def gkfo_correction(efnv_correction):
s1 = PotentialSite(specie="H",
distance=1.999,
potential=10,
pc_potential=None)
s2 = PotentialSite(specie="He",
distance=2.0001,
potential=15,
pc_potential=2)
s3 = PotentialSite(specie="He", distance=3.0, potential=20, pc_potential=3)
return GkfoCorrection(init_efnv_correction=efnv_correction,
additional_charge=1,
pc_2nd_term=10.0,
gkfo_sites=[s1, s2, s3],
ave_dielectric_tensor=4.0,
ave_electronic_dielectric_tensor=2.0)
def efnv_correction():
s1 = PotentialSite(specie="H",
distance=1.999,
potential=1.0,
pc_potential=None)
s2 = PotentialSite(specie="He",
distance=2.0001,
potential=1.5,
pc_potential=0.2)
s3 = PotentialSite(specie="He",
distance=3.0,
potential=2.0,
pc_potential=0.3)
return ExtendedFnvCorrection(charge=10,
point_charge_correction=1.0,
defect_region_radius=2.0,
sites=[s1, s2, s3],
defect_coords=(0.0, 0.0, 0.0))
def make_efnv_correction(charge: int,
calc_results: CalcResults,
perfect_calc_results: CalcResults,
dielectric_tensor: np.array,
accuracy: float = defaults.ewald_accuracy,
unit_conversion: float = 180.95128169876497):
"""
Notes:
(1) The formula written in YK2014 need to be divided by 4pi in the SI unit.
(2) When assuming an element charge locate at the defect_coords and
angstrom for length, relative dielectric tensor, Multiply
elementary_charge * 1e10 / epsilon_0 = 180.95128169876497
to make potential in V.
"""
if calc_results.structure.lattice != perfect_calc_results.structure.lattice:
raise SupercellError("The lattice constants for defect and perfect "
"models are different")
structure_analyzer = DefectStructureComparator(
calc_results.structure, perfect_calc_results.structure)
defect_coords = structure_analyzer.defect_center_coord
lattice = calc_results.structure.lattice
ewald = Ewald(lattice.matrix, dielectric_tensor, accuracy=accuracy)
point_charge_correction = \
0.0 if not charge else - ewald.lattice_energy * charge ** 2
defect_region_radius = calc_max_sphere_radius(lattice.matrix)
sites = []
for d, p in structure_analyzer.atom_mapping.items():
specie = str(calc_results.structure[d].specie)
frac_coords = calc_results.structure[d].frac_coords
distance, _ = lattice.get_distance_and_image(defect_coords,
frac_coords)
pot = calc_results.potentials[d] - perfect_calc_results.potentials[p]
coord = calc_results.structure[d].frac_coords
rel_coord = [x - y for x, y in zip(coord, defect_coords)]
if distance <= defect_region_radius:
pc_potential = None
else:
if charge == 0:
pc_potential = 0
else:
pc_potential = ewald.atomic_site_potential(rel_coord) * charge
pc_potential *= unit_conversion
sites.append(PotentialSite(specie, distance, pot, pc_potential))
return ExtendedFnvCorrection(
charge=charge,
point_charge_correction=point_charge_correction * unit_conversion,
defect_region_radius=defect_region_radius,
sites=sites,
defect_coords=tuple(defect_coords))
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),
]
def efnv_cor():
return ExtendedFnvCorrection(charge=1,
point_charge_correction=0.0,
defect_region_radius=2.8,
sites=[
PotentialSite(specie="H",
distance=1.0,
potential=-4,
pc_potential=None),
PotentialSite(specie="H",
distance=2.0,
potential=-3,
pc_potential=None),
PotentialSite(specie="He",
distance=3.0,
potential=-2,
pc_potential=-3),
PotentialSite(specie="He",
distance=4.0,
potential=-1,
pc_potential=-2)
],
defect_coords=(0.0, 0.0, 0.0))
def make_gkfo_correction(
efnv_correction: ExtendedFnvCorrection,
additional_charge: int,
final_calc_results: CalcResults,
initial_calc_results: CalcResults,
diele_tensor: np.array,
ion_clamped_diele_tensor: np.array,
accuracy: float = defaults.ewald_accuracy,
unit_conversion: float = 180.95128169876497) -> GkfoCorrection:
assert final_calc_results.structure == initial_calc_results.structure
assert abs(additional_charge) == 1
defect_coords = efnv_correction.defect_coords
lattice = initial_calc_results.structure.lattice
ewald_ele = Ewald(lattice.matrix,
ion_clamped_diele_tensor,
accuracy=accuracy)
defect_region_radius = efnv_correction.defect_region_radius
pc_2nd_term = -ewald_ele.lattice_energy
gkfo_sites = []
for index, site in enumerate(initial_calc_results.structure):
specie = site.specie
dist, _ = lattice.get_distance_and_image(site.frac_coords,
defect_coords)
pot = (final_calc_results.potentials[index] -
initial_calc_results.potentials[index])
rel_coord = [x - y for x, y in zip(site.frac_coords, defect_coords)]
if dist <= defect_region_radius:
pc_potential = None
else:
pc_potential = (ewald_ele.atomic_site_potential(rel_coord) *
additional_charge * unit_conversion)
gkfo_sites.append(PotentialSite(specie, dist, pot, pc_potential))
return GkfoCorrection(
init_efnv_correction=efnv_correction,
additional_charge=additional_charge,
pc_2nd_term=pc_2nd_term * unit_conversion,
gkfo_sites=gkfo_sites,
ave_dielectric_tensor=np.trace(diele_tensor) / 3,
ave_electronic_dielectric_tensor=np.trace(ion_clamped_diele_tensor) /
3)
def test_defect_site_msonable(efnv_correction):
assert_msonable(
PotentialSite(specie="H",
distance=1.999,
potential=1.0,
pc_potential=0.1))
def test_defect_site_diff_pot():
s = PotentialSite("H", distance=1.999, potential=1.0, pc_potential=0.1)
assert s.diff_pot == 1.0 - 0.1