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Molecular dynamics simulation
Published in Zhigang Li, Nanofluidics, 2018
The Large-scale Atomic/Molecular Massively Parallel Simulator, or LAMMPS, is a software package developed by Sandia National Laboratories. It is a free-to-use and open-source code that can conduct atomic, mesoscale, and Monte Carlo simulations. Predominantly, LAMMPS has been widely used to perform large-scale MD simulations in nanoscience and nanotechnologies, which involve most of the scientific fields, including chemistry, physics, biology, materials science, and mechanics. LAMMPS is integrated with rich force fields, which are capable of modeling a wide range of gases, liquids, and solids. LAMMPS can be used to simulate the dynamics of a variety of particles, such as atoms, coarse-grained particles, polymers, biomolecules, and granular materials. The latest version of LAMMPS is written in C++ and can be easily modified or extended with new constraints, force fields, and boundary conditions to meet user’s requirements.
Modeling of Deformation and Fracture Process of Layered Nanocomposites
Published in Satya Bir Singh, Prabhat Ranjan, Alexander V. Vakhrushev, A. K. Haghi, Mechatronic Systems Design and Solid Materials, 2021
A. Yu. Fedotov, A. T. Lekontsev, A. V. Vakhrushev
For the simulation, we used the free software package for classical molecular dynamics LAMMPS (large-scale atomic/molecular massively parallel simulator). To visualize the results obtained, the Ovito software package was used. The well-established embedded atom method (EAM) was chosen as the potential of interatomic interaction. Let us briefly describe this method.
Thermal and flow characterization in nanochannels with tunable surface wettability: A comprehensive molecular dynamics study
Published in Numerical Heat Transfer, Part A: Applications, 2020
Haiyi Sun, Zhike Liu, Gongming Xin, Qian Xin, Jingzhi Zhang, Bing-Yang Cao, Xinyu Wang
All simulations in this work are implemented through the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) package. In order to improve computational efficiency without affecting accuracy, only the attraction and repulsion forces are applied to describe the interatomic interactions, which are modeled as the 12-6 Lennard–Jones (L–J) potential: where ε is the energy parameter, r is the interatomic distance and σ is the length parameter. To describe the argon-argon interaction, σAr-Aris set to be 3.405 Å and εAr-Ar is equal to 0.0104 eV [36]. In addition, σCu-Cu = 2.338 Å and εCu-Cu = 0.410 eV are used for the Cu-Cu interaction in two solid walls [37]. The interaction parameters between argon atoms and copper atoms are as follows: σAr-Cu = 2.871 Å and εAr-Cu = 0.065 eV, which can be obtained by the Lorentz-Berthelot mixing rule [38]. In order to represent different surface wettabilities, we use a scaling parameter χ to tune the interfacial coupling strength between the fluid and walls. Here eight different scaling parameters are selected: χ = 0.25, 0.50, 0.75, 1.00, 1.25, 1.50, 1.75, 2.00. The actual energy parameters between the copper atoms and argon atoms are the product of their intrinsic energy parameters and the scaling parameter. With the aim of improving the computational efficiency, the cutoff radius rcut is set to be 10 Å and the atomic interactions beyond the cutoff radius are not taken into account [24].
Analysis of the influence of tool radius on mechanical state of monocrystalline silicon during nano-cutting
Published in Mechanics of Advanced Materials and Structures, 2022
Lai Lianfeng, Niu Qinchuan, Li Minglin
LAMMPs can support atomic and molecular systems including gas, liquid or solid phases, various ensembles, and millions of levels, and provide support for multiple potential functions, and LAMMPs has good parallel scalability. LAMMPs mainly program the model that needs to be created, combined with the potential function and boundary conditions set in advance, simulate the cutting process and get the relevant data, and then combine with visualization software such as OVITO to analyze and process the data.
Evaluation of Methods for Viscosity Simulations of Lubricants at Different Temperatures and Pressures: A Case Study on PAO-2
Published in Tribology Transactions, 2021
Dimitrios Mathas, Walter Holweger, Marcus Wolf, Christof Bohnert, Vasilios Bakolas, Joanna Procelewska, Ling Wang, Scott Bair, Chris-Kriton Skylaris
All equilibrium and nonequilibrium molecular dynamics simulations were carried out by using the LAMMPS software (45), combined with some in-house developed scripts to perform autocorrelation and averaging of viscosity. The necessary files, that included the coordinates of molecules, the simulation settings and atomic charges needed for LAMMPS, were generated with Moltemplate (46). Moltemplate is an open-source software that can generate LAMMPS input scripts. The molecular system structures needed in Moltemplate were generated with Packmol (47), which reads simple .xyz file coordinates in order to fill simulation boxes of specified size with molecules that have randomized arrangement. A box with a starting volume of Å3, containing 170 9,10-dimethyloctadecane molecules (10,540 atoms) was generated and periodic boundary conditions were applied in all three dimensions. In this work, the L-OPLS-AA and GAFF2-AA force fields were chosen. L-OPLS-AA (48) is a force field specifically optimized for long-chain hydrocarbons while GAFF2-AA is a general-purpose force field (49). The functional form of these force fields is expressed as: where defines the harmonic vibrational motion between bonded atoms with respect to the equilibrium bond length, defines the angular vibrational motion of three atoms with respect to the equilibrium bond angle, refers to torsional rotation of four atoms with respect to a central bond and refers to pairwise interactions (Lennard-Jones and electrostatics). All force field coefficients that were used in this work are available in the Supporting Information.