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

Abstract

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.

Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays

“… 42 Moreover, incorporating the Barnes-Hut treecode algorithm in XMDYN has recently shown significant improvement to the computational efficiency. 43 However, in these studies, the currently used ReaxFF module was not included. In the present calculation, no optimization of the interfacing between XMDYN and ReaxFF was performed.…”

Computational study of diffraction image formation from XFEL irradiated single ribosome molecule

“…We used the tree-code-extended XMDYN code 21 – 23 to simulate the dynamics of the irradiated ribosome molecule. XMDYN follows the ionization dynamics of atoms and ions, using a Monte Carlo scheme combined with first-principle atomic-structure calculations.…”

“…In this paper, we perform a comprehensive analysis of radiation damage during a realistic SPI study of a ribosome macromolecule, containing 142,429 non-hydrogen atoms. For the simulation, we use the SIMEX framework 16 , with a dedicated software for modeling X-ray induced radiation damage in large finite-size samples, the tree-code-extended XMDYN tool 21 – 23 . With these codes, we estimate the minimal number of simulated molecular-dynamics realizations of the X-ray irradiated molecule (performed under typical experimental conditions) needed to reliably compute its time-integrated and realization-averaged diffraction image.…”