Third round of examples clean-up (i-pi#278)

incomplete work towards these goals 
*  use lowercase names rather than Camel_Case
*  use underscores rather than hyphen consistently
 * flatten a bit the folder hierarchy - all the feature_type/feature/lammps_something should be just feature_type/feature
*  use driver whenever possible

---------

Co-authored-by: litman90 <[email protected]>

examples/features/Advanced_combinations/README.md → examples/features/advanced_combinations/README.md

@@ -3,8 +3,8 @@ Full-fledged demos of i-PI performing actual calculations
 
 - Existing examples in alphabetical orderd:
 
-	**Cav-MD**: Cavity molecular dynamics (CavMD) simulation of liquid water under vibrational strong coupling
-	**Spatially_localized_RPC**: Spatially localized ring-polymer contraction 
+	**cav_md**: Cavity molecular dynamics (CavMD) simulation of liquid water under vibrational strong coupling
+	**spatially_localized_rpc**: Spatially localized ring-polymer contraction 
 
 - Examples that need to be added
   **COMPLETE HERE**

examples/features/Classical_molecular_dynamics/README.md → examples/features/classical_molecular_dynamics/README.md

@@ -1,5 +1,5 @@
 Classical molecular dynamics. 
 =================================================
-NVT_ensemble: global thermostatted classical NVT simulations
+nvt_ensemble: global thermostatted classical NVT simulations
 NPzT_ensemble_BZP: classical NVT simulations with the BZP barostat with only the z-component cell allowed to fluctuate
 NPzT_ensemble_MTTK: classical NVT simulations with the MTTK barostat with only the z-component cell allowed to fluctuate

examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/input.xml → examples/features/classical_molecular_dynamics/nvt_ensemble/input.xml

@@ -8,16 +8,16 @@
   <prng>
     <seed>31415</seed>
   </prng>
-  <ffsocket name='lammps' mode='unix'>
-    <address>h2o-pimd.1</address>
+  <ffsocket name='driver-qtip4pf' mode='unix' pbc='false'>
+    <address>h2o-md.1</address>
   </ffsocket>
   <system>
     <initialize nbeads='1'>
       <file mode='xyz'> water_216.xyz </file>
       <velocities mode='thermal' units='kelvin'> 300 </velocities>
     </initialize>
     <forces>
-      <force forcefield='lammps'> </force>
+      <force forcefield='driver-qtip4pf'> </force>
     </forces>
     <motion mode='dynamics'>
       <dynamics mode='nvt'>

examples/features/classical_molecular_dynamics/nvt_ensemble/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/classical_molecular_dynamics/nvt_ensemble/water_216.xyz

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

examples/features/metadynamics/README.md

@@ -0,0 +1,17 @@
+Metadynamics calculations using PLUMED
+======================================
+
+There are three examples of different variations-on-a-theme of the use of `<ffplumed>`
+to perform metadynamics calculations with i-PI
+
+`pimd_metadynamics` : metadynamics using a centroid bias for a PIMD calculation
+`wte_metadynamics`  : well-tempered ensemble. requires a workaround to communicate the energy as a CV
+`remd_metadynamics` : replica exchange combined with metadynamics
+
+These examples can be run using the Zundel PES implemented in the i-pi driver,
+
+```bash
+i-pi--driver -u -h zundel -m zundel
+```
+
+However, they require having PLUMED libraries and Python bindings in the appropriate system paths.

examples/features/metadynamics/wte_metadynamics/h5o2.dms4B.coeff.com.dat

@@ -0,0 +1 @@
+../../../../drivers/f90/pes/h5o2.dms4B.coeff.com.dat

examples/features/metadynamics/wte_metadynamics/h5o2.pes4B.coeff.dat

@@ -0,0 +1 @@
+../../../../drivers/f90/pes/h5o2.pes4B.coeff.dat

examples/features/open_paths/README.md

@@ -1,6 +1,6 @@
 Open path integral calculations for momentum distribution. 
 =================================================
 
-`water_onepath`: An open-path integral calculation with one atom represented with an open path while all others are represented with a closed path. This setup can be used for rigorous estimation of the momentum distribution of a particle. 
+`one_path`: An open-path integral calculation with one atom represented with an open path while all others are represented with a closed path. This setup can be used for rigorous estimation of the momentum distribution of a particle. 
 
-`water_multipath`: An open-path integral calculation with multiple atoms of a single atom type are represented with an open path while all others are represented with a closed path. Practically, this allows to average the momentum distribution over multiple atoms but it is not a rigorous way to estimate the momentum distribution of an atom if the kinetic energies of the different atoms are correlated.  
+`multi_path`: An open-path integral calculation with multiple atoms of a single atom type are represented with an open path while all others are represented with a closed path. Practically, this allows to average the momentum distribution over multiple atoms but it is not a rigorous way to estimate the momentum distribution of an atom if the kinetic energies of the different atoms are correlated.  

examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/input.xml → examples/features/path_integral_molecular_dynamics/cayley_pimd/input.xml

@@ -8,8 +8,8 @@
   <prng>
     <seed>32415</seed>
   </prng>
-  <ffsocket name='lammps' mode='unix'>
-    <address> h2o-pimd.4-cay </address>
+  <ffsocket name='qtip4pf' mode='unix' pbc='false'>
+    <address> h2o-cayley </address>
   </ffsocket>
   <system>
     <normal_modes propagator="cayley"/>
@@ -18,7 +18,7 @@
       <velocities mode='thermal' units='kelvin'> 300 </velocities>
     </initialize>
     <forces>
-      <force forcefield='lammps'> </force>
+      <force forcefield='qtip4pf'> </force>
     </forces>
     <motion mode='dynamics'>
       <dynamics mode='nvt'>