BaseProblems updated and some Warnings removed

extensions/base_problems/BaseProblem.h

@@ -7,13 +7,14 @@
 #include "time/RosenbrockStationary.h"
 #include "CouplingTimeInterface.h"
 #include "VtuReader.h"
+#include "pugixml.hpp"
 
 using namespace AMDiS;
 
 const Flag MESH_ADOPTED = 1<<2;
 const Flag DATA_ADOPTED = 1<<3;
 
-template<typename ProblemType=ProblemStat>
+template<typename ProblemType=ProblemStat, bool safeguard = false>
 class BaseProblem : public ProblemIterationInterface,
 		    public ProblemInstatBase
 {
@@ -163,14 +164,13 @@ public:
   /// for rosenbrock-problems a special time-operator can be added
   void addTimeOperator(RosenbrockStationary *prob, int i, int j);
   
+  template<typename T>
+  static void initFileWriterFromFile(AdaptInfo* adaptInfo, FileWriterTemplated<T>& fileWriter, bool keep_all = false);
+  
 protected:
 
   ProblemType *prob;
 
-  /// catch errors and exceptions in solve-block and continue with last iteration on failure
-  /// standard: false
-  bool secureIteration; 
-
   /// dimension of the mesh (set in \ref initialize(...) )
   unsigned dim;
   

extensions/base_problems/BaseProblem.hh

 using namespace AMDiS;
 
-template<typename ProblemType>
-BaseProblem<ProblemType>::BaseProblem(const std::string &name_, bool createProblem) 
+template<typename ProblemType, bool safeguard>
+BaseProblem<ProblemType, safeguard>::BaseProblem(const std::string &name_, bool createProblem) 
   : ProblemInstatBase(name_,NULL),
     prob(NULL),
-    secureIteration(false),
     dim(1),
     dow(1),
     nTimesteps(-1),
@@ -16,13 +15,11 @@ BaseProblem<ProblemType>::BaseProblem(const std::string &name_, bool createProbl
     prob = new ProblemType(name + "->space");
   
   dow = Global::getGeo(WORLD);
-  
-  Initfile::get(name + "->secure iteration", secureIteration);
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::initialize(Flag initFlag,
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::initialize(Flag initFlag,
 					  ProblemStat *adoptProblem,
 					  Flag adoptFlag)
 { FUNCNAME("BaseProblem::initialize()");
@@ -34,8 +31,8 @@ void BaseProblem<ProblemType>::initialize(Flag initFlag,
 }
 
 
-template<typename ProblemType>
-Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
+template<typename ProblemType, bool safeguard>
+Flag BaseProblem<ProblemType, safeguard>::initDataFromFile(AdaptInfo *adaptInfo)
 { 
   FUNCNAME("BaseProblem::initDataFromFile()");
   
@@ -53,7 +50,8 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
   
   // read data and mesh from arh-files/dat-files
   MSG("read data from file...\n");
-  if (readFormat == "arh") {
+  if (readFormat == "arh") 
+  {
     std::string filename = "";
     Initfile::get(name + "->value file", filename);
     if (filename.size() == 0) return initFlag;
@@ -65,7 +63,8 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
       solutions.push_back(prob->getSolution()->getDOFVector(i));
     ArhReader::read(filename, prob->getMesh(), solutions);
   }
-  else if (readFormat == "dat") {
+  else if (readFormat == "dat") 
+  {
     bool preserveMacroFileInfo = false;
     Parameters::get(prob->getMesh()->getName() + "->preserve macroFileInfo", preserveMacroFileInfo);
     if (prob->getMesh()->getMacroFileInfo() == NULL || !preserveMacroFileInfo)
@@ -79,7 +78,8 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
       ValueReader::readValue(filename,prob->getMesh(),prob->getSolution()->getDOFVector(i),prob->getMesh()->getMacroFileInfo());
     }
   }
-  else if (readFormat == "vtu") {
+  else if (readFormat == "vtu") 
+  {
     std::vector<std::string> filenames;
     Initfile::get(name + "->value file", filenames);
     if (filenames.size() == 0)
@@ -115,7 +115,8 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
     } else
       throw(std::runtime_error("You have to specify a .vtu file!"));
   }
-  else if (readFormat == "multi-vtu") {
+  else if (readFormat == "multi-vtu") 
+  {
     size_t numFiles = 0;
     Initfile::get(name + "->number of files", numFiles);
     for (size_t n = 0; n < numFiles; n++) {
@@ -159,6 +160,17 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
     throw(std::runtime_error("Parameter 'read data from file' set to 'true', but no parameter 'read format' specified!"));
   }
   
+  bool readPvdFromFile = false;
+  Initfile::get(name + "->read pvd from file", readPvdFromFile, 2);
+  if (readPvdFromFile) {
+    vector<FileWriterInterface*>& fileWriters = prob->getFileWriterList();
+    for (size_t i = 0; i < fileWriters.size(); i++) {
+      FileWriterTemplated<double>* fileWriter = dynamic_cast<FileWriterTemplated<double>*>(fileWriters[i]);
+      if (fileWriter)
+	initFileWriterFromFile(adaptInfo, *fileWriter);
+    }
+  }
+  
   initFlag.setFlag(DATA_ADOPTED);
   initFlag.setFlag(MESH_ADOPTED);
 
@@ -166,8 +178,36 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::beginIteration(AdaptInfo *adaptInfo) 
+template<typename ProblemType, bool safeguard>
+template<typename T>
+void BaseProblem<ProblemType, safeguard>::initFileWriterFromFile(AdaptInfo* adaptInfo, FileWriterTemplated<T>& fileWriter, bool keep_all)
+{
+  using namespace pugi;
+      
+  if(!boost::filesystem::exists(fileWriter.getFilename() + ".pvd"))
+    return;
+  
+  xml_document vtu;
+  if(!vtu.load_file((fileWriter.getFilename() + ".pvd").c_str()))
+    throw(std::runtime_error("Could not load pvd file! Error in xml structure."));
+
+  xml_node VTKFile = vtu.child("VTKFile");
+  xml_node Collection = VTKFile.child("Collection");
+  
+  std::vector<std::pair<double, std::string> >& paraviewAnimationFrames = fileWriter.getParaviewAnimationFrames();
+
+  for (xml_node DataSet = Collection.child("DataSet"); DataSet; DataSet = DataSet.next_sibling("DataSet")) {
+    std::string timestepStr = DataSet.attribute("timestep").value();
+    std::string fileStr = DataSet.attribute("file").value();
+    double time = boost::lexical_cast<double>(timestepStr);
+    if (keep_all || time <= adaptInfo->getStartTime())
+      paraviewAnimationFrames.push_back(std::make_pair(time, fileStr));
+  }
+}
+  
+
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::beginIteration(AdaptInfo *adaptInfo) 
 { FUNCNAME("BaseProblem::beginIteration()");
 	
   MSG("\n");
@@ -190,8 +230,8 @@ void BaseProblem<ProblemType>::beginIteration(AdaptInfo *adaptInfo)
 }
 
 
-template<typename ProblemType>
-Flag BaseProblem<ProblemType>::oneIteration(AdaptInfo *adaptInfo, 
+template<typename ProblemType, bool safeguard>
+Flag BaseProblem<ProblemType, safeguard>::oneIteration(AdaptInfo *adaptInfo, 
                                 Flag toDo) 
 { 
   FUNCNAME("BaseProblem::oneIteration()");
@@ -220,7 +260,7 @@ Flag BaseProblem<ProblemType>::oneIteration(AdaptInfo *adaptInfo,
 #endif
 
   if (toDo.isSet(SOLVE)) {
-    if (secureIteration) {
+    if (safeguard) {
       try {
 	prob->solve(adaptInfo);
       } catch(std::exception &e) {
@@ -250,8 +290,8 @@ Flag BaseProblem<ProblemType>::oneIteration(AdaptInfo *adaptInfo,
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::endIteration(AdaptInfo *adaptInfo) 
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::endIteration(AdaptInfo *adaptInfo) 
 { FUNCNAME("BaseProblem::endIteration()");
 	
   MSG("\n");
@@ -259,20 +299,15 @@ void BaseProblem<ProblemType>::endIteration(AdaptInfo *adaptInfo)
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::closeTimestep(AdaptInfo *adaptInfo)
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::closeTimestep(AdaptInfo *adaptInfo)
 {
-  int outputPeriod = 1;
-  Initfile::get("user parameter->write every ith timestep", outputPeriod);
-  if (adaptInfo->getTimestepNumber() % outputPeriod == 0
-    && adaptInfo->getStartTime() < adaptInfo->getEndTime()) {
   writeFiles(adaptInfo, false);
-  }
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::addTimeOperator(ProblemStat *prob, int i, int j)
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::addTimeOperator(ProblemStat *prob, int i, int j)
 {
   Operator *op = new Operator(prob->getFeSpace(i), prob->getFeSpace(j));
     op->addZeroOrderTerm(new Simple_ZOT);
@@ -284,8 +319,8 @@ void BaseProblem<ProblemType>::addTimeOperator(ProblemStat *prob, int i, int j)
 }
 
 
-template<typename ProblemType>
-void BaseProblem<ProblemType>::addTimeOperator(RosenbrockStationary *prob, int i, int j)
+template<typename ProblemType, bool safeguard>
+void BaseProblem<ProblemType, safeguard>::addTimeOperator(RosenbrockStationary *prob, int i, int j)
 {
   prob->addTimeOperator(i,j);
 }