* The last Christmas update

AMDiS/src/DOFAdmin.cc

@@ -32,6 +32,9 @@ namespace AMDiS {
     init(); 
   }
 
+  DOFAdmin::~DOFAdmin() 
+  {}
+
   void DOFAdmin::init()
   {
     firstHole = 0;
@@ -336,10 +339,6 @@ namespace AMDiS {
     nr0DOF[i] = v; 
   }
 
-  DOFAdmin::~DOFAdmin()
-  {
-  }
-
   int DOFAdmin::calcMemoryUsage()
   {
     return sizeof(DOFAdmin);

AMDiS/src/DOFVector.hh

@@ -74,7 +74,6 @@ namespace AMDiS {
     if (feSpace && feSpace->getAdmin()) {
       (feSpace->getAdmin())->addDOFIndexed(this);
     }
-      
     this->boundaryManager = NEW BoundaryManager(f);
   }
 

AMDiS/src/FiniteElemSpace.cc

@@ -11,7 +11,8 @@ namespace AMDiS {
 
   FiniteElemSpace::FiniteElemSpace(DOFAdmin* admin_,
 				   const BasisFunction* bas_fcts_,
-				   Mesh* aMesh, const std::string& aString)
+				   Mesh* aMesh, 
+				   const std::string& aString)
     : name(aString), 
       admin(admin_), 
       basFcts(bas_fcts_), 
@@ -47,12 +48,10 @@ namespace AMDiS {
   }
   
   FiniteElemSpace::FiniteElemSpace()
-  {
-  }
+  {}
 
   FiniteElemSpace::~FiniteElemSpace()
-  {
-  }
+  {}
 
   FiniteElemSpace& FiniteElemSpace::operator=(const FiniteElemSpace& feSpace)
   {

AMDiS/src/FiniteElemSpace.h

@@ -71,37 +71,32 @@ namespace AMDiS {
 					   Mesh *mesh,
 					   const std::string& name_ = "");
 
-    /** \brief
-     * destructor
-     */
+    /// Destructor.
     ~FiniteElemSpace();
     
     FiniteElemSpace& operator=(const FiniteElemSpace& feSpace);
 
-    /** \brief
-     * Returns \ref name
-     */  
+    /// Returns \ref name.
     inline std::string getName() const { 
       return name;
     }
 
-    /** \brief
-     * Returns \ref admin
-     */
+    /// Returns \ref admin.
     inline DOFAdmin* getAdmin() const { 
       return admin;
     }
 
-    /** \brief
-     * Returns \ref basFcts
-     */
+    /// Set a new DOF admin.
+    inline void setAdmin(DOFAdmin* a) {
+      admin = a;
+    }
+
+    /// Returns \ref basFcts
     inline const BasisFunction* getBasisFcts() const { 
       return basFcts;
     }
 
-    /** \brief
-     * Returns \ref mesh
-     */
+    /// Returns \ref mesh
     inline Mesh* getMesh() const { 
       return mesh; 
     }

AMDiS/src/Serializer.h

@@ -41,15 +41,15 @@ namespace AMDiS {
 	problem_(problem), 
 	tsModulo_(1), 
 	timestepNumber_(-1)
-	  {
+    {
       GET_PARAMETER(0, problem_->getName() + "->output->serialization filename", 
 		    &name_);
       GET_PARAMETER(0, problem_->getName() + "->output->write every i-th timestep",
 		    "%d", &tsModulo_);
       TEST_EXIT(name_ != "")("no filename\n");
-    };
+    }
 
-    virtual ~Serializer() {};
+    virtual ~Serializer() {}
 
     virtual void writeFiles(AdaptInfo *adaptInfo, 
 			    bool force,
@@ -73,13 +73,13 @@ namespace AMDiS {
       out.close();
 
       MSG("problem serialized to %s \n", name_.c_str());
-    };
+    }
 
-    void writeDelayedFiles() {};
+    void writeDelayedFiles() {}
 
     bool isWritingDelayed() { 
       return false; 
-    };
+    }
 
   protected:
     /** \brief
@@ -108,28 +108,27 @@ namespace AMDiS {
   public:
     static void serializeInt(std::ostream &out, int* ptrInt) {
       out.write(reinterpret_cast<const char*>(ptrInt), sizeof(int));
-    };
+    }
 
     static void serializeDouble(std::ostream &out, double* ptrInt) {
       out.write(reinterpret_cast<const char*>(ptrInt), sizeof(double));
-    };
+    }
 
     static void serializeBool(std::ostream &out, bool* ptrBool) {
       out.write(reinterpret_cast<const char*>(ptrBool), sizeof(bool));
     }
 
-
     static void deserializeInt(std::istream &in, int* ptrInt) {
       in.read(reinterpret_cast<char*>(ptrInt), sizeof(int));
-    };
+    }
 
     static void deserializeDouble(std::istream &in, double* ptrInt) {
       in.read(reinterpret_cast<char*>(ptrInt), sizeof(double));
-    };
+    }
 
     static void deserializeBool(std::istream &in, bool* ptrBool) {
       in.read(reinterpret_cast<char*>(ptrBool), sizeof(bool));
-    };
+    }
 
   };
 }

AMDiS/src/SolutionDataStorage.h

@@ -2,6 +2,7 @@
 #define AMDIS_SOLUTION_DATA_STORAGE_H
 
 #include <iostream>
+#include <fstream>
 #include <vector>
 #include <map>
 #include "DOFVector.h"
@@ -23,107 +24,320 @@ namespace AMDiS {
   };
   
 
-  class DataContainer
-  {
-  public:
-  };
 
+  /** \brief
+   * Class to store solution data for one timestep.
+   *
+   * Within this class, the solution data for one timestep is stored. The 
+   * type of the solution data is the typename of the class, i.e., either
+   * DOFVector or SystemVector. The class is resonsible for serialization
+   * and deserialization of the solution.
+   *
+   * The class is used only from class \ref SolutionDataStorage, and must
+   * not be used by the user in other context.
+   */
   template<typename T>
-  class SolutionDataStorage 
+  class SolutionData 
   {
   public:
+
+    /** \brief 
+     * The constructor requires already the data. So no empty data class
+     * can be created.
+     */
+    SolutionData(T* sol, 
+		 typename SolutionHelper<T>::type fes,
+		 double ts,
+		 int i) 
+      : solution(sol),
+	feSpace(fes),
+	timestamp(ts),
+	id(i),
+	serialized(false),
+	filename("")
+    {}
+
     /** \brief
-     *
+     * The destructor either deletes the data files or deletes the pointers
+     * to the data.
      */
-    SolutionDataStorage(std::string name);
+    ~SolutionData() 
+    {
+      if (!serialized) {
+	DELETE solution;
+	deleteFeSpace(feSpace);
+      }
+    }
+
+    /// Serialize the data to a file.
+    void serialize(std::string fn) 
+    {
+      std::ofstream out(fn.c_str());
+      serializeFeSpace(out, feSpace);
+      solution->serialize(out);
+      out.close();
+
+      serialized = true;
+      filename = fn;   
+
+      DELETE solution;
+      deleteFeSpace(feSpace);
+    }
+
+    /// Deserialize the data from file.
+    void deserialize()
+    {
+      std::string feName = "";
+      int dim = 0;
+      int degree = 0;
+
+      std::ifstream in(filename.c_str());
+      deserializeFeSpace(in, feSpace);
+      solution = new T("", feSpace, 0);
+      solution->deserialize(in);
+      in.close();
+
+      serialized = false;
+      filename = "";
+    }
 
     /** \brief
+     * Returns the data. In the case the data was serialized to the disk,
+     * it will be first deserialized from the corresponding file.
+     */
+    void getData(T** ptrSolution, double *ptrTimestamp)
+    {
+      if (serialized) {
+ 	deserialize();
+      } 
+
+      *ptrSolution = solution;
+      *ptrTimestamp = timestamp;      
+    }
+
+    /// Returns \ref serialized.
+    bool isSerialized() {
+      return serialized;
+    }
+
+  protected:
+    /// Serialize a fe space to a file.
+    void serializeFeSpace(std::ofstream &out, FiniteElemSpace* fe) 
+    {     
+      // Write the mesh to file.
+      out << fe->getMesh()->getName() << "\n";
+
+      int dim = fe->getMesh()->getDim();
+      out.write(reinterpret_cast<const char*>(&dim), sizeof(int));
+
+      fe->getMesh()->serialize(out);
+
+      // Then, write all other fe space data to file.
+      dim = fe->getBasisFcts()->getDim();
+      int degree = fe->getBasisFcts()->getDegree();
+      out << ((fe->getName() != "") ? fe->getName() : "noname") << "\n";
+      out.write(reinterpret_cast<const char*>(&dim), sizeof(int));
+      out.write(reinterpret_cast<const char*>(&degree), sizeof(int));
+    }
+
+    /** \brief 
+     * Serialize a vector of fe spaces to a file. 
      *
+     * Takes special care about multiple fe space pointers, pointing to the
+     * same fe space. In this case, only the first fe space is serialized
+     * completely.
      */
-    ~SolutionDataStorage();
+    void serializeFeSpace(std::ofstream &out, std::vector<FiniteElemSpace*>& fe)
+    {
+      int size = fe.size();     
+      out.write(reinterpret_cast<const char*>(&size), sizeof(int));
+
+      for (int i = 0; i < size; i++) {
+	// Check, if the pointer points to an fe space serialized before.
+	int found = -1;
+	for (int j = 0; j < i; j++) {
+	  if (fe[j] == fe[i]) {
+	    found = j;
+	    break;
+	  }
+	}
+
+        out.write(reinterpret_cast<const char*>(&found), sizeof(int));
+	// Only in case this fe space was not serialized before, write it to the file.
+	if (found == -1) {
+	  serializeFeSpace(out, fe[i]);
+	}
+      }
+    }
 
+    void deserializeFeSpace(std::ifstream &in, FiniteElemSpace** fe) 
+    {
+      std::string name = "";
+      int dim = 0;
+      int degree = 0;
+
+      in >> name;
+      in.get();
+      in.read(reinterpret_cast<char*>(&dim), sizeof(int));
+      Mesh *mesh = new Mesh(name, dim);
+      mesh->deserialize(in);
+
+      in >> name;
+      in.get();
+      in.read(reinterpret_cast<char*>(&dim), sizeof(int));
+      in.read(reinterpret_cast<char*>(&degree), sizeof(int));
+
+      *fe = FiniteElemSpace::provideFESpace(NULL,
+					    Lagrange::getLagrange(dim, degree),
+					    mesh,
+					    name);
+      (*fe)->setAdmin(const_cast<DOFAdmin*>(&(mesh->getDOFAdmin(0))));
+    }
+
+    void deserializeFeSpace(std::ifstream &in, std::vector<FiniteElemSpace*>& fe)
+    {
+      int size;
+      in.read(reinterpret_cast<char*>(&size), sizeof(int));
+
+      fe.resize(size);
+      for (int i = 0; i < size; i++) {
+	int found;
+	in.read(reinterpret_cast<char*>(&found), sizeof(int));
+	if (found == -1) {
+	  deserializeFeSpace(in, &(fe[i]));
+	} else {
+	  fe[i] = fe[found];
+	}
+      }
+    }
+
+    /// Remove one fe space from memory.
+    void deleteFeSpace(FiniteElemSpace* fe)
+    {
+      if (fe) {
+	DELETE fe->getMesh();
+	DELETE fe;
+	fe = NULL;
+      }
+    }
+
+    /// Remove a vector of fe spaces from memory. 
+    void deleteFeSpace(std::vector<FiniteElemSpace*>& fe)
+    {
+      // Stores all pointers to fe spaces, that were deleted. This should
+      // avoid double deletion of pointer.
+      std::map<FiniteElemSpace*, bool> deletedFeSpaces;
+
+      for (int i = 0; i < static_cast<int>(fe.size()); i++) {
+	if (deletedFeSpaces.find(fe[i]) == deletedFeSpaces.end()) {
+	  deleteFeSpace(fe[i]);
+	  deletedFeSpaces[fe[i]] = true;
+	}
+      }
+
+      fe.clear();
+    }
+
+    public:
     /** \brief
-     * Set one fix FE Space. All solutions are defined only on the given FE Space.     
+     * Here, all the solutions (i.e. either DOFVectors or SystemVectors)
+     * are stored.
      */
-    void setFixFESpace(typename SolutionHelper<T>::type feSpace);
+    T* solution;
 
     /** \brief
-     *
+     * Stores to every solution its FE Space. If \ref fixedFESpace is set
+     * to true, only one entry exists. This is than the FE Space for all
+     * solutions.
      */
-    void push(T *solution,
-	      double timestamp);
+    typename SolutionHelper<T>::type feSpace;
 
     /** \brief
-     *
+     * Stores to every solutions the timestamp at which the solution was
+     * created in the adaption loop.
+     */
+    double timestamp;
+
+    /** \brief
+     * If true, the solution data is serialied to disk and the pointers
+     * are not valid.
+     */
+    bool serialized;
+
+    /// If solution data is serialied, here the corresponding filename is stored.
+    std::string filename;
+
+    int id;
+  };
+
+
+
+  /** \brief
+   * Storage for solution datas with optimization process.
+   *
+   * This class may be used to store solutions within an optimization process. 
+   * Within the forward step, solutions are stored within this data storage, and
+   * are then used within the backward step. The storage supports serialization
+   * and deserialization of solutions (and the corresponding fe spaces) to save
+   * memory.
+   *
+   * The template typename must be the type of the solution data to be stored, i.e,
+   * either DOFVector<double> or SystemVector.
+   */
+  template<typename T>
+  class SolutionDataStorage 
+  {
+  public:
+    /** \brief
+     * Constructor. The parameter is a string that will be used to search for 
+     * parameters of the storage within the init file.
      */
-    bool pop(T **solution,
-	     double *timestep);
+    SolutionDataStorage(std::string name);
 
     /** \brief
-     * Deletes all pointers and empties all internal vectors.
+     * Destructor. Deletes all stored solutions and deletes all serialized files.
      */
+    ~SolutionDataStorage();
+
+    /// Add a solution and its timestamp to the storage.
+    void push(T *solution, double timestamp);
+
+    /// Get solution data from storage. Returns true, if solution data is valid.
+    bool pop(T **solution, double *timestep);
+
+    /// Delete all pointers and empties all internal vectors.
     void clear();
 	     
-
     /** \brief
-     * Returns for a given solution number the corresponding fe Space. If the
+     * Return for a given solution number the corresponding fe Space. If the
      * the fe Space is fixed, the fe Space for all solutions is stored at
      * position 0.
      */
     typename SolutionHelper<T>::type getFeSpace(int i = 0) {
-      return feSpaces[i];
+      return solutions[i]->feSpace;
     }
 
-    /** \brief
-     *
-     */
+    /// Returns \ref poped.
     bool isPoped() {
       return poped;
     }
 
-    /** \brief
-     *
-     */
+    /// Add a new container to the storage.
     void addContainer(std::string name);
 
-    /** \brief
-     *
-     */
+    /// Add value to a container.