Extend protocols results with helpful quantities for analysis

[ijpulidos]

It is useful to think about appending to the protocol results values or quantities that are expected to be needed for the analysis.

Candidates of such quantities could be:

• Convergence of the free energy estimate (time series of FE)
• Mixing of replicas (for the Repex protocol)

Others?

[ijpulidos]

@JenkeScheen @jthorton Are there any in particular that could be useful for the work you are doing with asapdiscovery-alchemy?

[richardjgowers]

Just an FYI for how this works from a Gufe perspective. Anything you put in the output dictionary from ProtocolUnit._execute should get communicated back home. So for the perses eq-RFE Protocol we're including plenty of extra dicts: https://github.com/OpenFreeEnergy/openfe/blob/main/openfe/protocols/openmm_rfe/equil_rfe_methods.py#L1030C1-L1036C10