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[WIP] Functions to convert netcdfplus CVs to SimStore CVs#1005
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Still need to do some custom work on the func_config for MDTraj
codecovbot commentedApr 8, 2021 • edited
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Codecov Report
@@ Coverage Diff @@## master #1005 +/- ##======================================= Coverage 81.17% 81.17% ======================================= Files 139 139 Lines 15143 15143 ======================================= Hits 12292 12292 Misses 2851 2851 Continue to review full report at Codecov.
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@sroet,@hejung,@gyorgy-hantal (and anyone else who has some old CVs from netcdfplus and is comfortable trying an experimental branch): Could you try this branch out and see if the The following script is a rough template of I hope you can try, especially for any CV that might have an unusual setup: importopenpathsamplingaspathsfromopenpathsampling.experimental.storage.collective_variablesimportMDTrajFunctionCVstorage=paths.Storage("old_file.nc",mode='r')old=storage.cvs['phi']# was originally defined as a paths.MDTrajFunctionCV# create the new CV using the classmethod `from_netcdfplus_cv`new=MDTrajFunctionCV.from_netcdfplus_cv(old)snap=storage.snapshots[-1]# take an arbitrary snapshot from storageassertold(snap)==new(snap) So far, the CV types in the following table have been implemented in the new storage. (Only
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This adds a constructor to SimStore-based CVs to create the appropriate SimStore CV from a netcdfplus CV. This is a necessary step toward writing a script that converts netcdfplus files to SimStore files. That will be useful now for users who want to experiment with SimStore, and will be necessary in a pre-2.0 release so that users can upgrade.