Fix HDF5 files so that they compile

library/SpatialDomains/CMakeLists.txt

@@ -49,8 +49,8 @@ SpatialDomains.hpp
 )
 
 IF(NEKTAR_USE_HDF5)
-	SET(SPATIAL_DOMAINS_HEADERS ${SPATIAL_DOMAINS_HEADERS} MeshGraphHDF5.h FieldIOHdf5.h)
-	SET(SPATIAL_DOMAINS_SOURCES ${SPATIAL_DOMAINS_SOURCES} MeshGraphHDF5.cpp FieldIOHdf5.cpp)
+	SET(SPATIAL_DOMAINS_HEADERS ${SPATIAL_DOMAINS_HEADERS} MeshGraphHDF5.h)
+	SET(SPATIAL_DOMAINS_SOURCES ${SPATIAL_DOMAINS_SOURCES} MeshGraphHDF5.cpp)
 ENDIF()
 
 IF(NEKTAR_USE_SCOTCH)

library/SpatialDomains/MeshGraphHDF5.cpp

@@ -37,7 +37,6 @@
 #include "MeshGraphHDF5.h"
 
 #include <LibUtilities/BasicUtils/ParseUtils.h>
-#include <SpatialDomains/Equation.h>
 #include <SpatialDomains/MeshEntities.hpp>
 #include <boost/algorithm/string.hpp>
 #include <boost/filesystem.hpp>
@@ -51,18 +50,17 @@ namespace Nektar
 namespace SpatialDomains
 {
 
-MeshFileType MeshGraphHDF5::className =
+std::string MeshGraphHDF5::className =
     GetMeshGraphFactory().RegisterCreatorFunction(
-        eHDF5Mesh, MeshGraphHDF5::create, "IO with HDF5 geometry");
+        "HDF5", MeshGraphHDF5::create, "IO with HDF5 geometry");
 
-void MeshGraphHDF5::ReadGeometry(const SessionReaderSharedPtr &pSession,
-                                 DomainRangeShPtr &rng, bool fillGraph)
+void MeshGraphHDF5::ReadGeometry(
+    DomainRangeShPtr rng,
+    bool fillGraph)
 {
-    m_session = pSession;
-
     int err;
     //we use the xml geom to find information about the HDF5 file
-    m_xmlGeom            = pSession->GetElement("NEKTAR/GEOMETRY");
+    m_xmlGeom            = m_session->GetElement("NEKTAR/GEOMETRY");
     TiXmlAttribute *attr = m_xmlGeom->FirstAttribute();
     m_meshPartitioned    = false;
     m_meshDimension      = 3;
@@ -135,6 +133,11 @@ void MeshGraphHDF5::ReadGeometry(const SessionReaderSharedPtr &pSession,
     ReadDomain();
 }
 
+void MeshGraphHDF5::PartitionMesh(LibUtilities::SessionReaderSharedPtr session)
+{
+    // Don't do anything yet!
+}
+
 void MeshGraphHDF5::ReadVertices()
 {
     string nm = "vert";

library/SpatialDomains/MeshGraphHdf5.h → library/SpatialDomains/MeshGraphHDF5.h

@@ -68,12 +68,14 @@ public:
         return MemoryManager<MeshGraphHDF5>::AllocateSharedPtr();
     }
 
-    static MeshFileType className;
+    static std::string className;
 
 protected:
-    void ReadGeometry(const SessionReaderSharedPtr &pSession,
-                      DomainRangeShPtr &rng = NullDomainRangeShPtr,
-                      bool fillGraph        = true);
+    virtual void ReadGeometry(
+        DomainRangeShPtr rng,
+        bool             fillGraph);
+    virtual void PartitionMesh(
+        LibUtilities::SessionReaderSharedPtr session);
 
 private: