15 Apr 2009 mbanck   » (Journeyer)

Over the Easter holidays, I finally did a bit of real programming again, adding some quantum chemistry related C++ code to OpenBabel and Avogadro. I added support for molecular vibrations to the NWChem and Molden file formats, as well as writing support for the MOLPRO input and output formats mostly from scratch. The latter was something I wanted to do for a long time, as I have been almost exclusively using MOLPRO for my Ph.D. over the last couple of years. The event which sparked my interest was the addition of animated vibrations in the Avogadro 0.9.3 release on April 1st, something I considered one of the last missing features in Avogadro in order for it to be useful as a general purpose quantum chemistry visualization app.

Once I had started coding, I decided to also do contribute to the visualization of molecular orbitals in Avogadro. So far, it was required to have formatted Gaussian or Q-Chem checkpoint files (both seem to use the same format, but you do not usually have those around) or Mopac2000 logfiles (Mopac2000 is non-free, unlike Mopac7, which is in Debian). My patch adds support for reading orbitals from MOLPRO logfiles on top of that. It has to be said that rendering molecular orbitals (while a bit unintuitive from a GUI perspective) is really impressive in Avogadro, thanks to the work done by Marcus Hanwell. See for exampe this picture for a Povray rendered molecular orbital exported by Avogadro.

If I manage to find some more time, I would like to (i) move the basis set and molecular orbital parsing code to OpenBabel, where it rightfully belongs and (ii) enhance and unify the OpenBabel quantum chemistry input file export code, so that they can be used by Avogadro directly. Right now, Avogadro reimplements a GUI and code for exporting an input file for each supported quantum chemistry package (Gaussian, Q-Chem, GAMESS and Mopac2000, currently).

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