def get_structure(d=10, a=0, atom="Li"):
species = []
coords = []
# does not work with cluster
# parser = CifParser(
# "/home/srr70/coo2/other_compoun/group_1_atoms/test/licoo2.cif")
# structure = parser.get_structures()[0]
# does not work with cluster
structure = Structure.from_file(
"/home/srr70/coo2/other_compoun/group_1_atoms/test/licoo2.cif")
for i in structure:
if i.species_string == "Li":
species.append(i.species)
coords.append(i.coords + [0, 0, +.5 * d + a])
else:
species.append(i.species)
coords.append(i.coords)
a = structure.lattice.matrix.copy()
a[2][2] = a[2][2] - d
struc = Structure(Lattice(a), species, coords, coords_are_cartesian=True)
struc.replace_species({"Li": atom})
CifWriter(struc).write_file(f"{atom}" + 'coo2_' +
str(struc.lattice.c)[:4] + '.cif')
# CifWriter(struc).write_file(fname+'licoo2_big.cif')
# os.system("open "+fname+'licoo2_big.cif')
return p2ase().get_atoms(struc)
