def get_freysoldt_correction(defect_type, defect_specie, path_to_defect_locpot,path_to_pure_locpot,charge,
dielectric_constant,defect_site_coordinates,energy_cutoff=500,get_plot=False):
''' Function to perform charge corrections according to the method proposed py Freysoldt
If this correction is used, please reference Freysoldt's original paper.
doi: 10.1103/PhysRevLett.102.016402
Args:
defect_type: 'vacancy' or 'interstitial'
defect_specie: string with element occupying the defect site
path_to_defect_locpot: path to LOCPOT file of defect structure
path_to_pure_locpot: path to LOCPOT file of Pure structure
charge: Charge of the defected system
dielectric_constant: Dielectric constant
defect_site_coordinates: numpy array with fractional coordinates of defect site
energy_cutoff: Cut-off of plane wave expansion
get_plot: return also Matplotlib object with plot
Returns:
Freysoldt corrections values as a dictionary
'''
# acquiring data from LOCPOT files
locpot_pure = Locpot.from_file(path_to_pure_locpot)
vol_data_pure = VolumetricData(locpot_pure.structure,locpot_pure.data)
locpot_defect = Locpot.from_file(path_to_defect_locpot)
vol_data_defect = VolumetricData(locpot_defect.structure,locpot_defect.data)
parameters = {}
parameters['axis_grid'] = []
parameters['bulk_planar_averages'] = []
parameters['defect_planar_averages'] = []
for i in range(0,3):
parameters['axis_grid'].append(vol_data_pure.get_axis_grid(i))
parameters['bulk_planar_averages'].append(vol_data_pure.get_average_along_axis(i))
parameters['defect_planar_averages'].append(vol_data_defect.get_average_along_axis(i))
parameters['initial_defect_structure'] = locpot_defect.structure
parameters['defect_frac_sc_coords'] = defect_site_coordinates
structure_bulk = locpot_pure.structure
defect_site = PeriodicSite(defect_specie, coords=defect_site_coordinates, lattice = locpot_pure.structure.lattice)
module = importlib.import_module("pymatgen.analysis.defects.core")
defect_class = getattr(module,defect_type)
defect = defect_class(structure_bulk, defect_site, charge=charge, multiplicity=None)
defect_entry = DefectEntry(defect,None,corrections=None,parameters=parameters)
freysoldt_class = FreysoldtCorrection(dielectric_constant,energy_cutoff=energy_cutoff)
freysoldt_corrections = freysoldt_class.get_correction(defect_entry)
if get_plot:
plt = freysoldt_class.plot(1)
return freysoldt_corrections , plt
else:
return freysoldt_corrections
def perform_freysoldt(self, defect_entry):
FC = FreysoldtCorrection(defect_entry.parameters['dielectric'])
freycorr = FC.get_correction(defect_entry)
freysoldt_meta = FC.metadata.copy()
freysoldt_meta["freysoldt_potalign"] = defect_entry.parameters["potalign"]
freysoldt_meta["freysoldt_electrostatic"] = freycorr["freysoldt_electrostatic"]
freysoldt_meta["freysoldt_potential_alignment_correction"] = freycorr["freysoldt_potential_alignment"]
defect_entry.parameters.update({'freysoldt_meta': freysoldt_meta})
return defect_entry
def perform_freysoldt(self, defect_entry):
FC = FreysoldtCorrection(defect_entry.parameters['dielectric'])
freycorr = FC.get_correction(defect_entry)
freysoldt_meta = FC.metadata.copy()
freysoldt_meta["freysoldt_potalign"] = defect_entry.parameters["potalign"]
freysoldt_meta["freysoldt_electrostatic"] = freycorr["freysoldt_electrostatic"]
freysoldt_meta["freysoldt_potential_alignment_correction"] = freycorr["freysoldt_potential_alignment"]
defect_entry.parameters.update({'freysoldt_meta': freysoldt_meta})
return defect_entry
def perform_freysoldt(defect_entry):
"""
Perform Freysoldt correction.
Args:
defect_entry (DefectEntry): Defect to correct.
Returns:
Corrected DefectEntry
"""
FC = FreysoldtCorrection(defect_entry.parameters['dielectric'])
freycorr = FC.get_correction(defect_entry)
freysoldt_meta = FC.metadata.copy()
freysoldt_meta["freysoldt_potalign"] = defect_entry.parameters["potalign"]
freysoldt_meta["freysoldt_electrostatic"] = freycorr["freysoldt_electrostatic"]
freysoldt_meta["freysoldt_potential_alignment_correction"] = freycorr["freysoldt_potential_alignment"]
defect_entry.parameters.update({'freysoldt_meta': freysoldt_meta})
return defect_entry
def test_freysoldt(self):
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
struc = struc
vac = Vacancy(struc, struc.sites[0], charge=-3)
ids = vac.generate_defect_structure(1)
abc = struc.lattice.abc
axisdata = [np.arange(0.0, lattval, 0.2) for lattval in abc]
bldata = [
np.array([1.0 for u in np.arange(0.0, lattval, 0.2)]) for lattval in abc
]
dldata = [
np.array(
[
(-1 - np.cos(2 * np.pi * u / lattval))
for u in np.arange(0.0, lattval, 0.2)
]
)
for lattval in abc
]
params = {
"axis_grid": axisdata,
"bulk_planar_averages": bldata,
"defect_planar_averages": dldata,
"initial_defect_structure": ids,
"defect_frac_sc_coords": struc.sites[0].frac_coords,
}
fc = FreysoldtCorrection(15)
# test electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, -3)
self.assertAlmostEqual(es_corr, 0.975893)
# test potential alignment method
pot_corr = fc.perform_pot_corr(
axisdata[0], bldata[0], dldata[0], struc.lattice, -3, vac.site.coords, 0
)
self.assertAlmostEqual(pot_corr, 2.836369987722345)
# test entry full correction method
de = DefectEntry(vac, 0.0, corrections={}, parameters=params, entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val["freysoldt_electrostatic"], 0.975893)
self.assertAlmostEqual(val["freysoldt_potential_alignment"], 4.4700574)
# test the freysoldt plotter
for ax in range(3):
fcp = fc.plot(axis=ax)
self.assertTrue(fcp)
# check that uncertainty metadata exists
for ax in range(3):
self.assertAlmostEqual(
set(fc.metadata["pot_corr_uncertainty_md"][ax].keys()),
set(["potcorr", "stats"]),
)
# test a specified axis from entry
fc = FreysoldtCorrection(15, axis=[1])
val = fc.get_correction(de)
self.assertAlmostEqual(val["freysoldt_potential_alignment"], 5.2869010593283132)
# test a different charge
# for electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, 2)
self.assertAlmostEqual(es_corr, 0.43373)
# for potential alignment method
pot_corr = fc.perform_pot_corr(
axisdata[0], bldata[0], dldata[0], struc.lattice, 2, vac.site.coords, 0
)
self.assertAlmostEqual(pot_corr, -2.1375685936497768)
# test an input anisotropic dielectric constant
fc = FreysoldtCorrection([[1.0, 2.0, 3.0], [0.0, 3.0, 5.0], [4.0, 10.0, 8.0]])
self.assertAlmostEqual(fc.dielectric, 4.0)
val = fc.get_correction(de)
self.assertAlmostEqual(val["freysoldt_electrostatic"], 3.659599)
self.assertAlmostEqual(val["freysoldt_potential_alignment"], 3.3605255195745087)
# test potalign being added to defect entry
self.assertAlmostEqual(de.parameters["potalign"], 1.1201751731915028)
# test that metadata entries exist in defect entry
self.assertTrue("freysoldt_meta" in de.parameters.keys())
self.assertAlmostEqual(
set(de.parameters["freysoldt_meta"].keys()),
set(["pot_plot_data", "pot_corr_uncertainty_md"]),
)
# test a charge of zero
vac = Vacancy(struc, struc.sites[0], charge=0)
de = DefectEntry(vac, 0.0, corrections={}, parameters=params, entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val["freysoldt_electrostatic"], 0.0)
self.assertAlmostEqual(val["freysoldt_potential_alignment"], 0.0)
def test_freysoldt(self):
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
struc = struc
vac = Vacancy(struc, struc.sites[0], charge=-3)
abc = struc.lattice.abc
axisdata = [np.arange(0., lattval, 0.2) for lattval in abc]
bldata = [np.array([1. for u in np.arange(0., lattval, 0.2)]) for lattval in abc]
dldata = [
np.array([(-1 - np.cos(2 * np.pi * u / lattval)) for u in np.arange(0., lattval, 0.2)]) for lattval in abc
]
params = {'axis_grid': axisdata, 'bulk_planar_averages': bldata, 'defect_planar_averages': dldata}
fc = FreysoldtCorrection(15)
#test electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, -3)
self.assertAlmostEqual(es_corr, 0.975893)
#test potential alignment method
pot_corr = fc.perform_pot_corr(axisdata[0], bldata[0], dldata[0], struc.lattice, -3, vac.site.coords, 0)
self.assertAlmostEqual(pot_corr, 2.836369987722345)
#test entry full correction method
de = DefectEntry(vac, 0., corrections={}, parameters=params, entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 0.975893)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 4.4700574)
#test the freysoldt plotter and that plot metadata exists
pltsaver = []
for ax in range(3):
pltsaver.append(fc.plot(axis=ax))
self.assertAlmostEqual(len(pltsaver), 3)
#check that uncertainty metadata exists
for ax in range(3):
self.assertAlmostEqual(set(fc.metadata['pot_corr_uncertainty_md'][ax].keys()), set(['potcorr', 'stats']))
#test a specified axis from entry
fc = FreysoldtCorrection(15, axis=[1])
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 5.2869010593283132)
#test a different charge
# for electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, 2)
self.assertAlmostEqual(es_corr, 0.43373)
# for potential alignment method
pot_corr = fc.perform_pot_corr(axisdata[0], bldata[0], dldata[0], struc.lattice, 2, vac.site.coords, 0)
self.assertAlmostEqual(pot_corr, -2.1375685936497768)
#test an input anisotropic dielectric constant
fc = FreysoldtCorrection([[1., 2., 3.], [0., 3., 5.], [4., 10., 8.]])
self.assertAlmostEqual(fc.dielectric, 4.)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 3.659599)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 3.3605255195745087)
#test potalign being added to defect entry
self.assertAlmostEqual(de.parameters['potalign'], 1.1201751731915028)
#test that metadata entries exist in defect entry
self.assertTrue('freysoldt_meta' in de.parameters.keys())
self.assertAlmostEqual(
set(de.parameters['freysoldt_meta'].keys()), set(['pot_plot_data', 'pot_corr_uncertainty_md']))
#test a charge of zero
vac = Vacancy(struc, struc.sites[0], charge=0)
de = DefectEntry(vac, 0., corrections={}, parameters=params, entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 0.)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 0.)
def test_freysoldt(self):
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
struc = struc
vac = Vacancy(struc, struc.sites[0], charge=-3)
abc = struc.lattice.abc
axisdata = [np.arange(0., lattval, 0.2) for lattval in abc]
bldata = [
np.array([1. for u in np.arange(0., lattval, 0.2)])
for lattval in abc
]
dldata = [
np.array([(-1 - np.cos(2 * np.pi * u / lattval))
for u in np.arange(0., lattval, 0.2)]) for lattval in abc
]
params = {
'axis_grid': axisdata,
'bulk_planar_averages': bldata,
'defect_planar_averages': dldata
}
fc = FreysoldtCorrection(15)
#test electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, -3)
self.assertAlmostEqual(es_corr, 0.975893)
#test potential alignment method
pot_corr = fc.perform_pot_corr(axisdata[0], bldata[0], dldata[0],
struc.lattice, -3, vac.site.coords, 0)
self.assertAlmostEqual(pot_corr, 2.836369987722345)
#test entry full correction method
de = DefectEntry(vac,
0.,
corrections={},
parameters=params,
entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 0.975893)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 4.4700574)
#test the freysoldt plotter and that plot metadata exists
pltsaver = []
for ax in range(3):
pltsaver.append(fc.plot(axis=ax))
self.assertAlmostEqual(len(pltsaver), 3)
#check that uncertainty metadata exists
for ax in range(3):
self.assertAlmostEqual(
set(fc.metadata['pot_corr_uncertainty_md'][ax].keys()),
set(['potcorr', 'stats']))
#test a specified axis from entry
fc = FreysoldtCorrection(15, axis=[1])
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_potential_alignment'],
5.2869010593283132)
#test a different charge
# for electrostatic correction
es_corr = fc.perform_es_corr(struc.lattice, 2)
self.assertAlmostEqual(es_corr, 0.43373)
# for potential alignment method
pot_corr = fc.perform_pot_corr(axisdata[0], bldata[0], dldata[0],
struc.lattice, 2, vac.site.coords, 0)
self.assertAlmostEqual(pot_corr, -2.1375685936497768)
#test an input anisotropic dielectric constant
fc = FreysoldtCorrection([[1., 2., 3.], [0., 3., 5.], [4., 10., 8.]])
self.assertAlmostEqual(fc.dielectric, 4.)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 3.659599)
self.assertAlmostEqual(val['freysoldt_potential_alignment'],
3.3605255195745087)
#test potalign being added to defect entry
self.assertAlmostEqual(de.parameters['potalign'], 1.1201751731915028)
#test that metadata entries exist in defect entry
self.assertTrue('freysoldt_meta' in de.parameters.keys())
self.assertAlmostEqual(
set(de.parameters['freysoldt_meta'].keys()),
set(['pot_plot_data', 'pot_corr_uncertainty_md']))
#test a charge of zero
vac = Vacancy(struc, struc.sites[0], charge=0)
de = DefectEntry(vac,
0.,
corrections={},
parameters=params,
entry_id=None)
val = fc.get_correction(de)
self.assertAlmostEqual(val['freysoldt_electrostatic'], 0.)
self.assertAlmostEqual(val['freysoldt_potential_alignment'], 0.)
def get_correction_freysoldt(defect_entry,
epsilon,
title=None,
partflag='All',
axis=None):
"""
Function to compute the isotropic freysoldt correction for each defect.
If this correction is used, please reference Freysoldt's original paper.
doi: 10.1103/PhysRevLett.102.016402
Args:
defect_entry: DefectEntry object with the following
keys stored in defect.parameters:
required:
axis_grid (3 x NGX where NGX is the length of the NGX grid
in the x,y and z axis directions. Same length as planar
average lists):
A list of 3 numpy arrays which contain the cartesian axis
values (in angstroms) that correspond to each planar avg
potential supplied.
bulk_planar_averages (3 x NGX where NGX is the length of
the NGX grid in the x,y and z axis directions.):
A list of 3 numpy arrays which contain the planar averaged
electrostatic potential for the bulk supercell.
defect_planar_averages (3 x NGX where NGX is the length of
the NGX grid in the x,y and z axis directions.):
A list of 3 numpy arrays which contain the planar averaged
electrostatic potential for the defective supercell.
bulk_sc_structure (Structure) bulk structure corresponding to
defect supercell structure (uses Lattice for charge correction)
defect_frac_sc_coords (3 x 1 array) Fracitional co-ordinates of
defect location in supercell structure
optional:
'encut' : energy cutoff desired for Freysoldt correction
'madetol' : madelung tolerance for Freysoldt correction
'q_model' : Charge Model for Freysoldt correction
'q_model' : Charge Model for Freysoldt correction
epsilon (float or 3x3 matrix): Dielectric constant for the structure
title: decides whether to plot electrostatic potential plots or not...
if None, no plot is printed, if a string,
then the plot will be saved using the string
partflag: four options for correction output:
'pc' for just point charge correction, or
'potalign' for just potalign correction, or
'All' for both (added together), or
'AllSplit' for individual parts split up (form is [PC, potterm, full])
axis (int or None): if integer, then freysoldt correction is performed on the single axis.
If it is None, then averaging of the corrections for the three axes is used for the correction.
Returns Correction
"""
if partflag not in ['All', 'AllSplit', 'pc', 'potalign']:
print(
'{} is incorrect potalign type. Must be "All", "AllSplit", "pc", or '
'"potalign".'.format(partflag))
return
q_model = defect_entry.parameters.get('q_model', None)
encut = defect_entry.parameters.get('encut', 520)
madetol = defect_entry.parameters.get('madetol', 0.0001)
if not defect_entry.charge:
print('charge is zero so charge correction is zero')
return 0.
template_defect = defect_entry.copy()
corr_class = FreysoldtCorrection(epsilon,
q_model=q_model,
energy_cutoff=encut,
madetol=madetol,
axis=axis)
f_corr_summ = corr_class.get_correction(template_defect)
if title:
if axis is None:
ax_list = [[k, "axis" + str(k)]
for k in corr_class.metadata["pot_plot_data"].keys()]
else:
ax_list = [[axis, "axis" + str(axis + 1)]]
for ax_key, ax_title in ax_list:
p = corr_class.plot(ax_key, title=ax_title, saved=False)
p.savefig(title + '_' + ax_title + '_freysoldtplot.pdf',
bbox_inches='tight')
if partflag in ['AllSplit', 'All']:
freyval = np.sum(list(f_corr_summ.values()))
elif partflag == 'pc':
freyval = f_corr_summ['freysoldt_electrostatic']
elif partflag == 'potalign':
freyval = f_corr_summ['freysoldt_potential_alignment']
print('\n Final Freysoldt correction is {}'.format(freyval))
if partflag == 'AllSplit':
freyval = [
f_corr_summ['freysoldt_electrostatic'],
f_corr_summ['freysoldt_potential_alignment'], freyval
]
return freyval
