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

Show full item record



Permalink

http://hdl.handle.net/10138/307537

Citation

Fan , Z , Chen , W , Vierimaa , V & Harju , A 2017 , ' Efficient molecular dynamics simulations with many-body potentials on graphics processing units ' , Computer Physics Communications , vol. 218 , pp. 10-16 . https://doi.org/10.1016/j.cpc.2017.05.003

Title: Efficient molecular dynamics simulations with many-body potentials on graphics processing units
Author: Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari
Other contributor: University of Helsinki, Helsinki Institute of Physics
Date: 2017-09
Language: eng
Number of pages: 7
Belongs to series: Computer Physics Communications
ISSN: 0010-4655
DOI: https://doi.org/10.1016/j.cpc.2017.05.003
URI: http://hdl.handle.net/10138/307537
Abstract: 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 (Fan et al., 2015). 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). (C) 2017 Elsevier B.V. All rights reserved.
Subject: Molecular dynamics simulation
Many-body potential
Tersoff potential
Stillinger-Weber potential
Graphics processing units
Virial stress
Heat current
THERMAL-CONDUCTIVITY
PERFORMANCE
GPU
ORDER
IMPLEMENTATION
SYSTEMS
113 Computer and information sciences
114 Physical sciences
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
1610.03343.pdf 153.1Kb PDF View/Open

This item appears in the following Collection(s)

Show full item record