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feat(jacobian): Added regularization

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There are times when the jacobian matrix has infinities or nans. If
these cases correspond to species (rows or columns) which have
effectivley zero abundance (i.e. if Y(Cl-32) ~ 1e-310 and
(dY(H-2)/dt)/dY(Cl-32) is inf) then it is safe to regularize these
entries to 0. If this is not done then the solver will end up finding
NaN values for the molar abundances on subsequent steps. This has been
implimented through a small regularization function in the
CVODE_solver_strategy file.
This commit is contained in:
Emily Boudreaux
2025-11-14 18:49:29 -05:00
parent 2ed629e0bf
commit b5d76e3728
7 changed files with 365 additions and 16 deletions
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72
src/lib/engine/views/engine_multiscale.cpp
View File

@@ -163,19 +163,51 @@ namespace gridfire {
const double T9,
const double rho
) const {
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
LOG_TRACE_L2(m_logger, "Calculating RHS and Energy in MultiscalePartitioningEngineView at T9 = {}, rho = {}.", T9, rho);
LOG_TRACE_L2(m_logger, "Input composition is {}", [&comp]() -> std::string {
std::stringstream ss;
size_t i = 0;
for (const auto& [species, abundance] : comp) {
ss << species.name() << ": " << abundance;
if (i < comp.size() - 1) {
ss << ", ";
}
i++;
}
return ss.str();
}());
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
LOG_TRACE_L2(m_logger, "Equilibrated composition prior to calling base engine is {}", [&qseComposition, &comp]() -> std::string {
std::stringstream ss;
size_t i = 0;
for (const auto& [species, abundance] : qseComposition) {
ss << species.name() << ": " << abundance;
if (comp.contains(species)) {
ss << " (input: " << comp.getMolarAbundance(species) << ")";
}
if (i < qseComposition.size() - 1) {
ss << ", ";
}
i++;
}
return ss.str();
}());
const auto result = m_baseEngine.calculateRHSAndEnergy(comp, T9, rho);
LOG_TRACE_L2(m_logger, "Base engine calculation of RHS and Energy complete.");
if (!result) {
LOG_TRACE_L2(m_logger, "Base engine returned stale error during RHS and Energy calculation.");
return std::unexpected{result.error()};
}
auto deriv = result.value();
LOG_TRACE_L2(m_logger, "Zeroing out algebraic species derivatives.");
for (const auto& species : m_algebraic_species) {
deriv.dydt[species] = 0.0; // Fix the algebraic species to the equilibrium abundances we calculate.
}
LOG_TRACE_L2(m_logger, "Done Zeroing out algebraic species derivatives.");
return deriv;
}
@@ -1157,13 +1189,35 @@ namespace gridfire {
const double rho
) const {
LOG_TRACE_L1(m_logger, "Solving for QSE abundances...");
LOG_TRACE_L2(m_logger, "Composition before QSE solving: {}", [&comp]() -> std::string {
std::stringstream ss;
size_t i = 0;
for (const auto& [sp, y] : comp) {
ss << std::format("{}: {}", sp.name(), y);
if (i < comp.size() - 1) {
ss << ", ";
}
i++;
}
return ss.str();
}());
fourdst::composition::Composition outputComposition(comp.getRegisteredSpecies());
for (const auto& [sp, y]: comp) {
outputComposition.setMolarAbundance(sp, y);
}
fourdst::composition::Composition outputComposition(comp);
for (const auto&[is_in_equilibrium, algebraic_species, seed_species, mean_timescale] : m_qse_groups) {
LOG_TRACE_L2(m_logger, "Working on QSE group with algebraic species: {}",
[&]() -> std::string {
std::stringstream ss;
size_t count = 0;
for (const auto& species: algebraic_species) {
ss << species.name();
if (count < algebraic_species.size() - 1) {
ss << ", ";
}
count++;
}
return ss.str();
}());
if (!is_in_equilibrium || (algebraic_species.empty() && seed_species.empty())) {
continue;
}
@@ -1178,16 +1232,19 @@ namespace gridfire {
const double Y = std::max(initial_abundance, abundance_floor);
v_initial(i) = std::log(Y);
species_to_index_map.emplace(species, i);
LOG_TRACE_L2(m_logger, "For species {} initial molar abundance is {}, log scaled to {}. Species placed at index {}.", species.name(), Y, v_initial(i), i);
i++;
}
LOG_TRACE_L2(m_logger, "Setting up Eigen Levenberg-Marquardt solver for QSE group...");
EigenFunctor functor(*this, algebraic_species, comp, T9, rho, Y_scale, species_to_index_map);
Eigen::LevenbergMarquardt lm(functor);
lm.parameters.ftol = 1.0e-10;
lm.parameters.xtol = 1.0e-10;
LOG_TRACE_L1(m_logger, "Minimizing functor...");
LOG_TRACE_L2(m_logger, "Minimizing functor...");
Eigen::LevenbergMarquardtSpace::Status status = lm.minimize(v_initial);
LOG_TRACE_L2(m_logger, "Minimizing functor status: {}", lm_status_map.at(status));
if (status <= 0 || status >= 4) {
std::stringstream msg;
@@ -1459,13 +1516,14 @@ namespace gridfire {
}
LOG_TRACE_L2(
m_view.m_logger,
"Functor evaluation at T9 = {}, rho = {}, y_qse = <{}> complete. ||f|| = {}",
"Functor evaluation at T9 = {}, rho = {}, y_qse (v_qse) = <{}> complete. ||f|| = {}",
m_T9,
m_rho,
[&]() -> std::string {
std::stringstream ss;
for (long j = 0; j < y_qse.size(); ++j) {
ss << y_qse(j);
ss << "(" << v_qse(j) << ")";
if (j < y_qse.size() - 1) {
ss << ", ";
}