def test_corrections(self):
entry = DefectEntry(self.substitution, 2.5)
self.assertAlmostEqual(entry.energy, 2.5)
entry.corrections["pot_corr"] = -0.3
self.assertAlmostEqual(entry.energy, 2.2)
def test_corrections(self):
entry = DefectEntry(self.substitution, 2.5)
self.assertAlmostEqual(entry.energy, 2.5)
entry.corrections["pot_corr"] = -0.3
self.assertAlmostEqual(entry.energy, 2.2)
def test_process_entry(self):
# basic process with no corrections
dentry = DefectEntry(
self.vac,
0.0,
corrections={},
parameters={"vbm": 0.0, "cbm": 0.0},
entry_id=None,
)
dc = DefectCompatibility()
dentry = dc.process_entry(dentry)
self.assertIsNotNone(dentry)
# process with corrections from parameters used in other unit tests
params = self.frey_params.copy()
params.update(self.bandfill_params)
params.update(
{
"hybrid_cbm": params["cbm"] + 0.2,
"hybrid_vbm": params["vbm"] - 0.4,
}
)
dentry = DefectEntry(self.vac, 0.0, corrections={}, parameters=params, entry_id=None)
dc = DefectCompatibility()
dentry = dc.process_entry(dentry)
self.assertAlmostEqual(dentry.corrections["bandedgeshifting_correction"], 1.2)
self.assertAlmostEqual(dentry.corrections["bandfilling_correction"], 0.0)
self.assertAlmostEqual(dentry.corrections["charge_correction"], 5.44595036)
# test over delocalized free carriers which forces skipping charge correction
# modify the eigenvalue list to have free holes
hole_eigenvalues = {}
for spinkey, spinset in params["eigenvalues"].items():
hole_eigenvalues[spinkey] = []
for kptset in spinset:
hole_eigenvalues[spinkey].append([])
for eig in kptset:
if (eig[0] < params["vbm"]) and (eig[0] > params["vbm"] - 0.8):
hole_eigenvalues[spinkey][-1].append([eig[0], 0.5])
else:
hole_eigenvalues[spinkey][-1].append(eig)
params.update({"eigenvalues": hole_eigenvalues})
dentry = DefectEntry(self.vac, 0.0, corrections={}, parameters=params, entry_id=None)
dc = DefectCompatibility(free_chg_cutoff=0.8)
dentry = dc.process_entry(dentry)
self.assertAlmostEqual(dentry.corrections["bandedgeshifting_correction"], 1.19999999)
self.assertAlmostEqual(dentry.corrections["bandfilling_correction"], -1.62202400)
self.assertAlmostEqual(dentry.corrections["charge_correction"], 0.0)
# turn off band filling and band edge shifting
dc = DefectCompatibility(free_chg_cutoff=0.8, use_bandfilling=False, use_bandedgeshift=False)
dentry = dc.process_entry(dentry)
self.assertAlmostEqual(dentry.corrections["bandedgeshifting_correction"], 0.0)
self.assertAlmostEqual(dentry.corrections["bandfilling_correction"], 0.0)
self.assertAlmostEqual(dentry.corrections["charge_correction"], 0.0)
def test_defect_concentration(self):
entry = DefectEntry(self.substitution, .5, corrections={})
entry.defect._charge = -1
chem_pots = {"Sr": 0., "V": 0., "O": 0.}
self.assertAlmostEqual(entry.defect_concentration(chem_pots), 1.2878309944593931e14)
# #test temperature dependence
self.assertAlmostEqual(entry.defect_concentration(chem_pots, temperature=600), 2.040208007417593e+18)
# test fermi level dependence
self.assertAlmostEqual(entry.defect_concentration(chem_pots, fermi_level=.3), 1.4113592133771723e+19)
def test_defect_concentration(self):
entry = DefectEntry(self.substitution, .5, corrections={})
entry.defect._charge = -1
chem_pots = {"Sr": 0., "V": 0., "O": 0.}
self.assertAlmostEqual(entry.defect_concentration(chem_pots), 1.2878309944593931e14)
# #test temperature dependence
self.assertAlmostEqual(entry.defect_concentration(chem_pots, temperature=600), 2.040208007417593e+18)
# test fermi level dependence
self.assertAlmostEqual(entry.defect_concentration(chem_pots, fermi_level=.3), 1.4113592133771723e+19)
def setUpClass(cls):
cls.vbm_val = 2.6682
cls.gap = 1.5
cls.entries = list(loadfn(os.path.join(os.path.dirname(__file__), "GaAs_test_defentries.json")).values())
for entry in cls.entries:
entry.parameters.update({"vbm": cls.vbm_val})
cls.pd = DefectPhaseDiagram(cls.entries, cls.vbm_val, cls.gap)
cls.mu_elts = {Element("As"): -4.658070555, Element("Ga"): -3.7317319750000006}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
cls.extra_entry = DefectEntry(cls.entries[5].defect.copy(), 100.0)
sep_entries = [
ent for ent in cls.entries if not (ent.name == "Vac_As_mult4" and ent.charge in [-2, -1, 0, 1, 2])
]
sep_entries.append(cls.extra_entry.copy())
cls.sep_pd = DefectPhaseDiagram(sep_entries, cls.vbm_val, cls.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = cls.entries[:]
for entry in ls_entries:
if entry.name == "Vac_As_mult4" and entry.charge == -2.0:
entry.parameters["is_compatible"] = False
cls.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries, cls.vbm_val, cls.gap, filter_compatible=True)
cls.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries, cls.vbm_val, cls.gap, filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "complete_dos.json")) as f:
dos_dict = json.load(f)
cls.dos = CompleteDos.from_dict(dos_dict)
def setUp(self):
self.vbm_val = 2.6682
self.gap = 1.5
self.entries = list(loadfn(os.path.join(os.path.dirname(__file__), "GaAs_test_defentries.json")).values())
for entry in self.entries:
entry.parameters.update( {'vbm': self.vbm_val})
self.pd = DefectPhaseDiagram(self.entries, self.vbm_val, self.gap)
self.mu_elts = {Element("As"): -4.658070555, Element("Ga"): -3.7317319750000006}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
self.extra_entry = DefectEntry(self.entries[5].defect.copy(), 100.)
sep_entries = [ent for ent in self.entries if not (ent.name == 'Vac_As_mult4' and
ent.charge in [-2,-1,0,1,2])]
sep_entries.append( self.extra_entry.copy())
self.sep_pd = DefectPhaseDiagram( sep_entries, self.vbm_val, self.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = self.entries[:]
for entry in ls_entries:
if entry.name == 'Vac_As_mult4' and entry.charge == -2.:
entry.parameters['is_compatible'] = False
self.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=True)
self.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
dos_dict = json.load(f)
self.dos = CompleteDos.from_dict(dos_dict)
def from_dict(cls, d):
"""
Reconstitute a DefectPhaseDiagram object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of DefectPhaseDiagram.
Returns:
DefectPhaseDiagram object
"""
entries = [
DefectEntry.from_dict(entry_dict)
for entry_dict in d.get("entries")
]
vbm = d["vbm"]
band_gap = d["band_gap"]
filter_compatible = d.get("filter_compatible", True)
metadata = d.get("metadata", {})
if 'entry_id' in d.keys() and 'entry_id' not in metadata:
metadata['entry_id'] = d['entry_id']
return cls(entries,
vbm,
band_gap,
filter_compatible=filter_compatible,
metadata=metadata)
def test_check_freysoldt_delocalized(self):
de = DefectEntry(self.vac,
0.0,
corrections={},
parameters=self.frey_params,
entry_id=None)
de.parameters.update(
{"is_compatible":
True}) # needs to be initialized with this here for unittest
dc = DefectCompatibility(plnr_avg_var_tol=0.1, plnr_avg_minmax_tol=0.5)
dentry = dc.perform_freysoldt(de)
# check case which fits under compatibility constraints
dentry = dc.check_freysoldt_delocalized(dentry)
frey_delocal = dentry.parameters["delocalization_meta"]["plnr_avg"]
self.assertTrue(frey_delocal["is_compatible"])
ans_var = [0.00038993, 0.02119532, 0.02119532]
ans_window = [0.048331509, 0.36797169, 0.36797169]
for ax in range(3):
ax_metadata = frey_delocal["metadata"][ax]
self.assertTrue(ax_metadata["frey_variance_compatible"])
self.assertAlmostEqual(ax_metadata["frey_variance"], ans_var[ax])
self.assertTrue(ax_metadata["frey_minmax_compatible"])
self.assertAlmostEqual(ax_metadata["frey_minmax_window"],
ans_window[ax])
self.assertTrue(dentry.parameters["is_compatible"])
# check planar delocalization on 2nd and 3rd axes
dc = DefectCompatibility(plnr_avg_var_tol=0.1, plnr_avg_minmax_tol=0.2)
dentry.parameters.update({"is_compatible": True})
dentry = dc.check_freysoldt_delocalized(dentry)
frey_delocal = dentry.parameters["delocalization_meta"]["plnr_avg"]
self.assertFalse(frey_delocal["is_compatible"])
ax_metadata = frey_delocal["metadata"][0]
self.assertTrue(ax_metadata["frey_variance_compatible"])
self.assertTrue(ax_metadata["frey_minmax_compatible"])
for ax in [1, 2]:
ax_metadata = frey_delocal["metadata"][ax]
self.assertTrue(ax_metadata["frey_variance_compatible"])
self.assertFalse(ax_metadata["frey_minmax_compatible"])
self.assertFalse(dentry.parameters["is_compatible"])
# check variance based delocalization on 2nd and 3rd axes
dc = DefectCompatibility(plnr_avg_var_tol=0.01,
plnr_avg_minmax_tol=0.5)
dentry.parameters.update({"is_compatible": True})
dentry = dc.check_freysoldt_delocalized(dentry)
frey_delocal = dentry.parameters["delocalization_meta"]["plnr_avg"]
self.assertFalse(frey_delocal["is_compatible"])
ax_metadata = frey_delocal["metadata"][0]
self.assertTrue(ax_metadata["frey_variance_compatible"])
self.assertTrue(ax_metadata["frey_minmax_compatible"])
for ax in [1, 2]:
ax_metadata = frey_delocal["metadata"][ax]
self.assertFalse(ax_metadata["frey_variance_compatible"])
self.assertTrue(ax_metadata["frey_minmax_compatible"])
self.assertFalse(dentry.parameters["is_compatible"])
def test_formation_energy(self):
entry = DefectEntry(self.substitution, 2.5, corrections={"pot_corr": -0.3})
# Test chemical potentials on formation energy
self.assertAlmostEqual(entry.formation_energy(), 2.2)
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2}), 2.0)
self.assertAlmostEqual(entry.formation_energy({"V": 0.2}), 2.4)
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2, "V": 0.2}), 2.2)
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2, "V": 0.2, "O": 2}), 2.2)
# Test Fermi level on formation energy
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2, "V": 0.2}, fermi_level=0.2), 2.2)
entry.parameters["vbm"] = 0
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2, "V": 0.2}, fermi_level=0.2), 2.2)
entry.defect._charge = 1
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2, "V": 0.2}, fermi_level=0.2), 2.4)
def test_check_kumagai_delocalized(self):
de = DefectEntry(self.kumagai_vac, 0.0, parameters=self.kumagai_params)
de.parameters.update(
{"is_compatible":
True}) # needs to be initialized with this here for unittest
dc = DefectCompatibility(atomic_site_var_tol=13.3,
atomic_site_minmax_tol=20.95)
dentry = dc.perform_kumagai(de)
# check case which fits under compatibility constraints
dentry = dc.check_kumagai_delocalized(dentry)
kumagai_delocal = dentry.parameters["delocalization_meta"][
"atomic_site"]
self.assertTrue(kumagai_delocal["is_compatible"])
kumagai_md = kumagai_delocal["metadata"]
true_variance = 13.262304401193997
true_minmax = 20.9435
self.assertTrue(kumagai_md["kumagai_variance_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_variance"], true_variance)
self.assertTrue(kumagai_md["kumagai_minmax_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_minmax_window"],
true_minmax)
self.assertTrue(dentry.parameters["is_compatible"])
# break variable compatibility
dc = DefectCompatibility(atomic_site_var_tol=0.1,
atomic_site_minmax_tol=20.95)
de.parameters.update({"is_compatible": True})
dentry = dc.perform_kumagai(de)
dentry = dc.check_kumagai_delocalized(dentry)
kumagai_delocal = dentry.parameters["delocalization_meta"][
"atomic_site"]
self.assertFalse(kumagai_delocal["is_compatible"])
kumagai_md = kumagai_delocal["metadata"]
self.assertFalse(kumagai_md["kumagai_variance_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_variance"], true_variance)
self.assertTrue(kumagai_md["kumagai_minmax_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_minmax_window"],
true_minmax)
self.assertFalse(dentry.parameters["is_compatible"])
# break maxmin compatibility
dc = DefectCompatibility(atomic_site_var_tol=13.3,
atomic_site_minmax_tol=0.5)
de.parameters.update({"is_compatible": True})
dentry = dc.perform_kumagai(de)
dentry = dc.check_kumagai_delocalized(dentry)
kumagai_delocal = dentry.parameters["delocalization_meta"][
"atomic_site"]
self.assertFalse(kumagai_delocal["is_compatible"])
kumagai_md = kumagai_delocal["metadata"]
self.assertTrue(kumagai_md["kumagai_variance_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_variance"], true_variance)
self.assertFalse(kumagai_md["kumagai_minmax_compatible"])
self.assertAlmostEqual(kumagai_md["kumagai_minmax_window"],
true_minmax)
self.assertFalse(dentry.parameters["is_compatible"])
def test_bandfilling_SOC_calc(self):
v = Vasprun(os.path.join(PymatgenTest.TEST_FILES_DIR, "vasprun.xml.int_Te_SOC.gz"))
struc = v.structures[0]
interstitial = Interstitial(struc, struc.sites[-1], charge=-2)
eigenvalues = v.eigenvalues.copy()
kptweights = v.actual_kpoints_weights
potalign = -0.1
defect_incar = v.incar
bandfill_params = {
"eigenvalues": eigenvalues,
"kpoint_weights": kptweights,
"potalign": potalign,
"vbm": 1.6465, # bulk VBM
"cbm": 3.1451, # bulk CBM
"run_metadata": {"defect_incar": defect_incar},
}
soc_dentry = DefectEntry(
interstitial,
0.0,
corrections={},
parameters=bandfill_params,
entry_id=None,
)
dc = DefectCompatibility()
soc_dentry = dc.process_entry(soc_dentry)
self.assertAlmostEqual(soc_dentry.corrections["bandfilling_correction"], -1.9628402187500003)
def test_perform_all_corrections(self):
# return entry even if insufficent values are provided
# for freysoldt, kumagai, bandfilling, or band edge shifting
de = DefectEntry(self.vac, 0.0, corrections={}, parameters={}, entry_id=None)
dc = DefectCompatibility()
dentry = dc.perform_all_corrections(de)
self.assertIsNotNone(dentry)
def test_delocalization_analysis(self):
# return entry even if insufficent values are provided
# for delocalization analysis with freysoldt, kumagai,
# bandfilling, or band edge shifting
de = DefectEntry(self.vac, 0.0, corrections={}, parameters={}, entry_id=None)
dc = DefectCompatibility()
dentry = dc.delocalization_analysis(de)
self.assertIsNotNone(dentry)
def convert_cd_to_de( cd, b_cse):
"""
As of pymatgen v2.0, ComputedDefect objects were deprecated in favor
of DefectEntry objects in pymatgen.analysis.defects.core
This function takes a ComputedDefect (either as a dict or object) and
converts it into a DefectEntry object in order to handle legacy
PyCDT creation within the current paradigm of PyCDT.
:param cd (dict or ComputedDefect object): ComputedDefect as an object or as a dictionary
:params b_cse (dict or ComputedStructureEntry object): ComputedStructureEntry of bulk entry
associated with the ComputedDefect.
:return: de (DefectEntry): Resulting DefectEntry object
"""
if type(cd) != dict:
cd = cd.as_dict()
if type(b_cse) != dict:
b_cse = b_cse.as_dict()
bulk_sc_structure = Structure.from_dict( b_cse["structure"])
#modify defect_site as required for Defect object, confirming site exists in bulk structure
site_cls = cd["site"]
defect_site = PeriodicSite.from_dict( site_cls)
def_nom = cd["name"].lower()
if "sub_" in def_nom or "as_" in def_nom:
#modify site object for substitution site of Defect object
site_cls["species"][0]["element"] = cd["name"].split("_")[2]
defect_site = PeriodicSite.from_dict( site_cls)
poss_deflist = sorted(
bulk_sc_structure.get_sites_in_sphere(defect_site.coords, 0.1, include_index=True), key=lambda x: x[1])
if len(poss_deflist) != 1:
raise ValueError("ComputedDefect to DefectEntry conversion failed. "
"Could not determine periodic site position in bulk supercell.")
# create defect object
if "vac_" in def_nom:
defect_obj = Vacancy(bulk_sc_structure, defect_site, charge=cd["charge"])
elif "as_" in def_nom or "sub_" in def_nom:
defect_obj = Substitution(bulk_sc_structure, defect_site, charge=cd["charge"])
elif "int_" in def_nom:
defect_obj = Interstitial(bulk_sc_structure, defect_site, charge=cd["charge"])
else:
raise ValueError("Could not recognize defect type for {}".format( cd["name"]))
# assign proper energy and parameter metadata
uncorrected_energy = cd["entry"]["energy"] - b_cse["energy"]
def_path = os.path.split( cd["entry"]["data"]["locpot_path"])[0]
bulk_path = os.path.split( b_cse["data"]["locpot_path"])[0]
p = {"defect_path": def_path,
"bulk_path": bulk_path,
"encut": cd["entry"]["data"]["encut"]}
de = DefectEntry( defect_obj, uncorrected_energy, parameters = p)
return de
def test_defect_concentration(self):
entry = DefectEntry(self.substitution, 0.5, corrections={})
entry.defect._charge = -1
chem_pots = {"Sr": 0.0, "V": 0.0, "O": 0.0}
self.assertAlmostEqual(entry.defect_concentration(chem_pots) / 1.2878334860092098e14, 1)
# #test temperature dependence
self.assertAlmostEqual(
entry.defect_concentration(chem_pots, temperature=600) / 2.0402099809985405e18,
1,
)
# test fermi level dependence
self.assertAlmostEqual(
entry.defect_concentration(chem_pots, fermi_level=0.3) / 1.411360305591838e19,
1,
)
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 setUp(self):
self.vbm_val = 2.6682
self.gap = 1.5
self.entries = list(
loadfn(
os.path.join(os.path.dirname(__file__),
"GaAs_test_defentries.json")).values())
for entry in self.entries:
entry.parameters.update({'vbm': self.vbm_val})
self.pd = DefectPhaseDiagram(self.entries, self.vbm_val, self.gap)
self.mu_elts = {
Element("As"): -4.658070555,
Element("Ga"): -3.7317319750000006
}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
self.extra_entry = DefectEntry(self.entries[5].defect.copy(), 100.)
sep_entries = [
ent for ent in self.entries if not (
ent.name == 'Vac_As_mult4' and ent.charge in [-2, -1, 0, 1, 2])
]
sep_entries.append(self.extra_entry.copy())
self.sep_pd = DefectPhaseDiagram(sep_entries, self.vbm_val, self.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = self.entries[:]
for entry in ls_entries:
if entry.name == 'Vac_As_mult4' and entry.charge == -2.:
entry.parameters['is_compatible'] = False
self.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries,
self.vbm_val,
self.gap,
filter_compatible=True)
self.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries,
self.vbm_val,
self.gap,
filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
dos_dict = json.load(f)
self.dos = CompleteDos.from_dict(dos_dict)
def test_perform_freysoldt(self):
de = DefectEntry(self.vac, 0.0, corrections={}, parameters=self.frey_params, entry_id=None)
dc = DefectCompatibility()
dentry = dc.perform_freysoldt(de)
val = dentry.parameters["freysoldt_meta"]
self.assertAlmostEqual(val["freysoldt_electrostatic"], 0.975893)
self.assertAlmostEqual(val["freysoldt_potential_alignment_correction"], 4.4700574)
self.assertAlmostEqual(val["freysoldt_potalign"], 1.4900191)
self.assertTrue("pot_corr_uncertainty_md" in val.keys())
self.assertTrue("pot_plot_data" in val.keys())
def test_perform_kumagai(self):
de = DefectEntry(self.kumagai_vac, 0.0, parameters=self.kumagai_params)
dc = DefectCompatibility()
dentry = dc.perform_kumagai(de)
val = dentry.parameters["kumagai_meta"]
self.assertAlmostEqual(val["kumagai_electrostatic"], 0.88236299)
self.assertAlmostEqual(val["kumagai_potential_alignment_correction"], 2.09704862)
self.assertAlmostEqual(val["kumagai_potalign"], 0.69901620)
self.assertTrue("pot_corr_uncertainty_md" in val.keys())
self.assertTrue("pot_plot_data" in val.keys())
def test_bandedgeshifting(self):
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
struc = struc
vac = Vacancy(struc, struc.sites[0], charge=-3)
besc = BandEdgeShiftingCorrection()
params = {"hybrid_cbm": 1.0, "hybrid_vbm": -1.0, "vbm": -0.5, "cbm": 0.6}
de = DefectEntry(vac, 0.0, corrections={}, parameters=params, entry_id=None)
corr = besc.get_correction(de)
self.assertEqual(corr["bandedgeshifting_correction"], 1.5)
def test_run_band_edge_shifting(self):
de = DefectEntry(self.vac,
0.,
corrections={},
parameters=self.band_edge_params,
entry_id=None)
dc = DefectCompatibility()
dentry = dc.perform_band_edge_shifting(de)
val = dentry.parameters['bandshift_meta']
self.assertEqual(val['vbmshift'], -0.5)
self.assertEqual(val['cbmshift'], 0.4)
self.assertEqual(val['bandedgeshifting_correction'], 1.5)
def test_run_bandfilling(self):
de = DefectEntry(self.vac,
0.,
corrections={},
parameters=self.bandfill_params,
entry_id=None)
dc = DefectCompatibility()
dentry = dc.perform_bandfilling(de)
val = dentry.parameters['bandfilling_meta']
self.assertAlmostEqual(val['num_hole_vbm'], 0.)
self.assertAlmostEqual(val['num_elec_cbm'], 0.)
self.assertAlmostEqual(val['bandfilling_correction'], 0.)
def setUp(self):
self.epsilon = 15.
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
# load neccessary parameters for defect_entry to make use
# of Freysoldt and Kumagai corrections
p = {}
ids = vac.generate_defect_structure(1)
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
]
p.update({'axis_grid': axisdata, 'bulk_planar_averages': bldata, 'defect_planar_averages': dldata,
'initial_defect_structure': ids, 'defect_frac_sc_coords': struc.sites[0].frac_coords,
'bulk_sc_structure': struc})
bulk_atomic_site_averages, defect_atomic_site_averages = [], []
defect_site_with_sc_lattice = PeriodicSite( struc.sites[0].specie, struc.sites[0].coords,
struc.lattice, coords_are_cartesian = True)
max_dist = 9.6
pert_amnt = 1.
for site_ind, site in enumerate(struc.sites):
if site.specie.symbol == "O":
Oval = -30.6825
bulk_atomic_site_averages.append( Oval)
if site_ind:
dist_to_defect = site.distance_and_image( defect_site_with_sc_lattice)[0]
defect_site_val = Oval - .3 + pert_amnt * ((max_dist - dist_to_defect)/max_dist)**2
defect_atomic_site_averages.append( defect_site_val)
else:
Vval = -51.6833
bulk_atomic_site_averages.append( Vval)
if site_ind:
dist_to_defect = site.distance_and_image( defect_site_with_sc_lattice)[0]
defect_site_val = Vval - .3 + pert_amnt * ((max_dist - dist_to_defect)/max_dist)**2
defect_atomic_site_averages.append( defect_site_val)
site_matching_indices = [[ind, ind-1] for ind in range(len(struc.sites)) if ind != 0]
p.update({ "bulk_atomic_site_averages": bulk_atomic_site_averages,
"defect_atomic_site_averages": defect_atomic_site_averages,
"site_matching_indices": site_matching_indices})
self.defect_entry = DefectEntry( vac, 0., parameters = p)
def setUp(self):
l = Lattice([[3.52,0.0,2.033], [1.174,3.32,2.033], \
[0.0,0.0,4.066]])
s_bulk = Structure(l, ['Ga', 'As'], \
[[0.0000, 0.0000, 0.0000], \
[0.2500, 0.2500, 0.2500]])
defect_site = PeriodicSite('As', [0.25, 0.25, 0.25], l)
defect = Vacancy(s_bulk, defect_site, charge=1.)
defect_entry = DefectEntry(defect, 0.)
entries = [defect_entry]
vbm = 0.2
band_gap = 1.
dpd = DefectPhaseDiagram(entries, vbm, band_gap)
self.dp = DefectPlotter(dpd)
def test_run_bandfilling(self):
de = DefectEntry(self.vac,
0.,
corrections={},
parameters=self.bandfill_params,
entry_id=None)
dc = DefectCompatibility()
dentry = dc.perform_bandfilling(de)
val = dentry.parameters['bandfilling_meta']
self.assertAlmostEqual(val['num_hole_vbm'], 0.)
self.assertAlmostEqual(val['num_elec_cbm'], 0.)
self.assertAlmostEqual(val['bandfilling_correction'], 0.)
occu = [[1.457, 0.0833333], [1.5204, 0.0833333], [1.53465, 0.0833333],
[1.5498, 0.0416667]]
self.assertArrayAlmostEqual(
list(sorted(val['occupied_def_levels'], key=lambda x: x[0])),
list(sorted(occu, key=lambda x: x[0])))
self.assertAlmostEqual(val['total_occupation_defect_levels'],
0.29166669)
self.assertFalse(val['unoccupied_def_levels'])
def from_dict(cls, d):
"""
Reconstitute a DefectPhaseDiagram object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of DefectPhaseDiagram.
Returns:
DefectPhaseDiagram object
"""
entries = [DefectEntry.from_dict(entry_dict) for entry_dict in d.get("entries")]
vbm = d["vbm"]
band_gap = d["band_gap"]
filter_compatible = d.get("filter_compatible", True)
metadata = d.get("metadata", {})
if 'entry_id' in d.keys() and 'entry_id' not in metadata:
metadata['entry_id'] = d['entry_id']
return cls(entries, vbm, band_gap, filter_compatible=filter_compatible,
metadata=metadata)
def test_bandedgeshifting(self):
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
struc = struc
vac = Vacancy(struc, struc.sites[0], charge=-3)
besc = BandEdgeShiftingCorrection()
params = {
'hybrid_cbm': 1.,
'hybrid_vbm': -1.,
'vbm': -0.5,
'cbm': 0.6,
'num_hole_vbm': 0.,
'num_elec_cbm': 0.
}
de = DefectEntry(vac,
0.,
corrections={},
parameters=params,
entry_id=None)
#test with no free carriers
corr = besc.get_correction(de)
self.assertEqual(corr['vbm_shift_correction'], 1.5)
self.assertEqual(corr['elec_cbm_shift_correction'], 0.)
self.assertEqual(corr['hole_vbm_shift_correction'], 0.)
#test with free holes
de.parameters.update({'num_hole_vbm': 1.})
corr = besc.get_correction(de)
self.assertEqual(corr['vbm_shift_correction'], 1.5)
self.assertEqual(corr['elec_cbm_shift_correction'], 0.)
self.assertEqual(corr['hole_vbm_shift_correction'], 0.5)
#test with free electrons
de.parameters.update({'num_hole_vbm': 0., 'num_elec_cbm': 1.})
corr = besc.get_correction(de)
self.assertEqual(corr['vbm_shift_correction'], 1.5)
self.assertEqual(corr['elec_cbm_shift_correction'], 0.4)
self.assertEqual(corr['hole_vbm_shift_correction'], 0.)
def test_formation_energy(self):
entry = DefectEntry(self.substitution,
2.5,
corrections={"pot_corr": -0.3})
# Test chemical potentials on formation energy
self.assertAlmostEqual(entry.formation_energy(), 2.2)
self.assertAlmostEqual(entry.formation_energy({"Sr": 0.2}), 2.0)
self.assertAlmostEqual(entry.formation_energy({"V": 0.2}), 2.4)
self.assertAlmostEqual(entry.formation_energy({
"Sr": 0.2,
"V": 0.2
}), 2.2)
self.assertAlmostEqual(
entry.formation_energy({
"Sr": 0.2,
"V": 0.2,
"O": 2
}), 2.2)
# Test Fermi level on formation energy
self.assertAlmostEqual(
entry.formation_energy({
"Sr": 0.2,
"V": 0.2
}, fermi_level=0.2), 2.2)
entry.parameters["vbm"] = 0
self.assertAlmostEqual(
entry.formation_energy({
"Sr": 0.2,
"V": 0.2
}, fermi_level=0.2), 2.2)
entry.defect._charge = 1
self.assertAlmostEqual(
entry.formation_energy({
"Sr": 0.2,
"V": 0.2
}, fermi_level=0.2), 2.4)
def test_init(self):
entry = DefectEntry(self.substitution, 2.5)
entry_doc = entry.as_dict()
re_entry = DefectEntry.from_dict(entry_doc)
self.assertNotEqual(re_entry, None)
def test_check_final_relaxed_structure_delocalized(self):
# test structure delocalization analysis
# first test no movement in atoms
initial_defect_structure = self.vac.generate_defect_structure()
final_defect_structure = initial_defect_structure.copy()
sampling_radius = 4.55
defect_frac_sc_coords = self.vac.site.frac_coords[:]
params = {
"initial_defect_structure": initial_defect_structure,
"final_defect_structure": final_defect_structure,
"sampling_radius": sampling_radius,
"defect_frac_sc_coords": defect_frac_sc_coords,
"is_compatible": True,
}
dentry = DefectEntry(self.vac, 0.0, corrections={}, parameters=params, entry_id=None)
dc = DefectCompatibility(tot_relax_tol=0.1, perc_relax_tol=0.1, defect_tot_relax_tol=0.1)
dentry = dc.check_final_relaxed_structure_delocalized(dentry)
struc_delocal = dentry.parameters["delocalization_meta"]["structure_relax"]
self.assertTrue(dentry.parameters["is_compatible"])
self.assertTrue(struc_delocal["is_compatible"])
self.assertTrue(struc_delocal["metadata"]["structure_tot_relax_compatible"])
self.assertEqual(struc_delocal["metadata"]["tot_relax_outside_rad"], 0.0)
self.assertTrue(struc_delocal["metadata"]["structure_perc_relax_compatible"])
self.assertEqual(struc_delocal["metadata"]["perc_relax_outside_rad"], 0.0)
self.assertEqual(
len(struc_delocal["metadata"]["full_structure_relax_data"]),
len(initial_defect_structure),
)
self.assertIsNone(struc_delocal["metadata"]["defect_index"])
defect_delocal = dentry.parameters["delocalization_meta"]["defectsite_relax"]
self.assertTrue(defect_delocal["is_compatible"])
self.assertIsNone(defect_delocal["metadata"]["relax_amount"])
# next test for when structure has delocalized outside of radius from defect
pert_struct_fin_struct = initial_defect_structure.copy()
pert_struct_fin_struct.perturb(0.1)
dentry.parameters.update({"final_defect_structure": pert_struct_fin_struct})
dentry = dc.check_final_relaxed_structure_delocalized(dentry)
struc_delocal = dentry.parameters["delocalization_meta"]["structure_relax"]
self.assertFalse(dentry.parameters["is_compatible"])
self.assertFalse(struc_delocal["is_compatible"])
self.assertFalse(struc_delocal["metadata"]["structure_tot_relax_compatible"])
self.assertAlmostEqual(struc_delocal["metadata"]["tot_relax_outside_rad"], 12.5)
self.assertFalse(struc_delocal["metadata"]["structure_perc_relax_compatible"])
self.assertAlmostEqual(struc_delocal["metadata"]["perc_relax_outside_rad"], 77.63975155)
# now test for when an interstitial defect has migrated too much
inter_def_site = PeriodicSite(
"H",
[7.58857304, 11.70848069, 12.97817518],
self.vac.bulk_structure.lattice,
to_unit_cell=True,
coords_are_cartesian=True,
)
inter = Interstitial(self.vac.bulk_structure, inter_def_site, charge=0)
initial_defect_structure = inter.generate_defect_structure()
final_defect_structure = initial_defect_structure.copy()
poss_deflist = sorted(
final_defect_structure.get_sites_in_sphere(inter.site.coords, 2, include_index=True),
key=lambda x: x[1],
)
def_index = poss_deflist[0][2]
final_defect_structure.translate_sites(
indices=[def_index], vector=[0.0, 0.0, 0.008]
) # fractional coords translation
defect_frac_sc_coords = inter_def_site.frac_coords[:]
params = {
"initial_defect_structure": initial_defect_structure,
"final_defect_structure": final_defect_structure,
"sampling_radius": sampling_radius,
"defect_frac_sc_coords": defect_frac_sc_coords,
"is_compatible": True,
}
dentry = DefectEntry(inter, 0.0, corrections={}, parameters=params, entry_id=None)
dentry = dc.check_final_relaxed_structure_delocalized(dentry)
defect_delocal = dentry.parameters["delocalization_meta"]["defectsite_relax"]
self.assertFalse(defect_delocal["is_compatible"])
self.assertAlmostEqual(defect_delocal["metadata"]["relax_amount"], 0.10836054)
def parse_defect_calculations(self):
"""
Parses the defect calculations as DefectEntry objects,
from a PyCDT root_fldr file structure.
Charge correction is missing in the first run.
"""
logger = logging.getLogger(__name__)
parsed_defects = []
subfolders = glob.glob(os.path.join(self._root_fldr, "vac_*"))
subfolders += glob.glob(os.path.join(self._root_fldr, "as_*"))
subfolders += glob.glob(os.path.join(self._root_fldr, "sub_*"))
subfolders += glob.glob(os.path.join(self._root_fldr, "inter_*"))
def get_vr_and_check_locpot(fldr):
vr_file = os.path.join(fldr,"vasprun.xml")
if not os.path.exists(vr_file):
logger.warning("{} doesn't exit".format(vr_file))
error_msg = ": Failure, vasprun.xml doesn't exist."
return (None, error_msg) #Further processing is not useful
try:
vr = Vasprun(vr_file, parse_potcar_file=False)
except:
logger.warning("Couldn't parse {}".format(vr_file))
error_msg = ": Failure, couldn't parse vaprun.xml file."
return (None, error_msg)
if not vr.converged:
logger.warning(
"Vasp calculation at {} not converged".format(fldr))
error_msg = ": Failure, Vasp calculation not converged."
return (None, error_msg) # Further processing is not useful
# Check if locpot exists
locpot_file = os.path.join(fldr, "LOCPOT")
if not os.path.exists(locpot_file):
logger.warning("{} doesn't exit".format(locpot_file))
error_msg = ": Failure, LOCPOT doesn't exist"
return (None, error_msg) #Further processing is not useful
return (vr, None)
def get_encut_from_potcar(fldr):
potcar_file = os.path.join(fldr,"POTCAR")
if not os.path.exists(potcar_file):
logger.warning("Not POTCAR in {} to parse ENCUT".format(fldr))
error_msg = ": Failure, No POTCAR file."
return (None, error_msg) #Further processing is not useful
try:
potcar = Potcar.from_file(potcar_file)
except:
logger.warning("Couldn't parse {}".format(potcar_file))
error_msg = ": Failure, couldn't read POTCAR file."
return (None, error_msg)
encut = max(ptcr_sngl.enmax for ptcr_sngl in potcar)
return (encut, None)
# get bulk entry information first
fldr = os.path.join(self._root_fldr, "bulk")
vr, error_msg = get_vr_and_check_locpot(fldr)
if error_msg:
logger.error("Abandoning parsing of the calculations")
return {}
bulk_energy = vr.final_energy
bulk_sc_struct = vr.final_structure
try:
encut = vr.incar["ENCUT"]
except: # ENCUT not specified in INCAR. Read from POTCAR
encut, error_msg = get_encut_from_potcar(fldr)
if error_msg:
logger.error("Abandoning parsing of the calculations")
return {}
trans_dict = loadfn(
os.path.join(fldr, "transformation.json"),
cls=MontyDecoder)
supercell_size = trans_dict["supercell"]
bulk_file_path = fldr
bulk_entry = ComputedStructureEntry(
bulk_sc_struct, bulk_energy,
data={"bulk_path": bulk_file_path,
"encut": encut,
"supercell_size": supercell_size})
# get defect entry information
for fldr in subfolders:
fldr_name = os.path.split(fldr)[1]
chrg_fldrs = glob.glob(os.path.join(fldr,"charge*"))
for chrg_fldr in chrg_fldrs:
trans_dict = loadfn(
os.path.join(chrg_fldr, "transformation.json"),
cls=MontyDecoder)
chrg = trans_dict["charge"]
vr, error_msg = get_vr_and_check_locpot(chrg_fldr)
if error_msg:
logger.warning("Parsing the rest of the calculations")
continue
if "substitution_specie" in trans_dict and \
trans_dict["substitution_specie"] not in bulk_sc_struct.symbol_set:
self._substitution_species.add(
trans_dict["substitution_specie"])
elif "inter" in trans_dict["defect_type"] and \
trans_dict["defect_site"].specie.symbol not in bulk_sc_struct.symbol_set:
# added because extrinsic interstitials don't have
# "substitution_specie" character...
trans_dict["substitution_specie"] = trans_dict["defect_site"].specie.symbol
self._substitution_species.add(
trans_dict["defect_site"].specie.symbol)
defect_type = trans_dict.get("defect_type", None)
energy = vr.final_energy
try:
encut = vr.incar["ENCUT"]
except: # ENCUT not specified in INCAR. Read from POTCAR
encut, error_msg = get_encut_from_potcar(chrg_fldr)
if error_msg:
logger.warning("Not able to determine ENCUT "
"in {}".format(fldr_name))
logger.warning("Parsing the rest of the "
"calculations")
continue
comp_data = {"bulk_path": bulk_file_path,
"defect_path": chrg_fldr, "encut": encut,
"fldr_name": fldr_name, "supercell_size": supercell_size}
if "substitution_specie" in trans_dict:
comp_data["substitution_specie"] = \
trans_dict["substitution_specie"]
# create Defect Object as dict, then load to DefectEntry object
defect_dict = {"structure": bulk_sc_struct, "charge": chrg,
"@module": "pymatgen.analysis.defects.core"
}
defect_site = trans_dict["defect_supercell_site"]
if "vac_" in defect_type:
defect_dict["@class"] = "Vacancy"
elif "as_" in defect_type or "sub_" in defect_type:
defect_dict["@class"] = "Substitution"
substitution_specie = trans_dict["substitution_specie"]
defect_site = PeriodicSite( substitution_specie, defect_site.frac_coords,
defect_site.lattice, coords_are_cartesian=False)
elif "int_" in defect_type:
defect_dict["@class"] = "Interstitial"
else:
raise ValueError("defect type {} not recognized...".format(defect_type))
defect_dict.update( {"defect_site": defect_site})
defect = MontyDecoder().process_decoded( defect_dict)
parsed_defects.append( DefectEntry( defect, energy - bulk_energy,
parameters=comp_data))
try:
parsed_defects_data = {}
parsed_defects_data["bulk_entry"] = bulk_entry
parsed_defects_data["defects"] = parsed_defects
return parsed_defects_data
except:
return {} # Return Null dict due to failure
class DefectsThermodynamicsTest(PymatgenTest):
def setUp(self):
self.vbm_val = 2.6682
self.gap = 1.5
self.entries = list(loadfn(os.path.join(os.path.dirname(__file__), "GaAs_test_defentries.json")).values())
for entry in self.entries:
entry.parameters.update( {'vbm': self.vbm_val})
self.pd = DefectPhaseDiagram(self.entries, self.vbm_val, self.gap)
self.mu_elts = {Element("As"): -4.658070555, Element("Ga"): -3.7317319750000006}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
self.extra_entry = DefectEntry(self.entries[5].defect.copy(), 100.)
sep_entries = [ent for ent in self.entries if not (ent.name == 'Vac_As_mult4' and
ent.charge in [-2,-1,0,1,2])]
sep_entries.append( self.extra_entry.copy())
self.sep_pd = DefectPhaseDiagram( sep_entries, self.vbm_val, self.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = self.entries[:]
for entry in ls_entries:
if entry.name == 'Vac_As_mult4' and entry.charge == -2.:
entry.parameters['is_compatible'] = False
self.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=True)
self.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
dos_dict = json.load(f)
self.dos = CompleteDos.from_dict(dos_dict)
def test_good_test_data(self):
self.assertEqual(len(self.entries), 48)
def test_suggest_charges(self):
suggested_charges = self.pd.suggest_charges()
for k in [
"Vac_As_mult4@0-1-2-3-4-5", "Sub_Ga_on_As_mult4@6-7-8-9-10-11", "Vac_Ga_mult4@12-13-14-15",
"Sub_As_on_Ga_mult4@16-17-18-19-20-21", "Int_Ga_mult1@22-23-24-25",
"Int_As_mult1@26-27-28-29-30-31-32-33-34", "Int_As_mult1@35-36-37-38-39-40-41-42-43",
"Int_Ga_mult1@44-45-46-47"
]:
self.assertTrue(
len(suggested_charges[k]) > 0, "Could not find any suggested charges for {} with band_gap of {}".format(
k, self.pd.band_gap))
pd = DefectPhaseDiagram(self.entries, 2.6682, 1.0)
suggested_charges = self.pd.suggest_charges()
for k in ["Vac_As_mult4@0-1-2-3-4-5", "Vac_Ga_mult4@12-13-14-15"]:
self.assertTrue(
len(suggested_charges[k]) > 0, "Could not find any suggested charges for {} with band_gap of {}".format(
k, pd.band_gap))
#test again but with only one charge state stable for Vac_As
suggested_charges = self.sep_pd.suggest_charges()
self.assertEqual( set(suggested_charges['Vac_As_mult4@0-43']), set([-4]))
def test_suggest_larger_supercells(self):
suggested_larger_cells = self.pd_ls_fcFalse.suggest_larger_supercells()
self.assertEqual( suggested_larger_cells['Vac_As_mult4@0-1-2-3-4-5'], [-2])
# raise error if filter_compatibile = True
self.assertRaises( ValueError, self.pd_ls_fcTrue.suggest_larger_supercells)
def test_entries(self):
all_stable_entries = self.pd.all_stable_entries
self.assertEqual(len(self.pd.defect_types), 8)
self.assertEqual(len(all_stable_entries), sum([len(v) for v in self.pd.stable_charges.values()]))
#test again but with only one charge state stable for Vac_As
self.assertEqual( len(self.sep_pd.transition_level_map['Vac_As_mult4@0-43']), 0)
self.assertEqual( len(self.sep_pd.stable_entries['Vac_As_mult4@0-43']), 1)
self.assertEqual( len(self.sep_pd.finished_charges['Vac_As_mult4@0-43']), 2)
#
def test_solve_for_fermi_energy(self):
fermi_energy = self.pd.solve_for_fermi_energy( 100., self.mu_elts, self.dos)
self.assertAlmostEqual( fermi_energy, 0.57387314)
fermi_energy = self.pd.solve_for_fermi_energy( 1000., self.mu_elts, self.dos)
self.assertAlmostEqual( fermi_energy, 0.74139553)
def test_solve_for_non_equilibrium_fermi_energy(self):
fermi_energy = self.pd.solve_for_non_equilibrium_fermi_energy( 300., 1000., self.mu_elts, self.dos)
self.assertAlmostEqual( fermi_energy, 0.29500637)
fermi_energy = self.pd.solve_for_non_equilibrium_fermi_energy( 1000., 1000., self.mu_elts, self.dos)
self.assertAlmostEqual( fermi_energy, 0.74139553)
def test_get_dopability_limits(self):
lower_lim, upper_lim = self.pd.get_dopability_limits( self.mu_elts)
self.assertAlmostEqual( lower_lim, -0.39996272)
self.assertAlmostEqual( upper_lim, 1.064193047)
# raise error if defects are negative across gap
bad_mu_elts = self.mu_elts.copy()
bad_mu_elts[Element("Ga")] += 10.
lower_lim, upper_lim = self.pd.get_dopability_limits( bad_mu_elts)
self.assertIsNone( lower_lim)
self.assertIsNone( upper_lim)
def test_plot(self):
#simple test that plot is produced
p = self.pd.plot(saved=False)
self.assertTrue( p)
def test_init(self):
entry = DefectEntry(self.substitution, 2.5)
entry_doc = entry.as_dict()
re_entry = DefectEntry.from_dict(entry_doc)
self.assertNotEqual(re_entry, None)
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_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_kumagai(self):
gamma = 0.19357221
prec = 28
lattice = Lattice(
[[4.692882, -8.12831, 0.0], [4.692882, 8.12831, 0.0], [0.0, 0.0, 10.03391]]
)
# note that real/recip vector generation is not dependent on epsilon
g_vecs, _, r_vecs, _ = generate_R_and_G_vecs(
gamma, prec, lattice, 80.0 * np.identity(3)
)
# test real space summation (bigger for large epsilon)
kc_high_diel = KumagaiCorrection(80.0 * np.identity(3), gamma=gamma)
real_sum = kc_high_diel.get_real_summation(gamma, r_vecs[0])
self.assertAlmostEqual(real_sum, 0.00843104)
# test recip space summation (bigger for small epsilon)
kc_low_diel = KumagaiCorrection(0.1 * np.identity(3), gamma=gamma)
recip_sum = kc_low_diel.get_recip_summation(gamma, g_vecs[0], lattice.volume)
self.assertAlmostEqual(recip_sum, 0.31117099)
# test self interaction
si_corr = kc_low_diel.get_self_interaction(gamma)
self.assertAlmostEqual(si_corr, -0.54965249)
# test potenital shift interaction correction
ps_corr = kc_low_diel.get_potential_shift(gamma, lattice.volume)
self.assertAlmostEqual(ps_corr, -0.00871593)
# """Test Defect Entry approach to correction """
bulk_struc = Poscar.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "defect", "CONTCAR_bulk")
).structure
bulk_out = Outcar(os.path.join(PymatgenTest.TEST_FILES_DIR, "defect", "OUTCAR_bulk.gz"))
defect_out = Outcar(os.path.join(PymatgenTest.TEST_FILES_DIR, "defect", "OUTCAR_vac_Ga_-3.gz"))
epsilon = 18.118 * np.identity(3)
vac = Vacancy(bulk_struc, bulk_struc.sites[0], charge=-3)
defect_structure = vac.generate_defect_structure()
defect_frac_coords = [0.0, 0.0, 0.0]
parameters = {
"bulk_atomic_site_averages": bulk_out.electrostatic_potential,
"defect_atomic_site_averages": defect_out.electrostatic_potential,
"site_matching_indices": [[ind, ind - 1] for ind in range(len(bulk_struc))],
"initial_defect_structure": defect_structure,
"defect_frac_sc_coords": defect_frac_coords,
}
dentry = DefectEntry(vac, 0.0, parameters=parameters)
kc = KumagaiCorrection(epsilon)
kcorr = kc.get_correction(dentry)
self.assertAlmostEqual(kcorr["kumagai_electrostatic"], 0.88236299)
self.assertAlmostEqual(kcorr["kumagai_potential_alignment"], 2.09704862)
# test ES correction
high_diel_es_corr = kc_high_diel.perform_es_corr(gamma, prec, lattice, -3.0)
self.assertAlmostEqual(high_diel_es_corr, 0.25176240)
low_diel_es_corr = kc_low_diel.perform_es_corr(gamma, prec, lattice, -3.0)
self.assertAlmostEqual(low_diel_es_corr, 201.28810966)
# test pot correction
site_list = []
for bs_ind, ds_ind in dentry.parameters["site_matching_indices"]:
Vqb = -(
defect_out.electrostatic_potential[ds_ind]
- bulk_out.electrostatic_potential[bs_ind]
)
site_list.append([defect_structure[ds_ind], Vqb])
sampling_radius = dentry.parameters["kumagai_meta"]["sampling_radius"]
gamma = dentry.parameters["kumagai_meta"]["gamma"]
q = -3
g_vecs, _, r_vecs, _ = generate_R_and_G_vecs(
gamma, 28, defect_structure.lattice, np.identity(3)
)
high_diel_pot_corr = kc_high_diel.perform_pot_corr(
defect_structure,
defect_frac_coords,
site_list,
sampling_radius,
q,
r_vecs[0],
g_vecs[0],
gamma,
)
self.assertAlmostEqual(high_diel_pot_corr, 2.35840716)
low_diel_pot_corr = kc_low_diel.perform_pot_corr(
defect_structure,
defect_frac_coords,
site_list,
sampling_radius,
q,
r_vecs[0],
g_vecs[0],
gamma,
)
self.assertAlmostEqual(low_diel_pot_corr, -58.83598095)
# test the kumagai plotter
kcp = kc.plot()
self.assertTrue(kcp)
# check that uncertainty metadata exists
self.assertAlmostEqual(
set(kc.metadata["pot_corr_uncertainty_md"].keys()),
set(["number_sampled", "stats"]),
)