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[WIP] OpenMMToolsMCEngine #1041

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3a75a85
Add first draft of OpenMMToolsMCEngine
dwhswenson Jul 28, 2021
4290267
serialization, docstrings, mdtraj integration
dwhswenson Jul 31, 2021
d3b0537
start to tests on OpenMMToolsMCEngine
dwhswenson Jul 31, 2021
f4bcfd1
first few tests working
dwhswenson Jul 31, 2021
9942f71
more tests
dwhswenson Jul 31, 2021
311586e
that makes full test coverage!
dwhswenson Jul 31, 2021
a66b3e5
fix to tests when openmmtools not available
dwhswenson Jul 31, 2021
c2b51a5
copy openmmtools dicts when deserializing
dwhswenson Aug 2, 2021
4ee3d8b
add support for any kind of mover; more tests
dwhswenson Aug 3, 2021
207c0fb
Everything except last bits of example
dwhswenson Aug 4, 2021
116a9db
some cleanup to get the engine to run in example
dwhswenson Aug 7, 2021
e94fb60
update MC engine example
dwhswenson Aug 11, 2021
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add support for any kind of mover; more tests
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@dwhswenson
dwhswenson committed Aug 3, 2021
commit 4ee3d8bd543bb4c23f534f34ca439d17eb1c274f
9 changes: 7 additions & 2 deletions openpathsampling/engines/openmm/mcengine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,8 +108,13 @@ def current_snapshot(self, snapshot):


def _get_n_accepted(self):
return sum(dct['n_accepted']
for dct in self._sampler.move.statistics)
statistics = self._sampler.move.statistics
if isinstance(statistics, dict):
# single move
return statistics['n_accepted']
else:
# sequence or weighted move
return sum(dct['n_accepted'] for dct in statistics)


def generate_next_frame(self):
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27 changes: 24 additions & 3 deletions openpathsampling/tests/test_openmm_mcengine.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import pytest
import openpathsampling as paths
import copy
import numpy as np

from openpathsampling.engines.openmm.mcengine import *

Expand Down Expand Up @@ -103,7 +104,20 @@ def test_current_snapshot_set_same(self, mcengine, snapshot):
def test_current_snapshot_update(self, mcengine, snapshot):
# when we set a new snapshot (and one already exists) the
# internal information should be updated
pytest.skip()
unit = pytest.importorskip('simtk.unit')
pos = snapshot.coordinates.value_in_unit(unit.nanometers)
new_pos = np.random.random(pos.shape) * unit.nanometers
new_snapshot = snapshot.construct(
coordinates=new_pos,
velocities=snapshot.velocities,
box_vectors=snapshot.box_vectors,
engine=snapshot.engine
)
mcengine.current_snapshot = snapshot
mcengine.current_snapshot = new_snapshot
sampler_state = mcengine._sampler.sampler_state
assert not (sampler_state.positions == snapshot.coordinates).all()
assert (sampler_state.positions == new_snapshot.coordinates).all()

def test_current_snapshot_uninitialized_error(self, mcengine):
# if we try to get the current snapshot before the engine has been
Expand Down Expand Up @@ -156,11 +170,18 @@ def test_trajectory_to_mdtraj(self, snapshot, ad_vacuum_testsystem,
assert isinstance(mdt, md.Trajectory)
assert len(mdt) == len(traj)

@pytest.mark.parametrize('wrapper', [None, 'weighted', 'sequence'])
@pytest.mark.parametrize('accept', ['accept', 'reject'])
def test_get_n_accepted(self, accept, thermodynamic_state, snapshot):
def test_get_n_accepted(self, wrapper, accept, thermodynamic_state,
snapshot):
# (not API) ensure that we get the correct number of accepted steps
# from a mover
move = mcmc.WeightedMove([(AlwaysMove(accept), 1)])
wrap = {
None: lambda x: x,
'weighted': lambda x: mcmc.WeightedMove([(x, 1)]),
'sequence': lambda x: mcmc.SequenceMove([x]),
}[wrapper]
move = wrap(AlwaysMove(accept))
results = {'accept': [1, 2], 'reject': [0, 0]}[accept]
always_accept = OpenMMToolsMCEngine(
move=move,
Expand Down