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Move non-trivial functions out of header files

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This commit is contained in:
Ray Speth 2016-04-08 19:13:09 -04:00
parent 9e5362a762
commit 9ed23a57ab
14 changed files with 344 additions and 259 deletions
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91
include/cantera/oneD/Domain1D.h
View file

@ -43,21 +43,7 @@ public:
* @param points Number of grid points.
* @param time (unused)
*/
Domain1D(size_t nv=1, size_t points=1,
doublereal time = 0.0) :
m_rdt(0.0),
m_nv(0),
m_time(time),
m_container(0),
m_index(npos),
m_type(0),
m_iloc(0),
m_jstart(0),
m_left(0),
m_right(0),
m_bw(-1) {
resize(nv, points);
}
Domain1D(size_t nv=1, size_t points=1, double time=0.0);
virtual ~Domain1D() {}
@ -134,28 +120,7 @@ public:
* is virtual so that subclasses can perform other actions required to
* resize the domain.
*/
virtual void resize(size_t nv, size_t 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;
m_refiner.reset(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);
// Default error tolerances for all domains
m_rtol_ss.resize(m_nv, 1.0e-4);
m_atol_ss.resize(m_nv, 1.0e-9);
m_rtol_ts.resize(m_nv, 1.0e-4);
m_atol_ts.resize(m_nv, 1.0e-11);
m_points = np;
m_z.resize(np, 0.0);
m_slast.resize(m_nv * m_points, 0.0);
locate();
}
virtual void resize(size_t nv, size_t np);
//! Return a reference to the grid refiner.
Refiner& refiner() {
@ -207,13 +172,7 @@ public:
}
//! Name of the nth component. May be overloaded.
virtual std::string componentName(size_t n) const {
if (m_name[n] != "") {
return m_name[n];
} else {
return fmt::format("component {}", n);
}
}
virtual std::string componentName(size_t n) const;
void setComponentName(size_t n, const std::string& name) {
m_name[n] = name;
@ -229,16 +188,7 @@ public:
}
//! index of component with name \a name.
size_t componentIndex(const std::string& name) const {
size_t nc = nComponents();
for (size_t n = 0; n < nc; n++) {
if (name == componentName(n)) {
return n;
}
}
throw CanteraError("Domain1D::componentIndex",
"no component named "+name);
}
size_t componentIndex(const std::string& name) const;
void setBounds(size_t n, doublereal lower, doublereal upper) {
m_min[n] = lower;
@ -445,25 +395,7 @@ public:
* 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();
}
}
void locate();
/**
* Location of the start of the local solution vector in the global
@ -571,18 +503,7 @@ public:
return m_z[m_points - 1];
}
void setProfile(const std::string& name, doublereal* values, doublereal* soln) {
for (size_t n = 0; n < m_nv; n++) {
if (name == componentName(n)) {
for (size_t j = 0; j < m_points; j++) {
soln[index(n, j) + m_iloc] = values[j];
}
return;
}
}
throw CanteraError("Domain1D::setProfile",
"unknown component: "+name);
}
void setProfile(const std::string& name, double* values, double* soln);
vector_fp& grid() {
return m_z;

57
include/cantera/oneD/Inlet1D.h
View file

@ -109,10 +109,7 @@ protected:
class Inlet1D : public Bdry1D
{
public:
Inlet1D() : Bdry1D(), m_V0(0.0), m_nsp(0), m_flow(0) {
m_type = cInletType;
m_xstr = "";
}
Inlet1D();
/// set spreading rate
virtual void setSpreadRate(doublereal V0) {
@ -125,25 +122,9 @@ public:
return m_V0;
}
virtual void showSolution(const doublereal* x) {
writelog(" Mass Flux: {:10.4g} kg/m^2/s \n", m_mdot);
writelog(" Temperature: {:10.4g} K \n", m_temp);
if (m_flow) {
writelog(" Mass Fractions: \n");
for (size_t k = 0; k < m_flow->phase().nSpecies(); k++) {
if (m_yin[k] != 0.0) {
writelog(" {:>16s} {:10.4g} \n",
m_flow->phase().speciesName(k), m_yin[k]);
}
}
}
writelog("\n");
}
virtual void showSolution(const double* x);
virtual void _getInitialSoln(doublereal* x) {
x[0] = m_mdot;
x[1] = m_temp;
}
virtual void _getInitialSoln(double* x);
virtual size_t nSpecies() {
return m_nsp;
@ -256,10 +237,7 @@ public:
class OutletRes1D : public Bdry1D
{
public:
OutletRes1D() : Bdry1D(), m_nsp(0), m_flow(0) {
m_type = cOutletResType;
m_xstr = "";
}
OutletRes1D();
virtual void showSolution(const doublereal* x) {}
@ -317,10 +295,7 @@ public:
x[0] = m_temp;
}
virtual void showSolution_s(std::ostream& s, const doublereal* x) {
s << "------------------- Surface " << domainIndex() << " ------------------- " << std::endl;
s << " temperature: " << m_temp << " K" << " " << x[0] << std::endl;
}
virtual void showSolution_s(std::ostream& s, const double* x);
virtual void showSolution(const doublereal* x) {
writelog(" Temperature: {:10.4g} K \n\n", m_temp);
@ -334,18 +309,9 @@ public:
class ReactingSurf1D : public Bdry1D
{
public:
ReactingSurf1D() : Bdry1D(),
m_kin(0), m_surfindex(0), m_nsp(0) {
m_type = cSurfType;
}
ReactingSurf1D();
void setKineticsMgr(InterfaceKinetics* kin) {
m_kin = kin;
m_surfindex = kin->surfacePhaseIndex();
m_sphase = (SurfPhase*)&kin->thermo(m_surfindex);
m_nsp = m_sphase->nSpecies();
m_enabled = true;
}
void setKineticsMgr(InterfaceKinetics* kin);
void enableCoverageEquations(bool docov) {
m_enabled = docov;
@ -371,14 +337,7 @@ public:
std::copy(x+1,x+1+m_nsp,m_fixed_cov.begin());
}
virtual void showSolution(const doublereal* x) {
writelog(" Temperature: {:10.4g} K \n", x[0]);
writelog(" Coverages: \n");
for (size_t k = 0; k < m_nsp; k++) {
writelog(" {:>20s} {:10.4g} \n", m_sphase->speciesName(k), x[k+1]);
}
writelog("\n");
}
virtual void showSolution(const doublereal* x);
protected:
InterfaceKinetics* m_kin;

9
include/cantera/oneD/OneDim.h
View file

@ -237,14 +237,7 @@ public:
return m_nsteps_max;
}
void setJacAge(int ss_age, int ts_age=-1) {
m_ss_jac_age = ss_age;
if (ts_age > 0) {
m_ts_jac_age = ts_age;
} else {
m_ts_jac_age = m_ss_jac_age;
}
}
void setJacAge(int ss_age, int ts_age=-1);
/**
* Save statistics on function and Jacobian evaluation, and reset the

66
include/cantera/oneD/StFlow.h
View file

@ -97,12 +97,7 @@ public:
}
//! Write the initial solution estimate into array x.
virtual void _getInitialSoln(doublereal* x) {
for (size_t j = 0; j < m_points; j++) {
T(x,j) = m_thermo->temperature();
m_thermo->getMassFractions(&Y(x, 0, j));
}
}
virtual void _getInitialSoln(double* x);
virtual void _finalize(const doublereal* x);
@ -154,28 +149,7 @@ public:
return "<none>";
}
void solveEnergyEqn(size_t j=npos) {
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (!m_do_energy[i]) {
changed = true;
}
m_do_energy[i] = true;
}
} else {
if (!m_do_energy[j]) {
changed = true;
}
m_do_energy[j] = true;
}
m_refiner->setActive(0, true);
m_refiner->setActive(1, true);
m_refiner->setActive(2, true);
if (changed) {
needJacUpdate();
}
}
void solveEnergyEqn(size_t j=npos);
//! Turn radiation on / off.
/*!
@ -199,41 +173,9 @@ public:
* radiative term and writes them into the variables, which are used for the
* calculation.
*/
void setBoundaryEmissivities(doublereal e_left, doublereal e_right) {
if (e_left < 0 || e_left > 1) {
throw CanteraError("setBoundaryEmissivities",
"The left boundary emissivity must be between 0.0 and 1.0!");
} else if (e_right < 0 || e_right > 1) {
throw CanteraError("setBoundaryEmissivities",
"The right boundary emissivity must be between 0.0 and 1.0!");
} else {
m_epsilon_left = e_left;
m_epsilon_right = e_right;
}
}
void setBoundaryEmissivities(doublereal e_left, doublereal e_right);
void fixTemperature(size_t j=npos) {
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (m_do_energy[i]) {
changed = true;
}
m_do_energy[i] = false;
}
} else {
if (m_do_energy[j]) {
changed = true;
}
m_do_energy[j] = false;
}
m_refiner->setActive(0, false);
m_refiner->setActive(1, false);
m_refiner->setActive(2, false);
if (changed) {
needJacUpdate();
}
}
void fixTemperature(size_t j=npos);
bool doEnergy(size_t j) {
return m_do_energy[j];

8
include/cantera/thermo/ThermoPhase.h
View file

@ -484,13 +484,7 @@ public:
* @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 (size_t k = 0; k < m_kk; k++) {
mu[k] += ve*charge(k);
}
}
void getElectrochemPotentials(doublereal* mu) const;
//! Returns an array of partial molar enthalpies for the species
//! in the mixture. Units (J/kmol)

9
include/cantera/zeroD/Reactor.h
View file

@ -52,14 +52,7 @@ public:
setKineticsMgr(contents);
}
void setKineticsMgr(Kinetics& kin) {
m_kin = &kin;
if (m_kin->nReactions() == 0) {
disableChemistry();
} else {
enableChemistry();
}
}
void setKineticsMgr(Kinetics& kin);
//! Disable changes in reactor composition due to chemical reactions.
void disableChemistry() {

46
include/cantera/zeroD/ReactorNet.h
View file

@ -30,46 +30,21 @@ public:
//! Set initial time. Default = 0.0 s. Restarts integration from this time
//! using the current mixture state as the initial condition.
void setInitialTime(doublereal time) {
m_time = time;
m_integrator_init = false;
}
void setInitialTime(double time);
//! Set the maximum time step.
void setMaxTimeStep(double maxstep) {
m_maxstep = maxstep;
m_init = false;
}
void setMaxTimeStep(double maxstep);
//! Set the maximum number of error test failures permitted by the CVODES
//! integrator in a single time step.
void setMaxErrTestFails(int nmax) {
m_maxErrTestFails = nmax;
m_init = false;
}
void setMaxErrTestFails(int nmax);
//! Set the relative and absolute tolerances for the integrator.
void setTolerances(doublereal rtol, doublereal atol) {
if (rtol >= 0.0) {
m_rtol = rtol;
}
if (atol >= 0.0) {
m_atols = atol;
}
m_init = false;
}
void setTolerances(double rtol, double atol);
//! Set the relative and absolute tolerances for integrating the
//! sensitivity equations.
void setSensitivityTolerances(doublereal rtol, doublereal atol) {
if (rtol >= 0.0) {
m_rtolsens = rtol;
}
if (atol >= 0.0) {
m_atolsens = atol;
}
m_init = false;
}
void setSensitivityTolerances(double rtol, double atol);
//! Current value of the simulation time.
doublereal time() {
@ -153,16 +128,7 @@ public:
* rate constant (and implicitly on the reverse rate constant for
* reversible reactions).
*/
double sensitivity(size_t k, size_t p) {
if (!m_init) {
initialize();
}
if (p >= m_sensIndex.size()) {
throw IndexError("ReactorNet::sensitivity",
"m_sensIndex", p, m_sensIndex.size()-1);
}
return m_integ->sensitivity(k, m_sensIndex[p])/m_integ->solution(k);
}
double sensitivity(size_t k, size_t p);
//! Return the sensitivity of the component named *component* with respect to
//! the *p*-th sensitivity parameter.

94
src/oneD/Domain1D.cpp
View file

@ -11,6 +11,67 @@ using namespace std;
namespace Cantera
{
Domain1D::Domain1D(size_t nv, size_t points, double time) :
m_rdt(0.0),
m_nv(0),
m_time(time),
m_container(0),
m_index(npos),
m_type(0),
m_iloc(0),
m_jstart(0),
m_left(0),
m_right(0),
m_bw(-1)
{
resize(nv, points);
}
void Domain1D::resize(size_t nv, size_t 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;
m_refiner.reset(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);
// Default error tolerances for all domains
m_rtol_ss.resize(m_nv, 1.0e-4);
m_atol_ss.resize(m_nv, 1.0e-9);
m_rtol_ts.resize(m_nv, 1.0e-4);
m_atol_ts.resize(m_nv, 1.0e-11);
m_points = np;
m_z.resize(np, 0.0);
m_slast.resize(m_nv * m_points, 0.0);
locate();
}
std::string Domain1D::componentName(size_t n) const
{
if (m_name[n] != "") {
return m_name[n];
} else {
return fmt::format("component {}", n);
}
}
size_t Domain1D::componentIndex(const std::string& name) const
{
size_t nc = nComponents();
for (size_t n = 0; n < nc; n++) {
if (name == componentName(n)) {
return n;
}
}
throw CanteraError("Domain1D::componentIndex",
"no component named "+name);
}
void Domain1D::setTransientTolerances(doublereal rtol, doublereal atol, size_t n)
{
if (n == npos) {
@ -147,6 +208,26 @@ void Domain1D::restore(const XML_Node& dom, doublereal* soln, int loglevel)
}
}
void Domain1D::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();
}
}
void Domain1D::setupGrid(size_t n, const doublereal* z)
{
if (n > 1) {
@ -195,6 +276,19 @@ void Domain1D::showSolution(const doublereal* x)
writelog("\n");
}
void Domain1D::setProfile(const std::string& name, double* values, double* soln)
{
for (size_t n = 0; n < m_nv; n++) {
if (name == componentName(n)) {
for (size_t j = 0; j < m_points; j++) {
soln[index(n, j) + m_iloc] = values[j];
}
return;
}
}
throw CanteraError("Domain1D::setProfile", "unknown component: "+name);
}
void Domain1D::_getInitialSoln(doublereal* x)
{
for (size_t j = 0; j < m_points; j++) {

10
src/oneD/OneDim.cpp
View file

@ -101,6 +101,16 @@ MultiNewton& OneDim::newton()
return *m_newt;
}
void OneDim::setJacAge(int ss_age, int ts_age)
{
m_ss_jac_age = ss_age;
if (ts_age > 0) {
m_ts_jac_age = ts_age;
} else {
m_ts_jac_age = m_ss_jac_age;
}
}
void OneDim::writeStats(int printTime)
{
saveStats();

70
src/oneD/StFlow.cpp
View file

@ -181,6 +181,14 @@ void StFlow::enableSoret(bool withSoret)
}
}
void StFlow::_getInitialSoln(double* x)
{
for (size_t j = 0; j < m_points; j++) {
T(x,j) = m_thermo->temperature();
m_thermo->getMassFractions(&Y(x, 0, j));
}
}
void StFlow::setGas(const doublereal* x, size_t j)
{
m_thermo->setTemperature(T(x,j));
@ -819,6 +827,68 @@ XML_Node& StFlow::save(XML_Node& o, const doublereal* const sol)
return flow;
}
void StFlow::solveEnergyEqn(size_t j)
{
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (!m_do_energy[i]) {
changed = true;
}
m_do_energy[i] = true;
}
} else {
if (!m_do_energy[j]) {
changed = true;
}
m_do_energy[j] = true;
}
m_refiner->setActive(0, true);
m_refiner->setActive(1, true);
m_refiner->setActive(2, true);
if (changed) {
needJacUpdate();
}
}
void StFlow::setBoundaryEmissivities(doublereal e_left, doublereal e_right)
{
if (e_left < 0 || e_left > 1) {
throw CanteraError("setBoundaryEmissivities",
"The left boundary emissivity must be between 0.0 and 1.0!");
} else if (e_right < 0 || e_right > 1) {
throw CanteraError("setBoundaryEmissivities",
"The right boundary emissivity must be between 0.0 and 1.0!");
} else {
m_epsilon_left = e_left;
m_epsilon_right = e_right;
}
}
void StFlow::fixTemperature(size_t j)
{
bool changed = false;
if (j == npos) {
for (size_t i = 0; i < m_points; i++) {
if (m_do_energy[i]) {
changed = true;
}
m_do_energy[i] = false;
}
} else {
if (m_do_energy[j]) {
changed = true;
}
m_do_energy[j] = false;
}
m_refiner->setActive(0, false);
m_refiner->setActive(1, false);
m_refiner->setActive(2, false);
if (changed) {
needJacUpdate();
}
}
void AxiStagnFlow::evalRightBoundary(doublereal* x, doublereal* rsd,
integer* diag, doublereal rdt)
{

72
src/oneD/boundaries1D.cpp
View file

@ -73,6 +73,37 @@ void Bdry1D::_init(size_t n)
// ---------------- Inlet1D methods ----------------
Inlet1D::Inlet1D()
: m_V0(0.0)
, m_nsp(0)
, m_flow(0)
{
m_type = cInletType;
m_xstr = "";
}
void Inlet1D::showSolution(const double* x)
{
writelog(" Mass Flux: {:10.4g} kg/m^2/s \n", m_mdot);
writelog(" Temperature: {:10.4g} K \n", m_temp);
if (m_flow) {
writelog(" Mass Fractions: \n");
for (size_t k = 0; k < m_flow->phase().nSpecies(); k++) {
if (m_yin[k] != 0.0) {
writelog(" {:>16s} {:10.4g} \n",
m_flow->phase().speciesName(k), m_yin[k]);
}
}
}
writelog("\n");
}
void Inlet1D::_getInitialSoln(double* x)
{
x[0] = m_mdot;
x[1] = m_temp;
}
void Inlet1D::setMoleFractions(const std::string& xin)
{
m_xstr = xin;
@ -367,6 +398,14 @@ void Symm1D::restore(const XML_Node& dom, doublereal* soln, int loglevel)
// -------- Outlet1D --------
OutletRes1D::OutletRes1D()
: m_nsp(0)
, m_flow(0)
{
m_type = cOutletResType;
m_xstr = "";
}
string Outlet1D::componentName(size_t n) const
{
switch (n) {
@ -671,8 +710,31 @@ void Surf1D::restore(const XML_Node& dom, doublereal* soln, int loglevel)
resize(1,1);
}
void Surf1D::showSolution_s(std::ostream& s, const double* x)
{
s << "------------------- Surface " << domainIndex() << " ------------------- " << std::endl;
s << " temperature: " << m_temp << " K" << " " << x[0] << std::endl;
}
// -------- ReactingSurf1D --------
ReactingSurf1D::ReactingSurf1D()
: m_kin(0)
, m_surfindex(0)
, m_nsp(0)
{
m_type = cSurfType;
}
void ReactingSurf1D::setKineticsMgr(InterfaceKinetics* kin)
{
m_kin = kin;
m_surfindex = kin->surfacePhaseIndex();
m_sphase = (SurfPhase*)&kin->thermo(m_surfindex);
m_nsp = m_sphase->nSpecies();
m_enabled = true;
}
string ReactingSurf1D::componentName(size_t n) const
{
if (n == 0) {
@ -820,4 +882,14 @@ void ReactingSurf1D::restore(const XML_Node& dom, doublereal* soln,
resize(m_nsp+1,1);
}
void ReactingSurf1D::showSolution(const double* x)
{
writelog(" Temperature: {:10.4g} K \n", x[0]);
writelog(" Coverages: \n");
for (size_t k = 0; k < m_nsp; k++) {
writelog(" {:>20s} {:10.4g} \n", m_sphase->speciesName(k), x[k+1]);
}
writelog("\n");
}
}

9
src/thermo/ThermoPhase.cpp
View file

@ -125,6 +125,15 @@ void ThermoPhase::getLnActivityCoefficients(doublereal* lnac) const
}
}
void ThermoPhase::getElectrochemPotentials(doublereal* mu) const
{
getChemPotentials(mu);
double ve = Faraday * electricPotential();
for (size_t k = 0; k < m_kk; k++) {
mu[k] += ve*charge(k);
}
}
void ThermoPhase::setState_TPX(doublereal t, doublereal p, const doublereal* x)
{
setMoleFractions(x);

10
src/zeroD/Reactor.cpp
View file

@ -25,6 +25,16 @@ Reactor::Reactor() :
m_nsens(npos)
{}
void Reactor::setKineticsMgr(Kinetics& kin)
{
m_kin = &kin;
if (m_kin->nReactions() == 0) {
disableChemistry();
} else {
enableChemistry();
}
}
void Reactor::getInitialConditions(double t0, size_t leny, double* y)
{
warn_deprecated("Reactor::getInitialConditions",

52
src/zeroD/ReactorNet.cpp
View file

@ -31,6 +31,46 @@ ReactorNet::~ReactorNet()
delete m_integ;
}
void ReactorNet::setInitialTime(double time)
{
m_time = time;
m_integrator_init = false;
}
void ReactorNet::setMaxTimeStep(double maxstep)
{
m_maxstep = maxstep;
m_init = false;
}
void ReactorNet::setMaxErrTestFails(int nmax)
{
m_maxErrTestFails = nmax;
m_init = false;
}
void ReactorNet::setTolerances(double rtol, double atol)
{
if (rtol >= 0.0) {
m_rtol = rtol;
}
if (atol >= 0.0) {
m_atols = atol;
}
m_init = false;
}
void ReactorNet::setSensitivityTolerances(double rtol, double atol)
{
if (rtol >= 0.0) {
m_rtolsens = rtol;
}
if (atol >= 0.0) {
m_atolsens = atol;
}
m_init = false;
}
void ReactorNet::initialize()
{
size_t n, nv;
@ -141,6 +181,18 @@ void ReactorNet::eval(doublereal t, doublereal* y,
checkFinite("ydot", ydot, m_nv);
}
double ReactorNet::sensitivity(size_t k, size_t p)
{
if (!m_init) {
initialize();
}
if (p >= m_sensIndex.size()) {
throw IndexError("ReactorNet::sensitivity",
"m_sensIndex", p, m_sensIndex.size()-1);
}
return m_integ->sensitivity(k, m_sensIndex[p])/m_integ->solution(k);
}
void ReactorNet::evalJacobian(doublereal t, doublereal* y,
doublereal* ydot, doublereal* p, Array2D* j)
{