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[Input] Handle "declared-species" option for adding reactions from YAML

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This commit is contained in:
Ray Speth 2019-02-25 20:25:01 -05:00
parent 69371e5751
commit 0b04881b8d
4 changed files with 37 additions and 13 deletions
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6
include/cantera/kinetics/Kinetics.h
View file

@ -740,6 +740,9 @@ public:
void skipUndeclaredSpecies(bool skip) {
m_skipUndeclaredSpecies = skip;
}
bool skipUndeclaredSpecies() const {
return m_skipUndeclaredSpecies;
}
//! Determine behavior when adding a new reaction that contains third-body
//! efficiencies for species not defined in any of the phases associated
@ -749,6 +752,9 @@ public:
void skipUndeclaredThirdBodies(bool skip) {
m_skipUndeclaredThirdBodies = skip;
}
bool skipUndeclaredThirdBodies() const {
return m_skipUndeclaredThirdBodies;
}
//@}
//! @name Altering Reaction Rates

1
include/cantera/kinetics/reaction_defs.h
View file

@ -14,6 +14,7 @@
namespace Cantera
{
const int INVALID_RXN = 0;
const int NONE = 0;
/// @name Reaction Types

1
src/kinetics/Kinetics.cpp
View file

@ -289,7 +289,6 @@ string Kinetics::kineticsSpeciesName(size_t k) const
size_t Kinetics::kineticsSpeciesIndex(const std::string& nm) const
{
for (size_t n = 0; n < m_thermo.size(); n++) {
string id = thermo(n).id();
// Check the ThermoPhase object for a match
size_t k = thermo(n).speciesIndex(nm);
if (k != npos) {

42
src/kinetics/Reaction.cpp
View file

@ -287,8 +287,12 @@ Arrhenius readArrhenius(const XML_Node& arrhenius_node)
Units rateCoeffUnits(const Reaction& R, const Kinetics& kin,
int pressure_dependence=0)
{
if (R.reaction_type == INTERFACE_RXN
&& dynamic_cast<const InterfaceReaction&>(R).is_sticking_coefficient) {
if (R.reaction_type == INVALID_RXN) {
// If a reaction is invalid because of missing species in the Kinetics
// object, determining the units of the rate coefficient is impossible.
return Units();
} else if (R.reaction_type == INTERFACE_RXN
&& dynamic_cast<const InterfaceReaction&>(R).is_sticking_coefficient) {
// Sticking coefficients are dimensionless
return Units();
}
@ -448,7 +452,8 @@ void setupReaction(Reaction& R, const XML_Node& rxn_node)
R.reversible = (rev == "true" || rev == "yes");
}
void parseReactionEquation(Reaction& R, const AnyValue& equation) {
void parseReactionEquation(Reaction& R, const AnyValue& equation,
const Kinetics& kin) {
// Parse the reaction equation to determine participating species and
// stoichiometric coefficients
std::vector<std::string> tokens;
@ -487,6 +492,10 @@ void parseReactionEquation(Reaction& R, const AnyValue& equation) {
equation.asString(), tokens[i],
(last_used == npos) ? "n/a" : tokens[last_used]);
}
if (kin.kineticsSpeciesIndex(species) == npos
&& stoich != -1 && species != "M") {
R.reaction_type = INVALID_RXN;
}
if (reactants) {
R.reactants[species] += stoich;
@ -508,14 +517,17 @@ void parseReactionEquation(Reaction& R, const AnyValue& equation) {
}
}
void setupReaction(Reaction& R, const AnyMap& node)
void setupReaction(Reaction& R, const AnyMap& node, const Kinetics& kin)
{
parseReactionEquation(R, node["equation"]);
parseReactionEquation(R, node["equation"], kin);
// Non-stoichiometric reaction orders
std::map<std::string, double> orders;
if (node.hasKey("orders")) {
for (const auto& order : node["orders"].asMap<double>()) {
R.orders[order.first] = order.second;
if (kin.kineticsSpeciesIndex(order.first) == npos) {
R.reaction_type = INVALID_RXN;
}
}
}
@ -553,7 +565,7 @@ void setupElementaryReaction(ElementaryReaction& R, const XML_Node& rxn_node)
void setupElementaryReaction(ElementaryReaction& R, const AnyMap& node,
const Kinetics& kin)
{
setupReaction(R, node);
setupReaction(R, node, kin);
R.allow_negative_pre_exponential_factor = node.getBool("negative-A", false);
R.rate = readArrhenius(R, node["rate-constant"], kin, node.units());
}
@ -609,7 +621,7 @@ void setupFalloffReaction(FalloffReaction& R, const XML_Node& rxn_node)
void setupFalloffReaction(FalloffReaction& R, const AnyMap& node,
const Kinetics& kin)
{
setupReaction(R, node);
setupReaction(R, node, kin);
// setupReaction sets the stoichiometric coefficient for the falloff third
// body to -1.
std::string third_body;
@ -701,7 +713,7 @@ void setupPlogReaction(PlogReaction& R, const XML_Node& rxn_node)
void setupPlogReaction(PlogReaction& R, const AnyMap& node, const Kinetics& kin)
{
setupReaction(R, node);
setupReaction(R, node, kin);
std::multimap<double, Arrhenius> rates;
for (const auto& rate : node.at("rate-constants").asVector<AnyMap>()) {
rates.insert({rate.convert("P", "Pa"),
@ -742,7 +754,7 @@ void setupChebyshevReaction(ChebyshevReaction& R, const XML_Node& rxn_node)
void setupChebyshevReaction(ChebyshevReaction&R, const AnyMap& node,
const Kinetics& kin)
{
setupReaction(R, node);
setupReaction(R, node, kin);
R.reactants.erase("(+M)"); // remove optional third body notation
R.products.erase("(+M)");
const auto& T_range = node["temperature-range"].asVector<AnyValue>(2);
@ -800,7 +812,7 @@ void setupInterfaceReaction(InterfaceReaction& R, const XML_Node& rxn_node)
void setupInterfaceReaction(InterfaceReaction& R, const AnyMap& node,
const Kinetics& kin)
{
setupReaction(R, node);
setupReaction(R, node, kin);
R.allow_negative_pre_exponential_factor = node.getBool("negative-A", false);
if (node.hasKey("rate-constant")) {
@ -1029,7 +1041,7 @@ unique_ptr<Reaction> newReaction(const AnyMap& node, const Kinetics& kin)
if (kin.thermo().nDim() < 3) {
// See if this is an electrochemical reaction
Reaction testReaction(0);
parseReactionEquation(testReaction, node["equation"]);
parseReactionEquation(testReaction, node["equation"], kin);
if (isElectrochemicalReaction(testReaction, kin)) {
unique_ptr<ElectrochemicalReaction> R(new ElectrochemicalReaction());
setupElectrochemicalReaction(*R, node, kin);
@ -1085,7 +1097,13 @@ std::vector<shared_ptr<Reaction>> getReactions(const AnyValue& items,
{
std::vector<shared_ptr<Reaction>> all_reactions;
for (const auto& node : items.asVector<AnyMap>()) {
all_reactions.emplace_back(newReaction(node, kinetics));
shared_ptr<Reaction> R(newReaction(node, kinetics));
if (R->reaction_type != INVALID_RXN) {
all_reactions.emplace_back(R);
} else if (!kinetics.skipUndeclaredSpecies()) {
throw InputFileError("getReactions", node,
"Reaction '{}' contains undeclared species.", R->equation());
}
};
return all_reactions;
}