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Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN

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posted on 2022-10-21, 03:49 authored by M Stransky, Z Jurek, R Santra, Adrian MancusoAdrian Mancuso, B Ziaja
In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL.

Funding

A.P.M. and B.Z. gratefully acknowledge the funding received from an R&D grant of the European XFEL, with the contribution of IFJ PAN in Krakow.

History

Publication Date

2022-06-30

Journal

Molecules

Volume

27

Issue

13

Article Number

4206

Pagination

10p.

Publisher

MDPI

ISSN

1420-3049

Rights Statement

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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