PIGLE - Particles Interacting in Generalized Langevin Equation simulator
PIGLE - Particles Interacting in Generalized Langevin Equation simulator
复制标题
DOI：
10.1016/j.cpc.2019.04.013
复制
发表时间：
2019-09-01
影响因子：
6.3
通讯作者：
Allison, W.
中科院分区：
文献类型：
--
作者：
Avidor, N.;Townsend, P. S. M.;Allison, W.
我们提出了一个使用 Simulink 和 MATLAB 的软件包，可以对遵循广义朗之万方程的相互作用粒子进行分子动力学模拟。该软件包考虑了三个空间维度和类似刚体的旋转，经过调整以探索共吸附物质的表面扩散。物理参数是物种特定的，包括用户定义的有色噪声谱和独立作用于平移和旋转自由度的记忆摩擦内核。我们使用已建立的动态相关函数分析结果对模拟进行基准测试，并使用该软件包对有关耗散旋转运动和多指数摩擦内核的新颖分析结果进行数值验证。该软件包提供了一种直接的方法来扩展原子尺度超快表面扩散问题的建模。 程序摘要程序标题：PIGLE - 广义朗之万方程模拟器中的粒子交互程序文件 doi：http://dx.doi.org/10.17632/759j7vhfgp.1许可规定：GNU 通用公共许可证 3编程语言：MATLAB/Simulink 问题性质：理解分子扩散表面具有基础和工业意义，并且需要在实验和从头算理论之间建立桥梁。分子动力学模拟被广泛用于连接实验和理论世界，但通常表面动力学模拟要么在极端简化的情况下完成（二维朗之万用于单一物种吸附物），要么以昂贵的计算成本明确包含所有底物原子以及吸附物原子。解决方案方法：我们在这里提出了一个用于共吸附相互作用物种的广义朗之万动力学的模拟器，考虑了 3 个空间维度的表面扩散和刚体旋转。该软件包还允许对计算轨迹进行统计分析，考虑施加在平移和旋转质心上的散射中心的配置。 (C) 2019 Elsevier B.V. 保留所有权利。
We present a package using Simulink and MATLAB to perform molecular dynamics simulations of interacting particles obeying a Generalized Langevin Equation. The package, which accounts for three spatial dimensions and rigid-body like rotation, is tuned to explore surface diffusion of co-adsorbed species. The physical para(m)eters are species specific, and include user-defined colored noise spectra and memory friction kernels acting independently on translational and rotational degrees of freedom. We benchmark the simulations using established analytical results for dynamical correlation functions, and we use the package to numerically verify novel analytical results concerning dissipative rotational motion and multi-exponential friction kernels. The package provides a straight-forward way to expand the modeling of ultra-fast surface diffusion problems at the atomic scale.Program summaryProgram title: PIGLE - Particles Interacting in Generalized Langevin Equation simulatorProgram Files doi: http://dx.doi.org/10.17632/759j7vhfgp.1Licensing provisions: GNU General Public License 3Programming language: MATLAB/SimulinkNature of problem: Understanding molecular diffusion at surfaces is of fundamental and industrial interest, and requires bridging between the experiment and ab-initio theories. Molecular dynamics simulations are widely used to bridge the experimental and theoretical worlds, however normally surface dynamics simulations are done either under extreme simplifications (two dimensional Langevin with for single species adsorbate), or with all the substrate atoms as well as the adsorbate atoms included explicitly at expensive computational cost.Solution method: We here present a simulator for generalized Langevin dynamics of co-adsorbed interacting species, accounting for surface diffusion in 3 spatial dimensions and rigid body rotation. The package allows also to perform statistical analysis of the computed trajectories, considering a configuration of scattering centers which is imposed on the translating and rotating center-of-mass. (C) 2019 Elsevier B.V. All rights reserved.