More COSTly work – DALTON and VAMP

I am honoured to be a member of the COST D37 CCWF working group on interoperability in chemical computing (see Semantic Chemical Computing for the last meeting in Berlin). COST enables European collaboration by not only having group meetings but also by exchanging scientists (STSM – short term scientific missions).
We’re excited by this model because we’ve had two working visits from COST members. First was Kurt Mikkelsen from Copenhagen with the DALTON code (I was away so I may get details wrong). Kurt is interested in physical quantities such as hyperpolarizability and other tensors of high rank. Although the code is fairly ancient – and (I gather) has spaghetti in places – Kurt and colleagues here (Toby White, Andrew Walkingshaw) were able to put enough FoX in that DALTON can be said to be CMLized.
Now we’ve had a visit from Thomas Steinke from Berlin for 2 weeks (Thomas also helps run the COST process). Thomas is a developer on the VAMP program (Tim Clark) which is a semi-empirical code from the AMPAC phylogeny. The code is pretty hairy in places (e.g. backwards GOTOs out of loops) it took us (Thoams, Andrew, Toby and me) about 2 days to get a running version that emitted metadata, calculated NMR shifts, and final properties and coordinates. Yesterday we added the history (steps, cycles, etc.) which is not conceptually difficult but a spaghetti nightmare in places.
So – if you understand a code well – it is possible to make substantial progress to CMLizing it in about 2 days. Well structured code is easy and the difficulties arise primarily from unmaintainble code. I’ll blog this in detail later, but it’s straightforward to output coordinates, NMR shifts (peakList), energies, and a wide range of scalar, array and tensor/matrix properties.
The next phase was to run Andrew’s Golem over the outputs and create a dictionary and we’re now about to convert the results into RDF and put it into our molecular repository. More later…

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