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Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Zheyong Fan, Wei Chen, Ville Vierimaa, Ari Harju
School of Mathematics and Physics, Bohai University, Jinzhou, China
arXiv:1610.03343 [physics.comp-ph], (11 Oct 2016)

@article{fan2016efficient,

   title={Efficient molecular dynamics simulations with many-body potentials on graphics processing units},

   author={Fan, Zheyong and Chen, Wei and Vierimaa, Ville and Harju, Ari},

   year={2016},

   month={oct},

   archivePrefix={"arXiv"},

   primaryClass={physics.comp-ph}

}

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Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently [Phys. Rev. B 92 (2015) 094301]. In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz) and the single-precision performance of GPUMD reaches $10^8$ atom * step / second.
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