Nexus: Fix improperly formatted docstrings, and/or adapt them to numpydoc

[brockdyer03]

Proposed changes

The docstrings for the following functions were updated to be compliant with (play nice with) numpydoc:

• nexus_base.NexusCore.log()
• numerics.ndgrid()
• machines.Supercomputer.validate_queue_config()
• pseudopotential.GaussianPP.simplify()

What type(s) of changes does this code introduce?

• Documentation or build script changes

Does this introduce a breaking change?

• No

What systems has this change been tested on?

Laptop, Fedora Linux 43 (KDE Plasma Desktop Edition)
AMD Ryzen 7 PRO 7840U (8 cores, 16 logical processors)

Python        3.14.5
uv            0.11.19
cif2cell      2.1.0
coverage      7.13.5
h5py          3.16.0
matplotlib    3.10.9
numpy         2.4.4
pycifrw       4.4.6
pydot         4.0.1
pytest        9.0.3
pytest-cov    7.1.0
pytest-order  1.4.0
scipy         1.17.1
seekpath      2.2.1
spglib        2.7.0
sphinx        9.1.0

Checklist

• • I have read the pull request guidance and develop docs
• • This PR is up to date with the current state of 'develop'
• • Documentation has been added (if appropriate)

[prckent]

LGTM and safe enough to merge

[prckent]

Test this please