Merge remote-tracking branch 'upstream/master' into fix/xml-output

CHANGELOG.md

@@ -19,7 +19,7 @@ v4.4.1
 - Fix issue with FieldConvert when range flag used (!761)
 
 **NekMesh**:
-- Fix memory consumption issue with Gmsh output (!747)
+- Fix memory consumption issue with Gmsh output (!747, !762)
 - Rework meshing control so that if possible viewable meshes will be dumped
   when some part of the system fails (!756)
 - Add manifold meshing option (!756)

library/NekMeshUtils/MeshElements/Edge.h

@@ -73,8 +73,9 @@ public:
 
     /// Copies an existing edge.
     NEKMESHUTILS_EXPORT Edge(const Edge &pSrc)
-        : m_n1(pSrc.m_n1), m_n2(pSrc.m_n2), m_edgeNodes(pSrc.m_edgeNodes),
-          m_curveType(pSrc.m_curveType), m_geom(pSrc.m_geom)
+        : m_id(pSrc.m_id), m_n1(pSrc.m_n1), m_n2(pSrc.m_n2),
+          m_edgeNodes(pSrc.m_edgeNodes), m_curveType(pSrc.m_curveType),
+          m_elLink(pSrc.m_elLink), m_parentCAD(pSrc.m_parentCAD)
     {
     }
 

library/NekMeshUtils/MeshElements/Face.h

@@ -67,13 +67,18 @@ public:
                              std::vector<EdgeSharedPtr> pEdgeList,
                               LibUtilities::PointsType pCurveType)
                 : m_vertexList(pVertexList), m_edgeList(pEdgeList),
-                  m_faceNodes(pFaceNodes), m_curveType(pCurveType), m_geom(){}
+                  m_faceNodes(pFaceNodes), m_curveType(pCurveType), m_geom()
+    {
+    }
 
     /// Copy an existing face.
     NEKMESHUTILS_EXPORT Face(const Face &pSrc)
-            : m_vertexList(pSrc.m_vertexList), m_edgeList(pSrc.m_edgeList),
-              m_faceNodes(pSrc.m_faceNodes), m_curveType(pSrc.m_curveType),
-              m_geom(pSrc.m_geom){}
+        : m_id(pSrc.m_id), m_vertexList(pSrc.m_vertexList),
+          m_edgeList(pSrc.m_edgeList), m_faceNodes(pSrc.m_faceNodes),
+          m_curveType(pSrc.m_curveType), m_geom(pSrc.m_geom),
+          m_parentCAD(pSrc.m_parentCAD)
+    {
+    }
 
     NEKMESHUTILS_EXPORT ~Face()
     {

library/NekMeshUtils/MeshElements/Mesh.cpp

@@ -98,12 +98,10 @@ unsigned int Mesh::GetNumEntities()
  */
 void Mesh::MakeOrder(int order, LibUtilities::PointsType distType)
 {
-
-    // going to make a copy of the curavture information
-    // cheaper that geom objects
-    // currently the geometry objects which make up a 3D element
-    // dont use the volume nodes, they are just stored,
-    // so we can get away without copying them
+    // Going to make a copy of the curavture information, since this is cheaper
+    // than using Nektar's Geometry objects. Currently, the geometry objects
+    // which make up a 3D element dont use the volume nodes, they are just
+    // stored, so we can get away without copying them.
 
     int id = m_vertexSet.size();
 
@@ -141,19 +139,47 @@ void Mesh::MakeOrder(int order, LibUtilities::PointsType distType)
         ASSERTL1(false, "Mesh::MakeOrder does not support this points type.");
     }
 
-    // Begin by coping mesh objects for edges, faces
-    // so that we don't affect any neighbouring elements in the mesh as
-    // we process each element.
-    // at the same time we delete the curvature from the original edge
+    // Begin by copying mesh objects for edges and faces so that we don't affect
+    // any neighbouring elements in the mesh as we process each element. At the
+    // same time we delete the curvature from the original edge and face, which
+    // will be re-added with the MakeOrder routine.
+
+    // First, we fill in the volume-interior nodes. This preserves the original
+    // curvature of the mesh.
+    const int nElmt = m_element[m_expDim].size();
+    int tmpId = 0;
+    for (int i = 0; i < nElmt; ++i)
+    {
+        if (m_verbose)
+        {
+            LibUtilities::PrintProgressbar(i, nElmt, "MakeOrder: Elements: ");
+        }
+        ElementSharedPtr el                    = m_element[m_expDim][i];
+        SpatialDomains::GeometrySharedPtr geom = el->GetGeom(m_spaceDim);
+        geom->FillGeom();
+        el->MakeOrder(order, geom, pTypes[el->GetConf().m_e], m_spaceDim, tmpId);
+    }
+
+    // Now make copies of each of the edges.
     for (eit = m_edgeSet.begin(); eit != m_edgeSet.end(); eit++)
     {
         edgeCopies[(*eit)->m_id] = EdgeSharedPtr(new Edge(*(*eit)));
         (*eit)->m_edgeNodes.clear();
     }
 
+    // Now copy faces. Make sure that this is a "deep copy", so that the face's
+    // edge list corresponds to the copied edges, otherwise we end up in a
+    // non-consistent state.
     for (fit = m_faceSet.begin(); fit != m_faceSet.end(); fit++)
     {
-        faceCopies[(*fit)->m_id] = FaceSharedPtr(new Face(*(*fit)));
+        FaceSharedPtr tmpFace = FaceSharedPtr(new Face(*(*fit)));
+
+        for (int i = 0; i < tmpFace->m_edgeList.size(); ++i)
+        {
+            tmpFace->m_edgeList[i] = edgeCopies[tmpFace->m_edgeList[i]->m_id];
+        }
+
+        faceCopies[(*fit)->m_id] = tmpFace;
         (*fit)->m_faceNodes.clear();
     }
 
@@ -249,18 +275,13 @@ void Mesh::MakeOrder(int order, LibUtilities::PointsType distType)
         el->SetVolumeNodes(face->m_faceNodes);
     }
 
-    // Finally, fill in volumes.
-    const int nElmt = m_element[m_expDim].size();
     for (int i = 0; i < nElmt; ++i)
     {
-        if (m_verbose)
+        vector<NodeSharedPtr> tmp = m_element[m_expDim][i]->GetVolumeNodes();
+        for (int j = 0; j < tmp.size(); ++j)
         {
-            LibUtilities::PrintProgressbar(i, nElmt, "MakeOrder: Elements: ");
+            tmp[j]->m_id = id++;
         }
-        ElementSharedPtr el                    = m_element[m_expDim][i];
-        SpatialDomains::GeometrySharedPtr geom = el->GetGeom(m_spaceDim);
-        geom->FillGeom();
-        el->MakeOrder(order, geom, pTypes[el->GetConf().m_e], m_spaceDim, id);
     }
 
     if (m_verbose)