Pseudo-Verlet lists: a new, compact neighbour list representation
Pseudo-Verlet lists: a new, compact neighbour list representation
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Pseudo-Verlet 列表：一种新的、紧凑的邻居列表表示
DOI：
10.1080/08927022.2012.762097
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发表时间：
2013
影响因子：
2.1
通讯作者：
P. Gonnet
中科院分区：
文献类型：
--
作者：
P. Gonnet
Verlet列表或邻居列表是一种流行的设备，用于加速分子动力学和其他基于粒子的模拟中的非键相互作用的计算，其中给定几何形状的相互作用粒子列表被计算一次，并在几个时间步长内重复使用，直到几何形状发生显着变化。Verlet列表的大小通常是范围内的指数，其中N是颗粒的总数，ρN是颗粒数密度，rc和rs分别是截止距离和表皮距离。由于它们的内存需求，Verlet列表并不总是多核或图形处理单元系统的最佳选择，其中每个核的内存带宽是有限的。本文介绍了伪Verlet列表，一种替代的邻居列表表示，只需要13 N的索引范围内，从而需要更少的存储，并导致更好的缓存重用。
Verlet lists, or neighbour lists, are a popular device to speed up the computation of non-bonded interactions in molecular dynamics and other particle-based simulations, in which a list of interacting particles for a given geometry is computed once and reused over several time steps until the geometry changes significantly. The size of the Verlet list is generally indices in the range , where N is the total number of particles, ρN is the particle number density and rc and rs are the cutoff and skin distances, respectively. Due to their memory requirements, Verlet lists are not always an optimal choice on multi-core or graphics processing unit systems in which the memory bandwidth per core is limited. This paper introduces pseudo-Verlet lists, an alternative neighbour list representation which requires only 13N indices in the range , thus requiring less storage, and resulting in better cache reuse.