python box model iniital classes

src/box_model.py

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+from music_box_evolving_conditions import EvolvingConditions
+from music_box_reaction_list import ReactionList
+from music_box_species_list import SpeciesList
+from music_box_model_options import BoxModelOptions
+
+class BoxModel:
+    """
+    Represents a box model with attributes such as box model options, species list, reaction list,
+    initial conditions, and evolving conditions.
+
+    Attributes:
+        boxModelOptions (BoxModelOptions): Options for the box model simulation.
+        speciesList (SpeciesList): A list of species.
+        reactionList (ReactionList): A list of reactions.
+        initialConditions (Conditions): Initial conditions for the simulation.
+        evolvingConditions (List[EvolvingConditions]): List of evolving conditions over time.
+    """
+
+    def __init__(self, box_model_options, species_list, reaction_list, initial_conditions, evolving_conditions):
+        """
+        Initializes a new instance of the BoxModel class.
+
+        Args:
+            box_model_options (BoxModelOptions): Options for the box model simulation.
+            species_list (SpeciesList): A list of species.
+            reaction_list (ReactionList): A list of reactions.
+            initial_conditions (Conditions): Initial conditions for the simulation.
+            evolving_conditions (List[EvolvingConditions]): List of evolving conditions over time.
+        """
+        self.boxModelOptions = box_model_options
+        self.speciesList = species_list
+        self.reactionList = reaction_list
+        self.initialConditions = initial_conditions
+        self.evolvingConditions = evolving_conditions
+
+    def add_evolving_condition(self, time_point, conditions):
+        """
+        Add an evolving condition at a specific time point.
+
+        Args:
+            time_point (float): The time point for the evolving condition.
+            conditions (Conditions): The associated conditions at the given time point.
+        """
+        evolving_condition = EvolvingConditions(time=[time_point], conditions=[conditions])
+        self.evolvingConditions.append(evolving_condition)
+
+    def generateFiles(self):
+        """
+        TODO: Generate configuration JSON files for the box model simulation.
+        """
+        # TODO: Implement the logic to generate configuration files.
+        # This method is a placeholder, and the actual implementation is required.
+        pass

src/music_box_conditions.py

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+from typing import List
+
+class Conditions:
+    """
+    Represents conditions for a simulation with attributes such as pressure, temperature, species concentrations,
+    and reaction rates.
+
+    Attributes:
+        pressure (float): The pressure of the conditions in atmospheres.
+        temperature (float): The temperature of the conditions in Kelvin.
+        speciesConcentrations (List[SpeciesConcentration]): A list of species concentrations.
+        reactionRates (List[ReactionRate]): A list of reaction rates.
+    """
+
+    def __init__(self, pressure, temperature, species_concentrations=None, reaction_rates=None):
+        """
+        Initializes a new instance of the Conditions class.
+
+        Args:
+            pressure (float): The pressure of the conditions in atmospheres.
+            temperature (float): The temperature of the conditions in Kelvin.
+            species_concentrations (List[SpeciesConcentration]): A list of species concentrations. Default is an empty list.
+            reaction_rates (List[ReactionRate]): A list of reaction rates. Default is an empty list.
+        """
+        self.pressure = pressure
+        self.temperature = temperature
+        self.speciesConcentrations = species_concentrations if species_concentrations is not None else []
+        self.reactionRates = reaction_rates if reaction_rates is not None else []
+
+    def add_species_concentration(self, species_concentration):
+        """
+        Add a SpeciesConcentration instance to the list of species concentrations.
+
+        Args:
+            species_concentration (SpeciesConcentration): The SpeciesConcentration instance to be added.
+        """
+        self.speciesConcentrations.append(species_concentration)
+
+    def add_reaction_rate(self, reaction_rate):
+        """
+        Add a ReactionRate instance to the list of reaction rates.
+
+        Args:
+            reaction_rate (ReactionRate): The ReactionRate instance to be added.
+        """
+        self.reactionRates.append(reaction_rate)

src/music_box_evolving_conditions.py

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+from typing import List
+
+class EvolvingConditions:
+    """
+    Represents evolving conditions with attributes such as time and associated conditions.
+
+    Attributes:
+        time (List[float]): A list of time points.
+        conditions (List[Conditions]): A list of associated conditions.
+    """
+
+    def __init__(self, time=None, conditions=None):
+        """
+        Initializes a new instance of the EvolvingConditions class.
+
+        Args:
+            time (List[float]): A list of time points. Default is an empty list.
+            conditions (List[Conditions]): A list of associated conditions. Default is an empty list.
+        """
+        self.time = time if time is not None else []
+        self.conditions = conditions if conditions is not None else []
+
+    def add_condition(self, time_point, conditions):
+        """
+        Add an evolving condition at a specific time point.
+
+        Args:
+            time_point (float): The time point for the evolving condition.
+            conditions (Conditions): The associated conditions at the given time point.
+        """
+        self.time.append(time_point)
+        self.conditions.append(conditions)
+
+    def read_conditions_from_file(self, file_path):
+        """
+        TODO: Read conditions from a file and update the evolving conditions.
+
+        Args:
+            file_path (str): The path to the file containing conditions data.
+        """
+        # TODO: Implement the logic to read conditions from the specified file.
+        # This method is a placeholder, and the actual implementation is required.
+        pass

src/music_box_model_options.py

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+class BoxModelOptions:
+    """
+    Represents options for a box model simulation.
+
+    Attributes:
+        grid (str): The type of grid. Default is "box".
+        chemStepTime (float): Time step for chemical reactions in the simulation in minutes.
+        outputStepTime (float): Time step for output data in the simulation in hours.
+        simulationLength (float): Length of the simulation in hours.
+    """
+
+    def __init__(self, chem_step_time, output_step_time, simulation_length, grid="box"):
+        """
+        Initializes a new instance of the BoxModelOptions class.
+
+        Args:
+            chem_step_time (float): Time step for chemical reactions in the simulation in minutes.
+            output_step_time (float): Time step for output data in the simulation in hours.
+            simulation_length (float): Length of the simulation in hours.
+            grid (str): The type of grid. Default is "box".
+        """
+        self.chemStepTime = chem_step_time
+        self.outputStepTime = output_step_time
+        self.simulationLength = simulation_length
+        self.grid = grid

src/music_box_product.py

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+class Product:
+    """
+    Represents a product with attributes such as name and yield.
+
+    Attributes:
+        name (str): The name of the product.
+        species (Species): An instance of the Species class representing the product.
+        yield_value (float): The yield of the product.
+    """
+
+    def __init__(self, species, yield_value):
+        """
+        Initializes a new instance of the Product class.
+
+        Args:
+            species (Species): An instance of the Species class representing the product.
+            yield_value (float): The yield of the product.
+        """
+        self.name = species.name
+        self.species = species
+        self.yield_value = yield_value

src/music_box_reactant.py

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+class Reactant:
+    """
+    Represents a reactant with attributes such as name and quantity.
+
+    Attributes:
+        name (str): The name of the reactant.
+        quantity (float): The quantity of the reactant.
+    """
+
+    def __init__(self, species, quantity):
+        """
+        Initializes a new instance of the Reactant class.
+
+        Args:
+            species (Species): An instance of the Species class representing the reactant.
+            quantity (float): The quantity of the reactant.
+        """
+        self.name = species.name
+        self.species = species
+        self.quantity = quantity
+

src/music_box_reaction.py

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+from typing import List
+
+class Reaction:
+    """
+    Represents a chemical reaction with attributes such as name, type, reactants, and products.
+
+    Attributes:
+        name (str): The name of the reaction.
+        reaction_type (str): The type of the reaction.
+        reactants (List[Reactant]): A list of Reactant instances representing the reactants. Default is an empty list.
+        products (List[Product]): A list of Product instances representing the products. Default is an empty list.
+    """
+
+    def __init__(self, name, reaction_type, reactants=None, products=None):
+        """
+        Initializes a new instance of the Reaction class.
+
+        Args:
+            name (str): The name of the reaction.
+            reaction_type (str): The type of the reaction.
+            reactants (List[Reactant]): A list of Reactant instances representing the reactants. Default is an empty list.
+            products (List[Product]): A list of Product instances representing the products. Default is an empty list.
+        """
+        self.name = name
+        self.reaction_type = reaction_type
+        self.reactants = reactants if reactants is not None else []
+        self.products = products if products is not None else []
+
+    def add_reactant(self, reactant):
+        """
+        Add a Reactant instance to the list of reactants.
+
+        Args:
+            reactant (Reactant): The Reactant instance to be added.
+        """
+        self.reactants.append(reactant)
+
+    def add_product(self, product):
+        """
+        Add a Product instance to the list of products.
+
+        Args:
+            product (Product): The Product instance to be added.
+        """
+        self.products.append(product)

src/music_box_reaction_list.py

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+from typing import List
+
+class ReactionList:
+    """
+    Represents a list of chemical reactions.
+
+    Attributes:
+        mechanisms (List[Reaction]): A list of Reaction instances.
+    """
+
+    def __init__(self, mechanisms=None):
+        """
+        Initializes a new instance of the ReactionList class.
+
+        Args:
+            mechanisms (List[Reaction]): A list of Reaction instances. Default is an empty list.
+        """
+        self.mechanisms = mechanisms if mechanisms is not None else []
+
+    def add_reaction(self, reaction):
+        """
+        Add a Reaction instance to the ReactionList.
+
+        Args:
+            reaction (Reaction): The Reaction instance to be added.
+        """
+        self.mechanisms.append(reaction)

src/music_box_reaction_rate.py

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+class ReactionRate:
+    """
+    Represents a reaction rate with attributes such as the associated reaction and rate.
+
+    Attributes:
+        reaction (Reaction): The associated reaction.
+        rate (float): The rate of the reaction in 1/s (inverse seconds).
+    """
+
+    def __init__(self, reaction, rate):
+        """
+        Initializes a new instance of the ReactionRate class.
+
+        Args:
+            reaction (Reaction): The associated reaction.
+            rate (float): The rate of the reaction in 1/s (inverse seconds).
+        """
+        self.reaction = reaction
+        self.rate = rate

src/music_box_species.py

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+class Species:
+    """
+    Represents a species with various attributes such as name, absolute tolerance, phase, molecular weight, and density.
+
+    Attributes:
+        name (str): The name of the species.
+        absolute_tolerance (float): The absolute tolerance of the species.
+        phase (str): The phase of the species.
+        molecular_weight (float): The molecular weight of the species in kg mol^-1.
+        density (float): The density of the species in kg m^-3.
+    """
+
+    def __init__(self, name, absolute_tolerance, phase, molecular_weight, density):
+        """
+        Initializes a new instance of the Species class.
+
+        Args:
+            name (str): The name of the species.
+            absolute_tolerance (float): The absolute tolerance of the species.
+            phase (str): The phase of the species.
+            molecular_weight (float): The molecular weight of the species in kg mol^-1.
+            density (float): The density of the species in kg m^-3.
+        """
+        self.name = name
+        self.absolute_tolerance = absolute_tolerance
+        self.phase = phase
+        self.molecular_weight = molecular_weight
+        self.density = density 

src/music_box_species_concentration.py

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+class SpeciesConcentration:
+    """
+    Represents a species concentration with attributes such as the associated species and concentration.
+
+    Attributes:
+        species (Species): The associated species.
+        concentration (float): The concentration of the species.
+    """
+
+    def __init__(self, species, concentration):
+        """
+        Initializes a new instance of the SpeciesConcentration class.
+
+        Args:
+            species (Species): The associated species.
+            concentration (float): The concentration of the species.
+        """
+        self.species = species
+        self.concentration = concentration

src/music_box_species_list.py

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+from typing import List
+
+class SpeciesList:
+    """
+    Represents a list of species with a relative tolerance.
+
+    Attributes:
+        species (List[Species]): A list of Species instances.
+        relativeTolerance (float): The relative tolerance for the species list.
+    """
+
+    def __init__(self, species=None, relative_tolerance=0.0):
+        """
+        Initializes a new instance of the SpeciesList class.
+
+        Args:
+            species (List[Species]): A list of Species instances. Default is an empty list.
+            relative_tolerance (float): The relative tolerance for the species list. Default is 0.0.
+        """
+        self.species = species if species is not None else []
+        self.relativeTolerance = relative_tolerance
+
+    def add_species(self, species):
+        """
+        Add a Species instance to the list of species.
+
+        Args:
+            species (Species): The Species instance to be added.
+        """
+        self.species.append(species)