Chaste  Release::2018.1
AxisymmetricConductivityTensors.cpp
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35 
36 #include <vector>
37 #include "UblasIncludes.hpp"
38 #include "AxisymmetricConductivityTensors.hpp"
39 #include "Exception.hpp"
40 
41 
42 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
44 {
45  if (SPACE_DIM != 3)
46  {
47  EXCEPTION("Axisymmetric anisotropic conductivity only makes sense in 3D");
48  }
49 }
50 
51 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
53 {
54  //assert(SPACE_DIM == 3);//Otherwise constructor would have thrown
55  if (constantConductivities[1] != constantConductivities[2])
56  {
57  EXCEPTION("Axisymmetric media defined: transversal and normal conductivities should have the same value");
58  }
59 
60  this->mUseNonConstantConductivities = false;
61  this->mConstantConductivities = constantConductivities;
62 }
63 
64 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
66 {
67  this->mpMesh = pMesh;
68 
69  if (!this->mUseNonConstantConductivities && !this->mUseFibreOrientation)
70  {
71  // Constant tensor for every element
72  c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));
73 
74  for (unsigned dim=0; dim<SPACE_DIM; dim++)
75  {
76  assert(this->mConstantConductivities(dim) != DBL_MAX);
77  conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
78  }
79  this->mTensors.push_back(conductivity_matrix);
80  }
81  else
82  {
83  c_vector<double,SPACE_DIM> fibre_vector((zero_vector<double>(SPACE_DIM)));
84  fibre_vector[0]=1.0;
85 
86  if (this->mUseFibreOrientation)
87  {
88  // open file
89  this->mFileReader.reset(new FibreReader<SPACE_DIM>(this->mFibreOrientationFile, AXISYM));
90  if (this->mFileReader->GetNumLinesOfData() != this->mpMesh->GetNumElements())
91  {
92  EXCEPTION("The size of the fibre file does not match the number of elements in the mesh");
93  }
94  }
95 
96  if (this->mUseNonConstantConductivities)
97  {
98  if (this->mpNonConstantConductivities->size() != this->mpMesh->GetNumLocalElements())
99  {
100  EXCEPTION("The size of the conductivities vector does not match the number of elements in the mesh");
101  }
102  }
103 
104  // reserve() allocates all the memory at once, more efficient than relying
105  // on the automatic reallocation scheme.
106  this->mTensors.reserve(this->mpMesh->GetNumLocalElements());
107 
108  c_matrix<double, SPACE_DIM, SPACE_DIM> conductivity_matrix(zero_matrix<double>(SPACE_DIM,SPACE_DIM));
109 
110  unsigned local_element_index = 0;
111 
112  for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
113  it != this->mpMesh->GetElementIteratorEnd();
114  ++it)
115  {
116  /*
117  * For every element of the mesh we compute its tensor like (from
118  * "Laminar Arrangement of VentricularMyocites Influences Electrical
119  * Behavior of the Heart", Darren et al. 2007):
120  *
121  * [g_f 0 0 ] [a_f']
122  * tensor = [a_f a_l a_n] [ 0 g_l 0 ] [a_l']
123  * [ 0 0 g_n] [a_n']
124  *
125  * [x_i]
126  * where a_i = [y_i], i={f,l,n} are read from the fibre orientation file and
127  * [z_i]
128  *
129  * g_f = fibre/longitudinal conductivity (constant or element specific)
130  * g_l = laminar/transverse conductivity (constant or element specific)
131  * g_n = normal conductivity (constant or element specific)
132  *
133  *
134  * For axisymmetric anisotropic media (g_l = g_n) we can simplify previous expression to
135  *
136  *
137  * tensor = g_l * I + (g_f - g_l) * a_f * a_f'
138  *
139  */
140 
141  if (this->mUseNonConstantConductivities)
142  {
143  for (unsigned dim=0; dim<SPACE_DIM; dim++)
144  {
145  conductivity_matrix(dim,dim) = (*this->mpNonConstantConductivities)[local_element_index][dim];
146  }
147  }
148  else
149  {
150  for (unsigned dim=0; dim<SPACE_DIM; dim++)
151  {
152  assert(this->mConstantConductivities(dim) != DBL_MAX);
153  conductivity_matrix(dim,dim) = this->mConstantConductivities(dim);
154  }
155  }
156 
157  if (this->mUseFibreOrientation)
158  {
159  unsigned current_fibre_global_index = it->GetIndex();
160  this->mFileReader->GetFibreVector(current_fibre_global_index, fibre_vector);
161  }
162 
163  this->mTensors.push_back( conductivity_matrix(1,1) * identity_matrix<double>(SPACE_DIM) +
164  (conductivity_matrix(0,0) - conductivity_matrix(1,1)) * outer_prod(fibre_vector,fibre_vector));
165 
166  local_element_index++;
167  }
168 
169  assert(this->mTensors.size() == this->mpMesh->GetNumLocalElements());
170  assert(this->mTensors.size() == local_element_index);
171 
172  if (this->mUseFibreOrientation)
173  {
174  // close fibre file
175  this->mFileReader.reset();
176  }
177  }
178 
179  this->mInitialised = true;
180 }
181 
182 // Explicit instantiation
183 
184 // only makes sense for 3d elements in 3d, but we need the other to compile
185 // AbstractCardiacTissue and BidomainTissue.
#define EXCEPTION(message)
Definition: Exception.hpp:143
void SetConstantConductivities(c_vector< double, 3 > constantConductivities)
void Init(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)