Line data Source code
1 : // The libMesh Finite Element Library.
2 : // Copyright (C) 2002-2026 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
3 :
4 : // This library is free software; you can redistribute it and/or
5 : // modify it under the terms of the GNU Lesser General Public
6 : // License as published by the Free Software Foundation; either
7 : // version 2.1 of the License, or (at your option) any later version.
8 :
9 : // This library is distributed in the hope that it will be useful,
10 : // but WITHOUT ANY WARRANTY; without even the implied warranty of
11 : // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 : // Lesser General Public License for more details.
13 :
14 : // You should have received a copy of the GNU Lesser General Public
15 : // License along with this library; if not, write to the Free Software
16 : // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
17 :
18 :
19 :
20 : // Local includes
21 : #include "libmesh/replicated_mesh.h"
22 :
23 : #include "libmesh/boundary_info.h"
24 : #include "libmesh/elem.h"
25 : #include "libmesh/libmesh_logging.h"
26 : #include "libmesh/mesh_communication.h"
27 : #include "libmesh/parallel_implementation.h"
28 : #include "libmesh/partitioner.h"
29 : #include "libmesh/point.h"
30 : #include "libmesh/string_to_enum.h"
31 : #include "libmesh/utility.h"
32 :
33 : // C++ includes
34 : #include <unordered_map>
35 : #include <unordered_set>
36 :
37 : namespace libMesh
38 : {
39 :
40 : // ------------------------------------------------------------
41 : // ReplicatedMesh class member functions
42 69922 : ReplicatedMesh::ReplicatedMesh (const Parallel::Communicator & comm_in,
43 69922 : unsigned char d) :
44 : UnstructuredMesh (comm_in,d),
45 69922 : _n_nodes(0), _n_elem(0)
46 : {
47 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
48 : // In serial we just need to reset the next unique id to zero
49 : // here in the constructor.
50 69922 : _next_unique_id = 0;
51 : #endif
52 :
53 81834 : const std::string default_partitioner = "metis";
54 : const std::string my_partitioner =
55 : libMesh::command_line_value("--default-partitioner",
56 139844 : default_partitioner);
57 : _partitioner = Partitioner::build
58 127932 : (Utility::string_to_enum<PartitionerType>(my_partitioner));
59 69922 : }
60 :
61 :
62 2395 : bool ReplicatedMesh::subclass_locally_equals(const MeshBase & other_mesh_base) const
63 : {
64 1038 : const ReplicatedMesh * rep_mesh_ptr =
65 2395 : dynamic_cast<const ReplicatedMesh *>(&other_mesh_base);
66 2395 : if (!rep_mesh_ptr)
67 0 : return false;
68 1038 : const ReplicatedMesh & other_mesh = *rep_mesh_ptr;
69 :
70 5828 : if (_n_nodes != other_mesh._n_nodes ||
71 2395 : _n_elem != other_mesh._n_elem ||
72 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
73 7185 : _next_unique_id != other_mesh._next_unique_id ||
74 : #endif
75 2395 : !this->nodes_and_elements_equal(other_mesh))
76 78 : return false;
77 :
78 1034 : return true;
79 : }
80 :
81 :
82 84555 : ReplicatedMesh::~ReplicatedMesh ()
83 : {
84 74174 : this->ReplicatedMesh::clear(); // Free nodes and elements
85 84555 : }
86 :
87 :
88 : // This might be specialized later, but right now it's just here to
89 : // make sure the compiler doesn't give us a default (non-deep) copy
90 : // constructor instead.
91 4181 : ReplicatedMesh::ReplicatedMesh (const ReplicatedMesh & other_mesh) :
92 4181 : ReplicatedMesh(static_cast<const MeshBase&>(other_mesh))
93 : {
94 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
95 4181 : this->_next_unique_id = other_mesh._next_unique_id;
96 : #endif
97 4181 : }
98 :
99 :
100 4252 : ReplicatedMesh::ReplicatedMesh (const MeshBase & other_mesh) :
101 : UnstructuredMesh (other_mesh),
102 4252 : _n_nodes(0), _n_elem(0) // copy_* will increment this
103 : {
104 : // Just copy, skipping preparation
105 4252 : this->copy_nodes_and_elements(other_mesh, true, 0, 0, 0, nullptr, true);
106 :
107 1424 : this->allow_find_neighbors(other_mesh.allow_find_neighbors());
108 1424 : this->allow_detect_interior_parents(other_mesh.allow_detect_interior_parents());
109 1424 : this->allow_renumbering(other_mesh.allow_renumbering());
110 1424 : this->allow_remote_element_removal(other_mesh.allow_remote_element_removal());
111 1424 : this->skip_partitioning(other_mesh.skip_partitioning());
112 :
113 4252 : this->copy_constraint_rows(other_mesh);
114 :
115 724 : auto & this_boundary_info = this->get_boundary_info();
116 724 : const auto & other_boundary_info = other_mesh.get_boundary_info();
117 :
118 4252 : this_boundary_info = other_boundary_info;
119 :
120 724 : this->set_subdomain_name_map() = other_mesh.get_subdomain_name_map();
121 :
122 4252 : this->_preparation = other_mesh.preparation();
123 :
124 : // If other_mesh is distributed, then we've got parts of it on each
125 : // processor but we're not replicated yet; fix that.
126 4252 : if (!other_mesh.is_serial())
127 71 : MeshCommunication().allgather(*this);
128 4252 : }
129 :
130 156 : ReplicatedMesh & ReplicatedMesh::operator= (ReplicatedMesh && other_mesh)
131 : {
132 16 : LOG_SCOPE("operator=(&&)", "ReplicatedMesh");
133 :
134 : // Move assign as an UnstructuredMesh
135 8 : this->UnstructuredMesh::operator=(std::move(other_mesh));
136 :
137 : // Nodes and elements belong to ReplicatedMesh and have to be
138 : // moved before we can move arbitrary GhostingFunctor, Partitioner,
139 : // etc. subclasses.
140 156 : this->move_nodes_and_elements(std::move(other_mesh));
141 :
142 : // Handle those remaining moves.
143 156 : this->post_dofobject_moves(std::move(other_mesh));
144 :
145 164 : return *this;
146 : }
147 :
148 156 : MeshBase & ReplicatedMesh::assign(MeshBase && other_mesh)
149 : {
150 156 : *this = std::move(cast_ref<ReplicatedMesh&>(other_mesh));
151 :
152 156 : return *this;
153 : }
154 :
155 156 : void ReplicatedMesh::move_nodes_and_elements(MeshBase && other_meshbase)
156 : {
157 8 : ReplicatedMesh & other_mesh = cast_ref<ReplicatedMesh&>(other_meshbase);
158 :
159 156 : this->_nodes = std::move(other_mesh._nodes);
160 156 : this->_n_nodes = other_mesh.n_nodes();
161 :
162 156 : this->_elements = std::move(other_mesh._elements);
163 156 : this->_n_elem = other_mesh.n_elem();
164 156 : }
165 :
166 :
167 16014855 : const Point & ReplicatedMesh::point (const dof_id_type i) const
168 : {
169 16014855 : return this->node_ref(i);
170 : }
171 :
172 :
173 :
174 :
175 101596618 : const Node * ReplicatedMesh::node_ptr (const dof_id_type i) const
176 : {
177 5262824 : libmesh_assert_less (i, this->max_node_id());
178 5262824 : libmesh_assert(_nodes[i]);
179 5262824 : libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
180 :
181 106821548 : return _nodes[i];
182 : }
183 :
184 :
185 :
186 :
187 108134541 : Node * ReplicatedMesh::node_ptr (const dof_id_type i)
188 : {
189 10155925 : libmesh_assert_less (i, this->max_node_id());
190 10155925 : libmesh_assert(_nodes[i]);
191 10155925 : libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
192 :
193 117649116 : return _nodes[i];
194 : }
195 :
196 :
197 :
198 :
199 17381450 : const Node * ReplicatedMesh::query_node_ptr (const dof_id_type i) const
200 : {
201 17381450 : if (i >= this->max_node_id())
202 0 : return nullptr;
203 17131445 : libmesh_assert (_nodes[i] == nullptr ||
204 : _nodes[i]->id() == i); // This will change soon
205 :
206 17466632 : return _nodes[i];
207 : }
208 :
209 :
210 :
211 :
212 2779108 : Node * ReplicatedMesh::query_node_ptr (const dof_id_type i)
213 : {
214 2779108 : if (i >= this->max_node_id())
215 87059 : return nullptr;
216 223714 : libmesh_assert (_nodes[i] == nullptr ||
217 : _nodes[i]->id() == i); // This will change soon
218 :
219 2132623 : return _nodes[i];
220 : }
221 :
222 :
223 :
224 :
225 3220829 : const Elem * ReplicatedMesh::elem_ptr (const dof_id_type i) const
226 : {
227 515737 : libmesh_assert_less (i, this->max_elem_id());
228 515737 : libmesh_assert(_elements[i]);
229 515737 : libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
230 :
231 3640183 : return _elements[i];
232 : }
233 :
234 :
235 :
236 :
237 95646427 : Elem * ReplicatedMesh::elem_ptr (const dof_id_type i)
238 : {
239 5269618 : libmesh_assert_less (i, this->max_elem_id());
240 5269618 : libmesh_assert(_elements[i]);
241 5269618 : libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
242 :
243 100163421 : return _elements[i];
244 : }
245 :
246 :
247 :
248 :
249 15386750 : const Elem * ReplicatedMesh::query_elem_ptr (const dof_id_type i) const
250 : {
251 15386750 : if (i >= this->max_elem_id())
252 0 : return nullptr;
253 15302410 : libmesh_assert (_elements[i] == nullptr ||
254 : _elements[i]->id() == i); // This will change soon
255 :
256 15416334 : return _elements[i];
257 : }
258 :
259 :
260 :
261 :
262 1465357 : Elem * ReplicatedMesh::query_elem_ptr (const dof_id_type i)
263 : {
264 1465357 : if (i >= this->max_elem_id())
265 44881 : return nullptr;
266 188348 : libmesh_assert (_elements[i] == nullptr ||
267 : _elements[i]->id() == i); // This will change soon
268 :
269 809070 : return _elements[i];
270 : }
271 :
272 :
273 :
274 :
275 16048389 : Elem * ReplicatedMesh::add_elem (Elem * e)
276 : {
277 1162578 : libmesh_assert(e);
278 :
279 : // We no longer merely append elements with ReplicatedMesh
280 :
281 : // If the user requests a valid id that doesn't correspond to an
282 : // existing element, let's give them that id, resizing the elements
283 : // container if necessary.
284 16048389 : if (!e->valid_id())
285 822060 : e->set_id (cast_int<dof_id_type>(_elements.size()));
286 :
287 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
288 16048389 : if (!e->valid_unique_id())
289 5219609 : e->set_unique_id(_next_unique_id++);
290 : else
291 11687381 : _next_unique_id = std::max(_next_unique_id, e->unique_id()+1);
292 : #endif
293 :
294 2314268 : const dof_id_type id = e->id();
295 :
296 17200079 : if (id < _elements.size())
297 : {
298 : // This should *almost* never happen, but we rely on it when
299 : // using allgather to replicate a not-yet-actually-replicated
300 : // ReplicatedMesh under construction in parallel.
301 169275 : if (e == _elements[id])
302 0 : return e;
303 :
304 : // Overwriting existing elements is still probably a mistake.
305 17132 : libmesh_assert(!_elements[id]);
306 : }
307 : else
308 : {
309 15879114 : _elements.resize(id+1, nullptr);
310 : }
311 :
312 16048389 : ++_n_elem;
313 16048389 : _elements[id] = e;
314 :
315 : // We actually added a new element. Some of our caches might still
316 : // be valid, but we should clear the ones which definitely are not.
317 16048389 : this->clear_point_locator();
318 16048389 : this->clear_stored_ranges();
319 :
320 : // Make sure any new element is given space for any extra integers
321 : // we've requested
322 16048389 : e->add_extra_integers(_elem_integer_names.size(),
323 16048389 : _elem_integer_default_values);
324 :
325 : // And set mapping type and data on any new element
326 2314268 : e->set_mapping_type(this->default_mapping_type());
327 2314268 : e->set_mapping_data(this->default_mapping_data());
328 :
329 16048389 : return e;
330 : }
331 :
332 15234442 : Elem * ReplicatedMesh::add_elem (std::unique_ptr<Elem> e)
333 : {
334 : // The mesh now takes ownership of the Elem. Eventually the guts of
335 : // add_elem() will get moved to a private helper function, and
336 : // calling add_elem() directly will be deprecated.
337 15234442 : return add_elem(e.release());
338 : }
339 :
340 :
341 :
342 626045 : Elem * ReplicatedMesh::insert_elem (Elem * e)
343 : {
344 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
345 626045 : if (!e->valid_unique_id())
346 18176 : e->set_unique_id(_next_unique_id++);
347 : else
348 607869 : _next_unique_id = std::max(_next_unique_id, e->unique_id()+1);
349 : #endif
350 :
351 260196 : dof_id_type eid = e->id();
352 130098 : libmesh_assert_less (eid, _elements.size());
353 626045 : Elem * oldelem = _elements[eid];
354 :
355 626045 : if (oldelem)
356 : {
357 130098 : libmesh_assert_equal_to (oldelem->id(), eid);
358 626045 : this->delete_elem(oldelem);
359 : }
360 :
361 626045 : ++_n_elem;
362 626045 : _elements[eid] = e;
363 :
364 : // We actually added a new element. Some of our caches might still
365 : // be valid, but we should clear the ones which definitely are not.
366 626045 : this->clear_point_locator();
367 626045 : this->clear_stored_ranges();
368 :
369 : // Make sure any new element is given space for any extra integers
370 : // we've requested
371 626045 : e->add_extra_integers(_elem_integer_names.size(),
372 626045 : _elem_integer_default_values);
373 :
374 : // And set mapping type and data on any new element
375 260196 : e->set_mapping_type(this->default_mapping_type());
376 260196 : e->set_mapping_data(this->default_mapping_data());
377 :
378 626045 : return e;
379 : }
380 :
381 626045 : Elem * ReplicatedMesh::insert_elem (std::unique_ptr<Elem> e)
382 : {
383 : // The mesh now takes ownership of the Elem. Eventually the guts of
384 : // insert_elem(Elem*) will get moved to a private helper function, and
385 : // calling insert_elem(Elem*) directly will be deprecated.
386 626045 : return insert_elem(e.release());
387 : }
388 :
389 :
390 :
391 2434621 : void ReplicatedMesh::delete_elem(Elem * e)
392 : {
393 242305 : libmesh_assert(e);
394 :
395 : // Initialize an iterator to eventually point to the element we want to delete
396 242305 : std::vector<Elem *>::iterator pos = _elements.end();
397 :
398 : // In many cases, e->id() gives us a clue as to where e
399 : // is located in the _elements vector. Try that first
400 : // before trying the O(n_elem) search.
401 242305 : libmesh_assert_less (e->id(), _elements.size());
402 :
403 2676926 : if (_elements[e->id()] == e)
404 : {
405 : // We found it!
406 2192316 : pos = _elements.begin();
407 242305 : std::advance(pos, e->id());
408 : }
409 :
410 : else
411 : {
412 : // This search is O(n_elem)
413 0 : pos = std::find (_elements.begin(),
414 : _elements.end(),
415 0 : e);
416 : }
417 :
418 : // Huh? Element not in the vector?
419 242305 : libmesh_assert (pos != _elements.end());
420 :
421 : // Remove the element from the BoundaryInfo object
422 2434621 : this->get_boundary_info().remove(e);
423 :
424 : // delete the element
425 2434621 : --_n_elem;
426 2434621 : delete e;
427 :
428 : // explicitly zero the pointer
429 2434621 : *pos = nullptr;
430 :
431 : // Some of our caches might still be valid, but we should clear the
432 : // ones which definitely are not.
433 2434621 : this->clear_point_locator();
434 2434621 : this->clear_stored_ranges();
435 2434621 : }
436 :
437 :
438 :
439 21420 : void ReplicatedMesh::renumber_elem(const dof_id_type old_id,
440 : const dof_id_type new_id)
441 : {
442 : // This could be a no-op
443 21420 : if (old_id == new_id)
444 0 : return;
445 :
446 : // This doesn't get used in serial yet
447 21420 : Elem * el = _elements[old_id];
448 7140 : libmesh_assert (el);
449 :
450 28560 : if (new_id >= _elements.size())
451 288 : _elements.resize(new_id+1, nullptr);
452 :
453 7140 : el->set_id(new_id);
454 7140 : libmesh_assert (!_elements[new_id]);
455 28560 : _elements[new_id] = el;
456 21420 : _elements[old_id] = nullptr;
457 :
458 : // Should we delete any caches here? Our point locator indexes by
459 : // element pointer and should be fine with an id change. Our stored
460 : // ranges are no longer sorted, which is *probably* fine, but let's
461 : // just be safe.
462 21420 : this->clear_stored_ranges();
463 : }
464 :
465 :
466 :
467 11735707 : Node * ReplicatedMesh::add_point (const Point & p,
468 : const dof_id_type id,
469 : const processor_id_type proc_id)
470 : {
471 1806574 : Node * n = nullptr;
472 :
473 : // If the user requests a valid id, either
474 : // provide the existing node or resize the container
475 : // to fit the new node.
476 11735707 : if (id != DofObject::invalid_id)
477 7756065 : if (id < _nodes.size())
478 14819 : n = _nodes[id];
479 : else
480 6825808 : _nodes.resize(id+1);
481 : else
482 4895080 : _nodes.push_back (static_cast<Node *>(nullptr));
483 :
484 : // if the node already exists, then assign new (x,y,z) values
485 1819244 : if (n)
486 0 : *n = p;
487 : // otherwise build a new node, put it in the right spot, and return
488 : // a valid pointer.
489 : else
490 : {
491 22555976 : n = Node::build(p, (id == DofObject::invalid_id) ?
492 7590534 : cast_int<dof_id_type>(_nodes.size()-1) : id).release();
493 11735707 : n->processor_id() = proc_id;
494 :
495 11735707 : n->add_extra_integers(_node_integer_names.size(),
496 11735707 : _node_integer_default_values);
497 :
498 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
499 11735707 : if (!n->valid_unique_id())
500 11735707 : n->set_unique_id(_next_unique_id++);
501 : else
502 0 : _next_unique_id = std::max(_next_unique_id, n->unique_id()+1);
503 : #endif
504 :
505 11735707 : ++_n_nodes;
506 11735707 : if (id == DofObject::invalid_id)
507 4895080 : _nodes.back() = n;
508 : else
509 7756065 : _nodes[id] = n;
510 : }
511 :
512 : // better not pass back a nullptr.
513 1806574 : libmesh_assert (n);
514 :
515 11735707 : return n;
516 : }
517 :
518 :
519 :
520 945630 : Node * ReplicatedMesh::add_node (Node * n)
521 : {
522 96754 : libmesh_assert(n);
523 :
524 : // If the user requests a valid id, either set the existing
525 : // container entry or resize the container to fit the new node.
526 945630 : if (n->valid_id())
527 : {
528 96673 : const dof_id_type id = n->id();
529 1041891 : if (id < _nodes.size())
530 15076 : libmesh_assert(!_nodes[id]);
531 : else
532 748877 : _nodes.resize(id+1); // default nullptr
533 :
534 1041891 : _nodes[id] = n;
535 : }
536 : else
537 : {
538 162 : n->set_id (cast_int<dof_id_type>(_nodes.size()));
539 412 : _nodes.push_back(n);
540 : }
541 :
542 945630 : ++_n_nodes;
543 :
544 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
545 945630 : if (!n->valid_unique_id())
546 420 : n->set_unique_id(_next_unique_id++);
547 : else
548 1443695 : _next_unique_id = std::max(_next_unique_id, n->unique_id()+1);
549 : #endif
550 :
551 945630 : n->add_extra_integers(_node_integer_names.size(),
552 945630 : _node_integer_default_values);
553 :
554 945630 : return n;
555 : }
556 :
557 945630 : Node * ReplicatedMesh::add_node (std::unique_ptr<Node> n)
558 : {
559 : // The mesh now takes ownership of the Node. Eventually the guts of
560 : // add_node() will get moved to a private helper function, and
561 : // calling add_node() directly will be deprecated.
562 945630 : return add_node(n.release());
563 : }
564 :
565 250912 : void ReplicatedMesh::delete_node(Node * n)
566 : {
567 63787 : libmesh_assert(n);
568 63787 : libmesh_assert_less (n->id(), _nodes.size());
569 :
570 : // Initialize an iterator to eventually point to the element we want
571 : // to delete
572 63787 : std::vector<Node *>::iterator pos;
573 :
574 : // In many cases, e->id() gives us a clue as to where e
575 : // is located in the _elements vector. Try that first
576 : // before trying the O(n_elem) search.
577 314699 : if (_nodes[n->id()] == n)
578 : {
579 187125 : pos = _nodes.begin();
580 63787 : std::advance(pos, n->id());
581 : }
582 : else
583 : {
584 0 : pos = std::find (_nodes.begin(),
585 : _nodes.end(),
586 0 : n);
587 : }
588 :
589 : // Huh? Node not in the vector?
590 63787 : libmesh_assert (pos != _nodes.end());
591 :
592 : // Delete the node from the BoundaryInfo object
593 250912 : this->get_boundary_info().remove(n);
594 127574 : _constraint_rows.erase(n);
595 :
596 : // delete the node
597 250912 : --_n_nodes;
598 438037 : delete n;
599 :
600 : // explicitly zero the pointer
601 250912 : *pos = nullptr;
602 250912 : }
603 :
604 :
605 :
606 70092 : void ReplicatedMesh::renumber_node(const dof_id_type old_id,
607 : const dof_id_type new_id)
608 : {
609 : // This could be a no-op
610 70092 : if (old_id == new_id)
611 0 : return;
612 :
613 : // This doesn't get used in serial yet
614 70092 : Node * nd = _nodes[old_id];
615 23364 : libmesh_assert (nd);
616 :
617 93456 : if (new_id >= _nodes.size())
618 288 : _nodes.resize(new_id+1, nullptr);
619 :
620 23364 : nd->set_id(new_id);
621 23364 : libmesh_assert (!_nodes[new_id]);
622 93456 : _nodes[new_id] = nd;
623 70092 : _nodes[old_id] = nullptr;
624 : }
625 :
626 :
627 :
628 127185 : void ReplicatedMesh::clear ()
629 : {
630 : // Call parent clear function
631 127185 : MeshBase::clear();
632 :
633 : // Clear our elements and nodes
634 : // There is no need to remove them from
635 : // the BoundaryInfo data structure since we
636 : // already cleared it.
637 127185 : this->ReplicatedMesh::clear_elems();
638 :
639 10947439 : for (auto & node : _nodes)
640 19944869 : delete node;
641 :
642 127185 : _n_nodes = 0;
643 23980 : _nodes.clear();
644 127185 : }
645 :
646 :
647 :
648 127897 : void ReplicatedMesh::clear_elems ()
649 : {
650 14569024 : for (auto & elem : _elements)
651 14441127 : delete elem;
652 :
653 127897 : _n_elem = 0;
654 24186 : _elements.clear();
655 127897 : }
656 :
657 :
658 :
659 235474 : void ReplicatedMesh::update_parallel_id_counts()
660 : {
661 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
662 235474 : _next_unique_id = this->parallel_max_unique_id();
663 : #endif
664 :
665 : // Implicitly get max_elem_id/max_node_id by trimming the vectors
666 470948 : auto trim_vec = [](auto & dof_vec) {
667 583044 : auto last_non_null = std::find_if(dof_vec.rbegin(), dof_vec.rend(), [](DofObject * d) { return (d != nullptr); });
668 470948 : dof_vec.resize(last_non_null.base()-dof_vec.begin());
669 470948 : };
670 :
671 235474 : trim_vec(this->_nodes);
672 235474 : trim_vec(this->_elements);
673 :
674 235474 : _n_constraint_rows = this->count_constraint_rows();
675 :
676 235474 : this->_preparation.has_synched_id_counts = true;
677 235474 : }
678 :
679 :
680 :
681 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
682 252872 : unique_id_type ReplicatedMesh::parallel_max_unique_id() const
683 : {
684 : // This function must be run on all processors at once
685 44352 : parallel_object_only();
686 :
687 252872 : unique_id_type max_local = _next_unique_id;
688 252872 : this->comm().max(max_local);
689 252872 : return max_local;
690 : }
691 :
692 :
693 :
694 21166 : void ReplicatedMesh::set_next_unique_id(unique_id_type id)
695 : {
696 21166 : _next_unique_id = id;
697 21166 : }
698 : #endif
699 :
700 :
701 :
702 188379 : void ReplicatedMesh::renumber_nodes_and_elements ()
703 : {
704 109974 : LOG_SCOPE("renumber_nodes_and_elem()", "Mesh");
705 :
706 : // node and element id counters
707 36658 : dof_id_type next_free_elem = 0;
708 36658 : dof_id_type next_free_node = 0;
709 :
710 : // Will hold the set of nodes that are currently connected to elements
711 73316 : std::unordered_set<Node *> connected_nodes;
712 :
713 : // Loop over the elements. Note that there may
714 : // be nullptrs in the _elements vector from the coarsening
715 : // process. Pack the elements in to a contiguous array
716 : // and then trim any excess.
717 : {
718 36658 : std::vector<Elem *>::iterator in = _elements.begin();
719 36658 : std::vector<Elem *>::iterator out_iter = _elements.begin();
720 36658 : const std::vector<Elem *>::iterator end = _elements.end();
721 :
722 40557072 : for (; in != end; ++in)
723 40368693 : if (*in != nullptr)
724 : {
725 3122152 : Elem * el = *in;
726 :
727 38905815 : *out_iter = *in;
728 3122152 : ++out_iter;
729 :
730 : // Increment the element counter
731 38905815 : el->set_id (next_free_elem++);
732 :
733 38905815 : if (_skip_renumber_nodes_and_elements)
734 : {
735 : // Add this elements nodes to the connected list
736 2145255 : for (auto & n : el->node_ref_range())
737 1934776 : connected_nodes.insert(&n);
738 : }
739 : else // We DO want node renumbering
740 : {
741 : // Loop over this element's nodes. Number them,
742 : // if they have not been numbered already. Also,
743 : // position them in the _nodes vector so that they
744 : // are packed contiguously from the beginning.
745 240752224 : for (auto & n : el->node_ref_range())
746 202056888 : if (n.id() == next_free_node) // don't need to process
747 38581516 : next_free_node++; // [(src == dst) below]
748 :
749 163475372 : else if (n.id() > next_free_node) // need to process
750 : {
751 : // The source and destination indices
752 : // for this node
753 1182998 : const dof_id_type src_idx = n.id();
754 9125340 : const dof_id_type dst_idx = next_free_node++;
755 :
756 : // ensure we want to swap a valid nodes
757 1182998 : libmesh_assert(_nodes[src_idx]);
758 :
759 : // Swap the source and destination nodes
760 2925133 : std::swap(_nodes[src_idx],
761 2925133 : _nodes[dst_idx] );
762 :
763 : // Set proper indices where that makes sense
764 9125340 : if (_nodes[src_idx] != nullptr)
765 1168240 : _nodes[src_idx]->set_id (src_idx);
766 1182998 : _nodes[dst_idx]->set_id (dst_idx);
767 : }
768 : }
769 : }
770 :
771 : // Erase any additional storage. These elements have been
772 : // copied into nullptr voids by the procedure above, and are
773 : // thus repeated and unnecessary.
774 188379 : _elements.erase (out_iter, end);
775 : }
776 :
777 :
778 188379 : if (_skip_renumber_nodes_and_elements)
779 : {
780 : // Loop over the nodes. Note that there may
781 : // be nullptrs in the _nodes vector from the coarsening
782 : // process. Pack the nodes in to a contiguous array
783 : // and then trim any excess.
784 :
785 60 : std::vector<Node *>::iterator in = _nodes.begin();
786 60 : std::vector<Node *>::iterator out_iter = _nodes.begin();
787 60 : const std::vector<Node *>::iterator end = _nodes.end();
788 :
789 925936 : for (; in != end; ++in)
790 925541 : if (*in != nullptr)
791 : {
792 : // This is a reference so that if we change the pointer it will change in the vector
793 209684 : Node * & nd = *in;
794 :
795 : // If this node is still connected to an elem, put it in the list
796 419368 : if (connected_nodes.count(nd))
797 : {
798 673877 : *out_iter = nd;
799 137780 : ++out_iter;
800 :
801 : // Increment the node counter
802 673877 : nd->set_id (next_free_node++);
803 : }
804 : else // This node is orphaned, delete it!
805 : {
806 251664 : this->get_boundary_info().remove (nd);
807 143808 : _constraint_rows.erase(nd);
808 :
809 : // delete the node
810 251664 : --_n_nodes;
811 431424 : delete nd;
812 251664 : nd = nullptr;
813 : }
814 : }
815 :
816 : // Erase any additional storage. Whatever was
817 395 : _nodes.erase (out_iter, end);
818 : }
819 : else // We really DO want node renumbering
820 : {
821 : // Any nodes in the vector >= _nodes[next_free_node]
822 : // are not connected to any elements and may be deleted
823 : // if desired.
824 :
825 : // Now, delete the unused nodes
826 : {
827 151386 : std::vector<Node *>::iterator nd = _nodes.begin();
828 36598 : const std::vector<Node *>::iterator end = _nodes.end();
829 :
830 36598 : std::advance (nd, next_free_node);
831 :
832 1724476 : for (auto & node : as_range(nd, end))
833 : {
834 : // Mesh modification code might have already deleted some
835 : // nodes
836 1536492 : if (node == nullptr)
837 104431 : continue;
838 :
839 : // remove any boundary information associated with
840 : // this node
841 1396559 : this->get_boundary_info().remove (node);
842 220100 : _constraint_rows.erase(node);
843 :
844 : // delete the node
845 1396559 : --_n_nodes;
846 2683068 : delete node;
847 1396559 : node = nullptr;
848 : }
849 :
850 187984 : _nodes.erase (nd, end);
851 : }
852 : }
853 :
854 188379 : this->_preparation.has_removed_orphaned_nodes = true;
855 :
856 36658 : libmesh_assert_equal_to (next_free_elem, _elements.size());
857 36658 : libmesh_assert_equal_to (next_free_node, _nodes.size());
858 :
859 188379 : this->update_parallel_id_counts();
860 188379 : }
861 :
862 :
863 :
864 2220 : void ReplicatedMesh::fix_broken_node_and_element_numbering ()
865 : {
866 : // Nodes first
867 3180410 : for (auto n : index_range(_nodes))
868 3178190 : if (this->_nodes[n] != nullptr)
869 3178190 : this->_nodes[n]->set_id() = cast_int<dof_id_type>(n);
870 :
871 : // Elements next
872 3664758 : for (auto e : index_range(_elements))
873 3662538 : if (this->_elements[e] != nullptr)
874 3662538 : this->_elements[e]->set_id() = cast_int<dof_id_type>(e);
875 2220 : }
876 :
877 :
878 113514 : dof_id_type ReplicatedMesh::n_active_elem () const
879 : {
880 207898 : return static_cast<dof_id_type>(std::distance (this->active_elements_begin(),
881 321412 : this->active_elements_end()));
882 : }
883 :
884 : std::vector<dof_id_type>
885 142 : ReplicatedMesh::get_disconnected_subdomains(std::vector<subdomain_id_type> * subdomain_ids) const
886 : {
887 : // find number of disconnected subdomains
888 4 : std::vector<dof_id_type> representative_elem_ids;
889 :
890 : // use subdomain_ids as markers for all elements to indicate if the elements
891 : // have been visited. Note: here subdomain ID is unrelated with element
892 : // subdomain_id().
893 8 : std::vector<subdomain_id_type> subdomains;
894 142 : if (!subdomain_ids)
895 0 : subdomain_ids = &subdomains;
896 4 : subdomain_ids->clear();
897 142 : subdomain_ids->resize(max_elem_id() + 1, Elem::invalid_subdomain_id);
898 :
899 : // counter of disconnected subdomains
900 4 : subdomain_id_type subdomain_counter = 0;
901 :
902 : // a stack for visiting elements, make its capacity sufficiently large to avoid
903 : // memory allocation and deallocation when the vector size changes
904 8 : std::vector<const Elem *> list;
905 142 : list.reserve(n_elem());
906 :
907 : // counter of visited elements
908 4 : dof_id_type visited = 0;
909 142 : dof_id_type n_active = n_active_elem();
910 4 : do
911 : {
912 1672 : for (const auto & elem : active_element_ptr_range())
913 876 : if ((*subdomain_ids)[elem->id()] == Elem::invalid_subdomain_id)
914 : {
915 284 : list.push_back(elem);
916 284 : (*subdomain_ids)[elem->id()] = subdomain_counter;
917 284 : break;
918 268 : }
919 : // we should be able to find a seed here
920 8 : libmesh_assert(list.size() > 0);
921 :
922 284 : dof_id_type min_id = std::numeric_limits<dof_id_type>::max();
923 1988 : while (list.size() > 0)
924 : {
925 : // pop up an element
926 1704 : const Elem * elem = list.back(); list.pop_back(); ++visited;
927 :
928 3084 : min_id = std::min(elem->id(), min_id);
929 :
930 8520 : for (auto s : elem->side_index_range())
931 : {
932 6816 : const Elem * neighbor = elem->neighbor_ptr(s);
933 6816 : if (neighbor != nullptr && (*subdomain_ids)[neighbor->id()] == Elem::invalid_subdomain_id)
934 : {
935 : // neighbor must be active
936 40 : libmesh_assert(neighbor->active());
937 1420 : list.push_back(neighbor);
938 1460 : (*subdomain_ids)[neighbor->id()] = subdomain_counter;
939 : }
940 : }
941 : }
942 :
943 284 : representative_elem_ids.push_back(min_id);
944 284 : subdomain_counter++;
945 : }
946 284 : while (visited != n_active);
947 :
948 146 : return representative_elem_ids;
949 : }
950 :
951 : std::unordered_map<dof_id_type, std::vector<std::vector<Point>>>
952 142 : ReplicatedMesh::get_boundary_points() const
953 : {
954 142 : libmesh_error_msg_if(mesh_dimension() != 2,
955 : "Error: get_boundary_points only works for 2D now");
956 :
957 : // find number of disconnected subdomains
958 : // subdomains will hold the IDs of disconnected subdomains for all elements.
959 8 : std::vector<subdomain_id_type> subdomains;
960 146 : std::vector<dof_id_type> elem_ids = get_disconnected_subdomains(&subdomains);
961 :
962 4 : std::unordered_map<dof_id_type, std::vector<std::vector<Point>>> boundary_points;
963 :
964 : // get all boundary sides that are to be erased later during visiting
965 : // use a comparison functor to avoid run-time randomness due to pointers
966 : struct boundary_side_compare
967 : {
968 1584 : bool operator()(const std::pair<const Elem *, unsigned int> & lhs,
969 : const std::pair<const Elem *, unsigned int> & rhs) const
970 : {
971 42340 : if (lhs.first->id() < rhs.first->id())
972 328 : return true;
973 29298 : else if (lhs.first->id() == rhs.first->id())
974 : {
975 14668 : if (lhs.second < rhs.second)
976 112 : return true;
977 : }
978 1144 : return false;
979 : }
980 : };
981 8 : std::set<std::pair<const Elem *, unsigned int>, boundary_side_compare> boundary_elements;
982 3592 : for (const auto & elem : active_element_ptr_range())
983 8568 : for (auto s : elem->side_index_range())
984 7008 : if (elem->neighbor_ptr(s) == nullptr)
985 3542 : boundary_elements.insert(std::pair<const Elem *, unsigned int>(elem, s));
986 :
987 568 : while (!boundary_elements.empty())
988 : {
989 : // get the first entry as the seed
990 426 : const Elem * eseed = boundary_elements.begin()->first;
991 426 : unsigned int sseed = boundary_elements.begin()->second;
992 :
993 : // get the subdomain ID that these boundary sides attached to
994 438 : subdomain_id_type subdomain_id = subdomains[eseed->id()];
995 :
996 : // start visiting the mesh to find all boundary nodes with the seed
997 24 : std::vector<Point> bpoints;
998 426 : const Elem * elem = eseed;
999 12 : unsigned int s = sseed;
1000 438 : std::vector<unsigned int> local_side_nodes = elem->nodes_on_side(s);
1001 : while (true)
1002 : {
1003 96 : std::pair<const Elem *, unsigned int> side(elem, s);
1004 96 : libmesh_assert(boundary_elements.count(side));
1005 96 : boundary_elements.erase(side);
1006 :
1007 : // push all nodes on the side except the node on the other end of the side (index 1)
1008 11928 : for (auto i : index_range(local_side_nodes))
1009 8520 : if (i != 1)
1010 5400 : bpoints.push_back(*static_cast<const Point *>(elem->node_ptr(local_side_nodes[i])));
1011 :
1012 : // use the last node to find next element and side
1013 3408 : const Node * node = elem->node_ptr(local_side_nodes[1]);
1014 96 : std::set<const Elem *> neighbors;
1015 3408 : elem->find_point_neighbors(*node, neighbors);
1016 :
1017 : // if only one neighbor is found (itself), this node is a cornor node on boundary
1018 3408 : if (neighbors.size() != 1)
1019 64 : neighbors.erase(elem);
1020 :
1021 : // find the connecting side
1022 96 : bool found = false;
1023 3686 : for (const auto & neighbor : neighbors)
1024 : {
1025 10011 : for (auto ss : neighbor->side_index_range())
1026 9892 : if (neighbor->neighbor_ptr(ss) == nullptr && !(elem == neighbor && s == ss))
1027 : {
1028 4958 : local_side_nodes = neighbor->nodes_on_side(ss);
1029 : // we expect the starting point of the side to be the same as the end of the previous side
1030 5092 : if (neighbor->node_ptr(local_side_nodes[0]) == node)
1031 : {
1032 3408 : elem = neighbor;
1033 96 : s = ss;
1034 96 : found = true;
1035 96 : break;
1036 : }
1037 1588 : else if (neighbor->node_ptr(local_side_nodes[1]) == node)
1038 : {
1039 0 : elem = neighbor;
1040 0 : s = ss;
1041 0 : found = true;
1042 : // flip nodes in local_side_nodes because the side is in an opposite direction
1043 0 : auto temp(local_side_nodes);
1044 0 : local_side_nodes[0] = temp[1];
1045 0 : local_side_nodes[1] = temp[0];
1046 0 : for (unsigned int i = 2; i < temp.size(); ++i)
1047 0 : local_side_nodes[temp.size() + 1 - i] = temp[i];
1048 0 : break;
1049 : }
1050 : }
1051 108 : if (found)
1052 96 : break;
1053 : }
1054 :
1055 3408 : libmesh_error_msg_if(!found, "ERROR: mesh topology error on visiting boundary sides");
1056 :
1057 : // exit if we reach the starting point
1058 3408 : if (elem == eseed && s == sseed)
1059 12 : break;
1060 84 : }
1061 426 : boundary_points[elem_ids[subdomain_id]].push_back(bpoints);
1062 : }
1063 :
1064 146 : return boundary_points;
1065 : }
1066 :
1067 : } // namespace libMesh
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