fixed "sites" v. "size" problem, yaml_writer now works for catalysis …

…and gas phase. Time for pull request?

rmgpy/cantera.py

@@ -18,8 +18,7 @@
 from rmgpy.chemkin import get_species_identifier
 
 def write_cantera(spcs, rxns, surface_site_density=None, solvent=None, solvent_data=None, path="chem.yml"):
-    # result_dict = get_mech_dict(spcs, rxns, solvent=solvent, solvent_data=solvent_data)
-
+
     # intro to file will change depending on the presence of surface species
     is_surface = False
     for spc in spcs:
@@ -120,25 +119,16 @@ def write_surface_species(spcs,rxns, surface_site_density):
         #Dr. West, why can't i just write the above lines as: 
             #surface_species = [spc for spc in spcs if spc.contains_surface_site()]
             #gas_species = [spc for spc in spcs if not spc.contains_surface_site()]
-
-        #VERY INTERESTING: for some reason, the sample catalysis yaml that i was looking at split up the species (surface v. gas), but when I do that, I get an error in cantera
 
     sorted_surface_species = sorted(surface_species, key=lambda surface_species: surface_species.index)
     surface_species_to_write = [get_species_identifier(surface_species) for surface_species in sorted_surface_species]
 
     sorted_gas_species = sorted(gas_species, key=lambda gas_species: gas_species.index)
     gas_species_to_write = [get_species_identifier(gas_species) for gas_species in sorted_gas_species]
-    
-    #using this now instead because the separated species gave me errors? 
+
+
     sorted_species = sorted(spcs, key=lambda spcs: spcs.index)
     species_to_write = [get_species_identifier(spec) for spec in sorted_species]
-
-    # coverage_dependencies = {}
-    # for rxn in rxns:
-    #     coverage_dependence = getattr(rxn.kinetics, 'coverage_dependence', {})
-    #     if coverage_dependence:
-    #         coverage_dependencies.update(coverage_dependence)
-
 
 
     #gas part 
@@ -237,7 +227,6 @@ def get_mech_dict_nonsurface(spcs, rxns, solvent='solvent', solvent_data=None):
          if names.count(name) > 1:
              names[i] += "-"+str(names.count(name))
 
-    #  for spc in spcs:
      result_dict = dict()
      result_dict["species"]= [obj_to_dict(x, spcs, names=names) for x in spcs]
 
@@ -256,7 +245,6 @@ def reaction_to_dicts(obj, spcs):
     length 1, but a MultiArrhenius or MultiPDepArrhenius will be longer.
     """
 
-    #try:
     reaction_list = []
     if isinstance(obj.kinetics, MultiArrhenius) or isinstance(obj.kinetics, MultiPDepArrhenius):
         list_of_cantera_reactions = obj.to_cantera(use_chemkin_identifier=True)
@@ -268,28 +256,10 @@ def reaction_to_dicts(obj, spcs):
         efficiencies = getattr(obj.kinetics, 'efficiencies', {})
         if efficiencies:      
             reaction_data["efficiencies"] = {spcs[i].to_chemkin(): float(val) for i, val in enumerate(obj.kinetics.get_effective_collider_efficiencies(spcs)) if val != 1}
-        # if isinstance(obj.kinetics, StickingCoefficient):
-        #     reaction_data.pop('equation', None)
-        #     reaction_data['equation'] = str(obj)
         reaction_list.append(reaction_data)
 
-    # for reaction in list_of_cantera_reactions:
-    #     reaction_data = reaction.input_data   
-    #     efficiencies = getattr(obj.kinetics, 'efficiencies', {})
-    #     if efficiencies:      
-    #         reaction_data["efficiencies"] = {spcs[i].to_chemkin(): float(val) for i, val in enumerate(obj.kinetics.get_effective_collider_efficiencies(spcs)) if val != 1}
-
-    #     reaction_list.append(reaction_data)
-
-    # if isinstance[obj.kinetics, StickingCoefficient]:  
-    #      print(str(obj))
-
     return reaction_list
-    # except: 
-    #     print('passing')
-    #     print(type(obj.kinetics))
-    #     print(str(obj))
-    #     return []
+
 
 
 def obj_to_dict(obj, spcs, names=None, label="solvent"):
@@ -303,6 +273,10 @@ def obj_to_dict(obj, spcs, names=None, label="solvent"):
             result_dict['note'] = obj.transport_data.comment
         except:
             pass
+        if 'size' in species_data: 
+            sites = species_data['size']
+            species_data.pop('size', None)
+            species_data['sites'] = sites
         species_data.update(result_dict)
         return species_data #returns composition, name, thermo, and transport, and note
 

rmgpy/species.py

@@ -434,9 +434,17 @@ def to_cantera(self, use_chemkin_identifier=False):
             else:
                 element_dict[symbol] += 1
         if use_chemkin_identifier:
-            ct_species = ct.Species(self.to_chemkin(), element_dict)
+            label = self.to_chemkin()
         else:
-            ct_species = ct.Species(self.label, element_dict)
+            label = self.label
+
+        if self.contains_surface_site() and element_dict['X'] > 1:
+            # for multidentate adsorbates, 'size' is the same as 'sites'? for some reason, cantera won't take the input 'size,' so will need to use 'sites' 
+            ct_species = ct.Species(label, element_dict, size=element_dict['X'])
+            #hopefully this will be fixed soon, so that ct.Species can take a 'sites' parameter or that cantera can read input files with 'size' specified
+        else:
+            ct_species = ct.Species(label, element_dict)
+
         if self.thermo:
             try:
                 ct_species.thermo = self.thermo.to_cantera()