[WIP] Modify charge neutrality verification in DielectricConstant

[orionarcher]

This PR allows DielectricConstant to check charge neutrality at a customizable granularity.

I work with electrolyte systems where fragments are molecules in the system. In the current scheme, DielectricConstant will fail on my systems because ions have non-zero charge. This adds a keyword to modify the level at which charge neutrality is enforced.

I think changing the hard-coded option to "group" to simplify the API would also be a good fix, it's unclear to me why "fragments" is desirable.

Fixes #

Changes made in this Pull Request:

• add new check_neutrality_of kwarg to DielectricConstant

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4249.org.readthedocs.build/en/4249/

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[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.01% 🎉

Comparison is base (acfd122) 93.40% compared to head (5cf79a1) 93.41%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4249      +/-   ##
===========================================
+ Coverage    93.40%   93.41%   +0.01%     
===========================================
  Files          169      183      +14     
  Lines        22204    23310    +1106     
  Branches      4064     4064              
===========================================
+ Hits         20740    21776    +1036     
- Misses         948     1018      +70     
  Partials       516      516              

Files Changed	Coverage Δ
package/MDAnalysis/analysis/dielectric.py	100.00% <100.00%> (ø)

... and 14 files with indirect coverage changes

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[hmacdope]

Seems reasonable to me, would need some tests ofc, but understand its WIP.

[orionarcher]

Great thank you, wanted to get a second opinion before updating changelog and writing tests.

[PicoCentauri]

@orionarcher if your system has free charges/ions you can not use this module because the equation does not hold if you have free charges.

[orionarcher]

Got it. Thanks for the clarification @PicoCentauri.

[PicoCentauri]

Yes, you are not the first one that run into these problems. It might be worth to explain this in the docstring.

[orionarcher]

How challenging do you think it would be to implement a dielectric calculation that could handle free charges / ions?

[PicoCentauri]

What you have to do is to calculate the frequency dependent dielectric spectrum and take the zero frequency limit to get the dielectric constant. I did the implementation once, but the code never made it into the main branch, because I branched off too far. 😅 It would be wonderful too have this in mda.

Details on the theory are i.e. explained here. See equation (10) and section S6 in the SI.

[orionarcher]

Thanks for sharing! I'll need to implement this myself in the next couple months. I'll ping you when/if I pick it back up.

[PicoCentauri]

Sure! You can also always ask me on Discord!