Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex

doi:10.1016/j.jcp.2018.01.015

Title: Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

Journal Article · Fri Jan 12 00:00:00 EST 2018 · Journal of Computational Physics

DOI:https://doi.org/10.1016/j.jcp.2018.01.015· OSTI ID:1433659

^[1]; Zhang, Feng ^[2]; Wang, Cai-Zhuang ^[2]; Ho, Kai-Ming ^[1]; Travesset, Alex ^[1]

Iowa State Univ., Ames, IA (United States). Dept. of Physics; Ames Lab., Ames, IA (United States)
Ames Lab., Ames, IA (United States)

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 Ni₃Al. Our code scales well with the size of the simulating system 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.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Ames Lab., Ames, IA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-07CH11358

OSTI ID:: 1433659

Alternate ID(s):: OSTI ID: 1548813

Report Number(s):: IS-J-9610; PII: S0021999118300251; TRN: US1802809

Journal Information:: Journal of Computational Physics, Vol. 359, Issue C; ISSN 0021-9991

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 7 works

Citation information provided by
Web of Science

References (25)

Unified Approach for Molecular Dynamics and Density-Functional Theory Car, R.; Parrinello, M. Physical Review Letters, Vol. 55, Issue 22 https://doi.org/10.1103/PhysRevLett.55.2471	journal	November 1985
Ab initio molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium Kresse, G.; Hafner, J. Physical Review B, Vol. 49, Issue 20, p. 14251-14269 https://doi.org/10.1103/PhysRevB.49.14251	journal	May 1994
A simple empirical N -body potential for transition metals Finnis, M. W.; Sinclair, J. E. Philosophical Magazine A, Vol. 50, Issue 1 https://doi.org/10.1080/01418618408244210	journal	July 1984
Computer simulation of liquid metals Belashchenko, D. K. Physics-Uspekhi, Vol. 56, Issue 12 https://doi.org/10.3367/UFNe.0183.201312b.1281	journal	December 2013
Short-range structural signature of excess specific heat and fragility of metallic-glass-forming supercooled liquids Ding, Jun; Cheng, Yong-Qiang; Sheng, Hongwei Physical Review B, Vol. 85, Issue 6 https://doi.org/10.1103/PhysRevB.85.060201	journal	February 2012
Three decades of many-body potentials in materials research Sinnott, Susan B.; Brenner, Donald W. MRS Bulletin, Vol. 37, Issue 5 https://doi.org/10.1557/mrs.2012.88	journal	May 2012
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
GROMACS: A message-passing parallel molecular dynamics implementation Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00042-E	journal	September 1995
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
General purpose molecular dynamics simulations fully implemented on graphics processing units Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A. Journal of Computational Physics, Vol. 227, Issue 10 https://doi.org/10.1016/j.jcp.2008.01.047	journal	May 2008
A survey of computational molecular science using graphics processing units: Survey of computational molecular science on GPUs Harvey, M. J.; De Fabritiis, Gianni Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 5 https://doi.org/10.1002/wcms.1101	journal	April 2012
Strong scaling of general-purpose molecular dynamics simulations on GPUs Glaser, Jens; Nguyen, Trung Dac; Anderson, Joshua A. Computer Physics Communications, Vol. 192 https://doi.org/10.1016/j.cpc.2015.02.028	journal	July 2015
Scalable Metropolis Monte Carlo for simulation of hard shapes Anderson, Joshua A.; Eric Irrgang, M.; Glotzer, Sharon C. Computer Physics Communications, Vol. 204 https://doi.org/10.1016/j.cpc.2016.02.024	journal	July 2016
GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations Spellings, Matthew; Marson, Ryan L.; Anderson, Joshua A. Journal of Computational Physics, Vol. 334 https://doi.org/10.1016/j.jcp.2017.01.014	journal	April 2017
Probing the Statistical Validity of the Ductile-to-Brittle Transition in Metallic Nanowires Using GPU Computing French, William R.; Pervaje, Amulya K.; Santos, Andrew P. Journal of Chemical Theory and Computation, Vol. 9, Issue 12 https://doi.org/10.1021/ct400885z	journal	November 2013
Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs Morozov, I. V.; Kazennov, A. M.; Bystryi, R. G. Computer Physics Communications, Vol. 182, Issue 9 https://doi.org/10.1016/j.cpc.2010.12.026	journal	September 2011
Nosé–Hoover chains: The canonical ensemble via continuous dynamics Martyna, Glenn J.; Klein, Michael L.; Tuckerman, Mark The Journal of Chemical Physics, Vol. 97, Issue 4 https://doi.org/10.1063/1.463940	journal	August 1992
Glass Transition Temperatures of Polymers from Molecular Dynamics Simulations Han, Jie; Gee, Richard H.; Boyd, Richard H. Macromolecules, Vol. 27, Issue 26 https://doi.org/10.1021/ma00104a036	journal	December 1994
A Molecular Dynamics Approach for Predicting the Glass Transition Temperature and Plasticization Effect in Amorphous Pharmaceuticals Gupta, Jasmine; Nunes, Cletus; Jonnalagadda, Sriramakamal Molecular Pharmaceutics, Vol. 10, Issue 11 https://doi.org/10.1021/mp400118v	journal	October 2013
Bulk metallic glass formation in binary Cu-rich alloy series – Cu100−xZrx (x=34, 36, 38.2, 40 at.%) and mechanical properties of bulk Cu64Zr36 glass Xu, Donghua; Lohwongwatana, Boonrat; Duan, Gang Acta Materialia, Vol. 52, Issue 9 https://doi.org/10.1016/j.actamat.2004.02.009	journal	May 2004
Bulk metallic glass formation in the binary Cu–Zr system Wang, D.; Li, Y.; Sun, B. B. Applied Physics Letters, Vol. 84, Issue 20 https://doi.org/10.1063/1.1751219	journal	May 2004
Formation, Thermal Stability and Mechanical Properties of Cu-Zr and Cu-Hf Binary Glassy Alloy Rods Inoue, Akihisa; Zhang, Wei MATERIALS TRANSACTIONS, Vol. 45, Issue 2 https://doi.org/10.2320/matertrans.45.584	journal	January 2004
Development of suitable interatomic potentials for simulation of liquid and amorphous Cu–Zr alloys Mendelev, M. I.; Kramer, M. J.; Ott, R. T. Philosophical Magazine, Vol. 89, Issue 11 https://doi.org/10.1080/14786430902832773	journal	April 2009
Thermodynamic properties of Al, Ni, NiAl, and Ni3Al from first-principles calculations Wang, Y.; Liu, Z. -K.; Chen, L. -Q. Acta Materialia, Vol. 52, Issue 9 https://doi.org/10.1016/j.actamat.2004.02.014	journal	May 2004
Development of an interatomic potential for the Ni-Al system Purja Pun, G. P.; Mishin, Y. Philosophical Magazine, Vol. 89, Issue 34-36 https://doi.org/10.1080/14786430903258184	journal	December 2009

Cited By (1)

Classical molecular dynamics on graphics processing unit architectures Jász, Ádám; Rák, Ádám; Ladjánszki, István WIREs Computational Molecular Science, Vol. 10, Issue 2 https://doi.org/10.1002/wcms.1444	journal	August 2019