The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application
The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application
复制标题
基于非均匀快速傅立叶变换的ENUF方法-Ewald求和：实现、并行化与应用
DOI：
10.1002/jcc.26395
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发表时间：
2020
影响因子：
3
通讯作者：
Wang Yong-Lei
中科院分区：
文献类型：
--
作者：
Yang Sheng-Chun;Li Bin;Zhu You-Liang;Laaksonen Aatto;Wang Yong-Lei
模型系统的计算机模拟被广泛用于探索从物理、化学、生物学到材料科学和工程等有前途的应用中的惊人现象。带电粒子间的长程静电相互作用是决定模型系统结构和状态的重要因素。如何有效地计算部分或全周期边界条件下模拟系统中的静电相互作用一直是一个具有挑战性的课题。在过去的几十年里，人们提出了多种计算方案，其中埃瓦尔德求和方法是准确处理模拟系统中带电粒子之间静电相互作用的最可靠途径。此外，已经做了大量的努力来提高基于Ewald求和的方法的计算效率。代表性的例子是基于截断、反应场、多极、多重网格和粒子网格方案的方法。我们概述了ENUF方法，这是基于非均匀快速傅立叶变换技术的Ewald求和方法的缩写，并在基于粒子的模拟软件包中实现了该方法，以计算微观和介观水平的静电能量和力。对聚电解质、树枝状聚合物-膜复合物和离子流体的构象性质的广泛计算研究表明，ENUF方法及其衍生物将能量和动量守恒到浮点精度，并表现出最佳物理参数的计算复杂性。这些ENUF为基础的方法是有吸引力的替代品，在分子模拟中，需要高精度和高效率的模拟方法，以加速在扩展的时空尺度上的静电相互作用的计算。
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in simulation systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes has been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions between charged particles in simulation systems. In addition, extensive efforts have been done to improve computational efficiencies of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi‐poles, multi‐grids, and particle‐mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on the nonuniform fast Fourier transform technique, and have implemented this method in particle‐based simulation packages to calculate electrostatic energies and forces at micro‐ and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer‐membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales.