AxisymmetricConductivityTensors.cpp

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*/

#include <vector>
#include "UblasIncludes.hpp"
#include "AxisymmetricConductivityTensors.hpp"
#include "Exception.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AxisymmetricConductivityTensors<ELEMENT_DIM, SPACE_DIM>::AxisymmetricConductivityTensors()
{
    if (SPACE_DIM != 3)
    {
        EXCEPTION("Axisymmetric anisotropic conductivity only makes sense in 3D");
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AxisymmetricConductivityTensors<ELEMENT_DIM, SPACE_DIM>::SetConstantConductivities(c_vector<double, 3> constantConductivities)
{
    //assert(SPACE_DIM == 3);//Otherwise constructor would have thrown
    if (constantConductivities[1] != constantConductivities[2])
    {
        EXCEPTION("Axisymmetric media defined: transversal and normal conductivities should have the same value");
    }

    this->mUseNonConstantConductivities = false;
    this->mConstantConductivities = constantConductivities;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AxisymmetricConductivityTensors<ELEMENT_DIM, SPACE_DIM>::Init(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> *pMesh)
{
    this->mpMesh = pMesh;

    if (!this->mUseNonConstantConductivities && !this->mUseFibreOrientation)
    {
        // Constant tensor for every element
        c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));

        for (unsigned dim=0; dim<SPACE_DIM; dim++)
        {
            assert(this->mConstantConductivities(dim) != DBL_MAX);
            conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
        }
        this->mTensors.push_back(conductivity_matrix);
    }
    else
    {
        c_vector<double,SPACE_DIM> fibre_vector((zero_vector<double>(SPACE_DIM)));
        fibre_vector[0]=1.0;

        if (this->mUseFibreOrientation)
        {
            // open file
            this->mFileReader.reset(new FibreReader<SPACE_DIM>(this->mFibreOrientationFile, AXISYM));
            if (this->mFileReader->GetNumLinesOfData() != this->mpMesh->GetNumElements())
            {
                EXCEPTION("The size of the fibre file does not match the number of elements in the mesh");
            }
        }

        if (this->mUseNonConstantConductivities)
        {
            if (this->mpNonConstantConductivities->size() != this->mpMesh->GetNumLocalElements())
            {
                EXCEPTION("The size of the conductivities vector does not match the number of elements in the mesh");
            }
        }

        // reserve() allocates all the memory at once, more efficient than relying
        // on the automatic reallocation scheme.
        this->mTensors.reserve(this->mpMesh->GetNumLocalElements());

        c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));

        unsigned local_element_index = 0;

        for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
             it != this->mpMesh->GetElementIteratorEnd();
             ++it)
        {
            /*
             *  For every element of the mesh we compute its tensor like (from
             * "Laminar Arrangement of VentricularMyocites Influences Electrical
             * Behavior of the Heart", Darren et al. 2007):
             *
             *                         [g_f  0   0 ] [a_f']
             *  tensor = [a_f a_l a_n] [ 0  g_l  0 ] [a_l']
             *                         [ 0   0  g_n] [a_n']
             *
             *              [x_i]
             *  where a_i = [y_i], i={f,l,n} are read from the fibre orientation file and
             *              [z_i]
             *
             *  g_f = fibre/longitudinal conductivity (constant or element specific)
             *  g_l = laminar/transverse conductivity (constant or element specific)
             *  g_n = normal conductivity (constant or element specific)
             *
             *
             *  For axisymmetric anisotropic media (g_l = g_n) we can simplify previous expression to
             *
             *
             *  tensor = g_l * I + (g_f - g_l) * a_f * a_f'
             *
             */

            if (this->mUseNonConstantConductivities)
            {
                for (unsigned dim=0; dim<SPACE_DIM; dim++)
                {
                    conductivity_matrix(dim,dim) = (*this->mpNonConstantConductivities)[local_element_index][dim];
                }
            }
            else
            {
                for (unsigned dim=0; dim<SPACE_DIM; dim++)
                {
                    assert(this->mConstantConductivities(dim) != DBL_MAX);
                    conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
                }
            }

            if (this->mUseFibreOrientation)
            {
                unsigned current_fibre_global_index = it->GetIndex();
                this->mFileReader->GetFibreVector(current_fibre_global_index, fibre_vector);
            }

            this->mTensors.push_back( conductivity_matrix(1,1) * identity_matrix<double>(SPACE_DIM) +
                                      (conductivity_matrix(0,0) - conductivity_matrix(1,1)) * outer_prod(fibre_vector,fibre_vector));

            local_element_index++;
        }

        assert(this->mTensors.size() == this->mpMesh->GetNumLocalElements());
        assert(this->mTensors.size() == local_element_index);

        if (this->mUseFibreOrientation)
        {
            // close fibre file
            this->mFileReader.reset();
        }
    }

    this->mInitialised = true;
}

// Explicit instantiation

// only makes sense for 3d elements in 3d, but we need the other to compile
// AbstractCardiacTissue and BidomainTissue.
template class AxisymmetricConductivityTensors<1,1>;
template class AxisymmetricConductivityTensors<1,2>;
template class AxisymmetricConductivityTensors<1,3>;
template class AxisymmetricConductivityTensors<2,2>;
template class AxisymmetricConductivityTensors<2,3>;
template class AxisymmetricConductivityTensors<3,3>;