Fast neighbor lists for adaptive-resolution particle simulations

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Omar Awile - , ETH Zurich (Author)
  • Ferit Büyükkeçeci - , ETH Zurich (Author)
  • Sylvain Reboux - , ETH Zurich (Author)
  • Ivo F. Sbalzarini - , Center for Systems Biology Dresden (CSBD), ETH Zurich (Author)

Abstract

Particle methods provide a simple yet powerful framework for simulating both discrete and continuous systems either deterministically or stochastically. The inherent adaptivity of particle methods is particularly appealing when simulating multiscale models or systems that develop a wide spectrum of length scales. Evaluating particle-particle interactions using neighbor-finding algorithms such as cell lists or Verlet lists, however, quickly becomes inefficient in adaptive-resolution simulations where the interaction cutoff radius is a function of space. We present a novel adaptive-resolution cell list algorithm and the associated data structures that provide efficient access to the interaction partners of a particle, independent of the (potentially continuous) spectrum of cutoff radii present in a simulation. We characterize the computational cost of the proposed algorithm for a wide range of resolution spans and particle numbers, showing that the present algorithm outperforms conventional uniform-resolution cell lists in most adaptive-resolution settings.

Details

Original languageEnglish
Pages (from-to)1073-1081
Number of pages9
JournalComputer physics communications
Volume183
Issue number5
Publication statusPublished - May 2012
Peer-reviewedYes
Externally publishedYes

External IDs

ORCID /0000-0003-4414-4340/work/159608300

Keywords

Keywords

  • Adaptive-resolution simulations, Cell lists, Multiresolution simulations, Neighbor lists, Particle methods, Verlet lists