H5Fed: Add function for triangle boundary.

H5Fed/applications/gmsh2h5fed.cc

@@ -123,7 +123,10 @@ int main(int argc, char **argv)
   // Vector for the gmshs tetrahedrons.
   std::vector<std::vector<unsigned int> > gmshTetrahedronTag;
   gmshTetrahedronTag.clear();
-  
+  // Vector for the gmshs triangles.
+  std::vector<std::vector<unsigned int> > gmshTriangle;
+  gmshTriangle.clear();
+
   // Make an instance of the vtk class.
   gmsh gmshInFile;
 
@@ -148,9 +151,9 @@ int main(int argc, char **argv)
   // Open H5Fed file for writing. Filename and file write access comes
   // from command line parameters. 
   if (writeFileForce == false)
-    h5fedFile.open(hdf5fedOutputFile,FILE_CREATE);
+    h5fedFile.open(hdf5fedOutputFile,H5Fed::FILE_CREATE);
   else
-    h5fedFile.open(hdf5fedOutputFile,FILE_CREATE_FORCE);
+    h5fedFile.open(hdf5fedOutputFile,H5Fed::FILE_CREATE_FORCE);
 
   // Create the group hierarchie in the hdf5fed file.
   h5fedFile.createGroupHierarchie();
@@ -168,7 +171,6 @@ int main(int argc, char **argv)
     h5fedFile.wCoord3d(gmshNodes);
     // Every node in h5fed file, so we can save memory.
     gmshNodes.clear();
-  
     //Get a vector with all tetrahedrons from gmsh file.
     gmshTetrahedron = gmshInFile.gmshTetrahedron();
     for(int varI = 0; varI<gmshTetrahedron.size(); varI++)
@@ -189,7 +191,22 @@ int main(int argc, char **argv)
 //      rDebug("Elem: %d Nodes: %d; %d", varI, gmshTetrahedronTag[varI][0], gmshTetrahedronTag[varI][1]);
     }
 
-
+    //Get a vector with all triangles from gmsh file.
+    gmshTriangle = gmshInFile.gmshTriangle();
+    // Boundary Index
+    std::vector<unsigned int> gmshTriangleBoundaryIndex;
+    gmshTriangleBoundaryIndex.resize(0,gmshTriangle.size());
+    // Write the triangles to the h5fed file as  level zero boundary, the 
+    // first one.
+    h5fedFile.wTriangleB(0,0,gmshTriangle, gmshTriangleBoundaryIndex);
+    // Every triangle in h5fed file, so we can save memory.
+    gmshTriangle.clear();
+    /*
+    for(int varI = 0; varI<gmshTriangle.size(); varI++)
+    {
+      rDebug("Triangle: %d Nodes: %d; %d; %d; ", varI, gmshTriangle[varI][0], gmshTriangle[varI][1], gmshTriangle[varI][2]);
+    }
+    */
   
   // End with the automatic index mapping because we have no further actcion
   // with an gmsh file index.

H5Fed/applications/h5feddump.cc

@@ -100,15 +100,14 @@ int main(int argc, char **argv)
   
   // Open H5Fed file for reading. Filename comes from 
   // command line parameters. 
-  h5fedFile.open(hdf5fedFile,FILE_READ);
+  h5fedFile.open(hdf5fedFile,H5Fed::FILE_READ);
 
   // Vector for the tetrahedorn nodes and the material tag.
   std::vector< std::vector<unsigned int> > elem;
   std::vector<unsigned int> materialIndex;
 
-
   // Read the tetrahedrons of the h5fed file an print them.
-  h5fedFile.rTetrahedron((unsigned int)0, elem, materialIndex);
+/*  h5fedFile.rTetrahedron((unsigned int)0, elem, materialIndex);
   for(int varI = 0; varI<elem.size(); varI++)
   {
     rDebug("Tet number: %d; nodes: %d %d; %d %d; material index: %d",
@@ -119,8 +118,19 @@ int main(int argc, char **argv)
            elem[varI][3],
            materialIndex[varI]);
   }
-
-
+*/
+  // Read the boundary trianglel of the h5fed file an print them.
+  h5fedFile.rTriangleB((unsigned int)0, (unsigned int) 0, elem, materialIndex);
+  for(int varI = 0; varI<elem.size(); varI++)
+  {
+    rDebug("Triangle number: %d; nodes: %d %d; %d; material index: %d",
+           varI,
+           elem[varI][0],
+           elem[varI][1],
+           elem[varI][2],
+           materialIndex[varI]);
+  }
+/*
   // Read the 3d coordinates of the h5fed file an print them.
   std::vector<std::vector< double> > coord;
   h5fedFile.rCoord3d(coord);
@@ -132,6 +142,8 @@ int main(int argc, char **argv)
            coord[varI][1],
            coord[varI][2]);
   }
+  
+*/  
   // Close H5Fed file.
   h5fedFile.close();
     

H5Fed/applications/h5feddump.hh

@@ -50,7 +50,7 @@
 
 using namespace physicomath;
 using namespace nonsciconst;
-using namespace H5Fed;
+//using namespace H5Fed;
 //using namespace gmshtohdf5fed;
 
 #endif /*PHIDIAS3D_H_*/

H5Fed/libsrc/gmsh/gmsh.cc

@@ -373,3 +373,8 @@ std::vector< std::vector<unsigned int> > gmsh::gmshTetrahedronTag()
 {
   return gmshTetrahedronTag_;
 }
+
+std::vector< std::vector<unsigned int> > gmsh::gmshTriangle()
+{
+  return gmshTriangle_;
+}

H5Fed/libsrc/gmsh/gmsh.hh

@@ -92,6 +92,7 @@ namespace gmshtohdf5fed
       std::vector<unsigned int> gmshNodeNumber();
       std::vector< std::vector<unsigned int> > gmshTetrahedron();
       std::vector< std::vector<unsigned int> > gmshTetrahedronTag();
+      std::vector< std::vector<unsigned int> > gmshTriangle();
 
     private:
       string fileName_;

H5Fed/libsrc/h5fed/h5fed.hh

@@ -336,7 +336,7 @@ public:
     }
   };
 
-  // Write 3dim coordinates to h5fed file.
+  // Read 3dim coordinates from h5fed file.
   int rCoord3d (std::vector<std::vector<double> >& coord)
   {
     // All these operations are only allowed, if there is a valid file
@@ -457,7 +457,7 @@ public:
   {
     // Set the name of the dataset, we want to read.
     std::string datasetName = H5FED_D_TETMESH;
-    rElement_(datasetName, level, elem, materialIndex);
+    rElement_(datasetName, level, -1, elem, materialIndex);
     return OKCODE;
   };
 
@@ -473,17 +473,49 @@ public:
     // Select the data type in which the elements should be stored.
     hid_t dataType = H5FED_MESH_ELEM_DATATYPE;
     // This function does the real work for all elements.
-    wElement_(datasetName, level, elemDim, elem, materialIndex, dataType);
+    wElement_(datasetName, level, -1, elemDim, elem, materialIndex, dataType);
     return OKCODE;
-    
   }
   
+  int wTriangleB(unsigned int level,
+                 unsigned int number,
+                 std::vector< std::vector<unsigned int> >& elem,
+                 std::vector<unsigned int>& boundaryIndex)
+  {
+    // Set dimension of an elements vector.
+    unsigned int elemDim = H5FED_TRIANGLE_N_NODE;
+    // Set the name of the dataset, we want to operate.
+    std::string datasetName = H5FED_D_TRIANGLEBOUNDARY;
+    // Select the data type in which the elements should be stored.
+    hid_t dataType = H5FED_MESH_ELEM_DATATYPE;
+    // This function does the real work for all elements.
+    wElement_(datasetName, level, (int)number,  elemDim, elem, boundaryIndex, dataType);
+    return OKCODE;
+  }
+
+  // Read and return boundary triangles and respective boundary index of the
+  // given level and number.
+  int rTriangleB(unsigned int level,
+                 unsigned int number,
+                 std::vector<std::vector<unsigned int> >& elem,
+                 std::vector<unsigned int>& boundaryIndex)
+  {
+    // Set the name of the dataset, we want to read.
+    std::string datasetName = H5FED_D_TRIANGLEBOUNDARY;
+    rElement_(datasetName, level, (int)number, elem, boundaryIndex);
+    return OKCODE;
+  };
+
+  
   // This function gets some attributes of the element, it should insert and
   // insert it to the given dataset.
   // Here we do the index mapping.
   // datasetNameBlank: the name of the elements dataset without the level!
   //                   (example: ../TETMESH_L)
   // level: the hierarchy level of the elements.
+  // number: if there are different meshes on the same level (i.e. for
+  //         boudaries, they are numbered. For no numbering choose
+  //         number < 0.
   // elemDim: the number of nodes a single element has (tet = 4, line = 2, ..)
   // elem: the outer vector contains all elements,
   //       the inner vector contains the elements node numbers
@@ -492,6 +524,7 @@ public:
   //              the material index in the file.
   int wElement_(std::string datasetNameBlank,
                 unsigned int level,
+                int number,
                 unsigned int elemDim,
                 std::vector< std::vector<unsigned int> >& elem,
                 std::vector<unsigned int>& materialIndex,
@@ -503,6 +536,10 @@ public:
     {
       // Make datasetName with the datasetNameBlank and the level.
       std::string datasetName = datasetNameBlank + stringify(level);
+      if (number >= 0)
+      {
+        datasetName = datasetName + "_K" + stringify(number);
+      }
 
       // Check if the dataset with the given datasetName already exists:
       // if it exists, abort; 
@@ -616,7 +653,8 @@ public:
           // Set the appropriate material list!
           // ===> This is not implementes yet! <===
           // See warning above.
-          element[dim_out[1]-1] = materialIndex[varI];
+//          element[dim_out[1]-1] = materialIndex[varI];
+          element[dim_out[1]-1] = 0;
   
           // Select hyperslab ('region') in file dataspace.
           hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
@@ -658,12 +696,16 @@ public:
   // vetor of vectors and a vector.
   // datasetNameBlank: the name of the elements dataset without the level!
   //                   (example: ../TETMESH_L)
-  // level:            the hierarchy level of the elements.
+  // level:            the hierarchy level of the elements
+  // number: if there are different meshes on the same level (i.e. for
+  //         boudaries, they are numbered. For no numbering choose
+  //         number < 0.
   // elem: the outer vector gets all elements,
   //       the inner vectors get the elements node numbers.
   // materialIndex: the material index to an elemen.
   int rElement_(std::string datasetNameBlank,
                 unsigned int level,
+                int number,
                 std::vector< std::vector<unsigned int> >& elem,
                 std::vector<unsigned int>& materialIndex)
   {
@@ -673,6 +715,10 @@ public:
     {
       // Make datasetName with the datasetNameBlank and the level.
       std::string datasetName = datasetNameBlank + stringify(level);
+      if (number >= 0)
+      {
+        datasetName = datasetName + "_K" + stringify(number);
+      }
 
       // Check if the dataset with the given datasetName exists:
       // if it does not return errorcode, else continue. 

H5Fed/libsrc/h5fed/h5fedconst.hh

@@ -47,6 +47,7 @@ const std::string H5FED_D_PRISMATICMESH  (H5FED_G_VOLUME_MESH+"/PRISMATICMESH_L"
 const std::string H5FED_D_PYRAMIDMESH    (H5FED_G_VOLUME_MESH+"/PYRAMIDMESH_L");
 const std::string H5FED_D_TRIANGLEMESH   (H5FED_G_VOLUME_MESH+"/TRIANGLEMESH_L");
 const std::string H5FED_D_QUADRANGLEMESH (H5FED_G_VOLUME_MESH+"/QUADRANGLEMESH_L");
+const std::string H5FED_D_TRIANGLEBOUNDARY (H5FED_G_BOUNDARY_MESH+"/BOUNDARY_TRIANGLE_L");
 
 // How much nodes have a geometric figure. 
 const unsigned short int H5FED_TET_N_NODE        = 4;