STEMsalabim  
A high-performance computing cluster friendly code for scanning transmission electron microscopy image simulations of thin specimens
STEMSalaBim

The STEMsalabim software aims to provide accurate scanning transmission electron microscopy (STEM) image simulation of a specimen whose atomic structure is known. It implements the frozen lattice multislice algorithm as described in great detail in the book Advanced computing in electron microscopy by Earl J. Kirkland.

While there are multiple existing implementations of the same technique, none of them is suitable for running on high-performance computing (HPC) clusters, which is required in order to simulate large supercells or large sets of simulations, e.g. for parameter sweeps.

The purpose of STEMsalabim is to fill this gap by providing a multislice implementation that is well parallelizable both within and across computing nodes, using a mixture of threaded parallelization and message passing interface (MPI).

Downloads

Version Summary Download links
2.0.0-beta pre-release of version 2.0.0, that has not been tested extensively. stemsalabim-2.0.0-beta.tar.gz
1.0 Initial release stemsalabim-1.0.tar.gz

How to get started

We suggest you start reading General information to understand, and only then go on with Installing STEMsalabim and Running STEMsalabim.

Credits

We acknowledge the creators of the supplementary libraries that STEMsalabim depends on.

We would also like to acknowledge the creators of STEMsim, which we used as a reference implementation to test STEMsalabim.

Once again, we would like to highlight the book Advanced computing in electron microscopy by Earl J. Kirkland for its detailed description of the implementation of multislice algorithms.

STEMsalabim was written in the Structure & Technology Research Laboratory of the Philipps-Universit├Ąt Marburg.

Philipps-Universit├Ąt Marburg Structure & Technology Research Laboratory
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