import abtem
import ase
import matplotlib.pyplot as plt
from ase.io import write

PACBED quickstart

This notebook demonstrates a basic simulation of a position averaged convergent beam electron diffraction (PACBED) simulation of SrTiO\(_3\).

Configuration

We start by (optionally) setting our configuration. See documentation for details.

abtem.config.set(
    {
        "device": "cpu",
        "fft": "fftw",
        "diagnostics.task_progress": False,
        "diagnostics.progress_bar": False,
    }
);

Atomic model

We import a model of SrTiO₃. See our walkthrough or our tutorial on atomic models.

atoms = ase.io.read("data/SrTiO3.cif")

abtem.show_atoms(atoms);

Crystal potential

potential_unit = abtem.Potential(atoms, slice_thickness=0.5, sampling=0.05)

repetitions_xy = 5
repetitions_z = 10

potential = abtem.CrystalPotential(
    potential_unit, repetitions=(repetitions_xy, repetitions_xy, repetitions_z)
)

Probe

probe = abtem.Probe(energy=100e3, semiangle_cutoff=30)

probe.grid.match(potential)

Scan

scan = abtem.GridScan(potential=potential, start=(0, 0), end=(1 / repetitions_xy, 1 / repetitions_xy), fractional=True)

visualization = potential.show()

scan.add_to_plot(visualization)

Detect

detector = abtem.PixelatedDetector()

measurement = probe.scan(scan=scan, potential=potential, detectors=detector)

measurement.compute();

Average over scan positions

measurement.shape

(13, 13, 185, 185)

measurement.axes_metadata

type                 label     coordinates
-------------------  --------  --------------------
ScanAxis             x [Å]     0.00 0.30 ... 3.64
ScanAxis             y [Å]     0.00 0.30 ... 3.64
ReciprocalSpaceAxis  kx [1/Å]  -4.66 -4.61 ... 4.66
ReciprocalSpaceAxis  ky [1/Å]  -4.66 -4.61 ... 4.66

pacbed = measurement.mean(axis=(0,1))

pacbed.crop(50).show(power=0.5);

# this cell produces a thumbnail for the online documentation

visualization = pacbed.crop(50).show(power=0.5)
visualization.axis_off()
plt.savefig(
    "../thumbnails/pacbed_quickstart.png", bbox_inches="tight", pad_inches=0
)