def _get_soap_graph(feature, label):
spectrum = {
"data": [{
"coloraxis": "coloraxis",
#'hovertemplate': 'x: %{x}<br>y: %{y}<br>color: %{z}<extra></extra>',
"type": "heatmap",
"z": feature.tolist(),
}]
}
spectrum["layout"] = {
"xaxis": {
"visible": False
},
"yaxis": {
"visible": False
},
"paper_bgcolor": "rgba(0,0,0,0)",
"plot_bgcolor": "rgba(0,0,0,0)",
"coloraxis": {
"colorscale": [
[0.0, "#0d0887"],
[0.1111111111111111, "#46039f"],
[0.2222222222222222, "#7201a8"],
[0.3333333333333333, "#9c179e"],
[0.4444444444444444, "#bd3786"],
[0.5555555555555556, "#d8576b"],
[0.6666666666666666, "#ed7953"],
[0.7777777777777778, "#fb9f3a"],
[0.8888888888888888, "#fdca26"],
[1.0, "#f0f921"],
],
"showscale":
False,
},
"margin": {
"l": 0,
"b": 0,
"t": 0,
"r": 0,
"pad": 0
},
# "height": 20*feature.shape[0], # for fixed size plots
# "width": 20*feature.shape[1]
}
return Columns([
Column(Label(label), size="1"),
Column(
dcc.Graph(
figure=spectrum,
config={"displayModeBar": False},
responsive=True,
style={"height": "60px"},
)),
])
def update_contents(self, new_store_contents):
struct = self.from_data(new_store_contents)
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=1)
if not msa.is_magnetic:
# TODO: detect magnetic elements (?)
return html.Div(
"This structure is not magnetic or does not have "
"magnetic information associated with it."
)
mag_species_and_magmoms = msa.magnetic_species_and_magmoms
for k, v in mag_species_and_magmoms.items():
if not isinstance(v, list):
mag_species_and_magmoms[k] = [v]
magnetic_atoms = "\n".join(
[
f"{sp} ({', '.join([f'{magmom} µB' for magmom in magmoms])})"
for sp, magmoms in mag_species_and_magmoms.items()
]
)
magnetization_per_formula_unit = (
msa.total_magmoms
/ msa.structure.composition.get_reduced_composition_and_factor()[1]
)
rows = []
rows.append(
(
html.B("Total magnetization per formula unit"),
html.Br(),
f"{magnetization_per_formula_unit:.1f} µB",
)
)
rows.append((html.B("Atoms with local magnetic moments"), html.Br(),
magnetic_atoms))
data_block = html.Div([html.P([html.Span(cell) for cell in row]) for row in rows])
viewer = StructureMoleculeComponent(
struct,
id=self.id("structure"), color_scheme="magmom",
static=True
)
return Columns([
Column(html.Div([viewer.struct_layout], style={"height": "60vmin"})),
Column(data_block)
])
def layout(self):
if self.dim in [2, 3]:
return Columns([
Column([
html.Div(self._sub_layouts["energy"]),
self._sub_layouts["allow_shallow"]
]),
Column([self._sub_layouts["cpd"], self.vertex_list])
])
else:
return Columns([
Column([
self.vertex_list, self._sub_layouts["allow_shallow"],
self._sub_layouts["cpd_label"]
]),
Column(html.Div(self._sub_layouts["energy"]))
])
def update_contents(self, new_store_contents):
#JSONViewComponent(id=self.id("json-editor"),
# src=loads(new_store_contents))
return Columns(
[ #Column(self.editor_layout), Column(self.json_layout),
Column()
])
def _get_soap_graph(feature, label):
spectrum = px.imshow(feature,
aspect="equal",
color_continuous_scale="plasma")
coloraxis = spectrum.layout.coloraxis
coloraxis["showscale"] = False
layout = {
"xaxis": {
"visible": False
},
"yaxis": {
"visible": False
},
"paper_bgcolor": "rgba(0,0,0,0)",
"plot_bgcolor": "rgba(0,0,0,0)",
"coloraxis": coloraxis,
"margin": {
"l": 0,
"b": 0,
"t": 0,
"r": 0,
"pad": 0
},
# "height": 20*feature.shape[0], # for fixed size plots
# "width": 20*feature.shape[1]
}
spectrum.layout = layout
return Columns([
Column(Label(label), size="1"),
Column(
dcc.Graph(
figure=spectrum,
config={"displayModeBar": False},
responsive=True,
style={"height": "60px"},
)),
])
def initial_contents(self):
# TODO: this is so dumb, PanelComponent needs a rethink
# (this comment is definition of technical debt)
editor = dcc.Textarea(
id=self.id("editor"),
rows=16,
className="textarea",
style={
"max-width": "88%",
"max-height": "800px",
"height": "100%"
},
)
json = Box(
dcc.SyntaxHighlighter(id=self.id("highlighted"),
customStyle={
"height": "100%",
"max-height": "800px"
}))
return Columns([Column(editor), Column(json)])
def update_contents(self, new_store_contents):
editor = dcc.Textarea(
id=self.id("editor"),
rows=16,
className="textarea",
style={
"max-width": "88%",
"max-height": "800px",
"height": "100%"
},
value=new_store_contents,
)
json = Box(
dcc.SyntaxHighlighter(id=self.id("highlighted"),
customStyle={
"height": "100%",
"max-height": "800px"
},
children=new_store_contents))
return Columns([Column(editor), Column(json)])
def container_layout(self, state=None, structure=None) -> html.Div:
"""
:return: Layout defining transformation and its options.
"""
container = MessageContainer(
[
MessageHeader(
html.Div([
self._sub_layouts["enable"],
html.Span(
self.title,
style={
"vertical-align": "middle",
"margin-left": "1rem",
},
),
])),
MessageBody([
Columns([
Column([
self._sub_layouts["description"],
html.Br(),
html.Div(
self.options_layouts(state=state,
structure=structure)),
html.Br(),
self._sub_layouts["message"],
])
])
]),
],
kind="dark",
id=self.id("container"),
)
return container
def get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
kwargs = self.reconstruct_kwargs_from_state(
callback_context.inputs)
distance_cutoff = kwargs["distance_cutoff"]
angle_cutoff = kwargs["angle_cutoff"]
# TODO: remove these brittle guard statements, figure out more robust way to handle multiple input types
if isinstance(struct, StructureGraph):
struct = struct.structure
def get_valences(struct):
valences = [
getattr(site.specie, "oxi_state", None) for site in struct
]
valences = [v for v in valences if v is not None]
if len(valences) == len(struct):
return valences
else:
return "undefined"
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
valences=get_valences(struct),
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": unicodeify_species(struct[index].species_string),
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
disable_callbacks=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
)._sub_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
"The continuous symmetry measure (CSM) describes the similarity to an "
"ideal coordination environment. It can be understood as a 'distance' to "
"a shape and ranges from 0 to 100 in which 0 corresponds to a "
"coordination environment that is exactly identical to the ideal one. A "
"CSM larger than 5.0 already indicates a relatively strong distortion of "
"the investigated coordination environment.",
):
f"{env[0]['csm']:.2f}",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites, "
f"or try an alternative algorithm such as LocalEnv.")
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
def update_contents(self, new_store_contents):
return Columns([Column(self.editor_layout), Column(self.json_layout)])
def layout(self):
return html.Div([Columns(Column(self._sub_layouts["graph"]))])
def layout(self):
return Columns([
Column([self.vertex_list, self._sub_layouts["cpd_label"]]),
Column(html.Div(self._sub_layouts["energy"]))
])
def retrieve_grain_boundaries(mpid):
if not mpid or "mpid" not in mpid:
raise PreventUpdate
data = None
with MPRester() as mpr:
data = mpr.get_gb_data(mpid["mpid"])
if not data:
return (
"No grain boundary information computed for this crystal structure. "
"Grain boundary information has only been computed for elemental ground state "
"crystal structures at present.")
table_data = [{
"Sigma":
d["sigma"],
"Rotation Axis":
f"{d['rotation_axis']}",
"Rotation Angle / º":
f"{d['rotation_angle']:.2f}",
"Grain Boundary Plane":
f"({' '.join(map(str, d['gb_plane']))})",
"Grain Boundary Energy / Jm⁻²":
f"{d['gb_energy']:.2f}",
} for d in data]
df = pd.DataFrame(table_data)
table = dt.DataTable(
id=self.id("table"),
columns=[{
"name": i,
"id": i
} for i in df.columns],
data=df.to_dict("records"),
style_cell={
"minWidth": "0px",
"maxWidth": "200px",
"whiteSpace": "normal",
},
css=[{
"selector":
".dash-cell div.dash-cell-value",
"rule":
"display: inline; white-space: inherit; overflow: inherit; text-overflow: inherit;",
}],
sort_action="native",
sort_mode="multi",
)
view = html.Div(
[
StructureMoleculeComponent(
data[2]["initial_structure"],
id=self.id("struct"),
static=True,
color_scheme="grain_label",
).struct_layout
],
style={
"width": "400px",
"height": "400px"
},
)
return Columns([Column(table), Column(view)])
def update_contents(data, symprec, angle_tolerance):
if not data:
return html.Div()
struct = self.from_data(data)
if not isinstance(struct, Structure):
return html.Div(
"Can only analyze symmetry of crystal structures at present."
)
kwargs = self.reconstruct_kwargs_from_state(
callback_context.inputs)
symprec = kwargs["symprec"]
angle_tolerance = kwargs["angle_tolerance"]
if symprec <= 0:
return html.Span(
f"Please use a positive symmetry-finding tolerance (currently {symprec})."
)
sga = SpacegroupAnalyzer(struct,
symprec=symprec,
angle_tolerance=angle_tolerance)
try:
data = dict()
data["Crystal System"] = sga.get_crystal_system().title()
data["Lattice System"] = sga.get_lattice_type().title()
data["Hall Number"] = sga.get_hall()
data["International Number"] = sga.get_space_group_number()
data["Symbol"] = unicodeify_spacegroup(
sga.get_space_group_symbol())
data["Point Group"] = unicodeify_spacegroup(
sga.get_point_group_symbol())
sym_struct = sga.get_symmetrized_structure()
except Exception:
return html.Span(
f"Failed to calculate symmetry with this combination of "
f"symmetry-finding ({symprec}) and angle tolerances ({angle_tolerance})."
)
datalist = get_data_list(data)
wyckoff_contents = []
wyckoff_data = sorted(
zip(sym_struct.wyckoff_symbols, sym_struct.equivalent_sites),
key=lambda x: "".join(filter(lambda w: w.isalpha(), x[0])),
)
for symbol, equiv_sites in wyckoff_data:
wyckoff_contents.append(
html.Label(
f"{symbol}, {unicodeify_species(equiv_sites[0].species_string)}",
className="mpc-label",
))
site_data = [(
self.pretty_frac_format(site.frac_coords[0]),
self.pretty_frac_format(site.frac_coords[1]),
self.pretty_frac_format(site.frac_coords[2]),
) for site in equiv_sites]
wyckoff_contents.append(get_table(site_data))
return Columns([
Column([H5("Overview"), datalist]),
Column([H5("Wyckoff Positions"),
html.Div(wyckoff_contents)]),
])
CalcResults(structure=defect_structure, energy=0.5, **common)]
de_common = dict(name="Va_O1",
structure=defect_structure, site_symmetry="1",
perturbed_structure=defect_structure, defect_center=[[0]*3])
defect_entries = [DefectEntry(charge=0, **de_common),
DefectEntry(charge=1, **de_common)]
corrections = [ManualCorrection(correction_energy=1.0),
ManualCorrection(correction_energy=1.0)]
cpd_e_component = CpdEnergyComponent(cpd_plot_info,
perfect,
defects,
defect_entries,
corrections,
unitcell_vbm=0.0,
unitcell_cbm=1.0)
my_layout = html.Div([Column(cpd_e_component.layout)])
ctc.register_crystal_toolkit(app=app, layout=my_layout, cache=None)
# In[5]:
app.run_server(port=8099)
#app.run_server(mode='inline', port=8096)
def get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
distance_cutoff = float(distance_cutoff)
angle_cutoff = float(angle_cutoff)
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": struct[index].species_string,
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
static=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
).all_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
'"Continuous Symmetry Measure," a measure of how symmetrical a '
"local environment is from most symmetrical at 0% to least "
"symmetrical at 100%",
):
f"{env[0]['csm']:.2f}%",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites."
)
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
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")