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

作者：Kong, Ling Ti^*; Denniston, Colin; Mueser, Martin H.

来源：Computer Physics Communications, 2011, 182(2): 540-541.

DOI：10.1016/j.cpc.2010.10.006

• Elastic stiffness coefficients
• Elastic Green's function
• Molecular dynamics simulation
• Acoustic sum rule

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: http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
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 (http://lammps.sandia.gov/), MPI (http://www.mcs.anl.gov/research/projects/mpi/), FFT (http://www.fftw.org/)
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.

• 出版日期2011-2
• 单位上海交通大学