr), neq_); + /* * Set default values of Delta bounds constraints */ @@ -2718,7 +2712,7 @@ namespace Cantera { #ifdef DEBUG_DOGLEG m_normDeltaSoln_CP = doCauchyPointSolve(jac); - if (m_numTotalNewtIts == 1) { + if (num_newt_its == 1) { initializeTrustRegion(); } #else @@ -2773,7 +2767,7 @@ namespace Cantera { #ifdef DEBUG_DOGLEG - descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(ydot_new), DATA_PTR(stp)); + descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1)); #endif @@ -2783,7 +2777,7 @@ namespace Cantera { residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr)); #endif m = dampDogLeg(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), - stp, DATA_PTR(y_new), DATA_PTR(ydot_new), + stp, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), DATA_PTR(stp1), s1, jac, frst, i_backtracks); } #ifdef DEBUG_DOGLEG @@ -2804,7 +2798,7 @@ namespace Cantera { */ if (!doDogLeg_) { m = dampStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), - DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(ydot_new), + DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), DATA_PTR(stp1), s1, jac, frst, i_backtracks); frst = false; num_backtracks += i_backtracks; @@ -2832,7 +2826,7 @@ namespace Cantera { } - info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(ydot_new)); + info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1)); if (info != 1) { if (m_print_flag > 0) { printf("\t\t\tsolve_nonlinear_problem(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); @@ -2867,7 +2861,7 @@ namespace Cantera { bool m_filterIntermediate = false; if (m_filterIntermediate) { if (m == 0) { - (void) filterNewSolution(time_n, DATA_PTR(y_new), DATA_PTR(ydot_new)); + (void) filterNewSolution(time_n, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1)); } } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index adaa51369..ecf889fc8 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -637,7 +637,7 @@ namespace Cantera { * * This routine doesn't need to be called for the solution of the nonlinear problem. */ - void descentComparison(double time_curr ,double *ydot0, double *ydot1, const double *newtDir); + void descentComparison(double time_curr ,double *ydot0, double *ydot1); //! Setup the parameters for the double dog leg @@ -694,7 +694,6 @@ namespace Cantera { * @param step0 INPUT Trial step * @param y1 OUTPUT Solution values at the conditions which are evalulated for success * @param ydot1 OUTPUT Time derivates of solution at the conditions which are evalulated for success - * @param loglevel INPUT Current loglevel * @param trustDeltaOld INPUT Value of the trust length at the old conditions * * @@ -707,9 +706,9 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int decideStep(const doublereal time_curr, int leg, double alpha, const double* y0, const doublereal *ydot0, - std::vector & step0, - double* const y1, double* const ydot1, int& loglevel, double trustDeltaOld); + int decideStep(const doublereal time_curr, int leg, double alpha, const double* const y0, const doublereal * const ydot0, + const std::vector & step0, + const double* const y1, const double* const ydot1, double trustDeltaOld); //! Calculated the expected residual along the double dogleg curve. /*! @@ -801,8 +800,8 @@ namespace Cantera { //! Vector containing the solution at the previous time step std::vector m_y_nm1; - //! New value of the solution time derivative - std::vector ydot_new; + //! Value of the solution time derivative at the new point that is to be considered + std::vector m_ydot_n_1; //! Vector of column scaling factors std::vector m_colScales; From b1b6dd945ca6dbcc5e2ff949bf73763a2138d006 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 13 Sep 2011 17:49:33 +0000 Subject: [PATCH 394/446] Fixed some pivoting issues in mlequ. I've encountered a stoich matrix that causes this routine to signal a singular matrix when it isn't. This iteration uses a row swapping algorithm to get rid of the problem. Next, I'll add a gauss-jordon (with full pivoting) algorithm on top of the row swapping algorithm. --- Cantera/src/equil/vcs_solve_TP.cpp | 12 +- Cantera/src/equil/vcs_util.cpp | 279 ++++++++++++++++++++++++++++- 2 files changed, 279 insertions(+), 12 deletions(-) diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index bc660e603..03a4add54 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -3595,24 +3595,24 @@ namespace VCSnonideal { if (m_debug_print_lvl >= 2) { plogf(" --- Components:"); for (j = 0; j < ncTrial; j++) { - plogf(" %3d ", j); + plogf(" %3d", j); } plogf("\n --- Components Moles:"); for (j = 0; j < ncTrial; j++) { - plogf("%10.3g", m_molNumSpecies_old[j]); + plogf(" % -10.3E", m_molNumSpecies_old[j]); } - plogf("\n --- NonComponent| Moles | "); + plogf("\n --- NonComponent| Moles |"); for (j = 0; j < ncTrial; j++) { - plogf("%-10.10s", m_speciesName[j].c_str()); + plogf(" %10.10s", m_speciesName[j].c_str()); } //plogf("| m_scSize"); plogf("\n"); for (i = 0; i < m_numRxnTot; i++) { plogf(" --- %3d ", m_indexRxnToSpecies[i]); plogf("%-10.10s", m_speciesName[m_indexRxnToSpecies[i]].c_str()); - plogf("|%10.3g|", m_molNumSpecies_old[m_indexRxnToSpecies[i]]); + plogf("|% -10.3E|", m_molNumSpecies_old[m_indexRxnToSpecies[i]]); for (j = 0; j < ncTrial; j++) { - plogf(" %6.2f", m_stoichCoeffRxnMatrix[i][j]); + plogf(" %+7.3f", m_stoichCoeffRxnMatrix[i][j]); } //plogf(" | %6.2f", m_scSize[i]); plogf("\n"); diff --git a/Cantera/src/equil/vcs_util.cpp b/Cantera/src/equil/vcs_util.cpp index 463c383d0..fa6493e4e 100644 --- a/Cantera/src/equil/vcs_util.cpp +++ b/Cantera/src/equil/vcs_util.cpp @@ -233,10 +233,8 @@ namespace VCSnonideal { } return retn; } - /*****************************************************************************/ - /*****************************************************************************/ - /*****************************************************************************/ + //==================================================================================================================== // Swap values in a std vector string /* * Switches the value of vecStrings[i1] with vecStrings[i2] @@ -250,7 +248,7 @@ namespace VCSnonideal { vstr[i2] = vstr[i1]; vstr[i1] = tmp; } - + //==================================================================================================================== // Swap values in vector of doubles /* * Switches the value of x[i1] with x[i2] @@ -264,7 +262,7 @@ namespace VCSnonideal { x[i1] = x[i2]; x[i2] = t; } - + //==================================================================================================================== // Swap values in an integer array /* * Switches the value of x[i1] with x[i2] @@ -279,6 +277,148 @@ namespace VCSnonideal { x[i2] = t; } + //==================================================================================================================== +#ifdef DEBUG_HKM + static void mlequ_matrixDump(double *c, int idem, int n) { + int i, j; + printf("vcsUtil_mlequ() MATRIX DUMP --------------------------------------------------\n"); + printf(" "); + for (j = 0; j < n; ++j) { + printf(" % 3d ", j); + } + printf("\n"); + for (j = 0; j < n; ++j) { + printf("-----------"); + } + printf("\n"); + for (i = 0; i < n; ++i) { + printf(" %3d | ", i); + for (j = 0; j < n; ++j) { + printf("% 10.3e ", c[i + j * idem]); + } + printf("\n"); + } + for (j = 0; j < n; ++j) { + printf("-----------"); + } + printf("\n"); + printf("vcsUtil_mlequ() END MATRIX DUMP --------------------------------------------------\n"); + + } +#endif + //==================================================================================================================== + //! Swap rows in the c matrix and the b rhs matrix + /*! + * @param c Matrix of size nxn, row first + * @param idem C storage dimension for the number of rows + * @param n Size of the matrix + * @param b RHS of the Ax=b problem to solve + * @param m Number of rhs to solve + * @param irowa first row to swap + * @param irowb second row to swap + */ + static void vcsUtil_swapRows(double *c, int idem, int n, double *b, int m, int irowa, int irowb) { + double t1; + int j; + if (irowa == irowb) return; + for (j = 0; j < n; j++) { + SWAP(c[irowa + j * idem], c[irowb + j * idem], t1); + } + for (j = 0; j < m; j++) { + SWAP(b[irowa + j * idem], b[irowb + j * idem], t1); + } + } + //==================================================================================================================== + //! Swap rows in the c matrix and the b rhs matrix to lower the condition number of the matrix + /*! + * @param c Matrix of size nxn, row first + * @param idem C storage dimension for the number of rows + * @param n Size of the matrix + * @param b RHS of the Ax=b problem to solve + * @param m Number of rhs to solve + */ + static void vcsUtil_mlequ_preprocess(double *c, int idem, int n, double *b, int m) { + int j = 0; + std::vector irowUsed(n, 0); + + for (j = 0; j < n; j++) { + int numNonzero = 0; + int inonzero = -1; + for (int i = 0; i < n; i++) { + if (c[i + j * idem] != 0.0) { + numNonzero++; + inonzero = i; + } + } + if (numNonzero == 1 ) { + if (inonzero != j) { + if (irowUsed[inonzero] == 0) { + vcsUtil_swapRows(c, idem, n, b, m, j, inonzero); +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + } + } + irowUsed[j] = 1; + } + } + + for (j = 0; j < n; j++) { + if (c[j + j * idem] == 0.0) { + int numNonzero = 0; + int inonzero = -1; + for (int i = 0; i < n; i++) { + if (! irowUsed[i]) { + if (c[i + j * idem] != 0.0) { + if ((c[i + i * idem] == 0.0) || (c[j + i * idem] != 0.0)) { + numNonzero++; + inonzero = i; + } + } + } + } + if (numNonzero == 1) { + if (inonzero != j) { + if (irowUsed[inonzero] == 0) { + vcsUtil_swapRows(c, idem, n, b, m, j, inonzero); +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + } + } + irowUsed[j] = 1; + } + } + } + + for (j = 0; j < n; j++) { + if (c[j + j * idem] == 0.0) { + int numNonzero = 0; + int inonzero = -1; + for (int i = 0; i < n; i++) { + if (! irowUsed[i]) { + if (c[i + j * idem] != 0.0) { + if ((c[i + i * idem] == 0.0) || (c[j + i * idem] != 0.0)) { + numNonzero++; + inonzero = i; + } + } + } + } + if (inonzero != -1) { + if (inonzero != j) { + if (irowUsed[inonzero] == 0) { + vcsUtil_swapRows(c, idem, n, b, m, j, inonzero); +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + } + } + } + } + } + } + //==================================================================================================================== // Invert an n x n matrix and solve m rhs's /* * Solve a square matrix with multiple right hand sides @@ -310,13 +450,58 @@ namespace VCSnonideal { * @param m number of rhs's */ int vcsUtil_mlequ(double *c, int idem, int n, double *b, int m) { +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + vcsUtil_mlequ_preprocess(c, idem, n, b, m); +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + int dmatrix = 0; +#ifdef DEBUG_HKM + static int s_numCalls = 0; + s_numCalls++; +#endif + int i, j, k, l; double R; if (n > idem || n <= 0) { plogf("vcsUtil_mlequ ERROR: badly dimensioned matrix: %d %d\n", n, idem); return 1; } - + +#ifdef DEBUG_HKM + for (i = 0; i < n; ++i) { + bool notFound = true; + for (j = 0; j < n; ++j) { + if (c[i + j * idem] != 0.0) { + notFound = false; + } + } + if (notFound) { + printf(" vcsUtil_mlequ ERROR(): row %d is identically zero\n", i); + } + } + for (j = 0; j < n; ++j) { + bool notFound = true; + for (i = 0; i < n; ++i) { + if (c[i + j * idem] != 0.0) { + notFound = false; + } + } + if (notFound) { + printf(" vcsUtil_mlequ ERROR(): column %d is identically zero\n", j); + } + } + // if (s_numCalls >= 32) { + // printf("vcsUtil_mlequ: we are here\n"); + // dmatrix = 1; + // } + + if (dmatrix) { + mlequ_matrixDump(c, idem, n); + } +#endif /* * Loop over the rows * -> At the end of each loop, the only nonzero entry in the column @@ -332,6 +517,12 @@ namespace VCSnonideal { if (c[k + i * idem] != 0.0) goto FOUND_PIVOT; } plogf("vcsUtil_mlequ ERROR: Encountered a zero column: %d\n", i); +#ifdef DEBUG_HKM + plogf(" call # %d\n", s_numCalls); +#endif +#ifdef DEBUG_HKM + mlequ_matrixDump(c, idem, n); +#endif return 1; FOUND_PIVOT: ; for (j = 0; j < n; ++j) c[i + j * idem] += c[k + j * idem]; @@ -358,6 +549,80 @@ namespace VCSnonideal { } return 0; } + //==================================================================================================================== + //! Linear equation solution by Gauss-Jordan elimination for multiple rhs vectors + + static int vcsUtil_gaussj(double *c, int idem, int n, double *b, int m) { + int i, j, k, l, ll; + int irow = -1; + int icol = -1; + bool needInverse = false; + double pivinv, dum; + std::vector indxc(n); + std::vector indxr(n); + std::vector ipiv(n, 0); + doublereal big = 0.0; + /* + * This is the main loop over the columns to be reduced. + */ + for (i = 0; i < n; i++) { + big = 0.0; + for (j = 0; j < n; j++) { + if (ipiv[j] != 1) { + for (k = 0; k < n; k++) { + if (ipiv[k] == 0) { + if (fabs(c[j + idem * k]) >= big) { + big = fabs(c[j + idem * k]); + irow = j; + icol = k; + } + } + } + } + } + ++(ipiv[icol]); + if (irow != icol) { + vcsUtil_swapRows(c, idem, n, b, m, irow, icol); + } + indxr[i] = irow; + indxc[i] = icol; + if (c[icol + idem * icol] == 0.0) { + plogf("vcsUtil_gaussj ERROR: Encountered a zero column: %d\n", i); + return 1; + } + pivinv = 1.0 / c[icol + idem * icol]; + c[icol + idem * icol] = 1.0; + for (l = 0; l < n; l++) { + c[icol + idem * l] *= pivinv; + } + for (l = 0; l < m; l++) { + b[icol + idem * l] *= pivinv; + } + for (ll = 0; ll < n; ll++) { + if (ll != icol) { + dum = c[ll + idem * icol]; + c[ll + idem * icol] = 0; + for (l = 0; l < n; l++) { + c[ll + idem * l] -= c[icol + idem * l] * dum; + } + for (l = 0; l < m; l++) { + b[ll + idem * l] -= b[icol + idem * l] * dum; + } + } + } + } + if (needInverse) { + for (l = n-1; l >= 0; l--) { + if (indxr[l] != indxc[l]) { + for (k = 0; k < n; k++) { + SWAP(c[k + idem * indxr[l]], c[k + idem * indxr[l]], dum); + } + } + } + } + return 0; + } + //==================================================================================================================== // Returns the value of the gas constant in the units specified by a parameter /* @@ -550,3 +815,5 @@ namespace VCSnonideal { } } + + From c58697dbd3a91311294570c1a6472c73eba46059 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 13 Sep 2011 18:32:08 +0000 Subject: [PATCH 395/446] Replaced mlequ with gaussj full pivoting in a few spots. There were no changes above numerical roundoff in the test suite. --- Cantera/src/equil/vcs_internal.h | 2 ++ Cantera/src/equil/vcs_solve_TP.cpp | 10 ++++-- Cantera/src/equil/vcs_util.cpp | 57 +++++++++++++++++++++++++++++- 3 files changed, 66 insertions(+), 3 deletions(-) diff --git a/Cantera/src/equil/vcs_internal.h b/Cantera/src/equil/vcs_internal.h index b3d87bbf7..ec897b4be 100644 --- a/Cantera/src/equil/vcs_internal.h +++ b/Cantera/src/equil/vcs_internal.h @@ -158,6 +158,8 @@ namespace VCSnonideal { */ int vcsUtil_mlequ(double *c, int idem, int n, double *b, int m); + int vcsUtil_gaussj(double *c, int idem, int n, double *b, int m); + //! Swap values in vector of doubles /*! * Switches the value of x[i1] with x[i2] diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 03a4add54..1a169dd0f 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -3517,7 +3517,11 @@ namespace VCSnonideal { * Use Gauss-Jordon block elimination to calculate * the reaction matrix, m_stoichCoeffRxnMatrix[][]. */ - j = vcsUtil_mlequ(sm, m_numElemConstraints, ncTrial, m_stoichCoeffRxnMatrix[0], m_numRxnTot); + + j = vcsUtil_gaussj(sm, m_numElemConstraints, ncTrial, m_stoichCoeffRxnMatrix[0], m_numRxnTot); + // j = vcsUtil_mlequ(sm, m_numElemConstraints, ncTrial, m_stoichCoeffRxnMatrix[0], m_numRxnTot); + + if (j == 1) { plogf("vcs_solve_TP ERROR: mlequ returned an error condition\n"); return VCS_FAILED_CONVERGENCE; @@ -3566,7 +3570,9 @@ namespace VCSnonideal { } } } - j = vcsUtil_mlequ(sm, m_numElemConstraints, ncTrial, aw, 1); + + j = vcsUtil_gaussj(sm, m_numElemConstraints, ncTrial, aw, 1); + // j = vcsUtil_mlequ(sm, m_numElemConstraints, ncTrial, aw, 1); if (j == 1) { plogf("vcs_solve_TP ERROR: mlequ returned an error condition\n"); return VCS_FAILED_CONVERGENCE; diff --git a/Cantera/src/equil/vcs_util.cpp b/Cantera/src/equil/vcs_util.cpp index fa6493e4e..524ba39b1 100644 --- a/Cantera/src/equil/vcs_util.cpp +++ b/Cantera/src/equil/vcs_util.cpp @@ -551,13 +551,57 @@ namespace VCSnonideal { } //==================================================================================================================== //! Linear equation solution by Gauss-Jordan elimination for multiple rhs vectors + /* + * Solve a square matrix with multiple right hand sides + * + * \f[ + * C X + B = 0; + * \f] + * + * This routine uses Gauss elimination and is optimized for the solution + * of lots of rhs's. + * + * @return Routine returns an integer representing success: + * - 1 : Matrix is singluar + * - 0 : solution is OK + * The solution x[] is returned in the matrix b. + * + * @param c Matrix to be inverted. c is in fortran format, i.e., rows + * are the inner loop. Row numbers equal to idem. + * c[i+j*idem] = c_i_j = Matrix to be inverted: i = row number + * j = column number + * @param idem number of row dimensions in c + * @param n Number of rows and columns in c + * @param b Multiple RHS. Note, b is actually the negative of + * most formulations. Row numbers equal to idem. + * b[i+j*idem] = b_i_j = vectors of rhs's: i = row number + * j = column number + * (each column is a new rhs) + * @param m number of rhs's + */ + int vcsUtil_gaussj(double *c, int idem, int n, double *b, int m) { - static int vcsUtil_gaussj(double *c, int idem, int n, double *b, int m) { int i, j, k, l, ll; int irow = -1; int icol = -1; bool needInverse = false; double pivinv, dum; +#ifdef DEBUG_HKM + static int s_numCalls = 0; + s_numCalls++; +#endif +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + /* + * Preprocess the problem + */ + vcsUtil_mlequ_preprocess(c, idem, n, b, m); + +#ifdef DEBUG_HKM + // mlequ_matrixDump(c, idem, n); +#endif + std::vector indxc(n); std::vector indxr(n); std::vector ipiv(n, 0); @@ -620,6 +664,17 @@ namespace VCSnonideal { } } } + + + /* + * The negative in the last expression is due to the form of B upon + * input + */ + for (i = 0; i < n; ++i) { + for (j = 0; j < m; ++j) { + b[i + j * idem] = -b[i + j * idem]; + } + } return 0; } //==================================================================================================================== From cf730962a668c2ed047d1e77f25fb60f94dba23b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 13 Sep 2011 23:32:29 +0000 Subject: [PATCH 396/446] Protected against sundials not being compiled in --- Cantera/src/numerics/DAE_solvers.cpp | 4 ++-- Cantera/src/numerics/IDA_Solver.cpp | 5 +++++ Cantera/src/numerics/IDA_Solver.h | 2 ++ 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/Cantera/src/numerics/DAE_solvers.cpp b/Cantera/src/numerics/DAE_solvers.cpp index db3b8b339..02b58c5fe 100644 --- a/Cantera/src/numerics/DAE_solvers.cpp +++ b/Cantera/src/numerics/DAE_solvers.cpp @@ -12,12 +12,12 @@ namespace Cantera { - DAE_Solver* newDAE_Solver(string itype, ResidJacEval& f) { + DAE_Solver* newDAE_Solver(std::string itype, ResidJacEval& f) { if (itype == "IDA") { #ifdef HAS_SUNDIALS return new IDA_Solver(f); #else - raise CanteraError("newDAE_Solver","IDA solver requires sundials" + throw CanteraError("newDAE_Solver","IDA solver requires sundials" " package, but Cantera was not built with sundials."); #endif } diff --git a/Cantera/src/numerics/IDA_Solver.cpp b/Cantera/src/numerics/IDA_Solver.cpp index 7c269b040..0ff4eadce 100644 --- a/Cantera/src/numerics/IDA_Solver.cpp +++ b/Cantera/src/numerics/IDA_Solver.cpp @@ -10,6 +10,8 @@ #include +#ifdef HAS_SUNDIALS + #ifdef SUNDIALS_VERSION_22 #include #include @@ -30,6 +32,8 @@ using namespace std; + + inline static N_Vector nv(void* x) { return reinterpret_cast(x); } @@ -645,3 +649,4 @@ namespace Cantera { //==================================================================================================================== } +#endif diff --git a/Cantera/src/numerics/IDA_Solver.h b/Cantera/src/numerics/IDA_Solver.h index 928728969..7102c58ad 100644 --- a/Cantera/src/numerics/IDA_Solver.h +++ b/Cantera/src/numerics/IDA_Solver.h @@ -21,6 +21,7 @@ #include "DAE_Solver.h" #include "ctexceptions.h" +#ifdef HAS_SUNDIALS #ifdef SUNDIALS_VERSION_22 #include @@ -353,4 +354,5 @@ namespace Cantera { } #endif +#endif From 49ad882efc81f92189a818a5cc79e69c38bd9a59 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 20 Sep 2011 23:32:53 +0000 Subject: [PATCH 397/446] Added derivatives of molar volume wrt T and P to the main interface. --- Cantera/src/thermo/HMWSoln.cpp | 11 ++-- Cantera/src/thermo/HMWSoln_input.cpp | 77 +++++++++++++++++++++++++++- Cantera/src/thermo/SurfPhase.cpp | 2 + Cantera/src/thermo/ThermoPhase.h | 53 ++++++++++++++++++- 4 files changed, 135 insertions(+), 8 deletions(-) diff --git a/Cantera/src/thermo/HMWSoln.cpp b/Cantera/src/thermo/HMWSoln.cpp index 5147b705d..9059b492b 100644 --- a/Cantera/src/thermo/HMWSoln.cpp +++ b/Cantera/src/thermo/HMWSoln.cpp @@ -738,10 +738,13 @@ namespace Cantera { // Molar heat capacity at constant volume. Units: J/kmol/K. doublereal HMWSoln::cv_mole() const { - //getPartialMolarCv(m_tmpV.begin()); - //return mean_X(m_tmpV.begin()); - err("not implemented"); - return 0.0; + double kappa_t = isothermalCompressibility(); + double beta = thermalExpansionCoeff(); + double cp = cp_mole(); + double tt = temperature(); + double molarV = molarVolume(); + double cv = cp - beta * beta * tt * molarV / kappa_t; + return cv; } // diff --git a/Cantera/src/thermo/HMWSoln_input.cpp b/Cantera/src/thermo/HMWSoln_input.cpp index f4380c784..5faecbca2 100644 --- a/Cantera/src/thermo/HMWSoln_input.cpp +++ b/Cantera/src/thermo/HMWSoln_input.cpp @@ -1657,15 +1657,88 @@ namespace Cantera { MolalityVPSSTP::initThermoXML(phaseNode, id); /* - * Lastly set the state + * Lastly calculate the charge balance and then add stuff until the charges compensate */ + + vector_fp mf(m_kk, 0.0); + getMoleFractions(DATA_PTR(mf)); + bool notDone = true; + + do { + double sum = 0.0; + int kMaxC = -1; + double MaxC = 0.0; + for (int k = 0; k < m_kk; k++) { + sum += mf[k] * m_speciesCharge[k]; + if (fabs(mf[k] * m_speciesCharge[k]) > MaxC) { + kMaxC = k; + } + } + int kHp = speciesIndex("H+"); + int kOHm = speciesIndex("OH-"); + + + if (fabs(sum) > 1.0E-30) { + if (kHp >= 0) { + if (mf[kHp] > sum * 1.1) { + mf[kHp] -= sum; + mf[0] += sum; + notDone = false; + } else { + if (sum > 0.0) { + mf[kHp] *= 0.5; + mf[0] += mf[kHp]; + sum -= mf[kHp]; + } + } + } + if (notDone) { + if (kOHm >= 0) { + if (mf[kOHm] > -sum * 1.1) { + mf[kOHm] += sum; + mf[0] -= sum; + notDone = false; + } else { + if (sum < 0.0) { + mf[kOHm] *= 0.5; + mf[0] += mf[kOHm]; + sum += mf[kOHm]; + } + } + } + if (notDone) { + if (kMaxC >= 0) { + if (mf[kMaxC] > (1.1 * sum / m_speciesCharge[kMaxC])) { + mf[kMaxC] -= sum / m_speciesCharge[kMaxC]; + mf[0] += sum / m_speciesCharge[kMaxC]; + } else { + mf[kMaxC] *= 0.5; + mf[0] += mf[kMaxC]; + notDone = true; + } + } + } + } + setMoleFractions(DATA_PTR(mf)); + } else { + notDone = false; + } + } while (notDone); + + + + + + + + // if (phaseNode.hasChild("state")) { // XML_Node& stateNode = phaseNode.child("state"); // setStateFromXML(stateNode); //} } - + //==================================================================================================================== // Precalculate the IMS Cutoff parameters for typeCutoff = 2 void HMWSoln::calcIMSCutoffParams_() { IMS_afCut_ = 1.0 / (std::exp(1.0) * IMS_gamma_k_min_); diff --git a/Cantera/src/thermo/SurfPhase.cpp b/Cantera/src/thermo/SurfPhase.cpp index acd506062..ab0ecc4c7 100644 --- a/Cantera/src/thermo/SurfPhase.cpp +++ b/Cantera/src/thermo/SurfPhase.cpp @@ -211,6 +211,8 @@ namespace Cantera { } } + // HKM 9/1/11 The partial molar volumes returned here are really partial molar areas. + // Partial molar volumes for this phase should actually be equal to zero. void SurfPhase::getPartialMolarVolumes(doublereal* vbar) const { getStandardVolumes(vbar); } diff --git a/Cantera/src/thermo/ThermoPhase.h b/Cantera/src/thermo/ThermoPhase.h index 758919b3e..322a749f1 100644 --- a/Cantera/src/thermo/ThermoPhase.h +++ b/Cantera/src/thermo/ThermoPhase.h @@ -1264,7 +1264,31 @@ namespace Cantera { virtual void getPartialMolarVolumes(doublereal* vbar) const { err("getPartialMolarVolumes"); } - + + //! Return an array of derivatives of partial molar volumes wrt temperature for the + //! species in the mixture. Units: m^3/kmol. + /*! + * The derivative is at constant pressure + * + * @param d_vbar_dT Output vector of derivatives of species partial molar volumes wrt T. + * Length = m_kk. units are m^3/kmol/K. + */ + virtual void getdPartialMolarVolumes_dT(doublereal* d_vbar_dT) const { + err("getdPartialMolarVolumes_dT"); + } + + //! Return an array of derivatives of partial molar volumes wrt pressure for the + //! species in the mixture. Units: m^3/kmol. + /*! + * The derivative is at constant temperature + * + * @param d_vbar_dP Output vector of derivatives of species partial molar volumes wrt P. + * Length = m_kk. units are m^3/kmol/Pa. + */ + virtual void getdPartialMolarVolumes_dP(doublereal* d_vbar_dP) const { + err("getdPartialMolarVolumes_dP"); + } + //@} /// @name Properties of the Standard State of the Species in the Solution //@{ @@ -1357,11 +1381,36 @@ namespace Cantera { err("getStandardVolumes"); } + //! Get the derivative of the molar volumes of the species standard states wrt temperature at the current + //! T and P of the solution. + /*! + * The derivative is at constant pressure + * units = m^3 / kmol / K + * + * @param d_vol_dT Output vector containing derivatives of standard state volumes wrt T + * Length: m_kk. + */ + virtual void getdStandardVolumes_dT(doublereal *d_vol_dT) const { + err("getdStandardVolumes_dT"); + } + + //! Get the derivative molar volumes of the species standard states wrt pressure at the current + //! T and P of the solution. + /*! + * The derivative is at constant temperature. + * units = m^3 / kmol / Pa + * + * @param d_vol_dP Output vector containing the derivative of standard state volumes wrt P. + * Length: m_kk. + */ + virtual void getdStandardVolumes_dP(doublereal *d_vol_dP) const { + err("getdStandardVolumes_dP"); + } + //@} /// @name Thermodynamic Values for the Species Reference States //@{ - //! Returns the vector of nondimensional //! enthalpies of the reference state at the current temperature //! of the solution and the reference pressure for the species. From 626660102c0e92e511b9eb0ee00a10e03d015bbb Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 20 Sep 2011 23:41:17 +0000 Subject: [PATCH 398/446] Added a manual check for the satisfaction of Reaction Matrix's ability to conserve elements. --- Cantera/src/equil/vcs_solve_TP.cpp | 50 ++++++++++++++++++++++++++++++ Cantera/src/equil/vcs_util.cpp | 4 +-- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp index 1a169dd0f..59c4e9824 100644 --- a/Cantera/src/equil/vcs_solve_TP.cpp +++ b/Cantera/src/equil/vcs_solve_TP.cpp @@ -3623,9 +3623,59 @@ namespace VCSnonideal { //plogf(" | %6.2f", m_scSize[i]); plogf("\n"); } + + + /* + * Manual check on the satisfaction of the reaction matrix's ability + * to conserve elements + */ + double sum; + double sumMax = -1.0; + int iMax = -1; + int jMax = -1; + int n; + for (i = 0; i < m_numRxnTot; ++i) { + k = m_indexRxnToSpecies[i]; + for (j = 0; j < ncTrial; ++j) { + if (j == jlose) { + sum = m_formulaMatrix[juse][k]; + for (n = 0; n < ncTrial; n++) { + double numElements = m_formulaMatrix[juse][n]; + double coeff = m_stoichCoeffRxnMatrix[i][n]; + sum += coeff * numElements; + } + } else { + sum = m_formulaMatrix[j][k]; + for (n = 0; n < ncTrial; n++) { + double numElements = m_formulaMatrix[j][n]; + double coeff = m_stoichCoeffRxnMatrix[i][n]; + sum += coeff * numElements; + } + } + if (fabs(sum) > sumMax) { + sumMax = fabs(sum); + iMax = i; + jMax = j; + if (j == jlose) { + jMax = juse; + } + } + if (fabs(sum) > 1.0E-6) { + printf("we have a prob\n"); + exit(-1); + } + } + } + plogf(" --- largest error in Stoich coeff = %g at rxn = %d ", sumMax, iMax); + plogf("%-10.10s", m_speciesName[m_indexRxnToSpecies[iMax]].c_str()); + plogf(" element = %d ", jMax); + plogf("%-5.5s", m_elementName[jMax].c_str()); + plogf("\n"); plogf(" "); for(i=0; i<77; i++) plogf("-"); plogf("\n"); } #endif + + /* **************************************************** */ /* **** EVALUATE DELTA N VALUES *********************** */ /* **************************************************** */ diff --git a/Cantera/src/equil/vcs_util.cpp b/Cantera/src/equil/vcs_util.cpp index 524ba39b1..61e79511e 100644 --- a/Cantera/src/equil/vcs_util.cpp +++ b/Cantera/src/equil/vcs_util.cpp @@ -550,7 +550,7 @@ namespace VCSnonideal { return 0; } //==================================================================================================================== - //! Linear equation solution by Gauss-Jordan elimination for multiple rhs vectors + // Linear equation solution by Gauss-Jordan elimination for multiple rhs vectors /* * Solve a square matrix with multiple right hand sides * @@ -558,7 +558,7 @@ namespace VCSnonideal { * C X + B = 0; * \f] * - * This routine uses Gauss elimination and is optimized for the solution + * This routine uses Gauss-Jordan elimination with full pivoting and is optimized for the solution * of lots of rhs's. * * @return Routine returns an integer representing success: From 436bed3868a639ee2f59e16effb44f42ecf8f43d Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Sep 2011 01:03:45 +0000 Subject: [PATCH 399/446] Added doxygen fixes --- Cantera/src/thermo/Constituents.h | 4 ++++ Cantera/src/thermo/Elements.h | 3 +-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/Cantera/src/thermo/Constituents.h b/Cantera/src/thermo/Constituents.h index 3a31522c3..3f4e1b3fd 100644 --- a/Cantera/src/thermo/Constituents.h +++ b/Cantera/src/thermo/Constituents.h @@ -191,6 +191,8 @@ namespace Cantera { * the value ENTROPY298_UNKNOWN, which is * interpreted as an unknown, and if used * will cause Cantera to throw an error. + * @param elem_type Specifies the type of the element constraint equation. This defaults + * to CT_ELEM_TYPE_ABSPOS, i.e., an element. */ void addUniqueElement(const std::string& symbol, doublereal weight, int atomicNumber = 0, @@ -230,6 +232,8 @@ namespace Cantera { * the value ENTROPY298_UNKNOWN, which is * interpreted as an unknown, and if used * will cause Cantera to throw an error. + * @param elem_type Specifies the type of the element constraint equation. This defaults + * to CT_ELEM_TYPE_ABSPOS, i.e., an element. */ int addUniqueElementAfterFreeze(const std::string& symbol, doublereal weight, int atomicNumber, doublereal entropy298 = ENTROPY298_UNKNOWN, int elem_type = CT_ELEM_TYPE_ABSPOS); diff --git a/Cantera/src/thermo/Elements.h b/Cantera/src/thermo/Elements.h index 8f738acad..f0c46cb18 100644 --- a/Cantera/src/thermo/Elements.h +++ b/Cantera/src/thermo/Elements.h @@ -59,8 +59,7 @@ namespace Cantera { */ #define CT_ELEM_TYPE_CHARGENEUTRALITY 2 - //! Constraint associated with maintaing a fixed lattice stoichiometry int eh - //! solids + //! Constraint associated with maintaing a fixed lattice stoichiometry in a solid /*! * The constraint may have positive or negative values. The lattice 0 species will * have negative values while higher lattices will have positive values From fd1e408f25452c3c3f011fd5907bb293e788c136 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Sep 2011 16:18:26 +0000 Subject: [PATCH 400/446] Doxygen change Changed a function to be const --- Cantera/src/thermo/Elements.cpp | 10 ++++++++-- Cantera/src/thermo/Elements.h | 6 ++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/Cantera/src/thermo/Elements.cpp b/Cantera/src/thermo/Elements.cpp index 7641a2365..1c0357ec2 100644 --- a/Cantera/src/thermo/Elements.cpp +++ b/Cantera/src/thermo/Elements.cpp @@ -548,7 +548,13 @@ namespace Cantera { addUniqueElement(symbol); } } - + + // True if freezeElements has been called. + bool Elements::elementsFrozen() const + { + return m_elementsFrozen; + } + /* * clear() * @@ -562,7 +568,7 @@ namespace Cantera { m_elem_type.resize(0); m_elementsFrozen = false; } - + /* * ready(): * diff --git a/Cantera/src/thermo/Elements.h b/Cantera/src/thermo/Elements.h index f0c46cb18..c4a3ec499 100644 --- a/Cantera/src/thermo/Elements.h +++ b/Cantera/src/thermo/Elements.h @@ -294,6 +294,8 @@ namespace Cantera { * The default is to specify an ENTROPY298_UNKNOWN value, * which will cause a throw error if its ever * needed. + * @param elem_type New elem type to be assigned. + * The default is a regular element, CT_ELEM_TYPE_ABSPOS */ void addUniqueElement(const std::string& symbol, doublereal weight = -12345.0, int atomicNumber = 0, @@ -316,8 +318,8 @@ namespace Cantera { //! Prohibit addition of more elements, and prepare to add species. void freezeElements(); - /// True if freezeElements has been called. - bool elementsFrozen() { return m_elementsFrozen; } + //! True if freezeElements has been called. + bool elementsFrozen() const; /// Remove all elements void clear(); From 7bb60ff5960c3be083152c4685c8409235ff8d31 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Sep 2011 16:36:49 +0000 Subject: [PATCH 401/446] Doxygen changes. --- Cantera/src/thermo/LatticeSolidPhase.h | 30 ++++++++++++++------------ 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/Cantera/src/thermo/LatticeSolidPhase.h b/Cantera/src/thermo/LatticeSolidPhase.h index 961c42316..c9c7c47fa 100644 --- a/Cantera/src/thermo/LatticeSolidPhase.h +++ b/Cantera/src/thermo/LatticeSolidPhase.h @@ -106,7 +106,7 @@ namespace Cantera { * * * \f[ - * V_i = \sum_k{ \X_k V_k} + * V_i = \sum_k{ X_k V_k} * \f] * * where k is a species in the ith sublattice. @@ -325,7 +325,7 @@ namespace Cantera { //! Set the mole fractions to the specified values, and then //! normalize them so that they sum to 1.0 for each of the subphases - /* + /*! * On input, the mole fraction vector is assumed to sum to one for each of the sublattices. The sublattices * are updated with this mole fraction vector. The mole fractions are also storred within this object, after * they are normalized to one by dividing by the number of sublattices. @@ -567,29 +567,31 @@ namespace Cantera { /// @name Thermodynamic Values for the Species Reference States -------------------- //@{ - /** - * Returns the vector of nondimensional - * enthalpies of the reference state at the current temperature - * of the solution and the reference pressure for the species. - * + //! Returns the vector of nondimensional enthalpies of the reference state at the current + //! temperature of the solution and the reference pressure for the species. + /*! * This function fills in its one entry in hrt[] by calling * the underlying species thermo function for the * dimensionless gibbs free energy, calculated from the * dimensionless enthalpy and entropy. + * + * @param grt Vector of dimensionless Gibbs free energies of the reference state + * length = m_kk */ virtual void getGibbs_RT_ref(doublereal *grt) const; - /** - * Returns the vector of the - * gibbs function of the reference state at the current temperature - * of the solution and the reference pressure for the species. + //! Returns the vector of the gibbs function of the reference state at the current + //! temperatureof the solution and the reference pressure for the species. + /*! * units = J/kmol * - * This function fills in its one entry in g[] by calling - * the underlying species thermo functions for the - * gibbs free energy, calculated from enthalpy and the + * This function fills in its one entry in g[] by calling the underlying species thermo + * functions for the gibbs free energy, calculated from enthalpy and the * entropy, and the multiplying by RT. + * + * @param g Vector of Gibbs free energies of the reference state. + * length = m_kk */ virtual void getGibbs_ref(doublereal *g) const; From 445adce8fc2bc1f789180bb9e29b196d35ed1f87 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Sep 2011 16:40:51 +0000 Subject: [PATCH 402/446] Doxygen changes --- Cantera/src/numerics/NonlinearSolver.cpp | 285 +++++++++++++++-------- Cantera/src/numerics/NonlinearSolver.h | 68 ++++-- Cantera/src/numerics/ResidJacEval.h | 3 +- Cantera/src/numerics/RootFind.h | 2 + 4 files changed, 248 insertions(+), 110 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 4826270dd..bddd33567 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -147,6 +147,7 @@ namespace Cantera { lambdaStar_(0.0), Jd_(0), deltaX_trust_(0), + norm_deltaX_trust_(0.0), trustDelta_(1.0), Nuu_(0.0), dist_R0_(0.0), @@ -251,6 +252,7 @@ namespace Cantera { lambdaStar_(0.0), Jd_(0), deltaX_trust_(0), + norm_deltaX_trust_(0.0), trustDelta_(1.0), Nuu_(0.0), dist_R0_(0.0), @@ -331,6 +333,7 @@ namespace Cantera { lambdaStar_ = right.lambdaStar_; Jd_ = right.Jd_; deltaX_trust_ = right.deltaX_trust_; + norm_deltaX_trust_ = right.norm_deltaX_trust_; trustDelta_ = right.trustDelta_; Nuu_ = right.Nuu_; @@ -439,8 +442,7 @@ namespace Cantera { const int num_entries = printLargest; - printf("\t\t "); - print_line("-", 90); + printf("\t\t "); print_line("-", 90); printf("\t\t solnErrorNorm(): "); if (title) { printf("%s", title); @@ -452,12 +454,10 @@ namespace Cantera { doublereal dmax1, normContrib; int j; int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - printf("\t\t Printout of Largest Contributors:\n"); - printf("\t\t (damp = %g)\n", dampFactor); - printf("\t\t I weightdeltaY/sqtN| deltaY " + printf("\t\t Printout of Largest Contributors: (damp = %g)\n", dampFactor); + printf("\t\t I weightdeltaY/sqtN| deltaY " "ysolnOld ysolnNew Soln_Weights\n"); - printf("\t\t "); - print_line("-", 90); + printf("\t\t "); print_line("-", 88); for (int jnum = 0; jnum < num_entries; jnum++) { dmax1 = -1.0; @@ -479,13 +479,12 @@ namespace Cantera { if (i >= 0) { error = delta_y[i] / m_ewt[i]; normContrib = sqrt(error * error); - printf("\t\t %4d %12.4e | %12.4e %12.4e %12.4e %12.4e\n", i, normContrib/sqrt((double)neq_), + printf("\t\t %4d %12.4e | %12.4e %12.4e %12.4e %12.4e\n", i, normContrib/sqrt((double)neq_), delta_y[i], m_y_n_curr[i], m_y_n_curr[i] + dampFactor * delta_y[i], m_ewt[i]); } } - printf("\t\t "); - print_line("-", 90); + printf("\t\t "); print_line("-", 90); mdp::mdp_safe_free((void **) &imax); } } @@ -525,22 +524,30 @@ namespace Cantera { int j; int *imax = mdp::mdp_alloc_int_1(num_entries, -1); - - printf("\t "); - print_line("-", 90); - printf("\t\t residErrorNorm():"); - if (title) { - printf(" %s ", title); - } else { - printf(" residual L2 norm "); + if (m_print_flag >= 4 && m_print_flag <= 5) { + printf("\t "); + print_line("-", 90); + printf("\t\t residErrorNorm():"); + if (title) { + printf(" %s ", title); + } else { + printf(" residual L2 norm "); + } + printf("= %12.4E\n", sum_norm); } - printf("= %12.4E\n", sum_norm); - if (m_print_flag >= 6) { - printf("\t\t Printout of Largest Contributors to norm:\n"); - printf("\t\t I |Resid/ResWt| UnsclRes ResWt | y_curr\n"); - printf("\t\t "); - print_line("-", 80); + printf("\t\t "); print_line("-", 90); + printf("\t\t residErrorNorm(): "); + if (title) { + printf(" %s ", title); + } else { + printf(" residual L2 norm "); + } + printf("= %12.4E\n", sum_norm); + printf("\t\t Printout of Largest Contributors to norm:\n"); + printf("\t\t I |Resid/ResWt| UnsclRes ResWt | y_curr\n"); + printf("\t\t "); + print_line("-", 88); for (int jnum = 0; jnum < num_entries; jnum++) { dmax1 = -1.0; for (i = 0; i < neq_; i++) { @@ -561,12 +568,12 @@ namespace Cantera { if (i >= 0) { error = resid[i] / m_residWts[i]; normContrib = sqrt(error * error); - printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e\n", i, normContrib, resid[i], m_residWts[i], y[i]); + printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e\n", i, normContrib, resid[i], m_residWts[i], y[i]); } } printf("\t\t "); - print_line("-", 80); + print_line("-", 90); } mdp::mdp_safe_free((void **) &imax); } @@ -916,7 +923,7 @@ namespace Cantera { if (cond < 1.0E7) { doNewton = true; if (m_print_flag >= 3) { - printf("\t\t\tdoAffineNewtonSolve: Condition number = %g during regular solve\n", cond); + printf("\t\t doAffineNewtonSolve: Condition number = %g during regular solve\n", cond); } /* @@ -925,7 +932,7 @@ namespace Cantera { int info = jac.solve(DATA_PTR(delta_y)); if (info) { if (m_print_flag >= 2) { - printf("\t\t\tNonlinearSolver::doAffineSolve QRSolve returned INFO = %d. Switching to Hessian solve\n", info); + printf("\t\t NonlinearSolver::doAffineSolve() ERROR: QRSolve returned INFO = %d. Switching to Hessian solve\n", info); } doHessian = true; newtonGood = false; @@ -943,7 +950,7 @@ namespace Cantera { doHessian = true; newtonGood = false; if (m_print_flag >= 3) { - printf("\t\t\tdoAffineNewtonSolve: Condition number too large, %g. Doing a Hessian solve \n", cond); + printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g. Doing a Hessian solve \n", cond); } } @@ -1036,7 +1043,7 @@ namespace Cantera { ct_dpotrf(ctlapack::UpperTriangular, neq_, &(*(Hessian_.begin())), neq_, info); if (info) { if (m_print_flag >= 2) { - printf("\t\t\tNonlinearSolver::doAffineSolve DPOTRF returned INFO = %d\n", info); + printf("\t\t NonlinearSolver::doAffineSolve() ERROR: DPOTRF returned INFO = %d\n", info); } return info; } @@ -1077,7 +1084,7 @@ namespace Cantera { ct_dpotrs(ctlapack::UpperTriangular, neq_, 1,&(*(Hessian_.begin())), neq_, delta_y, neq_, info); if (info) { if (m_print_flag >= 2) { - printf("\t\t\tNonlinearSolver::doAffineSolve DPOTRS returned INFO = %d\n", info); + printf("\t\t NonlinearSolver::doAffineSolve() ERROR: DPOTRS returned INFO = %d\n", info); } return info; } @@ -1092,13 +1099,13 @@ namespace Cantera { if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("\t\t\t Comparison between Hessian deltaX and newton deltaX\n"); - printf("\t\t\t i Hessian+Junk Newton \n"); - printf("\t\t\t--------------------------------------------------------\n"); + printf("\t\t Comparison between Hessian deltaX and newton deltaX\n"); + printf("\t\t I Hessian+Junk Newton \n"); + printf("\t\t --------------------------------------------------------\n"); for (int i =0; i < neq_; i++) { - printf("\t\t\t%3d %12.5g %12.5g\n", i, delta_y[i], delyNewton[i]); + printf("\t\t %3d %12.5g %12.5g\n", i, delta_y[i], delyNewton[i]); } - printf("\t\t\t--------------------------------------------------------\n"); + printf("\t\t --------------------------------------------------------\n"); } @@ -1264,7 +1271,7 @@ namespace Cantera { normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 0); } if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("\t\t\tdoCauchyPointSolve: Steepest descent to Cauchy point: \n"); + printf("\t\t doCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid0); printf("\t\t\t Rpred = %g\n", residCauchy); printf("\t\t\t Rjd = %g\n", RJd_norm_); @@ -1330,10 +1337,10 @@ namespace Cantera { * The steepest direction is always largest even when there are variable solution weights */ if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); - printf("descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); - printf("descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); - printf("descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); + printf("\t\t descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); + printf("\t\t descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); + printf("\t\t descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); + printf("\t\t descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); } } @@ -1429,7 +1436,7 @@ namespace Cantera { * @return Returns the expected value of the residual at that point according to the quadratic model. * The residual at the newton point will always be zero. */ - double NonlinearSolver::expectedResidLeg(int leg, double alpha) const { + doublereal NonlinearSolver::expectedResidLeg(int leg, doublereal alpha) const { double resD2, res2, resNorm; double normResid02 = m_normResid0 * m_normResid0 * neq_; @@ -1489,15 +1496,21 @@ namespace Cantera { * @param time_curr INPUT current time * @param ydot0 INPUT Current value of the derivative of the solution vector for non-time dependent * determinations - * @param ydot1 INPUT Time derivate of solution at the conditions which are evalulated + * @param legBest OUTPUT leg of the dogleg that gives the lowest residual + * @param alphaBest OUTPUT distance along dogleg for best result. */ - void NonlinearSolver::residualComparisonLeg(const double time_curr, const double * const ydot0) const { + void NonlinearSolver::residualComparisonLeg(const doublereal time_curr, const doublereal * const ydot0, int &legBest, + doublereal &alphaBest) const { double *y1 = DATA_PTR(m_wksp); double *ydot1 = DATA_PTR(m_wksp_2); double sLen; + double alpha; + + double residSteepBest = 1.0E300; + double residSteepLinBest = 0.0; if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { - printf(" residualComparisonLeg() \n"); - printf(" Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); + printf("\t\t residualComparisonLeg() \n"); + printf("\t\t Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); } // First compare at 1/4 along SD curve std::vector alphaT; @@ -1509,7 +1522,7 @@ namespace Cantera { alphaT.push_back(0.75); alphaT.push_back(1.0); for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { - double alpha = alphaT[iteration]; + alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { y1[i] = m_y_n_curr[i] + alpha * deltaX_CP_[i]; } @@ -1530,10 +1543,16 @@ namespace Cantera { double residSteep = residErrorNorm(DATA_PTR(m_resid)); double residSteepLin = expectedResidLeg(0, alpha); + if (residSteep < residSteepBest) { + legBest = 0; + alphaBest = alpha; + residSteepBest = residSteep; + residSteepLinBest = residSteepLin; + } double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); + printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); } } @@ -1563,10 +1582,16 @@ namespace Cantera { double residSteep = residErrorNorm(DATA_PTR(m_resid)); double residSteepLin = expectedResidLeg(1, alpha); + if (residSteep < residSteepBest) { + legBest = 1; + alphaBest = alpha; + residSteepBest = residSteep; + residSteepLinBest = residSteepLin; + } double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); + printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); } } @@ -1593,20 +1618,46 @@ namespace Cantera { double residSteep = residErrorNorm(DATA_PTR(m_resid)); double residSteepLin = expectedResidLeg(2, alpha); - + if (residSteep < residSteepBest) { + legBest = 2; + alphaBest = alpha; + residSteepBest = residSteep; + residSteepLinBest = residSteepLin; + } double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { - printf(" (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); + printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); + } + } + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + printf("\t\t Best Result: \n"); + double relFit = (residSteepBest - residSteepLinBest) / (fabs(residSteepLinBest) + 1.0E-10); + if (m_print_flag <= 6) { + printf("\t\t Leg %2d alpha %5g: NonlinResid = %g LinResid = %g, relfit = %g\n", + legBest, alphaBest, residSteepBest, residSteepLinBest, relFit); + } else { + if (legBest == 0) { + sLen = alpha * solnErrorNorm(DATA_PTR(deltaX_CP_)); + } else if (legBest == 1) { + for (int i = 0; i < neq_; i++) { + y1[i] = (1.0 - alphaBest) * deltaX_CP_[i]; + y1[i] += alphaBest * Nuu_ * deltaX_Newton_[i]; + } + sLen = solnErrorNorm(DATA_PTR(y1)); + } else { + sLen = ( Nuu_ + alpha * (1.0 - Nuu_)) * solnErrorNorm(DATA_PTR(deltaX_Newton_)); + } + printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", legBest, alphaBest, sLen, + residSteepBest, residSteepLinBest , relFit); } } - } //==================================================================================================================== double NonlinearSolver::trustRegionLength() const { - double dlen = solnErrorNorm(DATA_PTR(deltaX_trust_)); - return (trustDelta_ * dlen); + norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); + return (trustDelta_ * norm_deltaX_trust_); } //==================================================================================================================== void NonlinearSolver::setDefaultDeltaBoundsMagnitudes() @@ -1789,15 +1840,16 @@ namespace Cantera { // Final renormalization. - trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); + norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); double sum = trustNormGoal / trustNorm; for (int i = 0; i < neq_; i++) { deltaX_trust_[i] = deltaX_trust_[i] * sum; - } + } + norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); trustDelta_ = 1.0; if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", + printf("\t\t calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", trustNorm, trustNormGoal); } } @@ -1810,13 +1862,13 @@ namespace Cantera { { double cpd = calcTrustDistance(deltaX_CP_); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } trustDelta_ = trustDelta_ * cpd; calcTrustVector(); cpd = calcTrustDistance(deltaX_CP_); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } } @@ -2213,16 +2265,21 @@ namespace Cantera { } return -2; } - //==================================================================================================================== - - - // Using Damping along a dog leg to calculate the next step - /*! + // Damp using the dog leg approach + /* + * + * @param time_curr INPUT Current value of the time + * @param y_n_curr INPUT Current value of the solution vector + * @param ydot_n_curr INPUT Current value of the derivative of the solution vector + * @param step_1 INPUT First trial step for the first iteration + * @param y_n_1 INPUT First trial value of the solution vector + * @param ydot_n_1 INPUT First trial value of the derivative of the solution vector + * @param s1 OUTPUT Norm of the vector step_1 + * @param jac INPUT jacobian + * @param num_backtracks OUTPUT number of backtracks taken in the current damping step * * - * @param step0 (output) On return this contains the suggested step vector for the current iteration - * * @return 1 Successful step was taken. The predicted residual norm is less than one * 2 Successful step: Next step's norm is less than 0.8 * 3 Success: The final residual is less than 1.0 @@ -2233,11 +2290,10 @@ namespace Cantera { * 0 Uncertain Success: s1 is about the same as s0 * -2 Unsuccessful step. */ - int NonlinearSolver::dampDogLeg(const doublereal time_curr, const double* y_n_curr, + int NonlinearSolver::dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, const doublereal *ydot_n_curr, std::vector & step_1, - double* const y_n_1, double* const ydot_n_1, double* stepLastGood, - double& s1, SquareMatrix& jac, bool writetitle, - int& num_backtracks) + doublereal* const y_n_1, doublereal* const ydot_n_1, + doublereal& s1, SquareMatrix& jac, int& num_backtracks) { double lambda; double alpha; @@ -2247,6 +2303,7 @@ namespace Cantera { int retn = 0; bool haveASuccess = false; double trustDeltaOld = trustDelta_; + doublereal* stepLastGood = DATA_PTR(m_wksp); //-------------------------------------------- // Attempt damped step //-------------------------------------------- @@ -2563,8 +2620,10 @@ namespace Cantera { int m = 0; bool forceNewJac = false; doublereal s1=1.e30; - - +#ifdef DEBUG_DOGLEG + int legBest; + doublereal alphaBest; +#endif // std::vector y_curr(neq_, 0.0); // std::vector ydot_curr(neq_, 0.0); std::vector stp(neq_, 0.0); @@ -2613,6 +2672,12 @@ namespace Cantera { m_numTotalNewtIts++; num_newt_its++; + if (m_print_flag > 3) { + printf("\t"); + print_line("=", 100); + printf("\tsolve_nonlinear_problem(): iteration %d:\n", + num_newt_its); + } /* * If we are far enough away from the solution, redo the solution weights and the trust vectors. */ @@ -2647,19 +2712,13 @@ namespace Cantera { setDefaultDeltaBoundsMagnitudes(); } - if (m_print_flag > 3) { - printf("\tsolve_nonlinear_problem(): iteration %d:\n", - num_newt_its); - } - - // Check whether the Jacobian should be re-evaluated. forceNewJac = true; if (forceNewJac) { if (m_print_flag > 3) { - printf("\tsolve_nonlinear_problem(): Getting a new Jacobian and solving system\n"); + printf("\t solve_nonlinear_problem(): Getting a new Jacobian\n"); } info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), num_newt_its); @@ -2670,7 +2729,7 @@ namespace Cantera { m_residCurrent = true; } else { if (m_print_flag > 1) { - printf("\tsolve_nonlinear_problem(): Solving system with old jacobian\n"); + printf("\t solve_nonlinear_problem(): Solving system with old jacobian\n"); } m_residCurrent = false; } @@ -2683,10 +2742,13 @@ namespace Cantera { /* * Calculate the base residual */ + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate the base residual\n"); + } info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr)); if (info != 1) { if (m_print_flag > 0) { - printf("\t\t\tsolve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); + printf("\t solve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); } m = -5; goto done; @@ -2711,14 +2773,26 @@ namespace Cantera { } #ifdef DEBUG_DOGLEG + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate the steepest descent direction and Cauchy Point\n"); + } m_normDeltaSoln_CP = doCauchyPointSolve(jac); if (num_newt_its == 1) { + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length to the Cauchy Point\n"); + } initializeTrustRegion(); } #else - if (doDogLeg_) { + if (doDogLeg_) { + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate the steepest descent direction and Cauchy Point\n"); + } m_normDeltaSoln_CP = doCauchyPointSolve(jac); if (m_numTotalNewtIts == 1) { + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length to the Cauchy Point\n"); + } initializeTrustRegion(); } } @@ -2726,8 +2800,14 @@ namespace Cantera { // compute the undamped Newton step if (doAffineSolve_) { + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate the Newton direction via an Affine solve\n"); + } info = doAffineNewtonSolve(DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); } else { + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate the Newton direction via a Newton solve\n"); + } info = doNewtonSolve(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); } @@ -2750,9 +2830,13 @@ namespace Cantera { double trustD = calcTrustDistance(stp); if (s_print_DogLeg || m_print_flag > 3) { if (trustD > trustDelta_) { - printf("newton's method trustD, %g, larger than trust region, %g\n", trustD, trustDelta_); + printf("\t\t newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", + trustD, trustDelta_); + printf("\t\t newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", + trustD, trustDelta_); } else { - printf("newton's method trustD, %g, smaller than trust region, %g\n", trustD, trustDelta_); + printf("\t\t newton's method step size, %g trustVectorUnits, smaller than trust region, %g trustVectorUnits\n", + trustD, trustDelta_); } } #endif @@ -2767,6 +2851,9 @@ namespace Cantera { #ifdef DEBUG_DOGLEG + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Compare descent rates for Cauchy and Newton directions\n"); + } descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1)); #endif @@ -2774,15 +2861,23 @@ namespace Cantera { if (doDogLeg_) { setupDoubleDogleg(); #ifdef DEBUG_DOGLEG - residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr)); + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Compare Linear and nonlinear residuals along double dog-leg path\n"); + } + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); #endif + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Calculate damping along dog-leg path to ensure residual decrease\n"); + } m = dampDogLeg(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), - stp, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), - DATA_PTR(stp1), s1, jac, frst, i_backtracks); + stp, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), s1, jac, i_backtracks); } #ifdef DEBUG_DOGLEG else { - residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr)); + if (m_print_flag > 3) { + printf("\t solve_nonlinear_problem(): Compare Linear and nonlinear residuals along double dog-leg path\n"); + } + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); } #endif @@ -2809,7 +2904,7 @@ namespace Cantera { if (num_newt_its < m_min_newt_its) { if (m > 0) { if (m_print_flag > 2) { - printf("\t Damped Newton successful (m=%d) but minimum newton iterations not attained. Resolving ...\n", m); + printf("\t solve_nonlinear_problem(): Damped Newton successful (m=%d) but minimum newton iterations not attained. Resolving ...\n", m); } m = 0; } @@ -2821,7 +2916,7 @@ namespace Cantera { if (num_newt_its > maxNewtIts_) { m = -7; if (m_print_flag > 1) { - printf("\t\tsolve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); + printf("\t solve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); } } @@ -2829,14 +2924,14 @@ namespace Cantera { info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1)); if (info != 1) { if (m_print_flag > 0) { - printf("\t\t\tsolve_nonlinear_problem(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + printf("\t solve_nonlinear_problem(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } m = -8; goto done; } if (m_print_flag > 3) { - residErrorNorm(DATA_PTR(m_resid), "Resulting Residual Norm", 10, DATA_PTR(y_new)); + residErrorNorm(DATA_PTR(m_resid), "\t solve_nonlinear_problem():Resulting Residual Norm", 10, DATA_PTR(y_new)); } convRes = 0; @@ -2846,13 +2941,13 @@ namespace Cantera { if (m_print_flag >= 4) { if (convRes > 0) { - printf("\t Damped Newton iteration successful, nonlin " + printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, nonlin " "converged, final estimate of the next solution update norm = %-12.4E\n", s1); } else if (m >= 0) { - printf("\t Damped Newton iteration successful, " + printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, " "final estimate of the next solution update norm = %-12.4E\n", s1); } else { - printf("\t Damped Newton unsuccessful, final estimate of the next solution update norm = %-12.4E\n", s1); + printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful, final estimate of the next solution update norm = %-12.4E\n", s1); } } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index ecf889fc8..82bd83c84 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -288,6 +288,7 @@ namespace Cantera { void setDeltaBoundsMagnitudes(const doublereal * const deltaBoundsMagnitudes); protected: + //! Calculate the trust region vectors /*! * The trust region is made up of the trust region vector calculation and the trustDelta_ value @@ -298,7 +299,6 @@ namespace Cantera { * * || delta_x dot 1/trustDeltaX_ || <= trustDelta_ * - * @param y current value of the solution */ void calcTrustVector(); @@ -636,6 +636,10 @@ namespace Cantera { * The actual residual decline in the newton direction determined by numerical differencing * * This routine doesn't need to be called for the solution of the nonlinear problem. + * + * @param time_curr Current time + * @param ydot0 INPUT Current value of the derivative of the solution vector + * @param ydot1 INPUT Time derivates of solution at the conditions which are evalulated for success */ void descentComparison(double time_curr ,double *ydot0, double *ydot1); @@ -660,7 +664,7 @@ namespace Cantera { //! Given a trust distance, this routine calculates the intersection of the this distance with the //! double dogleg curve /*! - * @param trustDelta (INPUT) Value of the trust distance + * @param trustVal (INPUT) Value of the trust distance * @param lambda (OUTPUT) Returns the internal coordinate of the double dogleg * @param alpha (OUTPUT) Returns the relative distance along the appropriate leg * @return leg (OUTPUT) Returns the leg ID (0, 1, or 2) @@ -673,11 +677,34 @@ namespace Cantera { */ void initializeTrustRegion(); - int dampDogLeg(const doublereal time_curr, const double* y0, - const doublereal *ydot0, std::vector & step0, - double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, bool writetitle, - int& num_backtracks); + + //! Damp using the dog leg approach + /*! + * + * @param time_curr INPUT Current value of the time + * @param y_n_curr INPUT Current value of the solution vector + * @param ydot_n_curr INPUT Current value of the derivative of the solution vector + * @param step_1 INPUT First trial step for the first iteration + * @param y_n_1 INPUT First trial value of the solution vector + * @param ydot_n_1 INPUT First trial value of the derivative of the solution vector + * @param s1 OUTPUT Norm of the vector step_1 + * @param jac INPUT jacobian + * @param num_backtracks OUTPUT number of backtracks taken in the current damping step + * + * @return 1 Successful step was taken. The predicted residual norm is less than one + * 2 Successful step: Next step's norm is less than 0.8 + * 3 Success: The final residual is less than 1.0 + * A predicted deltaSoln1 is not produced however. s1 is estimated. + * 4 Success: The final residual is less than the residual + * from the previous step. + * A predicted deltaSoln1 is not produced however. s1 is estimated. + * 0 Uncertain Success: s1 is about the same as s0 + * -2 Unsuccessful step. + */ + int dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, + const doublereal *ydot_n_curr, std::vector & step_1, + doublereal* const y_n_1, doublereal* const ydot_n_1, + doublereal& s1, SquareMatrix& jac, int& num_backtracks); //! Decide whether the current step is acceptable and adjust the trust region size /*! @@ -718,18 +745,21 @@ namespace Cantera { * @return Returns the expected value of the residual at that point according to the quadratic model. * The residual at the newton point will always be zero. */ - double expectedResidLeg(int leg, doublereal alpha) const; + doublereal expectedResidLeg(int leg, doublereal alpha) const; //! Here we print out the residual at various points along the double dogleg, comparing against the quadratic model //! in a table format - /* + /*! * @param time_curr INPUT current time * @param ydot0 INPUT Current value of the derivative of the solution vector for non-time dependent * determinations + * @param legBest OUTPUT leg of the dogleg that gives the lowest residual + * @param alphaBest OUTPUT distance along dogleg for best result. */ - void residualComparisonLeg(const double time_curr, const double * const ydot0) const; + void residualComparisonLeg(const doublereal time_curr, const doublereal * const ydot0, int & legBest, + doublereal & alphaBest) const; - //! Set the print level from the rootfinder + //! Set the print level from the nonlinear solver /*! * * 0 -> absolutely nothing is printed for a single time step. @@ -845,9 +875,10 @@ namespace Cantera { //! Norm of the residual before damping doublereal m_normResidFRaw; - //! Norm of the solution update created by the iteration in its raw, undamped form. + //! Norm of the solution update created by the iteration in its raw, undamped form, using the solution norm doublereal m_normDeltaSoln_Newton; + //! Norm of the distance to the cauchy point using the solution norm doublereal m_normDeltaSoln_CP; //! Norm of the residual for a trial calculation which may or may not be used @@ -1007,16 +1038,26 @@ namespace Cantera { //! Vector of trust region values. std::vector deltaX_trust_; - //! Current value of trust radius. This is used with trustDeltaX_ to + //! Current norm of the vector deltaX_trust_ in terms of the solution norm + mutable doublereal norm_deltaX_trust_; + + //! Current value of trust radius. This is used with deltaX_trust_ to //! calculate the max step size. doublereal trustDelta_; //! Relative distance down the Newton step that the second dogleg starts doublereal Nuu_; + //! Distance of the zeroeth leg of the dogleg in terms of the solution norm doublereal dist_R0_; + + //! Distance of the first leg of the dogleg in terms of the solution norm doublereal dist_R1_; + + //! Distance of the second leg of the dogleg in terms of the solution norm doublereal dist_R2_; + + //! Distance of the sum of all legs of the doglegs in terms of the solution norm doublereal dist_Total_; //! Dot product of the Jd_ variable defined above with itself. @@ -1028,7 +1069,6 @@ namespace Cantera { //! Norm of the Cauchy Step direction wrt trust region doublereal normTrust_CP_; - //! General toggle for turning on dog leg damping. int doDogLeg_; diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 678d3fe7b..9514a1635 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -341,7 +341,8 @@ namespace Cantera { * @param cj Coefficient of yprime used in the evalulation of the jacobian * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) - * @param J Reference to the SquareMatrix object to be calculated (output) + * @param jacobianColPts Pointer to the vector of pts to columns of the SquareMatrix + * object to be calculated (output) * @param resid Value of the residual that is computed (output) * * @return Returns a flag to indicate that operation is successful. diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 17b2eff9a..9d933ea4f 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -267,6 +267,7 @@ namespace Cantera { //! Delta X norm. This is the nominal value of deltaX that will be used by the program doublereal DeltaXnorm_; + //! Boolean indicating whether DeltaXnorm_ has been specified by the user or not int specifiedDeltaXnorm_; //! Delta X Max. This is the maximum value of deltaX that will be used by the program @@ -275,6 +276,7 @@ namespace Cantera { */ doublereal DeltaXMax_; + //! Boolean indicating whether DeltaXMax_ has been specified by the user or not int specifiedDeltaXMax_; //! Boolean indicating whether the function is an increasing with x From d251da7a848250465ff43f8f2946ba78f0eea180 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 23 Sep 2011 20:31:17 +0000 Subject: [PATCH 403/446] Revamped the rootfinder algorithm. Behavior is substantially different. A summary table is now written out at the end of the solve for some print levels. --- Cantera/src/numerics/RootFind.cpp | 480 +++++++++++++++++++++--------- Cantera/src/numerics/RootFind.h | 166 ++++++++++- 2 files changed, 510 insertions(+), 136 deletions(-) diff --git a/Cantera/src/numerics/RootFind.cpp b/Cantera/src/numerics/RootFind.cpp index 1b61f1779..4d5760fca 100644 --- a/Cantera/src/numerics/RootFind.cpp +++ b/Cantera/src/numerics/RootFind.cpp @@ -18,7 +18,7 @@ #ifdef DEBUG_MODE #include "mdp_allo.h" #endif - +#include "stringUtils.h" /* Standard include files */ #include @@ -48,6 +48,13 @@ namespace Cantera { #define DSIGN(x) (( (x) == (0.0) ) ? (0.0) : ( ((x) > 0.0) ? 1.0 : -1.0 )) #endif +#ifdef SWAP +#undef SWAP +#endif +#ifndef SWAP +#define SWAP(x1, x2, tmp) ((tmp) = (x2), (x2) = (x1), (x1) = (tmp)) +#endif + // turn on debugging for now #ifndef DEBUG_MODE #define DEBUG_MODE @@ -275,17 +282,20 @@ namespace Cantera { // Function to decide whether two real numbers are the same or not /* * A comparison is made between the two numbers to decide whether they - * are close to one another. This is defined as being within delXMeaningful() of each other + * are close to one another. This is defined as being within factor * delXMeaningful() of each other. * * @param x2 First number - * @param x2 second number + * @param x1 second number + * @param factor Multiplicative factor for delta X. defaults to 1 * * @return Returns a boolean indicating whether the two numbers are the same or not. */ - bool RootFind::theSame(doublereal x2, doublereal x1) const { + bool RootFind::theSame(doublereal x2, doublereal x1, doublereal factor) const { doublereal x = fabs(x2) + fabs(x1); doublereal deltaX = delXMeaningful(x); - if (fabs(x2 - x1) < deltaX) { + doublereal deltaXSmall = factor * deltaX; + deltaXSmall = MAX(deltaXSmall , x * 1.0E-15); + if (fabs(x2 - x1) < deltaXSmall) { return true; } return false; @@ -322,9 +332,10 @@ namespace Cantera { char fileName[80]; FILE *fp = 0; #endif + int doFinalFuncCall = 0; doublereal x1, x2, xnew, f1, f2, fnew, slope; doublereal deltaX1 = 0.0, deltaX2 = 0.0, deltaXnew = 0.0; - int its = 0; + int posStraddle = 0; int retn = ROOTFIND_FAILEDCONVERGENCE; int foundPosF = 0; @@ -335,11 +346,15 @@ namespace Cantera { doublereal xNegF = 0.0; doublereal fNegF = -1.0E300; doublereal fnorm; /* A valid norm for the making the function value dimensionless */ - doublereal c[9], f[3], xn1, xn2, x0 = 0.0, f0 = 0.0, root, theta, xquad, xDelMin; - doublereal CR0, CR1, CR2, CRnew, CRdenom; + doublereal x0 = 0.0, f0 = 0.0, xDelMin; doublereal sgn; - - + doublereal dtmp; + doublereal fnoise = 0.0; + rfHistory_.clear(); + rfTable rfT; + rfT.clear(); + rfT.reasoning = "First Point: "; + callNum++; #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { @@ -397,10 +412,14 @@ namespace Cantera { x1 = *xbest; if (x1 < xmin || x1 > xmax) { x1 = (xmin + xmax) / 2.0; + rfT.reasoning += " x1 set middle between xmin and xmax because entrance is outside bounds."; + } else { + rfT.reasoning += " x1 set to entrance x."; } x_maxTried_ = x1; x_minTried_ = x1; + int its = 1; f1 = func(x1); #ifdef DEBUG_MODE @@ -410,45 +429,62 @@ namespace Cantera { } #endif + if (f1 == 0.0) { *xbest = x1; return 0; - } else if (f1 > 0.0) { + } else if (f1 > fnoise) { foundPosF = 1; xPosF = x1; fPosF = f1; - } else { + } else if (f1 < -fnoise) { foundNegF = 1; xNegF = x1; - fNegF = x1; + fNegF = f1; } - + rfT.its = its; + rfT.TP_its = 0; + rfT.xval = x1; + rfT.fval = f1; + rfT.foundPos = foundPosF; + rfT.foundNeg = foundNegF; + rfT.deltaXConverged = m_rtolx * (fabs(x1) + 0.001); + rfT.deltaFConverged = fabs(f1) * m_rtolf; + rfT.delX = xmax - xmin; + rfHistory_.push_back(rfT); + rfT.clear(); + /* * Now, this is actually a tricky part of the algorithm - Find the x value for * the second point. It's tricky because we don't have a valid idea of the scale of x yet * */ + rfT.reasoning = "Second Point: "; if (x1 == 0.0) { x2 = x1 + 0.01 * DeltaXnorm_; + rfT.reasoning += "Set by DeltaXnorm_"; } else { x2 = x1 * 1.0001; + rfT.reasoning += "Set slightly higher."; } if (x2 > xmax) { x2 = x1 - 0.01 * DeltaXnorm_; + rfT.reasoning += " - But adjusted to be within bounds"; } /* * Find the second function value f2 = func(x2), Process it */ deltaX2 = x2 - x1; - f2 = func(x2); + its++; + f2 = func(x2); #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { print_funcEval(fp, x2, f2, its); fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", -1, 0, x2, f2); } #endif - + /* * Calculate the norm of the function, this is the nominal value of f. We try * to reduce the nominal value of f by rtolf, this is the main convergence requirement. @@ -458,23 +494,33 @@ namespace Cantera { } else { fnorm = 0.5*(fabs(f1) + fabs(f2)) + fabs(m_funcTargetValue) + m_atolf; } + fnoise = 1.0E-100; - if (f2 == 0.0) { - *xbest = x2; - return ROOTFIND_SUCCESS; - } else if (f2 > 0.0) { + + if (f2 > fnoise) { if (!foundPosF) { foundPosF = 1; xPosF = x2; - fPosF = x2; + fPosF = f2; } - } else { + } else if (f2 < - fnoise) { if (!foundNegF) { foundNegF = 1; xNegF = x2; fNegF = f2; } + } else if (f2 == 0.0) { + *xbest = x2; + return ROOTFIND_SUCCESS; } + rfT.its = its; + rfT.TP_its = 0; + rfT.xval = x2; + rfT.fval = f2; + rfT.foundPos = foundPosF; + rfT.foundNeg = foundNegF; + + /* * See if we have already achieved a straddle */ @@ -483,7 +529,7 @@ namespace Cantera { if (xPosF > xNegF) posStraddle = 1; else posStraddle = 0; } - bool doQuad = false; + bool useNextStrat = false; bool slopePointingToHigher = true; // --------------------------------------------------------------------------------------------- @@ -499,8 +545,13 @@ namespace Cantera { printf(" RootFind: we are here x2 = %g x1 = %g\n", x2, x1); } #endif + doublereal delXtmp = deltaXControlled(x2, x1); slope = (f2 - f1) / delXtmp; + rfT.slope = slope; + rfHistory_.push_back(rfT); + rfT.clear(); + rfT.reasoning = ""; if (fabs(slope) <= 1.0E-100) { if (printLvl >= 2) { writelogf("%s functions evals produced the same result, %g, at %g and %g\n", @@ -509,6 +560,7 @@ namespace Cantera { xnew = x2 + DeltaXnorm_; slopePointingToHigher = true; useNextStrat = true; + rfT.reasoning += "Slope is close to zero. "; } else { useNextStrat = false; xnew = x2 - f2 / slope; @@ -517,6 +569,7 @@ namespace Cantera { } else { slopePointingToHigher = false; } + rfT.reasoning += "Slope is good. "; } #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { @@ -530,13 +583,18 @@ namespace Cantera { if (!foundStraddle) { if (fabs(xnew - x2) > DeltaXMax_) { useNextStrat = true; + rfT.reasoning += "Too large change in xnew from slope. "; } if (fabs(deltaXnew) < fabs(deltaX2)) { deltaXnew = 1.2 * deltaXnew; xnew = x2 + deltaXnew; } } + /* + * If the slope can't be trusted using a different strategy for picking the next point + */ if (useNextStrat) { + rfT.reasoning += "Using DeltaXnorm, " + fp2str(DeltaXnorm_) + " and FuncIsGenerallyIncreasing hints. "; if (f2 < 0.0) { if (FuncIsGenerallyIncreasing_) { if (slopePointingToHigher) { @@ -580,53 +638,24 @@ namespace Cantera { } } - /* - * Do a quadratic fit -> Note this algorithm seems - * to work OK. The quadratic approximation doesn't kick in until - * the end of the run, when it becomes reliable. + * Here, if we have a straddle, we purposefully overshoot the smaller side by 5%. Yes it does lead to + * more iterations. However, we're interested in bounding x, and not just doing Newton's method. */ - if (its > 0 && doQuad) { - c[0] = 1.; c[1] = 1.; c[2] = 1.; - c[3] = x0; c[4] = x1; c[5] = x2; - c[6] = SQUARE(x0); c[7] = SQUARE(x1); c[8] = SQUARE(x2); - f[0] = - f0; f[1] = - f1; f[2] = - f2; - int rrr = smlequ(c, 3, 3, f, 1); - if (rrr == 1) goto QUAD_BAIL; - root = f[1]* f[1] - 4.0 * f[0] * f[2]; - if (root >= 0.0) { - xn1 = (- f[1] + sqrt(root)) / (2.0 * f[2]); - xn2 = (- f[1] - sqrt(root)) / (2.0 * f[2]); - if (fabs(xn2 - x2) < fabs(xn1 - x2) && xn2 > 0.0 ) xquad = xn2; - else xquad = xn1; - theta = fabs(xquad - xnew) / fabs(xnew - x2); - theta = MIN(1.0, theta); - xnew = theta * xnew + (1.0 - theta) * xquad; -#ifdef DEBUG_MODE - if (printLvl >= 3 && writeLogAllowed_) { - if (theta != 1.0) { - fprintf(fp, " | xquad = %-11.5E", xnew); - } - } -#endif - } else { - /* - * Pick out situations where the convergence may be - * accelerated. - */ - if ((DSIGN(xnew - x2) == DSIGN(x2 - x1)) && - (DSIGN(x2 - x1) == DSIGN(x1 - x0)) ) { - xnew += xnew - x2; -#ifdef DEBUG_MODE - if (printLvl >= 3 && writeLogAllowed_) { - fprintf(fp, " | xquada = %-11.5E", xnew); - } -#endif + if (foundStraddle) { + double delta = fabs(x2 - x1); + if (fabs(xnew - x1) < .01 * delta) { + xnew = x1 + 0.01 * (x2 - x1); + } else if (fabs(xnew - x2) < .01 * delta) { + xnew = x1 + 0.01 * (x2 - x1); + } else if ((xnew > x1 && xnew < x2) || (xnew < x1 && xnew > x2)) { + if (fabs(xnew - x1) < fabs(x2 - xnew)) { + xnew = x1 + 20./19. * (xnew - x1); + } else { + xnew = x2 + 20./19. * (xnew - x2); } } } - QUAD_BAIL: ; - /* * OK, we have an estimate xnew. * @@ -637,7 +666,7 @@ namespace Cantera { /* * If we are doing a jump in between the two previous points, make sure * the new trial is no closer that 10% of the distances between x2-x1 to - * any of the original points. + * any of the original points. This is an important part of finding a good bound. */ xDelMin = fabs(x2 - x1) / 10.; if (fabs(xnew - x1) < xDelMin) { @@ -674,13 +703,37 @@ namespace Cantera { if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | xlimitsize = %-11.5E", xnew); } +#endif + } + /* + * If we are doing a jump outside the two previous points, make sure + * the new trial is no closer that 10% of the distances between x2-x1 to + * any of the original points. This is an important part of finding a good bound. + */ + xDelMin = 0.1 * fabs(x2 - x1); + if (fabs(xnew - x2) < xDelMin) { + xnew = x2 + DSIGN(xnew - x2) * xDelMin; +#ifdef DEBUG_MODE + if (printLvl >= 3 && writeLogAllowed_) { + fprintf(fp, " | x10%% = %-11.5E", xnew); + } +#endif + } + if (fabs(xnew - x1) < xDelMin) { + xnew = x1 + DSIGN(xnew - x1) * xDelMin; +#ifdef DEBUG_MODE + if (printLvl >= 3 && writeLogAllowed_) { + fprintf(fp, " | x10%% = %-11.5E", xnew); + } #endif } } - + /* + * HKM -> Not sure this section is needed + */ if (foundStraddle) { #ifdef DEBUG_MODE - slope = xnew; + double xorig = xnew; #endif if (posStraddle) { if (f2 > 0.0) { @@ -717,7 +770,7 @@ namespace Cantera { } #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { - if (slope != xnew) { + if (xorig != xnew) { fprintf(fp, " | xstraddle = %-11.5E", xnew); } } @@ -735,6 +788,8 @@ namespace Cantera { sgn = -1.0; } deltaXnew = 1.2 * delXMeaningful(xnew) * sgn; + rfT.reasoning += "Enforcing minimum stepsize from " + fp2str(xnew - x2) + + " to " + fp2str(deltaXnew); xnew = x2 + deltaXnew; } } @@ -746,20 +801,18 @@ namespace Cantera { topBump++; if (topBump < 3) { xnew = x2 + (xmax - x2) / 2.0; + rfT.reasoning += ("xval reduced to " + fp2str(xnew) + " because predicted xnew was above max value of " + fp2str(xmax)); } else { if (x2 == xmax || x1 == xmax) { // we are here when we are bumping against the top limit. // No further action is possible - if (xnew > xmax) { - slope = (f2 - f1) / delXtmp; - xnew = x2 - f2 / slope; - if (xnew > xmax) { - retn = ROOTFIND_SOLNHIGHERTHANXMAX; - *xbest = xnew; - } - } + retn = ROOTFIND_SOLNHIGHERTHANXMAX; + *xbest = xnew; + rfT.slope = slope; + rfT.reasoning += "Giving up because we're at xmax and xnew point higher: " + fp2str(xnew); goto done; } else { + rfT.reasoning += "xval reduced from " + fp2str(xnew) + " to the max value, " + fp2str(xmax); xnew = xmax; } } @@ -772,21 +825,20 @@ namespace Cantera { if (xnew < xmin) { bottomBump++; if (bottomBump < 3) { + rfT.reasoning += ("xnew increased from " + fp2str(xnew) +" to " + fp2str(x2 - (x2 - xmin) / 2.0) + + " because above min value of " + fp2str(xmin)); xnew = x2 - (x2 - xmin) / 2.0; } else { if (x2 == xmin || x1 == xmin) { // we are here when we are bumping against the bottom limit. // No further action is possible - if (xnew < xmin) { - slope = (f2 - f1) / delXtmp; - xnew = x2 - f2 / slope; - if (xnew < xmin) { - retn = ROOTFIND_SOLNLOWERTHANXMIN; - *xbest = xnew; - } - } + retn = ROOTFIND_SOLNLOWERTHANXMIN; + *xbest = xnew; + rfT.slope = slope; + rfT.reasoning = "Giving up because we're already at xmin and xnew points lower: " + fp2str(xnew); goto done; - } else { + } else { + rfT.reasoning += "xval increased from " + fp2str(xnew) + " to the min value, " + fp2str(xmin); xnew = xmin; } } @@ -796,10 +848,10 @@ namespace Cantera { } #endif } - + + its++; fnew = func(xnew); - CRdenom = MAX(fabs(fnew), MAX(fabs(f2), MAX(fabs(f1), fnorm))); - CRnew = sqrt(fabs(fnew) / CRdenom); + #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp,"\n"); @@ -807,7 +859,9 @@ namespace Cantera { fprintf(fp, "%-5d %-5d %-15.5E %-15.5E", its, 0, xnew, fnew); } #endif - + rfT.xval = xnew; + rfT.fval = fnew; + rfT.its = its; if (foundStraddle) { if (posStraddle) { if (fnew > 0.0) { @@ -837,18 +891,20 @@ namespace Cantera { } if (! foundStraddle) { - if (fnew > 0.0) { + if (fnew > fnoise) { if (!foundPosF) { foundPosF = 1; + rfT.foundPos = 1; xPosF = xnew; fPosF = fnew; foundStraddle = 1; if (xPosF > xNegF) posStraddle = 1; else posStraddle = 0; } - } else { + } else if (fnew < - fnoise) { if (!foundNegF) { foundNegF = 1; + rfT.foundNeg = 1; xNegF = xnew; fNegF = fnew; foundStraddle = 1; @@ -860,15 +916,14 @@ namespace Cantera { x0 = x1; f0 = f1; - CR0 = CR1; x1 = x2; f1 = f2; - CR1 = CR2; + x2 = xnew; f2 = fnew; /* - * As we go on to new data points, we make sure that + * As we go on to new data points, we make sure that * we have the best straddle of the solution with the choice of F1 and F2 when * we do have a straddle to work with. */ @@ -947,64 +1002,190 @@ namespace Cantera { } } } - } + } + AssertThrow((f1 * f2 <= 0.0), "F1 and F2 aren't bounding"); } deltaX1 = deltaX2; deltaX2 = deltaXnew; - CR2 = CRnew; + deltaXnew = x2 - x1; deltaXConverged_ = 0.5 * deltaXConverged_ + 0.5 * (m_rtolx * 0.5 * (fabs(x2) + fabs(x1)) + m_atolx); - if (fabs(fnew / fnorm) < m_rtolf) { - if (deltaX2 < deltaXConverged_ && deltaXnew < deltaXConverged_) { - converged = 1; + rfT.deltaXConverged = deltaXConverged_; + rfT.deltaFConverged = fnorm * m_rtolf; + if (foundStraddle) { + rfT.delX = MAX(fabs(deltaX2), fabs(deltaXnew)); + } else { + rfT.delX = MAX(fabs(deltaX2), fabs(deltaXnew)); + if (x2 < x1) { + rfT.delX = MAX(rfT.delX, x2 - xmin); + } else { + rfT.delX = MAX(rfT.delX, xmax - x2); } - if (fabs(slope) > 1.0E-100) { - double xdels = fabs(fnew / slope); - if (xdels < deltaXConverged_ * 0.5) { - converged = 1; - } - } - } /* - * Check for excess convergence in the x coordinate + * Section To Determine CONVERGENCE criteria */ - if (foundStraddle) { - doublereal denom = fabs(x1) + fabs(x2); - if (denom < 1.0E-200) { - retn = ROOTFIND_FAILEDCONVERGENCE; - converged = true; + doFinalFuncCall = 0; + if ((fabs(fnew / fnorm) < m_rtolf) && foundStraddle) { + if (fabs(deltaX2) < deltaXConverged_ && fabs(deltaXnew) < deltaXConverged_) { + converged = 1; + rfT.reasoning += "NormalConvergence"; + retn = ROOTFIND_SUCCESS; + } + + else if (fabs(slope) > 1.0E-100) { + double xdels = fabs(fnew / slope); + if (xdels < deltaXConverged_ * 0.3) { + converged = 1; + rfT.reasoning += "NormalConvergence-SlopelimitsDelX"; + doFinalFuncCall = 1; + retn = ROOTFIND_SUCCESS; + } } - if (theSame(x2, x1)) { - converged = true; + + + /* + * Check for excess convergence in the x coordinate + */ + if (!converged) { + if (foundStraddle) { + doublereal denom = fabs(x1 - x2); + if (denom < 1.0E-200) { + retn = ROOTFIND_FAILEDCONVERGENCE; + converged = true; + rfT.reasoning += "ConvergenceFZero but X1X2Identical"; + } + if (theSame(x2, x1, 1.0E-2)) { + converged = true; + rfT.reasoning += " ConvergenceF and XSame"; + retn = ROOTFIND_SUCCESS; + } + } + } + } else { + /* + * We are here when F is not converged, but we may want to end anyway + */ + if (!converged) { + if (foundStraddle) { + doublereal denom = fabs(x1 - x2); + if (denom < 1.0E-200) { + retn = ROOTFIND_FAILEDCONVERGENCE; + converged = true; + rfT.reasoning += "FNotConverged but X1X2Identical"; + } + /* + * The premise here is that if x1 and x2 get close to one another, + * then the accuracy of the calculation gets destroyed. + */ + if (theSame(x2, x1, 1.0E-5)) { + converged = true; + retn = ROOTFIND_SUCCESS_XCONVERGENCEONLY; + rfT.reasoning += "FNotConverged but XSame"; + } + } } } - its++; } while (! converged && its < itmax); done: if (converged) { - retn = ROOTFIND_SUCCESS; - if (fabs(f1) < 2.0 * fabs(f2)) { - slope = (f2 - f1) / (x2 - x1); - xnew = x2 - f2 / slope; + rfT.slope = slope; + rfHistory_.push_back(rfT); + rfT.clear(); + rfT.its = its; + AssertThrow((f1 * f2 <= 0.0), "F1 and F2 aren't bounding"); + double x_fpos = x2; + double x_fneg = x1; + if (f2 < 0.0) { + x_fpos = x1; + x_fneg = x2; + } + rfT.delX = fabs(x_fpos - x_fneg); + if (doFinalFuncCall || (fabs(f1) < 2.0 * fabs(f2))) { + double delXtmp = deltaXControlled(x2, x1); + slope = (f2 - f1) / delXtmp; + xnew = x2 - f2 / slope; + its++; fnew = func(xnew); - if (fabs(fnew) < fabs(f2)) { + if (fnew > 0.0) { + if (fabs(xnew - x_fneg) < fabs(x_fpos - x_fneg)) { + x_fpos = xnew; + rfT.delX = fabs(xnew - x_fneg); + } + } else { + if (fabs(xnew - x_fpos) < fabs(x_fpos - x_fneg)) { + x_fneg = xnew; + rfT.delX = fabs(xnew - x_fpos); + } + } + rfT.its = its; + if (fabs(fnew) < fabs(f2) && (fabs(fnew) < fabs(f1))) { + *xbest = xnew; + if (doFinalFuncCall) { + rfT.reasoning += "CONVERGENCE: Another Evaluation Requested"; + rfT.delX = fabs(xnew - x2); + } else { + rfT.reasoning += "CONVERGENCE: Another Evaluation done because f1 < f2"; + rfT.delX = fabs(xnew - x1); + } + rfT.fval = fnew; + rfT.xval = xnew; x2 = xnew; f2 = fnew; + } else if (fabs(f1) < fabs(f2)) { + rfT.its = its; + rfT.xval = xnew; + rfT.fval = fnew; + + rfT.slope = slope; + rfT.reasoning += "CONVERGENCE: Another Evaluation not as good as Second Point "; + rfHistory_.push_back(rfT); + rfT.clear(); + rfT.its = its; + SWAP(f1, f2, dtmp); + SWAP(x1, x2, dtmp); *xbest = x2; + if (fabs(fnew) < fabs(f1)) { + if (f1 * fnew > 0.0) { + SWAP(f1, fnew, dtmp); + SWAP(x1, xnew, dtmp); + } + } + + rfT.its = its; + rfT.xval = *xbest; + rfT.fval = f2; + rfT.delX = fabs(x_fpos - x_fneg); + rfT.reasoning += "CONVERGENCE: NormalEnding -> Second point used"; + } else { + rfT.its = its; + rfT.xval = xnew; + rfT.fval = fnew; + + rfT.slope = slope; + rfT.reasoning += "CONVERGENCE: Another Evaluation not as good as First Point "; + rfHistory_.push_back(rfT); + rfT.clear(); + rfT.its = its; + *xbest = x2; + rfT.xval = *xbest; + rfT.fval = f2; + rfT.delX = fabs(x_fpos - x_fneg); + rfT.reasoning += "CONVERGENCE: NormalEnding -> Last point used"; } - if (fabs(f1) < fabs(f2)) { - x2 = x1; - f2 = f1; - *xbest = x1; - fnew = func(x2); - } + } else { + + *xbest = x2; + + rfT.xval = *xbest; + rfT.fval = f2; + rfT.delX = fabs(x2 - x1); + rfT.reasoning += "CONVERGENCE: NormalEnding -> Last point used"; } - - - + funcTargetValue = f2 + m_funcTargetValue; + rfT.slope = slope; if (printLvl >= 1) { writelogf("RootFind success: convergence achieved\n"); @@ -1013,35 +1194,50 @@ namespace Cantera { if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, " | RootFind success in %d its, fnorm = %g\n", its, fnorm); } -#endif +#endif + rfHistory_.push_back(rfT); } else { + rfT.reasoning = "FAILED CONVERGENCE "; + rfT.slope = slope; + rfT.its = its; if (retn == ROOTFIND_SOLNHIGHERTHANXMAX) { if (printLvl >= 1) { writelogf("RootFind ERROR: Soln probably lies higher than xmax, %g: best guess = %g\n", xmax, *xbest); } + rfT.reasoning += "Soln probably lies higher than xmax, " + fp2str(xmax) + ": best guess = " + fp2str(*xbest); } else if (retn == ROOTFIND_SOLNLOWERTHANXMIN) { if (printLvl >= 1) { writelogf("RootFind ERROR: Soln probably lies lower than xmin, %g: best guess = %g\n", xmin, *xbest); } + rfT.reasoning += "Soln probably lies lower than xmin, " + fp2str(xmin) + ": best guess = " + fp2str(*xbest); } else { retn = ROOTFIND_FAILEDCONVERGENCE; if (printLvl >= 1) { writelogf("RootFind ERROR: maximum iterations exceeded without convergence, cause unknown\n"); } + rfT.reasoning += "Maximum iterations exceeded without convergence, cause unknown"; } #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { fprintf(fp, "\nRootFind failure in %d its\n", its); } #endif + + *xbest = x2; + funcTargetValue = f2 + m_funcTargetValue; + rfT.xval = *xbest; + rfT.fval = f2; + rfHistory_.push_back(rfT); } - *xbest = x2; - funcTargetValue = f2 + m_funcTargetValue; #ifdef DEBUG_MODE if (printLvl >= 3 && writeLogAllowed_) { fclose(fp); } #endif + + if (printLvl >= 2) { + printTable(); + } return retn; } @@ -1173,4 +1369,22 @@ namespace Cantera { specifiedDeltaXMax_ = 1; } //==================================================================================================================== + + //==================================================================================================================== + void RootFind::printTable() { + printf("\t----------------------------------------------------------------------------------------------------------------------------------------\n"); + printf("\t RootFinder Summary table: \n"); + printf("\t FTarget = %g\n", m_funcTargetValue); + printf("\t Iter | xval delX deltaXConv | slope | foundP foundN| F - F_targ deltaFConv | Reasoning\n"); + printf("\t----------------------------------------------------------------------------------------------------------------------------------------\n"); + for (int i = 0; i < (int) rfHistory_.size(); i++) { + struct rfTable rfT = rfHistory_[i]; + printf("\t %3d |%- 17.11E %- 13.7E %- 13.7E |%- 13.5E| %3d %3d | %- 12.5E %- 12.5E | %s \n", + rfT.its, rfT.xval, rfT.delX, rfT.deltaXConverged, rfT.slope, rfT.foundPos, rfT.foundNeg, rfT.fval, + rfT.deltaFConverged, (rfT.reasoning).c_str()); + } + printf("\t----------------------------------------------------------------------------------------------------------------------------------------\n"); + } + //==================================================================================================================== + } diff --git a/Cantera/src/numerics/RootFind.h b/Cantera/src/numerics/RootFind.h index 9d933ea4f..016827660 100644 --- a/Cantera/src/numerics/RootFind.h +++ b/Cantera/src/numerics/RootFind.h @@ -29,6 +29,14 @@ namespace Cantera { //! This means that the root solver was a success #define ROOTFIND_SUCCESS 0 + //! This return value means that the root finder resolved a solution in the x coordinate + //! However, convergence in F was not achieved. + /*! + * A common situation for this to happen is that f(x) is discontinuous about f(x) = f_0, + * where we seek the x where the function is equal to f_0. f(x) spans the + * f_0 while not being equal to f_0 anywhere. + */ +#define ROOTFIND_SUCCESS_XCONVERGENCEONLY 1 //! This means that the root solver failed to achieve convergence #define ROOTFIND_FAILEDCONVERGENCE -1 //! This means that the input to the root solver was defective @@ -40,12 +48,96 @@ namespace Cantera { * */ #define ROOTFIND_SOLNHIGHERTHANXMAX -4 - //@{ + //@} + + + //! Root finder for 1D problems /*! * + * The root finder solves a single nonlinear equation described below. * + * \f[ + * f(x) = f_0 + * \f] + * + * \f$ f(x) \f$ is assumed to be single valued as a function of x.\f$ f(x) \f$ is not assumed to be continuous nor is + * its derivative assumed to be well formed. + * + * Root finders are significantly different in the sense that do not have to rely + * solely on Newton's method to find the answer to the problem. Instead they use a method to bound + * the solution between high and low values and then use a method to refine that bound. The eventual + * solution to the problem is presented as x_best and as a bound, delta_X, on the solution + * component. Because of this, they are far more stable for functions and Jacobians that have discontinuities + * or noise associated with them. + * + * The algorithm is a convolution of a local Secant method with an approach of finding a straddle in x. + * The Jacobian is never required. + * + * There is a general breakdown of the algorithm into stages. The first stage seeks to find a straddle of the + * function. The second stage seeks to reduce the bounds in x and f in order to satisfy the specification of the + * stopping criteria. In the last stage the algorithm seeks to find the base value of x that satisfies the + * original equation given what it current knows about the function. + * + * Globalization strategy + * + * Specifying the General Changes in x + * + * Supplying Hints with General Function Behavior Flags + * + * + * + * Stopping Criteria + * + * Specification of the Stopping Criteria + * + * + * Additional constraints + * + * Bounds Criteria For the Routine + * + * Example + * + * @code + * // Define a residual. The definition of a residual involves a lot more work than is shown here. + * ResidEval * ec; + * // Instantiate the root finder with the residual to be solved, ec. + * RootFind rf(&ec); + * // Set the relative and absolute tolerancess for f and x. + * rf.setTol(1.0E-5, 1.0E-10, 1.0E-5, 1.0E-11); + * // Give a hint about the function's dependence on x. This is needed, for example, if the function has + * // flat regions. + * rf.setFuncIsGenerallyIncreasing(true); + * rf.setDeltaX(0.01); + * // Supply an initial guess for the solution + * double xbest = phiM; + * double oldP = printLvl_; + * // Set the print level for the solver. Zero produces no output. Two produces a summary table of each iteration. + * rf.setPrintLvl(2); + * // Define a minimum and maximum for the independent variable. + * double phimin = 1.3; + * double phimax = 2.2; + * // Define a maximum iteration number + * int itmax = 100; + * // Define the f_0 value, and on return will contain the actual value of f(x) obtained + * double currentObtained; + * // Call the solver + * status = rf.solve(phimin, phimax, 100, currentObtained, &xbest); + * if (status == 0) { + * if (printLvl_ > 1) { + * printf("Electrode::integrateConstantCurrent(): Volts (%g amps) = %g\n", currentObtained, xbest); + * } + * } else { + * if (printLvl_) { + * printf("Electrode::integrateConstantCurrent(): bad status = %d Volts (%g amps) = %g\n", + * status, currentObtained, xbest); + * } + * } + * @endcode + * + * @todo Noise + * @todo General Search to be done when all else fails * */ class RootFind { @@ -110,14 +202,18 @@ namespace Cantera { //! Function to decide whether two real numbers are the same or not /*! * A comparison is made between the two numbers to decide whether they - * are close to one another. This is defined as being within delXMeaningful() of each other + * are close to one another. This is defined as being within factor * delXMeaningful() of each other. + * + * The basic premise here is that if the two numbers are too close, the noise + * will prevent an accurate calculation of the function and its slope. * * @param x1 First number * @param x2 second number + * @param factor Multiplicative factor to multiple deltaX with * * @return Returns a boolean indicating whether the two numbers are the same or not. */ - bool theSame(doublereal x2, doublereal x1) const; + bool theSame(doublereal x2, doublereal x1, doublereal factor = 1.0) const; public: @@ -233,6 +329,9 @@ namespace Cantera { */ void setDeltaXMax(doublereal deltaX); + //! Print the iteration history table + void printTable(); + public: //! Pointer to the residual function evaluator @@ -249,6 +348,7 @@ namespace Cantera { //! Relative tolerance for the value of f and x doublereal m_rtolf; + //! Relative tolerance for the value of x doublereal m_rtolx; @@ -256,10 +356,19 @@ namespace Cantera { doublereal m_maxstep; protected: + //! Print level + /*! + * 0 No printing of any kind + * 1 Single print line indicating success or failure of the routine. + * 2 Summary table printed at the end of the routine, with a convergence history + * 3 Printouts during the iteration are added. Summary table is printed out at the end. + * if writeLogAllowed_ is turned on, a file is written out with the convergence history. + */ int printLvl; public: + //! Boolean to turn on the possibility of writing a log file. bool writeLogAllowed_; @@ -304,6 +413,57 @@ namespace Cantera { //! Internal variable tracking f(x) of smallest x tried. doublereal fx_minTried_; + + //! Structure containing the iteration history + struct rfTable { + //@{ + int its; + int TP_its; + double slope; + double xval; + double fval; + int foundPos; + int foundNeg; + double deltaXConverged; + double deltaFConverged; + double delX; + + + std::string reasoning; + + void clear() { + its = 0; + TP_its = 0; + slope = -1.0E300; + xval = -1.0E300; + fval = -1.0E300; + reasoning = ""; + }; + + rfTable() : + its(-2), + TP_its(0), + slope(-1.0E300), + xval(-1.0E300), + fval(-1.0E300), + foundPos(0), + foundNeg(0), + deltaXConverged(-1.0E300), + deltaFConverged(-1.0E300), + delX(-1.0E300), + reasoning("") + { + }; + + + //@} + }; + + //! Vector of iteration histories + std::vector rfHistory_; + + + }; } #endif From d153aa8c0a10326b2cb5d89746df2f9c00c14996 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 23 Sep 2011 21:20:09 +0000 Subject: [PATCH 404/446] Fixed an error in the specification of a list length. --- Cantera/src/thermo/ThermoFactory.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 9704cae20..9c3a13f52 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -97,7 +97,7 @@ namespace Cantera { /*! * @deprecated This entire structure could be replaced with a std::map */ - static int ntypes = 19; + static int ntypes = 20; //! Define the string name of the %ThermoPhase types that are handled by this factory routine static string _types[] = {"IdealGas", "Incompressible", From 9af9a3e70220c8dfd426e6dafa1b6ac1d6a06fe7 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 29 Sep 2011 23:11:12 +0000 Subject: [PATCH 405/446] Made the double dogleg capability operational. It can now be used by users reliably. --- Cantera/src/numerics/NonlinearSolver.cpp | 1047 +++++++++++++--------- Cantera/src/numerics/NonlinearSolver.h | 174 ++-- 2 files changed, 742 insertions(+), 479 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index bddd33567..0f3f8d736 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -24,11 +24,10 @@ #include "clockWC.h" #include "vec_functions.h" -#include - #include "mdp_allo.h" -#include +#include +#include #include #include #include @@ -41,8 +40,9 @@ extern void print_line(const char *, int); #define MIN(x,y) (( (x) < (y) ) ? (x) : (y)) #endif #ifndef CONSTD_DATA_PTR -#define CONSTD_DATA_PTR(x) (( const double *) (&x[0])) +#define CONSTD_DATA_PTR(x) (( const doublereal *) (&x[0])) #endif + //@} using namespace std; @@ -86,7 +86,7 @@ namespace Cantera { * Turn this on if you want to compare the Hessian and Newton solve results. */ bool NonlinearSolver::s_doBothSolvesAndCompare(false); - //==================================================================================================================== + //==================================================================================================================== // Default constructor /* * @param func Residual and jacobian evaluator function object @@ -101,6 +101,7 @@ namespace Cantera { m_y_n_curr(0), m_ydot_n_curr(0), m_y_nm1(0), + m_y_n_1(0), m_ydot_n_1(0), m_colScales(0), m_rowScales(0), @@ -109,8 +110,9 @@ namespace Cantera { m_wksp(0), m_wksp_2(0), m_residWts(0), - m_normResid0(0.0), - m_normResidFRaw(0.0), + m_normResid_0(0.0), + m_normResid_Bound(0.0), + m_normResid_1(0.0), m_normDeltaSoln_Newton(0.0), m_normDeltaSoln_CP(0.0), m_normResidTrial(0.0), @@ -143,6 +145,8 @@ namespace Cantera { deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), + dogLegID_(0), + dogLegAlpha_(1.0), RJd_norm_(0.0), lambdaStar_(0.0), Jd_(0), @@ -158,7 +162,14 @@ namespace Cantera { normTrust_Newton_(0.0), normTrust_CP_(0.0), doDogLeg_(0), - doAffineSolve_(0) + doAffineSolve_(0) , + CurrentTrustFactor_(1.0), + NextTrustFactor_ (1.0), + ResidWtsReevaluated_(false), + ResidDecreaseSDExp_(0.0), + ResidDecreaseSD_(0.0), + ResidDecreaseNewtExp_(0.0), + ResidDecreaseNewt_(0.0) { neq_ = m_func->nEquations(); @@ -168,6 +179,7 @@ namespace Cantera { m_y_n_curr.resize(neq_, 0.0); m_ydot_n_curr.resize(neq_, 0.0); m_y_nm1.resize(neq_, 0.0); + m_y_n_1.resize(neq_, 0.0); m_ydot_n_1.resize(neq_, 0.0); m_colScales.resize(neq_, 1.0); m_rowScales.resize(neq_, 1.0); @@ -178,6 +190,8 @@ namespace Cantera { m_residWts.resize(neq_, 0.0); atolk_.resize(neq_, atolBase_); deltaX_Newton_.resize(neq_, 0.0); + m_step_1.resize(neq_, 0.0); + m_y_n_1.resize(neq_, 0.0); doublereal hb = std::numeric_limits::max(); m_y_high_bounds.resize(neq_, hb); m_y_low_bounds.resize(neq_, -hb); @@ -193,9 +207,8 @@ namespace Cantera { Jd_.resize(neq_, 0.0); deltaX_trust_.resize(neq_, 1.0); - } - //==================================================================================================================== + //==================================================================================================================== NonlinearSolver::NonlinearSolver(const NonlinearSolver &right) : m_func(right.m_func), solnType_(NSOLN_TYPE_STEADY_STATE), @@ -206,7 +219,9 @@ namespace Cantera { m_y_n_curr(0), m_ydot_n_curr(0), m_y_nm1(0), + m_y_n_1(0), m_ydot_n_1(0), + m_step_1(0), m_colScales(0), m_rowScales(0), m_rowWtScales(0), @@ -214,8 +229,9 @@ namespace Cantera { m_wksp(0), m_wksp_2(0), m_residWts(0), - m_normResid0(0.0), - m_normResidFRaw(0.0), + m_normResid_0(0.0), + m_normResid_Bound(0.0), + m_normResid_1(0.0), m_normDeltaSoln_Newton(0.0), m_normDeltaSoln_CP(0.0), m_normResidTrial(0.0), @@ -248,6 +264,8 @@ namespace Cantera { deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), + dogLegID_(0), + dogLegAlpha_(1.0), RJd_norm_(0.0), lambdaStar_(0.0), Jd_(0), @@ -263,15 +281,22 @@ namespace Cantera { normTrust_Newton_(0.0), normTrust_CP_(0.0), doDogLeg_(0), - doAffineSolve_(0) + doAffineSolve_(0), + CurrentTrustFactor_(1.0), + NextTrustFactor_ (1.0), + ResidWtsReevaluated_(false), + ResidDecreaseSDExp_(0.0), + ResidDecreaseSD_(0.0), + ResidDecreaseNewtExp_(0.0), + ResidDecreaseNewt_(0.0) { *this =operator=(right); } - //==================================================================================================================== + //==================================================================================================================== NonlinearSolver::~NonlinearSolver() { } - //==================================================================================================================== + //==================================================================================================================== NonlinearSolver& NonlinearSolver::operator=(const NonlinearSolver &right) { if (this == &right) { return *this; @@ -288,7 +313,9 @@ namespace Cantera { m_y_n_curr = right.m_y_n_curr; m_ydot_n_curr = right.m_ydot_n_curr; m_y_nm1 = right.m_y_nm1; + m_y_n_1 = right.m_y_n_1; m_ydot_n_1 = right.m_ydot_n_1; + m_step_1 = right.m_step_1; m_colScales = right.m_colScales; m_rowScales = right.m_rowScales; m_rowWtScales = right.m_rowWtScales; @@ -296,8 +323,9 @@ namespace Cantera { m_wksp = right.m_wksp; m_wksp_2 = right.m_wksp_2; m_residWts = right.m_residWts; - m_normResid0 = right.m_normResid0; - m_normResidFRaw = right.m_normResidFRaw; + m_normResid_0 = right.m_normResid_0; + m_normResid_Bound = right.m_normResid_Bound; + m_normResid_1 = right.m_normResid_1; m_normDeltaSoln_Newton = right.m_normDeltaSoln_Newton; m_normDeltaSoln_CP = right.m_normDeltaSoln_CP; m_normResidTrial = right.m_normResidTrial; @@ -329,6 +357,9 @@ namespace Cantera { Hessian_ = right.Hessian_; deltaX_CP_ = right.deltaX_CP_; deltaX_Newton_ = right.deltaX_Newton_; + residNorm2Cauchy_ = right.residNorm2Cauchy_; + dogLegID_ = right.dogLegID_; + dogLegAlpha_ = right.dogLegAlpha_; RJd_norm_ = right.RJd_norm_; lambdaStar_ = right.lambdaStar_; Jd_ = right.Jd_; @@ -346,6 +377,14 @@ namespace Cantera { normTrust_CP_ = right.normTrust_CP_; doDogLeg_ = right.doDogLeg_; doAffineSolve_ = right.doAffineSolve_; + CurrentTrustFactor_ = right.CurrentTrustFactor_; + NextTrustFactor_ = right.NextTrustFactor_; + + ResidWtsReevaluated_ = right.ResidWtsReevaluated_; + ResidDecreaseSDExp_ = right.ResidDecreaseSDExp_; + ResidDecreaseSD_ = right.ResidDecreaseSD_; + ResidDecreaseNewtExp_ = right.ResidDecreaseNewtExp_; + ResidDecreaseNewt_ = right.ResidDecreaseNewt_; return *this; } @@ -384,21 +423,13 @@ namespace Cantera { void NonlinearSolver::setSolverScheme(int doDogLeg, int doAffineSolve) { doDogLeg_ = doDogLeg; doAffineSolve_ = doAffineSolve; -#ifdef DEBUG_DOGLEG - -#else - // if (doDogLeg_) { - //throw CanteraError("NonlinearSolver::setSolverScheme", - // "ifdef block not on"); - //} -#endif } //==================================================================================================================== - std::vector & NonlinearSolver::lowBoundsConstraintVector() { + std::vector & NonlinearSolver::lowBoundsConstraintVector() { return m_y_low_bounds; } //==================================================================================================================== - std::vector & NonlinearSolver::highBoundsConstraintVector() { + std::vector & NonlinearSolver::highBoundsConstraintVector() { return m_y_high_bounds; } //==================================================================================================================== @@ -610,7 +641,7 @@ namespace Cantera { * -0 or neg value Means an unsuccessful operation */ int NonlinearSolver::doResidualCalc(const doublereal time_curr, const int typeCalc, const doublereal * const y_curr, - const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) const + const doublereal * const ydot_curr, const ResidEval_Type_Enum evalType) const { int retn = m_func->evalResidNJ(time_curr, delta_t_n, y_curr, ydot_curr, DATA_PTR(m_resid), evalType); m_nfe++; @@ -625,7 +656,8 @@ namespace Cantera { * @param ydot_comm Current value of the time derivative of the solution vector * @param time_curr current value of the time */ - void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr) + void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr, + int num_newt_its) { int irow, jcol; @@ -704,11 +736,11 @@ namespace Cantera { } } - - computeResidWts(); - + if (num_newt_its % 5 == 1) { + computeResidWts(); + } + } - } //==================================================================================================================== // Calculate the scaling factor for translating residual norms into solution norms. @@ -723,7 +755,7 @@ namespace Cantera { if (! jacCopy_.m_factored) { - double sum = 0.0; + doublereal sum = 0.0; for (int irow = 0; irow < neq_; irow++) { m_residWts[irow] = m_rowWtScales[irow] / neq_; sum += m_residWts[irow]; @@ -744,8 +776,8 @@ namespace Cantera { jptr++; } } - double resNormOld = 0.0; - double error; + doublereal resNormOld = 0.0; + doublereal error; for (int irow = 0; irow < neq_; irow++) { error = m_wksp[irow] / m_residWts[irow]; @@ -858,7 +890,8 @@ namespace Cantera { #endif - m_numTotalLinearSolves++; + m_numTotalLinearSolves++; + m_numLocalLinearSolves++; return info; } //==================================================================================================================== @@ -891,7 +924,7 @@ namespace Cantera { } // Factor the matrix - double cond = 1.0E300; + m_conditionNumber = 1.0E300; int info = 0; if (!jac.m_factored) { if (jac.useQR_) { @@ -905,14 +938,14 @@ namespace Cantera { * If we have failed to factor, we will fall back to calculating and factoring a modified Hessian */ if (info == 0) { - double rcond = 0.0; + doublereal rcond = 0.0; if (jac.useQR_) { rcond = jac.rcondQR(); } else { rcond = jac.rcond(jac.a1norm_); } if (rcond > 0.0) { - cond = 1.0 / rcond; + m_conditionNumber = 1.0 / rcond; } } bool doHessian = false; @@ -920,10 +953,10 @@ namespace Cantera { doHessian = true; } bool doNewton = false; - if (cond < 1.0E7) { + if (m_conditionNumber < 1.0E7) { doNewton = true; - if (m_print_flag >= 3) { - printf("\t\t doAffineNewtonSolve: Condition number = %g during regular solve\n", cond); + if (m_print_flag >= 4) { + printf("\t\t doAffineNewtonSolve: Condition number = %g during regular solve\n", m_conditionNumber); } /* @@ -950,7 +983,7 @@ namespace Cantera { doHessian = true; newtonGood = false; if (m_print_flag >= 3) { - printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g. Doing a Hessian solve \n", cond); + printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g. Doing a Hessian solve \n", m_conditionNumber); } } @@ -1156,7 +1189,8 @@ namespace Cantera { #endif - m_numTotalLinearSolves++; + m_numTotalLinearSolves++; + m_numLocalLinearSolves++; return info; } @@ -1167,8 +1201,8 @@ namespace Cantera { */ doublereal NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) { - double rowFac = 1.0; - double normSoln; + doublereal rowFac = 1.0; + doublereal normSoln; // Calculate the descent direction /* * For confirmation of the scaling factors, see Dennis and Schnabel p, 152, p, 156 and my notes @@ -1181,7 +1215,7 @@ namespace Cantera { */ for (int j = 0; j < neq_; j++) { deltaX_CP_[j] = 0.0; - double colFac = 1.0; + doublereal colFac = 1.0; if (m_colScaling) { colFac = 1.0 / m_colScales[j]; } @@ -1190,8 +1224,8 @@ namespace Cantera { rowFac = 1.0 / m_rowScales[i]; } deltaX_CP_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] - / (m_residWts[i] * m_residWts[i]); -#ifdef DEBUG_DOGLEG + / (m_residWts[i] * m_residWts[i]); +#ifdef DEBUG_MODE mdp::checkFinite(deltaX_CP_[j]); #endif } @@ -1243,104 +1277,140 @@ namespace Cantera { for (int i = 0; i < neq_; i++) { deltaX_CP_[i] *= lambdaStar_; } - double normResid02 = m_normResid0 * m_normResid0 * neq_; + + doublereal normResid02 = m_normResid_0 * m_normResid_0 * neq_; + + /* + * Calculate the expected square of the risdual at the Cauchy point if the linear model is correct + */ if (fabs(JdJd_norm_) < 1.0E-290) { residNorm2Cauchy_ = normResid02; } else { residNorm2Cauchy_ = normResid02 - RJd_norm_ * RJd_norm_ / (JdJd_norm_); } - if (m_print_flag > 2) { - double residCauchy = 0.0; + // Extra printout section + if (m_print_flag > 2) { + // Calculate the expected residual at the Cauchy point if the linear model is correct + doublereal residCauchy = 0.0; if (residNorm2Cauchy_ > 0.0) { residCauchy = sqrt(residNorm2Cauchy_ / neq_); } else { if (fabs(JdJd_norm_) < 1.0E-290) { - residCauchy = m_normResid0; + residCauchy = m_normResid_0; } else { - residCauchy = m_normResid0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); + residCauchy = m_normResid_0 - sqrt(RJd_norm_ * RJd_norm_ / (JdJd_norm_)); } - } - + } // Compute the weighted norm of the undamped step size descentDir_[] if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 10); } else { normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 0); } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { printf("\t\t doCauchyPointSolve: Steepest descent to Cauchy point: \n"); - printf("\t\t\t R0 = %g \n", m_normResid0); + printf("\t\t\t R0 = %g \n", m_normResid_0); printf("\t\t\t Rpred = %g\n", residCauchy); printf("\t\t\t Rjd = %g\n", RJd_norm_); printf("\t\t\t JdJd = %g\n", JdJd_norm_); printf("\t\t\t deltaX = %g\n", normSoln); printf("\t\t\t lambda = %g\n", lambdaStar_); } + } else { + // Calculate the norm of the Cauchy solution update in any case + normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 0); } return normSoln; } //=================================================================================================================== - void NonlinearSolver::descentComparison(double time_curr, double *ydot0, double *ydot1) + void NonlinearSolver::descentComparison(doublereal time_curr, doublereal *ydot0, doublereal *ydot1, int &numTrials) { int info; - double ff = 1.0E-5; - double *y1 = DATA_PTR(m_wksp); - double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + doublereal ff = 1.0E-5; + doublereal *y_n_1 = DATA_PTR(m_wksp); + doublereal cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + if (cauchyDistanceNorm < 1.0E-2) { + ff = 1.0E-9 / cauchyDistanceNorm; + if (ff > 1.0E-2) { + ff = 1.0E-2; + } + } for (int i = 0; i < neq_; i++) { - mdp::checkFinite(deltaX_CP_[i]); - y1[i] = m_y_n_curr[i] + ff * deltaX_CP_[i]; + y_n_1[i] = m_y_n_curr[i] + ff * deltaX_CP_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot1, Base_LaggedSolutionComponents); } else { - info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot0, Base_LaggedSolutionComponents); } - double normResid02 = m_normResid0 * m_normResid0 * neq_; - double residSteep = residErrorNorm(DATA_PTR(m_resid)); - double residSteep2 = residSteep * residSteep * neq_; - double funcDecrease2 = 0.5 * (residSteep2 - normResid02) / ( ff * cauchyDistanceNorm); + doublereal normResid02 = m_normResid_0 * m_normResid_0 * neq_; + doublereal residSteep = residErrorNorm(DATA_PTR(m_resid)); + doublereal residSteep2 = residSteep * residSteep * neq_; + doublereal funcDecreaseSD = 0.5 * (residSteep2 - normResid02) / ( ff * cauchyDistanceNorm); - double sNewt = solnErrorNorm(DATA_PTR(deltaX_Newton_)); + doublereal sNewt = solnErrorNorm(DATA_PTR(deltaX_Newton_)); for (int i = 0; i < neq_; i++) { - y1[i] = m_y_n_curr[i] + ff * deltaX_Newton_[i]; + y_n_1[i] = m_y_n_curr[i] + ff * deltaX_Newton_[i]; } /* - * Calculate the residual that would result if y1[] were the new solution vector + * Calculate the residual that would result if y1[] were the new solution vector. + * Here we use the lagged solution components in the residual calculation as well. We are + * interested in the linear model and its agreement with the nonlinear model. + * * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot1, Base_LaggedSolutionComponents); } else { - info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot0, Base_LaggedSolutionComponents); } - double residNewt = residErrorNorm(DATA_PTR(m_resid)); - double residNewt2 = residNewt * residNewt * neq_; + doublereal residNewt = residErrorNorm(DATA_PTR(m_resid)); + doublereal residNewt2 = residNewt * residNewt * neq_; - double funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); + doublereal funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); - // This is the expected inital rate of decrease in the cauchy direction. + // This is the expected inital rate of decrease in the Cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || - double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; + doublereal funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; - double funcDecreaseNewtExp2 = - normResid02 / sNewt; + doublereal funcDecreaseNewtExp2 = - normResid02 / sNewt; + + if ( m_normResid_0 > 1.0E-100) { + ResidDecreaseSDExp_ = funcDecreaseSDExp / neq_ / m_normResid_0; + ResidDecreaseSD_ = funcDecreaseSD / neq_ / m_normResid_0; + ResidDecreaseNewtExp_ = funcDecreaseNewtExp2 / neq_ / m_normResid_0; + ResidDecreaseNewt_ = funcDecreaseNewt2 / neq_ / m_normResid_0; + } else { + ResidDecreaseSDExp_ = 0.0; + ResidDecreaseSD_ = funcDecreaseSD / neq_; + ResidDecreaseNewtExp_ = 0.0; + ResidDecreaseNewt_ = funcDecreaseNewt2 / neq_; + } + numTrials += 2; /* * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights */ - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("\t\t descentComparison: initial rate of decrease in cauchy dir (expected) = %g\n", funcDecreaseSDExp); - printf("\t\t descentComparison: initial rate of decrease in cauchy dir = %g\n", funcDecrease2); - printf("\t\t descentComparison: initial rate of decrease in newton dir (expected) = %g\n", funcDecreaseNewtExp2); - printf("\t\t descentComparison: initial rate of decrease in newton dir = %g\n", funcDecreaseNewt2); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 5)) { + printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir (expected) = %g\n", funcDecreaseSDExp); + printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir = %g\n", funcDecreaseSD); + printf("\t\t descentComparison: initial rate of decrease of func in newton dir (expected) = %g\n", funcDecreaseNewtExp2); + printf("\t\t descentComparison: initial rate of decrease of func in newton dir = %g\n", funcDecreaseNewt2); + } + if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir (expected) = %g\n", ResidDecreaseSDExp_); + printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir = %g\n", ResidDecreaseSD_); + printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir (expected) = %g\n", ResidDecreaseNewtExp_); + printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir = %g\n", ResidDecreaseNewt_); } } @@ -1367,7 +1437,7 @@ namespace Cantera { // double fac1 = sumG / lambdaStar_; // double fac2 = sumH / lambdaStar_; // double gamma = fac1 / fac2; - // double gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; + // doublereal gamma = m_normDeltaSoln_CP / m_normDeltaSoln_Newton; /* * This hasn't worked. so will do it heuristically. One issue is that the newton * direction is not the inverse of the Hessian times the gradient. The Hession @@ -1382,12 +1452,12 @@ namespace Cantera { * Maybe we need to check that the linearized residual is * monotonic along that line. However, we haven't needed to yet. */ - double residSteepLin = expectedResidLeg(0, 1.0); - double Nres2CP = residSteepLin * residSteepLin * neq_; - double Nres2_o = m_normResid0 * m_normResid0 * neq_; - double a = Nres2CP / Nres2_o; - double betaEqual = (2.0 - sqrt(4.0 - 4 * (1.0 - a))) / 2.0; - double beta = (1.0 + betaEqual) / 2.0; + doublereal residSteepLin = expectedResidLeg(0, 1.0); + doublereal Nres2CP = residSteepLin * residSteepLin * neq_; + doublereal Nres2_o = m_normResid_0 * m_normResid_0 * neq_; + doublereal a = Nres2CP / Nres2_o; + doublereal betaEqual = (2.0 - sqrt(4.0 - 4 * (1.0 - a))) / 2.0; + doublereal beta = (1.0 + betaEqual) / 2.0; Nuu_ = beta; @@ -1415,7 +1485,7 @@ namespace Cantera { * * @return Returns the leg number ( 0, 1, or 2). */ - int NonlinearSolver::lambdaToLeg(const double lambda, double &alpha) const { + int NonlinearSolver::lambdaToLeg(const doublereal lambda, doublereal &alpha) const { if (lambda < dist_R0_ / dist_Total_) { alpha = lambda * dist_Total_ / dist_R0_; @@ -1438,8 +1508,8 @@ namespace Cantera { */ doublereal NonlinearSolver::expectedResidLeg(int leg, doublereal alpha) const { - double resD2, res2, resNorm; - double normResid02 = m_normResid0 * m_normResid0 * neq_; + doublereal resD2, res2, resNorm; + doublereal normResid02 = m_normResid_0 * m_normResid_0 * neq_; if (leg == 0) { /* @@ -1448,8 +1518,8 @@ namespace Cantera { * R2 = R2 + 2 lambda R dot Jd + lambda**2 Jd dot Jd */ - double tmp = - 2.0 * alpha + alpha * alpha; - double tmp2 = - RJd_norm_ * lambdaStar_; + doublereal tmp = - 2.0 * alpha + alpha * alpha; + doublereal tmp2 = - RJd_norm_ * lambdaStar_; resD2 = tmp2 * tmp; } else if (leg == 1) { @@ -1457,12 +1527,12 @@ namespace Cantera { /* * Same formula as above for lambda=1. */ - double tmp2 = - RJd_norm_ * lambdaStar_; - double RdotJS = - tmp2; - double JsJs = tmp2; + doublereal tmp2 = - RJd_norm_ * lambdaStar_; + doublereal RdotJS = - tmp2; + doublereal JsJs = tmp2; - double res0_2 = m_normResid0 * m_normResid0 * neq_; + doublereal res0_2 = m_normResid_0 * m_normResid_0 * neq_; res2 = res0_2 + (1.0 - alpha) * 2 * RdotJS - 2 * alpha * Nuu_ * res0_2 + (1.0 - alpha) * (1.0 - alpha) * JsJs @@ -1473,15 +1543,15 @@ namespace Cantera { return resNorm; } else { - double beta = Nuu_ + alpha * (1.0 - Nuu_); - double tmp2 = normResid02; - double tmp = 1.0 - 2.0 * beta + 1.0 * beta * beta - 1.0; + doublereal beta = Nuu_ + alpha * (1.0 - Nuu_); + doublereal tmp2 = normResid02; + doublereal tmp = 1.0 - 2.0 * beta + 1.0 * beta * beta - 1.0; resD2 = tmp * tmp2; } - res2 = m_normResid0 * m_normResid0 * neq_ + resD2; + res2 = m_normResid_0 * m_normResid_0 * neq_ + resD2; if (res2 < 0.0) { - resNorm = m_normResid0 - sqrt(resD2/neq_); + resNorm = m_normResid_0 - sqrt(resD2/neq_); } else { resNorm = sqrt(res2 / neq_); } @@ -1501,19 +1571,19 @@ namespace Cantera { */ void NonlinearSolver::residualComparisonLeg(const doublereal time_curr, const doublereal * const ydot0, int &legBest, doublereal &alphaBest) const { - double *y1 = DATA_PTR(m_wksp); - double *ydot1 = DATA_PTR(m_wksp_2); - double sLen; - double alpha; + doublereal *y1 = DATA_PTR(m_wksp); + doublereal *ydot1 = DATA_PTR(m_wksp_2); + doublereal sLen; + doublereal alpha; - double residSteepBest = 1.0E300; - double residSteepLinBest = 0.0; + doublereal residSteepBest = 1.0E300; + doublereal residSteepLinBest = 0.0; if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf("\t\t residualComparisonLeg() \n"); printf("\t\t Point StepLen Residual_Actual Residual_Linear RelativeMatch\n"); } // First compare at 1/4 along SD curve - std::vector alphaT; + std::vector alphaT; alphaT.push_back(0.00); alphaT.push_back(0.01); alphaT.push_back(0.1); @@ -1541,8 +1611,8 @@ namespace Cantera { } - double residSteep = residErrorNorm(DATA_PTR(m_resid)); - double residSteepLin = expectedResidLeg(0, alpha); + doublereal residSteep = residErrorNorm(DATA_PTR(m_resid)); + doublereal residSteepLin = expectedResidLeg(0, alpha); if (residSteep < residSteepBest) { legBest = 0; alphaBest = alpha; @@ -1550,14 +1620,14 @@ namespace Cantera { residSteepLinBest = residSteepLin; } - double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + doublereal relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 0, alpha, sLen, residSteep, residSteepLin , relFit); } } for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { - double alpha = alphaT[iteration]; + doublereal alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { y1[i] = m_y_n_curr[i] + (1.0 - alpha) * deltaX_CP_[i]; y1[i] += alpha * Nuu_ * deltaX_Newton_[i]; @@ -1580,8 +1650,8 @@ namespace Cantera { } sLen = solnErrorNorm(DATA_PTR(y1)); - double residSteep = residErrorNorm(DATA_PTR(m_resid)); - double residSteepLin = expectedResidLeg(1, alpha); + doublereal residSteep = residErrorNorm(DATA_PTR(m_resid)); + doublereal residSteepLin = expectedResidLeg(1, alpha); if (residSteep < residSteepBest) { legBest = 1; alphaBest = alpha; @@ -1589,14 +1659,14 @@ namespace Cantera { residSteepLinBest = residSteepLin; } - double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + doublereal relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 1, alpha, sLen, residSteep, residSteepLin , relFit); } } for (int iteration = 0; iteration < (int) alphaT.size(); iteration++) { - double alpha = alphaT[iteration]; + doublereal alpha = alphaT[iteration]; for (int i = 0; i < neq_; i++) { y1[i] = m_y_n_curr[i] + ( Nuu_ + alpha * (1.0 - Nuu_))* deltaX_Newton_[i]; } @@ -1616,25 +1686,25 @@ namespace Cantera { - double residSteep = residErrorNorm(DATA_PTR(m_resid)); - double residSteepLin = expectedResidLeg(2, alpha); + doublereal residSteep = residErrorNorm(DATA_PTR(m_resid)); + doublereal residSteepLin = expectedResidLeg(2, alpha); if (residSteep < residSteepBest) { legBest = 2; alphaBest = alpha; residSteepBest = residSteep; residSteepLinBest = residSteepLin; } - double relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); + doublereal relFit = (residSteep - residSteepLin) / (fabs(residSteepLin) + 1.0E-10); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf("\t\t (%2d - % 10.3g) % 15.8E % 15.8E % 15.8E % 15.8E\n", 2, alpha, sLen, residSteep, residSteepLin , relFit); } } if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { printf("\t\t Best Result: \n"); - double relFit = (residSteepBest - residSteepLinBest) / (fabs(residSteepLinBest) + 1.0E-10); + doublereal relFit = (residSteepBest - residSteepLinBest) / (fabs(residSteepLinBest) + 1.0E-10); if (m_print_flag <= 6) { - printf("\t\t Leg %2d alpha %5g: NonlinResid = %g LinResid = %g, relfit = %g\n", - legBest, alphaBest, residSteepBest, residSteepLinBest, relFit); + printf("\t\t Leg %2d alpha %5g: NonlinResid = %g LinResid = %g, relfit = %g\n", + legBest, alphaBest, residSteepBest, residSteepLinBest, relFit); } else { if (legBest == 0) { sLen = alpha * solnErrorNorm(DATA_PTR(deltaX_CP_)); @@ -1654,7 +1724,7 @@ namespace Cantera { } //==================================================================================================================== - double NonlinearSolver::trustRegionLength() const + doublereal NonlinearSolver::trustRegionLength() const { norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); return (trustDelta_ * norm_deltaX_trust_); @@ -1668,6 +1738,16 @@ namespace Cantera { } } //==================================================================================================================== + void NonlinearSolver::adjustUpStepMinimums() { + for (int i = 0; i < neq_; i++) { + doublereal goodVal = deltaX_trust_[i] * trustDelta_; + if (deltaX_trust_[i] * trustDelta_ > m_deltaStepMinimum[i]) { + m_deltaStepMinimum[i] = 1.1 * goodVal; + } + + } + } + //==================================================================================================================== void NonlinearSolver::setDeltaBoundsMagnitudes(const doublereal * const deltaStepMinimum) { @@ -1689,46 +1769,47 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 2 * - * @param y Initial value of the solution vector - * @param step0 initial proposed step size + * @param y_n_curr Initial value of the solution vector + * @param step_1 initial proposed step size * * @return returns the damping factor */ double - NonlinearSolver::deltaBoundStep(const doublereal * const y, const doublereal * const step0) { + NonlinearSolver::deltaBoundStep(const doublereal * const y_n_curr, const doublereal * const step_1) { int i_fbounds = 0; int ifbd = 0; int i_fbd = 0; + doublereal UPFAC = 2.0; doublereal sameSign = 0.0; doublereal ff; doublereal f_delta_bounds = 1.0; doublereal ff_alt; for (int i = 0; i < neq_; i++) { - doublereal y_new = y[i] + step0[i]; - sameSign = y_new * y[i]; + doublereal y_new = y_n_curr[i] + step_1[i]; + sameSign = y_new * y_n_curr[i]; /* * Now do a delta bounds - * Increase variables by a factor of 1.5 only + * Increase variables by a factor of UPFAC only * decrease variables by a factor of 2 only */ ff = 1.0; if (sameSign >= 0.0) { - if ((fabs(y_new) > 1.5 * fabs(y[i])) && - (fabs(y_new - y[i]) > m_deltaStepMinimum[i])) { - ff = 0.5 * fabs(y[i]/(y_new - y[i])); - ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); + if ((fabs(y_new) > UPFAC * fabs(y_n_curr[i])) && + (fabs(y_new - y_n_curr[i]) > m_deltaStepMinimum[i])) { + ff = (UPFAC - 1.0) * fabs(y_n_curr[i]/(y_new - y_n_curr[i])); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y_n_curr[i])); ff = MAX(ff, ff_alt); ifbd = 1; } - if ((fabs(2.0 * y_new) < fabs(y[i])) && - (fabs(y_new - y[i]) > m_deltaStepMinimum[i])) { - ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; - ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); + if ((fabs(2.0 * y_new) < fabs(y_n_curr[i])) && + (fabs(y_new - y_n_curr[i]) > m_deltaStepMinimum[i])) { + ff = y_n_curr[i]/(y_new - y_n_curr[i]) * (1.0 - 2.0)/2.0; + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y_n_curr[i])); ff = MAX(ff, ff_alt); ifbd = 0; } @@ -1737,11 +1818,11 @@ namespace Cantera { * This handles the case where the value crosses the origin. * - First we don't let it cross the origin until its shrunk to the size of m_deltaStepMinimum[i] */ - if (fabs(y[i]) > m_deltaStepMinimum[i]) { - ff = y[i]/(y_new - y[i]) * (1.0 - 2.0)/2.0; - ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); + if (fabs(y_n_curr[i]) > m_deltaStepMinimum[i]) { + ff = y_n_curr[i]/(y_new - y_n_curr[i]) * (1.0 - 2.0)/2.0; + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y_n_curr[i])); ff = MAX(ff, ff_alt); - if (y[i] >= 0.0) { + if (y_n_curr[i] >= 0.0) { ifbd = 0; } else { ifbd = 1; @@ -1750,9 +1831,9 @@ namespace Cantera { /* * Second when it does cross the origin, we make sure that its magnitude is only 50% of the previous value. */ - else if (fabs(y_new) > 0.5 * fabs(y[i])) { - ff = y[i]/(y_new - y[i]) * (-1.5); - ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y[i])); + else if (fabs(y_new) > 0.5 * fabs(y_n_curr[i])) { + ff = y_n_curr[i]/(y_new - y_n_curr[i]) * (-1.5); + ff_alt = fabs(m_deltaStepMinimum[i] / (y_new - y_n_curr[i])); ff = MAX(ff, ff_alt); ifbd = 0; } @@ -1771,16 +1852,18 @@ namespace Cantera { /* * Report on any corrections */ - if (m_print_flag > 1) { + if (m_print_flag >= 3) { if (f_delta_bounds < 1.0) { if (i_fbd) { printf("\t\tdeltaBoundStep: Increase of Variable %d causing " - "delta damping of %g\n", - i_fbounds, f_delta_bounds); + "delta damping of %g: origVal = %10.3g, undampedNew = %10.3g, dampedNew = %10.3g\n", + i_fbounds, f_delta_bounds, y_n_curr[i_fbounds], y_n_curr[i_fbounds] + step_1[i_fbounds], + y_n_curr[i_fbounds] + f_delta_bounds * step_1[i_fbounds] ); } else { printf("\t\tdeltaBoundStep: Decrease of variable %d causing" - "delta damping of %g\n", - i_fbounds, f_delta_bounds); + "delta damping of %g: origVal = %10.3g, undampedNew = %10.3g, dampedNew = %10.3g\n", + i_fbounds, f_delta_bounds, y_n_curr[i_fbounds], y_n_curr[i_fbounds] + step_1[i_fbounds], + y_n_curr[i_fbounds] + f_delta_bounds * step_1[i_fbounds]); } } } @@ -1797,25 +1880,25 @@ namespace Cantera { */ void NonlinearSolver::calcTrustVector() { - double wtSum = 0.0; + doublereal wtSum = 0.0; for (int i = 0; i < neq_; i++) { wtSum += m_ewt[i]; } wtSum /= neq_; - double trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); - double trustNormGoal = trustNorm * trustDelta_; + doublereal trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); + doublereal trustNormGoal = trustNorm * trustDelta_; // This is the size of each component. - double trustDeltaEach = trustDelta_ * trustNorm / neq_; - double oldVal; - double fabsy; + doublereal trustDeltaEach = trustDelta_ * trustNorm / neq_; + doublereal oldVal; + doublereal fabsy; // we use the old value of the trust region as an indicator for (int i = 0; i < neq_; i++) { oldVal = deltaX_trust_[i]; fabsy = fabs(m_y_n_curr[i]); // First off make sure that each trust region vector is 1/2 the size of each variable or smaller // unless overridden by the deltaStepMininum value. - double newValue = trustDeltaEach * m_ewt[i] / wtSum; + doublereal newValue = trustDeltaEach * m_ewt[i] / wtSum; if (newValue > 0.5 * fabsy) { if (fabsy * 0.5 > m_deltaStepMinimum[i]) { deltaX_trust_[i] = 0.5 * fabsy; @@ -1841,7 +1924,7 @@ namespace Cantera { // Final renormalization. norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); - double sum = trustNormGoal / trustNorm; + doublereal sum = trustNormGoal / trustNorm; for (int i = 0; i < neq_; i++) { deltaX_trust_[i] = deltaX_trust_[i] * sum; } @@ -1860,7 +1943,7 @@ namespace Cantera { */ void NonlinearSolver::initializeTrustRegion() { - double cpd = calcTrustDistance(deltaX_CP_); + doublereal cpd = calcTrustDistance(deltaX_CP_); if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } @@ -1882,7 +1965,7 @@ namespace Cantera { * @param alpha Relative length along the dog length that you are on. * @param deltaX Vector to be filled up */ - void NonlinearSolver::fillDogLegStep(int leg, double alpha, std::vector & deltaX) const { + void NonlinearSolver::fillDogLegStep(int leg, doublereal alpha, std::vector & deltaX) const { if (leg == 0) { for (int i = 0; i < neq_; i++) { deltaX[i] = alpha * deltaX_CP_[i]; @@ -1927,9 +2010,9 @@ namespace Cantera { * @param alpha (OUTPUT) Returns the relative distance along the appropriate leg * @return leg (OUTPUT) Returns the leg ID (0, 1, or 2) */ - int NonlinearSolver::calcTrustIntersection(double trustDelta, double &lambda, double &alpha) const + int NonlinearSolver::calcTrustIntersection(doublereal trustDelta, doublereal &lambda, doublereal &alpha) const { - double dist; + doublereal dist; if (normTrust_Newton_ < trustDelta) { lambda = 1.0; alpha = 1.0; @@ -1949,14 +2032,14 @@ namespace Cantera { alpha = trustDelta / normTrust_CP_; return 0; } - double sumv = 0.0; + doublereal sumv = 0.0; for (int i = 0; i < neq_; i++) { sumv += (deltaX_Newton_[i] / deltaX_trust_[i]) * (deltaX_CP_[i] / deltaX_trust_[i]); } - double a = normTrust_Newton_ * normTrust_Newton_ * Nuu_ * Nuu_; - double b = 2.0 * Nuu_ * sumv; - double c = normTrust_CP_ * normTrust_CP_ - trustDelta * trustDelta; + doublereal a = normTrust_Newton_ * normTrust_Newton_ * Nuu_ * Nuu_; + doublereal b = 2.0 * Nuu_ * sumv; + doublereal c = normTrust_CP_ * normTrust_CP_ - trustDelta * trustDelta; alpha =( -b + sqrt( b * b - 4.0 * a * c)) / (2.0 * a); @@ -2029,11 +2112,10 @@ namespace Cantera { } - /* * Report on any corrections */ - if (m_print_flag > 1) { + if (m_print_flag >= 3) { if (f_bounds != 1.0) { printf("\t\tboundStep: Variable %d causing bounds damping of %g\n", i_lower, f_bounds); } @@ -2044,10 +2126,9 @@ namespace Cantera { return fbound; } - //==================================================================================================================== - /* - * - * dampStep(): + //=================================================================================================================== + // Find a damping coefficient through a look-ahead mechanism + /* * * On entry, step0 must contain an undamped Newton step to the * current solution y0. This method attempts to find a damping coefficient @@ -2066,23 +2147,30 @@ namespace Cantera { * from the previous step. * A predicted deltaSoln1 is not produced however. s1 is estimated. * 0 Uncertain Success: s1 is about the same as s0 - * -2 Unsuccessful step. + * NSOLN_RETN_FAIL_DAMPSTEP + * Unsuccessful step. We can not find a damping factor that is suitable. */ - int NonlinearSolver::dampStep(const doublereal time_curr, const double* y0, - const doublereal *ydot0, const double* step0, - double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, bool writetitle, - int& num_backtracks) - { + int NonlinearSolver::dampStep(const doublereal time_curr, const doublereal * y_n_curr, + const doublereal * ydot_n_curr, doublereal * const step_1, + doublereal * const y_n_1, double* const ydot_n_1, doublereal * const step_2, + double& stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks) + { + int j, m; int info = 0; - int retnTrial = -2; - // Compute the weighted norm of the undamped step size step0 - doublereal s0 = solnErrorNorm(step0); + int retnTrial = NSOLN_RETN_FAIL_DAMPSTEP; + // Compute the weighted norm of the undamped step size step_1 + doublereal stepNorm_1 = solnErrorNorm(step_1); + + doublereal * step_1_orig = DATA_PTR(m_wksp); + for (j = 0; j < neq_; j++) { + step_1_orig[j] = step_1[j]; + } + // Compute the multiplier to keep all components in bounds.A value of one indicates that there is no limitation // on the current step size in the nonlinear method due to bounds constraints (either negative values of delta // bounds constraints. - m_dampBound = boundStep(y0, step0); + m_dampBound = boundStep(y_n_curr, step_1); // If fbound is very small, then y0 is already close to the boundary and step0 points out of the allowed domain. In // this case, the Newton algorithm fails, so return an error condition. @@ -2097,7 +2185,7 @@ namespace Cantera { // damping coefficient starts at 1.0 m_dampRes = 1.0; - int j, m; + doublereal ff = m_dampBound; num_backtracks = 0; for (m = 0; m < NDAMP; m++) { @@ -2110,20 +2198,21 @@ namespace Cantera { * update the time derivative. */ for (j = 0; j < neq_; j++) { - y1[j] = y0[j] + ff * step0[j]; + step_1[j] = ff * step_1_orig[j]; + y_n_1[j] = y_n_curr[j] + step_1[j]; } if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - calc_ydot(m_order, y1, ydot1); + calc_ydot(m_order, y_n_1, ydot_n_1); } /* * Calculate the residual that would result if y1[] were the new solution vector * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot_n_1, Base_LaggedSolutionComponents); } else { - info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot_n_curr, Base_LaggedSolutionComponents); } if (info != 1) { if (m_print_flag > 0) { @@ -2132,34 +2221,38 @@ namespace Cantera { return -1; } m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); + m_normResid_1 = m_normResidTrial; + if (m == 0) { + m_normResid_Bound = m_normResidTrial; + } - bool steepEnough = (m_normResidTrial < m_normResid0 * (0.9 * (1.0 - ff) * (1.0 - ff)* (1.0 - ff) + 0.1)); + bool steepEnough = (m_normResidTrial < m_normResid_0 * (0.9 * (1.0 - ff) * (1.0 - ff)* (1.0 - ff) + 0.1)); if (m_normResidTrial < 1.0 || steepEnough) { if (m_print_flag >= 5) { if (m_normResidTrial < 1.0) { printf("\t dampStep(): Current trial step and damping" " coefficient accepted because residTrial test step < 1:\n"); - printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid_0, m_normResidTrial); } else if (steepEnough) { printf("\t dampStep(): Current trial step and damping" " coefficient accepted because resid0 > residTrial and steep enough:\n"); - printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid_0, m_normResidTrial); } else { printf("\t dampStep(): Current trial step and damping" " coefficient accepted because residual solution damping is turned off:\n"); - printf("\t resid0 = %g, residTrial = %g\n", m_normResid0, m_normResidTrial); + printf("\t resid0 = %g, residTrial = %g\n", m_normResid_0, m_normResidTrial); } } /* * We aren't going to solve the system if we don't need to. Therefore, return an estimate * of the next solution update based on the ratio of the residual reduction. */ - if (m_normResid0 > 0.0) { - s1 = s0 * m_normResidTrial / m_normResid0; + if (m_normResid_0 > 0.0) { + stepNorm_2 = stepNorm_1 * m_normResidTrial / m_normResid_0; } else { - s1 = 0; + stepNorm_2 = 0; } if (m_normResidTrial < 1.0) { retnTrial = 3; @@ -2172,9 +2265,9 @@ namespace Cantera { // Compute the next undamped step, step1[], that would result if y1[] were accepted. // We now have two steps that we have calculated step0[] and step1[] if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doNewtonSolve(time_curr, y1, ydot1, step1, jac); + info = doNewtonSolve(time_curr, y_n_1, ydot_n_1, step_2, jac); } else { - info = doNewtonSolve(time_curr, y1, ydot0, step1, jac); + info = doNewtonSolve(time_curr, y_n_1, ydot_n_curr, step_2, jac); } if (info) { if (m_print_flag > 0) { @@ -2184,21 +2277,18 @@ namespace Cantera { } // compute the weighted norm of step1 - s1 = solnErrorNorm(step1); + stepNorm_2 = solnErrorNorm(step_2); // write log information - if (m_print_flag > 3) { - print_solnDelta_norm_contrib((const doublereal *) step0, - "DeltaSoln", - (const doublereal *) step1, - "DeltaSolnTrial", - "dampNewt: Important Entries for " - "Weighted Soln Updates:", - y0, y1, ff, 5); + if (m_print_flag >= 5) { + print_solnDelta_norm_contrib((const doublereal *) step_1_orig, "DeltaSoln", + (const doublereal *) step_2, "DeltaSolnTrial", + "dampNewt: Important Entries for Weighted Soln Updates:", + y_n_curr, y_n_1, ff, 5); } - if (m_print_flag > 1) { - printf("\t\t\tdampStep(): s0 = %g, s1 = %g, dampBound = %g," - "dampRes = %g\n", s0, s1, m_dampBound, m_dampRes); + if (m_print_flag >= 4) { + printf("\t\t\tdampStep(): s1 = %g, s2 = %g, dampBound = %g," + "dampRes = %g\n", stepNorm_1, stepNorm_2, m_dampBound, m_dampRes); } @@ -2207,13 +2297,12 @@ namespace Cantera { // step would result in a converged solution. Otherwise, // decrease the damping coefficient and try again. - if (s1 < 0.8 || s1 < s0) { - if (s1 < 1.0) { - if (m_print_flag > 2) { - if (s1 < 1.0) { - printf("\t\t\tdampStep: current trial step and damping" - " coefficient accepted because test step < 1\n"); - printf("\t\t\t s1 = %g, s0 = %g\n", s1, s0); + if (stepNorm_2 < 0.8 || stepNorm_2 < stepNorm_1) { + if (stepNorm_2 < 1.0) { + if (m_print_flag >= 3) { + if (stepNorm_2 < 1.0) { + printf("\t\t\tdampStep: current trial step and damping coefficient accepted because test step < 1\n"); + printf("\t\t\t s2 = %g, s1 = %g\n", stepNorm_2, stepNorm_1); } } retnTrial = 2; @@ -2224,7 +2313,7 @@ namespace Cantera { } else { if (m_print_flag > 1) { printf("\t\t\tdampStep: current step rejected: (s1 = %g > " - "s0 = %g)", s1, s0); + "s0 = %g)", stepNorm_2, stepNorm_1); if (m < (NDAMP-1)) { printf(" Decreasing damping factor and retrying"); } else { @@ -2240,20 +2329,20 @@ namespace Cantera { // If a damping coefficient was found, return 1 if the // solution after stepping by the damped step would represent // a converged solution, and return 0 otherwise. If no damping - // coefficient could be found, return -2. + // coefficient could be found, return NSOLN_RETN_FAIL_DAMPSTEP. if (m < NDAMP) { if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted retnTrial = %d, its = %d, damp = %g\n", retnTrial, m+1, ff); } return retnTrial; } else { - if (s1 < 0.5 && (s0 < 0.5)) { + if (stepNorm_2 < 0.5 && (stepNorm_1 < 0.5)) { if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted kindof retnTrial = %d, its = %d, damp = %g\n", 2, m+1, ff); } return 2; } - if (s1 < 1.0) { + if (stepNorm_2 < 1.0) { if (m_print_flag >= 4 ) { printf("\t dampStep(): current trial step accepted and soln converged retnTrial = %d, its = %d, damp = %g\n", 0, m+1, ff); } @@ -2261,9 +2350,10 @@ namespace Cantera { } } if (m_print_flag >= 4 ) { - printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", -2, m+1, ff); + printf("\t dampStep(): current direction is rejected! retnTrial = %d, its = %d, damp = %g\n", + NSOLN_RETN_FAIL_DAMPSTEP, m+1, ff); } - return -2; + return NSOLN_RETN_FAIL_DAMPSTEP; } //==================================================================================================================== // Damp using the dog leg approach @@ -2277,32 +2367,31 @@ namespace Cantera { * @param ydot_n_1 INPUT First trial value of the derivative of the solution vector * @param s1 OUTPUT Norm of the vector step_1 * @param jac INPUT jacobian - * @param num_backtracks OUTPUT number of backtracks taken in the current damping step + * @param numTrials OUTPUT number of trials taken in the current damping step * * - * @return 1 Successful step was taken. The predicted residual norm is less than one - * 2 Successful step: Next step's norm is less than 0.8 - * 3 Success: The final residual is less than 1.0 + * @return 1 Success: Good step was taken. The predicted residual norm is less than one + * 2 Success: Good step: Next step's norm is less than 0.8 + * 3 Success: The final residual is less than 1.0 * A predicted deltaSoln1 is not produced however. s1 is estimated. - * 4 Success: The final residual is less than the residual - * from the previous step. + * 4 Success: The final residual is less than the residual from the previous step. * A predicted deltaSoln1 is not produced however. s1 is estimated. - * 0 Uncertain Success: s1 is about the same as s0 - * -2 Unsuccessful step. + * 0 Unknown Uncertain Success: s1 is about the same as s0 + * NSOLN_RETN_FAIL_DAMPSTEP + * Unsuccessful step. Can not find a damping coefficient that is suitable */ int NonlinearSolver::dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, const doublereal *ydot_n_curr, std::vector & step_1, doublereal* const y_n_1, doublereal* const ydot_n_1, - doublereal& s1, SquareMatrix& jac, int& num_backtracks) + doublereal& stepNorm_1, doublereal& stepNorm_2, SquareMatrix& jac, int& numTrials) { - double lambda; - double alpha; + doublereal lambda; int info; - int leg = 2; + bool success = false; int retn = 0; bool haveASuccess = false; - double trustDeltaOld = trustDelta_; + doublereal trustDeltaOld = trustDelta_; doublereal* stepLastGood = DATA_PTR(m_wksp); //-------------------------------------------- // Attempt damped step @@ -2311,26 +2400,26 @@ namespace Cantera { // damping coefficient starts at 1.0 m_dampRes = 1.0; int j, m; - num_backtracks = 0; - double tlen; + doublereal tlen; for (m = 0; m < NDAMP; m++) { + numTrials++; /* * Find the initial value of lambda that satisfies the trust distance, trustDelta_ */ - leg = calcTrustIntersection(trustDelta_, lambda, alpha); + dogLegID_ = calcTrustIntersection(trustDelta_, lambda, dogLegAlpha_); if (m_print_flag > 5) { tlen = trustRegionLength(); printf("\tdampDogLeg: trust region with length %13.5E has intersection at leg = %d, alpha = %g\n", - tlen, leg, alpha); + tlen, dogLegID_, dogLegAlpha_); } /* * Figure out the new step vector, step0, based on (leg, alpha). Here we are using the * inter */ - fillDogLegStep(leg, alpha, step_1); + fillDogLegStep(dogLegID_, dogLegAlpha_, step_1); /* * OK, now that we have step0, Bound the step @@ -2358,29 +2447,29 @@ namespace Cantera { } /* * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria - * as a good step. + * as a good step. The overall outcome is returned in the variable info. */ - info = decideStep(time_curr, leg, alpha, y_n_curr, ydot_n_curr, step_1, y_n_1, ydot_n_1, trustDeltaOld); + info = decideStep(time_curr, dogLegID_, dogLegAlpha_, y_n_curr, ydot_n_curr, step_1, y_n_1, ydot_n_1, trustDeltaOld); + m_normResid_Bound = m_normResid_1; /* * The algorithm failed to find a solution vector sufficiently different than the current point */ if (info == -1) { - num_backtracks++; + if (m_print_flag >= 1) { - double stepNorm = solnErrorNorm(DATA_PTR(step_1)); + doublereal stepNorm = solnErrorNorm(DATA_PTR(step_1)); printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); success = false; - retn = -1; + retn = NSOLN_RETN_FAIL_STEPTOOSMALL; break; } } if (info == -2) { - num_backtracks++; if (m_print_flag >= 1) { printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); success = false; - retn = -1; + retn = NSOLN_RETN_MATRIXINVERSIONERROR; break; } } @@ -2388,7 +2477,8 @@ namespace Cantera { success = true; break; } - if (info == 3) { + if (info == 3) { + haveASuccess = true; // Store the good results in stepLastGood mdp::mdp_copy_dbl_1(DATA_PTR(stepLastGood), CONSTD_DATA_PTR(step_1), neq_); @@ -2412,23 +2502,22 @@ namespace Cantera { success = true; break; } else { - num_backtracks++; + } } - - } /* * Estimate s1, the norm after the next step */ - double stepNorm = solnErrorNorm(DATA_PTR(step_1)); + stepNorm_1 = solnErrorNorm(DATA_PTR(step_1)); + stepNorm_2 = stepNorm_1; if (m_dampBound < 1.0) { - stepNorm /= m_dampBound; + stepNorm_2 /= m_dampBound; } - stepNorm /= lambda; - stepNorm *= m_normResidTrial / m_normResid0; - s1 = stepNorm; + stepNorm_2 /= lambda; + stepNorm_2 *= m_normResidTrial / m_normResid_0; + if (success) { if (m_normResidTrial < 1.0) { @@ -2440,7 +2529,7 @@ namespace Cantera { } return 0; } - return -1; + return NSOLN_RETN_FAIL_DAMPSTEP; } //==================================================================================================================== // Decide whether the current step is acceptable and adjust the trust region size @@ -2470,44 +2559,47 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int NonlinearSolver::decideStep(const doublereal time_curr, int leg, double alpha, const double * const y0, - const doublereal * const ydot0, const std::vector & step0, - const double * const y1, const double* const ydot1, double trustDeltaOld) + int NonlinearSolver::decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y_n_curr, + const doublereal * const ydot_n_curr, const std::vector & step_1, + const doublereal * const y_n_1, const double* const ydot_n_1, doublereal trustDeltaOld) { int retn = 2; bool goodStep = false; int info; - double ll; + doublereal ll; // Calculate the solution step length - double stepNorm = solnErrorNorm(DATA_PTR(step0)); + doublereal stepNorm = solnErrorNorm(DATA_PTR(step_1)); // Calculate the initial (R**2 * neq) value for the old function - double normResid0_2 = m_normResid0 * m_normResid0 * neq_; + doublereal normResid0_2 = m_normResid_0 * m_normResid_0 * neq_; // Calculate the distance to the cauchy point - double cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); + doublereal cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); // This is the expected inital rate of decrease in the cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || - double funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; + doublereal funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; if (funcDecreaseSDExp > 0.0) { - if (m_print_flag > 0) { + if (m_print_flag >= 5) { printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); } } /* - * Calculate the residual that would result if y1[] were the new solution vector + * Calculate the residual that would result if y1[] were the new solution vector. + * The Lagged solution components are kept lagged here. Unfortunately, it just doesn't work in some cases to use a + * Jacobian from a lagged state and then use a residual from an unlagged condition. The linear model doesn't + * agree with the nonlinear model. * -> m_resid[] contains the result of the residual calculation */ if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - info = doResidualCalc(time_curr, solnType_, y1, ydot1, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot_n_1, Base_LaggedSolutionComponents); } else { - info = doResidualCalc(time_curr, solnType_, y1, ydot0, Base_LaggedSolutionComponents); + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot_n_curr, Base_LaggedSolutionComponents); } if (info != 1) { - if (m_print_flag > 0) { + if (m_print_flag >= 2) { printf("\t\tdecideStep: current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); } return -2; @@ -2517,19 +2609,22 @@ namespace Cantera { * m_normResidTrial */ m_normResidTrial = residErrorNorm(DATA_PTR(m_resid)); - double normResidTrial_2 = neq_ * m_normResidTrial * m_normResidTrial; + doublereal normResidTrial_2 = neq_ * m_normResidTrial * m_normResidTrial; /* * We have a minimal acceptance test for passage. deltaf < 1.0E-4 (CauchySlope) (deltS) * This is the condition that D&S use in 6.4.5 */ - double funcDecrease = 0.5 * (normResidTrial_2 - normResid0_2); - double acceptableDelF = funcDecreaseSDExp * stepNorm * 1.0E-4; + doublereal funcDecrease = 0.5 * (normResidTrial_2 - normResid0_2); + doublereal acceptableDelF = funcDecreaseSDExp * stepNorm * 1.0E-4; if (funcDecrease < acceptableDelF) { + m_normResid_1 = m_normResidTrial; goodStep = true; + m_normResid_1 = m_normResidTrial; retn = 0; } else { trustDelta_ *= 0.33; + CurrentTrustFactor_ *= 0.33; retn = 2; // error condition if step is getting too small if (rtol_ * stepNorm < 1.0E-6) { @@ -2543,44 +2638,72 @@ namespace Cantera { * If we had to bounds delta the update, decrease the trust region */ if (m_dampBound < 1.0) { - trustDelta_ *= 0.5; - ll = trustRegionLength(); - printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bounds constraint\n", - ll*2, ll); + // trustDelta_ *= 0.5; + // NextTrustFactor_ *= 0.5; + // ll = trustRegionLength(); + // if (m_print_flag >= 5) { + // printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bounds constraint\n", ll*2, ll); + //} } else { retn = 0; /* * Calculate the expected residual from the quadratic model */ - double expectedNormRes = expectedResidLeg(leg, alpha); - double expectedFuncDecrease = 0.5 * (neq_ * expectedNormRes * expectedNormRes - normResid0_2); + doublereal expectedNormRes = expectedResidLeg(leg, alpha); + doublereal expectedFuncDecrease = 0.5 * (neq_ * expectedNormRes * expectedNormRes - normResid0_2); if (funcDecrease > 0.1 * expectedFuncDecrease) { - if ((m_normResidTrial > 0.5 * m_normResid0) && (m_normResidTrial > 0.1)) { + if ((m_normResidTrial > 0.5 * m_normResid_0) && (m_normResidTrial > 0.1)) { trustDelta_ *= 0.5; + NextTrustFactor_ *= 0.5; ll = trustRegionLength(); - printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", - ll*2, ll); + if (m_print_flag >= 5) { + printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", + ll*2, ll); + } } } else { /* * If we are doing well, consider increasing the trust region and recalculating */ - if (funcDecrease < 0.8 * expectedFuncDecrease || (m_normResidTrial < 0.33 * m_normResid0)) { - if (trustDelta_ <= trustDeltaOld) { + if (funcDecrease < 0.8 * expectedFuncDecrease || (m_normResidTrial < 0.33 * m_normResid_0)) { + if (trustDelta_ <= trustDeltaOld && (leg != 2 || alpha < 0.75) ) { trustDelta_ *= 2.0; + CurrentTrustFactor_ *= 2; + adjustUpStepMinimums(); ll = trustRegionLength(); - printf("\td\tecideStep(): Trust region increased from %g to %g due to good quad approximation\n", - ll*0.5, ll); + if (m_print_flag >= 5) { + printf("\t\tdecideStep(): Trust region increased from %g to %g due to good quad approximation\n", + ll*0.5, ll); + } retn = 3; } else { /* * Increase the size of the trust region for the next calculation */ - if (m_normResidTrial < 0.75 * expectedNormRes) { - trustDelta_ *= 2.0; - ll = trustRegionLength(); - printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", - ll*0.5, ll); + if (m_normResidTrial < 0.75 * expectedNormRes || (m_normResidTrial < 0.20 * m_normResid_0)) { + if (leg == 2 && alpha == 1.0 ) { + ll = trustRegionLength(); + if (ll < 2.0 * m_normDeltaSoln_Newton) { + trustDelta_ *= 2.0; + NextTrustFactor_ *= 2.0; + adjustUpStepMinimums(); + ll = trustRegionLength(); + if (m_print_flag >= 5) { + printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + ll*0.5, ll); + } + } + } else { + ll = trustRegionLength(); + trustDelta_ *= 2.0; + NextTrustFactor_ *= 2.0; + adjustUpStepMinimums(); + ll = trustRegionLength(); + if (m_print_flag >= 5) { + printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + ll*0.5, ll); + } + } } } } @@ -2590,7 +2713,6 @@ namespace Cantera { } //==================================================================================================================== /* - * * solve_nonlinear_problem(): * * Find the solution to F(X) = 0 by damped Newton iteration. On @@ -2604,10 +2726,8 @@ namespace Cantera { * @return A positive value indicates a successful convergence * -1 Failed convergence */ - int NonlinearSolver::solve_nonlinear_problem(int SolnType, double* y_comm, - double* ydot_comm, doublereal CJ, - doublereal time_curr, - SquareMatrix& jac, + int NonlinearSolver::solve_nonlinear_problem(int SolnType, double* y_comm, double* ydot_comm, doublereal CJ, + doublereal time_curr, SquareMatrix& jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput) { @@ -2617,20 +2737,19 @@ namespace Cantera { int info = 0; bool m_residCurrent = false; - int m = 0; + num_linear_solves -= m_numTotalLinearSolves; + int retnDamp = 0; + int retnCode = 0; bool forceNewJac = false; - doublereal s1=1.e30; -#ifdef DEBUG_DOGLEG + + doublereal stepNorm_1; + doublereal stepNorm_2; +#ifdef DEBUG_MODE int legBest; doublereal alphaBest; #endif - // std::vector y_curr(neq_, 0.0); - // std::vector ydot_curr(neq_, 0.0); - std::vector stp(neq_, 0.0); - std::vector stp1(neq_, 0.0); - std::vector y_new(neq_, 0.0); - + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), DATA_PTR(y_comm), neq_); if (SolnType != NSOLN_TYPE_STEADY_STATE || ydot_comm) { @@ -2642,9 +2761,8 @@ namespace Cantera { m_normDeltaSoln_Newton = 1.0E1; bool frst = true; num_newt_its = 0; - num_linear_solves = - m_numTotalLinearSolves; num_backtracks = 0; - int i_backtracks; + int i_numTrials; m_print_flag = loglevelInput; if (m_print_flag > 1) { jac.m_printLevel = 1; @@ -2655,22 +2773,33 @@ namespace Cantera { trustDelta_ = 1.0; if (m_print_flag == 2 || m_print_flag == 3) { - printf("\tsolve_nonlinear_problem():\n\n"); - printf("\t Iter Resid NewJac | LinearIts Ax-b | Fbound Fdamp DampIts | DeltaSolnF ResidF\n"); - printf("\t-------------------------------------------------------------------------------------------------\n"); - + if (doDogLeg_) { + printf("\tWt Iter Resid NewJac log(CN)| dRdS_CDexp dRdS_CD dRdS_Newtexp dRdS_Newt |" + "DS_Cauchy DS_Newton DS_Trust | legID legAlpha Fbound | CTF NTF | nTr|" + "DS_Final ResidLag ResidFull\n"); + printf("\t---------------------------------------------------------------------------------------------------" + "--------------------------------------------------------------------------------\n"); + } else { + printf("\t Wt Iter Resid NewJac | Fbound ResidBound | DampIts Fdamp DS_Step1 DS_Step2" + "ResidLag | DS_Damp DS_Newton ResidFull\n"); + printf("\t--------------------------------------------------------------------------------------------------" + "----------------------------------\n"); + } } - - while (1 > 0) { + CurrentTrustFactor_ = 1.0; + NextTrustFactor_ = 1.0; + ResidWtsReevaluated_ = false; + i_numTrials = 0; /* * Increment Newton Solve counter */ m_numTotalNewtIts++; num_newt_its++; + m_numLocalLinearSolves = 0; if (m_print_flag > 3) { printf("\t"); @@ -2683,7 +2812,7 @@ namespace Cantera { */ if (m_normDeltaSoln_Newton > 1.0E2) { createSolnWeights(DATA_PTR(m_y_n_curr)); -#ifdef DEBUG_DOGLEG +#ifdef DEBUG_MODE calcTrustVector(); #else if (doDogLeg_) { @@ -2692,9 +2821,9 @@ namespace Cantera { #endif } else { // Do this stuff every 5 iterations - if ( (num_newt_its % 5) == 1) { + if ((num_newt_its % 5) == 1) { createSolnWeights(DATA_PTR(m_y_n_curr)); -#ifdef DEBUG_DOGLEG +#ifdef DEBUG_MODE calcTrustVector(); #else if (doDogLeg_) { @@ -2703,7 +2832,6 @@ namespace Cantera { #endif } } - /* * Set default values of Delta bounds constraints @@ -2723,7 +2851,7 @@ namespace Cantera { info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), num_newt_its); if (info == 0) { - m = -4; + retnDamp = NSOLN_RETN_JACOBIANFORMATIONERROR ; goto done; } m_residCurrent = true; @@ -2750,7 +2878,7 @@ namespace Cantera { if (m_print_flag > 0) { printf("\t solve_nonlinear_problem(): Residual Calc ERROR %d. Bailing\n", info); } - m = -5; + retnDamp = NSOLN_RETN_RESIDUALFORMATIONERROR; goto done; } @@ -2758,21 +2886,21 @@ namespace Cantera { * Scale the matrix and the rhs, if they aren't already scaled * Figure out and store the residual scaling factors. */ - scaleMatrix(jac, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), time_curr); + scaleMatrix(jac, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), time_curr, num_newt_its); /* * Optional print out the initial residual */ if (m_print_flag >= 6) { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n_curr)); + m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n_curr)); } else if (m_print_flag == 4 || m_print_flag == 5) { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); + m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); } else { - m_normResid0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); + m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); } -#ifdef DEBUG_DOGLEG +#ifdef DEBUG_MODE if (m_print_flag > 3) { printf("\t solve_nonlinear_problem(): Calculate the steepest descent direction and Cauchy Point\n"); } @@ -2812,30 +2940,29 @@ namespace Cantera { } if (info) { - m = -6; + retnDamp = NSOLN_RETN_MATRIXINVERSIONERROR; goto done; } - mdp::mdp_copy_dbl_1(DATA_PTR(stp), CONSTD_DATA_PTR(deltaX_Newton_), neq_); + mdp::mdp_copy_dbl_1(DATA_PTR(m_step_1), CONSTD_DATA_PTR(deltaX_Newton_), neq_); if (m_print_flag > 3) { - m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 10); + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Step of the iteration", 10); } else { - m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(stp), "Initial Undamped Step of the iteration", 0); - } + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Step of the iteration", 0); + } - if (doDogLeg_) { -#ifdef DEBUG_DOGLEG - double trustD = calcTrustDistance(stp); +#ifdef DEBUG_MODE + doublereal trustD = calcTrustDistance(m_step_1); if (s_print_DogLeg || m_print_flag > 3) { if (trustD > trustDelta_) { - printf("\t\t newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", + printf("\t\t Newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", trustD, trustDelta_); - printf("\t\t newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", + printf("\t\t Newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", trustD, trustDelta_); } else { - printf("\t\t newton's method step size, %g trustVectorUnits, smaller than trust region, %g trustVectorUnits\n", + printf("\t\t Newton's method step size, %g trustVectorUnits, smaller than trust region, %g trustVectorUnits\n", trustD, trustDelta_); } } @@ -2845,39 +2972,41 @@ namespace Cantera { /* * Filter out bad directions */ - filterNewStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(stp)); + filterNewStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_step_1)); - -#ifdef DEBUG_DOGLEG - if (m_print_flag > 3) { + if (s_print_DogLeg &&m_print_flag >= 4) { printf("\t solve_nonlinear_problem(): Compare descent rates for Cauchy and Newton directions\n"); + descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1), i_numTrials); + } else { + if (doDogLeg_) { + descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1), i_numTrials); + } } - descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1)); -#endif + if (doDogLeg_) { setupDoubleDogleg(); -#ifdef DEBUG_DOGLEG - if (m_print_flag > 3) { +#ifdef DEBUG_MODE + if (s_print_DogLeg && m_print_flag >= 5) { printf("\t solve_nonlinear_problem(): Compare Linear and nonlinear residuals along double dog-leg path\n"); + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); } - residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); #endif - if (m_print_flag > 3) { + if (m_print_flag >= 4) { printf("\t solve_nonlinear_problem(): Calculate damping along dog-leg path to ensure residual decrease\n"); } - m = dampDogLeg(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), - stp, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), s1, jac, i_backtracks); + retnDamp = dampDogLeg(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), + m_step_1, DATA_PTR(m_y_n_1), DATA_PTR(m_ydot_n_1), stepNorm_1, stepNorm_2, jac, i_numTrials); } -#ifdef DEBUG_DOGLEG +#ifdef DEBUG_MODE else { - if (m_print_flag > 3) { - printf("\t solve_nonlinear_problem(): Compare Linear and nonlinear residuals along double dog-leg path\n"); + if (s_print_DogLeg && m_print_flag >= 5) { + printf("\t solve_nonlinear_problem(): Compare Linear and nonlinear residuals along double dog-leg path\n"); + residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); } - residualComparisonLeg(time_curr, DATA_PTR(m_ydot_n_curr), legBest, alphaBest); } #endif @@ -2892,21 +3021,25 @@ namespace Cantera { * s1 */ if (!doDogLeg_) { - m = dampStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), - DATA_PTR(stp), DATA_PTR(y_new), DATA_PTR(m_ydot_n_1), - DATA_PTR(stp1), s1, jac, frst, i_backtracks); + retnDamp = dampStep(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), + DATA_PTR(m_step_1), DATA_PTR(m_y_n_1), DATA_PTR(m_ydot_n_1), + DATA_PTR(m_wksp_2), stepNorm_2, jac, frst, i_numTrials); frst = false; - num_backtracks += i_backtracks; + num_backtracks += i_numTrials; + stepNorm_1 = solnErrorNorm(DATA_PTR(m_step_1)); } + + /* * Impose the minimum number of newton iterations critera */ if (num_newt_its < m_min_newt_its) { - if (m > 0) { + if (retnDamp > NSOLN_RETN_CONTINUE) { if (m_print_flag > 2) { - printf("\t solve_nonlinear_problem(): Damped Newton successful (m=%d) but minimum newton iterations not attained. Resolving ...\n", m); + printf("\t solve_nonlinear_problem(): Damped Newton successful (m=%d) but minimum newton" + "iterations not attained. Resolving ...\n", retnDamp); } - m = 0; + retnDamp = NSOLN_RETN_CONTINUE; } } @@ -2914,40 +3047,56 @@ namespace Cantera { * Impose max newton iteration */ if (num_newt_its > maxNewtIts_) { - m = -7; + retnDamp = NSOLN_RETN_MAXIMUMITERATIONSEXCEEDED; if (m_print_flag > 1) { - printf("\t solve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", s1); + printf("\t solve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", + stepNorm_1); } } - - info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1)); + /* + * Do a full residual calculation with the unlagged solution components. + * Then get the norm of the residual + */ + info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n_1), DATA_PTR(m_ydot_n_1)); if (info != 1) { if (m_print_flag > 0) { - printf("\t solve_nonlinear_problem(): current trial step and damping led to Residual Calc ERROR %d. Bailing\n", info); + printf("\t solve_nonlinear_problem(): current trial step and damping led to Residual Calc " + "ERROR %d. Bailing\n", info); } - m = -8; + retnDamp = NSOLN_RETN_RESIDUALFORMATIONERROR; goto done; } - - if (m_print_flag > 3) { - residErrorNorm(DATA_PTR(m_resid), "\t solve_nonlinear_problem():Resulting Residual Norm", 10, DATA_PTR(y_new)); + if (m_print_flag >= 4) { + m_normResid_full = residErrorNorm(DATA_PTR(m_resid), "\t solve_nonlinear_problem():Resulting Residual Norm", + 10, DATA_PTR(m_y_n_1)); + if (fabs(m_normResid_full - m_normResid_1) > 1.0E-3 * ( m_normResid_1 + m_normResid_full + 1.0E-4)) { + if (m_print_flag >= 4) { + printf("\t solve_nonlinear_problem(): Residual norm changed from %g to %g due to " + "lagging of components\n", m_normResid_1, m_normResid_full); + } + } + } else { + m_normResid_full = residErrorNorm(DATA_PTR(m_resid)); } + /* + * Check the convergence criteria + */ convRes = 0; - if (m > 0) { - convRes = convergenceCheck(m, s1); - } - + if (retnDamp > NSOLN_RETN_CONTINUE) { + convRes = convergenceCheck(retnDamp, stepNorm_1); + } if (m_print_flag >= 4) { if (convRes > 0) { printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, nonlin " - "converged, final estimate of the next solution update norm = %-12.4E\n", s1); - } else if (m >= 0) { + "converged, final estimate of the next solution update norm = %-12.4E\n", stepNorm_2); + } else if (retnDamp >= NSOLN_RETN_CONTINUE) { printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, " - "final estimate of the next solution update norm = %-12.4E\n", s1); + "estimate of the next solution update norm = %-12.4E\n", stepNorm_2); } else { - printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful, final estimate of the next solution update norm = %-12.4E\n", s1); + printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful, final estimate " + "of the next solution update norm = %-12.4E\n", stepNorm_2); } } @@ -2955,14 +3104,14 @@ namespace Cantera { bool m_filterIntermediate = false; if (m_filterIntermediate) { - if (m == 0) { - (void) filterNewSolution(time_n, DATA_PTR(y_new), DATA_PTR(m_ydot_n_1)); + if (retnDamp == NSOLN_RETN_CONTINUE) { + (void) filterNewSolution(time_n, DATA_PTR(m_y_n_1), DATA_PTR(m_ydot_n_1)); } } // Exchange new for curr solutions - if (m >= 0) { - mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), CONSTD_DATA_PTR(y_new), neq_); + if (retnDamp >= NSOLN_RETN_CONTINUE) { + mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), CONSTD_DATA_PTR(m_y_n_1), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { calc_ydot(m_order, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr)); @@ -2970,17 +3119,36 @@ namespace Cantera { } if (m_print_flag == 2 || m_print_flag == 3) { - // printf("\t Iter Resid NewJac | LinearIts Ax-b | Fbound Fdamp DampIts | DeltaSolnF ResidF\n"); - - printf("\t%4d %11.3E", num_newt_its, m_normResid0); + // printf("\t Iter Resid NewJac | Fbound | ResidBound | Fdamp DampIts | DeltaSolnNewton ResidFinal \n"); + if (ResidWtsReevaluated_) { + printf("\t*"); + } else { + printf("\t "); + } + printf(" %3d %11.3E", num_newt_its, m_normResid_0); bool m_jacAge = false; if (!m_jacAge) { - printf(" Y |"); + printf(" Y "); } else { - printf(" N |"); + printf(" N "); + } + if (doDogLeg_) { + printf("%5.1F |", log10(m_conditionNumber)); + // printf("\t Iter Resid NewJac | DS_Cauchy DS_Newton DS_Trust | legID legAlpha Fbound | | DS_F ResidFinal \n"); + printf("%10.3E %10.3E %10.3E %10.3E|", ResidDecreaseSDExp_, ResidDecreaseSD_, + ResidDecreaseNewtExp_, ResidDecreaseNewt_); + printf("%10.3E %10.3E %10.3E|", m_normDeltaSoln_CP , m_normDeltaSoln_Newton, norm_deltaX_trust_ * trustDelta_); + printf("%2d %10.2E %10.2E", dogLegID_ , dogLegAlpha_, m_dampBound); + printf("| %3.2f %3.2f |", CurrentTrustFactor_, NextTrustFactor_); + printf(" %2d ", i_numTrials); + printf("| %10.3E %10.3E %10.3E", stepNorm_1, m_normResid_1, m_normResid_full); + } else { + printf(" |"); + printf("%10.2E %10.3E |", m_dampBound, m_normResid_Bound); + printf("%2d %10.2E %10.3E %10.3E %10.3E", i_numTrials + 1, m_dampRes, + stepNorm_1 / ( m_dampRes * m_dampBound), stepNorm_2, m_normResid_1); + printf("| %10.3E %10.3E %10.3E", stepNorm_1, m_normDeltaSoln_Newton, m_normResid_full); } - printf("%5d %11.3E | %10.2E %10.2E %2d | %11.3E %11.3E ", m_numTotalLinearSolves, 0.0, m_dampBound, m_dampRes, - i_backtracks, m_normDeltaSoln_Newton, m_normResidFRaw); printf("\n"); } @@ -2992,7 +3160,7 @@ namespace Cantera { // If dampStep fails, first try a new Jacobian if an old // one was being used. If it was a new Jacobian, then // return -1 to signify failure. - else if (m < 0) { + else if (retnDamp < NSOLN_RETN_CONTINUE) { goto done; } } @@ -3002,19 +3170,35 @@ namespace Cantera { if (m_print_flag == 2 || m_print_flag == 3) { if (convRes > 0) { - if (convRes == 3) { - printf("\t | | converged = 3 |(%11.3E) \n", s1); + if (doDogLeg_) { + if (convRes == 3) { + printf("\t | | " + " | | converged = 3 |(%11.3E) \n", stepNorm_2); + } else { + printf("\t | | " + " | | converged = %1d | %10.3E %10.3E\n", convRes, + stepNorm_2, m_normResidTrial); + } + printf("\t-----------------------------------------------------------------------------------------------------" + "------------------------------------------------------------------------------\n"); } else { - printf("\t | | converged = %1d | %11.3E %11.3E \n", convRes, - s1, m_normResidTrial); + if (convRes == 3) { + printf("\t | " + " | converged = 3 | (%11.3E) \n", stepNorm_2); + } else { + printf("\t | " + " | converged = %1d | %10.3E %10.3E\n", convRes, + stepNorm_2, m_normResidTrial); + } + printf("\t------------------------------------------------------------------------------------" + "-----------------------------------------------\n"); } } - printf("\t --------------------------------------------------------------------------------------------\n"); + } - mdp::mdp_copy_dbl_1(y_comm, CONSTD_DATA_PTR(m_y_n_curr), neq_); if (solnType_ != NSOLN_TYPE_STEADY_STATE) { mdp::mdp_copy_dbl_1(ydot_comm, CONSTD_DATA_PTR(m_ydot_n_curr), neq_); @@ -3024,7 +3208,7 @@ namespace Cantera { doublereal time_elapsed = wc.secondsWC(); if (m_print_flag > 1) { - if (m > 0) { + if (retnDamp > 0) { if (NonlinearSolver::s_TurnOffTiming) { printf("\t\tNonlinear problem solved successfully in %d its\n", num_newt_its); @@ -3036,31 +3220,37 @@ namespace Cantera { printf("\t\tNonlinear problem failed to solve after %d its\n", num_newt_its); } } - return m; + retnCode = retnDamp; + if (retnDamp > 0) { + retnCode = NSOLN_RETN_SUCCESS; + } + + + return retnCode; } //==================================================================================================================== // Print solution norm contribution /* * Prints out the most important entries to the update to the solution vector for the current step * - * @param solnDelta0 Raw update vector for the current nonlinear step - * @param s0 Norm of the vector solnDelta0 - * @param solnDelta1 Raw update vector for the next solution value based on the old matrix - * @param s1 Norm of the vector solnDelta1 + * @param step_1 Raw update vector for the current nonlinear step + * @param stepNorm_1 Norm of the vector step_1 + * @param step_2 Raw update vector for the next solution value based on the old matrix + * @param stepNorm_2 Norm of the vector step_2 * @param title title of the printout - * @param y0 Old value of the solution - * @param y1 New value of the solution after damping corrections + * @param y_n_curr Old value of the solution + * @param y_n_1 New value of the solution after damping corrections * @param damp Value of the damping factor * @param num_entries Number of entries to print out */ void NonlinearSolver:: - print_solnDelta_norm_contrib(const doublereal * const solnDelta0, - const char * const s0, - const doublereal * const solnDelta1, - const char * const s1, + print_solnDelta_norm_contrib(const doublereal * const step_1, + const char * const stepNorm_1, + const doublereal * const step_2, + const char * const stepNorm_2, const char * const title, - const doublereal * const y0, - const doublereal * const y1, + const doublereal * const y_n_curr, + const doublereal * const y_n_1, doublereal damp, int num_entries) { int i, j, jnum; @@ -3068,7 +3258,7 @@ namespace Cantera { doublereal dmax0, dmax1, error, rel_norm; printf("\t\t%s currentDamp = %g\n", title, damp); printf("\t\t I ysolnOld %13s ysolnNewRaw | ysolnNewTrial " - "%10s ysolnNewTrialRaw | solnWeight wtDelSoln wtDelSolnTrial\n", s0, s1); + "%10s ysolnNewTrialRaw | solnWeight wtDelSoln wtDelSolnTrial\n", stepNorm_1, stepNorm_2); int *imax = mdp::mdp_alloc_int_1(num_entries, -1); printf("\t\t "); print_line("-", 125); for (jnum = 0; jnum < num_entries; jnum++) { @@ -3079,9 +3269,9 @@ namespace Cantera { if (imax[j] == i) used = true; } if (!used) { - error = solnDelta0[i] / m_ewt[i]; + error = step_1[i] / m_ewt[i]; rel_norm = sqrt(error * error); - error = solnDelta1[i] / m_ewt[i]; + error = step_2[i] / m_ewt[i]; rel_norm += sqrt(error * error); if (rel_norm > dmax1) { imax[jnum] = i; @@ -3091,13 +3281,13 @@ namespace Cantera { } if (imax[jnum] >= 0) { i = imax[jnum]; - error = solnDelta0[i] / m_ewt[i]; + error = step_1[i] / m_ewt[i]; dmax0 = sqrt(error * error); - error = solnDelta1[i] / m_ewt[i]; + error = step_2[i] / m_ewt[i]; dmax1 = sqrt(error * error); printf("\t\t %4d %12.4e %12.4e %12.4e | %12.4e %12.4e %12.4e |%12.4e %12.4e %12.4e\n", - i, y0[i], solnDelta0[i], y0[i] + solnDelta0[i], y1[i], - solnDelta1[i], y1[i]+ solnDelta1[i], m_ewt[i], dmax0, dmax1); + i, y_n_curr[i], step_1[i], y_n_curr[i] + step_1[i], y_n_1[i], + step_2[i], y_n_1[i]+ step_2[i], m_ewt[i], dmax0, dmax1); } } printf("\t\t "); print_line("-", 125); @@ -3152,10 +3342,10 @@ namespace Cantera { * 0 Means an unsuccessful operation */ int NonlinearSolver::beuler_jac(SquareMatrix &J, doublereal * const f, - doublereal time_curr, doublereal CJ, - doublereal * const y, - doublereal * const ydot, - int num_newt_its) + doublereal time_curr, doublereal CJ, + doublereal * const y, + doublereal * const ydot, + int num_newt_its) { int i, j; double* col_j; @@ -3209,7 +3399,7 @@ namespace Cantera { printf("\t\tUnk m_ewt y dyVector ResN\n"); for (int iii = 0; iii < neq_; iii++){ printf("\t\t %4d %16.8e %16.8e %16.8e %16.8e \n", - iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); } } } @@ -3375,7 +3565,7 @@ namespace Cantera { */ doublereal NonlinearSolver::filterNewSolution(const doublereal timeCurrent, doublereal * const y_current, doublereal *const ydot_current) { - doublereal tmp = m_func->filterSolnPrediction(timeCurrent, y_current); + doublereal tmp = m_func->filterSolnPrediction(timeCurrent, y_current); return tmp; } //==================================================================================================================== @@ -3383,17 +3573,18 @@ namespace Cantera { /* * The residual weights are defined here to be equal to the inverse of the row scaling factors used to * row scale the matrix, after column scaling is used. They are multiplied by rtol and an atol factor - * is added as well so that if the residual is less than 1, then the calculation is deemed to be comverged. + * is added as well so that if the residual is less than 1, then the calculation is deemed to be converged. * * The basic idea is that a change in the solution vector on the order of the convergence tolerance * multiplied by [RJC] which is of order one after row scaling should give you the relative weight * of the row. Values of the residual for that row can then be normalized by the value of this weight. * When the tolerance in delta x is achieved, the tolerance in the residual should also be achieved - * and should be checked + * and should be checked. */ void NonlinearSolver::computeResidWts() { + ResidWtsReevaluated_ = true; doublereal sum = 0.0; for (int i = 0; i < neq_; i++) { m_residWts[i] = m_rowWtScales[i] / neq_; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 82bd83c84..a62c9425a 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -37,6 +37,32 @@ namespace Cantera { #define NSOLN_TYPE_STEADY_STATE 0 //@} + + //@{ + /// @name Constant which determines the Return int from the nonlinear solver + /*! + * This int is returned from the nonlinear solver + */ + //! The nonlinear solve is successful. +#define NSOLN_RETN_SUCCESS 1 + //! Problem isn't solved yet +#define NSOLN_RETN_CONTINUE 0 + //! The nonlinear problem started to take too small an update step. This indicates that either the + //! Jacobian is bad, or a constraint is being bumped up against. +#define NSOLN_RETN_FAIL_STEPTOOSMALL -1 + //! The nonlinear problem didn't solve the problem +#define NSOLN_RETN_FAIL_DAMPSTEP -2 + //! The nonlinear problem's jacobian is singular +#define NSOLN_RETN_MATRIXINVERSIONERROR -3 + //! The nonlinear problem's jacobian formation produced an error +#define NSOLN_RETN_JACOBIANFORMATIONERROR -4 + //! The nonlinear problem's base residual produced an error +#define NSOLN_RETN_RESIDUALFORMATIONERROR -5 + //! The nonlinear problem's max number of iterations has been exceeded +#define NSOLN_RETN_MAXIMUMITERATIONSEXCEEDED -7 + //@} + //@} + //@{ /// @name Constant which determines the type of the Jacobian //! The jacobian will be calculated from a numerical method @@ -162,7 +188,7 @@ namespace Cantera { * @return Returns the L2 norm of the delta */ doublereal solnErrorNorm(const doublereal * const delta_y, const char * title = 0, int printLargest = 0, - const doublereal dampFactor = 1.0) const; + const doublereal dampFactor = 1.0) const; //! L2 norm of the residual of the equation system /*! @@ -270,7 +296,7 @@ namespace Cantera { * We carry out a norm of deltaX_trust_ first. Then, we multiply that value * by trustDelta_ */ - double trustRegionLength() const; + doublereal trustRegionLength() const; //! Set default deulta bounds amounts /*! @@ -281,6 +307,8 @@ namespace Cantera { */ void setDefaultDeltaBoundsMagnitudes(); + void adjustUpStepMinimums(); + //! Set the delta Bounds magnitudes by hand /*! * @param deltaBoundsMagnitudes set the deltaBoundsMagnitude vector @@ -311,7 +339,7 @@ namespace Cantera { * @param alpha Relative length along the dog length that you are on. * @param deltaX Vector to be filled up */ - void fillDogLegStep(int leg, double alpha, std::vector & deltaX) const; + void fillDogLegStep(int leg, doublereal alpha, std::vector & deltaX) const; //! Calculate the trust distance of a step in the solution variables /*! @@ -370,10 +398,10 @@ namespace Cantera { const doublereal * const y_high_bounds); //! Return an editable vector of the low bounds constraints - std::vector & lowBoundsConstraintVector(); + std::vector & lowBoundsConstraintVector(); //! Return an editable vector of the high bounds constraints - std::vector & highBoundsConstraintVector(); + std::vector & highBoundsConstraintVector(); //! Internal function to calculate the time derivative of the solution at the new step /*! @@ -450,34 +478,34 @@ namespace Cantera { //! Find a damping coefficient through a look-ahead mechanism /*! - * On entry, step0 must contain an undamped Newton step for the - * solution x0. This method attempts to find a damping coefficient + * On entry, step_1 must contain an undamped Newton step for the + * solution y_n_curr. This method attempts to find a damping coefficient * such that all components stay in bounds, and the next * undamped step would have a norm smaller than - * that of step0. If successful, the new solution after taking the - * damped step is returned in y1, and the undamped step at y1 is - * returned in step1. + * that of step_1. If successful, the new solution after taking the + * damped step is returned in y_n_1, and the undamped step at y_n_1 is + * returned in step_2. * * @param time_curr Current physical time - * @param y0 Base value of the solution before any steps - * are taken - * @param ydot0 Base value of the time derivative of teh - * solution - * @param step0 Initial step suggested. - * @param y1 Value of y1, the suggested solution after damping - * @param ydot1 Value of the time derivative of the solution at y1 - * @param step1 Value of the step change from y0 to y1 - * @param s1 norm of the step change in going from y0 to y1 - * @param jac Jacobian - * @param writetitle Write a title line + * @param y_n_curr Base value of the solution before any steps + * are taken + * @param ydot_n_curr Base value of the time derivative of teh + * solution + * @param step_1 Initial step suggested. + * @param y_n_1 Value of y1, the suggested solution after damping + * @param ydot_n_1 Value of the time derivative of the solution at y_n_1 + * @param step_2 Value of the step change from y_n_1 to y_n_2 + * @param stepNorm_2 norm of the step change in going from y_n_1 to y_n_2 + * @param jac Jacobian + * @param writetitle Write a title line * @param num_backtracks Number of backtracks taken * * @return returns an integer indicating what happened. */ - int dampStep(const doublereal time_curr, const double* y0, - const doublereal *ydot0, const double* step0, - double* const y1, double* const ydot1, double* step1, - double& s1, SquareMatrix& jac, bool writetitle, + int dampStep(const doublereal time_curr, const double* y_n_curr, + const doublereal *ydot_n_curr, double * const step_1, + double* const y_n_1, double* const ydot_n_1, double* step_2, + double& stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks); //! Find the solution to F(X) = 0 by damped Newton iteration. @@ -521,27 +549,27 @@ namespace Cantera { * @param ydot_comm Current value of the time derivative of the solution vector * @param time_curr current value of the time */ - void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr); + void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr, int num_newt_its); //! Print solution norm contribution /*! * Prints out the most important entries to the update to the solution vector for the current step * - * @param solnDelta0 Raw update vector for the current nonlinear step - * @param s0 Norm of the vector solnDelta0 - * @param solnDelta1 Raw update vector for the next solution value based on the old matrix - * @param s1 Norm of the vector solnDelta1 + * @param step_1 Raw update vector for the current nonlinear step + * @param stepNorm_1 Norm of the vector step_1 + * @param step_2 Raw update vector for the next solution value based on the old matrix + * @param stepNorm_2 Norm of the vector step_2 * @param title title of the printout - * @param y0 Old value of the solution - * @param y1 New value of the solution after damping corrections + * @param y_n_curr Old value of the solution + * @param y_n_1 New value of the solution after damping corrections * @param damp Value of the damping factor * @param num_entries Number of entries to print out */ void - print_solnDelta_norm_contrib(const doublereal * const solnDelta0, const char * const s0, - const doublereal * const solnDelta1, const char * const s1, - const char * const title, const doublereal * const y0, const doublereal * const y1, - doublereal damp, int num_entries); + print_solnDelta_norm_contrib(const doublereal * const step_1, const char * const stepNorm_1, + const doublereal * const step_2, const char * const stepNorm_2, + const char * const title, const doublereal * const y_n_curr, + const doublereal * const y_n_1, doublereal damp, int num_entries); //! Compute the Residual Weights /*! @@ -640,8 +668,9 @@ namespace Cantera { * @param time_curr Current time * @param ydot0 INPUT Current value of the derivative of the solution vector * @param ydot1 INPUT Time derivates of solution at the conditions which are evalulated for success + * @param numTrials OUTPUT Counter for the number of residual evaluations */ - void descentComparison(double time_curr ,double *ydot0, double *ydot1); + void descentComparison(doublereal time_curr ,doublereal * ydot0, doublereal * ydot1, int &numTrials); //! Setup the parameters for the double dog leg @@ -659,7 +688,7 @@ namespace Cantera { * * @return Returns the leg number ( 0, 1, or 2). */ - int lambdaToLeg(const double lambda, double &alpha) const; + int lambdaToLeg(const doublereal lambda, doublereal &alpha) const; //! Given a trust distance, this routine calculates the intersection of the this distance with the //! double dogleg curve @@ -669,7 +698,7 @@ namespace Cantera { * @param alpha (OUTPUT) Returns the relative distance along the appropriate leg * @return leg (OUTPUT) Returns the leg ID (0, 1, or 2) */ - int calcTrustIntersection(double trustVal, double &lambda, double &alpha) const; + int calcTrustIntersection(doublereal trustVal, doublereal &lambda, doublereal &alpha) const; //! Initialize the size of the trust vector. /*! @@ -687,7 +716,8 @@ namespace Cantera { * @param step_1 INPUT First trial step for the first iteration * @param y_n_1 INPUT First trial value of the solution vector * @param ydot_n_1 INPUT First trial value of the derivative of the solution vector - * @param s1 OUTPUT Norm of the vector step_1 + * @param stepNorm_1 OUTPUT Norm of the vector step_1 + * @param stepNorm_2 OUTPUT Estimated norm of the vector step_2 * @param jac INPUT jacobian * @param num_backtracks OUTPUT number of backtracks taken in the current damping step * @@ -704,7 +734,7 @@ namespace Cantera { int dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, const doublereal *ydot_n_curr, std::vector & step_1, doublereal* const y_n_1, doublereal* const ydot_n_1, - doublereal& s1, SquareMatrix& jac, int& num_backtracks); + doublereal& stepNorm_1, doublereal& stepNorm_2, SquareMatrix& jac, int& num_backtracks); //! Decide whether the current step is acceptable and adjust the trust region size /*! @@ -733,9 +763,10 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int decideStep(const doublereal time_curr, int leg, double alpha, const double* const y0, const doublereal * const ydot0, + int decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y0, + const doublereal * const ydot0, const std::vector & step0, - const double* const y1, const double* const ydot1, double trustDeltaOld); + const doublereal * const y1, const doublereal * const ydot1, doublereal trustDeltaOld); //! Calculated the expected residual along the double dogleg curve. /*! @@ -830,9 +861,14 @@ namespace Cantera { //! Vector containing the solution at the previous time step std::vector m_y_nm1; + //! Vector containing the solution at the previous time step + std::vector m_y_n_1; + //! Value of the solution time derivative at the new point that is to be considered std::vector m_ydot_n_1; + std::vector m_step_1; + //! Vector of column scaling factors std::vector m_colScales; @@ -870,10 +906,16 @@ namespace Cantera { std::vector m_residWts; //! Norm of the residual at the start of each nonlinear iteration - doublereal m_normResid0; + doublereal m_normResid_0; - //! Norm of the residual before damping - doublereal m_normResidFRaw; + //! Norm of the residual after it has been bounded + doublereal m_normResid_Bound; + + //! Norm of the residual at the end of the first leg of the current iteration + doublereal m_normResid_1; + + //! Norm of the residual at the end of the first leg of the current iteration + doublereal m_normResid_full; //! Norm of the solution update created by the iteration in its raw, undamped form, using the solution norm doublereal m_normDeltaSoln_Newton; @@ -927,9 +969,12 @@ namespace Cantera { //! int indicating whether row scaling is turned on (1) or not (0) int m_rowScaling; - //! Total number of linear solves + //! Total number of linear solves taken by the solver object int m_numTotalLinearSolves; + //! Number of local linear solves done during the current iteration + int m_numLocalLinearSolves; + //! Total number of newton iterations int m_numTotalNewtIts; @@ -992,7 +1037,7 @@ namespace Cantera { int m_print_flag; //! Scale factor for turning residual norms into solution norms - double m_ScaleSolnNormToResNorm; + doublereal m_ScaleSolnNormToResNorm; //! Copy of the jacobian that doesn't get overwritten when the inverse is determined /*! @@ -1020,6 +1065,12 @@ namespace Cantera { //! were valid doublereal residNorm2Cauchy_; + //! Current leg + int dogLegID_; + + //! Current Alpha param along the leg + doublereal dogLegAlpha_; + //! Residual dot Jd norm /*! * This is equal to R_hat dot J_hat d_y_descent @@ -1075,13 +1126,34 @@ namespace Cantera { //! General toggle for turning on Affine solve with Hessian int doAffineSolve_; + //! Condition number of the matrix + doublereal m_conditionNumber; + //! Factor indicating how much trust region has been changed this iteration - output variable + doublereal CurrentTrustFactor_; + + //! Factor indicating how much trust region has been changed next iteration - output variable + doublereal NextTrustFactor_; + + //! Boolean indicating that the residual weights have been reevalulated this iteration - output variable + bool ResidWtsReevaluated_; + + //! Expected DResid_dS for the steepest descent path - output variable + doublereal ResidDecreaseSDExp_; + + //! Actual DResid_dS for the steepest descent path - output variable + doublereal ResidDecreaseSD_; + + //! Expected DResid_dS for the Newton path - output variable + doublereal ResidDecreaseNewtExp_; + + //! Actual DResid_dS for the newton path - output variable + doublereal ResidDecreaseNewt_; /******************************************************************************************* - * OTHER COUNTERS + * STATIC VARIABLES *****************************************************************************************/ - public: //! Turn off printing of time /*! @@ -1092,7 +1164,7 @@ namespace Cantera { //! Turn on or off printing of the Jacobian static bool s_print_NumJac; - //! Turn on all printing of dogleg information + //! Turn on extra printing of dogleg information static bool s_print_DogLeg; //! Turn on solving both the Newton and Hessian systems and comparing the results From 9197a283b61fb3aaf4ac3082f8df174773d8c1ee Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 Oct 2011 21:48:11 +0000 Subject: [PATCH 406/446] Stable intermediate step. Working on a new test problem where the Newton direction is fouled up by a large condition number. --- Cantera/src/numerics/NonlinearSolver.cpp | 127 +++++++++++++++++++---- Cantera/src/numerics/NonlinearSolver.h | 8 +- 2 files changed, 111 insertions(+), 24 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 0f3f8d736..0b74ff376 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -86,6 +86,13 @@ namespace Cantera { * Turn this on if you want to compare the Hessian and Newton solve results. */ bool NonlinearSolver::s_doBothSolvesAndCompare(false); + + // This toggle turns off the use of the Hessian when it is warranted by the condition number. + /* + * This is a debugging option. + */ + bool NonlinearSolver::s_alwaysAssumeNewtonGood(false); + //==================================================================================================================== // Default constructor /* @@ -923,7 +930,7 @@ namespace Cantera { } } - // Factor the matrix + // Factor the matrix using a standard Newton solve m_conditionNumber = 1.0E300; int info = 0; if (!jac.m_factored) { @@ -952,9 +959,9 @@ namespace Cantera { if (s_doBothSolvesAndCompare) { doHessian = true; } - bool doNewton = false; + bool useNewton = false; if (m_conditionNumber < 1.0E7) { - doNewton = true; + useNewton = true; if (m_print_flag >= 4) { printf("\t\t doAffineNewtonSolve: Condition number = %g during regular solve\n", m_conditionNumber); } @@ -965,7 +972,7 @@ namespace Cantera { int info = jac.solve(DATA_PTR(delta_y)); if (info) { if (m_print_flag >= 2) { - printf("\t\t NonlinearSolver::doAffineSolve() ERROR: QRSolve returned INFO = %d. Switching to Hessian solve\n", info); + printf("\t\t doAffineNewtonSolve() ERROR: QRSolve returned INFO = %d. Switching to Hessian solve\n", info); } doHessian = true; newtonGood = false; @@ -989,12 +996,12 @@ namespace Cantera { if (doHessian) { // Store the old value for later comparison - if (doNewton) { - delyNewton = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); - for (irow = 0; irow < neq_; irow++) { - delyNewton[irow] = delta_y[irow]; - } + + delyNewton = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + for (irow = 0; irow < neq_; irow++) { + delyNewton[irow] = delta_y[irow]; } + // Get memory if not done before if (Hessian_.nRows() == 0) { Hessian_.resize(neq_, neq_); @@ -1057,8 +1064,14 @@ namespace Cantera { } /* * Add junk to the Hessian diagonal + * -> Note, testing indicates that this will get too big for ill-conditioned systems. */ hcol = sqrt(neq_) * 1.0E-7 * hnorm; +#ifdef DEBUG_HKM_NOT + if (hcol > 1.0) { + hcol = 1.0E1; + } +#endif if (m_colScaling) { for (int i = 0; i < neq_; i++) { Hessian_(i,i) += hcol / (m_colScales[i] * m_colScales[i]); @@ -1076,7 +1089,7 @@ namespace Cantera { ct_dpotrf(ctlapack::UpperTriangular, neq_, &(*(Hessian_.begin())), neq_, info); if (info) { if (m_print_flag >= 2) { - printf("\t\t NonlinearSolver::doAffineSolve() ERROR: DPOTRF returned INFO = %d\n", info); + printf("\t\t doAffineNewtonSolve() ERROR: Hessian isn't positive definate DPOTRF returned INFO = %d\n", info); } return info; } @@ -1117,7 +1130,7 @@ namespace Cantera { ct_dpotrs(ctlapack::UpperTriangular, neq_, 1,&(*(Hessian_.begin())), neq_, delta_y, neq_, info); if (info) { if (m_print_flag >= 2) { - printf("\t\t NonlinearSolver::doAffineSolve() ERROR: DPOTRS returned INFO = %d\n", info); + printf("\t\t NonlinearSolver::doAffineNewtonSolve() ERROR: DPOTRS returned INFO = %d\n", info); } return info; } @@ -1131,18 +1144,40 @@ namespace Cantera { } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { - printf("\t\t Comparison between Hessian deltaX and newton deltaX\n"); - printf("\t\t I Hessian+Junk Newton \n"); - printf("\t\t --------------------------------------------------------\n"); - for (int i =0; i < neq_; i++) { - printf("\t\t %3d %12.5g %12.5g\n", i, delta_y[i], delyNewton[i]); + if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 7)) { + double normNewt = solnErrorNorm(CONSTD_DATA_PTR(delyNewton)); + double normHess = solnErrorNorm(CONSTD_DATA_PTR(delta_y)); + printf("\t\t doAffineNewtonSolve(): Printout Comparison between Hessian deltaX and Newton deltaX\n"); + + printf("\t\t I Hessian+Junk Newton"); + if (newtonGood || s_alwaysAssumeNewtonGood) { + printf(" (USING NEWTON DIRECTION)\n"); + } else { + printf(" (USING HESSIAN DIRECTION)\n"); + } + printf("\t\t Norm: %12.4E %12.4E\n", normHess, normNewt); + + printf("\t\t --------------------------------------------------------\n"); + for (int i =0; i < neq_; i++) { + printf("\t\t %3d %13.5E %13.5E\n", i, delta_y[i], delyNewton[i]); + } + printf("\t\t --------------------------------------------------------\n"); + } else if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + double normNewt = solnErrorNorm(CONSTD_DATA_PTR(delyNewton)); + double normHess = solnErrorNorm(CONSTD_DATA_PTR(delta_y)); + printf("\t\t doAffineNewtonSolve(): Hessian update norm = %12.4E \n" + "\t\t Newton update norm = %12.4E \n", normHess, normNewt); + if (newtonGood || s_alwaysAssumeNewtonGood) { + printf("\t\t (USING NEWTON DIRECTION)\n"); + } else { + printf("\t\t (USING HESSIAN DIRECTION)\n"); } - printf("\t\t --------------------------------------------------------\n"); - } - if (newtonGood) { + /* + * Choose the delta_y to use + */ + if (newtonGood || s_alwaysAssumeNewtonGood) { mdp::mdp_copy_dbl_1(DATA_PTR(delta_y), CONSTD_DATA_PTR(delyNewton), neq_); } mdp::mdp_safe_free((void **) &delyH); @@ -1330,6 +1365,7 @@ namespace Cantera { { int info; doublereal ff = 1.0E-5; + doublereal ffNewt = 1.0E-5; doublereal *y_n_1 = DATA_PTR(m_wksp); doublereal cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); if (cauchyDistanceNorm < 1.0E-2) { @@ -1357,8 +1393,11 @@ namespace Cantera { doublereal funcDecreaseSD = 0.5 * (residSteep2 - normResid02) / ( ff * cauchyDistanceNorm); doublereal sNewt = solnErrorNorm(DATA_PTR(deltaX_Newton_)); + if (sNewt > 1.0) { + ffNewt = ffNewt / sNewt; + } for (int i = 0; i < neq_; i++) { - y_n_1[i] = m_y_n_curr[i] + ff * deltaX_Newton_[i]; + y_n_1[i] = m_y_n_curr[i] + ffNewt * deltaX_Newton_[i]; } /* * Calculate the residual that would result if y1[] were the new solution vector. @@ -1375,7 +1414,7 @@ namespace Cantera { doublereal residNewt = residErrorNorm(DATA_PTR(m_resid)); doublereal residNewt2 = residNewt * residNewt * neq_; - doublereal funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); + doublereal funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ffNewt * sNewt); // This is the expected inital rate of decrease in the Cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || @@ -1397,8 +1436,14 @@ namespace Cantera { numTrials += 2; /* - * HKM These have been shown to exactly match up. + * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights + * + * HKM When a hessian is used with junk on the diagonal, funcDecreaseNewtExp2 is no longer accurate as the + * direction gets signficantly shorter with increasing condition number. This suggests an algorithm where the + * newton step from the Hessian should be increased so as to match funcDecreaseNewtExp2 = funcDecreaseNewt2. + * This roughly equals the ratio of the norms of the hessian and newton steps. This increased Newton step can + * then be used with the trust region double dogleg algorithm. */ if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 5)) { printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir (expected) = %g\n", funcDecreaseSDExp); @@ -1412,6 +1457,36 @@ namespace Cantera { printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir (expected) = %g\n", ResidDecreaseNewtExp_); printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir = %g\n", ResidDecreaseNewt_); } + + if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + if (funcDecreaseNewt2 >= 0.0) { + printf("\t\t %13.5E %22.16E\n", funcDecreaseNewtExp2, m_normResid_0); + double ff = ffNewt * 1.0E-5; + for (int ii = 0; ii < 13; ii++) { + ff *= 10.; + if (ii == 12) { + ff = ffNewt; + } + for (int i = 0; i < neq_; i++) { + y_n_1[i] = m_y_n_curr[i] + ff * deltaX_Newton_[i]; + } + numTrials += 1; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot1, Base_LaggedSolutionComponents); + } else { + info = doResidualCalc(time_curr, solnType_, y_n_1, ydot0, Base_LaggedSolutionComponents); + } + residNewt = residErrorNorm(DATA_PTR(m_resid)); + residNewt2 = residNewt * residNewt * neq_; + funcDecreaseNewt2 = 0.5 * (residNewt2 - normResid02) / ( ff * sNewt); + printf("\t\t %10.3E %13.5E %22.16E\n", ff, funcDecreaseNewt2, residNewt ); + } + + } + + + } + } //==================================================================================================================== @@ -2851,6 +2926,9 @@ namespace Cantera { info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), num_newt_its); if (info == 0) { + if (m_print_flag > 0) { + printf("\t solve_nonlinear_problem(): Jacobian Formation Error: %d Bailing\n", info); + } retnDamp = NSOLN_RETN_JACOBIANFORMATIONERROR ; goto done; } @@ -2941,6 +3019,9 @@ namespace Cantera { if (info) { retnDamp = NSOLN_RETN_MATRIXINVERSIONERROR; + if (m_print_flag > 0) { + printf("\t solve_nonlinear_problem(): Matrix Inversion Error: %d Bailing\n", info); + } goto done; } mdp::mdp_copy_dbl_1(DATA_PTR(m_step_1), CONSTD_DATA_PTR(deltaX_Newton_), neq_); diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index a62c9425a..ef7921103 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -588,7 +588,7 @@ namespace Cantera { /*! * @param residWts Vector of length neq_ */ - void getResidWts(doublereal * const residWts) const; + void getResidWts(doublereal * const residWts) const; //! Check to see if the nonlinear problem has converged /*! @@ -1173,6 +1173,12 @@ namespace Cantera { */ static bool s_doBothSolvesAndCompare; + //! This toggle turns off the use of the Hessian when it is warranted by the condition number. + /*! + * This is a debugging option. + */ + static bool s_alwaysAssumeNewtonGood; + }; } From 788697405fc995606b60fe84a954b99081ebf15f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 Oct 2011 23:32:13 +0000 Subject: [PATCH 407/446] Added documentation --- Cantera/src/equil/vcs_internal.h | 34 ++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/Cantera/src/equil/vcs_internal.h b/Cantera/src/equil/vcs_internal.h index ec897b4be..cda63dada 100644 --- a/Cantera/src/equil/vcs_internal.h +++ b/Cantera/src/equil/vcs_internal.h @@ -158,6 +158,40 @@ namespace VCSnonideal { */ int vcsUtil_mlequ(double *c, int idem, int n, double *b, int m); + //! Invert an n x n matrix and solve m rhs's + /*! + * Solve a square matrix with multiple right hand sides + * + * \f[ + * C X + B = 0; + * \f] + * + * This routine uses Gauss-Jordan elimination and is optimized for the solution + * of lots of rhs's. Full row and column pivoting is used here. It's been + * shown to be necessary in at least one case. + * The matrix C is destroyed during the solve. + * + * @return The solution x[] is returned in the matrix B. + * Routine returns an integer representing success: + * - 1 : Matrix is singluar + * - 0 : solution is OK + * + * @param c Matrix to be inverted. c is in fortran format, i.e., rows + * are the inner loop. Row numbers equal to idem. + * c[i+j*idem] = c_i_j = Matrix to be inverted: + * - i = row number + * - j = column number + * + * @param idem number of row dimensions in c + * @param n Number of rows and columns in c + * @param b Multiple RHS. Note, b is actually the negative of + * most formulations. Row numbers equal to idem. + * b[i+j*idem] = b_i_j = vectors of rhs's: + * - i = row number + * - j = column number + * (each column is a new rhs) + * @param m number of rhs's + */ int vcsUtil_gaussj(double *c, int idem, int n, double *b, int m); //! Swap values in vector of doubles From 6a3c7eabd4f486c4e69a997467cf20f8185ae77a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 4 Oct 2011 23:33:58 +0000 Subject: [PATCH 408/446] Added a getMoleFraction to GibbsExcess at the start of the calculation. Want the mole fraction to be synched at all times. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 1 + Cantera/src/thermo/StoichSubstance.h | 5 ++++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 94b366c79..339b0edd9 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -332,6 +332,7 @@ namespace Cantera { void GibbsExcessVPSSTP::initThermo() { initLengths(); VPStandardStateTP::initThermo(); + getMoleFractions(DATA_PTR(moleFractions_)); } diff --git a/Cantera/src/thermo/StoichSubstance.h b/Cantera/src/thermo/StoichSubstance.h index 991ef4962..a154f8096 100644 --- a/Cantera/src/thermo/StoichSubstance.h +++ b/Cantera/src/thermo/StoichSubstance.h @@ -394,7 +394,10 @@ namespace Cantera { protected: int m_kk; - doublereal m_tmin, m_tmax, m_press, m_p0; + doublereal m_tmin; + doublereal m_tmax; + doublereal m_press; + doublereal m_p0; mutable doublereal m_tlast; mutable array_fp m_h0_RT; From a510731dca8cc547f4476c1631d598da07cc3350 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 5 Oct 2011 17:30:08 +0000 Subject: [PATCH 409/446] Fixed a column scaling error for the dogleg method --- Cantera/src/numerics/NonlinearSolver.cpp | 105 +++++++++++++++++------ Cantera/src/numerics/NonlinearSolver.h | 52 +++++++++-- Cantera/src/numerics/ResidJacEval.cpp | 2 + 3 files changed, 127 insertions(+), 32 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 0b74ff376..4eec506e4 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -618,13 +618,61 @@ namespace Cantera { return sum_norm; } //==================================================================================================================== + // Set the column scaling that are used for the inversion of the matrix /* - * setColumnScales(): + * There are three ways to do this. + * + * The first method is to set the bool useColScaling to true, leaving the scaling factors unset. + * Then, the column scales will be set to the solution error weighting factors. This has the + * effect of ensuring that all delta variables will have the same order of magnitude at convergence + * end. + * + * The second way is the explicity set the column factors in the second argument of this function call. + * + * The final way to input the scales is to override the ResidJacEval member function call, + * + * calcSolnScales(double time_n, const double *m_y_n_curr, const double *m_y_nm1, double *m_colScales) + * + * Overriding this function call will trump all other ways to specify the column scaling factors. + * + * @param useColScaling Turn this on if you want to use column scaling in the calculations + * @param scaleFactors A vector of doubles that specifies the column factors. + */ + void NonlinearSolver::setColumnScaling(bool useColScaling, const double * const scaleFactors) { + if (useColScaling) { + if (scaleFactors) { + m_colScaling = 2; + for (int i = 0; i < neq_; i++) { + m_colScales[i] = scaleFactors[i]; + if (m_colScales[i] <= 1.0E-200) { + throw CanteraError("NonlinearSolver::setColumnScaling() ERROR", "Bad column scale factor"); + } + } + } else { + m_colScaling = 1; + } + } else { + m_colScaling = 0; + } + } + //==================================================================================================================== + // Set the rowscaling that are used for the inversion of the matrix + /* + * Row scaling is set here. Right now the row scaling is set internally in the code. + * + * @param useRowScaling Turn row scaling on or off. + */ + void NonlinearSolver::setRowScaling(bool useRowScaling) { + m_rowScaling = useRowScaling; + } + //==================================================================================================================== + /* + * calcColumnScales(): * * Set the column scaling vector at the current time */ - void NonlinearSolver::setColumnScales() { - if (m_colScaling) { + void NonlinearSolver::calcColumnScales() { + if (m_colScaling == 1) { for (int i = 0; i < neq_; i++) { m_colScales[i] = m_ewt[i]; } @@ -633,7 +681,9 @@ namespace Cantera { m_colScales[i] = 1.0; } } - m_func->calcSolnScales(time_n, DATA_PTR(m_y_n_curr), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); + if (m_colScaling) { + m_func->calcSolnScales(time_n, DATA_PTR(m_y_n_curr), DATA_PTR(m_y_nm1), DATA_PTR(m_colScales)); + } } //==================================================================================================================== // Compute the current residual @@ -667,9 +717,6 @@ namespace Cantera { int num_newt_its) { int irow, jcol; - - - /* * Column scaling -> We scale the columns of the Jacobian * by the nominal important change in the solution vector @@ -694,13 +741,10 @@ namespace Cantera { } } } - - /* * row sum scaling -> Note, this is an unequivical success * at keeping the small numbers well balanced and nonnegative. */ - if (! jac.m_factored) { /* * Ok, this is ugly. jac.begin() returns an vector iterator @@ -714,7 +758,9 @@ namespace Cantera { } for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { - //m_rowScales[irow] += fabs(*jptr); + if (m_rowScaling) { + m_rowScales[irow] += fabs(*jptr); + } if (m_colScaling) { // This is needed in order to mitgate the change in J_ij carried out just above this loop. // Alternatively, we could move this loop up to the top @@ -725,15 +771,19 @@ namespace Cantera { jptr++; } } - + if (m_rowScaling) { for (irow = 0; irow < neq_; irow++) { m_rowScales[irow] = 1.0/m_rowScales[irow]; } + } else { + for (irow = 0; irow < neq_; irow++) { + m_rowScales[irow] = 1.0; + } + } // What we have defined is a maximum value that the residual can be and still pass. // This isn't sufficient. if (m_rowScaling) { - jptr = &(*(jac.begin())); for (jcol = 0; jcol < neq_; jcol++) { for (irow = 0; irow < neq_; irow++) { @@ -1144,7 +1194,7 @@ namespace Cantera { } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 7)) { + if (doDogLeg_ && m_print_flag > 7) { double normNewt = solnErrorNorm(CONSTD_DATA_PTR(delyNewton)); double normHess = solnErrorNorm(CONSTD_DATA_PTR(delta_y)); printf("\t\t doAffineNewtonSolve(): Printout Comparison between Hessian deltaX and Newton deltaX\n"); @@ -1162,7 +1212,7 @@ namespace Cantera { printf("\t\t %3d %13.5E %13.5E\n", i, delta_y[i], delyNewton[i]); } printf("\t\t --------------------------------------------------------\n"); - } else if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + } else if (doDogLeg_ && m_print_flag >= 4) { double normNewt = solnErrorNorm(CONSTD_DATA_PTR(delyNewton)); double normHess = solnErrorNorm(CONSTD_DATA_PTR(delta_y)); printf("\t\t doAffineNewtonSolve(): Hessian update norm = %12.4E \n" @@ -1237,6 +1287,7 @@ namespace Cantera { doublereal NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) { doublereal rowFac = 1.0; + doublereal colFac = 1.0; doublereal normSoln; // Calculate the descent direction /* @@ -1250,7 +1301,6 @@ namespace Cantera { */ for (int j = 0; j < neq_; j++) { deltaX_CP_[j] = 0.0; - doublereal colFac = 1.0; if (m_colScaling) { colFac = 1.0 / m_colScales[j]; } @@ -1277,7 +1327,10 @@ namespace Cantera { rowFac = 1.0; } for (int j = 0; j < neq_; j++) { - Jd_[i] += deltaX_CP_[j] * jac.value(i,j) * rowFac/ m_residWts[i]; + if (m_colScaling) { + colFac = 1.0 / m_colScales[j]; + } + Jd_[i] += deltaX_CP_[j] * jac.value(i,j) * rowFac * colFac / m_residWts[i]; } } @@ -1445,20 +1498,20 @@ namespace Cantera { * This roughly equals the ratio of the norms of the hessian and newton steps. This increased Newton step can * then be used with the trust region double dogleg algorithm. */ - if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 5)) { + if ((s_print_DogLeg && m_print_flag >= 3) || (doDogLeg_ && m_print_flag >= 5)) { printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir (expected) = %g\n", funcDecreaseSDExp); printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir = %g\n", funcDecreaseSD); printf("\t\t descentComparison: initial rate of decrease of func in newton dir (expected) = %g\n", funcDecreaseNewtExp2); printf("\t\t descentComparison: initial rate of decrease of func in newton dir = %g\n", funcDecreaseNewt2); } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + if ((s_print_DogLeg && m_print_flag >= 3) || (doDogLeg_ && m_print_flag >= 4)) { printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir (expected) = %g\n", ResidDecreaseSDExp_); printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir = %g\n", ResidDecreaseSD_); printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir (expected) = %g\n", ResidDecreaseNewtExp_); printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir = %g\n", ResidDecreaseNewt_); } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + if ((s_print_DogLeg && m_print_flag >= 5) || (doDogLeg_ && m_print_flag >= 5)) { if (funcDecreaseNewt2 >= 0.0) { printf("\t\t %13.5E %22.16E\n", funcDecreaseNewtExp2, m_normResid_0); double ff = ffNewt * 1.0E-5; @@ -2006,7 +2059,7 @@ namespace Cantera { norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); trustDelta_ = 1.0; - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + if (doDogLeg_ && m_print_flag >= 4) { printf("\t\t calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", trustNorm, trustNormGoal); } @@ -2019,13 +2072,13 @@ namespace Cantera { void NonlinearSolver::initializeTrustRegion() { doublereal cpd = calcTrustDistance(deltaX_CP_); - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + if ((doDogLeg_ && m_print_flag >= 4)) { printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } trustDelta_ = trustDelta_ * cpd; calcTrustVector(); cpd = calcTrustDistance(deltaX_CP_); - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 3)) { + if ((doDogLeg_ && m_print_flag >= 4)) { printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); } } @@ -2942,7 +2995,7 @@ namespace Cantera { /* * Go get new scales */ - setColumnScales(); + calcColumnScales(); /* @@ -3036,7 +3089,7 @@ namespace Cantera { if (doDogLeg_) { #ifdef DEBUG_MODE doublereal trustD = calcTrustDistance(m_step_1); - if (s_print_DogLeg || m_print_flag > 3) { + if (m_print_flag >= 4) { if (trustD > trustDelta_) { printf("\t\t Newton's method step size, %g trustVectorUnits, larger than trust region, %g trustVectorUnits\n", trustD, trustDelta_); @@ -3057,7 +3110,7 @@ namespace Cantera { - if (s_print_DogLeg &&m_print_flag >= 4) { + if (s_print_DogLeg && m_print_flag >= 4) { printf("\t solve_nonlinear_problem(): Compare descent rates for Cauchy and Newton directions\n"); descentComparison(time_curr, DATA_PTR(m_ydot_n_curr), DATA_PTR(m_ydot_n_1), i_numTrials); } else { diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index ef7921103..574e70583 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -109,6 +109,10 @@ namespace Cantera { * help equilibrate a nonlinear steady state system. The time transient is not important in and of * itself. Many physical systems have a time dependence to them that provides a natural way to relax * the nonlinear system. + * + * MATRIX SCALING + * + * * * * @code @@ -539,8 +543,42 @@ namespace Cantera { doublereal time_curr, SquareMatrix& jac,int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput); + private: //! Set the column scales - void setColumnScales(); + void calcColumnScales(); + + public: + + //! Set the column scaling that are used for the inversion of the matrix + /*! + * There are three ways to do this. + * + * The first method is to set the bool useColScaling to true, leaving the scaling factors unset. + * Then, the column scales will be set to the solution error weighting factors. This has the + * effect of ensuring that all delta variables will have the same order of magnitude at convergence + * end. + * + * The second way is the explicity set the column factors in the second argument of this function call. + * + * The final way to input the scales is to override the ResidJacEval member function call, + * + * calcSolnScales(double time_n, const double *m_y_n_curr, const double *m_y_nm1, double *m_colScales) + * + * Overriding this function call will trump all other ways to specify the column scaling factors. + * + * @param useColScaling Turn this on if you want to use column scaling in the calculations + * @param scaleFactors A vector of doubles that specifies the column factors. + */ + void setColumnScaling(bool useColScaling, const double * const scaleFactors = 0); + + + //! Set the rowscaling that are used for the inversion of the matrix + /*! + * Row scaling is set here. Right now the row scaling is set internally in the code. + * + * @param useRowScaling Turn row scaling on or off. + */ + void setRowScaling(bool useRowScaling); //! Scale the matrix /*! @@ -590,6 +628,8 @@ namespace Cantera { */ void getResidWts(doublereal * const residWts) const; + + //! Check to see if the nonlinear problem has converged /*! * @@ -958,13 +998,13 @@ namespace Cantera { * MATRIX INFORMATION **************************************************************************************/ - //! The type of column scaled used in the solution of the problem + //! The type of column scaling used in the matrix inversion of the problem /*! - * If true then colScaling = m_ewt[] - * if false then colScaling = 1.0 - * Currently, this is not part of the interface + * If 1 then colScaling = m_ewt[] + * If 2 then colScaling = user set + * if 0 then colScaling = 1.0 */ - bool m_colScaling; + int m_colScaling; //! int indicating whether row scaling is turned on (1) or not (0) int m_rowScaling; diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index a0261c9f3..62ca74b79 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -209,11 +209,13 @@ namespace Cantera { calcSolnScales(const doublereal t, const doublereal * const ysoln, const doublereal * const ysolnOld, doublereal * const ysolnScales) { + if (ysolnScales) { if (ysolnScales[0] == 0.0) { for (int i = 0; i < neq_; i++) { ysolnScales[i] = 1.0; } } + } } //==================================================================================================================== // Filter the solution predictions From 7d63cd24d4c2ed33fa9559dcfc623fa8da5fd42a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 8 Oct 2011 01:02:29 +0000 Subject: [PATCH 410/446] Fixed the trust region calculation --- Cantera/src/numerics/NonlinearSolver.cpp | 174 ++++++++++++++++------- Cantera/src/numerics/NonlinearSolver.h | 37 ++++- 2 files changed, 153 insertions(+), 58 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 4eec506e4..da23cd897 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -160,6 +160,8 @@ namespace Cantera { deltaX_trust_(0), norm_deltaX_trust_(0.0), trustDelta_(1.0), + trustRegionInitializationMethod_(2), + trustRegionInitializationFactor_(1.0), Nuu_(0.0), dist_R0_(0.0), dist_R1_(0.0), @@ -279,6 +281,8 @@ namespace Cantera { deltaX_trust_(0), norm_deltaX_trust_(0.0), trustDelta_(1.0), + trustRegionInitializationMethod_(2), + trustRegionInitializationFactor_(1.0), Nuu_(0.0), dist_R0_(0.0), dist_R1_(0.0), @@ -373,7 +377,8 @@ namespace Cantera { deltaX_trust_ = right.deltaX_trust_; norm_deltaX_trust_ = right.norm_deltaX_trust_; trustDelta_ = right.trustDelta_; - + trustRegionInitializationMethod_ = right.trustRegionInitializationMethod_; + trustRegionInitializationFactor_ = right.trustRegionInitializationFactor_; Nuu_ = right.Nuu_; dist_R0_ = right.dist_R0_; dist_R1_ = right.dist_R1_; @@ -466,7 +471,7 @@ namespace Cantera { } sum_norm = sqrt(sum_norm / neq_); if (printLargest) { - if (m_print_flag >= 4 && m_print_flag <= 5) { + if ((printLargest == 1) || (m_print_flag >= 4 && m_print_flag <= 5)) { printf("\t\t solnErrorNorm(): "); if (title) { @@ -1393,12 +1398,12 @@ namespace Cantera { } } // Compute the weighted norm of the undamped step size descentDir_[] - if (s_print_DogLeg || (doDogLeg_ && m_print_flag > 6)) { + if ((s_print_DogLeg || doDogLeg_) && m_print_flag >= 6) { normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 10); } else { normSoln = solnErrorNorm(DATA_PTR(deltaX_CP_), "SteepestDescentDir", 0); } - if (s_print_DogLeg || (doDogLeg_ && m_print_flag >= 4)) { + if ((s_print_DogLeg || doDogLeg_) && m_print_flag >= 5) { printf("\t\t doCauchyPointSolve: Steepest descent to Cauchy point: \n"); printf("\t\t\t R0 = %g \n", m_normResid_0); printf("\t\t\t Rpred = %g\n", residCauchy); @@ -1852,6 +1857,11 @@ namespace Cantera { } //==================================================================================================================== + // Calculate the length of the current trust region in terms of the solution error norm + /* + * We carry out a norm of deltaX_trust_ first. Then, we multiply that value + * by trustDelta_ + */ doublereal NonlinearSolver::trustRegionLength() const { norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); @@ -2000,24 +2010,26 @@ namespace Cantera { return f_delta_bounds; } //==================================================================================================================== - // Calculate the trust region vectors + // Readjust the trust region vectors /* * The trust region is made up of the trust region vector calculation and the trustDelta_ value * We periodically recalculate the trustVector_ values so that they renormalize to the * correct length. */ - void NonlinearSolver::calcTrustVector() + void NonlinearSolver::readjustTrustVector() { + doublereal trustDeltaOld = trustDelta_; doublereal wtSum = 0.0; for (int i = 0; i < neq_; i++) { wtSum += m_ewt[i]; } wtSum /= neq_; doublereal trustNorm = solnErrorNorm(DATA_PTR(deltaX_trust_)); + doublereal deltaXSizeOld = trustNorm; doublereal trustNormGoal = trustNorm * trustDelta_; // This is the size of each component. - doublereal trustDeltaEach = trustDelta_ * trustNorm / neq_; + // doublereal trustDeltaEach = trustDelta_ * trustNorm / neq_; doublereal oldVal; doublereal fabsy; // we use the old value of the trust region as an indicator @@ -2026,7 +2038,8 @@ namespace Cantera { fabsy = fabs(m_y_n_curr[i]); // First off make sure that each trust region vector is 1/2 the size of each variable or smaller // unless overridden by the deltaStepMininum value. - doublereal newValue = trustDeltaEach * m_ewt[i] / wtSum; + // doublereal newValue = trustDeltaEach * m_ewt[i] / wtSum; + doublereal newValue = trustNormGoal * m_ewt[i]; if (newValue > 0.5 * fabsy) { if (fabsy * 0.5 > m_deltaStepMinimum[i]) { deltaX_trust_[i] = 0.5 * fabsy; @@ -2057,11 +2070,12 @@ namespace Cantera { deltaX_trust_[i] = deltaX_trust_[i] * sum; } norm_deltaX_trust_ = solnErrorNorm(DATA_PTR(deltaX_trust_)); - trustDelta_ = 1.0; + trustDelta_ = trustNormGoal / norm_deltaX_trust_; if (doDogLeg_ && m_print_flag >= 4) { - printf("\t\t calcTrustVector(): Trust vector size (SolnNorm Basis) changed from %g to %g \n", - trustNorm, trustNormGoal); + printf("\t\t reajustTrustVector(): Trust size = %11.3E: Old deltaX size = %11.3E trustDelta_ = %11.3E\n" + "\t\t new deltaX size = %11.3E trustdelta_ = %11.3E\n", + trustNormGoal, deltaXSizeOld, trustDeltaOld, norm_deltaX_trust_, trustDelta_ ); } } //==================================================================================================================== @@ -2071,15 +2085,44 @@ namespace Cantera { */ void NonlinearSolver::initializeTrustRegion() { - doublereal cpd = calcTrustDistance(deltaX_CP_); - if ((doDogLeg_ && m_print_flag >= 4)) { - printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + if (trustRegionInitializationMethod_ == 0) { + return; } - trustDelta_ = trustDelta_ * cpd; - calcTrustVector(); - cpd = calcTrustDistance(deltaX_CP_); - if ((doDogLeg_ && m_print_flag >= 4)) { - printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + if (trustRegionInitializationMethod_ == 1) { + for (int i = 0; i < neq_; i++) { + deltaX_trust_[i] = m_ewt[i] * trustRegionInitializationFactor_; + } + trustDelta_ = 1.0; + } + if (trustRegionInitializationMethod_ == 2) { + for (int i = 0; i < neq_; i++) { + deltaX_trust_[i] = m_ewt[i] * m_normDeltaSoln_CP * trustRegionInitializationFactor_; + } + doublereal cpd = calcTrustDistance(deltaX_CP_); + if ((doDogLeg_ && m_print_flag >= 4)) { + printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + } + trustDelta_ = trustDelta_ * cpd * trustRegionInitializationFactor_; + readjustTrustVector(); + cpd = calcTrustDistance(deltaX_CP_); + if ((doDogLeg_ && m_print_flag >= 4)) { + printf("\t\t initializeTrustRegion(): Relative Distance of Cauchy Vector wrt Trust Vector = %g\n", cpd); + } + } + if (trustRegionInitializationMethod_ == 3) { + for (int i = 0; i < neq_; i++) { + deltaX_trust_[i] = m_ewt[i] * m_normDeltaSoln_Newton * trustRegionInitializationFactor_; + } + doublereal cpd = calcTrustDistance(deltaX_Newton_); + if ((doDogLeg_ && m_print_flag >= 4)) { + printf("\t\t initializeTrustRegion(): Relative Distance of Newton Vector wrt Trust Vector = %g\n", cpd); + } + trustDelta_ = trustDelta_ * cpd; + readjustTrustVector(); + cpd = calcTrustDistance(deltaX_Newton_); + if ((doDogLeg_ && m_print_flag >= 4)) { + printf("\t\t initializeTrustRegion(): Relative Distance of Newton Vector wrt Trust Vector = %g\n", cpd); + } } } @@ -2537,15 +2580,14 @@ namespace Cantera { * Find the initial value of lambda that satisfies the trust distance, trustDelta_ */ dogLegID_ = calcTrustIntersection(trustDelta_, lambda, dogLegAlpha_); - - if (m_print_flag > 5) { + if (m_print_flag >= 4) { tlen = trustRegionLength(); - printf("\tdampDogLeg: trust region with length %13.5E has intersection at leg = %d, alpha = %g\n", - tlen, dogLegID_, dogLegAlpha_); + printf("\t\t dampDogLeg: trust region with length %13.5E has intersection at leg = %d, alpha = %g, lambda = %g\n", + tlen, dogLegID_, dogLegAlpha_, lambda); } /* - * Figure out the new step vector, step0, based on (leg, alpha). Here we are using the - * inter + * Figure out the new step vector, step_1, based on (leg, alpha). Here we are using the + * intersection of the trust oval with the dog-leg curve. */ fillDogLegStep(dogLegID_, dogLegAlpha_, step_1); @@ -2587,7 +2629,7 @@ namespace Cantera { if (m_print_flag >= 1) { doublereal stepNorm = solnErrorNorm(DATA_PTR(step_1)); - printf("\t\t\tdampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); + printf("\t\t dampDogLeg: Current direction rejected, update became too small %g\n", stepNorm); success = false; retn = NSOLN_RETN_FAIL_STEPTOOSMALL; break; @@ -2595,7 +2637,7 @@ namespace Cantera { } if (info == -2) { if (m_print_flag >= 1) { - printf("\t\t\tdampStep: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); + printf("\t\t dampDogLeg: current trial step and damping led to LAPACK ERROR %d. Bailing\n", info); success = false; retn = NSOLN_RETN_MATRIXINVERSIONERROR; break; @@ -2876,6 +2918,7 @@ namespace Cantera { int legBest; doublereal alphaBest; #endif + bool trInit = false; mdp::mdp_copy_dbl_1(DATA_PTR(m_y_n_curr), DATA_PTR(y_comm), neq_); @@ -2897,8 +2940,15 @@ namespace Cantera { } else { jac.m_printLevel = 0; } - mdp::mdp_init_dbl_1(DATA_PTR(deltaX_trust_), 1.0, neq_); - trustDelta_ = 1.0; + if (trustRegionInitializationMethod_ == 0) { + trInit = true; + } else if (trustRegionInitializationMethod_ == 1) { + trInit = true; + initializeTrustRegion(); + } else { + mdp::mdp_init_dbl_1(DATA_PTR(deltaX_trust_), 1.0, neq_); + trustDelta_ = 1.0; + } if (m_print_flag == 2 || m_print_flag == 3) { printf("\tsolve_nonlinear_problem():\n\n"); @@ -2941,10 +2991,12 @@ namespace Cantera { if (m_normDeltaSoln_Newton > 1.0E2) { createSolnWeights(DATA_PTR(m_y_n_curr)); #ifdef DEBUG_MODE - calcTrustVector(); + if (trInit) { + readjustTrustVector(); + } #else - if (doDogLeg_) { - calcTrustVector(); + if (doDogLeg_ && trInit) { + readjustTrustVector(); } #endif } else { @@ -2952,10 +3004,12 @@ namespace Cantera { if ((num_newt_its % 5) == 1) { createSolnWeights(DATA_PTR(m_y_n_curr)); #ifdef DEBUG_MODE - calcTrustVector(); + if (trInit) { + readjustTrustVector(); + } #else - if (doDogLeg_) { - calcTrustVector(); + if (doDogLeg_ && trInit) { + readjustTrustVector(); } #endif } @@ -3001,7 +3055,7 @@ namespace Cantera { /* * Calculate the base residual */ - if (m_print_flag > 3) { + if (m_print_flag >= 6) { printf("\t solve_nonlinear_problem(): Calculate the base residual\n"); } info = doResidualCalc(time_curr, NSOLN_TYPE_STEADY_STATE, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr)); @@ -3025,46 +3079,37 @@ namespace Cantera { */ if (m_print_flag >= 6) { m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 10, DATA_PTR(m_y_n_curr)); - } else if (m_print_flag == 4 || m_print_flag == 5) { - m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); } else { m_normResid_0 = residErrorNorm(DATA_PTR(m_resid), "Initial norm of the residual", 0, DATA_PTR(m_y_n_curr)); + if (m_print_flag == 4 || m_print_flag == 5 ) { + printf("\t solve_nonlinear_problem(): Initial Residual Norm = %13.4E\n", m_normResid_0); + } } + #ifdef DEBUG_MODE if (m_print_flag > 3) { printf("\t solve_nonlinear_problem(): Calculate the steepest descent direction and Cauchy Point\n"); } m_normDeltaSoln_CP = doCauchyPointSolve(jac); - if (num_newt_its == 1) { - if (m_print_flag > 3) { - printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length to the Cauchy Point\n"); - } - initializeTrustRegion(); - } + #else if (doDogLeg_) { if (m_print_flag > 3) { printf("\t solve_nonlinear_problem(): Calculate the steepest descent direction and Cauchy Point\n"); } m_normDeltaSoln_CP = doCauchyPointSolve(jac); - if (m_numTotalNewtIts == 1) { - if (m_print_flag > 3) { - printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length to the Cauchy Point\n"); - } - initializeTrustRegion(); - } } #endif // compute the undamped Newton step if (doAffineSolve_) { - if (m_print_flag > 3) { + if (m_print_flag >= 4) { printf("\t solve_nonlinear_problem(): Calculate the Newton direction via an Affine solve\n"); } info = doAffineNewtonSolve(DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); } else { - if (m_print_flag > 3) { + if (m_print_flag >= 4) { printf("\t solve_nonlinear_problem(): Calculate the Newton direction via a Newton solve\n"); } info = doNewtonSolve(time_curr, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), DATA_PTR(deltaX_Newton_), jac); @@ -3079,14 +3124,33 @@ namespace Cantera { } mdp::mdp_copy_dbl_1(DATA_PTR(m_step_1), CONSTD_DATA_PTR(deltaX_Newton_), neq_); - if (m_print_flag > 3) { - m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Step of the iteration", 10); + if (m_print_flag >= 6) { + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Newton Step of the iteration", 10); } else { - m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Step of the iteration", 0); + m_normDeltaSoln_Newton = solnErrorNorm(DATA_PTR(deltaX_Newton_), "Initial Undamped Newton Step of the iteration", 0); + } + + if (m_numTotalNewtIts == 1) { + if (trustRegionInitializationMethod_ == 2 || trustRegionInitializationMethod_ == 3) { + if (m_print_flag > 3) { + if (trustRegionInitializationMethod_ == 2) { + printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length of the Cauchy Vector times %f\n", + trustRegionInitializationFactor_); + } else { + printf("\t solve_nonlinear_problem(): Initialize the trust region size as the length of the Newton Vector times %f\n", + trustRegionInitializationFactor_); + } + } + initializeTrustRegion(); + trInit = true; + } } if (doDogLeg_) { + + + #ifdef DEBUG_MODE doublereal trustD = calcTrustDistance(m_step_1); if (m_print_flag >= 4) { diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 574e70583..a2861dddc 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -295,7 +295,7 @@ namespace Cantera { int doAffineNewtonSolve(const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, SquareMatrix& jac); - //! Calculate the size of the current trust region + //! Calculate the length of the current trust region in terms of the solution error norm /*! * We carry out a norm of deltaX_trust_ first. Then, we multiply that value * by trustDelta_ @@ -321,7 +321,7 @@ namespace Cantera { protected: - //! Calculate the trust region vectors + //! Readjust the trust region vectors /*! * The trust region is made up of the trust region vector calculation and the trustDelta_ value * We periodically recalculate the trustVector_ values so that they renormalize to the @@ -332,7 +332,7 @@ namespace Cantera { * || delta_x dot 1/trustDeltaX_ || <= trustDelta_ * */ - void calcTrustVector(); + void readjustTrustVector(); //! Fill a dogleg solution step vector /*! @@ -746,6 +746,22 @@ namespace Cantera { */ void initializeTrustRegion(); + //! Set Trust region initialization strategy + /*! + * The default is use method 2 with a factor of 1. + * Then, on subsequent invocations of solve_nonlinear_problem() the strategy flips to method 0. + * + * @param method Method to set the strategy + * 0 No strategy - Use the previous strategy + * 1 Factor of the solution error weights + * 2 Factor of the first Cauchy Point distance + * 3 Factor of the first Newton step distance + * + * @param factor Factor to use in combination with the method + * + */ + void setTrustRegionInitializationMethod(int method, doublereal factor); + //! Damp using the dog leg approach /*! @@ -1136,6 +1152,21 @@ namespace Cantera { //! calculate the max step size. doublereal trustDelta_; + //! Method for handling the trust region initialization + /*! + * Then, on subsequent invocations of solve_nonlinear_problem() the strategy flips to method 0. + * + * method Method to set the strategy + * 0 No strategy - Use the previous strategy + * 1 Factor of the solution error weights + * 2 Factor of the first Cauchy Point distance + * 3 Factor of the first Newton step distance + */ + int trustRegionInitializationMethod_; + + //! Factor used to set the initial trust region + doublereal trustRegionInitializationFactor_; + //! Relative distance down the Newton step that the second dogleg starts doublereal Nuu_; From 6cf9c46630efc5e5543fd76a807bc15c7468880e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 10 Oct 2011 16:51:52 +0000 Subject: [PATCH 411/446] Worked on lvl 4 printouts --- Cantera/src/numerics/NonlinearSolver.cpp | 90 +++++++++++++++--------- 1 file changed, 57 insertions(+), 33 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index da23cd897..91fa49d4b 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -568,9 +568,7 @@ namespace Cantera { int *imax = mdp::mdp_alloc_int_1(num_entries, -1); if (m_print_flag >= 4 && m_print_flag <= 5) { - printf("\t "); - print_line("-", 90); - printf("\t\t residErrorNorm():"); + printf("\t\t residErrorNorm():"); if (title) { printf(" %s ", title); } else { @@ -2792,7 +2790,13 @@ namespace Cantera { goodStep = true; m_normResid_1 = m_normResidTrial; retn = 0; + if (m_print_flag >= 4) { + printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E passes\n", dogLegID_, dogLegAlpha_, m_normResidTrial); + } } else { + if (m_print_flag >= 4) { + printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E failes\n", dogLegID_, dogLegAlpha_, m_normResidTrial); + } trustDelta_ *= 0.33; CurrentTrustFactor_ *= 0.33; retn = 2; @@ -2826,8 +2830,8 @@ namespace Cantera { trustDelta_ *= 0.5; NextTrustFactor_ *= 0.5; ll = trustRegionLength(); - if (m_print_flag >= 5) { - printf("\t\tdecideStep(): Trust region decreased from %g to %g due to bad quad approximation\n", + if (m_print_flag >= 4) { + printf("\t\t decideStep: Trust region decreased from %g to %g due to bad quad approximation\n", ll*2, ll); } } @@ -2841,16 +2845,22 @@ namespace Cantera { CurrentTrustFactor_ *= 2; adjustUpStepMinimums(); ll = trustRegionLength(); - if (m_print_flag >= 5) { - printf("\t\tdecideStep(): Trust region increased from %g to %g due to good quad approximation\n", - ll*0.5, ll); + if (m_print_flag >= 4) { + if (m_normResidTrial < 0.33 * m_normResid_0) { + printf("\t\t decideStep: Redo line search with trust region increased from %g to %g due to good nonlinear behavior\n", + ll*0.5, ll); + } else { + printf("\t\t decideStep: Redi line search with trust region increased from %g to %g due to good linear model approximation\n", + ll*0.5, ll); + } } retn = 3; } else { /* * Increase the size of the trust region for the next calculation */ - if (m_normResidTrial < 0.75 * expectedNormRes || (m_normResidTrial < 0.20 * m_normResid_0)) { + if (m_normResidTrial < 0.99 * expectedNormRes || (m_normResidTrial < 0.20 * m_normResid_0) || + (funcDecrease < -1.0E-50 && ( funcDecrease < 0.9 *expectedFuncDecrease)) ) { if (leg == 2 && alpha == 1.0 ) { ll = trustRegionLength(); if (ll < 2.0 * m_normDeltaSoln_Newton) { @@ -2858,8 +2868,8 @@ namespace Cantera { NextTrustFactor_ *= 2.0; adjustUpStepMinimums(); ll = trustRegionLength(); - if (m_print_flag >= 5) { - printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + if (m_print_flag >= 4) { + printf("\t\t decideStep: Trust region further increased from %g to %g next step due to good linear model behavior\n", ll*0.5, ll); } } @@ -2869,8 +2879,8 @@ namespace Cantera { NextTrustFactor_ *= 2.0; adjustUpStepMinimums(); ll = trustRegionLength(); - if (m_print_flag >= 5) { - printf("\t\tdecideStep(): Trust region further increased from %g to %g due to good nonlinear behavior\n", + if (m_print_flag >= 4) { + printf("\t\t decideStep: Trust region further increased from %g to %g next step due to good linear model behavior\n", ll*0.5, ll); } } @@ -2981,7 +2991,7 @@ namespace Cantera { if (m_print_flag > 3) { printf("\t"); - print_line("=", 100); + print_line("=", 119); printf("\tsolve_nonlinear_problem(): iteration %d:\n", num_newt_its); } @@ -3266,11 +3276,10 @@ namespace Cantera { goto done; } if (m_print_flag >= 4) { - m_normResid_full = residErrorNorm(DATA_PTR(m_resid), "\t solve_nonlinear_problem():Resulting Residual Norm", - 10, DATA_PTR(m_y_n_1)); + m_normResid_full = residErrorNorm(DATA_PTR(m_resid), " Resulting full residual norm", 10, DATA_PTR(m_y_n_1)); if (fabs(m_normResid_full - m_normResid_1) > 1.0E-3 * ( m_normResid_1 + m_normResid_full + 1.0E-4)) { if (m_print_flag >= 4) { - printf("\t solve_nonlinear_problem(): Residual norm changed from %g to %g due to " + printf("\t solve_nonlinear_problem(): Full residual norm changed from %g to %g due to " "lagging of components\n", m_normResid_1, m_normResid_full); } } @@ -3285,18 +3294,7 @@ namespace Cantera { if (retnDamp > NSOLN_RETN_CONTINUE) { convRes = convergenceCheck(retnDamp, stepNorm_1); } - if (m_print_flag >= 4) { - if (convRes > 0) { - printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, nonlin " - "converged, final estimate of the next solution update norm = %-12.4E\n", stepNorm_2); - } else if (retnDamp >= NSOLN_RETN_CONTINUE) { - printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, " - "estimate of the next solution update norm = %-12.4E\n", stepNorm_2); - } else { - printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful, final estimate " - "of the next solution update norm = %-12.4E\n", stepNorm_2); - } - } + @@ -3350,6 +3348,32 @@ namespace Cantera { printf("\n"); } + if (m_print_flag >= 4) { + if (doDogLeg_) { + if (convRes > 0) { + printf("\t solve_nonlinear_problem(): Problem Converged, stepNorm = %11.3E, reduction of res from %11.3E to %11.3E\n", + stepNorm_1, m_normResid_0, m_normResid_full); + printf("\t"); + print_line("=", 119); + } else { + printf("\t solve_nonlinear_problem(): Successfull step taken with stepNorm = %11.3E, reduction of res from %11.3E to %11.3E\n", + stepNorm_1, m_normResid_0, m_normResid_full); + } + } else { + if (convRes > 0) { + printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, nonlin " + "converged, final estimate of the next solution update norm = %-12.4E\n", stepNorm_2); + printf("\t"); + print_line("=", 119); + } else if (retnDamp >= NSOLN_RETN_CONTINUE) { + printf("\t solve_nonlinear_problem(): Damped Newton iteration successful, " + "estimate of the next solution update norm = %-12.4E\n", stepNorm_2); + } else { + printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful, final estimate " + "of the next solution update norm = %-12.4E\n", stepNorm_2); + } + } + } // convergence if (convRes) { goto done; @@ -3405,17 +3429,17 @@ namespace Cantera { num_linear_solves += m_numTotalLinearSolves; doublereal time_elapsed = wc.secondsWC(); - if (m_print_flag > 1) { + if (m_print_flag > 1 ) { if (retnDamp > 0) { if (NonlinearSolver::s_TurnOffTiming) { - printf("\t\tNonlinear problem solved successfully in %d its\n", + printf("\tNonlinear problem solved successfully in %d its\n", num_newt_its); } else { - printf("\t\tNonlinear problem solved successfully in %d its, time elapsed = %g sec\n", + printf("\tNonlinear problem solved successfully in %d its, time elapsed = %g sec\n", num_newt_its, time_elapsed); } } else { - printf("\t\tNonlinear problem failed to solve after %d its\n", num_newt_its); + printf("\tNonlinear problem failed to solve after %d its\n", num_newt_its); } } retnCode = retnDamp; From e8d6649c7b2284e96e059518f45f37c7fa734f5a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 13 Oct 2011 21:16:06 +0000 Subject: [PATCH 412/446] Doxygen updates -> Also moved implementation functions for BandMatrix into the cpp file --- Cantera/src/numerics/BandMatrix.cpp | 375 ++++++++++++++--------- Cantera/src/numerics/BandMatrix.h | 352 ++++++++++++++------- Cantera/src/numerics/NonlinearSolver.cpp | 18 +- Cantera/src/numerics/NonlinearSolver.h | 34 +- 4 files changed, 497 insertions(+), 282 deletions(-) diff --git a/Cantera/src/numerics/BandMatrix.cpp b/Cantera/src/numerics/BandMatrix.cpp index b643fe1b2..0571df81c 100644 --- a/Cantera/src/numerics/BandMatrix.cpp +++ b/Cantera/src/numerics/BandMatrix.cpp @@ -22,160 +22,243 @@ using namespace std; namespace Cantera { + //==================================================================================================================== + BandMatrix::BandMatrix() : + m_factored(false), + m_n(0), + m_kl(0), + m_ku(0), + m_zero(0.0) + { + data.clear(); + ludata.clear(); + } + //==================================================================================================================== + BandMatrix::BandMatrix(int n, int kl, int ku, doublereal v) : + m_factored(false), + m_n(n), + m_kl(kl), + m_ku(ku), + m_zero(0.0) + { + data.resize(n*(2*kl + ku + 1)); + ludata.resize(n*(2*kl + ku + 1)); + fill(data.begin(), data.end(), v); + fill(ludata.begin(), ludata.end(), 0.0); + m_ipiv.resize(m_n); + } + //==================================================================================================================== + BandMatrix::BandMatrix(const BandMatrix& y) : + m_factored(false), + m_n(0), + m_kl(0), + m_ku(0), + m_zero(0.0) + { + m_n = y.m_n; + m_kl = y.m_kl; + m_ku = y.m_ku; + data = y.data; + ludata = y.ludata; + m_factored = y.m_factored; + m_ipiv = y.m_ipiv; + } + //==================================================================================================================== + BandMatrix::~BandMatrix() { - /// Default constructor. - BandMatrix::BandMatrix() : m_factored(false), m_n(0), - m_kl(0), m_ku(0), m_zero(0.0) { - data.clear(); ludata.clear(); + } + //==================================================================================================================== + BandMatrix& BandMatrix::operator=(const BandMatrix & y) { + if (&y == this) return *this; + m_n = y.m_n; + m_kl = y.m_kl; + m_ku = y.m_ku; + m_ipiv = y.m_ipiv; + data = y.data; + ludata = y.ludata; + m_factored = y.m_factored; + return *this; + } + //==================================================================================================================== + void BandMatrix::resize(int n, int kl, int ku, doublereal v) { + m_n = n; + m_kl = kl; + m_ku = ku; + data.resize(n*(2*kl + ku + 1)); + ludata.resize(n*(2*kl + ku + 1)); + m_ipiv.resize(m_n); + fill(data.begin(), data.end(), v); + m_factored = false; + } + //==================================================================================================================== + void BandMatrix::bfill(doublereal v) { + std::fill(data.begin(), data.end(), v); + m_factored = false; + } + //==================================================================================================================== + doublereal& BandMatrix::operator()(int i, int j) { + return value(i,j); + } + //==================================================================================================================== + doublereal BandMatrix::operator()(int i, int j) const { + return value(i,j); + } + //==================================================================================================================== + doublereal& BandMatrix::value(int i, int j) { + m_factored = false; + if (i < j - m_ku || i > j + m_kl) { + return m_zero; } - - - /** - * Constructor. Create an n by n banded matrix. - * @param n number of rows and columns - * @param kl number of subdiagonals - * @param ku number of superdiagonals - * @param v initial value (default = 0.0) - */ - BandMatrix::BandMatrix(int n, int kl, int ku, doublereal v) - : m_factored(false), m_n(n), m_kl(kl), m_ku(ku) { - data.resize(n*(2*kl + ku + 1)); - ludata.resize(n*(2*kl + ku + 1)); - fill(data.begin(), data.end(), v); - fill(ludata.begin(), ludata.end(), 0.0); - m_ipiv.resize(m_n); + return data[index(i,j)]; + } + //==================================================================================================================== + doublereal BandMatrix::value( int i, int j) const { + if (i < j - m_ku || i > j + m_kl) return 0.0; + return data[index(i,j)]; + } + //==================================================================================================================== + int BandMatrix::index(int i, int j) const { + int rw = m_kl + m_ku + i - j; + return (2*m_kl + m_ku + 1)*j + rw; + } + //==================================================================================================================== + doublereal BandMatrix::_value(int i, int j) const { + return data[index(i,j)]; + } + //==================================================================================================================== + // Number of rows + int BandMatrix::nRows() const { + return m_n; + } + //==================================================================================================================== + // Number of columns + int BandMatrix::nColumns() const { + return m_n; + } + //==================================================================================================================== + // Number of subdiagonals + int BandMatrix::nSubDiagonals() const { + return m_kl; + } + //==================================================================================================================== + // Number of superdiagonals + int BandMatrix::nSuperDiagonals() const { + return m_ku; + } + //==================================================================================================================== + int BandMatrix::ldim() const { + return 2*m_kl + m_ku + 1; + } + //==================================================================================================================== + vector_int & BandMatrix::ipiv() { + return m_ipiv; + } + //==================================================================================================================== + /* + * Multiply A*b and write result to \c prod. + */ + void BandMatrix::mult(const doublereal * const b, doublereal * const prod) const { + int nr = nRows(); + doublereal sum = 0.0; + for (int m = 0; m < nr; m++) { + sum = 0.0; + for (int j = m - m_kl; j <= m + m_ku; j++) { + if (j >= 0 && j < m_n) + sum += _value(m,j) * b[j]; + } + prod[m] = sum; } - - /// copy constructor - BandMatrix::BandMatrix(const BandMatrix& y) { - m_n = y.m_n; - m_kl = y.m_kl; - m_ku = y.m_ku; - data = y.data; - ludata = y.ludata; - m_factored = y.m_factored; - m_ipiv = y.m_ipiv; + } + //==================================================================================================================== + /* + * Multiply b*A and write result to \c prod. + */ + void BandMatrix::leftMult(const doublereal * const b, doublereal * const prod) const { + int nc = nColumns(); + doublereal sum = 0.0; + for (int n = 0; n < nc; n++) { + sum = 0.0; + for (int i = n - m_ku; i <= n + m_kl; i++) { + if (i >= 0 && i < m_n) + sum += _value(i,n) * b[i]; + } + prod[n] = sum; } + } + //==================================================================================================================== + /* + * Perform an LU decomposition. LAPACK routine DGBTRF is used. + * The factorization is saved in ludata. + */ + int BandMatrix::factor() { + int info=0; + copy(data.begin(), data.end(), ludata.begin()); + ct_dgbtrf(nRows(), nColumns(), nSubDiagonals(), nSuperDiagonals(), + DATA_PTR(ludata), ldim(), DATA_PTR(ipiv()), info); - BandMatrix& BandMatrix::operator=(const BandMatrix& y) { - if (&y == this) return *this; - m_n = y.m_n; - m_kl = y.m_kl; - m_ku = y.m_ku; - m_ipiv = y.m_ipiv; - data = y.data; - ludata = y.ludata; - m_factored = y.m_factored; - return *this; + // if info = 0, LU decomp succeeded. + if (info == 0) { + m_factored = true; + } else { + m_factored = false; + ofstream fout("bandmatrix.csv"); + fout << *this << endl; + fout.close(); } + return info; + } + //==================================================================================================================== + int BandMatrix::solve(int n, const doublereal * const b, doublereal * const x) { + copy(b, b+n, x); + return solve(n, x); + } + //==================================================================================================================== + int BandMatrix::solve(int n, doublereal* b) { + int info = 0; + if (!m_factored) info = factor(); + if (info == 0) + ct_dgbtrs(ctlapack::NoTranspose, nColumns(), nSubDiagonals(), + nSuperDiagonals(), 1, DATA_PTR(ludata), ldim(), + DATA_PTR(ipiv()), b, nColumns(), info); - void BandMatrix::resize(int n, int kl, int ku, doublereal v) { - m_n = n; - m_kl = kl; - m_ku = ku; - data.resize(n*(2*kl + ku + 1)); - ludata.resize(n*(2*kl + ku + 1)); - m_ipiv.resize(m_n); - fill(data.begin(), data.end(), v); - fill(data.begin(), data.end(), 0.0); - m_factored = false; + // error handling + if (info != 0) { + ofstream fout("bandmatrix.csv"); + fout << *this << endl; + fout.close(); } - - - /** - * Multiply A*b and write result to \c prod. - */ - void BandMatrix::mult(const double* b, double* prod) const { - int nr = rows(); - int m, j; - double sum = 0.0; - for (m = 0; m < nr; m++) { - sum = 0.0; - for (j = m - m_kl; j <= m + m_ku; j++) { - if (j >= 0 && j < m_n) - sum += _value(m,j)*b[j]; - } - prod[m] = sum; - } - } - - - /** - * Multiply b*A and write result to \c prod. - */ - void BandMatrix::leftMult(const double* b, double* prod) const { - int nc = columns(); - int n, i; - double sum = 0.0; - for (n = 0; n < nc; n++) { - sum = 0.0; - for (i = n - m_ku; i <= n + m_kl; i++) { - if (i >= 0 && i < m_n) - sum += _value(i,n)*b[i]; - } - prod[n] = sum; - } - } - - - /** - * Perform an LU decomposition. LAPACK routine DGBTRF is used. - * The factorization is saved in ludata. - */ - int BandMatrix::factor() { - int info=0; - copy(data.begin(), data.end(), ludata.begin()); - ct_dgbtrf(rows(), columns(), nSubDiagonals(), nSuperDiagonals(), - DATA_PTR(ludata), ldim(), DATA_PTR(ipiv()), info); - - // if info = 0, LU decomp succeeded. - if (info == 0) { - m_factored = true; - } - else { - m_factored = false; - ofstream fout("bandmatrix.csv"); - fout << *this << endl; - fout.close(); - } - return info; - } - - - - int BandMatrix::solve(int n, const doublereal* b, doublereal* x) { - copy(b, b+n, x); - return solve(n, x); - } - - int BandMatrix::solve(int n, doublereal* b) { - int info = 0; - if (!m_factored) info = factor(); - if (info == 0) - ct_dgbtrs(ctlapack::NoTranspose, columns(), nSubDiagonals(), - nSuperDiagonals(), 1, DATA_PTR(ludata), ldim(), - DATA_PTR(ipiv()), b, columns(), info); - - // error handling - if (info != 0) { - ofstream fout("bandmatrix.csv"); - fout << *this << endl; - fout.close(); - } - return info; - } - - ostream& operator<<(ostream& s, const BandMatrix& m) { - int nr = m.rows(); - int nc = m.columns(); - int i,j; - for (i = 0; i < nr; i++) { - for (j = 0; j < nc; j++) { - s << m(i,j) << ", "; - } - s << endl; - } - return s; + return info; + } + //==================================================================================================================== + vector_fp::iterator BandMatrix::begin() { + m_factored = false; + return data.begin(); + } + //==================================================================================================================== + vector_fp::iterator BandMatrix::end() { + m_factored = false; + return data.end(); + } + //==================================================================================================================== + vector_fp::const_iterator BandMatrix::begin() const { + return data.begin(); + } + //==================================================================================================================== + vector_fp::const_iterator BandMatrix::end() const { + return data.end(); + } + //==================================================================================================================== + ostream& operator<<(ostream& s, const BandMatrix& m) { + int nr = m.nRows(); + int nc = m.nColumns(); + for (int i = 0; i < nr; i++) { + for (int j = 0; j < nc; j++) { + s << m(i,j) << ", "; + } + s << endl; } + return s; + } + //==================================================================================================================== } diff --git a/Cantera/src/numerics/BandMatrix.h b/Cantera/src/numerics/BandMatrix.h index d3f7fdd3e..148029c95 100644 --- a/Cantera/src/numerics/BandMatrix.h +++ b/Cantera/src/numerics/BandMatrix.h @@ -23,130 +23,258 @@ namespace Cantera { - /** - * A class for banded matrices. + /** + * A class for banded matrices. This class has matrix inversion processes. + * The class is based upon the LAPACK banded storage matrix format. + */ + class BandMatrix { + + public: + + //! Base Constructor + /*! + * * Create an \c 0 by \c 0 matrix, and initialize all elements to \c 0. */ - class BandMatrix { + BandMatrix(); - public: + //! Creates a banded matrix and sets all elements to zero + /*! + * Create an \c n by \c n banded matrix, and initialize all elements to \c v. + * + * @param n size of the square matrix + * @param kl band size on the lower portion of the matrix + * @param ku band size on the upper portion of the matrix + * @param v intial value of all matrix components. + */ + BandMatrix(int n, int kl, int ku, doublereal v = 0.0); - BandMatrix(); - BandMatrix(int n, int kl, int ku, doublereal v = 0.0); + //! Copy constructor + /*! + * @param y Matrix to be copied + */ + BandMatrix(const BandMatrix& y); - /// copy constructor - BandMatrix(const BandMatrix& y); + //! Destructor. Does nothing. + virtual ~BandMatrix(); - /// Destructor. Does nothing. - virtual ~BandMatrix(){} + //! assignment operator + /*! + * @param y reference to the matrix to be copied + */ + BandMatrix& operator=(const BandMatrix& y); - /// assignment. - BandMatrix& operator=(const BandMatrix& y); + //! Resize the matrix problem + /*! + * All data is lost + * + * @param n size of the square matrix + * @param kl band size on the lower portion of the matrix + * @param ku band size on the upper portion of the matrix + * @param v intial value of all matrix components. + */ + void resize(int n, int kl, int ku, doublereal v = 0.0); - void resize(int n, int kl, int ku, doublereal v = 0.0); + //! Fill or zero the matrix + /*! + * @param v Fill value, defaults to zero. + */ + void bfill(doublereal v = 0.0); - void bfill(doublereal v) { - std::fill(data.begin(), data.end(), v); - m_factored = false; - } - - doublereal& operator()( int i, int j) { - return value(i,j); - } - - doublereal operator() ( int i, int j) const { - return value(i,j); - } - - /// Return a reference to element (i,j). Since this method may - /// alter the element value, it may need to be refactored, so - /// the flag m_factored is set to false. - doublereal& value( int i, int j) { - m_factored = false; - if (i < j - m_ku || i > j + m_kl) { - m_zero = 0.0; - return m_zero; - } - return data[index(i,j)]; - } - - /// Return the value of element (i,j). This method does not - /// alter the array. - doublereal value( int i, int j) const { - if (i < j - m_ku || i > j + m_kl) return 0.0; - return data[index(i,j)]; - } - - /// Return the location in the internal 1D array corresponding to - /// the (i,j) element in the banded array. - int index(int i, int j) const { - int rw = m_kl + m_ku + i - j; - return (2*m_kl + m_ku + 1)*j + rw; - } - - /// Return the value of the (i,j) element for (i,j) within the - /// bandwidth. For efficiency, this method does not check that - /// (i,j) are within the bandwidth; it is up to the calling - /// program to insure that this is true. - doublereal _value(int i, int j) const { - return data[index(i,j)]; - } - - /// Number of rows - int nRows() const { return m_n; } - /// @deprecated Redundant. - int rows() const { return m_n; } - - /// Number of columns - int nColumns() const { return m_n; } - /// @deprecated Redundant. - int columns() const { return m_n; } - - /// Number of subdiagonals - int nSubDiagonals() const { return m_kl; } - - /// Number of superdiagonals - int nSuperDiagonals() const { return m_ku; } - - int ldim() const { return 2*m_kl + m_ku + 1; } - vector_int& ipiv() { return m_ipiv; } - - /// Multiply A*b and write result to prod. - void mult(const double* b, double* prod) const; - - /// Multiply b*A and write result to prod. - void leftMult(const double* b, double* prod) const; - - int factor(); - - //void solve(const vector_fp& b, vector_fp& x); - - int solve(int n, const doublereal* b, doublereal* x); - int solve(int n, doublereal* b); - - vector_fp::iterator begin() { - m_factored = false; - return data.begin(); - } - vector_fp::iterator end() { - m_factored = false; - return data.end(); - } - vector_fp::const_iterator begin() const { return data.begin(); } - vector_fp::const_iterator end() const { return data.end(); } - - protected: - vector_fp data; - vector_fp ludata; - bool m_factored; + //! Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * Returns a changeable reference to the matrix entry + */ + doublereal& operator()(int i, int j); - int m_n, m_kl, m_ku; - doublereal m_zero; - vector_int m_ipiv; + //! Constant Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * Returns an unchangeable reference to the matrix entry + */ + doublereal operator() (int i, int j) const; - }; + //! Return a changeable reference to element (i,j). + /*! + * Since this method may alter the element value, it may need to be refactored, so + * the flag m_factored is set to false. + * + * @param i row + * @param j column + * + * @return Returns a reference to the value of the matrix entry + */ + doublereal& value( int i, int j); - std::ostream& operator<<(std::ostream& s, const BandMatrix& m); + + //! Return the value of element (i,j). + /*! + * This method does not alter the array. + * @param i row + * @param j column + * + * @return Returns the value of the matrix entry + */ + doublereal value( int i, int j) const; + + //! Returns the location in the internal 1D array corresponding to the (i,j) element in the banded array + /*! + * @param i row + * @param j column + * + * @return Returns the index of the matrix entry + */ + int index(int i, int j) const; + + //! Return the value of the (i,j) element for (i,j) within the bandwidth. + /*! + * For efficiency, this method does not check that (i,j) are within the bandwidth; it is up to the calling + * program to insure that this is true. + * + * @param i row + * @param j column + * + * @return Returns the value of the matrix entry + */ + doublereal _value(int i, int j) const; + + //! Returns the number of rows + int nRows() const; + + //! Number of columns + int nColumns() const; + + //! Number of subdiagonals + int nSubDiagonals() const; + + //! Number of superdiagonals + int nSuperDiagonals() const; + + //! Return the number of rows of storage needed for the band storage + int ldim() const; + + //! Return a reference to the pivot vector + /*! + * @return return a reference to the pivot vector + */ + vector_int& ipiv(); + + //! Multiply A*b and write result to prod. + /*! + * @param b Vector to do the rh multiplcation + * @param prod OUTPUT vector to receive the result + */ + void mult(const doublereal * const b, doublereal * const prod) const; + + //! Multiply b*A and write result to prod. + /*! + * @param b Vector to do the lh multiplcation + * @param prod OUTPUT vector to receive the result + */ + void leftMult(const doublereal * const b, doublereal * const prod) const; + + //! Perform an LU decomposition, the LAPACK routine DGBTRF is used. + /*! + * + * The factorization is saved in ludata. + * + * @return Return a success flag. + * 0 indicates a success + * ~0 Some error occurred, see the LAPACK documentation + */ + int factor(); + + + //! Solve the matrix problem Ax = b + /*! + * @param n size of the matrix + * @param b INPUT rhs of the problem + * @param x OUTPUT solution to the problem + * + * @return Return a success flag + * 0 indicates a success + * ~0 Some error occurred, see the LAPACK documentation + */ + int solve(int n, const doublereal * const b, doublereal * const x); + + //! Solve the matrix problem Ax = b + /*! + * @param n size of the matrix + * @param b INPUT rhs of the problem + * OUTPUT solution to the problem + * + * @return Return a success flag + * 0 indicates a success + * ~0 Some error occurred, see the LAPACK documentation + */ + int solve(int n, doublereal * const b); + + + //! Returns an iterator for the start of the band storage data + /*! + * Iterator points to the beginning of the data, and it is changeable. + */ + vector_fp::iterator begin(); + + //! Returns an iterator for the end of the band storage data + /*! + * Iterator points to the end of the data, and it is changeable. + */ + vector_fp::iterator end(); + + //! Returns a const iterator for the start of the band storage data + /*! + * Iterator points to the beginning of the data, and it is not changeable. + */ + vector_fp::const_iterator begin() const; + + //! Returns a const iterator for the end of the band storage data + /*! + * Iterator points to the end of the data, and it is not changeable. + */ + vector_fp::const_iterator end() const; + + protected: + + //! Matrix data + vector_fp data; + + //! Factorized data + vector_fp ludata; + + //! Boolean indicating whether the matrix is factored + bool m_factored; + + //! Number of rows and columns of the matrix + int m_n; + + //! Number of subdiagonals of the matrix + int m_kl; + + //! Number of super diagonals of the matrix + int m_ku; + + //! value of zero + doublereal m_zero; + + //! Pivot vector + vector_int m_ipiv; + + }; + + //! Utility routine to print out the matrix + /*! + * @param s ostream to print the matrix out to + * @param m Matrix to be printed + * + * @return Returns a reference to the ostream + */ + std::ostream& operator<<(std::ostream& s, const BandMatrix& m); } diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 91fa49d4b..962389c64 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -716,8 +716,8 @@ namespace Cantera { * @param ydot_comm Current value of the time derivative of the solution vector * @param time_curr current value of the time */ - void NonlinearSolver::scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr, - int num_newt_its) + void NonlinearSolver::scaleMatrix(SquareMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, + doublereal time_curr, int num_newt_its) { int irow, jcol; /* @@ -2319,10 +2319,10 @@ namespace Cantera { * NSOLN_RETN_FAIL_DAMPSTEP * Unsuccessful step. We can not find a damping factor that is suitable. */ - int NonlinearSolver::dampStep(const doublereal time_curr, const doublereal * y_n_curr, - const doublereal * ydot_n_curr, doublereal * const step_1, - doublereal * const y_n_1, double* const ydot_n_1, doublereal * const step_2, - double& stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks) + int NonlinearSolver::dampStep(const doublereal time_curr, const doublereal * const y_n_curr, + const doublereal * const ydot_n_curr, doublereal * const step_1, + doublereal * const y_n_1, doublereal * const ydot_n_1, doublereal * const step_2, + doublereal & stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks) { int j, m; int info = 0; @@ -2729,7 +2729,7 @@ namespace Cantera { */ int NonlinearSolver::decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y_n_curr, const doublereal * const ydot_n_curr, const std::vector & step_1, - const doublereal * const y_n_1, const double* const ydot_n_1, doublereal trustDeltaOld) + const doublereal * const y_n_1, const doublereal * const ydot_n_1, doublereal trustDeltaOld) { int retn = 2; bool goodStep = false; @@ -2906,8 +2906,8 @@ namespace Cantera { * @return A positive value indicates a successful convergence * -1 Failed convergence */ - int NonlinearSolver::solve_nonlinear_problem(int SolnType, double* y_comm, double* ydot_comm, doublereal CJ, - doublereal time_curr, SquareMatrix& jac, + int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal * const y_comm, doublereal * const ydot_comm, + doublereal CJ, doublereal time_curr, SquareMatrix& jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput) { diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index a2861dddc..582c3fa6c 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -311,6 +311,7 @@ namespace Cantera { */ void setDefaultDeltaBoundsMagnitudes(); + //! Adjust the step minimums void adjustUpStepMinimums(); //! Set the delta Bounds magnitudes by hand @@ -506,10 +507,10 @@ namespace Cantera { * * @return returns an integer indicating what happened. */ - int dampStep(const doublereal time_curr, const double* y_n_curr, - const doublereal *ydot_n_curr, double * const step_1, - double* const y_n_1, double* const ydot_n_1, double* step_2, - double& stepNorm_2, SquareMatrix& jac, bool writetitle, + int dampStep(const doublereal time_curr, const doublereal * const y_n_curr, + const doublereal * const ydot_n_curr, doublereal * const step_1, + doublereal * const y_n_1, doublereal * const ydot_n_1, doublereal * step_2, + doublereal & stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks); //! Find the solution to F(X) = 0 by damped Newton iteration. @@ -539,7 +540,7 @@ namespace Cantera { * @return A positive value indicates a successful convergence * -1 Failed convergence */ - int solve_nonlinear_problem(int SolnType, double* y_comm,double* ydot_comm, doublereal CJ, + int solve_nonlinear_problem(int SolnType, doublereal * const y_comm, doublereal * const ydot_comm, doublereal CJ, doublereal time_curr, SquareMatrix& jac,int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput); @@ -586,8 +587,10 @@ namespace Cantera { * @param y_comm Current value of the solution vector * @param ydot_comm Current value of the time derivative of the solution vector * @param time_curr current value of the time + * @param num_newt_its Current value of the number of newt its */ - void scaleMatrix(SquareMatrix& jac, double* y_comm, double* ydot_comm, doublereal time_curr, int num_newt_its); + void scaleMatrix(SquareMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, + doublereal time_curr, int num_newt_its); //! Print solution norm contribution /*! @@ -802,11 +805,11 @@ namespace Cantera { * @param time_curr INPUT Current value of the time * @param leg INPUT Leg of the dogleg that we are on * @param alpha INPUT Distance down that leg that we are on - * @param y0 INPUT Current value of the solution vector - * @param ydot0 INPUT Current value of the derivative of the solution vector - * @param step0 INPUT Trial step - * @param y1 OUTPUT Solution values at the conditions which are evalulated for success - * @param ydot1 OUTPUT Time derivates of solution at the conditions which are evalulated for success + * @param y_n_curr INPUT Current value of the solution vector + * @param ydot_n_curr INPUT Current value of the derivative of the solution vector + * @param step_1 INPUT Trial step + * @param y_n_1 OUTPUT Solution values at the conditions which are evalulated for success + * @param ydot_n_1 OUTPUT Time derivates of solution at the conditions which are evalulated for success * @param trustDeltaOld INPUT Value of the trust length at the old conditions * * @@ -819,10 +822,10 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y0, - const doublereal * const ydot0, - const std::vector & step0, - const doublereal * const y1, const doublereal * const ydot1, doublereal trustDeltaOld); + int decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y_n_curr, + const doublereal * const ydot_n_curr, + const std::vector & step_1, + const doublereal * const y_n_1, const doublereal * const ydot_n_1, doublereal trustDeltaOld); //! Calculated the expected residual along the double dogleg curve. /*! @@ -923,6 +926,7 @@ namespace Cantera { //! Value of the solution time derivative at the new point that is to be considered std::vector m_ydot_n_1; + //! Value of the step to be taken in the solution std::vector m_step_1; //! Vector of column scaling factors From a292978c08bb438ad0d9bf37e749c278a2ca904e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 15:40:13 +0000 Subject: [PATCH 413/446] Added apps/lib apps/include and apps/bin to the install directory structure --- Makefile.in | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Makefile.in b/Makefile.in index 623726454..d683ad86f 100755 --- a/Makefile.in +++ b/Makefile.in @@ -193,6 +193,11 @@ endif finish-install: @INSTALL@ -d @ct_docdir@ @INSTALL@ -d @ct_bindir@ + @INSTALL@ -d @ct_dir@/apps + @INSTALL@ -d @ct_dir@/apps/include + @INSTALL@ -d @ct_dir@/apps/bin + @INSTALL@ -d @ct_dir@/apps/lib + -( cd @ct_dir/apps ; -$(RMDIRTREE) lib/* include/* bin/* ) -( cd bin ; @INSTALL@ -c exp3to2.sh "@ct_bindir@" ) -( cd bin ; @INSTALL@ -c csvdiff "@ct_bindir@" ) -( cd bin ; @INSTALL@ -c install_tsc "@ct_bindir@" ) @@ -244,6 +249,7 @@ uninstall: -$(RMDIRTREE) @ct_demodir@ -$(RMDIRTREE) @ct_docdir@ -$(RMDIRTREE) @ct_tutdir@ + -$(RMDIRTREE) @ct_dir@/apps -$(RMDIRTREE) @prefix@/matlab/toolbox/cantera cd tools; @MAKE@ uninstall From 5b06c6b2897d3f47afe7d6513cfd216344994bea Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 17:05:45 +0000 Subject: [PATCH 414/446] Added namespaces so that it would compile. --- Cantera/cxx/demos/combustor/combustor.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Cantera/cxx/demos/combustor/combustor.cpp b/Cantera/cxx/demos/combustor/combustor.cpp index b8a3c0c45..8f6c44ff4 100644 --- a/Cantera/cxx/demos/combustor/combustor.cpp +++ b/Cantera/cxx/demos/combustor/combustor.cpp @@ -12,6 +12,9 @@ #include using namespace CanteraZeroD; +using namespace Cantera; +using namespace Cantera_CXX; +using namespace std; void runexample() { From 8efa87d79162c9f3349abe40aead703f5fa6ddd5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 17:11:21 +0000 Subject: [PATCH 415/446] Added namespace to get it to compile --- Cantera/cxx/demos/flamespeed/flamespeed.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/Cantera/cxx/demos/flamespeed/flamespeed.cpp b/Cantera/cxx/demos/flamespeed/flamespeed.cpp index c55f6d7ba..8a43fe489 100644 --- a/Cantera/cxx/demos/flamespeed/flamespeed.cpp +++ b/Cantera/cxx/demos/flamespeed/flamespeed.cpp @@ -17,6 +17,7 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace std; int flamespeed(int np, void* p) { try { From 695868ef3815ad4c4a84b30e6cc575534c79d190 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 19:24:37 +0000 Subject: [PATCH 416/446] Added namespace to get it to compile --- Cantera/cxx/demos/NASA_coeffs/NASA_coeffs.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/Cantera/cxx/demos/NASA_coeffs/NASA_coeffs.cpp b/Cantera/cxx/demos/NASA_coeffs/NASA_coeffs.cpp index 913e9e362..d8efa570b 100644 --- a/Cantera/cxx/demos/NASA_coeffs/NASA_coeffs.cpp +++ b/Cantera/cxx/demos/NASA_coeffs/NASA_coeffs.cpp @@ -12,6 +12,7 @@ using namespace std; using namespace Cantera; +using namespace Cantera_CXX; // The program is put into a function so that error handling code can From 0d74e7ddd0114417782c91c0e4391eaf9b834887 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 19:28:56 +0000 Subject: [PATCH 417/446] Added namespace to get it to compile --- tools/templates/f77/demo_ftnlib.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/templates/f77/demo_ftnlib.cpp b/tools/templates/f77/demo_ftnlib.cpp index 2baa9bf06..b8e24b86d 100644 --- a/tools/templates/f77/demo_ftnlib.cpp +++ b/tools/templates/f77/demo_ftnlib.cpp @@ -37,6 +37,7 @@ using namespace Cantera; using namespace Cantera_CXX; +using namespace std; // store a pointer to an IdealGasMix object static IdealGasMix* _gas = 0; From b9c9f81761548226e0f473e7333872804509758a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 19 Oct 2011 20:45:06 +0000 Subject: [PATCH 418/446] Made the BandMatrix class and SquareMatrix inherit from a common parent so that they can be used interchangeably in other software. Removed PsuedBinaryVPSSTP in favor of MolarityIonicVPSSTP --- Cantera/fortran/f77demos/Makefile.in | 4 + Cantera/src/numerics/BEulerInt.cpp | 16 +- Cantera/src/numerics/BEulerInt.h | 14 +- Cantera/src/numerics/BandMatrix.cpp | 247 ++- Cantera/src/numerics/BandMatrix.h | 195 ++- Cantera/src/numerics/DenseMatrix.cpp | 2 +- Cantera/src/numerics/DenseMatrix.h | 3 +- Cantera/src/numerics/GeneralMatrix.cpp | 42 + Cantera/src/numerics/GeneralMatrix.h | 245 +++ Cantera/src/numerics/Makefile.in | 4 +- Cantera/src/numerics/NonlinearSolver.cpp | 519 ++++-- Cantera/src/numerics/NonlinearSolver.h | 20 +- Cantera/src/numerics/ResidJacEval.cpp | 4 +- Cantera/src/numerics/ResidJacEval.h | 9 +- Cantera/src/numerics/SquareMatrix.cpp | 142 +- Cantera/src/numerics/SquareMatrix.h | 168 +- Cantera/src/numerics/ctlapack.h | 43 + Cantera/src/oneD/MultiNewton.cpp | 2 +- Cantera/src/thermo/Makefile.in | 10 +- Cantera/src/thermo/MargulesVPSSTP.h | 2 +- .../src/thermo/MixedSolventElectrolyte.cpp | 16 +- Cantera/src/thermo/MixedSolventElectrolyte.h | 4 +- ...naryVPSSTP.cpp => MolarityIonicVPSSTP.cpp} | 179 +- ...doBinaryVPSSTP.h => MolarityIonicVPSSTP.h} | 66 +- Cantera/src/thermo/PureFluidPhase.cpp | 2 +- Cantera/src/thermo/ThermoFactory.cpp | 10 +- Cantera/src/thermo/mix_defs.h | 3 + configure | 1548 ++++++++++++++--- docs/Cantera.cfg.in | 8 +- .../linux.64_sierra_gcc444_python264_numpy | 3 + ext/f2c_lapack/Makefile.in | 3 + ext/f2c_lapack/dgbcon.c | 283 +++ ext/f2c_lapack/dgbequ.c | 321 ++++ ext/f2c_lapack/dlatbs.c | 855 +++++++++ ext/lapack/Makefile.in | 2 + ext/lapack/dgbcon.f | 222 +++ ext/lapack/dgbequ.f | 240 +++ ext/lapack/dlatbs.f | 724 ++++++++ .../cathermo/HMW_test_1/output_blessed.txt | 2 +- .../HMW_test_1/output_noD_blessed.txt | 274 ++- 40 files changed, 5850 insertions(+), 606 deletions(-) create mode 100644 Cantera/src/numerics/GeneralMatrix.cpp create mode 100644 Cantera/src/numerics/GeneralMatrix.h rename Cantera/src/thermo/{PseudoBinaryVPSSTP.cpp => MolarityIonicVPSSTP.cpp} (60%) rename Cantera/src/thermo/{PseudoBinaryVPSSTP.h => MolarityIonicVPSSTP.h} (84%) create mode 100644 ext/f2c_lapack/dgbcon.c create mode 100644 ext/f2c_lapack/dgbequ.c create mode 100644 ext/f2c_lapack/dlatbs.c create mode 100644 ext/lapack/dgbcon.f create mode 100644 ext/lapack/dgbequ.f create mode 100644 ext/lapack/dlatbs.f diff --git a/Cantera/fortran/f77demos/Makefile.in b/Cantera/fortran/f77demos/Makefile.in index d99410041..8ba8599e5 100644 --- a/Cantera/fortran/f77demos/Makefile.in +++ b/Cantera/fortran/f77demos/Makefile.in @@ -18,6 +18,10 @@ FORT = @F77@ # Fortran compile flags FORT_FLAGS = @FFLAGS@ +FCLIBS= @FCLIBS@ +FLIBS = @FLIBS@ + + # Fortran libraries FORT_LIBS = @LCXX_FLIBS@ @LCXX_END_LIBS@ @FLIBS@ diff --git a/Cantera/src/numerics/BEulerInt.cpp b/Cantera/src/numerics/BEulerInt.cpp index 78753267d..a2abc55fb 100644 --- a/Cantera/src/numerics/BEulerInt.cpp +++ b/Cantera/src/numerics/BEulerInt.cpp @@ -421,7 +421,7 @@ namespace Cantera { * Here a small weighting indicates that the change in solution is * very sensitive to that equation. */ - void BEulerInt::computeResidWts(SquareMatrix &jac) + void BEulerInt::computeResidWts(GeneralMatrix &jac) { int i, j; double *data = &(*(jac.begin())); @@ -637,7 +637,7 @@ namespace Cantera { * not have to be computed again. * */ - void BEulerInt::beuler_jac(SquareMatrix &J, double * const f, + void BEulerInt::beuler_jac(GeneralMatrix &J, double * const f, double time_curr, double CJ, double * const y, double * const ydot, @@ -1664,7 +1664,7 @@ namespace Cantera { */ void BEulerInt::doNewtonSolve(double time_curr, double *y_curr, double *ydot_curr, double* delta_y, - SquareMatrix& jac, int loglevel) + GeneralMatrix& jac, int loglevel) { int irow, jcol; @@ -1682,7 +1682,7 @@ namespace Cantera { * by the nominal important change in the solution vector */ if (m_colScaling) { - if (!jac.m_factored) { + if (!jac.factored()) { /* * Go get new scales */ @@ -1702,7 +1702,7 @@ namespace Cantera { } if (m_matrixConditioning) { - if (jac.m_factored) { + if (jac.factored()) { m_func->matrixConditioning(0, sz, delta_y); } else { double *jptr = &(*(jac.begin())); @@ -1716,7 +1716,7 @@ namespace Cantera { * nonnegative. */ if (m_rowScaling) { - if (! jac.m_factored) { + if (! jac.factored()) { /* * Ok, this is ugly. jac.begin() returns an vector iterator * to the first data location. @@ -1940,7 +1940,7 @@ namespace Cantera { int BEulerInt::dampStep(double time_curr, const double * y0, const double *ydot0, const double* step0, double* y1, double* ydot1, double* step1, - double& s1, SquareMatrix& jac, + double& s1, GeneralMatrix & jac, int& loglevel, bool writetitle, int& num_backtracks) { @@ -2107,7 +2107,7 @@ namespace Cantera { int BEulerInt::solve_nonlinear_problem(double * const y_comm, double * const ydot_comm, double CJ, double time_curr, - SquareMatrix& jac, + GeneralMatrix & jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, diff --git a/Cantera/src/numerics/BEulerInt.h b/Cantera/src/numerics/BEulerInt.h index 7481558fc..3a02a1368 100644 --- a/Cantera/src/numerics/BEulerInt.h +++ b/Cantera/src/numerics/BEulerInt.h @@ -24,7 +24,7 @@ #include "Integrator.h" #include "ResidJacEval.h" -#include "SquareMatrix.h" +#include "GeneralMatrix.h" #include "NonlinearSolver.h" #include "mdp_allo.h" @@ -119,7 +119,7 @@ namespace Cantera { bool printLargest = false); virtual void setInitialTimeStep(double delta_t); - void beuler_jac(SquareMatrix &, double * const, + void beuler_jac(GeneralMatrix &, double * const, double, double, double * const, double * const, int); @@ -175,7 +175,7 @@ namespace Cantera { int solve_nonlinear_problem(double * const y_comm, double * const ydot_comm, double CJ, double time_curr, - SquareMatrix& jac, + GeneralMatrix& jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, @@ -186,7 +186,7 @@ namespace Cantera { * evaluated at x, but the Jacobian is not recomputed. */ void doNewtonSolve(double, double *, double*, double *, - SquareMatrix&, int); + GeneralMatrix&, int); //! Bound the Newton step while relaxing the solution @@ -228,12 +228,12 @@ namespace Cantera { */ int dampStep(double, const double*, const double*, const double *, double*, double*, - double*, double&, SquareMatrix&, int&, bool, int&); + double*, double&, GeneralMatrix&, int&, bool, int&); /* * Compute Residual Weights */ - void computeResidWts(SquareMatrix &jac); + void computeResidWts(GeneralMatrix &jac); /* * Filter a new step @@ -421,7 +421,7 @@ namespace Cantera { * Pointer to the jacobian representing the * time dependent problem */ - SquareMatrix *tdjac_ptr; + GeneralMatrix *tdjac_ptr; /** * Determines the level of printing for each time * step. diff --git a/Cantera/src/numerics/BandMatrix.cpp b/Cantera/src/numerics/BandMatrix.cpp index 0571df81c..44a045dfb 100644 --- a/Cantera/src/numerics/BandMatrix.cpp +++ b/Cantera/src/numerics/BandMatrix.cpp @@ -17,6 +17,7 @@ #include "ctexceptions.h" #include "stringUtils.h" #include "global.h" +#include using namespace std; @@ -24,6 +25,7 @@ namespace Cantera { //==================================================================================================================== BandMatrix::BandMatrix() : + GeneralMatrix(1), m_factored(false), m_n(0), m_kl(0), @@ -35,6 +37,7 @@ namespace Cantera { } //==================================================================================================================== BandMatrix::BandMatrix(int n, int kl, int ku, doublereal v) : + GeneralMatrix(1), m_factored(false), m_n(n), m_kl(kl), @@ -46,9 +49,15 @@ namespace Cantera { fill(data.begin(), data.end(), v); fill(ludata.begin(), ludata.end(), 0.0); m_ipiv.resize(m_n); + m_colPtrs.resize(n); + int ldab = (2*kl + ku + 1); + for (int j = 0; j < n; j++) { + m_colPtrs[j] = &(data[ldab * j]); + } } //==================================================================================================================== BandMatrix::BandMatrix(const BandMatrix& y) : + GeneralMatrix(1), m_factored(false), m_n(0), m_kl(0), @@ -62,6 +71,11 @@ namespace Cantera { ludata = y.ludata; m_factored = y.m_factored; m_ipiv = y.m_ipiv; + m_colPtrs.resize(m_n); + int ldab = (2 *m_kl + m_ku + 1); + for (int j = 0; j < m_n; j++) { + m_colPtrs[j] = &(data[ldab * j]); + } } //==================================================================================================================== BandMatrix::~BandMatrix() { @@ -70,6 +84,7 @@ namespace Cantera { //==================================================================================================================== BandMatrix& BandMatrix::operator=(const BandMatrix & y) { if (&y == this) return *this; + GeneralMatrix::operator=(y); m_n = y.m_n; m_kl = y.m_kl; m_ku = y.m_ku; @@ -77,6 +92,11 @@ namespace Cantera { data = y.data; ludata = y.ludata; m_factored = y.m_factored; + m_colPtrs.resize(m_n); + int ldab = (2 * m_kl + m_ku + 1); + for (int j = 0; j < m_n; j++) { + m_colPtrs[j] = &(data[ldab * j]); + } return *this; } //==================================================================================================================== @@ -88,6 +108,11 @@ namespace Cantera { ludata.resize(n*(2*kl + ku + 1)); m_ipiv.resize(m_n); fill(data.begin(), data.end(), v); + m_colPtrs.resize(m_n); + int ldab = (2 * m_kl + m_ku + 1); + for (int j = 0; j < n; j++) { + m_colPtrs[j] = &(data[ldab * j]); + } m_factored = false; } //==================================================================================================================== @@ -96,6 +121,11 @@ namespace Cantera { m_factored = false; } //==================================================================================================================== + void BandMatrix::zero() { + std::fill(data.begin(), data.end(), 0.0); + m_factored = false; + } + //==================================================================================================================== doublereal& BandMatrix::operator()(int i, int j) { return value(i,j); } @@ -127,7 +157,16 @@ namespace Cantera { } //==================================================================================================================== // Number of rows - int BandMatrix::nRows() const { + size_t BandMatrix::nRows() const { + return m_n; + } + //==================================================================================================================== + // Number of rows + size_t BandMatrix::nRowsAndStruct(int * const iStruct) const { + if (iStruct) { + iStruct[0] = m_kl; + iStruct[1] = m_ku; + } return m_n; } //==================================================================================================================== @@ -208,12 +247,12 @@ namespace Cantera { return info; } //==================================================================================================================== - int BandMatrix::solve(int n, const doublereal * const b, doublereal * const x) { - copy(b, b+n, x); - return solve(n, x); + int BandMatrix::solve(const doublereal * const b, doublereal * const x) { + copy(b, b + m_n, x); + return solve(x); } //==================================================================================================================== - int BandMatrix::solve(int n, doublereal* b) { + int BandMatrix::solve(doublereal* b) { int info = 0; if (!m_factored) info = factor(); if (info == 0) @@ -259,6 +298,202 @@ namespace Cantera { } return s; } - //==================================================================================================================== + //==================================================================================================================== + void BandMatrix::err(std::string msg) const { + throw CanteraError("BandMatrix() unimplemented function", msg); + } + //==================================================================================================================== + // Factors the A matrix using the QR algorithm, overwriting A + /* + * we set m_factored to 2 to indicate the matrix is now QR factored + * + * @return Returns the info variable from lapack + */ + int BandMatrix::factorQR() { + factor(); + return 0; + } + //==================================================================================================================== + // Factors the A matrix using the QR algorithm, overwriting A + // Returns an estimate of the inverse of the condition number for the matrix + /* + * The matrix must have been previously factored using the QR algorithm + * + * @return returns the inverse of the condition number + */ + doublereal BandMatrix::rcondQR() { + double a1norm = oneNorm(); + return rcond(a1norm); + } + //==================================================================================================================== + // Returns an estimate of the inverse of the condition number for the matrix + /* + * The matrix must have been previously factored using the LU algorithm + * + * @param a1norm Norm of the matrix + * + * @return returns the inverse of the condition number + */ + doublereal BandMatrix::rcond(doublereal a1norm) { + int printLevel = 0; + int useReturnErrorCode = 0; + if ((int) iwork_.size() < m_n) { + iwork_.resize(m_n); + } + if ((int) work_.size() < 3 * m_n) { + work_.resize(3 * m_n); + } + doublereal rcond = 0.0; + if (m_factored != 1) { + throw CanteraError("BandMatrix::rcond()", "matrix isn't factored correctly"); + } + + // doublereal anorm = oneNorm(); + int ldab = (2 *m_kl + m_ku + 1); + int rinfo; + rcond = ct_dgbcon('1', m_n, m_kl, m_ku, DATA_PTR(ludata), ldab, DATA_PTR(m_ipiv), a1norm, DATA_PTR(work_), + DATA_PTR(iwork_), rinfo); + if (rinfo != 0) { + if (printLevel) { + writelogf("BandMatrix::rcond(): DGBCON returned INFO = %d\n", rinfo); + } + if (! useReturnErrorCode) { + throw CanteraError("BandMatrix::rcond()", "DGBCON returned INFO = " + int2str(rinfo)); + } + } + return rcond; + } + //==================================================================================================================== + // Change the way the matrix is factored + /* + * @param fAlgorithm integer + * 0 LU factorization + * 1 QR factorization + */ + void BandMatrix::useFactorAlgorithm(int fAlgorithm) { + // QR algorithm isn't implemented for banded matrix. + } + //==================================================================================================================== + int BandMatrix::factorAlgorithm() const { + return 0; + } + //==================================================================================================================== + // Returns the one norm of the matrix + doublereal BandMatrix::oneNorm() const { + doublereal value = 0.0; + for (int j = 0; j < m_n; j++) { + doublereal sum = 0.0; + doublereal *colP = m_colPtrs[j]; + for (int i = j - m_ku; i <= j + m_kl; i++) { + sum += fabs(colP[m_kl + m_ku + i - j]); + } + if (sum > value) { + value = sum; + } + } + return value; + } + //==================================================================================================================== + int BandMatrix::checkRows(doublereal &valueSmall) const { + valueSmall = 1.0E300; + int iSmall = -1; + double vv; + for (int i = 0; i < m_n; i++) { + double valueS = 0.0; + for (int j = i - m_kl; j <= i + m_ku; j++) { + if (j >= 0 && (j < m_n)) { + vv = fabs(value(i,j)); + if (vv > valueS) { + valueS = vv; + } + } + } + if (valueS < valueSmall) { + iSmall = i; + valueSmall = valueS; + if (valueSmall == 0.0) { + return iSmall; + } + } + } + return iSmall; + } + //==================================================================================================================== + int BandMatrix::checkColumns(doublereal &valueSmall) const { + valueSmall = 1.0E300; + int jSmall = -1; + double vv; + for (int j = 0; j < m_n; j++) { + double valueS = 0.0; + for (int i = j - m_ku; i <= j + m_kl; i++) { + if (i >= 0 && (i < m_n)) { + vv = fabs(value(i,j)); + if (vv > valueS) { + valueS = vv; + } + } + } + if (valueS < valueSmall) { + jSmall = j; + valueSmall = valueS; + if (valueSmall == 0.0) { + return jSmall; + } + } + } + return jSmall; + } + //==================================================================================================================== + GeneralMatrix * BandMatrix::duplMyselfAsGeneralMatrix() const { + BandMatrix *dd = new BandMatrix(*this); + return static_cast(dd); + } + //==================================================================================================================== + bool BandMatrix::factored() const { + return m_factored; + } + //==================================================================================================================== + // Return a pointer to the top of column j, columns are assumed to be contiguous in memory + /* + * @param j Value of the column + * + * @return Returns a pointer to the top of the column + */ + doublereal * BandMatrix::ptrColumn(int j) { + return m_colPtrs[j]; + } + //==================================================================================================================== + // Return a vector of const pointers to the columns + /* + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + doublereal * const * BandMatrix::colPts() { + return &(m_colPtrs[0]); + } + //==================================================================================================================== + // Copy the data from one array into another without doing any checking + /* + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + void BandMatrix::copyData(const GeneralMatrix& y) { + m_factored = false; + size_t n = sizeof(doublereal) * m_n * (2 *m_kl + m_ku + 1); + GeneralMatrix * yyPtr = const_cast(&y); + (void) memcpy(DATA_PTR(data), yyPtr->ptrColumn(0), n); + } + //==================================================================================================================== + /* + * clear the factored flag + */ + void BandMatrix::clearFactorFlag() { + m_factored = 0; + } + //==================================================================================================================== + //==================================================================================================================== } diff --git a/Cantera/src/numerics/BandMatrix.h b/Cantera/src/numerics/BandMatrix.h index 148029c95..6a756172e 100644 --- a/Cantera/src/numerics/BandMatrix.h +++ b/Cantera/src/numerics/BandMatrix.h @@ -1,7 +1,8 @@ /** * @file BandMatrix.h - * - * Banded matrices. + * Declarations for the class BandMatrix + * which is a child class of GeneralMatrix for banded matrices handled by solvers + * (see class \ref numerics and \link Cantera::BandMatrix BandMatrix\endlink). */ /* @@ -20,14 +21,26 @@ #include "ctlapack.h" #include "utilities.h" #include "ctexceptions.h" +#include "GeneralMatrix.h" namespace Cantera { - /** - * A class for banded matrices. This class has matrix inversion processes. - * The class is based upon the LAPACK banded storage matrix format. + //! A class for banded matrices, involving matrix inversion processes. + //! The class is based upon the LAPACK banded storage matrix format. + /*! + * An important issue with this class is that it stores both the original data + * and the LU factorization of the data. This means that the banded matrix typically + * will take up twice the room that it is expected to take. + * + * QR factorizations of banded matrices are not included in the original LAPACK work. + * Add-ons are available. However, they are not included here. Instead we just use the + * stock LU decompositions. + * + * This class is a derived class of the base class GeneralMatrix. However, withinin + * the oneD directory, the class is used as is, without reference to the GeneralMatrix + * base type. */ - class BandMatrix { + class BandMatrix : public GeneralMatrix { public: @@ -90,7 +103,7 @@ namespace Cantera { doublereal& operator()(int i, int j); - //! Constant Index into the (i,j) element + //! Constant index into the (i,j) element /*! * @param i row * @param j column @@ -144,7 +157,19 @@ namespace Cantera { doublereal _value(int i, int j) const; //! Returns the number of rows - int nRows() const; + virtual size_t nRows() const; + + //! Return the size and structure of the matrix + /*! + * This is inherited from GeneralMatrix + * + * @param iStruct OUTPUT Pointer to a vector of ints that describe the structure of the matrix. + * istruct[0] = kl + * istruct[1] = ku + * + * @return returns the number of rows and columns in the matrix. + */ + virtual size_t nRowsAndStruct(int * const iStruct = 0) const; //! Number of columns int nColumns() const; @@ -169,14 +194,14 @@ namespace Cantera { * @param b Vector to do the rh multiplcation * @param prod OUTPUT vector to receive the result */ - void mult(const doublereal * const b, doublereal * const prod) const; + virtual void mult(const doublereal * const b, doublereal * const prod) const; //! Multiply b*A and write result to prod. /*! * @param b Vector to do the lh multiplcation * @param prod OUTPUT vector to receive the result */ - void leftMult(const doublereal * const b, doublereal * const prod) const; + virtual void leftMult(const doublereal * const b, doublereal * const prod) const; //! Perform an LU decomposition, the LAPACK routine DGBTRF is used. /*! @@ -192,7 +217,6 @@ namespace Cantera { //! Solve the matrix problem Ax = b /*! - * @param n size of the matrix * @param b INPUT rhs of the problem * @param x OUTPUT solution to the problem * @@ -200,11 +224,10 @@ namespace Cantera { * 0 indicates a success * ~0 Some error occurred, see the LAPACK documentation */ - int solve(int n, const doublereal * const b, doublereal * const x); + int solve(const doublereal * const b, doublereal * const x); //! Solve the matrix problem Ax = b /*! - * @param n size of the matrix * @param b INPUT rhs of the problem * OUTPUT solution to the problem * @@ -212,14 +235,14 @@ namespace Cantera { * 0 indicates a success * ~0 Some error occurred, see the LAPACK documentation */ - int solve(int n, doublereal * const b); + int solve(doublereal * const b); //! Returns an iterator for the start of the band storage data /*! * Iterator points to the beginning of the data, and it is changeable. */ - vector_fp::iterator begin(); + virtual vector_fp::iterator begin(); //! Returns an iterator for the end of the band storage data /*! @@ -239,6 +262,130 @@ namespace Cantera { */ vector_fp::const_iterator end() const; + /** + * Zero the matrix + */ + virtual void zero(); + + //! Factors the A matrix using the QR algorithm, overwriting A + /*! + * we set m_factored to 2 to indicate the matrix is now QR factored + * + * @return Returns the info variable from lapack + */ + virtual int factorQR(); + + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the QR algorithm + * + * @return returns the inverse of the condition number + */ + virtual doublereal rcondQR(); + + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the LU algorithm + * + * @param a1norm Norm of the matrix + * + * @return returns the inverse of the condition number + */ + virtual doublereal rcond(doublereal a1norm); + + //! Change the way the matrix is factored + /*! + * @param fAlgorithm integer + * 0 LU factorization + * 1 QR factorization + */ + virtual void useFactorAlgorithm(int fAlgorithm); + + //! Returns the factor algorithm used + /*! + * 0 LU decomposition + * 1 QR decomposition + * + * This routine will always return 0 + */ + virtual int factorAlgorithm() const; + + //! Returns the one norm of the matrix + virtual doublereal oneNorm() const; + + //! Duplicate this object as a GeneralMatrix pointer + virtual GeneralMatrix * duplMyselfAsGeneralMatrix() const; + + //! Report whether the current matrix has been factored. + virtual bool factored() const; + + //! Return a pointer to the top of column j, column values are assumed to be contiguous in memory + /*! + * The LAPACK bandstructure has column values which are contiguous in memory: + * + * On entry, the matrix A in band storage, in rows KL+1 to + * 2*KL+KU+1; rows 1 to KL of the array need not be set. + * The j-th column of A is stored in the j-th column of the + * array AB as follows: + * AB(KL + KU + 1 + i - j,j) = A(i,j) for max(1, j - KU) <= i <= min(m, j + KL) + * + * This routine returns the position of AB(1,j) (fortran-1 indexing) in the above format + * + * So to address the (i,j) position, you use the following indexing: + * + * double *colP_j = matrix.ptrColumn(j); + * double a_i_j = colP_j[kl + ku + i - j]; + * + * + * @param j Value of the column + * + * @return Returns a pointer to the top of the column + */ + virtual doublereal * ptrColumn(int j); + + //! Return a vector of const pointers to the columns + /*! + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + virtual doublereal * const * colPts(); + + //! Copy the data from one array into another without doing any checking + /*! + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + virtual void copyData(const GeneralMatrix& y); + + + //! Clear the factored flag + virtual void clearFactorFlag(); + + //! Check to see if we have any zero rows in the jacobian + /*! + * This utility routine checks to see if any rows are zero. + * The smallest row is returned along with the largest coefficient in that row + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest row + * + * @return index of the row that is most nearly zero + */ + virtual int checkRows(doublereal & valueSmall) const; + + //! Check to see if we have any zero columns in the jacobian + /*! + * This utility routine checks to see if any columns are zero. + * The smallest column is returned along with the largest coefficient in that column + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest column + * + * @return index of the column that is most nearly zero + */ + virtual int checkColumns(doublereal & valueSmall) const; + protected: //! Matrix data @@ -265,6 +412,24 @@ namespace Cantera { //! Pivot vector vector_int m_ipiv; + //! Vector of column pointers + std::vector m_colPtrs; + + //! Extra work array needed - size = n + vector_int iwork_; + + //! Extra dp work array needed - size = 3n + vector_fp work_; + + private: + + //! Error function that gets called for unhandled cases + /*! + * @param msg String containing the message. + */ + void err(std::string msg) const; + + }; //! Utility routine to print out the matrix diff --git a/Cantera/src/numerics/DenseMatrix.cpp b/Cantera/src/numerics/DenseMatrix.cpp index c56f242fb..134acfe72 100644 --- a/Cantera/src/numerics/DenseMatrix.cpp +++ b/Cantera/src/numerics/DenseMatrix.cpp @@ -32,7 +32,7 @@ namespace Cantera { * all elements to \c v. */ DenseMatrix::DenseMatrix(int n, int m, doublereal v) : - Array2D(n, m, v), + Array2D(n, m, v), m_ipiv(0), m_useReturnErrorCode(0), m_printLevel(0) diff --git a/Cantera/src/numerics/DenseMatrix.h b/Cantera/src/numerics/DenseMatrix.h index b6d37af1c..c43018d4a 100644 --- a/Cantera/src/numerics/DenseMatrix.h +++ b/Cantera/src/numerics/DenseMatrix.h @@ -21,6 +21,7 @@ #include "ct_defs.h" #include "Array.h" + namespace Cantera { /** * @defgroup numerics Numerical Utilities within Cantera @@ -123,7 +124,7 @@ namespace Cantera { * @return returns a vector of pointers to the top of the columns * of the matrices. */ - doublereal * const * colPts(); + virtual doublereal * const * colPts(); //! Return a const vector of const pointers to the columns /*! diff --git a/Cantera/src/numerics/GeneralMatrix.cpp b/Cantera/src/numerics/GeneralMatrix.cpp new file mode 100644 index 000000000..5a76c5e6b --- /dev/null +++ b/Cantera/src/numerics/GeneralMatrix.cpp @@ -0,0 +1,42 @@ +/** + * @file GeneralMatrix.cpp + * + */ +/* + * $Revision: 725 $ + * $Date: 2011-05-16 18:45:08 -0600 (Mon, 16 May 2011) $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#include "GeneralMatrix.h" +using namespace std; + +namespace Cantera { + //==================================================================================================================== + GeneralMatrix::GeneralMatrix(int matType) : + matrixType_(matType) + { + } + //==================================================================================================================== + GeneralMatrix::GeneralMatrix(const GeneralMatrix &y) : + matrixType_(y.matrixType_) + { + } + //==================================================================================================================== + GeneralMatrix& GeneralMatrix::operator=(const GeneralMatrix &y) + { + if (&y == this) return *this; + matrixType_ = y.matrixType_; + return *this; + } + //==================================================================================================================== + GeneralMatrix::~GeneralMatrix() + { + } + //==================================================================================================================== +} diff --git a/Cantera/src/numerics/GeneralMatrix.h b/Cantera/src/numerics/GeneralMatrix.h new file mode 100644 index 000000000..8781ff524 --- /dev/null +++ b/Cantera/src/numerics/GeneralMatrix.h @@ -0,0 +1,245 @@ +/** + * @file GeneralMatrix.h + * Declarations for the class GeneralMatrix which is a virtual base class for matrices handled by solvers + * (see class \ref numerics and \link Cantera::GeneralMatrix GeneralMatrix\endlink). + */ + +/* + * $Date: 2011-10-13 15:16:06 -0600 (Thu, 13 Oct 2011) $ + * $Revision: 776 $ + */ +/* + * Copywrite 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government + * retains certain rights in this software. + * See file License.txt for licensing information. + */ + +#ifndef CT_GENERALMATRIX_H +#define CT_GENERALMATRIX_H + +#include "ct_defs.h" + +namespace Cantera { + + //! Generic matrix + class GeneralMatrix { + + + public: + + //! Base Constructor + /*! + * @param matType Matrix type + * 0 full + * 1 banded + */ + GeneralMatrix(int matType); + + //! Copy Constructor + /*! + * @param right Object to be copied + */ + GeneralMatrix(const GeneralMatrix& right); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + GeneralMatrix& operator=(const GeneralMatrix& right); + + //! Destructor. Does nothing. + virtual ~GeneralMatrix(); + + //! Duplicator member function + /*! + * This function will duplicate the matrix given a generic GeneralMatrix pointer + * + * @return Returns a pointer to the malloced object + */ + virtual GeneralMatrix * duplMyselfAsGeneralMatrix() const = 0; + + //! Zero the matrix elements + virtual void zero() = 0; + + //! Multiply A*b and write result to prod. + /*! + * @param b Vector to do the rh multiplcation + * @param prod OUTPUT vector to receive the result + */ + virtual void mult(const doublereal * const b, doublereal * const prod) const = 0; + + //! Multiply b*A and write result to prod. + /*! + * @param b Vector to do the lh multiplcation + * @param prod OUTPUT vector to receive the result + */ + virtual void leftMult(const doublereal * const b, doublereal * const prod) const = 0; + + //! Factors the A matrix, overwriting A. + /* + * We flip m_factored boolean to indicate that the matrix is now A-1. + */ + virtual int factor() = 0; + + //! Factors the A matrix using the QR algorithm, overwriting A + /*! + * we set m_factored to 2 to indicate the matrix is now QR factored + * + * @return Returns the info variable from lapack + */ + virtual int factorQR() = 0; + + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the QR algorithm + * + * @return returns the inverse of the condition number + */ + virtual doublereal rcondQR() = 0; + + //! Returns an estimate of the inverse of the condition number for the matrix + /*! + * The matrix must have been previously factored using the LU algorithm + * + * @param a1norm Norm of the matrix + * + * @return returns the inverse of the condition number + */ + virtual doublereal rcond(doublereal a1norm) = 0; + + //! Change the way the matrix is factored + /*! + * @param fAlgorithm integer + * 0 LU factorization + * 1 QR factorization + */ + virtual void useFactorAlgorithm(int fAlgorithm) = 0; + + //! Return the factor algorithm used + /*! + * + */ + virtual int factorAlgorithm() const = 0; + + //! Calculate the one norm of the matrix + /*! + * Returns the one norm of the matrix + */ + virtual doublereal oneNorm() const = 0; + + + //! Return the number of rows in the matrix + virtual size_t nRows() const = 0; + + + //! Return the size and structure of the matrix + /*! + * This is inherited from GeneralMatrix + * + * @param iStruct OUTPUT Pointer to a vector of ints that describe the structure of the matrix. + * + * @return returns the number of rows and columns in the matrix. + */ + virtual size_t nRowsAndStruct(int * const iStruct = 0) const = 0; + + //! clear the factored flag + virtual void clearFactorFlag() = 0; + + //! Solves the Ax = b system returning x in the b spot. + /*! + * @param b Vector for the rhs of the equation system + */ + virtual int solve(doublereal *b) = 0; + + //! true if the current factorization is up to date with the matrix + virtual bool factored() const = 0; + + //! Return a pointer to the top of column j, columns are assumed to be contiguous in memory + /*! + * @param j Value of the column + * + * @return Returns a pointer to the top of the column + */ + virtual doublereal * ptrColumn(int j) = 0; + + //! Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * Returns a changeable reference to the matrix entry + */ + virtual doublereal& operator()(int i, int j) = 0; + + + //! Constant Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * Returns an unchangeable reference to the matrix entry + */ + virtual doublereal operator() (int i, int j) const = 0; + + //! Copy the data from one array into another without doing any checking + /*! + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + virtual void copyData(const GeneralMatrix& y) = 0; + + //! Return an iterator pointing to the first element + /*! + * We might drop this later + */ + virtual vector_fp::iterator begin() = 0; + + //! Return a const iterator pointing to the first element + /*! + * We might drop this later + */ + virtual vector_fp::const_iterator begin() const = 0; + + //! Return a vector of const pointers to the columns + /*! + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + virtual doublereal * const * colPts() = 0; + + //! Check to see if we have any zero rows in the jacobian + /*! + * This utility routine checks to see if any rows are zero. + * The smallest row is returned along with the largest coefficient in that row + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest row + * + * @return index of the row that is most nearly zero + */ + virtual int checkRows (doublereal & valueSmall) const = 0; + + //! Check to see if we have any zero columns in the jacobian + /*! + * This utility routine checks to see if any columns are zero. + * The smallest column is returned along with the largest coefficient in that column + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest column + * + * @return index of the column that is most nearly zero + */ + virtual int checkColumns (doublereal & valueSmall) const = 0; + + //! Matrix type + /*! + * 0 Square + * 1 Banded + */ + int matrixType_; + + }; +} +#endif diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in index 8787bb236..e83028c68 100644 --- a/Cantera/src/numerics/Makefile.in +++ b/Cantera/src/numerics/Makefile.in @@ -37,14 +37,14 @@ CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) NUMERICS_OBJ = DenseMatrix.o funcs.o Func1.o \ ODE_integrators.o BandMatrix.o DAE_solvers.o \ funcs.o sort.o SquareMatrix.o ResidJacEval.o NonlinearSolver.o \ - solveProb.o BEulerInt.o RootFind.o IDA_Solver.o + solveProb.o BEulerInt.o RootFind.o IDA_Solver.o GeneralMatrix.o NUMERICS_H = ArrayViewer.h DenseMatrix.h \ funcs.h ctlapack.h Func1.h FuncEval.h \ polyfit.h\ BandMatrix.h Integrator.h DAE_Solver.h ResidEval.h sort.h \ SquareMatrix.h ResidJacEval.h NonlinearSolver.h \ - solveProb.h BEulerInt.h RootFind.h IDA_Solver.h + solveProb.h BEulerInt.h RootFind.h IDA_Solver.h GeneralMatrix.h ifeq ($(use_sundials), 1) ODEPACKAGE_H = CVodesIntegrator.h diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 962389c64..81c92ec00 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -19,6 +19,7 @@ #include #include "SquareMatrix.h" +#include "GeneralMatrix.h" #include "NonlinearSolver.h" #include "ctlapack.h" @@ -147,8 +148,8 @@ namespace Cantera { atolk_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), - jacCopy_(0), - Hessian_(0), + jacCopyPtr_(0), + HessianPtr_(0), deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), @@ -211,7 +212,7 @@ namespace Cantera { } - jacCopy_.resize(neq_, neq_, 0.0); + // jacCopyPtr_->resize(neq_, 0.0); deltaX_CP_.resize(neq_, 0.0); Jd_.resize(neq_, 0.0); deltaX_trust_.resize(neq_, 1.0); @@ -268,8 +269,8 @@ namespace Cantera { atolk_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), - jacCopy_(0), - Hessian_(0), + jacCopyPtr_(0), + HessianPtr_(0), deltaX_CP_(0), deltaX_Newton_(0), residNorm2Cauchy_(0.0), @@ -306,6 +307,12 @@ namespace Cantera { //==================================================================================================================== NonlinearSolver::~NonlinearSolver() { + if (jacCopyPtr_) { + delete jacCopyPtr_; + } + if (HessianPtr_) { + delete HessianPtr_; + } } //==================================================================================================================== NonlinearSolver& NonlinearSolver::operator=(const NonlinearSolver &right) { @@ -364,8 +371,15 @@ namespace Cantera { m_print_flag = right.m_print_flag; m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; - jacCopy_ = right.jacCopy_; - Hessian_ = right.Hessian_; + if (jacCopyPtr_) { + delete (jacCopyPtr_); + } + jacCopyPtr_ = (right.jacCopyPtr_)->duplMyselfAsGeneralMatrix(); + if (HessianPtr_) { + delete (HessianPtr_); + } + HessianPtr_ = (right.HessianPtr_)->duplMyselfAsGeneralMatrix(); + deltaX_CP_ = right.deltaX_CP_; deltaX_Newton_ = right.deltaX_Newton_; residNorm2Cauchy_ = right.residNorm2Cauchy_; @@ -716,39 +730,57 @@ namespace Cantera { * @param ydot_comm Current value of the time derivative of the solution vector * @param time_curr current value of the time */ - void NonlinearSolver::scaleMatrix(SquareMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, + void NonlinearSolver::scaleMatrix(GeneralMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, doublereal time_curr, int num_newt_its) { int irow, jcol; + int ku, kl; + int ivec[2]; + int n = jac.nRowsAndStruct(ivec); + double *colP_j; + /* * Column scaling -> We scale the columns of the Jacobian * by the nominal important change in the solution vector */ if (m_colScaling) { - if (!jac.m_factored) { - /* - * Go get new scales -> Took this out of this inner loop. - * Needs to be done at a larger scale. - */ - // setColumnScales(); + if (!jac.factored()) { + if (jac.matrixType_ == 0) { + /* + * Go get new scales -> Took this out of this inner loop. + * Needs to be done at a larger scale. + */ + // setColumnScales(); - /* - * Scale the new Jacobian - */ - doublereal *jptr = &(*(jac.begin())); - for (jcol = 0; jcol < neq_; jcol++) { - for (irow = 0; irow < neq_; irow++) { - *jptr *= m_colScales[jcol]; - jptr++; + /* + * Scale the new Jacobian + */ + doublereal *jptr = &(*(jac.begin())); + for (jcol = 0; jcol < neq_; jcol++) { + for (irow = 0; irow < neq_; irow++) { + *jptr *= m_colScales[jcol]; + jptr++; + } + } + } else if (jac.matrixType_ == 1) { + kl = ivec[0]; + ku = ivec[1]; + for (jcol = 0; jcol < neq_; jcol++) { + colP_j = (doublereal *) jac.ptrColumn(jcol); + for (irow = jcol - ku; irow <= jcol + kl; irow++) { + if (irow >= 0 && irow < neq_) { + colP_j[kl + ku + irow - jcol] *= m_colScales[jcol]; + } + } } } - } + } } /* * row sum scaling -> Note, this is an unequivical success * at keeping the small numbers well balanced and nonnegative. */ - if (! jac.m_factored) { + if (! jac.factored()) { /* * Ok, this is ugly. jac.begin() returns an vector iterator * to the first data location. @@ -759,39 +791,75 @@ namespace Cantera { m_rowScales[irow] = 0.0; m_rowWtScales[irow] = 0.0; } - for (jcol = 0; jcol < neq_; jcol++) { - for (irow = 0; irow < neq_; irow++) { - if (m_rowScaling) { - m_rowScales[irow] += fabs(*jptr); - } - if (m_colScaling) { - // This is needed in order to mitgate the change in J_ij carried out just above this loop. - // Alternatively, we could move this loop up to the top - m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol] / m_colScales[jcol]; - } else { - m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol]; + if (jac.matrixType_ == 0) { + for (jcol = 0; jcol < neq_; jcol++) { + for (irow = 0; irow < neq_; irow++) { + if (m_rowScaling) { + m_rowScales[irow] += fabs(*jptr); + } + if (m_colScaling) { + // This is needed in order to mitgate the change in J_ij carried out just above this loop. + // Alternatively, we could move this loop up to the top + m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol] / m_colScales[jcol]; + } else { + m_rowWtScales[irow] += fabs(*jptr) * m_ewt[jcol]; + } + jptr++; + } + } + } else if (jac.matrixType_ == 1) { + kl = ivec[0]; + ku = ivec[1]; + for (jcol = 0; jcol < neq_; jcol++) { + colP_j = (doublereal *) jac.ptrColumn(jcol); + for (irow = jcol - ku; irow <= jcol + kl; irow++) { + if (irow >= 0 && irow < neq_) { + double vv = fabs(colP_j[kl + ku + irow - jcol]); + if (m_rowScaling) { + m_rowScales[irow] += vv; + } + if (m_colScaling) { + // This is needed in order to mitgate the change in J_ij carried out just above this loop. + // Alternatively, we could move this loop up to the top + m_rowWtScales[irow] += vv * m_ewt[jcol] / m_colScales[jcol]; + } else { + m_rowWtScales[irow] += vv * m_ewt[jcol]; + } + } } - jptr++; } } if (m_rowScaling) { - for (irow = 0; irow < neq_; irow++) { - m_rowScales[irow] = 1.0/m_rowScales[irow]; - } + for (irow = 0; irow < neq_; irow++) { + m_rowScales[irow] = 1.0/m_rowScales[irow]; + } } else { - for (irow = 0; irow < neq_; irow++) { - m_rowScales[irow] = 1.0; - } + for (irow = 0; irow < neq_; irow++) { + m_rowScales[irow] = 1.0; + } } // What we have defined is a maximum value that the residual can be and still pass. // This isn't sufficient. - + if (m_rowScaling) { - jptr = &(*(jac.begin())); - for (jcol = 0; jcol < neq_; jcol++) { - for (irow = 0; irow < neq_; irow++) { - *jptr *= m_rowScales[irow]; - jptr++; + if (jac.matrixType_ == 0) { + jptr = &(*(jac.begin())); + for (jcol = 0; jcol < neq_; jcol++) { + for (irow = 0; irow < neq_; irow++) { + *jptr *= m_rowScales[irow]; + jptr++; + } + } + } else if (jac.matrixType_ == 1) { + kl = ivec[0]; + ku = ivec[1]; + for (jcol = 0; jcol < neq_; jcol++) { + colP_j = (doublereal *) jac.ptrColumn(jcol); + for (irow = jcol - ku; irow <= jcol + kl; irow++) { + if (irow >= 0 && irow < neq_) { + colP_j[kl + ku + irow - jcol] *= m_rowScales[irow]; + } + } } } } @@ -812,7 +880,7 @@ namespace Cantera { */ void NonlinearSolver::calcSolnToResNormVector() { - if (! jacCopy_.m_factored) { + if (! jacCopyPtr_->factored()) { doublereal sum = 0.0; @@ -829,7 +897,7 @@ namespace Cantera { for (int irow = 0; irow < neq_; irow++) { m_wksp[irow] = 0.0; } - doublereal *jptr = &(*(jacCopy_.begin())); + doublereal *jptr = &(jacCopyPtr_->operator()(0,0)); for (int jcol = 0; jcol < neq_; jcol++) { for (int irow = 0; irow < neq_; irow++) { m_wksp[irow] += (*jptr) * m_ewt[jcol]; @@ -873,7 +941,7 @@ namespace Cantera { */ int NonlinearSolver::doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, - SquareMatrix& jac) + GeneralMatrix& jac) { int irow; @@ -961,16 +1029,22 @@ namespace Cantera { * This is algorith A.6.5.1 in Dennis / Schnabel * * Compute the QR decomposition + * + * Notes on banded Hessian solve: + * The matrix for jT j has a larger band width. Both the top and bottom band widths + * are doubled, going from KU to KU+KL and KL to KU+KL in size. This is not an impossible increase in cost, but + * has to be considered. */ int NonlinearSolver::doAffineNewtonSolve(const doublereal * const y_curr, const doublereal * const ydot_curr, - doublereal * const delta_y, SquareMatrix& jac) + doublereal * const delta_y, GeneralMatrix& jac) { bool newtonGood = true; int irow; doublereal *delyNewton = 0; // We can default to QR here ( or not ) - jac.useQR_ = true; - // multiply the residual by -1 + jac.useFactorAlgorithm(1); + int useQR = jac.factorAlgorithm(); + // multiplyl the residual by -1 // Scale the residual if there is row scaling. Note, the matrix has already been scaled if (m_rowScaling && !m_resid_scaled) { for (int n = 0; n < neq_; n++) { @@ -986,8 +1060,8 @@ namespace Cantera { // Factor the matrix using a standard Newton solve m_conditionNumber = 1.0E300; int info = 0; - if (!jac.m_factored) { - if (jac.useQR_) { + if (!jac.factored()) { + if (useQR) { info = jac.factorQR(); } else { info = jac.factor(); @@ -999,14 +1073,27 @@ namespace Cantera { */ if (info == 0) { doublereal rcond = 0.0; - if (jac.useQR_) { + if (useQR) { rcond = jac.rcondQR(); } else { - rcond = jac.rcond(jac.a1norm_); + doublereal a1norm = jac.oneNorm(); + rcond = jac.rcond(a1norm); } if (rcond > 0.0) { m_conditionNumber = 1.0 / rcond; } + } else { + m_conditionNumber = 1.0E300; + newtonGood = false; + if (m_print_flag >= 1) { + printf("\t\t doAffineNewtonSolve: "); + if (useQR) { + printf("factorQR()"); + } else { + printf("factor()"); + } + printf(" returned with info = %d, indicating a zero row or column\n", info); + } } bool doHessian = false; if (s_doBothSolvesAndCompare) { @@ -1040,10 +1127,19 @@ namespace Cantera { } } else { - doHessian = true; - newtonGood = false; - if (m_print_flag >= 3) { - printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g. Doing a Hessian solve \n", m_conditionNumber); + if (jac.matrixType_ == 1) { + useNewton = true; + newtonGood = true; + if (m_print_flag >= 3) { + printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g, But Banded Hessian solve " + "not implemented yet \n", m_conditionNumber); + } + } else { + doHessian = true; + newtonGood = false; + if (m_print_flag >= 3) { + printf("\t\t doAffineNewtonSolve() WARNING: Condition number too large, %g. Doing a Hessian solve \n", m_conditionNumber); + } } } @@ -1056,30 +1152,32 @@ namespace Cantera { } // Get memory if not done before - if (Hessian_.nRows() == 0) { - Hessian_.resize(neq_, neq_); + if (HessianPtr_ == 0) { + HessianPtr_ = jac.duplMyselfAsGeneralMatrix(); } /* * Calculate the symmetric Hessian */ - Hessian_.zero(); + GeneralMatrix &hessian = *HessianPtr_; + GeneralMatrix &jacCopy = *jacCopyPtr_; + hessian.zero(); if (m_rowScaling) { for (int i = 0; i < neq_; i++) { for (int j = i; j < neq_; j++) { for (int k = 0; k < neq_; k++) { - Hessian_(i,j) += jacCopy_(k,i) * jacCopy_(k,j) * m_rowScales[k] * m_rowScales[k]; + hessian(i,j) += jacCopy(k,i) * jacCopy(k,j) * m_rowScales[k] * m_rowScales[k]; } - Hessian_(j,i) = Hessian_(i,j); + hessian(j,i) = hessian(i,j); } } } else { for (int i = 0; i < neq_; i++) { for (int j = i; j < neq_; j++) { for (int k = 0; k < neq_; k++) { - Hessian_(i,j) += jacCopy_(k,i) * jacCopy_(k,j); + hessian(i,j) += jacCopy(k,i) * jacCopy(k,j); } - Hessian_(j,i) = Hessian_(i,j); + hessian(j,i) = hessian(i,j); } } } @@ -1092,10 +1190,10 @@ namespace Cantera { if (m_colScaling) { for (int i = 0; i < neq_; i++) { for (int j = i; j < neq_; j++) { - hcol += fabs(Hessian_(j,i)) * m_colScales[j]; + hcol += fabs(hessian(j,i)) * m_colScales[j]; } for (int j = i+1; j < neq_; j++) { - hcol += fabs(Hessian_(i,j)) * m_colScales[j]; + hcol += fabs(hessian(i,j)) * m_colScales[j]; } hcol *= m_colScales[i]; if (hcol > hnorm) { @@ -1105,10 +1203,10 @@ namespace Cantera { } else { for (int i = 0; i < neq_; i++) { for (int j = i; j < neq_; j++) { - hcol += fabs(Hessian_(j,i)); + hcol += fabs(hessian(j,i)); } for (int j = i+1; j < neq_; j++) { - hcol += fabs(Hessian_(i,j)); + hcol += fabs(hessian(i,j)); } if (hcol > hnorm) { hnorm = hcol; @@ -1127,11 +1225,11 @@ namespace Cantera { #endif if (m_colScaling) { for (int i = 0; i < neq_; i++) { - Hessian_(i,i) += hcol / (m_colScales[i] * m_colScales[i]); + hessian(i,i) += hcol / (m_colScales[i] * m_colScales[i]); } } else { for (int i = 0; i < neq_; i++) { - Hessian_(i,i) += hcol; + hessian(i,i) += hcol; } } @@ -1139,7 +1237,7 @@ namespace Cantera { * Factor the Hessian */ int info; - ct_dpotrf(ctlapack::UpperTriangular, neq_, &(*(Hessian_.begin())), neq_, info); + ct_dpotrf(ctlapack::UpperTriangular, neq_, &(*(HessianPtr_->begin())), neq_, info); if (info) { if (m_print_flag >= 2) { printf("\t\t doAffineNewtonSolve() ERROR: Hessian isn't positive definate DPOTRF returned INFO = %d\n", info); @@ -1164,14 +1262,14 @@ namespace Cantera { for (int j = 0; j < neq_; j++) { delta_y[j] = 0.0; for (int i = 0; i < neq_; i++) { - delta_y[j] += delyH[i] * jacCopy_.value(i,j) * m_rowScales[i]; + delta_y[j] += delyH[i] * jacCopy(i,j) * m_rowScales[i]; } } } else { for (int j = 0; j < neq_; j++) { delta_y[j] = 0.0; for (int i = 0; i < neq_; i++) { - delta_y[j] += delyH[i] * jacCopy_.value(i,j); + delta_y[j] += delyH[i] * jacCopy(i,j); } } } @@ -1180,7 +1278,7 @@ namespace Cantera { /* * Solve the factored Hessian System */ - ct_dpotrs(ctlapack::UpperTriangular, neq_, 1,&(*(Hessian_.begin())), neq_, delta_y, neq_, info); + ct_dpotrs(ctlapack::UpperTriangular, neq_, 1,&(*(hessian.begin())), neq_, delta_y, neq_, info); if (info) { if (m_print_flag >= 2) { printf("\t\t NonlinearSolver::doAffineNewtonSolve() ERROR: DPOTRS returned INFO = %d\n", info); @@ -1287,7 +1385,7 @@ namespace Cantera { /* * This call must be made on the unfactored jacobian! */ - doublereal NonlinearSolver::doCauchyPointSolve(SquareMatrix& jac) + doublereal NonlinearSolver::doCauchyPointSolve(GeneralMatrix& jac) { doublereal rowFac = 1.0; doublereal colFac = 1.0; @@ -1311,7 +1409,7 @@ namespace Cantera { if (m_rowScaling) { rowFac = 1.0 / m_rowScales[i]; } - deltaX_CP_[j] -= m_resid[i] * jac.value(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] + deltaX_CP_[j] -= m_resid[i] * jac(i,j) * colFac * rowFac * m_ewt[j] * m_ewt[j] / (m_residWts[i] * m_residWts[i]); #ifdef DEBUG_MODE mdp::checkFinite(deltaX_CP_[j]); @@ -1333,7 +1431,7 @@ namespace Cantera { if (m_colScaling) { colFac = 1.0 / m_colScales[j]; } - Jd_[i] += deltaX_CP_[j] * jac.value(i,j) * rowFac * colFac / m_residWts[i]; + Jd_[i] += deltaX_CP_[j] * jac(i,j) * rowFac * colFac / m_residWts[i]; } } @@ -2322,7 +2420,7 @@ namespace Cantera { int NonlinearSolver::dampStep(const doublereal time_curr, const doublereal * const y_n_curr, const doublereal * const ydot_n_curr, doublereal * const step_1, doublereal * const y_n_1, doublereal * const ydot_n_1, doublereal * const step_2, - doublereal & stepNorm_2, SquareMatrix& jac, bool writetitle, int& num_backtracks) + doublereal & stepNorm_2, GeneralMatrix& jac, bool writetitle, int& num_backtracks) { int j, m; int info = 0; @@ -2552,7 +2650,7 @@ namespace Cantera { int NonlinearSolver::dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, const doublereal *ydot_n_curr, std::vector & step_1, doublereal* const y_n_1, doublereal* const ydot_n_1, - doublereal& stepNorm_1, doublereal& stepNorm_2, SquareMatrix& jac, int& numTrials) + doublereal& stepNorm_1, doublereal& stepNorm_2, GeneralMatrix& jac, int& numTrials) { doublereal lambda; int info; @@ -2907,7 +3005,7 @@ namespace Cantera { * -1 Failed convergence */ int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal * const y_comm, doublereal * const ydot_comm, - doublereal CJ, doublereal time_curr, SquareMatrix& jac, + doublereal CJ, doublereal time_curr, GeneralMatrix& jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput) { @@ -2921,6 +3019,11 @@ namespace Cantera { int retnDamp = 0; int retnCode = 0; bool forceNewJac = false; + + if (jacCopyPtr_) { + delete jacCopyPtr_; + } + jacCopyPtr_ = jac.duplMyselfAsGeneralMatrix(); doublereal stepNorm_1; doublereal stepNorm_2; @@ -2945,11 +3048,7 @@ namespace Cantera { num_backtracks = 0; int i_numTrials; m_print_flag = loglevelInput; - if (m_print_flag > 1) { - jac.m_printLevel = 1; - } else { - jac.m_printLevel = 0; - } + if (trustRegionInitializationMethod_ == 0) { trInit = true; } else if (trustRegionInitializationMethod_ == 1) { @@ -3563,10 +3662,9 @@ namespace Cantera { * 1 Means a successful operation * 0 Means an unsuccessful operation */ - int NonlinearSolver::beuler_jac(SquareMatrix &J, doublereal * const f, + int NonlinearSolver::beuler_jac(GeneralMatrix &J, doublereal * const f, doublereal time_curr, doublereal CJ, - doublereal * const y, - doublereal * const ydot, + doublereal * const y, doublereal * const ydot, int num_newt_its) { int i, j; @@ -3590,101 +3688,190 @@ namespace Cantera { return info; } } else { - /******************************************************************* - * Generic algorithm to calculate a numerical Jacobian - */ - /* - * Calculate the current value of the rhs given the - * current conditions. - */ + if (J.matrixType_ == 0) { + /******************************************************************* + * Generic algorithm to calculate a numerical Jacobian + */ + /* + * Calculate the current value of the rhs given the + * current conditions. + */ - info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); - m_nfe++; - if (info != 1) { - return info; - } - m_nJacEval++; + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); + m_nfe++; + if (info != 1) { + return info; + } + m_nJacEval++; - /* - * Malloc a vector and call the function object to return a set of - * deltaY's that are appropriate for calculating the numerical - * derivative. - */ - doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); - retn = m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); + /* + * Malloc a vector and call the function object to return a set of + * deltaY's that are appropriate for calculating the numerical + * derivative. + */ + doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + retn = m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); - if (s_print_NumJac) { - if (m_print_flag >= 7) { - if (neq_ < 20) { - printf("\t\tUnk m_ewt y dyVector ResN\n"); - for (int iii = 0; iii < neq_; iii++){ - printf("\t\t %4d %16.8e %16.8e %16.8e %16.8e \n", - iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + if (s_print_NumJac) { + if (m_print_flag >= 7) { + if (neq_ < 20) { + printf("\t\tUnk m_ewt y dyVector ResN\n"); + for (int iii = 0; iii < neq_; iii++){ + printf("\t\t %4d %16.8e %16.8e %16.8e %16.8e \n", + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + } } } } - } - /* - * Loop over the variables, formulating a numerical derivative - * of the dense matrix. - * For the delta in the variable, we will use a variety of approaches - * The original approach was to use the error tolerance amount. - * This may not be the best approach, as it could be overly large in - * some instances and overly small in others. - * We will first protect from being overly small, by using the usual - * sqrt of machine precision approach, i.e., 1.0E-7, - * to bound the lower limit of the delta. - */ - for (j = 0; j < neq_; j++) { + /* + * Loop over the variables, formulating a numerical derivative + * of the dense matrix. + * For the delta in the variable, we will use a variety of approaches + * The original approach was to use the error tolerance amount. + * This may not be the best approach, as it could be overly large in + * some instances and overly small in others. + * We will first protect from being overly small, by using the usual + * sqrt of machine precision approach, i.e., 1.0E-7, + * to bound the lower limit of the delta. + */ + for (j = 0; j < neq_; j++) { - /* - * Get a pointer into the column of the matrix - */ + /* + * Get a pointer into the column of the matrix + */ - col_j = (doublereal *) J.ptrColumn(j); - ysave = y[j]; - dy = dyVector[j]; - //dy = fmaxx(1.0E-6 * m_ewt[j], fabs(ysave)*1.0E-7); + col_j = (doublereal *) J.ptrColumn(j); + ysave = y[j]; + dy = dyVector[j]; + //dy = fmaxx(1.0E-6 * m_ewt[j], fabs(ysave)*1.0E-7); + + y[j] = ysave + dy; + dy = y[j] - ysave; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydotsave = ydot[j]; + ydot[j] += dy * CJ; + } + /* + * Call the function + */ + + + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), + JacDelta_ResidEval, j, dy); + m_nfe++; + if (info != 1) { + mdp::mdp_safe_free((void **) &dyVector); + return info; + } + + doublereal diff; + for (i = 0; i < neq_; i++) { + diff = subtractRD(m_wksp[i], f[i]); + col_j[i] = diff / dy; + } + y[j] = ysave; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydot[j] = ydotsave; + } - y[j] = ysave + dy; - dy = y[j] - ysave; - if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - ydotsave = ydot[j]; - ydot[j] += dy * CJ; } - /* - * Call the function - */ + /* + * Release memory + */ + mdp::mdp_safe_free((void **) &dyVector); + } else if (J.matrixType_ == 1) { + int ku, kl; + int ivec[2]; + int n = J.nRowsAndStruct(ivec); + kl = ivec[0]; + ku = ivec[1]; + if (n != neq_) { + printf("we have probs\n"); exit(-1); + } - - info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), - JacDelta_ResidEval, j, dy); - m_nfe++; + // --------------------------------- BANDED MATRIX BRAIN DEAD --------------------------------------------------- + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, f, JacBase_ResidEval); + m_nfe++; if (info != 1) { - mdp::mdp_safe_free((void **) &dyVector); return info; } + m_nJacEval++; - doublereal diff; - for (i = 0; i < neq_; i++) { - diff = subtractRD(m_wksp[i], f[i]); - col_j[i] = diff / dy; - } - y[j] = ysave; - if (solnType_ != NSOLN_TYPE_STEADY_STATE) { - ydot[j] = ydotsave; + + doublereal *dyVector = mdp::mdp_alloc_dbl_1(neq_, MDP_DBL_NOINIT); + retn = m_func->calcDeltaSolnVariables(time_curr, y, ydot, dyVector, DATA_PTR(m_ewt)); + if (s_print_NumJac) { + if (m_print_flag >= 7) { + if (neq_ < 20) { + printf("\t\tUnk m_ewt y dyVector ResN\n"); + for (int iii = 0; iii < neq_; iii++){ + printf("\t\t %4d %16.8e %16.8e %16.8e %16.8e \n", + iii, m_ewt[iii], y[iii], dyVector[iii], f[iii]); + } + } + } } + + for (j = 0; j < neq_; j++) { + + + col_j = (doublereal *) J.ptrColumn(j); + ysave = y[j]; + dy = dyVector[j]; + + + y[j] = ysave + dy; + dy = y[j] - ysave; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydotsave = ydot[j]; + ydot[j] += dy * CJ; + } + + info = m_func->evalResidNJ(time_curr, delta_t_n, y, ydot, DATA_PTR(m_wksp), JacDelta_ResidEval, j, dy); + m_nfe++; + if (info != 1) { + mdp::mdp_safe_free((void **) &dyVector); + return info; + } + + doublereal diff; + + + + for (int i = j - ku; i <= j + kl; i++) { + if (i >= 0 && i < neq_) { + diff = subtractRD(m_wksp[i], f[i]); + col_j[kl + ku + i - j] = diff / dy; + } + } + y[j] = ysave; + if (solnType_ != NSOLN_TYPE_STEADY_STATE) { + ydot[j] = ydotsave; + } + + } + + mdp::mdp_safe_free((void **) &dyVector); + double vSmall; + int ismall = J.checkRows(vSmall); + if (vSmall < 1.0E-100) { + printf("WE have a zero row, %d\n", ismall); + exit(-1); + } + ismall = J.checkColumns(vSmall); + if (vSmall < 1.0E-100) { + printf("WE have a zero column, %d\n", ismall); + exit(-1); + } + + // ---------------------BANDED MATRIX BRAIN DEAD ----------------------- } - /* - * Release memory - */ - mdp::mdp_safe_free((void **) &dyVector); } if (m_print_flag >= 7 && s_print_NumJac) { @@ -3721,7 +3908,7 @@ namespace Cantera { * Make a copy of the data. Note, this jacobian copy occurs before any matrix scaling operations. * It's the raw matrix producted by this routine. */ - jacCopy_.copyData(J); + jacCopyPtr_->copyData(J); return retn; } diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 582c3fa6c..6972934ac 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -259,7 +259,7 @@ namespace Cantera { */ int doNewtonSolve(const doublereal time_curr, const doublereal * const y_curr, const doublereal * const ydot_curr, doublereal * const delta_y, - SquareMatrix& jac); + GeneralMatrix& jac); //! Compute the newton step, either by direct newton's or by solving a close problem that is represented //! by a Hessian ( @@ -293,7 +293,7 @@ namespace Cantera { * else indicates a failure. */ int doAffineNewtonSolve(const doublereal * const y_curr, const doublereal * const ydot_curr, - doublereal * const delta_y, SquareMatrix& jac); + doublereal * const delta_y, GeneralMatrix& jac); //! Calculate the length of the current trust region in terms of the solution error norm /*! @@ -438,7 +438,7 @@ namespace Cantera { * 1 Means a successful operation * 0 Means an unsuccessful operation */ - int beuler_jac(SquareMatrix &J, doublereal * const f, + int beuler_jac(GeneralMatrix &J, doublereal * const f, doublereal time_curr, doublereal CJ, doublereal * const y, doublereal * const ydot, int num_newt_its); @@ -510,7 +510,7 @@ namespace Cantera { int dampStep(const doublereal time_curr, const doublereal * const y_n_curr, const doublereal * const ydot_n_curr, doublereal * const step_1, doublereal * const y_n_1, doublereal * const ydot_n_1, doublereal * step_2, - doublereal & stepNorm_2, SquareMatrix& jac, bool writetitle, + doublereal & stepNorm_2, GeneralMatrix& jac, bool writetitle, int& num_backtracks); //! Find the solution to F(X) = 0 by damped Newton iteration. @@ -541,7 +541,7 @@ namespace Cantera { * -1 Failed convergence */ int solve_nonlinear_problem(int SolnType, doublereal * const y_comm, doublereal * const ydot_comm, doublereal CJ, - doublereal time_curr, SquareMatrix& jac,int &num_newt_its, + doublereal time_curr, GeneralMatrix & jac, int &num_newt_its, int &num_linear_solves, int &num_backtracks, int loglevelInput); private: @@ -589,7 +589,7 @@ namespace Cantera { * @param time_curr current value of the time * @param num_newt_its Current value of the number of newt its */ - void scaleMatrix(SquareMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, + void scaleMatrix(GeneralMatrix& jac, doublereal * const y_comm, doublereal * const ydot_comm, doublereal time_curr, int num_newt_its); //! Print solution norm contribution @@ -689,7 +689,7 @@ namespace Cantera { * * @return Returns the norm of the solution update */ - doublereal doCauchyPointSolve(SquareMatrix& jac); + doublereal doCauchyPointSolve(GeneralMatrix& jac); //! This is a utility routine that can be used to print out the rates of the initial residual decline /*! @@ -793,7 +793,7 @@ namespace Cantera { int dampDogLeg(const doublereal time_curr, const doublereal* y_n_curr, const doublereal *ydot_n_curr, std::vector & step_1, doublereal* const y_n_1, doublereal* const ydot_n_1, - doublereal& stepNorm_1, doublereal& stepNorm_2, SquareMatrix& jac, int& num_backtracks); + doublereal& stepNorm_1, doublereal& stepNorm_2, GeneralMatrix& jac, int& num_backtracks); //! Decide whether the current step is acceptable and adjust the trust region size /*! @@ -1103,10 +1103,10 @@ namespace Cantera { /*! * The jacobian storred here is the raw matrix, before any row or column scaling is carried out */ - Cantera::SquareMatrix jacCopy_; + Cantera::GeneralMatrix * jacCopyPtr_; //! Hessian - Cantera::SquareMatrix Hessian_; + Cantera::GeneralMatrix * HessianPtr_; /********************************************************************************************* * VARIABLES ASSOCIATED WITH STEPS AND ASSOCIATED DOUBLE DOGLEG PARAMETERS diff --git a/Cantera/src/numerics/ResidJacEval.cpp b/Cantera/src/numerics/ResidJacEval.cpp index 62ca74b79..a4fc0ac22 100644 --- a/Cantera/src/numerics/ResidJacEval.cpp +++ b/Cantera/src/numerics/ResidJacEval.cpp @@ -333,7 +333,7 @@ namespace Cantera { evalJacobian(const doublereal t, const doublereal delta_t, doublereal cj, const doublereal * const y, const doublereal * const ydot, - SquareMatrix &J, + GeneralMatrix &J, doublereal * const resid) { doublereal * const * jac_colPts = J.colPts(); @@ -349,7 +349,7 @@ namespace Cantera { * @param c_j The current value of the coefficient of the time derivative * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) - * @param jac_colPts Reference to the SquareMatrix object to be calculated (output) + * @param jac_colPts Reference to the SquareMatrix object to be calculated (output) * @param resid Value of the residual that is computed (output) */ int ResidJacEval:: diff --git a/Cantera/src/numerics/ResidJacEval.h b/Cantera/src/numerics/ResidJacEval.h index 9514a1635..ccbaf4b98 100644 --- a/Cantera/src/numerics/ResidJacEval.h +++ b/Cantera/src/numerics/ResidJacEval.h @@ -21,7 +21,7 @@ #define CT_RESIDJACEVAL_H #include "ResidEval.h" -#include "SquareMatrix.h" +#include "GeneralMatrix.h" namespace Cantera { @@ -312,7 +312,7 @@ namespace Cantera { virtual int matrixConditioning(doublereal * const matrix, const int nrows, doublereal * const rhs); - //! Calculate an analytical jacobian and the residual at the current time and values. + //! Calculate an analytical jacobian and the residual at the current time and values. /*! * Only called if the jacFormation method is set to analytical * @@ -329,8 +329,9 @@ namespace Cantera { * -0 or neg value Means an unsuccessful operation */ virtual int evalJacobian(const doublereal t, const doublereal delta_t, doublereal cj, - const doublereal* const y, const doublereal* const ydot, - SquareMatrix &J, doublereal * const resid); + const doublereal* const y, const doublereal* const ydot, + GeneralMatrix &J, doublereal * const resid); + //! Calculate an analytical jacobian and the residual at the current time and values. /*! diff --git a/Cantera/src/numerics/SquareMatrix.cpp b/Cantera/src/numerics/SquareMatrix.cpp index 1724f8c93..29e16bef0 100644 --- a/Cantera/src/numerics/SquareMatrix.cpp +++ b/Cantera/src/numerics/SquareMatrix.cpp @@ -32,6 +32,7 @@ namespace Cantera { //==================================================================================================================== SquareMatrix::SquareMatrix() : DenseMatrix(), + GeneralMatrix(0), m_factored(0), a1norm_(0.0), useQR_(0) @@ -48,7 +49,8 @@ namespace Cantera { * @param v intial value of all matrix components. */ SquareMatrix::SquareMatrix(int n, doublereal v) : - DenseMatrix(n, n, v), + DenseMatrix(n, n, v), + GeneralMatrix(0), m_factored(0), a1norm_(0.0), useQR_(0) @@ -61,7 +63,8 @@ namespace Cantera { * copy constructor */ SquareMatrix::SquareMatrix(const SquareMatrix& y) : - DenseMatrix(y), + DenseMatrix(y), + GeneralMatrix(0), m_factored(y.m_factored), a1norm_(y.a1norm_), useQR_(y.useQR_) @@ -75,6 +78,7 @@ namespace Cantera { SquareMatrix& SquareMatrix::operator=(const SquareMatrix& y) { if (&y == this) return *this; DenseMatrix::operator=(y); + GeneralMatrix::operator=(y); m_factored = y.m_factored; a1norm_ = y.a1norm_; useQR_ = y.useQR_; @@ -87,7 +91,7 @@ namespace Cantera { /* * Solve Ax = b. Vector b is overwritten on exit with x. */ - int SquareMatrix::solve(double* b) + int SquareMatrix::solve(doublereal * b) { if (useQR_) { return solveQR(b); @@ -138,6 +142,25 @@ namespace Cantera { void SquareMatrix::resize(int n, int m, doublereal v) { DenseMatrix::resize(n, m, v); } + + //==================================================================================================================== + // Multiply A*b and write result to prod. + /* + * @param b Vector to do the rh multiplcation + * @param prod OUTPUT vector to receive the result + */ + void SquareMatrix::mult(const doublereal * const b, doublereal * const prod) const { + DenseMatrix::mult(b, prod); + } + //==================================================================================================================== + // Multiply b*A and write result to prod. + /* + * @param b Vector to do the lh multiplcation + * @param prod OUTPUT vector to receive the result + */ + void SquareMatrix::leftMult(const doublereal * const b, doublereal * const prod) const { + DenseMatrix::leftMult(b, prod); + } //==================================================================================================================== /* * Factor A. A is overwritten with the LU decomposition of A. @@ -206,7 +229,7 @@ namespace Cantera { /* * Solve Ax = b. Vector b is overwritten on exit with x. */ - int SquareMatrix::solveQR(double* b) + int SquareMatrix::solveQR(doublereal * b) { int info=0; /* @@ -288,7 +311,11 @@ namespace Cantera { } return rcond; } - //===================================================================================================================== + //===================================================================================================================== + doublereal SquareMatrix::oneNorm() const { + return a1norm_; + } + //===================================================================================================================== doublereal SquareMatrix::rcondQR() { if ((int) iwork_.size() < m_nrows) { @@ -316,6 +343,111 @@ namespace Cantera { return rcond; } //===================================================================================================================== + void SquareMatrix::useFactorAlgorithm(int fAlgorithm) { + useQR_ = fAlgorithm; + } + //===================================================================================================================== + int SquareMatrix::factorAlgorithm() const { + return (int) useQR_; + } + //===================================================================================================================== + bool SquareMatrix::factored() const { + return m_factored; + } + //===================================================================================================================== + // Return a pointer to the top of column j, columns are contiguous in memory + /* + * @param j Value of the column + * + * @return Returns a pointer to the top of the column + */ + doublereal * SquareMatrix::ptrColumn(int j) { + return Array2D::ptrColumn(j); + } + //===================================================================================================================== + // Copy the data from one array into another without doing any checking + /* + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + void SquareMatrix::copyData(const GeneralMatrix& y) { + const SquareMatrix *yy_ptr = dynamic_cast(& y); + Array2D::copyData(*yy_ptr); + } + //===================================================================================================================== + size_t SquareMatrix::nRows() const { + return m_nrows; + } + //===================================================================================================================== + size_t SquareMatrix::nRowsAndStruct(int * const iStruct) const { + return m_nrows; + } + //===================================================================================================================== + GeneralMatrix * SquareMatrix::duplMyselfAsGeneralMatrix() const { + SquareMatrix *dd = new SquareMatrix(*this); + return static_cast(dd); + } + //===================================================================================================================== + // Return an iterator pointing to the first element + vector_fp::iterator SquareMatrix::begin() { + return m_data.begin(); + } + //===================================================================================================================== + // Return a const iterator pointing to the first element + vector_fp::const_iterator SquareMatrix::begin() const { + return m_data.begin(); + } + //===================================================================================================================== + // Return a vector of const pointers to the columns + /* + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + doublereal * const * SquareMatrix::colPts() { + return DenseMatrix::colPts(); + } + //===================================================================================================================== + + int SquareMatrix::checkRows(doublereal &valueSmall) const { + valueSmall = 1.0E300; + int iSmall = -1; + for (int i = 0; i < m_nrows; i++) { + double valueS = 0.0; + for (int j = 0; j < m_nrows; j++) { + if (fabs(value(i,j)) > valueS) { + valueS = fabs(value(i,j)); + } + } + if (valueS < valueSmall) { + iSmall = i; + valueSmall = valueS; + } + } + return iSmall; + } + //===================================================================================================================== + int SquareMatrix::checkColumns(doublereal &valueSmall) const { + valueSmall = 1.0E300; + int jSmall = -1; + for (int j = 0; j < m_nrows; j++) { + double valueS = 0.0; + for (int i = 0; i < m_nrows; i++) { + if (fabs(value(i,j)) > valueS) { + valueS = fabs(value(i,j)); + } + } + if (valueS < valueSmall) { + jSmall = j; + valueSmall = valueS; + } + } + return jSmall; + } + //===================================================================================================================== + } diff --git a/Cantera/src/numerics/SquareMatrix.h b/Cantera/src/numerics/SquareMatrix.h index b95d3b35b..0eb03dbe8 100644 --- a/Cantera/src/numerics/SquareMatrix.h +++ b/Cantera/src/numerics/SquareMatrix.h @@ -18,6 +18,7 @@ #define CT_SQUAREMATRIX_H #include "DenseMatrix.h" +#include "GeneralMatrix.h" namespace Cantera { @@ -25,7 +26,7 @@ namespace Cantera { * A class for full (non-sparse) matrices with Fortran-compatible * data storage. Adds matrix inversion operations to this class from DenseMatrix. */ - class SquareMatrix: public DenseMatrix { + class SquareMatrix: public DenseMatrix, public GeneralMatrix { public: @@ -61,8 +62,7 @@ namespace Cantera { //! Destructor. Does nothing. virtual ~SquareMatrix(); - - //! Solves the Ax = b system returning x in the b spot. + //! Solves the Ax = b system returning x in the b spot. /*! * @param b Vector for the rhs of the equation system */ @@ -76,12 +76,25 @@ namespace Cantera { */ void resize(int n, int m, doublereal v = 0.0); - /** * Zero the matrix */ void zero(); + //! Multiply A*b and write result to prod. + /*! + * @param b Vector to do the rh multiplcation + * @param prod OUTPUT vector to receive the result + */ + virtual void mult(const doublereal * const b, doublereal * const prod) const; + + //! Multiply b*A and write result to prod. + /*! + * @param b Vector to do the lh multiplcation + * @param prod OUTPUT vector to receive the result + */ + virtual void leftMult(const doublereal * const b, doublereal * const prod) const; + /** * Factors the A matrix, overwriting A. We flip m_factored * boolean to indicate that the matrix is now A-1. @@ -94,7 +107,7 @@ namespace Cantera { * * @return Returns the info variable from lapack */ - int factorQR(); + virtual int factorQR(); //! Returns an estimate of the inverse of the condition number for the matrix /*! @@ -102,7 +115,7 @@ namespace Cantera { * * @return returns the inverse of the condition number */ - doublereal rcondQR(); + virtual doublereal rcondQR(); //! Returns an estimate of the inverse of the condition number for the matrix /*! @@ -112,7 +125,10 @@ namespace Cantera { * * @return returns the inverse of the condition number */ - doublereal rcond(doublereal a1norm); + virtual doublereal rcond(doublereal a1norm); + + //! Returns the one norm of the matrix + virtual doublereal oneNorm() const; //! Solves the linear problem Ax=b using the QR algorithm returning x in the b spot /*! @@ -122,17 +138,136 @@ namespace Cantera { //! clear the factored flag - void clearFactorFlag(); - /** - * set the factored flag - */ + virtual void clearFactorFlag(); + + //! set the factored flag void setFactorFlag(); - /* - * the factor flag + //! Report whether the current matrix has been factored. + virtual bool factored() const; + + //! Change the way the matrix is factored + /*! + * @param fAlgorithm integer + * 0 LU factorization + * 1 QR factorization */ + virtual void useFactorAlgorithm(int fAlgorithm); + + //! Returns the factor algorithm used + /*! + * 0 LU decomposition + * 1 QR decomposition + * + * This routine will always return 0 + */ + virtual int factorAlgorithm() const; + + //! Return a pointer to the top of column j, columns are assumed to be contiguous in memory + /*! + * @param j Value of the column + * + * @return Returns a pointer to the top of the column + */ + virtual doublereal * ptrColumn(int j); + + //! Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * (note, tried a using directive here, and it didn't seem to work) + * + * Returns a changeable reference to the matrix entry + */ + virtual doublereal& operator()(int i, int j) { + return Array2D::operator()(i, j); + } + + //! Copy the data from one array into another without doing any checking + /*! + * This differs from the assignment operator as no resizing is done and memcpy() is used. + * @param y Array to be copied + */ + virtual void copyData(const GeneralMatrix& y); + + //! Constant Index into the (i,j) element + /*! + * @param i row + * @param j column + * + * Returns an unchangeable reference to the matrix entry + */ + virtual doublereal operator() (int i, int j) const { + return Array2D::operator()(i, j); + } + + //! Return the number of rows in the matrix + virtual size_t nRows() const; + + //! Return the size and structure of the matrix + /*! + * This is inherited from GeneralMatrix + * + * @param iStruct OUTPUT Pointer to a vector of ints that describe the structure of the matrix. + * not used + * + * @return returns the number of rows and columns in the matrix. + */ + size_t nRowsAndStruct(int * const iStruct = 0) const; + + //! Duplicate this object + virtual GeneralMatrix * duplMyselfAsGeneralMatrix() const; + + + //! Return an iterator pointing to the first element + /*! + */ + virtual vector_fp::iterator begin(); + + + //! Return a const iterator pointing to the first element + virtual vector_fp::const_iterator begin() const; + + + //! Return a vector of const pointers to the columns + /*! + * Note the value of the pointers are protected by their being const. + * However, the value of the matrix is open to being changed. + * + * @return returns a vector of pointers to the top of the columns + * of the matrices. + */ + virtual doublereal * const * colPts(); + + //! Check to see if we have any zero rows in the jacobian + /*! + * This utility routine checks to see if any rows are zero. + * The smallest row is returned along with the largest coefficient in that row + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest row + * + * @return index of the row that is most nearly zero + */ + virtual int checkRows(doublereal & valueSmall) const; + + //! Check to see if we have any zero columns in the jacobian + /*! + * This utility routine checks to see if any columns are zero. + * The smallest column is returned along with the largest coefficient in that column + * + * @param valueSmall OUTPUT value of the largest coefficient in the smallest column + * + * @return index of the column that is most nearly zero + */ + virtual int checkColumns(doublereal & valueSmall) const; + + protected: + + //! the factor flag int m_factored; + public: //! Work vector for QR algorithm vector_fp tau; @@ -141,11 +276,10 @@ namespace Cantera { //! Integer work vector for QR algorithms std::vector iwork_; - + protected: //! 1-norm of the matrix. This is determined immediately before every factorization doublereal a1norm_; - - public: + //! Use the QR algorithm to factor and invert the matrix int useQR_; }; @@ -153,5 +287,3 @@ namespace Cantera { #endif - - diff --git a/Cantera/src/numerics/ctlapack.h b/Cantera/src/numerics/ctlapack.h index ea7083c1f..b1fae29b0 100644 --- a/Cantera/src/numerics/ctlapack.h +++ b/Cantera/src/numerics/ctlapack.h @@ -29,6 +29,7 @@ #define _DGETRS_ dgetrs #define _DGETRI_ dgetri #define _DGELSS_ dgelss +#define _DGBCON_ dgbcon #define _DGBSV_ dgbsv #define _DGBTRF_ dgbtrf #define _DGBTRS_ dgbtrs @@ -51,6 +52,7 @@ #define _DGETRS_ dgetrs_ #define _DGETRI_ dgetri_ #define _DGELSS_ dgelss_ +#define _DGBCON_ dgbcon_ #define _DGBSV_ dgbsv_ #define _DGBTRF_ dgbtrf_ #define _DGBTRS_ dgbtrs_ @@ -222,6 +224,16 @@ extern "C" { #endif +#ifdef LAPACK_FTN_STRING_LEN_AT_END + int _DGBCON_(const char *norm, const integer* n, integer *kl, integer *ku, doublereal* ab, const integer* ldab, + const integer *ipiv, const doublereal *anorm, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info, ftnlen nosize); +#else + int _DGBCON_(const char *norm, ftnlen nosize, const integer* n, integer *kl, integer *ku, doublereal* ab, const integer* ldab, + const integer *ipiv, const doublereal *anorm, const doublereal *rcond, + doublereal* work, const integer* iwork, integer *info); +#endif + #ifdef LAPACK_FTN_STRING_LEN_AT_END doublereal _DLANGE_(const char *norm, const integer* m, const integer* n, doublereal* a, const integer* lda, doublereal* work, ftnlen nosize); @@ -535,6 +547,37 @@ namespace Cantera { #else _DGECON_(&cnorm, trsize, &f_n, a, &f_lda, &anorm, &rcond, work, iwork, &f_info); #endif +#endif + info = f_info; + return rcond; + } + + //==================================================================================================================== + //! + /*! + */ + inline doublereal ct_dgbcon(const char norm, int n, int kl, int ku, doublereal* a, int ldab, int *ipiv, doublereal anorm, + doublereal* work, int *iwork, int &info) { + char cnorm = '1'; + if (norm) { + cnorm = norm; + } + integer f_n = n; + integer f_kl = kl; + integer f_ku = ku; + integer f_ldab = ldab; + integer f_info = info; + doublereal rcond; + +#ifdef NO_FTN_STRING_LEN_AT_END + _DGBCON_(&cnorm, &f_n , &f_kl, &f_ku, a, &f_ldab, ipiv, &anorm, &rcond, work, iwork, &f_info); +#else + ftnlen trsize = 1; +#ifdef LAPACK_FTN_STRING_LEN_AT_END + _DGBCON_(&cnorm, &f_n, &f_kl, &f_ku, a, &f_ldab, ipiv, &anorm, &rcond, work, iwork, &f_info, trsize); +#else + _DGBCON_(&cnorm, trsize, &f_n, &f_kl, &f_ku, a, &f_ldab, ipiv, &anorm, &rcond, work, iwork, &f_info); +#endif #endif info = f_info; return rcond; diff --git a/Cantera/src/oneD/MultiNewton.cpp b/Cantera/src/oneD/MultiNewton.cpp index e85f4da54..1f79e125f 100644 --- a/Cantera/src/oneD/MultiNewton.cpp +++ b/Cantera/src/oneD/MultiNewton.cpp @@ -133,7 +133,7 @@ namespace Cantera { } #endif - iok = jac.solve(sz, step, step); + iok = jac.solve(step, step); // if iok is non-zero, then solve failed if (iok > 0) { diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index 9a933701f..4cdc7580e 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -79,11 +79,13 @@ ELECTRO_H = MolalityVPSSTP.h VPStandardStateTP.h \ endif ifeq ($(do_issp),1) ISSP_OBJ = IdealSolidSolnPhase.o StoichSubstanceSSTP.o SingleSpeciesTP.o MineralEQ3.o \ - GibbsExcessVPSSTP.o PseudoBinaryVPSSTP.o MargulesVPSSTP.o \ - IonsFromNeutralVPSSTP.o PDSS_IonsFromNeutral.o FixedChemPotSSTP.o + GibbsExcessVPSSTP.o MolarityIonicVPSSTP.o MargulesVPSSTP.o \ + IonsFromNeutralVPSSTP.o PDSS_IonsFromNeutral.o FixedChemPotSSTP.o \ + MixedSolventElectrolyte.o ISSP_H = IdealSolidSolnPhase.h StoichSubstanceSSTP.h SingleSpeciesTP.h MineralEQ3.h \ - GibbsExcessVPSSTP.h PseudoBinaryVPSSTP.h MargulesVPSSTP.h \ - IonsFromNeutralVPSSTP.h PDSS_IonsFromNeutral.h FixedChemPotSSTP.h + GibbsExcessVPSSTP.h MolarityIonicVPSSTP.h MargulesVPSSTP.h \ + IonsFromNeutralVPSSTP.h PDSS_IonsFromNeutral.h FixedChemPotSSTP.h \ + MixedSolventElectrolyte.h endif CATHERMO_OBJ = $(THERMO_OBJ) $(ELECTRO_OBJ) $(ISSP_OBJ) diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 93adb082c..ebeb9d5e2 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -23,7 +23,7 @@ #ifndef CT_MARGULESVPSSTP_H #define CT_MARGULESVPSSTP_H -#include "PseudoBinaryVPSSTP.h" +#include "GibbsExcessVPSSTP.h" namespace Cantera { diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.cpp b/Cantera/src/thermo/MixedSolventElectrolyte.cpp index 64d4b9bd1..fc6edbfa4 100644 --- a/Cantera/src/thermo/MixedSolventElectrolyte.cpp +++ b/Cantera/src/thermo/MixedSolventElectrolyte.cpp @@ -31,7 +31,7 @@ namespace Cantera { * */ MixedSolventElectrolyte::MixedSolventElectrolyte() : - GibbsExcessVPSSTP(), + MolarityIonicVPSSTP(), numBinaryInteractions_(0), formMargules_(0), formTempModel_(0) @@ -48,7 +48,7 @@ namespace Cantera { */ MixedSolventElectrolyte::MixedSolventElectrolyte(std::string inputFile, std::string id) : - GibbsExcessVPSSTP(), + MolarityIonicVPSSTP(), numBinaryInteractions_(0), formMargules_(0), formTempModel_(0) @@ -57,7 +57,7 @@ namespace Cantera { } MixedSolventElectrolyte::MixedSolventElectrolyte(XML_Node& phaseRoot, std::string id) : - GibbsExcessVPSSTP(), + MolarityIonicVPSSTP(), numBinaryInteractions_(0), formMargules_(0), formTempModel_(0) @@ -73,7 +73,7 @@ namespace Cantera { * has a working copy constructor */ MixedSolventElectrolyte::MixedSolventElectrolyte(const MixedSolventElectrolyte &b) : - GibbsExcessVPSSTP() + MolarityIonicVPSSTP() { MixedSolventElectrolyte::operator=(b); } @@ -90,7 +90,7 @@ namespace Cantera { return *this; } - GibbsExcessVPSSTP::operator=(b); + MolarityIonicVPSSTP::operator=(b); numBinaryInteractions_ = b.numBinaryInteractions_ ; m_HE_b_ij = b.m_HE_b_ij; @@ -141,7 +141,7 @@ namespace Cantera { * */ MixedSolventElectrolyte::MixedSolventElectrolyte(int testProb) : - GibbsExcessVPSSTP(), + MolarityIonicVPSSTP(), numBinaryInteractions_(0), formMargules_(0), formTempModel_(0) @@ -659,7 +659,7 @@ namespace Cantera { */ void MixedSolventElectrolyte::initThermo() { initLengths(); - GibbsExcessVPSSTP::initThermo(); + MolarityIonicVPSSTP::initThermo(); } @@ -741,7 +741,7 @@ namespace Cantera { /* * Go down the chain */ - GibbsExcessVPSSTP::initThermoXML(phaseNode, id); + MolarityIonicVPSSTP::initThermoXML(phaseNode, id); } diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.h b/Cantera/src/thermo/MixedSolventElectrolyte.h index e91caaca2..7ffad1f05 100644 --- a/Cantera/src/thermo/MixedSolventElectrolyte.h +++ b/Cantera/src/thermo/MixedSolventElectrolyte.h @@ -23,7 +23,7 @@ #ifndef CT_MIXEDSOLVENTELECTROLYTEVPSSTP_H #define CT_MIXEDSOLVENTELECTROLYTEVPSSTP_H -#include "PseudoBinaryVPSSTP.h" +#include "MolarityIonicVPSSTP.h" namespace Cantera { @@ -311,7 +311,7 @@ namespace Cantera { * */ - class MixedSolventElectrolyte : public GibbsExcessVPSSTP { + class MixedSolventElectrolyte : public MolarityIonicVPSSTP { public: diff --git a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp similarity index 60% rename from Cantera/src/thermo/PseudoBinaryVPSSTP.cpp rename to Cantera/src/thermo/MolarityIonicVPSSTP.cpp index f909098a6..e657aea3d 100644 --- a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp @@ -1,9 +1,9 @@ /** - * @file PseudoBinaryVPSSTP.cpp + * @file MolarityIonicVPSSTP.cpp * Definitions for intermediate ThermoPhase object for phases which * employ excess gibbs free energy formulations * (see \ref thermoprops - * and class \link Cantera::PseudoBinaryVPSSTP PseudoBinaryVPSSTP\endlink). + * and class \link Cantera::MolarityIonicVPSSTP MolarityIonicVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating @@ -17,24 +17,24 @@ * U.S. Government retains certain rights in this software. */ /* - * $Date$ - * $Revision$ + * $Date: 2009-11-09 16:36:49 -0700 (Mon, 09 Nov 2009) $ + * $Revision: 255 $ */ -#include "PseudoBinaryVPSSTP.h" +#include "MolarityIonicVPSSTP.h" #include using namespace std; namespace Cantera { - + //==================================================================================================================== /* * Default constructor. * */ - PseudoBinaryVPSSTP::PseudoBinaryVPSSTP() : + MolarityIonicVPSSTP::MolarityIonicVPSSTP() : GibbsExcessVPSSTP(), PBType_(PBTYPE_PASSTHROUGH), numPBSpecies_(m_kk), @@ -42,19 +42,17 @@ namespace Cantera { numCationSpecies_(0), numAnionSpecies_(0), numPassThroughSpecies_(0), - neutralPBindexStart(0), - cationPhase_(0), - anionPhase_(0) + neutralPBindexStart(0) { } - + //==================================================================================================================== /* * Copy Constructor: * * Note this stuff will not work until the underlying phase * has a working copy constructor */ - PseudoBinaryVPSSTP::PseudoBinaryVPSSTP(const PseudoBinaryVPSSTP &b) : + MolarityIonicVPSSTP::MolarityIonicVPSSTP(const MolarityIonicVPSSTP &b) : GibbsExcessVPSSTP(), PBType_(PBTYPE_PASSTHROUGH), numPBSpecies_(m_kk), @@ -62,21 +60,19 @@ namespace Cantera { numCationSpecies_(0), numAnionSpecies_(0), numPassThroughSpecies_(0), - neutralPBindexStart(0), - cationPhase_(0), - anionPhase_(0) + neutralPBindexStart(0) { *this = operator=(b); } - + //==================================================================================================================== /* * operator=() * * Note this stuff will not work until the underlying phase * has a working assignment operator */ - PseudoBinaryVPSSTP& PseudoBinaryVPSSTP:: - operator=(const PseudoBinaryVPSSTP &b) { + MolarityIonicVPSSTP& MolarityIonicVPSSTP:: + operator=(const MolarityIonicVPSSTP &b) { if (&b != this) { GibbsExcessVPSSTP::operator=(b); } @@ -92,21 +88,19 @@ namespace Cantera { passThroughList_ = b.passThroughList_; numPassThroughSpecies_ = b.numPassThroughSpecies_; neutralPBindexStart = b.neutralPBindexStart; - cationPhase_ = b.cationPhase_; - anionPhase_ = b.anionPhase_; moleFractionsTmp_ = b.moleFractionsTmp_; return *this; } - + //==================================================================================================================== /** * - * ~PseudoBinaryVPSSTP(): (virtual) + * ~MolarityIonicVPSSTP(): (virtual) * * Destructor: does nothing: * */ - PseudoBinaryVPSSTP::~PseudoBinaryVPSSTP() { + MolarityIonicVPSSTP::~MolarityIonicVPSSTP() { } /* @@ -114,25 +108,25 @@ namespace Cantera { * a pointer to ThermoPhase. */ ThermoPhase* - PseudoBinaryVPSSTP::duplMyselfAsThermoPhase() const { - PseudoBinaryVPSSTP* mtp = new PseudoBinaryVPSSTP(*this); + MolarityIonicVPSSTP::duplMyselfAsThermoPhase() const { + MolarityIonicVPSSTP* mtp = new MolarityIonicVPSSTP(*this); return (ThermoPhase *) mtp; } /* * -------------- Utilities ------------------------------- */ - + //==================================================================================================================== // Equation of state type flag. /* * The ThermoPhase base class returns * zero. Subclasses should define this to return a unique * non-zero value. Known constants defined for this purpose are - * listed in mix_defs.h. The PseudoBinaryVPSSTP class also returns + * listed in mix_defs.h. The MolarityIonicVPSSTP class also returns * zero, as it is a non-complete class. */ - int PseudoBinaryVPSSTP::eosType() const { + int MolarityIonicVPSSTP::eosType() const { return 0; } @@ -147,32 +141,35 @@ namespace Cantera { * - Activities, Standard States, Activity Concentrations ----------- */ - - doublereal PseudoBinaryVPSSTP::standardConcentration(int k) const { + //==================================================================================================================== + doublereal MolarityIonicVPSSTP::standardConcentration(int k) const { err("standardConcentration"); return -1.0; } - - doublereal PseudoBinaryVPSSTP::logStandardConc(int k) const { + //==================================================================================================================== + doublereal MolarityIonicVPSSTP::logStandardConc(int k) const { err("logStandardConc"); return -1.0; } + //==================================================================================================================== - - - void PseudoBinaryVPSSTP::getElectrochemPotentials(doublereal* mu) const { + void MolarityIonicVPSSTP::getElectrochemPotentials(doublereal* mu) const { getChemPotentials(mu); double ve = Faraday * electricPotential(); for (int k = 0; k < m_kk; k++) { mu[k] += ve*charge(k); } } - - void PseudoBinaryVPSSTP::calcPseudoBinaryMoleFractions() const { + //==================================================================================================================== + void MolarityIonicVPSSTP::calcPseudoBinaryMoleFractions() const { int k; + int kCat; + int kMax; doublereal sumCat; doublereal sumAnion; + doublereal chP, chM; doublereal sum = 0.0; + doublereal sumMax; switch (PBType_) { case PBTYPE_PASSTHROUGH: for (k = 0; k < m_kk; k++) { @@ -185,26 +182,43 @@ namespace Cantera { for (k = 0; k < m_kk; k++) { moleFractionsTmp_[k] = moleFractions_[k]; } + kMax = -1; + sumMax = 0.0; for (k = 0; k < (int) cationList_.size(); k++) { - sumCat += moleFractions_[cationList_[k]]; + kCat = cationList_[k]; + chP = m_speciesCharge[kCat]; + if (moleFractions_[kCat] > sumMax) { + kMax = k; + sumMax = moleFractions_[kCat]; + } + sumCat += chP * moleFractions_[kCat]; + } + k = anionList_[0]; + chM = m_speciesCharge[k]; + sumAnion = moleFractions_[k] * chM; + sum = sumCat - sumAnion; + if (fabs(sum) > 1.0E-16) { + moleFractionsTmp_[cationList_[kMax]] -= sum / m_speciesCharge[kMax]; + sum = 0.0; + for (k = 0; k < numCationSpecies_; k++) { + sum += moleFractionsTmp_[k]; + } + for (k = 0; k < numCationSpecies_; k++) { + moleFractionsTmp_[k]/= sum; + } } - sumAnion = moleFractions_[anionList_[k]]; - PBMoleFractions_[0] = sumCat -sumAnion; - moleFractionsTmp_[indexSpecialSpecies_] -= PBMoleFractions_[0]; - for (k = 0; k < numCationSpecies_; k++) { - PBMoleFractions_[1+k] = moleFractionsTmp_[cationList_[k]]; + PBMoleFractions_[k] = moleFractionsTmp_[cationList_[k]]; } - for (k = 0; k < numPassThroughSpecies_; k++) { - PBMoleFractions_[neutralPBindexStart + k] = - moleFractions_[cationList_[k]]; + PBMoleFractions_[neutralPBindexStart + k] = moleFractions_[passThroughList_[k]]; } sum = fmaxx(0.0, PBMoleFractions_[0]); for (k = 1; k < numPBSpecies_; k++) { sum += PBMoleFractions_[k]; + } for (k = 0; k < numPBSpecies_; k++) { PBMoleFractions_[k] /= sum; @@ -226,19 +240,17 @@ namespace Cantera { } } - + //==================================================================================================================== /* * ------------ Partial Molar Properties of the Solution ------------ */ - - - doublereal PseudoBinaryVPSSTP::err(std::string msg) const { - throw CanteraError("PseudoBinaryVPSSTP","Base class method " + //==================================================================================================================== + doublereal MolarityIonicVPSSTP::err(std::string msg) const { + throw CanteraError("MolarityIonicVPSSTP","Base class method " +msg+" called. Equation of state type: "+int2str(eosType())); return 0; } - - + //==================================================================================================================== /* * @internal Initialize. This method is provided to allow * subclasses to perform any initialization required after all @@ -252,19 +264,49 @@ namespace Cantera { * * @see importCTML.cpp */ - void PseudoBinaryVPSSTP::initThermo() { - initLengths(); + void MolarityIonicVPSSTP::initThermo() { GibbsExcessVPSSTP::initThermo(); + initLengths(); + /* + * Go find the list of cations and anions + */ + double ch; + numCationSpecies_ = 0.0; + cationList_.clear(); + anionList_.clear(); + passThroughList_.clear(); + for (int k = 0; k < m_kk; k++) { + ch = m_speciesCharge[k]; + if (ch > 0.0) { + cationList_.push_back(k); + numCationSpecies_++; + } else if (ch < 0.0) { + anionList_.push_back(k); + numAnionSpecies_++; + } else { + passThroughList_.push_back(k); + numPassThroughSpecies_++; + } + } + numPBSpecies_ = numCationSpecies_ + numAnionSpecies_ - 1; + neutralPBindexStart = numPBSpecies_; + PBType_ = PBTYPE_MULTICATIONANION; + if (numAnionSpecies_ == 1) { + PBType_ = PBTYPE_SINGLEANION; + } else if (numCationSpecies_ == 1) { + PBType_ = PBTYPE_SINGLECATION; + } + if (numAnionSpecies_ == 0 && numCationSpecies_ == 0) { + PBType_ = PBTYPE_PASSTHROUGH; + } } - - - // Initialize lengths of local variables after all species have - // been identified. - void PseudoBinaryVPSSTP::initLengths() { + //==================================================================================================================== + // Initialize lengths of local variables after all species have been identified. + void MolarityIonicVPSSTP::initLengths() { m_kk = nSpecies(); - moleFractions_.resize(m_kk); + moleFractionsTmp_.resize(m_kk); } - + //==================================================================================================================== /* * initThermoXML() (virtual from ThermoPhase) * Import and initialize a ThermoPhase object @@ -280,18 +322,16 @@ namespace Cantera { * to see if phaseNode is pointing to the phase * with the correct id. */ - void PseudoBinaryVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { + void MolarityIonicVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { GibbsExcessVPSSTP::initThermoXML(phaseNode, id); } - - /** + //==================================================================================================================== + /* * Format a summary of the mixture state for output. */ - std::string PseudoBinaryVPSSTP::report(bool show_thermo) const { - - + std::string MolarityIonicVPSSTP::report(bool show_thermo) const { char p[800]; string s = ""; try { @@ -364,7 +404,6 @@ namespace Cantera { } return s; } - - + //==================================================================================================================== } diff --git a/Cantera/src/thermo/PseudoBinaryVPSSTP.h b/Cantera/src/thermo/MolarityIonicVPSSTP.h similarity index 84% rename from Cantera/src/thermo/PseudoBinaryVPSSTP.h rename to Cantera/src/thermo/MolarityIonicVPSSTP.h index 3cc9a9d5b..dd6c339e8 100644 --- a/Cantera/src/thermo/PseudoBinaryVPSSTP.h +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.h @@ -1,15 +1,15 @@ /** - * @file PseudoBinaryVPSSTP.h + * @file MolarityIonicVPSSTP.h * Header for intermediate ThermoPhase object for phases which * employ gibbs excess free energy based formulations * (see \ref thermoprops - * and class \link Cantera::gibbsExcessVPSSTP gibbsExcessVPSSTP\endlink). + * and class \link Cantera::MolarityIonicVPSSTP MolarityIonicVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based upon activities - * based on the molality scale. These include most of the methods for - * calculating liquid electrolyte thermodynamics. + * based on the molarity scale. In this class, we expect that there are + * ions, but they are treated on the molarity scale. */ /* * Copywrite (2006) Sandia Corporation. Under the terms of @@ -17,11 +17,11 @@ * U.S. Government retains certain rights in this software. */ /* - * $Id$ + * $Id: MolarityIonicVPSSTP.h 255 2009-11-09 23:36:49Z hkmoffa $ */ -#ifndef CT_PSEUDOBINARYVPSSTP_H -#define CT_PSEUDOBINARYVPSSTP_H +#ifndef CT_MOLARITYIONICVPSSTP_H +#define CT_MOLARITYIONICVPSSTP_H #include "GibbsExcessVPSSTP.h" @@ -32,22 +32,14 @@ namespace Cantera { */ /*! - * PseudoBinaryVPSSTP is a derived class of ThermoPhase + * MolarityIonicVPSSTP is a derived class of ThermoPhase * GibbsExcessVPSSTP that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based on * expressing the Excess Gibbs free energy as a function of - * the mole fractions (or pseudo mole fractions) of consitituents. - * This category is the workhorse for describing molten salts, - * solid-phase mixtures of semiconductors, and mixtures of miscible - * and semi-miscible compounds. - * - * It includes - * . regular solutions - * . Margueles expansions - * . NTRL equation - * . Wilson's equation - * . UNIQUAC equation of state. + * the mole fractions (or pseudo mole fractions) of the consitituents. + * This category is the workhorse for describing ionic systems which + * are not on the molality scale. * * This class adds additional functions onto the %ThermoPhase interface * that handles the calculation of the excess Gibbs free energy. The %ThermoPhase @@ -60,15 +52,14 @@ namespace Cantera { * symmetrical formulations. * * This layer will massage the mole fraction vector to implement - * cation and anion based mole numbers in an optional manner - * - * The way that it collects the cation and anion based mole numbers - * is via holding two extra ThermoPhase objects. These - * can include standard states for salts. - * + * cation and anion based mole numbers in an optional manner, such that + * it is expected that there exists a charge balance at all times. + * One of the ions must be a "special ion" in the sense that its' thermodynamic + * functions are set to zero, and the thermo functions of all other + * ions are based on a valuation relative to the special ion. * */ - class PseudoBinaryVPSSTP : public GibbsExcessVPSSTP { + class MolarityIonicVPSSTP : public GibbsExcessVPSSTP { public: @@ -81,7 +72,7 @@ namespace Cantera { * density conservation and therefore element conservation * is the more important principle to follow. */ - PseudoBinaryVPSSTP(); + MolarityIonicVPSSTP(); //! Copy constructor /*! @@ -90,17 +81,17 @@ namespace Cantera { * * @param b class to be copied */ - PseudoBinaryVPSSTP(const PseudoBinaryVPSSTP&b); + MolarityIonicVPSSTP(const MolarityIonicVPSSTP&b); /// Assignment operator /*! * * @param b class to be copied. */ - PseudoBinaryVPSSTP& operator=(const PseudoBinaryVPSSTP&b); + MolarityIonicVPSSTP& operator=(const MolarityIonicVPSSTP&b); /// Destructor. - virtual ~PseudoBinaryVPSSTP(); + virtual ~MolarityIonicVPSSTP(); //! Duplication routine for objects which inherit from ThermoPhase. /*! @@ -344,6 +335,13 @@ namespace Cantera { protected: + // Pseudobinary type + /*! + * PBTYPE_PASSTHROUGH All species are passthrough species + * PBTYPE_SINGLEANION there is only one anion in the mixture + * PBTYPE_SINGLECATION there is only one cation in the mixture + * PBTYPE_MULTICATIONANION Complex mixture + */ int PBType_; //! Number of pseudo binary species @@ -354,20 +352,20 @@ namespace Cantera { mutable std::vector PBMoleFractions_; + //! Vector of cation indecises in the mixture std::vector cationList_; + + //! Number of cations in the mixture int numCationSpecies_; - std::vectoranionList_; + std::vector anionList_; int numAnionSpecies_; std::vector passThroughList_; int numPassThroughSpecies_; int neutralPBindexStart; - ThermoPhase *cationPhase_; - ThermoPhase *anionPhase_; - mutable std::vector moleFractionsTmp_; private: diff --git a/Cantera/src/thermo/PureFluidPhase.cpp b/Cantera/src/thermo/PureFluidPhase.cpp index 7f1266f9e..0c30fe03e 100644 --- a/Cantera/src/thermo/PureFluidPhase.cpp +++ b/Cantera/src/thermo/PureFluidPhase.cpp @@ -354,7 +354,7 @@ namespace Cantera { void PureFluidPhase::getEnthalpy_RT_ref(doublereal *hrt) const { double psave = pressure(); double t = temperature(); - double pref = m_spthermo->refPressure(); + //double pref = m_spthermo->refPressure(); double plow = 1.0E-8; Set(tpx::TP, t, plow); getEnthalpy_RT(hrt); diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 9c3a13f52..ff9480d97 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -78,6 +78,8 @@ #include "HMWSoln.h" #include "DebyeHuckel.h" #include "IdealMolalSoln.h" +#include "MolarityIonicVPSSTP.h" +#include "MixedSolventElectrolyte.h" #endif #include "IdealSolnGasVPSS.h" @@ -97,7 +99,7 @@ namespace Cantera { /*! * @deprecated This entire structure could be replaced with a std::map */ - static int ntypes = 20; + static int ntypes = 22; //! Define the string name of the %ThermoPhase types that are handled by this factory routine static string _types[] = {"IdealGas", "Incompressible", @@ -106,7 +108,8 @@ namespace Cantera { "HMW", "IdealSolidSolution", "DebyeHuckel", "IdealMolalSolution", "IdealGasVPSS", "MineralEQ3", "MetalSHEelectrons", "Margules", "PhaseCombo_Interaction", - "IonsFromNeutralMolecule", "FixedChemPot" + "IonsFromNeutralMolecule", "FixedChemPot", "MolarityIonicVPSSTP", + "MixedSolventElectrolyte" }; //! Define the integer id of the %ThermoPhase types that are handled by this factory routine @@ -116,7 +119,8 @@ namespace Cantera { cHMW, cIdealSolidSolnPhase, cDebyeHuckel, cIdealMolalSoln, cVPSS_IdealGas, cMineralEQ3, cMetalSHEelectrons, - cMargulesVPSSTP, cPhaseCombo_Interaction, cIonsFromNeutral, cFixedChemPot + cMargulesVPSSTP, cPhaseCombo_Interaction, cIonsFromNeutral, cFixedChemPot, + cMolarityIonicVPSSTP, cMixedSolventElectrolyte }; /* diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index 3a4dec238..1aef185ea 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -79,6 +79,9 @@ namespace Cantera { const int cMargulesVPSSTP = 301; + const int cMolarityIonicVPSSTP = 401; + const int cMixedSolventElectrolyte = 402; + const int cPhaseCombo_Interaction = 305; const int cIonsFromNeutral = 2000; diff --git a/configure b/configure index ed3d01168..eafb4a6a6 100755 --- a/configure +++ b/configure @@ -308,7 +308,7 @@ ac_includes_default="\ # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' +ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS F77 FFLAGS LDFLAGS ac_ct_F77 EXEEXT OBJEXT FLIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS CPPFLAGS ac_ct_CXX use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS FC FCFLAGS ac_ct_FC FCLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' ac_subst_files='' # Initialize some variables set by options. @@ -749,6 +749,18 @@ ac_env_target_alias_set=${target_alias+set} ac_env_target_alias_value=$target_alias ac_cv_env_target_alias_set=${target_alias+set} ac_cv_env_target_alias_value=$target_alias +ac_env_F77_set=${F77+set} +ac_env_F77_value=$F77 +ac_cv_env_F77_set=${F77+set} +ac_cv_env_F77_value=$F77 +ac_env_FFLAGS_set=${FFLAGS+set} +ac_env_FFLAGS_value=$FFLAGS +ac_cv_env_FFLAGS_set=${FFLAGS+set} +ac_cv_env_FFLAGS_value=$FFLAGS +ac_env_LDFLAGS_set=${LDFLAGS+set} +ac_env_LDFLAGS_value=$LDFLAGS +ac_cv_env_LDFLAGS_set=${LDFLAGS+set} +ac_cv_env_LDFLAGS_value=$LDFLAGS ac_env_CXX_set=${CXX+set} ac_env_CXX_value=$CXX ac_cv_env_CXX_set=${CXX+set} @@ -757,10 +769,6 @@ ac_env_CXXFLAGS_set=${CXXFLAGS+set} ac_env_CXXFLAGS_value=$CXXFLAGS ac_cv_env_CXXFLAGS_set=${CXXFLAGS+set} ac_cv_env_CXXFLAGS_value=$CXXFLAGS -ac_env_LDFLAGS_set=${LDFLAGS+set} -ac_env_LDFLAGS_value=$LDFLAGS -ac_cv_env_LDFLAGS_set=${LDFLAGS+set} -ac_cv_env_LDFLAGS_value=$LDFLAGS ac_env_CPPFLAGS_set=${CPPFLAGS+set} ac_env_CPPFLAGS_value=$CPPFLAGS ac_cv_env_CPPFLAGS_set=${CPPFLAGS+set} @@ -777,14 +785,14 @@ ac_env_CXXCPP_set=${CXXCPP+set} ac_env_CXXCPP_value=$CXXCPP ac_cv_env_CXXCPP_set=${CXXCPP+set} ac_cv_env_CXXCPP_value=$CXXCPP -ac_env_F77_set=${F77+set} -ac_env_F77_value=$F77 -ac_cv_env_F77_set=${F77+set} -ac_cv_env_F77_value=$F77 -ac_env_FFLAGS_set=${FFLAGS+set} -ac_env_FFLAGS_value=$FFLAGS -ac_cv_env_FFLAGS_set=${FFLAGS+set} -ac_cv_env_FFLAGS_value=$FFLAGS +ac_env_FC_set=${FC+set} +ac_env_FC_value=$FC +ac_cv_env_FC_set=${FC+set} +ac_cv_env_FC_value=$FC +ac_env_FCFLAGS_set=${FCFLAGS+set} +ac_env_FCFLAGS_value=$FCFLAGS +ac_cv_env_FCFLAGS_set=${FCFLAGS+set} +ac_cv_env_FCFLAGS_value=$FCFLAGS # # Report the --help message. @@ -860,17 +868,19 @@ if test -n "$ac_init_help"; then cat <<\_ACEOF Some influential environment variables: - CXX C++ compiler command - CXXFLAGS C++ compiler flags + F77 Fortran 77 compiler command + FFLAGS Fortran 77 compiler flags LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory + CXX C++ compiler command + CXXFLAGS C++ compiler flags CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have headers in a nonstandard directory CC C compiler command CFLAGS C compiler flags CXXCPP C++ preprocessor - F77 Fortran 77 compiler command - FFLAGS Fortran 77 compiler flags + FC Fortran compiler command + FCFLAGS Fortran compiler flags Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. @@ -1303,6 +1313,726 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +ac_ext=f +ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' +ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_f77_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_F77+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$F77"; then + ac_cv_prog_F77="$F77" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_F77="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +F77=$ac_cv_prog_F77 +if test -n "$F77"; then + echo "$as_me:$LINENO: result: $F77" >&5 +echo "${ECHO_T}$F77" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$F77" && break + done +fi +if test -z "$F77"; then + ac_ct_F77=$F77 + for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_F77+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_F77"; then + ac_cv_prog_ac_ct_F77="$ac_ct_F77" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_F77="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_F77=$ac_cv_prog_ac_ct_F77 +if test -n "$ac_ct_F77"; then + echo "$as_me:$LINENO: result: $ac_ct_F77" >&5 +echo "${ECHO_T}$ac_ct_F77" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_F77" && break +done + + F77=$ac_ct_F77 +fi + + +# Provide some information about the compiler. +echo "$as_me:1410:" \ + "checking for Fortran 77 compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +rm -f a.out + +cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for Fortran 77 compiler default output file name" >&5 +echo $ECHO_N "checking for Fortran 77 compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: Fortran 77 compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: Fortran 77 compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the Fortran 77 compiler works" >&5 +echo $ECHO_N "checking whether the Fortran 77 compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run Fortran 77 compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run Fortran 77 compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +# If we don't use `.F' as extension, the preprocessor is not run on the +# input file. (Note that this only needs to work for GNU compilers.) +ac_save_ext=$ac_ext +ac_ext=F +echo "$as_me:$LINENO: checking whether we are using the GNU Fortran 77 compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU Fortran 77 compiler... $ECHO_C" >&6 +if test "${ac_cv_f77_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF + program main +#ifndef __GNUC__ + choke me +#endif + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_f77_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_f77_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_f77_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_f77_compiler_gnu" >&6 +ac_ext=$ac_save_ext +ac_test_FFLAGS=${FFLAGS+set} +ac_save_FFLAGS=$FFLAGS +FFLAGS= +echo "$as_me:$LINENO: checking whether $F77 accepts -g" >&5 +echo $ECHO_N "checking whether $F77 accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_f77_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + FFLAGS=-g +cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_f77_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_f77_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_f77_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_f77_g" >&5 +echo "${ECHO_T}$ac_cv_prog_f77_g" >&6 +if test "$ac_test_FFLAGS" = set; then + FFLAGS=$ac_save_FFLAGS +elif test $ac_cv_prog_f77_g = yes; then + if test "x$ac_cv_f77_compiler_gnu" = xyes; then + FFLAGS="-g -O2" + else + FFLAGS="-g" + fi +else + if test "x$ac_cv_f77_compiler_gnu" = xyes; then + FFLAGS="-O2" + else + FFLAGS= + fi +fi + +G77=`test $ac_compiler_gnu = yes && echo yes` +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +ac_ext=f +ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' +ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_f77_compiler_gnu +echo "$as_me:$LINENO: checking how to get verbose linking output from $F77" >&5 +echo $ECHO_N "checking how to get verbose linking output from $F77... $ECHO_C" >&6 +if test "${ac_cv_prog_f77_v+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_f77_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_f77_v= +# Try some options frequently used verbose output +for ac_verb in -v -verbose --verbose -V -\#\#\#; do + cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF + +# Compile and link our simple test program by passing a flag (argument +# 1 to this macro) to the Fortran compiler in order to get +# "verbose" output that we can then parse for the Fortran linker +# flags. +ac_save_FFLAGS=$FFLAGS +FFLAGS="$FFLAGS $ac_verb" +(eval echo $as_me:1787: \"$ac_link\") >&5 +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` +echo "$ac_f77_v_output" >&5 +FFLAGS=$ac_save_FFLAGS + +rm -f conftest* + +# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where +# /foo, /bar, and /baz are search directories for the Fortran linker. +# Here, we change these into -L/foo -L/bar -L/baz (and put it first): +ac_f77_v_output="`echo $ac_f77_v_output | + grep 'LPATH is:' | + sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + +case $ac_f77_v_output in + # If we are using xlf then replace all the commas with spaces. + *xlfentry*) + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/,/ /g'` ;; + + # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted + # $LIBS confuse us, and the libraries appear later in the output anyway). + *mGLOB_options_string*) + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + + # If we are using Cray Fortran then delete quotes. + # Use "\"" instead of '"' for font-lock-mode. + # FIXME: a more general fix for quoted arguments with spaces? + *cft90*) + ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; +esac + + + # look for -l* and *.a constructs in the output + for ac_arg in $ac_f77_v_output; do + case $ac_arg in + [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) + ac_cv_prog_f77_v=$ac_verb + break 2 ;; + esac + done +done +if test -z "$ac_cv_prog_f77_v"; then + { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $F77" >&5 +echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} +fi +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 +echo "$as_me: WARNING: compilation failed" >&2;} +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_f77_v" >&5 +echo "${ECHO_T}$ac_cv_prog_f77_v" >&6 +echo "$as_me:$LINENO: checking for Fortran libraries of $F77" >&5 +echo $ECHO_N "checking for Fortran libraries of $F77... $ECHO_C" >&6 +if test "${ac_cv_f77_libs+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test "x$FLIBS" != "x"; then + ac_cv_f77_libs="$FLIBS" # Let the user override the test. +else + +cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF + +# Compile and link our simple test program by passing a flag (argument +# 1 to this macro) to the Fortran compiler in order to get +# "verbose" output that we can then parse for the Fortran linker +# flags. +ac_save_FFLAGS=$FFLAGS +FFLAGS="$FFLAGS $ac_cv_prog_f77_v" +(eval echo $as_me:1865: \"$ac_link\") >&5 +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` +echo "$ac_f77_v_output" >&5 +FFLAGS=$ac_save_FFLAGS + +rm -f conftest* + +# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where +# /foo, /bar, and /baz are search directories for the Fortran linker. +# Here, we change these into -L/foo -L/bar -L/baz (and put it first): +ac_f77_v_output="`echo $ac_f77_v_output | + grep 'LPATH is:' | + sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + +case $ac_f77_v_output in + # If we are using xlf then replace all the commas with spaces. + *xlfentry*) + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/,/ /g'` ;; + + # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted + # $LIBS confuse us, and the libraries appear later in the output anyway). + *mGLOB_options_string*) + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + + # If we are using Cray Fortran then delete quotes. + # Use "\"" instead of '"' for font-lock-mode. + # FIXME: a more general fix for quoted arguments with spaces? + *cft90*) + ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; +esac + + + +ac_cv_f77_libs= + +# Save positional arguments (if any) +ac_save_positional="$@" + +set X $ac_f77_v_output +while test $# != 1; do + shift + ac_arg=$1 + case $ac_arg in + [\\/]*.a | ?:[\\/]*.a) + ac_exists=false + for ac_i in $ac_cv_f77_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" +fi + + ;; + -bI:*) + ac_exists=false + for ac_i in $ac_cv_f77_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + if test "$ac_compiler_gnu" = yes; then + for ac_link_opt in $ac_arg; do + ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" + done +else + ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" +fi +fi + + ;; + # Ignore these flags. + -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) + ;; + -lkernel32) + test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" + ;; + -[LRuY]) + # These flags, when seen by themselves, take an argument. + # We remove the space between option and argument and re-iterate + # unless we find an empty arg or a new option (starting with -) + case $2 in + "" | -*);; + *) + ac_arg="$ac_arg$2" + shift; shift + set X $ac_arg "$@" + ;; + esac + ;; + -YP,*) + for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do + ac_exists=false + for ac_i in $ac_cv_f77_libs; do + if test x"$ac_j" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_arg="$ac_arg $ac_j" + ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" +fi + + done + ;; + -[lLR]*) + ac_exists=false + for ac_i in $ac_cv_f77_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" +fi + + ;; + # Ignore everything else. + esac +done +# restore positional arguments +set X $ac_save_positional; shift + +# We only consider "LD_RUN_PATH" on Solaris systems. If this is seen, +# then we insist that the "run path" must be an absolute path (i.e. it +# must begin with a "/"). +case `(uname -sr) 2>/dev/null` in + "SunOS 5"*) + ac_ld_run_path=`echo $ac_f77_v_output | + sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` + test "x$ac_ld_run_path" != x && + if test "$ac_compiler_gnu" = yes; then + for ac_link_opt in $ac_ld_run_path; do + ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" + done +else + ac_cv_f77_libs="$ac_cv_f77_libs $ac_ld_run_path" +fi + ;; +esac +fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" + +fi +echo "$as_me:$LINENO: result: $ac_cv_f77_libs" >&5 +echo "${ECHO_T}$ac_cv_f77_libs" >&6 +FLIBS="$ac_cv_f77_libs" + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu ac_config_headers="$ac_config_headers config.h" @@ -1888,207 +2618,6 @@ ac_compiler=`set X $ac_compile; echo $2` echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ - -int -main () -{ - - ; - return 0; -} -_ACEOF -ac_clean_files_save=$ac_clean_files -ac_clean_files="$ac_clean_files a.out a.exe b.out" -# Try to create an executable without -o first, disregard a.out. -# It will help us diagnose broken compilers, and finding out an intuition -# of exeext. -echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5 -echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6 -ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` -if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 - (eval $ac_link_default) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - # Find the output, starting from the most likely. This scheme is -# not robust to junk in `.', hence go to wildcards (a.*) only as a last -# resort. - -# Be careful to initialize this variable, since it used to be cached. -# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. -ac_cv_exeext= -# b.out is created by i960 compilers. -for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out -do - test -f "$ac_file" || continue - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) - ;; - conftest.$ac_ext ) - # This is the source file. - ;; - [ab].out ) - # We found the default executable, but exeext='' is most - # certainly right. - break;; - *.* ) - ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - # FIXME: I believe we export ac_cv_exeext for Libtool, - # but it would be cool to find out if it's true. Does anybody - # maintain Libtool? --akim. - export ac_cv_exeext - break;; - * ) - break;; - esac -done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ { echo "$as_me:$LINENO: error: C++ compiler cannot create executables -See \`config.log' for more details." >&5 -echo "$as_me: error: C++ compiler cannot create executables -See \`config.log' for more details." >&2;} - { (exit 77); exit 77; }; } -fi - -ac_exeext=$ac_cv_exeext -echo "$as_me:$LINENO: result: $ac_file" >&5 -echo "${ECHO_T}$ac_file" >&6 - -# Check the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5 -echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6 -# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 -# If not cross compiling, check that we can run a simple program. -if test "$cross_compiling" != yes; then - if { ac_try='./$ac_file' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - cross_compiling=no - else - if test "$cross_compiling" = maybe; then - cross_compiling=yes - else - { { echo "$as_me:$LINENO: error: cannot run C++ compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run C++ compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } - fi - fi -fi -echo "$as_me:$LINENO: result: yes" >&5 -echo "${ECHO_T}yes" >&6 - -rm -f a.out a.exe conftest$ac_cv_exeext b.out -ac_clean_files=$ac_clean_files_save -# Check the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 -echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 -echo "$as_me:$LINENO: result: $cross_compiling" >&5 -echo "${ECHO_T}$cross_compiling" >&6 - -echo "$as_me:$LINENO: checking for suffix of executables" >&5 -echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - # If both `conftest.exe' and `conftest' are `present' (well, observable) -# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will -# work properly (i.e., refer to `conftest.exe'), while it won't with -# `rm'. -for ac_file in conftest.exe conftest conftest.*; do - test -f "$ac_file" || continue - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; - *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - export ac_cv_exeext - break;; - * ) break;; - esac -done -else - { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi - -rm -f conftest$ac_cv_exeext -echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 -echo "${ECHO_T}$ac_cv_exeext" >&6 - -rm -f conftest.$ac_ext -EXEEXT=$ac_cv_exeext -ac_exeext=$EXEEXT -echo "$as_me:$LINENO: checking for suffix of object files" >&5 -echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 -if test "${ac_cv_objext+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ - -int -main () -{ - - ; - return 0; -} -_ACEOF -rm -f conftest.o conftest.obj -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; - *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` - break;; - esac -done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi - -rm -f conftest.$ac_cv_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 -echo "${ECHO_T}$ac_cv_objext" >&6 -OBJEXT=$ac_cv_objext -ac_objext=$OBJEXT echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 if test "${ac_cv_cxx_compiler_gnu+set}" = set; then @@ -2991,6 +3520,7 @@ fi case $ac_sys_system in Linux) NEED_F2C=1 ;; esac +NEED_F2C= # # Create a variable build_f2c_lib that determines whether @@ -3002,7 +3532,7 @@ if test -n "$NEED_F2C" ; then build_f2c_lib=1 else case $ac_sys_system in - Linux) F2C_SYSTEMLIB="-lg2c" + Linux) F2C_SYSTEMLIB="" esac fi @@ -3142,7 +3672,7 @@ then RAW_LIBS_DEP=$RAW_LIBS_DEP' 'libctf2c.a else case $ac_sys_system in - Linux) LOCAL_LIBS=$LOCAL_LIBS' '-lg2c;; + Linux) LOCAL_LIBS=$LOCAL_LIBS;; esac fi # Darwin*) LOCAL_LIBS=$LOCAL_LIBS' '-lg2c;; @@ -9975,7 +10505,11 @@ echo 'checking for a strip symbol command ... ' $HAVE_STRIPSYMBOLS # Fortran #--------------------------------------------------------------------------- -#if test x"$build_with_f2c" = "x0"; then +# +# This macro sets the substitution variable, @F77@ and @G77@ +# +echo " this is $F77" +echo "this is a test" ac_ext=f ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10068,7 +10602,7 @@ fi # Provide some information about the compiler. -echo "$as_me:10071:" \ +echo "$as_me:10605:" \ "checking for Fortran 77 compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 @@ -10222,8 +10756,7 @@ else FFLAGS=$FFLAGS' -fno-second-underscore' fi fi - - +#F77LDRCLIBS= ac_ext=f ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10275,7 +10808,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10278: \"$ac_link\") >&5 +(eval echo $as_me:10811: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10353,7 +10886,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10356: \"$ac_link\") >&5 +(eval echo $as_me:10889: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10526,6 +11059,550 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +echo " Macro returned with FLIBS defined as " $FLIBS + + +# +ac_ext=${FC_SRCEXT-f} +ac_compile='$FC -c $FCFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext >&5' +ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_fc_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in f95 fort xlf95 ifc efc pgf95 lf95 gfortran f90 xlf90 pgf90 epcf90 g77 f77 xlf frt pgf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_FC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$FC"; then + ac_cv_prog_FC="$FC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_FC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +FC=$ac_cv_prog_FC +if test -n "$FC"; then + echo "$as_me:$LINENO: result: $FC" >&5 +echo "${ECHO_T}$FC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$FC" && break + done +fi +if test -z "$FC"; then + ac_ct_FC=$FC + for ac_prog in f95 fort xlf95 ifc efc pgf95 lf95 gfortran f90 xlf90 pgf90 epcf90 g77 f77 xlf frt pgf77 fort77 fl32 af77 +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_FC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_FC"; then + ac_cv_prog_ac_ct_FC="$ac_ct_FC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_FC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_FC=$ac_cv_prog_ac_ct_FC +if test -n "$ac_ct_FC"; then + echo "$as_me:$LINENO: result: $ac_ct_FC" >&5 +echo "${ECHO_T}$ac_ct_FC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_FC" && break +done + + FC=$ac_ct_FC +fi + + +# Provide some information about the compiler. +echo "$as_me:11158:" \ + "checking for Fortran compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +rm -f a.out + +# If we don't use `.F' as extension, the preprocessor is not run on the +# input file. (Note that this only needs to work for GNU compilers.) +ac_save_ext=$ac_ext +ac_ext=F +echo "$as_me:$LINENO: checking whether we are using the GNU Fortran compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU Fortran compiler... $ECHO_C" >&6 +if test "${ac_cv_fc_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF + program main +#ifndef __GNUC__ + choke me +#endif + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_fc_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_fc_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_fc_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_fc_compiler_gnu" >&6 +ac_ext=$ac_save_ext +ac_test_FFLAGS=${FCFLAGS+set} +ac_save_FFLAGS=$FCFLAGS +FCFLAGS= +echo "$as_me:$LINENO: checking whether $FC accepts -g" >&5 +echo $ECHO_N "checking whether $FC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_fc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + FCFLAGS=-g +cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_fc_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_fc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_fc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_fc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_fc_g" >&6 +if test "$ac_test_FFLAGS" = set; then + FCFLAGS=$ac_save_FFLAGS +elif test $ac_cv_prog_fc_g = yes; then + if test "x$ac_cv_fc_compiler_gnu" = xyes; then + FCFLAGS="-g -O2" + else + FCFLAGS="-g" + fi +else + if test "x$ac_cv_fc_compiler_gnu" = xyes; then + FCFLAGS="-O2" + else + FCFLAGS= + fi +fi + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +ac_ext=${FC_SRCEXT-f} +ac_compile='$FC -c $FCFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext >&5' +ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_fc_compiler_gnu +echo "$as_me:$LINENO: checking how to get verbose linking output from $FC" >&5 +echo $ECHO_N "checking how to get verbose linking output from $FC... $ECHO_C" >&6 +if test "${ac_cv_prog_fc_v+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_fc_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_fc_v= +# Try some options frequently used verbose output +for ac_verb in -v -verbose --verbose -V -\#\#\#; do + cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF + +# Compile and link our simple test program by passing a flag (argument +# 1 to this macro) to the Fortran compiler in order to get +# "verbose" output that we can then parse for the Fortran linker +# flags. +ac_save_FFLAGS=$FCFLAGS +FCFLAGS="$FCFLAGS $ac_verb" +(eval echo $as_me:11353: \"$ac_link\") >&5 +ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` +echo "$ac_fc_v_output" >&5 +FCFLAGS=$ac_save_FFLAGS + +rm -f conftest* + +# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where +# /foo, /bar, and /baz are search directories for the Fortran linker. +# Here, we change these into -L/foo -L/bar -L/baz (and put it first): +ac_fc_v_output="`echo $ac_fc_v_output | + grep 'LPATH is:' | + sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_fc_v_output" + +case $ac_fc_v_output in + # If we are using xlf then replace all the commas with spaces. + *xlfentry*) + ac_fc_v_output=`echo $ac_fc_v_output | sed 's/,/ /g'` ;; + + # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted + # $LIBS confuse us, and the libraries appear later in the output anyway). + *mGLOB_options_string*) + ac_fc_v_output=`echo $ac_fc_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + + # If we are using Cray Fortran then delete quotes. + # Use "\"" instead of '"' for font-lock-mode. + # FIXME: a more general fix for quoted arguments with spaces? + *cft90*) + ac_fc_v_output=`echo $ac_fc_v_output | sed "s/\"//g"` ;; +esac + + + # look for -l* and *.a constructs in the output + for ac_arg in $ac_fc_v_output; do + case $ac_arg in + [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) + ac_cv_prog_fc_v=$ac_verb + break 2 ;; + esac + done +done +if test -z "$ac_cv_prog_fc_v"; then + { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $FC" >&5 +echo "$as_me: WARNING: cannot determine how to obtain linking information from $FC" >&2;} +fi +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 +echo "$as_me: WARNING: compilation failed" >&2;} +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_fc_v" >&5 +echo "${ECHO_T}$ac_cv_prog_fc_v" >&6 +echo "$as_me:$LINENO: checking for Fortran libraries of $FC" >&5 +echo $ECHO_N "checking for Fortran libraries of $FC... $ECHO_C" >&6 +if test "${ac_cv_fc_libs+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test "x$FCLIBS" != "x"; then + ac_cv_fc_libs="$FCLIBS" # Let the user override the test. +else + +cat >conftest.$ac_ext <<_ACEOF + program main + + end +_ACEOF + +# Compile and link our simple test program by passing a flag (argument +# 1 to this macro) to the Fortran compiler in order to get +# "verbose" output that we can then parse for the Fortran linker +# flags. +ac_save_FFLAGS=$FCFLAGS +FCFLAGS="$FCFLAGS $ac_cv_prog_fc_v" +(eval echo $as_me:11431: \"$ac_link\") >&5 +ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` +echo "$ac_fc_v_output" >&5 +FCFLAGS=$ac_save_FFLAGS + +rm -f conftest* + +# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where +# /foo, /bar, and /baz are search directories for the Fortran linker. +# Here, we change these into -L/foo -L/bar -L/baz (and put it first): +ac_fc_v_output="`echo $ac_fc_v_output | + grep 'LPATH is:' | + sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_fc_v_output" + +case $ac_fc_v_output in + # If we are using xlf then replace all the commas with spaces. + *xlfentry*) + ac_fc_v_output=`echo $ac_fc_v_output | sed 's/,/ /g'` ;; + + # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted + # $LIBS confuse us, and the libraries appear later in the output anyway). + *mGLOB_options_string*) + ac_fc_v_output=`echo $ac_fc_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + + # If we are using Cray Fortran then delete quotes. + # Use "\"" instead of '"' for font-lock-mode. + # FIXME: a more general fix for quoted arguments with spaces? + *cft90*) + ac_fc_v_output=`echo $ac_fc_v_output | sed "s/\"//g"` ;; +esac + + + +ac_cv_fc_libs= + +# Save positional arguments (if any) +ac_save_positional="$@" + +set X $ac_fc_v_output +while test $# != 1; do + shift + ac_arg=$1 + case $ac_arg in + [\\/]*.a | ?:[\\/]*.a) + ac_exists=false + for ac_i in $ac_cv_fc_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" +fi + + ;; + -bI:*) + ac_exists=false + for ac_i in $ac_cv_fc_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + if test "$ac_compiler_gnu" = yes; then + for ac_link_opt in $ac_arg; do + ac_cv_fc_libs="$ac_cv_fc_libs -Xlinker $ac_link_opt" + done +else + ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" +fi +fi + + ;; + # Ignore these flags. + -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) + ;; + -lkernel32) + test x"$CYGWIN" != xyes && ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" + ;; + -[LRuY]) + # These flags, when seen by themselves, take an argument. + # We remove the space between option and argument and re-iterate + # unless we find an empty arg or a new option (starting with -) + case $2 in + "" | -*);; + *) + ac_arg="$ac_arg$2" + shift; shift + set X $ac_arg "$@" + ;; + esac + ;; + -YP,*) + for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do + ac_exists=false + for ac_i in $ac_cv_fc_libs; do + if test x"$ac_j" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_arg="$ac_arg $ac_j" + ac_cv_fc_libs="$ac_cv_fc_libs $ac_j" +fi + + done + ;; + -[lLR]*) + ac_exists=false + for ac_i in $ac_cv_fc_libs; do + if test x"$ac_arg" = x"$ac_i"; then + ac_exists=true + break + fi + done + + if test x"$ac_exists" = xtrue; then + : +else + ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" +fi + + ;; + # Ignore everything else. + esac +done +# restore positional arguments +set X $ac_save_positional; shift + +# We only consider "LD_RUN_PATH" on Solaris systems. If this is seen, +# then we insist that the "run path" must be an absolute path (i.e. it +# must begin with a "/"). +case `(uname -sr) 2>/dev/null` in + "SunOS 5"*) + ac_ld_run_path=`echo $ac_fc_v_output | + sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` + test "x$ac_ld_run_path" != x && + if test "$ac_compiler_gnu" = yes; then + for ac_link_opt in $ac_ld_run_path; do + ac_cv_fc_libs="$ac_cv_fc_libs -Xlinker $ac_link_opt" + done +else + ac_cv_fc_libs="$ac_cv_fc_libs $ac_ld_run_path" +fi + ;; +esac +fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" + +fi +echo "$as_me:$LINENO: result: $ac_cv_fc_libs" >&5 +echo "${ECHO_T}$ac_cv_fc_libs" >&6 +FCLIBS="$ac_cv_fc_libs" + + +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +echo 'FLIBS = ' $FLIBS + override_f77_libs=0; #case $ac_sys_system in @@ -10704,7 +11781,6 @@ F90BUILDFLAGS=${f90buildopts}' '${savef90flags} - # filename extensions for Fortran 77 if test -z "$F77_EXT"; then F77_EXT=f; fi @@ -11577,6 +12653,13 @@ s,@ECHO_C@,$ECHO_C,;t t s,@ECHO_N@,$ECHO_N,;t t s,@ECHO_T@,$ECHO_T,;t t s,@LIBS@,$LIBS,;t t +s,@F77@,$F77,;t t +s,@FFLAGS@,$FFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@ac_ct_F77@,$ac_ct_F77,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@FLIBS@,$FLIBS,;t t s,@BITCOMPILE@,$BITCOMPILE,;t t s,@BITHARDWARE@,$BITHARDWARE,;t t s,@BITCHANGE@,$BITCHANGE,;t t @@ -11627,11 +12710,8 @@ s,@USERDIR@,$USERDIR,;t t s,@INCL_USER_CODE@,$INCL_USER_CODE,;t t s,@CXX@,$CXX,;t t s,@CXXFLAGS@,$CXXFLAGS,;t t -s,@LDFLAGS@,$LDFLAGS,;t t s,@CPPFLAGS@,$CPPFLAGS,;t t s,@ac_ct_CXX@,$ac_ct_CXX,;t t -s,@EXEEXT@,$EXEEXT,;t t -s,@OBJEXT@,$OBJEXT,;t t s,@use_sundials@,$use_sundials,;t t s,@CVODE_LIBS@,$CVODE_LIBS,;t t s,@IDA_LIBS@,$IDA_LIBS,;t t @@ -11704,10 +12784,10 @@ s,@CXX_INCLUDES@,$CXX_INCLUDES,;t t s,@LCXX_FLAGS@,$LCXX_FLAGS,;t t s,@LCXX_END_LIBS@,$LCXX_END_LIBS,;t t s,@HAVE_STRIPSYMBOLS@,$HAVE_STRIPSYMBOLS,;t t -s,@F77@,$F77,;t t -s,@FFLAGS@,$FFLAGS,;t t -s,@ac_ct_F77@,$ac_ct_F77,;t t -s,@FLIBS@,$FLIBS,;t t +s,@FC@,$FC,;t t +s,@FCFLAGS@,$FCFLAGS,;t t +s,@ac_ct_FC@,$ac_ct_FC,;t t +s,@FCLIBS@,$FCLIBS,;t t s,@F90@,$F90,;t t s,@BUILD_F90@,$BUILD_F90,;t t s,@F90FLAGS@,$F90FLAGS,;t t diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index 789deaf44..f3f3a4dab 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -798,7 +798,13 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ RootFind.h \ RootFind.cpp \ NonlinearSolver.h \ - NonlinearSolver.cpp + NonlinearSolver.cpp \ + BandMatrix.h \ + BandMatrix.cpp \ + GeneralMatrix.h \ + GeneralMatrix.cpp \ + SquareMatrix.h \ + SquareMatrix.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. diff --git a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy index 32760d503..7ab813602 100755 --- a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy +++ b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy @@ -85,6 +85,9 @@ export CC F77='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/gfortran' export F77 +FFLAGS="-g -fno-second-underscore" +export FFLAGS + CFLAGS="-g -Wall" export CFLAGS diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in index 16c2f1a14..4b0e77110 100755 --- a/ext/f2c_lapack/Makefile.in +++ b/ext/f2c_lapack/Makefile.in @@ -111,6 +111,9 @@ dtrtrs.o \ dgecon.o \ dgeequ.o \ dgerfs.o \ +dgbcon.o \ +dgbequ.o \ +dlatbs.o \ ieeeck.o \ ilaenv.o diff --git a/ext/f2c_lapack/dgbcon.c b/ext/f2c_lapack/dgbcon.c new file mode 100644 index 000000000..72083f759 --- /dev/null +++ b/ext/f2c_lapack/dgbcon.c @@ -0,0 +1,283 @@ +/* dgbcon.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; + +/* Subroutine */ int dgbcon_(char *norm, integer *n, integer *kl, integer *ku, + doublereal *ab, integer *ldab, integer *ipiv, doublereal *anorm, + doublereal *rcond, doublereal *work, integer *iwork, integer *info, + ftnlen norm_len) +{ + /* System generated locals */ + integer ab_dim1, ab_offset, i__1, i__2, i__3; + doublereal d__1; + + /* Local variables */ + static integer j; + static doublereal t; + static integer kd, lm, jp, ix, kase; + extern doublereal ddot_(integer *, doublereal *, integer *, doublereal *, + integer *); + static integer kase1; + static doublereal scale; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + extern /* Subroutine */ int drscl_(integer *, doublereal *, doublereal *, + integer *); + static logical lnoti; + extern /* Subroutine */ int daxpy_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int dlacon_(integer *, doublereal *, doublereal *, + integer *, doublereal *, integer *); + extern integer idamax_(integer *, doublereal *, integer *); + extern /* Subroutine */ int dlatbs_(char *, char *, char *, char *, + integer *, integer *, doublereal *, integer *, doublereal *, + doublereal *, doublereal *, integer *, ftnlen, ftnlen, ftnlen, + ftnlen), xerbla_(char *, integer *, ftnlen); + static doublereal ainvnm; + static logical onenrm; + static char normin[1]; + static doublereal smlnum; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* September 30, 1994 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DGBCON estimates the reciprocal of the condition number of a real */ +/* general band matrix A, in either the 1-norm or the infinity-norm, */ +/* using the LU factorization computed by DGBTRF. */ + +/* An estimate is obtained for norm(inv(A)), and the reciprocal of the */ +/* condition number is computed as */ +/* RCOND = 1 / ( norm(A) * norm(inv(A)) ). */ + +/* Arguments */ +/* ========= */ + +/* NORM (input) CHARACTER*1 */ +/* Specifies whether the 1-norm condition number or the */ +/* infinity-norm condition number is required: */ +/* = '1' or 'O': 1-norm; */ +/* = 'I': Infinity-norm. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* KL (input) INTEGER */ +/* The number of subdiagonals within the band of A. KL >= 0. */ + +/* KU (input) INTEGER */ +/* The number of superdiagonals within the band of A. KU >= 0. */ + +/* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) */ +/* Details of the LU factorization of the band matrix A, as */ +/* computed by DGBTRF. U is stored as an upper triangular band */ +/* matrix with KL+KU superdiagonals in rows 1 to KL+KU+1, and */ +/* the multipliers used during the factorization are stored in */ +/* rows KL+KU+2 to 2*KL+KU+1. */ + +/* LDAB (input) INTEGER */ +/* The leading dimension of the array AB. LDAB >= 2*KL+KU+1. */ + +/* IPIV (input) INTEGER array, dimension (N) */ +/* The pivot indices; for 1 <= i <= N, row i of the matrix was */ +/* interchanged with row IPIV(i). */ + +/* ANORM (input) DOUBLE PRECISION */ +/* If NORM = '1' or 'O', the 1-norm of the original matrix A. */ +/* If NORM = 'I', the infinity-norm of the original matrix A. */ + +/* RCOND (output) DOUBLE PRECISION */ +/* The reciprocal of the condition number of the matrix A, */ +/* computed as RCOND = 1/(norm(A) * norm(inv(A))). */ + +/* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) */ + +/* IWORK (workspace) INTEGER array, dimension (N) */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters. */ + + /* Parameter adjustments */ + ab_dim1 = *ldab; + ab_offset = 1 + ab_dim1; + ab -= ab_offset; + --ipiv; + --work; + --iwork; + + /* Function Body */ + *info = 0; + onenrm = *(unsigned char *)norm == '1' || lsame_(norm, "O", (ftnlen)1, ( + ftnlen)1); + if (! onenrm && ! lsame_(norm, "I", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*kl < 0) { + *info = -3; + } else if (*ku < 0) { + *info = -4; + } else if (*ldab < (*kl << 1) + *ku + 1) { + *info = -6; + } else if (*anorm < 0.) { + *info = -8; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DGBCON", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + *rcond = 0.; + if (*n == 0) { + *rcond = 1.; + return 0; + } else if (*anorm == 0.) { + return 0; + } + + smlnum = dlamch_("Safe minimum", (ftnlen)12); + +/* Estimate the norm of inv(A). */ + + ainvnm = 0.; + *(unsigned char *)normin = 'N'; + if (onenrm) { + kase1 = 1; + } else { + kase1 = 2; + } + kd = *kl + *ku + 1; + lnoti = *kl > 0; + kase = 0; +L10: + dlacon_(n, &work[*n + 1], &work[1], &iwork[1], &ainvnm, &kase); + if (kase != 0) { + if (kase == kase1) { + +/* Multiply by inv(L). */ + + if (lnoti) { + i__1 = *n - 1; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + i__2 = *kl, i__3 = *n - j; + lm = min(i__2,i__3); + jp = ipiv[j]; + t = work[jp]; + if (jp != j) { + work[jp] = work[j]; + work[j] = t; + } + d__1 = -t; + daxpy_(&lm, &d__1, &ab[kd + 1 + j * ab_dim1], &c__1, & + work[j + 1], &c__1); +/* L20: */ + } + } + +/* Multiply by inv(U). */ + + i__1 = *kl + *ku; + dlatbs_("Upper", "No transpose", "Non-unit", normin, n, &i__1, & + ab[ab_offset], ldab, &work[1], &scale, &work[(*n << 1) + + 1], info, (ftnlen)5, (ftnlen)12, (ftnlen)8, (ftnlen)1); + } else { + +/* Multiply by inv(U'). */ + + i__1 = *kl + *ku; + dlatbs_("Upper", "Transpose", "Non-unit", normin, n, &i__1, &ab[ + ab_offset], ldab, &work[1], &scale, &work[(*n << 1) + 1], + info, (ftnlen)5, (ftnlen)9, (ftnlen)8, (ftnlen)1); + +/* Multiply by inv(L'). */ + + if (lnoti) { + for (j = *n - 1; j >= 1; --j) { +/* Computing MIN */ + i__1 = *kl, i__2 = *n - j; + lm = min(i__1,i__2); + work[j] -= ddot_(&lm, &ab[kd + 1 + j * ab_dim1], &c__1, & + work[j + 1], &c__1); + jp = ipiv[j]; + if (jp != j) { + t = work[jp]; + work[jp] = work[j]; + work[j] = t; + } +/* L30: */ + } + } + } + +/* Divide X by 1/SCALE if doing so will not cause overflow. */ + + *(unsigned char *)normin = 'Y'; + if (scale != 1.) { + ix = idamax_(n, &work[1], &c__1); + if (scale < (d__1 = work[ix], abs(d__1)) * smlnum || scale == 0.) + { + goto L40; + } + drscl_(n, &scale, &work[1], &c__1); + } + goto L10; + } + +/* Compute the estimate of the reciprocal condition number. */ + + if (ainvnm != 0.) { + *rcond = 1. / ainvnm / *anorm; + } + +L40: + return 0; + +/* End of DGBCON */ + +} /* dgbcon_ */ + diff --git a/ext/f2c_lapack/dgbequ.c b/ext/f2c_lapack/dgbequ.c new file mode 100644 index 000000000..1c26aadfd --- /dev/null +++ b/ext/f2c_lapack/dgbequ.c @@ -0,0 +1,321 @@ +/* dgbequ.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Subroutine */ int dgbequ_(integer *m, integer *n, integer *kl, integer *ku, + doublereal *ab, integer *ldab, doublereal *r__, doublereal *c__, + doublereal *rowcnd, doublereal *colcnd, doublereal *amax, integer * + info) +{ + /* System generated locals */ + integer ab_dim1, ab_offset, i__1, i__2, i__3, i__4; + doublereal d__1, d__2, d__3; + + /* Local variables */ + static integer i__, j, kd; + static doublereal rcmin, rcmax; + extern doublereal dlamch_(char *, ftnlen); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + static doublereal bignum, smlnum; + + +/* -- LAPACK routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* March 31, 1993 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DGBEQU computes row and column scalings intended to equilibrate an */ +/* M-by-N band matrix A and reduce its condition number. R returns the */ +/* row scale factors and C the column scale factors, chosen to try to */ +/* make the largest element in each row and column of the matrix B with */ +/* elements B(i,j)=R(i)*A(i,j)*C(j) have absolute value 1. */ + +/* R(i) and C(j) are restricted to be between SMLNUM = smallest safe */ +/* number and BIGNUM = largest safe number. Use of these scaling */ +/* factors is not guaranteed to reduce the condition number of A but */ +/* works well in practice. */ + +/* Arguments */ +/* ========= */ + +/* M (input) INTEGER */ +/* The number of rows of the matrix A. M >= 0. */ + +/* N (input) INTEGER */ +/* The number of columns of the matrix A. N >= 0. */ + +/* KL (input) INTEGER */ +/* The number of subdiagonals within the band of A. KL >= 0. */ + +/* KU (input) INTEGER */ +/* The number of superdiagonals within the band of A. KU >= 0. */ + +/* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) */ +/* The band matrix A, stored in rows 1 to KL+KU+1. The j-th */ +/* column of A is stored in the j-th column of the array AB as */ +/* follows: */ +/* AB(ku+1+i-j,j) = A(i,j) for max(1,j-ku)<=i<=min(m,j+kl). */ + +/* LDAB (input) INTEGER */ +/* The leading dimension of the array AB. LDAB >= KL+KU+1. */ + +/* R (output) DOUBLE PRECISION array, dimension (M) */ +/* If INFO = 0, or INFO > M, R contains the row scale factors */ +/* for A. */ + +/* C (output) DOUBLE PRECISION array, dimension (N) */ +/* If INFO = 0, C contains the column scale factors for A. */ + +/* ROWCND (output) DOUBLE PRECISION */ +/* If INFO = 0 or INFO > M, ROWCND contains the ratio of the */ +/* smallest R(i) to the largest R(i). If ROWCND >= 0.1 and */ +/* AMAX is neither too large nor too small, it is not worth */ +/* scaling by R. */ + +/* COLCND (output) DOUBLE PRECISION */ +/* If INFO = 0, COLCND contains the ratio of the smallest */ +/* C(i) to the largest C(i). If COLCND >= 0.1, it is not */ +/* worth scaling by C. */ + +/* AMAX (output) DOUBLE PRECISION */ +/* Absolute value of largest matrix element. If AMAX is very */ +/* close to overflow or very close to underflow, the matrix */ +/* should be scaled. */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -i, the i-th argument had an illegal value */ +/* > 0: if INFO = i, and i is */ +/* <= M: the i-th row of A is exactly zero */ +/* > M: the (i-M)-th column of A is exactly zero */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + +/* Test the input parameters */ + + /* Parameter adjustments */ + ab_dim1 = *ldab; + ab_offset = 1 + ab_dim1; + ab -= ab_offset; + --r__; + --c__; + + /* Function Body */ + *info = 0; + if (*m < 0) { + *info = -1; + } else if (*n < 0) { + *info = -2; + } else if (*kl < 0) { + *info = -3; + } else if (*ku < 0) { + *info = -4; + } else if (*ldab < *kl + *ku + 1) { + *info = -6; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DGBEQU", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*m == 0 || *n == 0) { + *rowcnd = 1.; + *colcnd = 1.; + *amax = 0.; + return 0; + } + +/* Get machine constants. */ + + smlnum = dlamch_("S", (ftnlen)1); + bignum = 1. / smlnum; + +/* Compute row scale factors. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + r__[i__] = 0.; +/* L10: */ + } + +/* Find the maximum element in each row. */ + + kd = *ku + 1; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MAX */ + i__2 = j - *ku; +/* Computing MIN */ + i__4 = j + *kl; + i__3 = min(i__4,*m); + for (i__ = max(i__2,1); i__ <= i__3; ++i__) { +/* Computing MAX */ + d__2 = r__[i__], d__3 = (d__1 = ab[kd + i__ - j + j * ab_dim1], + abs(d__1)); + r__[i__] = max(d__2,d__3); +/* L20: */ + } +/* L30: */ + } + +/* Find the maximum and minimum scale factors. */ + + rcmin = bignum; + rcmax = 0.; + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { +/* Computing MAX */ + d__1 = rcmax, d__2 = r__[i__]; + rcmax = max(d__1,d__2); +/* Computing MIN */ + d__1 = rcmin, d__2 = r__[i__]; + rcmin = min(d__1,d__2); +/* L40: */ + } + *amax = rcmax; + + if (rcmin == 0.) { + +/* Find the first zero scale factor and return an error code. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { + if (r__[i__] == 0.) { + *info = i__; + return 0; + } +/* L50: */ + } + } else { + +/* Invert the scale factors. */ + + i__1 = *m; + for (i__ = 1; i__ <= i__1; ++i__) { +/* Computing MIN */ +/* Computing MAX */ + d__2 = r__[i__]; + d__1 = max(d__2,smlnum); + r__[i__] = 1. / min(d__1,bignum); +/* L60: */ + } + +/* Compute ROWCND = min(R(I)) / max(R(I)) */ + + *rowcnd = max(rcmin,smlnum) / min(rcmax,bignum); + } + +/* Compute column scale factors */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + c__[j] = 0.; +/* L70: */ + } + +/* Find the maximum element in each column, */ +/* assuming the row scaling computed above. */ + + kd = *ku + 1; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MAX */ + i__3 = j - *ku; +/* Computing MIN */ + i__4 = j + *kl; + i__2 = min(i__4,*m); + for (i__ = max(i__3,1); i__ <= i__2; ++i__) { +/* Computing MAX */ + d__2 = c__[j], d__3 = (d__1 = ab[kd + i__ - j + j * ab_dim1], abs( + d__1)) * r__[i__]; + c__[j] = max(d__2,d__3); +/* L80: */ + } +/* L90: */ + } + +/* Find the maximum and minimum scale factors. */ + + rcmin = bignum; + rcmax = 0.; + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + d__1 = rcmin, d__2 = c__[j]; + rcmin = min(d__1,d__2); +/* Computing MAX */ + d__1 = rcmax, d__2 = c__[j]; + rcmax = max(d__1,d__2); +/* L100: */ + } + + if (rcmin == 0.) { + +/* Find the first zero scale factor and return an error code. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { + if (c__[j] == 0.) { + *info = *m + j; + return 0; + } +/* L110: */ + } + } else { + +/* Invert the scale factors. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ +/* Computing MAX */ + d__2 = c__[j]; + d__1 = max(d__2,smlnum); + c__[j] = 1. / min(d__1,bignum); +/* L120: */ + } + +/* Compute COLCND = min(C(J)) / max(C(J)) */ + + *colcnd = max(rcmin,smlnum) / min(rcmax,bignum); + } + + return 0; + +/* End of DGBEQU */ + +} /* dgbequ_ */ + diff --git a/ext/f2c_lapack/dlatbs.c b/ext/f2c_lapack/dlatbs.c new file mode 100644 index 000000000..eaea649f4 --- /dev/null +++ b/ext/f2c_lapack/dlatbs.c @@ -0,0 +1,855 @@ +/* dlatbs.f -- translated by f2c (version 20031025). + You must link the resulting object file with libf2c: + on Microsoft Windows system, link with libf2c.lib; + on Linux or Unix systems, link with .../path/to/libf2c.a -lm + or, if you install libf2c.a in a standard place, with -lf2c -lm + -- in that order, at the end of the command line, as in + cc *.o -lf2c -lm + Source for libf2c is in /netlib/f2c/libf2c.zip, e.g., + + http://www.netlib.org/f2c/libf2c.zip +*/ + +#include "f2c.h" + +/* Table of constant values */ + +static integer c__1 = 1; +static doublereal c_b36 = .5; + +/* Subroutine */ int dlatbs_(char *uplo, char *trans, char *diag, char * + normin, integer *n, integer *kd, doublereal *ab, integer *ldab, + doublereal *x, doublereal *scale, doublereal *cnorm, integer *info, + ftnlen uplo_len, ftnlen trans_len, ftnlen diag_len, ftnlen normin_len) +{ + /* System generated locals */ + integer ab_dim1, ab_offset, i__1, i__2, i__3, i__4; + doublereal d__1, d__2, d__3; + + /* Local variables */ + static integer i__, j; + static doublereal xj, rec, tjj; + static integer jinc, jlen; + extern doublereal ddot_(integer *, doublereal *, integer *, doublereal *, + integer *); + static doublereal xbnd; + static integer imax; + static doublereal tmax, tjjs, xmax, grow, sumj; + extern /* Subroutine */ int dscal_(integer *, doublereal *, doublereal *, + integer *); + static integer maind; + extern logical lsame_(char *, char *, ftnlen, ftnlen); + static doublereal tscal, uscal; + extern doublereal dasum_(integer *, doublereal *, integer *); + static integer jlast; + extern /* Subroutine */ int dtbsv_(char *, char *, char *, integer *, + integer *, doublereal *, integer *, doublereal *, integer *, + ftnlen, ftnlen, ftnlen), daxpy_(integer *, doublereal *, + doublereal *, integer *, doublereal *, integer *); + static logical upper; + extern doublereal dlamch_(char *, ftnlen); + extern integer idamax_(integer *, doublereal *, integer *); + extern /* Subroutine */ int xerbla_(char *, integer *, ftnlen); + static doublereal bignum; + static logical notran; + static integer jfirst; + static doublereal smlnum; + static logical nounit; + + +/* -- LAPACK auxiliary routine (version 3.0) -- */ +/* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., */ +/* Courant Institute, Argonne National Lab, and Rice University */ +/* June 30, 1992 */ + +/* .. Scalar Arguments .. */ +/* .. */ +/* .. Array Arguments .. */ +/* .. */ + +/* Purpose */ +/* ======= */ + +/* DLATBS solves one of the triangular systems */ + +/* A *x = s*b or A'*x = s*b */ + +/* with scaling to prevent overflow, where A is an upper or lower */ +/* triangular band matrix. Here A' denotes the transpose of A, x and b */ +/* are n-element vectors, and s is a scaling factor, usually less than */ +/* or equal to 1, chosen so that the components of x will be less than */ +/* the overflow threshold. If the unscaled problem will not cause */ +/* overflow, the Level 2 BLAS routine DTBSV is called. If the matrix A */ +/* is singular (A(j,j) = 0 for some j), then s is set to 0 and a */ +/* non-trivial solution to A*x = 0 is returned. */ + +/* Arguments */ +/* ========= */ + +/* UPLO (input) CHARACTER*1 */ +/* Specifies whether the matrix A is upper or lower triangular. */ +/* = 'U': Upper triangular */ +/* = 'L': Lower triangular */ + +/* TRANS (input) CHARACTER*1 */ +/* Specifies the operation applied to A. */ +/* = 'N': Solve A * x = s*b (No transpose) */ +/* = 'T': Solve A'* x = s*b (Transpose) */ +/* = 'C': Solve A'* x = s*b (Conjugate transpose = Transpose) */ + +/* DIAG (input) CHARACTER*1 */ +/* Specifies whether or not the matrix A is unit triangular. */ +/* = 'N': Non-unit triangular */ +/* = 'U': Unit triangular */ + +/* NORMIN (input) CHARACTER*1 */ +/* Specifies whether CNORM has been set or not. */ +/* = 'Y': CNORM contains the column norms on entry */ +/* = 'N': CNORM is not set on entry. On exit, the norms will */ +/* be computed and stored in CNORM. */ + +/* N (input) INTEGER */ +/* The order of the matrix A. N >= 0. */ + +/* KD (input) INTEGER */ +/* The number of subdiagonals or superdiagonals in the */ +/* triangular matrix A. KD >= 0. */ + +/* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) */ +/* The upper or lower triangular band matrix A, stored in the */ +/* first KD+1 rows of the array. The j-th column of A is stored */ +/* in the j-th column of the array AB as follows: */ +/* if UPLO = 'U', AB(kd+1+i-j,j) = A(i,j) for max(1,j-kd)<=i<=j; */ +/* if UPLO = 'L', AB(1+i-j,j) = A(i,j) for j<=i<=min(n,j+kd). */ + +/* LDAB (input) INTEGER */ +/* The leading dimension of the array AB. LDAB >= KD+1. */ + +/* X (input/output) DOUBLE PRECISION array, dimension (N) */ +/* On entry, the right hand side b of the triangular system. */ +/* On exit, X is overwritten by the solution vector x. */ + +/* SCALE (output) DOUBLE PRECISION */ +/* The scaling factor s for the triangular system */ +/* A * x = s*b or A'* x = s*b. */ +/* If SCALE = 0, the matrix A is singular or badly scaled, and */ +/* the vector x is an exact or approximate solution to A*x = 0. */ + +/* CNORM (input or output) DOUBLE PRECISION array, dimension (N) */ + +/* If NORMIN = 'Y', CNORM is an input argument and CNORM(j) */ +/* contains the norm of the off-diagonal part of the j-th column */ +/* of A. If TRANS = 'N', CNORM(j) must be greater than or equal */ +/* to the infinity-norm, and if TRANS = 'T' or 'C', CNORM(j) */ +/* must be greater than or equal to the 1-norm. */ + +/* If NORMIN = 'N', CNORM is an output argument and CNORM(j) */ +/* returns the 1-norm of the offdiagonal part of the j-th column */ +/* of A. */ + +/* INFO (output) INTEGER */ +/* = 0: successful exit */ +/* < 0: if INFO = -k, the k-th argument had an illegal value */ + +/* Further Details */ +/* ======= ======= */ + +/* A rough bound on x is computed; if that is less than overflow, DTBSV */ +/* is called, otherwise, specific code is used which checks for possible */ +/* overflow or divide-by-zero at every operation. */ + +/* A columnwise scheme is used for solving A*x = b. The basic algorithm */ +/* if A is lower triangular is */ + +/* x[1:n] := b[1:n] */ +/* for j = 1, ..., n */ +/* x(j) := x(j) / A(j,j) */ +/* x[j+1:n] := x[j+1:n] - x(j) * A[j+1:n,j] */ +/* end */ + +/* Define bounds on the components of x after j iterations of the loop: */ +/* M(j) = bound on x[1:j] */ +/* G(j) = bound on x[j+1:n] */ +/* Initially, let M(0) = 0 and G(0) = max{x(i), i=1,...,n}. */ + +/* Then for iteration j+1 we have */ +/* M(j+1) <= G(j) / | A(j+1,j+1) | */ +/* G(j+1) <= G(j) + M(j+1) * | A[j+2:n,j+1] | */ +/* <= G(j) ( 1 + CNORM(j+1) / | A(j+1,j+1) | ) */ + +/* where CNORM(j+1) is greater than or equal to the infinity-norm of */ +/* column j+1 of A, not counting the diagonal. Hence */ + +/* G(j) <= G(0) product ( 1 + CNORM(i) / | A(i,i) | ) */ +/* 1<=i<=j */ +/* and */ + +/* |x(j)| <= ( G(0) / |A(j,j)| ) product ( 1 + CNORM(i) / |A(i,i)| ) */ +/* 1<=i< j */ + +/* Since |x(j)| <= M(j), we use the Level 2 BLAS routine DTBSV if the */ +/* reciprocal of the largest M(j), j=1,..,n, is larger than */ +/* max(underflow, 1/overflow). */ + +/* The bound on x(j) is also used to determine when a step in the */ +/* columnwise method can be performed without fear of overflow. If */ +/* the computed bound is greater than a large constant, x is scaled to */ +/* prevent overflow, but if the bound overflows, x is set to 0, x(j) to */ +/* 1, and scale to 0, and a non-trivial solution to A*x = 0 is found. */ + +/* Similarly, a row-wise scheme is used to solve A'*x = b. The basic */ +/* algorithm for A upper triangular is */ + +/* for j = 1, ..., n */ +/* x(j) := ( b(j) - A[1:j-1,j]' * x[1:j-1] ) / A(j,j) */ +/* end */ + +/* We simultaneously compute two bounds */ +/* G(j) = bound on ( b(i) - A[1:i-1,i]' * x[1:i-1] ), 1<=i<=j */ +/* M(j) = bound on x(i), 1<=i<=j */ + +/* The initial values are G(0) = 0, M(0) = max{b(i), i=1,..,n}, and we */ +/* add the constraint G(j) >= G(j-1) and M(j) >= M(j-1) for j >= 1. */ +/* Then the bound on x(j) is */ + +/* M(j) <= M(j-1) * ( 1 + CNORM(j) ) / | A(j,j) | */ + +/* <= M(0) * product ( ( 1 + CNORM(i) ) / |A(i,i)| ) */ +/* 1<=i<=j */ + +/* and we can safely call DTBSV if 1/M(n) and 1/G(n) are both greater */ +/* than max(underflow, 1/overflow). */ + +/* ===================================================================== */ + +/* .. Parameters .. */ +/* .. */ +/* .. Local Scalars .. */ +/* .. */ +/* .. External Functions .. */ +/* .. */ +/* .. External Subroutines .. */ +/* .. */ +/* .. Intrinsic Functions .. */ +/* .. */ +/* .. Executable Statements .. */ + + /* Parameter adjustments */ + ab_dim1 = *ldab; + ab_offset = 1 + ab_dim1; + ab -= ab_offset; + --x; + --cnorm; + + /* Function Body */ + *info = 0; + upper = lsame_(uplo, "U", (ftnlen)1, (ftnlen)1); + notran = lsame_(trans, "N", (ftnlen)1, (ftnlen)1); + nounit = lsame_(diag, "N", (ftnlen)1, (ftnlen)1); + +/* Test the input parameters. */ + + if (! upper && ! lsame_(uplo, "L", (ftnlen)1, (ftnlen)1)) { + *info = -1; + } else if (! notran && ! lsame_(trans, "T", (ftnlen)1, (ftnlen)1) && ! + lsame_(trans, "C", (ftnlen)1, (ftnlen)1)) { + *info = -2; + } else if (! nounit && ! lsame_(diag, "U", (ftnlen)1, (ftnlen)1)) { + *info = -3; + } else if (! lsame_(normin, "Y", (ftnlen)1, (ftnlen)1) && ! lsame_(normin, + "N", (ftnlen)1, (ftnlen)1)) { + *info = -4; + } else if (*n < 0) { + *info = -5; + } else if (*kd < 0) { + *info = -6; + } else if (*ldab < *kd + 1) { + *info = -8; + } + if (*info != 0) { + i__1 = -(*info); + xerbla_("DLATBS", &i__1, (ftnlen)6); + return 0; + } + +/* Quick return if possible */ + + if (*n == 0) { + return 0; + } + +/* Determine machine dependent parameters to control overflow. */ + + smlnum = dlamch_("Safe minimum", (ftnlen)12) / dlamch_("Precision", ( + ftnlen)9); + bignum = 1. / smlnum; + *scale = 1.; + + if (lsame_(normin, "N", (ftnlen)1, (ftnlen)1)) { + +/* Compute the 1-norm of each column, not including the diagonal. */ + + if (upper) { + +/* A is upper triangular. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + i__2 = *kd, i__3 = j - 1; + jlen = min(i__2,i__3); + cnorm[j] = dasum_(&jlen, &ab[*kd + 1 - jlen + j * ab_dim1], & + c__1); +/* L10: */ + } + } else { + +/* A is lower triangular. */ + + i__1 = *n; + for (j = 1; j <= i__1; ++j) { +/* Computing MIN */ + i__2 = *kd, i__3 = *n - j; + jlen = min(i__2,i__3); + if (jlen > 0) { + cnorm[j] = dasum_(&jlen, &ab[j * ab_dim1 + 2], &c__1); + } else { + cnorm[j] = 0.; + } +/* L20: */ + } + } + } + +/* Scale the column norms by TSCAL if the maximum element in CNORM is */ +/* greater than BIGNUM. */ + + imax = idamax_(n, &cnorm[1], &c__1); + tmax = cnorm[imax]; + if (tmax <= bignum) { + tscal = 1.; + } else { + tscal = 1. / (smlnum * tmax); + dscal_(n, &tscal, &cnorm[1], &c__1); + } + +/* Compute a bound on the computed solution vector to see if the */ +/* Level 2 BLAS routine DTBSV can be used. */ + + j = idamax_(n, &x[1], &c__1); + xmax = (d__1 = x[j], abs(d__1)); + xbnd = xmax; + if (notran) { + +/* Compute the growth in A * x = b. */ + + if (upper) { + jfirst = *n; + jlast = 1; + jinc = -1; + maind = *kd + 1; + } else { + jfirst = 1; + jlast = *n; + jinc = 1; + maind = 1; + } + + if (tscal != 1.) { + grow = 0.; + goto L50; + } + + if (nounit) { + +/* A is non-unit triangular. */ + +/* Compute GROW = 1/G(j) and XBND = 1/M(j). */ +/* Initially, G(0) = max{x(i), i=1,...,n}. */ + + grow = 1. / max(xbnd,smlnum); + xbnd = grow; + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L50; + } + +/* M(j) = G(j-1) / abs(A(j,j)) */ + + tjj = (d__1 = ab[maind + j * ab_dim1], abs(d__1)); +/* Computing MIN */ + d__1 = xbnd, d__2 = min(1.,tjj) * grow; + xbnd = min(d__1,d__2); + if (tjj + cnorm[j] >= smlnum) { + +/* G(j) = G(j-1)*( 1 + CNORM(j) / abs(A(j,j)) ) */ + + grow *= tjj / (tjj + cnorm[j]); + } else { + +/* G(j) could overflow, set GROW to 0. */ + + grow = 0.; + } +/* L30: */ + } + grow = xbnd; + } else { + +/* A is unit triangular. */ + +/* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. */ + +/* Computing MIN */ + d__1 = 1., d__2 = 1. / max(xbnd,smlnum); + grow = min(d__1,d__2); + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L50; + } + +/* G(j) = G(j-1)*( 1 + CNORM(j) ) */ + + grow *= 1. / (cnorm[j] + 1.); +/* L40: */ + } + } +L50: + + ; + } else { + +/* Compute the growth in A' * x = b. */ + + if (upper) { + jfirst = 1; + jlast = *n; + jinc = 1; + maind = *kd + 1; + } else { + jfirst = *n; + jlast = 1; + jinc = -1; + maind = 1; + } + + if (tscal != 1.) { + grow = 0.; + goto L80; + } + + if (nounit) { + +/* A is non-unit triangular. */ + +/* Compute GROW = 1/G(j) and XBND = 1/M(j). */ +/* Initially, M(0) = max{x(i), i=1,...,n}. */ + + grow = 1. / max(xbnd,smlnum); + xbnd = grow; + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L80; + } + +/* G(j) = max( G(j-1), M(j-1)*( 1 + CNORM(j) ) ) */ + + xj = cnorm[j] + 1.; +/* Computing MIN */ + d__1 = grow, d__2 = xbnd / xj; + grow = min(d__1,d__2); + +/* M(j) = M(j-1)*( 1 + CNORM(j) ) / abs(A(j,j)) */ + + tjj = (d__1 = ab[maind + j * ab_dim1], abs(d__1)); + if (xj > tjj) { + xbnd *= tjj / xj; + } +/* L60: */ + } + grow = min(grow,xbnd); + } else { + +/* A is unit triangular. */ + +/* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. */ + +/* Computing MIN */ + d__1 = 1., d__2 = 1. / max(xbnd,smlnum); + grow = min(d__1,d__2); + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Exit the loop if the growth factor is too small. */ + + if (grow <= smlnum) { + goto L80; + } + +/* G(j) = ( 1 + CNORM(j) )*G(j-1) */ + + xj = cnorm[j] + 1.; + grow /= xj; +/* L70: */ + } + } +L80: + ; + } + + if (grow * tscal > smlnum) { + +/* Use the Level 2 BLAS solve if the reciprocal of the bound on */ +/* elements of X is not too small. */ + + dtbsv_(uplo, trans, diag, n, kd, &ab[ab_offset], ldab, &x[1], &c__1, ( + ftnlen)1, (ftnlen)1, (ftnlen)1); + } else { + +/* Use a Level 1 BLAS solve, scaling intermediate results. */ + + if (xmax > bignum) { + +/* Scale X so that its components are less than or equal to */ +/* BIGNUM in absolute value. */ + + *scale = bignum / xmax; + dscal_(n, scale, &x[1], &c__1); + xmax = bignum; + } + + if (notran) { + +/* Solve A * x = b */ + + i__1 = jlast; + i__2 = jinc; + for (j = jfirst; i__2 < 0 ? j >= i__1 : j <= i__1; j += i__2) { + +/* Compute x(j) = b(j) / A(j,j), scaling x if necessary. */ + + xj = (d__1 = x[j], abs(d__1)); + if (nounit) { + tjjs = ab[maind + j * ab_dim1] * tscal; + } else { + tjjs = tscal; + if (tscal == 1.) { + goto L100; + } + } + tjj = abs(tjjs); + if (tjj > smlnum) { + +/* abs(A(j,j)) > SMLNUM: */ + + if (tjj < 1.) { + if (xj > tjj * bignum) { + +/* Scale x by 1/b(j). */ + + rec = 1. / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + x[j] /= tjjs; + xj = (d__1 = x[j], abs(d__1)); + } else if (tjj > 0.) { + +/* 0 < abs(A(j,j)) <= SMLNUM: */ + + if (xj > tjj * bignum) { + +/* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM */ +/* to avoid overflow when dividing by A(j,j). */ + + rec = tjj * bignum / xj; + if (cnorm[j] > 1.) { + +/* Scale by 1/CNORM(j) to avoid overflow when */ +/* multiplying x(j) times column j. */ + + rec /= cnorm[j]; + } + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + x[j] /= tjjs; + xj = (d__1 = x[j], abs(d__1)); + } else { + +/* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and */ +/* scale = 0, and compute a solution to A*x = 0. */ + + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + x[i__] = 0.; +/* L90: */ + } + x[j] = 1.; + xj = 1.; + *scale = 0.; + xmax = 0.; + } +L100: + +/* Scale x if necessary to avoid overflow when adding a */ +/* multiple of column j of A. */ + + if (xj > 1.) { + rec = 1. / xj; + if (cnorm[j] > (bignum - xmax) * rec) { + +/* Scale x by 1/(2*abs(x(j))). */ + + rec *= .5; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + } + } else if (xj * cnorm[j] > bignum - xmax) { + +/* Scale x by 1/2. */ + + dscal_(n, &c_b36, &x[1], &c__1); + *scale *= .5; + } + + if (upper) { + if (j > 1) { + +/* Compute the update */ +/* x(max(1,j-kd):j-1) := x(max(1,j-kd):j-1) - */ +/* x(j)* A(max(1,j-kd):j-1,j) */ + +/* Computing MIN */ + i__3 = *kd, i__4 = j - 1; + jlen = min(i__3,i__4); + d__1 = -x[j] * tscal; + daxpy_(&jlen, &d__1, &ab[*kd + 1 - jlen + j * ab_dim1] + , &c__1, &x[j - jlen], &c__1); + i__3 = j - 1; + i__ = idamax_(&i__3, &x[1], &c__1); + xmax = (d__1 = x[i__], abs(d__1)); + } + } else if (j < *n) { + +/* Compute the update */ +/* x(j+1:min(j+kd,n)) := x(j+1:min(j+kd,n)) - */ +/* x(j) * A(j+1:min(j+kd,n),j) */ + +/* Computing MIN */ + i__3 = *kd, i__4 = *n - j; + jlen = min(i__3,i__4); + if (jlen > 0) { + d__1 = -x[j] * tscal; + daxpy_(&jlen, &d__1, &ab[j * ab_dim1 + 2], &c__1, &x[ + j + 1], &c__1); + } + i__3 = *n - j; + i__ = j + idamax_(&i__3, &x[j + 1], &c__1); + xmax = (d__1 = x[i__], abs(d__1)); + } +/* L110: */ + } + + } else { + +/* Solve A' * x = b */ + + i__2 = jlast; + i__1 = jinc; + for (j = jfirst; i__1 < 0 ? j >= i__2 : j <= i__2; j += i__1) { + +/* Compute x(j) = b(j) - sum A(k,j)*x(k). */ +/* k<>j */ + + xj = (d__1 = x[j], abs(d__1)); + uscal = tscal; + rec = 1. / max(xmax,1.); + if (cnorm[j] > (bignum - xj) * rec) { + +/* If x(j) could overflow, scale x by 1/(2*XMAX). */ + + rec *= .5; + if (nounit) { + tjjs = ab[maind + j * ab_dim1] * tscal; + } else { + tjjs = tscal; + } + tjj = abs(tjjs); + if (tjj > 1.) { + +/* Divide by A(j,j) when scaling x if A(j,j) > 1. */ + +/* Computing MIN */ + d__1 = 1., d__2 = rec * tjj; + rec = min(d__1,d__2); + uscal /= tjjs; + } + if (rec < 1.) { + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + + sumj = 0.; + if (uscal == 1.) { + +/* If the scaling needed for A in the dot product is 1, */ +/* call DDOT to perform the dot product. */ + + if (upper) { +/* Computing MIN */ + i__3 = *kd, i__4 = j - 1; + jlen = min(i__3,i__4); + sumj = ddot_(&jlen, &ab[*kd + 1 - jlen + j * ab_dim1], + &c__1, &x[j - jlen], &c__1); + } else { +/* Computing MIN */ + i__3 = *kd, i__4 = *n - j; + jlen = min(i__3,i__4); + if (jlen > 0) { + sumj = ddot_(&jlen, &ab[j * ab_dim1 + 2], &c__1, & + x[j + 1], &c__1); + } + } + } else { + +/* Otherwise, use in-line code for the dot product. */ + + if (upper) { +/* Computing MIN */ + i__3 = *kd, i__4 = j - 1; + jlen = min(i__3,i__4); + i__3 = jlen; + for (i__ = 1; i__ <= i__3; ++i__) { + sumj += ab[*kd + i__ - jlen + j * ab_dim1] * + uscal * x[j - jlen - 1 + i__]; +/* L120: */ + } + } else { +/* Computing MIN */ + i__3 = *kd, i__4 = *n - j; + jlen = min(i__3,i__4); + i__3 = jlen; + for (i__ = 1; i__ <= i__3; ++i__) { + sumj += ab[i__ + 1 + j * ab_dim1] * uscal * x[j + + i__]; +/* L130: */ + } + } + } + + if (uscal == tscal) { + +/* Compute x(j) := ( x(j) - sumj ) / A(j,j) if 1/A(j,j) */ +/* was not used to scale the dotproduct. */ + + x[j] -= sumj; + xj = (d__1 = x[j], abs(d__1)); + if (nounit) { + +/* Compute x(j) = x(j) / A(j,j), scaling if necessary. */ + + tjjs = ab[maind + j * ab_dim1] * tscal; + } else { + tjjs = tscal; + if (tscal == 1.) { + goto L150; + } + } + tjj = abs(tjjs); + if (tjj > smlnum) { + +/* abs(A(j,j)) > SMLNUM: */ + + if (tjj < 1.) { + if (xj > tjj * bignum) { + +/* Scale X by 1/abs(x(j)). */ + + rec = 1. / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + } + x[j] /= tjjs; + } else if (tjj > 0.) { + +/* 0 < abs(A(j,j)) <= SMLNUM: */ + + if (xj > tjj * bignum) { + +/* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM. */ + + rec = tjj * bignum / xj; + dscal_(n, &rec, &x[1], &c__1); + *scale *= rec; + xmax *= rec; + } + x[j] /= tjjs; + } else { + +/* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and */ +/* scale = 0, and compute a solution to A'*x = 0. */ + + i__3 = *n; + for (i__ = 1; i__ <= i__3; ++i__) { + x[i__] = 0.; +/* L140: */ + } + x[j] = 1.; + *scale = 0.; + xmax = 0.; + } +L150: + ; + } else { + +/* Compute x(j) := x(j) / A(j,j) - sumj if the dot */ +/* product has already been divided by 1/A(j,j). */ + + x[j] = x[j] / tjjs - sumj; + } +/* Computing MAX */ + d__2 = xmax, d__3 = (d__1 = x[j], abs(d__1)); + xmax = max(d__2,d__3); +/* L160: */ + } + } + *scale /= tscal; + } + +/* Scale the column norms by 1/TSCAL for return. */ + + if (tscal != 1.) { + d__1 = 1. / tscal; + dscal_(n, &d__1, &cnorm[1], &c__1); + } + + return 0; + +/* End of DLATBS */ + +} /* dlatbs_ */ + diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in index e0f242113..b71f30b4f 100755 --- a/ext/lapack/Makefile.in +++ b/ext/lapack/Makefile.in @@ -18,6 +18,7 @@ F_FLAGS = @FFLAGS@ $(PIC_FLAG) OBJS = \ dbdsqr.o \ +dgbcon.o \ dgbtrf.o \ dgbtf2.o \ dgbtrs.o \ @@ -59,6 +60,7 @@ dlasrt.o \ dlassq.o \ dlasv2.o \ dlaswp.o \ +dlatbs.o \ dorg2r.o \ dorgbr.o \ dorgl2.o \ diff --git a/ext/lapack/dgbcon.f b/ext/lapack/dgbcon.f new file mode 100644 index 000000000..ba613b735 --- /dev/null +++ b/ext/lapack/dgbcon.f @@ -0,0 +1,222 @@ + SUBROUTINE DGBCON( NORM, N, KL, KU, AB, LDAB, IPIV, ANORM, RCOND, + $ WORK, IWORK, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* September 30, 1994 +* +* .. Scalar Arguments .. + CHARACTER NORM + INTEGER INFO, KL, KU, LDAB, N + DOUBLE PRECISION ANORM, RCOND +* .. +* .. Array Arguments .. + INTEGER IPIV( * ), IWORK( * ) + DOUBLE PRECISION AB( LDAB, * ), WORK( * ) +* .. +* +* Purpose +* ======= +* +* DGBCON estimates the reciprocal of the condition number of a real +* general band matrix A, in either the 1-norm or the infinity-norm, +* using the LU factorization computed by DGBTRF. +* +* An estimate is obtained for norm(inv(A)), and the reciprocal of the +* condition number is computed as +* RCOND = 1 / ( norm(A) * norm(inv(A)) ). +* +* Arguments +* ========= +* +* NORM (input) CHARACTER*1 +* Specifies whether the 1-norm condition number or the +* infinity-norm condition number is required: +* = '1' or 'O': 1-norm; +* = 'I': Infinity-norm. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* KL (input) INTEGER +* The number of subdiagonals within the band of A. KL >= 0. +* +* KU (input) INTEGER +* The number of superdiagonals within the band of A. KU >= 0. +* +* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) +* Details of the LU factorization of the band matrix A, as +* computed by DGBTRF. U is stored as an upper triangular band +* matrix with KL+KU superdiagonals in rows 1 to KL+KU+1, and +* the multipliers used during the factorization are stored in +* rows KL+KU+2 to 2*KL+KU+1. +* +* LDAB (input) INTEGER +* The leading dimension of the array AB. LDAB >= 2*KL+KU+1. +* +* IPIV (input) INTEGER array, dimension (N) +* The pivot indices; for 1 <= i <= N, row i of the matrix was +* interchanged with row IPIV(i). +* +* ANORM (input) DOUBLE PRECISION +* If NORM = '1' or 'O', the 1-norm of the original matrix A. +* If NORM = 'I', the infinity-norm of the original matrix A. +* +* RCOND (output) DOUBLE PRECISION +* The reciprocal of the condition number of the matrix A, +* computed as RCOND = 1/(norm(A) * norm(inv(A))). +* +* WORK (workspace) DOUBLE PRECISION array, dimension (3*N) +* +* IWORK (workspace) INTEGER array, dimension (N) +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL LNOTI, ONENRM + CHARACTER NORMIN + INTEGER IX, J, JP, KASE, KASE1, KD, LM + DOUBLE PRECISION AINVNM, SCALE, SMLNUM, T +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER IDAMAX + DOUBLE PRECISION DDOT, DLAMCH + EXTERNAL LSAME, IDAMAX, DDOT, DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL DAXPY, DLACON, DLATBS, DRSCL, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + ONENRM = NORM.EQ.'1' .OR. LSAME( NORM, 'O' ) + IF( .NOT.ONENRM .AND. .NOT.LSAME( NORM, 'I' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( KL.LT.0 ) THEN + INFO = -3 + ELSE IF( KU.LT.0 ) THEN + INFO = -4 + ELSE IF( LDAB.LT.2*KL+KU+1 ) THEN + INFO = -6 + ELSE IF( ANORM.LT.ZERO ) THEN + INFO = -8 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGBCON', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + RCOND = ZERO + IF( N.EQ.0 ) THEN + RCOND = ONE + RETURN + ELSE IF( ANORM.EQ.ZERO ) THEN + RETURN + END IF +* + SMLNUM = DLAMCH( 'Safe minimum' ) +* +* Estimate the norm of inv(A). +* + AINVNM = ZERO + NORMIN = 'N' + IF( ONENRM ) THEN + KASE1 = 1 + ELSE + KASE1 = 2 + END IF + KD = KL + KU + 1 + LNOTI = KL.GT.0 + KASE = 0 + 10 CONTINUE + CALL DLACON( N, WORK( N+1 ), WORK, IWORK, AINVNM, KASE ) + IF( KASE.NE.0 ) THEN + IF( KASE.EQ.KASE1 ) THEN +* +* Multiply by inv(L). +* + IF( LNOTI ) THEN + DO 20 J = 1, N - 1 + LM = MIN( KL, N-J ) + JP = IPIV( J ) + T = WORK( JP ) + IF( JP.NE.J ) THEN + WORK( JP ) = WORK( J ) + WORK( J ) = T + END IF + CALL DAXPY( LM, -T, AB( KD+1, J ), 1, WORK( J+1 ), 1 ) + 20 CONTINUE + END IF +* +* Multiply by inv(U). +* + CALL DLATBS( 'Upper', 'No transpose', 'Non-unit', NORMIN, N, + $ KL+KU, AB, LDAB, WORK, SCALE, WORK( 2*N+1 ), + $ INFO ) + ELSE +* +* Multiply by inv(U'). +* + CALL DLATBS( 'Upper', 'Transpose', 'Non-unit', NORMIN, N, + $ KL+KU, AB, LDAB, WORK, SCALE, WORK( 2*N+1 ), + $ INFO ) +* +* Multiply by inv(L'). +* + IF( LNOTI ) THEN + DO 30 J = N - 1, 1, -1 + LM = MIN( KL, N-J ) + WORK( J ) = WORK( J ) - DDOT( LM, AB( KD+1, J ), 1, + $ WORK( J+1 ), 1 ) + JP = IPIV( J ) + IF( JP.NE.J ) THEN + T = WORK( JP ) + WORK( JP ) = WORK( J ) + WORK( J ) = T + END IF + 30 CONTINUE + END IF + END IF +* +* Divide X by 1/SCALE if doing so will not cause overflow. +* + NORMIN = 'Y' + IF( SCALE.NE.ONE ) THEN + IX = IDAMAX( N, WORK, 1 ) + IF( SCALE.LT.ABS( WORK( IX ) )*SMLNUM .OR. SCALE.EQ.ZERO ) + $ GO TO 40 + CALL DRSCL( N, SCALE, WORK, 1 ) + END IF + GO TO 10 + END IF +* +* Compute the estimate of the reciprocal condition number. +* + IF( AINVNM.NE.ZERO ) + $ RCOND = ( ONE / AINVNM ) / ANORM +* + 40 CONTINUE + RETURN +* +* End of DGBCON +* + END diff --git a/ext/lapack/dgbequ.f b/ext/lapack/dgbequ.f new file mode 100644 index 000000000..309798c98 --- /dev/null +++ b/ext/lapack/dgbequ.f @@ -0,0 +1,240 @@ + SUBROUTINE DGBEQU( M, N, KL, KU, AB, LDAB, R, C, ROWCND, COLCND, + $ AMAX, INFO ) +* +* -- LAPACK routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* March 31, 1993 +* +* .. Scalar Arguments .. + INTEGER INFO, KL, KU, LDAB, M, N + DOUBLE PRECISION AMAX, COLCND, ROWCND +* .. +* .. Array Arguments .. + DOUBLE PRECISION AB( LDAB, * ), C( * ), R( * ) +* .. +* +* Purpose +* ======= +* +* DGBEQU computes row and column scalings intended to equilibrate an +* M-by-N band matrix A and reduce its condition number. R returns the +* row scale factors and C the column scale factors, chosen to try to +* make the largest element in each row and column of the matrix B with +* elements B(i,j)=R(i)*A(i,j)*C(j) have absolute value 1. +* +* R(i) and C(j) are restricted to be between SMLNUM = smallest safe +* number and BIGNUM = largest safe number. Use of these scaling +* factors is not guaranteed to reduce the condition number of A but +* works well in practice. +* +* Arguments +* ========= +* +* M (input) INTEGER +* The number of rows of the matrix A. M >= 0. +* +* N (input) INTEGER +* The number of columns of the matrix A. N >= 0. +* +* KL (input) INTEGER +* The number of subdiagonals within the band of A. KL >= 0. +* +* KU (input) INTEGER +* The number of superdiagonals within the band of A. KU >= 0. +* +* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) +* The band matrix A, stored in rows 1 to KL+KU+1. The j-th +* column of A is stored in the j-th column of the array AB as +* follows: +* AB(ku+1+i-j,j) = A(i,j) for max(1,j-ku)<=i<=min(m,j+kl). +* +* LDAB (input) INTEGER +* The leading dimension of the array AB. LDAB >= KL+KU+1. +* +* R (output) DOUBLE PRECISION array, dimension (M) +* If INFO = 0, or INFO > M, R contains the row scale factors +* for A. +* +* C (output) DOUBLE PRECISION array, dimension (N) +* If INFO = 0, C contains the column scale factors for A. +* +* ROWCND (output) DOUBLE PRECISION +* If INFO = 0 or INFO > M, ROWCND contains the ratio of the +* smallest R(i) to the largest R(i). If ROWCND >= 0.1 and +* AMAX is neither too large nor too small, it is not worth +* scaling by R. +* +* COLCND (output) DOUBLE PRECISION +* If INFO = 0, COLCND contains the ratio of the smallest +* C(i) to the largest C(i). If COLCND >= 0.1, it is not +* worth scaling by C. +* +* AMAX (output) DOUBLE PRECISION +* Absolute value of largest matrix element. If AMAX is very +* close to overflow or very close to underflow, the matrix +* should be scaled. +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -i, the i-th argument had an illegal value +* > 0: if INFO = i, and i is +* <= M: the i-th row of A is exactly zero +* > M: the (i-M)-th column of A is exactly zero +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, J, KD + DOUBLE PRECISION BIGNUM, RCMAX, RCMIN, SMLNUM +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH + EXTERNAL DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters +* + INFO = 0 + IF( M.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( KL.LT.0 ) THEN + INFO = -3 + ELSE IF( KU.LT.0 ) THEN + INFO = -4 + ELSE IF( LDAB.LT.KL+KU+1 ) THEN + INFO = -6 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGBEQU', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + ROWCND = ONE + COLCND = ONE + AMAX = ZERO + RETURN + END IF +* +* Get machine constants. +* + SMLNUM = DLAMCH( 'S' ) + BIGNUM = ONE / SMLNUM +* +* Compute row scale factors. +* + DO 10 I = 1, M + R( I ) = ZERO + 10 CONTINUE +* +* Find the maximum element in each row. +* + KD = KU + 1 + DO 30 J = 1, N + DO 20 I = MAX( J-KU, 1 ), MIN( J+KL, M ) + R( I ) = MAX( R( I ), ABS( AB( KD+I-J, J ) ) ) + 20 CONTINUE + 30 CONTINUE +* +* Find the maximum and minimum scale factors. +* + RCMIN = BIGNUM + RCMAX = ZERO + DO 40 I = 1, M + RCMAX = MAX( RCMAX, R( I ) ) + RCMIN = MIN( RCMIN, R( I ) ) + 40 CONTINUE + AMAX = RCMAX +* + IF( RCMIN.EQ.ZERO ) THEN +* +* Find the first zero scale factor and return an error code. +* + DO 50 I = 1, M + IF( R( I ).EQ.ZERO ) THEN + INFO = I + RETURN + END IF + 50 CONTINUE + ELSE +* +* Invert the scale factors. +* + DO 60 I = 1, M + R( I ) = ONE / MIN( MAX( R( I ), SMLNUM ), BIGNUM ) + 60 CONTINUE +* +* Compute ROWCND = min(R(I)) / max(R(I)) +* + ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) + END IF +* +* Compute column scale factors +* + DO 70 J = 1, N + C( J ) = ZERO + 70 CONTINUE +* +* Find the maximum element in each column, +* assuming the row scaling computed above. +* + KD = KU + 1 + DO 90 J = 1, N + DO 80 I = MAX( J-KU, 1 ), MIN( J+KL, M ) + C( J ) = MAX( C( J ), ABS( AB( KD+I-J, J ) )*R( I ) ) + 80 CONTINUE + 90 CONTINUE +* +* Find the maximum and minimum scale factors. +* + RCMIN = BIGNUM + RCMAX = ZERO + DO 100 J = 1, N + RCMIN = MIN( RCMIN, C( J ) ) + RCMAX = MAX( RCMAX, C( J ) ) + 100 CONTINUE +* + IF( RCMIN.EQ.ZERO ) THEN +* +* Find the first zero scale factor and return an error code. +* + DO 110 J = 1, N + IF( C( J ).EQ.ZERO ) THEN + INFO = M + J + RETURN + END IF + 110 CONTINUE + ELSE +* +* Invert the scale factors. +* + DO 120 J = 1, N + C( J ) = ONE / MIN( MAX( C( J ), SMLNUM ), BIGNUM ) + 120 CONTINUE +* +* Compute COLCND = min(C(J)) / max(C(J)) +* + COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM ) + END IF +* + RETURN +* +* End of DGBEQU +* + END diff --git a/ext/lapack/dlatbs.f b/ext/lapack/dlatbs.f new file mode 100644 index 000000000..fe7dd11cb --- /dev/null +++ b/ext/lapack/dlatbs.f @@ -0,0 +1,724 @@ + SUBROUTINE DLATBS( UPLO, TRANS, DIAG, NORMIN, N, KD, AB, LDAB, X, + $ SCALE, CNORM, INFO ) +* +* -- LAPACK auxiliary routine (version 3.0) -- +* Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +* Courant Institute, Argonne National Lab, and Rice University +* June 30, 1992 +* +* .. Scalar Arguments .. + CHARACTER DIAG, NORMIN, TRANS, UPLO + INTEGER INFO, KD, LDAB, N + DOUBLE PRECISION SCALE +* .. +* .. Array Arguments .. + DOUBLE PRECISION AB( LDAB, * ), CNORM( * ), X( * ) +* .. +* +* Purpose +* ======= +* +* DLATBS solves one of the triangular systems +* +* A *x = s*b or A'*x = s*b +* +* with scaling to prevent overflow, where A is an upper or lower +* triangular band matrix. Here A' denotes the transpose of A, x and b +* are n-element vectors, and s is a scaling factor, usually less than +* or equal to 1, chosen so that the components of x will be less than +* the overflow threshold. If the unscaled problem will not cause +* overflow, the Level 2 BLAS routine DTBSV is called. If the matrix A +* is singular (A(j,j) = 0 for some j), then s is set to 0 and a +* non-trivial solution to A*x = 0 is returned. +* +* Arguments +* ========= +* +* UPLO (input) CHARACTER*1 +* Specifies whether the matrix A is upper or lower triangular. +* = 'U': Upper triangular +* = 'L': Lower triangular +* +* TRANS (input) CHARACTER*1 +* Specifies the operation applied to A. +* = 'N': Solve A * x = s*b (No transpose) +* = 'T': Solve A'* x = s*b (Transpose) +* = 'C': Solve A'* x = s*b (Conjugate transpose = Transpose) +* +* DIAG (input) CHARACTER*1 +* Specifies whether or not the matrix A is unit triangular. +* = 'N': Non-unit triangular +* = 'U': Unit triangular +* +* NORMIN (input) CHARACTER*1 +* Specifies whether CNORM has been set or not. +* = 'Y': CNORM contains the column norms on entry +* = 'N': CNORM is not set on entry. On exit, the norms will +* be computed and stored in CNORM. +* +* N (input) INTEGER +* The order of the matrix A. N >= 0. +* +* KD (input) INTEGER +* The number of subdiagonals or superdiagonals in the +* triangular matrix A. KD >= 0. +* +* AB (input) DOUBLE PRECISION array, dimension (LDAB,N) +* The upper or lower triangular band matrix A, stored in the +* first KD+1 rows of the array. The j-th column of A is stored +* in the j-th column of the array AB as follows: +* if UPLO = 'U', AB(kd+1+i-j,j) = A(i,j) for max(1,j-kd)<=i<=j; +* if UPLO = 'L', AB(1+i-j,j) = A(i,j) for j<=i<=min(n,j+kd). +* +* LDAB (input) INTEGER +* The leading dimension of the array AB. LDAB >= KD+1. +* +* X (input/output) DOUBLE PRECISION array, dimension (N) +* On entry, the right hand side b of the triangular system. +* On exit, X is overwritten by the solution vector x. +* +* SCALE (output) DOUBLE PRECISION +* The scaling factor s for the triangular system +* A * x = s*b or A'* x = s*b. +* If SCALE = 0, the matrix A is singular or badly scaled, and +* the vector x is an exact or approximate solution to A*x = 0. +* +* CNORM (input or output) DOUBLE PRECISION array, dimension (N) +* +* If NORMIN = 'Y', CNORM is an input argument and CNORM(j) +* contains the norm of the off-diagonal part of the j-th column +* of A. If TRANS = 'N', CNORM(j) must be greater than or equal +* to the infinity-norm, and if TRANS = 'T' or 'C', CNORM(j) +* must be greater than or equal to the 1-norm. +* +* If NORMIN = 'N', CNORM is an output argument and CNORM(j) +* returns the 1-norm of the offdiagonal part of the j-th column +* of A. +* +* INFO (output) INTEGER +* = 0: successful exit +* < 0: if INFO = -k, the k-th argument had an illegal value +* +* Further Details +* ======= ======= +* +* A rough bound on x is computed; if that is less than overflow, DTBSV +* is called, otherwise, specific code is used which checks for possible +* overflow or divide-by-zero at every operation. +* +* A columnwise scheme is used for solving A*x = b. The basic algorithm +* if A is lower triangular is +* +* x[1:n] := b[1:n] +* for j = 1, ..., n +* x(j) := x(j) / A(j,j) +* x[j+1:n] := x[j+1:n] - x(j) * A[j+1:n,j] +* end +* +* Define bounds on the components of x after j iterations of the loop: +* M(j) = bound on x[1:j] +* G(j) = bound on x[j+1:n] +* Initially, let M(0) = 0 and G(0) = max{x(i), i=1,...,n}. +* +* Then for iteration j+1 we have +* M(j+1) <= G(j) / | A(j+1,j+1) | +* G(j+1) <= G(j) + M(j+1) * | A[j+2:n,j+1] | +* <= G(j) ( 1 + CNORM(j+1) / | A(j+1,j+1) | ) +* +* where CNORM(j+1) is greater than or equal to the infinity-norm of +* column j+1 of A, not counting the diagonal. Hence +* +* G(j) <= G(0) product ( 1 + CNORM(i) / | A(i,i) | ) +* 1<=i<=j +* and +* +* |x(j)| <= ( G(0) / |A(j,j)| ) product ( 1 + CNORM(i) / |A(i,i)| ) +* 1<=i< j +* +* Since |x(j)| <= M(j), we use the Level 2 BLAS routine DTBSV if the +* reciprocal of the largest M(j), j=1,..,n, is larger than +* max(underflow, 1/overflow). +* +* The bound on x(j) is also used to determine when a step in the +* columnwise method can be performed without fear of overflow. If +* the computed bound is greater than a large constant, x is scaled to +* prevent overflow, but if the bound overflows, x is set to 0, x(j) to +* 1, and scale to 0, and a non-trivial solution to A*x = 0 is found. +* +* Similarly, a row-wise scheme is used to solve A'*x = b. The basic +* algorithm for A upper triangular is +* +* for j = 1, ..., n +* x(j) := ( b(j) - A[1:j-1,j]' * x[1:j-1] ) / A(j,j) +* end +* +* We simultaneously compute two bounds +* G(j) = bound on ( b(i) - A[1:i-1,i]' * x[1:i-1] ), 1<=i<=j +* M(j) = bound on x(i), 1<=i<=j +* +* The initial values are G(0) = 0, M(0) = max{b(i), i=1,..,n}, and we +* add the constraint G(j) >= G(j-1) and M(j) >= M(j-1) for j >= 1. +* Then the bound on x(j) is +* +* M(j) <= M(j-1) * ( 1 + CNORM(j) ) / | A(j,j) | +* +* <= M(0) * product ( ( 1 + CNORM(i) ) / |A(i,i)| ) +* 1<=i<=j +* +* and we can safely call DTBSV if 1/M(n) and 1/G(n) are both greater +* than max(underflow, 1/overflow). +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, HALF, ONE + PARAMETER ( ZERO = 0.0D+0, HALF = 0.5D+0, ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL NOTRAN, NOUNIT, UPPER + INTEGER I, IMAX, J, JFIRST, JINC, JLAST, JLEN, MAIND + DOUBLE PRECISION BIGNUM, GROW, REC, SMLNUM, SUMJ, TJJ, TJJS, + $ TMAX, TSCAL, USCAL, XBND, XJ, XMAX +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER IDAMAX + DOUBLE PRECISION DASUM, DDOT, DLAMCH + EXTERNAL LSAME, IDAMAX, DASUM, DDOT, DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL DAXPY, DSCAL, DTBSV, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN +* .. +* .. Executable Statements .. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + NOTRAN = LSAME( TRANS, 'N' ) + NOUNIT = LSAME( DIAG, 'N' ) +* +* Test the input parameters. +* + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'T' ) .AND. .NOT. + $ LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( .NOT.NOUNIT .AND. .NOT.LSAME( DIAG, 'U' ) ) THEN + INFO = -3 + ELSE IF( .NOT.LSAME( NORMIN, 'Y' ) .AND. .NOT. + $ LSAME( NORMIN, 'N' ) ) THEN + INFO = -4 + ELSE IF( N.LT.0 ) THEN + INFO = -5 + ELSE IF( KD.LT.0 ) THEN + INFO = -6 + ELSE IF( LDAB.LT.KD+1 ) THEN + INFO = -8 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLATBS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* Determine machine dependent parameters to control overflow. +* + SMLNUM = DLAMCH( 'Safe minimum' ) / DLAMCH( 'Precision' ) + BIGNUM = ONE / SMLNUM + SCALE = ONE +* + IF( LSAME( NORMIN, 'N' ) ) THEN +* +* Compute the 1-norm of each column, not including the diagonal. +* + IF( UPPER ) THEN +* +* A is upper triangular. +* + DO 10 J = 1, N + JLEN = MIN( KD, J-1 ) + CNORM( J ) = DASUM( JLEN, AB( KD+1-JLEN, J ), 1 ) + 10 CONTINUE + ELSE +* +* A is lower triangular. +* + DO 20 J = 1, N + JLEN = MIN( KD, N-J ) + IF( JLEN.GT.0 ) THEN + CNORM( J ) = DASUM( JLEN, AB( 2, J ), 1 ) + ELSE + CNORM( J ) = ZERO + END IF + 20 CONTINUE + END IF + END IF +* +* Scale the column norms by TSCAL if the maximum element in CNORM is +* greater than BIGNUM. +* + IMAX = IDAMAX( N, CNORM, 1 ) + TMAX = CNORM( IMAX ) + IF( TMAX.LE.BIGNUM ) THEN + TSCAL = ONE + ELSE + TSCAL = ONE / ( SMLNUM*TMAX ) + CALL DSCAL( N, TSCAL, CNORM, 1 ) + END IF +* +* Compute a bound on the computed solution vector to see if the +* Level 2 BLAS routine DTBSV can be used. +* + J = IDAMAX( N, X, 1 ) + XMAX = ABS( X( J ) ) + XBND = XMAX + IF( NOTRAN ) THEN +* +* Compute the growth in A * x = b. +* + IF( UPPER ) THEN + JFIRST = N + JLAST = 1 + JINC = -1 + MAIND = KD + 1 + ELSE + JFIRST = 1 + JLAST = N + JINC = 1 + MAIND = 1 + END IF +* + IF( TSCAL.NE.ONE ) THEN + GROW = ZERO + GO TO 50 + END IF +* + IF( NOUNIT ) THEN +* +* A is non-unit triangular. +* +* Compute GROW = 1/G(j) and XBND = 1/M(j). +* Initially, G(0) = max{x(i), i=1,...,n}. +* + GROW = ONE / MAX( XBND, SMLNUM ) + XBND = GROW + DO 30 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 50 +* +* M(j) = G(j-1) / abs(A(j,j)) +* + TJJ = ABS( AB( MAIND, J ) ) + XBND = MIN( XBND, MIN( ONE, TJJ )*GROW ) + IF( TJJ+CNORM( J ).GE.SMLNUM ) THEN +* +* G(j) = G(j-1)*( 1 + CNORM(j) / abs(A(j,j)) ) +* + GROW = GROW*( TJJ / ( TJJ+CNORM( J ) ) ) + ELSE +* +* G(j) could overflow, set GROW to 0. +* + GROW = ZERO + END IF + 30 CONTINUE + GROW = XBND + ELSE +* +* A is unit triangular. +* +* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. +* + GROW = MIN( ONE, ONE / MAX( XBND, SMLNUM ) ) + DO 40 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 50 +* +* G(j) = G(j-1)*( 1 + CNORM(j) ) +* + GROW = GROW*( ONE / ( ONE+CNORM( J ) ) ) + 40 CONTINUE + END IF + 50 CONTINUE +* + ELSE +* +* Compute the growth in A' * x = b. +* + IF( UPPER ) THEN + JFIRST = 1 + JLAST = N + JINC = 1 + MAIND = KD + 1 + ELSE + JFIRST = N + JLAST = 1 + JINC = -1 + MAIND = 1 + END IF +* + IF( TSCAL.NE.ONE ) THEN + GROW = ZERO + GO TO 80 + END IF +* + IF( NOUNIT ) THEN +* +* A is non-unit triangular. +* +* Compute GROW = 1/G(j) and XBND = 1/M(j). +* Initially, M(0) = max{x(i), i=1,...,n}. +* + GROW = ONE / MAX( XBND, SMLNUM ) + XBND = GROW + DO 60 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 80 +* +* G(j) = max( G(j-1), M(j-1)*( 1 + CNORM(j) ) ) +* + XJ = ONE + CNORM( J ) + GROW = MIN( GROW, XBND / XJ ) +* +* M(j) = M(j-1)*( 1 + CNORM(j) ) / abs(A(j,j)) +* + TJJ = ABS( AB( MAIND, J ) ) + IF( XJ.GT.TJJ ) + $ XBND = XBND*( TJJ / XJ ) + 60 CONTINUE + GROW = MIN( GROW, XBND ) + ELSE +* +* A is unit triangular. +* +* Compute GROW = 1/G(j), where G(0) = max{x(i), i=1,...,n}. +* + GROW = MIN( ONE, ONE / MAX( XBND, SMLNUM ) ) + DO 70 J = JFIRST, JLAST, JINC +* +* Exit the loop if the growth factor is too small. +* + IF( GROW.LE.SMLNUM ) + $ GO TO 80 +* +* G(j) = ( 1 + CNORM(j) )*G(j-1) +* + XJ = ONE + CNORM( J ) + GROW = GROW / XJ + 70 CONTINUE + END IF + 80 CONTINUE + END IF +* + IF( ( GROW*TSCAL ).GT.SMLNUM ) THEN +* +* Use the Level 2 BLAS solve if the reciprocal of the bound on +* elements of X is not too small. +* + CALL DTBSV( UPLO, TRANS, DIAG, N, KD, AB, LDAB, X, 1 ) + ELSE +* +* Use a Level 1 BLAS solve, scaling intermediate results. +* + IF( XMAX.GT.BIGNUM ) THEN +* +* Scale X so that its components are less than or equal to +* BIGNUM in absolute value. +* + SCALE = BIGNUM / XMAX + CALL DSCAL( N, SCALE, X, 1 ) + XMAX = BIGNUM + END IF +* + IF( NOTRAN ) THEN +* +* Solve A * x = b +* + DO 110 J = JFIRST, JLAST, JINC +* +* Compute x(j) = b(j) / A(j,j), scaling x if necessary. +* + XJ = ABS( X( J ) ) + IF( NOUNIT ) THEN + TJJS = AB( MAIND, J )*TSCAL + ELSE + TJJS = TSCAL + IF( TSCAL.EQ.ONE ) + $ GO TO 100 + END IF + TJJ = ABS( TJJS ) + IF( TJJ.GT.SMLNUM ) THEN +* +* abs(A(j,j)) > SMLNUM: +* + IF( TJJ.LT.ONE ) THEN + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by 1/b(j). +* + REC = ONE / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF + X( J ) = X( J ) / TJJS + XJ = ABS( X( J ) ) + ELSE IF( TJJ.GT.ZERO ) THEN +* +* 0 < abs(A(j,j)) <= SMLNUM: +* + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM +* to avoid overflow when dividing by A(j,j). +* + REC = ( TJJ*BIGNUM ) / XJ + IF( CNORM( J ).GT.ONE ) THEN +* +* Scale by 1/CNORM(j) to avoid overflow when +* multiplying x(j) times column j. +* + REC = REC / CNORM( J ) + END IF + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + X( J ) = X( J ) / TJJS + XJ = ABS( X( J ) ) + ELSE +* +* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and +* scale = 0, and compute a solution to A*x = 0. +* + DO 90 I = 1, N + X( I ) = ZERO + 90 CONTINUE + X( J ) = ONE + XJ = ONE + SCALE = ZERO + XMAX = ZERO + END IF + 100 CONTINUE +* +* Scale x if necessary to avoid overflow when adding a +* multiple of column j of A. +* + IF( XJ.GT.ONE ) THEN + REC = ONE / XJ + IF( CNORM( J ).GT.( BIGNUM-XMAX )*REC ) THEN +* +* Scale x by 1/(2*abs(x(j))). +* + REC = REC*HALF + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + END IF + ELSE IF( XJ*CNORM( J ).GT.( BIGNUM-XMAX ) ) THEN +* +* Scale x by 1/2. +* + CALL DSCAL( N, HALF, X, 1 ) + SCALE = SCALE*HALF + END IF +* + IF( UPPER ) THEN + IF( J.GT.1 ) THEN +* +* Compute the update +* x(max(1,j-kd):j-1) := x(max(1,j-kd):j-1) - +* x(j)* A(max(1,j-kd):j-1,j) +* + JLEN = MIN( KD, J-1 ) + CALL DAXPY( JLEN, -X( J )*TSCAL, + $ AB( KD+1-JLEN, J ), 1, X( J-JLEN ), 1 ) + I = IDAMAX( J-1, X, 1 ) + XMAX = ABS( X( I ) ) + END IF + ELSE IF( J.LT.N ) THEN +* +* Compute the update +* x(j+1:min(j+kd,n)) := x(j+1:min(j+kd,n)) - +* x(j) * A(j+1:min(j+kd,n),j) +* + JLEN = MIN( KD, N-J ) + IF( JLEN.GT.0 ) + $ CALL DAXPY( JLEN, -X( J )*TSCAL, AB( 2, J ), 1, + $ X( J+1 ), 1 ) + I = J + IDAMAX( N-J, X( J+1 ), 1 ) + XMAX = ABS( X( I ) ) + END IF + 110 CONTINUE +* + ELSE +* +* Solve A' * x = b +* + DO 160 J = JFIRST, JLAST, JINC +* +* Compute x(j) = b(j) - sum A(k,j)*x(k). +* k<>j +* + XJ = ABS( X( J ) ) + USCAL = TSCAL + REC = ONE / MAX( XMAX, ONE ) + IF( CNORM( J ).GT.( BIGNUM-XJ )*REC ) THEN +* +* If x(j) could overflow, scale x by 1/(2*XMAX). +* + REC = REC*HALF + IF( NOUNIT ) THEN + TJJS = AB( MAIND, J )*TSCAL + ELSE + TJJS = TSCAL + END IF + TJJ = ABS( TJJS ) + IF( TJJ.GT.ONE ) THEN +* +* Divide by A(j,j) when scaling x if A(j,j) > 1. +* + REC = MIN( ONE, REC*TJJ ) + USCAL = USCAL / TJJS + END IF + IF( REC.LT.ONE ) THEN + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF +* + SUMJ = ZERO + IF( USCAL.EQ.ONE ) THEN +* +* If the scaling needed for A in the dot product is 1, +* call DDOT to perform the dot product. +* + IF( UPPER ) THEN + JLEN = MIN( KD, J-1 ) + SUMJ = DDOT( JLEN, AB( KD+1-JLEN, J ), 1, + $ X( J-JLEN ), 1 ) + ELSE + JLEN = MIN( KD, N-J ) + IF( JLEN.GT.0 ) + $ SUMJ = DDOT( JLEN, AB( 2, J ), 1, X( J+1 ), 1 ) + END IF + ELSE +* +* Otherwise, use in-line code for the dot product. +* + IF( UPPER ) THEN + JLEN = MIN( KD, J-1 ) + DO 120 I = 1, JLEN + SUMJ = SUMJ + ( AB( KD+I-JLEN, J )*USCAL )* + $ X( J-JLEN-1+I ) + 120 CONTINUE + ELSE + JLEN = MIN( KD, N-J ) + DO 130 I = 1, JLEN + SUMJ = SUMJ + ( AB( I+1, J )*USCAL )*X( J+I ) + 130 CONTINUE + END IF + END IF +* + IF( USCAL.EQ.TSCAL ) THEN +* +* Compute x(j) := ( x(j) - sumj ) / A(j,j) if 1/A(j,j) +* was not used to scale the dotproduct. +* + X( J ) = X( J ) - SUMJ + XJ = ABS( X( J ) ) + IF( NOUNIT ) THEN +* +* Compute x(j) = x(j) / A(j,j), scaling if necessary. +* + TJJS = AB( MAIND, J )*TSCAL + ELSE + TJJS = TSCAL + IF( TSCAL.EQ.ONE ) + $ GO TO 150 + END IF + TJJ = ABS( TJJS ) + IF( TJJ.GT.SMLNUM ) THEN +* +* abs(A(j,j)) > SMLNUM: +* + IF( TJJ.LT.ONE ) THEN + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale X by 1/abs(x(j)). +* + REC = ONE / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + END IF + X( J ) = X( J ) / TJJS + ELSE IF( TJJ.GT.ZERO ) THEN +* +* 0 < abs(A(j,j)) <= SMLNUM: +* + IF( XJ.GT.TJJ*BIGNUM ) THEN +* +* Scale x by (1/abs(x(j)))*abs(A(j,j))*BIGNUM. +* + REC = ( TJJ*BIGNUM ) / XJ + CALL DSCAL( N, REC, X, 1 ) + SCALE = SCALE*REC + XMAX = XMAX*REC + END IF + X( J ) = X( J ) / TJJS + ELSE +* +* A(j,j) = 0: Set x(1:n) = 0, x(j) = 1, and +* scale = 0, and compute a solution to A'*x = 0. +* + DO 140 I = 1, N + X( I ) = ZERO + 140 CONTINUE + X( J ) = ONE + SCALE = ZERO + XMAX = ZERO + END IF + 150 CONTINUE + ELSE +* +* Compute x(j) := x(j) / A(j,j) - sumj if the dot +* product has already been divided by 1/A(j,j). +* + X( J ) = X( J ) / TJJS - SUMJ + END IF + XMAX = MAX( XMAX, ABS( X( J ) ) ) + 160 CONTINUE + END IF + SCALE = SCALE / TSCAL + END IF +* +* Scale the column norms by 1/TSCAL for return. +* + IF( TSCAL.NE.ONE ) THEN + CALL DSCAL( N, ONE / TSCAL, CNORM, 1 ) + END IF +* + RETURN +* +* End of DLATBS +* + END diff --git a/test_problems/cathermo/HMW_test_1/output_blessed.txt b/test_problems/cathermo/HMW_test_1/output_blessed.txt index 3d63f73b0..296945da9 100644 --- a/test_problems/cathermo/HMW_test_1/output_blessed.txt +++ b/test_problems/cathermo/HMW_test_1/output_blessed.txt @@ -1,7 +1,7 @@ Index Name MoleF MolalityCropped Charge 0 H2O(L) 8.1992706e-01 5.5508435e+01 0.0 1 Cl- 9.0036447e-02 6.0953986e+00 -1.0 - 2 H+ 3.1947185e-11 2.1628000e-09 1.0 + 2 H+ 3.1947189e-11 2.1628000e-09 1.0 3 Na+ 9.0036468e-02 6.0954000e+00 1.0 4 OH- 2.0645728e-08 1.3977000e-06 -1.0 diff --git a/test_problems/cathermo/HMW_test_1/output_noD_blessed.txt b/test_problems/cathermo/HMW_test_1/output_noD_blessed.txt index 966d76de0..296945da9 100644 --- a/test_problems/cathermo/HMW_test_1/output_noD_blessed.txt +++ b/test_problems/cathermo/HMW_test_1/output_noD_blessed.txt @@ -1,7 +1,7 @@ Index Name MoleF MolalityCropped Charge 0 H2O(L) 8.1992706e-01 5.5508435e+01 0.0 1 Cl- 9.0036447e-02 6.0953986e+00 -1.0 - 2 H+ 3.1947185e-11 2.1628000e-09 1.0 + 2 H+ 3.1947189e-11 2.1628000e-09 1.0 3 Na+ 9.0036468e-02 6.0954000e+00 1.0 4 OH- 2.0645728e-08 1.3977000e-06 -1.0 @@ -28,6 +28,278 @@ Index Name MoleF MolalityCropped Charge OH- Na+ Cl- -0.00600 a1 = 3.04284e-10 a2 = 3.04284e-10 + + Debugging information from hmw_act + Step 1: + ionic strenth = 6.0997000e+00 + total molar charge = 1.2199400e+01 + Is = 6.0997 + ij = 1, elambda = 0.0454012, elambda1 = -0.00306854 + ij = 2, elambda = 0.200776, elambda1 = -0.014532 + ij = 3, elambda = 0.47109, elambda1 = -0.0351127 + ij = 4, elambda = 0.857674, elambda1 = -0.0650149 + ij = 4, elambda = 0.857674, elambda1 = -0.0650149 + ij = 6, elambda = 1.98206, elambda1 = -0.153152 + ij = 8, elambda = 3.57685, elambda1 = -0.279391 + ij = 9, elambda = 4.55112, elambda1 = -0.356872 + ij = 12, elambda = 8.18289, elambda1 = -0.646977 + ij = 16, elambda = 14.6822, elambda1 = -1.16875 + Step 2: + z1= 1 z2= 1 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 1 z2= 2 E-theta(I) = -0.059044, E-thetaprime(I) = 0.004790 + z1= 1 z2= 3 E-theta(I) = -0.355533, E-thetaprime(I) = 0.028969 + z1= 1 z2= 4 E-theta(I) = -1.068400, E-thetaprime(I) = 0.087216 + z1= 2 z2= 1 E-theta(I) = -0.059044, E-thetaprime(I) = 0.004790 + z1= 2 z2= 2 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 2 z2= 3 E-theta(I) = -0.178237, E-thetaprime(I) = 0.014566 + z1= 2 z2= 4 E-theta(I) = -0.951372, E-thetaprime(I) = 0.077813 + z1= 3 z2= 1 E-theta(I) = -0.355533, E-thetaprime(I) = 0.028969 + z1= 3 z2= 2 E-theta(I) = -0.178237, E-thetaprime(I) = 0.014566 + z1= 3 z2= 3 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 3 z2= 4 E-theta(I) = -0.357010, E-thetaprime(I) = 0.029220 + z1= 4 z2= 1 E-theta(I) = -1.068400, E-thetaprime(I) = 0.087216 + z1= 4 z2= 2 E-theta(I) = -0.951372, E-thetaprime(I) = 0.077813 + z1= 4 z2= 3 E-theta(I) = -0.357010, E-thetaprime(I) = 0.029220 + z1= 4 z2= 4 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + Step 3: + Species Species g(x) hfunc(x) + Cl- H+ 0.07849 -0.07133 + Cl- Na+ 0.07849 -0.07133 + Cl- OH- 0.00000 0.00000 + H+ Na+ 0.00000 0.00000 + H+ OH- 0.07849 -0.07133 + Na+ OH- 0.07849 -0.07133 + Step 4: + Species Species BMX BprimeMX BphiMX +1 0.200614: 0.1775 0.2945 0 0.0784862 + Cl- H+ 0.2006142 -0.0034438 0.1796081 +2 0.0974087: 0.0765 0.2664 0 0.0784862 + Cl- Na+ 0.0974087 -0.0031152 0.0784069 + Cl- OH- 0.0000000 0.0000000 0.0000000 + H+ Na+ 0.0000000 0.0000000 0.0000000 +5 0: 0 0 0 0.0784862 + H+ OH- 0.0000000 0.0000000 0.0000000 +6 0.106257: 0.0864 0.253 0 0.0784862 + Na+ OH- 0.1062570 -0.0029585 0.0882110 + Step 5: + Species Species CMX + Cl- H+ 0.0004000 + Cl- Na+ 0.0006350 + Cl- OH- 0.0000000 + H+ Na+ 0.0000000 + H+ OH- 0.0000000 + Na+ OH- 0.0022000 + Step 6: + Species Species Phi_ij Phiprime_ij Phi^phi_ij + Cl- H+ 0.000000 0.000000 0.000000 + Cl- Na+ 0.000000 0.000000 0.000000 + Cl- OH- -0.050000 0.000000 -0.050000 + H+ Na+ 0.036000 0.000000 0.036000 + H+ OH- 0.000000 0.000000 0.000000 + Na+ OH- 0.000000 0.000000 0.000000 + Step 7: + initial value of F = -1.143942 + F = -1.143942 + F = -1.259847 + F = -1.259847 + F = -1.259847 + F = -1.259847 + F = -1.259847 + Step 8: Summing in All Contributions to Activity Coefficients + Contributions to ln(ActCoeff_Cl-): + Unary term: z*z*F = -1.25985 + Tern CMX term on Cl-,H+: abs(z_i) m_j m_k CMX = 0.00000 + Tern CMX term on Cl-,Na+: abs(z_i) m_j m_k CMX = 0.02363 + Bin term with H+: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Psi term on H+,Na+: m_j m_k psi_ijk = -0.00000 + Bin term with Na+: 2 m_j BMX = 1.18833 + m_j Z CMX = 0.04725 + Phi term with OH-: 2 m_j Phi_aa = -0.00000 + Psi term on OH-,Na+: m_j m_k psi_ijk = -0.00000 + Tern CMX term on OH-,Na+: abs(z_i) m_j m_k CMX = 0.00000 + Net Cl- lngamma[i] = -0.00064 gamma[i]= 0.999359 + Contributions to ln(ActCoeff_H+): + Unary term: z*z*F = -1.25985 + Bin term with Cl-: 2 m_j BMX = 2.44737 + m_j Z CMX = 0.02977 + Tern CMX term on H+,Cl-: abs(z_i) m_j m_k CMX = 0.00000 + Phi term with Na+: 2 m_j Phi_cc = 0.43918 + Psi term on Na+,Cl-: m_j m_k psi_ijk = -0.14883 + Tern CMX term on Na+,Cl-: abs(z_i) m_j m_k CMX = 0.02363 + Tern CMX term on Na+,OH-: abs(z_i) m_j m_k CMX = 0.00000 + Bin term with OH-: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Net H+ lngamma[i] = 1.53127 gamma[i]= 4.624042 + Contributions to ln(ActCoeff_Na+): + Unary term: z*z*F = -1.25985 + Bin term with Cl-: 2 m_j BMX = 1.18833 + m_j Z CMX = 0.04725 + Psi term on Cl-,OH-: m_j m_k psi_ijk = -0.00000 + Phi term with H+: 2 m_j Phi_cc = 0.00000 + Psi term on H+,Cl-: m_j m_k psi_ijk = -0.00000 + Tern CMX term on H+,Cl-: abs(z_i) m_j m_k CMX = 0.00000 + Tern CMX term on Na+,Cl-: abs(z_i) m_j m_k CMX = 0.02363 + Tern CMX term on Na+,OH-: abs(z_i) m_j m_k CMX = 0.00000 + Bin term with OH-: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Net Na+ lngamma[i] = -0.00064 gamma[i]= 0.999359 + Contributions to ln(ActCoeff_OH-): + Unary term: z*z*F = -1.25985 + Phi term with Cl-: 2 m_j Phi_aa = -0.60997 + Tern CMX term on Cl-,H+: abs(z_i) m_j m_k CMX = 0.00000 + Psi term on Cl-,Na+: m_j m_k psi_ijk = -0.22324 + Tern CMX term on Cl-,Na+: abs(z_i) m_j m_k CMX = 0.02363 + Bin term with H+: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Bin term with Na+: 2 m_j BMX = 1.29627 + m_j Z CMX = 0.16371 + Tern CMX term on OH-,Na+: abs(z_i) m_j m_k CMX = 0.00000 + Net OH- lngamma[i] = -0.60945 gamma[i]= 0.543650 + Step 9: + term1= -1.489777 sum1= 3.205458 sum2= 0.000000 sum3= -0.000001 sum4= 0.000000 sum5= 0.000000 + sum_m_phi_minus_1= 3.431360 osmotic_coef= 1.281273 + Step 10: + Weight of Solvent = 18.01528 + molalitySumUncropped = 12.1994 + ln_a_water= -0.281593 a_water= 0.754581 + + + Debugging information from hmw_act + Step 1: + ionic strenth = 6.0997000e+00 + total molar charge = 1.2199400e+01 + Is = 6.0997 + ij = 1, elambda = 0.0454012, elambda1 = -0.00306854 + ij = 2, elambda = 0.200776, elambda1 = -0.014532 + ij = 3, elambda = 0.47109, elambda1 = -0.0351127 + ij = 4, elambda = 0.857674, elambda1 = -0.0650149 + ij = 4, elambda = 0.857674, elambda1 = -0.0650149 + ij = 6, elambda = 1.98206, elambda1 = -0.153152 + ij = 8, elambda = 3.57685, elambda1 = -0.279391 + ij = 9, elambda = 4.55112, elambda1 = -0.356872 + ij = 12, elambda = 8.18289, elambda1 = -0.646977 + ij = 16, elambda = 14.6822, elambda1 = -1.16875 + Step 2: + z1= 1 z2= 1 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 1 z2= 2 E-theta(I) = -0.059044, E-thetaprime(I) = 0.004790 + z1= 1 z2= 3 E-theta(I) = -0.355533, E-thetaprime(I) = 0.028969 + z1= 1 z2= 4 E-theta(I) = -1.068400, E-thetaprime(I) = 0.087216 + z1= 2 z2= 1 E-theta(I) = -0.059044, E-thetaprime(I) = 0.004790 + z1= 2 z2= 2 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 2 z2= 3 E-theta(I) = -0.178237, E-thetaprime(I) = 0.014566 + z1= 2 z2= 4 E-theta(I) = -0.951372, E-thetaprime(I) = 0.077813 + z1= 3 z2= 1 E-theta(I) = -0.355533, E-thetaprime(I) = 0.028969 + z1= 3 z2= 2 E-theta(I) = -0.178237, E-thetaprime(I) = 0.014566 + z1= 3 z2= 3 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + z1= 3 z2= 4 E-theta(I) = -0.357010, E-thetaprime(I) = 0.029220 + z1= 4 z2= 1 E-theta(I) = -1.068400, E-thetaprime(I) = 0.087216 + z1= 4 z2= 2 E-theta(I) = -0.951372, E-thetaprime(I) = 0.077813 + z1= 4 z2= 3 E-theta(I) = -0.357010, E-thetaprime(I) = 0.029220 + z1= 4 z2= 4 E-theta(I) = 0.000000, E-thetaprime(I) = 0.000000 + Step 3: + Species Species g(x) hfunc(x) + Cl- H+ 0.07849 -0.07133 + Cl- Na+ 0.07849 -0.07133 + Cl- OH- 0.00000 0.00000 + H+ Na+ 0.00000 0.00000 + H+ OH- 0.07849 -0.07133 + Na+ OH- 0.07849 -0.07133 + Step 4: + Species Species BMX BprimeMX BphiMX +1 0.200614: 0.1775 0.2945 0 0.0784862 + Cl- H+ 0.2006142 -0.0034438 0.1796081 +2 0.0974087: 0.0765 0.2664 0 0.0784862 + Cl- Na+ 0.0974087 -0.0031152 0.0784069 + Cl- OH- 0.0000000 0.0000000 0.0000000 + H+ Na+ 0.0000000 0.0000000 0.0000000 +5 0: 0 0 0 0.0784862 + H+ OH- 0.0000000 0.0000000 0.0000000 +6 0.106257: 0.0864 0.253 0 0.0784862 + Na+ OH- 0.1062570 -0.0029585 0.0882110 + Step 5: + Species Species CMX + Cl- H+ 0.0004000 + Cl- Na+ 0.0006350 + Cl- OH- 0.0000000 + H+ Na+ 0.0000000 + H+ OH- 0.0000000 + Na+ OH- 0.0022000 + Step 6: + Species Species Phi_ij Phiprime_ij Phi^phi_ij + Cl- H+ 0.000000 0.000000 0.000000 + Cl- Na+ 0.000000 0.000000 0.000000 + Cl- OH- -0.050000 0.000000 -0.050000 + H+ Na+ 0.036000 0.000000 0.036000 + H+ OH- 0.000000 0.000000 0.000000 + Na+ OH- 0.000000 0.000000 0.000000 + Step 7: + initial value of F = -1.143942 + F = -1.143942 + F = -1.259847 + F = -1.259847 + F = -1.259847 + F = -1.259847 + F = -1.259847 + Step 8: Summing in All Contributions to Activity Coefficients + Contributions to ln(ActCoeff_Cl-): + Unary term: z*z*F = -1.25985 + Tern CMX term on Cl-,H+: abs(z_i) m_j m_k CMX = 0.00000 + Tern CMX term on Cl-,Na+: abs(z_i) m_j m_k CMX = 0.02363 + Bin term with H+: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Psi term on H+,Na+: m_j m_k psi_ijk = -0.00000 + Bin term with Na+: 2 m_j BMX = 1.18833 + m_j Z CMX = 0.04725 + Phi term with OH-: 2 m_j Phi_aa = -0.00000 + Psi term on OH-,Na+: m_j m_k psi_ijk = -0.00000 + Tern CMX term on OH-,Na+: abs(z_i) m_j m_k CMX = 0.00000 + Net Cl- lngamma[i] = -0.00064 gamma[i]= 0.999359 + Contributions to ln(ActCoeff_H+): + Unary term: z*z*F = -1.25985 + Bin term with Cl-: 2 m_j BMX = 2.44737 + m_j Z CMX = 0.02977 + Tern CMX term on H+,Cl-: abs(z_i) m_j m_k CMX = 0.00000 + Phi term with Na+: 2 m_j Phi_cc = 0.43918 + Psi term on Na+,Cl-: m_j m_k psi_ijk = -0.14883 + Tern CMX term on Na+,Cl-: abs(z_i) m_j m_k CMX = 0.02363 + Tern CMX term on Na+,OH-: abs(z_i) m_j m_k CMX = 0.00000 + Bin term with OH-: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Net H+ lngamma[i] = 1.53127 gamma[i]= 4.624042 + Contributions to ln(ActCoeff_Na+): + Unary term: z*z*F = -1.25985 + Bin term with Cl-: 2 m_j BMX = 1.18833 + m_j Z CMX = 0.04725 + Psi term on Cl-,OH-: m_j m_k psi_ijk = -0.00000 + Phi term with H+: 2 m_j Phi_cc = 0.00000 + Psi term on H+,Cl-: m_j m_k psi_ijk = -0.00000 + Tern CMX term on H+,Cl-: abs(z_i) m_j m_k CMX = 0.00000 + Tern CMX term on Na+,Cl-: abs(z_i) m_j m_k CMX = 0.02363 + Tern CMX term on Na+,OH-: abs(z_i) m_j m_k CMX = 0.00000 + Bin term with OH-: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Net Na+ lngamma[i] = -0.00064 gamma[i]= 0.999359 + Contributions to ln(ActCoeff_OH-): + Unary term: z*z*F = -1.25985 + Phi term with Cl-: 2 m_j Phi_aa = -0.60997 + Tern CMX term on Cl-,H+: abs(z_i) m_j m_k CMX = 0.00000 + Psi term on Cl-,Na+: m_j m_k psi_ijk = -0.22324 + Tern CMX term on Cl-,Na+: abs(z_i) m_j m_k CMX = 0.02363 + Bin term with H+: 2 m_j BMX = 0.00000 + m_j Z CMX = 0.00000 + Bin term with Na+: 2 m_j BMX = 1.29627 + m_j Z CMX = 0.16371 + Tern CMX term on OH-,Na+: abs(z_i) m_j m_k CMX = 0.00000 + Net OH- lngamma[i] = -0.60945 gamma[i]= 0.543650 + Step 9: + term1= -1.489777 sum1= 3.205458 sum2= 0.000000 sum3= -0.000001 sum4= 0.000000 sum5= 0.000000 + sum_m_phi_minus_1= 3.431360 osmotic_coef= 1.281273 + Step 10: + Weight of Solvent = 18.01528 + molalitySumUncropped = 12.1994 + ln_a_water= -0.281593 a_water= 0.754581 + Name Activity ActCoeffMolal MoleFract Molality H2O(L) 0.754581 0.92042 0.819823 55.5084 Cl- 6.09579 0.999359 0.0900885 6.0997 From 2191ad93e5a92fff2003aefbbe5a32e7d3eb6b54 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 20 Oct 2011 14:49:19 +0000 Subject: [PATCH 419/446] Fixed runtest --- Cantera/python/examples/surface_chemistry/diamond_cvd/runtest | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/python/examples/surface_chemistry/diamond_cvd/runtest b/Cantera/python/examples/surface_chemistry/diamond_cvd/runtest index c4b4c05a1..a194e6e53 100755 --- a/Cantera/python/examples/surface_chemistry/diamond_cvd/runtest +++ b/Cantera/python/examples/surface_chemistry/diamond_cvd/runtest @@ -40,7 +40,7 @@ then fi retnCSVTotal=1 -if test $retnStat_csv_0 = "1" +if test $retnStat_csv_0 = "0" then retnCSVTotal=0 fi From aa623afbd3df67f43145a551820cb6415d9f96a9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 20 Oct 2011 14:51:43 +0000 Subject: [PATCH 420/446] Fixed runtest --- .../catcomb_stagflow/output_blessed_0.txt | 38 +++++++++---------- .../catcomb_stagflow/runtest | 2 +- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/Cantera/python/examples/surface_chemistry/catcomb_stagflow/output_blessed_0.txt b/Cantera/python/examples/surface_chemistry/catcomb_stagflow/output_blessed_0.txt index e34efe4a3..917ccdfbb 100644 --- a/Cantera/python/examples/surface_chemistry/catcomb_stagflow/output_blessed_0.txt +++ b/Cantera/python/examples/surface_chemistry/catcomb_stagflow/output_blessed_0.txt @@ -729,27 +729,27 @@ no new points needed in flow C(S) 1.368e-07 O(S) 0.867 -Solution saved to file catcomb.xml as solution soln1. +Solution saved to file catcomb.xml as solution soln1_2. solution saved to catcomb.csv Statistics: Grid Functions Time Jacobians Time - 8 38 0.0400 3 0.2100 - 9 16 0.0300 2 0.1800 - 10 8 0.0300 1 0.1000 - 10 16 0.0500 2 0.2200 - 10 10 0.0200 1 0.1100 - 10 14 0.0300 2 0.2200 - 10 16 0.0500 2 0.2100 - 10 14 0.0300 2 0.2200 - 10 8 0.0300 1 0.1000 - 10 41 0.1200 3 0.3100 - 17 37 0.1100 3 0.4800 - 25 26 0.1500 2 0.4900 - 28 11 0.0700 1 0.2800 - 29 11 0.0600 1 0.2900 - 30 6 0.0300 1 0.3100 - 32 6 0.0500 1 0.3300 - 33 4 0.0200 1 0.3500 - 34 2 0.0000 1 0.3600 + 8 38 0.0400 3 0.1200 + 9 16 0.0100 2 0.0900 + 10 8 0.0100 1 0.0600 + 10 16 0.0300 2 0.1100 + 10 10 0.0200 1 0.0500 + 10 14 0.0200 2 0.1100 + 10 16 0.0400 2 0.1100 + 10 14 0.0200 2 0.1100 + 10 8 0.0100 1 0.0500 + 10 41 0.0500 3 0.1600 + 17 37 0.1100 3 0.3600 + 25 26 0.1100 2 0.3900 + 28 11 0.0500 1 0.2200 + 29 11 0.1000 1 0.2300 + 30 6 0.0300 1 0.2400 + 32 6 0.0400 1 0.2600 + 33 4 0.0300 1 0.2600 + 34 2 0.0000 1 0.2800 diff --git a/Cantera/python/examples/surface_chemistry/catcomb_stagflow/runtest b/Cantera/python/examples/surface_chemistry/catcomb_stagflow/runtest index 3048b8df8..d5c072113 100755 --- a/Cantera/python/examples/surface_chemistry/catcomb_stagflow/runtest +++ b/Cantera/python/examples/surface_chemistry/catcomb_stagflow/runtest @@ -40,7 +40,7 @@ then fi retnCSVTotal=1 -if test $retnStat_csv_0 = "1" +if test $retnStat_csv_0 = "0" then retnCSVTotal=0 fi From b80d34b66e23aa711eb44f38fd274a00edd677d9 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 20 Oct 2011 17:14:57 +0000 Subject: [PATCH 421/446] Fixed a memory leak. The gastran object is now officially owned by the dusty gas tran object. --- Cantera/src/transport/DustyGasTransport.cpp | 16 +++++++++++++--- Cantera/src/transport/DustyGasTransport.h | 3 +++ Cantera/src/transport/TransportBase.h | 10 ++++------ 3 files changed, 20 insertions(+), 9 deletions(-) diff --git a/Cantera/src/transport/DustyGasTransport.cpp b/Cantera/src/transport/DustyGasTransport.cpp index a6d3cd404..827a0bdd6 100644 --- a/Cantera/src/transport/DustyGasTransport.cpp +++ b/Cantera/src/transport/DustyGasTransport.cpp @@ -114,14 +114,19 @@ namespace Cantera { m_diam = right.m_diam; m_perm = right.m_perm; - // Warning -> This is a shallow pointer copy. gastran may not point to the correct object + // Warning -> gastran may not point to the correct object // after this copy. The routine initialize() must be called - m_gastran = right.m_gastran; + if (m_gastran) { + delete m_gastran; + } + m_gastran = right.duplMyselfAsTransport(); + return *this; } //==================================================================================================================== DustyGasTransport::~DustyGasTransport() { + delete m_gastran; } //==================================================================================================================== // Duplication routine for objects which inherit from %Transport @@ -182,7 +187,12 @@ namespace Cantera { // constant mixture attributes m_thermo = phase; m_nsp = m_thermo->nSpecies(); - m_gastran = gastr; + if (m_gastran != gastr) { + if (m_gastran) { + delete m_gastran; + } + m_gastran = gastr; + } // make a local copy of the molecular weights m_mw.resize(m_nsp); diff --git a/Cantera/src/transport/DustyGasTransport.h b/Cantera/src/transport/DustyGasTransport.h index 2a9e96813..83304364b 100644 --- a/Cantera/src/transport/DustyGasTransport.h +++ b/Cantera/src/transport/DustyGasTransport.h @@ -378,6 +378,9 @@ namespace Cantera { doublereal m_perm; //! Pointer to the transport object for the gas phase + /*! + * Note, this object owns the gastran object + */ Transport* m_gastran; }; diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h index 1e1d07e55..e605836ed 100644 --- a/Cantera/src/transport/TransportBase.h +++ b/Cantera/src/transport/TransportBase.h @@ -746,10 +746,9 @@ namespace Cantera { //! Set model parameters for derived classes /*! - * This method may be - * overloaded in subclasses to set model-specific parameters. - * The primary use of this class is to set parameters while in the - * middle of a calculation. + * This method may be derived in subclasses to set model-specific parameters. + * The primary use of this class is to set parameters while in the middle of a calculation + * without actually having to dynamically cast the base Transport pointer. * * @param type Specifies the type of parameters to set * 0 : Diffusion coefficient @@ -759,8 +758,7 @@ namespace Cantera { * @param p Vector of parameters. The length of the vector * varies with the parameterization */ - virtual void setParameters(const int type, const int k, - const doublereal* const p); + virtual void setParameters(const int type, const int k, const doublereal* const p); //! Sets the velocity basis /*! From 974fecdd5a55a0c5f9900474006c99be0912bf51 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 25 Oct 2011 15:57:20 +0000 Subject: [PATCH 422/446] Fixed this test case as an example. Took the timing out of the blessed solution The solution stayed the same. --- .../examples/flames/npflame1/npflame1.py | 2 +- .../flames/npflame1/output_blessed_0.txt | 22 +++++++++---------- .../python/examples/flames/npflame1/runtest | 6 ++--- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/Cantera/python/examples/flames/npflame1/npflame1.py b/Cantera/python/examples/flames/npflame1/npflame1.py index 692e3f1e4..96fe85294 100644 --- a/Cantera/python/examples/flames/npflame1/npflame1.py +++ b/Cantera/python/examples/flames/npflame1/npflame1.py @@ -117,7 +117,7 @@ fcsv.close() print 'solution saved to npflame1.csv' f.showSolution() -f.showStats() +f.showStats(0) diff --git a/Cantera/python/examples/flames/npflame1/output_blessed_0.txt b/Cantera/python/examples/flames/npflame1/output_blessed_0.txt index d0eeebeb9..355a57a1d 100644 --- a/Cantera/python/examples/flames/npflame1/output_blessed_0.txt +++ b/Cantera/python/examples/flames/npflame1/output_blessed_0.txt @@ -2588,14 +2588,14 @@ solution saved to npflame1.csv Statistics: Grid Functions Time Jacobians Time - 8 589 1.2400 22 1.3700 - 8 820 1.7500 49 3.2200 - 13 1341 6.2100 45 6.8000 - 20 2488 19.5700 45 12.2500 - 30 253 3.1500 17 7.8000 - 44 61 1.1300 3 2.1700 - 66 25 0.7400 2 2.4100 - 106 31 1.4700 2 4.4300 - 155 24 1.6800 2 7.2600 - 173 12 0.9400 1 4.2700 - 178 2 0.1600 1 4.4600 + 8 589 NA 22 NA + 8 820 NA 49 NA + 13 1341 NA 45 NA + 20 2488 NA 45 NA + 30 253 NA 17 NA + 44 61 NA 3 NA + 66 25 NA 2 NA + 106 31 NA 2 NA + 155 24 NA 2 NA + 173 12 NA 1 NA + 178 2 NA 1 NA diff --git a/Cantera/python/examples/flames/npflame1/runtest b/Cantera/python/examples/flames/npflame1/runtest index 5d830d68a..bbea0cef4 100755 --- a/Cantera/python/examples/flames/npflame1/runtest +++ b/Cantera/python/examples/flames/npflame1/runtest @@ -2,7 +2,7 @@ # # temp_success="1" -/bin/rm -f output_0.txt npflame1.csv diff_csv.txt diff_out_0.txt +/bin/rm -f output_0.txt npflame1.csv diff_csv.txt diff_out_0.txt npflame1.xml ########################################################################## prog=npflame1.py @@ -40,7 +40,7 @@ then fi retnCSVTotal=1 -if test $retnStat_csv_0 = "1" +if test $retnStat_csv_0 = "0" then retnCSVTotal=0 fi @@ -57,7 +57,7 @@ else echo " see diff_csv.txt " if test $retnTotal != "0" then - echo " ASCII files are different too - see diff_test*.txt" + echo " ASCII files are different too - see diff_out_0.txt" fi fi From 2560431f0725264b9ad45526e3d1f09575b53859 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 25 Oct 2011 16:02:05 +0000 Subject: [PATCH 423/446] Added a printTime option to writeStats() to turn off time printing in output files. Started moving blocks around in configure.in, and fixed an error that corrupted FLIBS. --- Cantera/clib/src/ctonedim.cpp | 7 +- Cantera/clib/src/ctonedim.h | 2 +- Cantera/clib/src/ctstagn.cpp | 4 +- Cantera/clib/src/ctstagn.h | 2 +- Cantera/python/Cantera/OneD/onedim.py | 11 +- .../examples/transport/output_blessed_0.txt | 42 +- Cantera/python/setup.py.in | 9 +- Cantera/python/src/ctonedim_methods.cpp | 11 +- Cantera/src/oneD/OneDim.cpp | 18 +- Cantera/src/oneD/OneDim.h | 8 +- configure | 5264 +++++------------ configure.in | 134 +- .../linux.64_sierra_gcc444_python264_numpy | 13 +- 13 files changed, 1518 insertions(+), 4007 deletions(-) diff --git a/Cantera/clib/src/ctonedim.cpp b/Cantera/clib/src/ctonedim.cpp index 9295c2ed5..7f592f3da 100644 --- a/Cantera/clib/src/ctonedim.cpp +++ b/Cantera/clib/src/ctonedim.cpp @@ -565,12 +565,13 @@ extern "C" { catch (CanteraError) { return -1; } } - int DLL_EXPORT sim1D_writeStats(int i) { + int DLL_EXPORT sim1D_writeStats(int i, int printTime) { try { - _sim1D(i)->writeStats(); + _sim1D(i)->writeStats(printTime); return 0; + } catch (CanteraError) { + return -1; } - catch (CanteraError) { return -1; } } int DLL_EXPORT sim1D_domainIndex(int i, char* name) { diff --git a/Cantera/clib/src/ctonedim.h b/Cantera/clib/src/ctonedim.h index 8bf95e442..76b00dd93 100644 --- a/Cantera/clib/src/ctonedim.h +++ b/Cantera/clib/src/ctonedim.h @@ -84,7 +84,7 @@ extern "C" { EEXXTT int DLL_CPREFIX sim1D_save(int i, char* fname, char* id, char* desc); EEXXTT int DLL_CPREFIX sim1D_restore(int i, char* fname, char* id); - EEXXTT int DLL_CPREFIX sim1D_writeStats(int i); + EEXXTT int DLL_CPREFIX sim1D_writeStats(int i, int printTime = 1); EEXXTT int DLL_CPREFIX sim1D_domainIndex(int i, char* name); EEXXTT double DLL_CPREFIX sim1D_value(int i, int idom, int icomp, int localPoint); EEXXTT double DLL_CPREFIX sim1D_workValue(int i, int idom, diff --git a/Cantera/clib/src/ctstagn.cpp b/Cantera/clib/src/ctstagn.cpp index f7bd67846..f32076cc1 100755 --- a/Cantera/clib/src/ctstagn.cpp +++ b/Cantera/clib/src/ctstagn.cpp @@ -429,8 +429,8 @@ extern "C" { return 0; } - int DLL_EXPORT onedim_writeStats(int i) { - _onedim(i)->writeStats(); + int DLL_EXPORT onedim_writeStats(int i, int printTime) { + _onedim(i)->writeStats(printTime); return 0; } diff --git a/Cantera/clib/src/ctstagn.h b/Cantera/clib/src/ctstagn.h index 4b4b721bf..86742055f 100755 --- a/Cantera/clib/src/ctstagn.h +++ b/Cantera/clib/src/ctstagn.h @@ -68,7 +68,7 @@ extern "C" { int DLL_IMPORT onedim_settransientmode(int i, double dt, double* x); int DLL_IMPORT onedim_setnewtonoptions(int i, int maxage); int DLL_IMPORT onedim_resize(int i); - int DLL_IMPORT onedim_writeStats(int i); + int DLL_IMPORT onedim_writeStats(int i, int printTime = 1); double DLL_IMPORT onedim_timestep(int i, int nsteps, double dt, double* x, double* xnew, int loglevel); int DLL_IMPORT onedim_save(int i, char* fname, char* id, char* desc, double* soln); diff --git a/Cantera/python/Cantera/OneD/onedim.py b/Cantera/python/Cantera/OneD/onedim.py index 3710100a0..9e6782815 100644 --- a/Cantera/python/Cantera/OneD/onedim.py +++ b/Cantera/python/Cantera/OneD/onedim.py @@ -615,9 +615,14 @@ class Stack: """ return _cantera.sim1D_restore(self._hndl, file, id) - def showStats(self): - """Show the statistics for the last solution.""" - return _cantera.sim1D_writeStats(self._hndl) + def showStats(self, printTime = 1): + """Show the statistics for the last solution. + If invoked with no arguments or with a non-zero argument, the + timing statistics will be printed. If invoked with a zero argument, + the timing will not be printed. + Default: print timing enabled. + """ + return _cantera.sim1D_writeStats(self._hndl, _onoff[printTime]) def domainIndex(self, name): """Integer index of the domain with name 'name'""" diff --git a/Cantera/python/examples/transport/output_blessed_0.txt b/Cantera/python/examples/transport/output_blessed_0.txt index 0e67ec2b6..d46c48f75 100644 --- a/Cantera/python/examples/transport/output_blessed_0.txt +++ b/Cantera/python/examples/transport/output_blessed_0.txt @@ -1,31 +1,31 @@ [[ 6.04406471e-06 1.01738100e-06 3.25467803e-15 9.44878921e-07 - 3.20196626e-07 3.45252809e-15 3.12341397e-15 3.09815027e-15 - 2.93166212e-15] + 3.20196626e-07 3.45252809e-15 3.12341397e-15 3.09815027e-15 + 2.93166212e-15] [ 5.08690499e-15 1.00940773e-05 2.95033119e-15 8.72973220e-07 - 2.90021521e-07 3.22819878e-15 2.88500792e-15 2.86100892e-15 - 2.70458750e-15] + 2.90021521e-07 3.22819878e-15 2.88500792e-15 2.86100892e-15 + 2.70458750e-15] [ 3.25467803e-15 5.90066238e-07 2.40899947e-06 8.67150386e-07 - 2.75178768e-07 3.02514701e-15 2.87336197e-15 2.85661971e-15 - 2.73675664e-15] + 2.75178768e-07 3.02514701e-15 2.87336197e-15 2.85661971e-15 + 2.73675664e-15] [ 3.14959640e-15 5.81982147e-07 2.89050129e-15 2.56318977e-06 - 2.87270338e-07 3.25199672e-15 3.05588867e-15 3.04247847e-15 - 2.94726056e-15] + 2.87270338e-07 3.25199672e-15 3.05588867e-15 3.04247847e-15 + 2.94726056e-15] [ 3.20196626e-15 5.80043042e-07 2.75178768e-15 8.61811015e-07 - 2.62146728e-06 2.99922209e-15 2.85602138e-15 2.83971549e-15 - 2.72221044e-15] + 2.62146728e-06 2.99922209e-15 2.85602138e-15 2.83971549e-15 + 2.72221044e-15] [ 3.45252809e-15 6.45639757e-07 3.02514701e-15 9.75599015e-07 - 2.99922209e-07 2.08849997e-06 3.19672263e-15 3.17885565e-15 - 3.07926377e-15] + 2.99922209e-07 2.08849997e-06 3.19672263e-15 3.17885565e-15 + 3.07926377e-15] [ 3.12341397e-15 5.77001585e-07 2.87336197e-15 9.16766600e-07 - 2.85602138e-07 3.19672263e-15 1.62315735e-06 3.02939857e-15 - 2.93566827e-15] + 2.85602138e-07 3.19672263e-15 1.62315735e-06 3.02939857e-15 + 2.93566827e-15] [ 3.09815027e-15 5.72201784e-07 2.85661971e-15 9.12743541e-07 - 2.83971549e-07 3.17885565e-15 3.02939857e-15 1.60480867e-06 - 2.92422492e-15] + 2.83971549e-07 3.17885565e-15 3.02939857e-15 1.60480867e-06 + 2.92422492e-15] [ 2.93166212e-15 5.40917501e-07 2.73675664e-15 8.84178169e-07 - 2.72221044e-07 3.07926377e-15 2.93566827e-15 2.92422492e-15 - 1.51904485e-06]] + 2.72221044e-07 3.07926377e-15 2.93566827e-15 2.92422492e-15 + 1.51904485e-06]] [-0. -0. -0. -0. -0. -0. -0. -0. -0.] -[ -7.04749149e-14 -1.88567695e-05 -3.64733235e-14 -9.21405522e-06 - -3.58390239e-06 -3.54030661e-14 -3.04704797e-14 -3.02364800e-14 - -2.89579939e-14] +[ -6.90966189e-14 -1.84036152e-05 -3.65042941e-14 -9.29059107e-06 + -3.58923841e-06 -3.54785016e-14 -3.07335477e-14 -3.05071031e-14 + -2.92655613e-14] diff --git a/Cantera/python/setup.py.in b/Cantera/python/setup.py.in index 957fa1e62..8d068621c 100644 --- a/Cantera/python/setup.py.in +++ b/Cantera/python/setup.py.in @@ -11,10 +11,11 @@ libs = [] platform = sys.platform flibs = [] -if @build_with_f2c@ <> 1: - flibstr = '@FLIBS@' - f1 = flibstr.replace('-l', ' ') - flibs = f1.split() +# HKM -> not clear we need FLIBS here +#if @build_with_f2c@ == 1: +# flibstr = '@FLIBS@' +# f1 = flibstr.replace('-l', ' ') +# flibs = f1.split() linkargs = '@LCXX_FLAGS@' diff --git a/Cantera/python/src/ctonedim_methods.cpp b/Cantera/python/src/ctonedim_methods.cpp index d1ac71e89..16f533134 100644 --- a/Cantera/python/src/ctonedim_methods.cpp +++ b/Cantera/python/src/ctonedim_methods.cpp @@ -870,11 +870,14 @@ py_sim1D_writeStats(PyObject *self, PyObject *args) { int _val; int i; - if (!PyArg_ParseTuple(args, "i:sim1D_writeStats", &i)) + int printTime; + if (!PyArg_ParseTuple(args, "ii:sim1D_writeStats", &i, &printTime)) { return NULL; - - _val = sim1D_writeStats(i); - if (int(_val) == -1) return reportCanteraError(); + } + _val = sim1D_writeStats(i, printTime); + if (int(_val) == -1) { + return reportCanteraError(); + } return Py_BuildValue("i",_val); } diff --git a/Cantera/src/oneD/OneDim.cpp b/Cantera/src/oneD/OneDim.cpp index a54602ce2..545c68cb1 100644 --- a/Cantera/src/oneD/OneDim.cpp +++ b/Cantera/src/oneD/OneDim.cpp @@ -101,20 +101,26 @@ namespace Cantera { MultiJac& OneDim::jacobian() { return *m_jac; } MultiNewton& OneDim::newton() { return *m_newt; } - void OneDim::writeStats() { + //============================================================================================================== + void OneDim::writeStats(int printTime) { saveStats(); char buf[100]; sprintf(buf,"\nStatistics:\n\n Grid Functions Time Jacobians Time \n"); writelog(buf); int n = m_gridpts.size(); for (int i = 0; i < n; i++) { - sprintf(buf,"%5i %5i %9.4f %5i %9.4f \n", - m_gridpts[i], m_funcEvals[i], m_funcElapsed[i], - m_jacEvals[i], m_jacElapsed[i]); - writelog(buf); + if (printTime) { + sprintf(buf,"%5i %5i %9.4f %5i %9.4f \n", + m_gridpts[i], m_funcEvals[i], m_funcElapsed[i], + m_jacEvals[i], m_jacElapsed[i]); + } else { + sprintf(buf,"%5i %5i NA %5i NA \n", + m_gridpts[i], m_funcEvals[i], m_jacEvals[i]); + } + writelog(buf); } } - + //============================================================================================================== /** * Save statistics on function and Jacobiab evaulation, and reset diff --git a/Cantera/src/oneD/OneDim.h b/Cantera/src/oneD/OneDim.h index 3dfac1b15..1f8382208 100644 --- a/Cantera/src/oneD/OneDim.h +++ b/Cantera/src/oneD/OneDim.h @@ -137,7 +137,13 @@ namespace Cantera { double timeStep(int nsteps, double dt, double* x, double* r, int loglevel); - void writeStats(); + //! Write statistics about the number of iterations and Jacobians at each grid level + /*! + * @param printTime Boolean that indicates whether time should be printed out + * The default is true. It's turned off for test problems where + * we don't want to print any times + */ + void writeStats(int printTime = 1); void save(std::string fname, std::string id, std::string desc, doublereal* sol); diff --git a/configure b/configure index eafb4a6a6..0f45c8d28 100755 --- a/configure +++ b/configure @@ -308,7 +308,7 @@ ac_includes_default="\ # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS F77 FFLAGS LDFLAGS ac_ct_F77 EXEEXT OBJEXT FLIBS BITCOMPILE BITHARDWARE BITCHANGE ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE CXX CXXFLAGS CPPFLAGS ac_ct_CXX use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS ac_ct_CC CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS FC FCFLAGS ac_ct_FC FCLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' +ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS BITCOMPILE BITHARDWARE BITCHANGE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT CC CFLAGS ac_ct_CC ldemulationarg CVF_LIBDIR USE_CLIB_DLL local_inst local_python_inst python_prefix python_win_prefix ctversion homedir ct_libdir ct_bindir ct_incdir ct_incroot ct_datadir ct_demodir ct_templdir ct_tutdir ct_docdir ct_dir ct_mandir build build_cpu build_vendor build_os host host_cpu host_vendor host_os target target_cpu target_vendor target_os username ctroot buildinc buildlib buildbin MAKE GRAPHVIZDIR ARCHIVE DO_RANLIB RANLIB CXX_DEPENDS USERDIR INCL_USER_CODE use_sundials CVODE_LIBS IDA_LIBS sundials_include sundials_lib_dir sundials_lib sundials_lib_dep CANTERA_DEBUG_MODE COMPILE_PURE_FLUIDS phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' ac_subst_files='' # Initialize some variables set by options. @@ -749,18 +749,6 @@ ac_env_target_alias_set=${target_alias+set} ac_env_target_alias_value=$target_alias ac_cv_env_target_alias_set=${target_alias+set} ac_cv_env_target_alias_value=$target_alias -ac_env_F77_set=${F77+set} -ac_env_F77_value=$F77 -ac_cv_env_F77_set=${F77+set} -ac_cv_env_F77_value=$F77 -ac_env_FFLAGS_set=${FFLAGS+set} -ac_env_FFLAGS_value=$FFLAGS -ac_cv_env_FFLAGS_set=${FFLAGS+set} -ac_cv_env_FFLAGS_value=$FFLAGS -ac_env_LDFLAGS_set=${LDFLAGS+set} -ac_env_LDFLAGS_value=$LDFLAGS -ac_cv_env_LDFLAGS_set=${LDFLAGS+set} -ac_cv_env_LDFLAGS_value=$LDFLAGS ac_env_CXX_set=${CXX+set} ac_env_CXX_value=$CXX ac_cv_env_CXX_set=${CXX+set} @@ -769,6 +757,10 @@ ac_env_CXXFLAGS_set=${CXXFLAGS+set} ac_env_CXXFLAGS_value=$CXXFLAGS ac_cv_env_CXXFLAGS_set=${CXXFLAGS+set} ac_cv_env_CXXFLAGS_value=$CXXFLAGS +ac_env_LDFLAGS_set=${LDFLAGS+set} +ac_env_LDFLAGS_value=$LDFLAGS +ac_cv_env_LDFLAGS_set=${LDFLAGS+set} +ac_cv_env_LDFLAGS_value=$LDFLAGS ac_env_CPPFLAGS_set=${CPPFLAGS+set} ac_env_CPPFLAGS_value=$CPPFLAGS ac_cv_env_CPPFLAGS_set=${CPPFLAGS+set} @@ -785,14 +777,14 @@ ac_env_CXXCPP_set=${CXXCPP+set} ac_env_CXXCPP_value=$CXXCPP ac_cv_env_CXXCPP_set=${CXXCPP+set} ac_cv_env_CXXCPP_value=$CXXCPP -ac_env_FC_set=${FC+set} -ac_env_FC_value=$FC -ac_cv_env_FC_set=${FC+set} -ac_cv_env_FC_value=$FC -ac_env_FCFLAGS_set=${FCFLAGS+set} -ac_env_FCFLAGS_value=$FCFLAGS -ac_cv_env_FCFLAGS_set=${FCFLAGS+set} -ac_cv_env_FCFLAGS_value=$FCFLAGS +ac_env_F77_set=${F77+set} +ac_env_F77_value=$F77 +ac_cv_env_F77_set=${F77+set} +ac_cv_env_F77_value=$F77 +ac_env_FFLAGS_set=${FFLAGS+set} +ac_env_FFLAGS_value=$FFLAGS +ac_cv_env_FFLAGS_set=${FFLAGS+set} +ac_cv_env_FFLAGS_value=$FFLAGS # # Report the --help message. @@ -868,19 +860,17 @@ if test -n "$ac_init_help"; then cat <<\_ACEOF Some influential environment variables: - F77 Fortran 77 compiler command - FFLAGS Fortran 77 compiler flags - LDFLAGS linker flags, e.g. -L if you have libraries in a - nonstandard directory CXX C++ compiler command CXXFLAGS C++ compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory CPPFLAGS C/C++ preprocessor flags, e.g. -I if you have headers in a nonstandard directory CC C compiler command CFLAGS C compiler flags CXXCPP C++ preprocessor - FC Fortran compiler command - FCFLAGS Fortran compiler flags + F77 Fortran 77 compiler command + FFLAGS Fortran 77 compiler flags Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. @@ -1314,725 +1304,6 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu - -ac_ext=f -ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' -ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_f77_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran - do - # 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= $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_f77_g=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_prog_f77_g=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_g" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_g" >&6 -if test "$ac_test_FFLAGS" = set; then - FFLAGS=$ac_save_FFLAGS -elif test $ac_cv_prog_f77_g = yes; then - if test "x$ac_cv_f77_compiler_gnu" = xyes; then - FFLAGS="-g -O2" - else - FFLAGS="-g" - fi -else - if test "x$ac_cv_f77_compiler_gnu" = xyes; then - FFLAGS="-O2" - else - FFLAGS= - fi -fi - -G77=`test $ac_compiler_gnu = yes && echo yes` -ac_ext=c -ac_cpp='$CPP $CPPFLAGS' -ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_c_compiler_gnu - - -ac_ext=f -ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' -ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_f77_compiler_gnu -echo "$as_me:$LINENO: checking how to get verbose linking output from $F77" >&5 -echo $ECHO_N "checking how to get verbose linking output from $F77... $ECHO_C" >&6 -if test "${ac_cv_prog_f77_v+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_f77_v= -# Try some options frequently used verbose output -for ac_verb in -v -verbose --verbose -V -\#\#\#; do - cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF - -# Compile and link our simple test program by passing a flag (argument -# 1 to this macro) to the Fortran compiler in order to get -# "verbose" output that we can then parse for the Fortran linker -# flags. -ac_save_FFLAGS=$FFLAGS -FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:1787: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 -FFLAGS=$ac_save_FFLAGS - -rm -f conftest* - -# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where -# /foo, /bar, and /baz are search directories for the Fortran linker. -# Here, we change these into -L/foo -L/bar -L/baz (and put it first): -ac_f77_v_output="`echo $ac_f77_v_output | - grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" - -case $ac_f77_v_output in - # If we are using xlf then replace all the commas with spaces. - *xlfentry*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/,/ /g'` ;; - - # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted - # $LIBS confuse us, and the libraries appear later in the output anyway). - *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; - - # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? - *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; -esac - - - # look for -l* and *.a constructs in the output - for ac_arg in $ac_f77_v_output; do - case $ac_arg in - [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) - ac_cv_prog_f77_v=$ac_verb - break 2 ;; - esac - done -done -if test -z "$ac_cv_prog_f77_v"; then - { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $F77" >&5 -echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} -fi -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 -echo "$as_me: WARNING: compilation failed" >&2;} -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_v" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_v" >&6 -echo "$as_me:$LINENO: checking for Fortran libraries of $F77" >&5 -echo $ECHO_N "checking for Fortran libraries of $F77... $ECHO_C" >&6 -if test "${ac_cv_f77_libs+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test "x$FLIBS" != "x"; then - ac_cv_f77_libs="$FLIBS" # Let the user override the test. -else - -cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF - -# Compile and link our simple test program by passing a flag (argument -# 1 to this macro) to the Fortran compiler in order to get -# "verbose" output that we can then parse for the Fortran linker -# flags. -ac_save_FFLAGS=$FFLAGS -FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:1865: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 -FFLAGS=$ac_save_FFLAGS - -rm -f conftest* - -# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where -# /foo, /bar, and /baz are search directories for the Fortran linker. -# Here, we change these into -L/foo -L/bar -L/baz (and put it first): -ac_f77_v_output="`echo $ac_f77_v_output | - grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" - -case $ac_f77_v_output in - # If we are using xlf then replace all the commas with spaces. - *xlfentry*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/,/ /g'` ;; - - # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted - # $LIBS confuse us, and the libraries appear later in the output anyway). - *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; - - # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? - *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; -esac - - - -ac_cv_f77_libs= - -# Save positional arguments (if any) -ac_save_positional="$@" - -set X $ac_f77_v_output -while test $# != 1; do - shift - ac_arg=$1 - case $ac_arg in - [\\/]*.a | ?:[\\/]*.a) - ac_exists=false - for ac_i in $ac_cv_f77_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" -fi - - ;; - -bI:*) - ac_exists=false - for ac_i in $ac_cv_f77_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - if test "$ac_compiler_gnu" = yes; then - for ac_link_opt in $ac_arg; do - ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" - done -else - ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" -fi -fi - - ;; - # Ignore these flags. - -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) - ;; - -lkernel32) - test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" - ;; - -[LRuY]) - # These flags, when seen by themselves, take an argument. - # We remove the space between option and argument and re-iterate - # unless we find an empty arg or a new option (starting with -) - case $2 in - "" | -*);; - *) - ac_arg="$ac_arg$2" - shift; shift - set X $ac_arg "$@" - ;; - esac - ;; - -YP,*) - for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do - ac_exists=false - for ac_i in $ac_cv_f77_libs; do - if test x"$ac_j" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_arg="$ac_arg $ac_j" - ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" -fi - - done - ;; - -[lLR]*) - ac_exists=false - for ac_i in $ac_cv_f77_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" -fi - - ;; - # Ignore everything else. - esac -done -# restore positional arguments -set X $ac_save_positional; shift - -# We only consider "LD_RUN_PATH" on Solaris systems. If this is seen, -# then we insist that the "run path" must be an absolute path (i.e. it -# must begin with a "/"). -case `(uname -sr) 2>/dev/null` in - "SunOS 5"*) - ac_ld_run_path=`echo $ac_f77_v_output | - sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` - test "x$ac_ld_run_path" != x && - if test "$ac_compiler_gnu" = yes; then - for ac_link_opt in $ac_ld_run_path; do - ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" - done -else - ac_cv_f77_libs="$ac_cv_f77_libs $ac_ld_run_path" -fi - ;; -esac -fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" - -fi -echo "$as_me:$LINENO: result: $ac_cv_f77_libs" >&5 -echo "${ECHO_T}$ac_cv_f77_libs" >&6 -FLIBS="$ac_cv_f77_libs" - - -ac_ext=c -ac_cpp='$CPP $CPPFLAGS' -ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_c_compiler_gnu ac_config_headers="$ac_config_headers config.h" @@ -2139,6 +1410,1333 @@ fi +# +#----------------------------------------------------------------------- +# C++ and C Compilation - INITIAL SECTION +#----------------------------------------------------------------------- +# +# CFLAGS: flags that get attached to the C compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# FFLAGS: flags that get attached to the Fortran compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# +# CXXFLAGS: Flags that get attached to the CXX compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# +if test -z "$AFLAGS" ; then + AFLAGS=" " +fi +if test -z "$CXXFLAGS" ; then + CXXFLAGS="$AFLAGS" +else + CXXFLAGS="$CXXFLAGS"" ""$AFLAGS" +fi +if test -z "$CFLAGS" ; then + CFLAGS="$AFLAGS" +else + CFLAGS="$CFLAGS"" ""$AFLAGS" +fi +if test -z "$FFLAGS" ; then + FFLAGS="$AFLAGS" +else + FFLAGS="$FFLAGS"" ""$AFLAGS" +fi +export CXXFLAGS +export AFLAGS +export CFLAGS +export FFLAGS +# +# Note these should not be within if blocks +# +ac_ext=cc +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +if test -n "$ac_tool_prefix"; then + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CXX"; then + ac_cv_prog_CXX="$CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CXX=$ac_cv_prog_CXX +if test -n "$CXX"; then + echo "$as_me:$LINENO: result: $CXX" >&5 +echo "${ECHO_T}$CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CXX" && break + done +fi +if test -z "$CXX"; then + ac_ct_CXX=$CXX + for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CXX"; then + ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CXX="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CXX=$ac_cv_prog_ac_ct_CXX +if test -n "$ac_ct_CXX"; then + echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 +echo "${ECHO_T}$ac_ct_CXX" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CXX" && break +done +test -n "$ac_ct_CXX" || ac_ct_CXX="g++" + + CXX=$ac_ct_CXX +fi + + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C++ compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5 +echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6 +ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` +if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 + (eval $ac_link_default) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Find the output, starting from the most likely. This scheme is +# not robust to junk in `.', hence go to wildcards (a.*) only as a last +# resort. + +# Be careful to initialize this variable, since it used to be cached. +# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. +ac_cv_exeext= +# b.out is created by i960 compilers. +for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) + ;; + conftest.$ac_ext ) + # This is the source file. + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + # FIXME: I believe we export ac_cv_exeext for Libtool, + # but it would be cool to find out if it's true. Does anybody + # maintain Libtool? --akim. + export ac_cv_exeext + break;; + * ) + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: C++ compiler cannot create executables +See \`config.log' for more details." >&5 +echo "$as_me: error: C++ compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; } +fi + +ac_exeext=$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_file" >&5 +echo "${ECHO_T}$ac_file" >&6 + +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5 +echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6 +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. +if test "$cross_compiling" != yes; then + if { ac_try='./$ac_file' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { echo "$as_me:$LINENO: error: cannot run C++ compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot run C++ compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + fi + fi +fi +echo "$as_me:$LINENO: result: yes" >&5 +echo "${ECHO_T}yes" >&6 + +rm -f a.out a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +# Check the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 +echo "$as_me:$LINENO: result: $cross_compiling" >&5 +echo "${ECHO_T}$cross_compiling" >&6 + +echo "$as_me:$LINENO: checking for suffix of executables" >&5 +echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 +if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + export ac_cv_exeext + break;; + * ) break;; + esac +done +else + { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest$ac_cv_exeext +echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +echo "${ECHO_T}$ac_cv_exeext" >&6 + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +echo "$as_me:$LINENO: checking for suffix of object files" >&5 +echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 +if test "${ac_cv_objext+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } +fi + +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +echo "${ECHO_T}$ac_cv_objext" >&6 +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_cxx_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 +GXX=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CXXFLAGS=${CXXFLAGS+set} +ac_save_CXXFLAGS=$CXXFLAGS +CXXFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 +echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cxx_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cxx_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cxx_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +if test "$ac_test_CXXFLAGS" = set; then + CXXFLAGS=$ac_save_CXXFLAGS +elif test $ac_cv_prog_cxx_g = yes; then + if test "$GXX" = yes; then + CXXFLAGS="-g -O2" + else + CXXFLAGS="-g" + fi +else + if test "$GXX" = yes; then + CXXFLAGS="-O2" + else + CXXFLAGS= + fi +fi +for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_cxx_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + CC=$ac_ct_CC +else + CC="$ac_cv_prog_CC" +fi + +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + echo "$as_me:$LINENO: result: $CC" >&5 +echo "${ECHO_T}$CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +echo "$as_me:$LINENO: checking for $ac_word" >&5 +echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +echo "${ECHO_T}$ac_ct_CC" >&6 +else + echo "$as_me:$LINENO: result: no" >&5 +echo "${ECHO_T}no" >&6 +fi + + test -n "$ac_ct_CC" && break +done + + CC=$ac_ct_CC +fi + +fi + + +test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; } + +# Provide some information about the compiler. +echo "$as_me:$LINENO:" \ + "checking for C compiler version" >&5 +ac_compiler=`set X $ac_compile; echo $2` +{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 + (eval $ac_compiler --version &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 + (eval $ac_compiler -v &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 + (eval $ac_compiler -V &5) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 +if test "${ac_cv_c_compiler_gnu+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_compiler_gnu=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_compiler_gnu=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 +GCC=`test $ac_compiler_gnu = yes && echo yes` +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +CFLAGS="-g" +echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_g+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_g=yes +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +ac_cv_prog_cc_g=no +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +fi +echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 +echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 +if test "${ac_cv_prog_cc_stdc+set}" = set; then + echo $ECHO_N "(cached) $ECHO_C" >&6 +else + ac_cv_prog_cc_stdc=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std1 is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std1. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +# Don't try gcc -ansi; that turns off useful extensions and +# breaks some systems' header files. +# AIX -qlanglvl=ansi +# Ultrix and OSF/1 -std1 +# HP-UX 10.20 and later -Ae +# HP-UX older versions -Aa -D_HPUX_SOURCE +# SVR4 -Xc -D__EXTENSIONS__ +for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_prog_cc_stdc=$ac_arg +break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext +done +rm -f conftest.$ac_ext conftest.$ac_objext +CC=$ac_save_CC + +fi + +case "x$ac_cv_prog_cc_stdc" in + x|xno) + echo "$as_me:$LINENO: result: none needed" >&5 +echo "${ECHO_T}none needed" >&6 ;; + *) + echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 +echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 + CC="$CC $ac_cv_prog_cc_stdc" ;; +esac + +# Some people use a C++ compiler to compile C. Since we use `exit', +# in C++ we need to declare it. In case someone uses the same compiler +# for both compiling C and C++ we need to have the C++ compiler decide +# the declaration of exit, since it's the most demanding environment. +cat >conftest.$ac_ext <<_ACEOF +#ifndef __cplusplus + choke me +#endif +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + for ac_declaration in \ + '' \ + 'extern "C" void std::exit (int) throw (); using std::exit;' \ + 'extern "C" void std::exit (int); using std::exit;' \ + 'extern "C" void exit (int) throw ();' \ + 'extern "C" void exit (int);' \ + 'void exit (int);' +do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +#include +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +continue +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_declaration +int +main () +{ +exit (42); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && + { ac_try='test -z "$ac_c_werror_flag" + || test ! -s conftest.err' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; } && + { ac_try='test -s conftest.$ac_objext' + { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 + (eval $ac_try) 2>&5 + ac_status=$? + echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + break +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +done +rm -f conftest* +if test -n "$ac_declaration"; then + echo '#ifdef __cplusplus' >>confdefs.h + echo $ac_declaration >>confdefs.h + echo '#endif' >>confdefs.h +fi + +else + echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +fi +rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + SHARED_CTLIB=0 @@ -2468,14 +3066,15 @@ fi #---------------------------------------- - - ######################################################### # User Code ######################################################### USERDIR="" INCL_USER_CODE=0 -if test -n "$USER_SRC_DIR"; then USERDIR=$USER_SRC_DIR; INCL_USER_CODE=1; fi +if test -n "$USER_SRC_DIR"; then + USERDIR=$USER_SRC_DIR + INCL_USER_CODE=1 +fi @@ -2492,11 +3091,11 @@ CVODE_LIBS='-lcvode' IDA_LIBS='' if test "x$SUNDIALS_HOME" = "x"; then -SUNDIALS_LIB_DIR=/usr/local/lib -SUNDIALS_INC_DIR=/usr/local/include + SUNDIALS_LIB_DIR=/usr/local/lib + SUNDIALS_INC_DIR=/usr/local/include else -SUNDIALS_LIB_DIR="$SUNDIALS_HOME/lib" -SUNDIALS_INC_DIR="$SUNDIALS_HOME/include" + SUNDIALS_LIB_DIR="$SUNDIALS_HOME/lib" + SUNDIALS_INC_DIR="$SUNDIALS_HOME/include" fi if test "$USE_SUNDIALS" = "default"; then @@ -2505,361 +3104,6 @@ if test "$USE_SUNDIALS" = "default"; then # SUNDIALS_LIB_DIR had a space in it, despite use of double quotes everywhere #ldsave="$LDFLAGS" #LDFLAGS='-L'"$SUNDIALS_LIB_DIR"' '"$ldsave" -ac_ext=cc -ac_cpp='$CXXCPP $CPPFLAGS' -ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC - do - # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. -set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$CXX"; then - ac_cv_prog_CXX="$CXX" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -CXX=$ac_cv_prog_CXX -if test -n "$CXX"; then - echo "$as_me:$LINENO: result: $CXX" >&5 -echo "${ECHO_T}$CXX" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$CXX" && break - done -fi -if test -z "$CXX"; then - ac_ct_CXX=$CXX - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC -do - # Extract the first word of "$ac_prog", so it can be a program name with args. -set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_CXX"; then - ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_CXX="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -ac_ct_CXX=$ac_cv_prog_ac_ct_CXX -if test -n "$ac_ct_CXX"; then - echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 -echo "${ECHO_T}$ac_ct_CXX" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$ac_ct_CXX" && break -done -test -n "$ac_ct_CXX" || ac_ct_CXX="g++" - - CXX=$ac_ct_CXX -fi - - -# Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C++ compiler version" >&5 -ac_compiler=`set X $ac_compile; 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then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-lsundials_cvodes \ --lsundials_cvodes -lsundials_nvecserial -lm $LIBS" +LIBS="-lsundials_cvodes -lsundials_cvodes -lsundials_nvecserial -lm $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF @@ -2941,7 +3184,7 @@ if test ${use_sundials} = 0 ; then fi if test ${use_sundials} = 1 ; then - echo SUNDIALS: succeeded in finding a sundials installation + echo "SUNDIALS: succeeded in finding a sundials installation" else echo SUNDIALS: failed at finding a sundials installation fi @@ -2949,8 +3192,9 @@ fi fi if test "x$USE_SUNDIALS" = "xy"; then -use_sundials=1 + use_sundials=1 fi +echo "Out of Block" sundials_lib_dir= sundials_lib= sundials_lib_dep= @@ -4238,2220 +4482,9 @@ esac # precompile_headers still relevant? # precompile_headers=no -# -# CFLAGS: flags that get attached to the C compiler -# statement. 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then - # We chose a different compiler from the bogus one. - # However, it has the same basename, so the bogon will be chosen - # first if we set CC to just the basename; use the full file name. - shift - ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" - fi -fi -fi -fi -CC=$ac_cv_prog_CC -if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - -fi -if test -z "$CC"; then - if test -n "$ac_tool_prefix"; then - for ac_prog in cl - do - # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. -set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$CC"; then - ac_cv_prog_CC="$CC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -CC=$ac_cv_prog_CC -if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$CC" && break - done -fi -if test -z "$CC"; then - ac_ct_CC=$CC - for ac_prog in cl -do - # Extract the first word of "$ac_prog", so it can be a program name with args. -set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_CC"; then - ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_CC="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -ac_ct_CC=$ac_cv_prog_ac_ct_CC -if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$ac_ct_CC" && break -done - - CC=$ac_ct_CC -fi - -fi - - -test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&5 -echo "$as_me: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } - -# Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } - -echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 -if test "${ac_cv_c_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ - -int -main () -{ -#ifndef __GNUC__ - choke me -#endif - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_compiler_gnu=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -ac_cv_c_compiler_gnu=$ac_compiler_gnu - -fi -echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 -GCC=`test $ac_compiler_gnu = yes && echo yes` -ac_test_CFLAGS=${CFLAGS+set} -ac_save_CFLAGS=$CFLAGS -CFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 -echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ - -int -main () -{ - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_cc_g=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_prog_cc_g=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 -if test "$ac_test_CFLAGS" = set; then - CFLAGS=$ac_save_CFLAGS -elif test $ac_cv_prog_cc_g = yes; then - if test "$GCC" = yes; then - CFLAGS="-g -O2" - else - CFLAGS="-g" - fi -else - if test "$GCC" = yes; then - CFLAGS="-O2" - else - CFLAGS= - fi -fi -echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 -echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - ac_cv_prog_cc_stdc=no -ac_save_CC=$CC -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -#include -#include -#include -#include -/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ -struct buf { int x; }; -FILE * (*rcsopen) (struct buf *, struct stat *, int); -static char *e (p, i) - char **p; - int i; -{ - return p[i]; -} -static char *f (char * (*g) (char **, int), char **p, ...) -{ - char *s; - va_list v; - va_start (v,p); - s = g (p, va_arg (v,int)); - va_end (v); - return s; -} - -/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has - function prototypes and stuff, but not '\xHH' hex character constants. - These don't provoke an error unfortunately, instead are silently treated - as 'x'. The following induces an error, until -std1 is added to get - proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an - array size at least. It's necessary to write '\x00'==0 to get something - that's true only with -std1. */ -int osf4_cc_array ['\x00' == 0 ? 1 : -1]; - -int test (int i, double x); -struct s1 {int (*f) (int a);}; -struct s2 {int (*f) (double a);}; -int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); -int argc; -char **argv; -int -main () -{ -return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; - ; - return 0; -} -_ACEOF -# Don't try gcc -ansi; that turns off useful extensions and -# breaks some systems' header files. -# AIX -qlanglvl=ansi -# Ultrix and OSF/1 -std1 -# HP-UX 10.20 and later -Ae -# HP-UX older versions -Aa -D_HPUX_SOURCE -# SVR4 -Xc -D__EXTENSIONS__ -for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" -do - CC="$ac_save_CC $ac_arg" - rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_cc_stdc=$ac_arg -break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext -done -rm -f conftest.$ac_ext conftest.$ac_objext -CC=$ac_save_CC - -fi - -case "x$ac_cv_prog_cc_stdc" in - x|xno) - echo "$as_me:$LINENO: result: none needed" >&5 -echo "${ECHO_T}none needed" >&6 ;; - *) - echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 - CC="$CC $ac_cv_prog_cc_stdc" ;; -esac - -# Some people use a C++ compiler to compile C. Since we use `exit', -# in C++ we need to declare it. In case someone uses the same compiler -# for both compiling C and C++ we need to have the C++ compiler decide -# the declaration of exit, since it's the most demanding environment. -cat >conftest.$ac_ext <<_ACEOF -#ifndef __cplusplus - choke me -#endif -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi - -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -ac_ext=cc -ac_cpp='$CXXCPP $CPPFLAGS' -ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_cxx_compiler_gnu - - - +if test "x$OS_IS_WIN" != "x1"; then echo "$as_me:$LINENO: checking for ability to precompile headers" >&5 echo $ECHO_N "checking for ability to precompile headers... $ECHO_C" >&6 - if test -n "$GCC"; then msg=`rm -f *h.gch; $CXX testpch.h &> /dev/null` if test -f testpch.h.gch; then @@ -10602,7 +8635,7 @@ fi # Provide some information about the compiler. -echo "$as_me:10605:" \ +echo "$as_me:8638:" \ "checking for Fortran 77 compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 @@ -10756,7 +8789,8 @@ else FFLAGS=$FFLAGS' -fno-second-underscore' fi fi -#F77LDRCLIBS= +F77LDRCLIBS= + ac_ext=f ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -10808,7 +8842,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:10811: \"$ac_link\") >&5 +(eval echo $as_me:8845: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -10886,7 +8920,7 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:10889: \"$ac_link\") >&5 +(eval echo $as_me:8923: \"$ac_link\") >&5 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS @@ -11061,548 +9095,6 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu echo " Macro returned with FLIBS defined as " $FLIBS - -# -ac_ext=${FC_SRCEXT-f} -ac_compile='$FC -c $FCFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext >&5' -ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_fc_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in f95 fort xlf95 ifc efc pgf95 lf95 gfortran f90 xlf90 pgf90 epcf90 g77 f77 xlf frt pgf77 fort77 fl32 af77 - do - # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. -set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_FC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$FC"; then - ac_cv_prog_FC="$FC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_FC="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -FC=$ac_cv_prog_FC -if test -n "$FC"; then - echo "$as_me:$LINENO: result: $FC" >&5 -echo "${ECHO_T}$FC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$FC" && break - done -fi -if test -z "$FC"; then - ac_ct_FC=$FC - for ac_prog in f95 fort xlf95 ifc efc pgf95 lf95 gfortran f90 xlf90 pgf90 epcf90 g77 f77 xlf frt pgf77 fort77 fl32 af77 -do - # Extract the first word of "$ac_prog", so it can be a program name with args. -set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_FC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_FC"; then - ac_cv_prog_ac_ct_FC="$ac_ct_FC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_FC="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done -done - -fi -fi -ac_ct_FC=$ac_cv_prog_ac_ct_FC -if test -n "$ac_ct_FC"; then - echo "$as_me:$LINENO: result: $ac_ct_FC" >&5 -echo "${ECHO_T}$ac_ct_FC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - test -n "$ac_ct_FC" && break -done - - FC=$ac_ct_FC -fi - - -# Provide some information about the compiler. -echo "$as_me:11158:" \ - "checking for Fortran compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -rm -f a.out - -# If we don't use `.F' as extension, the preprocessor is not run on the -# input file. (Note that this only needs to work for GNU compilers.) -ac_save_ext=$ac_ext -ac_ext=F -echo "$as_me:$LINENO: checking whether we are using the GNU Fortran compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU Fortran compiler... $ECHO_C" >&6 -if test "${ac_cv_fc_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF - program main -#ifndef __GNUC__ - choke me -#endif - - end -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_fc_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_compiler_gnu=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -ac_cv_fc_compiler_gnu=$ac_compiler_gnu - -fi -echo "$as_me:$LINENO: result: $ac_cv_fc_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_fc_compiler_gnu" >&6 -ac_ext=$ac_save_ext -ac_test_FFLAGS=${FCFLAGS+set} -ac_save_FFLAGS=$FCFLAGS -FCFLAGS= -echo "$as_me:$LINENO: checking whether $FC accepts -g" >&5 -echo $ECHO_N "checking whether $FC accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_fc_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - FCFLAGS=-g -cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_fc_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_fc_g=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_prog_fc_g=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_fc_g" >&5 -echo "${ECHO_T}$ac_cv_prog_fc_g" >&6 -if test "$ac_test_FFLAGS" = set; then - FCFLAGS=$ac_save_FFLAGS -elif test $ac_cv_prog_fc_g = yes; then - if test "x$ac_cv_fc_compiler_gnu" = xyes; then - FCFLAGS="-g -O2" - else - FCFLAGS="-g" - fi -else - if test "x$ac_cv_fc_compiler_gnu" = xyes; then - FCFLAGS="-O2" - else - FCFLAGS= - fi -fi - -ac_ext=cc -ac_cpp='$CXXCPP $CPPFLAGS' -ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_cxx_compiler_gnu - - -ac_ext=${FC_SRCEXT-f} -ac_compile='$FC -c $FCFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext >&5' -ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $FCFLAGS_SRCEXT conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_fc_compiler_gnu -echo "$as_me:$LINENO: checking how to get verbose linking output from $FC" >&5 -echo $ECHO_N "checking how to get verbose linking output from $FC... $ECHO_C" >&6 -if test "${ac_cv_prog_fc_v+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_fc_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_fc_v= -# Try some options frequently used verbose output -for ac_verb in -v -verbose --verbose -V -\#\#\#; do - cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF - -# Compile and link our simple test program by passing a flag (argument -# 1 to this macro) to the Fortran compiler in order to get -# "verbose" output that we can then parse for the Fortran linker -# flags. -ac_save_FFLAGS=$FCFLAGS -FCFLAGS="$FCFLAGS $ac_verb" -(eval echo $as_me:11353: \"$ac_link\") >&5 -ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_fc_v_output" >&5 -FCFLAGS=$ac_save_FFLAGS - -rm -f conftest* - -# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where -# /foo, /bar, and /baz are search directories for the Fortran linker. -# Here, we change these into -L/foo -L/bar -L/baz (and put it first): -ac_fc_v_output="`echo $ac_fc_v_output | - grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_fc_v_output" - -case $ac_fc_v_output in - # If we are using xlf then replace all the commas with spaces. - *xlfentry*) - ac_fc_v_output=`echo $ac_fc_v_output | sed 's/,/ /g'` ;; - - # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted - # $LIBS confuse us, and the libraries appear later in the output anyway). - *mGLOB_options_string*) - ac_fc_v_output=`echo $ac_fc_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; - - # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? - *cft90*) - ac_fc_v_output=`echo $ac_fc_v_output | sed "s/\"//g"` ;; -esac - - - # look for -l* and *.a constructs in the output - for ac_arg in $ac_fc_v_output; do - case $ac_arg in - [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) - ac_cv_prog_fc_v=$ac_verb - break 2 ;; - esac - done -done -if test -z "$ac_cv_prog_fc_v"; then - { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $FC" >&5 -echo "$as_me: WARNING: cannot determine how to obtain linking information from $FC" >&2;} -fi -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 -echo "$as_me: WARNING: compilation failed" >&2;} -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_fc_v" >&5 -echo "${ECHO_T}$ac_cv_prog_fc_v" >&6 -echo "$as_me:$LINENO: checking for Fortran libraries of $FC" >&5 -echo $ECHO_N "checking for Fortran libraries of $FC... $ECHO_C" >&6 -if test "${ac_cv_fc_libs+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test "x$FCLIBS" != "x"; then - ac_cv_fc_libs="$FCLIBS" # Let the user override the test. -else - -cat >conftest.$ac_ext <<_ACEOF - program main - - end -_ACEOF - -# Compile and link our simple test program by passing a flag (argument -# 1 to this macro) to the Fortran compiler in order to get -# "verbose" output that we can then parse for the Fortran linker -# flags. -ac_save_FFLAGS=$FCFLAGS -FCFLAGS="$FCFLAGS $ac_cv_prog_fc_v" -(eval echo $as_me:11431: \"$ac_link\") >&5 -ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_fc_v_output" >&5 -FCFLAGS=$ac_save_FFLAGS - -rm -f conftest* - -# On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where -# /foo, /bar, and /baz are search directories for the Fortran linker. -# Here, we change these into -L/foo -L/bar -L/baz (and put it first): -ac_fc_v_output="`echo $ac_fc_v_output | - grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_fc_v_output" - -case $ac_fc_v_output in - # If we are using xlf then replace all the commas with spaces. - *xlfentry*) - ac_fc_v_output=`echo $ac_fc_v_output | sed 's/,/ /g'` ;; - - # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted - # $LIBS confuse us, and the libraries appear later in the output anyway). - *mGLOB_options_string*) - ac_fc_v_output=`echo $ac_fc_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; - - # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? - *cft90*) - ac_fc_v_output=`echo $ac_fc_v_output | sed "s/\"//g"` ;; -esac - - - -ac_cv_fc_libs= - -# Save positional arguments (if any) -ac_save_positional="$@" - -set X $ac_fc_v_output -while test $# != 1; do - shift - ac_arg=$1 - case $ac_arg in - [\\/]*.a | ?:[\\/]*.a) - ac_exists=false - for ac_i in $ac_cv_fc_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" -fi - - ;; - -bI:*) - ac_exists=false - for ac_i in $ac_cv_fc_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - if test "$ac_compiler_gnu" = yes; then - for ac_link_opt in $ac_arg; do - ac_cv_fc_libs="$ac_cv_fc_libs -Xlinker $ac_link_opt" - done -else - ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" -fi -fi - - ;; - # Ignore these flags. - -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) - ;; - -lkernel32) - test x"$CYGWIN" != xyes && ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" - ;; - -[LRuY]) - # These flags, when seen by themselves, take an argument. - # We remove the space between option and argument and re-iterate - # unless we find an empty arg or a new option (starting with -) - case $2 in - "" | -*);; - *) - ac_arg="$ac_arg$2" - shift; shift - set X $ac_arg "$@" - ;; - esac - ;; - -YP,*) - for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do - ac_exists=false - for ac_i in $ac_cv_fc_libs; do - if test x"$ac_j" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_arg="$ac_arg $ac_j" - ac_cv_fc_libs="$ac_cv_fc_libs $ac_j" -fi - - done - ;; - -[lLR]*) - ac_exists=false - for ac_i in $ac_cv_fc_libs; do - if test x"$ac_arg" = x"$ac_i"; then - ac_exists=true - break - fi - done - - if test x"$ac_exists" = xtrue; then - : -else - ac_cv_fc_libs="$ac_cv_fc_libs $ac_arg" -fi - - ;; - # Ignore everything else. - esac -done -# restore positional arguments -set X $ac_save_positional; shift - -# We only consider "LD_RUN_PATH" on Solaris systems. If this is seen, -# then we insist that the "run path" must be an absolute path (i.e. it -# must begin with a "/"). -case `(uname -sr) 2>/dev/null` in - "SunOS 5"*) - ac_ld_run_path=`echo $ac_fc_v_output | - sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` - test "x$ac_ld_run_path" != x && - if test "$ac_compiler_gnu" = yes; then - for ac_link_opt in $ac_ld_run_path; do - ac_cv_fc_libs="$ac_cv_fc_libs -Xlinker $ac_link_opt" - done -else - ac_cv_fc_libs="$ac_cv_fc_libs $ac_ld_run_path" -fi - ;; -esac -fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" - -fi -echo "$as_me:$LINENO: result: $ac_cv_fc_libs" >&5 -echo "${ECHO_T}$ac_cv_fc_libs" >&6 -FCLIBS="$ac_cv_fc_libs" - - -ac_ext=cc -ac_cpp='$CXXCPP $CPPFLAGS' -ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_cxx_compiler_gnu - - -echo 'FLIBS = ' $FLIBS - override_f77_libs=0; #case $ac_sys_system in @@ -12653,16 +10145,19 @@ s,@ECHO_C@,$ECHO_C,;t t s,@ECHO_N@,$ECHO_N,;t t s,@ECHO_T@,$ECHO_T,;t t s,@LIBS@,$LIBS,;t t -s,@F77@,$F77,;t t -s,@FFLAGS@,$FFLAGS,;t t -s,@LDFLAGS@,$LDFLAGS,;t t -s,@ac_ct_F77@,$ac_ct_F77,;t t -s,@EXEEXT@,$EXEEXT,;t t -s,@OBJEXT@,$OBJEXT,;t t -s,@FLIBS@,$FLIBS,;t t s,@BITCOMPILE@,$BITCOMPILE,;t t s,@BITHARDWARE@,$BITHARDWARE,;t t s,@BITCHANGE@,$BITCHANGE,;t t +s,@CXX@,$CXX,;t t +s,@CXXFLAGS@,$CXXFLAGS,;t t +s,@LDFLAGS@,$LDFLAGS,;t t +s,@CPPFLAGS@,$CPPFLAGS,;t t +s,@ac_ct_CXX@,$ac_ct_CXX,;t t +s,@EXEEXT@,$EXEEXT,;t t +s,@OBJEXT@,$OBJEXT,;t t +s,@CC@,$CC,;t t +s,@CFLAGS@,$CFLAGS,;t t +s,@ac_ct_CC@,$ac_ct_CC,;t t s,@ldemulationarg@,$ldemulationarg,;t t s,@CVF_LIBDIR@,$CVF_LIBDIR,;t t s,@USE_CLIB_DLL@,$USE_CLIB_DLL,;t t @@ -12708,10 +10203,6 @@ s,@RANLIB@,$RANLIB,;t t s,@CXX_DEPENDS@,$CXX_DEPENDS,;t t s,@USERDIR@,$USERDIR,;t t s,@INCL_USER_CODE@,$INCL_USER_CODE,;t t -s,@CXX@,$CXX,;t t -s,@CXXFLAGS@,$CXXFLAGS,;t t -s,@CPPFLAGS@,$CPPFLAGS,;t t -s,@ac_ct_CXX@,$ac_ct_CXX,;t t s,@use_sundials@,$use_sundials,;t t s,@CVODE_LIBS@,$CVODE_LIBS,;t t s,@IDA_LIBS@,$IDA_LIBS,;t t @@ -12773,9 +10264,6 @@ s,@PIC@,$PIC,;t t s,@INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t s,@INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t s,@INSTALL_DATA@,$INSTALL_DATA,;t t -s,@CC@,$CC,;t t -s,@CFLAGS@,$CFLAGS,;t t -s,@ac_ct_CC@,$ac_ct_CC,;t t s,@CXXCPP@,$CXXCPP,;t t s,@EGREP@,$EGREP,;t t s,@SOEXT@,$SOEXT,;t t @@ -12784,10 +10272,10 @@ s,@CXX_INCLUDES@,$CXX_INCLUDES,;t t s,@LCXX_FLAGS@,$LCXX_FLAGS,;t t s,@LCXX_END_LIBS@,$LCXX_END_LIBS,;t t s,@HAVE_STRIPSYMBOLS@,$HAVE_STRIPSYMBOLS,;t t -s,@FC@,$FC,;t t -s,@FCFLAGS@,$FCFLAGS,;t t -s,@ac_ct_FC@,$ac_ct_FC,;t t -s,@FCLIBS@,$FCLIBS,;t t +s,@F77@,$F77,;t t +s,@FFLAGS@,$FFLAGS,;t t +s,@ac_ct_F77@,$ac_ct_F77,;t t +s,@FLIBS@,$FLIBS,;t t s,@F90@,$F90,;t t s,@BUILD_F90@,$BUILD_F90,;t t s,@F90FLAGS@,$F90FLAGS,;t t diff --git a/configure.in b/configure.in index c58010bc6..2b4c37672 100755 --- a/configure.in +++ b/configure.in @@ -2,6 +2,7 @@ dnl Process this file with autoconf to produce a configure script. define([AC_CACHE_LOAD], )dnl define([AC_CACHE_SAVE], )dnl AC_INIT(Cantera,1.7.0) + AC_CONFIG_HEADER(config.h) # AC_CONFIG_AUX_DIR(.) # AC_CONFIG_SRCDIR(./License.txt) @@ -79,6 +80,50 @@ fi AC_SUBST(BITCOMPILE) AC_SUBST(BITHARDWARE) AC_SUBST(BITCHANGE) +# +#----------------------------------------------------------------------- +# C++ and C Compilation - INITIAL SECTION +#----------------------------------------------------------------------- +# +# CFLAGS: flags that get attached to the C compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# FFLAGS: flags that get attached to the Fortran compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# +# CXXFLAGS: Flags that get attached to the CXX compiler +# statement. AFLAGS are base flags that +# get added to compilers and loaders. +# +if test -z "$AFLAGS" ; then + AFLAGS=" " +fi +if test -z "$CXXFLAGS" ; then + CXXFLAGS="$AFLAGS" +else + CXXFLAGS="$CXXFLAGS"" ""$AFLAGS" +fi +if test -z "$CFLAGS" ; then + CFLAGS="$AFLAGS" +else + CFLAGS="$CFLAGS"" ""$AFLAGS" +fi +if test -z "$FFLAGS" ; then + FFLAGS="$AFLAGS" +else + FFLAGS="$FFLAGS"" ""$AFLAGS" +fi +export CXXFLAGS +export AFLAGS +export CFLAGS +export FFLAGS +# +# Note these should not be within if blocks +# +AC_PROG_CXX() +AC_PROG_CC() + SHARED_CTLIB=0 @@ -306,14 +351,15 @@ AC_SUBST(CXX_DEPENDS) #---------------------------------------- - - ######################################################### # User Code ######################################################### USERDIR="" INCL_USER_CODE=0 -if test -n "$USER_SRC_DIR"; then USERDIR=$USER_SRC_DIR; INCL_USER_CODE=1; fi +if test -n "$USER_SRC_DIR"; then + USERDIR=$USER_SRC_DIR + INCL_USER_CODE=1 +fi AC_SUBST(USERDIR) AC_SUBST(INCL_USER_CODE) @@ -325,11 +371,11 @@ CVODE_LIBS='-lcvode' IDA_LIBS='' if test "x$SUNDIALS_HOME" = "x"; then -SUNDIALS_LIB_DIR=/usr/local/lib -SUNDIALS_INC_DIR=/usr/local/include + SUNDIALS_LIB_DIR=/usr/local/lib + SUNDIALS_INC_DIR=/usr/local/include else -SUNDIALS_LIB_DIR="$SUNDIALS_HOME/lib" -SUNDIALS_INC_DIR="$SUNDIALS_HOME/include" + SUNDIALS_LIB_DIR="$SUNDIALS_HOME/lib" + SUNDIALS_INC_DIR="$SUNDIALS_HOME/include" fi if test "$USE_SUNDIALS" = "default"; then @@ -338,8 +384,7 @@ if test "$USE_SUNDIALS" = "default"; then # SUNDIALS_LIB_DIR had a space in it, despite use of double quotes everywhere #ldsave="$LDFLAGS" #LDFLAGS='-L'"$SUNDIALS_LIB_DIR"' '"$ldsave" -AC_CHECK_LIB(sundials_cvodes, CVodeCreate, [use_sundials=1], [use_sundials=0],\ -[-lsundials_cvodes -lsundials_nvecserial -lm]) +AC_CHECK_LIB(sundials_cvodes, CVodeCreate, [use_sundials=1], [use_sundials=0], [-lsundials_cvodes -lsundials_nvecserial -lm] ) if test ${use_sundials} = 0 ; then tmpFile="$SUNDIALS_LIB_DIR/libsundials_cvodes.a" @@ -349,7 +394,7 @@ if test ${use_sundials} = 0 ; then fi if test ${use_sundials} = 1 ; then - echo SUNDIALS: succeeded in finding a sundials installation + echo "SUNDIALS: succeeded in finding a sundials installation" else echo SUNDIALS: failed at finding a sundials installation fi @@ -357,8 +402,9 @@ fi fi if test "x$USE_SUNDIALS" = "xy"; then -use_sundials=1 + use_sundials=1 fi +echo "Out of Block" sundials_lib_dir= sundials_lib= sundials_lib_dep= @@ -844,6 +890,7 @@ fi case $ac_sys_system in Linux) NEED_F2C=1 ;; esac +NEED_F2C= # # Create a variable build_f2c_lib that determines whether @@ -855,7 +902,7 @@ if test -n "$NEED_F2C" ; then build_f2c_lib=1 else case $ac_sys_system in - Linux) F2C_SYSTEMLIB="-lg2c" + Linux) F2C_SYSTEMLIB="" esac fi AC_SUBST(build_f2c_lib) @@ -995,7 +1042,7 @@ then RAW_LIBS_DEP=$RAW_LIBS_DEP' 'libctf2c.a else case $ac_sys_system in - Linux) LOCAL_LIBS=$LOCAL_LIBS' '-lg2c;; + Linux) LOCAL_LIBS=$LOCAL_LIBS;; esac fi # Darwin*) LOCAL_LIBS=$LOCAL_LIBS' '-lg2c;; @@ -1382,55 +1429,8 @@ esac # precompile_headers still relevant? # precompile_headers=no -# -# CFLAGS: flags that get attached to the C compiler -# statement. AFLAGS are base flags that -# get added to compilers and loaders. -# FFLAGS: flags that get attached to the Fortran compiler -# statement. AFLAGS are base flags that -# get added to compilers and loaders. -# -# CXXFLAGS: Flags that get attached to the CXX compiler -# statement. AFLAGS are base flags that -# get added to compilers and loaders. -# -if test -z "$AFLAGS" ; then - AFLAGS=" " -fi -if test -z "$CXXFLAGS" ; then - CXXFLAGS="$AFLAGS" -else - CXXFLAGS="$CXXFLAGS"" ""$AFLAGS" -fi -if test -z "$CFLAGS" ; then - CFLAGS="$AFLAGS" -else - CFLAGS="$CFLAGS"" ""$AFLAGS" -fi -if test -z "$FFLAGS" ; then - FFLAGS="$AFLAGS" -else - FFLAGS="$FFLAGS"" ""$AFLAGS" -fi - -if test "x$OS_IS_WIN" = "x1"; then - #CXX=cl.exe - #CC=cl.exe - #export CXX - AC_PROG_CXX() - AC_PROG_CC() -else - -# -# Determines the CXX compiler to use -# -export CXX -AC_PROG_CXX() -AC_PROG_CC() - - +if test "x$OS_IS_WIN" != "x1"; then AC_MSG_CHECKING(for ability to precompile headers) - if test -n "$GCC"; then msg=`rm -f *h.gch; $CXX testpch.h &> /dev/null` if test -f testpch.h.gch; then @@ -1549,7 +1549,11 @@ AC_SUBST(HAVE_STRIPSYMBOLS) # Fortran #--------------------------------------------------------------------------- -#if test x"$build_with_f2c" = "x0"; then +# +# This macro sets the substitution variable, @F77@ and @G77@ +# +echo " this is $F77" +echo "this is a test" AC_PROG_F77() # if G77 is defined, then add a flag to turn off adding a second underscore @@ -1561,10 +1565,11 @@ else FFLAGS=$FFLAGS' -fno-second-underscore' fi fi - -dnl Checks for libraries. +F77LDRCLIBS= AC_F77_LIBRARY_LDFLAGS() +echo " Macro returned with FLIBS defined as " $FLIBS + override_f77_libs=0; #case $ac_sys_system in @@ -1691,7 +1696,6 @@ AC_OBJEXT AC_EXEEXT AC_SUBST(precompile_headers) -AC_SUBST(FLIBS) AC_SUBST(OS_IS_DARWIN) AC_SUBST(OS_IS_WIN) AC_SUBST(OS_IS_CYGWIN) diff --git a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy index 7ab813602..39a93c332 100755 --- a/docs/install_examples/linux.64_sierra_gcc444_python264_numpy +++ b/docs/install_examples/linux.64_sierra_gcc444_python264_numpy @@ -43,7 +43,7 @@ export BUILD_MATLAB_TOOLBOX INSTALL_BIN=config/install-sh export INSTALL_BIN -MATLAB_CMD="/usr/local/matlab/7.9/bin/matlab" +MATLAB_CMD="/usr/local/matlab/7.13/bin/matlab" export MATLAB_CMD BUILD_F90_INTERFACE="y" @@ -85,20 +85,17 @@ export CC F77='/sierra/Sntools/extras/compilers/gcc-4.4.4/bin/gfortran' export F77 -FFLAGS="-g -fno-second-underscore" + +FFLAGS="-g " export FFLAGS - -CFLAGS="-g -Wall" +CFLAGS="-g " export CFLAGS #CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL -DDEBUG_NUMJAC" -CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL " +CXXFLAGS="-g -Wall -Woverloaded-virtual -DDEBUG_HKM -DDEBUG_HKM_EPEQUIL " export CXXFLAGS -FFLAGS="-g -DDEBUG_HKM -fno-second-underscore" -export FFLAGS - LDFLAGS=' ' export LDFLAGS From 5d1e55596d782049d229953ad0924bb35a7eb5ce Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 31 Oct 2011 22:05:07 +0000 Subject: [PATCH 424/446] Added the RedlichKisterVPSSTP thermo model to the system. Fixed an error in MultiPhase that Carlos found. --- Cantera/src/equil/MultiPhase.cpp | 8 +- Cantera/src/thermo/Makefile.in | 4 +- Cantera/src/thermo/RedlichKisterVPSSTP.cpp | 1136 ++++++++++++++++++++ Cantera/src/thermo/RedlichKisterVPSSTP.h | 983 +++++++++++++++++ Cantera/src/thermo/ThermoFactory.cpp | 12 +- Cantera/src/thermo/ThermoFactory.h | 5 +- Cantera/src/thermo/mix_defs.h | 2 + docs/Cantera.cfg.in | 2 + 8 files changed, 2142 insertions(+), 10 deletions(-) create mode 100644 Cantera/src/thermo/RedlichKisterVPSSTP.cpp create mode 100644 Cantera/src/thermo/RedlichKisterVPSSTP.h diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp index 96e49176c..53c17ef45 100644 --- a/Cantera/src/equil/MultiPhase.cpp +++ b/Cantera/src/equil/MultiPhase.cpp @@ -293,6 +293,9 @@ namespace Cantera { } //==================================================================================================================== int MultiPhase::speciesIndex(std::string speciesName, std::string phaseName) { + if (!m_init) { + init(); + } int p = phaseIndex(phaseName); if (p < 0) { throw CanteraError("MultiPhase::speciesIndex", "phase not found: " + phaseName); @@ -382,7 +385,7 @@ namespace Cantera { else return false; } - + //==================================================================================================================== /// The Gibbs free energy of the mixture (J). doublereal MultiPhase::gibbs() const { index_t i; @@ -455,6 +458,9 @@ namespace Cantera { /// Set the mole fractions of phase \a n to the values in /// array \a x. void MultiPhase::setPhaseMoleFractions(const index_t n, const doublereal* const x) { + if (!m_init) { + init(); + } phase_t* p = m_phase[n]; p->setState_TPX(m_temp, m_press, x); int nsp = p->nSpecies(); diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in index 4cdc7580e..a7f87e4ec 100644 --- a/Cantera/src/thermo/Makefile.in +++ b/Cantera/src/thermo/Makefile.in @@ -81,11 +81,11 @@ ifeq ($(do_issp),1) ISSP_OBJ = IdealSolidSolnPhase.o StoichSubstanceSSTP.o SingleSpeciesTP.o MineralEQ3.o \ GibbsExcessVPSSTP.o MolarityIonicVPSSTP.o MargulesVPSSTP.o \ IonsFromNeutralVPSSTP.o PDSS_IonsFromNeutral.o FixedChemPotSSTP.o \ - MixedSolventElectrolyte.o + MixedSolventElectrolyte.o RedlichKisterVPSSTP.o ISSP_H = IdealSolidSolnPhase.h StoichSubstanceSSTP.h SingleSpeciesTP.h MineralEQ3.h \ GibbsExcessVPSSTP.h MolarityIonicVPSSTP.h MargulesVPSSTP.h \ IonsFromNeutralVPSSTP.h PDSS_IonsFromNeutral.h FixedChemPotSSTP.h \ - MixedSolventElectrolyte.h + MixedSolventElectrolyte.h RedlichKisterVPSSTP.h endif CATHERMO_OBJ = $(THERMO_OBJ) $(ELECTRO_OBJ) $(ISSP_OBJ) diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.cpp b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp new file mode 100644 index 000000000..a97ee19d8 --- /dev/null +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp @@ -0,0 +1,1136 @@ +/** + * @file RedlichKisterVPSSTP.cpp + * Definitions for ThermoPhase object for phases which + * employ excess gibbs free energy formulations related to RedlichKister + * expansions (see \ref thermoprops + * and class \link Cantera::RedlichKisterVPSSTP RedlichKisterVPSSTP\endlink). + * + */ +/* + * Copywrite (2009) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Date: 2011-04-14 12:24:13 -0600 (Thu, 14 Apr 2011) $ + * $Revision: 713 $ + */ + + +#include "RedlichKisterVPSSTP.h" +#include "ThermoFactory.h" +#include + +using namespace std; + +namespace Cantera { + + static const double xxSmall = 1.0E-150; + //==================================================================================================================== + /* + * Default constructor. + * + */ + RedlichKisterVPSSTP::RedlichKisterVPSSTP() : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + m_pSpecies_A_ij(0), + m_pSpecies_B_ij(0), + m_N_ij(0), + m_HE_m_ij(0), + m_SE_m_ij(0), + formRedlichKister_(0), + formTempModel_(0), + dlnActCoeff_dX_() + { + } + //==================================================================================================================== + /* + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + + */ + RedlichKisterVPSSTP::RedlichKisterVPSSTP(std::string inputFile, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + m_pSpecies_A_ij(0), + m_pSpecies_B_ij(0), + m_N_ij(0), + m_HE_m_ij(0), + m_SE_m_ij(0), + formRedlichKister_(0), + formTempModel_(0), + dlnActCoeff_dX_() + { + constructPhaseFile(inputFile, id); + } + //==================================================================================================================== + RedlichKisterVPSSTP::RedlichKisterVPSSTP(XML_Node& phaseRoot, std::string id) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + m_pSpecies_A_ij(0), + m_pSpecies_B_ij(0), + m_N_ij(0), + m_HE_m_ij(0), + m_SE_m_ij(0), + formRedlichKister_(0), + formTempModel_(0), + dlnActCoeff_dX_() + { + constructPhaseXML(phaseRoot, id); + } + //==================================================================================================================== + // Special constructor for a hard-coded problem + /* + * + * LiKCl treating the PseudoBinary layer as passthrough. + * -> test to predict the eutectic and liquidus correctly. + * + */ + RedlichKisterVPSSTP::RedlichKisterVPSSTP(int testProb) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + m_pSpecies_A_ij(0), + m_pSpecies_B_ij(0), + m_N_ij(0), + m_HE_m_ij(0), + m_SE_m_ij(0), + formRedlichKister_(0), + formTempModel_(0), + dlnActCoeff_dX_() + { + constructPhaseFile("LiKCl_liquid.xml", ""); + numBinaryInteractions_ = 1; + + m_HE_m_ij.resize(0); + m_SE_m_ij.resize(0); + + vector_fp he(2); + he[0] = 0.0; + he[1] = 0.0; + vector_fp se(2); + se[0] = 0.0; + se[1] = 0.0; + + m_HE_m_ij.push_back(he); + m_SE_m_ij.push_back(se); + m_N_ij.push_back(1); + m_pSpecies_A_ij.resize(1); + m_pSpecies_B_ij.resize(1); + + int iLiLi = speciesIndex("LiLi"); + if (iLiLi < 0) { + throw CanteraError("RedlichKisterVPSSTP test1 constructor", + "Unable to find LiLi"); + } + m_pSpecies_A_ij[0] = iLiLi; + + + int iVLi = speciesIndex("VLi"); + if (iVLi < 0) { + throw CanteraError("RedlichKisterVPSSTP test1 constructor", + "Unable to find VLi"); + } + m_pSpecies_B_ij[0] = iVLi; + + + } + //==================================================================================================================== + /* + * Copy Constructor: + * + * Note this stuff will not work until the underlying phase + * has a working copy constructor + */ + RedlichKisterVPSSTP::RedlichKisterVPSSTP(const RedlichKisterVPSSTP &b) : + GibbsExcessVPSSTP(), + numBinaryInteractions_(0), + m_pSpecies_A_ij(0), + m_pSpecies_B_ij(0), + m_N_ij(0), + m_HE_m_ij(0), + m_SE_m_ij(0), + formRedlichKister_(0), + formTempModel_(0), + dlnActCoeff_dX_() + { + RedlichKisterVPSSTP::operator=(b); + } + //==================================================================================================================== + /* + * operator=() + * + * Note this stuff will not work until the underlying phase + * has a working assignment operator + */ + RedlichKisterVPSSTP& RedlichKisterVPSSTP:: + operator=(const RedlichKisterVPSSTP &b) { + if (&b == this) { + return *this; + } + + GibbsExcessVPSSTP::operator=(b); + + numBinaryInteractions_ = b.numBinaryInteractions_ ; + m_pSpecies_A_ij = b.m_pSpecies_A_ij; + m_pSpecies_B_ij = b.m_pSpecies_B_ij; + m_N_ij = b.m_N_ij; + m_HE_m_ij = b.m_HE_m_ij; + m_SE_m_ij = b.m_SE_m_ij; + formRedlichKister_ = b.formRedlichKister_; + formTempModel_ = b.formTempModel_; + dlnActCoeff_dX_ = b.dlnActCoeff_dX_; + + return *this; + } + //==================================================================================================================== + /* + * + * ~RedlichKisterVPSSTP(): (virtual) + * + * Destructor: does nothing: + * + */ + RedlichKisterVPSSTP::~RedlichKisterVPSSTP() { + } + //==================================================================================================================== + /* + * This routine duplicates the current object and returns + * a pointer to ThermoPhase. + */ + ThermoPhase* + RedlichKisterVPSSTP::duplMyselfAsThermoPhase() const { + RedlichKisterVPSSTP* mtp = new RedlichKisterVPSSTP(*this); + return (ThermoPhase *) mtp; + } + + //==================================================================================================================== + // Equation of state type flag. + /* + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The RedlichKisterVPSSTP class also returns + * zero, as it is a non-complete class. + */ + int RedlichKisterVPSSTP::eosType() const { + return 0; + } + //==================================================================================================================== + /* + * Import, construct, and initialize a phase + * specification from an XML tree into the current object. + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void RedlichKisterVPSSTP::constructPhaseFile(std::string inputFile, std::string id) { + + if ((int) inputFile.size() == 0) { + throw CanteraError("RedlichKisterVPSSTP:constructPhaseFile", + "input file is null"); + } + string path = findInputFile(inputFile); + std::ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("RedlichKisterVPSSTP:constructPhaseFile","could not open " + +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + XML_Node &phaseNode_XML = xml(); + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("RedlichKisterVPSSTP:constructPhaseFile", + "ERROR: Can not find phase named " + + id + " in file named " + inputFile); + } + fxml_phase->copy(&phaseNode_XML); + constructPhaseXML(*fxml_phase, id); + delete fxml; + } + //==================================================================================================================== + /* + * Import, construct, and initialize a HMWSoln phase + * specification from an XML tree into the current object. + * + * Most of the work is carried out by the cantera base + * routine, importPhase(). That routine imports all of the + * species and element data, including the standard states + * of the species. + * + * Then, In this routine, we read the information + * particular to the specification of the activity + * coefficient model for the Pitzer parameterization. + * + * We also read information about the molar volumes of the + * standard states if present in the XML file. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void RedlichKisterVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id) { + string stemp; + if ((int) id.size() > 0) { + string idp = phaseNode.id(); + if (idp != id) { + throw CanteraError("RedlichKisterVPSSTP::constructPhaseXML", + "phasenode and Id are incompatible"); + } + } + + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("RedlichKisterVPSSTP::constructPhaseXML", + "no thermo XML node"); + } + XML_Node& thermoNode = phaseNode.child("thermo"); + + /* + * Make sure that the thermo model is RedlichKister + */ + stemp = thermoNode.attrib("model"); + string formString = lowercase(stemp); + if (formString != "redlich-kister") { + throw CanteraError("RedlichKisterVPSSTP::constructPhaseXML", + "model name isn't Redlich-Kister: " + formString); + + } + + /* + * Call the Cantera importPhase() function. This will import + * all of the species into the phase. This will also handle + * all of the solvent and solute standard states + */ + bool m_ok = importPhase(phaseNode, this); + if (!m_ok) { + throw CanteraError("RedlichKisterVPSSTP::constructPhaseXML","importPhase failed "); + } + + } + //==================================================================================================================== + + + + /* + * ------------ Molar Thermodynamic Properties ---------------------- + */ + + + /* + * - Activities, Standard States, Activity Concentrations ----------- + */ + + // This method returns an array of generalized concentrations + /* + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * Here we define the activity concentrations as equal + * to the activities, because the standard concentration is 1. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + void RedlichKisterVPSSTP::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } + //==================================================================================================================== + doublereal RedlichKisterVPSSTP::standardConcentration(int k) const { + //err("standardConcentration"); + //return -1.0; + return 1.0; + } + //==================================================================================================================== + doublereal RedlichKisterVPSSTP::logStandardConc(int k) const { + //err("logStandardConc"); + //return -1.0; + return 0.0; + } + //==================================================================================================================== + // Get the array of non-dimensional molar-based activity coefficients at + // the current solution temperature, pressure, and solution concentration. + /* + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void RedlichKisterVPSSTP::getActivityCoefficients(doublereal* ac) const { + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + + /* + * take the exp of the internally storred coefficients. + */ + for (int k = 0; k < m_kk; k++) { + ac[k] = exp(lnActCoeff_Scaled_[k]); + } + } + //==================================================================================================================== + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + //==================================================================================================================== + void RedlichKisterVPSSTP::getElectrochemPotentials(doublereal* mu) const { + getChemPotentials(mu); + double ve = Faraday * electricPotential(); + for (int k = 0; k < m_kk; k++) { + mu[k] += ve*charge(k); + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::getChemPotentials(doublereal* mu) const { + doublereal xx; + /* + * First get the standard chemical potentials in + * molar form. + * -> this requires updates of standard state as a function + * of T and P + */ + getStandardChemPotentials(mu); + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + /* + * + */ + doublereal RT = GasConstant * temperature(); + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + mu[k] += RT * (log(xx) + lnActCoeff_Scaled_[k]); + } + } + //==================================================================================================================== + //Molar enthalpy. Units: J/kmol. + doublereal RedlichKisterVPSSTP::enthalpy_mole() const { + int kk = nSpecies(); + double hbar[kk], h = 0; + getPartialMolarEnthalpies(hbar); + for (int i = 0; i < kk; i++){ + h += moleFractions_[i]*hbar[i]; + } + return h; + } + //==================================================================================================================== + /// Molar entropy. Units: J/kmol. + doublereal RedlichKisterVPSSTP::entropy_mole() const { + int kk = nSpecies(); + double sbar[kk], s = 0; + getPartialMolarEntropies(sbar); + for (int i = 0; i < kk; i++){ + s += moleFractions_[i]*sbar[i]; + } + return s; + } + //==================================================================================================================== + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + doublereal RedlichKisterVPSSTP::cp_mole() const { + int kk = nSpecies(); + double cpbar[kk], cp = 0; + getPartialMolarCp(cpbar); + for (int i = 0; i < kk; i++){ + cp += moleFractions_[i]*cpbar[i]; + } + return cp; + } + //==================================================================================================================== + /// Molar heat capacity at constant volume. Units: J/kmol/K. + doublereal RedlichKisterVPSSTP::cv_mole() const { + return cp_mole() - GasConstant; + } + //==================================================================================================================== + // Returns an array of partial molar enthalpies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void RedlichKisterVPSSTP::getPartialMolarEnthalpies(doublereal* hbar) const { + /* + * Get the nondimensional standard state enthalpies + */ + getEnthalpy_RT(hbar); + /* + * dimensionalize it. + */ + double T = temperature(); + double RT = GasConstant * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] *= RT; + } + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + double RTT = RT * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] -= RTT * dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + // Returns an array of partial molar heat capacities for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void RedlichKisterVPSSTP::getPartialMolarCp(doublereal* cpbar) const { + /* + * Get the nondimensional standard state entropies + */ + getCp_R(cpbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + //==================================================================================================================== + // Returns an array of partial molar entropies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void RedlichKisterVPSSTP::getPartialMolarEntropies(doublereal* sbar) const { + double xx; + /* + * Get the nondimensional standard state entropies + */ + getEntropy_R(sbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + sbar[k] += - lnActCoeff_Scaled_[k] -log(xx) - T * dlnActCoeffdT_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + sbar[k] *= GasConstant; + } + } + + /* + * ------------ Partial Molar Properties of the Solution ------------ + */ + //==================================================================================================================== + // Return an array of partial molar volumes for the + // species in the mixture. Units: m^3/kmol. + /* + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void RedlichKisterVPSSTP::getPartialMolarVolumes(doublereal* vbar) const { + int iK; + /* + * Get the standard state values in m^3 kmol-1 + */ + getStandardVolumes(vbar); + for ( iK = 0; iK < m_kk; iK++ ){ + + vbar[iK] += 0.0; + } + } + //==================================================================================================================== + doublereal RedlichKisterVPSSTP::err(std::string msg) const { + throw CanteraError("RedlichKisterVPSSTP","Base class method " + +msg+" called. Equation of state type: "+int2str(eosType())); + return 0; + } + //==================================================================================================================== + /* + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + void RedlichKisterVPSSTP::initThermo() { + initLengths(); + GibbsExcessVPSSTP::initThermo(); + } + //==================================================================================================================== + // Initialize lengths of local variables after all species have + // been identified. + void RedlichKisterVPSSTP::initLengths() { + m_kk = nSpecies(); + dlnActCoeffdlnN_.resize(m_kk, m_kk); + } + //==================================================================================================================== + /* + * initThermoXML() (virtual from ThermoPhase) + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a complete XML tree + * description of the phase, including all of the species data. In other words while "phase" must + * point to an XML phase object, it must have sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done to see if phaseNode is pointing to the phase + * with the correct id. + */ + void RedlichKisterVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { + std::string subname = "RedlichKisterVPSSTP::initThermoXML"; + std::string stemp; + + /* + * Check on the thermo field. Must have: + * + */ + + XML_Node& thermoNode = phaseNode.child("thermo"); + std::string mStringa = thermoNode.attrib("model"); + std::string mString = lowercase(mStringa); + if (mString != "redlich-kister") { + throw CanteraError(subname.c_str(), + "Unknown thermo model: " + mStringa + " - This object only knows \"Redlich-Kister\" "); + } + + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + XML_Node *acNodePtr = 0; + if (thermoNode.hasChild("activityCoefficients")) { + XML_Node& acNode = thermoNode.child("activityCoefficients"); + acNodePtr = &acNode; + std::string mStringa = acNode.attrib("model"); + std::string mString = lowercase(mStringa); + if (mString != "redlich-kister") { + throw CanteraError(subname.c_str(), + "Unknown activity coefficient model: " + mStringa); + } + int n = acNodePtr->nChildren(); + for (int i = 0; i < n; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + stemp = xmlACChild.name(); + std::string nodeName = lowercase(stemp); + /* + * Process a binary salt field, or any of the other XML fields + * that make up the Pitzer Database. Entries will be ignored + * if any of the species in the entry isn't in the solution. + */ + if (nodeName == "binaryneutralspeciesparameters") { + readXMLBinarySpecies(xmlACChild); + } + } + } + /* + * Go down the chain + */ + GibbsExcessVPSSTP::initThermoXML(phaseNode, id); + } + //=================================================================================================================== + // Update the activity coefficients + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + */ + void RedlichKisterVPSSTP::s_update_lnActCoeff() const { + int iA, iB, m, k; + doublereal XA, XB; + doublereal T = temperature(); + doublereal RT = GasConstant * T; + + fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + doublereal deltaX = XA - XB; + int N = m_N_ij[i]; + vector_fp &he_vec = m_HE_m_ij[i]; + vector_fp &se_vec = m_SE_m_ij[i]; + doublereal poly = 1.0; + doublereal polyMm1 = 1.0; + doublereal sum = 0.0; + doublereal sumMm1 = 0.0; + doublereal sum2 = 0.0; + for (m = 0; m < N; m++) { + doublereal A_ge = he_vec[m] - T * se_vec[m]; + sum += A_ge * poly; + sum2 += A_ge * (m + 1) * poly; + poly *= deltaX; + if (m >= 1) { + sumMm1 += (A_ge * polyMm1 * m); + polyMm1 *= deltaX; + } + } + doublereal oneMXA = 1.0 - XA; + doublereal oneMXB = 1.0 - XB; + for (k = 0; k < m_kk; k++) { + if (iA == k) { + lnActCoeff_Scaled_[k] += (oneMXA * XB * sum) + (XA * XB * sumMm1 * (oneMXA + XB)); + } else if (iB == k) { + lnActCoeff_Scaled_[k] += (oneMXB * XA * sum) + (XA * XB * sumMm1 * (-oneMXB - XA)); + } else { + lnActCoeff_Scaled_[k] += -(XA * XB * sum2); + } + } + // Debug against formula in literature +#ifdef DEBUG_MODE_NOT + double lnA = 0.0; + double lnB = 0.0; + double polyk = 1.0; + double fac = 2.0 * XA - 1.0; + for (m = 0; m < N; m++) { + doublereal A_ge = he_vec[m] - T * se_vec[m]; + lnA += A_ge * oneMXA * oneMXA * polyk * (1.0 + 2.0 * XA * m / fac); + lnB += A_ge * XA * XA * polyk * (1.0 - 2.0 * oneMXA * m / fac); + polyk *= fac; + } + // This gives the same result as above + // printf("RT lnActCoeff_Scaled_[iA] = %15.8E , lnA = %15.8E\n", lnActCoeff_Scaled_[iA], lnA); + // printf("RT lnActCoeff_Scaled_[iB] = %15.8E , lnB = %15.8E\n", lnActCoeff_Scaled_[iB], lnB); + +#endif + + } + for (k = 0; k < m_kk; k++) { + lnActCoeff_Scaled_[k] /= RT; + } + } + //=================================================================================================================== + // Update the derivative of the log of the activity coefficients wrt T + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + + */ + void RedlichKisterVPSSTP::s_update_dlnActCoeff_dT() const { + int iA, iB, m, k; + doublereal XA, XB; + // doublereal T = temperature(); + + fvo_zero_dbl_1(dlnActCoeffdT_Scaled_, m_kk); + fvo_zero_dbl_1(d2lnActCoeffdT2_Scaled_, m_kk); + + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + doublereal deltaX = XA - XB; + int N = m_N_ij[i]; + doublereal poly = 1.0; + doublereal sum = 0.0; + + vector_fp &se_vec = m_SE_m_ij[i]; + doublereal sumMm1 = 0.0; + doublereal polyMm1 = 1.0; + doublereal sum2 = 0.0; + for (m = 0; m < N; m++) { + doublereal A_ge = - se_vec[m]; + sum += A_ge * poly; + sum2 += A_ge * (m + 1) * poly; + poly *= deltaX; + if (m >= 1) { + sumMm1 += (A_ge * polyMm1 * m); + polyMm1 *= deltaX; + } + } + doublereal oneMXA = 1.0 - XA; + doublereal oneMXB = 1.0 - XB; + for (k = 0; k < m_kk; k++) { + if (iA == k) { + dlnActCoeffdT_Scaled_[k] += (oneMXA * XB * sum) + (XA * XB * sumMm1 * (oneMXA + XB)); + } else if (iB == k) { + dlnActCoeffdT_Scaled_[k] += (oneMXB * XA * sum) + (XA * XB * sumMm1 * (-oneMXB - XA)); + } else { + dlnActCoeffdT_Scaled_[k] += -(XA * XB * sum2); + } + } + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::getdlnActCoeffdT(doublereal *dlnActCoeffdT) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdT[k] = dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const { + s_update_dlnActCoeff_dT(); + for (int k = 0; k < m_kk; k++) { + d2lnActCoeffdT2[k] = d2lnActCoeffdT2_Scaled_[k]; + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::s_update_dlnActCoeff_dX_() const { + + + int iA, iB, m, k; + doublereal XA, XB; + doublereal T = temperature(); + + dlnActCoeff_dX_.zero(); + + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + doublereal deltaX = XA - XB; + int N = m_N_ij[i]; + doublereal poly = 1.0; + doublereal sum = 0.0; + vector_fp &he_vec = m_HE_m_ij[i]; + vector_fp &se_vec = m_SE_m_ij[i]; + doublereal sumMm1 = 0.0; + doublereal polyMm1 = 1.0; + doublereal polyMm2 = 1.0; + doublereal sum2 = 0.0; + doublereal sum2Mm1 = 0.0; + doublereal sumMm2 = 0.0; + for (m = 0; m < N; m++) { + doublereal A_ge = he_vec[m] - T * se_vec[m]; + sum += A_ge * poly; + sum2 += A_ge * (m + 1) * poly; + poly *= deltaX; + if (m >= 1) { + sumMm1 += (A_ge * polyMm1 * m); + sum2Mm1 += (A_ge * polyMm1 * m * (1.0 + m)); + polyMm1 *= deltaX; + } + if (m >= 2) { + sumMm2 += (A_ge * polyMm2 * m * (m - 1.0)); + polyMm2 *= deltaX; + } + } + + for (k = 0; k < m_kk; k++) { + if (iA == k) { + + dlnActCoeff_dX_(k, iA) += (- XB * sum + (1.0 - XA) * XB * sumMm1 + + XB * sumMm1 * (1.0 - 2.0 * XA + XB) + + XA * XB * sumMm2 * (1.0 - XA + XB)); + + dlnActCoeff_dX_(k, iB) += ((1.0 - XA) * sum - (1.0 - XA) * XB * sumMm1 + + XA * sumMm1 * (1.0 + 2.0 * XB - XA) + - XA * XB * sumMm2 * (1.0 - XA + XB)); + + } else if (iB == k) { + + dlnActCoeff_dX_(k, iA) += ((1.0 - XB) * sum + (1.0 - XA) * XB * sumMm1 + + XB * sumMm1 * (1.0 - 2.0 * XA + XB) + + XA * XB * sumMm2 * (1.0 - XA + XB)); + + dlnActCoeff_dX_(k, iB) += (- XA * sum - (1.0 - XB) * XA * sumMm1 + + XA * sumMm1 * (XB - XA - (1.0 - XB)) + - XA * XB * sumMm2 * (-XA - (1.0 - XB))); + } else { + + dlnActCoeff_dX_(k, iA) += ( - XB * sum2 - XA * XB * sum2Mm1); + + dlnActCoeff_dX_(k, iB) += ( - XA * sum2 + XA * XB * sum2Mm1); + + } + } + } + } + //==================================================================================================================== + // Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + // a line in parameter space or along a line in physical space + /* + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + void RedlichKisterVPSSTP::getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, + doublereal *dlnActCoeffds) const { + s_update_dlnActCoeff_dT(); + s_update_dlnActCoeff_dX_(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffds[k] = dlnActCoeffdT_Scaled_[k] * dTds; + for (int l = 0; l < m_kk; l++) { + dlnActCoeffds[k] += dlnActCoeff_dX_(k, l) * dXds[l]; + } + } + } + + //==================================================================================================================== + void RedlichKisterVPSSTP::getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const { + s_update_dlnActCoeff_dX_(); + for (int l = 0; l < m_kk; l++) { + dlnActCoeffdlnN_diag[l] = dlnActCoeff_dX_(l, l); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnN_diag[k] -= dlnActCoeff_dX_(l, k) * moleFractions_[k]; + } + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const { + s_update_dlnActCoeff_dX_(); + for (int k = 0; k < m_kk; k++) { + dlnActCoeffdlnX_diag[k] = dlnActCoeffdlnX_diag_[k]; + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::getdlnActCoeffdlnN(const int ld, doublereal *dlnActCoeffdlnN) { + s_update_dlnActCoeff_dX_(); + double *data = & dlnActCoeffdlnN_(0,0); + for (int k = 0; k < m_kk; k++) { + for (int m = 0; m < m_kk; m++) { + dlnActCoeffdlnN[ld * k + m] = data[m_kk * k + m]; + } + } + } + //==================================================================================================================== + void RedlichKisterVPSSTP::resizeNumInteractions(const int num) { + numBinaryInteractions_ = num; + m_pSpecies_A_ij.resize(num, -1); + m_pSpecies_B_ij.resize(num, -1); + m_N_ij.resize(num, -1); + m_HE_m_ij.resize(num); + m_SE_m_ij.resize(num); + dlnActCoeff_dX_.resize(num, num, 0.0); + } + //==================================================================================================================== + // Process an XML node called "binaryNeutralSpeciesParameters" + /* + * This node contains all of the parameters necessary to describe the RedlichKister Interaction for + * a single binary interaction. This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + */ + void RedlichKisterVPSSTP::readXMLBinarySpecies(XML_Node &xmLBinarySpecies) { + std::string xname = xmLBinarySpecies.name(); + if (xname != "binaryNeutralSpeciesParameters") { + throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", + "Incorrect name for processing this routine: " + xname); + } + double *charge = DATA_PTR(m_speciesCharge); + std::string stemp; + int nParamsFound = 0; + int Npoly = 0; + vector_fp hParams, sParams, vParams; + std::string iName = xmLBinarySpecies.attrib("speciesA"); + if (iName == "") { + throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "no speciesA attrib"); + } + std::string jName = xmLBinarySpecies.attrib("speciesB"); + if (jName == "") { + throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "no speciesB attrib"); + } + /* + * Find the index of the species in the current phase. It's not + * an error to not find the species. This means that the interaction doesn't occur for the current + * implementation of the phase. + */ + int iSpecies = speciesIndex(iName); + if (iSpecies < 0) { + return; + } + string ispName = speciesName(iSpecies); + if (charge[iSpecies] != 0) { + throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "speciesA charge problem"); + } + int jSpecies = speciesIndex(jName); + if (jSpecies < 0) { + return; + } + std::string jspName = speciesName(jSpecies); + if (charge[jSpecies] != 0) { + throw CanteraError("RedlichKisterVPSSTP::readXMLBinarySpecies", "speciesB charge problem"); + } + /* + * Ok we have found a valid interaction + */ + numBinaryInteractions_++; + int iSpot = numBinaryInteractions_ - 1; + m_pSpecies_A_ij.resize(numBinaryInteractions_); + m_pSpecies_B_ij.resize(numBinaryInteractions_); + m_pSpecies_A_ij[iSpot] = iSpecies; + m_pSpecies_B_ij[iSpot] = jSpecies; + + int num = xmLBinarySpecies.nChildren(); + for (int iChild = 0; iChild < num; iChild++) { + XML_Node &xmlChild = xmLBinarySpecies.child(iChild); + stemp = xmlChild.name(); + string nodeName = lowercase(stemp); + /* + * Process the binary species interaction child elements + */ + if (nodeName == "excessenthalpy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, hParams, true, "toSI", "excessEnthalpy"); + nParamsFound = hParams.size(); + if (nParamsFound > Npoly) { + Npoly = nParamsFound; + } + + } + + if (nodeName == "excessentropy") { + /* + * Get the string containing all of the values + */ + ctml::getFloatArray(xmlChild, sParams, true, "toSI", "excessEntropy"); + nParamsFound = sParams.size(); + if (nParamsFound > Npoly) { + Npoly = nParamsFound; + } + } + } + hParams.resize(Npoly, 0.0); + sParams.resize(Npoly, 0.0); + m_HE_m_ij.push_back(hParams); + m_SE_m_ij.push_back(sParams); + m_N_ij.push_back(Npoly); + resizeNumInteractions(numBinaryInteractions_); + } + //==================================================================================================================== +#ifdef DEBUG_MODE + void RedlichKisterVPSSTP::Vint(double &VintOut, double &voltsOut) { + int iA, iB, m; + doublereal XA, XB; + doublereal T = temperature(); + doublereal RT = GasConstant * T; + double Volts = 0.0; + + fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + + for (int i = 0; i < numBinaryInteractions_; i++) { + iA = m_pSpecies_A_ij[i]; + iB = m_pSpecies_B_ij[i]; + XA = moleFractions_[iA]; + XB = moleFractions_[iB]; + if (XA <= 1.0E-14) { + XA = 1.0E-14; + } + if (XA >= (1.0 - 1.0E-14)) { + XA = 1.0 - 1.0E-14; + } + + int N = m_N_ij[i]; + vector_fp &he_vec = m_HE_m_ij[i]; + vector_fp &se_vec = m_SE_m_ij[i]; + double fac = 2.0 * XA - 1.0; + if (fabs(fac) < 1.0E-13) { + fac = 1.0E-13; + } + double polykp1 = fac; + double poly1mk = fac; + + for (m = 0; m < N; m++) { + doublereal A_ge = he_vec[m]; + Volts += A_ge * ( polykp1 - (2.0 * XA * m * (1.0-XA) ) / poly1mk ); + polykp1 *= fac; + poly1mk /= fac; + } + } + Volts /= Faraday; + + double termp = RT * log((1.0 - XA)/XA) / Faraday; + + VintOut = Volts; + voltsOut = Volts + termp; + } + #endif + //==================================================================================================================== +} + diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.h b/Cantera/src/thermo/RedlichKisterVPSSTP.h new file mode 100644 index 000000000..d11e9e2bd --- /dev/null +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.h @@ -0,0 +1,983 @@ +/** + * @file RedlichKisterVPSSTP.h + * Header for intermediate ThermoPhase object for phases which + * employ gibbs excess free energy based formulations + * (see \ref thermoprops + * and class \link Cantera::RedlichKisterVPSSTP RedlichKisterVPSSTP\endlink). + * + * Header file for a derived class of ThermoPhase that handles + * variable pressure standard state methods for calculating + * thermodynamic properties that are further based upon activities + * based on the molality scale. These include most of the methods for + * calculating liquid electrolyte thermodynamics. + */ +/* + * Copywrite (2006) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ +/* + * $Id: MargulesVPSSTP.h 782 2011-10-19 20:45:06Z hkmoffa $ + */ + +#ifndef CT_REDLICHKISTERVPSSTP_H +#define CT_REDLICHKISTERVPSSTP_H + +#include "GibbsExcessVPSSTP.h" +#include "Array.h" + +namespace Cantera { + + /** + * @ingroup thermoprops + */ + + + //! RedlichKisterVPSSTP is a derived class of GibbsExcessVPSSTP that employs + //! the Redlich-Kister approximation for the excess gibbs free energy + /*! + * + * %RedlichKisterVPSSTP derives from class GibbsExcessVPSSTP which is derived + * from VPStandardStateTP, and overloads the virtual methods defined there with ones that + * use expressions appropriate for the Redlich Kister Excess gibbs free energy approximation. + * + * The independent unknowns are pressure, temperature, and mass fraction. + * + * Several concepts are introduced. The first concept is there are temporary + * variables for holding the species standard state values of Cp, H, S, G, and V at the + * last temperature and pressure called. These functions are not recalculated + * if a new call is made using the previous temperature and pressure. Currently, + * these variables and the calculation method are handled by the VPSSMgr class, + * for which VPStandardStateTP owns a pointer to. + * + * To support the above functionality, pressure and temperature variables, + * m_plast_ss and m_tlast_ss, are kept which store the last pressure and temperature + * used in the evaluation of standard state properties. + * + * This class is usually used for nearly incompressible phases. For those phases, it + * makes sense to change the equation of state independent variable from + * density to pressure. The variable m_Pcurrent contains the current value of the + * pressure within the phase. + * + * + *
+ *

Specification of Species Standard %State Properties

+ *
+ * + * All species are defined to have standard states that depend upon both + * the temperature and the pressure. The Redlich-Kister approximation assumes + * symmetric standard states, where all of the standard state assume + * that the species are in pure component states at the temperatue + * and pressure of the solution. I don't think it prevents, however, + * some species from being dilute in the solution. + * + * + *
+ *

Specification of Solution Thermodynamic Properties

+ *
+ * + * The molar excess Gibbs free energy is given by the following formula which is a sum over interactions i. + * Each of the interactions are binary interactions involving two of the species in the phase, denoted, Ai + * and Bi. + * This is the generalization of the Redlich-Kister formulation for a phase that has more than 2 species. + * + * \f[ + * G^E = \sum_{i} G^E_{i} + * \f] + * + * where + * + * \f[ + * G^E_{i} = n X_{Ai} X_{Bi} \sum_m \left( A^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) + * \f] + * + * and where we can break down the gibbs free energy contributions into enthalpy and entropy contributions + * + * \f[ + * H^E_i = n X_{Ai} X_{Bi} \sum_m \left( H^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) + * \f] + * + * \f[ + * S^E_i = n X_{Ai} X_{Bi} \sum_m \left( S^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) + * \f] + * + * where n is the total moles in the solution. + * + * The activity of a species defined in the phase is given by an excess Gibbs free energy formulation. + * + * \f[ + * a_k = \gamma_k X_k + * \f] + * + * where + * + * \f[ + * R T \ln( \gamma_k )= \frac{d(n G^E)}{d(n_k)}\Bigg|_{n_i} + * \f] + * + * Taking the derivatives results in the following expression + * \f[ + * R T \ln( \gamma_k )= \sum_i \delta_{Ai,k} (1 - X_{Ai}) X_{Bi} \sum_m \left( A^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) + * + \sum_i \delta_{Ai,k} X_{Ai} X_{Bi} \sum_m \left( A^{i}_0 + A^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^{m-1} (1 - X_{Ai} + X_{Bi}) \right) + * \f] + * where + * + * + * This object inherits from the class VPStandardStateTP. Therefore, the specification and + * calculation of all standard state and reference state values are handled at that level. Various functional + * forms for the standard state are permissible. + * The chemical potential for species k is equal to + * + * \f[ + * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) + * \f] + * + * The partial molar entropy for species k is given by the following relation, + * + * \f[ + * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * The partial molar enthalpy for species k is given by + * + * \f[ + * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * The partial molar volume for species k is + * + * \f[ + * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} + * \f] + * + * The partial molar Heat Capacity for species k is + * + * \f[ + * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} + * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} + * \f] + * + *
+ *

%Application within %Kinetics Managers

+ *
+ * + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^s_k, \f$ where \f$ C^s_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. + * The activity concentration,\f$ C^a_k \f$,is given by the following expression. + * + * \f[ + * C^a_k = C^s_k X_k = \frac{P}{R T} X_k + * \f] + * + * The standard concentration for species k is independent of k and equal to + * + * \f[ + * C^s_k = C^s = \frac{P}{R T} + * \f] + * + * For example, a bulk-phase binary gas reaction between species j and k, producing + * a new gas species l would have the + * following equation for its rate of progress variable, \f$ R^1 \f$, which has + * units of kmol m-3 s-1. + * + * \f[ + * R^1 = k^1 C_j^a C_k^a = k^1 (C^s a_j) (C^s a_k) + * \f] + * where + * \f[ + * C_j^a = C^s a_j \mbox{\quad and \quad} C_k^a = C^s a_k + * \f] + * + * + * \f$ C_j^a \f$ is the activity concentration of species j, and + * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^s \f$ + * is the standard concentration. \f$ a_j \f$ is + * the activity of species j which is equal to the mole fraction of j. + * + * The reverse rate constant can then be obtained from the law of microscopic reversibility + * and the equilibrium expression for the system. + * + * \f[ + * \frac{a_j a_k}{ a_l} = K_a^{o,1} = \exp(\frac{\mu^o_l - \mu^o_j - \mu^o_k}{R T} ) + * \f] + * + * \f$ K_a^{o,1} \f$ is the dimensionless form of the equilibrium constant, associated with + * the pressure dependent standard states \f$ \mu^o_l(T,P) \f$ and their associated activities, + * \f$ a_l \f$, repeated here: + * + * \f[ + * \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l) + * \f] + * + * We can switch over to expressing the equilibrium constant in terms of the reference + * state chemical potentials + * + * \f[ + * K_a^{o,1} = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{P} + * \f] + * + * The concentration equilibrium constant, \f$ K_c \f$, may be obtained by changing over + * to activity concentrations. When this is done: + * + * \f[ + * \frac{C^a_j C^a_k}{ C^a_l} = C^o K_a^{o,1} = K_c^1 = + * \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) * \frac{P_{ref}}{RT} + * \f] + * + * %Kinetics managers will calculate the concentration equilibrium constant, \f$ K_c \f$, + * using the second and third part of the above expression as a definition for the concentration + * equilibrium constant. + * + * For completeness, the pressure equilibrium constant may be obtained as well + * + * \f[ + * \frac{P_j P_k}{ P_l P_{ref}} = K_p^1 = \exp(\frac{\mu^{ref}_l - \mu^{ref}_j - \mu^{ref}_k}{R T} ) + * \f] + * + * \f$ K_p \f$ is the simplest form of the equilibrium constant for ideal gases. However, it isn't + * necessarily the simplest form of the equilibrium constant for other types of phases; \f$ K_c \f$ is + * used instead because it is completely general. + * + * The reverse rate of progress may be written down as + * \f[ + * R^{-1} = k^{-1} C_l^a = k^{-1} (C^o a_l) + * \f] + * + * where we can use the concept of microscopic reversibility to + * write the reverse rate constant in terms of the + * forward reate constant and the concentration equilibrium + * constant, \f$ K_c \f$. + * + * \f[ + * k^{-1} = k^1 K^1_c + * \f] + * + * \f$k^{-1} \f$ has units of s-1. + * + * + *
+ *

Instantiation of the Class

+ *
+ * + * + * The constructor for this phase is located in the default ThermoFactory + * for %Cantera. A new %IdealGasPhase may be created by the following code + * snippet: + * + * @code + * XML_Node *xc = get_XML_File("silane.xml"); + * XML_Node * const xs = xc->findNameID("phase", "silane"); + * ThermoPhase *silane_tp = newPhase(*xs); + * IdealGasPhase *silaneGas = dynamic_cast (silane_tp); + * @endcode + * + * or by the following constructor: + * + * @code + * XML_Node *xc = get_XML_File("silane.xml"); + * XML_Node * const xs = xc->findNameID("phase", "silane"); + * IdealGasPhase *silaneGas = new IdealGasPhase(*xs); + * @endcode + * + *
+ *

XML Example

+ *
+ * An example of an XML Element named phase setting up a IdealGasPhase + * object named silane is given below. + * + * + * @verbatim + + + Si H He + + H2 H HE SIH4 SI SIH SIH2 SIH3 H3SISIH SI2H6 + H2SISIH2 SI3H8 SI2 SI3 + + + + + + + @endverbatim + * + * The model attribute "IdealGas" of the thermo XML element identifies the phase as + * being of the type handled by the IdealGasPhase object. + * + * @ingroup thermoprops + * + + */ + class RedlichKisterVPSSTP : public GibbsExcessVPSSTP { + + public: + + //! Constructor + /*! + * This doesn't do much more than initialize constants with + * default values. + */ + RedlichKisterVPSSTP(); + + //! Construct and initialize a RedlichKisterVPSSTP ThermoPhase object + //! directly from an xml input file + /*! + * Working constructors + * + * The two constructors below are the normal way the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the XML database to get the info for the phase. + * + * @param inputFile Name of the input file containing the phase XML data + * to set up the object + * @param id ID of the phase in the input file. Defaults to the + * empty string. + */ + RedlichKisterVPSSTP(std::string inputFile, std::string id = ""); + + //! Construct and initialize a RedlichKisterVPSSTP ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML phase node containing the description of the phase + * @param id id attribute containing the name of the phase. + * (default is the empty string) + */ + RedlichKisterVPSSTP(XML_Node& phaseRef, std::string id = ""); + + + //! Special constructor for a hard-coded problem + /*! + * + * @param testProb Hard-coded value. Only the value of 1 is + * used. It's for + * a LiKCl system + * -> test to predict the eutectic and liquidus correctly. + */ + RedlichKisterVPSSTP(int testProb); + + //! Copy constructor + /*! + * Note this stuff will not work until the underlying phase + * has a working copy constructor + * + * @param b class to be copied + */ + RedlichKisterVPSSTP(const RedlichKisterVPSSTP& b); + + //! Assignment operator + /*! + * + * @param b class to be copied. + */ + RedlichKisterVPSSTP& operator=(const RedlichKisterVPSSTP &b); + + //! Destructor + virtual ~RedlichKisterVPSSTP(); + + //! Duplication routine for objects which inherit from ThermoPhase. + /*! + * This virtual routine can be used to duplicate thermophase objects + * inherited from ThermoPhase even if the application only has + * a pointer to ThermoPhase to work with. + */ + virtual ThermoPhase *duplMyselfAsThermoPhase() const; + + /** + * + * @name Utilities + * @{ + */ + + + //! Equation of state type flag. + /*! + * The ThermoPhase base class returns + * zero. Subclasses should define this to return a unique + * non-zero value. Known constants defined for this purpose are + * listed in mix_defs.h. The MolalityVPSSTP class also returns + * zero, as it is a non-complete class. + */ + virtual int eosType() const; + + //! Initialization of a phase using an xml file + /*! + * This routine is a precursor to + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseFile(std::string inputFile, std::string id); + + //! Import and initialize a phase + //! specification in an XML tree into the current object. + /*! + * Here we read an XML description of the phase. + * We import descriptions of the elements that make up the + * species in a phase. + * We import information about the species, including their + * reference state thermodynamic polynomials. We then freeze + * the state of the species. + * + * Then, we read the species molar volumes from the xml + * tree to finish the initialization. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void constructPhaseXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Molar Thermodynamic Properties + * @{ + */ + + + /** + * @} + * @name Utilities for Solvent ID and Molality + * @{ + */ + + + + + /** + * @} + * @name Mechanical Properties + * @{ + */ + + /** + * @} + * @name Potential Energy + * + * Species may have an additional potential energy due to the + * presence of external gravitation or electric fields. These + * methods allow specifying a potential energy for individual + * species. + * @{ + */ + + /** + * @} + * @name Activities, Standard States, and Activity Concentrations + * + * The activity \f$a_k\f$ of a species in solution is + * related to the chemical potential by \f[ \mu_k = \mu_k^0(T) + * + \hat R T \log a_k. \f] The quantity \f$\mu_k^0(T,P)\f$ is + * the chemical potential at unit activity, which depends only + * on temperature and pressure. + * @{ + */ + + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + + + /** + * The standard concentration \f$ C^0_k \f$ used to normalize + * the generalized concentration. In many cases, this quantity + * will be the same for all species in a phase - for example, + * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this + * reason, this method returns a single value, instead of an + * array. However, for phases in which the standard + * concentration is species-specific (e.g. surface species of + * different sizes), this method may be called with an + * optional parameter indicating the species. + * + * @param k species index. Defaults to zero. + */ + virtual doublereal standardConcentration(int k=0) const; + + /** + * Returns the natural logarithm of the standard + * concentration of the kth species + * + * @param k species index + */ + virtual doublereal logStandardConc(int k=0) const; + + //! Get the array of non-dimensional molar-based activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + virtual void getActivityCoefficients(doublereal* ac) const; + + + + + //@} + /// @name Partial Molar Properties of the Solution + //@{ + + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ + virtual void getChemPotentials(doublereal* mu) const; + + /// Molar enthalpy. Units: J/kmol. + virtual doublereal enthalpy_mole() const; + + /// Molar entropy. Units: J/kmol. + virtual doublereal entropy_mole() const; + + /// Molar heat capacity at constant pressure. Units: J/kmol/K. + virtual doublereal cp_mole() const; + + /// Molar heat capacity at constant volume. Units: J/kmol/K. + virtual doublereal cv_mole() const; + + //! Returns an array of partial molar enthalpies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * @param hbar Vector of returned partial molar enthalpies + * (length m_kk, units = J/kmol) + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * @param sbar Vector of returned partial molar entropies + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????????? + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * ??????????????? + * \f] + * + * @param cpbar Vector of returned partial molar heat capacities + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + + + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //! Get the species electrochemical potentials. + /*! + * These are partial molar quantities. + * This method adds a term \f$ Fz_k \phi_k \f$ to the + * to each chemical potential. + * + * Units: J/kmol + * + * @param mu output vector containing the species electrochemical potentials. + * Length: m_kk., units = J/kmol + */ + void getElectrochemPotentials(doublereal* mu) const; + + //! Get the array of temperature second derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param d2lnActCoeffdT2 Output vector of temperature 2nd derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getd2lnActCoeffdT2(doublereal *d2lnActCoeffdT2) const; + + //! Get the array of temperature derivatives of the log activity coefficients + /*! + * This function is a virtual class, but it first appears in GibbsExcessVPSSTP + * class and derived classes from GibbsExcessVPSSTP. + * + * units = 1/Kelvin + * + * @param dlnActCoeffdT Output vector of temperature derivatives of the + * log Activity Coefficients. length = m_kk + * + */ + virtual void getdlnActCoeffdT(doublereal *dlnActCoeffdT) const; + + + + //@} + /// @name Properties of the Standard State of the Species in the Solution + //@{ + + + + //@} + /// @name Thermodynamic Values for the Species Reference States + //@{ + + + /////////////////////////////////////////////////////// + // + // The methods below are not virtual, and should not + // be overloaded. + // + ////////////////////////////////////////////////////// + + /** + * @name Specific Properties + * @{ + */ + + + /** + * @name Setting the State + * + * These methods set all or part of the thermodynamic + * state. + * @{ + */ + + + + //@} + + /** + * @name Chemical Equilibrium + * Routines that implement the Chemical equilibrium capability + * for a single phase, based on the element-potential method. + * @{ + */ + + + + //@} + + + + /// The following methods are used in the process of constructing + /// the phase and setting its parameters from a specification in an + /// input file. They are not normally used in application programs. + /// To see how they are used, see files importCTML.cpp and + /// ThermoFactory.cpp. + + + /*! + * @internal Initialize. This method is provided to allow + * subclasses to perform any initialization required after all + * species have been added. For example, it might be used to + * resize internal work arrays that must have an entry for + * each species. The base class implementation does nothing, + * and subclasses that do not require initialization do not + * need to overload this method. When importing a CTML phase + * description, this method is called just prior to returning + * from function importPhase. + * + * @see importCTML.cpp + */ + virtual void initThermo(); + + + /** + * Import and initialize a ThermoPhase object + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void initThermoXML(XML_Node& phaseNode, std::string id); + + /** + * @} + * @name Derivatives of Thermodynamic Variables needed for Applications + * @{ + */ + + //! Get the change in activity coefficients w.r.t. change in state (temp, mole fraction, etc.) along + //! a line in parameter space or along a line in physical space + /*! + * + * @param dTds Input of temperature change along the path + * @param dXds Input vector of changes in mole fraction along the path. length = m_kk + * Along the path length it must be the case that the mole fractions sum to one. + * @param dlnActCoeffds Output vector of the directional derivatives of the + * log Activity Coefficients along the path. length = m_kk + * units are 1/units(s). if s is a physical coordinate then the units are 1/m. + */ + virtual void getdlnActCoeffds(const doublereal dTds, const doublereal * const dXds, doublereal *dlnActCoeffds) const; + + //! Get the array of log concentration-like derivatives of the + //! log activity coefficients - diagonal component + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the mole fraction. + * + * units = dimensionless + * + * @param dlnActCoeffdlnX_diag Output vector of the diagonal component of the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnX_diag(doublereal *dlnActCoeffdlnX_diag) const; + + //! Get the array of derivatives of the log activity coefficients wrt mole numbers - diagonal only + /*! + * This function is a virtual method. For ideal mixtures + * (unity activity coefficients), this can return zero. + * Implementations should take the derivative of the + * logarithm of the activity coefficient with respect to the + * logarithm of the concentration-like variable (i.e. mole fraction, + * molality, etc.) that represents the standard state. + * + * units = dimensionless + * + * @param dlnActCoeffdlnN_diag Output vector of the diagonal entries for the log(mole fraction) + * derivatives of the log Activity Coefficients. + * length = m_kk + */ + virtual void getdlnActCoeffdlnN_diag(doublereal *dlnActCoeffdlnN_diag) const; + + + //! Get the array of derivatives of the ln activity coefficients with respect to the ln species mole numbers + /*! + * Implementations should take the derivative of the logarithm of the activity coefficient with respect to a + * log of a species mole number (with all other species mole numbers held constant) + * + * units = 1 / kmol + * + * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log act_coeff for the mth + * species with respect to the number of moles of the kth species. + * + * \f[ + * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} + * \f] + * + * @param ld Number of rows in the matrix + * @param dlnActCoeffdlnN Output vector of derivatives of the + * log Activity Coefficients. length = m_kk * m_kk + */ + virtual void getdlnActCoeffdlnN(const int ld, doublereal * const dlnActCoeffdlnN) ; + + //@} + + private: + + //! Process an XML node called "binaryNeutralSpeciesParameters" + /*! + * This node contains all of the parameters necessary to describe + * the Redlich-Kister model for a particular binary interaction. + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + * + * @param xmlBinarySpecies Reference to the XML_Node named "binaryNeutralSpeciesParameters" + * containing the binary interaction + */ + void readXMLBinarySpecies(XML_Node &xmlBinarySpecies); + + //! Resize internal arrays within the object that depend upon the number + //! of binary Redlich-Kister interaction terms + /*! + * @param num Number of binary Redlich-Kister interaction terms + */ + void resizeNumInteractions(const int num); + + + //! Initialize lengths of local variables after all species have + //! been identified. + void initLengths(); + + //! Update the activity coefficients + /*! + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + */ + void s_update_lnActCoeff() const; + + //! Update the derivative of the log of the activity coefficients wrt T + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt temperature. + */ + void s_update_dlnActCoeff_dT() const; + + //! Internal routine that calculates the derivative of the activity coefficients wrt + //! the mole fractions. + /*! + * This routine calculates the the derivative of the activity coefficients wrt to mole fraction + * with all other mole fractions held constant. This is strictly not permitted. However, if the + * resulting matrix is multiplied by a permissible deltaX vector then everything is ok. + * + * This is the natural way to handle concentration derivatives in this routine. + */ + void s_update_dlnActCoeff_dX_() const; + +#ifdef DEBUG_MODE + public: + //! Utility routine that calculates a literature expression + /*! + * @param VintOut Output contribution to the voltage corresponding to nonideal term + * @param voltsOut Output contribution to the voltage corresponding to nonideal term and mf term + */ + void Vint(double &VintOut, double &voltsOut) ; +#endif + + private: + //! Error function + /*! + * Print an error string and exit + * + * @param msg Message to be printed + */ + doublereal err(std::string msg) const; + + protected: + + //! number of binary interaction expressions + int numBinaryInteractions_; + + //! vector of species indices representing species A in the interaction + /*! + * Each Redlich-Kister excess Gibbs free energy term involves two species, A and B. + * This vector identifies species A. + */ + vector_int m_pSpecies_A_ij; + + //! vector of species indices representing species B in the interaction + /*! + * Each Redlich-Kisterexcess Gibbs free energy term involves two species, A and B. + * This vector identifies species B. + */ + vector_int m_pSpecies_B_ij; + + + //! Vector of the length of the polynomial for the interaction. + vector_int m_N_ij; + + + //! Enthalpy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable std::vector< vector_fp> m_HE_m_ij; + + + //! Entropy term for the binary mole fraction interaction of the + //! excess gibbs free energy expression + mutable std::vector< vector_fp> m_SE_m_ij; + + //! form of the RedlichKister interaction expression + /*! + * Currently there is only one form. + */ + int formRedlichKister_; + + //! form of the temperatuer dependence of the Redlich-Kister interaction expression + /*! + * Currently there is only one form -> constant wrt temperature. + */ + int formTempModel_; + + + //! Two dimensional array of derivatives of activity coefficients wrt mole fractions + mutable Array2D dlnActCoeff_dX_; + + + }; + + + +} + +#endif + + + + + diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index ff9480d97..0cf6338fc 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -28,6 +28,7 @@ #ifdef WITH_IDEAL_SOLUTIONS #include "IdealSolidSolnPhase.h" #include "MargulesVPSSTP.h" +#include "RedlichKisterVPSSTP.h" #include "IonsFromNeutralVPSSTP.h" #include "PhaseCombo_Interaction.h" #endif @@ -99,7 +100,7 @@ namespace Cantera { /*! * @deprecated This entire structure could be replaced with a std::map */ - static int ntypes = 22; + static int ntypes = 23; //! Define the string name of the %ThermoPhase types that are handled by this factory routine static string _types[] = {"IdealGas", "Incompressible", @@ -109,7 +110,7 @@ namespace Cantera { "IdealMolalSolution", "IdealGasVPSS", "MineralEQ3", "MetalSHEelectrons", "Margules", "PhaseCombo_Interaction", "IonsFromNeutralMolecule", "FixedChemPot", "MolarityIonicVPSSTP", - "MixedSolventElectrolyte" + "MixedSolventElectrolyte", "Redlich-Kister" }; //! Define the integer id of the %ThermoPhase types that are handled by this factory routine @@ -120,7 +121,7 @@ namespace Cantera { cIdealMolalSoln, cVPSS_IdealGas, cMineralEQ3, cMetalSHEelectrons, cMargulesVPSSTP, cPhaseCombo_Interaction, cIonsFromNeutral, cFixedChemPot, - cMolarityIonicVPSSTP, cMixedSolventElectrolyte + cMolarityIonicVPSSTP, cMixedSolventElectrolyte, cRedlichKisterVPSSTP }; /* @@ -162,6 +163,10 @@ namespace Cantera { th = new MargulesVPSSTP(); break; + case cRedlichKisterVPSSTP: + th = new RedlichKisterVPSSTP(); + break; + case cPhaseCombo_Interaction: th = new PhaseCombo_Interaction(); break; @@ -811,7 +816,6 @@ namespace Cantera { factory->installThermoForSpecies(k, s, &th, *spthermo_ptr, phaseNode_ptr); } - return true; } diff --git a/Cantera/src/thermo/ThermoFactory.h b/Cantera/src/thermo/ThermoFactory.h index 01ec78d12..b4af0abef 100644 --- a/Cantera/src/thermo/ThermoFactory.h +++ b/Cantera/src/thermo/ThermoFactory.h @@ -255,8 +255,7 @@ namespace Cantera { * * @ingroup thermoprops */ - bool importPhase(XML_Node& phase, ThermoPhase* th, - SpeciesThermoFactory* spfactory = 0); + bool importPhase(XML_Node& phase, ThermoPhase* th, SpeciesThermoFactory* spfactory = 0); //! Install a species into a ThermoPhase object, which defines //! the phase thermodynamics and speciation. @@ -305,7 +304,7 @@ namespace Cantera { VPSSMgr *vpss_ptr = 0, SpeciesThermoFactory* factory = 0); - //!Search an XML tree for species data. + //! Search an XML tree for species data. /*! * This utility routine will search the XML tree for the species * named by the string, kname. It will return the XML_Node diff --git a/Cantera/src/thermo/mix_defs.h b/Cantera/src/thermo/mix_defs.h index 1aef185ea..a74fb4ccf 100644 --- a/Cantera/src/thermo/mix_defs.h +++ b/Cantera/src/thermo/mix_defs.h @@ -79,6 +79,8 @@ namespace Cantera { const int cMargulesVPSSTP = 301; + const int cRedlichKisterVPSSTP = 303; + const int cMolarityIonicVPSSTP = 401; const int cMixedSolventElectrolyte = 402; diff --git a/docs/Cantera.cfg.in b/docs/Cantera.cfg.in index f3f3a4dab..5b260f5d0 100755 --- a/docs/Cantera.cfg.in +++ b/docs/Cantera.cfg.in @@ -707,6 +707,8 @@ FILE_PATTERNS = Kinetics.h Kinetics.cpp \ GibbsExcessVPSSTP.cpp \ MargulesVPSSTP.h \ MargulesVPSSTP.cpp \ + RedlichKisterVPSSTP.h \ + RedlichKisterVPSSTP.cpp \ IonsFromNeutralVPSSTP.h \ IonsFromNeutralVPSSTP.cpp \ VPSSMgr.h \ From 5f01cc30bbb45da43fca49765e73bf3542c3daf5 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 1 Nov 2011 21:09:58 +0000 Subject: [PATCH 425/446] Worked on MolarityIonicVPSSTP, filling it in a little bit. Changed GibbsExcessVPSSTP so that getLnActivityCoefficient() is central. The straight activity coefficients may not be representable within machine limits. --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 22 + Cantera/src/thermo/GibbsExcessVPSSTP.h | 7 + Cantera/src/thermo/MargulesVPSSTP.cpp | 10 +- Cantera/src/thermo/MargulesVPSSTP.h | 8 +- Cantera/src/thermo/MolarityIonicVPSSTP.cpp | 453 ++++++++++++++++++++- Cantera/src/thermo/MolarityIonicVPSSTP.h | 222 +++++++++- Cantera/src/thermo/RedlichKisterVPSSTP.cpp | 20 +- Cantera/src/thermo/RedlichKisterVPSSTP.h | 9 +- 8 files changed, 713 insertions(+), 38 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 339b0edd9..8f357a9e5 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -233,7 +233,29 @@ namespace Cantera { } } + //==================================================================================================================== + // Get the array of non-dimensional molar-based activity coefficients at + // the current solution temperature, pressure, and solution concentration. + /* + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void GibbsExcessVPSSTP::getActivityCoefficients(doublereal * const ac) const { + + getLnActivityCoefficients(ac); + // Protect against roundoff when taking exponentials + for (int k = 0; k < m_kk; k++) { + if (ac[k] > 700.) { + ac[k] = exp(700.); + } else if (ac[k] < -700.) { + ac[k] = exp(-700); + } else { + ac[k] = exp(ac[k]); + } + } + } + //==================================================================================================================== + void GibbsExcessVPSSTP::getElectrochemPotentials(doublereal* mu) const { getChemPotentials(mu); double ve = Faraday * electricPotential(); diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 521f7f344..8de94d8ff 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -289,6 +289,13 @@ namespace Cantera { */ virtual void getActivities(doublereal* ac) const; + //! Get the array of non-dimensional molar-based ln activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param lnac Output vector of ln activity coefficients. Length: m_kk. + */ + virtual void getActivityCoefficients(doublereal * const ac) const; + //! Get the array of temperature derivatives of the log activity coefficients /*! diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index 15fc3edb2..ebe7c89aa 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -376,12 +376,12 @@ namespace Cantera { return 0.0; } //==================================================================================================================== - // Get the array of non-dimensional molar-based activity coefficients at + // Get the array of non-dimensional molar-based ln activity coefficients at // the current solution temperature, pressure, and solution concentration. /* - * @param ac Output vector of activity coefficients. Length: m_kk. + * @param lnac Output vector of ln activity coefficients. Length: m_kk. */ - void MargulesVPSSTP::getActivityCoefficients(doublereal* ac) const { + void MargulesVPSSTP::getLnActivityCoefficients(doublereal* lnac) const { /* * Update the activity coefficients */ @@ -391,10 +391,10 @@ namespace Cantera { * take the exp of the internally storred coefficients. */ for (int k = 0; k < m_kk; k++) { - ac[k] = exp(lnActCoeff_Scaled_[k]); + lnac[k] = lnActCoeff_Scaled_[k]; } } - + //==================================================================================================================== /* * ------------ Partial Molar Properties of the Solution ------------ */ diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index ebeb9d5e2..5d675fb14 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -536,15 +536,13 @@ namespace Cantera { */ virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based activity coefficients at + //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! - * @param ac Output vector of activity coefficients. Length: m_kk. + * @param ac Output vector of ln activity coefficients. Length: m_kk. */ - virtual void getActivityCoefficients(doublereal* ac) const; + virtual void getLnActivityCoefficients(doublereal* lnac) const; - - //@} /// @name Partial Molar Properties of the Solution diff --git a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp index e657aea3d..1e7831ba9 100644 --- a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp @@ -23,12 +23,13 @@ #include "MolarityIonicVPSSTP.h" - +#include "ThermoFactory.h" #include using namespace std; namespace Cantera { + static const double xxSmall = 1.0E-150; //==================================================================================================================== /* * Default constructor. @@ -44,6 +45,40 @@ namespace Cantera { numPassThroughSpecies_(0), neutralPBindexStart(0) { + } + //==================================================================================================================== + /* + * Working constructors + * + * The two constructors below are the normal way + * the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the + * XML database to get the info for the phase. + */ + MolarityIonicVPSSTP::MolarityIonicVPSSTP(std::string inputFile, std::string id) : + GibbsExcessVPSSTP(), + PBType_(PBTYPE_PASSTHROUGH), + numPBSpecies_(m_kk), + indexSpecialSpecies_(-1), + numCationSpecies_(0), + numAnionSpecies_(0), + numPassThroughSpecies_(0), + neutralPBindexStart(0) + { + constructPhaseFile(inputFile, id); + } + //==================================================================================================================== + MolarityIonicVPSSTP::MolarityIonicVPSSTP(XML_Node& phaseRoot, std::string id) : + GibbsExcessVPSSTP(), + PBType_(PBTYPE_PASSTHROUGH), + numPBSpecies_(m_kk), + indexSpecialSpecies_(-1), + numCationSpecies_(0), + numAnionSpecies_(0), + numPassThroughSpecies_(0), + neutralPBindexStart(0) + { + constructPhaseXML(phaseRoot, id); } //==================================================================================================================== /* @@ -130,8 +165,120 @@ namespace Cantera { return 0; } - + //==================================================================================================================== + /* + * Import, construct, and initialize a phase + * specification from an XML tree into the current object. + * + * This routine is a precursor to constructPhaseXML(XML_Node*) + * routine, which does most of the work. + * + * @param infile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void MolarityIonicVPSSTP::constructPhaseFile(std::string inputFile, std::string id) { + if ((int) inputFile.size() == 0) { + throw CanteraError("MolarityIonicVPSSTP:constructPhaseFile", + "input file is null"); + } + string path = findInputFile(inputFile); + std::ifstream fin(path.c_str()); + if (!fin) { + throw CanteraError("MolarityIonicVPSSTP:constructPhaseFile","could not open " + +path+" for reading."); + } + /* + * The phase object automatically constructs an XML object. + * Use this object to store information. + */ + XML_Node &phaseNode_XML = xml(); + XML_Node *fxml = new XML_Node(); + fxml->build(fin); + XML_Node *fxml_phase = findXMLPhase(fxml, id); + if (!fxml_phase) { + throw CanteraError("MolarityIonicVPSSTP:constructPhaseFile", + "ERROR: Can not find phase named " + + id + " in file named " + inputFile); + } + fxml_phase->copy(&phaseNode_XML); + constructPhaseXML(*fxml_phase, id); + delete fxml; + } + //==================================================================================================================== + /* + * Import, construct, and initialize a HMWSoln phase + * specification from an XML tree into the current object. + * + * Most of the work is carried out by the cantera base + * routine, importPhase(). That routine imports all of the + * species and element data, including the standard states + * of the species. + * + * Then, In this routine, we read the information + * particular to the specification of the activity + * coefficient model for the Pitzer parameterization. + * + * We also read information about the molar volumes of the + * standard states if present in the XML file. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void MolarityIonicVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id) { + string stemp; + if ((int) id.size() > 0) { + string idp = phaseNode.id(); + if (idp != id) { + throw CanteraError("MolarityIonicVPSSTP::constructPhaseXML", + "phasenode and Id are incompatible"); + } + } + + /* + * Find the Thermo XML node + */ + if (!phaseNode.hasChild("thermo")) { + throw CanteraError("MolarityIonicVPSSTP::constructPhaseXML", + "no thermo XML node"); + } + XML_Node& thermoNode = phaseNode.child("thermo"); + + /* + * Make sure that the thermo model is MolarityIonic + */ + stemp = thermoNode.attrib("model"); + string formString = lowercase(stemp); + if (formString != "molarityionicvpss") { + throw CanteraError("MolarityIonicVPSSTP::constructPhaseXML", + "model name isn't MolarityIonicVPSS: " + formString); + + } + + /* + * Call the Cantera importPhase() function. This will import + * all of the species into the phase. This will also handle + * all of the solvent and solute standard states + */ + bool m_ok = importPhase(phaseNode, this); + if (!m_ok) { + throw CanteraError("MolarityIonicVPSSTP::constructPhaseXML","importPhase failed "); + } + + } + //==================================================================================================================== /* * ------------ Molar Thermodynamic Properties ---------------------- */ @@ -140,16 +287,78 @@ namespace Cantera { /* * - Activities, Standard States, Activity Concentrations ----------- */ - + // This method returns an array of generalized concentrations + /* + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * Here we define the activity concentrations as equal + * to the activities, because the standard concentration is 1. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + void MolarityIonicVPSSTP::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } //==================================================================================================================== doublereal MolarityIonicVPSSTP::standardConcentration(int k) const { - err("standardConcentration"); return -1.0; } //==================================================================================================================== doublereal MolarityIonicVPSSTP::logStandardConc(int k) const { - err("logStandardConc"); - return -1.0; + return 0.0; + } + //==================================================================================================================== + // Get the array of non-dimensional molar-based activity coefficients at + // the current solution temperature, pressure, and solution concentration. + /* + * @param ac Output vector of activity coefficients. Length: m_kk. + */ + void MolarityIonicVPSSTP::getLnActivityCoefficients(doublereal* lnac) const { + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + + /* + * take the exp of the internally storred coefficients. + */ + for (int k = 0; k < m_kk; k++) { + lnac[k] = lnActCoeff_Scaled_[k]; + } + } + //==================================================================================================================== + void MolarityIonicVPSSTP::getChemPotentials(doublereal* mu) const { + doublereal xx; + /* + * First get the standard chemical potentials in + * molar form. + * -> this requires updates of standard state as a function + * of T and P + */ + getStandardChemPotentials(mu); + /* + * Update the activity coefficients + */ + s_update_lnActCoeff(); + /* + * + */ + doublereal RT = GasConstant * temperature(); + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + mu[k] += RT * (log(xx) + lnActCoeff_Scaled_[k]); + } } //==================================================================================================================== @@ -160,6 +369,145 @@ namespace Cantera { mu[k] += ve*charge(k); } } + + //==================================================================================================================== + // Returns an array of partial molar enthalpies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MolarityIonicVPSSTP::getPartialMolarEnthalpies(doublereal* hbar) const { + /* + * Get the nondimensional standard state enthalpies + */ + getEnthalpy_RT(hbar); + /* + * dimensionalize it. + */ + double T = temperature(); + double RT = GasConstant * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] *= RT; + } + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + double RTT = RT * T; + for (int k = 0; k < m_kk; k++) { + hbar[k] -= RTT * dlnActCoeffdT_Scaled_[k]; + } + } + //==================================================================================================================== + // Returns an array of partial molar heat capacities for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????? \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MolarityIonicVPSSTP::getPartialMolarCp(doublereal* cpbar) const { + /* + * Get the nondimensional standard state entropies + */ + getCp_R(cpbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + cpbar[k] -= 2 * T * dlnActCoeffdT_Scaled_[k] + T * T * d2lnActCoeffdT2_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + cpbar[k] *= GasConstant; + } + } + //==================================================================================================================== + // Returns an array of partial molar entropies for the species + // in the mixture. + /* + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + */ + void MolarityIonicVPSSTP::getPartialMolarEntropies(doublereal* sbar) const { + double xx; + /* + * Get the nondimensional standard state entropies + */ + getEntropy_R(sbar); + double T = temperature(); + /* + * Update the activity coefficients, This also update the + * internally storred molalities. + */ + s_update_lnActCoeff(); + s_update_dlnActCoeff_dT(); + + for (int k = 0; k < m_kk; k++) { + xx = fmaxx(moleFractions_[k], xxSmall); + sbar[k] += - lnActCoeff_Scaled_[k] -log(xx) - T * dlnActCoeffdT_Scaled_[k]; + } + /* + * dimensionalize it. + */ + for (int k = 0; k < m_kk; k++) { + sbar[k] *= GasConstant; + } + } + // Return an array of partial molar volumes for the + // species in the mixture. Units: m^3/kmol. + /* + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + void MolarityIonicVPSSTP::getPartialMolarVolumes(doublereal* vbar) const { + int iK; + /* + * Get the standard state values in m^3 kmol-1 + */ + getStandardVolumes(vbar); + for ( iK = 0; iK < m_kk; iK++ ){ + + vbar[iK] += 0.0; + } + } //==================================================================================================================== void MolarityIonicVPSSTP::calcPseudoBinaryMoleFractions() const { int k; @@ -241,6 +589,38 @@ namespace Cantera { } } //==================================================================================================================== + + // Update the activity coefficients + /* + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + * + */ + void MolarityIonicVPSSTP::s_update_lnActCoeff() const { + int k; + for (k = 0; k < m_kk; k++) { + lnActCoeff_Scaled_[k] = 0.0; + } + } + //==================================================================================================================== + void MolarityIonicVPSSTP::s_update_dlnActCoeff_dT() const { + + + } + //==================================================================================================================== + // Internal routine that calculates the derivative of the activity coefficients wrt + // the mole fractions. + /* + * This routine calculates the the derivative of the activity coefficients wrt to mole fraction + * with all other mole fractions held constant. This is strictly not permitted. However, if the + * resulting matrix is multiplied by a permissible deltaX vector then everything is ok. + * + * This is the natural way to handle concentration derivatives in this routine. + */ + void MolarityIonicVPSSTP::s_update_dlnActCoeff_dX_() const { + + } + //==================================================================================================================== /* * ------------ Partial Molar Properties of the Solution ------------ */ @@ -323,11 +703,70 @@ namespace Cantera { * with the correct id. */ void MolarityIonicVPSSTP::initThermoXML(XML_Node& phaseNode, std::string id) { + std::string subname = "MolarityIonicVPSSTP::initThermoXML"; + std::string stemp; + /* + * Check on the thermo field. Must have: + * + */ + + XML_Node& thermoNode = phaseNode.child("thermo"); + std::string mStringa = thermoNode.attrib("model"); + std::string mString = lowercase(mStringa); + if (mString != "molarityionicvpss") { + throw CanteraError(subname.c_str(), + "Unknown thermo model: " + mStringa + " - This object only knows \"MolarityIonicVPSS\" "); + } + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + /* + * Go get all of the coefficients and factors in the + * activityCoefficients XML block + */ + XML_Node *acNodePtr = 0; + if (thermoNode.hasChild("activityCoefficients")) { + XML_Node& acNode = thermoNode.child("activityCoefficients"); + acNodePtr = &acNode; + std::string mStringa = acNode.attrib("model"); + std::string mString = lowercase(mStringa); + // if (mString != "redlich-kister") { + // throw CanteraError(subname.c_str(), + // "Unknown activity coefficient model: " + mStringa); + //} + int n = acNodePtr->nChildren(); + for (int i = 0; i < n; i++) { + XML_Node &xmlACChild = acNodePtr->child(i); + stemp = xmlACChild.name(); + std::string nodeName = lowercase(stemp); + /* + * Process a binary interaction + */ + if (nodeName == "binaryneutralspeciesparameters") { + readXMLBinarySpecies(xmlACChild); + } + } + } - + + /* + * Go down the chain + */ GibbsExcessVPSSTP::initThermoXML(phaseNode, id); } //==================================================================================================================== + // Process an XML node called "binaryNeutralSpeciesParameters" + /* + * This node contains all of the parameters necessary to describe + * a single binary interaction. This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + */ + void MolarityIonicVPSSTP::readXMLBinarySpecies(XML_Node &xmLBinarySpecies) { + std::string xname = xmLBinarySpecies.name(); + + } + //==================================================================================================================== /* * Format a summary of the mixture state for output. */ diff --git a/Cantera/src/thermo/MolarityIonicVPSSTP.h b/Cantera/src/thermo/MolarityIonicVPSSTP.h index dd6c339e8..e75531a8e 100644 --- a/Cantera/src/thermo/MolarityIonicVPSSTP.h +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.h @@ -38,8 +38,7 @@ namespace Cantera { * thermodynamic properties that are further based on * expressing the Excess Gibbs free energy as a function of * the mole fractions (or pseudo mole fractions) of the consitituents. - * This category is the workhorse for describing ionic systems which - * are not on the molality scale. + * This category is the workhorse for describing ionic systems which are not on the molality scale. * * This class adds additional functions onto the %ThermoPhase interface * that handles the calculation of the excess Gibbs free energy. The %ThermoPhase @@ -56,7 +55,7 @@ namespace Cantera { * it is expected that there exists a charge balance at all times. * One of the ions must be a "special ion" in the sense that its' thermodynamic * functions are set to zero, and the thermo functions of all other - * ions are based on a valuation relative to the special ion. + * ions are based on a valuation relative to that special ion. * */ class MolarityIonicVPSSTP : public GibbsExcessVPSSTP { @@ -74,6 +73,31 @@ namespace Cantera { */ MolarityIonicVPSSTP(); + //! Construct and initialize a MolarityIonicVPSSTP ThermoPhase object + //! directly from an xml input file + /*! + * Working constructors + * + * The two constructors below are the normal way the phase initializes itself. They are shells that call + * the routine initThermo(), with a reference to the XML database to get the info for the phase. + * + * @param inputFile Name of the input file containing the phase XML data + * to set up the object + * @param id ID of the phase in the input file. Defaults to the + * empty string. + */ + MolarityIonicVPSSTP(std::string inputFile, std::string id = ""); + + //! Construct and initialize a MolarityIonicVPSSTP ThermoPhase object + //! directly from an XML database + /*! + * @param phaseRef XML phase node containing the description of the phase + * @param id id attribute containing the name of the phase. + * (default is the empty string) + */ + MolarityIonicVPSSTP(XML_Node& phaseRef, std::string id = ""); + + //! Copy constructor /*! * Note this stuff will not work until the underlying phase @@ -118,7 +142,46 @@ namespace Cantera { */ virtual int eosType() const; - + //! Initialization of a phase using an xml file + /*! + * This routine is a precursor to + * routine, which does most of the work. + * + * @param inputFile XML file containing the description of the + * phase + * + * @param id Optional parameter identifying the name of the + * phase. If none is given, the first XML + * phase element will be used. + */ + void constructPhaseFile(std::string inputFile, std::string id); + + //! Import and initialize a phase + //! specification in an XML tree into the current object. + /*! + * Here we read an XML description of the phase. + * We import descriptions of the elements that make up the + * species in a phase. + * We import information about the species, including their + * reference state thermodynamic polynomials. We then freeze + * the state of the species. + * + * Then, we read the species molar volumes from the xml + * tree to finish the initialization. + * + * @param phaseNode This object must be the phase node of a + * complete XML tree + * description of the phase, including all of the + * species data. In other words while "phase" must + * point to an XML phase object, it must have + * sibling nodes "speciesData" that describe + * the species in the phase. + * + * @param id ID of the phase. If nonnull, a check is done + * to see if phaseNode is pointing to the phase + * with the correct id. + */ + void constructPhaseXML(XML_Node& phaseNode, std::string id); /** * @} @@ -165,7 +228,24 @@ namespace Cantera { * @{ */ - + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used + * by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; /** @@ -191,6 +271,15 @@ namespace Cantera { */ virtual doublereal logStandardConc(int k=0) const; + //! Get the array of non-dimensional molar-based ln activity coefficients at + //! the current solution temperature, pressure, and solution concentration. + /*! + * @param lnac Output vector of ln activity coefficients. Length: m_kk. + */ + virtual void getLnActivityCoefficients(doublereal* ac) const; + + + @@ -198,6 +287,16 @@ namespace Cantera { /// @name Partial Molar Properties of the Solution //@{ + //! Get the species chemical potentials. Units: J/kmol. + /*! + * This function returns a vector of chemical potentials of the + * species in solution at the current temperature, pressure + * and mole fraction of the solution. + * + * @param mu Output vector of species chemical + * potentials. Length: m_kk. Units: J/kmol + */ + virtual void getChemPotentials(doublereal* mu) const; /** * Get the species electrochemical potentials. @@ -212,7 +311,79 @@ namespace Cantera { */ void getElectrochemPotentials(doublereal* mu) const; + //! Returns an array of partial molar enthalpies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * molality-based activity coefficent wrt temperature + * + * \f[ + * \bar h_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * \f] + * + * @param hbar Vector of returned partial molar enthalpies + * (length m_kk, units = J/kmol) + */ + virtual void getPartialMolarEnthalpies(doublereal* hbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * \f] + * + * @param sbar Vector of returned partial molar entropies + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarEntropies(doublereal* sbar) const; + + //! Returns an array of partial molar entropies for the species + //! in the mixture. + /*! + * Units (J/kmol) + * + * For this phase, the partial molar enthalpies are equal to the + * standard state enthalpies modified by the derivative of the + * activity coefficent wrt temperature + * + * \f[ + * ??????????????? + * \bar s_k(T,P) = s^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} + * - R \ln( \gamma_k X_k) + * - R T \frac{d \ln(\gamma_k) }{dT} + * ??????????????? + * \f] + * + * @param cpbar Vector of returned partial molar heat capacities + * (length m_kk, units = J/kmol/K) + */ + virtual void getPartialMolarCp(doublereal* cpbar) const; + //! Return an array of partial molar volumes for the + //! species in the mixture. Units: m^3/kmol. + /*! + * Frequently, for this class of thermodynamics representations, + * the excess Volume due to mixing is zero. Here, we set it as + * a default. It may be overriden in derived classes. + * + * @param vbar Output vector of speciar partial molar volumes. + * Length = m_kk. units are m^3/kmol. + */ + virtual void getPartialMolarVolumes(doublereal* vbar) const; + + //@} /// @name Properties of the Standard State of the Species in the Solution //@{ @@ -318,11 +489,48 @@ namespace Cantera { private: - //! Initialize lengths of local variables after all species have - //! been identified. + //! Initialize lengths of local variables after all species have been identified. void initLengths(); + + //! Process an XML node called "binaryNeutralSpeciesParameters" + /*! + * This node contains all of the parameters necessary to describe + * the Redlich-Kister model for a particular binary interaction. + * This function reads the XML file and writes the coefficients + * it finds to an internal data structures. + * + * @param xmlBinarySpecies Reference to the XML_Node named "binaryNeutralSpeciesParameters" + * containing the binary interaction + */ + void readXMLBinarySpecies(XML_Node &xmlBinarySpecies); + //! Update the activity coefficients + /*! + * This function will be called to update the internally storred + * natural logarithm of the activity coefficients + */ + void s_update_lnActCoeff() const; + + //! Update the derivative of the log of the activity coefficients wrt T + /*! + * This function will be called to update the internally storred + * derivative of the natural logarithm of the activity coefficients + * wrt temperature. + */ + void s_update_dlnActCoeff_dT() const; + + //! Internal routine that calculates the derivative of the activity coefficients wrt + //! the mole fractions. + /*! + * This routine calculates the the derivative of the activity coefficients wrt to mole fraction + * with all other mole fractions held constant. This is strictly not permitted. However, if the + * resulting matrix is multiplied by a permissible deltaX vector then everything is ok. + * + * This is the natural way to handle concentration derivatives in this routine. + */ + void s_update_dlnActCoeff_dX_() const; + private: //! Error function diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.cpp b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp index a97ee19d8..b6dc57f3d 100644 --- a/Cantera/src/thermo/RedlichKisterVPSSTP.cpp +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp @@ -387,7 +387,7 @@ namespace Cantera { /* * @param ac Output vector of activity coefficients. Length: m_kk. */ - void RedlichKisterVPSSTP::getActivityCoefficients(doublereal* ac) const { + void RedlichKisterVPSSTP::getLnActivityCoefficients(doublereal* lnac) const { /* * Update the activity coefficients */ @@ -397,7 +397,7 @@ namespace Cantera { * take the exp of the internally storred coefficients. */ for (int k = 0; k < m_kk; k++) { - ac[k] = exp(lnActCoeff_Scaled_[k]); + lnac[k] = lnActCoeff_Scaled_[k]; } } //==================================================================================================================== @@ -728,6 +728,12 @@ namespace Cantera { doublereal RT = GasConstant * T; fvo_zero_dbl_1(lnActCoeff_Scaled_, m_kk); + + /* + * Scaling: I moved the division of RT higher so that we are always dealing with G/RT dimensionless terms + * within the routine. There is a severe problem with roundoff error in these calculations. The + * dimensionless terms help. + */ for (int i = 0; i < numBinaryInteractions_; i++) { iA = m_pSpecies_A_ij[i]; @@ -744,7 +750,7 @@ namespace Cantera { doublereal sumMm1 = 0.0; doublereal sum2 = 0.0; for (m = 0; m < N; m++) { - doublereal A_ge = he_vec[m] - T * se_vec[m]; + doublereal A_ge = (he_vec[m] - T * se_vec[m]) / RT; sum += A_ge * poly; sum2 += A_ge * (m + 1) * poly; poly *= deltaX; @@ -771,7 +777,7 @@ namespace Cantera { double polyk = 1.0; double fac = 2.0 * XA - 1.0; for (m = 0; m < N; m++) { - doublereal A_ge = he_vec[m] - T * se_vec[m]; + doublereal A_ge = (he_vec[m] - T * se_vec[m]) / RT; lnA += A_ge * oneMXA * oneMXA * polyk * (1.0 + 2.0 * XA * m / fac); lnB += A_ge * XA * XA * polyk * (1.0 - 2.0 * oneMXA * m / fac); polyk *= fac; @@ -783,9 +789,7 @@ namespace Cantera { #endif } - for (k = 0; k < m_kk; k++) { - lnActCoeff_Scaled_[k] /= RT; - } + } //=================================================================================================================== // Update the derivative of the log of the activity coefficients wrt T @@ -1117,7 +1121,7 @@ namespace Cantera { double poly1mk = fac; for (m = 0; m < N; m++) { - doublereal A_ge = he_vec[m]; + doublereal A_ge = he_vec[m] - T * se_vec[m]; Volts += A_ge * ( polykp1 - (2.0 * XA * m * (1.0-XA) ) / poly1mk ); polykp1 *= fac; poly1mk /= fac; diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.h b/Cantera/src/thermo/RedlichKisterVPSSTP.h index d11e9e2bd..d4d927d62 100644 --- a/Cantera/src/thermo/RedlichKisterVPSSTP.h +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.h @@ -533,15 +533,12 @@ namespace Cantera { */ virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based activity coefficients at + //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! - * @param ac Output vector of activity coefficients. Length: m_kk. + * @param lnac Output vector of ln activity coefficients. Length: m_kk. */ - virtual void getActivityCoefficients(doublereal* ac) const; - - - + virtual void getLnActivityCoefficients(doublereal* ac) const; //@} /// @name Partial Molar Properties of the Solution From 0d0e481e2fc5ea6a66298611bbca278488d12d64 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Thu, 3 Nov 2011 20:03:23 +0000 Subject: [PATCH 426/446] Added comments. --- Cantera/src/zeroD/Reactor.h | 45 ++++++++++++++++----------------- Cantera/src/zeroD/ReactorBase.h | 13 ++++++++-- 2 files changed, 33 insertions(+), 25 deletions(-) diff --git a/Cantera/src/zeroD/Reactor.h b/Cantera/src/zeroD/Reactor.h index d43760f08..510844405 100644 --- a/Cantera/src/zeroD/Reactor.h +++ b/Cantera/src/zeroD/Reactor.h @@ -59,10 +59,8 @@ namespace CanteraZeroD { public: - /** - * Default constructor. - */ - Reactor(); + //! Default constructor. + Reactor(); /** * Destructor. Deletes the integrator. @@ -121,26 +119,27 @@ namespace CanteraZeroD { virtual int componentIndex(std::string nm) const; protected: - - Cantera::Kinetics* m_kin; - - doublereal m_temp_atol; // tolerance on T - doublereal m_maxstep; // max step size - doublereal m_vdot, m_Q; - Cantera::vector_fp m_atol; - doublereal m_rtol; - Cantera::vector_fp m_work; - Cantera::vector_fp m_sdot; // surface production rates - bool m_chem; - bool m_energy; - int m_nv; - - int m_nsens; - Cantera::vector_int m_pnum; - std::vector m_pname; - Cantera::vector_int m_nsens_wall; - Cantera::vector_fp m_mult_save; + //! Pointer to the homogeneous Kinetics object that handles the reactions + Cantera::Kinetics* m_kin; + //! Tolerance on the temperature + doublereal m_temp_atol; + doublereal m_maxstep; // max step size + doublereal m_vdot, m_Q; + Cantera::vector_fp m_atol; + doublereal m_rtol; + Cantera::vector_fp m_work; + Cantera::vector_fp m_sdot; // surface production rates + bool m_chem; + bool m_energy; + int m_nv; + + int m_nsens; + Cantera::vector_int m_pnum; + std::vector m_pname; + Cantera::vector_int m_nsens_wall; + Cantera::vector_fp m_mult_save; + private: }; } diff --git a/Cantera/src/zeroD/ReactorBase.h b/Cantera/src/zeroD/ReactorBase.h index 008050bdb..4f0bc5a11 100644 --- a/Cantera/src/zeroD/ReactorBase.h +++ b/Cantera/src/zeroD/ReactorBase.h @@ -133,7 +133,14 @@ namespace CanteraZeroD { /// the current time (s). doublereal time() const { return m_time; } - doublereal volume() const { return m_vol; } + + //! Returns the current volume of the reactor + /*! + * @return Return the volume in m**3 + */ + doublereal volume() const { + return m_vol; + } doublereal density() const { return m_state[1]; } doublereal temperature() const { return m_state[0]; } doublereal enthalpy_mass() const { return m_enthalpy; } @@ -152,7 +159,9 @@ namespace CanteraZeroD { protected: - int m_nsp; + //! Number of homogeneous species in the mixture + int m_nsp; + Cantera::thermo_t* m_thermo; doublereal m_time; doublereal m_vol, m_vol0; From 973d1ad926439b890a56f57f6f21a98865e77a78 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 7 Nov 2011 21:51:51 +0000 Subject: [PATCH 427/446] Fixed a Makefile error --- Cantera/src/transport/Makefile.in | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index df4315d5a..73e74392f 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -70,12 +70,17 @@ all: $(LIB) .depends @(for lh in $(CATRAN_H) ; do \ $(INSTALL_TSC) "$${lh}" $(INCDIR) ; \ done) -%.d: Makefile %.o + +.cpp.d: @CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d .cpp.o: $(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES) +$(DEPENDS): Makefile + +$(CATRAN_OBJ): Makefile + $(LIB): $(CATRAN_OBJ) $(CATRAN_H) @ARCHIVE@ $(LIB) $(CATRAN_OBJ) > /dev/null ifeq ($(do_ranlib),1) From 75b3ed6ef9b884a802a45f2d5cb0dd24c0249a65 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 8 Nov 2011 21:01:07 +0000 Subject: [PATCH 428/446] Deleted a line that snuck in that caused ctft2c to not be used when it was requested to be used --- configure | 10537 +++++++++++++++++++------------------------------ configure.in | 1 - 2 files changed, 4013 insertions(+), 6525 deletions(-) diff --git a/configure b/configure index 0f45c8d28..d85b60181 100755 --- a/configure +++ b/configure @@ -1,81 +1,423 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.59 for Cantera 1.7.0. +# Generated by GNU Autoconf 2.68 for Cantera 1.7.0. +# +# +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software +# Foundation, Inc. +# # -# Copyright (C) 2003 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## -# Be Bourne compatible -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: - # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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'((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. -for as_var in \ - LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ - LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ - LC_TELEPHONE LC_TIME -do - if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then - eval $as_var=C; export $as_var - else - $as_unset $as_var - fi -done +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE -# Required to use basename. -if expr a : '\(a\)' >/dev/null 2>&1; then +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +if test "x$CONFIG_SHELL" = x; then + as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. 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Then install a modern shell, or manually run +$0: the script under such a shell if you do have one." + fi + exit 1 +fi +fi +fi +SHELL=${CONFIG_SHELL-/bin/sh} +export SHELL +# Unset more variables known to interfere with behavior of common tools. +CLICOLOR_FORCE= GREP_OPTIONS= +unset CLICOLOR_FORCE GREP_OPTIONS + +## --------------------- ## +## M4sh Shell Functions. ## +## --------------------- ## +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" + + +} # as_fn_mkdir_p +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with STATUS, using 1 if that was 0. +as_fn_error () +{ + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + fi + $as_echo "$as_me: error: $2" >&2 + as_fn_exit $as_status +} # as_fn_error + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi -if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. -as_me=`$as_basename "$0" || +as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)$' \| \ - . : '\(.\)' 2>/dev/null || -echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } - /^X\/\(\/\/\)$/{ s//\1/; q; } - /^X\/\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` - -# PATH needs CR, and LINENO needs CR and PATH. # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -83,146 +425,107 @@ as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits -# The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then - echo "#! /bin/sh" >conf$$.sh - echo "exit 0" >>conf$$.sh - chmod +x conf$$.sh - if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then - PATH_SEPARATOR=';' - else - PATH_SEPARATOR=: - fi - rm -f conf$$.sh -fi - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" || { - # Find who we are. Look in the path if we contain no path at all - # relative or not. - case $0 in - *[\\/]* ) as_myself=$0 ;; - *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done - - ;; - esac - # We did not find ourselves, most probably we were run as `sh COMMAND' - # in which case we are not to be found in the path. - if test "x$as_myself" = x; then - as_myself=$0 - fi - if test ! -f "$as_myself"; then - { echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2 - { (exit 1); exit 1; }; } - fi - case $CONFIG_SHELL in - '') - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for as_base in sh bash ksh sh5; do - case $as_dir in - /*) - if ("$as_dir/$as_base" -c ' - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then - $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } - $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } - CONFIG_SHELL=$as_dir/$as_base - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$0" ${1+"$@"} - fi;; - esac - done -done -;; - esac - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. The first 'sed' inserts a - # line-number line before each line; the second 'sed' does the real - # work. The second script uses 'N' to pair each line-number line - # with the numbered line, and appends trailing '-' during - # substitution so that $LINENO is not a special case at line end. - # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the - # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) - sed '=' <$as_myself | + as_lineno_1=$LINENO as_lineno_1a=$LINENO + as_lineno_2=$LINENO as_lineno_2a=$LINENO + eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && + test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { + # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno N - s,$,-, - : loop - s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3, + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ t loop - s,-$,, - s,^['$as_cr_digits']*\n,, + s/-\n.*// ' >$as_me.lineno && - chmod +x $as_me.lineno || - { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 - { (exit 1); exit 1; }; } + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the - # original and so on. Autoconf is especially sensible to this). - . ./$as_me.lineno + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" # Exit status is that of the last command. exit } - -case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in - *c*,-n*) ECHO_N= ECHO_C=' -' ECHO_T=' ' ;; - *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;; - *) ECHO_N= ECHO_C='\c' ECHO_T= ;; +ECHO_C= ECHO_N= ECHO_T= +case `echo -n x` in #((((( +-n*) + case `echo 'xy\c'` in + *c*) ECHO_T=' ';; # ECHO_T is single tab character. + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; + esac;; +*) + ECHO_N='-n';; esac -if expr a : '\(a\)' >/dev/null 2>&1; then - as_expr=expr -else - as_expr=false -fi - rm -f conf$$ conf$$.exe conf$$.file -echo >conf$$.file -if ln -s conf$$.file conf$$ 2>/dev/null; then - # We could just check for DJGPP; but this test a) works b) is more generic - # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04). - if test -f conf$$.exe; then - # Don't use ln at all; we don't have any links - as_ln_s='cp -p' - else +if test -d conf$$.dir; then + rm -f conf$$.dir/conf$$.file +else + rm -f conf$$.dir + mkdir conf$$.dir 2>/dev/null +fi +if (echo >conf$$.file) 2>/dev/null; then + if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' + # ... but there are two gotchas: + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -p'. + ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || + as_ln_s='cp -p' + elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln + else + as_ln_s='cp -p' fi -elif ln conf$$.file conf$$ 2>/dev/null; then - as_ln_s=ln else as_ln_s='cp -p' fi -rm -f conf$$ conf$$.exe conf$$.file +rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file +rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi -as_executable_p="test -f" +if test -x / >/dev/null 2>&1; then + as_test_x='test -x' +else + if ls -dL / >/dev/null 2>&1; then + as_ls_L_option=L + else + as_ls_L_option= + fi + as_test_x=' + eval sh -c '\'' + if test -d "$1"; then + test -d "$1/."; + else + case $1 in #( + -*)set "./$1";; + esac; + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + ???[sx]*):;;*)false;;esac;fi + '\'' sh + ' +fi +as_executable_p=$as_test_x # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" @@ -231,38 +534,25 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -# IFS -# We need space, tab and new line, in precisely that order. -as_nl=' -' -IFS=" $as_nl" - -# CDPATH. -$as_unset CDPATH - +test -n "$DJDIR" || exec 7<&0 &1 # Name of the host. -# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` -exec 6>&1 - # # Initializations. # ac_default_prefix=/usr/local +ac_clean_files= ac_config_libobj_dir=. +LIBOBJS= cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= -SHELL=${CONFIG_SHELL-/bin/sh} - -# Maximum number of lines to put in a shell here document. -# This variable seems obsolete. It should probably be removed, and -# only ac_max_sed_lines should be used. -: ${ac_max_here_lines=38} # Identity of this package. PACKAGE_NAME='Cantera' @@ -270,50 +560,264 @@ PACKAGE_TARNAME='cantera' PACKAGE_VERSION='1.7.0' PACKAGE_STRING='Cantera 1.7.0' PACKAGE_BUGREPORT='' +PACKAGE_URL='' # Factoring default headers for most tests. ac_includes_default="\ #include -#if HAVE_SYS_TYPES_H +#ifdef HAVE_SYS_TYPES_H # include #endif -#if HAVE_SYS_STAT_H +#ifdef HAVE_SYS_STAT_H # include #endif -#if STDC_HEADERS +#ifdef STDC_HEADERS # include # include #else -# if HAVE_STDLIB_H +# ifdef HAVE_STDLIB_H # include # endif #endif -#if HAVE_STRING_H -# if !STDC_HEADERS && HAVE_MEMORY_H +#ifdef HAVE_STRING_H +# if !defined STDC_HEADERS && defined HAVE_MEMORY_H # include # endif # include #endif -#if HAVE_STRINGS_H +#ifdef HAVE_STRINGS_H # include #endif -#if HAVE_INTTYPES_H +#ifdef HAVE_INTTYPES_H # include -#else -# if HAVE_STDINT_H -# include -# endif #endif -#if HAVE_UNISTD_H +#ifdef HAVE_STDINT_H +# include +#endif +#ifdef HAVE_UNISTD_H # include #endif" -ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME 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phase_object_files phase_header_files COMPILE_IDEAL_SOLUTIONS COMPILE_ELECTROLYTES NEED_CATHERMO COMPILE_KINETICS COMPILE_HETEROKIN COMPILE_RXNPATH WITH_REACTORS KERNEL KERNEL_OBJ BUILD_CK LIB_DIR COMPILE_VCSNONIDEAL COMPILE_H298MODIFY_CAPABILITY COMPILE_INTERMEDIATE_ZEROED_KINETICS BOOST_INCLUDE BOOST_LIB PURIFY build_lapack build_blas BLAS_LAPACK_LIBS BLAS_LAPACK_LINK BLAS_LAPACK_DIR build_with_f2c build_f2c_lib F2C_SYSTEMLIB BOOST_LIB_DIR LOCAL_LIB_DIRS LOCAL_LIBS LOCAL_LIBS_DEP INSTALL_LIBS_DEP RAW_LIBS_DEP CANTERA_CORE_LIBS CANTERA_CORE_LIBS_DEP CT_SHARED_LIB PYTHON_CMD BUILD_PYTHON NUMPY_INC_DIR NUMPY_HOME NUMARRAY_INC_DIR NUMARRAY_HOME CANTERA_PYTHON_HOME CVSTAG MATLAB_CMD BUILD_MATLAB BUILD_CLIB export_name PIC INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CXXCPP EGREP SOEXT SHARED CXX_INCLUDES LCXX_FLAGS LCXX_END_LIBS HAVE_STRIPSYMBOLS F77 FFLAGS ac_ct_F77 FLIBS F90 BUILD_F90 F90FLAGS F90BUILDFLAGS F90LIBS LCXX_FLIBS precompile_headers OS_IS_DARWIN OS_IS_WIN OS_IS_CYGWIN SHARED_CTLIB mex_ext F77_EXT CXX_EXT OBJ_EXT EXE_EXT math_libs SO LDSHARED EXTRA_LINK TSCOMPARE_abs INSTALL_abs INSTALL_VERBOSE LIBOBJS LTLIBOBJS' +ac_subst_vars='LTLIBOBJS +LIBOBJS +INSTALL_VERBOSE +INSTALL_abs +TSCOMPARE_abs +EXTRA_LINK +LDSHARED +SO +math_libs +EXE_EXT +OBJ_EXT +CXX_EXT +F77_EXT +mex_ext +SHARED_CTLIB +OS_IS_CYGWIN +OS_IS_WIN +OS_IS_DARWIN +precompile_headers +LCXX_FLIBS +F90LIBS +F90BUILDFLAGS +F90FLAGS +BUILD_F90 +F90 +FLIBS +ac_ct_F77 +FFLAGS +F77 +HAVE_STRIPSYMBOLS +LCXX_END_LIBS +LCXX_FLAGS +CXX_INCLUDES +SHARED +SOEXT +EGREP +GREP +CXXCPP +INSTALL_DATA +INSTALL_SCRIPT +INSTALL_PROGRAM +PIC +export_name +BUILD_CLIB +BUILD_MATLAB +MATLAB_CMD +CVSTAG +CANTERA_PYTHON_HOME +NUMARRAY_HOME +NUMARRAY_INC_DIR +NUMPY_HOME +NUMPY_INC_DIR +BUILD_PYTHON +PYTHON_CMD +CT_SHARED_LIB +CANTERA_CORE_LIBS_DEP +CANTERA_CORE_LIBS +RAW_LIBS_DEP +INSTALL_LIBS_DEP +LOCAL_LIBS_DEP +LOCAL_LIBS +LOCAL_LIB_DIRS +BOOST_LIB_DIR +F2C_SYSTEMLIB +build_f2c_lib +build_with_f2c +BLAS_LAPACK_DIR +BLAS_LAPACK_LINK +BLAS_LAPACK_LIBS +build_blas +build_lapack +PURIFY +BOOST_LIB +BOOST_INCLUDE +COMPILE_INTERMEDIATE_ZEROED_KINETICS +COMPILE_H298MODIFY_CAPABILITY +COMPILE_VCSNONIDEAL +LIB_DIR +BUILD_CK +KERNEL_OBJ +KERNEL +WITH_REACTORS +COMPILE_RXNPATH +COMPILE_HETEROKIN +COMPILE_KINETICS +NEED_CATHERMO +COMPILE_ELECTROLYTES +COMPILE_IDEAL_SOLUTIONS +phase_header_files +phase_object_files +COMPILE_PURE_FLUIDS +CANTERA_DEBUG_MODE +sundials_lib_dep +sundials_lib +sundials_lib_dir +sundials_include +IDA_LIBS +CVODE_LIBS +use_sundials +INCL_USER_CODE +USERDIR +CXX_DEPENDS +RANLIB +DO_RANLIB +ARCHIVE +GRAPHVIZDIR +MAKE +buildbin +buildlib +buildinc +ctroot +username +target_os +target_vendor +target_cpu +target +host_os +host_vendor +host_cpu +host +build_os +build_vendor +build_cpu +build +ct_mandir +ct_dir +ct_docdir +ct_tutdir +ct_templdir +ct_demodir +ct_datadir +ct_incroot +ct_incdir +ct_bindir +ct_libdir +homedir +ctversion +python_win_prefix +python_prefix +local_python_inst +local_inst +USE_CLIB_DLL +CVF_LIBDIR +ldemulationarg +ac_ct_CC +CFLAGS +CC +OBJEXT +EXEEXT +ac_ct_CXX +CPPFLAGS +LDFLAGS +CXXFLAGS +CXX +BITCHANGE +BITHARDWARE +BITCOMPILE +target_alias +host_alias +build_alias +LIBS +ECHO_T +ECHO_N +ECHO_C +DEFS +mandir +localedir +libdir +psdir +pdfdir +dvidir +htmldir +infodir +docdir +oldincludedir +includedir +localstatedir +sharedstatedir +sysconfdir +datadir +datarootdir +libexecdir +sbindir +bindir +program_transform_name +prefix +exec_prefix +PACKAGE_URL +PACKAGE_BUGREPORT +PACKAGE_STRING +PACKAGE_VERSION +PACKAGE_TARNAME +PACKAGE_NAME +PATH_SEPARATOR +SHELL' ac_subst_files='' +ac_user_opts=' +enable_option_checking +' + ac_precious_vars='build_alias +host_alias +target_alias +CXX +CXXFLAGS +LDFLAGS +LIBS +CPPFLAGS +CCC +CC +CFLAGS +CXXCPP +F77 +FFLAGS' + # Initialize some variables set by options. ac_init_help= ac_init_version=false +ac_unrecognized_opts= +ac_unrecognized_sep= # The variables have the same names as the options, with # dashes changed to underlines. cache_file=/dev/null @@ -336,34 +840,49 @@ x_libraries=NONE # and all the variables that are supposed to be based on exec_prefix # by default will actually change. # Use braces instead of parens because sh, perl, etc. also accept them. +# (The list follows the same order as the GNU Coding Standards.) bindir='${exec_prefix}/bin' sbindir='${exec_prefix}/sbin' libexecdir='${exec_prefix}/libexec' -datadir='${prefix}/share' +datarootdir='${prefix}/share' +datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' -libdir='${exec_prefix}/lib' includedir='${prefix}/include' oldincludedir='/usr/include' -infodir='${prefix}/info' -mandir='${prefix}/man' +docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' +infodir='${datarootdir}/info' +htmldir='${docdir}' +dvidir='${docdir}' +pdfdir='${docdir}' +psdir='${docdir}' +libdir='${exec_prefix}/lib' +localedir='${datarootdir}/locale' +mandir='${datarootdir}/man' ac_prev= +ac_dashdash= for ac_option do # If the previous option needs an argument, assign it. if test -n "$ac_prev"; then - eval "$ac_prev=\$ac_option" + eval $ac_prev=\$ac_option ac_prev= continue fi - ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'` + case $ac_option in + *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *=) ac_optarg= ;; + *) ac_optarg=yes ;; + esac # Accept the important Cygnus configure options, so we can diagnose typos. - case $ac_option in + case $ac_dashdash$ac_option in + --) + ac_dashdash=yes ;; -bindir | --bindir | --bindi | --bind | --bin | --bi) ac_prev=bindir ;; @@ -385,33 +904,59 @@ do --config-cache | -C) cache_file=config.cache ;; - -datadir | --datadir | --datadi | --datad | --data | --dat | --da) + -datadir | --datadir | --datadi | --datad) ac_prev=datadir ;; - -datadir=* | --datadir=* | --datadi=* | --datad=* | --data=* | --dat=* \ - | --da=*) + -datadir=* | --datadir=* | --datadi=* | --datad=*) datadir=$ac_optarg ;; + -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \ + | --dataroo | --dataro | --datar) + ac_prev=datarootdir ;; + -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \ + | --dataroot=* | --dataroo=* | --dataro=* | --datar=*) + datarootdir=$ac_optarg ;; + -disable-* | --disable-*) - ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid feature name: $ac_feature" >&2 - { (exit 1); exit 1; }; } - ac_feature=`echo $ac_feature | sed 's/-/_/g'` - eval "enable_$ac_feature=no" ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval enable_$ac_useropt=no ;; + + -docdir | --docdir | --docdi | --doc | --do) + ac_prev=docdir ;; + -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*) + docdir=$ac_optarg ;; + + -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv) + ac_prev=dvidir ;; + -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*) + dvidir=$ac_optarg ;; -enable-* | --enable-*) - ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid feature name: $ac_feature" >&2 - { (exit 1); exit 1; }; } - ac_feature=`echo $ac_feature | sed 's/-/_/g'` - case $ac_option in - *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;; - *) ac_optarg=yes ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; esac - eval "enable_$ac_feature='$ac_optarg'" ;; + eval enable_$ac_useropt=\$ac_optarg ;; -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \ @@ -438,6 +983,12 @@ do -host=* | --host=* | --hos=* | --ho=*) host_alias=$ac_optarg ;; + -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht) + ac_prev=htmldir ;; + -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \ + | --ht=*) + htmldir=$ac_optarg ;; + -includedir | --includedir | --includedi | --included | --include \ | --includ | --inclu | --incl | --inc) ac_prev=includedir ;; @@ -462,13 +1013,16 @@ do | --libexe=* | --libex=* | --libe=*) libexecdir=$ac_optarg ;; + -localedir | --localedir | --localedi | --localed | --locale) + ac_prev=localedir ;; + -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*) + localedir=$ac_optarg ;; + -localstatedir | --localstatedir | --localstatedi | --localstated \ - | --localstate | --localstat | --localsta | --localst \ - | --locals | --local | --loca | --loc | --lo) + | --localstate | --localstat | --localsta | --localst | --locals) ac_prev=localstatedir ;; -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \ - | --localstate=* | --localstat=* | --localsta=* | --localst=* \ - | --locals=* | --local=* | --loca=* | --loc=* | --lo=*) + | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*) localstatedir=$ac_optarg ;; -mandir | --mandir | --mandi | --mand | --man | --ma | --m) @@ -533,6 +1087,16 @@ do | --progr-tra=* | --program-tr=* | --program-t=*) program_transform_name=$ac_optarg ;; + -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd) + ac_prev=pdfdir ;; + -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*) + pdfdir=$ac_optarg ;; + + -psdir | --psdir | --psdi | --psd | --ps) + ac_prev=psdir ;; + -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*) + psdir=$ac_optarg ;; + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) silent=yes ;; @@ -583,26 +1147,36 @@ do ac_init_version=: ;; -with-* | --with-*) - ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid package name: $ac_package" >&2 - { (exit 1); exit 1; }; } - ac_package=`echo $ac_package| sed 's/-/_/g'` - case $ac_option in - *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;; - *) ac_optarg=yes ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig" + ac_unrecognized_sep=', ';; esac - eval "with_$ac_package='$ac_optarg'" ;; + eval with_$ac_useropt=\$ac_optarg ;; -without-* | --without-*) - ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'` + ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. - expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid package name: $ac_package" >&2 - { (exit 1); exit 1; }; } - ac_package=`echo $ac_package | sed 's/-/_/g'` - eval "with_$ac_package=no" ;; + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval with_$ac_useropt=no ;; --x) # Obsolete; use --with-x. @@ -622,27 +1196,26 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) { echo "$as_me: error: unrecognized option: $ac_option -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; } + -*) as_fn_error $? "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information" ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && - { echo "$as_me: error: invalid variable name: $ac_envvar" >&2 - { (exit 1); exit 1; }; } - ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` - eval "$ac_envvar='$ac_optarg'" + case $ac_envvar in #( + '' | [0-9]* | *[!_$as_cr_alnum]* ) + as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; + esac + eval $ac_envvar=\$ac_optarg export $ac_envvar ;; *) # FIXME: should be removed in autoconf 3.0. - echo "$as_me: WARNING: you should use --build, --host, --target" >&2 + $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && - echo "$as_me: WARNING: invalid host type: $ac_option" >&2 - : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option} + $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 + : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}" ;; esac @@ -650,31 +1223,36 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - { echo "$as_me: error: missing argument to $ac_option" >&2 - { (exit 1); exit 1; }; } + as_fn_error $? "missing argument to $ac_option" fi -# Be sure to have absolute paths. -for ac_var in exec_prefix prefix -do - eval ac_val=$`echo $ac_var` - case $ac_val in - [\\/$]* | ?:[\\/]* | NONE | '' ) ;; - *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 - { (exit 1); exit 1; }; };; +if test -n "$ac_unrecognized_opts"; then + case $enable_option_checking in + no) ;; + fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; + *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac -done +fi -# Be sure to have absolute paths. -for ac_var in bindir sbindir libexecdir datadir sysconfdir sharedstatedir \ - localstatedir libdir includedir oldincludedir infodir mandir +# Check all directory arguments for consistency. +for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ + datadir sysconfdir sharedstatedir localstatedir includedir \ + oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ + libdir localedir mandir do - eval ac_val=$`echo $ac_var` + eval ac_val=\$$ac_var + # Remove trailing slashes. case $ac_val in - [\\/$]* | ?:[\\/]* ) ;; - *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 - { (exit 1); exit 1; }; };; + */ ) + ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'` + eval $ac_var=\$ac_val;; esac + # Be sure to have absolute directory names. + case $ac_val in + [\\/$]* | ?:[\\/]* ) continue;; + NONE | '' ) case $ac_var in *prefix ) continue;; esac;; + esac + as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" done # There might be people who depend on the old broken behavior: `$host' @@ -688,8 +1266,8 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. - If a cross compiler is detected then cross compile mode will be used." >&2 + $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host. + If a cross compiler is detected then cross compile mode will be used" >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi @@ -701,90 +1279,72 @@ test -n "$host_alias" && ac_tool_prefix=$host_alias- test "$silent" = yes && exec 6>/dev/null +ac_pwd=`pwd` && test -n "$ac_pwd" && +ac_ls_di=`ls -di .` && +ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || + as_fn_error $? "working directory cannot be determined" +test "X$ac_ls_di" = "X$ac_pwd_ls_di" || + as_fn_error $? "pwd does not report name of working directory" + + # Find the source files, if location was not specified. if test -z "$srcdir"; then ac_srcdir_defaulted=yes - # Try the directory containing this script, then its parent. - ac_confdir=`(dirname "$0") 2>/dev/null || -$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$0" : 'X\(//\)[^/]' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| \ - . : '\(.\)' 2>/dev/null || -echo X"$0" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; } - /^X\(\/\/\)[^/].*/{ s//\1/; q; } - /^X\(\/\/\)$/{ s//\1/; q; } - /^X\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + # Try the directory containing this script, then the parent directory. + ac_confdir=`$as_dirname -- "$as_myself" || +$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_myself" : 'X\(//\)[^/]' \| \ + X"$as_myself" : 'X\(//\)$' \| \ + X"$as_myself" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_myself" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` srcdir=$ac_confdir - if test ! -r $srcdir/$ac_unique_file; then + if test ! -r "$srcdir/$ac_unique_file"; then srcdir=.. fi else ac_srcdir_defaulted=no fi -if test ! -r $srcdir/$ac_unique_file; then - if test "$ac_srcdir_defaulted" = yes; then - { echo "$as_me: error: cannot find sources ($ac_unique_file) in $ac_confdir or .." >&2 - { (exit 1); exit 1; }; } - else - { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 - { (exit 1); exit 1; }; } - fi +if test ! -r "$srcdir/$ac_unique_file"; then + test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." + as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" fi -(cd $srcdir && test -r ./$ac_unique_file) 2>/dev/null || - { echo "$as_me: error: sources are in $srcdir, but \`cd $srcdir' does not work" >&2 - { (exit 1); exit 1; }; } -srcdir=`echo "$srcdir" | sed 's%\([^\\/]\)[\\/]*$%\1%'` -ac_env_build_alias_set=${build_alias+set} -ac_env_build_alias_value=$build_alias -ac_cv_env_build_alias_set=${build_alias+set} -ac_cv_env_build_alias_value=$build_alias -ac_env_host_alias_set=${host_alias+set} -ac_env_host_alias_value=$host_alias -ac_cv_env_host_alias_set=${host_alias+set} -ac_cv_env_host_alias_value=$host_alias -ac_env_target_alias_set=${target_alias+set} -ac_env_target_alias_value=$target_alias -ac_cv_env_target_alias_set=${target_alias+set} -ac_cv_env_target_alias_value=$target_alias -ac_env_CXX_set=${CXX+set} -ac_env_CXX_value=$CXX -ac_cv_env_CXX_set=${CXX+set} -ac_cv_env_CXX_value=$CXX -ac_env_CXXFLAGS_set=${CXXFLAGS+set} -ac_env_CXXFLAGS_value=$CXXFLAGS -ac_cv_env_CXXFLAGS_set=${CXXFLAGS+set} -ac_cv_env_CXXFLAGS_value=$CXXFLAGS -ac_env_LDFLAGS_set=${LDFLAGS+set} -ac_env_LDFLAGS_value=$LDFLAGS -ac_cv_env_LDFLAGS_set=${LDFLAGS+set} -ac_cv_env_LDFLAGS_value=$LDFLAGS -ac_env_CPPFLAGS_set=${CPPFLAGS+set} -ac_env_CPPFLAGS_value=$CPPFLAGS -ac_cv_env_CPPFLAGS_set=${CPPFLAGS+set} -ac_cv_env_CPPFLAGS_value=$CPPFLAGS -ac_env_CC_set=${CC+set} -ac_env_CC_value=$CC -ac_cv_env_CC_set=${CC+set} -ac_cv_env_CC_value=$CC -ac_env_CFLAGS_set=${CFLAGS+set} -ac_env_CFLAGS_value=$CFLAGS -ac_cv_env_CFLAGS_set=${CFLAGS+set} -ac_cv_env_CFLAGS_value=$CFLAGS -ac_env_CXXCPP_set=${CXXCPP+set} -ac_env_CXXCPP_value=$CXXCPP -ac_cv_env_CXXCPP_set=${CXXCPP+set} -ac_cv_env_CXXCPP_value=$CXXCPP -ac_env_F77_set=${F77+set} -ac_env_F77_value=$F77 -ac_cv_env_F77_set=${F77+set} -ac_cv_env_F77_value=$F77 -ac_env_FFLAGS_set=${FFLAGS+set} -ac_env_FFLAGS_value=$FFLAGS -ac_cv_env_FFLAGS_set=${FFLAGS+set} -ac_cv_env_FFLAGS_value=$FFLAGS +ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" +ac_abs_confdir=`( + cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" + pwd)` +# When building in place, set srcdir=. +if test "$ac_abs_confdir" = "$ac_pwd"; then + srcdir=. +fi +# Remove unnecessary trailing slashes from srcdir. +# Double slashes in file names in object file debugging info +# mess up M-x gdb in Emacs. +case $srcdir in +*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;; +esac +for ac_var in $ac_precious_vars; do + eval ac_env_${ac_var}_set=\${${ac_var}+set} + eval ac_env_${ac_var}_value=\$${ac_var} + eval ac_cv_env_${ac_var}_set=\${${ac_var}+set} + eval ac_cv_env_${ac_var}_value=\$${ac_var} +done # # Report the --help message. @@ -807,20 +1367,17 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print \`checking...' messages + -q, --quiet, --silent do not print \`checking ...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files --srcdir=DIR find the sources in DIR [configure dir or \`..'] -_ACEOF - - cat <<_ACEOF Installation directories: --prefix=PREFIX install architecture-independent files in PREFIX - [$ac_default_prefix] + [$ac_default_prefix] --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX - [PREFIX] + [PREFIX] By default, \`make install' will install all the files in \`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify @@ -830,18 +1387,25 @@ for instance \`--prefix=\$HOME'. For better control, use the options below. 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We do this before executing the actions. + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_link + +# ac_fn_cxx_try_run LINENO +# ------------------------ +# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes +# that executables *can* be run. +ac_fn_cxx_try_run () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { ac_try='./conftest$ac_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then : + ac_retval=0 +else + $as_echo "$as_me: program exited with status $ac_status" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=$ac_status +fi + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_run + +# ac_fn_cxx_compute_int LINENO EXPR VAR INCLUDES +# ---------------------------------------------- +# Tries to find the compile-time value of EXPR in a program that includes +# INCLUDES, setting VAR accordingly. Returns whether the value could be +# computed +ac_fn_cxx_compute_int () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_lo=0 ac_mid=0 + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=$ac_mid; break +else + as_fn_arith $ac_mid + 1 && ac_lo=$as_val + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + as_fn_arith 2 '*' $ac_mid + 1 && ac_mid=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=-1 ac_mid=-1 + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_lo=$ac_mid; break +else + as_fn_arith '(' $ac_mid ')' - 1 && ac_hi=$as_val + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + as_fn_arith 2 '*' $ac_mid && ac_mid=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + ac_lo= ac_hi= +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + as_fn_arith '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo && ac_mid=$as_val + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +static int test_array [1 - 2 * !(($2) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_hi=$ac_mid +else + as_fn_arith '(' $ac_mid ')' + 1 && ac_lo=$as_val +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in #(( +?*) eval "$3=\$ac_lo"; ac_retval=0 ;; +'') ac_retval=1 ;; +esac + else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +static long int longval () { return $2; } +static unsigned long int ulongval () { return $2; } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (($2) < 0) + { + long int i = longval (); + if (i != ($2)) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ($2)) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_run "$LINENO"; then : + echo >>conftest.val; read $3 &5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } > conftest.i && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_cpp + +# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES +# --------------------------------------------------------- +# Tests whether HEADER exists and can be compiled using the include files in +# INCLUDES, setting the cache variable VAR accordingly. +ac_fn_cxx_check_header_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +#include <$2> +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + eval "$3=yes" +else + eval "$3=no" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_cxx_check_header_compile + +# ac_fn_f77_try_compile LINENO +# ---------------------------- +# Try to compile conftest.$ac_ext, and return whether this succeeded. +ac_fn_f77_try_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + rm -f conftest.$ac_objext + if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_f77_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_f77_try_compile +cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by Cantera $as_me 1.7.0, which was -generated by GNU Autoconf 2.59. Invocation command line was +generated by GNU Autoconf 2.68. Invocation command line was $ $0 $@ _ACEOF +exec 5>>config.log { cat <<_ASUNAME ## --------- ## @@ -1008,7 +1993,7 @@ uname -v = `(uname -v) 2>/dev/null || echo unknown` /bin/arch = `(/bin/arch) 2>/dev/null || echo unknown` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown` -hostinfo = `(hostinfo) 2>/dev/null || echo unknown` +/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown` /bin/machine = `(/bin/machine) 2>/dev/null || echo unknown` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown` /bin/universe = `(/bin/universe) 2>/dev/null || echo unknown` @@ -1020,8 +2005,9 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - echo "PATH: $as_dir" -done + $as_echo "PATH: $as_dir" + done +IFS=$as_save_IFS } >&5 @@ -1043,7 +2029,6 @@ _ACEOF ac_configure_args= ac_configure_args0= ac_configure_args1= -ac_sep= ac_must_keep_next=false for ac_pass in 1 2 do @@ -1054,13 +2039,13 @@ do -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil) continue ;; - *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*) - ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) + ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; + 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; 2) - ac_configure_args1="$ac_configure_args1 '$ac_arg'" + as_fn_append ac_configure_args1 " '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1076,104 +2061,115 @@ do -* ) ac_must_keep_next=true ;; esac fi - ac_configure_args="$ac_configure_args$ac_sep'$ac_arg'" - # Get rid of the leading space. - ac_sep=" " + as_fn_append ac_configure_args " '$ac_arg'" ;; esac done done -$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } -$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } +{ ac_configure_args0=; unset ac_configure_args0;} +{ ac_configure_args1=; unset ac_configure_args1;} # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there # would cause problems or look ugly. -# WARNING: Be sure not to use single quotes in there, as some shells, -# such as our DU 5.0 friend, will then `close' the trap. +# WARNING: Use '\'' to represent an apostrophe within the trap. +# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug. trap 'exit_status=$? # Save into config.log some information that might help in debugging. { echo - cat <<\_ASBOX -## ---------------- ## + $as_echo "## ---------------- ## ## Cache variables. ## -## ---------------- ## -_ASBOX +## ---------------- ##" echo # The following way of writing the cache mishandles newlines in values, -{ +( + for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do + eval ac_val=\$$ac_var + case $ac_val in #( + *${as_nl}*) + case $ac_var in #( + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 +$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + esac + case $ac_var in #( + _ | IFS | as_nl) ;; #( + BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( + *) { eval $ac_var=; unset $ac_var;} ;; + esac ;; + esac + done (set) 2>&1 | - case `(ac_space='"'"' '"'"'; set | grep ac_space) 2>&1` in - *ac_space=\ *) + case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #( + *${as_nl}ac_space=\ *) sed -n \ - "s/'"'"'/'"'"'\\\\'"'"''"'"'/g; - s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='"'"'\\2'"'"'/p" - ;; + "s/'\''/'\''\\\\'\'''\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p" + ;; #( *) - sed -n \ - "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p" + sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; - esac; -} + esac | + sort +) echo - cat <<\_ASBOX -## ----------------- ## + $as_echo "## ----------------- ## ## Output variables. ## -## ----------------- ## -_ASBOX +## ----------------- ##" echo for ac_var in $ac_subst_vars do - eval ac_val=$`echo $ac_var` - echo "$ac_var='"'"'$ac_val'"'"'" + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" done | sort echo if test -n "$ac_subst_files"; then - cat <<\_ASBOX -## ------------- ## -## Output files. ## -## ------------- ## -_ASBOX + $as_echo "## ------------------- ## +## File substitutions. ## +## ------------------- ##" echo for ac_var in $ac_subst_files do - eval ac_val=$`echo $ac_var` - echo "$ac_var='"'"'$ac_val'"'"'" + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" done | sort echo fi if test -s confdefs.h; then - cat <<\_ASBOX -## ----------- ## + $as_echo "## ----------- ## ## confdefs.h. ## -## ----------- ## -_ASBOX +## ----------- ##" echo - sed "/^$/d" confdefs.h | sort + cat confdefs.h echo fi test "$ac_signal" != 0 && - echo "$as_me: caught signal $ac_signal" - echo "$as_me: exit $exit_status" + $as_echo "$as_me: caught signal $ac_signal" + $as_echo "$as_me: exit $exit_status" } >&5 - rm -f core *.core && - rm -rf conftest* confdefs* conf$$* $ac_clean_files && + rm -f core *.core core.conftest.* && + rm -f -r conftest* confdefs* conf$$* $ac_clean_files && exit $exit_status - ' 0 +' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal + trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. -rm -rf conftest* confdefs.h -# AIX cpp loses on an empty file, so make sure it contains at least a newline. -echo >confdefs.h +rm -f -r conftest* confdefs.h + +$as_echo "/* confdefs.h */" > confdefs.h # Predefined preprocessor variables. @@ -1181,42 +2177,57 @@ cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF +cat >>confdefs.h <<_ACEOF +#define PACKAGE_URL "$PACKAGE_URL" +_ACEOF + # Let the site file select an alternate cache file if it wants to. -# Prefer explicitly selected file to automatically selected ones. -if test -z "$CONFIG_SITE"; then - if test "x$prefix" != xNONE; then - CONFIG_SITE="$prefix/share/config.site $prefix/etc/config.site" - else - CONFIG_SITE="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site" - fi +# Prefer an explicitly selected file to automatically selected ones. +ac_site_file1=NONE +ac_site_file2=NONE +if test -n "$CONFIG_SITE"; then + # We do not want a PATH search for config.site. + case $CONFIG_SITE in #(( + -*) ac_site_file1=./$CONFIG_SITE;; + */*) ac_site_file1=$CONFIG_SITE;; + *) ac_site_file1=./$CONFIG_SITE;; + esac +elif test "x$prefix" != xNONE; then + ac_site_file1=$prefix/share/config.site + ac_site_file2=$prefix/etc/config.site +else + ac_site_file1=$ac_default_prefix/share/config.site + ac_site_file2=$ac_default_prefix/etc/config.site fi -for ac_site_file in $CONFIG_SITE; do - if test -r "$ac_site_file"; then - { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 -echo "$as_me: loading site script $ac_site_file" >&6;} +for ac_site_file in "$ac_site_file1" "$ac_site_file2" +do + test "x$ac_site_file" = xNONE && continue + if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 +$as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 - . "$ac_site_file" + . "$ac_site_file" \ + || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "failed to load site script $ac_site_file +See \`config.log' for more details" "$LINENO" 5 ; } fi done @@ -1224,53 +2235,63 @@ done # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false -for ac_var in `(set) 2>&1 | - sed -n 's/^ac_env_\([a-zA-Z_0-9]*\)_set=.*/\1/p'`; do +for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set - eval ac_old_val="\$ac_cv_env_${ac_var}_value" - eval ac_new_val="\$ac_env_${ac_var}_value" + eval ac_old_val=\$ac_cv_env_${ac_var}_value + eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 -echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 -echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then - { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 -echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} - { echo "$as_me:$LINENO: former value: $ac_old_val" >&5 -echo "$as_me: former value: $ac_old_val" >&2;} - { echo "$as_me:$LINENO: current value: $ac_new_val" >&5 -echo "$as_me: current value: $ac_new_val" >&2;} - ac_cache_corrupted=: + # differences in whitespace do not lead to failure. + ac_old_val_w=`echo x $ac_old_val` + ac_new_val_w=`echo x $ac_new_val` + if test "$ac_old_val_w" != "$ac_new_val_w"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 +$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} + ac_cache_corrupted=: + else + { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 +$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} + eval $ac_var=\$ac_old_val + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 +$as_echo "$as_me: former value: \`$ac_old_val'" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 +$as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in - *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*) - ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 -echo "$as_me: error: changes in the environment can compromise the build" >&2;} - { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 -echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} - { (exit 1); exit 1; }; } + { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 +$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} + as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi +## -------------------- ## +## Main body of script. ## +## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -1280,59 +2301,38 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu - - - - - - - - - - - - - - - - - - - - - - - - - - ac_config_headers="$ac_config_headers config.h" +ac_config_headers="$ac_config_headers config.h" # AC_CONFIG_AUX_DIR(.) # AC_CONFIG_SRCDIR(./License.txt) ac_aux_dir= -for ac_dir in config $srcdir/config; do - if test -f $ac_dir/install-sh; then +for ac_dir in config "$srcdir"/config; do + if test -f "$ac_dir/install-sh"; then ac_aux_dir=$ac_dir ac_install_sh="$ac_aux_dir/install-sh -c" break - elif test -f $ac_dir/install.sh; then + elif test -f "$ac_dir/install.sh"; then ac_aux_dir=$ac_dir ac_install_sh="$ac_aux_dir/install.sh -c" break - elif test -f $ac_dir/shtool; then + elif test -f "$ac_dir/shtool"; then ac_aux_dir=$ac_dir ac_install_sh="$ac_aux_dir/shtool install -c" break fi done if test -z "$ac_aux_dir"; then - { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in config $srcdir/config" >&5 -echo "$as_me: error: cannot find install-sh or install.sh in config $srcdir/config" >&2;} - { (exit 1); exit 1; }; } + as_fn_error $? "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5 fi -ac_config_guess="$SHELL $ac_aux_dir/config.guess" -ac_config_sub="$SHELL $ac_aux_dir/config.sub" -ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure. + +# These three variables are undocumented and unsupported, +# and are intended to be withdrawn in a future Autoconf release. +# They can cause serious problems if a builder's source tree is in a directory +# whose full name contains unusual characters. +ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var. +ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var. +ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. + if test -z $CANTERA_VERSION ; then @@ -1357,9 +2357,7 @@ echo " " echo "--------------------------------------------------------------" echo " " -cat >>confdefs.h <<\_ACEOF -#define NDEBUG 1 -_ACEOF +$as_echo "#define NDEBUG 1" >>confdefs.h ac_sys_system=`uname -s` @@ -1451,20 +2449,24 @@ export FFLAGS # # Note these should not be within if blocks # -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -if test -n "$ac_tool_prefix"; then - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC +if test -z "$CXX"; then + if test -n "$CCC"; then + CXX=$CCC + else + if test -n "$ac_tool_prefix"; then + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CXX+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then ac_cv_prog_CXX="$CXX" # Let the user override the test. @@ -1474,39 +2476,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - echo "$as_me:$LINENO: result: $CXX" >&5 -echo "${ECHO_T}$CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 +$as_echo "$CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CXX" && break done fi if test -z "$CXX"; then ac_ct_CXX=$CXX - for ac_prog in $CCC g++ c++ gpp aCC CC cxx cc++ cl FCC KCC RCC xlC_r xlC + for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CXX+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test. @@ -1516,59 +2520,72 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 -echo "${ECHO_T}$ac_ct_CXX" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 +$as_echo "$ac_ct_CXX" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CXX" && break done -test -n "$ac_ct_CXX" || ac_ct_CXX="g++" - CXX=$ac_ct_CXX + if test "x$ac_ct_CXX" = x; then + CXX="g++" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CXX=$ac_ct_CXX + fi fi - + fi +fi # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C++ compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -1580,112 +2597,108 @@ main () } _ACEOF ac_clean_files_save=$ac_clean_files -ac_clean_files="$ac_clean_files a.out a.exe b.out" +ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. -echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5 -echo $ECHO_N "checking for C++ compiler default output file name... $ECHO_C" >&6 -ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` -if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 - (eval $ac_link_default) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - # Find the output, starting from the most likely. This scheme is -# not robust to junk in `.', hence go to wildcards (a.*) only as a last -# resort. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler works" >&5 +$as_echo_n "checking whether the C++ compiler works... " >&6; } +ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` -# Be careful to initialize this variable, since it used to be cached. -# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. -ac_cv_exeext= -# b.out is created by i960 compilers. -for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out +# The possible output files: +ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*" + +ac_rmfiles= +for ac_file in $ac_files +do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + * ) ac_rmfiles="$ac_rmfiles $ac_file";; + esac +done +rm -f $ac_rmfiles + +if { { ac_try="$ac_link_default" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link_default") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. +# So ignore a value of `no', otherwise this would lead to `EXEEXT = no' +# in a Makefile. We should not override ac_cv_exeext if it was cached, +# so that the user can short-circuit this test for compilers unknown to +# Autoconf. +for ac_file in $ac_files '' do test -f "$ac_file" || continue case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) - ;; - conftest.$ac_ext ) - # This is the source file. + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; [ab].out ) # We found the default executable, but exeext='' is most # certainly right. break;; *.* ) - ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - # FIXME: I believe we export ac_cv_exeext for Libtool, - # but it would be cool to find out if it's true. Does anybody - # maintain Libtool? --akim. - export ac_cv_exeext + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + then :; else + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + fi + # We set ac_cv_exeext here because the later test for it is not + # safe: cross compilers may not add the suffix if given an `-o' + # argument, so we may need to know it at that point already. + # Even if this section looks crufty: it has the advantage of + # actually working. break;; * ) break;; esac done +test "$ac_cv_exeext" = no && ac_cv_exeext= + else - echo "$as_me: failed program was:" >&5 + ac_file='' +fi +if test -z "$ac_file"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +$as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { echo "$as_me:$LINENO: error: C++ compiler cannot create executables -See \`config.log' for more details." >&5 -echo "$as_me: error: C++ compiler cannot create executables -See \`config.log' for more details." >&2;} - { (exit 77); exit 77; }; } +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "C++ compiler cannot create executables +See \`config.log' for more details" "$LINENO" 5 ; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } fi - +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5 +$as_echo_n "checking for C++ compiler default output file name... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +$as_echo "$ac_file" >&6; } ac_exeext=$ac_cv_exeext -echo "$as_me:$LINENO: result: $ac_file" >&5 -echo "${ECHO_T}$ac_file" >&6 -# Check the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5 -echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6 -# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 -# If not cross compiling, check that we can run a simple program. -if test "$cross_compiling" != yes; then - if { ac_try='./$ac_file' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - cross_compiling=no - else - if test "$cross_compiling" = maybe; then - cross_compiling=yes - else - { { echo "$as_me:$LINENO: error: cannot run C++ compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run C++ compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } - fi - fi -fi -echo "$as_me:$LINENO: result: yes" >&5 -echo "${ECHO_T}yes" >&6 - -rm -f a.out a.exe conftest$ac_cv_exeext b.out +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save -# Check the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 -echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6 -echo "$as_me:$LINENO: result: $cross_compiling" >&5 -echo "${ECHO_T}$cross_compiling" >&6 - -echo "$as_me:$LINENO: checking for suffix of executables" >&5 -echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6 -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : # If both `conftest.exe' and `conftest' are `present' (well, observable) # catch `conftest.exe'. For instance with Cygwin, `ls conftest' will # work properly (i.e., refer to `conftest.exe'), while it won't with @@ -1693,38 +2706,90 @@ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 for ac_file in conftest.exe conftest conftest.*; do test -f "$ac_file" || continue case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - export ac_cv_exeext break;; * ) break;; esac done else - { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details" "$LINENO" 5 ; } fi - -rm -f conftest$ac_cv_exeext -echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 -echo "${ECHO_T}$ac_cv_exeext" >&6 +rm -f conftest conftest$ac_cv_exeext +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } rm -f conftest.$ac_ext EXEEXT=$ac_cv_exeext ac_exeext=$EXEEXT -echo "$as_me:$LINENO: checking for suffix of object files" >&5 -echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6 -if test "${ac_cv_objext+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +FILE *f = fopen ("conftest.out", "w"); + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} _ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +ac_clean_files="$ac_clean_files conftest.out" +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +if test "$cross_compiling" != yes; then + { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } + if { ac_try='./conftest$ac_cv_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot run C++ compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details" "$LINENO" 5 ; } + fi + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +ac_clean_files=$ac_clean_files_save +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +$as_echo_n "checking for suffix of object files... " >&6; } +if ${ac_cv_objext+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -1736,45 +2801,46 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>&5 +if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>&5 ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then - for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + for ac_file in conftest.o conftest.obj conftest.*; do + test -f "$ac_file" || continue; case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;; + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;; *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` break;; esac done else - echo "$as_me: failed program was:" >&5 + $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot compute suffix of object files: cannot compile +See \`config.log' for more details" "$LINENO" 5 ; } fi - rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 -echo "${ECHO_T}$ac_cv_objext" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +$as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6 -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } +if ${ac_cv_cxx_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -1788,55 +2854,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6 -GXX=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +$as_echo "$ac_cv_cxx_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GXX=yes +else + GXX= +fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -CXXFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 -echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cxx_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +$as_echo_n "checking whether $CXX accepts -g... " >&6; } +if ${ac_cv_prog_cxx_g+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_cxx_werror_flag=$ac_cxx_werror_flag + ac_cxx_werror_flag=yes + ac_cv_prog_cxx_g=no + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -1847,39 +2892,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CXXFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cxx_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + +else + ac_cxx_werror_flag=$ac_save_cxx_werror_flag + CXXFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_cv_prog_cxx_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cxx_werror_flag=$ac_save_cxx_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +$as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS elif test $ac_cv_prog_cxx_g = yes; then @@ -1895,112 +2950,6 @@ else CXXFLAGS= fi fi -for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi - ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' @@ -2015,10 +2964,10 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -2028,35 +2977,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -2066,39 +3017,50 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="gcc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then - if test -n "$ac_tool_prefix"; then - # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -2108,77 +3070,37 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="${ac_tool_prefix}cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi -fi -if test -z "$ac_cv_prog_CC"; then - ac_ct_CC=$CC - # Extract the first word of "cc", so it can be a program name with args. -set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - if test -n "$ac_ct_CC"; then - ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. -else -as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_prog_ac_ct_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 + fi -done -done - -fi -fi -ac_ct_CC=$ac_cv_prog_ac_ct_CC -if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 -else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 -fi - - CC=$ac_ct_CC -else - CC="$ac_cv_prog_CC" -fi - fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -2189,18 +3111,19 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. @@ -2218,24 +3141,25 @@ fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. @@ -2245,39 +3169,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - echo "$as_me:$LINENO: result: $CC" >&5 -echo "${ECHO_T}$CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC - for ac_prog in cl + for ac_prog in cl.exe do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. @@ -2287,71 +3213,83 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 -echo "${ECHO_T}$ac_ct_CC" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_CC" && break done - CC=$ac_ct_CC + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi fi fi -test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&5 -echo "$as_me: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "no acceptable C compiler found in \$PATH +See \`config.log' for more details" "$LINENO" 5 ; } # Provide some information about the compiler. -echo "$as_me:$LINENO:" \ - "checking for C compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6 -if test "${ac_cv_c_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if ${ac_cv_c_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2365,55 +3303,34 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6 -GCC=`test $ac_compiler_gnu = yes && echo yes` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -CFLAGS="-g" -echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 -echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if ${ac_cv_prog_cc_g+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2424,39 +3341,49 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ -ac_cv_prog_cc_g=no +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_g" >&6 +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS elif test $ac_cv_prog_cc_g = yes; then @@ -2472,18 +3399,14 @@ else CFLAGS= fi fi -echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 -echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 -if test "${ac_cv_prog_cc_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if ${ac_cv_prog_cc_c89+:} false; then : + $as_echo_n "(cached) " >&6 else - ac_cv_prog_cc_stdc=no + ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -2511,12 +3434,17 @@ static char *f (char * (*g) (char **, int), char **p, ...) /* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has function prototypes and stuff, but not '\xHH' hex character constants. These don't provoke an error unfortunately, instead are silently treated - as 'x'. The following induces an error, until -std1 is added to get + as 'x'. The following induces an error, until -std is added to get proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an array size at least. It's necessary to write '\x00'==0 to get something - that's true only with -std1. */ + that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; @@ -2531,205 +3459,37 @@ return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; return 0; } _ACEOF -# Don't try gcc -ansi; that turns off useful extensions and -# breaks some systems' header files. -# AIX -qlanglvl=ansi -# Ultrix and OSF/1 -std1 -# HP-UX 10.20 and later -Ae -# HP-UX older versions -Aa -D_HPUX_SOURCE -# SVR4 -Xc -D__EXTENSIONS__ -for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_prog_cc_stdc=$ac_arg -break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg fi -rm -f conftest.err conftest.$ac_objext +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break done -rm -f conftest.$ac_ext conftest.$ac_objext +rm -f conftest.$ac_ext CC=$ac_save_CC fi - -case "x$ac_cv_prog_cc_stdc" in - x|xno) - echo "$as_me:$LINENO: result: none needed" >&5 -echo "${ECHO_T}none needed" >&6 ;; +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; *) - echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 -echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 - CC="$CC $ac_cv_prog_cc_stdc" ;; + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac - -# Some people use a C++ compiler to compile C. Since we use `exit', -# in C++ we need to declare it. In case someone uses the same compiler -# for both compiling C and C++ we need to have the C++ compiler decide -# the declaration of exit, since it's the most demanding environment. -cat >conftest.$ac_ext <<_ACEOF -#ifndef __cplusplus - choke me -#endif -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - for ac_declaration in \ - '' \ - 'extern "C" void std::exit (int) throw (); using std::exit;' \ - 'extern "C" void std::exit (int); using std::exit;' \ - 'extern "C" void exit (int) throw ();' \ - 'extern "C" void exit (int);' \ - 'void exit (int);' -do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -#include -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -continue -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_declaration -int -main () -{ -exit (42); - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_c_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if test "x$ac_cv_prog_cc_c89" != xno; then : fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -rm -f conftest* -if test -n "$ac_declaration"; then - echo '#ifdef __cplusplus' >>confdefs.h - echo $ac_declaration >>confdefs.h - echo '#endif' >>confdefs.h -fi -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' @@ -2886,79 +3646,107 @@ ct_mandir=${prefix} # Make sure we can run config.sub. -$ac_config_sub sun4 >/dev/null 2>&1 || - { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5 -echo "$as_me: error: cannot run $ac_config_sub" >&2;} - { (exit 1); exit 1; }; } +$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || + as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 -echo "$as_me:$LINENO: checking build system type" >&5 -echo $ECHO_N "checking build system type... $ECHO_C" >&6 -if test "${ac_cv_build+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +$as_echo_n "checking build system type... " >&6; } +if ${ac_cv_build+:} false; then : + $as_echo_n "(cached) " >&6 else - ac_cv_build_alias=$build_alias -test -z "$ac_cv_build_alias" && - ac_cv_build_alias=`$ac_config_guess` -test -z "$ac_cv_build_alias" && - { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 -echo "$as_me: error: cannot guess build type; you must specify one" >&2;} - { (exit 1); exit 1; }; } -ac_cv_build=`$ac_config_sub $ac_cv_build_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;} - { (exit 1); exit 1; }; } + ac_build_alias=$build_alias +test "x$ac_build_alias" = x && + ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` +test "x$ac_build_alias" = x && + as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 +ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 fi -echo "$as_me:$LINENO: result: $ac_cv_build" >&5 -echo "${ECHO_T}$ac_cv_build" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +$as_echo "$ac_cv_build" >&6; } +case $ac_cv_build in +*-*-*) ;; +*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;; +esac build=$ac_cv_build -build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_build +shift +build_cpu=$1 +build_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +build_os=$* +IFS=$ac_save_IFS +case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac -echo "$as_me:$LINENO: checking host system type" >&5 -echo $ECHO_N "checking host system type... $ECHO_C" >&6 -if test "${ac_cv_host+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +$as_echo_n "checking host system type... " >&6; } +if ${ac_cv_host+:} false; then : + $as_echo_n "(cached) " >&6 else - ac_cv_host_alias=$host_alias -test -z "$ac_cv_host_alias" && - ac_cv_host_alias=$ac_cv_build_alias -ac_cv_host=`$ac_config_sub $ac_cv_host_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;} - { (exit 1); exit 1; }; } + if test "x$host_alias" = x; then + ac_cv_host=$ac_cv_build +else + ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 +fi fi -echo "$as_me:$LINENO: result: $ac_cv_host" >&5 -echo "${ECHO_T}$ac_cv_host" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +$as_echo "$ac_cv_host" >&6; } +case $ac_cv_host in +*-*-*) ;; +*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;; +esac host=$ac_cv_host -host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_host +shift +host_cpu=$1 +host_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +host_os=$* +IFS=$ac_save_IFS +case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -echo "$as_me:$LINENO: checking target system type" >&5 -echo $ECHO_N "checking target system type... $ECHO_C" >&6 -if test "${ac_cv_target+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 +$as_echo_n "checking target system type... " >&6; } +if ${ac_cv_target+:} false; then : + $as_echo_n "(cached) " >&6 else - ac_cv_target_alias=$target_alias -test "x$ac_cv_target_alias" = "x" && - ac_cv_target_alias=$ac_cv_host_alias -ac_cv_target=`$ac_config_sub $ac_cv_target_alias` || - { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_target_alias failed" >&5 -echo "$as_me: error: $ac_config_sub $ac_cv_target_alias failed" >&2;} - { (exit 1); exit 1; }; } + if test "x$target_alias" = x; then + ac_cv_target=$ac_cv_host +else + ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 +fi fi -echo "$as_me:$LINENO: result: $ac_cv_target" >&5 -echo "${ECHO_T}$ac_cv_target" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 +$as_echo "$ac_cv_target" >&6; } +case $ac_cv_target in +*-*-*) ;; +*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;; +esac target=$ac_cv_target -target_cpu=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'` -target_vendor=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'` -target_os=`echo $ac_cv_target | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'` +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_target +shift +target_cpu=$1 +target_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +target_os=$* +IFS=$ac_save_IFS +case $target_os in *\ *) target_os=`echo "$target_os" | sed 's/ /-/g'`;; esac # The aliases save the names the user supplied, while $host etc. @@ -2967,6 +3755,7 @@ test -n "$target_alias" && test "$program_prefix$program_suffix$program_transform_name" = \ NONENONEs,x,x, && program_prefix=${target_alias}- + # the root of the source tree ctroot=`(pwd)` builddir=$target @@ -3078,7 +3867,7 @@ fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -3105,71 +3894,43 @@ if test "$USE_SUNDIALS" = "default"; then #ldsave="$LDFLAGS" #LDFLAGS='-L'"$SUNDIALS_LIB_DIR"' '"$ldsave" -echo "$as_me:$LINENO: checking for CVodeCreate in -lsundials_cvodes" >&5 -echo $ECHO_N "checking for CVodeCreate in -lsundials_cvodes... $ECHO_C" >&6 -if test "${ac_cv_lib_sundials_cvodes_CVodeCreate+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CVodeCreate in -lsundials_cvodes" >&5 +$as_echo_n "checking for CVodeCreate in -lsundials_cvodes... " >&6; } +if ${ac_cv_lib_sundials_cvodes_CVodeCreate+:} false; then : + $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsundials_cvodes -lsundials_cvodes -lsundials_nvecserial -lm $LIBS" -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ -/* Override any gcc2 internal prototype to avoid an error. */ +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif -/* We use char because int might match the return type of a gcc2 - builtin and then its argument prototype would still apply. */ char CVodeCreate (); int main () { -CVodeCreate (); +return CVodeCreate (); ; return 0; } _ACEOF -rm -f conftest.$ac_objext conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_sundials_cvodes_CVodeCreate=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_lib_sundials_cvodes_CVodeCreate=no + ac_cv_lib_sundials_cvodes_CVodeCreate=no fi -rm -f conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -echo "$as_me:$LINENO: result: $ac_cv_lib_sundials_cvodes_CVodeCreate" >&5 -echo "${ECHO_T}$ac_cv_lib_sundials_cvodes_CVodeCreate" >&6 -if test $ac_cv_lib_sundials_cvodes_CVodeCreate = yes; then +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sundials_cvodes_CVodeCreate" >&5 +$as_echo "$ac_cv_lib_sundials_cvodes_CVodeCreate" >&6; } +if test "x$ac_cv_lib_sundials_cvodes_CVodeCreate" = xyes; then : use_sundials=1 else use_sundials=0 @@ -3207,13 +3968,9 @@ CVODE_LIBS='-lsundials_cvodes -lsundials_nvecserial' IDA_LIBS='-lsundials_ida -lsundials_nvecserial' if test "$SUNDIALS_VERSION" = "2.2"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_22 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_22 1" >>confdefs.h sundials_include='-I'${SUNDIALS_HOME}'/include -I'${SUNDIALS_HOME}'/include/sundials -I'${SUNDIALS_HOME}'/include/cvodes -I'${SUNDIALS_HOME}'/include/ida' echo "sundials include directory: " ${sundials_include} @@ -3222,13 +3979,9 @@ _ACEOF sundials_lib="-L$SUNDIALS_LIB_DIR -lsundials_cvodes -lsundials_ida -lsundials_nvecserial" sundials_lib_dep="$SUNDIALS_LIB_DIR/libsundials_cvodes.a $SUNDIALS_LIB_DIR/libsundials_ida.a $SUNDIALS_LIB_DIR/libsundials_nvecserial.a" elif test "$SUNDIALS_VERSION" = "2.3"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_23 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_23 1" >>confdefs.h sundials_include='-I'${SUNDIALS_INC_DIR} echo "sundials include directory: " ${sundials_include} @@ -3238,13 +3991,9 @@ _ACEOF sundials_lib_dep="$SUNDIALS_LIB_DIR/libsundials_cvodes.a $SUNDIALS_LIB_DIR/libsundials_ida.a $SUNDIALS_LIB_DIR/libsundials_nvecserial.a" # python tools/src/sundials_version.py $SUNDIALS_HOME elif test "$SUNDIALS_VERSION" = "2.4"; then - cat >>confdefs.h <<\_ACEOF -#define HAS_SUNDIALS 1 -_ACEOF + $as_echo "#define HAS_SUNDIALS 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define SUNDIALS_VERSION_24 1 -_ACEOF + $as_echo "#define SUNDIALS_VERSION_24 1" >>confdefs.h sundials_include='-I'${SUNDIALS_INC_DIR} echo "sundials include directory: " ${sundials_include} @@ -3286,9 +4035,7 @@ fi DEBUG_MODE=${DEBUG_MODE:="n"} CANTERA_DEBUG_MODE=0 if test "$DEBUG_MODE" = "y" -o "$DEBUG_MODE" = "Y" ; then - cat >>confdefs.h <<\_ACEOF -#define DEBUG_MODE 1 -_ACEOF + $as_echo "#define DEBUG_MODE 1" >>confdefs.h CANTERA_DEBUG_MODE="1" else @@ -3315,32 +4062,24 @@ NEED_ZEROD= #fi if test "$WITH_METAL" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_METAL 1 -_ACEOF + $as_echo "#define WITH_METAL 1" >>confdefs.h hdrs=$hdrs' MetalPhase.h' fi if test "$WITH_SEMICONDUCTOR" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_SEMICONDUCTOR 1 -_ACEOF + $as_echo "#define WITH_SEMICONDUCTOR 1" >>confdefs.h hdrs=$hdrs' SemiconductorPhase.h' objs=$objs' SemiconductorPhase.o' fi if test "$WITH_ADSORBATE" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_ADSORBATE 1 -_ACEOF + $as_echo "#define WITH_ADSORBATE 1" >>confdefs.h hdrs=$hdrs' AdsorbateThermo.h' fi if test "$WITH_STOICH_SUBSTANCE" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_STOICH_SUBSTANCE 1 -_ACEOF + $as_echo "#define WITH_STOICH_SUBSTANCE 1" >>confdefs.h hdrs=$hdrs' StoichSubstance.h' objs=$objs' StoichSubstance.o' @@ -3348,9 +4087,7 @@ fi COMPILE_PURE_FLUIDS= if test "$WITH_PURE_FLUIDS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_PURE_FLUIDS 1 -_ACEOF + $as_echo "#define WITH_PURE_FLUIDS 1" >>confdefs.h COMPILE_PURE_FLUIDS=1 hdrs=$hdrs' PureFluidPhase.h' @@ -3359,9 +4096,7 @@ fi if test "$WITH_REAL_GASSES" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_REAL_GASSES 1 -_ACEOF + $as_echo "#define WITH_REAL_GASSES 1" >>confdefs.h hdrs=$hdrs' RedlichKwongMFTP.h' objs=$objs' RedlichKwongMFTP.o' @@ -3369,9 +4104,7 @@ fi if test "$WITH_LATTICE_SOLID" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_LATTICE_SOLID 1 -_ACEOF + $as_echo "#define WITH_LATTICE_SOLID 1" >>confdefs.h hdrs=$hdrs' LatticeSolidPhase.h' objs=$objs' LatticeSolidPhase.o' @@ -3387,9 +4120,7 @@ phase_header_files=$hdrs NEED_CATHERMO= COMPILE_IDEAL_SOLUTIONS=0 if test "$WITH_IDEAL_SOLUTIONS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_IDEAL_SOLUTIONS 1 -_ACEOF + $as_echo "#define WITH_IDEAL_SOLUTIONS 1" >>confdefs.h NEED_CATHERMO=1 COMPILE_IDEAL_SOLUTIONS=1 @@ -3398,9 +4129,7 @@ fi COMPILE_ELECTROLYTES=0 if test "$WITH_ELECTROLYTES" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_ELECTROLYTES 1 -_ACEOF + $as_echo "#define WITH_ELECTROLYTES 1" >>confdefs.h NEED_CATHERMO=1 COMPILE_ELECTROLYTES=1 @@ -3410,17 +4139,13 @@ fi if test "$WITH_PRIME" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_PRIME 1 -_ACEOF + $as_echo "#define WITH_PRIME 1" >>confdefs.h fi COMPILE_KINETICS=0 if test "$WITH_KINETICS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_KINETICS 1 -_ACEOF + $as_echo "#define WITH_KINETICS 1" >>confdefs.h COMPILE_KINETICS=1 fi @@ -3429,9 +4154,7 @@ fi COMPILE_HETEROKIN=0 if test "$WITH_HETERO_KINETICS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_HETEROKINETICS 1 -_ACEOF + $as_echo "#define WITH_HETEROKINETICS 1" >>confdefs.h COMPILE_HETEROKIN=1 fi @@ -3439,9 +4162,7 @@ fi COMPILE_RXNPATH=0 if test "$WITH_REACTION_PATHS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_REACTIONPATHS 1 -_ACEOF + $as_echo "#define WITH_REACTIONPATHS 1" >>confdefs.h COMPILE_RXNPATH=1 fi @@ -3490,17 +4211,13 @@ fi if test "$ENABLE_TPX" = "y" ; then KERNEL=$KERNEL' 'tpx NEED_TPX=1 - cat >>confdefs.h <<\_ACEOF -#define INCL_PURE_FLUIDS 1 -_ACEOF + $as_echo "#define INCL_PURE_FLUIDS 1" >>confdefs.h fi NEED_SPECTRA=0 if test "$WITH_SPECTRA" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_SPECTRA 1 -_ACEOF + $as_echo "#define WITH_SPECTRA 1" >>confdefs.h KERNEL=$KERNEL' 'spectra NEED_SPECTRA=1 @@ -3513,9 +4230,7 @@ fi COMPILE_VCSNONIDEAL=0 if test "$WITH_VCSNONIDEAL" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_VCSNONIDEAL 1 -_ACEOF + $as_echo "#define WITH_VCSNONIDEAL 1" >>confdefs.h COMPILE_VCSNONIDEAL=1 fi @@ -3523,9 +4238,7 @@ fi COMPILE_H298MODIFY_CAPABILITY=0 if test "$WITH_H298MODIFY_CAPABILITY" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define H298MODIFY_CAPABILITY 1 -_ACEOF + $as_echo "#define H298MODIFY_CAPABILITY 1" >>confdefs.h COMPILE_H298MODIFY_CAPABILITY=1 fi @@ -3534,9 +4247,7 @@ fi COMPILE_INTERMEDIATE_ZEROED_KINETICS=0 if test "$KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS 1 -_ACEOF + $as_echo "#define KINETICS_WITH_INTERMEDIATE_ZEROED_KINETICS 1" >>confdefs.h COMPILE_INTERMEDIATE_ZEROED_KINETICS=1 fi @@ -3544,18 +4255,14 @@ fi if test "$WITH_HTML_LOG_FILES" = "y"; then - cat >>confdefs.h <<\_ACEOF -#define WITH_HTML_LOGS 1 -_ACEOF + $as_echo "#define WITH_HTML_LOGS 1" >>confdefs.h fi BOOST_INCLUDE= BOOST_LIB= if test "$BUILD_THREAD_SAFE" = "y" ; then - cat >>confdefs.h <<\_ACEOF -#define THREAD_SAFE_CANTERA 1 -_ACEOF + $as_echo "#define THREAD_SAFE_CANTERA 1" >>confdefs.h BOOST_INCLUDE=-I$BOOST_INC_DIR BOOST_LIB=$BOOST_THREAD_LIB @@ -3695,9 +4402,7 @@ echo " " if test "x$PURIFY" != "x"; then - cat >>confdefs.h <<\_ACEOF -#define PURIFY_MODE 1 -_ACEOF + $as_echo "#define PURIFY_MODE 1" >>confdefs.h fi @@ -3764,7 +4469,6 @@ fi case $ac_sys_system in Linux) NEED_F2C=1 ;; esac -NEED_F2C= # # Create a variable build_f2c_lib that determines whether @@ -3964,9 +4668,7 @@ fi # case $ac_sys_system in SunOS* ) - cat >>confdefs.h <<\_ACEOF -#define NEEDS_GENERIC_TEMPL_STATIC_DECL 1 -_ACEOF + $as_echo "#define NEEDS_GENERIC_TEMPL_STATIC_DECL 1" >>confdefs.h echo 'Turned on special handing of static definitions in templated classes' ;; @@ -4004,9 +4706,7 @@ else exit 1 fi if test $BUILD_PYTHON = 0 ; then -cat >>confdefs.h <<\_ACEOF -#define HAS_NO_PYTHON 1 -_ACEOF +$as_echo "#define HAS_NO_PYTHON 1" >>confdefs.h fi @@ -4016,10 +4716,10 @@ if test "$PYTHON_CMD" = "default" -o \ do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_PYTHON_CMD+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_PYTHON_CMD+:} false; then : + $as_echo_n "(cached) " >&6 else case $PYTHON_CMD in [\\/]* | ?:[\\/]*) @@ -4031,28 +4731,29 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_PYTHON_CMD="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS ;; esac fi PYTHON_CMD=$ac_cv_path_PYTHON_CMD - if test -n "$PYTHON_CMD"; then - echo "$as_me:$LINENO: result: $PYTHON_CMD" >&5 -echo "${ECHO_T}$PYTHON_CMD" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PYTHON_CMD" >&5 +$as_echo "$PYTHON_CMD" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$PYTHON_CMD" && break done test -n "$PYTHON_CMD" || PYTHON_CMD=""none"" @@ -4080,24 +4781,18 @@ USE_NUMARRAY='y' if test "$USE_NUMERIC" = "y"; then USE_NUMARRAY='n' USE_NUMPY='n' -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMERIC 1 -_ACEOF +$as_echo "#define HAS_NUMERIC 1" >>confdefs.h fi if test "$USE_NUMPY" = "y"; then USE_NUMARRAY='n' -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMPY 1 -_ACEOF +$as_echo "#define HAS_NUMPY 1" >>confdefs.h fi if test "$USE_NUMARRAY" = "y"; then -cat >>confdefs.h <<\_ACEOF -#define HAS_NUMARRAY 1 -_ACEOF +$as_echo "#define HAS_NUMARRAY 1" >>confdefs.h fi @@ -4229,10 +4924,10 @@ if test "$BUILD_MATLAB_TOOLBOX" != "n"; then "$MATLAB_CMD"x = "x"; then # Extract the first word of "matlab", so it can be a program name with args. set dummy matlab; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_MATLAB_CMD+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_MATLAB_CMD+:} false; then : + $as_echo_n "(cached) " >&6 else case $MATLAB_CMD in [\\/]* | ?:[\\/]*) @@ -4244,29 +4939,30 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_MATLAB_CMD="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS test -z "$ac_cv_path_MATLAB_CMD" && ac_cv_path_MATLAB_CMD=""none"" ;; esac fi MATLAB_CMD=$ac_cv_path_MATLAB_CMD - if test -n "$MATLAB_CMD"; then - echo "$as_me:$LINENO: result: $MATLAB_CMD" >&5 -echo "${ECHO_T}$MATLAB_CMD" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MATLAB_CMD" >&5 +$as_echo "$MATLAB_CMD" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + if test "$MATLAB_CMD" = "none"; then MATLAB_CMD=`find /*/MATLAB*/bin/m* -name matlab` fi @@ -4285,8 +4981,8 @@ fi echo "Windows MATLAB command: ${MATLAB_CMD}" fi - echo "$as_me:$LINENO: checking MATLAB ($MATLAB_CMD)" >&5 -echo $ECHO_N "checking MATLAB ($MATLAB_CMD)... $ECHO_C" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking MATLAB ($MATLAB_CMD)" >&5 +$as_echo_n "checking MATLAB ($MATLAB_CMD)... " >&6; } rm -f diary cat >> testmat.m << EOF diary; @@ -4389,22 +5085,23 @@ echo 'checking for Position independent code command ... ' $PIC # SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" # OS/2's system install, which has a completely different semantic # ./install, which can be erroneously created by make from ./install.sh. -echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 -echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6 +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if test "${ac_cv_path_install+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +if ${ac_cv_path_install+:} false; then : + $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - # Account for people who put trailing slashes in PATH elements. -case $as_dir/ in - ./ | .// | /cC/* | \ + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in #(( + ./ | .// | /[cC]/* | \ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ - ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -4412,7 +5109,7 @@ case $as_dir/ in # by default. for ac_prog in ginstall scoinst install; do for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then if test $ac_prog = install && grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then # AIX install. It has an incompatible calling convention. @@ -4422,30 +5119,43 @@ case $as_dir/ in # program-specific install script used by HP pwplus--don't use. : else - ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" - break 3 + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi fi fi done done ;; esac -done + done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir fi if test "${ac_cv_path_install+set}" = set; then INSTALL=$ac_cv_path_install else - # As a last resort, use the slow shell script. We don't cache a - # path for INSTALL within a source directory, because that will + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will # break other packages using the cache if that directory is - # removed, or if the path is relative. + # removed, or if the value is a relative name. INSTALL=$ac_install_sh fi fi -echo "$as_me:$LINENO: result: $INSTALL" >&5 -echo "${ECHO_T}$INSTALL" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. # It thinks the first close brace ends the variable substitution. @@ -4483,34 +5193,32 @@ esac # precompile_headers=no if test "x$OS_IS_WIN" != "x1"; then -echo "$as_me:$LINENO: checking for ability to precompile headers" >&5 -echo $ECHO_N "checking for ability to precompile headers... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ability to precompile headers" >&5 +$as_echo_n "checking for ability to precompile headers... " >&6; } if test -n "$GCC"; then msg=`rm -f *h.gch; $CXX testpch.h &> /dev/null` if test -f testpch.h.gch; then precompile_headers=yes - cat >>confdefs.h <<\_ACEOF -#define USE_PCH 1 -_ACEOF + $as_echo "#define USE_PCH 1" >>confdefs.h fi fi -echo "$as_me:$LINENO: result: ${precompile_headers}" >&5 -echo "${ECHO_T}${precompile_headers}" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${precompile_headers}" >&5 +$as_echo "${precompile_headers}" >&6; } # End of the OS_IS_WIN section fi # Sizes of various common basic types -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5 -echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5 +$as_echo_n "checking how to run the C++ preprocessor... " >&6; } if test -z "$CXXCPP"; then - if test "${ac_cv_prog_CXXCPP+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 + if ${ac_cv_prog_CXXCPP+:} false; then : + $as_echo_n "(cached) " >&6 else # Double quotes because CXXCPP needs to be expanded for CXXCPP in "$CXX -E" "/lib/cpp" @@ -4524,11 +5232,7 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4537,78 +5241,34 @@ cat >>conftest.$ac_ext <<_ACEOF #endif Syntax error _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext - # OK, works on sane cases. Now check whether non-existent headers + # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then +if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.err conftest.$ac_ext -if $ac_preproc_ok; then +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : break fi @@ -4620,8 +5280,8 @@ fi else ac_cv_prog_CXXCPP=$CXXCPP fi -echo "$as_me:$LINENO: result: $CXXCPP" >&5 -echo "${ECHO_T}$CXXCPP" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5 +$as_echo "$CXXCPP" >&6; } ac_preproc_ok=false for ac_cxx_preproc_warn_flag in '' yes do @@ -4631,11 +5291,7 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4644,119 +5300,185 @@ cat >>conftest.$ac_ext <<_ACEOF #endif Syntax error _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then - : -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext - # OK, works on sane cases. Now check whether non-existent headers + # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 - (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } >/dev/null; then - if test -s conftest.err; then - ac_cpp_err=$ac_cxx_preproc_warn_flag - ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag - else - ac_cpp_err= - fi -else - ac_cpp_err=yes -fi -if test -z "$ac_cpp_err"; then +if ac_fn_cxx_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.err conftest.$ac_ext -if $ac_preproc_ok; then - : +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : + else - { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check -See \`config.log' for more details." >&5 -echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details" "$LINENO" 5 ; } fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -echo "$as_me:$LINENO: checking for egrep" >&5 -echo $ECHO_N "checking for egrep... $ECHO_C" >&6 -if test "${ac_cv_prog_egrep+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +$as_echo_n "checking for grep that handles long lines and -e... " >&6; } +if ${ac_cv_path_GREP+:} false; then : + $as_echo_n "(cached) " >&6 else - if echo a | (grep -E '(a|b)') >/dev/null 2>&1 - then ac_cv_prog_egrep='grep -E' - else ac_cv_prog_egrep='egrep' + if test -z "$GREP"; then + ac_path_GREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in grep ggrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue +# Check for GNU ac_path_GREP and select it if it is found. + # Check for GNU $ac_path_GREP +case `"$ac_path_GREP" --version 2>&1` in +*GNU*) + ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'GREP' >> "conftest.nl" + "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_GREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_GREP="$ac_path_GREP" + ac_path_GREP_max=$ac_count fi -fi -echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5 -echo "${ECHO_T}$ac_cv_prog_egrep" >&6 - EGREP=$ac_cv_prog_egrep + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac - -echo "$as_me:$LINENO: checking for ANSI C header files" >&5 -echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 -if test "${ac_cv_header_stdc+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 + $ac_path_GREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_GREP"; then + as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + ac_cv_path_GREP=$GREP +fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +$as_echo "$ac_cv_path_GREP" >&6; } + GREP="$ac_cv_path_GREP" + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +$as_echo_n "checking for egrep... " >&6; } +if ${ac_cv_path_EGREP+:} false; then : + $as_echo_n "(cached) " >&6 +else + if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 + then ac_cv_path_EGREP="$GREP -E" + else + if test -z "$EGREP"; then + ac_path_EGREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in egrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue +# Check for GNU ac_path_EGREP and select it if it is found. + # Check for GNU $ac_path_EGREP +case `"$ac_path_EGREP" --version 2>&1` in +*GNU*) + ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'EGREP' >> "conftest.nl" + "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_EGREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_EGREP="$ac_path_EGREP" + ac_path_EGREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_EGREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_EGREP"; then + as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi +else + ac_cv_path_EGREP=$EGREP +fi + + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +$as_echo "$ac_cv_path_EGREP" >&6; } + EGREP="$ac_cv_path_EGREP" + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +$as_echo_n "checking for ANSI C header files... " >&6; } +if ${ac_cv_header_stdc+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -4771,51 +5493,23 @@ main () return 0; } _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_header_stdc=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_header_stdc=no + ac_cv_header_stdc=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then - : + $EGREP "memchr" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -4825,18 +5519,14 @@ fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then - : + $EGREP "free" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -4846,16 +5536,13 @@ fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. - if test "$cross_compiling" = yes; then + if test "$cross_compiling" = yes; then : : else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include +#include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) @@ -4875,109 +5562,39 @@ main () for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) - exit(2); - exit (0); + return 2; + return 0; } _ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - : -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_run "$LINENO"; then : -( exit $ac_status ) -ac_cv_header_stdc=no +else + ac_cv_header_stdc=no fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext +fi + fi fi -fi -echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 -echo "${ECHO_T}$ac_cv_header_stdc" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +$as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -cat >>confdefs.h <<\_ACEOF -#define STDC_HEADERS 1 -_ACEOF +$as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. - - - - - - - - - for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h -do -as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` -echo "$as_me:$LINENO: checking for $ac_header" >&5 -echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 -if eval "test \"\${$as_ac_Header+set}\" = set"; then - echo $ECHO_N "(cached) $ECHO_C" >&6 -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default - -#include <$ac_header> -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - eval "$as_ac_Header=yes" -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -eval "$as_ac_Header=no" -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 -echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 -if test `eval echo '${'$as_ac_Header'}'` = yes; then +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default +" +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF -#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi @@ -4985,3313 +5602,265 @@ fi done -echo "$as_me:$LINENO: checking for int" >&5 -echo $ECHO_N "checking for int... $ECHO_C" >&6 -if test "${ac_cv_type_int+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of int" >&5 +$as_echo_n "checking size of int... " >&6; } +if ${ac_cv_sizeof_int+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((int *) 0) - return 0; -if (sizeof (int)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_int=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (int))" "ac_cv_sizeof_int" "$ac_includes_default"; then : -ac_cv_type_int=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_int" >&5 -echo "${ECHO_T}$ac_cv_type_int" >&6 - -echo "$as_me:$LINENO: checking size of int" >&5 -echo $ECHO_N "checking size of int... $ECHO_C" >&6 -if test "${ac_cv_sizeof_int+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_int" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (int) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_int=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_int" >&5 +$as_echo "$ac_cv_sizeof_int" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (int))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_int=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (int)); } -unsigned long ulongval () { return (long) (sizeof (int)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (int))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (int)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (int)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_int=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (int), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_int=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_int" >&5 -echo "${ECHO_T}$ac_cv_sizeof_int" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_INT $ac_cv_sizeof_int _ACEOF -echo "$as_me:$LINENO: checking for long" >&5 -echo $ECHO_N "checking for long... $ECHO_C" >&6 -if test "${ac_cv_type_long+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of long" >&5 +$as_echo_n "checking size of long... " >&6; } +if ${ac_cv_sizeof_long+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((long *) 0) - return 0; -if (sizeof (long)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? 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- grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (long) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_long=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_long" >&5 +$as_echo "$ac_cv_sizeof_long" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (long))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_long=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (long), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (long), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (long)); } -unsigned long ulongval () { return (long) (sizeof (long)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (long))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (long)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (long)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? 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" >&6; } +if ${ac_cv_sizeof_void_p+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((void * *) 0) - return 0; -if (sizeof (void *)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_void_p=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (void *))" "ac_cv_sizeof_void_p" "$ac_includes_default"; then : -ac_cv_type_void_p=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_void_p" >&5 -echo "${ECHO_T}$ac_cv_type_void_p" >&6 - -echo "$as_me:$LINENO: checking size of void *" >&5 -echo $ECHO_N "checking size of void *... $ECHO_C" >&6 -if test "${ac_cv_sizeof_void_p+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_void_p" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (void *) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_void_p=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_void_p" >&5 +$as_echo "$ac_cv_sizeof_void_p" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (void *))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_void_p=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (void *)); } -unsigned long ulongval () { return (long) (sizeof (void *)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (void *))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (void *)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (void *)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_void_p=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (void *), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_void_p=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_void_p" >&5 -echo "${ECHO_T}$ac_cv_sizeof_void_p" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_VOID_P $ac_cv_sizeof_void_p _ACEOF -echo "$as_me:$LINENO: checking for char" >&5 -echo $ECHO_N "checking for char... $ECHO_C" >&6 -if test "${ac_cv_type_char+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of char" >&5 +$as_echo_n "checking size of char... " >&6; } +if ${ac_cv_sizeof_char+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((char *) 0) - return 0; -if (sizeof (char)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_char=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (char))" "ac_cv_sizeof_char" "$ac_includes_default"; then : -ac_cv_type_char=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_char" >&5 -echo "${ECHO_T}$ac_cv_type_char" >&6 - -echo "$as_me:$LINENO: checking size of char" >&5 -echo $ECHO_N "checking size of char... $ECHO_C" >&6 -if test "${ac_cv_sizeof_char+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_char" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (char) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_char=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_char" >&5 +$as_echo "$ac_cv_sizeof_char" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (char))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? 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" >&6; } +if ${ac_cv_sizeof_short+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((short *) 0) - return 0; -if (sizeof (short)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_short=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (short))" "ac_cv_sizeof_short" "$ac_includes_default"; then : -ac_cv_type_short=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_short" >&5 -echo "${ECHO_T}$ac_cv_type_short" >&6 - -echo "$as_me:$LINENO: checking size of short" >&5 -echo $ECHO_N "checking size of short... $ECHO_C" >&6 -if test "${ac_cv_sizeof_short+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_short" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (short) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_short=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_short" >&5 +$as_echo "$ac_cv_sizeof_short" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (short))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_short=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (short)); } -unsigned long ulongval () { return (long) (sizeof (short)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (short))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (short)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (short)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_short=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (short), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_short=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_short" >&5 -echo "${ECHO_T}$ac_cv_sizeof_short" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_SHORT $ac_cv_sizeof_short _ACEOF -echo "$as_me:$LINENO: checking for float" >&5 -echo $ECHO_N "checking for float... $ECHO_C" >&6 -if test "${ac_cv_type_float+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of float" >&5 +$as_echo_n "checking size of float... " >&6; } +if ${ac_cv_sizeof_float+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((float *) 0) - return 0; -if (sizeof (float)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_float=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (float))" "ac_cv_sizeof_float" "$ac_includes_default"; then : -ac_cv_type_float=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_float" >&5 -echo "${ECHO_T}$ac_cv_type_float" >&6 - -echo "$as_me:$LINENO: checking size of float" >&5 -echo $ECHO_N "checking size of float... $ECHO_C" >&6 -if test "${ac_cv_sizeof_float+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_float" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (float) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_float=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_float" >&5 +$as_echo "$ac_cv_sizeof_float" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (float))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_float=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (float)); } -unsigned long ulongval () { return (long) (sizeof (float)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (float))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (float)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (float)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_float=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (float), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_float=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_float" >&5 -echo "${ECHO_T}$ac_cv_sizeof_float" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_FLOAT $ac_cv_sizeof_float _ACEOF -echo "$as_me:$LINENO: checking for double" >&5 -echo $ECHO_N "checking for double... $ECHO_C" >&6 -if test "${ac_cv_type_double+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of double" >&5 +$as_echo_n "checking size of double... " >&6; } +if ${ac_cv_sizeof_double+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((double *) 0) - return 0; -if (sizeof (double)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? 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- grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (double) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_double=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_double" >&5 +$as_echo "$ac_cv_sizeof_double" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (double))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_double=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (double)); } -unsigned long ulongval () { return (long) (sizeof (double)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (double))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (double)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (double)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_double=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (double), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_double=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_double" >&5 -echo "${ECHO_T}$ac_cv_sizeof_double" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_DOUBLE $ac_cv_sizeof_double _ACEOF -echo "$as_me:$LINENO: checking for fpos_t" >&5 -echo $ECHO_N "checking for fpos_t... $ECHO_C" >&6 -if test "${ac_cv_type_fpos_t+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking size of fpos_t" >&5 +$as_echo_n "checking size of fpos_t... " >&6; } +if ${ac_cv_sizeof_fpos_t+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if ((fpos_t *) 0) - return 0; -if (sizeof (fpos_t)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_type_fpos_t=yes -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 + if ac_fn_cxx_compute_int "$LINENO" "(long int) (sizeof (fpos_t))" "ac_cv_sizeof_fpos_t" "$ac_includes_default"; then : -ac_cv_type_fpos_t=no -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -echo "$as_me:$LINENO: result: $ac_cv_type_fpos_t" >&5 -echo "${ECHO_T}$ac_cv_type_fpos_t" >&6 - -echo "$as_me:$LINENO: checking size of fpos_t" >&5 -echo $ECHO_N "checking size of fpos_t... $ECHO_C" >&6 -if test "${ac_cv_sizeof_fpos_t+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$ac_cv_type_fpos_t" = yes; then - # The cast to unsigned long works around a bug in the HP C Compiler - # version HP92453-01 B.11.11.23709.GP, which incorrectly rejects - # declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. - # This bug is HP SR number 8606223364. - if test "$cross_compiling" = yes; then - # Depending upon the size, compute the lo and hi bounds. -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) >= 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=0 ac_mid=0 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) <= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_lo=`expr $ac_mid + 1` - if test $ac_lo -le $ac_mid; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid + 1` + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "cannot compute sizeof (fpos_t) +See \`config.log' for more details" "$LINENO" 5 ; } + else + ac_cv_sizeof_fpos_t=0 + fi fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) < 0)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=-1 ac_mid=-1 - while :; do - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) >= $ac_mid)]; -test_array [0] = 0 - - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_lo=$ac_mid; break -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_hi=`expr '(' $ac_mid ')' - 1` - if test $ac_mid -le $ac_hi; then - ac_lo= ac_hi= - break - fi - ac_mid=`expr 2 '*' $ac_mid` fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext - done -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sizeof_fpos_t" >&5 +$as_echo "$ac_cv_sizeof_fpos_t" >&6; } -ac_lo= ac_hi= -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -# Binary search between lo and hi bounds. -while test "x$ac_lo" != "x$ac_hi"; do - ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -static int test_array [1 - 2 * !(((long) (sizeof (fpos_t))) <= $ac_mid)]; -test_array [0] = 0 - ; - return 0; -} -_ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_hi=$ac_mid -else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -ac_lo=`expr '(' $ac_mid ')' + 1` -fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext -done -case $ac_lo in -?*) ac_cv_sizeof_fpos_t=$ac_lo;; -'') { { echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } ;; -esac -else - if test "$cross_compiling" = yes; then - { { echo "$as_me:$LINENO: error: cannot run test program while cross compiling -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot run test program while cross compiling -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -long longval () { return (long) (sizeof (fpos_t)); } -unsigned long ulongval () { return (long) (sizeof (fpos_t)); } -#include -#include -int -main () -{ - - FILE *f = fopen ("conftest.val", "w"); - if (! f) - exit (1); - if (((long) (sizeof (fpos_t))) < 0) - { - long i = longval (); - if (i != ((long) (sizeof (fpos_t)))) - exit (1); - fprintf (f, "%ld\n", i); - } - else - { - unsigned long i = ulongval (); - if (i != ((long) (sizeof (fpos_t)))) - exit (1); - fprintf (f, "%lu\n", i); - } - exit (ferror (f) || fclose (f) != 0); - - ; - return 0; -} -_ACEOF -rm -f conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && { ac_try='./conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then - ac_cv_sizeof_fpos_t=`cat conftest.val` -else - echo "$as_me: program exited with status $ac_status" >&5 -echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -( exit $ac_status ) -{ { echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&5 -echo "$as_me: error: cannot compute sizeof (fpos_t), 77 -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; } -fi -rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext -fi -fi -rm -f conftest.val -else - ac_cv_sizeof_fpos_t=0 -fi -fi -echo "$as_me:$LINENO: result: $ac_cv_sizeof_fpos_t" >&5 -echo "${ECHO_T}$ac_cv_sizeof_fpos_t" >&6 cat >>confdefs.h <<_ACEOF #define SIZEOF_FPOS_T $ac_cv_sizeof_fpos_t _ACEOF @@ -8327,71 +5896,43 @@ fi # # Check to see if we have a -lm line # -echo "$as_me:$LINENO: checking for printf in -lm" >&5 -echo $ECHO_N "checking for printf in -lm... $ECHO_C" >&6 -if test "${ac_cv_lib_m_printf+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for printf in -lm" >&5 +$as_echo_n "checking for printf in -lm... " >&6; } +if ${ac_cv_lib_m_printf+:} false; then : + $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ -/* Override any gcc2 internal prototype to avoid an error. */ +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif -/* We use char because int might match the return type of a gcc2 - builtin and then its argument prototype would still apply. */ char printf (); int main () { -printf (); +return printf (); ; return 0; } _ACEOF -rm -f conftest.$ac_objext conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_m_printf=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_lib_m_printf=no + ac_cv_lib_m_printf=no fi -rm -f conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -echo "$as_me:$LINENO: result: $ac_cv_lib_m_printf" >&5 -echo "${ECHO_T}$ac_cv_lib_m_printf" >&6 -if test $ac_cv_lib_m_printf = yes; then +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_printf" >&5 +$as_echo "$ac_cv_lib_m_printf" >&6; } +if test "x$ac_cv_lib_m_printf" = xyes; then : add_stm=1 else add_stm=0 @@ -8401,71 +5942,43 @@ fi # # Check to see if we have a -lstdc++ line # -echo "$as_me:$LINENO: checking for printf in -lstdc++" >&5 -echo $ECHO_N "checking for printf in -lstdc++... $ECHO_C" >&6 -if test "${ac_cv_lib_stdcpp_printf+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for printf in -lstdc++" >&5 +$as_echo_n "checking for printf in -lstdc++... " >&6; } +if ${ac_cv_lib_stdcpp_printf+:} false; then : + $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lstdc++ $LIBS" -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ -/* Override any gcc2 internal prototype to avoid an error. */ +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif -/* We use char because int might match the return type of a gcc2 - builtin and then its argument prototype would still apply. */ char printf (); int main () { -printf (); +return printf (); ; return 0; } _ACEOF -rm -f conftest.$ac_objext conftest$ac_exeext -if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 - (eval $ac_link) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_cxx_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest$ac_exeext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_stdcpp_printf=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_lib_stdcpp_printf=no + ac_cv_lib_stdcpp_printf=no fi -rm -f conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -echo "$as_me:$LINENO: result: $ac_cv_lib_stdcpp_printf" >&5 -echo "${ECHO_T}$ac_cv_lib_stdcpp_printf" >&6 -if test $ac_cv_lib_stdcpp_printf = yes; then +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_stdcpp_printf" >&5 +$as_echo "$ac_cv_lib_stdcpp_printf" >&6; } +if test "x$ac_cv_lib_stdcpp_printf" = xyes; then : add_stdc=1 else add_stdc=0 @@ -8502,8 +6015,8 @@ fi has_sstream=no -echo "$as_me:$LINENO: checking for sstream" >&5 -echo $ECHO_N "checking for sstream... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sstream" >&5 +$as_echo_n "checking for sstream... " >&6; } cat >> testsstream.cpp << EOF #include main() {} @@ -8512,14 +6025,12 @@ EOF if test -f testsstream.o; then has_sstream=yes rm testsstream.o - cat >>confdefs.h <<\_ACEOF -#define HAS_SSTREAM 1 -_ACEOF + $as_echo "#define HAS_SSTREAM 1" >>confdefs.h fi rm -f testsstream.cpp -echo "$as_me:$LINENO: result: ${has_sstream}" >&5 -echo "${ECHO_T}${has_sstream}" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${has_sstream}" >&5 +$as_echo "${has_sstream}" >&6; } # # Determine if we have a command to strip symbols from an object file @@ -8548,14 +6059,14 @@ ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_f77_compiler_gnu if test -n "$ac_tool_prefix"; then - for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran + for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_F77+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_F77+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$F77"; then ac_cv_prog_F77="$F77" # Let the user override the test. @@ -8565,39 +6076,41 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_F77="$ac_tool_prefix$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi F77=$ac_cv_prog_F77 if test -n "$F77"; then - echo "$as_me:$LINENO: result: $F77" >&5 -echo "${ECHO_T}$F77" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $F77" >&5 +$as_echo "$F77" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$F77" && break done fi if test -z "$F77"; then ac_ct_F77=$F77 - for ac_prog in g77 f77 xlf frt pgf77 fort77 fl32 af77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 ifc efc pgf95 lf95 gfortran + for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_prog_ac_ct_F77+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_F77+:} false; then : + $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_F77"; then ac_cv_prog_ac_ct_F77="$ac_ct_F77" # Let the user override the test. @@ -8607,64 +6120,81 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_F77="$ac_prog" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS fi fi ac_ct_F77=$ac_cv_prog_ac_ct_F77 if test -n "$ac_ct_F77"; then - echo "$as_me:$LINENO: result: $ac_ct_F77" >&5 -echo "${ECHO_T}$ac_ct_F77" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_F77" >&5 +$as_echo "$ac_ct_F77" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$ac_ct_F77" && break done - F77=$ac_ct_F77 + if test "x$ac_ct_F77" = x; then + F77="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + F77=$ac_ct_F77 + fi fi # Provide some information about the compiler. -echo "$as_me:8638:" \ - "checking for Fortran 77 compiler version" >&5 -ac_compiler=`set X $ac_compile; echo $2` -{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 - (eval $ac_compiler --version &5) 2>&5 +$as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 - (eval $ac_compiler -v &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } -{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 - (eval $ac_compiler -V &5) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done rm -f a.out # If we don't use `.F' as extension, the preprocessor is not run on the # input file. (Note that this only needs to work for GNU compilers.) ac_save_ext=$ac_ext ac_ext=F -echo "$as_me:$LINENO: checking whether we are using the GNU Fortran 77 compiler" >&5 -echo $ECHO_N "checking whether we are using the GNU Fortran 77 compiler... $ECHO_C" >&6 -if test "${ac_cv_f77_compiler_gnu+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU Fortran 77 compiler" >&5 +$as_echo_n "checking whether we are using the GNU Fortran 77 compiler... " >&6; } +if ${ac_cv_f77_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main #ifndef __GNUC__ choke me @@ -8672,90 +6202,42 @@ else end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_compiler_gnu=no + ac_compiler_gnu=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_f77_compiler_gnu=$ac_compiler_gnu fi -echo "$as_me:$LINENO: result: $ac_cv_f77_compiler_gnu" >&5 -echo "${ECHO_T}$ac_cv_f77_compiler_gnu" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_f77_compiler_gnu" >&5 +$as_echo "$ac_cv_f77_compiler_gnu" >&6; } ac_ext=$ac_save_ext ac_test_FFLAGS=${FFLAGS+set} ac_save_FFLAGS=$FFLAGS FFLAGS= -echo "$as_me:$LINENO: checking whether $F77 accepts -g" >&5 -echo $ECHO_N "checking whether $F77 accepts -g... $ECHO_C" >&6 -if test "${ac_cv_prog_f77_g+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $F77 accepts -g" >&5 +$as_echo_n "checking whether $F77 accepts -g... " >&6; } +if ${ac_cv_prog_f77_g+:} false; then : + $as_echo_n "(cached) " >&6 else FFLAGS=-g -cat >conftest.$ac_ext <<_ACEOF +cat > conftest.$ac_ext <<_ACEOF program main end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_cv_prog_f77_g=yes else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -ac_cv_prog_f77_g=no + ac_cv_prog_f77_g=no fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_g" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_g" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_f77_g" >&5 +$as_echo "$ac_cv_prog_f77_g" >&6; } if test "$ac_test_FFLAGS" = set; then FFLAGS=$ac_save_FFLAGS elif test $ac_cv_prog_f77_g = yes; then @@ -8772,8 +6254,12 @@ else fi fi -G77=`test $ac_compiler_gnu = yes && echo yes` -ac_ext=cc +if test $ac_compiler_gnu = yes; then + G77=yes +else + G77= +fi +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -8795,42 +6281,21 @@ ac_ext=f ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5' ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_f77_compiler_gnu -echo "$as_me:$LINENO: checking how to get verbose linking output from $F77" >&5 -echo $ECHO_N "checking how to get verbose linking output from $F77... $ECHO_C" >&6 -if test "${ac_cv_prog_f77_v+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $F77" >&5 +$as_echo_n "checking how to get verbose linking output from $F77... " >&6; } +if ${ac_cv_prog_f77_v+:} false; then : + $as_echo_n "(cached) " >&6 else - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main end _ACEOF -rm -f conftest.$ac_objext -if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 - (eval $ac_compile) 2>conftest.er1 - ac_status=$? - grep -v '^ *+' conftest.er1 >conftest.err - rm -f conftest.er1 - cat conftest.err >&5 - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } && - { ac_try='test -z "$ac_f77_werror_flag" - || test ! -s conftest.err' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; } && - { ac_try='test -s conftest.$ac_objext' - { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 - (eval $ac_try) 2>&5 - ac_status=$? - echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; }; then +if ac_fn_f77_try_compile "$LINENO"; then : ac_cv_prog_f77_v= # Try some options frequently used verbose output for ac_verb in -v -verbose --verbose -V -\#\#\#; do - cat >conftest.$ac_ext <<_ACEOF + cat > conftest.$ac_ext <<_ACEOF program main end @@ -8842,20 +6307,29 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_verb" -(eval echo $as_me:8845: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 +eval "set x $ac_link" +shift +$as_echo "$as_me:${as_lineno-$LINENO}: $*" >&5 +# gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH, +# LIBRARY_PATH; skip all such settings. +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | + sed '/^Driving:/d; /^Configured with:/d; + '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"` +$as_echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS -rm -f conftest* +rm -rf conftest* # On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where # /foo, /bar, and /baz are search directories for the Fortran linker. # Here, we change these into -L/foo -L/bar -L/baz (and put it first): ac_f77_v_output="`echo $ac_f77_v_output | grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + sed 's|.*LPATH is\(: *[^ ]*\).*|\1|;s|: */| -L/|g'` $ac_f77_v_output" +# FIXME: we keep getting bitten by quoted arguments; a more general fix +# that detects unbalanced quotes in FLIBS should be implemented +# and (ugh) tested at some point. case $ac_f77_v_output in # If we are using xlf then replace all the commas with spaces. *xlfentry*) @@ -8864,51 +6338,55 @@ case $ac_f77_v_output in # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted # $LIBS confuse us, and the libraries appear later in the output anyway). *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"-mGLOB[^"]*"/ /g'` ;; + + # Portland Group compiler has singly- or doubly-quoted -cmdline argument + # Singly-quoted arguments were reported for versions 5.2-4 and 6.0-4. + # Doubly-quoted arguments were reported for "PGF90/x86 Linux/x86 5.0-2". + *-cmdline\ * | *-ignore\ * | *-def\ *) + ac_f77_v_output=`echo $ac_f77_v_output | sed "\ + s/-cmdline *'[^']*'/ /g; s/-cmdline *\"[^\"]*\"/ /g + s/-ignore *'[^']*'/ /g; s/-ignore *\"[^\"]*\"/ /g + s/-def *'[^']*'/ /g; s/-def *\"[^\"]*\"/ /g"` ;; # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"//g'` ;; esac # look for -l* and *.a constructs in the output for ac_arg in $ac_f77_v_output; do case $ac_arg in - [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) - ac_cv_prog_f77_v=$ac_verb - break 2 ;; + [\\/]*.a | ?:[\\/]*.a | -[lLRu]*) + ac_cv_prog_f77_v=$ac_verb + break 2 ;; esac done done if test -z "$ac_cv_prog_f77_v"; then - { echo "$as_me:$LINENO: WARNING: cannot determine how to obtain linking information from $F77" >&5 -echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot determine how to obtain linking information from $F77" >&5 +$as_echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;} fi else - echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - -{ echo "$as_me:$LINENO: WARNING: compilation failed" >&5 -echo "$as_me: WARNING: compilation failed" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: compilation failed" >&5 +$as_echo "$as_me: WARNING: compilation failed" >&2;} fi -rm -f conftest.err conftest.$ac_objext conftest.$ac_ext +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -echo "$as_me:$LINENO: result: $ac_cv_prog_f77_v" >&5 -echo "${ECHO_T}$ac_cv_prog_f77_v" >&6 -echo "$as_me:$LINENO: checking for Fortran libraries of $F77" >&5 -echo $ECHO_N "checking for Fortran libraries of $F77... $ECHO_C" >&6 -if test "${ac_cv_f77_libs+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_f77_v" >&5 +$as_echo "$ac_cv_prog_f77_v" >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 libraries of $F77" >&5 +$as_echo_n "checking for Fortran 77 libraries of $F77... " >&6; } +if ${ac_cv_f77_libs+:} false; then : + $as_echo_n "(cached) " >&6 else if test "x$FLIBS" != "x"; then ac_cv_f77_libs="$FLIBS" # Let the user override the test. else -cat >conftest.$ac_ext <<_ACEOF +cat > conftest.$ac_ext <<_ACEOF program main end @@ -8920,20 +6398,29 @@ _ACEOF # flags. ac_save_FFLAGS=$FFLAGS FFLAGS="$FFLAGS $ac_cv_prog_f77_v" -(eval echo $as_me:8923: \"$ac_link\") >&5 -ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` -echo "$ac_f77_v_output" >&5 +eval "set x $ac_link" +shift +$as_echo "$as_me:${as_lineno-$LINENO}: $*" >&5 +# gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH, +# LIBRARY_PATH; skip all such settings. +ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | + sed '/^Driving:/d; /^Configured with:/d; + '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"` +$as_echo "$ac_f77_v_output" >&5 FFLAGS=$ac_save_FFLAGS -rm -f conftest* +rm -rf conftest* # On HP/UX there is a line like: "LPATH is: /foo:/bar:/baz" where # /foo, /bar, and /baz are search directories for the Fortran linker. # Here, we change these into -L/foo -L/bar -L/baz (and put it first): ac_f77_v_output="`echo $ac_f77_v_output | grep 'LPATH is:' | - sed 's,.*LPATH is\(: *[^ ]*\).*,\1,;s,: */, -L/,g'` $ac_f77_v_output" + sed 's|.*LPATH is\(: *[^ ]*\).*|\1|;s|: */| -L/|g'` $ac_f77_v_output" +# FIXME: we keep getting bitten by quoted arguments; a more general fix +# that detects unbalanced quotes in FLIBS should be implemented +# and (ugh) tested at some point. case $ac_f77_v_output in # If we are using xlf then replace all the commas with spaces. *xlfentry*) @@ -8942,13 +6429,20 @@ case $ac_f77_v_output in # With Intel ifc, ignore the quoted -mGLOB_options_string stuff (quoted # $LIBS confuse us, and the libraries appear later in the output anyway). *mGLOB_options_string*) - ac_f77_v_output=`echo $ac_f77_v_output | sed 's/\"-mGLOB[^\"]*\"/ /g'` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"-mGLOB[^"]*"/ /g'` ;; + + # Portland Group compiler has singly- or doubly-quoted -cmdline argument + # Singly-quoted arguments were reported for versions 5.2-4 and 6.0-4. + # Doubly-quoted arguments were reported for "PGF90/x86 Linux/x86 5.0-2". + *-cmdline\ * | *-ignore\ * | *-def\ *) + ac_f77_v_output=`echo $ac_f77_v_output | sed "\ + s/-cmdline *'[^']*'/ /g; s/-cmdline *\"[^\"]*\"/ /g + s/-ignore *'[^']*'/ /g; s/-ignore *\"[^\"]*\"/ /g + s/-def *'[^']*'/ /g; s/-def *\"[^\"]*\"/ /g"` ;; # If we are using Cray Fortran then delete quotes. - # Use "\"" instead of '"' for font-lock-mode. - # FIXME: a more general fix for quoted arguments with spaces? *cft90*) - ac_f77_v_output=`echo $ac_f77_v_output | sed "s/\"//g"` ;; + ac_f77_v_output=`echo $ac_f77_v_output | sed 's/"//g'` ;; esac @@ -8963,8 +6457,8 @@ while test $# != 1; do shift ac_arg=$1 case $ac_arg in - [\\/]*.a | ?:[\\/]*.a) - ac_exists=false + [\\/]*.a | ?:[\\/]*.a) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -8972,15 +6466,14 @@ while test $# != 1; do fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi - - ;; - -bI:*) - ac_exists=false + ;; + -bI:*) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -8988,8 +6481,8 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else if test "$ac_compiler_gnu" = yes; then for ac_link_opt in $ac_arg; do @@ -8999,18 +6492,18 @@ else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi fi - - ;; - # Ignore these flags. - -lang* | -lcrt[01].o | -lcrtbegin.o | -lc | -lgcc | -libmil | -LANG:=*) - ;; - -lkernel32) - test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" - ;; - -[LRuY]) - # These flags, when seen by themselves, take an argument. - # We remove the space between option and argument and re-iterate - # unless we find an empty arg or a new option (starting with -) + ;; + # Ignore these flags. + -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -little \ + |-LANG:=* | -LIST:* | -LNO:* | -link) + ;; + -lkernel32) + test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" + ;; + -[LRuYz]) + # These flags, when seen by themselves, take an argument. + # We remove the space between option and argument and re-iterate + # unless we find an empty arg or a new option (starting with -) case $2 in "" | -*);; *) @@ -9019,10 +6512,10 @@ fi set X $ac_arg "$@" ;; esac - ;; - -YP,*) - for ac_j in `echo $ac_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do - ac_exists=false + ;; + -YP,*) + for ac_j in `$as_echo "$ac_arg" | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_j" = x"$ac_i"; then ac_exists=true @@ -9030,17 +6523,16 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_arg="$ac_arg $ac_j" - ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" + ac_cv_f77_libs="$ac_cv_f77_libs $ac_j" fi - - done - ;; - -[lLR]*) - ac_exists=false + done + ;; + -[lLR]*) + ac_exists=false for ac_i in $ac_cv_f77_libs; do if test x"$ac_arg" = x"$ac_i"; then ac_exists=true @@ -9048,14 +6540,16 @@ fi fi done - if test x"$ac_exists" = xtrue; then - : + if test x"$ac_exists" = xtrue; then : + else ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" fi - - ;; - # Ignore everything else. + ;; + -zallextract*| -zdefaultextract) + ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg" + ;; + # Ignore everything else. esac done # restore positional arguments @@ -9066,10 +6560,10 @@ set X $ac_save_positional; shift # must begin with a "/"). case `(uname -sr) 2>/dev/null` in "SunOS 5"*) - ac_ld_run_path=`echo $ac_f77_v_output | - sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` + ac_ld_run_path=`$as_echo "$ac_f77_v_output" | + sed -n 's,^.*LD_RUN_PATH *= *\(/[^ ]*\).*$,-R\1,p'` test "x$ac_ld_run_path" != x && - if test "$ac_compiler_gnu" = yes; then + if test "$ac_compiler_gnu" = yes; then for ac_link_opt in $ac_ld_run_path; do ac_cv_f77_libs="$ac_cv_f77_libs -Xlinker $ac_link_opt" done @@ -9081,12 +6575,12 @@ esac fi # test "x$[]_AC_LANG_PREFIX[]LIBS" = "x" fi -echo "$as_me:$LINENO: result: $ac_cv_f77_libs" >&5 -echo "${ECHO_T}$ac_cv_f77_libs" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_f77_libs" >&5 +$as_echo "$ac_cv_f77_libs" >&6; } FLIBS="$ac_cv_f77_libs" -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -9129,10 +6623,10 @@ if test "x${BUILD_F90}" != "x0"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -echo "$as_me:$LINENO: checking for $ac_word" >&5 -echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 -if test "${ac_cv_path_F90+set}" = set; then - echo $ECHO_N "(cached) $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_F90+:} false; then : + $as_echo_n "(cached) " >&6 else case $F90 in [\\/]* | ?:[\\/]*) @@ -9144,28 +6638,29 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_F90="$as_dir/$ac_word$ac_exec_ext" - echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done +IFS=$as_save_IFS ;; esac fi F90=$ac_cv_path_F90 - if test -n "$F90"; then - echo "$as_me:$LINENO: result: $F90" >&5 -echo "${ECHO_T}$F90" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $F90" >&5 +$as_echo "$F90" >&6; } else - echo "$as_me:$LINENO: result: no" >&5 -echo "${ECHO_T}no" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } fi + test -n "$F90" && break done test -n "$F90" || F90=""none"" @@ -9186,8 +6681,8 @@ f90_module_dir='-I' f90_opts='' if test "x${BUILD_F90}" != "x0"; then - echo "$as_me:$LINENO: checking Fortran 90 compiler ($F90) type" >&5 -echo $ECHO_N "checking Fortran 90 compiler ($F90) type... $ECHO_C" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking Fortran 90 compiler ($F90) type" >&5 +$as_echo_n "checking Fortran 90 compiler ($F90) type... " >&6; } cat >> testf90.f90 << EOF module mt double precision, parameter :: x = 2.3 @@ -9241,8 +6736,8 @@ F90LIBS= f90buildopts="-p. -s -YEXT_NAMES=LCS -YEXT_SFX=_ -YCFRL=1" fi rm -f testf90.f90 - echo "$as_me:$LINENO: result: ${f90type}" >&5 -echo "${ECHO_T}${f90type}" >&6 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${f90type}" >&5 +$as_echo "${f90type}" >&6; } if test "x${BUILD_F90}" != "x0"; then if test "x${has_f90}" = "xno"; then echo " -> cannot build the Fortran 90 interface" @@ -9278,7 +6773,7 @@ if test -z "$F77_EXT"; then F77_EXT=f; fi -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -9303,27 +6798,19 @@ math_libs='-lcvode -lctmath' if test "$LAPACK_FTN_TRAILING_UNDERSCORE" = "y" then - cat >>confdefs.h <<\_ACEOF -#define LAPACK_FTN_TRAILING_UNDERSCORE 1 -_ACEOF + $as_echo "#define LAPACK_FTN_TRAILING_UNDERSCORE 1" >>confdefs.h - cat >>confdefs.h <<\_ACEOF -#define FTN_TRAILING_UNDERSCORE 1 -_ACEOF + $as_echo "#define FTN_TRAILING_UNDERSCORE 1" >>confdefs.h fi if test "$LAPACK_FTN_STRING_LEN_AT_END" = "y" -then cat >>confdefs.h <<\_ACEOF -#define LAPACK_FTN_STRING_LEN_AT_END 1 -_ACEOF +then $as_echo "#define LAPACK_FTN_STRING_LEN_AT_END 1" >>confdefs.h fi if test "$LAPACK_NAMES" = "lower" -then cat >>confdefs.h <<\_ACEOF -#define LAPACK_NAMES_LOWERCASE 1 -_ACEOF +then $as_echo "#define LAPACK_NAMES_LOWERCASE 1" >>confdefs.h fi @@ -9337,8 +6824,8 @@ fi # SO is the extension of shared libraries `(including the dot!) # -- usually .so, .sl on HP-UX, .dll on Cygwin -echo "$as_me:$LINENO: checking SO" >&5 -echo $ECHO_N "checking SO... $ECHO_C" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking SO" >&5 +$as_echo_n "checking SO... " >&6; } if test -z "$SO" then case $ac_sys_system in @@ -9348,12 +6835,12 @@ then *) SO=.so;; esac fi -echo "$as_me:$LINENO: result: $SO" >&5 -echo "${ECHO_T}$SO" >&6 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $SO" >&5 +$as_echo "$SO" >&6; } -ac_ext=cc +ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' @@ -9428,39 +6915,27 @@ fi - ac_config_files="$ac_config_files Makefile Cantera/Makefile Cantera/src/Makefile Cantera/src/base/Makefile Cantera/src/zeroD/Makefile Cantera/src/oneD/Makefile Cantera/src/converters/Makefile Cantera/src/transport/Makefile Cantera/src/thermo/Makefile Cantera/src/kinetics/Makefile Cantera/src/numerics/Makefile Cantera/src/spectra/Makefile Cantera/src/equil/Makefile Cantera/clib/src/Makefile Cantera/fortran/src/Makefile Cantera/fortran/f77demos/f77demos.mak Cantera/fortran/f77demos/Makefile Cantera/matlab/Makefile Cantera/matlab/setup_matlab.py Cantera/python/Makefile Cantera/python/setup.py Cantera/cxx/Makefile Cantera/cxx/src/Makefile Cantera/cxx/demos/Makefile Cantera/cxx/demos/combustor/Makefile Cantera/cxx/demos/combustor/Makefile.install Cantera/cxx/demos/flamespeed/Makefile Cantera/cxx/demos/flamespeed/Makefile.install Cantera/cxx/demos/kinetics1/Makefile Cantera/cxx/demos/kinetics1/Makefile.install Cantera/cxx/demos/NASA_coeffs/Makefile Cantera/cxx/demos/NASA_coeffs/Makefile.install Cantera/cxx/demos/rankine/Makefile Cantera/cxx/demos/rankine/Makefile.install Cantera/cxx/include/Cantera.mak Cantera/cxx/include/Cantera_bt.mak Cantera/user/Makefile Cantera/python/src/Makefile Cantera/python/examples/Makefile Cantera/python/examples/equilibrium/Makefile Cantera/python/examples/equilibrium/adiabatic_flame/Makefile Cantera/python/examples/equilibrium/multiphase_plasma/Makefile Cantera/python/examples/equilibrium/simple_test/Makefile Cantera/python/examples/equilibrium/stoich_flame/Makefile Cantera/python/examples/gasdynamics/isentropic/Makefile Cantera/python/examples/gasdynamics/soundSpeed/Makefile Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile Cantera/python/examples/reactors/surf_pfr_sim/Makefile Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile Cantera/python/examples/transport/Makefile Cantera/python/examples/flames/Makefile Cantera/python/examples/gasdynamics/Makefile Cantera/python/examples/liquid_vapor/Makefile Cantera/python/examples/reactors/Makefile Cantera/python/examples/surface_chemistry/Makefile ext/lapack/Makefile ext/blas/Makefile ext/cvode/Makefile ext/math/Makefile ext/recipes/Makefile ext/tpx/Makefile ext/Makefile ext/f2c_libs/Makefile ext/f2c_blas/Makefile ext/f2c_lapack/Makefile ext/f2c_math/Makefile examples/Makefile examples/cxx/Makefile docs/Makefile tools/Makefile docs/Cantera.cfg tools/src/Makefile 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test_problems/nasa9_reader/Makefile test_problems/nasa9_reader/runtest test_problems/min_python/Makefile test_problems/min_python/minDiamond/Makefile test_problems/min_python/negATest/Makefile test_problems/pureFluidTest/Makefile test_problems/rankine_democxx/Makefile test_problems/python/Makefile test_problems/cathermo/Makefile test_problems/cathermo/issp/Makefile test_problems/cathermo/ims/Makefile test_problems/cathermo/stoichSubSSTP/Makefile test_problems/cathermo/testIAPWS/Makefile test_problems/cathermo/testIAPWSPres/Makefile test_problems/cathermo/testIAPWSTripP/Makefile test_problems/cathermo/testWaterPDSS/Makefile test_problems/cathermo/testWaterTP/Makefile test_problems/cathermo/HMW_test_1/Makefile test_problems/cathermo/HMW_test_3/Makefile test_problems/cathermo/HMW_graph_GvT/Makefile test_problems/cathermo/HMW_graph_GvI/Makefile test_problems/cathermo/HMW_graph_HvT/Makefile test_problems/cathermo/HMW_graph_CpvT/Makefile test_problems/cathermo/HMW_graph_VvT/Makefile test_problems/cathermo/DH_graph_1/Makefile test_problems/cathermo/DH_graph_acommon/Makefile test_problems/cathermo/DH_graph_NM/Makefile test_problems/cathermo/DH_graph_Pitzer/Makefile test_problems/cathermo/DH_graph_bdotak/Makefile test_problems/cathermo/HMW_dupl_test/Makefile test_problems/cathermo/VPissp/Makefile test_problems/cathermo/wtWater/Makefile test_problems/VCSnonideal/Makefile test_problems/VPsilane_test/Makefile test_problems/VPsilane_test/runtest test_problems/VCSnonideal/NaCl_equil/Makefile bin/install_tsc" +ac_config_files="$ac_config_files Makefile Cantera/Makefile Cantera/src/Makefile Cantera/src/base/Makefile Cantera/src/zeroD/Makefile Cantera/src/oneD/Makefile Cantera/src/converters/Makefile Cantera/src/transport/Makefile Cantera/src/thermo/Makefile Cantera/src/kinetics/Makefile Cantera/src/numerics/Makefile Cantera/src/spectra/Makefile Cantera/src/equil/Makefile Cantera/clib/src/Makefile Cantera/fortran/src/Makefile Cantera/fortran/f77demos/f77demos.mak Cantera/fortran/f77demos/Makefile Cantera/matlab/Makefile Cantera/matlab/setup_matlab.py Cantera/python/Makefile Cantera/python/setup.py Cantera/cxx/Makefile Cantera/cxx/src/Makefile Cantera/cxx/demos/Makefile Cantera/cxx/demos/combustor/Makefile Cantera/cxx/demos/combustor/Makefile.install Cantera/cxx/demos/flamespeed/Makefile Cantera/cxx/demos/flamespeed/Makefile.install Cantera/cxx/demos/kinetics1/Makefile Cantera/cxx/demos/kinetics1/Makefile.install Cantera/cxx/demos/NASA_coeffs/Makefile Cantera/cxx/demos/NASA_coeffs/Makefile.install Cantera/cxx/demos/rankine/Makefile Cantera/cxx/demos/rankine/Makefile.install Cantera/cxx/include/Cantera.mak Cantera/cxx/include/Cantera_bt.mak Cantera/user/Makefile Cantera/python/src/Makefile Cantera/python/examples/Makefile Cantera/python/examples/equilibrium/Makefile Cantera/python/examples/equilibrium/adiabatic_flame/Makefile Cantera/python/examples/equilibrium/multiphase_plasma/Makefile Cantera/python/examples/equilibrium/simple_test/Makefile Cantera/python/examples/equilibrium/stoich_flame/Makefile Cantera/python/examples/gasdynamics/isentropic/Makefile Cantera/python/examples/gasdynamics/soundSpeed/Makefile Cantera/python/examples/flames/adiabatic_flame/Makefile Cantera/python/examples/flames/flame1/Makefile Cantera/python/examples/flames/flame2/Makefile Cantera/python/examples/flames/flame_fixed_T/Makefile Cantera/python/examples/flames/free_h2_air/Makefile Cantera/python/examples/flames/npflame1/Makefile Cantera/python/examples/flames/stflame1/Makefile Cantera/python/examples/fuel_cells/Makefile Cantera/python/examples/liquid_vapor/critProperties/Makefile Cantera/python/examples/liquid_vapor/rankine/Makefile Cantera/python/examples/kinetics/Makefile Cantera/python/examples/misc/Makefile Cantera/python/examples/reactors/combustor_sim/Makefile Cantera/python/examples/reactors/functors_sim/Makefile Cantera/python/examples/reactors/mix1_sim/Makefile Cantera/python/examples/reactors/mix2_sim/Makefile Cantera/python/examples/reactors/piston_sim/Makefile Cantera/python/examples/reactors/reactor1_sim/Makefile Cantera/python/examples/reactors/reactor2_sim/Makefile Cantera/python/examples/reactors/sensitivity_sim/Makefile Cantera/python/examples/reactors/surf_pfr_sim/Makefile Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile Cantera/python/examples/transport/Makefile Cantera/python/examples/flames/Makefile Cantera/python/examples/gasdynamics/Makefile Cantera/python/examples/liquid_vapor/Makefile Cantera/python/examples/reactors/Makefile Cantera/python/examples/surface_chemistry/Makefile ext/lapack/Makefile ext/blas/Makefile ext/cvode/Makefile ext/math/Makefile ext/recipes/Makefile ext/tpx/Makefile ext/Makefile ext/f2c_libs/Makefile ext/f2c_blas/Makefile ext/f2c_lapack/Makefile ext/f2c_math/Makefile examples/Makefile examples/cxx/Makefile docs/Makefile tools/Makefile docs/Cantera.cfg tools/src/Makefile tools/src/sample.mak tools/src/finish_install.py tools/src/package4mac tools/templates/f77/demo.mak tools/templates/f90/demo.mak tools/templates/cxx/demo.mak tools/testtools/Makefile data/inputs/Makefile data/inputs/mkxml test_problems/Makefile test_problems/cxx_ex/Makefile test_problems/silane_equil/Makefile test_problems/surfkin/Makefile test_problems/spectroscopy/Makefile test_problems/surfSolverTest/Makefile test_problems/diamondSurf/Makefile test_problems/diamondSurf_dupl/Makefile test_problems/ChemEquil_gri_matrix/Makefile test_problems/ChemEquil_gri_pairs/Makefile test_problems/ChemEquil_ionizedGas/Makefile test_problems/ChemEquil_red1/Makefile test_problems/CpJump/Makefile test_problems/mixGasTransport/Makefile test_problems/multiGasTransport/Makefile test_problems/printUtilUnitTest/Makefile test_problems/fracCoeff/Makefile test_problems/negATest/Makefile test_problems/NASA9poly_test/Makefile test_problems/ck2cti_test/Makefile test_problems/ck2cti_test/runtest test_problems/nasa9_reader/Makefile test_problems/nasa9_reader/runtest test_problems/min_python/Makefile test_problems/min_python/minDiamond/Makefile test_problems/min_python/negATest/Makefile test_problems/pureFluidTest/Makefile test_problems/rankine_democxx/Makefile test_problems/python/Makefile test_problems/cathermo/Makefile test_problems/cathermo/issp/Makefile test_problems/cathermo/ims/Makefile test_problems/cathermo/stoichSubSSTP/Makefile test_problems/cathermo/testIAPWS/Makefile test_problems/cathermo/testIAPWSPres/Makefile test_problems/cathermo/testIAPWSTripP/Makefile test_problems/cathermo/testWaterPDSS/Makefile test_problems/cathermo/testWaterTP/Makefile test_problems/cathermo/HMW_test_1/Makefile test_problems/cathermo/HMW_test_3/Makefile test_problems/cathermo/HMW_graph_GvT/Makefile test_problems/cathermo/HMW_graph_GvI/Makefile test_problems/cathermo/HMW_graph_HvT/Makefile test_problems/cathermo/HMW_graph_CpvT/Makefile test_problems/cathermo/HMW_graph_VvT/Makefile test_problems/cathermo/DH_graph_1/Makefile test_problems/cathermo/DH_graph_acommon/Makefile test_problems/cathermo/DH_graph_NM/Makefile test_problems/cathermo/DH_graph_Pitzer/Makefile test_problems/cathermo/DH_graph_bdotak/Makefile test_problems/cathermo/HMW_dupl_test/Makefile test_problems/cathermo/VPissp/Makefile test_problems/cathermo/wtWater/Makefile test_problems/VCSnonideal/Makefile test_problems/VPsilane_test/Makefile test_problems/VPsilane_test/runtest test_problems/VCSnonideal/NaCl_equil/Makefile bin/install_tsc" + test "x$prefix" = xNONE && prefix=$ac_default_prefix # Let make expand exec_prefix. test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' -# VPATH may cause trouble with some makes, so we remove $(srcdir), -# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and -# trailing colons and then remove the whole line if VPATH becomes empty -# (actually we leave an empty line to preserve line numbers). -if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=/{ -s/:*\$(srcdir):*/:/; -s/:*\${srcdir}:*/:/; -s/:*@srcdir@:*/:/; -s/^\([^=]*=[ ]*\):*/\1/; -s/:*$//; -s/^[^=]*=[ ]*$//; -}' -fi - DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= +U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. - ac_i=`echo "$ac_i" | - sed 's/\$U\././;s/\.o$//;s/\.obj$//'` - # 2. Add them. - ac_libobjs="$ac_libobjs $ac_i\$U.$ac_objext" - ac_ltlibobjs="$ac_ltlibobjs $ac_i"'$U.lo' + ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' + ac_i=`$as_echo "$ac_i" | sed "$ac_script"` + # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR + # will be set to the directory where LIBOBJS objects are built. + as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" + as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs @@ -9468,12 +6943,14 @@ LTLIBOBJS=$ac_ltlibobjs -: ${CONFIG_STATUS=./config.status} +: "${CONFIG_STATUS=./config.status}" +ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 -echo "$as_me: creating $CONFIG_STATUS" >&6;} -cat >$CONFIG_STATUS <<_ACEOF +{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: creating $CONFIG_STATUS" >&6;} +as_write_fail=0 +cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -9483,81 +6960,253 @@ cat >$CONFIG_STATUS <<_ACEOF debug=false ac_cs_recheck=false ac_cs_silent=false + SHELL=\${CONFIG_SHELL-$SHELL} -_ACEOF +export SHELL +_ASEOF +cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## -cat >>$CONFIG_STATUS <<\_ACEOF -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## - -# Be Bourne compatible -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: - # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' -elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then - set -o posix -fi -DUALCASE=1; export DUALCASE # for MKS sh - -# Support unset when possible. -if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then - as_unset=unset + setopt NO_GLOB_SUBST else - as_unset=false + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac fi -# Work around bugs in pre-3.0 UWIN ksh. -$as_unset ENV MAIL MAILPATH +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent editors from complaining about space-tab. +# (If _AS_PATH_WALK were called with IFS unset, it would disable word +# splitting by setting IFS to empty value.) +IFS=" "" $as_nl" + +# Find who we are. Look in the path if we contain no directory separator. +as_myself= +case $0 in #(( + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done +IFS=$as_save_IFS + + ;; +esac +# We did not find ourselves, most probably we were run as `sh COMMAND' +# in which case we are not to be found in the path. +if test "x$as_myself" = x; then + as_myself=$0 +fi +if test ! -f "$as_myself"; then + $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + exit 1 +fi + +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done PS1='$ ' PS2='> ' PS4='+ ' # NLS nuisances. -for as_var in \ - LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \ - LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \ - LC_TELEPHONE LC_TIME -do - if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then - eval $as_var=C; export $as_var - else - $as_unset $as_var - fi -done +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE -# Required to use basename. -if expr a : '\(a\)' >/dev/null 2>&1; then +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + + +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with STATUS, using 1 if that was 0. +as_fn_error () +{ + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + fi + $as_echo "$as_me: error: $2" >&2 + as_fn_exit $as_status +} # as_fn_error + + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr else as_expr=false fi -if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then as_basename=basename else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. -as_me=`$as_basename "$0" || +as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)$' \| \ - . : '\(.\)' 2>/dev/null || -echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } - /^X\/\(\/\/\)$/{ s//\1/; q; } - /^X\/\(\/\).*/{ s//\1/; q; } - s/.*/./; q'` + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` - -# PATH needs CR, and LINENO needs CR and PATH. # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -9565,148 +7214,123 @@ as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits -# The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then - echo "#! /bin/sh" >conf$$.sh - echo "exit 0" >>conf$$.sh - chmod +x conf$$.sh - if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then - PATH_SEPARATOR=';' - else - PATH_SEPARATOR=: - fi - rm -f conf$$.sh -fi - - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" || { - # Find who we are. Look in the path if we contain no path at all - # relative or not. - case $0 in - *[\\/]* ) as_myself=$0 ;; - *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done - - ;; - esac - # We did not find ourselves, most probably we were run as `sh COMMAND' - # in which case we are not to be found in the path. - if test "x$as_myself" = x; then - as_myself=$0 - fi - if test ! -f "$as_myself"; then - { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5 -echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;} - { (exit 1); exit 1; }; } - fi - case $CONFIG_SHELL in - '') - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for as_base in sh bash ksh sh5; do - case $as_dir in - /*) - if ("$as_dir/$as_base" -c ' - as_lineno_1=$LINENO - as_lineno_2=$LINENO - as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then - $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; } - $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; } - CONFIG_SHELL=$as_dir/$as_base - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$0" ${1+"$@"} - fi;; - esac - done -done -;; - esac - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. 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"cannot create directory $as_dir" + + +} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false fi -as_executable_p="test -f" +if test -x / >/dev/null 2>&1; then + as_test_x='test -x' +else + if ls -dL / >/dev/null 2>&1; then + as_ls_L_option=L + else + as_ls_L_option= + fi + as_test_x=' + eval sh -c '\'' + if test -d "$1"; then + test -d "$1/."; + else + case $1 in #( + -*)set "./$1";; + esac; + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + ???[sx]*):;;*)false;;esac;fi + '\'' sh + ' +fi +as_executable_p=$as_test_x # Sed expression to map a string onto a valid CPP name. as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" @@ -9715,31 +7339,20 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -# IFS -# We need space, tab and new line, in precisely that order. -as_nl=' -' -IFS=" $as_nl" - -# CDPATH. -$as_unset CDPATH - exec 6>&1 +## ----------------------------------- ## +## Main body of $CONFIG_STATUS script. ## +## ----------------------------------- ## +_ASEOF +test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 -# Open the log real soon, to keep \$[0] and so on meaningful, and to +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# Save the log message, to keep $0 and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their -# values after options handling. Logging --version etc. is OK. -exec 5>>config.log -{ - echo - sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX -## Running $as_me. ## -_ASBOX -} >&5 -cat >&5 <<_CSEOF - +# values after options handling. +ac_log=" This file was extended by Cantera $as_me 1.7.0, which was -generated by GNU Autoconf 2.59. Invocation command line was +generated by GNU Autoconf 2.68. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -9747,45 +7360,46 @@ generated by GNU Autoconf 2.59. Invocation command line was CONFIG_COMMANDS = $CONFIG_COMMANDS $ $0 $@ -_CSEOF -echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5 -echo >&5 +on `(hostname || uname -n) 2>/dev/null | sed 1q` +" + _ACEOF +case $ac_config_files in *" +"*) set x $ac_config_files; shift; ac_config_files=$*;; +esac + +case $ac_config_headers in *" +"*) set x $ac_config_headers; shift; ac_config_headers=$*;; +esac + + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 # Files that config.status was made for. -if test -n "$ac_config_files"; then - echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS -fi +config_files="$ac_config_files" +config_headers="$ac_config_headers" -if test -n "$ac_config_headers"; then - echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS -fi - -if test -n "$ac_config_links"; then - echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS -fi - -if test -n "$ac_config_commands"; then - echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS -fi - -cat >>$CONFIG_STATUS <<\_ACEOF +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files from templates according to the -current configuration. +\`$as_me' instantiates files and other configuration actions +from templates according to the current configuration. Unless the files +and actions are specified as TAGs, all are instantiated by default. -Usage: $0 [OPTIONS] [FILE]... +Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit - -V, --version print version number, then exit - -q, --quiet do not print progress messages + -V, --version print version number and configuration settings, then exit + --config print configuration, then exit + -q, --quiet, --silent + do not print progress messages -d, --debug don't remove temporary files --recheck update $as_me by reconfiguring in the same conditions - --file=FILE[:TEMPLATE] - instantiate the configuration file FILE - --header=FILE[:TEMPLATE] - instantiate the configuration header FILE + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE Configuration files: $config_files @@ -9793,84 +7407,90 @@ $config_files Configuration headers: $config_headers -Report bugs to ." -_ACEOF +Report bugs to the package provider." -cat >>$CONFIG_STATUS <<_ACEOF +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ Cantera config.status 1.7.0 -configured by $0, generated by GNU Autoconf 2.59, - with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" +configured by $0, generated by GNU Autoconf 2.68, + with options \\"\$ac_cs_config\\" -Copyright (C) 2003 Free Software Foundation, Inc. +Copyright (C) 2010 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." -srcdir=$srcdir -INSTALL="$INSTALL" + +ac_pwd='$ac_pwd' +srcdir='$srcdir' +INSTALL='$INSTALL' +test -n "\$AWK" || AWK=awk _ACEOF -cat >>$CONFIG_STATUS <<\_ACEOF -# If no file are specified by the user, then we need to provide default -# value. By we need to know if files were specified by the user. +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# The default lists apply if the user does not specify any file. ac_need_defaults=: while test $# != 0 do case $1 in - --*=*) - ac_option=`expr "x$1" : 'x\([^=]*\)='` - ac_optarg=`expr "x$1" : 'x[^=]*=\(.*\)'` + --*=?*) + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; - -*) + --*=) + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg= + ac_shift=: + ;; + *) ac_option=$1 ac_optarg=$2 ac_shift=shift ;; - *) # This is not an option, so the user has probably given explicit - # arguments. - ac_option=$1 - ac_need_defaults=false;; esac case $ac_option in # Handling of the options. -_ACEOF -cat >>$CONFIG_STATUS <<\_ACEOF -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) ac_cs_recheck=: ;; - --version | --vers* | -V ) - echo "$ac_cs_version"; exit 0 ;; - --he | --h) - # Conflict between --help and --header - { { echo "$as_me:$LINENO: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&5 -echo "$as_me: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&2;} - { (exit 1); exit 1; }; };; - --help | --hel | -h ) - echo "$ac_cs_usage"; exit 0 ;; - --debug | --d* | -d ) + --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) + $as_echo "$ac_cs_version"; exit ;; + --config | --confi | --conf | --con | --co | --c ) + $as_echo "$ac_cs_config"; exit ;; + --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift - CONFIG_FILES="$CONFIG_FILES $ac_optarg" + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + '') as_fn_error $? "missing file argument" ;; + esac + as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift - CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg" + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + esac + as_fn_append CONFIG_HEADERS " '$ac_optarg'" ac_need_defaults=false;; + --he | --h) + # Conflict between --help and --header + as_fn_error $? "ambiguous option: \`$1' +Try \`$0 --help' for more information.";; + --help | --hel | -h ) + $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil | --si | --s) ac_cs_silent=: ;; # This is an error. - -*) { { echo "$as_me:$LINENO: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&5 -echo "$as_me: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&2;} - { (exit 1); exit 1; }; } ;; + -*) as_fn_error $? "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; - *) ac_config_targets="$ac_config_targets $1" ;; + *) as_fn_append ac_config_targets " $1" + ac_need_defaults=false ;; esac shift @@ -9884,189 +7504,203 @@ if $ac_cs_silent; then fi _ACEOF -cat >>$CONFIG_STATUS <<_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 if \$ac_cs_recheck; then - echo "running $SHELL $0 " $ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6 - exec $SHELL $0 $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + shift + \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 + CONFIG_SHELL='$SHELL' + export CONFIG_SHELL + exec "\$@" fi _ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX + $as_echo "$ac_log" +} >&5 +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - - -cat >>$CONFIG_STATUS <<\_ACEOF +# Handling of arguments. for ac_config_target in $ac_config_targets do - case "$ac_config_target" in - # Handling of arguments. - "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;; 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- "Cantera/python/examples/kinetics/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/kinetics/Makefile" ;; - "Cantera/python/examples/misc/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/misc/Makefile" ;; - "Cantera/python/examples/reactors/combustor_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/combustor_sim/Makefile" ;; - "Cantera/python/examples/reactors/functors_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/functors_sim/Makefile" ;; - "Cantera/python/examples/reactors/mix1_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix1_sim/Makefile" ;; - "Cantera/python/examples/reactors/mix2_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix2_sim/Makefile" ;; - "Cantera/python/examples/reactors/piston_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/piston_sim/Makefile" ;; - "Cantera/python/examples/reactors/reactor1_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor1_sim/Makefile" ;; - "Cantera/python/examples/reactors/reactor2_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor2_sim/Makefile" ;; - "Cantera/python/examples/reactors/sensitivity_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/sensitivity_sim/Makefile" ;; - "Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ;; - "Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ;; - "Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ;; - "Cantera/python/examples/transport/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/transport/Makefile" ;; - "Cantera/python/examples/flames/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/Makefile" ;; - "Cantera/python/examples/gasdynamics/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/Makefile" ;; - "Cantera/python/examples/liquid_vapor/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/Makefile" ;; - "Cantera/python/examples/reactors/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/Makefile" ;; - "Cantera/python/examples/surface_chemistry/Makefile" ) CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/Makefile" ;; - "ext/lapack/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/lapack/Makefile" ;; - "ext/blas/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/blas/Makefile" ;; - "ext/cvode/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/cvode/Makefile" ;; - "ext/math/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/math/Makefile" ;; - "ext/recipes/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/recipes/Makefile" ;; - "ext/tpx/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/tpx/Makefile" ;; - "ext/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/Makefile" ;; - "ext/f2c_libs/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_libs/Makefile" ;; - "ext/f2c_blas/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_blas/Makefile" ;; - "ext/f2c_lapack/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_lapack/Makefile" ;; - "ext/f2c_math/Makefile" ) CONFIG_FILES="$CONFIG_FILES ext/f2c_math/Makefile" ;; - "examples/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;; - "examples/cxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES examples/cxx/Makefile" ;; - "docs/Makefile" ) CONFIG_FILES="$CONFIG_FILES docs/Makefile" ;; - "tools/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; - "docs/Cantera.cfg" ) CONFIG_FILES="$CONFIG_FILES docs/Cantera.cfg" ;; - "tools/src/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/src/Makefile" ;; - "tools/src/sample.mak" ) CONFIG_FILES="$CONFIG_FILES tools/src/sample.mak" ;; - "tools/src/finish_install.py" ) CONFIG_FILES="$CONFIG_FILES tools/src/finish_install.py" ;; - "tools/src/package4mac" ) CONFIG_FILES="$CONFIG_FILES tools/src/package4mac" ;; - "tools/templates/f77/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/f77/demo.mak" ;; - "tools/templates/f90/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/f90/demo.mak" ;; - "tools/templates/cxx/demo.mak" ) CONFIG_FILES="$CONFIG_FILES tools/templates/cxx/demo.mak" ;; - "tools/testtools/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/testtools/Makefile" ;; - "data/inputs/Makefile" ) CONFIG_FILES="$CONFIG_FILES data/inputs/Makefile" ;; - "data/inputs/mkxml" ) CONFIG_FILES="$CONFIG_FILES data/inputs/mkxml" ;; - "test_problems/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/Makefile" ;; - "test_problems/cxx_ex/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cxx_ex/Makefile" ;; - "test_problems/silane_equil/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/silane_equil/Makefile" ;; - "test_problems/surfkin/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/surfkin/Makefile" ;; - "test_problems/spectroscopy/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/spectroscopy/Makefile" ;; - "test_problems/surfSolverTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/surfSolverTest/Makefile" ;; - "test_problems/diamondSurf/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf/Makefile" ;; - "test_problems/diamondSurf_dupl/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf_dupl/Makefile" ;; - "test_problems/ChemEquil_gri_matrix/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_matrix/Makefile" ;; - "test_problems/ChemEquil_gri_pairs/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_pairs/Makefile" ;; - "test_problems/ChemEquil_ionizedGas/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_ionizedGas/Makefile" ;; - "test_problems/ChemEquil_red1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_red1/Makefile" ;; - "test_problems/CpJump/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/CpJump/Makefile" ;; - "test_problems/mixGasTransport/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/mixGasTransport/Makefile" ;; - "test_problems/multiGasTransport/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/multiGasTransport/Makefile" ;; - "test_problems/printUtilUnitTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/printUtilUnitTest/Makefile" ;; - "test_problems/fracCoeff/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/fracCoeff/Makefile" ;; - "test_problems/negATest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/negATest/Makefile" ;; - "test_problems/NASA9poly_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/NASA9poly_test/Makefile" ;; - "test_problems/ck2cti_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/Makefile" ;; - "test_problems/ck2cti_test/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/runtest" ;; - "test_problems/nasa9_reader/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/Makefile" ;; - "test_problems/nasa9_reader/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/runtest" ;; - "test_problems/min_python/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/Makefile" ;; - "test_problems/min_python/minDiamond/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/minDiamond/Makefile" ;; - "test_problems/min_python/negATest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/min_python/negATest/Makefile" ;; - "test_problems/pureFluidTest/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/pureFluidTest/Makefile" ;; - "test_problems/rankine_democxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/rankine_democxx/Makefile" ;; - "test_problems/python/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/python/Makefile" ;; - "test_problems/cathermo/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/Makefile" ;; - "test_problems/cathermo/issp/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/issp/Makefile" ;; - "test_problems/cathermo/ims/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/ims/Makefile" ;; - "test_problems/cathermo/stoichSubSSTP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/stoichSubSSTP/Makefile" ;; - "test_problems/cathermo/testIAPWS/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWS/Makefile" ;; - "test_problems/cathermo/testIAPWSPres/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSPres/Makefile" ;; - "test_problems/cathermo/testIAPWSTripP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSTripP/Makefile" ;; - "test_problems/cathermo/testWaterPDSS/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterPDSS/Makefile" ;; - "test_problems/cathermo/testWaterTP/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterTP/Makefile" ;; - "test_problems/cathermo/HMW_test_1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_1/Makefile" ;; - "test_problems/cathermo/HMW_test_3/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_3/Makefile" ;; - "test_problems/cathermo/HMW_graph_GvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_GvI/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvI/Makefile" ;; - "test_problems/cathermo/HMW_graph_HvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_HvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_CpvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_CpvT/Makefile" ;; - "test_problems/cathermo/HMW_graph_VvT/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_VvT/Makefile" ;; - "test_problems/cathermo/DH_graph_1/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_1/Makefile" ;; - "test_problems/cathermo/DH_graph_acommon/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_acommon/Makefile" ;; - "test_problems/cathermo/DH_graph_NM/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_NM/Makefile" ;; - "test_problems/cathermo/DH_graph_Pitzer/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_Pitzer/Makefile" ;; - "test_problems/cathermo/DH_graph_bdotak/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_bdotak/Makefile" ;; - "test_problems/cathermo/HMW_dupl_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_dupl_test/Makefile" ;; - "test_problems/cathermo/VPissp/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/VPissp/Makefile" ;; - "test_problems/cathermo/wtWater/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/wtWater/Makefile" ;; - "test_problems/VCSnonideal/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/Makefile" ;; - "test_problems/VPsilane_test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/Makefile" ;; - "test_problems/VPsilane_test/runtest" ) CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/runtest" ;; - "test_problems/VCSnonideal/NaCl_equil/Makefile" ) CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/NaCl_equil/Makefile" ;; - "bin/install_tsc" ) CONFIG_FILES="$CONFIG_FILES bin/install_tsc" ;; - "config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 -echo "$as_me: error: invalid argument: $ac_config_target" >&2;} - { (exit 1); exit 1; }; };; + case $ac_config_target in + "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; + "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; + "Cantera/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/Makefile" ;; + "Cantera/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/Makefile" ;; + "Cantera/src/base/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/base/Makefile" ;; + "Cantera/src/zeroD/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/zeroD/Makefile" ;; + "Cantera/src/oneD/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/oneD/Makefile" ;; + "Cantera/src/converters/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/converters/Makefile" ;; + "Cantera/src/transport/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/transport/Makefile" ;; + "Cantera/src/thermo/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/thermo/Makefile" ;; + "Cantera/src/kinetics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/kinetics/Makefile" ;; + "Cantera/src/numerics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/numerics/Makefile" ;; + "Cantera/src/spectra/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/spectra/Makefile" ;; + "Cantera/src/equil/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/src/equil/Makefile" ;; + "Cantera/clib/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/clib/src/Makefile" ;; + "Cantera/fortran/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/src/Makefile" ;; + "Cantera/fortran/f77demos/f77demos.mak") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/f77demos/f77demos.mak" ;; + "Cantera/fortran/f77demos/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/fortran/f77demos/Makefile" ;; + "Cantera/matlab/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/matlab/Makefile" ;; + "Cantera/matlab/setup_matlab.py") CONFIG_FILES="$CONFIG_FILES Cantera/matlab/setup_matlab.py" ;; + "Cantera/python/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/Makefile" ;; + "Cantera/python/setup.py") CONFIG_FILES="$CONFIG_FILES Cantera/python/setup.py" ;; + "Cantera/cxx/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/Makefile" ;; + "Cantera/cxx/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/src/Makefile" ;; + "Cantera/cxx/demos/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/Makefile" ;; + "Cantera/cxx/demos/combustor/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/combustor/Makefile" ;; + "Cantera/cxx/demos/combustor/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/combustor/Makefile.install" ;; + "Cantera/cxx/demos/flamespeed/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/flamespeed/Makefile" ;; + "Cantera/cxx/demos/flamespeed/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/flamespeed/Makefile.install" ;; + "Cantera/cxx/demos/kinetics1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/kinetics1/Makefile" ;; + "Cantera/cxx/demos/kinetics1/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/kinetics1/Makefile.install" ;; + "Cantera/cxx/demos/NASA_coeffs/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/NASA_coeffs/Makefile" ;; + "Cantera/cxx/demos/NASA_coeffs/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/NASA_coeffs/Makefile.install" ;; + "Cantera/cxx/demos/rankine/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/rankine/Makefile" ;; + "Cantera/cxx/demos/rankine/Makefile.install") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/demos/rankine/Makefile.install" ;; + "Cantera/cxx/include/Cantera.mak") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/include/Cantera.mak" ;; + "Cantera/cxx/include/Cantera_bt.mak") CONFIG_FILES="$CONFIG_FILES Cantera/cxx/include/Cantera_bt.mak" ;; + "Cantera/user/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/user/Makefile" ;; + "Cantera/python/src/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/src/Makefile" ;; + "Cantera/python/examples/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/Makefile" ;; + "Cantera/python/examples/equilibrium/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/Makefile" ;; + "Cantera/python/examples/equilibrium/adiabatic_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/adiabatic_flame/Makefile" ;; + "Cantera/python/examples/equilibrium/multiphase_plasma/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/multiphase_plasma/Makefile" ;; + "Cantera/python/examples/equilibrium/simple_test/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/simple_test/Makefile" ;; + "Cantera/python/examples/equilibrium/stoich_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/equilibrium/stoich_flame/Makefile" ;; + "Cantera/python/examples/gasdynamics/isentropic/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/isentropic/Makefile" ;; + "Cantera/python/examples/gasdynamics/soundSpeed/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/soundSpeed/Makefile" ;; + "Cantera/python/examples/flames/adiabatic_flame/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/adiabatic_flame/Makefile" ;; + "Cantera/python/examples/flames/flame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame1/Makefile" ;; + "Cantera/python/examples/flames/flame2/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame2/Makefile" ;; + "Cantera/python/examples/flames/flame_fixed_T/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/flame_fixed_T/Makefile" ;; + "Cantera/python/examples/flames/free_h2_air/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/free_h2_air/Makefile" ;; + "Cantera/python/examples/flames/npflame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/npflame1/Makefile" ;; + "Cantera/python/examples/flames/stflame1/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/stflame1/Makefile" ;; + "Cantera/python/examples/fuel_cells/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/fuel_cells/Makefile" ;; + "Cantera/python/examples/liquid_vapor/critProperties/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/critProperties/Makefile" ;; + "Cantera/python/examples/liquid_vapor/rankine/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/rankine/Makefile" ;; + "Cantera/python/examples/kinetics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/kinetics/Makefile" ;; + "Cantera/python/examples/misc/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/misc/Makefile" ;; + "Cantera/python/examples/reactors/combustor_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/combustor_sim/Makefile" ;; + "Cantera/python/examples/reactors/functors_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/functors_sim/Makefile" ;; + "Cantera/python/examples/reactors/mix1_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix1_sim/Makefile" ;; + "Cantera/python/examples/reactors/mix2_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/mix2_sim/Makefile" ;; + "Cantera/python/examples/reactors/piston_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/piston_sim/Makefile" ;; + "Cantera/python/examples/reactors/reactor1_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor1_sim/Makefile" ;; + "Cantera/python/examples/reactors/reactor2_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/reactor2_sim/Makefile" ;; + "Cantera/python/examples/reactors/sensitivity_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/sensitivity_sim/Makefile" ;; + "Cantera/python/examples/reactors/surf_pfr_sim/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/surf_pfr_sim/Makefile" ;; + "Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/diamond_cvd/Makefile" ;; + "Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/catcomb_stagflow/Makefile" ;; + "Cantera/python/examples/transport/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/transport/Makefile" ;; + "Cantera/python/examples/flames/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/flames/Makefile" ;; + "Cantera/python/examples/gasdynamics/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/gasdynamics/Makefile" ;; + "Cantera/python/examples/liquid_vapor/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/liquid_vapor/Makefile" ;; + "Cantera/python/examples/reactors/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/reactors/Makefile" ;; + "Cantera/python/examples/surface_chemistry/Makefile") CONFIG_FILES="$CONFIG_FILES Cantera/python/examples/surface_chemistry/Makefile" ;; + "ext/lapack/Makefile") CONFIG_FILES="$CONFIG_FILES ext/lapack/Makefile" ;; + "ext/blas/Makefile") CONFIG_FILES="$CONFIG_FILES ext/blas/Makefile" ;; + "ext/cvode/Makefile") CONFIG_FILES="$CONFIG_FILES ext/cvode/Makefile" ;; + "ext/math/Makefile") CONFIG_FILES="$CONFIG_FILES ext/math/Makefile" ;; + "ext/recipes/Makefile") CONFIG_FILES="$CONFIG_FILES ext/recipes/Makefile" ;; + "ext/tpx/Makefile") CONFIG_FILES="$CONFIG_FILES ext/tpx/Makefile" ;; + "ext/Makefile") CONFIG_FILES="$CONFIG_FILES ext/Makefile" ;; + "ext/f2c_libs/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_libs/Makefile" ;; + "ext/f2c_blas/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_blas/Makefile" ;; + "ext/f2c_lapack/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_lapack/Makefile" ;; + "ext/f2c_math/Makefile") CONFIG_FILES="$CONFIG_FILES ext/f2c_math/Makefile" ;; + "examples/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;; + "examples/cxx/Makefile") CONFIG_FILES="$CONFIG_FILES examples/cxx/Makefile" ;; + "docs/Makefile") CONFIG_FILES="$CONFIG_FILES docs/Makefile" ;; + "tools/Makefile") CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; + "docs/Cantera.cfg") CONFIG_FILES="$CONFIG_FILES docs/Cantera.cfg" ;; + "tools/src/Makefile") CONFIG_FILES="$CONFIG_FILES tools/src/Makefile" ;; + "tools/src/sample.mak") CONFIG_FILES="$CONFIG_FILES tools/src/sample.mak" ;; + "tools/src/finish_install.py") CONFIG_FILES="$CONFIG_FILES tools/src/finish_install.py" ;; + "tools/src/package4mac") CONFIG_FILES="$CONFIG_FILES tools/src/package4mac" ;; + "tools/templates/f77/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/f77/demo.mak" ;; + "tools/templates/f90/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/f90/demo.mak" ;; + "tools/templates/cxx/demo.mak") CONFIG_FILES="$CONFIG_FILES tools/templates/cxx/demo.mak" ;; + "tools/testtools/Makefile") CONFIG_FILES="$CONFIG_FILES tools/testtools/Makefile" ;; + "data/inputs/Makefile") CONFIG_FILES="$CONFIG_FILES data/inputs/Makefile" ;; + "data/inputs/mkxml") CONFIG_FILES="$CONFIG_FILES data/inputs/mkxml" ;; + "test_problems/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/Makefile" ;; + "test_problems/cxx_ex/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cxx_ex/Makefile" ;; + "test_problems/silane_equil/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/silane_equil/Makefile" ;; + "test_problems/surfkin/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/surfkin/Makefile" ;; + "test_problems/spectroscopy/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/spectroscopy/Makefile" ;; + "test_problems/surfSolverTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/surfSolverTest/Makefile" ;; + "test_problems/diamondSurf/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf/Makefile" ;; + "test_problems/diamondSurf_dupl/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/diamondSurf_dupl/Makefile" ;; + "test_problems/ChemEquil_gri_matrix/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_matrix/Makefile" ;; + "test_problems/ChemEquil_gri_pairs/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_gri_pairs/Makefile" ;; + "test_problems/ChemEquil_ionizedGas/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_ionizedGas/Makefile" ;; + "test_problems/ChemEquil_red1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ChemEquil_red1/Makefile" ;; + "test_problems/CpJump/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/CpJump/Makefile" ;; + "test_problems/mixGasTransport/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/mixGasTransport/Makefile" ;; + "test_problems/multiGasTransport/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/multiGasTransport/Makefile" ;; + "test_problems/printUtilUnitTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/printUtilUnitTest/Makefile" ;; + "test_problems/fracCoeff/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/fracCoeff/Makefile" ;; + "test_problems/negATest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/negATest/Makefile" ;; + "test_problems/NASA9poly_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/NASA9poly_test/Makefile" ;; + "test_problems/ck2cti_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/Makefile" ;; + "test_problems/ck2cti_test/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/ck2cti_test/runtest" ;; + "test_problems/nasa9_reader/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/Makefile" ;; + "test_problems/nasa9_reader/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/nasa9_reader/runtest" ;; + "test_problems/min_python/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/Makefile" ;; + "test_problems/min_python/minDiamond/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/minDiamond/Makefile" ;; + "test_problems/min_python/negATest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/min_python/negATest/Makefile" ;; + "test_problems/pureFluidTest/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/pureFluidTest/Makefile" ;; + "test_problems/rankine_democxx/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/rankine_democxx/Makefile" ;; + "test_problems/python/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/python/Makefile" ;; + "test_problems/cathermo/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/Makefile" ;; + "test_problems/cathermo/issp/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/issp/Makefile" ;; + "test_problems/cathermo/ims/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/ims/Makefile" ;; + "test_problems/cathermo/stoichSubSSTP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/stoichSubSSTP/Makefile" ;; + "test_problems/cathermo/testIAPWS/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWS/Makefile" ;; + "test_problems/cathermo/testIAPWSPres/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSPres/Makefile" ;; + "test_problems/cathermo/testIAPWSTripP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testIAPWSTripP/Makefile" ;; + "test_problems/cathermo/testWaterPDSS/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterPDSS/Makefile" ;; + "test_problems/cathermo/testWaterTP/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/testWaterTP/Makefile" ;; + "test_problems/cathermo/HMW_test_1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_1/Makefile" ;; + "test_problems/cathermo/HMW_test_3/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_test_3/Makefile" ;; + "test_problems/cathermo/HMW_graph_GvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_GvI/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_GvI/Makefile" ;; + "test_problems/cathermo/HMW_graph_HvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_HvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_CpvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_CpvT/Makefile" ;; + "test_problems/cathermo/HMW_graph_VvT/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_graph_VvT/Makefile" ;; + "test_problems/cathermo/DH_graph_1/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_1/Makefile" ;; + "test_problems/cathermo/DH_graph_acommon/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_acommon/Makefile" ;; + "test_problems/cathermo/DH_graph_NM/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_NM/Makefile" ;; + "test_problems/cathermo/DH_graph_Pitzer/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_Pitzer/Makefile" ;; + "test_problems/cathermo/DH_graph_bdotak/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/DH_graph_bdotak/Makefile" ;; + "test_problems/cathermo/HMW_dupl_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/HMW_dupl_test/Makefile" ;; + "test_problems/cathermo/VPissp/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/VPissp/Makefile" ;; + "test_problems/cathermo/wtWater/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/cathermo/wtWater/Makefile" ;; + "test_problems/VCSnonideal/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/Makefile" ;; + "test_problems/VPsilane_test/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/Makefile" ;; + "test_problems/VPsilane_test/runtest") CONFIG_FILES="$CONFIG_FILES test_problems/VPsilane_test/runtest" ;; + "test_problems/VCSnonideal/NaCl_equil/Makefile") CONFIG_FILES="$CONFIG_FILES test_problems/VCSnonideal/NaCl_equil/Makefile" ;; + "bin/install_tsc") CONFIG_FILES="$CONFIG_FILES bin/install_tsc" ;; + + *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; esac done + # If the user did not use the arguments to specify the items to instantiate, # then the envvar interface is used. Set only those that are not. # We use the long form for the default assignment because of an extremely @@ -10077,699 +7711,550 @@ if $ac_need_defaults; then fi # Have a temporary directory for convenience. Make it in the build tree -# simply because there is no reason to put it here, and in addition, +# simply because there is no reason against having it here, and in addition, # creating and moving files from /tmp can sometimes cause problems. -# Create a temporary directory, and hook for its removal unless debugging. +# Hook for its removal unless debugging. +# Note that there is a small window in which the directory will not be cleaned: +# after its creation but before its name has been assigned to `$tmp'. $debug || { - trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0 - trap '{ (exit 1); exit 1; }' 1 2 13 15 + tmp= ac_tmp= + trap 'exit_status=$? + : "${ac_tmp:=$tmp}" + { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status +' 0 + trap 'as_fn_exit 1' 1 2 13 15 } - # Create a (secure) tmp directory for tmp files. { - tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` && - test -n "$tmp" && test -d "$tmp" + tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && + test -d "$tmp" } || { - tmp=./confstat$$-$RANDOM - (umask 077 && mkdir $tmp) -} || + tmp=./conf$$-$RANDOM + (umask 077 && mkdir "$tmp") +} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 +ac_tmp=$tmp + +# Set up the scripts for CONFIG_FILES section. +# No need to generate them if there are no CONFIG_FILES. +# This happens for instance with `./config.status config.h'. +if test -n "$CONFIG_FILES"; then + + +ac_cr=`echo X | tr X '\015'` +# On cygwin, bash can eat \r inside `` if the user requested igncr. +# But we know of no other shell where ac_cr would be empty at this +# point, so we can use a bashism as a fallback. +if test "x$ac_cr" = x; then + eval ac_cr=\$\'\\r\' +fi +ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` +if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then + ac_cs_awk_cr='\\r' +else + ac_cs_awk_cr=$ac_cr +fi + +echo 'BEGIN {' >"$ac_tmp/subs1.awk" && +_ACEOF + + { - echo "$me: cannot create a temporary directory in ." >&2 - { (exit 1); exit 1; } + echo "cat >conf$$subs.awk <<_ACEOF" && + echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && + echo "_ACEOF" +} >conf$$subs.sh || + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 +ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` +ac_delim='%!_!# ' +for ac_last_try in false false false false false :; do + . ./conf$$subs.sh || + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + + ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` + if test $ac_delim_n = $ac_delim_num; then + break + elif $ac_last_try; then + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done +rm -f conf$$subs.sh + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK && +_ACEOF +sed -n ' +h +s/^/S["/; s/!.*/"]=/ +p +g +s/^[^!]*!// +:repl +t repl +s/'"$ac_delim"'$// +t delim +:nl +h +s/\(.\{148\}\)..*/\1/ +t more1 +s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ +p +n +b repl +:more1 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t nl +:delim +h +s/\(.\{148\}\)..*/\1/ +t more2 +s/["\\]/\\&/g; s/^/"/; s/$/"/ +p +b +:more2 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t delim +' >$CONFIG_STATUS || ac_write_fail=1 +rm -f conf$$subs.awk +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACAWK +cat >>"\$ac_tmp/subs1.awk" <<_ACAWK && + for (key in S) S_is_set[key] = 1 + FS = "" + +} +{ + line = $ 0 + nfields = split(line, field, "@") + substed = 0 + len = length(field[1]) + for (i = 2; i < nfields; i++) { + key = field[i] + keylen = length(key) + if (S_is_set[key]) { + value = S[key] + line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) + len += length(value) + length(field[++i]) + substed = 1 + } else + len += 1 + keylen + } + + print line } +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then + sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" +else + cat +fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \ + || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 _ACEOF -cat >>$CONFIG_STATUS <<_ACEOF +# VPATH may cause trouble with some makes, so we remove sole $(srcdir), +# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ +h +s/// +s/^/:/ +s/[ ]*$/:/ +s/:\$(srcdir):/:/g +s/:\${srcdir}:/:/g +s/:@srcdir@:/:/g +s/^:*// +s/:*$// +x +s/\(=[ ]*\).*/\1/ +G +s/\n// +s/^[^=]*=[ ]*$// +}' +fi -# -# CONFIG_FILES section. -# - -# No need to generate the scripts if there are no CONFIG_FILES. -# This happens for instance when ./config.status config.h -if test -n "\$CONFIG_FILES"; then - # Protect against being on the right side of a sed subst in config.status. - sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g; - s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' 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"could not create $ac_file" "$LINENO" 5 fi else - cat $tmp/config.h - rm -f $tmp/config.h + $as_echo "/* $configure_input */" \ + && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \ + || as_fn_error $? "could not create -" "$LINENO" 5 fi -done -_ACEOF + ;; -cat >>$CONFIG_STATUS <<\_ACEOF -{ (exit 0); exit 0; } + esac + +done # for ac_tag + + +as_fn_exit 0 _ACEOF -chmod +x $CONFIG_STATUS ac_clean_files=$ac_clean_files_save +test $ac_write_fail = 0 || + as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 + # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. @@ -10789,7 +8274,11 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || { (exit 1); exit 1; } + $ac_cs_success || as_fn_exit 1 +fi +if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 +$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi # ) diff --git a/configure.in b/configure.in index 2b4c37672..6cc3fc616 100755 --- a/configure.in +++ b/configure.in @@ -890,7 +890,6 @@ fi case $ac_sys_system in Linux) NEED_F2C=1 ;; esac -NEED_F2C= # # Create a variable build_f2c_lib that determines whether From 5b03c282d8e7f555e1b6acf53020321c41a887a8 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 8 Nov 2011 23:48:14 +0000 Subject: [PATCH 429/446] Fixed an error in the install script. --- Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile.in b/Makefile.in index d683ad86f..b672a59d6 100755 --- a/Makefile.in +++ b/Makefile.in @@ -197,7 +197,7 @@ finish-install: @INSTALL@ -d @ct_dir@/apps/include @INSTALL@ -d @ct_dir@/apps/bin @INSTALL@ -d @ct_dir@/apps/lib - -( cd @ct_dir/apps ; -$(RMDIRTREE) lib/* include/* bin/* ) + -( cd @ct_dir@/apps ; -$(RMDIRTREE) lib/* include/* bin/* ) -( cd bin ; @INSTALL@ -c exp3to2.sh "@ct_bindir@" ) -( cd bin ; @INSTALL@ -c csvdiff "@ct_bindir@" ) -( cd bin ; @INSTALL@ -c install_tsc "@ct_bindir@" ) From 8742d6addb3ae93d3273290f7ce3e202a2f9b59b Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 9 Nov 2011 18:39:51 +0000 Subject: [PATCH 430/446] Added MolarityIonicVPSS to the ThermoFactory --- Cantera/src/thermo/MolarityIonicVPSSTP.cpp | 9 ++++----- Cantera/src/thermo/ThermoFactory.cpp | 4 ++++ 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp index 1e7831ba9..99f715427 100644 --- a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp @@ -261,10 +261,9 @@ namespace Cantera { */ stemp = thermoNode.attrib("model"); string formString = lowercase(stemp); - if (formString != "molarityionicvpss") { + if (formString != "molarityionicvpss" && formString != "molarityionicvpsstp") { throw CanteraError("MolarityIonicVPSSTP::constructPhaseXML", - "model name isn't MolarityIonicVPSS: " + formString); - + "model name isn't MolarityIonicVPSSTP: " + formString); } /* @@ -713,9 +712,9 @@ namespace Cantera { XML_Node& thermoNode = phaseNode.child("thermo"); std::string mStringa = thermoNode.attrib("model"); std::string mString = lowercase(mStringa); - if (mString != "molarityionicvpss") { + if (mString != "molarityionicvpss" && mString != "molarityionicvpsstp") { throw CanteraError(subname.c_str(), - "Unknown thermo model: " + mStringa + " - This object only knows \"MolarityIonicVPSS\" "); + "Unknown thermo model: " + mStringa + " - This object only knows \"MolarityIonicVPSSTP\" "); } /* * Go get all of the coefficients and factors in the diff --git a/Cantera/src/thermo/ThermoFactory.cpp b/Cantera/src/thermo/ThermoFactory.cpp index 0cf6338fc..ea51c3f6d 100644 --- a/Cantera/src/thermo/ThermoFactory.cpp +++ b/Cantera/src/thermo/ThermoFactory.cpp @@ -167,6 +167,10 @@ namespace Cantera { th = new RedlichKisterVPSSTP(); break; + case cMolarityIonicVPSSTP: + th = new MolarityIonicVPSSTP(); + break; + case cPhaseCombo_Interaction: th = new PhaseCombo_Interaction(); break; From cc0b37123e0217432fef4c59c891b078eed4173c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 2 Dec 2011 02:31:54 +0000 Subject: [PATCH 431/446] Started to work on documentation. --- Cantera/src/transport/SimpleTransport.h | 44 +++++++++++++++++++++++-- 1 file changed, 41 insertions(+), 3 deletions(-) diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index b82d6120b..2d7c2734d 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -32,7 +32,7 @@ namespace Cantera { class LiquidTransportParams; - //! Class LiquidTransport implements mixture-averaged transport + //! Class SimpleTransport implements mixture-averaged transport //! properties for liquid phases. /*! * The model is based on that @@ -116,8 +116,46 @@ namespace Cantera { * * The viscosity calculation may be broken down into two parts. * In the first part, the viscosity of the pure species are calculated - * In the second part, a mixing rule is applied, based on the - * Wilkes correlation, to yield the mixture viscosity. + * In the second part, a mixing rule is applied. There are two mixing rules. + * Solvent-only and mixture-averaged. + * + * For the solvent-only mixing rule, we use the pure species viscosity calculated for + * the solvent as the viscosity of the entire mixture. For the mixture averaged rule + * we do a mole fraction based average of the pure species viscosities: + * + * Solvent-only: + * \f[ + * \mu = \mu_0 + * \f] + * Mixture-average: + * \f[ + * \mu = \sum_k {\mu_k X_k} + * \f] + * + * + *

Calculate of the Binary Diffusion Coefficients

+ * + * The binary diffusion coefficients are obtained from the pure species diffusion coefficients + * using an additive process + * + * \f[ + * D_{i,j} = \frac{1}{2} \left( D^0_i(T) + D^0_j(T) \right) + * \f] + * + * + * + * + *

Electrical Mobilities

+ * + * The mobility \f$ \mu^e_k \f$ is calculated from the diffusion coefficient using the Einstein relation. + * + * \f[ + * \mu^e_k = \frac{F D_k}{R T} + * \f] + * + * The diffusion coefficients, \f$ D_k \f$ , is calculated from a call to the mixture diffusion + * coefficient routine. + * * * @ingroup tranprops * From f59c07606a3d617fb4eb6a9b4857689ab30e0ea6 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 3 Dec 2011 03:32:18 +0000 Subject: [PATCH 432/446] Added diffusion velocity returns to SimpleTransport. Worked on documentation. --- Cantera/src/transport/LiquidTransport.h | 3 +- Cantera/src/transport/SimpleTransport.cpp | 117 ++++++++++++++++++++-- Cantera/src/transport/SimpleTransport.h | 115 +++++++++++++++++++++ 3 files changed, 224 insertions(+), 11 deletions(-) diff --git a/Cantera/src/transport/LiquidTransport.h b/Cantera/src/transport/LiquidTransport.h index 352687c47..080790f5f 100644 --- a/Cantera/src/transport/LiquidTransport.h +++ b/Cantera/src/transport/LiquidTransport.h @@ -482,8 +482,7 @@ namespace Cantera { doublereal* current); - //! Get the species diffusive velocities wrt to - //! the averaged velocity, + //! Get the species diffusive velocities wrt to the averaged velocity, //! given the gradients in mole fraction and temperature /*! * The average velocity can be computed on a mole-weighted diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index 6c9b62c64..cfd84f401 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -598,6 +598,104 @@ namespace Cantera { dt[k] = 0.0; } } + + //==================================================================================================================== + //! Get the species diffusive velocities wrt to the averaged velocity, + //! given the gradients in mole fraction and temperature + /*! + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * + * Units for the returned velocities are m s-1. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + void SimpleTransport::getSpeciesVdiff(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + doublereal* Vdiff) { + set_Grad_T(grad_T); + set_Grad_X(grad_X); + const doublereal* y = m_thermo->massFractions(); + const doublereal rho = m_thermo->density(); + + getSpeciesFluxesExt(m_nsp, DATA_PTR(Vdiff)); + + for (int n = 0; n < m_nDim; n++) { + for (int k = 0; k < m_nsp; k++) { + if (y[k] > 1.0E-200) { + Vdiff[n * m_nsp + k] *= 1.0 / (rho * y[k]); + } else { + Vdiff[n * m_nsp + k] = 0.0; + } + } + } + } + //================================================================================================ + // Get the species diffusive velocities wrt to the averaged velocity, + // given the gradients in mole fraction, temperature and electrostatic potential. + /* + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * + * Units for the returned velocities are m s-1. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * (length = ndim) + * @param Vdiff Output of the species diffusion velocities + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + void SimpleTransport::getSpeciesVdiffES(int ndim, const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, const doublereal* grad_Phi, + doublereal* Vdiff) { + set_Grad_T(grad_T); + set_Grad_X(grad_X); + set_Grad_V(grad_Phi); + const doublereal* y = m_thermo->massFractions(); + const doublereal rho = m_thermo->density(); + + getSpeciesFluxesExt(m_nsp, DATA_PTR(Vdiff)); + + for (int n = 0; n < m_nDim; n++) { + for (int k = 0; k < m_nsp; k++) { + if (y[k] > 1.0E-200) { + Vdiff[n * m_nsp + k] *= 1.0 / (rho * y[k]); + } else { + Vdiff[n * m_nsp + k] = 0.0; + } + } + } + } //================================================================================================ // Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, // given the gradients in mole fraction and temperature @@ -673,33 +771,34 @@ namespace Cantera { const array_fp& mw = m_thermo->molecularWeights(); const doublereal* y = m_thermo->massFractions(); - doublereal conc = m_thermo->molarDensity(); + doublereal concTotal = m_thermo->molarDensity(); // Unroll wrt ndim - vector_fp sum(m_nDim, 0.0); - + if (doMigration_) { double FRT = ElectronCharge / (Boltzmann * m_temp); for (n = 0; n < m_nDim; n++) { + rhoVc[n] = 0.0; for (k = 0; k < m_nsp; k++) { - fluxes[n*ldf + k] = -conc * mw[k] * m_spwork[k] * + fluxes[n*ldf + k] = - concTotal * mw[k] * m_spwork[k] * ( m_Grad_X[n*m_nsp + k] + FRT * m_molefracs[k] * m_chargeSpecies[k] * m_Grad_V[n]); - sum[n] += fluxes[n*ldf + k]; + rhoVc[n] += fluxes[n*ldf + k]; } } } else { for (n = 0; n < m_nDim; n++) { + rhoVc[n] = 0.0; for (k = 0; k < m_nsp; k++) { - fluxes[n*ldf + k] = -conc * mw[k] * m_spwork[k] * m_Grad_X[n*m_nsp + k]; - sum[n] += fluxes[n*ldf + k]; + fluxes[n*ldf + k] = - concTotal * mw[k] * m_spwork[k] * m_Grad_X[n*m_nsp + k]; + rhoVc[n] += fluxes[n*ldf + k]; } } } - // add correction flux to enforce sum to zero + // Add correction flux to enforce sum to zero for (n = 0; n < m_nDim; n++) { for (k = 0; k < m_nsp; k++) { - fluxes[n*ldf + k] -= y[k]*sum[n]; + fluxes[n*ldf + k] -= y[k] * rhoVc[n]; } } } diff --git a/Cantera/src/transport/SimpleTransport.h b/Cantera/src/transport/SimpleTransport.h index 2d7c2734d..3c60f1b90 100644 --- a/Cantera/src/transport/SimpleTransport.h +++ b/Cantera/src/transport/SimpleTransport.h @@ -156,6 +156,53 @@ namespace Cantera { * The diffusion coefficients, \f$ D_k \f$ , is calculated from a call to the mixture diffusion * coefficient routine. * + *

Species Diffusive Fluxes

+ * + * The diffusive mass flux of species \e k is computed from the following + * formula + * + * Usually the specified solution average velocity is the mass averaged velocity. + * This is changed in some subclasses, however. + * + * \f[ + * j_k = - c^T M_k D_k \nabla X_k - \rho Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * \rho V_c = - \sum_j {c^T M_j D_j \nabla X_j} + * \f] + * + * In the above equation, \f$ D_k \f$ is the mixture diffusivity for species k calculated for the current + * conditions, which may depend on T, P, and X_k. \f$ C^T \f$ is the total concentration of the phase. + * + * When this is electrical migration, the formulas above are enhanced to + * + * \f[ + * j_k = - C^T M_k D_k \nabla X_k + F C^T M_k \frac{D_k}{ R T } X_k z_k \nabla V - \rho Y_k V_c + * \f] + * + * where V_c is the correction velocity + * + * \f[ + * \rho V_c = - \sum_j {c^T M_j D_j \nabla X_j} + \sum_j F C^T M_j \frac{D_j}{ R T } X_j z_j \nabla V + * \f] + * + * + *

Species Diffusional Velocities

+ * + * Species diffusional velocities are calculated from the species diffusional fluxes, within this object, + * using the following formula for the diffusional velocity of the kth species, \f$ V_k^d \f$ + * + * \f[ + * j_k = \rho Y_k V_k^d + * \f] + * + * + * TODO + * This object has to be made compatible with different types of reference velocities. Right now, elements + * of the formulas are only compatible with the mass-averaged velocity. * * @ingroup tranprops * @@ -364,6 +411,69 @@ namespace Cantera { */ virtual void set_Grad_X(const doublereal * const grad_X); + //! Get the species diffusive velocities wrt to the averaged velocity, + //! given the gradients in mole fraction and temperature + /*! + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * + * Units for the returned velocities are m s-1. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param Vdiff Output of the diffusive velocities. + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + virtual void getSpeciesVdiff(int ndim, + const doublereal* grad_T, + int ldx, + const doublereal* grad_X, + int ldf, + doublereal* Vdiff); + + //! Get the species diffusive velocities wrt to the averaged velocity, + //! given the gradients in mole fraction, temperature and electrostatic potential. + /*! + * The average velocity can be computed on a mole-weighted + * or mass-weighted basis, or the diffusion velocities may + * be specified as relative to a specific species (i.e. a + * solvent) all according to the velocityBasis input parameter. + * + * Units for the returned velocities are m s-1. + * + * @param ndim Number of dimensions in the flux expressions + * @param grad_T Gradient of the temperature + * (length = ndim) + * @param ldx Leading dimension of the grad_X array + * (usually equal to m_nsp but not always) + * @param grad_X Gradients of the mole fraction + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + * @param ldf Leading dimension of the fluxes array + * (usually equal to m_nsp but not always) + * @param grad_Phi Gradients of the electrostatic potential + * (length = ndim) + * @param Vdiff Output of the species diffusion velocities + * Flat vector with the m_nsp in the inner loop. + * length = ldx * ndim + */ + virtual void getSpeciesVdiffES(int ndim, const doublereal* grad_T, + int ldx, const doublereal* grad_X, + int ldf, const doublereal* grad_Phi, + doublereal* Vdiff); + + //! Get the species diffusive mass fluxes wrt to the specified solution averaged velocity, //! given the gradients in mole fraction and temperature /*! @@ -723,6 +833,8 @@ namespace Cantera { */ vector_fp m_spwork; + vector_fp m_fluxes; + private: @@ -755,6 +867,9 @@ namespace Cantera { */ int m_nDim; + //! Temporary variable that stores the rho Vc value + double rhoVc[3]; + private: //! Throw an exception if this method is invoked. From 81d315e562bbbf090315410767653953b4942d94 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 14 Dec 2011 16:03:27 +0000 Subject: [PATCH 433/446] Start of a new Tortuosity treatment -> taking it into Cantera in a formal way. --- Cantera/src/transport/Makefile.in | 6 +- Cantera/src/transport/SimpleTransport.cpp | 48 ++++++- Cantera/src/transport/Tortuosity.h | 70 +++++++---- Cantera/src/transport/TortuosityBase.cpp | 96 ++++++++++++++ Cantera/src/transport/TortuosityBase.h | 108 ++++++++++++++++ Cantera/src/transport/TortuosityBruggeman.cpp | 99 +++++++++++++++ Cantera/src/transport/TortuosityBruggeman.h | 114 +++++++++++++++++ Cantera/src/transport/TortuosityMaxwell.cpp | 99 +++++++++++++++ Cantera/src/transport/TortuosityMaxwell.h | 118 ++++++++++++++++++ .../src/transport/TortuosityPercolation.cpp | 105 ++++++++++++++++ Cantera/src/transport/TortuosityPercolation.h | 108 ++++++++++++++++ 11 files changed, 937 insertions(+), 34 deletions(-) create mode 100644 Cantera/src/transport/TortuosityBase.cpp create mode 100644 Cantera/src/transport/TortuosityBase.h create mode 100644 Cantera/src/transport/TortuosityBruggeman.cpp create mode 100644 Cantera/src/transport/TortuosityBruggeman.h create mode 100644 Cantera/src/transport/TortuosityMaxwell.cpp create mode 100644 Cantera/src/transport/TortuosityMaxwell.h create mode 100644 Cantera/src/transport/TortuosityPercolation.cpp create mode 100644 Cantera/src/transport/TortuosityPercolation.h diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in index 73e74392f..4ec69c96a 100644 --- a/Cantera/src/transport/Makefile.in +++ b/Cantera/src/transport/Makefile.in @@ -37,12 +37,14 @@ CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG) TRAN_OBJ = TransportFactory.o MultiTransport.o MixTransport.o MMCollisionInt.o \ SolidTransport.o DustyGasTransport.o TransportBase.o WaterTransport.o \ SimpleTransport.o LiquidTransportData.o LiquidTransportParams.o LiquidTranInteraction.o \ - TransportParams.o + TransportParams.o \ + TortuosityBase.o TortuosityBruggeman.o TortuosityPercolation.o TortuosityMaxwell.o TRAN_H = TransportFactory.h MultiTransport.h MixTransport.h \ MMCollisionInt.h SolidTransport.h DustyGasTransport.h \ TransportBase.h L_matrix.h TransportParams.h WaterTransport.h \ - SimpleTransport.h LiquidTranInteraction.h Tortuosity.h + SimpleTransport.h LiquidTranInteraction.h Tortuosity.h \ + TortuosityBase.h TortuosityBruggeman.h TortuosityPercolation.h TortuosityMaxwell.h ifeq ($(do_electro),1) do_issp = 1 diff --git a/Cantera/src/transport/SimpleTransport.cpp b/Cantera/src/transport/SimpleTransport.cpp index cfd84f401..817b6527d 100644 --- a/Cantera/src/transport/SimpleTransport.cpp +++ b/Cantera/src/transport/SimpleTransport.cpp @@ -771,10 +771,12 @@ namespace Cantera { const array_fp& mw = m_thermo->molecularWeights(); const doublereal* y = m_thermo->massFractions(); + doublereal concTotal = m_thermo->molarDensity(); + // Unroll wrt ndim - + if (doMigration_) { double FRT = ElectronCharge / (Boltzmann * m_temp); for (n = 0; n < m_nDim; n++) { @@ -795,11 +797,47 @@ namespace Cantera { } } - // Add correction flux to enforce sum to zero - for (n = 0; n < m_nDim; n++) { - for (k = 0; k < m_nsp; k++) { - fluxes[n*ldf + k] -= y[k] * rhoVc[n]; + if (m_velocityBasis == VB_MASSAVG) { + for (n = 0; n < m_nDim; n++) { + rhoVc[n] = 0.0; + for (k = 0; k < m_nsp; k++) { + rhoVc[n] += fluxes[n*ldf + k]; + } } + for (n = 0; n < m_nDim; n++) { + for (k = 0; k < m_nsp; k++) { + fluxes[n*ldf + k] -= y[k] * rhoVc[n]; + } + } + } else if (m_velocityBasis == VB_MOLEAVG) { + for (n = 0; n < m_nDim; n++) { + rhoVc[n] = 0.0; + for (k = 0; k < m_nsp; k++) { + rhoVc[n] += fluxes[n*ldf + k] / mw[k]; + } + } + for (n = 0; n < m_nDim; n++) { + for (k = 0; k < m_nsp; k++) { + fluxes[n*ldf + k] -= m_molefracs[k] * rhoVc[n] * mw[k]; + } + } + } else if (m_velocityBasis >= 0) { + for (n = 0; n < m_nDim; n++) { + rhoVc[n] = - fluxes[n*ldf + m_velocityBasis] / mw[m_velocityBasis]; + for (k = 0; k < m_nsp; k++) { + rhoVc[n] += fluxes[n*ldf + k] / mw[k]; + } + } + for (n = 0; n < m_nDim; n++) { + for (k = 0; k < m_nsp; k++) { + fluxes[n*ldf + k] -= m_molefracs[k] * rhoVc[n] * mw[k]; + } + fluxes[n*ldf + m_velocityBasis] = 0.0; + } + + } else { + throw CanteraError("SimpleTransport::getSpeciesFluxesExt()", + "unknown velocity basis"); } } //================================================================================================ diff --git a/Cantera/src/transport/Tortuosity.h b/Cantera/src/transport/Tortuosity.h index b8b34b5d5..d3b1d4744 100644 --- a/Cantera/src/transport/Tortuosity.h +++ b/Cantera/src/transport/Tortuosity.h @@ -1,38 +1,54 @@ + /** - * @file Tortuosity.h - * Class to compute the increase in diffusive path length associated with - * tortuous path diffusion through, for example, porous media. + * @file TortuosityBruggeman.h + * Class to compute the increase in diffusive path length in porous media + * assuming the Bruggeman exponent relation */ +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ +#ifndef CT_TORTUOSITYBRUGGEMAN_H +#define CT_TORTUOSITYBRUGGEMAN_H + + namespace Cantera { -/** - * Class to compute the increase in diffusive path length associated with - * tortuous path diffusion through, for example, porous media. - * This base class implementation relates tortuosity to volume fraction - * through a power-law relationship that goes back to Bruggemann. The - * exponent is referred to as the Bruggemann exponent. - * - * Note that the total diffusional flux is generally written as - * - * \f[ - * \frac{ \phi C_T D_i \nabla X_i }{ \tau^2 } - * \f] - * - * where \f$ \phi \f$ is the volume fraction of the transported phase, - * \f$ \tau \f$ is referred to as the tortuosity. (Other variables are - * \f$ C_T \f$, the total concentration, \f$ D_i \f$, the diffusion - * coefficient, and \f$ X_i \f$, the mole fraction with Fickian - * transport assumed.) - * - * The tortuosity comes into play in conjunction the the - - */ - class Tortuosity { + //! Specific Class to handle tortuosity corrections for diffusive transport + //! in porous media using the Bruggeman exponent + /*! + * Class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + * This base class implementation relates tortuosity to volume fraction + * through a power-law relationship that goes back to Bruggemann. The + * exponent is referred to as the Bruggemann exponent. + * + * Note that the total diffusional flux is generally written as + * + * \f[ + * \frac{ \phi C_T D_i \nabla X_i }{ \tau^2 } + * \f] + * + * where \f$ \phi \f$ is the volume fraction of the transported phase, + * \f$ \tau \f$ is referred to as the tortuosity. (Other variables are + * \f$ C_T \f$, the total concentration, \f$ D_i \f$, the diffusion + * coefficient, and \f$ X_i \f$, the mole fraction with Fickian + * transport assumed.) + * + * The tortuosity comes into play in conjunction the the + */ + class TortuosityBruggeman { public: //! Default constructor uses Bruggemann exponent of 1.5 - Tortuosity( double setPower = 1.5 ) : expBrug_(setPower) { + TortuosityBruggeman(double setPower = 1.5 ) : expBrug_(setPower) { } //! The tortuosity factor models the effective increase in the diff --git a/Cantera/src/transport/TortuosityBase.cpp b/Cantera/src/transport/TortuosityBase.cpp new file mode 100644 index 000000000..4fe734dbb --- /dev/null +++ b/Cantera/src/transport/TortuosityBase.cpp @@ -0,0 +1,96 @@ +/** + * @file TortuosityBase.cpp + * Base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ + +#include "TortuosityBase.h" +#include "ctexceptions.h" + +#include + +namespace Cantera { + //==================================================================================================================== + static void err(const std::string r) { + throw Cantera::CanteraError("TortuosityBase", "Error calling base class " + r); + } + //==================================================================================================================== + // Default constructor + TortuosityBase::TortuosityBase() + { + } + //==================================================================================================================== + // Copy Constructor + /* + * @param right Object to be copied + */ + TortuosityBase::TortuosityBase(const TortuosityBase &right) + { + *this = right; + } + //==================================================================================================================== + // Default destructor for TortuosityBase + TortuosityBase::~TortuosityBase() { + + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + TortuosityBase & TortuosityBase::operator=(const TortuosityBase &right) { + if (&right == this) { + return *this; + } + return *this; + } + //==================================================================================================================== + // Duplication operator + /* + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + TortuosityBase * TortuosityBase::duplMyselfAsTortuosityBase() const { + TortuosityBase * tb = new TortuosityBase(*this); + return tb; + } + //==================================================================================================================== + // The tortuosity factor models the effective increase in the diffusive transport length. + /* + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + doublereal TortuosityBase::tortuosityFactor(doublereal porosity) { + err("tortuosityFactor"); + return 0.0; + } + //==================================================================================================================== + // The McMillan number is the ratio of the flux-like variable to the value it would have without porous flow. + /* + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + doublereal TortuosityBase::McMillanFactor(doublereal porosity) { + err("McMillanFactor"); + return 0.0; + } + //==================================================================================================================== +} diff --git a/Cantera/src/transport/TortuosityBase.h b/Cantera/src/transport/TortuosityBase.h new file mode 100644 index 000000000..5b4c2dacc --- /dev/null +++ b/Cantera/src/transport/TortuosityBase.h @@ -0,0 +1,108 @@ +/** + * @file TortuosityBase.h + * Virtual base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ +#ifndef CT_TORTUOSITYBASE_H +#define CT_TORTUOSITYBASE_H + +#include "ct_defs.h" + + +namespace Cantera { + + //! Base case to handle tortuosity corrections for diffusive transport + //! in porous media + /*! + * Class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + * This base class implementation relates tortuosity to volume fraction + * through a power-law relationship that goes back to Bruggemann. The + * exponent is referred to as the Bruggemann exponent. + * + * Note that the total diffusional flux is generally written as + * + * \f[ + * \frac{ \phi C_T D_i \nabla X_i }{ \tau^2 } + * \f] + * + * where \f$ \phi \f$ is the volume fraction of the transported phase, + * \f$ \tau \f$ is referred to as the tortuosity. (Other variables are + * \f$ C_T \f$, the total concentration, \f$ D_i \f$, the diffusion + * coefficient, and \f$ X_i \f$, the mole fraction with Fickian + * transport assumed.) + * + * The tortuosity comes into play in conjunction the the + */ + class TortuosityBase { + + public: + //! Default constructor uses Bruggemann exponent of 1.5 + TortuosityBase(); + + //! Copy Constructor + /*! + * @param right Object to be copied + */ + TortuosityBase(const TortuosityBase &right); + + //! Default destructor for TortuosityBase + virtual ~TortuosityBase(); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + TortuosityBase & operator=(const TortuosityBase &right); + + //! Duplication operator + /*! + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + virtual TortuosityBase * duplMyselfAsTortuosityBase() const; + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /*! + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + virtual doublereal tortuosityFactor(doublereal porosity); + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + virtual doublereal McMillanFactor(doublereal porosity); + + protected: + + }; + + + +} + +#endif + diff --git a/Cantera/src/transport/TortuosityBruggeman.cpp b/Cantera/src/transport/TortuosityBruggeman.cpp new file mode 100644 index 000000000..ca88e38cf --- /dev/null +++ b/Cantera/src/transport/TortuosityBruggeman.cpp @@ -0,0 +1,99 @@ +/** + * @file TortuosityBase.cpp + * Base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ + +#include "TortuosityBruggeman.h" +#include "ctexceptions.h" + +#include + +namespace Cantera { + + //==================================================================================================================== + // Default constructor + TortuosityBruggeman::TortuosityBruggeman(doublereal setPower) : + TortuosityBase(), + expBrug_(setPower) + { + } + //==================================================================================================================== + // Copy Constructor + /* + * @param right Object to be copied + */ + TortuosityBruggeman::TortuosityBruggeman(const TortuosityBruggeman &right) : + TortuosityBase(), + expBrug_(right.expBrug_) + { + *this = right; + } + //==================================================================================================================== + // Default destructor for TortuosityBruggeman + TortuosityBruggeman::~TortuosityBruggeman() { + + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + TortuosityBruggeman & TortuosityBruggeman::operator=(const TortuosityBruggeman &right) { + if (&right == this) { + return *this; + } + TortuosityBase::operator=(right); + + expBrug_ = right.expBrug_; + + return *this; + } + //==================================================================================================================== + // Duplication operator + /* + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + TortuosityBase * TortuosityBruggeman::duplMyselfAsTortuosityBase() const { + TortuosityBruggeman * tb = new TortuosityBruggeman(*this); + return dynamic_cast(tb); + } + //==================================================================================================================== + // The tortuosity factor models the effective increase in the diffusive transport length. + /* + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + doublereal TortuosityBruggeman::tortuosityFactor(doublereal porosity) { + return pow(porosity, expBrug_ - 1.0); + } + //==================================================================================================================== + // The McMillan number is the ratio of the flux-like variable to the value it would have without porous flow. + /* + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + doublereal TortuosityBruggeman::McMillanFactor(doublereal porosity) { + return pow(porosity, expBrug_); + } + //==================================================================================================================== +} diff --git a/Cantera/src/transport/TortuosityBruggeman.h b/Cantera/src/transport/TortuosityBruggeman.h new file mode 100644 index 000000000..d20e10665 --- /dev/null +++ b/Cantera/src/transport/TortuosityBruggeman.h @@ -0,0 +1,114 @@ +/** + * @file TortuosityBase.h + * Virtual base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ +#ifndef CT_TORTUOSITYBRUGGEMAN_H +#define CT_TORTUOSITYBRUGGEMAN_H + +#include "TortuosityBase.h" + + +namespace Cantera { + + //! Base case to handle tortuosity corrections for diffusive transport + //! in porous media using the Bruggeman exponential approximation + /*! + * Class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + * This base class implementation relates tortuosity to volume fraction + * through a power-law relationship that goes back to Bruggemann. The + * exponent is referred to as the Bruggemann exponent. + * + * Note that the total diffusional flux is generally written as + * + * \f[ + * \frac{ \phi C_T D_i \nabla X_i }{ \tau^2 } + * \f] + * + * where \f$ \phi \f$ is the volume fraction of the transported phase, + * \f$ \tau \f$ is referred to as the tortuosity. (Other variables are + * \f$ C_T \f$, the total concentration, \f$ D_i \f$, the diffusion + * coefficient, and \f$ X_i \f$, the mole fraction with Fickian + * transport assumed.) + * + * The tortuosity comes into play in conjunction the the + */ + class TortuosityBruggeman : public TortuosityBase { + + public: + //! Default constructor uses Bruggemann exponent of 1.5 + /*! + * @param setPower Exponent in the Bruggeman factor. The default is 1.5 + */ + TortuosityBruggeman(doublereal setPower = 1.5); + + //! Copy Constructor + /*! + * @param right Object to be copied + */ + TortuosityBruggeman(const TortuosityBruggeman &right); + + //! Default destructor for TortuosityBruggeman + virtual ~TortuosityBruggeman(); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + TortuosityBruggeman & operator=(const TortuosityBruggeman &right); + + //! Duplication operator + /*! + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + virtual TortuosityBase * duplMyselfAsTortuosityBase() const; + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /*! + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + virtual doublereal tortuosityFactor(doublereal porosity); + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + virtual doublereal McMillanFactor(doublereal porosity); + + + protected: + //! Bruggemann exponent: power to which the tortuosity depends on the volume fraction + doublereal expBrug_; + + }; + + + +} + +#endif + diff --git a/Cantera/src/transport/TortuosityMaxwell.cpp b/Cantera/src/transport/TortuosityMaxwell.cpp new file mode 100644 index 000000000..782567202 --- /dev/null +++ b/Cantera/src/transport/TortuosityMaxwell.cpp @@ -0,0 +1,99 @@ +/** + * @file TortuosityBase.cpp + * Base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ + +#include "TortuosityMaxwell.h" +#include "ctexceptions.h" + +#include + +namespace Cantera { + + //==================================================================================================================== + // Default constructor + TortuosityMaxwell::TortuosityMaxwell(doublereal relativeConductivities) : + TortuosityBase(), + relativeConductivities_(relativeConductivities) + { + } + //==================================================================================================================== + // Copy Constructor + /* + * @param right Object to be copied + */ + TortuosityMaxwell::TortuosityMaxwell(const TortuosityMaxwell &right) : + TortuosityBase(), + relativeConductivities_(right.relativeConductivities_) + { + *this = right; + } + //==================================================================================================================== + // Default destructor for TortuosityMaxwell + TortuosityMaxwell::~TortuosityMaxwell() { + + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + TortuosityMaxwell & TortuosityMaxwell::operator=(const TortuosityMaxwell &right) { + if (&right == this) { + return *this; + } + TortuosityBase::operator=(right); + + relativeConductivities_ = right.relativeConductivities_; + + return *this; + } + //==================================================================================================================== + // Duplication operator + /* + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + TortuosityBase * TortuosityMaxwell::duplMyselfAsTortuosityBase() const { + TortuosityMaxwell * tb = new TortuosityMaxwell(*this); + return dynamic_cast(tb); + } + //==================================================================================================================== + // The tortuosity factor models the effective increase in the diffusive transport length. + /* + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + */ + doublereal TortuosityMaxwell::tortuosityFactor(doublereal porosity) { + return McMillanFactor(porosity) / porosity; + } + //==================================================================================================================== + // The McMillan number is the ratio of the flux-like variable to the value it would have without porous flow. + /* + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + doublereal TortuosityMaxwell::McMillanFactor(doublereal porosity) { + doublereal tmp = 1 + 3 * ( 1.0 - porosity ) * ( relativeConductivities_ - 1.0 ) / ( relativeConductivities_ + 2 ); + return tmp; + } + //==================================================================================================================== +} diff --git a/Cantera/src/transport/TortuosityMaxwell.h b/Cantera/src/transport/TortuosityMaxwell.h new file mode 100644 index 000000000..861145fad --- /dev/null +++ b/Cantera/src/transport/TortuosityMaxwell.h @@ -0,0 +1,118 @@ +/** + * @file TortuosityBase.h + * Virtual base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ +#ifndef CT_TORTUOSITYBRUGGEMAN_H +#define CT_TORTUOSITYBRUGGEMAN_H + +#include "TortuosityBase.h" + + +namespace Cantera { + + //! Maxwell model for tortuosity + /*! + * + * This class implements transport coefficient corrections + * appropriate for porous media with a dispersed phase. + * This model goes back to Maxwell. The formula for the + * conductivity is expressed in terms of the volume fraction + * of the continuous phase, \f$ \phi \f$, and the relative + * conductivities of the dispersed and continuous phases, + * \f$ r = \kappa_d / \kappa_0 \f$. For dilute particle + * suspensions the effective conductivity is + * + * \f[ + * \kappa / \kappa_0 = 1 + 3 ( 1 - \phi ) ( r - 1 ) / ( r + 2 ) + * + O(\phi^2) + * \f] + * + * The class is derived from the TortuosityBase class. + * + */ + class TortuosityMaxwell : public TortuosityBase { + + public: + //! Default constructor uses Maxwelln exponent of 1.5 + /*! + * @param setPower Exponent in the Maxwell factor. The default is 1.5 + */ + TortuosityMaxwell(double relativeConductivites = 0.0); + + //! Copy Constructor + /*! + * @param right Object to be copied + */ + TortuosityMaxwell(const TortuosityMaxwell &right); + + //! Default destructor for TortuosityMaxwell + virtual ~TortuosityMaxwell(); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + TortuosityMaxwell & operator=(const TortuosityMaxwell &right); + + //! Duplication operator + /*! + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + virtual TortuosityBase * duplMyselfAsTortuosityBase() const; + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /*! + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + virtual doublereal tortuosityFactor(doublereal porosity); + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /** + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + virtual doublereal McMillanFactor(doublereal porosity); + + + protected: + + //! Relative conductivities of the dispersed and continuous phases, + /*! + * + * \f[ + * \code{relativeConductivites_} = \kappa_d / \kappa_0 + * \f] + */ + doublereal relativeConductivities_; + + }; + + + +} + +#endif + diff --git a/Cantera/src/transport/TortuosityPercolation.cpp b/Cantera/src/transport/TortuosityPercolation.cpp new file mode 100644 index 000000000..49f0f4724 --- /dev/null +++ b/Cantera/src/transport/TortuosityPercolation.cpp @@ -0,0 +1,105 @@ +/** + * @file TortuosityPercolation.cpp + * Base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ + +#include "TortuosityPercolation.h" +#include "ctexceptions.h" + +#include + +namespace Cantera { + + //==================================================================================================================== + // Default constructor + TortuosityPercolation::TortuosityPercolation(double percolationThreshold, double conductivityExponent) : + TortuosityBase(), + percolationThreshold_(percolationThreshold), + conductivityExponent_(conductivityExponent) + { + + } + //==================================================================================================================== + // Copy Constructor + /* + * @param right Object to be copied + */ + TortuosityPercolation::TortuosityPercolation(const TortuosityPercolation &right) : + TortuosityBase(), + percolationThreshold_(right.percolationThreshold_), + conductivityExponent_(right.conductivityExponent_) + { + *this = right; + } + //==================================================================================================================== + // Default destructor for TortuosityPercolation + TortuosityPercolation::~TortuosityPercolation() { + + } + //==================================================================================================================== + // Assignment operator + /* + * @param right Object to be copied + */ + TortuosityPercolation & TortuosityPercolation::operator=(const TortuosityPercolation &right) { + if (&right == this) { + return *this; + } + TortuosityBase::operator=(right); + + percolationThreshold_ = right.percolationThreshold_; + conductivityExponent_ = right.conductivityExponent_; + + return *this; + } + //==================================================================================================================== + // Duplication operator + /* + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + TortuosityBase * TortuosityPercolation::duplMyselfAsTortuosityBase() const { + TortuosityPercolation * tb = new TortuosityPercolation(*this); + return dynamic_cast(tb); + } + //==================================================================================================================== + // The tortuosity factor models the effective increase in the diffusive transport length. + /* + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + */ + doublereal TortuosityPercolation::tortuosityFactor(doublereal porosity) { + return McMillanFactor(porosity) / porosity; + } + //==================================================================================================================== + // The McMillan number is the ratio of the flux-like variable to the value it would have without porous flow. + /* + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + doublereal TortuosityPercolation::McMillanFactor(doublereal porosity) { + doublereal tmp = pow(((porosity - percolationThreshold_) + / ( 1.0 - percolationThreshold_ )) , + conductivityExponent_); + return tmp; + } + //==================================================================================================================== +} diff --git a/Cantera/src/transport/TortuosityPercolation.h b/Cantera/src/transport/TortuosityPercolation.h new file mode 100644 index 000000000..fd11f9ec2 --- /dev/null +++ b/Cantera/src/transport/TortuosityPercolation.h @@ -0,0 +1,108 @@ +/** + * @file TortuosityBase.h + * Virtual base class to compute the increase in diffusive path length associated with + * tortuous path diffusion through, for example, porous media. + */ + +/* + * Copywrite (2005) Sandia Corporation. Under the terms of + * Contract DE-AC04-94AL85000 with Sandia Corporation, the + * U.S. Government retains certain rights in this software. + */ + +/* + * $Revision: 572 $ + * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ + */ +#ifndef CT_TORTUOSITYPERCOLATION_H +#define CT_TORTUOSITYPERCOLATION_H + +#include "TortuosityBase.h" + + +namespace Cantera { + + //! This class implements transport coefficient corrections + //! appropriate for porous media where percollation theory applies. + /*! + * + * + */ + class TortuosityPercolation : public TortuosityBase { + + public: + //! Default constructor uses Percolationn exponent of 1.5 + /*! + * @param setPower Exponent in the Percolation factor. The default is 1.5 + */ + TortuosityPercolation(double percolationThreshold = 0.4, double conductivityExponent = 2.0); + + //! Copy Constructor + /*! + * @param right Object to be copied + */ + TortuosityPercolation(const TortuosityPercolation &right); + + //! Default destructor for TortuosityPercolation + virtual ~TortuosityPercolation(); + + //! Assignment operator + /*! + * @param right Object to be copied + */ + TortuosityPercolation & operator=(const TortuosityPercolation &right); + + //! Duplication operator + /*! + * @return Returns a pointer to a duplicate of the current object given a + * base class pointer + */ + virtual TortuosityBase * duplMyselfAsTortuosityBase() const; + + //! The tortuosity factor models the effective increase in the + //! diffusive transport length. + /*! + * This method returns \f$ 1/\tau^2 \f$ in the description of the flux + * + * \f$ C_T D_i \nabla X_i / \tau^2 \f$. + * + * + */ + virtual doublereal tortuosityFactor(doublereal porosity); + + //! The McMillan number is the ratio of the flux-like + //! variable to the value it would have without porous flow. + /*! + * The McMillan number combines the effect of toruosity + * and volume fraction of the transported phase. The net flux + * observed is then the product of the McMillan number and the + * non-porous transport rate. For a conductivity in a non-porous + * media, \f$ \kappa_0 \f$, the conductivity in the porous media + * would be \f$ \kappa = (\rm McMillan) \kappa_0 \f$. + */ + virtual doublereal McMillanFactor(doublereal porosity); + + + protected: + + //! Critical volume fraction / site density for percolation + double percolationThreshold_; + + //! Conductivity exponent + /*! + * The McMillan number (ratio of effective conductivity to non-porous conductivity) is + * \f[ \kappa/\kappa_0 = ( \phi - \phi_c )^\mu \f] + * where \f$ \mu \f$ is the conductivity exponent (typical values range from 1.6 to 2.0) and \f$ \phi_c \f$ + * is the percolation threshold. + */ + double conductivityExponent_; + + + }; + + + +} + +#endif + From 12a7f447fc718f63ddffc6236637f4fe5a44fc0a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 21 Dec 2011 22:47:50 +0000 Subject: [PATCH 434/446] Added a missing #endif --- Cantera/src/transport/Tortuosity.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Cantera/src/transport/Tortuosity.h b/Cantera/src/transport/Tortuosity.h index d3b1d4744..2fa72717c 100644 --- a/Cantera/src/transport/Tortuosity.h +++ b/Cantera/src/transport/Tortuosity.h @@ -1,4 +1,3 @@ - /** * @file TortuosityBruggeman.h * Class to compute the increase in diffusive path length in porous media @@ -15,8 +14,8 @@ * $Revision: 572 $ * $Date: 2010-08-13 20:21:57 -0600 (Fri, 13 Aug 2010) $ */ -#ifndef CT_TORTUOSITYBRUGGEMAN_H -#define CT_TORTUOSITYBRUGGEMAN_H +#ifndef CT_TORTUOSITY_H +#define CT_TORTUOSITY_H namespace Cantera { @@ -44,11 +43,11 @@ namespace Cantera { * * The tortuosity comes into play in conjunction the the */ - class TortuosityBruggeman { + class Tortuosity { public: //! Default constructor uses Bruggemann exponent of 1.5 - TortuosityBruggeman(double setPower = 1.5 ) : expBrug_(setPower) { + Tortuosity(double setPower = 1.5 ) : expBrug_(setPower) { } //! The tortuosity factor models the effective increase in the @@ -190,3 +189,4 @@ namespace Cantera { }; } +#endif From 267ac5b0e7297047a9cc4dc31aa9bec924d13641 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Jan 2012 15:51:02 +0000 Subject: [PATCH 435/446] another trial --- Cantera/src/oneD/OneDim.h | 9 ++++++--- Cantera/src/oneD/Sim1D.cpp | 14 +++++++++----- Cantera/src/oneD/Sim1D.h | 15 ++++++++------- 3 files changed, 23 insertions(+), 15 deletions(-) diff --git a/Cantera/src/oneD/OneDim.h b/Cantera/src/oneD/OneDim.h index 1f8382208..bd199ec53 100644 --- a/Cantera/src/oneD/OneDim.h +++ b/Cantera/src/oneD/OneDim.h @@ -32,8 +32,8 @@ namespace Cantera { /// Add a domain. void addDomain(Domain1D* d); - /// Return a reference to the Jacobian evaluator. - MultiJac& jacobian(); + //! Return a reference to the Jacobian evaluator. + MultiJac& jacobian(); /// Return a reference to the Newton iterator. MultiNewton& newton(); @@ -173,7 +173,10 @@ namespace Cantera { MultiNewton* m_newt; // Newton iterator doublereal m_rdt; // reciprocal of time step bool m_jac_ok; // if true, Jacobian is current - int m_nd; // number of domains + + //! number of domains + int m_nd; + int m_bw; // Jacobian bandwidth int m_size; // solution vector size diff --git a/Cantera/src/oneD/Sim1D.cpp b/Cantera/src/oneD/Sim1D.cpp index d804a4564..921e0da72 100644 --- a/Cantera/src/oneD/Sim1D.cpp +++ b/Cantera/src/oneD/Sim1D.cpp @@ -22,12 +22,16 @@ namespace Cantera { s += '\n'; writelog(s.c_str()); } - - Sim1D::Sim1D() : OneDim() { + //==================================================================================================================== + Sim1D::Sim1D() : + OneDim() + { //writelog("Sim1D default constructor\n"); } - - Sim1D::Sim1D(vector& domains) : OneDim(domains) { + //==================================================================================================================== + Sim1D::Sim1D(vector& domains) : + OneDim(domains) + { // resize the internal solution vector and the wprk array, // and perform domain-specific initialization of the @@ -49,7 +53,7 @@ namespace Cantera { m_steps.push_back(10); } - + //==================================================================================================================== // added by Karl Meredith void Sim1D::setInitialGuess(string component, vector_fp& locs, vector_fp& vals){ diff --git a/Cantera/src/oneD/Sim1D.h b/Cantera/src/oneD/Sim1D.h index 8b50cc098..e3717e15b 100644 --- a/Cantera/src/oneD/Sim1D.h +++ b/Cantera/src/oneD/Sim1D.h @@ -23,13 +23,14 @@ namespace Cantera { public: - /** - * Default constructor. This constructor is provided to make - * the class default-constructible, but is not meant to be - * used in most applications. Use the next constructor - * instead. - */ - Sim1D(); + + //! Default constructor. + /*! + * This constructor is provided to make + * the class default-constructible, but is not meant to be + * used in most applications. Use the next constructor + */ + Sim1D(); /** From 701bcc53b16302100fb79fdc94ab2e74d2bff865 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Jan 2012 16:24:09 +0000 Subject: [PATCH 436/446] Added a print statement. --- Cantera/src/numerics/NonlinearSolver.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index 81c92ec00..cbc3af79f 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -3141,7 +3141,7 @@ namespace Cantera { } info = beuler_jac(jac, DATA_PTR(m_resid), time_curr, CJ, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), num_newt_its); - if (info == 0) { + if (info != 1) { if (m_print_flag > 0) { printf("\t solve_nonlinear_problem(): Jacobian Formation Error: %d Bailing\n", info); } From 89497de36975d078d11a922182ec4b3a14e0b07e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Jan 2012 16:59:02 +0000 Subject: [PATCH 437/446] Moved the getActivityConcentration() function and related functions up to the parent level, GibbsExcessVPSSTP --- Cantera/src/thermo/GibbsExcessVPSSTP.cpp | 13 +-- Cantera/src/thermo/GibbsExcessVPSSTP.h | 44 ++++++++- Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp | 97 +------------------ Cantera/src/thermo/IonsFromNeutralVPSSTP.h | 83 ---------------- Cantera/src/thermo/MargulesVPSSTP.cpp | 42 +------- Cantera/src/thermo/MargulesVPSSTP.h | 42 -------- .../src/thermo/MixedSolventElectrolyte.cpp | 44 +-------- Cantera/src/thermo/MixedSolventElectrolyte.h | 43 -------- Cantera/src/thermo/MolarityIonicVPSSTP.cpp | 34 +------ Cantera/src/thermo/MolarityIonicVPSSTP.h | 48 --------- Cantera/src/thermo/PhaseCombo_Interaction.cpp | 40 +------- Cantera/src/thermo/RedlichKisterVPSSTP.cpp | 42 +------- Cantera/src/thermo/RedlichKisterVPSSTP.h | 43 -------- 13 files changed, 62 insertions(+), 553 deletions(-) diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp index 8f357a9e5..feba2c49e 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.cpp +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.cpp @@ -213,16 +213,17 @@ namespace Cantera { /* * - Activities, Standard States, Activity Concentrations ----------- */ + void GibbsExcessVPSSTP::getActivityConcentrations(doublereal* c) const { + getActivities(c); + } doublereal GibbsExcessVPSSTP::standardConcentration(int k) const { - err("standardConcentration"); - return -1.0; + return 1.0; } doublereal GibbsExcessVPSSTP::logStandardConc(int k) const { - err("logStandardConc"); - return -1.0; + return 0.0; } void GibbsExcessVPSSTP::getActivities(doublereal* ac) const { @@ -328,8 +329,8 @@ namespace Cantera { */ void GibbsExcessVPSSTP::getUnitsStandardConc(double *uA, int k, int sizeUA) const { for (int i = 0; i < sizeUA; i++) { - if (i == 0) uA[0] = 1.0; - if (i == 1) uA[1] = -nDim(); + if (i == 0) uA[0] = 0.0; + if (i == 1) uA[1] = 0.0; if (i == 2) uA[2] = 0.0; if (i == 3) uA[3] = 0.0; if (i == 4) uA[4] = 0.0; diff --git a/Cantera/src/thermo/GibbsExcessVPSSTP.h b/Cantera/src/thermo/GibbsExcessVPSSTP.h index 8de94d8ff..46c7a4369 100644 --- a/Cantera/src/thermo/GibbsExcessVPSSTP.h +++ b/Cantera/src/thermo/GibbsExcessVPSSTP.h @@ -74,7 +74,27 @@ namespace Cantera { * fraction vector. That's one of its primary usages. In order to keep the mole fraction * vector constant, all of the setState functions are redesigned at this layer. * - *

SetState Strategy

+ * + *

+ * Activity Concentrations: Relationship of %ThermoPhase to %Kinetics Expressions + *

+ * + * As explained in a similar discussion in the ThermoPhase class, the actual units used + * in kinetics expressions must be specified in the ThermoPhase class for the corresponding + * species. These units vary with the field of study. %Cantera uses the concept of + * activity concentrations to represent this. Activity concentrations are used directly + * in the expressions for kinetics. Standard concentrations are used as the multiplicative + * constant that takes the activity of a species and turns it into an activity concentration. + * Standard concentrations must not depend on the concentration of the species in the phase. + * + * Here we set a standard for the specification of the standard concentrations for this class + * and all child classes underneath it. We specify here that the standard concentration is + * equal to 1 for all species. Therefore, the activities appear directly in kinetics expressions + * involving species in underlying %GibbsExcessVPSSTP phases. + * + *

+ * SetState Strategy + *

* * All setState functions that set the internal state of the ThermoPhase object are * overloaded at this level, so that a current mole fraction vector is maintained within @@ -223,7 +243,24 @@ namespace Cantera { * @{ */ - + //! This method returns an array of generalized concentrations + /*! + * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / + * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration + * defined below and \f$ a_k \f$ are activities used in the + * thermodynamic functions. These activity (or generalized) + * concentrations are used by kinetics manager classes to compute the forward and + * reverse rates of elementary reactions. Note that they may + * or may not have units of concentration --- they might be + * partial pressures, mole fractions, or surface coverages, + * for example. + * + * @param c Output array of generalized concentrations. The + * units depend upon the implementation of the + * reaction rate expressions within the phase. + */ + virtual void getActivityConcentrations(doublereal* c) const; + /** @@ -237,6 +274,9 @@ namespace Cantera { * different sizes), this method may be called with an * optional parameter indicating the species. * + * The standard concentration for defaulted to 1. In other words + * the activity concentration is assumed to be 1. + * * @param k species index. Defaults to zero. */ virtual doublereal standardConcentration(int k=0) const; diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp index f7c9a79f6..029fd29cd 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -323,109 +323,18 @@ namespace Cantera { //err("not implemented"); //return 0.0; } - + //=========================================================================================================== /* * - Activities, Standard States, Activity Concentrations ----------- */ - - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void IonsFromNeutralVPSSTP::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - + //=========================================================================================================== void IonsFromNeutralVPSSTP::getDissociationCoeffs(vector_fp& coeffs, vector_fp& charges, std::vector& neutMolIndex) const { coeffs = fm_neutralMolec_ions_; charges = m_speciesCharge; neutMolIndex = fm_invert_ionForNeutral; } - - // Return the standard concentration for the kth species - /* - * The standard concentration \f$ C^0_k \f$ used to normalize - * the activity (i.e., generalized) concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k Optional parameter indicating the species. The default - * is to assume this refers to species 0. - * @return - * Returns the standard concentration. The units are by definition - * dependent on the ThermoPhase and kinetics manager representation. - */ - doublereal IonsFromNeutralVPSSTP::standardConcentration(int k) const { - return 1.0; - } - - // Natural logarithm of the standard concentration of the kth species. - /* - * @param k index of the species (defaults to zero) - */ - doublereal IonsFromNeutralVPSSTP::logStandardConc(int k) const { - return 0.0; - } - - // Returns the units of the standard and generalized concentrations. - /* - * Note they have the same units, as their - * ratio is defined to be equal to the activity of the kth - * species in the solution, which is unitless. - * - * This routine is used in print out applications where the - * units are needed. Usually, MKS units are assumed throughout - * the program and in the XML input files. - * - * The base %ThermoPhase class assigns the default quantities - * of (kmol/m3) for all species. - * Inherited classes are responsible for overriding the default - * values if necessary. - * - * @param uA Output vector containing the units - * uA[0] = kmol units - default = 1 - * uA[1] = m units - default = -nDim(), the number of spatial - * dimensions in the Phase class. - * uA[2] = kg units - default = 0; - * uA[3] = Pa(pressure) units - default = 0; - * uA[4] = Temperature units - default = 0; - * uA[5] = time units - default = 0 - * @param k species index. Defaults to 0. - * @param sizeUA output int containing the size of the vector. - * Currently, this is equal to 6. - */ - void IonsFromNeutralVPSSTP::getUnitsStandardConc(double *uA, int k, - int sizeUA) const { - uA[0] = 0; - uA[1] = 0; - uA[2] = 0; - uA[3] = 0; - uA[4] = 0; - uA[5] = 0; - } - + //=========================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. /* diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h index d0c62c20a..33b6d5d8c 100644 --- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.h +++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.h @@ -264,88 +264,6 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - //! Return the standard concentration for the kth species - /*! - * The standard concentration \f$ C^0_k \f$ used to normalize - * the activity (i.e., generalized) concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * Here we define the standard concentration as being equal to 1.0. - * Therefore, the kinetics operators will be dealing in unitless - * activities for all kinetics expressions involving the molten - * salts. This assignment is subject to further assessment. - * - * @param k Optional parameter indicating the species. The default - * is to assume this refers to species 0. - * @return - * Returns the standard concentration. The units are by definition - * dependent on the ThermoPhase and kinetics manager representation. - */ - virtual doublereal standardConcentration(int k=0) const; - - - //! Natural logarithm of the standard concentration of the kth species. - /*! - * @param k index of the species (defaults to zero) - */ - virtual doublereal logStandardConc(int k=0) const; - - //! Returns the units of the standard and generalized concentrations. - /*! - * Note they have the same units, as their - * ratio is defined to be equal to the activity of the kth - * species in the solution, which is unitless. - * - * This routine is used in print out applications where the - * units are needed. Usually, MKS units are assumed throughout - * the program and in the XML input files. - * - * The base %ThermoPhase class assigns the default quantities - * of (kmol/m3) for all species. - * Inherited classes are responsible for overriding the default - * values if necessary. - * - * @param uA Output vector containing the units - * uA[0] = kmol units - default = 1 - * uA[1] = m units - default = -nDim(), the number of spatial - * dimensions in the Phase class. - * uA[2] = kg units - default = 0; - * uA[3] = Pa(pressure) units - default = 0; - * uA[4] = Temperature units - default = 0; - * uA[5] = time units - default = 0 - * @param k species index. Defaults to 0. - * @param sizeUA output int containing the size of the vector. - * Currently, this is equal to 6. - */ - virtual void getUnitsStandardConc(double *uA, int k = 0, - int sizeUA = 6) const; - - //! Get the array of non-dimensional molar-based activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! @@ -353,7 +271,6 @@ namespace Cantera { */ virtual void getActivityCoefficients(doublereal* ac) const; - //@} /// @name Partial Molar Properties of the Solution diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp index ebe7c89aa..2af8706cb 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.cpp +++ b/Cantera/src/thermo/MargulesVPSSTP.cpp @@ -340,41 +340,7 @@ namespace Cantera { * - Activities, Standard States, Activity Concentrations ----------- */ - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void MargulesVPSSTP::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - doublereal MargulesVPSSTP::standardConcentration(int k) const { - //err("standardConcentration"); - //return -1.0; - return 1.0; - } - - doublereal MargulesVPSSTP::logStandardConc(int k) const { - //err("logStandardConc"); - //return -1.0; - return 0.0; - } //==================================================================================================================== // Get the array of non-dimensional molar-based ln activity coefficients at // the current solution temperature, pressure, and solution concentration. @@ -1151,7 +1117,7 @@ namespace Cantera { if (nParamsFound != 2) { throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessEnthalpy for " + ispName + "::" + jspName, - "wrong number of params found"); + "wrong number of params found. Need 2"); } m_HE_b_ij[iSpot] = vParams[0]; m_HE_c_ij[iSpot] = vParams[1]; @@ -1167,7 +1133,7 @@ namespace Cantera { if (nParamsFound != 2) { throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessEntropy for " + ispName + "::" + jspName, - "wrong number of params found"); + "wrong number of params found. Need 2"); } m_SE_b_ij[iSpot] = vParams[0]; m_SE_c_ij[iSpot] = vParams[1]; @@ -1183,7 +1149,7 @@ namespace Cantera { if (nParamsFound != 2) { throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessVolume_Enthalpy for " + ispName + "::" + jspName, - "wrong number of params found"); + "wrong number of params found. Need 2"); } m_VHE_b_ij[iSpot] = vParams[0]; m_VHE_c_ij[iSpot] = vParams[1]; @@ -1199,7 +1165,7 @@ namespace Cantera { if (nParamsFound != 2) { throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies::excessVolume_Entropy for " + ispName + "::" + jspName, - "wrong number of params found"); + "wrong number of params found. Need 2"); } m_VSE_b_ij[iSpot] = vParams[0]; m_VSE_c_ij[iSpot] = vParams[1]; diff --git a/Cantera/src/thermo/MargulesVPSSTP.h b/Cantera/src/thermo/MargulesVPSSTP.h index 5d675fb14..6b38baa33 100644 --- a/Cantera/src/thermo/MargulesVPSSTP.h +++ b/Cantera/src/thermo/MargulesVPSSTP.h @@ -493,48 +493,6 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - - /** - * The standard concentration \f$ C^0_k \f$ used to normalize - * the generalized concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k species index. Defaults to zero. - */ - virtual doublereal standardConcentration(int k=0) const; - - /** - * Returns the natural logarithm of the standard - * concentration of the kth species - * - * @param k species index - */ - virtual doublereal logStandardConc(int k=0) const; //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.cpp b/Cantera/src/thermo/MixedSolventElectrolyte.cpp index fc6edbfa4..922a40bfa 100644 --- a/Cantera/src/thermo/MixedSolventElectrolyte.cpp +++ b/Cantera/src/thermo/MixedSolventElectrolyte.cpp @@ -329,52 +329,14 @@ namespace Cantera { } } - - + //==================================================================================================================== /* * ------------ Molar Thermodynamic Properties ---------------------- */ - - + //==================================================================================================================== /* * - Activities, Standard States, Activity Concentrations ----------- */ - - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void MixedSolventElectrolyte::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - - doublereal MixedSolventElectrolyte::standardConcentration(int k) const { - //err("standardConcentration"); - //return -1.0; - return 1.0; - } - - doublereal MixedSolventElectrolyte::logStandardConc(int k) const { - //err("logStandardConc"); - //return -1.0; - return 0.0; - } //==================================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. @@ -394,7 +356,7 @@ namespace Cantera { ac[k] = exp(lnActCoeff_Scaled_[k]); } } - + //==================================================================================================================== /* * ------------ Partial Molar Properties of the Solution ------------ */ diff --git a/Cantera/src/thermo/MixedSolventElectrolyte.h b/Cantera/src/thermo/MixedSolventElectrolyte.h index 7ffad1f05..21a33cde8 100644 --- a/Cantera/src/thermo/MixedSolventElectrolyte.h +++ b/Cantera/src/thermo/MixedSolventElectrolyte.h @@ -493,49 +493,6 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - - /** - * The standard concentration \f$ C^0_k \f$ used to normalize - * the generalized concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k species index. Defaults to zero. - */ - virtual doublereal standardConcentration(int k=0) const; - - /** - * Returns the natural logarithm of the standard - * concentration of the kth species - * - * @param k species index - */ - virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! diff --git a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp index 99f715427..6f02b9ce1 100644 --- a/Cantera/src/thermo/MolarityIonicVPSSTP.cpp +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.cpp @@ -281,42 +281,10 @@ namespace Cantera { /* * ------------ Molar Thermodynamic Properties ---------------------- */ - - + //==================================================================================================================== /* * - Activities, Standard States, Activity Concentrations ----------- */ - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void MolarityIonicVPSSTP::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - //==================================================================================================================== - doublereal MolarityIonicVPSSTP::standardConcentration(int k) const { - return -1.0; - } - //==================================================================================================================== - doublereal MolarityIonicVPSSTP::logStandardConc(int k) const { - return 0.0; - } //==================================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. diff --git a/Cantera/src/thermo/MolarityIonicVPSSTP.h b/Cantera/src/thermo/MolarityIonicVPSSTP.h index e75531a8e..1ab7cd25f 100644 --- a/Cantera/src/thermo/MolarityIonicVPSSTP.h +++ b/Cantera/src/thermo/MolarityIonicVPSSTP.h @@ -228,49 +228,6 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - - /** - * The standard concentration \f$ C^0_k \f$ used to normalize - * the generalized concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k species index. Defaults to zero. - */ - virtual doublereal standardConcentration(int k=0) const; - - /** - * Returns the natural logarithm of the standard - * concentration of the kth species - * - * @param k species index - */ - virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! @@ -278,11 +235,6 @@ namespace Cantera { */ virtual void getLnActivityCoefficients(doublereal* ac) const; - - - - - //@} /// @name Partial Molar Properties of the Solution //@{ diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.cpp b/Cantera/src/thermo/PhaseCombo_Interaction.cpp index 574d3477e..ef01eb6d7 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.cpp +++ b/Cantera/src/thermo/PhaseCombo_Interaction.cpp @@ -342,51 +342,13 @@ namespace Cantera { } } //==================================================================================================================== - /* * ------------ Molar Thermodynamic Properties ---------------------- */ - - + //==================================================================================================================== /* * - Activities, Standard States, Activity Concentrations ----------- */ - - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void PhaseCombo_Interaction::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - //==================================================================================================================== - doublereal PhaseCombo_Interaction::standardConcentration(int k) const { - //err("standardConcentration"); - //return -1.0; - return 1.0; - } - //==================================================================================================================== - doublereal PhaseCombo_Interaction::logStandardConc(int k) const { - //err("logStandardConc"); - //return -1.0; - return 0.0; - } //==================================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.cpp b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp index b6dc57f3d..1f3944cd3 100644 --- a/Cantera/src/thermo/RedlichKisterVPSSTP.cpp +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.cpp @@ -334,53 +334,13 @@ namespace Cantera { } //==================================================================================================================== - - - /* * ------------ Molar Thermodynamic Properties ---------------------- */ - - + //==================================================================================================================== /* * - Activities, Standard States, Activity Concentrations ----------- */ - - // This method returns an array of generalized concentrations - /* - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * Here we define the activity concentrations as equal - * to the activities, because the standard concentration is 1. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - void RedlichKisterVPSSTP::getActivityConcentrations(doublereal* c) const { - getActivities(c); - } - //==================================================================================================================== - doublereal RedlichKisterVPSSTP::standardConcentration(int k) const { - //err("standardConcentration"); - //return -1.0; - return 1.0; - } - //==================================================================================================================== - doublereal RedlichKisterVPSSTP::logStandardConc(int k) const { - //err("logStandardConc"); - //return -1.0; - return 0.0; - } //==================================================================================================================== // Get the array of non-dimensional molar-based activity coefficients at // the current solution temperature, pressure, and solution concentration. diff --git a/Cantera/src/thermo/RedlichKisterVPSSTP.h b/Cantera/src/thermo/RedlichKisterVPSSTP.h index d4d927d62..87d11f306 100644 --- a/Cantera/src/thermo/RedlichKisterVPSSTP.h +++ b/Cantera/src/thermo/RedlichKisterVPSSTP.h @@ -490,49 +490,6 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - - /** - * The standard concentration \f$ C^0_k \f$ used to normalize - * the generalized concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k species index. Defaults to zero. - */ - virtual doublereal standardConcentration(int k=0) const; - - /** - * Returns the natural logarithm of the standard - * concentration of the kth species - * - * @param k species index - */ - virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based ln activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! From 34d3ad6a69938ff8552a0ca878dbbff53c27e70f Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Jan 2012 17:05:28 +0000 Subject: [PATCH 438/446] Added some comments to this file. --- Cantera/cxx/include/Cantera.h | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/Cantera/cxx/include/Cantera.h b/Cantera/cxx/include/Cantera.h index 08dad4bb9..8ac96d93e 100755 --- a/Cantera/cxx/include/Cantera.h +++ b/Cantera/cxx/include/Cantera.h @@ -1,7 +1,6 @@ /** * @file Cantera.h - * Basic include file to be used in all Cantera application - * environments. + * Basic include file to be used in all Cantera application environments. */ /* @@ -11,16 +10,24 @@ // Copyright 2001 California Institute of Technology +/* + * Note, this include should be the first include that code containing the + * Cantera namespace sees when in the Cantera application environment. + */ + #ifndef CANTERA_H_INCL #define CANTERA_H_INCL -// definitions +// If we are using this file, then we are in the Cantera Apps environment. +// Define a variable to signify this fact. #ifndef CANTERA_APP #define CANTERA_APP #endif +// define the presence of the Cantera_CXX namespace namespace Cantera_CXX{ } +// Include global typedefs and values for physical constants using SI units #include "kernel/ct_defs.h" // some useful functions @@ -29,9 +36,6 @@ namespace Cantera_CXX{ } // the CanteraError exception class #include "kernel/ctexceptions.h" -// -//#include "kernel/importCTML.h" - // The Cantera logger class #include "kernel/logger.h" @@ -44,10 +48,9 @@ namespace Cantera_CXX{ } // Include string utility routines #include "kernel/stringUtils.h" +// Include the array object +#include "kernel/Array.h" + #endif - - - - From b605f1e049daa44ac91b040d12c29fe9399fbc75 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Tue, 3 Jan 2012 17:09:08 +0000 Subject: [PATCH 439/446] Forgot to take out the definitions from one file. --- Cantera/src/thermo/PhaseCombo_Interaction.h | 46 --------------------- 1 file changed, 46 deletions(-) diff --git a/Cantera/src/thermo/PhaseCombo_Interaction.h b/Cantera/src/thermo/PhaseCombo_Interaction.h index a14049990..8e42709f5 100644 --- a/Cantera/src/thermo/PhaseCombo_Interaction.h +++ b/Cantera/src/thermo/PhaseCombo_Interaction.h @@ -527,58 +527,12 @@ namespace Cantera { * @{ */ - //! This method returns an array of generalized concentrations - /*! - * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / - * C^0_k, \f$ where \f$ C^0_k \f$ is a standard concentration - * defined below and \f$ a_k \f$ are activities used in the - * thermodynamic functions. These activity (or generalized) - * concentrations are used - * by kinetics manager classes to compute the forward and - * reverse rates of elementary reactions. Note that they may - * or may not have units of concentration --- they might be - * partial pressures, mole fractions, or surface coverages, - * for example. - * - * @param c Output array of generalized concentrations. The - * units depend upon the implementation of the - * reaction rate expressions within the phase. - */ - virtual void getActivityConcentrations(doublereal* c) const; - - - /** - * The standard concentration \f$ C^0_k \f$ used to normalize - * the generalized concentration. In many cases, this quantity - * will be the same for all species in a phase - for example, - * for an ideal gas \f$ C^0_k = P/\hat R T \f$. For this - * reason, this method returns a single value, instead of an - * array. However, for phases in which the standard - * concentration is species-specific (e.g. surface species of - * different sizes), this method may be called with an - * optional parameter indicating the species. - * - * @param k species index. Defaults to zero. - */ - virtual doublereal standardConcentration(int k=0) const; - - /** - * Returns the natural logarithm of the standard - * concentration of the kth species - * - * @param k species index - */ - virtual doublereal logStandardConc(int k=0) const; - //! Get the array of non-dimensional molar-based activity coefficients at //! the current solution temperature, pressure, and solution concentration. /*! * @param ac Output vector of activity coefficients. Length: m_kk. */ virtual void getActivityCoefficients(doublereal* ac) const; - - - //@} /// @name Partial Molar Properties of the Solution From 5f9c515e03bbdb9322aa80540eebf53d4a2bcf2a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Jan 2012 16:12:23 +0000 Subject: [PATCH 440/446] Added a new function getNamedStringValue --- Cantera/src/base/ctml.cpp | 70 ++++++++++++++++++++++++++++++++++-- Cantera/src/base/ctml.h | 75 +++++++++++++++++++++++++++++++-------- Cantera/src/base/xml.cpp | 2 +- Cantera/src/base/xml.h | 2 +- 4 files changed, 130 insertions(+), 19 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index ec6c4983d..a4856bbff 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -416,7 +416,7 @@ namespace ctml { if (!parent.hasChild(nameString)) return ""; return parent(nameString); } - //==================================================================================================================== + //==================================================================================================================== // This function reads a child node with the name, "string", with a specific // title attribute named "titleString" /* @@ -440,10 +440,11 @@ namespace ctml { <\string> @endverbatum * - * @param node reference to the XML_Node object of the parent XML element + * @param node Reference to the XML_Node object of the parent XML element * @param titleString String name of the title attribute of the child node * @param valueString Value string that is found in the child node. output variable - * @param typeString String type. This is an optional output variable + * @param typeString String type. This is an optional output variable. It is filled + * with the attribute "type" of the XML entry. */ void getString(const Cantera::XML_Node& node, const std::string &titleString, std::string& valueString, std::string& typeString) { @@ -458,6 +459,69 @@ namespace ctml { } } + //==================================================================================================================== + // This function attempts to read a named child node and returns with the contents in the value string. + // title attribute named "titleString" + /* + * This function will read a child node to the current XML node, with the + * name "string". It must have a title attribute, named titleString, and the body + * of the XML node will be read into the valueString output argument. + * + * If the child node is not found then the empty string is returned. + * + * Example: + * + * Code snipet: + * @verbatum + const XML_Node &node; + std::string valueString; + std::string typeString; + std::string nameString = "timeIncrement"; + getString(XML_Node& node, nameString, valueString, valueString, typeString); + @endverbatum + * + * Reads the following the snippet in the XML file: + * + * * @verbatum + + valueString + <\nameString> + @endverbatum + * + * or alternatively as a retrofit and special case, it also reads the following case + * + * @verbatum + + valueString + <\string> + @endverbatum + * + * @param node Reference to the XML_Node object of the parent XML element + * @param nameString Name of the XML Node input variable + * @param valueString Value string that is found in the child node. output variable + * @param typeString String type. This is an optional output variable. It is filled + * with the attribute "type" of the XML entry. output variable + */ + void getNamedStringValue(const Cantera::XML_Node& node, const std::string &nameString, std::string& valueString, + std::string& typeString) + { + valueString = ""; + typeString = ""; + if (node.hasChild(nameString)) { + XML_Node &xc = node.child(nameString); + valueString = xc.value(); + typeString = xc["type"]; + } else { + XML_Node* s = getByTitle(node, nameString); + if (s) { + if (s->name() == "string") { + valueString = (*s).value(); + typeString = (*s)["type"]; + return; + } + } + } + } //==================================================================================================================== // Get a vector of integer values from a child element. /* diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 6c57abdee..bd0614b16 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -851,6 +851,40 @@ namespace ctml { //! This function reads a child node with the name string with a specific //! title attribute named titleString + /*! + * This function will read a child node to the current XML node with the name "string". + * It must have a title attribute, named titleString, and the body + * of the XML node will be read into the valueString output argument. + * + * If the child node is not found then the empty string is returned. + * + * Example: + * + * Code snipet: + * @verbatim + const XML_Node &node; + getString(XML_Node& node, std::string titleString, std::string valueString, + std::string typeString); + @endverbatim + * + * Reads the following the snippet in the XML file: + * @verbatim + + valueString + <\string> + @endverbatim + * + * @param node Reference to the XML_Node object of the parent XML element + * @param titleString String name of the title attribute of the child node + * @param valueString Value string that is found in the child node. output variable + * @param typeString String type. This is an optional output variable. It is filled + * with the attribute "type" of the XML entry. + */ + void getString(const Cantera::XML_Node& node, const std::string &titleString, + std::string& valueString, std::string& typeString); + + //! This function attempts to read a named child node and returns with the contents in the value string. + //! title attribute named "titleString" /*! * This function will read a child node to the current XML node, with the * name "string". It must have a title attribute, named titleString, and the body @@ -861,26 +895,39 @@ namespace ctml { * Example: * * Code snipet: - * @verbatim - const XML_Node &node; - getString(XML_Node& node, std::string titleString, std::string valueString, - std::string typeString); - @endverbatim + * @verbatum + const XML_Node &node; + std::string valueString; + std::string typeString; + std::string nameString = "timeIncrement"; + getString(XML_Node& node, nameString, valueString, valueString, typeString); + @endverbatum * * Reads the following the snippet in the XML file: - * @verbatim - + * + * * @verbatum + + valueString + <\nameString> + @endverbatum + * + * or alternatively as a retrofit and special case, it also reads the following case + * + * @verbatum + valueString <\string> - @endverbatim + @endverbatum * - * @param node reference to the XML_Node object of the parent XML element - * @param titleString String name of the title attribute of the child node - * @param valueString Value string that is found in the child node. output variable - * @param typeString String type. This is an optional output variable + * @param node Reference to the XML_Node object of the parent XML element + * @param nameString Name of the XML Node input variable + * @param valueString Value string that is found in the child node. output variable + * @param typeString String type. This is an optional output variable. It is filled + * with the attribute "type" of the XML entry. output variable */ - void getString(const Cantera::XML_Node& node, const std::string &titleString, - std::string& valueString, std::string& typeString); + void getNamedStringValue(const Cantera::XML_Node& node, const std::string &nameString, std::string& valueString, + std::string& typeString); + //! This function reads a child node with the name, nameString, and returns //! its xml value as the return string diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 1484c1b6f..65de68887 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -925,7 +925,7 @@ namespace Cantera { } // This routine carries out a recursive search for an XML node based - // on the xml element attribute ID. + // on the xml element attribute, "id" . /* * If exact match is found, the pointer * to the matching XML Node is returned. If not, 0 is returned. diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index 3be1378a3..cf9ece36d 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -517,7 +517,7 @@ namespace Cantera { const std::string &idTarget) const; //! This routine carries out a recursive search for an XML node based - //! on the xml element attribute ID. + //! on the xml element attribute, "id" /*! * If exact match is found, the pointer * to the matching XML Node is returned. If not, 0 is returned. From 8c39c0307b7a07f8a0b621c65866690b8cc4a052 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 9 Jan 2012 22:32:55 +0000 Subject: [PATCH 441/446] Clarified the API for addChild. The function always mallocs a new copy of the child. Added a new function, mergeAsChild(XML_Node &), for the case where a malloc is not wanted. Made setRoot() a recursive function, as it should be. --- Cantera/src/base/xml.cpp | 99 ++++++++++++++++++++++++++++------------ Cantera/src/base/xml.h | 38 ++++++++++++--- 2 files changed, 100 insertions(+), 37 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 65de68887..69b1e51be 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -393,13 +393,15 @@ namespace Cantera { ////////////////////////// XML_Node ///////////////////////////////// - XML_Node::XML_Node(const char * cnm) - : m_name(""), - m_value(""), - m_parent(0), - m_locked(false), - m_nchildren(0), - m_iscomment(false) + XML_Node::XML_Node(const char * cnm) : + m_name(""), + m_value(""), + m_parent(0), + m_root(0), + m_locked(false), + m_nchildren(0), + m_iscomment(false) , + m_linenum(0) { if (! cnm) { m_name = "--"; @@ -417,19 +419,21 @@ namespace Cantera { * @param nm Name of the node. * The default name of the node is "--" * - * @param p pointer to the root for this node in the tree. - * The default is 0 indicating this is the top of the tree. + * @param parent Pointer to the parent for this node in the tree. + * A value of zero 0 indicates this is the top of the tree. */ - XML_Node::XML_Node(const std::string nm, XML_Node * const p) - : m_name(nm), - m_value(""), - m_parent(p), - m_locked(false), - m_nchildren(0), - m_iscomment(false) + XML_Node::XML_Node(const std::string nm, XML_Node * const parent) : + m_name(nm), + m_value(""), + m_parent(parent), + m_root(0), + m_locked(false), + m_nchildren(0), + m_iscomment(false), + m_linenum(0) { - if (!p) m_root = this; - else m_root = &p->root(); + if (!parent) m_root = this; + else m_root = &(parent->root()); } // Copy constructor @@ -440,11 +444,15 @@ namespace Cantera { m_name(""), m_value(""), m_parent(0), + m_root(0), m_locked(false), m_nchildren(0), - m_iscomment(false) + m_iscomment(right.m_iscomment), + m_linenum(right.m_linenum) { - m_root = this; + m_root = & right.root(); + m_name = right.m_name; + m_value = right.m_value; right.copy(this); } @@ -517,17 +525,18 @@ namespace Cantera { addChild("comment", comment); } - // Add a child node to the current node - /* - * This will add an XML_Node as a child to the current node. - * Note, this actually adds the node. Therefore, node is changed. - * There is no copy made of the child node. + + //! Merge an existing node as a child node to the current node + /*! + * This will merge an XML_Node as a child to the current node. + * Note, this actually adds the node. Therefore, the current node is changed. + * There is no copy made of the child node. The child node should not be deleted in the future. * * @param node Reference to a child XML_Node object * - * @return returns a reference to the added node + * @return Returns a reference to the added child node */ - XML_Node& XML_Node::addChild(XML_Node& node) { + XML_Node& XML_Node::mergeAsChild(XML_Node& node) { m_children.push_back(&node); m_nchildren = static_cast(m_children.size()); m_childindex[node.name()] = m_children.back(); @@ -536,7 +545,27 @@ namespace Cantera { return *m_children.back(); } - // Add a child node to the current node with a specified name + // Add a child node to the current node by makeing a copy of an existing node tree + /* + * This will add an XML_Node as a child to the current node. + * Note, this actually adds the node. Therefore, node is changed. + * A copy is made of the underlying tree. + * + * @param node Reference to a child XML_Node object + * + * @return returns a reference to the added node + */ + XML_Node& XML_Node::addChild(const XML_Node& node) { + XML_Node *xx = new XML_Node(node); + m_children.push_back(xx); + m_nchildren = static_cast(m_children.size()); + m_childindex[xx->name()] = m_children.back(); + xx->setRoot(root()); + xx->setParent(this); + return *m_children.back(); + } + + // Add a new malloced child node to the current node with a specified name /* * This will add an XML_Node as a child to the current node. * The node will be blank except for the specified name. @@ -555,7 +584,11 @@ namespace Cantera { return *m_children.back(); } - // Add a child node to the current xml node, and at the + XML_Node& XML_Node::addChild(const char *cstring) { + return addChild(std::string(cstring)); + } + + // Add a new malloced child node to the current xml node, and at the // same time add a value to the child /* * Resulting XML string: @@ -1179,12 +1212,15 @@ namespace Cantera { for (int n = 0; n < m_nchildren; n++) { sc = m_children[n]; ndc = node_dest->nChildren(); + // Here is where we do a malloc of the child node. (void) node_dest->addChild(sc->name()); dc = vsc[ndc]; sc->copy(dc); } } + + // Set the lock for this node void XML_Node::lock() { m_locked = true; @@ -1402,7 +1438,10 @@ namespace Cantera { } void XML_Node::setRoot(const XML_Node& root) { - m_root = const_cast(&root); + m_root = const_cast(&root); + for (int i = 0; i < m_nchildren; i++) { + m_children[i]->setRoot(root); + } } XML_Node * findXMLPhase(XML_Node *root, diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index cf9ece36d..305942618 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -175,10 +175,10 @@ namespace Cantera { * @param nm Name of the node. * The default name of the node is "--" * - * @param p pointer to the root for this node in the tree. - * The default is 0 indicating this is the top of the tree. + * @param parent Pointer to the parent for this node in the tree. + * A value of 0 indicates this is the top of the tree. */ - XML_Node(const std::string nm, XML_Node * const p); + XML_Node(const std::string nm, XML_Node * const parent); //! Copy constructor /*! @@ -203,18 +203,31 @@ namespace Cantera { */ void addComment(const std::string &comment); - //! Add a child node to the current node + //! Merge an existing node as a child node to the current node /*! - * This will add an XML_Node as a child to the current node. + * This will merge an XML_Node as a child to the current node. * Note, this actually adds the node. Therefore, the current node is changed. - * There is no copy made of the child node. + * There is no copy made of the child node. The child node should not be deleted in the future * * @param node Reference to a child XML_Node object * * @return Returns a reference to the added child node */ - XML_Node& addChild(XML_Node& node); + XML_Node& mergeAsChild(XML_Node& node); + // Add a child node to the current node by makeing a copy of an existing node tree + /* + * This will add an XML_Node as a child to the current node. + * Note, this actually adds the node. Therefore, node is changed. + * A copy is made of the underlying tree + * + * @param node Reference to a child XML_Node object + * + * @return returns a reference to the added node + */ + XML_Node& addChild(const XML_Node& node); + + //! Add a child node to the current node with a specified name /*! * This will add an XML_Node as a child to the current node. @@ -226,6 +239,17 @@ namespace Cantera { */ XML_Node& addChild(const std::string &sname); + //! Add a child node to the current node with a specified name + /*! + * This will add an XML_Node as a child to the current node. + * The node will be blank except for the specified name. + * + * @param cstring Name of the new child as a c string + * + * @return Returns a reference to the added node + */ + XML_Node& addChild(const char * cstring); + //! Add a child node to the current xml node, and at the //! same time add a value to the child /*! From 8e1563b07dbac7aaba8b95a2939d8cd08fe1dd25 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Fri, 13 Jan 2012 02:24:48 +0000 Subject: [PATCH 442/446] Added a recursive limit to the writes. --- Cantera/src/base/xml.cpp | 26 ++++++++++++++++---------- Cantera/src/base/xml.h | 33 +++++++++++++++++++++------------ 2 files changed, 37 insertions(+), 22 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 69b1e51be..09c286eed 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -450,7 +450,7 @@ namespace Cantera { m_iscomment(right.m_iscomment), m_linenum(right.m_linenum) { - m_root = & right.root(); + m_root = this; m_name = right.m_name; m_value = right.m_value; right.copy(this); @@ -797,6 +797,10 @@ namespace Cantera { return m_attribs; } + const std::map& XML_Node::attribsConst() const { + return m_attribs; + } + // Set the line number /* * @param n the member data m_linenum is set to n @@ -1127,8 +1131,7 @@ namespace Cantera { } else { if (node->name() != nm.substr(1,nm.size()-1)) - throw XML_TagMismatch(node->name(), - nm.substr(1,nm.size()-1), lnum); + throw XML_TagMismatch(node->name(), nm.substr(1,nm.size()-1), lnum); node = node->parent(); } } @@ -1202,6 +1205,7 @@ namespace Cantera { int ndc; node_dest->addValue(m_value); node_dest->setName(m_name); + node_dest->setLineNumber(m_linenum); if (m_name == "") return; map::const_iterator b = m_attribs.begin(); for (; b != m_attribs.end(); ++b) { @@ -1292,7 +1296,7 @@ namespace Cantera { * main recursive routine. It doesn't put a final endl * on. This is fixed up in the public method. */ - void XML_Node::write_int(std::ostream& s, int level) const { + void XML_Node::write_int(std::ostream& s, int level, int numRecursivesAllowed) const { if (m_name == "") return; @@ -1402,9 +1406,11 @@ namespace Cantera { } } int i; - for (i = 0; i < m_nchildren; i++) { - s << endl; - m_children[i]->write_int(s,level + 2); + if (numRecursivesAllowed > 0) { + for (i = 0; i < m_nchildren; i++) { + s << endl; + m_children[i]->write_int(s,level + 2, numRecursivesAllowed - 1); + } } if (m_nchildren > 0) s << endl << indent; s << ""; @@ -1421,14 +1427,14 @@ namespace Cantera { * is skipped and the children are processed. "--" is used * to denote the top of the tree. */ - void XML_Node::write(std::ostream& s, const int level) const { + void XML_Node::write(std::ostream& s, const int level, int numRecursivesAllowed) const { if (m_name == "--" && m_root == this) { for (int i = 0; i < m_nchildren; i++) { - m_children[i]->write_int(s,level); + m_children[i]->write_int(s,level, numRecursivesAllowed-1); s << endl; } } else { - write_int(s, level); + write_int(s, level, numRecursivesAllowed); s << endl; } } diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index 305942618..faeb41711 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -45,8 +45,7 @@ namespace Cantera { */ XML_Reader(std::istream& input); - //! Read a single character from the input stream - //! and return it + //! Read a single character from the input stream and returns it /*! * All low level reads occur through this function. * The function also keeps track of the line numbers. @@ -130,13 +129,14 @@ namespace Cantera { std::string readValue(); protected: - //! Input Stream containing the XML file + + //! Input stream containing the XML file std::istream& m_s; public: + //! Line count int m_line; - }; @@ -412,6 +412,7 @@ namespace Cantera { void clear(); private: + //! Returns a changeable value of the attributes map for the current node /*! * Note this is a simple accessor routine. And, it is a private function. @@ -421,6 +422,13 @@ namespace Cantera { public: + //! Returns an unchangeable value of the attributs map for the current node + /*! + * + * @return Returns an unchangeable reference to the attributes map + */ + const std::map& attribsConst() const; + //! Set the line number /*! * @param n the member data m_linenum is set to n @@ -432,7 +440,6 @@ namespace Cantera { * @return returns the member data m_linenum */ int lineNumber() const; - //! Returns a pointer to the parent node of the current node XML_Node* parent() const; @@ -642,9 +649,10 @@ namespace Cantera { * to denote the top of the tree. * * @param s ostream to write to - * @param level Indentation level to work from + * @param level Indentation level to work from + * @param numRecursivesAllowed Number of recursive calls allowed */ - void write(std::ostream& s, const int level = 0) const; + void write(std::ostream& s, const int level = 0, int numRecursivesAllowed = 60000) const; //! Return the root of the current XML_Node tree /*! @@ -705,15 +713,16 @@ namespace Cantera { //! Write an XML subtree to an output stream. /*! - * This is the - * main recursive routine. It doesn't put a final endl - * on. This is fixed up in the public method. + * This is the main recursive routine. It doesn't put a final endl + * on. This is fixed up in the public method. A method to only write out a limited + * amount of the xml tree has been added. * * * @param s ostream to write to * @param level Indentation level to work from + * @param numRecurvivesAllowed Number of recursive calls allowed */ - void write_int(std::ostream& s, int level = 0) const; + void write_int(std::ostream& s, int level = 0, int numRecursivesAllowed = 60000) const; protected: @@ -785,7 +794,7 @@ namespace Cantera { //! True if the current node is a comment node bool m_iscomment; - //! the member data m_linenum + //! The member data m_linenum /*! * Currently, unimplemented functionality */ From 8c98b3560e76e8a86a25bccb8b53024f1482b90e Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Sat, 14 Jan 2012 02:20:48 +0000 Subject: [PATCH 443/446] Added an index lookup up capability. Added a depth gauge to findByAttr. --- Cantera/src/base/xml.cpp | 72 ++++++++++++++++++++++++++++++++++++---- Cantera/src/base/xml.h | 28 +++++++++++++++- 2 files changed, 92 insertions(+), 8 deletions(-) diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 09c286eed..e5cb9aa94 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -960,7 +960,63 @@ namespace Cantera { } return scResult; } - + //==================================================================================================================== + // This routine carries out a search for an XML node based + // on both the xml element name and the attribute ID and an integer index. + /* + * If exact matches are found for all fields, the pointer + * to the matching XML Node is returned. The search is only carried out on + * the current element and the child elements of the current element. + * + * The "id" attribute may be defaulted by setting it to "". + * In this case the pointer to the first xml element matching the name + * only is returned. + * + * @param nameTarget Name of the XML Node that is being searched for + * @param idTarget "id" attribute of the XML Node that the routine + * looks for + * @param index Integer describing the index. The index is an + * attribute of the form index = "3" + * + * @return Returns the pointer to the XML node that fits the criteria + * + */ + XML_Node* XML_Node::findNameIDIndex(const std::string & nameTarget, + const std::string & idTarget, const int index_i) const { + XML_Node *scResult = 0; + XML_Node *sc; + std::string idattrib = id(); + std::string ii = attrib("index"); + std::string index_s = int2str(index_i); + int iMax = -1000000; + if (name() == nameTarget) { + if (idTarget == "" || idTarget == idattrib) { + if (index_s == ii) { + return const_cast(this); + } + } + } + for (int n = 0; n < m_nchildren; n++) { + sc = m_children[n]; + if (sc->name() == nameTarget) { + ii = sc->attrib("index"); + int indexR = atoi(ii.c_str()); + idattrib = sc->id(); + if (idTarget == idattrib || idTarget == "") { + if (index_s == ii) { + return sc; + } + } + if (indexR > iMax) { + scResult = sc; + iMax = indexR; + } + } + } + + return scResult; + } + //==================================================================================================================== // This routine carries out a recursive search for an XML node based // on the xml element attribute, "id" . /* @@ -1014,17 +1070,19 @@ namespace Cantera { * */ XML_Node* XML_Node::findByAttr(const std::string& attr, - const std::string& val) const { + const std::string& val, int depth) const { if (hasAttrib(attr)) { if (attrib(attr) == val) { return const_cast(this); } } - XML_Node* r = 0; - int n = nChildren(); - for (int i = 0; i < n; i++) { - r = m_children[i]->findByAttr(attr, val); - if (r != 0) return r; + if (depth > 0) { + XML_Node* r = 0; + int n = nChildren(); + for (int i = 0; i < n; i++) { + r = m_children[i]->findByAttr(attr, val, depth - 1); + if (r != 0) return r; + } } return 0; } diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index faeb41711..890470fe9 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -547,6 +547,29 @@ namespace Cantera { XML_Node* findNameID(const std::string &nameTarget, const std::string &idTarget) const; + //! This routine carries out a search for an XML node based + //! on both the xml element name and the attribute ID and an integer index. + /*! + * If exact matches are found for all fields, the pointer + * to the matching XML Node is returned. The search is only carried out on + * the current element and the child elements of the current element. + * + * The "id" attribute may be defaulted by setting it to "". + * In this case the pointer to the first xml element matching the name + * only is returned. + * + * @param nameTarget Name of the XML Node that is being searched for + * @param idTarget "id" attribute of the XML Node that the routine + * looks for + * @param index Integer describing the index. The index is an + * attribute of the form index = "3" + * + * @return Returns the pointer to the XML node that fits the criteria + * + */ + XML_Node* findNameIDIndex(const std::string &nameTarget, + const std::string &idTarget, const int index) const; + //! This routine carries out a recursive search for an XML node based //! on the xml element attribute, "id" /*! @@ -581,11 +604,14 @@ namespace Cantera { * @param attr Attribute of the XML Node that the routine * looks for * @param val Value of the attribute + * @param depth Depth of the search. A value of 1 means that only the + * immediate children are searched. * * @return Returns the pointer to the XML node that fits the criteria * */ - XML_Node* findByAttr(const std::string& attr, const std::string& val) const; + XML_Node* findByAttr(const std::string& attr, const std::string& val, + int depth = 100000) const; //! This routine carries out a recursive search for an XML node based //! on the name of the node. From fdd37f5f2dc4da37ffc089aeef8fd4488c29573a Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Mon, 23 Jan 2012 20:59:38 +0000 Subject: [PATCH 444/446] Added addNamedFloat Array() to ctml. Easy way to read and write float arrays. volt and coulomb added to units added depth argument to several xml calls. --- Cantera/src/base/ctml.cpp | 198 ++++++++++++++++++++++++++++++++++++-- Cantera/src/base/ctml.h | 9 ++ Cantera/src/base/units.h | 6 ++ Cantera/src/base/xml.cpp | 34 ++++--- Cantera/src/base/xml.h | 23 +++-- 5 files changed, 242 insertions(+), 28 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index a4856bbff..2305aa6a7 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -125,8 +125,13 @@ namespace ctml { */ void addInteger(Cantera::XML_Node& node, const std::string &title, const int val, const std::string units, const std::string type) { - XML_Node& f = node.addChild("integer",val); - f.addAttribute("title",title); +#ifdef CTML_VERSION_1_4 + XML_Node& f = node.addChild("integer", val); + f.addAttribute("title", title); +#else + XML_Node& f = node.addChild(title, val); +#endif + f.addAttribute("vtype", "integer"); if (type != "") f.addAttribute("type",type); if (units != "") f.addAttribute("units",units); } @@ -195,10 +200,17 @@ namespace ctml { else if (i > 0 && (i+1) % 3 == 0) v += ",\n"; else v += ", "; } - XML_Node& f = node.addChild("intArray",v); +#ifdef CTML_VERSION_1_4 + XML_Node& f = node.addChild("intArray",v); f.addAttribute("title",title); +#else + XML_Node& f = node.addChild(title, v); +#endif if (type != "") f.addAttribute("type",type); f.addAttribute("size",n); +#ifndef CTML_VERSION_1_4 + f.addAttribute("vtype", "intArray"); +#endif if (units != "") f.addAttribute("units",units); if (minval != Undef) f.addAttribute("min",minval); if (maxval != Undef) f.addAttribute("max",maxval); @@ -252,13 +264,14 @@ namespace ctml { const doublereal maxval) { string fmt = "%17.9E"; #ifdef CTML_VERSION_1_4 - XML_Node& f = node.addChild("float",val,fmt); - f.addAttribute("title",title); + XML_Node& f = node.addChild("float", val, fmt); + f.addAttribute("title", title); #else - XML_Node& f = node.addChild(title,val,fmt); + XML_Node& f = node.addChild(title, val, fmt); #endif if (type != "") f.addAttribute("type",type); if (units != "") f.addAttribute("units",units); + f.addAttribute("vtype", "float"); if (minval != Undef) f.addAttribute("min",minval); if (maxval != Undef) f.addAttribute("max",maxval); } @@ -300,7 +313,7 @@ namespace ctml { * @param unitsString String name of the Units attribute. This is an optional * parameter. The default is to * have an empty string. - * @param typeString String type. This is an optional parameter. The default + * @param type String type. This is an optional parameter. The default * is to have an empty string. * @param minval Minimum allowed value of the int. This is an optional * parameter. The default is the @@ -337,6 +350,87 @@ namespace ctml { if (maxval != Undef) f.addAttribute("max",maxval); } //==================================================================================================================== + // This function adds a child node with the name given by the first parameter with a value + // consisting of a comma separated list of floats + /* + * This function will add a child node to the current XML node, with the + * name given in the list. It will have a title attribute, and the body + * of the XML node will be filled out with a comma separated list of + * integers + * + * Example: + * + * Code snipet: + * @verbatum + const XML_Node &node; + std::string titleString = "additionalTemperatures"; + int n = 3; + int Tcases[3] = [273.15, 298.15, 373.15]; + std::string typeString = "optional"; + std::string units = "Kelvin"; + addNamedFloatArray(node, titleString, n, &cases[0], typeString, units); + @endverbatum + * + * Creates the following the snippet in the XML file: + * @verbatum + + + 273.15, 298.15, 373.15 + <\additionalTemperatures> + <\parentNode> + @endverbatum + * + * @param node reference to the XML_Node object of the parent XML element + * @param name Name of the XML node + * @param n Length of the doubles vector. + * @param values Pointer to a vector of doubles + * @param unitsString String name of the Units attribute. This is an optional + * parameter. The default is to + * have an empty string. + * @param type String type. This is an optional parameter. The default + * is to have an empty string. + * @param minval Minimum allowed value of the int. This is an optional + * parameter. The default is the + * special double, Cantera::Undef, which means to ignore the + * entry. + * @param maxval Maximum allowed value of the int. This is an optional + * parameter. The default is the + * special double, Cantera::Undef, which means to ignore the + * entry. + * + * @todo I don't think this is used. Figure out what is used for writing integers, + * and codify that. unitsString shouldn't be here, since it's an int. + * typeString should be codified as to its usage. + */ + void addNamedFloatArray(Cantera::XML_Node& node, const std::string &name, const int n, + const doublereal* const vals, const std::string units, + const std::string type, const doublereal minval, + const doublereal maxval) { + std::string fmt = "%17.9E"; + int i; + std::string v = ""; + for (i = 0; i < n; i++) { + v += fp2str(vals[i],fmt); + if (i == n-1) v += "\n"; + else if (i > 0 && (i+1) % 3 == 0) v += ",\n"; + else v += ", "; + } + XML_Node& f = node.addChild(name, v); + if (type != "") { + f.addAttribute("type",type); + } + /* + * Add vtype, which indicates the type of the value. Here we specify it as a list of floats separated + * by commas, with a length given by size attribute. + */ + f.addAttribute("vtype", "floatArray"); + + f.addAttribute("size", n); + if (units != "") f.addAttribute("units", units); + if (minval != Undef) f.addAttribute("min", minval); + if (maxval != Undef) f.addAttribute("max", maxval); + } + //==================================================================================================================== // This function adds a child node with the name string with a string value // to the current node /* @@ -1114,6 +1208,96 @@ namespace ctml { return v.size(); } //==================================================================================================================== + int getNamedFloatArray(const Cantera::XML_Node& parentNode, const std::string & nodeName, std::vector & v, + const bool convert, const std::string unitsString) { + std::string::size_type icom; + std::string numstr; + doublereal dtmp; + std::string nn = parentNode.name(); + v.clear(); + const Cantera::XML_Node *readNode = parentNode.findByName(nodeName); + if (!readNode) { + return 0; + } + + doublereal vmin = Undef; + doublereal vmax = Undef; + doublereal funit = 1.0; + /* + * Get the attributes field, units, from the XML node + */ + std::string units = (*readNode)["units"]; + if (units != "" && convert) { + if (unitsString == "actEnergy" && units != "") { + funit = actEnergyToSI(units); + } else if (unitsString != "" && units != "") { + funit = toSI(units); + } + } + + if ((*readNode)["min"] != "") + vmin = atofCheck((*readNode)["min"].c_str()); + if ((*readNode)["max"] != "") + vmax = atofCheck((*readNode)["max"].c_str()); + + int expectedSize = 0; + nn = (*readNode)["size"]; + expectedSize = atoi(nn.c_str()); + + nn = (*readNode)["vtype"]; + if (nn != "floatArray") { + throw CanteraError("getNamedFloatArray", + "node named " + nodeName + "didn't have correct vtype"); + } + + doublereal vv; + std::string val = readNode->value(); + while (1 > 0) { + icom = val.find(','); + if (icom != string::npos) { + numstr = val.substr(0,icom); + val = val.substr(icom+1,val.size()); + dtmp = atofCheck(numstr.c_str()); + v.push_back(dtmp); + } + else { + /* + * This little bit of code is to allow for the + * possibility of a comma being the last + * item in the value text. This was allowed in + * previous versions of Cantera, even though it + * would appear to be odd. So, we keep the + * possibilty in for backwards compatibility. + */ + int nlen = strlen(val.c_str()); + if (nlen > 0) { + dtmp = atofCheck(val.c_str()); + v.push_back(dtmp); + } + break; + } + vv = v.back(); + if (vmin != Undef && vv < vmin - Tiny) { + writelog("\nWarning: value "+fp2str(vv)+ + " is below lower limit of " +fp2str(vmin)+".\n"); + } + if (vmax != Undef && vv > vmax + Tiny) { + writelog("\nWarning: value "+fp2str(vv)+ + " is above upper limit of " +fp2str(vmin)+".\n"); + } + } + int nv = v.size(); + for (int n = 0; n < nv; n++) { + v[n] *= funit; + } + if (nv != expectedSize) { + throw CanteraError("getNamedFloatArray", + "node named " + nodeName + "didn't have correct number of floats" + + int2str(expectedSize) + " vs " + int2str(nv)); + } + return nv; + } + //==================================================================================================================== // This routine is used to interpret the value portions of XML // elements that contain colon separated pairs. /* diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index bd0614b16..434e5fa02 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -282,6 +282,15 @@ namespace ctml { const doublereal minval = Cantera::Undef, const doublereal maxval = Cantera::Undef); + void addNamedFloatArray(Cantera::XML_Node& parentNode, const std::string &name, const int n, + const doublereal* const vals, const std::string units = "", + const std::string type = "", + const doublereal minval = Cantera::Undef, + const doublereal maxval = Cantera::Undef); + + + + //! This function adds a child node with the name string with a string value //! to the current node /*! diff --git a/Cantera/src/base/units.h b/Cantera/src/base/units.h index bf81f8820..ac988cb23 100644 --- a/Cantera/src/base/units.h +++ b/Cantera/src/base/units.h @@ -216,6 +216,7 @@ namespace Cantera { // temperature m_u["K"] = 1.0; m_u["C"] = 1.0; + m_u["Kelvin"] = 1.0; // mass m_u["gm"] = 1.0e-3; @@ -233,6 +234,11 @@ namespace Cantera { m_u["hr"] = 3600.0; m_u["ms"] = 0.001; + // electric potential + m_u["volt"] = 1.0; + + // charge + m_u["coulomb"] = 1.0; /* // frequency - Took frequency out to reevaluate it. Inverse cm is probably the wrong default unit diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index e5cb9aa94..0db1dc8f3 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -539,7 +539,7 @@ namespace Cantera { XML_Node& XML_Node::mergeAsChild(XML_Node& node) { m_children.push_back(&node); m_nchildren = static_cast(m_children.size()); - m_childindex[node.name()] = m_children.back(); + m_childindex.insert(pair(node.name(), m_children.back())); node.setRoot(root()); node.setParent(this); return *m_children.back(); @@ -559,7 +559,7 @@ namespace Cantera { XML_Node *xx = new XML_Node(node); m_children.push_back(xx); m_nchildren = static_cast(m_children.size()); - m_childindex[xx->name()] = m_children.back(); + m_childindex.insert( pair(xx->name(), xx)); xx->setRoot(root()); xx->setParent(this); return *m_children.back(); @@ -578,7 +578,7 @@ namespace Cantera { XML_Node *xxx = new XML_Node(sname, this); m_children.push_back(xxx); m_nchildren = static_cast(m_children.size()); - m_childindex[sname] = m_children.back(); + m_childindex.insert(pair(sname, xxx)); xxx->setRoot(root()); xxx->setParent(this); return *m_children.back(); @@ -1098,15 +1098,17 @@ namespace Cantera { * * @return Returns the pointer to the XML node that fits the criteria */ - XML_Node* XML_Node::findByName(const std::string& nm) { + XML_Node* XML_Node::findByName(const std::string& nm, int depth) { if (name() == nm) { return this; } - XML_Node* r = 0; - int n = nChildren(); - for (int i = 0; i < n; i++) { - r = m_children[i]->findByName(nm); - if (r != 0) return r; + if (depth > 0) { + XML_Node* r = 0; + int n = nChildren(); + for (int i = 0; i < n; i++) { + r = m_children[i]->findByName(nm); + if (r != 0) return r; + } } return 0; } @@ -1122,15 +1124,17 @@ namespace Cantera { * * @return Returns the pointer to the XML node that fits the criteria */ - const XML_Node* XML_Node::findByName(const std::string& nm) const { + const XML_Node* XML_Node::findByName(const std::string& nm, int depth) const { if (name() == nm) { return const_cast(this); } - const XML_Node* r = 0; - int n = nChildren(); - for (int i = 0; i < n; i++) { - r = m_children[i]->findByName(nm); - if (r != 0) return r; + if (depth > 0) { + const XML_Node* r = 0; + int n = nChildren(); + for (int i = 0; i < n; i++) { + r = m_children[i]->findByName(nm); + if (r != 0) return r; + } } return 0; } diff --git a/Cantera/src/base/xml.h b/Cantera/src/base/xml.h index 890470fe9..b81fe6c00 100644 --- a/Cantera/src/base/xml.h +++ b/Cantera/src/base/xml.h @@ -156,6 +156,10 @@ namespace Cantera { class XML_Node { public: + //! Value_type for the lookup multimap m_childindex. This is a convenience definition + //! for manipulating the multimap + typedef std::pair CIPair; + //! Default constructor for XML_Node, representing a tree structure /*! * Constructor for an XML_Node, which is a node in a tree-like structure @@ -621,10 +625,12 @@ namespace Cantera { * This is the const version of the routine. * * @param nm Name of the XML node + * @param depth Depth of the search. A value of 1 means that only the + * immediate children are searched. * * @return Returns the pointer to the XML node that fits the criteria */ - const XML_Node* findByName(const std::string& nm) const; + const XML_Node* findByName(const std::string& nm, int depth = 100000) const; //! This routine carries out a recursive search for an XML node based //! on the name of the node. @@ -634,10 +640,12 @@ namespace Cantera { * This is the non-const version of the routine. * * @param nm Name of the XML node + * @param depth Depth of the search. A value of 1 means that only the + * immediate children are searched. * * @return Returns the pointer to the XML node that fits the criteria */ - XML_Node* findByName(const std::string& nm); + XML_Node* findByName(const std::string& nm, int depth = 100000); //! Get a vector of pointers to XML_Node containing all of the children //! of the current node which matches the input name @@ -649,9 +657,11 @@ namespace Cantera { */ void getChildren(const std::string &name, std::vector& children) const; - //! Return a changeable reference to a child of the current node, - //! named by the argument + //! Return a changeable reference to a child of the current node, named by the argument /*! + * Note the underlying data allows for more than one XML element with the same name. + * This routine returns the first child with the given name. + * * @param loc Name of the child to return */ XML_Node& child(const std::string &loc) const; @@ -782,9 +792,10 @@ namespace Cantera { /*! * m_childindex[node.name()] = XML_Node *pointer * - * This object helps to speed up searches + * This object helps to speed up searches. + * The value_type for this multimap is CIPair. */ - std::map m_childindex; + std::multimap m_childindex; //! Storage of attributes for a node /*! From cb4048249c8d9d6f0cf67753bd658f3af575b915 Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 8 Feb 2012 15:59:11 +0000 Subject: [PATCH 445/446] Added a way to specify weighting norms for the residuals. --- Cantera/src/numerics/NonlinearSolver.cpp | 127 ++++++++++++++++++----- Cantera/src/numerics/NonlinearSolver.h | 45 ++++++++ 2 files changed, 145 insertions(+), 27 deletions(-) diff --git a/Cantera/src/numerics/NonlinearSolver.cpp b/Cantera/src/numerics/NonlinearSolver.cpp index cbc3af79f..a79765aa4 100644 --- a/Cantera/src/numerics/NonlinearSolver.cpp +++ b/Cantera/src/numerics/NonlinearSolver.cpp @@ -146,6 +146,9 @@ namespace Cantera { atolBase_(1.0E-10), m_ydot_nm1(0), atolk_(0), + userResidAtol_(0), + userResidRtol_(1.0E-3), + checkUserResidualTols_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopyPtr_(0), @@ -267,6 +270,9 @@ namespace Cantera { atolBase_(1.0E-10), m_ydot_nm1(0), atolk_(0), + userResidAtol_(0), + userResidRtol_(1.0E-3), + checkUserResidualTols_(0), m_print_flag(0), m_ScaleSolnNormToResNorm(0.001), jacCopyPtr_(0), @@ -368,6 +374,9 @@ namespace Cantera { rtol_ = right.rtol_; atolBase_ = right.atolBase_; atolk_ = right.atolk_; + userResidAtol_ = right.userResidAtol_; + userResidRtol_ = right.userResidRtol_; + checkUserResidualTols_ = right.checkUserResidualTols_; m_print_flag = right.m_print_flag; m_ScaleSolnNormToResNorm = right.m_ScaleSolnNormToResNorm; @@ -736,7 +745,7 @@ namespace Cantera { int irow, jcol; int ku, kl; int ivec[2]; - int n = jac.nRowsAndStruct(ivec); + jac.nRowsAndStruct(ivec); double *colP_j; /* @@ -882,15 +891,25 @@ namespace Cantera { { if (! jacCopyPtr_->factored()) { - - doublereal sum = 0.0; - for (int irow = 0; irow < neq_; irow++) { - m_residWts[irow] = m_rowWtScales[irow] / neq_; - sum += m_residWts[irow]; - } - sum /= neq_; - for (int irow = 0; irow < neq_; irow++) { - m_residWts[irow] = (m_residWts[irow] + atolBase_ * atolBase_ * sum); + if (checkUserResidualTols_ != 1) { + doublereal sum = 0.0; + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = m_rowWtScales[irow] / neq_; + sum += m_residWts[irow]; + } + sum /= neq_; + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = (m_residWts[irow] + atolBase_ * atolBase_ * sum); + } + if (checkUserResidualTols_ == 2) { + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = MIN(m_residWts[irow], userResidAtol_[irow] + userResidRtol_ * m_rowWtScales[irow] / neq_); + } + } + } else { + for (int irow = 0; irow < neq_; irow++) { + m_residWts[irow] = userResidAtol_[irow] + userResidRtol_ * m_rowWtScales[irow] / neq_; + } } @@ -919,6 +938,7 @@ namespace Cantera { if (m_ScaleSolnNormToResNorm < 1.0E-8) { m_ScaleSolnNormToResNorm = 1.0E-8; } + // Recalculate the residual weights now that we know the value of m_ScaleSolnNormToResNorm computeResidWts(); } else { @@ -2232,7 +2252,7 @@ namespace Cantera { * @param alpha Relative length along the dog length that you are on. * @param deltaX Vector to be filled up */ - void NonlinearSolver::fillDogLegStep(int leg, doublereal alpha, std::vector & deltaX) const { + void NonlinearSolver::fillDogLegStep(int leg, doublereal alpha, std::vector & deltaX) const { if (leg == 0) { for (int i = 0; i < neq_; i++) { deltaX[i] = alpha * deltaX_CP_[i]; @@ -2343,7 +2363,8 @@ namespace Cantera { * Maximum decrease in variable in any one newton iteration: * factor of 5 */ - doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0) { + doublereal NonlinearSolver::boundStep(const doublereal * const y, const doublereal * const step0) + { int i, i_lower = -1; doublereal fbound = 1.0, f_bounds = 1.0; doublereal ff, y_new; @@ -2611,7 +2632,8 @@ namespace Cantera { } if (stepNorm_2 < 1.0) { if (m_print_flag >= 4 ) { - printf("\t dampStep(): current trial step accepted and soln converged retnTrial = %d, its = %d, damp = %g\n", 0, m+1, ff); + printf("\t dampStep(): current trial step accepted and soln converged retnTrial =" + "%d, its = %d, damp = %g\n", 0, m+1, ff); } return 0; } @@ -2715,7 +2737,8 @@ namespace Cantera { * OK, we have the step0. Now, ask the question whether it satisfies the acceptance criteria * as a good step. The overall outcome is returned in the variable info. */ - info = decideStep(time_curr, dogLegID_, dogLegAlpha_, y_n_curr, ydot_n_curr, step_1, y_n_1, ydot_n_1, trustDeltaOld); + info = decideStep(time_curr, dogLegID_, dogLegAlpha_, y_n_curr, ydot_n_curr, step_1, + y_n_1, ydot_n_1, trustDeltaOld); m_normResid_Bound = m_normResid_1; /* @@ -2825,9 +2848,11 @@ namespace Cantera { * -2 Current value of the solution vector caused a residual error in its evaluation. * Step is a failure, and the step size must be reduced in order to proceed further. */ - int NonlinearSolver::decideStep(const doublereal time_curr, int leg, doublereal alpha, const doublereal * const y_n_curr, + int NonlinearSolver::decideStep(const doublereal time_curr, int leg, doublereal alpha, + const doublereal * const y_n_curr, const doublereal * const ydot_n_curr, const std::vector & step_1, - const doublereal * const y_n_1, const doublereal * const ydot_n_1, doublereal trustDeltaOld) + const doublereal * const y_n_1, const doublereal * const ydot_n_1, + doublereal trustDeltaOld) { int retn = 2; bool goodStep = false; @@ -2889,11 +2914,13 @@ namespace Cantera { m_normResid_1 = m_normResidTrial; retn = 0; if (m_print_flag >= 4) { - printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E passes\n", dogLegID_, dogLegAlpha_, m_normResidTrial); + printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E passes\n", + dogLegID_, dogLegAlpha_, m_normResidTrial); } } else { if (m_print_flag >= 4) { - printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E failes\n", dogLegID_, dogLegAlpha_, m_normResidTrial); + printf("\t\t decideStep: Norm Residual(leg=%1d, alpha=%10.2E) = %11.4E failes\n", + dogLegID_, dogLegAlpha_, m_normResidTrial); } trustDelta_ *= 0.33; CurrentTrustFactor_ *= 0.33; @@ -3994,14 +4021,26 @@ namespace Cantera { NonlinearSolver::computeResidWts() { ResidWtsReevaluated_ = true; - doublereal sum = 0.0; - for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_rowWtScales[i] / neq_; - sum += m_residWts[i]; - } - sum /= neq_; - for (int i = 0; i < neq_; i++) { - m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * atolBase_ * sum); + if (checkUserResidualTols_ == 1) { + for (int i = 0; i < neq_; i++) { + m_residWts[i] = userResidAtol_[i] + userResidRtol_ * m_rowWtScales[i] / neq_; + } + } else { + doublereal sum = 0.0; + for (int i = 0; i < neq_; i++) { + m_residWts[i] = m_rowWtScales[i] / neq_; + sum += m_residWts[i]; + } + sum /= neq_; + for (int i = 0; i < neq_; i++) { + m_residWts[i] = m_ScaleSolnNormToResNorm * (m_residWts[i] + atolBase_ * atolBase_ * sum); + } + if (checkUserResidualTols_ == 2) { + for (int i = 0; i < neq_; i++) { + double uR = userResidAtol_[i] + userResidRtol_ * m_rowWtScales[i] / neq_; + m_residWts[i] = MIN(m_residWts[i], uR); + } + } } } //===================================================================================================================== @@ -4093,7 +4132,7 @@ namespace Cantera { //===================================================================================================================== // Set the relative tolerances for the solution variables /* - * Set the relative tolerances used in the calculation + * Set the relative tolerances used in the calculation for the solution variables. * * @param rtol single double */ @@ -4102,6 +4141,40 @@ namespace Cantera { rtol_ = rtol; } //===================================================================================================================== + // Set the relative and absolute tolerances for the Residual norm comparisons, if used + /* + * + * residWeightNorm[i] = residAtol[i] + residRtol * m_rowWtScales[i] / neq + * + * @param residNormHandling Parameter that sets the default handling of the residual norms + * 0 The residual weighting vector is calculated to make sure that the solution + * norms are roughly 1 when the residual norm is roughly 1. + * This is the default if this routine is not called. + * 1 Use the user residual norm specified by the parameters in this routine + * 2 Use the minimum value of the residual weights calculcated by method 1 and 2. + * This is the default if this routine is called and this parameter isn't specified. + */ + void NonlinearSolver::setResidualTols(double residRtol, double * residATol, int residNormHandling) + { + if (residNormHandling < 0 || residNormHandling > 2) { + throw CanteraError("NonlinearSolver::setResidualTols()", + "Unknown int for residNormHandling"); + } + checkUserResidualTols_ = residNormHandling; + userResidRtol_ = residRtol; + if (residATol) { + userResidAtol_.resize(neq_); + for (int i = 0; i < neq_; i++) { + userResidAtol_[i] = residATol[i]; + } + } else { + if (residNormHandling ==1 || residNormHandling == 2) { + throw CanteraError("NonlinearSolver::setResidualTols()", + "Must set residATol vector"); + } + } + } + //===================================================================================================================== void NonlinearSolver::setPrintLvl(int printLvl) { m_print_flag = printLvl; diff --git a/Cantera/src/numerics/NonlinearSolver.h b/Cantera/src/numerics/NonlinearSolver.h index 6972934ac..c6c92c366 100644 --- a/Cantera/src/numerics/NonlinearSolver.h +++ b/Cantera/src/numerics/NonlinearSolver.h @@ -667,6 +667,35 @@ namespace Cantera { */ void setRtol(const doublereal rtol); + //! Set the relative and absolute tolerances for the Residual norm comparisons, if used + /*! + * Residual norms are used to calculate convergence within the nonlinear solver, since + * these are the norms that are associated with convergence proofs, especially for ill-conditioned systems. + * Usually the residual weights for each row are calculated by the program such that they + * correlate with the convergence requirements on the solution variables input by the user using + * the routines setAtol() and setRtol(). + * The residual weights are essentially calculated from the value + * + * residWeightNorm[i] = m_ScaleSolnNormToResNorm * sum_j ( fabs(A_i,j) ewt(j)) + * + * The factor, m_ScaleSolnNormToResNorm, is computed periodically to ensure that the solution norms + * and the residual norms are converging at the same time and thus accounts for some-illconditioning issues + * but not all. + * + * The user specified tolerance for the residual is given by the following quantity + * + * residWeightNorm[i] = residAtol[i] + residRtol * m_rowWtScales[i] / neq + * + * @param residNormHandling Parameter that sets the default handling of the residual norms + * 0 The residual weighting vector is calculated to make sure that the solution + * norms are roughly 1 when the residual norm is roughly 1. + * This is the default if this routine is not called. + * 1 Use the user residual norm specified by the parameters in this routine + * 2 Use the minimum value of the residual weights calculcated by method 1 and 2. + * This is the default if this routine is called and this parameter isn't specified. + */ + void setResidualTols(double residRtol, double * residATol, int residNormHandling = 2); + //! Set the value of the maximum # of newton iterations /*! * @param maxNewtIts Maximum number of newton iterations @@ -878,6 +907,8 @@ namespace Cantera { */ void setSolverScheme(int doDogLeg, int doAffineSolve); + + /* * ----------------------------------------------------------------------------------------------------------------- * MEMBER DATA @@ -1082,6 +1113,20 @@ namespace Cantera { */ std::vector atolk_; + //! absolute tolerance in the unscaled solution unknowns + std::vector userResidAtol_; + + //! absolute tolerance in the unscaled solution unknowns + doublereal userResidRtol_; + + //! Check the residual tolerances explictly against user input + /*! + * 0 Don't calculate residual weights from residual tolerance inputs + * 1 Calculate residual weights from residual tolerance inputs only + * 2 Calculate residual weights from a minimum of the solution error weights process and the direct residual tolerance inputs + */ + int checkUserResidualTols_; + //! Determines the level of printing for each time step. /*! * 0 -> absolutely nothing is printed for a single time step. From 39f2e4786aa10a0fd1203e53aa556004706e488c Mon Sep 17 00:00:00 2001 From: Harry Moffat Date: Wed, 8 Feb 2012 16:00:55 +0000 Subject: [PATCH 446/446] Changed the default number of digits that are saved to an xml file. This crucial change is needed if xml files are to be used as restart files, where we will need close to machine precision. --- Cantera/src/base/ctml.cpp | 17 ++++++++--------- Cantera/src/base/ctml.h | 4 ++++ Cantera/src/base/xml.cpp | 2 +- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp index 2305aa6a7..ca4185b91 100644 --- a/Cantera/src/base/ctml.cpp +++ b/Cantera/src/base/ctml.cpp @@ -37,6 +37,9 @@ using namespace Cantera; namespace ctml { + std::string FP_Format = "%23.15E"; + std::string INT_Format = "%8d"; + //==================================================================================================================== //! Convert a floating point value from a string to a double /*! @@ -191,11 +194,10 @@ namespace ctml { void addIntegerArray(Cantera::XML_Node& node, const std::string &title, const int n, const int* const vals, const std::string units, const std::string type, const doublereal minval, const doublereal maxval) { - std::string fmt = "%8d"; int i; std::string v = ""; for (i = 0; i < n; i++) { - v += int2str(vals[i],fmt); + v += int2str(vals[i],INT_Format); if (i == n-1) v += "\n"; else if (i > 0 && (i+1) % 3 == 0) v += ",\n"; else v += ", "; @@ -262,12 +264,11 @@ namespace ctml { const doublereal val, const std::string units, const std::string type, const doublereal minval, const doublereal maxval) { - string fmt = "%17.9E"; #ifdef CTML_VERSION_1_4 - XML_Node& f = node.addChild("float", val, fmt); + XML_Node& f = node.addChild("float", val, ctml::FP_Format); f.addAttribute("title", title); #else - XML_Node& f = node.addChild(title, val, fmt); + XML_Node& f = node.addChild(title, val, ctml::FP_Format); #endif if (type != "") f.addAttribute("type",type); if (units != "") f.addAttribute("units",units); @@ -332,11 +333,10 @@ namespace ctml { const doublereal* const vals, const std::string units, const std::string type, const doublereal minval, const doublereal maxval) { - std::string fmt = "%17.9E"; int i; std::string v = ""; for (i = 0; i < n; i++) { - v += fp2str(vals[i],fmt); + v += fp2str(vals[i],FP_Format); if (i == n-1) v += "\n"; else if (i > 0 && (i+1) % 3 == 0) v += ",\n"; else v += ", "; @@ -406,11 +406,10 @@ namespace ctml { const doublereal* const vals, const std::string units, const std::string type, const doublereal minval, const doublereal maxval) { - std::string fmt = "%17.9E"; int i; std::string v = ""; for (i = 0; i < n; i++) { - v += fp2str(vals[i],fmt); + v += fp2str(vals[i],FP_Format); if (i == n-1) v += "\n"; else if (i > 0 && (i+1) % 3 == 0) v += ",\n"; else v += ", "; diff --git a/Cantera/src/base/ctml.h b/Cantera/src/base/ctml.h index 434e5fa02..6199a3e3d 100644 --- a/Cantera/src/base/ctml.h +++ b/Cantera/src/base/ctml.h @@ -33,6 +33,10 @@ namespace ctml { */ const std::string CTML_Version = "1.4.1"; + extern std::string FP_Format; + + extern std::string INT_Format; + //! This function adds a child node with the name, "bool", with a value //! consisting of a single bool /*! diff --git a/Cantera/src/base/xml.cpp b/Cantera/src/base/xml.cpp index 0db1dc8f3..2fd3ea015 100644 --- a/Cantera/src/base/xml.cpp +++ b/Cantera/src/base/xml.cpp @@ -1437,7 +1437,7 @@ namespace Cantera { bool doSpace = true; bool doNewLine = false; int ll = static_cast(m_value.size()) - 1; - if (ll > 15) { + if (ll > 25) { doNewLine = true; } if (m_name == "floatArray") {