Quantized bounding volume hierarchies for neighbor search in molecular simulations on graphics processing units

Michael P. Howard, Antonia Statt, Felix Madutsa, Thomas M. Truskett, Athanassios Z. Panagiotopoulos

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

We present an algorithm for neighbor search in molecular simulations on graphics processing units (GPUs) based on bounding volume hierarchies (BVHs). The BVH is compressed into a low-precision, quantized representation to increase the BVH traversal speed compared to a previous implementation. We find that neighbor search using the quantized BVH is roughly two to four times faster than current state-of-the-art methods using uniform grids (cell lists) for a suite of benchmarks for common molecular simulation models. Based on the benchmark results, we recommend using the BVH instead of a single cell list for neighbor list generation in molecular simulations on GPUs.

Original languageEnglish (US)
Pages (from-to)139-146
Number of pages8
JournalComputational Materials Science
Volume164
DOIs
StatePublished - Jun 15 2019

All Science Journal Classification (ASJC) codes

  • Computer Science(all)
  • Chemistry(all)
  • Materials Science(all)
  • Mechanics of Materials
  • Physics and Astronomy(all)
  • Computational Mathematics

Keywords

  • Bounding volume hierarchy
  • GPU
  • Molecular simulation
  • Neighbor search

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