Source code for crystal_toolkit.components.xas

import plotly.graph_objs as go
from dash import dcc, html
from dash.dependencies import Input, Output, State
from dash.exceptions import PreventUpdate

from crystal_toolkit.core.mpcomponent import MPComponent
from crystal_toolkit.core.panelcomponent import PanelComponent
from crystal_toolkit.helpers.layouts import MessageBody, MessageContainer

# Author: Matthew McDermott
# Contact:

[docs]class XASComponent(MPComponent): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.create_store("mpid") self.create_store("elements") default_xas_layout = dict( xaxis={ "title": "Energy (eV)", "anchor": "y", "mirror": "ticks", "nticks": 8, "showgrid": True, "showline": True, "side": "bottom", "tickfont": {"size": 16.0}, "ticks": "inside", "titlefont": {"size": 16.0}, "type": "linear", "zeroline": False, }, yaxis={ "title": "Absorption Coeff, μ (a.u.)", "anchor": "x", "mirror": "ticks", "nticks": 7, "showgrid": True, "showline": True, "side": "left", "tickfont": {"size": 16.0}, "ticks": "inside", "titlefont": {"size": 16.0}, "type": "linear", "zeroline": False, }, autosize=True, height=300, hovermode="x", showlegend=False, paper_bgcolor="rgba(0,0,0,0)", plot_bgcolor="rgba(0,0,0,0)", margin=dict(l=60, b=50, t=50, pad=0, r=30), ) line_colors = [ "rgb(128, 0, 0)", "rgb(0, 0, 128)", "rgb(60, 180, 75)", "rgb(145,30,180)", "rgb(230,25,75)", "rgb(240,50,230)", ] empty_plot_style = { "xaxis": {"visible": False}, "yaxis": {"visible": False}, "paper_bgcolor": "rgba(0,0,0,0)", "plot_bgcolor": "rgba(0,0,0,0)", } @property def _sub_layouts(self): graph = html.Div( [ dcc.Graph( figure=go.Figure(layout=XASComponent.empty_plot_style), config={"displayModeBar": False}, ) ],"xas-div"), ) element_selector = html.Div( [ html.P("Select an Element:"), dcc.RadioItems("element-selector"), options=[], inputClassName="mpc-radio", labelClassName="mpc-radio", ), ] ) return {"graph": graph, "element_selector": element_selector} @property def layout(self): return html.Div( [self._sub_layouts["graph"], self._sub_layouts["element_selector"]] )
[docs] def generate_callbacks(self, app, cache): @app.callback( Output("xas-div"), "children"), [Input(, "data")] ) def update_graph(plotdata): if not plotdata: raise PreventUpdate if plotdata == "error": search_error = ( MessageContainer( [ MessageBody( dcc.Markdown( "XANES pattern not available for this selection." ) ) ], kind="warning", ), ) return search_error else: return [ dcc.Graph( figure=go.Figure(data=plotdata, layout=self.default_xas_layout), config={"displayModeBar": False}, ) ] @app.callback( [Output(, "data"), Output("elements"), "data")][ Input("element-selector"), "value") ], [State("mpid"), "data"), State("elements"), "data")], ) def pattern_from_mpid(element, mpid, elements): if not element or not elements: raise PreventUpdate url_path = f"/materials/{mpid['mpid']}/xas/{element}" from mp_api.client import MPRester with MPRester() as mpr: data = mpr._make_request(url_path) # querying MP database via MAPI if len(data) == 0: plotdata = "error" else: x = data[0]["spectrum"].x y = data[0]["spectrum"].y plotdata = [ go.Scatter( x=x, y=y, line=dict(color=self.line_colors[elements.index(element)]), ) ] with MPRester() as mpr: entry = mpr.get_entry_by_material_id(mpid["mpid"]) comp = entry.composition elem_options = [str(comp.elements[i]) for i in range(0, len(comp))] return plotdata, elem_options @app.callback( Output("element-selector"), "options"), [Input("elements"), "data")], ) def generate_element_options(elements): return [{"label": i, "value": i} for i in elements] @app.callback( Output("element-selector"), "value"), [Input("element-selector"), "options")], ) def set_xas_value(options): if not options or not options[0]: raise PreventUpdate return options[0]["value"]
[docs]class XASPanelComponent(PanelComponent): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.xas = XASComponent() self.xas.attach_from(self, this_store_name="mpid") @property def title(self): return "X-Ray Absorption Spectra" @property def description(self): return ( "Display the K-edge X-Ray Absorption Near Edge Structure (XANES) for this structure, " "if it has been calculated by the Materials Project." ) @property def loading_text(self): return "Searching for calculated XANES pattern on Materials Project..." @property def initial_contents(self): return html.Div([super().initial_contents, html.Div([self.xas.layout])])
[docs] def update_contents(self, new_store_contents, *args): return self.xas.layout
# def generate_callbacks(self, app, cache): # # super().generate_callbacks(app, cache) # # @app.callback( # Output("inner_contents"), "children"), [Input(, "data")] # ) # def add_xas(mpid): # if not mpid: # raise PreventUpdate # return self.xas.layout