musica 0.12.2__cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

musica/musica.cpp

@@ -0,0 +1,201 @@
+// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+#include <musica/micm/cuda_availability.hpp>
+#include <musica/micm/micm.hpp>
+#include <musica/micm/micm_c_interface.hpp>
+#include <musica/micm/state.hpp>
+#include <musica/micm/state_c_interface.hpp>
+
+#include <mechanism_configuration/v1/types.hpp>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/stl_bind.h>
+
+namespace py = pybind11;
+namespace v1 = mechanism_configuration::v1::types;
+
+PYBIND11_MAKE_OPAQUE(std::vector<double>)
+PYBIND11_MAKE_OPAQUE(std::vector<micm::Conditions>)
+
+void bind_musica(py::module_ &core)
+{
+  py::bind_vector<std::vector<double>>(core, "VectorDouble");
+  py::bind_vector<std::vector<micm::Conditions>>(core, "VectorConditions");
+
+  py::class_<micm::Conditions>(core, "_Conditions")
+      .def(py::init<>())
+      .def_readwrite("temperature", &micm::Conditions::temperature_)
+      .def_readwrite("pressure", &micm::Conditions::pressure_)
+      .def_readwrite("air_density", &micm::Conditions::air_density_);
+
+  py::class_<musica::State>(core, "_State")
+      .def(py::init<>())
+      .def("__del__", [](musica::State &state) {})
+      .def("number_of_grid_cells", [](musica::State &state) { return state.NumberOfGridCells(); })
+      .def_property(
+          "conditions",
+          [](musica::State &state) -> std::vector<micm::Conditions> & { return state.GetConditions(); },
+          nullptr,
+          "list of conditions structs for each grid cell")
+      .def_property(
+          "concentrations",
+          [](musica::State &state) -> std::vector<double> & { return state.GetOrderedConcentrations(); },
+          nullptr,
+          "native 1D list of concentrations, ordered by species and grid cell according to matrix type")
+      .def_property(
+          "user_defined_rate_parameters",
+          [](musica::State &state) -> std::vector<double> & { return state.GetOrderedRateParameters(); },
+          nullptr,
+          "native 1D list of user-defined rate parameters, ordered by parameter and grid cell according to matrix type")
+      .def("concentration_strides", [](musica::State &state) { return state.GetConcentrationsStrides(); })
+      .def(
+          "user_defined_rate_parameter_strides",
+          [](musica::State &state) { return state.GetUserDefinedRateParametersStrides(); });
+
+  py::enum_<musica::MICMSolver>(core, "_SolverType")
+      .value("rosenbrock", musica::MICMSolver::Rosenbrock)
+      .value("rosenbrock_standard_order", musica::MICMSolver::RosenbrockStandardOrder)
+      .value("backward_euler", musica::MICMSolver::BackwardEuler)
+      .value("backward_euler_standard_order", musica::MICMSolver::BackwardEulerStandardOrder)
+      .value("cuda_rosenbrock", musica::MICMSolver::CudaRosenbrock);
+
+  py::class_<musica::MICM>(core, "_Solver");
+
+  core.def(
+      "_vector_size",
+      [](const musica::MICMSolver solver_type)
+      {
+        switch (solver_type)
+        {
+          case musica::MICMSolver::Rosenbrock:
+          case musica::MICMSolver::BackwardEuler:
+          case musica::MICMSolver::CudaRosenbrock: return musica::MUSICA_VECTOR_SIZE;
+          case musica::MICMSolver::RosenbrockStandardOrder:
+          case musica::MICMSolver::BackwardEulerStandardOrder: return static_cast<std::size_t>(0);
+          default: throw py::value_error("Invalid MICM solver type.");
+        }
+      },
+      "Returns the vector dimension for vector-ordered solvers, 0 otherwise.");
+
+  core.def(
+      "_create_solver",
+      [](const char *config_path, musica::MICMSolver solver_type)
+      {
+        musica::Error error;
+        musica::MICM *micm = musica::CreateMicm(config_path, solver_type, &error);
+        if (!musica::IsSuccess(error))
+        {
+          std::cout << "Error creating solver: " << error.message_.value_ << " solver_type: " << solver_type
+                    << " config_path: " << config_path << std::endl;
+          std::string message = "Error creating solver: " + std::string(error.message_.value_);
+          DeleteError(&error);
+          throw py::value_error(message);
+        }
+        return micm;
+      });
+
+  core.def(
+      "_create_solver_from_mechanism",
+      [](const v1::Mechanism &mechanism, musica::MICMSolver solver_type, bool ignore_non_gas_phases)
+      {
+        musica::Error error;
+        musica::Chemistry chemistry = musica::ConvertV1Mechanism(mechanism, ignore_non_gas_phases);
+        musica::MICM *micm = musica::CreateMicmFromChemistryMechanism(&chemistry, solver_type, &error);
+        if (!musica::IsSuccess(error))
+        {
+          std::string message = "Error creating solver: " + std::string(error.message_.value_);
+          DeleteError(&error);
+          throw py::value_error(message);
+        }
+        return micm;
+      });
+
+  core.def(
+      "_create_state",
+      [](musica::MICM *micm, std::size_t number_of_grid_cells)
+      {
+        musica::Error error;
+        musica::State *state = musica::CreateMicmState(micm, number_of_grid_cells, &error);
+        if (!musica::IsSuccess(error))
+        {
+          std::string message = "Error creating state: " + std::string(error.message_.value_);
+          DeleteError(&error);
+          throw py::value_error(message);
+        }
+        return state;
+      });
+
+  core.def(
+      "_micm_solve",
+      [](musica::MICM *micm, musica::State *state, double time_step)
+      {
+        musica::String solver_state;
+        musica::SolverResultStats solver_stats;
+        musica::Error error;
+        musica::MicmSolve(micm, state, time_step, &solver_state, &solver_stats, &error);
+        if (!musica::IsSuccess(error))
+        {
+          std::string message = "Error solving system: " + std::string(error.message_.value_);
+          DeleteError(&error);
+          throw py::value_error(message);
+        }
+      },
+      "Solve the chemistry system");
+
+  core.def(
+      "_species_ordering",
+      [](musica::State *state)
+      {
+        std::map<std::string, std::size_t> map;
+        std::visit([&map](auto &state) { map = state.variable_map_; }, state->state_variant_);
+        return map;
+      },
+      "Return map of species names to their indices in the state concentrations vector");
+
+  core.def(
+      "_user_defined_rate_parameters_ordering",
+      [](musica::State *state)
+      {
+        std::map<std::string, std::size_t> map;
+
+        std::visit([&map](auto &state) { map = state.custom_rate_parameter_map_; }, state->state_variant_);
+        return map;
+      },
+      "Return map of reaction rate parameters to their indices in the state user-defined rate parameters vector");
+
+  core.def("_is_cuda_available", &musica::IsCudaAvailable, "Check if CUDA is available");
+
+  core.def(
+      "_print_state",
+      [](musica::State *state, const double current_time)
+      {
+        std::visit(
+            [&current_time](auto &state)
+            {
+              std::cout << "Current time: " << current_time << std::endl;
+              std::cout << "State variables: " << std::endl;
+              std::vector<std::string> species_names(state.variable_map_.size());
+              for (const auto &species : state.variable_map_)
+                species_names[species.second] = species.first;
+              for (const auto &name : species_names)
+                std::cout << name << ",";
+              std::cout << std::endl << state.variables_ << std::endl;
+              std::cout << "User-defined rate parameters: " << std::endl;
+              std::vector<std::string> rate_param_names(state.custom_rate_parameter_map_.size());
+              for (const auto &rate : state.custom_rate_parameter_map_)
+                rate_param_names[rate.second] = rate.first;
+              for (const auto &name : rate_param_names)
+                std::cout << name << ",";
+              std::cout << std::endl << state.custom_rate_parameters_ << std::endl;
+              std::cout << "Conditions: " << std::endl;
+              std::cout << "Temperature,Pressure,Air density" << std::endl;
+              for (const auto &condition : state.conditions_)
+              {
+                std::cout << condition.temperature_ << "," << condition.pressure_ << "," << condition.air_density_
+                          << std::endl;
+              }
+            },
+            state->state_variant_);
+      },
+      "Print the state to stdout with the current time");
+}

musica/test/examples/v1/full_configuration/full_configuration.json

@@ -0,0 +1,466 @@
+{
+  "version": "1.0.0",
+  "name": "Full Configuration",
+  "species": [
+    {
+      "name": "A",
+      "__absolute tolerance": 1.0e-30
+    },
+    {
+      "name": "B",
+      "tracer type": "AEROSOL"
+    },
+    {
+      "name": "C",
+      "tracer type": "THIRD_BODY"
+    },
+    {
+      "name": "M"
+    },
+    {
+      "name": "H2O2",
+      "HLC(298K) [mol m-3 Pa-1]": 1.011596348,
+      "HLC exponential factor [K]": 6340,
+      "diffusion coefficient [m2 s-1]": 1.46E-05,
+      "N star": 1.74,
+      "molecular weight [kg mol-1]": 0.0340147,
+      "density [kg m-3]": 1000.0,
+      "__absolute tolerance": 1.0e-10
+    },
+    {
+      "name": "ethanol",
+      "diffusion coefficient [m2 s-1]": 0.95E-05,
+      "N star": 2.55,
+      "molecular weight [kg mol-1]": 0.04607,
+      "__absolute tolerance": 1.0e-20
+    },
+    {
+      "name": "ethanol_aq",
+      "molecular weight [kg mol-1]": 0.04607,
+      "density [kg m-3]": 1000.0,
+      "__absolute tolerance": 1.0e-20
+    },
+    {
+      "name": "H2O2_aq",
+      "molecular weight [kg mol-1]": 0.0340147,
+      "density [kg m-3]": 1000.0,
+      "__absolute tolerance": 1.0e-10
+    },
+    {
+      "name": "H2O_aq",
+      "density [kg m-3]": 1000.0,
+      "molecular weight [kg mol-1]": 0.01801
+    },
+    {
+      "name": "aerosol stuff",
+      "molecular weight [kg mol-1]": 0.5,
+      "density [kg m-3]": 1000.0,
+      "__absolute tolerance": 1.0e-20
+    },
+    {
+      "name": "more aerosol stuff",
+      "molecular weight [kg mol-1]": 0.2,
+      "density [kg m-3]": 1000.0,
+      "__absolute tolerance": 1.0e-20
+    }
+  ],
+  "phases": [
+    {
+      "name": "gas",
+      "species": [
+        "A",
+        "B",
+        "C",
+        "ethanol"
+      ]
+    },
+    {
+      "name": "aqueous aerosol",
+      "species": [
+        "H2O2_aq",
+        "H2O_aq",
+        "ethanol_aq",
+        "A",
+        "B",
+        "C"
+      ]
+    },
+    {
+      "name": "surface reacting phase",
+      "species": [
+        "aerosol stuff",
+        "more aerosol stuff"
+      ]
+    },
+    {
+      "name": "cloud",
+      "species": [
+        "B",
+        "C"
+      ]
+    }
+  ],
+  "reactions": [
+    {
+      "type": "SIMPOL_PHASE_TRANSFER",
+      "gas phase": "gas",
+      "gas-phase species": "ethanol",
+      "condensed phase": "aqueous aerosol",
+      "condensed-phase species": "ethanol_aq",
+      "B": [
+        -1.97E+03,
+        2.91E+00,
+        1.96E-03,
+        -4.96E-01
+      ],
+      "name": "my simpol",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "AQUEOUS_EQUILIBRIUM",
+      "condensed phase": "aqueous aerosol",
+      "condensed-phase water": "H2O_aq",
+      "A": 1.14e-2,
+      "C": 2300.0,
+      "k_reverse": 0.32,
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 2
+        }
+      ],
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "name": "my aqueous eq",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "condensed phase": "aqueous aerosol",
+      "A": 123.45,
+      "Ea": 123.45,
+      "B": 1.3,
+      "D": 300.0,
+      "E": 0.6E-5,
+      "reactants": [
+        {
+          "species name": "H2O2_aq",
+          "coefficient": 1
+        },
+        {
+          "species name": "H2O_aq",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "ethanol_aq",
+          "coefficient": 1
+        }
+      ],
+      "name": "my condensed arrhenius",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "CONDENSED_PHASE_ARRHENIUS",
+      "condensed phase": "aqueous aerosol",
+      "A": 123.45,
+      "C": 123.45,
+      "B": 1.3,
+      "D": 300.0,
+      "E": 0.6E-5,
+      "reactants": [
+        {
+          "species name": "H2O2_aq",
+          "coefficient": 1
+        },
+        {
+          "species name": "H2O_aq",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "ethanol_aq",
+          "coefficient": 1
+        }
+      ],
+      "name": "my other condensed arrhenius"
+    },
+    {
+      "type": "CONDENSED_PHASE_PHOTOLYSIS",
+      "condensed phase": "aqueous aerosol",
+      "reactants": [
+        {
+          "species name": "H2O2_aq",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "ethanol_aq",
+          "coefficient": 1
+        }
+      ],
+      "scaling factor": 12.3,
+      "name": "condensed photo B",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "EMISSION",
+      "gas phase": "gas",
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "name": "my emission",
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
+    },
+    {
+      "type": "FIRST_ORDER_LOSS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "name": "my first order loss",
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
+    },
+    {
+      "type": "PHOTOLYSIS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "name": "photo B",
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
+    },
+    {
+      "type": "SURFACE",
+      "gas phase": "gas",
+      "gas-phase species": "A",
+      "reaction probability": 2.0e-2,
+      "gas-phase products": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "condensed phase": "surface reacting phase",
+      "name": "my surface",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "TROE",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "M",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "k0_A": 1.2e-12,
+      "k0_B": 167,
+      "k0_C": 3,
+      "kinf_A": 136,
+      "kinf_B": 5,
+      "kinf_C": 24,
+      "Fc": 0.9,
+      "N": 0.8,
+      "name": "my troe",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "TERNARY_CHEMICAL_ACTIVATION",
+      "gas phase": "gas",
+      "name": "my ternary chemical activation",
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "M",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "k0_A": 32.1,
+      "k0_B": -2.3,
+      "k0_C": 102.3,
+      "kinf_A": 63.4,
+      "kinf_B": -1.3,
+      "kinf_C": 908.5,
+      "Fc": 1.3,
+      "N": 32.1,
+      "__irrelevant": "2"
+    },
+    {
+      "type": "BRANCHED_NO_RO2",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 1
+        }
+      ],
+      "alkoxy products": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "nitrate products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "X": 1.2e-4,
+      "Y": 167,
+      "a0": 0.15,
+      "n": 9,
+      "name": "my branched",
+      "__irrelevant": "2"
+    },
+    {
+      "gas phase": "gas",
+      "name": "my tunneling",
+      "type": "TUNNELING",
+      "A": 123.45,
+      "B": 1200.0,
+      "C": 1.0e8,
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "__irrelevant": "2"
+    },
+    {
+      "type": "WET_DEPOSITION",
+      "condensed phase": "cloud",
+      "name": "rxn cloud",
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
+    },
+    {
+      "type": "ARRHENIUS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "A": 32.1,
+      "B": -2.3,
+      "C": 102.3,
+      "D": 63.4,
+      "E": -1.3,
+      "name": "my arrhenius",
+      "__irrelevant": "2"
+    },
+    {
+      "type": "ARRHENIUS",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "B",
+          "coefficient": 1.2
+        }
+      ],
+      "A": 29.3,
+      "B": -1.5,
+      "Ea": 101.2,
+      "D": 82.6,
+      "E": -0.98,
+      "name": "my other arrhenius"
+    },
+    {
+      "type": "USER_DEFINED",
+      "gas phase": "gas",
+      "reactants": [
+        {
+          "species name": "A",
+          "coefficient": 1
+        },
+        {
+          "species name": "B",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1.3
+        }
+      ],
+      "name": "my user defined",
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
+    }
+  ]
+}