Hi Peter (et al.), It was a really positive meeting and I'm looking forward to lots of good things coming out of it over the next few months.
The infrastructure is there to provide a suite of tools that could change the way that we do computational chemistry, so it's now just a case of keeping the momentum going and building on what has already been done. I was actually thinking that the dictionaries - and particularly the top "compchem" one - could become a really valuable resource by themselves. Currently there is no "official" site where you can go to find out what MP2 or CCSD(T) means, what a basis set is etc. If the definition within the dictionary was reasonably thorough and had links to the relevant papers etc, with a bit of stylesheet magic, it could be turned into the first place people would turn to when looking to start learning about a particular aspect of computational chemistry. Also, as Peter has already pointed out, with a minimal bit of web programming, it would be possible to use the other dictionaries to provide a list of which codes provided which functionality, so that if you wanted to run an MP2 calculation with a cc-pvdz basis set, the site would list which codes supported that functionality. I was thinking that sort of thing might make the perfect final-year project for a chemistry/cheminformatics student? Many, many thanks for the Blue Obelisk Peter. I'm not entirely sure I deserve it having seen all the great stuff that Sam and Noel did before they got theirs, but I am extremely grateful. Unfortunately, I'm of no-fixed-abode for the next 6-months to a year, but hopefully we'll meet again in the not too distant future and you can give it to me then. I'm only going to be in sporadic email contact from now on, so I wish you all well and look forward to seeing what happens with the project. Best wishes, Jens On 25 March 2011 09:26, Peter Murray-Rust <pm...@cam.ac.uk> wrote: > Just a quick note to record an extremely successful event at Daresbury, > sponsored by Daresbury and EPSRC where we were able to build a > proof-of-concept infrastructure which takes log files and converts them to > CML. The CML obeys the CMLComp convention and so can be read into a semantic > repository (chempound). We have made varying amounts of progress on the > following codes: > * GAMESS-US > * GAMESS-UK > * Gaussian (various flavours) > * NWChem > * Molcas > * Turbomole > * QuantumEspresso > * Dalton > > For all of these there is now a framework that translates raw logfiles into > semantic CML. These files can be directly read and analysed by Avogadro and > we hope to soon have a semantic logfile browser in it. > > Some of the programs are highly parsed, others are more stublike. The > framework allows a collaborative community to increase the functionality of > the parser without needing to write procedural code. > > All parsed material must conform to the convention and dictionaries. This > makes it possible to build a reliable toolchain for converting the output of > any program into the input of any other. (The input facility is less > generally advanced at this stage). For details (and please get involved!) > http://quixote.wikispot.org/Front_Page. > > I would particularly like to thank Jens Thomas from Daresbury who has put > huge amounts of effort into this and is now taking a break from Science. We > shall miss you Jens. > > Had I had a minute to think about it I would have brought a Blue Obelisk. So > please accept the award of a Blue Obelisk even though it's virtual at > present. Let me know where to send it... > > P. > > > > > -- > Peter Murray-Rust > Reader in Molecular Informatics > Unilever Centre, Dep. Of Chemistry > University of Cambridge > CB2 1EW, UK > +44-1223-763069 > ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
