Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units

Michael P. Howard, Joshua A. Anderson, Arash Nikoubashman, Sharon C. Glotzer, Athanassios Z. Panagiotopoulos

Research output: Contribution to journalArticlepeer-review

30 Scopus citations

Abstract

We present an algorithm based on linear bounding volume hierarchies (LBVHs) for computing neighbor (Verlet) lists using graphics processing units (GPUs) for colloidal systems characterized by large size disparities. We compare this to a GPU implementation of the current state-of-the-art CPU algorithm based on stenciled cell lists. We report benchmarks for both neighbor list algorithms in a Lennard-Jones binary mixture with synthetic interaction range disparity and a realistic colloid solution. LBVHs outperformed the stenciled cell lists for systems with moderate or large size disparity and dilute or semidilute fractions of large particles, conditions typical of colloidal systems.

Original languageEnglish (US)
Pages (from-to)45-52
Number of pages8
JournalComputer Physics Communications
Volume203
DOIs
StatePublished - Jun 1 2016

All Science Journal Classification (ASJC) codes

  • Hardware and Architecture
  • Physics and Astronomy(all)

Keywords

  • Bounding volume hierarchy
  • Colloid
  • GPU
  • Molecular simulation
  • Neighbor list
  • Non-uniform
  • Size disparity

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