Voluminous

Voluminous: Volume Visualization Tool

Authors:

Installers and example data download at: https://code.renci.org/gf/project/voluminous/frs/

Description

Voluminous is a tool developed to assist in the visualization of volumetric scalar fields and in particular for finding and emphasizing locations in the field that separate positive and negative regions.  It was originally developed for the visualization of computational chemistry electron density fields where the input volume represents the difference between two scalar fields.  However, other scientific disciplines that require the interpretation of the difference between fields may also benefit from Voluminous.

We demonstrate the application of Voluminous to data from a computational chemistry project. The visualized data are derived from the difference of the charge density of a Uranium atom calculated with relativistic corrections versus using non-relativistic methods. In the visualization, positive surfaces are red and negative surfaces are blue. The inner, fully opaque surfaces have high (abs) magnitude, and the outer, semi-transparent surfaces have low (abs) magnitude. Slices through the center of the data are also pasted onto the sides of the cube that represents the entire simulation space.

voluminousimage

Specifically this visualization illustrates the angular momentum (orbital) differential mixing that occurs in Uranium using a relativistic method versus a more conventional non-relativistic method.  These visualization techniques are  equally useful in understanding bonding, for example by subtracting from the molecular density the sum of the atomic (or fragment) densities superimposed on the molecular geometry.

This early use of Voluminous was initially revealed at the TeraGrid 2008 visualization gallery and competition.

Support

Partial support (Tilson) for the creation of these and other data sets as well as the computational chemistry codes that generated the raw data was provided by US DOE SciDAC-e award DE-FC02-06ER25764. Additional support from the Renaissance Computing Institute is greatly appreciated.

We also thank our collaborators (esp W.C.Ermler, UT San Antonio) for important feedback on the usability of the tool.

Toolkits

Voluminous is developed using Qt for the application framework and GUI, and the Visualization ToolKit (VTK) for the visualization.

Visualization features

Voluminous enables the rendering of two isovalues in the volume, for each of which a positive and negative surface is drawn.  Surface visibility can be toggled, as can view-dependent transparency, which modulates the opacity of the surface based on the angle between the surface and the current viewpoint, enabling clearer visibility of any surfaces  behind the translucent surface, and better shape-perception of the  translucent surface itself.  In addition, color-mapped slices through the middle of the volume are pasted onto the edges of the volume, with a color map applied.  Additional features include labeled axes, a data label, and the ability to render in a grayscale mode non-color publications.

Examples

Two examples from the quantum chemistry (QC) community are provided at the RENCI download site. For both, all files required to reproduce the QC results are provided. To demonstrate Voluminous, however, only the pre-generated vtk files will be needed. A tool for data conversion is provided. This converts the raw QC data on a grid to the proper vtk format. It can be used as a template for customization.