使用 Tamm-Dancoff 近似和范围分离混合函数的超大规模 GPU 加速时变密度泛函理论的核梯度。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI:10.1021/acs.jctc.4c01003
Inkoo Kim, Daun Jeong, Leah P Weisburn, Alexandra Alexiu, Troy Van Voorhis, Young Min Rhee, Won-Joon Son, Hyung-Jin Kim, Jinkyu Yim, Sungmin Kim, Yeonchoo Cho, Inkook Jang, Seungmin Lee, Dae Sin Kim
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引用次数: 0

摘要

现代图形处理器(GPU)提供了前所未有的计算能力。在本研究中,我们采用塔姆-丹可夫近似(TDA)和高斯型原子轨道作为基函数,介绍了 Kohn-Sham 时变密度泛函理论(TDDFT)分析核梯度的高性能多 GPU 实现。我们讨论了在量程分离方案中电子斥力积分和交换相关函数导数的 GPU 高效算法。作为一个示例,我们在ωB97X/def2-SVP 理论水平上计算了带有明确水溶液分子(共 4353 个原子)的全尺度绿色荧光蛋白 S1 态的 TDA-TDDFT 梯度。我们的算法在配备256个Nvidia A100 GPU的高速分布式系统上显示出良好的并行效率,最多64个GPU的并行效率大于70%,256个GPU的并行效率为31%,有效地利用了现代高性能计算系统的能力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals.

Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals.

Modern graphics processing units (GPUs) provide an unprecedented level of computing power. In this study, we present a high-performance, multi-GPU implementation of the analytical nuclear gradient for Kohn-Sham time-dependent density functional theory (TDDFT), employing the Tamm-Dancoff approximation (TDA) and Gaussian-type atomic orbitals as basis functions. We discuss GPU-efficient algorithms for the derivatives of electron repulsion integrals and exchange-correlation functionals within the range-separated scheme. As an illustrative example, we calculate the TDA-TDDFT gradient of the S1 state of a full-scale green fluorescent protein with explicit water solvent molecules, totaling 4353 atoms, at the ωB97X/def2-SVP level of theory. Our algorithm demonstrates favorable parallel efficiencies on a high-speed distributed system equipped with 256 Nvidia A100 GPUs, achieving >70% with up to 64 GPUs and 31% with 256 GPUs, effectively leveraging the capabilities of modern high-performance computing systems.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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