Dan Wilson

Over the last couple of years, I’ve spent quite a bit of time working with Chemical Markup Language (CML) as part of my day job. As its name suggests, this is an XML language for chemistry, and it is gaining more and more traction in the field of computational chemistry.

Many of our codes now output CML directly, in addition to their normal output files, which greatly simplifies post-analysis. Rather than writing tools which read proprietary output files, and which have to be modified for use with each different code, we can write tools which work with the CML, and (theoretically, at least) they will work everywhere. For complex analysis tasks, Andrew Walkingshaw’s Golem toolkit provides libraries for dictionary-driven processing of CML files. For visualisation, Jmol can display chemical structures, and Toby White’s ccViz is very useful for turning CML into XHTML, for visualisation with a web browser.

Anyway, to get to the point of this post… There are two announcements I would like to make! First, my work with Andrew Walkingshaw on adding CML output to the CASTEP code, is at long last available to UK academics via the CCPForge website. Hopefully it will also be available in the next commercial release from Accelrys. Not all calculated properties are currently marked-up. If you have any specific requests, please let me know.

Secondly, I’ve opened a public repository of CML-related post-processing utilities on GitHub (if you haven’t heard of it, think Sourceforge done right). It’s a little barren at the moment, but I have quite a few things I plan to upload in the near future. If you have anything to contribute, please let me know.

That’s it for now!