Literature DB >> 29047123

Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations.

Yoshifumi Nishimura1, Hiromi Nakai1,2,3,4.   

Abstract

A low-computational-cost algorithm and its parallel implementation for periodic divide-and-conquer density-functional tight-binding (DC-DFTB) calculations are presented. The developed algorithm enables rapid computation of the interaction between atomic partial charges, which is the bottleneck for applications to large systems, by means of multipole- and interpolation-based approaches for long- and short-range contributions. The numerical errors of energy and forces with respect to the conventional Ewald-based technique can be under the control of the multipole expansion order, level of unit cell replication, and interpolation grid size. The parallel performance of four different evaluation schemes combining previous approaches and the proposed one are assessed using test calculations of a cubic water box on the K computer. The largest benchmark system consisted of 3,295,500 atoms. DC-DFTB energy and forces for this system were obtained in only a few minutes when the proposed algorithm was activated and parallelized over 16,000 nodes in the K computer. The high performance using a single node workstation was also confirmed. In addition to liquid water systems, the feasibility of the present method was examined by testing solid systems such as diamond form of carbon, face-centered cubic form of copper, and rock salt form of sodium chloride.
© 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Entities:  

Keywords:  density-functional tight-binding method; divide-and-conquer method; massively parallel calculation; multipole expansion; periodic boundary condition

Year:  2017        PMID: 29047123     DOI: 10.1002/jcc.25086

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  2 in total

1.  Reversible Sodium Metal Electrodes: Is Fluorine an Essential Interphasial Component?

Authors:  Kyosuke Doi; Yuki Yamada; Masaki Okoshi; Junichi Ono; Chien-Pin Chou; Hiromi Nakai; Atsuo Yamada
Journal:  Angew Chem Int Ed Engl       Date:  2019-05-14       Impact factor: 15.336

2.  Using Accelerated Molecular Dynamics Simulation to elucidate the effects of the T198F mutation on the molecular flexibility of the West Nile virus envelope protein.

Authors:  Renan Patrick da Penha Valente; Rafael Conceição de Souza; Gabriela de Medeiros Muniz; João Elias Vidueira Ferreira; Ricardo Morais de Miranda; Anderson Henrique Lima E Lima; João Lídio da Silva Gonçalves Vianez Junior
Journal:  Sci Rep       Date:  2020-06-15       Impact factor: 4.379

  2 in total

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