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fba2ae6
better key handling for pathmovechanges
jhprinz Apr 30, 2015
552c3ed
better key handling for pathmovechanges
jhprinz Apr 30, 2015
90323f8
Merge branch 'master' of github.com:choderalab/msm-tis into pathchang…
jhprinz Apr 30, 2015
474e0a7
analysis of pathmovers
jhprinz Apr 30, 2015
448fd4d
fix __init__
jhprinz Apr 30, 2015
0cf1c98
Merge branch 'master' of github.com:choderalab/msm-tis into pathchang…
jhprinz Apr 30, 2015
826c8b1
add fast sampleset load
jhprinz May 3, 2015
4b466a8
Merge branch 'master' of github.com:choderalab/msm-tis into fastsampl…
jhprinz May 3, 2015
10e8be9
Merge branch 'master' of github.com:choderalab/msm-tis into pathchang…
jhprinz May 3, 2015
240be52
fix numpy int index bug
jhprinz May 3, 2015
b90bc6b
Merge branch 'fixcache' into fastsampleset
jhprinz May 3, 2015
36ba029
fix numpy int index bug
jhprinz May 3, 2015
da5607b
removed storage of .valid
jhprinz May 3, 2015
de56741
simplify apply_to and remove to_dict
jhprinz May 3, 2015
bb18b00
fast load of pmc
jhprinz May 3, 2015
e80fd0a
fast load of pmc
jhprinz May 3, 2015
14fbd6c
cleanup
jhprinz May 3, 2015
5af7482
rename samples to results
jhprinz May 4, 2015
53fd843
adding sample generators
jhprinz May 5, 2015
ce9b92c
little fixes
jhprinz May 5, 2015
667048a
remove collapsed
jhprinz May 5, 2015
596db6b
remove collapsed
jhprinz May 5, 2015
937ff51
fix
jhprinz May 5, 2015
21b6869
fix
jhprinz May 5, 2015
08617ea
fix
jhprinz May 10, 2015
65b3ec2
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 11, 2015
e894bee
treelogic
jhprinz May 11, 2015
ed9ff47
Merge branch 'movepathvis' into pmc
jhprinz May 11, 2015
b55e5bb
treelogic
jhprinz May 11, 2015
cb5e98d
Merge branch 'pathchangekey' into pmc
jhprinz May 11, 2015
c21c365
treelogic
jhprinz May 11, 2015
399fb00
Merge branch 'movepathvis' into pmc
jhprinz May 11, 2015
5c142e9
little fixes
jhprinz May 12, 2015
a406c70
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 12, 2015
9bf6990
remove keep_samples
jhprinz May 12, 2015
0c06597
add trial and result
jhprinz May 12, 2015
c006e20
fixes
jhprinz May 12, 2015
e05c8a4
nosetests pass
jhprinz May 12, 2015
3296b3d
fix bootstrap
jhprinz May 12, 2015
879e029
fixed alanine example
jhprinz May 12, 2015
18d28b1
fix toy example
jhprinz May 12, 2015
f6e31f1
fix step in PathSimulationMover
jhprinz May 12, 2015
9ae36db
add canonical_mover
jhprinz May 12, 2015
95fd9fe
better vis
jhprinz May 12, 2015
b800876
better vis
jhprinz May 12, 2015
3d6dcce
fix test
jhprinz May 12, 2015
dab4227
fix test
jhprinz May 12, 2015
228e696
fix use of networkx
jhprinz May 12, 2015
6ead03a
nb updates
jhprinz May 13, 2015
44cdc8b
cleanup of PM and PMC
jhprinz May 13, 2015
92e8831
removed force ensemble switch
jhprinz May 13, 2015
43ffc4d
little fixes
jhprinz May 13, 2015
5faebe7
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 15, 2015
8796db4
remove trialgenerator.py
jhprinz May 15, 2015
1cfbc55
allow to add PMC to SampleSets
jhprinz May 15, 2015
e8bfb13
tree docs
jhprinz May 15, 2015
18da881
PMC docs
jhprinz May 15, 2015
99e524b
PM docs
jhprinz May 15, 2015
d293064
Merge branch 'fixnamestorage' into pmc
jhprinz May 15, 2015
bfce32c
fix merge
jhprinz May 15, 2015
fcfce31
remove immutable name
jhprinz May 16, 2015
b694f76
Merge branch 'fixnamestorage' into pmc
jhprinz May 16, 2015
09e4608
removed class_list
jhprinz May 16, 2015
41523c4
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 16, 2015
fcb3a5f
fix merge conflicts
jhprinz May 16, 2015
83bc407
fix merge conflicts
jhprinz May 16, 2015
235fcdb
remove ForceEnsembleChange
jhprinz May 16, 2015
2e75f0a
fix toy_retis.nc name
jhprinz May 16, 2015
9a99257
add mcstep
jhprinz May 16, 2015
1714d81
add mcstep
jhprinz May 16, 2015
983a899
add mcstep
jhprinz May 16, 2015
d04ca79
add mcstep
jhprinz May 16, 2015
8e1248d
add mcstep
jhprinz May 16, 2015
60312f2
fix analysis
jhprinz May 16, 2015
43f14d6
fix minus test after changing PM structure
jhprinz May 16, 2015
61e3323
analysis tests
jhprinz May 17, 2015
8fa7fca
fix lookup_function
jhprinz May 17, 2015
fa41f8a
update nb
jhprinz May 17, 2015
615779a
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 17, 2015
7de24db
fix test after better PMC filtering
jhprinz May 17, 2015
be65765
change mcstep attributes
jhprinz May 17, 2015
df3d756
Merge branch 'master' of github.com:choderalab/msm-tis into pmc
jhprinz May 17, 2015
954c13c
post merge fixes
jhprinz May 17, 2015
ccecbdf
post merge fixes
jhprinz May 17, 2015
6028231
fix loading pathsimulator
jhprinz May 17, 2015
6e31051
fix analysis
jhprinz May 17, 2015
d7661c2
add flag class for Swapping Moves
jhprinz May 17, 2015
5150ab9
replica swap count
jhprinz May 17, 2015
f108ad0
replica swap count
jhprinz May 18, 2015
f1a43ba
add mcstep store
jhprinz May 18, 2015
f3b694c
precompute cvs in pathsimulation
jhprinz May 18, 2015
095c48b
avoid snapshot loading for analysis
jhprinz May 19, 2015
61d2c1f
extreme speedup for analysis
jhprinz May 19, 2015
b787f75
canonical to property
jhprinz May 19, 2015
5faed01
canonical to property
jhprinz May 19, 2015
aa43bf8
add StateSwapMover
jhprinz May 19, 2015
13c5b65
fix automatic cvs storage
jhprinz May 20, 2015
5faf86e
fix automatic cvs storage
jhprinz May 20, 2015
42f6209
reduce steps in toy_tis
jhprinz May 20, 2015
a2f26f6
docs for PathSimulator
jhprinz May 20, 2015
2da238a
fix from_dict signature
jhprinz May 20, 2015
7d73723
add OPSObject inheritance for networks
jhprinz May 20, 2015
fb6fbc2
var renames
jhprinz May 20, 2015
61e5545
change to mccycle
jhprinz May 20, 2015
47f694f
add fast iter for trajectories
jhprinz May 20, 2015
3c6da40
fix networks
jhprinz May 20, 2015
b41c2ea
Generators to GeneratingMover
jhprinz May 20, 2015
f695be7
add cache_all for cv
jhprinz May 20, 2015
70d20bf
fix renaming
jhprinz May 20, 2015
0163041
change in and out
jhprinz May 28, 2015
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fix test
  • Loading branch information
jhprinz committed May 12, 2015
commit dab42277af620ddc6d33b0500b0a5659b49b5bc5
30 changes: 15 additions & 15 deletions openpathsampling/pathmover.py
Original file line number Diff line number Diff line change
Expand Up @@ -372,7 +372,7 @@ def _accept(self, trials):
###############################################################################

class ShootGenerator(SampleGenerator):
def __init__(self, selector, ensembles, replicas=None):
def __init__(self, selector, ensembles=None, replicas=None):
# TODO: Remove replicas
super(ShootGenerator, self).__init__(ensembles)
self.selector = selector
Expand Down Expand Up @@ -583,7 +583,7 @@ class RandomSubtrajectorySelectGenerator(SampleGenerator):


'''
def __init__(self, subensemble, n_l, ensembles=None):
def __init__(self, subensemble, n_l=None, ensembles=None):
super(RandomSubtrajectorySelectGenerator, self).__init__(
ensembles
)
Expand Down Expand Up @@ -613,22 +613,22 @@ def __call__(self, trial):
if (self.n_l is None and len(subtrajs) > 0) or \
(self.n_l is not None and len(subtrajs) == self.n_l):
subtraj = self._choose(subtrajs)
else:
# return zero-length trajectory otherwise
subtraj = paths.Trajectory([])

bias = 1.0
bias = 1.0

trial = paths.Sample(
replica=replica,
trajectory=subtraj,
ensemble=self.subensemble,
parent=trial,
mover=self,
bias=bias
)
trial = paths.Sample(
replica=replica,
trajectory=subtraj,
ensemble=self.subensemble,
parent=trial,
mover=self,
bias=bias
)

trials = [trial]
else:
trials = []

trials = [trial]
return trials

@ops_object
Expand Down
5 changes: 3 additions & 2 deletions openpathsampling/tests/testpathmover.py
Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@ def setup(self):

class testForwardShootMover(testShootingMover):
def test_move(self):
mover = ForwardShootMover(UniformSelector(), ensemble=self.tps)
mover = ForwardShootMover(UniformSelector(), ensembles=self.tps)
self.dyn.initialized = True
change = mover.move(self.init_samp)
newsamp = self.init_samp + change
Expand All @@ -149,7 +149,7 @@ def test_move(self):

class testBackwardShootMover(testShootingMover):
def test_move(self):
mover = BackwardShootMover(UniformSelector(), ensemble=self.tps)
mover = BackwardShootMover(UniformSelector(), ensembles=self.tps)
self.dyn.initialized = True
change = mover.move(self.init_samp)
newsamp = self.init_samp + change
Expand Down Expand Up @@ -595,6 +595,7 @@ def test_nothing_allowed(self):
change = mover.move(self.gs)
samples = change.results
assert_equal(len(samples), 0)
print change.samples
assert_equal(len(change.samples), 0)

class testFirstSubtrajectorySelectMover(SubtrajectorySelectTester):
Expand Down