musica 0.11.1.3__cp311-cp311-win32.whl → 0.12.0__cp311-cp311-win32.whl

musica/mechanism_configuration/condensed_phase_arrhenius.py

@@ -0,0 +1,116 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _CondensedPhaseArrhenius, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+from musica.constants import BOLTZMANN
+
+
+class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
+    """
+    A class representing a condensed phase Arrhenius rate constant.
+
+    Attributes:
+        name (str): The name of the condensed phase Arrhenius rate constant.
+        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
+        B (float): Temperature exponent [unitless].
+        C (float): Exponential term [K-1].
+        Ea (float): Activation energy [J molecule-1].
+        D (float): Reference Temperature [K].
+        E (float): Pressure scaling term [Pa-1].
+        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.
+        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+        aerosol_phase_water (Species): The water species in the aerosol phase.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase Arrhenius rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        A: Optional[float] = None,
+        B: Optional[float] = None,
+        C: Optional[float] = None,
+        Ea: Optional[float] = None,
+        D: Optional[float] = None,
+        E: Optional[float] = None,
+        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        aerosol_phase: Optional[Phase] = None,
+        aerosol_phase_water: Optional[Species] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the CondensedPhaseArrhenius object with the given parameters.
+
+        Args:
+            name (str): The name of the condensed phase Arrhenius rate constant.
+            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1].
+            B (float): Temperature exponent [unitless].
+            C (float): Exponential term [K-1].
+            Ea (float): Activation energy [J molecule-1].
+            D (float): Reference Temperature [K].
+            E (float): Pressure scaling term [Pa-1].
+            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.
+            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+            aerosol_phase_water (Species): The water species in the aerosol phase.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase Arrhenius 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
+        if C is not None and Ea is not None:
+            raise ValueError("Cannot specify both C and Ea.")
+        self.C = -Ea / BOLTZMANN if Ea is not None else C if C is not None else self.C
+        self.D = D if D is not None else self.D
+        self.E = E if E is not None else self.E
+        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.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
+        self.aerosol_phase_water = (
+            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
+        )
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance) -> Dict:
+        serialize_dict = {
+            "type": "CONDENSED_PHASE_ARRHENIUS",
+            "name": instance.name,
+            "A": instance.A,
+            "B": instance.B,
+            "C": instance.C,
+            "D": instance.D,
+            "E": instance.E,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
+            "products":  ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
+            "aerosol phase": instance.aerosol_phase,
+            "aerosol-phase water": instance.aerosol_phase_water,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/condensed_phase_photolysis.py

@@ -0,0 +1,91 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _CondensedPhasePhotolysis, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+
+class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
+    """
+    A class representing a condensed phase photolysis reaction rate constant.
+
+    Attributes:
+        name (str): The name of the condensed phase 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.
+        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+        aerosol_phase_water (float): The water species in the aerosol phase [unitless].
+        other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase 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,
+        aerosol_phase: Optional[Phase] = None,
+        aerosol_phase_water: Optional[Species] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the CondensedPhasePhotolysis object with the given parameters.
+
+        Args:
+            name (str): The name of the condensed phase 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.
+            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+            aerosol_phase_water (Species): The water species in the aerosol phase [unitless].
+            other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase 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.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
+        self.aerosol_phase_water = (
+            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
+        )
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance) -> Dict:
+        serialize_dict = {
+            "type": "CONDENSED_PHASE_PHOTOLYSIS",
+            "name": instance.name,
+            "scaling factor": instance.scaling_factor,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
+            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
+            "aerosol phase": instance.aerosol_phase,
+            "aerosol-phase water": instance.aerosol_phase_water,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/emission.py

@@ -0,0 +1,67 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _Emission, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class Emission(_Emission):
+    """
+    A class representing an emission reaction rate constant.
+
+    Attributes:
+        name (str): The name of the emission reaction rate constant.
+        scaling_factor (float): The scaling factor for the emission rate constant.
+        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 emission reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        scaling_factor: Optional[float] = None,
+        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        gas_phase: Optional[Phase] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the Emission object with the given parameters.
+
+        Args:
+            name (str): The name of the emission reaction rate constant.
+            scaling_factor (float): The scaling factor for the emission rate constant.
+            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 emission 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.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": "EMISSION",
+            "name": instance.name,
+            "scaling factor": instance.scaling_factor,
+            "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/first_order_loss.py

@@ -0,0 +1,67 @@
+from typing import Optional, Any, Dict, List, Union, Tuple
+from musica import _FirstOrderLoss, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class FirstOrderLoss(_FirstOrderLoss):
+    """
+    A class representing a first-order loss reaction rate constant.
+
+    Attributes:
+        name (str): The name of the first-order loss reaction rate constant.
+        scaling_factor (float): The scaling factor for the first-order loss rate constant.
+        reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved 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 first-order loss reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        scaling_factor: Optional[float] = None,
+        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        gas_phase: Optional[Phase] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the FirstOrderLoss object with the given parameters.
+
+        Args:
+            name (str): The name of the first-order loss reaction rate constant.
+            scaling_factor (float): The scaling factor for the first-order loss rate constant.
+            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved 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 first-order loss 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.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": "FIRST_ORDER_LOSS",
+            "name": instance.name,
+            "scaling factor": instance.scaling_factor,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
+            "gas phase": instance.gas_phase,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/henrys_law.py

@@ -0,0 +1,85 @@
+from typing import Optional, Any, Dict, Union, Tuple
+from musica import _HenrysLaw, _ReactionComponent
+from .phase import Phase
+from .species import Species
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class HenrysLaw(_HenrysLaw):
+    """
+    A class representing a Henry's law reaction rate constant.
+
+    Attributes:
+        name (str): The name of the Henry's law reaction rate constant.
+        gas_phase (Phase): The gas phase in which the reaction occurs.
+        gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
+        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+        aerosol_phase_water (Species): The water species in the aerosol phase.
+        aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the Henry's law reaction rate constant.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        gas_phase: Optional[Phase] = None,
+        gas_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
+        aerosol_phase: Optional[Phase] = None,
+        aerosol_phase_water: Optional[Species] = None,
+        aerosol_phase_species: Optional[Union[Species, Tuple[float, Species]]] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the HenrysLaw object with the given parameters.
+
+        Args:
+            name (str): The name of the Henry's law reaction rate constant.
+            gas_phase (Phase): The gas phase in which the reaction occurs.
+            gas_phase_species (Union[Species, Tuple[float, Species]]): The gas phase species involved in the reaction.
+            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
+            aerosol_phase_water (Species): The water species in the aerosol phase.
+            aerosol_phase_species (Union[Species, Tuple[float, Species]]): The aerosol phase species involved in the reaction.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the Henry's law reaction rate constant.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
+        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.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
+        self.aerosol_phase_water = (
+            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
+        )
+        self.aerosol_phase_species = (
+            (
+                _ReactionComponent(aerosol_phase_species.name)
+                if isinstance(aerosol_phase_species, Species)
+                else _ReactionComponent(
+                    aerosol_phase_species[1].name, aerosol_phase_species[0]
+                )
+            )
+            if aerosol_phase_species is not None
+            else self.aerosol_phase_species
+        )
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance) -> Dict:
+        serialize_dict = {
+            "type": "HL_PHASE_TRANSFER",
+            "name": instance.name,
+            "gas phase": instance.gas_phase,
+            "gas-phase species": instance.gas_phase_species.species_name,
+            "aerosol phase": instance.aerosol_phase,
+            "aerosol-phase water": instance.aerosol_phase_water,
+            "aerosol-phase species": instance.aerosol_phase_species.species_name,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)

musica/mechanism_configuration/mechanism_configuration.py

@@ -0,0 +1,161 @@
+# Copyright (C) 2025 University Corporation for Atmospheric Research
+# SPDX-License-Identifier: Apache-2.0
+#
+# This file is part of the musica Python package.
+# For more information, see the LICENSE file in the top-level directory of this distribution.
+import os
+import json
+import yaml
+from typing import Optional, Any, Dict, List
+from musica import _Mechanism, _Version, _Parser
+from .species import Species
+from .phase import Phase
+from .arrhenius import Arrhenius, _Arrhenius
+from .condensed_phase_arrhenius import CondensedPhaseArrhenius, _CondensedPhaseArrhenius
+from .troe import Troe, _Troe
+from .branched import Branched, _Branched
+from .tunneling import Tunneling, _Tunneling
+from .surface import Surface, _Surface
+from .photolysis import Photolysis, _Photolysis
+from .condensed_phase_photolysis import CondensedPhasePhotolysis, _CondensedPhasePhotolysis
+from .emission import Emission, _Emission
+from .first_order_loss import FirstOrderLoss, _FirstOrderLoss
+from .aqueous_equilibrium import AqueousEquilibrium, _AqueousEquilibrium
+from .wet_deposition import WetDeposition, _WetDeposition
+from .henrys_law import HenrysLaw, _HenrysLaw
+from .simpol_phase_transfer import SimpolPhaseTransfer, _SimpolPhaseTransfer
+from .user_defined import UserDefined, _UserDefined
+from .reactions import Reactions, ReactionType
+
+
+class Version(_Version):
+    """
+    A class representing the version of the mechanism.
+    """
+
+
+class Mechanism(_Mechanism):
+    """
+    A class representing a chemical mechanism.
+
+    Attributes:
+        name (str): The name of the mechanism.
+        reactions (List[Reaction]): A list of reactions in the mechanism.
+        species (List[Species]): A list of species in the mechanism.
+        phases (List[Phase]): A list of phases in the mechanism.
+        version (Version): The version of the mechanism.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        reactions: Optional[List[Any]] = None,
+        species: Optional[List[Species]] = None,
+        phases: Optional[List[Phase]] = None,
+        version: Optional[Version] = None,
+    ):
+        """
+        Initializes the Mechanism object with the given parameters.
+
+        Args:
+            name (str): The name of the mechanism.
+            reactions (List[]): A list of reactions in the mechanism.
+            species (List[Species]): A list of species in the mechanism.
+            phases (List[Phase]): A list of phases in the mechanism.
+            version (Version): The version of the mechanism.
+        """
+        super().__init__()
+        self.name = name
+        self.species = species if species is not None else []
+        self.phases = phases if phases is not None else []
+        self.reactions = Reactions(reactions=reactions if reactions is not None else [])
+        self.version = version if version is not None else Version()
+
+    def to_dict(self) -> Dict:
+        species_list = []
+        for species in self.species:
+            species_list.append(Species.serialize(species))
+
+        phases_list = []
+        for phase in self.phases:
+            phases_list.append(Phase.serialize(phase))
+
+        reactions_list = []
+        for reaction in self.reactions:
+            if isinstance(reaction, (_Arrhenius, Arrhenius)):
+                reactions_list.append(Arrhenius.serialize(reaction))
+            elif isinstance(reaction, (_Branched, Branched)):
+                reactions_list.append(Branched.serialize(reaction))
+            elif isinstance(reaction, (_CondensedPhaseArrhenius, CondensedPhaseArrhenius)):
+                reactions_list.append(CondensedPhaseArrhenius.serialize(reaction))
+            elif isinstance(reaction, (_CondensedPhasePhotolysis, CondensedPhasePhotolysis)):
+                reactions_list.append(CondensedPhasePhotolysis.serialize(reaction))
+            elif isinstance(reaction, (_Emission, Emission)):
+                reactions_list.append(Emission.serialize(reaction))
+            elif isinstance(reaction, (_FirstOrderLoss, FirstOrderLoss)):
+                reactions_list.append(FirstOrderLoss.serialize(reaction))
+            elif isinstance(reaction, (_SimpolPhaseTransfer, SimpolPhaseTransfer)):
+                reactions_list.append(SimpolPhaseTransfer.serialize(reaction))
+            elif isinstance(reaction, (_AqueousEquilibrium, AqueousEquilibrium)):
+                reactions_list.append(AqueousEquilibrium.serialize(reaction))
+            elif isinstance(reaction, (_WetDeposition, WetDeposition)):
+                reactions_list.append(WetDeposition.serialize(reaction))
+            elif isinstance(reaction, (_HenrysLaw, HenrysLaw)):
+                reactions_list.append(HenrysLaw.serialize(reaction))
+            elif isinstance(reaction, (_Photolysis, Photolysis)):
+                reactions_list.append(Photolysis.serialize(reaction))
+            elif isinstance(reaction, (_Surface, Surface)):
+                reactions_list.append(Surface.serialize(reaction))
+            elif isinstance(reaction, (_Troe, Troe)):
+                reactions_list.append(Troe.serialize(reaction))
+            elif isinstance(reaction, (_Tunneling, Tunneling)):
+                reactions_list.append(Tunneling.serialize(reaction))
+            elif isinstance(reaction, (_UserDefined, UserDefined)):
+                reactions_list.append(UserDefined.serialize(reaction))
+            else:
+                raise TypeError(f'Reaction type {type(reaction)} is not supported for export.')
+
+        return {
+            "name": self.name,
+            "reactions": reactions_list,
+            "species": species_list,
+            "phases": phases_list,
+            "version": self.version.to_string(),
+        }
+
+    def export(self, file_path: str) -> None:
+        MechanismSerializer.serialize(self, file_path)
+
+
+class Parser(_Parser):
+    """
+    A class for parsing a chemical mechanism.
+    """
+
+
+class MechanismSerializer():
+    """
+    A class for exporting a chemical mechanism.
+    """
+
+    @staticmethod
+    def serialize(mechanism: Mechanism, file_path: str = "./mechanism.json") -> None:        
+        if not isinstance(mechanism, Mechanism):
+            raise TypeError(f"Object {mechanism} is not of type Mechanism.")
+
+        directory, file = os.path.split(file_path)
+        if directory:
+            os.makedirs(directory, exist_ok=True)
+        dictionary = mechanism.to_dict()
+        
+        _, file_ext = os.path.splitext(file)
+        file_ext = file_ext.lower()
+        if file_ext in ['.yaml', '.yml']:
+            with open(file_path, 'w') as file:
+                yaml.dump(dictionary, file)
+        elif '.json' == file_ext:
+            json_str = json.dumps(dictionary, indent=4)
+            with open(file_path, 'w') as file:
+                file.write(json_str)
+        else:
+            raise Exception('Allowable write formats are .json, .yaml, and .yml')

musica/mechanism_configuration/phase.py

@@ -0,0 +1,43 @@
+from typing import Optional, Any, Dict, List
+from musica import _Phase
+from .species import Species
+from .utils import _add_other_properties, _remove_empty_keys
+
+
+class Phase(_Phase):
+    """
+    A class representing a phase in a chemical mechanism.
+
+    Attributes:
+        name (str): The name of the phase.
+        species (List[Species]): A list of species in the phase.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        species: Optional[List[Species]] = None,
+        other_properties: Optional[Dict[str, Any]] = None,
+    ):
+        """
+        Initializes the Phase object with the given parameters.
+
+        Args:
+            name (str): The name of the phase.
+            species (List[Species]): A list of species in the phase.
+            other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
+        """
+        super().__init__()
+        self.name = name if name is not None else self.name
+        self.species = [s.name for s in species] if species is not None else self.species
+        self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+    @staticmethod
+    def serialize(instance):
+        serialize_dict = {
+            "name": instance.name,
+            "species": instance.species,
+        }
+        _add_other_properties(serialize_dict, instance.other_properties)
+        return _remove_empty_keys(serialize_dict)