Chaste  Release::2018.1
BidomainCorrectionTermAssembler.cpp
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35 
36 
37 #include "BidomainCorrectionTermAssembler.hpp"
38 #include "UblasIncludes.hpp"
39 #include <boost/numeric/ublas/vector_proxy.hpp>
40 
41 template<unsigned ELEM_DIM, unsigned SPACE_DIM>
45  : AbstractCorrectionTermAssembler<ELEM_DIM,SPACE_DIM,2>(pMesh,pTissue)
46 {
49 }
50 
51 template<unsigned ELEM_DIM, unsigned SPACE_DIM>
53  c_vector<double, ELEM_DIM+1> &rPhi,
54  c_matrix<double, SPACE_DIM, ELEM_DIM+1> &rGradPhi /* not used */,
55  ChastePoint<SPACE_DIM> &rX /* not used */,
56  c_vector<double,2> &rU,
57  c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
58  Element<ELEM_DIM,SPACE_DIM>* pElement /* not used */)
59 {
60  double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
61 
62  // compute the ionic current at this quadrature point using the
63  // interpolated state variables, and a random choice of cell (all
64  // should be the same)
65  unsigned node_global_index = pElement->GetNodeGlobalIndex(0);
66  AbstractCardiacCellInterface* p_any_cell = this->mpCardiacTissue->GetCardiacCellOrHaloCell(node_global_index);
67  double ionic_sv_interp = p_any_cell->GetIIonic(&(this->mStateVariablesAtQuadPoint));
68 
69  c_vector<double,2*(ELEM_DIM+1)> ret;
70 
71  ublas::vector_slice<c_vector<double, 2*(ELEM_DIM+1)> > slice_V (ret, slice (0, 2, ELEM_DIM+1));
72  ublas::vector_slice<c_vector<double, 2*(ELEM_DIM+1)> > slice_Phi(ret, slice (1, 2, ELEM_DIM+1));
73 
74  // add on the SVI ionic current, and take away the original NCI (linearly
75  // interpolated ionic current) that would have been added as part of
76  // the matrix-based assembly stage.
77  noalias(slice_V) = rPhi * (-Am) * ( ionic_sv_interp - this->mIionicInterp );
78  // no correction needed for elliptic equation
79  noalias(slice_Phi) = zero_vector<double>(ELEM_DIM+1);
80 
81  return ret;
82 }
83 
84 // Explicit instantiation
BidomainCorrectionTermAssembler(AbstractTetrahedralMesh< ELEM_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue)
unsigned GetNodeGlobalIndex(unsigned localIndex) const
bool GetUseStateVariableInterpolation() const
virtual double GetIIonic(const std::vector< double > *pStateVariables=NULL)=0
c_vector< double, 2 *(ELEM_DIM+1)> ComputeVectorTerm(c_vector< double, ELEM_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEM_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 2 > &rU, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEM_DIM, SPACE_DIM > *pElement)
static HeartConfig * Instance()