OffLatticeSimulation.hpp

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*/
 
#ifndef OFFLATTICESIMULATION_HPP_
#define OFFLATTICESIMULATION_HPP_
 
#include "AbstractCellBasedSimulation.hpp"
#include "AbstractForce.hpp"
#include "AbstractCellPopulationBoundaryCondition.hpp"
#include "AbstractNumericalMethod.hpp"
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
class OffLatticeSimulation : public AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>
{
private:
 
    friend class boost::serialization::access;
    friend class TestOffLatticeSimulation;
    friend class TestOffLatticeSimulationWithNodeBasedCellPopulation;
 
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM> >(*this);
        archive & mForceCollection;
        archive & mBoundaryConditions;
        archive & mpNumericalMethod;
    }
 
protected:
 
    std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > > mForceCollection;
 
    std::vector<boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> > > mBoundaryConditions;
 
    boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > mpNumericalMethod;
 
    unsigned mMaxAdaptiveTimeSteps = 5;
 
    virtual void UpdateCellLocationsAndTopology();
 
    void RevertToOldLocations(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > oldNodeLoctions);
 
    void ApplyBoundaries(std::map<Node<SPACE_DIM>*, c_vector<double, SPACE_DIM> > oldNodeLoctions);
 
    virtual void SetupSolve();
 
    virtual void WriteVisualizerSetupFile();
 
public:
 
    OffLatticeSimulation(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
                         bool deleteCellPopulationInDestructor=false,
                         bool initialiseCells=true);
 
    void AddForce(boost::shared_ptr<AbstractForce<ELEMENT_DIM,SPACE_DIM> > pForce);
 
    void RemoveAllForces();
 
    void AddCellPopulationBoundaryCondition(boost::shared_ptr<AbstractCellPopulationBoundaryCondition<ELEMENT_DIM,SPACE_DIM> >  pBoundaryCondition);
 
    void RemoveAllCellPopulationBoundaryConditions();
 
    void SetNumericalMethod(boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > pNumericalMethod);
 
    const boost::shared_ptr<AbstractNumericalMethod<ELEMENT_DIM, SPACE_DIM> > GetNumericalMethod() const;
 
    void SetMaxAdaptiveTimeStep(const unsigned maxAdaptiveTimeStep);
 
    unsigned GetMaxAdaptiveTimeStep() const;
 
    void OutputAdditionalSimulationSetup(out_stream& rParamsFile);
 
    virtual void OutputSimulationParameters(out_stream& rParamsFile);
 
    const std::vector<boost::shared_ptr<AbstractForce<ELEMENT_DIM, SPACE_DIM> > >& rGetForceCollection() const;
};
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(OffLatticeSimulation)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>* p_cell_population = &(t->rGetCellPopulation());
    ar & p_cell_population;
}
 
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>* p_cell_population;
    ar >> p_cell_population;
 
    // Invoke inplace constructor to initialise instance, middle two variables set extra
    // member variables to be deleted as they are loaded from archive and to not initialise cells.
    ::new(t)OffLatticeSimulation<ELEMENT_DIM,SPACE_DIM>(*p_cell_population, true, false);
}
}
} // namespace
 
#endif /*OFFLATTICESIMULATION_HPP_*/