outputs results to file and creates file for initial test

src/box_model.py

@@ -11,7 +11,7 @@
 from music_box_conditions import Conditions
 from music_box_species_concentration import SpeciesConcentration
 from music_box_reaction_rate import ReactionRate
-import utils
+import csv
 import musica
 
 class BoxModel:
@@ -263,7 +263,7 @@ def create_solver(self, path_to_config):
         self.solver = musica.create_micm(path_to_config)
 
 
-    def solve(self):
+    def solve(self, path_to_output = None):
         """
         TODO: Solve the box model simulation.
         """
@@ -275,9 +275,6 @@ 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
         next_conditions = None
@@ -287,11 +284,32 @@ def solve(self):
             next_conditions_index = 0
             next_conditions = self.evolving_conditions.conditions[0]
             next_conditions_time = self.evolving_conditions.times[0]
+
+        #initializes file headers if output file is present
+        output_array = []
+        if(path_to_output != None):
+            headers = []
+            headers.append("time")
+            headers.append("ENV.temperature")
+            headers.append("ENV.pressure")
+            for spec in self.species_list:
+                headers.append("CONC." + spec.name)
+
+            output_array.append(headers)
 
         #runs the simulation at each timestep
         curr_time = 0
-        while(curr_time <= (self.box_model_options.simulation_length)):
-            print(curr_concentrations)
+        while(curr_time <= self.box_model_options.simulation_length):
+
+            #appends row to output if file is present
+            if(path_to_output != None):
+                row = []
+                row.append(curr_time)
+                row.append(curr_conditions.temperature)
+                row.append(curr_conditions.pressure)
+                for conc in curr_concentrations:
+                    row.append(conc)
+                output_array.append(row)
 
             #iterates evolvings conditons if enough time has elapsed
             if(next_conditions != None and next_conditions_time <= curr_time):
@@ -311,10 +329,19 @@ def solve(self):
 
             #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  
 
+        #outputs to file if output is present
+        if(path_to_output != None):
+            with open(path_to_output, 'w', newline='') as output:
+                writer = csv.writer(output)
+                writer.writerows(output_array)
+
     def readFromUIJson(self, path_to_json):
         """
         TODO: Read the box model configuration from json and sets config
@@ -354,13 +381,8 @@ def readConditionsFromJson(self, path_to_json):
 def __main__():
     # Create a new instance of the BoxModel class.
 
-    box_model = BoxModel()
-    box_model.readConditionsFromJson("configs/test_config/my_config.json")
-    box_model.create_solver("configs/test_config/camp_data")
-    box_model.solve()
-
+    pass
 
-    box_model.solve()
 
 
 

src/configs/test_config_2/camp_data/config.json

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

src/configs/test_config_2/camp_data/reactions.json

@@ -0,0 +1 @@
+{"camp-data": [{"type": "MECHANISM", "name": "music box interactive configuration", "reactions": [{"type": "PHOTOLYSIS", "scaling_factor": 1, "MUSICA name": "O3_2", "reactants": {"O3": {}}, "products": {"O": {"yield": 1}, "O2": {"yield": 1}, "irr__0665f4f2-132e-4f99-a2d7-7b0cf35b1b5f": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 3.3e-11, "Ea": -7.59e-22, "B": 0, "D": 300, "E": 0, "reactants": {"O1D": {"qty": 1}, "O2": {"qty": 1}}, "products": {"O": {"yield": 1}, "O2": {"yield": 1}, "irr__21732b9a-3601-4739-acdc-48466559aeee": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 6e-34, "Ea": 0, "B": -2.4, "D": 300, "E": 0, "reactants": {"O": {"qty": 1}, "O2": {"qty": 1}, "M": {"qty": 1}}, "products": {"O3": {"yield": 1}, "M": {"yield": 1}, "irr__6b0bb4ae-f671-4f2a-92c9-e88992346583": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 2.15e-11, "Ea": -1.518e-21, "B": 0, "D": 300, "E": 0, "reactants": {"O1D": {"qty": 1}, "N2": {"qty": 1}}, "products": {"O": {"yield": 1}, "N2": {"yield": 1}, "irr__8be08086-a796-4c88-b56f-a695a0c22ddd": {"yield": 1}}}, {"type": "PHOTOLYSIS", "scaling_factor": 1, "MUSICA name": "O3_1", "reactants": {"O3": {}}, "products": {"O1D": {"yield": 1}, "O2": {"yield": 1}, "irr__90a4d7ba-c694-424b-a0eb-1146f2afee8e": {"yield": 1}}}, {"type": "ARRHENIUS", "A": 8e-12, "Ea": 2.8428e-20, "B": 0, "D": 300, "E": 0, "reactants": {"O": {"qty": 1}, "O3": {"qty": 1}}, "products": {"O2": {"yield": 2}, "irr__b3c93679-40cf-419a-8914-818b5d40b117": {"yield": 1}}}, {"type": "PHOTOLYSIS", "scaling_factor": 1, "MUSICA name": "O2_1", "reactants": {"O2": {}}, "products": {"O": {"yield": 2}, "irr__ce5b7d7f-dd7e-4daa-8e49-f1db924b50f6": {"yield": 1}}}]}]}

src/configs/test_config_2/camp_data/species.json

@@ -0,0 +1 @@
+{"camp-data": [{"name": "M", "type": "CHEM_SPEC", "tracer type": "CONSTANT"}, {"name": "Ar", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "CO2", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "H2O", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "O1D", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "O", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "O2", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "O3", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "N2", "type": "CHEM_SPEC", "absolute tolerance": 1e-12}, {"name": "irr__0665f4f2-132e-4f99-a2d7-7b0cf35b1b5f", "type": "CHEM_SPEC"}, {"name": "irr__21732b9a-3601-4739-acdc-48466559aeee", "type": "CHEM_SPEC"}, {"name": "irr__6b0bb4ae-f671-4f2a-92c9-e88992346583", "type": "CHEM_SPEC"}, {"name": "irr__8be08086-a796-4c88-b56f-a695a0c22ddd", "type": "CHEM_SPEC"}, {"name": "irr__90a4d7ba-c694-424b-a0eb-1146f2afee8e", "type": "CHEM_SPEC"}, {"name": "irr__b3c93679-40cf-419a-8914-818b5d40b117", "type": "CHEM_SPEC"}, {"name": "irr__ce5b7d7f-dd7e-4daa-8e49-f1db924b50f6", "type": "CHEM_SPEC"}]}