Work on some general PETSc solver.

AMDiS/CMakeLists.txt

@@ -197,6 +197,7 @@ if(ENABLE_PARALLEL_DOMAIN)
 	find_package(PETSc REQUIRED)
 	include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
 	SET(PARALLEL_DOMAIN_AMDIS_SRC
+		${SOURCE_DIR}/parallel/CheckerPartitioner.cc
 		${SOURCE_DIR}/parallel/ElementObjectData.cc
 		${SOURCE_DIR}/parallel/MeshDistributor.cc 
 		${SOURCE_DIR}/parallel/MeshManipulation.cc

AMDiS/other/include/Makefile_AMDiS.mk

@@ -77,7 +77,7 @@ ifeq ($(strip $(USE_PARALLEL_AMDIS)), 1)
 	endif
 
 	CPPFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS
-	INCLUDES += $(PETSC_INCLUDE)
+	INCLUDES += $(PETSC_CC_INCLUDES)
 	LIBS += $(PARMETIS_LIB) -lmpi $(PETSC_LIB)
 	LIBS += $(ZOLTAN_LIB)
 else

AMDiS/src/Element.cc

@@ -18,6 +18,7 @@
 #include "ElementRegion_ED.h"
 #include "Serializer.h"
 #include "MeshStructure.h"
+#include "BasisFunction.h"
 
 namespace AMDiS {
 
@@ -622,4 +623,15 @@ namespace AMDiS {
     file.close();
   }
 
+
+  void Element::getAllDofs(FiniteElemSpace* feSpace, 
+			   BoundaryObject bound, 
+			   DofContainer& dofs)
+  {
+    getNodeDofs(feSpace, bound, dofs);
+
+    if (feSpace->getBasisFcts()->getDegree() > 1)
+      getHigherOrderDofs(feSpace, bound, dofs);
+  }
+
 }

AMDiS/src/Element.h

@@ -411,32 +411,38 @@ namespace AMDiS {
     virtual int getChildType(int elType) const = 0;
 
     /** \brief
-     * Traverses an edge/face of a given element (this includes also all children of 
-     * the element having the same edge/face). All vertex dofs alonge this edge/face
-     * are assembled and put together to a list. 
+     * Traverses a vertex/edge/face of a given element (this includes also all
+     * children of the element having the same edge/face). All DOFs on mesh
+     * nodes alonge this vertex/edge/face are assembled and put together to 
+     * a list.
      *
      * \param[in]  feSpace         FE space which is used to get the dofs.
-     * \param[in]  bound           Defines the edge/face of the element on which
-     *                             all vertex dofs are assembled.
+     * \param[in]  bound           Defines the vertex/edge/face of the element on
+     *                             which all vertex dofs are assembled.
      * \param[out] dofs            List of dofs, where the result is stored.
      */
-    virtual void getVertexDofs(FiniteElemSpace* feSpace, 
-			       BoundaryObject bound,
-			       DofContainer& dofs) const = 0;
+    virtual void getNodeDofs(FiniteElemSpace* feSpace, 
+			     BoundaryObject bound,
+			     DofContainer& dofs) const = 0;
 
     /** \brief
-     * Traverses an edge/face of a given element (this includes also all children of 
-     * the element having the same edge/face). All non vertex dofs alonge this edge/face 
-     * are assembled and put together to a list.
+     * Traverses a vertex/edge/face of a given element (this includes also all
+     * children of the element having the same edge/face). All DOFs belonging
+     * to higher order basis functions alonge this vertex/edge/face are 
+     * assembled and put together to a list.
      *
      * \param[in]  feSpace         FE space which is used to get the dofs.
      * \param[in]  bound           Defines the edge/face of the element on which
      *                             all non vertex dofs are assembled.
      * \param[out] dofs            All dofs are put to this dof list.
      */
-    virtual void getNonVertexDofs(FiniteElemSpace* feSpace, 
-				  BoundaryObject bound,
-				  DofContainer& dofs) const = 0;
+    virtual void getHigherOrderDofs(FiniteElemSpace* feSpace, 
+				    BoundaryObject bound,
+				    DofContainer& dofs) const = 0;
+
+    void getAllDofs(FiniteElemSpace* feSpace, 
+		    BoundaryObject bound, 
+		    DofContainer& dofs);
 
 
     /** \} */

AMDiS/src/Line.h

@@ -173,15 +173,15 @@ namespace AMDiS {
       return "Line"; 
     }
 
-    void getVertexDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
+    void getNodeDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
     {
-      FUNCNAME("Line::getVertexDofs()");
+      FUNCNAME("Line::getNodeDofs()");
       ERROR_EXIT("Not yet implemented!\n");
     }
 
-    void getNonVertexDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
+    void getHigherOrderDofs(FiniteElemSpace*, BoundaryObject, DofContainer&) const
     {
-      FUNCNAME("Line::getNonVertexDofs()");
+      FUNCNAME("Line::getHigherOrderDofs()");
       ERROR_EXIT("Not yet implemented!\n");
     }
 

AMDiS/src/Makefile.am

@@ -12,6 +12,7 @@ PARALLEL_INCLUDES =
 
 if USE_PARALLEL_DOMAIN_AMDIS
   PARALLEL_AMDIS_SOURCES += \
+  parallel/CheckerPartitioner.cc \
   parallel/ElementObjectData.cc \
   parallel/MeshDistributor.cc \
   parallel/MeshManipulation.cc \
@@ -247,6 +248,7 @@ io/ValueWriter.h \
 io/VtkWriter.h \
 io/VtkWriter.hh \
 itl/minres.hpp \
+parallel/CheckerPartitioner.h \
 parallel/ElementObjectData.h \
 parallel/InteriorBoundary.h \
 parallel/MeshDistributor.h \

AMDiS/src/Makefile.in

@@ -38,6 +38,7 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_1 = \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@  parallel/CheckerPartitioner.cc \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@  parallel/ElementObjectData.cc \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@  parallel/MeshDistributor.cc \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@  parallel/MeshManipulation.cc \
@@ -88,10 +89,11 @@ am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
 libLTLIBRARIES_INSTALL = $(INSTALL)
 LTLIBRARIES = $(lib_LTLIBRARIES)
 libamdis_la_LIBADD =
-am__libamdis_la_SOURCES_DIST = parallel/ElementObjectData.cc \
-	parallel/MeshDistributor.cc parallel/MeshManipulation.cc \
-	parallel/MeshPartitioner.cc parallel/MpiHelper.cc \
-	parallel/ParallelDebug.cc parallel/ParallelProblemStatBase.cc \
+am__libamdis_la_SOURCES_DIST = parallel/CheckerPartitioner.cc \
+	parallel/ElementObjectData.cc parallel/MeshDistributor.cc \
+	parallel/MeshManipulation.cc parallel/MeshPartitioner.cc \
+	parallel/MpiHelper.cc parallel/ParallelDebug.cc \
+	parallel/ParallelProblemStatBase.cc \
 	parallel/ParMetisPartitioner.cc parallel/PetscProblemStat.cc \
 	parallel/PetscSolver.cc parallel/StdMpi.cc \
 	parallel/ZoltanPartitioner.cc AdaptBase.cc AdaptInfo.cc \
@@ -130,7 +132,8 @@ am__libamdis_la_SOURCES_DIST = parallel/ElementObjectData.cc \
 	io/ValueWriter.cc io/VtkWriter.cc parallel/InteriorBoundary.cc \
 	time/RosenbrockAdaptInstationary.cc time/RosenbrockMethod.cc \
 	time/RosenbrockStationary.cc
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-ElementObjectData.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-CheckerPartitioner.lo \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@	libamdis_la-ElementObjectData.lo \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@	libamdis_la-MeshDistributor.lo \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@	libamdis_la-MeshManipulation.lo \
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@	libamdis_la-MeshPartitioner.lo \
@@ -568,6 +571,7 @@ io/ValueWriter.h \
 io/VtkWriter.h \
 io/VtkWriter.hh \
 itl/minres.hpp \
+parallel/CheckerPartitioner.h \
 parallel/ElementObjectData.h \
 parallel/InteriorBoundary.h \
 parallel/MeshDistributor.h \
@@ -822,6 +826,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BasisFunction.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Boundary.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BoundaryManager.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CheckerPartitioner.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Cholesky.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-CoarseningManager1d.Plo@am__quote@
@@ -976,6 +981,13 @@ distclean-compile:
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(LTCXXCOMPILE) -c -o $@ $<
 
+libamdis_la-CheckerPartitioner.lo: parallel/CheckerPartitioner.cc
+@am__fastdepCXX_TRUE@	if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-CheckerPartitioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo" -c -o libamdis_la-CheckerPartitioner.lo `test -f 'parallel/CheckerPartitioner.cc' || echo '$(srcdir)/'`parallel/CheckerPartitioner.cc; \
+@am__fastdepCXX_TRUE@	then mv -f "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo" "$(DEPDIR)/libamdis_la-CheckerPartitioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-CheckerPartitioner.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='parallel/CheckerPartitioner.cc' object='libamdis_la-CheckerPartitioner.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@	$(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-CheckerPartitioner.lo `test -f 'parallel/CheckerPartitioner.cc' || echo '$(srcdir)/'`parallel/CheckerPartitioner.cc
+
 libamdis_la-ElementObjectData.lo: parallel/ElementObjectData.cc
 @am__fastdepCXX_TRUE@	if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ElementObjectData.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo" -c -o libamdis_la-ElementObjectData.lo `test -f 'parallel/ElementObjectData.cc' || echo '$(srcdir)/'`parallel/ElementObjectData.cc; \
 @am__fastdepCXX_TRUE@	then mv -f "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo" "$(DEPDIR)/libamdis_la-ElementObjectData.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ElementObjectData.Tpo"; exit 1; fi

AMDiS/src/Mesh.cc

@@ -77,11 +77,11 @@ namespace AMDiS {
   const Flag Mesh::CALL_REVERSE_MODE       = 0X8000L;
 
 
-  std::vector<DegreeOfFreedom> Mesh::dof_used;
+  vector<DegreeOfFreedom> Mesh::dof_used;
   const int Mesh::MAX_DOF = 100;
-  std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
+  map<pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
 
-  Mesh::Mesh(std::string aName, int dimension) 
+  Mesh::Mesh(string aName, int dimension) 
     : name(aName), 
       dim(dimension), 
       nVertices(0),
@@ -186,7 +186,7 @@ namespace AMDiS {
   
     // mapIndex[i] is the index of the MacroElement element in the vector
     // macroElements, for which holds: element->getIndex() = i    
-    std::map<int, int> mapIndex;
+    map<int, int> mapIndex;
 
     // We use this map for coping the DOFs of the Elements within the
     // MacroElements objects.
@@ -198,7 +198,7 @@ namespace AMDiS {
 
     // Go through all MacroElements of mesh m, and create for every a new
     // MacroElement in this mesh.
-    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
+    for (deque<MacroElement*>::const_iterator it = m.macroElements.begin();
 	 it != m.macroElements.end(); ++it, insertCounter++) {
 
       // Create new MacroElement.
@@ -214,13 +214,13 @@ namespace AMDiS {
       macroElements.push_back(el);
 
       // Update the index map.
-      mapIndex.insert(std::pair<int, int>(el->getIndex(), insertCounter));
+      mapIndex.insert(pair<int, int>(el->getIndex(), insertCounter));
     }
 
     // Now we have to go through all the new MacroElements, and update the neighbour
     // connections.
     insertCounter = 0;
-    for (std::deque<MacroElement*>::const_iterator it = m.macroElements.begin();
+    for (deque<MacroElement*>::const_iterator it = m.macroElements.begin();
 	 it != m.macroElements.end();
 	 ++it, insertCounter++) {
       // Go through all neighbours.
@@ -275,8 +275,8 @@ namespace AMDiS {
   {
     FUNCNAME("Mesh::removeMacroElement()");
 
-    typedef std::map<const DegreeOfFreedom*, std::set<MacroElement*> > DofElMap;
-    typedef std::map<const DegreeOfFreedom*, GeoIndex> DofPosMap;
+    typedef map<const DegreeOfFreedom*, std::set<MacroElement*> > DofElMap;
+    typedef map<const DegreeOfFreedom*, GeoIndex> DofPosMap;
 
     TEST_EXIT(admin.size() == 1)("Not yet implemented for multiple admins!\n");
     TEST_EXIT(admin[0])("There is something wrong!\n");
@@ -305,12 +305,12 @@ namespace AMDiS {
 
     // === Remove macro elements from mesh macro element list. ===
 
-    // Removing arbitrary elements from an std::deque is very slow. Therefore, we
+    // Removing arbitrary elements from an deque is very slow. Therefore, we
     // create a new deque with all macro elements that should not be deleted. The
     // macro element deque is than replaced by the new created one.
 
-    std::deque<MacroElement*> newMacroElements;
-    for (std::deque<MacroElement*>::iterator elIter = macroElements.begin();
+    deque<MacroElement*> newMacroElements;
+    for (deque<MacroElement*>::iterator elIter = macroElements.begin();
 	 elIter != macroElements.end(); ++elIter) {
       // If the current mesh macro element should not be deleted, i.e., it is not a
       // member of the list of macro elements to be deleted, is is inserted to the new
@@ -416,7 +416,7 @@ namespace AMDiS {
 
     localAdmin->setMesh(this);
 
-    TEST_EXIT(std::find(admin.begin(), admin.end(), localAdmin) == admin.end())
+    TEST_EXIT(find(admin.begin(), admin.end(), localAdmin) == admin.end())
       ("admin %s is already associated to mesh %s\n",
        localAdmin->getName().c_str(), this->getName().c_str());
 
@@ -479,7 +479,7 @@ namespace AMDiS {
 	  compressAdmin->getHoleCount() < 1)    
 	continue;
 
-      std::vector<int> newDofIndex(size);     
+      vector<int> newDofIndex(size);     
       compressAdmin->compress(newDofIndex);
 
       Flag fill_flag = (preserveCoarseDOFs ?  
@@ -559,7 +559,7 @@ namespace AMDiS {
   }
 
 
-  const DOFAdmin *Mesh::createDOFAdmin(std::string lname, DimVec<int> lnDof)
+  const DOFAdmin *Mesh::createDOFAdmin(string lname, DimVec<int> lnDof)
   {
     FUNCNAME("Mesh::createDOFAdmin()");
     
@@ -905,10 +905,12 @@ namespace AMDiS {
 			       const FiniteElemSpace* feSpace,
 			       WorldVector<double>& coords)
   {
+    FUNCNAME("Mesh::getDofIndexCoords()");
+
     DimVec<double>* baryCoords;
     bool found = false;
     TraverseStack stack;
-    std::vector<DegreeOfFreedom> dofVec(feSpace->getBasisFcts()->getNumber());
+    vector<DegreeOfFreedom> dofVec(feSpace->getBasisFcts()->getNumber());
 
     ElInfo *elInfo = stack.traverseFirst(this, -1, 
 					 Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);    
@@ -938,9 +940,11 @@ namespace AMDiS {
   void Mesh::getDofIndexCoords(const FiniteElemSpace* feSpace,
 			       DOFVector<WorldVector<double> >& coords)
   {
+    FUNCNAME("Mesh::getDofIndexCoords()");
+
     const BasisFunction* basFcts = feSpace->getBasisFcts();
     int nBasFcts = basFcts->getNumber();
-    std::vector<DegreeOfFreedom> dofVec(nBasFcts);
+    vector<DegreeOfFreedom> dofVec(nBasFcts);
 
     TraverseStack stack;
     ElInfo *elInfo = 
@@ -958,6 +962,27 @@ namespace AMDiS {
   }
 
 
+  void Mesh::getAllDofs(FiniteElemSpace *feSpace, 
+			std::set<const DegreeOfFreedom*>& allDofs)
+  {
+    FUNCNAME("Mesh::getAllDofs()");
+
+    ElementDofIterator elDofIt(feSpace);   
+    allDofs.clear();
+
+    TraverseStack stack;
+    ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_LEAF_EL);
+    while (elInfo) {
+      elDofIt.reset(elInfo->getElement());
+      do {
+	allDofs.insert(elDofIt.getDofPtr());
+      } while(elDofIt.next());
+
+      elInfo = stack.traverseNext(elInfo);
+    }
+  }
+
+
   void Mesh::setDiameter(const WorldVector<double>& w) 
   { 
     diam = w; 
@@ -970,7 +995,7 @@ namespace AMDiS {
   }
 
 
-  void Mesh::serialize(std::ostream &out)
+  void Mesh::serialize(ostream &out)
   {
     serializedDOFs.clear();
 
@@ -1022,7 +1047,7 @@ namespace AMDiS {
     // === Write periodic associations. ===
     int mapSize = periodicAssociations.size();
     SerUtil::serialize(out, mapSize);
-    for (std::map<BoundaryType, VertexVector*>::iterator it = periodicAssociations.begin();
+    for (map<BoundaryType, VertexVector*>::iterator it = periodicAssociations.begin();
 	 it != periodicAssociations.end(); ++it) {
       BoundaryType b = it->first;
 
@@ -1046,7 +1071,7 @@ namespace AMDiS {
   }
 
 
-  void Mesh::deserialize(std::istream &in)
+  void Mesh::deserialize(istream &in)
   {
     FUNCNAME("Mesh::deserialize()");
 
@@ -1100,7 +1125,7 @@ namespace AMDiS {
     }
 
     SerUtil::deserialize(in, size);
-    std::vector< std::vector<int> > neighbourIndices(size);
+    vector< vector<int> > neighbourIndices(size);
 
     deleteMeshStructure();
 
@@ -1110,7 +1135,7 @@ namespace AMDiS {
     // decomposition based parallelization. Therefore we create a temporary map
     // from macro element indices to the continous index of \ref macroElements. This
     // will be used later to find the correct neighbours of the macro elements.
-    std::map<int, int> elIndexVecIndex;
+    map<int, int> elIndexVecIndex;
 
     macroElements.resize(size);
     for (int i = 0; i < size; i++) {
@@ -1177,9 +1202,9 @@ namespace AMDiS {
 
     TEST_EXIT(admin.size() > 0)("No DOF admin defined!\n");
 
-    std::string macroFilename("");
-    std::string valueFilename("");
-    std::string periodicFilename("");
+    string macroFilename("");
+    string valueFilename("");
+    string periodicFilename("");
     int check = 1;
 
     GET_PARAMETER(0, name + "->macro file name",  &macroFilename);
@@ -1206,8 +1231,8 @@ namespace AMDiS {
 
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-  void Mesh::checkParallelMacroFile(std::string &macroFilename, 
-				    std::string &periodicFilename,
+  void Mesh::checkParallelMacroFile(string &macroFilename, 
+				    string &periodicFilename,
 				    int check)
   {
     FUNCNAME("Mesh::checkParallelMacroFile()");
@@ -1260,7 +1285,8 @@ namespace AMDiS {
     //    =>  gr = log_2(nProcs * 10 / nMacroElements)
     
     double scale = 10.0 * MPI::COMM_WORLD.Get_size() / nMacroElements;
-    nParallelPreRefinements = static_cast<int>(std::max(0.0, ceil(log(scale) / log(2))));
+    nParallelPreRefinements = 
+      static_cast<int>(std::max(0.0, ceil(log(scale) / log(2))));
     
     if (dim == 3) {
       int newElType = (elType + nParallelPreRefinements) % 3;
@@ -1299,7 +1325,7 @@ namespace AMDiS {
 
     // === If macro weights are explicitly given, we cannot change the mesh. ===
 
-    std::string macroWeightsFilename = "";
+    string macroWeightsFilename = "";
     GET_PARAMETER(0, name + "->macro weights", &macroWeightsFilename);
     if (macroWeightsFilename != "") {
       ERROR_EXIT("Should not happen!\n");
@@ -1315,12 +1341,14 @@ namespace AMDiS {
       srand(time(NULL));
       filenameRandomNumber = rand() % 1000000;
     }
+    MPI::COMM_WORLD.Barrier();
     MPI::COMM_WORLD.Bcast(&filenameRandomNumber, 1, MPI_INT, 0);
+    MPI::COMM_WORLD.Barrier();
 
-    std::stringstream newMacroFilename;
+    stringstream newMacroFilename;
     newMacroFilename << macroFilename << "." << filenameRandomNumber << ".tmp";
 
-    std::stringstream newPeriodicFilename;
+    stringstream newPeriodicFilename;
     newPeriodicFilename << periodicFilename << "." << filenameRandomNumber << ".tmp";
 
 
@@ -1363,7 +1391,7 @@ namespace AMDiS {
     else 
       globalRefinements -= nParallelPreRefinements;
 
-    std::stringstream oss;
+    stringstream oss;
     oss << globalRefinements;
     ADD_PARAMETER(0, name + "->global refinements", oss.str().c_str());
 
@@ -1382,8 +1410,8 @@ namespace AMDiS {
 
   bool Mesh::associated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) 
   {
-    std::map<BoundaryType, VertexVector*>::iterator it;
-    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
+    map<BoundaryType, VertexVector*>::iterator it;
+    map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
     for (it = periodicAssociations.begin(); it != end; ++it)
       if ((*(it->second))[dof1] == dof2)
 	return true;
@@ -1394,9 +1422,9 @@ namespace AMDiS {
 
   bool Mesh::indirectlyAssociated(DegreeOfFreedom dof1, DegreeOfFreedom dof2) 
   {
-    std::vector<DegreeOfFreedom> associatedToDOF1;
-    std::map<BoundaryType, VertexVector*>::iterator it;
-    std::map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
+    vector<DegreeOfFreedom> associatedToDOF1;
+    map<BoundaryType, VertexVector*>::iterator it;
+    map<BoundaryType, VertexVector*>::iterator end = periodicAssociations.end();
     DegreeOfFreedom dof, assDOF;
 
     associatedToDOF1.push_back(dof1);
@@ -1444,7 +1472,7 @@ namespace AMDiS {
   {
     Element::deletedDOFs.clear();
     
-    for (std::deque<MacroElement*>::const_iterator it = macroElements.begin();
+    for (deque<MacroElement*>::const_iterator it = macroElements.begin();
 	 it != macroElements.end(); ++it) {
       (*it)->getElement()->deleteElementDOFs();
       delete *it;

AMDiS/src/Mesh.h

@@ -50,6 +50,9 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
+
   /** \ingroup Triangulation 
    * \brief
    * A Mesh holds all information about a triangulation. 
@@ -58,7 +61,7 @@ namespace AMDiS {
   {
   public:
     /// Creates a mesh with the given name of dimension dim
-    Mesh(std::string name, int dim);
+    Mesh(string name, int dim);
 
     /// Destructor
     virtual ~Mesh();
@@ -83,7 +86,7 @@ namespace AMDiS {
     }
 
     /// Returns \ref name of the mesh
-    inline std::string getName() const 
+    inline string getName() const 
     { 
       return name; 
     }
@@ -197,7 +200,7 @@ namespace AMDiS {
      * are needed at the different positions (see \ref DOFAdmin::nrDOF).
      * A pointer to the created DOFAdmin is returned.
      */
-    const DOFAdmin* createDOFAdmin(std::string lname, DimVec<int> nDof);
+    const DOFAdmin* createDOFAdmin(string lname, DimVec<int> nDof);
 
     /** \brief
      * Returns the size of \ref admin which is the number of the DOFAdmins
@@ -230,7 +233,7 @@ namespace AMDiS {
     }
 
     /// Returns an iterator to the begin of \ref macroElements
-    inline std::deque<MacroElement*>::iterator firstMacroElement() 
+    inline deque<MacroElement*>::iterator firstMacroElement() 
     {
       return macroElements.begin();
     }
@@ -242,13 +245,13 @@ namespace AMDiS {
     }
 
     /// Returns an iterator to the end of \ref macroElements
-    inline std::deque<MacroElement*>::iterator endOfMacroElements() 
+    inline deque<MacroElement*>::iterator endOfMacroElements() 
     {
       return macroElements.end();
     }
 
     /// Returns \ref macroElements, the list of all macro elements in the mesh.
-    std::deque<MacroElement*>& getMacroElements()
+    deque<MacroElement*>& getMacroElements()
     {
       return macroElements;
     }
@@ -260,7 +263,7 @@ namespace AMDiS {
      */
 
     /// Sets \ref name of the mesh
-    inline void setName(std::string aName) 
+    inline void setName(string aName) 
     { 
       name = aName;
     }
@@ -496,16 +499,25 @@ namespace AMDiS {
 			   WorldVector<double>& coords);
 
     /** \brief
-     * Traverse the whole mesh and stores to each DOF of the given finite element space
-     * the coordinates in a given DOFVector. Works in the same way as the function
-     * \ref getDofIndexCoords defined above.
+     * Traverse the whole mesh and stores to each DOF of the given finite
+     * element space the coordinates in a given DOFVector. Works in the same
+     * way as the function \ref getDofIndexCoords defined above.
      *
-     * @param[in]   feSpace   The fe soace to be used for the search.
-     * @param[out]  coords    DOF vector that stores the coordinates to each dof.
+     * @param[in]   feSpace   The FE space to be used for the search.
+     * @param[out]  coords    DOF vector that stores the coordinates to each DOF.
      */
     void getDofIndexCoords(const FiniteElemSpace* feSpace,
 			   DOFVector<WorldVector<double> >& coords);
 
+    /** \brief
+     * Traverse the mesh and get all DOFs in this mesh for a given FE space.
+     *
+     * @param[in]   feSpace   The FE space to be used for collecting DOFs.
+     * @param[out]  allDofs   The set which is filled with all DOFs.
+     */
+    void getAllDofs(FiniteElemSpace *feSpace, 
+		    std::set<const DegreeOfFreedom*>& allDofs);
+
     /// Returns FILL_ANY_?D
     inline static const Flag& getFillAnyFlag(int dim) 
     {
@@ -526,10 +538,10 @@ namespace AMDiS {
     }
 
     /// Serialize the mesh to a file.
-    void serialize(std::ostream &out);
+    void serialize(ostream &out);
 
     /// Deserialize a mesh from a file.
-    void deserialize(std::istream &in);
+    void deserialize(istream &in);
 
     /// Returns \ref elementIndex and increments it by 1.
     inline int getNextElementIndex() 
@@ -544,7 +556,7 @@ namespace AMDiS {
     }
   
     ///
-    inline std::map<BoundaryType, VertexVector*>& getPeriodicAssociations() 
+    inline map<BoundaryType, VertexVector*>& getPeriodicAssociations() 
     {
       return periodicAssociations;
     }
@@ -707,8 +719,8 @@ namespace AMDiS {
      *                                    AMDiS macro mesh, the value must be 1 and 0
      *                                    otherwise.
      */
-    void checkParallelMacroFile(std::string &macroFilename, 
-				std::string &periodicFilename,
+    void checkParallelMacroFile(string &macroFilename, 
+				string &periodicFilename,
 				int check);
 #endif
 
@@ -717,7 +729,7 @@ namespace AMDiS {
     static const int MAX_DOF;
 
     /// Name of this Mesh
-    std::string name;
+    string name;