def test_site_diff():
site_diff_vac = SiteDiff(removed=[(1, "H", (0.0, 0.0, 0.0))],
inserted=[],
removed_by_sub=[],
inserted_by_sub=[])
site_diff_int = SiteDiff(removed=[],
inserted=[(1, "H", (0.0, 0.0, 0.0))],
removed_by_sub=[],
inserted_by_sub=[])
site_diff_sub = SiteDiff(removed=[],
inserted=[],
removed_by_sub=[(1, "H", (0.0, 0.0, 0.0))],
inserted_by_sub=[(1, "He", (0.0, 0.0, 0.0))])
assert site_diff_vac.is_complex_defect is False
assert site_diff_sub.is_complex_defect is False
assert site_diff_vac.is_vacancy
assert site_diff_int.is_vacancy is False
assert site_diff_sub.is_vacancy is False
assert site_diff_vac.is_interstitial is False
assert site_diff_int.is_interstitial
assert site_diff_sub.is_interstitial is False
assert site_diff_vac.is_substituted is False
assert site_diff_int.is_substituted is False
assert site_diff_sub.is_substituted
def def_str_info(displacements):
site_diff = SiteDiff(removed=[(0, 'H', (0.25, 0.25, 0.25))],
inserted=[(0, 'H', (0.27, 0.25, 0.25))],
removed_by_sub=[(2, 'Li', (0.5, 0.5, 0.5))],
inserted_by_sub=[(2, 'Be', (0.5, 0.5, 0.5009))])
site_diff_from_init = SiteDiff(removed=[(0, 'H', (0.25, 0.25, 0.25))],
inserted=[(0, 'H', (0.27, 0.25, 0.25))],
removed_by_sub=[(2, 'Li', (0.5, 0.5, 0.5))],
inserted_by_sub=[(2, 'Be', (0.5, 0.5, 0.5))
])
shifted_final = Structure(Lattice.cubic(10),
species=["H", "He", "Be", "U"],
coords=[[0.27, 0.25, 0.25], [0.76, 0.75, 0.75],
[0.5, 0.5, 0.5009], [0.0, 0.0, 0.0]])
return DefectStructureInfo(shifted_final_structure=shifted_final,
initial_site_sym="3m",
final_site_sym="m",
site_diff=site_diff,
site_diff_from_initial=site_diff_from_init,
symprec=0.1,
dist_tol=0.2,
anchor_atom_idx=3,
neighbor_atom_indices=[0],
neighbor_cutoff_factor=1.2,
drift_vector=(0.0, 0.0, 0.0001),
drift_dist=0.001,
center=(0.38, 0.375, 0.375175),
displacements=displacements)
def test_judge_defect_type():
"""The structures remain as they could be used in the future"""
perfect = Structure(Lattice.cubic(10), species=["H"]*4,
coords=[[0.0, 0.0, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
defect = Structure(Lattice.cubic(10), species=["H"]*3,
coords=[[0.0, 0.0, 0.0], [0.25, 0.25, 0.5],
[0.5, 0.5, 0.0]])
site_diff = SiteDiff(removed=[(1, "H", (0.0, 0.5, 0.5)),
(2, "H", (0.5, 0.0, 0.5))],
inserted=[(1, "H", (0.25, 0.25, 0.5))],
removed_by_sub=[], inserted_by_sub=[])
assert judge_defect_type(site_diff) == DefectType.vacancy_split
defect_2 = Structure(Lattice.cubic(10), species=["H"]*5,
coords=[[0.0, 0.0, 0.0], [0.25, 0.25, 0.5],
[0.75, 0.25, 0.5], [0.25, 0.75, 0.5],
[0.5, 0.5, 0.0]])
site_diff_2 = SiteDiff(removed=[(1, "H", (0.0, 0.5, 0.5)),
(2, "H", (0.5, 0.0, 0.5))],
inserted=[(1, "H", (0.25, 0.25, 0.5)),
(2, "H", (0.75, 0.25, 0.5)),
(3, "H", (0.25, 0.75, 0.5))],
removed_by_sub=[], inserted_by_sub=[])
assert judge_defect_type(site_diff_2) == DefectType.interstitial_split
defect_3 = Structure(Lattice.cubic(10), species=["H", "He", "H"],
coords=[[0.0, 0.0, 0.0], [0.25, 0.25, 0.5],
[0.5, 0.5, 0.0]])
site_diff_3 = SiteDiff(removed=[(1, "H", (0.0, 0.5, 0.5)),
(2, "H", (0.5, 0.0, 0.5))],
inserted=[(1, "He", (0.25, 0.25, 0.5))],
removed_by_sub=[], inserted_by_sub=[])
assert judge_defect_type(site_diff_3) == DefectType.unknown
def test_site_diff_is_no_diff():
site_diff = SiteDiff(removed=[],
inserted=[],
removed_by_sub=[],
inserted_by_sub=[])
assert site_diff.is_no_diff is True
site_diff = SiteDiff(removed=[(1, "H", (0.0, 0.0, 0.0))],
inserted=[],
removed_by_sub=[],
inserted_by_sub=[])
assert site_diff.is_no_diff is False
def test_make_site_diff_wo_diff():
s1 = IStructure(Lattice.cubic(10), species=["H"], coords=[[0] * 3])
s2 = s1.copy()
structure_comparator = DefectStructureComparator(s1, s2)
site_diff = structure_comparator.make_site_diff()
assert site_diff == SiteDiff([], [], [], [])
assert site_diff.is_no_diff
s1 = IStructure(Lattice.cubic(10),
species=["H", "He"],
coords=[[0] * 3, [0.5] * 3])
s2 = IStructure(Lattice.cubic(10), species=["H"], coords=[[0] * 3])
structure_comparator = DefectStructureComparator(defect_structure=s2,
perfect_structure=s1)
site_diff = structure_comparator.make_site_diff()
assert site_diff == SiteDiff([(1, "He", (0.5, 0.5, 0.5))], [], [], [])
assert site_diff.is_no_diff is False
def site_diff():
return SiteDiff(removed=[(1, "Cu", (0.25, 0.74, 0.74))],
inserted=[(0, "Cu", (0.25, 0.5, 0.5))],
removed_by_sub=[(0, "Cu", (0.25, 0.25, 0.25))],
inserted_by_sub=[(5, "H", (0.25, 0.25, 0.25))])