orca.py stucks in a loop if no NBO analysis was done

[vbochenkov]

Hi @xiki-tempula,
qforce seems to be stuck trying to find the string "Now starting NBO analysis" (in line 468, in _read_orca_nbo_analysis) in orca output file. Here is the file: propane_hessian.log

[selimsami]

This shouldn't cause Q-Force to be stuck and it should be handled more gracefully, but note that you do not seem to have set NBO environment variable for ORCA, Q-Force needs this for the bond order analysis:

Environment variable NBOEXE for nbo6.exe or nbo5.exe not set! Skipping NBO-Analysis

[xiki-tempula]

@vbochenkov Thanks for reporting. Do you mind uploading a new ORCA log file with the NBO set up correctly? It seems that ORCA has now removed the string Now starting NBO, which is used to locate the NBO file. So I could fix this issue if I could know what are the new string to indicate the start of the NBO analysis.

[vbochenkov]

Unfortunately, I don't have NBO, so I cannot set it up. I didn't realize that it is mandatory to have it to run qforce. :(

[selimsami]

@vbochenkov, if you have access to Gaussian, Q-Chem, or xTB, all these methods have either NBO or a bond order analysis tool included in them.

[vbochenkov]

@selimsami, I have access to Firefly, it has NBO tool. So, perhaps, I'll have to work to add a module for Qforce to support Firefly :)

[selimsami]

Appreciated! Note that xTB is free and open source, so you could use it to to test Q-Force before you decide to help the development.

[vbochenkov]

Cool! Thanks for the idea! I'll check it.

[xiki-tempula]

@selimsami Do you have a plan of deprecating the lone pair? If the requirement for lone pair is deprecated, I could make it that ORCA will not need NBO and we won't have these issues.

[selimsami]

Oh nice! Then I will work on this

[selimsami]

@xiki-tempula, this will take me a bit longer. There is some dependency on lone pairs for atom type detection. But I should be able get around that, probably next week.

[selimsami]

@xiki-tempula, depreciation done, see #55

[xiki-tempula]

@vbochenkov Do you mind trying the latest version? The ORCA requirement for NBO has been removed now.

[vbochenkov]

Hi @xiki-tempula, I've got the following error message while testing the new version:
....
Selected QM Software: "orca"
Necessary Hessian output files and the corresponding extensions are:

• out_file: ['.out', '.log']
• hess_file: ['_opt.hess']
• pc_file: ['_charge.pc_chelpg']
• coord_file: ['_opt.xyz']

NOTE: QM atomic charges are scaled by 1.2 to account for the condensed phase polarization.
Set this value to 1 for gas phase simulations.

Traceback (most recent call last):
File "/usr/local/bin/qforce", line 11, in
load_entry_point('qforce==0.6.4', 'console_scripts', 'qforce')()
File "/usr/local/lib/python3.8/dist-packages/pycolt-0.5.3-py3.8.egg/colt/colt.py", line 363, in call
return self._func(**answers)
File "/usr/local/lib/python3.8/dist-packages/qforce-0.6.4-py3.8.egg/qforce/main.py", line 37, in run
File "/usr/local/lib/python3.8/dist-packages/qforce-0.6.4-py3.8.egg/qforce/main.py", line 49, in run_qforce
File "/usr/local/lib/python3.8/dist-packages/qforce-0.6.4-py3.8.egg/qforce/molecule/molecule.py", line 15, in init
File "/usr/local/lib/python3.8/dist-packages/qforce-0.6.4-py3.8.egg/qforce/molecule/non_bonded.py", line 65, in from_topology
File "/usr/local/lib/python3.8/dist-packages/qforce-0.6.4-py3.8.egg/qforce/molecule/non_bonded.py", line 633, in sum_charges_to_qtotal
File "/usr/local/lib/python3.8/dist-packages/PuLP-2.1-py3.8.egg/pulp/pulp.py", line 1686, in solve
status = solver.actualSolve(self, **kwargs)
archive.zip

AttributeError: 'NoneType' object has no attribute 'actualSolve'

The Orca produced files are attached.

[selimsami]

@vbochenkov , I did not manage to reproduce your issue with the files you have provided, it worked fine for me.

Were you using the latest GitHub version or the pypi version? I have now pushed the update to pypi as well (0.6.5), so could you please try again with:

pip install --upgrade qforce

If that doesn't work, can you try upgrading PuLP:

pip install --upgrade pulp

And let me know which step solved your problem.

[vbochenkov]

@selimsami, thank you for the suggestion. I had to upgrade PuLP, and now it works fine! I'm closing the issue. Thanks for your help!