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fix(weakRates): major progress in resolving bugs

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bigs were introduced by the interface change from accepting raw molar abundance vectors to using the composition vector. This commit resolves many of these, including preformant ways to report that a species is not present in the composition and unified index lookups using composition object tooling.

BREAKING CHANGE:
This commit is contained in:
Emily Boudreaux
2025-10-10 09:12:40 -04:00
parent 13e2ea9ffa
commit 2f1077c02d
21 changed files with 17953 additions and 375 deletions
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52
src/lib/engine/views/engine_multiscale.cpp
View File

@@ -17,7 +17,13 @@
namespace {
using namespace fourdst::atomic;
std::vector<double> packCompositionToVector(const fourdst::composition::Composition& composition, const gridfire::GraphEngine& engine) {
//TODO: Replace all calls to this function with composition.getMolarAbundanceVector() so that
// we don't have to keep this function around. (Cant do this right now because there is not a
// guarantee that this function will return the same ordering as the canonical vector representation)
std::vector<double> packCompositionToVector(
const fourdst::composition::Composition& composition,
const gridfire::GraphEngine& engine
) {
std::vector<double> Y(engine.getNetworkSpecies().size(), 0.0);
const auto& allSpecies = engine.getNetworkSpecies();
for (size_t i = 0; i < allSpecies.size(); ++i) {
@@ -780,6 +786,7 @@ namespace gridfire {
LOG_TRACE_L1(m_logger, "Partitioning by timescale...");
const auto result= m_baseEngine.getSpeciesDestructionTimescales(comp, T9, rho);
const auto netTimescale = m_baseEngine.getSpeciesTimescales(comp, T9, rho);
if (!result) {
LOG_ERROR(m_logger, "Failed to get species destruction timescales due to stale engine state");
m_logger->flush_log();
@@ -792,6 +799,14 @@ namespace gridfire {
}
const std::unordered_map<Species, double>& all_timescales = result.value();
const std::unordered_map<Species, double>& net_timescales = netTimescale.value();
for (const auto& [species, destructionTimescale] : all_timescales) {
std::cout << "Species: " << species.name()
<< ", Destruction Timescale: " << (std::isfinite(destructionTimescale) ? std::to_string(destructionTimescale) : "inf")
<< " s, Net Timescale: " << (std::isfinite(net_timescales.at(species)) ? std::to_string(net_timescales.at(species)) : "inf")
<< " s\n";
}
const auto& all_species = m_baseEngine.getNetworkSpecies();
std::vector<std::pair<double, Species>> sorted_timescales;
@@ -1075,6 +1090,11 @@ namespace gridfire {
normalized_composition.setMassFraction(species, 0.0);
}
}
bool normCompFinalizedOkay = normalized_composition.finalize(true);
if (!normCompFinalizedOkay) {
LOG_ERROR(m_logger, "Failed to finalize composition before QSE solve.");
throw std::runtime_error("Failed to finalize composition before QSE solve.");
}
Eigen::VectorXd Y_scale(algebraic_species.size());
Eigen::VectorXd v_initial(algebraic_species.size());
@@ -1330,10 +1350,18 @@ namespace gridfire {
Eigen::VectorXd y_qse = m_Y_scale.array() * v_qse.array().sinh(); // Convert to physical abundances using asinh scaling
for (const auto& species: m_qse_solve_species) {
if (!comp_trial.contains(species)) {
if (!comp_trial.hasSymbol(std::string(species.name()))) {
comp_trial.registerSpecies(species);
}
comp_trial.setMassFraction(species, y_qse[static_cast<long>(m_qse_solve_species_index_map.at(species))]);
const double molarAbundance = y_qse[static_cast<long>(m_qse_solve_species_index_map.at(species))];
const double massFraction = molarAbundance * species.mass();
comp_trial.setMassFraction(species, massFraction);
}
const bool didFinalize = comp_trial.finalize(false);
if (!didFinalize) {
std::string msg = std::format("Failed to finalize composition (comp_trial) in {} at line {}", __FILE__, __LINE__);
throw std::runtime_error(msg);
}
const auto result = m_view->getBaseEngine().calculateRHSAndEnergy(comp_trial, m_T9, m_rho);
@@ -1357,10 +1385,18 @@ namespace gridfire {
Eigen::VectorXd y_qse = m_Y_scale.array() * v_qse.array().sinh(); // Convert to physical abundances using asinh scaling
for (const auto& species: m_qse_solve_species) {
if (!comp_trial.contains(species)) {
if (!comp_trial.hasSymbol(std::string(species.name()))) {
comp_trial.registerSpecies(species);
}
comp_trial.setMassFraction(species, y_qse[static_cast<long>(m_qse_solve_species_index_map.at(species))]);
const double molarAbundance = y_qse[static_cast<long>(m_qse_solve_species_index_map.at(species))];
const double massFraction = molarAbundance * species.mass();
comp_trial.setMassFraction(species, massFraction);
}
const bool didFinalize = comp_trial.finalize(false);
if (!didFinalize) {
std::string msg = std::format("Failed to finalize composition (comp_trial) in {} at line {}", __FILE__, __LINE__);
throw std::runtime_error(msg);
}
m_view->getBaseEngine().generateJacobianMatrix(comp_trial, m_T9, m_rho);
@@ -1368,14 +1404,16 @@ namespace gridfire {
const long N = static_cast<long>(m_qse_solve_species.size());
J_qse.resize(N, N);
long rowID = 0;
long colID = 0;
for (const auto& rowSpecies : m_qse_solve_species) {
long colID = 0;
for (const auto& colSpecies: m_qse_solve_species) {
J_qse(rowID++, colID++) = m_view->getBaseEngine().getJacobianMatrixEntry(
J_qse(rowID, colID) = m_view->getBaseEngine().getJacobianMatrixEntry(
rowSpecies,
colSpecies
);
colID += 1;
}
rowID += 1;
}
// Chain rule for asinh scaling: