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

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The python bindings now work with the polymorphic reaction class and the CVODE solver
This commit is contained in:
Emily Boudreaux
2025-10-30 15:05:08 -04:00
parent 23df87f915
commit 7fded59814
27 changed files with 962 additions and 255 deletions
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54
src/python/reaction/bindings.cpp
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@@ -48,7 +48,7 @@ void register_reaction_bindings(py::module &m) {
.def(
"calculate_rate",
[](const gridfire::reaction::ReaclibReaction& self, const double T9, const double rho, const std::vector<double>& Y) -> double {
return self.calculate_rate(T9, rho, 0, TODO, Y, TODO);
return self.calculate_rate(T9, rho, 0, {}, Y, {});
},
py::arg("T9"),
py::arg("rho"),
@@ -183,9 +183,15 @@ void register_reaction_bindings(py::module &m) {
py::class_<gridfire::reaction::LogicalReaclibReaction, gridfire::reaction::ReaclibReaction>(m, "LogicalReaclibReaction")
.def(
py::init<const std::vector<gridfire::reaction::Reaction>>(),
py::init<const std::vector<gridfire::reaction::ReaclibReaction>>(),
py::arg("reactions"),
"Construct a LogicalReaclibReaction from a vector of Reaction objects."
"Construct a LogicalReaclibReaction from a vector of ReaclibReaction objects."
)
.def(
py::init<const std::vector<gridfire::reaction::ReaclibReaction>, bool>(),
py::arg("reactions"),
py::arg("is_reverse"),
"Construct a LogicalReaclibReaction from a vector of ReaclibReaction objects."
)
.def(
"add_reaction",
@@ -210,26 +216,56 @@ void register_reaction_bindings(py::module &m) {
)
.def(
"calculate_rate",
[](const gridfire::reaction::LogicalReaclibReaction& self, const double T9, const double rho, const std::vector<double>& Y) -> double {
return self.calculate_rate(T9, rho, 0, TODO, Y, TODO);
[](
const gridfire::reaction::LogicalReaclibReaction& self,
const double T9,
const double rho,
const double Ye,
const double mue,
const std::vector<double>& Y,
const std::unordered_map<size_t, Species>& index_to_species_map
) -> double {
return self.calculate_rate(T9, rho, Ye, mue, Y, index_to_species_map);
},
py::arg("T9"),
"Calculate the reaction rate at a given temperature T9 (in units of 10^9 K)."
py::arg("rho"),
py::arg("Ye"),
py::arg("mue"),
py::arg("Y"),
py::arg("index_to_species_map"),
"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(
"calculate_forward_rate_log_derivative",
&gridfire::reaction::LogicalReaclibReaction::calculate_forward_rate_log_derivative,
&gridfire::reaction::LogicalReaclibReaction::calculate_log_rate_partial_deriv_wrt_T9,
py::arg("T9"),
py::arg("rho"),
py::arg("Ye"),
py::arg("mue"),
py::arg("Composition"),
"Calculate the forward rate log derivative at a given temperature T9 (in units of 10^9 K)."
);
py::class_<gridfire::reaction::ReactionSet>(m, "ReactionSet")
// TODO: Fix the constructor to accept a vector of unique ptrs to Reaclib Reactions
.def(
py::init<const std::vector<gridfire::reaction::Reaction>>(),
py::init<const std::vector<gridfire::reaction::Reaction*>>(),
py::arg("reactions"),
py::keep_alive<1, 2>(), // Keep arg 2 (reactions) alive as long as arg 1 (self) is alive. This helps mitigate use-after-free errors
"Construct a LogicalReactionSet from a vector of LogicalReaclibReaction objects."
)
.def_static(
"from_clones",
[](const std::vector<gridfire::reaction::Reaction*>& py_reactions) {
std::vector<std::unique_ptr<gridfire::reaction::Reaction>> cpp_reactions;
cpp_reactions.reserve(py_reactions.size());
for (const auto& reaction : py_reactions) {
cpp_reactions.emplace_back(reaction->clone());
}
return std::make_unique<gridfire::reaction::ReactionSet>(std::move(cpp_reactions));
},
py::arg("reactions"),
"Create a ReactionSet that takes ownership of the reactions by cloning the input reactions."
)
.def(
py::init<>(),
"Default constructor for an empty LogicalReactionSet."