merge with old repo

cmake/modules/CTestTestfile.cmake

-# CMake generated Testfile for 
-# Source directory: /home/dion/codes/dorie/dorie/cmake/modules
-# Build directory: /home/dion/codes/dorie/dorie/cmake/modules
-# 
-# This file includes the relevant testing commands required for 
-# testing this directory and lists subdirectories to be tested as well.

cmake/modules/DorieMacros.cmake

 # File for module specific CMake tests.
 
 # find all required packages
-FIND_PACKAGE(HDF5 REQUIRED COMPONENTS C)
-FIND_PACKAGE(FFTW REQUIRED)
-FIND_PACKAGE(SuperLU REQUIRED)
-FIND_PACKAGE(MPI REQUIRED)
-FIND_PACKAGE(UG REQUIRED)
-
-FIND_PACKAGE(METIS)
-FIND_PACKAGE(ParMETIS)
+FIND_PACKAGE (HDF5 REQUIRED)
+FIND_PACKAGE (FFTW REQUIRED)
+FIND_PACKAGE (SuperLU REQUIRED)
+FIND_PACKAGE (MPI REQUIRED)
+FIND_PACKAGE (METIS REQUIRED)
+FIND_PACKAGE (ParMETIS REQUIRED)
+FIND_PACKAGE (UG REQUIRED)
 
 include_directories(${FFTW_INCLUDES})
 include_directories(${HDF5_INCLUDE_DIRS})

cmake/modules/InstallPythonPackage.cmake

+# This cmake module provides macros that install python packages into the virtualenv
+# that is shared by all dune modules that depend on dune-python.
+#
+# .. cmake_function:: dune_install_python_package
+#
+#    .. cmake_param:: PATH
+#       :required:
+#       :single:
+#
+#       Relative path to the given python package source code.
+#
+#    .. cmake_param:: MAJOR_VERSION
+#       :single:
+#
+#       Set to "2" or "3" if your python package only works with
+#       python2 or python3. This will restrict the installation process to that
+#       python version.
+#
+#    .. cmake_param:: NO_PIP
+#       :option:
+#
+#       Instead of :code:`pip -e`, `python setup.py develop` will be used as
+#       the installation command.
+#
+#    .. cmake_param:: NO_EDIT
+#       :option:
+#
+#       Will drop :code:`pip`s :code:`-e` option (or switch :code:`develop` to :code:`install`).
+#       Only use this option if your package is incompatible with :code:`-e`.
+#
+#    Installs the python package located at path into the virtualenv used by dune-python
+#    The package at the given location is expected to be a pip installable package.
+#    Also marks the given python package for global installation during :code:`make install`.
+#    By default, the python package will then be installed into the system-wide site-packages
+#    location. If you do not want to install it there, or you do not have permission to,
+#    you may optionally set :ref:`DUNE_PYTHON_INSTALL_USER` to a username. The
+#    packages will then be installed in the home directory of that user.
+#    This is done through pips :code:`--user` option. Installation in arbitrary locations is not
+#    supported to minimize :code:`PYTHONPATH` issues.
+#
+# .. cmake_variable:: DUNE_PYTHON_INSTALL_USER
+#
+#    dune-python only supports two ways of globally installing python packages during
+#    :code:`make install`:
+#
+#    * Into standard system paths (default)
+#    * Into the standard python path of a users home directory (through :code:`pip --user`)
+#
+#    Set this variable to a username to use the latter.
+#
+
+include(CheckPythonPackage)
+
+function(dorie_install_python_package)
+  # Parse Arguments
+  set(OPTION NO_PIP NO_EDIT QUIET)
+  set(SINGLE PATH MAJOR_VERSION)
+  set(MULTI)
+  include(CMakeParseArguments)
+  cmake_parse_arguments(PYINST "${OPTION}" "${SINGLE}" "${MULTI}" ${ARGN})
+  if(PYINST_UNPARSED_ARGUMENTS)
+    message(WARNING "Unparsed arguments in dune_install_python_package: This often indicates typos!")
+  endif()
+
+  # apply defaults
+  if(NOT PYINST_MAJOR_VERSION)
+    set(PYINST_MAJOR_VERSION 2 3)
+  endif()
+
+  # check for available pip packages
+  check_python_package(PACKAGE pip
+                       INTERPRETER ${PYTHON2_EXECUTABLE}
+                       RESULT PIP2_FOUND)
+  check_python_package(PACKAGE pip
+                       INTERPRETER ${PYTHON3_EXECUTABLE}
+                       RESULT PIP3_FOUND)
+
+  # Construct the installation command strings from the given options
+  if(PYINST_NO_PIP)
+    if(PYINST_NO_EDIT)
+      set(INST_COMMAND install)
+    else()
+      set(INST_COMMAND develop)
+    endif()
+    set(VENV_INSTALL_COMMAND python setup.py ${INST_COMMAND})
+  else()
+    set(EDIT_OPTION)
+    if(NOT PYINST_NO_EDIT)
+      set(EDIT_OPTION -e)
+    endif()
+    if(PYINST_QUIET)
+      set(EDIT_OPTION "-q ${EDIT_OPTION}")
+    endif()
+    set(VENV_INSTALL_COMMAND python -m pip install ${EDIT_OPTION} .)
+  endif()
+
+  # Construct the interpreter options for global installation
+  if(PYINST_NO_PIP)
+    set(SYSTEM_INSTALL_OPTIONS setup.py install)
+    if(DUNE_PYTHON_INSTALL_USER)
+      message("Error message: Incompatible options - NO_PIP and DUNE_PYTHON_INSTALL_USER")
+    endif()
+  else()
+    set(USER_STRING "")
+    if(DUNE_PYTHON_INSTALL_USER)
+      set(USER_STRING --user ${DUNE_PYTHON_INSTALL_USER})
+    endif()
+    set(SYSTEM_INSTALL_OPTIONS -m pip install ${USER_STRING} .)
+  endif()
+
+  # iterate over the given interpreters
+  foreach(version ${PYINST_MAJOR_VERSION})
+    # install the package into the virtual env
+    execute_process(COMMAND ${CMAKE_BINARY_DIR}/dune-env-${version} ${VENV_INSTALL_COMMAND}
+                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${PYINST_PATH})
+
+    # define a rule on how to install the package during make install
+    if(PIP${version}_FOUND)
+      install(CODE "execute_process(COMMAND ${PYTHON${version}_EXECUTABLE} ${SYSTEM_INSTALL_OPTIONS}
+                                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${PYINST_PATH})
+                   ")
+    else()
+      install(CODE "message(FATAL_ERROR \"You need the python${version} package pip installed on the host system to install a module that contains python code\")")
+    endif()
+  endforeach()
+endfunction()

cmake/modules/Makefile

-# CMAKE generated file: DO NOT EDIT!
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-
-# Default target executed when no arguments are given to make.
-default_target: all
-
-.PHONY : default_target
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-.SUFFIXES:
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-.SUFFIXES: .hpux_make_needs_suffix_list
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-
-# The shell in which to execute make rules.
-SHELL = /bin/sh
-
-# The CMake executable.
-CMAKE_COMMAND = /usr/bin/cmake
-
-# The command to remove a file.
-RM = /usr/bin/cmake -E remove -f
-
-# Escaping for special characters.
-EQUALS = =
-
-# The top-level source directory on which CMake was run.
-CMAKE_SOURCE_DIR = /home/dion/codes/dorie/dorie
-
-# The top-level build directory on which CMake was run.
-CMAKE_BINARY_DIR = /home/dion/codes/dorie/dorie
-
-#=============================================================================
-# Targets provided globally by CMake.
-
-# Special rule for the target test
-test:
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running tests..."
-	/usr/bin/ctest --force-new-ctest-process $(ARGS)
-.PHONY : test
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-.PHONY : test/fast
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-# Special rule for the target package
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-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool..."
-	cd /home/dion/codes/dorie/dorie && /usr/bin/cpack --config ./CPackConfig.cmake
-.PHONY : package
-
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-
-.PHONY : package/fast
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-.PHONY : edit_cache
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-package_source:
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool for source..."
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-.PHONY : package_source
-
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-.PHONY : rebuild_cache
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-install/strip: preinstall
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-	/usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
-.PHONY : install/strip
-
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-install/strip/fast: install/strip
-
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-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
-	/usr/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
-.PHONY : install/local
-
-# Special rule for the target install/local
-install/local/fast: install/local
-
-.PHONY : install/local/fast
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-# Special rule for the target list_install_components
-list_install_components:
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
-.PHONY : list_install_components
-
-# Special rule for the target list_install_components
-list_install_components/fast: list_install_components
-
-.PHONY : list_install_components/fast
-
-# Special rule for the target install
-install: preinstall
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install
-
-# Special rule for the target install
-install/fast: preinstall/fast
-	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
-	/usr/bin/cmake -P cmake_install.cmake
-.PHONY : install/fast
-
-# The main all target
-all: cmake_check_build_system
-	cd /home/dion/codes/dorie/dorie && $(CMAKE_COMMAND) -E cmake_progress_start /home/dion/codes/dorie/dorie/CMakeFiles /home/dion/codes/dorie/dorie/cmake/modules/CMakeFiles/progress.marks
-	cd /home/dion/codes/dorie/dorie && $(MAKE) -f CMakeFiles/Makefile2 cmake/modules/all
-	$(CMAKE_COMMAND) -E cmake_progress_start /home/dion/codes/dorie/dorie/CMakeFiles 0
-.PHONY : all
-
-# The main clean target
-clean:
-	cd /home/dion/codes/dorie/dorie && $(MAKE) -f CMakeFiles/Makefile2 cmake/modules/clean
-.PHONY : clean
-
-# The main clean target
-clean/fast: clean
-
-.PHONY : clean/fast
-
-# Prepare targets for installation.
-preinstall: all
-	cd /home/dion/codes/dorie/dorie && $(MAKE) -f CMakeFiles/Makefile2 cmake/modules/preinstall
-.PHONY : preinstall
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-# Prepare targets for installation.
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-	cd /home/dion/codes/dorie/dorie && $(MAKE) -f CMakeFiles/Makefile2 cmake/modules/preinstall
-.PHONY : preinstall/fast
-
-# clear depends
-depend:
-	cd /home/dion/codes/dorie/dorie && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
-.PHONY : depend
-
-# Help Target
-help:
-	@echo "The following are some of the valid targets for this Makefile:"
-	@echo "... all (the default if no target is provided)"
-	@echo "... clean"
-	@echo "... depend"
-	@echo "... test"
-	@echo "... package"
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-
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-# No rule that depends on this can have commands that come from listfiles
-# because they might be regenerated.
-cmake_check_build_system:
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-.PHONY : cmake_check_build_system
-

cmake/modules/cmake_install.cmake

-# Install script for directory: /home/dion/codes/dorie/dorie/cmake/modules
-
-# Set the install prefix
-if(NOT DEFINED CMAKE_INSTALL_PREFIX)
-  set(CMAKE_INSTALL_PREFIX "/usr/local")
-endif()
-string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
-
-# Set the install configuration name.
-if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
-  if(BUILD_TYPE)
-    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
-           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
-  else()
-    set(CMAKE_INSTALL_CONFIG_NAME "")
-  endif()
-  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
-endif()
-
-# Set the component getting installed.
-if(NOT CMAKE_INSTALL_COMPONENT)
-  if(COMPONENT)
-    message(STATUS "Install component: \"${COMPONENT}\"")
-    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
-  else()
-    set(CMAKE_INSTALL_COMPONENT)
-  endif()
-endif()
-
-# Install shared libraries without execute permission?
-if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
-  set(CMAKE_INSTALL_SO_NO_EXE "1")
-endif()
-
-if(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
-  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/dune/cmake/modules" TYPE FILE FILES "/home/dion/codes/dorie/dorie/cmake/modules/DorieMacros.cmake")
-endif()
-

doc/CMakeLists.txt

+message(STATUS "Python modules path: ${DORIE_PYTHON_MODULES}")
+
 add_subdirectory("doxygen")
-add_subdirectory("parameters")
-add_subdirectory("sphinx")
+add_subdirectory("default_files")
+
+# copy static files to build tree
+file(COPY ${CMAKE_CURRENT_LIST_DIR}/examples DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+file(COPY ${CMAKE_CURRENT_LIST_DIR}/figures DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
+include(DuneSphinxCMakeDoc)
+dune_cmake_sphinx_doc()
 if(TARGET sphinx_html)
   add_dependencies(sphinx_html doxygen_dorie)
 endif()

doc/sphinx/conf.py.in → doc/conf.py.in

@@ -26,15 +26,19 @@ import shlex
 
 deploy_mode = '@DEPLOY_SPHINX@' in ['1',"True","true"]
 
+rst_prolog = """
+.. |branch| replace:: @DEPLOY_SPHINX_GITBRANCH@
+"""
+
 def setup(app): # pass this along
     app.add_config_value('deploy_mode', '', 'env')
 
 
 sys.path.append('@DUNE_SPHINX_EXT_PATH@')
-python_modules = '@DORIE_PYTHON_MODULES@'
+#python_modules = '@DORIE_PYTHON_MODULES@'
 
-for module in python_modules.split(";"):
-    sys.path.append(module)
+#for module in python_modules.split(";"):
+#    sys.path.append(module)
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #needs_sphinx = '1.0'
@@ -319,5 +323,5 @@ texinfo_documents = [
 
 # -- Breathe configuration -----------------------------------------------
 
-breathe_projects = { "dorie": "@CMAKE_CURRENT_BINARY_DIR@/../doxygen/xml" }
+breathe_projects = { "dorie": "@CMAKE_CURRENT_BINARY_DIR@/doxygen/xml" }
 breathe_default_project = "dorie"

doc/default_files/2d_infiltr.bcdat

+spatial_resolution_north 0
+spatial_resolution_south 0
+spatial_resolution_west -1
+spatial_resolution_east -1
+number_BC_change_times 1
+0 neumann -5.55e-6 dirichlet 0
\ No newline at end of file

doc/default_files/3d_infiltr.bcdat

+spatial_resolution_north_we 0
+spatial_resolution_north_fb 0
+spatial_resolution_south_we 0
+spatial_resolution_south_fb 0
+spatial_resolution_west_sn -1
+spatial_resolution_west_fb -1
+spatial_resolution_east_sn -1
+spatial_resolution_east_fb -1
+spatial_resolution_front_sn -1
+spatial_resolution_front_we -1
+spatial_resolution_back_sn -1
+spatial_resolution_back_we -1
+number_BC_change_times 1
+0 neumann -5.55e-6 dirichlet 0
\ No newline at end of file

doc/default_files/CMakeLists.txt

+function(scrape_parameters SOURCE_DIR XML_FILE CSS OUTPUT RESULT_NAME)
+    message(STATUS "Running parameter scraper on sources ${SOURCE_DIR}")
+    if(DEPLOY_SPHINX_SOURCE_URL)
+        execute_process(COMMAND ${CMAKE_BINARY_DIR}/dune-env scrape_folder.py --source ${SOURCE_DIR}
+                          --xml ${XML_FILE} --out ${OUTPUT} --css ${CSS}
+                          --source_url ${DEPLOY_SPHINX_SOURCE_URL}
+                          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                          RESULT_VARIABLE RETURN_CODE)
+    else()
+        execute_process(COMMAND ${CMAKE_BINARY_DIR}/dune-env scrape_folder.py --source ${SOURCE_DIR}
+                          --xml ${XML_FILE} --out ${OUTPUT} --css ${CSS}
+                          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                          RESULT_VARIABLE RETURN_CODE)
+    endif()
+    set(${RESULT_NAME} ${RETURN_CODE} PARENT_SCOPE)
+endfunction()
+
+file(COPY ${CMAKE_CURRENT_LIST_DIR} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/..)
+
+scrape_parameters(${PROJECT_SOURCE_DIR}/dune/dorie-rfg ${CMAKE_CURRENT_SOURCE_DIR}/field-parameters.xml ${CMAKE_CURRENT_SOURCE_DIR}/parameters.css "default_pf.ini field-parameters.html field-parameters.rst" FIELDPARSCRAPE_RETURN)
+if (${FIELDPARSCRAPE_RETURN} GREATER 0)
+    message(FATAL_ERROR "Parameter scraper failed. DORiE can not be built.")
+endif()
+
+scrape_parameters(${PROJECT_SOURCE_DIR}/dune/dorie ${CMAKE_CURRENT_SOURCE_DIR}/parameters.xml ${CMAKE_CURRENT_SOURCE_DIR}/parameters.css "default.ini parameters.html parameters.rst" PARSCRAPE_RETURN)
+if (${PARSCRAPE_RETURN} GREATER 0)
+    message(FATAL_ERROR "Parameter scraper failed. DORiE can not be built.")
+endif()

doc/default_files/field-parameters.xml

+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+If you want to use any special characters, you will need to define them here.
+A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
+-->
+
+<!DOCTYPE naughtyxml [
+    <!ENTITY alpha "&#945;">
+    <!ENTITY beta "&#946;">
+    <!ENTITY eta "&#951;">
+    <!ENTITY tau "&#964;">
+    <!ENTITY times "&#215;">
+]>
+
+<!--
+XML file hierarchy:
+<dorie> -> <category> -> <parameter> -> (parameter attributes)
+
+Possible parameter attributes:
+
+  definition: meaning of the parameter, will only show up in html output
+  suggestion: standard value in created parameter files
+  values: possible values, will only show up in html output
+  comment: extra comment, will only show up in parameter files
+
+All attributes are optional.
+
+The parser supports rudimentary markdown / styling. You can add a paragraph by
+adding an empty line, make text **bold** or ``monospaced``.
+-->
+
+<dorie>
+  <category name="general" hidden="true">
+
+    <parameter name="generator">
+      <definition>
+        Specifies which parameter field generator module should be used.
+      </definition>
+      <values> image, csv, fft, hdf5 </values>
+      <suggestion> csv </suggestion>
+      <comment> One of: image, csv, fft, hdf5 </comment>
+    </parameter>
+
+    <parameter name="inputFile">
+      <definition>
+        Path to file holding the parameter distribution data (i.e., image, CSV file,
+        or HDF5 file). Has no effect when using FFT generator.
+      </definition>
+      <values> path </values>
+    </parameter>
+
+    <parameter name="outputFile">
+      <definition>
+        Output file name of the parameter field array.
+      </definition>
+      <values> path </values>
+      <suggestion> field.h5 </suggestion>
+    </parameter>
+
+    <parameter name="parameterization">
+      <definition>
+        Parameterization to be used when mapping field value to parameter.
+        Essentially sets which ``parameters.&lt;parameterization&gt;.&lt;x&gt;``
+        values should be used.
+      </definition>
+      <values> vanGenuchten </values>
+      <suggestion> vanGenuchten </suggestion>
+    </parameter>
+
+    <parameter name="overwrite">
+      <definition>
+        Whether an existing parameter field array should be overwritten.
+      </definition>
+      <values> bool </values>
+      <suggestion> false </suggestion>
+    </parameter>
+  </category>
+
+  <category name="parameters.vanGenuchten.1" hidden="true">
+    <parameter name="theta_r">
+      <definition>
+        Residual water content of medium 1, used in the Mualem-van Genuchten
+        parameterization. Default values for sand, according to Soil Physics, p. 92.
+      </definition>
+      <values> float </values>
+      <suggestion> 0.03 </suggestion>
+    </parameter>
+
+    <parameter name="theta_s">
+      <definition> Saturated water content. </definition>
+      <values> float </values>
+      <suggestion> 0.32 </suggestion>
+    </parameter>
+
+    <parameter name="alpha">
+      <definition> log10(&alpha;) in the van Genuchten parameterization. Units: [1/m] </definition>
+      <values> float </values>
+      <suggestion> -2.3 </suggestion>
+    </parameter>
+
+    <parameter name="tau">
+      <definition> &tau; in the Mualem parameterization of the hydraulic permeability. </definition>
+      <values> float </values>
+      <suggestion> -1.1 </suggestion>
+    </parameter>
+
+    <parameter name="n">
+      <definition> n in the van Genuchten parameterization. </definition>
+      <values> float </values>
+      <suggestion> 4.17 </suggestion>
+    </parameter>
+
+    <parameter name="k0">
+      <definition> Saturated hydraulic conductivity. Units: [m/s] </definition>
+      <values> float </values>
+      <suggestion> 2.2E-5 </suggestion>
+    </parameter>
+  </category>
+
+  <category name="parameters.vanGenuchten.2" hidden="true">
+    <parameter name="theta_r">
+      <definition>
+        Residual water content of medium 2, used in the Mualem-van Genuchten
+        parameterization. Default values for silt, according to Soil Physics, p. 92.
+      </definition>
+      <values> float </values>
+      <suggestion> 0.01 </suggestion>
+    </parameter>
+
+    <parameter name="theta_s">
+      <definition> Saturated water content. </definition>
+      <values> float </values>
+      <suggestion> 0.41 </suggestion>
+    </parameter>
+
+    <parameter name="alpha">
+      <definition> log10(&alpha;) in the van Genuchten parameterization. Units: [1/m] </definition>
+      <values> float </values>
+      <suggestion> -0.7 </suggestion>
+    </parameter>
+
+    <parameter name="tau">
+      <definition> &tau; in the Mualem parameterization of the hydraulic permeability. </definition>
+      <values> float </values>
+      <suggestion> .0 </suggestion>
+    </parameter>
+
+    <parameter name="n">
+      <definition> n in the van Genuchten parameterization. </definition>
+      <values> float </values>
+      <suggestion> 1.3 </suggestion>
+    </parameter>
+