ExtendedBidomainTissue.cpp

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#include "ExtendedBidomainTissue.hpp"

#include "DistributedVector.hpp"
#include "OrthotropicConductivityTensors.hpp"
#include "AxisymmetricConductivityTensors.hpp"
#include "AbstractStimulusFunction.hpp"
#include "ChastePoint.hpp"
#include "AbstractChasteRegion.hpp"
#include "HeartEventHandler.hpp"

template <unsigned SPACE_DIM>
ExtendedBidomainTissue<SPACE_DIM>::ExtendedBidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory,
                                                          AbstractCardiacCellFactory<SPACE_DIM>* pCellFactorySecondCell,
                                                          AbstractStimulusFactory<SPACE_DIM>* pExtracellularStimulusFactory)
    : AbstractCardiacTissue<SPACE_DIM>(pCellFactory),
      mpIntracellularConductivityTensorsSecondCell(NULL),
      mUserSuppliedExtracellularStimulus(false)
{
    //First, do the same that the abstract constructor does, but applied to the second cell

    assert(pCellFactorySecondCell != NULL);
    assert(pCellFactorySecondCell->GetMesh() != NULL);
    assert(pCellFactorySecondCell->GetNumberOfCells() == pCellFactory->GetNumberOfCells() );
    assert(pExtracellularStimulusFactory != NULL);
    assert(pExtracellularStimulusFactory->GetMesh() != NULL);
    assert(pExtracellularStimulusFactory->GetNumberOfCells() == pCellFactorySecondCell->GetNumberOfCells() );

    unsigned num_local_nodes = this->mpDistributedVectorFactory->GetLocalOwnership();
    unsigned ownership_range_low = this->mpDistributedVectorFactory->GetLow();
    mCellsDistributedSecondCell.resize(num_local_nodes);
    mGgapDistributed.resize(num_local_nodes);
    mExtracellularStimuliDistributed.resize(num_local_nodes);

    try
    {
        for (unsigned local_index = 0; local_index < num_local_nodes; local_index++)
        {
            unsigned global_index = local_index + ownership_range_low;
            Node<SPACE_DIM>* p_node = this->mpMesh->GetNode(global_index);
            mCellsDistributedSecondCell[local_index] = pCellFactorySecondCell->CreateCardiacCellForNode(p_node);
            mCellsDistributedSecondCell[local_index]->SetUsedInTissueSimulation();
            mGgapDistributed[local_index] = 0.0;//default. It will be changed by specific method later when user input will be obtained
            mExtracellularStimuliDistributed[local_index] = pExtracellularStimulusFactory->CreateStimulusForNode(p_node);
        }

        pCellFactorySecondCell->FinaliseCellCreation(&mCellsDistributedSecondCell,
                                                     this->mpDistributedVectorFactory->GetLow(),
                                                     this->mpDistributedVectorFactory->GetHigh());
    }
    catch (const Exception& e)
    {
#define COVERAGE_IGNORE //don't really know how to cover this...
        // Errors thrown creating cells will often be process-specific
        PetscTools::ReplicateException(true);
        // Should really do this for other processes too, but this is all we need
        // to get memory testing to pass, and leaking when we're about to die isn't
        // that bad! Delete second cells
        for (std::vector<AbstractCardiacCellInterface*>::iterator cell_iterator = mCellsDistributedSecondCell.begin();
             cell_iterator != mCellsDistributedSecondCell.end();
             ++cell_iterator)
        {
            delete (*cell_iterator);
        }
        throw e;
#undef COVERAGE_IGNORE
    }
    PetscTools::ReplicateException(false);

    HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
    mIionicCacheReplicatedSecondCell.Resize( pCellFactory->GetNumberOfCells() );
    mIntracellularStimulusCacheReplicatedSecondCell.Resize( pCellFactorySecondCell->GetNumberOfCells() );
    mGgapCacheReplicated.Resize(pCellFactorySecondCell->GetNumberOfCells());//this is a bit of a hack...
    mExtracellularStimulusCacheReplicated.Resize(pExtracellularStimulusFactory->GetNumberOfCells());
    HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);

    //Create the extracellular conductivity tensor
    CreateExtracellularConductivityTensors();
}

//archiving constructor
template <unsigned SPACE_DIM>
ExtendedBidomainTissue<SPACE_DIM>::ExtendedBidomainTissue(std::vector<AbstractCardiacCellInterface*> & rCellsDistributed,
                                                          std::vector<AbstractCardiacCellInterface*> & rSecondCellsDistributed,
                                                          std::vector<boost::shared_ptr<AbstractStimulusFunction> > & rExtraStimuliDistributed,
                                                          std::vector<double> & rGgapsDistributed,
                                                          AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh,
                                                          c_vector<double, SPACE_DIM>  intracellularConductivitiesSecondCell)
        :   AbstractCardiacTissue<SPACE_DIM>(pMesh),
            mpIntracellularConductivityTensorsSecondCell(NULL),
            mIntracellularConductivitiesSecondCell(intracellularConductivitiesSecondCell),
            mCellsDistributedSecondCell(rSecondCellsDistributed),
            mExtracellularStimuliDistributed(rExtraStimuliDistributed),
            mGgapDistributed(rGgapsDistributed),
            mUserSuppliedExtracellularStimulus(false)
{
    //segfault guards in case we failed to load anything from the archive
    assert(mCellsDistributedSecondCell.size() > 0);
    assert(mExtracellularStimuliDistributed.size() > 0);
    assert(mGgapDistributed.size() > 0);
    //allocate memory for the caches
    mIionicCacheReplicatedSecondCell.Resize( this->mpDistributedVectorFactory->GetProblemSize());
    mIntracellularStimulusCacheReplicatedSecondCell.Resize( this->mpDistributedVectorFactory->GetProblemSize() );
    mGgapCacheReplicated.Resize(this->mpDistributedVectorFactory->GetProblemSize());
    mExtracellularStimulusCacheReplicated.Resize(this->mpDistributedVectorFactory->GetProblemSize());

    CreateIntracellularConductivityTensorSecondCell();
    CreateExtracellularConductivityTensors();
}


template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetGgapHeterogeneities(std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > >& rGgapHeterogeneityRegions,
                                                               std::vector<double> rGgapValues)
{
    assert( rGgapHeterogeneityRegions.size() == rGgapValues.size() );//problem class (which calls this method should have thrown otherwise)
    mGgapHeterogeneityRegions = rGgapHeterogeneityRegions;
    mGgapValues =rGgapValues;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::CreateGGapConductivities()
{
    assert(mGgapHeterogeneityRegions.size() == mGgapValues.size());
    assert(this->mpMesh != NULL);

    unsigned ownership_range_low = this->mpDistributedVectorFactory->GetLow();
    unsigned num_local_nodes = this->mpDistributedVectorFactory->GetLocalOwnership();
    assert(mGgapDistributed.size() == num_local_nodes);//the constructor should have allocated memory.
    try
    {
        for (unsigned local_index = 0; local_index < num_local_nodes; local_index++)
        {
            unsigned global_index = ownership_range_low + local_index;
            Node<SPACE_DIM>* p_node = this->mpMesh->GetNode(global_index);
            mGgapDistributed[local_index] = mGGap;//assign default uniform value everywhere first

            //then change where and if necessary
            for (unsigned het_index = 0; het_index < mGgapHeterogeneityRegions.size(); het_index++)
            {
                if ( mGgapHeterogeneityRegions[het_index]->DoesContain ( p_node->GetPoint() ) )
                {
                    mGgapDistributed[local_index] = mGgapValues[het_index];
                }
            }
        }
    }
    catch (const Exception& e)
    {
#define COVERAGE_IGNORE
        PetscTools::ReplicateException(true);
        throw e;
#undef COVERAGE_IGNORE
    }
    PetscTools::ReplicateException(false);
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::CreateIntracellularConductivityTensorSecondCell()
{
    HeartEventHandler::BeginEvent(HeartEventHandler::READ_MESH);
    this->mpConfig = HeartConfig::Instance();

    if (this->mpConfig->IsMeshProvided() && this->mpConfig->GetLoadMesh())
    {
        assert(this->mFibreFilePathNoExtension != "");

        switch (this->mpConfig->GetConductivityMedia())
        {
            case cp::media_type::Orthotropic:
            {
                mpIntracellularConductivityTensorsSecondCell =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder ortho_file(this->mFibreFilePathNoExtension + ".ortho", RelativeTo::AbsoluteOrCwd);
                assert(ortho_file.Exists());
                mpIntracellularConductivityTensorsSecondCell->SetFibreOrientationFile(ortho_file);
                break;
            }

            case cp::media_type::Axisymmetric:
            {
                mpIntracellularConductivityTensorsSecondCell =  new AxisymmetricConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder axi_file(this->mFibreFilePathNoExtension + ".axi", RelativeTo::AbsoluteOrCwd);
                assert(axi_file.Exists());
                mpIntracellularConductivityTensorsSecondCell->SetFibreOrientationFile(axi_file);
                break;
            }

            case cp::media_type::NoFibreOrientation:
                mpIntracellularConductivityTensorsSecondCell =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                break;

            default :
                NEVER_REACHED;
        }
    }
    else // Slab defined in config file or SetMesh() called; no fibre orientation assumed
    {
        mpIntracellularConductivityTensorsSecondCell =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
    }

    // this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
    // a pointer to it and we don't want it to go out of scope before Init() is called
    unsigned num_elements = this->mpMesh->GetNumElements();
    std::vector<c_vector<double, SPACE_DIM> > hetero_intra_conductivities;

    c_vector<double, SPACE_DIM> intra_conductivities;
    this->mpConfig->GetIntracellularConductivities(intra_conductivities);//this one is used just for resizing

    if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
    {
        try
        {
            assert(hetero_intra_conductivities.size()==0);
            hetero_intra_conductivities.resize(num_elements, intra_conductivities);
        }
        catch(std::bad_alloc &badAlloc)
        {
#define COVERAGE_IGNORE
            std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
            PetscTools::ReplicateException(true);
            throw badAlloc;
#undef COVERAGE_IGNORE
        }
        PetscTools::ReplicateException(false);

        std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
        std::vector< c_vector<double,3> > intra_h_conductivities;
        std::vector< c_vector<double,3> > extra_h_conductivities;
        HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
                                                                intra_h_conductivities,
                                                                extra_h_conductivities);
        unsigned local_element_index = 0;
        for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
             it != this->mpMesh->GetElementIteratorEnd();
             ++it)
        {
            //unsigned element_index = it->GetIndex();
            // if element centroid is contained in the region
            ChastePoint<SPACE_DIM> element_centroid(it->CalculateCentroid());
            for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
            {
                if ( conductivities_heterogeneity_areas[region_index]->DoesContain(element_centroid) )
                {
                    //We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
                    for (unsigned i=0; i<SPACE_DIM; i++)
                    {
                        hetero_intra_conductivities[local_element_index][i] = intra_h_conductivities[region_index][i];
                    }
                }
            }
            local_element_index++;
        }

        mpIntracellularConductivityTensorsSecondCell->SetNonConstantConductivities(&hetero_intra_conductivities);
    }
    else
    {
        mpIntracellularConductivityTensorsSecondCell->SetConstantConductivities(mIntracellularConductivitiesSecondCell);
    }

    mpIntracellularConductivityTensorsSecondCell->Init(this->mpMesh);
    HeartEventHandler::EndEvent(HeartEventHandler::READ_MESH);
}

template <unsigned SPACE_DIM>
bool ExtendedBidomainTissue<SPACE_DIM>::HasTheUserSuppliedExtracellularStimulus()
{
    return mUserSuppliedExtracellularStimulus;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetUserSuppliedExtracellularStimulus(bool flag)
{
    mUserSuppliedExtracellularStimulus = flag;
}

template <unsigned SPACE_DIM>
const std::vector<AbstractCardiacCellInterface*>& ExtendedBidomainTissue<SPACE_DIM>::rGetSecondCellsDistributed() const
{
    return mCellsDistributedSecondCell;
}

template <unsigned SPACE_DIM>
const std::vector<double>& ExtendedBidomainTissue<SPACE_DIM>::rGetGapsDistributed() const
{
    return mGgapDistributed;
}

template <unsigned SPACE_DIM>
const std::vector<boost::shared_ptr<AbstractStimulusFunction> >& ExtendedBidomainTissue<SPACE_DIM>::rGetExtracellularStimulusDistributed() const
{
    return mExtracellularStimuliDistributed;
}


template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::CreateExtracellularConductivityTensors()
{
    if (this->mpConfig->IsMeshProvided() && this->mpConfig->GetLoadMesh())
    {
        assert(this->mFibreFilePathNoExtension != "");
        switch (this->mpConfig->GetConductivityMedia())
        {
            case cp::media_type::Orthotropic:
            {
                mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder ortho_file(this->mFibreFilePathNoExtension + ".ortho", RelativeTo::AbsoluteOrCwd);
                assert(ortho_file.Exists());
                mpExtracellularConductivityTensors->SetFibreOrientationFile(ortho_file);
                break;
            }

            case cp::media_type::Axisymmetric:
            {
                mpExtracellularConductivityTensors =  new AxisymmetricConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder axi_file(this->mFibreFilePathNoExtension + ".axi", RelativeTo::AbsoluteOrCwd);
                assert(axi_file.Exists());
                mpExtracellularConductivityTensors->SetFibreOrientationFile(axi_file);
                break;
            }

            case cp::media_type::NoFibreOrientation:
                mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                break;

            default :
                NEVER_REACHED;
        }
    }
    else // no fibre orientation assumed
    {
        mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
    }

    c_vector<double, SPACE_DIM> extra_conductivities;
    this->mpConfig->GetExtracellularConductivities(extra_conductivities);

    // this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
    // a pointer to it and we don't want it to go out of scope before Init() is called
    unsigned num_elements = this->mpMesh->GetNumElements();
    std::vector<c_vector<double, SPACE_DIM> > hetero_extra_conductivities;

    if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
    {
        try
        {
            assert(hetero_extra_conductivities.size()==0);
            //initialise with the values of teh default conductivity tensor
            hetero_extra_conductivities.resize(num_elements, extra_conductivities);
        }
        catch(std::bad_alloc &badAlloc)
        {
#define COVERAGE_IGNORE
            std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
            PetscTools::ReplicateException(true);
            throw badAlloc;
#undef COVERAGE_IGNORE
        }
        PetscTools::ReplicateException(false);

        std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
        std::vector< c_vector<double,3> > intra_h_conductivities;
        std::vector< c_vector<double,3> > extra_h_conductivities;
        HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
                                                                intra_h_conductivities,
                                                                extra_h_conductivities);
        unsigned local_element_index = 0;
        for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator iter = (this->mpMesh)->GetElementIteratorBegin();
             iter != (this->mpMesh)->GetElementIteratorEnd();
             ++iter)
        {
            //unsigned element_index = iter->GetIndex();
            // if element centroid is contained in the region
            ChastePoint<SPACE_DIM> element_centroid(iter->CalculateCentroid());
            for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
            {
                // if element centroid is contained in the region
                if ( conductivities_heterogeneity_areas[region_index]->DoesContain( element_centroid ) )
                {
                    //We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
                    for (unsigned i=0; i<SPACE_DIM; i++)
                    {
                        hetero_extra_conductivities[local_element_index][i] = extra_h_conductivities[region_index][i];
                    }
                }
            }
            local_element_index++;
        }

        mpExtracellularConductivityTensors->SetNonConstantConductivities(&hetero_extra_conductivities);
    }
    else
    {
        mpExtracellularConductivityTensors->SetConstantConductivities(extra_conductivities);
    }
    mpExtracellularConductivityTensors->Init(this->mpMesh);
}

template <unsigned SPACE_DIM>
ExtendedBidomainTissue<SPACE_DIM>::~ExtendedBidomainTissue()
{
    // Delete (second) cells
    for (std::vector<AbstractCardiacCellInterface*>::iterator cell_iterator = mCellsDistributedSecondCell.begin();
         cell_iterator != mCellsDistributedSecondCell.end();
         ++cell_iterator)
    {
        delete (*cell_iterator);
    }

    if (mpExtracellularConductivityTensors)
    {
        delete mpExtracellularConductivityTensors;
    }

    if (mpIntracellularConductivityTensorsSecondCell)
    {
        delete mpIntracellularConductivityTensorsSecondCell;
    }
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetIntracellularConductivitiesSecondCell(c_vector<double, SPACE_DIM> conductivities)
{
    for (unsigned i = 0; i < SPACE_DIM; i++)
    {
        mIntracellularConductivitiesSecondCell[i] = conductivities[i];
    }
}

template <unsigned SPACE_DIM>
c_vector<double, SPACE_DIM>  ExtendedBidomainTissue<SPACE_DIM>::GetIntracellularConductivitiesSecondCell() const
{
    return mIntracellularConductivitiesSecondCell;
}

template <unsigned SPACE_DIM>
const c_matrix<double, SPACE_DIM, SPACE_DIM>& ExtendedBidomainTissue<SPACE_DIM>::rGetExtracellularConductivityTensor(unsigned elementIndex)
{
    assert(mpExtracellularConductivityTensors);
    if (this->mpConductivityModifier==NULL)
    {
        return (*mpExtracellularConductivityTensors)[elementIndex];
    }
    else
    {
        return this->mpConductivityModifier->rGetModifiedConductivityTensor(elementIndex, (*mpExtracellularConductivityTensors)[elementIndex], 1u);
    }
}

template <unsigned SPACE_DIM>
const c_matrix<double, SPACE_DIM, SPACE_DIM>& ExtendedBidomainTissue<SPACE_DIM>::rGetIntracellularConductivityTensorSecondCell(unsigned elementIndex)
{
    assert(mpIntracellularConductivityTensorsSecondCell);
    if (this->mpConductivityModifier==NULL)
    {
        return (*mpIntracellularConductivityTensorsSecondCell)[elementIndex];
    }
    else
    {
        return this->mpConductivityModifier->rGetModifiedConductivityTensor(elementIndex, (*mpIntracellularConductivityTensorsSecondCell)[elementIndex], 2u);
    }
}

template <unsigned SPACE_DIM>
AbstractCardiacCellInterface* ExtendedBidomainTissue<SPACE_DIM>::GetCardiacSecondCell( unsigned globalIndex )
{
    return mCellsDistributedSecondCell[globalIndex - this->mpDistributedVectorFactory->GetLow()];
}

template <unsigned SPACE_DIM>
boost::shared_ptr<AbstractStimulusFunction> ExtendedBidomainTissue<SPACE_DIM>::GetExtracellularStimulus( unsigned globalIndex )
{
    return mExtracellularStimuliDistributed[globalIndex - this->mpDistributedVectorFactory->GetLow()];
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SolveCellSystems(Vec existingSolution, double time, double nextTime, bool updateVoltage)
{
    HeartEventHandler::BeginEvent(HeartEventHandler::SOLVE_ODES);

    DistributedVector dist_solution = this->mpDistributedVectorFactory->CreateDistributedVector(existingSolution);
    DistributedVector::Stripe V_first_cell(dist_solution, 0);
    DistributedVector::Stripe V_second_cell(dist_solution, 1);
    DistributedVector::Stripe phi_e(dist_solution, 2);

    for (DistributedVector::Iterator index = dist_solution.Begin();
         index != dist_solution.End();
         ++index)
    {
        // overwrite the voltage with the input value
        this->mCellsDistributed[index.Local]->SetVoltage( V_first_cell[index] );
        mCellsDistributedSecondCell[index.Local]->SetVoltage( V_second_cell[index] );
        try
        {
            // solve
            // Note: Voltage should not be updated. GetIIonic will be called later
            // and needs the old voltage. The voltage will be updated from the pde.
            this->mCellsDistributed[index.Local]->ComputeExceptVoltage(time, nextTime);
            mCellsDistributedSecondCell[index.Local]->ComputeExceptVoltage(time, nextTime);
        }
        catch (Exception &e)
        {
#define COVERAGE_IGNORE
            PetscTools::ReplicateException(true);
            throw e;
#undef COVERAGE_IGNORE
        }

        // update the Iionic and stimulus caches
        this->UpdateCaches(index.Global, index.Local, nextTime);//in parent class
        UpdateAdditionalCaches(index.Global, index.Local, nextTime);//extended bidomain specific caches
    }
    PetscTools::ReplicateException(false);
    HeartEventHandler::EndEvent(HeartEventHandler::SOLVE_ODES);

    HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
    if ( this->mDoCacheReplication )
    {
        this->ReplicateCaches();
        ReplicateAdditionalCaches();//extended bidomain specific caches
    }
    HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::UpdateAdditionalCaches(unsigned globalIndex, unsigned localIndex, double nextTime)
{
    mIionicCacheReplicatedSecondCell[globalIndex] = mCellsDistributedSecondCell[localIndex]->GetIIonic();
    mIntracellularStimulusCacheReplicatedSecondCell[globalIndex] = mCellsDistributedSecondCell[localIndex]->GetIntracellularStimulus(nextTime);
    mExtracellularStimulusCacheReplicated[globalIndex] = mExtracellularStimuliDistributed[localIndex]->GetStimulus(nextTime);
    mGgapCacheReplicated[globalIndex] = mGgapDistributed[localIndex];
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::ReplicateAdditionalCaches()
{
    mIionicCacheReplicatedSecondCell.Replicate(this->mpDistributedVectorFactory->GetLow(), this->mpDistributedVectorFactory->GetHigh());
    mIntracellularStimulusCacheReplicatedSecondCell.Replicate(this->mpDistributedVectorFactory->GetLow(), this->mpDistributedVectorFactory->GetHigh());
    mExtracellularStimulusCacheReplicated.Replicate(this->mpDistributedVectorFactory->GetLow(), this->mpDistributedVectorFactory->GetHigh());
    mGgapCacheReplicated.Replicate(this->mpDistributedVectorFactory->GetLow(), this->mpDistributedVectorFactory->GetHigh());
}

template <unsigned SPACE_DIM>
ReplicatableVector& ExtendedBidomainTissue<SPACE_DIM>::rGetIionicCacheReplicatedSecondCell()
{
    return mIionicCacheReplicatedSecondCell;
}

template <unsigned SPACE_DIM>
ReplicatableVector& ExtendedBidomainTissue<SPACE_DIM>::rGetIntracellularStimulusCacheReplicatedSecondCell()
{
    return mIntracellularStimulusCacheReplicatedSecondCell;
}

template <unsigned SPACE_DIM>
ReplicatableVector& ExtendedBidomainTissue<SPACE_DIM>::rGetExtracellularStimulusCacheReplicated()
{
    return mExtracellularStimulusCacheReplicated;
}

template <unsigned SPACE_DIM>
ReplicatableVector& ExtendedBidomainTissue<SPACE_DIM>::rGetGgapCacheReplicated()
{
    return mGgapCacheReplicated;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetAmFirstCell()
{
    return mAmFirstCell;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetAmSecondCell()
{
    return mAmSecondCell;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetAmGap()
{
    return mAmGap;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetCmFirstCell()
{
    return mCmFirstCell;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetCmSecondCell()
{
    return mCmSecondCell;
}

template <unsigned SPACE_DIM>
double ExtendedBidomainTissue<SPACE_DIM>::GetGGap()
{
    return mGGap;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetAmFirstCell(double value)
{
    mAmFirstCell = value;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetAmSecondCell(double value)
{
    mAmSecondCell = value;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetAmGap(double value)
{
    mAmGap = value;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetGGap(double value)
{
    mGGap = value;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetCmFirstCell(double value)
{
    mCmFirstCell = value;
}

template <unsigned SPACE_DIM>
void ExtendedBidomainTissue<SPACE_DIM>::SetCmSecondCell(double value)
{
    mCmSecondCell = value;
}

// Explicit instantiation

template class ExtendedBidomainTissue<1>;
template class ExtendedBidomainTissue<2>;
template class ExtendedBidomainTissue<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainTissue)