[WIP] Builders for solvent and electrolyte classical molecular dynamics runs #1135
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….py files for package structure.
…lob instead of byte encoded.
orionarcher
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1135 +/- ##
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- Coverage 90.42% 89.10% -1.33%
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Files 147 116 -31
Lines 14448 11042 -3406
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- Hits 13065 9839 -3226
+ Misses 1383 1203 -180 ☔ View full report in Codecov by Sentry. |
orionarcher
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This PR implements ElectrolyteBuilder and SolventBenchmarkBuilder classes for analysis of trajectories generated by atomate2.openmm.
The core Builder classes are supported by a variety of utility functions that interact with MDAnalysis, SolvationAnalysis, and TransportAnalysis. In addition to the usual get_items, process_items, update_targets workflow, users can also manually create an MDAnalysis.Universe directly from the taskdoc with ElectrolyteBuilder.instantiate_universe. This makes manual analysis of a small number of systems much easier.
Everything is reasonably well tested but there is one outstanding error where some file types are not being deserialized correctly.