musica 0.11.1.1__cp312-cp312-win_amd64.whl → 0.14.2__cp312-cp312-win_amd64.whl

musica/musica.cpp

@@ -1,214 +0,0 @@
-// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
-// SPDX-License-Identifier: Apache-2.0
-#include <musica/micm/micm.hpp>
-#include <musica/micm/micm_c_interface.hpp>
-#include <musica/micm/state_c_interface.hpp>
-#include <musica/micm/state.hpp>
-#include <mechanism_configuration/v1/types.hpp>
-#include <musica/micm/cuda_availability.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)
-      {
-        musica::Error error;
-        musica::Chemistry chemistry = musica::ConvertV1Mechanism(mechanism);
-        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/v0/config.json

@@ -1,7 +0,0 @@
-{
-    "camp-files": [
-      "species.json",
-      "reactions.json"
-    ]
-  }
-  

musica/test/examples/v0/config.yaml

@@ -1,3 +0,0 @@
-camp-files:
-- species.yaml
-- reactions.yaml

musica/test/examples/v0/reactions.json

@@ -1,193 +0,0 @@
-{
-  "camp-data": [
-    {
-      "type": "MECHANISM",
-      "name": "music box interactive configuration",
-      "reactions": [
-        {
-          "type": "PHOTOLYSIS",
-          "scaling factor": 1,
-          "MUSICA name": "foo",
-          "reactants": {
-            "foo": {}
-          },
-          "products": {
-            "buz": {
-              "yield": 1
-            },
-            "bar": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "ARRHENIUS",
-          "A": 6e-34,
-          "Ea": 0,
-          "B": -2.4,
-          "D": 300,
-          "E": 0,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "quuz": {
-              "qty": 1
-            },
-            "M": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            },
-            "M": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "TROE",
-          "k0_A": 2.5e-31,
-          "k0_B": -1.8,
-          "k0_C": 0,
-          "kinf_A": 2.2e-11,
-          "kinf_B": -0.7,
-          "kinf_C": 0,
-          "Fc": 0.6,
-          "N": 1,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "foo": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "EMISSION",
-          "scaling factor": 1,
-          "MUSICA name": "buz",
-          "species": "buz"
-        },
-        {
-          "type": "FIRST_ORDER_LOSS",
-          "species": "bar",
-          "MUSICA name": "bar",
-          "scaling factor": 2.5
-        },
-        {
-          "type": "TERNARY_CHEMICAL_ACTIVATION",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "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
-        },
-        {
-          "type": "BRANCHED",
-          "reactants": {
-            "foo" : { },
-            "quz" : { "qty" :2 }
-          },
-          "alkoxy products": {
-            "bar": { "yield": 1.0 },
-            "baz": { "yield": 3.2 }
-          },
-          "nitrate products": {
-            "quz": { "yield": 1.0 }
-          },
-          "Y" : 42.3,
-          "X" : 12.3,
-          "a0" : 1.0e-5,
-          "n" : 3
-        },
-        {
-          "type": "WENNBERG_NO_RO2",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "alkoxy products": {
-            "baz": { }
-          },
-          "nitrate products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "Y" : 2.3e8,
-          "X" : 0.32,
-          "a0" : 0.423,
-          "n" : 6
-        },
-        {
-          "type": "TUNNELING",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "A": 32.1,
-          "B": -2.3,
-          "C": 102.3
-        },
-        {
-          "type": "WENNBERG_TUNNELING",
-          "reactants": {
-            "bar2" : { },
-            "baz2" : { }
-          },
-          "products": {
-            "bar2": { "yield": 0.5 },
-            "foo2": { }
-          },
-          "A": 2.1,
-          "B": -1.3,
-          "C": 12.3
-        },
-        {
-          "type": "SURFACE",
-          "gas-phase reactant": "bar",
-          "gas-phase products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "reaction probability": 0.5,
-          "MUSICA name": "kbar"
-        },
-        {
-          "type": "USER_DEFINED",
-          "MUSICA name": "bar",
-          "reactants": { 
-            "foo" : { "qty": 2 }
-          },
-          "products": {
-            "bar" : { }
-          }, 
-          "scaling factor": 2.5
-        }
-      ]
-    }
-  ]
-}

musica/test/examples/v0/reactions.yaml

@@ -1,142 +0,0 @@
-camp-data:
-- name: music box interactive configuration
-  reactions:
-  - MUSICA name: foo
-    products:
-      bar:
-        yield: 1
-      buz:
-        yield: 1
-    reactants:
-      foo: {}
-    scaling factor: 1
-    type: PHOTOLYSIS
-  - A: 6.0e-34
-    B: -2.4
-    D: 300
-    E: 0
-    Ea: 0
-    products:
-      M:
-        yield: 1
-      baz:
-        yield: 1
-    reactants:
-      M:
-        qty: 1
-      bar:
-        qty: 1
-      quuz:
-        qty: 1
-    type: ARRHENIUS
-  - Fc: 0.6
-    N: 1
-    k0_A: 2.5e-31
-    k0_B: -1.8
-    k0_C: 0
-    kinf_A: 2.2e-11
-    kinf_B: -0.7
-    kinf_C: 0
-    products:
-      baz:
-        yield: 1
-    reactants:
-      bar:
-        qty: 1
-      foo:
-        qty: 1
-    type: TROE
-  - MUSICA name: buz
-    scaling factor: 1
-    species: buz
-    type: EMISSION
-  - MUSICA name: bar
-    scaling factor: 2.5
-    species: bar
-    type: FIRST_ORDER_LOSS
-  - Fc: 1.3
-    N: 32.1
-    k0_A: 32.1
-    k0_B: -2.3
-    k0_C: 102.3
-    kinf_A: 63.4
-    kinf_B: -1.3
-    kinf_C: 908.5
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TERNARY_CHEMICAL_ACTIVATION
-  - X: 12.3
-    Y: 42.3
-    a0: 1.0e-05
-    alkoxy products:
-      bar:
-        yield: 1.0
-      baz:
-        yield: 3.2
-    n: 3
-    nitrate products:
-      quz:
-        yield: 1.0
-    reactants:
-      foo: {}
-      quz:
-        qty: 2
-    type: BRANCHED
-  - X: 0.32
-    Y: 230000000.0
-    a0: 0.423
-    alkoxy products:
-      baz: {}
-    n: 6
-    nitrate products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: WENNBERG_NO_RO2
-  - A: 32.1
-    B: -2.3
-    C: 102.3
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TUNNELING
-  - A: 2.1
-    B: -1.3
-    C: 12.3
-    products:
-      bar2:
-        yield: 0.5
-      foo2: {}
-    reactants:
-      bar2: {}
-      baz2: {}
-    type: WENNBERG_TUNNELING
-  - MUSICA name: kbar
-    gas-phase products:
-      bar:
-        yield: 0.5
-      foo: {}
-    gas-phase reactant: bar
-    reaction probability: 0.5
-    type: SURFACE
-  - MUSICA name: bar
-    products:
-      bar: {}
-    reactants:
-      foo:
-        qty: 2
-    scaling factor: 2.5
-    type: USER_DEFINED
-  type: MECHANISM

musica/test/examples/v0/species.json

@@ -1,40 +0,0 @@
-{
-  "camp-data": [
-    {
-      "name": "foo",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "buz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "quuz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "foo2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "M",
-      "type": "CHEM_SPEC"
-    }
-  ]
-}

musica/test/examples/v0/species.yaml

@@ -1,19 +0,0 @@
-camp-data:
-- name: foo
-  type: CHEM_SPEC
-- name: bar
-  type: CHEM_SPEC
-- name: buz
-  type: CHEM_SPEC
-- name: quuz
-  type: CHEM_SPEC
-- name: foo2
-  type: CHEM_SPEC
-- name: bar2
-  type: CHEM_SPEC
-- name: baz
-  type: CHEM_SPEC
-- name: baz2
-  type: CHEM_SPEC
-- name: M
-  type: CHEM_SPEC