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DL_MG:用于真空和溶液中电子结构计算的并行多重网格泊松和泊松-玻尔兹曼求解器

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

作者信息

Womack James C, Anton Lucian, Dziedzic Jacek, Hasnip Phil J, Probert Matt I J, Skylaris Chris-Kriton

机构信息

Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.

Cray U.K. Ltd. , Broad Quay House, Prince Street , Bristol BS1 4DJ , United Kingdom.

出版信息

J Chem Theory Comput. 2018 Mar 13;14(3):1412-1432. doi: 10.1021/acs.jctc.7b01274. Epub 2018 Mar 2.

DOI:10.1021/acs.jctc.7b01274
PMID:29447447
Abstract

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.

摘要

泊松方程的求解是电子结构计算中的关键步骤,它能得出静电势——这是量子力学哈密顿量的关键组成部分。近几十年来,理论的进步和计算机性能的提升使得在复杂环境中模拟扩展系统的电子结构成为可能。这就需要求解更复杂的泊松方程变体,这些变体具有非均匀介电常数、非线性依赖的离子浓度以及多样的边界条件。通常用于求解真空(或具有均匀介电常数)中泊松方程的解析解在这些情况下并不适用,必须使用数值方法。在这项工作中,我们展示了DL_MG,这是一个灵活、可扩展且精确的求解器库,专门为应对在并行计算机上进行现代大规模电子结构计算时求解泊松方程所面临的挑战而开发。我们的求解器基于多重网格方法,并使用迭代高阶缺陷校正方法来提高解的精度。使用两个与化学相关的模型系统,我们测试了DL_MG在求解广义泊松方程和泊松 - 玻尔兹曼方程时的准确性和计算性能,结果表明它与解析解高度吻合,并且能够高效扩展到约10个未知数和100多个CPU核心。我们还将DL_MG应用于实际的大规模电子结构计算中,使用ONETEP线性缩放电子结构软件包,利用常规可用的计算资源研究了一个包含2615个原子的蛋白质 - 配体复合物。在这些计算中,使用DL_MG的总体执行时间并不显著长于使用传统基于快速傅里叶变换(FFT)的求解器所需的时间。

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