Literature DB >> 22562950

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

Xavier Andrade1, Joseba Alberdi-Rodriguez, David A Strubbe, Micael J T Oliveira, Fernando Nogueira, Alberto Castro, Javier Muguerza, Agustin Arruabarrena, Steven G Louie, Alán Aspuru-Guzik, Angel Rubio, Miguel A L Marques.   

Abstract

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

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Year:  2012        PMID: 22562950     DOI: 10.1088/0953-8984/24/23/233202

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  13 in total

1.  Application of compressed sensing to the simulation of atomic systems.

Authors:  Xavier Andrade; Jacob N Sanders; Alán Aspuru-Guzik
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-13       Impact factor: 11.205

2.  Time-resolved spectroscopy in time-dependent density functional theory: an exact condition.

Authors:  Johanna I Fuks; Kai Luo; Ernesto D Sandoval; Neepa T Maitra
Journal:  Phys Rev Lett       Date:  2015-05-05       Impact factor: 9.161

3.  Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin.

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4.  Insights into colour-tuning of chlorophyll optical response in green plants.

Authors:  Joaquim Jornet-Somoza; Joseba Alberdi-Rodriguez; Bruce F Milne; Xavier Andrade; Miguel A L Marques; Fernando Nogueira; Micael J T Oliveira; James J P Stewart; Angel Rubio
Journal:  Phys Chem Chem Phys       Date:  2015-10-28       Impact factor: 3.676

5.  Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II.

Authors:  Muhamed Amin; Ashraf Badawi; S S Obayya
Journal:  Sci Rep       Date:  2016-11-09       Impact factor: 4.379

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Authors:  Brian E Conn; Aydar Atnagulov; Bokwon Yoon; Robert N Barnett; Uzi Landman; Terry P Bigioni
Journal:  Sci Adv       Date:  2016-11-25       Impact factor: 14.136

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Authors:  Alexander Ryabov; Iskander Akhatov; Petr Zhilyaev
Journal:  Sci Rep       Date:  2020-05-14       Impact factor: 4.379

8.  Photoinduced Electron Transfer in Donor-Acceptor Complexes: Isotope Effect and Dynamic Symmetry Breaking.

Authors:  Jan Paul Menzel; Huub J M de Groot; Francesco Buda
Journal:  J Phys Chem Lett       Date:  2019-10-11       Impact factor: 6.475

9.  Indirect to Direct Charge Transfer Transition in Plasmon-Enabled CO2 Photoreduction.

Authors:  Yimin Zhang; Lei Yan; Mengxue Guan; Daqiang Chen; Zhe Xu; Haizhong Guo; Shiqi Hu; Shengjie Zhang; Xinbao Liu; Zhengxiao Guo; Shunfang Li; Sheng Meng
Journal:  Adv Sci (Weinh)       Date:  2021-11-12       Impact factor: 16.806

10.  Extreme nonlinear strong-field photoemission from carbon nanotubes.

Authors:  Chi Li; Ke Chen; Mengxue Guan; Xiaowei Wang; Xu Zhou; Feng Zhai; Jiayu Dai; Zhenjun Li; Zhipei Sun; Sheng Meng; Kaihui Liu; Qing Dai
Journal:  Nat Commun       Date:  2019-10-25       Impact factor: 14.919

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