AbstractCellBasedSimulation.hpp

/*

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*/

#ifndef ABSTRACTCELLBASEDSIMULATION_HPP_
#define ABSTRACTCELLBASEDSIMULATION_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/vector.hpp>
#include <boost/serialization/string.hpp>

#include <vector>

#include "CellBasedPdeHandler.hpp"
#include "AbstractCellKiller.hpp"
#include "AbstractCellBasedSimulationModifier.hpp"
#include "AbstractForce.hpp"
#include "RandomNumberGenerator.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
class AbstractCellBasedSimulation : public Identifiable
{
    // Allow tests to access private members, in order to test computation of private functions e.g. DoCellBirth()
    friend class TestCryptSimulation2d;
    friend class TestOffLatticeSimulation3d;
    friend class TestOffLatticeSimulation;

private:

    friend class boost::serialization::access;

    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        SerializableSingleton<SimulationTime>* p_time_wrapper = SimulationTime::Instance()->GetSerializationWrapper();
        archive & p_time_wrapper;

        SerializableSingleton<RandomNumberGenerator>* p_rng_wrapper = RandomNumberGenerator::Instance()->GetSerializationWrapper();
        archive & p_rng_wrapper;

        archive & mDt;
        archive & mEndTime;
        archive & mNoBirth;
        archive & mUpdateCellPopulation;
        archive & mOutputDirectory;
        archive & mNumBirths;
        archive & mNumDeaths;
        archive & mOutputDivisionLocations;
        archive & mOutputCellVelocities;
        archive & mCellKillers;
        archive & mSimulationModifiers;
        archive & mSamplingTimestepMultiple;
        archive & mpCellBasedPdeHandler;
    }

protected:

    double mDt;

    double mEndTime;

    AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>& mrCellPopulation;

    bool mDeleteCellPopulationInDestructor;

    bool mInitialiseCells;

    bool mNoBirth;

    bool mUpdateCellPopulation;

    std::string mOutputDirectory;

    std::string mSimulationOutputDirectory;

    out_stream mpVizSetupFile;

    unsigned mNumBirths;

    unsigned mNumDeaths;

    bool mOutputDivisionLocations;

    out_stream mpDivisionLocationFile;

    bool mOutputCellVelocities;

    out_stream mpCellVelocitiesFile;

    std::vector<boost::shared_ptr<AbstractCellKiller<SPACE_DIM> > > mCellKillers;

    std::vector<boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM, SPACE_DIM> > > mSimulationModifiers;

    unsigned mSamplingTimestepMultiple;

    CellBasedPdeHandler<SPACE_DIM>* mpCellBasedPdeHandler;

    virtual void WriteVisualizerSetupFile()
    {
    }

    virtual unsigned DoCellBirth();

    virtual c_vector<double, SPACE_DIM> CalculateCellDivisionVector(CellPtr pParentCell)=0;

    unsigned DoCellRemoval();

    virtual void SetupSolve()
    {
    }

    virtual bool StoppingEventHasOccurred();

    virtual void UpdateCellPopulation();

    virtual void UpdateCellLocationsAndTopology()=0;

    void OutputSimulationSetup();

    virtual void OutputAdditionalSimulationSetup(out_stream& rParamsFile)
    {
    }

public:

    AbstractCellBasedSimulation(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
                                bool deleteCellPopulationInDestructor=false,
                                bool initialiseCells=true);

    virtual ~AbstractCellBasedSimulation();

    void SetCellBasedPdeHandler(CellBasedPdeHandler<SPACE_DIM>* pCellBasedPdeHandler);

    CellBasedPdeHandler<SPACE_DIM>* GetCellBasedPdeHandler();

    std::vector<double> GetNodeLocation(const unsigned& rNodeIndex);

    double GetDt();

    unsigned GetNumBirths();

    unsigned GetNumDeaths();

    std::string GetOutputDirectory();

    void SetDt(double dt);

    void SetEndTime(double endTime);

    void SetOutputDirectory(std::string outputDirectory);

    void SetSamplingTimestepMultiple(unsigned samplingTimestepMultiple);

    void SetNoBirth(bool noBirth);

    void SetUpdateCellPopulationRule(bool updateCellPopulation);

    bool GetUpdateCellPopulationRule();

    void AddCellKiller(boost::shared_ptr<AbstractCellKiller<SPACE_DIM> > pCellKiller);

    void RemoveAllCellKillers();

    void AddSimulationModifier(boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM,SPACE_DIM> > pSimulationModifier);

    std::vector<boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM, SPACE_DIM> > >* GetSimulationModifiers();

    void Solve();

    AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rGetCellPopulation();

    const AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rGetCellPopulation() const;

    bool GetOutputDivisionLocations();

    void SetOutputDivisionLocations(bool outputDivisionLocations);

    bool GetOutputCellVelocities();

    void SetOutputCellVelocities(bool outputCellVelocities);

    virtual void OutputSimulationParameters(out_stream& rParamsFile)=0;
};

#endif /*ABSTRACTCELLBASEDSIMULATION_HPP_*/