renamed path dune/amdis to amdis

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)
@@ -17,33 +11,30 @@ 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")
 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})
+  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})
+      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)
+      target_compile_definitions(amdis PUBLIC MTL_HAS_UMFPACK)
   endif ()
 endif (MTL_FOUND)
 

cmake/modules/AmdisMacros.cmake

 # File for module specific CMake tests.
 
-include(AMDiSCXXFeatures)
\ No newline at end of file
+include(AMDiSCXXFeatures)
+
+#find_package(SuiteSparse)
+#find_package(Alberta)
\ No newline at end of file

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; };

src/vecellipt.cc → examples/vecellipt.cc

 #include <iostream>
 
-#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>
 
 using namespace AMDiS;
 

src/CMakeLists.txt

-
-set(projects2d "ellipt" "heat" "vecellipt" "expressions" "stokes0" "stokes1" "stokes3")
-
-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
+add_subdirectory(amdis)
\ No newline at end of file

src/amdis.cc

-// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
-// vi: set et ts=4 sw=2 sts=2:
-
-#include <iostream>
-
-#include <dune/amdis/AMDiS.hpp>
-#include <dune/amdis/ProblemStat.hpp>
-#include <dune/amdis/Terms.hpp>
-
-using namespace AMDiS;
-
-// 1 component with polynomial degree 1
-using HeatParam   = TestTraits<AMDIS_DIM, 2>;
-using HeatProblem = ProblemStat<HeatParam>;
-
-int main(int argc, char** argv)
-{
-    AMDiS::init(argc, argv);
-
-    HeatProblem prob("heat");
-    prob.initialize(INIT_ALL);
-
-    AdaptInfo adaptInfo("adapt");
-
-    double tau = adaptInfo.getTimestep();
-    AMDIS_MSG("timestep = " << tau);
-
-    using Op = HeatProblem::ElementOperator;
-    Op opLhs;
-    opLhs.addZOT( constant(1.0/tau) );
-    opLhs.addSOT( constant(1.0) );
-
-    Op opRhs;
-    opRhs.addZOT( valueOf(prob.getSolution<0>(), 1.0/tau) );
-    opRhs.addZOT( eval([](auto const& x) { return -1.0; }) );
-
-    prob.addMatrixOperator(opLhs, 0, 0);
-    prob.addVectorOperator(opRhs, 0);
-
-    // set boundary condition
-    auto predicate = [](auto const& p){ return p[0] < 1.e-8 || p[1] < 1.e-8; };
-    auto dbcValues = [](auto const& p){ return 0.0; };
-    prob.addDirichletBC(predicate, 0, 0, dbcValues);
-
-    prob.getSolution<0>().getVector() = 0.0;
-    double t = 0.0;
-    for (t = adaptInfo.getStartTime();
-         t < adaptInfo.getEndTime();
-         t+= adaptInfo.getTimestep())
-    {
-        prob.writeFiles(adaptInfo, t);
-        prob.buildAfterCoarsen(adaptInfo, Flag(0));
-        prob.solve(adaptInfo);
-    }
-
-    prob.writeFiles(adaptInfo, t);
-    AMDiS::finalize();
-    return 0;
-}
\ No newline at end of file

dune/amdis/AMDiS.cpp → src/amdis/AMDiS.cpp

 #include "AMDiS.hpp"
 
 // AMDiS includes
-#include <dune/amdis/Initfile.hpp>
-#include <dune/amdis/Output.hpp>
+#include <amdis/Initfile.hpp>
+#include <amdis/Output.hpp>
 
 namespace AMDiS
 {

dune/amdis/AdaptInfo.cpp → src/amdis/AdaptInfo.cpp

@@ -4,7 +4,7 @@
 #include <string>
 #include <iostream>
 
-#include <dune/amdis/Initfile.hpp>
+#include <amdis/Initfile.hpp>
 
 namespace AMDiS
 {

dune/amdis/AdaptInfo.hpp → src/amdis/AdaptInfo.hpp

@@ -8,8 +8,8 @@
 #include <vector>
 
 // AMDiS includes
-#include <dune/amdis/Output.hpp>
-#include <dune/amdis/common/Math.hpp>
+#include <amdis/Output.hpp>
+#include <amdis/common/Math.hpp>
 
 namespace AMDiS
 {

dune/amdis/AdaptInstationary.cpp → src/amdis/AdaptInstationary.cpp

 #include "AdaptInstationary.hpp"
 
 // AMDiS includes
-#include <dune/amdis/AdaptInfo.hpp>
-#include <dune/amdis/Flag.hpp>
-#include <dune/amdis/Initfile.hpp>
-#include <dune/amdis/Output.hpp>
-#include <dune/amdis/ProblemIterationInterface.hpp>
-#include <dune/amdis/ProblemTimeInterface.hpp>
+#include <amdis/AdaptInfo.hpp>
+#include <amdis/Flag.hpp>
+#include <amdis/Initfile.hpp>
+#include <amdis/Output.hpp>
+#include <amdis/ProblemIterationInterface.hpp>
+#include <amdis/ProblemTimeInterface.hpp>
 
 namespace AMDiS
 {

dune/amdis/Assembler.hpp → src/amdis/Assembler.hpp

@@ -6,11 +6,11 @@
 #include <dune/common/fmatrix.hh>
 #include <dune/common/fvector.hh>
 
-#include <dune/amdis/DirichletBC.hpp>
-#include <dune/amdis/LinearAlgebra.hpp>
-#include <dune/amdis/LocalAssemblerBase.hpp>
-#include <dune/amdis/common/Mpl.hpp>
-#include <dune/amdis/common/TypeDefs.hpp>
+#include <amdis/DirichletBC.hpp>
+#include <amdis/LinearAlgebra.hpp>
+#include <amdis/LocalAssemblerBase.hpp>
+#include <amdis/common/Mpl.hpp>
+#include <amdis/common/TypeDefs.hpp>
 
 namespace AMDiS
 {

dune/amdis/Assembler.inc.hpp → src/amdis/Assembler.inc.hpp

 #pragma once
 
 #include <dune/functions/functionspacebases/subspacebasis.hh>
-#include <dune/amdis/utility/TreePath.hpp>
-#include <dune/amdis/utility/Visitor.hpp>
+#include <amdis/utility/TreePath.hpp>
+#include <amdis/utility/Visitor.hpp>
 
-#include <dune/amdis/common/Math.hpp>
+#include <amdis/common/Math.hpp>
 
 namespace AMDiS {
 

dune/amdis/CMakeLists.txt → src/amdis/CMakeLists.txt

@@ -13,6 +13,7 @@ dune_library_add_sources(amdis SOURCES
     ProblemStat.cpp
     StandardProblemIteration.cpp
 )
+link_libraries(amdis)
 
 install(FILES
     AdaptBase.hpp
@@ -50,7 +51,7 @@ install(FILES
     ProblemStatTraits.hpp
     ProblemTimeInterface.hpp
     StandardProblemIteration.hpp
-DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/dune/amdis)
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/amdis)
 
 add_subdirectory("assembler")
 add_subdirectory("common")

dune/amdis/CreatorInterface.hpp → src/amdis/CreatorInterface.hpp

@@ -3,8 +3,8 @@
 #include <memory>
 #include <string>
 
-#include <dune/amdis/common/Utility.hpp>
-#include <dune/amdis/Output.hpp>
+#include <amdis/common/Utility.hpp>
+#include <amdis/Output.hpp>
 
 namespace AMDiS
 {

dune/amdis/CreatorMap.hpp → src/amdis/CreatorMap.hpp

@@ -5,7 +5,7 @@
 #include <string>
 
 // AMDiS includes
-#include <dune/amdis/CreatorInterface.hpp>
+#include <amdis/CreatorInterface.hpp>
 
 namespace AMDiS
 {

dune/amdis/DirichletBC.hpp → src/amdis/DirichletBC.hpp

@@ -5,11 +5,11 @@
 #include <type_traits>
 #include <vector>
 
-#include <dune/amdis/Output.hpp>