Chaste  Release::2017.1
PottsMeshGenerator.cpp
1 /*
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3 Copyright (c) 2005-2017, University of Oxford.
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34 */
35 
36 #include "PottsMeshGenerator.hpp"
37 
38 #include <boost/scoped_array.hpp>
39 
40 template<unsigned DIM>
41 PottsMeshGenerator<DIM>::PottsMeshGenerator(unsigned numNodesAcross, unsigned numElementsAcross, unsigned elementWidth,
42  unsigned numNodesUp, unsigned numElementsUp, unsigned elementHeight,
43  unsigned numNodesDeep, unsigned numElementsDeep, unsigned elementDepth,
44  bool startAtBottomLeft, bool isPeriodicInX, bool isPeriodicInY ,bool isPeriodicInZ)
45 {
46  assert(numNodesAcross > 0);
47  assert(numNodesUp > 0);
48  assert(numNodesDeep > 0);
49 
50  assert(numElementsAcross*elementWidth <= numNodesAcross);
51  assert(numElementsUp*elementHeight <= numNodesUp);
52  assert(numElementsDeep*elementDepth <= numNodesDeep);
53 
54  std::vector<Node<DIM>*> nodes;
55  std::vector<PottsElement<DIM>*> elements;
56  std::vector<std::set<unsigned> > moore_neighbours;
57  std::vector<std::set<unsigned> > von_neumann_neighbours;
58 
59  unsigned num_nodes = numNodesAcross*numNodesUp*numNodesDeep;
60 
61  unsigned next_node_index = 0;
62  boost::scoped_array<unsigned> node_indices(new unsigned[elementWidth*elementHeight*elementDepth]);
63  unsigned element_index;
64 
65  unsigned index_offset = 0;
66 
67  if (!startAtBottomLeft) // Elements in centre of mesh
68  {
69  // Calculate the width of the medium on the edge and offset the node index so that the elements are in the centre of the mesh.
70  unsigned across_gap = (numNodesAcross - numElementsAcross*elementWidth)/2;
71  unsigned up_gap = (numNodesUp - numElementsUp*elementHeight)/2;
72  unsigned deep_gap = (numNodesDeep - numElementsDeep*elementDepth)/2;
73 
74  index_offset = deep_gap*numNodesAcross*numNodesUp + up_gap*numNodesAcross + across_gap;
75  }
76 
77  /*
78  * Create the nodes, row by row, from the bottom up
79  * On the first and last row we have numNodesAcross nodes, all of which are boundary
80  * nodes. On each interior row we have numNodesAcross nodes, the first and last nodes
81  * are boundary nodes.
82  */
83  for (unsigned k=0; k<numNodesDeep; k++)
84  {
85  for (unsigned j=0; j<numNodesUp; j++)
86  {
87  for (unsigned i=0; i<numNodesAcross; i++)
88  {
89  bool is_boundary_node=false;
90  if (DIM==2)
91  {
92  is_boundary_node = (j==0 || j==numNodesUp-1 || (i==0 && !isPeriodicInX) || (i==numNodesAcross-1 && !isPeriodicInX) ) ? true : false;
93  }
94  if (DIM==3)
95  {
96  is_boundary_node = (j==0 || j==numNodesUp-1 || (i==0 && !isPeriodicInX) || (i==numNodesAcross-1 && !isPeriodicInX) || k==0 || k==numNodesDeep-1) ? true : false;
97  }
98  Node<DIM>* p_node = new Node<DIM>(next_node_index, is_boundary_node, i, j, k);
99  nodes.push_back(p_node);
100  next_node_index++;
101  }
102  }
103  }
104  assert(nodes.size()==num_nodes);
105 
106  /*
107  * Create the elements. The array node_indices contains the
108  * global node indices, in increasing order.
109  */
110  for (unsigned n=0; n<numElementsDeep; n++)
111  {
112  for (unsigned j=0; j<numElementsUp; j++)
113  {
114  for (unsigned i=0; i<numElementsAcross; i++)
115  {
116  for (unsigned m=0; m<elementDepth; m++)
117  {
118  for (unsigned l=0; l<elementHeight; l++)
119  {
120  for (unsigned k=0; k<elementWidth; k++)
121  {
122  node_indices[m*elementHeight*elementWidth + l*elementWidth + k] = n*elementDepth*numNodesUp*numNodesAcross +
123  j*elementHeight*numNodesAcross +
124  i*elementWidth +
125  m*numNodesAcross*numNodesUp +
126  l*numNodesAcross +
127  k + index_offset;
128  }
129  }
130  }
131  std::vector<Node<DIM>*> element_nodes;
132  for (unsigned k=0; k<elementDepth*elementHeight*elementWidth; k++)
133  {
134  element_nodes.push_back(nodes[node_indices[k]]);
135  }
136 
137  element_index = n*numElementsAcross*numElementsUp + j*numElementsAcross + i;
138  PottsElement<DIM>* p_element = new PottsElement<DIM>(element_index, element_nodes);
139  elements.push_back(p_element);
140  }
141  }
142  }
143 
144  /*
145  * Create the neighborhoods of each node
146  */
147 
148  moore_neighbours.resize(num_nodes);
149  von_neumann_neighbours.resize(num_nodes);
150 
151  for (unsigned node_index=0; node_index<num_nodes; node_index++)
152  {
153  // Clear the set of neighbouring node indices
154 
155  moore_neighbours[node_index].clear();
156 
157  switch (DIM)
158  {
159  case 2:
160  {
161  assert(DIM == 2);
162  /*
163  * This stores the available neighbours using the following numbering:
164  *
165  * 1-----0-----7
166  * | | |
167  * | | |
168  * 2-----x-----6
169  * | | |
170  * | | |
171  * 3-----4-----5
172  */
173 
174  // Create a vector of possible neighbouring node indices
175  std::vector<unsigned> moore_neighbour_indices_vector(8, node_index);
176  moore_neighbour_indices_vector[0] += numNodesAcross;
177  moore_neighbour_indices_vector[1] += numNodesAcross - 1;
178  moore_neighbour_indices_vector[2] -= 1;
179  moore_neighbour_indices_vector[3] -= numNodesAcross + 1;
180  moore_neighbour_indices_vector[4] -= numNodesAcross;
181  moore_neighbour_indices_vector[5] -= numNodesAcross - 1;
182  moore_neighbour_indices_vector[6] += 1;
183  moore_neighbour_indices_vector[7] += numNodesAcross + 1;
184 
185  // Work out whether this node lies on any edge of the mesh
186  bool on_south_edge = (node_index < numNodesAcross);
187  bool on_north_edge = ((int) node_index > (int)numNodesAcross*((int)numNodesUp - 1) - 1);
188  bool on_west_edge = (node_index%numNodesAcross == 0);
189  bool on_east_edge = (node_index%numNodesAcross == numNodesAcross - 1);
190 
191  if (isPeriodicInX)
192  {
193  if (on_west_edge)
194  {
195  moore_neighbour_indices_vector[1] = node_index + 2*numNodesAcross - 1;
196  moore_neighbour_indices_vector[2] = node_index + numNodesAcross - 1;
197  moore_neighbour_indices_vector[3] = node_index - 1;
198  }
199 
200  if (on_east_edge)
201  {
202  moore_neighbour_indices_vector[5] = node_index - 2*numNodesAcross + 1;
203  moore_neighbour_indices_vector[6] = node_index - numNodesAcross + 1;
204  moore_neighbour_indices_vector[7] = node_index + 1;
205  }
206  }
207 
208  if (isPeriodicInY)
209  {
210  if (on_north_edge)
211  {
212  moore_neighbour_indices_vector[0] = node_index - numNodesAcross*(numNodesUp-1);
213  moore_neighbour_indices_vector[1] = moore_neighbour_indices_vector[0] - 1;
214  moore_neighbour_indices_vector[7] = moore_neighbour_indices_vector[0] + 1;
215 
216  if (on_west_edge)
217  {
218  moore_neighbour_indices_vector[1] = moore_neighbour_indices_vector[1] + numNodesAcross;
219  }
220  if (on_east_edge)
221  {
222  moore_neighbour_indices_vector[7] = moore_neighbour_indices_vector[7] - numNodesAcross;
223  }
224  }
225 
226  if (on_south_edge)
227  {
228  moore_neighbour_indices_vector[4] = node_index + numNodesAcross*(numNodesUp-1);
229  moore_neighbour_indices_vector[3] = moore_neighbour_indices_vector[4] - 1;
230  moore_neighbour_indices_vector[5] = moore_neighbour_indices_vector[4] + 1;
231 
232  if (on_west_edge)
233  {
234  moore_neighbour_indices_vector[3] = moore_neighbour_indices_vector[3] + numNodesAcross;
235  }
236  if (on_east_edge)
237  {
238  moore_neighbour_indices_vector[5] = moore_neighbour_indices_vector[5] - numNodesAcross;
239  }
240  }
241  }
242 
243  if (isPeriodicInX)
244  {
245  on_east_edge = false;
246  on_west_edge = false;
247  }
248  if (isPeriodicInY)
249  {
250  on_south_edge = false;
251  on_north_edge = false;
252  }
253 
254  // Create a vector of booleans for which neighbours are available
255  // Use the order N, NW, W, SW, S, SE, E, NE
256  std::vector<bool> available_neighbours = std::vector<bool>(8, true);
257  available_neighbours[0] = !on_north_edge;
258  available_neighbours[1] = !(on_north_edge || on_west_edge);
259  available_neighbours[2] = !on_west_edge;
260  available_neighbours[3] = !(on_south_edge || on_west_edge);
261  available_neighbours[4] = !on_south_edge;
262  available_neighbours[5] = !(on_south_edge || on_east_edge);
263  available_neighbours[6] = !on_east_edge;
264  available_neighbours[7] = !(on_north_edge || on_east_edge);
265 
266  // Using neighbour_indices_vector and available_neighbours, store the indices of all available neighbours to the set all_neighbours
267  for (unsigned i=0; i<8; i++)
268  {
269  if (available_neighbours[i])
270  {
271  assert(moore_neighbour_indices_vector[i] < nodes.size());
272  moore_neighbours[node_index].insert(moore_neighbour_indices_vector[i]);
273  }
274  }
275  break;
276  }
277  case 3:
278  {
279  assert(DIM ==3);
280  /*
281  * This stores the available neighbours using the following numbering:
282  * FRONT BACK
283  * 1-----0-----7 10-----9---16 19----18---25
284  * | | | | | | | | |
285  * | | | | | | | | |
286  * 2-----x-----6 11----8-----15 20----17---24
287  * | | | | | | | | |
288  * | | | | | | | | |
289  * 3-----4-----5 12----13----14 21---22----23
290  */
291 
292  // Create a vector of possible neighbouring node indices
293  std::vector<unsigned> moore_neighbour_indices_vector(26, node_index);
294  moore_neighbour_indices_vector[0] += numNodesAcross;
295  moore_neighbour_indices_vector[1] += numNodesAcross - 1;
296  moore_neighbour_indices_vector[2] -= 1;
297  moore_neighbour_indices_vector[3] -= numNodesAcross + 1;
298  moore_neighbour_indices_vector[4] -= numNodesAcross;
299  moore_neighbour_indices_vector[5] -= numNodesAcross - 1;
300  moore_neighbour_indices_vector[6] += 1;
301  moore_neighbour_indices_vector[7] += numNodesAcross + 1;
302  moore_neighbour_indices_vector[8] -= numNodesAcross*numNodesUp;
303  for (unsigned i=9; i<17; i++)
304  {
305  moore_neighbour_indices_vector[i] = moore_neighbour_indices_vector[i-9]-numNodesAcross*numNodesUp;
306  }
307  moore_neighbour_indices_vector[17] += numNodesAcross*numNodesUp;
308  for (unsigned i=18; i<26; i++)
309  {
310  moore_neighbour_indices_vector[i]=moore_neighbour_indices_vector[i-18]+numNodesAcross*numNodesUp;
311  }
312 
313  // Work out whether this node lies on any edge of the mesh
314  bool on_south_edge = (node_index%(numNodesAcross*numNodesUp)<numNodesAcross);
315  bool on_north_edge = (node_index%(numNodesAcross*numNodesUp)>(numNodesAcross*numNodesUp-numNodesAcross-1));
316  bool on_west_edge = (node_index%numNodesAcross == 0);
317  bool on_east_edge = (node_index%numNodesAcross == numNodesAcross - 1);
318  bool on_front_edge = (node_index < numNodesAcross*numNodesUp);
319  bool on_back_edge = (node_index > numNodesAcross*numNodesUp*(numNodesDeep-1)-1);
320 
321  if (isPeriodicInX)
322  {
323  if (on_west_edge)
324  {
325  moore_neighbour_indices_vector[1] = node_index + 2*numNodesAcross - 1;
326  moore_neighbour_indices_vector[2] = node_index + numNodesAcross - 1;
327  moore_neighbour_indices_vector[3] = node_index - 1;
328 
329  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[1] - numNodesAcross*numNodesUp;
330  moore_neighbour_indices_vector[11] = moore_neighbour_indices_vector[2] - numNodesAcross*numNodesUp;
331  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[3] - numNodesAcross*numNodesUp;
332 
333  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[1] + numNodesAcross*numNodesUp;
334  moore_neighbour_indices_vector[20] = moore_neighbour_indices_vector[2] + numNodesAcross*numNodesUp;
335  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[3] + numNodesAcross*numNodesUp;
336  }
337 
338  if (on_east_edge)
339  {
340  moore_neighbour_indices_vector[5] = node_index - 2*numNodesAcross + 1;
341  moore_neighbour_indices_vector[6] = node_index - numNodesAcross + 1;
342  moore_neighbour_indices_vector[7] = node_index + 1;
343 
344  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[5] - numNodesAcross*numNodesUp;
345  moore_neighbour_indices_vector[15] = moore_neighbour_indices_vector[6] - numNodesAcross*numNodesUp;
346  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[7] - numNodesAcross*numNodesUp;
347 
348  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[5] + numNodesAcross*numNodesUp;
349  moore_neighbour_indices_vector[24] = moore_neighbour_indices_vector[6] + numNodesAcross*numNodesUp;
350  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[7] + numNodesAcross*numNodesUp;
351  }
352  }
353 
354  if (isPeriodicInY)
355  {
356  if (on_north_edge)
357  {
358  moore_neighbour_indices_vector[0] = node_index - numNodesAcross*(numNodesUp-1);
359  moore_neighbour_indices_vector[1] = moore_neighbour_indices_vector[0] - 1;
360  moore_neighbour_indices_vector[7] = moore_neighbour_indices_vector[0] + 1;
361 
362  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[1] - numNodesAcross*numNodesUp;
363  moore_neighbour_indices_vector[9] = moore_neighbour_indices_vector[0] - numNodesAcross*numNodesUp;
364  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[7] - numNodesAcross*numNodesUp;
365 
366  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[1] + numNodesAcross*numNodesUp;
367  moore_neighbour_indices_vector[18] = moore_neighbour_indices_vector[0] + numNodesAcross*numNodesUp;
368  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[7] + numNodesAcross*numNodesUp;
369 
370  if (on_west_edge)
371  {
372  moore_neighbour_indices_vector[1] = moore_neighbour_indices_vector[1] + numNodesAcross;
373  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[10] + numNodesAcross;
374  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[19] + numNodesAcross;
375  }
376  if (on_east_edge)
377  {
378  moore_neighbour_indices_vector[7] = moore_neighbour_indices_vector[7] - numNodesAcross;
379  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[16] - numNodesAcross;
380  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[25] - numNodesAcross;
381  }
382  }
383 
384  if (on_south_edge)
385  {
386  moore_neighbour_indices_vector[4] = node_index + numNodesAcross*(numNodesUp-1);
387  moore_neighbour_indices_vector[3] = moore_neighbour_indices_vector[4] - 1;
388  moore_neighbour_indices_vector[5] = moore_neighbour_indices_vector[4] + 1;
389 
390  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[3] - numNodesAcross*numNodesUp;
391  moore_neighbour_indices_vector[13] = moore_neighbour_indices_vector[4] - numNodesAcross*numNodesUp;
392  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[5] - numNodesAcross*numNodesUp;
393 
394  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[3] + numNodesAcross*numNodesUp;
395  moore_neighbour_indices_vector[22] = moore_neighbour_indices_vector[4] + numNodesAcross*numNodesUp;
396  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[5] + numNodesAcross*numNodesUp;
397 
398  if (on_west_edge)
399  {
400  moore_neighbour_indices_vector[3] = moore_neighbour_indices_vector[3] + numNodesAcross;
401  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[12] + numNodesAcross;
402  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[21] + numNodesAcross;
403  }
404  if (on_east_edge)
405  {
406  moore_neighbour_indices_vector[5] = moore_neighbour_indices_vector[5] - numNodesAcross;
407  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[14] - numNodesAcross;
408  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[23] - numNodesAcross;
409  }
410  }
411  }
412 
413  if (isPeriodicInZ)
414  {
415  if (on_back_edge)
416  {
417  moore_neighbour_indices_vector[17] = node_index - numNodesAcross*numNodesUp*(numNodesDeep-1);
418  moore_neighbour_indices_vector[20] = moore_neighbour_indices_vector[17] - 1;
419  moore_neighbour_indices_vector[24] = moore_neighbour_indices_vector[17] + 1;
420 
421  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[20] - numNodesAcross;
422  moore_neighbour_indices_vector[22] = moore_neighbour_indices_vector[17] - numNodesAcross;
423  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[24] - numNodesAcross;
424 
425  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[20] + numNodesAcross;
426  moore_neighbour_indices_vector[18] = moore_neighbour_indices_vector[17] + numNodesAcross;
427  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[24] + numNodesAcross;
428 
429  if (on_west_edge)
430  {
431  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[19] + numNodesAcross;
432  moore_neighbour_indices_vector[20] = moore_neighbour_indices_vector[20] + numNodesAcross;
433  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[21] + numNodesAcross;
434  }
435  if (on_east_edge)
436  {
437  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[23] - numNodesAcross;
438  moore_neighbour_indices_vector[24] = moore_neighbour_indices_vector[24] - numNodesAcross;
439  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[25] - numNodesAcross;
440  }
441 
442  if (on_south_edge)
443  {
444  moore_neighbour_indices_vector[21] = moore_neighbour_indices_vector[21] + numNodesAcross*numNodesUp;
445  moore_neighbour_indices_vector[22] = moore_neighbour_indices_vector[22] + numNodesAcross*numNodesUp;
446  moore_neighbour_indices_vector[23] = moore_neighbour_indices_vector[23] + numNodesAcross*numNodesUp;
447  }
448 
449  if (on_north_edge)
450  {
451  moore_neighbour_indices_vector[18] = moore_neighbour_indices_vector[18] - numNodesAcross*numNodesUp;
452  moore_neighbour_indices_vector[19] = moore_neighbour_indices_vector[19] - numNodesAcross*numNodesUp;
453  moore_neighbour_indices_vector[25] = moore_neighbour_indices_vector[25] - numNodesAcross*numNodesUp;
454  }
455  }
456 
457  if (on_front_edge)
458  {
459  moore_neighbour_indices_vector[8] = node_index + numNodesAcross*numNodesUp*(numNodesDeep-1);
460  moore_neighbour_indices_vector[11] = moore_neighbour_indices_vector[8] - 1;
461  moore_neighbour_indices_vector[15] = moore_neighbour_indices_vector[8] + 1;
462 
463  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[11] - numNodesAcross;
464  moore_neighbour_indices_vector[13] = moore_neighbour_indices_vector[8] - numNodesAcross;
465  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[15] - numNodesAcross;
466 
467  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[11] + numNodesAcross;
468  moore_neighbour_indices_vector[9] = moore_neighbour_indices_vector[8] + numNodesAcross;
469  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[15] + numNodesAcross;
470 
471  if (on_west_edge)
472  {
473  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[10] + numNodesAcross;
474  moore_neighbour_indices_vector[11] = moore_neighbour_indices_vector[11] + numNodesAcross;
475  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[12] + numNodesAcross;
476  }
477  if (on_east_edge)
478  {
479  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[14] - numNodesAcross;
480  moore_neighbour_indices_vector[15] = moore_neighbour_indices_vector[15] - numNodesAcross;
481  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[16] - numNodesAcross;
482  }
483 
484  if (on_south_edge)
485  {
486  moore_neighbour_indices_vector[12] = moore_neighbour_indices_vector[12] + numNodesAcross*numNodesUp;
487  moore_neighbour_indices_vector[13] = moore_neighbour_indices_vector[13] + numNodesAcross*numNodesUp;
488  moore_neighbour_indices_vector[14] = moore_neighbour_indices_vector[14] + numNodesAcross*numNodesUp;
489  }
490 
491  if (on_north_edge)
492  {
493  moore_neighbour_indices_vector[9] = moore_neighbour_indices_vector[9] - numNodesAcross*numNodesUp;
494  moore_neighbour_indices_vector[10] = moore_neighbour_indices_vector[10] - numNodesAcross*numNodesUp;
495  moore_neighbour_indices_vector[16] = moore_neighbour_indices_vector[16] - numNodesAcross*numNodesUp;
496  }
497  }
498  }
499 
500  if (isPeriodicInX)
501  {
502  on_east_edge = false;
503  on_west_edge = false;
504  }
505  if (isPeriodicInY)
506  {
507  on_south_edge = false;
508  on_north_edge = false;
509  }
510  if (isPeriodicInZ)
511  {
512  on_front_edge = false;
513  on_back_edge = false;
514  }
515 
516  // Create a vector of booleans for which neighbours are available
517  // Use the order N, NW, W, SW, S, SE, E, NE
518  std::vector<bool> available_neighbours = std::vector<bool>(26, true);
519  available_neighbours[0] = !on_north_edge;
520  available_neighbours[1] = !(on_north_edge || on_west_edge);
521  available_neighbours[2] = !on_west_edge;
522  available_neighbours[3] = !(on_south_edge || on_west_edge);
523  available_neighbours[4] = !on_south_edge;
524  available_neighbours[5] = !(on_south_edge || on_east_edge);
525  available_neighbours[6] = !on_east_edge;
526  available_neighbours[7] = !(on_north_edge || on_east_edge);
527  available_neighbours[8] = !(on_front_edge);
528  for (unsigned i=9; i<17; i++)
529  {
530  available_neighbours[i] = (available_neighbours[i-9] && !(on_front_edge));
531  }
532  available_neighbours[17] = !(on_back_edge);
533  for (unsigned i=18; i<26; i++)
534  {
535  available_neighbours[i] = (available_neighbours[i-18] && !(on_back_edge));
536  }
537 
538  // Using neighbour_indices_vector and available_neighbours, store the indices of all available neighbours to the set all_neighbours
539  for (unsigned i=0; i<26; i++)
540  {
541  if (available_neighbours[i] && moore_neighbour_indices_vector[i] < numNodesAcross*numNodesUp*numNodesDeep)
542  {
543  assert(moore_neighbour_indices_vector[i] < nodes.size());
544  moore_neighbours[node_index].insert(moore_neighbour_indices_vector[i]);
545  }
546  }
547  break;
548  }
549  default:
550  NEVER_REACHED;
551  }
552 
553  // Clear the set of neighbouring node indices
554  von_neumann_neighbours[node_index].clear();
555 
556  switch (DIM)
557  {
558  case 2:
559  {
560  assert(DIM == 2);
561  /*
562  * This stores the available neighbours using the following numbering:
563  *
564  * 0
565  * |
566  * |
567  * 1-----x-----3
568  * |
569  * |
570  * 2
571  */
572  // Create a vector of possible neighbouring node indices
573  std::vector<unsigned> von_neumann_neighbour_indices_vector(4, node_index);
574  von_neumann_neighbour_indices_vector[0] += numNodesAcross;
575  von_neumann_neighbour_indices_vector[1] -= 1;
576  von_neumann_neighbour_indices_vector[2] -= numNodesAcross;
577  von_neumann_neighbour_indices_vector[3] += 1;
578 
579  // Work out whether this node lies on any edge of the mesh
580  bool on_south_edge = (node_index < numNodesAcross);
581  bool on_north_edge = ((int)node_index > (int)numNodesAcross*((int)numNodesUp - 1) - 1);
582  bool on_west_edge = (node_index%numNodesAcross == 0);
583  bool on_east_edge = (node_index%numNodesAcross == numNodesAcross - 1);
584 
585  if (isPeriodicInX)
586  {
587  if (on_west_edge)
588  {
589  von_neumann_neighbour_indices_vector[1] = node_index + numNodesAcross - 1;
590  on_west_edge = false;
591  }
592 
593  if (on_east_edge)
594  {
595  von_neumann_neighbour_indices_vector[3] = node_index - numNodesAcross + 1;
596  on_east_edge = false;
597  }
598  }
599 
600  if (isPeriodicInY)
601  {
602  if (on_north_edge)
603  {
604  von_neumann_neighbour_indices_vector[0] = node_index - numNodesAcross*(numNodesUp-1);
605  on_north_edge = false;
606  }
607 
608  if (on_south_edge)
609  {
610  von_neumann_neighbour_indices_vector[2] = node_index + numNodesAcross*(numNodesUp-1);
611  on_south_edge = false;
612  }
613  }
614 
615  // Create a vector of booleans for which neighbours are available
616  // Use the order N, W, S, E
617  std::vector<bool> available_neighbours = std::vector<bool>(2*DIM, true);
618  available_neighbours[0] = !on_north_edge;
619  available_neighbours[1] = !on_west_edge;
620  available_neighbours[2] = !on_south_edge;
621  available_neighbours[3] = !on_east_edge;
622 
623  // Using von_neumann_neighbour_indices_vector and available_neighbours, store the indices of all available neighbours to the set all_neighbours
624  for (unsigned i=0; i<4; i++)
625  {
626  if (available_neighbours[i])
627  {
628  assert(von_neumann_neighbour_indices_vector[i] < nodes.size());
629  von_neumann_neighbours[node_index].insert(von_neumann_neighbour_indices_vector[i]);
630  }
631  }
632  break;
633  }
634  case 3:
635  {
636  assert(DIM == 3);
637 
638  /*
639  * This stores the available neighbours using the following numbering:
640  *
641  * 0 5
642  * | /
643  * |/
644  * 1-----x-----3
645  * / |
646  * / |
647  * 4 2
648  */
649  // Create a vector of possible neighbouring node indices
650  std::vector<unsigned> von_neumann_neighbour_indices_vector(6, node_index);
651  von_neumann_neighbour_indices_vector[0] += numNodesAcross;
652  von_neumann_neighbour_indices_vector[1] -= 1;
653  von_neumann_neighbour_indices_vector[2] -= numNodesAcross;
654  von_neumann_neighbour_indices_vector[3] += 1;
655  von_neumann_neighbour_indices_vector[4] -= numNodesAcross*numNodesUp;
656  von_neumann_neighbour_indices_vector[5] += numNodesAcross*numNodesUp;
657 
658  // Work out whether this node lies on any edge of the mesh
659  bool on_south_edge = (node_index%(numNodesAcross*numNodesUp)<numNodesAcross);
660  bool on_north_edge = (node_index%(numNodesAcross*numNodesUp)>(numNodesAcross*numNodesUp-numNodesAcross-1));
661  bool on_west_edge = (node_index%numNodesAcross== 0);
662  bool on_east_edge = (node_index%numNodesAcross == numNodesAcross - 1);
663  bool on_front_edge = (node_index < numNodesAcross*numNodesUp);
664  bool on_back_edge = (node_index > numNodesAcross*numNodesUp*(numNodesDeep-1)-1);
665 
666  if (isPeriodicInX)
667  {
668  if (on_west_edge)
669  {
670  von_neumann_neighbour_indices_vector[1] = node_index + numNodesAcross - 1;
671  on_west_edge = false;
672  }
673 
674  if (on_east_edge)
675  {
676  von_neumann_neighbour_indices_vector[3] = node_index - numNodesAcross + 1;
677  on_east_edge = false;
678  }
679  }
680 
681  if (isPeriodicInY)
682  {
683  if (on_north_edge)
684  {
685  von_neumann_neighbour_indices_vector[0] = node_index - numNodesAcross*(numNodesUp-1);
686  on_north_edge = false;
687  }
688 
689  if (on_south_edge)
690  {
691  von_neumann_neighbour_indices_vector[2] = node_index + numNodesAcross*(numNodesUp-1);
692  on_south_edge = false;
693  }
694  }
695 
696  if (isPeriodicInZ)
697  {
698  if (on_front_edge)
699  {
700  von_neumann_neighbour_indices_vector[4] = node_index + numNodesAcross*numNodesUp*(numNodesDeep-1);
701  on_front_edge = false;
702  }
703 
704  if (on_back_edge)
705  {
706  von_neumann_neighbour_indices_vector[5] = node_index - numNodesAcross*numNodesUp*(numNodesDeep-1);
707  on_back_edge = false;
708  }
709  }
710 
711  // Create a vector of booleans for which neighbours are available
712  // Use the order N, W, S, E, F, B
713  std::vector<bool> available_neighbours = std::vector<bool>(2*DIM, true);
714  available_neighbours[0] = !on_north_edge;
715  available_neighbours[1] = !on_west_edge;
716  available_neighbours[2] = !on_south_edge;
717  available_neighbours[3] = !on_east_edge;
718  available_neighbours[4] = !on_front_edge;
719  available_neighbours[5] = !on_back_edge;
720 
721  // Using von_neumann_neighbour_indices_vector and available_neighbours, store the indices of all available neighbours to the set all_neighbours
722  for (unsigned i=0; i<6; i++)
723  {
724  if (available_neighbours[i] && von_neumann_neighbour_indices_vector[i]<numNodesAcross*numNodesUp*numNodesDeep)
725  {
726  assert(von_neumann_neighbour_indices_vector[i] < nodes.size());
727  von_neumann_neighbours[node_index].insert(von_neumann_neighbour_indices_vector[i]);
728  }
729  }
730  break;
731  }
732  default:
733  NEVER_REACHED;
734  }
735  }
736 
737  mpMesh = new PottsMesh<DIM>(nodes, elements, von_neumann_neighbours, moore_neighbours);
738 }
739 
740 template<unsigned DIM>
741 PottsMeshGenerator<DIM>::~PottsMeshGenerator()
742 {
743  delete mpMesh;
744 }
745 
746 template<unsigned DIM>
747 PottsMesh<DIM>* PottsMeshGenerator<DIM>::GetMesh()
748 {
749  return mpMesh;
750 }
751 
752 // Explicit instantiation
753 template class PottsMeshGenerator<1>;
754 template class PottsMeshGenerator<2>;
755 template class PottsMeshGenerator<3>;
Node
Definition: Node.hpp:58
NEVER_REACHED
#define NEVER_REACHED
Definition: Exception.hpp:206
PottsMeshGenerator::GetMesh
virtual PottsMesh< DIM > * GetMesh()
Definition: PottsMeshGenerator.cpp:747
PottsMeshGenerator::PottsMeshGenerator
PottsMeshGenerator(unsigned numNodesAcross, unsigned numElementsAcross, unsigned elementWidth, unsigned numNodesUp=1u, unsigned numElementsUp=1u, unsigned elementHeight=1u, unsigned numNodesDeep=1u, unsigned numElementsDeep=1u, unsigned elementDepth=1u, bool startAtBottomLeft=false, bool isPeriodicInX=false, bool isPeriodicInY=false, bool isPeriodicInZ=false)
Definition: PottsMeshGenerator.cpp:41