DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.
DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.
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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。
DOI：
10.1021/acs.jctc.7b01274
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发表时间：
2018
影响因子：
5.5
通讯作者：
Chris
中科院分区：
文献类型：
--
作者：
J. C. Womack;L. Anton;J. Dziedzic;P. Hasnip;Matt Probert;Chris
泊松方程的求解是电子结构计算中的关键步骤，产生静电势——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高使得在复杂环境中模拟扩展系统的电子结构成为可能。这需要求解更复杂的泊松方程变体，具有非均匀介电常数、具有非线性依赖性的离子浓度以及不同的边界条件。通常用于求解真空（或均匀介电常数）泊松方程的解析解不适用于这些情况，必须使用数值方法。在这项工作中，我们提出了 DL_MG，一个灵活、可扩展且准确的求解器库，专门为解决并行计算机上现代大规模电子结构计算中求解泊松方程的挑战而开发。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准确性。使用两个化学相关的模型系统，我们测试了 DL_MG 在求解广义泊松和泊松-玻尔兹曼方程时的准确性和计算性能，证明了与解析解的良好一致性，并有效扩展到约 109 个未知数和 100 个 CPU 内核。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 线性缩放电子结构包来研究具有常规可用计算资源的 2615 个原子蛋白质-配体复合物。在这些计算中，DL_MG 的总体执行时间并不比使用传统的基于 FFT 的求解器进行计算所需的时间长很多。
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 ∼109 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.
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影响因子：
5.5
作者：
Stefan Ringe;H. Oberhofer;C. Hille;S. Matera;K. Reuter
通讯作者：
Stefan Ringe;H. Oberhofer;C. Hille;S. Matera;K. Reuter
影响因子：
5.5
作者：
Karl A. Wilkinson;N. Hine;Chris-Kriton Skylaris
通讯作者：
Karl A. Wilkinson;N. Hine;Chris-Kriton Skylaris
影响因子：
5.5
作者：
Parrish RM;Burns LA;Smith DGA;Simmonett AC;DePrince AE 3rd;Hohenstein EG;Bozkaya U;Sokolov AY;Di Remigio R;Richard RM;Gonthier JF;James AM;McAlexander HR;Kumar A;Saitow M;Wang X;Pritchard BP;Verma P;Schaefer HF 3rd;Patkowski K;King RA;Valeev EF;Evangelista FA;Turney JM;Crawford TD;Sherrill CD
通讯作者：
Sherrill CD
影响因子：
4.4
作者：
Hine, Nicholas D. M.;Dziedzic, Jacek;Skylaris, Chris-Kriton
通讯作者：
Skylaris, Chris-Kriton