An improved version of the Green's function molecular dynamics method

LT Kong and C Denniston and MH Muser, COMPUTER PHYSICS COMMUNICATIONS, 182, 540-541 (2011).

DOI: 10.1016/j.cpc.2010.10.006

This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campana and Maser, 2004 1,2), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Gamma-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Gamma (Kong, 2010 3) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summary Program title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL: Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, No. of lines in distributed program, including test data, etc.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS (, MPI (, FFT ( Catalogue identifier of previous version: AECW_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1004 Does the new version supersede the previous version?: Yes Nature of problem: Green's function molecular dynamics (GFMD) is a coarse-graining method that enables one to investigate the full elastic response of an interface between a semi-infinite solid and a contact while taking only the surface atoms in the solid into consideration. The effect of long-range elastic deformations on the surface atoms from the semi-infinite solid is replaced by effective elastic interactions, thus reducing the problem from three dimensions to two dimensions without compromising the physical essence of the problem.

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