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)
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.)
