some updates of extensions

extensions/ExtendedProblemStat.h

@@ -323,6 +323,9 @@ protected:
 
       // erase the rows for all first indices
       for (size_t i = 0; i < indices.size(); i++) {
+	if (indices[i].first == indices[i].second)
+	  continue;
+	
 	if (asmMatrix) {
 	  c_type cursor(begin<tag::row>(m)+indices[i].first);
 	  for (ic_type icursor(begin<tag::nz>(cursor)), icend(end<tag::nz>(cursor)); icursor != icend; ++icursor) {
@@ -341,11 +344,15 @@ protected:
 	matrix::inserter<Matrix, update_plus<double> > ins(m);
 	if (row == col) {
 	  for (size_t i = 0; i < indices.size(); i++) {
+	    if (indices[i].first == indices[i].second)
+	      continue;
 	    ins[indices[i].first][indices[i].first] << 1.0;
 	    ins[indices[i].first][indices[i].second] << -1.0;
 	  }
 	}
 	for (size_t i = 0; i < indices.size(); i++) {
+	  if (indices[i].first == indices[i].second)
+	    continue;
 	  for (size_t j = 0; j < row_values[i].size(); j++) {
 	    ins[indices[i].second][row_values[i][j].first] << row_values[i][j].second;
 	  }

extensions/Refinement_Level.h

@@ -247,16 +247,8 @@ public:
 
   void markElements(Flag &markFlag) 
   {
-    FUNCNAME("RefinementLevelDOF::markElements()");
-
-    const DOFAdmin* admin = feSpace->getAdmin();
-    const BasisFunction *basFcts = feSpace->getBasisFcts();
-    int numBasFcts = basFcts->getNumber();
-
-    DegreeOfFreedom *localIndices = new DegreeOfFreedom[numBasFcts];
-    FixVec<WorldVector<double>, VERTEX> coords(mesh->getDim(), NO_INIT);
-    double meanValue;
-
+    FUNCNAME("RefinementLevelDOFList::markElements()");
+    
     bool elMarkRefine = false, elMarkCoarsen = false;
 
     std::vector<ElementFunctionDOFVec<double>*> elFcts;
@@ -291,8 +283,6 @@ public:
 	    markFlag= 1;
     if(elMarkCoarsen) 
 	    markFlag|= 2;
-    
-    delete [] localIndices;
   };
 private:
 	std::vector<DOFVector<double>*> vecs;

extensions/VtuReader.hh

@@ -113,6 +113,9 @@ namespace AMDiS {
 	  (*it_results[i])++;
 	}
       }
+      
+      
+      MSG("VTU file read from: %s\n", filename.c_str());
     }
   } // end namespace VtuReader
   

extensions/base_problems/BaseProblem.hh

@@ -47,7 +47,7 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
   
   std::string readFormat = "arh";
   Initfile::get(name + "->read format", readFormat, 2);
-  if (readFormat != "arh" && readFormat != "dat" && readFormat != "vtu") {
+  if (readFormat != "arh" && readFormat != "dat" && readFormat != "vtu" && readFormat != "multi-vtu") {
     WARNING("You can not read data from formats other than .arh, .dat or .vtu! The .arh-format is selected.\n");
   }
   
@@ -98,17 +98,63 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
     if (arh_idx >= 0) {
       ArhReader::read(filenames[arh_idx], prob->getMesh());
     }
-    if (vtu_idx >= 0) {
+    if (vtu_idx >= 0) {      
+      std::vector<int> readComponents;
+      Initfile::get(name + "->read components", readComponents);
+      if (readComponents.size() == 0)
+	for (size_t i = 0; i < prob->getNumComponents(); i++)
+	  readComponents.push_back(i);
+	
       std::vector<DOFVector<double>*> solutions;
       std::vector<std::string> names;
-      for (size_t i = 0; i < prob->getNumComponents(); i++) {
-	solutions.push_back(prob->getSolution()->getDOFVector(i));
-	names.push_back(prob->getComponentName(i));
+      for (size_t i = 0; i < readComponents.size(); i++) {
+	solutions.push_back(prob->getSolution()->getDOFVector(readComponents[i]));
+	names.push_back(prob->getComponentName(readComponents[i]));
       }
       VtuReader::readValue(filenames[vtu_idx], prob->getMesh(), solutions, names);
     } else
       throw(std::runtime_error("You have to specify a .vtu file!"));
   }
+  else if (readFormat == "multi-vtu") {
+    size_t numFiles = 0;
+    Initfile::get(name + "->number of files", numFiles);
+    for (size_t n; n < numFiles; n++) {
+      std::vector<std::string> filenames;
+      Initfile::get(name + "->value file[" + boost::lexical_cast<std::string>(n) + "]", filenames);
+      if (filenames.size() == 0)
+	return initFlag;
+      int arh_idx = -1, vtu_idx = -1;
+      for (size_t i = 0; i < filenames.size(); i++) {
+	if (!file_exists(filenames[i]))
+	  throw(std::runtime_error("The file '" + filenames[i] + "' does not exist!"));
+	if (filenames[i].find(".vtu") != std::string::npos)
+	  vtu_idx = i;
+	else if (filenames[i].find(".arh") != std::string::npos)
+	  arh_idx = i;
+	else
+	  throw(std::runtime_error("The file '" + filenames[i] + "' must have the extension .arh or .vtu!"));
+      }
+      if (arh_idx >= 0) {
+	ArhReader::read(filenames[arh_idx], prob->getMesh());
+      }
+      if (vtu_idx >= 0) {      
+	std::vector<int> readComponents;
+	Initfile::get(name + "->read components[" + boost::lexical_cast<std::string>(n) + "]", readComponents);
+	if (readComponents.size() == 0)
+	  for (size_t i = 0; i < prob->getNumComponents(); i++)
+	    readComponents.push_back(i);
+	  
+	std::vector<DOFVector<double>*> solutions;
+	std::vector<std::string> names;
+	for (size_t i = 0; i < readComponents.size(); i++) {
+	  solutions.push_back(prob->getSolution()->getDOFVector(readComponents[i]));
+	  names.push_back(prob->getComponentName(readComponents[i]));
+	}
+	VtuReader::readValue(filenames[vtu_idx], prob->getMesh(), solutions, names);
+      } else
+	throw(std::runtime_error("You have to specify a .vtu file!"));
+    }
+  }
   else {
     throw(std::runtime_error("Parameter 'read data from file' set to 'true', but no parameter 'read format' specified!"));
   }