We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.
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14 May 2014
Research Article|
March 28 2014
A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations
Fuyuki Shimojo;
Fuyuki Shimojo
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
2Department of Physics,
Kumamoto University
, Kumamoto 860-8555, Japan
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Shinnosuke Hattori;
Shinnosuke Hattori
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
2Department of Physics,
Kumamoto University
, Kumamoto 860-8555, Japan
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Rajiv K. Kalia;
Rajiv K. Kalia
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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Manaschai Kunaseth;
Manaschai Kunaseth
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
3
National Nanotechnology Center
, Pathumthani 12120, Thailand
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Weiwei Mou;
Weiwei Mou
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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Aiichiro Nakano;
Aiichiro Nakano
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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Ken-ichi Nomura;
Ken-ichi Nomura
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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Satoshi Ohmura;
Satoshi Ohmura
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
2Department of Physics,
Kumamoto University
, Kumamoto 860-8555, Japan
4Department of Physics,
Kyoto University
, Kyoto 606-8502, Japan
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Pankaj Rajak;
Pankaj Rajak
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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Kohei Shimamura;
Kohei Shimamura
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
2Department of Physics,
Kumamoto University
, Kumamoto 860-8555, Japan
5Department of Applied Quantum Physics and Nuclear Engineering,
Kyushu University
, Fukuoka 819-0395, Japan
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Priya Vashishta
Priya Vashishta
1Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science,
University of Southern California
, Los Angeles, California 90089-0242, USA
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J. Chem. Phys. 140, 18A529 (2014)
Article history
Received:
November 25 2013
Accepted:
March 12 2014
Citation
Fuyuki Shimojo, Shinnosuke Hattori, Rajiv K. Kalia, Manaschai Kunaseth, Weiwei Mou, Aiichiro Nakano, Ken-ichi Nomura, Satoshi Ohmura, Pankaj Rajak, Kohei Shimamura, Priya Vashishta; A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations. J. Chem. Phys. 14 May 2014; 140 (18): 18A529. https://doi.org/10.1063/1.4869342
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