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Computational aspects of many-body potentials

Published online by Cambridge University Press:  09 May 2012

Steven J. Plimpton
Affiliation:
Sandia National Laboratories, Albuquerque, NM; email sjplimp@sandia.gov
Aidan P. Thompson
Affiliation:
Scalable Algorithms Department, Sandia National Laboratories, Albuquerque, NM; athomps@sandia.gov

Abstract

We discuss the relative complexity and computational cost of several popular many-body empirical potentials, developed by the materials science community over the past 30 years. The inclusion of more detailed many-body effects has come at a computational cost, but the cost still scales linearly with the number of atoms modeled. This is enabling very large molecular dynamics simulations with unprecedented atomic-scale fidelity to physical and chemical phenomena. The cost and scalability of the potentials, run in serial and parallel, are benchmarked in the LAMMPS molecular dynamics code. Several recent large calculations performed with these potentials are highlighted to illustrate what is now possible on current supercomputers. We conclude with a brief mention of high-performance computing architecture trends and the research issues they raise for continued potential development and use.

Information

Type
Research Article
Copyright
Copyright © Materials Research Society 2012
Figure 0

Table I. Many-body potentials.

Figure 1

Figure 1. Performance of eight many-body potentials and an SPC/E water potential on varying numbers of cores of a Cray XT5 machine, as implemented in LAMMPS.19 The red curves are for 32 K-atom systems; the green curves are for 1 M-atom systems; and the blue curves are for scaled systems with 32 K atoms per processor. Definitions of fixed-size and scaled-size parallel efficiency and the dotted line are discussed in the text. Single-core CPU times per-atom per-time step are listed in Table I. EAM, embedded-atom method; MEAM, modified embedded-atom method; REBO, reactive empirical bond-order; BOP, bond order potential; AIREBO, adaptive intermolecular REBO; ReaxFF, reactive force field; COMB, charge optimized many-body.

Figure 2

Figure 2. Single CPU cost in seconds per-atom per-time step versus year for the potentials of Table I (closed symbols) and others (open symbols). The line represents a doubling in computational cost every two years, akin to Moore’s Law for hardware complexity.19 EAM, embedded-atom method; MEAM, modified embedded-atom method; REBO, reactive empirical bond order; BOP, bond-order potential; AIREBO, adaptive intermolecular REBO; ReaxFF, reactive force field; COMB, charge optimized many-body; GAP, Gaussian approximation potential.

Figure 3

Figure 3. Tree structure of an 85 keV collision cascade in δ-Pu at 600 K, simulated with a modified embedded-atom method potential. The colors represent the kinetic energy of the atom; red = high, yellow = medium, green = low. Reprinted with permission from Reference 31. ©2007, Springer Science + Business Media.

Figure 4

Figure 4. Fracture of a bundle of carbon nanotubes (800 nm in length) undergoing tensile strain, simulated with the adaptive intermolecular reactive empirical bond-order potential. (a) A side view of a portion of the unstrained fiber; (b) an end view showing cross-links between fibers; and (c) after fracture occurs, with strain applied in the lateral direction. Reprinted with permission from Reference 32. ©2011, American Institute of Physics.

Figure 5

Figure 5. Ductile fracture of a polycrystalline sample (10 nm grains) of (a) pure Ni versus (b) brittle fracture of Ni with 20% S-doped (yellow atoms) grain boundary layers. (c) The bottom view of the pure Ni simulation is colored via the common neighborhood parameter34 to highlight defects (non-blue) appearing at different scales. Reprinted with permission from Reference 33. ©2010, American Physical Society.

Figure 6

Figure 6. Shock compression response of a low-density polymer foam,35 simulated using the reactive force field potential.14 (a) The initial 80-nm length foam sample and void structure. (b) A magnified view of the shock wave moving from left to right through the sample. The dark patches are locations where the voids connect to adjacent voids on the back side of the sample. Small molecular fragments are ejected into the void space ahead of the main shock front.