Chaste  Release::2018.1
AbstractBoxDomainPdeModifier.hpp
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35 
36 #ifndef ABSTRACTBOXDOMAINPDEMODIFIER_HPP_
37 #define ABSTRACTBOXDOMAINPDEMODIFIER_HPP_
38 
39 #include "ChasteSerialization.hpp"
40 #include <boost/serialization/base_object.hpp>
41 
42 #include "AbstractPdeModifier.hpp"
43 
49 template<unsigned DIM>
51 {
52  friend class TestEllipticBoxDomainPdeModifier;
53  friend class TestParabolicBoxDomainPdeModifier;
54  friend class TestOffLatticeSimulationWithPdes;
55 
56 private:
57 
67  template<class Archive>
68  void serialize(Archive & archive, const unsigned int version)
69  {
70  archive & boost::serialization::base_object<AbstractPdeModifier<DIM> >(*this);
71  archive & mpMeshCuboid;
72  archive & mStepSize;
73  archive & mSetBcsOnBoxBoundary;
74  }
75 
76 protected:
77 
79  std::map<CellPtr, unsigned> mCellPdeElementMap;
80 
85  boost::shared_ptr<ChasteCuboid<DIM> > mpMeshCuboid;
86 
91  double mStepSize;
92 
98 
99 public:
100 
112  AbstractBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=boost::shared_ptr<AbstractLinearPde<DIM,DIM> >(),
113  boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
114  bool isNeumannBoundaryCondition=true,
115  boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid=boost::shared_ptr<ChasteCuboid<DIM> >(),
116  double stepSize=1.0,
117  Vec solution=nullptr);
118 
123 
127  double GetStepSize();
128 
134  void SetBcsOnBoxBoundary(bool setBcsOnBoxBoundary);
135 
139  bool AreBcsSetOnBoxBoundary();
140 
151  virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
152 
159  void GenerateFeMesh(boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid, double stepSize);
160 
168  void UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
169 
176 
186 
193  void OutputSimulationModifierParameters(out_stream& rParamsFile);
194 };
195 
198 
199 #endif /*ABSTRACTBOXDOMAINPDEMODIFIER_HPP_*/
AbstractBoxDomainPdeModifier(boost::shared_ptr< AbstractLinearPde< DIM, DIM > > pPde=boost::shared_ptr< AbstractLinearPde< DIM, DIM > >(), boost::shared_ptr< AbstractBoundaryCondition< DIM > > pBoundaryCondition=boost::shared_ptr< AbstractBoundaryCondition< DIM > >(), bool isNeumannBoundaryCondition=true, boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid=boost::shared_ptr< ChasteCuboid< DIM > >(), double stepSize=1.0, Vec solution=nullptr)
void InitialiseCellPdeElementMap(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
#define TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(T)
boost::shared_ptr< ChasteCuboid< DIM > > mpMeshCuboid
void UpdateCellPdeElementMap(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
std::map< CellPtr, unsigned > mCellPdeElementMap
friend class boost::serialization::access
void SetBcsOnBoxBoundary(bool setBcsOnBoxBoundary)
void GenerateFeMesh(boost::shared_ptr< ChasteCuboid< DIM > > pMeshCuboid, double stepSize)
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
gcov doesn't like this file...
void serialize(Archive &archive, const unsigned int version)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)