Visualizing the frequency calculation result on Molden 5.0?

1

I am new in PSI4. I know PSI4 can write output file in Molden format, which can be done by setting MOLDEN_WRITE to be true. It works very well.

I tried to set MOLDEN_WRITE to be true in frequency calculation. I got a file in molden format after the frequency calculation. However, it seems that vibration of the molecule cannot be visualized on Molden 5.0, even though the MOs and charge density can be seen. My input file is as below:

set basis cc-pVDZ
molecule {
0 1
H 0.63109 -0.02651 0.47485
O 0.14793 0.02998 -0.34219
H -0.77901 -0.00348 -0.13266
}
set molden_write true
frequencies(‘scf’)

1 Like
2

@cpjwong

I believe that the option molden_write will only write the MOs in molden format currently. I don’t know if this functionality exists in PSI4, but my knowledge of PSI’s features is far from exhaustive.

3

@amjames

Thank you for your answer. I think it may be possible to do so if I can write a program that can output a molden format file for visualization of vibration of atoms. As the psi4 frequency calculation result contains the displacement of atoms at different frequencies. However, I have no idea of the format of a molden file for visualization of vibration. Would you mind telling me where I can get this information?

Regards,
Jeremy

4

@cpjwong This page has the molden documentation for input files.

If you get a script/program working to do this and you put it out in the open (ie github) feel free to post a link back here so others can use it!

5

Psi4 is interfaced with WebMO, which can nicely animate vibrational frequencies

1 Like
6

Thank you, Prof. Sherrill.

I learn quantum chemistry by watching your lecture videos on youtube. Then, I got to know PSI4 when I read the notes on your homepage. I love the free software and the course materials, and got very excited when I read your note on how to code Hartree-Fock method. Thanks for making these materials free for everybody in the world.

7

Hi Jeremy,

Molden works great with reformated and complemented PSI4- standard output. Rules are given here: http://www.cmbi.ru.nl/molden/molden_format.html.

Regards
Bernhard

8

Sorry for the late reply. I have written a script to read the output file of frequency calculation and generate a molden input file for vibration visualization. My script is not well-written, but it could do the job for me. Thanks for all your comments and advice.freq_gen.py (2.5 KB)