Atomistic visualization: space-time multiresolution integration of data analysis and rendering.

作者信息

Bhattarai Dipesh, Karki Bijaya B

机构信息

Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

出版信息

J Mol Graph Model. 2009 Jun-Jul;27(8):951-68. doi: 10.1016/j.jmgm.2009.02.005. Epub 2009 Feb 20.

Abstract

Time-varying three-dimensional scattered data representing snapshots of atomic configurations produced by molecular dynamics simulations are not illuminating by themselves; gaining insight into them poses a tremendous challenge. In order to take the advantage of maximal information offered by these simulations, we have proposed an efficient scheme, which integrates various analysis and rendering tasks together in order to support interactive visualization of the data at space-time multiresolution. Additional data produced by various analytical techniques on the fly represent the atomic system under consideration at diverse length- (e.g., nearest neighbor, next-nearest neighbor or beyond) and time- (e.g., instantaneous, finite intervals or overall averages) scales. In particular, the radial distribution functions, coordination environments, clusters and rings are computed and visualized to understand the structural behavior whereas a variety of displacement data and covariance matrices are explored to understand the dynamical behavior. While the spatial distributions of atoms need to be reproduced correctly during rendering, we take the advantage of high flexibility in rendering other attributes because of the lack of their direct physical relevance. A combination of different techniques including animation, color maps, pathlines, different types of glyphs, and graphics hardware accelerated approach is exploited to render the original and extracted data. First-principles molecular dynamics simulation data for liquid systems are used to justify the effectiveness and usefulness of the proposed scheme.

摘要

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