Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
OffLatticeSimulation.hpp
1/*
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34*/
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
45#include <boost/serialization/base_object.hpp>
46#include <boost/serialization/set.hpp>
47#include <boost/serialization/vector.hpp>
48
70template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
71class OffLatticeSimulation : public AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>
72{
73private:
74
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
95protected:
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
138public:
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
217namespace boost
218{
219namespace serialization
220{
224template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
225inline 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
236template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
237inline 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_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
Definition Node.hpp:59
std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > mForceCollection
const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > GetNumericalMethod() const
virtual void UpdateCellLocationsAndTopology()
void OutputAdditionalSimulationSetup(out_stream &rParamsFile)
void AddCellPopulationBoundaryCondition(boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > pBoundaryCondition)
std::vector< boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM > > > mBoundaryConditions
const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > > & rGetForceCollection() const
void SetNumericalMethod(boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > pNumericalMethod)
void ApplyBoundaries(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
friend class boost::serialization::access
virtual void WriteVisualizerSetupFile()
virtual void OutputSimulationParameters(out_stream &rParamsFile)
void RevertToOldLocations(std::map< Node< SPACE_DIM > *, c_vector< double, SPACE_DIM > > oldNodeLoctions)
void AddForce(boost::shared_ptr< AbstractForce< ELEMENT_DIM, SPACE_DIM > > pForce)
void serialize(Archive &archive, const unsigned int version)
boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, SPACE_DIM > > mpNumericalMethod