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[Kinetics] Refactor and deprecate installReagents

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This commit is contained in:
Ray Speth 2014-10-29 23:32:27 +00:00
parent a8659c86cc
commit 6f0fb5cf8d
8 changed files with 67 additions and 206 deletions
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2
include/cantera/kinetics/AqueousKinetics.h
View file

@ -164,8 +164,6 @@ protected:
private:
void addElementaryReaction(ReactionData& r);
void installReagents(const ReactionData& r);
/**
* Update the equilibrium constants in molar units.
*/

2
include/cantera/kinetics/GasKinetics.h
View file

@ -162,8 +162,6 @@ private:
void addPlogReaction(ReactionData& r);
void addChebyshevReaction(ReactionData& r);
virtual void installReagents(const ReactionData& r);
//! Update the equilibrium constants in molar units.
void updateKc();

2
include/cantera/kinetics/InterfaceKinetics.h
View file

@ -307,8 +307,6 @@ public:
void addGlobalReaction(ReactionData& r);
void installReagents(const ReactionData& r);
//! Update the equilibrium constants and stored electrochemical potentials
//! in molar units for all reversible reactions and for all species.
/*!

2
include/cantera/kinetics/Kinetics.h
View file

@ -779,6 +779,8 @@ public:
*/
virtual void addReaction(ReactionData& r);
//! @deprecated To be removed after Cantera 2.2. No longer called as part
//! of addReaction.
virtual void installReagents(const ReactionData& r) {
throw NotImplementedError("Kinetics::installReagents");
}

67
src/kinetics/AqueousKinetics.cpp
View file

@ -339,6 +339,16 @@ void AqueousKinetics::addReaction(ReactionData& r)
if (r.reactionType == ELEMENTARY_RXN) {
addElementaryReaction(r);
}
m_dn.push_back(accumulate(r.pstoich.begin(), r.pstoich.end(), 0.0) -
accumulate(r.rstoich.begin(), r.rstoich.end(), 0.0));
if (r.reversible) {
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_irrev.push_back(nReactions());
m_nirrev++;
}
Kinetics::addReaction(r);
}
@ -348,63 +358,6 @@ void AqueousKinetics::addElementaryReaction(ReactionData& r)
m_rates.install(nReactions(), r);
}
void AqueousKinetics::installReagents(const ReactionData& r)
{
size_t n, ns, m;
doublereal nsFlt;
doublereal reactantGlobalOrder = 0.0;
doublereal productGlobalOrder = 0.0;
size_t rnum = nReactions();
std::vector<size_t> rk;
size_t nr = r.reactants.size();
for (n = 0; n < nr; n++) {
nsFlt = r.rstoich[n];
reactantGlobalOrder += nsFlt;
ns = (size_t) nsFlt;
if ((doublereal) ns != nsFlt) {
ns = std::max<size_t>(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);
std::vector<size_t> pk;
size_t np = r.products.size();
for (n = 0; n < np; n++) {
nsFlt = r.pstoich[n];
productGlobalOrder += nsFlt;
ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(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_rxnstoich.add(nReactions(), r);
if (r.reversible) {
m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
m_irrev.push_back(nReactions());
m_nirrev++;
}
}
void AqueousKinetics::init()
{
m_kk = thermo().nSpecies();

66
src/kinetics/GasKinetics.cpp
View file

@ -451,6 +451,16 @@ void GasKinetics::addReaction(ReactionData& r)
}
// operations common to all reaction types
m_dn.push_back(accumulate(r.pstoich.begin(), r.pstoich.end(), 0.0) -
accumulate(r.rstoich.begin(), r.rstoich.end(), 0.0));
if (r.reversible) {
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_irrev.push_back(nReactions());
m_nirrev++;
}
Kinetics::addReaction(r);
}
@ -507,62 +517,6 @@ void GasKinetics::addChebyshevReaction(ReactionData& r)
m_cheb_rates.install(nReactions(), r);
}
void GasKinetics::installReagents(const ReactionData& r)
{
size_t n, ns, m;
doublereal nsFlt;
doublereal reactantGlobalOrder = 0.0;
doublereal productGlobalOrder = 0.0;
size_t rnum = nReactions();
std::vector<size_t> rk;
size_t nr = r.reactants.size();
for (n = 0; n < nr; n++) {
nsFlt = r.rstoich[n];
reactantGlobalOrder += nsFlt;
ns = (size_t) nsFlt;
if ((doublereal) ns != nsFlt) {
ns = std::max<size_t>(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);
std::vector<size_t> pk;
size_t np = r.products.size();
for (n = 0; n < np; n++) {
nsFlt = r.pstoich[n];
productGlobalOrder += nsFlt;
ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(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_rxnstoich.add(nReactions(), r);
if (r.reversible) {
m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_dn.push_back(productGlobalOrder - reactantGlobalOrder);
m_irrev.push_back(nReactions());
m_nirrev++;
}
}
void GasKinetics::init()
{
m_kk = thermo().nSpecies();

93
src/kinetics/InterfaceKinetics.cpp
View file

@ -798,6 +798,13 @@ void InterfaceKinetics::addReaction(ReactionData& r)
addElementaryReaction(r);
}
if (r.reversible) {
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_irrev.push_back(nReactions());
m_nirrev++;
}
Kinetics::addReaction(r);
m_rxnPhaseIsReactant.push_back(std::vector<bool>(nPhases(), false));
@ -975,92 +982,6 @@ void InterfaceKinetics::setIOFlag(int ioFlag)
}
}
void InterfaceKinetics::installReagents(const ReactionData& r)
{
size_t n, ns, m;
doublereal nsFlt;
/*
* Obtain the current reaction index for the reaction that we
* are adding. The first reaction is labeled 0.
*/
size_t rnum = nReactions();
// vectors rk and pk are lists of species numbers, with
// repeated entries for species with stoichiometric
// coefficients > 1. This allows the reaction to be defined
// with unity reaction order for each reactant, and so the
// faster method 'multiply' can be used to compute the rate of
// progress instead of 'power'.
std::vector<size_t> rk;
size_t nr = r.reactants.size();
for (n = 0; n < nr; n++) {
nsFlt = r.rstoich[n];
ns = (size_t) nsFlt;
if ((doublereal) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
/*
* Add to m_rrxn. m_rrxn is a vector of maps. m_rrxn has a length
* equal to the total number of species for each species, there
* exists a map, with the reaction number being the key, and the
* reactant stoichiometric coefficient being the value.
*/
m_rrxn[r.reactants[n]][rnum] = nsFlt;
for (m = 0; m < ns; m++) {
rk.push_back(r.reactants[n]);
}
}
/*
* Now that we have rk[], we add it into the vector<vector_int> m_reactants
* in the rnum index spot. Thus m_reactants[rnum] yields a vector
* of reactants for the rnum'th reaction
*/
m_reactants.push_back(rk);
std::vector<size_t> pk;
size_t np = r.products.size();
for (n = 0; n < np; n++) {
nsFlt = r.pstoich[n];
ns = (size_t) nsFlt;
if ((doublereal) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
/*
* Add to m_prxn. m_prxn is a vector of maps. m_prxn has a length
* equal to the total number of species for each species, there
* exists a map, with the reaction number being the key, and the
* product stoichiometric coefficient being the value.
*/
m_prxn[r.products[n]][rnum] = nsFlt;
for (m = 0; m < ns; m++) {
pk.push_back(r.products[n]);
}
}
/*
* Now that we have pk[], we add it into the vector<vector_int> m_products
* in the rnum index spot. Thus m_products[rnum] yields a vector
* of products for the rnum'th reaction
*/
m_products.push_back(pk);
/*
* Add this reaction to the stoichiometric coefficient manager. This
* calculates rates of species production from reaction rates of
* progress.
*/
m_rxnstoich.add(nReactions(), r);
/*
* register reaction in lists of reversible and irreversible rxns.
*/
if (r.reversible) {
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_irrev.push_back(nReactions());
m_nirrev++;
}
}
void InterfaceKinetics::addPhase(thermo_t& thermo)
{
Kinetics::addPhase(thermo);

39
src/kinetics/Kinetics.cpp
View file

@ -334,7 +334,44 @@ void Kinetics::finalize()
}
void Kinetics::addReaction(ReactionData& r) {
installReagents(r);
// vectors rk and pk are lists of species numbers, with repeated entries
// for species with stoichiometric coefficients > 1. This allows the
// reaction to be defined with unity reaction order for each reactant, and
// so the faster method 'multiply' can be used to compute the rate of
// progress instead of 'power'.
std::vector<size_t> rk;
for (size_t n = 0; n < r.reactants.size(); n++) {
double nsFlt = r.rstoich[n];
size_t ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
if (r.rstoich[n] != 0.0) {
m_rrxn[r.reactants[n]][m_ii] += r.rstoich[n];
}
for (size_t m = 0; m < ns; m++) {
rk.push_back(r.reactants[n]);
}
}
m_reactants.push_back(rk);
std::vector<size_t> pk;
for (size_t n = 0; n < r.products.size(); n++) {
double nsFlt = r.pstoich[n];
size_t ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
if (r.pstoich[n] != 0.0) {
m_prxn[r.products[n]][m_ii] += r.pstoich[n];
}
for (size_t m = 0; m < ns; m++) {
pk.push_back(r.products[n]);
}
}
m_products.push_back(pk);
m_rxnstoich.add(nReactions(), r);
installGroups(nReactions(), r.rgroups, r.pgroups);
incrementRxnCount();
m_rxneqn.push_back(r.equation);