Added a stub of an example, and have something that "just runs"

examples/features/o3_averaging/random_liquid_water/input.xml

@@ -0,0 +1,35 @@
+<simulation verbosity='high'>
+  <output prefix='simulation'>
+    <properties stride='1' filename='out'>  [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal} ] </properties>
+    <trajectory filename='pos' stride='20' cell_units='angstrom'> positions{angstrom} </trajectory>
+    <checkpoint stride='200'/>
+  </output>
+  <total_steps>100</total_steps>
+  <prng>
+    <seed>31415</seed>
+  </prng>
+  <ffrotations name='driver-qtip4pf' mode='unix' pbc='false'>
+      <address>h2o-md.1</address>
+      <grid> 2 </grid>
+  </ffrotations>
+  <system>
+    <initialize nbeads='1'>
+      <file mode='xyz'> water_216.xyz </file>
+      <velocities mode='thermal' units='kelvin'> 300 </velocities>
+    </initialize>
+    <forces>
+      <force forcefield='driver-qtip4pf'> </force>
+    </forces>
+    <motion mode='dynamics'>
+      <dynamics mode='nvt'>
+        <timestep units='femtosecond'> 0.5 </timestep>
+        <thermostat mode='svr'>
+          <tau units='femtosecond'> 100 </tau>
+        </thermostat>
+      </dynamics>
+    </motion>
+    <ensemble>
+      <temperature units='kelvin'> 300 </temperature>
+    </ensemble>
+  </system>
+</simulation>

examples/features/o3_averaging/random_liquid_water/run.sh

@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m qtip4pf -u -a h2o-md.1"
+sleep_time=4
+
+${ipi} input.xml > log.i-pi & 
+echo "# i-PI is running"
+
+echo "# Waiting for ${sleep_time} (s) before executing driver"
+sleep ${sleep_time}
+
+${driver} > /dev/null & 
+echo "# Driver is running"
+
+wait
+
+echo "# Simulation complete"

examples/features/o3_averaging/random_liquid_water/water_216.xyz

@@ -0,0 +1 @@
+../../../init_files/water_216.xyz

ipi/engine/atoms.py

@@ -156,9 +156,9 @@ def copy(self):
         """
 
         newat = Atoms(self.natoms)
-        newat.q[:] = self.q
-        newat.p[:] = self.p
-        newat.m[:] = self.m
+        newat.q[:] = dstrip(self.q)
+        newat.p[:] = dstrip(self.p)
+        newat.m[:] = dstrip(self.m)
         newat.names[:] = self.names
         return newat