musica 0.11.1.4__cp312-cp312-win_amd64.whl → 0.12.1__cp312-cp312-win_amd64.whl

musica/musica.cpp

@@ -1,12 +1,12 @@
 // 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_c_interface.hpp>
 #include <musica/micm/state.hpp>
-#include <mechanism_configuration/v1/types.hpp>
-#include <musica/micm/cuda_availability.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>
@@ -21,7 +21,7 @@ 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_)
@@ -30,40 +30,27 @@ void bind_musica(py::module_ &core)
 
   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("__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();
-          },
+          [](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();
-          },
+          [](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();
-          },
+          [](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();
-          });
+      .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)
@@ -74,20 +61,18 @@ void bind_musica(py::module_ &core)
 
   py::class_<musica::MICM>(core, "_Solver");
 
-  core.def("_vector_size",
+  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::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.");
+          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.");
@@ -111,10 +96,10 @@ void bind_musica(py::module_ &core)
 
   core.def(
       "_create_solver_from_mechanism",
-      [](const v1::Mechanism &mechanism, musica::MICMSolver solver_type)
+      [](const v1::Mechanism &mechanism, musica::MICMSolver solver_type, bool ignore_non_gas_phases)
       {
         musica::Error error;
-        musica::Chemistry chemistry = musica::ConvertV1Mechanism(mechanism);
+        musica::Chemistry chemistry = musica::ConvertV1Mechanism(mechanism, ignore_non_gas_phases);
         musica::MICM *micm = musica::CreateMicmFromChemistryMechanism(&chemistry, solver_type, &error);
         if (!musica::IsSuccess(error))
         {
@@ -124,7 +109,7 @@ void bind_musica(py::module_ &core)
         }
         return micm;
       });
-  
+
   core.def(
       "_create_state",
       [](musica::MICM *micm, std::size_t number_of_grid_cells)
@@ -184,31 +169,33 @@ void bind_musica(py::module_ &core)
       "_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_);
+        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

@@ -101,33 +101,25 @@
     }
   ],
   "reactions": [
-    {
-      "type": "HL_PHASE_TRANSFER",
-      "gas phase": "gas",
-      "gas-phase species": "H2O2",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase species": "H2O2_aq",
-      "aerosol-phase water": "H2O_aq",
-      "name": "my henry's law"
-    },
     {
       "type": "SIMPOL_PHASE_TRANSFER",
       "gas phase": "gas",
       "gas-phase species": "ethanol",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase species": "ethanol_aq",
+      "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"
+      "name": "my simpol",
+      "__irrelevant": "2"
     },
     {
       "type": "AQUEOUS_EQUILIBRIUM",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
+      "condensed-phase water": "H2O_aq",
       "A": 1.14e-2,
       "C": 2300.0,
       "k_reverse": 0.32,
@@ -147,12 +139,12 @@
           "coefficient": 1
         }
       ],
-      "name": "my aqueous eq"
+      "name": "my aqueous eq",
+      "__irrelevant": "2"
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "A": 123.45,
       "Ea": 123.45,
       "B": 1.3,
@@ -174,12 +166,12 @@
           "coefficient": 1
         }
       ],
-      "name": "my condensed arrhenius"
+      "name": "my condensed arrhenius",
+      "__irrelevant": "2"
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "A": 123.45,
       "C": 123.45,
       "B": 1.3,
@@ -205,8 +197,7 @@
     },
     {
       "type": "CONDENSED_PHASE_PHOTOLYSIS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "reactants": [
         {
           "species name": "H2O2_aq",
@@ -220,7 +211,8 @@
         }
       ],
       "scaling factor": 12.3,
-      "name": "condensed photo B"
+      "name": "condensed photo B",
+      "__irrelevant": "2"
     },
     {
       "type": "EMISSION",
@@ -232,7 +224,8 @@
         }
       ],
       "name": "my emission",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "FIRST_ORDER_LOSS",
@@ -244,7 +237,8 @@
         }
       ],
       "name": "my first order loss",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "PHOTOLYSIS",
@@ -262,7 +256,8 @@
         }
       ],
       "name": "photo B",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "SURFACE",
@@ -279,8 +274,9 @@
           "coefficient": 1
         }
       ],
-      "aerosol phase": "surface reacting phase",
-      "name": "my surface"
+      "condensed phase": "surface reacting phase",
+      "name": "my surface",
+      "__irrelevant": "2"
     },
     {
       "type": "TROE",
@@ -309,7 +305,38 @@
       "kinf_C": 24,
       "Fc": 0.9,
       "N": 0.8,
-      "name": "my troe"
+      "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",
@@ -336,7 +363,8 @@
       "Y": 167,
       "a0": 0.15,
       "n": 9,
-      "name": "my branched"
+      "name": "my branched",
+      "__irrelevant": "2"
     },
     {
       "gas phase": "gas",
@@ -356,13 +384,15 @@
           "species name": "C",
           "coefficient": 1
         }
-      ]
+      ],
+      "__irrelevant": "2"
     },
     {
       "type": "WET_DEPOSITION",
-      "aerosol phase": "cloud",
+      "condensed phase": "cloud",
       "name": "rxn cloud",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "ARRHENIUS",
@@ -384,7 +414,8 @@
       "C": 102.3,
       "D": 63.4,
       "E": -1.3,
-      "name": "my arrhenius"
+      "name": "my arrhenius",
+      "__irrelevant": "2"
     },
     {
       "type": "ARRHENIUS",
@@ -428,7 +459,8 @@
         }
       ],
       "name": "my user defined",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     }
   ]
 }

musica/test/examples/v1/full_configuration/full_configuration.yaml

@@ -65,27 +65,21 @@ phases:
   - B
   - C
 reactions:
-- type: HL_PHASE_TRANSFER
-  gas phase: gas
-  gas-phase species: H2O2
-  aerosol phase: aqueous aerosol
-  aerosol-phase species: H2O2_aq
-  aerosol-phase water: H2O_aq
-  name: my henry's law
 - type: SIMPOL_PHASE_TRANSFER
   gas phase: gas
   gas-phase species: ethanol
-  aerosol phase: aqueous aerosol
-  aerosol-phase species: ethanol_aq
+  condensed phase: aqueous aerosol
+  condensed-phase species: ethanol_aq
   B:
   - -1970
   - 2.91
   - 0.00196
   - -0.496
   name: my simpol
+  __irrelevant: "2"
 - type: AQUEOUS_EQUILIBRIUM
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
+  condensed-phase water: H2O_aq
   A: 0.0114
   C: 2300
   k_reverse: 0.32
@@ -98,9 +92,9 @@ reactions:
   - species name: C
     coefficient: 1
   name: my aqueous eq
+  __irrelevant: "2"
 - type: CONDENSED_PHASE_ARRHENIUS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   A: 123.45
   Ea: 123.45
   B: 1.3
@@ -115,9 +109,9 @@ reactions:
   - species name: ethanol_aq
     coefficient: 1
   name: my condensed arrhenius
+  __irrelevant: "2"
 - type: CONDENSED_PHASE_ARRHENIUS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   A: 123.45
   C: 123.45
   B: 1.3
@@ -133,8 +127,7 @@ reactions:
     coefficient: 1
   name: my other condensed arrhenius
 - type: CONDENSED_PHASE_PHOTOLYSIS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   reactants:
   - species name: H2O2_aq
     coefficient: 1
@@ -143,6 +136,7 @@ reactions:
     coefficient: 1
   scaling factor: 12.3
   name: condensed photo B
+  __irrelevant: "2"
 - type: EMISSION
   gas phase: gas
   products:
@@ -150,6 +144,7 @@ reactions:
     coefficient: 1
   name: my emission
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: FIRST_ORDER_LOSS
   gas phase: gas
   reactants:
@@ -157,6 +152,7 @@ reactions:
     coefficient: 1
   name: my first order loss
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: PHOTOLYSIS
   gas phase: gas
   reactants:
@@ -167,6 +163,7 @@ reactions:
     coefficient: 1
   name: photo B
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: SURFACE
   gas phase: gas
   gas-phase species: A
@@ -176,8 +173,9 @@ reactions:
     coefficient: 1
   - species name: C
     coefficient: 1
-  aerosol phase: surface reacting phase
+  condensed phase: surface reacting phase
   name: my surface
+  __irrelevant: "2"
 - type: TROE
   gas phase: gas
   reactants:
@@ -197,6 +195,27 @@ reactions:
   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:
@@ -213,6 +232,7 @@ reactions:
   a0: 0.15
   "n": 9
   name: my branched
+  __irrelevant: "2"
 - gas phase: gas
   type: TUNNELING
   name: "my tunneling"
@@ -225,10 +245,12 @@ reactions:
   products:
   - species name: C
     coefficient: 1
+  __irrelevant: "2"
 - type: WET_DEPOSITION
-  aerosol phase: cloud
+  condensed phase: cloud
   name: rxn cloud
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: ARRHENIUS
   gas phase: gas
   reactants:
@@ -243,6 +265,7 @@ reactions:
   D: 63.4
   E: -1.3
   name: my arrhenius
+  __irrelevant: "2"
 - type: ARRHENIUS
   gas phase: gas
   reactants:
@@ -268,4 +291,5 @@ reactions:
   - species name: C
     coefficient: 1.3
   name: my user defined
-  scaling factor: 12.3
+  scaling factor: 12.3
+  __irrelevant: "2"

musica/test/{test_analytical.py → integration/test_analytical.py}

@@ -4,12 +4,12 @@ import musica
 import random
 import musica.mechanism_configuration as mc
 from musica.cuda import is_cuda_available
+from musica.constants import GAS_CONSTANT
 
 
 def TestSingleGridCell(solver, state, time_step, places=5):
     temperature = 272.5
     pressure = 101253.3
-    GAS_CONSTANT = 8.31446261815324
     air_density = pressure / (GAS_CONSTANT * temperature)
 
     rate_constants = {
@@ -118,7 +118,6 @@ def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
         rate_constants["USER.reaction 2"].append(
             0.002 + random.uniform(-0.0001, 0.0001))
 
-
     state.set_conditions(temperatures, pressures)  # Air density should be calculated in the state
     state.set_concentrations(concentrations)
     state.set_user_defined_rate_parameters(rate_constants)