Merge branch 'issue/doc_build_params' into 'master'

Fix directories in Doxyfile

See merge request !217

docs/Doxyfile

@@ -122,29 +122,32 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 
 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                  = ../amdis \
+                         ../amdis/common \
+                         ../amdis/functions \
+                         ../amdis/gridfunctions \
+                         ../amdis/io \
+                         ../amdis/linearalgebra \
+                         ../amdis/linearalgebra/eigen \
+                         ../amdis/linearalgebra/istl \
+                         ../amdis/linearalgebra/mtl \
+                         ../amdis/linearalgebra/petsc \
+                         ../amdis/localoperators \
+                         ../amdis/operations \
+                         ../amdis/typetree \
+                         ../amdis/utility
 INPUT_ENCODING         = UTF-8
 RECURSIVE              = NO
-EXCLUDE                = ../src/amdis/linearalgebra/eigen \
-                         ../src/amdis/linearalgebra/istl \
-                         ../src/amdis/linearalgebra/petsc
+EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       =
 EXCLUDE_SYMBOLS        = AMDiS::Impl \
                          AMDiS::Math::Impl_ \
                          AMDiS::Concepts::Impl_ \
                          AMDiS::detail \
+                         Dune \
                          itl::details
-EXAMPLE_PATH           = examples
+EXAMPLE_PATH           = ../examples
 EXAMPLE_PATTERNS       = *
 EXAMPLE_RECURSIVE      = NO
 IMAGE_PATH             =
@@ -168,7 +171,7 @@ SOURCE_TOOLTIPS        = YES
 USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
 CLANG_ASSISTED_PARSING = NO
-CLANG_OPTIONS          = -std=c++14
+CLANG_OPTIONS          = -std=c++17
 
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index

docs/tutorials/backup-restore.md

+# How to backup and restore problem data?
+
+In very long simulations, i.e. many timesteps, it is recommended to backup an
+intermediate state from time to time, so that it is possible to resume a
+simulation from the last stored backup file. Therefore, you mostly need
+a representation of the grid in memory incorporating the grid hierarchy and
+the data for the solution vector. Other parameters are fixed or problem specific,
+so need to be stored manually.
+
+In the `ProblemStat` there is a pair of functions `backup()` and `restore()`
+that can be used for this purpose. The backup function saves the grid and the
+solution vector to files and the restore function initializes a new problem from
+stored files.
+
+```c++
+ProblemStat prob("prob");
+prob.initialize(INIT_ALL);
+AdaptInfo adaptInfo("adapt");
+
+// some calculation ...
+
+prob.backup(adaptInfo);
+```
+
+This create at least two files, one for the grid and one for the solution, where
+the filenames are either fixed to `backup_TIMESTEP.grid` and `backup_TIMESTEP.solution`
+or specified in the initfile as
+
+```
+prob->backup->grid: backup_xyz.grid
+prob->backup->solution: backup_xyz.solution
+```
+
+To restart a simulation it is recommended to initialize the problem directly with
+the grid and solution file, i.e.
+
+```c++
+ProblemStat prob("prob");
+prob.restore(INIT_ALL);
+
+// some more calculation ...
+```
+
+where the restore filenames **must** be given in the initfile as
+
+```
+prob->restore->grid: backup_xyz.grid
+prob->restore->solution: backup_xyz.solution
+```

docs/howto.md → docs/tutorials/block-mat-vec.md

-# How To
+# How to use block matrices and vectors?
 
-[TOC]
-
-## How to use block matrices and vectors?
 When using the default `BasisCreator` provided by AMDiS, like `LagrangeBasis` or
 `TaylorHoodBasis`, the resulting indexing scheme is *flat*, meaning we need to
 use one (sparse) matrix and one vector to describe the linear system. Sometimes
@@ -67,51 +64,4 @@ auto& vec_vel_y = vec_vel[1];
 
 Note: Currently the blocking is implemented for the ISTL backend only.
 
-## How to backup and restore problem data?
-In very long simulations, i.e. many timesteps, it is recommended to backup an
-intermediate state from time to time, so that it is possible to resume a
-simulation from the last stored backup file. Therefore, you mostly need
-a representation of the grid in memory incorporating the grid hierarchy and
-the data for the solution vector. Other parameters are fixed or problem specific,
-so need to be stored manually.
-
-In the `ProblemStat` there is a pair of functions `backup()` and `restore()`
-that can be used for this purpose. The backup function saves the grid and the
-solution vector to files and the restore function initializes a new problem from
-stored files.
-
-```c++
-ProblemStat prob("prob");
-prob.initialize(INIT_ALL);
-AdaptInfo adaptInfo("adapt");
-
-// some calculation ...
-
-prob.backup(adaptInfo);
-```
-
-This create at least two files, one for the grid and one for the solution, where
-the filenames are either fixed to `backup_TIMESTEP.grid` and `backup_TIMESTEP.solution`
-or specified in the initfile as
-
-```
-prob->backup->grid: backup_xyz.grid
-prob->backup->solution: backup_xyz.solution
-```
-
-To restart a simulation it is recommended to initialize the problem directly with
-the grid and solution file, i.e.
-
-```c++
-ProblemStat prob("prob");
-prob.restore(INIT_ALL);
 
-// some more calculation ...
-```
-
-where the restore filenames **must** be given in the initfile as
-
-```
-prob->restore->grid: backup_xyz.grid
-prob->restore->solution: backup_xyz.solution
-```

docs/tutorials/tutorials.md

@@ -12,27 +12,34 @@ functions.
 Create a problem class as a container for the grid, basis, solution vector and
 linear system and many more. What can a problem class do for your workflow.
 
-3. [Operators](../reference/Operators.md):
+3. [Backup and Restore](backup-restore.md)
+Write intermediate states of your lengthy conmputations to file and resume the
+simulation from a backup file.
+
+4. [Operators](../reference/Operators.md):
 Define your PDE in terms of operator terms. Learn how to add operators to a
 problem and how to define your own operators.
 
-4. [Boundary Conditions](boundary-conditions.md):
+5. [Block Matrices and Vectors](block-mat-vec.md)
+Use block matrices and vectors instead of the default flat versions.
+
+6. [Boundary Conditions]():
 Select parts of the grid boundary and assign boundary conditions or boundary
 operators. Learn how to specify the boundary parts and how to set different
 types of boundary conditions, like Dirichlet or periodic conditions, or
 Neumann/Robin-type boundary integrals.
 
-5. [Linear Solvers](linear-solvers.md):
+7. [Linear Solvers]():
 Control the solution of the assembled linear system, which linear solver to use
 and which preconditioner. How to control solver parameters and how to add an
 own linear solver.
 
-6. [Adaptivity and Grid Refinement](grid-adaptivity.md):
+8. [Adaptivity and Grid Refinement]():
 Grid adaptivity needs control of marking and refinement strategies. Learn how to
 define and add a marker to the problem, learn about interpolation during grid
 adaptivity and how to load balance your grid.
 
-7. [FileWriters](filewriters.md):
+9. [FileWriters]():
 Output and backup/restore of data is an important topic for simulations and
 for postprocessing. Different Writers are introduced and the configuration and control
 of these writers discussed.