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Simulation of Graphene Elastomer Composites
Published in Titash Mondal, Anil K. Bhowmick, Graphene-Rubber Nanocomposites, 2023
Sumit Sharma, Pramod Rakt Patel
Berendsen thermostat: The Berendsen thermostat (Berendsen et al. 1984) is an algorithm to re-scale the velocities of particles in MD simulations to control the simulation temperature. In this scheme, the system is weakly coupled to a heat bath with some temperature. The thermostat suppresses fluctuations of the kinetic energy of the system and therefore cannot produce trajectories consistent with the canonical ensemble. The temperature of the system is corrected such that the deviation exponentially decays with some time constant τ.
Multiphysics in molecular dynamics simulation
Published in Ken P. Chong, Arthur P. Boresi, Sunil Saigal, James D. Lee, Numerical Methods in Mechanics of Materials, 2017
James D. Lee, Jiaoyan Li, Zhen Zhang, Kerlin P. Robert
In MD, temperature is not an independent variable as in continuum mechanics (CM), but related to the microscopic random motions of atoms. Currently, popular techniques to control temperature include velocity rescaling, the Berendsen thermostat (Berendsen et al., 1984), the Andersen thermostat (Andersen, 1980), the Nosé–Hoover thermostat (Hoover, 1985; Nosé, 1984a, 1984b), Nosé–Hoover chains (Martyna et al., 1992), and Langevin dynamics (Lemons and Gythiel, 1997). Velocity rescaling is straightforward to implement. However, this thermostat does not allow the proper temperature fluctuations, cannot remove localized correlation, and is not time reversible. As a result, it is good for use in initialization state of a system, or say to warm up a system. The Berendsen thermostat is actually a specialized velocity rescaling thermostat, such that it has same advantages and disadvantages as velocity rescaling. Andersen thermostat maintains constant temperature condition for a material system by reassigning velocities of atoms or molecules that have collisions based on Maxwell-Boltzmann statistics. Even though the algorithm allows sampling from the canonical ensemble, the dynamics in fact is not physical. Langevin dynamics allows controlling the temperature of the canonical ensemble by the use of stochastic differential equations where a friction force term and a random force term are introduced. Compared to Langevin dynamics, Nosé–Hoover thermostat is deterministic, time reversible, and easy to implement. It has been widely used to calculate material properties. However, Nosé–Hoover thermostat is not suitable for a nanomaterial system whose temperature varies spatially and temporally during the simulation with the imposition of a temperature gradient. Li and Lee (2014a) reformulated the Nosé–Hoover thermostat to locally regulate temperatures at many distinct regions without introducing the physical linear and angular momenta and finally extend the feedback temperature force to a more general level.
Theoretical Models for Investigating The Processes of Nanofilm Deposition onto Porous Templates of Aluminum Oxide
Published in Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov, A. N. Beltiukov, A. L. Trigub, A. V. Severyukhin, Nanostructured Semiconductors in Porous Alumina Matrices, 2019
Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov
It is known that the application of Berendsen thermostat, especially for relatively small systems and at long trajectories, results in physically incorrect results due to the uneven distribution of energy by degrees of freedom.64,65
Thermal Decomposition Mechanism of Nitroglycerin by ReaxFF Reactive Molecular Dynamics Simulations
Published in Combustion Science and Technology, 2021
Tao Zeng, Rongjie Yang, Jianmin Li, Weiqiang Tang, Dinghua Li
Firstly, MD simulation is performed for 20 ps to relax the amorphous cell at 300 K, where the temperature is controlled using the Berendsen thermostat with the canonical ensemble (NVT) that refers to a constant number of atoms and a constant volume. The relaxed systems are heated from 300 to 2500, 2750, 3000, 3250 and 3500 K, respectively. The five subsequent separate simulations are equilibrated for 200 ps with the NVT ensemble. We control the temperature using the Berendsen thermostat with damping constant of 0.1 ps (Chen et al. 2018). The simulation system applies the periodic boundary conditions, and the time step of 0.1 fs is set. A 0.3 bond-order cutoff for all atom pairs is used to analyze the products for the recognition of molecules. The connection table of the atoms, molecular species, and dynamic trajectories are determined every 500 steps. These data are applied to obtain the evolution of the products and the mechanism of the NG thermal decomposition.
Reactive molecular dynamics simulation of oil shale combustion using the ReaxFF reactive force field
Published in Energy Sources, Part A: Recovery, Utilization, and Environmental Effects, 2021
Zhijun Zhang, Hanyu Zhang, Jun Chai, Liang Zhao, Li Zhuang
The system was energy-optimized via low-temperature (10 K) ReaxFF simulation (time step of 0.25 femtosecond) for 10 picoseconds (ps) to prevent chemical reactions from occurring during equilibration, the temperature was controlled using the Berendsen thermostat (Berendsen et al. 1984) with a 0.1 ps damping constant, then used the molecular dynamics simulation with NVT (constant number, constant volume, and constant temperature) ensemble including a heating process from 10 K to 300 K at a rate of 14.5 K/ps and a constant temperature process for 50 ps. Then, this system was compressed by no-reaction NPT (constant number, constant pressure, and constant temperature) MD simulation at temperature of 300 K and a pressure of 500 MPa for 20 ps. The density of the system after compression was 1.12 kg/dm3, which was in accordance with the experimental kerogen density. Next, the system was relaxed at 300 K using the NVT ensemble for 50 ps to optimize some unreasonable structures produced by compression.
Effects of stretching on molecular transfer from cell membrane by forming pores
Published in Soft Materials, 2019
Amin Hadi, Abbas Rastgoo, Azam Bolhassani, Nooshin Haghighipour
A periodic boundary condition was applied in three directions, so that if an atom crosses a boundary, it will enter the simulation system from the opposite direction. In MD simulations, the motion of N individual particles in a specified volume V evolves according to Newton’s laws. Hence, since the energy is conserved, from a thermodynamic point of view the resulting system is a micro-canonical ensemble (NVE) (34,35). However, in order to mimic experimental conditions, it is often necessary to simulate systems at constant temperature rather than energy, obtaining a canonical ensemble (NVT) (36). The control of the temperature is achieved by coupling the system to a so-called “thermostat”, which acts as a thermal bath. Several methods have been introduced to keep the temperature constant while using the micro-canonical ensemble (36). Popular techniques to control temperature include velocity rescaling, the Andersen thermostat (37), the Nosé–Hoover thermostat (38), Nosé–Hoover chains (39), the Berendsen thermostat (40), and Langevin dynamics (41,42). Initially, the system was used to the thermal relaxation in the NVE ensemble with the Langevin thermostat 42 at a temperature of 310 K and for 1 ns. For this purpose, a Velocity-Verlet algorithm for a Langevin thermostat (43) with 1fs time step was employed. Typical advantage for Langevin thermostat is that we need fewer computations per time step since we eliminate many atoms and include them implicitly by stochastic terms (44). After the thermal relaxation, we fix three edges out of four edges of the membrane for t ns and stretch it from the fourth edge at a speed of V (Fig. 2). The final tension and strain can be calculated as follow: