fixed inital conditions for reaction rates

NCAR · Apr 16, 2024 · 3081ab8 · 3081ab8
1 parent 4afde18
commit 3081ab8
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Showing 6 changed files with 3,620 additions and 3,610 deletions.
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
@@ -121,8 +121,9 @@ 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
 
             data["model components"] = [
                 {

diff --git a/src/acom_music_box/music_box_conditions.py b/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)
 
 

diff --git a/tests/configs/wall_loss_config/camp_data/reactions.json b/tests/configs/wall_loss_config/camp_data/reactions.json
@@ -7,7 +7,7 @@
                 {
                     "type": "PHOTOLYSIS",
 
-
+                    "scaling factor": 1,
                     "MUSICA name": "LOSS_SOA1 wall loss",
                     "reactants": {
                         "SOA1": {}
@@ -21,7 +21,7 @@
                 {
                     "type": "PHOTOLYSIS",
 
-
+                    "scaling factor": 1,
                     "MUSICA name": "LOSS_SOA2 wall loss",
                     "reactants": {
                         "SOA2": {}

diff --git a/tests/configs/wall_loss_config/initial_conditions.csv b/tests/configs/wall_loss_config/initial_conditions.csv
diff --git a/tests/configs/wall_loss_config/my_config.json b/tests/configs/wall_loss_config/my_config.json
@@ -22,7 +22,8 @@
         }
     },
     "initial conditions": {
-        "initial_conditions.csv": {}
+        "PHOT.LOSS_SOA1 wall loss.s-1": 0.01,
+        "PHOT.LOSS_SOA2 wall loss.s-1": 0.05
     },
     "model components": [
         {