Merge pull request #392 from ajsilveira/master

SamplerStates accepts simtk.unit.Quantities as inputs

openmmtools/states.py

@@ -1754,7 +1754,7 @@ class SamplerState(object):
         Position vectors for N particles (length units).
     velocities : Nx3 simtk.unit.Quantity, optional
         Velocity vectors for N particles (velocity units).
-    box_vectors : 3x3 simtk.unit.Quantity
+    box_vectors : 3x3 simtk.unit.Quantity 
         Current box vectors (length units).
 
     Attributes
@@ -1834,7 +1834,13 @@ def __init__(self, positions, velocities=None, box_vectors=None):
         self._collective_variables = None
         self._kinetic_energy = None
         self._potential_energy = None
-        self._initialize(copy.deepcopy(positions), copy.deepcopy(velocities), copy.deepcopy(box_vectors))
+        args = []
+        for input in [positions, velocities, box_vectors]:
+            if isinstance(input, unit.Quantity) and not isinstance(input._value, np.ndarray):
+                args.append(np.array(input/input.unit)*input.unit)
+            else:
+               args.append(copy.deepcopy(input))    
+        self._initialize(*args)
 
     @classmethod
     def from_context(cls, context_state, ignore_collective_variables=False):