diff --git a/Makefile.am b/Makefile.am
index d426d8adc6c9a01eee8689d6030bad389d525cb8..2c1af34d8df7b0bf83e6421c02db711c160cae3e 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 5c32bd3c4ec4f426278d424e4e5396d11bd901dc..e04d081c0bb635b3334c05b5438cbbfcd7f2bd7a 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 710613ec9a431a007ed7b83e2d5634ee24eea7ec..2bf33de8a0217f0b7e1c2a70f0446678355529cd 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 28b5465a52f8e5e46cccc192398819c872b0d34f..d83974dd34c71310d1eca7c7376de83fd20d3210 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 ba7b00467928774dd832f8007509a1b0d7f99fd7..e22a3c50d166873c060a723533c8e5b7ace08367 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 fa71cf5d8ac45ed67440f5138d81bfc0d8400f0d..1c7346b2b478e3a7c67403a5ecd56689f75b029a 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 c9bf2aea7edd33886219dd4db822d930baff7d47..d771ac8aaa0cbfbe5c25fedc72117228efc910b4 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 310ea98f898c4327adf511f854b48fe6c50c4a2e..c0bb534c40c42c8085e9ef9ffb45ca606484f07a 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 5e3853f1e196a2bedfcb32579209fd2f614cfadc..e2ff84caa59af30ad50977e676e7106075957a32 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 d709955bfc3f8a158ecd6d6410a766559eeb94e4..34b0dffd8d5f5dde8314c23d00cc2bb8ad08577a 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 521700093411b034aad3500e0ee0f54993f2f7ec..73afff14c7e399be5062b56901848a11a226eee1 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 205af5a415c04c71cc8c2a3c8144bd8f9789dd8a..42ee57ddfbd62c45752314ac43e39d943c6acbb8 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 04951925eff6e4aa67cec620d96a3b79fcf9cee0..29b8de6a975a0800b5b580b06e946a79e984156e 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 9c0e0ccdcbbdd52b14230d98393637e99d9ad80f..384744e0d791dbc8f2ce82e94d7a0753b288eb92 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 d0122d103199d7c2468a6081d1b2921620929e02..e070ed6e3ad3697333a61dce5514b39339b76c12 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 85013713f1293b79a0ca5962cb6f7da8f8cdef07..4eef7c46471f1d4189a595b4b3b9cb6980fe379f 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 be3cdd8e3cbc4cdbb0d8ab039bbbaa0f8e9ce2a1..5c118c26dd2c2226abfff15f6930e0903671de8b 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 669fa49823cd65ff336c60964e5e565e925c53c5..c065cef8f612709480ab62b842a7beb1d2fe58a4 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 6d96edda655c7bf2d18ab8312417722f78bdb7e0..fd6e36b1db16ebdc375abfb1150cb5f06d4c060e 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 8a08d0b0408c39f58a53aeff660123f6afc5777b..069e0efc31d623e7e8fd58a711ea647b95f09626 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 8b40bdda3674e646219bf44f906cf3ce1b299940..7b2d0e95bc83036cddba847e0acb405a198dbb13 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 aaba58f266ffd6dc77707c45be0bec0218282328..0140f598a2697209756731934121186b946fcdfa 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 1e7d79fe57e18ff6ec1a43696675867caba8202c..04635c149fa19181386880f79034f413c96f8848 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 1db1a6e96f1d58c1ad0a594b17bb3b192450a9e6..200fab538cb38515c0df665c9191139fd9cd9960 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 e49cc93f2d4ded7f98ece06fe86b533d6a6a7969..026019b44d05d8d8272b49c5baa2d7c2b8f4ef6c 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 9d4cca708513cc89218547ddde27482e052b7e7c..83f388aeb01c968aa4aac2cd50b9065993cee96b 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 51f7295d982798fe123e160345301713adad374b..aa1064d380a97740c918ee961a7316822b5b8f43 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 28571d4803cb8c26bf67d84870c10a2e7dcf534c..2e22a655c855dea8aaa3cc175ee1d6b102db6eb2 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 bceddf338ae797abcc32c24fb2642320d9091ba9..80c76970b75909fc6ea50a95af051bbe8846e78e 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 ea14dbde3293bb28f98de29eb035d53bc7caa1e6..aae44b01a1c116407293a22ca5c79dd9f6ef551a 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 e2f2836900bacf612acb289154de973cda90eccb..5a053a4054a4397939530209428100b8080e241c 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 aec7449e2dbec7f5aadc5e075fd1f75a31da5d83..f7db75e6e3667f20c8fb50003955a0f82c19a32c 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 cab3a822a9b61aa9c32558e60296af66d3b0db8a..f0438966ed61e966318c03621e2450935bd7f037 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 6d8609cb0fd26b5daa5bf6593b8e5c929abcc5d7..0ff0482c5c9285074e35e4aff93ff85d325506e4 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 b2956e086d61a5042fb131bdc061c9b8950899fc..9a32b86a479f2c32108ec973b0f1ccc2dd308b73 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 8760786e1ebee86037c9ac8575415d8a10498e62..141e6af26f5a1052690c665dab3fdf676a31f34d 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 5716b254b6751a89a31bfde61389bc853fd8b80f..2986b8a7ea938da7e1cde6b8d7605d95600f74c8 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 0e18efb2b25eac98a64d676e48880c2d79d1a1db..73cc77029ef1b5812850147e6fe146b45c88634c 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 c732f5e8c0e05c79517f75b1fd95c396a84bc3d6..54e48c923c198cf461a106ad98a990c95b3391b6 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 3d1655649181819d18d7cb869a1e64b7219abd12..5b4973ab7967a06f8f1c7939224f0c636f6d5aac 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 382b72c14c0d9bec6382748f2d189862ed7f01ee..2b015311b1b10c3e03b638f49d8c2babfdb64faf 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 c7ff7ede11aca5e7608588f2edf62d6291980eb6..9b04385a5b186a6088f8061a903d90d391dac62c 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 b1075399ffb6c7fd833be5e284991e379c193fef..ed7aea4cee33dd33bc38e5172e59dd173b3728d6 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 ebc6749b2e2230c6fb3b06c8d085883a144602ea..5fba6714f7cf83fa0e65552dbede7465ac26c234 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 3a0fbe424896e011550a3668ae717323632fb142..bab705720d7787b3abda704b70c88f15bf3014b2 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 255ee48d8dc1932d02dec0b797865336fdd6cf4e..6d9fb639b5903b0b953e49ccfb86ae98f2af6cd6 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 f94f7c10c3cd50ae066539c771737fb8de7c5519..eeae68c7a7f1d0a7b97aa62140419d7026b4c076 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 15c87c734e239a120863fc5b12c87a8b7f2d5ecc..87cb2dd2b6a63999d16f521c8dced85cf2342825 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 9d25f52432c6f934f42d0109e057fd4f8d47f820..38871c80c1bfd20dcfb2d1047e65a83ae9db619d 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 cb6d98cae7ecfb160b85f4aacd620315f3c54233..d665a5970c1899891ed75fce6bfe43636358a809 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 e52a6e32c72e1d7370f67cab8d6dc80f309ecc12..0e1d99f89ec65b74f4bca7604cfd0bfa1c4194b9 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 8a9767404b2de4f35a6a0d68ee338a23dd369ea3..e6427788bd08041c31eab6ba1a514009e5ebfefb 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 d8075a89ce014b8cd237e6624acf6c6cb25a7218..fa994d00971b2fff5e421aa1e313aec7ff99b3d8 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 1127ab925b4bd66fc406bb8620b76387da529cae..1d7686e7fe9dfc49e3a2c42b774680624a338efa 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 54a35b2c7919cbf6578ed5519a389e6a3130d098..9139835bdbea88a80026f4a264a44bb60638882a 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 8d70102a297a377b772ce649b3847f689a8207e8..479de1398092dac3fc1275ffd1fc5741ff4c8c61 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 8d70102a297a377b772ce649b3847f689a8207e8..479de1398092dac3fc1275ffd1fc5741ff4c8c61 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 bedc6e6f2119bcb13cba863dcb79bc160f8042e4..583d270a7a0092f606bf782809aae66628862120 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 05af93484634e0d1ee2e851cd80ab765fc6a8c43..0ac9317f910ec265b1d9ea001e6c1ee09fc91a7d 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 b11a0c1e52f2792447ffe39efbdf5c7b2ddda437..daf743309663c6c3e84c90d53daea720917f411f 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 0260ce10352b865e4ac9884fbd91a13d63759c99..fa8793964ad3cf00e1ee6168ddea47ca94042a90 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 1239ca1bc2f66eb961686502603030a34dc84e2d..8a4740897cbb5b8e5d878436338e165f990f757a 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 9a72fa7caaaa7b526ef92ea7b32752a1d7a88b5c..f004b1e1628accb6be22262cd136ed979cbd42ff 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 1f6e29d35d09611297ff4a242a51599177f4b0b1..2090b49cd264eb41202fd413aa18434ae314ced1 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 765c28f3d51f101abd6a2de39da4791ff1eb9267..5d5a73fb331f16c8ab818ae6b2625b506d3d5293 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 fb894e204b54d688700d6abb29c41a35f0ee85db..fb82605166cbd9116160ff3e362d72590d2ecd1d 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 60723f75db0fca29745f72f8c576c9c337aa6e5a..04b3a39658b1056ad8dcede360f5f91bb67fb083 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 a884d68dd407295b49399229a3fff0f7900c6cfc..10fc83f69ef7b1b046ea2b197b60e4807db89d97 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 670f34383a07784095712db137225c57fa4c2e71..ed2e5d220ad0dc28cb9f69deca2d7e7eab446401 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 670f34383a07784095712db137225c57fa4c2e71..ed2e5d220ad0dc28cb9f69deca2d7e7eab446401 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 670f34383a07784095712db137225c57fa4c2e71..ed2e5d220ad0dc28cb9f69deca2d7e7eab446401 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 b2881737bd343e2d52c171860d0c7a4083bf3b5c..c73a2cc6693df5c1b4d5323879b676cb6f30aafa 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 4c5d16d78ddef94d25d7b3d6cccfacd406c084ca..c4738438a702415e375b235cbff46430d32074ea 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 62580ac39709bf63b7e383ea2521df1b7f11bb49..b8bb071037e4278a90aed3a40131021f86d90db0 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 f112c403a448343909b8fe7bdba8d7f43f0a821f..b3cf134fc76f3dd7ce7c1fc8feaaffe681c35750 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 f84e7c31368f131e9f32e0bb560393b3e9463f61..04440bb7fa0c71cf23b5c8e27bb181467f421627 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 4efc2d1f34c31ee91cc34d21a823a6ef896b932f..a845838b180420a59ef0dbaaa7b3a6503540bb22 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 d966705d264d4903cb62657f74f19cbe188f6e8e..e6bd3191c51ab961816d9bbffdf4084a8e48cb7c 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 abbef91a103187c71e92c4ff5e86cdfaae9775f9..022c8548389e42b4f27615fd3e7be5d62fb64e40 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 3c78528ee607acb60f35e36538bcce3824e39d35..f99b85432ec43e1497c7316dc526c832a7ea2c55 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 908b01b751752f3cfba829f5dd14c2b8a82b5367..14fb22d2e0f2ad4a93d965fe775c2dbf39647a60 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 baaeb63b1c084f71de5715597ae908c5146e5c85..83afecc5e9ec7b017f21b85446d056f911c66b80 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 86e7ad3fb4cdce8566baec1c659e2dd1f4dd3a3f..45bb31743aeebbc37271643182e04597488cf6bb 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 3d124340f9669742964330ccd92c1751d640b4aa..981a1d70e767a1784d53044642b7d19fb116c5a4 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 2db5eece8fb8c2e02aaeb81855e85ea8ca93ef3c..8db8b47a216523acd8bd21ce7e47bd7f10dc392f 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 bada61690fa1c694a8b0d5d2f4a8b5acc64efec6..224ba4afb964d40502fb806f1c322e87f9eff017 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 5fb0f920acc6bfe84404f23c9b5a4f19d144a12f..90c3c57bb562b17c0156a90784918735a26b7f28 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 25c8c925fd7eff3b0274049f06634f509f73e5d9..855a006327ae2c859af255f4c09eaada32a54de5 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 cef06239482d1056eccacbf0c630bc8990bcdb92..6a777d4e3e8f08d41b3108f2e5668f902ec4e672 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 f807a3adb45973f756e1b0872c27a626288dbbe3..23108949920137da29db249128d10a35431c704c 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 a7a9580e7fc498a869d4bf47f5fdb0fd88d260dd..38500cd97aaed093402cc2c45eef867d73762109 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 492eddc7b7fcf2e0a192a7408bdf888f1ef5a1a6..a11b784b49dc19ae936acaab9b09cd72291c6b5c 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 b2dba5ab940d65bc8dd3e1f0869cb162385e90b8..e0077289f675dad6e21564f7dd26b65fb6034e08 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 4c0315a26606c31e01fc7272f1ebe8e08b30d3c9..702e6a2c3f355e4ea037179e2e945f90062c70d1 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 b4c1a4581f3c0565153d659b462acde5c68d717e..0356ba18155283c8bad8c558b406e841b78948db 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 dd61a52d4b8a7273629d549270dffbbaa5faf08a..d23ced0a634a913b111df4b22444726a8b3f7564 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_sink/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_sink/run.sh
@@ -14,4 +14,4 @@ then
./getIC.sh $filename
fi
-../../swift --hydro --sinks --stars --external-gravity --self-gravity --threads=8 isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --hydro --sinks --stars --external-gravity --self-gravity --threads=8 isolated_galaxy.yml 2>&1 | tee output.log
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
index 65f2f9ba0af75423260f6d8921e66e83baba967b..842caee52f224d98959d3a946e9400e7dcc759ba 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
@@ -30,7 +30,7 @@ then
../getEaglePhotometryTable.sh
fi
-../../swift --threads=16 --external-gravity --self-gravity --stars --star-formation --cooling --hydro isolated_galaxy.yml 2>&1 | tee output.log
+../../../swift --threads=16 --external-gravity --self-gravity --stars --star-formation --cooling --hydro isolated_galaxy.yml 2>&1 | tee output.log
# Kennicutt-Schmidt law plot
python3 plotSolution.py
diff --git a/examples/Makefile.am b/examples/Makefile.am
index 5dc5f613e2c23eede866ab25f47144d207ef4dcf..3d865c8f99e757b50d98a02afa1614bd25adc189 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -15,75 +15,6 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-# Common flags
-MYFLAGS =
-
-# Add the source directory and the non-standard paths to the included library headers to CFLAGS
-AM_CFLAGS = -I$(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 40ddcbb63a74751fc9a623e17a0d9bbe94360cb2..b73dea6e0c938ace0de0fe4fa82d5a6c1102fc2a 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 e96abc6d590312700d41fd4f594bf57cb2da0d99..98e868bd1037d38251c0587d981f4364acc5d61b 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 f834a3904670bc9beaa80d7f764c547aa0b25b09..06ca28c934ddbd64fe251ebced0e4f5d1f231c54 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 385dbb8b0a5039b95830727811a2fe823c3d49f6..da6121423688415d08dd1fdcd26bb457a5c8a9eb 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 4b9bd2e2771e57036c59ed606ff69700916b9bb2..652d760b3023354fa1179a8bc4985664e2c132cc 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 4095bbc909131f8f46fff413acb776319cd9f472..c62022fef2ae34ab8331b31a192538bf8a48f0ac 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 d3a457632a9af7e34af4c06120394600cf09741e..6ba2a475d8f37c4e6aa0f00ae858691436887a5f 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 07e531811c983aca11127eac6b08bf81c060535d..f0a3f3faa9e0283359adbbe1aede36edfa01853d 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 18f4267d504bc6a477e6ed6f9a9e099b4642631e..2ea05d8e385609e23036943121b2b2a1f13838f1 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 2cd76ea807e8c55beca5d8e78aba37c88d792132..1b193840caec2c81b69e10924bb79c5ed66a77a0 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 0fbb8d9d4df6c5c5d38d45b3cb9422ea11242086..24fe522a77d5278fba767579f419468d1a96b148 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 51346e2509df292d3368b7bcbd08b982d626ad0d..b5cff76a3f2d0985e32b5510416583cb4682b17d 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 9899b7cc7de3b1eae6f8ca3a8a571e94c6686c3e..3933238a5ebddeed6d724adf9627a98e156c8597 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 5446a4c5b212461c1d4a4626ee624d03f5e430e4..174fda2baad152abcd52c3abcd2afc1f34801e88 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 0cd01f0c2a4e106bd5eadf922be063b853123a77..ccbcf316aa1bba1c05e73f6b2748e0d69de0dce4 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 8a5df06928252dcd417c7843cbb86cfbeea33134..d1140fa1e97542b5d29b1fe479676bde292504cb 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 e5edd2c7d3dcb6a9febd71904d12e396cfb42ddb..f9a1e1fc128e321fb4242feffd51e062182bcb09 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 06b3683b80216c37ab37139c323752e08b6ed84d..3134a61e732a516b529ba5ca6a997b4cbffea8c8 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 e3cebd4932ef1b28bca6077d0cdcc051d2c83875..9f81af658a3af253ce1faf407ac39b4cdffe0867 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 72c219acb201b3a3541b6a08d799b21ba4638009..b965ed13559218cfe96ec35285e9129da0816b16 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 72c219acb201b3a3541b6a08d799b21ba4638009..b965ed13559218cfe96ec35285e9129da0816b16 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 f909a7c98dd03759d75927d4a7c277573833c790..842dfea7624417e9536b8e21d1b38574b0904e40 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 7008adcaf4f828ae9c97bb989cd3e51d41e54955..cf8009dfdd8b3f6883ea709702ef30a0931f5130 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 12019fa48625ff3c2e093177c33a53d5a66bba60..1dbbda548414824630f51ec3886c3500e4f4c3b1 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 aa1f8e5da1e3cbf6f7afbc2cf00b9ee527f02665..be0b80ed8bad5bc6a12f6a11ae34deb3405efed1 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 7008adcaf4f828ae9c97bb989cd3e51d41e54955..cf8009dfdd8b3f6883ea709702ef30a0931f5130 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 bd87ae715d751f83b92496ad8cdb2dfd930b0316..314d173f7cbdb6e838ad9dbe60e027f78f3390db 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 d670f8a65d32821f468f87a95ac2d184c0caeb01..c54d1005cc8c37f9b3e848fc7b457d9d5a19b18d 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 4dcefb9e715674785972288dc73b4b954bc38fcc..9ce32ccf6e42cbc10cb295a32947739f076aebac 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 cb0ba2042bb4853f3098269c3f96d4d17a021a83..3fecdb9b33a5e6e97956919fccd3459f6419dcee 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 bc477def4e04a3b88c9b6fc24c2fa9ce7c87e675..caa9e32dc8543a769826ddf390cff2d3565f1962 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 a3fa284be151b7f5d5da6e888d9839c00bbf34a5..7d2759e71e1b1d9639ac0ef8338733fde7e3f487 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 7c9451fa36f55102ffae74dde5f462f6a6d1a15d..351874e30eaeadb649ceff76f7b5036694a018c1 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