added method for generating species config

src/box_model.py

@@ -1,7 +1,12 @@
+import json
+
 from music_box_evolving_conditions import EvolvingConditions
 from music_box_reaction_list import ReactionList
+from music_box_reaction import Reaction
 from music_box_species_list import SpeciesList
+from music_box_species import Species
 from music_box_model_options import BoxModelOptions
+from music_box_conditions import Conditions
 
 class BoxModel:
     """
@@ -16,7 +21,8 @@ class BoxModel:
         evolvingConditions (List[EvolvingConditions]): List of evolving conditions over time.
     """
 
-    def __init__(self, box_model_options, species_list, reaction_list, initial_conditions, evolving_conditions):
+    def __init__(self, box_model_options=None, species_list=None, reaction_list=None,
+             initial_conditions=None, evolving_conditions=None, config_file=None):
         """
         Initializes a new instance of the BoxModel class.
 
@@ -26,12 +32,15 @@ def __init__(self, box_model_options, species_list, reaction_list, initial_condi
             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.
+            config_file (String): File path for the configuration file to be located. Default is "camp_data/config.json".
         """
-        self.boxModelOptions = box_model_options
-        self.speciesList = species_list
-        self.reactionList = reaction_list
-        self.initialConditions = initial_conditions
-        self.evolvingConditions = evolving_conditions
+        self.box_model_options = box_model_options
+        self.species_list = species_list
+        self.reaction_list = reaction_list
+        self.initial_conditions = initial_conditions
+        self.evolving_conditions = evolving_conditions
+        self.config_file = config_file if config_file is not None else "camp_data/config.json"
+
 
     def add_evolving_condition(self, time_point, conditions):
         """
@@ -44,10 +53,65 @@ def add_evolving_condition(self, time_point, conditions):
         evolving_condition = EvolvingConditions(time=[time_point], conditions=[conditions])
         self.evolvingConditions.append(evolving_condition)
 
-    def generateFiles(self):
+    def generateConfig(self):
         """
-        TODO: Generate configuration JSON files for the box model simulation.
+        TODO: Generate configuration JSON for the box model simulation.
         """
         # TODO: Implement the logic to generate configuration files.
         # This method is a placeholder, and the actual implementation is required.
+
+        speciesConfig = self.generateSpeciesConfig()
+        print(speciesConfig)
+
         pass
+    def generateSpeciesConfig(self):
+        """
+        Generate a JSON configuration for the species in the box model.
+
+        Returns:
+            str: A JSON-formatted string representing the species configuration.
+        """
+
+        #Established relative tolerance
+        relTolerance = {
+            "type" : "RELATIVE_TOLERANCE",
+            "value" : self.species_list.relative_tolerance
+        }
+
+        speciesArray = []
+
+        #Adds species to config
+        for species in self.species_list.species:
+            spec = {}
+
+            #Add species name if value is set
+            if(species.name != None):
+                spec["name"] = species.name
+
+            spec["type"] = "CHEM_SPEC"
+
+            #Add species absoluate tolerance if value is set
+            if(species.absolute_tolerance != None):
+                spec["absolute tolerance"] = species.absolute_tolerance
+
+            #Add species phase if value is set
+            if(species.phase != None):
+                spec["phase"] = species.phase            
+
+            #Add species molecular weight if value is set
+            if(species.molecular_weight != None):
+                spec["molecular weight [kg mol-1]"] = species.molecular_weight
+
+            #Add species density if value is set
+            if(species.density != None):
+                spec["density [kg m-3]"] = species.density
+
+            speciesArray.append(spec)
+
+        species_json = {
+            "camp-data" : speciesArray
+        }
+
+        return json.dumps(species_json)
+
+

src/music_box_conditions.py

@@ -24,8 +24,8 @@ def __init__(self, pressure, temperature, species_concentrations=None, reaction_
         """
         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 []
+        self.species_concentrations = species_concentrations if species_concentrations is not None else []
+        self.reaction_rates = reaction_rates if reaction_rates is not None else []
 
     def add_species_concentration(self, species_concentration):
         """
@@ -34,7 +34,7 @@ def add_species_concentration(self, species_concentration):
         Args:
             species_concentration (SpeciesConcentration): The SpeciesConcentration instance to be added.
         """
-        self.speciesConcentrations.append(species_concentration)
+        self.species_concentration.append(species_concentration)
 
     def add_reaction_rate(self, reaction_rate):
         """
@@ -43,4 +43,4 @@ def add_reaction_rate(self, reaction_rate):
         Args:
             reaction_rate (ReactionRate): The ReactionRate instance to be added.
         """
-        self.reactionRates.append(reaction_rate)
+        self.reaction_rates.append(reaction_rate)

src/music_box_model_options.py

@@ -19,7 +19,7 @@ def __init__(self, chem_step_time, output_step_time, simulation_length, grid="bo
             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.chem_step_time = chem_step_time
+        self.output_step_time = output_step_time
+        self.simulation_length = simulation_length
         self.grid = grid

src/music_box_reaction.py

@@ -16,7 +16,7 @@ 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.
+            type (str): The type 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.

src/music_box_reaction_list.py

@@ -5,17 +5,17 @@ class ReactionList:
     Represents a list of chemical reactions.
 
     Attributes:
-        mechanisms (List[Reaction]): A list of Reaction instances.
+        reactions (List[Reaction]): A list of Reaction instances.
     """
 
-    def __init__(self, mechanisms=None):
+    def __init__(self, reactions=None):
         """
         Initializes a new instance of the ReactionList class.
 
         Args:
-            mechanisms (List[Reaction]): A list of Reaction instances. Default is an empty list.
+            reactions (List[Reaction]): A list of Reaction instances. Default is an empty list.
         """
-        self.mechanisms = mechanisms if mechanisms is not None else []
+        self.reactions = reactions if reactions is not None else []
 
     def add_reaction(self, reaction):
         """
@@ -24,4 +24,4 @@ def add_reaction(self, reaction):
         Args:
             reaction (Reaction): The Reaction instance to be added.
         """
-        self.mechanisms.append(reaction)
+        self.reactions.append(reaction)

src/music_box_species.py

@@ -10,7 +10,7 @@ class Species:
         density (float): The density of the species in kg m^-3.
     """
 
-    def __init__(self, name, absolute_tolerance, phase, molecular_weight, density):
+    def __init__(self, name=None, absolute_tolerance=None, phase=None, molecular_weight=None, density=None):
         """
         Initializes a new instance of the Species class.
 

src/music_box_species_list.py

@@ -18,7 +18,7 @@ def __init__(self, species=None, relative_tolerance=0.0):
             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
+        self.relative_tolerance = relative_tolerance
 
     def add_species(self, species):
         """