Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
VertexMesh.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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34*/
35#ifndef VERTEXMESH_HPP_
36#define VERTEXMESH_HPP_
37
38// Forward declaration prevents circular include chain
39template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
41
42#include <algorithm>
43#include <iostream>
44#include <map>
45
46#include <boost/serialization/base_object.hpp>
47#include <boost/serialization/split_member.hpp>
48#include <boost/serialization/vector.hpp>
50
51#include "AbstractMesh.hpp"
52#include "Edge.hpp"
53#include "EdgeHelper.hpp"
54#include "ArchiveLocationInfo.hpp"
55#include "TetrahedralMesh.hpp"
56#include "VertexElement.hpp"
57#include "VertexElementMap.hpp"
58#include "VertexMeshReader.hpp"
59#include "VertexMeshWriter.hpp"
60
61
76template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
77class VertexMesh : public AbstractMesh<ELEMENT_DIM, SPACE_DIM>
78{
79 friend class TestVertexMesh;
80
81
82protected:
84 std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> mElements;
85
87 std::vector<VertexElement<ELEMENT_DIM - 1, SPACE_DIM>*> mFaces;
88
91
99 std::map<unsigned, unsigned> mVoronoiElementIndexMap;
100
109
117 unsigned SolveNodeMapping(unsigned index) const;
118
126 unsigned SolveElementMapping(unsigned index) const;
127
135 unsigned SolveBoundaryElementMapping(unsigned index) const;
136
142
151
172 bool ElementIncludesPoint(const c_vector<double, SPACE_DIM>& rTestPoint, unsigned elementIndex);
173
183 unsigned GetLocalIndexForElementEdgeClosestToPoint(const c_vector<double, SPACE_DIM>& rTestPoint, unsigned elementIndex);
184
187
195 template <class Archive>
196 void save(Archive& archive, const unsigned int version) const
197 {
198 archive& boost::serialization::base_object<AbstractMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
199 // Create a mesh writer pointing to the correct file and directory
202 false);
203 mesh_writer.WriteFilesUsingMesh(*(const_cast<VertexMesh<ELEMENT_DIM, SPACE_DIM>*>(this)));
204 }
205
212 template <class Archive>
213 void load(Archive& archive, const unsigned int version)
214 {
215 archive& boost::serialization::base_object<AbstractMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
216
218 this->ConstructFromMeshReader(mesh_reader);
219 }
220 BOOST_SERIALIZATION_SPLIT_MEMBER()
221
222public:
224 class VertexElementIterator;
225
231 inline VertexElementIterator GetElementIteratorBegin(bool skipDeletedElements = true);
232
236 inline VertexElementIterator GetElementIteratorEnd();
237
244 VertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
245 std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> vertexElements);
246
254 VertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
255 std::vector<VertexElement<ELEMENT_DIM - 1, SPACE_DIM>*> faces,
256 std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> vertexElements);
257
276 bool isPeriodic = false,
277 bool isBounded = false,
278 bool scaleBoundByEdgeLength = true,
279 double maxDelaunayEdgeLength = DBL_MAX,
280 bool offsetNewBoundaryNodes = false);
281
291
295 VertexMesh();
296
300 virtual ~VertexMesh();
301
306 unsigned GetNumEdges() const;
307
314 Edge<SPACE_DIM>* GetEdge(unsigned index) const;
315
320 const EdgeHelper<SPACE_DIM>& rGetEdgeHelper() const;
321
325 virtual unsigned GetNumNodes() const;
326
330 virtual unsigned GetNumElements() const;
331
335 unsigned GetNumAllElements() const;
336
340 virtual unsigned GetNumFaces() const;
341
347 VertexElement<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;
348
354 VertexElement<ELEMENT_DIM - 1, SPACE_DIM>* GetFace(unsigned index) const;
355
371 virtual c_vector<double, SPACE_DIM> GetCentroidOfElement(unsigned index);
372
378 void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader);
379
383 virtual void Clear();
384
390 unsigned GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(unsigned elementIndex);
391
400
410 unsigned GetRosetteRankOfElement(unsigned index);
411
423 virtual c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocationA,
424 const c_vector<double, SPACE_DIM>& rLocationB);
425
435 virtual double GetVolumeOfElement(unsigned index);
436
446 virtual double GetSurfaceAreaOfElement(unsigned index);
447
459 c_vector<double, SPACE_DIM> GetAreaGradientOfElementAtNode(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement, unsigned localIndex);
460
472 c_vector<double, SPACE_DIM> GetPreviousEdgeGradientOfElementAtNode(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement, unsigned localIndex);
473
485 c_vector<double, SPACE_DIM> GetNextEdgeGradientOfElementAtNode(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement, unsigned localIndex);
486
496 c_vector<double, SPACE_DIM> GetPerimeterGradientOfElementAtNode(VertexElement<ELEMENT_DIM, SPACE_DIM>* pElement, unsigned localIndex);
497
527 virtual c_vector<double, 3> CalculateMomentsOfElement(unsigned index);
528
535 double GetEdgeLength(unsigned elementIndex1, unsigned elementIndex2);
536
547 double GetElongationShapeFactorOfElement(unsigned elementIndex);
548
560 double CalculateUnitNormalToFaceWithArea(VertexElement<ELEMENT_DIM - 1, SPACE_DIM>* pFace, c_vector<double, SPACE_DIM>& rNormal);
561
571 virtual double CalculateAreaOfFace(VertexElement<ELEMENT_DIM - 1, SPACE_DIM>* pFace);
572
598 c_vector<double, SPACE_DIM> GetShortAxisOfElement(unsigned index);
599
606 std::set<unsigned> GetNeighbouringNodeIndices(unsigned nodeIndex);
607
620 std::set<unsigned> GetNeighbouringNodeNotAlsoInElement(unsigned nodeIndex, unsigned elemIndex);
621
628 std::set<unsigned> GetNeighbouringElementIndices(unsigned elementIndex);
629
638 virtual VertexMesh<ELEMENT_DIM, SPACE_DIM>* GetMeshForVtk();
639
650 bool IsNearExistingNodes(c_vector<double,SPACE_DIM> newNodeLocation, std::vector<Node<SPACE_DIM> *> nodesToCheck, double minClearance);
651
658 {
659 public:
666
672
678 inline bool operator!=(const typename VertexMesh<ELEMENT_DIM, SPACE_DIM>::VertexElementIterator& rOther);
679
684 inline VertexElementIterator& operator++();
685
696 VertexElementIterator(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
697 typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*>::iterator elementIter,
698 bool skipDeletedElements = true);
699
700 private:
703
705 typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*>::iterator mElementIter;
706
709
714 inline bool IsAtEnd();
715
720 inline bool IsAllowedElement();
721 };
722};
723
726
727
728// VertexElementIterator class implementation - most methods are inlined //
730
731template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
733 bool skipDeletedElements)
734{
735 return VertexElementIterator(*this, mElements.begin(), skipDeletedElements);
736}
737
738template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
743
744template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
750
751template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
757
758template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
763
764template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
766{
767 do
768 {
769 ++mElementIter;
770 } while (!IsAtEnd() && !IsAllowedElement());
771
772 return (*this);
773}
774
775template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
778 typename std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*>::iterator elementIter,
779 bool skipDeletedElements)
780 : mrMesh(rMesh),
781 mElementIter(elementIter),
782 mSkipDeletedElements(skipDeletedElements)
783{
784 if (mrMesh.mElements.empty())
785 {
786 // Cope with empty meshes
788 }
789 else
790 {
791 // Make sure we start at an allowed element
792 if (mElementIter == mrMesh.mElements.begin() && !IsAllowedElement())
793 {
794 ++(*this);
795 }
796 }
797}
798
799template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
801{
802 return mElementIter == mrMesh.mElements.end();
803}
804
805template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
807{
808 return !(mSkipDeletedElements && (*this)->IsDeleted());
809}
810
811#endif /*VERTEXMESH_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
static std::string GetMeshFilename()
static std::string GetArchiveDirectory()
static std::string GetArchiveRelativePath()
Definition Edge.hpp:52
Definition Node.hpp:59
void WriteFilesUsingMesh(VertexMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
VertexElementIterator(VertexMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, typename std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * >::iterator elementIter, bool skipDeletedElements=true)
std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * >::iterator mElementIter
VertexElementIterator & operator++()
bool operator!=(const typename VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexElementIterator &rOther)
VertexElement< ELEMENT_DIM, SPACE_DIM > & operator*()
VertexElement< ELEMENT_DIM, SPACE_DIM > * operator->()
std::vector< VertexElement< ELEMENT_DIM - 1, SPACE_DIM > * > mFaces
virtual c_vector< double, SPACE_DIM > GetVectorFromAtoB(const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)
double CalculateUnitNormalToFaceWithArea(VertexElement< ELEMENT_DIM - 1, SPACE_DIM > *pFace, c_vector< double, SPACE_DIM > &rNormal)
VertexElement< ELEMENT_DIM - 1, SPACE_DIM > * GetFace(unsigned index) const
VertexElementIterator GetElementIteratorEnd()
virtual unsigned GetNumNodes() const
virtual double GetSurfaceAreaOfElement(unsigned index)
std::set< unsigned > GetNeighbouringNodeIndices(unsigned nodeIndex)
std::set< unsigned > GetNeighbouringNodeNotAlsoInElement(unsigned nodeIndex, unsigned elemIndex)
void GenerateEdgesFromElements(std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > &rElements)
virtual double CalculateAreaOfFace(VertexElement< ELEMENT_DIM - 1, SPACE_DIM > *pFace)
const EdgeHelper< SPACE_DIM > & rGetEdgeHelper() const
c_vector< double, SPACE_DIM > GetNextEdgeGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
virtual unsigned GetNumFaces() const
VertexElement< ELEMENT_DIM, SPACE_DIM > * GetElement(unsigned index) const
EdgeHelper< SPACE_DIM > mEdgeHelper
unsigned GetLocalIndexForElementEdgeClosestToPoint(const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)
double GetElongationShapeFactorOfElement(unsigned elementIndex)
unsigned GetNumAllElements() const
unsigned SolveNodeMapping(unsigned index) const
TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpDelaunayMesh
bool ElementIncludesPoint(const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)
c_vector< double, SPACE_DIM > GetAreaGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
bool IsNearExistingNodes(c_vector< double, SPACE_DIM > newNodeLocation, std::vector< Node< SPACE_DIM > * > nodesToCheck, double minClearance)
std::set< unsigned > GetNeighbouringElementIndices(unsigned elementIndex)
VertexElementIterator GetElementIteratorBegin(bool skipDeletedElements=true)
void save(Archive &archive, const unsigned int version) const
c_vector< double, SPACE_DIM > GetPerimeterGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
double GetEdgeLength(unsigned elementIndex1, unsigned elementIndex2)
c_vector< double, SPACE_DIM > GetShortAxisOfElement(unsigned index)
unsigned GetRosetteRankOfElement(unsigned index)
Edge< SPACE_DIM > * GetEdge(unsigned index) const
unsigned SolveBoundaryElementMapping(unsigned index) const
unsigned SolveElementMapping(unsigned index) const
unsigned GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(unsigned nodeIndex)
virtual c_vector< double, SPACE_DIM > GetCentroidOfElement(unsigned index)
std::map< unsigned, unsigned > mVoronoiElementIndexMap
friend class boost::serialization::access
void load(Archive &archive, const unsigned int version)
void ConstructFromMeshReader(AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)
unsigned GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(unsigned elementIndex)
virtual void Clear()
unsigned GetNumEdges() const
c_vector< double, SPACE_DIM > GetPreviousEdgeGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > mElements
virtual c_vector< double, 3 > CalculateMomentsOfElement(unsigned index)
virtual VertexMesh< ELEMENT_DIM, SPACE_DIM > * GetMeshForVtk()
virtual double GetVolumeOfElement(unsigned index)
virtual unsigned GetNumElements() const
void GenerateVerticesFromElementCircumcentres(TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)