Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization

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• 作者：Chuanfu Luo ; Jens-Uwe Sommer
• 关键词：Molecular dynamics (MD) ; Coarse grained polymer model ; LAMMPS ; Polymer crystallization ; Parallel computing
• 刊名：Computer Physics Communications
• 出版年：2009
• 出版时间：August 2009
• 年：2009
• 卷：180
• 期：8
• 页码：1382-1391
• 全文大小：1572 K

文摘

We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations.

This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations.

Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters.

Program summary

Program title: lammps-cgpva

Catalogue identifier: AEDE_v1_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html

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

Licensing provisions: GNU's GPL

No. of lines in distributed program, including test data, etc.: 940 798

No. of bytes in distributed program, including test data, etc.: 12 536 245

Distribution format: tar.gz

Programming language: C++/MPI

Computer: Tested on Intel-x86 and AMD64 architectures. Should run on any architecture providing a C++ compiler

Operating system: Tested under Linux. Any other OS with C++ compiler and MPI library should suffice

Has the code been vectorized or parallelized?: Yes

RAM: Depends on system size and how many CPUs are used

Classification: 7.7

External routines: LAMMPS (http://lammps.sandia.gov/), FFTW (http://www.fftw.org/)

Nature of problem: Implementing special tabular angle potentials and Lennard-Jones-9-6 style interactions of a coarse grained polymer model for LAMMPS code.

Solution method: Cubic spline interpolation of input tabulated angle potential data.

Restrictions: The code is based on a former version of LAMMPS.

Unusual features.: Any special angular potential can be used if it can be tabulated.

Running time: Seconds to weeks, depending on system size, speed of CPU and how many CPUs are used. The test run provided with the package takes about 5 minutes on 4 AMD's opteron (2.6 GHz) CPUs.

References:

[1] D. Reith, H. Meyer, F. Müller-Plathe, Macromolecules 34 (2001) 2335–2345.

[2] H. Meyer, F. Müller-Plathe, J. Chem. Phys. 115 (2001) 7807.

[3] H. Meyer, F. Müller-Plathe, Macromolecules 35 (2002) 1241–1252.