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SimStore part 2: Storable functions (and more)#929

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dwhswenson merged 37 commits into
openpathsampling:masterfrom
dwhswenson:storable_functions
Oct 31, 2020
Merged

SimStore part 2: Storable functions (and more)#929
dwhswenson merged 37 commits into
openpathsampling:masterfrom
dwhswenson:storable_functions

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@dwhswenson

@dwhswenson dwhswenson commented Sep 25, 2020

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This is the second PR in the process of updating the OPS storage subsystem, following on #928. See #928 for overall motivation.

Major improvements in this PR:

  • StorableFunction: a new base class for CVs that is designed to handle parallel simulation
  • Storable storages: you can now restart a simulation without manually recreating the storage object it saved to
  • Support for Gromacs snapshots (NB: some Gromacs improvements here will be cherry-picked into a separate PR)
  • snapshots table that combines all the individual (engine-specific) snapshot tables.

This includes #928, and therefore should only be merged after that.

Start to safemode; not sure that it works yet.

Still need to get the storable function results to store correctly
This was mainly causing errors in tests
@dwhswenson dwhswenson marked this pull request as ready for review October 23, 2020 16:03
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This is ready for review and comment. Since this is another big PR, I will leave it open for at least a week, merging no earlier than Sat 31 Oct 13:00 local (12:00 GMT).

An example showing how to use this is in dwhswenson/ops-storage-notebooks#5, in the 01_simple_usage.ipynb notebook.

The good news is, these are the two really big SimStore PRs. From here, I can add smaller chunks that might actually be reviewable.

@dwhswenson dwhswenson merged commit 86eafe2 into openpathsampling:master Oct 31, 2020
@dwhswenson dwhswenson deleted the storable_functions branch October 31, 2020 12:44
@dwhswenson dwhswenson mentioned this pull request Oct 31, 2020
@dwhswenson dwhswenson mentioned this pull request Dec 23, 2020
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