Merge branch 'change_directory_structure' into 'develop'

Change directory structure

See merge request spraetor/dune-amdis!4

CMakeLists.txt

 cmake_minimum_required(VERSION 3.1)
-project(dune-amdis CXX)
-
-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
-      ${PROJECT_BINARY_DIR})
-endif()
+project(amdis CXX)
 
 #find dune-common and set the module path
 find_package(dune-common REQUIRED)
@@ -17,35 +11,19 @@ include(DuneMacros)
 
 # start a dune project with information from dune.module
 dune_project()
+
 dune_enable_all_packages(MODULE_LIBRARIES amdis)
 
-include(AmdisMacros)
 add_subdirectory("src")
 add_subdirectory("test")
-add_subdirectory("dune")
+add_subdirectory("examples" EXCLUDE_FROM_ALL)
 add_subdirectory("doc")
 add_subdirectory("cmake/modules")
 
-
-# some additional packages and flags
-add_dune_alberta_flags("amdis" OBJECT USE_GENERIC)
-target_compile_definitions("amdis" PUBLIC AMDIS_BACKEND_MTL=1)
-target_compile_options("amdis" PUBLIC -ftemplate-backtrace-limit=0 -Wall -pedantic -Wno-unused-parameter)
-
-find_package(MTL REQUIRED
-             PATHS /usr/local/lib/mtl4 /opt/sources/mtl4 /opt/development/mtl4)
-if (MTL_FOUND)
-  target_include_directories("amdis" PUBLIC ${MTL_INCLUDE_DIRS})
-
-  set (CXX_ELEVEN_FEATURE_LIST "MOVE" "AUTO" "RANGEDFOR" "INITLIST" "STATICASSERT" "DEFAULTIMPL")
-  foreach (feature ${CXX_ELEVEN_FEATURE_LIST})
-      target_compile_definitions("amdis" PUBLIC MTL_WITH_${feature})
-  endforeach ()
-
-  if (HAVE_UMFPACK OR ENABLE_SUITESPARSE OR SuiteSparse_FOUND)
-      target_compile_definitions("amdis" PUBLIC MTL_HAS_UMFPACK)
-  endif ()
-endif (MTL_FOUND)
+target_include_directories(amdis PUBLIC
+  $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
+target_compile_definitions(amdis PUBLIC AMDIS_BACKEND_MTL=1)
+target_compile_options(amdis PUBLIC -Wall -pedantic -Wno-unused-parameter) #-ftemplate-backtrace-limit=0
 
 # finalize the dune project, e.g. generating config.h etc.
 finalize_dune_project(GENERATE_CONFIG_H_CMAKE)

cmake/modules/AmdisMacros.cmake

 # File for module specific CMake tests.
 
-include(AMDiSCXXFeatures)
\ No newline at end of file
+include(AMDiSCXXFeatures)
+
+# some additional packages and flags
+find_package(MTL REQUIRED
+             PATHS /usr/local/lib/mtl4 /opt/sources/mtl4 /opt/development/mtl4)
+
+set(CXX_ELEVEN_FEATURE_LIST "MOVE" "AUTO" "RANGEDFOR" "INITLIST" "STATICASSERT" "DEFAULTIMPL")
+set(MTL_COMPILE_DEFINITIONS "")
+foreach(feature ${CXX_ELEVEN_FEATURE_LIST})
+  list(APPEND MTL_COMPILE_DEFINITIONS "MTL_WITH_${feature}")
+endforeach()
+
+if(HAVE_UMFPACK OR ENABLE_SUITESPARSE OR SuiteSparse_FOUND)
+  list(APPEND MTL_COMPILE_DEFINITIONS "MTL_HAS_UMFPACK")
+endif()
+
+dune_register_package_flags(
+  COMPILE_DEFINITIONS ${MTL_COMPILE_DEFINITIONS}
+  INCLUDE_DIRS ${MTL_INCLUDE_DIRS})

cmake/modules/CMakeLists.txt

-set(modules "AmdisMacros.cmake")
 
-install(FILES ${modules} DESTINATION ${DUNE_INSTALL_MODULEDIR})
+install(FILES 
+    AmdisMacros.cmake
+    AMDiSCXXFeatures.cmake
+  DESTINATION ${DUNE_INSTALL_MODULEDIR})

doc/Mainpage.md

@@ -13,10 +13,10 @@ and \f$ g(x) \equiv 0 \f$, the domain \f$ \Omega \f$ a square domain \f$ [0,1]^2
 and \f$ \Gamma \f$ the lower and left edge of the boundary.
 
 ~~~~~~~~~~~~~~~{.cpp}
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/AdaptInfo.hpp>
-#include <dune/amdis/AdaptStationary.hpp>
-#include <dune/amdis/ProblemStat.hpp>
+#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;

dune.module

@@ -3,7 +3,7 @@
 ################################
 
 #Name of the module
-Module: dune-amdis
+Module: amdis
 Version: 0.1
 Maintainer: simon.praetorius@tu-dresden.de
 #depending on

dune/CMakeLists.txt

-add_subdirectory(amdis)
-# add_subdirectory(amdis/test)
\ No newline at end of file

dune/amdis/LinearAlgebra.hpp

-#pragma once
-
-#include <dune/amdis/linear_algebra/LinearSolverInterface.hpp>
-#include <dune/amdis/linear_algebra/SolverInfo.hpp>
-
-#if defined(AMDIS_BACKEND_ISTL)
-
-#include <dune/amdis/linear_algebra/istl/SystemVector.hpp>
-#include <dune/amdis/linear_algebra/istl/SystemMatrix.hpp>
-#include <dune/amdis/linear_algebra/istl/LinearSolver.hpp>
-
-#elif defined(AMDIS_BACKEND_MTL)
-
-#include <dune/amdis/linear_algebra/mtl/SystemVector.hpp>
-#include <dune/amdis/linear_algebra/mtl/SystemMatrix.hpp>
-#include <dune/amdis/linear_algebra/mtl/LinearSolver.hpp>
-#include <dune/amdis/linear_algebra/mtl/ITL_Solver.hpp>
-#include <dune/amdis/linear_algebra/mtl/BITL_Solver.hpp>
-
-#elif defined(AMDIS_BACKEND_PETSC)
-
-#include <dune/amdis/linear_algebra/petsc/SystemVector.hpp>
-#include <dune/amdis/linear_algebra/petsc/SystemMatrix.hpp>
-#include <dune/amdis/linear_algebra/petsc/LinearSolver.hpp>
-
-#else
-
-#error "Unknown linear algebra backend!. Set corresponding variable \
-        AMDIS_BACKEND_ISTL, AMDIS_BACKEND_MTL or AMDIS_BACKEND_PETSC."
-
-#endif
\ No newline at end of file

examples/CMakeLists.txt

+
+set(projects2d "ellipt" "heat" "vecellipt" "stokes0" "stokes1" "stokes3" "navier_stokes")
+
+foreach(project ${projects2d})
+    add_executable(${project}.2d ${project}.cc)
+    add_dune_alberta_flags(GRIDDIM 2 WORLDDIM 2 ${project}.2d)
+    target_link_dune_default_libraries(${project}.2d)
+    target_link_libraries(${project}.2d "amdis")
+    target_compile_definitions(${project}.2d PRIVATE AMDIS_DIM=2 AMDIS_DOW=2)
+endforeach()
+
+set(projects3d "ellipt" "heat")
+
+foreach(project ${projects3d})
+    add_executable(${project}.3d ${project}.cc)
+    add_dune_alberta_flags(GRIDDIM 3 WORLDDIM 3 ${project}.3d)
+    target_link_dune_default_libraries(${project}.3d)
+    target_link_libraries(${project}.3d "amdis")
+    target_compile_definitions(${project}.3d PRIVATE AMDIS_DIM=3 AMDIS_DOW=3)
+endforeach()
\ No newline at end of file

src/ellipt.cc → examples/ellipt.cc

@@ -3,10 +3,10 @@
 
 #include <iostream>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Operators.hpp>
-#include <dune/amdis/common/Literals.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/Operators.hpp>
+#include <amdis/common/Literals.hpp>
 
 using namespace AMDiS;
 

src/heat.cc → examples/heat.cc

@@ -3,13 +3,13 @@
 
 #include <iostream>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/AdaptInstationary.hpp>
-#include <dune/amdis/ProblemInstat.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Operators.hpp>
-#include <dune/amdis/GridFunctions.hpp>
-#include <dune/amdis/common/Literals.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/AdaptInstationary.hpp>
+#include <amdis/ProblemInstat.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/Operators.hpp>
+#include <amdis/GridFunctions.hpp>
+#include <amdis/common/Literals.hpp>
 
 using namespace AMDiS;
 

src/navier_stokes.cc → examples/navier_stokes.cc

@@ -2,27 +2,18 @@
 #include <ctime>
 #include <cmath>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/AdaptInstationary.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/ProblemInstat.hpp>
-#include <dune/amdis/Operators.hpp>
-#include <dune/amdis/assembler/StokesOperator.hpp>
-
-#ifdef DOW
-#undef DOW
-#endif
-#define DOW AMDIS_DOW
-
-#ifndef STRATEGY
-#define STRATEGY 1
-#endif
+#include <amdis/AMDiS.hpp>
+#include <amdis/AdaptInstationary.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/ProblemInstat.hpp>
+#include <amdis/Operators.hpp>
+#include <amdis/assembler/StokesOperator.hpp>
 
 using namespace AMDiS;
 
 struct NavierStokesBasis
 {
-  using Grid = Dune::AlbertaGrid<AMDIS_DIM,AMDIS_DOW>;
+  using Grid = Dune::YaspGrid<AMDIS_DIM>;
   using GlobalBasis = typename TaylorHoodBasis<Grid::LeafGridView>::GlobalBasis;
 };
 
@@ -69,7 +60,7 @@ int main(int argc, char** argv)
   auto opNonlin1 = makeOperator(tag::testvec_trialvec{}, density * trans(gradientAtQP(prob.getSolution(_v))));
   prob.addMatrixOperator(opNonlin1, _v, _v);
 
-  for (std::size_t i = 0; i < DOW; ++i) {
+  for (std::size_t i = 0; i < AMDIS_DOW; ++i) {
     // <(u^old * nabla)u_i, v_i>
     auto opNonlin2 = makeOperator(tag::test_gradtrial{}, density * prob.getSolution(_v));
     prob.addMatrixOperator(opNonlin2, treepath(_v,i), treepath(_v,i));

src/BlockPreconditioner.hpp → examples/old/BlockPreconditioner.hpp

 #pragma once
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/LinearAlgebra.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/LinearAlgebra.hpp>
 
 namespace AMDiS
 {

src/MTLPfcPrecon.hpp → examples/old/MTLPfcPrecon.hpp

 #pragma once
 
 #include "BlockPreconditioner.hpp"
-#include <dune/amdis/common/Literals.hpp>
+#include <amdis/common/Literals.hpp>
 
 namespace AMDiS
 {

src/PfcPrecon.hpp → examples/old/PfcPrecon.hpp

@@ -9,7 +9,7 @@
 #include <dune/istl/multitypeblockvector.hh>
 #include <dune/istl/preconditioner.hh>
 
-#include <dune/amdis/common/Mpl.hpp>
+#include <amdis/common/Mpl.hpp>
 
 namespace AMDiS {
 

src/pfc.cc → examples/old/pfc.cc

@@ -5,11 +5,11 @@
 #include <ctime>
 #include <cmath>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/AdaptInstationary.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/ProblemInstat.hpp>
-#include <dune/amdis/Terms.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/AdaptInstationary.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/ProblemInstat.hpp>
+#include <amdis/Terms.hpp>
 
 #include "MTLPfcPrecon.hpp"
 

src/stokes0.cc → examples/stokes0.cc

@@ -2,9 +2,9 @@
 #include <ctime>
 #include <cmath>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Operators.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/Operators.hpp>
 
 #ifdef DOW
 #undef DOW
@@ -47,6 +47,8 @@ int main(int argc, char** argv)
       prob.addMatrixOperator(opDiv, _p, treepath(_v,i));
     }
 
+    auto opZero = makeOperator(tag::test_trial{}, 0.0);
+    prob.addMatrixOperator(opZero, _p, _p);
 
     // define boundary regions
     auto left = [](auto const& x) { return x[0] < 1.e-8; };
@@ -74,6 +76,11 @@ int main(int argc, char** argv)
     // assemble and solve system
     prob.buildAfterCoarsen(adaptInfo, Flag(0));
 
+    // write matrix to file
+    mtl::io::matrix_market_ostream out("matrix_stokes0.mtx");
+    out << prob.getSystemMatrix()->getMatrix();
+    std::cout << prob.getSystemMatrix()->getMatrix() << '\n';
+
     prob.solve(adaptInfo);
 
     // output solution

src/stokes1.cc → examples/stokes1.cc

@@ -2,9 +2,9 @@
 #include <ctime>
 #include <cmath>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Operators.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/Operators.hpp>
 
 #ifdef DOW
 #undef DOW
@@ -78,14 +78,9 @@ int main(int argc, char** argv)
     prob.buildAfterCoarsen(adaptInfo, Flag(0));
 
     // write matrix to file
-    if (Parameters::get<int>("stokesMesh->global refinements").value_or(0) < 2) {
-      mtl::io::matrix_market_ostream out("stokes_matrix.mtx");
-      out << prob.getSystemMatrix()->getMatrix();
-
-      std::cout << "A = \n" << prob.getSystemMatrix()->getMatrix() << '\n';
-      std::cout << "x = \n" << prob.getSolution()->getVector() << '\n';
-      std::cout << "b = \n" << prob.getRhs()->getVector() << '\n';
-    }
+    mtl::io::matrix_market_ostream out("matrix_stokes1.mtx");
+    out << prob.getSystemMatrix()->getMatrix();
+    std::cout << prob.getSystemMatrix()->getMatrix() << '\n';
 
     prob.solve(adaptInfo);
 

src/stokes3.cc → examples/stokes3.cc

@@ -2,10 +2,10 @@
 #include <ctime>
 #include <cmath>
 
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Operators.hpp>
-#include <dune/amdis/assembler/StokesOperator.hpp>
+#include <amdis/AMDiS.hpp>
+#include <amdis/ProblemStat.hpp>
+#include <amdis/Operators.hpp>
+#include <amdis/assembler/StokesOperator.hpp>
 
 using namespace AMDiS;
 
@@ -30,6 +30,9 @@ int main(int argc, char** argv)
   auto opStokes = makeOperator(tag::stokes{}, viscosity);
   prob.addMatrixOperator(opStokes, treepath(), treepath());
 
+  auto opZero = makeOperator(tag::test_trial{}, 0.0);
+  prob.addMatrixOperator(opZero, _p, _p);
+
   // define boundary regions
   auto left = [](auto const& x) { return x[0] < 1.e-8; };
   auto not_left = [](auto const& x) { return x[0] > 1.0 - 1.e-8 || x[1] < 1.e-8 || x[1] > 1.0 - 1.e-8; };