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feat(bindings): ported most bindings over from serif

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Emily Boudreaux
2025-07-22 13:51:43 -04:00
parent 706f47f807
commit dd0025232a
28 changed files with 1252 additions and 0 deletions
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163
src-pybind/composition/bindings.cpp Normal file
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#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 <string>
#include "fourdst/composition/composition.h"
#include "fourdst/composition/atomicSpecies.h"
#include "bindings.h"
#include "fourdst/composition/species.h"
namespace py = pybind11;
std::string sv_to_string(std::string_view sv) {
return std::string(sv);
}
std::string get_ostream_str(const fourdst::composition::Composition& comp) {
std::ostringstream oss;
oss << comp;
return oss.str();
}
void register_comp_bindings(pybind11::module &comp_submodule) {
// --- Bindings for composition and species module ---
py::class_<fourdst::composition::GlobalComposition>(comp_submodule, "GlobalComposition")
.def_readonly("specificNumberDensity", &fourdst::composition::GlobalComposition::specificNumberDensity)
.def_readonly("meanParticleMass", &fourdst::composition::GlobalComposition::meanParticleMass)
.def("__repr__", // Add a string representation for easy printing in Python
[](const fourdst::composition::GlobalComposition &gc) {
return "<GlobalComposition(specNumDens=" + std::to_string(gc.specificNumberDensity) +
", meanMass=" + std::to_string(gc.meanParticleMass) + ")>";
});
py::class_<fourdst::composition::CompositionEntry>(comp_submodule, "CompositionEntry")
.def("symbol", &fourdst::composition::CompositionEntry::symbol)
.def("mass_fraction",
py::overload_cast<>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
"Gets the mass fraction of the species.")
.def("mass_fraction",
py::overload_cast<double>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
py::arg("meanMolarMass"), // Name the argument in Python
"Gets the mass fraction of the species given the mean molar mass.")
.def("number_fraction",
py::overload_cast<>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
"Gets the number fraction of the species.")
.def("number_fraction",
py::overload_cast<double>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
py::arg("totalMoles"),
"Gets the number fraction of the species given the total moles.")
.def("rel_abundance", &fourdst::composition::CompositionEntry::rel_abundance)
.def("isotope", &fourdst::composition::CompositionEntry::isotope) // Assuming Species is bound or convertible
.def("getMassFracMode", &fourdst::composition::CompositionEntry::getMassFracMode)
.def("__repr__", // Optional: nice string representation
[](const fourdst::composition::CompositionEntry &ce) {
// You might want to include more info here now
return "<CompositionEntry(symbol='" + ce.symbol() + "', " +
"mass_frac=" + std::to_string(ce.mass_fraction()) + ", " +
"num_frac=" + std::to_string(ce.number_fraction()) + ")>";
});
// --- Binding for the main Composition class ---
py::class_<fourdst::composition::Composition>(comp_submodule, "Composition")
// Constructors
.def(py::init<>(), "Default constructor")
.def(py::init<const std::vector<std::string>&>(),
py::arg("symbols"),
"Constructor taking a list of symbols to register (defaults to mass fraction mode)")
// .def(py::init<const std::set<std::string>&>(), py::arg("symbols")) // Binding std::set constructor is possible but often less convenient from Python
.def(py::init<const std::vector<std::string>&, const std::vector<double>&, bool>(),
py::arg("symbols"), py::arg("fractions"), py::arg("massFracMode") = true,
"Constructor taking symbols, fractions, and mode (True=Mass, False=Number)")
// Methods
.def("finalize", &fourdst::composition::Composition::finalize, py::arg("norm") = false,
"Finalize the composition, optionally normalizing fractions to sum to 1.")
.def("registerSymbol", py::overload_cast<const std::string&, bool>(&fourdst::composition::Composition::registerSymbol),
py::arg("symbol"), py::arg("massFracMode") = true, "Register a single symbol.")
.def("registerSymbol", py::overload_cast<const std::vector<std::string>&, bool>(&fourdst::composition::Composition::registerSymbol),
py::arg("symbols"), py::arg("massFracMode") = true, "Register multiple symbols.")
.def("getRegisteredSymbols", &fourdst::composition::Composition::getRegisteredSymbols,
"Get the set of registered symbols.")
.def("setMassFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setMassFraction),
py::arg("symbol"), py::arg("mass_fraction"), "Set mass fraction for a single symbol (requires massFracMode). Returns old value.")
.def("setMassFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setMassFraction),
py::arg("symbols"), py::arg("mass_fractions"), "Set mass fractions for multiple symbols (requires massFracMode). Returns list of old values.")
.def("setNumberFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setNumberFraction),
py::arg("symbol"), py::arg("number_fraction"), "Set number fraction for a single symbol (requires !massFracMode). Returns old value.")
.def("setNumberFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setNumberFraction),
py::arg("symbols"), py::arg("number_fractions"), "Set number fractions for multiple symbols (requires !massFracMode). Returns list of old values.")
.def("mix", &fourdst::composition::Composition::mix, py::arg("other"), py::arg("fraction"),
"Mix with another composition. Returns new Composition.")
.def("getMassFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getMassFraction, py::const_),
py::arg("symbol"), "Get mass fraction for a symbol (calculates if needed). Requires finalization.")
.def("getMassFraction", py::overload_cast<>(&fourdst::composition::Composition::getMassFraction, py::const_),
"Get dictionary of all mass fractions. Requires finalization.")
.def("getNumberFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getNumberFraction, py::const_),
py::arg("symbol"), "Get number fraction for a symbol (calculates if needed). Requires finalization.")
.def("getNumberFraction", py::overload_cast<>(&fourdst::composition::Composition::getNumberFraction, py::const_),
"Get dictionary of all number fractions. Requires finalization.")
// Note: pybind11 automatically converts std::pair to a Python tuple
.def("getComposition", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getComposition, py::const_),
py::arg("symbol"), "Returns a tuple (CompositionEntry, GlobalComposition) for the symbol. Requires finalization.")
// Binding the version returning map<string, Entry> requires a bit more care or helper function
// to convert the map to a Python dict if needed directly. Let's bind the pair version for now.
.def("getComposition", py::overload_cast<>(&fourdst::composition::Composition::getComposition, py::const_),
"Returns a tuple (dict[str, CompositionEntry], GlobalComposition) for all symbols. Requires finalization.")
.def("subset", &fourdst::composition::Composition::subset, py::arg("symbols"), py::arg("method") = "norm",
"Create a new Composition containing only the specified symbols.")
.def("hasSymbol", &fourdst::composition::Composition::hasSymbol, py::arg("symbol"),
"Check if a symbol is registered.")
.def("setCompositionMode", &fourdst::composition::Composition::setCompositionMode, py::arg("massFracMode"),
"Set the mode (True=Mass, False=Number). Requires finalization before switching.")
// Operator overload
.def(py::self + py::self, "Mix equally with another composition.") // Binds operator+
// Add __repr__ or __str__
.def("__repr__", [](const fourdst::composition::Composition &comp) {
return get_ostream_str(comp); // Use helper for C++ operator<<
});
}
void register_species_bindings(pybind11::module &chem_submodule) {
// --- Bindings for species module ---
py::class_<fourdst::atomic::Species>(chem_submodule, "Species")
.def("mass", &fourdst::atomic::Species::mass, "Get atomic mass (amu)")
.def("massUnc", &fourdst::atomic::Species::massUnc, "Get atomic mass uncertainty (amu)")
.def("bindingEnergy", &fourdst::atomic::Species::bindingEnergy, "Get binding energy (keV/nucleon?)") // Check units
.def("betaDecayEnergy", &fourdst::atomic::Species::betaDecayEnergy, "Get beta decay energy (keV?)") // Check units
.def("betaCode", [](const fourdst::atomic::Species& s){ return sv_to_string(s.betaCode()); }, "Get beta decay code") // Convert string_view
.def("name", [](const fourdst::atomic::Species& s){ return sv_to_string(s.name()); }, "Get species name (e.g., 'H-1')") // Convert string_view
.def("el", [](const fourdst::atomic::Species& s){ return sv_to_string(s.el()); }, "Get element symbol (e.g., 'H')") // Convert string_view
.def("nz", &fourdst::atomic::Species::nz, "Get NZ value")
.def("n", &fourdst::atomic::Species::n, "Get neutron number N")
.def("z", &fourdst::atomic::Species::z, "Get proton number Z")
.def("a", &fourdst::atomic::Species::a, "Get mass number A")
.def("__repr__",
[](const fourdst::atomic::Species &s) {
std::ostringstream oss;
oss << s;
return oss.str();
});
chem_submodule.attr("species") = py::cast(fourdst::atomic::species); // Expose the species map
}

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src-pybind/composition/bindings.h Normal file
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#pragma once
#include <pybind11/pybind11.h>
void register_comp_bindings(pybind11::module &m);
void register_species_bindings(pybind11::module &m);

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src-pybind/composition/meson.build Normal file
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# Define the library
bindings_sources = files('bindings.cpp')
bindings_headers = files('bindings.h')
dependencies = [
composition_dep,
python3_dep,
pybind11_dep,
]
shared_module('py_composition',
bindings_sources,
cpp_args: ['-fvisibility=default'],
install : true,
dependencies: dependencies,
include_directories: include_directories('.')
)