diff --git a/examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/in.lmp b/examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/in.lmp
deleted file mode 100644
index b335a251d..000000000
--- a/examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/in.lmp
+++ /dev/null
@@ -1,32 +0,0 @@
-units electron
-atom_style full
-
-#pair_style lj/cut/coul/long 17.01
-pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007
-#bond_style harmonic
-bond_style class2
-angle_style harmonic
-#kspace_style pppm 0.0001
-kspace_style pppm/tip4p 0.0001
-
-read_data data.lmp
-pair_coeff * * 0 0
-pair_coeff 1 1 0.000295147 5.96946
-
-neighbor 2.0 bin
-
-timestep 0.00025
-
-#velocity all create 298.0 2345187
-
-#thermo_style multi
-#thermo 1
-
-#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1
-#fix 1 all nve
-fix 1 all ipi h2o-pimd.1 32345 unix
-
-#dump 1 all xyz 25 dump.xyz
-
-run 100000000
-
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.dms4B.coeff.com.dat b/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.dms4B.coeff.com.dat
deleted file mode 120000
index 35e54d55e..000000000
--- a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.dms4B.coeff.com.dat
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../drivers/f90/pes/h5o2.dms4B.coeff.com.dat
\ No newline at end of file
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.pes4B.coeff.dat b/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.pes4B.coeff.dat
deleted file mode 120000
index a279745bc..000000000
--- a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/h5o2.pes4B.coeff.dat
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../drivers/f90/pes/h5o2.pes4B.coeff.dat
\ No newline at end of file
diff --git a/examples/features/Metadynamics/README.md b/examples/features/Metadynamics/README.md
deleted file mode 100644
index 304627ac1..000000000
--- a/examples/features/Metadynamics/README.md
+++ /dev/null
@@ -1,10 +0,0 @@
-Metadynamics calculations using PLUMED
-======================================
-
-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.
diff --git a/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/data.lmp b/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/data.lmp
deleted file mode 100644
index 13c75e993..000000000
--- a/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/data.lmp
+++ /dev/null
@@ -1,1331 +0,0 @@
-LAMMPS Description
-
- 648 atoms
- 432 bonds
- 216 angles
-
- 2 atom types
- 1 bond types
- 1 angle types
-
- 0 35.233 xlo xhi
- 0 35.233 ylo yhi
- 0 35.233 zlo zhi
-
-Masses
-
- 1 15.9994
- 2 1.0080
-
-Bond Coeffs
-
- 1 1.78 0.2708585 -0.327738785 0.231328959
-
-Angle Coeffs
-
- 1 0.0700 107.400000
-
-Atoms
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diff --git a/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/water_216.xyz b/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/water_216.xyz
deleted file mode 120000
index 95291df24..000000000
--- a/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/water_216.xyz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../init_files/water_216.xyz
\ No newline at end of file
diff --git a/examples/features/Vibrations/harmonic/eNMFD-NormalModes/lammps_h2o-molecule/run.sh b/examples/features/Vibrations/harmonic/eNMFD-NormalModes/lammps_h2o-molecule/run.sh
deleted file mode 100644
index 802f8e4b6..000000000
--- a/examples/features/Vibrations/harmonic/eNMFD-NormalModes/lammps_h2o-molecule/run.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-ipi=i-pi
-lmp=lmp_mpi
-sleep_time=10
-
-${ipi} input.xml > log.i-pi &
-echo "# i-PI is running"
-
-echo "# Waiting for ${sleep_time} (s) before executing LAMMPS"
-sleep ${sleep_time}
-
-${lmp} < in.lmp > /dev/null &
-echo "# LAMMPS is running"
-
-wait
-
-echo "# Simulation complete"
diff --git a/examples/features/Advanced_combinations/README.md b/examples/features/advanced_combinations/README.md
similarity index 68%
rename from examples/features/Advanced_combinations/README.md
rename to examples/features/advanced_combinations/README.md
index 20c4eb235..f7ad369bf 100644
--- a/examples/features/Advanced_combinations/README.md
+++ b/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**
diff --git a/examples/features/Advanced_combinations/Cav-MD/README.md b/examples/features/advanced_combinations/cav_md/README.md
similarity index 100%
rename from examples/features/Advanced_combinations/Cav-MD/README.md
rename to examples/features/advanced_combinations/cav_md/README.md
diff --git a/examples/features/Advanced_combinations/Cav-MD/data.lmp b/examples/features/advanced_combinations/cav_md/data.lmp
similarity index 100%
rename from examples/features/Advanced_combinations/Cav-MD/data.lmp
rename to examples/features/advanced_combinations/cav_md/data.lmp
diff --git a/examples/features/Advanced_combinations/Cav-MD/in.lmp b/examples/features/advanced_combinations/cav_md/in.lmp
similarity index 100%
rename from examples/features/Advanced_combinations/Cav-MD/in.lmp
rename to examples/features/advanced_combinations/cav_md/in.lmp
diff --git a/examples/features/Advanced_combinations/Cav-MD/input.xml b/examples/features/advanced_combinations/cav_md/input.xml
similarity index 100%
rename from examples/features/Advanced_combinations/Cav-MD/input.xml
rename to examples/features/advanced_combinations/cav_md/input.xml
diff --git a/examples/features/Advanced_combinations/Cav-MD/water_216_photons.xyz b/examples/features/advanced_combinations/cav_md/water_216_photons.xyz
similarity index 100%
rename from examples/features/Advanced_combinations/Cav-MD/water_216_photons.xyz
rename to examples/features/advanced_combinations/cav_md/water_216_photons.xyz
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/CH.airebo b/examples/features/advanced_combinations/spatially_localized_rpc/CH.airebo
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/CH.airebo
rename to examples/features/advanced_combinations/spatially_localized_rpc/CH.airebo
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/README.md b/examples/features/advanced_combinations/spatially_localized_rpc/README.md
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/README.md
rename to examples/features/advanced_combinations/spatially_localized_rpc/README.md
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/data.full b/examples/features/advanced_combinations/spatially_localized_rpc/data.full
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/data.full
rename to examples/features/advanced_combinations/spatially_localized_rpc/data.full
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/data.part b/examples/features/advanced_combinations/spatially_localized_rpc/data.part
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/data.part
rename to examples/features/advanced_combinations/spatially_localized_rpc/data.part
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/in.full b/examples/features/advanced_combinations/spatially_localized_rpc/in.full
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/in.full
rename to examples/features/advanced_combinations/spatially_localized_rpc/in.full
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/in.partbeads b/examples/features/advanced_combinations/spatially_localized_rpc/in.partbeads
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/in.partbeads
rename to examples/features/advanced_combinations/spatially_localized_rpc/in.partbeads
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/in.partcontr b/examples/features/advanced_combinations/spatially_localized_rpc/in.partcontr
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/in.partcontr
rename to examples/features/advanced_combinations/spatially_localized_rpc/in.partcontr
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/init.xyz b/examples/features/advanced_combinations/spatially_localized_rpc/init.xyz
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/init.xyz
rename to examples/features/advanced_combinations/spatially_localized_rpc/init.xyz
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/input.xml b/examples/features/advanced_combinations/spatially_localized_rpc/input.xml
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/input.xml
rename to examples/features/advanced_combinations/spatially_localized_rpc/input.xml
diff --git a/examples/features/Advanced_combinations/Spatially_localized_RPC/test_settings.dat b/examples/features/advanced_combinations/spatially_localized_rpc/test_settings.dat
similarity index 100%
rename from examples/features/Advanced_combinations/Spatially_localized_RPC/test_settings.dat
rename to examples/features/advanced_combinations/spatially_localized_rpc/test_settings.dat
diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/data.lmp b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/data.lmp
similarity index 100%
rename from examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/data.lmp
rename to examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/data.lmp
diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/ice_96.xyz b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/ice_96.xyz
similarity index 100%
rename from examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/ice_96.xyz
rename to examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/ice_96.xyz
diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/in.lmp b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/in.lmp
similarity index 100%
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rename to examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/in.lmp
diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/input.xml b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/input.xml
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/run.sh b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/run.sh
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/test_settings.dat b/examples/features/classical_molecular_dynamics/NPzT_ensemble_BZP/lammps_h2o_bulk_Ih/test_settings.dat
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/.driver_info b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/.driver_info
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/data.lmp b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/data.lmp
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/ice_96.xyz b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/ice_96.xyz
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/in.lmp b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/in.lmp
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/input.xml b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/input.xml
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/run.sh b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/run.sh
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/simulation.restart b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/simulation.restart
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diff --git a/examples/features/Classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/simulation.xc.pdb b/examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/simulation.xc.pdb
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rename to examples/features/classical_molecular_dynamics/NPzT_ensemble_MTTK/lammps_h2o_bulk_Ih/simulation.xc.pdb
diff --git a/examples/features/Classical_molecular_dynamics/README.md b/examples/features/classical_molecular_dynamics/README.md
similarity index 84%
rename from examples/features/Classical_molecular_dynamics/README.md
rename to examples/features/classical_molecular_dynamics/README.md
index 5198193c0..a3730455c 100644
--- a/examples/features/Classical_molecular_dynamics/README.md
+++ b/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
diff --git a/examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/input.xml b/examples/features/classical_molecular_dynamics/nvt_ensemble/input.xml
similarity index 88%
rename from examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/input.xml
rename to examples/features/classical_molecular_dynamics/nvt_ensemble/input.xml
index adf34b9ed..d4621aa5f 100644
--- a/examples/features/Classical_molecular_dynamics/NVT_ensemble/lammps_h2o_liquid_water/input.xml
+++ b/examples/features/classical_molecular_dynamics/nvt_ensemble/input.xml
@@ -8,8 +8,8 @@
31415
-
- h2o-pimd.1
+
+ h2o-md.1
@@ -17,7 +17,7 @@
300
-
+
diff --git a/examples/features/classical_molecular_dynamics/nvt_ensemble/run.sh b/examples/features/classical_molecular_dynamics/nvt_ensemble/run.sh
new file mode 100644
index 000000000..976f961e8
--- /dev/null
+++ b/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"
diff --git a/examples/features/classical_molecular_dynamics/nvt_ensemble/water_216.xyz b/examples/features/classical_molecular_dynamics/nvt_ensemble/water_216.xyz
new file mode 120000
index 000000000..58a9ede12
--- /dev/null
+++ b/examples/features/classical_molecular_dynamics/nvt_ensemble/water_216.xyz
@@ -0,0 +1 @@
+../../../init_files/water_216.xyz
\ No newline at end of file
diff --git a/examples/features/Committee_models/BASELINED-COMMITTEE/lammps_h2o_liquid_water/.driver_info b/examples/features/committee_models/BASELINED-COMMITTEE/lammps_h2o_liquid_water/.driver_info
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diff --git a/examples/features/Geometry_optimization/BFGS/lammps_NaCl/run.sh b/examples/features/geometry_optimization/LBFGS/lammps_paracetamol/run.sh
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rename from examples/features/Geometry_optimization/BFGS/lammps_NaCl/run.sh
rename to examples/features/geometry_optimization/LBFGS/lammps_paracetamol/run.sh
diff --git a/examples/features/Geometry_optimization/README.md b/examples/features/geometry_optimization/README.md
similarity index 100%
rename from examples/features/Geometry_optimization/README.md
rename to examples/features/geometry_optimization/README.md
diff --git a/examples/features/Geometry_optimization/SD/lammps_h2o_molecule/data.lmp b/examples/features/geometry_optimization/SD/lammps_h2o_molecule/data.lmp
similarity index 100%
rename from examples/features/Geometry_optimization/SD/lammps_h2o_molecule/data.lmp
rename to examples/features/geometry_optimization/SD/lammps_h2o_molecule/data.lmp
diff --git a/examples/features/Geometry_optimization/SD/lammps_h2o_molecule/in.lmp b/examples/features/geometry_optimization/SD/lammps_h2o_molecule/in.lmp
similarity index 100%
rename from examples/features/Geometry_optimization/SD/lammps_h2o_molecule/in.lmp
rename to examples/features/geometry_optimization/SD/lammps_h2o_molecule/in.lmp
diff --git a/examples/features/Geometry_optimization/SD/lammps_h2o_molecule/init.xyz b/examples/features/geometry_optimization/SD/lammps_h2o_molecule/init.xyz
similarity index 100%
rename from examples/features/Geometry_optimization/SD/lammps_h2o_molecule/init.xyz
rename to examples/features/geometry_optimization/SD/lammps_h2o_molecule/init.xyz
diff --git a/examples/features/Geometry_optimization/SD/lammps_h2o_molecule/input.xml b/examples/features/geometry_optimization/SD/lammps_h2o_molecule/input.xml
similarity index 100%
rename from examples/features/Geometry_optimization/SD/lammps_h2o_molecule/input.xml
rename to examples/features/geometry_optimization/SD/lammps_h2o_molecule/input.xml
diff --git a/examples/features/Geometry_optimization/LBFGS/lammps_paracetamol/run.sh b/examples/features/geometry_optimization/SD/lammps_h2o_molecule/run.sh
similarity index 100%
rename from examples/features/Geometry_optimization/LBFGS/lammps_paracetamol/run.sh
rename to examples/features/geometry_optimization/SD/lammps_h2o_molecule/run.sh
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/README.md b/examples/features/geometry_optimization/nudged_elastic_band/README.md
similarity index 100%
rename from examples/features/Geometry_optimization/Nudge_elastic_band/zundel/README.md
rename to examples/features/geometry_optimization/nudged_elastic_band/README.md
diff --git a/examples/features/Metadynamics/zundel-metad/h5o2.dms4B.coeff.com.dat b/examples/features/geometry_optimization/nudged_elastic_band/h5o2.dms4B.coeff.com.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-metad/h5o2.dms4B.coeff.com.dat
rename to examples/features/geometry_optimization/nudged_elastic_band/h5o2.dms4B.coeff.com.dat
diff --git a/examples/features/Metadynamics/zundel-metad/h5o2.pes4B.coeff.dat b/examples/features/geometry_optimization/nudged_elastic_band/h5o2.pes4B.coeff.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-metad/h5o2.pes4B.coeff.dat
rename to examples/features/geometry_optimization/nudged_elastic_band/h5o2.pes4B.coeff.dat
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/init.xyz b/examples/features/geometry_optimization/nudged_elastic_band/init.xyz
similarity index 100%
rename from examples/features/Geometry_optimization/Nudge_elastic_band/zundel/init.xyz
rename to examples/features/geometry_optimization/nudged_elastic_band/init.xyz
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/input.xml b/examples/features/geometry_optimization/nudged_elastic_band/input.xml
similarity index 100%
rename from examples/features/Geometry_optimization/Nudge_elastic_band/zundel/input.xml
rename to examples/features/geometry_optimization/nudged_elastic_band/input.xml
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/plot-bells.plt b/examples/features/geometry_optimization/nudged_elastic_band/plot-bells.plt
similarity index 100%
rename from examples/features/Geometry_optimization/Nudge_elastic_band/zundel/plot-bells.plt
rename to examples/features/geometry_optimization/nudged_elastic_band/plot-bells.plt
diff --git a/examples/features/Geometry_optimization/Nudge_elastic_band/zundel/plot-converg.plt b/examples/features/geometry_optimization/nudged_elastic_band/plot-converg.plt
similarity index 100%
rename from examples/features/Geometry_optimization/Nudge_elastic_band/zundel/plot-converg.plt
rename to examples/features/geometry_optimization/nudged_elastic_band/plot-converg.plt
diff --git a/examples/features/Input-Output/README.md b/examples/features/input_output/README.md
similarity index 100%
rename from examples/features/Input-Output/README.md
rename to examples/features/input_output/README.md
diff --git a/examples/features/Input-Output/cif/K2S2O8_rotated.cif b/examples/features/input_output/cif/K2S2O8_rotated.cif
similarity index 100%
rename from examples/features/Input-Output/cif/K2S2O8_rotated.cif
rename to examples/features/input_output/cif/K2S2O8_rotated.cif
diff --git a/examples/features/Input-Output/cif/K2S2O8_rotated.xyz b/examples/features/input_output/cif/K2S2O8_rotated.xyz
similarity index 100%
rename from examples/features/Input-Output/cif/K2S2O8_rotated.xyz
rename to examples/features/input_output/cif/K2S2O8_rotated.xyz
diff --git a/examples/features/Input-Output/cif/README b/examples/features/input_output/cif/README
similarity index 100%
rename from examples/features/Input-Output/cif/README
rename to examples/features/input_output/cif/README
diff --git a/examples/features/Input-Output/cif/input.xml b/examples/features/input_output/cif/input.xml
similarity index 100%
rename from examples/features/Input-Output/cif/input.xml
rename to examples/features/input_output/cif/input.xml
diff --git a/examples/features/Input-Output/replay/input.xml b/examples/features/input_output/replay/input.xml
similarity index 100%
rename from examples/features/Input-Output/replay/input.xml
rename to examples/features/input_output/replay/input.xml
diff --git a/examples/features/Input-Output/replay/traj.extxyz b/examples/features/input_output/replay/traj.extxyz
similarity index 100%
rename from examples/features/Input-Output/replay/traj.extxyz
rename to examples/features/input_output/replay/traj.extxyz
diff --git a/examples/features/metadynamics/README.md b/examples/features/metadynamics/README.md
new file mode 100644
index 000000000..a4e4f5454
--- /dev/null
+++ b/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 ``
+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.
diff --git a/examples/features/Metadynamics/zundel-metad/h5o2+.xyz b/examples/features/metadynamics/pimd_metadynamics/h5o2+.xyz
similarity index 100%
rename from examples/features/Metadynamics/zundel-metad/h5o2+.xyz
rename to examples/features/metadynamics/pimd_metadynamics/h5o2+.xyz
diff --git a/examples/features/Metadynamics/zundel-remd-metad/h5o2.dms4B.coeff.com.dat b/examples/features/metadynamics/pimd_metadynamics/h5o2.dms4B.coeff.com.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/h5o2.dms4B.coeff.com.dat
rename to examples/features/metadynamics/pimd_metadynamics/h5o2.dms4B.coeff.com.dat
diff --git a/examples/features/Metadynamics/zundel-remd-metad/h5o2.pes4B.coeff.dat b/examples/features/metadynamics/pimd_metadynamics/h5o2.pes4B.coeff.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/h5o2.pes4B.coeff.dat
rename to examples/features/metadynamics/pimd_metadynamics/h5o2.pes4B.coeff.dat
diff --git a/examples/features/Metadynamics/zundel-metad/input.xml b/examples/features/metadynamics/pimd_metadynamics/input.xml
similarity index 100%
rename from examples/features/Metadynamics/zundel-metad/input.xml
rename to examples/features/metadynamics/pimd_metadynamics/input.xml
diff --git a/examples/features/Metadynamics/zundel-metad/plumed/plumed.dat b/examples/features/metadynamics/pimd_metadynamics/plumed/plumed.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-metad/plumed/plumed.dat
rename to examples/features/metadynamics/pimd_metadynamics/plumed/plumed.dat
diff --git a/examples/features/Metadynamics/zundel-remd-metad/h5o2+.xyz b/examples/features/metadynamics/remd_metadynamics/h5o2+.xyz
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/h5o2+.xyz
rename to examples/features/metadynamics/remd_metadynamics/h5o2+.xyz
diff --git a/examples/features/Metadynamics/zundel-wte/h5o2.dms4B.coeff.com.dat b/examples/features/metadynamics/remd_metadynamics/h5o2.dms4B.coeff.com.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-wte/h5o2.dms4B.coeff.com.dat
rename to examples/features/metadynamics/remd_metadynamics/h5o2.dms4B.coeff.com.dat
diff --git a/examples/features/Metadynamics/zundel-wte/h5o2.pes4B.coeff.dat b/examples/features/metadynamics/remd_metadynamics/h5o2.pes4B.coeff.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-wte/h5o2.pes4B.coeff.dat
rename to examples/features/metadynamics/remd_metadynamics/h5o2.pes4B.coeff.dat
diff --git a/examples/features/Metadynamics/zundel-remd-metad/input.xml b/examples/features/metadynamics/remd_metadynamics/input.xml
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/input.xml
rename to examples/features/metadynamics/remd_metadynamics/input.xml
diff --git a/examples/features/Metadynamics/zundel-remd-metad/plumed-200K/plumed.dat b/examples/features/metadynamics/remd_metadynamics/plumed-200K/plumed.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/plumed-200K/plumed.dat
rename to examples/features/metadynamics/remd_metadynamics/plumed-200K/plumed.dat
diff --git a/examples/features/Metadynamics/zundel-remd-metad/plumed-250K/plumed.dat b/examples/features/metadynamics/remd_metadynamics/plumed-250K/plumed.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/plumed-250K/plumed.dat
rename to examples/features/metadynamics/remd_metadynamics/plumed-250K/plumed.dat
diff --git a/examples/features/Metadynamics/zundel-remd-metad/plumed-320K/plumed.dat b/examples/features/metadynamics/remd_metadynamics/plumed-320K/plumed.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-remd-metad/plumed-320K/plumed.dat
rename to examples/features/metadynamics/remd_metadynamics/plumed-320K/plumed.dat
diff --git a/examples/features/Metadynamics/zundel-wte/h5o2+.xyz b/examples/features/metadynamics/wte_metadynamics/h5o2+.xyz
similarity index 100%
rename from examples/features/Metadynamics/zundel-wte/h5o2+.xyz
rename to examples/features/metadynamics/wte_metadynamics/h5o2+.xyz
diff --git a/examples/features/metadynamics/wte_metadynamics/h5o2.dms4B.coeff.com.dat b/examples/features/metadynamics/wte_metadynamics/h5o2.dms4B.coeff.com.dat
new file mode 120000
index 000000000..35797e5cc
--- /dev/null
+++ b/examples/features/metadynamics/wte_metadynamics/h5o2.dms4B.coeff.com.dat
@@ -0,0 +1 @@
+../../../../drivers/f90/pes/h5o2.dms4B.coeff.com.dat
\ No newline at end of file
diff --git a/examples/features/metadynamics/wte_metadynamics/h5o2.pes4B.coeff.dat b/examples/features/metadynamics/wte_metadynamics/h5o2.pes4B.coeff.dat
new file mode 120000
index 000000000..d5173136a
--- /dev/null
+++ b/examples/features/metadynamics/wte_metadynamics/h5o2.pes4B.coeff.dat
@@ -0,0 +1 @@
+../../../../drivers/f90/pes/h5o2.pes4B.coeff.dat
\ No newline at end of file
diff --git a/examples/features/Metadynamics/zundel-wte/input.xml b/examples/features/metadynamics/wte_metadynamics/input.xml
similarity index 100%
rename from examples/features/Metadynamics/zundel-wte/input.xml
rename to examples/features/metadynamics/wte_metadynamics/input.xml
diff --git a/examples/features/Metadynamics/zundel-wte/plumed/plumed.dat b/examples/features/metadynamics/wte_metadynamics/plumed/plumed.dat
similarity index 100%
rename from examples/features/Metadynamics/zundel-wte/plumed/plumed.dat
rename to examples/features/metadynamics/wte_metadynamics/plumed/plumed.dat
diff --git a/examples/features/open_paths/README.md b/examples/features/open_paths/README.md
index 84d61aa23..4caf7080a 100644
--- a/examples/features/open_paths/README.md
+++ b/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.
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/input.xml b/examples/features/path_integral_molecular_dynamics/cayley_pimd/input.xml
similarity index 88%
rename from examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/input.xml
rename to examples/features/path_integral_molecular_dynamics/cayley_pimd/input.xml
index b8cab55be..e2936f687 100644
--- a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/input.xml
+++ b/examples/features/path_integral_molecular_dynamics/cayley_pimd/input.xml
@@ -8,8 +8,8 @@
32415
-
- h2o-pimd.4-cay
+
+ h2o-cayley
@@ -18,7 +18,7 @@
300
-
+
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/data.lmp b/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/data.lmp
deleted file mode 100644
index 13c75e993..000000000
--- a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/data.lmp
+++ /dev/null
@@ -1,1331 +0,0 @@
-LAMMPS Description
-
- 648 atoms
- 432 bonds
- 216 angles
-
- 2 atom types
- 1 bond types
- 1 angle types
-
- 0 35.233 xlo xhi
- 0 35.233 ylo yhi
- 0 35.233 zlo zhi
-
-Masses
-
- 1 15.9994
- 2 1.0080
-
-Bond Coeffs
-
- 1 1.78 0.2708585 -0.327738785 0.231328959
-
-Angle Coeffs
-
- 1 0.0700 107.400000
-
-Atoms
-
- 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000
- 2 1 2 0.5564 2.97900000 7.05400000 0.85700000
- 3 1 2 0.5564 5.52500001 5.69700001 0.45100000
- 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000
- 5 2 2 0.5564 33.72200001 34.68900000 4.84000001
- 6 2 2 0.5564 36.02900000 33.22000001 3.71100001
- 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000
- 8 3 2 0.5564 7.26500000 1.86400000 13.85100001
- 9 3 2 0.5564 5.00899999 3.55500000 13.91599999
- 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001
- 11 4 2 0.5564 0.75700000 0.26100000 21.82000000
- 12 4 2 0.5564 0.21300001 3.01299999 23.04700000
- 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999
- 14 5 2 0.5564 0.81800000 1.88399999 30.73200000
- 15 5 2 0.5564 2.88300001 1.82500000 29.01100000
- 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001
- 17 6 2 0.5564 2.39200001 2.89799999 34.84600000
- 18 6 2 0.5564 0.81400000 0.53200001 35.83600000
- 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999
- 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000
- 21 7 2 0.5564 30.91999999 11.59399999 1.67700000
- 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000
- 23 8 2 0.5564 0.30500000 10.64300001 2.79300000
- 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000
- 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000
- 26 9 2 0.5564 33.61600000 7.67300000 8.85700000
- 27 9 2 0.5564 35.11500000 5.25999999 7.61800001
- 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999
- 29 10 2 0.5564 31.62400000 6.90800001 23.52100001
- 30 10 2 0.5564 32.54400000 4.99000000 24.98200000
- 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000
- 32 11 2 0.5564 1.85600000 10.17500000 25.57899999
- 33 11 2 0.5564 0.51900000 8.09899999 26.38599999
- 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999
- 35 12 2 0.5564 2.16699999 8.72700000 30.49400000
- 36 12 2 0.5564 2.37400001 10.51300000 33.03799999
- 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000
- 38 13 2 0.5564 4.12700001 15.87200001 4.44600001
- 39 13 2 0.5564 2.90500001 18.33899999 3.15999999
- 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000
- 41 14 2 0.5564 5.21100000 16.75600000 8.29900001
- 42 14 2 0.5564 2.56000000 15.49200001 8.86000000
- 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000
- 44 15 2 0.5564 2.86900001 8.02300001 18.05000000
- 45 15 2 0.5564 3.96000000 8.46700001 15.15400000
- 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000
- 47 16 2 0.5564 4.65300000 4.63800000 21.48000000
- 48 16 2 0.5564 6.40500000 6.20800000 22.52899999
- 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999
- 50 17 2 0.5564 2.83200000 14.80400001 23.42200000
- 51 17 2 0.5564 1.43400000 13.50900000 21.19599999
- 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001
- 53 18 2 0.5564 3.65500000 17.20000000 26.76599999
- 54 18 2 0.5564 4.77200001 18.97699999 24.49999999
- 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001
- 56 19 2 0.5564 35.20999999 21.26700001 2.81599999
- 57 19 2 0.5564 35.96200001 21.72599999 0.13099999
- 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000
- 59 20 2 0.5564 2.79500000 22.34599999 14.87600001
- 60 20 2 0.5564 2.41399999 24.11500000 17.13000001
- 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000
- 62 21 2 0.5564 34.63999999 24.80400001 15.01299999
- 63 21 2 0.5564 32.40100000 25.76400000 14.29500001
- 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999
- 65 22 2 0.5564 1.35300001 27.24800000 24.98700001
- 66 22 2 0.5564 1.54600001 28.05000000 22.31700001
- 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999
- 68 23 2 0.5564 35.66899999 20.15100000 25.31700001
- 69 23 2 0.5564 32.96000000 21.18000000 23.99200000
- 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000
- 71 24 2 0.5564 33.31399999 18.78200000 33.88300001
- 72 24 2 0.5564 32.74300001 18.18100001 30.87100000
- 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000
- 74 25 2 0.5564 5.85600000 23.08400001 3.39999999
- 75 25 2 0.5564 3.98600000 22.18000000 5.60200000
- 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000
- 77 26 2 0.5564 5.76700000 27.69300001 8.47600000
- 78 26 2 0.5564 7.20200001 25.50600000 10.18600000
- 79 27 1 -1.1128 0.60099999 29.73699999 12.74700001
- 80 27 2 0.5564 -0.68500000 30.84200000 12.34999999
- 81 27 2 0.5564 1.33600000 30.71600000 14.03099999
- 82 28 1 -1.1128 7.56300000 28.19100001 24.33300000
- 83 28 2 0.5564 9.20100000 28.82800000 24.68400000
- 84 28 2 0.5564 7.38100001 27.62100000 22.79900000
- 85 29 1 -1.1128 3.65300000 27.10900001 27.77200001
- 86 29 2 0.5564 5.12600000 27.01500000 26.77200001
- 87 29 2 0.5564 3.03099999 28.75600000 27.69800000
- 88 30 1 -1.1128 2.59600001 23.99100001 32.47600000
- 89 30 2 0.5564 2.87900000 24.79099999 30.85899999
- 90 30 2 0.5564 4.00300000 22.91299999 32.70099999
- 91 31 1 -1.1128 3.08300000 31.31700001 3.64399999
- 92 31 2 0.5564 4.13300000 30.58900001 2.53900001
- 93 31 2 0.5564 4.21800000 32.17300001 5.03700001
- 94 32 1 -1.1128 4.66100001 30.55500000 9.36799999
- 95 32 2 0.5564 3.18400001 29.84300000 10.13200000
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diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/in.lmp b/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/in.lmp
deleted file mode 100644
index 6c9a8f819..000000000
--- a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/in.lmp
+++ /dev/null
@@ -1,33 +0,0 @@
-units electron
-atom_style full
-
-#pair_style lj/cut/coul/long 17.01
-pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007
-#bond_style harmonic
-bond_style class2
-angle_style harmonic
-#kspace_style pppm 0.0001
-kspace_style pppm/tip4p 0.0001
-
-read_data data.lmp
-pair_coeff * * 0 0
-pair_coeff 1 1 0.000295147 5.96946
-
-neighbor 2.0 bin
-
-timestep 0.00025
-
-#velocity all create 298.0 2345187
-
-#thermo_style multi
-#thermo 1
-
-#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1
-#fix 1 all nve
-fix 1 all ipi h2o-pimd.4-cay 32345 unix
-
-
-#dump 1 all xyz 25 dump.xyz
-
-run 100000000
-
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/run.sh b/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/run.sh
deleted file mode 100644
index 802f8e4b6..000000000
--- a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/run.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-ipi=i-pi
-lmp=lmp_mpi
-sleep_time=10
-
-${ipi} input.xml > log.i-pi &
-echo "# i-PI is running"
-
-echo "# Waiting for ${sleep_time} (s) before executing LAMMPS"
-sleep ${sleep_time}
-
-${lmp} < in.lmp > /dev/null &
-echo "# LAMMPS is running"
-
-wait
-
-echo "# Simulation complete"
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/water_216.xyz b/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/water_216.xyz
deleted file mode 120000
index 95291df24..000000000
--- a/examples/features/path_integral_molecular_dynamics/cayley_pimd/lammps_h2o_bulk_liquid/water_216.xyz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../init_files/water_216.xyz
\ No newline at end of file
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/run.sh b/examples/features/path_integral_molecular_dynamics/cayley_pimd/run.sh
new file mode 100644
index 000000000..36b87f390
--- /dev/null
+++ b/examples/features/path_integral_molecular_dynamics/cayley_pimd/run.sh
@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m qtip4pf -u -a h2o-cayley"
+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"
diff --git a/examples/features/path_integral_molecular_dynamics/cayley_pimd/water_216.xyz b/examples/features/path_integral_molecular_dynamics/cayley_pimd/water_216.xyz
new file mode 120000
index 000000000..58a9ede12
--- /dev/null
+++ b/examples/features/path_integral_molecular_dynamics/cayley_pimd/water_216.xyz
@@ -0,0 +1 @@
+../../../init_files/water_216.xyz
\ No newline at end of file
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/input.xml b/examples/features/path_integral_molecular_dynamics/piglet/input.xml
similarity index 99%
rename from examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/input.xml
rename to examples/features/path_integral_molecular_dynamics/piglet/input.xml
index 5a8f40482..8065346ea 100644
--- a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/input.xml
+++ b/examples/features/path_integral_molecular_dynamics/piglet/input.xml
@@ -7,8 +7,8 @@
32343
-
- h2o-piglet.4
+
+ h2o-piglet
@@ -16,7 +16,7 @@
298
-
+
298
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/data.lmp b/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/data.lmp
deleted file mode 100644
index 13c75e993..000000000
--- a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/data.lmp
+++ /dev/null
@@ -1,1331 +0,0 @@
-LAMMPS Description
-
- 648 atoms
- 432 bonds
- 216 angles
-
- 2 atom types
- 1 bond types
- 1 angle types
-
- 0 35.233 xlo xhi
- 0 35.233 ylo yhi
- 0 35.233 zlo zhi
-
-Masses
-
- 1 15.9994
- 2 1.0080
-
-Bond Coeffs
-
- 1 1.78 0.2708585 -0.327738785 0.231328959
-
-Angle Coeffs
-
- 1 0.0700 107.400000
-
-Atoms
-
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diff --git a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/in.lmp b/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/in.lmp
deleted file mode 100644
index 0f7ec33ef..000000000
--- a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/in.lmp
+++ /dev/null
@@ -1,32 +0,0 @@
-units electron
-atom_style full
-
-#pair_style lj/cut/coul/long 17.01
-pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007
-#bond_style harmonic
-bond_style class2
-angle_style harmonic
-#kspace_style pppm 0.0001
-kspace_style pppm/tip4p 0.0001
-
-read_data data.lmp
-pair_coeff * * 0 0
-pair_coeff 1 1 0.000295147 5.96946
-
-neighbor 2.0 bin
-
-timestep 0.00025
-
-#velocity all create 298.0 2345187
-
-#thermo_style multi
-#thermo 1
-
-#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1
-#fix 1 all nve
-fix 1 all ipi h2o-piglet.4 32344 unix
-
-#dump 1 all xyz 25 dump.xyz
-
-run 100000000
-
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/run.sh b/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/run.sh
deleted file mode 100644
index 802f8e4b6..000000000
--- a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/run.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-ipi=i-pi
-lmp=lmp_mpi
-sleep_time=10
-
-${ipi} input.xml > log.i-pi &
-echo "# i-PI is running"
-
-echo "# Waiting for ${sleep_time} (s) before executing LAMMPS"
-sleep ${sleep_time}
-
-${lmp} < in.lmp > /dev/null &
-echo "# LAMMPS is running"
-
-wait
-
-echo "# Simulation complete"
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/water_216.xyz b/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/water_216.xyz
deleted file mode 120000
index 95291df24..000000000
--- a/examples/features/path_integral_molecular_dynamics/piglet/lammps_h2o_bulk_liquid/water_216.xyz
+++ /dev/null
@@ -1 +0,0 @@
-../../../../init_files/water_216.xyz
\ No newline at end of file
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/run.sh b/examples/features/path_integral_molecular_dynamics/piglet/run.sh
new file mode 100644
index 000000000..4ae2a39c5
--- /dev/null
+++ b/examples/features/path_integral_molecular_dynamics/piglet/run.sh
@@ -0,0 +1,16 @@
+ipi=i-pi
+driver="i-pi-driver -m qtip4pf -u -a h2o-piglet"
+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"
diff --git a/examples/features/path_integral_molecular_dynamics/piglet/water_216.xyz b/examples/features/path_integral_molecular_dynamics/piglet/water_216.xyz
new file mode 120000
index 000000000..58a9ede12
--- /dev/null
+++ b/examples/features/path_integral_molecular_dynamics/piglet/water_216.xyz
@@ -0,0 +1 @@
+../../../init_files/water_216.xyz
\ No newline at end of file
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similarity index 100%
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diff --git a/examples/features/Path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/in.lmp b/examples/features/path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/in.lmp
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diff --git a/examples/features/Geometry_optimization/SD/lammps_h2o_molecule/run.sh b/examples/features/path_integral_quantum_dynamics/TRPMD/lammps_h2o_liquid_water/run.sh
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diff --git a/ipi_tests/examples/excluded_test.txt b/ipi_tests/examples/excluded_test.txt
index c9f628c51..ae001c944 100644
--- a/ipi_tests/examples/excluded_test.txt
+++ b/ipi_tests/examples/excluded_test.txt
@@ -17,6 +17,6 @@ clients/yaff/mil53_ffsocket
clients/ffsgdml/benzene-pimd.10
clients/ffsgdml/benzene-scpimd.10
-features/Metadynamics/zundel-remd-metad
-features/Metadynamics/zundel-metad
-features/Metadynamics/zundel-wte
+features/metadynamics/pimd_metadynamics
+features/metadynamics/wte_metadynamics
+features/metadynamics/remd_metadynamics