def perform_bandfilling(defect_entry):
"""
Perform bandfilling correction.
Args:
defect_entry (DefectEntry): Defect to correct.
Returns:
Corrected DefectEntry
"""
BFC = BandFillingCorrection()
bfc_dict = BFC.get_correction(defect_entry)
bandfilling_meta = defect_entry.parameters["bandfilling_meta"].copy()
bandfilling_meta.update(
{"bandfilling_correction": bfc_dict["bandfilling_correction"]})
defect_entry.parameters.update({
"bandfilling_meta":
bandfilling_meta,
# also update free holes and electrons for shallow level shifting correction...
"num_hole_vbm":
bandfilling_meta["num_hole_vbm"],
"num_elec_cbm":
bandfilling_meta["num_elec_cbm"],
})
return defect_entry
def perform_bandfilling(self, defect_entry):
"""
Perform bandfilling correction.
Args:
defect_entry (DefectEntry): Defect to correct.
Returns:
Corrected DefectEntry
"""
BFC = BandFillingCorrection()
bfc_dict = BFC.get_correction(defect_entry)
bandfilling_meta = defect_entry.parameters['bandfilling_meta'].copy()
bandfilling_meta.update(
{'bandfilling_correction': bfc_dict['bandfilling_correction']})
defect_entry.parameters.update({
'bandfilling_meta':
bandfilling_meta,
# also update free holes and electrons for shallow level shifting correction...
'num_hole_vbm':
bandfilling_meta['num_hole_vbm'],
'num_elec_cbm':
bandfilling_meta['num_elec_cbm']
})
return defect_entry
def perform_bandfilling(self, defect_entry):
BFC = BandFillingCorrection()
bfc_dict = BFC.get_correction(defect_entry)
bandfilling_meta = defect_entry.parameters['bandfilling_meta'].copy()
bandfilling_meta.update( {'bandfilling_correction': bfc_dict['bandfilling']})
defect_entry.parameters.update({'bandfilling_meta': bandfilling_meta,
# also update free holes and electrons for band edge shifting correction...
'num_hole_vbm': bandfilling_meta['num_hole_vbm'],
'num_elec_cbm': bandfilling_meta['num_elec_cbm']})
return defect_entry
def perform_bandfilling(self, defect_entry):
BFC = BandFillingCorrection()
bfc_dict = BFC.get_correction(defect_entry)
bandfilling_meta = defect_entry.parameters['bandfilling_meta'].copy()
bandfilling_meta.update(
{'bandfilling_correction': bfc_dict['bandfilling']})
defect_entry.parameters.update({
'bandfilling_meta':
bandfilling_meta,
# also update free holes and electrons for band edge shifting correction...
'num_hole_vbm':
bandfilling_meta['num_hole_vbm'],
'num_elec_cbm':
bandfilling_meta['num_elec_cbm']
})
return defect_entry
def test_bandfilling(self):
v = Vasprun(os.path.join(PymatgenTest.TEST_FILES_DIR, "vasprun.xml"))
eigenvalues = v.eigenvalues.copy()
kptweights = v.actual_kpoints_weights
potalign = 0.0
vbm = v.eigenvalue_band_properties[2]
cbm = v.eigenvalue_band_properties[1]
params = {
"eigenvalues": eigenvalues,
"kpoint_weights": kptweights,
"potalign": potalign,
"vbm": vbm,
"cbm": cbm,
}
bfc = BandFillingCorrection()
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
# test trivial performing bandfilling correction
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bf_corr, 0.0)
self.assertFalse(bfc.metadata["num_elec_cbm"])
self.assertFalse(bfc.metadata["num_hole_vbm"])
self.assertFalse(bfc.metadata["potalign"])
# test trivial full entry bandfill evaluation
de = DefectEntry(vac, 0.0, corrections={}, parameters=params, entry_id=None)
corr = bfc.get_correction(de)
self.assertAlmostEqual(corr["bandfilling_correction"], 0.0)
# modify the eigenvalue list to have free holes
hole_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
hole_eigenvalues[spinkey] = []
for kptset in spinset:
hole_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] < vbm) and (eig[0] > vbm - 0.8):
hole_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
hole_eigenvalues[spinkey][-1].append(eig)
hole_bf_corr = bfc.perform_bandfill_corr(
hole_eigenvalues, kptweights, potalign, vbm, cbm
)
self.assertAlmostEqual(hole_bf_corr, -0.41138336)
self.assertAlmostEqual(bfc.metadata["num_hole_vbm"], 0.8125000649)
self.assertFalse(bfc.metadata["num_elec_cbm"])
# test case with only one spin and eigen-occupations are 1.
one_spin_eigen = hole_eigenvalues.copy()
del one_spin_eigen[list(eigenvalues.keys())[0]]
bf_corr = bfc.perform_bandfill_corr(
one_spin_eigen, kptweights, potalign, vbm, cbm
)
self.assertAlmostEqual(bf_corr, -0.14487501159000005)
# test case with only one spin and eigen-occupations are 2.
one_spin_eigen_twooccu = one_spin_eigen.copy()
for kptset in one_spin_eigen_twooccu.values():
for bandset in kptset:
for occuset in bandset:
if occuset[1] == 1.0:
occuset[1] = 2.0
elif occuset[1] == 0.5:
occuset[1] = 1.0
bf_corr = bfc.perform_bandfill_corr(
one_spin_eigen_twooccu, kptweights, potalign, vbm, cbm
)
self.assertAlmostEqual(bf_corr, -0.14487501159000005)
def test_bandfilling(self):
v = Vasprun(os.path.join(test_dir, 'vasprun.xml'))
eigenvalues = v.eigenvalues.copy()
kptweights = v.actual_kpoints_weights
potalign = 0.
vbm = v.eigenvalue_band_properties[2]
cbm = v.eigenvalue_band_properties[1]
params = {
'eigenvalues': eigenvalues,
'kpoint_weights': kptweights,
'potalign': potalign,
'vbm': vbm,
'cbm': cbm
}
bfc = BandFillingCorrection()
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
#test trivial performing bandfilling correction
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bf_corr, 0.)
self.assertFalse(bfc.metadata['occupied_def_levels'])
self.assertFalse(bfc.metadata['unoccupied_def_levels'])
self.assertFalse(bfc.metadata['total_occupation_defect_levels'])
self.assertFalse(bfc.metadata['num_elec_cbm'])
self.assertFalse(bfc.metadata['num_hole_vbm'])
self.assertFalse(bfc.metadata['potalign'])
#test trivial full entry bandfill evaluation
de = DefectEntry(vac, 0., corrections={}, parameters=params, entry_id=None)
corr = bfc.get_correction(de)
self.assertAlmostEqual(corr['bandfilling'], 0.)
#modify the eigenvalue list to have free holes
hole_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
hole_eigenvalues[spinkey] = []
for kptset in spinset:
hole_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] < vbm) and (eig[0] > vbm - .8):
hole_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
hole_eigenvalues[spinkey][-1].append(eig)
hole_bf_corr = bfc.perform_bandfill_corr(hole_eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(hole_bf_corr, -0.41138336)
self.assertAlmostEqual(bfc.metadata['num_hole_vbm'], 0.8125000649)
self.assertFalse(bfc.metadata['num_elec_cbm'])
#modify the eigenvalue list to have free electrons
elec_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
elec_eigenvalues[spinkey] = []
for kptset in spinset:
elec_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] > cbm) and (eig[0] < cbm + .2):
elec_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
elec_eigenvalues[spinkey][-1].append(eig)
elec_bf_corr = bfc.perform_bandfill_corr(elec_eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(elec_bf_corr, -0.0903187572254)
self.assertAlmostEqual(bfc.metadata['num_elec_cbm'], 0.8541667349)
self.assertFalse(bfc.metadata['num_hole_vbm'])
#modify the potalignment and introduce new occupied defect levels from vbm states
potalign = -0.1
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bfc.metadata['num_hole_vbm'], 0.)
self.assertAlmostEqual(bf_corr, 0.)
occu = [[1.457, 0.0833333], [1.5204, 0.0833333], [1.53465, 0.0833333], [1.5498, 0.0416667]]
self.assertArrayAlmostEqual(
list(sorted(bfc.metadata['occupied_def_levels'], key=lambda x: x[0])), list(
sorted(occu, key=lambda x: x[0])))
self.assertAlmostEqual(bfc.metadata['total_occupation_defect_levels'], 0.29166669)
self.assertFalse(bfc.metadata['unoccupied_def_levels'])
def test_bandfilling(self):
v = Vasprun(os.path.join(test_dir, 'vasprun.xml'))
eigenvalues = v.eigenvalues.copy()
kptweights = v.actual_kpoints_weights
potalign = 0.
vbm = v.eigenvalue_band_properties[2]
cbm = v.eigenvalue_band_properties[1]
params = {
'eigenvalues': eigenvalues,
'kpoint_weights': kptweights,
'potalign': potalign,
'vbm': vbm,
'cbm': cbm
}
bfc = BandFillingCorrection()
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
#test trivial performing bandfilling correction
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign,
vbm, cbm)
self.assertAlmostEqual(bf_corr, 0.)
self.assertFalse(bfc.metadata['occupied_def_levels'])
self.assertFalse(bfc.metadata['unoccupied_def_levels'])
self.assertFalse(bfc.metadata['total_occupation_defect_levels'])
self.assertFalse(bfc.metadata['num_elec_cbm'])
self.assertFalse(bfc.metadata['num_hole_vbm'])
self.assertFalse(bfc.metadata['potalign'])
#test trivial full entry bandfill evaluation
de = DefectEntry(vac,
0.,
corrections={},
parameters=params,
entry_id=None)
corr = bfc.get_correction(de)
self.assertAlmostEqual(corr['bandfilling'], 0.)
#modify the eigenvalue list to have free holes
hole_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
hole_eigenvalues[spinkey] = []
for kptset in spinset:
hole_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] < vbm) and (eig[0] > vbm - .8):
hole_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
hole_eigenvalues[spinkey][-1].append(eig)
hole_bf_corr = bfc.perform_bandfill_corr(hole_eigenvalues, kptweights,
potalign, vbm, cbm)
self.assertAlmostEqual(hole_bf_corr, -0.41138336)
self.assertAlmostEqual(bfc.metadata['num_hole_vbm'], 0.8125000649)
self.assertFalse(bfc.metadata['num_elec_cbm'])
#modify the eigenvalue list to have free electrons
elec_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
elec_eigenvalues[spinkey] = []
for kptset in spinset:
elec_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] > cbm) and (eig[0] < cbm + .2):
elec_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
elec_eigenvalues[spinkey][-1].append(eig)
elec_bf_corr = bfc.perform_bandfill_corr(elec_eigenvalues, kptweights,
potalign, vbm, cbm)
self.assertAlmostEqual(elec_bf_corr, -0.0903187572254)
self.assertAlmostEqual(bfc.metadata['num_elec_cbm'], 0.8541667349)
self.assertFalse(bfc.metadata['num_hole_vbm'])
#modify the potalignment and introduce new occupied defect levels from vbm states
potalign = -0.1
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign,
vbm, cbm)
self.assertAlmostEqual(bfc.metadata['num_hole_vbm'], 0.)
self.assertAlmostEqual(bf_corr, 0.)
occu = [[1.457, 0.0833333], [1.5204, 0.0833333], [1.53465, 0.0833333],
[1.5498, 0.0416667]]
self.assertArrayAlmostEqual(
list(
sorted(bfc.metadata['occupied_def_levels'],
key=lambda x: x[0])),
list(sorted(occu, key=lambda x: x[0])))
self.assertAlmostEqual(bfc.metadata['total_occupation_defect_levels'],
0.29166669)
self.assertFalse(bfc.metadata['unoccupied_def_levels'])
def test_bandfilling(self):
v = Vasprun(os.path.join(test_dir, 'vasprun.xml'))
eigenvalues = v.eigenvalues.copy()
kptweights = v.actual_kpoints_weights
potalign = 0.
vbm = v.eigenvalue_band_properties[2]
cbm = v.eigenvalue_band_properties[1]
params = {
'eigenvalues': eigenvalues,
'kpoint_weights': kptweights,
'potalign': potalign,
'vbm': vbm,
'cbm': cbm
}
bfc = BandFillingCorrection()
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
#test trivial performing bandfilling correction
bf_corr = bfc.perform_bandfill_corr(eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bf_corr, 0.)
self.assertFalse(bfc.metadata['num_elec_cbm'])
self.assertFalse(bfc.metadata['num_hole_vbm'])
self.assertFalse(bfc.metadata['potalign'])
#test trivial full entry bandfill evaluation
de = DefectEntry(vac, 0., corrections={}, parameters=params, entry_id=None)
corr = bfc.get_correction(de)
self.assertAlmostEqual(corr['bandfilling_correction'], 0.)
#modify the eigenvalue list to have free holes
hole_eigenvalues = {}
for spinkey, spinset in eigenvalues.items():
hole_eigenvalues[spinkey] = []
for kptset in spinset:
hole_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] < vbm) and (eig[0] > vbm - .8):
hole_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
hole_eigenvalues[spinkey][-1].append(eig)
hole_bf_corr = bfc.perform_bandfill_corr(hole_eigenvalues, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(hole_bf_corr, -0.41138336)
self.assertAlmostEqual(bfc.metadata['num_hole_vbm'], 0.8125000649)
self.assertFalse(bfc.metadata['num_elec_cbm'])
#test case with only one spin and eigen-occupations are 1.
one_spin_eigen = hole_eigenvalues.copy()
del one_spin_eigen[list(eigenvalues.keys())[0]]
bf_corr = bfc.perform_bandfill_corr(one_spin_eigen, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bf_corr, -0.14487501159000005)
#test case with only one spin and eigen-occupations are 2.
one_spin_eigen_twooccu = one_spin_eigen.copy()
for kptset in one_spin_eigen_twooccu.values():
for bandset in kptset:
for occuset in bandset:
if occuset[1] == 1.:
occuset[1] = 2.
elif occuset[1] == .5:
occuset[1] = 1.
bf_corr = bfc.perform_bandfill_corr(one_spin_eigen_twooccu, kptweights, potalign, vbm, cbm)
self.assertAlmostEqual(bf_corr, -0.14487501159000005)