still many errors to go...

Common/include/geometry/CGeometry.hpp

@@ -190,7 +190,7 @@ class CGeometry {
   CPrimalGrid** elem;                    /*!< \brief Element vector (primal grid information). */
   CPrimalGrid** face;                    /*!< \brief Face vector (primal grid information). */
   CPrimalGrid*** bound;	                 /*!< \brief Boundary vector (primal grid information). */
-  CPoint** node;                         /*!< \brief Node vector (dual grid information). */
+  CPoint* nodes;                         /*!< \brief Node vector (dual grid information). */
   CEdge* edges;                          /*!< \brief Edge vector (dual grid information). */
   CVertex*** vertex;                     /*!< \brief Boundary Vertex vector (dual grid information). */
   CTurboVertex**** turbovertex;          /*!< \brief Boundary Vertex vector ordered for turbomachinery calculation(dual grid information). */

Common/include/geometry/CPhysicalGeometry.hpp

@@ -799,7 +799,7 @@ class CPhysicalGeometry final : public CGeometry {
    */
   void SetWallDistance(su2double val) override {
     for (unsigned long iPoint = 0; iPoint < GetnPoint(); iPoint++){
-      node[iPoint]->SetWall_Distance(val);
+      nodes->SetWall_Distance(iPoint,val);
     }
   }
 

Common/include/toolboxes/C2DContainer.hpp

@@ -485,6 +485,45 @@ class C2DContainer :
   }
 };
 
+/*!
+ * \brief Useful typedefs with default template parameters
+ */
+template<class T> using su2vector = C2DContainer<unsigned long, T, StorageType::ColumnMajor, 64, DynamicSize, 1>;
+template<class T> using su2matrix = C2DContainer<unsigned long, T, StorageType::RowMajor,    64, DynamicSize, DynamicSize>;
+
+using su2activevector = su2vector<su2double>;
+using su2activematrix = su2matrix<su2double>;
+
+using su2passivevector = su2vector<passivedouble>;
+using su2passivematrix = su2matrix<passivedouble>;
+
+/*!
+ * \class CVectorOfMatrix
+ * \brief  This contrived container is used to store matrices in a contiguous manner
+ *         but still present the "su2double**" interface to the outside world,
+ *         it will be replaced by something more efficient (at some point...).
+ */
+struct CVectorOfMatrix {
+  su2activevector storage;
+  su2matrix<su2double*> interface;
+  unsigned long M, N;
+
+  void resize(unsigned long length, unsigned long rows, unsigned long cols, su2double value) {
+    M = rows;
+    N = cols;
+    storage.resize(length*rows*cols) = value;
+    interface.resize(length,rows);
+
+    for(unsigned long i=0; i<length; ++i)
+      for(unsigned long j=0; j<rows; ++j)
+        interface(i,j) = &(*this)(i,j,0);
+  }
+
+  su2double& operator() (unsigned long i, unsigned long j, unsigned long k) { return storage(i*M*N + j*N + k); }
+  const su2double& operator() (unsigned long i, unsigned long j, unsigned long k) const { return storage(i*M*N + j*N + k); }
+
+  su2double** operator[] (unsigned long i) { return interface[i]; }
+};
 
 /*!
  * \class C2DDummyLastView
@@ -549,15 +588,3 @@ struct C3DDummyMiddleView
     return data(i,k);
   }
 };
-
-/*!
- * \brief Useful typedefs with default template parameters
- */
-template<class T> using su2vector = C2DContainer<unsigned long, T, StorageType::ColumnMajor, 64, DynamicSize, 1>;
-template<class T> using su2matrix = C2DContainer<unsigned long, T, StorageType::RowMajor,    64, DynamicSize, DynamicSize>;
-
-using su2activevector = su2vector<su2double>;
-using su2activematrix = su2matrix<su2double>;
-
-using su2passivevector = su2vector<passivedouble>;
-using su2passivematrix = su2matrix<passivedouble>;

Common/include/toolboxes/graph_toolbox.hpp

@@ -335,14 +335,12 @@ CCompressedSparsePattern<Index_t> buildCSRPattern(Geometry_t& geometry,
        *    neighbors, not duplicating any existing neighbor. ---*/
       for(auto jPoint : addedNeighbors)
       {
-        auto point = geometry.node[jPoint];
-
         if(type == ConnectivityType::FiniteVolume)
         {
           /*--- For FVM we know the neighbors of point j directly. ---*/
-          for(unsigned short iNeigh = 0; iNeigh < point->GetnPoint(); ++iNeigh)
+          for(unsigned short iNeigh = 0; iNeigh < geometry.nodes->GetnPoint(jPoint); ++iNeigh)
           {
-            Index_t kPoint = point->GetPoint(iNeigh);
+            Index_t kPoint = geometry.nodes->GetPoint(jPoint,iNeigh);
 
             if(neighbors.count(kPoint) == 0) // no duplication
               newNeighbors.insert(kPoint);
@@ -351,9 +349,9 @@ CCompressedSparsePattern<Index_t> buildCSRPattern(Geometry_t& geometry,
         else // FiniteElement
         {
           /*--- For FEM we need the nodes of all elements that contain point j. ---*/
-          for(unsigned short iNeigh = 0; iNeigh < point->GetnElem(); ++iNeigh)
+          for(unsigned short iNeigh = 0; iNeigh < geometry.nodes->GetnElem(jPoint); ++iNeigh)
           {
-            auto elem = geometry.elem[point->GetElem(iNeigh)];
+            auto elem = geometry.elem[geometry.nodes->GetElem(jPoint,iNeigh)];
 
             for(unsigned short iNode = 0; iNode < elem->GetnNodes(); ++iNode)
             {

Common/src/CMultiGridQueue.cpp

@@ -6,7 +6,7 @@
  *
  * SU2 Project Website: https://su2code.github.io
  *
- * The SU2 Project is maintained by the SU2 Foundation 
+ * The SU2 Project is maintained by the SU2 Foundation
  * (http://su2foundation.org)
  *
  * Copyright 2012-2020, SU2 Contributors (cf. AUTHORS.md)
@@ -29,154 +29,154 @@
 
 CMultiGridQueue::CMultiGridQueue(unsigned long val_npoint) {
   unsigned long iPoint;
-  
+
   nPoint = val_npoint;
   Priority = new short[nPoint];
   RightCV = new bool[nPoint];
-  
+
   QueueCV.resize(1);
-  
+
   /*--- Queue initialization with all the points in the finer grid ---*/
   for (iPoint = 0; iPoint < nPoint; iPoint ++) {
     QueueCV[0].push_back(iPoint);
     Priority[iPoint] = 0;
     RightCV[iPoint] = true;
   }
-  
+
 }
 
 CMultiGridQueue::~CMultiGridQueue(void) {
-  
+
   delete[] Priority;
   delete[] RightCV;
-  
+
 }
 
 void CMultiGridQueue::AddCV(unsigned long val_new_point, unsigned short val_number_neighbors) {
-  
+
   unsigned short Max_Neighbors = QueueCV.size()-1;
-  
+
   /*--- Basic check ---*/
   if (val_new_point > nPoint) {
     SU2_MPI::Error("The index of the CV is greater than the size of the priority list.", CURRENT_FUNCTION);
   }
-  
+
   /*--- Resize the list ---*/
   if (val_number_neighbors > Max_Neighbors)
   QueueCV.resize(val_number_neighbors+1);
-  
+
   /*--- Find the point in the queue ---*/
   bool InQueue = false;
   if (Priority[val_new_point] == val_number_neighbors) InQueue = true;
-  
+
   if (!InQueue) {
     /*--- Add the control volume, and update the priority list ---*/
     QueueCV[val_number_neighbors].push_back(val_new_point);
     Priority[val_new_point] = val_number_neighbors;
   }
-  
+
 }
 
 void CMultiGridQueue::RemoveCV(unsigned long val_remove_point) {
   unsigned short iPoint;
   bool check;
-  
+
   /*--- Basic check ---*/
   if (val_remove_point > nPoint) {
     SU2_MPI::Error("The index of the CV is greater than the size of the priority list." , CURRENT_FUNCTION);
   }
-  
+
   /*--- Find priority of the Control Volume ---*/
   short Number_Neighbors = Priority[val_remove_point];
   if (Number_Neighbors == -1) {
     char buf[200];
     SPRINTF(buf, "The CV %lu is not in the priority list.", val_remove_point);
     SU2_MPI::Error(string(buf), CURRENT_FUNCTION);
   }
-  
+
   /*--- Find the point in the queue ---*/
   vector<unsigned long>::iterator ItQueue = find(QueueCV[Number_Neighbors].begin(),
                                                  QueueCV[Number_Neighbors].end(),
                                                  val_remove_point);
   if ( ItQueue != QueueCV[Number_Neighbors].end() ) QueueCV[Number_Neighbors].erase(ItQueue);
-  
+
   Priority[val_remove_point] = -1;
-  
+
   /*--- Check that the size of the queue is the right one ---*/
   unsigned short Size_QueueCV = 0;
   check = false;
   for (iPoint = 0; iPoint < QueueCV.size(); iPoint ++)
   if (QueueCV[iPoint].size() != 0) { Size_QueueCV = iPoint; check = true;}
-  
+
   /*--- Resize the queue, if check = false, the queue is empty, at least
    we need one element in the queue ---*/
   if (check) QueueCV.resize(Size_QueueCV+1);
   else QueueCV.resize(1);
-  
+
 }
 
 void CMultiGridQueue::MoveCV(unsigned long val_move_point, short val_number_neighbors) {
-  
+
   if (val_number_neighbors < 0) {
     val_number_neighbors = 0;
     RightCV[val_move_point] = false;
   }
   else {
     RightCV[val_move_point] = true;
   }
-  
+
   /*--- Remove the control volume ---*/
   RemoveCV(val_move_point);
-  
+
   /*--- Add a new control volume ---*/
   AddCV(val_move_point, val_number_neighbors);
-  
+
 }
 
 void CMultiGridQueue::IncrPriorityCV(unsigned long val_incr_point) {
-  
+
   /*--- Find the priority list ---*/
   short Number_Neighbors = Priority[val_incr_point];
   if (Number_Neighbors == -1) {
     char buf[200];
     SPRINTF(buf, "The CV %lu is not in the priority list.", val_incr_point);
     SU2_MPI::Error(string(buf), CURRENT_FUNCTION);
   }
-  
+
   /*--- Remove the control volume ---*/
   RemoveCV(val_incr_point);
-  
+
   /*--- Increase the priority ---*/
   AddCV(val_incr_point, Number_Neighbors+1);
-  
+
 }
 
 void CMultiGridQueue::RedPriorityCV(unsigned long val_red_point) {
-  
+
   /*--- Find the priority list ---*/
   short Number_Neighbors = Priority[val_red_point];
   if (Number_Neighbors == -1) {
     char buf[200];
     SPRINTF(buf, "The CV %lu is not in the priority list.", val_red_point);
     SU2_MPI::Error(string(buf), CURRENT_FUNCTION);
   }
-  
+
   if (Number_Neighbors != 0) {
-    
+
     /*--- Remove the control volume ---*/
     RemoveCV(val_red_point);
-    
+
     /*--- Increase the priority ---*/
     AddCV(val_red_point, Number_Neighbors-1);
-    
+
   }
-  
+
 }
 
 void CMultiGridQueue::VisualizeQueue(void) {
   unsigned short iPoint;
   unsigned long jPoint;
-  
+
   cout << endl;
   for (iPoint = 0; iPoint < QueueCV.size(); iPoint ++) {
     cout << "Number of neighbors " << iPoint <<": ";
@@ -185,15 +185,15 @@ void CMultiGridQueue::VisualizeQueue(void) {
     }
     cout << endl;
   }
-  
+
 }
 
 void CMultiGridQueue::VisualizePriority(void) {
   unsigned long iPoint;
-  
+
   for (iPoint = 0; iPoint < nPoint; iPoint ++)
   cout << "Control Volume: " << iPoint <<" Priority: " << Priority[iPoint] << endl;
-  
+
 }
 
 long CMultiGridQueue::NextCV(void) {
@@ -203,11 +203,11 @@ long CMultiGridQueue::NextCV(void) {
 
 bool CMultiGridQueue::EmptyQueue(void) {
   unsigned short iPoint;
-  
+
   /*--- In case there is only the no agglomerated elements,
    check if they can be agglomerated or we have already finished ---*/
   bool check = true;
-  
+
   if ( QueueCV.size() == 1 ) {
     for (iPoint = 0; iPoint < QueueCV[0].size(); iPoint ++) {
       if (RightCV[QueueCV[0][iPoint]]) { check = false; break; }
@@ -217,30 +217,30 @@ bool CMultiGridQueue::EmptyQueue(void) {
     for (iPoint = 1; iPoint < QueueCV.size(); iPoint ++)
     if (QueueCV[iPoint].size() != 0) { check = false; break;}
   }
-  
+
   return check;
 }
 
 unsigned long CMultiGridQueue::TotalCV(void) {
   unsigned short iPoint;
   unsigned long TotalCV;
-  
+
   TotalCV = 0;
   for (iPoint = 0; iPoint < QueueCV.size(); iPoint ++)
   if (QueueCV[iPoint].size() != 0) { TotalCV += QueueCV[iPoint].size(); }
-  
+
   return TotalCV;
 }
 
 void CMultiGridQueue::Update(unsigned long iPoint, CGeometry *fine_grid) {
   unsigned short iNode;
   unsigned long jPoint;
-  
+
   RemoveCV(iPoint);
-  for (iNode = 0; iNode < fine_grid->node[iPoint]->GetnPoint(); iNode ++) {
-    jPoint = fine_grid->node[iPoint]->GetPoint(iNode);
-    if (fine_grid->node[jPoint]->GetAgglomerate() == false)
-    IncrPriorityCV(jPoint);
+  for (iNode = 0; iNode < fine_grid->nodes->GetnPoint(iPoint); iNode ++) {
+    jPoint = fine_grid->nodes->GetPoint(iPoint,iNode);
+    if (!fine_grid->nodes->GetAgglomerate(jPoint))
+      IncrPriorityCV(jPoint);
   }
-  
+
 }