Molecular Dynamics Simulation With Interval-Valued Interatomic Potentials

2016 ◽  
Author(s):  
Anh Tran ◽  
Yan Wang
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Interatomic Potential ◽  
Thermal Fluctuation ◽  
Potential Functions ◽  
Dynamics Simulation ◽  
Computational Time ◽  
System Control ◽  
Interatomic Potentials ◽  
Time Step

In molecular dynamics (MD) simulation, the two main sources of uncertainty are the interatomic potential functions and thermal fluctuation. The accuracy of the interatomic potential functions plays a vital role toward the reliability of MD simulation prediction. Reliable molecular dynamics (R-MD) is an interval-based MD simulation platform, where atomistic positions and velocities are represented as Kaucher (or generalized) intervals to capture the uncertainty associated with the inter-atomic potentials. The advantage of this uncertainty quantification (UQ) approach is that the uncertainty effect can be assessed on-the-fly with only one run of simulation, and thus the computational time for UQ is significantly reduced. In this paper, an extended interval statistical ensemble is introduced to quantify the uncertainty associated with the system control variables, such as temperature and pressure at each time-step. This method allows for quantifying and propagating the uncertainty in the system as MD simulation advances. An example of interval isothermal-isobaric (NPT) ensemble is implemented to demonstrate the feasibility of applying the intrusive UQ technique toward MD simulation.

COMPUTER SIMULATION OF EPITAXIAL GROWTH OF SILICON ON Si (001) SURFACE

2002 ◽  
Vol 16 (01n02) ◽  
pp. 227-232 ◽  
Author(s):  
M. H. LIANG ◽  
X. XIE ◽  
S. LI
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Epitaxial Growth ◽  
Interatomic Potential ◽  
Simulation Method ◽  
Growth Direction ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Weber Potential ◽  
Deposition Conditions

Epitaxial growth of silicon on Si (001) surface has been studied with interatomic potential based molecular dynamics simulation method. Three silicon interatomic potentials developed separately by Stillinger-Weber, Tersoff, and Bazant-Kaxiras were used. Energetic beam of 8 eV, substrate temperature of 500K and deposition rate of 1.15 ps/atom were used as the deposition conditions. Morphologies of the growth were obtained and densities in the growth direction analyzed. Epitaxial growth under the deposition conditions imposed was found possible only using the Stillinger-Weber potential. Disordered growths of differing degree were obtained using the Bazant-Kaxiras and Tersoff potentials. The disordered growth may be attributed to the existence of an epitaxial transition temperature higher than 500K that these potentials might have.

scholarly journals Molecular dynamics lattice gas equilibrium distribution function for Lennard–Jones particles

2021 ◽  
Vol 379 (2208) ◽  
pp. 20200404 ◽  
Author(s):  
Aleksandra Pachalieva ◽  
Alexander J. Wagner
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Lattice Boltzmann ◽  
Md Simulation ◽  
Lattice Gas ◽  
Equilibrium Distribution ◽  
Dynamics Simulation ◽  
Equilibrium Distribution Function ◽  
Weighted Sum ◽  
Time Step

The molecular dynamics lattice gas (MDLG) method maps a molecular dynamics (MD) simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method (LBM) by taking a Boltzmann average over the MDLG. A key property of the LBM is the equilibrium distribution function, which was originally derived by assuming that the particle displacements in the MD simulation are Boltzmann distributed. However, we recently discovered that a single Gaussian distribution function is not sufficient to describe the particle displacements in a broad transition regime between free particles and particles undergoing many collisions in one time step. In a recent publication, we proposed a Poisson weighted sum of Gaussians which shows better agreement with the MD data. We derive a lattice Boltzmann equilibrium distribution function from the Poisson weighted sum of Gaussians model and compare it to a measured equilibrium distribution function from MD data and to an analytical approximation of the equilibrium distribution function from a single Gaussian probability distribution function. This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.

Equilibrium Molecular Dynamics and the Thermal Behavior of Small Systems

2010 ◽  
Author(s):  
Alejandro Guajardo-Cue´llar ◽  
David B. Go ◽  
Mihir Sen
Keyword(s):  
Molecular Dynamics ◽  
Thermal Behavior ◽  
Interatomic Potential ◽  
Model System ◽  
Dynamics Simulation ◽  
Small Scale ◽  
Interatomic Potentials ◽  
Power Spectral ◽  
Anharmonic Potential ◽  
Dynamics Calculation

Equilibrium molecular dynamics can be used to investigate the heat transport due to conduction in small scale systems. The results from a molecular dynamics simulation can be used to extract the thermal behavior. In this study, an equilibrium molecular dynamics calculation of a model system using three interatomic potentials, a harmonic potential, an anharmonic potential, and the Tersoff interatomic potential, has been conducted. The characteristics of the transport are studied from the kinetic energies in the frequency domain. The power spectral density of the kinetic energy of the three different potentials is compared. This study helps to understand how heat is transported in a small system of atoms.

scholarly journals On Time Step in the Molecular Dynamics (MD) Simulation of Nanomachining

2017 ◽  
Vol 261 ◽  
pp. 108-114
Author(s):  
Akinjide O. Oluwajobi ◽  
Xun Chen
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Integration Time ◽  
Interatomic Potentials ◽  
Material Behaviour ◽  
Major Focus ◽  
Time Step ◽  
Critical Issues ◽  
Computationally Expensive ◽  
Selection Of

The study of nanoscale machining phenomena and processes are effectively been carried out by using the molecular dynamics (MD) simulation. The MD provides explanation of material behaviour that are difficult to observe or even impossible through experiments. To carry out reliable simulations, the method depends on critical issues, which include the choice of appropriate interatomic potentials and the integration time step. The selection of the timestep in the MD simulation of nanomachining is the major focus of this investigation. A too low timestep would be computationally expensive and also a too high timestep would cause chaotic behaviour in the simulation. Computational experiments were conducted to check for the range of timestep that is appropriate for the simulation of nanomachining of copper. It was observed from the total energy variations, that time step in the range of 0.1 to 0.4 fs could be used to procure stable simulations in copper, for the configuation employed.

Preliminary Studies on Molecular Dynamics Simulation of Friction Stir Processing of Aluminium Alloys

2019 ◽  
Vol 796 ◽  
pp. 155-163
Author(s):  
Oyindamola Kayode ◽  
Oluwole A. Olufayo ◽  
Esther Titilayo Akinlabi
Keyword(s):  
Molecular Dynamics ◽  
Aluminium Alloy ◽  
Friction Stir Processing ◽  
Md Simulation ◽  
Equations Of Motion ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Friction Stir ◽  
Atoms And Molecules

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules at nanoscale. It allows interaction between the atoms and molecules for a fixed period, giving an understanding of the system as they dynamically begin to evolve. The paths of the atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting atoms, where interatomic potentials or molecular mechanics force fields are used to calculate forces and potential energies between the atoms. In this study, the basic parameters used in MD simulations are briefly discussed. An MD simulation of the friction stir processing (FSP) of aluminium alloy 6061-T6 was carried out to explain the invisible thermodynamic microscopic details which occurred during the process. However, the aim of the MD simulation is not to predict precisely the process, but to predict the average thermodynamic behavior of the process if conducted in a practical state. This is to further enhance the understanding of the FSP process. The results obtained from the MD simulation prove that it may be possible to adequately represent the MD simulation of the FSP of an aluminium alloy.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

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