def test_sites_for_bio2():
bio2_structure = Structure.from_str("""Bi4 O8
1.0
4.880207 0.000000 -2.019673
-0.667412 5.402283 -1.612690
-0.040184 -0.016599 6.808846
Bi O
4 8
direct
0.729106 0.250000 1.000000 Bi
0.270894 0.750000 0.000000 Bi
0.000000 0.000000 0.500000 Bi
0.500000 0.500000 0.500000 Bi
0.321325 0.021684 0.814642 O
0.114894 0.650123 0.351314 O
0.885106 0.349877 0.648686 O
0.763580 0.849877 0.648686 O
0.236420 0.150123 0.351314 O
0.493318 0.521684 0.814642 O
0.506682 0.478316 0.185358 O
0.678675 0.978316 0.185358 O""",
fmt="POSCAR")
symmetrizer = StructureSymmetrizer(bio2_structure)
actual = symmetrizer.sites
expected = \
{'Bi1': Site(element='Bi', wyckoff_letter='e', site_symmetry='2', equivalent_atoms=[0, 1]),
'Bi2': Site(element='Bi', wyckoff_letter='c', site_symmetry='-1', equivalent_atoms=[2, 3]),
'O1': Site(element='O', wyckoff_letter='f', site_symmetry='1', equivalent_atoms=[4, 9, 10, 11]),
'O2': Site(element='O', wyckoff_letter='f', site_symmetry='1', equivalent_atoms=[5, 6, 7, 8])}
assert actual == expected
def test_sites(complex_monoclinic_structure):
symmetrizer = StructureSymmetrizer(complex_monoclinic_structure)
actual = symmetrizer.sites
expected = {"H1": Site("H", "a", "2/m", [0]),
"He1": Site("He", "m", "m", [1, 2]),
"He2": Site("He", "m", "m", [3, 4])}
assert actual == expected
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 _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 site():
return Site(element="H",
wyckoff_letter="a",
site_symmetry="m3m",
equivalent_atoms=[0, 1, 2, 3, 5, 6])