Merge pull request #484 from jhprinz/fixboxvectors

fix setting box_vectors
openpathsampling · May 19, 2016 · 5e03a00 · 5e03a00
2 parents efe4149 + c2d94b4
commit 5e03a00
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/openpathsampling/engines/openmm/engine.py b/openpathsampling/engines/openmm/engine.py
@@ -218,13 +218,19 @@ def _changed(self):
 
     @current_snapshot.setter
     def current_snapshot(self, snapshot):
-
         self.check_snapshot_type(snapshot)
 
         if snapshot is not self._current_snapshot:
             if snapshot.coordinates is not None:
                 self.simulation.context.setPositions(snapshot.coordinates)
 
+            if snapshot.box_vectors is not None:
+                self.simulation.context.setPeriodicBoxVectors(
+                    snapshot.box_vectors[0],
+                    snapshot.box_vectors[1],
+                    snapshot.box_vectors[2]
+                )
+
             if snapshot.velocities is not None:
                 self.simulation.context.setVelocities(snapshot.velocities)
 

diff --git a/openpathsampling/tests/testopenmmengine.py b/openpathsampling/tests/testopenmmengine.py
@@ -96,17 +96,21 @@ def test_snapshot_set(self):
                           )
             testvel.append([0.1*i, 0.1*i, 0.1*i])
 
+        testbvecs = 5.0 * np.identity(3)
+
         self.engine.current_snapshot = peng.Snapshot.construct(
             coordinates=np.array(testpos) * u.nanometers,
-            box_vectors=np.zeros((3, 3)),
+            box_vectors=np.array(testbvecs) * u.nanometers,
             velocities=np.array(testvel) * u.nanometers / u.picoseconds
         )
         state = self.engine.simulation.context.getState(getPositions=True,
                                                         getVelocities=True)
         sim_coords = state.getPositions(asNumpy=True) / u.nanometers
+        sim_bvecs = state.getPeriodicBoxVectors(asNumpy=True) / u.nanometers
         sim_vels = state.getVelocities(asNumpy=True) / (u.nanometers/u.picoseconds)
 
         np.testing.assert_almost_equal(testpos, sim_coords, decimal=5)
+        np.testing.assert_almost_equal(testbvecs, sim_bvecs, decimal=5)
         np.testing.assert_almost_equal(testvel, sim_vels, decimal=5)
 
     def test_generate_next_frame(self):