AbstractCellBasedSimulation.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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 "CellwiseData.hpp"
#include "RandomNumberGenerator.hpp"

template<unsigned 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<CellwiseData<DIM> >* p_cellwise_data_wrapper = CellwiseData<DIM>::Instance()->GetSerializationWrapper();
        archive & p_cellwise_data_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 & mCellKillers;
        archive & mSamplingTimestepMultiple;
        archive & mpCellBasedPdeHandler;
    }

protected:

    double mDt;

    double mEndTime;

    AbstractCellPopulation<DIM>& mrCellPopulation;

    bool mDeleteCellPopulationInDestructor;

    bool mInitialiseCells;

    bool mNoBirth;

    bool mUpdateCellPopulation;

    std::string mOutputDirectory;

    std::string mSimulationOutputDirectory;

    out_stream mpVizSetupFile;

    unsigned mNumBirths;

    unsigned mNumDeaths;

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

    unsigned mSamplingTimestepMultiple;

    CellBasedPdeHandler<DIM>* mpCellBasedPdeHandler;

    virtual void WriteVisualizerSetupFile()
    {
    }

    virtual unsigned DoCellBirth();

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

    unsigned DoCellRemoval();

    virtual void PostSolve();

    virtual void SetupSolve();

    virtual void AfterSolve();

    virtual bool StoppingEventHasOccurred();

    virtual void UpdateCellPopulation();

    virtual void UpdateCellLocationsAndTopology()=0;

    void OutputSimulationSetup();

    virtual void OutputAdditionalSimulationSetup(out_stream& rParamsFile)
    {
    }

public:

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

    virtual ~AbstractCellBasedSimulation();

    void SetCellBasedPdeHandler(CellBasedPdeHandler<DIM>* pCellBasedPdeHandler);

    CellBasedPdeHandler<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);

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

    void Solve();

    AbstractCellPopulation<DIM>& rGetCellPopulation();

    const AbstractCellPopulation<DIM>& rGetCellPopulation() const;

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

#endif /*ABSTRACTCELLBASEDSIMULATION_HPP_*/