correcting reaction rate setting

src/acom_music_box/conditions.py

@@ -222,18 +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)):
+                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_rate = headers[i]
-
-                    match = filter(
-                        lambda x: x.name == reaction_rate.split('.')[1],
-                        reaction_list.reactions)
-
-                    reaction = next(match, None)
-                    rate = rates[i]
-
-                    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)
@@ -712,21 +714,16 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering):
                 key = "EMIS." + rate.reaction.name
             rate_constants[key] = rate.rate
 
-        # print(curr_conditions.reaction_rates)
-        print(len(rate_constant_ordering.keys()))
-        print(len(rate_constants.keys()))
+        logger.debug(f"MUSICA provided {len(rate_constant_ordering.keys())} user defined reaction rates")
+        logger.debug(f"Music box expects {len(rate_constants.keys())}")
 
-        musica_rates = set(rate_constants.keys())
-        box_rates = set(rate_constant_ordering.keys())
+        musica_rates = set(rate_constant_ordering.keys())
+        box_rates = set(rate_constants.keys())
 
-        print(box_rates.difference(musica_rates))
+        logger.debug(f"Musica contains these rates, and music box doesn't' {musica_rates.difference(box_rates)}")
 
         ordered_rate_constants = len(rate_constants.keys()) * [0.0]
-        # print(sorted(rate_constant_ordering.values()))
-        # print(len(ordered_rate_constants))
         for key, value in rate_constants.items():
-            # print(f"key: {key}, rate_constant_ordering[key]: {rate_constant_ordering[key]}")
-            # print(ordered_rate_constants)
             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):

tests/test_chapman.py

@@ -55,7 +55,7 @@ def test_run(self):
                     float(test_output_concs[i][j]),
                     rel_tol=1e-8,
                     abs_tol=1e-15,
-                ), f"Arrays differ at index ({i}, {j}) for "
+                ), f"Arrays differ at index ({i}, {j}) for species {concs_to_test[j]}"
 
 
 if __name__ == "__main__":

tests/test_wall_loss.py

@@ -16,7 +16,7 @@ def test_run(self):
         box_model.create_solver(camp_path)
 
         # solves and saves output
-        model_output = box_model.solve()
+        model_output = box_model.solve(output_path="output/wall_loss_test.csv")
 
         # read wall_loss_test.csv into test_output
         with open("expected_results/wall_loss_test.csv", "r") as file:
@@ -46,7 +46,8 @@ def test_run(self):
                     float(model_output_concs[i][j]),
                     float(test_output_concs[i][j]),
                     rel_tol=1e-8,
-                ), f"Arrays differ at index ({i}, {j}) for "
+                    abs_tol=1e-8,
+                ), f"Arrays differ at index ({i}, {j}) for species {concs_to_test[j]}"
 
 
 if __name__ == "__main__":