def test(vasp_files):
d = vasp_files / "KInO2_Va_O_2"
defect_entry: DefectEntry = loadfn(d / "Va_O1_2/defect_entry.json")
calc_results: CalcResults = loadfn(d / "Va_O1_2/calc_results.json")
perfect_calc_results: CalcResults = loadfn(d / "perfect_calc_results.json")
unitcell: Unitcell = loadfn(d / "unitcell.json")
make_efnv_correction(defect_entry.charge,
calc_results,
perfect_calc_results,
unitcell.dielectric_constant,
1)
def _inner(_dir: Path):
calc_results = get_calc_results(_dir, args.check_calc_results)
defect_entry = loadfn(_dir / "defect_entry.json")
efnv = make_efnv_correction(defect_entry.charge, calc_results,
args.perfect_calc_results,
args.unitcell.dielectric_constant)
efnv.to_json_file(_dir / "correction.json")
title = defect_entry.full_name
plotter = SitePotentialMplPlotter.from_efnv_corr(title=title,
efnv_correction=efnv)
plotter.construct_plot()
plotter.plt.savefig(fname=_dir / "correction.pdf")
plotter.plt.clf()
def make_efnv_correction_from_vasp(args):
for d in args.dirs:
logger.info(f"Parsing data in {d} ...")
defect_entry: DefectEntry = loadfn(d / "defect_entry.json")
calc_results = loadfn(d / "calc_results.json")
efnv = make_efnv_correction(defect_entry.charge, calc_results,
args.perfect_calc_results,
args.unitcell.dielectric_constant)
efnv.to_json_file(d / "correction.json")
title = defect_entry.full_name
plotter = SitePotentialMplPlotter.from_efnv_corr(title=title,
efnv_correction=efnv)
plotter.construct_plot()
plotter.plt.savefig(fname=d / "correction.pdf")
plotter.plt.clf()
def test_make_efnv_correction(mocker):
mock_perfect = mocker.Mock(spec=CalcResults, autospec=True)
mock_defect = mocker.Mock(spec=CalcResults, autospec=True)
mock_perfect.structure = IStructure(Lattice.cubic(10),
species=["H"] + ["He"] * 3 + ["Li"],
coords=[[0, 0, 0], [1 / 2, 1 / 2, 0],
[1 / 2, 0, 1 / 2],
[0, 1 / 2, 1 / 2],
[0, 0, 1 / 2]])
mock_defect.structure = IStructure(Lattice.cubic(10),
species=["He"] * 3 + ["Li"],
coords=[[1 / 2, 1 / 2, 0],
[1 / 2, 0, 1 / 2],
[0, 1 / 2, 1 / 2],
[0, 0, 1 / 2]])
mock_perfect.potentials = [3.0, 4.0, 5.0, 6.0, 7.0]
mock_defect.potentials = [14.0, 25.0, 36.0, 47.0]
mock_ewald = mocker.patch("pydefect.cli.vasp.make_efnv_correction.Ewald")
ewald = mocker.Mock()
ewald.lattice_energy = 1e3
ewald.atomic_site_potential.return_value = 1e4
mock_ewald.return_value = ewald
efnvc = make_efnv_correction(charge=2,
calc_results=mock_defect,
perfect_calc_results=mock_perfect,
dielectric_tensor=np.eye(3))
unit_conversion = 180.95128169876497
assert efnvc.charge == 2
assert efnvc.point_charge_correction == -4e3 * unit_conversion
assert efnvc.defect_region_radius == 5.0
assert efnvc.sites == [
PotentialSite("He", 5 * np.sqrt(2), 10.0, 2e4 * unit_conversion),
PotentialSite("He", 5 * np.sqrt(2), 20.0, 2e4 * unit_conversion),
PotentialSite("He", 5 * np.sqrt(2), 30.0, 2e4 * unit_conversion),
PotentialSite("Li", 5.0, 40.0, None),
]
