Acceleration of environmental electrostatic potential using cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method

Yoshio Okiyama; Tatsuya Nakano; Chiduru Watanabe; Kaori Fukuzawa; Yuto Komeiji; Katsunori Segawa; Yuji Mochizuki

doi:10.1246/BCSJ.20200227

Acceleration of environmental electrostatic potential using cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki

Research output: Contribution to journal › Article › peer-review

Abstract

The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer electrostatic potential (dimer-es). These approximations were previously implemented by introducing the Cholesky decomposition with adaptive metric (CDAM) method to the FMO (Okiyama et al., Chem. Phys. Lett. 2010, 490, 84). In this study, a distributed memory algorithm of CDAM was introduced to reduce the necessary memory size. The improved version of CDAM was applied to the ESP approximation and was shown to give sufficiently precise energy values while halving the calculation time.

Original language	English
Pages (from-to)	91-96
Number of pages	6
Journal	Bulletin of the Chemical Society of Japan
Volume	94
Issue number	1
DOIs	https://doi.org/10.1246/BCSJ.20200227
Publication status	Published - 2021
Externally published	Yes

Keywords

CDAM
ESP approximation
FMO

ASJC Scopus subject areas

Chemistry(all)

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10.1246/BCSJ.20200227

Cite this

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title = "Acceleration of environmental electrostatic potential using cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method",

abstract = "The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer electrostatic potential (dimer-es). These approximations were previously implemented by introducing the Cholesky decomposition with adaptive metric (CDAM) method to the FMO (Okiyama et al., Chem. Phys. Lett. 2010, 490, 84). In this study, a distributed memory algorithm of CDAM was introduced to reduce the necessary memory size. The improved version of CDAM was applied to the ESP approximation and was shown to give sufficiently precise energy values while halving the calculation time.",

keywords = "CDAM, ESP approximation, FMO",

author = "Yoshio Okiyama and Tatsuya Nakano and Chiduru Watanabe and Kaori Fukuzawa and Yuto Komeiji and Katsunori Segawa and Yuji Mochizuki",

note = "Funding Information: This work was partially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) as a social and scientific priority issue #6 (Accelerated Development of Innovative Clean Energy Systems) to be tackled using post-K computer (“Fugaku”). Additional support was provided by Grant-in-Aid for Scientific Research (Kakenhi-JP16H04635 and JP19K12010), AMED-BINDS (Grant Number JP19am0101113) and the Rikkyo SFR. Publisher Copyright: {\textcopyright} 2021 The Chemical Society of Japan.",

year = "2021",

doi = "10.1246/BCSJ.20200227",

language = "English",

volume = "94",

pages = "91--96",

journal = "Bulletin of the Chemical Society of Japan",

issn = "0009-2673",

publisher = "Chemical Society of Japan",

number = "1",

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TY - JOUR

T1 - Acceleration of environmental electrostatic potential using cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method

AU - Okiyama, Yoshio

AU - Nakano, Tatsuya

AU - Watanabe, Chiduru

AU - Fukuzawa, Kaori

AU - Komeiji, Yuto

AU - Segawa, Katsunori

AU - Mochizuki, Yuji

N1 - Funding Information: This work was partially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) as a social and scientific priority issue #6 (Accelerated Development of Innovative Clean Energy Systems) to be tackled using post-K computer (“Fugaku”). Additional support was provided by Grant-in-Aid for Scientific Research (Kakenhi-JP16H04635 and JP19K12010), AMED-BINDS (Grant Number JP19am0101113) and the Rikkyo SFR. Publisher Copyright: © 2021 The Chemical Society of Japan.

PY - 2021

Y1 - 2021

N2 - The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer electrostatic potential (dimer-es). These approximations were previously implemented by introducing the Cholesky decomposition with adaptive metric (CDAM) method to the FMO (Okiyama et al., Chem. Phys. Lett. 2010, 490, 84). In this study, a distributed memory algorithm of CDAM was introduced to reduce the necessary memory size. The improved version of CDAM was applied to the ESP approximation and was shown to give sufficiently precise energy values while halving the calculation time.

AB - The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer electrostatic potential (dimer-es). These approximations were previously implemented by introducing the Cholesky decomposition with adaptive metric (CDAM) method to the FMO (Okiyama et al., Chem. Phys. Lett. 2010, 490, 84). In this study, a distributed memory algorithm of CDAM was introduced to reduce the necessary memory size. The improved version of CDAM was applied to the ESP approximation and was shown to give sufficiently precise energy values while halving the calculation time.

KW - CDAM

KW - ESP approximation

KW - FMO

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VL - 94

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EP - 96

JO - Bulletin of the Chemical Society of Japan

JF - Bulletin of the Chemical Society of Japan

IS - 1

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Acceleration of environmental electrostatic potential using cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method

Abstract

Keywords

ASJC Scopus subject areas

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