def plot_chem_pot_diag(args) -> None:
cpd = ChemPotDiag.from_yaml(args.yaml)
if cpd.dim == 2:
plotter = ChemPotDiagMpl2DMplPlotter(CpdPlotInfo(cpd))
elif cpd.dim == 3:
plotter = ChemPotDiagMpl3DMplPlotter(CpdPlotInfo(cpd))
else:
raise CpdNotSupportedError("Number of elements must be 2 or 3. "
f"Now {cpd.vertex_elements}.")
print(cpd)
plt = plotter.draw_diagram()
plt.savefig(fname="cpd.pdf")
plt.show()
def cpd_plot_info_2d():
energies = [
CompositionEnergy(Composition("H"), 0.0, ""),
CompositionEnergy(Composition("O"), 1.0, ""),
CompositionEnergy(Composition("H4O2"), -4.0, "")
]
cpd = ChemPotDiag(energies, target=Composition("H2O"))
return CpdPlotInfo(cpd, min_range=-10)
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_layouts(structure: Structure, dos_plot_data, band_plot_data,
perfect_dirname, defect_dirnames, supercell_info,
chem_pot_diag):
cpd_plot_info = CpdPlotInfo(ChemPotDiag.from_yaml(chem_pot_diag))
perfect: CalcResults = loadfn(perfect_dirname / "calc_results.json")
defects, defect_entries, corrections, single_defect_layouts = [], [], [], []
for d in defect_dirnames:
#TODO: check convergence
defects.append(loadfn(d / "calc_results.json"))
defect_entry = loadfn(d / "defect_entry.json")
defect_entries.append(defect_entry)
corrections.append(loadfn(d / "correction.json"))
defect_entry: DefectEntry = loadfn(d / "defect_entry.json")
efnv_correction = loadfn(d / "correction.json")
eigval = loadfn(d / "band_edge_eigenvalues.json")
pot = SitePotentialPlotlyPlotter(title=defect_entry.full_name,
efnv_correction=efnv_correction)
eig = EigenvaluePlotlyPlotter(title=defect_entry.full_name,
band_edge_eigenvalues=eigval,
supercell_vbm=perfect.vbm,
supercell_cbm=perfect.cbm)
scene_dicts = loadfn(d / "parchgs" / "scene_dicts.json")
if isinstance(scene_dicts, dict):
scene_dicts = SceneDicts.from_dict(scene_dicts)
single_defect_layouts.append(
SingleDefectComponent(pot,
eig,
scene_dicts,
defect_entry.full_name,
id=f"{defect_entry.full_name}").layout())
if cpd_plot_info.cpd.dim in [2, 3]:
cpd_energy_comp = CpdEnergy2D3DComponent(cpd_plot_info, perfect,
defects, defect_entries,
corrections)
else:
cpd_energy_comp = CpdEnergyOtherComponent(cpd_plot_info, perfect,
defects, defect_entries,
corrections)
structure_component = StructureComponent(structure)
comp = structure.composition.reduced_formula
band_dos_component = BandDosComponent(
dos_plot_data,
band_plot_data,
id=f"band_dos_{comp}",
)
supercell_component = SupercellComponent(supercell_info)
symmetrizer = StructureSymmetrizer(structure)
return create_ctk(structure_component, symmetry_layout(structure),
mpid_and_link(symmetrizer), site_layout(symmetrizer),
band_dos_component, supercell_component.layout,
cpd_energy_comp.layout, single_defect_layouts)
def cpd_3d_info():
energies = [
CompositionEnergy(Composition("H"), 0.0, ""),
CompositionEnergy(Composition("O"), 1.0, ""),
CompositionEnergy(Composition("H4O2"), -4.0, ""),
CompositionEnergy(Composition("MgH2O"), -10.0, ""),
CompositionEnergy(Composition("Mg"), 0.0, ""),
CompositionEnergy(Composition("MgO"), -3.0, "")
]
cpd = ChemPotDiag(energies, target=Composition("MgH2O"))
return CpdPlotInfo(cpd)
app = JupyterDash(suppress_callback_exceptions=True,
assets_folder=SETTINGS.ASSETS_PATH)
from vise.analyzer.band_edge_properties import BandEdge
comp_energies = [
CompositionEnergy(Composition("Mg"), 0.0, "a"),
CompositionEnergy(Composition("Ca"), 0.0, "a"),
CompositionEnergy(Composition("Sr"), 0.0, "a"),
CompositionEnergy(Composition("O"), 0.0, "a"),
CompositionEnergy(Composition("H"), 0.0, "a"),
# CompositionEnergy(Composition("MgCaO3"), -100.0, "a"),
CompositionEnergy(Composition("MgCaSrO3"), -100.0, "a"),
]
#cpd = ChemPotDiag(comp_energies, target=Composition("MgCaO3"))
cpd = ChemPotDiag(comp_energies, target=Composition("MgCaSrO3"))
cpd_plot_info = CpdPlotInfo(cpd)
# In[2]:
print(cpd.target.elements)
print(cpd.dim)
print(cpd.target_vertices)
print(cpd.all_compounds)
print(cpd.impurity_abs_energy(Element.H, label="A"))
# In[3]:
def cpd_plot_info_wo_min_range(cpd):
return CpdPlotInfo(cpd)
def cpd_plot_info():
cpd = ChemPotDiag(energies, target=Composition("H2O"))
return CpdPlotInfo(cpd, min_range=-10)
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")
def remove_higher_energy_comp(comp_energies: List[CompositionEnergy]):
result = []
for _, grouped_comp_energies in groupby(
comp_energies, key=lambda x: x.composition.reduced_formula):
result.append(min(list(grouped_comp_energies),
key=lambda y: y.abs_energy_per_atom))
return result
def parse_args(args):
parser = argparse.ArgumentParser(description="")
parser.add_argument("-e", "--elements", type=str, nargs="+")
parser.add_argument("-he", "--host_elements", type=Element, nargs="+")
parser.add_argument("-t", "--target", type=Composition)
parser.add_argument("-f", "--functional", type=str)
return parser.parse_args(args)
if __name__ == "__main__":
x = parse_args(sys.argv[1:])
cpd = make_chem_pot_diag_from_mp(x.elements, x.target,
x.host_elements, x.functional)
cpd.to_yaml()
if cpd.dim == 2:
plotter = ChemPotDiagPlotly2DMplPlotter(CpdPlotInfo(cpd))
elif cpd.dim == 3:
plotter = ChemPotDiagPlotly3DMplPlotter(CpdPlotInfo(cpd))
plotter.figure.show()