some small errors and warnings corrected

AMDiS/src/Expressions.hh

@@ -213,7 +213,7 @@ transformDOF_mm(Term term, DOFVector<T>* result)
   assigned.set(0);
   temp.set(tmp);
   
-  while (cont) {      
+  while (cont) {
     term.initElement(&ot, dualElInfo.colElInfo, NULL, NULL, basisFcts);
     basisFcts->getLocalIndices(dualElInfo.rowElInfo->getElement(), resultFeSpace->getAdmin(), localIndices);
     
@@ -245,6 +245,8 @@ transformDOF_mm(Term term, DOFVector<T>* result)
     *resultIter = (*tempIter);
     *resultIter/= (*assignedIter);
   }
+  
+  delete lambda_1;
 }
 
 } // end namespace AMDiS

AMDiS/src/Mesh.cc

@@ -1461,9 +1461,10 @@ namespace AMDiS {
       else
       {
         ERROR_EXIT("Parallel model only support dim = 2 or 3.\n");
+	return;
       }
 
-      refManager->globalRefine(&testMesh, nParallelPreRefinements);      
+      refManager->globalRefine(&testMesh, nParallelPreRefinements);
       delete refManager;
 
       Lagrange* basFcts = Lagrange::getLagrange(dim, 1);

AMDiS/src/ProblemStat.cc

@@ -178,20 +178,23 @@ namespace AMDiS {
       if (adoptProblem && 
 	  (adoptFlag.isSet(INIT_MESH) ||
 	   adoptFlag.isSet(INIT_SYSTEM) ||
-	   adoptFlag.isSet(INIT_FE_SPACE))) {
+	   adoptFlag.isSet(INIT_FE_SPACE))) 
+      {
 	meshes = adoptProblem->getMeshes();
-	componentMeshes = adoptProblem->componentMeshes;
-      
-	TEST_EXIT(adoptProblem->getNumAddComponents() + nAddComponents > 0)
-	  ("Not yet implemented.\n");
-	// If the adopt problem has fewer components than this problem, but only one
-	// mesh for all component, than scal up the componentMeshes array.
-	if (adoptProblem->getNumComponents() < nComponents) {
-	  TEST_EXIT(meshes.size() == 1)("Daran muss ich noch arbeiten!\n");
-	  
+	if (meshes.size() == 1)
+	  componentMeshes.resize(nComponents, meshes[0]);
+	else if (adoptProblem->getNumComponents() >= nComponents) {
 	  componentMeshes.resize(nComponents);
-	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
-	    componentMeshes[i] = componentMeshes[0];
+	  std::copy(adoptProblem->componentMeshes.begin(), 
+		    adoptProblem->componentMeshes.begin() + nComponents, 
+		    componentMeshes.begin());
+	} else {
+	  componentMeshes.resize(nComponents, meshes[0]);
+	  WARNING("componentMeshes may not be derived correctly from the adoptProblem. You have to do this manually!\n");
+	}
+	
+	if (nAddComponents > 0) {
+	  WARNING("Additional meshed can not be adopted from adoptProblem. You have to initialize these meshes manually!\n");
 	}
       }
     }
@@ -229,24 +232,26 @@ namespace AMDiS {
 	createFeSpace(NULL);
 
       if (adoptProblem &&
-	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
+	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) 
+      {
 	feSpaces = adoptProblem->getFeSpaces();
-	componentSpaces = adoptProblem->componentSpaces;
 	traverseInfo = adoptProblem->traverseInfo;
-      
-	TEST_EXIT(adoptProblem->getNumAddComponents() + nAddComponents > 0)
-	  ("Not yet implemented.\n");
-
-	// If the adopt problem has fewer components than this problem, but only one
-	// fe space for all component, than scal up the componentSpaces array.
-	if (adoptProblem->getNumComponents() < nComponents) {
-	  TEST_EXIT(feSpaces.size() == 1)("Daran muss ich noch arbeiten!\n");
-	  
+	
+	if (feSpaces.size() == 1)
+	  componentSpaces.resize(nComponents, feSpaces[0]);
+	else if (adoptProblem->getNumComponents() >= nComponents) {
 	  componentSpaces.resize(nComponents);
-	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
-	    componentSpaces[i] = componentSpaces[0];
+	  std::copy(adoptProblem->componentSpaces.begin(), 
+		    adoptProblem->componentSpaces.begin() + nComponents,
+		    componentSpaces.begin());
+	} else {
+	  componentSpaces.resize(nComponents, feSpaces[0]);
+	  WARNING("componentSpaces may not be derived correctly from the adoptProblem. You have to do this manually!\n");
+	}
+	
+	if (nAddComponents > 0) {
+	  WARNING("Additional feSpaces can not be adopted from adoptProblem. You have to initialize these fespaces manually!\n");
 	}
-
       }
     }
 
@@ -276,10 +281,8 @@ namespace AMDiS {
       }
     }
 
-// #ifndef HAVE_PARALLEL_DOMAIN_AMDIS
     if (!solver) 
       WARNING("no solver created\n");
-// #endif
 
     // === create estimator ===
     if (initFlag.isSet(INIT_ESTIMATOR))

AMDiS/src/ProblemStat.h

@@ -147,17 +147,6 @@ namespace AMDiS {
     void dualAssemble(AdaptInfo *adaptInfo, Flag flag, 
 		      bool asmMatrix = true, bool asmVector = true);
 
-    /// Determines the execution order of the single adaption steps. If adapt is
-    /// true, mesh adaption will be performed. This allows to avoid mesh adaption,
-    /// e.g. in timestep adaption loops of timestep adaptive strategies.
-    Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION) override;
-
-    /// Returns number of managed problems
-    int getNumProblems() override
-    { 
-      return 1; 
-    }
-
     /// Implementation of ProblemStatBase::getNumComponents(), TODO: Wrong!!
     virtual int getNumComponents() 
     { 
@@ -169,13 +158,6 @@ namespace AMDiS {
       return nAddComponents;
     }
 
-    /// Returns the problem with the given number. If only one problem
-    /// is managed by this master problem, the number hasn't to be given.
-    ProblemStatBase *getProblem(int number = 0) override
-    { 
-      return this; 
-    }
-
     /// Writes output files. TODO: Make obsolete.
     void writeFiles(AdaptInfo *adaptInfo, bool force);
 
@@ -557,11 +539,13 @@ namespace AMDiS {
       return fileWriters;
     }
     
+    /// Returns \ref solutionTime.
     double getSolutionTime()
     {
       return solutionTime;
     }
     
+    /// Returns \ref buildTime.
     double getBuildTime()
     {
       return buildTime;
@@ -687,36 +671,64 @@ namespace AMDiS {
 
     std::map<Operator*, std::vector<OperatorPos> > operators;
     
+    /// time needed to solve the linear system
     double solutionTime;
+    
+    /// time needed to assemble the linear system
     double buildTime;
     
     template <class> friend class detail::CouplingProblemStat;
   };
-
-#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
-  struct ProblemStat : public ProblemStatSeq, 
-		       public StandardProblemIteration
+  
+  namespace detail
   {
-    typedef ProblemStatSeq super;
-    using super::getName;
-    
-    ProblemStat(std::string nameStr,
-		ProblemIterationInterface *problemIteration = NULL)
-      : super(nameStr, problemIteration),
-	StandardProblemIteration(this)
-    { }
-
-    Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo)
+    template <class ProblemStatType>
+    struct ProblemStat : public ProblemStatType, 
+			 public StandardProblemIteration
     {
-      for (int i = 0; i < getNumComponents(); i++)
-	if (adaptInfo->spaceToleranceReached(i))
-	  adaptInfo->allowRefinement(false, i);
-	else
-	  adaptInfo->allowRefinement(true, i);	
-
-      return StandardProblemIteration::oneIteration(adaptInfo, toDo);
-    }
-  };
+      using ProblemStatType::getName;
+      
+      /// Constructor
+      ProblemStat(std::string nameStr,
+		  ProblemIterationInterface *problemIteration = NULL)
+	: ProblemStatType(nameStr, problemIteration),
+	  StandardProblemIteration(this)
+      { }
+
+      /// Returns number of managed problems
+      // implements StandardProblemIteration::getNumProblems()
+      virtual int getNumProblems() override
+      { 
+	return 1; 
+      }
+
+      /// Returns the problem with the given number. If only one problem
+      /// is managed by this master problem, the number hasn't to be given.
+      // implements StandardProblemIteration::getProblem(int)
+      virtual ProblemStatBase *getProblem(int number = 0) override
+      { 
+	return this; 
+      }
+
+      /// Determines the execution order of the single adaption steps. If adapt is
+      /// true, mesh adaption will be performed. This allows to avoid mesh adaption,
+      /// e.g. in timestep adaption loops of timestep adaptive strategies.
+      // implements StandardProblemIteration::oneIteration(AdaptInfo*, Flag)
+      virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION) override
+      {	
+	for (int i = 0; i < ProblemStatType::getNumComponents(); i++)
+	  if (adaptInfo->spaceToleranceReached(i))
+	    adaptInfo->allowRefinement(false, i);
+	  else
+	    adaptInfo->allowRefinement(true, i);	
+
+	return StandardProblemIteration::oneIteration(adaptInfo, toDo);
+      }
+    };
+  }
+  
+#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
+  typedef detail::ProblemStat<ProblemStatSeq> ProblemStat;
 #endif
 }
 

AMDiS/src/io/detail/Arh3Reader.cc

@@ -35,16 +35,16 @@ namespace AMDiS { namespace io {
     
 	file.read(const_cast<char*>(typeId.data()), 4);
 	TEST_EXIT(typeId == id)
-	  ("Cannot read Arh2 format: this file is not \"arh2\" format.\n");
+	  ("Cannot read Arh format: this file is not \"%s\" format.\n", id.c_str());
 
 	file.read(reinterpret_cast<char*>(&major_), 1);
 	TEST_EXIT(major == major_)
-	  ("Cannot read Arh2 format: Arh2Reader major version is %i, the file major version is %i. \n",
+	  ("Cannot read Arh format: Arh2Reader major version is %i, the file major version is %i. \n",
 	  major, major_);
 
 	file.read(reinterpret_cast<char*>(&minor_), 1);
 	TEST_EXIT(minor <= minor_)
-	  ("Cannot read Arh2 format: Arh2Reader minor version is %i is smaller than the file minor version %i.\n", 
+	  ("Cannot read Arh format: ArhReader minor version is %i is smaller than the file minor version %i.\n", 
 	  minor, minor_);
       }
       
@@ -344,7 +344,7 @@ namespace AMDiS { namespace io {
 		if ((*nDOF)[0] != feSpaceDOFs[vecsFeSpaceNum[i]][3])
 		  matchdof = false;
 		else {
-		  for(size_t j = 1; j < nDOF->getSize(); j++) {
+		  for(int j = 1; j < nDOF->getSize(); j++) {
 		    if((*nDOF)[j] != feSpaceDOFs[vecsFeSpaceNum[i]][j-1]){
 		      matchdof = false;
 		      break;
@@ -373,7 +373,7 @@ namespace AMDiS { namespace io {
 	      
 	      TEST_EXIT((*nDOF)[0] == feSpaceDOFs[vecsFeSpaceNum[i]][3])
 		  ("The fespace of vec number %i is not equal to the correspond fespace.\n", i+1);
-	      for(size_t j = 1; j < nDOF->getSize(); j++)
+	      for(int j = 1; j < nDOF->getSize(); j++)
 		TEST_EXIT((*nDOF)[j] == feSpaceDOFs[vecsFeSpaceNum[i]][j-1])
 		  ("The fespace of vec number %i is not equal to the correspond fespace.\n", i+1);
 	    }
@@ -498,12 +498,13 @@ namespace AMDiS { namespace io {
       template<typename T>
       void readValues(stringstream& file, vector<double>& values)
       {
-	int size = values.size();
-	T data[size];
+	size_t size = values.size();
+	T* data = new T[size];
 	file.read(reinterpret_cast<char*>(&data[0]), sizeof(T) * size);
 	
 	for (size_t i = 0; i < size; i++)
 	  values[i] = static_cast<double>(data[i]);
+	delete data;
       }
     
       void readFile(string filename, Mesh *mesh,
@@ -585,11 +586,13 @@ namespace AMDiS { namespace io {
 	    nMacros = mesh->getNumberOfMacros();
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
 	    Parallel::mpi::globalAdd(nMacros);
-	    if(MPI::COMM_WORLD.Get_rank() == 0) 
+	    if(MPI::COMM_WORLD.Get_rank() == 0)
 #endif	      
+	    {
 	      TEST_EXIT(nMacros == nMacros_)
 		  ("Number of macro elements in parallel ARH files doesn't match to the current runtime. %d vs %d\n",
 		  nMacros, nMacros_); 
+	    }
 
 	    if (!parh) {
 	      for (int i = 0; i < nProcs; i++) {
@@ -818,7 +821,7 @@ namespace AMDiS { namespace io {
 	file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
 	
 	uint32_t rank = 0;
-	for (size_t i = 0; i < nMacros; i++) {
+	for (int i = 0; i < nMacros; i++) {
 	  file.read(reinterpret_cast<char*>(&rank), 4);
 	  partition.push_back(rank);
 	}

AMDiS/src/io/detail/Arh3Writer.cc

@@ -120,9 +120,7 @@ namespace AMDiS { namespace io {
 	  Mesh* mesh_ = mesh ? mesh : vecs[0]->getFeSpace()->getMesh();
 	  
 	  if (MPI::COMM_WORLD.Get_rank() == 0) {
-	    writeParallelFile(name + ".parh", 
-			      mesh ? mesh : vecs[0]->getFeSpace()->getMesh(),
-			      filenameType);
+	    writeParallelFile(name + ".parh", mesh_, filenameType);
 	  }
 	  
 	  TEST_EXIT(filenameType == "cont")("Only filename type \"cont\".\n");
@@ -195,7 +193,7 @@ namespace AMDiS { namespace io {
 			       string dataformat)
       {
         FUNCNAME("Arh3Writer::detail::writeHeader()");
-	int nbits = boost::lexical_cast<int>(dataformat.substr(2, 2));
+// 	int nbits = boost::lexical_cast<int>(dataformat.substr(2, 2));
         TEST_EXIT(file.is_open())("the file is not open. should not happen.\n");
 	
 	map<const FiniteElemSpace*, string> AFEDfileName;
@@ -277,11 +275,11 @@ namespace AMDiS { namespace io {
 	  file.write(nameStr.c_str(), nameStrLen);
 	  DimVec<int>* nDOF = feSpaceIt->first->getBasisFcts()->getNumberOfDofs();
 	  //
-	  for(size_t j = 1; j < nDOF->getSize(); j++) {
+	  for(int j = 1; j < nDOF->getSize(); j++) {
             posDOFs = (*nDOF)[j];
             file.write(reinterpret_cast<char*>(&posDOFs), 4);
           }
-          for(size_t j = nDOF->getSize(); j < 4 ; j++) {
+          for(int j = nDOF->getSize(); j < 4 ; j++) {
             posDOFs = 0;
             file.write(reinterpret_cast<char*>(&posDOFs), 4);
           }
@@ -537,12 +535,13 @@ namespace AMDiS { namespace io {
       template<typename T>
       int writeValues(stringstream& file, vector<double>& values)
       {
-	int size = values.size();
-	T data[size];
+	size_t size = values.size();
+	T* data = new T[size];
 	for (size_t i = 0; i < size; i++)
 	  data[i] = static_cast<T>(values[i]);
 	
 	file.write(reinterpret_cast<char*>(&data[0]), sizeof(T) * size);
+	delete data;
 	return sizeof(T) * size;
       }
       

AMDiS/src/parallel/ParallelProblemStat.cc

@@ -88,7 +88,7 @@ namespace AMDiS { namespace Parallel {
     std::vector<const FiniteElemSpace*> tmpFeSpaces, tmpComponentSpaces(getComponentSpaces().begin(),
 							   getComponentSpaces().begin() + getNumComponents());
 							   
-    for (int i = 0; i < tmpComponentSpaces.size(); i++)
+    for (size_t i = 0; i < tmpComponentSpaces.size(); i++)
       if (std::find(tmpFeSpaces.begin(), tmpFeSpaces.end(), tmpComponentSpaces[i]) == tmpFeSpaces.end())
 	tmpFeSpaces.push_back(tmpComponentSpaces[i]);
       

AMDiS/src/parallel/ParallelProblemStat.h

@@ -77,29 +77,7 @@ namespace AMDiS
   } // end namespace Parallel
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-  struct ProblemStat : public Parallel::ParallelProblemStat, 
-		       public StandardProblemIteration
-  {
-    typedef Parallel::ParallelProblemStat super;
-    using super::getName;
-    
-    ProblemStat(std::string nameStr,
-		ProblemIterationInterface *problemIteration = NULL)
-      : super(nameStr, problemIteration),
-	StandardProblemIteration(this)
-    { }
-
-    Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo)
-    {
-      for (int i = 0; i < getNumComponents(); i++)
-	if (adaptInfo->spaceToleranceReached(i))
-	  adaptInfo->allowRefinement(false, i);
-	else
-	  adaptInfo->allowRefinement(true, i);	
-
-      return StandardProblemIteration::oneIteration(adaptInfo, toDo);
-    }
-  };
+  typedef detail::ProblemStat<Parallel::ParallelProblemStat> ProblemStat; 
 #endif
   
 } // end namespace AMDiS

AMDiS/src/parallel/StdMpi.cc

@@ -633,7 +633,7 @@ namespace AMDiS { namespace Parallel {
 
   void StdMpiHelper<vector<Matrix<int> > >::createBuffer(vector<Matrix<int> > &data, int *buf)
   {
-    int dimOfWorld = Global::getGeo(WORLD);
+//     int dimOfWorld = Global::getGeo(WORLD);
     int pos = 0;
     buf[pos++] = data.size() > 0 ? data[0].getNumRows() : 0;
     buf[pos++] = data.size() > 0 ? data[0].getNumCols() : 0;

extensions/BackgroundMesh.hh

@@ -30,7 +30,7 @@ namespace AMDiS { namespace extensions {
   template<typename T>
   T Box::evalAtPoint(const DOFVector<T>& vec, const PointType& x, int strategy, int nrOfPoints)
   {
-    T value;
+    T value = 0;
     switch (strategy) {
       case 0:
 	value = evalAtPoint_simple(vec, x);