Visual Computing

University of Konstanz
2011 IEEE Pacific Visualization Symposium

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

S. Frey, T. Schlömer, S. Grottel, C. Dachsbacher, O. Deussen, T. Ertl
Teaser of Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics


Paper (.pdf, 23.8 MB)


Molecular dynamics is a widely used simulation technique to investigate material properties and structural changes under external forces. The availability of more powerful clusters and algorithms continues to increase the spatial and temporal extents of the simulation domain. This poses a particular challenge for the visualization of the underlying processes which might consist of millions of particles and thousands of time steps. Some application domains have developed special visual metaphors to only represent the relevant information of such data sets but these approaches typically require detailed domain knowledge that might not always be available or applicable. We propose a general technique that replaces the huge amount of simulated particles by a smaller set of representatives that are used for the visualization instead. The representatives capture the characteristics of the underlying particle density and exhibit coherency over time. We introduce loose capacity-constrained Voronoi diagrams for the generation of these representatives by means of a GPU-friendly, parallel algorithm. This way we achieve visualizations that reflect the particle distribution and geometric structure of the original data very faithfully. We evaluate our approach using real-world data sets from the application domains of material science, thermodynamics and dynamical systems theory.


  author     = {S. Frey and T. Schlömer and S. Grottel and C. Dachsbacher and O. Deussen and T. Ertl},
  booktitle  = {2011 IEEE Pacific Visualization Symposium},
  doi        = {10.1109/PACIFICVIS.2011.5742372},
  issn       = {2165-8765},
  keywords   = {computational geometry;data analysis;data visualisation;molecular dynamics method;GPU-friendly algorithm;dynamical systems theory;external forces;loose capacity-constrained Voronoi diagrams;loose capacity-constrained representatives;material properties;material science;molecular dynamics;parallel algorithm;qualitative visual analysis;real-world data sets;simulation technique;structural changes;thermodynamics;visual metaphors;Clustering algorithms;Data visualization;Density functional theory;Graphics processing unit;Measurement;Parallel algorithms;Visualization;clustering;molecular dynamics;particle-based visualization;time-dependent data},
  month      = {mar},
  pages      = {51-58},
  title      = {Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics},
  year       = {2011},
  url        = {},