def test_grids_joblib_roundtrip(tmpdir, grids):
tmpdir.chdir()
print(tmpdir)
with open("tmp.joblib", mode="wb") as f:
joblib.dump(grids, f, compress=3)
with open("tmp.joblib", mode="rb") as f:
actual = joblib.load(f)
assert_dataclass_almost_equal(actual, grids)
def test_make_defect_structure_info(structures, def_str_info):
perf, initial, final = structures
info = MakeDefectStructureInfo(perf,
initial,
final,
dist_tol=0.2,
symprec=0.1,
neighbor_cutoff_factor=1.2)
actual = info.defect_structure_info
print(actual)
assert_dataclass_almost_equal(actual, def_str_info)
def test_assert_dataclass_almost_equal_float():
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(1.0), 1.0)
assert_dataclass_almost_equal(TestData(1.0), TestData(1.0))
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(1.0), TestData(2.0))
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(1.0), TestData(1.01), digit=2)
assert_dataclass_almost_equal(TestData(1.0), TestData(1.01), digit=1)
def test_perturbed_structure(ortho_conventional, mocker):
mock = mocker.patch(
"pydefect.input_maker.defect_entries_maker.random_3d_vector")
mock.return_value = ([0.0, 0.0, 0.35], 1.0)
structure = copy_to_structure(ortho_conventional)
actual = perturb_structure(structure,
center=[0.0, 0.0, 0.0], cutoff=2.5-1e-5)
expected_structure = structure
expected_structure[0].frac_coords = [0.0, 0.0, 0.05]
expected_site = PerturbedSite(element='H',
distance=0.0,
initial_coords=(0.0, 0.0, 0.0),
perturbed_coords=(0.0, 0.0, 0.05),
displacement=1.0)
mock.assert_called_with(defaults.displace_distance)
assert actual[0] == expected_structure
assert_dataclass_almost_equal(actual[1][0], expected_site)
def test_assert_dataclass_almost_equal_dataclass_attribute():
assert_dataclass_almost_equal(TestData(d=Data(1.0)), TestData(d=Data(1.0)))
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(d=Data(1.0)),
TestData(d=Data(1.01)),
digit=2)
assert_dataclass_almost_equal(TestData(d=Data(1.0)),
TestData(d=Data(1.001)),
digit=2)
def test_grids_from_chgcar(grids, chgcar):
actual = Grids.from_chgcar(chgcar)
assert_dataclass_almost_equal(actual, grids)
def test_grids_np_save_load_roundtrip(tmpdir, grids):
tmpdir.chdir()
print(tmpdir)
grids.dump()
actual = grids.from_file()
assert_dataclass_almost_equal(actual, grids)
def test_assert_dataclass_almost_equal_nested_iterable():
assert_dataclass_almost_equal(TestData(c=[(1.0,)]), TestData(c=[(1.0,)]))
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(c=[(1.0,)]),
TestData(c=[(2.0,)]), digit=2)
def test_assert_dataclass_almost_equal_iterable():
assert_dataclass_almost_equal(TestData(b=[1.0]), TestData(b=[1.0]))
with pytest.raises(AssertionError):
assert_dataclass_almost_equal(TestData(b=[1.0]), TestData(b=[2.0]))
def test_make_band_edge_orbital_infos(mocker):
mock_procar = mocker.Mock(spec=Procar, autospec=True)
mock_vasprun = mocker.Mock(spec=Vasprun, autospec=True)
mock_str_info = mocker.Mock(spec=DefectStructureInfo, autospec=True)
mock_vasprun.actual_kpoints = [[0.0, 0.0, 0.0]]
mock_vasprun.actual_kpoints_weights = [1.0]
mock_vasprun.final_structure = Structure(Lattice.cubic(1),
species=["H", "H", "He"],
coords=[[0] * 3] * 3)
mock_vasprun.eigenvalues = {
Spin.up:
np.array([
[
[-3.01, 1.],
[-2.90, 1.], # vbm
[8.01, 0.]
],
[[-3.01, 1.], [-2.99, 1.], [7.90, 0.]]
]), # cbm
# shift one band for testing magnetization
Spin.down:
np.array([[[-2.99, 1.], [7.99, 0.], [10.00, 0.]],
[[-3.01, 1.], [8.00, 0.], [10.00, 0.]]])
}
mock_vasprun.efermi = 20.0
# s: 1, p: 3, d: 5, f: 7 = 16 orbitals
mock_procar.data = {
Spin.up:
np.array([
[
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 0th band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 0th band, 2nd atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
], # 1st kpt, 0th band, 3rd atom
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 1st band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]
],
[
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 2nd kpt, 0th band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]
]
]),
Spin.down:
np.array([
[
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 0th band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 0th band, 2nd atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
], # 1st kpt, 0th band, 3rd atom
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 1st kpt, 1st band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]
],
[
[
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0], # 2nd kpt, 0th band, 1st atom
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]],
[[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]]
]
]),
}
mock_str_info.neighbor_atom_indices = [0]
actual = make_band_edge_orbital_infos(mock_procar,
mock_vasprun,
vbm=0.0,
cbm=5.0,
str_info=mock_str_info)
expected = BandEdgeOrbitalInfos(
orbital_infos=[[[
OrbitalInfo(energy=-2.9,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=1.0,
participation_ratio=1.0),
OrbitalInfo(energy=8.01,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0)
],
[
OrbitalInfo(energy=-2.99,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=1.0,
participation_ratio=1.0),
OrbitalInfo(energy=7.90,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0)
]],
[[
OrbitalInfo(energy=7.99,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0),
OrbitalInfo(energy=10.00,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0)
],
[
OrbitalInfo(energy=8.00,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0),
OrbitalInfo(energy=10.00,
orbitals={
"H": [1.0, 0.0, 0.0, 0.0],
"He": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0,
participation_ratio=1.0)
]]],
kpt_coords=[(0.0, 0.0, 0.0)],
kpt_weights=[1.0],
lowest_band_index=1,
fermi_level=20.0)
assert_dataclass_almost_equal(actual, expected)