correction of MeshManipulation

extensions/base_problems/CouplingBaseProblem.h

@@ -46,9 +46,9 @@ public:
 
   ~CouplingBaseProblem() { }  
   
-  virtual void initialize(Flag initFlag,
-			  ProblemStat *adoptProblem = NULL,
-			  Flag adoptFlag = INIT_NOTHING)
+  void initialize(Flag initFlag,
+			  ProblemStatSeq *adoptProblem = NULL,
+			  Flag adoptFlag = INIT_NOTHING) _OVERRIDE_
   {  
     for (size_t i = 0; i < baseProblems.size(); i++) {
       for (size_t j = 0; j < baseProblems[i]->getNumProblems(); j++)

extensions/base_problems/CouplingBaseProblem2.h

@@ -83,6 +83,8 @@ public:
 
   #define BASEPROBLEM_ARGS(z, n, text) BOOST_PP_COMMA_IF(n) _BaseProblemType ## n &prob ## n
   #define BASEPROBLEM_TYPES(z, n, text) class _BaseProblemType ## n
+    
+  // constructors created by C-Macros for each number of arguments, using BOOST_PP-Macros
   
   #define COUPLED_BASEPROBLEM_CONSTRUCTOR(z, n, text) \
       template<BOOST_PP_ENUM(BOOST_PP_INC(n), BASEPROBLEM_TYPES, BaseProblemType)> \
@@ -110,7 +112,7 @@ public:
   ~CouplingBaseProblem() { }  
   
   void initialize(Flag initFlag,
-		  ProblemStat *adoptProblem = NULL,
+		  ProblemStatSeq *adoptProblem = NULL,
 		  Flag adoptFlag = INIT_NOTHING) _OVERRIDE_
   {  
     tools::FOR_EACH< detail::AddProblem >::loop2(*this, baseProblems);

extensions/base_problems/CouplingBaseProblem2_cxx11.h

@@ -88,9 +88,18 @@ public:
   }
 
   ~CouplingBaseProblem() { }  
-  
+
+  /**
+   * Add the problems to the iterationInterface, timeInterface and couplingProblemStat.
+   * As a consequence all problem can be initialized one after another and in the
+   * adaption loop they are solved in rotation.
+   *
+   * In the adaption loop the problems are solved the same order as they are added to the
+   * iterationInterface in this method. This order can be changed manually in the oneIteration
+   * method.
+   **/
   void initialize(Flag initFlag,
-		  ProblemStat *adoptProblem = NULL,
+		  ProblemStatSeq *adoptProblem = NULL,
 		  Flag adoptFlag = INIT_NOTHING) _OVERRIDE_
   {
     tools::FOR_EACH< detail::AddProblem >::loop2(*this, baseProblems);
@@ -106,6 +115,12 @@ public:
   
   virtual void initData() {}  
   
+  
+  /**
+   * At first the initData method is called for all baseProblems, then
+   * the problems are filled with operators and coupling operators as well as
+   * boundary conditions are added.
+   **/
   virtual void initTimeInterface()
   {
     tools::FOR_EACH< detail::InitData >::loop(baseProblems);

extensions/base_problems/CouplingBaseProblem_RB.h

@@ -28,7 +28,7 @@ public:
   typedef BaseProblem_RB BaseProblemType;
   typedef CouplingProblemStatImpl<ExtendedRosenbrockStationary> CProblemStat;
 
-  CoupledBaseProblem_RB(std::string name_, 
+  CouplingBaseProblem_RB(std::string name_, 
 			BaseProblemType *prob0_,
 			BaseProblemType *prob1_=NULL, 
 			BaseProblemType *prob2_=NULL, 
@@ -43,11 +43,11 @@ public:
     }
   }
 
-  ~CoupledBaseProblem_RB() { }  
+  ~CouplingBaseProblem_RB() { }  
   
   /// get the j-th stage-solution-vector of the i-th problem
   DOFVector<double> *getStageSolution(int i, int j)
-  { FUNCNAME("CoupledBaseProblem::getStageSolution(i,j)");
+  { FUNCNAME("CouplingBaseProblem_RB::getStageSolution(i,j)");
   
     TEST_EXIT(0<=i && 0<=j && i<baseProblems.size() && j<=baseProblems[i]->getNumComponents())
       ("Indices out of range!\n");
@@ -56,7 +56,7 @@ public:
   
   /// get the j-th unVec-vector of the i-th problem
   DOFVector<double> *getUnVec(int i, int j=0) 
-  { FUNCNAME("CoupledBaseProblem::getUnVec(i,j)");
+  { FUNCNAME("CouplingBaseProblem_RB::getUnVec(i,j)");
   
     TEST_EXIT(0<=i && 0<=j && i<baseProblems.size() && j<=baseProblems[i]->getNumComponents())
       ("Indices out of range!\n");

extensions/demo/NavierStokesCahnHilliard_PC/init/cahnHilliard.inc.2d

@@ -31,6 +31,7 @@ ch->space->dim: 2
 
 % ================== SOLVER ======================================
 ch->space->solver: petsc-ch % umfpack %petsc-ch
+ch->space->solver->backend: no
 ch->space->solver->use old initial guess: 1
 ch->space->solver->symmetric strategy: 0
 ch->space->solver->store symbolic: 0

extensions/demo/NavierStokesCahnHilliard_PC/init/navierStokes_TaylorHood.inc.2d

@@ -48,6 +48,7 @@ ns->space->dim: 2
 
 % ================== SOLVER ======================================
 ns->space->solver: petsc-navierstokes %umfpack % petsc-navierstokes
+ns->space->solver->backend: no
 ns->space->solver->navierstokes->use old initial guess: 1
 parallel->use zero start vector: 0
 ns->space->solver->navierstokes->pressure component: 2

extensions/demo/NavierStokesCahnHilliard_PC/src/CahnHilliardNavierStokes_.h

@@ -18,10 +18,14 @@
 #ifndef CAHN_HILLIARD_NAVIER_STOKES_H
 #define CAHN_HILLIARD_NAVIER_STOKES_H
 
+#include "AMDiS.h"
+
 // coupling structures
-#include "CouplingIterationInterface.h"
-#include "CouplingTimeInterface.h"
-#include "CouplingProblemStat.h"
+#if __cplusplus > 199711L
+  #include "CouplingBaseProblem2_cxx11.h"
+#else
+  #include "CouplingBaseProblem2.h"
+#endif
 
 #include "CahnHilliard_.h"
 
@@ -33,38 +37,6 @@
 
 using namespace AMDiS;
 
-
-
-class ID : public AbstractFunction<double, double>
-{
-public:
-  ID()
-    : AbstractFunction<double, double>(2)  {};
-  double operator()(const double& x) const  {
-    return x;
-  }
-};
-
-
-
-
-
-class Y : public AbstractFunction<double, WorldVector<double> >
-{
-public:
-  Y()
-    : AbstractFunction<double, WorldVector<double> >(1)  {};
-  double operator()(const WorldVector<double>& x) const  {
-    return x[1];
-  }
-};
-
-
-
-
-
-
-
 /**
   * \ingroup Problem 
   *
@@ -72,90 +44,87 @@ public:
   */
 template<typename CH_Type = CahnHilliard_,
 	 typename NS_Type = NavierStokes_TaylorHood>
-class CahnHilliardNavierStokes_ : public CouplingIterationInterface,
-                                 public CouplingTimeInterface,
-                                 public CouplingProblemStat
+class CahnHilliardNavierStokes_ : public CouplingBaseProblem<ProblemStat, CH_Type, NS_Type>
 {
+public:
+  
+  typedef CouplingBaseProblem<ProblemStat, CH_Type, NS_Type> super;
+  
 public:
 
   CahnHilliardNavierStokes_(std::string name_, CH_Type *chProb_, NS_Type *nsProb_)
-  : CouplingProblemStat(name_),
+  : super(name_, *chProb_, *nsProb_),
     chProb(chProb_),
     nsProb(nsProb_),
     refFunction(NULL),
     refinement(NULL),
     sigma(0.0),
-    surfaceTension(0.0)
+    surfaceTension(0.0),
+    y(NULL),
+    yc1(NULL),
+    yc2(NULL)
   {
-    dow = Global::getGeo(WORLD);
-
-    Parameters::get(name + "->sigma", sigma);
+    Parameters::get(super::name + "->sigma", sigma);
     surfaceTension = sigma/chProb->getEpsilon() * 3.0/2.0/sqrt(2.0);
-    
-
   }
 
 
-  ~CahnHilliardNavierStokes_() {
-    if (refFunction != NULL)
+  ~CahnHilliardNavierStokes_() 
+  {
+    if (refFunction) {
       delete refFunction;
-    if (refinement != NULL)
+      refFunction = NULL;
+    }
+    if (refinement) {
       delete refinement;
+      refinement = NULL;
+    }
+    if (y) {
+      delete y;
+      y = NULL;
+    }
+    if (yc1) {
+      delete yc1;
+      yc1 = NULL;
+    }
+    if (yc2) {
+      delete yc2;
+      yc2 = NULL;
+    }
   }
 
-
+  
   /**
-   * Add the problems to the iterationInterface, timeInterface and couplingProblemStat.
-   * As a consequence all problem can be initialized one after another and in the
-   * adaption loop they are solved in rotation.
-   * At the end the problems are filled with operators and coupling operators as well as
-   * boundary conditions are added.
-   *
-   * In the adaption loop the problems are solved the same order as they are added to the
-   * iterationInterface in this method. This order can be changed manually in the oneIteration
-   * method.
+   * All needed DOFVectors are initialized so that they can be used inside
+   * of the operators.
    **/
-  void initialize(AdaptInfo *adaptInfo)
+  void initData()
   {
-    for (size_t i = 0; i < chProb->getNumProblems(); i++)
-      addProblem(chProb->getProblem(i));
-    for (size_t i = 0; i < nsProb->getNumProblems(); i++)
-      addProblem(nsProb->getProblem(i));
-    
-    addIterationInterface(chProb);
-    addIterationInterface(nsProb);
-   // setSolveProblem("ch",false);
- 
-
-    addTimeInterface(chProb);
-    addTimeInterface(nsProb);
-
-    CouplingProblemStat::initialize(INIT_ALL);
-    dim = getMesh()->getDim();
-    fillCouplingOperators();
-    // fillOperators and fillBoundaryConditions for chProb and nsProb
-    nsProb->initTimeInterface();
-    chProb->initTimeInterface();
-    
     y = new DOFVector<double>(chProb->getFeSpace(0), "volume");
     yc1 = new DOFVector<double>(chProb->getFeSpace(0), "volume");
     yc2 = new DOFVector<double>(chProb->getFeSpace(0), "volume");
+    
     output = fopen( "output_data", "w" );
     fprintf(output, "time u_b center_old\n");
     fclose(output);
-    u_b=0;
-//     fillCouplingBoundaryConditions();
-  }
-
-  
-  Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo)
-  { FUNCNAME("CouplingIterationInterface::oneIteration()");
-    Flag flag = CouplingIterationInterface::oneIteration(adaptInfo, toDo);
+    u_b = 0;
     
-    //chProb->solveInitialProblem(adaptInfo);
     
-    return flag;
-  };
+    // meshFunction for k local refinement around the interface of the phasefield-DOFVector
+    refFunction = new PhaseFieldRefinement(chProb->getMesh());
+
+    if (chProb->getDoubleWellType() == 0) {
+      refinement = new RefinementLevelDOF(
+	chProb->getFeSpace(),
+	refFunction,
+	chProb->getSolution()->getDOFVector(1)); // phaseField-DOFVector in [0,1]
+    } else {
+      refinement = new RefinementLevelDOF(
+	chProb->getFeSpace(),
+	refFunction,
+	new PhaseDOFView<double>(chProb->getSolution()->getDOFVector(1))); // phaseField-DOFVector in [-1,1]
+    }
+  }
   
 
   /**
@@ -166,18 +135,21 @@ public:
   void fillCouplingOperators()
   { FUNCNAME("CahnHilliardNavierStokes::fillCouplingOperators()");
     MSG("CahnHilliardNavierStokes::fillCouplingOperators()");
+    
+    int degree = nsProb->getFeSpace(0)->getBasisFcts()->getDegree();
 
-    for (size_t i = 0; i < dow; i++) {
+    for (size_t i = 0; i < super::dow; i++) {
       // < nu * d_i(c) , theta >
       Operator *opNuGradC = new Operator(nsProb->getFeSpace(i), chProb->getFeSpace(0));
-      opNuGradC->addTerm(new VecAndPartialDerivative_ZOT(chProb->getSolution()->getDOFVector(0), chProb->getSolution()->getDOFVector(1), i));
+      opNuGradC->addTerm(new VecAndPartialDerivative_ZOT(chProb->getSolution()->getDOFVector(0), 
+							 chProb->getSolution()->getDOFVector(1), i));
       nsProb->getProblem(0)->addVectorOperator(opNuGradC, i, &surfaceTension, &surfaceTension);
     }
 
-     for (size_t i = 0; i < dow; i++) {
+     for (size_t i = 0; i < super::dow; i++) {
 	// < v * grad(c) , theta >
 	Operator *opVGradC = new Operator(chProb->getFeSpace(0), chProb->getFeSpace(1));
-	opVGradC->addTerm(new VecAtQP_FOT(nsProb->getSolution()->getDOFVector(i), new ID(), i), GRD_PHI);
+	opVGradC->addTerm(new VecAndPartialDerivative_FOT(nsProb->getSolution()->getDOFVector(i), i), GRD_PHI);
 	chProb->getProblem()->addMatrixOperator(opVGradC, 1, 1,  chProb->getTau());
      }
    /**/ 
@@ -191,27 +163,12 @@ public:
    **/ 
   void solveInitialProblem(AdaptInfo *adaptInfo)
   {
-    // meshFunction for klocal refinement around the interface of the phasefield-DOFVector
-    refFunction = new PhaseFieldRefinement(chProb->getMesh());
-
-    if (chProb->getDoubleWellType() == 0) {
-      refinement = new RefinementLevelDOF(
-	chProb->getFeSpace(),
-	refFunction,
-	chProb->getSolution()->getDOFVector(1)); // phaseField-DOFVector in [0,1]
-    } else {
-      refinement = new RefinementLevelDOF(
-	chProb->getFeSpace(),
-	refFunction,
-	new PhaseDOFView<double>(chProb->getSolution()->getDOFVector(1))); // phaseField-DOFVector in [-1,1]
-    }
-
     // initial refinement
     refinement->refine(0);
 
-    for (int i = 0; i < 3; i++) {
+    for (int i = 0; i < 5; i++) {
       chProb->solveInitialProblem(adaptInfo); 	// update phaseField-DOFVector
-      refinement->refine((i < 4 ? 4 : 10));	// do k steps of local refinement
+      refinement->refine(5);			// do k steps of local refinement
     }
 
     // solve all initial problems of the problems added to the CouplingTimeInterface
@@ -226,16 +183,14 @@ public:
   void closeTimestep(AdaptInfo *adaptInfo)
   {
     CouplingTimeInterface::closeTimestep(adaptInfo);
-
     
-    
-    Y yFun;
+    AMDiS::Component<1> yFun(y->getFeSpace()->getBasisFcts()->getDegree());
     y->interpol(&yFun);
 
-    DOFVector<double>::Iterator phiIt(dynamic_cast<DOFIndexed<double>*>(const_cast<DOFVector<double>*>(chProb->getSolution()->getDOFVector(1))), USED_DOFS);
-    DOFVector<double>::Iterator yIt(dynamic_cast<DOFIndexed<double>*>(y), USED_DOFS);
-    DOFVector<double>::Iterator yc1It(dynamic_cast<DOFIndexed<double>*>(yc1), USED_DOFS);
-    DOFVector<double>::Iterator yc2It(dynamic_cast<DOFIndexed<double>*>(yc2), USED_DOFS);
+    DOFIterator<double> phiIt(chProb->getSolution()->getDOFVector(1), USED_DOFS);
+    DOFIterator<double> yIt(y, USED_DOFS);
+    DOFIterator<double> yc1It(yc1, USED_DOFS);
+    DOFIterator<double> yc2It(yc2, USED_DOFS);
 
     for (phiIt.reset(), yIt.reset(),yc1It.reset(),yc2It.reset();
          !phiIt.end();
@@ -244,25 +199,18 @@ public:
                 *yc1It = *yc2It * *yIt;
 	}
 
-        if (adaptInfo->getTimestepNumber() <= 1) center_old = (yc1->Int())/(yc2->Int());
-        u_b = - (center_old - (yc1->Int())/(yc2->Int()) ) / adaptInfo->getTimestep();
-	center_old = (yc1->Int())/(yc2->Int());
+    if (adaptInfo->getTimestepNumber() <= 1) 
+      center_old = (yc1->Int()) / (yc2->Int());
+    u_b = - (center_old - (yc1->Int()) / (yc2->Int()) ) / adaptInfo->getTimestep();
+    center_old = (yc1->Int()) / (yc2->Int());
     
+    // append values to file
     output = fopen( "output_data", "a" );
-    fprintf(output, "%f, %f, %f\n",
-                adaptInfo->getTime(),
-                u_b,
-                center_old);
+    fprintf(output, "%f, %f, %f\n", adaptInfo->getTime(), u_b, center_old);
     fclose(output);
-
-//chProb->solveInitialProblem(adaptInfo);
     
     refinement->refine(2);
   }
-  
-  
-  
-  
 
 protected:
 
@@ -272,9 +220,6 @@ protected:
   PhaseFieldRefinement* refFunction;
   RefinementLevelDOF *refinement;
 
-  unsigned dim;		// dimension of the mesh
-  unsigned dow;		// dimension of the world
-
   double sigma;		// coupling parameter to calculate the surface tension
   double surfaceTension;// := sigma/epsilon
   double u_b, center_old;

extensions/demo/NavierStokesCahnHilliard_PC/src/CahnHilliard_.cc

@@ -115,11 +115,11 @@ void CahnHilliard_::solveInitialProblem(AdaptInfo *adaptInfo)
 
     /// create phase-field from signed-dist-function
     if (doubleWell == 0) {
-      transformDOF(prob->getSolution()->getDOFVector(1),
-        new SignedDistToPhaseField(initialEps));
+      forEachDOF(prob->getSolution()->getDOFVector(1),
+        new SignedDistToPhaseField(initialEps, 1.0/(2.0*sqrt(2.0))));
     } else {
-      transformDOF(prob->getSolution()->getDOFVector(1),
-        new SignedDistToCh(initialEps));
+      forEachDOF(prob->getSolution()->getDOFVector(1),
+        new SignedDistToCh(initialEps, 1.0/sqrt(2.0)));
     }
   }
 }
@@ -130,6 +130,7 @@ void CahnHilliard_::fillOperators()
   MSG("CahnHilliard_::fillOperators()\n");