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

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

doi:10.1016/j.jcp.2018.01.015

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

Lin Yang, Feng Zhang^*, Cai Zhuang Wang, Kai Ming Ho, Alex Travesset

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

Abstract

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 g(r) 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. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

Original language	English
Pages (from-to)	352-360
Number of pages	9
Journal	Journal of Computational Physics
Volume	359
DOIs	https://doi.org/10.1016/j.jcp.2018.01.015
Publication status	Published - 15 Apr 2018
Externally published	Yes

Keywords

Embedded atom method
GPU computing
Metallic system simulation
Molecular dynamics

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Yang, L., Zhang, F., Wang, C. Z., Ho, K. M., & Travesset, A. (2018). Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software. Journal of Computational Physics, 359, 352-360. https://doi.org/10.1016/j.jcp.2018.01.015

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

abstract = "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 Cu64.5Zr35.5, and pair correlation function g(r) 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. The source code can be accessed through the HOOMD-blue web page for free by any interested user.",

keywords = "Embedded atom method, GPU computing, Metallic system simulation, Molecular dynamics",

author = "Lin Yang and Feng Zhang and Wang, {Cai Zhuang} and Ho, {Kai Ming} and Alex Travesset",

note = "Publisher Copyright: {\textcopyright} 2018",

year = "2018",

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doi = "10.1016/j.jcp.2018.01.015",

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T2 - A GPU-accelerated molecular dynamics software

AU - Yang, Lin

AU - Zhang, Feng

AU - Wang, Cai Zhuang

AU - Ho, Kai Ming

AU - Travesset, Alex

PY - 2018/4/15

Y1 - 2018/4/15

N2 - 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 Cu64.5Zr35.5, and pair correlation function g(r) 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. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

AB - 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 Cu64.5Zr35.5, and pair correlation function g(r) 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. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

KW - Embedded atom method

KW - GPU computing

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ER -

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

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Keywords

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