Coherent Culling and Shading for Large Molecular Dynamics Visualization

• Published in: Computer graphics forum Vol. 29; no. 3; pp. 953 - 962
• Main Authors: Grottel, Sebastian, Reina, Guido, Dachsbacher, Carsten, Ertl, Thomas
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-06-2010
• Subjects: Computer graphics; Computer simulation; Culling; Datasets; Dynamical systems; Dynamics; I.3.7 [Computer Graphics]: Computer Graphics-Three-Dimensional Graphics and Realism; Molecular dynamics; Molecular physics; Molecular structure; Rendering; Simulation; Studies; Visualization
• ISSN: 0167-7055; 1467-8659
• DOI: 10.1111/j.1467-8659.2009.01698.x

Molecular dynamics simulations are a principal tool for studying molecular systems. Such simulations are used to investigate molecular structure, dynamics, and thermodynamical properties, as well as a replacement for, or complement to, costly and dangerous experiments. With the increasing availability of computational power the resulting data sets are becoming increasingly larger, and benchmarks indicate that the interactive visualization on desktop computers poses a challenge when rendering substantially more than millions of glyphs. Trading visual quality for rendering performance is a common approach when interactivity has to be guaranteed. In this paper we address both problems and present a method for high‐quality visualization of massive molecular dynamics data sets. We employ several optimization strategies on different levels of granularity, such as data quantization, data caching in video memory, and a two‐level occlusion culling strategy: coarse culling via hardware occlusion queries and a vertex‐level culling using maximum depth mipmaps. To ensure optimal image quality we employ GPU raycasting and deferred shading with smooth normal vector generation. We demonstrate that our method allows us to interactively render data sets containing tens of millions of high‐quality glyphs.