Fixed bugs with chapman example (#148)

* does not add rel tolerance to species list

* updates m according to temp and pressure

* commented out concentration array override

* changed Type to type

* removes unecessary code

src/acom_music_box/music_box.py

@@ -182,11 +182,11 @@ def generateSpeciesConfig(self):
         speciesArray = []
 
         #Adds relative tolerance if value is set
-        # if(self.species_list.relative_tolerance != None):
-        #     relativeTolerance = {}
-        #     relativeTolerance["Type"] = "RELATIVE_TOLERANCE"
-        #     relativeTolerance["value"] = self.species_list.relative_tolerance
-        #     speciesArray.append(relativeTolerance)
+        if(self.species_list.relative_tolerance != None):
+            relativeTolerance = {}
+            relativeTolerance["type"] = "RELATIVE_TOLERANCE"
+            relativeTolerance["value"] = self.species_list.relative_tolerance
+            speciesArray.append(relativeTolerance)
 
         #Adds species to config
         for species in self.species_list.species:
@@ -420,6 +420,7 @@ def solve(self, path_to_output = None):
 
         rate_constant_ordering = musica.user_defined_reaction_rates(self.solver)
         species_constant_ordering = musica.species_ordering(self.solver)
+
 
         #adds species headers to output
         ordered_species_headers =  [k for k, v in sorted(species_constant_ordering.items(), key=lambda item: item[1])]
@@ -428,6 +429,7 @@ def solve(self, path_to_output = None):
 
         ordered_concentrations = self.order_species_concentrations(curr_conditions, species_constant_ordering)
         ordered_rate_constants = self.order_reaction_rates(curr_conditions, rate_constant_ordering)
+
 
         output_array.append(headers)
 
@@ -453,28 +455,30 @@ def solve(self, path_to_output = None):
             #iterates evolvings conditons if enough time has elapsed
             while(next_conditions != None and next_conditions_time <= curr_time):
 
-                #curr_conditions = next_conditions
                 curr_conditions.update_conditions(next_conditions)
 
-
                 #iterates next_conditions if there are remaining evolving conditions
                 if(len(self.evolving_conditions) > next_conditions_index + 1):
                     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):
-                        ordered_concentrations = self.order_species_concentrations(curr_conditions, species_constant_ordering)
 
                     ordered_rate_constants = self.order_reaction_rates(curr_conditions, rate_constant_ordering)
 
                 else:
                     next_conditions = None
 
+
+            #updates M accordingly
+            if 'M' in species_constant_ordering:
+                BOLTZMANN_CONSTANT = 1.380649e-23
+                AVOGADRO_CONSTANT = 6.02214076e23;  
+                GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
+                ordered_concentrations[species_constant_ordering['M']] = curr_conditions.pressure / (GAS_CONSTANT * curr_conditions.temperature)
+
             #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, ordered_concentrations, ordered_rate_constants)
+
 
 
 
@@ -582,13 +586,13 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering):
     @classmethod
     def order_species_concentrations(self, curr_conditions, species_constant_ordering):
         concentrations = {}
+
         for concentraton in curr_conditions.species_concentrations:
             concentrations[concentraton.species.name] = concentraton.concentration
 
         ordered_concentrations = len(concentrations.keys()) * [0.0]
 
         for key, value in concentrations.items():
-
             ordered_concentrations[species_constant_ordering[key]] = value
         return ordered_concentrations
 

src/acom_music_box/music_box_species_list.py

@@ -12,7 +12,7 @@ class SpeciesList:
         relativeTolerance (float): The relative tolerance for the species list.
     """
 
-    def __init__(self, species=None, relative_tolerance=0.0):
+    def __init__(self, species=None, relative_tolerance=1.0e-4):
         """
         Initializes a new instance of the SpeciesList class.
 
@@ -66,8 +66,9 @@ def from_config_JSON(cls, path_to_json, config_JSON):
                     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))
+                        if properties.get('name') is not None:
+                            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