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 journalArticlepeer-review

10 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

  • General Computer Science
  • General Chemistry
  • General Materials Science
  • Mechanics of Materials
  • General Physics and Astronomy
  • Computational Mathematics

Keywords

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

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