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refactor(reaction): refactored to an abstract reaction class in prep for weak reactions

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This commit is contained in:
Emily Boudreaux
2025-08-14 13:33:46 -04:00
parent d920a55ba6
commit 0b77f2e269
81 changed files with 1050041 additions and 913 deletions
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27
src/lib/engine/procedures/priming.cpp
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@@ -24,11 +24,11 @@ namespace gridfire {
const reaction::Reaction* dominateReaction = nullptr;
double maxFlow = -1.0;
for (const auto& reaction : engine.getNetworkReactions()) {
if (reaction.contains(species) && reaction.stoichiometry(species) > 0) {
const double flow = engine.calculateMolarReactionFlow(reaction, Y, T9, rho);
if (reaction->contains(species) && reaction->stoichiometry(species) > 0) {
const double flow = engine.calculateMolarReactionFlow(*reaction, Y, T9, rho);
if (flow > maxFlow) {
maxFlow = flow;
dominateReaction = &reaction;
dominateReaction = reaction.get();
}
}
}
@@ -105,9 +105,8 @@ namespace gridfire {
const auto Y = primer.mapNetInToMolarAbundanceVector(tempNetIn);
const double destructionRateConstant = calculateDestructionRateConstant(primer, primingSpecies, Y, T9, rho);
double equilibriumMassFraction = 0.0;
if (destructionRateConstant > 1e-99) {
double equilibriumMassFraction = 0.0;
const double creationRate = calculateCreationRate(primer, primingSpecies, Y, T9, rho);
equilibriumMassFraction = (creationRate / destructionRateConstant) * primingSpecies.mass();
if (std::isnan(equilibriumMassFraction)) {
@@ -116,9 +115,7 @@ namespace gridfire {
}
LOG_TRACE_L3(logger, "Found equilibrium for {}: X_eq = {:.4e}", primingSpecies.name(), equilibriumMassFraction);
const reaction::Reaction* dominantChannel = findDominantCreationChannel(primer, primingSpecies, Y, T9, rho);
if (dominantChannel) {
if (const reaction::Reaction* dominantChannel = findDominantCreationChannel(primer, primingSpecies, Y, T9, rho)) {
LOG_TRACE_L3(logger, "Dominant creation channel for {}: {}", primingSpecies.name(), dominantChannel->peName());
double totalReactantMass = 0.0;
@@ -170,7 +167,7 @@ namespace gridfire {
std::vector<std::string> final_symbols;
std::vector<double> final_mass_fractions;
for(const auto& [species, mass_fraction] : currentMassFractions) {
final_symbols.push_back(std::string(species.name()));
final_symbols.emplace_back(species.name());
if (mass_fraction < 0.0 && std::abs(mass_fraction) < 1e-16) {
final_mass_fractions.push_back(0.0); // Avoid negative mass fractions
} else {
@@ -197,14 +194,14 @@ namespace gridfire {
const double T9,
const double rho
) {
const int speciesIndex = engine.getSpeciesIndex(species);
const size_t speciesIndex = engine.getSpeciesIndex(species);
std::vector<double> Y_scaled(Y.begin(), Y.end());
Y_scaled[speciesIndex] = 1.0; // Set the abundance of the species to 1.0 for rate constant calculation
double destructionRateConstant = 0.0;
for (const auto& reaction: engine.getNetworkReactions()) {
if (reaction.contains_reactant(species)) {
const int stoichiometry = reaction.stoichiometry(species);
destructionRateConstant += std::abs(stoichiometry) * engine.calculateMolarReactionFlow(reaction, Y_scaled, T9, rho);
if (reaction->contains_reactant(species)) {
const int stoichiometry = reaction->stoichiometry(species);
destructionRateConstant += std::abs(stoichiometry) * engine.calculateMolarReactionFlow(*reaction, Y_scaled, T9, rho);
}
}
return destructionRateConstant;
@@ -219,9 +216,9 @@ namespace gridfire {
) {
double creationRate = 0.0;
for (const auto& reaction: engine.getNetworkReactions()) {
const int stoichiometry = reaction.stoichiometry(species);
const int stoichiometry = reaction->stoichiometry(species);
if (stoichiometry > 0) {
creationRate += stoichiometry * engine.calculateMolarReactionFlow(reaction, Y, T9, rho);
creationRate += stoichiometry * engine.calculateMolarReactionFlow(*reaction, Y, T9, rho);
}
}
return creationRate;