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Visual Verification and Analysis of Cluster Detection for Molecular Dynamics
November/December 2007 (vol. 13 no. 6)
pp. 1624-1631
A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.

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Index Terms:
Cluster detection analysis, molecular dynamics visualization, time-dependent scattered data, glyph visualization, out-of-core techniques, evolution graph view
Citation:
Sebastian Grottel, Guido Reina, Jadran Vrabec, Thomas Ertl, "Visual Verification and Analysis of Cluster Detection for Molecular Dynamics," IEEE Transactions on Visualization and Computer Graphics, vol. 13, no. 6, pp. 1624-1631, Nov.-Dec. 2007, doi:10.1109/TVCG.2007.70614
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