fixed "sites" v. "size" problem, yaml_writer now works for catalysis and gas phase.

Time for pull request?

Author: Nora-Khalil

rmgpy/cantera.py

@@ -330,6 +330,10 @@ 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()