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fix(python-bindings): Updated python bindings to new interface

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The python bindings now work with the polymorphic reaction class and the CVODE solver
This commit is contained in:
Emily Boudreaux
2025-10-30 15:05:08 -04:00
parent 23df87f915
commit 7fded59814
27 changed files with 962 additions and 255 deletions
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90
src/python/engine/trampoline/py_engine.cpp
View File

@@ -33,12 +33,12 @@ const std::vector<fourdst::atomic::Species>& PyEngine::getNetworkSpecies() const
py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\"");
}
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyEngine::calculateRHSAndEnergy(const std::vector<double> &Y, double T9, double rho) const {
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyEngine::calculateRHSAndEnergy(const fourdst::composition::Composition &comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError>),
gridfire::Engine,
calculateRHSAndEnergy,
Y, T9, rho
comp, T9, rho
);
}
@@ -65,39 +65,62 @@ const std::vector<fourdst::atomic::Species>& PyDynamicEngine::getNetworkSpecies(
py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\"");
}
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::calculateRHSAndEnergy(const std::vector<double> &Y, double T9, double rho) const {
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::calculateRHSAndEnergy(const fourdst::composition::Composition &comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError>),
gridfire::Engine,
calculateRHSAndEnergy,
Y, T9, rho
comp, T9, rho
);
}
void PyDynamicEngine::generateJacobianMatrix(const std::vector<double> &Y_dynamic, double T9, double rho) const {
void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composition& comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
void,
gridfire::DynamicEngine,
generateJacobianMatrix,
Y_dynamic, T9, rho
comp,
T9,
rho
);
}
void PyDynamicEngine::generateJacobianMatrix(const std::vector<double> &Y_dynamic, double T9, double rho, const gridfire::SparsityPattern &sparsityPattern) const {
void PyDynamicEngine::generateJacobianMatrix(
const fourdst::composition::Composition &comp,
const double T9,
const double rho,
const std::vector<fourdst::atomic::Species> &activeSpecies
) const {
PYBIND11_OVERRIDE_PURE(
void,
gridfire::DynamicEngine,
generateJacobianMatrix,
Y_dynamic, T9, rho, sparsityPattern
comp,
T9,
rho,
activeSpecies
);
}
double PyDynamicEngine::getJacobianMatrixEntry(int i, int j) const {
void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composition &comp, double T9, double rho, const gridfire::SparsityPattern &sparsityPattern) const {
PYBIND11_OVERRIDE_PURE(
void,
gridfire::DynamicEngine,
generateJacobianMatrix,
comp,
T9,
rho,
sparsityPattern
);
}
double PyDynamicEngine::getJacobianMatrixEntry(const fourdst::atomic::Species& rowSpecies, const fourdst::atomic::Species& colSpecies) const {
PYBIND11_OVERRIDE_PURE(
double,
gridfire::DynamicEngine,
getJacobianMatrixEntry,
i, j
rowSpecies,
colSpecies
);
}
@@ -109,21 +132,25 @@ void PyDynamicEngine::generateStoichiometryMatrix() {
);
}
int PyDynamicEngine::getStoichiometryMatrixEntry(int speciesIndex, int reactionIndex) const {
int PyDynamicEngine::getStoichiometryMatrixEntry(const fourdst::atomic::Species& species, const gridfire::reaction::Reaction& reaction) const {
PYBIND11_OVERRIDE_PURE(
int,
gridfire::DynamicEngine,
getStoichiometryMatrixEntry,
speciesIndex, reactionIndex
species,
reaction
);
}
double PyDynamicEngine::calculateMolarReactionFlow(const gridfire::reaction::Reaction &reaction, const std::vector<double> &Y, double T9, double rho) const {
double PyDynamicEngine::calculateMolarReactionFlow(const gridfire::reaction::Reaction &reaction, const fourdst::composition::Composition &comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
double,
gridfire::DynamicEngine,
calculateMolarReactionFlow,
reaction, Y, T9, rho
reaction,
comp,
T9,
rho
);
}
@@ -144,21 +171,23 @@ void PyDynamicEngine::setNetworkReactions(const gridfire::reaction::ReactionSet&
);
}
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesTimescales(const std::vector<double> &Y, double T9, double rho) const {
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesTimescales(const fourdst::composition::Composition &comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError>),
gridfire::DynamicEngine,
getSpeciesTimescales,
Y, T9, rho
comp,
T9,
rho
);
}
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesDestructionTimescales(const std::vector<double> &Y, double T9, double rho) const {
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesDestructionTimescales(const fourdst::composition::Composition &comp, double T9, double rho) const {
PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError>),
gridfire::DynamicEngine,
getSpeciesDestructionTimescales,
Y, T9, rho
comp, T9, rho
);
}
@@ -224,6 +253,31 @@ gridfire::PrimingReport PyDynamicEngine::primeEngine(const gridfire::NetIn &netI
);
}
gridfire::EnergyDerivatives PyDynamicEngine::calculateEpsDerivatives(
const fourdst::composition::Composition &comp,
const double T9,
const double rho) const {
PYBIND11_OVERRIDE_PURE(
gridfire::EnergyDerivatives,
gridfire::DynamicEngine,
calculateEpsDerivatives,
comp,
T9,
rho
);
}
fourdst::composition::Composition PyDynamicEngine::collectComposition(
fourdst::composition::Composition &comp
) const {
PYBIND11_OVERRIDE_PURE(
fourdst::composition::Composition,
gridfire::DynamicEngine,
collectComposition,
comp
);
}
const gridfire::Engine& PyEngineView::getBaseEngine() const {
PYBIND11_OVERRIDE_PURE(
const gridfire::Engine&,

130
src/python/engine/trampoline/py_engine.h
View File

@@ -12,7 +12,12 @@
class PyEngine final : public gridfire::Engine {
public:
const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
std::expected<gridfire::StepDerivatives<double>,gridfire::expectations::StaleEngineError> calculateRHSAndEnergy(const std::vector<double> &Y, double T9, double rho) const override;
std::expected<gridfire::StepDerivatives<double>,gridfire::expectations::StaleEngineError> calculateRHSAndEnergy(
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
private:
mutable std::vector<fourdst::atomic::Species> m_species_cache;
};
@@ -20,41 +25,124 @@ private:
class PyDynamicEngine final : public gridfire::DynamicEngine {
public:
const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
std::expected<gridfire::StepDerivatives<double>,gridfire::expectations::StaleEngineError> calculateRHSAndEnergy(const std::vector<double> &Y, double T9, double rho) const override;
void generateJacobianMatrix(const std::vector<double> &Y_dynamic, double T9, double rho) const override;
void generateJacobianMatrix(const std::vector<double> &Y_dynamic, double T9, double rho, const gridfire::SparsityPattern &sparsityPattern) const override;
double getJacobianMatrixEntry(int i, int j) const override;
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> calculateRHSAndEnergy(
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
void generateJacobianMatrix(
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
void generateJacobianMatrix(
const fourdst::composition::Composition &comp,
double T9,
double rho,
const std::vector<fourdst::atomic::Species> &activeSpecies
) const override;
void generateJacobianMatrix(
const fourdst::composition::Composition& comp,
double T9,
double rho,
const gridfire::SparsityPattern &sparsityPattern
) const override;
double getJacobianMatrixEntry(
const fourdst::atomic::Species& rowSpecies,
const fourdst::atomic::Species& colSpecies
) const override;
void generateStoichiometryMatrix() override;
int getStoichiometryMatrixEntry(int speciesIndex, int reactionIndex) const override;
double calculateMolarReactionFlow(const gridfire::reaction::Reaction &reaction, const std::vector<double> &Y, double T9, double rho) const override;
int getStoichiometryMatrixEntry(
const fourdst::atomic::Species& species,
const gridfire::reaction::Reaction& reaction
) const override;
double calculateMolarReactionFlow(
const gridfire::reaction::Reaction &reaction,
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
const gridfire::reaction::ReactionSet& getNetworkReactions() const override;
void setNetworkReactions(const gridfire::reaction::ReactionSet& reactions) override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesTimescales(const std::vector<double> &Y, double T9, double rho) const override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesDestructionTimescales(const std::vector<double> &Y, double T9, double rho) const override;
fourdst::composition::Composition update(const gridfire::NetIn &netIn) override;
bool isStale(const gridfire::NetIn &netIn) override;
void setScreeningModel(gridfire::screening::ScreeningType model) override;
void setNetworkReactions(
const gridfire::reaction::ReactionSet& reactions
) override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesTimescales(
const fourdst::composition::Composition& comp,
double T9,
double rho
) const override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesDestructionTimescales(
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
fourdst::composition::Composition update(
const gridfire::NetIn &netIn
) override;
bool isStale(
const gridfire::NetIn &netIn
) override;
void setScreeningModel(
gridfire::screening::ScreeningType model
) override;
gridfire::screening::ScreeningType getScreeningModel() const override;
size_t getSpeciesIndex(const fourdst::atomic::Species &species) const override;
std::vector<double> mapNetInToMolarAbundanceVector(const gridfire::NetIn &netIn) const override;
gridfire::PrimingReport primeEngine(const gridfire::NetIn &netIn) override;
size_t getSpeciesIndex(
const fourdst::atomic::Species &species
) const override;
std::vector<double> mapNetInToMolarAbundanceVector(
const gridfire::NetIn &netIn
) const override;
gridfire::PrimingReport primeEngine(
const gridfire::NetIn &netIn
) override;
gridfire::BuildDepthType getDepth() const override {
throw std::logic_error("Network depth not supported by this engine.");
}
void rebuild(const fourdst::composition::Composition& comp, gridfire::BuildDepthType depth) override {
void rebuild(
const fourdst::composition::Composition& comp,
gridfire::BuildDepthType depth
) override {
throw std::logic_error("Setting network depth not supported by this engine.");
}
[[nodiscard]] gridfire::EnergyDerivatives calculateEpsDerivatives(
const fourdst::composition::Composition &comp,
double T9,
double rho
) const override;
fourdst::composition::Composition collectComposition(
fourdst::composition::Composition &comp
) const override;
private:
mutable std::vector<fourdst::atomic::Species> m_species_cache;
};
class PyEngineView final : public gridfire::EngineView<gridfire::Engine> {
const gridfire::Engine& getBaseEngine() const override;
[[nodiscard]] const gridfire::Engine& getBaseEngine() const override;
};
class PyDynamicEngineView final : public gridfire::EngineView<gridfire::DynamicEngine> {
const gridfire::DynamicEngine& getBaseEngine() const override;
[[nodiscard]] const gridfire::DynamicEngine& getBaseEngine() const override;
};