def test_local_extrema_append_sites_to_supercell_info(local_extrema,
simple_cubic):
sites = {
"H1":
Site(element="H",
wyckoff_letter="a",
site_symmetry="mmm",
equivalent_atoms=[0, 1, 2, 3, 4, 5, 6, 7])
}
actual_cubic = Structure.from_dict(simple_cubic.as_dict())
supercell_info = SupercellInfo(actual_cubic * [2, 2, 2], "Pm-3m",
[[2, 0, 0], [0, 2, 0], [0, 0, 2]], sites,
[])
actual = local_extrema.append_sites_to_supercell_info(supercell_info,
indices=[1, 2])
interstitials = [
Interstitial(frac_coords=[0.05] * 3,
site_symmetry="3m",
info="test #1"),
Interstitial(frac_coords=[0.05, 0.0, 0.0],
site_symmetry="4mm",
info="test #2")
]
expected = SupercellInfo(actual_cubic * [2, 2, 2], "Pm-3m",
[[2, 0, 0], [0, 2, 0], [0, 0, 2]], sites,
interstitials)
assert actual == expected
def append_interstitial(supercell_info: SupercellInfo,
unitcell_structure: Union[Structure, IStructure],
frac_coords: List[Union[List[float], Coords]],
infos: List[str]) -> SupercellInfo:
"""
inv_trans_mat must be multiplied with coords from the right as the
trans_mat is multiplied to the unitcell lattice vector from the left.
see __mul__ of IStructure in pymatgen.
x_u, x_s means the frac coordinates in unitcell and supercell,
while a, b, c are the unitcell lattice vector.
(a_u, b_u, c_u) . (a, b, c) = (a_s, b_s, c_s) . trans_mat . (a, b, c)
(a_u, b_u, c_u) = (a_s, b_s, c_s) . trans_mat
so, (a_s, b_s, c_s) = (a_u, b_u, c_u) . inv_trans_ma
"""
if supercell_info.unitcell_structure and \
supercell_info.unitcell_structure != unitcell_structure:
raise NotPrimitiveError
if isinstance(frac_coords[0], float):
frac_coords = [frac_coords]
for fcoord, info in zip(frac_coords, infos):
us = Structure.from_dict(unitcell_structure.as_dict())
us.append(species=Element.H, coords=fcoord)
symmetrizer = StructureSymmetrizer(us)
site_symm = symmetrizer.spglib_sym_data["site_symmetry_symbols"][-1]
inv_matrix = inv(np.array(supercell_info.transformation_matrix))
new_coords = np.dot(fcoord, inv_matrix).tolist()
supercell_info.interstitials.append(
Interstitial(frac_coords=new_coords,
site_symmetry=site_symm,
info=info))
return supercell_info
def append_interstitial(supercell_info: SupercellInfo,
unitcell_structure: Structure,
frac_coords: List[float]) -> SupercellInfo:
"""
inv_trans_mat must be multiplied with coords from the right as the
trans_mat is multiplied to the unitcell lattice vector from the left.
see __mul__ of IStructure in pymatgen.
x_u, x_s means the frac coordinates in unitcell and supercell,
while a, b, c are the unitcell lattice vector.
(a_u, b_u, c_u) . (a, b, c) = (a_s, b_s, c_s) . trans_mat . (a, b, c)
(a_u, b_u, c_u) = (a_s, b_s, c_s) . trans_mat
so, (a_s, b_s, c_s) = (a_u, b_u, c_u) . inv_trans_mat
"""
if supercell_info.unitcell_structure and \
supercell_info.unitcell_structure != unitcell_structure:
raise NotPrimitiveError
unitcell_structure.append(species=Element.H, coords=frac_coords)
symmetrizer = StructureSymmetrizer(unitcell_structure)
wyckoff_letter = (symmetrizer.spglib_sym_data["wyckoffs"][-1])
site_symmetry = (symmetrizer.spglib_sym_data["site_symmetry_symbols"][-1])
inv_matrix = inv(np.array(supercell_info.transformation_matrix))
new_coords = np.dot(frac_coords, inv_matrix).tolist()
supercell_info.interstitials.append(
Interstitial(frac_coords=new_coords,
wyckoff_letter=wyckoff_letter,
site_symmetry=site_symmetry))
return supercell_info
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])
expected = Interstitial(frac_coords=[1 / 8, 1 / 8, 1 / 8],
wyckoff_letter="d",
site_symmetry="-43m")
assert new_supercell_info.interstitials[0] == expected
def cubic_supercell_info(cubic_supercell):
sites = {"H1": Site(element="H", wyckoff_letter="a", site_symmetry="m-3m",
equivalent_atoms=list(range(32))),
"He1": Site(element="He", wyckoff_letter="b", site_symmetry="m-3m",
equivalent_atoms=list(range(32, 64)))}
interstitial = Interstitial([0.25]*3, site_symmetry="yy")
return SupercellInfo(cubic_supercell,
"Fm-3m",
[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
sites,
interstitials=[interstitial])
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 supercell_info(ortho_conventional):
sites = {
"H1":
Site(element="H",
wyckoff_letter="a",
site_symmetry="mmm",
equivalent_atoms=[0, 1, 2, 3]),
"He1":
Site(element="He",
wyckoff_letter="b",
site_symmetry="mmm",
equivalent_atoms=[4, 5, 6, 7])
}
interstitial = Interstitial(frac_coords=[0.25] * 3,
site_symmetry="yy",
info="test")
return SupercellInfo(ortho_conventional, "Fmmm",
[[1, 0, 0], [0, 1, 0], [0, 0, 1]], sites,
[interstitial])
def supercell_info(mocker, ortho_conventional):
mock = mocker.patch("pydefect.util.structure_tools.defaults")
mock.same_distance_criterion = defaults.same_distance_criterion
mock.cutoff_distance_factor = 1.7
sites = {
"H1":
Site(element="H",
wyckoff_letter="a",
site_symmetry="mmm",
equivalent_atoms=[0, 1, 2, 3]),
"He1":
Site(element="He",
wyckoff_letter="b",
site_symmetry="mmm",
equivalent_atoms=[4, 5, 6, 7])
}
interstitial = Interstitial([0.25] * 3,
wyckoff_letter="x",
site_symmetry="yy")
return SupercellInfo(ortho_conventional, "Fmmm",
[[1, 0, 0], [0, 1, 0], [0, 0, 1]], sites,
[interstitial])
def interstitial():
return Interstitial(frac_coords=[0.25, 0.25, 0.25],
wyckoff_letter="a",
site_symmetry="m3m")
