break Pynta so that it does not detect the uniqueness of adsorbates

handle naming of duplicate adsorbates properly
this is intended for scale testing only

pynta/main.py

@@ -187,18 +187,19 @@ def generate_mol_dict(self):
                     mols.append(mol)
                     r["product_mols"].append(mol)
 
-        unique_mols = []
-        for mol in mols:
-            for m in unique_mols:
-                if mol.is_isomorphic(m):
-                    break
-            else:
-                unique_mols.append(mol)
-
+        # unique_mols = []
+        # for mol in mols:
+        #     for m in unique_mols:
+        #         if mol.is_isomorphic(m):
+        #             break
+        #     else:
+        #         unique_mols.append(mol)
+        unique_mols = mols[:]
         for mol in unique_mols:
             mol.multiplicity = mol.get_radical_count() + 1
-
-        mol_dict = {get_name(mol):mol for mol in unique_mols}
+        mol_dict = dict()
+        for mol in unique_mols:
+            mol_dict[get_name(mol,mol_dict.keys())] = mol
         self.mol_dict = mol_dict
         self.name_to_adjlist_dict = {sm:mol.to_adjacency_list() for sm,mol in mol_dict.items()}
 

pynta/mol.py

@@ -812,8 +812,14 @@ def get_bond_lengths_sites(mol,ads,atom_map,surf_atom_map,nslab,facet="fcc111",m
 
     return bondlengths,sites,sitelengths
 
-def get_name(mol):
+def get_name(mol,mol_names):
     try:
-        return mol.to_smiles()
+        basename = mol.to_smiles()
     except:
-        return mol.to_adjacency_list().replace("\n"," ")[:-1]
+        basename = mol.to_adjacency_list().replace("\n"," ")[:-1]
+    i = 0 
+    name = basename
+    while name in mol_names:
+        i += 1
+        name = basename + "-" + str(i)
+    return name