Several small features added.

AMDiS/libtool

@@ -44,7 +44,7 @@ available_tags=" CXX F77"
 
 # ### BEGIN LIBTOOL CONFIG
 
-# Libtool was configured on host deimos101:
+# Libtool was configured on host p2d108:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -82,13 +82,13 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+CC="gcc"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
@@ -174,7 +174,7 @@ dlopen_self=unknown
 dlopen_self_static=unknown
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
 
 # Compiler flag to turn off builtin functions.
 no_builtin_flag=" -fno-builtin"
@@ -6763,7 +6763,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
 # End:
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
-# Libtool was configured on host deimos101:
+# Libtool was configured on host p2d108:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -6801,13 +6801,13 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
+CC="g++"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
@@ -6893,7 +6893,7 @@ dlopen_self=unknown
 dlopen_self_static=unknown
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
 
 # Compiler flag to turn off builtin functions.
 no_builtin_flag=" -fno-builtin"
@@ -6960,11 +6960,11 @@ predeps=""
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
 
 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path=`echo "-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+compiler_lib_search_path=`echo "-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Method to check whether dependent libraries are shared objects.
 deplibs_check_method="pass_all"
@@ -7071,7 +7071,7 @@ include_expsyms=""
 
 # ### BEGIN LIBTOOL TAG CONFIG: F77
 
-# Libtool was configured on host deimos101:
+# Libtool was configured on host p2d108:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7109,7 +7109,7 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"

AMDiS/src/AdaptInfo.h

@@ -47,19 +47,18 @@ namespace AMDiS {
       /// Constructor.
       ScalContent(std::string prefix) 
 	: est_sum(0.0),
-	est_t_sum(0.0),
-	est_max(0.0),
-	est_t_max(0.0),
-	fac_max(0.0),
-	fac_sum(1.0),
-	spaceTolerance(0.0),
-	timeTolerance(0.0),
-	timeErrLow(0.0),
-	coarsenAllowed(0),
-	refinementAllowed(1),
-	refineBisections(1),
-	coarseBisections(1)
-	
+	  est_t_sum(0.0),
+	  est_max(0.0),
+	  est_t_max(0.0),
+	  fac_max(0.0),
+	  fac_sum(1.0),
+	  spaceTolerance(0.0),
+	  timeTolerance(0.0),
+	  timeErrLow(0.0),
+	  coarsenAllowed(0),
+	  refinementAllowed(1),
+	  refineBisections(1),
+	  coarseBisections(1)	  	
       {
 	double timeTheta2 = 0.3;
 
@@ -147,7 +146,8 @@ namespace AMDiS {
 	solverTolerance(1e-8),
 	solverResidual(0.0),
         scalContents(size),
-	isDeserialized_(false)
+	deserialized(false),
+	rosenbrockMode(false)
     {
       GET_PARAMETER(0, name_ + "->start time", "%f", &startTime);
       time = startTime;
@@ -615,13 +615,18 @@ namespace AMDiS {
     inline const int getCoarseBisections(int index) const 
     {
       return scalContents[index]->coarseBisections;
-    }
+    }    
 
     inline int getSize() 
     { 
       return scalContents.size(); 
     }
 
+    inline bool getRosenbrockMode()
+    {
+      return rosenbrockMode;
+    }
+
     inline void setSolverIterations(int it) 
     {
       solverIterations = it;
@@ -665,12 +670,17 @@ namespace AMDiS {
     /// Returns true, if the adaptive procedure was deserialized from a file.
     const bool isDeserialized() const 
     {
-      return isDeserialized_;
+      return deserialized;
     }
 
     inline void setIsDeserialized(bool b) 
     {
-      isDeserialized_ = b;
+      deserialized = b;
+    }
+
+    inline void setRosenbrockMode(bool b)
+    {
+      rosenbrockMode = b;
     }
 
     /// Creates new scalContents with the given size.
@@ -767,7 +777,10 @@ namespace AMDiS {
     std::vector<ScalContent*> scalContents;
 
     /// Is true, if the adaptive procedure was deserialized from a file.
-    bool isDeserialized_;
+    bool deserialized;
+
+    /// Is true, if the time adaption is controlled by a Rosenbrock Method.
+    bool rosenbrockMode;
   };
 
 }

AMDiS/src/DOFVector.h

@@ -523,19 +523,22 @@ namespace AMDiS {
     /// vec[i] = v.vec[i]
     void copy(const DOFVector<T>& v); 
 
-    /// Returns minimum of DOFVector
+    /// Returns minimum of DOFVector.
     T min() const; 
 
-    /// Returns maximum of DOFVector
+    /// Returns maximum of DOFVector.
     T max() const;
 
-    /// Returns absolute maximum of DOFVector
+    /// Returns absolute maximum of DOFVector.
     T absMax() const;
 
-    /// Used by interpol while mesh traversal
+    /// Returns the average value of the DOFVector.
+    T average() const;
+
+    /// Used by interpol while mesh traversal.
     void interpolFct(ElInfo* elinfo);
 
-    /// Prints \ref vec to stdout
+    /// Prints \ref vec to stdout.
     void print() const; 
 
     ///

AMDiS/src/DOFVector.hh

@@ -289,6 +289,7 @@ namespace AMDiS {
     return m;
   }
 
+
   template<typename T>
   T DOFVector<T>::max() const 
   {
@@ -302,6 +303,7 @@ namespace AMDiS {
       m = std::max(m, *vecIterator);
 
     return m;
+
   }
 
   template<typename T>
@@ -310,6 +312,26 @@ namespace AMDiS {
     return std::max(abs(max()), abs(min()));
   }
 
+
+  template<typename T>
+  T DOFVector<T>::average() const
+  {
+    FUNCNAME("DOFVector<T>::average()");
+    
+    checkFeSpace(this->feSpace, vec);
+
+    int count = 0;
+    T m = 0;
+    Iterator vecIterator(const_cast<DOFIndexed<T>*>(dynamic_cast<const DOFIndexed<T>*>(this)), USED_DOFS);
+    for (vecIterator.reset(); !vecIterator.end(); ++vecIterator) {
+      m += *vecIterator;
+      count++;
+    }
+
+    return m / count;
+  }
+
+
   template<typename T>
   void DOFVector<T>::print() const
   {

AMDiS/src/ProblemVec.cc

@@ -538,10 +538,11 @@ namespace AMDiS {
 
 	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
 	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);
-	  adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
-	  adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
-	} else {
-	  WARNING("No estimator for component %d\n" , i);
+
+	  if (adaptInfo->getRosenbrockMode() == false) {
+	    adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
+	    adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
+	  }
 	}
       }
     }
@@ -623,7 +624,7 @@ namespace AMDiS {
     FUNCNAME("ProblemVec::buildAfterCoarsen()");
 
     if (dualMeshTraverseRequired()) {
-      dualAssemble(adaptInfo, flag);
+      dualAssemble(adaptInfo, flag, asmMatrix, asmVector);
       return;
     }
 
@@ -779,10 +780,13 @@ namespace AMDiS {
   }
   
 
-  void ProblemVec::dualAssemble(AdaptInfo *adaptInfo, Flag flag)
+  void ProblemVec::dualAssemble(AdaptInfo *adaptInfo, Flag flag, 
+				bool asmMatrix, bool asmVector)
   {
     FUNCNAME("ProblemVec::dualAssemble()");
 
+    TEST_EXIT(asmVector)("Not yet implemented!\n");
+
     for (unsigned int i = 0; i < meshes.size(); i++)
       meshes[i]->dofCompress();
 
@@ -828,7 +832,7 @@ namespace AMDiS {
 	bool assembleMatrix = true;
 	// The DOFMatrix which should be assembled (or not, if assembleMatrix
 	// will be set to false).
-	DOFMatrix *matrix = (*systemMatrix)[i][j];
+	DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
 
 	if (writeAsmInfo && matrix) {
 	  for (std::vector<Operator*>::iterator it = matrix->getOperatorsBegin();
@@ -874,6 +878,10 @@ namespace AMDiS {
 	if (!assembleMatrix && i != j)
 	  if (matrix)
 	    nnz += matrix->getBaseMatrix().nnz();
+
+	if (matrix && !assembleMatrix) {
+	  ERROR_EXIT("Not yet implemented!\n");
+	}
       }
     }
 
@@ -899,7 +907,7 @@ namespace AMDiS {
 
       for (int i = 0; i < nComponents; i++) {
 	for (int j = 0; j < nComponents; j++) {
-	  DOFMatrix *matrix = (*systemMatrix)[i][j];
+	  DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
 
 	  if (!matrix)
 	    continue;
@@ -983,19 +991,18 @@ namespace AMDiS {
 
     for (int i = 0; i < nComponents; i++) {
       for (int j = 0; j < nComponents; j++) {
-	DOFMatrix *matrix = (*systemMatrix)[i][j];
+	DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
 
-	if (matrix)
-	  matrix->removeRowsWithDBC(matrix->getApplyDBCs());      
+	if (!matrix)
+	  continue;
 
-	if (matrix)
-	  matrix->finishInsertion();
+	matrix->removeRowsWithDBC(matrix->getApplyDBCs());      
+	matrix->finishInsertion();
 
- 	if (matrix && matrix->getBoundaryManager())
+ 	if (matrix->getBoundaryManager())
  	  matrix->getBoundaryManager()->exitMatrix(matrix);	
 
-	if (matrix)
-	  nnz += matrix->getBaseMatrix().nnz();	 
+	nnz += matrix->getBaseMatrix().nnz();	 
       }
 
       // And now assemble boundary conditions on the vectors

AMDiS/src/ProblemVec.h

@@ -182,7 +182,8 @@ namespace AMDiS {
 
     bool dualMeshTraverseRequired();
 
-    void dualAssemble(AdaptInfo *adaptInfo, Flag flag);
+    void dualAssemble(AdaptInfo *adaptInfo, Flag flag, 
+		      bool asmMatrix = true, bool asmVector = true);
 
     void createPrecon();
 

AMDiS/src/ResidualEstimator.cc

@@ -179,9 +179,9 @@ namespace AMDiS {
     }
 
     if (output) {
-      MSG("estimate   = %.8e\n", est_sum);
+      MSG("estimate for component %d = %.8e\n", row, est_sum);
       if (C3)
-	MSG("time estimate   = %.8e\n", est_t_sum);
+	MSG("time estimate for component %d = %.8e\n", row, est_t_sum);
     }
 
     delete [] riq;

AMDiS/src/VtkWriter.hh

@@ -126,7 +126,8 @@ namespace AMDiS {
     DOFVector<double>::Iterator valueIt(values, USED_DOFS);
     DOFVector< std::list<WorldVector<double> > >::Iterator coordIt(dofCoords, USED_DOFS);
 
-    file << std::fixed;
+    file << std::scientific;
+    file.precision(15);
          
     // Write the values for all vertex DOFs.
     for (intPointIt.reset(), valueIt.reset(), coordIt.reset();

AMDiS/src/time/RosenbrockAdaptInstationary.cc

@@ -15,15 +15,23 @@ namespace AMDiS {
       firstTimestep(true),
       lastTimestepRejected(false),
       succRejection(false),
+      fixFirstTimesteps(0),
       tauGamma(1.0)
   {
+    FUNCNAME("RosenbrockAdaptInstationary::RosenbrockAdaptInstationary()");
+
     std::string str;
     GET_PARAMETER(0, name + "->rosenbrock method", &str);
     RosenbrockMethodCreator *creator = 
       dynamic_cast<RosenbrockMethodCreator*>(CreatorMap<RosenbrockMethod>::getCreator(str));
     rosenbrockMethod = creator->create();
 
+    TEST_EXIT_DBG(rosenbrockMethod)("This should not happen!\n");
+
+    GET_PARAMETER(0, name + "->fix first timesteps", "%d", &fixFirstTimesteps);
     problemStat->setRosenbrockMethod(rosenbrockMethod);
+
+    adaptInfo->setRosenbrockMode(true);
   }
 
 
@@ -58,61 +66,63 @@ namespace AMDiS {
       double newTimestep = 0.0;
       double order = rosenbrockMethod->getOrder();
 
-      if (errorEst < timeTol) {
+      if (errorEst < timeTol || fixFirstTimesteps > 0 || firstTimestep) {
 	double fac = 1.0;
-
-	if (firstTimestep || succRejection) {
-	  fac = pow((timeTol / errorEst), 1.0 / order);
+	
+	if (fixFirstTimesteps > 0) {
+	  newTimestep = adaptInfo->getTimestep();
 	} else {
-	  fac = adaptInfo->getTimestep() / tauAcc * 
-	    pow((timeTol * estAcc / (errorEst * errorEst)), 1.0 / order);
+	  if (firstTimestep || succRejection) {
+	    fac = pow((timeTol / errorEst), 1.0 / order);
+	  } else {
+	    fac = adaptInfo->getTimestep() / tauAcc * 
+	      pow((timeTol * estAcc / (errorEst * errorEst)), 1.0 / order);
+	  }
+	  fac = std::min(fac, 3.0);
+	  newTimestep = fac * adaptInfo->getTimestep();
+	  newTimestep *= 0.95;
 	}
-	fac = std::min(fac, 3.0);
-	newTimestep = fac * adaptInfo->getTimestep();
 
 	tauAcc = adaptInfo->getTimestep();
 	estAcc = errorEst;
-
+	
 	lastTimestepRejected = false;
 	succRejection = false;