**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:
http://cpc.cs.qub.ac.uk/summaries/AECW_v1_0.html 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
(http://www.fftw.org/). LAMMPS version May 21, 2008
(http://lammps.sandia.gov/) 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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