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;

    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 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_*/