def plot_chem_pot_diag(args) -> None:
cpd = ChemPotDiag.from_yaml(args.yaml)
if cpd.dim == 1:
logger.warning("Single element is not supported for the plot.")
return
print(cpd)
if cpd.dim == 2:
plotter = ChemPotDiagMpl2DMplPlotter(CpdPlotInfo(cpd))
elif cpd.dim == 3:
plotter = ChemPotDiagMpl3DMplPlotter(CpdPlotInfo(cpd))
else:
logger.info("Number of elements must be 2 or 3. "
f"Now, elements are {cpd.vertex_elements}.")
return
plt = plotter.draw_diagram()
plt.savefig(fname="cpd.pdf")
plt.show()
def make_chem_pot_diag(args) -> None:
if args.elements:
cpd = make_chem_pot_diag_from_mp(additional_elements=args.elements,
target=args.target,
atom_energy_yaml=args.atom_energy_yaml)
else:
comp_es = []
for d in args.dirs:
vasprun = Vasprun(d / defaults.vasprun)
composition = vasprun.final_structure.composition
energy = float(vasprun.final_energy) # type is FloatWithUnit
comp_es.append(CompositionEnergy(composition, energy, "local"))
if args.update:
cpd = ChemPotDiag.from_yaml(args.yaml)
replace_comp_energy(cpd, comp_es)
else:
cpd = ChemPotDiag(comp_es, args.target)
cpd.to_yaml(args.yaml)
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")
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")
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Kumagai group.
import argparse
import sys
from pydefect.chem_pot_diag.chem_pot_diag import ChemPotDiag, CpdPlotInfo
from pydefect.chem_pot_diag.cpd_plotter import ChemPotDiag3DPlotlyPlotter
def parse_args(args):
parser = argparse.ArgumentParser(description="")
parser.add_argument("-c", "--chem_pot_diag", type=str)
parser.add_argument("--port", type=int)
return parser.parse_args(args)
if __name__ == "__main__":
args = parse_args(sys.argv[1:])
cpd = ChemPotDiag.from_yaml(args.chem_pot_diag)
print(cpd.target_vertices)
print(cpd.vertex_coords)
cpd_plot_info = CpdPlotInfo(cpd)
print(cpd_plot_info.comp_vertices)
plotter = ChemPotDiag3DPlotlyPlotter(cpd_plot_info)
fig = plotter.figure
fig.show()
# ctc.register_crystal_toolkit(app=app, layout=layout, cache=None)
# app.run_server(debug=True, port=args.port)