ccViz

The eMinerals project has done a lot of work on adding CML output to our simulation codes with the development of the FoX library.

For much of our data, we use a subset of the Chemical Markup Language (CML); this subset is defined within the document [link]

This subset of CML is intended to be sufficient to describe and contain all data produced as the output of a computational atomic-scale physical/chemical/materials-science simulation. Currently it is used by the following list of codes: SIESTA, DL_POLY_3, CASTEP, GULP, but we anticipate that it will be of use to any similar code.

One important use of this CML subset is to provide a rich user interface to the code output - to help the simulation scientist visualize the output in a much more direct and appealing fashion than scanning through a text file.

To this end, we have written a tool, called ccViz (for "computational chemistry Visualizer") which uses XSLT to transform the CML into assorted formats for easy browser-based visualization.

Content is produced in three forms: XHTML for textual output; SVG for 2-dimensional plots of relevant quantities (eg graphs of energy by timestep, or radial distribution functions), and embedded Java applets, Jmol[link] for viewing molecular structures. 

All of these are produced by a single transformation as a single file, which can be viewed within any modern web browser, degrading gracefully where appropriate facilities do not exist, and which may be easily saved or transferred.

Examples for SIESTA and DL_POLY output are available here[link] and here[link]. Note that these are produced on-the-fly from the raw CML (which is available here[link] or here[link] for comparison, so may load slowly.

The XSLT is freely available, and may be used simply by referencing "http://www.eminerals.org/XSLT/ccViz.xslt" in an XSLT transformation process. 

Documentation is available here[link], and the scripts themselves may be downloaded by interested parties from here[link]. It is recommended that all users use the canonical copy at http://www.eminerals.org/XSLT/ccViz.xslt whenever possible, since that will be updated to include any new features and bug fixes automatically.

General references

A more detailed description of ccViz and its design may be obtained as a pdf file from the following link:

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