Chaste  Release::3.4
AbstractMesh.hpp
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35 
36 #ifndef ABSTRACTMESH_HPP_
37 #define ABSTRACTMESH_HPP_
38 
39 #include "ChasteSerialization.hpp"
40 #include "ClassIsAbstract.hpp"
41 
42 #include "UblasVectorInclude.hpp"
43 #include "UblasMatrixInclude.hpp"
44 
45 #include <vector>
46 #include <string>
47 #include <cassert>
48 
49 #include "Node.hpp"
50 #include "DistributedVectorFactory.hpp"
51 #include "ProcessSpecificArchive.hpp"
52 #include "ChasteCuboid.hpp"
53 
54 #include <boost/utility.hpp>
55 
59 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
60 class AbstractMesh : private boost::noncopyable
61 {
62  friend class TestDistributedTetrahedralMesh;
63  template <unsigned A_DIMENSION> friend class NodesOnlyMesh; //NodesOnlyMesh is able to grab the node information in order to copy
64  template <unsigned A_DIMENSION> friend class QuadraticMeshHelper;
65 
66 private:
76  virtual unsigned SolveNodeMapping(unsigned index) const = 0;
77 
79  friend class boost::serialization::access;
86  template<class Archive>
87  void serialize(Archive & archive, const unsigned int version)
88  {
91  }
92 
93 protected: // Give access of these variables to subclasses
94 
96  std::vector<Node<SPACE_DIM> *> mNodes;
97 
99  std::vector<Node<SPACE_DIM> *> mBoundaryNodes;
100 
106 
114  std::vector<unsigned> mNodePermutation;
115 
120  std::string mMeshFileBaseName;
121 
126 
130  virtual void SetElementOwnerships();
131 
139  ChasteCuboid<SPACE_DIM> CalculateBoundingBox(const std::vector<Node<SPACE_DIM>* >& rNodes) const;
140 
141 public:
142 
144  // Iterators //
146 
148  typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator BoundaryNodeIterator;
149 
151  class NodeIterator;
152 
158  inline NodeIterator GetNodeIteratorBegin(bool skipDeletedNodes=true);
159 
163  inline NodeIterator GetNodeIteratorEnd();
164 
166  // Methods //
168 
172  AbstractMesh();
173 
177  virtual ~AbstractMesh();
178 
184  virtual unsigned GetNumNodes() const;
185 
189  unsigned GetNumBoundaryNodes() const;
190 
194  virtual unsigned GetNumAllNodes() const;
195 
201  unsigned GetNumNodeAttributes() const;
202 
209  Node<SPACE_DIM>* GetNode(unsigned index) const;
210 
217  virtual Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;
218 
233  Node<SPACE_DIM>* GetNodeFromPrePermutationIndex(unsigned index) const;
234 
240  virtual void ReadNodesPerProcessorFile(const std::string& rNodesPerProcessorFile);
241 
246 
256 
261  virtual void PermuteNodes();
262 
267 
273 
277  std::string GetMeshFileBaseName() const;
278 
284  bool IsMeshOnDisk() const;
285 
294  const std::vector<unsigned>& rGetNodePermutation() const;
295 
306  virtual c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocationA,
307  const c_vector<double, SPACE_DIM>& rLocationB);
308 
320  double GetDistanceBetweenNodes(unsigned indexA, unsigned indexB);
321 
330  virtual double GetWidth(const unsigned& rDimension) const;
331 
340 
353  virtual unsigned GetNearestNodeIndex(const ChastePoint<SPACE_DIM>& rTestPoint);
354 
362  virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);
363 
371  virtual void Translate(const c_vector<double, SPACE_DIM>& rDisplacement);
372 
380  void Translate(const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0);
381 
389  virtual void Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotationMatrix);
390 
397  void Rotate(c_vector<double,3> axis, double angle);
398 
404  void RotateX(const double theta);
405 
411  void RotateY(const double theta);
412 
418  void RotateZ(const double theta);
419 
425  void Rotate(double theta);
426 
431  virtual void RefreshMesh();
432 
436  bool IsMeshChanging() const;
437 
443 
450 
452  // Nested classes //
454 
459  {
460  public:
466  inline Node<SPACE_DIM>& operator*();
467 
472  inline Node<SPACE_DIM>* operator->();
473 
479  inline bool operator!=(const typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator& rOther);
480 
485  inline NodeIterator& operator++();
486 
498  typename std::vector<Node<SPACE_DIM> *>::iterator nodeIter,
499  bool skipDeletedNodes=true);
500  private:
503 
505  typename std::vector<Node<SPACE_DIM> *>::iterator mNodeIter;
506 
509 
514  inline bool IsAtEnd();
515 
520  inline bool IsAllowedNode();
521  };
522 
523 
524 };
525 
527 
528 // NodeIterator class implementation - most methods are inlined //
531 
532 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
533 typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeIteratorBegin(
534  bool skipDeletedNodes)
535 {
536  return NodeIterator(*this, mNodes.begin(), skipDeletedNodes);
537 }
538 
539 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
541 {
542  return NodeIterator(*this, mNodes.end());
543 }
544 
545 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
547 {
548  assert(!IsAtEnd());
549  return **mNodeIter;
550 }
551 
552 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
554 {
555  assert(!IsAtEnd());
556  return *mNodeIter;
557 }
558 
559 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
561 {
562  return mNodeIter != rOther.mNodeIter;
563 }
564 
565 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
567 {
568  do
569  {
570  ++mNodeIter;
571  }
572  while (!IsAtEnd() && !IsAllowedNode());
573 
574  return (*this);
575 }
576 
577 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
580  typename std::vector<Node<SPACE_DIM> *>::iterator nodeIter,
581  bool skipDeletedNodes)
582  : mrMesh(rMesh),
583  mNodeIter(nodeIter),
584  mSkipDeletedNodes(skipDeletedNodes)
585 {
586  if (mrMesh.mNodes.size() == 0)
587  {
588  // Cope with empty meshes
589  mNodeIter = mrMesh.mNodes.end();
590  }
591  else
592  {
593  // Make sure we start at an allowed node
594  if (mNodeIter == mrMesh.mNodes.begin() && !IsAllowedNode())
595  {
596  ++(*this);
597  }
598  }
599 }
600 
601 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
603 {
604  return mNodeIter == mrMesh.mNodes.end();
605 }
606 
607 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
609 {
610  return !(mSkipDeletedNodes && (*this)->IsDeleted());
611 }
612 
613 
614 #endif /*ABSTRACTMESH_HPP_*/
virtual DistributedVectorFactory * GetDistributedVectorFactory()
#define TEMPLATED_CLASS_IS_ABSTRACT_2_UNSIGNED(T)
std::vector< Node< SPACE_DIM > * > mBoundaryNodes
virtual void ReadNodesPerProcessorFile(const std::string &rNodesPerProcessorFile)
virtual unsigned GetNearestNodeIndex(const ChastePoint< SPACE_DIM > &rTestPoint)
Definition: Node.hpp:58
virtual void RefreshMesh()
virtual Node< SPACE_DIM > * GetNodeOrHaloNode(unsigned index) const
virtual unsigned SolveNodeMapping(unsigned index) const =0
const std::vector< unsigned > & rGetNodePermutation() const
Node< SPACE_DIM > * operator->()
bool IsMeshChanging() const
virtual void Translate(const c_vector< double, SPACE_DIM > &rDisplacement)
std::vector< unsigned > mNodePermutation
Node< SPACE_DIM > * GetNode(unsigned index) const
std::vector< Node< SPACE_DIM > * >::iterator mNodeIter
void serialize(Archive &archive, const unsigned int version)
NodeIterator GetNodeIteratorEnd()
unsigned CalculateMaximumContainingElementsPerProcess() const
std::string GetMeshFileBaseName() const
virtual ChasteCuboid< SPACE_DIM > CalculateBoundingBox() const
virtual unsigned GetNumNodes() const
virtual void PermuteNodes()
Node< SPACE_DIM > & operator*()
BoundaryNodeIterator GetBoundaryNodeIteratorBegin() const
virtual unsigned GetNumAllNodes() const
NodeIterator & operator++()
virtual void SetElementOwnerships()
std::string mMeshFileBaseName
static Archive * Get(void)
double GetDistanceBetweenNodes(unsigned indexA, unsigned indexB)
bool mMeshChangesDuringSimulation
std::vector< Node< SPACE_DIM > * > mNodes
DistributedVectorFactory * mpDistributedVectorFactory
unsigned GetNumBoundaryNodes() const
bool operator!=(const typename AbstractMesh< ELEMENT_DIM, SPACE_DIM >::NodeIterator &rOther)
unsigned GetNumNodeAttributes() const
std::vector< Node< SPACE_DIM > * >::const_iterator BoundaryNodeIterator
NodeIterator GetNodeIteratorBegin(bool skipDeletedNodes=true)
bool IsMeshOnDisk() const
virtual ~AbstractMesh()
void SetMeshHasChangedSinceLoading()
virtual double GetWidth(const unsigned &rDimension) const
virtual void Rotate(c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)
virtual c_vector< double, SPACE_DIM > GetVectorFromAtoB(const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)
BoundaryNodeIterator GetBoundaryNodeIteratorEnd() const
virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)
NodeIterator(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, typename std::vector< Node< SPACE_DIM > * >::iterator nodeIter, bool skipDeletedNodes=true)
virtual void SetDistributedVectorFactory(DistributedVectorFactory *pFactory)
void RotateY(const double theta)
void RotateZ(const double theta)
Node< SPACE_DIM > * GetNodeFromPrePermutationIndex(unsigned index) const
void RotateX(const double theta)