for matkey in st_json.keys():
tmp_st = st_json[matkey]
st = Structure.from_dict(tmp_st['st_after'])
bulkkey = ext_bulk_soap(matkey, bulkkeys)
st_bulk = Structure.from_dict(st_bulk_json[bulkkey])
slab = Slab(lattice=st.lattice,
species=st.species,
coords=st.frac_coords,
miller_index=[1, 1, 1],
oriented_unit_cell=st_bulk,
shift=0,
scale_factor=1,
reorient_lattice=False)
print(slab.is_symmetric(), slab.have_equivalent_surfaces())
surface_sites = []
surface_sites_prop = []
for tol in [0.0, 0.25, 0.5]:
tmp_surface_sites = get_surface_sites(slab, tol=tol)
surface_sites_prop.append(slab.site_properties['is_surf_site'])
surface_sites_prop = np.asarray(surface_sites_prop)
surface_sites_prop = np.any(surface_sites_prop, axis=0)
surface_sites = np.arange(0, slab.num_sites, 1)[surface_sites_prop]
surface_sites = [
i for i in surface_sites
if slab[i].frac_coords[2] > slab.center_of_mass[2]
] # top only
surface_sites_top = np.zeros(slab.num_sites, dtype=bool)
surface_sites_top[surface_sites] = True
