Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
OrthotropicConductivityTensors.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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15 this list of conditions and the following disclaimer.
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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33
34*/
35
36#include "OrthotropicConductivityTensors.hpp"
37#include "Exception.hpp"
38
39template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
41{
42 this->mpMesh = pMesh;
43
44 if (!this->mUseNonConstantConductivities && !this->mUseFibreOrientation)
45 {
46 // Constant tensor for every element
47 c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));
48
49 for (unsigned dim=0; dim<SPACE_DIM; dim++)
50 {
51 assert(this->mConstantConductivities(dim) != DBL_MAX);
52 conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
53 }
54
55 this->mTensors.push_back(conductivity_matrix);
56 }
57 else
58 {
59 c_matrix<double,SPACE_DIM,SPACE_DIM> orientation_matrix((identity_matrix<double>(SPACE_DIM)));
60
61 if (this->mUseFibreOrientation)
62 {
63 // open file
64 this->mFileReader.reset(new FibreReader<SPACE_DIM>(this->mFibreOrientationFile, ORTHO));
65 if (this->mFileReader->GetNumLinesOfData() != this->mpMesh->GetNumElements())
66 {
67 EXCEPTION("The size of the fibre file does not match the number of elements in the mesh");
68 }
69 }
70
71 if (this->mUseNonConstantConductivities)
72 {
73 if (this->mpNonConstantConductivities->size() != this->mpMesh->GetNumLocalElements())
74 {
75 EXCEPTION("The size of the conductivities vector does not match the number of elements in the mesh");
76 }
77 }
78
79 // reserve() allocates all the memory at once, more efficient than relying
80 // on the automatic reallocation scheme.
81 this->mTensors.reserve(this->mpMesh->GetNumLocalElements());
82
83 c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));
84
85 unsigned local_element_index = 0;
86
87 for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
88 it != this->mpMesh->GetElementIteratorEnd();
89 ++it)
90 {
91 /*
92 * For every element of the mesh we compute its tensor like (from
93 * "Laminar Arrangement of Ventricular Myocytes Influences Electrical
94 * Behavior of the Heart, DA Hooks et al. 2007):
95 *
96 *
97 * [g_f 0 0 ] [a_f']
98 * tensor = [a_f a_l a_n] [ 0 g_l 0 ] [a_l']
99 * [ 0 0 g_n] [a_n']
100 *
101 * [x_i]
102 * where a_i = [y_i], i={f,l,n} are read from the fibre orientation file and
103 * [z_i]
104 *
105 * g_f = fibre/longitudinal conductivity (constant or element specific)
106 * g_l = laminar/transverse conductivity (constant or element specific)
107 * g_n = normal conductivity (constant or element specific)
108 *
109 */
110 if (this->mUseNonConstantConductivities)
111 {
112 for (unsigned dim=0; dim<SPACE_DIM; dim++)
113 {
114 conductivity_matrix(dim,dim) = (*this->mpNonConstantConductivities)[local_element_index][dim];
115 }
116 }
117 else
118 {
119 for (unsigned dim=0; dim<SPACE_DIM; dim++)
120 {
121 assert(this->mConstantConductivities(dim) != DBL_MAX);
122 conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
123 }
124 }
125
126 if (this->mUseFibreOrientation)
127 {
128 unsigned current_fibre_global_index = it->GetIndex();
129 this->mFileReader->GetFibreSheetAndNormalMatrix(current_fibre_global_index, orientation_matrix);
130 }
131
132 c_matrix<double,SPACE_DIM,SPACE_DIM> temp;
133 noalias(temp) = prod(orientation_matrix, conductivity_matrix);
134 this->mTensors.push_back( prod(temp, trans(orientation_matrix) ) );
135
136 local_element_index++;
137 }
138 assert(this->mTensors.size() == this->mpMesh->GetNumLocalElements());
139 assert(this->mTensors.size() == local_element_index);
140
141 if (this->mUseFibreOrientation)
142 {
143 // Close fibre file
144 this->mFileReader.reset();
145 }
146 }
147
148 this->mInitialised = true;
149}
150
151// Explicit instantiation
#define EXCEPTION(message)
void Init(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)