Nektar++
MeshGraphIOHDF5.h
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1////////////////////////////////////////////////////////////////////////////////
2//
3// File: MeshGraphIOHDF5.h
4//
5// For more information, please see: http://www.nektar.info/
6//
7// The MIT License
8//
9// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10// Department of Aeronautics, Imperial College London (UK), and Scientific
11// Computing and Imaging Institute, University of Utah (USA).
12//
13// Permission is hereby granted, free of charge, to any person obtaining a
14// copy of this software and associated documentation files (the "Software"),
15// to deal in the Software without restriction, including without limitation
16// the rights to use, copy, modify, merge, publish, distribute, sublicense,
17// and/or sell copies of the Software, and to permit persons to whom the
18// Software is furnished to do so, subject to the following conditions:
19//
20// The above copyright notice and this permission notice shall be included
21// in all copies or substantial portions of the Software.
22//
23// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
24// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
25// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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29// DEALINGS IN THE SOFTWARE.
30//
31// Description:
32//
33////////////////////////////////////////////////////////////////////////////////
34
35#ifndef NEKTAR_SPATIALDOMAINS_MGIOHDF5_H
36#define NEKTAR_SPATIALDOMAINS_MGIOHDF5_H
37
41
43{
44
46{
47public:
48 friend class MemoryManager<MeshGraphIOHDF5>;
49
51 {
53 }
54
55 static std::string className, cmdSwitch;
56
57protected:
58 TiXmlElement *m_xmlGeom{};
59
60 MeshGraphIOHDF5() = default;
61 ~MeshGraphIOHDF5() override = default;
62
63 // some of these functions are going to be virtual because they will be
64 // inherited by the XmlCompressed version
65
67 const std::string &outfilename, bool defaultExp = false,
68 const LibUtilities::FieldMetaDataMap &metadata =
71 LibUtilities::DomainRangeShPtr rng, bool fillGraph) final;
74
75private:
76 void ReadCurveMap(CurveMap &curveMap, std::string dsName,
77 const std::unordered_set<int> &readIds);
78 void ReadDomain();
79 void ReadComposites();
80
81 template <class T>
82 void WriteGeometryMap(std::map<int, std::shared_ptr<T>> &geomMap,
83 std::string datasetName);
84
85 template <class T, typename DataType>
86 void ReadGeometryData(std::map<int, std::shared_ptr<T>> &geomMap,
87 std::string dataSet,
88 const std::unordered_set<int> &readIds,
89 std::vector<int> &ids,
90 std::vector<DataType> &geomData);
91 template <class T, typename DataType>
92 void FillGeomMap(std::map<int, std::shared_ptr<T>> &geomMap,
93 const CurveMap &curveMap, std::vector<int> &ids,
94 std::vector<DataType> &geomData);
95 template <class T, typename DataType>
96 void ConstructGeomObject(std::map<int, std::shared_ptr<T>> &geomMap, int id,
97 DataType *data, CurveSharedPtr curve);
98
100 std::unordered_map<int, int> &id2row);
101
102 void WriteCurveMap(CurveMap &curves, std::string dsName,
103 MeshCurvedPts &curvedPts, int &ptOffset, int &newIdx);
104 void WriteCurvePoints(MeshCurvedPts &curvedPts);
105
106 void WriteComposites(CompositeMap &comps);
107 void WriteDomain(std::map<int, CompositeMap> &domain);
108
109 std::string m_hdf5Name;
114 unsigned int m_inFormatVersion;
115
116 static const unsigned int FORMAT_VERSION;
117};
118
119} // namespace Nektar::SpatialDomains
120
121#endif
#define SPATIAL_DOMAINS_EXPORT
General purpose memory allocation routines with the ability to allocate from thread specific memory p...
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
void v_PartitionMesh(LibUtilities::SessionReaderSharedPtr session) final
Partition the mesh.
LibUtilities::H5::GroupSharedPtr m_mesh
LibUtilities::H5::GroupSharedPtr m_maps
void FillGeomMap(std::map< int, std::shared_ptr< T > > &geomMap, const CurveMap &curveMap, std::vector< int > &ids, std::vector< DataType > &geomData)
void WriteDomain(std::map< int, CompositeMap > &domain)
void WriteGeometryMap(std::map< int, std::shared_ptr< T > > &geomMap, std::string datasetName)
void ConstructGeomObject(std::map< int, std::shared_ptr< T > > &geomMap, int id, DataType *data, CurveSharedPtr curve)
void v_ReadGeometry(LibUtilities::DomainRangeShPtr rng, bool fillGraph) final
static const unsigned int FORMAT_VERSION
Version of the Nektar++ HDF5 geometry format, which is embedded into the main NEKTAR/GEOMETRY group a...
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)
void WriteCurveMap(CurveMap &curves, std::string dsName, MeshCurvedPts &curvedPts, int &ptOffset, int &newIdx)
void v_WriteGeometry(const std::string &outfilename, bool defaultExp=false, const LibUtilities::FieldMetaDataMap &metadata=LibUtilities::NullFieldMetaDataMap) final
void WriteCurvePoints(MeshCurvedPts &curvedPts)
LibUtilities::H5::FileSharedPtr m_file
void ReadCurveMap(CurveMap &curveMap, std::string dsName, const std::unordered_set< int > &readIds)
LibUtilities::H5::PListSharedPtr m_readPL
static MeshGraphIOSharedPtr create()
CompositeDescriptor CreateCompositeDescriptor()
std::shared_ptr< PList > PListSharedPtr
Definition: H5.h:92
std::shared_ptr< File > FileSharedPtr
Definition: H5.h:88
std::shared_ptr< Group > GroupSharedPtr
Definition: FieldIOHdf5.h:48
std::map< std::string, std::string > FieldMetaDataMap
Definition: FieldIO.h:50
std::shared_ptr< SessionReader > SessionReaderSharedPtr
static FieldMetaDataMap NullFieldMetaDataMap
Definition: FieldIO.h:51
std::shared_ptr< DomainRange > DomainRangeShPtr
Definition: DomainRange.h:64
std::shared_ptr< MeshGraphIO > MeshGraphIOSharedPtr
Definition: MeshGraphIO.h:46
std::map< int, std::pair< LibUtilities::ShapeType, std::vector< int > > > CompositeDescriptor
Definition: MeshGraph.h:61
std::shared_ptr< Curve > CurveSharedPtr
Definition: Curve.hpp:58
std::unordered_map< int, CurveSharedPtr > CurveMap
Definition: Curve.hpp:59
std::map< int, CompositeSharedPtr > CompositeMap
Definition: MeshGraph.h:136