Chaste  Release::2018.1
OrthotropicConductivityTensors.cpp
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35 
36 #include "OrthotropicConductivityTensors.hpp"
37 #include "Exception.hpp"
38 
39 template<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
void Init(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
#define EXCEPTION(message)
Definition: Exception.hpp:143