Efficient and scalable electrostatics via spherical grids and treecode summation.

IF 3.1 2区 化学 Q3 CHEMISTRY, PHYSICAL
Andrew C Simmonett, Bernard R Brooks, Thomas A Darden
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引用次数: 0

Abstract

Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self-consistent field calculations. These difficulties are a result of the Coulomb operator's slow decay, which necessitates the evaluation of large numbers of interactions. In this work, we use a combination of cubature techniques to factorize the Coulomb operator and devise a hierarchical summation scheme, arriving at a novel technique that requires O(N⁡log(N)) effort to evaluate electrostatic interactions. The factorization may be made arbitrarily accurate, allowing full control between computational expense and accuracy. By avoiding the fast Fourier transform to evaluate terms, the resulting algorithm bears a resemblance to that of the fast multipole method and offers many opportunities for highly scalable parallel implementations.

高效和可扩展的静电通过球面网格和树码求和。
非共价静电相互作用的评估是经典分子动力学模拟的主要瓶颈,库仑矩阵元素的评估同样限制了量子力学自洽场的计算。这些困难是由于库仑算符的缓慢衰减造成的,这就需要对大量的相互作用进行评估。在这项工作中,我们结合了培养技术来分解库仑算子,并设计了一个分层求和方案,得到了一种新的技术,需要O(N N log(N))的努力来评估静电相互作用。因式分解可以精确到任意程度,从而可以完全控制计算费用和精度。通过避免快速傅里叶变换来评估项,所得算法与快速多极方法相似,并为高度可扩展的并行实现提供了许多机会。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Chemical Physics
Journal of Chemical Physics 物理-物理:原子、分子和化学物理
CiteScore
7.40
自引率
15.90%
发文量
1615
审稿时长
2 months
期刊介绍: The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance. Topical coverage includes: Theoretical Methods and Algorithms Advanced Experimental Techniques Atoms, Molecules, and Clusters Liquids, Glasses, and Crystals Surfaces, Interfaces, and Materials Polymers and Soft Matter Biological Molecules and Networks.
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