add debug asserts

pynta/coveragedependence.py

@@ -2212,22 +2212,30 @@ def mol_to_atoms(admol,slab,sites,metal,partial_atoms=None,partial_admol=None):
     Returns:
         _type_: Atoms object corresponding to the admol 2D configuration
     """
+    assert admol.atoms[1].site == "bridge"
+    assert partial_admol.atoms[1].site == "bridge"
     if partial_atoms and partial_admol:
         atoms = deepcopy(partial_atoms)
         gpartial_admol = partial_admol.to_group()
         admol_atom_order = admol.atoms[:]
         gpartial_admol_order = gpartial_admol.atoms[:]
+        assert admol.atoms[1].site == "bridge"
+        assert partial_admol.atoms[1].site == "bridge"
         try:
             subisos = admol.find_subgraph_isomorphisms(gpartial_admol,save_order=True)
         except ValueError:
             subisos = admol.find_subgraph_isomorphisms(gpartial_admol)
             admol.atoms = admol_atom_order
             gpartial_admol.atoms = gpartial_admol_order
+        assert admol.atoms[1].site == "bridge"
+        assert partial_admol.atoms[1].site == "bridge"
         if len(subisos) == 0:
             raise ValueError("partial_admol is not subgraph isomorphic to admol: {0}, {1}".format(gpartial_admol.to_adjacency_list(),admol.to_adjacency_list()))
         subiso = subisos[0]
         atoms_in_partial = [a for a in subiso.keys() if not a.is_surface_site()]
         split_structs,adsorbed_atom_dict = split_adsorbed_structures(admol,clear_site_info=False,adsorption_info=True,atoms_to_skip=atoms_in_partial)
+        assert admol.atoms[1].site == "bridge"
+        assert partial_admol.atoms[1].site == "bridge"
     elif partial_atoms is None and partial_admol is None:
         atoms = deepcopy(slab)
         split_structs,adsorbed_atom_dict = split_adsorbed_structures(admol,clear_site_info=False,adsorption_info=True)
@@ -2249,7 +2257,8 @@ def mol_to_atoms(admol,slab,sites,metal,partial_atoms=None,partial_admol=None):
             ad.rotate(rot_vec,[0.0,0.0,1.0]) #rotate bonds toward the +z-axis
         else:
             adatom_molind = st.atoms.index([a for a in st.atoms if not a.is_surface_site()][0])
-
+        assert admol.atoms[1].site == "bridge"
+        assert partial_admol.atoms[1].site == "bridge"
         atom_surf_inds = []
         ad_sites = []
         for a,sind in adsorbed_atom_dict.items():
@@ -2258,4 +2267,6 @@ def mol_to_atoms(admol,slab,sites,metal,partial_atoms=None,partial_admol=None):
                 atom_surf_inds.append(mol_to_atoms_map[adatom_molind])
                 ad_sites.append(sites[sind])
         atoms,_,_ = place_adsorbate(ad,atoms,atom_surf_inds,ad_sites,metal)
+    assert admol.atoms[1].site == "bridge"
+    assert partial_admol.atoms[1].site == "bridge"
     return atoms

pynta/tasks.py

@@ -1242,14 +1242,18 @@ def run_task(self, fw_spec):
         sample_fws = []
         calculation_directories = []
         for i,config in enumerate(configs_for_calculation):
+            assert config.atoms[1].site == "bridge"
             adname = None
             for admol_name,config_list in admol_to_config_for_calculation.items():
                 if config in config_list:
                     adname = admol_name
                     break
             else:
                 raise ValueError
+            assert config.atoms[1].site == "bridge"
+
             partial_admol = admol_name_structure_dict[adname]
+            assert partial_admol.atoms[1].site == "bridge"
             admol_path = admol_name_path_dict[adname]
             partial_atoms = read(admol_path)
             init_atoms = mol_to_atoms(config,slab,sites,metal,partial_atoms=partial_atoms,partial_admol=partial_admol)