diff --git a/doc/RTD/source/ParameterFiles/output_selection.rst b/doc/RTD/source/ParameterFiles/output_selection.rst index b84a776c7dcac2136dedd2324cfef43d7a5455ea..728079023b937d699819e595d18b5a233773c29b 100644 --- a/doc/RTD/source/ParameterFiles/output_selection.rst +++ b/doc/RTD/source/ParameterFiles/output_selection.rst @@ -6,12 +6,11 @@ Output List ~~~~~~~~~~~ -In the sections ``Snapshots`` and ``Statistics``, you can specify the -options ``output_list_on`` and ``output_list`` which receive an int -and a filename. The ``output_list_on`` enable or not the output list -and ``output_list`` is the filename containing the output times. With -the file header, you can choose between writing redshifts, scale -factors or times. +In the sections ``Snapshots``, ``Statistics`` and ``StructureFinding``, you can +specify the options ``output_list_on`` and ``output_list`` which receive an int +and a filename. The ``output_list_on`` enable or not the output list and +``output_list`` is the filename containing the output times. With the file +header, you can choose between writing redshifts, scale factors or times. Example of file containing with times (in internal units):: diff --git a/doc/RTD/source/ParameterFiles/parameter_description.rst b/doc/RTD/source/ParameterFiles/parameter_description.rst index 0454d30a6139a9b43b09908b7ba44155d37f11b4..9f2ed813accc3e4aa91b2b916fb0c27a391544ee 100644 --- a/doc/RTD/source/ParameterFiles/parameter_description.rst +++ b/doc/RTD/source/ParameterFiles/parameter_description.rst @@ -438,7 +438,7 @@ in the internal units of time. Users also have to provide the difference in 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 +equally spaced 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 @@ -935,8 +935,8 @@ to control whether they are used or not. If enabled these will be used to repartition after the second step, which will generally give as good a repartition immediately as you get at the first unforced repartition. -Also once these have been enabled you can change the `trigger:` value to -numbers greater than 2, and repartitioning will be forced every `trigger` +Also once these have been enabled you can change the ``trigger`` value to +numbers greater than 2, and repartitioning will be forced every ``trigger`` steps. This latter option is probably only useful for developers, but tuning the second step to use fixed costs can give some improvements. @@ -945,7 +945,70 @@ the second step to use fixed costs can give some improvements. Structure finding (VELOCIraptor) -------------------------------- +This section describes the behaviour of the on-the-fly structure +finding using the VELOCIraptor library (see +:ref:`VELOCIraptor_interface`). The section is named +``StructureFinding`` and also governs the behaviour of the +structure finding code when invoked at snapshots dumping time via +the parameter ``Snapshots:invoke_stf``. +The main parameters are: + + * The VELOCIraptor parameter file to use for the run: + ``config_file_name``, + * The directory in which the structure catalogs will be written: ``basename``. + +Both these parameters must always be specified when running SWIFT with +on-the-fly calls to the structure finding code. In particular, when +only running VELOCIraptor when snapshots are written, nothing more is +necessary and one would use: + +.. code:: YAML + + Snapshots: + invoke_stf: 1 # We want VELOCIraptor to be called when snapshots are dumped. + # ... + # Rest of the snapshots properties + + StructureFinding: + config_file_name: my_stf_configuration_file.cfg # See the VELOCIraptor manual for the content of this file. + basename: ./haloes/ # Write the catalogs in this sub-directory + +If one additionally want to call VELOCIraptor at times not linked with +snapshots, the additional parameters need to be supplied. + +The time of the first call is controlled by the two following options: + +* Time of the first call to VELOCIraptor (non-cosmological runs): ``time_first``, +* Scale-factor of the first call to VELOCIraptor (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 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``. + +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 call. This implies that the outputs are +equally spaced in :math:`\log(a)` (See :ref:`Output_list_label` to have +calls not regularly spaced in time). + +Showing all the parameters for a basic cosmologica test-case, one would have: + +.. code:: YAML + + StructureFinding: + config_file_name: my_stf_configuration_file.cfg # See the VELOCIraptor manual for the content of this file. + basename: ./haloes/ # Write the catalogs in this sub-directory + scale_factor_first: 0.1 # Scale-factor of the first output + delta_time: 1.1 # Delta log-a between outputs + + +------------------------ + + .. [#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}`. diff --git a/doc/RTD/source/VELOCIraptorInterface/index.rst b/doc/RTD/source/VELOCIraptorInterface/index.rst index 312b9cd3f893dd44f814ad80ac40748db12bd4d5..2ef4533ca8d1f5e47f01b761b68528e9040048a2 100644 --- a/doc/RTD/source/VELOCIraptorInterface/index.rst +++ b/doc/RTD/source/VELOCIraptorInterface/index.rst @@ -1,6 +1,8 @@ .. VELOCIraptor Interface Folkert Nobels, 8th October 2018 +.. _VELOCIraptor_interface: + VELOCIraptor Interface ======================