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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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68
src/lib/engine/views/engine_adaptive.cpp
View File

@@ -70,12 +70,12 @@ namespace gridfire {
reactionIndexMap.reserve(m_activeReactions.size());
for (const auto& active_reaction_ptr : m_activeReactions) {
auto it = fullReactionReverseMap.find(active_reaction_ptr.id());
auto it = fullReactionReverseMap.find(active_reaction_ptr->id());
if (it != fullReactionReverseMap.end()) {
reactionIndexMap.push_back(it->second);
} else {
LOG_ERROR(m_logger, "Active reaction '{}' not found in base engine during reaction index map construction.", active_reaction_ptr.id());
LOG_ERROR(m_logger, "Active reaction '{}' not found in base engine during reaction index map construction.", active_reaction_ptr->id());
m_logger->flush_log();
throw std::runtime_error("Mismatch between active reactions and base engine.");
}
@@ -89,11 +89,6 @@ namespace gridfire {
fourdst::composition::Composition baseUpdatedComposition = m_baseEngine.update(netIn);
NetIn updatedNetIn = netIn;
// for (const auto &entry: netIn.composition | std::views::values) {
// if (baseUpdatedComposition.contains(entry.isotope())) {
// updatedNetIn.composition.setMassFraction(entry.isotope(), baseUpdatedComposition.getMassFraction(entry.isotope()));
// }
// }
updatedNetIn.composition = baseUpdatedComposition;
updatedNetIn.composition.finalize(false);
@@ -115,7 +110,7 @@ namespace gridfire {
const std::unordered_set<Species> reachableSpecies = findReachableSpecies(updatedNetIn);
LOG_DEBUG(m_logger, "Found {} reachable species in adaptive engine view.", reachableSpecies.size());
const std::vector<const reaction::LogicalReaction*> finalReactions = cullReactionsByFlow(allFlows, reachableSpecies, Y_Full, maxFlow);
const std::vector<const reaction::Reaction*> finalReactions = cullReactionsByFlow(allFlows, reachableSpecies, Y_Full, maxFlow);
finalizeActiveSet(finalReactions);
@@ -191,7 +186,7 @@ namespace gridfire {
const size_t i_full = mapCulledToFullSpeciesIndex(i_culled);
const size_t j_full = mapCulledToFullSpeciesIndex(j_culled);
return m_baseEngine.getJacobianMatrixEntry(i_full, j_full);
return m_baseEngine.getJacobianMatrixEntry(static_cast<int>(i_full), static_cast<int>(j_full));
}
void AdaptiveEngineView::generateStoichiometryMatrix() {
@@ -206,7 +201,7 @@ namespace gridfire {
validateState();
const size_t speciesIndex_full = mapCulledToFullSpeciesIndex(speciesIndex_culled);
const size_t reactionIndex_full = mapCulledToFullReactionIndex(reactionIndex_culled);
return m_baseEngine.getStoichiometryMatrixEntry(speciesIndex_full, reactionIndex_full);
return m_baseEngine.getStoichiometryMatrixEntry(static_cast<int>(speciesIndex_full), static_cast<int>(reactionIndex_full));
}
double AdaptiveEngineView::calculateMolarReactionFlow(
@@ -226,11 +221,11 @@ namespace gridfire {
return m_baseEngine.calculateMolarReactionFlow(reaction, Y, T9, rho);
}
const reaction::LogicalReactionSet & AdaptiveEngineView::getNetworkReactions() const {
const reaction::ReactionSet & AdaptiveEngineView::getNetworkReactions() const {
return m_activeReactions;
}
void AdaptiveEngineView::setNetworkReactions(const reaction::LogicalReactionSet &reactions) {
void AdaptiveEngineView::setNetworkReactions(const reaction::ReactionSet &reactions) {
LOG_CRITICAL(m_logger, "AdaptiveEngineView does not support setting network reactions directly. Use update() with NetIn instead. Perhaps you meant to call this on the base engine?");
throw exceptions::UnableToSetNetworkReactionsError("AdaptiveEngineView does not support setting network reactions directly. Use update() with NetIn instead. Perhaps you meant to call this on the base engine?");
}
@@ -248,7 +243,7 @@ namespace gridfire {
return std::unexpected{result.error()};
}
const std::unordered_map<Species, double> fullTimescales = result.value();
const std::unordered_map<Species, double>& fullTimescales = result.value();
std::unordered_map<Species, double> culledTimescales;
@@ -262,22 +257,21 @@ namespace gridfire {
}
std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError>
std::expected<std::unordered_map<Species, double>, expectations::StaleEngineError>
AdaptiveEngineView::getSpeciesDestructionTimescales(
const std::vector<double> &Y,
double T9,
double rho
const double T9,
const double rho
) const {
validateState();
const auto Y_full = mapCulledToFull(Y);
const auto result = m_baseEngine.getSpeciesDestructionTimescales(Y_full, T9, rho);
const std::vector<double> Y_full = mapCulledToFull(Y);
const auto result = m_baseEngine.getSpeciesDestructionTimescales(Y_full, T9, rho);
if (!result) {
return std::unexpected{result.error()};
}
const std::unordered_map<Species, double> destructionTimescales = result.value();
const std::unordered_map<Species, double>& destructionTimescales = result.value();
std::unordered_map<Species, double> culledTimescales;
culledTimescales.reserve(m_activeSpecies.size());
@@ -309,7 +303,7 @@ namespace gridfire {
return m_baseEngine.primeEngine(netIn);
}
int AdaptiveEngineView::getSpeciesIndex(const fourdst::atomic::Species &species) const {
size_t AdaptiveEngineView::getSpeciesIndex(const fourdst::atomic::Species &species) const {
const auto it = std::ranges::find(m_activeSpecies, species);
if (it != m_activeSpecies.end()) {
return static_cast<int>(std::distance(m_activeSpecies.begin(), it));
@@ -389,8 +383,8 @@ namespace gridfire {
const auto& fullReactionSet = m_baseEngine.getNetworkReactions();
reactionFlows.reserve(fullReactionSet.size());
for (const auto& reaction : fullReactionSet) {
const double flow = m_baseEngine.calculateMolarReactionFlow(reaction, out_Y_Full, T9, rho);
reactionFlows.push_back({&reaction, flow});
const double flow = m_baseEngine.calculateMolarReactionFlow(*reaction, out_Y_Full, T9, rho);
reactionFlows.push_back({reaction.get(), flow});
LOG_TRACE_L1(m_logger, "Reaction '{}' has flow rate: {:0.3E} [mol/s/g]", reaction.id(), flow);
}
return reactionFlows;
@@ -418,14 +412,14 @@ namespace gridfire {
new_species_found_in_pass = false;
for (const auto& reaction: m_baseEngine.getNetworkReactions()) {
bool all_reactants_reachable = true;
for (const auto& reactant: reaction.reactants()) {
for (const auto& reactant: reaction->reactants()) {
if (!reachable.contains(reactant)) {
all_reactants_reachable = false;
break;
}
}
if (all_reactants_reachable) {
for (const auto& product: reaction.products()) {
for (const auto& product: reaction->products()) {
if (!reachable.contains(product)) {
reachable.insert(product);
new_species_found_in_pass = true;
@@ -439,7 +433,7 @@ namespace gridfire {
return reachable;
}
std::vector<const reaction::LogicalReaction *> AdaptiveEngineView::cullReactionsByFlow(
std::vector<const reaction::Reaction *> AdaptiveEngineView::cullReactionsByFlow(
const std::vector<ReactionFlow> &allFlows,
const std::unordered_set<fourdst::atomic::Species> &reachableSpecies,
const std::vector<double> &Y_full,
@@ -449,7 +443,7 @@ namespace gridfire {
const auto relative_culling_threshold = m_config.get<double>("gridfire:AdaptiveEngineView:RelativeCullingThreshold", 1e-75);
double absoluteCullingThreshold = relative_culling_threshold * maxFlow;
LOG_DEBUG(m_logger, "Relative culling threshold: {:0.3E} ({})", relative_culling_threshold, absoluteCullingThreshold);
std::vector<const reaction::LogicalReaction*> culledReactions;
std::vector<const reaction::Reaction*> culledReactions;
for (const auto& [reactionPtr, flowRate]: allFlows) {
bool keepReaction = false;
if (flowRate > absoluteCullingThreshold) {
@@ -487,7 +481,7 @@ namespace gridfire {
const double T9,
const double rho,
const std::vector<Species> &activeSpecies,
const reaction::LogicalReactionSet &activeReactions
const reaction::ReactionSet &activeReactions
) const {
const auto result = m_baseEngine.getSpeciesTimescales(Y_full, T9, rho);
if (!result) {
@@ -497,7 +491,7 @@ namespace gridfire {
std::unordered_map<Species, double> timescales = result.value();
std::set<Species> onlyProducedSpecies;
for (const auto& reaction : activeReactions) {
const std::vector<Species> products = reaction.products();
const std::vector<Species>& products = reaction->products();
onlyProducedSpecies.insert(products.begin(), products.end());
}
@@ -506,7 +500,7 @@ namespace gridfire {
onlyProducedSpecies,
[&](const Species &species) {
for (const auto& reaction : activeReactions) {
if (reaction.contains_reactant(species)) {
if (reaction->contains_reactant(species)) {
return true; // If any active reaction consumes the species then erase it from the set.
}
}
@@ -545,26 +539,26 @@ namespace gridfire {
}()
);
std::unordered_map<Species, const reaction::LogicalReaction*> reactionsToRescue;
std::unordered_map<Species, const reaction::Reaction*> reactionsToRescue;
for (const auto& species : onlyProducedSpecies) {
double maxSpeciesConsumptionRate = 0.0;
for (const auto& reaction : m_baseEngine.getNetworkReactions()) {
const bool speciesToCheckIsConsumed = reaction.contains_reactant(species);
const bool speciesToCheckIsConsumed = reaction->contains_reactant(species);
if (!speciesToCheckIsConsumed) {
continue; // If the species is not consumed by this reaction, skip it.
}
bool allOtherReactantsAreAvailable = true;
for (const auto& reactant : reaction.reactants()) {
for (const auto& reactant : reaction->reactants()) {
const bool reactantIsAvailable = std::ranges::contains(activeSpecies, reactant);
if (!reactantIsAvailable && reactant != species) {
allOtherReactantsAreAvailable = false;
}
}
if (allOtherReactantsAreAvailable && speciesToCheckIsConsumed) {
double rate = reaction.calculate_rate(T9);
double rate = reaction->calculate_rate(T9, rho, Y_full);
if (rate > maxSpeciesConsumptionRate) {
maxSpeciesConsumptionRate = rate;
reactionsToRescue[species] = &reaction;
reactionsToRescue[species] = reaction.get();
}
}
}
@@ -626,7 +620,7 @@ namespace gridfire {
);
RescueSet rescueSet;
std::unordered_set<const reaction::LogicalReaction*> newReactions;
std::unordered_set<const reaction::Reaction*> newReactions;
std::unordered_set<Species> newSpecies;
for (const auto &reactionPtr: reactionsToRescue | std::views::values) {
@@ -639,7 +633,7 @@ namespace gridfire {
}
void AdaptiveEngineView::finalizeActiveSet(
const std::vector<const reaction::LogicalReaction *> &finalReactions
const std::vector<const reaction::Reaction *> &finalReactions
) {
std::unordered_set<Species>finalSpeciesSet;
m_activeReactions.clear();