BMIM Cl bond formation benchmark

[PythonFZ]

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Summary

This benchmark introduces a check for the formation of a Cl-C bond in the ionic liquid BMIM Cl.
Some models show a bond formation which should not happen.
The test runs

1. Build BMIM Cl system
2. Run geometry optimization
3. Run 5 ps MD
4. Compute C-Cl RDF
5. Check if the RDF shows bond lengths shorter than 2 A (furthest covalent bond distance), if so mark as failed.

Added https://github.com/zincware/molify for creating initial configurations to the list of depedencies.
This package is the successor of https://github.com/zincware/rdkit2ase
which is already included via
https://github.com/basf/mlipx/blob/9ee4a5453aeaafc3109c2cac399de0363249367b/pyproject.toml#L21

Linked issue

Resolves #

Progress

• Calculations
• Analysis
• Application
• Documentation

Testing

[ElliottKasoar]

Thanks for this! I'm testing it now, but overall it looks great! Please can you rebase as I think there are conflicts with uv.lock due to recently merged changes

[PythonFZ]

Thanks for this! I'm testing it now, but overall it looks great! Please can you rebase as I think there are conflicts with uv.lock due to recently merged changes

I hope to have addressed all comments and rebased onto main

[ElliottKasoar]

Thanks for this, @PythonFZ!

I may return to this with some minor requests following some changes being added in #360, but I think this looks great!