Small changes and a new test for parallel interior boundaries.

AMDiS/src/AMDiS.h

@@ -142,6 +142,7 @@
 #if HAVE_PARALLEL_DOMAIN_AMDIS
 #include "parallel/InteriorBoundary.h"
 #include "parallel/MpiHelper.h"
+#include "parallel/ParallelDebug.h"
 #include "parallel/StdMpi.h"
 
 #if HAVE_PARALLEL_MTL4

AMDiS/src/BoundaryObject.cc

@@ -135,4 +135,11 @@ namespace AMDiS {
 	    type == other.type);
   }
 
+  bool AtomicBoundary::operator!=(const AtomicBoundary& other) const
+  {
+    return (rankObj != other.rankObj ||
+	    neighObj != other.neighObj ||
+	    type != other.type);
+  }
+
 }

AMDiS/src/BoundaryObject.h

@@ -110,6 +110,8 @@ namespace AMDiS {
 
     bool operator==(const AtomicBoundary& other) const;
 
+    bool operator!=(const AtomicBoundary& other) const;
+
     /// The rank's part of the boundary.
     BoundaryObject rankObj;
 

AMDiS/src/Mesh.cc

@@ -1498,4 +1498,16 @@ namespace AMDiS {
 
     Element::deletedDOFs.clear();
   }
+
+
+  void Mesh::getElementIndexMap(map<int, Element*> &elIndexMap)
+  {
+    TraverseStack stack;
+    ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_EVERY_EL_PREORDER);
+    while (elInfo) {
+      Element *el = elInfo->getElement();
+      elIndexMap[el->getIndex()] = el;      
+      elInfo = stack.traverseNext(elInfo);
+    }
+  }
 }

AMDiS/src/Mesh.h

@@ -629,6 +629,10 @@ namespace AMDiS {
     }
 #endif
 
+    /// Creates a map for all elements in mesh that maps from element indices
+    /// to the corresponding pointers.
+    void getElementIndexMap(map<int, Element*> &elIndexMap);
+
   public:
     ///
     static const Flag FILL_NOTHING;

AMDiS/src/Serializer.h

@@ -37,6 +37,8 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
   template<typename ProblemType>
   class Serializer : public FileWriterInterface
   {
@@ -64,7 +66,7 @@ namespace AMDiS {
     }
 
 
-    Serializer(ProblemType *prob, std::string filename, int writeEveryIth)
+    Serializer(ProblemType *prob, string filename, int writeEveryIth)
       : name(filename),
 	problem(prob),
 	tsModulo(writeEveryIth),
@@ -119,10 +121,10 @@ namespace AMDiS {
       }
 
 #if HAVE_PARALLEL_DOMAIN_AMDIS
-      filename += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
+      filename += ".p" + boost::lexical_cast<string>(MPI::COMM_WORLD.Get_rank());
 #endif
 
-      std::ofstream out(filename.c_str());
+      ofstream out(filename.c_str());
       TEST_EXIT(out.is_open())("Cannot open serialization file!\n");
       out.write(reinterpret_cast<const char*>(&amdisRevisionNumber), sizeof(int));
       problem->serialize(out);
@@ -134,7 +136,7 @@ namespace AMDiS {
 
   protected:
     /// Name of file to which the problem is serialized.
-    std::string name;
+    string name;
 
     /// Pointer to the problem.
     ProblemType *problem;
@@ -159,40 +161,40 @@ namespace AMDiS {
   namespace SerUtil {
 
     template<typename T>
-    void serialize(std::ostream& out, T& data)
+    void serialize(ostream& out, T& data)
     {
       out.write(reinterpret_cast<const char*>(&data), sizeof(T));
     }   
 
     template<typename T>
-    void deserialize(std::istream& in, T& data)
+    void deserialize(istream& in, T& data)
     {
       in.read(reinterpret_cast<char*>(&data), sizeof(T));
     }   
 
 
 
-    void serialize(std::ostream& out, DofEdge& data);
+    void serialize(ostream& out, DofEdge& data);
 
-    void deserialize(std::istream& in, DofEdge& data);
+    void deserialize(istream& in, DofEdge& data);
 
 
 
-    void serialize(std::ostream& out, DofFace& data);
+    void serialize(ostream& out, DofFace& data);
 
-    void deserialize(std::istream& in, DofFace& data);
+    void deserialize(istream& in, DofFace& data);
 
 
 
     template<typename T, typename U>
-    void serialize(std::ostream& out, std::pair<T, U>& data)
+    void serialize(ostream& out, pair<T, U>& data)
     {
       serialize(out, data.first);
       serialize(out, data.second);
     }
 
     template<typename T, typename U>
-    void deserialize(std::istream& in, std::pair<T, U>& data)
+    void deserialize(istream& in, pair<T, U>& data)
     {
       deserialize(in, data.first);
       deserialize(in, data.second);
@@ -201,11 +203,11 @@ namespace AMDiS {
 
 
     template<typename T>
-    void serialize(std::ostream& out, std::vector<T>& data)
+    void serialize(ostream& out, vector<T>& data)
     {
       int vecSize = data.size();
       serialize(out, vecSize);
-      for (typename std::vector<T>::iterator it = data.begin(); 
+      for (typename vector<T>::iterator it = data.begin(); 
 	   it != data.end(); ++it) {
 	T v = *it;
 	serialize(out, v);
@@ -213,7 +215,7 @@ namespace AMDiS {
     }
 
     template<typename T>
-    void deserialize(std::istream& in, std::vector<T>& data)
+    void deserialize(istream& in, vector<T>& data)
     {
       data.clear();
 
@@ -231,7 +233,7 @@ namespace AMDiS {
 
 
     template<typename T>
-    void serialize(std::ostream& out, std::set<T>& data)
+    void serialize(ostream& out, std::set<T>& data)
     {
       int setSize = data.size();
       serialize(out, setSize);
@@ -243,7 +245,7 @@ namespace AMDiS {
     }
 
     template<typename T>
-    void deserialize(std::istream& in, std::set<T>& data)
+    void deserialize(istream& in, std::set<T>& data)
     {
       data.clear();
 
@@ -260,12 +262,12 @@ namespace AMDiS {
 
 
     template<typename T1, typename T2>
-    void serialize(std::ostream& out, std::map<T1, T2>& data)
+    void serialize(ostream& out, map<T1, T2>& data)
     {
       int mapSize = data.size();
       serialize(out, mapSize);
 
-      for (typename std::map<T1,T2>::iterator it = data.begin(); 
+      for (typename map<T1,T2>::iterator it = data.begin(); 
 	   it != data.end(); ++it) {
 	T1 v1 = it->first;
 	T2 v2 = it->second;
@@ -275,7 +277,7 @@ namespace AMDiS {
     }
 
     template<typename T1, typename T2>
-    void deserialize(std::istream& in, std::map<T1, T2>& data)
+    void deserialize(istream& in, map<T1, T2>& data)
     {
       data.clear();
 

AMDiS/src/io/FileWriter.hh

@@ -174,10 +174,10 @@ namespace AMDiS {
 
   template<typename T>
   void FileWriterTemplated<T>::writeFiles(AdaptInfo *adaptInfo,
-			      bool force,
-			      int level,
-			      Flag flag,
-			      bool (*writeElem)(ElInfo*))
+					  bool force,
+					  int level,
+					  Flag flag,
+					  bool (*writeElem)(ElInfo*))
   {
     FUNCNAME("FileWriterTemplated<T>::writeFiles()");
 
@@ -186,19 +186,19 @@ namespace AMDiS {
 
     // Containers, which store the data to be written;
     std::vector<DataCollector<T>*> dataCollectors(solutionVecs.size());
-
+    
     if (writeElem) {
       for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)
 	dataCollectors[i] = new DataCollector<T>(feSpace, solutionVecs[i], 
-					      level, flag, writeElem);
+						 level, flag, writeElem);
     } else {
       for (int i = 0; i < static_cast<int>(dataCollectors.size()); i++)
 	dataCollectors[i] = new DataCollector<T>(feSpace, solutionVecs[i], 
-					      traverseLevel, 
-					      flag | traverseFlag, 
-					      writeElement);
+						 traverseLevel, 
+						 flag | traverseFlag, 
+						 writeElement);
     }
-
+    
     std::string fn = filename;
 
 #if HAVE_PARALLEL_DOMAIN_AMDIS

AMDiS/src/parallel/DofComm.cc

@@ -18,6 +18,30 @@ namespace AMDiS {
 
   using namespace std;
 
+
+  void DofComm::init(int level, 
+		     MeshLevelData &ld,
+		     vector<const FiniteElemSpace*> &fe)
+  {
+    FUNCNAME("DofComm::init()");
+    
+    meshLevel = level;
+    levelData = &ld;
+    feSpaces = fe;
+    
+    nLevel = levelData->getLevelNumber() - meshLevel;
+    TEST_EXIT_DBG(nLevel >= 1)("Should not happen!\n");
+
+    sendDofs.clear();
+    recvDofs.clear();
+    periodicDofs.clear();
+    
+    sendDofs.resize(nLevel);
+    recvDofs.resize(nLevel);
+    periodicDofs.resize(nLevel);
+  }
+
+
   void DofComm::create(InteriorBoundary &boundary)
   {
     createContainer(boundary.getOwn(), sendDofs);
@@ -28,6 +52,8 @@ namespace AMDiS {
   void DofComm::createContainer(RankToBoundMap &boundary,
 				LevelDataType &data)
   {
+    FUNCNAME("DofComm::createContainer()");
+
     // === Fill data. ===
 
     for (unsigned int i = 0; i < feSpaces.size(); i++)

AMDiS/src/parallel/DofComm.h

@@ -38,7 +38,10 @@ namespace AMDiS {
     DofComm() 
       : recvDofs(1),
 	sendDofs(1),
-	periodicDofs(0)
+	periodicDofs(0),
+	meshLevel(-1),
+	nLevel(0),
+	levelData(NULL)
     {}
     
     typedef map<const FiniteElemSpace*, DofContainer> FeMapType;
@@ -48,23 +51,9 @@ namespace AMDiS {
     // meshLevel: map[rank -> map[feSpace -> DofContainer]]
     typedef vector<DataType> LevelDataType;
 
-    void init(int n, vector<const FiniteElemSpace*> &fe)
-    {
-      FUNCNAME("DofComm::init()");
-
-      TEST_EXIT_DBG(n >= 1)("Should not happen!\n");
-
-      nLevel = n;
-      feSpaces = fe;
-
-      sendDofs.clear();
-      recvDofs.clear();
-      periodicDofs.clear();
-
-      sendDofs.resize(nLevel);
-      recvDofs.resize(nLevel);
-      periodicDofs.resize(nLevel);
-    }
+    void init(int level, 
+	      MeshLevelData &levelData, 
+	      vector<const FiniteElemSpace*> &fe);
 
     void create(InteriorBoundary &boundary);
 
@@ -119,8 +108,12 @@ namespace AMDiS {
     /// considered here. 
     LevelDataType periodicDofs;
 
+    int meshLevel;
+
     int nLevel;
 
+    MeshLevelData *levelData;
+
     vector<const FiniteElemSpace*> feSpaces;
 
     friend class Iterator;

AMDiS/src/parallel/ElementObjectDatabase.cc

@@ -579,35 +579,23 @@ namespace AMDiS {
     TEST_EXIT_DBG(macroElementRankMap)("Should not happen!\n");
 
     int owner = -1;
-
-    switch (iterGeoPos) {
-    case VERTEX:
-      {
-	vector<ElementObjectData>& vertexData = vertexElements[vertexIter->first];
-	for (vector<ElementObjectData>::iterator it = vertexData.begin();
-	     it != vertexData.end(); ++it)
-	  owner = std::max(owner, (*macroElementRankMap)[it->elIndex]);
-      }
-      break;
-    case EDGE:
-      {
-	vector<ElementObjectData>& edgeData = edgeElements[edgeIter->first];
-	for (vector<ElementObjectData>::iterator it = edgeData.begin();
-	     it != edgeData.end(); ++it)
-	  owner = std::max(owner, (*macroElementRankMap)[it->elIndex]);
-      }
-      break;
-    case FACE:
-      {
-      	vector<ElementObjectData>& faceData = faceElements[faceIter->first];
-	for (vector<ElementObjectData>::iterator it = faceData.begin();
-	     it != faceData.end(); ++it)
-	  owner = std::max(owner, (*macroElementRankMap)[it->elIndex]);
-      }
-      break;
-    default:
-	ERROR_EXIT("Should not happen!\n");
-    }    
+    vector<ElementObjectData> *objData;
+    
+   switch (iterGeoPos) {
+   case VERTEX:
+     objData = &(vertexElements[vertexIter->first]);
+     break;
+   case EDGE:
+     objData = &(edgeElements[edgeIter->first]);
+     break;
+   case FACE:
+     objData = &(faceElements[faceIter->first]);
+     break;
+   }
+
+   for (vector<ElementObjectData>::iterator it = objData->begin();
+	it != objData->end(); ++it)
+     owner = std::max(owner, (*macroElementRankMap)[it->elIndex]);
 
     return owner;
   }
@@ -641,10 +629,12 @@ namespace AMDiS {
       }
       break;
     case FACE:
-      vector<ElementObjectData>& faceData = faceElements[faceIter->first];
-      for (vector<ElementObjectData>::iterator it = faceData.begin();
-	   it != faceData.end(); ++it)
-	ranksInLevel[0].insert((*macroElementRankMap)[it->elIndex]);
+      {
+	vector<ElementObjectData>& faceData = faceElements[faceIter->first];
+	for (vector<ElementObjectData>::iterator it = faceData.begin();
+	     it != faceData.end(); ++it)
+	  ranksInLevel[0].insert((*macroElementRankMap)[it->elIndex]);
+      }
       break;
     default:
       ERROR_EXIT("Should not happen!\n");

AMDiS/src/parallel/InteriorBoundary.cc

@@ -19,6 +19,9 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
+
   void InteriorBoundary::create(MPI::Intracomm &mpiComm,
 				ElementObjectDatabase &elObjDb)
   { 
@@ -345,13 +348,19 @@ namespace AMDiS {
   }
 
 
-  void InteriorBoundary::serialize(std::ostream &out)
+  void InteriorBoundary::serialize(ostream &out)
   {
-    FUNCNAME("InteriorBoundary::serialize()");
+    serialize(out, own);
+    serialize(out, other);
+    serialize(out, periodic);
+  }
 
-    ERROR_EXIT("REWRITE TO MULTILEVEL STRUCTURE!\n");
 
-#if 0
+  void InteriorBoundary::serialize(ostream &out,
+				   RankToBoundMap& boundary)
+  {
+    FUNCNAME("InteriorBoundary::serialize()");
+
     int mSize = boundary.size();
     SerUtil::serialize(out, mSize);
     for (RankToBoundMap::iterator it = boundary.begin(); 
@@ -380,18 +389,26 @@ namespace AMDiS {
 	SerUtil::serialize(out, bound.type);
       }
     }
-#endif
   }