def energy_fig(self, abs_chem_pot, label):
single_energies = []
for d, e, c in zip(self.defects, self.defect_entries,
self.corrections):
single_energies.append(
make_single_defect_energy(self.perfect, d, e, abs_chem_pot, c))
defect_energies = make_defect_energies(single_energies)
plotter = DefectEnergyPlotlyPlotter(title=f"Label {label[0]}",
defect_energies=defect_energies,
vbm=self.perfect.vbm,
cbm=self.perfect.cbm,
supercell_vbm=self.perfect.vbm,
supercell_cbm=self.perfect.cbm)
return plotter.create_figure()
def test_generate_defect_energies():
defect_energies = [
SingleDefectEnergy("Va_O1", 0, -1, 1),
SingleDefectEnergy("Va_Mg1", 0, -2, 2),
SingleDefectEnergy("Va_O1", 1, 7, 3),
SingleDefectEnergy("Va_Mg1", -1, -14, 4),
SingleDefectEnergy("Va_O1", 2, 15, 5),
SingleDefectEnergy("Va_Mg1", -2, -14, 6)
]
actual = make_defect_energies(defect_energies)
expected = [
DefectEnergy("Va_Mg1", [0, -1, -2], [-2, -14, -14], [2, 4, 6]),
DefectEnergy("Va_O1", [0, 1, 2], [-1, 7, 15], [1, 3, 5])
]
assert actual == expected
def make_defect_formation_energy(args):
title = latexify(
args.perfect_calc_results.structure.composition.reduced_formula)
chem_pot_diag = ChemPotDiag.from_yaml(args.chem_pot_diag)
abs_chem_pot = chem_pot_diag.abs_chem_pot_dict(args.label)
single_energies = []
for d in args.dirs:
if args.skip_shallow and loadfn(
d / "band_edge_states.json").is_shallow:
continue
single_energies.append(
make_single_defect_energy(args.perfect_calc_results,
loadfn(d / "calc_results.json"),
loadfn(d / "defect_entry.json"),
abs_chem_pot,
loadfn(d / "correction.json")))
defect_energies = make_defect_energies(single_energies)
if args.print:
print(" charge E_f correction ")
for e in defect_energies:
print(e)
print("")
print("-- cross points -- ")
for e in defect_energies:
print(e.name)
print(e.cross_points(args.unitcell.vbm, args.unitcell.cbm))
print("")
return
plotter = DefectEnergyMplPlotter(
title=title,
defect_energies=defect_energies,
vbm=args.unitcell.vbm,
cbm=args.unitcell.cbm,
supercell_vbm=args.perfect_calc_results.vbm,
supercell_cbm=args.perfect_calc_results.cbm,
y_range=args.y_range)
plotter.construct_plot()
plotter.plt.savefig(f"energy_{args.label}.pdf")