Reactive bond-order simulations using both spatial and temporal approaches to parallelism
SJ Stuart and Y Li and O Kum and JW Mintmire and AF Voter, STRUCTURAL CHEMISTRY, 15, 479-486 (2004).
We describe two different approaches to exploiting parallel computing architecture that have been used successfully for reactive molecular simulation using bond-order potentials. These potentials are based on the Tersoff bond-order formalism, and allow accurate treatement of covalent bonding reactions in the framework of a classical potential. They include both Brenner's reactive empirical bond order (REBO) potential and our adaptive intermolecular version of this potential (AIREBO). Traditional spatial and atom-based parallel decompositioon techniques have been employed in the RMD-CE program developed for parallel molecular dynamics simulations with a variety of reactive potentials. Key features of this implementation, including the object- oriented approach and novel algorithms for the integrator and neighbor lists, are discussed. The resulting code provides efficient scaling down to system sizes of 400 atoms per processor, and has been applied successfully to systems of as many as half a million atoms. For smaller systems, the parallel replica dynamics algorithm has been successfully applied to take advantage of parallelism in the time domain for rare- event systems. This approach takes advantage of the independence of different parts of a dynamics trajectory, and provides excellent parallel efficiencies for systems as small as tens of atoms, where other parallel simulation techniques are not applicable. This technique has been used to model the pyrolysis of hexadecane on the microsecond timescale, at more realistic temperatures than are achievable with other simulation methods.
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