Debugging2

src/acom_music_box/music_box.py

@@ -121,8 +121,15 @@ def generateConfig(self, directory):
             data["initial conditions"] = {}
 
             for reaction_rate in self.initial_conditions.reaction_rates:
-                name = "PHOT." + reaction_rate.reaction.name + ".s-1"
-                data["initial conditions"][name] = reaction_rate.rate
+                if(reaction_rate.reaction.reaction_type == "PHOTOLYSIS"):
+                    name = "PHOT." + reaction_rate.reaction.name + ".s-1"
+                    data["initial conditions"][name] = reaction_rate.rate
+                elif(reaction_rate.reaction.reaction_type == "LOSS"):
+                    name = "LOSS." + reaction_rate.reaction.name + ".s-1"
+                    data["initial conditions"][name] = reaction_rate.rate
+                elif (reaction_rate.reaction.reaction_type =="EMISSION"):
+                    name = "EMISSION." + reaction_rate.reaction.name + ".s-1"
+                    data["initial conditions"][name] = reaction_rate.rate
 
             data["model components"] = [
                 {
@@ -358,6 +365,9 @@ def generateReactionConfig(self):
             if(reaction.name != None):
                 reac["MUSICA name"] = reaction.name
 
+            if(reaction.scaling_factor != None):
+                reac["scaling factor"] = reaction.scaling_factor
+
             reactionsArray.append(reac)
 
         reacList["reactions"] = reactionsArray

src/acom_music_box/music_box_conditions.py

@@ -84,11 +84,22 @@ def from_config_JSON(cls, config_JSON, species_list, reaction_list):
 
         # Set initial species concentrations
         species_concentrations = []
+        reaction_rates = []
 
         #reads initial conditions from csv if it is given
         if 'initial conditions' in config_JSON:
-            initial_conditions_csv = config_JSON['initial conditions']
+            #initial_conditions_csv = config_JSON['initial conditions']
+
             #read_initial_conditions_from_csv(initial_conditions_csv)
+            for reaction_rate in config_JSON['initial conditions']:
+
+                match = filter(lambda x: x.name == reaction_rate.split('.')[1], reaction_list.reactions)
+
+                reaction = next(match, None)
+
+                rate = config_JSON['initial conditions'][reaction_rate]
+
+                reaction_rates.append(ReactionRate(reaction, rate))
 
         #reads from config file directly if present
         if 'chemical species' in config_JSON:
@@ -105,13 +116,12 @@ def from_config_JSON(cls, config_JSON, species_list, reaction_list):
 
         #TODO: may or may not be necessary
         # Set initial reaction rates
-        reaction_rates = []
 
         for reaction in reaction_list.reactions:
             if reaction.name != None and not any(reac.reaction.name == reaction.name for reac in reaction_rates):
                 reaction_rates.append(ReactionRate(reaction, 0)) 
 
-
+        
         return cls(pressure, temperature, species_concentrations, reaction_rates)
 
 

src/acom_music_box/music_box_reaction.py

@@ -11,7 +11,7 @@ class Reaction:
         products (List[Product]): A list of Product instances representing the products. Default is an empty list.
     """
 
-    def __init__(self, name=None, reaction_type=None, reactants=None, products=None):
+    def __init__(self, name=None, reaction_type=None, reactants=None, products=None, scaling_factor=None):
         """
         Initializes a new instance of the Reaction class.
 
@@ -25,6 +25,7 @@ def __init__(self, name=None, reaction_type=None, reactants=None, products=None)
         self.reaction_type = reaction_type
         self.reactants = reactants if reactants is not None else []
         self.products = products if products is not None else []
+        self.scaling_factor = scaling_factor
 
     def add_reactant(self, reactant):
         """

src/acom_music_box/music_box_reaction_list.py

@@ -111,6 +111,7 @@ def get_products_from_JSON(self, reaction, species_list):
     def get_reactions_from_JSON(self, reaction, species_list):
 
         name = reaction['MUSICA name'] if 'MUSICA name' in reaction else None
+        scaling_factor = reaction['scaling factor'] if 'scaling factor' in reaction else None
         reaction_type = reaction['type']
 
         reactants = ReactionList.get_reactants_from_JSON(reaction, species_list)
@@ -163,4 +164,4 @@ def get_reactions_from_JSON(self, reaction, species_list):
             N = reaction.get('N')
             return Troe_Ternary(name, reaction_type, reactants, products, k0_A, k0_B, k0_C, kinf_A, kinf_B, kinf_C, Fc, N)
         else:
-            return Reaction(name, reaction_type, reactants, products)
+            return Reaction(name, reaction_type, reactants, products, scaling_factor)