Journal
COMPUTER PHYSICS COMMUNICATIONS
Volume 192, Issue -, Pages 91-96Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.cpc.2015.02.023
Keywords
Reactive molecular dynamics; Extended Lagrangian scheme; Parallel computing
Funding
- Department of Energy, Office of Science, Basic Energy Sciences, Materials Science and Engineering Division [DE-FG02-04ER-46130]
- National Science Foundation [1125317]
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [1125317] Funding Source: National Science Foundation
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Reactive molecular dynamics (RMD) simulations describe chemical reactions at orders-of-magnitude faster computing speed compared with quantum molecular dynamics (QMD) simulations. A major computational bottleneck of RMD is charge-equilibration (QEq) calculation to describe charge transfer between atoms. Here, we eliminate the speed-limiting iterative minimization of the Coulombic energy in QEq calculation by adapting an extended-Lagrangian scheme that was recently proposed in the context of QMD simulations, Souvatzis and Niklasson (2014). The resulting XRMD simulation code drastically improves energy conservation compared with our previous RMD code, Nomura et al. (2008), while substantially reducing the time-to-solution. The XRMD code has been implemented on parallel computers based on spatial decomposition, achieving a weak-scaling parallel efficiency of 0.977 on 786,432 IBM Blue Gene/Q cores for a 67.6 billion-atom system. (C) 2015 Elsevier B.V. All rights reserved.
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