Work on Rosenbrock methods.

AMDiS/src/ProblemStat.cc

@@ -515,17 +515,8 @@ namespace AMDiS {
 					     solution->getDOFVector(i)));      
     }
 
-    // Check for serializer
     int writeSerialization = 0;
-    Parameters::get(name + "->write serialization", writeSerialization);
-    if (writeSerialization) {
-      MSG("Use are using the obsolete parameter: %s->write serialization\n", name.c_str());
-      MSG("Please use instead the following parameter: %s->output->write serialization\n", name.c_str());
-      ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
-    }
-
     Parameters::get(name + "->output->write serialization", writeSerialization);
-
     if (writeSerialization)
       fileWriters.push_back(new Serializer<ProblemStatSeq>(this));
   }

AMDiS/src/Serializer.h

@@ -45,7 +45,10 @@ namespace AMDiS {
       : name(""), 
 	problem(prob),
 	tsModulo(1), 
-	timestepNumber(-1)
+	timestepNumber(-1),
+	appendIndex(0),
+	indexLength(5),
+	indexDecimals(3)
     {
       FUNCNAME("Serializer::Serializer()");
 
@@ -55,9 +58,9 @@ namespace AMDiS {
 		      tsModulo);
       TEST_EXIT(name != "")("No filename!\n");
 
-#if HAVE_PARALLEL_DOMAIN_AMDIS
-      name += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
-#endif
+      Parameters::get(problem->getName() + "->output->append index", appendIndex);
+      Parameters::get(problem->getName() + "->output->index length", indexLength);
+      Parameters::get(problem->getName() + "->output->index decimals", indexDecimals);
     }
 
 
@@ -65,15 +68,18 @@ namespace AMDiS {
       : name(filename),
 	problem(prob),
 	tsModulo(writeEveryIth),
-	timestepNumber(-1)
+	timestepNumber(-1),
+	appendIndex(0),
+	indexLength(5),
+	indexDecimals(3)
     {
       FUNCNAME("Serializer::Serializer()");
 
       TEST_EXIT(name != "")("No filename!\n");
 
-#if HAVE_PARALLEL_DOMAIN_AMDIS
-      name += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
-#endif      
+      Parameters::get(problem->getName() + "->output->append index", appendIndex);
+      Parameters::get(problem->getName() + "->output->index length", indexLength);
+      Parameters::get(problem->getName() + "->output->index decimals", indexDecimals);
     }
 
 
@@ -97,14 +103,35 @@ namespace AMDiS {
 
       TEST_EXIT(adaptInfo)("No AdaptInfo\n");
 
-      std::ofstream out(name.c_str());
+      string filename = name;
+      if (appendIndex) {
+	TEST_EXIT(indexLength <= 99)("index lenght > 99\n");
+	TEST_EXIT(indexDecimals <= 97)("index decimals > 97\n");
+	TEST_EXIT(indexDecimals < indexLength)("index length <= index decimals\n");
+	
+	char formatStr[9];
+	char timeStr[20];
+	
+	sprintf(formatStr, "%%0%d.%df", indexLength, indexDecimals);
+	sprintf(timeStr, formatStr, adaptInfo ? adaptInfo->getTime() : 0.0);
+	
+	filename += string(timeStr);
+      }
+
+      filename += ".ser";
+      
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+      filename += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
+#endif
+
+      std::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);
       adaptInfo->serialize(out);
       out.close();
 
-      MSG("problem serialized to %s \n", name.c_str());
+      MSG("Problem serialized to %s \n", filename.c_str());
     }
 
   protected:
@@ -117,6 +144,16 @@ namespace AMDiS {
     /// The problem is serialized every tsModulo-th timestep.
     int tsModulo;
 
+    /// 0: Don't append time index to filename prefix.
+    /// 1: Append time index to filename prefix.
+    int appendIndex;
+
+    /// Total length of appended time index.
+    int indexLength;
+
+    /// Number of decimals in time index.
+    int indexDecimals;
+
     /// Current timestep number.
     int timestepNumber;
   };

AMDiS/src/ZeroOrderTerm.h

@@ -97,7 +97,7 @@ namespace AMDiS {
   public:
     /// Constructor.
     VecAtQP_ZOT(DOFVectorBase<double> *dv,
-		AbstractFunction<double, double> *ab);
+		AbstractFunction<double, double> *ab = NULL);
 
     /// Implementation of \ref OperatorTerm::initElement().
     void initElement(const ElInfo* elInfo, 

AMDiS/src/io/FileWriter.cc

@@ -261,14 +261,16 @@ namespace AMDiS {
 #if HAVE_PARALLEL_DOMAIN_AMDIS
       if (MPI::COMM_WORLD.Get_rank() == 0) {
 	VtkWriter vtkWriter(&dataCollectors);
-	vtkWriter.updateAnimationFile(paraFilename + paraviewParallelFileExt, 
+	vtkWriter.updateAnimationFile(adaptInfo,
+				      paraFilename + paraviewParallelFileExt, 
 				      &paraviewAnimationFrames,
 				      filename + ".pvd");
 
       }
 #else
       VtkWriter vtkWriter(&dataCollectors);
-      vtkWriter.updateAnimationFile(fn + paraviewFileExt, 
+      vtkWriter.updateAnimationFile(adaptInfo,
+				    fn + paraviewFileExt, 
 				    &paraviewAnimationFrames,
 				    filename + ".pvd");
 #endif

AMDiS/src/io/FileWriter.h

@@ -35,6 +35,8 @@
 
 namespace AMDiS {
 
+  using namespace std;
+
   typedef enum {
     NONE = 0,
     GZIP = 1,
@@ -73,19 +75,19 @@ namespace AMDiS {
       writeElement = writeElem;
     }
 
-    std::string getFilename() 
+    string getFilename() 
     { 
       return filename; 
     }
     
-    void setFilename(std::string n) 
+    void setFilename(string n) 
     { 
       filename = n; 
     }
 
   protected:
     /// Used filename prefix.
-    std::string filename;
+    string filename;
 
     int traverseLevel;
 
@@ -105,18 +107,18 @@ namespace AMDiS {
   {
   public:
     /// Constructor for a filewriter for one data component.
-    FileWriter(std::string name, Mesh *mesh, DOFVector<double> *vec);
+    FileWriter(string name, Mesh *mesh, DOFVector<double> *vec);
 
     /// Constructor for a filewriter with more than one data component.
-    FileWriter(std::string name, 
+    FileWriter(string name, 
 	       Mesh *mesh,
-	       std::vector< DOFVector<double>* > vecs);
+	       vector< DOFVector<double>* > vecs);
 
     /** \brief
      * Constructor for a filewriter, when the solution vector is a vector
      * of WorldVectors.
      */
-    FileWriter(std::string name,
+    FileWriter(string name,
 	       Mesh *mesh,
 	       DOFVector< WorldVector<double> > *vec);
 
@@ -137,22 +139,22 @@ namespace AMDiS {
     void readParameters();
 
     /// Name of the writer.
-    std::string name;
+    string name;
 
     /// AMDiS mesh-file extension.
-    std::string amdisMeshExt;
+    string amdisMeshExt;
 
     /// AMDiS solution-file extension.
-    std::string amdisDataExt;
+    string amdisDataExt;
 
     /// VTK file extension.
-    std::string paraviewFileExt;
+    string paraviewFileExt;
 
     /// Parallel VTK file extension.
-    std::string paraviewParallelFileExt;
+    string paraviewParallelFileExt;
 
     /// Periodic file extension.
-    std::string periodicFileExt;
+    string periodicFileExt;
 
     /// 0: Don't write AMDiS files; 1: Write AMDiS files. 
     int writeAMDiSFormat;
@@ -182,18 +184,16 @@ namespace AMDiS {
     int writeArhFormat;
 
     /// camera position for povray script files
-    std::string povrayCameraLocation;
+    string povrayCameraLocation;
 
     /// orientation for camera in povray script files
-    std::string povrayCameraLookAt;
+    string povrayCameraLookAt;
 
     /// name of the template file that will be prepended to all created *.pov files 
-    std::string povrayTemplate;
+    string povrayTemplate;
 
-    /** \brief
-     * 0: Don't append time index to filename prefix.
-     * 1: Append time index to filename prefix.
-     */
+    /// 0: Don't append time index to filename prefix.
+    /// 1: Append time index to filename prefix.
     int appendIndex;
 
     /// Total length of appended time index.
@@ -205,8 +205,9 @@ namespace AMDiS {
     /// Timestep modulo: write only every tsModulo-th timestep! 
     int tsModulo;
 
-    /// Stores all writen filename to a ParaView animation file.
-    std::vector< std::string > paraviewAnimationFrames;
+    /// Stores a set of pairs of timepoint and filename to write a ParaView 
+    /// animation file.
+    vector<pair<double, string> > paraviewAnimationFrames;
 
     ///
     int timestepNumber;
@@ -218,7 +219,7 @@ namespace AMDiS {
     const FiniteElemSpace *feSpace;
 
     /// Pointers to the vectors which store the solution.
-    std::vector<DOFVector<double>*> solutionVecs;
+    vector<DOFVector<double>*> solutionVecs;
 
     /** \brief
      * Stores the number of temporal solutions vectors, which have been created

AMDiS/src/io/VtkWriter.cc

@@ -31,7 +31,9 @@
 
 namespace AMDiS { 
 
-  int VtkWriter::writeFile(std::string name)
+  using namespace std;
+
+  int VtkWriter::writeFile(string name)
   {
     FUNCNAME("VtkWriter::writeFile()");
     
@@ -50,32 +52,32 @@ namespace AMDiS {
     }
 
     {
-      std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
+      ofstream swapfile(name.c_str(), ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", name.c_str());
       swapfile.close();
     }
 
-    file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc));
+    file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc));
     writeFileToStream(file);
 
     return 0;
   }
 
 
-  void VtkWriter::writeParallelFile(std::string name, int nRanks,
-				    std::string fnPrefix, std::string fnPostfix)
+  void VtkWriter::writeParallelFile(string name, int nRanks,
+				    string fnPrefix, string fnPostfix)
   {
     FUNCNAME("VtkWriter::writeParallelFile()");
 
     boost::iostreams::filtering_ostream file;
     {
-      std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
+      ofstream swapfile(name.c_str(), ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", name.c_str());
       swapfile.close();
     }
-    file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc)); 
+    file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc)); 
 
     file << "<?xml version=\"1.0\"?>\n";
     file << "<VTKFile type=\"PUnstructuredGrid\">\n";
@@ -97,7 +99,7 @@ namespace AMDiS {
     file << "    </PPointData>\n";
 
     for (int i = 0; i < nRanks; i++) {
-      std::stringstream oss;
+      stringstream oss;
       oss << fnPrefix << "-p" << i << "-" << fnPostfix;
       boost::filesystem::path filepath(oss.str());
       file << "    <Piece Source=\"" 
@@ -111,38 +113,36 @@ namespace AMDiS {
   }
 
 
-  int VtkWriter::updateAnimationFile(std::string valueFilename,
-				     std::vector< std::string > *paraViewAnimationFrames,
-				     std::string animationFilename)
+  int VtkWriter::updateAnimationFile(AdaptInfo *adaptInfo,
+				     string valueFilename,
+				     vector<pair<double, string > > *paraViewAnimationFrames,
+				     string animationFilename)
   {
     FUNCNAME("VtkWriter::updateAnimationFile()");
 
     size_t found = valueFilename.find_last_of("/\\");
-    paraViewAnimationFrames->push_back(valueFilename.substr(found + 1));
+    paraViewAnimationFrames->push_back(make_pair(adaptInfo->getTime(), 
+						 valueFilename.substr(found + 1)));
 
     boost::iostreams::filtering_ostream file;
     {
-      std::ofstream swapfile(animationFilename.c_str(), 
-			     std::ios::out | std::ios::trunc);
+      ofstream swapfile(animationFilename.c_str(), 
+			     ios::out | ios::trunc);
       TEST_EXIT(swapfile.is_open())
 	("Cannot open file %s for writing!\n", animationFilename.c_str());
       swapfile.close();
     }
     file.push(boost::iostreams::file_descriptor_sink(animationFilename, 
-						     std::ios::trunc)); 
+						     ios::trunc)); 
 
     file << "<?xml version=\"1.0\"?>\n";
     file << "<VTKFile type=\"Collection\" version=\"0.1\" >"  << "\n";
     file << "<Collection>\n";
 
-    int counter = 0;
-    std::vector< std::string >::iterator it;
-    for (it = paraViewAnimationFrames->begin(); 
-	 it < paraViewAnimationFrames->end(); 
-	 ++it, counter++) {
-      file << "<DataSet timestep=\"" << counter
-	   << "\" part=\"0\" file=\"" << (*it) << "\"/>\n";      
-    }
+    for (vector<pair<double, string> >::iterator it = paraViewAnimationFrames->begin(); 
+	 it < paraViewAnimationFrames->end(); ++it)
+      file << "<DataSet timestep=\"" << it->first
+	   << "\" part=\"0\" file=\"" << it->second << "\"/>\n"; 
 
     file << "</Collection>\n";
     file << "</VTKFile>\n";
@@ -152,23 +152,23 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(DOFVector<double> *values, 
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
     FUNCNAME("VtkWriter::writeFile()");
 
     DataCollector dc(values->getFeSpace(), values);
-    std::vector<DataCollector*> dcList(0);
+    vector<DataCollector*> dcList(0);
     dcList.push_back(&dc);
     writeFile(dcList, filename, writeParallel);
   }
 
 
-  void VtkWriter::writeFile(std::vector<DOFVector<double>* > &values,
-			    std::string filename,
+  void VtkWriter::writeFile(vector<DOFVector<double>* > &values,
+			    string filename,
 			    bool writeParallel)
   {
-    std::vector<DataCollector*> dcList(0);
+    vector<DataCollector*> dcList(0);
     for (unsigned int i = 0; i < values.size(); i++)
       dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));	
     writeFile(dcList, filename, writeParallel);
@@ -178,10 +178,10 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(WorldVector<DOFVector<double>* > &values,
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
-    std::vector<DataCollector*> dcList(0);
+    vector<DataCollector*> dcList(0);
     for (int i = 0; i < values.getSize(); i++)
       dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));	
     writeFile(dcList, filename, writeParallel);
@@ -191,7 +191,7 @@ namespace AMDiS {
 
 
   void VtkWriter::writeFile(DOFVector<WorldVector<double> > *values,
-			    std::string filename,
+			    string filename,
 			    bool writeParallel)
   {
     WorldVector<DOFVector<double>*> valuesWV;
@@ -205,10 +205,10 @@ namespace AMDiS {