{
  "annotation_id": "2e065bb7-3e90-4cf2-8e02-2f15882c8256",
  "date_created": "2026-03-02T18:00:46.814000Z",
  "date_modified": "2026-03-02T18:00:46.814000Z",
  "file_hash": "4b26b8288f7c9d5588a0e73c6888392e78f39d3c75ab9810e775bbe3a434fba8",
  "private": false,
  "record": {
    "abstract": "An improved neighbor list algorithm is proposed to reduce unnecessary\ninteratomic distance calculations in molecular simulations. It combines the\nadvantages of Verlet table and cell linked list algorithms by using cell\ndecomposition approach to accelerate the neighbor list construction speed, and\ndata sorting method to lower the CPU data cache miss rate, as well as partial\nupdating method to minimize the unnecessary reconstruction of the neighbor\nlist. Both serial and parallel performance of molecular dynamics simulation are\nevaluated using the proposed algorithm and compared with those using\nconventional Verlet table and cell linked list algorithms. Results show that\nthe new algorithm outperforms the conventional algorithms by a factor of 2~3 in\ncases of both small and large number of atoms.",
    "arxiv_id": "physics/0311055",
    "authors": [
      "Zhenhua Yao",
      "Jian-Sheng Wang",
      "Gui-Rong Liu",
      "Min Cheng"
    ],
    "categories": [
      "physics.comp-ph"
    ],
    "doi": "10.1016/j.cpc.2004.04.004",
    "title": "Improved neighbor list algorithm in molecular simulations using cell   decomposition and data sorting method",
    "url": "https://arxiv.org/abs/physics/0311055"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "2f34d180-19e6-4c49-a389-a1fad99e6de7",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}