Merge pull request i-pi#266 from sabia-group/feat/hot-cmd-ensemble

PILE thermostats with a different temperature on the centroid

examples/features/Path_integral_quantum_dynamics/README.md

@@ -2,3 +2,4 @@ Path-integral quantum dynamics
 =================================================
 
 TRPMD: thermostatted ring polymer molecular dynamics
+two_temperature_PILE: an example of how one could run PACMD with a two-temperature PILE protocol. Settings cannot prevent "temperature leakage", do not use for production.

examples/features/Path_integral_quantum_dynamics/two_temperature_PILE/README

@@ -0,0 +1,6 @@
+This can be run with the driver.x code as a client, by using the pswater potential.
+A command to launch the client is
+
+i-pi-driver -u -a driver -m pswater
+
+This is an example for CMD. Be warned, the current settings CANNOT prevent energy leakage from the internal degrees of freedom to the centroid. This is just an example of the functionality. 

examples/features/Path_integral_quantum_dynamics/two_temperature_PILE/input.xml

@@ -0,0 +1,40 @@
+<simulation verbosity='low' threading='False'>
+  <output prefix='simulation'>
+    <properties stride='20' filename='out'>  [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_md{electronvolt}, kinetic_cv{electronvolt}, potential{electronvolt} ] </properties>
+    <trajectory filename='vel' stride='20' bead='1' flush='200'> velocities </trajectory>
+    <trajectory filename='xc' stride='20' flush='200'> x_centroid{angstrom} </trajectory> 
+    <trajectory filename='vc' stride='20' flush='200' > v_centroid </trajectory> 
+  </output>
+  <total_steps>1000</total_steps>
+  <prng>
+    <seed>3337</seed>
+  </prng>
+  <ffsocket name='driver' mode='unix'>
+    <address>driver</address>
+  </ffsocket>
+  <system>
+  <normal_modes>
+     <frequencies style='pa-cmd' units="inversecm"> [13000]   </frequencies>
+  </normal_modes>
+    <initialize nbeads='16'>
+      <file mode='chk'> therm_checkpoint.chk </file>
+    </initialize>
+    <forces>
+      <force forcefield='driver'> </force>
+    </forces>
+    <motion mode='dynamics'>
+      <fixcom> False </fixcom>
+      <dynamics mode='nvt'>
+        <timestep units='femtosecond'> 0.05 </timestep>
+        <thermostat mode='pile_l'>
+          <tau units='femtosecond'> 100 </tau> 
+          <pile_lambda> 0.01 </pile_lambda> 
+          <pile_centroid_t units='kelvin'> 200 </pile_centroid_t> 
+        </thermostat> 
+      </dynamics>
+    </motion>
+    <ensemble>
+      <temperature units='kelvin'> 600 </temperature>
+    </ensemble>
+  </system>
+</simulation>