From 7d87ceb80ff708eef28d7e77ed2f8c23ffa1f601 Mon Sep 17 00:00:00 2001
From: "Peter W. Draper" <p.w.draper@durham.ac.uk>
Date: Fri, 30 Nov 2018 15:22:11 +0000
Subject: [PATCH] Update all example scripts with long options

---
 examples/AgoraDisk/run.sh                     | 2 +-
 examples/ConstantCosmoVolume/run.sh           | 2 +-
 examples/CoolingBox/run.sh                    | 2 +-
 examples/CoolingHalo/run.sh                   | 2 +-
 examples/CoolingHaloWithSpin/run.sh           | 2 +-
 examples/DiscPatch/GravityOnly/run.sh         | 2 +-
 examples/DiscPatch/HydroStatic/run.sh         | 2 +-
 examples/DiscPatch/HydroStatic_1D/run.sh      | 2 +-
 examples/DwarfGalaxy/run.sh                   | 2 +-
 examples/EAGLE_100/run.sh                     | 2 +-
 examples/EAGLE_12/run.sh                      | 2 +-
 examples/EAGLE_25/run.sh                      | 2 +-
 examples/EAGLE_50/run.sh                      | 2 +-
 examples/EAGLE_6/run.sh                       | 2 +-
 examples/EAGLE_6/testVELOCIraptor.sh          | 8 ++++----
 examples/EAGLE_DMO_100/run.sh                 | 2 +-
 examples/EAGLE_DMO_12/run.sh                  | 2 +-
 examples/EAGLE_DMO_25/run.sh                  | 2 +-
 examples/EAGLE_DMO_50/run.sh                  | 2 +-
 examples/EvrardCollapse_3D/run.sh             | 2 +-
 examples/ExternalPointMass/run.sh             | 2 +-
 examples/Gradients/run.sh                     | 6 +++---
 examples/GreshoVortex_2D/run.sh               | 2 +-
 examples/GreshoVortex_3D/run.sh               | 2 +-
 examples/Hernquist_circularorbit/run.sh       | 2 +-
 examples/Hernquist_radialinfall/run.sh        | 2 +-
 examples/HydrostaticHalo/run.sh               | 2 +-
 examples/InteractingBlastWaves_1D/run.sh      | 2 +-
 examples/IsolatedGalaxy_dmparticles/run.sh    | 2 +-
 examples/IsolatedGalaxy_potential/run.sh      | 2 +-
 examples/IsothermalPotential/run.sh           | 2 +-
 examples/KelvinHelmholtzGrowthRate_2D/run.sh  | 2 +-
 examples/KelvinHelmholtzGrowthRate_3D/run.sh  | 2 +-
 examples/KelvinHelmholtz_2D/run.sh            | 2 +-
 examples/KeplerianRing/README.md              | 2 +-
 examples/KeplerianRing/run.sh                 | 2 +-
 examples/MultiTypes/run.sh                    | 2 +-
 examples/NFW_Halo/run.sh                      | 2 +-
 examples/Noh_1D/run.sh                        | 2 +-
 examples/Noh_2D/run.sh                        | 2 +-
 examples/Noh_3D/run.sh                        | 2 +-
 examples/PerturbedBox_3D/run.sh               | 2 +-
 examples/SantaBarbara/run.sh                  | 2 +-
 examples/SantaBarbara_low/run.sh              | 2 +-
 examples/SedovBlast_1D/run.sh                 | 2 +-
 examples/SedovBlast_2D/run.sh                 | 2 +-
 examples/SedovBlast_3D/run.sh                 | 2 +-
 examples/SineWavePotential_1D/run.sh          | 2 +-
 examples/SineWavePotential_2D/run.sh          | 2 +-
 examples/SineWavePotential_3D/run.sh          | 2 +-
 examples/SmallCosmoVolume/run.sh              | 2 +-
 examples/SmallCosmoVolume_DM/run.sh           | 2 +-
 examples/SmallCosmoVolume_VELOCIraptor/run.sh | 2 +-
 examples/SmallCosmoVolume_cooling/run.sh      | 2 +-
 examples/SmoothedMetallicity/run.sh           | 2 +-
 examples/SodShockSpherical_2D/run.sh          | 2 +-
 examples/SodShockSpherical_3D/run.sh          | 2 +-
 examples/SodShock_1D/run.sh                   | 2 +-
 examples/SodShock_2D/run.sh                   | 2 +-
 examples/SodShock_3D/run.sh                   | 2 +-
 examples/SquareTest_2D/run.sh                 | 2 +-
 examples/SupernovaeFeedback/run.sh            | 2 +-
 examples/UniformBox_2D/run.sh                 | 2 +-
 examples/UniformBox_3D/run.sh                 | 2 +-
 examples/VacuumSpherical_2D/run.sh            | 2 +-
 examples/VacuumSpherical_3D/run.sh            | 2 +-
 examples/Vacuum_1D/run.sh                     | 2 +-
 examples/Vacuum_2D/run.sh                     | 2 +-
 examples/Vacuum_3D/run.sh                     | 2 +-
 examples/ZeldovichPancake_3D/run.sh           | 2 +-
 examples/ZoomIn/run.sh                        | 2 +-
 examples/main.c                               | 4 ++--
 72 files changed, 78 insertions(+), 78 deletions(-)

diff --git a/examples/AgoraDisk/run.sh b/examples/AgoraDisk/run.sh
index d7e284db52..6bf9a98342 100755
--- a/examples/AgoraDisk/run.sh
+++ b/examples/AgoraDisk/run.sh
@@ -38,7 +38,7 @@ cp $sim.hdf5 agora_disk.hdf5
 python3 changeType.py agora_disk.hdf5
 
 # Run SWIFT
-#../swift $flag -s -G -t 4 agora_disk.yml 2>&1 | tee output.log
+#../swift $flag --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
 
 
 echo "Changing smoothing length to be Gadget compatible"
diff --git a/examples/ConstantCosmoVolume/run.sh b/examples/ConstantCosmoVolume/run.sh
index a2d9cdc63f..c7180b5232 100755
--- a/examples/ConstantCosmoVolume/run.sh
+++ b/examples/ConstantCosmoVolume/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -c -G -t 8 constant_volume.yml 2>&1 | tee output.log
+../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py $i
diff --git a/examples/CoolingBox/run.sh b/examples/CoolingBox/run.sh
index 30b2177a6e..685836375b 100755
--- a/examples/CoolingBox/run.sh
+++ b/examples/CoolingBox/run.sh
@@ -21,7 +21,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -C -t 1 coolingBox.yml
+../swift --hydro --cooling --threads=1 coolingBox.yml
 
 # Check energy conservation and cooling rate
 python energy_plot.py
diff --git a/examples/CoolingHalo/run.sh b/examples/CoolingHalo/run.sh
index 60ceae649d..c7c00fe81c 100755
--- a/examples/CoolingHalo/run.sh
+++ b/examples/CoolingHalo/run.sh
@@ -4,7 +4,7 @@
 echo "Generating initial conditions for the isothermal potential box example..."
 python makeIC.py 10000 
 
-../swift -g -s -C -t 16 cooling_halo.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
 
 python radial_profile.py 2. 200 100
 
diff --git a/examples/CoolingHaloWithSpin/run.sh b/examples/CoolingHaloWithSpin/run.sh
index 131fbf3cb1..90d0cc84e7 100755
--- a/examples/CoolingHaloWithSpin/run.sh
+++ b/examples/CoolingHaloWithSpin/run.sh
@@ -5,7 +5,7 @@ echo "Generating initial conditions for the isothermal potential box example..."
 python makeIC.py 10000 
 
 # Run SWIFT with external potential, SPH and cooling
-../swift -g -s -C -t 1 cooling_halo.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
 
 # python radial_profile.py 10
 
diff --git a/examples/DiscPatch/GravityOnly/run.sh b/examples/DiscPatch/GravityOnly/run.sh
index 9af1011ee6..999ffa120f 100755
--- a/examples/DiscPatch/GravityOnly/run.sh
+++ b/examples/DiscPatch/GravityOnly/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 1000
 fi
 
-../../swift -g -t 2 disc-patch.yml
+../../swift --external-gravity --threads=2 disc-patch.yml
diff --git a/examples/DiscPatch/HydroStatic/run.sh b/examples/DiscPatch/HydroStatic/run.sh
index e1f47ecad5..2dccc93f04 100755
--- a/examples/DiscPatch/HydroStatic/run.sh
+++ b/examples/DiscPatch/HydroStatic/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
 python plotSolution.py
diff --git a/examples/DiscPatch/HydroStatic_1D/run.sh b/examples/DiscPatch/HydroStatic_1D/run.sh
index e9d073a6cc..3e22727ada 100755
--- a/examples/DiscPatch/HydroStatic_1D/run.sh
+++ b/examples/DiscPatch/HydroStatic_1D/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 # Run SWIFT
-../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
 python plotSolution.py
diff --git a/examples/DwarfGalaxy/run.sh b/examples/DwarfGalaxy/run.sh
index ced1959de3..17c0ac0c7e 100755
--- a/examples/DwarfGalaxy/run.sh
+++ b/examples/DwarfGalaxy/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -b -G -s -S -t 8 $@ dwarf_galaxy.yml 2>&1 | tee output.log
+../swift --feedback --self-gravity --hydro --stars --threads=8 $@ dwarf_galaxy.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_100/run.sh b/examples/EAGLE_100/run.sh
index 9c990a902a..12b6ff2a6e 100755
--- a/examples/EAGLE_100/run.sh
+++ b/examples/EAGLE_100/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -s -G -S -t 16 eagle_100.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_100.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_12/run.sh b/examples/EAGLE_12/run.sh
index 67f1c24a1e..90128c4f6c 100755
--- a/examples/EAGLE_12/run.sh
+++ b/examples/EAGLE_12/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -s -G -S -t 16 eagle_12.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_12.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_25/run.sh b/examples/EAGLE_25/run.sh
index 0b6cf77d7b..af1218f707 100755
--- a/examples/EAGLE_25/run.sh
+++ b/examples/EAGLE_25/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -s -G -S -t 16 eagle_25.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --stars--threads=16 eagle_25.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_50/run.sh b/examples/EAGLE_50/run.sh
index a0d5dee11d..a08e3125b1 100755
--- a/examples/EAGLE_50/run.sh
+++ b/examples/EAGLE_50/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -s -G -S -t 16 eagle_50.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_50.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_6/run.sh b/examples/EAGLE_6/run.sh
index 7ef3fc2abd..6df5902a05 100755
--- a/examples/EAGLE_6/run.sh
+++ b/examples/EAGLE_6/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -s -G -S -t 16 eagle_6.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_6.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_6/testVELOCIraptor.sh b/examples/EAGLE_6/testVELOCIraptor.sh
index 14ec304870..3f0ae1d6f0 100755
--- a/examples/EAGLE_6/testVELOCIraptor.sh
+++ b/examples/EAGLE_6/testVELOCIraptor.sh
@@ -36,8 +36,8 @@ if [ "$RUN_DM" = "1" ]; then
     rm $VEL_OUTPUT/vel_$TEST*
 
     # Run test using SWIFT + VELOCIraptor
-    echo "Running: mpirun -np $NUM_MPI_PROC ../swift_mpi -G -t 8 eagle_6.yml -x -n 5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_dmonly"
-    mpirun -np $NUM_MPI_PROC ../swift_mpi -G -t 8 eagle_6.yml -x -n 5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_dmonly
+    echo "Running: mpirun -np $NUM_MPI_PROC ../swift_mpi --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_dmonly"
+    mpirun -np $NUM_MPI_PROC ../swift_mpi --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_dmonly
 
     # Run test using VELOCIraptor
     echo "Running: mpirun -np $NUM_MPI_PROC $VELOCIRAPTOR_PATH/bin/stf-gas -I 2 -i eagle_dmonly_0000 -C $VELOCIRAPTOR_PATH/stf_input_$TEST.cfg -o ./$VEL_OUTPUT/vel_$TEST"
@@ -80,8 +80,8 @@ if [ "$RUN_GAS" = "1" ]; then
     rm $VEL_OUTPUT/vel_$TEST*
 
     # Run test using SWIFT + VELOCIraptor
-    echo "Running: mpirun -np $NUM_MPI_PROC ../swift_mpi -s -G -t 8 eagle_6.yml -x -n 5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_gas"
-    mpirun -np $NUM_MPI_PROC ../swift_mpi -s -G -t 8 eagle_6.yml -x -n 5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_gas
+    echo "Running: mpirun -np $NUM_MPI_PROC ../swift_mpi --hydro --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_gas"
+    mpirun -np $NUM_MPI_PROC ../swift_mpi --hydro --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$OUTPUT/stf -P StructureFinding:config_file_name:./stf_input_$TEST.cfg -P Snapshots:basename:./eagle_gas
 
     # Run test using VELOCIraptor
     echo "Running: mpirun -np $NUM_MPI_PROC $VELOCIRAPTOR_PATH/bin/stf-gas -I 2 -i eagle_gas_0000 -C ./stf_input_$TEST.cfg -o ./$VEL_OUTPUT/vel_$TEST"
diff --git a/examples/EAGLE_DMO_100/run.sh b/examples/EAGLE_DMO_100/run.sh
index 642c9247cf..6a3b3a00d6 100755
--- a/examples/EAGLE_DMO_100/run.sh
+++ b/examples/EAGLE_DMO_100/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -G -t 16 eagle_100.yml 2>&1 | tee output.log
+../swift --cosmology --self-gravity --threads=16 eagle_100.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_12/run.sh b/examples/EAGLE_DMO_12/run.sh
index ebf24ee6a5..f5e7e72947 100755
--- a/examples/EAGLE_DMO_12/run.sh
+++ b/examples/EAGLE_DMO_12/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -G -t 16 eagle_12.yml 2>&1 | tee output.log
+../swift --cosmology --self-gravity --threads=16 eagle_12.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_25/run.sh b/examples/EAGLE_DMO_25/run.sh
index ae0a6d3c49..6387472050 100755
--- a/examples/EAGLE_DMO_25/run.sh
+++ b/examples/EAGLE_DMO_25/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -G -t 16 eagle_25.yml 2>&1 | tee output.log
+../swift --cosmology --self-gravity --threads=16 eagle_25.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_50/run.sh b/examples/EAGLE_DMO_50/run.sh
index 31980a5a88..486f7f33f7 100755
--- a/examples/EAGLE_DMO_50/run.sh
+++ b/examples/EAGLE_DMO_50/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -c -G -t 16 eagle_50.yml 2>&1 | tee output.log
+../swift --cosmology --self-gravity --threads=16 eagle_50.yml 2>&1 | tee output.log
 
diff --git a/examples/EvrardCollapse_3D/run.sh b/examples/EvrardCollapse_3D/run.sh
index abb7614f66..d9005a7214 100755
--- a/examples/EvrardCollapse_3D/run.sh
+++ b/examples/EvrardCollapse_3D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -G -t 4 evrard.yml 2>&1 | tee output.log
+../swift --hydro --self-gravity --threads=4 evrard.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference result if not present.
 if [ ! -e evrardCollapse3D_exact.txt ]
diff --git a/examples/ExternalPointMass/run.sh b/examples/ExternalPointMass/run.sh
index e074c384c4..fa3a40e20c 100755
--- a/examples/ExternalPointMass/run.sh
+++ b/examples/ExternalPointMass/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 rm -rf pointMass_*.hdf5
-../swift -g -t 1 externalPointMass.yml 2>&1 | tee output.log
+../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
 
 python energy_plot.py
diff --git a/examples/Gradients/run.sh b/examples/Gradients/run.sh
index 44c25ac569..4a0a80a3ae 100755
--- a/examples/Gradients/run.sh
+++ b/examples/Gradients/run.sh
@@ -1,13 +1,13 @@
 #! /bin/bash
 
 python makeICs.py stretched
-../swift -s -t 2 gradientsStretched.yml
+../swift --hydro --threads=2 gradientsStretched.yml
 python plot.py gradients_stretched_0001.hdf5 stretched
 
 python makeICs.py cartesian
-../swift -s -t 2 gradientsCartesian.yml
+../swift --hydro --threads=2 gradientsCartesian.yml
 python plot.py gradients_cartesian_0001.hdf5 cartesian
 
 python makeICs.py random
-../swift -s -t 2 gradientsRandom.yml
+../swift --hydro --threads=2 gradientsRandom.yml
 python plot.py gradients_random_0001.hdf5 random
diff --git a/examples/GreshoVortex_2D/run.sh b/examples/GreshoVortex_2D/run.sh
index 6d537bcc96..855d528bdf 100755
--- a/examples/GreshoVortex_2D/run.sh
+++ b/examples/GreshoVortex_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 gresho.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 gresho.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 11
diff --git a/examples/GreshoVortex_3D/run.sh b/examples/GreshoVortex_3D/run.sh
index da7d6cee11..1967a77ba7 100755
--- a/examples/GreshoVortex_3D/run.sh
+++ b/examples/GreshoVortex_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 gresho.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 11
diff --git a/examples/Hernquist_circularorbit/run.sh b/examples/Hernquist_circularorbit/run.sh
index a2fedd0914..fe2eb0bd07 100755
--- a/examples/Hernquist_circularorbit/run.sh
+++ b/examples/Hernquist_circularorbit/run.sh
@@ -12,7 +12,7 @@ then
 fi
 
 # self gravity G, external potential g, hydro s, threads t and high verbosity v
-../swift -g -t 6 hernquistcirc.yml 2>&1 | tee output.log
+../swift --external-gravity --threads=6 hernquistcirc.yml 2>&1 | tee output.log
 
 
 echo "Save plots of the circular orbits"
diff --git a/examples/Hernquist_radialinfall/run.sh b/examples/Hernquist_radialinfall/run.sh
index b2bcd99f9e..0ad64e2dd2 100755
--- a/examples/Hernquist_radialinfall/run.sh
+++ b/examples/Hernquist_radialinfall/run.sh
@@ -12,7 +12,7 @@ then
 fi
 
 rm -rf hernquist_*.hdf5
-../swift -g -t 1 hernquist.yml 2>&1 | tee output.log
+../swift --external-gravity --threads=1 hernquist.yml 2>&1 | tee output.log
 
 
 
diff --git a/examples/HydrostaticHalo/run.sh b/examples/HydrostaticHalo/run.sh
index 8258428255..cb67be62aa 100755
--- a/examples/HydrostaticHalo/run.sh
+++ b/examples/HydrostaticHalo/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run for 10 dynamical times
-../swift -g -s -t 1 hydrostatic.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --threads=1 hydrostatic.yml 2>&1 | tee output.log
 
 echo "Plotting density profiles"
 mkdir plots
diff --git a/examples/InteractingBlastWaves_1D/run.sh b/examples/InteractingBlastWaves_1D/run.sh
index 31717bd806..cb8519e7f9 100755
--- a/examples/InteractingBlastWaves_1D/run.sh
+++ b/examples/InteractingBlastWaves_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 interactingBlastWaves.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 interactingBlastWaves.yml 2>&1 | tee output.log
 
 # Get the high resolution reference solution if not present.
 if [ ! -e interactingBlastWaves1D_exact.txt ]
diff --git a/examples/IsolatedGalaxy_dmparticles/run.sh b/examples/IsolatedGalaxy_dmparticles/run.sh
index 10fb9d3b0e..5a4d5b6ce4 100755
--- a/examples/IsolatedGalaxy_dmparticles/run.sh
+++ b/examples/IsolatedGalaxy_dmparticles/run.sh
@@ -6,7 +6,7 @@ then
     ./getIC.sh
 fi 
 
-../swift -g -G -S -t 16 isolated_galaxy.yml 2>&1 | tee output.log
+../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
 
 
 echo "Make plots of conservation of total angular momentum" 
diff --git a/examples/IsolatedGalaxy_potential/run.sh b/examples/IsolatedGalaxy_potential/run.sh
index 18a9da50df..e93b43b55b 100755
--- a/examples/IsolatedGalaxy_potential/run.sh
+++ b/examples/IsolatedGalaxy_potential/run.sh
@@ -6,7 +6,7 @@ then
     ./getIC.sh
 fi 
 
-../swift -g -G -S -t 16 isolated_galaxy.yml 2>&1 | tee output.log
+../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
 
 
 echo "Make plots of conservation of total angular momentum" 
diff --git a/examples/IsothermalPotential/run.sh b/examples/IsothermalPotential/run.sh
index a5f03f32f8..bc44b2bd1f 100755
--- a/examples/IsothermalPotential/run.sh
+++ b/examples/IsothermalPotential/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 rm -rf Isothermal_*.hdf5
-../swift -g -t 1 isothermal.yml 2>&1 | tee output.log
+../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
 
 python energy_plot.py
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/run.sh b/examples/KelvinHelmholtzGrowthRate_2D/run.sh
index 3e6e026f66..505d644984 100755
--- a/examples/KelvinHelmholtzGrowthRate_2D/run.sh
+++ b/examples/KelvinHelmholtzGrowthRate_2D/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 100
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/run.sh b/examples/KelvinHelmholtzGrowthRate_3D/run.sh
index 3e6e026f66..505d644984 100755
--- a/examples/KelvinHelmholtzGrowthRate_3D/run.sh
+++ b/examples/KelvinHelmholtzGrowthRate_3D/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 100
diff --git a/examples/KelvinHelmholtz_2D/run.sh b/examples/KelvinHelmholtz_2D/run.sh
index dbb39caf38..ef823cb85b 100755
--- a/examples/KelvinHelmholtz_2D/run.sh
+++ b/examples/KelvinHelmholtz_2D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 kelvinHelmholtz.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 6
diff --git a/examples/KeplerianRing/README.md b/examples/KeplerianRing/README.md
index 1c361f275d..1cb2e2119d 100644
--- a/examples/KeplerianRing/README.md
+++ b/examples/KeplerianRing/README.md
@@ -69,7 +69,7 @@ Plotting
 
 Once you have ran swift (we suggest that you use the following)
 
-    ../swift -g -S -s -t 16 keplerian_ring.yml 2>&1 | tee output.log
+    ../swift --external-gravity --stars --hydro --threads=16 keplerian_ring.yml 2>&1 | tee output.log
 
 there will be around 350 ```.hdf5``` files in your directory. To check out
 the results of the example use the plotting script:
diff --git a/examples/KeplerianRing/run.sh b/examples/KeplerianRing/run.sh
index 0195846a88..236f512d1c 100755
--- a/examples/KeplerianRing/run.sh
+++ b/examples/KeplerianRing/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 rm -rf keplerian_ring_*.hdf5
-../swift -g -s -t 1 -v 1 keplerian_ring.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --threads=1 --verbose=1 keplerian_ring.yml 2>&1 | tee output.log
 
 echo
 echo
diff --git a/examples/MultiTypes/run.sh b/examples/MultiTypes/run.sh
index 38cba70393..b0a3953e32 100755
--- a/examples/MultiTypes/run.sh
+++ b/examples/MultiTypes/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 9 13 7 1
 fi
 
-../swift -s -g -S -t 1 multiTypes.yml 2>&1 | tee output.log
+../swift --hydro --external-gravity --stars --threads=1 multiTypes.yml 2>&1 | tee output.log
diff --git a/examples/NFW_Halo/run.sh b/examples/NFW_Halo/run.sh
index 5501f09ef4..3a21c96784 100755
--- a/examples/NFW_Halo/run.sh
+++ b/examples/NFW_Halo/run.sh
@@ -11,7 +11,7 @@ then
 fi
 
 # self gravity G, external potential g, hydro s, threads t and high verbosity v
-../swift -g -t 6 test.yml 2>&1 | tee output.log
+../swift --external-gravity --threads=6 test.yml 2>&1 | tee output.log
 
 if command -v python3 &>/dev/null; then
     python3 makePlots.py
diff --git a/examples/Noh_1D/run.sh b/examples/Noh_1D/run.sh
index 77788bfa84..15efd56e7b 100755
--- a/examples/Noh_1D/run.sh
+++ b/examples/Noh_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 noh.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/Noh_2D/run.sh b/examples/Noh_2D/run.sh
index cff2008010..5595ad8439 100755
--- a/examples/Noh_2D/run.sh
+++ b/examples/Noh_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 2 noh.yml 2>&1 | tee output.log
+../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/Noh_3D/run.sh b/examples/Noh_3D/run.sh
index b9e4fb145b..7ff7b084f4 100755
--- a/examples/Noh_3D/run.sh
+++ b/examples/Noh_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 2 noh.yml 2>&1 | tee output.log
+../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/PerturbedBox_3D/run.sh b/examples/PerturbedBox_3D/run.sh
index e20bff52d1..ab771ea1f0 100755
--- a/examples/PerturbedBox_3D/run.sh
+++ b/examples/PerturbedBox_3D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 50
 fi
 
-../swift -s -t 16 perturbedBox.yml 2>&1 | tee output.log
+../swift --hydro --threads=16 perturbedBox.yml 2>&1 | tee output.log
diff --git a/examples/SantaBarbara/run.sh b/examples/SantaBarbara/run.sh
index 044f9f4ef3..206ba7bad0 100755
--- a/examples/SantaBarbara/run.sh
+++ b/examples/SantaBarbara/run.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Run SWIFT
-../swift -c -s -G -t 28 santa_barbara.yml
+../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
 
diff --git a/examples/SantaBarbara_low/run.sh b/examples/SantaBarbara_low/run.sh
index 044f9f4ef3..206ba7bad0 100755
--- a/examples/SantaBarbara_low/run.sh
+++ b/examples/SantaBarbara_low/run.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Run SWIFT
-../swift -c -s -G -t 28 santa_barbara.yml
+../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
 
diff --git a/examples/SedovBlast_1D/run.sh b/examples/SedovBlast_1D/run.sh
index 4b9a84f069..ba47921496 100755
--- a/examples/SedovBlast_1D/run.sh
+++ b/examples/SedovBlast_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 sedov.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/SedovBlast_2D/run.sh b/examples/SedovBlast_2D/run.sh
index a32c8f0d6f..b481d45552 100755
--- a/examples/SedovBlast_2D/run.sh
+++ b/examples/SedovBlast_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 sedov.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/SedovBlast_3D/run.sh b/examples/SedovBlast_3D/run.sh
index 00d5e5b91c..88aec36a7b 100755
--- a/examples/SedovBlast_3D/run.sh
+++ b/examples/SedovBlast_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 sedov.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/SineWavePotential_1D/run.sh b/examples/SineWavePotential_1D/run.sh
index 077cf1c0cc..a725a88a17 100755
--- a/examples/SineWavePotential_1D/run.sh
+++ b/examples/SineWavePotential_1D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/SineWavePotential_2D/run.sh b/examples/SineWavePotential_2D/run.sh
index 077cf1c0cc..a725a88a17 100755
--- a/examples/SineWavePotential_2D/run.sh
+++ b/examples/SineWavePotential_2D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/SineWavePotential_3D/run.sh b/examples/SineWavePotential_3D/run.sh
index 077cf1c0cc..a725a88a17 100755
--- a/examples/SineWavePotential_3D/run.sh
+++ b/examples/SineWavePotential_3D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
+../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/SmallCosmoVolume/run.sh b/examples/SmallCosmoVolume/run.sh
index e243215813..12c98d1b63 100755
--- a/examples/SmallCosmoVolume/run.sh
+++ b/examples/SmallCosmoVolume/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -c -s -G -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 # Plot the temperature evolution
 python plotTempEvolution.py
diff --git a/examples/SmallCosmoVolume_DM/run.sh b/examples/SmallCosmoVolume_DM/run.sh
index 8a4cd944c7..9c002f4643 100755
--- a/examples/SmallCosmoVolume_DM/run.sh
+++ b/examples/SmallCosmoVolume_DM/run.sh
@@ -8,5 +8,5 @@ then
 fi
 
 # Run SWIFT
-../swift -c -G -t 8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
+../swift --cosmology --self-gravity --threads=8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
 
diff --git a/examples/SmallCosmoVolume_VELOCIraptor/run.sh b/examples/SmallCosmoVolume_VELOCIraptor/run.sh
index f3c82c2171..cde550f0a5 100755
--- a/examples/SmallCosmoVolume_VELOCIraptor/run.sh
+++ b/examples/SmallCosmoVolume_VELOCIraptor/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -c -s -G -x -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --velociraptor --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 echo "Make a plot of the HMF"
 if command -v python3 &>/dev/null; then
diff --git a/examples/SmallCosmoVolume_cooling/run.sh b/examples/SmallCosmoVolume_cooling/run.sh
index 454ed27950..b5d01cf232 100755
--- a/examples/SmallCosmoVolume_cooling/run.sh
+++ b/examples/SmallCosmoVolume_cooling/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -c -s -G -C -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
+../swift --cosmology --hydro --self-gravity --cooling --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 # Plot the temperature evolution
 python plotTempEvolution.py
diff --git a/examples/SmoothedMetallicity/run.sh b/examples/SmoothedMetallicity/run.sh
index de8c55d678..9f31eac369 100755
--- a/examples/SmoothedMetallicity/run.sh
+++ b/examples/SmoothedMetallicity/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -n 1 -s -t 4 smoothed_metallicity.yml 2>&1 | tee output.log
+../swift --steps=1 --hydro --threads=4 smoothed_metallicity.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 1
diff --git a/examples/SodShockSpherical_2D/run.sh b/examples/SodShockSpherical_2D/run.sh
index d662d20f40..90be0cc83c 100755
--- a/examples/SodShockSpherical_2D/run.sh
+++ b/examples/SodShockSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 sodShock.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference solution if not present.
 if [ ! -e sodShockSpherical2D_exact.txt ]
diff --git a/examples/SodShockSpherical_3D/run.sh b/examples/SodShockSpherical_3D/run.sh
index faf979869e..b28b69e0aa 100755
--- a/examples/SodShockSpherical_3D/run.sh
+++ b/examples/SodShockSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 sodShock.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference solution if not present.
 if [ ! -e sodShockSpherical3D_exact.txt ]
diff --git a/examples/SodShock_1D/run.sh b/examples/SodShock_1D/run.sh
index 4be4254baa..fb2ba77dac 100755
--- a/examples/SodShock_1D/run.sh
+++ b/examples/SodShock_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 sodShock.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1 
diff --git a/examples/SodShock_2D/run.sh b/examples/SodShock_2D/run.sh
index 9e6bbfdf1c..730cabcb9d 100755
--- a/examples/SodShock_2D/run.sh
+++ b/examples/SodShock_2D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 sodShock.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/SodShock_3D/run.sh b/examples/SodShock_3D/run.sh
index 8ed85baf73..fee82ce3e1 100755
--- a/examples/SodShock_3D/run.sh
+++ b/examples/SodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 sodShock.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/SquareTest_2D/run.sh b/examples/SquareTest_2D/run.sh
index 7d77e9c5bd..f96bd4c0e1 100755
--- a/examples/SquareTest_2D/run.sh
+++ b/examples/SquareTest_2D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 square.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 square.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/SupernovaeFeedback/run.sh b/examples/SupernovaeFeedback/run.sh
index d468bf02dc..984cee2b41 100644
--- a/examples/SupernovaeFeedback/run.sh
+++ b/examples/SupernovaeFeedback/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -g -b -s -S -t 4 SN_feedback.yml 2>&1 | tee output.log
+../swift --external-gravity --feedback --hydro --stars --threads=4 SN_feedback.yml 2>&1 | tee output.log
 
 # Plot the solution
 # TODO
diff --git a/examples/UniformBox_2D/run.sh b/examples/UniformBox_2D/run.sh
index ee3ef10996..3c146d8b48 100755
--- a/examples/UniformBox_2D/run.sh
+++ b/examples/UniformBox_2D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 100
 fi
 
-../swift -s -t 16 uniformPlane.yml 2>&1 | tee output.log
+../swift --hydro --threads=16 uniformPlane.yml 2>&1 | tee output.log
diff --git a/examples/UniformBox_3D/run.sh b/examples/UniformBox_3D/run.sh
index 08891cdd08..eb2648cc52 100755
--- a/examples/UniformBox_3D/run.sh
+++ b/examples/UniformBox_3D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 100
 fi
 
-../swift -s -t 16 uniformBox.yml 2>&1 | tee output.log
+../swift --hydro --threads=16 uniformBox.yml 2>&1 | tee output.log
diff --git a/examples/VacuumSpherical_2D/run.sh b/examples/VacuumSpherical_2D/run.sh
index 51d32b4de6..c88095abf3 100755
--- a/examples/VacuumSpherical_2D/run.sh
+++ b/examples/VacuumSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 vacuum.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
 
 # Get the 1D high resolution reference result if not present.
 if [ ! -e vacuumSpherical2D_exact.txt ]
diff --git a/examples/VacuumSpherical_3D/run.sh b/examples/VacuumSpherical_3D/run.sh
index a136929678..ef6a84be13 100755
--- a/examples/VacuumSpherical_3D/run.sh
+++ b/examples/VacuumSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 16 vacuum.yml 2>&1 | tee output.log
+../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
 
 # Get the reference solution if it is not present.
 if [ ! -e vacuumSpherical3D_exact.txt ]
diff --git a/examples/Vacuum_1D/run.sh b/examples/Vacuum_1D/run.sh
index b141f91f87..a840f7c1ba 100755
--- a/examples/Vacuum_1D/run.sh
+++ b/examples/Vacuum_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 vacuum.yml 2>&1 | tee output.log
+../swift --hydro --threads=1 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/Vacuum_2D/run.sh b/examples/Vacuum_2D/run.sh
index 5c0b2ca5e1..5a526bb506 100755
--- a/examples/Vacuum_2D/run.sh
+++ b/examples/Vacuum_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 4 vacuum.yml 2>&1 | tee output.log
+../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/Vacuum_3D/run.sh b/examples/Vacuum_3D/run.sh
index 5029626f67..eaf7a32d4f 100755
--- a/examples/Vacuum_3D/run.sh
+++ b/examples/Vacuum_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 16 vacuum.yml 2>&1 | tee output.log
+../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/ZeldovichPancake_3D/run.sh b/examples/ZeldovichPancake_3D/run.sh
index b3f802f978..4ced5ec57d 100755
--- a/examples/ZeldovichPancake_3D/run.sh
+++ b/examples/ZeldovichPancake_3D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -c -G -t 8 zeldovichPancake.yml 2>&1 | tee output.log
+../swift ---hydro --cosmology --self-gravity --threads=8 zeldovichPancake.yml 2>&1 | tee output.log
 
 # Plot the result
 for i in {0..119}
diff --git a/examples/ZoomIn/run.sh b/examples/ZoomIn/run.sh
index 99eda1cfc7..d9650dd778 100755
--- a/examples/ZoomIn/run.sh
+++ b/examples/ZoomIn/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -b -c -G -s -S -t 8 zoom_in.yml 2>&1 | tee output.log
+../swift --feedback --cosmology --self-gravity --hydro --stars --threads=8 zoom_in.yml 2>&1 | tee output.log
 
diff --git a/examples/main.c b/examples/main.c
index 4708f05a01..b897be3d79 100644
--- a/examples/main.c
+++ b/examples/main.c
@@ -193,14 +193,14 @@ int main(int argc, char *argv[]) {
                   "Run with self-gravity.", NULL, 0, 0),
       OPT_BOOLEAN('M', "multipole-reconstruction", &with_mpole_reconstruction,
                   "Reconstruct the multipoles every time-step.", NULL, 0, 0),
-      OPT_BOOLEAN('s', "hydrodynamics", &with_hydro, "Run with hydrodynamics.",
+      OPT_BOOLEAN('s', "hydro", &with_hydro, "Run with hydrodynamics.",
                   NULL, 0, 0),
       OPT_BOOLEAN('S', "stars", &with_stars, "Run with stars", NULL, 0, 0),
       OPT_BOOLEAN('x', "velociraptor", &with_structure_finding,
                   "Run with structure finding", NULL, 0, 0),
 
       OPT_GROUP("  Control options:"),
-      OPT_BOOLEAN('a', "affinity", &with_aff,
+      OPT_BOOLEAN('a', "pin", &with_aff,
                   "Pin runners using processor affinity.", NULL, 0, 0),
       OPT_BOOLEAN('d', "dry-run", &dry_run,
                   "Dry run. Read the parameter file, allocates memory but does "
-- 
GitLab