Added some parallel debuging test for periodic boundary conditions.

AMDiS/src/AdaptInfo.h

@@ -367,7 +367,7 @@ namespace AMDiS {
     /// Sets \ref timestepNumber.
     inline void setTimestepNumber(int num) 
     {
-      timestepNumber = AMDiS::min(nTimesteps,num);
+      timestepNumber = std::min(nTimesteps, num);
     }
     
     /// Returns \ref nTimesteps.
@@ -379,7 +379,7 @@ namespace AMDiS {
     /// Sets \ref nTimesteps.
     inline void setNumberOfTimesteps(int num) 
     {
-      nTimesteps = AMDiS::max(0,num);
+      nTimesteps = std::max(0, num);
     }
 
     /// Increments \ref timestepNumber by 1;

AMDiS/src/Boundary.h

@@ -43,4 +43,4 @@ namespace AMDiS {
 
 }
 
-#endif  // _Boundary_H_ 
+#endif

AMDiS/src/CoarseningManager.cc

@@ -45,7 +45,7 @@ namespace AMDiS {
 
       if (el->getChild(0)) {
 	// interior node of the tree
-	int mark = max(el->getChild(0)->getMark(), el->getChild(1)->getMark());
+	int mark = std::max(el->getChild(0)->getMark(), el->getChild(1)->getMark());
 	el->setMark(std::min(mark + 1, 0));
       } else {
 	// leaf node of the tree                                 
@@ -63,7 +63,7 @@ namespace AMDiS {
     ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
     while (elInfo) {
       Element *el = elInfo->getElement();
-      el->setMark(max(el->getMark(), 0));
+      el->setMark(std::max(el->getMark(), 0));
       elInfo = stack.traverseNext(elInfo);
     }
   }

AMDiS/src/CoarseningManager1d.cc

@@ -57,7 +57,7 @@ namespace AMDiS {
       int  mark0 = coarsenRecursive(dynamic_cast<Line*>(const_cast<Element*>(parent->getChild(0))));
       int  mark1 = coarsenRecursive(dynamic_cast<Line*>(const_cast<Element*>( parent->getChild(1))));
 
-      mark = max(mark0, mark1);
+      mark = std::max(mark0, mark1);
 
       child[0] = dynamic_cast<Line*>(const_cast<Element*>( parent->getChild(0)));
       child[1] = dynamic_cast<Line*>(const_cast<Element*>( parent->getChild(1))); 

AMDiS/src/DOFAdmin.cc

@@ -167,7 +167,7 @@ namespace AMDiS {
     usedCount++;
     if (holeCount > 0) 
       holeCount--;
-    sizeUsed = max(sizeUsed, dof + 1);
+    sizeUsed = std::max(sizeUsed, dof + 1);
 
     return dof;
   }
@@ -182,7 +182,7 @@ namespace AMDiS {
       if (old > minsize) 
 	return;
   
-    int newval = max(minsize, static_cast<int>((dofFree.size() + sizeIncrement)));
+    int newval = std::max(minsize, static_cast<int>((dofFree.size() + sizeIncrement)));
 
     size = newval;
   
@@ -324,7 +324,7 @@ namespace AMDiS {
 
     for (std::list<DOFContainer*>::iterator dc = dofContainerList.begin(); 
 	 dc != dofContainerList.end(); ++dc)
-      (*dc)->compressDofContainer(n, newDofIndex);    
+      (*dc)->compressDofContainer(n, newDofIndex);
   }
 
 

AMDiS/src/DOFIterator.h

@@ -173,7 +173,7 @@ namespace AMDiS {
     }
   
     /// Dereferntiation of the \ref dofFreeIterator
-    virtual bool isDOFFree() 
+    virtual bool isDofFree() 
     {
       return *dofFreeIterator;
     }

AMDiS/src/Error.hh

@@ -77,7 +77,7 @@ namespace AMDiS {
       
       for (int i = 0; i < nPoints; i++) {
 	err = u_vec[i] > uh_vec[i] ? u_vec[i] - uh_vec[i] : uh_vec[i] - u_vec[i];
-	maxErr = max(maxErr, err);
+	maxErr = std::max(maxErr, err);
       }
 
       elInfo = stack.traverseNext(elInfo);

AMDiS/src/Global.h

@@ -117,17 +117,6 @@ namespace AMDiS {
 
   // ===== some simple template functions ====================================== 
 
-  ///  template<typename T> T max(T a,T b ) {return  ((a) > (b) ? (a) : (b));}
-  template<typename T,typename S> inline T max(T a,S b )
-  {
-    return  ((a) > (b) ? (a) : (b));
-  }
-
-  template<typename T> inline T min(T a,T b) 
-  {
-    return  ((a) < (b)) ? (a) : (b);
-  }
-
   template<typename T> inline T abs(T a) 
   {
     return  ((a) >= 0 ? (a) : -(a));

AMDiS/src/MathFunctions.h

@@ -42,15 +42,17 @@ namespace AMDiS {
     return 0;
   }
 
-  inline double Phi1ToR(double p1, double eps) {
-    double x = max(-1.0 + numeric_limits< double >::epsilon(), 
-		    min(1.0 - numeric_limits< double >::epsilon(), p1));
+  inline double Phi1ToR(double p1, double eps) 
+  {
+    double x = std::max(-1.0 + numeric_limits<double>::epsilon(), 
+		    std::min(1.0 - numeric_limits<double>::epsilon(), p1));
     return eps / 3.0 * log((1 + x) / (1 - x)) * 0.5;
   }
 
-  inline double Phi2ToR(double p2, double eps) {
-    double x = max(-1.0 + numeric_limits< double >::epsilon(), 
-		    min(1.0 - numeric_limits< double >::epsilon(), 1 + 2 * p2));
+  inline double Phi2ToR(double p2, double eps) 
+  {
+    double x = std::max(-1.0 + numeric_limits<double>::epsilon(), 
+		    std::min(1.0 - numeric_limits<double>::epsilon(), 1 + 2 * p2));
     return eps / 3.0 * log( (1 + x) / (1 - x) );
   }
 

AMDiS/src/Mesh.cc

@@ -102,9 +102,12 @@ namespace AMDiS {
       changeIndex(0),
       final_lambda(dimension, DEFAULT_VALUE, 0.0)
   {
-
     FUNCNAME("Mesh::Mesh()");
 
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    nParallelPreRefinements = 0;
+#endif
+
     // set default element prototype
     switch(dim) {
     case 1:
@@ -1248,42 +1251,41 @@ namespace AMDiS {
     //        nMacroElements * 2^gr >= nProcs * 10
     //    =>  gr = log_2(nProcs * 10 / nMacroElements)
     
-    double tmp = 10.0 * MPI::COMM_WORLD.Get_size() / nMacroElements;
-    int nrRefine = ceil(log(tmp) / log(2));
-    if (nrRefine < 0)
-      nrRefine = 0;
+    double scale = 10.0 * MPI::COMM_WORLD.Get_size() / nMacroElements;
+    nParallelPreRefinements = static_cast<int>(std::max(0.0, ceil(log(scale) / log(2))));
     
     if (dim == 3) {
-      int newElType = (elType + nrRefine) % 3;
+      int newElType = (elType + nParallelPreRefinements) % 3;
       switch (newElType) {
       case 1:
-	if (nrRefine > 0)
-	  nrRefine--;
+	if (nParallelPreRefinements > 0)
+	  nParallelPreRefinements--;
 	else 
-	  nrRefine = 2;
+	  nParallelPreRefinements = 2;
 	break;
       case 2:
-	nrRefine++;
+	nParallelPreRefinements++;
 	break;	
       }
       
-      TEST_EXIT((elType + nrRefine) % 3 == 0)("This should not happen!\n");
+      TEST_EXIT((elType + nParallelPreRefinements) % 3 == 0)
+	("This should not happen!\n");
     }	    
 
 
     // === Check if number of pre refinements is set ini init file. ===
 
-    int nPreRefine = 0;
-    GET_PARAMETER(0, "parallel->pre refine", "%d", &nPreRefine);
-    if (nPreRefine != 0) {
+    int tmp = 0;
+    GET_PARAMETER(0, "parallel->pre refine", "%d", &tmp);
+    if (tmp != 0) {
       MSG("Calculated %d pre refines to be useful, but %d are set in init file!\n",
-	  nrRefine, nPreRefine);
-      nrRefine = nPreRefine;
+	  nParallelPreRefinements, tmp);
+      nParallelPreRefinements = tmp;
     }
 
     // === If we do not need to refine the mesh, return back. ===
 
-    if (nrRefine == 0)
+    if (nParallelPreRefinements == 0)
       return;
 
 
@@ -1323,7 +1325,7 @@ namespace AMDiS {
       else
        	refManager = new RefinementManager3d();
 
-      refManager->globalRefine(&testMesh, nrRefine);      
+      refManager->globalRefine(&testMesh, nParallelPreRefinements);      
       delete refManager;
 
       Lagrange* basFcts = Lagrange::getLagrange(dim, 1);
@@ -1348,21 +1350,20 @@ namespace AMDiS {
     int globalRefinements = 0;
     GET_PARAMETER(0, name + "->global refinements", "%d", &globalRefinements);
 
-    if (globalRefinements < nrRefine)
+    if (globalRefinements < nParallelPreRefinements)
       globalRefinements = 0;
     else 
-      globalRefinements -= nrRefine;
+      globalRefinements -= nParallelPreRefinements;
 
     std::stringstream oss;
     oss << globalRefinements;
-
     ADD_PARAMETER(0, name + "->global refinements", oss.str().c_str());
 
 
     // === Print a note to the screen that another mesh file will be used. ===
 
     MSG("The macro mesh file \"%s\" was refined %d times and stored to file \"%s\".\n",
-	macroFilename.c_str(), nrRefine, newMacroFilename.str().c_str());
+	macroFilename.c_str(), nParallelPreRefinements, newMacroFilename.str().c_str());
 
     macroFilename = newMacroFilename.str();
     if (periodicFilename != "")

AMDiS/src/Mesh.h

@@ -608,6 +608,21 @@ namespace AMDiS {
     ///
     void deleteMeshStructure();
 
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    /// In parallel computations the level of all macro elements is equal to the number
+    /// of global pre refinements, \ref nParallelPreRefinements.
+    inline int getMacroElementLevel()
+    {
+      return nParallelPreRefinements;
+    }
+#else
+    /// In sequentiel computations the level of all macro elements is always 0.
+    inline int getMacroElementLevel()
+    {
+      return 0;
+    }
+#endif
+
   public:
     ///
     static const Flag FILL_NOTHING;
@@ -702,6 +717,12 @@ namespace AMDiS {
     void checkParallelMacroFile(std::string &macroFilename, 
 				std::string &periodicFilename,
 				int check);
+
+    /// Returns \ref nParallelPreRefinements
+    int getParallelPreRefinements() const
+    {
+      return nParallelPreRefinements;
+    }
 #endif
 
   protected:
@@ -855,6 +876,13 @@ namespace AMDiS {
      */
     long changeIndex;
 
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    /// In parallel computations the mesh may be globally prerefined to achieve a fine
+    /// enought starting mesh for the given number of ranks. The value of the variable
+    /// will be defined in function \ref checkParallelMacroFile.
+    int nParallelPreRefinements;
+#endif
+
   protected:
     /// for findElement-Fcts
     DimVec<double> final_lambda;

AMDiS/src/Operator.cc

@@ -53,7 +53,7 @@ namespace AMDiS {
 
     for (int i = 0; i < static_cast<int>(terms->size()); i++) {
       OperatorTerm *term = (*terms)[i];
-      maxTermDegree = max(maxTermDegree, term->degree);
+      maxTermDegree = std::max(maxTermDegree, term->degree);
     }
    
     return psiDegree + phiDegree - order + maxTermDegree;

AMDiS/src/Parameters.cc

@@ -50,7 +50,7 @@ namespace AMDiS {
 
     if (Parameters::singlett->paramInfo) {
       if (Parameters::singlett->paramInfo > 1)
-	info = max(info, Parameters::singlett->paramInfo - 1);
+	info = std::max(info, Parameters::singlett->paramInfo - 1);
     } else {
       info = 0;
     }

AMDiS/src/RefinementManager1d.cc

@@ -41,7 +41,7 @@ namespace AMDiS {
     child[0] = dynamic_cast<Line*>(mesh->createNewElement(el));
     child[1] = dynamic_cast<Line*>(mesh->createNewElement(el));
 
-    int mark = max(0, el->getMark() - 1);
+    int mark = std::max(0, el->getMark() - 1);
     child[0]->setMark(mark);
     child[1]->setMark(mark);
     el->setMark(0);

AMDiS/src/RefinementManager2d.cc

@@ -257,7 +257,7 @@ namespace AMDiS {
     child[0] = dynamic_cast<Triangle*>(mesh->createNewElement(el));
     child[1] = dynamic_cast<Triangle*>(mesh->createNewElement(el));
 
-    int newMark = max(0, el->getMark() - 1);
+    int newMark = std::max(0, el->getMark() - 1);
     child[0]->setMark(newMark);
     child[1]->setMark(newMark);
     el->setMark(0);
@@ -334,7 +334,7 @@ namespace AMDiS {
       int opp_vertex = (*elInfo)->getOppVertex(2);
       
       ElInfo *neigh_info = stack->traverseNeighbour2d(*elInfo, 2);
-      neigh_info->getElement()->setMark(max(neigh_info->getElement()->getMark(), 1));
+      neigh_info->getElement()->setMark(std::max(neigh_info->getElement()->getMark(), 1));
       neigh_info = refineFunction(neigh_info);
 
       // === Now go back to the original element and refine the patch. ===

AMDiS/src/RefinementManager3d.cc

@@ -25,6 +25,7 @@
 #include "DOFVector.h"
 #include "PeriodicBC.h"
 #include "VertexVector.h"
+#include "Debug.h"
 
 namespace AMDiS {
 
@@ -41,7 +42,7 @@ namespace AMDiS {
     child[0] = dynamic_cast<Tetrahedron*>(mesh->createNewElement(el));
     child[1] = dynamic_cast<Tetrahedron*>(mesh->createNewElement(el));
   
-    int mark = max(0, el->getMark() - 1);
+    int mark = std::max(0, el->getMark() - 1);
     child[0]->setMark(mark);
     child[1]->setMark(mark);
     el->setMark(0);
@@ -249,6 +250,8 @@ namespace AMDiS {
 
   int RefinementManager3d::newCoordsFct(ElInfo *el_info)
   {
+    FUNCNAME("RefinementManager3d::newCoordsFct()");
+
     Element *el = el_info->getElement();
     DegreeOfFreedom *edge[2];
     ElInfo *elinfo = el_info;
@@ -474,7 +477,7 @@ namespace AMDiS {
 	// Only 0 can be a compatible commen refinement edge. Thus, neigh has not 
 	// a compatible refinement edge. Refine it first.
 
-	neigh->setMark(max(neigh->getMark(), 1));
+	neigh->setMark(std::max(neigh->getMark(), 1));
 
 	neighInfo = refineFunction(neighInfo);
 

AMDiS/src/ResidualEstimator.cc

@@ -256,7 +256,7 @@ namespace AMDiS {
     el->setEstimation(est_el, row);
     el->setMark(0);
     est_sum += est_el;
-    est_max = max(est_max, est_el);
+    est_max = std::max(est_max, est_el);
   }
 
 
@@ -295,7 +295,7 @@ namespace AMDiS {
 	    }
 	    double v = C3 * det * result;
 	    est_t_sum += v;
-	    est_t_max = max(est_t_max, v);
+	    est_t_max = std::max(est_t_max, v);
 	  }
 	}
       }

AMDiS/src/Tetrahedron.h

@@ -274,7 +274,7 @@ namespace AMDiS {
 
       DegreeOfFreedom dof0 = dof[vertexOfEdge[localEdgeIndex][0]][0];
       DegreeOfFreedom dof1 = dof[vertexOfEdge[localEdgeIndex][1]][0];
-      DofEdge edge = std::make_pair(min(dof0, dof1), max(dof0, dof1));
+      DofEdge edge = std::make_pair(std::min(dof0, dof1), std::max(dof0, dof1));
 
       return edge;
     }

AMDiS/src/Triangle.h

@@ -178,7 +178,7 @@ namespace AMDiS {
 
       DegreeOfFreedom dof0 = dof[vertexOfEdge[localEdgeIndex][0]][0];
       DegreeOfFreedom dof1 = dof[vertexOfEdge[localEdgeIndex][1]][0];
-      DofEdge edge = std::make_pair(min(dof0, dof1), max(dof0, dof1));
+      DofEdge edge = std::make_pair(std::min(dof0, dof1), std::max(dof0, dof1));
 
       return edge;
     }

AMDiS/src/VertexVector.cc

@@ -26,29 +26,33 @@ namespace AMDiS {
     const_cast<DOFAdmin*>(admin)->addDOFContainer(this);
   }
 
+
   VertexVector::~VertexVector()
   {
     const_cast<DOFAdmin*>(admin)->removeDOFIndexed(this);
     const_cast<DOFAdmin*>(admin)->removeDOFContainer(this);
   }
 
+
   void VertexVector::set(DegreeOfFreedom val)
   {
     DOFIteratorBase it(const_cast<DOFAdmin*>(admin), USED_DOFS);
     for (it.reset(); !it.end(); ++it)
-      if (!it.isDOFFree()) 
+      if (!it.isDofFree()) 
 	operator[](it.getDOFIndex()) = val;
   } 
 
+
   void VertexVector::print()
   {
     DOFIteratorBase it(const_cast<DOFAdmin*>(admin), USED_DOFS);
     for (it.reset(); !it.end(); ++it)
-      if (!it.isDOFFree())
+      if (!it.isDofFree())
 	std::cout << "DOF " << it.getDOFIndex() << " -> " 
 		  << operator[](it.getDOFIndex()) << "\n";
   }
 
+
   void VertexVector::changeDofIndices(std::map<int, int>& dofIndexMap)
   {
     FUNCNAME("VertexVector::changedofIndices()");