musica 0.11.1.4__cp312-cp312-win32.whl → 0.12.0__cp312-cp312-win32.whl

musica/mechanism_configuration/surface.py

@@ -0,0 +1,89 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _Surface, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class Surface(_Surface):
+    """
+    A class representing a surface in a chemical mechanism.
+
+    (TODO: get details from MusicBox)
+
+    Attributes:
+        name (str): The name of the surface.
+        reaction_probability (float): The probability of a reaction occurring on the surface.
+        gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
+        gas_phase_products (List[Union[Species, Tuple[float, Species]]]): The gas phase products formed in the reaction.
+        gas_phase (Phase): The gas phase in which the reaction occurs.
+        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the surface.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        reaction_probability: Optional[float] = None,
+        gas_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
+        gas_phase_products: Optional[
+            List[Union[Species, Tuple[float, Species]]]
+        ] = None,
+        gas_phase: Optional[Phase] = None,
+        aerosol_phase: Optional[Phase] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the Surface object with the given parameters.
+
+        Args:
+            name (str): The name of the surface.
+            reaction_probability (float): The probability of a reaction occurring on the surface.
+            gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
+            gas_phase_products (List[Union[Species, Tuple[float, Species]]]): The gas phase products formed in the reaction.
+            gas_phase (Phase): The gas phase in which the reaction occurs.
+            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the surface.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.reaction_probability = reaction_probability if reaction_probability is not None else self.reaction_probability
+        self.gas_phase_species = (
+            (
+                _ReactionComponent(gas_phase_species.name)
+                if isinstance(gas_phase_species, Species)
+                else _ReactionComponent(gas_phase_species[1].name, gas_phase_species[0])
+            )
+            if gas_phase_species is not None
+            else self.gas_phase_species
+        )
+        self.gas_phase_products = (
+            [
+                (
+                    _ReactionComponent(p.name)
+                    if isinstance(p, Species)
+                    else _ReactionComponent(p[1].name, p[0])
+                )
+                for p in gas_phase_products
+            ]
+            if gas_phase_products is not None
+            else self.gas_phase_products
+        )
+        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
+        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": "SURFACE",
+            "name": instance.name,
+            "reaction probability": instance.reaction_probability,
+            "gas-phase species": instance.gas_phase_species.species_name,
+            "gas-phase products": ReactionComponentSerializer.serialize_list_reaction_components(instance.gas_phase_products),
+            "gas phase": instance.gas_phase,
+            "aerosol phase": instance.aerosol_phase,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/troe.py

@@ -0,0 +1,137 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _Troe, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class Troe(_Troe):
+    """
+    A class representing a Troe rate constant.
+
+    Attributes:
+        name (str): The name of the Troe rate constant.
+        k0_A (float): Pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1].
+        k0_B (float): Temperature exponent for the low-pressure limit [unitless].
+        k0_C (float): Exponential term for the low-pressure limit [K-1].
+        kinf_A (float): Pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1].
+        kinf_B (float): Temperature exponent for the high-pressure limit [unitless].
+        kinf_C (float): Exponential term for the high-pressure limit [K-1].
+        Fc (float): Troe parameter [unitless].
+        N (float): Troe parameter [unitless].
+        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 Troe rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        k0_A: Optional[float] = None,
+        k0_B: Optional[float] = None,
+        k0_C: Optional[float] = None,
+        kinf_A: Optional[float] = None,
+        kinf_B: Optional[float] = None,
+        kinf_C: Optional[float] = None,
+        Fc: Optional[float] = None,
+        N: 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 Troe object with the given parameters.
+
+        k0 = k0_A * exp( k0_C / T ) * ( T / 300.0 )^k0_B
+        kinf = kinf_A * exp( kinf_C / T ) * ( T / 300.0 )^kinf_B
+        k = k0[M] / ( 1 + k0[M] / kinf ) * Fc^(1 + 1/N*(log10(k0[M]/kinf))^2)^-1
+
+        where:
+            k = rate constant
+            k0 = low-pressure limit rate constant
+            kinf = high-pressure limit rate constant
+            k0_A = pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1]
+            k0_B = temperature exponent for the low-pressure limit [unitless]
+            k0_C = exponential term for the low-pressure limit [K-1]
+            kinf_A = pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1]
+            kinf_B = temperature exponent for the high-pressure limit [unitless]
+            kinf_C = exponential term for the high-pressure limit [K-1]
+            Fc = Troe parameter [unitless]
+            N = Troe parameter [unitless]
+            T = temperature [K]
+            M = concentration of the third body [mol m-3]
+
+        Args:
+            name (str): The name of the Troe rate constant.
+            k0_A (float): Pre-exponential factor for the low-pressure limit [(mol m-3)^(n-1)s-1].
+            k0_B (float): Temperature exponent for the low-pressure limit [unitless].
+            k0_C (float): Exponential term for the low-pressure limit [K-1].
+            kinf_A (float): Pre-exponential factor for the high-pressure limit [(mol m-3)^(n-1)s-1].
+            kinf_B (float): Temperature exponent for the high-pressure limit [unitless].
+            kinf_C (float): Exponential term for the high-pressure limit [K-1].
+            Fc (float): Troe parameter [unitless].
+            N (float): Troe parameter [unitless].
+            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 Troe rate constant.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.k0_A = k0_A if k0_A is not None else self.k0_A
+        self.k0_B = k0_B if k0_B is not None else self.k0_B
+        self.k0_C = k0_C if k0_C is not None else self.k0_C
+        self.kinf_A = kinf_A if kinf_A is not None else self.kinf_A
+        self.kinf_B = kinf_B if kinf_B is not None else self.kinf_B
+        self.kinf_C = kinf_C if kinf_C is not None else self.kinf_C
+        self.Fc = Fc if Fc is not None else self.Fc
+        self.N = N if N is not None else self.N
+        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": "TROE",
+            "name": instance.name,
+            "k0_A": instance.k0_A,
+            "k0_B": instance.k0_B,
+            "k0_C": instance.k0_C,
+            "kinf_A": instance.kinf_A,
+            "kinf_B": instance.kinf_B,
+            "kinf_C": instance.kinf_C,
+            "Fc": instance.Fc,
+            "N": instance.N,
+            "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/tunneling.py

@@ -0,0 +1,103 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _Tunneling, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class Tunneling(_Tunneling):
+    """
+    A class representing a quantum tunneling reaction rate constant.
+
+    k = A * exp( -B / T ) * exp( C / T^3 )
+
+    where:
+        k = rate constant
+        A = pre-exponential factor [(mol m-3)^(n-1)s-1]
+        B = tunneling parameter [K^-1]
+        C = tunneling parameter [K^-3]
+        T = temperature [K]
+        n = number of reactants
+
+    Attributes:
+        name (str): The name of the tunneling reaction rate constant.
+        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
+        B (float): Tunneling parameter [K^-1].
+        C (float): Tunneling parameter [K^-3].
+        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 tunneling reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        A: Optional[float] = None,
+        B: Optional[float] = None,
+        C: 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 Tunneling object with the given parameters.
+
+        Args:
+            name (str): The name of the tunneling reaction rate constant.
+            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
+            B (float): Tunneling parameter [K^-1].
+            C (float): Tunneling parameter [K^-3].
+            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 tunneling reaction rate constant.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.A = A if A is not None else self.A
+        self.B = B if B is not None else self.B
+        self.C = C if C is not None else self.C
+        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": "TUNNELING",
+            "name": instance.name,
+            "A": instance.A,
+            "B": instance.B,
+            "C": instance.C,
+            "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/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/test/examples/v1/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"
     }
   ]
 }