Gauss-Legendre-spherical-t (GLST) cubature-based factorization of long-range electrostatics in simulations.

IF 3.1 2区 化学 Q3 CHEMISTRY, PHYSICAL
Wonmuk Hwang, James E Gonzales, Bernard R Brooks
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Abstract

We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss-Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and treecode method, we utilize the Gauss-Legendre quadrature for integration over a finite range and spherical t-design for integration over a unit sphere. The resulting GLST cubature breaks the long-range interaction term into a sum of terms that can be calculated in parallel with minimal inter-processor communication. The simulation box is divided into cells that are grouped with a separate GLST cubature applied to each group, based on their distance from the atom or cell for which the long-range interaction is calculated. Periodic boundary conditions are handled at two levels: first by "wrapping-around" other cells about the cell under consideration, then by repeating the wrapped-around box over a pre-computed number of times to make the relative error of the calculated force meet the target accuracy. With its high granularity, tunable accuracy, and adaptability to different box geometries, the GLST method is suitable for the simulation of large systems on computer hardware where many cores or threads are available.

模拟中基于gauss - legende - sphere -t (GLST)模型的远程静电分解。
我们开发了一种高度并行的算法来计算远程静电相互作用,称为高斯-勒让德-球-t (GLST)培养法。在我们最近的球面网格和树码方法的激励下,我们利用高斯-勒让德正交在有限范围内进行积分,利用球面t设计在单位球面上进行积分。由此产生的GLST模型将远程交互项分解为一组项,这些项可以通过最小的处理器间通信并行计算。模拟盒被分成不同的单元,根据它们与计算远程相互作用的原子或单元的距离,对每一组应用单独的GLST培养。周期边界条件在两个层次上处理:首先通过“缠绕”所考虑的单元周围的其他单元,然后通过在预先计算的次数上重复缠绕的框,使计算力的相对误差满足目标精度。由于其高粒度、可调精度和对不同盒子几何形状的适应性,GLST方法适合在具有许多内核或线程的计算机硬件上模拟大型系统。
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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