D. Bhattarai

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

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.

Atomistic visualization: on-the-fly data extraction and rendering

In this paper, we present an approach involving on-the-fly data extraction and rendering to achieve a real-time integration between analysis and visualization of atomistic simulation data. The integration is demonstrated along two directions: The first direction is to explore coordination environments by rendering spatial variation and temporal stability of the coordination states computed for each atom, and the second direction is to explore the aggregate atomic movement by computing ellipsoids. Ellipsoids are computed from covariance matrices of the time-varying positional data. The proposed approach is applied to visualize the data from first-principles molecular dynamics simulations.