[WIP] Atomate2 support in OpenMM

[orionarcher]

Summary

This PR ports over functionality from atomate2-openmm developed by @xperrylinn and myself. It includes:

• Support for setting up OpenMM InputSets using pymatgen.io.openmm
• Standard classical MD workflows operating on OpenMM inputsets
• Optionally recording trajectory and simulation state information to AWS
• Rich metadata on simulation setup for downstream analysis with Emmett

Additional dependencies introduced

• openmm
• openff-toolkit
• mdanalysis
• pymatgen.io.openmm
• packmol
• openbabel

These are all necessary for the classical MD setup and execution workflow.

TODO (if any)

• Tests are not fully passing yet in atomate2
• OpenMM input sets, which are used as the input and output of jobs, can be very large and a more compact solution is needed

Checklist

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• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.

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Questions:

Best way to deal with new requirements?

[utf]

Hi @orionarcher and @xperrylinn, this looks great. Thanks for contributing this back to atomate2.

On first glance, the code looks very nice. I'll try and get some proper comments back to you in the next few days.

[orionarcher]

Thanks @utf!

Head's up that we are working to reorganize the code around the OpenFF Interchange object, which is a much closer analog to Molecule or Structure than an OpenMMInputSet, which is what we are currently using. This should let us better delineate what is being simulated vs the details of the simulation. Much of the OpenMM code will remain the same but the basic input and output of jobs will change. I'm hoping to add that to the PR in the next week or so. May be best to hold off on a close review until then.

[utf]

Ok, thanks for the heads up. I'll hold off reviewing for now. Let me know when you want me to take a look.