Basis optimization CLI

[pfebrer]

Here is the PR with the basis optimization CLI.

Probably I should add something to the documentation.

@zerothi could you test if it works fine for you? You just need to have the inputs for a calculation in a directory and then run:

stoolbox basis optim --geometry file.fdf

The only constraint is that the fdf file can't be named RUN.fdf.

EDIT: If you want to optimize with BADS (the default optimizer) you just need to install pybads:

pip install pybads

[zerothi]

Seems like we should move the basis optim writer to the _yaml_reader and rename it.

[zerothi]

@pfebrer could you please review my comments, then we should get it in asap (note I forced pushed a rebase!)

[pfebrer]

Hey, I have answered them, sorry I think I was too busy when I saw the review

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 22.09302% with 67 lines in your changes missing coverage. Please review.

Project coverage is 86.82%. Comparing base (58d60d8) to head (ec336e9). Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/sisl/_lib/_argparse.py	22.61%	65 Missing :warning:
src/sisl/_core/periodictable.py	0.00%	2 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #910      +/-   ##
==========================================
- Coverage   86.92%   86.82%   -0.10%     
==========================================
  Files         412      412              
  Lines       54332    54413      +81     
==========================================
+ Hits        47227    47244      +17     
- Misses       7105     7169      +64     

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[zerothi]

I have some questions, the charge-confinement scheme is not only targeted polarization orbitals. AFAIK, it's use is for non-populated orbitals, and so could be either regular empty orbitals or something else.

I will also add the soft-confinement to play with. Do you have any comments on this before I make changes?

[zerothi]

@pfebrer could you have a look at the latest commit I made, I added soft-confinement, and changed the logic of the charge-confinement (now for q=0 orbitals + polarization orbitals).

Plus some other minor details.

[pfebrer]

Regarding the charge confinement and soft-confinement, the basis optimization follows a workflow that Federico determined was general and good enough to optimize the basis in "any" system. So it was not meant to be very flexible in what you can optimize, but that was more a feature than a bug I would say. If you want to change something about the workflow, I would talk to Federico