def test_local_extrema_append_sites_to_supercell_info2(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_2 = local_extrema.append_sites_to_supercell_info(supercell_info,
indices=[2])
interstitials = [
Interstitial(frac_coords=[0.05, 0.0, 0.0],
site_symmetry="4mm",
info="test #2")
]
expected_2 = SupercellInfo(actual_cubic * [2, 2, 2], "Pm-3m",
[[2, 0, 0], [0, 2, 0], [0, 0, 2]], sites,
interstitials)
assert actual_2 == expected_2
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 _generate_supercell_info(self):
symmetrizer = StructureSymmetrizer(self.supercell.structure)
if symmetrizer.sg_number != self.sg:
raise SupercellError
self.supercell_info = SupercellInfo(
self.supercell.structure,
self.sg_symbol,
self.transformation_matrix,
symmetrizer.sites,
unitcell_structure=self.primitive_structure)
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 _generate_supercell_info(self):
multiplicity = int(round(det(self.transformation_matrix)))
sites = {}
for site_name, site in self.symmetrizer.sites.items():
atoms = []
for i in site.equivalent_atoms:
atoms.extend(
list(range(i * multiplicity, (i + 1) * multiplicity)))
sites[site_name] = Site(element=site.element,
wyckoff_letter=site.wyckoff_letter,
site_symmetry=site.site_symmetry,
equivalent_atoms=atoms)
self.supercell_info = \
SupercellInfo(structure=self.supercell.structure,
space_group=self.sg_symbol,
transformation_matrix=self.transformation_matrix,
sites=sites,
unitcell_structure=self.primitive_structure)
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)
def test_supercell_info_from_dict(supercell_info):
d = supercell_info.as_dict()
d["transform_matrix"] = d.pop("transformation_matrix")
expected = SupercellInfo.from_dict(d)
assert expected == supercell_info
