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Eliminate unnecessary counter variable Kinetics::m_ii

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This commit is contained in:
Ray Speth 2015-07-16 15:37:41 -04:00
parent 571eaeda24
commit 761f54f241
7 changed files with 51 additions and 58 deletions
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4
include/cantera/kinetics/InterfaceKinetics.h
View file

@ -114,8 +114,8 @@ public:
*
* units = J kmol-1
*
* @param deltaG Output vector of deltaG's for reactions Length: m_ii.
* If 0, this updates the internally stored values only.
* @param deltaG Output vector of deltaG's for reactions Length:
* nReactions(). If 0, this updates the internally stored values only.
*/
virtual void getDeltaGibbs(doublereal* deltaG);

47
include/cantera/kinetics/Kinetics.h
View file

@ -189,7 +189,7 @@ public:
//! Number of reactions in the reaction mechanism.
size_t nReactions() const {
return m_ii;
return m_reactions.size();
}
//! Check that the specified reaction index is in range
@ -401,7 +401,7 @@ public:
* least as large as the total number of reactions.
*
* @param fwdROP Output vector containing forward rates
* of progress of the reactions. Length: m_ii.
* of progress of the reactions. Length: nReactions().
*/
virtual void getFwdRatesOfProgress(doublereal* fwdROP);
@ -411,7 +411,7 @@ public:
* dimensioned at least as large as the total number of reactions.
*
* @param revROP Output vector containing reverse rates
* of progress of the reactions. Length: m_ii.
* of progress of the reactions. Length: nReactions().
*/
virtual void getRevRatesOfProgress(doublereal* revROP);
@ -420,7 +420,7 @@ public:
* progress in array netROP, which must be dimensioned at least as large
* as the total number of reactions.
*
* @param netROP Output vector of the net ROP. Length: m_ii.
* @param netROP Output vector of the net ROP. Length: nReactions().
*/
virtual void getNetRatesOfProgress(doublereal* netROP);
@ -435,7 +435,7 @@ public:
* \f]
*
* @param kc Output vector containing the equilibrium constants.
* Length: m_ii.
* Length: nReactions().
*/
virtual void getEquilibriumConstants(doublereal* kc) {
throw NotImplementedError("Kinetics::getEquilibriumConstants");
@ -455,7 +455,7 @@ public:
* reaction.
*
* @param property Input vector of property value. Length: m_kk.
* @param deltaProperty Output vector of deltaRxn. Length: m_ii.
* @param deltaProperty Output vector of deltaRxn. Length: nReactions().
*/
virtual void getReactionDelta(const doublereal* property,
doublereal* deltaProperty);
@ -479,7 +479,8 @@ public:
*
* units = J kmol-1
*
* @param deltaG Output vector of deltaG's for reactions Length: m_ii.
* @param deltaG Output vector of deltaG's for reactions Length:
* nReactions().
*/
virtual void getDeltaGibbs(doublereal* deltaG) {
throw NotImplementedError("Kinetics::getDeltaGibbs");
@ -493,7 +494,8 @@ public:
*
* units = J kmol-1
*
* @param deltaM Output vector of deltaM's for reactions Length: m_ii.
* @param deltaM Output vector of deltaM's for reactions Length:
* nReactions().
*/
virtual void getDeltaElectrochemPotentials(doublereal* deltaM) {
throw NotImplementedError("Kinetics::getDeltaElectrochemPotentials");
@ -505,7 +507,8 @@ public:
*
* units = J kmol-1
*
* @param deltaH Output vector of deltaH's for reactions Length: m_ii.
* @param deltaH Output vector of deltaH's for reactions Length:
* nReactions().
*/
virtual void getDeltaEnthalpy(doublereal* deltaH) {
throw NotImplementedError("Kinetics::getDeltaEnthalpy");
@ -517,7 +520,8 @@ public:
*
* units = J kmol-1 Kelvin-1
*
* @param deltaS Output vector of deltaS's for reactions Length: m_ii.
* @param deltaS Output vector of deltaS's for reactions Length:
* nReactions().
*/
virtual void getDeltaEntropy(doublereal* deltaS) {
throw NotImplementedError("Kinetics::getDeltaEntropy");
@ -530,7 +534,8 @@ public:
*
* units = J kmol-1
*
* @param deltaG Output vector of ss deltaG's for reactions Length: m_ii.
* @param deltaG Output vector of ss deltaG's for reactions Length:
* nReactions().
*/
virtual void getDeltaSSGibbs(doublereal* deltaG) {
throw NotImplementedError("Kinetics::getDeltaSSGibbs");
@ -543,7 +548,8 @@ public:
*
* units = J kmol-1
*
* @param deltaH Output vector of ss deltaH's for reactions Length: m_ii.
* @param deltaH Output vector of ss deltaH's for reactions Length:
* nReactions().
*/
virtual void getDeltaSSEnthalpy(doublereal* deltaH) {
throw NotImplementedError("Kinetics::getDeltaSSEnthalpy");
@ -556,7 +562,8 @@ public:
*
* units = J kmol-1 Kelvin-1
*
* @param deltaS Output vector of ss deltaS's for reactions Length: m_ii.
* @param deltaS Output vector of ss deltaS's for reactions Length:
* nReactions().
*/
virtual void getDeltaSSEntropy(doublereal* deltaS) {
throw NotImplementedError("Kinetics::getDeltaSSEntropy");
@ -695,7 +702,7 @@ public:
* length is the number of reactions. units depends on many issues.
*
* @param kfwd Output vector containing the forward reaction rate
* constants. Length: m_ii.
* constants. Length: nReactions().
*/
virtual void getFwdRateConstants(doublereal* kfwd) {
throw NotImplementedError("Kinetics::getFwdRateConstants");
@ -842,15 +849,6 @@ public:
//@}
/**
* Increment the number of reactions in the mechanism by one.
* @todo Should be protected?
*/
void incrementRxnCount() {
m_ii++;
m_perturb.push_back(1.0);
}
/**
* Returns true if the kinetics manager has been properly
* initialized and finalized.
@ -929,9 +927,6 @@ protected:
StoichManagerN m_irrevProductStoich;
//@}
//! Number of reactions in the mechanism
size_t m_ii;
//! The number of species in all of the phases
//! that participate in this kinetics mechanism.
size_t m_kk;

6
src/kinetics/AqueousKinetics.cpp
View file

@ -87,7 +87,7 @@ void AqueousKinetics::getEquilibriumConstants(doublereal* kc)
getReactionDelta(&m_grt[0], &m_rkcn[0]);
doublereal rrt = 1.0/(GasConstant * thermo().temperature());
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
kc[i] = exp(-m_rkcn[i]*rrt);
}
@ -124,7 +124,7 @@ void AqueousKinetics::updateROP()
// for reversible reactions, multiply ropr by concentration products
m_revProductStoich.multiply(&m_conc[0], &m_ropr[0]);
for (size_t j = 0; j != m_ii; ++j) {
for (size_t j = 0; j != nReactions(); ++j) {
m_ropnet[j] = m_ropf[j] - m_ropr[j];
}
@ -142,7 +142,7 @@ void AqueousKinetics::getFwdRateConstants(doublereal* kfwd)
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
kfwd[i] = m_ropf[i];
}
}

6
src/kinetics/BulkKinetics.cpp
View file

@ -104,12 +104,12 @@ void BulkKinetics::getRevRateConstants(doublereal* krev, bool doIrreversible)
if (doIrreversible) {
getEquilibriumConstants(&m_ropnet[0]);
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
krev[i] /= m_ropnet[i];
}
} else {
// m_rkcn[] is zero for irreversible reactions
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
krev[i] *= m_rkcn[i];
}
}
@ -168,7 +168,7 @@ void BulkKinetics::finalize()
// Guarantee that these arrays can be converted to double* even in the
// special case where there are no reactions defined.
if (!m_ii) {
if (!nReactions()) {
m_perturb.resize(1, 1.0);
m_ropf.resize(1, 0.0);
m_ropr.resize(1, 0.0);

6
src/kinetics/GasKinetics.cpp
View file

@ -127,7 +127,7 @@ void GasKinetics::getEquilibriumConstants(doublereal* kc)
getReactionDelta(&m_grt[0], &m_rkcn[0]);
doublereal rrt = 1.0/(GasConstant * thermo().temperature());
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
kc[i] = exp(-m_rkcn[i]*rrt + m_dn[i]*m_logStandConc);
}
@ -199,7 +199,7 @@ void GasKinetics::updateROP()
// for reversible reactions, multiply ropr by concentration products
m_revProductStoich.multiply(&m_conc[0], &m_ropr[0]);
for (size_t j = 0; j != m_ii; ++j) {
for (size_t j = 0; j != nReactions(); ++j) {
m_ropnet[j] = m_ropf[j] - m_ropr[j];
}
@ -235,7 +235,7 @@ void GasKinetics::getFwdRateConstants(doublereal* kfwd)
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
kfwd[i] = m_ropf[i];
}
}

24
src/kinetics/InterfaceKinetics.cpp
View file

@ -294,11 +294,11 @@ void InterfaceKinetics::getEquilibriumConstants(doublereal* kc)
updateMu0();
doublereal rrt = 1.0 / (GasConstant * thermo(0).temperature());
std::fill(kc, kc + m_ii, 0.0);
std::fill(kc, kc + nReactions(), 0.0);
getReactionDelta(DATA_PTR(m_mu0_Kc), kc);
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
kc[i] = exp(-kc[i]*rrt);
}
}
@ -333,7 +333,7 @@ void InterfaceKinetics::updateExchangeCurrentQuantities()
getReactionDelta(DATA_PTR(m_mu0), DATA_PTR(m_deltaG0));
// Calculate the product of the standard concentrations of the reactants
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
m_ProdStanConcReac[i] = 1.0;
}
m_reactantStoich.multiply(DATA_PTR(m_StandardConc), DATA_PTR(m_ProdStanConcReac));
@ -463,7 +463,7 @@ void InterfaceKinetics::getRevRateConstants(doublereal* krev, bool doIrreversibl
getFwdRateConstants(krev);
if (doIrreversible) {
getEquilibriumConstants(&m_ropnet[0]);
for (size_t i = 0; i < m_ii; i++) {
for (size_t i = 0; i < nReactions(); i++) {
krev[i] /= m_ropnet[i];
}
} else {
@ -506,7 +506,7 @@ void InterfaceKinetics::updateROP()
// Fix up these calculations for cases where the above formalism doesn't hold
double OCV = 0.0;
for (size_t jrxn = 0; jrxn != m_ii; ++jrxn) {
for (size_t jrxn = 0; jrxn != nReactions(); ++jrxn) {
int reactionType = m_rxntype[jrxn];
if (reactionType == BUTLERVOLMER_RXN) {
//
@ -543,7 +543,7 @@ void InterfaceKinetics::updateROP()
}
}
for (size_t j = 0; j != m_ii; ++j) {
for (size_t j = 0; j != nReactions(); ++j) {
m_ropnet[j] = m_ropf[j] - m_ropr[j];
}
@ -553,7 +553,7 @@ void InterfaceKinetics::updateROP()
* phases that are stoichiometric phases containing one species with a unity activity
*/
if (m_phaseExistsCheck) {
for (size_t j = 0; j != m_ii; ++j) {
for (size_t j = 0; j != nReactions(); ++j) {
if ((m_ropr[j] > m_ropf[j]) && (m_ropr[j] > 0.0)) {
for (size_t p = 0; p < nPhases(); p++) {
if (m_rxnPhaseIsProduct[j][p]) {
@ -624,7 +624,7 @@ void InterfaceKinetics::getDeltaGibbs(doublereal* deltaG)
// Use the stoichiometric manager to find deltaG for each reaction.
getReactionDelta(DATA_PTR(m_mu), DATA_PTR(m_deltaG));
if (deltaG != 0 && (DATA_PTR(m_deltaG) != deltaG)) {
for (size_t j = 0; j < m_ii; ++j) {
for (size_t j = 0; j < nReactions(); ++j) {
deltaG[j] = m_deltaG[j];
}
}
@ -967,7 +967,7 @@ void InterfaceKinetics::init()
void InterfaceKinetics::finalize()
{
Kinetics::finalize();
size_t safe_reaction_size = std::max<size_t>(m_ii, 1);
size_t safe_reaction_size = std::max<size_t>(nReactions(), 1);
deltaElectricEnergy_.resize(safe_reaction_size);
size_t ks = reactionPhaseIndex();
if (ks == npos) throw CanteraError("InterfaceKinetics::finalize",
@ -992,7 +992,7 @@ void InterfaceKinetics::finalize()
// Guarantee that these arrays can be converted to double* even in the
// special case where there are no reactions defined.
if (!m_ii) {
if (!nReactions()) {
m_perturb.resize(1, 1.0);
m_ropf.resize(1, 0.0);
m_ropr.resize(1, 0.0);
@ -1170,7 +1170,7 @@ void EdgeKinetics::finalize()
// handled by the InterfaceKinetics::finalize() call.
Kinetics::finalize();
size_t safe_reaction_size = std::max<size_t>(m_ii, 1);
size_t safe_reaction_size = std::max<size_t>(nReactions(), 1);
deltaElectricEnergy_.resize(safe_reaction_size);
size_t ks = reactionPhaseIndex();
if (ks == npos) throw CanteraError("EdgeKinetics::finalize",
@ -1195,7 +1195,7 @@ void EdgeKinetics::finalize()
// Guarantee that these arrays can be converted to double* even in the
// special case where there are no reactions defined.
if (!m_ii) {
if (!nReactions()) {
m_perturb.resize(1, 1.0);
m_ropf.resize(1, 0.0);
m_ropr.resize(1, 0.0);

16
src/kinetics/Kinetics.cpp
View file

@ -16,7 +16,6 @@ using namespace std;
namespace Cantera
{
Kinetics::Kinetics() :
m_ii(0),
m_kk(0),
m_thermo(0),
m_surfphase(npos),
@ -49,7 +48,6 @@ Kinetics& Kinetics::operator=(const Kinetics& right)
m_reactantStoich = right.m_reactantStoich;
m_revProductStoich = right.m_revProductStoich;
m_irrevProductStoich = right.m_irrevProductStoich;
m_ii = right.m_ii;
m_kk = right.m_kk;
m_perturb = right.m_perturb;
m_reactions = right.m_reactions;
@ -94,15 +92,15 @@ int Kinetics::type() const
void Kinetics::checkReactionIndex(size_t i) const
{
if (i >= m_ii) {
throw IndexError("checkReactionIndex", "reactions", i, m_ii-1);
if (i >= nReactions()) {
throw IndexError("checkReactionIndex", "reactions", i, nReactions()-1);
}
}
void Kinetics::checkReactionArraySize(size_t ii) const
{
if (m_ii > ii) {
throw ArraySizeError("checkReactionArraySize", ii, m_ii);
if (nReactions() > ii) {
throw ArraySizeError("checkReactionArraySize", ii, nReactions());
}
}
@ -452,7 +450,7 @@ void Kinetics::getNetRatesOfProgress(doublereal* netROP)
void Kinetics::getReactionDelta(const double* prop, double* deltaProp)
{
fill(deltaProp, deltaProp + m_ii, 0.0);
fill(deltaProp, deltaProp + nReactions(), 0.0);
// products add
m_revProductStoich.incrementReactions(prop, deltaProp);
m_irrevProductStoich.incrementReactions(prop, deltaProp);
@ -462,7 +460,7 @@ void Kinetics::getReactionDelta(const double* prop, double* deltaProp)
void Kinetics::getRevReactionDelta(const double* prop, double* deltaProp)
{
fill(deltaProp, deltaProp + m_ii, 0.0);
fill(deltaProp, deltaProp + nReactions(), 0.0);
// products add
m_revProductStoich.incrementReactions(prop, deltaProp);
// reactants subtract
@ -652,7 +650,6 @@ bool Kinetics::addReaction(shared_ptr<Reaction> r)
m_irrevProductStoich.add(irxn, pk, pstoich, pstoich);
}
incrementRxnCount();
m_reactions.push_back(r);
m_rxneqn.push_back(r->equation());
m_reactantStrings.push_back(r->reactantString());
@ -663,6 +660,7 @@ bool Kinetics::addReaction(shared_ptr<Reaction> r)
m_ropf.push_back(0.0);
m_ropr.push_back(0.0);
m_ropnet.push_back(0.0);
m_perturb.push_back(1.0);
return true;
}