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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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Add engine to StaticContainer/KineticContainer 
Ran tests and reloaded old files, so this shouldn't break things
  • Loading branch information
@dwhswenson
dwhswenson committed Dec 4, 2020
commit d4546e21d61167e4c6d35a04a65ec0eb830994ad
67 changes: 11 additions & 56 deletions openpathsampling/engines/features/shared.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ def unmask_quantity(quantity):
return quantity
return np.array(quantity.value_in_unit(q_unit)) * q_unit


# =============================================================================
# SIMULATION CONFIGURATION
# =============================================================================
Expand All @@ -36,53 +37,24 @@ class StaticContainer(StorableObject):
Simulation configuration. Only Coordinates, the associated boxvectors
and the potential_energy

Attributes
Parameters
----------
coordinates : simtk.unit.Quantity wrapping Nx3 np array of dimension length
atomic coordinates
box_vectors : periodic box vectors
the periodic box vectors

engine : :class:`.DynamicsEngine`
the engine that creating this data
"""

# Class variables to store the global storage and the system context
# describing the system to be saved as configuration_indices

def __init__(self, coordinates, box_vectors):
"""
Create a simulation configuration from either an OpenMM context or
individually-specified components.

Parameters
----------
coordinates
box_vectors
"""

def __init__(self, coordinates, box_vectors, engine=None):
super(StaticContainer, self).__init__()

self.coordinates = copy.deepcopy(coordinates)
self.box_vectors = copy.deepcopy(box_vectors)

# if self.coordinates is not None:
# # Check for nans in coordinates, and raise an exception if
# # something is wrong.
# if type(self.coordinates) is unit.Quantity:
# coords = self.coordinates._value
# else:
# coords = self.coordinates
#
# if np.any(np.isnan(coords)):
# bad_atoms = [i for i in range(len(coords))
# if np.any(np.isnan(coords[i]))]
# raise ValueError("Coordinates went 'nan' for atoms: " +
# str(bad_atoms))

return

# =========================================================================
# Comparison functions
# =========================================================================
self.engine = engine

@property
def n_atoms(self):
Expand All @@ -91,10 +63,6 @@ def n_atoms(self):
"""
return self.coordinates.shape[0]

# =========================================================================
# Utility functions
# =========================================================================

def copy(self):
"""
Returns a deep copy of the instance itself using a subset of coordinates.
Expand All @@ -112,6 +80,7 @@ def copy(self):
)

def to_dict(self):
# note: to_dict not used here in SimStore, so no need to change
return {
'coordinates': self.coordinates,
'box_vectors': self.box_vectors
Expand Down Expand Up @@ -214,26 +183,14 @@ class KineticContainer(StorableObject):
----------
velocities : simtk.unit.Quantity wrapping Nx3 np array of dimension length
atomic velocities

engine : :class:`.DynamicsEngine`
the engine that creating this data
"""

def __init__(self, velocities):
"""
Create a simulation momentum from either an OpenMM context or
individually-specified components.

Parameters
----------
velocities
"""

def __init__(self, velocities, engine=None):
super(KineticContainer, self).__init__()

self.velocities = copy.deepcopy(velocities)

# =========================================================================
# Utility functions
# =========================================================================
self.engine = engine

def copy(self):
"""
Expand All @@ -245,9 +202,7 @@ def copy(self):
Momentum()
the shallow copy
"""

this = KineticContainer(velocities=self.velocities)

return this

def to_dict(self):
Expand Down