CellBasedSimulation.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 CELLBASEDSIMULATION_HPP_
#define CELLBASEDSIMULATION_HPP_

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

#include <vector>

#include "AbstractForce.hpp"
#include "AbstractCellKiller.hpp"
#include "AbstractCellPopulation.hpp"
#include "RandomNumberGenerator.hpp"
#include "Identifiable.hpp"

template<unsigned DIM>
class CellBasedSimulation : public Identifiable
{
    // Allow tests to access private members, in order to test computation of
    // private functions eg. DoCellBirth
    friend class TestCryptSimulation2d;
    friend class TestCellBasedSimulation3d;
    friend class TestCellBasedSimulation;

protected:

    double mDt;

    double mEndTime;

    AbstractCellPopulation<DIM>& mrCellPopulation;

    bool mDeleteCellPopulation;

    bool mAllocatedMemoryForForceCollection;

    bool mInitialiseCells;

    bool mNoBirth;

    bool mUpdateCellPopulation;

    std::string mOutputDirectory;

    std::string mSimulationOutputDirectory;

    out_stream mpVizSetupFile;

    out_stream mpNodeVelocitiesFile;

    RandomNumberGenerator* mpRandomGenerator;

    unsigned mNumBirths;

    unsigned mNumDeaths;

    unsigned mSamplingTimestepMultiple;

    std::vector<AbstractCellKiller<DIM>*> mCellKillers;

    std::vector<AbstractForce<DIM>*> mForceCollection;

    bool mOutputNodeVelocities;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        mpRandomGenerator = RandomNumberGenerator::Instance();
        archive & *mpRandomGenerator;
        archive & mpRandomGenerator;

        // If Archive is an output archive, then & resolves to <<
        // If Archive is an input archive, then & resolves to >>
        archive & mDt;
        archive & mEndTime;
        archive & mNoBirth;
        archive & mUpdateCellPopulation;
        archive & mOutputDirectory;
        archive & mNumBirths;
        archive & mNumDeaths;
        archive & mCellKillers;
        archive & mSamplingTimestepMultiple;
        archive & mForceCollection;
        archive & mOutputNodeVelocities;
    }

    virtual void WriteVisualizerSetupFile()
    {
    }

    virtual unsigned DoCellBirth();

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

    unsigned DoCellRemoval();

    virtual void UpdateNodePositions(const std::vector< c_vector<double, DIM> >& rNodeForces);

    virtual void ApplyCellPopulationBoundaryConditions(const std::vector< c_vector<double, DIM> >& rOldLocations)
    {
    }

    virtual void PostSolve()
    {
    }

    virtual void SetupSolve()
    {
    }

    virtual void AfterSolve()
    {
    }

    virtual bool StoppingEventHasOccurred();

    void UpdateCellPopulation();

    void OutputSimulationSetup();


public:

    CellBasedSimulation(AbstractCellPopulation<DIM>& rCellPopulation,
                        bool deleteCellPopulationAndForceCollection=false,
                        bool initialiseCells=true);

    virtual ~CellBasedSimulation();

    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(AbstractCellKiller<DIM>* pCellKiller);

    void AddForce(AbstractForce<DIM>* pForce);

    void Solve();

    AbstractCellPopulation<DIM>& rGetCellPopulation();

    const AbstractCellPopulation<DIM>& rGetCellPopulation() const;

    const std::vector<AbstractForce<DIM>*> rGetForceCollection() const;

    bool GetOutputNodeVelocities();

    void SetOutputNodeVelocities(bool outputNodeVelocities);

    virtual void OutputSimulationParameters(out_stream& rParamsFile);
};


#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellBasedSimulation)


namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const CellBasedSimulation<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, CellBasedSimulation<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
    ::new(t)CellBasedSimulation<DIM>(*p_cell_population, true, false);
}
}
} // namespace


#endif /*CELLBASEDSIMULATION_HPP_*/

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