Re: [cclib-devel] XML output of comp chem programs

[Noel O'B. <bao...@gm...>]

Thanks for the info.

Just to be clear. It's not at all the main aim of cclib to XMLise the
output of comp chem programs - we are not even that interested in
extracting data that isn't useful for visualisation (we like
frequencies and cartesian displacement vectors) or implementing
algorithms (we like matrices).

But it would be nice, and not very difficult, to write extracted data
from cclib's internal representation to an XML file if a standard
existed for harmonic frequencies, and so on.

I'm happy to give a demo at the least excuse, although your place is
probably better than mine for that purpose...:-)

Regards,
   Noel


On 16/02/07, peter murray-rust <pm...@ca...> wrote:
> At 10:07 14/02/2007, Noel O'Boyle wrote:
> >Hello Peter,
> >
> >I was wondering do you have any names/contacts who could fill me in on
> >the current state of interoperable XML output for computational
> >chemistry packages. According to google, there have been some meetings
> >regarding this, but this is nothing concrete on the web.
>
> I have now looked at the cclib home page and think progress could be
> made fast. I have copied Toby in case he has comments.  We should
> meet informally soon and you can show me cclib
>
> P.
>
>
>
> The major efforts in this area come from:
> - eMinerals - a uk-based eScience group with some other connections.
> This includes programs such as GULP, SIESTA, CASTEP, METADISE,
> DL_POLY, and some others
> - COST D37. A Euro project at an early stage. We are starting to
> address aspects of interoperability in mainly atomic codes such as
> VAMP, DALTON, etc.
> - MOPAC, GAMESS-US. I am doing this in conjunction with the authors
> - CECAM2006 - this covers ABINIT, MOLPRO, GAMESS-UK, etc.
>
> The key approach is via libraries. Toby White has developed FoX for
> FORTRAN - I have copied him.
>
> In general a code requires a dictionary. The creation of a stub
> dictionary and CMLised code is of the order of 2-4 weeks depending on
> the level of rigour and comprehensiveness. (There are some outputs
> which never need to be marked up)
>
> >There has been some talk among the cclib developers regarding this,
> >but I'm not keen on doing it if there isn't an agreed standard. It
> >doesn't have to be a complete spec from our point of view, but just
> >enough to cover information that is commonly read into visualisation
> >programs, for example.
>
> Java programs can use JUMBO. C++ is not formally supported, nor is
> Python. It shouldn't be too difficult to extract those from (say)
> OpenBabel and other sources if you only want a library.
>
> What programs do you wish to do and what does it entail?
>
> P.
>
>
>
> >Regards,
> >   Noel
>
> Peter Murray-Rust
> Unilever Centre for Molecular Sciences Informatics
> University of Cambridge,
> Lensfield Road,  Cambridge CB2 1EW, UK
> +44-1223-763069
>
>