GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows
GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows
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DOI：
10.1016/j.jcp.2010.03.047
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发表时间：
2010-08
期刊：
影响因子：
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通讯作者：
A. Sunarso;T. Tsuji;S. Chono
中科院分区：
文献类型：
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作者：
A. Sunarso;T. Tsuji;S. Chono
我们开发了一种基于GPU的分子动力学模拟，用于研究具有各向异性分子（如液晶）的流体的流动。应用模拟的宏观流动（回流）产生的研究下，在一个电场的应用程序的液晶分子重新取向。采用单元列表法在GPU上实现了分子间力和力矩的并行计算，并提出了一种高效的单元列表更新算法。在具有有限的高速存储器资源的GPU上实现涉及大量算术运算和数据的计算中的一些重要问题被广泛地解决。尽管在计算分子间力和扭矩时GPU占用率相对较低，但在最近的GPU上的计算速度比在最近的CPU的单核上快约50倍，因此使用个人计算机进行涉及大量分子的模拟是可能的。基于GPU的模拟应该允许广泛的调查的分子水平的机制下的各种宏观流动现象的流体与各向异性分子。
We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.