From d0999769d2f2cbf36c1f8977d273cdb81833072b Mon Sep 17 00:00:00 2001
From: "Peter W. Draper" <p.w.draper@durham.ac.uk>
Date: Mon, 11 Jul 2022 14:25:44 +0000
Subject: [PATCH] Move executable out of examples
---
Makefile.am | 69 +++++++++++++++++++
.../source/GettingStarted/compiling_code.rst | 5 +-
.../Cooling/ConstantCosmoTempEvolution/run.sh | 2 +-
examples/Cooling/CoolingBox/run.sh | 2 +-
examples/Cooling/CoolingHalo/run.sh | 2 +-
examples/Cooling/CoolingHaloWithSpin/run.sh | 2 +-
.../Cooling/CoolingRedshiftDependence/run.sh | 2 +-
examples/Cooling/FeedbackEvent_3D/run.sh | 2 +-
examples/Cooling/FeedbackEvent_3D/runs.sh | 4 +-
examples/Cosmology/ComovingSodShock_1D/run.sh | 2 +-
examples/Cosmology/ComovingSodShock_2D/run.sh | 2 +-
examples/Cosmology/ComovingSodShock_3D/run.sh | 2 +-
.../Cosmology/ComovingToroTest2_1D/run.sh | 2 +-
examples/Cosmology/ConstantCosmoVolume/run.sh | 2 +-
examples/Cosmology/NeutrinoCosmo/run.sh | 2 +-
examples/Cosmology/ZeldovichPancake_3D/run.sh | 2 +-
examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh | 2 +-
examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh | 2 +-
examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh | 2 +-
examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_100/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_12/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_25/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_25_low_res/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_50/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_50_low_res/run.sh | 2 +-
examples/EAGLE_ICs/EAGLE_6/run.sh | 2 +-
examples/EAGLE_low_z/EAGLE_100/run.sh | 2 +-
examples/EAGLE_low_z/EAGLE_12/run.sh | 2 +-
examples/EAGLE_low_z/EAGLE_25/run.sh | 2 +-
examples/EAGLE_low_z/EAGLE_50/run.sh | 2 +-
examples/EAGLE_low_z/EAGLE_6/run.sh | 4 +-
.../EAGLE_low_z/EAGLE_6/testVELOCIraptor.sh | 8 +--
examples/GEAR/AgoraCosmo/run.sh | 2 +-
examples/GEAR/AgoraDisk/run.sh | 2 +-
examples/GEAR/ZoomIn/run.sh | 2 +-
.../GravityTests/DiscPatch/GravityOnly/run.sh | 2 +-
.../GravityTests/DiscPatch/HydroStatic/run.sh | 2 +-
.../DiscPatch/HydroStatic_1D/run.sh | 2 +-
.../GravityTests/ExternalPointMass/run.sh | 2 +-
.../Hernquist_circularorbit/run.sh | 2 +-
.../Hernquist_radialinfall/run.sh | 2 +-
examples/GravityTests/HydrostaticHalo/run.sh | 2 +-
.../GravityTests/IsothermalPotential/run.sh | 2 +-
.../GravityTests/JeansFragmentation/run.sh | 2 +-
examples/GravityTests/NFW_Halo/run.sh | 2 +-
.../Plummer_Selfgravitating/run.sh | 2 +-
examples/HydroTests/BlobTest_3D/run.sh | 2 +-
examples/HydroTests/Diffusion_1D/run.sh | 2 +-
examples/HydroTests/Diffusion_1D/run_set.sh | 2 +-
examples/HydroTests/EvrardCollapse_3D/run.sh | 2 +-
examples/HydroTests/Gradients/run.sh | 6 +-
examples/HydroTests/GreshoVortex_2D/run.sh | 2 +-
examples/HydroTests/GreshoVortex_3D/run.sh | 2 +-
.../InteractingBlastWaves_1D/run.sh | 2 +-
.../KelvinHelmholtzGrowthRate_2D/run.sh | 2 +-
.../KelvinHelmholtzGrowthRate_3D/run.sh | 2 +-
examples/HydroTests/KelvinHelmholtz_2D/run.sh | 2 +-
examples/HydroTests/KeplerianRing/README.md | 2 +-
examples/HydroTests/KeplerianRing/run.sh | 2 +-
examples/HydroTests/Noh_1D/run.sh | 2 +-
examples/HydroTests/Noh_2D/run.sh | 2 +-
examples/HydroTests/Noh_3D/run.sh | 2 +-
examples/HydroTests/PerturbedBox_3D/run.sh | 2 +-
examples/HydroTests/Rayleigh-Taylor_2D/run.sh | 2 +-
examples/HydroTests/SedovBlast_1D/run.sh | 2 +-
examples/HydroTests/SedovBlast_2D/run.sh | 2 +-
examples/HydroTests/SedovBlast_3D/run.sh | 2 +-
.../HydroTests/SineWavePotential_1D/run.sh | 2 +-
.../HydroTests/SineWavePotential_2D/run.sh | 2 +-
.../HydroTests/SineWavePotential_3D/run.sh | 2 +-
.../HydroTests/SodShockSpherical_2D/run.sh | 2 +-
.../HydroTests/SodShockSpherical_3D/run.sh | 2 +-
examples/HydroTests/SodShock_1D/run.sh | 2 +-
examples/HydroTests/SodShock_2D/run.sh | 2 +-
examples/HydroTests/SodShock_3D/run.sh | 2 +-
examples/HydroTests/SodShock_BCC_3D/run.sh | 2 +-
examples/HydroTests/SquareTest_2D/run.sh | 2 +-
examples/HydroTests/ToroTest2_1D/run.sh | 2 +-
examples/HydroTests/ToroTest2_2D/run.sh | 2 +-
examples/HydroTests/ToroTest2_3D/run.sh | 2 +-
examples/HydroTests/UniformBox_2D/run.sh | 2 +-
examples/HydroTests/UniformBox_3D/run.sh | 2 +-
examples/HydroTests/VacuumSpherical_2D/run.sh | 2 +-
examples/HydroTests/VacuumSpherical_3D/run.sh | 2 +-
examples/HydroTests/Vacuum_1D/run.sh | 2 +-
examples/HydroTests/Vacuum_2D/run.sh | 2 +-
examples/HydroTests/Vacuum_3D/run.sh | 2 +-
.../IdealisedCluster_M13/run.sh | 2 +-
.../IdealisedCluster_M135/run.sh | 2 +-
.../IdealisedCluster_M14/run.sh | 2 +-
.../IsolatedGalaxy_NFW_MN/run.sh | 2 +-
.../IsolatedGalaxy_dmparticles/run.sh | 2 +-
.../IsolatedGalaxy_feedback/run.sh | 2 +-
.../IsolatedGalaxy_potential/run.sh | 2 +-
.../IsolatedGalaxy/IsolatedGalaxy_sink/run.sh | 2 +-
.../IsolatedGalaxy_starformation/run.sh | 2 +-
examples/Makefile.am | 69 -------------------
examples/Planetary/EarthImpact/run.sh | 2 +-
examples/Planetary/EvrardCollapse_3D/run.sh | 2 +-
examples/Planetary/GreshoVortex_3D/run.sh | 2 +-
examples/Planetary/KelvinHelmholtz_2D/run.sh | 2 +-
examples/Planetary/SodShock_3D/run.sh | 2 +-
examples/Planetary/SquareTest_2D/run.sh | 2 +-
examples/QuickLymanAlpha/L050N0752/run.sh | 2 +-
.../Advection_1D/run.sh | 2 +-
.../Advection_2D/run.sh | 2 +-
.../RadiativeTransferTests/CoolingTest/run.sh | 4 +-
.../RadiativeTransferTests/HeatingTest/run.sh | 2 +-
.../IonMassFractionAdvectionTest_2D/run.sh | 2 +-
.../IonizationEquilibriumICSetupTest/run.sh | 2 +-
.../RandomizedBox_3D/run.sh | 4 +-
.../StromgrenSphere_2D/run.sh | 2 +-
.../StromgrenSphere_2D/runPropagationTest.sh | 2 +-
.../StromgrenSphere_3D/run.sh | 2 +-
.../StromgrenSphere_3D/runPropagationTest.sh | 2 +-
.../UniformBox_3D/run.sh | 4 +-
examples/SantaBarbara/SantaBarbara-128/run.sh | 2 +-
examples/SantaBarbara/SantaBarbara-256/run.sh | 2 +-
.../SmallCosmoVolume_DM/run.sh | 2 +-
.../SmallCosmoVolume_Snipshots/run.sh | 2 +-
.../SmallCosmoVolume_VELOCIraptor/run.sh | 2 +-
.../SmallCosmoVolume_cooling/run.sh | 2 +-
.../SmallCosmoVolume_hydro/run.sh | 2 +-
.../SmallCosmoVolume_lightcone/run.sh | 2 +-
.../CosmologicalStellarEvolution/run.sh | 10 +--
.../SubgridTests/ParticleSplitting/run.sh | 2 +-
examples/SubgridTests/PressureFloor/run.sh | 2 +-
.../SubgridTests/SmoothedMetallicity/run.sh | 2 +-
examples/SubgridTests/StellarEvolution/run.sh | 10 +--
examples/nIFTyCluster/Baryonic/run.sh | 2 +-
examples/main.c => swift.c | 0
examples/main_fof.c => swift_fof.c | 0
133 files changed, 216 insertions(+), 219 deletions(-)
rename examples/main.c => swift.c (100%)
rename examples/main_fof.c => swift_fof.c (100%)
diff --git a/Makefile.am b/Makefile.am
index d426d8adc6..2c1af34d8d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -30,5 +30,74 @@ SUBDIRS += examples/Cooling/CoolingRates
endif
DIST_SUBDIRS = $(SUBDIRS) examples/Cooling/CoolingRates
+# Common flags
+MYFLAGS =
+
+# Add the source directory and the non-standard paths to the included library headers to CFLAGS
+AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/argparse $(HDF5_CPPFLAGS) \
+ $(GSL_INCS) $(FFTW_INCS) $(NUMA_INCS) $(GRACKLE_INCS) $(OPENMP_CFLAGS) \
+ $(CHEALPIX_CFLAGS)
+
+AM_LDFLAGS = $(HDF5_LDFLAGS)
+
+# Extra libraries.
+EXTRA_LIBS = $(GSL_LIBS) $(HDF5_LIBS) $(FFTW_LIBS) $(NUMA_LIBS) $(PROFILER_LIBS) \
+ $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) \
+ $(CHEALPIX_LIBS)
+
+# MPI libraries.
+MPI_LIBS = $(PARMETIS_LIBS) $(METIS_LIBS) $(MPI_THREAD_LIBS) $(FFTW_MPI_LIBS)
+MPI_FLAGS = -DWITH_MPI $(PARMETIS_INCS) $(METIS_INCS) $(FFTW_MPI_INCS)
+
+# Programs.
+bin_PROGRAMS = swift
+
+# Also build the FOF tool?
+if HAVESTANDALONEFOF
+bin_PROGRAMS += fof
+endif
+
+# Do we have the CSDS?
+if HAVECSDS
+LD_CSDS = csds/src/.libs/libcsds_writer.a
+else
+LD_CSDS =
+endif
+
+# Build MPI versions as well?
+if HAVEMPI
+bin_PROGRAMS += swift_mpi
+if HAVESTANDALONEFOF
+bin_PROGRAMS += fof_mpi
+endif
+endif
+
+# engine_policy_setaffinity is available?
+if HAVESETAFFINITY
+ENGINE_POLICY_SETAFFINITY=| engine_policy_setaffinity
+else
+ENGINE_POLICY_SETAFFINITY=
+endif
+
+# Sources for swift
+swift_SOURCES = swift.c
+swift_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+swift_LDADD = src/libswiftsim.la argparse/libargparse.la $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for swift_mpi, do we need an affinity policy for MPI?
+swift_mpi_SOURCES = swift.c
+swift_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+swift_mpi_LDADD = src/libswiftsim_mpi.la argparse/libargparse.la $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for fof
+fof_SOURCES = swift_fof.c
+fof_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+fof_LDADD = src/.libs/libswiftsim.a argparse/.libs/libargparse.a $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
+# Sources for fof_mpi, do we need an affinity policy for MPI?
+fof_mpi_SOURCES = swift_fof.c
+fof_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
+fof_mpi_LDADD = src/.libs/libswiftsim_mpi.a argparse/.libs/libargparse.a $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
+
# Non-standard files that should be part of the distribution.
EXTRA_DIST = INSTALL.swift .clang-format format.sh
diff --git a/doc/RTD/source/GettingStarted/compiling_code.rst b/doc/RTD/source/GettingStarted/compiling_code.rst
index 5c32bd3c4e..e04d081c0b 100644
--- a/doc/RTD/source/GettingStarted/compiling_code.rst
+++ b/doc/RTD/source/GettingStarted/compiling_code.rst
@@ -107,15 +107,14 @@ This may be required as a dependency of HEALPix.
Initial Setup
-------------
-We use autotools for setup. To get a basic running version of the code
-(the binary is created in swiftsim/examples) on most platforms, run
-
+We use autotools for setup. To get a basic running version of the code use:
.. code-block:: bash
./autogen.sh
./configure
make
+the executable binaries are found in the top directory.
MacOS Specific Oddities
~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/run.sh b/examples/Cooling/ConstantCosmoTempEvolution/run.sh
index 710613ec9a..2bf33de8a0 100755
--- a/examples/Cooling/ConstantCosmoTempEvolution/run.sh
+++ b/examples/Cooling/ConstantCosmoTempEvolution/run.sh
@@ -20,7 +20,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --cosmology --cooling --threads=4 const_cosmo_temp_evol.yml 2>&1 | tee output.log
+../../../swift --hydro --cosmology --cooling --threads=4 const_cosmo_temp_evol.yml 2>&1 | tee output.log
# Plot the result
python3 plot_thermal_history.py cooling_box
diff --git a/examples/Cooling/CoolingBox/run.sh b/examples/Cooling/CoolingBox/run.sh
index 28b5465a52..d83974dd34 100755
--- a/examples/Cooling/CoolingBox/run.sh
+++ b/examples/Cooling/CoolingBox/run.sh
@@ -21,7 +21,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --cooling --threads=4 -n 1000 coolingBox.yml
+../../../swift --hydro --cooling --threads=4 -n 1000 coolingBox.yml
# Check energy conservation and cooling rate
python3 plotEnergy.py
diff --git a/examples/Cooling/CoolingHalo/run.sh b/examples/Cooling/CoolingHalo/run.sh
index ba7b004679..e22a3c50d1 100755
--- a/examples/Cooling/CoolingHalo/run.sh
+++ b/examples/Cooling/CoolingHalo/run.sh
@@ -4,7 +4,7 @@
echo "Generating initial conditions for the isothermal potential box example..."
python3 makeIC.py 10000
-../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
+../../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
python3 radial_profile.py 2. 200 100
diff --git a/examples/Cooling/CoolingHaloWithSpin/run.sh b/examples/Cooling/CoolingHaloWithSpin/run.sh
index fa71cf5d8a..1c7346b2b4 100755
--- a/examples/Cooling/CoolingHaloWithSpin/run.sh
+++ b/examples/Cooling/CoolingHaloWithSpin/run.sh
@@ -5,7 +5,7 @@ echo "Generating initial conditions for the isothermal potential box example..."
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
+../../../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
# python3 radial_profile.py 10
diff --git a/examples/Cooling/CoolingRedshiftDependence/run.sh b/examples/Cooling/CoolingRedshiftDependence/run.sh
index c9bf2aea7e..d771ac8aaa 100755
--- a/examples/Cooling/CoolingRedshiftDependence/run.sh
+++ b/examples/Cooling/CoolingRedshiftDependence/run.sh
@@ -14,7 +14,7 @@ then
python3 makeIC.py
fi
-swift_location="../../swift"
+swift_location="../../../swift"
rm data/redshift_dependence_*_z_*.hdf5
diff --git a/examples/Cooling/FeedbackEvent_3D/run.sh b/examples/Cooling/FeedbackEvent_3D/run.sh
index 310ea98f89..c0bb534c40 100755
--- a/examples/Cooling/FeedbackEvent_3D/run.sh
+++ b/examples/Cooling/FeedbackEvent_3D/run.sh
@@ -12,7 +12,7 @@ if [ ! -f feedback.hdf5 ]; then
fi
# Run SWIFT
-../../swift --hydro --cooling --limiter --threads=4 feedback.yml 2>&1 | tee output.log
+../../../swift --hydro --cooling --limiter --threads=4 feedback.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 5
diff --git a/examples/Cooling/FeedbackEvent_3D/runs.sh b/examples/Cooling/FeedbackEvent_3D/runs.sh
index 5e3853f1e1..e2ff84caa5 100644
--- a/examples/Cooling/FeedbackEvent_3D/runs.sh
+++ b/examples/Cooling/FeedbackEvent_3D/runs.sh
@@ -17,7 +17,7 @@ do
cd default_diffmax_$diffusion_alpha_max
- ../../../swift --hydro --cooling --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log
+ ../../../../swift --hydro --cooling --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log
cd ..
@@ -25,7 +25,7 @@ do
cd nocool_diffmax_$diffusion_alpha_max
- ../../../swift --hydro --temperature --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log
+ ../../../../swift --hydro --temperature --limiter --threads=16 --param="SPH:diffusion_alpha_max:${diffusion_alpha_max}" ../feedback.yml 2>&1 | tee output.log
cd ..
done
diff --git a/examples/Cosmology/ComovingSodShock_1D/run.sh b/examples/Cosmology/ComovingSodShock_1D/run.sh
index d709955bfc..34b0dffd8d 100755
--- a/examples/Cosmology/ComovingSodShock_1D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/Cosmology/ComovingSodShock_2D/run.sh b/examples/Cosmology/ComovingSodShock_2D/run.sh
index 5217000934..73afff14c7 100755
--- a/examples/Cosmology/ComovingSodShock_2D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_2D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/Cosmology/ComovingSodShock_3D/run.sh b/examples/Cosmology/ComovingSodShock_3D/run.sh
index 205af5a415..42ee57ddfb 100755
--- a/examples/Cosmology/ComovingSodShock_3D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/Cosmology/ComovingToroTest2_1D/run.sh b/examples/Cosmology/ComovingToroTest2_1D/run.sh
index 04951925ef..29b8de6a97 100755
--- a/examples/Cosmology/ComovingToroTest2_1D/run.sh
+++ b/examples/Cosmology/ComovingToroTest2_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
+../../../swift --cosmology --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/Cosmology/ConstantCosmoVolume/run.sh b/examples/Cosmology/ConstantCosmoVolume/run.sh
index 9c0e0ccdcb..384744e0d7 100755
--- a/examples/Cosmology/ConstantCosmoVolume/run.sh
+++ b/examples/Cosmology/ConstantCosmoVolume/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --cosmology --self-gravity --threads=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
python3 plotSolution.py $i
diff --git a/examples/Cosmology/NeutrinoCosmo/run.sh b/examples/Cosmology/NeutrinoCosmo/run.sh
index d0122d1031..e070ed6e3a 100755
--- a/examples/Cosmology/NeutrinoCosmo/run.sh
+++ b/examples/Cosmology/NeutrinoCosmo/run.sh
@@ -8,4 +8,4 @@ then
fi
# Run SWIFT
-../../swift -c -G --threads=8 neutrino_cosmo.yml 2>&1 | tee output.log
+../../../swift -c -G --threads=8 neutrino_cosmo.yml 2>&1 | tee output.log
diff --git a/examples/Cosmology/ZeldovichPancake_3D/run.sh b/examples/Cosmology/ZeldovichPancake_3D/run.sh
index 85013713f1..4eef7c4647 100755
--- a/examples/Cosmology/ZeldovichPancake_3D/run.sh
+++ b/examples/Cosmology/ZeldovichPancake_3D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --cosmology --self-gravity --threads=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/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
index be3cdd8e3c..5c118c26dd 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --self-gravity --threads=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_low_z/EAGLE_DMO_12/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
index 669fa49823..c065cef8f6 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --self-gravity --threads=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_low_z/EAGLE_DMO_25/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
index 6d96edda65..fd6e36b1db 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --self-gravity --threads=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_low_z/EAGLE_DMO_50/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
index 8a08d0b040..069e0efc31 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --self-gravity --threads=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/EAGLE_ICs/EAGLE_100/run.sh b/examples/EAGLE_ICs/EAGLE_100/run.sh
index 8b40bdda36..7b2d0e95bc 100755
--- a/examples/EAGLE_ICs/EAGLE_100/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_100/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_100.yml
diff --git a/examples/EAGLE_ICs/EAGLE_12/run.sh b/examples/EAGLE_ICs/EAGLE_12/run.sh
index aaba58f266..0140f598a2 100755
--- a/examples/EAGLE_ICs/EAGLE_12/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_12/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_12.yml
diff --git a/examples/EAGLE_ICs/EAGLE_25/run.sh b/examples/EAGLE_ICs/EAGLE_25/run.sh
index 1e7d79fe57..04635c149f 100755
--- a/examples/EAGLE_ICs/EAGLE_25/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_25/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_25.yml
diff --git a/examples/EAGLE_ICs/EAGLE_25_low_res/run.sh b/examples/EAGLE_ICs/EAGLE_25_low_res/run.sh
index 1db1a6e96f..200fab538c 100755
--- a/examples/EAGLE_ICs/EAGLE_25_low_res/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_25_low_res/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_25.yml
diff --git a/examples/EAGLE_ICs/EAGLE_50/run.sh b/examples/EAGLE_ICs/EAGLE_50/run.sh
index e49cc93f2d..026019b44d 100755
--- a/examples/EAGLE_ICs/EAGLE_50/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_50/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_50.yml
diff --git a/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh b/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh
index 9d4cca7085..83f388aeb0 100755
--- a/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_50.yml
diff --git a/examples/EAGLE_ICs/EAGLE_6/run.sh b/examples/EAGLE_ICs/EAGLE_6/run.sh
index 51f7295d98..aa1064d380 100755
--- a/examples/EAGLE_ICs/EAGLE_6/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_6/run.sh
@@ -35,7 +35,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --eagle \
--threads=16 --pin \
eagle_6.yml
diff --git a/examples/EAGLE_low_z/EAGLE_100/run.sh b/examples/EAGLE_low_z/EAGLE_100/run.sh
index 28571d4803..2e22a655c8 100755
--- a/examples/EAGLE_low_z/EAGLE_100/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_100/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --hydro --self-gravity --stars --threads=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_low_z/EAGLE_12/run.sh b/examples/EAGLE_low_z/EAGLE_12/run.sh
index bceddf338a..80c76970b7 100755
--- a/examples/EAGLE_low_z/EAGLE_12/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_12/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --hydro --self-gravity --stars --threads=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_low_z/EAGLE_25/run.sh b/examples/EAGLE_low_z/EAGLE_25/run.sh
index ea14dbde32..aae44b01a1 100755
--- a/examples/EAGLE_low_z/EAGLE_25/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_25/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --hydro --self-gravity --stars --threads=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_low_z/EAGLE_50/run.sh b/examples/EAGLE_low_z/EAGLE_50/run.sh
index e2f2836900..5a053a4054 100755
--- a/examples/EAGLE_low_z/EAGLE_50/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_50/run.sh
@@ -7,5 +7,5 @@ then
./getIC.sh
fi
-../../swift --cosmology --hydro --self-gravity --stars --threads=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_low_z/EAGLE_6/run.sh b/examples/EAGLE_low_z/EAGLE_6/run.sh
index aec7449e2d..f7db75e6e3 100755
--- a/examples/EAGLE_low_z/EAGLE_6/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_6/run.sh
@@ -7,7 +7,5 @@ then
./getIC.sh
fi
-../../swift --hydro --threads=4 -n 16 -y 1 eagle_6.yml \
- -PInitialConditions:metadata_group_name:NoRuntimePars \
- | tee output.log
+../../../swift -v 1 --interleave --hydro --threads=4 -n 16 -y 1 eagle_6.yml | tee output.log
diff --git a/examples/EAGLE_low_z/EAGLE_6/testVELOCIraptor.sh b/examples/EAGLE_low_z/EAGLE_6/testVELOCIraptor.sh
index cab3a822a9..f0438966ed 100755
--- a/examples/EAGLE_low_z/EAGLE_6/testVELOCIraptor.sh
+++ b/examples/EAGLE_low_z/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 $NUM_MPI_PROC ../swift_mpi --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$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
+ 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 $NUM_MPI_PROC ../swift_mpi --hydro --self-gravity --threads=8 eagle_6.yml --velociraptor --steps=5 -P StructureFinding:basename:./$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
+ 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/GEAR/AgoraCosmo/run.sh b/examples/GEAR/AgoraCosmo/run.sh
index 6d8609cb0f..0ff0482c5c 100644
--- a/examples/GEAR/AgoraCosmo/run.sh
+++ b/examples/GEAR/AgoraCosmo/run.sh
@@ -26,4 +26,4 @@ echo "Converting the initial conditions into a SWIFT compatible format"
python3 convert_ic.py
echo "Running SWIFT"
-../../swift --cooling --feedback --cosmology --limiter --sync --self-gravity --hydro --stars --star-formation --threads=24 agora_cosmo.yml 2>&1 | tee output.log
+../../../swift --cooling --feedback --cosmology --limiter --sync --self-gravity --hydro --stars --star-formation --threads=24 agora_cosmo.yml 2>&1 | tee output.log
diff --git a/examples/GEAR/AgoraDisk/run.sh b/examples/GEAR/AgoraDisk/run.sh
index b2956e086d..9a32b86a47 100755
--- a/examples/GEAR/AgoraDisk/run.sh
+++ b/examples/GEAR/AgoraDisk/run.sh
@@ -36,7 +36,7 @@ cp $sim.hdf5 agora_disk.hdf5
python3 changeType.py agora_disk.hdf5
# Run SWIFT
-../../swift --sync --limiter --cooling --hydro --self-gravity --star-formation --feedback --stars --threads=8 agora_disk.yml 2>&1 | tee output.log
+../../../swift --sync --limiter --cooling --hydro --self-gravity --star-formation --feedback --stars --threads=8 agora_disk.yml 2>&1 | tee output.log
echo "Changing smoothing length to be Gadget compatible"
diff --git a/examples/GEAR/ZoomIn/run.sh b/examples/GEAR/ZoomIn/run.sh
index 8760786e1e..141e6af26f 100755
--- a/examples/GEAR/ZoomIn/run.sh
+++ b/examples/GEAR/ZoomIn/run.sh
@@ -3,4 +3,4 @@
echo "Fetching initial conditions for the zoom in example..."
./getIC.sh
-../../swift --cooling --feedback --cosmology --limiter --sync --self-gravity --hydro --stars --star-formation --threads=8 zoom_in.yml 2>&1 | tee output.log
+../../../swift --cooling --feedback --cosmology --limiter --sync --self-gravity --hydro --stars --star-formation --threads=8 zoom_in.yml 2>&1 | tee output.log
diff --git a/examples/GravityTests/DiscPatch/GravityOnly/run.sh b/examples/GravityTests/DiscPatch/GravityOnly/run.sh
index 5716b254b6..2986b8a7ea 100755
--- a/examples/GravityTests/DiscPatch/GravityOnly/run.sh
+++ b/examples/GravityTests/DiscPatch/GravityOnly/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../../swift --external-gravity --threads=2 disc-patch.yml
+../../../../swift --external-gravity --threads=2 disc-patch.yml
# Verify energy conservation
python3 test.py
diff --git a/examples/GravityTests/DiscPatch/HydroStatic/run.sh b/examples/GravityTests/DiscPatch/HydroStatic/run.sh
index 0e18efb2b2..73cc77029e 100755
--- a/examples/GravityTests/DiscPatch/HydroStatic/run.sh
+++ b/examples/GravityTests/DiscPatch/HydroStatic/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../../swift --external-gravity --hydro --threads=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
python3 plotSolution.py
diff --git a/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh b/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
index c732f5e8c0..54e48c923c 100755
--- a/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
+++ b/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
@@ -8,6 +8,6 @@ then
fi
# Run SWIFT
-../../../swift --external-gravity --hydro --threads=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
python3 plotSolution.py
diff --git a/examples/GravityTests/ExternalPointMass/run.sh b/examples/GravityTests/ExternalPointMass/run.sh
index 3d16556491..5b4973ab79 100755
--- a/examples/GravityTests/ExternalPointMass/run.sh
+++ b/examples/GravityTests/ExternalPointMass/run.sh
@@ -8,6 +8,6 @@ then
fi
rm -rf pointMass_*.hdf5
-../../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
+../../../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
python3 energy_plot.py
diff --git a/examples/GravityTests/Hernquist_circularorbit/run.sh b/examples/GravityTests/Hernquist_circularorbit/run.sh
index 382b72c14c..2b015311b1 100755
--- a/examples/GravityTests/Hernquist_circularorbit/run.sh
+++ b/examples/GravityTests/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 --external-gravity --threads=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/GravityTests/Hernquist_radialinfall/run.sh b/examples/GravityTests/Hernquist_radialinfall/run.sh
index c7ff7ede11..9b04385a5b 100755
--- a/examples/GravityTests/Hernquist_radialinfall/run.sh
+++ b/examples/GravityTests/Hernquist_radialinfall/run.sh
@@ -12,7 +12,7 @@ then
fi
rm -rf hernquist_*.hdf5
-../../swift --external-gravity --threads=1 hernquist.yml 2>&1 | tee output.log
+../../../swift --external-gravity --threads=1 hernquist.yml 2>&1 | tee output.log
diff --git a/examples/GravityTests/HydrostaticHalo/run.sh b/examples/GravityTests/HydrostaticHalo/run.sh
index b1075399ff..ed7aea4cee 100755
--- a/examples/GravityTests/HydrostaticHalo/run.sh
+++ b/examples/GravityTests/HydrostaticHalo/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run for 10 dynamical times
-../../swift --external-gravity --hydro --threads=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/GravityTests/IsothermalPotential/run.sh b/examples/GravityTests/IsothermalPotential/run.sh
index ebc6749b2e..5fba6714f7 100755
--- a/examples/GravityTests/IsothermalPotential/run.sh
+++ b/examples/GravityTests/IsothermalPotential/run.sh
@@ -8,6 +8,6 @@ then
fi
rm -rf Isothermal_*.hdf5
-../../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
+../../../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
python3 energy_plot.py
diff --git a/examples/GravityTests/JeansFragmentation/run.sh b/examples/GravityTests/JeansFragmentation/run.sh
index 3a0fbe4248..bab705720d 100755
--- a/examples/GravityTests/JeansFragmentation/run.sh
+++ b/examples/GravityTests/JeansFragmentation/run.sh
@@ -14,4 +14,4 @@ then
fi
# Run for some sound crossing time
-../../swift --hydro --self-gravity --threads=1 jeansfragmentation.yml 2>&1 | tee output.log
+../../../swift --hydro --self-gravity --threads=1 jeansfragmentation.yml 2>&1 | tee output.log
diff --git a/examples/GravityTests/NFW_Halo/run.sh b/examples/GravityTests/NFW_Halo/run.sh
index 255ee48d8d..6d9fb639b5 100755
--- a/examples/GravityTests/NFW_Halo/run.sh
+++ b/examples/GravityTests/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 --external-gravity --threads=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/GravityTests/Plummer_Selfgravitating/run.sh b/examples/GravityTests/Plummer_Selfgravitating/run.sh
index f94f7c10c3..eeae68c7a7 100755
--- a/examples/GravityTests/Plummer_Selfgravitating/run.sh
+++ b/examples/GravityTests/Plummer_Selfgravitating/run.sh
@@ -12,7 +12,7 @@ then
mkdir snap
fi
-../../swift --self-gravity --threads=8 params.yml 2>&1 | tee output.log
+../../../swift --self-gravity --threads=8 params.yml 2>&1 | tee output.log
echo "Plotting results..."
# If params.yml is left at default values, should produce 10 snapshots
diff --git a/examples/HydroTests/BlobTest_3D/run.sh b/examples/HydroTests/BlobTest_3D/run.sh
index 15c87c734e..87cb2dd2b6 100755
--- a/examples/HydroTests/BlobTest_3D/run.sh
+++ b/examples/HydroTests/BlobTest_3D/run.sh
@@ -8,6 +8,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=2 blob.yml
+../../../swift --hydro --threads=2 blob.yml
python3 makeMovie.py
diff --git a/examples/HydroTests/Diffusion_1D/run.sh b/examples/HydroTests/Diffusion_1D/run.sh
index 9d25f52432..38871c80c1 100755
--- a/examples/HydroTests/Diffusion_1D/run.sh
+++ b/examples/HydroTests/Diffusion_1D/run.sh
@@ -8,4 +8,4 @@ then
fi
# Run SWIFT
-../../swift --hydro --limiter --threads=1 diffusion.yml 2>&1 | tee output.log
+../../../swift --hydro --limiter --threads=1 diffusion.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/Diffusion_1D/run_set.sh b/examples/HydroTests/Diffusion_1D/run_set.sh
index cb6d98cae7..d665a5970c 100644
--- a/examples/HydroTests/Diffusion_1D/run_set.sh
+++ b/examples/HydroTests/Diffusion_1D/run_set.sh
@@ -1,7 +1,7 @@
#!/bin/bash
beta=(1.0 0.1 0.01 0.001)
-swift_location="../../swift"
+swift_location="../../../swift"
flags="--hydro --limiter --threads=2"
parameter="diffusion.yml"
parameter_fixed="diffusion_fixed_alpha.yml"
diff --git a/examples/HydroTests/EvrardCollapse_3D/run.sh b/examples/HydroTests/EvrardCollapse_3D/run.sh
index e52a6e32c7..0e1d99f89e 100755
--- a/examples/HydroTests/EvrardCollapse_3D/run.sh
+++ b/examples/HydroTests/EvrardCollapse_3D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --self-gravity --threads=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/HydroTests/Gradients/run.sh b/examples/HydroTests/Gradients/run.sh
index 8a9767404b..e6427788bd 100755
--- a/examples/HydroTests/Gradients/run.sh
+++ b/examples/HydroTests/Gradients/run.sh
@@ -1,13 +1,13 @@
#! /bin/bash
python3 makeICs.py stretched
-../../swift --hydro --threads=2 gradientsStretched.yml
+../../../swift --hydro --threads=2 gradientsStretched.yml
python3 plot.py gradients_stretched_0001.hdf5 stretched
python3 makeICs.py cartesian
-../../swift --hydro --threads=2 gradientsCartesian.yml
+../../../swift --hydro --threads=2 gradientsCartesian.yml
python3 plot.py gradients_cartesian_0001.hdf5 cartesian
python3 makeICs.py random
-../../swift --hydro --threads=2 gradientsRandom.yml
+../../../swift --hydro --threads=2 gradientsRandom.yml
python3 plot.py gradients_random_0001.hdf5 random
diff --git a/examples/HydroTests/GreshoVortex_2D/run.sh b/examples/HydroTests/GreshoVortex_2D/run.sh
index d8075a89ce..fa994d0097 100755
--- a/examples/HydroTests/GreshoVortex_2D/run.sh
+++ b/examples/HydroTests/GreshoVortex_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 gresho.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 gresho.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 11
diff --git a/examples/HydroTests/GreshoVortex_3D/run.sh b/examples/HydroTests/GreshoVortex_3D/run.sh
index 1127ab925b..1d7686e7fe 100755
--- a/examples/HydroTests/GreshoVortex_3D/run.sh
+++ b/examples/HydroTests/GreshoVortex_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 11
diff --git a/examples/HydroTests/InteractingBlastWaves_1D/run.sh b/examples/HydroTests/InteractingBlastWaves_1D/run.sh
index 54a35b2c79..9139835bdb 100755
--- a/examples/HydroTests/InteractingBlastWaves_1D/run.sh
+++ b/examples/HydroTests/InteractingBlastWaves_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=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/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh b/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
index 8d70102a29..479de13980 100755
--- a/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
@@ -9,7 +9,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 100
diff --git a/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh b/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
index 8d70102a29..479de13980 100755
--- a/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
@@ -9,7 +9,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 100
diff --git a/examples/HydroTests/KelvinHelmholtz_2D/run.sh b/examples/HydroTests/KelvinHelmholtz_2D/run.sh
index bedc6e6f21..583d270a7a 100755
--- a/examples/HydroTests/KelvinHelmholtz_2D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtz_2D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
# Plot the solution
diff --git a/examples/HydroTests/KeplerianRing/README.md b/examples/HydroTests/KeplerianRing/README.md
index 05af934846..0ac9317f91 100644
--- a/examples/HydroTests/KeplerianRing/README.md
+++ b/examples/HydroTests/KeplerianRing/README.md
@@ -66,7 +66,7 @@ Plotting
Once you have ran swift (we suggest that you use the following)
- ../swift --external-gravity --stars --hydro --threads=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/HydroTests/KeplerianRing/run.sh b/examples/HydroTests/KeplerianRing/run.sh
index b11a0c1e52..daf7433096 100755
--- a/examples/HydroTests/KeplerianRing/run.sh
+++ b/examples/HydroTests/KeplerianRing/run.sh
@@ -9,7 +9,7 @@ then
fi
rm -rf keplerian_ring_*.hdf5
-../../swift --external-gravity --hydro --threads=1 --verbose=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/HydroTests/Noh_1D/run.sh b/examples/HydroTests/Noh_1D/run.sh
index 0260ce1035..fa8793964a 100755
--- a/examples/HydroTests/Noh_1D/run.sh
+++ b/examples/HydroTests/Noh_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 noh.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 noh.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 12
diff --git a/examples/HydroTests/Noh_2D/run.sh b/examples/HydroTests/Noh_2D/run.sh
index 1239ca1bc2..8a4740897c 100755
--- a/examples/HydroTests/Noh_2D/run.sh
+++ b/examples/HydroTests/Noh_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 12
diff --git a/examples/HydroTests/Noh_3D/run.sh b/examples/HydroTests/Noh_3D/run.sh
index 9a72fa7caa..f004b1e162 100755
--- a/examples/HydroTests/Noh_3D/run.sh
+++ b/examples/HydroTests/Noh_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 12
diff --git a/examples/HydroTests/PerturbedBox_3D/run.sh b/examples/HydroTests/PerturbedBox_3D/run.sh
index 1f6e29d35d..2090b49cd2 100755
--- a/examples/HydroTests/PerturbedBox_3D/run.sh
+++ b/examples/HydroTests/PerturbedBox_3D/run.sh
@@ -7,4 +7,4 @@ then
python3 makeIC.py 50
fi
-../../swift --hydro --threads=16 perturbedBox.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=16 perturbedBox.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/Rayleigh-Taylor_2D/run.sh b/examples/HydroTests/Rayleigh-Taylor_2D/run.sh
index 765c28f3d5..5d5a73fb33 100644
--- a/examples/HydroTests/Rayleigh-Taylor_2D/run.sh
+++ b/examples/HydroTests/Rayleigh-Taylor_2D/run.sh
@@ -10,6 +10,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --external-gravity --threads=8 rayleigh_taylor.yml 2>&1 | tee output.log
+../../../swift --hydro --external-gravity --threads=8 rayleigh_taylor.yml 2>&1 | tee output.log
python3 makeMovie.py -i 0 -f 1001
diff --git a/examples/HydroTests/SedovBlast_1D/run.sh b/examples/HydroTests/SedovBlast_1D/run.sh
index fb894e204b..fb82605166 100755
--- a/examples/HydroTests/SedovBlast_1D/run.sh
+++ b/examples/HydroTests/SedovBlast_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
+../../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 5
diff --git a/examples/HydroTests/SedovBlast_2D/run.sh b/examples/HydroTests/SedovBlast_2D/run.sh
index 60723f75db..04b3a39658 100755
--- a/examples/HydroTests/SedovBlast_2D/run.sh
+++ b/examples/HydroTests/SedovBlast_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
+../../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 5
diff --git a/examples/HydroTests/SedovBlast_3D/run.sh b/examples/HydroTests/SedovBlast_3D/run.sh
index a884d68dd4..10fc83f69e 100755
--- a/examples/HydroTests/SedovBlast_3D/run.sh
+++ b/examples/HydroTests/SedovBlast_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --limiter --threads=4 sedov.yml 2>&1 | tee output.log
+../../../swift --hydro --limiter --threads=4 sedov.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 5
diff --git a/examples/HydroTests/SineWavePotential_1D/run.sh b/examples/HydroTests/SineWavePotential_1D/run.sh
index 670f34383a..ed2e5d220a 100755
--- a/examples/HydroTests/SineWavePotential_1D/run.sh
+++ b/examples/HydroTests/SineWavePotential_1D/run.sh
@@ -6,7 +6,7 @@ then
python3 makeIC.py
fi
-../../swift --external-gravity --hydro --threads=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/HydroTests/SineWavePotential_2D/run.sh b/examples/HydroTests/SineWavePotential_2D/run.sh
index 670f34383a..ed2e5d220a 100755
--- a/examples/HydroTests/SineWavePotential_2D/run.sh
+++ b/examples/HydroTests/SineWavePotential_2D/run.sh
@@ -6,7 +6,7 @@ then
python3 makeIC.py
fi
-../../swift --external-gravity --hydro --threads=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/HydroTests/SineWavePotential_3D/run.sh b/examples/HydroTests/SineWavePotential_3D/run.sh
index 670f34383a..ed2e5d220a 100755
--- a/examples/HydroTests/SineWavePotential_3D/run.sh
+++ b/examples/HydroTests/SineWavePotential_3D/run.sh
@@ -6,7 +6,7 @@ then
python3 makeIC.py
fi
-../../swift --external-gravity --hydro --threads=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/HydroTests/SodShockSpherical_2D/run.sh b/examples/HydroTests/SodShockSpherical_2D/run.sh
index b2881737bd..c73a2cc669 100755
--- a/examples/HydroTests/SodShockSpherical_2D/run.sh
+++ b/examples/HydroTests/SodShockSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=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/HydroTests/SodShockSpherical_3D/run.sh b/examples/HydroTests/SodShockSpherical_3D/run.sh
index 4c5d16d78d..c4738438a7 100755
--- a/examples/HydroTests/SodShockSpherical_3D/run.sh
+++ b/examples/HydroTests/SodShockSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=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/HydroTests/SodShock_1D/run.sh b/examples/HydroTests/SodShock_1D/run.sh
index 62580ac397..b8bb071037 100755
--- a/examples/HydroTests/SodShock_1D/run.sh
+++ b/examples/HydroTests/SodShock_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/HydroTests/SodShock_2D/run.sh b/examples/HydroTests/SodShock_2D/run.sh
index f112c403a4..b3cf134fc7 100755
--- a/examples/HydroTests/SodShock_2D/run.sh
+++ b/examples/HydroTests/SodShock_2D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/HydroTests/SodShock_3D/run.sh b/examples/HydroTests/SodShock_3D/run.sh
index f84e7c3136..04440bb7fa 100755
--- a/examples/HydroTests/SodShock_3D/run.sh
+++ b/examples/HydroTests/SodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/HydroTests/SodShock_BCC_3D/run.sh b/examples/HydroTests/SodShock_BCC_3D/run.sh
index 4efc2d1f34..a845838b18 100755
--- a/examples/HydroTests/SodShock_BCC_3D/run.sh
+++ b/examples/HydroTests/SodShock_BCC_3D/run.sh
@@ -10,6 +10,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/HydroTests/SquareTest_2D/run.sh b/examples/HydroTests/SquareTest_2D/run.sh
index d966705d26..e6bd3191c5 100755
--- a/examples/HydroTests/SquareTest_2D/run.sh
+++ b/examples/HydroTests/SquareTest_2D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 square.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 square.yml 2>&1 | tee output.log
# Plot the solution
python3 plotSolution.py 40
diff --git a/examples/HydroTests/ToroTest2_1D/run.sh b/examples/HydroTests/ToroTest2_1D/run.sh
index abbef91a10..022c854838 100755
--- a/examples/HydroTests/ToroTest2_1D/run.sh
+++ b/examples/HydroTests/ToroTest2_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/HydroTests/ToroTest2_2D/run.sh b/examples/HydroTests/ToroTest2_2D/run.sh
index 3c78528ee6..f99b85432e 100755
--- a/examples/HydroTests/ToroTest2_2D/run.sh
+++ b/examples/HydroTests/ToroTest2_2D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 toroTest2.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/HydroTests/ToroTest2_3D/run.sh b/examples/HydroTests/ToroTest2_3D/run.sh
index 908b01b751..14fb22d2e0 100755
--- a/examples/HydroTests/ToroTest2_3D/run.sh
+++ b/examples/HydroTests/ToroTest2_3D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 toroTest2.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 toroTest2.yml 2>&1 | tee output.log
python3 plotSolution.py 1
diff --git a/examples/HydroTests/UniformBox_2D/run.sh b/examples/HydroTests/UniformBox_2D/run.sh
index baaeb63b1c..83afecc5e9 100755
--- a/examples/HydroTests/UniformBox_2D/run.sh
+++ b/examples/HydroTests/UniformBox_2D/run.sh
@@ -7,4 +7,4 @@ then
python3 makeIC.py 100
fi
-../../swift --hydro --threads=16 uniformPlane.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=16 uniformPlane.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/UniformBox_3D/run.sh b/examples/HydroTests/UniformBox_3D/run.sh
index 86e7ad3fb4..45bb31743a 100755
--- a/examples/HydroTests/UniformBox_3D/run.sh
+++ b/examples/HydroTests/UniformBox_3D/run.sh
@@ -7,4 +7,4 @@ then
python3 makeIC.py 100
fi
-../../swift --hydro --threads=16 uniformBox.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=16 uniformBox.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/VacuumSpherical_2D/run.sh b/examples/HydroTests/VacuumSpherical_2D/run.sh
index 3d124340f9..981a1d70e7 100755
--- a/examples/HydroTests/VacuumSpherical_2D/run.sh
+++ b/examples/HydroTests/VacuumSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=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/HydroTests/VacuumSpherical_3D/run.sh b/examples/HydroTests/VacuumSpherical_3D/run.sh
index 2db5eece8f..8db8b47a21 100755
--- a/examples/HydroTests/VacuumSpherical_3D/run.sh
+++ b/examples/HydroTests/VacuumSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=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/HydroTests/Vacuum_1D/run.sh b/examples/HydroTests/Vacuum_1D/run.sh
index bada61690f..224ba4afb9 100755
--- a/examples/HydroTests/Vacuum_1D/run.sh
+++ b/examples/HydroTests/Vacuum_1D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=1 vacuum.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=1 vacuum.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/HydroTests/Vacuum_2D/run.sh b/examples/HydroTests/Vacuum_2D/run.sh
index 5fb0f920ac..90c3c57bb5 100755
--- a/examples/HydroTests/Vacuum_2D/run.sh
+++ b/examples/HydroTests/Vacuum_2D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/HydroTests/Vacuum_3D/run.sh b/examples/HydroTests/Vacuum_3D/run.sh
index 25c8c925fd..855a006327 100755
--- a/examples/HydroTests/Vacuum_3D/run.sh
+++ b/examples/HydroTests/Vacuum_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
# Plot the result
python3 plotSolution.py 1
diff --git a/examples/IdealisedCluster/IdealisedCluster_M13/run.sh b/examples/IdealisedCluster/IdealisedCluster_M13/run.sh
index cef0623948..6a777d4e3e 100755
--- a/examples/IdealisedCluster/IdealisedCluster_M13/run.sh
+++ b/examples/IdealisedCluster/IdealisedCluster_M13/run.sh
@@ -24,4 +24,4 @@ then
../getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
+../../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
diff --git a/examples/IdealisedCluster/IdealisedCluster_M135/run.sh b/examples/IdealisedCluster/IdealisedCluster_M135/run.sh
index f807a3adb4..2310894992 100755
--- a/examples/IdealisedCluster/IdealisedCluster_M135/run.sh
+++ b/examples/IdealisedCluster/IdealisedCluster_M135/run.sh
@@ -24,4 +24,4 @@ then
../getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
+../../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
diff --git a/examples/IdealisedCluster/IdealisedCluster_M14/run.sh b/examples/IdealisedCluster/IdealisedCluster_M14/run.sh
index a7a9580e7f..38500cd97a 100755
--- a/examples/IdealisedCluster/IdealisedCluster_M14/run.sh
+++ b/examples/IdealisedCluster/IdealisedCluster_M14/run.sh
@@ -24,4 +24,4 @@ then
../getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
+../../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro --limiter --sync --black-holes idealised_cluster_M13.yml 2>&1 | tee output.log
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_NFW_MN/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_NFW_MN/run.sh
index 492eddc7b7..a11b784b49 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_NFW_MN/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_NFW_MN/run.sh
@@ -6,4 +6,4 @@ then
./getIC.sh
fi
-../../swift -g -G -s --threads=16 isolated_galaxy.yml
+../../../swift -g -G -s --threads=16 isolated_galaxy.yml
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
index b2dba5ab94..e0077289f6 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
@@ -6,7 +6,7 @@ then
./getIC.sh
fi
-../../swift --external-gravity --self-gravity --stars --threads=4 isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --external-gravity --self-gravity --stars --threads=4 isolated_galaxy.yml 2>&1 | tee output.log
echo "Make plots of conservation of total angular momentum"
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_feedback/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_feedback/run.sh
index 4c0315a266..702e6a2c3f 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_feedback/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_feedback/run.sh
@@ -30,7 +30,7 @@ then
./getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --hydro --limiter --sync isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --threads=16 --feedback --external-gravity --self-gravity --stars --star-formation --cooling --hydro --limiter --sync isolated_galaxy.yml 2>&1 | tee output.log
# Kennicutt-Schmidt law plot
python3 plotSolution.py 100
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
index b4c1a4581f..0356ba1815 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
@@ -6,7 +6,7 @@ then
./getIC.sh
fi
-../../swift --external-gravity --self-gravity --stars --threads=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/IsolatedGalaxy_sink/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_sink/run.sh
index dd61a52d4b..d23ced0a63 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_sink/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_sink/run.sh
@@ -14,4 +14,4 @@ then
./getIC.sh $filename
fi
-../../swift --hydro --sinks --stars --external-gravity --self-gravity --threads=8 isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --hydro --sinks --stars --external-gravity --self-gravity --threads=8 isolated_galaxy.yml 2>&1 | tee output.log
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
index 65f2f9ba0a..842caee52f 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
@@ -30,7 +30,7 @@ then
../getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --external-gravity --self-gravity --stars --star-formation --cooling --hydro isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --threads=16 --external-gravity --self-gravity --stars --star-formation --cooling --hydro isolated_galaxy.yml 2>&1 | tee output.log
# Kennicutt-Schmidt law plot
python3 plotSolution.py
diff --git a/examples/Makefile.am b/examples/Makefile.am
index 5dc5f613e2..3d865c8f99 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -15,75 +15,6 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-# Common flags
-MYFLAGS =
-
-# Add the source directory and the non-standard paths to the included library headers to CFLAGS
-AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/argparse $(HDF5_CPPFLAGS) \
- $(GSL_INCS) $(FFTW_INCS) $(NUMA_INCS) $(GRACKLE_INCS) $(OPENMP_CFLAGS) \
- $(CHEALPIX_CFLAGS)
-
-AM_LDFLAGS = $(HDF5_LDFLAGS)
-
-# Extra libraries.
-EXTRA_LIBS = $(GSL_LIBS) $(HDF5_LIBS) $(FFTW_LIBS) $(NUMA_LIBS) $(PROFILER_LIBS) \
- $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) \
- $(CHEALPIX_LIBS)
-
-# MPI libraries.
-MPI_LIBS = $(PARMETIS_LIBS) $(METIS_LIBS) $(MPI_THREAD_LIBS) $(FFTW_MPI_LIBS)
-MPI_FLAGS = -DWITH_MPI $(PARMETIS_INCS) $(METIS_INCS) $(FFTW_MPI_INCS)
-
-# Programs.
-bin_PROGRAMS = swift
-
-# Also build the FOF tool?
-if HAVESTANDALONEFOF
-bin_PROGRAMS += fof
-endif
-
-# Do we have the CSDS?
-if HAVECSDS
-LD_CSDS = ../csds/src/.libs/libcsds_writer.a
-else
-LD_CSDS =
-endif
-
-# Build MPI versions as well?
-if HAVEMPI
-bin_PROGRAMS += swift_mpi
-if HAVESTANDALONEFOF
-bin_PROGRAMS += fof_mpi
-endif
-endif
-
-# engine_policy_setaffinity is available?
-if HAVESETAFFINITY
-ENGINE_POLICY_SETAFFINITY=| engine_policy_setaffinity
-else
-ENGINE_POLICY_SETAFFINITY=
-endif
-
-# Sources for swift
-swift_SOURCES = main.c
-swift_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_LDADD = ../src/.libs/libswiftsim.a ../argparse/.libs/libargparse.a $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
-
-# Sources for swift_mpi, do we need an affinity policy for MPI?
-swift_mpi_SOURCES = main.c
-swift_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-swift_mpi_LDADD = ../src/.libs/libswiftsim_mpi.a ../argparse/.libs/libargparse.a $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
-
-# Sources for fof
-fof_SOURCES = main_fof.c
-fof_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-fof_LDADD = ../src/.libs/libswiftsim.a ../argparse/.libs/libargparse.a $(VELOCIRAPTOR_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
-
-# Sources for fof_mpi, do we need an affinity policy for MPI?
-fof_mpi_SOURCES = main_fof.c
-fof_mpi_CFLAGS = $(MYFLAGS) $(AM_CFLAGS) $(MPI_FLAGS) -DENGINE_POLICY="engine_policy_keep $(ENGINE_POLICY_SETAFFINITY)"
-fof_mpi_LDADD = ../src/.libs/libswiftsim_mpi.a ../argparse/.libs/libargparse.a $(MPI_LIBS) $(VELOCIRAPTOR_MPI_LIBS) $(EXTRA_LIBS) $(LD_CSDS)
-
# Scripts to generate ICs
EXTRA_DIST = Cooling/CoolingBox/coolingBox.yml Cooling/CoolingBox/plotEnergy.py Cooling/CoolingBox/makeIC.py Cooling/CoolingBox/run.sh Cooling/CoolingBox/getGlass.sh \
Cosmology/ConstantCosmoVolume/run.sh Cosmology/ConstantCosmoVolume/makeIC.py Cosmology/ConstantCosmoVolume/plotSolution.py Cosmology/ConstantCosmoVolume/constant_volume.yml \
diff --git a/examples/Planetary/EarthImpact/run.sh b/examples/Planetary/EarthImpact/run.sh
index 40ddcbb63a..b73dea6e0c 100755
--- a/examples/Planetary/EarthImpact/run.sh
+++ b/examples/Planetary/EarthImpact/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift -s -G -t 8 earth_impact.yml 2>&1 | tee output.log
+../../../swift -s -G -t 8 earth_impact.yml 2>&1 | tee output.log
# Plot the snapshots
python3 plot_solution.py
diff --git a/examples/Planetary/EvrardCollapse_3D/run.sh b/examples/Planetary/EvrardCollapse_3D/run.sh
index e96abc6d59..98e868bd10 100755
--- a/examples/Planetary/EvrardCollapse_3D/run.sh
+++ b/examples/Planetary/EvrardCollapse_3D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --self-gravity --threads=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/Planetary/GreshoVortex_3D/run.sh b/examples/Planetary/GreshoVortex_3D/run.sh
index f834a39046..06ca28c934 100755
--- a/examples/Planetary/GreshoVortex_3D/run.sh
+++ b/examples/Planetary/GreshoVortex_3D/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
# Plot the solution
python3 ../../HydroTests/GreshoVortex_3D/plotSolution.py 11
diff --git a/examples/Planetary/KelvinHelmholtz_2D/run.sh b/examples/Planetary/KelvinHelmholtz_2D/run.sh
index 385dbb8b0a..da61214236 100755
--- a/examples/Planetary/KelvinHelmholtz_2D/run.sh
+++ b/examples/Planetary/KelvinHelmholtz_2D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
# Plot the solution
diff --git a/examples/Planetary/SodShock_3D/run.sh b/examples/Planetary/SodShock_3D/run.sh
index 4b9bd2e277..652d760b30 100755
--- a/examples/Planetary/SodShock_3D/run.sh
+++ b/examples/Planetary/SodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
python3 ../../HydroTests/SodShock_3D/plotSolution.py 1
diff --git a/examples/Planetary/SquareTest_2D/run.sh b/examples/Planetary/SquareTest_2D/run.sh
index 4095bbc909..c62022fef2 100755
--- a/examples/Planetary/SquareTest_2D/run.sh
+++ b/examples/Planetary/SquareTest_2D/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --hydro --threads=4 square.yml 2>&1 | tee output.log
+../../../swift --hydro --threads=4 square.yml 2>&1 | tee output.log
# Plot the solution
python3 ../../HydroTests/SquareTest_2D/plotSolution.py 40
diff --git a/examples/QuickLymanAlpha/L050N0752/run.sh b/examples/QuickLymanAlpha/L050N0752/run.sh
index d3a457632a..6ba2a475d8 100755
--- a/examples/QuickLymanAlpha/L050N0752/run.sh
+++ b/examples/QuickLymanAlpha/L050N0752/run.sh
@@ -18,7 +18,7 @@ fi
# Threading options - run with threads and pinning (latter not required but improves performance)
# The corresponding parameter file for this run
-../../swift \
+../../../swift \
--cosmology --quick-lyman-alpha \
--threads=16 --pin \
qla_50.yml
diff --git a/examples/RadiativeTransferTests/Advection_1D/run.sh b/examples/RadiativeTransferTests/Advection_1D/run.sh
index 07e531811c..f0a3f3faa9 100755
--- a/examples/RadiativeTransferTests/Advection_1D/run.sh
+++ b/examples/RadiativeTransferTests/Advection_1D/run.sh
@@ -10,7 +10,7 @@ if [ ! -f advection_1D.hdf5 ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro \
--threads=4 \
--verbose=0 \
diff --git a/examples/RadiativeTransferTests/Advection_2D/run.sh b/examples/RadiativeTransferTests/Advection_2D/run.sh
index 18f4267d50..2ea05d8e38 100755
--- a/examples/RadiativeTransferTests/Advection_2D/run.sh
+++ b/examples/RadiativeTransferTests/Advection_2D/run.sh
@@ -17,7 +17,7 @@ then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro \
--threads=4 \
--verbose=0 \
diff --git a/examples/RadiativeTransferTests/CoolingTest/run.sh b/examples/RadiativeTransferTests/CoolingTest/run.sh
index 2cd76ea807..1b193840ca 100755
--- a/examples/RadiativeTransferTests/CoolingTest/run.sh
+++ b/examples/RadiativeTransferTests/CoolingTest/run.sh
@@ -10,7 +10,7 @@ if [ ! -f ./cooling_test.hdf5 ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro \
--threads=4 \
--verbose=0 \
@@ -21,7 +21,7 @@ fi
./rt_cooling_test.yml 2>&1 | tee output.log
# Wanna run with cooling, but no RT? This should do the trick
-# ../../swift \
+# ../../../swift \
# --hydro \
# --threads=4 \
# --verbose=0 \
diff --git a/examples/RadiativeTransferTests/HeatingTest/run.sh b/examples/RadiativeTransferTests/HeatingTest/run.sh
index 0fbb8d9d4d..24fe522a77 100755
--- a/examples/RadiativeTransferTests/HeatingTest/run.sh
+++ b/examples/RadiativeTransferTests/HeatingTest/run.sh
@@ -10,7 +10,7 @@ if [ ! -f ./heating_test.hdf5 ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro \
--threads=4 \
--verbose=0 \
diff --git a/examples/RadiativeTransferTests/IonMassFractionAdvectionTest_2D/run.sh b/examples/RadiativeTransferTests/IonMassFractionAdvectionTest_2D/run.sh
index 51346e2509..b5cff76a3f 100755
--- a/examples/RadiativeTransferTests/IonMassFractionAdvectionTest_2D/run.sh
+++ b/examples/RadiativeTransferTests/IonMassFractionAdvectionTest_2D/run.sh
@@ -16,7 +16,7 @@ if [ ! -f 'advect_ions.hdf5' ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro --threads=4 --stars --external-gravity \
--feedback --radiation \
advect_ions.yml 2>&1 | tee output.log
diff --git a/examples/RadiativeTransferTests/IonizationEquilibriumICSetupTest/run.sh b/examples/RadiativeTransferTests/IonizationEquilibriumICSetupTest/run.sh
index 9899b7cc7d..3933238a5e 100755
--- a/examples/RadiativeTransferTests/IonizationEquilibriumICSetupTest/run.sh
+++ b/examples/RadiativeTransferTests/IonizationEquilibriumICSetupTest/run.sh
@@ -9,7 +9,7 @@ if [ ! -f ./ionization_equilibrium_test.hdf5 ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro \
--threads=1 \
--verbose=0 \
diff --git a/examples/RadiativeTransferTests/RandomizedBox_3D/run.sh b/examples/RadiativeTransferTests/RandomizedBox_3D/run.sh
index 5446a4c5b2..174fda2baa 100755
--- a/examples/RadiativeTransferTests/RandomizedBox_3D/run.sh
+++ b/examples/RadiativeTransferTests/RandomizedBox_3D/run.sh
@@ -9,11 +9,11 @@ if [ ! -f 'randomized-sine.hdf5' ]; then
python3 makeIC.py
fi
-cmd=../../swift
+cmd=../../../swift
if [ $# -gt 0 ]; then
case "$1" in
g | gdb)
- cmd='gdb --args ../../swift'
+ cmd='gdb --args ../../../swift'
;;
*)
echo unknown cmdline param, running without gdb
diff --git a/examples/RadiativeTransferTests/StromgrenSphere_2D/run.sh b/examples/RadiativeTransferTests/StromgrenSphere_2D/run.sh
index 0cd01f0c2a..ccbcf316aa 100755
--- a/examples/RadiativeTransferTests/StromgrenSphere_2D/run.sh
+++ b/examples/RadiativeTransferTests/StromgrenSphere_2D/run.sh
@@ -20,7 +20,7 @@ if [ ! -f 'stromgrenSphere-2D.hdf5' ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro --threads=4 --stars --external-gravity \
--feedback --radiation \
stromgrenSphere-2D.yml 2>&1 | tee output.log
diff --git a/examples/RadiativeTransferTests/StromgrenSphere_2D/runPropagationTest.sh b/examples/RadiativeTransferTests/StromgrenSphere_2D/runPropagationTest.sh
index 8a5df06928..d1140fa1e9 100755
--- a/examples/RadiativeTransferTests/StromgrenSphere_2D/runPropagationTest.sh
+++ b/examples/RadiativeTransferTests/StromgrenSphere_2D/runPropagationTest.sh
@@ -21,7 +21,7 @@ if [ ! -f 'propagationTest-2D.hdf5' ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro --threads=4 --stars --external-gravity \
--feedback --radiation \
./propagationTest-2D.yml 2>&1 | tee output.log
diff --git a/examples/RadiativeTransferTests/StromgrenSphere_3D/run.sh b/examples/RadiativeTransferTests/StromgrenSphere_3D/run.sh
index e5edd2c7d3..f9a1e1fc12 100755
--- a/examples/RadiativeTransferTests/StromgrenSphere_3D/run.sh
+++ b/examples/RadiativeTransferTests/StromgrenSphere_3D/run.sh
@@ -16,7 +16,7 @@ if [ ! -f 'stromgrenSphere-3D.hdf5' ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro --threads=4 --stars --external-gravity \
--feedback --radiation \
stromgrenSphere-3D.yml 2>&1 | tee output.log
diff --git a/examples/RadiativeTransferTests/StromgrenSphere_3D/runPropagationTest.sh b/examples/RadiativeTransferTests/StromgrenSphere_3D/runPropagationTest.sh
index 06b3683b80..3134a61e73 100755
--- a/examples/RadiativeTransferTests/StromgrenSphere_3D/runPropagationTest.sh
+++ b/examples/RadiativeTransferTests/StromgrenSphere_3D/runPropagationTest.sh
@@ -16,7 +16,7 @@ if [ ! -f 'propagationTest-3D.hdf5' ]; then
fi
# Run SWIFT with RT
-../../swift \
+../../../swift \
--hydro --threads=4 --stars --external-gravity \
--feedback --radiation \
./propagationTest-3D.yml 2>&1 | tee output.log
diff --git a/examples/RadiativeTransferTests/UniformBox_3D/run.sh b/examples/RadiativeTransferTests/UniformBox_3D/run.sh
index e3cebd4932..9f81af658a 100755
--- a/examples/RadiativeTransferTests/UniformBox_3D/run.sh
+++ b/examples/RadiativeTransferTests/UniformBox_3D/run.sh
@@ -9,11 +9,11 @@ if [ ! -f 'uniformBox-rt.hdf5' ]; then
python3 makeIC.py
fi
-cmd=../../swift
+cmd=../../../swift
if [ $# -gt 0 ]; then
case "$1" in
g | gdb)
- cmd='gdb --args ../../swift'
+ cmd='gdb --args ../../../swift'
;;
*)
echo unknown cmdline param, running without gdb
diff --git a/examples/SantaBarbara/SantaBarbara-128/run.sh b/examples/SantaBarbara/SantaBarbara-128/run.sh
index 72c219acb2..b965ed1355 100755
--- a/examples/SantaBarbara/SantaBarbara-128/run.sh
+++ b/examples/SantaBarbara/SantaBarbara-128/run.sh
@@ -1,4 +1,4 @@
#!/bin/bash
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
+../../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
diff --git a/examples/SantaBarbara/SantaBarbara-256/run.sh b/examples/SantaBarbara/SantaBarbara-256/run.sh
index 72c219acb2..b965ed1355 100755
--- a/examples/SantaBarbara/SantaBarbara-256/run.sh
+++ b/examples/SantaBarbara/SantaBarbara-256/run.sh
@@ -1,4 +1,4 @@
#!/bin/bash
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
+../../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
index f909a7c98d..842dfea762 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
@@ -8,5 +8,5 @@ then
fi
# Run SWIFT
-../../swift --cosmology --self-gravity --power --threads=8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
+../../../swift --cosmology --self-gravity --power --threads=8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/run.sh
index 7008adcaf4..cf8009dfdd 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_Snipshots/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --threads=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
python3 plotTempEvolution.py
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
index 12019fa486..1dbbda5484 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --velociraptor --threads=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/SmallCosmoVolume_cooling/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
index aa1f8e5da1..be0b80ed8b 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
@@ -19,7 +19,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --cooling --threads=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
python3 plotTempEvolution.py
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
index 7008adcaf4..cf8009dfdd 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
@@ -8,7 +8,7 @@ then
fi
# Run SWIFT
-../../swift --cosmology --hydro --self-gravity --threads=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
python3 plotTempEvolution.py
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_lightcone/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_lightcone/run.sh
index bd87ae715d..314d173f7c 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_lightcone/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_lightcone/run.sh
@@ -33,6 +33,6 @@ fi
# Run SWIFT
-../../swift --cosmology --eagle --lightcone --pin --threads=8 \
+../../../swift --cosmology --eagle --lightcone --pin --threads=8 \
small_cosmo_volume.yml 2>&1 | tee output.log
diff --git a/examples/SubgridTests/CosmologicalStellarEvolution/run.sh b/examples/SubgridTests/CosmologicalStellarEvolution/run.sh
index d670f8a65d..c54d1005cc 100755
--- a/examples/SubgridTests/CosmologicalStellarEvolution/run.sh
+++ b/examples/SubgridTests/CosmologicalStellarEvolution/run.sh
@@ -32,22 +32,22 @@ then
./getSolutions.sh
fi
-../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.08 -P EAGLEChemistry:init_abundance_Hydrogen:0.71 -P EAGLEChemistry:init_abundance_Helium:0.21 2>&1 | tee output_0p08.log
+../../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.08 -P EAGLEChemistry:init_abundance_Hydrogen:0.71 -P EAGLEChemistry:init_abundance_Helium:0.21 2>&1 | tee output_0p08.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.04 -P EAGLEChemistry:init_abundance_Hydrogen:0.74 -P EAGLEChemistry:init_abundance_Helium:0.23 2>&1 | tee output_0p04.log
+../../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.04 -P EAGLEChemistry:init_abundance_Hydrogen:0.74 -P EAGLEChemistry:init_abundance_Helium:0.23 2>&1 | tee output_0p04.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.01 2>&1 | tee output_0p01.log
+../../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.01 2>&1 | tee output_0p01.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.001 2>&1 | tee output_0p001.log
+../../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.001 2>&1 | tee output_0p001.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.0001 2>&1 | tee output_0p0001.log
+../../../swift --temperature --feedback --stars --hydro --cosmology --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.0001 2>&1 | tee output_0p0001.log
python3 plot_box_evolution.py
diff --git a/examples/SubgridTests/ParticleSplitting/run.sh b/examples/SubgridTests/ParticleSplitting/run.sh
index 4dcefb9e71..9ce32ccf6e 100644
--- a/examples/SubgridTests/ParticleSplitting/run.sh
+++ b/examples/SubgridTests/ParticleSplitting/run.sh
@@ -8,6 +8,6 @@ fi
# A very simple invocation for this one...
-../../swift --hydro -t 4 particle_splitting.yml
+../../../swift --hydro -t 4 particle_splitting.yml
python3 plotSolution.py
diff --git a/examples/SubgridTests/PressureFloor/run.sh b/examples/SubgridTests/PressureFloor/run.sh
index cb0ba2042b..3fecdb9b33 100644
--- a/examples/SubgridTests/PressureFloor/run.sh
+++ b/examples/SubgridTests/PressureFloor/run.sh
@@ -15,7 +15,7 @@ fi
rm pressureFloor_*
# Run SWIFT
-../../swift --self-gravity --hydro --cooling --threads=8 pressureFloor.yml
+../../../swift --self-gravity --hydro --cooling --threads=8 pressureFloor.yml
# Check if the simulation collapsed
python3 plotDensity.py 80
diff --git a/examples/SubgridTests/SmoothedMetallicity/run.sh b/examples/SubgridTests/SmoothedMetallicity/run.sh
index bc477def4e..caa9e32dc8 100755
--- a/examples/SubgridTests/SmoothedMetallicity/run.sh
+++ b/examples/SubgridTests/SmoothedMetallicity/run.sh
@@ -13,7 +13,7 @@ then
fi
# Run SWIFT
-../../swift --steps=1 --hydro --threads=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
python3 plotSolution.py 1
diff --git a/examples/SubgridTests/StellarEvolution/run.sh b/examples/SubgridTests/StellarEvolution/run.sh
index a3fa284be1..7d2759e71e 100755
--- a/examples/SubgridTests/StellarEvolution/run.sh
+++ b/examples/SubgridTests/StellarEvolution/run.sh
@@ -32,22 +32,22 @@ then
./getSolutions.sh
fi
-../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.08 -P EAGLEChemistry:init_abundance_Hydrogen:0.71 -P EAGLEChemistry:init_abundance_Helium:0.21 2>&1 | tee output_0p08.log
+../../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.08 -P EAGLEChemistry:init_abundance_Hydrogen:0.71 -P EAGLEChemistry:init_abundance_Helium:0.21 2>&1 | tee output_0p08.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.04 -P EAGLEChemistry:init_abundance_Hydrogen:0.74 -P EAGLEChemistry:init_abundance_Helium:0.23 2>&1 | tee output_0p04.log
+../../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.04 -P EAGLEChemistry:init_abundance_Hydrogen:0.74 -P EAGLEChemistry:init_abundance_Helium:0.23 2>&1 | tee output_0p04.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.01 2>&1 | tee output_0p01.log
+../../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.01 2>&1 | tee output_0p01.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.001 2>&1 | tee output_0p001.log
+../../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.001 2>&1 | tee output_0p001.log
python3 plot_box_evolution.py
-../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.0001 2>&1 | tee output_0p0001.log
+../../../swift --temperature --feedback --stars --hydro --external-gravity --threads=4 stellar_evolution.yml -P EAGLEChemistry:init_abundance_metal:0.0001 2>&1 | tee output_0p0001.log
python3 plot_box_evolution.py
diff --git a/examples/nIFTyCluster/Baryonic/run.sh b/examples/nIFTyCluster/Baryonic/run.sh
index 7c9451fa36..351874e30e 100755
--- a/examples/nIFTyCluster/Baryonic/run.sh
+++ b/examples/nIFTyCluster/Baryonic/run.sh
@@ -10,4 +10,4 @@
#SBATCH -t 72:00:00
-../../swift --cosmology --hydro --self-gravity -v 1 --pin --threads=56 nifty.yml
+../../../swift --cosmology --hydro --self-gravity -v 1 --pin --threads=56 nifty.yml
diff --git a/examples/main.c b/swift.c
similarity index 100%
rename from examples/main.c
rename to swift.c
diff --git a/examples/main_fof.c b/swift_fof.c
similarity index 100%
rename from examples/main_fof.c
rename to swift_fof.c
--
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