dorsal/arxiv
View SchemaNeighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids
| Authors | Aleksandar Donev, Salvatore Torquato, Frank H. Stillinger |
|---|---|
| Categories | |
| ArXiv ID | physics/0405089 |
| URL | https://arxiv.org/abs/physics/0405089 |
Abstract
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.
{
"annotation_id": "ab3be78b-d0ab-4c14-9415-7d9e795547d0",
"date_created": "2026-03-02T18:00:49.727000Z",
"date_modified": "2026-03-02T18:00:49.727000Z",
"file_hash": "ca99cb0b92cc9ac6792f5481a237f07f814eb0969af24b492c7308e885bb969d",
"private": false,
"record": {
"abstract": "In the first part of a series of two papers, we present in considerable\ndetail a collision-driven molecular dynamics algorithm for a system of\nnonspherical particles, within a parallelepiped simulation domain, under both\nperiodic or hard-wall boundary conditions. The algorithm extends previous\nevent-driven molecular dynamics algorithms for spheres. We present a novel\npartial-update near-neighbor list (NNL) algorithm that is superior to previous\nalgorithms at high densities, without compromising the correctness of the\nalgorithm. This efficiency of the algorithm is further increased for systems of\nvery aspherical particles by using bounding sphere complexes (BSC). In the\nsecond part of this series of papers we apply the algorithm presented in the\nfirst part of this series of papers to systems of hard ellipses and ellipsoids.\nThe theoretical machinery needed to treat such particles, including the overlap\npotentials, is developed in full detail. We describe an algorithm for\npredicting the time of collision for two moving ellipses or ellipsoids. We\npresent performance results for our implementation of the algorithm. The\npractical utility of the algorithm is demonstrated by presenting several\ninteresting physical applications, including the generation of jammed packings\ninside spherical containers, the study of contact force chains in jammed\npackings, and melting the densest-known equilibrium crystals of prolate\nspheroids.",
"arxiv_id": "physics/0405089",
"authors": [
"Aleksandar Donev",
"Salvatore Torquato",
"Frank H. Stillinger"
],
"categories": [
"physics.comp-ph",
"physics.chem-ph"
],
"title": "Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids",
"url": "https://arxiv.org/abs/physics/0405089"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "a90f0164-e03d-4280-bcf8-b2e177b9416e",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}