Merge branch 'python_box_model' of https://github.com/NCAR/music-box …

…into python_box_model

src/box_model.py

@@ -366,18 +366,22 @@ def solve(self, path_to_output = None):
 
         output_array.append(headers)
 
-        #runs the simulation at each timestep
-
+
         curr_time = 0
+        next_output_time = curr_time
+        #runs the simulation at each timestep
         while(curr_time <= self.box_model_options.simulation_length):
 
-            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)
+            #outputs to output_array if enough time has elapsed
+            if(next_output_time <= curr_time):   
+                row = []
+                row.append(next_output_time)
+                row.append(curr_conditions.temperature)
+                row.append(curr_conditions.pressure)
+                for conc in curr_concentrations:
+                    row.append(conc)
+                output_array.append(row)
+                next_output_time += self.box_model_options.output_step_time
 
             #iterates evolvings conditons if enough time has elapsed
             if(next_conditions != None and next_conditions_time <= curr_time):

src/configs/test_config_2/camp_data/reactions.json

@@ -1 +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}}}]}]}
+{"camp-data": [{"type": "MECHANISM", "name": "music box interactive configuration", "reactions": [{"type": "ARRHENIUS", "A": 8.8e-17, "Ea": 0, "B": 0, "D": 300, "E": 0, "reactants": {"O3": {"qty": 1}, "a-pinene": {"qty": 1}}, "products": {"SOA1": {"yield": 0.18}, "SOA2": {"yield": 0.09}, "irr__bab3e78d-d1d7-4c6b-9f6f-bbbd303c0901": {"yield": 1}}}]}]}

src/configs/test_config_2/camp_data/species.json

@@ -1 +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"}]}
+{"camp-data": [ {"name": "a-pinene", "type": "CHEM_SPEC"}, {"name": "O3", "type": "CHEM_SPEC"}, {"name": "SOA1", "type": "CHEM_SPEC"}, {"name": "SOA2", "type": "CHEM_SPEC"}, {"name": "irr__bab3e78d-d1d7-4c6b-9f6f-bbbd303c0901", "type": "CHEM_SPEC"}]}