Fix issues 213, 215, and 219

[lohedges]

This PR closes #219 by only excluding non-bonded interactions between from/to ghost atoms within the same molecule. This is one of several possible solutions (probably) the easiest. The issue in #219 can also be avoided by using a distance restraint between the alchemical ion and perturbable molecule, but this isn't used in somd1 and the implementation works without issues. Regardless, I think that the logic to exclude the non-bonded interactions was only intended for atoms within a perturbable molecule anyway.

In the fix I've just reused the existing start_indices vector to work out the molecule index. I'm happy to also create a atom_to_mol container or similar to avoid the double molecule index search. (This was just a quick fix, re-using what we had.)

Note that I've currently skipped the CI. I can trigger once we resolved issue #217. This PR supersedes #216.

• 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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Suggested reviewers:

@chryswoods

[chryswoods]

This looks good - I am happy with the code you've used to detect molecules. It is very simple. We can look to optimise it in the future if needed. I guess this would only possibly impact things when we have, e.g. perturbable proteins?

[lohedges]

Yes, I doubt it's much of a performance issue. If needed, it's trivial to keep track of the molecule indices as the ghosts are detected. I just did this as the simple first fix and thought I'd optimise once we knew it fixed the problem. (And if optimisation was needed.)