def test_add_interstitial_not_primitive_error(cubic_supercell_info_wo_int):
conventional_cell = Structure(Lattice.cubic(10),
species=["H"] * 4 + ["He"] * 4,
coords=[[0.0, 0.0, 0.0],
[0.5, 0.5, 0.0],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.0, 0.0, 0.5],
[0.0, 0.5, 0.0],
[0.5, 0.0, 0.0],
[0.5, 0.5, 0.5],
])
with pytest.raises(NotPrimitiveError):
append_interstitial(cubic_supercell_info_wo_int, conventional_cell,
[[1/4, 1/4, 1/4]], ["test1"])
def append_sites_to_supercell_info(self, supercell_info, indices):
frac_coords, infos = [], []
for idx, ep in enumerate(self.extrema_points, 1):
if idx in indices:
frac_coords.append(ep.frac_coords[0])
infos.append(f"{self.info} #{idx}")
result = append_interstitial(supercell_info,
self.unit_cell,
frac_coords=frac_coords,
infos=infos)
return result
def test_add_interstitial(cubic_supercell_info_wo_int):
primitive = Structure(Lattice.rhombohedral(7.071068, 60),
species=["H", "He"],
coords=[[0.0]*3, [0.5]*3])
new_supercell_info = append_interstitial(cubic_supercell_info_wo_int,
primitive,
[[1/4, 1/4, 1/4]],
infos=["test1"])
expected = Interstitial(frac_coords=[1/8, 1/8, 1/8],
site_symmetry="-43m",
info="test1")
assert new_supercell_info.interstitials[0] == expected
def test_add_interstitial2(mocker, simple_cubic):
mock_supercell_info = mocker.Mock()
mock_supercell_info.unitcell_structure = simple_cubic
mock_supercell_info.transformation_matrix = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
mock_supercell_info.interstitials = []
unitcell = Structure.from_dict(simple_cubic.as_dict())
new_supercell_info = append_interstitial(mock_supercell_info,
unitcell,
[(0.0, 0.0, 0.1)],
infos=["test1"])
expected = Interstitial(frac_coords=[0.0, 0.0, 0.05],
site_symmetry="4mm",
info="test1")
assert new_supercell_info.interstitials[0] == expected
def append_interstitial_to_supercell_info(args):
supercell_info = append_interstitial(args.supercell_info,
args.base_structure,
[args.frac_coords], args.info)
supercell_info.to_json_file()