Merge branch 'master' into snapshot_meta_data

.gitignore

@@ -36,6 +36,7 @@ examples/*/*/*.rst
 examples/*/*/*.hdf5
 examples/*/*/*.csv
 examples/*/*/*.dot
+examples/*/*/partition_fixed_costs.h
 examples/*/*/memuse_report-step*.dat
 examples/*/*/memuse_report-step*.log
 examples/*/*/restart/*

README

@@ -6,6 +6,7 @@
  /____/ |__/|__/___/_/    /_/
  SPH With Inter-dependent Fine-grained Tasking
 
+ Version : 0.8.3
  Website: www.swiftsim.com
  Twitter: @SwiftSimulation
 
@@ -25,7 +26,7 @@ Parameters:
     -b, --feedback                    Run with stars feedback.
     -c, --cosmology                   Run with cosmological time integration.
     --temperature                     Run with temperature calculation.
-    -C, --cooling                     Run with cooling (also switches on --with-temperature).
+    -C, --cooling                     Run with cooling (also switches on --temperature).
     -D, --drift-all                   Always drift all particles even the ones
                                       far from active particles. This emulates
                                       Gadget-[23] and GIZMO's default behaviours.
@@ -57,8 +58,8 @@ Parameters:
     -n, --steps=<int>                 Execute a fixed number of time steps.
                                       When unset use the time_end parameter
                                       to stop.
-    -o, --output-params=<str>         Generate a default output parameter
-                                      file.
+    -o, --output-params=<str>         Generate a parameter file with the options
+                                      for selecting the output fields.
     -P, --param=<str>                 Set parameter value, overiding the value
                                       read from the parameter file. Can be used
                                       more than once {sec:par:value}.

README.md

@@ -45,6 +45,9 @@ Any contributions that fail any of the automated tests will not be accepted.
 Contributions that include tests of the proposed modules (or any current ones!)
 are highly encouraged.
 
+Runtime parameters
+------------------
+
 ```
  Welcome to the cosmological hydrodynamical code
     ______       _________________
@@ -54,6 +57,7 @@ are highly encouraged.
  /____/ |__/|__/___/_/    /_/
  SPH With Inter-dependent Fine-grained Tasking
 
+ Version : 0.8.3
  Website: www.swiftsim.com
  Twitter: @SwiftSimulation
 
@@ -73,7 +77,7 @@ Parameters:
     -b, --feedback                    Run with stars feedback.
     -c, --cosmology                   Run with cosmological time integration.
     --temperature                     Run with temperature calculation.
-    -C, --cooling                     Run with cooling (also switches on --with-temperature).
+    -C, --cooling                     Run with cooling (also switches on --temperature).
     -D, --drift-all                   Always drift all particles even the ones
                                       far from active particles. This emulates
                                       Gadget-[23] and GIZMO's default behaviours.
@@ -84,6 +88,8 @@ Parameters:
     -s, --hydro                       Run with hydrodynamics.
     -S, --stars                       Run with stars.
     -B, --black-holes                 Run with black holes.
+    -u, --fof                         Run Friends-of-Friends algorithm to
+                                      perform black hole seeding.
     -x, --velociraptor                Run with structure finding.
     --limiter                         Run with time-step limiter.
 
@@ -103,8 +109,8 @@ Parameters:
     -n, --steps=<int>                 Execute a fixed number of time steps.
                                       When unset use the time_end parameter
                                       to stop.
-    -o, --output-params=<str>         Generate a default output parameter
-                                      file.
+    -o, --output-params=<str>         Generate a parameter file with the options
+                                      for selecting the output fields.
     -P, --param=<str>                 Set parameter value, overiding the value
                                       read from the parameter file. Can be used
                                       more than once {sec:par:value}.

configure.ac

@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # Init the project.
-AC_INIT([SWIFT],[0.8.2],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
+AC_INIT([SWIFT],[0.8.3],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
 swift_config_flags="$*"
 
 #  We want to stop when given unrecognised options. No subdirs so this is safe.
@@ -225,6 +225,16 @@ if test "x$enable_debug" = "xyes"; then
    fi
 fi
 
+# Check if stand-alone FoF is on.
+AC_ARG_ENABLE([stand-alone-fof],
+   [AS_HELP_STRING([--enable-stand-alone-fof],
+     [Activate the compilation of the stand-alone friends-of-friends post-processing tool.],
+   )],
+   [enable_standalone_fof="$enableval"],
+   [enable_standalone_fof="no"]
+)
+AM_CONDITIONAL([HAVEFOF],[test $enable_standalone_fof = "yes"])
+
 # Check if task debugging is on.
 AC_ARG_ENABLE([task-debugging],
    [AS_HELP_STRING([--enable-task-debugging],
@@ -2003,6 +2013,7 @@ AC_MSG_RESULT([
    Star feedback model  : $with_feedback
    Black holes model    : $with_black_holes
 
+   Stand-alone FoF tool:       : $enable_standalone_fof
    Individual timers           : $enable_timers
    Task debugging              : $enable_task_debugging
    Threadpool debugging        : $enable_threadpool_debugging

doc/RTD/source/CommandLineOptions/index.rst

@@ -20,7 +20,7 @@ can be found by typing ``./swift -h``::
     -b, --feedback                    Run with stars feedback.
     -c, --cosmology                   Run with cosmological time integration.
     --temperature                     Run with temperature calculation. 
-    -C, --cooling                     Run with cooling (also switches on --with-temperature).
+    -C, --cooling                     Run with cooling (also switches on --temperature).
     -D, --drift-all                   Always drift all particles even the ones
                                       far from active particles. This emulates
                                       Gadget-[23] and GIZMO's default behaviours.
@@ -31,8 +31,8 @@ can be found by typing ``./swift -h``::
     -s, --hydro                       Run with hydrodynamics.
     -S, --stars                       Run with stars.
     -B, --black-holes                 Run with black holes.
-    -u, --fof                         Run Friends-of-Friends algorithm and 
-                                      black holes seeding.
+    -u, --fof                         Run Friends-of-Friends algorithm to
+                                      perform black hole seeding.
     -x, --velociraptor                Run with structure finding.
     --limiter                         Run with time-step limiter.
 
@@ -52,8 +52,8 @@ can be found by typing ``./swift -h``::
     -n, --steps=<int>                 Execute a fixed number of time steps.
                                       When unset use the time_end parameter
                                       to stop.
-    -o, --output-params=<str>         Generate a default output parameter
-                                      file.
+    -o, --output-params=<str>         Generate a parameter file with the options
+                                      for selecting the output fields.
     -P, --param=<str>                 Set parameter value, overiding the value
                                       read from the parameter file. Can be used
                                       more than once {sec:par:value}.

doc/RTD/source/FriendsOfFriends/algorithm_description.rst

+.. Friends Of Friends
+   Matthieu Schaller 15th June 2019
+
+.. _fof_algorithm_description_label:
+
+Friends-Of-Friends Algorithm
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Friends-Of-Friends (FOF) is a common tool used to identify groups of
+particles in a simulation. This can, for instance, be used to identify
+haloes in a cosmological simulation.
+
+In practice, this is done by using a *linking length* ``l`` and
+demanding that any particle that finds another particle within a
+distance ``l`` is linked to it to form a group. A particle is linked
+directly to all other particles within a distance ``l`` (its
+*friends*) and indirectly to all particles that are linked to its
+friends (its *friends-of-friends*). This creates networks of linked particles
+which are called *groups*. The size (or length) of
+a group is the number of particles in that group. If a particle does not
+find any other particle within ``l`` then it forms its own group of
+size 1. For a given distribution of particles the resulting list of
+groups is unique and unambiguously defined.
+
+Small groups are typically discarded, the final catalogue only contains
+objects with a length above a minimal threshold, typically of the
+order of ``20`` particles. Smaller groups can often be spurious.
+
+Once the groups have been identified, properties can be computed for
+each of them. The total mass or the centre of mass are common
+examples. These are then stored in catalogues alongside a unique
+identifier for each group.
+
+SWIFT implements FOF using a Union-Find approach. It also exploits the
+domain decomposition and tree structure that is created for the other
+parts of the code. The tree can be easily used to find neighbours of
+particles within the linking length.
+
+Depending on the application, the choice of linking length and
+minimal group size can vary. For cosmological applications, bound
+structures (dark matter haloes) are traditionally identified using a
+linking length expressed as :math:`0.2` of the mean inter-particle
+separation :math:`d` in the simulation which is given by :math:`d =
+\sqrt[3]{\frac{V}{N}}`, where :math:`N` is the number of particles in
+the simulation and :math:`V` is the simulation (co-moving)
+volume. Usually only dark matter particles are considered for the
+number :math:`N`. Other particle types are linked but do not
+participate in the calculation of the linking length. Experience shows
+that this produces groups that are similar to the commonly adopted
+(but much more complex) definition of virialised haloes. A minimal
+group length of :math:`32` is often adopted in order to get a robust
+catalogue of haloes and compute a good halo mass function.
+
+For non-cosmological applications of the FOF algorithm, the choice of
+the linking length is more difficult and left to the user. The choice
+of the minimal group size to consider is also application dependent.
+
+In SWIFT, FOF is also used to identify haloes in which to seed black
+holes in a cosmological run. When used in this mode, the code does not
+produce any outputs but uses the catalogue internally to convert some
+gas particles into black hole particles.
+

doc/RTD/source/FriendsOfFriends/index.rst

+.. Friends Of Friends
+   Matthieu Schaller 15th June 2019
+
+.. _Friends_Of_Friends_label:
+
+Friends-Of-Friends (FOF) Halo Finder
+====================================
+
+This section describes the Friends-Of-Friends group
+finder and related parameters
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   algorithm_description
+   stand_alone_fof
+   on_the_fly_fof
+   parameter_description
+

doc/RTD/source/FriendsOfFriends/on_the_fly_fof.rst

+.. Friends Of Friends
+   Matthieu Schaller 15th June 2019
+
+.. _fof_on_the_fly_label:
+
+On-the-fly Friends-Of-Friends and Black Hole seeding
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The main purpose of the on-the-fly FOF is to identify haloes during a
+cosmological simulation in order to seed some of them with black holes
+based on physical considerations.
+
+**In this mode, no group catalogue is written to the disk. The resulting list
+of haloes is only used internally by SWIFT.**
+
+Once the haloes have been identified by the FOF code, SWIFT will iterate
+over the list of groups and will check whether each halo obeys the
+following criteria:
+
+  * Is above a user-specified mass threshold (typically
+    :math:`10^{10}~\rm{M}_\odot` or more).
+  * Contains *at least* one gas particle.
+  * Does *not* contain any already existing black hole particle.
+
+If a group satisfies all these requirements then the *densest* gas particle
+(based on their SPH density) in the group will be converted to a black
+hole. In practice this means that the gas particle is removed and a black
+hole particle with the same dynamical mass is inserted at the same position
+in the domain and with the same velocity. Additional properties are copied
+from the gas particle to the black hole particle depending on the specifics
+of the sub-grid model in use (see :ref:`subgrid`).
+
+Given that the halo mass considered for seeding black holes is usually many
+hundred times the mass of a single particle, it can be advantageous to
+raise the minimal group length required for a halo to appear in the catalogue
+of objects. This reduces the number of groups that are kept in memory and
+speeds up the seeding procedure by removing haloes that are obviously too
+small. For instance, in the case of EAGLE-like runs, the dark matter
+particle mass is around :math:`10^7\rm~{M}_\odot` and the minimal halo mass
+considered for seeding a black hole is of order
+:math:`10^{10}~\rm{M}_\odot`. Groups will hence need to have at least 1000
+particles to pass the first criterion outlined above. In this case, using a
+minimal group length of order 500 is beneficial over the more traditional
+value of 32 as it will reduce the number of haloes to consider by about a
+factor 10 (assuming a normal cosmology) whilst still being far enough from
+the actual user-defined mass limit to be safe.

doc/RTD/source/FriendsOfFriends/parameter_description.rst

+.. Friends Of Friends
+   Matthieu Schaller 15th June 2019
+
+.. _Fof_Parameter_Description_label:
+
+Friends-Of-Friends Parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ``FOF`` section of the parameter file contains all the options related
+to the group finder. Some parameters only make sense in the stand-alone
+version and some only in the on-the-fly version of the module.
+
+The main parameter is the linking length that will be used. The easiest way
+to define it is to set the ratio of the linking length to the mean *dark
+matter* inter-particle separation (irrespective of whether there are other
+kinds of particles present in the run). This is done using the parameter
+``linking_length_ratio`` and the typical value used is
+``0.2``. Users can optionally overwrite the linking length by imposing an
+absolute value using the parameter ``absolute_linking_length``. This is
+expressed in internal units. This value will be ignored (and the ratio of
+the mean inter-particle separation will be used) when set to ``-1``.
+
+The second important parameter is the minimal size of groups to retain in
+the catalogues. This is given in terms of number of particles (of all types)
+via the parameter ``min_group_size``. When analysing simulations, to
+identify haloes, the common practice is to set this to ``32`` in order to
+not plague the catalogue with too many small, likely unbound, structures.
+When using the FOF code on-the-fly for black hole seeding, larger values
+are recommended as there is no need to store groups much smaller than the
+minimal halo mass (see below).
+
+------------------------
+
+In the case of black holes seeding, we run the FOF module on-the-fly during
+a cosmological simulation. The time of the first FOF call is controlled by
+the following two options:
+
+  * Time of the first FOF call (non-cosmological runs): ``time_first``,
+  * Scale-factor of the first FOF call (cosmological runs):
+    ``scale_factor_first``.
+
+One of those two parameters has to be provided depending on the type of
+run. In the case of non-cosmological runs, the time of the first FOF call
+is expressed in the internal units of time. Users also have to provide the
+difference in time (or scale-factor) between consecutive outputs:
+
+  * Time difference between consecutive outputs: ``delta_time``.
+
+The last parameter relevant to the on-the-fly FOF module is the minimal
+halo (group) mass considered for seeding black holes. This is specified by
+the parameter ``black_hole_seed_halo_mass_Msun`` which is expressed in
+solar masses.
+
+------------------------
+
+In the case of the stand-alone module, the four seeding parameters
+described above are ignored but an additional one needs to be
+specified. This is the name of the file in which the catalogue of groups will
+be written. This is specified by the parameter ``fof_output``. The linking
+length and minimal group to keep are set in the way described above.
+
+There are two additional optional parameters that can be used to modify
+details of the stand-alone FOF code. The ``GroupID`` of the particles that
+do not belong to any groups is by default set to 2147483647
+(i.e. :math:`2^{31}-1`). A different value can be specified by changing the
+optional parameter ``group_id_default``. Similarly, the first group in the
+catalogue (i.e. the largest group) carries the ``GroupID`` 1. This can be
+changed by tweaking the optional parameter ``group_id_offset``.
+
+
+------------------------
+
+A full FOF section of the YAML parameter file looks like:
+
+.. code:: YAML
+
+    # Parameters of the Friends-Of-Friends module
+    FOF:
+       basename:                        fof_output  # Filename for the FOF outputs.
+       scale_factor_first:              0.91        # Scale-factor of first FoF black hole seeding calls.
+       time_first:                      0.2         # Time of first FoF black hole seeding calls.
+       delta_time:                      1.005       # Time between consecutive FoF black hole seeding calls.
+       min_group_size:                  256         # 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).
+       absolute_linking_length:         -1.         # (Optional) Absolute linking length (in internal units).
+       group_id_default:                2147483647  # (Optional) Sets the group ID of particles in groups below the minimum size.
+       group_id_offset:                 1           # (Optional) Sets the offset of group ID labelling. Defaults to 1 if unspecified.

doc/RTD/source/FriendsOfFriends/stand_alone_fof.rst

+.. Friends Of Friends
+   Matthieu Schaller 15th June 2019
+
+.. _fof_stand_alone_label:
+
+Stand-Alone Friends-Of-Friends
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The stand-alone version of the Friends-Of-Friends module can be
+compiled by configuring the code with the option
+``--enable-stand-alone-fof``. The ``fof`` and ``fof_mpi`` executables
+will then be generated alongside the regular SWIFT ones.
+
+The executable takes a parameter file as an argument. It will then
+read the snapshot specified in the parameter file and extract all
+the dark matter particles by default. FOF is then run on these
+particles and a catalogue of groups is written to disk. Additional
+particle types can be read and processed by the stand-alone FOF
+code by adding any of the following runtime parameters to the
+command line:
+
+ * ``--hydro``: Read and process the gas particles,
+ * ``--stars``: Read and process the star particles,
+ * ``--black-holes``: Read and process the black hole particles.
+
+The group catalogues contain a unique identifier for each group as
+well as the number of particles in each group and their total mass (in
+internal units). The FOF code will also write a snapshot with an
+additional field for each particle. This contains the ``GroupID`` of
+each particle and can be used to find all the particles in a given
+halo and to link them to the information stored in the catalogue.

doc/RTD/source/ParameterFiles/parameter_description.rst

@@ -517,6 +517,14 @@ 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_fof:
+
+Friends-Of-Friends (FOF)
+------------------------
+
+The parameters are described separately on the page
+:ref:`Fof_Parameter_Description_label` within the more general
+:ref:`Friends_Of_Friends_label` description.
 
 .. _Parameters_statistics:
 
@@ -568,8 +576,9 @@ been activated, the previous set of restart files will be named
 ``basename_000000.rst.prev``.
 
 SWIFT can also be stopped by creating an empty file called ``stop`` in the
-directory where the code runs. This will make SWIFT dump a fresh set of restart
-file (irrespective of the specified ``delta_time`` between dumps) and exit
+directory where the restart files are written (i.e. the directory speicified by
+the parameter ``subdir``). This will make SWIFT dump a fresh set of restart file
+(irrespective of the specified ``delta_time`` between dumps) and exit
 cleanly. One parameter governs this behaviour:
 
 * Number of steps between two checks for the presence of a ``stop`` file:

doc/RTD/source/SubgridModels/EAGLE/index.rst

@@ -508,10 +508,10 @@ For a normal EAGLE run, that section of the parameter file reads:
      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.
-     KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+     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.
-     KS_temperature_margin_dex:         0.5       # (Optional) Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+     EOS_temperature_margin_dex:        0.5       # (Optional) Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
      KS_max_density_threshold_H_p_cm3:  1e5       # (Optional) Hydrogen number density above which a particle gets automatically turned into a star in Hydrogen atoms per cm^3.
      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.

doc/RTD/source/conf.py

@@ -25,7 +25,7 @@ author = 'SWIFT Team'
 # The short X.Y version
 version = '0.8'
 # The full version, including alpha/beta/rc tags
-release = '0.8.2'
+release = '0.8.3'
 
 
 # -- General configuration ---------------------------------------------------

doc/RTD/source/index.rst

@@ -21,6 +21,7 @@ difference is the parameter file that will need to be adapted for SWIFT.
    Snapshots/index
    HydroSchemes/index
    SubgridModels/index
+   FriendsOfFriends/index
    EquationOfState/index
    ExternalPotentials/index
    NewOption/index

examples/EAGLE_ICs/EAGLE_12/eagle_12.yml

@@ -105,10 +105,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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

examples/EAGLE_ICs/EAGLE_25/eagle_25.yml

@@ -106,10 +106,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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

examples/EAGLE_ICs/EAGLE_50/eagle_50.yml

@@ -106,10 +106,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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

examples/EAGLE_low_z/EAGLE_12/eagle_12.yml

@@ -94,10 +94,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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

examples/EAGLE_low_z/EAGLE_25/eagle_25.yml

@@ -101,10 +101,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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

examples/EAGLE_low_z/EAGLE_50/eagle_50.yml

@@ -96,10 +96,10 @@ EAGLEStarFormation:
   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.
-  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  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.
-  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  EOS_temperature_margin_dex:        0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
   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