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Cleaned up Doxygen docs for class ImplicitSurfChem

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This commit is contained in:
Ray Speth 2013-04-12 23:05:46 +00:00
parent 76d3a03921
commit 68c0270958
2 changed files with 47 additions and 143 deletions
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121
include/cantera/kinetics/ImplicitSurfChem.h
View file

@ -17,54 +17,46 @@
namespace Cantera
{
class solveSP;
//! Advances the surface coverages of the associated set of SurfacePhase
//! objects in time
/*!
* This function advances a set of SurfacePhase objects, each
* associated with one InterfaceKinetics object, in time.
* The following equation is used for each surface phase, <I>i</I>.
* This function advances a set of SurfPhase objects, each associated with one
* InterfaceKinetics object, in time. The following equation is used for each
* surface phase, *i*.
*
* \f[
* \dot \theta_k = \dot s_k (\sigma_k / s_0)
* \f]
*
* In this equation,
* \f$ \theta_k \f$ is the site coverage for the kth species.
* \f$ \dot s_k \f$ is the source term for the kth species
* \f$ \sigma_k \f$ is the number of surface sites covered by
* each species k.
* \f$ s_0 \f$ is the total site density of the interfacial phase.
* In this equation,
* - \f$ \theta_k \f$ is the site coverage for the kth species.
* - \f$ \dot s_k \f$ is the source term for the kth species
* - \f$ \sigma_k \f$ is the number of surface sites covered by each species k.
* - \f$ s_0 \f$ is the total site density of the interfacial phase.
*
* Additionally, the 0'th equation in the set is discarded. Instead the
* alternate equation is solved for
* Additionally, the 0'th equation in the set is discarded. Instead the
* alternate equation is solved for
*
* \f[
* \sum_{k=0}^{N-1} \dot \theta_k = 0
* \f]
* \f[
* \sum_{k=0}^{N-1} \dot \theta_k = 0
* \f]
*
* This last equation serves to ensure that sum of the \f$ \theta_k \f$
* values stays constant.
* This last equation serves to ensure that sum of the \f$ \theta_k \f$ values
* stays constant.
*
* The object uses the CVODE software to advance the surface equations.
* The object uses the CVODE software to advance the surface equations.
*
* The solution vector used by this object is as follows.
* For each surface phase with \f$ N_s \f$ surface sites,
* it consists of the surface coverages
* \f$ \theta_k \f$ for \f$ k = 0, N_s - 1 \f$
* The solution vector used by this object is as follows: For each surface
* phase with \f$ N_s \f$ surface sites, it consists of the surface coverages
* \f$ \theta_k \f$ for \f$ k = 0, N_s - 1 \f$
*
* @ingroup kineticsmgr
*
*/
class ImplicitSurfChem : public FuncEval
{
public:
//! Constructor for multiple surfaces.
/*!
* @param k Vector of pointers to InterfaceKinetics objects
@ -79,13 +71,11 @@ public:
*/
virtual ~ImplicitSurfChem();
/**
* Overloads the virtual function
* declared in FuncEval.
/*!
* Must be called before calling method 'advance'
*/
virtual void initialize(doublereal t0 = 0.0);
//! Integrate from t0 to t1. The integrator is reinitialized first.
/*!
* This routine does a time accurate solve from t = t0 to t = t1.
@ -96,19 +86,16 @@ public:
*/
void integrate(doublereal t0, doublereal t1);
//! Integrate from t0 to t1 without reinitializing the integrator.
/*!
* Use when the coverages have not changed from
* their values on return from the last call to integrate or
* integrate0.
* Use when the coverages have not changed from their values on return
* from the last call to integrate or integrate0.
*
* @param t0 Initial Time -> this is an input
* @param t1 Final Time -> This is an input
*/
void integrate0(doublereal t0, doublereal t1);
//! Solve for the pseudo steady-state of the surface problem
/*!
* Solve for the steady state of the surface problem.
@ -118,13 +105,13 @@ public:
* Note, a direct solve is carried out under the hood here,
* to reduce the computational time.
*
* @param ifuncOverride 4 values are possible
* 1 SFLUX_INITIALIZE
* 2 SFLUX_RESIDUAL
* 3 SFLUX_JACOBIAN
* 4 SFLUX_TRANSIENT
* The default is -1, which means that the program
* will decide.
* @param ifuncOverride 4 values are possible. The default is -1, which
* means that the program will decide:
* - 1 SFLUX_INITIALIZE
* - 2 SFLUX_RESIDUAL
* - 3 SFLUX_JACOBIAN
* - 4 SFLUX_TRANSIENT
*
* @param timeScaleOverride When a pseudo transient is
* selected this value can be used to override
* the default time scale for integration which
@ -138,7 +125,6 @@ public:
void solvePseudoSteadyStateProblem(int ifuncOverride = -1,
doublereal timeScaleOverride = 1.0);
// overloaded methods of class FuncEval
//! Return the number of equations
@ -168,27 +154,24 @@ public:
virtual void getInitialConditions(doublereal t0,
size_t leny, doublereal* y);
/*
/*!
* Get the specifications for the problem from the values
* in the ThermoPhase objects for all phases.
*
* 1) concentrations of all species in all phases, m_concSpecies[]
* 2) Temperature and pressure
* 1. concentrations of all species in all phases, #m_concSpecies
* 2. Temperature and pressure
*
*
* @param vecConcSpecies Vector of concentrations. The
* phase concentration vectors are contiguous
* within the object, in the same order as the
* unknown vector.
* @param vecConcSpecies Vector of concentrations. The phase
* concentration vectors are contiguous within the
* object, in the same order as the unknown vector.
*/
void getConcSpecies(doublereal* const vecConcSpecies) const;
//! Sets the concentrations within phases that are unknowns in
//! the surface problem
/*!
* Fills the local concentration vector for all of the
* species in all of the phases that are unknowns in the surface
* problem.
* Fills the local concentration vector for all of the species in all of
* the phases that are unknowns in the surface problem.
*
* @param vecConcSpecies Vector of concentrations. The
* phase concentration vectors are contiguous
@ -205,12 +188,10 @@ public:
*/
void setCommonState_TP(doublereal TKelvin, doublereal PresPa);
//! Returns a reference to the vector of pointers to the
//! InterfaceKinetics objects
/*!
* This should probably go away in the future, as it opens up the
* class.
* This should probably go away in the future, as it opens up the class.
*/
std::vector<InterfaceKinetics*> & getObjects() {
return m_vecKinPtrs;
@ -223,18 +204,14 @@ public:
}
protected:
//! Set the mixture to a state consistent with solution
//! vector y.
/*!
* This function will set the surface site factions
* in the underlying %SurfPhase objects to the current
* value of the solution vector.
* This function will set the surface site factions in the underlying
* SurfPhase objects to the current value of the solution vector.
*
* @param y Current value of the solution vector.
* The lenth is equal to the sum of the number of surface
* sites in all the surface phases
* @param y Current value of the solution vector. The lenth is equal to
* the sum of the number of surface sites in all the surface phases.
*/
void updateState(doublereal* y);
@ -278,15 +255,13 @@ protected:
//! Pointer to the cvode integrator
Integrator* m_integ;
doublereal m_atol, m_rtol; // tolerances
doublereal m_maxstep; // max step size
doublereal m_maxstep; //!< max step size
vector_fp m_work;
/**
* Temporary vector - length num species in the Kinetics object.
* This is the sum of the number of species
* in each phase included in the kinetics object.
* Temporary vector - length num species in the Kinetics object. This is
* the sum of the number of species in each phase included in the kinetics
* object.
*/
vector_fp m_concSpecies;
vector_fp m_concSpeciesSave;
@ -327,7 +302,6 @@ protected:
friend class solveSS;
private:
//! Controls the amount of printing from this routine
//! and underlying routines.
int m_ioFlag;
@ -335,4 +309,3 @@ private:
}
#endif

69
src/kinetics/ImplicitSurfChem.cpp
View file

@ -15,7 +15,6 @@ using namespace std;
namespace Cantera
{
// Constructor
ImplicitSurfChem::ImplicitSurfChem(vector<InterfaceKinetics*> k) :
FuncEval(),
m_nsurf(0),
@ -109,17 +108,12 @@ int ImplicitSurfChem::checkMatch(std::vector<ThermoPhase*> m_vec, ThermoPhase* t
return retn;
}
/*
* Destructor. Deletes the integrator.
*/
ImplicitSurfChem::~ImplicitSurfChem()
{
delete m_integ;
delete m_surfSolver;
}
// overloaded method of FuncEval. Called by the integrator to
// get the initial conditions.
void ImplicitSurfChem::getInitialConditions(doublereal t0, size_t lenc,
doublereal* c)
{
@ -130,24 +124,12 @@ void ImplicitSurfChem::getInitialConditions(doublereal t0, size_t lenc,
}
}
/*
* Must be called before calling method 'advance'
*/
void ImplicitSurfChem::initialize(doublereal t0)
{
m_integ->setTolerances(m_rtol, m_atol);
m_integ->initialize(t0, *this);
}
// Integrate from t0 to t1. The integrator is reinitialized first.
/*
* This routine does a time accurate solve from t = t0 to t = t1.
* of the surface problem.
*
* @param t0 Initial Time -> this is an input
* @param t1 Final Time -> This is an input
*/
void ImplicitSurfChem::integrate(doublereal t0, doublereal t1)
{
m_integ->initialize(t0, *this);
@ -156,15 +138,6 @@ void ImplicitSurfChem::integrate(doublereal t0, doublereal t1)
updateState(m_integ->solution());
}
// Integrate from t0 to t1 without reinitializing the integrator.
/*
* Use when the coverages have not changed from
* their values on return from the last call to integrate or
* integrate0.
*
* @param t0 Initial Time -> this is an input
* @param t1 Final Time -> This is an input
*/
void ImplicitSurfChem::integrate0(doublereal t0, doublereal t1)
{
m_integ->integrate(t1);
@ -180,9 +153,6 @@ void ImplicitSurfChem::updateState(doublereal* c)
}
}
/*
* Called by the integrator to evaluate ydot given y at time 'time'.
*/
void ImplicitSurfChem::eval(doublereal time, doublereal* y,
doublereal* ydot, doublereal* p)
{
@ -204,19 +174,9 @@ void ImplicitSurfChem::eval(doublereal time, doublereal* y,
}
}
// Solve for the pseudo steady-state of the surface problem
/*
* Solve for the steady state of the surface problem.
* This is the same thing as the advanceCoverages() function,
* but at infinite times.
*
* Note, a direct solve is carried out under the hood here,
* to reduce the computational time.
*/
void ImplicitSurfChem::solvePseudoSteadyStateProblem(int ifuncOverride,
doublereal timeScaleOverride)
{
int ifunc;
/*
* set bulkFunc
@ -306,17 +266,6 @@ void ImplicitSurfChem::solvePseudoSteadyStateProblem(int ifuncOverride,
}
}
/*
* getConcSpecies():
*
* Fills the local concentration vector, m_concSpecies for all of the
* species in all of the phases that are unknowns in the surface
* problem.
*
* m_concSpecies[]
*/
void ImplicitSurfChem::getConcSpecies(doublereal* const vecConcSpecies) const
{
size_t kstart;
@ -333,15 +282,6 @@ void ImplicitSurfChem::getConcSpecies(doublereal* const vecConcSpecies) const
}
}
/*
* setConcSpecies():
*
* Fills the local concentration vector, m_concSpecies for all of the
* species in all of the phases that are unknowns in the surface
* problem.
*
* m_concSpecies[]
*/
void ImplicitSurfChem::setConcSpecies(const doublereal* const vecConcSpecies)
{
size_t kstart;
@ -358,15 +298,6 @@ void ImplicitSurfChem::setConcSpecies(const doublereal* const vecConcSpecies)
}
}
/*
* setCommonState_TP():
*
* Sets a common temperature and pressure amongst the
* thermodynamic objects in the interfacial kinetics object.
*
* Units Temperature = Kelvin
* Pressure = Pascal
*/
void ImplicitSurfChem::
setCommonState_TP(doublereal TKelvin, doublereal PresPa)
{