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Commit 6f6c3499 authored by Matthieu Schaller's avatar Matthieu Schaller
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Revert "Merge branch 'master' into 'updated_MAC'" 

This reverts commit bfc539fa, reversing
changes made to 861e5f8b.
parent 4dec23e9
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1 merge request!1077Improved multipole acceptance criterion (MAC)
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README
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......@@ -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.
......
README.md
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......@@ -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.
......
configure.ac
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......@@ -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().
......
doc/RTD/source/CommandLineOptions/index.rst
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......@@ -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.
......
doc/RTD/source/ImplementationDetails/index.rst
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......@@ -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
......
doc/RTD/source/LineOfSights/index.rst deleted 100644 → 0
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.. 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.
doc/RTD/source/ParameterFiles/parameter_description.rst
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......@@ -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
would have:
Showing all the parameters for a basic hydro test-case, one 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)
......
doc/RTD/source/index.rst
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......@@ -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
doc/RTD/source/random.rst 0 → 100644
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.. 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.
examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
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......@@ -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.
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.
subgrid_seed_mass_Msun: 1.5e5 # Black hole subgrid mass at creation time in solar masses.
max_eddington_fraction: 1.0 # 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.
with_angmom_limiter: 1 # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
viscous_alpha: 1e6 # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
radiative_efficiency: 0.1 # Fraction of the accreted mass that gets radiated.
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.
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'
examples/EAGLE_ICs/EAGLE_12/run.sh
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......@@ -11,7 +11,7 @@ fi
if [ ! -e yieldtables ]
then
echo "Fetching EAGLE yield tables..."
../getEagleYieldTable.sh
../getEagleYieldtable.sh
fi
if [ ! -e coolingtables ]
......
examples/EAGLE_ICs/EAGLE_25/eagle_25.yml
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......@@ -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.
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.
subgrid_seed_mass_Msun: 1.5e5 # Black hole subgrid mass at creation time in solar masses.
max_eddington_fraction: 1.0 # 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.
with_angmom_limiter: 1 # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
viscous_alpha: 1e6 # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
radiative_efficiency: 0.1 # Fraction of the accreted mass that gets radiated.
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.
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'
examples/EAGLE_ICs/EAGLE_25/run.sh
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......@@ -11,7 +11,7 @@ fi
if [ ! -e yieldtables ]
then
echo "Fetching EAGLE yield tables..."
../getEagleYieldTable.sh
../getEagleYieldtable.sh
fi
if [ ! -e coolingtables ]
......
examples/EAGLE_ICs/EAGLE_50/eagle_50.yml
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− 29
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......@@ -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.
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.
\ No newline at end of file
subgrid_seed_mass_Msun: 1.5e5 # Black hole subgrid mass at creation time in solar masses.
max_eddington_fraction: 1.0 # 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.
with_angmom_limiter: 1 # Are we applying the Rosas-Guevara (2015) viscous time-scale reduction term?
viscous_alpha: 1e6 # Normalisation constant of the Bondi viscuous time-scale accretion reduction term
radiative_efficiency: 0.1 # Fraction of the accreted mass that gets radiated.
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.
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'
examples/EAGLE_ICs/EAGLE_50/run.sh
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......@@ -11,7 +11,7 @@ fi
if [ ! -e yieldtables ]
then
echo "Fetching EAGLE yield tables..."
../getEagleYieldTable.sh
../getEagleYieldtable.sh
fi
if [ ! -e coolingtables ]
......
examples/EAGLE_ICs/EAGLE_50_low_res/README deleted 100644 → 0
+ 0
− 3
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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.
examples/EAGLE_ICs/EAGLE_50_low_res/eagle_50.yml deleted 100644 → 0
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− 209
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# 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.
examples/EAGLE_ICs/EAGLE_50_low_res/getIC.sh deleted 100755 → 0
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#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0376_ICs.hdf5
examples/EAGLE_ICs/EAGLE_50_low_res/output_list.txt deleted 100644 → 0
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# 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
examples/EAGLE_ICs/EAGLE_50_low_res/run.sh deleted 100755 → 0
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#!/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
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