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

• Published in: Computer physics communications Vol. 218; pp. 10 - 16
• Main Authors: Fan, Zheyong, Chen, Wei, Vierimaa, Ville, Harju, Ari
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.09.2017
• Subjects: Graphics processing units; Heat current; Many-body potential; Molecular dynamics simulation; Stillinger–Weber potential; Tersoff potential; Virial stress; Heat current; Tersoff potential; Many-body potential; Graphics processing units; Stillinger–Weber potential; Molecular dynamics simulation; Virial stress
• ISSN: 0010-4655; 1879-2944
• DOI: 10.1016/j.cpc.2017.05.003

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).