refineable_line_element.cc
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26 // Non-inline and non-templated functions for RefineableQElement<1> class
27 
28 #include <algorithm>
29 
30 // oomph-lib headers
31 #include "mesh.h"
32 #include "algebraic_elements.h"
35 
36 namespace oomph
37 {
38  //==========================================================================
39  /// Setup static matrix for coincidence between son nodal points and father
40  /// boundaries:
41  ///
42  /// Father_bound[nnode_1d](nnode_son,son_type) = {L/R/OMEGA}
43  ///
44  /// so that node nnode_son in element of type son_type lies on boundary/
45  /// vertex Father_bound[nnode_1d](nnode_son,son_type) in its father
46  /// element. If the node doesn't lie on a boundary the value is OMEGA.
47  //==========================================================================
49  {
50  using namespace BinaryTreeNames;
51 
52  // Find the number of nodes along a 1D edge (which is the number of nodes
53  // in the element for a 1D element!)
54  const unsigned n_node = nnode_1d();
55 
56  // Allocate space for the boundary information
57  Father_bound[n_node].resize(n_node, 2);
58 
59  // Initialise: By default points are not on the boundary
60  for (unsigned n = 0; n < n_node; n++)
61  {
62  for (unsigned ison = 0; ison < 2; ison++)
63  {
64  Father_bound[n_node](n, ison) = Tree::OMEGA;
65  }
66  }
67 
68  // Left-hand son:
69  // --------------
70 
71  // L node (0) is the L node of the parent
72  Father_bound[n_node](0, L) = L;
73 
74  // Other boundary is in the interior
75 
76  // Right-hand son:
77  // ---------------
78 
79  // R node (n_node-1) is the R node of the parent
80  Father_bound[n_node](n_node - 1, R) = R;
81 
82  // Other boundary is in the interior
83  }
84 
85  //==========================================================================
86  /// If a neighbouring element has already created a node at a position
87  /// corresponding to the local fractional position within the present
88  /// element, s_fraction, return a pointer to that node. If not, return
89  /// NULL (0). If the node is periodic the flag is_periodic will be true.
90  //==========================================================================
92  const Vector<double>& s_fraction, bool& is_periodic)
93  {
94  using namespace BinaryTreeNames;
95 
96  // Initialise edge of current element on which node lies
97  int edge_in_current = OMEGA;
98 
99  // Determine the edge of the current element on which the node lies
100  if (s_fraction[0] == 0.0)
101  {
102  edge_in_current = L;
103  }
104  if (s_fraction[0] == 1.0)
105  {
106  edge_in_current = R;
107  }
108 
109  // If the node does not lie on an edge then there is no neighbour:
110  // return NULL
111  if (edge_in_current == OMEGA)
112  {
113  return 0;
114  }
115 
116  // Allocate storage for edge in neighbouring element
117  int edge_in_neighbour;
118 
119  // Allocate storage for difference in size between current and
120  // neighbouring element
121  int diff_level;
122 
123  // Allocate storage for local coordinate of node in neighbouring tree
124  Vector<double> s_in_neighbour(1);
125 
126  // Allocate storage for flag indicating if the node is not in the same
127  // binary tree
128  bool in_neighbouring_tree;
129 
130  // Allocate storage for the pointer to the neighbouring element
131  // (using its binary tree representation)
132  BinaryTree* neighbour_pt;
133 
134  // Find pointer to neighbouring element along the edge in question and
135  // calculate the local coordinate of the node within that element
136  // s_in_neighbour
137  neighbour_pt = binary_tree_pt()->gteq_edge_neighbour(edge_in_current,
138  s_in_neighbour,
139  edge_in_neighbour,
140  diff_level,
141  in_neighbouring_tree);
142 
143  // If a neighbour exists...
144  if (neighbour_pt != 0)
145  {
146  // ...check whether its nodes have been created yet
147  if (neighbour_pt->object_pt()->nodes_built())
148  {
149  // If they have, find the node in question in the neighbour
150  Node* neighbour_node_pt =
151  neighbour_pt->object_pt()->get_node_at_local_coordinate(
152  s_in_neighbour);
153 
154  // If there is no node at this position, there is a problem, since in
155  // a 1D element (whose nodes have already been built) there should
156  // ALWAYS be a node at each edge of the element.
157  if (neighbour_node_pt == 0)
158  {
159  std::string error_message =
160  "Problem: an element claims to have had its nodes built, yet\n";
161  error_message += "it is missing (a least) a node at its edge.\n";
162  throw OomphLibError(
163  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
164  }
165  // Otherwise, carry on
166  else
167  {
168  // Now work out whether it's a periodic boundary (this is only
169  // (possible if we have moved into a neighbouring tree)
170  if (in_neighbouring_tree)
171  {
172  // Return whether the neighbour is periodic
173  is_periodic = binary_tree_pt()->root_pt()->is_neighbour_periodic(
174  edge_in_current);
175  }
176  // Return the pointer to the neighbouring node
177  return neighbour_node_pt;
178  }
179  }
180  }
181  // Node not found, return null
182  return 0;
183  }
184 
185  //==========================================================================
186  /// Build the element by doing the following:
187  /// - Give it nodal positions (by establishing the pointers to its nodes).
188  /// In the process create new nodes where required (i.e. if they don't
189  /// already exist in the father element and have not already been created
190  /// whilst building new neighbouring elements). Node building involves
191  /// the following steps:
192  /// - Get the nodal position from the father element.
193  /// - Establish the time-history of the newly created nodal point
194  /// (its coordinates and previous values) consistent with the father's
195  /// history.
196  /// - Add the new node to the mesh itself.
197  /// - Doc newly created nodes in "new_nodes.dat" stored in the directory
198  /// of the DocInfo object (only if it's open!).
199  /// - NOTE: Unlike in higher-dimensional elements, in 1D it is impossible
200  /// for newly-created nodes to be on a mesh boundary, since any boundary
201  /// nodes must exist in the initial (coarse) mesh. Therefore it is not
202  /// necessary to add any nodes to the mesh's boundary node storage
203  /// schemes, and we always create normal "bulk" nodes.
204  /// - Once the element has a full complement of nodes, excute the element-
205  /// specific further_build() (empty by default -- must be overloaded for
206  /// specific elements). This deals with any build operations that are not
207  /// included in the generic process outlined above. For instance, in
208  /// Crouzeix Raviart elements we need to initialise the internal pressure
209  /// pressure values in a manner consistent with the pressure distribution
210  /// in the father element.
211  //==========================================================================
213  Vector<Node*>& new_node_pt,
214  bool& was_already_built,
215  std::ofstream& new_nodes_file)
216  {
217  using namespace BinaryTreeNames;
218 
219  // Find the number of nodes along a 1D edge (which is the number of nodes
220  // in the element for a 1D element!)
221  const unsigned n_node = nnode_1d();
222 
223  // Check whether static father_bound needs to be created
224  if (Father_bound[n_node].nrow() == 0)
225  {
226  setup_father_bounds();
227  }
228 
229  // Pointer to the current element's father (in binary tree impersonation)
230  BinaryTree* father_pt =
231  dynamic_cast<BinaryTree*>(binary_tree_pt()->father_pt());
232 
233  // What type of son is the current element?
234  // Ask its binary tree representation...
235  const int son_type = Tree_pt->son_type();
236 
237  // Has somebody built the current element already?
238  // Check this by determining whether or not the first node has been built
239 
240  // If this element has not already been built...
241  if (!nodes_built())
242  {
243 #ifdef PARANOID
244  if (father_pt == 0)
245  {
246  std::string error_message =
247  "Something fishy here: I have no father and yet \n";
248  error_message += "I have no nodes. Who has created me then?!\n";
249 
250  throw OomphLibError(
251  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
252  }
253 #endif
254 
255  // Indicate status
256  was_already_built = false;
257 
258  // Return pointer to father element
259  RefineableQElement<1>* father_el_pt =
260  dynamic_cast<RefineableQElement<1>*>(father_pt->object_pt());
261 
262  // Timestepper should be the same for all nodes in father element.
263  // Use it create timesteppers for new nodes.
264  TimeStepper* time_stepper_pt =
265  father_el_pt->node_pt(0)->time_stepper_pt();
266 
267  // Determine number of history values (including present)
268  const unsigned ntstorage = time_stepper_pt->ntstorage();
269 
270  // Currently we can't handle the case of generalised coordinates
271  // since we haven't established how they should be interpolated.
272  // Buffer this case:
273  if (father_el_pt->node_pt(0)->nposition_type() != 1)
274  {
275  throw OomphLibError("Can't handle generalised nodal positions (yet).",
276  OOMPH_CURRENT_FUNCTION,
277  OOMPH_EXCEPTION_LOCATION);
278  }
279 
280  // Set up vertex coordinates in the father element:
281  // ------------------------------------------------
282 
283  // Allocate storage for the vertex coordinates s_left and s_right of
284  // the current element as viewed by this element's father (i.e. s_left[0]
285  // stores the local coordinate within the father element at which the
286  // node on the current element's left-hand edge is located. Likewise,
287  // s_right[0] stores the local coordinate within the father element at
288  // which the node on the current element's right-hand edge is located).
289  Vector<double> s_left(1);
290  Vector<double> s_right(1);
291 
292  // In order to set up the vertex coordinates we need to know which
293  // type of son the current element is
294  switch (son_type)
295  {
296  case L:
297  s_left[0] = -1.0;
298  s_right[0] = 0.0;
299  break;
300 
301  case R:
302  s_left[0] = 0.0;
303  s_right[0] = 1.0;
304  break;
305  }
306 
307  // Pass macro element pointer on to sons and set coordinates in
308  // macro element
309  // hierher why can I see this?
310  if (father_el_pt->Macro_elem_pt != 0)
311  {
312  set_macro_elem_pt(father_el_pt->Macro_elem_pt);
313 
314  s_macro_ll(0) =
315  father_el_pt->s_macro_ll(0) +
316  0.5 * (s_left[0] + 1.0) *
317  (father_el_pt->s_macro_ur(0) - father_el_pt->s_macro_ll(0));
318  s_macro_ur(0) =
319  father_el_pt->s_macro_ll(0) +
320  0.5 * (s_right[0] + 1.0) *
321  (father_el_pt->s_macro_ur(0) - father_el_pt->s_macro_ll(0));
322  }
323 
324  // If the father element hasn't been generated yet, we're stuck...
325  if (father_el_pt->node_pt(0) == 0)
326  {
327  throw OomphLibError(
328  "Trouble: father_el_pt->node_pt(0)==0\n Can't build son element!\n",
329  OOMPH_CURRENT_FUNCTION,
330  OOMPH_EXCEPTION_LOCATION);
331  }
332  // Otherwise, carry on
333  else
334  {
335  // Allocate storage for the location of a node in terms of the local
336  // coordinate of the father element
337  Vector<double> s_in_father(1);
338 
339  // Allocate storage for the fractional position (in the current
340  // element) of the node in the direction of s[0]
341  Vector<double> s_fraction(1);
342 
343  // Loop over all nodes in the element
344  for (unsigned n = 0; n < n_node; n++)
345  {
346  // Get the fractional position (in the current element) of the node
347  // in the direction of s[0]
348  s_fraction[0] = local_one_d_fraction_of_node(n, 0);
349 
350  // Evaluate the local coordinate of the node in the father element
351  s_in_father[0] = s_left[0] + (s_right[0] - s_left[0]) * s_fraction[0];
352 
353  // Initialise flag: So far, this node hasn't been built or copied yet
354  bool node_done = false;
355 
356  // Get the pointer to the node in the father (returns NULL if there
357  // is no node at this position)
358  Node* created_node_pt =
359  father_el_pt->get_node_at_local_coordinate(s_in_father);
360 
361  // Does this node already exist in father element?
362  // -----------------------------------------------
363 
364  // If it does...
365  if (created_node_pt != 0)
366  {
367  // ...copy node across
368  node_pt(n) = created_node_pt;
369 
370  // Make sure that we update the values at the node so that they
371  // are consistent with the present representation. This is only
372  // needed for mixed interpolation where the value at the father
373  // could now become active.
374 
375  // Loop over all history values
376  for (unsigned t = 0; t < ntstorage; t++)
377  {
378  // Get values from father element
379  // Note: get_interpolated_values() sets Vector size itself
380  Vector<double> prev_values;
381  father_el_pt->get_interpolated_values(
382  t, s_in_father, prev_values);
383 
384  // Find the minimum number of values (either those stored at the
385  // node, or those returned by the function)
386  unsigned n_val_at_node = created_node_pt->nvalue();
387  unsigned n_val_from_function = prev_values.size();
388 
389  // Use the ternary conditional operator here
390  unsigned n_var = n_val_at_node < n_val_from_function ?
391  n_val_at_node :
392  n_val_from_function;
393 
394  // Assign the values that we can
395  for (unsigned k = 0; k < n_var; k++)
396  {
397  created_node_pt->set_value(t, k, prev_values[k]);
398  }
399  }
400 
401  // Indicate that node has been created by copy
402  node_done = true;
403  }
404 
405  // Node does not exist in father element but might already
406  // -------------------------------------------------------
407  // have been created by neighbouring elements
408  // ------------------------------------------
409 
410  else
411  {
412  // Was the node created by one of its neighbours? Whether or not
413  // the node lies on an edge can be calculated from the fractional
414  // position.
415  bool is_periodic = false;
416  created_node_pt =
417  node_created_by_neighbour(s_fraction, is_periodic);
418 
419  // If the node was so created...
420  if (created_node_pt != 0)
421  {
422  // ...assign the pointer
423  node_pt(n) = created_node_pt;
424 
425  // Indicate that node has been created by copy
426  node_done = true;
427 
428  // In a 1D mesh there is no way that a periodic node (which must
429  // be on a boundary) can exist without being part of the initial
430  // (coarse) mesh. Therefore issue an error message if
431  // node_created_by_neighbour(...) returns `is_periodic==true'.
432 #ifdef PARANOID
433  if (is_periodic)
434  {
435  std::string error_message =
436  "node_created_by_neighbour returns a node which claims\n";
437  error_message += "to be periodic. In a 1D mesh any periodic "
438  "nodes must exist\n";
439  error_message += "in the initial (coarse) mesh.";
440 
441  throw OomphLibError(error_message,
442  OOMPH_CURRENT_FUNCTION,
443  OOMPH_EXCEPTION_LOCATION);
444  }
445 #endif
446  }
447  }
448 
449  // Node does not exist in father element or neighbouring element
450  // -------------------------------------------------------------
451 
452  // If the node has not been built anywhere ---> build it here
453  if (!node_done)
454  {
455  // In a 1D mesh any node which lies on the boundary must exist in
456  // the initial (coarse) mesh, so any newly-built nodes cannot be
457  // boundary nodes. Therefore we always create a normal "bulk" node.
458 
459  // Create node and set the pointer to it from the element
460  created_node_pt = construct_node(n, time_stepper_pt);
461 
462  // Add to vector of new nodes
463  new_node_pt.push_back(created_node_pt);
464 
465  // Now we set the position and values at the newly created node.
466  // In the first instance use macro element or FE representation
467  // to create past and present nodal positions.
468  // (THIS STEP SHOULD NOT BE SKIPPED FOR ALGEBRAIC ELEMENTS AS NOT
469  // ALL OF THEM NECESSARILY IMPLEMENT NONTRIVIAL NODE UPDATE
470  // FUNCTIONS. CALLING THE NODE UPDATE FOR SUCH ELEMENTS/NODES WILL
471  // LEAVE THEIR NODAL POSITIONS WHERE THEY WERE (THIS IS APPROPRIATE
472  // ONCE THEY HAVE BEEN GIVEN POSITIONS) BUT WILL NOT ASSIGN SENSIBLE
473  // INITIAL POSITIONS!)
474 
475  // Loop over history values
476  for (unsigned t = 0; t < ntstorage; t++)
477  {
478  // Allocate storage for the previous position of the node
479  Vector<double> x_prev(1);
480 
481  // Get position from father element -- this uses the macro
482  // element representation if appropriate.
483  father_el_pt->get_x(t, s_in_father, x_prev);
484 
485  // Set the previous position of the new node
486  created_node_pt->x(t, 0) = x_prev[0];
487 
488  // Allocate storage for the previous values at the node
489  // NOTE: the size of this vector is equal to the number of values
490  // (e.g. 3 velocity components and 1 pressure, say)
491  // associated with each node and NOT the number of history values
492  // which the node stores!
493  Vector<double> prev_values;
494 
495  // Get values from father element
496  // Note: get_interpolated_values() sets Vector size itself.
497  father_el_pt->get_interpolated_values(
498  t, s_in_father, prev_values);
499 
500  // Determine the number of values at the new node
501  const unsigned n_value = created_node_pt->nvalue();
502 
503  // Loop over all values and set the previous values
504  for (unsigned v = 0; v < n_value; v++)
505  {
506  created_node_pt->set_value(t, v, prev_values[v]);
507  }
508  } // End of loop over history values
509 
510  // Add new node to mesh
511  mesh_pt->add_node_pt(created_node_pt);
512 
513  } // End of case where we build the node ourselves
514 
515  // Check if the element is an algebraic element
516  AlgebraicElementBase* alg_el_pt =
517  dynamic_cast<AlgebraicElementBase*>(this);
518 
519  // If it is, set up node position (past and present) from algebraic
520  // node position (past and present) from algebraic node update
521  // node update function. This over-writes previous assingments that
522  // were made based on the macro-element/FE representation.
523  // NOTE: YES, THIS NEEDS TO BE CALLED REPEATEDLY IF THE NODE IS A
524  // MEMBER OF MULTIPLE ELEMENTS: THEY ALL ASSIGN THE SAME NODAL
525  // POSITIONS BUT WE NEED TO ADD THE REMESH INFO FOR *ALL* ROOT
526  // ELEMENTS!
527  if (alg_el_pt != 0)
528  {
529  // Build algebraic node update info for new node. This sets up
530  // the node update data for all node update functions that are
531  // shared by all nodes in the father element.
532  alg_el_pt->setup_algebraic_node_update(
533  node_pt(n), s_in_father, father_el_pt);
534  }
535 
536  // If we have built the node and we are documenting our progress,
537  // write the (hopefully consistent position) to the outputfile
538  if ((!node_done) && (new_nodes_file.is_open()))
539  {
540  new_nodes_file << node_pt(n)->x(0) << std::endl;
541  }
542  } // End of loop over all nodes in element
543 
544 
545  // If the element is a MacroElementNodeUpdateElement, set the update
546  // parameters for the current element's nodes -- all this needs is
547  // the vector of (pointers to the) geometric objects that affect the
548  // MacroElement-based node update. This is the same as that in the
549  // father element
550  MacroElementNodeUpdateElementBase* father_m_el_pt =
551  dynamic_cast<MacroElementNodeUpdateElementBase*>(father_el_pt);
552  if (father_m_el_pt != 0)
553  {
554  // Get Vector of geometric objects from father (construct Vector
555  // via copy operation)
556  Vector<GeomObject*> geom_object_pt(father_m_el_pt->geom_object_pt());
557 
558  // Cast current element to MacroElementNodeUpdateElement:
560  dynamic_cast<MacroElementNodeUpdateElementBase*>(this);
561 
562 #ifdef PARANOID
563  if (m_el_pt == 0)
564  {
565  std::string error_message =
566  "Failed to cast to MacroElementNodeUpdateElementBase*\n";
567  error_message +=
568  "Strange -- if the father is a MacroElementNodeUpdateElement\n";
569  error_message += "the son should be too....\n";
570 
571  throw OomphLibError(
572  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
573  }
574 #endif
575  // Build update info by passing Vector of geometric objects:
576  // This sets the current element to be the update element for all
577  // of the element's nodes. This is reversed if the element is
578  // ever un-refined in the father element's rebuild_from_sons()
579  // function which overwrites this assignment to avoid nasty
580  // segmentation faults that occur when a node tries to update
581  // itself via an element that no longer exists...
582  m_el_pt->set_node_update_info(geom_object_pt);
583  }
584 
585 #ifdef OOMPH_HAS_MPI
586  // Pass on non-halo proc ID
587  Non_halo_proc_ID =
588  tree_pt()->father_pt()->object_pt()->non_halo_proc_ID();
589 #endif
590 
591  // Is the new element an ElementWithMovingNodes?
592  ElementWithMovingNodes* aux_el_pt =
593  dynamic_cast<ElementWithMovingNodes*>(this);
594 
595  // Pass down the information re the method for the evaluation
596  // of the shape derivatives
597  if (aux_el_pt != 0)
598  {
599  ElementWithMovingNodes* aux_father_el_pt =
600  dynamic_cast<ElementWithMovingNodes*>(father_el_pt);
601 
602 #ifdef PARANOID
603  if (aux_father_el_pt == 0)
604  {
605  std::string error_message =
606  "Failed to cast to ElementWithMovingNodes*\n";
607  error_message +=
608  "Strange -- if the son is a ElementWithMovingNodes\n";
609  error_message += "the father should be too....\n";
610 
611  throw OomphLibError(
612  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
613  }
614 #endif
615 
616  // If evaluating the residuals by finite differences in the father
617  // continue to do so in the child
618  if (aux_father_el_pt
619  ->are_dresidual_dnodal_coordinates_always_evaluated_by_fd())
620  {
621  aux_el_pt
623  }
624 
625  aux_el_pt->method_for_shape_derivs() =
626  aux_father_el_pt->method_for_shape_derivs();
627 
628  // If bypassing the evaluation of fill_in_jacobian_from_geometric_data
629  // continue to do so
630  if (aux_father_el_pt
631  ->is_fill_in_jacobian_from_geometric_data_bypassed())
632  {
634  }
635  }
636 
637 
638  // Now do further build (if any)
639  further_build();
640 
641  } // Sanity check: Father element has been generated
642 
643  } // End of if element has not already been built
644 
645  // If element has already been built, say so
646  else
647  {
648  was_already_built = true;
649  }
650  }
651 
652  //==========================================================================
653  /// Print corner nodes, use colour (default "BLACK")
654  //==========================================================================
655  void RefineableQElement<1>::output_corners(std::ostream& outfile,
656  const std::string& colour) const
657  {
658  // Allocate storage for local coordinate s
659  Vector<double> s(1);
660 
661  // Allocate storage for global coordinate of element vertex
662  Vector<double> vertex(1);
663 
664  outfile << "ZONE I=2,J=2, C=" << colour << std::endl;
665 
666  // Left-hand vertex
667  s[0] = -1.0;
668  get_x(s, vertex);
669  outfile << vertex[0] << " " << Number << std::endl;
670 
671  // Right-hand vertex
672  s[0] = 1.0;
673  get_x(s, vertex);
674  outfile << vertex[0] << " " << Number << std::endl;
675 
676  outfile << "TEXT CS = GRID, X = " << vertex[0]
677  << ", HU = GRID, H = 0.01, AN = MIDCENTER, T =\"" << Number << "\""
678  << std::endl;
679  }
680 
681  //==========================================================================
682  /// Check inter-element continuity of
683  /// - nodal positions
684  /// - (nodally) interpolated function values
685  //==========================================================================
687  {
688  using namespace BinaryTreeNames;
689 
690  // Calculate number of nodes
691  const unsigned n_node = nnode_1d();
692 
693  // Number of timesteps (including present) for which continuity is
694  // to be checked
695  const unsigned n_time = 1;
696 
697  // Initialise errors
698  max_error = 0.0;
699  Vector<double> max_error_x(1, 0.0);
700  double max_error_val = 0.0;
701 
702  // Initialise vector of element edges in the current element
703  Vector<int> edge_in_current(2);
704  edge_in_current[0] = L;
705  edge_in_current[1] = R;
706 
707  // Loop over both edges
708  for (unsigned edge_counter = 0; edge_counter < 2; edge_counter++)
709  {
710  // Allocate storage for the fractional position (in the current
711  // element) of the node in the direction of s[0]
712  Vector<double> s_fraction(1);
713 
714  // Allocate storage for the location of a node in terms of the local
715  // coordinate of the current element
716  Vector<double> s_in_current(1);
717 
718  // Allocate storage for the location of a node in terms of the local
719  // coordinate of the neighbouring element
720  Vector<double> s_in_neighbour(1);
721 
722  // Allocate storage for edge in neighbouring element
723  int edge_in_neighbour;
724 
725  // Allocate storage for difference in size between current and
726  // neighbouring element
727  int diff_level;
728 
729  // Allocate storage for flag indicating if the node is not in the same
730  // binary tree
731  bool in_neighbouring_tree;
732 
733  // Calculate the local coordinate and the local coordinate as viewed
734  // from the neighbour
735 
736  // Allocate storage for the pointer to the neighbouring element
737  // (using its binary tree representation)
738  BinaryTree* neighbour_pt;
739 
740  // Find pointer to neighbouring element along the edge in question and
741  // calculate the local coordinate of the node within that element,
742  // s_in_neighbour
743  neighbour_pt =
744  binary_tree_pt()->gteq_edge_neighbour(edge_in_current[edge_counter],
745  s_in_neighbour,
746  edge_in_neighbour,
747  diff_level,
748  in_neighbouring_tree);
749 
750  // If neighbour exists and has existing nodes
751  if ((neighbour_pt != 0) && (neighbour_pt->object_pt()->nodes_built()))
752  {
753  // Need to exclude periodic nodes from this check.
754  // There are only periodic nodes if we are in a neighbouring tree...
755  bool is_periodic = false;
756  if (in_neighbouring_tree)
757  {
758  // Is it periodic?
759  is_periodic = tree_pt()->root_pt()->is_neighbour_periodic(
760  edge_in_current[edge_counter]);
761  }
762 
763  // Allocate storage for pointer to the local node
764  Node* local_node_pt = 0;
765 
766  switch (edge_counter)
767  {
768  case 0:
769  // Local fraction of node
770  s_fraction[0] = 0.0;
771  // Get pointer to local node
772  local_node_pt = node_pt(0);
773  break;
774 
775  case 1:
776  // Local fraction of node
777  s_fraction[0] = 1.0;
778  // Get pointer to local node
779  local_node_pt = node_pt(n_node - 1);
780  break;
781  }
782 
783  // Evaluate the local coordinate of the node in the current element
784  s_in_current[0] = -1.0 + 2.0 * s_fraction[0];
785 
786  // NOTE: We have already calculated the local coordinate of the node
787  // in the neighbouring element above when calling gteq_edge_neighbour()
788 
789  // Loop over timesteps
790  for (unsigned t = 0; t < n_time; t++)
791  {
792  // Allocate storage for the nodal position in the neighbouring element
793  Vector<double> x_in_neighbour(1);
794 
795  // Get the nodal position from the neighbouring element
796  neighbour_pt->object_pt()->interpolated_x(
797  t, s_in_neighbour, x_in_neighbour);
798 
799  // Check error only if the node is NOT periodic
800  if (is_periodic == false)
801  {
802  // Find the spatial error
803  double err = std::fabs(local_node_pt->x(t, 0) - x_in_neighbour[0]);
804 
805  // If it's bigger than our tolerance, say so
806  if (err > 1e-9)
807  {
808  oomph_info << "errx " << err << " " << t << " "
809  << local_node_pt->x(t, 0) << " " << x_in_neighbour[0]
810  << std::endl;
811 
812  oomph_info << "at " << local_node_pt->x(0) << std::endl;
813  }
814 
815  // If it's bigger than the previous max error, it is the
816  // new max error!
817  if (err > max_error_x[0])
818  {
819  max_error_x[0] = err;
820  }
821  }
822  // Allocate storage for the nodal values in the neighbouring element
823  Vector<double> values_in_neighbour;
824 
825  // Get the values from neighbouring element. NOTE: Number of values
826  // gets set by routine (because in general we don't know how many
827  // interpolated values a certain element has.
828  neighbour_pt->object_pt()->get_interpolated_values(
829  t, s_in_neighbour, values_in_neighbour);
830 
831  // Allocate storage for the nodal values in the current element
832  Vector<double> values_in_current;
833 
834  // Get the values in current element
835  get_interpolated_values(t, s_in_current, values_in_current);
836 
837  // Now figure out how many continuously interpolated values there are
838  const unsigned num_val =
839  neighbour_pt->object_pt()->ncont_interpolated_values();
840 
841  // Check error
842  for (unsigned ival = 0; ival < num_val; ival++)
843  {
844  // Find the spatial error
845  double err =
846  std::fabs(values_in_current[ival] - values_in_neighbour[ival]);
847 
848  // If it's bigger than our tolerance, say so
849  if (err > 1.0e-10)
850  {
851  oomph_info << local_node_pt->x(0) << "\n# "
852  << "erru " << err << " " << ival << " "
853  << get_node_number(local_node_pt) << " "
854  << values_in_current[ival] << " "
855  << values_in_neighbour[ival] << std::endl;
856  }
857 
858  // If it's bigger than the previous max error, it is the
859  // new max error!
860  if (err > max_error_val)
861  {
862  max_error_val = err;
863  }
864  }
865  } // End of loop over timesteps
866  } // End of if neighbour exists and has existing nodes
867  } // End of loop over edges
868 
869  // Update max_error if necessary
870  max_error = max_error_x[0];
871  if (max_error_val > max_error)
872  {
873  max_error = max_error_val;
874  }
875 
876  // Output max_error information
877  if (max_error > 1e-9)
878  {
879  oomph_info << "\n#------------------------------------ \n#Max error ";
880  oomph_info << max_error_x[0] << " " << max_error_val << std::endl;
881  oomph_info << "#------------------------------------ \n " << std::endl;
882  }
883  }
884 
885  //==========================================================================
886  /// Static matrix for coincidence between son nodal points and father
887  /// boundaries
888  //==========================================================================
889  std::map<unsigned, DenseMatrix<int>> RefineableQElement<1>::Father_bound;
890 
891 } // namespace oomph
e
Definition: cfortran.h:571
static char t char * s
Definition: cfortran.h:568
char t
Definition: cfortran.h:568
////////////////////////////////////////////////////////////////////
void setup_algebraic_node_update(Node *&node_pt, const Vector< double > &s_father, FiniteElement *father_el_pt) const
Set up node update info for (newly created) algebraic node: I.e. work out its node update information...
BinaryTree class: Recursively defined, generalised binary tree.
Definition: binary_tree.h:92
BinaryTree * gteq_edge_neighbour(const int &direction, Vector< double > &s_in_neighbour, int &edge, int &diff_level, bool &in_neighbouring_tree) const
Return pointer to greater or equal-sized edge neighbour in specified direction; also provide info reg...
Definition: binary_tree.cc:172
TimeStepper *& time_stepper_pt()
Return the pointer to the timestepper.
Definition: nodes.h:238
void set_value(const unsigned &i, const double &value_)
Set the i-th stored data value to specified value. The only reason that we require an explicit set fu...
Definition: nodes.h:271
unsigned nvalue() const
Return number of values stored in data object (incl pinned ones).
Definition: nodes.h:483
/////////////////////////////////////////////////////////////////////// /////////////////////////////...
void enable_bypass_fill_in_jacobian_from_geometric_data()
Bypass the call to fill_in_jacobian_from_geometric_data.
int & method_for_shape_derivs()
Access to method (enumerated flag) for determination of shape derivs.
void enable_always_evaluate_dresidual_dnodal_coordinates_by_fd()
Insist that shape derivatives are always evaluated by fd (using FiniteElement::get_dresidual_dnodal_c...
Node *& node_pt(const unsigned &n)
Return a pointer to the local node n.
Definition: elements.h:2179
virtual Node * get_node_at_local_coordinate(const Vector< double > &s) const
If there is a node at this local coordinate, return the pointer to the node.
Definition: elements.cc:3912
virtual double interpolated_x(const Vector< double > &s, const unsigned &i) const
Return FE interpolated coordinate x[i] at local coordinate s.
Definition: elements.cc:3992
MacroElement * Macro_elem_pt
Pointer to the element's macro element (NULL by default)
Definition: elements.h:1687
void get_x(const Vector< double > &s, Vector< double > &x) const
Global coordinates as function of local coordinates. Either via FE representation or via macro-elemen...
Definition: elements.h:1889
////////////////////////////////////////////////////////////////////
Vector< GeomObject * > & geom_object_pt()
Vector of (pointers to) geometric objects involved in node update function.
virtual void set_node_update_info(const Vector< GeomObject * > &geom_object_pt)=0
Set node update information: Pass the vector of (pointers to) the geometric objects that affect the n...
A general mesh class.
Definition: mesh.h:67
void add_node_pt(Node *const &node_pt)
Add a (pointer to a) node to the mesh.
Definition: mesh.h:611
Nodes are derived from Data, but, in addition, have a definite (Eulerian) position in a space of a gi...
Definition: nodes.h:906
double & x(const unsigned &i)
Return the i-th nodal coordinate.
Definition: nodes.h:1060
unsigned nposition_type() const
Number of coordinate types needed in the mapping between local and global coordinates.
Definition: nodes.h:1016
An OomphLibError object which should be thrown when an run-time error is encountered....
double & s_macro_ll(const unsigned &i)
Access fct to the i-th coordinate of the element's "lower left" vertex in the associated MacroElement...
Definition: Qelements.h:186
double & s_macro_ur(const unsigned &i)
Access fct to the i-th coordinate of the element's "upper right" vertex in the associated MacroElemen...
Definition: Qelements.h:202
virtual bool nodes_built()
Return true if all the nodes have been built, false if not.
virtual unsigned ncont_interpolated_values() const =0
Number of continuously interpolated values. Note: We assume that they are located at the beginning of...
virtual void get_interpolated_values(const Vector< double > &s, Vector< double > &values)
Get all continously interpolated function values in this element as a Vector. Note: Vector sets is ow...
Refineable version of QElement<1,NNODE_1D>.
A class that is used to template the refineable Q elements by dimension. It's really nothing more tha...
Definition: Qelements.h:2259
////////////////////////////////////////////////////////////////////// //////////////////////////////...
Definition: timesteppers.h:231
bool is_neighbour_periodic(const int &direction)
Return whether the neighbour in the particular direction is periodic.
Definition: tree.h:364
RefineableElement * object_pt() const
Return the pointer to the object (RefineableElement) represented by the tree.
Definition: tree.h:88
int son_type() const
Return son type.
Definition: tree.h:214
static const int OMEGA
Default value for an unassigned neighbour.
Definition: tree.h:262
TreeRoot *& root_pt()
Return pointer to root of the tree.
Definition: tree.h:141
std::string string(const unsigned &i)
Return the i-th string or "" if the relevant string hasn't been defined.
unsigned Number
The unsigned.
Vector< std::string > colour
Tecplot colours.
//////////////////////////////////////////////////////////////////// ////////////////////////////////...
OomphInfo oomph_info
Single (global) instantiation of the OomphInfo object – this is used throughout the library as a "rep...