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feat(python): Repaired python bindings

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Python bindings have now been brought back up to feature pairity with
C++. Further, stubs have been added for all python features so that code
completion will work
This commit is contained in:
Emily Boudreaux
2025-11-25 14:08:58 -05:00
parent 22b52abc30
commit bb1d6bbb24
51 changed files with 3798 additions and 460 deletions
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2
Doxyfile
View File

@@ -48,7 +48,7 @@ PROJECT_NAME = GridFire
# could be handy for archiving the generated documentation or if some version # could be handy for archiving the generated documentation or if some version
# control system is used. # control system is used.
PROJECT_NUMBER = v0.7.0-alpha PROJECT_NUMBER = v0.7.0_alpha_2025_10_25
# Using the PROJECT_BRIEF tag one can provide an optional one line description # Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewers a # for a project that appears at the top of each page and should give viewers a

48
build-python/meson.build
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@@ -1,5 +1,5 @@
# --- Python Extension Setup --- # --- Python Extension Setup ---
py_installation = import('python').find_installation('python3') py_installation = import('python').find_installation('python3', pure: false)
gridfire_py_deps = [ gridfire_py_deps = [
pybind11_dep, pybind11_dep,
@@ -10,11 +10,10 @@ gridfire_py_deps = [
] ]
py_mod = py_installation.extension_module( py_mod = py_installation.extension_module(
'gridfire', # Name of the generated .so/.pyd file (without extension) '_gridfire', # Name of the generated .so/.pyd file (without extension)
sources: [ sources: [
meson.project_source_root() + '/src/python/bindings.cpp', meson.project_source_root() + '/src/python/bindings.cpp',
meson.project_source_root() + '/src/python/types/bindings.cpp', meson.project_source_root() + '/src/python/types/bindings.cpp',
meson.project_source_root() + '/src/python/expectations/bindings.cpp',
meson.project_source_root() + '/src/python/partition/bindings.cpp', meson.project_source_root() + '/src/python/partition/bindings.cpp',
meson.project_source_root() + '/src/python/partition/trampoline/py_partition.cpp', meson.project_source_root() + '/src/python/partition/trampoline/py_partition.cpp',
meson.project_source_root() + '/src/python/reaction/bindings.cpp', meson.project_source_root() + '/src/python/reaction/bindings.cpp',
@@ -27,9 +26,52 @@ py_mod = py_installation.extension_module(
meson.project_source_root() + '/src/python/engine/trampoline/py_engine.cpp', meson.project_source_root() + '/src/python/engine/trampoline/py_engine.cpp',
meson.project_source_root() + '/src/python/solver/bindings.cpp', meson.project_source_root() + '/src/python/solver/bindings.cpp',
meson.project_source_root() + '/src/python/solver/trampoline/py_solver.cpp', meson.project_source_root() + '/src/python/solver/trampoline/py_solver.cpp',
meson.project_source_root() + '/src/python/policy/bindings.cpp',
meson.project_source_root() + '/src/python/policy/trampoline/py_policy.cpp',
meson.project_source_root() + '/src/python/utils/bindings.cpp', meson.project_source_root() + '/src/python/utils/bindings.cpp',
], ],
dependencies : gridfire_py_deps, dependencies : gridfire_py_deps,
cpp_args : ['-UNDEBUG'], # Example: Ensure assertions are enabled if needed cpp_args : ['-UNDEBUG'], # Example: Ensure assertions are enabled if needed
install : true, install : true,
subdir: 'gridfire',
)
py_installation.install_sources(
files(
meson.project_source_root() + '/src/python/gridfire/__init__.py',
meson.project_source_root() + '/stubs/gridfire/_gridfire/__init__.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/exceptions.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/partition.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/reaction.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/screening.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/io.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/solver.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/policy.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/type.pyi'
),
subdir: 'gridfire',
)
py_installation.install_sources(
files(
meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/__init__.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/engine/diagnostics.pyi',
),
subdir: 'gridfire/engine',
)
py_installation.install_sources(
files(
meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/__init__.pyi',
),
subdir: 'gridfire/utils',
)
py_installation.install_sources(
files(
meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/__init__.pyi',
meson.project_source_root() + '/stubs/gridfire/_gridfire/utils/hashing/reaction.pyi',
),
subdir: 'gridfire/utils/hashing',
) )

2
meson.build
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@@ -18,7 +18,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# #
# *********************************************************************** # # *********************************************************************** #
project('GridFire', 'cpp', version: 'v0.7.0-alpha', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0') project('GridFire', 'cpp', version: 'v0.7.0_alpha_2025_10_25', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
# Add default visibility for all C++ targets # Add default visibility for all C++ targets
add_project_arguments('-fvisibility=default', language: 'cpp') add_project_arguments('-fvisibility=default', language: 'cpp')

4
pip_install_mac_patch.sh
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@@ -67,10 +67,10 @@ echo ""
echo -e "${GREEN}Step 3: Locating installed gridfire extension module...${NC}" echo -e "${GREEN}Step 3: Locating installed gridfire extension module...${NC}"
# Find the .so file # Find the .so file
SO_FILE=$(find "$SITE_PACKAGES" -name "gridfire.cpython-*-darwin.so" 2>/dev/null | head -n 1) SO_FILE=$(find "$SITE_PACKAGES/gridfire" -name "_gridfire.cpython-*-darwin.so" 2>/dev/null | head -n 1)
if [ -z "$SO_FILE" ]; then if [ -z "$SO_FILE" ]; then
echo -e "${RED}Error: Could not find gridfire.cpython-*-darwin.so in $SITE_PACKAGES/gridfire${NC}" echo -e "${RED}Error: Could not find _gridfire.cpython-*-darwin.so in $SITE_PACKAGES/gridfire${NC}"
echo "Installation may have failed or the file is in an unexpected location." echo "Installation may have failed or the file is in an unexpected location."
exit 1 exit 1
fi fi

1
src/include/gridfire/engine/engine.h
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@@ -180,3 +180,4 @@
#include "gridfire/engine/views/engine_views.h" #include "gridfire/engine/views/engine_views.h"
#include "gridfire/engine/procedures/engine_procedures.h" #include "gridfire/engine/procedures/engine_procedures.h"
#include "gridfire/engine/types/engine_types.h" #include "gridfire/engine/types/engine_types.h"
#include "gridfire/engine/diagnostics/dynamic_engine_diagnostics.h"

36
src/include/gridfire/engine/procedures/construction.h
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@@ -24,23 +24,21 @@ namespace gridfire::engine {
enum class NetworkConstructionFlags : uint32_t { enum class NetworkConstructionFlags : uint32_t {
NONE = 0, NONE = 0,
STRONG = 1 << 0, // 1 REACLIB_STRONG = 1 << 0, // 1
BETA_MINUS = 1 << 1, // 2 WRL_BETA_MINUS = 1 << 1, // 2
BETA_PLUS = 1 << 2, // 4 WRL_BETA_PLUS = 1 << 2, // 4
ELECTRON_CAPTURE = 1 << 3, // 8 WRL_ELECTRON_CAPTURE = 1 << 3, // 8
POSITRON_CAPTURE = 1 << 4, // 16 WRL_POSITRON_CAPTURE = 1 << 4, // 16
REACLIB_WEAK = 1 << 5, REACLIB_WEAK = 1 << 5,
WRL_WEAK = BETA_MINUS | BETA_PLUS | ELECTRON_CAPTURE | POSITRON_CAPTURE, WRL_WEAK = WRL_BETA_MINUS | WRL_BETA_PLUS | WRL_ELECTRON_CAPTURE | WRL_POSITRON_CAPTURE,
REACLIB = STRONG | REACLIB_WEAK, REACLIB = REACLIB_STRONG | REACLIB_WEAK,
// Currently we default to just reaclib reactions but include both their strong and weak set // Currently we default to just reaclib reactions but include both their strong and weak set
DEFAULT = REACLIB, DEFAULT = REACLIB,
ALL = STRONG | WRL_WEAK
}; };
/** @brief Helper function to convert NetworkConstructionFlags to their underlying integer type. /** @brief Helper function to convert NetworkConstructionFlags to their underlying integer type.
@@ -103,20 +101,20 @@ namespace gridfire::engine {
inline std::string NetworkConstructionFlagsToString(NetworkConstructionFlags flags) { inline std::string NetworkConstructionFlagsToString(NetworkConstructionFlags flags) {
std::stringstream ss; std::stringstream ss;
constexpr std::array<NetworkConstructionFlags, 6> bases_flags_array = { constexpr std::array<NetworkConstructionFlags, 6> bases_flags_array = {
NetworkConstructionFlags::STRONG, NetworkConstructionFlags::REACLIB_STRONG,
NetworkConstructionFlags::BETA_MINUS, NetworkConstructionFlags::WRL_BETA_MINUS,
NetworkConstructionFlags::BETA_PLUS, NetworkConstructionFlags::WRL_BETA_PLUS,
NetworkConstructionFlags::ELECTRON_CAPTURE, NetworkConstructionFlags::WRL_ELECTRON_CAPTURE,
NetworkConstructionFlags::POSITRON_CAPTURE, NetworkConstructionFlags::WRL_POSITRON_CAPTURE,
NetworkConstructionFlags::REACLIB_WEAK NetworkConstructionFlags::REACLIB_WEAK
}; };
const std::unordered_map<NetworkConstructionFlags, std::string> bases_string_map = { const std::unordered_map<NetworkConstructionFlags, std::string> bases_string_map = {
{NetworkConstructionFlags::STRONG, "Strong"}, {NetworkConstructionFlags::REACLIB_STRONG, "Strong"},
{NetworkConstructionFlags::BETA_MINUS, "BetaMinus"}, {NetworkConstructionFlags::WRL_BETA_MINUS, "BetaMinus"},
{NetworkConstructionFlags::BETA_PLUS, "BetaPlus"}, {NetworkConstructionFlags::WRL_BETA_PLUS, "BetaPlus"},
{NetworkConstructionFlags::ELECTRON_CAPTURE, "ElectronCapture"}, {NetworkConstructionFlags::WRL_ELECTRON_CAPTURE, "ElectronCapture"},
{NetworkConstructionFlags::POSITRON_CAPTURE, "PositronCapture"}, {NetworkConstructionFlags::WRL_POSITRON_CAPTURE, "PositronCapture"},
{NetworkConstructionFlags::REACLIB_WEAK, "ReaclibWeak"} {NetworkConstructionFlags::REACLIB_WEAK, "ReaclibWeak"}
}; };

50
src/include/gridfire/engine/procedures/priming.h
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@@ -31,54 +31,4 @@ namespace gridfire::engine {
GraphEngine& engine, GraphEngine& engine,
const std::optional<std::vector<reaction::ReactionType>>& ignoredReactionTypes const std::optional<std::vector<reaction::ReactionType>>& ignoredReactionTypes
); );
/**
* @brief Computes the destruction rate constant for a specific species.
*
* Calculates the sum of molar reaction flows for all reactions where the species
* is a reactant (negative stoichiometry) after scaling its abundance to unity.
*
* @param engine Engine providing the current set of network reactions and flow calculations.
* @param species The atomic species whose destruction rate is computed.
* @param composition Current composition providing abundances for all species.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density of the medium.
* @param reactionTypesToIgnore types of reactions to ignore during calculation.
* @pre Y.size() matches engine.getNetworkReactions().size() mapping species order.
* @post Returned rate constant is non-negative.
* @return Sum of absolute stoichiometry-weighted destruction flows for the species.
*/
double calculateDestructionRateConstant(
const DynamicEngine& engine,
const fourdst::atomic::Species& species,
const fourdst::composition::Composition& composition,
double T9,
double rho,
const std::optional<std::vector<reaction::ReactionType>> &reactionTypesToIgnore
);
/**
* @brief Computes the creation rate for a specific species.
*
* Sums molar reaction flows for all reactions where the species
* appears as a product (positive stoichiometry).
*
* @param engine Engine providing the current set of network reactions and flow calculations.
* @param species The atomic species whose creation rate is computed.
* @param composition Composition object containing current abundances.
* @param T9 Temperature in units of 10^9 K.
* @param rho Density of the medium.
* @param reactionTypesToIgnore types of reactions to ignore during calculation.
* @pre Y.size() matches engine.getNetworkReactions().size() mapping species order.
* @post Returned creation rate is non-negative.
* @return Sum of stoichiometry-weighted creation flows for the species.
*/
double calculateCreationRate(
const DynamicEngine& engine,
const fourdst::atomic::Species& species,
const fourdst::composition::Composition& composition,
double T9,
double rho,
const std::optional<std::vector<reaction::ReactionType>> &reactionTypesToIgnore
);
} }

2
src/include/gridfire/engine/types/engine_types.h
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@@ -1,5 +1,7 @@
#pragma once #pragma once
#include <string_view>
namespace gridfire::engine { namespace gridfire::engine {
/** /**
* @enum EngineTypes * @enum EngineTypes

2
src/include/gridfire/policy/policy_abstract.h
View File

@@ -153,7 +153,7 @@ namespace gridfire::policy {
* if (s != NetworkPolicyStatus::INITIALIZED_VERIFIED) { // handle error } * if (s != NetworkPolicyStatus::INITIALIZED_VERIFIED) { // handle error }
* @endcode * @endcode
*/ */
[[nodiscard]] virtual NetworkPolicyStatus getStatus() const = 0; [[nodiscard]] virtual NetworkPolicyStatus get_status() const = 0;
[[nodiscard]] virtual const std::vector<std::unique_ptr<engine::DynamicEngine>> &get_engine_stack() const = 0; [[nodiscard]] virtual const std::vector<std::unique_ptr<engine::DynamicEngine>> &get_engine_stack() const = 0;

2
src/include/gridfire/policy/stellar_policy.h
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@@ -141,7 +141,7 @@ namespace gridfire::policy {
* @brief Gets the current status of the policy. * @brief Gets the current status of the policy.
* @return NetworkPolicyStatus The construction and verification status. * @return NetworkPolicyStatus The construction and verification status.
*/ */
[[nodiscard]] NetworkPolicyStatus getStatus() const override; [[nodiscard]] NetworkPolicyStatus get_status() const override;
[[nodiscard]] const std::vector<std::unique_ptr<engine::DynamicEngine>> &get_engine_stack() const override; [[nodiscard]] const std::vector<std::unique_ptr<engine::DynamicEngine>> &get_engine_stack() const override;

2
src/lib/engine/diagnostics/dynamic_engine_diagnostics.cpp
View File

@@ -15,7 +15,7 @@ namespace gridfire::engine::diagnostics {
const double relTol, const double relTol,
const double absTol, const double absTol,
const size_t top_n, const size_t top_n,
bool json const bool json
) { ) {
struct SpeciesError { struct SpeciesError {
std::string name; std::string name;

20
src/lib/engine/procedures/construction.cpp
View File

@@ -63,7 +63,7 @@ namespace {
parent_species.z() - 1 parent_species.z() - 1
); );
if (downProduct.has_value()) { // Only add the reaction if the Species map contains the product if (downProduct.has_value()) { // Only add the reaction if the Species map contains the product
if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::BETA_PLUS)) { if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::WRL_BETA_PLUS)) {
weak_reaction_pool.add_reaction( weak_reaction_pool.add_reaction(
std::make_unique<gridfire::rates::weak::WeakReaction>( std::make_unique<gridfire::rates::weak::WeakReaction>(
parent_species, parent_species,
@@ -72,7 +72,7 @@ namespace {
) )
); );
} }
if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::ELECTRON_CAPTURE)) { if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::WRL_ELECTRON_CAPTURE)) {
weak_reaction_pool.add_reaction( weak_reaction_pool.add_reaction(
std::make_unique<gridfire::rates::weak::WeakReaction>( std::make_unique<gridfire::rates::weak::WeakReaction>(
parent_species, parent_species,
@@ -83,7 +83,7 @@ namespace {
} }
} }
if (upProduct.has_value()) { // Only add the reaction if the Species map contains the product if (upProduct.has_value()) { // Only add the reaction if the Species map contains the product
if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::BETA_MINUS)) { if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::WRL_BETA_MINUS)) {
weak_reaction_pool.add_reaction( weak_reaction_pool.add_reaction(
std::make_unique<gridfire::rates::weak::WeakReaction>( std::make_unique<gridfire::rates::weak::WeakReaction>(
parent_species, parent_species,
@@ -92,7 +92,7 @@ namespace {
) )
); );
} }
if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::POSITRON_CAPTURE)) { if (has_flag(reactionTypes, gridfire::engine::NetworkConstructionFlags::WRL_POSITRON_CAPTURE)) {
weak_reaction_pool.add_reaction( weak_reaction_pool.add_reaction(
std::make_unique<gridfire::rates::weak::WeakReaction>( std::make_unique<gridfire::rates::weak::WeakReaction>(
parent_species, parent_species,
@@ -111,7 +111,7 @@ namespace {
const gridfire::engine::NetworkConstructionFlags reaction_types const gridfire::engine::NetworkConstructionFlags reaction_types
) { ) {
gridfire::reaction::ReactionSet strong_reaction_pool; gridfire::reaction::ReactionSet strong_reaction_pool;
if (has_flag(reaction_types, gridfire::engine::NetworkConstructionFlags::STRONG)) { if (has_flag(reaction_types, gridfire::engine::NetworkConstructionFlags::REACLIB_STRONG)) {
const auto& allReaclibReactions = gridfire::reaclib::get_all_reaclib_reactions(); const auto& allReaclibReactions = gridfire::reaclib::get_all_reaclib_reactions();
for (const auto& reaction : allReaclibReactions) { for (const auto& reaction : allReaclibReactions) {
const bool isWeakReaction = reaclib_reaction_is_weak(*reaction); const bool isWeakReaction = reaclib_reaction_is_weak(*reaction);
@@ -129,11 +129,11 @@ namespace {
bool validate_unique_weak_set(gridfire::engine::NetworkConstructionFlags flag) { bool validate_unique_weak_set(gridfire::engine::NetworkConstructionFlags flag) {
// This method ensures that weak reactions will only be fetched from either reaclib or the weak reaction library (WRL) // This method ensures that weak reactions will only be fetched from either reaclib or the weak reaction library (WRL)
// but not both // but not both
std::array<gridfire::engine::NetworkConstructionFlags, 4> WRL_Flags = { const std::array<gridfire::engine::NetworkConstructionFlags, 4> WRL_Flags = {
gridfire::engine::NetworkConstructionFlags::BETA_PLUS, gridfire::engine::NetworkConstructionFlags::WRL_BETA_PLUS,
gridfire::engine::NetworkConstructionFlags::ELECTRON_CAPTURE, gridfire::engine::NetworkConstructionFlags::WRL_ELECTRON_CAPTURE,
gridfire::engine::NetworkConstructionFlags::POSITRON_CAPTURE, gridfire::engine::NetworkConstructionFlags::WRL_POSITRON_CAPTURE,
gridfire::engine::NetworkConstructionFlags::BETA_MINUS gridfire::engine::NetworkConstructionFlags::WRL_BETA_MINUS
}; };
if (!has_flag(flag, gridfire::engine::NetworkConstructionFlags::REACLIB_WEAK)) { if (!has_flag(flag, gridfire::engine::NetworkConstructionFlags::REACLIB_WEAK)) {

2
src/lib/policy/stellar_policy.cpp
View File

@@ -92,7 +92,7 @@ namespace gridfire::policy {
return std::make_unique<partition::CompositePartitionFunction>(partitionFunction); return std::make_unique<partition::CompositePartitionFunction>(partitionFunction);
} }
inline NetworkPolicyStatus MainSequencePolicy::getStatus() const { inline NetworkPolicyStatus MainSequencePolicy::get_status() const {
return m_status; return m_status;
} }

10
src/python/bindings.cpp
View File

@@ -3,7 +3,6 @@
#include "types/bindings.h" #include "types/bindings.h"
#include "partition/bindings.h" #include "partition/bindings.h"
#include "expectations/bindings.h"
#include "engine/bindings.h" #include "engine/bindings.h"
#include "exceptions/bindings.h" #include "exceptions/bindings.h"
#include "io/bindings.h" #include "io/bindings.h"
@@ -11,8 +10,9 @@
#include "screening/bindings.h" #include "screening/bindings.h"
#include "solver/bindings.h" #include "solver/bindings.h"
#include "utils/bindings.h" #include "utils/bindings.h"
#include "policy/bindings.h"
PYBIND11_MODULE(gridfire, m) { PYBIND11_MODULE(_gridfire, m) {
m.doc() = "Python bindings for the fourdst utility modules which are a part of the 4D-STAR project."; m.doc() = "Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.";
pybind11::module::import("fourdst.constants"); pybind11::module::import("fourdst.constants");
@@ -26,9 +26,6 @@ PYBIND11_MODULE(gridfire, m) {
auto partitionMod = m.def_submodule("partition", "GridFire partition function bindings"); auto partitionMod = m.def_submodule("partition", "GridFire partition function bindings");
register_partition_bindings(partitionMod); register_partition_bindings(partitionMod);
auto expectationMod = m.def_submodule("expectations", "GridFire expectations bindings");
register_expectation_bindings(expectationMod);
auto reactionMod = m.def_submodule("reaction", "GridFire reaction bindings"); auto reactionMod = m.def_submodule("reaction", "GridFire reaction bindings");
register_reaction_bindings(reactionMod); register_reaction_bindings(reactionMod);
@@ -47,6 +44,9 @@ PYBIND11_MODULE(gridfire, m) {
auto solverMod = m.def_submodule("solver", "GridFire numerical solver bindings"); auto solverMod = m.def_submodule("solver", "GridFire numerical solver bindings");
register_solver_bindings(solverMod); register_solver_bindings(solverMod);
auto policyMod = m.def_submodule("policy", "GridFire network policy bindings");
register_policy_bindings(policyMod);
auto utilsMod = m.def_submodule("utils", "GridFire utility method bindings"); auto utilsMod = m.def_submodule("utils", "GridFire utility method bindings");
register_utils_bindings(utilsMod); register_utils_bindings(utilsMod);
} }

425
src/python/engine/bindings.cpp
View File

@@ -5,8 +5,8 @@
#include "bindings.h" #include "bindings.h"
#include "gridfire/engine/engine.h" #include "gridfire/engine/engine.h"
#include "gridfire/engine/diagnostics/dynamic_engine_diagnostics.h"
#include "gridfire/exceptions/exceptions.h" #include "gridfire/exceptions/exceptions.h"
#include "pybind11/numpy.h"
#include "trampoline/py_engine.h" #include "trampoline/py_engine.h"
@@ -15,21 +15,21 @@ namespace py = pybind11;
namespace { namespace {
template <typename T> template <typename T>
concept IsDynamicEngine = std::is_base_of_v<gridfire::DynamicEngine, T>; concept IsDynamicEngine = std::is_base_of_v<gridfire::engine::DynamicEngine, T>;
template <IsDynamicEngine T, IsDynamicEngine BaseT> template <IsDynamicEngine T, IsDynamicEngine BaseT>
void registerDynamicEngineDefs(py::class_<T, BaseT> pyClass) { void registerDynamicEngineDefs(py::class_<T, BaseT> pyClass) {
pyClass.def( pyClass.def(
"calculateRHSAndEnergy", "calculateRHSAndEnergy",
[]( [](
const gridfire::DynamicEngine& self, const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp, const fourdst::composition::Composition& comp,
const double T9, const double T9,
const double rho const double rho
) { ) {
auto result = self.calculateRHSAndEnergy(comp, T9, rho); auto result = self.calculateRHSAndEnergy(comp, T9, rho);
if (!result.has_value()) { if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update()."); throw gridfire::exceptions::EngineError(std::format("calculateRHSAndEnergy returned a potentially recoverable error {}", gridfire::engine::EngineStatus_to_string(result.error())));
} }
return result.value(); return result.value();
}, },
@@ -39,21 +39,32 @@ namespace {
"Calculate the right-hand side (dY/dt) and energy generation rate." "Calculate the right-hand side (dY/dt) and energy generation rate."
) )
.def("calculateEpsDerivatives", .def("calculateEpsDerivatives",
&gridfire::DynamicEngine::calculateEpsDerivatives, &gridfire::engine::DynamicEngine::calculateEpsDerivatives,
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
"Calculate deps/dT and deps/drho" "Calculate deps/dT and deps/drho"
) )
.def("generateJacobianMatrix", .def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&T::generateJacobianMatrix, py::const_), [](const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho) -> gridfire::engine::NetworkJacobian {
return self.generateJacobianMatrix(comp, T9, rho);
},
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
"Generate the Jacobian matrix for the current state." "Generate the Jacobian matrix for the current state."
) )
.def("generateJacobianMatrix", .def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double, const std::vector<fourdst::atomic::Species>&>(&T::generateJacobianMatrix, py::const_), [](const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho,
const std::vector<fourdst::atomic::Species>& activeSpecies) -> gridfire::engine::NetworkJacobian {
return self.generateJacobianMatrix(comp, T9, rho, activeSpecies);
},
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
@@ -61,7 +72,13 @@ namespace {
"Generate the jacobian matrix only for the subset of the matrix representing the active species." "Generate the jacobian matrix only for the subset of the matrix representing the active species."
) )
.def("generateJacobianMatrix", .def("generateJacobianMatrix",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::SparsityPattern&>(&T::generateJacobianMatrix, py::const_), [](const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp,
const double T9,
const double rho,
const gridfire::engine::SparsityPattern& sparsityPattern) -> gridfire::engine::NetworkJacobian {
return self.generateJacobianMatrix(comp, T9, rho, sparsityPattern);
},
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
@@ -73,7 +90,7 @@ namespace {
) )
.def("calculateMolarReactionFlow", .def("calculateMolarReactionFlow",
[]( [](
const gridfire::DynamicEngine& self, const gridfire::engine::DynamicEngine& self,
const gridfire::reaction::Reaction& reaction, const gridfire::reaction::Reaction& reaction,
const fourdst::composition::Composition& comp, const fourdst::composition::Composition& comp,
const double T9, const double T9,
@@ -97,11 +114,6 @@ namespace {
py::arg("reactions"), py::arg("reactions"),
"Set the network reactions to a new set of reactions." "Set the network reactions to a new set of reactions."
) )
.def("getJacobianMatrixEntry", &T::getJacobianMatrixEntry,
py::arg("rowSpecies"),
py::arg("colSpecies"),
"Get an entry from the previously generated Jacobian matrix."
)
.def("getStoichiometryMatrixEntry", &T::getStoichiometryMatrixEntry, .def("getStoichiometryMatrixEntry", &T::getStoichiometryMatrixEntry,
py::arg("species"), py::arg("species"),
py::arg("reaction"), py::arg("reaction"),
@@ -109,14 +121,14 @@ namespace {
) )
.def("getSpeciesTimescales", .def("getSpeciesTimescales",
[]( [](
const gridfire::DynamicEngine& self, const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp, const fourdst::composition::Composition& comp,
const double T9, const double T9,
const double rho const double rho
) -> std::unordered_map<fourdst::atomic::Species, double> { ) -> std::unordered_map<fourdst::atomic::Species, double> {
const auto result = self.getSpeciesTimescales(comp, T9, rho); const auto result = self.getSpeciesTimescales(comp, T9, rho);
if (!result.has_value()) { if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update()."); throw gridfire::exceptions::EngineError(std::format("getSpeciesTimescales has returned a potentially recoverable error {}", gridfire::engine::EngineStatus_to_string(result.error())));
} }
return result.value(); return result.value();
}, },
@@ -127,14 +139,14 @@ namespace {
) )
.def("getSpeciesDestructionTimescales", .def("getSpeciesDestructionTimescales",
[]( [](
const gridfire::DynamicEngine& self, const gridfire::engine::DynamicEngine& self,
const fourdst::composition::Composition& comp, const fourdst::composition::Composition& comp,
const double T9, const double T9,
const double rho const double rho
) -> std::unordered_map<fourdst::atomic::Species, double> { ) -> std::unordered_map<fourdst::atomic::Species, double> {
const auto result = self.getSpeciesDestructionTimescales(comp, T9, rho); const auto result = self.getSpeciesDestructionTimescales(comp, T9, rho);
if (!result.has_value()) { if (!result.has_value()) {
throw gridfire::exceptions::StaleEngineError("Engine reports stale state, call update()."); throw gridfire::exceptions::EngineError(std::format("getSpeciesDestructionTimescales has returned a potentially recoverable error {}", gridfire::engine::EngineStatus_to_string(result.error())));
} }
return result.value(); return result.value();
}, },
@@ -179,7 +191,7 @@ namespace {
.def("rebuild", .def("rebuild",
&T::rebuild, &T::rebuild,
py::arg("composition"), py::arg("composition"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full, py::arg("depth") = gridfire::engine::NetworkBuildDepth::Full,
"Rebuild the engine with a new composition and build depth." "Rebuild the engine with a new composition and build depth."
) )
.def("isStale", .def("isStale",
@@ -190,7 +202,14 @@ namespace {
.def("collectComposition", .def("collectComposition",
&T::collectComposition, &T::collectComposition,
py::arg("composition"), py::arg("composition"),
py::arg("T9"),
py::arg("rho"),
"Recursively collect composition from current engine and any sub engines if they exist." "Recursively collect composition from current engine and any sub engines if they exist."
)
.def("getSpeciesStatus",
&T::getSpeciesStatus,
py::arg("species"),
"Get the status of a species in the network."
); );
} }
@@ -206,11 +225,11 @@ void register_engine_bindings(py::module &m) {
void register_base_engine_bindings(const pybind11::module &m) { void register_base_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::StepDerivatives<double>>(m, "StepDerivatives") py::class_<gridfire::engine::StepDerivatives<double>>(m, "StepDerivatives")
.def_readonly("dYdt", &gridfire::StepDerivatives<double>::dydt, "The right-hand side (dY/dt) of the ODE system.") .def_readonly("dYdt", &gridfire::engine::StepDerivatives<double>::dydt, "The right-hand side (dY/dt) of the ODE system.")
.def_readonly("energy", &gridfire::StepDerivatives<double>::nuclearEnergyGenerationRate, "The energy generation rate."); .def_readonly("energy", &gridfire::engine::StepDerivatives<double>::nuclearEnergyGenerationRate, "The energy generation rate.");
py::class_<gridfire::SparsityPattern> py_sparsity_pattern(m, "SparsityPattern"); py::class_<gridfire::engine::SparsityPattern> py_sparsity_pattern(m, "SparsityPattern");
abs_stype_register_engine_bindings(m); abs_stype_register_engine_bindings(m);
abs_stype_register_dynamic_engine_bindings(m); abs_stype_register_dynamic_engine_bindings(m);
@@ -218,148 +237,219 @@ void register_base_engine_bindings(const pybind11::module &m) {
} }
void abs_stype_register_engine_bindings(const pybind11::module &m) { void abs_stype_register_engine_bindings(const pybind11::module &m) {
py::class_<gridfire::Engine, PyEngine>(m, "Engine"); py::class_<gridfire::engine::Engine, PyEngine>(m, "Engine");
} }
void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m) { void abs_stype_register_dynamic_engine_bindings(const pybind11::module &m) {
const auto a = py::class_<gridfire::DynamicEngine, PyDynamicEngine>(m, "DynamicEngine"); const auto a = py::class_<gridfire::engine::DynamicEngine, PyDynamicEngine>(m, "DynamicEngine");
} }
void register_engine_procedural_bindings(pybind11::module &m) { void register_engine_procedural_bindings(pybind11::module &m) {
auto procedures = m.def_submodule("procedures", "Procedural functions associated with engine module"); register_engine_construction_bindings(m);
register_engine_construction_bindings(procedures); register_engine_priming_bindings(m);
register_engine_construction_bindings(procedures);
} }
void register_engine_diagnostic_bindings(pybind11::module &m) { void register_engine_diagnostic_bindings(pybind11::module &m) {
auto diagnostics = m.def_submodule("diagnostics", "A submodule for engine diagnostics"); auto diagnostics = m.def_submodule("diagnostics", "A submodule for engine diagnostics");
diagnostics.def("report_limiting_species", diagnostics.def("report_limiting_species",
&gridfire::diagnostics::report_limiting_species, &gridfire::engine::diagnostics::report_limiting_species,
py::arg("engine"), py::arg("engine"),
py::arg("Y_full"), py::arg("Y_full"),
py::arg("E_full"), py::arg("E_full"),
py::arg("dydt_full"),
py::arg("relTol"), py::arg("relTol"),
py::arg("absTol"), py::arg("absTol"),
py::arg("top_n") = 10 py::arg("top_n"),
py::arg("json")
); );
diagnostics.def("inspect_species_balance", diagnostics.def("inspect_species_balance",
&gridfire::diagnostics::inspect_species_balance, &gridfire::engine::diagnostics::inspect_species_balance,
py::arg("engine"), py::arg("engine"),
py::arg("species_name"), py::arg("species_name"),
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho") py::arg("rho"),
py::arg("json")
); );
diagnostics.def("inspect_jacobian_stiffness", diagnostics.def("inspect_jacobian_stiffness",
&gridfire::diagnostics::inspect_jacobian_stiffness, &gridfire::engine::diagnostics::inspect_jacobian_stiffness,
py::arg("engine"), py::arg("engine"),
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho") py::arg("rho"),
py::arg("json")
); );
} }
void register_engine_construction_bindings(pybind11::module &m) { void register_engine_construction_bindings(pybind11::module &m) {
m.def("build_nuclear_network", &gridfire::build_nuclear_network, py::enum_<gridfire::engine::NetworkConstructionFlags>(m, "NetworkConstructionFlags")
.value("NONE", gridfire::engine::NetworkConstructionFlags::NONE, "No special construction flags.")
.value("REACLIB_STRONG", gridfire::engine::NetworkConstructionFlags::REACLIB_STRONG, "Include strong reactions from reaclib.")
.value("WRL_BETA_MINUS", gridfire::engine::NetworkConstructionFlags::WRL_BETA_MINUS, "Include beta-minus decay reactions from weak rate library.")
.value("WRL_BETA_PLUS", gridfire::engine::NetworkConstructionFlags::WRL_BETA_PLUS, "Include beta-plus decay reactions from weak rate library.")
.value("WRL_ELECTRON_CAPTURE", gridfire::engine::NetworkConstructionFlags::WRL_ELECTRON_CAPTURE, "Include electron capture reactions from weak rate library.")
.value("WRL_POSITRON_CAPTURE", gridfire::engine::NetworkConstructionFlags::WRL_POSITRON_CAPTURE, "Include positron capture reactions from weak rate library.")
.value("REACLIB_WEAK", gridfire::engine::NetworkConstructionFlags::REACLIB_WEAK, "Include weak reactions from reaclib.")
.value("WRL_WEAK", gridfire::engine::NetworkConstructionFlags::WRL_WEAK, "Include all weak reactions from weak rate library.")
.value("REACLIB", gridfire::engine::NetworkConstructionFlags::REACLIB, "Include all reactions from reaclib.")
.value("DEFAULT", gridfire::engine::NetworkConstructionFlags::DEFAULT, "Default construction flags (Reaclib strong and weak).")
.export_values()
.def("__repr__", [](const gridfire::engine::NetworkConstructionFlags& flags) {
return gridfire::engine::NetworkConstructionFlagsToString(flags);
});
m.def("build_nuclear_network", &gridfire::engine::build_nuclear_network,
py::arg("composition"), py::arg("composition"),
py::arg("weakInterpolator"), py::arg("weakInterpolator"),
py::arg("maxLayers") = gridfire::NetworkBuildDepth::Full, py::arg("maxLayers") = gridfire::engine::NetworkBuildDepth::Full,
py::arg("reverse") = false, py::arg("ReactionTypes") = gridfire::engine::NetworkConstructionFlags::DEFAULT,
"Build a nuclear network from a composition using all archived reaction data." "Build a nuclear network from a composition using all archived reaction data."
); );
} }
void register_engine_priming_bindings(pybind11::module &m) { void register_engine_priming_bindings(pybind11::module &m) {
m.def("primeNetwork",
m.def("calculateDestructionRateConstant", &gridfire::engine::primeNetwork,
&gridfire::calculateDestructionRateConstant, py::arg("netIn"),
py::arg("engine"), py::arg("engine"),
py::arg("species"), py::arg("ignoredReactionTypes") = std::nullopt,
py::arg("composition"), "Prime a network with a short timescale ignition"
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) { void register_engine_type_bindings(pybind11::module &m) {
auto types = m.def_submodule("types", "Types associated with engine module"); register_engine_building_type_bindings(m);
register_engine_building_type_bindings(types); register_engine_reporting_type_bindings(m);
register_engine_reporting_type_bindings(types); register_engine_types_bindings(m);
register_jacobian_type_bindings(m);
} }
void register_engine_building_type_bindings(pybind11::module &m) { void register_engine_building_type_bindings(const pybind11::module &m) {
py::enum_<gridfire::NetworkBuildDepth>(m, "NetworkBuildDepth") py::enum_<gridfire::engine::NetworkBuildDepth>(m, "NetworkBuildDepth")
.value("Full", gridfire::NetworkBuildDepth::Full, "Full network build depth") .value("Full", gridfire::engine::NetworkBuildDepth::Full, "Full network build depth")
.value("Shallow", gridfire::NetworkBuildDepth::Shallow, "Shallow network build depth") .value("Shallow", gridfire::engine::NetworkBuildDepth::Shallow, "Shallow network build depth")
.value("SecondOrder", gridfire::NetworkBuildDepth::SecondOrder, "Second order network build depth") .value("SecondOrder", gridfire::engine::NetworkBuildDepth::SecondOrder, "Second order network build depth")
.value("ThirdOrder", gridfire::NetworkBuildDepth::ThirdOrder, "Third order network build depth") .value("ThirdOrder", gridfire::engine::NetworkBuildDepth::ThirdOrder, "Third order network build depth")
.value("FourthOrder", gridfire::NetworkBuildDepth::FourthOrder, "Fourth order network build depth") .value("FourthOrder", gridfire::engine::NetworkBuildDepth::FourthOrder, "Fourth order network build depth")
.value("FifthOrder", gridfire::NetworkBuildDepth::FifthOrder, "Fifth order network build depth") .value("FifthOrder", gridfire::engine::NetworkBuildDepth::FifthOrder, "Fifth order network build depth")
.export_values(); .export_values();
py::class_<gridfire::BuildDepthType> py_build_depth_type(m, "BuildDepthType"); py::class_<gridfire::engine::BuildDepthType> py_build_depth_type(m, "BuildDepthType");
} }
void register_engine_reporting_type_bindings(pybind11::module &m) { void register_engine_reporting_type_bindings(const pybind11::module &m) {
py::enum_<gridfire::PrimingReportStatus>(m, "PrimingReportStatus") py::enum_<gridfire::engine::PrimingReportStatus>(m, "PrimingReportStatus")
.value("FULL_SUCCESS", gridfire::PrimingReportStatus::FULL_SUCCESS, "Priming was full successful.") .value("FULL_SUCCESS", gridfire::engine::PrimingReportStatus::SUCCESS, "Priming was full successful.")
.value("NO_SPECIES_TO_PRIME", gridfire::PrimingReportStatus::NO_SPECIES_TO_PRIME, "No species to prime.") .value("NO_SPECIES_TO_PRIME", gridfire::engine::PrimingReportStatus::SOLVER_FAILURE, "Solver Failed to converge during priming.")
.value("MAX_ITERATIONS_REACHED", gridfire::PrimingReportStatus::MAX_ITERATIONS_REACHED, "Maximum iterations reached during priming.") .value("MAX_ITERATIONS_REACHED", gridfire::engine::PrimingReportStatus::ALREADY_PRIMED, "Engine has already been primed.")
.value("FAILED_TO_FINALIZE_COMPOSITION", gridfire::PrimingReportStatus::FAILED_TO_FINALIZE_COMPOSITION, "Failed to finalize the composition after priming.")
.value("FAILED_TO_FIND_CREATION_CHANNEL", gridfire::PrimingReportStatus::FAILED_TO_FIND_CREATION_CHANNEL, "Failed to find a creation channel for the priming species.")
.value("FAILED_TO_FIND_PRIMING_REACTIONS", gridfire::PrimingReportStatus::FAILED_TO_FIND_PRIMING_REACTIONS, "Failed to find priming reactions for the species.")
.value("BASE_NETWORK_TOO_SHALLOW", gridfire::PrimingReportStatus::BASE_NETWORK_TOO_SHALLOW, "The base network is too shallow for priming.")
.export_values() .export_values()
.def("__repr__", [](const gridfire::PrimingReportStatus& status) { .def("__repr__", [](const gridfire::engine::PrimingReportStatus& status) {
std::stringstream ss; std::stringstream ss;
ss << gridfire::PrimingReportStatusStrings.at(status) << "\n"; ss << gridfire::engine::PrimingReportStatusStrings.at(status) << "\n";
return ss.str(); return ss.str();
}, },
"String representation of the PrimingReport." "String representation of the PrimingReport."
); );
py::class_<gridfire::PrimingReport>(m, "PrimingReport") py::class_<gridfire::engine::PrimingReport>(m, "PrimingReport")
.def_readonly("success", &gridfire::PrimingReport::success, "Indicates if the priming was successful.") .def_readonly("success", &gridfire::engine::PrimingReport::success, "Indicates if the priming was successful.")
.def_readonly("massFractionChanges", &gridfire::PrimingReport::massFractionChanges, "Map of species to their mass fraction changes after priming.") .def_readonly("primedComposition", &gridfire::engine::PrimingReport::primedComposition, "The composition after priming.")
.def_readonly("primedComposition", &gridfire::PrimingReport::primedComposition, "The composition after priming.") .def_readonly("status", &gridfire::engine::PrimingReport::status, "Status message from the priming process.")
.def_readonly("status", &gridfire::PrimingReport::status, "Status message from the priming process.") .def("__repr__", [](const gridfire::engine::PrimingReport& report) {
.def("__repr__", [](const gridfire::PrimingReport& report) {
std::stringstream ss; std::stringstream ss;
ss << report; ss << report;
return ss.str(); return ss.str();
} }
); );
py::enum_<gridfire::engine::SpeciesStatus>(m, "SpeciesStatus")
.value("ACTIVE", gridfire::engine::SpeciesStatus::ACTIVE, "Species is active in the network.")
.value("EQUILIBRIUM", gridfire::engine::SpeciesStatus::EQUILIBRIUM, "Species is in equilibrium.")
.value("INACTIVE_FLOW", gridfire::engine::SpeciesStatus::INACTIVE_FLOW, "Species is inactive due to flow.")
.value("NOT_PRESENT", gridfire::engine::SpeciesStatus::NOT_PRESENT, "Species is not present in the network.")
.export_values()
.def("__repr__", [](const gridfire::engine::SpeciesStatus& status) {
return gridfire::engine::SpeciesStatus_to_string(status);
});
} }
void register_engine_types_bindings(const pybind11::module &m) {
py::enum_<gridfire::engine::EngineTypes>(m, "EngineTypes")
.value("GRAPH_ENGINE", gridfire::engine::EngineTypes::GRAPH_ENGINE, "The standard graph-based engine.")
.value("ADAPTIVE_ENGINE_VIEW", gridfire::engine::EngineTypes::ADAPTIVE_ENGINE_VIEW, "An engine that adapts based on certain criteria.")
.value("MULTISCALE_PARTITIONING_ENGINE_VIEW", gridfire::engine::EngineTypes::MULTISCALE_PARTITIONING_ENGINE_VIEW, "An engine that partitions the system at multiple scales.")
.value("PRIMING_ENGINE_VIEW", gridfire::engine::EngineTypes::PRIMING_ENGINE_VIEW, "An engine that uses a priming strategy for simulations.")
.value("DEFINED_ENGINE_VIEW", gridfire::engine::EngineTypes::DEFINED_ENGINE_VIEW, "An engine defined by user specifications.")
.value("FILE_DEFINED_ENGINE_VIEW", gridfire::engine::EngineTypes::FILE_DEFINED_ENGINE_VIEW, "An engine defined through external files.")
.export_values()
.def("__repr__", [](const gridfire::engine::EngineTypes& type) {
return std::string(gridfire::engine::engine_type_to_string(type));
},
"String representation of the EngineTypes."
);
}
void register_jacobian_type_bindings(pybind11::module &m) {
py::class_<gridfire::engine::NetworkJacobian>(m, "NetworkJacobian")
.def("rank", &gridfire::engine::NetworkJacobian::rank, "Get the rank of the Jacobian matrix.")
.def("nnz", &gridfire::engine::NetworkJacobian::nnz, "Get the number of non-zero entries in the Jacobian matrix.")
.def("singular", &gridfire::engine::NetworkJacobian::singular, "Check if the Jacobian matrix is singular.")
.def("infs", &gridfire::engine::NetworkJacobian::infs, "Get all infinite entries in the Jacobian matrix.")
.def("nans", &gridfire::engine::NetworkJacobian::nans, "Get all NaN entries in the Jacobian matrix.")
.def("data", &gridfire::engine::NetworkJacobian::data, "Get the underlying sparse matrix data.")
.def("mapping", &gridfire::engine::NetworkJacobian::mapping, "Get the species-to-index mapping.")
.def("shape", &gridfire::engine::NetworkJacobian::shape, "Get the shape of the Jacobian matrix as (rows, columns).")
.def("to_csv", &gridfire::engine::NetworkJacobian::to_csv, py::arg("filename"), "Export the Jacobian matrix to a CSV file.")
.def("__getitem__", [](const gridfire::engine::NetworkJacobian &self, const std::pair<fourdst::atomic::Species, fourdst::atomic::Species>& speciesPair) {
return self(speciesPair.first, speciesPair.second);
}, py::arg("key"), "Get an entry from the Jacobian matrix using species identifiers.")
.def("__getitem__", [](const gridfire::engine::NetworkJacobian &self, const std::pair<size_t, size_t>& indexPair) {
return self(indexPair.first, indexPair.second);
}, py::arg("key"), "Get an entry from the Jacobian matrix using indices.")
.def("__setitem__", [](gridfire::engine::NetworkJacobian &self, const std::pair<fourdst::atomic::Species, fourdst::atomic::Species>& speciesPair, double value) {
self.set(speciesPair.first, speciesPair.second, value);
}, py::arg("key"), py::arg("value"), "Set an entry in the Jacobian matrix using species identifiers.")
.def("__setitem__", [](gridfire::engine::NetworkJacobian &self, const std::pair<size_t, size_t>& indexPair, double value) {
self.set(indexPair.first, indexPair.second, value);
}, py::arg("key"), py::arg("value"), "Set an entry in the Jacobian matrix using indices.")
.def("to_numpy", [](const gridfire::engine::NetworkJacobian &self) {
auto denseMatrix = Eigen::MatrixXd(self.data());
return pybind11::array_t<double>(
{std::get<0>(self.shape()), std::get<1>(self.shape())},
{sizeof(double) * std::get<1>(self.shape()), sizeof(double)},
denseMatrix.data()
);
}, "Convert the Jacobian matrix to a NumPy array.");
m.def(
"regularize_jacobian",
[](const gridfire::engine::NetworkJacobian& jac, const fourdst::composition::Composition& comp) {
return regularize_jacobian(jac, comp, std::nullopt);
},
py::arg("jacobian"),
py::arg("composition"),
"regularize_jacobian"
);
}
void con_stype_register_graph_engine_bindings(const pybind11::module &m) { void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
auto py_graph_engine_bindings = py::class_<gridfire::GraphEngine, gridfire::DynamicEngine>(m, "GraphEngine"); auto py_graph_engine_bindings = py::class_<gridfire::engine::GraphEngine, gridfire::engine::DynamicEngine>(m, "GraphEngine");
// Register the Graph Engine Specific Bindings // Register the Graph Engine Specific Bindings
py_graph_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::engine::BuildDepthType>(),
py::arg("composition"), py::arg("composition"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full, py::arg("depth") = gridfire::engine::NetworkBuildDepth::Full,
"Initialize GraphEngine with a composition and build depth." "Initialize GraphEngine with a composition and build depth."
); );
py_graph_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::engine::BuildDepthType>(),
py::arg("composition"), py::arg("composition"),
py::arg("partitionFunction"), py::arg("partitionFunction"),
py::arg("depth") = gridfire::NetworkBuildDepth::Full, py::arg("depth") = gridfire::engine::NetworkBuildDepth::Full,
"Initialize GraphEngine with a composition, partition function and build depth." "Initialize GraphEngine with a composition, partition function and build depth."
); );
py_graph_engine_bindings.def(py::init<const gridfire::reaction::ReactionSet &>(), py_graph_engine_bindings.def(py::init<const gridfire::reaction::ReactionSet &>(),
@@ -367,54 +457,66 @@ void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
"Initialize GraphEngine with a set of reactions." "Initialize GraphEngine with a set of reactions."
); );
py_graph_engine_bindings.def_static("getNetReactionStoichiometry", py_graph_engine_bindings.def_static("getNetReactionStoichiometry",
&gridfire::GraphEngine::getNetReactionStoichiometry, &gridfire::engine::GraphEngine::getNetReactionStoichiometry,
py::arg("reaction"), py::arg("reaction"),
"Get the net stoichiometry for a given reaction." "Get the net stoichiometry for a given reaction."
); );
py_graph_engine_bindings.def("getSpeciesTimescales", py_graph_engine_bindings.def("getSpeciesTimescales",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::reaction::ReactionSet&>(&gridfire::GraphEngine::getSpeciesTimescales, py::const_), [](const gridfire::engine::GraphEngine& self,
const fourdst::composition::Composition& composition,
const double T9,
const double rho,
const gridfire::reaction::ReactionSet& activeReactions) {
return self.getSpeciesTimescales(composition, T9, rho, activeReactions);
},
py::arg("composition"), py::arg("composition"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
py::arg("activeReactions") py::arg("activeReactions")
); );
py_graph_engine_bindings.def("getSpeciesDestructionTimescales", py_graph_engine_bindings.def("getSpeciesDestructionTimescales",
py::overload_cast<const fourdst::composition::Composition&, double, double, const gridfire::reaction::ReactionSet&>(&gridfire::GraphEngine::getSpeciesDestructionTimescales, py::const_), [](const gridfire::engine::GraphEngine& self,
const fourdst::composition::Composition& composition,
const double T9,
const double rho,
const gridfire::reaction::ReactionSet& activeReactions) {
return self.getSpeciesDestructionTimescales(composition, T9, rho, activeReactions);
},
py::arg("composition"), py::arg("composition"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
py::arg("activeReactions") py::arg("activeReactions")
); );
py_graph_engine_bindings.def("involvesSpecies", py_graph_engine_bindings.def("involvesSpecies",
&gridfire::GraphEngine::involvesSpecies, &gridfire::engine::GraphEngine::involvesSpecies,
py::arg("species"), py::arg("species"),
"Check if a given species is involved in the network." "Check if a given species is involved in the network."
); );
py_graph_engine_bindings.def("exportToDot", py_graph_engine_bindings.def("exportToDot",
&gridfire::GraphEngine::exportToDot, &gridfire::engine::GraphEngine::exportToDot,
py::arg("filename"), py::arg("filename"),
"Export the network to a DOT file for visualization." "Export the network to a DOT file for visualization."
); );
py_graph_engine_bindings.def("exportToCSV", py_graph_engine_bindings.def("exportToCSV",
&gridfire::GraphEngine::exportToCSV, &gridfire::engine::GraphEngine::exportToCSV,
py::arg("filename"), py::arg("filename"),
"Export the network to a CSV file for analysis." "Export the network to a CSV file for analysis."
); );
py_graph_engine_bindings.def("setPrecomputation", py_graph_engine_bindings.def("setPrecomputation",
&gridfire::GraphEngine::setPrecomputation, &gridfire::engine::GraphEngine::setPrecomputation,
py::arg("precompute"), py::arg("precompute"),
"Enable or disable precomputation for the engine." "Enable or disable precomputation for the engine."
); );
py_graph_engine_bindings.def("isPrecomputationEnabled", py_graph_engine_bindings.def("isPrecomputationEnabled",
&gridfire::GraphEngine::isPrecomputationEnabled, &gridfire::engine::GraphEngine::isPrecomputationEnabled,
"Check if precomputation is enabled for the engine." "Check if precomputation is enabled for the engine."
); );
py_graph_engine_bindings.def("getPartitionFunction", py_graph_engine_bindings.def("getPartitionFunction",
&gridfire::GraphEngine::getPartitionFunction, &gridfire::engine::GraphEngine::getPartitionFunction,
"Get the partition function used by the engine." "Get the partition function used by the engine."
); );
py_graph_engine_bindings.def("calculateReverseRate", py_graph_engine_bindings.def("calculateReverseRate",
&gridfire::GraphEngine::calculateReverseRate, &gridfire::engine::GraphEngine::calculateReverseRate,
py::arg("reaction"), py::arg("reaction"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
@@ -422,7 +524,7 @@ void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
"Calculate the reverse rate for a given reaction at a specific temperature, density, and composition." "Calculate the reverse rate for a given reaction at a specific temperature, density, and composition."
); );
py_graph_engine_bindings.def("calculateReverseRateTwoBody", py_graph_engine_bindings.def("calculateReverseRateTwoBody",
&gridfire::GraphEngine::calculateReverseRateTwoBody, &gridfire::engine::GraphEngine::calculateReverseRateTwoBody,
py::arg("reaction"), py::arg("reaction"),
py::arg("T9"), py::arg("T9"),
py::arg("forwardRate"), py::arg("forwardRate"),
@@ -430,7 +532,7 @@ void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
"Calculate the reverse rate for a two-body reaction at a specific temperature." "Calculate the reverse rate for a two-body reaction at a specific temperature."
); );
py_graph_engine_bindings.def("calculateReverseRateTwoBodyDerivative", py_graph_engine_bindings.def("calculateReverseRateTwoBodyDerivative",
&gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative, &gridfire::engine::GraphEngine::calculateReverseRateTwoBodyDerivative,
py::arg("reaction"), py::arg("reaction"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
@@ -439,126 +541,96 @@ void con_stype_register_graph_engine_bindings(const pybind11::module &m) {
"Calculate the derivative of the reverse rate for a two-body reaction at a specific temperature." "Calculate the derivative of the reverse rate for a two-body reaction at a specific temperature."
); );
py_graph_engine_bindings.def("isUsingReverseReactions", py_graph_engine_bindings.def("isUsingReverseReactions",
&gridfire::GraphEngine::isUsingReverseReactions, &gridfire::engine::GraphEngine::isUsingReverseReactions,
"Check if the engine is using reverse reactions." "Check if the engine is using reverse reactions."
); );
py_graph_engine_bindings.def("setUseReverseReactions", py_graph_engine_bindings.def("setUseReverseReactions",
&gridfire::GraphEngine::setUseReverseReactions, &gridfire::engine::GraphEngine::setUseReverseReactions,
py::arg("useReverse"), py::arg("useReverse"),
"Enable or disable the use of reverse reactions in the engine." "Enable or disable the use of reverse reactions in the engine."
); );
// Register the general dynamic engine bindings // Register the general dynamic engine bindings
registerDynamicEngineDefs<gridfire::GraphEngine, gridfire::DynamicEngine>(py_graph_engine_bindings); registerDynamicEngineDefs<gridfire::engine::GraphEngine, gridfire::engine::DynamicEngine>(py_graph_engine_bindings);
} }
void register_engine_view_bindings(const pybind11::module &m) { void register_engine_view_bindings(const pybind11::module &m) {
auto py_defined_engine_view_bindings = py::class_<gridfire::DefinedEngineView, gridfire::DynamicEngine>(m, "DefinedEngineView"); auto py_defined_engine_view_bindings = py::class_<gridfire::engine::DefinedEngineView, gridfire::engine::DynamicEngine>(m, "DefinedEngineView");
py_defined_engine_view_bindings.def(py::init<std::vector<std::string>, gridfire::GraphEngine&>(), py_defined_engine_view_bindings.def(py::init<std::vector<std::string>, gridfire::engine::GraphEngine&>(),
py::arg("peNames"), py::arg("peNames"),
py::arg("baseEngine"), 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, py_defined_engine_view_bindings.def("getBaseEngine", &gridfire::engine::DefinedEngineView::getBaseEngine,
"Get the base engine associated with this defined engine view."); "Get the base engine associated with this defined engine view.");
registerDynamicEngineDefs<gridfire::DefinedEngineView, gridfire::DynamicEngine>(py_defined_engine_view_bindings); registerDynamicEngineDefs<gridfire::engine::DefinedEngineView, gridfire::engine::DynamicEngine>(py_defined_engine_view_bindings);
auto py_file_defined_engine_view_bindings = py::class_<gridfire::FileDefinedEngineView, gridfire::DefinedEngineView>(m, "FileDefinedEngineView"); auto py_file_defined_engine_view_bindings = py::class_<gridfire::engine::FileDefinedEngineView, gridfire::engine::DefinedEngineView>(m, "FileDefinedEngineView");
py_file_defined_engine_view_bindings.def( py_file_defined_engine_view_bindings.def(
py::init<gridfire::GraphEngine&, const std::string&, const gridfire::io::NetworkFileParser&>(), py::init<gridfire::engine::GraphEngine&, const std::string&, const gridfire::io::NetworkFileParser&>(),
py::arg("baseEngine"), py::arg("baseEngine"),
py::arg("fileName"), py::arg("fileName"),
py::arg("parser"), py::arg("parser"),
"Construct a defined engine view from a file and a base engine." "Construct a defined engine view from a file and a base engine."
); );
py_file_defined_engine_view_bindings.def("getNetworkFile", &gridfire::FileDefinedEngineView::getNetworkFile, py_file_defined_engine_view_bindings.def("getNetworkFile", &gridfire::engine::FileDefinedEngineView::getNetworkFile,
"Get the network file associated with this defined engine view." "Get the network file associated with this defined engine view."
); );
py_file_defined_engine_view_bindings.def("getParser", &gridfire::FileDefinedEngineView::getParser, py_file_defined_engine_view_bindings.def("getParser", &gridfire::engine::FileDefinedEngineView::getParser,
"Get the parser used for this defined engine view." "Get the parser used for this defined engine view."
); );
py_file_defined_engine_view_bindings.def("getBaseEngine", &gridfire::FileDefinedEngineView::getBaseEngine, py_file_defined_engine_view_bindings.def("getBaseEngine", &gridfire::engine::FileDefinedEngineView::getBaseEngine,
"Get the base engine associated with this file defined engine view."); "Get the base engine associated with this file defined engine view.");
registerDynamicEngineDefs<gridfire::FileDefinedEngineView, gridfire::DefinedEngineView>(py_file_defined_engine_view_bindings); registerDynamicEngineDefs<gridfire::engine::FileDefinedEngineView, gridfire::engine::DefinedEngineView>(py_file_defined_engine_view_bindings);
auto py_priming_engine_view_bindings = py::class_<gridfire::NetworkPrimingEngineView, gridfire::DefinedEngineView>(m, "NetworkPrimingEngineView"); auto py_priming_engine_view_bindings = py::class_<gridfire::engine::NetworkPrimingEngineView, gridfire::engine::DefinedEngineView>(m, "NetworkPrimingEngineView");
py_priming_engine_view_bindings.def(py::init<const std::string&, gridfire::GraphEngine&>(), py_priming_engine_view_bindings.def(py::init<const std::string&, gridfire::engine::GraphEngine&>(),
py::arg("primingSymbol"), py::arg("primingSymbol"),
py::arg("baseEngine"), py::arg("baseEngine"),
"Construct a priming engine view with a priming symbol and a base engine."); "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::GraphEngine&>(), py_priming_engine_view_bindings.def(py::init<const fourdst::atomic::Species&, gridfire::engine::GraphEngine&>(),
py::arg("primingSpecies"), py::arg("primingSpecies"),
py::arg("baseEngine"), py::arg("baseEngine"),
"Construct a priming engine view with a priming species and a base engine."); "Construct a priming engine view with a priming species and a base engine.");
py_priming_engine_view_bindings.def("getBaseEngine", &gridfire::NetworkPrimingEngineView::getBaseEngine, py_priming_engine_view_bindings.def("getBaseEngine", &gridfire::engine::NetworkPrimingEngineView::getBaseEngine,
"Get the base engine associated with this priming engine view."); "Get the base engine associated with this priming engine view.");
registerDynamicEngineDefs<gridfire::NetworkPrimingEngineView, gridfire::DefinedEngineView>(py_priming_engine_view_bindings); registerDynamicEngineDefs<gridfire::engine::NetworkPrimingEngineView, gridfire::engine::DefinedEngineView>(py_priming_engine_view_bindings);
auto py_adaptive_engine_view_bindings = py::class_<gridfire::AdaptiveEngineView, gridfire::DynamicEngine>(m, "AdaptiveEngineView"); auto py_adaptive_engine_view_bindings = py::class_<gridfire::engine::AdaptiveEngineView, gridfire::engine::DynamicEngine>(m, "AdaptiveEngineView");
py_adaptive_engine_view_bindings.def(py::init<gridfire::DynamicEngine&>(), py_adaptive_engine_view_bindings.def(py::init<gridfire::engine::DynamicEngine&>(),
py::arg("baseEngine"), py::arg("baseEngine"),
"Construct an adaptive engine view with a base engine."); "Construct an adaptive engine view with a base engine.");
py_adaptive_engine_view_bindings.def("getBaseEngine", py_adaptive_engine_view_bindings.def("getBaseEngine",
&gridfire::AdaptiveEngineView::getBaseEngine, &gridfire::engine::AdaptiveEngineView::getBaseEngine,
"Get the base engine associated with this adaptive engine view." "Get the base engine associated with this adaptive engine view."
); );
registerDynamicEngineDefs<gridfire::AdaptiveEngineView, gridfire::DynamicEngine>(py_adaptive_engine_view_bindings); registerDynamicEngineDefs<gridfire::engine::AdaptiveEngineView, gridfire::engine::DynamicEngine>(py_adaptive_engine_view_bindings);
auto py_qse_cache_config = py::class_<gridfire::QSECacheConfig>(m, "QSECacheConfig"); auto py_multiscale_engine_view_bindings = py::class_<gridfire::engine::MultiscalePartitioningEngineView, gridfire::engine::DynamicEngine>(m, "MultiscalePartitioningEngineView");
auto py_qse_cache_key = py::class_<gridfire::QSECacheKey>(m, "QSECacheKey"); py_multiscale_engine_view_bindings.def(py::init<gridfire::engine::GraphEngine&>(),
py_qse_cache_key.def(py::init<double, double, const std::vector<double>&>(),
py::arg("T9"),
py::arg("rho"),
py::arg("Y")
);
py_qse_cache_key.def("hash", &gridfire::QSECacheKey::hash,
"Get the pre-computed hash value of the key");
py_qse_cache_key.def_static("bin", &gridfire::QSECacheKey::bin,
py::arg("value"),
py::arg("tol"),
"bin a value based on a tolerance");
py_qse_cache_key.def("__eq__", &gridfire::QSECacheKey::operator==,
py::arg("other"),
"Check if two QSECacheKeys are equal");
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"), py::arg("baseEngine"),
"Construct a multiscale partitioning engine view with a base engine." "Construct a multiscale partitioning engine view with a base engine."
); );
py_multiscale_engine_view_bindings.def("getBaseEngine", py_multiscale_engine_view_bindings.def("getBaseEngine",
&gridfire::MultiscalePartitioningEngineView::getBaseEngine, &gridfire::engine::MultiscalePartitioningEngineView::getBaseEngine,
"Get the base engine associated with this multiscale partitioning engine view." "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("comp"),
py::arg("T9"),
py::arg("rho"),
"Analyze the connectivity of timescale pools in the network."
);
py_multiscale_engine_view_bindings.def("partitionNetwork", py_multiscale_engine_view_bindings.def("partitionNetwork",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork), &gridfire::engine::MultiscalePartitioningEngineView::partitionNetwork,
py::arg("comp"), py::arg("netIn"),
py::arg("T9"),
py::arg("rho"),
"Partition the network based on species timescales and connectivity."); "Partition the network based on species timescales and connectivity.");
py_multiscale_engine_view_bindings.def("partitionNetwork", py_multiscale_engine_view_bindings.def("partitionNetwork",
py::overload_cast<const gridfire::NetIn&>(&gridfire::MultiscalePartitioningEngineView::partitionNetwork), py::overload_cast<const gridfire::NetIn&>(&gridfire::engine::MultiscalePartitioningEngineView::partitionNetwork),
py::arg("netIn"), py::arg("netIn"),
"Partition the network based on a NetIn object." "Partition the network based on a NetIn object."
); );
py_multiscale_engine_view_bindings.def("exportToDot", py_multiscale_engine_view_bindings.def("exportToDot",
&gridfire::MultiscalePartitioningEngineView::exportToDot, &gridfire::engine::MultiscalePartitioningEngineView::exportToDot,
py::arg("filename"), py::arg("filename"),
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
@@ -566,26 +638,37 @@ void register_engine_view_bindings(const pybind11::module &m) {
"Export the network to a DOT file for visualization." "Export the network to a DOT file for visualization."
); );
py_multiscale_engine_view_bindings.def("getFastSpecies", py_multiscale_engine_view_bindings.def("getFastSpecies",
&gridfire::MultiscalePartitioningEngineView::getFastSpecies, &gridfire::engine::MultiscalePartitioningEngineView::getFastSpecies,
"Get the list of fast species in the network." "Get the list of fast species in the network."
); );
py_multiscale_engine_view_bindings.def("getDynamicSpecies", py_multiscale_engine_view_bindings.def("getDynamicSpecies",
&gridfire::MultiscalePartitioningEngineView::getDynamicSpecies, &gridfire::engine::MultiscalePartitioningEngineView::getDynamicSpecies,
"Get the list of dynamic species in the network." "Get the list of dynamic species in the network."
); );
py_multiscale_engine_view_bindings.def("equilibrateNetwork", py_multiscale_engine_view_bindings.def("involvesSpecies",
py::overload_cast<const fourdst::composition::Composition&, double, double>(&gridfire::MultiscalePartitioningEngineView::equilibrateNetwork), &gridfire::engine::MultiscalePartitioningEngineView::involvesSpecies,
py::arg("species"),
"Check if a given species is involved in the network (in either the algebraic or dynamic set)."
);
py_multiscale_engine_view_bindings.def("involvesSpeciesInQSE",
&gridfire::engine::MultiscalePartitioningEngineView::involvesSpeciesInQSE,
py::arg("species"),
"Check if a given species is involved in the network's algebraic set."
);
py_multiscale_engine_view_bindings.def("involvesSpeciesInDynamic",
&gridfire::engine::MultiscalePartitioningEngineView::involvesSpeciesInDynamic,
py::arg("species"),
"Check if a given species is involved in the network's dynamic set."
);
py_multiscale_engine_view_bindings.def("getNormalizedEquilibratedComposition",
&gridfire::engine::MultiscalePartitioningEngineView::getNormalizedEquilibratedComposition,
py::arg("comp"), py::arg("comp"),
py::arg("T9"), py::arg("T9"),
py::arg("rho"), py::arg("rho"),
"Equilibrate the network based on species abundances and conditions."); "Get the normalized equilibrated composition for the algebraic species."
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."
); );
registerDynamicEngineDefs<gridfire::MultiscalePartitioningEngineView, gridfire::DynamicEngine>( registerDynamicEngineDefs<gridfire::engine::MultiscalePartitioningEngineView, gridfire::engine::DynamicEngine>(
py_multiscale_engine_view_bindings py_multiscale_engine_view_bindings
); );

6
src/python/engine/bindings.h
View File

@@ -20,7 +20,9 @@ void register_engine_construction_bindings(pybind11::module &m);
void register_engine_priming_bindings(pybind11::module &m); void register_engine_priming_bindings(pybind11::module &m);
void register_engine_type_bindings(pybind11::module &m); void register_engine_type_bindings(pybind11::module &m);
void register_engine_building_type_bindings(pybind11::module &m); void register_engine_building_type_bindings(const pybind11::module &m);
void register_engine_reporting_type_bindings(pybind11::module &m); void register_engine_reporting_type_bindings(const pybind11::module &m);
void register_engine_types_bindings(const pybind11::module &m);
void register_jacobian_type_bindings(pybind11::module &m);

160
src/python/engine/trampoline/py_engine.cpp
View File

@@ -33,10 +33,14 @@ const std::vector<fourdst::atomic::Species>& PyEngine::getNetworkSpecies() const
py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\""); py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\"");
} }
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyEngine::calculateRHSAndEnergy(const fourdst::composition::Composition &comp, double T9, double rho) const { std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus> PyEngine::calculateRHSAndEnergy(
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError>), PYBIND11_TYPE(std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus>),
gridfire::Engine, gridfire::engine::Engine,
calculateRHSAndEnergy, calculateRHSAndEnergy,
comp, T9, rho comp, T9, rho
); );
@@ -65,19 +69,29 @@ const std::vector<fourdst::atomic::Species>& PyDynamicEngine::getNetworkSpecies(
py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\""); py::pybind11_fail("Tried to call pure virtual function \"DynamicEngine::getNetworkSpecies\"");
} }
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::calculateRHSAndEnergy(const fourdst::composition::Composition &comp, double T9, double rho) const {
std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus> PyDynamicEngine::calculateRHSAndEnergy(
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError>), PYBIND11_TYPE(std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus>),
gridfire::Engine, gridfire::engine::DynamicEngine,
calculateRHSAndEnergy, calculateRHSAndEnergy,
comp, T9, rho comp, T9, rho
); );
} }
void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composition& comp, double T9, double rho) const { gridfire::engine::NetworkJacobian PyDynamicEngine::generateJacobianMatrix(
const fourdst::composition::CompositionAbstract& comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, gridfire::engine::NetworkJacobian,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
generateJacobianMatrix, generateJacobianMatrix,
comp, comp,
T9, T9,
@@ -85,15 +99,15 @@ void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composi
); );
} }
void PyDynamicEngine::generateJacobianMatrix( gridfire::engine::NetworkJacobian PyDynamicEngine::generateJacobianMatrix(
const fourdst::composition::Composition &comp, const fourdst::composition::CompositionAbstract &comp,
const double T9, const double T9,
const double rho, const double rho,
const std::vector<fourdst::atomic::Species> &activeSpecies const std::vector<fourdst::atomic::Species> &activeSpecies
) const { ) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, gridfire::engine::NetworkJacobian,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
generateJacobianMatrix, generateJacobianMatrix,
comp, comp,
T9, T9,
@@ -102,10 +116,15 @@ void PyDynamicEngine::generateJacobianMatrix(
); );
} }
void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composition &comp, double T9, double rho, const gridfire::SparsityPattern &sparsityPattern) const { gridfire::engine::NetworkJacobian PyDynamicEngine::generateJacobianMatrix(
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho,
const gridfire::engine::SparsityPattern &sparsityPattern
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, gridfire::engine::NetworkJacobian,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
generateJacobianMatrix, generateJacobianMatrix,
comp, comp,
T9, T9,
@@ -114,38 +133,36 @@ void PyDynamicEngine::generateJacobianMatrix(const fourdst::composition::Composi
); );
} }
double PyDynamicEngine::getJacobianMatrixEntry(const fourdst::atomic::Species& rowSpecies, const fourdst::atomic::Species& colSpecies) const {
PYBIND11_OVERRIDE_PURE(
double,
gridfire::DynamicEngine,
getJacobianMatrixEntry,
rowSpecies,
colSpecies
);
}
void PyDynamicEngine::generateStoichiometryMatrix() { void PyDynamicEngine::generateStoichiometryMatrix() {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, void,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
generateStoichiometryMatrix generateStoichiometryMatrix
); );
} }
int PyDynamicEngine::getStoichiometryMatrixEntry(const fourdst::atomic::Species& species, const gridfire::reaction::Reaction& reaction) const { int PyDynamicEngine::getStoichiometryMatrixEntry(
const fourdst::atomic::Species& species,
const gridfire::reaction::Reaction& reaction
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
int, int,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getStoichiometryMatrixEntry, getStoichiometryMatrixEntry,
species, species,
reaction reaction
); );
} }
double PyDynamicEngine::calculateMolarReactionFlow(const gridfire::reaction::Reaction &reaction, const fourdst::composition::Composition &comp, double T9, double rho) const { double PyDynamicEngine::calculateMolarReactionFlow(
const gridfire::reaction::Reaction &reaction,
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
double, double,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
calculateMolarReactionFlow, calculateMolarReactionFlow,
reaction, reaction,
comp, comp,
@@ -157,7 +174,7 @@ double PyDynamicEngine::calculateMolarReactionFlow(const gridfire::reaction::Rea
const gridfire::reaction::ReactionSet& PyDynamicEngine::getNetworkReactions() const { const gridfire::reaction::ReactionSet& PyDynamicEngine::getNetworkReactions() const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
const gridfire::reaction::ReactionSet&, const gridfire::reaction::ReactionSet&,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getNetworkReactions getNetworkReactions
); );
} }
@@ -165,16 +182,20 @@ const gridfire::reaction::ReactionSet& PyDynamicEngine::getNetworkReactions() co
void PyDynamicEngine::setNetworkReactions(const gridfire::reaction::ReactionSet& reactions) { void PyDynamicEngine::setNetworkReactions(const gridfire::reaction::ReactionSet& reactions) {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, void,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
setNetworkReactions, setNetworkReactions,
reactions reactions
); );
} }
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesTimescales(const fourdst::composition::Composition &comp, double T9, double rho) const { std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus> PyDynamicEngine::getSpeciesTimescales(
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError>), PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus>),
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getSpeciesTimescales, getSpeciesTimescales,
comp, comp,
T9, T9,
@@ -182,10 +203,14 @@ std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::ex
); );
} }
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> PyDynamicEngine::getSpeciesDestructionTimescales(const fourdst::composition::Composition &comp, double T9, double rho) const { std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus> PyDynamicEngine::getSpeciesDestructionTimescales(
const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError>), PYBIND11_TYPE(std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus>),
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getSpeciesDestructionTimescales, getSpeciesDestructionTimescales,
comp, T9, rho comp, T9, rho
); );
@@ -194,7 +219,7 @@ std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::ex
fourdst::composition::Composition PyDynamicEngine::update(const gridfire::NetIn &netIn) { fourdst::composition::Composition PyDynamicEngine::update(const gridfire::NetIn &netIn) {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
fourdst::composition::Composition, fourdst::composition::Composition,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
update, update,
netIn netIn
); );
@@ -203,7 +228,7 @@ fourdst::composition::Composition PyDynamicEngine::update(const gridfire::NetIn
bool PyDynamicEngine::isStale(const gridfire::NetIn &netIn) { bool PyDynamicEngine::isStale(const gridfire::NetIn &netIn) {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
bool, bool,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
isStale, isStale,
netIn netIn
); );
@@ -212,7 +237,7 @@ bool PyDynamicEngine::isStale(const gridfire::NetIn &netIn) {
void PyDynamicEngine::setScreeningModel(gridfire::screening::ScreeningType model) { void PyDynamicEngine::setScreeningModel(gridfire::screening::ScreeningType model) {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
void, void,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
setScreeningModel, setScreeningModel,
model model
); );
@@ -221,7 +246,7 @@ void PyDynamicEngine::setScreeningModel(gridfire::screening::ScreeningType model
gridfire::screening::ScreeningType PyDynamicEngine::getScreeningModel() const { gridfire::screening::ScreeningType PyDynamicEngine::getScreeningModel() const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
gridfire::screening::ScreeningType, gridfire::screening::ScreeningType,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getScreeningModel getScreeningModel
); );
} }
@@ -229,7 +254,7 @@ gridfire::screening::ScreeningType PyDynamicEngine::getScreeningModel() const {
size_t PyDynamicEngine::getSpeciesIndex(const fourdst::atomic::Species &species) const { size_t PyDynamicEngine::getSpeciesIndex(const fourdst::atomic::Species &species) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
int, int,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
getSpeciesIndex, getSpeciesIndex,
species species
); );
@@ -238,28 +263,28 @@ size_t PyDynamicEngine::getSpeciesIndex(const fourdst::atomic::Species &species)
std::vector<double> PyDynamicEngine::mapNetInToMolarAbundanceVector(const gridfire::NetIn &netIn) const { std::vector<double> PyDynamicEngine::mapNetInToMolarAbundanceVector(const gridfire::NetIn &netIn) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
std::vector<double>, std::vector<double>,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
mapNetInToMolarAbundanceVector, mapNetInToMolarAbundanceVector,
netIn netIn
); );
} }
gridfire::PrimingReport PyDynamicEngine::primeEngine(const gridfire::NetIn &netIn) { gridfire::engine::PrimingReport PyDynamicEngine::primeEngine(const gridfire::NetIn &netIn) {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
gridfire::PrimingReport, gridfire::engine::PrimingReport,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
primeEngine, primeEngine,
netIn netIn
); );
} }
gridfire::EnergyDerivatives PyDynamicEngine::calculateEpsDerivatives( gridfire::engine::EnergyDerivatives PyDynamicEngine::calculateEpsDerivatives(
const fourdst::composition::Composition &comp, const fourdst::composition::CompositionAbstract &comp,
const double T9, const double T9,
const double rho) const { const double rho) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
gridfire::EnergyDerivatives, gridfire::engine::EnergyDerivatives,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
calculateEpsDerivatives, calculateEpsDerivatives,
comp, comp,
T9, T9,
@@ -268,28 +293,41 @@ gridfire::EnergyDerivatives PyDynamicEngine::calculateEpsDerivatives(
} }
fourdst::composition::Composition PyDynamicEngine::collectComposition( fourdst::composition::Composition PyDynamicEngine::collectComposition(
fourdst::composition::Composition &comp const fourdst::composition::CompositionAbstract &comp,
const double T9,
const double rho
) const { ) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
fourdst::composition::Composition, fourdst::composition::Composition,
gridfire::DynamicEngine, gridfire::engine::DynamicEngine,
collectComposition, collectComposition,
comp comp,
T9,
rho
); );
} }
const gridfire::Engine& PyEngineView::getBaseEngine() const { gridfire::engine::SpeciesStatus PyDynamicEngine::getSpeciesStatus(const fourdst::atomic::Species &species) const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
const gridfire::Engine&, gridfire::engine::SpeciesStatus,
gridfire::EngineView<gridfire::Engine>, gridfire::engine::DynamicEngine,
getSpeciesStatus,
species
);
}
const gridfire::engine::Engine& PyEngineView::getBaseEngine() const {
PYBIND11_OVERRIDE_PURE(
const gridfire::engine::Engine&,
gridfire::engine::EngineView<gridfire::engine::Engine>,
getBaseEngine getBaseEngine
); );
} }
const gridfire::DynamicEngine& PyDynamicEngineView::getBaseEngine() const { const gridfire::engine::DynamicEngine& PyDynamicEngineView::getBaseEngine() const {
PYBIND11_OVERRIDE_PURE( PYBIND11_OVERRIDE_PURE(
const gridfire::DynamicEngine&, const gridfire::engine::DynamicEngine&,
gridfire::EngineView<gridfire::DynamicEngine>, gridfire::engine::EngineView<gridfire::engine::DynamicEngine>,
getBaseEngine getBaseEngine
); );
} }

58
src/python/engine/trampoline/py_engine.h
View File

@@ -1,7 +1,6 @@
#pragma once #pragma once
#include "gridfire/engine/engine.h" #include "gridfire/engine/engine.h"
#include "gridfire/expectations/expected_engine.h"
#include "fourdst/atomic/atomicSpecies.h" #include "fourdst/atomic/atomicSpecies.h"
@@ -9,11 +8,11 @@
#include <expected> #include <expected>
class PyEngine final : public gridfire::Engine { class PyEngine final : public gridfire::engine::Engine {
public: public:
const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override; const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
std::expected<gridfire::StepDerivatives<double>,gridfire::expectations::StaleEngineError> calculateRHSAndEnergy( std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus> calculateRHSAndEnergy(
const fourdst::composition::CompositionAbstract &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho double rho
@@ -22,39 +21,34 @@ private:
mutable std::vector<fourdst::atomic::Species> m_species_cache; mutable std::vector<fourdst::atomic::Species> m_species_cache;
}; };
class PyDynamicEngine final : public gridfire::DynamicEngine { class PyDynamicEngine final : public gridfire::engine::DynamicEngine {
public: public:
const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override; const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
std::expected<gridfire::StepDerivatives<double>, gridfire::expectations::StaleEngineError> calculateRHSAndEnergy( std::expected<gridfire::engine::StepDerivatives<double>, gridfire::engine::EngineStatus> calculateRHSAndEnergy(
const fourdst::composition::CompositionAbstract &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho double rho
) const override; ) const override;
void generateJacobianMatrix( gridfire::engine::NetworkJacobian generateJacobianMatrix(
const fourdst::composition::Composition& comp, const fourdst::composition::CompositionAbstract& comp,
double T9, double T9,
double rho double rho
) const override; ) const override;
void generateJacobianMatrix( gridfire::engine::NetworkJacobian generateJacobianMatrix(
const fourdst::composition::CompositionAbstract &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho, double rho,
const std::vector<fourdst::atomic::Species> &activeSpecies const std::vector<fourdst::atomic::Species> &activeSpecies
) const override; ) const override;
void generateJacobianMatrix( gridfire::engine::NetworkJacobian generateJacobianMatrix(
const fourdst::composition::Composition& comp, const fourdst::composition::CompositionAbstract& comp,
double T9, double T9,
double rho, double rho,
const gridfire::SparsityPattern &sparsityPattern const gridfire::engine::SparsityPattern &sparsityPattern
) const override;
double getJacobianMatrixEntry(
const fourdst::atomic::Species& rowSpecies,
const fourdst::atomic::Species& colSpecies
) const override; ) const override;
void generateStoichiometryMatrix() override; void generateStoichiometryMatrix() override;
@@ -77,14 +71,14 @@ public:
const gridfire::reaction::ReactionSet& reactions const gridfire::reaction::ReactionSet& reactions
) override; ) override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesTimescales( std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus> getSpeciesTimescales(
const fourdst::composition::CompositionAbstract &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho double rho
) const override; ) const override;
std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::expectations::StaleEngineError> getSpeciesDestructionTimescales( std::expected<std::unordered_map<fourdst::atomic::Species, double>, gridfire::engine::EngineStatus> getSpeciesDestructionTimescales(
const fourdst::composition::Composition &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho double rho
) const override; ) const override;
@@ -111,38 +105,44 @@ public:
const gridfire::NetIn &netIn const gridfire::NetIn &netIn
) const override; ) const override;
gridfire::PrimingReport primeEngine( gridfire::engine::PrimingReport primeEngine(
const gridfire::NetIn &netIn const gridfire::NetIn &netIn
) override; ) override;
gridfire::BuildDepthType getDepth() const override { gridfire::engine::BuildDepthType getDepth() const override {
throw std::logic_error("Network depth not supported by this engine."); throw std::logic_error("Network depth not supported by this engine.");
} }
void rebuild( void rebuild(
const fourdst::composition::CompositionAbstract &comp, const fourdst::composition::CompositionAbstract &comp,
gridfire::BuildDepthType depth gridfire::engine::BuildDepthType depth
) override { ) override {
throw std::logic_error("Setting network depth not supported by this engine."); throw std::logic_error("Setting network depth not supported by this engine.");
} }
[[nodiscard]] gridfire::EnergyDerivatives calculateEpsDerivatives( [[nodiscard]] gridfire::engine::EnergyDerivatives calculateEpsDerivatives(
const fourdst::composition::Composition &comp, const fourdst::composition::CompositionAbstract &comp,
double T9, double T9,
double rho double rho
) const override; ) const override;
fourdst::composition::Composition collectComposition( fourdst::composition::Composition collectComposition(
fourdst::composition::Composition &comp const fourdst::composition::CompositionAbstract &comp,
double T9,
double rho
) const override;
gridfire::engine::SpeciesStatus getSpeciesStatus(
const fourdst::atomic::Species &species
) const override; ) const override;
private: private:
mutable std::vector<fourdst::atomic::Species> m_species_cache; mutable std::vector<fourdst::atomic::Species> m_species_cache;
}; };
class PyEngineView final : public gridfire::EngineView<gridfire::Engine> { class PyEngineView final : public gridfire::engine::EngineView<gridfire::engine::Engine> {
[[nodiscard]] const gridfire::Engine& getBaseEngine() const override; [[nodiscard]] const gridfire::engine::Engine& getBaseEngine() const override;
}; };
class PyDynamicEngineView final : public gridfire::EngineView<gridfire::DynamicEngine> { class PyDynamicEngineView final : public gridfire::engine::EngineView<gridfire::engine::DynamicEngine> {
[[nodiscard]] const gridfire::DynamicEngine& getBaseEngine() const override; [[nodiscard]] const gridfire::engine::DynamicEngine& getBaseEngine() const override;
}; };

61
src/python/exceptions/bindings.cpp
View File

@@ -7,48 +7,41 @@ namespace py = pybind11;
#include "gridfire/exceptions/exceptions.h" #include "gridfire/exceptions/exceptions.h"
void register_exception_bindings(const py::module &m) { void register_exception_bindings(const py::module &m) {
py::register_exception<gridfire::exceptions::EngineError>(m, "GridFireEngineError"); py::register_exception<gridfire::exceptions::GridFireError>(m, "GridFireError");
// TODO: Make it so that we can grab the stale state in python py::register_exception<gridfire::exceptions::DebugException>(m, "DebugException", m.attr("GridFireError"));
// m.attr("StaleEngineTrigger") = py::register_exception<gridfire::exceptions::StaleEngineTrigger>(m, "StaleEngineTrigger", m.attr("GridFireEngineError"));
m.attr("StaleEngineError") = py::register_exception<gridfire::exceptions::StaleEngineError>(m, "StaleEngineError", m.attr("GridFireEngineError"));
m.attr("FailedToPartitionEngineError") = py::register_exception<gridfire::exceptions::FailedToPartitionEngineError>(m, "FailedToPartitionEngineError", m.attr("GridFireEngineError"));
m.attr("NetworkResizedError") = py::register_exception<gridfire::exceptions::NetworkResizedError>(m, "NetworkResizedError", m.attr("GridFireEngineError"));
m.attr("UnableToSetNetworkReactionsError") = py::register_exception<gridfire::exceptions::UnableToSetNetworkReactionsError>(m, "UnableToSetNetworkReactionsError", m.attr("GridFireEngineError"));
py::class_<gridfire::exceptions::StaleEngineTrigger::state>(m, "StaleEngineState") py::register_exception<gridfire::exceptions::EngineError>(m, "EngineError", m.attr("GridFireError"));
.def(py::init<>())
.def_readwrite("T9", &gridfire::exceptions::StaleEngineTrigger::state::m_T9)
.def_readwrite("rho", &gridfire::exceptions::StaleEngineTrigger::state::m_rho)
.def_readwrite("Y", &gridfire::exceptions::StaleEngineTrigger::state::m_Y)
.def_readwrite("t", &gridfire::exceptions::StaleEngineTrigger::state::m_t)
.def_readwrite("total_steps", &gridfire::exceptions::StaleEngineTrigger::state::m_total_steps)
.def_readwrite("eps_nuc", &gridfire::exceptions::StaleEngineTrigger::state::m_eps_nuc);
py::class_<gridfire::exceptions::StaleEngineTrigger>(m, "StaleEngineTrigger") py::register_exception<gridfire::exceptions::FailedToPartitionEngineError>(m, "FailedToPartitionEngineError", m.attr("EngineError"));
.def(py::init<const gridfire::exceptions::StaleEngineTrigger::state &>()) py::register_exception<gridfire::exceptions::NetworkResizedError>(m, "NetworkResizedError", m.attr("EngineError"));
.def("getState", &gridfire::exceptions::StaleEngineTrigger::getState) py::register_exception<gridfire::exceptions::UnableToSetNetworkReactionsError>(m, "UnableToSetNetworkReactionsError", m.attr("EngineError"));
.def("numSpecies", &gridfire::exceptions::StaleEngineTrigger::numSpecies) py::register_exception<gridfire::exceptions::BadCollectionError>(m, "BadCollectionError", m.attr("EngineError"));
.def("totalSteps", &gridfire::exceptions::StaleEngineTrigger::totalSteps) py::register_exception<gridfire::exceptions::InvalidQSESolutionError>(m, "InvalidQSESolutionError", m.attr("EngineError"));
.def("energy", &gridfire::exceptions::StaleEngineTrigger::energy) py::register_exception<gridfire::exceptions::BadRHSEngineError>(m, "BadRHSEngineError", m.attr("EngineError"));
.def("getMolarAbundance", &gridfire::exceptions::StaleEngineTrigger::getMolarAbundance)
.def("temperature", &gridfire::exceptions::StaleEngineTrigger::temperature)
.def("density", &gridfire::exceptions::StaleEngineTrigger::density)
.def("__repr__", [&](const gridfire::exceptions::StaleEngineTrigger& self) {
return self.what();
});
py::register_exception<gridfire::exceptions::FailedToPartitionEngineError>(m, "FailedToPartitionEngineError", m.attr("GridFireEngineError")); py::register_exception<gridfire::exceptions::JacobianError>(m, "JacobianError", m.attr("EngineError"));
py::register_exception<gridfire::exceptions::NetworkResizedError>(m, "NetworkResizedError", m.attr("GridFireEngineError"));
py::register_exception<gridfire::exceptions::UnableToSetNetworkReactionsError>(m, "UnableToSetNetworkReactionsError", m.attr("GridFireEngineError"));
py::register_exception<gridfire::exceptions::BadCollectionError>(m, "BadCollectionError", m.attr("GridFireEngineError"));
py::register_exception<gridfire::exceptions::JacobianError>(m, "JacobianError", m.attr("GridFireEngineError"));
py::register_exception<gridfire::exceptions::StaleJacobianError>(m, "StaleJacobianError", m.attr("JacobianError")); py::register_exception<gridfire::exceptions::StaleJacobianError>(m, "StaleJacobianError", m.attr("JacobianError"));
py::register_exception<gridfire::exceptions::UninitializedJacobianError>(m, "UninitializedJacobianError", m.attr("JacobianError")); py::register_exception<gridfire::exceptions::UninitializedJacobianError>(m, "UninitializedJacobianError", m.attr("JacobianError"));
py::register_exception<gridfire::exceptions::UnknownJacobianError>(m, "UnknownJacobianError", m.attr("JacobianError")); py::register_exception<gridfire::exceptions::UnknownJacobianError>(m, "UnknownJacobianError", m.attr("JacobianError"));
py::register_exception<gridfire::exceptions::UtilityError>(m, "UtilityError"); py::register_exception<gridfire::exceptions::UtilityError>(m, "UtilityError", m.attr("GridFireError"));
py::register_exception<gridfire::exceptions::HashingError>(m, "HashingError", m.attr("UtilityError")); py::register_exception<gridfire::exceptions::HashingError>(m, "HashingError", m.attr("UtilityError"));
py::register_exception<gridfire::exceptions::PolicyError>(m, "PolicyError", m.attr("GridFireError"));
py::register_exception<gridfire::exceptions::MissingBaseReactionError>(m, "MissingBaseReactionError", m.attr("PolicyError"));
py::register_exception<gridfire::exceptions::MissingSeedSpeciesError>(m, "MissingSeedSpeciesError", m.attr("PolicyError"));
py::register_exception<gridfire::exceptions::MissingKeyReactionError>(m, "MissingKeyReactionError", m.attr("PolicyError"));
py::register_exception<gridfire::exceptions::ReactionError>(m, "ReactionError", m.attr("GridFireError"));
py::register_exception<gridfire::exceptions::ReactionParsingError>(m, "ReactionParsingError", m.attr("ReactionError"));
py::register_exception<gridfire::exceptions::SolverError>(m, "SolverError", m.attr("GridFireError"));
py::register_exception<gridfire::exceptions::SingularJacobianError>(m, "SingularJacobianError", m.attr("SolverError"));
py::register_exception<gridfire::exceptions::IllConditionedJacobianError>(m, "IllConditionedJacobianError", m.attr("SolverError"));
py::register_exception<gridfire::exceptions::SUNDIALSError>(m, "SUNDIALSError", m.attr("SolverError"));
py::register_exception<gridfire::exceptions::CVODESolverFailureError>(m, "CVODESolverFailureError", m.attr("SUNDIALSError"));
py::register_exception<gridfire::exceptions::KINSolSolverFailureError>(m, "KINSolSolverFailureError", m.attr("SUNDIALSError"));
} }

43
src/python/expectations/bindings.cpp
View File

@@ -1,43 +0,0 @@
#include <pybind11/pybind11.h>
#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc. if needed directly
#include "bindings.h"
namespace py = pybind11;
#include "gridfire/expectations/expectations.h"
void register_expectation_bindings(const py::module &m) {
py::enum_<gridfire::expectations::EngineErrorTypes>(m, "EngineErrorTypes")
.value("FAILURE", gridfire::expectations::EngineErrorTypes::FAILURE)
.value("INDEX", gridfire::expectations::EngineErrorTypes::INDEX)
.value("STALE", gridfire::expectations::EngineErrorTypes::STALE)
.export_values();
py::enum_<gridfire::expectations::StaleEngineErrorTypes>(m, "StaleEngineErrorTypes")
.value("SYSTEM_RESIZED", gridfire::expectations::StaleEngineErrorTypes::SYSTEM_RESIZED)
.export_values();
// Bind the base class
py::class_<gridfire::expectations::EngineError>(m, "EngineError")
.def_readonly("message", &gridfire::expectations::EngineError::m_message)
.def_readonly("type", &gridfire::expectations::EngineError::type)
.def("__str__", [](const gridfire::expectations::EngineError &e) {return e.m_message;});
// Bind the EngineIndexError, specifying EngineError as the base
py::class_<gridfire::expectations::EngineIndexError, gridfire::expectations::EngineError>(m, "EngineIndexError")
.def(py::init<int>(), py::arg("index"))
.def_readonly("index", &gridfire::expectations::EngineIndexError::m_index)
.def("__str__", [](const gridfire::expectations::EngineIndexError &e) {
return e.m_message + " at index " + std::to_string(e.m_index);
});
// Bind the StaleEngineError, specifying EngineError as the base
py::class_<gridfire::expectations::StaleEngineError, gridfire::expectations::EngineError>(m, "StaleEngineError")
.def(py::init<gridfire::expectations::StaleEngineErrorTypes>(), py::arg("stale_type"))
.def_readonly("stale_type", &gridfire::expectations::StaleEngineError::staleType)
.def("__str__", [](const gridfire::expectations::StaleEngineError &e) {
return static_cast<std::string>(e);
});
}

5
src/python/expectations/bindings.h
View File

@@ -1,5 +0,0 @@
#pragma once
#include <pybind11/pybind11.h>
void register_expectation_bindings(const pybind11::module &m);

20
src/python/gridfire/__init__.py Normal file
View File

@@ -0,0 +1,20 @@
from ._gridfire import *
import sys
from ._gridfire import type, utils, engine, solver, exceptions, partition, reaction, screening, io, policy
sys.modules['gridfire.type'] = type
sys.modules['gridfire.utils'] = utils
sys.modules['gridfire.engine'] = engine
sys.modules['gridfire.solver'] = solver
sys.modules['gridfire.exceptions'] = exceptions
sys.modules['gridfire.partition'] = partition
sys.modules['gridfire.reaction'] = reaction
sys.modules['gridfire.screening'] = screening
sys.modules['gridfire.policy'] = policy
sys.modules['gridfire.io'] = io
__all__ = ['type', 'utils', 'engine', 'solver', 'exceptions', 'partition', 'reaction', 'screening', 'io', 'policy']
__version__ = "v0.7.0_alpha_2025_10_25"

5
src/python/io/bindings.cpp
View File

@@ -19,9 +19,4 @@ auto register_io_bindings(const py::module &m) -> void {
.def("parse", &gridfire::io::SimpleReactionListFileParser::parse, .def("parse", &gridfire::io::SimpleReactionListFileParser::parse,
py::arg("filename"), py::arg("filename"),
"Parse a simple reaction list file and return a ParsedNetworkData object."); "Parse a simple reaction list file and return a ParsedNetworkData object.");
// py::class_<gridfire::io::MESANetworkFileParser, gridfire::io::NetworkFileParser>(m, "MESANetworkFileParser")
// .def("parse", &gridfire::io::MESANetworkFileParser::parse,
// py::arg("filename"),
// "Parse a MESA network file and return a ParsedNetworkData object.");
} }

2
src/python/meson.build
View File

@@ -1,10 +1,10 @@
subdir('types') subdir('types')
subdir('utils') subdir('utils')
subdir('expectations')
subdir('exceptions') subdir('exceptions')
subdir('io') subdir('io')
subdir('partition') subdir('partition')
subdir('reaction') subdir('reaction')
subdir('screening') subdir('screening')
subdir('engine') subdir('engine')
subdir('policy')
subdir('solver') subdir('solver')

233
src/python/policy/bindings.cpp Normal file
View File

@@ -0,0 +1,233 @@
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <memory>
#include "bindings.h"
#include "trampoline/py_policy.h"
#include "gridfire/policy/policy.h"
PYBIND11_DECLARE_HOLDER_TYPE(T, std::unique_ptr<T>, true) // Declare unique_ptr as a holder type for pybind11
namespace py = pybind11;
namespace {
template <typename T>
concept IsReactionChainPolicy = std::is_base_of_v<gridfire::policy::ReactionChainPolicy, T>;
template <typename T>
concept IsNetworkPolicy = std::is_base_of_v<gridfire::policy::NetworkPolicy, T>;
template<IsReactionChainPolicy T, IsReactionChainPolicy BaseT>
void registerReactionChainPolicyDefs(py::class_<T, BaseT>& pyClass) {
pyClass.def(
"get_reactions",
&T::get_reactions,
"Get the ReactionSet representing this reaction chain."
)
.def(
"contains",
py::overload_cast<const std::string&>(&T::contains, py::const_),
py::arg("id"),
"Check if the reaction chain contains a reaction with the given ID."
)
.def(
"contains",
py::overload_cast<const gridfire::reaction::Reaction&>(&T::contains, py::const_),
py::arg("reaction"),
"Check if the reaction chain contains the given reaction."
)
.def(
"name",
&T::name,
"Get the name of the reaction chain policy."
)
.def(
"hash",
&T::hash,
py::arg("seed"),
"Compute a hash value for the reaction chain policy."
)
.def(
"__eq__",
&T::operator==,
py::arg("other"),
"Check equality with another ReactionChainPolicy."
)
.def(
"__ne__",
&T::operator!=,
py::arg("other"),
"Check inequality with another ReactionChainPolicy."
)
.def("__hash__", [](const T &self) {
return self.hash(0);
}
)
.def("__repr__", [](const T &self) {
std::stringstream ss;
ss << self;
return ss.str();
});
}
template<IsNetworkPolicy T, IsNetworkPolicy BaseT>
void registerNetworkPolicyDefs(py::class_<T, BaseT> pyClass) {
pyClass.def(
"name",
&T::name,
"Get the name of the network policy."
)
.def(
"get_seed_species",
&T::get_seed_species,
"Get the set of seed species required by the network policy."
)
.def(
"get_seed_reactions",
&T::get_seed_reactions,
"Get the set of seed reactions required by the network policy."
)
.def(
"get_status",
&T::get_status,
"Get the current status of the network policy."
)
.def(
"get_engine_types_stack",
&T::get_engine_types_stack,
"Get the types of engines in the stack constructed by the network policy."
)
.def(
"construct",
&T::construct,
py::return_value_policy::reference,
"Construct the network according to the policy."
);
}
}
void register_policy_bindings(pybind11::module &m) {
register_reaction_chain_policy_bindings(m);
register_network_policy_bindings(m);
}
void register_reaction_chain_policy_bindings(pybind11::module &m) {
using namespace gridfire::policy;
py::class_<ReactionChainPolicy, PyReactionChainPolicy> py_reactionChainPolicy(m, "ReactionChainPolicy");
py::class_<MultiReactionChainPolicy, ReactionChainPolicy> py_multiChainPolicy(m, "MultiReactionChainPolicy");
py::class_<TemperatureDependentChainPolicy, ReactionChainPolicy> py_tempDepChainPolicy(m, "TemperatureDependentChainPolicy");
py::class_<ProtonProtonIChainPolicy, TemperatureDependentChainPolicy> py_ppI(m, "ProtonProtonIChainPolicy");
py_ppI.def(py::init<>());
py_ppI.def("name", &ProtonProtonIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<ProtonProtonIIChainPolicy, TemperatureDependentChainPolicy> py_ppII(m, "ProtonProtonIIChainPolicy");
py_ppII.def(py::init<>());
py_ppII.def("name", &ProtonProtonIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<ProtonProtonIIIChainPolicy, TemperatureDependentChainPolicy> py_ppIII(m, "ProtonProtonIIIChainPolicy");
py_ppIII.def(py::init<>());
py_ppIII.def("name", &ProtonProtonIIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<ProtonProtonChainPolicy, MultiReactionChainPolicy> py_ppChain(m, "ProtonProtonChainPolicy");
py_ppChain.def(py::init<>());
py_ppChain.def("name", &ProtonProtonChainPolicy::name, "Get the name of the reaction chain policy.");
registerReactionChainPolicyDefs(py_ppI);
registerReactionChainPolicyDefs(py_ppII);
registerReactionChainPolicyDefs(py_ppIII);
registerReactionChainPolicyDefs(py_ppChain);
py::class_<CNOIChainPolicy, TemperatureDependentChainPolicy> py_cnoI(m, "CNOIChainPolicy");
py_cnoI.def(py::init<>());
py_cnoI.def("name", &CNOIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<CNOIIChainPolicy, TemperatureDependentChainPolicy> py_cnoII(m, "CNOIIChainPolicy");
py_cnoII.def(py::init<>());
py_cnoII.def("name", &CNOIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<CNOIIIChainPolicy, TemperatureDependentChainPolicy> py_cnoIII(m, "CNOIIIChainPolicy");
py_cnoIII.def(py::init<>());
py_cnoIII.def("name", &CNOIIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<CNOIVChainPolicy, TemperatureDependentChainPolicy> py_cnoIV(m, "CNOIVChainPolicy");
py_cnoIV.def(py::init<>());
py_cnoIV.def("name", &CNOIVChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<CNOChainPolicy, MultiReactionChainPolicy> py_cnoChain(m, "CNOChainPolicy");
py_cnoChain.def(py::init<>());
py_cnoChain.def("name", &CNOChainPolicy::name, "Get the name of the reaction chain policy.");
registerReactionChainPolicyDefs(py_cnoI);
registerReactionChainPolicyDefs(py_cnoII);
registerReactionChainPolicyDefs(py_cnoIII);
registerReactionChainPolicyDefs(py_cnoIV);
registerReactionChainPolicyDefs(py_cnoChain);
py::class_<HotCNOIChainPolicy, TemperatureDependentChainPolicy> py_hotCNOI(m, "HotCNOIChainPolicy");
py_hotCNOI.def(py::init<>());
py_hotCNOI.def("name", &HotCNOIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<HotCNOIIChainPolicy, TemperatureDependentChainPolicy> py_hotCNOII(m, "HotCNOIIChainPolicy");
py_hotCNOII.def(py::init<>());
py_hotCNOII.def("name", &HotCNOIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<HotCNOIIIChainPolicy, TemperatureDependentChainPolicy> py_hotCNOIII(m, "HotCNOIIIChainPolicy");
py_hotCNOIII.def(py::init<>());
py_hotCNOIII.def("name", &HotCNOIIIChainPolicy::name, "Get the name of the reaction chain policy.");
py::class_<HotCNOChainPolicy, MultiReactionChainPolicy> py_hotCNOChain(m, "HotCNOChainPolicy");
py_hotCNOChain.def(py::init<>());
py_hotCNOChain.def("name", &HotCNOChainPolicy::name, "Get the name of the reaction chain policy.");
registerReactionChainPolicyDefs(py_hotCNOI);
registerReactionChainPolicyDefs(py_hotCNOII);
registerReactionChainPolicyDefs(py_hotCNOIII);
registerReactionChainPolicyDefs(py_hotCNOChain);
py::class_<TripleAlphaChainPolicy, TemperatureDependentChainPolicy> py_tripleAlpha(m, "TripleAlphaChainPolicy");
py_tripleAlpha.def(py::init<>());
py_tripleAlpha.def("name", &TripleAlphaChainPolicy::name, "Get the name of the reaction chain policy.");
registerReactionChainPolicyDefs(py_tripleAlpha);
py::class_<MainSequenceReactionChainPolicy, MultiReactionChainPolicy> py_mainSeq(m, "MainSequenceReactionChainPolicy");
py_mainSeq.def(py::init<>());
py_mainSeq.def("name", &MainSequenceReactionChainPolicy::name, "Get the name of the reaction chain policy.");
registerReactionChainPolicyDefs(py_mainSeq);
}
void register_network_policy_bindings(pybind11::module &m) {
py::enum_<gridfire::policy::NetworkPolicyStatus>(m, "NetworkPolicyStatus")
.value("UNINITIALIZED", gridfire::policy::NetworkPolicyStatus::UNINITIALIZED)
.value("INITIALIZED_UNVERIFIED", gridfire::policy::NetworkPolicyStatus::INITIALIZED_UNVERIFIED)
.value("MISSING_KEY_REACTION", gridfire::policy::NetworkPolicyStatus::MISSING_KEY_REACTION)
.value("MISSING_KEY_SPECIES", gridfire::policy::NetworkPolicyStatus::MISSING_KEY_SPECIES)
.value("INITIALIZED_VERIFIED", gridfire::policy::NetworkPolicyStatus::INITIALIZED_VERIFIED)
.export_values();
py::class_<gridfire::policy::NetworkPolicy, PyNetworkPolicy> py_networkPolicy(m, "NetworkPolicy");
py::class_<gridfire::policy::MainSequencePolicy, gridfire::policy::NetworkPolicy> py_mainSeqPolicy(m, "MainSequencePolicy");
py_mainSeqPolicy.def(
py::init<const fourdst::composition::Composition&>(),
py::arg("composition"),
"Construct MainSequencePolicy from an existing composition."
);
py_mainSeqPolicy.def(
py::init<std::vector<fourdst::atomic::Species>, const std::vector<double>&>(),
py::arg("seed_species"),
py::arg("mass_fractions"),
"Construct MainSequencePolicy from seed species and mass fractions."
);
registerNetworkPolicyDefs(py_mainSeqPolicy);
}

7
src/python/policy/bindings.h Normal file
View File

@@ -0,0 +1,7 @@
#pragma once
#include <pybind11/pybind11.h>
void register_policy_bindings(pybind11::module& m);
void register_reaction_chain_policy_bindings(pybind11::module& m);
void register_network_policy_bindings(pybind11::module& m);

4
src/python/expectations/meson.build → src/python/policy/meson.build
View File

@@ -1,4 +1,6 @@
# Define the library # Define the library
subdir('trampoline')
bindings_sources = files('bindings.cpp') bindings_sources = files('bindings.cpp')
bindings_headers = files('bindings.h') bindings_headers = files('bindings.h')
@@ -8,7 +10,7 @@ dependencies = [
pybind11_dep, pybind11_dep,
] ]
shared_module('py_gf_expectations', shared_module('py_gf_policy',
bindings_sources, bindings_sources,
cpp_args: ['-fvisibility=default'], cpp_args: ['-fvisibility=default'],
install : true, install : true,

21
src/python/policy/trampoline/meson.build Normal file
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@@ -0,0 +1,21 @@
gf_policy_trampoline_sources = files('py_policy.cpp')
gf_policy_trapoline_dependencies = [
gridfire_dep,
pybind11_dep,
python3_dep,
]
gf_policy_trampoline_lib = static_library(
'policy_trampolines',
gf_policy_trampoline_sources,
include_directories: include_directories('.'),
dependencies: gf_policy_trapoline_dependencies,
install: false,
)
gr_policy_trampoline_dep = declare_dependency(
link_with: gf_policy_trampoline_lib,
include_directories: ('.'),
dependencies: gf_policy_trapoline_dependencies,
)

149
src/python/policy/trampoline/py_policy.cpp Normal file
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@@ -0,0 +1,149 @@
#include "py_policy.h"
#include "pybind11/pybind11.h"
#include "pybind11/stl.h"
#include "fourdst/atomic/atomicSpecies.h"
#include "gridfire/reaction/reaction.h"
#include "gridfire/engine/engine.h"
#include "gridfire/policy/policy.h"
#include <string>
#include <set>
namespace py = pybind11;
std::string PyNetworkPolicy::name() const {
PYBIND11_OVERRIDE_PURE(
std::string,
gridfire::policy::NetworkPolicy,
name
);
}
const std::set<fourdst::atomic::Species>& PyNetworkPolicy::get_seed_species() const {
PYBIND11_OVERRIDE_PURE(
const std::set<fourdst::atomic::Species>&,
gridfire::policy::NetworkPolicy,
get_seed_species
);
}
const gridfire::reaction::ReactionSet& PyNetworkPolicy::get_seed_reactions() const {
PYBIND11_OVERRIDE_PURE(
const gridfire::reaction::ReactionSet&,
gridfire::policy::NetworkPolicy,
get_seed_reactions
);
}
gridfire::engine::DynamicEngine& PyNetworkPolicy::construct() {
PYBIND11_OVERRIDE_PURE(
gridfire::engine::DynamicEngine&,
gridfire::policy::NetworkPolicy,
construct
);
}
gridfire::policy::NetworkPolicyStatus PyNetworkPolicy::get_status() const {
PYBIND11_OVERRIDE_PURE(
gridfire::policy::NetworkPolicyStatus,
gridfire::policy::NetworkPolicy,
getStatus
);
}
const std::vector<std::unique_ptr<gridfire::engine::DynamicEngine>> &PyNetworkPolicy::get_engine_stack() const {
PYBIND11_OVERRIDE_PURE(
const std::vector<std::unique_ptr<gridfire::engine::DynamicEngine>> &,
gridfire::policy::NetworkPolicy,
get_engine_stack
);
}
std::vector<gridfire::engine::EngineTypes> PyNetworkPolicy::get_engine_types_stack() const {
PYBIND11_OVERRIDE_PURE(
std::vector<gridfire::engine::EngineTypes>,
gridfire::policy::NetworkPolicy,
get_engine_types_stack
);
}
const std::unique_ptr<gridfire::partition::PartitionFunction>& PyNetworkPolicy::get_partition_function() const {
PYBIND11_OVERRIDE_PURE(
const std::unique_ptr<gridfire::partition::PartitionFunction>&,
gridfire::policy::NetworkPolicy,
get_partition_function
);
}
const gridfire::reaction::ReactionSet &PyReactionChainPolicy::get_reactions() const {
PYBIND11_OVERRIDE_PURE(
const gridfire::reaction::ReactionSet &,
gridfire::policy::ReactionChainPolicy,
get_reactions
);
}
bool PyReactionChainPolicy::contains(const std::string &id) const {
PYBIND11_OVERRIDE_PURE(
bool,
gridfire::policy::ReactionChainPolicy,
contains,
id
);
}
bool PyReactionChainPolicy::contains(const gridfire::reaction::Reaction &reaction) const {
PYBIND11_OVERRIDE_PURE(
bool,
gridfire::policy::ReactionChainPolicy,
contains,
reaction
);
}
std::unique_ptr<gridfire::policy::ReactionChainPolicy> PyReactionChainPolicy::clone() const {
PYBIND11_OVERRIDE_PURE(
std::unique_ptr<gridfire::policy::ReactionChainPolicy>,
gridfire::policy::ReactionChainPolicy,
clone
);
}
std::string PyReactionChainPolicy::name() const {
PYBIND11_OVERRIDE_PURE(
std::string,
gridfire::policy::ReactionChainPolicy,
name
);
}
uint64_t PyReactionChainPolicy::hash(uint64_t seed) const {
PYBIND11_OVERRIDE_PURE(
uint64_t,
gridfire::policy::ReactionChainPolicy,
hash,
seed
);
}
bool PyReactionChainPolicy::operator==(const ReactionChainPolicy &other) const {
PYBIND11_OVERRIDE_PURE(
bool,
gridfire::policy::ReactionChainPolicy,
operator==,
other
);
}
bool PyReactionChainPolicy::operator!=(const ReactionChainPolicy &other) const {
PYBIND11_OVERRIDE_PURE(
bool,
gridfire::policy::ReactionChainPolicy,
operator!=,
other
);
}

44
src/python/policy/trampoline/py_policy.h Normal file
View File

@@ -0,0 +1,44 @@
#pragma once
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include "gridfire/policy/policy.h"
class PyNetworkPolicy final : public gridfire::policy::NetworkPolicy {
public:
[[nodiscard]] std::string name() const override;
[[nodiscard]] const std::set<fourdst::atomic::Species>& get_seed_species() const override;
[[nodiscard]] const gridfire::reaction::ReactionSet& get_seed_reactions() const override;
[[nodiscard]] gridfire::engine::DynamicEngine& construct() override;
[[nodiscard]] gridfire::policy::NetworkPolicyStatus get_status() const override;
[[nodiscard]] const std::vector<std::unique_ptr<gridfire::engine::DynamicEngine>> &get_engine_stack() const override;
[[nodiscard]] std::vector<gridfire::engine::EngineTypes> get_engine_types_stack() const override;
[[nodiscard]] const std::unique_ptr<gridfire::partition::PartitionFunction>& get_partition_function() const override;
};
class PyReactionChainPolicy final : public gridfire::policy::ReactionChainPolicy {
public:
[[nodiscard]] const gridfire::reaction::ReactionSet & get_reactions() const override;
[[nodiscard]] bool contains(const std::string &id) const override;
[[nodiscard]] bool contains(const gridfire::reaction::Reaction &reaction) const override;
[[nodiscard]] std::unique_ptr<ReactionChainPolicy> clone() const override;
[[nodiscard]] std::string name() const override;
[[nodiscard]] uint64_t hash(uint64_t seed) const override;
[[nodiscard]] bool operator==(const ReactionChainPolicy &other) const override;
[[nodiscard]] bool operator!=(const ReactionChainPolicy &other) const override;
};

38
src/python/solver/bindings.cpp
View File

@@ -1,12 +1,10 @@
#include <pybind11/pybind11.h> #include <pybind11/pybind11.h>
#include <pybind11/functional.h> // needed for std::function
#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings #include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc. if needed directly #include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc. if needed directly
#include <pybind11/numpy.h> #include <pybind11/numpy.h>
#include <pybind11/functional.h>
#include <functional> #include <functional>
#include <boost/numeric/ublas/vector.hpp>
#include "bindings.h" #include "bindings.h"
#include "gridfire/solver/strategies/CVODE_solver_strategy.h" #include "gridfire/solver/strategies/CVODE_solver_strategy.h"
@@ -37,7 +35,7 @@ void register_solver_bindings(const py::module &m) {
py_cvode_timestep_context.def_readonly("currentNonlinearIterations", &gridfire::solver::CVODESolverStrategy::TimestepContext::currentNonlinearIterations); py_cvode_timestep_context.def_readonly("currentNonlinearIterations", &gridfire::solver::CVODESolverStrategy::TimestepContext::currentNonlinearIterations);
py_cvode_timestep_context.def_property_readonly( py_cvode_timestep_context.def_property_readonly(
"engine", "engine",
[](const gridfire::solver::CVODESolverStrategy::TimestepContext& self) -> const gridfire::DynamicEngine& { [](const gridfire::solver::CVODESolverStrategy::TimestepContext& self) -> const gridfire::engine::DynamicEngine& {
return self.engine; return self.engine;
} }
); );
@@ -66,7 +64,7 @@ void register_solver_bindings(const py::module &m) {
auto py_cvode_solver_strategy = py::class_<gridfire::solver::CVODESolverStrategy, gridfire::solver::DynamicNetworkSolverStrategy>(m, "CVODESolverStrategy"); auto py_cvode_solver_strategy = py::class_<gridfire::solver::CVODESolverStrategy, gridfire::solver::DynamicNetworkSolverStrategy>(m, "CVODESolverStrategy");
py_cvode_solver_strategy.def( py_cvode_solver_strategy.def(
py::init<gridfire::DynamicEngine&>(), py::init<gridfire::engine::DynamicEngine&>(),
py::arg("engine"), py::arg("engine"),
"Initialize the CVODESolverStrategy object." "Initialize the CVODESolverStrategy object."
); );
@@ -75,7 +73,7 @@ void register_solver_bindings(const py::module &m) {
"evaluate", "evaluate",
py::overload_cast<const gridfire::NetIn&, bool>(&gridfire::solver::CVODESolverStrategy::evaluate), py::overload_cast<const gridfire::NetIn&, bool>(&gridfire::solver::CVODESolverStrategy::evaluate),
py::arg("netIn"), py::arg("netIn"),
py::arg("display_trigger"), py::arg("display_trigger") = false,
"evaluate the dynamic engine using the dynamic engine class" "evaluate the dynamic engine using the dynamic engine class"
); );
@@ -92,6 +90,32 @@ void register_solver_bindings(const py::module &m) {
"Enable logging to standard output." "Enable logging to standard output."
); );
py_cvode_solver_strategy.def(
"set_absTol",
&gridfire::solver::CVODESolverStrategy::set_absTol,
py::arg("absTol"),
"Set the absolute tolerance for the CVODE solver."
);
py_cvode_solver_strategy.def(
"set_relTol",
&gridfire::solver::CVODESolverStrategy::set_relTol,
py::arg("relTol"),
"Set the relative tolerance for the CVODE solver."
);
py_cvode_solver_strategy.def(
"get_absTol",
&gridfire::solver::CVODESolverStrategy::get_absTol,
"Get the absolute tolerance for the CVODE solver."
);
py_cvode_solver_strategy.def(
"get_relTol",
&gridfire::solver::CVODESolverStrategy::get_relTol,
"Get the relative tolerance for the CVODE solver."
);
py_cvode_solver_strategy.def( py_cvode_solver_strategy.def(
"set_callback", "set_callback",
[]( [](
@@ -103,7 +127,5 @@ void register_solver_bindings(const py::module &m) {
py::arg("cb"), py::arg("cb"),
"Set a callback function which will run at the end of every successful timestep" "Set a callback function which will run at the end of every successful timestep"
); );
} }

2
src/python/solver/trampoline/py_solver.h
View File

@@ -8,7 +8,7 @@
#include <any> #include <any>
class PyDynamicNetworkSolverStrategy final : public gridfire::solver::DynamicNetworkSolverStrategy { class PyDynamicNetworkSolverStrategy final : public gridfire::solver::DynamicNetworkSolverStrategy {
explicit PyDynamicNetworkSolverStrategy(gridfire::DynamicEngine &engine) : gridfire::solver::DynamicNetworkSolverStrategy(engine) {} explicit PyDynamicNetworkSolverStrategy(gridfire::engine::DynamicEngine &engine) : gridfire::solver::DynamicNetworkSolverStrategy(engine) {}
gridfire::NetOut evaluate(const gridfire::NetIn &netIn) override; gridfire::NetOut evaluate(const gridfire::NetIn &netIn) override;
void set_callback(const std::any &callback) override; void set_callback(const std::any &callback) override;
[[nodiscard]] std::vector<std::tuple<std::string, std::string>> describe_callback_context() const override; [[nodiscard]] std::vector<std::tuple<std::string, std::string>> describe_callback_context() const override;

2
src/python/types/bindings.cpp
View File

@@ -7,7 +7,7 @@
namespace py = pybind11; namespace py = pybind11;
#include "gridfire/network.h" #include "gridfire/types/types.h"
void register_type_bindings(const pybind11::module &m) { void register_type_bindings(const pybind11::module &m) {
py::class_<gridfire::NetIn>(m, "NetIn") py::class_<gridfire::NetIn>(m, "NetIn")

15
stubs/gridfire/__init__.pyi Normal file
View File

@@ -0,0 +1,15 @@
from __future__ import annotations
from gridfire._gridfire import engine
from gridfire._gridfire import exceptions
from gridfire._gridfire import io
from gridfire._gridfire import partition
from gridfire._gridfire import policy
from gridfire._gridfire import reaction
from gridfire._gridfire import screening
from gridfire._gridfire import solver
from gridfire._gridfire import type
from gridfire._gridfire import utils
import sys as sys
from . import _gridfire
__all__: list = ['type', 'utils', 'engine', 'solver', 'exceptions', 'partition', 'reaction', 'screening', 'io', 'core', 'cli']
__version__: str = 'v0.7.0_alpha_2025_10_25'

15
stubs/gridfire/_gridfire/__init__.pyi Normal file
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@@ -0,0 +1,15 @@
"""
Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.
"""
from __future__ import annotations
from . import engine
from . import exceptions
from . import io
from . import partition
from . import policy
from . import reaction
from . import screening
from . import solver
from . import type
from . import utils
__all__: list[str] = ['engine', 'exceptions', 'io', 'partition', 'policy', 'reaction', 'screening', 'solver', 'type', 'utils']

1170
stubs/gridfire/_gridfire/engine/__init__.pyi Normal file
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File diff suppressed because it is too large Load Diff

15
stubs/gridfire/_gridfire/engine/diagnostics.pyi Normal file
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@@ -0,0 +1,15 @@
"""
A submodule for engine diagnostics
"""
from __future__ import annotations
import collections.abc
import fourdst._phys.composition
import gridfire._gridfire.engine
import typing
__all__: list[str] = ['inspect_jacobian_stiffness', 'inspect_species_balance', 'report_limiting_species']
def inspect_jacobian_stiffness(engine: gridfire._gridfire.engine.DynamicEngine, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat, json: bool) -> ... | None:
...
def inspect_species_balance(engine: gridfire._gridfire.engine.DynamicEngine, species_name: str, comp: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat, json: bool) -> ... | None:
...
def report_limiting_species(engine: gridfire._gridfire.engine.DynamicEngine, Y_full: collections.abc.Sequence[typing.SupportsFloat], E_full: collections.abc.Sequence[typing.SupportsFloat], relTol: typing.SupportsFloat, absTol: typing.SupportsFloat, top_n: typing.SupportsInt, json: bool) -> ... | None:
...

59
stubs/gridfire/_gridfire/exceptions.pyi Normal file
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@@ -0,0 +1,59 @@
"""
GridFire exceptions bindings
"""
from __future__ import annotations
__all__: list[str] = ['BadCollectionError', 'BadRHSEngineError', 'CVODESolverFailureError', 'DebugException', 'EngineError', 'FailedToPartitionEngineError', 'GridFireError', 'HashingError', 'IllConditionedJacobianError', 'InvalidQSESolutionError', 'JacobianError', 'KINSolSolverFailureError', 'MissingBaseReactionError', 'MissingKeyReactionError', 'MissingSeedSpeciesError', 'NetworkResizedError', 'PolicyError', 'ReactionError', 'ReactionParsingError', 'SUNDIALSError', 'SingularJacobianError', 'SolverError', 'StaleJacobianError', 'UnableToSetNetworkReactionsError', 'UninitializedJacobianError', 'UnknownJacobianError', 'UtilityError']
class BadCollectionError(EngineError):
pass
class BadRHSEngineError(EngineError):
pass
class CVODESolverFailureError(SUNDIALSError):
pass
class DebugException(GridFireError):
pass
class EngineError(GridFireError):
pass
class FailedToPartitionEngineError(EngineError):
pass
class GridFireError(Exception):
pass
class HashingError(UtilityError):
pass
class IllConditionedJacobianError(SolverError):
pass
class InvalidQSESolutionError(EngineError):
pass
class JacobianError(EngineError):
pass
class KINSolSolverFailureError(SUNDIALSError):
pass
class MissingBaseReactionError(PolicyError):
pass
class MissingKeyReactionError(PolicyError):
pass
class MissingSeedSpeciesError(PolicyError):
pass
class NetworkResizedError(EngineError):
pass
class PolicyError(GridFireError):
pass
class ReactionError(GridFireError):
pass
class ReactionParsingError(ReactionError):
pass
class SUNDIALSError(SolverError):
pass
class SingularJacobianError(SolverError):
pass
class SolverError(GridFireError):
pass
class StaleJacobianError(JacobianError):
pass
class UnableToSetNetworkReactionsError(EngineError):
pass
class UninitializedJacobianError(JacobianError):
pass
class UnknownJacobianError(JacobianError):
pass
class UtilityError(GridFireError):
pass

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stubs/gridfire/_gridfire/io.pyi Normal file
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"""
GridFire io bindings
"""
from __future__ import annotations
__all__: list[str] = ['NetworkFileParser', 'ParsedNetworkData', 'SimpleReactionListFileParser']
class NetworkFileParser:
pass
class ParsedNetworkData:
pass
class SimpleReactionListFileParser(NetworkFileParser):
def parse(self, filename: str) -> ParsedNetworkData:
"""
Parse a simple reaction list file and return a ParsedNetworkData object.
"""

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stubs/gridfire/_gridfire/partition.pyi Normal file
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"""
GridFire partition function bindings
"""
from __future__ import annotations
import collections.abc
import typing
__all__: list[str] = ['BasePartitionType', 'CompositePartitionFunction', 'GroundState', 'GroundStatePartitionFunction', 'PartitionFunction', 'RauscherThielemann', 'RauscherThielemannPartitionDataRecord', 'RauscherThielemannPartitionFunction', 'basePartitionTypeToString', 'stringToBasePartitionType']
class BasePartitionType:
"""
Members:
RauscherThielemann
GroundState
"""
GroundState: typing.ClassVar[BasePartitionType] # value = <BasePartitionType.GroundState: 1>
RauscherThielemann: typing.ClassVar[BasePartitionType] # value = <BasePartitionType.RauscherThielemann: 0>
__members__: typing.ClassVar[dict[str, BasePartitionType]] # value = {'RauscherThielemann': <BasePartitionType.RauscherThielemann: 0>, 'GroundState': <BasePartitionType.GroundState: 1>}
def __eq__(self, other: typing.Any) -> bool:
...
def __getstate__(self) -> int:
...
def __hash__(self) -> int:
...
def __index__(self) -> int:
...
def __init__(self, value: typing.SupportsInt) -> None:
...
def __int__(self) -> int:
...
def __ne__(self, other: typing.Any) -> bool:
...
def __repr__(self) -> str:
...
def __setstate__(self, state: typing.SupportsInt) -> None:
...
def __str__(self) -> str:
...
@property
def name(self) -> str:
...
@property
def value(self) -> int:
...
class CompositePartitionFunction:
@typing.overload
def __init__(self, partitionFunctions: collections.abc.Sequence[BasePartitionType]) -> None:
"""
Create a composite partition function from a list of base partition types.
"""
@typing.overload
def __init__(self, arg0: CompositePartitionFunction) -> None:
"""
Copy constructor for CompositePartitionFunction.
"""
def evaluate(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the composite partition function for given Z, A, and T9.
"""
def evaluateDerivative(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the derivative of the composite partition function for given Z, A, and T9.
"""
def get_type(self) -> str:
"""
Get the type of the partition function (should return 'Composite').
"""
def supports(self, z: typing.SupportsInt, a: typing.SupportsInt) -> bool:
"""
Check if the composite partition function supports given Z and A.
"""
class GroundStatePartitionFunction(PartitionFunction):
def __init__(self) -> None:
...
def evaluate(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the ground state partition function for given Z, A, and T9.
"""
def evaluateDerivative(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the derivative of the ground state partition function for given Z, A, and T9.
"""
def get_type(self) -> str:
"""
Get the type of the partition function (should return 'GroundState').
"""
def supports(self, z: typing.SupportsInt, a: typing.SupportsInt) -> bool:
"""
Check if the ground state partition function supports given Z and A.
"""
class PartitionFunction:
pass
class RauscherThielemannPartitionDataRecord:
@property
def a(self) -> int:
"""
Mass number
"""
@property
def ground_state_spin(self) -> float:
"""
Ground state spin
"""
@property
def normalized_g_values(self) -> float:
"""
Normalized g-values for the first 24 energy levels
"""
@property
def z(self) -> int:
"""
Atomic number
"""
class RauscherThielemannPartitionFunction(PartitionFunction):
def __init__(self) -> None:
...
def evaluate(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the Rauscher-Thielemann partition function for given Z, A, and T9.
"""
def evaluateDerivative(self, z: typing.SupportsInt, a: typing.SupportsInt, T9: typing.SupportsFloat) -> float:
"""
Evaluate the derivative of the Rauscher-Thielemann partition function for given Z, A, and T9.
"""
def get_type(self) -> str:
"""
Get the type of the partition function (should return 'RauscherThielemann').
"""
def supports(self, z: typing.SupportsInt, a: typing.SupportsInt) -> bool:
"""
Check if the Rauscher-Thielemann partition function supports given Z and A.
"""
def basePartitionTypeToString(type: BasePartitionType) -> str:
"""
Convert BasePartitionType to string.
"""
def stringToBasePartitionType(typeStr: str) -> BasePartitionType:
"""
Convert string to BasePartitionType.
"""
GroundState: BasePartitionType # value = <BasePartitionType.GroundState: 1>
RauscherThielemann: BasePartitionType # value = <BasePartitionType.RauscherThielemann: 0>

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stubs/gridfire/_gridfire/policy.pyi Normal file
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"""
GridFire network policy bindings
"""
from __future__ import annotations
import collections.abc
import fourdst._phys.atomic
import fourdst._phys.composition
import gridfire._gridfire.engine
import gridfire._gridfire.reaction
import typing
__all__: list[str] = ['CNOChainPolicy', 'CNOIChainPolicy', 'CNOIIChainPolicy', 'CNOIIIChainPolicy', 'CNOIVChainPolicy', 'HotCNOChainPolicy', 'HotCNOIChainPolicy', 'HotCNOIIChainPolicy', 'HotCNOIIIChainPolicy', 'INITIALIZED_UNVERIFIED', 'INITIALIZED_VERIFIED', 'MISSING_KEY_REACTION', 'MISSING_KEY_SPECIES', 'MainSequencePolicy', 'MainSequenceReactionChainPolicy', 'MultiReactionChainPolicy', 'NetworkPolicy', 'NetworkPolicyStatus', 'ProtonProtonChainPolicy', 'ProtonProtonIChainPolicy', 'ProtonProtonIIChainPolicy', 'ProtonProtonIIIChainPolicy', 'ReactionChainPolicy', 'TemperatureDependentChainPolicy', 'TripleAlphaChainPolicy', 'UNINITIALIZED']
class CNOChainPolicy(MultiReactionChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class CNOIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class CNOIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class CNOIIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class CNOIVChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class HotCNOChainPolicy(MultiReactionChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class HotCNOIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class HotCNOIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class HotCNOIIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class MainSequencePolicy(NetworkPolicy):
@typing.overload
def __init__(self, composition: fourdst._phys.composition.Composition) -> None:
"""
Construct MainSequencePolicy from an existing composition.
"""
@typing.overload
def __init__(self, seed_species: collections.abc.Sequence[fourdst._phys.atomic.Species], mass_fractions: collections.abc.Sequence[typing.SupportsFloat]) -> None:
"""
Construct MainSequencePolicy from seed species and mass fractions.
"""
def construct(self) -> gridfire._gridfire.engine.DynamicEngine:
"""
Construct the network according to the policy.
"""
def get_engine_types_stack(self) -> list[gridfire._gridfire.engine.EngineTypes]:
"""
Get the types of engines in the stack constructed by the network policy.
"""
def get_seed_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the set of seed reactions required by the network policy.
"""
def get_seed_species(self) -> set[fourdst._phys.atomic.Species]:
"""
Get the set of seed species required by the network policy.
"""
def get_status(self) -> NetworkPolicyStatus:
"""
Get the current status of the network policy.
"""
def name(self) -> str:
"""
Get the name of the network policy.
"""
class MainSequenceReactionChainPolicy(MultiReactionChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class MultiReactionChainPolicy(ReactionChainPolicy):
pass
class NetworkPolicy:
pass
class NetworkPolicyStatus:
"""
Members:
UNINITIALIZED
INITIALIZED_UNVERIFIED
MISSING_KEY_REACTION
MISSING_KEY_SPECIES
INITIALIZED_VERIFIED
"""
INITIALIZED_UNVERIFIED: typing.ClassVar[NetworkPolicyStatus] # value = <NetworkPolicyStatus.INITIALIZED_UNVERIFIED: 1>
INITIALIZED_VERIFIED: typing.ClassVar[NetworkPolicyStatus] # value = <NetworkPolicyStatus.INITIALIZED_VERIFIED: 4>
MISSING_KEY_REACTION: typing.ClassVar[NetworkPolicyStatus] # value = <NetworkPolicyStatus.MISSING_KEY_REACTION: 2>
MISSING_KEY_SPECIES: typing.ClassVar[NetworkPolicyStatus] # value = <NetworkPolicyStatus.MISSING_KEY_SPECIES: 3>
UNINITIALIZED: typing.ClassVar[NetworkPolicyStatus] # value = <NetworkPolicyStatus.UNINITIALIZED: 0>
__members__: typing.ClassVar[dict[str, NetworkPolicyStatus]] # value = {'UNINITIALIZED': <NetworkPolicyStatus.UNINITIALIZED: 0>, 'INITIALIZED_UNVERIFIED': <NetworkPolicyStatus.INITIALIZED_UNVERIFIED: 1>, 'MISSING_KEY_REACTION': <NetworkPolicyStatus.MISSING_KEY_REACTION: 2>, 'MISSING_KEY_SPECIES': <NetworkPolicyStatus.MISSING_KEY_SPECIES: 3>, 'INITIALIZED_VERIFIED': <NetworkPolicyStatus.INITIALIZED_VERIFIED: 4>}
def __eq__(self, other: typing.Any) -> bool:
...
def __getstate__(self) -> int:
...
def __hash__(self) -> int:
...
def __index__(self) -> int:
...
def __init__(self, value: typing.SupportsInt) -> None:
...
def __int__(self) -> int:
...
def __ne__(self, other: typing.Any) -> bool:
...
def __repr__(self) -> str:
...
def __setstate__(self, state: typing.SupportsInt) -> None:
...
def __str__(self) -> str:
...
@property
def name(self) -> str:
...
@property
def value(self) -> int:
...
class ProtonProtonChainPolicy(MultiReactionChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class ProtonProtonIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class ProtonProtonIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class ProtonProtonIIIChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
class ReactionChainPolicy:
pass
class TemperatureDependentChainPolicy(ReactionChainPolicy):
pass
class TripleAlphaChainPolicy(TemperatureDependentChainPolicy):
def __eq__(self, other: ReactionChainPolicy) -> bool:
"""
Check equality with another ReactionChainPolicy.
"""
def __hash__(self) -> int:
...
def __init__(self) -> None:
...
def __ne__(self, other: ReactionChainPolicy) -> bool:
"""
Check inequality with another ReactionChainPolicy.
"""
def __repr__(self) -> str:
...
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the reaction chain contains a reaction with the given ID.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the reaction chain contains the given reaction.
"""
def get_reactions(self) -> gridfire._gridfire.reaction.ReactionSet:
"""
Get the ReactionSet representing this reaction chain.
"""
def hash(self, seed: typing.SupportsInt) -> int:
"""
Compute a hash value for the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
@typing.overload
def name(self) -> str:
"""
Get the name of the reaction chain policy.
"""
INITIALIZED_UNVERIFIED: NetworkPolicyStatus # value = <NetworkPolicyStatus.INITIALIZED_UNVERIFIED: 1>
INITIALIZED_VERIFIED: NetworkPolicyStatus # value = <NetworkPolicyStatus.INITIALIZED_VERIFIED: 4>
MISSING_KEY_REACTION: NetworkPolicyStatus # value = <NetworkPolicyStatus.MISSING_KEY_REACTION: 2>
MISSING_KEY_SPECIES: NetworkPolicyStatus # value = <NetworkPolicyStatus.MISSING_KEY_SPECIES: 3>
UNINITIALIZED: NetworkPolicyStatus # value = <NetworkPolicyStatus.UNINITIALIZED: 0>

249
stubs/gridfire/_gridfire/reaction.pyi Normal file
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"""
GridFire reaction bindings
"""
from __future__ import annotations
import collections.abc
import fourdst._phys.atomic
import fourdst._phys.composition
import typing
__all__: list[str] = ['LogicalReaclibReaction', 'RateCoefficientSet', 'ReaclibReaction', 'ReactionSet', 'get_all_reactions', 'packReactionSet']
class LogicalReaclibReaction(ReaclibReaction):
@typing.overload
def __init__(self, reactions: collections.abc.Sequence[ReaclibReaction]) -> None:
"""
Construct a LogicalReaclibReaction from a vector of ReaclibReaction objects.
"""
@typing.overload
def __init__(self, reactions: collections.abc.Sequence[ReaclibReaction], is_reverse: bool) -> None:
"""
Construct a LogicalReaclibReaction from a vector of ReaclibReaction objects.
"""
def __len__(self) -> int:
"""
Overload len() to return the number of source rates.
"""
def add_reaction(self, reaction: ReaclibReaction) -> None:
"""
Add another Reaction source to this logical reaction.
"""
def calculate_forward_rate_log_derivative(self, T9: typing.SupportsFloat, rho: typing.SupportsFloat, Ye: typing.SupportsFloat, mue: typing.SupportsFloat, Composition: fourdst._phys.composition.Composition) -> float:
"""
Calculate the forward rate log derivative at a given temperature T9 (in units of 10^9 K).
"""
def calculate_rate(self, T9: typing.SupportsFloat, rho: typing.SupportsFloat, Ye: typing.SupportsFloat, mue: typing.SupportsFloat, Y: collections.abc.Sequence[typing.SupportsFloat], index_to_species_map: collections.abc.Mapping[typing.SupportsInt, fourdst._phys.atomic.Species]) -> float:
"""
Calculate the reaction rate at a given temperature T9 (in units of 10^9 K). Note that for a reaclib reaction only T9 is actually used, all other parameters are there for interface compatibility.
"""
def size(self) -> int:
"""
Get the number of source rates contributing to this logical reaction.
"""
def sources(self) -> list[str]:
"""
Get the list of source labels for the aggregated rates.
"""
class RateCoefficientSet:
def __init__(self, a0: typing.SupportsFloat, a1: typing.SupportsFloat, a2: typing.SupportsFloat, a3: typing.SupportsFloat, a4: typing.SupportsFloat, a5: typing.SupportsFloat, a6: typing.SupportsFloat) -> None:
"""
Construct a RateCoefficientSet with the given parameters.
"""
class ReaclibReaction:
__hash__: typing.ClassVar[None] = None
def __eq__(self, arg0: ReaclibReaction) -> bool:
"""
Equality operator for reactions based on their IDs.
"""
def __init__(self, id: str, peName: str, chapter: typing.SupportsInt, reactants: collections.abc.Sequence[fourdst._phys.atomic.Species], products: collections.abc.Sequence[fourdst._phys.atomic.Species], qValue: typing.SupportsFloat, label: str, sets: RateCoefficientSet, reverse: bool = False) -> None:
"""
Construct a Reaction with the given parameters.
"""
def __neq__(self, arg0: ReaclibReaction) -> bool:
"""
Inequality operator for reactions based on their IDs.
"""
def __repr__(self) -> str:
...
def all_species(self) -> set[fourdst._phys.atomic.Species]:
"""
Get all species involved in the reaction (both reactants and products) as a set.
"""
def calculate_rate(self, T9: typing.SupportsFloat, rho: typing.SupportsFloat, Y: collections.abc.Sequence[typing.SupportsFloat]) -> float:
"""
Calculate the reaction rate at a given temperature T9 (in units of 10^9 K).
"""
def chapter(self) -> int:
"""
Get the REACLIB chapter number defining the reaction structure.
"""
def contains(self, species: fourdst._phys.atomic.Species) -> bool:
"""
Check if the reaction contains a specific species.
"""
def contains_product(self, arg0: fourdst._phys.atomic.Species) -> bool:
"""
Check if the reaction contains a specific product species.
"""
def contains_reactant(self, arg0: fourdst._phys.atomic.Species) -> bool:
"""
Check if the reaction contains a specific reactant species.
"""
def excess_energy(self) -> float:
"""
Calculate the excess energy from the mass difference of reactants and products.
"""
def hash(self, seed: typing.SupportsInt = 0) -> int:
"""
Compute a hash for the reaction based on its ID.
"""
def id(self) -> str:
"""
Get the unique identifier of the reaction.
"""
def is_reverse(self) -> bool:
"""
Check if this is a reverse reaction rate.
"""
def num_species(self) -> int:
"""
Count the number of species in the reaction.
"""
def peName(self) -> str:
"""
Get the reaction name in (projectile, ejectile) notation (e.g., 'p(p,g)d').
"""
def product_species(self) -> set[fourdst._phys.atomic.Species]:
"""
Get the product species of the reaction as a set.
"""
def products(self) -> list[fourdst._phys.atomic.Species]:
"""
Get a list of product species in the reaction.
"""
def qValue(self) -> float:
"""
Get the Q-value of the reaction in MeV.
"""
def rateCoefficients(self) -> RateCoefficientSet:
"""
get the set of rate coefficients.
"""
def reactant_species(self) -> set[fourdst._phys.atomic.Species]:
"""
Get the reactant species of the reaction as a set.
"""
def reactants(self) -> list[fourdst._phys.atomic.Species]:
"""
Get a list of reactant species in the reaction.
"""
def sourceLabel(self) -> str:
"""
Get the source label for the rate data (e.g., 'wc12w', 'st08').
"""
@typing.overload
def stoichiometry(self, species: fourdst._phys.atomic.Species) -> int:
"""
Get the stoichiometry of the reaction as a map from species to their coefficients.
"""
@typing.overload
def stoichiometry(self) -> dict[fourdst._phys.atomic.Species, int]:
"""
Get the stoichiometry of the reaction as a map from species to their coefficients.
"""
class ReactionSet:
__hash__: typing.ClassVar[None] = None
@staticmethod
def from_clones(reactions: collections.abc.Sequence[...]) -> ReactionSet:
"""
Create a ReactionSet that takes ownership of the reactions by cloning the input reactions.
"""
def __eq__(self, LogicalReactionSet: ReactionSet) -> bool:
"""
Equality operator for LogicalReactionSets based on their contents.
"""
def __getitem__(self, index: typing.SupportsInt) -> ...:
"""
Get a LogicalReaclibReaction by index.
"""
def __getitem___(self, id: str) -> ...:
"""
Get a LogicalReaclibReaction by its ID.
"""
@typing.overload
def __init__(self, reactions: collections.abc.Sequence[...]) -> None:
"""
Construct a LogicalReactionSet from a vector of LogicalReaclibReaction objects.
"""
@typing.overload
def __init__(self) -> None:
"""
Default constructor for an empty LogicalReactionSet.
"""
@typing.overload
def __init__(self, other: ReactionSet) -> None:
"""
Copy constructor for LogicalReactionSet.
"""
def __len__(self) -> int:
"""
Overload len() to return the number of LogicalReactions.
"""
def __ne__(self, LogicalReactionSet: ReactionSet) -> bool:
"""
Inequality operator for LogicalReactionSets based on their contents.
"""
def __repr__(self) -> str:
...
def add_reaction(self, reaction: ...) -> None:
"""
Add a LogicalReaclibReaction to the set.
"""
def clear(self) -> None:
"""
Remove all LogicalReactions from the set.
"""
@typing.overload
def contains(self, id: str) -> bool:
"""
Check if the set contains a specific LogicalReaclibReaction.
"""
@typing.overload
def contains(self, reaction: ...) -> bool:
"""
Check if the set contains a specific Reaction.
"""
def contains_product(self, species: fourdst._phys.atomic.Species) -> bool:
"""
Check if any reaction in the set has the species as a product.
"""
def contains_reactant(self, species: fourdst._phys.atomic.Species) -> bool:
"""
Check if any reaction in the set has the species as a reactant.
"""
def contains_species(self, species: fourdst._phys.atomic.Species) -> bool:
"""
Check if any reaction in the set involves the given species.
"""
def getReactionSetSpecies(self) -> set[fourdst._phys.atomic.Species]:
"""
Get all species involved in the reactions of the set as a set of Species objects.
"""
def hash(self, seed: typing.SupportsInt = 0) -> int:
"""
Compute a hash for the LogicalReactionSet based on its contents.
"""
def remove_reaction(self, reaction: ...) -> None:
"""
Remove a LogicalReaclibReaction from the set.
"""
def size(self) -> int:
"""
Get the number of LogicalReactions in the set.
"""
def get_all_reactions() -> ReactionSet:
"""
Get all reactions from the REACLIB database.
"""
def packReactionSet(reactionSet: ReactionSet) -> ReactionSet:
"""
Convert a ReactionSet to a LogicalReactionSet by aggregating reactions with the same peName.
"""

68
stubs/gridfire/_gridfire/screening.pyi Normal file
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"""
GridFire plasma screening bindings
"""
from __future__ import annotations
import collections.abc
import fourdst._phys.atomic
import gridfire._gridfire.reaction
import typing
__all__: list[str] = ['BARE', 'BareScreeningModel', 'ScreeningModel', 'ScreeningType', 'WEAK', 'WeakScreeningModel', 'selectScreeningModel']
class BareScreeningModel:
def __init__(self) -> None:
...
def calculateScreeningFactors(self, reactions: gridfire._gridfire.reaction.ReactionSet, species: collections.abc.Sequence[fourdst._phys.atomic.Species], Y: collections.abc.Sequence[typing.SupportsFloat], T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> list[float]:
"""
Calculate the bare plasma screening factors. This always returns 1.0 (bare)
"""
class ScreeningModel:
pass
class ScreeningType:
"""
Members:
BARE
WEAK
"""
BARE: typing.ClassVar[ScreeningType] # value = <ScreeningType.BARE: 0>
WEAK: typing.ClassVar[ScreeningType] # value = <ScreeningType.WEAK: 1>
__members__: typing.ClassVar[dict[str, ScreeningType]] # value = {'BARE': <ScreeningType.BARE: 0>, 'WEAK': <ScreeningType.WEAK: 1>}
def __eq__(self, other: typing.Any) -> bool:
...
def __getstate__(self) -> int:
...
def __hash__(self) -> int:
...
def __index__(self) -> int:
...
def __init__(self, value: typing.SupportsInt) -> None:
...
def __int__(self) -> int:
...
def __ne__(self, other: typing.Any) -> bool:
...
def __repr__(self) -> str:
...
def __setstate__(self, state: typing.SupportsInt) -> None:
...
def __str__(self) -> str:
...
@property
def name(self) -> str:
...
@property
def value(self) -> int:
...
class WeakScreeningModel:
def __init__(self) -> None:
...
def calculateScreeningFactors(self, reactions: gridfire._gridfire.reaction.ReactionSet, species: collections.abc.Sequence[fourdst._phys.atomic.Species], Y: collections.abc.Sequence[typing.SupportsFloat], T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> list[float]:
"""
Calculate the weak plasma screening factors using the Salpeter (1954) model.
"""
def selectScreeningModel(type: ScreeningType) -> ScreeningModel:
"""
Select a screening model based on the specified type. Returns a pointer to the selected model.
"""
BARE: ScreeningType # value = <ScreeningType.BARE: 0>
WEAK: ScreeningType # value = <ScreeningType.WEAK: 1>

92
stubs/gridfire/_gridfire/solver.pyi Normal file
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"""
GridFire numerical solver bindings
"""
from __future__ import annotations
import collections.abc
import fourdst._phys.atomic
import gridfire._gridfire.engine
import gridfire._gridfire.type
import typing
__all__: list[str] = ['CVODESolverStrategy', 'CVODETimestepContext', 'DynamicNetworkSolverStrategy', 'SolverContextBase']
class CVODESolverStrategy(DynamicNetworkSolverStrategy):
def __init__(self, engine: gridfire._gridfire.engine.DynamicEngine) -> None:
"""
Initialize the CVODESolverStrategy object.
"""
def evaluate(self, netIn: gridfire._gridfire.type.NetIn, display_trigger: bool = False) -> gridfire._gridfire.type.NetOut:
"""
evaluate the dynamic engine using the dynamic engine class
"""
def get_absTol(self) -> float:
"""
Get the absolute tolerance for the CVODE solver.
"""
def get_relTol(self) -> float:
"""
Get the relative tolerance for the CVODE solver.
"""
def get_stdout_logging_enabled(self) -> bool:
"""
Check if solver logging to standard output is enabled.
"""
def set_absTol(self, absTol: typing.SupportsFloat) -> None:
"""
Set the absolute tolerance for the CVODE solver.
"""
def set_callback(self, cb: collections.abc.Callable[[CVODETimestepContext], None]) -> None:
"""
Set a callback function which will run at the end of every successful timestep
"""
def set_relTol(self, relTol: typing.SupportsFloat) -> None:
"""
Set the relative tolerance for the CVODE solver.
"""
def set_stdout_logging_enabled(self, logging_enabled: bool) -> None:
"""
Enable logging to standard output.
"""
class CVODETimestepContext(SolverContextBase):
@property
def T9(self) -> float:
...
@property
def currentConvergenceFailures(self) -> int:
...
@property
def currentNonlinearIterations(self) -> int:
...
@property
def dt(self) -> float:
...
@property
def engine(self) -> gridfire._gridfire.engine.DynamicEngine:
...
@property
def last_step_time(self) -> float:
...
@property
def networkSpecies(self) -> list[fourdst._phys.atomic.Species]:
...
@property
def num_steps(self) -> int:
...
@property
def rho(self) -> float:
...
@property
def state(self) -> list[float]:
...
@property
def t(self) -> float:
...
class DynamicNetworkSolverStrategy:
def describe_callback_context(self) -> list[tuple[str, str]]:
"""
Get a structure representing what data is in the callback context in a human readable format
"""
def evaluate(self, netIn: gridfire._gridfire.type.NetIn) -> gridfire._gridfire.type.NetOut:
"""
evaluate the dynamic engine using the dynamic engine class
"""
class SolverContextBase:
pass

61
stubs/gridfire/_gridfire/type.pyi Normal file
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"""
GridFire type bindings
"""
from __future__ import annotations
import fourdst._phys.composition
import typing
__all__: list[str] = ['NetIn', 'NetOut']
class NetIn:
composition: fourdst._phys.composition.Composition
def __init__(self) -> None:
...
def __repr__(self) -> str:
...
@property
def density(self) -> float:
...
@density.setter
def density(self, arg0: typing.SupportsFloat) -> None:
...
@property
def dt0(self) -> float:
...
@dt0.setter
def dt0(self, arg0: typing.SupportsFloat) -> None:
...
@property
def energy(self) -> float:
...
@energy.setter
def energy(self, arg0: typing.SupportsFloat) -> None:
...
@property
def tMax(self) -> float:
...
@tMax.setter
def tMax(self, arg0: typing.SupportsFloat) -> None:
...
@property
def temperature(self) -> float:
...
@temperature.setter
def temperature(self, arg0: typing.SupportsFloat) -> None:
...
class NetOut:
def __repr__(self) -> str:
...
@property
def composition(self) -> fourdst._phys.composition.Composition:
...
@property
def dEps_dRho(self) -> float:
...
@property
def dEps_dT(self) -> float:
...
@property
def energy(self) -> float:
...
@property
def num_steps(self) -> int:
...

17
stubs/gridfire/_gridfire/utils/__init__.pyi Normal file
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"""
GridFire utility method bindings
"""
from __future__ import annotations
import fourdst._phys.composition
import gridfire._gridfire.engine
import typing
from . import hashing
__all__: list[str] = ['formatNuclearTimescaleLogString', 'hash_atomic', 'hash_reaction', 'hashing']
def formatNuclearTimescaleLogString(engine: gridfire._gridfire.engine.DynamicEngine, Y: fourdst._phys.composition.Composition, T9: typing.SupportsFloat, rho: typing.SupportsFloat) -> str:
"""
Format a string for logging nuclear timescales based on temperature, density, and energy generation rate.
"""
def hash_atomic(a: typing.SupportsInt, z: typing.SupportsInt) -> int:
...
def hash_reaction(reaction: ...) -> int:
...

6
stubs/gridfire/_gridfire/utils/hashing/__init__.pyi Normal file
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@@ -0,0 +1,6 @@
"""
module for gridfire hashing functions
"""
from __future__ import annotations
from . import reaction
__all__: list[str] = ['reaction']

12
stubs/gridfire/_gridfire/utils/hashing/reaction.pyi Normal file
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@@ -0,0 +1,12 @@
"""
utility module for hashing gridfire reaction functions
"""
from __future__ import annotations
import typing
__all__: list[str] = ['mix_species', 'multiset_combine', 'splitmix64']
def mix_species(a: typing.SupportsInt, z: typing.SupportsInt) -> int:
...
def multiset_combine(acc: typing.SupportsInt, x: typing.SupportsInt) -> int:
...
def splitmix64(x: typing.SupportsInt) -> int:
...

2
subprojects/fourdst.wrap
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@@ -1,4 +1,4 @@
[wrap-git] [wrap-git]
url = https://github.com/4D-STAR/fourdst url = https://github.com/4D-STAR/fourdst
revision = v0.9.5 revision = v0.9.6
depth = 1 depth = 1

4
tests/graphnet_sandbox/main.cpp
View File

@@ -270,6 +270,10 @@ int main(int argc, char** argv) {
CLI11_PARSE(app, argc, argv); CLI11_PARSE(app, argc, argv);
const NetIn netIn = init(temp, rho, tMax); const NetIn netIn = init(temp, rho, tMax);
std::println("Starting Integration with T = {} K, ρ = {} g/cm³, tMax = {} s", temp, rho, tMax);
std::println("Composition is: {}", utils::iterable_to_delimited_string(netIn.composition, ", ", [&netIn](std::pair<const fourdst::atomic::Species&, double> arg) {
return std::format("{:5}: {:10.4E}", arg.first.name(), arg.second);
}));
policy::MainSequencePolicy stellarPolicy(netIn.composition); policy::MainSequencePolicy stellarPolicy(netIn.composition);
stellarPolicy.construct(); stellarPolicy.construct();

95
validation/pynucastro/GridFireEquiv/GridFireEvolve.py Normal file
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@@ -0,0 +1,95 @@
from fourdst.composition import Composition
from gridfire.type import NetIn
from gridfire.policy import MainSequencePolicy
from gridfire.solver import CVODESolverStrategy
from enum import Enum
from typing import Dict, Union, SupportsFloat
import json
import dicttoxml
def init_composition() -> Composition:
Y = [7.0262E-01, 9.7479E-06, 6.8955E-02, 2.5000E-04, 7.8554E-05, 6.0144E-04, 8.1031E-05, 2.1513E-05]
S = ["H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"]
return Composition(S, Y)
def init_netIn(temp: float, rho: float, time: float, comp: Composition) -> NetIn:
netIn = NetIn()
netIn.temperature = temp
netIn.density = rho
netIn.tMax = time
netIn.dt0 = 1e-12
netIn.composition = comp
return netIn
class StepData(Enum):
TIME = 0
DT = 1
COMP = 2
CONTRIB = 3
class StepLogger:
def __init__(self):
self.num_steps: int = 0
self.step_data: Dict[int, Dict[StepData, Union[SupportsFloat, Dict[str, SupportsFloat]]]] = {}
def log_step(self, context):
engine = context.engine
self.step_data[self.num_steps] = {}
self.step_data[self.num_steps][StepData.TIME] = context.t
self.step_data[self.num_steps][StepData.DT] = context.dt
comp_data: Dict[str, SupportsFloat] = {}
for species in engine.getNetworkSpecies():
sid = engine.getSpeciesIndex(species)
comp_data[species.name()] = context.state[sid]
self.step_data[self.num_steps][StepData.COMP] = comp_data
self.num_steps += 1
def to_json (self, filename: str):
serializable_data = {
stepNum: {
StepData.TIME.name: step[StepData.TIME],
StepData.DT.name: step[StepData.DT],
StepData.COMP.name: step[StepData.COMP],
}
for stepNum, step in self.step_data.items()
}
with open(filename, 'w') as f:
json.dump(serializable_data, f, indent=4)
def to_xml(self, filename: str):
serializable_data = {
stepNum: {
StepData.TIME.name: step[StepData.TIME],
StepData.DT.name: step[StepData.DT],
StepData.COMP.name: step[StepData.COMP],
}
for stepNum, step in self.step_data.items()
}
xml_data = dicttoxml.dicttoxml(serializable_data, custom_root='StepLog', attr_type=False)
with open(filename, 'wb') as f:
f.write(xml_data)
def main(temp: float, rho: float, time: float):
comp = init_composition()
netIn = init_netIn(temp, rho, time, comp)
policy = MainSequencePolicy(comp)
engine = policy.construct()
solver = CVODESolverStrategy(engine)
step_logger = StepLogger()
solver.set_callback(lambda context: step_logger.log_step(context))
solver.evaluate(netIn, False)
step_logger.to_xml("log_data.xml")
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Simple python example of GridFire usage")
parser.add_argument("-t", "--temp", type=float, help="Temperature in K", default=1.5e7)
parser.add_argument("-r", "--rho", type=float, help="Density in g/cm^3", default=1.5e2)
parser.add_argument("--tMax", type=float, help="Time in s", default=3.1536 * 1e17)
args = parser.parse_args()
main(args.temp, args.rho, args.tMax)