Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation

被引:84
作者
Nishizawa, Hiroaki [1 ]
Nishimura, Yoshifumi [1 ,2 ]
Kobayashi, Masato [3 ,4 ,5 ]
Irle, Stephan [6 ,7 ]
Nakai, Hiromi [2 ,4 ,8 ,9 ]
机构
[1] Inst Mol Sci, Dept Theoret & Computat Mol Sci, Okazaki, Aichi 4448585, Japan
[2] Waseda Univ, Res Inst Sci & Engn, Tokyo 1698555, Japan
[3] Hokkaido Univ, Dept Chem, Fac Sci, Sapporo, Hokkaido 0600810, Japan
[4] Kyoto Univ, ESICB, Kyoto 6158520, Japan
[5] Japan Sci & Technol Agcy, PRESTO, Kawaguchi, Saitama 3320012, Japan
[6] Nagoya Univ, Dept Chem, Grad Sch Sci, Nagoya, Aichi 4648602, Japan
[7] Nagoya Univ, Inst Transformat Biomol WPI ITbM, Nagoya, Aichi 4648602, Japan
[8] Waseda Univ, Sch Adv Sci & Engn, Dept Chem & Biochem, Tokyo 1698555, Japan
[9] Japan Sci & Technol Agcy, CREST, Kawaguchi, Saitama 3320012, Japan
关键词
quantum mechanical molecular dynamics; linear-scaling divide-and-conquer method; density-functional tight-binding method; massively parallel computation; OPEN-SHELL SYSTEMS; ELECTRONIC-STRUCTURE CALCULATIONS; IMPLEMENTATION; FRAGMENTATION; ENERGY; FIELD; HYDROCARBONS; FRAMEWORK; WATER;
D O I
10.1002/jcc.24419
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. (c) 2016 Wiley Periodicals, Inc.
引用
收藏
页码:1983 / 1992
页数:10
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