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NCAR · Oct 11, 2024 · 21eba37 · 21eba37
1 parent 135e76f
commit 21eba37
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Showing 2 changed files with 10 additions and 11 deletions.
diff --git a/src/acom_music_box/conditions.py b/src/acom_music_box/conditions.py
@@ -29,8 +29,8 @@ def __init__(
         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.
+            species_concentrations (Dict[Species, float]): A dictionary of species concentrations.
+            reaction_rates (Dict[Reaction, float]): A dictionary of reaction rates.
         """
         self.pressure = pressure
         self.temperature = temperature
@@ -117,9 +117,7 @@ def from_config_JSON(
 
         Args:
             path_to_json (str): The path to the JSON file containing the initial conditions and settings.
-            config_JSON (dict): The configuration JSON object containing the initial conditions and settings.
-            species_list (SpeciesList): A SpeciesList containing the species involved in the simulation.
-            reaction_list (ReactionList): A ReactionList containing the reactions involved in the simulation.
+            object (dict): The configuration JSON object containing the initial conditions and settings.
 
         Returns:
             object: An instance of the Conditions class with the settings from the configuration JSON object.
@@ -172,10 +170,9 @@ def read_initial_rates_from_file(cls, file_path):
 
         Args:
             file_path (str): The path to the file containing the initial reaction rates.
-            reaction_list (ReactionList): A ReactionList containing the reactions involved in the simulation.
 
         Returns:
-            list: A list where each element represents the initial rate of a reaction.
+            dict: A dictionary of initial reaction rates.
         """
 
         reaction_rates = {}
@@ -192,7 +189,9 @@ def read_initial_rates_from_file(cls, file_path):
             elif len(parts) == 2:
                 reaction_type, label = parts
             else:
-                logger.error(f"Unexpected format in key: {key}")
+                error = f"Unexpected format in key: {key}"
+                logger.error(error)
+                raise ValueError(error)
             rate_name = f'{reaction_type}.{label}'
             if rate_name in reaction_rates:
                 raise ValueError(f"Duplicate reaction rate found: {rate_name}")

diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
@@ -238,7 +238,7 @@ def loadJson(self, path_to_json):
             # Set initial conditions
             self.initial_conditions = Conditions.from_config_JSON(path_to_json, data)
 
-            # Set initial conditions
+            # Set evolving conditions
             self.evolving_conditions = EvolvingConditions.from_config_JSON(path_to_json, data)
 
         camp_path = os.path.join(os.path.dirname(path_to_json), self.config_file)
@@ -255,8 +255,8 @@ def order_reaction_rates(curr_conditions, rate_constant_ordering):
         and reorders the reaction rates accordingly.
 
         Args:
-            rate_constants (dict): A dictionary of rate constants.
-            rate_constant_ordering (dict): A dictionary that maps rate constant keys to indices for ordering.
+            curr_conditions: A Condition with the current state information
+            rate_constant_ordering: A dictionary which maps reaction names to their index in the reaction rates array
 
         Returns:
             list: An ordered list of rate constants.