BidomainProblem.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 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 "AbstractCardiacPde.hpp"
#include "AbstractDynamicAssemblerMixin.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "Electrodes.hpp"
#include "BidomainPde.hpp"
#include "BidomainDg0Assembler.hpp"
#include "HeartRegionCodes.hpp"
#include "DistributedTetrahedralMesh.hpp"

template<unsigned DIM>
class BidomainProblem : public AbstractCardiacProblem<DIM,DIM, 2>
{

    friend class boost::serialization::access;
    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 2> >(*this);
        archive & mpBidomainPde;
        //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 & mpBidomainPde;
        //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 TestBidomainWithBathAssembler;
    friend class TestCardiacSimulationArchiver;

protected:
    BidomainPde<DIM>* mpBidomainPde;

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

    bool mHasBath;

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

    Vec CreateInitialCondition();

    void AnalyseMeshForBath();

    BidomainDg0Assembler<DIM,DIM>* mpAssembler;

    virtual AbstractCardiacPde<DIM> *CreateCardiacPde();

    virtual AbstractDynamicAssemblerMixin<DIM, DIM, 2>* CreateAssembler();

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

    BidomainProblem();

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

    void SetNodeForAverageOfPhiZeroed(unsigned node);

    BidomainPde<DIM>* GetBidomainPde();

    void WriteInfo(double time);

    virtual void DefineWriterColumns(bool extending);

    virtual void WriteOneStep(double time, Vec voltageVec);

    void PreSolveChecks();

    void SetElectrodes(boost::shared_ptr<Electrodes<DIM> > pElectrodes);

    void AtBeginningOfTimestep(double time);

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

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

#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_*/