def test_make_defect_energy_info(mocker):
defect_entry = mocker.Mock(DefectEntry, autospec=True)
defect_entry.name = "Va_Mg1"
defect_entry.charge = -1
calc_results = mocker.Mock(CalcResults, autospec=True)
calc_results.structure = IStructure(Lattice.cubic(1.0), ["O"], [[0.0]*3])
calc_results.energy = 10.0
calc_results.electronic_conv = False
correction = mocker.Mock(Correction, autospec=True)
correction.correction_dict = {"a": 10.0}
p_calc_results = mocker.Mock(CalcResults, autospec=True)
p_calc_results.structure = IStructure(Lattice.cubic(1.0),
["Mg", "O"], [[0.0]*3]*2)
p_calc_results.energy = 1.0
standard_energies = StandardEnergies({"Mg": 10.0, "O": 20.0})
unitcell = mocker.Mock()
unitcell.vbm = 100.0
actual = make_defect_energy_info(defect_entry, calc_results, correction,
p_calc_results, standard_energies, unitcell)
energy = DefectEnergy(formation_energy=10.0 - 1.0 + 10 - 100.0,
energy_corrections={"a": 10.0},
is_shallow=None)
expected = DefectEnergyInfo(name="Va_Mg1", charge=-1,
atom_io={"Mg": -1}, defect_energy=energy)
assert actual == expected
def make_defect_energy_info(
defect_entry: DefectEntry,
calc_results: CalcResults,
correction: Correction,
perfect_calc_results: CalcResults,
standard_energies: StandardEnergies,
unitcell: Unitcell,
band_edge_states: BandEdgeStates = None) -> DefectEnergyInfo:
atom_io = num_atom_differences(calc_results.structure,
perfect_calc_results.structure)
formation_energy = calc_results.energy - perfect_calc_results.energy
formation_energy += defect_entry.charge * unitcell.vbm
for k, v in atom_io.items():
formation_energy -= standard_energies[k] * v
is_shallow = band_edge_states.is_shallow if band_edge_states else None
energy = DefectEnergy(formation_energy=formation_energy,
energy_corrections=correction.correction_dict,
is_shallow=is_shallow)
return DefectEnergyInfo(defect_entry.name,
defect_entry.charge,
atom_io=atom_io,
defect_energy=energy)
def test_make_defect_energy_summary(mocker):
energy1 = DefectEnergy(0.0, {"PC correction": 2.0}, False)
energy2 = DefectEnergy(1.0, {"PC correction": 3.0}, True)
defect_infos = [
DefectEnergyInfo("Va_Mg1", 0, {"Mg": -1}, energy1),
DefectEnergyInfo("Va_Mg1", 1, {"Mg": -1}, energy2)
]
target_vertices = TargetVertices(target="MgO",
vertices={"A": TargetVertex({"Mg": 5.0})})
unitcell = mocker.Mock()
unitcell.vbm = 1.0
unitcell.cbm = 11.0
perf_be_state = mocker.Mock()
perf_be_state.vbm_info.energy = 0.0
perf_be_state.cbm_info.energy = 12.0
actual = make_defect_energy_summary(defect_infos, target_vertices,
unitcell, perf_be_state)
defect_energies = {
"Va_Mg1":
DefectEnergies(atom_io={"Mg": -1},
charges=[0, 1],
defect_energies=[energy1, energy2])
}
expected = DefectEnergySummary(title=unitcell.system,
defect_energies=defect_energies,
rel_chem_pots={"A": {
"Mg": 5.0
}},
cbm=10.0,
supercell_vbm=-1.0,
supercell_cbm=11.0)
assert actual == expected
def defect_energy_info2():
energy = DefectEnergy(formation_energy=0.0,
energy_corrections={"no correction": 0.0})
return DefectEnergyInfo(name="hole polaron", charge=1, atom_io={},
defect_energy=energy)
def defect_energy_info(defect_energy):
return DefectEnergyInfo(name="Va_O1", charge=1, atom_io={"O": -1},
defect_energy=defect_energy)
def _inner(_dir: Path):
return DefectEnergyInfo.from_yaml(str(_dir /
"defect_energy_info.yaml"))