scholarly journals Effective Implementation of Elastohydrodynamic Lubrication of Rough Surfaces into Multibody Dynamics Software

2021 ◽  
Vol 11 (4) ◽  
pp. 1488
Author(s):  
Jozef Dlugoš ◽  
Pavel Novotný
Keyword(s):  
Multibody Dynamics ◽  
Degrees Of Freedom ◽  
Combustion Engine ◽  
Rough Surfaces ◽  
Elastohydrodynamic Lubrication ◽  
Shape Reconstruction ◽  
General Purpose ◽  
Dynamics Simulation ◽  
Computational Time ◽  
Dynamics Simulations

Currently, multibody dynamics simulations are moving away from issues exclusive to dynamics to more multiphysical problems. Most mechanical systems contain contact pairs that influence the dynamics of the entire mechanism, such as friction loss, wear, vibration and noise. In addition, deformation often affects the interaction between the contact bodies. If that is the case, this effect must be considered. However, a major disadvantage arises in that it leads to an increase in the number of degrees of freedom and the computational time. Often, the general-purpose multibody dynamics software does not take into account advanced phenomena, such as a lubricated contact pair. This paper can serve as a guide to implementing the elastohydrodynamic lubrication of rough surfaces into general-purpose multibody dynamics software (in this case MSC Adams), which remains challenging. In this paper, the deformation shape reconstruction of the reduced flexible bodies is described, as well as a solution to the increase in the computational speed issues thereby caused. To alleviate this burden, advanced sensitivity analysis techniques are used. In this paper, parallel computing has been employed. The proposed method leads to reasonable computational times for the multibody dynamics simulations, including elastohydrodynamic lubrication. The proposed method is applied to the multibody dynamics simulation of the piston–liner interaction of an internal combustion engine.

scholarly journals Identification of Important Normal Modes in Nonadiabatic Dynamics Simulations by Coherence, Correlation, and Frequency Analyses

2019 ◽  
Author(s):  
Sebastian Mai ◽  
Leticia Gonzalez
Keyword(s):  
Wave Function ◽  
Degrees Of Freedom ◽  
Normal Modes ◽  
Dynamics Simulation ◽  
Nuclear Motion ◽  
Nonadiabatic Dynamics ◽  
Excitation Energies ◽  
Time Frequency ◽  
Dynamics Simulations ◽  
Low Dimensional

<div>Nonadiabatic dynamics simulations of molecular systems with a large number of nuclear degrees of freedom become increasingly feasible, but there is still a need to extract from such simulations a small number of most important modes of nuclear motion, for example to obtain general insight or to construct low-dimensional model potentials for further simulations. Standard techniques for this dimensionality reduction employ statistical methods that identify the modes that account for the largest variance in nuclear positions. However, large-amplitude motion is not necessarily a good proxy for the influence of a mode on the excited-state wave function evolution. Hence, here we report a number of analysis techniques aimed at extracting from nonadiabatic dynamics simulations the vibrational modes that are most strongly affected by the electronic excitation process and that most significantly affect the interaction of the electronic states. The first technique identifies coherent nuclear motion after excitation from the ratio between total variance and variance of the average trajectory. The second strategy employs linear regression to find normal modes that have a statistically significant effect on excitation energies, energy gaps, or wave function overlaps. The third approach uses time-frequency analysis to find normal modes where the vibrational frequencies change in the course of the dynamics simulation. All three techniques are applied to the case of surface hopping trajectories of [Re(CO)<sub>3</sub>(Im)(Phen)]<sup>+</sup> (Im=imidazole; Phen=1,10-phenanthroline), showing that in this transition metal complex the nonadiabatic dynamics is dominated by a small number of carbonyl and phenanthroline in-plane stretch modes.</div><div><br></div>

Linearized dynamics equations for the balance and steer of a bicycle: a benchmark and review

2007 ◽  
Vol 463 (2084) ◽  
pp. 1955-1982 ◽  
Author(s):  
J.P Meijaard ◽  
Jim M Papadopoulos ◽  
Andy Ruina ◽  
A.L Schwab
Keyword(s):  
Degrees Of Freedom ◽  
Numerical Solutions ◽  
Equations Of Motion ◽  
Point Contact ◽  
Ground Level ◽  
Conservative System ◽  
Rear Wheel ◽  
General Purpose ◽  
Dynamic Programs ◽  
Dynamics Simulations

We present canonical linearized equations of motion for the Whipple bicycle model consisting of four rigid laterally symmetric ideally hinged parts: two wheels, a frame and a front assembly. The wheels are also axisymmetric and make ideal knife-edge rolling point contact with the ground level. The mass distribution and geometry are otherwise arbitrary. This conservative non-holonomic system has a seven-dimensional accessible configuration space and three velocity degrees of freedom parametrized by rates of frame lean, steer angle and rear wheel rotation. We construct the terms in the governing equations methodically for easy implementation. The equations are suitable for e.g. the study of bicycle self-stability. We derived these equations by hand in two ways and also checked them against two nonlinear dynamics simulations. In the century-old literature, several sets of equations fully agree with those here and several do not. Two benchmarks provide test cases for checking alternative formulations of the equations of motion or alternative numerical solutions. Further, the results here can also serve as a check for general purpose dynamic programs. For the benchmark bicycles, we accurately calculate the eigenvalues (the roots of the characteristic equation) and the speeds at which bicycle lean and steer are self-stable, confirming the century-old result that this conservative system can have asymptotic stability.

scholarly journals Identification of Important Normal Modes in Nonadiabatic Dynamics Simulations by Coherence, Correlation, and Frequency Analyses

2019 ◽  
Author(s):  
Sebastian Mai ◽  
Leticia Gonzalez
Keyword(s):  
Wave Function ◽  
Degrees Of Freedom ◽  
Normal Modes ◽  
Dynamics Simulation ◽  
Nuclear Motion ◽  
Nonadiabatic Dynamics ◽  
Excitation Energies ◽  
Time Frequency ◽  
Dynamics Simulations ◽  
Low Dimensional

<div>Nonadiabatic dynamics simulations of molecular systems with a large number of nuclear degrees of freedom become increasingly feasible, but there is still a need to extract from such simulations a small number of most important modes of nuclear motion, for example to obtain general insight or to construct low-dimensional model potentials for further simulations. Standard techniques for this dimensionality reduction employ statistical methods that identify the modes that account for the largest variance in nuclear positions. However, large-amplitude motion is not necessarily a good proxy for the influence of a mode on the excited-state wave function evolution. Hence, here we report a number of analysis techniques aimed at extracting from nonadiabatic dynamics simulations the vibrational modes that are most strongly affected by the electronic excitation process and that most significantly affect the interaction of the electronic states. The first technique identifies coherent nuclear motion after excitation from the ratio between total variance and variance of the average trajectory. The second strategy employs linear regression to find normal modes that have a statistically significant effect on excitation energies, energy gaps, or wave function overlaps. The third approach uses time-frequency analysis to find normal modes where the vibrational frequencies change in the course of the dynamics simulation. All three techniques are applied to the case of surface hopping trajectories of [Re(CO)<sub>3</sub>(Im)(Phen)]<sup>+</sup> (Im=imidazole; Phen=1,10-phenanthroline), showing that in this transition metal complex the nonadiabatic dynamics is dominated by a small number of carbonyl and phenanthroline in-plane stretch modes.</div><div><br></div>

Multibody Molecular Dynamics II: Applications and Results

2007 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Paul Crozier ◽  
Kurt S. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Multibody Dynamics ◽  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Future Research ◽  
Conservation Of Energy ◽  
Order Of Magnitude ◽  
Speed Up ◽  
The Stability ◽  
Dynamics Simulations

This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nano-second simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

scholarly journals Chrono::Render: A Graphical Visualization Pipeline for Multibody Dynamics Simulations

2014 ◽  
Author(s):  
Daniel Kaczmarek ◽  
Aaron Bartholomew ◽  
Felipe Gutierrez ◽  
Hammad Mazhar ◽  
Dan Negrut
Keyword(s):  
Open Source ◽  
Multibody Dynamics ◽  
High Performance ◽  
Dynamics Simulation ◽  
High Quality ◽  
Front End ◽  
Modeling Software ◽  
Dynamics Simulations ◽  
Client Side ◽  
Rendering Engine

This paper describes a web-enabled tool capable of generating high quality videos and images from multibody dynamics simulation results. This tool, called Chrono::Render, uses the Blender modeling software as the front end with Pixars RenderMan used to create high quality images. Blender is a free and open source tool used to create and visualize 3D content and provides a robust plugin framework which Chrono::Render leverages. To produce the final image, the Blender front end passes data to a RenderMan compliant rendering engine. Along with Pixars PhotoRealistic RenderMan (PRMan), several open source options such as Aqsis, JrMan, or Pixie can be used. Preprocessing is performed on the client side, where the front end generates a work order for the RenderMan compliant rendering engine to process. This work order, which contains several scripts that define the visualization parameters, along with the pre-processed simulation data and other user-defined geometry assets is uploaded to a remote server hosted by the Simulation Based Engineering Lab. This server contains more than a thousand CPU cores used for high performance computing applications, which can be used to render many frames of an animation in parallel. Chrono::Render is free and open source software released under a BSD3 license.

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.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Sign in / Sign up

Export Citation Format

Share Document