Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units
Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units
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DOI：
10.1016/j.cpc.2016.02.003
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发表时间：
2016-06-01
影响因子：
6.3
通讯作者：
Panagiotopoulos, Athanassios Z.
中科院分区：
文献类型：
--
作者：
Howard, Michael P.;Anderson, Joshua A.;Panagiotopoulos, Athanassios Z.
我们提出了一种基于线性包围体层次结构（LBVH）的算法，用于计算邻居（Verlet）列表，使用图形处理单元（GPU）的胶体系统，其特征在于大尺寸的差异。我们将其与基于模板单元列表的当前最先进CPU算法的GPU实现进行比较。我们报告基准的邻居列表算法在一个Lennard-琼斯二进制混合物与合成的相互作用范围的差距和一个现实的胶体溶液。LBVH优于模板细胞列表的系统具有中等或大的尺寸差异和大颗粒的稀释或半稀释部分，胶体系统的典型条件。(C)© 2016 Elsevier B. V.版权所有。
We present an algorithm based on linear bounding volume hierarchies (LBVHs) for computing neighbor (Verlet) lists using graphics processing units (GPUs) for colloidal systems characterized by large size disparities. We compare this to a GPU implementation of the current state-of-the-art CPU algorithm based on stenciled cell lists. We report benchmarks for both neighbor list algorithms in a Lennard-jones binary mixture with synthetic interaction range disparity and a realistic colloid solution. LBVHs outperformed the stenciled cell lists for systems with moderate or large size disparity and dilute or semidilute fractions of large particles, conditions typical of colloidal systems. (C) 2016 Elsevier B.V. All rights reserved.