def options_layout(self):
miller_index = get_matrix_input(self.id(), label="Miller index",
default=((1, 0, 0), ),
help="The surface plane defined by its Miller index (h, k, l)")
min_slab_size = dcc.Input(id=self.id("min_slab_size"), value=6)
min_vacuum_size = dcc.Input(id=self.id("min_vacuum_size"), value=10)
#lll_reduce = dcc.Checklist()
center_slab = dcc.Checklist(id=self.id("center_slab"), options=[{"label": " ", "value": "center_slab"}], values=[])
#in_unit_planes = ...
#primitive = ...
#max_normal_search = ...
#shift = ...
#tol = ...
# get_layout(name, display_name, type)
# get_inputs(name, type)
# get_value(type, inputs)
options = html.Div([miller_index,
Label("Min slab size:"), min_slab_size,
Label("Min vacuum size:"), min_vacuum_size,
Label("Center slab:"), center_slab])
return options
def add_initial_layout(data):
algorithm_choices = html.Div([
Label("Algorithm:"),
dcc.RadioItems(
id=self.id("algorithm"),
options=[
{
"label": "ChemEnv Analysis",
"value": "chemenv"
},
{
"label": "LocalEnv Analysis",
"value": "localenv"
},
{
"label": "Bonding Graph",
"value": "bondinggraph"
},
],
inputClassName="mpc-radio",
labelClassName="mpc-radio",
value="chemenv",
),
])
analysis = html.Div(id=self.id("analysis"))
return html.Div(
[algorithm_choices,
html.Br(), analysis,
html.Br()])
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 _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 update_contents(self, new_store_contents):
"""
Structure -> mpid -> BibTeX references from MP -> (optional doi lookup
via Crossref) -> formatting.
Formatting is very messy right now.
DOI lookup and (possibly) formatting should be cached in a builder.
"""
struct = self.from_data(new_store_contents)
if not isinstance(struct, Structure):
raise PreventUpdate(
"Literature mentions can only be retrieved for crystallographic "
"structures at present and not molecules. Please make a feature "
"request if this would be useful for you, and it will be "
"prioritized."
)
with MPRester() as mpr:
mpids = mpr.find_structure(struct)
if len(mpids) == 0:
raise PreventUpdate(
"No structures in the Materials Project database match this "
"crystal structure, so literature mentions cannot be retrieved. "
"Please submit this structure to Materials Project if you'd "
"like it to be added to the Materials Project database."
)
all_references = []
for mpid in mpids:
all_references.append(mpr.get_materials_id_references(mpid))
self.logger.debug(f"Retrieved references for {mpid}.")
if self.use_crossref:
cr = Crossref(mailto=CROSSREF_MAILTO)
individual_references = set()
for references in all_references:
individual_references.update(set(references.split("\n\n")))
# exclude Materials Proect references (these are intended to be
# references for the structure specifically)
refs_to_remove = set()
for ref in individual_references:
if "Jain2013" in ref:
refs_to_remove.add(ref)
individual_references -= refs_to_remove
works = [cr.works(query=ref, limit=1) for ref in individual_references]
self.logger.debug(f"Retrieved {len(works)} works from Crossref.")
items = [
work["message"]["items"][0]
for work in works
if len(work["message"]["items"]) > 0
]
dois_to_item = {
item["DOI"]: {
"cited-by": item.get("is-referenced-by-count", 0),
"score": item["score"],
"title": item.get("title", None),
"authors": item.get("author", []),
"journal": item.get("container-title", [None])[0],
"issue": item.get("issue", None),
"volume": item.get("volume", None),
"pages": item.get("page", None),
"date-parts": item.get("issued", {}).get("date-parts", [[None]]),
}
for item in items
if item["score"] > 40
}
num_refs = len(dois_to_item)
sorted_dois = sorted(
list(dois_to_item.keys()),
key=lambda doi: -dois_to_item[doi]["cited-by"],
)
if self.use_crossref_formatting:
# use Crossref to retrieve pre-formatted text
# remove leading "1. " from Science CSL style
refs = {
doi: content_negotiation(ids=doi, format="text", style="science")[
3:
]
for doi in dois_to_item.keys()
}
self.logger.debug(
f"Retrieved {len(refs)} formatted references from Crossref."
)
md = " \n\n".join(
f"> [{refs[doi]}](https://dx.doi.org/{doi}) "
f"Cited by {dois_to_item[doi]['cited-by']}."
for doi in sorted_dois
)
formatted_references = dcc.Markdown(
md, className="mpc-markdown"
)
else:
# else retrieve BibTeX entries to extract a nice author list
# and perform our own formatting
entries = {
doi: content_negotiation(ids=doi, format="bibtex")
for doi in sorted_dois
}
formatted_entries = []
for doi, entry in entries.items():
author_string = self._bibtex_entry_to_author_text(entry)
journal_div = self._item_to_journal_div(dois_to_item[doi])
formatted_entries.append(
html.Blockquote(
[
html.A(
[
html.Div(
[
html.I(
# necessary since titles can contain HTML for superscripts etc.
dcc.Markdown(
dois_to_item[doi]["title"],
dangerously_allow_html=True
)
)
]
),
html.Div([author_string]),
html.Div(
[
journal_div,
html.Span(
f" Cited by {dois_to_item[doi]['cited-by']}."
),
]
),
],
href=f"https://dx.doi.org/{doi}",
)
],
className="mpc",
style={"padding-left": "1rem", "margin-bottom": "1rem"}
)
)
formatted_references = html.Div(formatted_entries)
else:
# this uses pybtex directly on stored BibTeX entries from MP
# most-accurate references and faster since no Crossref lookup
# is required but no dois/hyperlinks available
all_entries = {}
for references in all_references:
all_entries.update(Parser().parse_string(references).entries)
md = self._pybtex_entries_to_markdown(all_entries)
formatted_references = dcc.Markdown(md, className="mpc-markdown")
num_refs = len(all_entries)
return html.Div(
[
Label(f"{num_refs} references found{':' if num_refs>0 else '.'}"),
formatted_references,
],
style={"max-height": "20rem", "overflow-y": "scroll"},
)
def options_layout(self):
options = html.Div([
html.Div([
Label("Rotation axis"),
dcc.Input(
value="[1, 0, 0]",
id=self.id("gb_rotation_axis"),
type="text",
className="input",
),
]),
html.Br(),
html.Div([
Label("Choose Σ"),
dcc.Dropdown(
id=self.id("gb_sigma_options"),
options=[],
placeholder="...",
),
]),
html.Br(),
html.Div([
Label("Choose rotation angle"),
dcc.Dropdown(
id=self.id("gb_rotation_options"),
options=[],
placeholder="...",
),
]),
html.Br(),
html.Div([
Label("Grain width"),
dcc.Slider(
id=self.id("gb_expand_times"),
min=1,
max=6,
step=1,
value=2,
marks={
2: "2",
4: "4",
6: "6"
},
),
]),
html.Br(),
html.Div([
Label("Distance between grains in Å"),
dcc.Input(
value="0.0",
id=self.id("gb_vacuum_thickness"),
type="text",
className="input",
),
]),
html.Br(),
html.Div([
Label("Plane"),
dcc.Input(
value="None",
id=self.id("gb_plane"),
type="text",
className="input",
),
]),
])
return options