Chaste  Release::3.4
OffLatticeSimulation.hpp
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35 
36 #ifndef OFFLATTICESIMULATION_HPP_
37 #define OFFLATTICESIMULATION_HPP_
38 
39 #include "AbstractCellBasedSimulation.hpp"
40 #include "AbstractForce.hpp"
41 #include "AbstractCellPopulationBoundaryCondition.hpp"
42 
43 #include "ChasteSerialization.hpp"
44 #include <boost/serialization/base_object.hpp>
45 #include <boost/serialization/set.hpp>
46 #include <boost/serialization/vector.hpp>
47 
68 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
69 class OffLatticeSimulation : public AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>
70 {
71 private:
72 
74  friend class boost::serialization::access;
75  friend class TestOffLatticeSimulationWithNodeBasedCellPopulation;
76 
83  template<class Archive>
84  void serialize(Archive & archive, const unsigned int version)
85  {
86  archive & boost::serialization::base_object<AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM> >(*this);
87  archive & mForceCollection;
88  archive & mBoundaryConditions;
89  }
90 
91 protected:
92 
94  std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > > mForceCollection;
95 
97  std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > > mBoundaryConditions;
98 
104  virtual void UpdateCellLocationsAndTopology();
105 
112  virtual void UpdateNodePositions();
113 
117  virtual void SetupSolve();
118 
136  virtual c_vector<double, SPACE_DIM> CalculateCellDivisionVector(CellPtr pParentCell);
137 
141  virtual void WriteVisualizerSetupFile();
142 
143 public:
144 
155  bool deleteCellPopulationInDestructor=false,
156  bool initialiseCells=true);
157 
163  void AddForce(boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > pForce);
164 
168  void RemoveAllForces();
169 
176 
181 
188  void OutputAdditionalSimulationSetup(out_stream& rParamsFile);
189 
198  virtual void OutputSimulationParameters(out_stream& rParamsFile);
199 };
200 
201 // Serialization for Boost >= 1.36
204 
205 namespace boost
206 {
207 namespace serialization
208 {
212 template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
213 inline void save_construct_data(
214  Archive & ar, const OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
215 {
216  // Save data required to construct instance
217  const AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>* p_cell_population = &(t->rGetCellPopulation());
218  ar & p_cell_population;
219 }
220 
224 template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
225 inline void load_construct_data(
226  Archive & ar, OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
227 {
228  // Retrieve data from archive required to construct new instance
230  ar >> p_cell_population;
231 
232  // Invoke inplace constructor to initialise instance, last two variables set extra
233  // member variables to be deleted as they are loaded from archive and to not initialise sells.
234  ::new(t)OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>(*p_cell_population, true, false);
235 }
236 }
237 } // namespace
238 
239 #endif /*OFFLATTICESIMULATION_HPP_*/
void OutputAdditionalSimulationSetup(out_stream &rParamsFile)
virtual void WriteVisualizerSetupFile()
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & rGetCellPopulation()
std::vector< boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > > mBoundaryConditions
void serialize(Archive &archive, const unsigned int version)
void AddForce(boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce)
virtual void UpdateNodePositions()
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > mForceCollection
virtual c_vector< double, SPACE_DIM > CalculateCellDivisionVector(CellPtr pParentCell)
OffLatticeSimulation(AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
virtual void OutputSimulationParameters(out_stream &rParamsFile)
virtual void UpdateCellLocationsAndTopology()
void AddCellPopulationBoundaryCondition(boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition)