def test_slide_energy():
energies = [
DefectEnergy("Va_Mg1", [0], [0], [0]),
DefectEnergy("Va_O1", [1], [0], [0]),
DefectEnergy("Va_O2", [2], [0], [0]),
DefectEnergy("Mg_i1", [0], [0], [0])
]
actual = slide_energy(energies, 1.0)
expected = [
DefectEnergy("Va_Mg1", [0], [0], [0]),
DefectEnergy("Va_O1", [1], [1.0], [0]),
DefectEnergy("Va_O2", [2], [2.0], [0]),
DefectEnergy("Mg_i1", [0], [0], [0])
]
assert actual == expected
"""
def __init__(self,
title: str,
defect_energies: List[DefectEnergy],
vbm: float,
cbm: float,
supercell_vbm: float,
supercell_cbm: float,
supercell_edge: bool = False,
y_range: Optional[List[float]] = None,
vline_threshold: float = 0.02,
x_unit: Optional[str] = "eV",
y_unit: Optional[str] = "eV",
**plot_settings):
self._title = title
self._supercell_edge = supercell_edge
self._base_level = vbm
if supercell_edge:
self._x_range = [supercell_vbm - vbm, supercell_cbm - vbm]
self._vbm = vbm - self._base_level
self._cbm = cbm - self._base_level
else:
self._x_range = [0, cbm - vbm]
self._supercell_vbm = supercell_vbm - self._base_level
self._supercell_cbm = supercell_cbm - self._base_level
self._defect_energies = slide_energy(defect_energies, self._base_level)
if y_range:
self._y_range = y_range
else:
all_y = []
for de in self._defect_energies:
cp = de.cross_points(self._x_range[0], self._x_range[1])
xs, ys = cp.t_all_sorted_points
all_y.extend(ys)
self._y_range = [min(all_y) - 0.2, max(all_y) + 0.2]
self._vline_threshold = vline_threshold
self._x_unit = x_unit
self._y_unit = y_unit
def make_defect_formation_energy(args):
formula = args.perfect_calc_results.structure.composition.reduced_formula
chem_pot_diag = ChemPotDiag.from_yaml(args.cpd_yaml)
pcr = args.perfect_calc_results
defects, defect_entries, corrections, edge_states = [], [], [], []
for d in args.dirs:
if args.skip_shallow:
edge_states = BandEdgeStates.from_yaml(d / "band_edge_states.yaml")
if edge_states.is_shallow:
continue
defects.append(loadfn(d / "calc_results.json"))
defect_entries.append(loadfn(d / "defect_entry.json"))
corrections.append(loadfn(d / "correction.json"))
if args.web_gui:
from crystal_toolkit.settings import SETTINGS
import dash_html_components as html
from crystal_toolkit.helpers.layouts import Column
import crystal_toolkit.components as ctc
import dash
edge_states = []
for d in args.dirs:
edge_states.append(
BandEdgeStates.from_yaml(d / "band_edge_states.yaml"))
app = dash.Dash(__name__,
suppress_callback_exceptions=True,
assets_folder=SETTINGS.ASSETS_PATH,
external_stylesheets=[
'https://codepen.io/chriddyp/pen/bWLwgP.css'
])
cpd_plot_info = CpdPlotInfo(chem_pot_diag)
cpd_e_component = CpdEnergyComponent(cpd_plot_info, pcr, defects,
defect_entries, corrections,
args.unitcell.vbm,
args.unitcell.cbm, edge_states)
my_layout = html.Div([Column(cpd_e_component.layout)])
ctc.register_crystal_toolkit(app=app, layout=my_layout, cache=None)
app.run_server(port=args.port)
return
abs_chem_pot = chem_pot_diag.abs_chem_pot_dict(args.label)
title = " ".join([latexify(formula), "point", args.label])
defect_energies = make_energies(pcr, defects, defect_entries, corrections,
abs_chem_pot)
if args.print:
defect_energies = slide_energy(defect_energies, args.unitcell.vbm)
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(ef_min=args.unitcell.vbm,
ef_max=args.unitcell.cbm,
base_ef=args.unitcell.vbm))
print("")
return
plotter = DefectEnergyMplPlotter(title=title,
defect_energies=defect_energies,
vbm=args.unitcell.vbm,
cbm=args.unitcell.cbm,
supercell_vbm=pcr.vbm,
supercell_cbm=pcr.cbm,
y_range=args.y_range,
supercell_edge=args.supercell_edge,
label_line=args.label_line,
add_charges=args.add_charges)
plotter.construct_plot()
plotter.plt.savefig(f"energy_{args.label}.pdf")