diff --git a/Documentation/gh-pages/source/compiling.rst b/Documentation/gh-pages/source/compiling.rst index 68a56f2e9..91c9fa9bd 100644 --- a/Documentation/gh-pages/source/compiling.rst +++ b/Documentation/gh-pages/source/compiling.rst @@ -1,4 +1,4 @@ -Getting starting with Kassiopiea +Getting started with Kassiopiea ********************************** .. contents:: On this page diff --git a/Documentation/gh-pages/source/conf.py b/Documentation/gh-pages/source/conf.py index 65d280f85..85dad36b0 100644 --- a/Documentation/gh-pages/source/conf.py +++ b/Documentation/gh-pages/source/conf.py @@ -11,7 +11,21 @@ # documentation root, use os.path.abspath to make it absolute, like shown here. # import os -# import sys + +import sys + +sys.path.insert(0, os.path.abspath('/Gon-na/Kassiopeia/Kassiopeia/LICENSEtest.rst')) + +sys.path.insert(0, os.path.abspath('/Gon-na/Kassiopeia/LICENSEtest.rst')) + +sys.path.insert(0, os.path.abspath('/Kassiopeia/LICENSEtest.rst')) + +sys.path.insert(0, os.path.abspath('/Kassiopeia/Kassiopeia/LICENSEtest.rst')) + +sys.path.insert(0, os.path.abspath('/home/runner/work/Kassiopeia/Kassiopeia/LICENSEtest.rst')) + + + # sys.path.insert(0, os.path.abspath('.')) diff --git a/Documentation/gh-pages/source/contact.rst b/Documentation/gh-pages/source/contact.rst new file mode 100644 index 000000000..8417f0834 --- /dev/null +++ b/Documentation/gh-pages/source/contact.rst @@ -0,0 +1,46 @@ + +Contact, Meeting and References +********************************* + +You can `contribute changes `_, `report issues `_ and `join discussions `_ on Github. + +Join the Kassiopeia community on `Gitter `_. + +Contact +======= + +* Kasper development list: katrin-kasper@lists.kit.edu +* Richard Salomon: richardsalomon@uni-muenster.de +* Benedikt Bieringer: benedikt.b@uni-muenster.de + + + +Regular Meeting +======= + +We also organize a regular meeting via Zoom. + +Kassiopeia **users as well as developers** can join, ask questions, raise issues and discuss development topics. +It does not matter whether you are already an expert or a complete beginner. **Everyone is welcome!** + +The meeting is announced via email. +Please register for the `mailing list `_ if you are interested. + + +References and Citation +========== + +**Cite** |our paper|_\ **:** + +.. |our paper| replace:: **our paper** +.. _our paper: https://iopscience.iop.org/article/10.1088/1367-2630/aa6950 + +.. code-block:: bash + + D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950) + + +In addition to this user guide, *Kassiopeia* and its associated libraries have been documented extensively in several +PhD theses. Many of these can be found under the list of KATRIN publications_. + +.. _publications: https://www.katrin.kit.edu/375.php \ No newline at end of file diff --git a/Documentation/gh-pages/source/external_documentation.rst b/Documentation/gh-pages/source/external_documentation.rst deleted file mode 100644 index abbb22fa3..000000000 --- a/Documentation/gh-pages/source/external_documentation.rst +++ /dev/null @@ -1,29 +0,0 @@ -References, Citation and Contact -******************************** - -.. contents:: On this page - :local: - :depth: 2 - -External references -=================== - -To cite the use of and/or data produced with the assistance of *Kassiopeia* or its associated libraries (*KGeoBag*, -*KEMField*, or *Kommon*). Please refer to the paper: - - D. Furse *et al.* (2017) New J. Phys. **19** 053012: - "Kassiopeia: A Modern, Extensible C++ Particle Tracking Package" - (`doi:10.1088/1367-2630/aa6950 `_) - -In addition to this user guide, *Kassiopeia* and its associated libraries have been documented extensively in several -PhD theses. Many of these can be found under the list of KATRIN publications_. - -Developer contact -================= - -To make bug reports, propose additional features and/or patches, please use the pull-request and issue tracker available -on the *Kassiopeia* GitHub repository here_. Additional unrelated inquiries may be directed towards: katrin-kasper (at) -lists (dot) kit (dot) edu. - -.. _publications: https://www.katrin.kit.edu/375.php -.. _here: https://github.com/KATRIN-Experiment/Kassiopeia diff --git a/Documentation/gh-pages/source/index.rst b/Documentation/gh-pages/source/index.rst index b6a2dc17a..25651ad45 100644 --- a/Documentation/gh-pages/source/index.rst +++ b/Documentation/gh-pages/source/index.rst @@ -40,8 +40,8 @@ Welcome to Kassiopeia's documentation! .. toctree:: :maxdepth: 4 - Introduction - References, Citation and Contact + Contact, Meeting and References + Introduction Getting Started Examples and Tests Configuring Your Own Simulation @@ -52,9 +52,10 @@ Welcome to Kassiopeia's documentation! Visualization Techniques XML Bindings License + LicenseTEST Authors - + @@ -94,6 +95,9 @@ to run your first simulation! *Note: A VTK error indicates that the "VNC (Deskto D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950) +In addition to this user guide, *Kassiopeia* and its associated libraries have been documented extensively in several +PhD theses. Many of these can be found under the list of KATRIN publications_. + **Docker images** -------------- @@ -106,6 +110,6 @@ The `kassiopeia/full` image comes with a JupyterLab installation, can run on Kub .. |More information| replace:: **More information** .. _More information: https://github.com/KATRIN-Experiment/Kassiopeia/blob/main/Docker/README.md - +.. _publications: https://www.katrin.kit.edu/375.php diff --git a/Documentation/gh-pages/source/licensetest.rst b/Documentation/gh-pages/source/licensetest.rst new file mode 100644 index 000000000..68447d8b6 --- /dev/null +++ b/Documentation/gh-pages/source/licensetest.rst @@ -0,0 +1 @@ +/home/runner/work/Kassiopeia \ No newline at end of file diff --git a/Documentation/gh-pages/source/linktolicense.rst b/Documentation/gh-pages/source/linktolicense.rst new file mode 100644 index 000000000..2f46982fb --- /dev/null +++ b/Documentation/gh-pages/source/linktolicense.rst @@ -0,0 +1,23 @@ + + +.. include:: ../Gon-na/Kassiopeia/LICENSEtest.rst + +.. include:: ../Gon-na/Kassiopeia/blob/main/LICENSEtest.rst + +.. include:: ../Gon-na/Kassiopeia/Kassiopeia/blob/main/LICENSEtest.rst + +.. include:: ../Kassiopeia/LICENSEtest.rst + +BREAKER 0 + +.. include:: licensetest.rst + +BREAKER 1 + +.. include:: ../home/runner/work/Kassiopeia/Kassiopeia/LICENSEtest.rst + + +BREAKER 2 + + +.. include:: license.rst \ No newline at end of file diff --git a/LICENSEtest.rst b/LICENSEtest.rst new file mode 100644 index 000000000..8294b6c13 --- /dev/null +++ b/LICENSEtest.rst @@ -0,0 +1,6 @@ +testlicense file +no content HOWEVER + +fieldsd +fieldsf +fields \ No newline at end of file diff --git a/README.md b/README.md index a1bc6312d..75f873b9a 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,6 @@ This simulation package by [the KATRIN collaboration](https://katrin.kit.edu) allows to run highly customizable particle tracking simulations along with calculations of electric and magnetic fields. -**Full user guide:** http://katrin-experiment.github.io/Kassiopeia/index.html - **Quick start:** [**Try it out online**](https://mybinder.org/v2/gh/KATRIN-Experiment/KassiopeiaBinder/HEAD) in an interactive Binder session. Open a "VNC (Desktop)" tab and a terminal tab and run @@ -31,159 +29,15 @@ to run your first simulation! *Note: A VTK error indicates that the "VNC (Deskto D. Furse et al. (2017) New J. Phys. 19 053012: “Kassiopeia: A Modern, Extensible C++ Particle Tracking Package” (doi:10.1088/1367-2630/aa6950) ``` - Docker images --------------- - -**All images:** https://github.com/orgs/KATRIN-Experiment/packages - -The `kassiopeia/full` image comes with a JupyterLab installation, can run on Kubernetes based JupyterHubs and is also used for the "try it out online" link above. - -**More information:** [Docker README](Docker/README.md) - - System requirements: ----------------------- - -NOTE: Kasper requires Linux/MacOS. Windows+cygwin should work too, but has not been tested. - -Some dependencies are only required if certain module are compiled in. - -Dependencies: -* CMake (https://www.cmake.org) version 3.14 or higher -* G++ (https://gcc.gnu.org) version 6.1 or higher (if compiling with GCC) -* Clang++ (https://clang.llvm.org) version 3.4 or higher (if compiling with clang) -* Boost (https://www.boost.org) version 1.65 or higher -* GSL (https://www.gnu.org/software/gsl) -* ROOT (https://www.cern.ch/root) version 6.16 or higher - + --enable-minuit2 (if you want to use KaFit) - + --enable-fftw3 (if you want to use KEMField) - -Optional Dependencies: -* FFTW (https://fftw.org) version 3.3.4 or higher -* HDF5 (https://support.hdfgroup.org/HDF5/) -* Log4CXX (https://logging.apache.org/log4cxx) -* MPI (https://www.open-mpi.org or mpich.org) -* OpenCL (https://www.khronos.org/opencl), installation details depend on your system -* PETSc (https://mcs.anl.gov/petsc) -* VTK (https://www.vtk.org) version 6.1 or higher -* pdflatex (for making the documentation; minimum version not known) -* doxygen (for making the documentation; minimum version not known) - -### Ubuntu Linux 18.04 LTS (bionic) - -* Make sure to update CMake to version 3.13 or newer. See www.cmake.org or use this - [direct link](https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz). -* Download ROOT libraries from cern.root.ch or use this - [direct link](https://root.cern/download/root_v6.18.04.Linux-ubuntu18-x86_64-gcc7.4.tar.gz). - Another option is to build your own version from the source files. -* To install all build dependencies: - ``` - > apt-get update -y && apt-get install -y \ - build-essential cmake cmake-curses-gui \ - libqt4-dev libx11-dev libxext-dev libxft-dev libxpm-dev \ - libboost-all-dev libfftw3-dev libgsl0-dev libhdf5-dev liblog4cxx-dev libomp-dev libopenmpi-dev \ - libpcl-dev libsqlite3-dev libssl-dev libvtk6-dev libxml2-dev ocl-icd-opencl-dev zlib1g-dev - ``` - -### Fedora Linux 31 - -* The ROOT libraries can be installed easily with the package manager. -* To install all build dependencies: - ``` - > dnf install -y \ - @development-tools cmake cmake-gui \ - root-core root-io-xmlparser root-minuit2 root-spectrum \ - vtk vtk-qt vtk-java \ - boost-devel fftw-devel gsl-devel hdf5-devel libomp-devel libxml2-devel log4cxx-devel \ - ocl-icd-devel openmpi-devel openssl-devel pcl-devel sqlite-devel vtk-devel zlib-devel - ``` - - Installation --------------- - -1. Make a separate directory for the build tree, and enter that directory: - ``` - > mkdir build - > cd build - ``` - - * Consider setting important environmental variables now. - Selecting a specific compiler to be configured by CMake is done for example by - ``` - > export CXX=clang++ - > export CC=clang - ``` - to use the Clang/LLVM compiler, or - ``` - > export CXX=g++ - > export CC=gcc - ``` - to use the GNU compiler (GCC). - -2. Run cmake (or ccmake, or cmake-gui, if you prefer): - ``` - > cmake .. - > ccmake .. - ``` - - * If applicable, make any changes you need to the configuration, and - (re)generate the makefiles. e.g. You may want to change the install - prefix. (NOTE: Most users will probably want to do this.) - - The default is `/install`. If you're not doing - a general install for your system, or if you just want to use a - different location, you should change `CMAKE_INSTALL_PREFIX` to - your desired location. Also note the `CMAKE_BUILD_TYPE`. If you - do not plan to debug Kasper applications, 'Release' will give you - the best execution performance. - - If you use one of the GUI variants (ccmake or cmake-gui), you can - just go through a list of all the available build options. Most - options also have a short description. Note that some variables - have dependencies (e.g. `BUILD_KASSIOPEIA` will also enable - `BUILD_KEMFIELD`). - -3. Then type - ``` - > make - ``` - to start the build process. This can take some time, depending on the - modules you activated in CMake. If you have more than one CPU core on - your system, you can build several files in parallel: - ``` - > make -j2 - ``` - Make sure to keep the number passed to 'make' smaller than the number - of actual CPU cores. Instead of 'make' you could also use 'ninja' - or any other build tool that works with CMake. - -4. Install the executables and libraries with - ``` - > make install - ``` - Executables are installed in the `bin/` directory, and libraries are - installed in the `lib/` directory (or `lib64/` on some systems.) - -5. Include `kasperenv.sh` in your `~/.bashrc` (or similar, depending on - your shell) with - ``` - > source /path/to/Kasper/install/bin/kasperenv.sh - ``` - This script adds the `bin/` directory to your `$PATH` so you can call - any Kasper executables directly from the commandline. Furthermore this - sets the `$KASPERSYS` environment variable to the install directory. - - - Documentation ---------------- - -1. Documentation distributed with Kasper - 1. This `README.md` file - 2. The Kassiopeia documentation is an HTML page hosted on GitHub - that will guide you through the installation process and - explains how to get started with your first simulation: - http://katrin-experiment.github.io/Kassiopeia/index.html - - Open Source +**[Documentation](http://katrin-experiment.github.io/Kassiopeia/index.html)** +============================================================================================= + +* **[System requirements & installation](https://katrin-experiment.github.io/Kassiopeia/compiling.html)** +* **[Docker images](https://github.com/orgs/KATRIN-Experiment/packages), [more information](Docker/README.md)** +* **[Meeting & Getting help](https://katrin-experiment.github.io/Kassiopeia/discussion.html)** + + +Open source ------------- This software is distributed "as-is" under an open source license @@ -196,24 +50,15 @@ Kassiopeia includes the following open-source libraries: * stl_reader (https://github.com/sreiter/stl_reader) - Getting help --------------- +Contact +----------------------- -Join the Kassiopeia community on Gitter: https://gitter.im/kassiopeia-simulation/community +* Kasper development list: katrin-kasper@lists.kit.edu +* Richard Salomon: richardsalomon@uni-muenster.de +* Benedikt Bieringer: benedikt.b@uni-muenster.de -You can [contribute changes](https://github.com/KATRIN-Experiment/Kassiopeia/compare), [report issues](https://github.com/KATRIN-Experiment/Kassiopeia/issues/new) and [join discussions](https://github.com/KATRIN-Experiment/Kassiopeia/discussions) on Github. -### Regular Meeting -We also organize a regular meeting via Zoom. -Kassiopeia **users as well as developers** can join, ask questions, raise issues and discuss development topics. -It does not matter whether you are already an expert or a complete beginner. **Everyone is welcome!** -The meeting is announced via email. -Please register for the [mailing list](https://www.lists.kit.edu/sympa/subscribe/kassiopeia-user) if you are interested. -Primary email contacts: -* Kasper development list: katrin-kasper@lists.kit.edu -* Richard Salomon: richardsalomon@uni-muenster.de -* Benedikt Bieringer: benedikt.b@uni-muenster.de