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Add CG_System class #19
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Codecov Report
@@ Coverage Diff @@
## master #19 +/- ##
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+ Coverage 96.33% 96.91% +0.57%
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Files 4 4
Lines 218 356 +138
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+ Hits 210 345 +135
- Misses 8 11 +3
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- Check if bonds exist before trying to shift or save them - Account for bead count in `shift_value`
- `save_mapping` requires filename and uses numpy serializer - `save` now stops at end of file
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Fixes: #16
OK, so I've been going round and round for how to fix this. Chris mentioned the CG_Compound class would still be useful to him for building up systems, so it makes sense to keep it because it works pretty well with a small system and mbuild has useful functions for initializing systems. In addition to this class, maybe we create a separate class for if a user just wants to use this package for msibi--a workflow something like:
(atomistic gsd) ->
(freud clustering - get the molecules) ->
(openbabel molecule - SMARTS matching) ->
(scale out that mapping to other molecules) ->
(coarse gsd)
In which case there's no reason to get mbuild involved. Maybe we want to keep this simple and not specific to gsd; any system of points, types, bonds, and box should work.
Maybe additionally we can get some speedup by not forcing any optimization steps when placing fine-grain structures... instead these can be optional.
TODO:
a way to visualize that this new method is correct?Use OVITO 😅