GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions
GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions
复制标题
GPU 加速模拟具有直接流体动力相互作用的胶体悬浮液
DOI：
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发表时间：
2012
期刊：
影响因子：
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通讯作者：
Felix Hofling
中科院分区：
文献类型：
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作者：
Michael Kopp;Felix Hofling
溶剂介导的胶体颗粒之间的流体动力学相互作用可以显着改变它们的动力学。我们讨论了最新图形处理器 (GPU) 的计算统一设备架构 (CUDA) 所提供的流处理器领先近似中斯托克斯动力学的实现。因此，避免了显式溶剂颗粒的模拟，并且可以在现有的、高度加速的分子动力学模拟中轻松地解释流体动力学相互作用。特别强调高效的内存访问和数值稳定性。该算法应用于四个悬浮颗粒簇的周期性沉降。最后，我们研究了依赖于硬件缓存或共享内存的各种 GPU 算法的复杂度为 O(N2) 的通用内存访问模式的运行时性能。
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(N2) for various GPU algorithms relying on either hardware cache or shared memory.
影响因子：
5.5
作者：
Ruymgaart, A. Peter;Cardenas, Alfredo E.;Elber, Ron
通讯作者：
Elber, Ron