NodeBasedCellPopulation.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 NODEBASEDCELLPOPULATION_HPP_
#define NODEBASEDCELLPOPULATION_HPP_

#include "AbstractCentreBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"
#include "BoxCollection.hpp"

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

template<unsigned DIM>
class NodeBasedCellPopulation : public AbstractCentreBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulation;
    friend class TestBoxCollection;

protected:

    NodesOnlyMesh<DIM>& mrMesh;

private:

    BoxCollection<DIM>* mpBoxCollection;

    c_vector<double, DIM> mMinSpatialPositions;

    c_vector<double, DIM> mMaxSpatialPositions;

    std::set< std::pair<Node<DIM>*, Node<DIM>* > > mNodePairs;

    bool mDeleteMesh;

    double mMechanicsCutOffLength;

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

        this->Validate();
    }

    unsigned AddNode(Node<DIM>* pNewNode);


protected:
    void SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation);

private:
    void Validate();

    void SplitUpIntoBoxes(double cutOffLength, c_vector<double, 2*DIM> domainSize);

    void FindMaxAndMin();

    void WriteCellVolumeResultsToFile();

    void WriteVtkResultsToFile();

public:

    NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh,
                            std::vector<CellPtr>& rCells,
                            const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                            bool deleteMesh=false);

    NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh);

    ~NodeBasedCellPopulation();

    NodesOnlyMesh<DIM>& rGetMesh();

    const NodesOnlyMesh<DIM>& rGetMesh() const;

    unsigned GetNumNodes();

    Node<DIM>* GetNode(unsigned index);

    unsigned RemoveDeadCells();

    void Clear();

    void Update(bool hasHadBirthsOrDeaths=true);

    BoxCollection<DIM>* GetBoxCollection();

    std::set< std::pair<Node<DIM>*, Node<DIM>* > >& rGetNodePairs();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetMechanicsCutOffLength();

    void SetMechanicsCutOffLength(double mechanicsCutOffLength);

    double GetWidth(const unsigned& rDimension);

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);

    virtual CellPtr AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr());
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodeBasedCellPopulation)

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

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

    // Invoke inplace constructor to initialise instance
    ::new(t)NodeBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*NODEBASEDCELLPOPULATION_HPP_*/