Numerical distortion and effects of thermostat in molecular dynamics simulations of single-walled carbon nanotubes
Li Rui (李 瑞)a, Hu Yuan-Zhong (胡元中)a, Wang Hui (王 慧)a, Zhang Yu-Jun (张宇军)b
aState Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China; bAdvanced Technology Institute of Technology Center, Baoshan Iron & Steel Co., Ltd., Shanghai 201900, China
Abstract In this paper, single-walled carbon nanotubes (SWCNTs) are studied through molecular dynamics (MD) simulation. The simulations are performed at temperatures of 1 and 300 K separately, with atomic interactions characterized by the second Reactive Empirical Bond Order (REBO) potential, and temperature controlled by a certain thermostat, i.e. by separately using the velocity scaling, the Berendsen scheme, the Nose--Hoover scheme, and the generalized Langevin scheme. Results for a (5,5) SWCNT with a length of 24.5 nm show apparent distortions in nanotube configuration, which can further enter into periodic vibrations, except in simulations using the generalized Langevin thermostat, which is ascribed to periodic boundary conditions used in simulation. The periodic boundary conditions may implicitly be applied in the form of an inconsistent constraint along the axis of the nanotube. The combination of the inconsistent constraint with the cumulative errors in calculation causes the distortions of nanotubes. When the generalized Langevin thermostat is applied, inconsistently distributed errors are dispersed by the random forces, and so the distortions and vibrations disappear. This speculation is confirmed by simulation in the case without periodic boundary conditions, where no apparent distortion and vibration occur. It is also revealed that numerically induced distortions and vibrations occur only in simulation of nanotubes with a small diameter and a large length-to-diameter ratio. When MD simulation is applied to a system with a particular geometry, attention should be paid to avoiding the numerical distortion and the result infidelity.
Received: 20 November 2007
Revised: 09 April 2008
Accepted manuscript online:
PACS:
61.46.Fg
(Nanotubes)
Fund: Project supported
by the Specialized Research Fund for the Doctoral Program of Higher
Education of China (Grant No 20060003025) and the State Key Program
for Basic Research of China (Grant No 2003CB716201).
Cite this article:
Li Rui (李 瑞), Hu Yuan-Zhong (胡元中), Wang Hui (王 慧), Zhang Yu-Jun (张宇军) Numerical distortion and effects of thermostat in molecular dynamics simulations of single-walled carbon nanotubes 2008 Chin. Phys. B 17 4253
Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Chin. Phys. B, 2022, 31(9): 096401.
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
