def test_randomized_committor(self):
raise SkipTest
# this shows that we get both states even with forward-only
# shooting, if the randomizer gives the negative velocities
randomizer = paths.RandomVelocities(beta=1.0)
sim = CommittorSimulation(storage=self.storage,
engine=self.engine,
states=[self.left, self.right],
randomizer=randomizer,
initial_snapshots=self.snap0,
direction=1)
sim.run(50)
assert_equal(len(sim.storage.steps), 50)
counts = {'None-Right' : 0,
'Left-None' : 0,
'None-Left' : 0,
'Right-None' : 0}
for step in sim.storage.steps:
step.active.sanity_check() # traj is in ensemble
traj = step.active[0].trajectory
traj_str = traj.summarize_by_volumes_str(self.state_labels)
try:
counts[traj_str] += 1
except KeyError:
msg = "Got trajectory described as '{0}', length {1}"
# this might be okay if it is 'None', length 100000
raise AssertionError(msg.format(traj_str, len(traj)))
assert_equal(counts['Left-None'], 0)
assert_equal(counts['Right-None'], 0)
assert_true(counts['None-Left'] > 0)
assert_true(counts['None-Right'] > 0)
assert_equal(sum(counts.values()), 50)
def create_randomizer(engine):
from simtk import unit as u
# only support OpenMM so far
# this might raise an AttributeError if using an engine or
# integrator that isn't supported
# integrator = engine.integrator
# temperature = integrator.temperature
temperature = 300 * u.kelvin # TODO: hard coding this for now
beta = 1.0 / (temperature * u.BOLTZMANN_CONSTANT_kB)
randomizer = paths.RandomVelocities(beta=beta, engine=engine)
return randomizer