Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
BidomainWithBathAssembler.cpp
1
2/*
3
4Copyright (c) 2005-2024, University of Oxford.
5All rights reserved.
6
7University of Oxford means the Chancellor, Masters and Scholars of the
8University of Oxford, having an administrative office at Wellington
9Square, Oxford OX1 2JD, UK.
10
11This file is part of Chaste.
12
13Redistribution and use in source and binary forms, with or without
14modification, are permitted provided that the following conditions are met:
15 * Redistributions of source code must retain the above copyright notice,
16 this list of conditions and the following disclaimer.
17 * Redistributions in binary form must reproduce the above copyright notice,
18 this list of conditions and the following disclaimer in the documentation
19 and/or other materials provided with the distribution.
20 * Neither the name of the University of Oxford nor the names of its
21 contributors may be used to endorse or promote products derived from this
22 software without specific prior written permission.
23
24THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
25AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
26IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
27ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
28LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
29CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
30GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
31HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
32LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
33OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
34
35*/
36
37#include "BidomainWithBathAssembler.hpp"
38
39template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
40c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)>
42 c_vector<double, ELEMENT_DIM+1> &rPhi,
43 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
45 c_vector<double,2> &rU,
46 c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
48{
49 if (!HeartRegionCode::IsRegionBath( pElement->GetUnsignedAttribute() )) // ie if a tissue element
50 {
51 return BidomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(rPhi,rGradPhi,rX,rU,rGradU,pElement);
52 }
53 else // bath element
54 {
55 double bath_cond=HeartConfig::Instance()->GetBathConductivity(pElement->GetUnsignedAttribute());
56
57 c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_b_grad_phi =
58 bath_cond * prod(trans(rGradPhi), rGradPhi);
59
60 c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ret = zero_matrix<double>(2*(ELEMENT_DIM+1));
61
62 // even rows, even columns
63 //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
64 //slice00(ret, slice (0, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
65 //slice00 = 0;
66
67 // odd rows, even columns
68 //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
69 //slice10(ret, slice (1, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
70 //slice10 = 0
71
72 // even rows, odd columns
73 //matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
74 //slice01(ret, slice (0, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
75 //slice01 = 0;
76
77 // odd rows, odd columns
78 matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
79 slice11(ret, slice (1, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
80 slice11 = grad_phi_sigma_b_grad_phi;
81
82 return ret;
83 }
84}
85
86// Explicit instantiation
unsigned GetUnsignedAttribute()
virtual c_matrix< double, 2 *(ELEMENT_DIM+1), 2 *(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, 2 > &rU, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
virtual c_matrix< double, 2 *(ELEMENT_DIM+1), 2 *(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, 2 > &rU, c_matrix< double, 2, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
double GetBathConductivity(unsigned bathRegion=UINT_MAX) const
static HeartConfig * Instance()
static bool IsRegionBath(HeartRegionType regionId)