def make_band_edge_states(orbital_infos: BandEdgeOrbitalInfos,
p_edge_state: PerfectBandEdgeState,
defect_charge_info: DefectChargeInfo = None
) -> BandEdgeStates:
vbm_k_idx = orbital_infos.kpt_idx(p_edge_state.vbm_info.kpt_coord)
cbm_k_idx = orbital_infos.kpt_idx(p_edge_state.cbm_info.kpt_coord)
vbm_info = p_edge_state.vbm_info
cbm_info = p_edge_state.cbm_info
states = []
lowest_idx = orbital_infos.lowest_band_index
for spin_idx, orb_info_by_spin in enumerate(orbital_infos.orbital_infos):
if defect_charge_info:
localized_orbs = defect_charge_info.localized_orbitals()[spin_idx]
localized_orbs = [i - lowest_idx for i in localized_orbs]
else:
localized_orbs = None
vbm_idx, vbm_diff = get_similar_orb_idx(orb_info_by_spin[vbm_k_idx],
vbm_info, localized_orbs,
_reversed=True)
vbm_info = EdgeInfo(band_idx=vbm_idx + lowest_idx,
kpt_coord=vbm_info.kpt_coord,
orbital_info=orb_info_by_spin[vbm_k_idx][vbm_idx])
cbm_idx, cbm_diff = get_similar_orb_idx(orb_info_by_spin[cbm_k_idx],
cbm_info, localized_orbs)
cbm_info = EdgeInfo(band_idx=cbm_idx + lowest_idx,
kpt_coord=cbm_info.kpt_coord,
orbital_info=orb_info_by_spin[cbm_k_idx][cbm_idx])
loc_idx_range = [vbm_info.band_idx + 1, cbm_info.band_idx - 1]
localized_orbs = get_localized_orbs(orb_info_by_spin,
loc_idx_range,
orbital_infos.lowest_band_index,
orbital_infos.kpt_weights)
vbm_hole = num_hole_in_vbm(orb_info_by_spin,
vbm_idx=vbm_idx,
weights=orbital_infos.kpt_weights)
cbm_electron = num_electron_in_cbm(orb_info_by_spin,
cbm_idx=cbm_idx,
weights=orbital_infos.kpt_weights)
states.append(BandEdgeState(vbm_info=vbm_info,
cbm_info=cbm_info,
vbm_orbital_diff=vbm_diff,
cbm_orbital_diff=cbm_diff,
localized_orbitals=localized_orbs,
vbm_hole_occupation=vbm_hole,
cbm_electron_occupation=cbm_electron))
return BandEdgeStates(states=states)
def test_plot_wo_spin():
be_orbital_info = BandEdgeOrbitalInfos(orbital_infos=[orb],
kpt_coords=[(0.0, 0.0, 0.0),
(0.25, 0.0, 0.0)],
kpt_weights=[0.5, 0.5],
lowest_band_index=10,
fermi_level=0.5)
plotter = EigenvalueMplPlotter(title="test",
band_edge_orb_infos=be_orbital_info,
supercell_vbm=0.1,
supercell_cbm=0.9)
plotter.construct_plot()
plotter.plt.show()
def test_band_edge_orbital_info_repr():
orbital_info_1 = OrbitalInfo(energy=1.23456789,
orbitals={
"Mn": [0.5, 0.4, 0.0, 0.0],
"Fe": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.99998,
participation_ratio=0.1111111)
orbital_info_2 = OrbitalInfo(energy=2.34567890,
orbitals={
"Mn": [0.1, 0.1, 0.0, 0.0],
"Fe": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.0001,
participation_ratio=0.2222222)
band_edge_orbital_infos = \
BandEdgeOrbitalInfos(orbital_infos=[[[orbital_info_1, orbital_info_2]]],
kpt_coords=[(0.0, 0.0, 0.0)],
kpt_weights=[1.0],
lowest_band_index=10,
fermi_level=0.5)
actual = band_edge_orbital_infos.__str__()
print(actual)
expected = """ -- band-edge orbitals info
K-points info
Index Coords Weight
1 ( 0.000, 0.000, 0.000) 1.000
Band info near band edges
Index Kpoint index Energy Occupation P-ratio Orbital
11 1 1.23 1.0 0.1 Mn-s: 0.50, Mn-p: 0.40
--
12 1 2.35 0.0 0.2
--
"""
assert actual == expected
def orb_infos():
orbital_infos = [[[
OrbitalInfo(energy=-1.1,
orbitals={
"Mn": [0.5, 0.6, 0.0, 0.0],
"O": [0.0, 0.0, 0.0, 0.0]
},
occupation=1.0,
participation_ratio=0.1),
OrbitalInfo(energy=-0.9,
orbitals={
"Mn": [0.5, 0.7, 0.0, 0.0],
"O": [0.0, 0.0, 0.0, 0.0]
},
occupation=1.0,
participation_ratio=0.1), # vbm
OrbitalInfo(energy=0.0,
orbitals={
"Mn": [0.1, 0.2, 0.0, 0.0],
"O": [0.3, 0.4, 0.0, 0.0]
},
occupation=1.0,
participation_ratio=0.1), # in-gap
OrbitalInfo(energy=1.0,
orbitals={
"Mn": [0.5, 0.8, 0.0, 0.0],
"O": [0.0, 0.0, 0.0, 0.0]
},
occupation=0.05,
participation_ratio=0.1), # in-gap
OrbitalInfo(energy=1.2,
orbitals={
"Mn": [0.0, 0.0, 0.0, 0.0],
"O": [0.1, 0.3, 0.0, 0.0]
},
occupation=0.02,
participation_ratio=0.1),
OrbitalInfo(energy=1.2,
orbitals={
"Mn": [0.0, 0.0, 0.0, 0.0],
"O": [0.1, 0.3, 0.0, 0.0]
},
occupation=0.01,
participation_ratio=0.1)
]]] # cbm
return BandEdgeOrbitalInfos(kpt_coords=[(0.0, 0.0, 0.0)],
kpt_weights=[1.0],
orbital_infos=orbital_infos,
lowest_band_index=8,
fermi_level=0.5)
def make_band_edge_orbital_infos(procar: Procar,
vasprun: Vasprun,
vbm: float, cbm: float,
str_info: DefectStructureInfo):
eigval_range = defaults.eigval_range
kpt_coords = [tuple(coord) for coord in vasprun.actual_kpoints]
max_energy_by_spin, min_energy_by_spin = [], []
neighbors = str_info.neighbor_atom_indices
for e in vasprun.eigenvalues.values():
max_energy_by_spin.append(np.amax(e[:, :, 0], axis=0))
min_energy_by_spin.append(np.amin(e[:, :, 0], axis=0))
max_energy_by_band = np.amax(np.vstack(max_energy_by_spin), axis=0)
min_energy_by_band = np.amin(np.vstack(min_energy_by_spin), axis=0)
lower_idx = np.argwhere(max_energy_by_band > vbm - eigval_range)[0][0]
upper_idx = np.argwhere(min_energy_by_band < cbm + eigval_range)[-1][-1]
orbs, s = procar.data, vasprun.final_structure
orb_infos = []
for spin, eigvals in vasprun.eigenvalues.items():
orb_infos.append([])
for k_idx in range(len(kpt_coords)):
orb_infos[-1].append([])
for b_idx in range(lower_idx, upper_idx + 1):
e, occ = eigvals[k_idx, b_idx, :]
orbitals = calc_orbital_character(orbs, s, spin, k_idx, b_idx)
p_ratio = calc_participation_ratio(orbs, spin, k_idx, b_idx, neighbors)
orb_infos[-1][-1].append(OrbitalInfo(e, orbitals, occ, p_ratio))
return BandEdgeOrbitalInfos(
orbital_infos=orb_infos,
kpt_coords=kpt_coords,
kpt_weights=vasprun.actual_kpoints_weights,
# need to convert numpy.int64 to int for mongoDB.
lowest_band_index=int(lower_idx),
fermi_level=vasprun.efermi)
orbitals={},
occupation=1.0,
participation_ratio=0.3),
OrbitalInfo(0.5,
orbitals={},
occupation=0.5,
participation_ratio=0.3),
OrbitalInfo(1.0,
orbitals={},
occupation=0.0,
participation_ratio=0.3)
]]
orbital_infos = BandEdgeOrbitalInfos(orbital_infos=[orb, orb],
kpt_coords=[(0.0, 0.0, 0.0),
(0.25, 0.0, 0.0)],
kpt_weights=[0.5, 0.5],
lowest_band_index=10,
fermi_level=0.5)
@pytest.fixture
def eigenvalue_mpl_plotter():
return EigenvalueMplPlotter(title="test",
band_edge_orb_infos=orbital_infos,
supercell_vbm=0.1,
supercell_cbm=0.9)
def test_plot(eigenvalue_mpl_plotter):
eigenvalue_mpl_plotter.construct_plot()
eigenvalue_mpl_plotter.plt.show()
def band_edge_orbital_infos(orbital_info):
return BandEdgeOrbitalInfos(orbital_infos=[[[orbital_info]]],
kpt_coords=[(0.0, 0.0, 0.0)],
kpt_weights=[1.0],
lowest_band_index=10,
fermi_level=0.5)
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)