class testMinusMover(object):
def setup(self):
op = CV_Function("myid", f=lambda snap :
snap.coordinates[0][0])
volA = CVRangeVolume(op, -100, 0.0)
volB = CVRangeVolume(op, 1.0, 100)
volX = CVRangeVolume(op, -100, 0.25)
self.dyn = CalvinistDynamics([
# successful move: (backward extension then forward)
-0.13, 0.13, 0.33, -0.11, -0.12, 0.12, 0.32, -0.131,
# never leaves state:
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.25,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
# goes to other state:
1.16, 1.26, 1.16, -0.16, 1.16, 1.26, 1.16
])
SampleMover.engine = self.dyn
self.dyn.initialized = True
self.innermost = paths.TISEnsemble(volA, volB, volX)
self.minus = paths.MinusInterfaceEnsemble(volA, volX)
self.mover = MinusMover(
minus_ensemble=self.minus,
innermost_ensembles=self.innermost
)
self.first_segment = [-0.1, 0.1, 0.3, 0.1, -0.15]
self.list_innermost = [-0.11, 0.11, 0.31, 0.11, -0.12]
self.second_segment = [-0.25, 0.2, 0.4, 0.2, -0.2]
init_minus = make_1d_traj(
coordinates=self.first_segment + [-0.35] + self.second_segment,
velocities=[1.0]*11
)
self.minus_sample = Sample(
replica=-1,
trajectory=init_minus,
ensemble=self.minus
)
def test_is_ensemble_change_mover(self):
assert_equal(self.mover.is_ensemble_change_mover, True)
def test_is_canonical(self):
assert_equal(self.mover.is_canonical, True)
def test_setup_sanity(self):
# sanity checks to make sure that what we set up makes sense
assert_equal(self.minus_sample.ensemble(self.minus_sample.trajectory),
True)
first_subtraj = FirstSubtrajectorySelectMover(
ensemble=self.minus,
sub_ensemble=self.minus._segment_ensemble
)
change = first_subtraj.move(SampleSet(self.minus_sample))
samples = change.results
assert_equal(samples[0].ensemble(samples[0].trajectory), True)
final_subtraj = FinalSubtrajectorySelectMover(
ensemble=self.minus,
sub_ensemble=self.minus._segment_ensemble
)
change = final_subtraj.move(SampleSet(self.minus_sample))
samples = change.results
assert_equal(samples[0].ensemble(samples[0].trajectory), True)
assert_equal(samples[0].ensemble, self.minus._segment_ensemble)
def test_successful_move(self):
init_innermost = make_1d_traj(self.list_innermost, [1.0]*5)
init_sample = Sample(
replica=0,
trajectory=init_innermost,
ensemble=self.innermost
)
gs = SampleSet([init_sample, self.minus_sample])
extend_forward = self.list_innermost + [0.12, 0.32, -0.131]
extend_backward = [-0.13, 0.13, 0.33] + self.list_innermost
assert_equal(self.minus(make_1d_traj(extend_forward)), True)
assert_equal(self.minus(make_1d_traj(extend_backward)), True)
seg_dir = {}
for i in range(100):
change = self.mover.move(gs)
samples = change.results
sub_samples = change.subchange.subchange.results
assert_equal(len(samples), 2)
assert_equal(len(sub_samples), 4)
s_inner = [s for s in sub_samples if s.ensemble==self.innermost]
s_minus = [s for s in sub_samples if s.ensemble==self.minus]
s_sub = [s for s in sub_samples if s.ensemble==self.minus._segment_ensemble]
assert_equal(len(s_inner), 1)
assert_equal(len(s_minus), 1)
assert_equal(len(s_sub), 2)
for c in change:
assert_equal(c.accepted, True)
assert_equal(change.canonical.mover, self.mover)
key = ""
s_inner0_xvals = [s.coordinates[0,0] for s in s_inner[0].trajectory]
if items_equal(s_inner0_xvals, self.first_segment):
key += "1"
elif items_equal(s_inner0_xvals, self.second_segment):
key += "2"
else:
print "s_inner0_xvals:", s_inner0_xvals
raise RuntimeError("Chosen segment neither first nor last!")
# final sample s_minus is accepted
s_minus_xvals = [s.coordinates[0,0] for s in s_minus[-1].trajectory]
if items_equal(s_minus_xvals, extend_forward):
key += "f"
elif items_equal(s_minus_xvals, extend_backward):
key += "b"
else:
print "s_minus_xvals:", s_minus_xvals
raise RuntimeError("Unexpected minus extension result!")
try:
seg_dir[key] += 1
except KeyError:
seg_dir[key] = 1
assert_equal(len(seg_dir.keys()), 4)
def test_repex_fails_other_ensemble(self):
innermost_other_ensemble = make_1d_traj([-0.11, 0.1, -0.12])
samp_other_ensemble = Sample(
replica=0,
trajectory=innermost_other_ensemble,
ensemble=self.innermost
)
gs = SampleSet([samp_other_ensemble, self.minus_sample])
change = self.mover.move(gs)
assert_equal(len(change.trials), 1)
sub = change.subchange.subchange
assert_equal(self.innermost(innermost_other_ensemble), False)
assert_equal(sub[0].accepted, True)
assert_equal(sub[1].accepted, False)
assert_equal(len(sub.trials), 3) # stop after failed repex
# only one sample which is not a segment
def test_repex_fails_innermost_crosses_state(self):
innermost_crosses_to_state = make_1d_traj([-0.11, 0.5, 1.8])
samp_crosses_to_state = Sample(
replica=0,
trajectory=innermost_crosses_to_state,
ensemble=self.innermost
)
gs = SampleSet([samp_crosses_to_state, self.minus_sample])
change = self.mover.move(gs)
assert_equal(len(change.trials), 1) # stop after failed repex
sub = change.subchange.subchange
assert_equal(self.innermost(innermost_crosses_to_state), True)
assert_equal(len(sub.trials), 3) # stop after failed repex
assert_subchanges_set_accepted(sub, [True, False, False])
def test_repex_fails_minus_crosses_to_state(self):
minus_crosses_to_state = make_1d_traj(
[-0.11, 0.5, 1.8, 0.6, -0.12, 0.7, 1.7, 0.4, -0.13]
)
badminus_sample = Sample(
replica=-1,
trajectory=minus_crosses_to_state,
ensemble=self.minus
)
init_sample = Sample(
replica=0,
trajectory=make_1d_traj(self.list_innermost, [1.0]*5),
ensemble=self.innermost
)
gs = SampleSet([badminus_sample, init_sample])
assert_equal(self.minus(minus_crosses_to_state), True)
change = self.mover.move(gs)
sub = change.subchange.subchange
assert_equal(len(sub.trials), 3) # stop after failed repex
assert_equal(len(change.trials), 1)
assert_subchanges_set_accepted(sub, [True, False, False])
def test_extension_fails(self):
innermost_bad_extension = [-0.25, 0.1, 0.5, 0.1, -0.25]
traj_bad_extension = make_1d_traj(innermost_bad_extension, [1.0]*5)
samp_bad_extension = Sample(
replica=0,
trajectory=traj_bad_extension,
ensemble=self.innermost
)
assert_equal(self.innermost(traj_bad_extension), True)
gs = SampleSet([self.minus_sample, samp_bad_extension])
change = self.mover.move(gs)
assert_equal(change.accepted, False) # whole minus has failed
sub = change.subchange.subchange
assert_equal(len(sub.trials), 4)
# after filtering there are only 2 trials
assert_equal(len(change.trials), 2)
assert_subchanges_set_accepted(sub, [True] * 2 + [False])
# first two work and the extention fails
# this only happens due to length
assert_equal(
len(sub[-1][0].trials[0].trajectory),
len(traj_bad_extension)+self.dyn.n_frames_max-1
)
class testMinusMover(object):
def setup(self):
op = CV_Function("myid", fcn=lambda snap :
snap.coordinates[0][0])
volA = CVRangeVolume(op, -100, 0.0)
volB = CVRangeVolume(op, 1.0, 100)
volX = CVRangeVolume(op, -100, 0.25)
self.dyn = CalvinistDynamics([
# successful move: (backward extension then forward)
-0.13, 0.13, 0.33, -0.11, -0.12, 0.12, 0.32, -0.131,
# never leaves state:
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.25,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
-0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15, -0.15,
# goes to other state:
1.16, 1.26, 1.16, -0.16, 1.16, 1.26, 1.16
])
SampleGeneratingMover.engine = self.dyn
self.dyn.initialized = True
self.innermost = paths.TISEnsemble(volA, volB, volX)
self.minus = paths.MinusInterfaceEnsemble(volA, volX)
self.mover = MinusMover(
minus_ensemble=self.minus,
innermost_ensembles=self.innermost
)
self.first_segment = [-0.1, 0.1, 0.3, 0.1, -0.15]
self.list_innermost = [-0.11, 0.11, 0.31, 0.11, -0.12]
self.second_segment = [-0.25, 0.2, 0.4, 0.2, -0.2]
init_minus = make_1d_traj(
coordinates=self.first_segment + [-0.35] + self.second_segment,
velocities=[1.0]*11
)
self.minus_sample = Sample(
replica=-1,
trajectory=init_minus,
ensemble=self.minus
)
def test_is_ensemble_change_mover(self):
assert_equal(self.mover.is_ensemble_change_mover, True)
def test_is_canonical(self):
assert_equal(self.mover.is_canonical, True)
def test_setup_sanity(self):
# sanity checks to make sure that what we set up makes sense
assert_equal(self.minus_sample.ensemble(self.minus_sample.trajectory),
True)
first_subtraj = FirstSubtrajectorySelectMover(
ensemble=self.minus,
sub_ensemble=self.minus._segment_ensemble
)
change = first_subtraj.move(SampleSet(self.minus_sample))
samples = change.results
assert_equal(samples[0].ensemble(samples[0].trajectory), True)
final_subtraj = FinalSubtrajectorySelectMover(
ensemble=self.minus,
sub_ensemble=self.minus._segment_ensemble
)
change = final_subtraj.move(SampleSet(self.minus_sample))
samples = change.results
assert_equal(samples[0].ensemble(samples[0].trajectory), True)
assert_equal(samples[0].ensemble, self.minus._segment_ensemble)
def test_successful_move(self):
init_innermost = make_1d_traj(self.list_innermost, [1.0]*5)
init_sample = Sample(
replica=0,
trajectory=init_innermost,
ensemble=self.innermost
)
gs = SampleSet([init_sample, self.minus_sample])
extend_forward = self.list_innermost + [0.12, 0.32, -0.131]
extend_backward = [-0.13, 0.13, 0.33] + self.list_innermost
assert_equal(self.minus(make_1d_traj(extend_forward)), True)
assert_equal(self.minus(make_1d_traj(extend_backward)), True)
seg_dir = {}
for i in range(100):
change = self.mover.move(gs)
samples = change.results
sub_samples = change.subchange.subchange.results
assert_equal(len(samples), 2)
assert_equal(len(sub_samples), 4)
s_inner = [s for s in sub_samples if s.ensemble==self.innermost]
s_minus = [s for s in sub_samples if s.ensemble==self.minus]
s_sub = [s for s in sub_samples if s.ensemble==self.minus._segment_ensemble]
assert_equal(len(s_inner), 1)
assert_equal(len(s_minus), 1)
assert_equal(len(s_sub), 2)
for c in change:
assert_equal(c.accepted, True)
assert_equal(change.canonical.mover, self.mover)
key = ""
s_inner0_xvals = [s.coordinates[0,0] for s in s_inner[0].trajectory]
if items_equal(s_inner0_xvals, self.first_segment):
key += "1"
elif items_equal(s_inner0_xvals, self.second_segment):
key += "2"
else:
print "s_inner0_xvals:", s_inner0_xvals
raise RuntimeError("Chosen segment neither first nor last!")
# final sample s_minus is accepted
s_minus_xvals = [s.coordinates[0,0] for s in s_minus[-1].trajectory]
if items_equal(s_minus_xvals, extend_forward):
key += "f"
elif items_equal(s_minus_xvals, extend_backward):
key += "b"
else:
print "s_minus_xvals:", s_minus_xvals
raise RuntimeError("Unexpected minus extension result!")
try:
seg_dir[key] += 1
except KeyError:
seg_dir[key] = 1
assert_equal(len(seg_dir.keys()), 4)
def test_repex_fails_other_ensemble(self):
innermost_other_ensemble = make_1d_traj([-0.11, 0.1, -0.12])
samp_other_ensemble = Sample(
replica=0,
trajectory=innermost_other_ensemble,
ensemble=self.innermost
)
gs = SampleSet([samp_other_ensemble, self.minus_sample])
change = self.mover.move(gs)
assert_equal(len(change.trials), 1)
sub = change.subchange.subchange
assert_equal(self.innermost(innermost_other_ensemble), False)
assert_equal(sub[0].accepted, True)
assert_equal(sub[1].accepted, False)
assert_equal(len(sub.trials), 3) # stop after failed repex
# only one sample which is not a segment
def test_repex_fails_innermost_crosses_state(self):
innermost_crosses_to_state = make_1d_traj([-0.11, 0.5, 1.8])
samp_crosses_to_state = Sample(
replica=0,
trajectory=innermost_crosses_to_state,
ensemble=self.innermost
)
gs = SampleSet([samp_crosses_to_state, self.minus_sample])
change = self.mover.move(gs)
assert_equal(len(change.trials), 1) # stop after failed repex
sub = change.subchange.subchange
assert_equal(self.innermost(innermost_crosses_to_state), True)
assert_equal(len(sub.trials), 3) # stop after failed repex
assert_subchanges_set_accepted(sub, [True, False, False])
def test_repex_fails_minus_crosses_to_state(self):
minus_crosses_to_state = make_1d_traj(
[-0.11, 0.5, 1.8, 0.6, -0.12, 0.7, 1.7, 0.4, -0.13]
)
badminus_sample = Sample(
replica=-1,
trajectory=minus_crosses_to_state,
ensemble=self.minus
)
init_sample = Sample(
replica=0,
trajectory=make_1d_traj(self.list_innermost, [1.0]*5),
ensemble=self.innermost
)
gs = SampleSet([badminus_sample, init_sample])
assert_equal(self.minus(minus_crosses_to_state), True)
change = self.mover.move(gs)
sub = change.subchange.subchange
assert_equal(len(sub.trials), 3) # stop after failed repex
assert_equal(len(change.trials), 1)
assert_subchanges_set_accepted(sub, [True, False, False])
def test_extension_fails(self):
innermost_bad_extension = [-0.25, 0.1, 0.5, 0.1, -0.25]
traj_bad_extension = make_1d_traj(innermost_bad_extension, [1.0]*5)
samp_bad_extension = Sample(
replica=0,
trajectory=traj_bad_extension,
ensemble=self.innermost
)
assert_equal(self.innermost(traj_bad_extension), True)
gs = SampleSet([self.minus_sample, samp_bad_extension])
change = self.mover.move(gs)
assert_equal(change.accepted, False) # whole minus has failed
sub = change.subchange.subchange
assert_equal(len(sub.trials), 4)
# after filtering there are only 2 trials
assert_equal(len(change.trials), 2)
assert_subchanges_set_accepted(sub, [True] * 2 + [False])
# first two work and the extention fails
# this only happens due to length
assert_equal(
len(sub[-1][0].trials[0].trajectory),
len(traj_bad_extension)+self.dyn.n_frames_max-1
)
