European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany.
Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland.
Molecules. 2022 Jun 30;27(13):4206. doi: 10.3390/molecules27134206.
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.
在这项工作中，我们首次将基于树算法的求解器集成到分子动力学代码 XMDYN 中。XMDYN 是为描述超快 X 射线脉冲与原子组装体的相互作用而开发的。它也是为在欧洲 XFEL 设施的 SPB/SFX 仪器上进行计算单粒子成像研究而开发的 SIMEX 模拟平台的一部分。为了提高 XMDYN 的性能，我们将现有的基于树算法的库仑求解器 PEPC 集成到代码中，并开发了一个专用的基于树算法的二次离子化求解器，现在也包含在 XMDYN 代码中。这些扩展使对 X 射线辐照的大型原子组装体（例如，对超快 X 射线科学有强烈兴趣的大型蛋白质系统或病毒）的计算效率模拟成为可能。基于 XMDYN 的预备模拟现在可以为在自由电子激光设施 EuXFEL 上进行的未来单粒子成像实验提供指导。
