Commit ce0fece2 authored by Praetorius, Simon's avatar Praetorius, Simon

documentation extended

parent 90400883
Pipeline #947 passed with stage
in 6 minutes and 59 seconds
......@@ -8,6 +8,14 @@
*.parh
*.tarh
# ignore matrix-market files
*.mtx
error.txt
lint.txt
# ignore build directories
build*/
install*/
\ No newline at end of file
install*/
.vscode/
\ No newline at end of file
cmake_minimum_required(VERSION 3.1)
project(dune-amdis CXX)
#set(CXX_MAX_STANDARD 14 CACHE BOOL "" FORCE)
if(NOT (dune-common_DIR OR dune-common_ROOT OR
"${CMAKE_PREFIX_PATH}" MATCHES ".*dune-common.*"))
string(REPLACE ${CMAKE_PROJECT_NAME} dune-common dune-common_DIR
......
# GIT Workflow
Follow the ideas of [a-successful-git-branching-model](http://nvie.com/posts/a-successful-git-branching-model), especially
- Create a new branch for all new features, following the naming convention `feature/XYZ`
Follow the ideas of [a-successful-git-branching-model](http://nvie.com/posts/a-successful-git-branching-model),
especially
- Create a new branch for all new features, following the naming convention
`feature/XYZ`
- Merge features in the `develop` branch only
- Correct Bugs in issue branches, following the naming convention `issue/XYZ`
- Merge issues in the `develop` branch, except when it is a hotfix, then merge to `master` and `develop`
- Merge issues in the `develop` branch, except when it is a hotfix, then merge
to `master` and `develop`
- For all merges create a meaningful *Merge Request* in GitLab
# Code Style-Guide
This style-guide is intended for developers writing code for AMDiS, is not complete and probably not applied to all parts of the AMDiS code. Feel free to edit existing source files in order to fulfill the styles.
This style-guide is intended for developers writing code for AMDiS, is not complete
and probably not applied to all parts of the AMDiS code. Feel free to edit existing
source files in order to fulfill the styles.
Parts of this convention are taken from well established style guides, like the *Google C++ Style Guide*.
Parts of this convention are taken from well established style guides, like the
*Google C++ Style Guide*.
In general, the code should follow the [C++ Core Guidelines](https://github.com/isocpp/CppCoreGuidelines).
## File naming conventions
Filenames should be mixed lower and upper case, starting with an uppercase letter. They should not include underscores or dashed. Use an uppercase letter to indicate a new subword. Sourcefiles should end in `.cpp` and header files should end in `.hpp`. In case you move the code of a template class to a separate file, included textually at the end of the corresponding header file, use the extensions `.inc.hpp`.
Filenames should be mixed lower and upper case, starting with an uppercase letter.
They should not include underscores or dashed. Use an uppercase letter to indicate
a new subword. Sourcefiles should end in `.cpp` and header files should end in `.hpp`.
In case you move the code of a template class to a separate file, included textually
at the end of the corresponding header file, use the extensions `.inc.hpp`.
The name of a file should follow the name of the implemented class in this file.
......@@ -26,21 +36,26 @@ Examples of valid filenames:
* `AdaptInstat.cpp`
* `DOFVector.hpp`
* `DOFVector.cpp`
* `DOFVector.inc.hpp` (the implementation of the methods of the template class `DOFVector<T>`)
* `DOFVector.inc.hpp` (the implementation of the methods of the template class
`DOFVector<T>`)
Do not use filenames that already exist in /usr/include or are stdandard C/C++ include files, such as `math.h` (remember that windows files-systems are case insensitive and thus, there is no difference between `math.h` and `Math.H`.)
Do not use filenames that already exist in /usr/include or are stdandard C/C++ include
files, such as `math.h` (remember that windows files-systems are case insensitive and
thus, there is no difference between `math.h` and `Math.H`.)
## Generale file structure
Every header file should start with a copyright notice and an include guard `#pragma once`, where the text of the copyright notice is given in the file `tools/license.templ.txt` and can automatically by added, using the script files in the `tools` directory:
Every header file should start with a copyright notice and an include guard `#pragma once`,
where the text of the copyright notice is given in the file `tools/license.templ.txt`
and can automatically by added, using the script files in the `tools` directory:
``` c++
// Software License for dune-amdis
// Software License for AMDiS
//
// Copyright (c) 2015 Institute for Scientific Computing, Technische Universitaet Dresden
// All rights reserved.
// Authors: Simon Praetorius
//
// This file is part of the dune-amdis Library
// This file is part of the AMDiS Library
// see also the LICENSE file in the distribution.
#pragma once
......@@ -50,14 +65,18 @@ After the include guard a list of include files can be added, see *Names and Ord
### Names and Order of Includes
All of a project's header files should be listed as descendants of the project's source directory. The includes should be grouped following the rules:
* [class header file] ... for source files that implement an interface specified in a header file
All of a project's header files should be listed as descendants of the project's
source directory. The includes should be grouped following the rules:
* [class header file] ... for source files that implement an interface specified
in a header file
* C system files.
* C++ system files.
* Other external libraries' header files.
* Your project's header files.
For better readability a comment above each group can be added. Within each section the includes should be ordered alphabetically. Project's header files should be surrounded by `"`, while external header files should be surrounded by `<...>`.
For better readability a comment above each group can be added. Within each section
the includes should be ordered alphabetically. Project's header files should be
surrounded by `"`, while external header files should be surrounded by `<...>`.
For example, the includes in `io/VtkWriter.cpp` might look like this:
......@@ -86,7 +105,8 @@ For example, the includes in `io/VtkWriter.cpp` might look like this:
### Namespaces
All implementation should be put into the namespace `AMDiS`. When a namespace closes, a corresponding comment should be added to the closing brackets:
All implementation should be put into the namespace `AMDiS`. When a namespace closes,
a corresponding comment should be added to the closing brackets:
``` c++
namespace AMDiS
......@@ -95,7 +115,9 @@ namespace AMDiS
} // end namespace AMDiS
```
Implementation details are put into a subnamespace `Impl`. A few more subnamespaces of `AMDiS` are allowed, e.g., `Concepts`. If onw of these subnamespaces need another subsubnamespace for implementation details, it should be names `_Impl`.
Implementation details are put into a subnamespace `Impl`. A few more subnamespaces
of `AMDiS` are allowed, e.g., `Concepts`. If one of these subnamespaces need another
subsubnamespace for implementation details, it should be named `Impl_`.
## Line length
......@@ -112,4 +134,5 @@ Use two spaces instead of tabs!
## Documentation
Use Doxygen-Style comments for the documentation of functions and classes, except when the function name already indicates its meaning completely.
Use Doxygen-Style comments for the documentation of functions and classes, except
when the function name already indicates its meaning completely.
Preparing the Sources
=========================
The project *dune-amdis* requires a modern compiler supporting c++14 standard
and an up-to-date cmake >= 3.1 installed on the system.
AMDiS
=====
The *Adaptive Multi-Dimensional Simulation Toolbox* (AMDiS) is implemented as a
discretization module on top of the Dune framework.
Installation
============
We provide a *cmake*-based configuration and use the `dunecontrol` build system.
Simply run
Installation using dune-docker
------------------------------
```
dunecontrol --current all
```
The easyest way to compile and run the code is to use the prepared docker images.
Therefore, 1. install *docker*, 2. clone the project *dune-docker*, 3. create the
image `dune:git`, 4. run this docker image with interactive shell.
(See also the `README.md` in the *dune-docker* project for details).
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-typetree](https://gitlab.dune-project.org/staging/dune-typetree)
- [dune-functions](https://gitlab.dune-project.org/staging/dune-functions)
Prepare for installation
------------------------
(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.
In order to resolve external dependencies, run the script `contrib/ci-setup`. This
will download the latest MTL4 library (and maybe more).
Additionally we require the following libraries to be found:
- [MTL4](https://gitlab.math.tu-dresden.de/spraetor/mtl4) (use this fork to get up-to-date changes)
- [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html) (optional)
- libalberta >= 3.0 (For Alberta-Grids)
Compile and link the library and examples
-----------------------------------------
And a compiler that supports the C++14 standard, e.g. g++ >= 4.9 and clang >= 3.6, and cmake >= 3.1.
Simply run
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:
```
dunecontrol --opts=/duneci/opts.gcc --current all
CMAKE_FLAGS="-DMTL_DIR:PATH=[MTL_ROOT]" dunecontrol --current configure
cmake --build build-cmake
```
to build the library and to compile and link the examples from the `src/` directory.
\ No newline at end of file
This compiles the library and all examples in the `src/` directory.
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-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 we require the following libraries to be found:
- [MTL4](https://gitlab.math.tu-dresden.de/spraetor/mtl4) (use this fork to get up-to-date changes)
- [Boost](http://www.boost.org) >= 1.40
- [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html) (optional)
- libalberta >= 3.0 (For Alberta-Grids)
And a compiler that supports the C++14 standard, e.g. `g++` >= 4.9 and `clang` >= 3.6,
and `cmake` >= 3.1.
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="-DMTL_DIR:PATH=[MTL_ROOT]" dunecontrol --current configure
cmake --build build-cmake
```
This compiles the library and all examples in the `src/` directory.
AMDiS {#mainpage}
=====
The *Adaptive Multi-Dimensional Simulation Toolbox* (AMDiS) is implemented as a
discretization module on top of the [Dune](https://dune-project.org) framework.
Example
-------
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. Adaption-modules for the time- and space adaptive solution of the problem, see \ref Adaption.
**Poisson equation:**
The most simple elliptic PDE is the Poisson equation:
\f{eqnarray*}{
-\Delta u &=& f(x),\quad\mbox{ in }\Omega \\
u &=& g(x),\quad\mbox{ on }\partial\Omega
\f}
where \f$ f(x) \f$ and \f$ g(x) \f$ are parameters describing the volume and
boundary forces of the problem.
The corresponding weak form of the equation reads:
\f[
\langle \nabla v, \nabla u\rangle_\Omega = (f(x)\,v)_\Omega,\quad\forall v\in V_0
\f]
with \f$ u\in V_g \f$.
Thus, we need to define a grid (discretization of \f$ \Omega \f$) and a finite
element space (discretization of \f$ V_0 \f$ and \f$ V_g \f$). This needs to be
provided as `Traits` parameter in the ProblemStat class:
~~~~~~~~~~~~~~~{.cpp}
using Grid = Dune::AlbertaGrid<AMDIS_DIM, AMDIS_DOW>;
using Traits = LagrangeBasis<Grid::LeafGridView, 1>;
~~~~~~~~~~~~~~~
This defines and `AlbertaGrid` as grid and a Lagrange Finite-Element space with
local polynomial degree 1 on the elements.
All AMDiS programs start with initialization of the library, using `AMDiS::init`
~~~~~~~~~~~~~~~{.cpp}
using namespace AMDiS;
int main(int argc, char** argv)
{
AMDiS::init(argc, argv);
ProblemStat<Traits> prob("name");
~~~~~~~~~~~~~~~
The Problem class is initialized with a name, that is used as identifier in the
parameter files. In order to initialize the Finite-Element space, the grid and
all other parts of the problem class, call `initialize(Flag)` where `Flag`
specifies what to initialize. For now, we initialize everything: `INIT_ALL`:
~~~~~~~~~~~~~~~{.cpp}
prob.initialize(INIT_ALL);
~~~~~~~~~~~~~~~
Operators specify the (bi-)linear-form and the coefficient function in the term,
see \ref operators for a list of possible types. The bilinear-form in the Poisson
equation consists of second-order term with coefficitn = 1 and the linear-form
includes the function \f$ f(x)=-1 \f$:
~~~~~~~~~~~~~~~{.cpp}
auto opL = makeOperator(tag::gradtest_gradtrial{}, 1.0);
prob.addMatrixOperator(opL, 0, 0);
auto opF = makeOperator(tag::test{}, [](auto const& x) { return -1.0; }, 0);
prob.addVectorOperator(opF, 0);
~~~~~~~~~~~~~~~
Boundary conditions, in the example above a Dirichlet condition, is specified by
defining a predicate for the boundary \f$ \partial\Omega \f$ and the values on the
boundary \f$ g(x) = 0 \f$:
~~~~~~~~~~~~~~~{.cpp}
auto predicate = [](auto const& x){ return x[0] < 1.e-8 || x[1] < 1.e-8; };
prob.addDirichletBC(predicate, 0, 0, 0.0);
~~~~~~~~~~~~~~~
The final step is the assembling and solution of the linear system. (Maybe including
grid adaption). This is realized using an \ref AdaptStationary class:
~~~~~~~~~~~~~~~{.cpp}
AdaptInfo adaptInfo("adapt");
AdaptStationary adapt("adapt", prob);
adapt.adapt(); // assemble and solve
~~~~~~~~~~~~~~~
Finally, finish the AMDiS program with `AMDiS::finish()`.
In complete program then reads:
~~~~~~~~~~~~~~~{.cpp}
#include <dune/amdis/AMDiS.hpp>
#include <dune/amdis/AdaptInfo.hpp>
#include <dune/amdis/AdaptStationary.hpp>
#include <dune/amdis/ProblemStat.hpp>
using namespace AMDiS;
using Grid = Dune::AlbertaGrid<AMDIS_DIM, AMDIS_DOW>;
using Traits = LagrangeBasis<Grid::LeafGridView, 1>;
int main(int argc, char** argv)
{
AMDiS::init(argc, argv);
ProblemStat<Traits> prob("poisson");
prob.initialize(INIT_ALL);
auto opL = makeOperator(tag::gradtest_gradtrial{}, 1.0);
prob.addMatrixOperator(opL, 0, 0);
auto opF = makeOperator(tag::test{}, [](auto const& x) { return -1.0; }, 0);
prob.addVectorOperator(opF, 0);
// set boundary condition
auto predicate = [](auto const& x){ return x[0] < 1.e-8 || x[1] < 1.e-8; };
prob.addDirichletBC(predicate, 0, 0, 0.0);
// assemble and solve
AdaptInfo adaptInfo("adapt");
AdaptStationary adapt("adapt", prob);
adapt.adapt();
AMDiS::finalize();
return 0;
}
~~~~~~~~~~~~~~~
\ No newline at end of file
......@@ -2,7 +2,8 @@
# please us '+=' to add file/directories to the lists
FILE_PATTERNS += *.hpp \
*.cpp
*.cpp \
*.md
HIDE_SCOPE_NAMES = YES
HIDE_UNDOC_CLASSES = NO
......@@ -33,7 +34,8 @@ INPUT += @top_srcdir@/dune/amdis \
@top_srcdir@/dune/amdis/linear_algebra \
@top_srcdir@/dune/amdis/linear_algebra/mtl \
@top_srcdir@/dune/amdis/operations \
@top_srcdir@/dune/amdis/utility
@top_srcdir@/dune/amdis/utility \
@top_srcdir@/doc
# see e.g. dune-grid for the examples of mainpage and modules
#INPUT += @srcdir@/mainpage \
# @srcdir@/modules
......
......@@ -10,7 +10,7 @@ Name: @PACKAGE_NAME@
Version: @VERSION@
Description: AMDiS dune-module
URL: https://gitlab.math.tu-dresden.de/spraetor/dune-amdis
Requires: dune-common dune-geometry dune-localfunctions dune-istl dune-typetree dune-grid dune-functions
Suggests: dune-uggrid dune-alugrid
Requires: dune-common dune-geometry dune-localfunctions dune-typetree dune-grid dune-functions
Suggests: dune-uggrid dune-alugrid dune-foamgrid
Libs: -L${libdir}
Cflags: -I${includedir}
......@@ -7,5 +7,5 @@ Module: dune-amdis
Version: 0.1
Maintainer: simon.praetorius@tu-dresden.de
#depending on
Depends: dune-common dune-geometry dune-localfunctions dune-istl dune-typetree dune-grid dune-functions
Suggests: dune-uggrid dune-alugrid
Depends: dune-common dune-geometry dune-localfunctions dune-typetree dune-grid dune-functions
Suggests: dune-uggrid dune-alugrid dune-foamgrid
......@@ -150,6 +150,9 @@ namespace AMDiS
} // end namespace Definition
/// \brief Concepts that is true for all ''simple'' types that can be
/// converted automatically to a GridFunction, e.g. arithmetic types,
/// FieldVectors, and `std::reference_wrapper`.
template <class T>
constexpr bool ConstantToGridFunction =
Definition::ConstantToGridFunction<T>::value;
......
......@@ -75,24 +75,32 @@ namespace AMDiS
} // end namespace Definition
/// \brief GridFunction F has free function `localFunction(F)`
template <class F>
constexpr bool HasLocalFunction = models<Definition::HasLocalFunction(F)>;
/// \brief GridFunction F has free function `derivative(F)`
template <class F>
constexpr bool HasDerivative = models<Definition::HasDerivative(F)>;
/// \brief GridFunction F has free function `derivative(localFunction(F))`
template <class F>
constexpr bool HasLocalFunctionDerivative = models<Definition::HasLocalFunctionDerivative(F)>;
/// \brief GridFunction F has free function `order(localFunction(F))`
template <class F>
constexpr bool HasLocalFunctionOrder = models<Definition::HasLocalFunctionOrder(F)>;
/// \brief Functor F has free function `partial(F,_0)`
template <class F>
constexpr bool HasPartial = models<Definition::HasPartial(F)>;
/// \brief Functor F has free function `order(F)`
template <class F>
constexpr bool HasOrder = models<Definition::HasOrder(F)>;
/// \brief Functor F is collable with GlobalCoordinates `F(Dune::FieldVector<double,DOW>)`
#ifndef AMDIS_DOW
template <class F>
constexpr bool CallableDomain =
......@@ -103,11 +111,14 @@ namespace AMDiS
Definition::CallableDow<F, AMDIS_DOW>;
#endif
// types that is a GridFunction
/// \brief GridFunction GF is a Type that has LocalFunction and provides some
/// typedefs for `Domain`, `Range`, and `EntitySet`.
template <class GF>
constexpr bool GridFunction =
HasLocalFunction<GF> && models<Definition::HasGridFunctionTypes(GF)>;
/// \brief Concept is fulfilled, if at least one of the massed Expressions
/// can be converted to a GridFunction, or is already a GridFunction.
template <class... GFs>
constexpr bool AnyGridFunction =
any_of_v<GridFunction<std::decay_t<GFs>>...> ||
......
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