The abTEM code

Author(s)
Jacob Madsen, Toma Susi
Abstract

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document. This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fast implementation of the PRISM algorithm for a decahedral 20000-atom gold nanoparticle.

Organisation(s)
Physics of Nanostructured Materials
Journal
Open Research Europe
Volume
1
ISSN
2732-5121
DOI
https://doi.org/10.12688/openreseurope.13015.2
Publication date
03-2021
Peer reviewed
Yes
Austrian Fields of Science 2012
103042 Electron microscopy, 102009 Computer simulation, 103018 Materials physics, 103030 Radiation physics
Keywords
ASJC Scopus subject areas
Medicine (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Immunology and Microbiology (miscellaneous) , Health Policy, Public Health, Environmental and Occupational Health
Portal url
https://ucris.univie.ac.at/portal/en/publications/the-abtem-code(b5d0499d-ec15-44c3-913e-b5abe80e964d).html