BidomainAssembler.cpp

/*

Copyright (c) 2005-2012, University of Oxford.
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   software without specific prior written permission.

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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/

#include "BidomainAssembler.hpp"
#include "PdeSimulationTime.hpp"
#include "UblasIncludes.hpp"
#include <boost/numeric/ublas/vector_proxy.hpp>


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)>
    BidomainAssembler<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)
{
    // get bidomain parameters
    double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
    double Cm = mpConfig->GetCapacitance();

    const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_i = this->mpCardiacTissue->rGetIntracellularConductivityTensor(pElement->GetIndex());
    const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_e = this->mpCardiacTissue->rGetExtracellularConductivityTensor(pElement->GetIndex());


    c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp = prod(sigma_i, rGradPhi);
    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_i_grad_phi =
        prod(trans(rGradPhi), temp);

    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> basis_outer_prod =
        outer_prod(rPhi, rPhi);

    c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp2 = prod(sigma_e, rGradPhi);
    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_e_grad_phi =
        prod(trans(rGradPhi), temp2);


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

    // 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 = (Am*Cm*PdeSimulationTime::GetPdeTimeStepInverse())*basis_outer_prod + grad_phi_sigma_i_grad_phi;

    // 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 = grad_phi_sigma_i_grad_phi;

    // 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 = grad_phi_sigma_i_grad_phi;

    // 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_i_grad_phi + grad_phi_sigma_e_grad_phi;

    return ret;
}




template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainAssembler<ELEMENT_DIM,SPACE_DIM>::BidomainAssembler(
            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            BidomainTissue<SPACE_DIM>* pTissue,
            unsigned numQuadPoints)
    : AbstractCardiacFeVolumeIntegralAssembler<ELEMENT_DIM,SPACE_DIM,2,false,true,CARDIAC>(pMesh,pTissue,numQuadPoints)
{
    assert(pTissue != NULL);
    mpConfig = HeartConfig::Instance();
}



// explicit instantiation

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