Cell list algorithms for nonequilibrium molecular dynamics

JOURNAL OF COMPUTATIONAL PHYSICS

卷:315

Article

Dobson, Matthew¹  Fox, Ian¹  Saracino, Alexandra¹ 

[1] Univ Massachusetts, Dept Math & Stat, 710 N Pleasant St, Amherst, MA 01003 USA

关键词: Nonequilibrium;    Molecular dynamics;    Elongational flow;    Cell list;   

DOI  :  10.1016/j.jcp.2016.03.056

来源: Elsevier

【 摘 要 】

We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N-2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm. (C) 2016 Elsevier Inc. All rights reserved.

【 授权许可】

Free