* Global refinement bug fix (for different meshes of different components)

AMDiS/src/DOFVector.cc

@@ -279,7 +279,8 @@ namespace AMDiS {
 	}
       }
     } else {
-      DimVec<double> grdPhi(dim, DEFAULT_VALUE, 0.0);
+      //      DimVec<double> grdPhi(dim, DEFAULT_VALUE, 0.0);
+      DimVec<double>* grdPhi = grdPhis[omp_get_thread_num()];
 
       for (int i = 0; i < numPoints; i++) {
 	for (int j = 0; j < dim + 1; j++) {
@@ -287,9 +288,9 @@ namespace AMDiS {
 	}
 
 	for (int j = 0; j < nBasFcts; j++) {
-	  (*(basFcts->getGrdPhi(j)))(quad->getLambda(i), grdPhi);
+	  (*(basFcts->getGrdPhi(j)))(quad->getLambda(i), *grdPhi);
 	  for (int k = 0; k < parts; k++) {
-	    grd1[k] += grdPhi[k] * localVec[j];
+	    grd1[k] += (*grdPhi)[k] * localVec[j];
 	  }
 	}
 
@@ -379,7 +380,9 @@ namespace AMDiS {
 	  }
       }
     } else {
-      DimMat<double> D2Phi(dim, NO_INIT);
+      //      DimMat<double> D2Phi(dim, NO_INIT);
+      DimMat<double>* D2Phi = D2Phis[omp_get_thread_num()];
+
       for (iq = 0; iq < numPoints; iq++) {
 	for (k = 0; k < parts; k++)
 	  for (l = 0; l < parts; l++)
@@ -387,11 +390,11 @@ namespace AMDiS {
 
 	for (i = 0; i < nBasFcts; i++) {
 	  WARNING("not tested after index correction\n");
-	  (*(basFcts->getD2Phi(i)))(quad->getLambda(iq), D2Phi);
+	  (*(basFcts->getD2Phi(i)))(quad->getLambda(iq), *D2Phi);
 
 	  for (k = 0; k < parts; k++)
 	    for (l = 0; l < parts; l++)
-	      D2Tmp[k][l] += localVec[i] * D2Phi[k][l];
+	      D2Tmp[k][l] += localVec[i] * (*D2Phi)[k][l];
 	}
 
 	for (i = 0; i < dow; i++)

AMDiS/src/DOFVector.h

@@ -228,7 +228,17 @@ namespace AMDiS {
      * Are used to store temporary local dofs of an element. 
      * Thread safe.
      */
-    std::vector<DegreeOfFreedom* > localIndices;
+    std::vector<DegreeOfFreedom*> localIndices;
+
+    /** \brief
+     * Temporarly used in \ref getGrdAtQPs. Thread safe.
+     */
+    std::vector<DimVec<double>*> grdPhis;
+
+    /** \brief
+     * Temporarly used in \ref getD2AtQPs. Thread safe.
+     */
+    std::vector<DimMat<double>*> D2Phis;
   };
 
 

AMDiS/src/DOFVector.hh

@@ -25,11 +25,16 @@ namespace AMDiS {
       boundaryManager(NULL)
   {
     nBasFcts = feSpace->getBasisFcts()->getNumber();
+    int dim = feSpace->getMesh()->getDim();
 
     localIndices.resize(omp_get_max_threads());
+    grdPhis.resize(omp_get_max_threads());
+    D2Phis.resize(omp_get_max_threads());
 
     for (int i = 0; i < omp_get_max_threads(); i++) {
       localIndices[i] = GET_MEMORY(DegreeOfFreedom, this->nBasFcts);      
+      grdPhis[i] = NEW DimVec<double>(dim, DEFAULT_VALUE, 0.0);
+      D2Phis[i] = NEW DimMat<double>(dim, NO_INIT);
     }
   }
   
@@ -38,6 +43,8 @@ namespace AMDiS {
   {
     for (int i = 0; i < static_cast<int>(localIndices.size()); i++) {
       FREE_MEMORY(localIndices[i], DegreeOfFreedom, this->nBasFcts);
+      DELETE grdPhis[i];
+      DELETE D2Phis[i];
     }
   }
   

AMDiS/src/ElInfo.cc

@@ -30,8 +30,6 @@ namespace AMDiS {
       neighbourCoord_(mesh_->getDim(), NO_INIT),
       oppVertex_(mesh_->getDim(), NO_INIT),
       grdLambda_(mesh_->getDim(), NO_INIT) 
-		//parametric_(false)
-  
   {
     projection_.set(NULL);
 
@@ -58,7 +56,7 @@ namespace AMDiS {
   {
     int dim = l.getSize() - 1;
 
-    static WorldVector<double> world[2];
+    static WorldVector<double> world[4];
     WorldVector<double> *ret = w ? w : &world[omp_get_thread_num()];
     double c = l[0];
 
@@ -106,9 +104,9 @@ namespace AMDiS {
 
     for (int i = 0; i < dow; i++) {
       e1[i] = coords[1][i] - v0[i];
-      if(dim > 1)
+      if (dim > 1)
 	e2[i] = coords[2][i] - v0[i];
-      if(dim > 2)
+      if (dim > 2)
 	e3[i] = coords[3][i] - v0[i];
     }
   
@@ -117,10 +115,10 @@ namespace AMDiS {
       det = coords[1][0] - coords[0][0];
       break;
     case 2:
-      if(dim == 1) {
+      if (dim == 1) {
 	det = norm(&e1);
       } else {
-	det = e1[0]*e2[1] - e1[1]*e2[0];
+	det = e1[0] * e2[1] - e1[1] * e2[0];
       }
       break;
     case 3: 

AMDiS/src/ProblemNonLin.cc

@@ -159,7 +159,7 @@ namespace AMDiS {
     nonLinSolver_ = nonLinSolverCreator->create();
     nonLinSolver_->setVectorCreator(NEW SystemVector::Creator("temp",
 							      componentSpaces_, 
-							      numComponents_));
+							      nComponents));
   }
 
 
@@ -171,13 +171,13 @@ namespace AMDiS {
   void ProblemNonLinVec::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag) 
   {
     FUNCNAME("ProblemNonLinVec::buildAfterCoarsen()");
-    int i, numMeshes = static_cast<int>(meshes_.size());
+    int nMeshes = static_cast<int>(meshes_.size());
 
-    for(i = 0; i < numMeshes; i++) {
+    for (int i = 0; i < nMeshes; i++) {
       meshes_[i]->dofCompress();
     }
 
-    for(i = 0; i < numComponents_; i++) {
+    for (int i = 0; i < nComponents; i++) {
       MSG("%d DOFs for %s\n", 
 	  componentSpaces_[i]->getAdmin()->getUsedSize(), 
 	  componentSpaces_[i]->getName().c_str());
@@ -187,15 +187,15 @@ namespace AMDiS {
     ElInfo *elInfo;
     
     // for all elements ...
-    for(i = 0; i < numComponents_; i++) {
+    for (int i = 0; i < nComponents; i++) {
       elInfo = stack.traverseFirst(componentMeshes_[i], -1, 
 				   Mesh::CALL_LEAF_EL | 
 				   Mesh::FILL_BOUND |
 				   Mesh::FILL_COORDS |
 				   Mesh::FILL_DET |
 				   Mesh::FILL_GRD_LAMBDA);
-      while(elInfo) {
-	if(solution_->getDOFVector(i)->getBoundaryManager()) {
+      while (elInfo) {
+	if (solution_->getDOFVector(i)->getBoundaryManager()) {
 	  solution_->getDOFVector(i)->
 	    getBoundaryManager()->fillBoundaryConditions(elInfo, solution_->getDOFVector(i));
 	}

AMDiS/src/ProblemNonLin.h

@@ -167,7 +167,7 @@ namespace AMDiS {
 	nonLinSolver_(NULL),
 	updater_(NULL)
     {
-      u0_.resize(numComponents_);
+      u0_.resize(nComponents);
       u0_.set(NULL);
     };
 
@@ -178,7 +178,7 @@ namespace AMDiS {
 		      int index) 
     {
       FUNCNAME("ProblemNonLinVec::setU0()");
-      TEST_EXIT(index < numComponents_)("invalid index\n");
+      TEST_EXIT(index < nComponents)("invalid index\n");
       u0_[index] = u0Fct;
       solution_->getDOFVector(index)->interpol(u0Fct);
     };

AMDiS/src/ProblemVec.cc

@@ -130,7 +130,7 @@ namespace AMDiS {
     // before timeout of the runqueue.
 
     int readSerialization = 0;
-    ::std::string serializationFilename = "";
+    std::string serializationFilename = "";
     GET_PARAMETER(0, "argv->rs", &serializationFilename);
 
     // If the parameter -rs is set, we do nothing here, because the problem will be
@@ -153,24 +153,21 @@ namespace AMDiS {
 	TEST_EXIT(serializationFilename != "")("no serialization file\n");
 
 	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
-	::std::ifstream in(serializationFilename.c_str());
+	std::ifstream in(serializationFilename.c_str());
 	deserialize(in);
 	in.close();
       } else {
+	int globalRefinements = 0;
+	GET_PARAMETER(0, meshes_[0]->getName() + "->global refinements", "%d", 
+		      &globalRefinements);
+
 	// Initialize the meshes if there is no serialization file.
 	for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
 	  if (initFlag.isSet(INIT_MESH) && 
 	      meshes_[i] && 
 	      !(meshes_[i]->isInitialized())) {
 	    meshes_[i]->initialize();	    
-	    
-	    // do global refinements
-	    int globalRefinements = 0;
-	    GET_PARAMETER(0, meshes_[0]->getName() + "->global refinements", "%d", 
-			  &globalRefinements);
-	    for (int gr = 0; gr < static_cast<int>(meshes_.size()); gr++) {
-	      refinementManager_->globalRefine(meshes_[gr], globalRefinements);
-	    }
+	    refinementManager_->globalRefine(meshes_[i], globalRefinements);
 	  }
 	}	
       }
@@ -183,23 +180,22 @@ namespace AMDiS {
   {
     FUNCNAME("ProblemVec::createMesh()");
 
-    componentMeshes_.resize(numComponents_);
-    ::std::map<int, Mesh*> meshForRefinementSet;
+    componentMeshes_.resize(nComponents);
+    std::map<int, Mesh*> meshForRefinementSet;
     char number[3];
 
-    ::std::string meshName("");
+    std::string meshName("");
     GET_PARAMETER(0, name_ + "->mesh", &meshName);
     TEST_EXIT(meshName != "")("no mesh name spezified\n");
     int dim = 0;
     GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
     TEST_EXIT(dim)("no problem dimension spezified!\n");
 
-    for (int i = 0; i < numComponents_; i++) {
+    for (int i = 0; i < nComponents; i++) {
       sprintf(number, "%d", i);
       int refSet = -1;
       GET_PARAMETER(0, name_ + "->refinement set[" + number + "]", "%d", &refSet);
       if (refSet < 0) {
-	WARNING("refinement set for component %d not set\n", i);
 	refSet = 0;
       }
       if (meshForRefinementSet[refSet] == NULL) {
@@ -234,30 +230,30 @@ namespace AMDiS {
     int degree = 1;
     char number[3];
 
-    ::std::map< ::std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
+    std::map< std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
     int dim = -1;
     GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
     TEST_EXIT(dim != -1)("no problem dimension spezified!\n");
 
-    componentSpaces_.resize(numComponents_, NULL);
+    componentSpaces_.resize(nComponents, NULL);
 
-    for (int i = 0; i < numComponents_; i++) {
+    for (int i = 0; i < nComponents; i++) {
       sprintf(number, "%d", i);
       GET_PARAMETER(0, name_ + "->polynomial degree[" + number + "]","%d", &degree);
 
       TEST_EXIT(componentSpaces_[i] == NULL)("feSpace already created\n");
 
-      if (feSpaceMap[::std::pair<Mesh*, int>(componentMeshes_[i], degree)] == NULL) {
+      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)] == NULL) {
 	FiniteElemSpace *newFESpace = 
 	  FiniteElemSpace::provideFESpace(NULL,
 					  Lagrange::getLagrange(dim, degree),
 					  componentMeshes_[i],
 					  name_ + "->feSpace");
-	feSpaceMap[::std::pair<Mesh*, int>(componentMeshes_[i], degree)] = newFESpace;
+	feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)] = newFESpace;
 	feSpaces_.push_back(newFESpace);
       }
       componentSpaces_[i] = 
-	feSpaceMap[::std::pair<Mesh*, int>(componentMeshes_[i], degree)];
+	feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)];
     }
 
     // create dof admin for vertex dofs if neccessary
@@ -278,21 +274,21 @@ namespace AMDiS {
 
     // === create vectors and system matrix ===
 
-    systemMatrix_ = NEW Matrix<DOFMatrix*>(numComponents_, numComponents_);
+    systemMatrix_ = NEW Matrix<DOFMatrix*>(nComponents, nComponents);
     systemMatrix_->set(NULL);
-    rhs_ = NEW SystemVector("rhs", componentSpaces_, numComponents_);
-    solution_ = NEW SystemVector("solution", componentSpaces_, numComponents_);
+    rhs_ = NEW SystemVector("rhs", componentSpaces_, nComponents);
+    solution_ = NEW SystemVector("solution", componentSpaces_, nComponents);
 
     char number[10];
-    ::std::string numberedName;
-    for (i = 0; i < numComponents_; i++) {
+    std::string numberedName;
+    for (i = 0; i < nComponents; i++) {
       (*systemMatrix_)[i][i] = NEW DOFMatrix(componentSpaces_[i], 
 					     componentSpaces_[i], "A_ii");
       (*systemMatrix_)[i][i]->setCoupleMatrix(false);
       sprintf(number, "[%d]", i);
-      numberedName = "rhs" + ::std::string(number);
+      numberedName = "rhs" + std::string(number);
       rhs_->setDOFVector(i, NEW DOFVector<double>(componentSpaces_[i], numberedName));
-      numberedName = name_ + ::std::string(number);
+      numberedName = name_ + std::string(number);
       solution_->setDOFVector(i, NEW DOFVector<double>(componentSpaces_[i], 
 						       numberedName));
       solution_->getDOFVector(i)->refineInterpol(true);
@@ -309,7 +305,7 @@ namespace AMDiS {
     FUNCNAME("ProblemVec::createSolver()");
 
     // === create solver ===
-    ::std::string solverType("no");
+    std::string solverType("no");
     GET_PARAMETER(0, name_ + "->solver", &solverType);
     OEMSolverCreator<SystemVector> *solverCreator = 
       dynamic_cast<OEMSolverCreator<SystemVector>*>(
@@ -322,10 +318,10 @@ namespace AMDiS {
     solver_->initParameters();
 
     // === create preconditioners ===
-    ::std::string preconType("no");
+    std::string preconType("no");
 
     PreconditionerScal *scalPrecon;
-    PreconditionerVec *vecPrecon = NEW PreconditionerVec(numComponents_);
+    PreconditionerVec *vecPrecon = NEW PreconditionerVec(nComponents);
 
     GET_PARAMETER(0, name_ + "->solver->left precon", &preconType);
     CreatorInterface<PreconditionerScal> *preconCreator =
@@ -337,12 +333,12 @@ namespace AMDiS {
       dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
 	setName(name_ + "->solver->left precon");
 
-      for(i = 0; i < numComponents_; i++) {
+      for(i = 0; i < nComponents; i++) {
 	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
-	  setSizeAndRow(numComponents_, i);
+	  setSizeAndRow(nComponents, i);
     
 	scalPrecon = preconCreator->create();
-	for(j = 0; j < numComponents_; j++) {
+	for(j = 0; j < nComponents; j++) {
 	  scalPrecon->setMatrix(&(*systemMatrix_)[i][j], j);
 	}
 	vecPrecon->setScalarPrecon(i, scalPrecon);
@@ -351,7 +347,7 @@ namespace AMDiS {
     }
 
 
-    vecPrecon = NEW PreconditionerVec(numComponents_);
+    vecPrecon = NEW PreconditionerVec(nComponents);
 
     GET_PARAMETER(0, name_ + "->solver->right precon", &preconType);
     preconCreator = 
@@ -362,12 +358,12 @@ namespace AMDiS {
 	setName(name_ + "->solver->left precon");
 
 
-      for(i = 0; i < numComponents_; i++) {
+      for(i = 0; i < nComponents; i++) {
 	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
-	  setSizeAndRow(numComponents_, i);
+	  setSizeAndRow(nComponents, i);
     
 	scalPrecon = preconCreator->create();
-	for(j = 0; j < numComponents_; j++) {
+	for(j = 0; j < nComponents; j++) {
 	  scalPrecon->setMatrix(&(*systemMatrix_)[i][j], j);
 	}
 	vecPrecon->setScalarPrecon(i, scalPrecon);
@@ -379,7 +375,7 @@ namespace AMDiS {
     // === create vector creator ===
     solver_->setVectorCreator(NEW SystemVector::Creator("temp",
 							componentSpaces_, 
-							numComponents_));
+							nComponents));
   }
 
   void ProblemVec::createEstimator()
@@ -395,15 +391,15 @@ namespace AMDiS {
     }  
 
     char number[3];
-    ::std::string estName;
+    std::string estName;
 
-    for(i = 0; i < numComponents_; i++) {
+    for(i = 0; i < nComponents; i++) {
       TEST_EXIT(estimator_[i] == NULL)("estimator already created\n");
       sprintf(number, "%d", i);
-      estName = name_ + "->estimator[" + ::std::string(number) + "]";
+      estName = name_ + "->estimator[" + std::string(number) + "]";