TeraChem: A graphical processing unit‐accelerated electronic structure package for large‐scale ab initio molecular dynamics,Wiley Interdisciplinary Reviews: Computational Molecular Science

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TeraChem: A graphical processing unit‐accelerated electronic structure package for large‐scale ab initio molecular dynamics
Wiley Interdisciplinary Reviews: Computational Molecular Science ( IF 16.8 ) Pub Date : 2020-07-26 , DOI: 10.1002/wcms.1494
Stefan Seritan _{1,

2} , Christoph Bannwarth _{1,

2} , Bryan S. Fales _{1,

2} , Edward G. Hohenstein _{1,

2} , Christine M. Isborn ₃ , Sara I. L. Kokkila‐Schumacher ₄ , Xin Li ₅ , Fang Liu ₆ , Nathan Luehr ₇ , James W. Snyder ₈ , Chenchen Song _{9,

10} , Alexey V. Titov ₁₁ , Ivan S. Ufimtsev ₁₂ , Lee‐Ping Wang ₁₃ , Todd J. Martínez _{1,

2}

Affiliation

Department of Chemistry and the PULSE InstituteStanford University Stanford California USA
SLAC National Accelerator Laboratory Menlo Park California USA
Department of ChemistryUniversity of California Merced Merced California USA
IBM Thomas J. Watson Research Center Yorktown Heights New York USA
Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of Technology Stockholm Sweden
Department of Chemical EngineeringMassachusetts Institute of Technology Cambridge Massachusetts USA
NVIDIA Santa Clara California USA
Adobe San Jose California USA
Department of PhysicsUniversity of California Berkeley Berkeley California USA
Molecular FoundryLawrence Berkeley National Laboratory Berkeley California USA
Intel Corporation Santa Clara California USA
Department of Structural BiologyStanford University School of Medicine Stanford California USA
Department of ChemistryUniversity of California Davis Davis California USA

TeraChem was born in 2008 with the goal of providing fast on‐the‐fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low‐cost parallel computer architecture that became more accessible for general‐purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large‐scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large‐scale nonadiabatic dynamics simulations.

中文翻译：

TeraChem：用于大规模从头算分子动力学的图形处理单元加速电子结构包

TeraChem于2008年诞生，其目标是提供快速的实时电子结构计算，以促进大型生物化学系统（如可光转换蛋白和多发色天线复合体）的从头算分子动力学研究。图形处理单元（GPU）最初是为视频游戏应用开发的，它提供了一种低成本的并行计算机体系结构，随着CUDA于2007年发布，通用的GPU计算变得更加易于使用。电子斥力积分（ERI）的评估是一项艰巨的任务。电子结构代码的主要瓶颈，并为GPU的加速提供了有吸引力的目标。因此，在TeraChem中实施了用于评估ERI和密度矩阵以及在其之间收缩的高效程序。开发并实施了电子结构方法以利用这些积分收缩程序，从而产生了第一个专为GPU设计的量子化学软件包。GPU的这种加速使TeraChem能够在气相和冷凝相中执行大规模的基态和激发态计算。如今，TeraChem的速度已成为一系列量子化学应用程序的基础，包括蛋白质的优化和动力学，自动化和交互式化学发现工具以及大规模非绝热动力学模拟。

更新日期：2020-07-26

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