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Merged
jhprinz merged 8 commits into from
Mar 13, 2017
Merged

Fast ensemble check #669

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2c9d585
Add "candidate" flag, plus speed-up in TISEnsemble
dwhswenson Feb 10, 2017
256d8d2
Add check for states in TISEnsemble w/candidate
dwhswenson Feb 10, 2017
fca2f38
Merge remote-tracking branch 'upstream/master' into fast_ensemble_check
dwhswenson Feb 16, 2017
81e7a07
Better way to select using "candidate" in TIS
dwhswenson Feb 16, 2017
4f5ebfc
Tests for TIS with candidate=True
dwhswenson Feb 18, 2017
5f2d042
Merge remote-tracking branch 'upstream/master' into fast_ensemble_check
dwhswenson Feb 27, 2017
6a921af
Added `candidate` to PathReversalMover & test
dwhswenson Feb 27, 2017
4577855
Use `candidate` in RepEx, & tests
dwhswenson Feb 27, 2017
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Tests for TIS with candidate=True
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@dwhswenson
dwhswenson committed Feb 18, 2017
commit 4f5ebfc4d832800dceb78be5be5449a24606d90d
18 changes: 13 additions & 5 deletions openpathsampling/ensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2792,18 +2792,26 @@ def __init__(self, initial_states, final_states, interface,
self.orderparameter = orderparameter
# TODO: add max_orderparameter as a traj CV
self.lambda_i = lambda_i
self._initial_volumes = volumes_a
self._final_volumes = volumes_b
self._initial_volumes = volume_a
self._final_volumes = volume_b | volume_a

def __call__(self, trajectory, trusted=None, candidate=False):
use_candidate = (candidate and self.lambda_i is not None
and self.orderparameter is not None)
if use_candidate:
# as a candidate trajectory, we assume that only the first and
# final frames can be in a state
return (self._initial_volumes(trajectory[0])
& self._final_volumes(trajectory[-1])
& max(self.orderparameter(trajectory)) >= self.lambda_i)
#logger.debug("initial: " +
#str(self._initial_volumes(trajectory[0])))
#logger.debug("final: " +
#str(self._final_volumes(trajectory[0])))
#logger.debug("max: " +
#str(max(self.orderparameter(trajectory))))
return (
self._initial_volumes(trajectory[0])
& self._final_volumes(trajectory[-1])
& (max(self.orderparameter(trajectory)) > self.lambda_i)
)
else:
# it still works fine if we use the slower algorithm
return super(TISEnsemble, self).__call__(trajectory, trusted)
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22 changes: 21 additions & 1 deletion openpathsampling/tests/testensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1282,7 +1282,7 @@ def test_strict_can_prepend(self):

class testTISEnsemble(EnsembleTest):
def setUp(self):
self.tis = TISEnsemble(vol1, vol3, vol2, op)
self.tis = TISEnsemble(vol1, vol3, vol2, op)
self.traj = ttraj['upper_in_out_cross_out_in']
self.minl = min(op(self.traj))
self.maxl = max(op(self.traj))
Expand All @@ -1300,6 +1300,26 @@ def test_tis_trajectory_summary_str(self):
str(self.minl) + " max_lambda=" + str(self.maxl) + " ")
assert_equal(mystr, teststr)

def test_tis_ensemble_candidate(self):
tis = TISEnsemble(vol1, vol3, vol2, op, lambda_i=0.7)
test_f = lambda t: tis(t, candidate=True)
results = {}
upper_keys = [k for k in ttraj.keys() if k[:6] == "upper_"]
for test in upper_keys:
results[test] = False
# results where we SHOULD get True
results['upper_in_out_cross_out_in'] = True
results['upper_in_cross_in'] = True
# results where the input isn't actually a candidate trajectory, so
# it accepts the path even though it shouldn't
results['upper_in_cross_in_cross_in'] = True
results['upper_in_out_cross_out_in_out_in_out_cross_out_in'] = True
results['upper_in_in_cross_in'] = True

for test in results.keys():
failmsg = "Failure in "+test+"("+str(ttraj[test])+"): "
self._single_test(test_f, ttraj[test], results[test], failmsg)

class EnsembleCacheTest(EnsembleTest):
def _was_cache_reset(self, cache):
return cache.contents == { }
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