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adapt to changes in get_bond_lengths_sites function
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@mjohnson541
mjohnson541 committed Apr 25, 2024
1 parent 10526b7 commit bbe031f
Showing 1 changed file with 8 additions and 4 deletions.
12 changes: 8 additions & 4 deletions pynta/transitionstate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,8 @@ def get_unique_TS_structs(adsorbates,species_names,slab,cas,nslab,num_surf_sites
Generate unique initial structures for TS guess generation
"""
tsstructs = []
slab_sites = cas.get_sites()
site_adjacency = cas.get_neighbor_site_list()
ordered_adsorbates = [adsorbates[name] for name in species_names]
for adss in itertools.product(*ordered_adsorbates):
if num_surf_sites[0] > 0:
Expand All @@ -184,7 +186,7 @@ def get_unique_TS_structs(adsorbates,species_names,slab,cas,nslab,num_surf_sites
ad = adss[1][nslab:]
bondlengths1,sites1,site_lengths1 = get_bond_lengths_sites(mol_dict[name],adss[1],gratom_to_molecule_atom_maps[name],
gratom_to_molecule_surface_atom_maps[name],nslab,
facet=facet,metal=metal,cas=cas)
slab_sites,site_adjacency,facet=facet,metal=metal)
sitetype1 = list(sites1.values())[0]
height1 = list(site_lengths1.values())[0]
surf_ind1 = list(gratom_to_molecule_surface_atom_maps[name].keys())[0]
Expand All @@ -201,7 +203,7 @@ def get_unique_TS_structs(adsorbates,species_names,slab,cas,nslab,num_surf_sites
ad2 = adss[2][nslab:]
bondlengths2,sites2,site_lengths2 = get_bond_lengths_sites(mol_dict[name2],adss[2],gratom_to_molecule_atom_maps[name2],
gratom_to_molecule_surface_atom_maps[name2],nslab,
facet=facet,metal=metal,cas=cas)
slab_sites,site_adjacency,facet=facet,metal=metal)
sitetype2 = list(sites2.values())[0]
height2 = list(site_lengths2.values())[0]
surf_ind2 = list(gratom_to_molecule_surface_atom_maps[name2].keys())[0]
Expand Down Expand Up @@ -263,6 +265,8 @@ def generate_constraints_harmonic_parameters(tsstructs,adsorbates,slab,forward_t
site_bond_potential_lists = []
site_bond_dict_list = []
out_structs = []
slab_sites = cas.get_sites()
site_adjacency = cas.get_neighbor_site_list()

nodes_file = os.path.join(os.path.split(pynta.models.__file__)[0],"TS_tree_nodes.json")
nodes = read_nodes(nodes_file)
Expand All @@ -286,7 +290,7 @@ def generate_constraints_harmonic_parameters(tsstructs,adsorbates,slab,forward_t
bondlengths,sites,site_lengths = get_bond_lengths_sites(mol_dict[name],ads,
gratom_to_molecule_atom_maps[name],
gratom_to_molecule_surface_atom_maps[name],
nslab,facet=facet,metal=metal,cas=cas)
nslab,slab_sites,site_adjacency,facet=facet,metal=metal)
bdlength_list.append(bondlengths)
sites_list.append(sites)
site_lengths_list.append(site_lengths)
Expand All @@ -312,7 +316,7 @@ def generate_constraints_harmonic_parameters(tsstructs,adsorbates,slab,forward_t
bondlengths,sites,site_lengths = get_bond_lengths_sites(mol_dict[name],ads,
gratom_to_molecule_atom_maps[name],
gratom_to_molecule_surface_atom_maps[name],
nslab,facet=facet,metal=metal,cas=cas)
nslab,slab_sites,site_adjacency,facet=facet,metal=metal)
bdlength_list.append(bondlengths)
sites_list.append(sites)
site_lengths_list.append(site_lengths)
Expand Down

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