Nektar++
MeshGraph.h
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3 // File: MeshGraph.h
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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).
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30 //
31 // Description:
32 //
33 ////////////////////////////////////////////////////////////////////////////////
34 
35 #ifndef NEKTAR_SPATIALDOMAINS_MESHGRAPH_H
36 #define NEKTAR_SPATIALDOMAINS_MESHGRAPH_H
37 
38 #include <unordered_map>
39 
43 
44 #include <SpatialDomains/HexGeom.h>
47 #include <SpatialDomains/PyrGeom.h>
49 #include <SpatialDomains/SegGeom.h>
50 #include <SpatialDomains/TetGeom.h>
51 #include <SpatialDomains/TriGeom.h>
52 
53 #include <SpatialDomains/Curve.hpp>
55 
56 class TiXmlDocument;
57 
58 namespace Nektar
59 {
60 namespace SpatialDomains
61 {
62 typedef std::map<int, std::pair<LibUtilities::ShapeType, std::vector<int>>>
64 
66 {
86 };
87 
88 // Keep this consistent with the enums in ExpansionType.
89 // This is used in the BC file to specify the expansion type.
90 const std::string kExpansionTypeStr[] = {"NOTYPE",
91  "MODIFIED",
92  "MODIFIEDQUADPLUS1",
93  "MODIFIEDQUADPLUS2",
94  "MODIFIEDGLLRADAU10",
95  "ORTHOGONAL",
96  "GLL_LAGRANGE",
97  "GLL_LAGRANGE_SEM",
98  "GAUSS_LAGRANGE",
99  "GAUSS_LAGRANGE_SEM",
100  "FOURIER",
101  "FOURIERSINGLEMODE",
102  "FOURIERHALFMODERE",
103  "FOURIERHALFMODEIM",
104  "CHEBYSHEV",
105  "FOURIER-CHEBYSHEV",
106  "CHEBYSHEV-FOURIER",
107  "FOURIER-MODIFIED"};
108 
109 typedef std::map<int, std::vector<unsigned int>> CompositeOrdering;
110 typedef std::map<int, std::vector<unsigned int>> BndRegionOrdering;
111 
112 // set restriction on domain range for post-processing.
113 // struct DomainRange
114 // {
115 // bool m_doXrange;
116 // NekDouble m_xmin;
117 // NekDouble m_xmax;
118 // bool m_doYrange;
119 // NekDouble m_ymin;
120 // NekDouble m_ymax;
121 // bool m_doZrange;
122 // NekDouble m_zmin;
123 // NekDouble m_zmax;
124 
125 // bool m_checkShape;
126 // LibUtilities::ShapeType m_shapeType;
127 // };
128 
129 // typedef std::shared_ptr<DomainRange> DomainRangeShPtr;
130 // static DomainRangeShPtr NullDomainRangeShPtr;
131 
132 struct Composite
133 {
134  std::vector<std::shared_ptr<Geometry>> m_geomVec;
135 };
136 
137 typedef std::shared_ptr<Composite> CompositeSharedPtr;
138 typedef std::map<int, CompositeSharedPtr> CompositeMap;
139 
140 struct ExpansionInfo;
141 
142 typedef std::shared_ptr<ExpansionInfo> ExpansionInfoShPtr;
143 typedef std::map<int, ExpansionInfoShPtr> ExpansionInfoMap;
144 
145 typedef std::shared_ptr<ExpansionInfoMap> ExpansionInfoMapShPtr;
146 typedef std::map<std::string, ExpansionInfoMapShPtr> ExpansionInfoMapShPtrMap;
147 
149 {
151  const LibUtilities::BasisKeyVector basiskeyvec)
152  : m_geomShPtr(geomShPtr), m_basisKeyVector(basiskeyvec)
153  {
154  }
155 
157  : m_geomShPtr(ExpInfo->m_geomShPtr),
159  {
160  }
161 
164 };
165 
166 typedef std::map<std::string, std::string> GeomInfoMap;
167 typedef std::shared_ptr<std::vector<std::pair<GeometrySharedPtr, int>>>
169 
170 typedef std::map<std::string, std::string> MeshMetaDataMap;
171 
172 class MeshGraph;
173 typedef std::shared_ptr<MeshGraph> MeshGraphSharedPtr;
174 
175 /// Base class for a spectral/hp element mesh.
177 {
178 public:
181 
185  bool fillGraph = true);
186 
188  std::string &outfilename, bool defaultExp = false,
189  const LibUtilities::FieldMetaDataMap &metadata =
191 
192  void Empty(int dim, int space)
193  {
194  m_meshDimension = dim;
195  m_spaceDimension = space;
196  }
197 
198  /*transfers the minial data structure to full meshgraph*/
200 
202 
205 
206  ////////////////////
208 
209  /* ---- Helper functions ---- */
210  /// Dimension of the mesh (can be a 1D curve in 3D space).
212  {
213  return m_meshDimension;
214  }
215 
216  /// Dimension of the space (can be a 1D curve in 3D space).
218  {
219  return m_spaceDimension;
220  }
221 
222  /* Range definitions for postprorcessing */
224  NekDouble xmin, NekDouble xmax,
229 
230  /// Check if goemetry is in range definition if activated
232 
233  /// Check if goemetry is in range definition if activated
235 
236  /* ---- Composites and Domain ---- */
237  CompositeSharedPtr GetComposite(int whichComposite)
238  {
239  ASSERTL0(m_meshComposites.find(whichComposite) !=
240  m_meshComposites.end(),
241  "Composite not found.");
242  return m_meshComposites.find(whichComposite)->second;
243  }
244 
246  GetCompositeItem(int whichComposite, int whichItem);
247 
249  const std::string &compositeStr, CompositeMap &compositeVector) const;
250 
251  std::map<int, CompositeSharedPtr> &GetComposites()
252  {
253  return m_meshComposites;
254  }
255 
256  std::map<int, std::string> &GetCompositesLabels()
257  {
258  return m_compositesLabels;
259  }
260 
261  std::map<int, std::map<int, CompositeSharedPtr>> &GetDomain()
262  {
263  return m_domain;
264  }
265 
266  std::map<int, CompositeSharedPtr> &GetDomain(int domain)
267  {
268  ASSERTL1(m_domain.count(domain),
269  "Request for domain which does not exist");
270  return m_domain[domain];
271  }
272 
274  const std::string variable = "DefaultVar");
275 
277  GeometrySharedPtr geom, const std::string variable = "DefaultVar");
278 
279  /// Sets expansions given field definitions
281  std::vector<LibUtilities::FieldDefinitionsSharedPtr> &fielddef);
282 
283  /// Sets expansions given field definition, quadrature points.
285  std::vector<LibUtilities::FieldDefinitionsSharedPtr> &fielddef,
286  std::vector<std::vector<LibUtilities::PointsType>> &pointstype);
287 
288  /// Sets expansions to have equispaced points
290  int npoints = 0);
291 
292  /// Reset expansion to have specified polynomial order \a nmodes
294 
295  /// Reset expansion to have specified point order \a
296  /// npts
298  /// This function sets the expansion #exp in map with
299  /// entry #variable
300 
301  inline void SetExpansionInfo(const std::string variable,
302  ExpansionInfoMapShPtr &exp);
303 
305 
306  /// Sets the basis key for all expansions of the given shape.
309  std::string var = "DefaultVar");
310 
312  ExpansionInfoMapShPtr &expansionMap, LibUtilities::ShapeType shape,
314 
315  inline bool SameExpansionInfo(const std::string var1,
316  const std::string var2);
317 
318  inline bool ExpansionInfoDefined(const std::string var);
319 
320  inline bool CheckForGeomInfo(std::string parameter);
321 
322  inline const std::string GetGeomInfo(std::string parameter);
323 
326  const int order);
327 
330  GeometrySharedPtr in, ExpansionType type_x, ExpansionType type_y,
331  ExpansionType type_z, const int nummodes_x, const int nummodes_y,
332  const int nummodes_z);
333 
334  /* ---- Manipulation of mesh ---- */
336  {
337  return m_vertSet.size();
338  }
339 
341  {
342  return m_vertSet[id];
343  }
344 
346  {
347  return m_segGeoms[id];
348  }
349 
351  {
352  return m_curvedEdges;
353  }
355  {
356  return m_curvedFaces;
357  }
358 
359  SPATIAL_DOMAINS_EXPORT std::map<int, PointGeomSharedPtr> &GetAllPointGeoms()
360  {
361  return m_vertSet;
362  }
363  SPATIAL_DOMAINS_EXPORT std::map<int, SegGeomSharedPtr> &GetAllSegGeoms()
364  {
365  return m_segGeoms;
366  }
368  {
369  return m_triGeoms;
370  }
372  {
373  return m_quadGeoms;
374  }
376  {
377  return m_tetGeoms;
378  }
380  {
381  return m_pyrGeoms;
382  }
384  {
385  return m_prismGeoms;
386  }
388  {
389  return m_hexGeoms;
390  }
391 
393 
395  {
396  auto it1 = m_triGeoms.find(gID);
397  if (it1 != m_triGeoms.end())
398  return it1->second;
399 
400  auto it2 = m_quadGeoms.find(gID);
401  if (it2 != m_quadGeoms.end())
402  return it2->second;
403 
404  return Geometry2DSharedPtr();
405  };
406 
408  SegGeomSharedPtr edge, const std::string variable = "DefaultVar");
409 
412 
415 
417  Geometry2DSharedPtr face, const int facedir,
418  const std::string variable = "DefaultVar");
419 
421  {
422  return m_compOrder;
423  }
424 
426  {
427  return m_bndRegOrder;
428  }
429 
430  /*an inital read which loads a very light weight data structure*/
432  LibUtilities::DomainRangeShPtr rng, bool fillGraph) = 0;
435 
436  SPATIAL_DOMAINS_EXPORT std::map<int, MeshEntity> CreateMeshEntities();
438 
439 protected:
440  void PopulateFaceToElMap(Geometry3DSharedPtr element, int kNfaces);
442  std::string GetCompositeString(CompositeSharedPtr comp);
443 
446 
449 
451 
458 
463 
465  std::map<int, std::string> m_compositesLabels;
466  std::map<int, CompositeMap> m_domain;
468 
470 
472 
473  std::unordered_map<int, GeometryLinkSharedPtr> m_faceToElMap;
474 
475  TiXmlElement *m_xmlGeom;
476 
479 
480  struct GeomRTree;
481  std::unique_ptr<GeomRTree> m_boundingBoxTree;
482 };
483 typedef std::shared_ptr<MeshGraph> MeshGraphSharedPtr;
485 
487 
488 /**
489  *
490  */
491 void MeshGraph::SetExpansionInfo(const std::string variable,
493 {
494  if (m_expansionMapShPtrMap.count(variable) != 0)
495  {
496  ASSERTL0(
497  false,
498  (std::string("ExpansionInfo field is already set for variable ") +
499  variable)
500  .c_str());
501  }
502  else
503  {
504  m_expansionMapShPtrMap[variable] = exp;
505  }
506 }
507 
508 /**
509  *
510  */
511 inline bool MeshGraph::SameExpansionInfo(const std::string var1,
512  const std::string var2)
513 {
514  ExpansionInfoMapShPtr expVec1 = m_expansionMapShPtrMap.find(var1)->second;
515  ExpansionInfoMapShPtr expVec2 = m_expansionMapShPtrMap.find(var2)->second;
516 
517  if (expVec1.get() == expVec2.get())
518  {
519  return true;
520  }
521 
522  return false;
523 }
524 
525 /**
526  *
527  */
528 inline bool MeshGraph::ExpansionInfoDefined(const std::string var)
529 {
530  return m_expansionMapShPtrMap.count(var);
531 }
532 
533 /**
534  *
535  */
536 inline bool MeshGraph::CheckForGeomInfo(std::string parameter)
537 {
538  return m_geomInfo.find(parameter) != m_geomInfo.end();
539 }
540 
541 /**
542  *
543  */
544 inline const std::string MeshGraph::GetGeomInfo(std::string parameter)
545 {
546  ASSERTL1(m_geomInfo.find(parameter) != m_geomInfo.end(),
547  "Parameter " + parameter + " does not exist.");
548  return m_geomInfo[parameter];
549 }
550 
551 } // namespace SpatialDomains
552 } // namespace Nektar
553 #endif
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:215
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode....
Definition: ErrorUtil.hpp:249
#define SPATIAL_DOMAINS_EXPORT
Describes the specification for a Basis.
Definition: Basis.h:50
Provides a generic Factory class.
Definition: NekFactory.hpp:105
2D geometry information
Definition: Geometry2D.h:69
3D geometry information
Definition: Geometry3D.h:68
Base class for a spectral/hp element mesh.
Definition: MeshGraph.h:177
std::map< int, PointGeomSharedPtr > & GetAllPointGeoms()
Definition: MeshGraph.h:359
std::map< int, std::string > & GetCompositesLabels()
Definition: MeshGraph.h:256
void SetDomainRange(NekDouble xmin, NekDouble xmax, NekDouble ymin=NekConstants::kNekUnsetDouble, NekDouble ymax=NekConstants::kNekUnsetDouble, NekDouble zmin=NekConstants::kNekUnsetDouble, NekDouble zmax=NekConstants::kNekUnsetDouble)
Definition: MeshGraph.cpp:3985
PrismGeomMap & GetAllPrismGeoms()
Definition: MeshGraph.h:383
bool CheckRange(Geometry2D &geom)
Check if goemetry is in range definition if activated.
Definition: MeshGraph.cpp:310
int GetMeshDimension()
Dimension of the mesh (can be a 1D curve in 3D space).
Definition: MeshGraph.h:211
const std::string GetGeomInfo(std::string parameter)
Definition: MeshGraph.h:544
void PopulateFaceToElMap(Geometry3DSharedPtr element, int kNfaces)
Given a 3D geometry object #element, populate the face to element map m_faceToElMap which maps faces ...
Definition: MeshGraph.cpp:3833
BndRegionOrdering & GetBndRegionOrdering()
Definition: MeshGraph.h:425
Geometry2DSharedPtr GetGeometry2D(int gID)
Definition: MeshGraph.h:394
static MeshGraphSharedPtr Read(const LibUtilities::SessionReaderSharedPtr pSession, LibUtilities::DomainRangeShPtr rng=LibUtilities::NullDomainRangeShPtr, bool fillGraph=true)
Definition: MeshGraph.cpp:110
void SetExpansionInfoToEvenlySpacedPoints(int npoints=0)
Sets expansions to have equispaced points.
Definition: MeshGraph.cpp:1454
virtual void ReadGeometry(LibUtilities::DomainRangeShPtr rng, bool fillGraph)=0
LibUtilities::SessionReaderSharedPtr m_session
Definition: MeshGraph.h:444
std::map< int, CompositeMap > m_domain
Definition: MeshGraph.h:466
std::unique_ptr< GeomRTree > m_boundingBoxTree
Definition: MeshGraph.h:480
ExpansionInfoMapShPtr SetUpExpansionInfoMap()
Definition: MeshGraph.cpp:2540
void SetExpansionInfoToPointOrder(int npts)
Reset expansion to have specified point order npts.
Definition: MeshGraph.cpp:1529
bool SameExpansionInfo(const std::string var1, const std::string var2)
Definition: MeshGraph.h:511
CompositeOrdering m_compOrder
Definition: MeshGraph.h:477
bool ExpansionInfoDefined(const std::string var)
Definition: MeshGraph.h:528
void GetCompositeList(const std::string &compositeStr, CompositeMap &compositeVector) const
Definition: MeshGraph.cpp:557
std::map< int, std::map< int, CompositeSharedPtr > > & GetDomain()
Definition: MeshGraph.h:261
void Empty(int dim, int space)
Definition: MeshGraph.h:192
virtual void PartitionMesh(LibUtilities::SessionReaderSharedPtr session)=0
const ExpansionInfoMap & GetExpansionInfo(const std::string variable="DefaultVar")
Definition: MeshGraph.cpp:612
std::map< int, SegGeomSharedPtr > & GetAllSegGeoms()
Definition: MeshGraph.h:363
GeometryLinkSharedPtr GetElementsFromEdge(Geometry1DSharedPtr edge)
Definition: MeshGraph.cpp:3525
GeometrySharedPtr GetCompositeItem(int whichComposite, int whichItem)
Definition: MeshGraph.cpp:518
ExpansionInfoMapShPtrMap m_expansionMapShPtrMap
Definition: MeshGraph.h:469
int GetSpaceDimension()
Dimension of the space (can be a 1D curve in 3D space).
Definition: MeshGraph.h:217
std::string GetCompositeString(CompositeSharedPtr comp)
Returns a string representation of a composite.
Definition: MeshGraph.cpp:2589
void ResetExpansionInfoToBasisKey(ExpansionInfoMapShPtr &expansionMap, LibUtilities::ShapeType shape, LibUtilities::BasisKeyVector &keys)
Definition: MeshGraph.cpp:1574
void SetExpansionInfoToNumModes(int nmodes)
Reset expansion to have specified polynomial order nmodes.
Definition: MeshGraph.cpp:1496
std::map< int, CompositeSharedPtr > & GetComposites()
Definition: MeshGraph.h:251
std::unordered_map< int, GeometryLinkSharedPtr > m_faceToElMap
Definition: MeshGraph.h:473
CompositeSharedPtr GetComposite(int whichComposite)
Definition: MeshGraph.h:237
void SetExpansionInfo(std::vector< LibUtilities::FieldDefinitionsSharedPtr > &fielddef)
Sets expansions given field definitions.
Definition: MeshGraph.cpp:665
CompositeOrdering & GetCompositeOrdering()
Definition: MeshGraph.h:420
LibUtilities::BasisKey GetEdgeBasisKey(SegGeomSharedPtr edge, const std::string variable="DefaultVar")
Definition: MeshGraph.cpp:3581
std::map< int, MeshEntity > CreateMeshEntities()
Create mesh entities for this graph.
Definition: MeshGraph.cpp:3864
LibUtilities::BasisKeyVector DefineBasisKeyFromExpansionTypeHomo(GeometrySharedPtr in, ExpansionType type_x, ExpansionType type_y, ExpansionType type_z, const int nummodes_x, const int nummodes_y, const int nummodes_z)
Definition: MeshGraph.cpp:2306
bool CheckForGeomInfo(std::string parameter)
Definition: MeshGraph.h:536
LibUtilities::BasisKey GetFaceBasisKey(Geometry2DSharedPtr face, const int facedir, const std::string variable="DefaultVar")
3D functions
Definition: MeshGraph.cpp:3757
SegGeomSharedPtr GetSegGeom(int id)
Definition: MeshGraph.h:345
CompositeDescriptor CreateCompositeDescriptor()
Definition: MeshGraph.cpp:3964
GeometryLinkSharedPtr GetElementsFromFace(Geometry2DSharedPtr face)
Definition: MeshGraph.cpp:3815
std::map< int, CompositeSharedPtr > & GetDomain(int domain)
Definition: MeshGraph.h:266
void SetBasisKey(LibUtilities::ShapeType shape, LibUtilities::BasisKeyVector &keys, std::string var="DefaultVar")
Sets the basis key for all expansions of the given shape.
Definition: MeshGraph.cpp:1566
std::map< int, std::string > m_compositesLabels
Definition: MeshGraph.h:465
std::vector< int > GetElementsContainingPoint(PointGeomSharedPtr p)
Definition: MeshGraph.cpp:256
PointGeomSharedPtr GetVertex(int id)
Definition: MeshGraph.h:340
virtual void WriteGeometry(std::string &outfilename, bool defaultExp=false, const LibUtilities::FieldMetaDataMap &metadata=LibUtilities::NullFieldMetaDataMap)=0
static LibUtilities::BasisKeyVector DefineBasisKeyFromExpansionType(GeometrySharedPtr in, ExpansionType type, const int order)
Definition: MeshGraph.cpp:1591
void SetSession(LibUtilities::SessionReaderSharedPtr pSession)
LibUtilities::DomainRangeShPtr m_domainRange
Definition: MeshGraph.h:467
BndRegionOrdering m_bndRegOrder
Definition: MeshGraph.h:478
std::vector< BasisKey > BasisKeyVector
Name for a vector of BasisKeys.
std::map< std::string, std::string > FieldMetaDataMap
Definition: FieldIO.h:52
std::shared_ptr< SessionReader > SessionReaderSharedPtr
static FieldMetaDataMap NullFieldMetaDataMap
Definition: FieldIO.h:53
std::shared_ptr< DomainRange > DomainRangeShPtr
Definition: DomainRange.h:66
static DomainRangeShPtr NullDomainRangeShPtr
Definition: DomainRange.h:67
static const NekDouble kNekUnsetDouble
std::map< int, TriGeomSharedPtr > TriGeomMap
Definition: TriGeom.h:59
std::map< std::string, std::string > GeomInfoMap
Definition: MeshGraph.h:166
std::map< int, std::vector< unsigned int > > CompositeOrdering
Definition: MeshGraph.h:109
std::map< int, PyrGeomSharedPtr > PyrGeomMap
Definition: PyrGeom.h:78
std::map< int, QuadGeomSharedPtr > QuadGeomMap
Definition: QuadGeom.h:54
std::map< int, std::pair< LibUtilities::ShapeType, std::vector< int > > > CompositeDescriptor
Definition: MeshGraph.h:63
std::shared_ptr< std::vector< std::pair< GeometrySharedPtr, int > > > GeometryLinkSharedPtr
Definition: MeshGraph.h:168
std::map< int, std::vector< unsigned int > > BndRegionOrdering
Definition: MeshGraph.h:110
std::shared_ptr< ExpansionInfoMap > ExpansionInfoMapShPtr
Definition: MeshGraph.h:145
std::map< int, SegGeomSharedPtr > SegGeomMap
Definition: SegGeom.h:52
std::unordered_map< int, CurveSharedPtr > CurveMap
Definition: Curve.hpp:61
std::map< int, CompositeSharedPtr > CompositeMap
Definition: MeshGraph.h:138
LibUtilities::NekFactory< std::string, MeshGraph > MeshGraphFactory
Definition: MeshGraph.h:484
std::shared_ptr< SegGeom > SegGeomSharedPtr
Definition: Geometry2D.h:62
std::map< int, TetGeomSharedPtr > TetGeomMap
Definition: TetGeom.h:86
std::shared_ptr< ExpansionInfo > ExpansionInfoShPtr
Definition: MeshGraph.h:140
const std::string kExpansionTypeStr[]
Definition: MeshGraph.h:90
std::shared_ptr< MeshGraph > MeshGraphSharedPtr
Definition: MeshGraph.h:172
std::map< std::string, std::string > MeshMetaDataMap
Definition: MeshGraph.h:170
std::map< int, PrismGeomSharedPtr > PrismGeomMap
Definition: PrismGeom.h:85
std::shared_ptr< PointGeom > PointGeomSharedPtr
Definition: Geometry.h:59
std::shared_ptr< Geometry2D > Geometry2DSharedPtr
Definition: Geometry.h:65
std::shared_ptr< Geometry > GeometrySharedPtr
Definition: Geometry.h:53
MeshGraphFactory & GetMeshGraphFactory()
Definition: MeshGraph.cpp:73
std::shared_ptr< Composite > CompositeSharedPtr
Definition: MeshGraph.h:137
std::shared_ptr< Geometry1D > Geometry1DSharedPtr
Definition: Geometry.h:63
std::map< std::string, ExpansionInfoMapShPtr > ExpansionInfoMapShPtrMap
Definition: MeshGraph.h:146
std::map< int, HexGeomSharedPtr > HexGeomMap
Definition: HexGeom.h:87
std::map< int, PointGeomSharedPtr > PointGeomMap
Definition: PointGeom.h:54
std::map< int, ExpansionInfoShPtr > ExpansionInfoMap
Definition: MeshGraph.h:143
std::shared_ptr< Geometry3D > Geometry3DSharedPtr
Definition: Geometry3D.h:52
The above copyright notice and this permission notice shall be included.
Definition: CoupledSolver.h:1
double NekDouble
std::vector< std::shared_ptr< Geometry > > m_geomVec
Definition: MeshGraph.h:134
ExpansionInfo(GeometrySharedPtr geomShPtr, const LibUtilities::BasisKeyVector basiskeyvec)
Definition: MeshGraph.h:150
LibUtilities::BasisKeyVector m_basisKeyVector
Definition: MeshGraph.h:163
ExpansionInfo(ExpansionInfoShPtr ExpInfo)
Definition: MeshGraph.h:156