Chaste  Release::2018.1
VertexBasedCellPopulation.hpp
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35 
36 #ifndef VERTEXBASEDCELLPOPULATION_HPP_
37 #define VERTEXBASEDCELLPOPULATION_HPP_
38 
39 #include "AbstractOffLatticeCellPopulation.hpp"
40 #include "MutableVertexMesh.hpp"
41 
42 #include "ChasteSerialization.hpp"
43 #include <boost/serialization/base_object.hpp>
44 #include <boost/serialization/set.hpp>
45 #include <boost/serialization/vector.hpp>
46 
47 template<unsigned DIM>
48 class AbstractVertexBasedDivisionRule; // Forward declaration to prevent circular include chain
49 
57 template<unsigned DIM>
59 {
60 private:
61 
66 
72 
78 
81 
84  boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > mpVertexBasedDivisionRule;
85 
90  std::vector< c_vector<double, DIM> > mLocationsOfT2Swaps;
91 
96  std::vector< unsigned > mCellIdsOfT2Swaps;
97 
103 
109  virtual void WriteVtkResultsToFile(const std::string& rDirectory);
110 
111  friend class boost::serialization::access;
123  template<class Archive>
124  void serialize(Archive & archive, const unsigned int version)
125  {
126  archive & boost::serialization::base_object<AbstractOffLatticeCellPopulation<DIM> >(*this);
128  archive & mpVertexBasedDivisionRule;
129  archive & mRestrictVertexMovement;
130  }
131 
136  void Validate();
137 
138 public:
139 
153  std::vector<CellPtr>& rCells,
154  bool deleteMesh=false,
155  bool validate=true,
156  const std::vector<unsigned> locationIndices=std::vector<unsigned>());
157 
164 
168  virtual ~VertexBasedCellPopulation();
169 
176  double GetDampingConstant(unsigned nodeIndex);
177 
182 
186  const MutableVertexMesh<DIM, DIM>& rGetMesh() const;
187 
195  VertexElement<DIM, DIM>* GetElement(unsigned elementIndex);
196 
200  unsigned GetNumElements();
201 
207  unsigned GetNumNodes();
208 
220  c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);
221 
229  Node<DIM>* GetNode(unsigned index);
230 
239  std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
240 
249  unsigned AddNode(Node<DIM>* pNewNode);
250 
260  virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector<double,DIM>& rDisplacement, double dt);
261 
270  void SetNode(unsigned index, ChastePoint<DIM>& rNewLocation);
271 
280 
290  CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());
291 
301  unsigned RemoveDeadCells();
302 
309  bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);
310 
319  void Update(bool hasHadBirthsOrDeaths=true);
320 
328  virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
329 
336  virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<DIM, DIM> > pPopulationWriter);
337 
344  virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<DIM, DIM> > pPopulationCountWriter);
345 
353  virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<DIM, DIM> > pCellWriter, CellPtr pCell);
354 
363  unsigned GetRosetteRankOfCell(CellPtr pCell);
364 
371  double GetVolumeOfCell(CellPtr pCell);
372 
378  std::vector< c_vector< double, DIM > > GetLocationsOfT2Swaps();
379 
385  std::vector< unsigned > GetCellIdsOfT2Swaps();
386 
392  void AddLocationOfT2Swap(c_vector< double, DIM> locationOfT2Swap);
393 
399  void AddCellIdOfT2Swap(unsigned idOfT2Swap);
400 
405 
410 
416  void SetOutputCellRearrangementLocations(bool outputCellRearrangementLocations);
417 
423  void OutputCellPopulationParameters(out_stream& rParamsFile);
424 
434  double GetWidth(const unsigned& rDimension);
435 
442  std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
443 
454 
464  virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex);
465 
481  virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
482  std::string& rVariableName,
483  bool dirichletBoundaryConditionApplies=false,
484  double dirichletBoundaryValue=0.0);
485 
489  boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > GetVertexBasedDivisionRule();
490 
496  void SetVertexBasedDivisionRule(boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > pVertexBasedDivisionRule);
497 
508  virtual double GetDefaultTimeStep();
509 
517  virtual void WriteDataToVisualizerSetupFile(out_stream& pVizSetupFile);
518 
533 
540 
546  void SetRestrictVertexMovementBoolean(bool restrictVertexMovement);
547 };
548 
551 
552 namespace boost
553 {
554 namespace serialization
555 {
559 template<class Archive, unsigned DIM>
560 inline void save_construct_data(
561  Archive & ar, const VertexBasedCellPopulation<DIM> * t, const unsigned int file_version)
562 {
563  // Save data required to construct instance
564  const MutableVertexMesh<DIM,DIM>* p_mesh = &(t->rGetMesh());
565  ar & p_mesh;
566 }
567 
572 template<class Archive, unsigned DIM>
573 inline void load_construct_data(
574  Archive & ar, VertexBasedCellPopulation<DIM> * t, const unsigned int file_version)
575 {
576  // Retrieve data from archive required to construct new instance
578  ar >> p_mesh;
579 
580  // Invoke inplace constructor to initialise instance
581  ::new(t)VertexBasedCellPopulation<DIM>(*p_mesh);
582 }
583 }
584 } // namespace ...
585 
586 #endif /*VERTEXBASEDCELLPOPULATION_HPP_*/
587 
void SetOutputCellRearrangementLocations(bool outputCellRearrangementLocations)
std::vector< c_vector< double, DIM > > GetLocationsOfT2Swaps()
virtual void AcceptPopulationCountWriter(boost::shared_ptr< AbstractCellPopulationCountWriter< DIM, DIM > > pPopulationCountWriter)
Definition: Node.hpp:58
virtual void SimulationSetupHook(AbstractCellBasedSimulation< DIM, DIM > *pSimulation)
boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > mpVertexBasedDivisionRule
virtual void AcceptCellWriter(boost::shared_ptr< AbstractCellWriter< DIM, DIM > > pCellWriter, CellPtr pCell)
void SetVertexBasedDivisionRule(boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > pVertexBasedDivisionRule)
std::vector< unsigned > GetCellIdsOfT2Swaps()
virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex)
virtual void WriteDataToVisualizerSetupFile(out_stream &pVizSetupFile)
std::vector< c_vector< double, DIM > > mLocationsOfT2Swaps
std::set< unsigned > GetNeighbouringNodeIndices(unsigned index)
std::vector< unsigned > mCellIdsOfT2Swaps
boost::shared_ptr< AbstractVertexBasedDivisionRule< DIM > > GetVertexBasedDivisionRule()
bool IsCellAssociatedWithADeletedLocation(CellPtr pCell)
double GetDampingConstant(unsigned nodeIndex)
void SetRestrictVertexMovementBoolean(bool restrictVertexMovement)
std::set< unsigned > GetNeighbouringLocationIndices(CellPtr pCell)
unsigned GetRosetteRankOfCell(CellPtr pCell)
MutableVertexMesh< DIM, DIM > & rGetMesh()
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void AcceptPopulationWriter(boost::shared_ptr< AbstractCellPopulationWriter< DIM, DIM > > pPopulationWriter)
void Update(bool hasHadBirthsOrDeaths=true)
void AddLocationOfT2Swap(c_vector< double, DIM > locationOfT2Swap)
VertexBasedCellPopulation(MutableVertexMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, bool deleteMesh=false, bool validate=true, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
Node< DIM > * GetNode(unsigned index)
virtual TetrahedralMesh< DIM, DIM > * GetTetrahedralMeshForPdeModifier()
virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector< double, DIM > &rDisplacement, double dt)
void OutputCellPopulationParameters(out_stream &rParamsFile)
virtual void OpenWritersFiles(OutputFileHandler &rOutputFileHandler)
void SetNode(unsigned index, ChastePoint< DIM > &rNewLocation)
void AddCellIdOfT2Swap(unsigned idOfT2Swap)
double GetWidth(const unsigned &rDimension)
c_vector< double, DIM > GetLocationOfCellCentre(CellPtr pCell)
unsigned AddNode(Node< DIM > *pNewNode)
CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr())
MutableVertexMesh< DIM, DIM > * mpMutableVertexMesh
virtual void WriteVtkResultsToFile(const std::string &rDirectory)
virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)
gcov doesn't like this file...
VertexElement< DIM, DIM > * GetElement(unsigned elementIndex)
void serialize(Archive &archive, const unsigned int version)
VertexElement< DIM, DIM > * GetElementCorrespondingToCell(CellPtr pCell)