diff --git a/.gitignore b/.gitignore
index 801010414..79e7da401 100644
--- a/.gitignore
+++ b/.gitignore
@@ -138,3 +138,5 @@ vignettes/*.pdf
 /*_files/
 
 # End of https://www.toptal.com/developers/gitignore/api/c,c++,r,cmake
+
+build/
diff --git a/CMake/FindR.cmake b/CMake/FindR.cmake
new file mode 100644
index 000000000..f07d36bd3
--- /dev/null
+++ b/CMake/FindR.cmake
@@ -0,0 +1,25 @@
+# prepare R environment (Rcpp + RInside)
+find_program(R_EXE "R")
+
+# search for R executable, R header file and library path
+if(R_EXE)
+  execute_process(COMMAND ${R_EXE} RHOME
+    OUTPUT_VARIABLE R_ROOT_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+
+  find_path(R_INCLUDE_DIR R.h
+    HINTS ${R_ROOT_DIR}
+    PATHS /usr/inlcude /usr/local/include /usr/share
+    PATH_SUFFIXES include/R R/include
+  )
+
+  find_library(R_LIBRARY R
+    HINTS ${R_ROOT_DIR}/lib
+  )
+else()
+  message(FATAL_ERROR "No R runtime found!")
+endif()
+
+set(R_LIBRARIES ${R_LIBRARY})
+set(R_INCLUDE_DIRS ${R_INCLUDE_DIR})
\ No newline at end of file
diff --git a/CMake/FindRInside.cmake b/CMake/FindRInside.cmake
new file mode 100644
index 000000000..c7757700f
--- /dev/null
+++ b/CMake/FindRInside.cmake
@@ -0,0 +1,23 @@
+# find RInside libraries and include path
+execute_process(COMMAND echo "cat(find.package('RInside'))"
+  COMMAND ${R_EXE} --vanilla --slave
+  RESULT_VARIABLE RINSIDE_NOT_FOUND
+  ERROR_QUIET
+  OUTPUT_VARIABLE RINSIDE_PATH
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+if(RInside_NOT_FOUND)
+  message(FATAL_ERROR "RInside not found!")
+endif()
+
+find_library(R_RInside_LIBRARY libRInside.so
+  HINTS ${RINSIDE_PATH}/lib)
+
+list(APPEND R_LIBRARIES ${R_RInside_LIBRARY})
+
+find_path(R_RInside_INCLUDE_DIR RInside.h
+  HINTS ${RINSIDE_PATH}
+  PATH_SUFFIXES include)
+
+list(APPEND R_INCLUDE_DIRS ${R_RInside_INCLUDE_DIR})
\ No newline at end of file
diff --git a/CMake/FindRcpp.cmake b/CMake/FindRcpp.cmake
new file mode 100644
index 000000000..be88a3780
--- /dev/null
+++ b/CMake/FindRcpp.cmake
@@ -0,0 +1,23 @@
+# find Rcpp include directory
+execute_process(COMMAND echo "cat(find.package('Rcpp'))"
+  COMMAND ${R_EXE} --vanilla --slave
+  RESULT_VARIABLE RCPP_NOT_FOUND
+  ERROR_QUIET
+  OUTPUT_VARIABLE RCPP_PATH
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+if(RCPP_NOT_FOUND)
+  message(FATAL_ERROR "Rcpp not found!")
+endif()
+
+# find_library(R_Rcpp_LIBRARY Rcpp.so
+#   HINTS ${RCPP_PATH}/libs)
+
+# list(APPEND R_LIBRARIES ${R_Rcpp_LIBRARY})
+
+find_path(R_Rcpp_INCLUDE_DIR Rcpp.h
+  HINTS ${RCPP_PATH}
+  PATH_SUFFIXES include)
+
+list(APPEND R_INCLUDE_DIRS ${R_Rcpp_INCLUDE_DIR})
\ No newline at end of file
diff --git a/CMake/POET_Scripts.cmake b/CMake/POET_Scripts.cmake
new file mode 100644
index 000000000..69760cc44
--- /dev/null
+++ b/CMake/POET_Scripts.cmake
@@ -0,0 +1,28 @@
+# Set or get version
+macro(get_POET_version)
+  if(EXISTS ${PROJECT_SOURCE_DIR}/.git)
+    find_program(GIT_EXECUTABLE git DOC "git executable")
+    mark_as_advanced(GIT_EXECUTABLE)
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
+      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+      OUTPUT_VARIABLE POET_GIT_BRANCH
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} describe --always
+      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+      OUTPUT_VARIABLE POET_GIT_VERSION
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT POET_GIT_BRANCH STREQUAL "master")
+      set(POET_VERSION "${POET_GIT_BRANCH}/${POET_GIT_VERSION}")
+    else()
+      set(POET_VERSION "${POET_GIT_VERSION}")
+    endif()
+  elseif(EXISTS ${PROJECT_SOURCE_DIR}/.svn)
+    file(STRINGS .gitversion POET_VERSION)
+  else()
+    set(POET_VERSION "0.1")
+  endif()
+
+  message(STATUS "Configuring POET version ${POET_VERSION}")
+endmacro(get_POET_version)
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 000000000..3f1a0f4fb
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,31 @@
+# Version 3.9+ offers new MPI package variables
+cmake_minimum_required(VERSION 3.9)
+
+project(POET CXX C)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+include("CMake/POET_Scripts.cmake")
+list(APPEND CMAKE_MODULE_PATH "${POET_SOURCE_DIR}/CMake")
+
+# set(GCC_CXX_FLAGS "-D STRICT_R_HEADERS") add_definitions(${GCC_CXX_FLAGS})
+
+find_package(MPI REQUIRED)
+
+find_package(R REQUIRED)
+find_package(Rcpp REQUIRED)
+find_package(RInside REQUIRED)
+
+add_subdirectory(src)
+add_subdirectory(R_lib)
+add_subdirectory(data)
+
+option(BUILD_DOC "Build documentation with doxygen" ON)
+
+if(BUILD_DOC)
+  add_subdirectory(docs)
+endif(BUILD_DOC)
diff --git a/README.md b/README.md
index 66bfabe01..3663e87dd 100644
--- a/README.md
+++ b/README.md
@@ -1,63 +1,201 @@
-
+
 <!--
-    Time-stamp: "Last modified 2020-02-01 18:14:13 delucia"
+    Time-stamp: "Last modified 2021-02-08 13:46:00 mluebke"
 -->
 
-# install libraries from MDL
+# POET
 
-    library(devtools)
-    devtools::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de")
-    devtools::install_gitlab("delucia/Rmufits", host="https://git.gfz-potsdam.de")
-  
-# USAGE
+POET is a coupled reactive transport simulator implementing a parallel
+architecture and a fast, original MPI-based Distributed Hash Table.
 
-mpirun ./kin <OPTIONS> <simfile.R> <DIRECTORY>
+## External Libraries
 
-OPTIONS:
+The following external header library is shipped with POET:
 
---work-package-size=<1-n>     ... size of work packages (default 5)
+- **argh** - https://github.com/adishavit/argh (BSD license)
 
---ignore-result         ... disables store of simulation resuls
+## Installation
 
-DHT:
+### Requirements
 
---dht                   ... enable dht (default is off)
+To compile POET you need several software to be installed:
 
---dht-log               ... enable logarithm application before rounding (default is off)
+- C/C++ compiler (tested with GCC)
+- MPI-Implementation (tested with OpenMPI and MVAPICH)
+- R language and environment
+- CMake 3.9+
 
---dht-signif=<1-n>      ... set rounding to number of significant digits (default 5) 
-                            (only used if no vector is given in setup file)
-                            (for individual values per column use R vector "signif_vector" in setup file)
+If you want to build documentation during compilation, `doxygen`and `graphviz` must be provided too.
 
---dht-strategy=<0-1>    ... change dht strategy, not implemented yet (default 0, dht on workers)
+The following R libraries must then be installed, which will get the needed dependencies automatically:
 
---dht-size=<1-n>        ... size of dht per process involved (see dht-strategy) in byte (default 1GiB)
+- [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)
 
---dht-snaps=<0-2>	... enable or disable storage of DHT snapshots
-			    0 = snapshots are disabled
-			    1 = only stores snapshot at the end of the simulation with name <DIRECTORY>.dht
-			    2 = stores snapshot at the end and after each iteration
-			        iteration snapshot files are stored in <DIRECTORY>/iter<n>.dht
+### Compiling source code
 
---dht-file=<snapshot> 	... initializes DHT with the given snapshot file
+The generation of makefiles is done with CMake. If you obtained POET from git, you should be able to generate Makefiles by running
 
-###############################################################################
+```sh
+mkdir build && cd build
+cmake ..
+```
 
+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.
 
-# about the usage of MPI_Wtime()
-From the OpenMPI Man Page:
+If POET was obtained from the official SVN repository or the redmine at <https://redmine.cs.uni-potsdam.de/projects/poet> the branch or tag to be used have to be set via
 
-For example, on platforms that support it, the clock_gettime() function will be used 
-to obtain a monotonic clock value with whatever precision is supported on that platform (e.g., nanoseconds). 
+```sh
+mkdir build && cd build
+cmake -D POET_SET_BRANCH="<BRANCH>" ..
+```
 
-# External Libraries
-Cmdline Parsing -> https://github.com/adishavit/argh
+where currently available branches/tags are:
 
+- dev
 
-# Examples included (more to come)
-1) SimDol2D.R     ... simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20 time steps
-2) SimDolKtz.R    ... simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k elements), 20 time steps
-                      The flow snapshots are NOT INCLUDED in svn but must be provided separately
+If everything went well you'll find the executable at `build/src/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 <option>=<value> [...]`. Currently there are the following available options:
 
+- **DHT_Debug**=_boolean_ - toggles the output of detailed statistics about DHT
+  usage (`cmake -D DHT_Debug=ON`). Defaults to _OFF_.
+- **BUILD_DOC**=_boolean_ - toggles the generation of documantiation during
+  compilation process. Defaults to _ON_.
+- _only from svn version:_ **POET_SET_BRANCH**=_string_ - set branch or tag whose code is used
 
+### Example: Build from scratch
+
+Assuming that only the C/C++ compiler, MPI libraries, R runtime environment and
+CMake have been installed, POET can be installed as follows:
+
+```sh
+# start R environment
+$ R
+
+# install R dependencies
+> install.packages(c("devtools", "Rcpp", "RInside"))
+> devtools::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de")
+> devtools::install_gitlab("delucia/Rmufits", host="https://git.gfz-potsdam.de")
+> q(save="no")
+
+# cd into POET project root
+$ cd <POET_dir>
+
+# Build process
+$ mkdir build && cd build
+$ cmake -DCMAKE_INSTALL_PREFIX=/home/<user>/poet ..
+$ make -j<max_numprocs>
+$ make install
+```
+
+This will install a POET project structure into `/home/<user>/poet` which is
+called hereinafter `<POET_INSTALL_DIR>`. With this version of POET we **do not
+recommend** to install to hierarchies like `/usr/local/` etc.
+
+The correspondending directory tree would look like this:
+
+```sh
+.
+└── poet/
+    ├── bin/
+    │   └── poet
+    ├── data/
+    │   └── SimDol2D.R
+    ├── docs/
+    │    └── html/
+    │       ├── index.html
+    │       └── ...
+    └── R_lib/
+        ├── kin_r_library.R
+        └── parallel_r_library.R
+```
+
+The R libraries will be loaded at runtime and the paths are hardcoded
+absolute paths inside `poet.cpp`. So, if you consider to move `bin/poet` either
+change paths of the R source files and recompile POET or also move `R_lib/*`
+according to the binary.
+
+To display the generated html documentation just open `docs/html/index.html`
+with the browser of your choice.
+
+## Running
+
+Before POET is ready to run, a working directory must be created. In this
+directory you should find the executable file, the R scripts
+`<POET_ROOT>/R_lib/kin_r_library.R` and `<POET_ROOT>/R_lib/parallel_r_library.R`
+and the simulation description e.g. `<POET_ROOT>/data/chem_problems/SimDol2D.R`.
+
+Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>` where:
+
+- **OPTIONS** - runtime parameters (explained below)
+- **SIMFILE** - simulation described as R script (currently supported:
+  `<POET_INSTALL_DIR>/data/SimDol2D.R`)
+- **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
+
+### Runtime options
+
+The following parameters can be set:
+
+| Option                   | Value        | Description                                                    |
+| ------------------------ | ------------ | -------------------------------------------------------------- |
+| **--work-package-size=** | _1..n_       | size of work packages (defaults to _5_)                        |
+| **--ignore-result**      |              | disables store of simulation resuls                            |
+| **--dht**                |              | enabling DHT usage (defaults to _OFF_)                         |
+| **--dht-nolog**          |              | disabling applying of logarithm before rounding                |
+| **--dht-signif=**        | _1..n_       | set rounding to number of significant digits (defaults to _5_) |
+| **--dht-strategy=**      | _0-1_        | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
+| **--dht-size=**          | _1-n_        | size of DHT per process involved in byte (defaults to _1 GiB_) |
+| **--dht-snaps=**         | _0-2_        | disable or enable storage of DHT snapshots                     |
+| **--dht-file=**          | `<SNAPSHOT>` | initializes DHT with the given snapshot file                   |
+
+#### Additions to `dht-signif`
+
+Only used if no vector is given in setup file. For individual values per column
+use R vector `signif_vector` in `SIMFILE`.
+
+#### Additions to `dht-snaps`
+
+Following values can be set:
+
+- _0_ = snapshots are disabled
+- _1_ = only stores snapshot at the end of the simulation with name
+  `<OUTPUT_DIRECTORY>.dht`
+- _2_ = stores snapshot at the end and after each iteration iteration
+  snapshot files are stored in `<DIRECTORY>/iter<n>.dht`
+
+### Example: Running from scratch
+
+We will continue the above example and start a simulation with `SimDol2D.R`,
+which is the only simulation supported at this moment. The required flow velocities 
+snapshots are included in the R package Rmufits. It's a 2D, 50x50 grid, with 20 time 
+steps. To start the simulation with 4 processes `cd` into your previously installed 
+POET-dir `<POET_INSTALL_DIR>/bin` and run:
+
+```sh
+mpirun -n 4 ./poet ../data/SimDol2D.R output
+```
+
+After a finished simulation all data generated by POET will be found in the
+directory `output`.
+
+You might want to use the DHT to cache previously simulated data and
+reuse them in further time-steps. Just append `--dht` to the options of POET to
+activate the usage of the DHT. The resulting call would look like this:
+
+```sh
+mpirun -n 4 ./poet --dht SimDol2D.R output
+```
+
+## About the usage of MPI_Wtime()
+
+Implemented time measurement functions uses `MPI_Wtime()`. Some important
+informations from the OpenMPI Man Page:
+
+For example, on platforms that support it, the clock_gettime() function will be
+used to obtain a monotonic clock value with whatever precision is supported on
+that platform (e.g., nanoseconds).
diff --git a/R_lib/CMakeLists.txt b/R_lib/CMakeLists.txt
new file mode 100644
index 000000000..46896d88e
--- /dev/null
+++ b/R_lib/CMakeLists.txt
@@ -0,0 +1 @@
+install(FILES kin_r_library.R parallel_r_library.R DESTINATION R_lib)
diff --git a/src/kin_r_library.R b/R_lib/kin_r_library.R
similarity index 96%
rename from src/kin_r_library.R
rename to R_lib/kin_r_library.R
index fe39533ef..abaf86004 100644
--- a/src/kin_r_library.R
+++ b/R_lib/kin_r_library.R
@@ -1,3 +1,18 @@
+### Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+###
+### POET is free software; you can redistribute it and/or modify it under the
+### terms of the GNU General Public License as published by the Free Software
+### Foundation; either version 2 of the License, or (at your option) any later
+### version.
+###
+### POET is distributed in the hope that it will be useful, but WITHOUT ANY
+### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+### A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+###
+### You should have received a copy of the GNU General Public License along with
+### this program; if not, write to the Free Software Foundation, Inc., 51
+### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
 ## Simple function to check file extension. It is needed to check if
 ## the GridFile is SUM (MUFITS format) or rds/RData
 FileExt <- function (x)
diff --git a/src/kin_r_library_warnings.R b/R_lib/kin_r_library_warnings.R
similarity index 96%
rename from src/kin_r_library_warnings.R
rename to R_lib/kin_r_library_warnings.R
index f7ad279b0..bc0374965 100644
--- a/src/kin_r_library_warnings.R
+++ b/R_lib/kin_r_library_warnings.R
@@ -1,3 +1,18 @@
+### Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+###
+### POET is free software; you can redistribute it and/or modify it under the
+### terms of the GNU General Public License as published by the Free Software
+### Foundation; either version 2 of the License, or (at your option) any later
+### version.
+###
+### POET is distributed in the hope that it will be useful, but WITHOUT ANY
+### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+### A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+###
+### You should have received a copy of the GNU General Public License along with
+### this program; if not, write to the Free Software Foundation, Inc., 51
+### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
 ## Simple function to check file extension. It is needed to check if
 ## the GridFile is SUM (MUFITS format) or rds/RData
 FileExt <- function (x)
diff --git a/src/parallel_r_library.R b/R_lib/parallel_r_library.R
similarity index 55%
rename from src/parallel_r_library.R
rename to R_lib/parallel_r_library.R
index 1b1f1c035..ecaecbcc5 100644
--- a/src/parallel_r_library.R
+++ b/R_lib/parallel_r_library.R
@@ -1,3 +1,18 @@
+### Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+###
+### POET is free software; you can redistribute it and/or modify it under the
+### terms of the GNU General Public License as published by the Free Software
+### Foundation; either version 2 of the License, or (at your option) any later
+### version.
+###
+### POET is distributed in the hope that it will be useful, but WITHOUT ANY
+### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+### A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+###
+### You should have received a copy of the GNU General Public License along with
+### this program; if not, write to the Free Software Foundation, Inc., 51
+### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
 distribute_work_packages <- function(len, package_size) 
 {
     ## Check if work_package is a divisor of grid length and act
diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
new file mode 100644
index 000000000..59a6f9255
--- /dev/null
+++ b/data/CMakeLists.txt
@@ -0,0 +1 @@
+install(FILES SimDol2D.R DESTINATION data)
diff --git a/data/chem_problems/SimComp2D.R b/data/SimComp2D.R
similarity index 100%
rename from data/chem_problems/SimComp2D.R
rename to data/SimComp2D.R
diff --git a/data/chem_problems/SimCompKtz.R b/data/SimCompKtz.R
similarity index 100%
rename from data/chem_problems/SimCompKtz.R
rename to data/SimCompKtz.R
diff --git a/data/chem_problems/SimDol2D.R b/data/SimDol2D.R
similarity index 100%
rename from data/chem_problems/SimDol2D.R
rename to data/SimDol2D.R
diff --git a/data/chem_problems/SimDolKtz.R b/data/SimDolKtz.R
similarity index 100%
rename from data/chem_problems/SimDolKtz.R
rename to data/SimDolKtz.R
diff --git a/data/chem_problems/mdl_quint_kin.dat b/data/mdl_quint_kin.dat
similarity index 100%
rename from data/chem_problems/mdl_quint_kin.dat
rename to data/mdl_quint_kin.dat
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
new file mode 100644
index 000000000..1df5575e5
--- /dev/null
+++ b/docs/CMakeLists.txt
@@ -0,0 +1,18 @@
+find_package(Doxygen)
+if(DOXYGEN_FOUND)
+
+  set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/./Doxyfile.in)
+  set(DOXYGEN_OUT ${CMAKE_BINARY_DIR}/Doxyfile)
+
+  configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+
+  add_custom_target(doc_doxygen ALL
+    COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    COMMENT "Generating documantation with doxygen"
+    VERBATIM)
+
+  install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doxygen/ DESTINATION docs)
+else(DOXYGEN_FOUND)
+  message("Doxygen not found. Please install.")
+endif(DOXYGEN_FOUND)
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
new file mode 100644
index 000000000..2d21ebad3
--- /dev/null
+++ b/docs/Doxyfile.in
@@ -0,0 +1,2633 @@
+# Doxyfile 1.9.1
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+###############################################################################
+#########################GENERATED BY CMAKE####################################
+###############################################################################
+
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = @CMAKE_PROJECT_NAME@
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         = @CMAKE_PROJECT_VERSION@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = @CMAKE_CURRENT_BINARY_DIR@/doxygen
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = @SRC_CODE_DIR@ \
+                         @PROJECT_SOURCE_DIR@/./README.md \
+                         @CMAKE_CURRENT_SOURCE_DIR@/./Output.md
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE = @PROJECT_SOURCE_DIR@/./README.md
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                = @SRC_CODE_DIR@/./util/argh.h
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the configuration
+# file that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = "A coupled reactive transport simulator"
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           =
+
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE        = English
+
+# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all generated output in the proper direction.
+# Possible values are: None, LTR, RTL and Context.
+# The default value is: None.
+
+OUTPUT_TEXT_DIRECTION  = None
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
+# such as
+# /***************
+# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
+# Javadoc-style will behave just like regular comments and it will not be
+# interpreted by doxygen.
+# The default value is: NO.
+
+JAVADOC_BANNER         = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines (in the resulting output). You can put ^^ in the value part of an
+# alias to insert a newline as if a physical newline was in the original file.
+# When you need a literal { or } or , in the value part of an alias you have to
+# escape them by means of a backslash (\), this can lead to conflicts with the
+# commands \{ and \} for these it is advised to use the version @{ and @} or use
+# a double escape (\\{ and \\})
+
+ALIASES                =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
+# sources only. Doxygen will then generate output that is more tailored for that
+# language. For instance, namespaces will be presented as modules, types will be
+# separated into more groups, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_SLICE  = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
+# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
+# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
+# tries to guess whether the code is fixed or free formatted code, this is the
+# default for Fortran type files). For instance to make doxygen treat .inc files
+# as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen. When specifying no_extension you should add
+# * to the FILE_PATTERNS.
+#
+# Note see also the list of default file extension mappings.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See https://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 5.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 5
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use
+# during processing. When set to 0 doxygen will based this on the number of
+# cores available in the system. You can set it explicitly to a value larger
+# than 0 to get more control over the balance between CPU load and processing
+# speed. At this moment only the input processing can be done using multiple
+# threads. Since this is still an experimental feature the default is set to 1,
+# which efficively disables parallel processing. Please report any issues you
+# encounter. Generating dot graphs in parallel is controlled by the
+# DOT_NUM_THREADS setting.
+# Minimum value: 0, maximum value: 32, default value: 1.
+
+NUM_PROC_THREADS       = 1
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = YES
+
+# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
+# methods of a class will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIV_VIRTUAL   = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If this flag is set to YES, the name of an unnamed parameter in a declaration
+# will be determined by the corresponding definition. By default unnamed
+# parameters remain unnamed in the output.
+# The default value is: YES.
+
+RESOLVE_UNNAMED_PARAMS = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# declarations. If set to NO, these declarations will be included in the
+# documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
+# able to match the capabilities of the underlying filesystem. In case the
+# filesystem is case sensitive (i.e. it supports files in the same directory
+# whose names only differ in casing), the option must be set to YES to properly
+# deal with such files in case they appear in the input. For filesystems that
+# are not case sensitive the option should be be set to NO to properly deal with
+# output files written for symbols that only differ in casing, such as for two
+# classes, one named CLASS and the other named Class, and to also support
+# references to files without having to specify the exact matching casing. On
+# Windows (including Cygwin) and MacOS, users should typically set this option
+# to NO, whereas on Linux or other Unix flavors it should typically be set to
+# YES.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation. If
+# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
+# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
+# at the end of the doxygen process doxygen will return with a non-zero status.
+# Possible values are: NO, YES and FAIL_ON_WARNINGS.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see:
+# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# Note the list of default checked file patterns might differ from the list of
+# default file extension mappings.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
+# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
+# *.ucf, *.qsf and *.ice.
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.idl \
+                         *.ddl \
+                         *.odl \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.cs \
+                         *.d \
+                         *.php \
+                         *.php4 \
+                         *.php5 \
+                         *.phtml \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.pyw \
+                         *.f90 \
+                         *.f95 \
+                         *.f03 \
+                         *.f08 \
+                         *.f18 \
+                         *.f \
+                         *.for \
+                         *.vhd \
+                         *.vhdl \
+                         *.ucf \
+                         *.qsf \
+                         *.ice
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = YES
+
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# entity all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see https://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = NO
+
+# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
+# documentation will contain a main index with vertical navigation menus that
+# are dynamically created via JavaScript. If disabled, the navigation index will
+# consists of multiple levels of tabs that are statically embedded in every HTML
+# page. Disable this option to support browsers that do not have JavaScript,
+# like the Qt help browser.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_MENUS     = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see:
+# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
+# create a documentation set, doxygen will generate a Makefile in the HTML
+# output directory. Running make will produce the docset in that directory and
+# running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
+# genXcode/_index.html for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see:
+# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the main .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location (absolute path
+# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
+# run qhelpgenerator on the generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
+# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
+# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
+# the HTML output. These images will generally look nicer at scaled resolutions.
+# Possible values are: png (the default) and svg (looks nicer but requires the
+# pdf2svg or inkscape tool).
+# The default value is: png.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FORMULA_FORMAT    = png
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
+# to create new LaTeX commands to be used in formulas as building blocks. See
+# the section "Including formulas" for details.
+
+FORMULA_MACROFILE      =
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# https://www.mathjax.org) which uses client side JavaScript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from https://www.mathjax.org before deployment.
+# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using JavaScript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see:
+# https://xapian.org/). See the section "External Indexing and Searching" for
+# details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when not enabling USE_PDFLATEX the default is latex when enabling
+# USE_PDFLATEX the default is pdflatex and when in the later case latex is
+# chosen this is overwritten by pdflatex. For specific output languages the
+# default can have been set differently, this depends on the implementation of
+# the output language.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         =
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# Note: This tag is used in the Makefile / make.bat.
+# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
+# (.tex).
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
+# generate index for LaTeX. In case there is no backslash (\) as first character
+# it will be automatically added in the LaTeX code.
+# Note: This tag is used in the generated output file (.tex).
+# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
+# The default value is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_MAKEINDEX_CMD    = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
+# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
+# files. Set this option to YES, to get a higher quality PDF documentation.
+#
+# See also section LATEX_CMD_NAME for selecting the engine.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
+# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
+# path from which the emoji images will be read. If a relative path is entered,
+# it will be relative to the LATEX_OUTPUT directory. If left blank the
+# LATEX_OUTPUT directory will be used.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EMOJI_DIRECTORY  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# configuration file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's configuration file. A template extensions file can be
+# generated using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION          = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
+# namespace members in file scope as well, matching the HTML output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_NS_MEMB_FILE_SCOPE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# the structure of the code including all documentation. Note that this feature
+# is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to Sqlite3 output
+#---------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = NO
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT               = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS        = 0
+
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME           = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH           =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK               = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
+# If the DOT_UML_DETAILS tag is set to NO, doxygen will show attributes and
+# methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
+# tag is set to YES, doxygen will add type and arguments for attributes and
+# methods in the UML graphs. If the DOT_UML_DETAILS tag is set to NONE, doxygen
+# will not generate fields with class member information in the UML graphs. The
+# class diagrams will look similar to the default class diagrams but using UML
+# notation for the relationships.
+# Possible values are: NO, YES and NONE.
+# The default value is: NO.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+DOT_UML_DETAILS        = NO
+
+# The DOT_WRAP_THRESHOLD tag can be used to set the maximum number of characters
+# to display on a single line. If the actual line length exceeds this threshold
+# significantly it will wrapped across multiple lines. Some heuristics are apply
+# to avoid ugly line breaks.
+# Minimum value: 0, maximum value: 1000, default value: 17.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_WRAP_THRESHOLD     = 17
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDE_GRAPH          = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH             = YES
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH           = YES
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH        = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT       = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG        = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH               =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS           =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS           =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      =
+
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES    = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_TRANSPARENT        = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate
+# files that are used to generate the various graphs.
+#
+# Note: This setting is not only used for dot files but also for msc and
+# plantuml temporary files.
+# The default value is: YES.
+
+DOT_CLEANUP            = YES
diff --git a/docs/Output.md b/docs/Output.md
new file mode 100644
index 000000000..05b3fa284
--- /dev/null
+++ b/docs/Output.md
@@ -0,0 +1,66 @@
+# Output Files
+
+POET will place all simulation data and other files inside the given
+`<OUTPUT_DIRECTORY>`. The directory will look like this:
+
+``` {.example}
+.
+└── <OUTPUT_DIRECTORY>/
+    ├── iter000.rds
+    ├── iter000.dht
+    ├── ...
+    ├── iter<n>.rds
+    ├── iter<n>.dht
+    ├── setup.rds
+    └── timings.rds
+```
+
+## Description
+
+All `.rds` file can be read into an R runtime using e.g.
+`readRDS("<FILE>")`. The following description can be given to the
+files:
+
+| File          | Description                                                                                                       |
+|---------------|-------------------------------------------------------------------------------------------------------------------|
+| iter<*n*>.rds | Defines the state of the grid after *n* iteration, especially the state after transport (`T`) and chemistry (`C`) |
+| iter<*n*>.dht | DHT-snapshot of the *n* th iteration                                                                              |
+| setup.rds     | Summary of all simulation parameters given at startup                                                             |
+| timings.rds   | Various measured timings by POET                                                                                  |
+
+## Timings
+
+POET provides built-in time measurements of (sub) routines. The
+corresponding values can be found in `<OUTPUT_DIRECTORY>/timings.rds`
+and possible to read out within a R runtime with
+`readRDS("timings.rds")`. There you will find the following values:
+
+| Value              | Description                                                                |
+|--------------------|----------------------------------------------------------------------------|
+| simtime            | time spent in whole simulation loop without any initialization and cleanup |
+| simtime\_transport | measured time in *transport* subroutine                                    |
+| simtime\_chemistry | measured time in *chemistry* subroutine (actual parallelized part)         |
+
+### chemistry subsetting
+
+If running parallel there are also measured timings which are subsets of
+*simtime\_​chemistry*.
+
+| Value                      | Description                                        |
+|----------------------------|----------------------------------------------------|
+| simtime\_workers           | time spent in send/​recv loop of master             |
+| simtime\_chemistry\_master | sequential part of master chemistry                |
+| phreeqc                    | measured time of each worker in PHREEQC subroutine |
+
+### DHT usage {#DHT-usage}
+
+If running in parallel and with activated DHT, two more timings and also
+some profiling about the DHT usage are given:
+
+| Value           | Description                                             |
+|-----------------|---------------------------------------------------------|
+| dht\_fill\_time | time to write data to DHT                               |
+| dht\_get\_time  | time to retreive data from DHT                          |
+| dh\_hits        | count of data points retrieved from DHT                 |
+| dht\_miss       | count of misses/count of data points written to DHT     |
+| dht\_evictions  | count of data points evicted by another write operation |
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 000000000..11b5710dc
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,18 @@
+set(SRC_CODE_DIR
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    CACHE INTERNAL "directory indicating which source code version is used")
+
+get_poet_version()
+
+configure_file(poet.h.in poet.h)
+
+add_executable(poet poet.cpp)
+target_include_directories(poet PUBLIC "${CMAKE_CURRENT_BINARY_DIR}")
+target_link_libraries(poet PUBLIC POET_Model POET_Util MPI::MPI_C)
+target_compile_definitions(poet PRIVATE OMPI_SKIP_MPICXX)
+
+install(TARGETS poet DESTINATION bin)
+
+add_subdirectory(DHT)
+add_subdirectory(model)
+add_subdirectory(util)
diff --git a/src/DHT.cpp b/src/DHT.cpp
deleted file mode 100644
index 546f7aa50..000000000
--- a/src/DHT.cpp
+++ /dev/null
@@ -1,423 +0,0 @@
-#include "DHT.h"
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <stdio.h>
-
-/*
- * determining destination rank and index by hash of key
- *
- * return values by reference
- */
-static void determine_dest(uint64_t hash, int comm_size, unsigned int table_size, unsigned int *dest_rank, unsigned int *index, unsigned int index_count) {
-    uint64_t tmp;
-    int char_hop = 9-index_count;
-    unsigned int i;
-    for (i = 0; i < index_count ; i++) {
-        tmp = 0;
-        memcpy(&tmp,(unsigned char *)&hash+i, char_hop);
-        index[i] = (unsigned int) (tmp % table_size);
-    }
-    *dest_rank = (unsigned int) (hash % comm_size);
-}
-
-/**
- * set write flag to 1
- */
-static void set_flag(char* flag_byte) {
-    *flag_byte = 0;
-    *flag_byte |= (1 << 0);
-} 
-
-/**
- * return 1 if write flag is set
- * else 0
- */
-static int read_flag(char flag_byte) {
-    if ((flag_byte & 0x01) == 0x01) {
-        return 1;
-    } else return 0;
-}
-
-/*
- * allocating memory for DHT object and buckets.
- * creating MPI window for OSC
- * filling DHT object with passed by parameters, window, 2 counters for R/W errors and 2 pointers with allocated memory for further use
- * return DHT object
- */
-DHT* DHT_create(MPI_Comm comm, unsigned int size, int data_size, int key_size, uint64_t(*hash_func) (int, void*)) {
-    DHT *object;
-    MPI_Win window;
-    void* mem_alloc;
-    int comm_size, tmp;
-
-    tmp = (int) ceil(log2(size));
-    if (tmp%8 != 0) tmp = tmp + (8-(tmp%8));
-
-    object = (DHT*) malloc(sizeof(DHT));
-    if (object == NULL) return NULL;
-
-    //every memory allocation has 1 additional byte for flags etc.
-    if (MPI_Alloc_mem(size * (1 + data_size + key_size), MPI_INFO_NULL, &mem_alloc) != 0) return NULL;
-    if (MPI_Comm_size(comm, &comm_size) != 0) return NULL;
-
-    memset(mem_alloc, '\0', size * (1 + data_size + key_size));
-
-    if (MPI_Win_create(mem_alloc, size * (1 + data_size + key_size), (1 + data_size + key_size), MPI_INFO_NULL, comm, &window) != 0) return NULL;
-
-    object->data_size = data_size;
-    object->key_size = key_size;
-    object->table_size = size;
-    object->window = window;
-    object->hash_func = hash_func;
-    object->comm_size = comm_size;
-    object->communicator = comm;
-    object->read_misses = 0;
-    object->collisions = 0;
-    object->recv_entry = malloc(1 + data_size + key_size);
-    object->send_entry = malloc(1 + data_size + key_size);
-    object->index_count = 9-(tmp/8);
-    object->index = (unsigned int*) malloc((9-(tmp/8))*sizeof(int));
-    object->mem_alloc = mem_alloc;
-
-    DHT_stats *stats;
-
-    stats = (DHT_stats*) malloc(sizeof(DHT_stats));
-    if (stats == NULL) return NULL;
-
-    object->stats = stats;
-    object->stats->writes_local = (int*) calloc(comm_size, sizeof(int));
-    object->stats->old_writes = 0;
-    object->stats->read_misses = 0;
-    object->stats->collisions = 0;
-    object->stats->w_access = 0;
-    object->stats->r_access = 0;
-
-    return object;
-}
-
-/*
- * puts passed by data with key to DHT
- *
- * returning DHT_MPI_ERROR = -1 if MPI error occurred
- * else  DHT_SUCCESS = 0 if success
- */
-int DHT_write(DHT *table, void* send_key, void* send_data) {
-    unsigned int dest_rank, i;
-    int result = DHT_SUCCESS;
-
-    table->stats->w_access++;
-
-    //determine destination rank and index by hash of key
-    determine_dest(table->hash_func(table->key_size, send_key), table->comm_size, table->table_size, &dest_rank, table->index, table->index_count);
-
-    //concatenating key with data to write entry to DHT
-    set_flag((char *) table->send_entry);
-    memcpy((char *) table->send_entry + 1, (char *) send_key, table->key_size);
-    memcpy((char *) table->send_entry + table->key_size + 1, (char *) send_data, table->data_size);
-
-    //locking window of target rank with exclusive lock
-    if (MPI_Win_lock(MPI_LOCK_EXCLUSIVE, dest_rank, 0, table->window) != 0)
-        return DHT_MPI_ERROR;
-    for (i = 0; i < table->index_count; i++)
-    {
-        if (MPI_Get(table->recv_entry, 1 + table->data_size + table->key_size, MPI_BYTE, dest_rank, table->index[i], 1 + table->data_size + table->key_size, MPI_BYTE, table->window) != 0) return DHT_MPI_ERROR;
-        if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-
-        //increment collision counter if receiving key doesn't match sending key
-        //,entry has write flag + last index is reached
-
-        if (read_flag(*(char *)table->recv_entry)) {
-            if (memcmp(send_key, (char *) table->recv_entry + 1, table->key_size) != 0) {
-                if (i == (table->index_count)-1) {
-                    table->collisions += 1;
-                    table->stats->collisions += 1;
-                    result = DHT_WRITE_SUCCESS_WITH_COLLISION;
-                    break;
-                }
-            } else break;
-        } else {
-            table->stats->writes_local[dest_rank]++;
-            break;
-        }
-    }
-
-    //put data to DHT
-    if (MPI_Put(table->send_entry, 1 + table->data_size + table->key_size, MPI_BYTE, dest_rank, table->index[i], 1 + table->data_size + table->key_size, MPI_BYTE, table->window) != 0) return DHT_MPI_ERROR;
-    //unlock window of target rank
-    if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-
-    return result;
-}
-
-/*
- * gets data from the DHT by key
- *
- * return  DHT_SUCCESS = 0 if success
- * DHT_MPI_ERROR = -1 if MPI error occurred
- * DHT_READ_ERROR = -2 if receiving key doesn't match sending key
- */
-int DHT_read(DHT *table, void* send_key, void* destination) {
-    unsigned int dest_rank, i;
-
-    table->stats->r_access++;
-
-    //determine destination rank and index by hash of key
-    determine_dest(table->hash_func(table->key_size, send_key), table->comm_size, table->table_size, &dest_rank, table->index, table->index_count);
-
-    //locking window of target rank with shared lock
-    if (MPI_Win_lock(MPI_LOCK_SHARED, dest_rank, 0, table->window) != 0) return DHT_MPI_ERROR;
-    //receive data
-    for (i = 0; i < table->index_count; i++) {
-        if (MPI_Get(table->recv_entry, 1 + table->data_size + table->key_size, MPI_BYTE, dest_rank, table->index[i], 1 + table->data_size + table->key_size, MPI_BYTE, table->window) != 0) return DHT_MPI_ERROR;
-        if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-        
-        //increment read error counter if write flag isn't set or key doesn't match passed by key + last index reached
-        //else copy data to dereference of passed by destination pointer
-
-        if ((read_flag(*(char *) table->recv_entry)) == 0) {
-            table->read_misses += 1;
-            table->stats->read_misses += 1;
-            if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-            return DHT_READ_ERROR;
-        }
-
-        if (memcmp(((char*)table->recv_entry) + 1, send_key, table->key_size) != 0) {
-            if (i == (table->index_count)-1) {
-                table->read_misses += 1;
-                table->stats->read_misses += 1;
-                if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-                return DHT_READ_ERROR;
-            }
-        } else break;
-    }
-
-    //unlock window of target rank
-    if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
-
-    memcpy((char *) destination, (char *) table->recv_entry + table->key_size + 1, table->data_size);
-
-    return DHT_SUCCESS;
-}
-
-int DHT_to_file(DHT* table, char* filename) {
-    //open file
-    MPI_File file;
-    if (MPI_File_open(table->communicator, filename, MPI_MODE_CREATE|MPI_MODE_WRONLY, MPI_INFO_NULL, &file) != 0) return DHT_FILE_IO_ERROR;
-
-    int rank;
-    MPI_Comm_rank(table->communicator, &rank);
-
-    //write header (key_size and data_size)
-    if (rank == 0) {
-        if (MPI_File_write(file, &table->key_size, 1, MPI_INT, MPI_STATUS_IGNORE) != 0) return DHT_FILE_WRITE_ERROR;
-        if (MPI_File_write(file, &table->data_size, 1, MPI_INT, MPI_STATUS_IGNORE) != 0) return DHT_FILE_WRITE_ERROR;
-    }
-
-    if (MPI_File_seek_shared(file, DHT_HEADER_SIZE, MPI_SEEK_SET) != 0) return DHT_FILE_IO_ERROR;
-
-    char* ptr;
-    int bucket_size = table->key_size + table->data_size + 1;
-
-    //iterate over local memory
-    for (unsigned int i = 0; i < table->table_size; i++) {
-        ptr = (char *) table->mem_alloc + (i * bucket_size);
-        //if bucket has been written to (checked by written_flag)...
-        if (read_flag(*ptr)) {
-            //write key and data to file
-            if (MPI_File_write_shared(file, ptr + 1, bucket_size - 1, MPI_BYTE, MPI_STATUS_IGNORE) != 0) return DHT_FILE_WRITE_ERROR;
-        }
-    }
-    //close file
-    if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR;
-
-    return DHT_SUCCESS;  
-}
-
-int DHT_from_file(DHT* table, char* filename) {
-    MPI_File file;
-    MPI_Offset f_size;
-    int e_size, m_size, cur_pos, rank, offset;
-    char* buffer;
-    void* key;
-    void* data;
-
-    if (MPI_File_open(table->communicator, filename, MPI_MODE_RDONLY, MPI_INFO_NULL, &file) != 0) return DHT_FILE_IO_ERROR;
-
-    if (MPI_File_get_size(file, &f_size) != 0) return DHT_FILE_IO_ERROR;
-
-    MPI_Comm_rank(table->communicator, &rank);
-
-    e_size = table->key_size + table->data_size;
-    m_size = e_size > DHT_HEADER_SIZE ? e_size : DHT_HEADER_SIZE;
-    buffer = (char *) malloc(m_size);
-
-    if (MPI_File_read(file, buffer, DHT_HEADER_SIZE, MPI_BYTE, MPI_STATUS_IGNORE) != 0) return DHT_FILE_READ_ERROR;
-
-    if (*(int *) buffer != table->key_size) return DHT_WRONG_FILE;
-    if (*(int *) (buffer + 4) != table->data_size) return DHT_WRONG_FILE;
-
-    offset = e_size*table->comm_size;
-
-    if (MPI_File_seek(file, DHT_HEADER_SIZE, MPI_SEEK_SET) != 0) return DHT_FILE_IO_ERROR;
-    cur_pos = DHT_HEADER_SIZE + (rank * e_size);
-
-    while(cur_pos < f_size) {
-        if (MPI_File_seek(file, cur_pos, MPI_SEEK_SET) != 0) return DHT_FILE_IO_ERROR;
-        MPI_Offset tmp;
-        MPI_File_get_position(file, &tmp);
-        if (MPI_File_read(file, buffer, e_size, MPI_BYTE, MPI_STATUS_IGNORE) != 0) return DHT_FILE_READ_ERROR;
-        key = buffer;
-        data = (buffer+table->key_size);
-        if (DHT_write(table, key, data) == DHT_MPI_ERROR) return DHT_MPI_ERROR;
-
-        cur_pos += offset;
-    }
-
-    free (buffer);
-    if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR; 
-
-    return DHT_SUCCESS;
-}
-
-/*
- * frees up memory and accumulate counter
- */
-int DHT_free(DHT* table, int* collision_counter, int* readerror_counter) {
-    int buf;
-
-    if (collision_counter != NULL) {
-        buf = 0;
-        if (MPI_Reduce(&table->collisions, &buf, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-        *collision_counter = buf;
-    }
-    if (readerror_counter != NULL) {
-        buf = 0;
-        if (MPI_Reduce(&table->read_misses, &buf, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-        *readerror_counter = buf;
-    }
-    if (MPI_Win_free(&(table->window)) != 0) return DHT_MPI_ERROR;
-    if (MPI_Free_mem(table->mem_alloc) != 0) return DHT_MPI_ERROR;
-    free(table->recv_entry);
-    free(table->send_entry);
-    free(table->index);
-
-    free(table->stats->writes_local);
-    free(table->stats);
-
-    free(table);
-
-    return DHT_SUCCESS;
-}
-
-/*
- * prints a table with statistics about current use of DHT 
- * for each participating process and summed up results containing:
-    *  1. occupied buckets (in respect to the memory of this process)
-    *  2. free buckets (in respect to the memory of this process)
-    *  3. calls of DHT_write (w_access)
-    *  4. calls of DHT_read (r_access)
-    *  5. read misses (see DHT_READ_ERROR)
-    *  6. collisions (see DHT_WRITE_SUCCESS_WITH_COLLISION)
- * 3-6 will reset with every call of this function
- * finally the amount of new written entries is printed out (in relation to last call of this funtion)
- */
-int DHT_print_statistics(DHT *table) {
-    int *written_buckets;
-    int *read_misses, sum_read_misses;
-    int *collisions, sum_collisions;
-    int sum_w_access, sum_r_access, *w_access, *r_access;
-    int rank;
-
-    MPI_Comm_rank(table->communicator, &rank);
-
-    //disable possible warning of unitialized variable, which is not the case
-    //since we're using MPI_Gather to obtain all values only on rank 0
-    #pragma GCC diagnostic push
-    #pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
-
-    //obtaining all values from all processes in the communicator
-    if (rank == 0) read_misses = (int*) malloc(table->comm_size*sizeof(int));
-    if (MPI_Gather(&table->stats->read_misses, 1, MPI_INT, read_misses, 1, MPI_INT, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    if (MPI_Reduce(&table->stats->read_misses, &sum_read_misses, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    table->stats->read_misses = 0;
-    
-    if (rank == 0) collisions = (int*) malloc(table->comm_size*sizeof(int));
-    if (MPI_Gather(&table->stats->collisions, 1, MPI_INT, collisions, 1, MPI_INT, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    if (MPI_Reduce(&table->stats->collisions, &sum_collisions, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    table->stats->collisions = 0;
-
-    if (rank == 0) w_access = (int*) malloc(table->comm_size*sizeof(int));
-    if (MPI_Gather(&table->stats->w_access, 1, MPI_INT, w_access, 1, MPI_INT, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    if (MPI_Reduce(&table->stats->w_access, &sum_w_access, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    table->stats->w_access = 0;
-
-    if (rank == 0) r_access = (int*) malloc(table->comm_size*sizeof(int));
-    if (MPI_Gather(&table->stats->r_access, 1, MPI_INT, r_access, 1, MPI_INT, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    if (MPI_Reduce(&table->stats->r_access, &sum_r_access, 1, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-    table->stats->r_access = 0;
-    
-    if (rank == 0) written_buckets = (int*) calloc(table->comm_size, sizeof(int));
-    if (MPI_Reduce(table->stats->writes_local, written_buckets, table->comm_size, MPI_INT, MPI_SUM, 0, table->communicator) != 0) return DHT_MPI_ERROR;
-
-    if (rank == 0) { //only process with rank 0 will print out results as a table
-        int sum_written_buckets = 0;
-
-        for (int i=0; i < table->comm_size; i++) {
-            sum_written_buckets += written_buckets[i];
-        }
-
-        int members = 7;
-        int padsize = (members*12)+1;
-        char pad[padsize+1];
-
-        memset(pad, '-', padsize*sizeof(char));
-        pad[padsize]= '\0';
-        printf("\n");
-        printf("%-35s||resets with every call of this function\n", " ");
-        printf("%-11s|%-11s|%-11s||%-11s|%-11s|%-11s|%-11s\n", 
-            "rank", 
-            "occupied", 
-            "free", 
-            "w_access",
-            "r_access",
-            "read misses",
-            "collisions");
-        printf("%s\n", pad);
-        for (int i = 0; i < table->comm_size; i++) {
-            printf("%-11d|%-11d|%-11d||%-11d|%-11d|%-11d|%-11d\n", 
-                i, 
-                written_buckets[i], 
-                table->table_size-written_buckets[i], 
-                w_access[i],
-                r_access[i],
-                read_misses[i],
-                collisions[i]);
-        }
-        printf("%s\n", pad);
-        printf("%-11s|%-11d|%-11d||%-11d|%-11d|%-11d|%-11d\n", 
-            "sum", 
-            sum_written_buckets, 
-            (table->table_size*table->comm_size)-sum_written_buckets, 
-            sum_w_access,
-            sum_r_access,
-            sum_read_misses,
-            sum_collisions);
-
-        printf("%s\n", pad);
-        printf("%s %d\n", 
-            "new entries:", 
-            sum_written_buckets - table->stats->old_writes);
-
-        printf("\n");
-        fflush(stdout);
-
-        table->stats->old_writes = sum_written_buckets;
-    }
-
-    //enable warning again
-    #pragma GCC diagnostic pop
-
-    MPI_Barrier(table->communicator);
-    return DHT_SUCCESS;
-}
\ No newline at end of file
diff --git a/src/DHT.h b/src/DHT.h
deleted file mode 100644
index 1b118e690..000000000
--- a/src/DHT.h
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * File:   DHT.h
- * Author: max luebke
- *
- * Created on 16. November 2017, 09:14
- */
-
-#ifndef DHT_H
-#define DHT_H
-
-#include <mpi.h>
-#include <stdint.h>
-
-#define DHT_MPI_ERROR -1
-#define DHT_READ_ERROR -2
-#define DHT_SUCCESS 0
-#define DHT_WRITE_SUCCESS_WITH_COLLISION 1
-
-#define DHT_WRONG_FILE 11
-#define DHT_FILE_IO_ERROR 12
-#define DHT_FILE_READ_ERROR 13
-#define DHT_FILE_WRITE_ERROR 14
-
-#define DHT_HEADER_SIZE 8
-
-typedef struct {;
-    int *writes_local, old_writes;
-    int read_misses, collisions;
-    int w_access, r_access;
-} DHT_stats;
-
-typedef struct {
-    MPI_Win window;
-    int data_size;
-    int key_size;
-    unsigned int table_size;
-    MPI_Comm communicator;
-    int comm_size;
-    uint64_t(*hash_func) (int, void*);
-    void* recv_entry;
-    void* send_entry;
-    void* mem_alloc;
-    int read_misses;
-    int collisions;
-    unsigned int *index;
-    unsigned int index_count;
-    DHT_stats *stats;
-} DHT;
-
-
-
-/*
- * parameters:
- * MPI_Comm comm - communicator of processes that are holding the DHT
- * int size_per_process - number of buckets each process will create
- * int data_size - size of data in bytes
- * int key_size - size of key in bytes
- * *hash_func - pointer to hashfunction
- *
- * return:
- * NULL if error during initialization
- * DHT* if success
- */
-extern DHT* DHT_create(MPI_Comm comm, unsigned int size_per_process, int data_size, int key_size, uint64_t(*hash_func)(int, void*));
-
-/*
- * parameters:
- * DHT *table - DHT_object created by DHT_create
- * void* data - pointer to data
- * void* - pointer to key
- *
- * return:
- * error value (see above)
- */
-extern int DHT_write(DHT *table, void* key, void* data);
-
-/*
- * parameters:
- * DHT *table - DHT_object created by DHT_create
- * void* key - pointer to key
- * void* destination - pointer which will hold the resulting data from DHT
- *
- * return:
- * error value (see above)
- */
-extern int DHT_read(DHT *table, void* key, void* destination);
-
-extern int DHT_to_file(DHT *table, char* filename);
-
-extern int DHT_from_file(DHT *table, char* filename);
-
-/*
- * parameters:
- * DHT *table - DHT_object created by DHT_create
- * int* collision_counter - pointer which will hold the total count of collisions
- * int* readerror_counter - pointer which will hold the total count of read errors
- *
- * return:
- * error value (see above)
- */
-extern int DHT_free(DHT *table, int* collision_counter, int* readerror_counter);
-
-/*
- * parameters:
- * DHT *table - DHT_object created by DHT_create
- * 
- * return:
- * error value (DHT_SUCCESS or DHT_MPI_ERROR)
- */
-extern int DHT_print_statistics(DHT *table);
-
-#endif /* DHT_H */
\ No newline at end of file
diff --git a/src/DHT/CMakeLists.txt b/src/DHT/CMakeLists.txt
new file mode 100644
index 000000000..8346f7e25
--- /dev/null
+++ b/src/DHT/CMakeLists.txt
@@ -0,0 +1,17 @@
+add_library(DHT DHT.c DHT.h)
+target_include_directories(DHT PUBLIC ${MPI_C_INCLUDE_DIRS})
+target_link_libraries(DHT PRIVATE MPI::MPI_C)
+target_compile_definitions(DHT PUBLIC OMPI_SKIP_MPICXX)
+
+option(DHT_Debug "Toggle output of stastic table for each iteration" OFF)
+
+if (DHT_Debug)
+  target_compile_definitions(DHT PUBLIC DHT_STATISTICS)
+endif()
+
+find_library(MATH_LIBRARY m)
+find_library(CRYPTO_LIBRARY crypto)
+
+add_library(DHT_Wrapper DHT_Wrapper.cpp DHT_Wrapper.h)
+target_include_directories(DHT_Wrapper PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_link_libraries(DHT_Wrapper PRIVATE DHT ${MATH_LIBRARY} ${CRYPTO_LIBRARY} POET_Util)
diff --git a/src/DHT/DHT.c b/src/DHT/DHT.c
new file mode 100644
index 000000000..b773cba06
--- /dev/null
+++ b/src/DHT/DHT.c
@@ -0,0 +1,497 @@
+/*
+** Copyright (C) 2017-2021 Max Luebke (University of Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "DHT.h"
+
+#include <inttypes.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+
+static void determine_dest(uint64_t hash, int comm_size,
+                           unsigned int table_size, unsigned int *dest_rank,
+                           uint64_t *index, unsigned int index_count) {
+  /** temporary index */
+  uint64_t tmp_index;
+  /** how many bytes do we need for one index? */
+  int index_size = sizeof(double) - (index_count - 1);
+  for (int i = 0; i < index_count; i++) {
+    tmp_index = 0;
+    memcpy(&tmp_index, (char *)&hash + i, index_size);
+    index[i] = (uint64_t)(tmp_index % table_size);
+  }
+  *dest_rank = (unsigned int)(hash % comm_size);
+}
+
+static void set_flag(char *flag_byte) {
+  *flag_byte = 0;
+  *flag_byte |= (1 << 0);
+}
+
+static int read_flag(char flag_byte) {
+  if ((flag_byte & 0x01) == 0x01) {
+    return 1;
+  } else
+    return 0;
+}
+
+DHT *DHT_create(MPI_Comm comm, uint64_t size, unsigned int data_size,
+                unsigned int key_size, uint64_t (*hash_func)(int, void *)) {
+  DHT *object;
+  MPI_Win window;
+  void *mem_alloc;
+  int comm_size, index_bytes;
+
+  // calculate how much bytes for the index are needed to address count of
+  // buckets per process
+  index_bytes = (int)ceil(log2(size));
+  if (index_bytes % 8 != 0) index_bytes = index_bytes + (8 - (index_bytes % 8));
+
+  // allocate memory for dht-object
+  object = (DHT *)malloc(sizeof(DHT));
+  if (object == NULL) return NULL;
+
+  // every memory allocation has 1 additional byte for flags etc.
+  if (MPI_Alloc_mem(size * (1 + data_size + key_size), MPI_INFO_NULL,
+                    &mem_alloc) != 0)
+    return NULL;
+  if (MPI_Comm_size(comm, &comm_size) != 0) return NULL;
+
+  // since MPI_Alloc_mem doesn't provide memory allocation with the memory set
+  // to zero, we're doing this here
+  memset(mem_alloc, '\0', size * (1 + data_size + key_size));
+
+  // create windows on previously allocated memory
+  if (MPI_Win_create(mem_alloc, size * (1 + data_size + key_size),
+                     (1 + data_size + key_size), MPI_INFO_NULL, comm,
+                     &window) != 0)
+    return NULL;
+
+  // fill dht-object
+  object->data_size = data_size;
+  object->key_size = key_size;
+  object->table_size = size;
+  object->window = window;
+  object->hash_func = hash_func;
+  object->comm_size = comm_size;
+  object->communicator = comm;
+  object->read_misses = 0;
+  object->evictions = 0;
+  object->recv_entry = malloc(1 + data_size + key_size);
+  object->send_entry = malloc(1 + data_size + key_size);
+  object->index_count = 9 - (index_bytes / 8);
+  object->index = (uint64_t *)malloc((object->index_count) * sizeof(uint64_t));
+  object->mem_alloc = mem_alloc;
+
+  // if set, initialize dht_stats
+#ifdef DHT_STATISTICS
+  DHT_stats *stats;
+
+  stats = (DHT_stats *)malloc(sizeof(DHT_stats));
+  if (stats == NULL) return NULL;
+
+  object->stats = stats;
+  object->stats->writes_local = (int *)calloc(comm_size, sizeof(int));
+  object->stats->old_writes = 0;
+  object->stats->read_misses = 0;
+  object->stats->evictions = 0;
+  object->stats->w_access = 0;
+  object->stats->r_access = 0;
+#endif
+
+  return object;
+}
+
+int DHT_write(DHT *table, void *send_key, void *send_data) {
+  unsigned int dest_rank, i;
+  int result = DHT_SUCCESS;
+
+#ifdef DHT_STATISTICS
+  table->stats->w_access++;
+#endif
+
+  // determine destination rank and index by hash of key
+  determine_dest(table->hash_func(table->key_size, send_key), table->comm_size,
+                 table->table_size, &dest_rank, table->index,
+                 table->index_count);
+
+  // concatenating key with data to write entry to DHT
+  set_flag((char *)table->send_entry);
+  memcpy((char *)table->send_entry + 1, (char *)send_key, table->key_size);
+  memcpy((char *)table->send_entry + table->key_size + 1, (char *)send_data,
+         table->data_size);
+
+  // locking window of target rank with exclusive lock
+  if (MPI_Win_lock(MPI_LOCK_EXCLUSIVE, dest_rank, 0, table->window) != 0)
+    return DHT_MPI_ERROR;
+  for (i = 0; i < table->index_count; i++) {
+    if (MPI_Get(table->recv_entry, 1 + table->data_size + table->key_size,
+                MPI_BYTE, dest_rank, table->index[i],
+                1 + table->data_size + table->key_size, MPI_BYTE,
+                table->window) != 0)
+      return DHT_MPI_ERROR;
+    if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+
+    // increment eviction counter if receiving key doesn't match sending key
+    // entry has write flag and last index is reached.
+    if (read_flag(*(char *)table->recv_entry)) {
+      if (memcmp(send_key, (char *)table->recv_entry + 1, table->key_size) !=
+          0) {
+        if (i == (table->index_count) - 1) {
+          table->evictions += 1;
+#ifdef DHT_STATISTICS
+          table->stats->evictions += 1;
+#endif
+          result = DHT_WRITE_SUCCESS_WITH_EVICTION;
+          break;
+        }
+      } else
+        break;
+    } else {
+#ifdef DHT_STATISTICS
+      table->stats->writes_local[dest_rank]++;
+#endif
+      break;
+    }
+  }
+
+  // put data to DHT (with last selected index by value i)
+  if (MPI_Put(table->send_entry, 1 + table->data_size + table->key_size,
+              MPI_BYTE, dest_rank, table->index[i],
+              1 + table->data_size + table->key_size, MPI_BYTE,
+              table->window) != 0)
+    return DHT_MPI_ERROR;
+  // unlock window of target rank
+  if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+
+  return result;
+}
+
+int DHT_read(DHT *table, void *send_key, void *destination) {
+  unsigned int dest_rank, i;
+
+#ifdef DHT_STATISTICS
+  table->stats->r_access++;
+#endif
+
+  // determine destination rank and index by hash of key
+  determine_dest(table->hash_func(table->key_size, send_key), table->comm_size,
+                 table->table_size, &dest_rank, table->index,
+                 table->index_count);
+
+  // locking window of target rank with shared lock
+  if (MPI_Win_lock(MPI_LOCK_SHARED, dest_rank, 0, table->window) != 0)
+    return DHT_MPI_ERROR;
+  // receive data
+  for (i = 0; i < table->index_count; i++) {
+    if (MPI_Get(table->recv_entry, 1 + table->data_size + table->key_size,
+                MPI_BYTE, dest_rank, table->index[i],
+                1 + table->data_size + table->key_size, MPI_BYTE,
+                table->window) != 0)
+      return DHT_MPI_ERROR;
+    if (MPI_Win_flush(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+
+    // increment read error counter if write flag isn't set ...
+    if ((read_flag(*(char *)table->recv_entry)) == 0) {
+      table->read_misses += 1;
+#ifdef DHT_STATISTICS
+      table->stats->read_misses += 1;
+#endif
+      // unlock window and return
+      if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+      return DHT_READ_MISS;
+    }
+
+    // ... or key doesn't match passed by key and last index reached.
+    if (memcmp(((char *)table->recv_entry) + 1, send_key, table->key_size) !=
+        0) {
+      if (i == (table->index_count) - 1) {
+        table->read_misses += 1;
+#ifdef DHT_STATISTICS
+        table->stats->read_misses += 1;
+#endif
+        // unlock window an return
+        if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+        return DHT_READ_MISS;
+      }
+    } else
+      break;
+  }
+
+  // unlock window of target rank
+  if (MPI_Win_unlock(dest_rank, table->window) != 0) return DHT_MPI_ERROR;
+
+  // if matching key was found copy data into memory of passed pointer
+  memcpy((char *)destination, (char *)table->recv_entry + table->key_size + 1,
+         table->data_size);
+
+  return DHT_SUCCESS;
+}
+
+int DHT_to_file(DHT *table, const char *filename) {
+  // open file
+  MPI_File file;
+  if (MPI_File_open(table->communicator, filename,
+                    MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL,
+                    &file) != 0)
+    return DHT_FILE_IO_ERROR;
+
+  int rank;
+  MPI_Comm_rank(table->communicator, &rank);
+
+  // write header (key_size and data_size)
+  if (rank == 0) {
+    if (MPI_File_write(file, &table->key_size, 1, MPI_INT, MPI_STATUS_IGNORE) !=
+        0)
+      return DHT_FILE_WRITE_ERROR;
+    if (MPI_File_write(file, &table->data_size, 1, MPI_INT,
+                       MPI_STATUS_IGNORE) != 0)
+      return DHT_FILE_WRITE_ERROR;
+  }
+
+  // seek file pointer behind header for all processes
+  if (MPI_File_seek_shared(file, DHT_FILEHEADER_SIZE, MPI_SEEK_SET) != 0)
+    return DHT_FILE_IO_ERROR;
+
+  char *ptr;
+  int bucket_size = table->key_size + table->data_size + 1;
+
+  // iterate over local memory
+  for (unsigned int i = 0; i < table->table_size; i++) {
+    ptr = (char *)table->mem_alloc + (i * bucket_size);
+    // if bucket has been written to (checked by written_flag)...
+    if (read_flag(*ptr)) {
+      // write key and data to file
+      if (MPI_File_write_shared(file, ptr + 1, bucket_size - 1, MPI_BYTE,
+                                MPI_STATUS_IGNORE) != 0)
+        return DHT_FILE_WRITE_ERROR;
+    }
+  }
+  // close file
+  if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR;
+
+  return DHT_SUCCESS;
+}
+
+int DHT_from_file(DHT *table, const char *filename) {
+  MPI_File file;
+  MPI_Offset f_size;
+  int bucket_size, buffer_size, cur_pos, rank, offset;
+  char *buffer;
+  void *key;
+  void *data;
+
+  // open file
+  if (MPI_File_open(table->communicator, filename, MPI_MODE_RDONLY,
+                    MPI_INFO_NULL, &file) != 0)
+    return DHT_FILE_IO_ERROR;
+
+  // get file size
+  if (MPI_File_get_size(file, &f_size) != 0) return DHT_FILE_IO_ERROR;
+
+  MPI_Comm_rank(table->communicator, &rank);
+
+  // calculate bucket size
+  bucket_size = table->key_size + table->data_size;
+  // buffer size is either bucket size or, if bucket size is smaller than the
+  // file header, the size of DHT_FILEHEADER_SIZE
+  buffer_size =
+      bucket_size > DHT_FILEHEADER_SIZE ? bucket_size : DHT_FILEHEADER_SIZE;
+  // allocate buffer
+  buffer = (char *)malloc(buffer_size);
+
+  // read file header
+  if (MPI_File_read(file, buffer, DHT_FILEHEADER_SIZE, MPI_BYTE,
+                    MPI_STATUS_IGNORE) != 0)
+    return DHT_FILE_READ_ERROR;
+
+  // compare if written header data and key size matches current sizes
+  if (*(int *)buffer != table->key_size) return DHT_WRONG_FILE;
+  if (*(int *)(buffer + 4) != table->data_size) return DHT_WRONG_FILE;
+
+  // set offset for each process
+  offset = bucket_size * table->comm_size;
+
+  // seek behind header of DHT file
+  if (MPI_File_seek(file, DHT_FILEHEADER_SIZE, MPI_SEEK_SET) != 0)
+    return DHT_FILE_IO_ERROR;
+
+  // current position is rank * bucket_size + OFFSET
+  cur_pos = DHT_FILEHEADER_SIZE + (rank * bucket_size);
+
+  // loop over file and write data to DHT with DHT_write
+  while (cur_pos < f_size) {
+    if (MPI_File_seek(file, cur_pos, MPI_SEEK_SET) != 0)
+      return DHT_FILE_IO_ERROR;
+    // TODO: really necessary?
+    MPI_Offset tmp;
+    MPI_File_get_position(file, &tmp);
+    if (MPI_File_read(file, buffer, bucket_size, MPI_BYTE, MPI_STATUS_IGNORE) !=
+        0)
+      return DHT_FILE_READ_ERROR;
+    // extract key and data and write to DHT
+    key = buffer;
+    data = (buffer + table->key_size);
+    if (DHT_write(table, key, data) == DHT_MPI_ERROR) return DHT_MPI_ERROR;
+
+    // increment current position
+    cur_pos += offset;
+  }
+
+  free(buffer);
+  if (MPI_File_close(&file) != 0) return DHT_FILE_IO_ERROR;
+
+  return DHT_SUCCESS;
+}
+
+int DHT_free(DHT *table, int *eviction_counter, int *readerror_counter) {
+  int buf;
+
+  if (eviction_counter != NULL) {
+    buf = 0;
+    if (MPI_Reduce(&table->evictions, &buf, 1, MPI_INT, MPI_SUM, 0,
+                   table->communicator) != 0)
+      return DHT_MPI_ERROR;
+    *eviction_counter = buf;
+  }
+  if (readerror_counter != NULL) {
+    buf = 0;
+    if (MPI_Reduce(&table->read_misses, &buf, 1, MPI_INT, MPI_SUM, 0,
+                   table->communicator) != 0)
+      return DHT_MPI_ERROR;
+    *readerror_counter = buf;
+  }
+  if (MPI_Win_free(&(table->window)) != 0) return DHT_MPI_ERROR;
+  if (MPI_Free_mem(table->mem_alloc) != 0) return DHT_MPI_ERROR;
+  free(table->recv_entry);
+  free(table->send_entry);
+  free(table->index);
+
+#ifdef DHT_STATISTICS
+  free(table->stats->writes_local);
+  free(table->stats);
+#endif
+  free(table);
+
+  return DHT_SUCCESS;
+}
+
+int DHT_print_statistics(DHT *table) {
+#ifdef DHT_STATISTICS
+  int *written_buckets;
+  int *read_misses, sum_read_misses;
+  int *evictions, sum_evictions;
+  int sum_w_access, sum_r_access, *w_access, *r_access;
+  int rank;
+  MPI_Comm_rank(table->communicator, &rank);
+
+// disable possible warning of unitialized variable, which is not the case
+// since we're using MPI_Gather to obtain all values only on rank 0
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
+
+  // obtaining all values from all processes in the communicator
+  if (rank == 0) read_misses = (int *)malloc(table->comm_size * sizeof(int));
+  if (MPI_Gather(&table->stats->read_misses, 1, MPI_INT, read_misses, 1,
+                 MPI_INT, 0, table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  if (MPI_Reduce(&table->stats->read_misses, &sum_read_misses, 1, MPI_INT,
+                 MPI_SUM, 0, table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  table->stats->read_misses = 0;
+
+  if (rank == 0) evictions = (int *)malloc(table->comm_size * sizeof(int));
+  if (MPI_Gather(&table->stats->evictions, 1, MPI_INT, evictions, 1, MPI_INT, 0,
+                 table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  if (MPI_Reduce(&table->stats->evictions, &sum_evictions, 1, MPI_INT, MPI_SUM,
+                 0, table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  table->stats->evictions = 0;
+
+  if (rank == 0) w_access = (int *)malloc(table->comm_size * sizeof(int));
+  if (MPI_Gather(&table->stats->w_access, 1, MPI_INT, w_access, 1, MPI_INT, 0,
+                 table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  if (MPI_Reduce(&table->stats->w_access, &sum_w_access, 1, MPI_INT, MPI_SUM, 0,
+                 table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  table->stats->w_access = 0;
+
+  if (rank == 0) r_access = (int *)malloc(table->comm_size * sizeof(int));
+  if (MPI_Gather(&table->stats->r_access, 1, MPI_INT, r_access, 1, MPI_INT, 0,
+                 table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  if (MPI_Reduce(&table->stats->r_access, &sum_r_access, 1, MPI_INT, MPI_SUM, 0,
+                 table->communicator) != 0)
+    return DHT_MPI_ERROR;
+  table->stats->r_access = 0;
+
+  if (rank == 0) written_buckets = (int *)calloc(table->comm_size, sizeof(int));
+  if (MPI_Reduce(table->stats->writes_local, written_buckets, table->comm_size,
+                 MPI_INT, MPI_SUM, 0, table->communicator) != 0)
+    return DHT_MPI_ERROR;
+
+  if (rank == 0) {  // only process with rank 0 will print out results as a
+                    // table
+    int sum_written_buckets = 0;
+
+    for (int i = 0; i < table->comm_size; i++) {
+      sum_written_buckets += written_buckets[i];
+    }
+
+    int members = 7;
+    int padsize = (members * 12) + 1;
+    char pad[padsize + 1];
+
+    memset(pad, '-', padsize * sizeof(char));
+    pad[padsize] = '\0';
+    printf("\n");
+    printf("%-35s||resets with every call of this function\n", " ");
+    printf("%-11s|%-11s|%-11s||%-11s|%-11s|%-11s|%-11s\n", "rank", "occupied",
+           "free", "w_access", "r_access", "read misses", "evictions");
+    printf("%s\n", pad);
+    for (int i = 0; i < table->comm_size; i++) {
+      printf("%-11d|%-11d|%-11d||%-11d|%-11d|%-11d|%-11d\n", i,
+             written_buckets[i], table->table_size - written_buckets[i],
+             w_access[i], r_access[i], read_misses[i], evictions[i]);
+    }
+    printf("%s\n", pad);
+    printf("%-11s|%-11d|%-11d||%-11d|%-11d|%-11d|%-11d\n", "sum",
+           sum_written_buckets,
+           (table->table_size * table->comm_size) - sum_written_buckets,
+           sum_w_access, sum_r_access, sum_read_misses, sum_evictions);
+
+    printf("%s\n", pad);
+    printf("%s %d\n",
+           "new entries:", sum_written_buckets - table->stats->old_writes);
+
+    printf("\n");
+    fflush(stdout);
+
+    table->stats->old_writes = sum_written_buckets;
+  }
+
+// enable warning again
+#pragma GCC diagnostic pop
+
+  MPI_Barrier(table->communicator);
+  return DHT_SUCCESS;
+#endif
+}
diff --git a/src/DHT/DHT.h b/src/DHT/DHT.h
new file mode 100644
index 000000000..1acba5022
--- /dev/null
+++ b/src/DHT/DHT.h
@@ -0,0 +1,312 @@
+/*
+** Copyright (C) 2017-2021 Max Luebke (University of Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+/**
+ * @file DHT.h
+ * @author Max Lübke (mluebke@uni-potsdam.de)
+ * @brief API to interact with the DHT
+ * @version 0.1
+ * @date 16 Nov 2017
+ *
+ * This file implements the creation of a DHT by using the MPI
+ * one-sided-communication. There is also the possibility to write or read data
+ * from or to the DHT. In addition, the current state of the DHT can be written
+ * to a file and read in again later.
+ */
+
+#ifndef DHT_H
+#define DHT_H
+
+#include <mpi.h>
+#include <stdint.h>
+
+/** Returned if some error in MPI routine occurs. */
+#define DHT_MPI_ERROR -1
+/** Returned by a call of DHT_read if no bucket with given key was found. */
+#define DHT_READ_MISS -2
+/** Returned by DHT_write if a bucket was evicted. */
+#define DHT_WRITE_SUCCESS_WITH_EVICTION -3
+/** Returned when no errors occured. */
+#define DHT_SUCCESS 0
+
+/** Returned by DHT_from_file if the given file does not match expected file. */
+#define DHT_WRONG_FILE -11
+/** Returned by DHT file operations if MPI file operation fails. */
+#define DHT_FILE_IO_ERROR -12
+/** Returned by DHT file operations if error occured in MPI_Read operation. */
+#define DHT_FILE_READ_ERROR -13
+/** Returned by DHT file operations if error occured in MPI_Write operation. */
+#define DHT_FILE_WRITE_ERROR -14
+
+/** Size of the file header in byte. */
+#define DHT_FILEHEADER_SIZE 8
+
+/**
+ * Internal struct to store statistics about read and write accesses and also
+ * read misses and evictions.
+ * <b>All values will be resetted to zero after a call of
+ * DHT_print_statistics().</b>
+ * Internal use only!
+ *
+ * @todo There's maybe a better solution than DHT_print_statistics and this
+ * struct
+ */
+typedef struct {
+  /** Count of writes to specific process this process did. */
+  int* writes_local;
+  /** Writes after last call of DHT_print_statistics. */
+  int old_writes;
+  /** How many read misses occur? */
+  int read_misses;
+  /** How many buckets where evicted? */
+  int evictions;
+  /** How many calls of DHT_write() did this process? */
+  int w_access;
+  /** How many calls of DHT_read() did this process? */
+  int r_access;
+} DHT_stats;
+
+/**
+ * Struct which serves as a handler or so called \a DHT-object. Will
+ * be created by DHT_create and must be passed as a parameter to every following
+ * function. Stores all relevant data.
+ * Do not touch outside DHT functions!
+ */
+typedef struct {
+  /** Created MPI Window, which serves as the DHT memory area of the process. */
+  MPI_Win window;
+  /** Size of the data of a bucket entry in byte. */
+  int data_size;
+  /** Size of the key of a bucket entry in byte. */
+  int key_size;
+  /** Count of buckets for each process. */
+  unsigned int table_size;
+  /** MPI communicator of all participating processes. */
+  MPI_Comm communicator;
+  /** Size of the MPI communicator respectively all participating processes. */
+  int comm_size;
+  /** Pointer to a hashfunction. */
+  uint64_t (*hash_func)(int, void*);
+  /** Pre-allocated memory where a bucket can be received. */
+  void* recv_entry;
+  /** Pre-allocated memory where a bucket to send can be stored. */
+  void* send_entry;
+  /** Allocated memory on which the MPI window was created. */
+  void* mem_alloc;
+  /** Count of read misses over all time. */
+  int read_misses;
+  /** Count of evictions over all time. */
+  int evictions;
+  /** Array of indeces where a bucket can be stored. */
+  uint64_t* index;
+  /** Count of possible indeces. */
+  unsigned int index_count;
+#ifdef DHT_STATISTICS
+  /** Detailed statistics of the usage of the DHT. */
+  DHT_stats* stats;
+#endif
+} DHT;
+
+/**
+ * @brief Create a DHT.
+ *
+ * When calling this function, the required memory is allocated and a
+ * MPI_Window is created. This allows the execution of MPI_Get and
+ * MPI_Put operations for one-sided communication. Then the number of
+ * indexes is calculated and finally all relevant data is entered into the
+ * \a DHT-object which is returned.
+ *
+ * @param comm MPI communicator which addresses all participating process of the
+ * DHT.
+ * @param size_per_process Number of buckets per process.
+ * @param data_size Size of data in byte.
+ * @param key_size Size of the key in byte.
+ * @param hash_func Pointer to a hash function. This function must take the size
+ * of the key and a pointer to the key as input parameters and return a 64 bit
+ * hash.
+ * @return DHT* The returned value is the \a DHT-object which serves as a handle
+ * for all DHT operations. If an error occured NULL is returned.
+ */
+extern DHT* DHT_create(MPI_Comm comm, uint64_t size_per_process,
+                       unsigned int data_size, unsigned int key_size,
+                       uint64_t (*hash_func)(int, void*));
+
+/**
+ * @brief Write data into DHT.
+ *
+ * When DHT_write is called, the address window is locked with a
+ * LOCK_EXCLUSIVE for write access. Now the first bucket is received
+ * using MPI_Get and it is checked if the bucket is empty or if the received key
+ * matches the passed key. If this is the case, the data of the bucket is
+ * overwritten with the new value. If not, the function continues with the next
+ * index until no more indexes are available. When the last index is reached and
+ * there are no more indexes available, the last examined bucket is replaced.
+ * After successful writing, the memory window is released and the function
+ * returns.
+ *
+ * @param table Pointer to the \a DHT-object.
+ * @param key Pointer to the key.
+ * @param data Pointer to the data.
+ * @return int Returns either DHT_SUCCESS on success or correspondending error
+ * value on eviction or error.
+ */
+extern int DHT_write(DHT* table, void* key, void* data);
+
+/**
+ * @brief Read data from DHT.
+ *
+ * At the beginning, the target process and all possible indices are determined.
+ * After that a SHARED lock on the address window for read access is done
+ * and the first entry is retrieved. Now the received key is compared
+ * with the key passed to the function. If they coincide the correct data
+ * was found. If not it continues with the next index. If the last
+ * possible bucket is reached and the keys still do not match the read
+ * error counter is incremented. After the window has been released
+ * again, the function returns with a corresponding return value (read
+ * error or error-free read). The data to be read out is also written to
+ * the memory area of the passed pointer.
+ *
+ * @param table Pointer to the \a DHT-object.
+ * @param key Pointer to the key.
+ * @param destination Pointer to memory area where retreived data should be
+ * stored.
+ * @return int Returns either DHT_SUCCESS on success or correspondending error
+ * value on read miss or error.
+ */
+extern int DHT_read(DHT* table, void* key, void* destination);
+
+/**
+ * @brief Write current state of DHT to file.
+ *
+ * All contents are written as a memory dump, so that no conversion takes place.
+ * First, an attempt is made to open or create a file. If this is successful the
+ * file header consisting of data and key size is written. Then each process
+ * reads its memory area of the DHT and each bucket that was marked as written
+ * is added to the file using MPI file operations.
+ *
+ * @param table Pointer to the \a DHT-object.
+ * @param filename Name of the file to write to.
+ * @return int Returns DHT_SUCCESS on succes, DHT_FILE_IO_ERROR if file can't be
+ * opened/closed or DHT_WRITE_ERROR if file is not writable.
+ */
+extern int DHT_to_file(DHT* table, const char* filename);
+
+/**
+ * @brief Read state of DHT from file.
+ *
+ * One needs a previously written DHT file (by DHT_from_file).
+ * First of all, an attempt is made to open the specified file. If this is
+ * succeeded the file header is read and compared with the current values of the
+ * DHT. If the data and key sizes do not differ, one can continue. Each process
+ * reads one line of the file and writes it to the DHT with DHT_write. This
+ * happens until no more lines are left. The writing is done by the
+ * implementation of DHT_write.
+ *
+ * @param table Pointer to the \a DHT-object.
+ * @param filename Name of the file to read from.
+ * @return int Returns DHT_SUCCESS on succes, DHT_FILE_IO_ERROR if file can't be
+ * opened/closed, DHT_READ_MISS if file is not readable or DHT_WRONG_FILE if
+ * file doesn't match expectation. This is possible if the data size or key size
+ * is different.
+ */
+extern int DHT_from_file(DHT* table, const char* filename);
+
+/**
+ * @brief Free ressources of DHT.
+ *
+ * Finally, to free all resources after using the DHT, the function
+ * DHT_free must be used. This will free the MPI\_Window, as well as the
+ * associated memory. Also all internal variables are released. Optionally, the
+ * count of evictions and read misses can also be obtained.
+ *
+ * @param table Pointer to the \a DHT-object.
+ * @param eviction_counter \a optional: Pointer to integer where the count of
+ * evictions should be stored.
+ * @param readerror_counter \a optional: Pointer to integer where the count of
+ * read errors should be stored.
+ * @return int Returns either DHT_SUCCESS on success or DHT_MPI_ERROR on
+ * internal MPI error.
+ */
+extern int DHT_free(DHT* table, int* eviction_counter, int* readerror_counter);
+
+/**
+ * @brief Prints a table with statistics about current use of DHT.
+ *
+ * These statistics are from each participated process and also summed up over
+ * all processes. Detailed statistics are:
+ *  -# occupied buckets (in respect to the memory of this process)
+ *  -# free buckets (in respect to the memory of this process)
+ *  -# calls of DHT_write (w_access)
+ *  -# calls of DHT_read (r_access)
+ *  -# read misses (see DHT_READ_MISS)
+ *  -# collisions (see DHT_WRITE_SUCCESS_WITH_EVICTION)
+ * 3-6 will reset with every call of this function finally the amount of new
+ * written entries is printed out (since the last call of this funtion).
+ *
+ * This is done by collective MPI operations with the root process with rank 0,
+ * which will also print a table with all informations to stdout.
+ *
+ * Also, as this function was implemented for a special case (POET project) one
+ * need to define DHT_STATISTICS to the compiler macros to use this
+ * function (eg. <emph>gcc -DDHT_STATISTICS ... </emph>).
+ * @param table Pointer to the \a DHT-object.
+ * @return int Returns DHT_SUCCESS on success or DHT_MPI_ERROR on internal MPI
+ * error.
+ */
+extern int DHT_print_statistics(DHT* table);
+
+/**
+ * @brief Determine destination rank and index.
+ *
+ * This is done by looping over all possbile indices. First of all, set a
+ * temporary index to zero and copy count of bytes for each index into the
+ * memory area of the temporary index. After that the current index is
+ * calculated by the temporary index modulo the table size. The destination rank
+ * of the process is simply determined by hash modulo the communicator size.
+ *
+ * @param hash Calculated 64 bit hash.
+ * @param comm_size Communicator size.
+ * @param table_size Count of buckets per process.
+ * @param dest_rank Reference to the destination rank variable.
+ * @param index Pointer to the array index.
+ * @param index_count Count of possible indeces.
+ */
+static void determine_dest(uint64_t hash, int comm_size,
+                           unsigned int table_size, unsigned int* dest_rank,
+                           uint64_t* index, unsigned int index_count);
+
+/**
+ * @brief Set the occupied flag.
+ *
+ * This will set the first bit of a bucket to 1.
+ *
+ * @param flag_byte First byte of a bucket.
+ */
+static void set_flag(char* flag_byte);
+
+/**
+ * @brief Get the occupied flag.
+ *
+ * This function determines whether the occupied flag of a bucket was set or
+ * not.
+ *
+ * @param flag_byte First byte of a bucket.
+ * @return int Returns 1 for true or 0 for false.
+ */
+static int read_flag(char flag_byte);
+
+#endif /* DHT_H */
diff --git a/src/DHT/DHT_Wrapper.cpp b/src/DHT/DHT_Wrapper.cpp
new file mode 100644
index 000000000..d254717ed
--- /dev/null
+++ b/src/DHT/DHT_Wrapper.cpp
@@ -0,0 +1,232 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "DHT_Wrapper.h"
+
+#include <math.h>
+#include <openssl/md5.h>
+
+#include <iostream>
+
+using namespace poet;
+using namespace std;
+
+uint64_t poet::get_md5(int key_size, void *key) {
+  MD5_CTX ctx;
+  unsigned char sum[MD5_DIGEST_LENGTH];
+  uint64_t retval, *v1, *v2;
+
+  // calculate md5 using MD5 functions
+  MD5_Init(&ctx);
+  MD5_Update(&ctx, key, key_size);
+  MD5_Final(sum, &ctx);
+
+  // divide hash in 2 64 bit parts and XOR them
+  v1 = (uint64_t *)&sum[0];
+  v2 = (uint64_t *)&sum[8];
+  retval = *v1 ^ *v2;
+
+  return retval;
+}
+
+DHT_Wrapper::DHT_Wrapper(SimParams &params, MPI_Comm dht_comm,
+                         int buckets_per_process, int data_size, int key_size) {
+  // initialize DHT object
+  dht_object =
+      DHT_create(dht_comm, buckets_per_process, data_size, key_size, &get_md5);
+  // allocate memory for fuzzing buffer
+  fuzzing_buffer = (double *)malloc(key_size);
+
+  // extract needed values from sim_param struct
+  t_simparams tmp = params.getNumParams();
+
+  this->dt_differ = tmp.dt_differ;
+  this->dht_log = tmp.dht_log;
+
+  this->dht_signif_vector = params.getDHTSignifVector();
+  this->dht_prop_type_vector = params.getDHTPropTypeVector();
+}
+
+DHT_Wrapper::~DHT_Wrapper() {
+  // free DHT
+  DHT_free(dht_object, NULL, NULL);
+  // free fuzzing buffer
+  free(fuzzing_buffer);
+}
+
+void DHT_Wrapper::checkDHT(int length, std::vector<bool> &out_result_index,
+                           double *work_package, double dt) {
+  void *key;
+  int res;
+  // var count -> count of variables per grid cell
+  int var_count = dht_prop_type_vector.size();
+  // loop over every grid cell contained in work package
+  for (int i = 0; i < length; i++) {
+    // point to current grid cell
+    key = (void *)&(work_package[i * var_count]);
+
+    // fuzz data (round, logarithm etc.)
+    fuzzForDHT(var_count, key, dt);
+
+    // overwrite input with data from DHT, IF value is found in DHT
+    res = DHT_read(dht_object, fuzzing_buffer, key);
+
+    // if DHT_SUCCESS value was found ...
+    if (res == DHT_SUCCESS) {
+      // ... and grid cell will be marked as 'not to be simulating'
+      out_result_index[i] = false;
+      dht_hits++;
+
+    }
+    // ... otherwise ...
+    else if (res == DHT_READ_MISS) {
+      // grid cell needs to be simulated by PHREEQC
+      out_result_index[i] = true;
+      dht_miss++;
+    } else {
+      // MPI ERROR ... WHAT TO DO NOW?
+      // RUNNING CIRCLES WHILE SCREAMING
+    }
+  }
+}
+
+void DHT_Wrapper::fillDHT(int length, std::vector<bool> &result_index,
+                          double *work_package, double *results, double dt) {
+  void *key;
+  void *data;
+  int res;
+  // var count -> count of variables per grid cell
+  int var_count = dht_prop_type_vector.size();
+  // loop over every grid cell contained in work package
+  for (int i = 0; i < length; i++) {
+    key = (void *)&(work_package[i * var_count]);
+    data = (void *)&(results[i * var_count]);
+
+    // If true grid cell was simulated, needs to be inserted into dht
+    if (result_index[i]) {
+      // fuzz data (round, logarithm etc.)
+      fuzzForDHT(var_count, key, dt);
+
+      // insert simulated data with fuzzed key into DHT
+      res = DHT_write(dht_object, fuzzing_buffer, data);
+
+      // if data was successfully written ...
+      if (res != DHT_SUCCESS) {
+        // ... also check if a previously written value was evicted
+        if (res == DHT_WRITE_SUCCESS_WITH_EVICTION) {
+          // and increment internal eviciton counter
+          dht_evictions++;
+        } else {
+          // MPI ERROR ... WHAT TO DO NOW?
+          // RUNNING CIRCLES WHILE SCREAMING
+        }
+      }
+    }
+  }
+}
+
+int DHT_Wrapper::tableToFile(const char *filename) {
+  int res = DHT_to_file(dht_object, filename);
+  return res;
+}
+
+int DHT_Wrapper::fileToTable(const char *filename) {
+  int res = DHT_from_file(dht_object, filename);
+  if (res != DHT_SUCCESS) return res;
+
+#ifdef DHT_STATISTICS
+  DHT_print_statistics(dht_object);
+#endif
+
+  return DHT_SUCCESS;
+}
+
+void DHT_Wrapper::printStatistics() {
+  int res;
+
+  res = DHT_print_statistics(dht_object);
+
+  if (res != DHT_SUCCESS) {
+    // MPI ERROR ... WHAT TO DO NOW?
+    // RUNNING CIRCLES WHILE SCREAMING
+  }
+}
+
+uint64_t DHT_Wrapper::getHits() { return this->dht_hits; }
+
+uint64_t DHT_Wrapper::getMisses() { return this->dht_miss; }
+
+uint64_t DHT_Wrapper::getEvictions() { return this->dht_evictions; }
+
+void DHT_Wrapper::fuzzForDHT(int var_count, void *key, double dt) {
+  unsigned int i = 0;
+  // introduce fuzzing to allow more hits in DHT
+  // loop over every variable of grid cell
+  for (i = 0; i < (unsigned int)var_count; i++) {
+    // check if variable is defined as 'act'
+    if (dht_prop_type_vector[i] == "act") {
+      // if log is enabled (default)
+      if (dht_log) {
+        // if variable is smaller than 0, which would be a strange result,
+        // warn the user and set fuzzing_buffer to 0 at this index
+        if (((double *)key)[i] < 0) {
+          cerr << "dht_wrapper.cpp::fuzz_for_dht(): Warning! Negative value in "
+                  "key!"
+               << endl;
+          fuzzing_buffer[i] = 0;
+        }
+        // if variable is 0 set fuzzing buffer to 0
+        else if (((double *)key)[i] == 0)
+          fuzzing_buffer[i] = 0;
+        // otherwise ...
+        else
+          // round current variable value by applying log with base 10, negate
+          // (since the actual values will be between 0 and 1) and cut result
+          // after significant digit
+          fuzzing_buffer[i] =
+              ROUND(-(std::log10(((double *)key)[i])), dht_signif_vector[i]);
+      }
+      // if log is disabled
+      else {
+        // just round by cutting after signifanct digit
+        fuzzing_buffer[i] = ROUND((((double *)key)[i]), dht_signif_vector[i]);
+      }
+    }
+    // if variable is defined as 'logact' (log was already applied e.g. pH)
+    else if (dht_prop_type_vector[i] == "logact") {
+      // just round by cutting after signifanct digit
+      fuzzing_buffer[i] = ROUND((((double *)key)[i]), dht_signif_vector[i]);
+    }
+    // if defined ass 'ignore' ...
+    else if (dht_prop_type_vector[i] == "ignore") {
+      // ... just set fuzzing buffer to 0
+      fuzzing_buffer[i] = 0;
+    }
+    // and finally, if type is not defined, print error message
+    else {
+      cerr << "dht_wrapper.cpp::fuzz_for_dht(): Warning! Probably wrong "
+              "prop_type!"
+           << endl;
+    }
+  }
+  // if timestep differs over iterations set current current time step at the
+  // end of fuzzing buffer
+  if (dt_differ) fuzzing_buffer[var_count] = dt;
+}
diff --git a/src/DHT/DHT_Wrapper.h b/src/DHT/DHT_Wrapper.h
new file mode 100644
index 000000000..dd7612f5e
--- /dev/null
+++ b/src/DHT/DHT_Wrapper.h
@@ -0,0 +1,300 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef DHT_WRAPPER_H
+#define DHT_WRAPPER_H
+
+#include <SimParams.h>
+
+#include <string>
+#include <vector>
+
+extern "C" {
+#include <DHT.h>
+}
+
+#include <mpi.h>
+
+/**
+ * @brief Cut double value after signif digit
+ *
+ * Macro to round a double value by cutting every digit after significant digit
+ *
+ */
+#define ROUND(value, signif) \
+  (((int)(pow(10.0, (double)signif) * value)) * pow(10.0, (double)-signif))
+
+namespace poet {
+/**
+ * @brief Return user-defined md5sum
+ *
+ * This function will calculate a hashsum with the help of md5sum. Therefore the
+ * md5sum for a given key is calculated and divided into two 64-bit parts. These
+ * will be XORed and returned as the hash.
+ *
+ * @param key_size Size of key in bytes
+ * @param key Pointer to key
+ * @return uint64_t Hashsum as an unsigned 64-bit integer
+ */
+static uint64_t get_md5(int key_size, void *key);
+
+/**
+ * @brief C++-Wrapper around DHT implementation
+ *
+ * Provides an API to interact with the current DHT implentation. This class is
+ * POET specific and can't be used outside the POET application.
+ *
+ */
+class DHT_Wrapper {
+ public:
+  /**
+   * @brief Construct a new dht wrapper object
+   *
+   * The constructor will initialize the private dht_object of this class by
+   * calling DHT_create with all given parameters. Also the fuzzing buffer will
+   * be allocated and all needed parameters extracted from simparams struct.
+   *
+   * @param params Simulation parameter object
+   * @param dht_comm Communicator which addresses all participating DHT
+   * processes
+   * @param buckets_per_process Count of buckets to allocate for each process
+   * @param data_size Size of data in bytes
+   * @param key_size Size of key in bytes
+   */
+  DHT_Wrapper(SimParams &params, MPI_Comm dht_comm, int buckets_per_process,
+              int data_size, int key_size);
+  /**
+   * @brief Destroy the dht wrapper object
+   *
+   * By destroying this object the DHT will also be freed. Since all statistics
+   * are stored inside this object, no statistics will be retrieved during the
+   * call of DHT_free. After freeing the DHT the fuzzing buffer will be also
+   * freed.
+   *
+   */
+  ~DHT_Wrapper();
+
+  /**
+   * @brief Check if values of workpackage are stored in DHT
+   *
+   * Call DHT_read for all grid cells of the given workpackage and if a
+   * previously simulated grid cell was found mark this grid cell as 'not be
+   * simulated'. Therefore all values of a grid cell are fuzzed by fuzzForDHT
+   * and used as input key. The correspondending retrieved value might be stored
+   * directly into the memory area of the work_package and out_result_index is
+   * marked with false ('not to be simulated').
+   *
+   * @param length Count of grid cells inside work package
+   * @param[out] out_result_index Indexing work packages which should be
+   * simulated
+   * @param[in,out] work_package Pointer to current work package
+   * @param dt Current timestep of simulation
+   */
+  void checkDHT(int length, std::vector<bool> &out_result_index,
+                double *work_package, double dt);
+
+  /**
+   * @brief Write simulated values into DHT
+   *
+   * Call DHT_write for all grid cells of the given workpackage which was
+   * simulated shortly before by the worker. Whether the grid cell was simulated
+   * is given by result_index. For every grid cell indicated with true inside
+   * result_index write the simulated value into the DHT.
+   *
+   * @param length Count of grid cells inside work package
+   * @param result_index Indexing work packages which was simulated
+   * @param work_package Pointer to current work package which was used as input
+   * of PHREEQC
+   * @param results Pointer to current work package which are the resulting
+   * outputs of the PHREEQC simulation
+   * @param dt Current timestep of simulation
+   */
+  void fillDHT(int length, std::vector<bool> &result_index,
+               double *work_package, double *results, double dt);
+
+  /**
+   * @brief Dump current DHT state into file.
+   *
+   * This function will simply execute DHT_to_file with given file name (see
+   * DHT.h for more info).
+   *
+   * @param filename Name of the dump file
+   * @return int Returns 0 on success, otherwise an error value
+   */
+  int tableToFile(const char *filename);
+
+  /**
+   * @brief Load dump file into DHT.
+   *
+   * This function will simply execute DHT_from_file with given file name (see
+   * DHT.h for more info).
+   *
+   * @param filename Name of the dump file
+   * @return int Returns 0 on success, otherwise an error value
+   */
+  int fileToTable(const char *filename);
+
+  /**
+   * @brief Print a detailed statistic of DHT usage.
+   *
+   * This function will simply execute DHT_print_statistics with given file name
+   * (see DHT.h for more info).
+   *
+   */
+  void printStatistics();
+
+  /**
+   * @brief Get the Hits object
+   *
+   * @return uint64_t Count of hits
+   */
+  uint64_t getHits();
+
+  /**
+   * @brief Get the Misses object
+   *
+   * @return uint64_t Count of read misses
+   */
+  uint64_t getMisses();
+
+  /**
+   * @brief Get the Evictions object
+   *
+   * @return uint64_t Count of evictions
+   */
+  uint64_t getEvictions();
+
+ private:
+  /**
+   * @brief Transform given workpackage into DHT key
+   *
+   * A given workpackage will be transformed into a DHT key by rounding each
+   * value of a workpackage to a given significant digit. Three different types
+   * of variables 'act', 'logact' and 'ignore' are used. Those types are given
+   * via the dht_signif_vector.
+   *
+   * If a variable is defined as 'act', dht_log is true and non-negative, the
+   * logarithm with base 10 will be applied. After that the value is negated. In
+   * case the value is 0 the fuzzing_buffer is also set to 0 at this position.
+   * If the value is negative a correspondending warning will be printed to
+   * stderr and the fuzzing buffer will be set to 0 at this index.
+   *
+   * If a variable is defined as 'logact' the value will be cut after the
+   * significant digit.
+   *
+   * If a variable ist defined as 'ignore' the fuzzing_buffer will be set to 0
+   * at the index of the variable.
+   *
+   * If dt_differ is true the current time step of the simulation will be set at
+   * the end of the fuzzing_buffer.
+   *
+   * @param var_count Count of variables for the current work package
+   * @param key Pointer to work package handled as the key
+   * @param dt Current time step of the simulation
+   */
+  void fuzzForDHT(int var_count, void *key, double dt);
+
+  /**
+   * @brief DHT handle
+   *
+   * Stores information about the DHT. Will be used as a handle for each DHT
+   * library call.
+   *
+   */
+  DHT *dht_object;
+
+  /**
+   * @brief Count of hits
+   *
+   * The counter will be incremented if a previously simulated workpackage can
+   * be retrieved with a given key.
+   *
+   */
+  uint64_t dht_hits = 0;
+
+  /**
+   * @brief Count of read misses
+   *
+   * The counter will be incremented if a given key doesn't retrieve a value
+   * from the DHT.
+   *
+   */
+  uint64_t dht_miss = 0;
+
+  /**
+   * @brief Count of evictions
+   *
+   * If a value in the DHT must be evicted because of lack of space/reaching the
+   * last index etc., this counter will be incremented.
+   *
+   */
+  uint64_t dht_evictions = 0;
+
+  /**
+   * @brief Rounded work package values
+   *
+   * Stores rounded work package values and serves as the DHT key pointer.
+   *
+   */
+  double *fuzzing_buffer;
+
+  /**
+   * @brief Indicates change in time step during simulation
+   *
+   * If set to true, the time step of simulation will differ between iterations,
+   * so the current time step must be stored inside the DHT key. Otherwise wrong
+   * values would be obtained.
+   *
+   * If set to false the time step doesn't need to be stored in the DHT key.
+   *
+   */
+  bool dt_differ;
+
+  /**
+   * @brief Logarithm before rounding
+   *
+   * Indicates if the logarithm with base 10 will be applied to a variable
+   * before rounding.
+   *
+   * Defaults to true.
+   *
+   */
+  bool dht_log;
+
+  /**
+   * @brief Significant digits for each variable
+   *
+   * Stores the rounding/significant digits for each variable of the work
+   * package.
+   *
+   */
+  std::vector<int> dht_signif_vector;
+
+  /**
+   * @brief Type of each variable
+   *
+   * Defines the type of each variable of the work package.
+   *
+   */
+  std::vector<std::string> dht_prop_type_vector;
+};
+}  // namespace poet
+
+#endif  // DHT_WRAPPER_H
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index e8f8c3036..000000000
--- a/src/Makefile
+++ /dev/null
@@ -1,51 +0,0 @@
-## Simple Makefile for MPI use of RInside
-
-## comment this out if you need a different version of R, 
-## and set R_HOME accordingly as an environment variable
-R_HOME := 		$(shell R RHOME)
-
-sources := 		$(wildcard *.cpp)
-programs := 		kin
-
-
-# OpenMPI header and libraries
-MPICPPFLAGS :=		$(shell mpic++ -showme:compile)
-MPILIBS :=		$(shell mpic++ -showme:link)
-
-## include headers and libraries for R 
-RCPPFLAGS := 		$(shell $(R_HOME)/bin/R CMD config --cppflags)
-RLDFLAGS := 		$(shell $(R_HOME)/bin/R CMD config --ldflags)
-RBLAS := 		$(shell $(R_HOME)/bin/R CMD config BLAS_LIBS)
-RLAPACK := 		$(shell $(R_HOME)/bin/R CMD config LAPACK_LIBS)
-
-
-## include headers and libraries for Rcpp interface classes
-## note that RCPPLIBS will be empty with Rcpp (>= 0.11.0) and can be omitted
-RCPPINCL := 		$(shell echo 'Rcpp:::CxxFlags()' | $(R_HOME)/bin/R --vanilla --slave)
-RCPPLIBS := 		$(shell echo 'Rcpp:::LdFlags()'  | $(R_HOME)/bin/R --vanilla --slave)
-
-
-## include headers and libraries for RInside embedding classes
-RINSIDEINCL := 		$(shell echo 'RInside:::CxxFlags()' | $(R_HOME)/bin/R --vanilla --slave)
-RINSIDELIBS := 		$(shell echo 'RInside:::LdFlags()'  | $(R_HOME)/bin/R --vanilla --slave)
-
-
-## compiler etc settings used in default make rules
-CXX := 			$(shell $(R_HOME)/bin/R CMD config CXX)
-CPPFLAGS := 		-D STRICT_R_HEADERS -Wall -ggdb -O3 $(shell $(R_HOME)/bin/R CMD config CPPFLAGS)
-CXXFLAGS := 		$(MPICPPFLAGS) $(RCPPFLAGS) $(RCPPINCL) $(RINSIDEINCL) $(shell $(R_HOME)/bin/R CMD config CXXFLAGS)
-LDLIBS := 		$(MPILIBS) $(RLDFLAGS) $(RBLAS) $(RLAPACK) $(RCPPLIBS) $(RINSIDELIBS) -lcrypto ## -fpermissive
-
-default: all
-
-kin :			DHT.cpp worker.cpp dht_wrapper.cpp r_utils.cpp kin.cpp
-
-all : 			$(programs)
-			@test -x /usr/bin/strip && strip $^
-
-run :			$(programs)
-			@test -x /usr/bin/mpirun && for p in $(programs); do echo; echo "Running $$p:"; mpirun -n 4 ./$$p; done
-
-clean:
-			rm -vf $(programs)
-
diff --git a/src/dht_wrapper.cpp b/src/dht_wrapper.cpp
deleted file mode 100644
index 44f0a865c..000000000
--- a/src/dht_wrapper.cpp
+++ /dev/null
@@ -1,175 +0,0 @@
-#include "dht_wrapper.h"
-#include <openssl/md5.h>
-
-/*init globals*/
-bool dht_enabled;
-int dht_snaps;
-int dht_strategy;
-int dht_significant_digits;
-std::string dht_file;
-std::vector<int> dht_significant_digits_vector;
-std::vector<string> prop_type_vector;
-bool dht_logarithm;
-uint64_t dht_size_per_process;
-uint64_t dht_hits, dht_miss, dht_collision;
-RInside *R_DHT;
-std::vector<bool> dht_flags;
-DHT *dht_object;
-
-double *fuzzing_buffer;
-
-bool dt_differ;
-/*functions*/
-
-uint64_t get_md5(int key_size, void *key) {
-    MD5_CTX ctx;
-    unsigned char sum[MD5_DIGEST_LENGTH];
-    uint64_t retval, *v1, *v2;
-
-    MD5_Init(&ctx);
-    MD5_Update(&ctx, key, key_size);
-    MD5_Final(sum, &ctx);
-
-    v1 = (uint64_t *)&sum[0];
-    v2 = (uint64_t *)&sum[8];
-    retval = *v1 ^ *v2;
-
-    return retval;
-}
-
-double Round_off(RInside &R, double N, double n) {
-    double result;
-    R["roundsig"] = n;
-    R["roundin"] = N;
-
-    result = R.parseEval("signif(roundin, digits=roundsig)");
-
-    return result;
-}
-
-/*
-*   Stores fuzzed version of key in fuzzing_buffer
-*/
-void fuzz_for_dht(RInside &R, int var_count, void *key, double dt) {
-    unsigned int i = 0;
-    //introduce fuzzing to allow more hits in DHT
-    for (i = 0; i < (unsigned int)var_count; i++) {
-        if (prop_type_vector[i] == "act") {
-            //with log10
-            if (dht_logarithm) {
-                if (((double *)key)[i] < 0)
-                    cerr << "dht_wrapper.cpp::fuzz_for_dht(): Warning! Negative value at key!" << endl;
-                else if (((double *)key)[i] == 0)
-                    fuzzing_buffer[i] = 0;
-                else
-                    //fuzzing_buffer[i] = Round_off(R, std::log10(((double *)key)[i]), dht_significant_digits_vector[i] - 1);
-                    fuzzing_buffer[i] = ROUND(-(std::log10(((double *)key)[i])), dht_significant_digits_vector[i]);
-            } else {
-                //without log10
-                //fuzzing_buffer[i] = Round_off(R, ((double *)key)[i], dht_significant_digits_vector[i]);
-                fuzzing_buffer[i] = ROUND((((double *)key)[i]), dht_significant_digits_vector[i]);
-            }
-        } else if (prop_type_vector[i] == "logact") {
-            //fuzzing_buffer[i] = Round_off(R, ((double *)key)[i], dht_significant_digits_vector[i]);
-            fuzzing_buffer[i] = ROUND((((double *)key)[i]), dht_significant_digits_vector[i]);
-        } else if (prop_type_vector[i] == "ignore") {
-            fuzzing_buffer[i] = 0;
-        } else {
-            cerr << "dht_wrapper.cpp::fuzz_for_dht(): Warning! Probably wrong prop_type!" << endl;
-        }
-    }
-    if (dt_differ)
-        fuzzing_buffer[var_count] = dt;
-}
-
-void check_dht(RInside &R, int length, std::vector<bool> &out_result_index, double *work_package) {
-    void *key;
-    int res;
-    int var_count = prop_type_vector.size();
-    double dt;
-
-    dt = R.parseEval("mysetup$dt");
-
-    for (int i = 0; i < length; i++) {
-        key = (void *)&(work_package[i * var_count]);
-
-        //fuzz data (round, logarithm etc.)
-        fuzz_for_dht(R, var_count, key, dt);
-
-        //overwrite input with data from DHT, IF value is found in DHT
-        res = DHT_read(dht_object, fuzzing_buffer, key);
-
-        if (res == DHT_SUCCESS) {
-            //flag that this line is replaced by DHT-value, do not simulate!!
-            out_result_index[i] = false;
-            dht_hits++;
-        } else if (res == DHT_READ_ERROR) {
-            //this line is untouched, simulation is needed
-            out_result_index[i] = true;
-            dht_miss++;
-        } else {
-            //MPI ERROR ... WHAT TO DO NOW?
-            //RUNNING CIRCLES WHILE SCREAMING
-        }
-    }
-}
-
-void fill_dht(RInside &R, int length, std::vector<bool> &result_index, double *work_package, double *results) {
-    void *key;
-    void *data;
-    int res;
-    int var_count = prop_type_vector.size();
-    double dt;
-
-    dt = R.parseEval("mysetup$dt");
-
-    for (int i = 0; i < length; i++) {
-        key = (void *)&(work_package[i * var_count]);
-        data = (void *)&(results[i * var_count]);
-
-        if (result_index[i]) {
-            //If true -> was simulated, needs to be inserted into dht
-
-            //fuzz data (round, logarithm etc.)
-            fuzz_for_dht(R, var_count, key, dt);
-
-            res = DHT_write(dht_object, fuzzing_buffer, data);
-
-            if (res != DHT_SUCCESS) {
-                if (res == DHT_WRITE_SUCCESS_WITH_COLLISION) {
-                    dht_collision++;
-                } else {
-                    //MPI ERROR ... WHAT TO DO NOW?
-                    //RUNNING CIRCLES WHILE SCREAMING
-                }
-            }
-        }
-    }
-}
-
-void print_statistics() {
-    int res;
-
-    res = DHT_print_statistics(dht_object);
-
-    if (res != DHT_SUCCESS) {
-        //MPI ERROR ... WHAT TO DO NOW?
-        //RUNNING CIRCLES WHILE SCREAMING
-    }
-}
-
-int table_to_file(char *filename) {
-    int res = DHT_to_file(dht_object, filename);
-    return res;
-}
-
-int file_to_table(char *filename) {
-
-    int res = DHT_from_file(dht_object, filename);
-    if (res != DHT_SUCCESS) 
-        return res;
-
-    DHT_print_statistics(dht_object);
-
-    return DHT_SUCCESS;
-}
diff --git a/src/dht_wrapper.h b/src/dht_wrapper.h
deleted file mode 100644
index 3557f7f5b..000000000
--- a/src/dht_wrapper.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#pragma once
-#include <RInside.h> 
-#include <string>
-#include <vector>
-#include <math.h>
-#include "DHT.h"
-
-using namespace std;
-using namespace Rcpp;
-
-/*Functions*/
-uint64_t get_md5(int key_size, void* key);
-void fuzz_for_dht(RInside &R, int var_count, void *key, double dt);
-void check_dht(RInside &R, int length, std::vector<bool> &out_result_index, double *work_package);
-void fill_dht(RInside &R, int length, std::vector<bool> &result_index, double *work_package, double *results);
-void print_statistics();
-int table_to_file(char* filename);
-int file_to_table(char* filename);
-
-/*globals*/
-extern bool dht_enabled;
-extern int dht_snaps;
-extern std::string dht_file;
-extern bool dt_differ;
-
-//Default DHT Size per process in Byte (defaults to 1 GiB)
-#define DHT_SIZE_PER_PROCESS 1073741824
-
-//sets default dht access and distribution strategy
-#define DHT_STRATEGY 0
-// 0 -> DHT is on workers, access from workers only
-// 1 -> DHT is on workers + master, access from master only !NOT IMPLEMENTED YET!
-
-#define ROUND(value,signif) (((int) (pow(10.0, (double) signif) * value)) * pow(10.0, (double) -signif))
-
-extern int dht_strategy;
-extern int dht_significant_digits;
-extern std::vector<int> dht_significant_digits_vector;
-extern std::vector<string> prop_type_vector;
-extern bool dht_logarithm;
-extern uint64_t dht_size_per_process;
-
-//global DHT object, can be NULL if not initialized, check strategy
-extern DHT* dht_object;
-
-//DHT Performance counter
-extern uint64_t dht_hits, dht_miss, dht_collision;
-
-extern double* fuzzing_buffer;
-extern std::vector<bool> dht_flags;
diff --git a/src/global_buffer.h b/src/global_buffer.h
deleted file mode 100644
index 69cc742f2..000000000
--- a/src/global_buffer.h
+++ /dev/null
@@ -1,9 +0,0 @@
-#pragma once
-
-#define BUFFER_OFFSET 5
-
-/*Globals*/
-extern double* mpi_buffer;
-extern double* mpi_buffer_results;
-
-extern uint32_t work_package_size; 
\ No newline at end of file
diff --git a/src/kin.cpp b/src/kin.cpp
deleted file mode 100644
index 63a57ba2d..000000000
--- a/src/kin.cpp
+++ /dev/null
@@ -1,818 +0,0 @@
-#include <string>
-#include <vector>
-#include <iostream>
-#include <cstring>
-
-#include <RInside.h>  // for the embedded R via RInside
- 
-#include <mpi.h>      // mpi header file
-
-#include "argh.h"     // Argument handler https://github.com/adishavit/argh BSD-licenced
-#include "DHT.h"      // MPI-DHT Implementation
-#include "worker.h"
-#include "r_utils.h"
-#include "dht_wrapper.h"
-#include "global_buffer.h"
-
-using namespace std;
-using namespace Rcpp;
-
-double* mpi_buffer;
-double* mpi_buffer_results;
-
-uint32_t work_package_size; 
-#define WORK_PACKAGE_SIZE_DEFAULT 5
-
-bool store_result;
-
-std::set<std::string> paramList() {
-    std::set<std::string> options;
-    //global
-    options.insert("work-package-size");
-    //only DHT
-    options.insert("dht-signif");
-    options.insert("dht-strategy");
-    options.insert("dht-size");
-    options.insert("dht-snaps");
-    options.insert("dht-file");
-
-    return options;
-}
-
-std::set<std::string> flagList() {
-    std::set<std::string> options;
-    //global
-    options.insert("ignore-result");
-    //only DHT
-    options.insert("dht");
-    options.insert("dht-log");
-
-    return options;
-}
-
-std::list<std::string> checkOptions(argh::parser cmdl) {
-    std::list<std::string> retList;
-    std::set<std::string> flist = flagList();
-    std::set<std::string> plist = paramList();
-
-    for (auto& flag: cmdl.flags()) {
-        if (!(flist.find(flag) != flist.end())) retList.push_back(flag);
-    }
-
-    for (auto& param: cmdl.params()) {
-        if (!(plist.find(param.first) != plist.end())) retList.push_back(param.first);
-    }
-
-    return retList;
-}
-
-typedef struct 
-{
-    char has_work;
-    double* send_addr;
-} worker_struct;
-
-
-int main(int argc, char *argv[]) {
-    double sim_start, sim_b_transport, sim_a_transport, sim_b_chemistry, sim_a_chemistry,
-	sim_end;
-
-    double cummul_transport = 0.f;
-    double cummul_chemistry = 0.f;
-    double cummul_workers   = 0.f;
-    double cummul_chemistry_master   = 0.f;
-
-    double cummul_master_seq_pre_loop = 0.f;
-    double cummul_master_seq_loop = 0.f;
-    double master_idle = 0.f;
-
-    double master_send_a, master_send_b;
-    double cummul_master_send = 0.f;
-    double master_recv_a, master_recv_b;
-    double cummul_master_recv = 0.f;
-
-    double sim_a_seq, sim_b_seq, sim_c_seq, sim_d_seq;
-    double idle_a, idle_b;
-
-    double sim_c_chemistry, sim_d_chemistry;
-    double sim_e_chemistry, sim_f_chemistry;
-
-    argh::parser cmdl(argv);
-
-    // cout << "CPP: Start Init (MPI)" << endl;
-
-    MPI_Init( &argc, &argv );
-
-    int world_size;
-    MPI_Comm_size(MPI_COMM_WORLD, &world_size);
-
-    int world_rank;
-    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
-
-    /*Create custom Communicator with all processes except 0 (the master) for DHT storage*/
-    //only needed if strategy == 0, but done anyway
-    MPI_Group group_world;
-    MPI_Group dht_group;
-    MPI_Comm  dht_comm;
-    int* process_ranks;
-    
-    // make a list of processes in the new communicator
-    process_ranks= (int*) malloc(world_size*sizeof(int));
-    for(int I = 1; I < world_size; I++)
-        process_ranks[I-1] = I; 
-        
-    //get the group under MPI_COMM_WORLD
-    MPI_Comm_group(MPI_COMM_WORLD, &group_world); 
-    //create the new group
-    MPI_Group_incl(group_world, world_size-1, process_ranks, &dht_group); 
-    // create the new communicator
-    MPI_Comm_create(MPI_COMM_WORLD, dht_group, &dht_comm);
-    free (process_ranks); //cleanup
-    // cout << "Done";
-
-    if (cmdl[{"help", "h"}]) {
-        if (world_rank == 0) {
-            cout << "Todo" << endl <<
-            "See README.md for further information." << endl;
-        }
-        MPI_Finalize();
-        return EXIT_SUCCESS;
-    }
-
-    /*INIT is now done separately in an R file provided here as argument!*/
-    if (!cmdl(2)) {
-        if (world_rank == 0) {
-            cerr << "ERROR. Kin needs 2 positional arguments: " << endl <<
-            "1) the R script defining your simulation and" << endl <<
-            "2) the directory prefix where to save results and profiling" << endl;
-        }
-        MPI_Finalize();
-        return EXIT_FAILURE;
-    }
-    
-    std::list<std::string> optionsError = checkOptions(cmdl);
-    if (!optionsError.empty()) {
-        if (world_rank == 0) {
-            cerr << "Unrecognized option(s):\n" << endl;
-            for (auto option: optionsError) {
-                cerr << option << endl;
-            }
-            cerr << "\nMake sure to use available options. Exiting!" << endl;
-        }
-        MPI_Finalize();
-        return EXIT_FAILURE;
-    }
-
-    /*Parse DHT arguments*/
-    dht_enabled = cmdl["dht"];
-    // cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';
-    
-    if (dht_enabled) {
-        cmdl("dht-strategy", 0) >> dht_strategy;
-        // cout << "CPP: DHT strategy is " << dht_strategy << endl;
-        
-        cmdl("dht-signif", 5) >> dht_significant_digits;
-        // cout << "CPP: DHT significant digits = " << dht_significant_digits << endl;
-        
-        dht_logarithm = cmdl["dht-log"];
-        // cout << "CPP: DHT logarithm before rounding: " << ( dht_logarithm ? "ON" : "OFF" ) << endl;
-        
-        cmdl("dht-size", DHT_SIZE_PER_PROCESS) >> dht_size_per_process;
-        // cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process << endl;
-
-        cmdl("dht-snaps", 0) >> dht_snaps;
-
-        cmdl("dht-file") >> dht_file;
-    }
-
-    /*Parse work package size*/
-    cmdl("work-package-size", WORK_PACKAGE_SIZE_DEFAULT) >> work_package_size;
-
-
-    /*Parse output options*/
-    store_result = !cmdl["ignore-result"];
-
-
-    if (world_rank==0) {
-        cout << "CPP: Complete results storage is " << ( store_result ? "ON" : "OFF" ) << endl;
-        cout << "CPP: Work Package Size: " << work_package_size << endl;
-        cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';
-
-        if (dht_enabled) {
-            cout << "CPP: DHT strategy is " << dht_strategy << endl;
-            cout << "CPP: DHT key default digits (ignored if 'signif_vector' is defined) = " << dht_significant_digits << endl;
-            cout << "CPP: DHT logarithm before rounding: " << ( dht_logarithm ? "ON" : "OFF" ) << endl;
-            cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process << endl;
-            cout << "CPP: DHT save snapshots is " << dht_snaps << endl;
-            cout << "CPP: DHT load file is " << dht_file << endl;
-        }
-    }
-
-    cout << "CPP: R Init (RInside) on process " << world_rank << endl;
-    RInside R(argc, argv); 
-
-    // if local_rank == 0 then master else worker
-    R["local_rank"] = world_rank;
-
-    /*Loading Dependencies*/
-    std::string r_load_dependencies = 
-        "suppressMessages(library(Rmufits));"
-        "suppressMessages(library(RedModRphree));"
-        "source('kin_r_library.R');"
-        "source('parallel_r_library.R');";
-    R.parseEvalQ(r_load_dependencies);
-    
-    std::string filesim;
-    cmdl(1) >> filesim;               // <- first positional argument
-    R["filesim"] = wrap(filesim);     // assign a char* (string) to 'filesim'
-    R.parseEvalQ("source(filesim)");  // eval the init string, ignoring any returns
-
-    std::string out_dir;
-    if (world_rank == 0) {            // only rank 0 initializes goes through the whole initialization 
-        cmdl(2) >> out_dir;           // <- second positional argument 
-        R["fileout"] = wrap(out_dir); // assign a char* (string) to 'fileout'
-
-        // Note: R::sim_init() checks if the directory already exists,
-        // if not it makes it
-
-        // pass the boolean "store_result" to the R process
-        R["store_result"] = store_result;
-
-        //get timestep vector from grid_init function ...
-        std::string master_init_code = "mysetup <- master_init(setup=setup)";
-        R.parseEval(master_init_code);
-
-        dt_differ = R.parseEval("mysetup$dt_differ");
-        MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
-    } else {                           // workers will only read the setup DataFrame defined by input file
-        R.parseEval("mysetup <- setup");
-        MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
-    }
-
-    if (world_rank==0) {
-        cout << "CPP: R init done on process with rank " << world_rank << endl;
-    }
-
-    //initialize chemistry on all processes
-    std::string init_chemistry_code = "mysetup <- init_chemistry(setup=mysetup)";
-    R.parseEval(init_chemistry_code);
-
-    /* Retrieve state_C from R context for MPI buffer generation */
-    Rcpp::DataFrame state_C = R.parseEval("mysetup$state_C");
-
-    /* Init Parallel helper functions */
-    R["n_procs"] = world_size-1; /* worker count */
-    R["work_package_size"] = work_package_size;
-
-    // Removed additional field for ID in previous versions
-    if (world_rank == 0)
-    {
-        mpi_buffer = (double*) calloc(state_C.nrow() * (state_C.ncol()), sizeof(double));
-    } else
-    {
-        mpi_buffer = (double*) calloc((work_package_size * (state_C.ncol())) + BUFFER_OFFSET, sizeof(double));
-        mpi_buffer_results = (double*) calloc(work_package_size * (state_C.ncol()), sizeof(double));
-    }
-
-    if (world_rank==0) {
-        cout << "CPP: parallel init completed (buffers allocated)!" << endl;
-    }
-
-    // MDL: pass to R the DHT stuff (basically, only for storing of
-    // simulation parameters). These 2 variables are always defined:
-    R["dht_enabled"] = dht_enabled;
-    R["dht_log"] = dht_logarithm;
-
-    if (dht_enabled)
-    {
-        //cout << "\nCreating DHT\n";
-        //determine size of dht entries
-        int dht_data_size = state_C.ncol() * sizeof(double);
-        int dht_key_size  = state_C.ncol() * sizeof(double) + (dt_differ * sizeof(double));
-
-        //determine bucket count for preset memory usage
-        //bucket size is key + value + 1 byte for status
-        int dht_buckets_per_process = dht_size_per_process / (1 + dht_data_size + dht_key_size);
-
-        // MDL : following code moved here from worker.cpp 
-        /*Load significance vector from R setup file (or set default)*/
-        bool signif_vector_exists = R.parseEval("exists('signif_vector')");
-        if (signif_vector_exists)
-        { 
-            dht_significant_digits_vector = as<std::vector<int>>(R["signif_vector"]);
-        } else 
-        {
-            dht_significant_digits_vector.assign(dht_object->key_size / sizeof(double), dht_significant_digits);
-        }
-
-        /*Load property type vector from R setup file (or set default)*/
-        bool prop_type_vector_exists = R.parseEval("exists('prop_type')");
-        if (prop_type_vector_exists)
-        { 
-            prop_type_vector = as<std::vector<string>>(R["prop_type"]);
-        } else 
-        {
-            prop_type_vector.assign(dht_object->key_size / sizeof(double), "act");
-        }
-
-        if(world_rank == 0)
-        {
-            //print only on master, values are equal on all workes
-            cout << "CPP: dht_data_size: " << dht_data_size << "\n";
-            cout << "CPP: dht_key_size: " << dht_key_size << "\n";
-            cout << "CPP: dht_buckets_per_process: " << dht_buckets_per_process << endl;
-
-            // MDL: new output on signif_vector and prop_type
-            if (signif_vector_exists) {
-                cout << "CPP: using problem-specific rounding digits: " << endl;
-                R.parseEval("print(data.frame(prop=prop, type=prop_type, digits=signif_vector))");
-            } else
-            {
-                cout << "CPP: using DHT default rounding digits = " << dht_significant_digits << endl;
-            }
-
-            // MDL: pass to R the DHT stuff. These variables exist
-            // only if dht_enabled is true
-            R["dht_final_signif"] = dht_significant_digits_vector;
-            R["dht_final_proptype"] = prop_type_vector;
-        }
-
-        if (dht_strategy == 0)
-        {
-            if(world_rank != 0) {
-                dht_object = DHT_create(dht_comm, dht_buckets_per_process, dht_data_size, dht_key_size, get_md5);   
-                 
-                //storing for access from worker and callback functions
-                fuzzing_buffer = (double   *) malloc (dht_key_size);    
-            }
-        } else {
-            dht_object = DHT_create(MPI_COMM_WORLD, dht_buckets_per_process, dht_data_size, dht_key_size, get_md5);        
-        }
-
-        if (world_rank==0) {
-            cout << "CPP: DHT successfully created!" << endl;
-        }
-    }
-
-
-    // MDL: store all parameters
-    if (world_rank==0) {
-        cout << "CPP: Calling R Function to store calling parameters" << endl;
-        R.parseEvalQ("StoreSetup(setup=mysetup)");
-
-    }
-    
-    MPI_Barrier(MPI_COMM_WORLD);
-
-    if (world_rank == 0) 
-    {   /* This is executed by the master */
-
-        Rcpp::NumericVector master_send;
-        Rcpp::NumericVector master_recv;
-
-        sim_a_seq = MPI_Wtime();
-
-        worker_struct* workerlist = (worker_struct*) calloc(world_size-1, sizeof(worker_struct));
-        int need_to_receive;
-        MPI_Status probe_status;
-        double* timings;
-        uint64_t* dht_perfs = NULL;
-
-        int local_work_package_size;
-
-        // a temporary send buffer
-        double* send_buffer;
-        send_buffer = (double*) calloc((work_package_size * (state_C.ncol() )) + BUFFER_OFFSET, sizeof(double));
-
-        // helper variables
-        int iteration;
-        double dt, current_sim_time;
-
-
-        int n_wp = 1; // holds the actual number of wp which is
-                      // computed later in R::distribute_work_packages()
-        std::vector<int> wp_sizes_vector; // vector with the sizes of
-                                          // each package
-
-        sim_start = MPI_Wtime();
-
-        //Iteration Count is dynamic, retrieving value from R (is only needed by master for the following loop)
-        uint32_t maxiter = R.parseEval("mysetup$maxiter");
-
-        sim_b_seq = MPI_Wtime();
-
-        cummul_master_seq_pre_loop += sim_b_seq - sim_a_seq;
-
-        /*SIMULATION LOOP*/
-        for(uint32_t iter = 1; iter < maxiter+1; iter++)
-        {
-            sim_a_seq = MPI_Wtime();
-
-            cummul_master_send = 0.f;
-            cummul_master_recv = 0.f;
-
-
-            cout << "CPP: Evaluating next time step" << endl;
-            R.parseEvalQ("mysetup <- master_iteration_setup(mysetup)");
-
-            /*displaying iteration number, with C++ and R iterator*/
-            cout << "CPP: Going through iteration " << iter << endl;
-            cout << "CPP: R's $iter: "<< ((uint32_t) (R.parseEval("mysetup$iter"))) <<". Iteration" << endl; 
-
-            cout << "CPP: Calling Advection" << endl;
-	        
-            sim_b_transport = MPI_Wtime();
-            R.parseEvalQ("mysetup <- master_advection(setup=mysetup)");
-            sim_a_transport = MPI_Wtime();
-            
-            
-            cout << "CPP: Chemistry" << endl;
-            /*Fallback for sequential execution*/
-            sim_b_chemistry = MPI_Wtime();
-
-            if(world_size == 1) 
-            {
-                // MDL : the transformation of values into pH and pe
-                // takes now place in master_advection() so the
-                // following line is unneeded
-                // R.parseEvalQ("mysetup$state_T <- RedModRphree::Act2pH(mysetup$state_T)");
-                R.parseEvalQ("result <- slave_chemistry(setup=mysetup, data=mysetup$state_T)");
-                R.parseEvalQ("mysetup <- master_chemistry(setup=mysetup, data=result)");
-            } else { /*send work to workers*/
-
-                
-                // NEW: only in the first iteration we call
-                // R::distribute_work_packages()!!
-                if (iter==1)
-                {
-                    R.parseEvalQ("wp_ids <- distribute_work_packages(len=nrow(mysetup$state_T), package_size=work_package_size)");
-
-                    // we only sort once the vector
-                    R.parseEvalQ("ordered_ids <- order(wp_ids)");
-                    R.parseEvalQ("wp_sizes_vector <- compute_wp_sizes(wp_ids)");
-                    n_wp = (int) R.parseEval("length(wp_sizes_vector)");
-                    wp_sizes_vector = as<std::vector<int>>(R["wp_sizes_vector"]);
-                    cout << "CPP: Total number of work packages: " << n_wp << endl;
-                    R.parseEval("stat_wp_sizes(wp_sizes_vector)");
-                    
-                }
-
-                /* shuffle and extract data
-                   MDL: we now apply :Act2pH directly in master_advection
-                 */
-                // R.parseEval("tmp <- shuffle_field(RedModRphree::Act2pH(mysetup$state_T), ordered_ids)");
-                R.parseEval("tmp <- shuffle_field(mysetup$state_T, ordered_ids)");
-                Rcpp::DataFrame chemistry_data = R.parseEval("tmp");
-
-                convert_R_Dataframe_2_C_buffer(mpi_buffer, chemistry_data);
-                // cout << "CPP: shuffle_field() done" << endl;
-
-                /* send and receive work; this is done by counting
-                 * the wp */
-                int pkg_to_send = n_wp;
-                int pkg_to_recv = n_wp;
-                size_t colCount = chemistry_data.ncol();
-                int free_workers = world_size-1;
-                double* work_pointer = mpi_buffer;
-                sim_c_chemistry = MPI_Wtime();
-
-                /* visual progress */
-                float progress = 0.0;
-                int barWidth = 70;
-
-                //retrieve data from R runtime
-                iteration = (int) R.parseEval("mysetup$iter");
-                dt = (double) R.parseEval("mysetup$requested_dt");
-                current_sim_time = (double) R.parseEval("mysetup$simulation_time-mysetup$requested_dt");
-
-                int count_pkgs = 0;
-
-                sim_b_seq = MPI_Wtime();
-
-                sim_c_chemistry = MPI_Wtime();
-
-                while (pkg_to_recv > 0) // start dispatching work packages
-                {
-                    /* visual progress */
-                    progress = (float) (count_pkgs+1)/n_wp;
-                        
-                    cout << "[";
-                    int pos = barWidth * progress;
-                    for (int iprog = 0; iprog < barWidth; ++iprog) {
-                        if (iprog < pos)
-                            cout << "=";
-                        else if (iprog == pos)
-                            cout << ">";
-                        else
-                            cout << " ";
-                    }
-                    std::cout << "] " << int(progress * 100.0) << " %\r";
-                    std::cout.flush();
-                    /* end visual progress */
-
-                    
-                    if (pkg_to_send > 0) {
-
-                        master_send_a = MPI_Wtime();
-                        /*search for free workers and send work*/
-                        for (int p = 0; p < world_size-1; p++) {
-                            if (workerlist[p].has_work == 0 && pkg_to_send > 0) /* worker is free */ {
-                                
-                                // to enable different work_package_size, set local copy of work_package_size to 
-                                // either global work_package size or remaining 'to_send' packages
-                              	// to_send >= work_package_size ? local_work_package_size = work_package_size : local_work_package_size = to_send;
-
-                                local_work_package_size = (int) wp_sizes_vector[count_pkgs];
-                                count_pkgs++;
-
-                                // cout << "CPP: sending pkg n. " << count_pkgs << " with size " << local_work_package_size << endl;
-
-                                /*push pointer forward to next work package, after taking the current one*/
-                                workerlist[p].send_addr = work_pointer;
-
-                                int end_of_wp = local_work_package_size * colCount;
-                                work_pointer = &(work_pointer[end_of_wp]);
-
-                                // fill send buffer starting with work_package ...
-                                std::memcpy(send_buffer, workerlist[p].send_addr, (end_of_wp) * sizeof(double));
-                                // followed by: work_package_size
-                                send_buffer[end_of_wp] = (double) local_work_package_size;
-                                // current iteration of simulation
-                                send_buffer[end_of_wp + 1] = (double) iteration;
-                                // size of timestep in seconds
-                                send_buffer[end_of_wp + 2] = dt;
-                                // current time of simulation (age) in seconds
-                                send_buffer[end_of_wp + 3] = current_sim_time;
-                                // placeholder for work_package_count
-                                send_buffer[end_of_wp + 4] = 0.; 
-                                
-                                /* ATTENTION Worker p has rank p+1 */
-                                MPI_Send(send_buffer, end_of_wp + BUFFER_OFFSET, MPI_DOUBLE, p+1, TAG_WORK, MPI_COMM_WORLD);
-
-                                workerlist[p].has_work = 1;
-                                free_workers--;
-                                pkg_to_send -= 1;
-                            }
-                        }
-                        master_send_b = MPI_Wtime();
-                        cummul_master_send += master_send_b - master_send_a;
-                    }
-
-                    
-
-                    /*check if there are results to receive and receive them*/  
-                    need_to_receive = 1;
-                    master_recv_a = MPI_Wtime();
-                    while(need_to_receive && pkg_to_recv > 0)
-                    {
-                        
-                        if (pkg_to_send > 0 && free_workers > 0)
-                            MPI_Iprobe(MPI_ANY_SOURCE, TAG_WORK, MPI_COMM_WORLD, &need_to_receive, &probe_status);
-                        else {
-                            idle_a = MPI_Wtime();
-                            MPI_Probe(MPI_ANY_SOURCE, TAG_WORK, MPI_COMM_WORLD, &probe_status);
-                            idle_b = MPI_Wtime();
-                            master_idle += idle_b - idle_a;
-                        }
-
-                        if(need_to_receive) 
-                            {
-                                int p = probe_status.MPI_SOURCE;
-                                int size;
-                                MPI_Get_count(&probe_status, MPI_DOUBLE, &size);
-                                MPI_Recv(workerlist[p-1].send_addr, size, MPI_DOUBLE, p, TAG_WORK, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-                                workerlist[p-1].has_work = 0;
-                                pkg_to_recv -= 1;
-                                free_workers++;
-                            } 
-                    }
-                    master_recv_b = MPI_Wtime();
-                    cummul_master_recv += master_recv_b - master_recv_a;
-                }
-
-                sim_c_seq = MPI_Wtime();
-
-                // don't overwrite last progress
-                cout << endl;
-                
-                sim_d_chemistry = MPI_Wtime();
-                cummul_workers   += sim_d_chemistry - sim_c_chemistry;
-
-                convert_C_buffer_2_R_Dataframe(mpi_buffer, chemistry_data);
-
-                R["chemistry_data"] = chemistry_data;
-
-                /* unshuffle results */
-                R.parseEval("result <- unshuffle_field(chemistry_data, ordered_ids)");
-
-                /* do master stuff */
-                sim_e_chemistry = MPI_Wtime();
-                R.parseEvalQ("mysetup <- master_chemistry(setup=mysetup, data=result)");
-                sim_f_chemistry = MPI_Wtime();
-                cummul_chemistry_master   += sim_f_chemistry - sim_e_chemistry;
-
-            }
-            sim_a_chemistry = MPI_Wtime();
-
-	    // MDL master_iteration_end just writes on disk state_T and
-	    // state_C after every iteration if the cmdline option
-	    // --ignore-results is not given (and thus the R variable
-	    // store_result is TRUE)
-            R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)");
-
-    	    cummul_transport += sim_a_transport - sim_b_transport;
-            cummul_chemistry += sim_a_chemistry - sim_b_chemistry;
-
-            cout << endl << "CPP: End of *coupling* iteration "<< iter <<"/" << maxiter << endl << endl;
-
-            if (dht_enabled) {
-                for (int i=1; i < world_size; i++) {
-                    MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_STATS, MPI_COMM_WORLD);
-                }
-
-                MPI_Barrier(MPI_COMM_WORLD);
-
-                if (dht_snaps == 2) {
-                    std::stringstream outfile;
-                    outfile << out_dir << "/iter_" << std::setfill('0') << std::setw(3) << iter << ".dht";
-                    for (int i=1; i < world_size; i++) {
-                        MPI_Send(outfile.str().c_str(), outfile.str().size(), MPI_CHAR, i, TAG_DHT_STORE, MPI_COMM_WORLD);
-                    }
-                    MPI_Barrier(MPI_COMM_WORLD);
-                }
-            }
-
-
-        sim_d_seq = MPI_Wtime();
-
-        cummul_master_seq_loop += ((sim_b_seq - sim_a_seq) - (sim_a_transport - sim_b_transport)) + (sim_d_seq - sim_c_seq); 
-        master_send.push_back(cummul_master_send, "it_" + to_string(iter));
-        master_recv.push_back(cummul_master_recv, "it_" + to_string(iter));           
-
-        } // END SIMULATION LOOP
-
-        sim_end = MPI_Wtime();
-
-        if (dht_enabled && dht_snaps > 0) {
-            cout << "CPP: Master: Instruct workers to write DHT to file ..." << endl;
-            std::string outfile;
-            outfile = out_dir + ".dht";
-            for (int i=1; i < world_size; i++) {
-                MPI_Send(outfile.c_str(), outfile.size(), MPI_CHAR, i, TAG_DHT_STORE, MPI_COMM_WORLD);
-            }
-            MPI_Barrier(MPI_COMM_WORLD);
-            cout << "CPP: Master: ... done" << endl;
-        }
-
-        Rcpp::NumericVector phreeqc_time;
-        Rcpp::NumericVector dht_get_time;
-        Rcpp::NumericVector dht_fill_time;
-        Rcpp::IntegerVector phreeqc_counts;
-        Rcpp::NumericVector idle_worker;
-
-        int phreeqc_tmp;
-
-        timings = (double*) calloc(3, sizeof(double));
-
-        if (dht_enabled) {
-            dht_hits = 0;
-            dht_miss = 0;
-            dht_collision = 0;
-            dht_perfs = (uint64_t*) calloc(3, sizeof(uint64_t));
-        }
-
-        double idle_worker_tmp;
-
-        for (int p = 0; p < world_size-1; p++)
-        {
-            /* ATTENTION Worker p has rank p+1 */
-            /* Send termination message to worker */
-            MPI_Send(NULL, 0, MPI_DOUBLE, p+1, TAG_FINISH, MPI_COMM_WORLD);
-
-            
-            MPI_Recv(timings, 3, MPI_DOUBLE, p+1, TAG_TIMING, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-            phreeqc_time.push_back(timings[0], "w" + to_string(p+1));
-
-            MPI_Recv(&phreeqc_tmp, 1, MPI_INT, p+1, TAG_TIMING, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-            phreeqc_counts.push_back(phreeqc_tmp, "w" + to_string(p+1));
-
-            MPI_Recv(&idle_worker_tmp, 1, MPI_DOUBLE, p+1, TAG_TIMING, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-            idle_worker.push_back(idle_worker_tmp, "w" + to_string(p+1));
-
-            if (dht_enabled)
-            {
-                dht_get_time.push_back(timings[1], "w" + to_string(p+1));
-                dht_fill_time.push_back(timings[2], "w" + to_string(p+1));
-
-                MPI_Recv(dht_perfs, 3, MPI_UNSIGNED_LONG_LONG, p+1, TAG_DHT_PERF, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-                dht_hits += dht_perfs[0];
-                dht_miss += dht_perfs[1];
-                dht_collision += dht_perfs[2];
-            }
-        }
-
-        R.parseEvalQ("profiling <- list()");
-
-        R["simtime"] = sim_end - sim_start;
-        R.parseEvalQ("profiling$simtime <- simtime");
-        R["simtime_transport"] = cummul_transport;
-        R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
-        R["simtime_chemistry"] = cummul_chemistry;
-        R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
-        R["simtime_workers"] = cummul_workers;
-        R.parseEvalQ("profiling$simtime_workers <- simtime_workers");
-        R["simtime_chemistry_master"] = cummul_chemistry_master;
-        R.parseEvalQ("profiling$simtime_chemistry_master <- simtime_chemistry_master");
-
-        R["seq_master_prep"] = cummul_master_seq_pre_loop;
-        R.parseEvalQ("profiling$seq_master_prep <- seq_master_prep");
-        R["seq_master_loop"] = cummul_master_seq_loop;
-        R.parseEvalQ("profiling$seq_master_loop <- seq_master_loop");
-
-        // R["master_send"] = master_send;
-        // R.parseEvalQ("profiling$master_send <- master_send");
-        // R["master_recv"] = master_recv;
-        // R.parseEvalQ("profiling$master_recv <- master_recv");
-
-        R["idle_master"] = master_idle;
-        R.parseEvalQ("profiling$idle_master <- idle_master");
-        R["idle_worker"] = idle_worker;
-        R.parseEvalQ("profiling$idle_worker <- idle_worker");
-
-        R["phreeqc_time"] = phreeqc_time;
-        R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
-
-        R["phreeqc_count"] = phreeqc_counts;
-        R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
-
-        if (dht_enabled)
-        {
-            R["dht_hits"] = dht_hits;
-            R.parseEvalQ("profiling$dht_hits <- dht_hits");
-            R["dht_miss"] = dht_miss;
-            R.parseEvalQ("profiling$dht_miss <- dht_miss");
-            R["dht_collision"] = dht_collision;
-            R.parseEvalQ("profiling$dht_collisions <- dht_collision");
-            R["dht_get_time"] = dht_get_time;
-            R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
-            R["dht_fill_time"] = dht_fill_time;
-            R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
-        }
-
-        
-        free(workerlist);
-        free(timings);
-
-        if (dht_enabled)
-            free(dht_perfs);
-
-        cout << "CPP: Done! Results are stored as R objects into <" << out_dir << "/timings.rds>" << endl;
-        /*exporting results and profiling data*/
-	
-        std::string r_vis_code;
-        r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
-        R.parseEval(r_vis_code);
-    } else { /*This is executed by the workers*/
-        if (!dht_file.empty()) {
-            int res = file_to_table((char *) dht_file.c_str());
-            if (res != DHT_SUCCESS) {
-                if (res == DHT_WRONG_FILE) {
-                    if (world_rank == 2) cerr << "CPP: Worker: Wrong File" << endl;
-                } else {
-                    if (world_rank == 2) cerr << "CPP: Worker: Error in loading current state of DHT from file" << endl;
-                }
-                return EXIT_FAILURE;
-            } else {
-                if (world_rank == 2) cout << "CPP: Worker: Successfully loaded state of DHT from file " << dht_file << endl;
-                std::cout.flush();
-            }
-        }
-        worker_function(R);
-        free(mpi_buffer_results);
-    }
-    
-    cout << "CPP: finished, cleanup of process " << world_rank << endl;
-
-    if (dht_enabled)
-    {
-        
-        if (dht_strategy == 0)
-        {
-            if(world_rank != 0) {
-                DHT_free(dht_object, NULL, NULL);
-            }
-        } else {
-            DHT_free(dht_object, NULL, NULL);
-        }
-    }
-
-    free(mpi_buffer);
-    MPI_Finalize();
-    
-    if (world_rank==0) {
-        cout << "CPP: done, bye!" << endl;
-    }
-    
-    exit(0);
-}
-
diff --git a/src/model/CMakeLists.txt b/src/model/CMakeLists.txt
new file mode 100644
index 000000000..955da1094
--- /dev/null
+++ b/src/model/CMakeLists.txt
@@ -0,0 +1,4 @@
+add_library(POET_Model ChemSim.cpp ChemSim.h ChemMaster.cpp ChemWorker.cpp TransportSim.cpp Grid.cpp)
+target_include_directories(POET_Model PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${MPI_C_INCLUDE_DIRS})
+target_link_libraries(POET_Model PRIVATE POET_Util MPI::MPI_C PUBLIC DHT_Wrapper)
+target_compile_definitions(POET_Model PRIVATE OMPI_SKIP_MPICXX)
\ No newline at end of file
diff --git a/src/model/ChemMaster.cpp b/src/model/ChemMaster.cpp
new file mode 100644
index 000000000..3e01b8941
--- /dev/null
+++ b/src/model/ChemMaster.cpp
@@ -0,0 +1,380 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include <Rcpp.h>
+
+#include <iostream>
+
+#include "ChemSim.h"
+
+using namespace poet;
+using namespace std;
+using namespace Rcpp;
+
+ChemMaster::ChemMaster(SimParams &params, RRuntime &R_, Grid &grid_)
+    : ChemSim(params, R_, grid_) {
+  t_simparams tmp = params.getNumParams();
+
+  this->wp_size = tmp.wp_size;
+  this->dht_enabled = tmp.dht_enabled;
+
+  this->out_dir = params.getOutDir();
+
+  /* allocate memory */
+  workerlist = (worker_struct *)calloc(world_size - 1, sizeof(worker_struct));
+  send_buffer = (double *)calloc((wp_size * (grid.getCols())) + BUFFER_OFFSET,
+                                 sizeof(double));
+  mpi_buffer =
+      (double *)calloc(grid.getRows() * grid.getCols(), sizeof(double));
+
+  /* calculate distribution of work packages */
+  R.parseEvalQ(
+      "wp_ids <- distribute_work_packages(len=nrow(mysetup$state_C), "
+      "package_size=work_package_size)");
+
+  // we only sort once the vector
+  R.parseEvalQ("ordered_ids <- order(wp_ids)");
+  R.parseEvalQ("wp_sizes_vector <- compute_wp_sizes(wp_ids)");
+  R.parseEval("stat_wp_sizes(wp_sizes_vector)");
+  wp_sizes_vector = as<std::vector<int>>(R["wp_sizes_vector"]);
+}
+
+ChemMaster::~ChemMaster() {
+  free(mpi_buffer);
+  free(workerlist);
+}
+
+void ChemMaster::run() {
+  /* declare most of the needed variables here */
+  double chem_a, chem_b;
+  double seq_a, seq_b, seq_c, seq_d;
+  double worker_chemistry_a, worker_chemistry_b;
+  double sim_e_chemistry, sim_f_chemistry;
+  int pkg_to_send, pkg_to_recv;
+  int free_workers;
+  int i_pkgs;
+
+  /* start time measurement of whole chemistry simulation */
+  chem_a = MPI_Wtime();
+
+  /* start time measurement of sequential part */
+  seq_a = MPI_Wtime();
+
+  /* shuffle grid */
+  grid.shuffleAndExport(mpi_buffer);
+
+  /* retrieve needed data from R runtime */
+  iteration = (int)R.parseEval("mysetup$iter");
+  dt = (double)R.parseEval("mysetup$requested_dt");
+  current_sim_time =
+      (double)R.parseEval("mysetup$simulation_time-mysetup$requested_dt");
+
+  /* setup local variables */
+  pkg_to_send = wp_sizes_vector.size();
+  pkg_to_recv = wp_sizes_vector.size();
+  work_pointer = mpi_buffer;
+  free_workers = world_size - 1;
+  i_pkgs = 0;
+
+  /* end time measurement of sequential part */
+  seq_b = MPI_Wtime();
+  seq_t += seq_b - seq_a;
+
+  /* start time measurement of chemistry time needed for send/recv loop */
+  worker_chemistry_a = MPI_Wtime();
+
+  /* start send/recv loop */
+  // while there are still packages to recv
+  while (pkg_to_recv > 0) {
+    // print a progressbar to stdout
+    printProgressbar((int)i_pkgs, (int)wp_sizes_vector.size());
+    // while there are still packages to send
+    if (pkg_to_send > 0) {
+      // send packages to all free workers ...
+      sendPkgs(pkg_to_send, i_pkgs, free_workers);
+    }
+    // ... and try to receive them from workers who has finished their work
+    recvPkgs(pkg_to_recv, pkg_to_send > 0, free_workers);
+  }
+
+  // Just to complete the progressbar
+  cout << endl;
+
+  /* stop time measurement of chemistry time needed for send/recv loop */
+  worker_chemistry_b = MPI_Wtime();
+  worker_t = worker_chemistry_b - worker_chemistry_a;
+
+  /* start time measurement of sequential part */
+  seq_c = MPI_Wtime();
+
+  /* unshuffle grid */
+  grid.importAndUnshuffle(mpi_buffer);
+
+  /* do master stuff */
+
+  /* start time measurement of master chemistry */
+  sim_e_chemistry = MPI_Wtime();
+
+  R.parseEvalQ("mysetup <- master_chemistry(setup=mysetup, data=result)");
+
+  /* end time measurement of master chemistry */
+  sim_f_chemistry = MPI_Wtime();
+  chem_master += sim_f_chemistry - sim_e_chemistry;
+
+  /* end time measurement of sequential part */
+  seq_d = MPI_Wtime();
+  seq_t += seq_d - seq_c;
+
+  /* end time measurement of whole chemistry simulation */
+  chem_b = MPI_Wtime();
+  chem_t += chem_b - chem_a;
+
+  /* advise workers to end chemistry iteration */
+  for (int i = 1; i < world_size; i++) {
+    MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_ITER, MPI_COMM_WORLD);
+  }
+}
+
+void ChemMaster::sendPkgs(int &pkg_to_send, int &count_pkgs,
+                          int &free_workers) {
+  /* declare variables */
+  double master_send_a, master_send_b;
+  int local_work_package_size;
+  int end_of_wp;
+
+  /* start time measurement */
+  master_send_a = MPI_Wtime();
+
+  /* search for free workers and send work */
+  for (int p = 0; p < world_size - 1; p++) {
+    if (workerlist[p].has_work == 0 && pkg_to_send > 0) /* worker is free */ {
+      /* to enable different work_package_size, set local copy of
+       * work_package_size to pre-calculated work package size vector */
+
+      local_work_package_size = (int)wp_sizes_vector[count_pkgs];
+      count_pkgs++;
+
+      /* note current processed work package in workerlist */
+      workerlist[p].send_addr = work_pointer;
+
+      /* push work pointer to next work package */
+      end_of_wp = local_work_package_size * grid.getCols();
+      work_pointer = &(work_pointer[end_of_wp]);
+
+      // fill send buffer starting with work_package ...
+      std::memcpy(send_buffer, workerlist[p].send_addr,
+                  (end_of_wp) * sizeof(double));
+      // followed by: work_package_size
+      send_buffer[end_of_wp] = (double)local_work_package_size;
+      // current iteration of simulation
+      send_buffer[end_of_wp + 1] = (double)iteration;
+      // size of timestep in seconds
+      send_buffer[end_of_wp + 2] = dt;
+      // current time of simulation (age) in seconds
+      send_buffer[end_of_wp + 3] = current_sim_time;
+      // placeholder for work_package_count
+      send_buffer[end_of_wp + 4] = 0.;
+
+      /* ATTENTION Worker p has rank p+1 */
+      MPI_Send(send_buffer, end_of_wp + BUFFER_OFFSET, MPI_DOUBLE, p + 1,
+               TAG_WORK, MPI_COMM_WORLD);
+
+      /* Mark that worker has work to do */
+      workerlist[p].has_work = 1;
+      free_workers--;
+      pkg_to_send -= 1;
+    }
+  }
+  master_send_b = MPI_Wtime();
+  send_t += master_send_b - master_send_a;
+}
+
+void ChemMaster::recvPkgs(int &pkg_to_recv, bool to_send, int &free_workers) {
+  /* declare most of the variables here */
+  int need_to_receive = 1;
+  double master_recv_a, master_recv_b;
+  double idle_a, idle_b;
+  int p, size;
+
+  MPI_Status probe_status;
+  master_recv_a = MPI_Wtime();
+  /* start to loop as long there are packages to recv and the need to receive
+   */
+  while (need_to_receive && pkg_to_recv > 0) {
+    // only of there are still packages to send and free workers are available
+    if (to_send && free_workers > 0)
+      // non blocking probing
+      MPI_Iprobe(MPI_ANY_SOURCE, TAG_WORK, MPI_COMM_WORLD, &need_to_receive,
+                 &probe_status);
+    else {
+      idle_a = MPI_Wtime();
+      // blocking probing
+      MPI_Probe(MPI_ANY_SOURCE, TAG_WORK, MPI_COMM_WORLD, &probe_status);
+      idle_b = MPI_Wtime();
+      master_idle += idle_b - idle_a;
+    }
+
+    /* if need_to_receive was set to true above, so there is a message to
+     * receive */
+    if (need_to_receive) {
+      p = probe_status.MPI_SOURCE;
+      MPI_Get_count(&probe_status, MPI_DOUBLE, &size);
+      MPI_Recv(workerlist[p - 1].send_addr, size, MPI_DOUBLE, p, TAG_WORK,
+               MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+      workerlist[p - 1].has_work = 0;
+      pkg_to_recv -= 1;
+      free_workers++;
+    }
+  }
+  master_recv_b = MPI_Wtime();
+  recv_t += master_recv_b - master_recv_a;
+}
+
+void ChemMaster::printProgressbar(int count_pkgs, int n_wp, int barWidth) {
+  /* visual progress */
+  double progress = (float)(count_pkgs + 1) / n_wp;
+
+  cout << "[";
+  int pos = barWidth * progress;
+  for (int iprog = 0; iprog < barWidth; ++iprog) {
+    if (iprog < pos)
+      cout << "=";
+    else if (iprog == pos)
+      cout << ">";
+    else
+      cout << " ";
+  }
+  std::cout << "] " << int(progress * 100.0) << " %\r";
+  std::cout.flush();
+  /* end visual progress */
+}
+
+void ChemMaster::end() {
+  /* call end() from base class */
+  ChemSim::end();
+
+  /* now we get to the part of the master */
+  double *timings;
+  int *dht_perfs;
+
+  Rcpp::NumericVector phreeqc_time;
+  Rcpp::NumericVector dht_get_time;
+  Rcpp::NumericVector dht_fill_time;
+  Rcpp::IntegerVector phreeqc_counts;
+  Rcpp::NumericVector idle_worker;
+
+  int phreeqc_tmp;
+
+  timings = (double *)calloc(3, sizeof(double));
+
+  int dht_hits = 0;
+  int dht_miss = 0;
+  int dht_evictions = 0;
+
+  if (dht_enabled) {
+    dht_perfs = (int *)calloc(3, sizeof(int));
+  }
+
+  double idle_worker_tmp;
+
+  /* loop over all workers *
+   * ATTENTION Worker p has rank p+1 */
+  for (int p = 0; p < world_size - 1; p++) {
+    /* Send termination message to worker */
+    MPI_Send(NULL, 0, MPI_DOUBLE, p + 1, TAG_FINISH, MPI_COMM_WORLD);
+
+    /* ... and receive all timings and metrics from each worker */
+    MPI_Recv(timings, 3, MPI_DOUBLE, p + 1, TAG_TIMING, MPI_COMM_WORLD,
+             MPI_STATUS_IGNORE);
+    phreeqc_time.push_back(timings[0], "w" + to_string(p + 1));
+
+    MPI_Recv(&phreeqc_tmp, 1, MPI_INT, p + 1, TAG_TIMING, MPI_COMM_WORLD,
+             MPI_STATUS_IGNORE);
+    phreeqc_counts.push_back(phreeqc_tmp, "w" + to_string(p + 1));
+
+    MPI_Recv(&idle_worker_tmp, 1, MPI_DOUBLE, p + 1, TAG_TIMING, MPI_COMM_WORLD,
+             MPI_STATUS_IGNORE);
+    idle_worker.push_back(idle_worker_tmp, "w" + to_string(p + 1));
+
+    if (dht_enabled) {
+      dht_get_time.push_back(timings[1], "w" + to_string(p + 1));
+      dht_fill_time.push_back(timings[2], "w" + to_string(p + 1));
+
+      MPI_Recv(dht_perfs, 3, MPI_INT, p + 1, TAG_DHT_PERF, MPI_COMM_WORLD,
+               MPI_STATUS_IGNORE);
+      dht_hits += dht_perfs[0];
+      dht_miss += dht_perfs[1];
+      dht_evictions += dht_perfs[2];
+    }
+  }
+
+  /* distribute all data to the R runtime */
+  R["simtime_chemistry"] = chem_t;
+  R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
+  R["simtime_workers"] = worker_t;
+  R.parseEvalQ("profiling$simtime_workers <- simtime_workers");
+  R["simtime_chemistry_master"] = chem_master;
+  R.parseEvalQ(
+      "profiling$simtime_chemistry_master <- simtime_chemistry_master");
+
+  R["seq_master"] = seq_t;
+  R.parseEvalQ("profiling$seq_master <- seq_master");
+
+  R["idle_master"] = master_idle;
+  R.parseEvalQ("profiling$idle_master <- idle_master");
+  R["idle_worker"] = idle_worker;
+  R.parseEvalQ("profiling$idle_worker <- idle_worker");
+
+  R["phreeqc_time"] = phreeqc_time;
+  R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
+
+  R["phreeqc_count"] = phreeqc_counts;
+  R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
+
+  if (dht_enabled) {
+    R["dht_hits"] = dht_hits;
+    R.parseEvalQ("profiling$dht_hits <- dht_hits");
+    R["dht_miss"] = dht_miss;
+    R.parseEvalQ("profiling$dht_miss <- dht_miss");
+    R["dht_evictions"] = dht_evictions;
+    R.parseEvalQ("profiling$dht_evictions <- dht_evictions");
+    R["dht_get_time"] = dht_get_time;
+    R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
+    R["dht_fill_time"] = dht_fill_time;
+    R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
+  }
+
+  /* do some cleanup */
+  free(timings);
+
+  if (dht_enabled) free(dht_perfs);
+}
+
+double ChemMaster::getSendTime() { return this->send_t; }
+
+double ChemMaster::getRecvTime() { return this->recv_t; }
+
+double ChemMaster::getIdleTime() { return this->master_idle; }
+
+double ChemMaster::getWorkerTime() { return this->worker_t; }
+
+double ChemMaster::getChemMasterTime() { return this->chem_master; }
+
+double ChemMaster::getSeqTime() { return this->seq_t; }
diff --git a/src/model/ChemSim.cpp b/src/model/ChemSim.cpp
new file mode 100644
index 000000000..2b5a265ab
--- /dev/null
+++ b/src/model/ChemSim.cpp
@@ -0,0 +1,60 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "ChemSim.h"
+
+#include <Rcpp.h>
+
+#include <iostream>
+
+using namespace Rcpp;
+using namespace poet;
+
+ChemSim::ChemSim(SimParams &params, RRuntime &R_, Grid &grid_)
+    : R(R_), grid(grid_) {
+  t_simparams tmp = params.getNumParams();
+  this->world_rank = tmp.world_rank;
+  this->world_size = tmp.world_size;
+  this->wp_size = tmp.wp_size;
+  this->out_dir = params.getOutDir();
+}
+
+void ChemSim::run() {
+  double chem_a, chem_b;
+
+  /* start time measuring */
+  chem_a = MPI_Wtime();
+
+  R.parseEvalQ(
+      "result <- slave_chemistry(setup=mysetup, data=mysetup$state_T)");
+  R.parseEvalQ("mysetup <- master_chemistry(setup=mysetup, data=result)");
+
+  /* end time measuring */
+  chem_b = MPI_Wtime();
+
+  chem_t += chem_b - chem_a;
+}
+
+void ChemSim::end() {
+  R["simtime_chemistry"] = chem_t;
+  R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
+}
+
+double ChemSim::getChemistryTime() { return this->chem_t; }
diff --git a/src/model/ChemSim.h b/src/model/ChemSim.h
new file mode 100644
index 000000000..dc5fb12a4
--- /dev/null
+++ b/src/model/ChemSim.h
@@ -0,0 +1,573 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef CHEMSIM_H
+#define CHEMSIM_H
+
+#include <DHT_Wrapper.h>
+#include <RRuntime.h>
+#include <SimParams.h>
+#include <mpi.h>
+
+#include <vector>
+
+#include "Grid.h"
+
+/** Number of data elements that are kept free at each work package */
+#define BUFFER_OFFSET 5
+
+/** Message tag indicating work */
+#define TAG_WORK 42
+/** Message tag indicating to finish loop */
+#define TAG_FINISH 43
+/** Message tag indicating timing profiling */
+#define TAG_TIMING 44
+/** Message tag indicating collecting DHT performance */
+#define TAG_DHT_PERF 45
+/** Message tag indicating simulation reached the end of an itertation */
+#define TAG_DHT_ITER 47
+
+namespace poet {
+/**
+ * @brief Base class of the chemical simulation
+ *
+ * Providing member functions to run an iteration and to end a simulation. Also
+ * containing basic parameters for simulation.
+ *
+ */
+class ChemSim {
+ public:
+  /**
+   * @brief Construct a new ChemSim object
+   *
+   * Creating a new instance of class ChemSim will just extract simulation
+   * parameters from SimParams object.
+   *
+   * @param params SimParams object
+   * @param R_ R runtime
+   * @param grid_ Initialized grid
+   */
+  ChemSim(SimParams &params, RRuntime &R_, Grid &grid_);
+
+  /**
+   * @brief Run iteration of simulation in sequential mode
+   *
+   * This will call the correspondending R function slave_chemistry, followed by
+   * the execution of master_chemistry.
+   *
+   * @todo change function name. Maybe 'slave' to 'seq'.
+   *
+   */
+  virtual void run();
+
+  /**
+   * @brief End simulation
+   *
+   * End the simulation by distribute the measured runtime of simulation to the
+   * R runtime.
+   *
+   */
+  virtual void end();
+
+  /**
+   * @brief Get the Chemistry Time
+   *
+   * @return double Runtime of sequential chemistry simulation in seconds
+   */
+  double getChemistryTime();
+
+ protected:
+  /**
+   * @brief Current simulation time or 'age' of simulation
+   *
+   */
+  double current_sim_time = 0;
+
+  /**
+   * @brief Current iteration
+   *
+   */
+  int iteration = 0;
+
+  /**
+   * @brief Current simulation timestep
+   *
+   */
+  int dt = 0;
+
+  /**
+   * @brief Rank of process in MPI_COMM_WORLD
+   *
+   */
+  int world_rank;
+
+  /**
+   * @brief Size of communicator MPI_COMM_WORLD
+   *
+   */
+  int world_size;
+
+  /**
+   * @brief Number of grid cells in each work package
+   *
+   */
+  unsigned int wp_size;
+
+  /**
+   * @brief Instance of RRuntime object
+   *
+   */
+  RRuntime &R;
+
+  /**
+   * @brief Initialized grid object
+   *
+   */
+  Grid &grid;
+
+  /**
+   * @brief Stores information about size of the current work package
+   *
+   */
+  std::vector<int> wp_sizes_vector;
+
+  /**
+   * @brief Absolute path to output path
+   *
+   */
+  std::string out_dir;
+
+  /**
+   * @brief Pointer to sending buffer
+   *
+   */
+  double *send_buffer;
+
+  /**
+   * @brief Worker struct
+   *
+   * This struct contains information which worker as work and which work
+   * package he is working on.
+   *
+   */
+  typedef struct {
+    char has_work;
+    double *send_addr;
+  } worker_struct;
+
+  /**
+   * @brief Pointer to worker_struct
+   *
+   */
+  worker_struct *workerlist;
+
+  /**
+   * @brief Pointer to mpi_buffer
+   *
+   * Typically for the master this is a continous C memory area containing the
+   * grid. For worker the memory area will just have the size of a work package.
+   *
+   */
+  double *mpi_buffer;
+
+  /**
+   * @brief Total chemistry runtime
+   *
+   */
+  double chem_t = 0.f;
+};
+
+/**
+ * @brief Class providing execution of master chemistry
+ *
+ * Providing member functions to run an iteration and to end a simulation. Also
+ * a loop to send and recv pkgs from workers is implemented.
+ *
+ */
+class ChemMaster : public ChemSim {
+ public:
+  /**
+   * @brief Construct a new ChemMaster object
+   *
+   * The following steps are executed to create a new object of ChemMaster:
+   * -# all needed simulation parameters are extracted
+   * -# memory is allocated
+   * -# distribution of work packages is calculated
+   *
+   * @param params Simulation parameters as SimParams object
+   * @param R_ R runtime
+   * @param grid_ Grid object
+   */
+  ChemMaster(SimParams &params, RRuntime &R_, Grid &grid_);
+
+  /**
+   * @brief Destroy the ChemMaster object
+   *
+   * By freeing ChemMaster all buffers allocated in the Constructor are freed.
+   *
+   */
+  ~ChemMaster();
+
+  /**
+   * @brief Run iteration of simulation in parallel mode
+   *
+   * To run the chemistry simulation parallel following steps are done:
+   *
+   * -# 'Shuffle' the grid by previously calculated distribution of work
+   * packages. Convert R grid to C memory area.
+   * -# Start the send/recv loop.
+   * Detailed description in sendPkgs respectively in recvPkgs.
+   * -# 'Unshuffle'
+   * the grid and convert C memory area to R grid.
+   * -# Run 'master_chemistry'
+   *
+   * The main tasks are instrumented with time measurements.
+   *
+   */
+  void run() override;
+
+  /**
+   * @brief End chemistry simulation.
+   *
+   * Notify the worker to finish their 'work'-loop. This is done by sending
+   * every worker an empty message with the tag TAG_FINISH. Now the master will
+   * receive measured times and DHT metrics from all worker one after another.
+   * Finally he will write all data to the R runtime and return this function.
+   *
+   */
+  void end() override;
+
+  /**
+   * @brief Get the send time
+   *
+   * Time spent in send loop.
+   *
+   * @return double sent time in seconds
+   */
+  double getSendTime();
+
+  /**
+   * @brief Get the recv time
+   *
+   * Time spent in recv loop.
+   *
+   * @return double recv time in seconds
+   */
+  double getRecvTime();
+
+  /**
+   * @brief Get the idle time
+   *
+   * Time master was idling in MPI_Probe of recv loop.
+   *
+   * @return double idle time in seconds
+   */
+  double getIdleTime();
+
+  /**
+   * @brief Get the Worker time
+   *
+   * Time spent in whole send/recv loop.
+   *
+   * @return double worker time in seconds
+   */
+  double getWorkerTime();
+
+  /**
+   * @brief Get the ChemMaster time
+   *
+   * Time spent in 'master_chemistry' R function.
+   *
+   * @return double ChemMaster time in seconds
+   */
+  double getChemMasterTime();
+
+  /**
+   * @brief Get the sequential time
+   *
+   * Time master executed code which must be run sequential.
+   *
+   * @return double seqntial time in seconds.
+   */
+  double getSeqTime();
+
+ private:
+  /**
+   * @brief Print a progressbar
+   *
+   * Prints a progressbar to stdout according to count of processed work
+   * packages in this iteration.
+   *
+   * @param count_pkgs Last processed index of work package
+   * @param n_wp Number of work packages
+   * @param barWidth Width of the progressbar/Count of characters to display the
+   * bar
+   */
+  void printProgressbar(int count_pkgs, int n_wp, int barWidth = 70);
+
+  /**
+   * @brief Start send loop
+   *
+   * Send a work package to every free worker, which are noted in a worker
+   * struct. After a work package was sent move pointer on work grid to the next
+   * work package. Use MPI_Send to transfer work package to worker.
+   *
+   * @param pkg_to_send Pointer to variable containing how much work packages
+   * are still to send
+   * @param count_pkgs Pointer to variable indexing the current work package
+   * @param free_workers Pointer to variable with the count of free workers
+   */
+  void sendPkgs(int &pkg_to_send, int &count_pkgs, int &free_workers);
+
+  /**
+   * @brief Start recv loop
+   *
+   * Receive processed work packages by worker. This is done by first probing
+   * for a message. If a message is receivable, receive it and put result into
+   * respective memory area. Continue, but now with a non blocking MPI_Probe. If
+   * a message is receivable or if no work packages are left to send, receive
+   * it. Otherwise or if all remaining work packages are received exit loop.
+   *
+   * @param pkg_to_recv Pointer to variable counting the to receiving work
+   * packages
+   * @param to_send Bool indicating if there are still work packages to send
+   * @param free_workers Pointer to worker to variable holding the number of
+   * free workers
+   */
+  void recvPkgs(int &pkg_to_recv, bool to_send, int &free_workers);
+
+  /**
+   * @brief Indicating usage of DHT
+   *
+   */
+  bool dht_enabled;
+
+  /**
+   * @brief Default number of grid cells in each work package
+   *
+   */
+  unsigned int wp_size;
+
+  /**
+   * @brief Pointer to current to be processed work package
+   *
+   */
+  double *work_pointer;
+
+  /**
+   * @brief Time spent in send loop
+   *
+   */
+  double send_t = 0.f;
+
+  /**
+   * @brief Time spent in recv loop
+   *
+   */
+  double recv_t = 0.f;
+
+  /**
+   * @brief Time master is idling in MPI_Probe
+   *
+   */
+  double master_idle = 0.f;
+
+  /**
+   * @brief Time spent in send/recv loop
+   *
+   */
+  double worker_t = 0.f;
+
+  /**
+   * @brief Time spent in sequential chemistry part
+   *
+   */
+  double chem_master = 0.f;
+
+  /**
+   * @brief Time spent in sequential instructions
+   *
+   */
+  double seq_t = 0.f;
+};
+
+/**
+ * @brief Class providing execution of worker chemistry
+ *
+ * Providing mainly a function to loop and wait for messages from the master.
+ *
+ */
+class ChemWorker : public ChemSim {
+ public:
+  /**
+   * @brief Construct a new ChemWorker object
+   *
+   * The following steps are executed to create a new object of ChemWorker:
+   * -# all needed simulation parameters are extracted
+   * -# memory is allocated
+   * -# Preparetion to create a DHT
+   * -# and finally create a new DHT_Wrapper
+   *
+   * @param params Simulation parameters as SimParams object
+   * @param R_ R runtime
+   * @param grid_ Grid object
+   * @param dht_comm Communicator addressing all processes marked as worker
+   */
+  ChemWorker(SimParams &params, RRuntime &R_, Grid &grid_, MPI_Comm dht_comm);
+
+  /**
+   * @brief Destroy the ChemWorker object
+   *
+   * Therefore all buffers are freed and the DHT_Wrapper object is destroyed.
+   *
+   */
+  ~ChemWorker();
+
+  /**
+   * @brief Start the 'work' loop
+   *
+   * Loop in an endless loop. At the beginning probe for a message from the
+   * master process. If there is a receivable message evaluate the message tag.
+   *
+   */
+  void loop();
+
+ private:
+  /**
+   * @brief Evaluating message to receive as work package
+   *
+   * These steps are done:
+   *
+   * -# Receive message
+   * -# Evaluate message header containing information about work package size,
+   * current iteration and timestep, simulation age
+   * -# if DHT is enabled check DHT for previously simulated results
+   * -# run simulation of work package
+   * -# send results back to master
+   * -# if DHT is enabled write simulated grid points to DHT
+   *
+   * @param probe_status message status of produced by MPI_Probe in loop
+   */
+  void doWork(MPI_Status &probe_status);
+
+  /**
+   * @brief Action to do after iteration
+   *
+   * If DHT is enabled print statistics and if dht_snaps is set to 2 write DHT
+   * snapshots.
+   *
+   */
+  void postIter();
+
+  /**
+   * @brief Message tag evaluates to TAG_FINISH
+   *
+   * Send all the collected timings and (possbile) DHT metrics to the master.
+   *
+   */
+  void finishWork();
+
+  /**
+   * @brief Write DHT snapshot
+   *
+   */
+  void writeFile();
+
+  /**
+   * @brief Read DHT snapshot
+   *
+   */
+  void readFile();
+
+  /**
+   * @brief Indicates usage of DHT
+   *
+   */
+  bool dht_enabled;
+
+  /**
+   * @brief Boolean if dt differs between iterations
+   *
+   */
+  bool dt_differ;
+
+  /**
+   * @brief Value between 0 and 2, indicating when to write DHT snapshots
+   *
+   */
+  int dht_snaps;
+
+  /**
+   * @brief Absolute path to DHT snapshot file
+   *
+   */
+  std::string dht_file;
+
+  /**
+   * @brief Count of bytes each process should allocate for the DHT
+   *
+   */
+  unsigned int dht_size_per_process;
+
+  /**
+   * @brief Indicates which grid cells were previously simulated and don't need
+   * to be simulated now
+   *
+   */
+  std::vector<bool> dht_flags;
+
+  /**
+   * @brief simulated results are stored here
+   *
+   */
+  double *mpi_buffer_results;
+
+  /**
+   * @brief Instance of DHT_Wrapper
+   *
+   */
+  DHT_Wrapper *dht;
+
+  /**
+   * @brief Array to store timings
+   *
+   * The values are stored in following order
+   *
+   * -# PHREEQC time
+   * -# DHT_get time
+   * -# DHT_fill time
+   *
+   */
+  double timing[3];
+
+  /**
+   * @brief Time worker is idling in MPI_Probe
+   *
+   */
+  double idle_t = 0.f;
+
+  /**
+   * @brief Count of PHREEQC calls
+   *
+   */
+  int phreeqc_count = 0;
+};
+}  // namespace poet
+#endif  // CHEMSIM_H
diff --git a/src/model/ChemWorker.cpp b/src/model/ChemWorker.cpp
new file mode 100644
index 000000000..c2db69341
--- /dev/null
+++ b/src/model/ChemWorker.cpp
@@ -0,0 +1,316 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include <Rcpp.h>
+
+#include <iostream>
+#include <string>
+
+#include "ChemSim.h"
+
+using namespace poet;
+using namespace std;
+using namespace Rcpp;
+
+ChemWorker::ChemWorker(SimParams &params, RRuntime &R_, Grid &grid_,
+                       MPI_Comm dht_comm)
+    : ChemSim(params, R_, grid_) {
+  t_simparams tmp = params.getNumParams();
+
+  this->dt_differ = tmp.dt_differ;
+  this->dht_enabled = tmp.dht_enabled;
+  this->dht_size_per_process = tmp.dht_size_per_process;
+  this->dht_snaps = tmp.dht_snaps;
+
+  this->dht_file = params.getDHTFile();
+
+  mpi_buffer = (double *)calloc((wp_size * (grid.getCols())) + BUFFER_OFFSET,
+                                sizeof(double));
+  mpi_buffer_results =
+      (double *)calloc(wp_size * (grid.getCols()), sizeof(double));
+
+  if (world_rank == 1)
+    cout << "CPP: Worker: DHT usage is " << (dht_enabled ? "ON" : "OFF")
+         << endl;
+
+  if (dht_enabled) {
+    int data_size = grid.getCols() * sizeof(double);
+    int key_size =
+        grid.getCols() * sizeof(double) + (dt_differ * sizeof(double));
+    int dht_buckets_per_process =
+        dht_size_per_process / (1 + data_size + key_size);
+
+    if (world_rank == 1)
+      cout << "CPP: Worker: data size: " << data_size << " bytes" << endl
+           << "CPP: Worker: key size: " << key_size << " bytes" << endl
+           << "CPP: Worker: buckets per process " << dht_buckets_per_process
+           << endl;
+
+    dht = new DHT_Wrapper(params, dht_comm, dht_buckets_per_process, data_size,
+                          key_size);
+
+    if (world_rank == 1) cout << "CPP: Worker: DHT created!" << endl;
+
+    if (!dht_file.empty()) readFile();
+    // set size
+    dht_flags.resize(wp_size, true);
+    // assign all elements to true (default)
+    dht_flags.assign(wp_size, true);
+  }
+
+  timing[0] = 0.0;
+  timing[1] = 0.0;
+  timing[2] = 0.0;
+}
+
+ChemWorker::~ChemWorker() {
+  free(mpi_buffer);
+  free(mpi_buffer_results);
+  if (dht_enabled) delete dht;
+}
+
+void ChemWorker::loop() {
+  MPI_Status probe_status;
+  while (1) {
+    double idle_a = MPI_Wtime();
+    MPI_Probe(0, MPI_ANY_TAG, MPI_COMM_WORLD, &probe_status);
+    double idle_b = MPI_Wtime();
+
+    /* there is a work package to receive */
+    if (probe_status.MPI_TAG == TAG_WORK) {
+      idle_t += idle_b - idle_a;
+      doWork(probe_status);
+    }
+    /* end of iteration */
+    else if (probe_status.MPI_TAG == TAG_DHT_ITER) {
+      postIter();
+    }
+    /* end of simulation */
+    else if (probe_status.MPI_TAG == TAG_FINISH) {
+      finishWork();
+      break;
+    }
+  }
+}
+
+void ChemWorker::doWork(MPI_Status &probe_status) {
+  int count;
+  int local_work_package_size = 0;
+
+  double dht_get_start, dht_get_end;
+  double phreeqc_time_start, phreeqc_time_end;
+  double dht_fill_start, dht_fill_end;
+
+  /* get number of doubles to be received */
+  MPI_Get_count(&probe_status, MPI_DOUBLE, &count);
+
+  /* receive */
+  MPI_Recv(mpi_buffer, count, MPI_DOUBLE, 0, TAG_WORK, MPI_COMM_WORLD,
+           MPI_STATUS_IGNORE);
+
+  /* decrement count of work_package by BUFFER_OFFSET */
+  count -= BUFFER_OFFSET;
+  
+  /* check for changes on all additional variables given by the 'header' of
+   * mpi_buffer */
+
+  // work_package_size
+  if (mpi_buffer[count] != local_work_package_size) {  // work_package_size
+    local_work_package_size = mpi_buffer[count];
+    R["work_package_size"] = local_work_package_size;
+    R.parseEvalQ("mysetup$work_package_size <- work_package_size");
+  }
+
+  // current iteration of simulation
+  if (mpi_buffer[count + 1] != iteration) {
+    iteration = mpi_buffer[count + 1];
+    R["iter"] = iteration;
+    R.parseEvalQ("mysetup$iter <- iter");
+  }
+
+  // current timestep size
+  if (mpi_buffer[count + 2] != dt) {
+    dt = mpi_buffer[count + 2];
+    R["dt"] = dt;
+    R.parseEvalQ("mysetup$dt <- dt");
+  }
+
+  // current simulation time ('age' of simulation)
+  if (mpi_buffer[count + 3] != current_sim_time) {
+    current_sim_time = mpi_buffer[count + 3];
+    R["simulation_time"] = current_sim_time;
+    R.parseEvalQ("mysetup$simulation_time <- simulation_time");
+  }
+  /* 4th double value is currently a placeholder */
+  // if (mpi_buffer[count+4] != placeholder) {
+  //     placeholder = mpi_buffer[count+4];
+  //     R["mysetup$placeholder"] = placeholder;
+  // }
+
+  if (dht_enabled) {
+    /* resize helper vector dht_flags of work_package_size changes */
+    if ((int)dht_flags.size() != local_work_package_size) {
+      dht_flags.resize(local_work_package_size, true);  // set size
+      dht_flags.assign(local_work_package_size,
+                       true);  // assign all elements to true (default)
+    }
+
+    /* check for values in DHT */
+    dht_get_start = MPI_Wtime();
+    dht->checkDHT(local_work_package_size, dht_flags, mpi_buffer, dt);
+    dht_get_end = MPI_Wtime();
+
+    /* distribute dht_flags to R Runtime */
+    R["dht_flags"] = as<LogicalVector>(wrap(dht_flags));
+  }
+
+  /* Convert grid to R runtime */
+  grid.importWP(mpi_buffer, wp_size);
+
+  if (dht_enabled) {
+    R.parseEvalQ("work_package <- work_package_full[dht_flags,]");
+  } else {
+    R.parseEvalQ("work_package <- work_package_full");
+  }
+
+  R.parseEvalQ("work_package <- as.matrix(work_package)");
+
+  unsigned int nrows = R.parseEval("nrow(work_package)");
+
+  if (nrows > 0) {
+    /*Single Line error Workaround*/
+    if (nrows <= 1) {
+      // duplicate line to enable correct simmulation
+      R.parseEvalQ(
+          "work_package <- work_package[rep(1:nrow(work_package), "
+          "times = 2), ]");
+    }
+    /* Run PHREEQC */
+    phreeqc_time_start = MPI_Wtime();
+    R.parseEvalQ(
+        "result <- as.data.frame(slave_chemistry(setup=mysetup, "
+        "data = work_package))");
+    phreeqc_time_end = MPI_Wtime();
+  } else {
+    // undefined behaviour, isn't it?
+  }
+
+  phreeqc_count++;
+
+  if (dht_enabled) {
+    R.parseEvalQ("result_full <- work_package_full");
+    if (nrows > 0) R.parseEvalQ("result_full[dht_flags,] <- result");
+  } else {
+    R.parseEvalQ("result_full <- result");
+  }
+
+  /* convert grid to C domain */
+  grid.exportWP(mpi_buffer_results);
+  /* send results to master */
+  MPI_Request send_req;
+  MPI_Isend(mpi_buffer_results, count, MPI_DOUBLE, 0, TAG_WORK, MPI_COMM_WORLD,
+            &send_req);
+
+  if (dht_enabled) {
+    /* write results to DHT */
+    dht_fill_start = MPI_Wtime();
+    dht->fillDHT(local_work_package_size, dht_flags, mpi_buffer,
+                 mpi_buffer_results, dt);
+    dht_fill_end = MPI_Wtime();
+
+    timing[1] += dht_get_end - dht_get_start;
+    timing[2] += dht_fill_end - dht_fill_start;
+  }
+
+  timing[0] += phreeqc_time_end - phreeqc_time_start;
+
+  MPI_Wait(&send_req, MPI_STATUS_IGNORE);
+}
+
+void ChemWorker::postIter() {
+  MPI_Recv(NULL, 0, MPI_DOUBLE, 0, TAG_DHT_ITER, MPI_COMM_WORLD,
+           MPI_STATUS_IGNORE);
+  if (dht_enabled) {
+    dht->printStatistics();
+
+    if (dht_snaps == 2) {
+      writeFile();
+    }
+  }
+  // synchronize all processes
+  MPI_Barrier(MPI_COMM_WORLD);
+}
+
+void ChemWorker::writeFile() {
+  cout.flush();
+  std::stringstream out;
+  out << out_dir << "/iter_" << setfill('0') << setw(3) << iteration << ".dht";
+  int res = dht->tableToFile(out.str().c_str());
+  if (res != DHT_SUCCESS && world_rank == 2)
+    cerr << "CPP: Worker: Error in writing current state of DHT to file."
+         << endl;
+  else if (world_rank == 2)
+    cout << "CPP: Worker: Successfully written DHT to file " << out.str()
+         << endl;
+}
+
+void ChemWorker::readFile() {
+  int res = dht->fileToTable((char *)dht_file.c_str());
+  if (res != DHT_SUCCESS) {
+    if (res == DHT_WRONG_FILE) {
+      if (world_rank == 1)
+        cerr << "CPP: Worker: Wrong file layout! Continue with empty DHT ..."
+             << endl;
+    } else {
+      if (world_rank == 1)
+        cerr << "CPP: Worker: Error in loading current state of DHT from "
+                "file. Continue with empty DHT ..."
+             << endl;
+    }
+  } else {
+    if (world_rank == 2)
+      cout << "CPP: Worker: Successfully loaded state of DHT from file "
+           << dht_file << endl;
+    std::cout.flush();
+  }
+}
+
+void ChemWorker::finishWork() {
+  /* before death, submit profiling/timings to master*/
+  MPI_Recv(NULL, 0, MPI_DOUBLE, 0, TAG_FINISH, MPI_COMM_WORLD,
+           MPI_STATUS_IGNORE);
+
+  // timings
+  MPI_Send(timing, 3, MPI_DOUBLE, 0, TAG_TIMING, MPI_COMM_WORLD);
+
+  MPI_Send(&phreeqc_count, 1, MPI_INT, 0, TAG_TIMING, MPI_COMM_WORLD);
+  MPI_Send(&idle_t, 1, MPI_DOUBLE, 0, TAG_TIMING, MPI_COMM_WORLD);
+
+  if (dht_enabled) {
+    // dht_perf
+    int dht_perf[3];
+    dht_perf[0] = dht->getHits();
+    dht_perf[1] = dht->getMisses();
+    dht_perf[2] = dht->getEvictions();
+    MPI_Send(dht_perf, 3, MPI_INT, 0, TAG_DHT_PERF, MPI_COMM_WORLD);
+  }
+
+  if (dht_enabled && dht_snaps > 0) writeFile();
+}
diff --git a/src/model/Grid.cpp b/src/model/Grid.cpp
new file mode 100644
index 000000000..ec475e6af
--- /dev/null
+++ b/src/model/Grid.cpp
@@ -0,0 +1,65 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "Grid.h"
+
+using namespace poet;
+using namespace Rcpp;
+
+void Grid::init() {
+  R.parseEval("GRID_TMP <- mysetup$state_C");
+  this->ncol = R.parseEval("ncol(GRID_TMP)");
+  this->nrow = R.parseEval("nrow(GRID_TMP)");
+}
+
+unsigned int Grid::getCols() { return this->ncol; }
+
+unsigned int Grid::getRows() { return this->nrow; }
+
+void Grid::shuffleAndExport(double *buffer) {
+  R.parseEval("tmp <- shuffle_field(mysetup$state_T, ordered_ids)");
+  R.setBufferDataFrame("tmp");
+  R.to_C_domain(buffer);
+}
+
+void Grid::importAndUnshuffle(double *buffer) {
+  R.setBufferDataFrame("GRID_TMP");
+  R.from_C_domain(buffer);
+  R["GRID_CHEM_DATA"] = R.getBufferDataFrame();
+  R.parseEval("result <- unshuffle_field(GRID_CHEM_DATA, ordered_ids)");
+}
+
+void Grid::importWP(double *buffer, unsigned int wp_size) {
+  R["GRID_WP_SKELETON"] = getSkeletonDataFrame(wp_size);
+  R.setBufferDataFrame("GRID_WP_SKELETON");
+  R.from_C_domain(buffer);
+  R["work_package_full"] = R.getBufferDataFrame();
+}
+void Grid::exportWP(double *buffer) {
+  R.setBufferDataFrame("result_full");
+  R.to_C_domain(buffer);
+}
+
+Rcpp::DataFrame Grid::getSkeletonDataFrame(unsigned int rows) {
+  R["GRID_ROWS"] = rows;
+
+  Rcpp::DataFrame tmp = R.parseEval("head(GRID_TMP,GRID_ROWS)");
+  return tmp;
+}
diff --git a/src/model/Grid.h b/src/model/Grid.h
new file mode 100644
index 000000000..75011f891
--- /dev/null
+++ b/src/model/Grid.h
@@ -0,0 +1,146 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef GRID_H
+#define GRID_H
+
+#include <RRuntime.h>
+#include <Rcpp.h>
+
+namespace poet {
+/**
+ * @brief Class describing the grid
+ *
+ * Providing methods to shuffle and unshuffle grid (for the master) as also to
+ * import and export a work package (for worker).
+ *
+ * @todo find better abstraction
+ *
+ */
+class Grid {
+ public:
+  /**
+   * @brief Construct a new Grid object
+   *
+   * This will call the default constructor and initializes private RRuntime
+   * with given R runtime.
+   *
+   * @param R
+   */
+  Grid(RRuntime &R) : R(R){};
+
+  /**
+   * @brief Init the grid
+   *
+   * At this moment init will only declare and define a variable inside the R
+   * runtime called grid_tmp since the whole Grid initialization and management
+   * is done by the R runtime. This may change in the future.
+   *
+   */
+  void init();
+
+  /**
+   * @brief Returns the number of elements for each gridcell
+   *
+   * @return unsigned int Number of elements
+   */
+  unsigned int getCols();
+
+  /**
+   * @brief Returns the number of grid cells
+   *
+   * @return unsigned int Number of grid cells
+   */
+  unsigned int getRows();
+
+  /**
+   * @brief Shuffle the grid and export it to C memory area
+   *
+   * This will call shuffle_field inside R runtime, set the resulting grid as
+   * buffered data frame in RRuntime object and write R grid to continous C
+   * memory area.
+   *
+   * @param[in,out] buffer Pointer to C memory area
+   */
+  void shuffleAndExport(double *buffer);
+
+  /**
+   * @brief Unshuffle the grid and import it from C memory area into R runtime
+   *
+   * Write C memory area into temporary R grid variable and unshuffle it.
+   *
+   * @param buffer Pointer to C memory area
+   */
+  void importAndUnshuffle(double *buffer);
+
+  /**
+   * @brief Import a C memory area as a work package into R runtime
+   *
+   * Get a skeleton from getSkeletonDataFrame inside R runtime and set this as
+   * buffer data frame of RRuntime object. Now convert C memory area to R data
+   * structure.
+   *
+   * @param buffer Pointer to C memory area
+   * @param wp_size Count of grid cells per work package
+   */
+  void importWP(double *buffer, unsigned int wp_size);
+
+  /**
+   * @brief Export a work package from R runtime into C memory area
+   *
+   * Set buffer data frame in RRuntime object to data frame holding the results
+   * and convert this to C memory area.
+   *
+   * @param buffer Pointer to C memory area
+   */
+  void exportWP(double *buffer);
+
+ private:
+  /**
+   * @brief Instance of RRuntime
+   *
+   */
+  RRuntime R;
+
+  /**
+   * @brief Number of columns of grid
+   *
+   */
+  unsigned int ncol;
+
+  /**
+   * @brief Number of rows of grid
+   *
+   */
+  unsigned int nrow;
+
+  /**
+   * @brief Get a SkeletonDataFrame
+   *
+   * Return a skeleton with \e n rows of current grid
+   *
+   * @param rows number of rows to return skeleton
+   * @return Rcpp::DataFrame Can be seen as a skeleton. The content of the data
+   * frame might be irrelevant.
+   */
+  Rcpp::DataFrame getSkeletonDataFrame(unsigned int rows);
+};
+}  // namespace poet
+#endif  // GRID_H
diff --git a/src/model/TransportSim.cpp b/src/model/TransportSim.cpp
new file mode 100644
index 000000000..711820d14
--- /dev/null
+++ b/src/model/TransportSim.cpp
@@ -0,0 +1,44 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "TransportSim.h"
+
+#include <mpi.h>
+
+using namespace poet;
+
+TransportSim::TransportSim(RRuntime &R_) : R(R_) {}
+
+void TransportSim::run() {
+  double sim_a_transport, sim_b_transport;
+
+  sim_b_transport = MPI_Wtime();
+  R.parseEvalQ("mysetup <- master_advection(setup=mysetup)");
+  sim_a_transport = MPI_Wtime();
+
+  transport_t += sim_a_transport - sim_b_transport;
+}
+
+void TransportSim::end() {
+  R["simtime_transport"] = transport_t;
+  R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
+}
+
+double TransportSim::getTransportTime() { return this->transport_t; }
diff --git a/src/model/TransportSim.h b/src/model/TransportSim.h
new file mode 100644
index 000000000..f5bc9b0bf
--- /dev/null
+++ b/src/model/TransportSim.h
@@ -0,0 +1,82 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef TRANSPORT_SIM_H
+#define TRANSPORT_SIM_H
+
+#include <RRuntime.h>
+
+namespace poet {
+/**
+ * @brief Class describing transport simulation
+ *
+ * Offers simple methods to run an iteration and end the simulation.
+ *
+ */
+class TransportSim {
+ public:
+  /**
+   * @brief Construct a new TransportSim object
+   *
+   * The instance will only be initialized with given R object.
+   *
+   * @param R RRuntime object
+   */
+  TransportSim(RRuntime &R);
+
+  /**
+   * @brief Run simulation for one iteration
+   *
+   * This will simply call the R function 'master_advection'
+   *
+   */
+  void run();
+
+  /**
+   * @brief End simulation
+   *
+   * All measured timings are distributed to the R runtime
+   *
+   */
+  void end();
+
+  /**
+   * @brief Get the transport time
+   *
+   * @return double time spent in transport
+   */
+  double getTransportTime();
+
+ private:
+  /**
+   * @brief Instance of RRuntime
+   *
+   */
+  RRuntime &R;
+
+  /**
+   * @brief time spent for transport
+   *
+   */
+  double transport_t = 0.f;
+};
+}  // namespace poet
+
+#endif  // TRANSPORT_SIM_H
diff --git a/src/poet.cpp b/src/poet.cpp
new file mode 100644
index 000000000..8eda62a7d
--- /dev/null
+++ b/src/poet.cpp
@@ -0,0 +1,218 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include <ChemSim.h>
+#include <Grid.h>
+#include <RRuntime.h>
+#include <Rcpp.h>
+#include <SimParams.h>
+#include <TransportSim.h>
+
+#include <cstring>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include <poet.h>
+
+using namespace std;
+using namespace poet;
+using namespace Rcpp;
+
+int main(int argc, char *argv[]) {
+  double sim_start, sim_end;
+
+  int world_size, world_rank;
+
+  MPI_Init(&argc, &argv);
+
+  MPI_Comm_size(MPI_COMM_WORLD, &world_size);
+
+  MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
+
+  /*Create custom Communicator with all processes except 0 (the master) for DHT
+   * storage */
+  MPI_Comm dht_comm;
+
+  if (world_rank == 0) {
+    MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED, world_rank, &dht_comm);
+  } else {
+    MPI_Comm_split(MPI_COMM_WORLD, 1, world_rank, &dht_comm);
+  }
+
+  if (world_rank == 0) {
+    cout << "Running POET in version " << poet_version << endl << endl;
+  }
+
+  /* initialize R runtime */
+  RRuntime R(argc, argv);
+
+  /*Loading Dependencies*/
+  std::string r_load_dependencies = "suppressMessages(library(Rmufits));"
+                                    "suppressMessages(library(RedModRphree));"
+                                    "source('../R_lib/kin_r_library.R');"
+                                    "source('../R_lib/parallel_r_library.R');";
+  R.parseEvalQ(r_load_dependencies);
+
+  SimParams params(world_rank, world_size);
+  int pret = params.parseFromCmdl(argv, R);
+
+  if (pret == PARSER_ERROR) {
+    MPI_Finalize();
+    return EXIT_FAILURE;
+  } else if (pret == PARSER_HELP) {
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+  }
+
+  cout << "CPP: R Init (RInside) on process " << world_rank << endl;
+
+  bool dt_differ;
+  if (world_rank == 0) {
+    // get timestep vector from grid_init function ...
+    std::string master_init_code = "mysetup <- master_init(setup=setup)";
+    R.parseEval(master_init_code);
+
+    dt_differ = R.parseEval("mysetup$dt_differ");
+    // ... and broadcast it to every other rank unequal to 0
+    MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
+  }
+  /* workers will only read the setup DataFrame defined by input file */
+  else {
+    R.parseEval("mysetup <- setup");
+    MPI_Bcast(&dt_differ, 1, MPI_C_BOOL, 0, MPI_COMM_WORLD);
+  }
+
+  params.setDtDiffer(dt_differ);
+
+  // initialize chemistry on all processes
+  std::string init_chemistry_code = "mysetup <- init_chemistry(setup=mysetup)";
+  R.parseEval(init_chemistry_code);
+
+  Grid grid(R);
+  grid.init();
+
+  params.initVectorParams(R, grid.getCols());
+
+  // MDL: store all parameters
+  if (world_rank == 0) {
+    cout << "CPP: Calling R Function to store calling parameters" << endl;
+    R.parseEvalQ("StoreSetup(setup=mysetup)");
+  }
+
+  if (world_rank == 0) {
+    cout << "CPP: Init done on process with rank " << world_rank << endl;
+  }
+
+  MPI_Barrier(MPI_COMM_WORLD);
+
+  /* THIS IS EXECUTED BY THE MASTER */
+  if (world_rank == 0) {
+    ChemMaster master(params, R, grid);
+    TransportSim trans(R);
+
+    sim_start = MPI_Wtime();
+
+    /* Iteration Count is dynamic, retrieving value from R (is only needed by
+     * master for the following loop) */
+    uint32_t maxiter = R.parseEval("mysetup$maxiter");
+
+    /* SIMULATION LOOP */
+    for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
+      cout << "CPP: Evaluating next time step" << endl;
+      R.parseEvalQ("mysetup <- master_iteration_setup(mysetup)");
+
+      /* displaying iteration number, with C++ and R iterator */
+      cout << "CPP: Going through iteration " << iter << endl;
+      cout << "CPP: R's $iter: " << ((uint32_t)(R.parseEval("mysetup$iter")))
+           << ". Iteration" << endl;
+
+      cout << "CPP: Calling Advection" << endl;
+
+      /* run transport */
+      trans.run();
+
+      cout << "CPP: Chemistry" << endl;
+
+      /* Fallback for sequential execution */
+      if (world_size == 1) {
+        master.ChemSim::run();
+      }
+      /* otherwise run parallel */
+      else {
+        master.run();
+      }
+
+      // MDL master_iteration_end just writes on disk state_T and
+      // state_C after every iteration if the cmdline option
+      // --ignore-results is not given (and thus the R variable
+      // store_result is TRUE)
+      R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)");
+
+      cout << endl
+           << "CPP: End of *coupling* iteration " << iter << "/" << maxiter
+           << endl
+           << endl;
+
+      MPI_Barrier(MPI_COMM_WORLD);
+
+    } // END SIMULATION LOOP
+
+    cout << "CPP: finished simulation loop" << endl;
+
+    sim_end = MPI_Wtime();
+
+    cout << "CPP: start timing profiling" << endl;
+
+    R.parseEvalQ("profiling <- list()");
+
+    R["simtime"] = sim_end - sim_start;
+    R.parseEvalQ("profiling$simtime <- simtime");
+
+    trans.end();
+
+    if (world_size == 1) {
+      master.ChemSim::end();
+    } else {
+      master.end();
+    }
+
+    string r_vis_code;
+    r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
+    R.parseEval(r_vis_code);
+
+    cout << "CPP: Done! Results are stored as R objects into <"
+         << params.getOutDir() << "/timings.rds>" << endl;
+  }
+  /* THIS IS EXECUTED BY THE WORKERS */
+  else {
+    ChemWorker worker(params, R, grid, dht_comm);
+    worker.loop();
+  }
+
+  cout << "CPP: finished, cleanup of process " << world_rank << endl;
+  MPI_Finalize();
+
+  if (world_rank == 0) {
+    cout << "CPP: done, bye!" << endl;
+  }
+
+  exit(0);
+}
diff --git a/src/poet.h.in b/src/poet.h.in
new file mode 100644
index 000000000..5f5279a2e
--- /dev/null
+++ b/src/poet.h.in
@@ -0,0 +1,6 @@
+#ifndef POET_H
+#define POET_H
+
+const char *poet_version = "@POET_VERSION@";
+
+#endif // POET_H
diff --git a/src/r_utils.cpp b/src/r_utils.cpp
deleted file mode 100644
index eafa33fa6..000000000
--- a/src/r_utils.cpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#include "r_utils.h"
-
-/* This function converts a pure double dataframe into a double array.
-    buffer      <- double array, needs to be allocated before
-    df          <- reference to input dataframe
-*/
-void convert_R_Dataframe_2_C_buffer(double* buffer, Rcpp::DataFrame &df)
-{
-    size_t rowCount = df.nrow();
-    size_t colCount = df.ncol();
-
-    for (size_t i = 0; i < rowCount; i++)
-    {
-        for (size_t j = 0; j < colCount; j++)
-        {
-            /* Access column vector j and extract value of line i */
-            Rcpp::DoubleVector col = df[j];
-            buffer[i * colCount + j] = col[i];
-        }
-    }
-}
-
-/* This function converts a double array into a double dataframe.
-    buffer      <- input double array
-    df          <- reference to output dataframe, needs to be of fitting size, structure will be taken from it
-*/
-void convert_C_buffer_2_R_Dataframe(double* buffer, Rcpp::DataFrame &df)
-{
-    size_t rowCount = df.nrow();
-    size_t colCount = df.ncol();
-
-    for (size_t i = 0; i < rowCount; i++)
-    {
-        for (size_t j = 0; j < colCount; j++)
-        {
-            /* Access column vector j and extract value of line i */
-            Rcpp::DoubleVector col = df[j];
-            col[i] = buffer[i * colCount + j];
-        }
-    }
-}
-
-
-
diff --git a/src/r_utils.h b/src/r_utils.h
deleted file mode 100644
index 95000e97f..000000000
--- a/src/r_utils.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#pragma once
-#include <RInside.h> 
-
-/*Functions*/
-void convert_R_Dataframe_2_C_buffer(double* buffer, Rcpp::DataFrame &df);
-void convert_C_buffer_2_R_Dataframe(double* buffer, Rcpp::DataFrame &df);
\ No newline at end of file
diff --git a/src/util/CMakeLists.txt b/src/util/CMakeLists.txt
new file mode 100644
index 000000000..13cac93e4
--- /dev/null
+++ b/src/util/CMakeLists.txt
@@ -0,0 +1,4 @@
+add_library(POET_Util RRuntime.cpp SimParams.cpp)
+target_include_directories(POET_Util PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${R_INCLUDE_DIRS})
+target_link_libraries(POET_Util PUBLIC ${R_LIBRARIES})
+target_compile_definitions(POET_Util PUBLIC STRICT_R_HEADERS)
diff --git a/src/util/RRuntime.cpp b/src/util/RRuntime.cpp
new file mode 100644
index 000000000..fccf8726b
--- /dev/null
+++ b/src/util/RRuntime.cpp
@@ -0,0 +1,64 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "RRuntime.h"
+
+#include <RInside.h>
+#include <Rcpp.h>
+
+#include <string>
+
+using namespace poet;
+
+void RRuntime::to_C_domain(double *buffer) {
+  size_t rowCount = dfbuff.nrow();
+  size_t colCount = dfbuff.ncol();
+
+  for (size_t i = 0; i < rowCount; i++) {
+    for (size_t j = 0; j < colCount; j++) {
+      /* Access column vector j and extract value of line i */
+      Rcpp::DoubleVector col = dfbuff[j];
+      buffer[i * colCount + j] = col[i];
+    }
+  }
+}
+
+void RRuntime::from_C_domain(double *buffer) {
+  size_t rowCount = dfbuff.nrow();
+  size_t colCount = dfbuff.ncol();
+
+  for (size_t i = 0; i < rowCount; i++) {
+    for (size_t j = 0; j < colCount; j++) {
+      /* Access column vector j and extract value of line i */
+      Rcpp::DoubleVector col = dfbuff[j];
+      col[i] = buffer[i * colCount + j];
+    }
+  }
+}
+
+void RRuntime::setBufferDataFrame(std::string dfname) {
+  this->dfbuff = parseEval(dfname);
+}
+
+Rcpp::DataFrame RRuntime::getBufferDataFrame() { return this->dfbuff; }
+
+size_t RRuntime::getBufferNCol() { return (this->dfbuff).ncol(); }
+
+size_t RRuntime::getBufferNRow() { return (this->dfbuff).nrow(); }
diff --git a/src/util/RRuntime.h b/src/util/RRuntime.h
new file mode 100644
index 000000000..f09933a72
--- /dev/null
+++ b/src/util/RRuntime.h
@@ -0,0 +1,137 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef RRUNTIME_H
+#define RRUNTIME_H
+
+#include <RInside.h>
+#include <Rcpp.h>
+
+#include <string>
+
+namespace poet {
+
+/**
+ * @brief Provides an interface to a R runtime.
+ *
+ * RRuntime is a wrapper class around a RInside (R) runtime and provides several
+ * simplified methods to use R commands inside POET.
+ *
+ */
+class RRuntime : public RInside {
+ public:
+  /**
+   * @brief Construct a new RRuntime object
+   *
+   * Since this is an inherited class of RInside the constructor of the super
+   * class is just called.
+   *
+   * @param argc Argument counter of the program
+   * @param argv Argument values of the program
+   */
+  RRuntime(const int argc, const char *const argv[]) : RInside(argc, argv){};
+
+  /**
+   * Convert a R dataframe into a C continious memory area.
+   *
+   * @param buffer Name of the R internal variable name.
+   */
+
+  /**
+   * @brief Convert a R dataframe into a C continious memory area.
+   *
+   * A buffer data frame must be set beforehand with setBufferDataFrame. Then
+   * each value will be set into the continious memory area. This is done row
+   * wise.
+   *
+   * @todo: Might be more performant if all columns would be loaded at once and
+   * not for each column seperatly
+   *
+   * @param buffer Pointer to pre-allocated memory
+   */
+  void to_C_domain(double *buffer);
+
+  /**
+   * @brief Convert continious C memory area into R dataframe and puts it into R
+   * runtime.
+   *
+   * A buffer data frame must be set beforehand with setBufferDataFrame. Then
+   * each value will be set into buffered data frame of this object. This is
+   * done row wise.
+   *
+   * @todo: Might be more performant if all columns would be loaded at once and
+   * not for each column seperatly
+   *
+   * @param buffer Pointer to memory area which should be converted into R
+   * dataframe.
+   */
+  void from_C_domain(double *buffer);
+
+  /**
+   * @brief Set the Buffer Data Frame object
+   *
+   * Set the buffered data frame (will be mostly the grid) of this object.
+   *
+   * @param dfname Name of the data frame inside R runtime
+   */
+  void setBufferDataFrame(std::string dfname);
+
+  /**
+   * @brief Get the Buffer Data Frame object
+   *
+   * Returning the current buffered data frame as a Rcpp data frame.
+   *
+   * @return Rcpp::DataFrame Current buffered data frame
+   */
+  Rcpp::DataFrame getBufferDataFrame();
+
+  /**
+   * @brief Get the Buffer N Col object
+   *
+   * Get the numbers of columns of the buffered data frame.
+   *
+   * @return size_t Count of columns of buffered data frame
+   */
+  size_t getBufferNCol();
+
+  /**
+   * @brief Get the Buffer N Row object
+   *
+   * Get the numbers of rows of the buffered data frame.
+   *
+   * @return size_t Count of rows of buffered data frame
+   */
+  size_t getBufferNRow();
+
+ private:
+  /**
+   * @brief Buffered data frame
+   *
+   * This is used to convert a R data frame into continious memory used by C/C++
+   * runtime and vice versa. Must be set with setBufferDataFrame and can be
+   * manipulated with from_C_domain.
+   * 
+   * @todo: Find a cleaner solution. Maybe abstraction via another class.
+   *
+   */
+  Rcpp::DataFrame dfbuff;
+};
+}  // namespace poet
+#endif  // RRUNTIME_H
diff --git a/src/util/SimParams.cpp b/src/util/SimParams.cpp
new file mode 100644
index 000000000..623a298db
--- /dev/null
+++ b/src/util/SimParams.cpp
@@ -0,0 +1,219 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#include "SimParams.h"
+
+#include <Rcpp.h>
+
+#include <iostream>
+
+using namespace poet;
+using namespace std;
+using namespace Rcpp;
+
+SimParams::SimParams(int world_rank_, int world_size_) {
+  this->simparams.world_rank = world_rank_;
+  this->simparams.world_size = world_size_;
+}
+
+int SimParams::parseFromCmdl(char *argv[], RRuntime &R) {
+  // initialize argh object
+  argh::parser cmdl(argv);
+
+  // if user asked for help
+  if (cmdl[{"help", "h"}]) {
+    if (simparams.world_rank == 0) {
+      cout << "Todo" << endl
+           << "See README.md for further information." << endl;
+    }
+    return PARSER_HELP;
+  }
+  // if positional arguments are missing
+  else if (!cmdl(2)) {
+    if (simparams.world_rank == 0) {
+      cerr << "ERROR. Kin needs 2 positional arguments: " << endl
+           << "1) the R script defining your simulation and" << endl
+           << "2) the directory prefix where to save results and profiling"
+           << endl;
+    }
+    return PARSER_ERROR;
+  }
+
+  // collect all parameters which are not known, print them to stderr and return
+  // with PARSER_ERROR
+  std::list<std::string> optionsError = validateOptions(cmdl);
+  if (!optionsError.empty()) {
+    if (simparams.world_rank == 0) {
+      cerr << "Unrecognized option(s):\n" << endl;
+      for (auto option : optionsError) {
+        cerr << option << endl;
+      }
+      cerr << "\nMake sure to use available options. Exiting!" << endl;
+    }
+    return PARSER_ERROR;
+  }
+
+  /*Parse DHT arguments*/
+  simparams.dht_enabled = cmdl["dht"];
+  // cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';
+
+  if (simparams.dht_enabled) {
+    cmdl("dht-strategy", 0) >> simparams.dht_strategy;
+    // cout << "CPP: DHT strategy is " << dht_strategy << endl;
+
+    cmdl("dht-signif", 5) >> simparams.dht_significant_digits;
+    // cout << "CPP: DHT significant digits = " << dht_significant_digits <<
+    // endl;
+
+    simparams.dht_log = !(cmdl["dht-nolog"]);
+    // cout << "CPP: DHT logarithm before rounding: " << ( dht_logarithm ? "ON"
+    // : "OFF" ) << endl;
+
+    cmdl("dht-size", DHT_SIZE_PER_PROCESS) >> simparams.dht_size_per_process;
+    // cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process <<
+    // endl;
+
+    cmdl("dht-snaps", 0) >> simparams.dht_snaps;
+
+    cmdl("dht-file") >> dht_file;
+  }
+  /*Parse work package size*/
+  cmdl("work-package-size", WORK_PACKAGE_SIZE_DEFAULT) >> simparams.wp_size;
+
+  /*Parse output options*/
+  simparams.store_result = !cmdl["ignore-result"];
+
+  if (simparams.world_rank == 0) {
+    cout << "CPP: Complete results storage is "
+         << (simparams.store_result ? "ON" : "OFF") << endl;
+    cout << "CPP: Work Package Size: " << simparams.wp_size << endl;
+    cout << "CPP: DHT is " << (simparams.dht_enabled ? "ON" : "OFF") << '\n';
+
+    if (simparams.dht_enabled) {
+      cout << "CPP: DHT strategy is " << simparams.dht_strategy << endl;
+      cout << "CPP: DHT key default digits (ignored if 'signif_vector' is "
+              "defined) = "
+           << simparams.dht_significant_digits << endl;
+      cout << "CPP: DHT logarithm before rounding: "
+           << (simparams.dht_log ? "ON" : "OFF") << endl;
+      cout << "CPP: DHT size per process (Byte) = "
+           << simparams.dht_size_per_process << endl;
+      cout << "CPP: DHT save snapshots is " << simparams.dht_snaps << endl;
+      cout << "CPP: DHT load file is " << dht_file << endl;
+    }
+  }
+
+  cmdl(1) >> filesim;
+  cmdl(2) >> out_dir;
+
+  /* distribute information to R runtime */
+  // if local_rank == 0 then master else worker
+  R["local_rank"] = simparams.world_rank;
+  // assign a char* (string) to 'filesim'
+  R["filesim"] = wrap(filesim);
+  // assign a char* (string) to 'fileout'
+  R["fileout"] = wrap(out_dir);
+  // pass the boolean "store_result" to the R process
+  R["store_result"] = simparams.store_result;
+  // worker count
+  R["n_procs"] = simparams.world_size - 1;
+  // work package size
+  R["work_package_size"] = simparams.wp_size;
+  // dht enabled?
+  R["dht_enabled"] = simparams.dht_enabled;
+  // log before rounding?
+  R["dht_log"] = simparams.dht_log;
+
+  // eval the init string, ignoring any returns
+  R.parseEvalQ("source(filesim)");
+
+  return PARSER_OK;
+}
+
+void SimParams::initVectorParams(RRuntime &R, int col_count) {
+  if (simparams.dht_enabled) {
+    /*Load significance vector from R setup file (or set default)*/
+    bool signif_vector_exists = R.parseEval("exists('signif_vector')");
+    if (signif_vector_exists) {
+      dht_signif_vector = as<std::vector<int>>(R["signif_vector"]);
+    } else {
+      dht_signif_vector.assign(col_count, simparams.dht_significant_digits);
+    }
+
+    /*Load property type vector from R setup file (or set default)*/
+    bool prop_type_vector_exists = R.parseEval("exists('prop_type')");
+    if (prop_type_vector_exists) {
+      dht_prop_type_vector = as<std::vector<string>>(R["prop_type"]);
+    } else {
+      dht_prop_type_vector.assign(col_count, "act");
+    }
+
+    if (simparams.world_rank == 0) {
+      // MDL: new output on signif_vector and prop_type
+      if (signif_vector_exists) {
+        cout << "CPP: using problem-specific rounding digits: " << endl;
+        R.parseEval(
+            "print(data.frame(prop=prop, type=prop_type, "
+            "digits=signif_vector))");
+      } else {
+        cout << "CPP: using DHT default rounding digits = "
+             << simparams.dht_significant_digits << endl;
+      }
+
+      // MDL: pass to R the DHT stuff. These variables exist
+      // only if dht_enabled is true
+      R["dht_final_signif"] = dht_signif_vector;
+      R["dht_final_proptype"] = dht_prop_type_vector;
+    }
+  }
+}
+
+void SimParams::setDtDiffer(bool dt_differ) { simparams.dt_differ = dt_differ; }
+
+t_simparams SimParams::getNumParams() { return this->simparams; }
+
+std::vector<int> SimParams::getDHTSignifVector() {
+  return this->dht_signif_vector;
+}
+std::vector<std::string> SimParams::getDHTPropTypeVector() {
+  return this->dht_prop_type_vector;
+}
+std::string SimParams::getDHTFile() { return this->dht_file; }
+
+std::string SimParams::getFilesim() { return this->filesim; }
+std::string SimParams::getOutDir() { return this->out_dir; }
+
+std::list<std::string> SimParams::validateOptions(argh::parser cmdl) {
+  /* store all unknown parameters here */
+  std::list<std::string> retList;
+
+  /* loop over all flags and compare to given flaglist*/
+  for (auto &flag : cmdl.flags()) {
+    if (!(flaglist.find(flag) != flaglist.end())) retList.push_back(flag);
+  }
+
+  /* and loop also over params and compare to given paramlist */
+  for (auto &param : cmdl.params()) {
+    if (!(paramlist.find(param.first) != paramlist.end()))
+      retList.push_back(param.first);
+  }
+
+  return retList;
+}
diff --git a/src/util/SimParams.h b/src/util/SimParams.h
new file mode 100644
index 000000000..86de2d710
--- /dev/null
+++ b/src/util/SimParams.h
@@ -0,0 +1,274 @@
+/*
+** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
+** Potsdam)
+**
+** Copyright (C) 2018-2021 Marco De Lucia (GFZ Potsdam)
+**
+** POET is free software; you can redistribute it and/or modify it under the
+** terms of the GNU General Public License as published by the Free Software
+** Foundation; either version 2 of the License, or (at your option) any later
+** version.
+**
+** POET is distributed in the hope that it will be useful, but WITHOUT ANY
+** WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+** A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+**
+** You should have received a copy of the GNU General Public License along with
+** this program; if not, write to the Free Software Foundation, Inc., 51
+** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+*/
+
+#ifndef PARSER_H
+#define PARSER_H
+
+#include <string>
+
+#include "RRuntime.h"
+#include "argh.h"  // Argument handler https://github.com/adishavit/argh
+// BSD-licenced
+
+/** Return value if no error occured */
+#define PARSER_OK 0
+/** Return value if error occured during parsing of program arguments */
+#define PARSER_ERROR -1
+/** Return value if user asked for help message with program parameter */
+#define PARSER_HELP -2
+
+/** Standard DHT Size (Defaults to 1 GiB) */
+#define DHT_SIZE_PER_PROCESS 1073741824
+/** Standard work package size */
+#define WORK_PACKAGE_SIZE_DEFAULT 5
+
+namespace poet {
+
+/**
+ * @brief Defining all simulation parameters
+ *
+ */
+typedef struct {
+  /** Count of processes in MPI_COMM_WORLD */
+  int world_size;
+  /** rank of proces in MPI_COMM_WORLD */
+  int world_rank;
+  /** indicates if DHT should be used */
+  bool dht_enabled;
+  /** apply logarithm to key before rounding */
+  bool dht_log;
+  /** indicates if timestep dt differs between iterations */
+  bool dt_differ;
+  /** Indicates, when a DHT snapshot should be written */
+  int dht_snaps;
+  /** <b>not implemented</b>: How a DHT is distributed over processes */
+  int dht_strategy;
+  /** Size of DHt per process in byter */
+  unsigned int dht_size_per_process;
+  /** Default significant digit for rounding */
+  int dht_significant_digits;
+  /** Default work package size */
+  unsigned int wp_size;
+  /** indicates if resulting grid should be stored after every iteration */
+  bool store_result;
+} t_simparams;
+
+/**
+ * @brief Reads information from program arguments and R runtime
+ *
+ * Providing functions to initialize parameters of the simulation using command
+ * line parameters and parameters from the R runtime. This class will also parse
+ * arguments from the commandline and decides if argument is known or unknown.
+ *
+ * Stores and distribute current simulation parameters at any time.
+ *
+ */
+class SimParams {
+ public:
+  /**
+   * @brief Construct a new SimParams object
+   *
+   * With all given parameters a new instance of this class will be created.
+   *
+   * @param world_rank Rank of process inside MPI_COMM_WORLD
+   * @param world_size Size of communicator MPI_COMM_WORLD
+   */
+  SimParams(int world_rank, int world_size);
+
+  /**
+   * @brief Parse program arguments
+   *
+   * This is done by the argh.h library.
+   *
+   * First, the function will check if there is a flag 'help' or 'h'. If this is
+   * the case a help message is printed and the function will return with
+   * PARSER_HELP.
+   *
+   * Second, if there are not 2 positional arguments an error will be printed to
+   * stderr and the function returns with PARSER_ERROR.
+   *
+   * Then all given program parameters and flags will be read and checked, if
+   * there are known by validateOptions. A list of all unknown options might be
+   * returned, printed out and the function will return with PARSER_ERROR.
+   * Oterhwise the function continuos.
+   *
+   * Now all program arguments will be stored inside t_simparams struct, printed
+   * out and the function returns with PARSER_OK.
+   *
+   * Also, all parsed agruments are distributed to the R runtime.
+   *
+   * @param argv Argument value of the program
+   * @param R Instantiated R runtime
+   * @return int Returns with 0 if no error occured, otherwise value less than 0
+   * is returned.
+   */
+  int parseFromCmdl(char *argv[], RRuntime &R);
+
+  /**
+   * @brief Init std::vector values
+   *
+   * This will initialize dht_signif_vector and dht_prop_type_vector internally
+   * depending on whether vectors are defined by R-Simulation file or not.
+   * 'init_chemistry' must be run beforehand.
+   *
+   * @param R R runtime
+   * @param col_count Count of variables per grid cell (typically the count of
+   * columns of each grid cell)
+   */
+  void initVectorParams(RRuntime &R, int col_count);
+
+  /**
+   * @brief Set if dt differs
+   *
+   * Set a boolean variable if the timestep differs between iterations of
+   * simulation.
+   *
+   * @param dt_differ Boolean value, if dt differs
+   */
+  void setDtDiffer(bool dt_differ);
+
+  /**
+   * @brief Get the numerical params struct
+   *
+   * Returns a struct which contains all numerical or boolean simulation
+   * parameters.
+   *
+   * @return t_simparams Parameter struct
+   */
+  t_simparams getNumParams();
+
+  /**
+   * @brief Get the DHT_Signif_Vector
+   *
+   * Returns a vector indicating which significant values are used for each
+   * variable of a grid cell.
+   *
+   * @return std::vector<int> Vector of integers containing information about
+   * significant digits
+   */
+  std::vector<int> getDHTSignifVector();
+
+  /**
+   * @brief Get the DHT_Prop_Type_Vector
+   *
+   * Returns a vector indicating of which type a variable of a grid cell is.
+   *
+   * @return std::vector<std::string> Vector if strings defining a type of a
+   * variable
+   */
+  std::vector<std::string> getDHTPropTypeVector();
+
+  /**
+   * @brief Return name of DHT snapshot.
+   *
+   * Name of the DHT file which is used to initialize the DHT with a previously
+   * written snapshot.
+   *
+   * @return std::string Absolute paht to the DHT snapshot
+   */
+  std::string getDHTFile();
+
+  /**
+   * @brief Get the filesim name
+   *
+   * Returns a string containing the absolute path to a R file defining the
+   * simulation.
+   *
+   * @return std::string Absolute path to R file
+   */
+  std::string getFilesim();
+
+  /**
+   * @brief Get the output directory
+   *
+   * Returns the name of an absolute path where all output files should be
+   * stored.
+   *
+   * @return std::string Absolute path to output path
+   */
+  std::string getOutDir();
+
+ private:
+  /**
+   * @brief Validate program parameters and flags
+   *
+   * Therefore this function iterates over the list of flags and parameters and
+   * compare them to the class member flagList and paramList. If a program
+   * argument is not included it is put to a list. This list will be returned.
+   *
+   * @return std::list<std::string> List with all unknown parameters. Might be
+   * empty.
+   */
+  std::list<std::string> validateOptions(argh::parser cmdl);
+
+  /**
+   * @brief Contains all valid program flags.
+   *
+   */
+  std::set<std::string> flaglist{"ignore-result", "dht", "dht-nolog"};
+
+  /**
+   * @brief Contains all valid program parameters.
+   *
+   */
+  std::set<std::string> paramlist{"work-package-size", "dht-signif",
+                                  "dht-strategy",      "dht-size",
+                                  "dht-snaps",         "dht-file"};
+
+  /**
+   * @brief Struct containing all simulation parameters
+   *
+   * Contains only those values which are standard arithmetic C types.
+   *
+   */
+  t_simparams simparams;
+
+  /**
+   * @brief Defines significant digits for each variable of a grid cell
+   *
+   */
+  std::vector<int> dht_signif_vector;
+
+  /**
+   * @brief Defines the type of a variable
+   *
+   */
+  std::vector<std::string> dht_prop_type_vector;
+
+  /**
+   * @brief Absolute path to a DHT snapshot
+   *
+   */
+  std::string dht_file;
+
+  /**
+   * @brief Absolute path to R file containing simulation definitions
+   *
+   */
+  std::string filesim;
+
+  /**
+   * @brief Absolute path to output dir
+   *
+   */
+  std::string out_dir;
+};
+}  // namespace poet
+#endif  // PARSER_H
diff --git a/src/argh.h b/src/util/argh.h
similarity index 88%
rename from src/argh.h
rename to src/util/argh.h
index 422aa4c78..2b2609cd6 100644
--- a/src/argh.h
+++ b/src/util/argh.h
@@ -1,3 +1,30 @@
+/*
+** Copyright (c) 2016, Adi Shavit All rights reserved.
+**
+** Redistribution and use in source and binary forms, with or without
+** modification, are permitted provided that the following conditions are met:
+**
+** * Redistributions of source code must retain the above copyright notice, this
+**   list of conditions and the following disclaimer. * Redistributions in
+**   binary form must reproduce the above copyright notice, this list of
+**   conditions and the following disclaimer in the documentation and/or other
+**   materials provided with the distribution. * Neither the name of nor the
+**   names of its contributors may be used to endorse or promote products
+**   derived from this software without specific prior written permission.
+**
+** THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+** AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+** IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+** ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+** LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+** CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+** SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+** INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+** CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+** ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+** POSSIBILITY OF SUCH DAMAGE.
+ */
+
 #pragma once
 
 #include <algorithm>
diff --git a/src/worker.cpp b/src/worker.cpp
deleted file mode 100644
index 880b71f51..000000000
--- a/src/worker.cpp
+++ /dev/null
@@ -1,277 +0,0 @@
-#include "worker.h"
-#include "dht_wrapper.h"
-#include "global_buffer.h"
-#include "r_utils.h"
-#include <mpi.h>
-#include <iostream>
-
-void worker_function(RInside& R) 
-{
-    int world_rank;
-    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
-    MPI_Status probe_status;
-    int count;
-
-    int local_work_package_size;
-    int iteration;
-    double dt, current_sim_time;
-
-    double idle_a, idle_b;
-    double cummul_idle = 0.f;
-
-    double dht_get_start=0, dht_get_end=0;
-    double dht_fill_start=0, dht_fill_end=0;
-    double phreeqc_time_start=0, phreeqc_time_end=0;
-    int phreeqc_count = 0;
-
-    //timing[0] -> phreeqc
-    //timing[1] -> dht_get
-    //timing[2] -> dht_fill
-    double timing[3];
-    timing[0] = 0.0;
-    timing[1] = 0.0;
-    timing[2] = 0.0;
-
-    //dht_perf[0] -> hits
-    //dht_perf[1] -> miss
-    //dht_perf[2] -> collisions
-    uint64_t dht_perf[3];
-
-    if (dht_enabled) 
-    {
-        dht_flags.resize(work_package_size, true); //set size
-        dht_flags.assign(work_package_size, true); //assign all elements to true (default)
-        dht_hits = 0;
-        dht_miss = 0;
-        dht_collision = 0;
-
-
-        // MDL: This code has now been moved to kin.cpp 
-        // /*Load significance vector from R setup file (or set default)*/
-        // bool signif_vector_exists = R.parseEval("exists('signif_vector')");
-        // if (signif_vector_exists)
-        // { 
-        //     dht_significant_digits_vector = as<std::vector<int>>(R["signif_vector"]);
-        // } else 
-        // {
-        //     dht_significant_digits_vector.assign(dht_object->key_size / sizeof(double), dht_significant_digits);
-        // }
-
-        // /*Load property type vector from R setup file (or set default)*/
-        // bool prop_type_vector_exists = R.parseEval("exists('prop_type')");
-        // if (prop_type_vector_exists)
-        // { 
-        //     prop_type_vector = as<std::vector<string>>(R["prop_type"]);
-        // } else 
-        // {
-        //     prop_type_vector.assign(dht_object->key_size / sizeof(double), "normal");
-        // }
-    }
-
-    //initialization of helper variables
-    iteration = 0;
-    dt = 0;
-    current_sim_time = 0;
-    local_work_package_size = 0;
-
-    /*worker loop*/
-    while(1)
-    {
-        /*Wait for Message*/
-        idle_a = MPI_Wtime();
-        MPI_Probe(0, MPI_ANY_TAG, MPI_COMM_WORLD, &probe_status);
-        idle_b = MPI_Wtime();
-
-        if (probe_status.MPI_TAG == TAG_WORK) 
-        {   /* do work */
-            
-            cummul_idle += idle_b - idle_a;
-
-            /* get number of doubles sent */
-            MPI_Get_count(&probe_status, MPI_DOUBLE, &count);
-
-            /* receive */
-            MPI_Recv(mpi_buffer, count, MPI_DOUBLE, 0, TAG_WORK, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-
-            //decrement count of work_package by BUFFER_OFFSET
-            count -= BUFFER_OFFSET;
-            //check for changes on all additional variables given by the 'header' of mpi_buffer
-            if (mpi_buffer[count] != local_work_package_size) { //work_package_size
-                local_work_package_size = mpi_buffer[count];
-                R["work_package_size"] = local_work_package_size;
-                R.parseEvalQ("mysetup$work_package_size <- work_package_size");
-            }
-            if (mpi_buffer[count+1] != iteration) { //current iteration of simulation
-                iteration = mpi_buffer[count+1];
-                R["iter"] = iteration;
-                R.parseEvalQ("mysetup$iter <- iter");
-            }
-            if (mpi_buffer[count+2] != dt) { //current timestep size
-                dt = mpi_buffer[count+2];
-                R["dt"] = dt;
-                R.parseEvalQ("mysetup$dt <- dt");
-            }
-            if (mpi_buffer[count+3] != current_sim_time) { //current simulation time ('age' of simulation)
-                current_sim_time = mpi_buffer[count+3];
-                R["simulation_time"] = current_sim_time;
-                R.parseEvalQ("mysetup$simulation_time <- simulation_time");
-            }
-            /* 4th double value is currently a placeholder */
-            // if (mpi_buffer[count+4] != placeholder) {
-            //     placeholder = mpi_buffer[count+4];
-            //     R["mysetup$placeholder"] = placeholder;
-            // }
-
-            /* get df with right structure to fill in work package */
-            R.parseEvalQ("tmp2 <- head(mysetup$state_C, work_package_size)");
-            // R.parseEval("print(rownames(tmp2)[1:5])");
-            // R.parseEval("print(head(tmp2, 2))");
-            // R.parseEvalQ("tmp2$id <- as.double(rownames(tmp2))");
-
-            Rcpp::DataFrame buffer = R.parseEval("tmp2");
-
-            if (dht_enabled)
-            {
-                // DEBUG
-                // cout << "RANK " << world_rank << " start checking DHT\n";
-
-                //resize helper vector dht_flags of work_package_size changes
-                if ((int) dht_flags.size() != local_work_package_size) {
-                    dht_flags.resize(local_work_package_size, true); //set size
-                    dht_flags.assign(local_work_package_size, true); //assign all elements to true (default)
-                } 
-                
-                dht_get_start = MPI_Wtime();
-                check_dht(R, local_work_package_size, dht_flags, mpi_buffer);
-                dht_get_end = MPI_Wtime();
-
-                //DEBUG
-                //cout << "RANK " << world_rank << " checking DHT complete \n";
-
-                R["dht_flags"] = as<LogicalVector>(wrap(dht_flags));
-                //R.parseEvalQ("print(head(dht_flags))");
-            }
-
-            /* work */
-            convert_C_buffer_2_R_Dataframe(mpi_buffer, buffer);
-            R["work_package_full"] = buffer;
-            //R["work_package"] = buffer;
-            
-            //DEBUG
-            //R.parseEvalQ("print(head(work_package_full))");
-            //R.parseEvalQ("print( c(length(dht_flags), nrow(work_package_full)) )");
-
-            if (dht_enabled)
-            {
-                R.parseEvalQ("work_package <- work_package_full[dht_flags,]");
-            } else {
-                R.parseEvalQ("work_package <- work_package_full");
-            }
-
-            //DEBUG
-            // R.parseEvalQ("print(head(work_package),2)");
-            
-            // R.parseEvalQ("rownames(work_package) <- work_package$id");
-            // R.parseEval("print(paste('id %in% colnames(work_package)', 'id' %in% colnames(work_package)");
-            // R.parseEvalQ("id_store <- rownames(work_package)"); //"[, ncol(work_package)]");
-            // R.parseEvalQ("work_package$id <- NULL");
-            R.parseEvalQ("work_package <- as.matrix(work_package)");
-            
-            unsigned int nrows = R.parseEval("nrow(work_package)");
-
-            if (nrows > 0)
-            {
-                /*Single Line error Workaround*/
-                if (nrows <=1)
-                {
-                    //duplicate line to enable correct simmulation
-                    R.parseEvalQ("work_package <- work_package[rep(1:nrow(work_package), times = 2), ]");
-                }
-
-                phreeqc_count++;
-
-                phreeqc_time_start = MPI_Wtime();
-                // MDL
-                // R.parseEvalQ("print('Work_package:\n'); print(head(work_package , 2)); cat('RCpp: worker_function:', local_rank, ' \n')");
-                R.parseEvalQ("result <- as.data.frame(slave_chemistry(setup=mysetup, data = work_package))");
-                phreeqc_time_end = MPI_Wtime();
-                // R.parseEvalQ("result$id <- id_store");
-            } else 
-            {
-                //cout << "Work-Package is empty, skipping phreeqc!" << endl;
-            }
-
-
-            if (dht_enabled)
-            {
-                R.parseEvalQ("result_full <- work_package_full");
-                if (nrows > 0)
-                    R.parseEvalQ("result_full[dht_flags,] <- result");
-            } else {
-                R.parseEvalQ("result_full <- result");
-            }
-
-            Rcpp::DataFrame result = R.parseEval("result_full");
-            convert_R_Dataframe_2_C_buffer(mpi_buffer_results, result);
-
-            /* send results to master */
-            MPI_Request send_req;
-            MPI_Isend(mpi_buffer_results, count, MPI_DOUBLE, 0, TAG_WORK, MPI_COMM_WORLD, &send_req);
-
-            if (dht_enabled)
-            {
-                dht_fill_start = MPI_Wtime();
-                fill_dht(R, local_work_package_size, dht_flags, mpi_buffer, mpi_buffer_results);
-                dht_fill_end = MPI_Wtime();
-
-                timing[1] += dht_get_end - dht_get_start;
-                timing[2] += dht_fill_end - dht_fill_start;
-            }
-
-            timing[0] += phreeqc_time_end - phreeqc_time_start;
-
-            MPI_Wait(&send_req,MPI_STATUS_IGNORE);
-
-        } else if (probe_status.MPI_TAG == TAG_FINISH) 
-        {   /* recv and die */
-            /* before death, submit profiling/timings to master*/
-
-            MPI_Recv(NULL, 0, MPI_DOUBLE, 0, TAG_FINISH, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-
-            //timings
-            MPI_Send(timing, 3, MPI_DOUBLE, 0, TAG_TIMING, MPI_COMM_WORLD);
-
-            MPI_Send(&phreeqc_count, 1, MPI_INT, 0, TAG_TIMING, MPI_COMM_WORLD);
-            MPI_Send(&cummul_idle, 1, MPI_DOUBLE, 0, TAG_TIMING, MPI_COMM_WORLD);
-
-            if(dht_enabled) 
-            {
-                //dht_perf
-                dht_perf[0] = dht_hits;
-                dht_perf[1] = dht_miss;
-                dht_perf[2] = dht_collision;
-                MPI_Send(dht_perf, 3, MPI_UNSIGNED_LONG_LONG, 0, TAG_DHT_PERF, MPI_COMM_WORLD);
-            }
-
-            break;
-
-        } else if ((probe_status.MPI_TAG == TAG_DHT_STATS)) {
-            MPI_Recv(NULL, 0, MPI_DOUBLE, 0, TAG_DHT_STATS, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-            print_statistics();
-            MPI_Barrier(MPI_COMM_WORLD);
-        } else if ((probe_status.MPI_TAG == TAG_DHT_STORE)) {
-            char* outdir;
-            MPI_Get_count(&probe_status, MPI_CHAR, &count);
-            outdir = (char *) calloc(count + 1, sizeof(char));
-            MPI_Recv(outdir, count, MPI_CHAR, 0, TAG_DHT_STORE, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-            int res = table_to_file((char *) outdir);
-            if (res != DHT_SUCCESS) {
-                if (world_rank == 2) cerr << "CPP: Worker: Error in writing current state of DHT to file (TAG_DHT_STORE)" << endl;
-            } else {
-                if (world_rank == 2) cout << "CPP: Worker: Successfully written DHT to file " << outdir << endl;
-            }
-            free(outdir);
-            MPI_Barrier(MPI_COMM_WORLD);
-        }
-    }
-}
diff --git a/src/worker.h b/src/worker.h
deleted file mode 100644
index 221a1f7a3..000000000
--- a/src/worker.h
+++ /dev/null
@@ -1,17 +0,0 @@
-#pragma once
-#include <RInside.h>
-
-using namespace std;
-using namespace Rcpp;
-
-/*Functions*/
-void worker_function(RInside &R);
-
-
-/*Globals*/
-#define TAG_WORK 42
-#define TAG_FINISH 43
-#define TAG_TIMING 44
-#define TAG_DHT_PERF 45
-#define TAG_DHT_STATS 46
-#define TAG_DHT_STORE 47
\ No newline at end of file