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Documentation: Seperate file for links
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Gon-na authored Apr 12, 2024
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10 changes: 9 additions & 1 deletion Documentation/gh-pages/source/conf.py
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Expand Up @@ -63,7 +63,15 @@
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []

# Exclude link file
exclude_patterns = ['links.rst']

# make rst_epilog a variable, so you can add other epilog parts to it
rst_epilog =""
# Read link all targets from file
with open('links.rst') as f:
rst_epilog += f.read()

highlight_language = ''

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12 changes: 0 additions & 12 deletions Documentation/gh-pages/source/configuring_simulation.rst
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Expand Up @@ -65,15 +65,3 @@ declared before their first use.
configuring_simulation_messagingsystem
configuring_simulation_pitfalls


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
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Expand Up @@ -79,16 +79,3 @@ natively understood by TinyExpr_. The standard functions (and mathematical const
+-------------+---------------+--------------------------+------------------------------------------------+
| ``pi`` | ``M_PI`` | ``TMath::E()`` | Fundamental constant. |
+-------------+---------------+--------------------------+------------------------------------------------+


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
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Expand Up @@ -162,14 +162,3 @@ redirecting output to a log file, or customizing the message format.
In *Kassiopeia*, *KEMField* and *KGeoBag*, most messages use the *KMessage* interface.


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
12 changes: 0 additions & 12 deletions Documentation/gh-pages/source/configuring_simulation_pitfalls.rst
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Expand Up @@ -41,15 +41,3 @@ the message::
Depening on where the element is referenced, the error may look different. For example::

[KSOBJECT ERROR MESSAGE] component <Y> could not build command named <X> (invalid child component)

.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
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Expand Up @@ -256,17 +256,6 @@ included by the syntax:
As shown above, a comment can span multiple lines. Any text between ``<!-- ... -->`` is ignored by the XML initializer,
including any XML elements. This makes it possible to quickly comment out parts of the file, e.g. for debugging.

.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/


.. rubric:: Footnotes
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3 changes: 0 additions & 3 deletions Documentation/gh-pages/source/contact.rst
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Expand Up @@ -48,6 +48,3 @@ In addition to this user guide, *Kassiopeia* and its associated libraries have b
PhD theses. Many of these can be found under the list of KATRIN publications_.



.. _publications: https://www.katrin.kit.edu/375.php
.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
9 changes: 0 additions & 9 deletions Documentation/gh-pages/source/examples.rst
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Expand Up @@ -196,13 +196,4 @@ also distributed with Kassiopeia, and are described in the following table.
+-----------------------------------------+---------------------------------------------------------------+




.. _VTK: http://www.vtk.org/
.. _Paraview: http://www.paraview.org/
.. _TBrowser: https://root.cern.ch/doc/master/classTBrowser.html
.. _PyROOT: https://root.cern/manual/python/
.. _uproot: https://pypi.org/project/uproot/
.. _STL: https://en.wikipedia.org/wiki/STL_%28file_format%29

.. [*] D. Furse *et al.* (2017) New J. Phys. **19** 053012, `doi:10.1088/1367-2630/aa6950 <https://doi.org/10.1088/1367-2630/aa6950>`_
7 changes: 0 additions & 7 deletions Documentation/gh-pages/source/index.rst
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Expand Up @@ -129,10 +129,3 @@ For more information and a guide on how to set up `Kassiopeia` see chapter :ref:




.. _`Try it out online`: https://mybinder.org/v2/gh/KATRIN-Experiment/KassiopeiaBinder/HEAD
.. _`the KATRIN collaboration`: https://katrin.kit.edu
.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950
.. _publications: https://www.katrin.kit.edu/375.php


2 changes: 0 additions & 2 deletions Documentation/gh-pages/source/introduction.rst
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Expand Up @@ -45,5 +45,3 @@ Furthermore, the object oriented approach of *Kassiopeia* provides a clear path
certain specific features in their own novel applications. Code contributions that extend *Kassiopeia's* functionality
can be submitted through GitHub and are always welcome.


.. _KATRIN: https://www.katrin.kit.edu
13 changes: 0 additions & 13 deletions Documentation/gh-pages/source/kassiopeia_generation.rst
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Expand Up @@ -233,16 +233,3 @@ pre-existing terminator might be useful for their purpose. As will be explained
terminators dynamically during the simulation. This allows a very flexible configuration of particle termination.


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/
14 changes: 0 additions & 14 deletions Documentation/gh-pages/source/kassiopeia_navigation.rst
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Expand Up @@ -118,17 +118,3 @@ nesting of the navigation elements should follow the same order as the underlyin



.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/

15 changes: 0 additions & 15 deletions Documentation/gh-pages/source/kassiopeia_output.rst
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Expand Up @@ -476,18 +476,3 @@ The following suffixes are available for the vector and matrix types.
| Trace | ``trace`` | ``KThreeMatrix`` |
+--------------------+-------------------------------------+------------------+


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/

15 changes: 0 additions & 15 deletions Documentation/gh-pages/source/kassiopeia_propagation.rst
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Expand Up @@ -278,18 +278,3 @@ Similarly, one may use the following code to employ fully specular reflection:
In order for this interaction to operate on any particles it must be associated with a surface in the simulation command
structure.

.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/

15 changes: 0 additions & 15 deletions Documentation/gh-pages/source/kassiopeia_simulation.rst
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Expand Up @@ -37,18 +37,3 @@ modify the actual objects used during the course of a simulation.
Following the declaration of ``ks_simulation``, the closing tag ``</kassiopeia>`` is placed to complete the simulation
configuration. When this tag is encountered by the XML parser, it triggers the simulation to run.


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/

16 changes: 0 additions & 16 deletions Documentation/gh-pages/source/kassiopeia_visualization.rst
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Expand Up @@ -130,19 +130,3 @@ Using Python

The track painters export VTK_ output files that can be visualized in Python with the PyVista_ module, as shown in :ref:`kgeobag-visualization`.



.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _Gnuplot: http://www.gnuplot.info/
.. _PyVista: https://www.pyvista.org/

12 changes: 0 additions & 12 deletions Documentation/gh-pages/source/kemfield_fields.rst
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Expand Up @@ -138,18 +138,6 @@ A complete list and set of examples of the XML bindings for magnetic fields can
Further documentation on the exact methods and parameters used in *KEMField* can be found in [2] and [3].


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _PyVista: https://www.pyvista.org/


.. rubric:: Footnotes
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16 changes: 0 additions & 16 deletions Documentation/gh-pages/source/kemfield_visualization.rst
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Expand Up @@ -96,19 +96,3 @@ the dimensions is equal to zero.) To speed up the computation, it is possible to
(``compute_gradient``) or electric field (``compute_field``), or to make use of existing symmetries in either dimension.
Note that the symmetry is not checked against the actual geometry, so it's a responsibility of the user to set this up
correctly.


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _PyVista: https://www.pyvista.org/


14 changes: 0 additions & 14 deletions Documentation/gh-pages/source/kgeobag_complex_shapes.rst
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Expand Up @@ -451,17 +451,3 @@ An XML example is as follows:
.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/

14 changes: 0 additions & 14 deletions Documentation/gh-pages/source/kgeobag_geometry.rst
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Expand Up @@ -317,17 +317,3 @@ supported shapes are the cylinder surface, describing a simple coil, and the rod
For further demonstrations of the possible geometry extensions please see the provided example XML files located
at :gh-code:`KGeoBag/Source/XML/Examples`.


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _PyVista: https://www.pyvista.org/

12 changes: 0 additions & 12 deletions Documentation/gh-pages/source/kgeobag_simple_shapes.rst
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Expand Up @@ -1052,15 +1052,3 @@ The parameters are:
- z_mesh_count: z mesh count
- z_mesh_power: z mesh power


.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
12 changes: 0 additions & 12 deletions Documentation/gh-pages/source/kgeobag_visualization.rst
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Expand Up @@ -77,15 +77,3 @@ create a slice that transforms the 3D surfaces into 2D lines.
plt.ylim(ylim)
.. _TFormula: http://root.cern.ch/root/htmldoc/TFormula.html
.. _TMath: http://root.cern.ch/root/htmldoc/TMath.html
.. _PDG: http://pdg.lbl.gov/mc_particle_id_contents.html
.. _Paraview: http://www.paraview.org/
.. _ROOT: https://root.cern.ch/
.. _VTK: http://www.vtk.org/
.. _MKS: https://scienceworld.wolfram.com/physics/MKS.html
.. _XML: https://www.w3.org/TR/xml11/
.. _Xpath: https://www.w3.org/TR/xpath-10/
.. _TinyExpr: https://github.com/codeplea/tinyexpr/
.. _Log4CXX: https://logging.apache.org/log4cxx/
.. _PyVista: https://www.pyvista.org/
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