Apply patches to NekMesh

library/NekMeshUtils/MeshElements/Composite.h

@@ -55,56 +55,6 @@ public:
     {
     }
 
-    /**
-     * @brief Generate a Nektar++ string describing the composite.
-     *
-     * The list of composites may include individual element IDs or ranges of
-     * element IDs.
-     */
-    NEKMESHUTILS_EXPORT std::string GetXmlString(bool doSort = true)
-    {
-        std::stringstream st;
-        std::vector<ElementSharedPtr>::iterator it;
-        bool range = false;
-        int vId    = m_items[0]->GetId();
-        int prevId = vId;
-
-        st << " " << m_tag << "[" << vId;
-
-        for (it = m_items.begin() + 1; it != m_items.end(); ++it)
-        {
-            // store previous element ID and get current one
-            prevId = vId;
-            vId    = (*it)->GetId();
-
-            // continue an already started range
-            if (prevId > -1 && vId == prevId + 1)
-            {
-                range = true;
-                // if this is the last element, it's the end of a range, so
-                // write
-                if (*it == m_items.back())
-                {
-                    st << "-" << vId;
-                }
-                continue;
-            }
-
-            // terminate a range, if present
-            if (range)
-            {
-                st << "-" << prevId;
-                range = false;
-            }
-
-            // write what will be either a single entry or start of new range
-            st << "," << vId;
-        }
-        // terminate
-        st << "] ";
-        return st.str();
-    }
-
     /// ID of composite.
     unsigned int m_id;
     /// Element type tag.

library/NekMeshUtils/MeshElements/Edge.cpp

@@ -102,6 +102,8 @@ SpatialDomains::SegGeomSharedPtr Edge::GetGeom(int coordDim)
             m_id, coordDim, p);
     }
 
+    ret->Setup();
+
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Face.cpp

@@ -334,7 +334,7 @@ SpatialDomains::Geometry2DSharedPtr Face::GetGeom(int coordDim)
             }
 
             ret = MemoryManager<SpatialDomains::TriGeom>::AllocateSharedPtr(
-                m_id, edges, edgeo, c);
+                m_id, edges, c);
         }
         else
         {
@@ -399,7 +399,7 @@ SpatialDomains::Geometry2DSharedPtr Face::GetGeom(int coordDim)
 
             ret =
                 MemoryManager<SpatialDomains::QuadGeom>::AllocateSharedPtr(
-                    m_id, edges, edgeo, c);
+                    m_id, edges, c);
         }
     }
     else
@@ -407,16 +407,17 @@ SpatialDomains::Geometry2DSharedPtr Face::GetGeom(int coordDim)
         if (nEdge == 3)
         {
             ret = MemoryManager<SpatialDomains::TriGeom>::AllocateSharedPtr(
-                m_id, edges, edgeo);
+                m_id, edges);
         }
         else
         {
             ret =
                 MemoryManager<SpatialDomains::QuadGeom>::AllocateSharedPtr(
-                    m_id, edges, edgeo);
+                    m_id, edges);
         }
     }
 
+    ret->Setup();
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Hexahedron.cpp

@@ -170,8 +170,10 @@ SpatialDomains::GeometrySharedPtr Hexahedron::GetGeom(int coordDim)
             m_face[i]->GetGeom(coordDim));
     }
 
-    ret = MemoryManager<SpatialDomains::HexGeom>::AllocateSharedPtr(faces);
+    ret = MemoryManager<SpatialDomains::HexGeom>::AllocateSharedPtr(
+        m_id, faces);
 
+    ret->Setup();
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Line.cpp

@@ -107,6 +107,7 @@ SpatialDomains::GeometrySharedPtr Line::GetGeom(int coordDim)
             m_id, 2, p);
     }
 
+    ret->Setup();
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Mesh.h

@@ -36,6 +36,8 @@
 #ifndef NEKMESHUTILS_MESHELEMENTS_MESH
 #define NEKMESHUTILS_MESHELEMENTS_MESH
 
+#include <set>
+
 #include <NekMeshUtils/NekMeshUtilsDeclspec.h>
 #include <NekMeshUtils/MeshElements/Element.h>
 #include <NekMeshUtils/MeshElements/Composite.h>

library/NekMeshUtils/MeshElements/Prism.cpp

@@ -253,8 +253,10 @@ SpatialDomains::GeometrySharedPtr Prism::GetGeom(int coordDim)
         faces[i] = m_face[i]->GetGeom(coordDim);
     }
 
-    ret = MemoryManager<SpatialDomains::PrismGeom>::AllocateSharedPtr(faces);
+    ret = MemoryManager<SpatialDomains::PrismGeom>::AllocateSharedPtr(
+        m_id, faces);
 
+    ret->Setup();
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Pyramid.cpp

@@ -164,7 +164,9 @@ SpatialDomains::GeometrySharedPtr Pyramid::GetGeom(int coordDim)
         faces[i] = m_face[i]->GetGeom(coordDim);
     }
 
-    m_geom = MemoryManager<SpatialDomains::PyrGeom>::AllocateSharedPtr(faces);
+    m_geom = MemoryManager<SpatialDomains::PyrGeom>::AllocateSharedPtr(
+        m_id, faces);
+    m_geom->Setup();
 
     return m_geom;
 }

library/NekMeshUtils/MeshElements/Quadrilateral.cpp

@@ -205,24 +205,17 @@ void Quadrilateral::MakeOrder(int                                order,
 SpatialDomains::GeometrySharedPtr Quadrilateral::GetGeom(int coordDim)
 {
     SpatialDomains::SegGeomSharedPtr edges[4];
-    SpatialDomains::PointGeomSharedPtr verts[4];
     SpatialDomains::QuadGeomSharedPtr ret;
 
     for (int i = 0; i < 4; ++i)
     {
         edges[i] = m_edge[i]->GetGeom(coordDim);
-        verts[i] = m_vertex[i]->GetGeom(coordDim);
     }
 
-    StdRegions::Orientation edgeorient[4] = {
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[0], *edges[1]),
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[1], *edges[2]),
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[2], *edges[3]),
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[3], *edges[0])};
-
     ret = MemoryManager<SpatialDomains::QuadGeom>::AllocateSharedPtr(
-        m_id, verts, edges, edgeorient);
+        m_id, edges);
 
+    ret->Setup();
     return ret;
 }
 

library/NekMeshUtils/MeshElements/Tetrahedron.cpp

@@ -239,7 +239,9 @@ SpatialDomains::GeometrySharedPtr Tetrahedron::GetGeom(int coordDim)
             m_face[i]->GetGeom(coordDim));
     }
 
-    ret = MemoryManager<SpatialDomains::TetGeom>::AllocateSharedPtr(tfaces);
+    ret = MemoryManager<SpatialDomains::TetGeom>::AllocateSharedPtr(
+        m_id, tfaces);
+    ret->Setup();
 
     return ret;
 }

library/NekMeshUtils/MeshElements/Triangle.cpp

@@ -121,22 +121,16 @@ Triangle::Triangle(ElmtConfig pConf,
 SpatialDomains::GeometrySharedPtr Triangle::GetGeom(int coordDim)
 {
     SpatialDomains::SegGeomSharedPtr edges[3];
-    SpatialDomains::PointGeomSharedPtr verts[3];
     SpatialDomains::TriGeomSharedPtr ret;
 
     for (int i = 0; i < 3; ++i)
     {
         edges[i] = m_edge[i]->GetGeom(coordDim);
-        verts[i] = m_vertex[i]->GetGeom(coordDim);
     }
 
-    StdRegions::Orientation edgeorient[3] = {
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[0], *edges[1]),
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[1], *edges[2]),
-        SpatialDomains::SegGeom::GetEdgeOrientation(*edges[2], *edges[0])};
-
     ret = MemoryManager<SpatialDomains::TriGeom>::AllocateSharedPtr(
-        m_id, verts, edges, edgeorient);
+        m_id, edges);
+    ret->Setup();
 
     return ret;
 }

utilities/NekMesh/InputModules/InputMCF.cpp

@@ -71,6 +71,7 @@ void InputMCF::ParseFile(string nm)
     filename.push_back(nm);
     LibUtilities::SessionReaderSharedPtr pSession =
         LibUtilities::SessionReader::CreateInstance(0, NULL, filename);
+    pSession->InitSession();
 
     ASSERTL0(pSession->DefinesElement("NEKTAR/MESHING"), "no meshing tag");
     ASSERTL0(pSession->DefinesElement("NEKTAR/MESHING/INFORMATION"),

utilities/NekMesh/InputModules/InputNekpp.cpp

@@ -81,11 +81,11 @@ void InputNekpp::Process()
 
     // Copy vertices.
     map<int, NodeSharedPtr> vIdMap;
-    for (auto &vit : graph->GetVertSet())
+    for (auto &vit : graph->GetAllPointGeoms())
     {
         SpatialDomains::PointGeomSharedPtr vert = vit.second;
         NodeSharedPtr n(
-            new Node(vert->GetVid(), (*vert)(0), (*vert)(1), (*vert)(2)));
+            new Node(vert->GetGlobalID(), (*vert)(0), (*vert)(1), (*vert)(2)));
         m_mesh->m_vertexSet.insert(n);
         vIdMap[vert->GetVid()] = n;
     }
@@ -107,13 +107,13 @@ void InputNekpp::Process()
             int id0 = it.second->GetVid(0);
             int id1 = it.second->GetVid(1);
             LibUtilities::PointsType ptype =
-                it.second->GetPointsKeys()[0].GetPointsType();
+                it.second->GetXmap()->GetPointsKeys()[0].GetPointsType();
             EdgeSharedPtr ed =
                 EdgeSharedPtr(new Edge(vIdMap[id0], vIdMap[id1], curve, ptype));
 
             auto testIns = m_mesh->m_edgeSet.insert(ed);
-            (*(testIns.first))->m_id = it.second->GetEid();
-            eIdMap[it.second->GetEid()] = ed;
+            (*(testIns.first))->m_id = it.second->GetGlobalID();
+            eIdMap[it.second->GetGlobalID()] = ed;
         }
     }
 
@@ -142,8 +142,8 @@ void InputNekpp::Process()
                                        faceEdges,
                                        LibUtilities::ePolyEvenlySpaced));
             auto testIns = m_mesh->m_faceSet.insert(fac);
-            (*(testIns.first))->m_id = it.second->GetFid();
-            fIdMap[it.second->GetFid()] = fac;
+            (*(testIns.first))->m_id = it.second->GetGlobalID();
+            fIdMap[it.second->GetGlobalID()] = fac;
         }
 
         for (auto &it : graph->GetAllQuadGeoms())
@@ -169,8 +169,8 @@ void InputNekpp::Process()
                                        faceEdges,
                                        LibUtilities::ePolyEvenlySpaced));
             auto testIns = m_mesh->m_faceSet.insert(fac);
-            (*(testIns.first))->m_id = it.second->GetFid();
-            fIdMap[it.second->GetFid()] = fac;
+            (*(testIns.first))->m_id = it.second->GetGlobalID();
+            fIdMap[it.second->GetGlobalID()] = fac;
         }
     }
 
@@ -241,10 +241,10 @@ void InputNekpp::Process()
     for (auto &compIt : graph->GetComposites())
     {
         // Get hold of dimension
-        int dim = (*compIt.second)[0]->GetShapeDim();
+        int dim = compIt.second->m_geomVec[0]->GetShapeDim();
 
         // compIt->second is a GeometryVector
-        for (auto &geomIt : *compIt.second)
+        for (auto &geomIt : compIt.second->m_geomVec)
         {
             ElmtConfig conf(geomIt->GetShapeType(), 1, true, true, false);
 

utilities/NekMesh/OutputModules/OutputNekpp.h

@@ -36,8 +36,6 @@
 #ifndef UTILITIES_NEKMESH_OUTPUTNEKPP
 #define UTILITIES_NEKMESH_OUTPUTNEKPP
 
-#include <tinyxml.h>
-
 #include <NekMeshUtils/Module/Module.h>
 
 namespace Nektar
@@ -54,7 +52,7 @@ public:
     {
         return MemoryManager<OutputNekpp>::AllocateSharedPtr(m);
     }
-    static NekMeshUtils::ModuleKey className;
+    static NekMeshUtils::ModuleKey className1, className2;
 
     OutputNekpp(NekMeshUtils::MeshSharedPtr m);
     virtual ~OutputNekpp();
@@ -63,24 +61,13 @@ public:
     virtual void Process();
 
 private:
-    /// Writes the <NODES> section of the XML file.
-    void WriteXmlNodes(TiXmlElement *pRoot);
-    /// Writes the <EDGES> section of the XML file.
-    void WriteXmlEdges(TiXmlElement *pRoot);
-    /// Writes the <FACES> section of the XML file if needed.
-    void WriteXmlFaces(TiXmlElement *pRoot);
-    /// Writes the <ELEMENTS> section of the XML file.
-    void WriteXmlElements(TiXmlElement *pRoot);
-    /// Writes the <CURVES> section of the XML file if needed.
-    void WriteXmlCurves(TiXmlElement *pRoot);
-    /// Writes the <COMPOSITES> section of the XML file.
-    void WriteXmlComposites(TiXmlElement *pRoot);
-    /// Writes the <DOMAIN> section of the XML file.
-    void WriteXmlDomain(TiXmlElement *pRoot);
-    /// Writes the <EXPANSIONS> section of the XML file.
-    void WriteXmlExpansions(TiXmlElement *pRoot);
-    /// Writes the <CONDITIONS> section of the XML file.
-    void WriteXmlConditions(TiXmlElement *pRoot);
+    void TransferVertices(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferEdges(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferFaces(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferElements(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferCurves(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferComposites(SpatialDomains::MeshGraphSharedPtr graph);
+    void TransferDomain(SpatialDomains::MeshGraphSharedPtr graph);
 };
 }
 }

utilities/NekMesh/ProcessModules/ProcessBL.cpp

@@ -197,7 +197,7 @@ void ProcessBL::BoundaryLayer2D()
     if (surf.size() > 0)
     {
         vector<unsigned int> surfs;
-        ParseUtils::GenerateSeqVector(surf, surfs);
+        ParseUtils::GenerateVector(surf, surfs);
         sort(surfs.begin(), surfs.end());
 
         // If surface is defined, process list of elements to find those
@@ -729,7 +729,7 @@ void ProcessBL::BoundaryLayer3D()
     if (surf.size() > 0)
     {
         vector<unsigned int> surfs;
-        ParseUtils::GenerateSeqVector(surf, surfs);
+        ParseUtils::GenerateVector(surf, surfs);
         sort(surfs.begin(), surfs.end());
 
         // If surface is defined, process list of elements to find those

utilities/NekMesh/ProcessModules/ProcessJac.cpp

@@ -98,7 +98,7 @@ void ProcessJac::Process()
         // Generate geometric factors.
         SpatialDomains::GeomFactorsSharedPtr gfac = geom->GetGeomFactors();
 
-        LibUtilities::PointsKeyVector p = geom->GetPointsKeys();
+        LibUtilities::PointsKeyVector p = geom->GetXmap()->GetPointsKeys();
         SpatialDomains::DerivStorage deriv = gfac->GetDeriv(p);
         const int pts = deriv[0][0].num_elements();
         Array<OneD,NekDouble> jc(pts);

utilities/NekMesh/ProcessModules/ProcessLinear.cpp

@@ -264,7 +264,7 @@ bool ProcessLinear::Invalid(ElementSharedPtr el, NekDouble thr)
     SpatialDomains::GeometrySharedPtr geomL = elL->GetGeom(m_mesh->m_spaceDim);
     SpatialDomains::GeomFactorsSharedPtr gfacL = geomL->GetGeomFactors();
 
-    LibUtilities::PointsKeyVector p = geom->GetPointsKeys();
+    LibUtilities::PointsKeyVector p = geom->GetXmap()->GetPointsKeys();
     SpatialDomains::DerivStorage deriv = gfac->GetDeriv(p);
     SpatialDomains::DerivStorage derivL = gfacL->GetDeriv(p);
     const int pts = deriv[0][0].num_elements();