Abstract
Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned over a sample's surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging methods have made STEM one of the most important tools for atomic-resolution materials science. Many of these imaging methods rely on accurate imaging and diffraction simulations in order to interpret experimental results. However, STEM simulations have traditionally required large calculation times, as modeling the electron scattering requires a separate simulation for each of the typically millions of probe positions. We have created the Prismatic simulation code for fast simulation of STEM experiments with support for multi-CPU and multi-GPU (graphics processing unit) systems, using both the conventional multislice and our recently-introduced PRISM method. In this paper, we introduce Prismatic version 2.0, which adds many new algorithmic improvements, an updated graphical user interface (GUI), post-processing of simulation data, and additional operating modes such as plane-wave TEM. We review various aspects of the simulation methods and codes in detail and provide various simulation examples. Prismatic 2.0 is freely available both as an open-source package that can be run using a C++ or Python command line interface, or GUI, as well within a Docker container environment.
Highlights
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record
Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned f over a sample’s surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization
Prismatic implements Poisson noise application for high-resolution transmission J electron microscopy (HRTEM) images with electron dose measured in counts per area; for STEM images, dose is applied in counts per probe
Summary
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging o methods have made STEM one of the most important tools for atomic-resolution materials science. We have added several improvements to enhance the accuracy and speed of simulations, including a new approach for the correct sub-slicing of 3D atomic potentials with sub-pixel shifting, a refocusing approach to the scattering matrix calculation for PRISM simulations that increases accuracy for thicker samples and delocalized probes, and various post-processing methods for coherence or shot-noise limitations. Prismatic is intended for use as a fully-featured TEM/STEM simulation software for electron microscopy, for diverse use cases such as experimental validation, database generation, or teaching It serves as the reference implementation for the of the command-line and pyprismatic interfaces. Prismatic is an open-source and cross-platform software package that
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