def setup(self):
traj = Trajectory([-0.5, 0.7, 1.1])
op = CallIdentity()
volA = CVRangeVolume(op, -100, 0.0)
volB = CVRangeVolume(op, 1.0, 100)
volX = CVRangeVolume(op, -100, 0.25)
tis = paths.TISEnsemble(volA, volB, volX)
tps = ef.A2BEnsemble(volA, volB)
len3 = LengthEnsemble(3)
len2 = LengthEnsemble(2)
self.hop_to_tis = RandomAllowedChoiceMover(
map(lambda ens : EnsembleHopMover(*ens),
[[tis, tis],
[tps, tis],
[len3, tis],
[len2, tis]]
)
)
self.hop_to_tps = RandomAllowedChoiceMover(
map(lambda ens : EnsembleHopMover(*ens),
[[tis, tps],
[tps, tps],
[len3, tps],
[len2, tps]]
)
)
self.hop_to_len3 = RandomAllowedChoiceMover(
map(lambda ens : EnsembleHopMover(*ens),
[[tis, len3],
[tps, len3],
[len3, len3],
[len2, len3]]
)
)
self.hop_to_len2 = RandomAllowedChoiceMover(
map(lambda ens : EnsembleHopMover(*ens),
[[tis, len2],
[tps, len2],
[len3, len2],
[len2, len2]]
)
)
self.init_sample = Sample(trajectory=traj,
ensemble=len3,
replica=0)
self.tis = tis
self.tps = tps
self.len3 = len3
self.len2 = len2
self.everything_accepted_movers = [
self.hop_to_tis, self.hop_to_len3, self.hop_to_tps
]
self.first_rejected_movers = [
self.hop_to_len2, self.hop_to_len3, self.hop_to_tps
]
self.last_rejected_movers = [
self.hop_to_tis, self.hop_to_tps, self.hop_to_len2
]
def setup(self):
self.l1 = LengthEnsemble(1)
self.l2 = LengthEnsemble(2)
self.l3 = LengthEnsemble(3)
self.s1 = Sample(replica=1, ensemble=self.l2)
self.s2 = Sample(replica=2, ensemble=self.l1)
self.s3 = Sample(replica=3, ensemble=self.l1)
self.s4 = Sample(replica=2, ensemble=self.l3)
self.sset = SampleSet([self.s1, self.s2, self.s3, self.s4])
def setup(self):
self.ensA = LengthEnsemble(1)
self.ensB = LengthEnsemble(2)
traj0A = Trajectory([0.5])
traj1A = Trajectory([1.0])
traj2B = Trajectory([0.5, 0.75])
traj2B_ = Trajectory([0.8, 0.9])
self.s0A = Sample(replica=0, trajectory=traj0A, ensemble=self.ensA)
self.s1A = Sample(replica=1, trajectory=traj1A, ensemble=self.ensA)
self.s2B = Sample(replica=2, trajectory=traj2B, ensemble=self.ensB)
self.s2B_ = Sample(replica=2, trajectory=traj2B_, ensemble=self.ensB)
self.testset = SampleSet([self.s0A, self.s1A, self.s2B])
def test_setitem_replica(self):
ensC = LengthEnsemble(3)
traj3C = Trajectory([-0.5, -0.25, 0.1])
s3C = Sample(replica=3, trajectory=traj3C, ensemble=ensC)
self.testset[3] = s3C
self.testset.consistency_check()
assert_equal(len(self.testset), 4)
def setup(self):
self.mytraj = make_1d_traj(coordinates=[-0.5, 0.1, 0.2, 0.3, 0.5],
velocities=[1.0, 1.0, 1.0, 1.0, 1.0])
self.dyn = CalvinistDynamics(
[-0.5, -0.4, -0.3, -0.2, -0.1, 0.1, 0.2, 0.3, 0.4, 0.5])
self.dyn.initialized = True
self.ens = LengthEnsemble(5)
self.gs = SampleSet(
Sample(replica=0, trajectory=self.mytraj, ensemble=self.ens))
def setup(self):
traj = Trajectory([-0.5, 0.7, 1.1])
op = CallIdentity()
volA = CVRangeVolume(op, -100, 0.0)
volB = CVRangeVolume(op, 1.0, 100)
volX = CVRangeVolume(op, -100, 0.25)
self.tis = paths.TISEnsemble(volA, volB, volX)
self.tps = ef.A2BEnsemble(volA, volB)
self.len3 = LengthEnsemble(3)
self.init_samp = SampleSet([Sample(trajectory=traj,
ensemble=self.len3,
replica=0)])
self.hop_to_tis = EnsembleHopMover(
ensemble=self.len3,
target_ensemble=self.tis
)
self.hop_to_tps = EnsembleHopMover(
ensemble=self.len3,
target_ensemble=self.tps
)
self.mover = RandomChoiceMover([self.hop_to_tis, self.hop_to_tps])