Commit b8a64877 authored by Spencer Sherwin's avatar Spencer Sherwin

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
parent f78cc199
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})
......
......@@ -37,7 +37,7 @@
#include <iostream>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputGmsh.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,7 +33,7 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputNek.h"
#include <LibUtilities/Foundations/ManagerAccess.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -39,7 +39,7 @@ using namespace std;
#include <SpatialDomains/MeshGraph.h>
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputNekpp.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEKPP
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEKPP
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -37,7 +37,7 @@
#include <iostream>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputPly.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTPLY
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTPLY
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -37,7 +37,7 @@
#include <iostream>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputSem.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSEM
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSEM
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -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"
......
......@@ -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
{
......
......@@ -36,7 +36,7 @@
#include <iostream>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputSwan.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSWAN
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSWAN
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -43,7 +43,7 @@ using namespace std;
#include <vtkPoints.h>
#include <vtkCellArray.h>
#include "MeshElements.h"
#include "../MeshElements.h"
#include "InputVtk.h"
namespace Nektar
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTVTK
#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTVTK
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,9 +33,9 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "OutputGmsh.h"
#include "InputGmsh.h"
#include "../InputModules/InputGmsh.h"
#include <map>
#include <vector>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTGMSH
#define UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTGMSH
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -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
......
......@@ -37,7 +37,7 @@
#define UTILITIES_PREPROCESSING_MESHCONVERT_OUTPUTNEKPP
#include <tinyxml.h>
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
////////////////////////////////////////////////////////////////////////////////
//
// 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();
}
}
}
////////////////////////////////////////////////////////////////////////////////
//
// 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
......@@ -36,7 +36,7 @@
#include <string>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessBL.h"
#include <LibUtilities/Foundations/ManagerAccess.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
#include <string>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessCyl.h"
#include <LocalRegions/SegExp.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSCHECK
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSCHECK
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,7 +33,7 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessDetectSurf.h"
#include <SpatialDomains/MeshGraph.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,7 +33,7 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessExtractSurf.h"
#include <SpatialDomains/MeshGraph.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSEXTRACTSURF
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,7 +33,7 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessJac.h"
#include <SpatialDomains/MeshGraph.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -36,7 +36,7 @@
#include <string>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessPerAlign.h"
#include <LocalRegions/SegExp.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSPERALIGN
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSPERALIGN
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -33,7 +33,7 @@
//
////////////////////////////////////////////////////////////////////////////////
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessScalar.h"
#include <SpatialDomains/MeshGraph.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSSCALAR
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSSCALAR
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
......@@ -36,7 +36,7 @@
#include <string>
using namespace std;
#include "MeshElements.h"
#include "../MeshElements.h"
#include "ProcessSpherigon.h"
#include <LocalRegions/SegExp.h>
......
......@@ -37,8 +37,8 @@
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#include "Module.h"
#include "InputPly.h"
#include "../Module.h"
#include "../InputModules/InputPly.h"
namespace Nektar
{
......
......@@ -36,8 +36,8 @@
#include <string>
using namespace std;
#include "MeshElements.h"
#include "InputNek.h"
#include "../MeshElements.h"
#include "../InputModules/InputNek.h"
#include "ProcessTetSplit.h"
#include <StdRegions/StdNodalPrismExp.h>
......
......@@ -36,7 +36,7 @@
#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#define UTILITIES_PREPROCESSING_MESHCONVERT_PROCESSJAC
#include "Module.h"
#include "../Module.h"
namespace Nektar
{
......
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