BidomainCorrectionTermAssembler.cpp

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#include "BidomainCorrectionTermAssembler.hpp"
#include "UblasIncludes.hpp"
#include <boost/numeric/ublas/vector_proxy.hpp>
 
template<unsigned ELEM_DIM, unsigned SPACE_DIM>
BidomainCorrectionTermAssembler<ELEM_DIM,SPACE_DIM>::BidomainCorrectionTermAssembler(
     AbstractTetrahedralMesh<ELEM_DIM,SPACE_DIM>* pMesh,
     BidomainTissue<SPACE_DIM>* pTissue)
        : AbstractCorrectionTermAssembler<ELEM_DIM,SPACE_DIM,2>(pMesh,pTissue)
{
    mpConfig = HeartConfig::Instance();
    assert(mpConfig->GetUseStateVariableInterpolation());
}
 
template<unsigned ELEM_DIM, unsigned SPACE_DIM>
c_vector<double,2*(ELEM_DIM+1)> BidomainCorrectionTermAssembler<ELEM_DIM,SPACE_DIM>::ComputeVectorTerm(
    c_vector<double, ELEM_DIM+1> &rPhi,
    c_matrix<double, SPACE_DIM, ELEM_DIM+1> &rGradPhi /* not used */,
    ChastePoint<SPACE_DIM> &rX /* not used */,
    c_vector<double,2> &rU,
    c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
    Element<ELEM_DIM,SPACE_DIM>* pElement /* not used */)
{
    double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
 
    // compute the ionic current at this quadrature point using the
    // interpolated state variables, and a random choice of cell (all
    // should be the same)
    unsigned node_global_index = pElement->GetNodeGlobalIndex(0);
    AbstractCardiacCellInterface* p_any_cell = this->mpCardiacTissue->GetCardiacCellOrHaloCell(node_global_index);
    double ionic_sv_interp = p_any_cell->GetIIonic(&(this->mStateVariablesAtQuadPoint));
 
    c_vector<double,2*(ELEM_DIM+1)> ret;
 
    ublas::vector_slice<c_vector<double, 2*(ELEM_DIM+1)> > slice_V  (ret, slice (0, 2, ELEM_DIM+1));
    ublas::vector_slice<c_vector<double, 2*(ELEM_DIM+1)> > slice_Phi(ret, slice (1, 2, ELEM_DIM+1));
 
    // add on the SVI ionic current, and take away the original NCI (linearly
    // interpolated ionic current) that would have been added as part of
    // the matrix-based assembly stage.
    noalias(slice_V)   = rPhi * (-Am) * ( ionic_sv_interp - this->mIionicInterp );
    // no correction needed for elliptic equation
    noalias(slice_Phi) = zero_vector<double>(ELEM_DIM+1);
 
    return ret;
}
 
// Explicit instantiation
template class BidomainCorrectionTermAssembler<1,1>;
template class BidomainCorrectionTermAssembler<2,2>;
template class BidomainCorrectionTermAssembler<3,3>;