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PRISM and Prismatic - a new algorithm and code for very fast scanning transmission electron microscopy (STEM) simulations

Banff International Research Station for Mathematical Innovation and Discovery

Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, namely the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor f that has typical values of 4–20 for atomic resolution simulations. We show that in many cases PRISM can provide a speedup that scales with f^4 compared to multislice simulations, with a negligible loss of accuracy. We demonstrate the usefulness of this method with large-scale scanning transmission electron microscopy image simulations of a crystalline nanoparticle on an amorphous carbon substrate. We also present a software package called Prismatic for parallelized simulation of image formation in STEM using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000x for PRISM and 15x for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine.Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface for Windows and OSX, and as a Python package.

Mathematics; Numerical analysis; Approximations and expansions; Control/optimization/operation research

video/mp4

Author affiliation: Lawrence Berkeley National Lab

2018-04-17

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/65426

Unreviewed

http://creativecommons.org/licenses/by-nc-nd/4.0/