MeshGraphHDF5.h

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////////////////////////////////////////////////////////////////////////////////
//
//  File:  Geometry.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).
//
//  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:  This file contains the base class specification for the
//                Geometry class.
//
//
////////////////////////////////////////////////////////////////////////////////
#ifndef NEKTAR_SPATIALDOMAINS_MGHDF5_H
#define NEKTAR_SPATIALDOMAINS_MGHDF5_H
 
#include <LibUtilities/BasicUtils/H5.h>
#include <SpatialDomains/MeshEntities.hpp>
#include <SpatialDomains/MeshGraph.h>
 
namespace Nektar
{
namespace SpatialDomains
{
 
class MeshGraphHDF5 : public MeshGraph
{
public:
    MeshGraphHDF5()
    {
    }
 
    SPATIAL_DOMAINS_EXPORT virtual void WriteGeometry(
        std::string &outfilename, bool defaultExp = false,
        const LibUtilities::FieldMetaDataMap &metadata =
            LibUtilities::NullFieldMetaDataMap);
 
    virtual ~MeshGraphHDF5()
    {
    }
 
    static MeshGraphSharedPtr create()
    {
        return MemoryManager<MeshGraphHDF5>::AllocateSharedPtr();
    }
 
    static std::string className, cmdSwitch;
 
protected:
    SPATIAL_DOMAINS_EXPORT virtual void ReadGeometry(
        LibUtilities::DomainRangeShPtr rng, bool fillGraph);
    SPATIAL_DOMAINS_EXPORT virtual void PartitionMesh(
        LibUtilities::SessionReaderSharedPtr session);
 
private:
    void ReadCurveMap(CurveMap &curveMap, std::string dsName,
                      const std::unordered_set<int> &readIds);
    void ReadDomain();
    void ReadComposites();
 
    template <class T>
    void WriteGeometryMap(std::map<int, std::shared_ptr<T>> &geomMap,
                          std::string datasetName);
 
    template <class T, typename DataType>
    void ReadGeometryData(std::map<int, std::shared_ptr<T>> &geomMap,
                          std::string dataSet,
                          const std::unordered_set<int> &readIds,
                          std::vector<int> &ids,
                          std::vector<DataType> &geomData);
    template <class T, typename DataType>
    void FillGeomMap(std::map<int, std::shared_ptr<T>> &geomMap,
                     const CurveMap &curveMap, std::vector<int> &ids,
                     std::vector<DataType> &geomData);
    template <class T, typename DataType>
    void ConstructGeomObject(std::map<int, std::shared_ptr<T>> &geomMap, int id,
                             DataType *data, CurveSharedPtr curve);
 
    CompositeDescriptor CreateCompositeDescriptor(
        std::unordered_map<int, int> &id2row);
 
    void WriteCurveMap(CurveMap &curves, std::string dsName,
                       MeshCurvedPts &curvedPts, int &ptOffset, int &newIdx);
    void WriteCurvePoints(MeshCurvedPts &curvedPts);
 
    void WriteComposites(CompositeMap &comps);
    void WriteDomain(std::map<int, CompositeMap> &domain);
 
    std::string m_hdf5Name;
    LibUtilities::H5::FileSharedPtr m_file;
    LibUtilities::H5::PListSharedPtr m_readPL;
    LibUtilities::H5::GroupSharedPtr m_mesh;
    LibUtilities::H5::GroupSharedPtr m_maps;
 
    static const unsigned int FORMAT_VERSION;
};
 
} // namespace SpatialDomains
} // namespace Nektar
 
#endif