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GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions
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 for various GPU algorithms relying on either hardware cache
or shared memory.Comment: to appear in a special issue of Eur. Phys. J. Special Topics on
"Computer Simulations on GPUs
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