quantem.diffsim

An interactive electron diffraction simulator for web pages and Dash apps. It shows a crystal and its diffraction pattern side by side for any orientation: nanobeam, convergent beam (CBED) and Kikuchi patterns, with kinematical or Bloch wave intensities, thickness, convergence, precession and beam energy controls. Every calculation runs in the browser, so the server only sends the structure.

The structure factors use the Lobato and Van Dyck electron scattering factors (Acta Cryst. A 70, 636 (2014)), and the Bloch wave couplings use the absorptive Weickenmeier and Kohl scattering factors with a Debye-Waller factor (Acta Cryst. A 47, 590 (1991)), as computed in quantEM. The same simulator runs in Jupyter as quantem.widget.DiffractionSim.

The package has no dependencies. It ships the browser bundle (one ES module, about 1.2 MB) and a few Python helpers.

Standalone page

from pymatgen.core import Lattice, Structure
import quantem.diffsim as diffsim

si = Structure.from_spacegroup("Fd-3m", Lattice.cubic(5.431), ["Si"], [[0, 0, 0]])
diffsim.save_html("si.html", si, zone_axis=[1, 1, 0], mode="nanobeam", title="Si")

structure_to_cif accepts a pymatgen Structure, an ASE Atoms object, CIF text or a CIF path. A pymatgen structure is converted to its conventional standard cell first (conventional=False keeps the given cell), so zone axes refer to the conventional lattice.

Dash

from dash import Dash, Input, Output, dcc, html
from quantem.diffsim import dash as diffsim_dash
import quantem.diffsim as diffsim

app = Dash(__name__)
diffsim_dash.register(app)
app.layout = html.Div([dcc.Store(id="structure"), diffsim_dash.layout("tem")])

@app.callback(Output(diffsim_dash.settings_id("tem"), "data"), Input("structure", "data"))
def show(structure):
    return diffsim.settings(Structure.from_dict(structure), zone_axis=[0, 0, 1], mode="nanobeam")

register(app) serves the bundle from the app's Flask server and adds one clientside callback that draws every simulator in the layout. Each new settings dictionary redraws that simulator.

Settings

settings() checks the names below. Lengths are in Å, angles in mrad unless named _deg, and scattering vectors in 1/Å.

License

MIT. Source and issues: electronmicroscopy/quantem.widget.