Add feature to enable overlaying the atoms to the generated AFM images.

[huangchieh]

Fix #363

1. Pass the atoms to the method eval in AFMulator.
2. To distinguish from the default output, prefix can be used when overlaying the atoms.

[NikoOinonen]

I'm not sure I like adding more plotting arguments to eval. The plot_to_dir argument was meant as just a easy thing to use when you just quickly need some basic image output. I think I would only add this option to plot_images and let the user call that method themselves when needed. So the workflow would be:

afm = afmulator(xyzs, Zs, ...)
afmulator.plot_images(afm, ..., atoms=atoms)

We could also do this in a more generic way by passing all possible arguments to the underlying plotting function plotImages with something like:

def plot_images(self, X, ..., **plot_kwargs):
    ...
    plotImages(
        ...
        **plot_kwargs
    )

[huangchieh]

Indeed, passing all possible arguments to the plotting function plotImages is much more elegant. I updated.

[codecov]

Codecov Report

❌ Patch coverage is 16.66667% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.58%. Comparing base (c6e7e74) to head (0448c4f).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
ppafm/ocl/AFMulator.py	16.66%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #364      +/-   ##
==========================================
- Coverage   55.61%   55.58%   -0.04%     
==========================================
  Files          40       44       +4     
  Lines        6252     6268      +16     
==========================================
+ Hits         3477     3484       +7     
- Misses       2775     2784       +9     

Flag	Coverage Δ
python-3.10	55.58% <16.66%> (?)
python-3.11	55.55% <16.66%> (?)
python-3.12	55.55% <16.66%> (-0.06%)	⬇️
python-3.13	55.55% <16.66%> (?)
python-3.8	55.50% <16.66%> (?)
python-3.9	55.50% <16.66%> (?)

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[NikoOinonen]

Thanks, looks good now.