Exclude alchemical ions from the REST2 region

[lohedges]

This PR applies a small fix by excluding alchemical ions from the REST2 region. These are tagged in somd2 using the is_alchemical_ion property, then excluded via a REST2 mask.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
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[mb2055]

There seems to be an issue when running without explicitly defining lambda_windows.
To recreate:

import sire as sr

mols = sr.load(sr.expand(sr.tutorial_url, "merged_molecule.s3"))

mols = sr.morph.link_to_reference(mols)

mols = mols.minimisation(lambda_value=0.5).run().commit()

d = mols.dynamics(lambda_value=0.5, timestep="4fs", temperature="25oC")

d.run("10ps", save_frequency="1ps")

raises TypeError: object of type 'NoneType' has no len() due to line 393. Can probably be fixed by just setting lambda_windows equal to lambda_value in the case where the user doesn't set it.

[lohedges]

Ah yes, good point, I'll just only store num_lambda_windows if not None.

[mb2055]

Looks good