def supercell_calc_results(args):
if args.print:
print(SupercellCalcResults.load_json(args.json))
return
if args.defect_center:
if len(args.defect_center) != 1 and len(args.defect_center) != 3:
raise ValueError("Length of the defect center is neither 1 or 3")
results = SupercellCalcResults.load_json(args.json)
results.defect_center = args.defect_center
results.to_json_file(filename=args.json)
return
if args.dir_all:
dirs = glob('*[0-9]/')
dirs.insert(0, "perfect/")
else:
dirs = args.dirs
for d in dirs:
if os.path.isdir(d):
logger.info(f"Parsing data in {d} ...")
if d in ["perfect", "perfect/"]:
try:
dft_results = SupercellCalcResults.from_vasp_files(
directory_path=d,
vasprun=args.vasprun,
contcar=args.contcar,
procar=args.procar,
outcar=args.outcar)
except IOError:
raise IOError("Parsing data in perfect failed.")
else:
try:
de = DefectEntry.load_json(
Path(d) / args.defect_entry_name)
dft_results = SupercellCalcResults.from_vasp_files(
directory_path=d,
vasprun=args.vasprun,
contcar=args.contcar,
outcar=args.outcar,
procar=args.procar,
cutoff=args.cutoff,
defect_entry=de,
defect_symprec=args.defect_symprec,
angle_tolerance=args.angle_tolerance)
except IOError as e:
logger.warning(f"Parsing data in {d} failed.")
logger.warning(e)
continue
dft_results.to_json_file(filename=Path(d) / "dft_results.json")
else:
logger.warning(f"{d} does not exist, so nothing is done.")
def setUp(self):
""" Va_O in the 2+ charge state in 64-atom supercells"""
self.mgO_perfect = \
SupercellCalcResults.from_vasp_files(
directory_path=self.DEFECTS_MGO_DIR / "perfect")
filepath = ["defects", "MgO", "Va_O1_2", "defect_entry.json"]
defect_entry = self.get_object_by_name(DefectEntry.load_json, filepath)
self.mgo_va_o1_2 = SupercellCalcResults.from_vasp_files(
directory_path=self.DEFECTS_MGO_DIR / "Va_O1_2",
defect_entry=defect_entry)
def vertical_transition_input_maker(args):
if abs(args.additional_charge) != 1:
raise ValueError(f"{args.additional_charge} is invalid.")
initial_dirname = Path(args.initial_dir_name)
de_filename = initial_dirname / "defect_entry.json"
de = DefectEntry.load_json(de_filename)
src_filename = initial_dirname / "dft_results.json"
src = SupercellCalcResults.load_json(src_filename)
new_charge = de.charge + args.additional_charge
vis = ViseInputSet.from_prev_calc(initial_dirname,
user_incar_settings={"NSW": 0},
parse_calc_results=False,
contcar_filename=args.contcar,
charge=new_charge)
de.charge += args.additional_charge
de.initial_structure = src.final_structure
de.perturbed_initial_structure = src.final_structure
de.initial_site_symmetry = src.site_symmetry
# FIX MAGNETIZATION?
new_dirname = initial_dirname / f"add_charge_{args.additional_charge}"
make_dir(str(new_dirname),
vis,
force_overwrite=False,
defect_entry_obj=de,
add_neighbor=False)
new_de_filename = new_dirname / "defect_entry.json"
de.to_json_file(new_de_filename)
def vertical_transition_energy(args):
initial_dir = Path(args.initial_dir)
initial_calc_results = \
SupercellCalcResults.load_json(initial_dir / "dft_results.json")
final_dir = Path(args.dir)
final_calc_results = \
SupercellCalcResults.load_json(final_dir / "dft_results.json")
unitcell = UnitcellCalcResults.load_json(args.unitcell_json)
if args.print:
vtec = VerticalTransitionEnergyCorrection.load_json(args.json)
vtec.plot_potential()
print(vtec)
if vtec.additional_charge == 1:
cbm = unitcell.band_edge[1]
print(f"CBM position (eV): {cbm}")
band_edge_related_energy = cbm
else:
vbm = unitcell.band_edge[0]
print(f"VBM position (eV): {vbm}")
band_edge_related_energy = -vbm
vte_wo_corr = (final_calc_results.total_energy -
initial_calc_results.total_energy +
band_edge_related_energy)
vte = vte_wo_corr + vtec.correction_energy
print(f"Vertical transition energy w/o correction (eV): {vte_wo_corr}")
print(f"Vertical transition energy w/ correction (eV): {vte}")
return
dielectric_tensor = unitcell.total_dielectric_tensor
static_dielectric_tensor = unitcell.static_dielectric_tensor
initial_efnv = \
ExtendedFnvCorrection.load_json(initial_dir / "correction.json")
initial_calc_results = \
SupercellCalcResults.load_json(initial_dir / "dft_results.json")
final_defect_entry = DefectEntry.load_json(final_dir / "defect_entry.json")
c = VerticalTransitionEnergyCorrection.from_files(
dielectric_tensor, static_dielectric_tensor, initial_efnv,
initial_calc_results, final_defect_entry, final_calc_results)
c.to_json_file(args.json)
print(c)
def defects(args):
if args.band_edge:
if args.band_edge[0] == "up":
spin = Spin.up
elif args.band_edge[0] == "down":
spin = Spin.down
else:
raise ValueError(
"band edge is inadequate (e.g. -be up no_in_gap).")
state = args.band_edge[1]
defect = Defect.load_json(args.json)
defect.set_band_edge_state(spin=spin, state=state)
defect.to_json_file(args.json)
return True
try:
perfect = SupercellCalcResults.load_json(args.perfect)
except FileNotFoundError:
print(f"{args.perfect} not found.")
raise
defects_dirs = args.defect_dirs or glob('*[0-9]/')
for d in defects_dirs:
filename = os.path.join(d, args.json)
if args.diagnose:
print(d.rjust(12), end=" ")
try:
print(Defect.load_json(filename).diagnose)
except FileNotFoundError:
logger.warning("No supercell results file.")
except Exception as e:
logger.warning(f"An error {e} is caught.")
continue
logger.info(f"parsing directory {d}...")
files = [args.defect_entry, args.dft_results, args.correction]
classes = [DefectEntry, SupercellCalcResults, ExtendedFnvCorrection]
input_objects = generate_objects_from_json_files(d,
files,
classes,
raise_error=False)
if input_objects:
try:
defect = Defect.from_objects(defect_entry=input_objects[0],
dft_results=input_objects[1],
perfect_dft_results=perfect,
correction=input_objects[2])
defect.to_json_file(filename)
except StructureError:
logger.warning(f"defect.json is not generated in {d}.")
else:
logger.warning(f"Generating {filename} failed.")
continue
def setUp(self) -> None:
unitcell = UnitcellCalcResults.load_json(parent / "MgO_unitcell.json")
dielectric_tensor = unitcell.total_dielectric_tensor
static_dielectric_tensor = unitcell.static_dielectric_tensor
initial_efnv_cor = ExtendedFnvCorrection.load_json(
parent / "MgO_Va_O_1_correction.json")
initial_calc_results = SupercellCalcResults.load_json(
parent / "MgO_Va_O_1_dft_results.json")
final_defect_entry = DefectEntry.load_json(
parent / "MgO_Va_O_1-added_defect_entry.json")
final_calc_results = SupercellCalcResults.load_json(
parent / "MgO_Va_O_1-added_dft_results.json")
self.vertical_correction = \
VerticalTransitionEnergyCorrection.from_files(
dielectric_tensor,
static_dielectric_tensor,
initial_efnv_cor,
initial_calc_results,
final_defect_entry,
final_calc_results,
8)
def plot_energy(args):
if args.reload_defects:
os.remove(args.energies)
try:
defect_energies = DefectEnergies.load_json(args.energies)
except FileNotFoundError:
unitcell = UnitcellCalcResults.load_json(args.unitcell)
perfect = SupercellCalcResults.load_json(args.perfect)
defects_dirs = args.defect_dirs or glob('*[0-9]/')
defect_list = []
for d in defects_dirs:
filename = Path(d) / 'defect.json'
logger.info(f"parsing directory {filename}...")
try:
defect_list.append(Defect.load_json(filename))
except FileNotFoundError:
logger.warning(f"Parsing {filename} failed.")
continue
chem_pot = ChemPotDiag.load_json(args.chem_pot_json)
# First construct DefectEnergies class object.
defect_energies = \
DefectEnergies.from_objects(unitcell=unitcell,
perfect=perfect,
defects=defect_list,
chem_pot=chem_pot,
chem_pot_label=args.chem_pot_label,
filtering_words=args.filtering,
system=args.name)
if args.print:
print(defect_energies)
return
defect_energies.to_json_file(filename=args.energies)
# if args.concentration:
# defect_concentration = \
# DefectConcentration.from_defect_energies(
# energies=energies,
# temperature=args.temperature[0],
# unitcell=unitcell,
# num_sites_filename=args.num_site_file)
# # if len(args.temperature) == 2:
# defect_concentration = \
# DefectConcentration.from_defect_energies(
# energies=energies,
# temperature=args.temperature[1],
# unitcell=unitcell,
# num_sites_filename=args.num_site_file,
# previous_concentration=defect_concentration)
# else:
# defect_concentration = None
# plt = defect_energies.plot_energy(filtering_words=args.filtering,
# x_range=args.x_range,
# y_range=args.y_range,
# show_transition_levels=args.show_tl,
# show_all_energies=args.show_all)
plt = defect_energies.plot_energy(
x_range=args.x_range,
y_range=args.y_range,
show_transition_levels=args.show_transition_level,
show_all_energies=args.show_all)
if args.save_file:
plt.savefig(args.save_file, format="pdf", transparent=True)
else:
plt.show()
def efnv_correction(args):
if args.print:
print(ExtendedFnvCorrection.load_json(args.json_file))
return
dirs = glob('*[0-9]/') if args.dir_all else args.dirs
if args.plot_potential:
for directory in dirs:
d = Path(directory)
c = ExtendedFnvCorrection.load_json(d / "correction.json")
c.plot_potential(d / "potential.pdf", args.y_range)
return
if args.nocorr:
for directory in dirs:
c = ManualCorrection(manual_correction_energy=args.manual)
c.to_json_file(Path(directory) / "correction.json")
return
try:
ucr = UnitcellCalcResults.load_json(args.unitcell_json)
dielectric_tensor = ucr.total_dielectric_tensor
except IOError:
raise FileNotFoundError("JSON for the unitcell info is not found.")
try:
perfect_dft_data = SupercellCalcResults.load_json(args.perfect_json)
except IOError:
raise FileNotFoundError("JSON for the perfect supercell is not found.")
# Ewald parameter related
if not Path(args.ewald_json).is_file():
logger.info("optimizing ewald...")
ewald = Ewald.from_optimization(
structure=perfect_dft_data.final_structure,
dielectric_tensor=dielectric_tensor,
initial_ewald_param=args.ewald_initial_param,
convergence=args.ewald_convergence,
prod_cutoff_fwhm=args.ewald_accuracy)
ewald.to_json_file(args.ewald_json)
for directory in dirs:
d = Path(directory)
json_to_make = d / "correction.json"
if json_to_make.exists() and not args.force_overwrite:
logger.warning(f"{json_to_make} already exists, so nothing done.")
continue
logger.info(f"correcting {directory} ...")
entry = DefectEntry.load_json(d / "defect_entry.json")
try:
defect_dft_data = \
SupercellCalcResults.load_json(d / "dft_results.json")
except IOError:
logger.warning(f"dft_results.json in {directory} does not exist.")
continue
c = ExtendedFnvCorrection. \
compute_correction(defect_entry=entry,
defect_dft=defect_dft_data,
perfect_dft=perfect_dft_data,
dielectric_tensor=dielectric_tensor,
defect_center=args.defect_center,
ewald=args.ewald_json)
c.plot_potential(d / "potential.pdf", args.y_range)
c.to_json_file(d / "correction.json")
def test_json(self):
tmp_file = tempfile.NamedTemporaryFile()
self.mgo_va_o1_2.to_json_file(tmp_file.name)
actual = SupercellCalcResults.load_json(tmp_file.name)
np.testing.assert_equal(actual.eigenvalues[Spin.up],
self.mgo_va_o1_2.eigenvalues[Spin.up])
def test_dict(self):
expected = self.mgo_va_o1_2.as_dict()
actual = SupercellCalcResults.from_dict(expected).as_dict()
self.assertEqual(expected, actual)