Revert "Merge branch 'master' into 'updated_MAC'"

This reverts commit bfc539fa, reversing changes made to 861e5f8b.

Revert "Merge branch 'master' into 'updated_MAC'"
6f6c3499 · Matthieu Schaller · 4dec23e9 · 6f6c3499 · 6f6c3499 · 6f6c3499
Commit 6f6c3499 authored 5 years ago by Matthieu Schaller
--- a/README
+++ b/README
@@ -40,7 +40,6 @@ Parameters:
    -u, --fof                         Run Friends-of-Friends algorithm and 
                                      black holes seeding.
    -x, --velociraptor                Run with structure finding.
-    --line-of-sight                   Run with line-of-sight outputs.
    --limiter                         Run with time-step limiter.
    --sync                            Run with time-step synchronization
                                      of particles hit by feedback events.

--- a/README.md
+++ b/README.md
@@ -127,7 +127,6 @@ Parameters:
    -u, --fof                         Run Friends-of-Friends algorithm to
                                      perform black hole seeding.
    -x, --velociraptor                Run with structure finding.
-    --line-of-sight                   Run with line-of-sight outputs.
    --limiter                         Run with time-step limiter.
    --sync                            Run with time-step synchronization
                                      of particles hit by feedback events.

--- a/configure.ac
+++ b/configure.ac
@@ -1383,17 +1383,6 @@ if test "$ax_cv_c_compiler_vendor" = "clang"; then
      AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
 fi
-# Check if we have native sincos and sincosf functions. If not failback to our
-# implementations. On Apple/CLANG we have __sincos, so also check for that
-# if the compiler is clang.
-AC_CHECK_LIB([m],[sincos], [AC_DEFINE([HAVE_SINCOS],1,[The sincos function is present.])])
-AC_CHECK_LIB([m],[sincosf], [AC_DEFINE([HAVE_SINCOSF],1,[The sincosf function is present.])])
-if test "$ax_cv_c_compiler_vendor" = "clang"; then
-      AC_CHECK_LIB([m],[__sincos], [AC_DEFINE([HAVE___SINCOS],1,[The __sincos function is present.])])
-      AC_CHECK_LIB([m],[__sincosf], [AC_DEFINE([HAVE___SINCOSF],1,[The __sincosf function is present.])])
-fi
 # Add warning flags by default, if these can be used. Option =error adds
 # -Werror to GCC, clang and Intel.  Note do this last as compiler tests may
 # become errors, if that's an issue don't use CFLAGS for these, use an AC_SUBST().

--- a/doc/RTD/source/CommandLineOptions/index.rst
+++ b/doc/RTD/source/CommandLineOptions/index.rst
@@ -37,7 +37,6 @@ can be found by typing ``./swift -h``:
    -u, --fof                         Run Friends-of-Friends algorithm to
                                      perform black hole seeding.
    -x, --velociraptor                Run with structure finding.
-    --line-of-sight                   Run with line-of-sight outputs.
    --limiter                         Run with time-step limiter.
    --sync                            Run with time-step synchronization
                                      of particles hit by feedback events.

--- a/doc/RTD/source/ImplementationDetails/index.rst
+++ b/doc/RTD/source/ImplementationDetails/index.rst
@@ -7,75 +7,8 @@
 Implementation details
 ======================
-This section contains technical information about internals of the code.
-Random number generator
-~~~~~~~~~~~~~~~~~~~~~~~
-Often subgrid models require random numbers, for this purpose 
-SWIFT has a random number generator. The random number generator
-of SWIFT is based on a combination of the standard `rand_r` and `erand48`
-random number generators. Since for some applications in cosmology
-we want to be able to sample random numbers with a probability lower than 
-:math:`10^{-8}`, we could not simply use the 32-bit `rand_r` due to its cut-off
-and spacing of around :math:`2^{-32} \approx 2 \times 10^{-10}`.
-For the `erand48` algorithm with 48 bits the spacing and cutoff are 
-significantly smaller and around :math:`2^{-48} \approx 3.5 \times 10^{-15}`,
-so this is very suitable for our applications. 
-Reproducible random numbers
---------------------------
-In our simulations we want to be able to reproduce the exact same random 
-numbers if we do exactly the same simulation twice. Because of this we 
-want to seed the random number generator in a reproducible way. In order to do this
-we seed with the particle ID of the current particle and the current 
-integer simulation time. 
-To produce several different types of random numbers we have an additional
-argument called the type of random number which is basically the nth random
-number for the specified seed, which is added to the particle ID, thus providing
-a distinct state per random number type.
-If the user wishes to run a simulation with a different set of random number,
-an option during the configuration (``--with-random-seed=INT``) is available.
-This option simply flip some bits in the initial number composed of the ID and the
-current simulation time through the binary operator XOR.
-Implementation
--------------
-Our random number generator packs the particle ID (plus the random number type) and
-the current simulation time as two 64-bit values, plus a constant 16-bit value,
-into a 144-bit buffer. This buffer is treated as an array of 9 `uint16` values.
-In a first pass we initialize the seed to 0 and run through the 9 `uint16` values,
-xor-ing them with the seed and calling `rand_r` on the seed to advance it. Using
-`rand_r` with the thus-generated seed, we generate a sequence of 9 16-bit values
-and xor them with the original 144-bit buffer.
-The 9 bytes of this modified buffer are then used for three passes of `erand48`,
-xor-ing the state in the same way as before. `erand48` is then called one final
-time with the last state, producing a random double-precision value with a
-48-bit mantissa.
-What to do if we break the random number generator?
---------------------------------------------------
-The most likely case is that the RNG is not strong enough for our application,
-in this case we could simply do multiple passes of both shuffling the state and
-generating the final value from the state. This increases the computational cost but
-will make the random number generator stronger. 
-An other case is that we need probabilities that are lower than :math:`1 \times 10^{-17}`,
-in this case we simply cannot use our random number generator and for example
-need to generate two random numbers in order to probe these low probabilities. 
------------------------------------------------------
 Generating new unique IDs
-~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------
 When spawning new particles (not converting them) for star formation or other
 similar processes, the code needs to create new unique particle IDs. This is

--- a/doc/RTD/source/LineOfSights/index.rst
+++ b/doc/RTD/source/LineOfSights/index.rst
-.. Snapshots
-   Matthieu Schaller, 23rd May 2020
-.. _line_of_sight:
-Line-of-sights outputs
-======================
-The line-of-sight outputs are designed to be processed by the
-``SpecWizard`` tool (`Theuns et al. 1998 <https://ui.adsabs.harvard.edu/abs/1998MNRAS.301..478T/>`_, 
-`Tepper-Garcia et al. 2011
-<https://ui.adsabs.harvard.edu/abs/2011MNRAS.413..190T/>`_).
-TO BE DONE.
--- a/doc/RTD/source/ParameterFiles/parameter_description.rst
+++ b/doc/RTD/source/ParameterFiles/parameter_description.rst
@@ -742,8 +742,7 @@ full section would be:
     delta_time:          1.02
     invoke_stf:          1
-Showing all the parameters for a basic non-cosmological hydro test-case, one
+Showing all the parameters for a basic hydro test-case, one would have:
-would have:
 .. code:: YAML
@@ -768,36 +767,6 @@ following pages:
 * :ref:`Output_list_label` (to have snapshots not evenly spaced in time),
 * :ref:`Output_selection_label` (to select what particle fields to write).
-.. _Parameters_line_of_sight:
-Line-of-sight outputs
---------------------
-The ``LineOfSight`` section of the parameter file contains all the options related to
-the dump of simulation outputs in the form of HDF5 :ref:`line_of_sight` data to
-be processed by the ``SpecWizard`` tool
-(See `Theuns et al. 1998 <https://ui.adsabs.harvard.edu/abs/1998MNRAS.301..478T/>`_,
-`Tepper-Garcia et al. 2011
-<https://ui.adsabs.harvard.edu/abs/2011MNRAS.413..190T/>`_). The parameters are:
-.. code:: YAML
-   LineOfSight:
-     basename:            los
-     scale_factor_first:  0.02    # Only used when running in cosmological mode
-     delta_time:          1.02
-     time_first:          0.01    # Only used when running in non-cosmological mode
-     output_list_on:      0       # Overwrite the regular output times with a list of output times
-     num_along_x:         0
-     num_along_y:         0
-     num_along_z:         100
-     allowed_los_range_x: [0, 100.]   # Range along the x-axis where LoS along Y or Z are allowed
-     allowed_los_range_y: [0, 100.]   # Range along the y-axis where LoS along X or Z are allowed
-     allowed_los_range_z: [0, 100.]   # Range along the z-axis where LoS along X or Y are allowed
-     range_when_shooting_down_x: 100. # Range along the x-axis of LoS along x
-     range_when_shooting_down_y: 100. # Range along the y-axis of LoS along y
-     range_when_shooting_down_z: 100. # Range along the z-axis of LoS along z
 .. _Parameters_fof:
 Friends-Of-Friends (FOF)

--- a/doc/RTD/source/index.rst
+++ b/doc/RTD/source/index.rst
@@ -23,14 +23,14 @@ difference is the parameter file that will need to be adapted for SWIFT.
   HydroSchemes/index
   TimeStepping/index
   SubgridModels/index
+   random
   Planetary/index
   FriendsOfFriends/index
-   VELOCIraptorInterface/index
-   LineOfSights/index
   EquationOfState/index
   ExternalPotentials/index
   NewOption/index
   Task/index
+   VELOCIraptorInterface/index
   AnalysisTools/index
   Logger/index
   ImplementationDetails/index
--- a/doc/RTD/source/random.rst
+++ b/doc/RTD/source/random.rst
+.. Random number generator
+   Folkert Nobels, 11th of July 2019
+Random number generator
+=======================
+Often subgrid models require random numbers, for this purpose 
+SWIFT has a random number generator. The random number generator
+of SWIFT is based on a combination of the standard `rand_r` and `erand48`
+random number generators. Since for some applications in cosmology
+we want to be able to sample random numbers with a probability lower than 
+:math:`10^{-8}`, we could not simply use the 32-bit `rand_r` due to its cut-off
+and spacing of around :math:`2^{-32} \approx 2 \times 10^{-10}`.
+For the `erand48` algorithm with 48 bits the spacing and cutoff are 
+significantly smaller and around :math:`2^{-48} \approx 3.5 \times 10^{-15}`,
+so this is very suitable for our applications. 
+Reproducible random numbers
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In our simulations we want to be able to reproduce the exact same random 
+numbers if we do exactly the same simulation twice. Because of this we 
+want to seed the random number generator in a reproducible way. In order to do this
+we seed with the particle ID of the current particle and the current 
+integer simulation time. 
+To produce several different types of random numbers we have an additional
+argument called the type of random number which is basically the nth random
+number for the specified seed, which is added to the particle ID, thus providing
+a distinct state per random number type.
+If the user wishes to run a simulation with a different set of random number,
+an option during the configuration (``--with-random-seed=INT``) is available.
+This option simply flip some bits in the initial number composed of the ID and the
+current simulation time through the binary operator XOR.
+Implementation
+~~~~~~~~~~~~~~
+Our random number generator packs the particle ID (plus the random number type) and
+the current simulation time as two 64-bit values, plus a constant 16-bit value,
+into a 144-bit buffer. This buffer is treated as an array of 9 `uint16` values.
+In a first pass we initialize the seed to 0 and run through the 9 `uint16` values,
+xor-ing them with the seed and calling `rand_r` on the seed to advance it. Using
+`rand_r` with the thus-generated seed, we generate a sequence of 9 16-bit values
+and xor them with the original 144-bit buffer.
+The 9 bytes of this modified buffer are then used for three passes of `erand48`,
+xor-ing the state in the same way as before. `erand48` is then called one final
+time with the last state, producing a random double-precision value with a
+48-bit mantissa.
+What to do if we break the random number generator?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The most likely case is that the RNG is not strong enough for our application,
+in this case we could simply do multiple passes of both shuffling the state and
+generating the final value from the state. This increases the computational cost but
+will make the random number generator stronger. 
+An other case is that we need probabilities that are lower than :math:`1 \times 10^{-17}`,
+in this case we simply cannot use our random number generator and for example
+need to generate two random numbers in order to probe these low probabilities. 
--- a/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
+++ b/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
@@ -91,15 +91,6 @@ InitialConditions:
  generate_gas_in_ics: 1             # Generate gas particles from the DM-only ICs
  cleanup_smoothing_lengths: 1       # Since we generate gas, make use of the (expensive) cleaning-up procedure.
-# Parameters of the line-of-sight outputs
-LineOfSight:
-  basename:            eagle_los
-  num_along_x:         0
-  num_along_y:         0
-  num_along_z:         100
-  scale_factor_first:  0.1
-  delta_time:          1.1
 # Impose primoridal metallicity
 EAGLEChemistry:
  init_abundance_metal:     0.
@@ -113,7 +104,6 @@ EAGLEChemistry:
  init_abundance_Silicon:   0.0
  init_abundance_Iron:      0.0
-# EAGLE cooling parameters
 EAGLECooling:
  dir_name:                ./coolingtables/
  H_reion_z:               7.5                 # Planck 2018
@@ -190,23 +180,15 @@ EAGLEFeedback:
 # EAGLE AGN model
 EAGLEAGN:
-  subgrid_seed_mass_Msun:             1.5e5      # Black hole subgrid mass at creation time in solar masses.
+  subgrid_seed_mass_Msun:           1.5e5      # Black hole subgrid mass at creation time in solar masses.
-  multi_phase_bondi:                  0          # Compute Bondi rates per neighbour particle?
+  max_eddington_fraction:           1.0        # Maximal allowed accretion rate in units of the Eddington rate.
-  with_angmom_limiter:                1          # Are we applying the Rosas-Guevara et al. (2015) viscous time-scale reduction term?
+  eddington_fraction_for_recording: 0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
-  viscous_alpha:                      1e6        # Normalisation constant of the viscous time-scale in the accretion reduction term
+  with_angmom_limiter:              1          # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
-  radiative_efficiency:               0.1        # Fraction of the accreted mass that gets radiated.
+  viscous_alpha:                    1e6        # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
-  max_eddington_fraction:             1.         # Maximal allowed accretion rate in units of the Eddington rate.
+  radiative_efficiency:             0.1        # Fraction of the accreted mass that gets radiated.
-  eddington_fraction_for_recording:   0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
+  coupling_efficiency:              0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
-  coupling_efficiency:                0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
+  AGN_delta_T_K:                    3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
-  AGN_delta_T_K:                      3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
+  AGN_num_ngb_to_heat:              1.         # Target number of gas neighbours to heat in an AGN feedback event.
-  AGN_num_ngb_to_heat:                1.         # Target number of gas neighbours to heat in an AGN feedback event.
+  max_reposition_mass:              2e8        # Maximal BH mass considered for BH repositioning in solar masses.
-  max_reposition_mass:                2e8        # Maximal BH mass considered for BH repositioning in solar masses.
+  threshold_major_merger:           0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  max_reposition_distance_ratio:      3.0        # Maximal distance a BH can be repositioned, in units of the softening length.
+  threshold_minor_merger:           0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  with_reposition_velocity_threshold: 1          # Should we only reposition to particles that move slowly w.r.t. the black hole?
-  max_reposition_velocity_ratio:      0.5        # Maximal velocity offset of a particle to reposition a BH to, in units of the ambient sound speed of the BH. Only meaningful if with_reposition_velocity_ratio is 1.
-  min_reposition_velocity_threshold: -1.0        # Minimal value of the velocity threshold for repositioning [km/s], set to < 0 for no effect. Only meaningful if with_reposition_velocity_ratio is 1.
-  set_reposition_speed:               0          # Should we reposition black holes with (at most) a prescribed speed towards the potential minimum?
-  threshold_major_merger:             0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  threshold_minor_merger:             0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  merger_threshold_type:              2          # Type of velocity threshold for BH mergers (0: v_circ at kernel edge, 1: v_esc at actual distance, with softening, 2: v_esc at actual distance, no softening).
-  merger_max_distance_ratio:          3.0        # Maximal distance over which two BHs can merge, in units of the softening length.
--- a/examples/EAGLE_ICs/EAGLE_12/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_12/run.sh
@@ -11,7 +11,7 @@ fi
 if [ ! -e yieldtables ]
 then
    echo "Fetching EAGLE yield tables..."
-    ../getEagleYieldTable.sh
+    ../getEagleYieldtable.sh
 fi
 if [ ! -e coolingtables ]

--- a/examples/EAGLE_ICs/EAGLE_25/eagle_25.yml
+++ b/examples/EAGLE_ICs/EAGLE_25/eagle_25.yml
@@ -91,15 +91,6 @@ InitialConditions:
  generate_gas_in_ics: 1             # Generate gas particles from the DM-only ICs
  cleanup_smoothing_lengths: 1       # Since we generate gas, make use of the (expensive) cleaning-up procedure.
-# Parameters of the line-of-sight outputs
-LineOfSight:
-  basename:            eagle_los
-  num_along_x:         0
-  num_along_y:         0
-  num_along_z:         100
-  scale_factor_first:  0.1
-  delta_time:          1.1
 # Impose primoridal metallicity
 EAGLEChemistry:
  init_abundance_metal:     0.
@@ -190,23 +181,15 @@ EAGLEFeedback:
 # EAGLE AGN model
 EAGLEAGN:
-  subgrid_seed_mass_Msun:             1.5e5      # Black hole subgrid mass at creation time in solar masses.
+  subgrid_seed_mass_Msun:           1.5e5      # Black hole subgrid mass at creation time in solar masses.
-  multi_phase_bondi:                  0          # Compute Bondi rates per neighbour particle?
+  max_eddington_fraction:           1.0        # Maximal allowed accretion rate in units of the Eddington rate.
-  with_angmom_limiter:                1          # Are we applying the Rosas-Guevara et al. (2015) viscous time-scale reduction term?
+  eddington_fraction_for_recording: 0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
-  viscous_alpha:                      1e6        # Normalisation constant of the viscous time-scale in the accretion reduction term
+  with_angmom_limiter:              1          # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
-  radiative_efficiency:               0.1        # Fraction of the accreted mass that gets radiated.
+  viscous_alpha:                    1e6        # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
-  max_eddington_fraction:             1.         # Maximal allowed accretion rate in units of the Eddington rate.
+  radiative_efficiency:             0.1        # Fraction of the accreted mass that gets radiated.
-  eddington_fraction_for_recording:   0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
+  coupling_efficiency:              0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
-  coupling_efficiency:                0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
+  AGN_delta_T_K:                    3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
-  AGN_delta_T_K:                      3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
+  AGN_num_ngb_to_heat:              1.         # Target number of gas neighbours to heat in an AGN feedback event.
-  AGN_num_ngb_to_heat:                1.         # Target number of gas neighbours to heat in an AGN feedback event.
+  max_reposition_mass:              2e8        # Maximal BH mass considered for BH repositioning in solar masses.
-  max_reposition_mass:                2e8        # Maximal BH mass considered for BH repositioning in solar masses.
+  threshold_major_merger:           0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  max_reposition_distance_ratio:      3.0        # Maximal distance a BH can be repositioned, in units of the softening length.
+  threshold_minor_merger:           0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  with_reposition_velocity_threshold: 1          # Should we only reposition to particles that move slowly w.r.t. the black hole?
-  max_reposition_velocity_ratio:      0.5        # Maximal velocity offset of a particle to reposition a BH to, in units of the ambient sound speed of the BH. Only meaningful if with_reposition_velocity_ratio is 1.
-  min_reposition_velocity_threshold: -1.0        # Minimal value of the velocity threshold for repositioning [km/s], set to < 0 for no effect. Only meaningful if with_reposition_velocity_ratio is 1.
-  set_reposition_speed:               0          # Should we reposition black holes with (at most) a prescribed speed towards the potential minimum?
-  threshold_major_merger:             0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  threshold_minor_merger:             0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  merger_threshold_type:              2          # Type of velocity threshold for BH mergers (0: v_circ at kernel edge, 1: v_esc at actual distance, with softening, 2: v_esc at actual distance, no softening).
-  merger_max_distance_ratio:          3.0        # Maximal distance over which two BHs can merge, in units of the softening length.
--- a/examples/EAGLE_ICs/EAGLE_25/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_25/run.sh
@@ -11,7 +11,7 @@ fi
 if [ ! -e yieldtables ]
 then
    echo "Fetching EAGLE yield tables..."
-    ../getEagleYieldTable.sh
+    ../getEagleYieldtable.sh
 fi
 if [ ! -e coolingtables ]

--- a/examples/EAGLE_ICs/EAGLE_50/eagle_50.yml
+++ b/examples/EAGLE_ICs/EAGLE_50/eagle_50.yml
@@ -89,15 +89,6 @@ InitialConditions:
  generate_gas_in_ics: 1             # Generate gas particles from the DM-only ICs
  cleanup_smoothing_lengths: 1       # Since we generate gas, make use of the (expensive) cleaning-up procedure.
-# Parameters of the line-of-sight outputs
-LineOfSight:
-  basename:            eagle_los
-  num_along_x:         0
-  num_along_y:         0
-  num_along_z:         100
-  scale_factor_first:  0.1
-  delta_time:          1.1
 # Impose primoridal metallicity
 EAGLEChemistry:
  init_abundance_metal:     0.
@@ -188,23 +179,15 @@ EAGLEFeedback:
 # EAGLE AGN model
 EAGLEAGN:
-  subgrid_seed_mass_Msun:             1.5e5      # Black hole subgrid mass at creation time in solar masses.
+  subgrid_seed_mass_Msun:           1.5e5      # Black hole subgrid mass at creation time in solar masses.
-  multi_phase_bondi:                  0          # Compute Bondi rates per neighbour particle?
+  max_eddington_fraction:           1.0        # Maximal allowed accretion rate in units of the Eddington rate.
-  with_angmom_limiter:                1          # Are we applying the Rosas-Guevara et al. (2015) viscous time-scale reduction term?
+  eddington_fraction_for_recording: 0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
-  viscous_alpha:                      1e6        # Normalisation constant of the viscous time-scale in the accretion reduction term
+  with_angmom_limiter:              1          # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
-  radiative_efficiency:               0.1        # Fraction of the accreted mass that gets radiated.
+  viscous_alpha:                    1e6        # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
-  max_eddington_fraction:             1.         # Maximal allowed accretion rate in units of the Eddington rate.
+  radiative_efficiency:             0.1        # Fraction of the accreted mass that gets radiated.
-  eddington_fraction_for_recording:   0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
+  coupling_efficiency:              0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
-  coupling_efficiency:                0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
+  AGN_delta_T_K:                    3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
-  AGN_delta_T_K:                      3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
+  AGN_num_ngb_to_heat:              1.         # Target number of gas neighbours to heat in an AGN feedback event.
-  AGN_num_ngb_to_heat:                1.         # Target number of gas neighbours to heat in an AGN feedback event.
+  max_reposition_mass:              2e8        # Maximal BH mass considered for BH repositioning in solar masses.
-  max_reposition_mass:                2e8        # Maximal BH mass considered for BH repositioning in solar masses.
+  threshold_major_merger:           0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  max_reposition_distance_ratio:      3.0        # Maximal distance a BH can be repositioned, in units of the softening length.
+  threshold_minor_merger:           0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  with_reposition_velocity_threshold: 1          # Should we only reposition to particles that move slowly w.r.t. the black hole?
-  max_reposition_velocity_ratio:      0.5        # Maximal velocity offset of a particle to reposition a BH to, in units of the ambient sound speed of the BH. Only meaningful if with_reposition_velocity_ratio is 1.
-  min_reposition_velocity_threshold: -1.0        # Minimal value of the velocity threshold for repositioning [km/s], set to < 0 for no effect. Only meaningful if with_reposition_velocity_ratio is 1.
-  set_reposition_speed:               0          # Should we reposition black holes with (at most) a prescribed speed towards the potential minimum?
-  threshold_major_merger:             0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  threshold_minor_merger:             0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  merger_threshold_type:              2          # Type of velocity threshold for BH mergers (0: v_circ at kernel edge, 1: v_esc at actual distance, with softening, 2: v_esc at actual distance, no softening).
-  merger_max_distance_ratio:          3.0        # Maximal distance over which two BHs can merge, in units of the softening length.
\ No newline at end of file
--- a/examples/EAGLE_ICs/EAGLE_50/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_50/run.sh
@@ -11,7 +11,7 @@ fi
 if [ ! -e yieldtables ]
 then
    echo "Fetching EAGLE yield tables..."
-    ../getEagleYieldTable.sh
+    ../getEagleYieldtable.sh
 fi
 if [ ! -e coolingtables ]

--- a/examples/EAGLE_ICs/EAGLE_50_low_res/README
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/README
-Initial conditions corresponding to the 50 Mpc volume
-of the EAGLE suite at 8x lower resolution.
-The ICs only contain DM particles. The gas particles will be generated in SWIFT.
--- a/examples/EAGLE_ICs/EAGLE_50_low_res/eagle_50.yml
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/eagle_50.yml
-# Define some meta-data about the simulation
-MetaData:
-  run_name:   EAGLE-L0050N0376-Ref
-# Define the system of units to use internally. 
-InternalUnitSystem:
-  UnitMass_in_cgs:     1.98841e43    # 10^10 M_sun in grams
-  UnitLength_in_cgs:   3.08567758e24 # Mpc in centimeters
-  UnitVelocity_in_cgs: 1e5           # km/s in centimeters per second
-  UnitCurrent_in_cgs:  1             # Amperes
-  UnitTemp_in_cgs:     1             # Kelvin
-# Cosmological parameters
-Cosmology:
-  h:              0.6777        # Reduced Hubble constant
-  a_begin:        0.0078125     # Initial scale-factor of the simulation
-  a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
-  Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0482519     # Baryon density parameter
-# Parameters governing the time integration
-TimeIntegration:
-  dt_min:     1e-10 # The minimal time-step size of the simulation (in internal units).
-  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
-# Parameters governing the snapshots
-Snapshots:
-  basename:            eagle # Common part of the name of output files
-  output_list_on:      1
-  output_list:         ./output_list.txt
-# Parameters governing the conserved quantities statistics
-Statistics:
-  delta_time:           1.02
-  scale_factor_first:   0.05
-# Parameters for the self-gravity scheme
-Gravity:
-  eta:                    0.025     # Constant dimensionless multiplier for time integration.
-  theta:                  0.7       # Opening angle (Multipole acceptance criterion)
-  mesh_side_length:       128
-  comoving_DM_softening:         0.006640 # Comoving softening for DM (6.67 ckpc)
-  max_physical_DM_softening:     0.002600 # Physical softening for DM (2.60 pkpc)
-  comoving_baryon_softening:     0.003580 # Comoving softening for baryons (3.58 ckpc)
-  max_physical_baryon_softening: 0.001400 # Physical softening for baryons (1.40 pkpc)
-  dithering:             0
-# Parameters for the hydrodynamics scheme
-SPH:
-  resolution_eta:                    1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
-  h_min_ratio:                       0.1      # Minimal smoothing length in units of softening.
-  h_max:                             0.5      # Maximal smoothing length in co-moving internal units.
-  CFL_condition:                     0.2      # Courant-Friedrich-Levy condition for time integration.
-  minimal_temperature:               100.0    # (internal units)
-  initial_temperature:               268.7    # (internal units)
-  particle_splitting:                1        # Particle splitting is ON
-  particle_splitting_mass_threshold: 5.6e-3   # (internal units, i.e. 5.6e7 Msun ~ 4x initial gas particle mass)
-# Parameters of the stars neighbour search
-Stars:
-  resolution_eta:        1.1642   # Target smoothing length in units of the mean inter-particle separation
-  h_tolerance:           7e-3
-# Parameters for the Friends-Of-Friends algorithm
-FOF:
-  basename:                        fof_output  # Filename for the FOF outputs.
-  min_group_size:                  32         # The minimum no. of particles required for a group.
-  linking_length_ratio:            0.2         # Linking length in units of the main inter-particle separation.
-  black_hole_seed_halo_mass_Msun:  1.5e10      # Minimal halo mass in which to seed a black hole (in solar masses).
-  scale_factor_first:              0.05        # Scale-factor of first FoF black hole seeding calls.
-  delta_time:                      1.00751     # Scale-factor ratio between consecutive FoF black hole seeding calls.
-Scheduler:
-  max_top_level_cells:   16
-  cell_split_size:       200
-Restarts:
-  onexit:       1
-  delta_hours:  6.0
-# Parameters related to the initial conditions
-InitialConditions:
-  file_name:  EAGLE_L0050N0376_ICs.hdf5
-  periodic:   1
-  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
-  cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
-  generate_gas_in_ics: 1             # Generate gas particles from the DM-only ICs
-  cleanup_smoothing_lengths: 1       # Since we generate gas, make use of the (expensive) cleaning-up procedure.
-# Parameters of the line-of-sight outputs
-LineOfSight:
-  basename:            eagle_los
-  num_along_x:         0
-  num_along_y:         0
-  num_along_z:         100
-  scale_factor_first:  0.1
-  delta_time:          1.1
-# Impose primoridal metallicity
-EAGLEChemistry:
-  init_abundance_metal:     0.
-  init_abundance_Hydrogen:  0.752
-  init_abundance_Helium:    0.248
-  init_abundance_Carbon:    0.0
-  init_abundance_Nitrogen:  0.0
-  init_abundance_Oxygen:    0.0
-  init_abundance_Neon:      0.0
-  init_abundance_Magnesium: 0.0
-  init_abundance_Silicon:   0.0
-  init_abundance_Iron:      0.0
-# EAGLE cooling parameters
-EAGLECooling:
-  dir_name:                ./coolingtables/
-  H_reion_z:               7.5                 # Planck 2018
-  H_reion_eV_p_H:          2.0
-  He_reion_z_centre:       3.5
-  He_reion_z_sigma:        0.5
-  He_reion_eV_p_H:         2.0
-# EAGLE star formation parameters
-EAGLEStarFormation:
-  EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
-  EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
-  EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
-  KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
-  KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
-  min_over_density:                  57.7      # The over-density above which star-formation is allowed.
-  KS_high_density_threshold_H_p_cm3: 1e3       # Hydrogen number density above which the Kennicut-Schmidt law changes slope in Hydrogen atoms per cm^3.
-  KS_high_density_exponent:          2.0       # Slope of the Kennicut-Schmidt law above the high-density threshold.
-  EOS_entropy_margin_dex:            0.5       # Logarithm base 10 of the maximal entropy above the EOS at which stars can form.
-  threshold_norm_H_p_cm3:            0.1       # Normalisation of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
-  threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
-  threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
-  threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
-# Parameters for the EAGLE "equation of state"
-EAGLEEntropyFloor:
-  Jeans_density_threshold_H_p_cm3: 0.1       # Physical density above which the EAGLE Jeans limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
-  Jeans_over_density_threshold:    10.       # Overdensity above which the EAGLE Jeans limiter entropy floor can kick in.
-  Jeans_temperature_norm_K:        8000      # Temperature of the EAGLE Jeans limiter entropy floor at the density threshold expressed in Kelvin.
-  Jeans_gamma_effective:           1.3333333 # Slope the of the EAGLE Jeans limiter entropy floor
-  Cool_density_threshold_H_p_cm3: 1e-5       # Physical density above which the EAGLE Cool limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
-  Cool_over_density_threshold:    10.        # Overdensity above which the EAGLE Cool limiter entropy floor can kick in.
-  Cool_temperature_norm_K:        8000       # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin.
-  Cool_gamma_effective:           1.         # Slope the of the EAGLE Cool limiter entropy floor
-# EAGLE feedback model
-EAGLEFeedback:
-  use_SNII_feedback:                1               # Global switch for SNII thermal (stochastic) feedback.
-  use_SNIa_feedback:                1               # Global switch for SNIa thermal (continuous) feedback.
-  use_AGB_enrichment:               1               # Global switch for enrichement from AGB stars.
-  use_SNII_enrichment:              1               # Global switch for enrichement from SNII stars.
-  use_SNIa_enrichment:              1               # Global switch for enrichement from SNIa stars.
-  filename:                         ./yieldtables/  # Path to the directory containing the EAGLE yield tables.
-  IMF_min_mass_Msun:                0.1             # Minimal stellar mass considered for the Chabrier IMF in solar masses.
-  IMF_max_mass_Msun:              100.0             # Maximal stellar mass considered for the Chabrier IMF in solar masses.
-  SNII_min_mass_Msun:               8.0             # Minimal mass considered for SNII stars in solar masses.
-  SNII_max_mass_Msun:             100.0             # Maximal mass considered for SNII stars in solar masses.
-  SNII_sampled_delay:               1               # Sample the SNII lifetimes to do feedback.
-  SNII_delta_T_K:                   3.16228e7       # Change in temperature to apply to the gas particle in a SNII thermal feedback event in Kelvin.
-  SNII_energy_erg:                  1.0e51          # Energy of one SNII explosion in ergs.
-  SNII_energy_fraction_min:         0.3             # Minimal fraction of energy applied in a SNII feedback event.
-  SNII_energy_fraction_max:         3.0             # Maximal fraction of energy applied in a SNII feedback event.
-  SNII_energy_fraction_Z_0:         0.0012663729    # Pivot point for the metallicity dependance of the SNII energy fraction (metal mass fraction).
-  SNII_energy_fraction_n_0_H_p_cm3: 1.4588          # Pivot point for the birth density dependance of the SNII energy fraction in cm^-3.
-  SNII_energy_fraction_n_Z:         0.8686          # Power-law for the metallicity dependance of the SNII energy fraction.
-  SNII_energy_fraction_n_n:         0.8686          # Power-law for the birth density dependance of the SNII energy fraction.
-  SNIa_DTD:                         Exponential     # Functional form of the SNIa delay time distribution.
-  SNIa_DTD_delay_Gyr:               0.04            # Stellar age after which SNIa start in Gyr (40 Myr corresponds to stars ~ 8 Msun).
-  SNIa_DTD_exp_timescale_Gyr:       2.0             # Time-scale of the exponential decay of the SNIa rates in Gyr.
-  SNIa_DTD_exp_norm_p_Msun:         0.002           # Normalisation of the SNIa rates in inverse solar masses.
-  SNIa_energy_erg:                 1.0e51           # Energy of one SNIa explosion in ergs.
-  AGB_ejecta_velocity_km_p_s:      10.0             # Velocity of the AGB ejectas in km/s.
-  stellar_evolution_age_cut_Gyr:    0.1             # Stellar age in Gyr above which the enrichment is down-sampled.
-  stellar_evolution_sampling_rate:   10             # Number of time-steps in-between two enrichment events for a star above the age threshold.
-  SNII_yield_factor_Hydrogen:       1.0             # (Optional) Correction factor to apply to the Hydrogen yield from the SNII channel.
-  SNII_yield_factor_Helium:         1.0             # (Optional) Correction factor to apply to the Helium yield from the SNII channel.
-  SNII_yield_factor_Carbon:         0.5             # (Optional) Correction factor to apply to the Carbon yield from the SNII channel.
-  SNII_yield_factor_Nitrogen:       1.0             # (Optional) Correction factor to apply to the Nitrogen yield from the SNII channel.
-  SNII_yield_factor_Oxygen:         1.0             # (Optional) Correction factor to apply to the Oxygen yield from the SNII channel.
-  SNII_yield_factor_Neon:           1.0             # (Optional) Correction factor to apply to the Neon yield from the SNII channel.
-  SNII_yield_factor_Magnesium:      2.0             # (Optional) Correction factor to apply to the Magnesium yield from the SNII channel.
-  SNII_yield_factor_Silicon:        1.0             # (Optional) Correction factor to apply to the Silicon yield from the SNII channel.
-  SNII_yield_factor_Iron:           0.5             # (Optional) Correction factor to apply to the Iron yield from the SNII channel.
-# EAGLE AGN model
-EAGLEAGN:
-  subgrid_seed_mass_Msun:             1.5e5      # Black hole subgrid mass at creation time in solar masses.
-  multi_phase_bondi:                  0          # Compute Bondi rates per neighbour particle?
-  with_angmom_limiter:                1          # Are we applying the Rosas-Guevara et al. (2015) viscous time-scale reduction term?
-  viscous_alpha:                      1e6        # Normalisation constant of the viscous time-scale in the accretion reduction term
-  radiative_efficiency:               0.1        # Fraction of the accreted mass that gets radiated.
-  max_eddington_fraction:             1.         # Maximal allowed accretion rate in units of the Eddington rate.
-  eddington_fraction_for_recording:   0.1        # Record the last time BHs reached an Eddington ratio above this threshold.
-  coupling_efficiency:                0.15       # Fraction of the radiated energy that couples to the gas in feedback events.
-  AGN_delta_T_K:                      3.16228e8  # Change in temperature to apply to the gas particle in an AGN feedback event in Kelvin.
-  AGN_num_ngb_to_heat:                1.         # Target number of gas neighbours to heat in an AGN feedback event.
-  max_reposition_mass:                2e8        # Maximal BH mass considered for BH repositioning in solar masses.
-  max_reposition_distance_ratio:      3.0        # Maximal distance a BH can be repositioned, in units of the softening length.
-  with_reposition_velocity_threshold: 1          # Should we only reposition to particles that move slowly w.r.t. the black hole?
-  max_reposition_velocity_ratio:      0.5        # Maximal velocity offset of a particle to reposition a BH to, in units of the ambient sound speed of the BH. Only meaningful if with_reposition_velocity_ratio is 1.
-  min_reposition_velocity_threshold: -1.0        # Minimal value of the velocity threshold for repositioning [km/s], set to < 0 for no effect. Only meaningful if with_reposition_velocity_ratio is 1.
-  set_reposition_speed:               0          # Should we reposition black holes with (at most) a prescribed speed towards the potential minimum?
-  threshold_major_merger:             0.333      # Mass ratio threshold to consider a BH merger as 'major'
-  threshold_minor_merger:             0.1        # Mass ratio threshold to consider a BH merger as 'minor'
-  merger_threshold_type:              2          # Type of velocity threshold for BH mergers (0: v_circ at kernel edge, 1: v_esc at actual distance, with softening, 2: v_esc at actual distance, no softening).
-  merger_max_distance_ratio:          3.0        # Maximal distance over which two BHs can merge, in units of the softening length.
--- a/examples/EAGLE_ICs/EAGLE_50_low_res/getIC.sh
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/getIC.sh
-#!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0376_ICs.hdf5
--- a/examples/EAGLE_ICs/EAGLE_50_low_res/output_list.txt
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/output_list.txt
-# Redshift
-18.08
-15.28
-13.06
-11.26
-9.79
-8.57
-7.54
-6.67
-5.92
-5.28
-4.72
-4.24
-3.81
-3.43
-3.09
-2.79
-2.52
-2.28
-2.06
-1.86
-1.68
-1.51
-1.36
-1.21
-1.08
-0.96
-0.85
-0.74
-0.64
-0.55
-0.46
-0.37
-0.29
-0.21
-0.14
-0.07
-0.00
--- a/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh
+++ b/examples/EAGLE_ICs/EAGLE_50_low_res/run.sh
-#!/bin/bash
- # Generate the initial conditions if they are not present.
-if [ ! -e EAGLE_L0050N0376_ICs.hdf5 ]
-then
-    echo "Fetching initial conditions for the EAGLE 50Mpc low-res. example..."
-    ./getIC.sh
-fi
-# Grab the cooling and yield tables if they are not present.
-if [ ! -e yieldtables ]
-then
-    echo "Fetching EAGLE yield tables..."
-    ../getEagleYieldTable.sh
-fi
-if [ ! -e coolingtables ]
-then
-    echo "Fetching EAGLE cooling tables..."
-    ../getEagleCoolingTable.sh
-fi
-# The following run-time options are broken down by line as:
-# Basic run-time options
-# Create and run with stars
-# Radiative options - run with cooling and stellar feedback
-# Run with the time-step limiter required to capture feedback
-# Run with black holes - fof is needed for the seeding
-# Threading options - run with threads and pinning (latter not required but improves performance)
-# The corresponding parameter file for this run
-../../swift \
-    --cosmology --eagle \
-    --threads=16 --pin \
-    eagle_50.yml