molden files and orbkit

[Audiochemie]

Hi Felix, thanks for the nice program. It is really helpful!

I ran into trouble though trying to compute particle hole densities and transition densities with the orbkit interface.

  File "xxx/TheoDORE_3.1.1/theodore/lib_tden.py", line 745, in compute_rho_0_n
    cube_ids=lib_orbkit.compute_rho_0_n(
  File "xxx/TheoDORE_3.1.1/theodore/orbkit_full.py", line 139, in compute_rho_0_n
    qc = self.orbkit_geo_ao_conversion(mos, molden_file=molden_file)
  File "xxx/TheoDORE_3.1.1/theodore/orbkit_full.py", line 47, in orbkit_geo_ao_conversion
    qc = read.read_molden(tmp)
  File "xxx/orbkit/orbkit/read/molden.py", line 370, in read_molden
    sym = sym[0].split('.')[-1]

Presumably this is linked to the fact that not the molden file specified in the input is used, but a temporary file which only contains the molden file header and a bit of a mo section. orbkit fails to read as it (rightfully) awaits mo coefficients. As I do not see a good reason for a temporary file to be passed to orbkit, I'd suggest to simply use the molden file specified by the user this should fix the issue.

Best regards Timo

[felixplasser]

Hi Timo, I am happy to have a look at that if you upload the full set of files TheoDORE reads.

The orbkit interface is not super robust. So, there might be an easy fix ...

[Audiochemie]

Thanks for the fast response. The involved files still create a gz > 50Mb so I created a smaller example, which throws the same exception. I think it should be an easy fix. Maybe extend the orbkit interface to accept **kwargs and pass sth like molden_file=xxx?

theodore_troubleshooting.tar.gz

Best Timo

[Audiochemie]

Thanks for the fast response. The involved files still create a gz > 50Mb so I created a smaller example, which throws the same exception. I think it should be an easy fix. Maybe extend the orbkit interface to accept **kwargs and pass sth like molden_file=xxx?

theodore_troubleshooting.tar.gz

Best Timo

I forgot to adapt the molden file. As I mentioned here orbkit has a problem with negative floats without leading zeros.

[felixplasser]

Hi, I had a look at this. In the first instance this tells me

FileNotFoundError: [Errno 2] No such file or directory: 'singlet1.in.out'

So, I guess we'd need that file as well.

Does the test work for you.

cd EXAMPLES
pytest-3 EXTRA/fa2.orbkit

[Audiochemie]

Whoops... I renamed the file to mrci.log and didn't change it in the dens_ana.in. Don't know why I did that. Here's a - hopefully - working archive: theodore_troubleshooting.tar.gz The test fails with the same error message as posted above.

[felixplasser]

Ok, if the test also fails, then this indicates a problem with the installation or orbkit version. I had a go with your files. It all works. As a proof I am attaching some figures made with qc_pymol.

[felixplasser]

Maybe the safest way to do it is to clone the git repo with all the same versions that I am using git clone --recursive https://github.com/felixplasser/theodore-qc.git

This sets symlinks to orbkit and cclib.

Then you install orbkit as described here https://theodore-qc.sourceforge.io/docs/installation.html#external-packages

Do you want to give this a go?

[Audiochemie]

Yeah I'll try to sort it out! Thanks for the help.

[Audiochemie]

A reinstall with the recursively cloned repo worked. :-)