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The European Physical Journal Special Topics

, Volume 210, Issue 1, pp 101–117 | Cite as

GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions

  • M. Kopp
  • F. Höfling
Regular Article

Abstract

Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute unified device architecture (CUDA) of recent graphics processors (GPUs). Thereby, the simulation of explicit solvent particles is avoided and hydrodynamic interactions can easily be accounted for in already available, highly accelerated molecular dynamics simulations. Special emphasis is put on efficient memory access and numerical stability. The algorithm is applied to the periodic sedimentation of a cluster of four suspended particles. Finally, we investigate the runtime performance of generic memory access patterns of complexity O(N 2) for various GPU algorithms relying on either hardware cache or shared memory.

Keywords

Graphic Processing Unit Memory Access European Physical Journal Special Topic Shared Memory Global Memory 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© EDP Sciences and Springer 2012

Authors and Affiliations

  • M. Kopp
    • 1
    • 2
  • F. Höfling
    • 1
    • 2
  1. 1.Max-Planck-Institut für Intelligente SystemeStuttgartGermany
  2. 2.Institut für Theoretische und Angewandte PhysikUniversität StuttgartStuttgartGermany

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