Chaste  Release::2018.1
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 #include "AbstractNumericalMethod.hpp"
43 
44 #include "ChasteSerialization.hpp"
45 #include <boost/serialization/base_object.hpp>
46 #include <boost/serialization/set.hpp>
47 #include <boost/serialization/vector.hpp>
48 
70 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
71 class OffLatticeSimulation : public AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>
72 {
73 private:
74 
76  friend class boost::serialization::access;
77  friend class TestOffLatticeSimulation;
78  friend class TestOffLatticeSimulationWithNodeBasedCellPopulation;
79 
86  template<class Archive>
87  void serialize(Archive & archive, const unsigned int version)
88  {
89  archive & boost::serialization::base_object<AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM> >(*this);
90  archive & mForceCollection;
91  archive & mBoundaryConditions;
92  archive & mpNumericalMethod;
93  }
94 
95 protected:
96 
98  std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > > mForceCollection;
99 
101  std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > > mBoundaryConditions;
102 
104  boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > mpNumericalMethod;
105 
111  virtual void UpdateCellLocationsAndTopology();
112 
119  void RevertToOldLocations(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > oldNodeLoctions);
120 
126  void ApplyBoundaries(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > oldNodeLoctions);
127 
131  virtual void SetupSolve();
132 
136  virtual void WriteVisualizerSetupFile();
137 
138 public:
139 
150  bool deleteCellPopulationInDestructor=false,
151  bool initialiseCells=true);
152 
158  void AddForce(boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > pForce);
159 
163  void RemoveAllForces();
164 
171 
176 
182  void SetNumericalMethod(boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > pNumericalMethod);
183 
187  const boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > GetNumericalMethod() const;
188 
196  void OutputAdditionalSimulationSetup(out_stream& rParamsFile);
197 
203  virtual void OutputSimulationParameters(out_stream& rParamsFile);
204 
210  const std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >& rGetForceCollection() const;
211 };
212 
213 // Serialization for Boost >= 1.36
216 
217 namespace boost
218 {
219 namespace serialization
220 {
224 template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
225 inline void save_construct_data(
226  Archive & ar, const OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
227 {
228  // Save data required to construct instance
229  const AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>* p_cell_population = &(t->rGetCellPopulation());
230  ar & p_cell_population;
231 }
232 
236 template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
237 inline void load_construct_data(
238  Archive & ar, OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
239 {
240  // Retrieve data from archive required to construct new instance
242  ar >> p_cell_population;
243 
244  // Invoke inplace constructor to initialise instance, middle two variables set extra
245  // member variables to be deleted as they are loaded from archive and to not initialise cells.
246  ::new(t)OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>(*p_cell_population, true, false);
247 }
248 }
249 } // namespace
250 
251 #endif /*OFFLATTICESIMULATION_HPP_*/
boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > mpNumericalMethod
const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > GetNumericalMethod() const
void OutputAdditionalSimulationSetup(out_stream &rParamsFile)
Definition: Node.hpp:58
virtual void WriteVisualizerSetupFile()
const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > & rGetForceCollection() const
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & rGetCellPopulation()
std::vector< boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > > mBoundaryConditions
void SetNumericalMethod(boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > pNumericalMethod)
void serialize(Archive &archive, const unsigned int version)
void ApplyBoundaries(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
void AddForce(boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce)
void RemoveAllCellPopulationBoundaryConditions()
void RevertToOldLocations(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > mForceCollection
OffLatticeSimulation(AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
gcov doesn't like this file...
virtual void OutputSimulationParameters(out_stream &rParamsFile)
virtual void UpdateCellLocationsAndTopology()
void AddCellPopulationBoundaryCondition(boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition)