BidomainTissue.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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*/


#ifndef BIDOMAINTISSUE_HPP_
#define BIDOMAINTISSUE_HPP_

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

#include <vector>
#include <boost/numeric/ublas/matrix.hpp>

#include "AbstractCardiacTissue.hpp"
#include "AbstractConductivityTensors.hpp"




template <unsigned SPACE_DIM>
class BidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
{
private:
    friend class TestBidomainTissue; // for testing.

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
        // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.
    }

    AbstractConductivityTensors<SPACE_DIM,SPACE_DIM> *mpExtracellularConductivityTensors;

    void CreateExtracellularConductivityTensors();

public:
    BidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory, bool exchangeHalos=false);

    BidomainTissue(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh);

    ~BidomainTissue();

     const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(BidomainTissue)

namespace boost
{
namespace serialization
{

template<class Archive, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
{
    const AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh = t->pGetMesh();
    ar & p_mesh;

    // CreateIntracellularConductivityTensor() is called by constructor and uses HeartConfig. So make sure that it is
    // archived too (needs doing before construction so appears here instead of usual archive location).
    HeartConfig* p_config = HeartConfig::Instance();
    ar & *p_config;
    ar & p_config;
}

template<class Archive, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
{
    AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh;
    ar & p_mesh;

    // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
    // (as does CreateExtracellularConductivityTensor). So make sure that it is
    // archived too (needs doing before construction so appears here instead of usual archive location).
    HeartConfig* p_config = HeartConfig::Instance();
    ar & *p_config;
    ar & p_config;

    ::new(t)BidomainTissue<SPACE_DIM>(p_mesh);
}
}
} // namespace ...


#endif /*BIDOMAINTISSUE_HPP_*/