reads species name from config

src/box_model.py

@@ -292,7 +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:
+            for spec in self.species_list.species:
                 headers.append("CONC." + spec.name)
 
             output_array.append(headers)
@@ -376,6 +376,9 @@ def readConditionsFromJson(self, path_to_json):
             # Set initial conditions
             self.initial_conditions = Conditions.from_config_JSON(data)
 
+            # Set species list
+            self.species_list = SpeciesList.from_config_JSON(data)
+
 
 # for testing purposes
 def __main__():

src/music_box_species_list.py

@@ -44,6 +44,22 @@ def from_UI_JSON(cls, UI_JSON):
             species_from_json.append(Species(name, absolute_tolerance, None, molecular_weight, None))
 
         return cls(species_from_json)
+
+    @classmethod
+    def from_config_JSON(cls, 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')
+
+            # TODO: Add phase and density to species
+
+            species_from_json.append(Species(name, absolute_tolerance, None, molecular_weight, None))
+
+        return cls(species_from_json)
+
 
     def add_species(self, species):
         """

src/test_config_1_out.csv

@@ -1,4 +1,4 @@
-time,ENV.temperature,ENV.pressure
+time,ENV.temperature,ENV.pressure,CONC.A,CONC.B,CONC.C
 0,272.5,101253.3,1.0,0.0,0.0
 1.0,272.5,101253.3,0.99520593465931,7.2584865869196184e-09,0.004794058082203489
 2.0,272.5,101253.3,0.9904348523811104,7.223688927947401e-09,0.009565140395200417