ExtendedBidomainProblem.hpp

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#ifndef EXTENDEDBIDOMAINPROBLEM_HPP_
#define EXTENDEDBIDOMAINPROBLEM_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 "AbstractExtendedBidomainSolver.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "Electrodes.hpp"
#include "ExtendedBidomainTissue.hpp"

#include "HeartRegionCodes.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "AbstractStimulusFactory.hpp"
#include "ElectrodesStimulusFactory.hpp"

template<unsigned DIM>
class ExtendedBidomainProblem : public AbstractCardiacProblem<DIM,DIM, 3>
{
    friend class boost::serialization::access;

    friend class TestArchivingExtendedBidomain;//for testing

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
        archive & mpExtendedBidomainTissue;
        archive & mFixedExtracellularPotentialNodes;
        //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
        archive & mVariablesIDs;
        archive & mUserSpecifiedSecondCellConductivities;
        archive & mUserHasSetBidomainValuesExplicitly;
        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mGgapHeterogeneityRegions;
        archive & mGgapHeterogenousValues;
        archive & mRowForAverageOfPhiZeroed;
        archive & mApplyAveragePhieZeroConstraintAfterSolving;
        archive & mUserSuppliedExtracellularStimulus;
        archive & mHasBath;
        //archive & mpSolver;

        //archive the values for the conductivies of the second cell
        for (unsigned i = 0; i < DIM; i++)
        {
            double conductivity = mIntracellularConductivitiesSecondCell(i);
            archive & conductivity;
        }

        bool has_solution = (this->mSolution != NULL);
        archive & has_solution;
        if (has_solution)
        {
            std::string filename = ArchiveLocationInfo::GetArchiveDirectory() + "AbstractCardiacProblem_mSolution.vec";

            Hdf5DataWriter writer(*this->mpMesh->GetDistributedVectorFactory(), ArchiveLocationInfo::GetArchiveRelativePath(), "AbstractCardiacProblem_mSolution", false);
            writer.DefineFixedDimension(this->mpMesh->GetDistributedVectorFactory()->GetProblemSize());
            writer.DefineUnlimitedDimension("Time", "msec", 1);

            // Make sure the file does not take more disc space than really needed (#1200)
            writer.SetFixedChunkSize(1);

            assert(HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() == false );

            int V = writer.DefineVariable("V","mV");
            int V_2 = writer.DefineVariable("V_2","mV");
            int phie = writer.DefineVariable("Phi_e","mV");
            std::vector<int> variable_ids;
            variable_ids.push_back(V);
            variable_ids.push_back(V_2);
            variable_ids.push_back(phie);
            writer.EndDefineMode();
            writer.PutUnlimitedVariable(0.0);

            //re-arrange to write out voltages...
            Vec voltages_to_be_written =  this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
            DistributedVector wrapped_voltages_to_be_written = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(voltages_to_be_written);

            DistributedVector distr_solution = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mSolution);
            DistributedVector::Stripe phi_i_first_cell_stripe(distr_solution,0);
            DistributedVector::Stripe phi_i_second_cell_stripe(distr_solution,1);
            DistributedVector::Stripe phi_e_stripe(distr_solution,2);


            DistributedVector::Stripe wrapped_voltages_to_be_written_first_stripe(wrapped_voltages_to_be_written,0);
            DistributedVector::Stripe wrapped_voltages_to_be_written_second_stripe(wrapped_voltages_to_be_written,1);
            DistributedVector::Stripe wrapped_voltages_to_be_written_third_stripe(wrapped_voltages_to_be_written,2);

            for (DistributedVector::Iterator index = distr_solution.Begin();
                 index != distr_solution.End();
                 ++index)
            {
                wrapped_voltages_to_be_written_first_stripe[index] = phi_i_first_cell_stripe[index] - phi_e_stripe[index];
                wrapped_voltages_to_be_written_second_stripe[index] = phi_i_second_cell_stripe[index] - phi_e_stripe[index];
                wrapped_voltages_to_be_written_third_stripe[index] = phi_e_stripe[index];
            }
            distr_solution.Restore();
            wrapped_voltages_to_be_written.Restore();

            writer.PutStripedVector(variable_ids, voltages_to_be_written);
            PetscTools::Destroy(voltages_to_be_written);
        }
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
        archive & mpExtendedBidomainTissue;
        archive & mFixedExtracellularPotentialNodes;
        //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
        archive & mVariablesIDs;
        archive & mUserSpecifiedSecondCellConductivities;
        archive & mUserHasSetBidomainValuesExplicitly;
        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mGgapHeterogeneityRegions;
        archive & mGgapHeterogenousValues;
        archive & mRowForAverageOfPhiZeroed;
        archive & mApplyAveragePhieZeroConstraintAfterSolving;
        archive & mUserSuppliedExtracellularStimulus;
        archive & mHasBath;
        //archive & mpSolver;

        //load the values for the conductivies of the second cell
        for (unsigned i = 0; i < DIM; i++)
        {
            double conductivity;
            archive & conductivity;
            mIntracellularConductivitiesSecondCell(i) = conductivity;
        }

        bool has_solution;
        archive & has_solution;

        if (has_solution)
        {
            std::string filename = ArchiveLocationInfo::GetArchiveDirectory() + "AbstractCardiacProblem_mSolution.vec";

            this->mSolution = this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
            DistributedVector mSolution_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mSolution);

            std::string archive_dir = ArchiveLocationInfo::GetArchiveRelativePath();
            Hdf5DataReader reader(archive_dir, "AbstractCardiacProblem_mSolution", !FileFinder::IsAbsolutePath(archive_dir));

            Vec V = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
            Vec V_2 = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
            Vec phie = this->mpMesh->GetDistributedVectorFactory()->CreateVec();

            reader.GetVariableOverNodes(V, "V", 0);
            reader.GetVariableOverNodes(V_2, "V_2", 0);
            reader.GetVariableOverNodes(phie, "Phi_e", 0);

            //from transmembrane voltages back to phi_i now...
            DistributedVector vm_first_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V);
            DistributedVector vm_second_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V_2);
            DistributedVector phie_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(phie);

            DistributedVector::Stripe mSolution_phi_1(mSolution_distri,0);
            DistributedVector::Stripe mSolution_phi_2(mSolution_distri,1);
            DistributedVector::Stripe mSolution_phie(mSolution_distri,2);

            for (DistributedVector::Iterator index = mSolution_distri.Begin();
                 index != mSolution_distri.End();
                 ++index)
            {
                mSolution_phi_1[index] = vm_first_cell_distri[index] + phie_distri[index];//phi_i = Vm + phi_e
                mSolution_phi_2[index] = vm_second_cell_distri[index] + phie_distri[index];
                mSolution_phie[index] = phie_distri[index];
            }
            PetscTools::Destroy(V);
            PetscTools::Destroy(V_2);
            PetscTools::Destroy(phie);

            mSolution_distri.Restore();
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()


protected:

    AbstractCardiacCellFactory<DIM,DIM>* mpSecondCellFactory;

    ExtendedBidomainTissue<DIM>* mpExtendedBidomainTissue;

    std::vector<unsigned> mFixedExtracellularPotentialNodes;

    c_vector<double, DIM>  mIntracellularConductivitiesSecondCell;

    unsigned mVoltageColumnId_Vm1;
    unsigned mVoltageColumnId_Vm2;
    unsigned mVoltageColumnId_Phie;
    std::vector<signed int> mVariablesIDs;

    bool mUserSpecifiedSecondCellConductivities;

    bool mUserHasSetBidomainValuesExplicitly;

    double mAmFirstCell;
    double mAmSecondCell;
    double mAmGap;
    double mCmFirstCell;
    double mCmSecondCell;
    double mGGap;

    std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > > mGgapHeterogeneityRegions;

    std::vector<double> mGgapHeterogenousValues;


    AbstractStimulusFactory<DIM>* mpExtracellularStimulusFactory;

    int mRowForAverageOfPhiZeroed;

    unsigned mApplyAveragePhieZeroConstraintAfterSolving;

    bool mUserSuppliedExtracellularStimulus;

    bool mHasBath;

    Vec CreateInitialCondition();

    void AnalyseMeshForBath();

    void ProcessExtracellularStimulus();

    AbstractExtendedBidomainSolver<DIM,DIM>* mpSolver;

    virtual AbstractCardiacTissue<DIM> *CreateCardiacTissue();

    virtual AbstractDynamicLinearPdeSolver<DIM,DIM,3>* CreateSolver();

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

    ExtendedBidomainProblem();

    ~ExtendedBidomainProblem();

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

    void SetIntracellularConductivitiesForSecondCell(c_vector<double, DIM> conductivities);

    void SetExtendedBidomainParameters(double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap);

    void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > >& rGgapHeterogeneityRegions, std::vector<double>& rGgapValues);

    void SetExtracellularStimulusFactory( AbstractStimulusFactory<DIM>* pFactory);


    void SetNodeForAverageOfPhiZeroed(unsigned node);


    ExtendedBidomainTissue<DIM>* GetExtendedBidomainTissue();

    void WriteInfo(double time);

    virtual void DefineWriterColumns(bool extending);

    virtual void WriteOneStep(double time, Vec voltageVec);

    void PreSolveChecks();


    bool GetHasBath();

    void SetHasBath(bool hasBath);

};

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

#endif /*EXTENDEDBIDOMAINPROBLEM_HPP_*/