A decade of particle-based scientific visualization

In this manuscript, we review the evolution of atomistic visualization over the last 12 years and put the development of the community in context with our own efforts within the DFG collaborative research center 716. The goal is to provide a comprehensive summary of all relevant work that has been conducted under the auspices of project D.3. In this project, we focused on the visualization and analysis of particle-based data sets, and on how to bring these visualizations onto the workstation of domain scientists without the need for a large rendering infrastructure. We discuss how our decisions and goals evolved over time and show the success stories and publications. Finally, we give an outlook on the challenges that still require additional research and to which extent the requirements and constraints of current research have changed the way visualization works after these 12 years.

[1]  Paul A. Navrátil,et al.  Visualization of Cosmological Particle-Based Datasets , 2007, IEEE Transactions on Visualization and Computer Graphics.

[2]  James P. Ahrens,et al.  In‐situ Sampling of a Large‐Scale Particle Simulation for Interactive Visualization and Analysis , 2011, Comput. Graph. Forum.

[3]  Jens H. Krüger,et al.  Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering , 2014, IEEE Transactions on Visualization and Computer Graphics.

[4]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[5]  Brian Wyvill,et al.  Robust iso-surface tracking for interactive character skinning , 2014, ACM Trans. Graph..

[6]  Hans-Christian Hege,et al.  amira: A Highly Interactive System for Visual Data Analysis , 2005, The Visualization Handbook.

[7]  Martin Falk,et al.  VoxLink—Combining sparse volumetric data and geometry for efficient rendering , 2016, Computational Visual Media.

[8]  Min Chen,et al.  Over Two Decades of Integration‐Based, Geometric Flow Visualization , 2010, Comput. Graph. Forum.

[9]  Thomas Ertl,et al.  Visual Abstractions of Solvent Pathlines near Protein Cavities , 2008, Comput. Graph. Forum.

[10]  Scott Klasky,et al.  In Situ Methods, Infrastructures, and Applications on High Performance Computing Platforms , 2016, Comput. Graph. Forum.

[11]  David S. Ebert,et al.  Hub-based Simulation and Graphics Hardware Accelerated Visualization for Nanotechnology Applications , 2006, IEEE Transactions on Visualization and Computer Graphics.

[12]  Cheng Li,et al.  GlyphLens: View-Dependent Occlusion Management in the Interactive Glyph Visualization , 2017, IEEE Transactions on Visualization and Computer Graphics.

[13]  Thomas Ertl,et al.  MegaMol—A Prototyping Framework for Particle-Based Visualization , 2015, IEEE Transactions on Visualization and Computer Graphics.

[14]  Thomas Ertl,et al.  2016 IEEE Scientific Visualization Contest Winner: Visual and Structural Analysis of Point-based Simulation Ensembles , 2018, IEEE Computer Graphics and Applications.

[15]  J. Peacock,et al.  Simulations of the formation, evolution and clustering of galaxies and quasars , 2005, Nature.

[16]  Guido Reina,et al.  Homogeneous nucleation in supersaturated vapors of methane, ethane, and carbon dioxide predicted by brute force molecular dynamics. , 2008, The Journal of chemical physics.

[17]  J. Barker,et al.  Perturbation Theory and Equation of State for Fluids. II. A Successful Theory of Liquids , 1967 .

[18]  Bruno Lévy,et al.  Iterative Methods for Visualization of Implicit Surfaces On GPU , 2007, ISVC.

[19]  Thomas Ertl,et al.  Evaluation of per-pixel linked lists for distributed rendering and comparative analysis , 2012, Comput. Vis. Sci..

[20]  Daniel Baum,et al.  Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale , 2012, Comput. Graph. Forum.

[21]  Rüdiger Westermann,et al.  Efficient High-Quality Volume Rendering of SPH Data , 2010, IEEE Transactions on Visualization and Computer Graphics.

[22]  Derek Bruening,et al.  Efficient, transparent, and comprehensive runtime code manipulation , 2004 .

[23]  Thomas Ertl,et al.  Image-Space GPU Metaballs for Time-Dependent Particle Data Sets , 2007, VMV.

[24]  Nelson Max,et al.  Hierarchical molecular modelling with ellipsoids. , 2004, Journal of molecular graphics & modelling.

[25]  Mohamed Ibrahim,et al.  Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data , 2018, IEEE Transactions on Visualization and Computer Graphics.

[26]  Sebastian Grottel,et al.  Visualization of Particle‐based Data with Transparency and Ambient Occlusion , 2015, Comput. Graph. Forum.

[27]  C. C. Law,et al.  ParaView: An End-User Tool for Large-Data Visualization , 2005, The Visualization Handbook.

[28]  Aaron Knoll,et al.  OSPRay - A CPU Ray Tracing Framework for Scientific Visualization , 2017, IEEE Transactions on Visualization and Computer Graphics.

[29]  Hans Hagen,et al.  Fast Ray Tracing of Arbitrary Implicit Surfaces with Interval and Affine Arithmetic , 2009, Comput. Graph. Forum.

[30]  Thomas Ertl,et al.  Visualization of Electrostatic Dipoles in Molecular Dynamics of Metal Oxides , 2012, IEEE Transactions on Visualization and Computer Graphics.

[31]  Kelly P. Gaither,et al.  RBF Volume Ray Casting on Multicore and Manycore CPUs , 2014, Comput. Graph. Forum.

[32]  P. Basser,et al.  Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. 1996. , 1996, Journal of magnetic resonance.

[33]  Thomas Ertl,et al.  Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Coherent Culling and Shading for Large Molecular Dynamics Visualization , 2022 .

[34]  Min Chen,et al.  Ray-driven dynamic working set rendering , 2007, The Visual Computer.

[35]  Thomas Ertl,et al.  Visual Verification and Analysis of Cluster Detection for Molecular Dynamics , 2007, IEEE Transactions on Visualization and Computer Graphics.

[36]  Ingo Wald,et al.  A Coherent Grid Traversal Approach to Visualizing Particle-Based Simulation Data , 2007, IEEE Transactions on Visualization and Computer Graphics.

[37]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[38]  Jens Schneider,et al.  Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets , 2009, IEEE Transactions on Visualization and Computer Graphics.