Feature vsites

[tom-potter-cresset]

This PR adds virtual site support to the Sire-to-OpenMM conversion, via the OpenMM LocalCoordinatesSite virtual site type.

• 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 test for any new functionality in this pull request: y
• I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y/n]
• 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
• I confirm that I have permission to release this code under the GPL3 license: y

Suggested reviewers:

@chryswoods, @lohedges

Any additional context of information?

Virtual site parameters are passed to Sire via properties added to a sr.mol.Molecule, which are converted to OpenMM LocalCoordinatesSites by sire_to_openmm(). Virtual sites are not considered as separate atoms by Sire, so their positions and velocities are not stored in the Molecule or output to trajectories by Sire.

For example:

vsite_dict = {
    "0": {
        "vs_indices": [0, 1, 2],
        "vs_ows": [1, 0, 0],
        "vs_xs": [1, -1, 0],
         vs_ys": [0, 1, -1],
        "vs_local": [0.03, 0, 0],
    }
}
vs_charges = [0.5]
parents = {str(i): [] for i in range(mol.num_atoms())}
parents["0"].append(0)

cursor = mol.cursor()
cursor.set("n_virtual_sites", 1)
cursor.set("vs_charges0", vs_charges)
cursor.set("virtual_sites", vsite_dict)
cursor.set("parents", parents)
mol = cursor.commit()

[lohedges]

If this is redundant, could the comment line be removed.

[lohedges]

Remove if no longer needed.

[lohedges]

Thanks for this great contribution. I'll work on updating loch to support OpenMM systems containing virtual sites.