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SimStore: Support for OpenMM snapshots #949

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Merged
dwhswenson merged 15 commits into from
Dec 23, 2020
Merged

SimStore: Support for OpenMM snapshots #949

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a67f164
Refactor for attribute handler factories
dwhswenson Dec 1, 2020
51cbccd
redo attribute handlers; integrate for ndarray
dwhswenson Dec 3, 2020
31892e9
complete transition to attribute handlers (numpy)
dwhswenson Dec 3, 2020
1a2ae80
support for simtk units (needs tests)
dwhswenson Dec 3, 2020
c4d0ade
most of the way to storing OpenMM snapshots
dwhswenson Dec 4, 2020
d4546e2
Add engine to StaticContainer/KineticContainer
dwhswenson Dec 4, 2020
b8fa05d
Seems like I can store/load OpenMM snapshots now!
dwhswenson Dec 5, 2020
1523850
move proxy and UUID stuff to their own files
dwhswenson Dec 12, 2020
7224f2e
Fix test for new file locs
dwhswenson Dec 12, 2020
4e29269
docstrings
dwhswenson Dec 12, 2020
c5b6f78
Misc fixes to get the new tutorial to work
dwhswenson Dec 12, 2020
1bf7a16
tests for attribute_handler.py
dwhswenson Dec 19, 2020
9e901bf
Additional test for scalarize_singletons
dwhswenson Dec 19, 2020
8f97732
tests for simstore/simtk-quantity serialization
dwhswenson Dec 20, 2020
62d09d6
integration tests for openmm snapshots
dwhswenson Dec 20, 2020
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tests for simstore/simtk-quantity serialization
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@dwhswenson
dwhswenson committed Dec 20, 2020
commit 8f97732091cc9c01cda4db30888b371cead9c85d
5 changes: 2 additions & 3 deletions openpathsampling/experimental/storage/simtk_unit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,7 @@ def unit_from_dict(dct):
return unit

def quantity_to_dict(obj):
return {
'value': obj.value,
return {'value': obj.value_in_unit(obj.unit),
'__simtk_unit__': unit_to_dict(obj.unit)}

def quantity_from_dict(dct):
Expand All @@ -41,7 +40,7 @@ def quantity_from_dict(dct):
simtk_quantity_codec = JSONCodec(
cls=simtk.unit.Quantity,
to_dict=quantity_to_dict,
from_dict=quantity_to_dict,
from_dict=quantity_from_dict,
is_my_dict=lambda x: '__simtk_unit__' in x
)

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