Implementation of Green's function molecular dynamics: An extension to LAMMPS

LT Kong and G Bartels and C Campana and C Denniston and MH Muser, COMPUTER PHYSICS COMMUNICATIONS, 180, 1004-1010 (2009).

DOI: 10.1016/j.cpc.2008.12.035

The Green's function molecular dynamics method, which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only the surface atoms, was implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. This was done in the style of fixes. The first fix, FixGFC, measures the elastic stiffness coefficients for a (small) solid block of a given material by making use of the fluctuation-dissipation theorem. With the help of the second fix, FixGFMD, the coefficients obtained from FixGFC can then be used to compute the elastic forces for a (large) block of the same material. Both fixes are designed to be run in parallel and to exploit the functions provided by LAMMPS. Program summary Program title: FixGFC/FixGFMD Catalogue identifier: AECW_v1_0 Program summary URL: Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 33 469 No. of bytes in distributed program, including test data, etc.: 1383631 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Parallelized via MPI RAM: Depends on the problem Classification: 7.7 External routines: MPI, FFTW 2.1.5 ( LAMMPS version May 21, 2008 ( Nature of problem: Using molecular dynamics to study elastically deforming solids imposes very high computational costs because portions of the solid far away from the interface or contact points need to be included in the simulation to reproduce the effects of long-range elastic deformations. Green's function molecular dynamics (GFMD) incorporates the full elastic response of semi-infinite solids so that only surface atoms have to be considered in molecular dynamics simulations, thus reducing the problem from three dimensions to two dimensions without compromising the physical essence of the problem. Solution method: See "Nature of problem". Restrictions: The mean equilibrium positions of the GFMD surface atoms must be in a plane and be periodic in the plane, so that the Born-von Karman boundary condition can be used. In addition, only deformation within the harmonic regime is expected in the surface layer during Green's function molecular dynamics. Running time: FixGFC varies from minutes to days, depending on the system size, the numbers of processors used, and the complexity of the force field. FixGFMD varies from seconds to days depending on the system size and numbers of processors used. References: 1 C. Campana, M.H. Muser, Phys. Rev. B 74 (2006) 075420. (C) 2008 Elsevier B.V. All rights reserved.

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