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feat(Jacobian): Jacobian generation is now stateless.

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Previously Jacobians were stored by engines and accessed through engine
accessors (e.g getJacobianMatrixEntry); however, this resulted in
desynced jacobian states. We have changed to a pattern of Engine creates
a jacobian and returns it to the caller. The caller can then do what
they will with it. Because of this the getJacobianMatrixEntry method has
been removed.

BREAKING CHANGE:
    - There is no longer any getJacobianMatrixEntry method on
DynamicEngine classes
    - the generateJacobian method signature has changed to return a
NetworkJacobian object. Internally this uses an Eigen Sparse Matrix to
store its data.
This commit is contained in:
Emily Boudreaux
2025-11-14 10:51:40 -05:00
parent 1500f863b6
commit 9417b79a32
14 changed files with 352 additions and 440 deletions
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86
src/lib/engine/views/engine_multiscale.cpp
View File

@@ -163,9 +163,9 @@ namespace gridfire {
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
const auto result = m_baseEngine.calculateRHSAndEnergy(qseComposition, T9, rho);
const auto result = m_baseEngine.calculateRHSAndEnergy(comp, T9, rho);
if (!result) {
return std::unexpected{result.error()};
@@ -184,28 +184,29 @@ namespace gridfire {
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.calculateEpsDerivatives(qseComposition, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.calculateEpsDerivatives(comp, T9, rho);
}
void MultiscalePartitioningEngineView::generateJacobianMatrix(
NetworkJacobian MultiscalePartitioningEngineView::generateJacobianMatrix(
const fourdst::composition::CompositionAbstract &comp,
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
m_baseEngine.generateJacobianMatrix(qseComposition, T9, rho, m_dynamic_species);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.generateJacobianMatrix(comp, T9, rho, m_dynamic_species);
}
void MultiscalePartitioningEngineView::generateJacobianMatrix(
NetworkJacobian MultiscalePartitioningEngineView::generateJacobianMatrix(
const fourdst::composition::CompositionAbstract &comp,
const double T9,
const double rho,
const std::vector<Species> &activeSpecies
) const {
const bool activeSpeciesIsSubset = std::ranges::any_of(activeSpecies, [&](const auto& species) -> bool {
return !involvesSpecies(species);
});
bool activeSpeciesIsSubset = true;
for (const auto& species : activeSpecies) {
if (!involvesSpecies(species)) activeSpeciesIsSubset = false;
}
if (!activeSpeciesIsSubset) {
std::string msg = std::format(
"Active species set contains species ({}) not present in network partition. Cannot generate jacobian matrix due to this.",
@@ -230,33 +231,19 @@ namespace gridfire {
}
}
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
m_baseEngine.generateJacobianMatrix(qseComposition, T9, rho, dynamicActiveSpeciesIntersection);
return m_baseEngine.generateJacobianMatrix(comp, T9, rho, dynamicActiveSpeciesIntersection);
}
void MultiscalePartitioningEngineView::generateJacobianMatrix(
NetworkJacobian MultiscalePartitioningEngineView::generateJacobianMatrix(
const fourdst::composition::CompositionAbstract &comp,
const double T9,
const double rho,
const SparsityPattern &sparsityPattern
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.generateJacobianMatrix(qseComposition, T9, rho, sparsityPattern);
}
double MultiscalePartitioningEngineView::getJacobianMatrixEntry(
const Species& rowSpecies,
const Species& colSpecies
) const {
// Check if the species we are differentiating with respect to is algebraic or dynamic. If it is algebraic we can reduce the work significantly...
if (std::ranges::contains(m_algebraic_species, colSpecies)) {
return 0.0;
}
if (std::ranges::contains(m_algebraic_species, rowSpecies)) {
return 0.0;
}
return m_baseEngine.getJacobianMatrixEntry(rowSpecies, colSpecies);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.generateJacobianMatrix(comp, T9, rho, sparsityPattern);
}
void MultiscalePartitioningEngineView::generateStoichiometryMatrix() {
@@ -276,9 +263,9 @@ namespace gridfire {
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
return m_baseEngine.calculateMolarReactionFlow(reaction, qseComposition, T9, rho);
return m_baseEngine.calculateMolarReactionFlow(reaction, comp, T9, rho);
}
const reaction::ReactionSet & MultiscalePartitioningEngineView::getNetworkReactions() const {
@@ -295,8 +282,8 @@ namespace gridfire {
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
const auto result = m_baseEngine.getSpeciesTimescales(qseComposition, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
const auto result = m_baseEngine.getSpeciesTimescales(comp, T9, rho);
if (!result) {
return std::unexpected{result.error()};
}
@@ -313,8 +300,8 @@ namespace gridfire {
const double T9,
const double rho
) const {
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
const auto result = m_baseEngine.getSpeciesDestructionTimescales(qseComposition, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
const auto result = m_baseEngine.getSpeciesDestructionTimescales(comp, T9, rho);
if (!result) {
return std::unexpected{result.error()};
}
@@ -524,6 +511,14 @@ namespace gridfire {
std::ranges::sort(m_qse_groups, [](const QSEGroup& a, const QSEGroup& b) {
return a.mean_timescale < b.mean_timescale;
});
for (const auto& species : m_baseEngine.getNetworkSpecies()) {
bool involvesAlgebraic = involvesSpeciesInQSE(species);
if (std::ranges::find(m_dynamic_species, species) == m_dynamic_species.end() && !involvesAlgebraic) {
// Species is classed as neither dynamic nor algebraic at end of partitioning → add to dynamic set
m_dynamic_species.push_back(species);
}
}
return getNormalizedEquilibratedComposition(comp, T9, rho);
}
@@ -554,7 +549,7 @@ namespace gridfire {
}
}
const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
// const fourdst::composition::Composition qseComposition = getNormalizedEquilibratedComposition(comp, T9, rho);
// Calculate reaction flows and find min/max for logarithmic scaling of transparency
std::vector<double> reaction_flows;
reaction_flows.reserve(all_reactions.size());
@@ -562,7 +557,7 @@ 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, qseComposition, T9, rho));
double flow = std::abs(m_baseEngine.calculateMolarReactionFlow(*reaction, comp, T9, rho));
reaction_flows.push_back(flow);
if (flow > 1e-99) { // Avoid log(0)
double log_flow = std::log10(flow);
@@ -826,6 +821,14 @@ namespace gridfire {
return qseComposition;
}
SpeciesStatus MultiscalePartitioningEngineView::getSpeciesStatus(const Species &species) const {
const SpeciesStatus status = m_baseEngine.getSpeciesStatus(species);
if (status == SpeciesStatus::ACTIVE && involvesSpeciesInQSE(species)) {
return SpeciesStatus::EQUILIBRIUM;
}
return status;
}
size_t MultiscalePartitioningEngineView::getSpeciesIndex(const Species &species) const {
return m_baseEngine.getSpeciesIndex(species);
}
@@ -1499,7 +1502,7 @@ namespace gridfire {
}
std::vector<Species> qse_species_vector(m_qse_solve_species.begin(), m_qse_solve_species.end());
m_view.getBaseEngine().generateJacobianMatrix(comp_trial, m_T9, m_rho, qse_species_vector);
NetworkJacobian jac = m_view.getBaseEngine().generateJacobianMatrix(comp_trial, m_T9, m_rho, qse_species_vector);
const auto result = m_view.getBaseEngine().calculateRHSAndEnergy(comp_trial, m_T9, m_rho);
if (!result) {
throw exceptions::StaleEngineError("Failed to calculate RHS and energy due to stale engine state");
@@ -1512,10 +1515,7 @@ namespace gridfire {
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(
rowSpecies,
colSpecies
);
J_qse(rowID, colID) = jac(rowSpecies, colSpecies);
colID += 1;
LOG_TRACE_L3(m_view.m_logger, "Jacobian[{}, {}] (d(dY({}))/dY({})) = {}", rowID, colID - 1, rowSpecies.name(), colSpecies.name(), J_qse(rowID, colID - 1));
}