BidomainTissue.cpp

/*

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*/

#include "BidomainTissue.hpp"

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

template <unsigned SPACE_DIM>
BidomainTissue<SPACE_DIM>::BidomainTissue(
            AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory,
            bool exchangeHalos)
    : AbstractCardiacTissue<SPACE_DIM>(pCellFactory, exchangeHalos)
{
    CreateExtracellularConductivityTensors();
}

template <unsigned SPACE_DIM>
BidomainTissue<SPACE_DIM>::BidomainTissue(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh)
        :  AbstractCardiacTissue<SPACE_DIM>(pMesh)
{
    CreateExtracellularConductivityTensors();
}

template <unsigned SPACE_DIM>
void BidomainTissue<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 // Slab defined in config file or SetMesh() called; 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_local_elements = this->mpMesh->GetNumLocalElements();
    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 the default conductivity tensor
            hetero_extra_conductivities.resize(num_local_elements, extra_conductivities);
        }
        // LCOV_EXCL_START
        catch(std::bad_alloc &r_bad_alloc)
        {
            std::cout << "Failed to allocate std::vector of size " << num_local_elements << std::endl;
            PetscTools::ReplicateException(true);
            throw r_bad_alloc;
        }
        // LCOV_EXCL_STOP

        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)
        {
            // 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>
BidomainTissue<SPACE_DIM>::~BidomainTissue()
{
    if (mpExtracellularConductivityTensors)
    {
        delete mpExtracellularConductivityTensors;
    }
}


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

// Explicit instantiation
template class BidomainTissue<1>;
template class BidomainTissue<2>;
template class BidomainTissue<3>;

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