Examples cleanup part 4 (i-pi#283)

* use underscores rather than hyphen consistently: Done. Update some README.md and add note on conventions in the main README.md
* flatten examples structure
* move profiling to ipi_test folder. update the readme
* Fixed a warning in an obscure s-c-related property
* (partial) removal of LAMMPS dependency of the examples 

---------

Co-authored-by: Yair Litman <[email protected]>

examples/README.md

@@ -20,3 +20,7 @@ If you want to add an example for a new feature, please respect the folder struc
 - Keep the size of the example to the minimum. If you need large files to run the client (e.g. a pseudopotential, or the parameters of a ML potential) give instructions on how to download the file from a repository. If the file is shared by many examples, put it in `init_files` and make a symlink
 - Include a README that briefly explains what the example is about, and what a user should be aware of when running it (what it does, what special setup is needed, etc.)
 
+Notes on file naming conventions and formats:
+  - Please use lowercase names rather than Camel_Case
+  - Please use use underscores rather than hyphen 
+  - Please use driver whenever possible

examples/clients/vasp/Makefile

@@ -18,12 +18,12 @@ define run_vasp
 endef
 
 h2o:
-	cd water-1-npt-md-vasp; $(IPI) input.xml & sleep 5; \
+	cd water_1_npt_md_vasp; $(IPI) input.xml & sleep 5; \
 	$(call run_vasp,1) \
 	wait
 
 dia:
-	cd dia-npt-pimd-vasp; $(IPI) input.xml & sleep 5; \
+	cd dia_npt_pimd_vasp; $(IPI) input.xml & sleep 5; \
 	$(call run_vasp,4) \
 	wait
 

examples/features/advanced_combinations/README.md

@@ -1,10 +1,12 @@
-Full-fledged demos of i-PI performing actual calculations
-=========================================================
+Examples of advanced features
+=============================
 
-- Existing examples in alphabetical orderd:
+This folder contains examples that are somewhat more complicated, requiring
+either a particular setup of the drivers, or post-processing of the output. 
+More thoroughly-commented examples of advanced simulations can be found in the
+`demos` folder: these are more minimalistic, and probably require careful study
+of the reference papers to fully understand the simulation setup. 
 
-	**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/advanced_combinations/cav_md/input.xml → examples/features/advanced_combinations/cav_md_liquid_water/input.xml

@@ -4,11 +4,11 @@
     <trajectory filename='xc' stride='4' format='xyz'> x_centroid{angstrom} </trajectory>
     <checkpoint filename='checkpoint' stride='4' overwrite='True'/>
   </output>
-  <total_steps>40000</total_steps>
+  <total_steps>4000</total_steps>
   <prng>
     <seed>31415</seed>
   </prng>
-  <ffcavphsocket name='lammps' mode='unix' pbc='True'>
+  <ffcavphsocket name='qtip4pf' mode='unix' pbc='False'>
     <address>h2o-cl-cavmd</address>
     <latency> 1e-3 </latency>
     <apply_photon> True </apply_photon>
@@ -25,7 +25,7 @@
       <velocities mode='thermal' units='kelvin'> 300 </velocities>
     </initialize>
     <forces>
-      <force forcefield='lammps'> </force>
+      <force forcefield='qtip4pf'> </force>
     </forces>
     <motion mode='dynamics'>
       <dynamics mode='nve'>

examples/features/advanced_combinations/cav_md_liquid_water/run.sh

@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m qtip4pf -u -a h2o-cl-cavmd"
+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/advanced_combinations/spatially_localized_rpc_graphene_benzene/README.md

@@ -0,0 +1,7 @@
+Spatially localized ring-polymer contraction
+--------------------------------------------
+
+NB: requires LAMMPS as a driver code
+
+- Client code: Lammps
+- Theory: Litman, et al. J. Chem. Phys. 148, 102320 (2018) https://doi.org/10.1063/1.5002537 

examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP_ice/ice_96.xyz

@@ -0,0 +1 @@
+../../../init_files/ice_96.xyz