Add mkdocs documentation

CMakeLists.txt

@@ -16,7 +16,6 @@ dune_enable_all_packages(MODULE_LIBRARIES amdis fmt)
 
 add_subdirectory("bin")
 add_subdirectory("cmake/modules")
-add_subdirectory("doc")
 add_subdirectory("examples" EXCLUDE_FROM_ALL)
 add_subdirectory("libs")
 add_subdirectory("src")

doc/CMakeLists.txt

-add_subdirectory("doxygen")

doc/Installation.md

-Installation instructions
-=========================
-We provide a *cmake*-based configuration and use the `dunecontrol` build system.
-Simply run
-
-```
-dunecontrol --current all
-```
-
-The `dunecontrol` script searches for the required
-(and suggested) dune modules this library depends on. These include:
-- [dune-common](https://gitlab.dune-project.org/core/dune-common)
-- [dune-geometry](https://gitlab.dune-project.org/core/dune-geometry)
-- [dune-grid](https://gitlab.dune-project.org/core/dune-grid)
-- [dune-localfunctions](https://gitlab.dune-project.org/core/dune-localfunctions)
-- [dune-istl](https://gitlab.dune-project.org/core/dune-istl)
-- [dune-typetree](https://gitlab.dune-project.org/staging/dune-typetree)
-- [dune-functions](https://gitlab.dune-project.org/staging/dune-functions)
-
-(See the file `dune.module` for an up-to-date list of dependencies). The dune modules
-can be obtained from https://gitlab.dune-project.org and need to be found in a
-subdirectory of `DUNE_CONTROL_PATH`. See also https://dune-project.org/doc/installation
-for details about the installation of dune modules.
-
-Additionally the following optional libraries can be used:
-- [MTL4](https://gitlab.math.tu-dresden.de/spraetor/mtl4) (use this fork to get up-to-date changes)
-- [Eigen3](http://eigen.tuxfamily.org) >= 3.3
-- [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
-- libalberta >= 3.0 (For Alberta-Grids)
-
-And a compiler that supports the C++14 standard, e.g. g++ >= 5.0 and clang >= 3.6, and cmake >= 3.1.
-
-By default, the `dune-istl` linear-algebra backend is used. To choose one of `ISTL`, `MTL`, or `EIGEN`, you can specify the cmake parameter `-DBACKEND=[ISTL,MTL,EIGEN]`.
-
-If your MTL4 installation is not found by default, you have to specify the path,
-where the file `MTLConfig.cmake` is found, here called `MTL_ROOT`. Then simply use
-`dunecontrol` to configure and `cmake` to build:
-
-```
-CMAKE_FLAGS="-DBACKEND=MTL -DMTL_DIR:PATH=[MTL_ROOT]" dunecontrol --current configure
-cmake --build build-cmake
-```
-
-Install Dune modules
---------------------
-To install all required Dune modules you can either install a debian package (Version 2.6 required), using source packages (e.g. [Version 2.6](https://dune-project.org/releases/2.6.0/)), or install everything from the repository:
-
-```bash
-cd ${SOURCE_DIR}
-git clone https://gitlab.dune-project.org/core/dune-common.git
-git clone https://gitlab.dune-project.org/core/dune-geometry.git
-git clone https://gitlab.dune-project.org/core/dune-grid.git
-git clone https://gitlab.dune-project.org/core/dune-localfunctions.git
-git clone https://gitlab.dune-project.org/core/dune-istl.git
-git clone https://gitlab.dune-project.org/staging/dune-typetree.git
-git clone https://gitlab.dune-project.org/staging/dune-functions.git
-```
-
-If additional grid types are required in the application (e.g. [AlbertaGrid](http://www.mathematik.uni-stuttgart.de/fak8/ians/lehrstuhl/nmh/downloads/alberta/), [dune-alugrid](https://gitlab.dune-project.org/extensions/dune-alugrid), or [dune-uggrid](https://gitlab.dune-project.org/staging/dune-uggrid). See also the list of dune modules on [dune-project.org](https://dune-project.org/groups/grid/)), these must be installed separately. Thereby, all Dune modules can be downloaded into the `${SOURCE_DIR}` folder. AlbertaGrid requires to set the cmake flag `-DALBERTA_ROOT` when configuring the dune-grid module.
-
-To compile all Dune modules maybe some flags need to be given to cmake. When using the `dunecontrol` script this can be accomplished by providing an options file `dune.opts`
-
-```bash
-CMAKE_FLAGS="-DALBERTA_ROOT:PATH=${ALBERTA_ROOT} \
-             -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR}"
-MAKE_FLAGS="-j4 install"
-```
-
-This specifies the location of the AlbertaGrid installation and an installation dir `${INSTALL_DIR}` for the Dune modules.
-
-I prefer an out-of-source build and thus specify a common build directory for all Dune modules:
-
-```bash
-mkdir -p /tmp/dune/build
-DUNE_CONTROL_PATH=${SOURCE_DIR} ${SOURCE_DIR}/dune-common/bin/dunecontrol --opts=dune.opts --builddir=/tmp/dune/build all
-```
-
-When the Dune modules are installed, the `bin/` directory in `${INSTALL_DIR}` can be added to the PATH variable to make `dunecontrol` and other scripts available directly.

doc/Mainpage.md

-AMDiS    {#mainpage}
-=====
-The *Adaptive Multi-Dimensional Simulation Toolbox* (AMDiS) is a Finite-Element
-discretization module allowing for fast prototyping of PDEs on adaptively refined
-grids. It is implemented on top of the [Dune](https://dune-project.org) framework.
-
-Tutorial
---------
-As an example of usage, we want to solve an elliptic PDE, the Poisson equation,
-\f$ -\Delta u = f \f$ in \f$ \Omega \f$ with \f$ u = g \f$ on a subset of the boundary
-\f$ \Gamma\subset\partial\Omega \f$. For simplicity, we assume \f$ f(x) \equiv -1 \f$
-and \f$ g(x) \equiv 0 \f$, the domain \f$ \Omega \f$ a square domain \f$ [0,1]^2 \f$
-and \f$ \Gamma \f$ the lower and left edge of the boundary.
-
-~~~~~~~~~~~~~~~{.cpp}
-#include <amdis/AMDiS.hpp>
-#include <amdis/AdaptInfo.hpp>
-#include <amdis/AdaptStationary.hpp>
-#include <amdis/ProblemStat.hpp>
-
-// The namespace all AMDiS classes and functions are defined in
-using namespace AMDiS;
-
-// A dune grid type
-using Grid = Dune::AlbertaGrid<GRIDDIM, WORLDDIM>;
-
-// A dune-functions globalBasis wrapped in a struct,
-// here representing local polynomial shape functions of degree 1
-using Traits = LagrangeBasis<Grid::LeafGridView, 1>;
-
-int main(int argc, char* argv[])
-{
-  // Initialize linear-algebra backend and read parameters from file
-  Environment env(argc, argv);
-
-  // Create a problem class containing all data for assembling
-  ProblemStat<Traits> prob("poisson");
-  // Initialize grid, globalBasis, solution vector and systenmatrix
-  prob.initialize(INIT_ALL);
-
-  // An operator representing the weak laplacian with coefficient = 1.0
-  auto opL = makeOperator(tag::gradtest_gradtrial{}, 1.0);
-  prob.addMatrixOperator(opL, 0, 0);
-
-  // An rhs-operator representing an analytic function f(x) = -1
-  auto opF = makeOperator(tag::test{}, [](auto const& x) { return -1.0; }, 0);
-  prob.addVectorOperator(opF, 0);
-
-  // Define the boundary Gamma
-  auto predicate = [](auto const& x){ return x[0] < 1.e-8 || x[1] < 1.e-8; };
-  // Set a value g(x) = 0 at this part of the boundary
-  prob.addDirichletBC(predicate, 0, 0, 0.0);
-
-  // assemble and solve the linear system
-  AdaptInfo adaptInfo("adapt");
-  AdaptStationary adapt("adapt", prob);
-  adapt.adapt();
-
-  return 0;
-}
-~~~~~~~~~~~~~~~
-
-Notes
------
-An AMDiS program consists of three main incredients:
-1. A Problem class that holds all information necessary for assembling a linear
-   system, see \ref ProblemStat.
-2. Operators describing the (bi)linear-form of your PDE, see \ref operators.
-3. A parameter file controlling several parts of the solution process, see \ref Initfile.

doc/doxygen/CMakeLists.txt

-# shortcut for creating the Doxyfile.in and Doxyfile
-add_doxygen_target()

doc/doxygen/Doxylocal

-# This file contains local changes to the doxygen configuration
-# please us '+=' to add file/directories to the lists
-
-PROJECT_NAME = AMDiS
-FILE_PATTERNS          += *.hpp \
-                          *.cpp \
-                          *.md
-
-HIDE_SCOPE_NAMES       = YES
-HIDE_UNDOC_CLASSES     = NO
-INTERNAL_DOCS          = NO
-MARKDOWN_SUPPORT       = YES
-GENERATE_XML           = YES
-
-EXCLUDE_SYMBOLS        = AMDiS::Impl \
-                         AMDiS::Math::Impl_ \
-                         AMDiS::Concepts::Impl_ \
-                         AMDiS::detail \
-                         itl::details
-
-PREDEFINED            += HAVE_UMFPACK \
-                         HAVE_ALBERTA \
-                         HAVE_UG \
-                         AMDIS_HAS_MTL \
-                         AMDIS_HAS_HYPRE 
-
-# The INPUT tag can be 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.
-
-INPUT                 += @top_srcdir@/src/amdis \
-                         @top_srcdir@/src/amdis/common \
-                         @top_srcdir@/src/amdis/functions \
-                         @top_srcdir@/src/amdis/gridfunctions \
-                         @top_srcdir@/src/amdis/linearalgebra \
-                         @top_srcdir@/src/amdis/linearalgebra/mtl \
-                         @top_srcdir@/src/amdis/localoperators \
-                         @top_srcdir@/src/amdis/operations \
-                         @top_srcdir@/src/amdis/typetree \
-                         @top_srcdir@/src/amdis/utility \
-                         @top_srcdir@/doc
-# see e.g. dune-grid for the examples of mainpage and modules
-#INPUT                 += @srcdir@/mainpage \
-#                         @srcdir@/modules
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# 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.
-
-EXCLUDE               += @top_srcdir@/src/amdis/linearalgebra/eigen \
-                         @top_srcdir@/src/amdis/linearalgebra/istl \
-                         @top_srcdir@/src/amdis/linearalgebra/petsc
-
-# 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          += @top_srcdir@/examples
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-# IMAGE_PATH            += @top_srcdir@/doc/pics

docs/Doxyfile

+# Doxyfile 1.8.13
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+DOXYFILE_ENCODING      = UTF-8
+PROJECT_NAME           = AMDiS
+PROJECT_NUMBER         = 0.1
+PROJECT_BRIEF          = "The Adaptive Multi-Dimensional Simulation Toolbox"
+PROJECT_LOGO           =
+OUTPUT_DIRECTORY       =
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+
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+                         "The $name widget" \
+                         "The $name file" \
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+                         a \
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+OPTIMIZE_OUTPUT_JAVA   = NO
+OPTIMIZE_FOR_FORTRAN   = NO
+OPTIMIZE_OUTPUT_VHDL   = NO
+EXTENSION_MAPPING      =
+MARKDOWN_SUPPORT       = YES
+TOC_INCLUDE_HEADINGS   = 0
+AUTOLINK_SUPPORT       = YES
+BUILTIN_STL_SUPPORT    = NO
+CPP_CLI_SUPPORT        = NO
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+INLINE_GROUPED_CLASSES = NO
+INLINE_SIMPLE_STRUCTS  = NO
+TYPEDEF_HIDES_STRUCT   = NO
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+EXTRACT_ALL            = NO
+EXTRACT_PRIVATE        = NO
+EXTRACT_PACKAGE        = NO
+EXTRACT_STATIC         = YES
+EXTRACT_LOCAL_CLASSES  = NO
+EXTRACT_LOCAL_METHODS  = NO
+EXTRACT_ANON_NSPACES   = NO
+HIDE_UNDOC_MEMBERS     = NO
+HIDE_UNDOC_CLASSES     = NO
+HIDE_FRIEND_COMPOUNDS  = NO
+HIDE_IN_BODY_DOCS      = YES
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+HIDE_SCOPE_NAMES       = YES
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+FORCE_LOCAL_INCLUDES   = NO
+INLINE_INFO            = YES
+SORT_MEMBER_DOCS       = YES
+SORT_BRIEF_DOCS        = NO
+SORT_MEMBERS_CTORS_1ST = YES
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+SHOW_NAMESPACES        = YES
+FILE_VERSION_FILTER    =
+LAYOUT_FILE            = Doxylayout.xml
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+QUIET                  = NO
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_DOC_ERROR      = YES
+WARN_NO_PARAMDOC       = NO
+WARN_AS_ERROR          = NO
+WARN_FORMAT            = "$file:$line: $text"
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+FILE_PATTERNS          = *.hpp *.cpp *.md
+INPUT                  = ../src/amdis \
+                         ../src/amdis/common \
+                         ../src/amdis/functions \
+                         ../src/amdis/gridfunctions \
+                         ../src/amdis/linearalgebra \
+                         ../src/amdis/linearalgebra/mtl \
+                         ../src/amdis/localoperators \
+                         ../src/amdis/operations \
+                         ../src/amdis/typetree \
+                         ../src/amdis/utility
+INPUT_ENCODING         = UTF-8
+RECURSIVE              = NO
+EXCLUDE                = ../src/amdis/linearalgebra/eigen \
+                         ../src/amdis/linearalgebra/istl \
+                         ../src/amdis/linearalgebra/petsc
+EXCLUDE_SYMLINKS       = NO
+EXCLUDE_PATTERNS       =
+EXCLUDE_SYMBOLS        = AMDiS::Impl \
+                         AMDiS::Math::Impl_ \
+                         AMDiS::Concepts::Impl_ \
+                         AMDiS::detail \
+                         itl::details
+EXAMPLE_PATH           = examples
+EXAMPLE_PATTERNS       = *
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+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
+FILTER_SOURCE_FILES    = NO
+FILTER_SOURCE_PATTERNS =
+USE_MDFILE_AS_MAINPAGE =
+
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+SOURCE_BROWSER         = NO
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+
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+ALPHABETICAL_INDEX     = YES
+COLS_IN_ALPHA_INDEX    = 5
+IGNORE_PREFIX          =
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+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+GENERATE_HTML          = YES
+HTML_OUTPUT            = html
+HTML_FILE_EXTENSION    = .html
+HTML_HEADER            =
+HTML_FOOTER            =
+HTML_STYLESHEET        =
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+HTML_TIMESTAMP         = NO
+HTML_DYNAMIC_SECTIONS  = NO
+HTML_INDEX_NUM_ENTRIES = 100
+
+GENERATE_DOCSET        = NO
+DOCSET_FEEDNAME        = "Doxygen generated docs"
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+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+DOCSET_PUBLISHER_NAME  = Publisher
+
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+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_EXTENSIONS     =
+MATHJAX_CODEFILE       =
+
+SEARCHENGINE           = YES
+SERVER_BASED_SEARCH    = NO
+EXTERNAL_SEARCH        = NO
+SEARCHENGINE_URL       =
+SEARCHDATA_FILE        = searchdata.xml
+EXTERNAL_SEARCH_ID     =
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+GENERATE_LATEX         = NO
+GENERATE_RTF           = NO
+GENERATE_MAN           = NO
+GENERATE_XML           = NO
+GENERATE_DOCBOOK       = NO
+GENERATE_AUTOGEN_DEF   = NO
+GENERATE_PERLMOD       = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = NO
+EXPAND_ONLY_PREDEF     = NO
+SEARCH_INCLUDES        = YES
+INCLUDE_PATH           =
+INCLUDE_FILE_PATTERNS  =
+PREDEFINED             = HAVE_UMFPACK \
+                         HAVE_ALBERTA \
+                         HAVE_UG \
+                         AMDIS_HAS_MTL \
+                         AMDIS_HAS_HYPRE
+EXPAND_AS_DEFINED      =
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
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+EXTERNAL_GROUPS        = YES
+EXTERNAL_PAGES         = YES
+PERL_PATH              = /usr/bin/perl
+
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+      <interfaces title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <allmemberslink visible="yes"/>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>