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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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442
src/python/engine/bindings.cpp
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@@ -5,6 +5,8 @@
#include "bindings.h"
#include "gridfire/engine/engine.h"
#include "gridfire/engine/diagnostics/dynamic_engine_diagnostics.h"
#include "gridfire/exceptions/exceptions.h"
#include "trampoline/py_engine.h"
@@ -17,23 +19,70 @@ namespace {
template <IsDynamicEngine T, IsDynamicEngine BaseT>
void registerDynamicEngineDefs(py::class_<T, BaseT> pyClass) {
pyClass.def("calculateRHSAndEnergy", &T::calculateRHSAndEnergy,
py::arg("Y"),
pyClass.def(
"calculateRHSAndEnergy",
[](
const gridfire::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho
) {
auto result = self.calculateRHSAndEnergy(comp, T9, rho);
if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update().");
}
return result.value();
},
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Calculate the right-hand side (dY/dt) and energy generation rate."
)
.def("generateJacobianMatrix", py::overload_cast<const std::vector<double>&, double, double>(&T::generateJacobianMatrix, py::const_),
py::arg("Y_dynamic"),
.def("calculateEpsDerivatives",
&gridfire::DynamicEngine::calculateEpsDerivatives,
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Calculate deps/dT and deps/drho"
)
.def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&T::generateJacobianMatrix, py::const_),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Generate the Jacobian matrix for the current state."
)
.def("generateStoichiometryMatrix", &T::generateStoichiometryMatrix)
.def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double, const std::vector<fourdst::atomic::Species>&>(&T::generateJacobianMatrix, py::const_),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
py::arg("activeSpecies"),
"Generate the jacobian matrix only for the subset of the matrix representing the active species."
)
.def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::SparsityPattern&>(&T::generateJacobianMatrix, py::const_),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
py::arg("sparsityPattern"),
"Generate the jacobian matrix for the given sparsity pattern"
)
.def("generateStoichiometryMatrix",
&T::generateStoichiometryMatrix
)
.def("calculateMolarReactionFlow",
static_cast<double (T::*)(const gridfire::reaction::Reaction&, const std::vector<double>&, const double, const double) const>(&T::calculateMolarReactionFlow),
[](
const gridfire::DynamicEngine& self,
const gridfire::reaction::Reaction& reaction,
const fourdst::composition::Composition& comp,
const double T9,
const double rho
) -> double {
return self.calculateMolarReactionFlow(reaction, comp, T9, rho);
},
py::arg("reaction"),
py::arg("Y"),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Calculate the molar reaction flow for a given reaction."
@@ -49,61 +98,99 @@ namespace {
"Set the network reactions to a new set of reactions."
)
.def("getJacobianMatrixEntry", &T::getJacobianMatrixEntry,
py::arg("i"),
py::arg("j"),
py::arg("rowSpecies"),
py::arg("colSpecies"),
"Get an entry from the previously generated Jacobian matrix."
)
.def("getStoichiometryMatrixEntry", &T::getStoichiometryMatrixEntry,
py::arg("speciesIndex"),
py::arg("reactionIndex"),
py::arg("species"),
py::arg("reaction"),
"Get an entry from the stoichiometry matrix."
)
.def("getSpeciesTimescales", &T::getSpeciesTimescales,
py::arg("Y"),
.def("getSpeciesTimescales",
[](
const gridfire::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho
) -> std::unordered_map<fourdst::atomic::Species, double> {
const auto result = self.getSpeciesTimescales(comp, T9, rho);
if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update().");
}
return result.value();
},
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Get the timescales for each species in the network."
)
.def("getSpeciesDestructionTimescales", &T::getSpeciesDestructionTimescales,
py::arg("Y"),
.def("getSpeciesDestructionTimescales",
[](
const gridfire::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho
) -> std::unordered_map<fourdst::atomic::Species, double> {
const auto result = self.getSpeciesDestructionTimescales(comp, T9, rho);
if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update().");
}
return result.value();
},
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Get the destruction timescales for each species in the network."
)
.def("update", &T::update,
.def("update",
&T::update,
py::arg("netIn"),
"Update the engine state based on the provided NetIn object."
)
.def("setScreeningModel", &T::setScreeningModel,
.def("setScreeningModel",
&T::setScreeningModel,
py::arg("screeningModel"),
"Set the screening model for the engine."
)
.def("getScreeningModel", &T::getScreeningModel,
.def("getScreeningModel",
&T::getScreeningModel,
"Get the current screening model of the engine."
)
.def("getSpeciesIndex", &T::getSpeciesIndex,
.def("getSpeciesIndex",
&T::getSpeciesIndex,
py::arg("species"),
"Get the index of a species in the network."
)
.def("mapNetInToMolarAbundanceVector", &T::mapNetInToMolarAbundanceVector,
.def("mapNetInToMolarAbundanceVector",
&T::mapNetInToMolarAbundanceVector,
py::arg("netIn"),
"Map a NetIn object to a vector of molar abundances."
)
.def("primeEngine", &T::primeEngine,
.def("primeEngine",
&T::primeEngine,
py::arg("netIn"),
"Prime the engine with a NetIn object to prepare for calculations."
)
.def("getDepth", &T::getDepth,
.def("getDepth",
&T::getDepth,
"Get the current build depth of the engine."
)
.def("rebuild", &T::rebuild,
.def("rebuild",
&T::rebuild,
py::arg("composition"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full,
"Rebuild the engine with a new composition and build depth."
)
.def("isStale", &T::isStale,
.def("isStale",
&T::isStale,
py::arg("netIn"),
"Check if the engine is stale based on the provided NetIn object."
)
.def("collectComposition",
&T::collectComposition,
py::arg("composition"),
"Recursively collect composition from current engine and any sub engines if they exist."
);
}
@@ -112,14 +199,123 @@ namespace {
void register_engine_bindings(py::module &m) {
register_base_engine_bindings(m);
register_engine_view_bindings(m);
register_engine_diagnostic_bindings(m);
register_engine_procedural_bindings(m);
register_engine_type_bindings(m);
}
m.def("build_reaclib_nuclear_network", &gridfire::build_reaclib_nuclear_network,
py::arg("composition"),
py::arg("maxLayers") = gridfire::NetworkBuildDepth::Full,
py::arg("reverse") = false,
"Build a nuclear network from a composition using ReacLib data."
void register_base_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::StepDerivatives<double>>(m, "StepDerivatives")
.def_readonly("dYdt", &gridfire::StepDerivatives<double>::dydt, "The right-hand side (dY/dt) of the ODE system.")
.def_readonly("energy", &gridfire::StepDerivatives<double>::nuclearEnergyGenerationRate, "The energy generation rate.");
py::class_<gridfire::SparsityPattern> py_sparsity_pattern(m, "SparsityPattern");
abs_stype_register_engine_bindings(m);
abs_stype_register_dynamic_engine_bindings(m);
con_stype_register_graph_engine_bindings(m);
}
void abs_stype_register_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::Engine, PyEngine>(m, "Engine");
}
void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m) {
const auto a = py::class_<gridfire::DynamicEngine, PyDynamicEngine>(m, "DynamicEngine");
}
void register_engine_procedural_bindings(pybind11::module &m) {
auto procedures = m.def_submodule("procedures", "Procedural functions associated with engine module");
register_engine_construction_bindings(procedures);
register_engine_construction_bindings(procedures);
}
void register_engine_diagnostic_bindings(pybind11::module &m) {
auto diagnostics = m.def_submodule("diagnostics", "A submodule for engine diagnostics");
diagnostics.def("report_limiting_species",
&gridfire::diagnostics::report_limiting_species,
py::arg("engine"),
py::arg("Y_full"),
py::arg("E_full"),
py::arg("dydt_full"),
py::arg("relTol"),
py::arg("absTol"),
py::arg("top_n") = 10
);
diagnostics.def("inspect_species_balance",
&gridfire::diagnostics::inspect_species_balance,
py::arg("engine"),
py::arg("species_name"),
py::arg("comp"),
py::arg("T9"),
py::arg("rho")
);
diagnostics.def("inspect_jacobian_stiffness",
&gridfire::diagnostics::inspect_jacobian_stiffness,
py::arg("engine"),
py::arg("comp"),
py::arg("T9"),
py::arg("rho")
);
}
void register_engine_construction_bindings(pybind11::module &m) {
m.def("build_nuclear_network", &gridfire::build_nuclear_network,
py::arg("composition"),
py::arg("weakInterpolator"),
py::arg("maxLayers") = gridfire::NetworkBuildDepth::Full,
py::arg("reverse") = false,
"Build a nuclear network from a composition using all archived reaction data."
);
}
void register_engine_priming_bindings(pybind11::module &m) {
m.def("calculateDestructionRateConstant",
&gridfire::calculateDestructionRateConstant,
py::arg("engine"),
py::arg("species"),
py::arg("composition"),
py::arg("T9"),
py::arg("rho"),
py::arg("reactionTypesToIgnore")
);
m.def("calculateCreationRate",
&gridfire::calculateCreationRate,
py::arg("engine"),
py::arg("species"),
py::arg("composition"),
py::arg("T9"),
py::arg("rho"),
py::arg("reactionTypesToIgnore")
);
}
void register_engine_type_bindings(pybind11::module &m) {
auto types = m.def_submodule("types", "Types associated with engine module");
register_engine_building_type_bindings(types);
register_engine_reporting_type_bindings(types);
}
void register_engine_building_type_bindings(pybind11::module &m) {
py::enum_<gridfire::NetworkBuildDepth>(m, "NetworkBuildDepth")
.value("Full", gridfire::NetworkBuildDepth::Full, "Full network build depth")
.value("Shallow", gridfire::NetworkBuildDepth::Shallow, "Shallow network build depth")
.value("SecondOrder", gridfire::NetworkBuildDepth::SecondOrder, "Second order network build depth")
.value("ThirdOrder", gridfire::NetworkBuildDepth::ThirdOrder, "Third order network build depth")
.value("FourthOrder", gridfire::NetworkBuildDepth::FourthOrder, "Fourth order network build depth")
.value("FifthOrder", gridfire::NetworkBuildDepth::FifthOrder, "Fifth order network build depth")
.export_values();
py::class_<gridfire::BuildDepthType> py_build_depth_type(m, "BuildDepthType");
}
void register_engine_reporting_type_bindings(pybind11::module &m) {
py::enum_<gridfire::PrimingReportStatus>(m, "PrimingReportStatus")
.value("FULL_SUCCESS", gridfire::PrimingReportStatus::FULL_SUCCESS, "Priming was full successful.")
.value("NO_SPECIES_TO_PRIME", gridfire::PrimingReportStatus::NO_SPECIES_TO_PRIME, "No species to prime.")
@@ -150,135 +346,128 @@ void register_engine_bindings(py::module &m) {
);
}
void register_base_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::StepDerivatives<double>>(m, "StepDerivatives")
.def_readonly("dYdt", &gridfire::StepDerivatives<double>::dydt, "The right-hand side (dY/dt) of the ODE system.")
.def_readonly("energy", &gridfire::StepDerivatives<double>::nuclearEnergyGenerationRate, "The energy generation rate.");
py::class_<gridfire::SparsityPattern>(m, "SparsityPattern");
abs_stype_register_engine_bindings(m);
abs_stype_register_dynamic_engine_bindings(m);
con_stype_register_graph_engine_bindings(m);
}
void abs_stype_register_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::Engine, PyEngine>(m, "Engine");
}
void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m) {
const auto a = py::class_<gridfire::DynamicEngine, PyDynamicEngine>(m, "DynamicEngine");
}
void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
py::enum_<gridfire::NetworkBuildDepth>(m, "NetworkBuildDepth")
.value("Full", gridfire::NetworkBuildDepth::Full, "Full network build depth")
.value("Shallow", gridfire::NetworkBuildDepth::Shallow, "Shallow network build depth")
.value("SecondOrder", gridfire::NetworkBuildDepth::SecondOrder, "Second order network build depth")
.value("ThirdOrder", gridfire::NetworkBuildDepth::ThirdOrder, "Third order network build depth")
.value("FourthOrder", gridfire::NetworkBuildDepth::FourthOrder, "Fourth order network build depth")
.value("FifthOrder", gridfire::NetworkBuildDepth::FifthOrder, "Fifth order network build depth")
.export_values();
py::class_<gridfire::BuildDepthType>(m, "BuildDepthType");
auto py_dynamic_engine_bindings = py::class_<gridfire::GraphEngine, gridfire::DynamicEngine>(m, "GraphEngine");
auto py_graph_engine_bindings = py::class_<gridfire::GraphEngine, gridfire::DynamicEngine>(m, "GraphEngine");
// Register the Graph Engine Specific Bindings
py_dynamic_engine_bindings.def(py::init<const fourdst::composition::Composition &, const gridfire::BuildDepthType>(),
py_graph_engine_bindings.def(py::init<const fourdst::composition::Composition &, const gridfire::BuildDepthType>(),
py::arg("composition"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full,
"Initialize GraphEngine with a composition and build depth."
);
py_dynamic_engine_bindings.def(py::init<const fourdst::composition::Composition &, const gridfire::partition::PartitionFunction &, const gridfire::BuildDepthType>(),
py_graph_engine_bindings.def(py::init<const fourdst::composition::Composition &,const gridfire::partition::PartitionFunction &, const gridfire::BuildDepthType>(),
py::arg("composition"),
py::arg("partitionFunction"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full,
"Initialize GraphEngine with a composition, partition function and build depth."
);
py_dynamic_engine_bindings.def(py::init<const gridfire::reaction::ReactionSet &>(),
py_graph_engine_bindings.def(py::init<const gridfire::reaction::ReactionSet &>(),
py::arg("reactions"),
"Initialize GraphEngine with a set of reactions."
);
py_dynamic_engine_bindings.def("generateJacobianMatrix", py::overload_cast<const std::vector<double>&, double, double, const gridfire::SparsityPattern&>(&gridfire::GraphEngine::generateJacobianMatrix, py::const_),
py::arg("Y_dynamic"),
py::arg("T9"),
py::arg("rho"),
py::arg("sparsityPattern"),
"Generate the Jacobian matrix for the current state with a specified sparsity pattern."
);
py_dynamic_engine_bindings.def_static("getNetReactionStoichiometry", &gridfire::GraphEngine::getNetReactionStoichiometry,
py_graph_engine_bindings.def_static("getNetReactionStoichiometry",
&gridfire::GraphEngine::getNetReactionStoichiometry,
py::arg("reaction"),
"Get the net stoichiometry for a given reaction."
);
py_dynamic_engine_bindings.def("involvesSpecies", &gridfire::GraphEngine::involvesSpecies,
py_graph_engine_bindings.def("getSpeciesTimescales",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::reaction::ReactionSet&>(&gridfire::GraphEngine::getSpeciesTimescales, py::const_),
py::arg("composition"),
py::arg("T9"),
py::arg("rho"),
py::arg("activeReactions")
);
py_graph_engine_bindings.def("getSpeciesDestructionTimescales",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::reaction::ReactionSet&>(&gridfire::GraphEngine::getSpeciesDestructionTimescales, py::const_),
py::arg("composition"),
py::arg("T9"),
py::arg("rho"),
py::arg("activeReactions")
);
py_graph_engine_bindings.def("involvesSpecies",
&gridfire::GraphEngine::involvesSpecies,
py::arg("species"),
"Check if a given species is involved in the network."
);
py_dynamic_engine_bindings.def("exportToDot", &gridfire::GraphEngine::exportToDot,
py_graph_engine_bindings.def("exportToDot",
&gridfire::GraphEngine::exportToDot,
py::arg("filename"),
"Export the network to a DOT file for visualization."
);
py_dynamic_engine_bindings.def("exportToCSV", &gridfire::GraphEngine::exportToCSV,
py_graph_engine_bindings.def("exportToCSV",
&gridfire::GraphEngine::exportToCSV,
py::arg("filename"),
"Export the network to a CSV file for analysis."
);
py_dynamic_engine_bindings.def("setPrecomputation", &gridfire::GraphEngine::setPrecomputation,
py_graph_engine_bindings.def("setPrecomputation",
&gridfire::GraphEngine::setPrecomputation,
py::arg("precompute"),
"Enable or disable precomputation for the engine."
);
py_dynamic_engine_bindings.def("isPrecomputationEnabled", &gridfire::GraphEngine::isPrecomputationEnabled,
py_graph_engine_bindings.def("isPrecomputationEnabled",
&gridfire::GraphEngine::isPrecomputationEnabled,
"Check if precomputation is enabled for the engine."
);
py_dynamic_engine_bindings.def("getPartitionFunction", &gridfire::GraphEngine::getPartitionFunction,
py_graph_engine_bindings.def("getPartitionFunction",
&gridfire::GraphEngine::getPartitionFunction,
"Get the partition function used by the engine."
);
py_dynamic_engine_bindings.def("calculateReverseRate", &gridfire::GraphEngine::calculateReverseRate,
py_graph_engine_bindings.def("calculateReverseRate",
&gridfire::GraphEngine::calculateReverseRate,
py::arg("reaction"),
py::arg("T9"),
"Calculate the reverse rate for a given reaction at a specific temperature."
py::arg("rho"),
py::arg("composition"),
"Calculate the reverse rate for a given reaction at a specific temperature, density, and composition."
);
py_dynamic_engine_bindings.def("calculateReverseRateTwoBody", &gridfire::GraphEngine::calculateReverseRateTwoBody,
py_graph_engine_bindings.def("calculateReverseRateTwoBody",
&gridfire::GraphEngine::calculateReverseRateTwoBody,
py::arg("reaction"),
py::arg("T9"),
py::arg("forwardRate"),
py::arg("expFactor"),
"Calculate the reverse rate for a two-body reaction at a specific temperature."
);
py_dynamic_engine_bindings.def("calculateReverseRateTwoBodyDerivative", &gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative,
py_graph_engine_bindings.def("calculateReverseRateTwoBodyDerivative",
&gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative,
py::arg("reaction"),
py::arg("T9"),
py::arg("rho"),
py::arg("composition"),
py::arg("reverseRate"),
"Calculate the derivative of the reverse rate for a two-body reaction at a specific temperature."
);
py_dynamic_engine_bindings.def("isUsingReverseReactions", &gridfire::GraphEngine::isUsingReverseReactions,
py_graph_engine_bindings.def("isUsingReverseReactions",
&gridfire::GraphEngine::isUsingReverseReactions,
"Check if the engine is using reverse reactions."
);
py_dynamic_engine_bindings.def("setUseReverseReactions", &gridfire::GraphEngine::setUseReverseReactions,
py_graph_engine_bindings.def("setUseReverseReactions",
&gridfire::GraphEngine::setUseReverseReactions,
py::arg("useReverse"),
"Enable or disable the use of reverse reactions in the engine."
);
// Register the general dynamic engine bindings
registerDynamicEngineDefs<gridfire::GraphEngine, gridfire::DynamicEngine>(py_dynamic_engine_bindings);
registerDynamicEngineDefs<gridfire::GraphEngine, gridfire::DynamicEngine>(py_graph_engine_bindings);
}
void register_engine_view_bindings(const pybind11::module &m) {
auto py_defined_engine_view_bindings = py::class_<gridfire::DefinedEngineView, gridfire::DynamicEngine>(m, "DefinedEngineView");
py_defined_engine_view_bindings.def(py::init<std::vector<std::string>, gridfire::DynamicEngine&>(),
py_defined_engine_view_bindings.def(py::init<std::vector<std::string>, gridfire::GraphEngine&>(),
py::arg("peNames"),
py::arg("baseEngine"),
"Construct a defined engine view with a list of tracked reactions and a base engine.");
"Construct a defined engine view with a list of tracked reactions and a base engine."
);
py_defined_engine_view_bindings.def("getBaseEngine", &gridfire::DefinedEngineView::getBaseEngine,
"Get the base engine associated with this defined engine view.");
registerDynamicEngineDefs<gridfire::DefinedEngineView, gridfire::DynamicEngine>(py_defined_engine_view_bindings);
auto py_file_defined_engine_view_bindings = py::class_<gridfire::FileDefinedEngineView, gridfire::DefinedEngineView>(m, "FileDefinedEngineView");
py_file_defined_engine_view_bindings.def(py::init<gridfire::DynamicEngine&, const std::string&, const gridfire::io::NetworkFileParser&>(),
py_file_defined_engine_view_bindings.def(
py::init<gridfire::GraphEngine&, const std::string&, const gridfire::io::NetworkFileParser&>(),
py::arg("baseEngine"),
py::arg("fileName"),
py::arg("parser"),
@@ -296,11 +485,11 @@ void register_engine_view_bindings(const pybind11::module &m) {
registerDynamicEngineDefs<gridfire::FileDefinedEngineView, gridfire::DefinedEngineView>(py_file_defined_engine_view_bindings);
auto py_priming_engine_view_bindings = py::class_<gridfire::NetworkPrimingEngineView, gridfire::DefinedEngineView>(m, "NetworkPrimingEngineView");
py_priming_engine_view_bindings.def(py::init<const std::string&, gridfire::DynamicEngine&>(),
py_priming_engine_view_bindings.def(py::init<const std::string&, gridfire::GraphEngine&>(),
py::arg("primingSymbol"),
py::arg("baseEngine"),
"Construct a priming engine view with a priming symbol and a base engine.");
py_priming_engine_view_bindings.def(py::init<const fourdst::atomic::Species&, gridfire::DynamicEngine&>(),
py_priming_engine_view_bindings.def(py::init<const fourdst::atomic::Species&, gridfire::GraphEngine&>(),
py::arg("primingSpecies"),
py::arg("baseEngine"),
"Construct a priming engine view with a priming species and a base engine.");
@@ -313,8 +502,10 @@ void register_engine_view_bindings(const pybind11::module &m) {
py_adaptive_engine_view_bindings.def(py::init<gridfire::DynamicEngine&>(),
py::arg("baseEngine"),
"Construct an adaptive engine view with a base engine.");
py_adaptive_engine_view_bindings.def("getBaseEngine", &gridfire::AdaptiveEngineView::getBaseEngine,
"Get the base engine associated with this adaptive engine view.");
py_adaptive_engine_view_bindings.def("getBaseEngine",
&gridfire::AdaptiveEngineView::getBaseEngine,
"Get the base engine associated with this adaptive engine view."
);
registerDynamicEngineDefs<gridfire::AdaptiveEngineView, gridfire::DynamicEngine>(py_adaptive_engine_view_bindings);
@@ -341,43 +532,63 @@ void register_engine_view_bindings(const pybind11::module &m) {
auto py_multiscale_engine_view_bindings = py::class_<gridfire::MultiscalePartitioningEngineView, gridfire::DynamicEngine>(m, "MultiscalePartitioningEngineView");
py_multiscale_engine_view_bindings.def(py::init<gridfire::GraphEngine&>(),
py::arg("baseEngine"),
"Construct a multiscale partitioning engine view with a base engine.");
py_multiscale_engine_view_bindings.def("getBaseEngine", &gridfire::MultiscalePartitioningEngineView::getBaseEngine,
"Get the base engine associated with this multiscale partitioning engine view.");
py_multiscale_engine_view_bindings.def("analyzeTimescalePoolConnectivity", &gridfire::MultiscalePartitioningEngineView::analyzeTimescalePoolConnectivity,
"Construct a multiscale partitioning engine view with a base engine."
);
py_multiscale_engine_view_bindings.def("getBaseEngine",
&gridfire::MultiscalePartitioningEngineView::getBaseEngine,
"Get the base engine associated with this multiscale partitioning engine view."
);
py_multiscale_engine_view_bindings.def("analyzeTimescalePoolConnectivity",
&gridfire::MultiscalePartitioningEngineView::analyzeTimescalePoolConnectivity,
py::arg("timescale_pools"),
py::arg("Y"),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Analyze the connectivity of timescale pools in the network.");
py_multiscale_engine_view_bindings.def("partitionNetwork", py::overload_cast<const std::vector<double>&, double, double>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork),
py::arg("Y"),
"Analyze the connectivity of timescale pools in the network."
);
py_multiscale_engine_view_bindings.def("partitionNetwork",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Partition the network based on species timescales and connectivity.");
py_multiscale_engine_view_bindings.def("partitionNetwork", py::overload_cast<const gridfire::NetIn&>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork),
py_multiscale_engine_view_bindings.def("partitionNetwork",
py::overload_cast<const gridfire::NetIn&>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork),
py::arg("netIn"),
"Partition the network based on a NetIn object.");
py_multiscale_engine_view_bindings.def("exportToDot", &gridfire::MultiscalePartitioningEngineView::exportToDot,
"Partition the network based on a NetIn object."
);
py_multiscale_engine_view_bindings.def("exportToDot",
&gridfire::MultiscalePartitioningEngineView::exportToDot,
py::arg("filename"),
py::arg("Y"),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Export the network to a DOT file for visualization.");
py_multiscale_engine_view_bindings.def("getFastSpecies", &gridfire::MultiscalePartitioningEngineView::getFastSpecies,
"Get the list of fast species in the network.");
py_multiscale_engine_view_bindings.def("getDynamicSpecies", &gridfire::MultiscalePartitioningEngineView::getDynamicSpecies,
"Get the list of dynamic species in the network.");
py_multiscale_engine_view_bindings.def("equilibrateNetwork", py::overload_cast<const std::vector<double>&, double, double>(&gridfire::MultiscalePartitioningEngineView::equilibrateNetwork),
py::arg("Y"),
"Export the network to a DOT file for visualization."
);
py_multiscale_engine_view_bindings.def("getFastSpecies",
&gridfire::MultiscalePartitioningEngineView::getFastSpecies,
"Get the list of fast species in the network."
);
py_multiscale_engine_view_bindings.def("getDynamicSpecies",
&gridfire::MultiscalePartitioningEngineView::getDynamicSpecies,
"Get the list of dynamic species in the network."
);
py_multiscale_engine_view_bindings.def("equilibrateNetwork",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&gridfire::MultiscalePartitioningEngineView::equilibrateNetwork),
py::arg("comp"),
py::arg("T9"),
py::arg("rho"),
"Equilibrate the network based on species abundances and conditions.");
py_multiscale_engine_view_bindings.def("equilibrateNetwork", py::overload_cast<const gridfire::NetIn&>(&gridfire::MultiscalePartitioningEngineView::equilibrateNetwork),
py_multiscale_engine_view_bindings.def("equilibrateNetwork",
py::overload_cast<const gridfire::NetIn&>(&gridfire::MultiscalePartitioningEngineView::equilibrateNetwork),
py::arg("netIn"),
"Equilibrate the network based on a NetIn object.");
"Equilibrate the network based on a NetIn object."
);
registerDynamicEngineDefs<gridfire::MultiscalePartitioningEngineView, gridfire::DynamicEngine>(
py_multiscale_engine_view_bindings
);
registerDynamicEngineDefs<gridfire::MultiscalePartitioningEngineView, gridfire::DynamicEngine>(py_multiscale_engine_view_bindings);
}
@@ -387,3 +598,4 @@ void register_engine_view_bindings(const pybind11::module &m) {

10
src/python/engine/bindings.h
View File

@@ -13,4 +13,14 @@ void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m);
void con_stype_register_graph_engine_bindings(const pybind11::module &m);
void register_engine_diagnostic_bindings(pybind11::module &m);
void register_engine_procedural_bindings(pybind11::module &m);
void register_engine_construction_bindings(pybind11::module &m);
void register_engine_priming_bindings(pybind11::module &m);
void register_engine_type_bindings(pybind11::module &m);
void register_engine_building_type_bindings(pybind11::module &m);
void register_engine_reporting_type_bindings(pybind11::module &m);

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;
};