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 "AbstractCellKiller.hpp"
#include "AbstractCellBasedSimulationModifier.hpp"
#include "AbstractForce.hpp"
#include "RandomNumberGenerator.hpp"
 
// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class AbstractCellPopulation;
 
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 & mTopologyUpdateSimulationModifiers;
        archive & mSamplingTimestepMultiple;
        archive & mUpdatingTimestepMultiple;
    }
 
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;
 
    std::vector<boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM, SPACE_DIM> > > mTopologyUpdateSimulationModifiers;
 
    unsigned mSamplingTimestepMultiple;
 
    unsigned mUpdatingTimestepMultiple;
 
    virtual void WriteVisualizerSetupFile()
    {
    }
 
    virtual unsigned DoCellBirth();
 
    unsigned DoCellRemoval();
 
    virtual void SetupSolve()
    {
    }
 
    virtual bool StoppingEventHasOccurred();
 
    virtual void UpdateCellPopulation();
 
    virtual void UpdateCellLocationsAndTopology()=0;
 
    void OutputSimulationSetup();
 
    virtual void OutputAdditionalSimulationSetup(out_stream& rParamsFile)=0;
 
public:
 
    AbstractCellBasedSimulation(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation,
                                bool deleteCellPopulationInDestructor=false,
                                bool initialiseCells=true);
 
    virtual ~AbstractCellBasedSimulation();
 
    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 SetUpdatingTimestepMultiple(unsigned updatingTimestepMultiple);
 
    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 AddTopologyUpdateSimulationModifier(boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM,SPACE_DIM> > pSimulationModifier);
 
    std::vector<boost::shared_ptr<AbstractCellBasedSimulationModifier<ELEMENT_DIM, SPACE_DIM> > >* GetTopologyUpdateSimulationModifiers();
 
    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_*/