skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

Publication Date:
Sponsoring Org.:
OSTI Identifier:
Grant/Contract Number:
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Volume: 212; Journal Issue: C; Related Information: CHORUS Timestamp: 2017-12-12 22:14:30; Journal ID: ISSN 0010-4655
Country of Publication:

Citation Formats

Nguyen, Trung Dac. GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations. Netherlands: N. p., 2017. Web. doi:10.1016/j.cpc.2016.10.020.
Nguyen, Trung Dac. GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations. Netherlands. doi:10.1016/j.cpc.2016.10.020.
Nguyen, Trung Dac. Wed . "GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations". Netherlands. doi:10.1016/j.cpc.2016.10.020.
title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
author = {Nguyen, Trung Dac},
abstractNote = {},
doi = {10.1016/j.cpc.2016.10.020},
journal = {Computer Physics Communications},
number = C,
volume = 212,
place = {Netherlands},
year = {Wed Mar 01 00:00:00 EST 2017},
month = {Wed Mar 01 00:00:00 EST 2017}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/j.cpc.2016.10.020

Citation Metrics:
Cited by: 3works
Citation information provided by
Web of Science

Save / Share:
  • Abstract not provided.
  • We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less
  • Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method ismore » a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.« less
  • A class of uniform pseudorandom number generators is proposed for modeling and simulations on massively parallel computers. The algorithm is simple, nonrecursive, and is easily transported to serial or vector computers. We have tested the procedure for uniformity, independence, and correlations by several methods. Related, less complex sequences passed some of these tests well enough; however, inadequacies were revealed by tests for correlations and in an interesting application, namely, annealing from an initial lattice that is mechanically unstable. In the latter case, initial velocities chosen by a random number generator that is not sufficiently random lead quickly to unphysical regularitymore » in grain structure. The new class of generators passes this dynamical diagnostic for unwanted correlations.« less