UC-IEG-IX

From EGI Knowledge Base

Use Case title: Visualization of Quantum Chemistry

Short description: Gaussian is a quantum chemistry commercial package which performs ab initio molecular orbit calculations by solving the Schroedinger equation. Gaussian is a much extended software among the quantum chemistry community interested in semi-empirical calculations, therefore we find it extremely interesting to give some kind of support for visualization of Gaussian runs. We have established contact with the chemistry group from the Johannes Kepler University in Linz and demonstrated the interactive & visualisation capabilities of I2G. They seemed to be very interested, since the analysis of the files produced by 'gaussian' was done in a post-mortem manner, with the researchers examining the text file by hand to detect end-of-job conditions

Actors involved:

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The targets of supporting an "interactive gaussian" would be:

• Examining the computational process of Gaussian, (www.gaussian.com), to replace the current post-mortem mode with a real-time/online mode.
• Development of modules instead of monolithic software. These modules should be able to work as data-importer/exporter for other independent renderers such as: Jmol, Molscript, maybe ParaView and Molden.
• A user-interface should be designed and developed in close cooperation with the researchers to make sure that the final result fits their needs.
• Input format
• Gaussian produces data in a "logfile" format. this is a pure text file, in which the information of each computational step is recorded after the step has finished. *The layout of this file is not perfectly clear, so as part of the project, the layout of this file should be analysed and documented as detailed as necessary.

To examine the feasibility of the project (and also to demonstrated the idea about interactive Quantum Chemistry), a logfile-viewer has been already developed written. The logfile-viewer ("logview") is able to read an unfinished gaussian outputfile and display its contents in a 3d graphical window. It is possible to step through the file by pressing the <enter> key, and to go to the beginning of the file by pressing the "w" key. Switching from "space-filling" to "balls-and-sticks" model and back is done by pressing the "m" key, turning molecule labels on/off is done by pressing the "l" key. Navigation is done just as in VTK with left/middle/right mouse buttons and the control-key, to rotate/shift/zoom or rolls the scene. Other buttons affect the representation of the molecules as spheres (flat vs. smooth shading, etc) Distributed tiled rendering was explored too by writing a library to intercept openGL calls and modify them accordingly.

The project itself looks therefore feasible and we have identified the following goals:

• Visualisation. It is the case in Quantum Chemistry visualization that it is relatively simple to display all the information concerning positions of atoms in molecules, but not so easy to isolate what is the relevant information of a particular simulation.
• Density
• Orbitals
• Molecular-display (already present in VMD)
• Vibrations

Interactivity:

• Request Information for Molecules (eg: Mouse over connection displays length)
• Order molecules in a DNA-sequence (w/ partly Intercalation, full Intercalation, outside binding)
• Create new Structure and store it as base for new calculations
• Submit changed Structure as a new Gaussian Job via a Grid interface
• Allow to select a particular Atom and examine more closely
• VMD: create extensions for interacting with a "ReachIn" display (haptic experiencing molecules)
• Eventually: extensions for (interactively) create movie, etc...