VertexBasedCellPopulation.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 VERTEXBASEDCELLPOPULATION_HPP_
#define VERTEXBASEDCELLPOPULATION_HPP_

#include "AbstractOffLatticeCellPopulation.hpp"
#include "MutableVertexMesh.hpp"

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

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"

template<unsigned DIM>
class VertexBasedCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
private:

    MutableVertexMesh<DIM, DIM>& mrMesh;

    bool mDeleteMesh;

    out_stream mpVizElementsFile;

    out_stream mpT1SwapLocationsFile;

    out_stream mpT3SwapLocationsFile;

    void WriteVtkResultsToFile();

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

    void Validate();

public:

    VertexBasedCellPopulation(MutableVertexMesh<DIM, DIM>& rMesh,
                      std::vector<CellPtr>& rCells,
                      bool deleteMesh=false,
                      bool validate=true,
                      const std::vector<unsigned> locationIndices=std::vector<unsigned>());

    VertexBasedCellPopulation(MutableVertexMesh<DIM, DIM>& rMesh);

    virtual ~VertexBasedCellPopulation();

    double GetDampingConstant(unsigned nodeIndex);

    MutableVertexMesh<DIM, DIM>& rGetMesh();

    const MutableVertexMesh<DIM, DIM>& rGetMesh() const;

    VertexElement<DIM, DIM>* GetElement(unsigned elementIndex);

    unsigned GetNumElements();

    unsigned GetNumNodes();

    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);

    Node<DIM>* GetNode(unsigned index);

    unsigned AddNode(Node<DIM>* pNewNode);

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

    void SetNode(unsigned index, ChastePoint<DIM>& rNewLocation);

    VertexElement<DIM, DIM>* GetElementCorrespondingToCell(CellPtr pCell);

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

    unsigned RemoveDeadCells();

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    void CreateOutputFiles(const std::string& rDirectory, bool cleanOutputDirectory);
    void CloseOutputFiles();

    void WriteResultsToFiles();

    void WriteCellVolumeResultsToFile();

    virtual void GenerateCellResultsAndWriteToFiles();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetWidth(const unsigned& rDimension);

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

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(VertexBasedCellPopulation)

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

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

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

#endif /*VERTEXBASEDCELLPOPULATION_HPP_*/