Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ExtendedBidomainAssembler.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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34*/
35
36#include "ExtendedBidomainAssembler.hpp"
37
38#include "Exception.hpp"
39#include "DistributedVector.hpp"
40#include "PdeSimulationTime.hpp"
41#include "ConstBoundaryCondition.hpp"
42
43template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
44c_matrix<double,3*(ELEMENT_DIM+1),3*(ELEMENT_DIM+1)>
46 c_vector<double, ELEMENT_DIM+1> &rPhi,
47 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
49 c_vector<double,3> &rU,
50 c_matrix<double, 3, SPACE_DIM> &rGradU /* not used */,
52{
53 // get bidomain parameters
54 double Am1 = mpExtendedBidomainTissue->GetAmFirstCell();
55 double Am2 = mpExtendedBidomainTissue->GetAmSecondCell();
56 double Cm1 = mpExtendedBidomainTissue->GetCmFirstCell();
57 double Cm2 = mpExtendedBidomainTissue->GetCmSecondCell();
58
59 const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_i_first_cell = mpExtendedBidomainTissue->rGetIntracellularConductivityTensor(pElement->GetIndex());
60 const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_i_second_cell = mpExtendedBidomainTissue->rGetIntracellularConductivityTensorSecondCell(pElement->GetIndex());
61 const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_e = mpExtendedBidomainTissue->rGetExtracellularConductivityTensor(pElement->GetIndex());
62
63 double delta_t = PdeSimulationTime::GetPdeTimeStep();
64
65 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp_1 = prod(sigma_i_first_cell, rGradPhi);
66 c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_i_first_cell_grad_phi =
67 prod(trans(rGradPhi), temp_1);
68
69 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp_2 = prod(sigma_i_second_cell, rGradPhi);
70 c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_i_second_cell_grad_phi =
71 prod(trans(rGradPhi), temp_2);
72
73 c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> basis_outer_prod =
74 outer_prod(rPhi, rPhi);
75
76 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp_ext = prod(sigma_e, rGradPhi);
77 c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_e_grad_phi =
78 prod(trans(rGradPhi), temp_ext);
79
80
81 c_matrix<double,3*(ELEMENT_DIM+1),3*(ELEMENT_DIM+1)> ret;
82
83 // first equation, first unknown
84 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
85 slice100(ret, slice (0, 3, ELEMENT_DIM+1), slice (0, 3, ELEMENT_DIM+1));
86 slice100 = (Am1*Cm1/delta_t)*basis_outer_prod + grad_phi_sigma_i_first_cell_grad_phi;
87
88 // first equation, second unknown
89 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
90 slice200(ret, slice (0, 3, ELEMENT_DIM+1), slice (1, 3, ELEMENT_DIM+1));
91 slice200 = zero_matrix<double>(ELEMENT_DIM+1, ELEMENT_DIM+1);
92
93 // first equation, third unknown
94 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
95 slice300(ret, slice (0, 3, ELEMENT_DIM+1), slice (2, 3, ELEMENT_DIM+1));
96 slice300 = grad_phi_sigma_i_first_cell_grad_phi;
97
98 // second equation, first unknown
99 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
100 slice010(ret, slice (1, 3, ELEMENT_DIM+1), slice (0, 3, ELEMENT_DIM+1));
101 slice010 = zero_matrix<double>(ELEMENT_DIM+1, ELEMENT_DIM+1);
102
103 // second equation, second unknown
104 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
105 slice020(ret, slice (1, 3, ELEMENT_DIM+1), slice (1, 3, ELEMENT_DIM+1));
106 slice020 = (Am2*Cm2/delta_t)*basis_outer_prod + grad_phi_sigma_i_second_cell_grad_phi;
107
108 // second equation, third unknown
109 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
110 slice030(ret, slice (1, 3, ELEMENT_DIM+1), slice (2, 3, ELEMENT_DIM+1));
111 slice030 = grad_phi_sigma_i_second_cell_grad_phi;
112
113 // third equation, first unknown
114 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
115 slice001(ret, slice (2, 3, ELEMENT_DIM+1), slice (0, 3, ELEMENT_DIM+1));
116 slice001 = grad_phi_sigma_i_first_cell_grad_phi;
117
118 // third equation, second unknown
119 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
120 slice002(ret, slice (2, 3, ELEMENT_DIM+1), slice (1, 3, ELEMENT_DIM+1));
121 slice002 = grad_phi_sigma_i_second_cell_grad_phi;
122
123 // third equation, third unknown
124 matrix_slice<c_matrix<double, 3*ELEMENT_DIM+3, 3*ELEMENT_DIM+3> >
125 slice003(ret, slice (2, 3, ELEMENT_DIM+1), slice (2, 3, ELEMENT_DIM+1));
126 slice003 = grad_phi_sigma_e_grad_phi + grad_phi_sigma_i_first_cell_grad_phi + grad_phi_sigma_i_second_cell_grad_phi;
127
128 return ret;
129}
130
131template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
135 : AbstractCardiacFeVolumeIntegralAssembler<ELEMENT_DIM,SPACE_DIM,3,true,true,NORMAL>(pMesh,pTissue),
136 mpExtendedBidomainTissue(pTissue)
137{
138 assert(pTissue != NULL);
139}
140
141template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
145
146// Explicit instantiation
147template class ExtendedBidomainAssembler<1,1>;
148template class ExtendedBidomainAssembler<2,2>;
149template class ExtendedBidomainAssembler<3,3>;
unsigned GetIndex() const
ExtendedBidomainAssembler(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, ExtendedBidomainTissue< SPACE_DIM > *pTissue)
virtual c_matrix< double, 3 *(ELEMENT_DIM+1), 3 *(ELEMENT_DIM+1)> ComputeMatrixTerm(c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 3 > &rU, c_matrix< double, 3, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
static double GetPdeTimeStep()