BidomainProblem.hpp

/*

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*/


#ifndef BIDOMAINPROBLEM_HPP_
#define BIDOMAINPROBLEM_HPP_

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

#include <vector>
#include <boost/shared_ptr.hpp>
#include <boost/serialization/shared_ptr.hpp>

#include "AbstractCardiacProblem.hpp"
#include "AbstractCardiacTissue.hpp"
#include "AbstractBidomainSolver.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "Electrodes.hpp"
#include "BidomainTissue.hpp"
#include "HeartRegionCodes.hpp"
#include "DistributedTetrahedralMesh.hpp"

template<unsigned DIM>
class BidomainProblem : public AbstractCardiacProblem<DIM,DIM, 2>
{
    friend class boost::serialization::access;

    // #1082
    friend class TestPCTwoLevelsBlockDiagonal;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 2> >(*this);
        archive & mpBidomainTissue;
        //archive & mExtracelluarColumnId; // Created by InitialiseWriter, called from Solve
        archive & mRowForAverageOfPhiZeroed;
        archive & mHasBath;
        archive & mpElectrodes;
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 2> >(*this);
        archive & mpBidomainTissue;
        //archive & mExtracelluarColumnId; // Created by InitialiseWriter, called from Solve
        archive & mRowForAverageOfPhiZeroed;
        archive & mHasBath;
        archive & mpElectrodes;

        if (mHasBath)
        {
            // We only save element annotations, so annotate bath nodes from these
            AnalyseMeshForBath();
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

    friend class TestBidomainWithBathProblem;
    friend class TestCardiacSimulationArchiver;

protected:
    BidomainTissue<DIM>* mpBidomainTissue;

    std::vector<unsigned> mFixedExtracellularPotentialNodes;
    unsigned mExtracelluarColumnId;
    unsigned mRowForAverageOfPhiZeroed;

    bool mHasBath;

    boost::shared_ptr<Electrodes<DIM> > mpElectrodes;

    Vec CreateInitialCondition();

    void AnalyseMeshForBath();

    AbstractBidomainSolver<DIM,DIM>* mpSolver;

    virtual AbstractCardiacTissue<DIM> *CreateCardiacTissue();

    virtual AbstractDynamicLinearPdeSolver<DIM,DIM,2>* CreateSolver();

public:
    BidomainProblem(AbstractCardiacCellFactory<DIM>* pCellFactory, bool hasBath=false);

    BidomainProblem();

    void SetFixedExtracellularPotentialNodes(std::vector<unsigned> nodes);

    void SetNodeForAverageOfPhiZeroed(unsigned node);

    BidomainTissue<DIM>* GetBidomainTissue();

    void WriteInfo(double time);

    virtual void DefineWriterColumns(bool extending);

    virtual void WriteOneStep(double time, Vec voltageVec);

    void PreSolveChecks();



    void AtBeginningOfTimestep(double time);

    void OnEndOfTimestep(double time);

    void SetUpAdditionalStoppingTimes(std::vector<double>& rAdditionalStoppingTimes);

    template<class Archive>
    void LoadExtraArchiveForBidomain(Archive & archive, unsigned version);

    bool GetHasBath();

    void SetElectrodes();
};

#include "SerializationExportWrapper.hpp" // Must be last
EXPORT_TEMPLATE_CLASS_SAME_DIMS(BidomainProblem)


template<unsigned DIM>
template<class Archive>
void BidomainProblem<DIM>::LoadExtraArchiveForBidomain(Archive & archive, unsigned version)
{
    // Not all bidomain problems have electrodes...
    if (mpElectrodes)
    {
        // Electrodes will always have a BCC object by this point
        assert(mpElectrodes->GetBoundaryConditionsContainer());
        // We might need to get some of the boundary conditions from this archive, but it might be
        // the case that the problem's BCC is the same object as the Electrodes' (if they are turned
        // on) in which case we need to do 'nothing'.
        boost::shared_ptr<BoundaryConditionsContainer<DIM, DIM, 2> > p_bcc;
        archive >> p_bcc;
        if (mpElectrodes->GetBoundaryConditionsContainer() != this->mpBoundaryConditionsContainer)
        {
            // The BCs will only actually be different if using a distributed tetrahedral mesh
            DistributedTetrahedralMesh<DIM,DIM>* p_dist_mesh = dynamic_cast<DistributedTetrahedralMesh<DIM,DIM>*>(this->mpMesh);
            if (p_dist_mesh)
            {
                mpElectrodes->GetBoundaryConditionsContainer()->MergeFromArchive(archive, this->mpMesh);
            }
            else
            {
                // Load into the temporary container, which will get thrown away shortly
                p_bcc->LoadFromArchive(archive, this->mpMesh);
            }
        }
    }
}

#endif /*BIDOMAINPROBLEM_HPP_*/