TY - JOUR

T1 - 3D visualization of molecular simulations in high-performance parallel computing environments

AU - Meier, Karsten

AU - Holzknecht, Christopher

AU - Kabelac, Stephan

AU - Olbrich, Stephan

AU - Chmielewski, Karsten

N1 - Funding Information: This project was part of a gigabit (LAN/WAN) testbed project in the DFN (German Academic Network) and financially supported by the German Federal Ministry of Education and Research (BMBF). Computational resources were provided by the Regionales Rechenzentrum für Niedersachsen (RRZN) at the Universität Hannover and the Konrad-Zuse-Zentrum für Informationstechnologie (ZIB) in Berlin. Copyright: Copyright 2008 Elsevier B.V., All rights reserved.

PY - 2004/6/15

Y1 - 2004/6/15

N2 - This paper presents a novel tool for interactive 3D visualization and computational steering of molecular simulations and other computer simulation techniques such as computational fluid dynamics in parallel computing environments. The visualization system consists of three major components - data source, streaming server and viewer - which are distributed in intra/internet networks. A parallelized data extraction and visualization library, which generates 3D scenes, is integrated in the simulation software. The 3D scenes can be stored locally or sent to the streaming server parallel to the simulation, where they are stored on a fast RAID hard disk system. The streaming server transfers the 3D scenes to viewer clients on demand for display. A multi-platform 3D viewer software is provided as a plug-in embeddable into different WWW browsers. Many models of broad interest in molecular simulations can be visualized, from simple spherical particles to moderately complex molecules, and several volume visualization methods are implemented efficiently. Examples from thermophysical property research applications demonstrate the utility of the visualization system. One example shows that the transport coefficients of the Lennard-Jones fluid at subcritical temperatures in the gas region are influenced by the formation of small clusters of particles.

AB - This paper presents a novel tool for interactive 3D visualization and computational steering of molecular simulations and other computer simulation techniques such as computational fluid dynamics in parallel computing environments. The visualization system consists of three major components - data source, streaming server and viewer - which are distributed in intra/internet networks. A parallelized data extraction and visualization library, which generates 3D scenes, is integrated in the simulation software. The 3D scenes can be stored locally or sent to the streaming server parallel to the simulation, where they are stored on a fast RAID hard disk system. The streaming server transfers the 3D scenes to viewer clients on demand for display. A multi-platform 3D viewer software is provided as a plug-in embeddable into different WWW browsers. Many models of broad interest in molecular simulations can be visualized, from simple spherical particles to moderately complex molecules, and several volume visualization methods are implemented efficiently. Examples from thermophysical property research applications demonstrate the utility of the visualization system. One example shows that the transport coefficients of the Lennard-Jones fluid at subcritical temperatures in the gas region are influenced by the formation of small clusters of particles.

KW - 3D visualization

KW - Cluster formation

KW - Lennard-Jones potential

KW - Molecular simulation

KW - Parallel computing

UR - http://www.scopus.com/inward/record.url?scp=11144321235&partnerID=8YFLogxK

U2 - 10.1080/08927020410001680778

DO - 10.1080/08927020410001680778

M3 - Article

AN - SCOPUS:11144321235

VL - 30

SP - 469

EP - 477

JO - Molecular Simulation

JF - Molecular Simulation

SN - 0892-7022

IS - 7

T2 - Foundations of Molecular Modelling and Simulation

Y2 - 6 July 2003 through 11 July 2003

ER -