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 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 cubic_supercell_info_wo_int(cubic_supercell):
sites = {
"H1":
Site(element="H",
wyckoff_letter="a",
site_symmetry="m-3m",
equivalent_atoms=[0, 1, 2, 3]),
"He1":
Site(element="He",
wyckoff_letter="b",
site_symmetry="m-3m",
equivalent_atoms=[4, 5, 6, 7])
}
unitcell = Structure(Lattice.rhombohedral(7.071068, 60),
species=["H", "He"],
coords=[[0.0] * 3, [0.5] * 3])
return SupercellInfo(cubic_supercell,
"Fm-3m", [[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
sites,
unitcell_structure=unitcell)
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 cubic_supercell_info_wo_int(mocker, cubic_supercell):
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="m-3m",
equivalent_atoms=[0, 1, 2, 3]),
"He1":
Site(element="He",
wyckoff_letter="b",
site_symmetry="m-3m",
equivalent_atoms=[4, 5, 6, 7])
}
unitcell = Structure(Lattice.rhombohedral(7.071068, 60),
species=["H", "He"],
coords=[[0.0] * 3, [0.5] * 3])
return SupercellInfo(cubic_supercell,
"Fm-3m", [[-2, 2, 2], [2, -2, 2], [2, 2, -2]],
sites,
unitcell_structure=unitcell)