Update all example scripts with long options

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"

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

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

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
 

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
 

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

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

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

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
 

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
 

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
 

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
 

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
 

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
 

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"

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
 

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
 

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
 

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
 

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 ]