Visualization of natural orbitals

General Discussion Support
1

Environment Information

Avogadro version: 1.2.0
Operating system and version: Windows 11 64-bit
Dear all,
I would like to visualize in Avogadro natural orbitals, which I calculated by MP2 method with ORCA 5.0.4 software. I created .fchk file by Multiwfn, but in Avogadro only canonical orbitals are seen.
Could you tell me, what should I do to visualize them?

2

If you calculated the natural orbitals in Orca, are they in the output? If so, that may be the easier way (or getting Orca to output them to molden via orca2mkl)

I’d be happy to take a look at the fchk file, but there’s nothing we can do for the Avogadro 1.2 series - it is not supported. (We cannot even build it because the libraries are too old.) On the other hand, it would be fairly easy to add for Avogadro2 nightly build (e.g. https://two.avogadro.cc/)

3

Yes, they are in input.
Files are available below:
https://drive.google.com/drive/folders/1v1nrnJOg-lZOKpNPMPIRJobTjAw_MHqU?usp=sharing

4

The output file has Natural Orbital Occupation Numbers but no coefficients / eigenvectors for them. I don’t see anything specific in the fchk file for natural orbitals. Since I’ve never used Multiwfn - are you sure that when it writes the fchk that it’s writing the natural orbitals?

The Multiwfn manual mentions generating natural orbitals from the fchk, but I don’t see anything about writing the SNO out after the analysis. As I said, I’ve never used it so I might be missing something.

As for the Orca output - the Avogadro2 import will read / plot orbitals when the basis set information is printed. But it’s missing in that file.

5

Please provide all information on how you created the fchk file. Especially the command line syntax you used.

Without that, I can only guess:

  1. I assume you used ‘orca_2mkl basename.gbw basename.molden -molden -allorbs’ to create the molden file for multiwfn.
  2. you opened the basename.molden file in multiwfn and saved it as fchk file.
  3. you opened the basename.fchk file with avogadro2

If this was the case, you used the wrong wave function file !
You have to use orca_2mkl with basename.mp2nat instead of basename.gbw. Orca writes the mp2 natural orbitals into basename.mp2nat and the delocalized molecular orbitals into the basename.gbw.

Try:

  1. orca_2mkl basename.mp2nat basename.molden -molden -allorbs
  2. open basename.molden file with multiwfn and saved it as fchk file.
  3. open basename.fchk file with avogadro2
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6

I tried something similar and now it works!
Thank you!

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7

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