musica 0.11.1.3__cp312-cp312-macosx_11_0_arm64.whl → 0.12.0__cp312-cp312-macosx_11_0_arm64.whl

musica/mechanism_configuration/user_defined.py

@@ -0,0 +1,83 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _UserDefined, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class UserDefined(_UserDefined):
+    """
+    A class representing a user-defined reaction rate constant.
+
+    Attributes:
+        name (str): The name of the photolysis reaction rate constant.
+        scaling_factor (float): The scaling factor for the photolysis rate constant.
+        reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+        products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
+        gas_phase (Phase): The gas phase in which the reaction occurs.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        scaling_factor: Optional[float] = None,
+        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        gas_phase: Optional[Phase] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the UserDefined object with the given parameters.
+
+        Args:
+            name (str): The name of the photolysis reaction rate constant.
+            scaling_factor (float): The scaling factor for the photolysis rate constant.
+            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+            products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
+            gas_phase (Phase): The gas phase in which the reaction occurs.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis reaction rate constant.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
+        self.reactants = (
+            [
+                (
+                    _ReactionComponent(r.name)
+                    if isinstance(r, Species)
+                    else _ReactionComponent(r[1].name, r[0])
+                )
+                for r in reactants
+            ]
+            if reactants is not None
+            else self.reactants
+        )
+        self.products = (
+            [
+                (
+                    _ReactionComponent(p.name)
+                    if isinstance(p, Species)
+                    else _ReactionComponent(p[1].name, p[0])
+                )
+                for p in products
+            ]
+            if products is not None
+            else self.products
+        )
+        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance) -> Dict:
+        serialize_dict = {
+            "type": "USER_DEFINED",
+            "name": instance.name,
+            "scaling factor": instance.scaling_factor,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
+            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
+            "gas phase": instance.gas_phase,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/utils.py

@@ -0,0 +1,10 @@
+from typing import Dict
+
+
+def _remove_empty_keys(dictionary: Dict) -> Dict:
+    return {k: v for k, v in dictionary.items() if v is not None and v != "" and v != [] and v != {}}
+
+
+def _add_other_properties(serialize_dict: Dict, other_properties: Dict) -> None:
+    for key in other_properties:
+        serialize_dict[key] = other_properties[key]

musica/mechanism_configuration/wet_deposition.py

@@ -0,0 +1,49 @@
+from typing import Optional, Any, Dict
+from musica import _WetDeposition
+from .phase import Phase
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class WetDeposition(_WetDeposition):
+    """
+    A class representing a wet deposition reaction rate constant.
+
+    Attributes:
+        name (str): The name of the wet deposition reaction rate constant.
+        scaling_factor (float): The scaling factor for the wet deposition rate constant.
+        aerosol_phase (Phase): The aerosol phase which undergoes wet deposition.
+        unknown_properties (Dict[str, Any]): A dictionary of other properties of the wet deposition reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        scaling_factor: Optional[float] = None,
+        aerosol_phase: Optional[Phase] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the WetDeposition object with the given parameters.
+
+        Args:
+            name (str): The name of the wet deposition reaction rate constant.
+            scaling_factor (float): The scaling factor for the wet deposition rate constant.
+            aerosol_phase (Phase): The aerosol phase which undergoes wet deposition.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the wet deposition reaction rate constant.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
+        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance) -> Dict:
+        serialize_dict = {
+            "type": "WET_DEPOSITION",
+            "name": instance.name,
+            "scaling factor": instance.scaling_factor,
+            "aerosol phase": instance.aerosol_phase,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration.cpp

@@ -374,7 +374,6 @@ void bind_mechanism_configuration(py::module_ & mechanism_configuration)
   py::class_<AqueousEquilibrium>(mechanism_configuration, "_AqueousEquilibrium")
       .def(py::init<>())
       .def_readwrite("name", &AqueousEquilibrium::name)
-      .def_readwrite("gas_phase", &AqueousEquilibrium::gas_phase)
       .def_readwrite("aerosol_phase", &AqueousEquilibrium::aerosol_phase)
       .def_readwrite("aerosol_phase_water", &AqueousEquilibrium::aerosol_phase_water)
       .def_readwrite("reactants", &AqueousEquilibrium::reactants)

musica/musica.cpp

@@ -211,4 +211,4 @@ void bind_musica(py::module_ &core)
         }, state->state_variant_);
       },
       "Print the state to stdout with the current time");
-}
+}

musica/test/examples/v1/{full_configuration.json → full_configuration/full_configuration.json}

@@ -108,7 +108,8 @@
       "aerosol phase": "aqueous aerosol",
       "aerosol-phase species": "H2O2_aq",
       "aerosol-phase water": "H2O_aq",
-      "name": "my henry's law"
+      "name": "my henry's law",
+      "__irrelevant": "2"
     },
     {
       "type": "SIMPOL_PHASE_TRANSFER",
@@ -122,7 +123,8 @@
         1.96E-03,
         -4.96E-01
       ],
-      "name": "my simpol"
+      "name": "my simpol",
+      "__irrelevant": "2"
     },
     {
       "type": "AQUEOUS_EQUILIBRIUM",
@@ -147,7 +149,8 @@
           "coefficient": 1
         }
       ],
-      "name": "my aqueous eq"
+      "name": "my aqueous eq",
+      "__irrelevant": "2"
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
@@ -174,7 +177,8 @@
           "coefficient": 1
         }
       ],
-      "name": "my condensed arrhenius"
+      "name": "my condensed arrhenius",
+      "__irrelevant": "2"
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
@@ -220,7 +224,8 @@
         }
       ],
       "scaling factor": 12.3,
-      "name": "condensed photo B"
+      "name": "condensed photo B",
+      "__irrelevant": "2"
     },
     {
       "type": "EMISSION",
@@ -232,7 +237,8 @@
         }
       ],
       "name": "my emission",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "FIRST_ORDER_LOSS",
@@ -244,7 +250,8 @@
         }
       ],
       "name": "my first order loss",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "PHOTOLYSIS",
@@ -262,7 +269,8 @@
         }
       ],
       "name": "photo B",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "SURFACE",
@@ -280,7 +288,8 @@
         }
       ],
       "aerosol phase": "surface reacting phase",
-      "name": "my surface"
+      "name": "my surface",
+      "__irrelevant": "2"
     },
     {
       "type": "TROE",
@@ -309,7 +318,8 @@
       "kinf_C": 24,
       "Fc": 0.9,
       "N": 0.8,
-      "name": "my troe"
+      "name": "my troe",
+      "__irrelevant": "2"
     },
     {
       "type": "BRANCHED_NO_RO2",
@@ -336,7 +346,8 @@
       "Y": 167,
       "a0": 0.15,
       "n": 9,
-      "name": "my branched"
+      "name": "my branched",
+      "__irrelevant": "2"
     },
     {
       "gas phase": "gas",
@@ -356,13 +367,15 @@
           "species name": "C",
           "coefficient": 1
         }
-      ]
+      ],
+      "__irrelevant": "2"
     },
     {
       "type": "WET_DEPOSITION",
       "aerosol phase": "cloud",
       "name": "rxn cloud",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     },
     {
       "type": "ARRHENIUS",
@@ -384,7 +397,8 @@
       "C": 102.3,
       "D": 63.4,
       "E": -1.3,
-      "name": "my arrhenius"
+      "name": "my arrhenius",
+      "__irrelevant": "2"
     },
     {
       "type": "ARRHENIUS",
@@ -428,7 +442,8 @@
         }
       ],
       "name": "my user defined",
-      "scaling factor": 12.3
+      "scaling factor": 12.3,
+      "__irrelevant": "2"
     }
   ]
 }

musica/test/examples/v1/{full_configuration.yaml → full_configuration/full_configuration.yaml}

@@ -72,6 +72,7 @@ reactions:
   aerosol-phase species: H2O2_aq
   aerosol-phase water: H2O_aq
   name: my henry's law
+  __irrelevant: "2"
 - type: SIMPOL_PHASE_TRANSFER
   gas phase: gas
   gas-phase species: ethanol
@@ -83,6 +84,7 @@ reactions:
   - 0.00196
   - -0.496
   name: my simpol
+  __irrelevant: "2"
 - type: AQUEOUS_EQUILIBRIUM
   aerosol phase: aqueous aerosol
   aerosol-phase water: H2O_aq
@@ -98,6 +100,7 @@ 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
@@ -115,6 +118,7 @@ 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
@@ -143,6 +147,7 @@ reactions:
     coefficient: 1
   scaling factor: 12.3
   name: condensed photo B
+  __irrelevant: "2"
 - type: EMISSION
   gas phase: gas
   products:
@@ -150,6 +155,7 @@ reactions:
     coefficient: 1
   name: my emission
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: FIRST_ORDER_LOSS
   gas phase: gas
   reactants:
@@ -157,6 +163,7 @@ reactions:
     coefficient: 1
   name: my first order loss
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: PHOTOLYSIS
   gas phase: gas
   reactants:
@@ -167,6 +174,7 @@ reactions:
     coefficient: 1
   name: photo B
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: SURFACE
   gas phase: gas
   gas-phase species: A
@@ -178,6 +186,7 @@ reactions:
     coefficient: 1
   aerosol phase: surface reacting phase
   name: my surface
+  __irrelevant: "2"
 - type: TROE
   gas phase: gas
   reactants:
@@ -197,6 +206,7 @@ reactions:
   Fc: 0.9
   N: 0.8
   name: my troe
+  __irrelevant: "2"
 - type: BRANCHED_NO_RO2
   gas phase: gas
   reactants:
@@ -213,6 +223,7 @@ reactions:
   a0: 0.15
   "n": 9
   name: my branched
+  __irrelevant: "2"
 - gas phase: gas
   type: TUNNELING
   name: "my tunneling"
@@ -225,10 +236,12 @@ reactions:
   products:
   - species name: C
     coefficient: 1
+  __irrelevant: "2"
 - type: WET_DEPOSITION
   aerosol phase: cloud
   name: rxn cloud
   scaling factor: 12.3
+  __irrelevant: "2"
 - type: ARRHENIUS
   gas phase: gas
   reactants:
@@ -243,6 +256,7 @@ reactions:
   D: 63.4
   E: -1.3
   name: my arrhenius
+  __irrelevant: "2"
 - type: ARRHENIUS
   gas phase: gas
   reactants:
@@ -268,4 +282,5 @@ 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

@@ -3,13 +3,13 @@ import numpy as np
 import musica
 import random
 import musica.mechanism_configuration as mc
-from musica._musica._core import _is_cuda_available
+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 = {
@@ -118,6 +118,7 @@ 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)
@@ -127,6 +128,7 @@ def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
     initial_temperatures = state.get_conditions()["temperature"]
     initial_pressures = state.get_conditions()["pressure"]
     initial_air_density = state.get_conditions()["air_density"]
+
     for i in range(num_grid_cells):
         assert np.isclose(initial_concentrations["A"][i], concentrations["A"][i], atol=1e-13)
         assert np.isclose(initial_concentrations["B"][i], concentrations["B"][i], atol=1e-13)
@@ -242,7 +244,7 @@ def GetMechanism():
 
 def test_single_grid_cell_standard_rosenbrock():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.rosenbrock_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 200.0, 5)
@@ -251,16 +253,16 @@ def test_single_grid_cell_standard_rosenbrock():
 def test_multiple_grid_cells_standard_rosenbrock():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.rosenbrock_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 200.0, 5)
 
 
 def test_cuda_rosenbrock():
-    if _is_cuda_available():
+    if is_cuda_available():
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.cuda_rosenbrock)
         state = solver.create_state()
         TestSingleGridCell(solver, state, 200.0, 5)
@@ -270,7 +272,7 @@ def test_cuda_rosenbrock():
 
 def test_single_grid_cell_backward_euler():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.backward_euler_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 10.0, places=2)
@@ -279,7 +281,7 @@ def test_single_grid_cell_backward_euler():
 def test_multiple_grid_cells_backward_euler():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.backward_euler_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 10.0, places=2)
@@ -287,7 +289,7 @@ def test_multiple_grid_cells_backward_euler():
 
 def test_single_grid_cell_rosenbrock():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.rosenbrock)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 200.0, 5)
@@ -296,7 +298,7 @@ def test_single_grid_cell_rosenbrock():
 def test_multiple_grid_cells_rosenbrock():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.rosenbrock)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 200.0, 5)
@@ -304,7 +306,7 @@ def test_multiple_grid_cells_rosenbrock():
 
 def test_single_grid_cell_backward_euler_standard_order():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.backward_euler_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 10.0, places=2)
@@ -313,7 +315,7 @@ def test_single_grid_cell_backward_euler_standard_order():
 def test_multiple_grid_cells_backward_euler_standard_order():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.backward_euler_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 10.0, places=2)

musica/test/test_chapman.py

@@ -3,9 +3,25 @@ import musica
 import musica.mechanism_configuration as mc
 
 
-def test_solve_with_config_path():
+def test_solve_with_config_path_v0():
     solver = musica.MICM(
-        config_path="configs/chapman",
+        config_path="configs/v0/chapman",
+        solver_type=musica.SolverType.rosenbrock_standard_order,
+    )
+    TestSolve(solver)
+
+
+def test_solve_with_config_path_v1_json():
+    solver = musica.MICM(
+        config_path="configs/v1/chapman/config.json",
+        solver_type=musica.SolverType.rosenbrock_standard_order,
+    )
+    TestSolve(solver)
+
+
+def test_solve_with_config_path_v1_yaml():
+    solver = musica.MICM(
+        config_path="configs/v1/chapman/config.yaml",
         solver_type=musica.SolverType.rosenbrock_standard_order,
     )
     TestSolve(solver)