Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids

Details Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids

2004-05-17

arxiv.org/abs/physics/0405089v1

Physics

Computational Physics

Two-paper series, 45 pages per paper, 90 pages total. To be submitted to JCP

Scientific paper

In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or hard-wall boundary conditions. The algorithm extends previous event-driven molecular dynamics algorithms for spheres. We present a novel partial-update near-neighbor list (NNL) algorithm that is superior to previous algorithms at high densities, without compromising the correctness of the algorithm. This efficiency of the algorithm is further increased for systems of very aspherical particles by using bounding sphere complexes (BSC). In the second part of this series of papers we apply the algorithm presented in the first part of this series of papers to systems of hard ellipses and ellipsoids. The theoretical machinery needed to treat such particles, including the overlap potentials, is developed in full detail. We describe an algorithm for predicting the time of collision for two moving ellipses or ellipsoids. We present performance results for our implementation of the algorithm. The practical utility of the algorithm is demonstrated by presenting several interesting physical applications, including the generation of jammed packings inside spherical containers, the study of contact force chains in jammed packings, and melting the densest-known equilibrium crystals of prolate spheroids.

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