Linked Cell Traversal Algorithms for Three-Body Interactions in Molecular Dynamics

TL;DR

This paper introduces parallel algorithms for efficiently computing three-body interactions in molecular dynamics, extending linked cell traversal methods to handle complex interactions across three cells, validated through Lennard-Jones fluid simulations.

Contribution

It develops a general framework for linked cell traversal algorithms for three-body interactions and analyzes their performance with cutoff conditions in molecular dynamics simulations.

Findings

Validated algorithms with Lennard-Jones fluid scenarios

Demonstrated scalability and performance at node level

Extended traversal methods to three-cell interactions

Abstract

In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals are extended to allow for the computation between molecules stored across three cells. A general framework for the computation of three-body interactions in linked cells is described, and then used to implement the corresponding traversals. In addition, our analysis is combined with the commonly used cutoff conditions, because they influence the total workload of the computation of interactions. The combinations between traversals and truncation conditions are validated using the well-known Lennard-Jones fluid. Validation case studies are taken from the literature and configured into homogeneous and inhomogeneous scenarios. Finally, strong scalability and performance in terms of molecule updates are measured at node-level.