LAMMPS engine updates#8
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Still need to complete the analysis cleanup.
…til_decorrelated `run_until_decorrelated` should account for time reversibility
Updates to docs/examples
…alysis Fix pandas API change: set_value -> at
…omvelocity Refactor RandomVelocity so engine can do the work
…-1.2 Release 1.2
Bump master version to 1.3.0.dev0
Fix pandas Deprepaction and Future Warnings
…l_ensemble Fix missing newline in the VisitAllStatesEnsemble
Ran tests and reloaded old files, so this shouldn't break things
np.array with no shape should return float
SimStore: Support for OpenMM snapshots
…lify SimStore: Simplify OPS Storage constructor
fix numpy 1.19 DeprecationWarning: tostring()
Fix: OPS hangs when external engine errors/exits unexpectedly
…houldn't be put on master" This reverts commit c2d47f0.
…updated_pr Reactive flux (updated PR)
…-1.4.0 Release 1.4.0
Bump 1.4.1.dev0
fix omt is None error in test suite
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This PR is a sub-PR of openpathsampling#697. If you merge this now, it will become part of that PR (not part of the OPS core).
I'm giving a talk about the OPS/LAMMPS interface on Tuesday, so I thought I should learn how to use it. I put together a little TPS demo -- LJ phase transition from gas to droplet, which was part of a the PRL on nested TPS that came out this week (Peter and Gabor Csanyi). I'll add that example sometime soon, too.
Updates:
configurationstostaticsandmomentumtokineticscomputestatement in an OPS CV.Still to do: write unit tests and docstrings for these updates. But that might be a while. Your choice on whether you want to merge this in as part of your main PR or wait on it until the tests are in place.