Hi Peter,
The way I understand it is that CML allows one to store all kinds of information in a very hierarchical fashion, e.g., a optimized geometry with additional information, the list of structures, possibly with their own frequency structures, that led to the final geometry and possibly a list of structures with the associated vibrational information (frequencies, symmetry, intensity,...). Please correct me if I am wrong in my assumption/understanding of what CML can do. I have to look a bit closer at the CML specifications to be able to put a CML file together that shows what I have in mind.
As Miguel pointed out earlier, I think that one needs to figure out within a context about how a bunch of structures/vibrations are dealt with. What I was hoping for (and maybe this is a proposal), is that Jmol could maintain the hierarchical information and have a tree-like representation for one to pick the visuals for a particular CML node. I think that would required a different way of storing the internals of what Jmol is dealing with. It would allow one to put each of the structures in a certain 'context', as opposed to having a single list of structures/vibrations.
Ren�
On Oct 14, 2004, at 10:32 AM, Peter Murray-Rust wrote:
At 09:15 10/10/2004 -0400, Miguel wrote:Rene wrote:
> I would like to get your input on whether you think it may be better to
write a conversion program that creates a CML2 file which then could be
read by JMol. I was hoping that one could add additional information
about each molecule in the file. For instance if one had calculated the
ground state and excited state energies for a set of configurations, or
energies of occupied valence shell orbitals, it may be nice to be able
to show one or more of these as a function of the configuration, or
better still the nuclear coordinate that was used in generating the set
of molecules.
We are currently working with CCP1 (a UK Research Council centered on Daresbury Lab) on basis sets in CML. There is not complete agreement yet on their representation. Your input would be valuable
> I downloaded some CML stuff, but that is incredibly hard to follow....
If you want to learn more about CML then Egon can help.
Feel free to write to me as well. CML is extensive (it covers a considerable amount of chemistry). If you are familiar with XML it shouldn't look so difficult. There is a summary of the components on http:?/wwmm.ch.cam.ac.uk/moin/ChemicalMarkupLanguage
HTH
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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