JSON handling for parameterized topologies

[CalCraven]

Seems like there's an issue saving the JSON state of a topology, where the parameters aren't stored at all. Maybe this is a good place to discuss if that's a feature we would want to have.

import gmso
from gmso.parameterization import apply
top = gmso.Topology.load("ethane.json")
assert not top.is_typed()
ff = gmso.ForceField("ethane.xml")
ptop = apply(top, ff, identify_connections=True)
assert ptop.is_typed()
ptop.save("ethane-typed.json")
newtop = gmso.Topology("ethane-typed.json")
print(newtop.is_typed("topology"))

output

False

[daico007]

I think this is already supported, likely need to change the default options and clarify the documentation for this method (https://github.com/mosdef-hub/gmso/blob/main/gmso/formats/json.py#L24-L42)

[CalCraven]

You're right. However, maybe we should make this clear at the topology.save() documentation, because that's the standard way to write things out and it's easy to miss that only a partial topology was saved without the keyword.

[daico007]

Yes, totally support changing the default to True (for saving out a typed structure)

[daico007]

This has been updated in the latest commit in #794

[daico007]

Addressed in #794