PIGLE — Particles Interacting in Generalized Langevin Equation simulator

Abstract

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 parameters 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 Program title: PIGLE — Particles Interacting in Generalized Langevin Equation simulator Program Files doi: http://dx.doi.org/10.17632/759j7vhfgp.1 Licensing provisions: GNU General Public License 3 Programming language: MATLAB/Simulink Nature 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.