3D Visualization of Molecular Simulations in High-performance Parallel Computing Environments

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

Acknowledgements

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.

Notes

Paper presented at FOMMS 2003—Foundations of Molecular Modeling and Simulation, July 6–11, 2003, Keystone, Colorado, USA.