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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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107
src/lib/engine/views/engine_multiscale.cpp
View File

@@ -44,7 +44,7 @@ namespace {
std::unordered_set<size_t> visited;
for (const size_t& start_node : nodes) {
if (visited.find(start_node) == visited.end()) {
if (!visited.contains(start_node)) {
std::vector<size_t> current_component;
std::queue<size_t> q;
@@ -56,9 +56,9 @@ namespace {
q.pop();
current_component.push_back(u);
if (graph.count(u)) {
if (graph.contains(u)) {
for (const auto& v : graph.at(u)) {
if (visited.find(v) == visited.end()) {
if (!visited.contains(v)) {
visited.insert(v);
q.push(v);
}
@@ -194,8 +194,7 @@ namespace gridfire {
}
auto deriv = result.value();
for (size_t i = 0; i < m_algebraic_species_indices.size(); ++i) {
const size_t species_index = m_algebraic_species_indices[i];
for (const size_t species_index : m_algebraic_species_indices) {
deriv.dydt[species_index] = 0.0; // Fix the algebraic species to the equilibrium abundances we calculate.
}
return deriv;
@@ -283,11 +282,11 @@ namespace gridfire {
return m_baseEngine.calculateMolarReactionFlow(reaction, Y_mutable, T9, rho);
}
const reaction::LogicalReactionSet & MultiscalePartitioningEngineView::getNetworkReactions() const {
const reaction::ReactionSet & MultiscalePartitioningEngineView::getNetworkReactions() const {
return m_baseEngine.getNetworkReactions();
}
void MultiscalePartitioningEngineView::setNetworkReactions(const reaction::LogicalReactionSet &reactions) {
void MultiscalePartitioningEngineView::setNetworkReactions(const reaction::ReactionSet &reactions) {
LOG_CRITICAL(m_logger, "setNetworkReactions is not supported in MultiscalePartitioningEngineView. Did you mean to call this on the base engine?");
throw exceptions::UnableToSetNetworkReactionsError("setNetworkReactions is not supported in MultiscalePartitioningEngineView. Did you mean to call this on the base engine?");
}
@@ -508,7 +507,7 @@ namespace gridfire {
}()
);
m_qse_groups = std::move(validated_groups);
m_qse_groups = validated_groups;
LOG_TRACE_L1(m_logger, "Identified {} QSE groups.", m_qse_groups.size());
for (const auto& group : m_qse_groups) {
@@ -589,7 +588,7 @@ namespace gridfire {
double max_log_flow = std::numeric_limits<double>::lowest();
for (const auto& reaction : all_reactions) {
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(reaction, Y, T9, rho));
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(*reaction, Y, T9, rho));
reaction_flows.push_back(flow);
if (flow > 1e-99) { // Avoid log(0)
double log_flow = std::log10(flow);
@@ -627,7 +626,7 @@ namespace gridfire {
// Group species by mass number for ranked layout.
// If species.a() returns incorrect values (e.g., 0 for many species), they will be grouped together here.
species_by_mass[species.a()].push_back(std::string(species.name()));
species_by_mass[species.a()].emplace_back(species.name());
}
dotFile << "\n";
@@ -843,7 +842,7 @@ namespace gridfire {
return equilibrateNetwork(Y, T9, rho);
}
int MultiscalePartitioningEngineView::getSpeciesIndex(const fourdst::atomic::Species &species) const {
size_t MultiscalePartitioningEngineView::getSpeciesIndex(const fourdst::atomic::Species &species) const {
return m_baseEngine.getSpeciesIndex(species);
}
@@ -859,14 +858,14 @@ namespace gridfire {
m_logger->flush_log();
throw exceptions::StaleEngineError("Failed to get species timescales due to stale engine state");
}
std::unordered_map<Species, double> all_timescales = result.value();
const std::unordered_map<Species, double>& all_timescales = result.value();
const auto& all_species = m_baseEngine.getNetworkSpecies();
std::vector<std::pair<double, size_t>> sorted_timescales;
for (size_t i = 0; i < all_species.size(); ++i) {
double timescale = all_timescales.at(all_species[i]);
if (std::isfinite(timescale) && timescale > 0) {
sorted_timescales.push_back({timescale, i});
sorted_timescales.emplace_back(timescale, i);
}
}
@@ -972,32 +971,6 @@ namespace gridfire {
}
// std::unordered_map<size_t, std::vector<size_t>> MultiscalePartitioningEngineView::buildConnectivityGraph(
// const std::unordered_set<size_t> &fast_reaction_indices
// ) const {
// const auto& all_reactions = m_baseEngine.getNetworkReactions();
// std::unordered_map<size_t, std::vector<size_t>> connectivity;
// for (const size_t reaction_idx : fast_reaction_indices) {
// const auto& reaction = all_reactions[reaction_idx];
// const auto& reactants = reaction.reactants();
// const auto& products = reaction.products();
//
// // For each fast reaction, create edges between all reactants and all products.
// // This represents that nucleons can flow quickly between these species.
// for (const auto& reactant : reactants) {
// const size_t reactant_idx = m_baseEngine.getSpeciesIndex(reactant);
// for (const auto& product : products) {
// const size_t product_idx = m_baseEngine.getSpeciesIndex(product);
//
// // Add a two-way edge to the adjacency list.
// connectivity[reactant_idx].push_back(product_idx);
// connectivity[product_idx].push_back(reactant_idx);
// }
// }
// }
// return connectivity;
// }
std::vector<MultiscalePartitioningEngineView::QSEGroup>
MultiscalePartitioningEngineView::validateGroupsWithFluxAnalysis(
const std::vector<QSEGroup> &candidate_groups,
@@ -1016,14 +989,14 @@ namespace gridfire {
);
for (const auto& reaction: m_baseEngine.getNetworkReactions()) {
const double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(reaction, Y, T9, rho));
const double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(*reaction, Y, T9, rho));
if (flow == 0.0) {
continue; // Skip reactions with zero flow
}
bool has_internal_reactant = false;
bool has_external_reactant = false;
for (const auto& reactant : reaction.reactants()) {
for (const auto& reactant : reaction->reactants()) {
if (group_members.contains(m_baseEngine.getSpeciesIndex(reactant))) {
has_internal_reactant = true;
} else {
@@ -1034,7 +1007,7 @@ namespace gridfire {
bool has_internal_product = false;
bool has_external_product = false;
for (const auto& product : reaction.products()) {
for (const auto& product : reaction->products()) {
if (group_members.contains(m_baseEngine.getSpeciesIndex(product))) {
has_internal_product = true;
} else {
@@ -1231,7 +1204,7 @@ namespace gridfire {
Eigen::VectorXd Y_scale(qse_solve_indices.size());
Eigen::VectorXd v_initial(qse_solve_indices.size());
for (size_t i = 0; i < qse_solve_indices.size(); ++i) {
for (long i = 0; i < qse_solve_indices.size(); ++i) {
constexpr double abundance_floor = 1.0e-15;
const double initial_abundance = Y_full[qse_solve_indices[i]];
Y_scale(i) = std::max(initial_abundance, abundance_floor);
@@ -1273,7 +1246,7 @@ namespace gridfire {
}
LOG_TRACE_L1(m_logger, "Minimization succeeded!");
Eigen::VectorXd Y_final_qse = Y_scale.array() * v_initial.array().sinh(); // Convert back to physical abundances using asinh scaling
for (size_t i = 0; i < qse_solve_indices.size(); ++i) {
for (long i = 0; i < qse_solve_indices.size(); ++i) {
LOG_TRACE_L1(
m_logger,
"Species {} (index {}) started with abundance {} and ended with {}.",
@@ -1314,7 +1287,7 @@ namespace gridfire {
const double timescale = all_timescales.at(all_species[species_idx]);
mean_timescale += timescale;
}
mean_timescale = mean_timescale / pool.size();
mean_timescale = mean_timescale / static_cast<double>(pool.size());
if (std::isinf(mean_timescale)) {
LOG_CRITICAL(m_logger, "Encountered infinite mean timescale for pool {} with species: {}",
count, [&]() -> std::string {
@@ -1355,8 +1328,8 @@ namespace gridfire {
return result;
}();
std::map<size_t, std::vector<reaction::LogicalReaction*>> speciesReactionMap;
std::vector<const reaction::LogicalReaction*> candidate_reactions;
std::map<size_t, std::vector<reaction::LogicalReaclibReaction*>> speciesReactionMap;
std::vector<const reaction::LogicalReaclibReaction*> candidate_reactions;
auto getSpeciesIdx = [&](const std::vector<Species> &species) -> std::vector<size_t> {
std::vector<size_t> result;
@@ -1369,8 +1342,8 @@ namespace gridfire {
};
for (const auto& reaction : m_baseEngine.getNetworkReactions()) {
const std::vector<Species> &reactants = reaction.reactants();
const std::vector<Species> &products = reaction.products();
const std::vector<Species> &reactants = reaction->reactants();
const std::vector<Species> &products = reaction->products();
std::unordered_set<Species> reactant_set(reactants.begin(), reactants.end());
std::unordered_set<Species> product_set(products.begin(), products.end());
@@ -1422,15 +1395,15 @@ namespace gridfire {
if (pool.empty()) continue; // Skip empty pools
// For each pool first identify all topological bridge connections
std::vector<std::pair<reaction::LogicalReaction, double>> bridge_reactions;
std::vector<std::pair<const reaction::Reaction*, double>> bridge_reactions;
for (const auto& species_idx : pool) {
Species ash = all_species[species_idx];
for (const auto& reaction : all_reactions) {
if (reaction.contains(ash)) {
if (reaction->contains(ash)) {
// Check to make sure there is at least one reactant that is not in the pool
// This lets seed nuclei bring mass into the QSE group.
bool has_external_reactant = false;
for (const auto& reactant : reaction.reactants()) {
for (const auto& reactant : reaction->reactants()) {
if (std::ranges::find(pool, m_baseEngine.getSpeciesIndex(reactant)) == pool.end()) {
has_external_reactant = true;
LOG_TRACE_L3(m_logger, "Found external reactant {} in reaction {} for species {}.", reactant.name(), reaction.id(), ash.name());
@@ -1438,9 +1411,9 @@ namespace gridfire {
}
}
if (has_external_reactant) {
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(reaction, Y, T9, rho));
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(*reaction, Y, T9, rho));
LOG_TRACE_L3(m_logger, "Found bridge reaction {} with flow {} for species {}.", reaction.id(), flow, ash.name());
bridge_reactions.push_back({reaction, flow});
bridge_reactions.emplace_back(reaction.get(), flow);
}
}
}
@@ -1467,8 +1440,8 @@ namespace gridfire {
}
std::vector<size_t> seed_indices;
for (size_t i = 0; i < bridge_reactions.size(); ++i) {
for (const auto& fuel : bridge_reactions[i].first.reactants()) {
for (auto &reaction: bridge_reactions | std::views::keys) {
for (const auto& fuel : reaction->reactants()) {
size_t fuel_idx = m_baseEngine.getSpeciesIndex(fuel);
// Only add the fuel if it is not already in the pool
if (std::ranges::find(pool, fuel_idx) == pool.end()) {
@@ -1492,7 +1465,7 @@ namespace gridfire {
mean_timescale += species.halfLife();
}
}
mean_timescale /= poolSet.size();
mean_timescale /= static_cast<double>(poolSet.size());
QSEGroup qse_group(all_indices, false, poolSet, seedSet, mean_timescale);
candidate_groups.push_back(qse_group);
}
@@ -1505,7 +1478,7 @@ namespace gridfire {
std::vector<double> y_trial = m_Y_full_initial;
Eigen::VectorXd y_qse = m_Y_scale.array() * v_qse.array().sinh(); // Convert to physical abundances using asinh scaling
for (size_t i = 0; i < m_qse_solve_indices.size(); ++i) {
for (long i = 0; i < m_qse_solve_indices.size(); ++i) {
y_trial[m_qse_solve_indices[i]] = y_qse(i);
}
@@ -1514,8 +1487,8 @@ namespace gridfire {
throw exceptions::StaleEngineError("Failed to calculate RHS and energy due to stale engine state");
}
const auto&[dydt, nuclearEnergyGenerationRate] = result.value();
f_qse.resize(m_qse_solve_indices.size());
for (size_t i = 0; i < m_qse_solve_indices.size(); ++i) {
f_qse.resize(static_cast<long>(m_qse_solve_indices.size()));
for (long i = 0; i < m_qse_solve_indices.size(); ++i) {
f_qse(i) = dydt[m_qse_solve_indices[i]];
}
@@ -1526,20 +1499,18 @@ namespace gridfire {
std::vector<double> y_trial = m_Y_full_initial;
Eigen::VectorXd y_qse = m_Y_scale.array() * v_qse.array().sinh(); // Convert to physical abundances using asinh scaling
for (size_t i = 0; i < m_qse_solve_indices.size(); ++i) {
for (long i = 0; i < m_qse_solve_indices.size(); ++i) {
y_trial[m_qse_solve_indices[i]] = y_qse(i);
}
// TODO: Think about if the jacobian matrix should be mutable so that generateJacobianMatrix can be const
m_view->getBaseEngine().generateJacobianMatrix(y_trial, m_T9, m_rho);
// TODO: Think very carefully about the indices here.
J_qse.resize(m_qse_solve_indices.size(), m_qse_solve_indices.size());
for (size_t i = 0; i < m_qse_solve_indices.size(); ++i) {
for (size_t j = 0; j < m_qse_solve_indices.size(); ++j) {
J_qse.resize(static_cast<long>(m_qse_solve_indices.size()), static_cast<long>(m_qse_solve_indices.size()));
for (long i = 0; i < m_qse_solve_indices.size(); ++i) {
for (long j = 0; j < m_qse_solve_indices.size(); ++j) {
J_qse(i, j) = m_view->getBaseEngine().getJacobianMatrixEntry(
m_qse_solve_indices[i],
m_qse_solve_indices[j]
static_cast<int>(m_qse_solve_indices[i]),
static_cast<int>(m_qse_solve_indices[j])
);
}
}