BidomainProblem.hpp

/*

Copyright (c) 2005-2016, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/


#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_*/