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Parallel algorithms for hyperdynamics and local hyperdynamics
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DOI：10.1063/5.0014448.png)
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Abstract
En 中文
Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In the work of Kim et al. [J. Chem. Phys. 139, 144110 (2013)], a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. Here, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost of 2-4x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of the Pt(100) surface for 80 mu s and 160 mu s.
Keywords:
ACCELERATED MOLECULAR-DYNAMICS
MARKOV STATE MODELS
REPLICA DYNAMICS
TIME-SCALE
SIMULATION
DIFFUSION
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