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

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 lar...

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Published in:	Journal of computational chemistry Vol. 37; no. 21; pp. 1983 - 1992
Main Authors:	Nishizawa, Hiroaki, Nishimura, Yoshifumi, Kobayashi, Masato, Irle, Stephan, Nakai, Hiromi
Format:	Journal Article
Language:	English
Published:	United States Blackwell Publishing Ltd 05.08.2016 Wiley Subscription Services, Inc
Subjects:	Chemical reactions Computer simulation density-functional tight-binding method Geometry Interpolation linear-scaling divide-and-conquer method massively parallel computation Optimization algorithms quantum mechanical molecular dynamics Quantum theory quantum mechanical molecular dynamics density-functional tight-binding method massively parallel computation linear-scaling divide-and-conquer method
ISSN:	0192-8651, 1096-987X, 1096-987X
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Abstract	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. © 2016 Wiley Periodicals, Inc. 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 called DC‐DFTB‐K that can be routinely applied to on‐the‐fly molecular reaction dynamics simulations of large systems. Numerical tests based on calculations of water clusters in a cubic box show a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer.
AbstractList	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. 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. © 2016 Wiley Periodicals, Inc. 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. © 2016 Wiley Periodicals, Inc.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. © 2016 Wiley Periodicals, Inc. 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. © 2016 Wiley Periodicals, Inc. 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 called DC‐DFTB‐K that can be routinely applied to on‐the‐fly molecular reaction dynamics simulations of large systems. Numerical tests based on calculations of water clusters in a cubic box show a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer.
Author	Irle, Stephan Nakai, Hiromi Kobayashi, Masato Nishimura, Yoshifumi Nishizawa, Hiroaki
Author_xml	– sequence: 1 givenname: Hiroaki surname: Nishizawa fullname: Nishizawa, Hiroaki organization: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 444-8585, Okazaki, Japan – sequence: 2 givenname: Yoshifumi surname: Nishimura fullname: Nishimura, Yoshifumi organization: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 444-8585, Okazaki, Japan – sequence: 3 givenname: Masato surname: Kobayashi fullname: Kobayashi, Masato organization: Department of Chemistry, Faculty of Science, Hokkaido University, 060-0810, Sapporo, Japan – sequence: 4 givenname: Stephan surname: Irle fullname: Irle, Stephan organization: Department of Chemistry, Graduate School of Science, and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, 464-8602, Nagoya, Japan – sequence: 5 givenname: Hiromi surname: Nakai fullname: Nakai, Hiromi email: nakai@waseda.jp organization: Research Institute for Science and Engineering, Waseda University, 169-8555, Tokyo, Japan
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Snippet	The linear‐scaling divide‐and‐conquer (DC) quantum chemical methodology is applied to the density‐functional tight‐binding (DFTB) theory to develop a massively... The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively...
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StartPage	1983
SubjectTerms	Chemical reactions Computer simulation density-functional tight-binding method Geometry Interpolation linear-scaling divide-and-conquer method massively parallel computation Optimization algorithms quantum mechanical molecular dynamics Quantum theory
Title	Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation
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Volume	37
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