Put modules into separate sub-directories and fixed the include references....

Put modules into separate sub-directories and fixed the include references. This version seems to compile correctly

utilities/MeshConvert/CMakeLists.txt

 SET(MeshConvertHeaders 
-    InputGmsh.h
-    InputNek.h
-    InputNekpp.h
-    InputPly.h
-    InputSem.h
-    InputSwan.h
-    InputStarTec.h
+    InputModules/InputGmsh.h
+    InputModules/InputNek.h
+    InputModules/InputNekpp.h
+    InputModules/InputPly.h
+    InputModules/InputSem.h
+    InputModules/InputSwan.h
+    InputModules/InputStarTec.h
     MeshElements.h
     Module.h
-    OutputGmsh.h
-    OutputNekpp.h
-    ProcessBL.h
-    ProcessCyl.h
-    ProcessDetectSurf.h
-    ProcessExtractSurf.h
-    ProcessJac.h
-    ProcessPerAlign.h
-    ProcessScalar.h
-    ProcessSpherigon.h
-    ProcessTetSplit.h
+    OutputModules/OutputGmsh.h
+    OutputModules/OutputNekpp.h
+    ProcessModules/ProcessBL.h
+    ProcessModules/ProcessCyl.h
+    ProcessModules/ProcessDetectSurf.h
+    ProcessModules/ProcessExtractSurf.h
+    ProcessModules/ProcessJac.h
+    ProcessModules/ProcessPerAlign.h
+    ProcessModules/ProcessScalar.h
+    ProcessModules/ProcessSpherigon.h
+    ProcessModules/ProcessTetSplit.h
 )
 
 SET(MeshConvertSources 
-    InputGmsh.cpp
-    InputNek.cpp
-    InputNekpp.cpp
-    InputPly.cpp
-    InputSem.cpp
-    InputSwan.cpp
-    InputStarTec.cpp
+    InputModules/InputGmsh.cpp
+    InputModules/InputNek.cpp
+    InputModules/InputNekpp.cpp
+    InputModules/InputPly.cpp
+    InputModules/InputSem.cpp
+    InputModules/InputSwan.cpp
+    InputModules/InputStarTec.cpp
     MeshConvert.cpp
     MeshElements.cpp
     Module.cpp
-    OutputGmsh.cpp
-    OutputNekpp.cpp
-    ProcessBL.cpp
-    ProcessCyl.cpp
-    ProcessDetectSurf.cpp
-    ProcessExtractSurf.cpp
-    ProcessJac.cpp
-    ProcessPerAlign.cpp
-    ProcessScalar.cpp
-    ProcessSpherigon.cpp
-    ProcessTetSplit.cpp
+    OutputModules/OutputGmsh.cpp
+    OutputModules/OutputNekpp.cpp
+    ProcessModules/ProcessBL.cpp
+    ProcessModules/ProcessCyl.cpp
+    ProcessModules/ProcessDetectSurf.cpp
+    ProcessModules/ProcessExtractSurf.cpp
+    ProcessModules/ProcessJac.cpp
+    ProcessModules/ProcessPerAlign.cpp
+    ProcessModules/ProcessScalar.cpp
+    ProcessModules/ProcessSpherigon.cpp
+    ProcessModules/ProcessTetSplit.cpp
 )
 
 IF (NEKTAR_USE_CCM)
-    SET(MeshConvertHeaders ${MeshConvertHeaders} InputStar.h)
-    SET(MeshConvertSources ${MeshConvertSources} InputStar.cpp)
+    SET(MeshConvertHeaders ${MeshConvertHeaders} InputModules/InputStar.h)
+    SET(MeshConvertSources ${MeshConvertSources} InputModules/InputStar.cpp)
 ENDIF (NEKTAR_USE_CCM)
 
 
 IF (NEKTAR_USE_VTK)
-    SET(MeshConvertHeaders ${MeshConvertHeaders} InputVtk.h OutputVtk.h)
-    SET(MeshConvertSources ${MeshConvertSources} InputVtk.cpp OutputVtk.cpp)
+    SET(MeshConvertHeaders ${MeshConvertHeaders} InputModules/InputVtk.h OutputModules/OutputVtk.h)
+    SET(MeshConvertSources ${MeshConvertSources} InputModules/InputVtk.cpp OutputModules/OutputVtk.cpp)
 ENDIF (NEKTAR_USE_VTK)
 
 ADD_UTILITIES_EXECUTABLE(MeshConvert util ${MeshConvertSources} ${MeshConvertHeaders})

utilities/MeshConvert/InputGmsh.cpp → utilities/MeshConvert/InputModules/InputGmsh.cpp

@@ -37,7 +37,7 @@
 #include <iostream>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputGmsh.h"
 
 namespace Nektar

utilities/MeshConvert/InputGmsh.h → utilities/MeshConvert/InputModules/InputGmsh.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputNek.cpp → utilities/MeshConvert/InputModules/InputNek.cpp

@@ -33,7 +33,7 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputNek.h"
 
 #include <LibUtilities/Foundations/ManagerAccess.h>

utilities/MeshConvert/InputNek.h → utilities/MeshConvert/InputModules/InputNek.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputNekpp.cpp → utilities/MeshConvert/InputModules/InputNekpp.cpp

@@ -39,7 +39,7 @@ using namespace std;
 
 #include <SpatialDomains/MeshGraph.h>
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputNekpp.h"
 
 namespace Nektar

utilities/MeshConvert/InputNekpp.h → utilities/MeshConvert/InputModules/InputNekpp.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEKPP
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEKPP
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputPly.cpp → utilities/MeshConvert/InputModules/InputPly.cpp

@@ -37,7 +37,7 @@
 #include <iostream>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputPly.h"
 
 namespace Nektar

utilities/MeshConvert/InputPly.h → utilities/MeshConvert/InputModules/InputPly.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTPLY
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTPLY
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputSem.cpp → utilities/MeshConvert/InputModules/InputSem.cpp

@@ -37,7 +37,7 @@
 #include <iostream>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputSem.h"
 
 namespace Nektar

utilities/MeshConvert/InputSem.h → utilities/MeshConvert/InputModules/InputSem.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSEM
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSEM
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputStar.h → utilities/MeshConvert/InputModules/InputStar.h

@@ -36,8 +36,8 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSTAR
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSTAR
 
-#include "Module.h"
-#include "MeshElements.h"
+#include "../Module.h"
+#include "../MeshElements.h"
 #include "ccmio.h"
 
 

utilities/MeshConvert/InputStarTec.h → utilities/MeshConvert/InputModules/InputStarTec.h

@@ -36,8 +36,8 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTTEC
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTTEC
 
-#include "Module.h"
-#include "MeshElements.h"
+#include "../Module.h"
+#include "../MeshElements.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputSwan.cpp → utilities/MeshConvert/InputModules/InputSwan.cpp

@@ -36,7 +36,7 @@
 #include <iostream>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputSwan.h"
 
 namespace Nektar

utilities/MeshConvert/InputSwan.h → utilities/MeshConvert/InputModules/InputSwan.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSWAN
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSWAN
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/InputVtk.cpp → utilities/MeshConvert/InputModules/InputVtk.cpp

@@ -43,7 +43,7 @@ using namespace std;
 #include <vtkPoints.h>
 #include <vtkCellArray.h>
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "InputVtk.h"
 
 namespace Nektar

utilities/MeshConvert/InputVtk.h → utilities/MeshConvert/InputModules/InputVtk.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTVTK
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTVTK
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/OutputGmsh.cpp → utilities/MeshConvert/OutputModules/OutputGmsh.cpp

@@ -33,9 +33,9 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "OutputGmsh.h"
-#include "InputGmsh.h"
+#include "../InputModules/InputGmsh.h"
 
 #include <map>
 #include <vector>

utilities/MeshConvert/OutputGmsh.h → utilities/MeshConvert/OutputModules/OutputGmsh.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTGMSH
 #define UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTGMSH
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/OutputNekpp.cpp → utilities/MeshConvert/OutputModules/OutputNekpp.cpp

@@ -46,7 +46,7 @@ namespace io = boost::iostreams;
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SpatialDomains/MeshGraph.h>
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "OutputNekpp.h"
 
 namespace Nektar

utilities/MeshConvert/OutputNekpp.h → utilities/MeshConvert/OutputModules/OutputNekpp.h

@@ -37,7 +37,7 @@
 #define UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTNEKPP
 
 #include <tinyxml.h>
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/OutputVtk.cpp

-////////////////////////////////////////////////////////////////////////////////
-//
-//  File: OutputVtk.cpp
-//
-//  For more information, please see: http://www.nektar.info/
-//
-//  The MIT License
-//
-//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
-//  Department of Aeronautics, Imperial College London (UK), and Scientific
-//  Computing and Imaging Institute, University of Utah (USA).
-//
-//  License for the specific language governing rights and limitations under
-//  Permission is hereby granted, free of charge, to any person obtaining a
-//  copy of this software and associated documentation files (the "Software"),
-//  to deal in the Software without restriction, including without limitation
-//  the rights to use, copy, modify, merge, publish, distribute, sublicense,
-//  and/or sell copies of the Software, and to permit persons to whom the
-//  Software is furnished to do so, subject to the following conditions:
-//
-//  The above copyright notice and this permission notice shall be included
-//  in all copies or substantial portions of the Software.
-//
-//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-//  DEALINGS IN THE SOFTWARE.
-//
-//  Description: VTK file format output.
-//
-////////////////////////////////////////////////////////////////////////////////
-
-#include <set>
-#include <string>
-using namespace std;
-
-#include <vtkPolyDataWriter.h>
-#include <vtkPolyData.h>
-#include <vtkPoints.h>
-#include <vtkCellArray.h>
-
-#include "MeshElements.h"
-#include "OutputVtk.h"
-
-namespace Nektar
-{
-    namespace Utilities
-    {
-        ModuleKey OutputVtk::className =
-            GetModuleFactory().RegisterCreatorFunction(
-                ModuleKey(eOutputModule, "vtk"), OutputVtk::create,
-                "Writes a VTK file.");
-
-        OutputVtk::OutputVtk(MeshSharedPtr m) : OutputModule(m)
-        {
-            
-        }
-
-        OutputVtk::~OutputVtk()
-        {
-
-        }
-        
-        void OutputVtk::Process()
-        {
-            if (m_mesh->m_verbose)
-            {
-                cout << "OutputVtk: Writing file..." << endl;
-            }
-
-            vtkPolyData *vtkMesh = vtkPolyData::New();
-            vtkPoints *vtkPoints = vtkPoints::New();
-            vtkCellArray *vtkPolys = vtkCellArray::New();
-
-            std::set<NodeSharedPtr>::iterator it;
-
-            std::set<NodeSharedPtr> tmp(
-                    m_mesh->m_vertexSet.begin(),
-                    m_mesh->m_vertexSet.end());
-
-            for (it = tmp.begin(); it != tmp.end(); ++it)
-            {
-                NodeSharedPtr n = *it;
-                vtkPoints->InsertPoint(n->m_id, n->m_x, n->m_y, n->m_z);
-            }
-
-            vtkIdType p[8];
-            vector<ElementSharedPtr> &elmt = 
-                                    m_mesh->m_element[m_mesh->m_expDim];
-            for(int i = 0; i < elmt.size(); ++i)
-            {
-                int vertexCount = elmt[i]->GetVertexCount();
-                for (int j = 0; j < vertexCount; ++j)
-                {
-                    p[j] = elmt[i]->GetVertex(j)->m_id;
-                }
-                vtkPolys->InsertNextCell(vertexCount, &p[0]);
-            }
-
-            vtkMesh->SetPoints(vtkPoints);
-            vtkMesh->SetPolys(vtkPolys);
-
-            // Write out the new mesh
-            vtkPolyDataWriter *vtkMeshWriter = vtkPolyDataWriter::New();
-            vtkMeshWriter->SetFileName(m_config["outfile"].as<string>().c_str());
-#if VTK_MAJOR_VERSION <= 5
-            vtkMeshWriter->SetInput(vtkMesh);
-#else
-            vtkMeshWriter->SetInputData(vtkMesh);
-#endif
-            vtkMeshWriter->Update();
-        }        
-    }
-}

utilities/MeshConvert/OutputVtk.h

-////////////////////////////////////////////////////////////////////////////////
-//
-//  File: OutputVtk.h
-//
-//  For more information, please see: http://www.nektar.info/
-//
-//  The MIT License
-//
-//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
-//  Department of Aeronautics, Imperial College London (UK), and Scientific
-//  Computing and Imaging Institute, University of Utah (USA).
-//
-//  License for the specific language governing rights and limitations under
-//  Permission is hereby granted, free of charge, to any person obtaining a
-//  copy of this software and associated documentation files (the "Software"),
-//  to deal in the Software without restriction, including without limitation
-//  the rights to use, copy, modify, merge, publish, distribute, sublicense,
-//  and/or sell copies of the Software, and to permit persons to whom the
-//  Software is furnished to do so, subject to the following conditions:
-//
-//  The above copyright notice and this permission notice shall be included
-//  in all copies or substantial portions of the Software.
-//
-//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-//  DEALINGS IN THE SOFTWARE.
-//
-//  Description: Vtk output module
-//
-////////////////////////////////////////////////////////////////////////////////
-
-#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTVTK
-#define UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTVTK
-
-#include <tinyxml.h>
-#include "Module.h"
-
-namespace Nektar
-{
-    namespace Utilities
-    {
-        /// Converter for Gmsh files.
-        class OutputVtk : public OutputModule
-        {
-        public:
-            /// Creates an instance of this class
-            static boost::shared_ptr<Module> create(MeshSharedPtr m) {
-                return MemoryManager<OutputVtk>::AllocateSharedPtr(m);
-            }
-            static ModuleKey className;
-            
-            OutputVtk(MeshSharedPtr m);
-            virtual ~OutputVtk();
-            
-            /// Write mesh to output file.
-            virtual void Process();
-        };
-    }
-}
-
-#endif

utilities/MeshConvert/ProcessBL.cpp → utilities/MeshConvert/ProcessModules/ProcessBL.cpp

@@ -36,7 +36,7 @@
 #include <string>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessBL.h"
 
 #include <LibUtilities/Foundations/ManagerAccess.h>

utilities/MeshConvert/ProcessBL.h → utilities/MeshConvert/ProcessModules/ProcessBL.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/ProcessCyl.cpp → utilities/MeshConvert/ProcessModules/ProcessCyl.cpp

 #include <string>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessCyl.h"
 
 #include <LocalRegions/SegExp.h>

utilities/MeshConvert/ProcessCyl.h → utilities/MeshConvert/ProcessModules/ProcessCyl.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSCHECK
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSCHECK
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/ProcessDetectSurf.cpp → utilities/MeshConvert/ProcessModules/ProcessDetectSurf.cpp

@@ -33,7 +33,7 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessDetectSurf.h"
 
 #include <SpatialDomains/MeshGraph.h>

utilities/MeshConvert/ProcessDetectSurf.h → utilities/MeshConvert/ProcessModules/ProcessDetectSurf.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/ProcessExtractSurf.cpp → utilities/MeshConvert/ProcessModules/ProcessExtractSurf.cpp

@@ -33,7 +33,7 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessExtractSurf.h"
 
 #include <SpatialDomains/MeshGraph.h>

utilities/MeshConvert/ProcessExtractSurf.h → utilities/MeshConvert/ProcessModules/ProcessExtractSurf.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/ProcessJac.cpp → utilities/MeshConvert/ProcessModules/ProcessJac.cpp

@@ -33,7 +33,7 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessJac.h"
 
 #include <SpatialDomains/MeshGraph.h>

utilities/MeshConvert/ProcessJac.h → utilities/MeshConvert/ProcessModules/ProcessJac.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
 
-#include "Module.h"
+#include "../Module.h"
 
 namespace Nektar
 {

utilities/MeshConvert/ProcessPerAlign.cpp → utilities/MeshConvert/ProcessModules/ProcessPerAlign.cpp

@@ -36,7 +36,7 @@
 #include <string>
 using namespace std;
 
-#include "MeshElements.h"
+#include "../MeshElements.h"
 #include "ProcessPerAlign.h"
 
 #include <LocalRegions/SegExp.h>

utilities/MeshConvert/ProcessPerAlign.h → utilities/MeshConvert/ProcessModules/ProcessPerAlign.h

@@ -36,7 +36,7 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSPERALIGN
 #define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSPERALIGN