Merge pull request #894 from dwhswenson/update_run_until_decorrelated

`run_until_decorrelated` should account for time reversibility
openpathsampling · Jan 29, 2020 · eeb6665 · eeb6665
2 parents 99603ea + b5fdc86
commit eeb6665
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Showing 2 changed files with 28 additions and 8 deletions.
diff --git a/openpathsampling/pathsimulators/path_sampling.py b/openpathsampling/pathsimulators/path_sampling.py
@@ -187,7 +187,7 @@ def run_until(self, n_steps):
         n_steps_to_run = n_steps - self.step
         self.run(n_steps_to_run)
 
-    def run_until_decorrelated(self):
+    def run_until_decorrelated(self, time_reversal=True):
         """Run until all trajectories are decorrelated.
 
         This runs until all the replicas in ``self.sample_set`` have
@@ -204,7 +204,8 @@ def run_until_decorrelated(self):
         self.output_stream = open(os.devnull, 'w')
 
         def n_correlated(sample_set, originals):
-            return sum([originals[r].is_correlated(sample_set[r])
+            return sum([originals[r].is_correlated(sample_set[r],
+                                                   time_reversal)
                         for r in originals])
 
         original_output_stream.write("Decorrelating trajectories....\n")
@@ -220,6 +221,12 @@ def n_correlated(sample_set, originals):
             self.run(1)
             to_decorrelate = n_correlated(self.sample_set, originals)
 
+        paths.tools.refresh_output(
+            "Step {}: All trajectories decorrelated!\n".format(self.step+1),
+            refresh=False,
+            output_stream=original_output_stream
+        )
+
         self.output_stream = original_output_stream
 
     def run(self, n_steps):

diff --git a/openpathsampling/tests/test_pathsimulator.py b/openpathsampling/tests/test_pathsimulator.py
@@ -662,13 +662,22 @@ def setup(self):
                                               pes=pes)
         self.engine = paths.engines.toy.Engine(options={'integ': integ},
                                                topology=topology)
-        network = paths.TPSNetwork(self.state_A, self.state_B)
+
+        interfaces = paths.VolumeInterfaceSet(self.cv, float("-inf"),
+                                              [0.0, 0.1, 0.2])
+        network = paths.MISTISNetwork([
+            (self.state_A, interfaces, self.state_B)
+        ])
         init_traj = make_1d_traj([-0.1, 0.2, 0.5, 0.8, 1.1])
-        scheme = paths.OneWayShootingMoveScheme(
-            network=network,
-            selector=paths.UniformSelector(),
-            engine=self.engine
-        )
+        scheme = paths.MoveScheme(network)
+        scheme.append([
+            paths.strategies.OneWayShootingStrategy(
+                selector=paths.UniformSelector(),
+                engine=self.engine
+            ),
+            paths.strategies.PathReversalStrategy(),
+            paths.strategies.OrganizeByMoveGroupStrategy()
+        ])
         init_cond = scheme.initial_conditions_from_trajectories(init_traj)
         self.sim = PathSampling(storage=None, move_scheme=scheme,
                                 sample_set=init_cond)
@@ -680,3 +689,7 @@ def all_snaps(sample_set):
         self.sim.run_until_decorrelated()
         final_snaps = all_snaps(self.sim.sample_set)
         assert initial_snaps & final_snaps == set([])
+        # test time reversal
+        init_xyz = set(s.xyz.tostring() for s in initial_snaps)
+        final_xyz = set(s.xyz.tostring() for s in final_snaps)
+        assert init_xyz & final_xyz == set([])