Add note to documentation for usage of CrystalNN

[JaGeo]

Closes #3762 with additional information provided in the documentation.

If you want to add something (e.g., a citation), @Andrew-S-Rosen , please feel free.

Summary by CodeRabbit

• Documentation
  • Enhanced documentation for CrystalNN with details on default weights for inorganic crystal structures and added initialization examples for MOFs.

[coderabbitai]

Walkthrough

The update to pymatgen/analysis/local_env.py includes a note on default weights optimized for inorganic crystal structures and introduces an initialization example for Metal-Organic Frameworks (MOFs) using CrystalNN. This change aims to enhance the functionality and applicability of the CrystalNN class for different types of crystal structures.

Changes

File	Change Summary
local_env.py	Added note on default weights for inorganic structures; added MOF initialization example using CrystalNN.

Assessment against linked issues

Objective	Addressed	Explanation
CrystalNN gives incorrect result for simple aromatic ring (#3762)	❌	The changes do not address the issue of incorrect neighbor detection in aromatic rings.

🐇✨
In the code where atoms lay,
A rabbit hopped by, fixing away.
With a tweak and a hop, structures align,
Now MOFs and crystals, perfectly fine.
Cheers to the code, let's celebrate,
For every atom finds its accurate mate!
🎉🐰

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[JaGeo]

Test failures are unrelated, @janosh ... Not sure qhy they suddenly showed up

[janosh]

failing tests were discussed here #3763 (comment)

[JaGeo]

failing tests were discussed here #3763 (comment)

Thanks!

[Andrew-S-Rosen]

Personally, I'd avoid the recommendation for specific parameters for MOFs in the docstring. There was no formal benchmarking on this (was quite literally whatever we thought looked nice when visualized on MP). I would recommend a more general statement that, for organic and hybrid metal-organic materials one may need to modify x_diff_weight and search_cutoff.

[JaGeo]

Personally, I'd avoid the recommendation for specific parameters for MOFs in the docstring. There was no formal benchmarking on this (was quite literally whatever we thought looked nice when visualized on MP). I would recommend a more general statement that, for organic and hybrid metal-organic materials one may need to modify x_diff_weight and search_cutoff.

Okay, I will adapt. However, a starting point for testing might be helpful.

[JaGeo]

@janosh could be merged if you are happy

[JaGeo]

Merged this now, as it is only a tiny documentation change and all tests are passing.