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Merged
jmsexton03 merged 4 commits into from
Dec 10, 2025
Merged

Update docs #106

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69ce909
Updating docs
Dec 8, 2025
57befa1
Updating docs
Dec 9, 2025
3f7e406
Adding references to conf.py
Dec 9, 2025
95c6e8e
Adding halo inputs
Dec 9, 2025
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44 changes: 42 additions & 2 deletions Docs/sphinx_documentation/source/NyxInputs.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -626,6 +626,17 @@ List of Parameters
| | after | | |
| | restarting | | |
+---------------------------------+----------------+----------------+----------------+
| **nyx.checkpoint_z_values** | The redshift | list of | NONE |
| | values at which| redshift values| |
| | checkpoint file| | |
| | should be | | |
| | written in | | |
| | addition to | | |
| | what is | | |
| | specified | | |
| | using | | |
| | **check_int** | | |
+---------------------------------+----------------+----------------+----------------+

.. _notes-4:

Expand Down Expand Up @@ -683,8 +694,8 @@ To restart from *chk_run00061*,for example, then set

.. _sec:PlotFiles:

Controlling PlotFile Generation
===============================
Controlling PlotFile and Generation
================================================

The main output from  is in the form of plotfiles (which are really
directories). The following options in the inputs file control the
Expand Down Expand Up @@ -743,6 +754,15 @@ List of Parameters
| | double or single | | |
| | precision | | |
+-----------------------------+------------------+------------------+---------+
| **nyx.plot_z_values** | The redshift | list of redshift | NONE |
| | values at which | values | |
| | plot files should| | |
| | be written in | | |
| | addition to what | | |
| | is specified | | |
| | using | | |
| | **nyx.plot_int** | | |
+-----------------------------+------------------+------------------+---------+

All the options for **amr.derive_plot_vars** are kept in ``derive_lst``
in ``Nyx_setup.cpp``. Feel free to look at it and see what’s there.
Expand Down Expand Up @@ -1137,7 +1157,27 @@ List of Parameters
| | heat input | | |
+----------------------------------+------------------+-----------------+-------------+

Dark matter halo output using Reeber
====================================

.. _list-of-parameters-halos:

List of Parameters
------------------

+-------------------------------------+----------------------------------------------+-----------------+-------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+=====================================+==============================================+=================+=============+
| **reeber.min_halo_n_cells** | Minimum number of cells required for a halo | integer | 10 |
| | to be considered a valid structure | | |
+-------------------------------------+----------------------------------------------+-----------------+-------------+
| **reeber.halo_component_threshold** | Threshold for identifying connected | real | 81.66 |
| | components within a halo | | |
+-------------------------------------+----------------------------------------------+-----------------+-------------+
| **reeber.halo_extrema_threshold** | Threshold for detecting local maxima or | real | 160.0 |
| | extrema in the density field | | |
+-------------------------------------+----------------------------------------------+-----------------+-------------+

Multigrid Inputs
================
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2 changes: 2 additions & 0 deletions Docs/sphinx_documentation/source/conf.py
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Expand Up @@ -71,6 +71,8 @@ def get_version():
'breathe']
todo_include_todos=True

bibtex_bibfiles = ['refs.bib']

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

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