musica 0.12.2__cp313-cp313-win_amd64.whl → 0.13.0__cp313-cp313-win_amd64.whl

musica/mechanism_configuration/arrhenius.py

@@ -2,18 +2,120 @@ from typing import Optional, Any, Dict, List, Union, Tuple
 from .. import backend
 from .phase import Phase
 from .species import Species
-from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties
+from .utils import _add_other_properties, _remove_empty_keys
 from ..constants import BOLTZMANN
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_Arrhenius = _backend._mechanism_configuration._Arrhenius
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
-ReactionType = _backend._mechanism_configuration._ReactionType
+Arrhenius = _backend._mechanism_configuration._Arrhenius
+
+original_init = Arrhenius.__init__
+
+
+@property
+def type(self):
+    """Get the reaction type."""
+    return ReactionType.Arrhenius
+
+
+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,
+    gas_phase: Optional[Phase] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
+    """
+    Initializes the Arrhenius object with the given parameters.
 
+    Args:
+        name (str): The name of the Arrhenius rate constant.
+        A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1] where n is the number of reactants.
+        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.
+        gas_phase (Phase): The gas phase in which the reaction occurs.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the Arrhenius rate constant.
+    """
+    original_init(self)
+
+    # Validate mutually exclusive parameters
+    if C is not None and Ea is not None:
+        raise ValueError("Cannot specify both C and Ea.")
+    if Ea is not None:
+        C = -Ea / BOLTZMANN
+
+    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.D = D if D is not None else self.D
+    self.E = E if E is not None else self.E
+    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
+    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
+    )
+
+
+def serialize(self) -> Dict:
+    """
+    Serialize the Arrhenius object to a dictionary using only Python-visible data.
 
-class Arrhenius:
+    Returns:
+        Dict: A dictionary representation of the Arrhenius object.
     """
+    serialize_dict = {
+        "type": "ARRHENIUS",
+        "name": self.name,
+        "A": self.A,
+        "B": self.B,
+        "C": self.C,
+        "D": self.D,
+        "E": self.E,
+        "reactants": [r.serialize() for r in self.reactants],
+        "products": [r.serialize() for r in self.products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
+
+Arrhenius.__doc__ = """
     A class representing an Arrhenius rate constant.
 
     k = A * exp( C / T ) * ( T / D )^B * exp( 1 - E * P )
@@ -42,266 +144,6 @@ class Arrhenius:
         other_properties (Dict[str, Any]): A dictionary of other properties of the 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,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Arrhenius object with the given parameters.
-
-        Args:
-            name (str): The name of the Arrhenius rate constant.
-            A (float): Pre-exponential factor [(mol m-3)^(n-1)s-1] where n is the number of reactants.
-            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.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the Arrhenius rate constant.
-        """
-        # Create the internal C++ instance
-        self._instance = _Arrhenius()
-
-        # Validate mutually exclusive parameters
-        if C is not None and Ea is not None:
-            raise ValueError("Cannot specify both C and Ea.")
-
-        # Set all parameters
-        if name is not None:
-            self.name = name
-        if A is not None:
-            self.A = A
-        if B is not None:
-            self.B = B
-        if Ea is not None:
-            self.C = -Ea / BOLTZMANN
-        elif C is not None:
-            self.C = C
-        if D is not None:
-            self.D = D
-        if E is not None:
-            self.E = E
-        if reactants is not None:
-            self.reactants = reactants
-        if products is not None:
-            self.products = products
-        if gas_phase is not None:
-            self.gas_phase = gas_phase
-        if other_properties is not None:
-            self.other_properties = other_properties
-
-    # Property delegation to self._instance
-    @property
-    def name(self) -> str:
-        """Get the name of the Arrhenius rate constant."""
-        return self._instance.name
-
-    @name.setter
-    def name(self, value: str):
-        """Set the name of the Arrhenius rate constant."""
-        self._instance.name = value
-
-    @property
-    def A(self) -> float:
-        """Get the pre-exponential factor."""
-        return self._instance.A
-
-    @A.setter
-    def A(self, value: float):
-        """Set the pre-exponential factor."""
-        self._instance.A = value
-
-    @property
-    def B(self) -> float:
-        """Get the temperature exponent."""
-        return self._instance.B
-
-    @B.setter
-    def B(self, value: float):
-        """Set the temperature exponent."""
-        self._instance.B = value
-
-    @property
-    def C(self) -> float:
-        """Get the exponential term."""
-        return self._instance.C
-
-    @C.setter
-    def C(self, value: float):
-        """Set the exponential term."""
-        self._instance.C = value
-
-    @property
-    def D(self) -> float:
-        """Get the reference temperature."""
-        return self._instance.D
-
-    @D.setter
-    def D(self, value: float):
-        """Set the reference temperature."""
-        self._instance.D = value
-
-    @property
-    def E(self) -> float:
-        """Get the pressure scaling term."""
-        return self._instance.E
-
-    @E.setter
-    def E(self, value: float):
-        """Set the pressure scaling term."""
-        self._instance.E = value
-
-    @property
-    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
-        """Get the reactants as Python objects."""
-        # Convert from C++ _ReactionComponent objects to Python Species objects
-        result = []
-        for rc in self._instance.reactants:
-            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
-                # Create a tuple with coefficient and species
-                species = Species(name=rc.species_name)
-                result.append((rc.coefficient, species))
-            else:
-                # Just the species
-                species = Species(name=rc.species_name)
-                result.append(species)
-        return result
-
-    @reactants.setter
-    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
-        """Set the reactants, converting from Python to C++ objects."""
-        cpp_reactants = []
-        for r in value:
-            if isinstance(r, Species):
-                cpp_reactants.append(_ReactionComponent(r.name))
-            elif isinstance(r, tuple) and len(r) == 2:
-                coefficient, species = r
-                cpp_reactants.append(_ReactionComponent(species.name, coefficient))
-            else:
-                raise ValueError(f"Invalid reactant format: {r}")
-        self._instance.reactants = cpp_reactants
-
-    @property
-    def products(self) -> List[Union[Species, Tuple[float, Species]]]:
-        """Get the products as Python objects."""
-        # Convert from C++ _ReactionComponent objects to Python Species objects
-        result = []
-        for rc in self._instance.products:
-            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
-                # Create a tuple with coefficient and species
-                species = Species(name=rc.species_name)
-                result.append((rc.coefficient, species))
-            else:
-                # Just the species
-                species = Species(name=rc.species_name)
-                result.append(species)
-        return result
-
-    @products.setter
-    def products(self, value: List[Union[Species, Tuple[float, Species]]]):
-        """Set the products, converting from Python to C++ objects."""
-        cpp_products = []
-        for p in value:
-            if isinstance(p, Species):
-                cpp_products.append(_ReactionComponent(p.name))
-            elif isinstance(p, tuple) and len(p) == 2:
-                coefficient, species = p
-                cpp_products.append(_ReactionComponent(species.name, coefficient))
-            else:
-                raise ValueError(f"Invalid product format: {p}")
-        self._instance.products = cpp_products
-
-    @property
-    def gas_phase(self) -> str:
-        """Get the gas phase name."""
-        return self._instance.gas_phase
-
-    @gas_phase.setter
-    def gas_phase(self, value: Union[Phase, str]):
-        """Set the gas phase."""
-        if isinstance(value, Phase):
-            self._instance.gas_phase = value.name
-        elif isinstance(value, str):
-            self._instance.gas_phase = value
-        else:
-            raise ValueError(f"Invalid gas_phase type: {type(value)}")
-
-    @property
-    def other_properties(self) -> Dict[str, Any]:
-        """Get the other properties."""
-        return self._instance.other_properties
-
-    @other_properties.setter
-    def other_properties(self, value: Dict[str, Any]):
-        """Set the other properties."""
-        self._instance.other_properties = value
-
-    @property
-    def type(self):
-        """Get the reaction type."""
-        return ReactionType.Arrhenius
-
-    def _create_serialize_dict(self, instance) -> Dict:
-        """
-        Helper method to create the serialization dictionary.
-
-        Args:
-            instance: The instance to serialize (either self._instance or a _Arrhenius object).
-
-        Returns:
-            Dict: Base serialization dictionary.
-        """
-        return {
-            "type": "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),
-            "gas phase": instance.gas_phase,
-        }
-
-    def serialize(self) -> Dict:
-        """
-        Serialize the Arrhenius object to a dictionary using only Python-visible data.
-
-        Returns:
-            Dict: A dictionary representation of the Arrhenius object.
-        """
-        serialize_dict = self._create_serialize_dict(self._instance)
-        _add_other_properties(serialize_dict, self.other_properties)
-        return serialize_dict
-
-    @staticmethod
-    def serialize_static(instance) -> Dict:
-        """
-        Static serialize method for compatibility with C++ _Arrhenius objects.
-
-        Args:
-            instance: The _Arrhenius instance to serialize.
-
-        Returns:
-            Dict: A dictionary representation of the Arrhenius object.
-        """
-        # Create a temporary Arrhenius object to use the helper method
-        temp_arrhenius = Arrhenius()
-        serialize_dict = temp_arrhenius._create_serialize_dict(instance)
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return serialize_dict
+Arrhenius.__init__ = __init__
+Arrhenius.serialize = serialize
+Arrhenius.type = type