reads species from json from camp_data

src/box_model.py

@@ -292,6 +292,7 @@ def solve(self, path_to_output = None):
         headers.append("time")
         headers.append("ENV.temperature")
         headers.append("ENV.pressure")
+
         for spec in self.species_list.species:
             headers.append("CONC." + spec.name)
 
@@ -377,11 +378,13 @@ def readConditionsFromJson(self, path_to_json):
             # Set box model options
             self.box_model_options = BoxModelOptions.from_config_JSON(data)
 
+            # Set species list
+            self.species_list = SpeciesList.from_config_JSON(path_to_json, data)
+
             # Set initial conditions
-            self.initial_conditions = Conditions.from_config_JSON(data)
+            self.initial_conditions = Conditions.from_config_JSON(data, self.species_list )
 
-            # Set species list
-            self.species_list = SpeciesList.from_config_JSON(data)
+
 
 
 # for testing purposes

src/configs/test_config_2/camp_data/reactions.json

@@ -1 +1,37 @@
-{"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}}}]}]}
+{
+    "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 +1,24 @@
-{"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"}]}
+{
+    "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"
+        }
+    ]
+}

src/configs/test_config_2/my_config.json

@@ -1 +1,39 @@
-{"box model options": {"grid": "box", "chemistry time step [sec]": 1, "output time step [sec]": 1, "simulation length [hr]": 1}, "chemical species": {"a-pinene": {"initial value [mol m-3]": 8e-08}, "O3": {"initial value [mol m-3]": 2e-05}}, "environmental conditions": {"temperature": {"initial value [K]": 298.15}, "pressure": {"initial value [Pa]": 101325}}, "initial conditions": {}, "model components": [{"type": "CAMP", "configuration file": "camp_data/config.json", "override species": {"M": {"mixing ratio mol mol-1": 1}}, "suppress output": {"M": {}}}]}
+{
+    "box model options": {
+        "grid": "box",
+        "chemistry time step [sec]": 1,
+        "output time step [sec]": 1,
+        "simulation length [hr]": 1
+    },
+    "chemical species": {
+        "a-pinene": {
+            "initial value [mol m-3]": 8e-08
+        },
+        "O3": {
+            "initial value [mol m-3]": 2e-05
+        }
+    },
+    "environmental conditions": {
+        "temperature": {
+            "initial value [K]": 298.15
+        },
+        "pressure": {
+            "initial value [Pa]": 101325
+        }
+    },
+    "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

@@ -70,7 +70,7 @@ def from_UI_JSON(cls, UI_JSON, species_list, reaction_list):
         return cls(pressure, temperature, species_concentrations, reaction_rates)
 
     @classmethod
-    def from_config_JSON(cls, config_JSON):
+    def from_config_JSON(cls, config_JSON, species_list):
         pressure = utils.convert_pressure(config_JSON['environmental conditions']['pressure'], 'initial value')
 
         temperature = utils.convert_temperature(config_JSON['environmental conditions']['temperature'], 'initial value')
@@ -91,6 +91,11 @@ def from_config_JSON(cls, config_JSON):
                 concentration = utils.convert_concentration(config_JSON['chemical species'][chem_spec], 'initial value')
 
                 species_concentrations.append(SpeciesConcentration(species, concentration))
+
+        for species in species_list.species:
+            if not any(conc.species.name == species.name for conc in species_concentrations):
+                species_concentrations.append(SpeciesConcentration(species, 0)) 
+
 
         #TODO: may or may not be necessary
         # Set initial reaction rates

src/music_box_species_list.py

@@ -1,3 +1,5 @@
+import json
+import os
 from typing import List
 from music_box_species import Species
 
@@ -46,17 +48,43 @@ def from_UI_JSON(cls, UI_JSON):
         return cls(species_from_json)
 
     @classmethod
-    def from_config_JSON(cls, config_JSON):
+    def from_config_JSON(cls, path_to_json, config_JSON):
 
         species_from_json = []
 
-        for name, properties in config_JSON['chemical species'].items():
-            absolute_tolerance = properties.get('absolute tolerance')
-            molecular_weight = properties.get('molecular weight')
+        #gets config file path
+        config_file_path = os.path.dirname(path_to_json) + "/" + config_JSON['model components'][0]['configuration file']
+
+        #opnens config path to read species file
+        with open(config_file_path, 'r') as json_file:
+            config = json.load(json_file)
+
+            #assumes species file is first in the list
+            if(len(config['camp-files']) > 0):
+                species_file_path = os.path.dirname(config_file_path) + "/" + config['camp-files'][0]
+                with open(species_file_path, 'r') as species_file:
+                    species_data = json.load(species_file)
+                    #loads species by names from camp files
+                    for properties in species_data['camp-data']:
+                        name = properties.get('name')
+                        species_from_json.append(Species(name, None, None, None, None))
+
+
+        #chceks if species are in the config file and updates attributes accordingly
+        for chem_spec in config_JSON['chemical species']:
+            for species in species_from_json:
+                if species.name == chem_spec:
+                    # Add attributes to species
+                    if 'absolute tolerance' in chem_spec:
+                        species.absolute_tolerance = chem_spec['absolute tolerance']
+                    if 'molecular weight' in chem_spec:
+                        species.molecular_weight = chem_spec['molecular weight']
+                    if 'density' in chem_spec:
+                        species.density = chem_spec['density']
+                    if 'phase' in chem_spec:
+                        species.phase = chem_spec['phase']
+
 
-            # TODO: Add phase and density to species
-
-            species_from_json.append(Species(name, absolute_tolerance, None, molecular_weight, None))
 
         return cls(species_from_json)