Add support to LOBSTER >=5.0

[naik-aakash]

Summary

This PR aims to update the lobster.io.inputs and lobster.io.outputs modules to support LOBSTER v5. There are some changes in v5.1, mainly with the format of output files. Also, new output files are generated from fragment orbital analysis. A few new keywords have also been added.

Todos

• add new keywords from lobster >= v5 to the inputs module
• update ICOHPLIST parser
• update GROSSPOP parser
• update Lobsterout parser
• Add parser for POLARIZATION.lobster lobster file (LOBSTER >=5.0 generates this)
• Add parser for BWDF.lobster lobster file
• Add support for COXXCAR.LCFO.lobster, ICOXXLIST.LCFO.lobster, GROSSPOP.LCFO.lobster file parsing
• Add support for DOSCAR.LCFO.lobster, CHARGE.LCFO.lobster file parsing
• Add attributes to lobsterout parser for MOFE generated files
• Add tests

[JaGeo]

@naik-aakash thanks! I was about to start doing it myself 🙈

[JaGeo]

I think we also don't have a parser for the polarization file 😅. But maybe, this can be done in a subsequent pull request

[JaGeo]

@naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?

[QuantumChemist]

@naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?

I was in contact with the LOBSTER developers and they will release a hotfix this week for a bug that prevents the LCFO anaylsis currently. I would suggest to wait with merging until then.

[naik-aakash]

@naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?

Hi @JaGeo , we can do this. I can add test for this updates in next 1 or 2 days.

Also, a bug was found in the new MOFE feature. Thus, I could not generate test files or write parsers for outputs for that specific analysis. In anycase a new version for LOBSTER is expected soon.

[naik-aakash]

Hi @JaGeo, this PR can now be reviewed. I am happy to address any issues that are spotted or needs some change.

[JaGeo]

I left some thoughts. Overall, nice work 😃

[naik-aakash]

Hi @JaGeo, I have now addressed all the review comments where possible. For the Cohpcar and Doscar parsers, I do not see any other way to extract file types from the data within the file itself, so I have left them as they are, and it seems to work for now.

[JaGeo]

So far, we mostly let users choose the filetype (eg Icohps, Icoops). I would do the same here.

[naik-aakash]

So far, we mostly let users choose the filetype (eg Icohps, Icoops). I would do the same here.

Oh, okay. This way sounds much simpler. I have now added the is_lcfo arg to the relevant parsers with the docstrings.

[JaGeo]

This looks great @naik-aakash ! Thank you!

@shyuep @mkhorton this would be ready to merge from my side. Please let us know if we should change anything else. Thank you. The test that fails currently is related to matplotlib and windows and I don't think this has anything to do with our pull request.

[naik-aakash]

Hi @shyuep , now all tests also pass after last merge. If there are no specific comments on the changes, PR is ready to be merged.

[shyuep]

Great. Thanks!