@@ -414,12 +414,13 @@ parameter is the base name that will be used for all the outputs in the run:
* The base name of the HDF5 snapshots: ``basename``.
This name will then be appended by an under-score and 6 digits followed by
``.hdf5`` (e.g. ``base_name_001234.hdf5``). The 6 digits are used to label the
different outputs, starting at ``000000``. In the default setup the digits
simply increase by one for each snapshot. However, if the optional parameter
``int_time_label_on`` is switched on, then the 6-digits will the physical time
of the simulation rounded to the nearest integer [#f3]_.
This name will then be appended by an under-score and 4 digits followed by
``.hdf5`` (e.g. ``base_name_1234.hdf5``). The 4 digits are used to label the
different outputs, starting at ``0000``. In the default setup the digits simply
increase by one for each snapshot. However, if the optional parameter
``int_time_label_on`` is switched on, then we use 6 digits and these will the
physical time of the simulation rounded to the nearest integer
(e.g. ``base_name_001234.hdf5``) [#f3]_.
The time of the first snapshot is controlled by the two following options:
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@@ -434,11 +435,28 @@ in the internal units of time. Users also have to provide the difference in time
* Time difference between consecutive outputs: ``delta_time``.
In non-cosmological runs this is also expressed in internal units. For
cosmological runs, this value is *multiplied* to obtain the scale-factor of the
next snapshot. This implies that the outputs are equally space in
:math:`\log(a)` (See :ref:`Output_list_label` to have snapshots not regularly spaced in time).
Users can optionally specify the level of compression used by the HDF5 libary
cosmological runs, this value is *multiplied* to obtain the
scale-factor of the next snapshot. This implies that the outputs are
equally space in :math:`\log(a)` (See :ref:`Output_list_label` to have
snapshots not regularly spaced in time).
When running the code with structure finding activated, it is often
useful to have a structure catalog written at the same simulation time
as the snapshots. To activate this, the following parameter can be
switched on:
* Run VELOCIraptor every time a snapshot is dumped: ``invoke_stf``
(default: ``0``).
This produces catalogs using the options specified for the stand-alone
VELOCIraptor outputs (see the section :ref:`Parameters_structure_finding`) but
with a base name and output number that matches the snapshot name
(e.g. ``stf_base_name_1234.hdf5``) irrespective of the name specified in the
section dedicated to VELOCIraptor. Note that the invocation of VELOCIraptor at
every dump is done additionally to the stand-alone dumps that can be specified
in the corresponding section of the YAML parameter file.
Users can optionally specify the level of compression used by the HDF5 library
using the parameter:
* GZIP compression level of the HDF5 arrays: ``compression`` (default: ``0``).
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@@ -464,14 +482,16 @@ When un-specified, these all take the same value as assumed by the internal
system of units. These are rarely used but can offer a practical alternative to
converting data in the post-processing of the simulations.
For a standard cosmological run, the full section would be:
For a standard cosmological run with structure finding activated, the
full section would be:
.. code:: YAML
Snapshots:
basename: output
scale_factor_first: 0.02 # z = 49
delta_time: 1.02
delta_time: 1.02
invoke_stf: 1
Showing all the parameters for a basic hydro test-case, one would have:
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@@ -481,6 +501,7 @@ Showing all the parameters for a basic hydro test-case, one would have:
basename: sedov
time_first: 0.01
delta_time: 0.005
invoke_stf: 0
int_time_label_on: 0
compression: 3
UnitLength_in_cgs: 1. # Use cm in outputs
...
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@@ -598,6 +619,12 @@ Scheduler
Domain Decomposition
--------------------
.. _Parameters_structure_finding:
Structure finding (VELOCIraptor)
--------------------------------
.. [#f1] The thorough reader (or overly keen SWIFT tester) would find that the speed of light is :math:`c=1.8026\times10^{12}\,\rm{fur}\,\rm{ftn}^{-1}`, Newton's constant becomes :math:`G_N=4.896735\times10^{-4}~\rm{fur}^3\,\rm{fir}^{-1}\,\rm{ftn}^{-2}` and Planck's constant turns into :math:`h=4.851453\times 10^{-34}~\rm{fur}^2\,\rm{fir}\,\rm{ftn}^{-1}`.
config_file_name:stf_input.cfg# Name of the STF config file.
basename:./stf# Common part of the name of output files.
output_time_format:0# Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
scale_factor_first:0.92# Scale-factor of the first snaphot (cosmological run)
time_first:0.01# Time of the first structure finding output (in internal units).
delta_step:1000# Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
delta_time:1.10# Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
config_file_name:stf_input.cfg# Name of the STF config file.
basename:./stf# Common part of the name of output files.
output_time_format:0# Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
scale_factor_first:0.92# Scale-factor of the first snaphot (cosmological run)
time_first:0.01# Time of the first structure finding output (in internal units).
delta_step:1000# Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
delta_time:1.10# Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
config_file_name:stf_input.cfg# Name of the STF config file.
basename:./stf# Common part of the name of output files.
output_time_format:0# Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
scale_factor_first:0.92# Scale-factor of the first snaphot (cosmological run)
time_first:0.01# Time of the first structure finding output (in internal units).
delta_step:1000# Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
delta_time:1.10# Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
config_file_name:stf_input.cfg# Name of the STF config file.
basename:./stf# Common part of the name of output files.
output_time_format:0# Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
scale_factor_first:0.92# Scale-factor of the first snaphot (cosmological run)
time_first:0.01# Time of the first structure finding output (in internal units).
delta_step:1000# Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
delta_time:1.10# Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
output_list_on:0 # (Optional) Enable the output list
output_list:stflist.txt# (Optional) File containing the output times (see documentation in "Parameter File" section)
