Cell List Algorithms for Nonequilibrium Molecular Dynamics

TL;DR

This paper introduces two modified cell list algorithms tailored for nonequilibrium molecular dynamics simulations involving deforming simulation boxes under linear flows, improving computational efficiency for such complex systems.

Contribution

The paper develops and compares two new cell list algorithms that adapt to dynamic, deforming simulation geometries in nonequilibrium molecular dynamics.

Findings

The algorithms effectively handle deforming simulation boxes.

They reduce computational complexity from O(N^2) to O(N).

The comparison shows differences in efficiency and complexity.

Abstract

We present two modifications of the standard cell list algorithm for nonequilibrium molecular dynamics simulations of homogeneous, linear flows. When such a flow is modeled with periodic boundary conditions, the simulation box deforms with the flow, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. For the typical case of short-ranged, pairwise interactions, the cell list algorithm reduces 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. The new versions of the cell list algorithm handle the dynamic, deforming simulation geometry. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.