Hi Miguel,
Part of the problem is also that I am not completely sure of the direction that Jmol goes with dealing with multiple structures, vibrations and other meta information for a particular nuclear arrangement. That was the reason I tried looking at the CML format, hoping that it would allow me to define the information in a very hierarchical fashion by encapsulating molecular structures (i.e., the vibration, with the symmetry, energy, transition moment etc) and optimization steps as a different set of structures within a molecular structure (the final optimized geometry, which has its energy, symmetry, orbital energies, dipole moment, quadrupole moment and all kinds of other things). By allowing a list of those, one could handle a run where a particular run does a scan over a nuclear coordinate (e.g. a changing bond distance) and have each geometry optimization as a set of structures associated with the final geometry for each of the steps in the scan (and possibly also a frequency analysis for each step, if one calculated that too). I can't see from the current Readers how that may be done, and I haven't been able to figure that out from the adapter either. (A lot of code to look through and try to understand :-).
We spent Tuesday working out how to support the output of compChem programs in CML. It's not trivial as the order and type of information is very variable. There are methods in Jmol to support vibrations but the semantics are implicit (i.e. concatenating files of equal size). There is a difficult balance between being very specific (elements called <vibration>) and more general (<eigen>) for example. For every element someone has to write some code :-) - and not just to render the object.
If you have specific requirements please feel free to mail.
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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