BidomainPde.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 BIDOMAINPDE_HPP_
#define BIDOMAINPDE_HPP_

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

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

#include "AbstractCardiacPde.hpp"
#include "AbstractConductivityTensors.hpp"

template <unsigned SPACE_DIM>
class BidomainPde : public virtual AbstractCardiacPde<SPACE_DIM>
{
private:
    friend class TestBidomainPde; // for testing.

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

    AbstractConductivityTensors<SPACE_DIM> *mpExtracellularConductivityTensors;

    ReplicatableVector mExtracellularStimulusCacheReplicated;

    void CreateExtracellularConductivityTensors();

public:
    BidomainPde(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory);

    BidomainPde(std::vector<AbstractCardiacCell*> & rCellsDistributed,AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh);

    ~BidomainPde();

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

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

namespace boost
{
namespace serialization
{

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

    // Don't use the std::vector serialization for cardiac cells, so that we can load them
    // more cleverly when migrating checkpoints.
    t->SaveCardiacCells(ar, file_version);

    // 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, BidomainPde<SPACE_DIM> * t, const unsigned int file_version)
{
    std::vector<AbstractCardiacCell*> cells_distributed;
    AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh;

    ar & p_mesh;
    // Load only the cells we actually own
    AbstractCardiacPde<SPACE_DIM,SPACE_DIM>::LoadCardiacCells(
            *ProcessSpecificArchive<Archive>::Get(), file_version, cells_distributed, p_mesh);

    // CreateIntracellularConductivityTensor() is called by AbstractCardiacPde 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)BidomainPde<SPACE_DIM>(cells_distributed, p_mesh);
}
}
} // namespace ...


#endif /*BIDOMAINPDE_HPP_*/