adds function to read config json and tests basic reaction

src/box_model.py

@@ -41,8 +41,8 @@ def __init__(self, box_model_options=None, species_list=None, reaction_list=None
             config_file (String): File path for the configuration file to be located. Default is "camp_data/config.json".
         """
         self.box_model_options = box_model_options
-        self.species_list = species_list
-        self.reaction_list = reaction_list
+        self.species_list = species_list if species_list is not None else []
+        self.reaction_list = reaction_list if reaction_list is not None else []
         self.initial_conditions = initial_conditions
         self.evolving_conditions = evolving_conditions if evolving_conditions is not None else []
         self.config_file = config_file if config_file is not None else "camp_data/config.json"
@@ -279,6 +279,8 @@ def solve(self):
 
         #sets up initial concentraion values
         curr_concentrations = self.initial_conditions.get_concentration_array()
+
+
 
 
         #sets up next condition if evolving conditions is not empty
@@ -304,27 +306,29 @@ def solve(self):
                     next_conditions_index += 1
                     next_conditions = self.evolving_conditions.conditions[next_conditions_index]
                     next_conditions_time = self.evolving_conditions.times[next_conditions_index]
+
+                    #overrides concentrations if specified by conditions
+                    if(len(curr_conditions.get_concentration_array()) != 0):
+                        curr_concentrations = curr_conditions.get_concentration_array()
                 else:
                     next_conditions = None
 
-            #updates concentrations if they are present in the evolving conditions
-            if(len(curr_conditions.get_concentration_array()) != 0):
-                curr_concentrations = curr_conditions.get_concentration_array()
-
-            curr_concentations = musica.micm_solve(self.solver, self.box_model_options.chem_step_time, curr_conditions.temperature, curr_conditions.pressure, curr_concentrations)
-
+            #solves and updates concentration values in concentration array
+            musica.micm_solve(self.solver, self.box_model_options.chem_step_time, curr_conditions.temperature, curr_conditions.pressure, curr_concentrations)
+
             #increments time
             curr_time += self.box_model_options.chem_step_time
-            #print(curr_concentrations)
 
+            print(curr_concentrations)
+
 
     def readFromJson(self, path_to_json):
         """
         TODO: Read the box model configuration from json and sets config
         """
         # TODO: Implement the logic to update the box model config using a json.
 
-        with open(path_to_json, 'r', encoding='utf-16') as json_file:
+        with open(path_to_json, 'r') as json_file:
             data = json.load(json_file)
 
             # Set box model options
@@ -342,20 +346,24 @@ def readFromJson(self, path_to_json):
             # Set evolving conditions
             self.evolving_conditions = EvolvingConditions.from_UI_JSON(data, self.species_list, self.reaction_list)    
 
+    def readConditionsFromJson(self, path_to_json):
+
+        with open(path_to_json, 'r') as json_file:
+            data = json.load(json_file)
+            # Set box model options
+            self.box_model_options = BoxModelOptions.from_config_JSON(data)
+
+            # Set initial conditions
+            self.initial_conditions = Conditions.from_config_JSON(data)
+
+
 # for testing purposes
 def __main__():
     # Create a new instance of the BoxModel class.
 
-    options = BoxModelOptions(5, 1, 2.5)
-    inital_condtions = Conditions(1.0, 298.0)
-    inital_condtions.add_species_concentration(SpeciesConcentration(Species(name="N2"),  3.29e1 ))
-    inital_condtions.add_species_concentration(SpeciesConcentration(Species(name="O2"), 8.84e0))
-    inital_condtions.add_species_concentration(SpeciesConcentration(Species(name="Ar"), 3.92e-1))
-    inital_condtions.add_species_concentration(SpeciesConcentration(Species(name="CO2"),  1.69e-2))
-    inital_condtions.add_species_concentration(SpeciesConcentration(Species(name="O"), 1.0e-5))
-    box_model = BoxModel(box_model_options=options, initial_conditions=inital_condtions)
-
-    box_model.create_solver("configs/chapman")
+    box_model = BoxModel()
+    box_model.readConditionsFromJson("configs/test_config/my_config.json")
+    box_model.create_solver("configs/test_config/camp_data")
     box_model.solve()
 
 

src/configs/test_config/camp_data/config.json

@@ -0,0 +1 @@
+{"camp-files": ["species.json", "reactions.json"]}

src/configs/test_config/camp_data/reactions.json

@@ -0,0 +1 @@
+{"camp-data": [{"type": "MECHANISM", "name": "music box interactive configuration", "reactions": [{"type": "ARRHENIUS", "A": 0.00012, "Ea": 1.0354868e-21, "B": 7, "D": 50, "E": 0.5, "reactants": {"B": {"qty": 1}}, "products": {"C": {"yield": 1}, "irr__089f1f45-4cd8-4278-83d5-d638e98e4315": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 0.004, "Ea": -6.903245e-22, "B": 0, "D": 300, "E": 0, "reactants": {"A": {"qty": 1}}, "products": {"B": {"yield": 1}, "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7": {"yield": 1}}}]}]}

src/configs/test_config/camp_data/species.json

@@ -0,0 +1 @@
+{"camp-data": [{"name": "A", "type": "CHEM_SPEC"}, {"name": "B", "type": "CHEM_SPEC"}, {"name": "C", "type": "CHEM_SPEC"},  {"name": "irr__089f1f45-4cd8-4278-83d5-d638e98e4315", "type": "CHEM_SPEC"}, {"name": "irr__2a109b21-bb24-41ae-8f06-7485fd36f1a7", "type": "CHEM_SPEC"}]}

src/configs/test_config/evolving_conditions.csv

@@ -0,0 +1,2 @@
+time.s
+0

src/configs/test_config/my_config.json

@@ -0,0 +1,46 @@
+
+{
+  "box model options": {
+    "grid": "box",
+    "chemistry time step [sec]": 1,
+    "output time step [sec]": 1,
+    "simulation length [sec]": 100
+  },
+  "chemical species": {
+    "A": {
+      "initial value [mol m-3]": 1
+    },
+    "B": {
+      "initial value [mol m-3]": 0
+    },
+    "C": {
+      "initial value [mol m-3]": 0
+    }
+  },
+  "environmental conditions": {
+    "pressure": {
+      "initial value [Pa]": 101253.3
+    },
+    "temperature": {
+      "initial value [K]": 272.5
+    }
+  },
+  "evolving conditions": {
+    "evolving_conditions.csv": {}
+  },
+  "initial conditions": {},
+  "model components": [
+    {
+      "type": "CAMP",
+      "configuration file": "camp_data/config.json",
+      "override species": {
+        "M": {
+          "mixing ratio mol mol-1": 1
+        }
+      },
+      "suppress output": {
+        "M": {}
+      }
+    }
+  ]
+}

src/music_box_conditions.py

@@ -1,5 +1,6 @@
 from typing import List
 from music_box_reaction_rate import ReactionRate
+from music_box_species import Species
 from music_box_species_concentration import SpeciesConcentration
 import utils
 
@@ -67,6 +68,36 @@ def from_UI_JSON(cls, UI_JSON, species_list, reaction_list):
             reaction_rates.append(ReactionRate(reaction_from_list, rate))
 
         return cls(pressure, temperature, species_concentrations, reaction_rates)
+
+    @classmethod
+    def from_config_JSON(cls, config_JSON):
+        pressure = utils.convert_pressure(config_JSON['environmental conditions']['pressure'], 'initial value')
+
+        temperature = utils.convert_temperature(config_JSON['environmental conditions']['temperature'], 'initial value')
+
+        # Set initial species concentrations
+        species_concentrations = []
+        for chem_spec in config_JSON['chemical species']:
+            species = Species(name = chem_spec)
+
+            concentration = utils.convert_concentration(config_JSON['chemical species'][chem_spec], 'initial value')
+
+            species_concentrations.append(SpeciesConcentration(species, concentration))
+
+        # Set initial reaction rates
+        reaction_rates = []
+
+        for reaction in config_JSON['initial conditions']:
+
+            reaction_from_list = Species(name=reaction)
+
+            rate = config_JSON['conditions']['initial conditions'][reaction]
+
+            reaction_rates.append(ReactionRate(reaction_from_list, rate))
+
+        return cls(pressure, temperature, species_concentrations, reaction_rates)
+
+
 
     def add_species_concentration(self, species_concentration):
         """

src/music_box_model_options.py

@@ -44,3 +44,15 @@ def from_UI_JSON(cls, UI_JSON):
         grid = UI_JSON['conditions']['box model options']['grid']
 
         return cls(chem_step_time, output_step_time, simulation_length, grid)
+
+
+    @classmethod
+    def from_config_JSON(cls, config_JSON):
+
+        chem_step_time = utils.convert_time(config_JSON['box model options'], 'chemistry time step') * 60
+        output_step_time = utils.convert_time(config_JSON['box model options'], 'output time step')
+        simulation_length = utils.convert_time(config_JSON['box model options'], 'simulation length')
+
+        grid = config_JSON['box model options']['grid']
+
+        return cls(chem_step_time, output_step_time, simulation_length, grid)