Chaste  Release::2018.1
MeshBasedCellPopulationWithGhostNodes.hpp
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35 
36 #ifndef MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_
37 #define MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_
38 
39 #include "ChasteSerialization.hpp"
40 #include <boost/serialization/base_object.hpp>
41 #include <boost/serialization/vector.hpp>
42 
43 #include "MeshBasedCellPopulation.hpp"
44 
55 template<unsigned DIM>
57 {
58 private:
59 
62 
64  std::vector<bool> mIsGhostNode;
65 
70 
84  template<class Archive>
85  void serialize(Archive & archive, const unsigned int version)
86  {
87  // This needs to be first so that MeshBasedCellPopulation::Validate() doesn't go mental.
88  archive & mIsGhostNode;
89  archive & mGhostSpringStiffness;
90  archive & boost::serialization::base_object<MeshBasedCellPopulation<DIM, DIM> >(*this);
91  }
92 
98  void SetGhostNodes(const std::set<unsigned>& rGhostNodeIndices);
99 
109  void Validate();
110 
111 protected:
118  virtual void AcceptCellWritersAcrossPopulation();
119 
120 public:
121 
132  std::vector<CellPtr>& rCells,
133  const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
134  bool deleteMesh=false,
135  double ghostSpringStiffness=15.0);
136 
144  double ghostSpringStiffness=15.0);
145 
150 
159 
168  std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
169 
174  void ApplyGhostForces();
175 
179  std::vector<bool>& rGetGhostNodes();
180 
191  bool IsGhostNode(unsigned index);
192 
196  std::set<unsigned> GetGhostNodeIndices();
197 
198 
205 
214  c_vector<double, DIM> CalculateForceBetweenGhostNodes(const unsigned& rNodeAGlobalIndex, const unsigned& rNodeBGlobalIndex);
215 
226  CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell);
227 
235  virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
236 
242  virtual void WriteVtkResultsToFile(const std::string& rDirectory);
243 
252  void OutputCellPopulationParameters(out_stream& rParamsFile);
253 };
254 
255 
258 
259 namespace boost
260 {
261 namespace serialization
262 {
266 template<class Archive, unsigned DIM>
267 inline void save_construct_data(
268  Archive & ar, const MeshBasedCellPopulationWithGhostNodes<DIM> * t, const unsigned int file_version)
269 {
270  // Save data required to construct instance
271  const MutableMesh<DIM,DIM>* p_mesh = &(t->rGetMesh());
272  ar & p_mesh;
273 }
274 
279 template<class Archive, unsigned DIM>
280 inline void load_construct_data(
281  Archive & ar, MeshBasedCellPopulationWithGhostNodes<DIM> * t, const unsigned int file_version)
282 {
283  // Retrieve data from archive required to construct new instance
284  MutableMesh<DIM,DIM>* p_mesh;
285  ar >> p_mesh;
286 
287  // Invoke inplace constructor to initialise instance
288  ::new(t)MeshBasedCellPopulationWithGhostNodes<DIM>(*p_mesh);
289 }
290 }
291 } // namespace
292 
293 #endif /*MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_*/
virtual TetrahedralMesh< DIM, DIM > * GetTetrahedralMeshForPdeModifier()
std::set< unsigned > GetNeighbouringLocationIndices(CellPtr pCell)
virtual void WriteVtkResultsToFile(const std::string &rDirectory)
virtual void OpenWritersFiles(OutputFileHandler &rOutputFileHandler)
c_vector< double, DIM > CalculateForceBetweenGhostNodes(const unsigned &rNodeAGlobalIndex, const unsigned &rNodeBGlobalIndex)
MutableMesh< ELEMENT_DIM, ELEMENT_DIM > & rGetMesh()
void serialize(Archive &archive, const unsigned int version)
MeshBasedCellPopulationWithGhostNodes(MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, double ghostSpringStiffness=15.0)
CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
void SetGhostNodes(const std::set< unsigned > &rGhostNodeIndices)
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