BidomainWithBathAssembler.cpp

/*

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*/

#include "BidomainWithBathAssembler.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)>
    BidomainWithBathAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(
            c_vector<double, ELEMENT_DIM+1> &rPhi,
            c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
            ChastePoint<SPACE_DIM> &rX,
            c_vector<double,2> &rU,
            c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
            Element<ELEMENT_DIM,SPACE_DIM>* pElement)
{
    if (!HeartRegionCode::IsRegionBath( pElement->GetUnsignedAttribute() )) // ie if a tissue element
    {
        return BidomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(rPhi,rGradPhi,rX,rU,rGradU,pElement);
    }
    else // bath element
    {
        double bath_cond=HeartConfig::Instance()->GetBathConductivity(pElement->GetAttribute());

        c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_b_grad_phi =
            bath_cond * prod(trans(rGradPhi), rGradPhi);

        c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ret = zero_matrix<double>(2*(ELEMENT_DIM+1));

        // even rows, even columns
        //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
        //slice00(ret, slice (0, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
        //slice00 = 0;

        // odd rows, even columns
        //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
        //slice10(ret, slice (1, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
        //slice10 = 0

        // even rows, odd columns
        //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
        //slice01(ret, slice (0, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
        //slice01 = 0;

        // odd rows, odd columns
        matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
        slice11(ret, slice (1, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
        slice11 = grad_phi_sigma_b_grad_phi;

        return ret;
    }
}



// explicit instantiation

template class BidomainWithBathAssembler<1,1>;
template class BidomainWithBathAssembler<2,2>;
template class BidomainWithBathAssembler<3,3>;