Fixed compilation problem on atlas with gcc.

AMDiS/CMakeLists.txt

@@ -89,6 +89,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/Element.cc
 	      ${SOURCE_DIR}/ElementData.cc
 	      ${SOURCE_DIR}/ElementDofIterator.cc
+	      ${SOURCE_DIR}/ElementRegion_ED.cc	
 	      ${SOURCE_DIR}/FiniteElemSpace.cc
 	      ${SOURCE_DIR}/FirstOrderAssembler.cc
 	      ${SOURCE_DIR}/FirstOrderTerm.cc
@@ -134,6 +135,8 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/SubElInfo.cc
 	      ${SOURCE_DIR}/SubQuadrature.cc
 	      ${SOURCE_DIR}/SurfaceQuadrature.cc
+	      ${SOURCE_DIR}/SurfaceRegion_ED.cc
+	      ${SOURCE_DIR}/SystemVector.cc
 	      ${SOURCE_DIR}/Tetrahedron.cc
 	      ${SOURCE_DIR}/Timer.cc
 	      ${SOURCE_DIR}/Traverse.cc

AMDiS/src/AMDiS.h

@@ -116,6 +116,7 @@
 
 #include "io/ArhReader.h"
 #include "io/ArhWriter.h"
+#include "io/DataCollector.h"
 #include "io/FileWriter.h"
 #include "io/GNUPlotWriter.h"
 #include "io/GridWriter.h"
@@ -128,10 +129,6 @@
 #include "io/VtkWriter.h"
 #include "io/VtkVectorWriter.h"
 
-#include "io/DataCollector.hh"
-#include "io/FileWriter.hh"
-#include "io/VtkVectorWriter.hh"
-
 #include "nonlin/ProblemNonLin.h"
 #include "nonlin/NonLinSolver.h"
 

AMDiS/src/ElementRegion_ED.cc

+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology 
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "ElementRegion_ED.h"
+#include "Serializer.h"
+
+namespace AMDiS {
+  
+  bool ElementRegion_ED::refineElementData(Element* parent, 
+					   Element* child1,
+					   Element* child2,
+					   int elType)
+  {
+    ElementData::refineElementData(parent, child1, child2, elType);
+    
+    ElementRegion_ED *ep;
+    
+    ep = new ElementRegion_ED(child1->getElementData());
+    ep->region = region;
+    child1->setElementData(ep);
+    
+    ep = new ElementRegion_ED(child2->getElementData());
+    ep->region = region;
+    child2->setElementData(ep);
+    
+    return false;
+  }
+
+  
+  ElementData *ElementRegion_ED::clone() const
+  { 
+    ElementRegion_ED *newObj = new ElementRegion_ED;
+    newObj->region = region;
+    newObj->decorated = ElementData::clone();
+    return newObj; 
+  }
+
+  void ElementRegion_ED::serialize(std::ostream& out) 
+  {
+    ElementData::serialize(out);
+    SerUtil::serialize(out, region);
+  }
+
+  
+  void ElementRegion_ED::deserialize(std::istream& in) 
+  {
+    ElementData::deserialize(in);
+    SerUtil::deserialize(in, region);
+  }
+}

AMDiS/src/ElementRegion_ED.h

@@ -25,7 +25,6 @@
 
 #include "ElementData.h"
 #include "FixVec.h"
-#include "Serializer.h"
 
 namespace AMDiS {
 
@@ -56,30 +55,9 @@ namespace AMDiS {
     bool refineElementData(Element* parent, 
 			   Element* child1,
 			   Element* child2,
-			   int elType)
-    {
-      ElementData::refineElementData(parent, child1, child2, elType);
-
-      ElementRegion_ED *ep;
+			   int elType);
 
-      ep = new ElementRegion_ED(child1->getElementData());
-      ep->region = region;
-      child1->setElementData(ep);
-
-      ep = new ElementRegion_ED(child2->getElementData());
-      ep->region = region;
-      child2->setElementData(ep);
-
-      return false;
-    }
-
-    ElementData *clone() const 
-    { 
-      ElementRegion_ED *newObj = new ElementRegion_ED;
-      newObj->region = region;
-      newObj->decorated = ElementData::clone();
-      return newObj; 
-    }
+    ElementData *clone() const;
 
     inline std::string getTypeName() const 
     { 
@@ -91,17 +69,9 @@ namespace AMDiS {
       return ELEMENT_REGION; 
     }
 
-    void serialize(std::ostream& out) 
-    {
-      ElementData::serialize(out);
-      SerUtil::serialize(out, region);
-    }
+    void serialize(std::ostream& out);
 
-    void deserialize(std::istream& in) 
-    {
-      ElementData::deserialize(in);
-      SerUtil::deserialize(in, region);
-    }
+    void deserialize(std::istream& in); 
 
     inline void setRegion(int r) 
     { 

AMDiS/src/ProblemInstat.cc

@@ -19,7 +19,6 @@
 #include "StandardProblemIteration.h"
 #include "est/Estimator.h"
 #include "io/FileWriter.h"
-#include "io/FileWriter.hh"
 
 namespace AMDiS {
   

AMDiS/src/ProblemStat.cc

@@ -23,7 +23,6 @@
 #include "Marker.h"
 #include "AdaptInfo.h"
 #include "io/FileWriter.h"
-#include "io/FileWriter.hh"
 #include "CoarseningManager.h"
 #include "RefinementManager.h"
 #include "DualTraverse.h"

AMDiS/src/SurfaceRegion_ED.cc

+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology 
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "SurfaceRegion_ED.h"
+#include "Serializer.h"
+
+namespace AMDiS {
+  
+  bool SurfaceRegion_ED::refineElementData(Element* parent, 
+					   Element* child1,
+					   Element* child2,
+					   int elType)
+  {
+    ElementData::refineElementData(parent, child1, child2, elType);
+    
+    int sideOfChild;
+    SurfaceRegion_ED *surfaceRegion;
+    
+    sideOfChild = parent->getSideOfChild(0, side, elType);
+    if (sideOfChild >= 0) {
+      surfaceRegion = new SurfaceRegion_ED(child1->getElementData());
+      surfaceRegion->setSide(sideOfChild);
+      surfaceRegion->setRegion(region);
+      child1->setElementData(surfaceRegion);
+    }    
+    
+    sideOfChild = parent->getSideOfChild(1, side, elType);
+    if (sideOfChild >= 0) {
+      surfaceRegion = new SurfaceRegion_ED(child2->getElementData());
+      surfaceRegion->side = sideOfChild;
+      surfaceRegion->region = region;
+      child2->setElementData(surfaceRegion);
+    }
+    
+    return false;
+  }
+  
+  
+  ElementData *SurfaceRegion_ED::clone() const 
+  { 
+    SurfaceRegion_ED *newObj = new SurfaceRegion_ED;
+    newObj->side = side;
+    newObj->region = region;
+    newObj->decorated = ElementData::clone();
+    return newObj; 
+  }
+
+
+  void SurfaceRegion_ED::serialize(std::ostream& out)
+  {
+    ElementData::serialize(out);
+    SerUtil::serialize(out, side);
+    SerUtil::serialize(out, region);
+  }
+  
+
+  void SurfaceRegion_ED::deserialize(std::istream& in) 
+  {
+    ElementData::deserialize(in);
+    SerUtil::deserialize(in, side);
+    SerUtil::deserialize(in, region);
+  }
+}
+

AMDiS/src/SurfaceRegion_ED.h

@@ -25,7 +25,6 @@
 
 #include "ElementData.h"
 #include "FixVec.h"
-#include "Serializer.h"
 
 namespace AMDiS {
 
@@ -57,40 +56,9 @@ namespace AMDiS {
     bool refineElementData(Element* parent, 
 			   Element* child1,
 			   Element* child2,
-			   int elType)
-    {
-      ElementData::refineElementData(parent, child1, child2, elType);
-
-      int sideOfChild;
-      SurfaceRegion_ED *surfaceRegion;
-
-      sideOfChild = parent->getSideOfChild(0, side, elType);
-      if (sideOfChild >= 0) {
-	surfaceRegion = new SurfaceRegion_ED(child1->getElementData());
-	surfaceRegion->setSide(sideOfChild);
-	surfaceRegion->setRegion(region);
-	child1->setElementData(surfaceRegion);
-      }    
-
-      sideOfChild = parent->getSideOfChild(1, side, elType);
-      if (sideOfChild >= 0) {
-	surfaceRegion = new SurfaceRegion_ED(child2->getElementData());
-	surfaceRegion->side = sideOfChild;
-	surfaceRegion->region = region;
-	child2->setElementData(surfaceRegion);
-      }
+			   int elType);
 
-      return false;
-    }
-
-    ElementData *clone() const 
-    { 
-      SurfaceRegion_ED *newObj = new SurfaceRegion_ED;
-      newObj->side = side;
-      newObj->region = region;
-      newObj->decorated = ElementData::clone();
-      return newObj; 
-    }
+    ElementData *clone() const ;
 
     inline std::string getTypeName() const 
     { 
@@ -102,19 +70,9 @@ namespace AMDiS {
       return SURFACE_REGION; 
     }
 
-    void serialize(std::ostream& out) 
-    {
-      ElementData::serialize(out);
-      SerUtil::serialize(out, side);
-      SerUtil::serialize(out, region);
-    }
+    void serialize(std::ostream& out);
 
-    void deserialize(std::istream& in) 
-    {
-      ElementData::deserialize(in);
-      SerUtil::deserialize(in, side);
-      SerUtil::deserialize(in, region);
-    }
+    void deserialize(std::istream& in);
 
     inline void setSide(int s) 
     { 

AMDiS/src/SystemVector.cc

+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology 
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "SystemVector.h"
+#include "Serializer.h"
+
+namespace AMDiS {
+
+  void SystemVector::serialize(std::ostream &out) 
+  {
+    int size = vectors.getSize();
+    SerUtil::serialize(out, size);
+    for (int i = 0; i < size; i++)
+      vectors[i]->serialize(out);
+  }
+
+
+  void SystemVector::deserialize(std::istream &in) 
+  {
+    int size, oldSize = vectors.getSize();
+    SerUtil::deserialize(in, size);
+    vectors.resize(size);
+    for (int i = oldSize; i < size; i++)
+      vectors[i] = new DOFVector<double>(feSpace[i], "");
+    for (int i = 0; i < size; i++)
+      vectors[i]->deserialize(in);
+  }
+
+}

AMDiS/src/SystemVector.h

@@ -27,7 +27,6 @@
 #include "DOFVector.h"
 #include "CreatorInterface.h"
 #include "Serializable.h"
-#include "Serializer.h"
 
 namespace AMDiS {
 
@@ -193,24 +192,9 @@ namespace AMDiS {
       return *this;
     }
 
-    void serialize(std::ostream &out) 
-    {
-      int size = vectors.getSize();
-      SerUtil::serialize(out, size);
-      for (int i = 0; i < size; i++)
-	vectors[i]->serialize(out);
-    }
+    void serialize(std::ostream &out);
 
-    void deserialize(std::istream &in) 
-    {
-      int size, oldSize = vectors.getSize();
-      SerUtil::deserialize(in, size);
-      vectors.resize(size);
-      for (int i = oldSize; i < size; i++)
-	vectors[i] = new DOFVector<double>(feSpace[i], "");
-      for (int i = 0; i < size; i++)
-	vectors[i]->deserialize(in);
-    }
+    void deserialize(std::istream &in);
 
     void copy(const SystemVector& rhs) 
     {

AMDiS/src/io/DataCollector.h

@@ -231,5 +231,7 @@ namespace AMDiS {
   };
 }
 
+#include "DataCollector.hh"
+
 #endif
 

AMDiS/src/io/DataCollector.hh

@@ -23,13 +23,12 @@
 
 namespace AMDiS {
 
-
   template<typename T>
   DataCollector<T>::DataCollector(const FiniteElemSpace *fe,
-			       DOFVector<T> *val,
-			       int l,
-			       Flag flag,
-			       bool (*writeElemFct)(ElInfo*))
+				  DOFVector<T> *val,
+				  int l,
+				  Flag flag,
+				  bool (*writeElemFct)(ElInfo*))
     : values(val),
       level(l),
       traverseFlag(flag),

AMDiS/src/io/FileCompression.h

+// ============================================================================
+// ==                                                                        ==
+// == AMDiS - Adaptive multidimensional simulations                          ==
+// ==                                                                        ==
+// ==  http://www.amdis-fem.org                                              ==
+// ==                                                                        ==
+// ============================================================================
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology 
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+#ifndef AMDIS_FILE_COMPRESSION_H
+#define AMDIS_FILE_COMPRESSION_H
+
+namespace AMDiS {
+
+  typedef enum {
+    NONE = 0,
+    GZIP = 1,
+    BZIP2 = 2
+  } FileCompression;
+
+}
+
+#endif

AMDiS/src/io/FileWriter.cc

@@ -12,13 +12,11 @@
 
 #include "boost/lexical_cast.hpp"
 #include "FileWriter.h"
-#include "FileWriter.hh"
 #include "Initfile.h"
 #include "ValueWriter.h"
 #include "MacroWriter.h"
 #include "VtkWriter.h"
 #include "VtkVectorWriter.h"
-#include "VtkVectorWriter.hh"
 #include "PngWriter.h"
 #include "PovrayWriter.h"
 #include "DofWriter.h"
@@ -28,7 +26,7 @@
 #include "Flag.h"
 #include "ElInfo.h"
 #include "Mesh.h"
-#include "DataCollector.hh"
+#include "DataCollector.h"
 
 #if HAVE_PARALLEL_DOMAIN_AMDIS
 #include <mpi.h>

AMDiS/src/io/FileWriter.h

@@ -32,18 +32,12 @@
 #include "AMDiS_fwd.h"
 #include "Mesh.h"
 #include "DataCollector.h"
+#include "FileCompression.h"
 
 namespace AMDiS {
 
   using namespace std;
 
-  typedef enum {
-    NONE = 0,
-    GZIP = 1,
-    BZIP2 = 2
-  } FileCompression;
-
-
   class FileWriterInterface
   {
   public:
@@ -100,8 +94,8 @@ namespace AMDiS {
    * \ingroup Output
    *
    * \brief
-   * Base class of FileWriterScal and FileWriterVec. Manages the file output
-   * of solution vectors.
+   * Base class of FileWriterScal and FileWriterVec. Manages the file
+   * output of solution vectors.
    */
   template<typename T>
   class FileWriterTemplated : public FileWriterInterface
@@ -112,14 +106,14 @@ namespace AMDiS {
 
     /// Constructor for a filewriter with more than one data component.
     FileWriterTemplated(string name,
-	       Mesh *mesh,
-	       vector< DOFVector<T>* > vecs);
+			Mesh *mesh,
+			vector< DOFVector<T>* > vecs);
 
     /// Constructor for a filewriter with more than one data component.
     FileWriterTemplated(std::string name,
-	       Mesh *mesh,
-	       SystemVector *vecs);
-
+			Mesh *mesh,
+			SystemVector *vecs);
+    
     /// Destructor
     virtual ~FileWriterTemplated();
 
@@ -253,7 +247,8 @@ namespace AMDiS {
   
   typedef FileWriterTemplated<double> FileWriter;
   typedef FileWriterTemplated<WorldVector<double> > FileVectorWriter;
-
 }
 
+#include "FileWriter.hh"
+
 #endif // AMDIS_FILEWRITER_H

AMDiS/src/io/FileWriter.hh

@@ -21,7 +21,6 @@
 #include "MacroWriter.h"
 #include "VtkWriter.h"
 #include "VtkVectorWriter.h"
-#include "VtkVectorWriter.hh"
 #include "PngWriter.h"
 #include "PovrayWriter.h"
 #include "DofWriter.h"
@@ -32,7 +31,7 @@
 #include "ElInfo.h"
 #include "Mesh.h"
 #include "SystemVector.h"
-#include "DataCollector.hh"
+#include "DataCollector.h"
 
 #if HAVE_PARALLEL_DOMAIN_AMDIS
 #include <mpi.h>

AMDiS/src/io/MacroWriter.cc

@@ -24,7 +24,6 @@
 #include "ElementRegion_ED.h"
 #include <string>
 #include "Traverse.h"
-#include "DataCollector.hh"
 
 namespace AMDiS {
 

AMDiS/src/io/PngWriter.cc

@@ -18,7 +18,7 @@
 #include "PngWriter.h"
 #include "Traverse.h"
 #include "DOFVector.h"
-#include "DataCollector.hh"
+#include "DataCollector.h"
 
 namespace AMDiS {
   int PngWriter::writeFile(std::string filename, int imageType) 

AMDiS/src/io/PovrayWriter.cc

@@ -19,7 +19,7 @@
 #include <map>
 #include <algorithm>
 #include "Traverse.h"
-#include "DataCollector.hh"
+#include "DataCollector.h"
 
 using namespace std;
 

AMDiS/src/io/ValueWriter.cc

@@ -18,7 +18,7 @@
 #include "DOFAdmin.h"
 #include "ElInfo.h"
 #include "BasisFunction.h"
-#include "DataCollector.hh"
+#include "DataCollector.h"
 
 namespace AMDiS {
 

AMDiS/src/io/VtkVectorWriter.cc

@@ -24,9 +24,7 @@
 #endif
 
 #include "VtkVectorWriter.h"
-#include "VtkVectorWriter.hh"
 #include "DataCollector.h"
-#include "DataCollector.hh"
 #include "DOFVector.h"
 #include "SurfaceRegion_ED.h"
 #include "ElementRegion_ED.h"

AMDiS/src/io/VtkVectorWriter.h

@@ -31,8 +31,8 @@
 #include <fstream>
 #include "BasisFunction.h"
 #include "DataCollector.h"
-#include "FileWriter.h"
 #include "SystemVector.h"
+#include "FileCompression.h"
 
 namespace AMDiS {
 
@@ -66,7 +66,8 @@ namespace AMDiS {
       compress = c;
     }
 
-    void setWriteAs3dVector(bool w) {
+    void setWriteAs3dVector(bool w) 
+    {
       writeAs3dVector = w;
     }
 
@@ -275,4 +276,6 @@ namespace AMDiS {
   };
 }
 
+#include "VtkVectorWriter.hh"
+
 #endif // AMDIS_VTKVECTORWRITER_H

AMDiS/src/io/VtkWriter.cc

@@ -25,10 +25,10 @@
 
 #include "VtkWriter.h"
 #include "DataCollector.h"
-#include "DataCollector.hh"
 #include "DOFVector.h"
 #include "SurfaceRegion_ED.h"
 #include "ElementRegion_ED.h"
+#include "AdaptInfo.h"
 
 namespace AMDiS { 
 

AMDiS/src/io/VtkWriter.h

@@ -31,7 +31,7 @@
 #include <fstream>
 #include "BasisFunction.h"
 #include "DataCollector.h"
-#include "FileWriter.h"
+#include "FileCompression.h"
 #include "SystemVector.h"
 
 namespace AMDiS {

AMDiS/src/parallel/MeshPartitioner.cc

@@ -31,7 +31,7 @@ namespace AMDiS {
     elementInRank.clear();
 
     // Is used in box partitioning mode only. 
-    map<DofEdge, set<int> > vertexElements;
+    map<DofEdge, std::set<int> > vertexElements;
 
     TraverseStack stack;
     ElInfo *elInfo = 
@@ -79,13 +79,13 @@ namespace AMDiS {
       // === to be in the same box.                                         ===
 
       int boxCounter = 0;
-      for (map<DofEdge, set<int> >::iterator it = vertexElements.begin();
+      for (map<DofEdge, std::set<int> >::iterator it = vertexElements.begin();
 	   it != vertexElements.end(); ++it) {
 	TEST_EXIT_DBG(it->second.size() == 6)("Should not happen!\n");
 	
 	boxSplitting[boxCounter] = it->second;
 
-	for (set<int>::iterator elIt = it->second.begin();
+	for (std::set<int>::iterator elIt = it->second.begin();
 	     elIt != it->second.end(); ++elIt)
 	  elInBox[*elIt] = boxCounter;
 
@@ -114,11 +114,11 @@ namespace AMDiS {
 
       int boxPerRank = boxCounter / mpiSize;
 
-      for (map<int, set<int> >::iterator it = boxSplitting.begin();
+      for (map<int, std::set<int> >::iterator it = boxSplitting.begin();
 	   it != boxSplitting.end(); ++it) {
 	int boxInRank = std::min(it->first / boxPerRank, mpiSize - 1);
 
-	for (set<int>::iterator elIt = it->second.begin();
+	for (std::set<int>::iterator elIt = it->second.begin();
 	     elIt != it->second.end(); ++elIt) {
 	  elementInRank[*elIt] = (boxInRank == mpiRank);
 	  partitionMap[*elIt] = boxInRank;