diff --git a/Documentation/gh-pages/source/conf.py b/Documentation/gh-pages/source/conf.py index 69570985..156da15c 100644 --- a/Documentation/gh-pages/source/conf.py +++ b/Documentation/gh-pages/source/conf.py @@ -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 = '' diff --git a/Documentation/gh-pages/source/configuring_simulation.rst b/Documentation/gh-pages/source/configuring_simulation.rst index 72a96691..7aa1ed35 100644 --- a/Documentation/gh-pages/source/configuring_simulation.rst +++ b/Documentation/gh-pages/source/configuring_simulation.rst @@ -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/ diff --git a/Documentation/gh-pages/source/configuring_simulation_expressions.rst b/Documentation/gh-pages/source/configuring_simulation_expressions.rst index 545d3197..2712ec82 100644 --- a/Documentation/gh-pages/source/configuring_simulation_expressions.rst +++ b/Documentation/gh-pages/source/configuring_simulation_expressions.rst @@ -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/ diff --git a/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst b/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst index 5f30a7db..abef55d4 100644 --- a/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst +++ b/Documentation/gh-pages/source/configuring_simulation_messagingsystem.rst @@ -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/ diff --git a/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst b/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst index e336f8d4..c0e1da15 100644 --- a/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst +++ b/Documentation/gh-pages/source/configuring_simulation_pitfalls.rst @@ -41,15 +41,3 @@ the message:: Depening on where the element is referenced, the error may look different. For example:: [KSOBJECT ERROR MESSAGE] component could not build command named (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/ diff --git a/Documentation/gh-pages/source/configuring_simulation_statements.rst b/Documentation/gh-pages/source/configuring_simulation_statements.rst index 747649bd..0cd8fbbb 100644 --- a/Documentation/gh-pages/source/configuring_simulation_statements.rst +++ b/Documentation/gh-pages/source/configuring_simulation_statements.rst @@ -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 diff --git a/Documentation/gh-pages/source/contact.rst b/Documentation/gh-pages/source/contact.rst index d41b6da3..9c9778f9 100644 --- a/Documentation/gh-pages/source/contact.rst +++ b/Documentation/gh-pages/source/contact.rst @@ -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 \ No newline at end of file diff --git a/Documentation/gh-pages/source/examples.rst b/Documentation/gh-pages/source/examples.rst index 413190d8..747b8ce5 100644 --- a/Documentation/gh-pages/source/examples.rst +++ b/Documentation/gh-pages/source/examples.rst @@ -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 `_ diff --git a/Documentation/gh-pages/source/index.rst b/Documentation/gh-pages/source/index.rst index 14a06ba8..78337b06 100644 --- a/Documentation/gh-pages/source/index.rst +++ b/Documentation/gh-pages/source/index.rst @@ -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 - - diff --git a/Documentation/gh-pages/source/introduction.rst b/Documentation/gh-pages/source/introduction.rst index a414f102..aedd1956 100644 --- a/Documentation/gh-pages/source/introduction.rst +++ b/Documentation/gh-pages/source/introduction.rst @@ -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 \ No newline at end of file diff --git a/Documentation/gh-pages/source/kassiopeia_generation.rst b/Documentation/gh-pages/source/kassiopeia_generation.rst index bc16ba61..21609ae1 100644 --- a/Documentation/gh-pages/source/kassiopeia_generation.rst +++ b/Documentation/gh-pages/source/kassiopeia_generation.rst @@ -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/ diff --git a/Documentation/gh-pages/source/kassiopeia_navigation.rst b/Documentation/gh-pages/source/kassiopeia_navigation.rst index 7b116593..7a239272 100644 --- a/Documentation/gh-pages/source/kassiopeia_navigation.rst +++ b/Documentation/gh-pages/source/kassiopeia_navigation.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kassiopeia_output.rst b/Documentation/gh-pages/source/kassiopeia_output.rst index 646844be..df3a110d 100644 --- a/Documentation/gh-pages/source/kassiopeia_output.rst +++ b/Documentation/gh-pages/source/kassiopeia_output.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kassiopeia_propagation.rst b/Documentation/gh-pages/source/kassiopeia_propagation.rst index 8eeefcb1..0e871786 100644 --- a/Documentation/gh-pages/source/kassiopeia_propagation.rst +++ b/Documentation/gh-pages/source/kassiopeia_propagation.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kassiopeia_simulation.rst b/Documentation/gh-pages/source/kassiopeia_simulation.rst index cf75a49c..cd20964d 100644 --- a/Documentation/gh-pages/source/kassiopeia_simulation.rst +++ b/Documentation/gh-pages/source/kassiopeia_simulation.rst @@ -37,18 +37,3 @@ modify the actual objects used during the course of a simulation. Following the declaration of ``ks_simulation``, the closing tag ```` 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/ - diff --git a/Documentation/gh-pages/source/kassiopeia_visualization.rst b/Documentation/gh-pages/source/kassiopeia_visualization.rst index 9629f44d..10b69980 100644 --- a/Documentation/gh-pages/source/kassiopeia_visualization.rst +++ b/Documentation/gh-pages/source/kassiopeia_visualization.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kemfield_fields.rst b/Documentation/gh-pages/source/kemfield_fields.rst index 51b53523..0a00527a 100644 --- a/Documentation/gh-pages/source/kemfield_fields.rst +++ b/Documentation/gh-pages/source/kemfield_fields.rst @@ -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 diff --git a/Documentation/gh-pages/source/kemfield_visualization.rst b/Documentation/gh-pages/source/kemfield_visualization.rst index f98fcdae..78da48fa 100644 --- a/Documentation/gh-pages/source/kemfield_visualization.rst +++ b/Documentation/gh-pages/source/kemfield_visualization.rst @@ -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/ - - diff --git a/Documentation/gh-pages/source/kgeobag_complex_shapes.rst b/Documentation/gh-pages/source/kgeobag_complex_shapes.rst index 567246e3..0249ba57 100644 --- a/Documentation/gh-pages/source/kgeobag_complex_shapes.rst +++ b/Documentation/gh-pages/source/kgeobag_complex_shapes.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kgeobag_geometry.rst b/Documentation/gh-pages/source/kgeobag_geometry.rst index a3dbdfac..38c2251d 100644 --- a/Documentation/gh-pages/source/kgeobag_geometry.rst +++ b/Documentation/gh-pages/source/kgeobag_geometry.rst @@ -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/ - diff --git a/Documentation/gh-pages/source/kgeobag_simple_shapes.rst b/Documentation/gh-pages/source/kgeobag_simple_shapes.rst index 8346617f..eb3dbd71 100644 --- a/Documentation/gh-pages/source/kgeobag_simple_shapes.rst +++ b/Documentation/gh-pages/source/kgeobag_simple_shapes.rst @@ -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/ diff --git a/Documentation/gh-pages/source/kgeobag_visualization.rst b/Documentation/gh-pages/source/kgeobag_visualization.rst index c3b4687a..19e59bfc 100644 --- a/Documentation/gh-pages/source/kgeobag_visualization.rst +++ b/Documentation/gh-pages/source/kgeobag_visualization.rst @@ -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/ diff --git a/Documentation/gh-pages/source/links.rst b/Documentation/gh-pages/source/links.rst new file mode 100644 index 00000000..2cb7a07a --- /dev/null +++ b/Documentation/gh-pages/source/links.rst @@ -0,0 +1,65 @@ +.. _publications: https://www.katrin.kit.edu/375.php +.. _`our paper`: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950 + +.. _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 + +.. _`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 + +.. _KATRIN: https://www.katrin.kit.edu + +.. _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/ + +.. _NumPy: https://numpy.org/ +.. _Pandas: https://pandas.pydata.org/ + +.. _CMake: https://www.cmake.org/ +.. _GCC: https://gcc.gnu.org/ +.. _Clang: https://clang.llvm.org/ +.. _HDF5: https://support.hdfgroup.org/HDF5/ +.. _LibXml2: https://www.xmlsoft.org/ +.. _PCL: https://www.pointclouds.org/ +.. _PETSc: https://mcs.anl.gov/petsc/ +.. _DoxyGen: https://www.doxygen.nl/ +.. _GSL: https://www.gnu.org/software/gsl/ +.. _Boost: http://www.boost.org/ + +.. _TBB: https://www.threadingbuildingblocks.org/ + +.. _OpenMPI: https://www.open-mpi.org/ +.. _MPICH: http://www.mpich.org/ +.. _FFTW: http://www.fftw.org/ +.. _CUDA: https://developer.nvidia.com/cuda-toolkit +.. _OpenCL: https://www.khronos.org/opencl/ +.. _ZLIB: http://www.zlib.net/ +.. _miniz: https://code.google.com/archive/p/miniz/ +.. _Docker: https://www.docker.com/ +.. _GoogleTest: https://github.com/google/googletest/ +.. _gperftools: https://github.com/gperftools/gperftools/ +.. |gccVersion| replace:: 6.1 +.. |clangVersion| replace:: 3.4 +.. |CMakeVersion| replace:: 3.14 +.. |BoostVersion| replace:: 1.65 +.. |ROOTVersion| replace:: 6.24 +.. |FFTWVersion| replace:: 3.3.4 +.. |VTKVersion| replace:: 7.0 + + + diff --git a/Documentation/gh-pages/source/output.rst b/Documentation/gh-pages/source/output.rst index 09b6e10c..f923eda7 100644 --- a/Documentation/gh-pages/source/output.rst +++ b/Documentation/gh-pages/source/output.rst @@ -777,10 +777,3 @@ However, because the storage is rather inefficient it should not be used for lar the order of several Gigabytes can be easily produced by a typical Monte-Carlo simulation! -.. _Paraview: http://www.paraview.org/ -.. _ROOT: https://root.cern.ch/ -.. _VTK: http://www.vtk.org/ -.. _NumPy: https://numpy.org/ -.. _Pandas: https://pandas.pydata.org/ -.. _uproot: https://pypi.org/project/uproot/ -.. _Gnuplot: http://www.gnuplot.info/ diff --git a/Documentation/gh-pages/source/runningKassiopeia.rst b/Documentation/gh-pages/source/runningKassiopeia.rst index c653ec00..5c4708e1 100644 --- a/Documentation/gh-pages/source/runningKassiopeia.rst +++ b/Documentation/gh-pages/source/runningKassiopeia.rst @@ -51,11 +51,5 @@ just once in the terminal. To immediately exit the simulation (without cleaning the key combination ``Crtl-C`` again, which leads to program termination. -.. _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 `_ diff --git a/Documentation/gh-pages/source/setup_manual.rst b/Documentation/gh-pages/source/setup_manual.rst index c6781941..b61169da 100644 --- a/Documentation/gh-pages/source/setup_manual.rst +++ b/Documentation/gh-pages/source/setup_manual.rst @@ -422,36 +422,3 @@ The ``COMPILER_TUNE_OPTIONS`` flag activates the compiler options: Since this produces code compiled for the current CPU, this option should not be used on a computing cluster or other architectures where compiled code is shared between different machines. Be aware that this option is largely untested. - -.. _CMake: https://www.cmake.org/ -.. _GCC: https://gcc.gnu.org/ -.. _Clang: https://clang.llvm.org/ -.. _HDF5: https://support.hdfgroup.org/HDF5/ -.. _LibXml2: https://www.xmlsoft.org/ -.. _PCL: https://www.pointclouds.org/ -.. _PETSc: https://mcs.anl.gov/petsc/ -.. _DoxyGen: https://www.doxygen.nl/ -.. _GSL: https://www.gnu.org/software/gsl/ -.. _ROOT: https://root.cern.ch/ -.. _Boost: http://www.boost.org/ -.. _Log4CXX: https://logging.apache.org/log4cxx/latest_stable/ -.. _TBB: https://www.threadingbuildingblocks.org/ -.. _VTK: http://www.vtk.org/ -.. _OpenMPI: https://www.open-mpi.org/ -.. _MPICH: http://www.mpich.org/ -.. _FFTW: http://www.fftw.org/ -.. _CUDA: https://developer.nvidia.com/cuda-toolkit -.. _OpenCL: https://www.khronos.org/opencl/ -.. _ZLIB: http://www.zlib.net/ -.. _miniz: https://code.google.com/archive/p/miniz/ -.. _Docker: https://www.docker.com/ -.. _GoogleTest: https://github.com/google/googletest/ -.. _gperftools: https://github.com/gperftools/gperftools/ -.. |gccVersion| replace:: 6.1 -.. |clangVersion| replace:: 3.4 -.. |CMakeVersion| replace:: 3.14 -.. |BoostVersion| replace:: 1.65 -.. |ROOTVersion| replace:: 6.24 -.. |FFTWVersion| replace:: 3.3.4 -.. |VTKVersion| replace:: 7.0 - diff --git a/Documentation/gh-pages/source/tools.rst b/Documentation/gh-pages/source/tools.rst index 9a148e21..1c4f7556 100644 --- a/Documentation/gh-pages/source/tools.rst +++ b/Documentation/gh-pages/source/tools.rst @@ -159,5 +159,3 @@ Finally, some helper tools are provided with *Kassiopeia* that can be used toget All listed programs will show a brief usage summary if called without arguments. -.. _ROOT: https://root.cern.ch/ -.. _VTK: http://www.vtk.org/