OnLatticeSimulation.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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*/

#ifndef ONLATTICESIMULATION_HPP_
#define ONLATTICESIMULATION_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include "AbstractCellBasedSimulation.hpp"
#include "AbstractPottsUpdateRule.hpp"
#include "AbstractMultipleCaUpdateRule.hpp"

template<unsigned DIM>
class OnLatticeSimulation : public AbstractCellBasedSimulation<DIM>
{
private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellBasedSimulation<DIM> >(*this);
        archive & mOutputCellVelocities;
    }

protected:

    bool mOutputCellVelocities;

    out_stream mpCellVelocitiesFile;

    void UpdateCellPopulation();

    void UpdateCellLocationsAndTopology();

    virtual c_vector<double, DIM> CalculateCellDivisionVector(CellPtr pParentCell);

    virtual void WriteVisualizerSetupFile();


public:

    OnLatticeSimulation(AbstractCellPopulation<DIM>& rCellPopulation,
                        bool deleteCellPopulationInDestructor=false,
                        bool initialiseCells=true);

    void AddMultipleCaUpdateRule(boost::shared_ptr<AbstractMultipleCaUpdateRule<DIM> > pUpdateRule);

    void RemoveAllMultipleCaUpdateRules();

    void AddPottsUpdateRule(boost::shared_ptr<AbstractPottsUpdateRule<DIM> > pUpdateRule);

    void RemoveAllPottsUpdateRules();

    bool GetOutputCellVelocities();

    void SetOutputCellVelocities(bool outputCellVelocities);

    virtual void SetupSolve();

    virtual void UpdateAtEndOfSolve();

    void OutputAdditionalSimulationSetup(out_stream& rParamsFile);

    void OutputSimulationParameters(out_stream& rParamsFile);
};

// Serialization for Boost >= 1.36
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(OnLatticeSimulation)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const OnLatticeSimulation<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const AbstractCellPopulation<DIM>* p_cell_population = &(t->rGetCellPopulation());
    ar & p_cell_population;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, OnLatticeSimulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    AbstractCellPopulation<DIM>* p_cell_population;
    ar >> p_cell_population;

    // Invoke inplace constructor to initialise instance, last two variables set extra
    // member variables to be deleted as they are loaded from archive and to not initialise sells.
    ::new(t)OnLatticeSimulation<DIM>(*p_cell_population, true, false);
}
}
} // namespace

#endif /*ONLATTICESIMULATION_HPP_*/