Details
| Original language | English |
|---|---|
| Pages (from-to) | 469-477 |
| Number of pages | 9 |
| Journal | Molecular Simulation |
| Volume | 30 |
| Issue number | 7 |
| Publication status | Published - 15 Jun 2004 |
| Externally published | Yes |
| Event | Foundations of Molecular Modelling and Simulation - Keystone Resort, CO, USA, United States Duration: 6 Jul 2003 → 11 Jul 2003 http://fomms.org/fomms-2003 |
Abstract
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.
Keywords
- 3D visualization, Cluster formation, Lennard-Jones potential, Molecular simulation, Parallel computing
ASJC Scopus subject areas
- Chemistry(all)
- General Chemistry
- Computer Science(all)
- Information Systems
- Mathematics(all)
- Modelling and Simulation
- Chemical Engineering(all)
- General Chemical Engineering
- Materials Science(all)
- General Materials Science
- Physics and Astronomy(all)
- Condensed Matter Physics
Cite this
- Standard
- Harvard
- Apa
- Vancouver
- BibTeX
- RIS
In: Molecular Simulation, Vol. 30, No. 7, 15.06.2004, p. 469-477.
Research output: Contribution to journal › Article › Research › peer review
}
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 -