Chaste  Release::2018.1
AbstractCentreBasedCellPopulation.hpp
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35 
36 #ifndef ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
37 #define ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
38 
39 #include "AbstractOffLatticeCellPopulation.hpp"
40 #include "AbstractCentreBasedDivisionRule.hpp"
41 
42 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class AbstractCentreBasedDivisionRule; // Circular definition thing.
43 
48 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
50 {
51 private:
56 
58  friend class boost::serialization::access;
65  template<class Archive>
66  void serialize(Archive & archive, const unsigned int version)
67  {
68  archive & boost::serialization::base_object<AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM> >(*this);
70  archive & mMarkedSprings;
71  archive & mpCentreBasedDivisionRule;
72  }
73 
74 protected:
80 
86  std::set<std::pair<CellPtr,CellPtr> > mMarkedSprings;
87 
91  boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > mpCentreBasedDivisionRule;
92 
99 
108  virtual void WriteVtkResultsToFile(const std::string& rDirectory)=0;
109 
115  virtual void AcceptCellWritersAcrossPopulation();
116 
117 public:
118 
127  std::vector<CellPtr>& rCells,
128  const std::vector<unsigned> locationIndices=std::vector<unsigned>());
129 
138  c_vector<double, SPACE_DIM> GetLocationOfCellCentre(CellPtr pCell);
139 
148 
164  virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
165  std::string& rVariableName,
166  bool dirichletBoundaryConditionApplies=false,
167  double dirichletBoundaryValue=0.0);
168 
177  CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());
178 
188  std::pair<CellPtr,CellPtr> CreateCellPair(CellPtr pCell1, CellPtr pCell2);
189 
195  bool IsMarkedSpring(const std::pair<CellPtr,CellPtr>& rCellPair);
196 
202  void MarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);
203 
209  void UnmarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);
210 
218  bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);
219 
228  virtual std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
229 
239  virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector<double,SPACE_DIM>& rDisplacement, double dt);
240 
257  virtual double GetDampingConstant(unsigned nodeIndex);
258 
267  virtual bool IsGhostNode(unsigned index);
268 
277  virtual bool IsParticle(unsigned index);
278 
287  virtual std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& rGetNodePairs()=0;
288 
293 
299  void SetMeinekeDivisionSeparation(double divisionSeparation);
300 
304  boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > GetCentreBasedDivisionRule();
305 
311  void SetCentreBasedDivisionRule(boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > pCentreBasedDivisionRule);
312 
318  virtual void OutputCellPopulationParameters(out_stream& rParamsFile);
319 
330  virtual double GetDefaultTimeStep();
331 };
332 
333 #endif /*ABSTRACTCENTREBASEDCELLPOPULATION_HPP_*/
boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > mpCentreBasedDivisionRule
virtual void WriteVtkResultsToFile(const std::string &rDirectory)=0
void UnmarkSpring(std::pair< CellPtr, CellPtr > &rCellPair)
Definition: Node.hpp:58
void serialize(Archive &archive, const unsigned int version)
virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)
std::pair< CellPtr, CellPtr > CreateCellPair(CellPtr pCell1, CellPtr pCell2)
virtual std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & rGetNodePairs()=0
virtual void OutputCellPopulationParameters(out_stream &rParamsFile)
virtual std::set< unsigned > GetNeighbouringLocationIndices(CellPtr pCell)
AbstractCentreBasedCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
Node< SPACE_DIM > * GetNodeCorrespondingToCell(CellPtr pCell)
boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > GetCentreBasedDivisionRule()
CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr())
void MarkSpring(std::pair< CellPtr, CellPtr > &rCellPair)
bool IsMarkedSpring(const std::pair< CellPtr, CellPtr > &rCellPair)
void SetMeinekeDivisionSeparation(double divisionSeparation)
virtual double GetDampingConstant(unsigned nodeIndex)
c_vector< double, SPACE_DIM > GetLocationOfCellCentre(CellPtr pCell)
std::set< std::pair< CellPtr, CellPtr > > mMarkedSprings
virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector< double, SPACE_DIM > &rDisplacement, double dt)
void SetCentreBasedDivisionRule(boost::shared_ptr< AbstractCentreBasedDivisionRule< ELEMENT_DIM, SPACE_DIM > > pCentreBasedDivisionRule)