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.

Design of Analog Front-end Circuit for Audio-frequency Magnetotelluric Instrument

2018 ◽  
Vol 23 (3) ◽  
pp. 305-318
Author(s):  
Yinglu Zhang ◽  
Zhenzhu Xi ◽  
Xingpeng Chen ◽  
Honglan Wei ◽  
Long Huang ◽  
...  
Keyword(s):  
Electric Field ◽  
High Performance ◽  
Notch Filter ◽  
Noise Levels ◽  
High Quality ◽  
Pass Filter ◽  
Input Noise ◽  
Front End ◽  
Analog Front End ◽  
Power Frequency

High-performance audio-frequency magnetotelluric (AMT) instrument is one means of obtaining high-quality electromagnetic (EM) data. To improve the ability of AMT system to obtain high-quality data, this paper presents a design for a high-performance analog front-end circuit for AMT instrument. It mainly consists of the input protection, preamplifier, passive high pass filter, power frequency notch filter, programmable amplifier, and active low pass filter. In addition, this paper proposes a design of low-noise, high-performance preamplifier, which improves the common-mode rejection ratio (CMRR) of analog front-end circuit and effectively enhances the signal-to-noise ratio (SNR) of the circuit. The front-end circuit utilized two-stage twin-T notch filter to effectively suppress the strong interference of fundamental component of power frequency. Also, it used signal relays to control circuit gain and selection of cutoff frequency of anti-aliasing filter, resulting in the improvement of the capability of the analog-to-digital Converter (ADC) to distinguish weak EM signal. The measured results of the electric field and magnetic field channel showed that: 1) The circuit works in frequency range of 1 Hz∼100 kHz; 2) The CMRR values of the preamplifier of electric field channel at low frequencies (1 Hz∼1 kHz) are 111 dB and 97 dB when the gains are 20 dB and 6 dB respectively; 3) The maximum attenuation fundamental power frequency can reach −39.46 dB and −39.04 dB respectively; 4) The total harmonic distortion rate at 1 kHz is 0.022% and 0.029% respectively; 5) The input noise levels of electric field channel are 12.67nV / [Formula: see text] @10Hz and 8.15V / [Formula: see text] @1kHz, while the input noise levels of magnetic field channel are 8.97nV / [Formula: see text] @10Hz and 6.16V / [Formula: see text] @1kHz; and 6) In conclusion, the analog front-end circuit is superior to meet the requirements of the AMT methods, and provides a useful reference for the development of AMT instrument.

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 IOb-Cache: A High-Performance Configurable Open-Source Cache

Algorithms ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 218
Author(s):  
João V. Roque ◽  
João D. Lopes ◽  
Mário P. Véstias ◽  
José T. de Sousa
Keyword(s):  
Open Source ◽  
High Performance ◽  
System On Chip ◽  
Processing Unit ◽  
Central Processing ◽  
Front End ◽  
Front End Module ◽  
Memory Accesses ◽  
On Chip ◽  
Access Policies

Open-source processors are increasingly being adopted by the industry, which requires all sorts of open-source implementations of peripherals and other system-on-chip modules. Despite the recent advent of open-source hardware, the available open-source caches have low configurability, limited lack of support for single-cycle pipelined memory accesses, and use non-standard hardware interfaces. In this paper, the IObundle cache (IOb-Cache), a high-performance configurable open-source cache is proposed, developed and deployed. The cache has front-end and back-end modules for fast integration with processors and memory controllers. The front-end module supports the native interface, and the back-end module supports the native interface and the standard Advanced eXtensible Interface (AXI). The cache is highly configurable in structure and access policies. The back-end can be configured to read bursts of multiple words per transfer to take advantage of the available memory bandwidth. To the best of our knowledge, IOb-Cache is currently the only configurable cache that supports pipelined Central Processing Unit (CPU) interfaces and AXI memory bus interface. Additionally, it has a write-through buffer and an independent controller for fast, most of the time 1-cycle writing together with 1-cycle reading, while previous works only support 1-cycle reading. This allows the best clocks-per-Instruction (CPI) to be close to one (1.055). IOb-Cache is integrated into IOb System-on-Chip (IOb-SoC) Github repository, which has 29 stars and is already being used in 50 projects (forks).

scholarly journals Open Source Software to Visualize Complex Data on Remote CEA's Supercomputing Facilities

2014 ◽  
Author(s):  
Fabien Vivodtzev ◽  
Thierry Carrard
Keyword(s):  
Numerical Simulation ◽  
Open Source ◽  
High Performance Computing ◽  
Open Source Software ◽  
High Performance ◽  
End Users ◽  
Dynamics Simulation ◽  
Complex Data ◽  
Simulation Code ◽  
Performance Computing

In order to guaranty performances of complex systems using numerical simulation, CEA is performing advanced data analysis and scientific visualization with open source software using High Performance Computing (HPC) capability. The diversity of the physics to study produces results of growing complexity in terms of large-scale, high dimensional and multivariate data. Moreover, the HPC approach introduces another layer of complexity by allowing computation amongst thousands of remote cores accessed from sites located hundreds of kilometers away from the computing facility. This paper presents how CEA deploys and contributes to open source software to enable production class visualization tools in a high performance computing context. Among several open source projects used at CEA, this presentation will focus on Visit, VTK and Paraview. In the first part we will address specific issues encountered when deploying VisIt and Paraview in a multi-site supercomputing facility for end-users. Several examples will be given on how such tools can be adapted to take advantage of a parallel setting to explore large multi-block dataset or perform remote visualization on material interface reconstructions of billions of cells. Then, the specific challenges faced to deliver Paraview’s Catalyst capabilities to end-users will be discussed. In the second part, we will describe how CEA contributes to open source visualization software and associated software development strategy by emphasizing on two recent development projects. The first is an integrated simulation workbench providing plugins for every step required to achieve numerical simulation independently on a local or a remote computer. Embedded in an Eclipse RCP environment, VTK views allow the users to perform data input using interaction or mesh preview before running the simulation code. Contributions to VTK have been made in order to smoothly integrate these technologies. The second details how recent developments at CEA have helped to visualize and to analyze results from ExaStamp, a parallel molecular dynamics simulation code dealing with molecular systems ranging from a few millions up to a billion atoms. These developments include a GPU intensive rendering method specialized for atoms and specific parallel algorithms to process molecular data sets.

scholarly journals HyperBeta: characterizing the structural dynamics of proteins and self-assembling peptides

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marco S. Nobile ◽  
Federico Fontana ◽  
Luca Manzoni ◽  
Paolo Cazzaniga ◽  
Giancarlo Mauri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Complex Structure ◽  
Molecular Structures ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
High Quality ◽  
Self Assembling ◽  
Coarse Grained Molecular Dynamics

AbstractSelf-assembling processes are ubiquitous phenomena that drive the organization and the hierarchical formation of complex molecular systems. The investigation of assembling dynamics, emerging from the interactions among biomolecules like amino-acids and polypeptides, is fundamental to determine how a mixture of simple objects can yield a complex structure at the nano-scale level. In this paper we present HyperBeta, a novel open-source software that exploits an innovative algorithm based on hyper-graphs to efficiently identify and graphically represent the dynamics of $$\beta$$ β -sheets formation. Differently from the existing tools, HyperBeta directly manipulates data generated by means of coarse-grained molecular dynamics simulation tools (GROMACS), performed using the MARTINI force field. Coarse-grained molecular structures are visualized using HyperBeta ’s proprietary real-time high-quality 3D engine, which provides a plethora of analysis tools and statistical information, controlled by means of an intuitive event-based graphical user interface. The high-quality renderer relies on a variety of visual cues to improve the readability and interpretability of distance and depth relationships between peptides. We show that HyperBeta is able to track the $$\beta$$ β -sheets formation in coarse-grained molecular dynamics simulations, and provides a completely new and efficient mean for the investigation of the kinetics of these nano-structures. HyperBeta will therefore facilitate biotechnological and medical research where these structural elements play a crucial role, such as the development of novel high-performance biomaterials in tissue engineering, or a better comprehension of the molecular mechanisms at the basis of complex pathologies like Alzheimer’s disease.

HeroMDAnalysis: an automagical tool for GROMACS-based molecular dynamics simulation analysis

2021 ◽  
Vol 13 (5) ◽  
pp. 447-456
Author(s):  
Ravi Rawat ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Kajal Bhati ◽  
Saurabh M. Verma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Graphical User Interface ◽  
Simulation Analysis ◽  
Prior Experience ◽  
Dynamics Simulation ◽  
Command Line ◽  
Command Line Interface ◽  
High Quality ◽  
Dynamics Simulations

Background & objective: Molecular dynamics simulations (MDS) using GROMACS are among the commonly used computational experiments in the area of molecular biology and drug discovery. This article presents a project called HeroMDAnalysis, an automagical tool to analyze the GROMACS-based MDS trajectories and generate plots as high-quality images for various parameters. Materials & methods: The tool was built using bash shell programming, and graphical user interface was built using Zenity engine. Results & conclusion: This tool offers a simple, semiautomated, and relatively fast framework for what was previously a complex, manual, time-consuming and error-prone task, presenting a useful method for biochemists and synthetic chemists with no prior experience of the command line interface.

FMM/GPU Accelerated Molecular Dynamics Simulation of Phase Transitions in Water-Nitrogen-Metal Systems

2012 ◽  
Author(s):  
Elena Moiseeva ◽  
Constantin Mikhaylenko ◽  
Victor Malyshev ◽  
Dmitry Maryin ◽  
Nail Gumerov
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Units ◽  
High Performance ◽  
Fast Multipole Method ◽  
Pure Water ◽  
Water Dynamics ◽  
Dynamics Simulation ◽  
Problem Size ◽  
Central Processing ◽  
Dynamics Simulations

To characterize the behavior of water with dissolved gas (nitrogen) near a solid metallic substrate, which is important for realistic modeling of flows in nanochannels, the method of molecular dynamics is used. High performance computing is achieved via the Fast Multipole Method (FMM) for the force evaluation and via utilization of heterogeneous architectures which consists of central processing units (CPUs) and graphics processing units (GPUs). The FMM allows one to speed up computations of the long-range interactions (Coulomb potential) due to the linear scaling of the algorithm with the problem size. Utilization of the GPU provides significant acceleration of computations. Realization of the FMM on GPUs allows one to perform computational experiments for very large systems. The paper shows that the described technique can be used for water dynamics simulations in a region of size up to 100 nanometers, or of the order 100 millions molecules on personal supercomputers equipped with several GPUs. Results of numerical experiments on structure formation on the contact interface of a water droplet and metal surface both for pure water and for water with dissolved air are reported.

Microstructures in Elastic Media

1994 ◽  
Author(s):  
Nhan Phan-Thien ◽  
Sangtae Kim
Keyword(s):  
Computational Methods ◽  
High Performance ◽  
Chemical Engineering ◽  
Elliptic Partial Differential Equations ◽  
Parallel Computers ◽  
Computational Algorithms ◽  
Applied Physics ◽  
Advanced Students ◽  
Particulate Solids ◽  
Modeling Software

This monograph describes various methods for solving deformation problems of particulate solids, taking the reader from analytical to computational methods. The book is the first to present the topic of linear elasticity in mathematical terms that will be familiar to anyone with a grounding in fluid mechanics. It incorporates the latest advances in computational algorithms for elliptic partial differential equations, and provides the groundwork for simulations on high performance parallel computers. Numerous exercises complement the theoretical discussions, and a related set of self-documented programs is available to readers with Internet access. The work will be of interest to advanced students and practicing researchers in mechanical engineering, chemical engineering, applied physics, computational methods, and developers of numerical modeling software.

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