An analytical benchmark and a Mathematica program for MD codes: Testing LAMMPS on the 2nd generation Brenner potential

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• 作者：Antonino Favata^a ; ^{antonino.favata@uniroma1.it" class="auth_mail" title="E-mail the corresponding author} ; Andrea Micheletti^b ; Seunghwa Ryu^c ; Nicola M. Pugno^d ; ^e ; ^f
• 关键词：REBO potentials ; 2nd generation Brenner potential ; LAMMPS ; Benchmark ; Carbon nanotubes
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：October 2016
• 年：2016
• 卷：207
• 期：Complete
• 页码：426-431
• 全文大小：413 K

文摘

An analytical benchmark and a simple consistent Mathematica program are proposed for graphene and carbon nanotubes, that may serve to test any molecular dynamics code implemented with REBO potentials. By exploiting the benchmark, we checked results produced by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) when adopting the second generation Brenner potential, we made evident that this code in its current implementation produces results which are offset from those of the benchmark by a significant amount, and provide evidence of the reason.

Program summary

Program title: MDBenchmarks

Catalogue identifier: AFAS_v1_0

Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAS_v1_0.html

Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland

Licensing provisions: GNU GPL v3

No. of lines in distributed program, including test data, etc.: 22854

No. of bytes in distributed program, including test data, etc.: 369171

Distribution format: tar.gz

Programming language: Mathematica 9.

Computer: Any PC.

Operating system: Any which supports Mathematica; tested under OS Yosemite.

RAM:  <$<$5 gigabytes

Classification: 7.7, 16.1, 16.13.

Nature of problem: Testing commercial or open-source molecular dynamics codes implementing off-the-shelf REBO potentials on an analytical benchmark.

Solution method: Analytical equilibrium conditions for achiral carbon nanotubes are implemented and solved, delivering benchmark values for the corresponding natural radius and cohesive energy; material properties (Young’s modulus and Poisson coefficient) are also computed.

Running time: Instantaneous, or a few seconds, depending on computer hardware