On Sun, Mar 29, 2009 at 8:32 PM, Jonas Baltrusaitis email@example.com wrote:
What about the variety of other spectroscopic data calculated which I mentioned before? Can those easily be incorporated (selected from some drop down menu). What about other packages (NWChem, ORCA etc)
That’s something I wouldn’t mind working on – I’ll have to read up on
how to get the calculated data to transform into spectra, but it might
be a good idea at some point to move vibrationplot.* out of the
Vibrations extension and into a new spectra extension.
For now I’d just like to get the vibrational spectra cleaned up and
finalized (ish), then it should be a simple matter to extend it to
plot other spectra.
I’m thinking that the vibrationplot.* dialog would be the main dialog
for the extension, but as Jonas has suggested, put a drop down
menu in that contains the various types of spectra that can done with
the loaded molecule, and just update the plot when the selection changes.
While on the topic, does anyone know if there is a better way to
convert from the calculated intensities to transmittance than what
I’ve got right now? As it stands, transmittance is being calculated
t = i / maxIntensity; // Normalize
t = 0.97 * t; // Keeps the peaks from extending to the
limits of the plot
t = 1 - t; // Simulate transmittance
where i is the intensity of the vibration.
Also, I’m toying with the idea of fitting a gaussian to the peaks. The
more I think about it, it seems like it would just be aesthetic and
rather useless. At worst, misleading even, since AFAIK there is no way
to get the width of the peak from the calculated data. Any thoughts?
A third question for the experienced folks (e.g. not me ): Is there
a way to separate out the vibrations that are IR vs. Raman active? I
imagine it would be possible to go through and calculate dipole
moments and polarizability tensors for each mode, but that sounds like
a nuts&bolts-type job for the openbabel package. Does something like
this already exist?