SimStore: Fix issue with internalized snapshot box vectors

openpathsampling/engines/features/box_vectors.py

@@ -3,6 +3,10 @@
 
 dimensions = ['n_spatial']
 
+schema_entries = [
+    ('box_vectors', 'ndarray.float32({n_spatial},{n_spatial})')
+]
+
 
 def netcdfplus_init(store):
     store.create_variable(

openpathsampling/experimental/storage/test_snapshot_integrations.py

@@ -7,6 +7,7 @@
 
 import numpy as np
 import openpathsampling as paths
+from openpathsampling.integration_tools import unit
 
 from openpathsampling.tests.test_helpers import data_filename
 
@@ -48,21 +49,46 @@ def _make_gromacs_snap(self):
         )
         return snap
 
+    def _make_gromacs_int_snap(self):
+        snap = self._make_gromacs_snap()
+        return snap.internalize()
+
     def _make_openmm_snap(self):
         mm = pytest.importorskip('simtk.openmm')
         traj_file = data_filename('ala_small_traj.pdb')
         traj = paths.engines.openmm.tools.ops_load_trajectory(traj_file)
         snap = traj[0]
         return snap
 
-    @pytest.mark.parametrize('integration', ['gromacs', 'openmm'])
+    @pytest.mark.parametrize('integration', ['gromacs', 'openmm',
+                                             'gromacs_int'])
     def test_integration(self, integration):
         make_snap = {
             'gromacs': self._make_gromacs_snap,
             'openmm': self._make_openmm_snap,
+            'gromacs_int': self._make_gromacs_int_snap,
         }[integration]
+
         snap = make_snap()
 
+        def get_velocities(snap):
+            return snap.velocities
+
+        def get_box_vectors(snap):
+            return snap.box_vectors
+
+        if integration == 'openmm':
+            # already skipping if OpenMM isn't available, so we can use unit
+            nm = unit.nanometer
+            ps = unit.picosecond
+            def extract_unit(func, units):
+                def inner(snap):
+                    return func(snap).value_in_unit(units)
+                return inner
+
+            get_velocities = extract_unit(get_velocities, nm/ps)
+            get_box_vectors = extract_unit(get_box_vectors, nm)
+
         storage = self._make_storage(mode='w')
         assert not storage.backend.has_table('snapshot0')
         storage.save(snap)
@@ -73,6 +99,9 @@ def test_integration(self, integration):
         assert storage.backend.has_table('snapshot0')
         snap2 = storage.snapshots.tables['snapshot0'][0]
 
+        assert not snap is snap2
         np.testing.assert_array_equal(snap.xyz, snap2.xyz)
-
-
+        np.testing.assert_array_equal(get_velocities(snap),
+                                      get_velocities(snap2))
+        np.testing.assert_array_equal(get_box_vectors(snap),
+                                      get_box_vectors(snap2))