diff --git a/CMakeLists.txt b/CMakeLists.txt index ed299ea61..49861573b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,6 +14,8 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) include("CMake/POET_Scripts.cmake") list(APPEND CMAKE_MODULE_PATH "${POET_SOURCE_DIR}/CMake") +get_poet_version() + # set(GCC_CXX_FLAGS "-D STRICT_R_HEADERS") add_definitions(${GCC_CXX_FLAGS}) find_package(MPI REQUIRED) diff --git a/README.md b/README.md index 774fd3f31..224271910 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,6 @@ - -**Po**tsdamer **R**eactive **T**ransport - - # Forked Project *PORT* is a fork of [POET](https://doi.org/10.5281/zenodo.4757913) @@ -19,11 +15,20 @@ also applicable for this project. POET is a coupled reactive transport simulator implementing a parallel architecture and a fast, original MPI-based Distributed Hash Table. +## Parsed code documentiation + +A parsed version of POET's documentiation can be found at [Gitlab +pages](https://sec34.git-pages.gfz-potsdam.de/port). + ## External Libraries The following external header library is shipped with POET: - **argh** - https://github.com/adishavit/argh (BSD license) +- **PhreeqcRM** with patches from GFZ - + https://www.usgs.gov/software/phreeqc-version-3 - + https://git.gfz-potsdam.de/mluebke/phreeqcrm-gfz +- **tug** - https://git.gfz-potsdam.de/sec34/tug ## Installation @@ -35,23 +40,18 @@ To compile POET you need several software to be installed: - MPI-Implementation (tested with OpenMPI and MVAPICH) - R language and environment - CMake 3.9+ - -If you want to build documentation during compilation, `doxygen`and -`graphviz` must be provided too. +- *optional*: `doxygen` with `dot` bindings for documentiation The following R libraries must then be installed, which will get the needed dependencies automatically: -- [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html) - [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html) - [RInside](https://cran.r-project.org/web/packages/RInside/index.html) -- [RedModRphree](https://git.gfz-potsdam.de/delucia/RedModRphree) -- [Rmufits](https://git.gfz-potsdam.de/delucia/Rmufits) ### Compiling source code -The generation of makefiles is done with CMake. If you obtained POET -from git, you should be able to generate Makefiles by running +The generation of makefiles is done with CMake. You should be able to generate +Makefiles by running: ```sh mkdir build && cd build @@ -62,34 +62,21 @@ This will create the directory `build` and processes the CMake files and generate Makefiles from it. You're now able to run `make` to start build process. -If POET was obtained from the official SVN repository or the redmine -at the branch or tag -to be used have to be set via - -```sh -mkdir build && cd build -cmake -D POET_SET_BRANCH="" .. -``` - -where currently available branches/tags are: - -- dev - If everything went well you'll find the executable at -`build/src/poet`, but it is recommended to install the POET project +`build/app/poet`, but it is recommended to install the POET project structure to a desired `CMAKE_INSTALL_PREFIX` with `make install`. During the generation of Makefiles, various options can be specified -via `cmake -D