Merge pull request #192 from NCAR/updates

Updates

src/acom_music_box/conditions.py

@@ -179,8 +179,13 @@ def from_config_JSON(
         for reaction in reaction_list.reactions:
             if (reaction.name is None):
                 continue
-            if not any(rate.reaction.name ==
-                       reaction.name for rate in reaction_rates):
+            reaction_exists = False
+            for rate in reaction_rates:
+                if rate.reaction.name == reaction.name:
+                    reaction_exists = True
+                    break
+
+            if not reaction_exists:
                 reaction_rates.append(ReactionRate(reaction, 0))
 
         return cls(
@@ -217,18 +222,12 @@ def read_initial_rates_from_file(cls, file_path, reaction_list):
                 # The second row of the CSV contains rates
                 rates = initial_conditions[1]
 
-                for i in range(0, len(headers)):
-
-                    reaction_rate = headers[i]
-
-                    match = filter(
-                        lambda x: x.name == reaction_rate.split('.')[1],
-                        reaction_list.reactions)
-
-                    reaction = next(match, None)
-                    rate = rates[i]
+                for reaction_rate, rate in zip(headers, rates):
+                    type, name, *rest = reaction_rate.split('.')
+                    for reaction in reaction_list.reactions:
+                        if reaction.name == name and reaction.short_type() == type:
+                            reaction_rates.append(ReactionRate(reaction, rate))
 
-                    reaction_rates.append(ReactionRate(reaction, rate))
         return reaction_rates
 
     def add_species_concentration(self, species_concentration):

src/acom_music_box/music_box.py

@@ -10,6 +10,7 @@
 import os
 
 import logging
+logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 
@@ -554,6 +555,7 @@ def solve(self, output_path=None):
         # outputs to file if output is present
         if (output_path is not None):
             logger.info("path_to_output = {}".format(output_path))
+            os.makedirs(os.path.dirname(output_path), exist_ok=True)
             with open(output_path, 'w', newline='') as output:
                 writer = csv.writer(output)
                 writer.writerows(output_array)
@@ -706,15 +708,14 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering):
 
             if (rate.reaction.reaction_type == "PHOTOLYSIS"):
                 key = "PHOTO." + rate.reaction.name
-            elif (rate.reaction.reaction_type == "LOSS"):
+            elif (rate.reaction.reaction_type == "FIRST_ORDER_LOSS"):
                 key = "LOSS." + rate.reaction.name
             elif (rate.reaction.reaction_type == "EMISSION"):
                 key = "EMIS." + rate.reaction.name
             rate_constants[key] = rate.rate
 
         ordered_rate_constants = len(rate_constants.keys()) * [0.0]
         for key, value in rate_constants.items():
-
             ordered_rate_constants[rate_constant_ordering[key]] = float(value)
         return ordered_rate_constants
 

src/acom_music_box/reaction.py

@@ -59,6 +59,24 @@ def add_product(self, product):
             product (Product): The Product instance to be added.
         """
         self.products.append(product)
+
+    def short_type(self):
+        """
+        Return the first letter of the reaction type.
+
+        Returns:
+            str: The first letter of the reaction type.
+        """
+        type_map = {
+            "EMISSION": "EMIS",
+            "PHOTOLYSIS": "PHOT",
+            "FIRST_ORDER_LOSS": "LOSS",
+            "BRANCHED": "BRAN",
+            "ARRHENIUS": "ARRH",
+            "TUNNELING": "TUNN",
+            "TROE_TERNARY": "TROE",
+        }
+        return type_map.get(self.reaction_type, "UNKNOWN")
 
 
 class Branched(Reaction):