Change the python invocation command in all the run script to python3

INSTALL.swift

@@ -180,7 +180,7 @@ before you can build it.
         documentation.
 
  - python:
-	Examples and solution script use python and rely on the numpy
+	Examples and solution script use python 3 and rely on the numpy
 	library version 1.8.2 or higher.
 
 

examples/Cooling/CoolingBox/run.sh

@@ -10,7 +10,7 @@ fi
 if [ ! -e coolingBox.hdf5 ]
 then
     echo "Generating initial conditions for the cooling box example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Get the Grackle cooling table
@@ -24,4 +24,4 @@ fi
 ../../swift --hydro --cooling --threads=4 -n 1000 coolingBox.yml
 
 # Check energy conservation and cooling rate
-python plotEnergy.py
+python3 plotEnergy.py

examples/Cooling/CoolingHalo/makeIC.py

@@ -24,7 +24,7 @@
 import random
 
 # Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
-# usage: python makeIC.py 1000: generate 1000 particles
+# usage: python3 makeIC.py 1000: generate 1000 particles
 
 # Some constants
 

examples/Cooling/CoolingHalo/makeIC_random_box.py

@@ -24,7 +24,7 @@
 import random
 
 # Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
-# usage: python makeIC.py 1000: generate 1000 particles
+# usage: python3 makeIC.py 1000: generate 1000 particles
 
 # Some constants
 

examples/Cooling/CoolingHalo/run.sh

@@ -2,12 +2,12 @@
 
 # Generate the initial conditions if they are not present.
 echo "Generating initial conditions for the isothermal potential box example..."
-python makeIC.py 10000 
+python3 makeIC.py 10000 
 
 ../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
 
-python radial_profile.py 2. 200 100
+python3 radial_profile.py 2. 200 100
 
-python internal_energy_profile.py 2. 200 100
+python3 internal_energy_profile.py 2. 200 100
 
-python test_energy_conservation.py 2. 200 100
+python3 test_energy_conservation.py 2. 200 100

examples/Cooling/CoolingHaloWithSpin/makeIC.py

@@ -24,7 +24,7 @@
 import random
 
 # Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
-# usage: python makeIC.py 1000: generate 1000 particles
+# usage: python3 makeIC.py 1000: generate 1000 particles
 
 # Some constants
 

examples/Cooling/CoolingHaloWithSpin/makeIC_random_box.py

@@ -24,7 +24,7 @@
 import random
 
 # Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
-# usage: python makeIC.py 1000: generate 1000 particles
+# usage: python3 makeIC.py 1000: generate 1000 particles
 
 # Some constants
 

examples/Cooling/CoolingHaloWithSpin/run.sh

@@ -2,13 +2,13 @@
 
 # Generate the initial conditions if they are not present.
 echo "Generating initial conditions for the isothermal potential box example..."
-python makeIC.py 10000 
+python3 makeIC.py 10000 
 
 # Run SWIFT with external potential, SPH and cooling
 ../../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
 
-# python radial_profile.py 10
+# python3 radial_profile.py 10
 
-# python internal_energy_profile.py 10
+# python3 internal_energy_profile.py 10
 
-# python test_energy_conservation.py
+# python3 test_energy_conservation.py

examples/Cooling/CoolingRates/README

@@ -3,12 +3,12 @@ rate from each of the elements depending on internal energy, density
 and redshift based on the EAGLE tables. To do so, the function in
 src/cooling/EAGLE returning the cooling rate is run for multiple
 values of the internal energy. The resulting cooling rates are written
-to files and plotted with a python script (cooling_rates_plot.py).
+to files and plotted with a python3 script (cooling_rates_plot.py).
 
 The test may be run by:
 ./getCoolingTables.sh
 ./cooling_rates -z X -d Y
-python plot_cooling_rates.py
+python3 plot_cooling_rates.py
 
 where X is the redshift at which the cooling rates are evaluated and Y
 is the base 10 logarithm of the hydrogen number density expressed in

examples/Cosmology/ComovingSodShock_1D/run.sh

@@ -4,11 +4,11 @@
 if [ ! -e sodShock.hdf5 ]
 then
     echo "Generating initial conditions for the 1D SodShock example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
 ../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Plot the result
-python plotSolution.py 1
+python3 plotSolution.py 1

examples/Cosmology/ComovingSodShock_2D/run.sh

@@ -9,10 +9,10 @@ fi
 if [ ! -e sodShock.hdf5 ]
 then
     echo "Generating initial conditions for the Sod shock example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
 ../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
-python plotSolution.py 1
+python3 plotSolution.py 1

examples/Cosmology/ComovingSodShock_3D/run.sh

@@ -9,10 +9,10 @@ fi
 if [ ! -e sodShock.hdf5 ]
 then
     echo "Generating initial conditions for the Sod shock example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
 ../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
-python plotSolution.py 1
+python3 plotSolution.py 1

examples/Cosmology/ZeldovichPancake_3D/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e zeldovichPancake.hdf5 ]
 then
     echo "Generating initial conditions for the 3D Zeldovich pancake example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
@@ -13,5 +13,5 @@ fi
 # Plot the result
 for i in {0..119}
 do 
-    python plotSolution.py $i
+    python3 plotSolution.py $i
 done

examples/EAGLE_low_z/EAGLE_6/testVELOCIraptor.sh

@@ -43,13 +43,13 @@ if [ "$RUN_DM" = "1" ]; then
     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"
     mpirun -np $NUM_MPI_PROC $VELOCIRAPTOR_PATH/bin/stf-gas -I 2 -i eagle_dmonly_0000 -C ./stf_input_$TEST.cfg -o ./$VEL_OUTPUT/vel_$TEST
 
-    # Create info file for python comparison script
+    # Create info file for python3 comparison script
     echo -e $INFO_FILE_TEXT > infoFile_$TEST.txt
     echo "vel_$TEST $VEL_OUTPUT/vel_$TEST" >> infoFile_$TEST.txt
     echo "stf_$TEST $OUTPUT/stf_0000.VELOCIraptor" >> infoFile_$TEST.txt
 
     # Run comparison script on VELOCIraptor output
-    if python $SCRIPT_PATH/catalogcomparisontolerancecheck.py infoFile_$TEST.txt toIfile.txt
+    if python3 $SCRIPT_PATH/catalogcomparisontolerancecheck.py infoFile_$TEST.txt toIfile.txt
     then
       echo "Catalog comparison passed: "$TEST
     else
@@ -87,13 +87,13 @@ if [ "$RUN_GAS" = "1" ]; then
     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"
     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
 
-    # Create info file for python comparison script
+    # Create info file for python3 comparison script
     echo -e $INFO_FILE_TEXT > infoFile_$TEST.txt
     echo "vel_$TEST $VEL_OUTPUT/vel_$TEST" >> infoFile_$TEST.txt
     echo "stf_$TEST $OUTPUT/stf_0000.VELOCIraptor" >> infoFile_$TEST.txt
 
     # Run comparison script on VELOCIraptor output
-    if python $SCRIPT_PATH/catalogcomparisontolerancecheck.py infoFile_$TEST.txt toIfile.txt
+    if python3 $SCRIPT_PATH/catalogcomparisontolerancecheck.py infoFile_$TEST.txt toIfile.txt
     then
       echo "Catalog comparison passed: "$TEST
     else

examples/GEAR/AgoraCosmo/README

@@ -1,7 +1,7 @@
 Initial conditions for the AGORA simulation presented in Roca-Fabrega et al. 2021.
 The initial conditions are generated by MUSIC (and thus the path to the binary
 should be set in run.sh). The initial conditions are generated for AREPO and
-then converted into SWIFT compatible IC with a python script.
+then converted into SWIFT compatible IC with a python3 script.
 We will use SWIFT to cancel the h- and a-factors from the ICs.
 
 The IC consists in a halo evolving to a virial mass of ∼ 1e12 Msun at z = 0 with a relatively

examples/GravityTests/DiscPatch/GravityOnly/makeIC.py

@@ -38,7 +38,7 @@
 # to obtain the 1/ch^2(x/b) profile from a uniform profile (a glass, say, or a uniform random variable), note that, when integrating in x
 # \int 0^x dx/ch^2(x) = tanh(x)-tanh(0) = \int_0^u du = u (where the last integral refers to a uniform density distribution), so that x = atanh(u)
 #
-# usage: python makeIC.py 1000
+# usage: python3 makeIC.py 1000
 
 # physical constants in cgs
 NEWTON_GRAVITY_CGS = 6.67430e-8

examples/GravityTests/DiscPatch/GravityOnly/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e Disc-Patch.hdf5 ]
 then
     echo "Generating initial conditions for the disc-patch example..."
-    python makeIC.py 1000
+    python3 makeIC.py 1000
 fi
 
 # Run SWIFT

examples/GravityTests/DiscPatch/HydroStatic/run.sh

@@ -9,10 +9,10 @@ fi
 if [ ! -e Disc-Patch.hdf5 ]
 then
     echo "Generating initial conditions for the disc patch example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
 ../../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
-python plotSolution.py
+python3 plotSolution.py

examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh

@@ -4,10 +4,10 @@
 if [ ! -e Disc-Patch.hdf5 ]
 then
     echo "Generating initial conditions for the disc patch example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT
 ../../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
-python plotSolution.py
+python3 plotSolution.py

examples/GravityTests/ExternalPointMass/run.sh

@@ -4,10 +4,10 @@
 if [ ! -e PointMass.hdf5 ]
 then
     echo "Generating initial conditions for the point mass potential box example..."
-    python makeIC.py 10000
+    python3 makeIC.py 10000
 fi
 
 rm -rf pointMass_*.hdf5
 ../../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
 
-python energy_plot.py
+python3 energy_plot.py

examples/GravityTests/Hernquist_circularorbit/run.sh

@@ -6,7 +6,7 @@ then
     if command -v python3 &>/dev/null; then
         python3 makeIC.py
     else 
-        python makeIC.py
+        python3 makeIC.py
     fi
 
 fi
@@ -19,5 +19,5 @@ echo "Save plots of the circular orbits"
 if command -v python3 &>/dev/null; then
     python3 plotprog.py
 else 
-    python plotprog.py
+    python3 plotprog.py
 fi

examples/GravityTests/Hernquist_radialinfall/makeIC.py

@@ -25,8 +25,8 @@
 import numpy as np
 
 # Generates N particles in a spherical distribution centred on [0,0,0], to be moved in an isothermal potential
-# usage: python makeIC.py 1000 0 : generate 1000 particles on circular orbits
-#        python makeIC.py 1000 1 : generate 1000 particles with Lz/L uniform in [0,1]
+# usage: python3 makeIC.py 1000 0 : generate 1000 particles on circular orbits
+#        python3 makeIC.py 1000 1 : generate 1000 particles with Lz/L uniform in [0,1]
 # all particles move in the xy plane, and start at y=0
 
 # physical constants in cgs

examples/GravityTests/Hernquist_radialinfall/run.sh

@@ -7,7 +7,7 @@ then
     if command -v python3 &>/dev/null; then
         python3 makeIC.py 
     else 
-        python makeIC.py
+        python3 makeIC.py
     fi
 fi
 
@@ -20,5 +20,5 @@ echo "Make plots of the radially free falling particles"
 if command -v python3 &>/dev/null; then
     python3 plotprog.py 
 else 
-    python plotprog.py
+    python3 plotprog.py
 fi

examples/GravityTests/HydrostaticHalo/makeIC.py

@@ -24,7 +24,7 @@
 import random
 
 # Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
-# usage: python makeIC.py 1000: generate 1000 particles
+# usage: python3 makeIC.py 1000: generate 1000 particles
 
 # Some constants
 

examples/GravityTests/HydrostaticHalo/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e Hydrostatic.hdf5 ]
 then
     echo "Generating initial conditions for the isothermal potential box example..."
-    python makeIC.py 100000
+    python3 makeIC.py 100000
 fi
 
 # Run for 10 dynamical times
@@ -13,15 +13,15 @@ fi
 echo "Plotting density profiles"
 mkdir plots
 mkdir plots/density_profile
-python density_profile.py 2. 200 300
+python3 density_profile.py 2. 200 300
 
 echo "Plotting internal energy profiles"
 mkdir plots/internal_energy
-python internal_energy_profile.py 2. 200 300
+python3 internal_energy_profile.py 2. 200 300
 
 echo "Plotting radial velocity profiles"
 mkdir plots/radial_velocity_profile
-python velocity_profile.py 2. 200 300
+python3 velocity_profile.py 2. 200 300
 
 echo "Plotting energy as a function of time"
-python test_energy_conservation.py 300
+python3 test_energy_conservation.py 300

examples/GravityTests/IsothermalPotential/makeIC.py

@@ -25,8 +25,8 @@
 import random
 
 # Generates N particles in a spherical distribution centred on [0,0,0], to be moved in an isothermal potential
-# usage: python makeIC.py 1000 0 : generate 1000 particles on circular orbits
-#        python makeIC.py 1000 1 : generate 1000 particles with Lz/L uniform in [0,1]
+# usage: python3 makeIC.py 1000 0 : generate 1000 particles on circular orbits
+#        python3 makeIC.py 1000 1 : generate 1000 particles with Lz/L uniform in [0,1]
 # all particles move in the xy plane, and start at y=0
 
 # physical constants in cgs

examples/GravityTests/IsothermalPotential/run.sh

@@ -4,10 +4,10 @@
 if [ ! -e Isothermal.hdf5 ]
 then
     echo "Generating initial conditions for the isothermal potential box example..."
-    python makeIC.py 1000 0
+    python3 makeIC.py 1000 0
 fi
 
 rm -rf Isothermal_*.hdf5
 ../../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
 
-python energy_plot.py
+python3 energy_plot.py

examples/GravityTests/NFW_Halo/run.sh

@@ -6,7 +6,7 @@ then
     if command -v python3 &>/dev/null; then
         python3 makeIC.py
     else 
-        python makeIC.py
+        python3 makeIC.py
     fi
 fi
 
@@ -16,5 +16,5 @@ fi
 if command -v python3 &>/dev/null; then
     python3 makePlots.py
 else 
-    python makePlots.py
+    python3 makePlots.py
 fi

examples/HydroTests/Diffusion_1D/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e diffusion.hdf5 ]
 then
     echo "Generating initial conditions for the Sedov blast example..."
-    python makeIC.py
+    python3 makeIC.py
 fi
 
 # Run SWIFT