I want to visualize the vibrational modes of some molecules and present them alongside their predicted spectra. Using Psi4 (1.3.2) and these commands:
set normal_modes_write on and
molden(wfn, 'struc.molden', density_a=wfn.Da()), I was able to combine the structure and vibrational frequencies into a single Molden input file. But together, they still didn’t give me IR or Raman intensities when read by either Avogadro or Molden. A minimum working example of my h2o.in is here.
Somehow, I don’t know which command did it for me (maybe someone can let me know, so I can learn), I got the IR intensities to be summarized alongside each vibrational mode in the Psi4 output file with the command:
e, wfn = freq('hf', return_wfn=True). Example output files after running the above input file are here.
I have cobbled together a Molden input file using my own python script combining the two Molden output files and the overall Psi4 output file, all produced when I run Psi4, into a combined Molden input file that has the IR intensities. But I still am not able to get something that looks like the Raman intensities, or polarizability of each mode.
As an aside, I got Avogadro to read the file produced by my script and use the vibrational information sometimes (but not every time…I don’t know why). Screen capture here. It doesn’t read in the intensities, although I feed them, but only the frequencies. Otherwise, I cannot get Avogadro to read vibrational information at all. Maybe someone could tell me why.
It is highly likely I am going about this all wrong, and I welcome someone helping point me in a better direction. Is there a command I am not finding which gives me these intensities and puts them in the right format for Avogadro or Molden to read?
Thanks for any help, and especially for your patience if this post is wordy and unhelpful.