The abTEM code: transmission electron microscopy from first principles

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.

ReciPro: free and open-source multipurpose crystallographic software integrating a crystal model database and viewer, diffraction and microscopy simulators, and diffraction data analysis tools

“…Tempas (Kilaas et al, 1987), JEMS (Stadelmann, 1987), xHREM (Ishizuka & Uyeda, 1977), QSTEM (Koch, 2002), MULTEM (Lobato & Van Dyck, 2015), Prismatic (Pryor et al, 2017) and Dr. Probe (Barthel, 2018) are currently maintained GUI-based S/TEM simulation programs based on the dynamical electron scattering theory. A recent trend has been the development of Python-based software which can be flexibly customized by even non-expert programmers, such as ASE (Larsen et al, 2017) and pymatgen (Ong et al, 2013) for handling atoms and crystal models, diffPy (Juha ´s et al, 2015) for powder diffraction data analyses, and abTEM (Madsen & Susi, 2021) and py_multislice (Brown et al, 2020) for S/TEM image simulations. Most of these programs were developed for specific purposes (e.g.…”

Hybrid Deep Learning Crystallographic Mapping of Polymorphic Phases in Polycrystalline Hf0.5Zr0.5O2 Thin Films

“…Simulated PACBED patterns were obtained by a multislice algorithm implemented in an open software package, abTEM. [ 35 ] To obtain ground truth results for validation, multislice calculations were performed for many artificially constructed supercell models of HZO with different crystallographic parameters, such as phase, orientation, local tilt, rotation, grain overlap, and thickness, with the microscope parameters approximate to the experimental conditions described above. Tilted PACBED patterns for three polymorphic phases (i.e., monoclinic, orthorhombic, and tetragonal) were simulated for the tilt range of ±10 mrad with a 1 mrad interval and the thickness range of 15–35 nm with a 1 nm interval.…”

Mechanism of Electron-Beam Manipulation of Single-Dopant Atoms in Silicon

“…All image simulations were performed using the multislice code abTEM . Based on the experimental HAADF contrast, we assumed a slab thickness of 15 nm and that the dopants were near the center of the slab.…”

“…All image simulations were performed using the multislice code abTEM. 38 Based on the experimental HAADF contrast, we assumed a slab thickness of 15 nm and that the dopants were near the center of the slab. The size of the structure prohibits fully optimizing all the positions at the ab initio level of theory; hence, smaller supercells around the defects were optimized and inserted into an idealized slab.…”