Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractTetrahedralElement.cpp
1/*
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34*/
35
37#include "AbstractTetrahedralElement.hpp"
38#include "Exception.hpp"
39
40#include <cassert>
41
43// Implementation
45
46template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
47void AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::RefreshJacobian(c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian)
48{
49 if (this->mIsDeleted)
50 {
51 EXCEPTION("Attempting to Refresh a deleted element");
52 }
53 for (unsigned i=0; i<SPACE_DIM; i++)
54 {
55 for (unsigned j=0; j!=ELEMENT_DIM; j++) // Does a j<ELEMENT_DIM without ever having to test j<0U (#186: pointless comparison of unsigned integer with zero)
56 {
57 rJacobian(i,j) = this->GetNodeLocation(j+1,i) - this->GetNodeLocation(0,i);
58 }
59 }
60}
61
62template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
64 : AbstractElement<ELEMENT_DIM, SPACE_DIM>(index, rNodes)
65{
66 // Sanity checking
67 unsigned num_vectices = ELEMENT_DIM+1;
68
69 double det;
70
71 if (SPACE_DIM == ELEMENT_DIM)
72 {
73 // This is so we know it's the first time of asking
74 // Create Jacobian
75 c_matrix<double, SPACE_DIM, ELEMENT_DIM> jacobian;
76 try
77 {
78 CalculateJacobian(jacobian, det);
79 }
80 catch (const Exception&)
81 {
82 // if the Jacobian is negative the orientation of the element is probably
83 // wrong, so swap the last two nodes around.
84
85 this->mNodes[num_vectices-1] = rNodes[num_vectices-2];
86 this->mNodes[num_vectices-2] = rNodes[num_vectices-1];
87
88 CalculateJacobian(jacobian, det);
89 // If determinant < 0 then element nodes are listed clockwise.
90 // We want them anticlockwise.
91 assert(det > 0.0);
92 }
93 }
94 else
95 {
96 //This is not a full-dimensional element
97 c_vector<double, SPACE_DIM> weighted_direction;
98 CalculateWeightedDirection(weighted_direction, det);
99 }
100
101}
102
103template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
107
108template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
109void AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::CalculateJacobian(c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian, double& rJacobianDeterminant)
110{
111
112 assert(ELEMENT_DIM <= SPACE_DIM);
113 RefreshJacobian(rJacobian);
114
115 {
116 rJacobianDeterminant = Determinant(rJacobian);
117 if (rJacobianDeterminant <= DBL_EPSILON)
118 {
119 std::stringstream message;
120 message << "Jacobian determinant is non-positive: "
121 << "determinant = " << rJacobianDeterminant
122 << " for element " << this->mIndex << " (" << ELEMENT_DIM
123 << "D element in " << SPACE_DIM << "D space). Nodes are at:" << std::endl;
124
125 for (unsigned local_node_index=0u; local_node_index != ELEMENT_DIM+1; local_node_index++)
126 {
127 c_vector<double, SPACE_DIM> location = this->GetNodeLocation(local_node_index);
128 message << "Node " << this->GetNodeGlobalIndex(local_node_index) << ":\t";
129
130 for (unsigned i=0; i<SPACE_DIM; i++)
131 {
132 message << location[i];
133 if (i==SPACE_DIM - 1u)
134 {
135 message << std::endl;
136 }
137 else
138 {
139 message << "\t";
140 }
141 }
142 }
143 EXCEPTION(message.str());
144 }
145 }
146}
147
148template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
149void AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::CalculateWeightedDirection(c_vector<double, SPACE_DIM>& rWeightedDirection, double& rJacobianDeterminant)
150{
151
152 if (ELEMENT_DIM >= SPACE_DIM)
153 {
154 assert(ELEMENT_DIM == SPACE_DIM);
155 EXCEPTION("WeightedDirection undefined for fully dimensional element");
156 }
157
158 c_matrix<double, SPACE_DIM, ELEMENT_DIM> jacobian;
159 RefreshJacobian(jacobian);
160
161 /*
162 * At this point we're only dealing with subspace (ELEMENT_DIM < SPACE_DIM) elem.
163 * We assume that the rWeightedDirection vector and rJacobianDeterminant (length
164 * of vector) are the values from a previous call.
165 */
166
167 // This code is only used when ELEMENT_DIM<SPACE_DIM
168 switch (ELEMENT_DIM)
169 {
170 case 0:
171 // See specialised template for ELEMENT_DIM==0
173 break;
174 case 1:
175 // Linear edge in a 2D plane or in 3D
176 rWeightedDirection=matrix_column<c_matrix<double,SPACE_DIM,ELEMENT_DIM> >(jacobian, 0);
177 break;
178 case 2:
179 // Surface triangle in a 3d mesh
180 assert(SPACE_DIM == 3);
181 rWeightedDirection(0) = -SubDeterminant(jacobian, 0, 2);
182 rWeightedDirection(1) = SubDeterminant(jacobian, 1, 2);
183 rWeightedDirection(2) = -SubDeterminant(jacobian, 2, 2);
184 break;
185 default:
186 ; // Not going to happen
187 }
188 rJacobianDeterminant = norm_2(rWeightedDirection);
189
190 if (rJacobianDeterminant < DBL_EPSILON)
191 {
192 EXCEPTION("Jacobian determinant is zero");
193 }
194}
195
196template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
198{
199 if (ELEMENT_DIM == 1 && SPACE_DIM == 3)
200 {
201 EXCEPTION("Don't have enough information to calculate a normal vector");
202 }
203 c_vector<double, SPACE_DIM> normal;
204 double determinant;
205 CalculateWeightedDirection(normal, determinant);
206 normal /= determinant;
207 if (ELEMENT_DIM == 1)
208 {
209 // Need to rotate so tangent becomes normal
210 double x = normal[0];
211 normal[0] = normal[1];
212 normal[1] = -x;
213 }
214 return normal;
215}
216
217template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
219{
220 c_vector<double, SPACE_DIM> centroid = zero_vector<double>(SPACE_DIM);
221 for (unsigned i=0; i<=ELEMENT_DIM; i++)
222 {
223 centroid += this->mNodes[i]->rGetLocation();
224 }
225 return centroid/((double)(ELEMENT_DIM + 1));
226}
227
228template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
229void AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::CalculateInverseJacobian(c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian, double& rJacobianDeterminant, c_matrix<double, ELEMENT_DIM, SPACE_DIM>& rInverseJacobian)
230{
231 assert(ELEMENT_DIM <= SPACE_DIM); // LCOV_EXCL_LINE
232 CalculateJacobian(rJacobian, rJacobianDeterminant);
233
234 // CalculateJacobian should make sure that the determinant is not close to zero (or, in fact, negative)
235 assert(rJacobianDeterminant > 0.0);
236 rInverseJacobian = Inverse(rJacobian);
237}
238
239template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
241{
242
243 if (this->mIsDeleted)
244 {
245 return 0.0;
246 }
247
248 double scale_factor = 1.0;
249
250 if (ELEMENT_DIM == 2)
251 {
252 scale_factor = 2.0; // both the volume of the canonical triangle is 1/2
253 }
254 else if (ELEMENT_DIM == 3)
255 {
256 scale_factor = 6.0; // both the volume of the canonical triangle is 1/6
257 }
258 return determinant/scale_factor;
259}
260
261template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
263{
264 for (unsigned local_index=0; local_index<ELEMENT_DIM+1; local_index++)
265 {
266 unsigned node = this->GetNodeGlobalIndex(local_index);
267
268 for (unsigned problem_index=0; problem_index<problemDim; problem_index++)
269 {
270 //std::cout << local_index*problemDim + problem_index << std::endl;
271 pIndices[local_index*problemDim + problem_index] = node*problemDim + problem_index;
272 }
273 }
274}
275
276
278// Specialization for 0d elements //
280
285template<unsigned SPACE_DIM>
287 : AbstractElement<0, SPACE_DIM>(index, rNodes)
288{
289 // Sanity checking
290 //unsigned total_nodes = 1;
291 assert(this->mNodes.size() == 1);
292 assert(SPACE_DIM > 0); // LCOV_EXCL_LINE
293
294 // This is so we know it's the first time of asking
295 // Create Jacobian
296 c_vector<double, SPACE_DIM> weighted_direction;
297 double det;
298
299 CalculateWeightedDirection(weighted_direction, det);
300
301 // If determinant < 0 then element nodes are listed clockwise.
302 // We want them anticlockwise.
303 assert(det > 0.0);
304}
305
306template<unsigned SPACE_DIM>
311
312template<unsigned SPACE_DIM>
314 c_vector<double, SPACE_DIM>& rWeightedDirection,
315 double& rJacobianDeterminant)
316{
317 assert(SPACE_DIM > 0); // LCOV_EXCL_LINE
318
319 // End point of a line
320 rWeightedDirection = zero_vector<double>(SPACE_DIM);
321 rWeightedDirection(0) = 1.0;
322
323 rJacobianDeterminant = 1.0;
324}
325
326template<unsigned SPACE_DIM>
328{
329 assert(SPACE_DIM > 0); // LCOV_EXCL_LINE
330
331 // End point of a line
332 c_vector<double, SPACE_DIM> normal = zero_vector<double>(SPACE_DIM);
334 return normal;
335}
336
337template<unsigned SPACE_DIM>
339{
340 c_vector<double, SPACE_DIM> centroid = this->mNodes[0]->rGetLocation();
341 return centroid;
342}
343
344template<unsigned SPACE_DIM>
345void AbstractTetrahedralElement<0, SPACE_DIM>::GetStiffnessMatrixGlobalIndices(unsigned problemDim, unsigned* pIndices) const
346{
347 for (unsigned local_index=0; local_index<1; local_index++)
348 {
349 unsigned node = this->GetNodeGlobalIndex(local_index);
350
351 for (unsigned problem_index=0; problem_index<problemDim; problem_index++)
352 {
353 //std::cout << local_index*problemDim + problem_index << std::endl;
354 pIndices[local_index*problemDim + problem_index] = node*problemDim + problem_index;
355 }
356 }
357}
358
359// Explicit instantiation
#define EXCEPTION(message)
#define NEVER_REACHED
T Determinant(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
T SubDeterminant(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM, const unsigned missrow, const unsigned misscol)
boost::numeric::ublas::c_matrix< T, 1, 1 > Inverse(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
std::vector< Node< SPACE_DIM > * > mNodes
void RefreshJacobian(c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian)
void CalculateInverseJacobian(c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant, c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian)
double GetVolume(double determinant) const
void CalculateWeightedDirection(c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant)
AbstractTetrahedralElement(unsigned index, const std::vector< Node< SPACE_DIM > * > &rNodes)
c_vector< double, SPACE_DIM > CalculateCentroid() const
void GetStiffnessMatrixGlobalIndices(unsigned problemDim, unsigned *pIndices) const
void CalculateJacobian(c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant)
c_vector< double, SPACE_DIM > CalculateNormal()
Definition Node.hpp:59