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 56118 : ReplicatedMesh::ReplicatedMesh (const Parallel::Communicator & comm_in,
43 56118 : unsigned char d) :
44 : UnstructuredMesh (comm_in,d),
45 56118 : _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 56118 : _next_unique_id = 0;
51 : #endif
52 :
53 65710 : const std::string default_partitioner = "metis";
54 : const std::string my_partitioner =
55 : libMesh::command_line_value("--default-partitioner",
56 112236 : default_partitioner);
57 : _partitioner = Partitioner::build
58 102644 : (Utility::string_to_enum<PartitionerType>(my_partitioner));
59 56118 : }
60 :
61 :
62 26399 : std::string_view ReplicatedMesh::subclass_first_difference_from (const MeshBase & other_mesh_base) const
63 : {
64 25042 : const ReplicatedMesh * rep_mesh_ptr =
65 26399 : dynamic_cast<const ReplicatedMesh *>(&other_mesh_base);
66 26399 : if (!rep_mesh_ptr)
67 0 : return "ReplicatedMesh class";
68 25042 : const ReplicatedMesh & other_mesh = *rep_mesh_ptr;
69 :
70 : #define CHECK_MEMBER(member_name) \
71 : if (member_name != other_mesh.member_name) \
72 : return #member_name;
73 :
74 26399 : CHECK_MEMBER(_n_nodes);
75 26399 : CHECK_MEMBER(_n_elem);
76 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
77 26399 : CHECK_MEMBER(_next_unique_id);
78 : #endif
79 26399 : if (!this->nodes_and_elements_equal(other_mesh))
80 78 : return "nodes and/or elements";
81 :
82 26321 : return "";
83 : }
84 :
85 :
86 94542 : ReplicatedMesh::~ReplicatedMesh ()
87 : {
88 72372 : this->ReplicatedMesh::clear(); // Free nodes and elements
89 94542 : }
90 :
91 :
92 : // This might be specialized later, but right now it's just here to
93 : // make sure the compiler doesn't give us a default (non-deep) copy
94 : // constructor instead.
95 16183 : ReplicatedMesh::ReplicatedMesh (const ReplicatedMesh & other_mesh) :
96 16183 : ReplicatedMesh(static_cast<const MeshBase&>(other_mesh))
97 : {
98 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
99 16183 : this->_next_unique_id = other_mesh._next_unique_id;
100 : #endif
101 16183 : }
102 :
103 :
104 16254 : ReplicatedMesh::ReplicatedMesh (const MeshBase & other_mesh) :
105 : UnstructuredMesh (other_mesh),
106 16254 : _n_nodes(0), _n_elem(0) // copy_* will increment this
107 : {
108 : // Just copy, skipping preparation
109 16254 : this->copy_nodes_and_elements(other_mesh, true, 0, 0, 0, nullptr, true);
110 :
111 13426 : this->allow_find_neighbors(other_mesh.allow_find_neighbors());
112 13426 : this->allow_detect_interior_parents(other_mesh.allow_detect_interior_parents());
113 13426 : this->allow_renumbering(other_mesh.allow_renumbering());
114 13426 : this->allow_remote_element_removal(other_mesh.allow_remote_element_removal());
115 13426 : this->skip_partitioning(other_mesh.skip_partitioning());
116 :
117 16254 : this->copy_constraint_rows(other_mesh);
118 :
119 12726 : auto & this_boundary_info = this->get_boundary_info();
120 12726 : const auto & other_boundary_info = other_mesh.get_boundary_info();
121 :
122 16254 : this_boundary_info = other_boundary_info;
123 :
124 12726 : this->set_subdomain_name_map() = other_mesh.get_subdomain_name_map();
125 :
126 16254 : this->_preparation = other_mesh.preparation();
127 :
128 : // If other_mesh is distributed, then we've got parts of it on each
129 : // processor but we're not replicated yet; fix that.
130 16254 : if (!other_mesh.is_serial())
131 71 : MeshCommunication().allgather(*this);
132 16254 : }
133 :
134 156 : ReplicatedMesh & ReplicatedMesh::operator= (ReplicatedMesh && other_mesh)
135 : {
136 8 : LOG_SCOPE("operator=(&&)", "ReplicatedMesh");
137 :
138 : // Move assign as an UnstructuredMesh
139 8 : this->UnstructuredMesh::operator=(std::move(other_mesh));
140 :
141 : // Nodes and elements belong to ReplicatedMesh and have to be
142 : // moved before we can move arbitrary GhostingFunctor, Partitioner,
143 : // etc. subclasses.
144 156 : this->move_nodes_and_elements(std::move(other_mesh));
145 :
146 : // Handle those remaining moves.
147 156 : this->post_dofobject_moves(std::move(other_mesh));
148 :
149 164 : return *this;
150 : }
151 :
152 156 : MeshBase & ReplicatedMesh::assign(MeshBase && other_mesh)
153 : {
154 156 : *this = std::move(cast_ref<ReplicatedMesh&>(other_mesh));
155 :
156 156 : return *this;
157 : }
158 :
159 156 : void ReplicatedMesh::move_nodes_and_elements(MeshBase && other_meshbase)
160 : {
161 8 : ReplicatedMesh & other_mesh = cast_ref<ReplicatedMesh&>(other_meshbase);
162 :
163 156 : this->_nodes = std::move(other_mesh._nodes);
164 156 : this->_n_nodes = other_mesh.n_nodes();
165 :
166 156 : this->_elements = std::move(other_mesh._elements);
167 156 : this->_n_elem = other_mesh.n_elem();
168 156 : }
169 :
170 :
171 15660045 : const Point & ReplicatedMesh::point (const dof_id_type i) const
172 : {
173 15660045 : return this->node_ref(i);
174 : }
175 :
176 :
177 :
178 :
179 101253656 : const Node * ReplicatedMesh::node_ptr (const dof_id_type i) const
180 : {
181 5175882 : libmesh_assert_less (i, this->max_node_id());
182 5175882 : libmesh_assert(_nodes[i]);
183 5175882 : libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
184 :
185 106379464 : return _nodes[i];
186 : }
187 :
188 :
189 :
190 :
191 130856165 : Node * ReplicatedMesh::node_ptr (const dof_id_type i)
192 : {
193 22420534 : libmesh_assert_less (i, this->max_node_id());
194 22420534 : libmesh_assert(_nodes[i]);
195 22420534 : libmesh_assert_equal_to (_nodes[i]->id(), i); // This will change soon
196 :
197 142715281 : return _nodes[i];
198 : }
199 :
200 :
201 :
202 :
203 34094120 : const Node * ReplicatedMesh::query_node_ptr (const dof_id_type i) const
204 : {
205 34094120 : if (i >= this->max_node_id())
206 0 : return nullptr;
207 33844115 : libmesh_assert (_nodes[i] == nullptr ||
208 : _nodes[i]->id() == i); // This will change soon
209 :
210 34179302 : return _nodes[i];
211 : }
212 :
213 :
214 :
215 :
216 4388044 : Node * ReplicatedMesh::query_node_ptr (const dof_id_type i)
217 : {
218 4388044 : if (i >= this->max_node_id())
219 86978 : return nullptr;
220 2036573 : libmesh_assert (_nodes[i] == nullptr ||
221 : _nodes[i]->id() == i); // This will change soon
222 :
223 3783911 : return _nodes[i];
224 : }
225 :
226 :
227 :
228 :
229 3239203 : const Elem * ReplicatedMesh::elem_ptr (const dof_id_type i) const
230 : {
231 540526 : libmesh_assert_less (i, this->max_elem_id());
232 540526 : libmesh_assert(_elements[i]);
233 540526 : libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
234 :
235 3655522 : return _elements[i];
236 : }
237 :
238 :
239 :
240 :
241 96613464 : Elem * ReplicatedMesh::elem_ptr (const dof_id_type i)
242 : {
243 6343989 : libmesh_assert_less (i, this->max_elem_id());
244 6343989 : libmesh_assert(_elements[i]);
245 6343989 : libmesh_assert_equal_to (_elements[i]->id(), i); // This will change soon
246 :
247 101111131 : return _elements[i];
248 : }
249 :
250 :
251 :
252 :
253 26984650 : const Elem * ReplicatedMesh::query_elem_ptr (const dof_id_type i) const
254 : {
255 26984650 : if (i >= this->max_elem_id())
256 0 : return nullptr;
257 26900409 : libmesh_assert (_elements[i] == nullptr ||
258 : _elements[i]->id() == i); // This will change soon
259 :
260 27014225 : return _elements[i];
261 : }
262 :
263 :
264 :
265 :
266 2336237 : Elem * ReplicatedMesh::query_elem_ptr (const dof_id_type i)
267 : {
268 2336237 : if (i >= this->max_elem_id())
269 44850 : return nullptr;
270 1081198 : libmesh_assert (_elements[i] == nullptr ||
271 : _elements[i]->id() == i); // This will change soon
272 :
273 1673745 : return _elements[i];
274 : }
275 :
276 :
277 :
278 :
279 17187733 : Elem * ReplicatedMesh::add_elem (Elem * e)
280 : {
281 2462232 : libmesh_assert(e);
282 :
283 : // We no longer merely append elements with ReplicatedMesh
284 :
285 : // If the user requests a valid id that doesn't correspond to an
286 : // existing element, let's give them that id, resizing the elements
287 : // container if necessary.
288 17187733 : if (!e->valid_id())
289 819058 : e->set_id (cast_int<dof_id_type>(_elements.size()));
290 :
291 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
292 17187733 : if (!e->valid_unique_id())
293 5041554 : e->set_unique_id(_next_unique_id++);
294 : else
295 12999794 : _next_unique_id = std::max(_next_unique_id, e->unique_id()+1);
296 : #endif
297 :
298 3586944 : const dof_id_type id = e->id();
299 :
300 18312445 : if (id < _elements.size())
301 : {
302 : // This should *almost* never happen, but we rely on it when
303 : // using allgather to replicate a not-yet-actually-replicated
304 : // ReplicatedMesh under construction in parallel.
305 165331 : if (e == _elements[id])
306 0 : return e;
307 :
308 : // Overwriting existing elements is still probably a mistake.
309 16044 : libmesh_assert(!_elements[id]);
310 : }
311 : else
312 : {
313 17022402 : _elements.resize(id+1, nullptr);
314 : }
315 :
316 17187733 : ++_n_elem;
317 17187733 : _elements[id] = e;
318 :
319 : // We actually added a new element. Some of our caches might still
320 : // be valid, but we should clear the ones which definitely are not.
321 17187733 : this->clear_point_locator();
322 17187733 : this->clear_stored_ranges();
323 :
324 : // Make sure any new element is given space for any extra integers
325 : // we've requested
326 17187733 : e->add_extra_integers(_elem_integer_names.size(),
327 17187733 : _elem_integer_default_values);
328 :
329 : // And set mapping type and data on any new element
330 3586944 : e->set_mapping_type(this->default_mapping_type());
331 3586944 : e->set_mapping_data(this->default_mapping_data());
332 :
333 17187733 : return e;
334 : }
335 :
336 16374371 : Elem * ReplicatedMesh::add_elem (std::unique_ptr<Elem> e)
337 : {
338 : // The mesh now takes ownership of the Elem. Eventually the guts of
339 : // add_elem() will get moved to a private helper function, and
340 : // calling add_elem() directly will be deprecated.
341 16374371 : return add_elem(e.release());
342 : }
343 :
344 :
345 :
346 582121 : Elem * ReplicatedMesh::insert_elem (Elem * e)
347 : {
348 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
349 582121 : if (!e->valid_unique_id())
350 18176 : e->set_unique_id(_next_unique_id++);
351 : else
352 563945 : _next_unique_id = std::max(_next_unique_id, e->unique_id()+1);
353 : #endif
354 :
355 235316 : dof_id_type eid = e->id();
356 117658 : libmesh_assert_less (eid, _elements.size());
357 582121 : Elem * oldelem = _elements[eid];
358 :
359 582121 : if (oldelem)
360 : {
361 117658 : libmesh_assert_equal_to (oldelem->id(), eid);
362 582121 : this->delete_elem(oldelem);
363 : }
364 :
365 582121 : ++_n_elem;
366 582121 : _elements[eid] = e;
367 :
368 : // We actually added a new element. Some of our caches might still
369 : // be valid, but we should clear the ones which definitely are not.
370 582121 : this->clear_point_locator();
371 582121 : this->clear_stored_ranges();
372 :
373 : // Make sure any new element is given space for any extra integers
374 : // we've requested
375 582121 : e->add_extra_integers(_elem_integer_names.size(),
376 582121 : _elem_integer_default_values);
377 :
378 : // And set mapping type and data on any new element
379 235316 : e->set_mapping_type(this->default_mapping_type());
380 235316 : e->set_mapping_data(this->default_mapping_data());
381 :
382 582121 : return e;
383 : }
384 :
385 582121 : Elem * ReplicatedMesh::insert_elem (std::unique_ptr<Elem> e)
386 : {
387 : // The mesh now takes ownership of the Elem. Eventually the guts of
388 : // insert_elem(Elem*) will get moved to a private helper function, and
389 : // calling insert_elem(Elem*) directly will be deprecated.
390 582121 : return insert_elem(e.release());
391 : }
392 :
393 :
394 :
395 2306530 : void ReplicatedMesh::delete_elem(Elem * e)
396 : {
397 228957 : libmesh_assert(e);
398 :
399 : // Initialize an iterator to eventually point to the element we want to delete
400 228957 : std::vector<Elem *>::iterator pos = _elements.end();
401 :
402 : // In many cases, e->id() gives us a clue as to where e
403 : // is located in the _elements vector. Try that first
404 : // before trying the O(n_elem) search.
405 228957 : libmesh_assert_less (e->id(), _elements.size());
406 :
407 2532845 : if (_elements[e->id()] == e)
408 : {
409 : // We found it!
410 2080215 : pos = _elements.begin();
411 228957 : std::advance(pos, e->id());
412 : }
413 :
414 : else
415 : {
416 : // This search is O(n_elem)
417 0 : pos = std::find (_elements.begin(),
418 : _elements.end(),
419 0 : e);
420 : }
421 :
422 : // Huh? Element not in the vector?
423 228957 : libmesh_assert (pos != _elements.end());
424 :
425 : // Remove the element from the BoundaryInfo object
426 2306530 : this->get_boundary_info().remove(e);
427 :
428 : // delete the element
429 2306530 : --_n_elem;
430 2306530 : delete e;
431 :
432 : // explicitly zero the pointer
433 2306530 : *pos = nullptr;
434 :
435 : // Some of our caches might still be valid, but we should clear the
436 : // ones which definitely are not.
437 2306530 : this->clear_point_locator();
438 2306530 : this->clear_stored_ranges();
439 2306530 : }
440 :
441 :
442 :
443 21420 : void ReplicatedMesh::renumber_elem(const dof_id_type old_id,
444 : const dof_id_type new_id)
445 : {
446 : // This could be a no-op
447 21420 : if (old_id == new_id)
448 0 : return;
449 :
450 : // This doesn't get used in serial yet
451 21420 : Elem * el = _elements[old_id];
452 7140 : libmesh_assert (el);
453 :
454 28560 : if (new_id >= _elements.size())
455 288 : _elements.resize(new_id+1, nullptr);
456 :
457 7140 : el->set_id(new_id);
458 7140 : libmesh_assert (!_elements[new_id]);
459 28560 : _elements[new_id] = el;
460 21420 : _elements[old_id] = nullptr;
461 :
462 : // Should we delete any caches here? Our point locator indexes by
463 : // element pointer and should be fine with an id change. Our stored
464 : // ranges are no longer sorted, which is *probably* fine, but let's
465 : // just be safe.
466 21420 : this->clear_stored_ranges();
467 : }
468 :
469 :
470 :
471 13774698 : Node * ReplicatedMesh::add_point (const Point & p,
472 : const dof_id_type id,
473 : const processor_id_type proc_id)
474 : {
475 4152081 : Node * n = nullptr;
476 :
477 : // If the user requests a valid id, either
478 : // provide the existing node or resize the container
479 : // to fit the new node.
480 13774698 : if (id != DofObject::invalid_id)
481 9875363 : if (id < _nodes.size())
482 14655 : n = _nodes[id];
483 : else
484 9008363 : _nodes.resize(id+1);
485 : else
486 4751680 : _nodes.push_back (static_cast<Node *>(nullptr));
487 :
488 : // if the node already exists, then assign new (x,y,z) values
489 4164636 : if (n)
490 0 : *n = p;
491 : // otherwise build a new node, put it in the right spot, and return
492 : // a valid pointer.
493 : else
494 : {
495 26697051 : n = Node::build(p, (id == DofObject::invalid_id) ?
496 9752145 : cast_int<dof_id_type>(_nodes.size()-1) : id).release();
497 13774698 : n->processor_id() = proc_id;
498 :
499 13774698 : n->add_extra_integers(_node_integer_names.size(),
500 13774698 : _node_integer_default_values);
501 :
502 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
503 13774698 : if (!n->valid_unique_id())
504 13774698 : n->set_unique_id(_next_unique_id++);
505 : else
506 0 : _next_unique_id = std::max(_next_unique_id, n->unique_id()+1);
507 : #endif
508 :
509 13774698 : ++_n_nodes;
510 13774698 : if (id == DofObject::invalid_id)
511 4751680 : _nodes.back() = n;
512 : else
513 9875363 : _nodes[id] = n;
514 : }
515 :
516 : // better not pass back a nullptr.
517 4152081 : libmesh_assert (n);
518 :
519 13774698 : return n;
520 : }
521 :
522 :
523 :
524 939498 : Node * ReplicatedMesh::add_node (Node * n)
525 : {
526 96530 : libmesh_assert(n);
527 :
528 : // If the user requests a valid id, either set the existing
529 : // container entry or resize the container to fit the new node.
530 939498 : if (n->valid_id())
531 : {
532 96472 : const dof_id_type id = n->id();
533 1035639 : if (id < _nodes.size())
534 15076 : libmesh_assert(!_nodes[id]);
535 : else
536 742826 : _nodes.resize(id+1); // default nullptr
537 :
538 1035639 : _nodes[id] = n;
539 : }
540 : else
541 : {
542 116 : n->set_id (cast_int<dof_id_type>(_nodes.size()));
543 331 : _nodes.push_back(n);
544 : }
545 :
546 939498 : ++_n_nodes;
547 :
548 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
549 939498 : if (!n->valid_unique_id())
550 331 : n->set_unique_id(_next_unique_id++);
551 : else
552 1436272 : _next_unique_id = std::max(_next_unique_id, n->unique_id()+1);
553 : #endif
554 :
555 939498 : n->add_extra_integers(_node_integer_names.size(),
556 939498 : _node_integer_default_values);
557 :
558 939498 : return n;
559 : }
560 :
561 939498 : Node * ReplicatedMesh::add_node (std::unique_ptr<Node> n)
562 : {
563 : // The mesh now takes ownership of the Node. Eventually the guts of
564 : // add_node() will get moved to a private helper function, and
565 : // calling add_node() directly will be deprecated.
566 939498 : return add_node(n.release());
567 : }
568 :
569 250688 : void ReplicatedMesh::delete_node(Node * n)
570 : {
571 63723 : libmesh_assert(n);
572 63723 : libmesh_assert_less (n->id(), _nodes.size());
573 :
574 : // Initialize an iterator to eventually point to the element we want
575 : // to delete
576 63723 : std::vector<Node *>::iterator pos;
577 :
578 : // In many cases, e->id() gives us a clue as to where e
579 : // is located in the _elements vector. Try that first
580 : // before trying the O(n_elem) search.
581 314411 : if (_nodes[n->id()] == n)
582 : {
583 186965 : pos = _nodes.begin();
584 63723 : std::advance(pos, n->id());
585 : }
586 : else
587 : {
588 0 : pos = std::find (_nodes.begin(),
589 : _nodes.end(),
590 0 : n);
591 : }
592 :
593 : // Huh? Node not in the vector?
594 63723 : libmesh_assert (pos != _nodes.end());
595 :
596 : // Delete the node from the BoundaryInfo object
597 250688 : this->get_boundary_info().remove(n);
598 127446 : _constraint_rows.erase(n);
599 :
600 : // delete the node
601 250688 : --_n_nodes;
602 437653 : delete n;
603 :
604 : // explicitly zero the pointer
605 250688 : *pos = nullptr;
606 250688 : }
607 :
608 :
609 :
610 70092 : void ReplicatedMesh::renumber_node(const dof_id_type old_id,
611 : const dof_id_type new_id)
612 : {
613 : // This could be a no-op
614 70092 : if (old_id == new_id)
615 0 : return;
616 :
617 : // This doesn't get used in serial yet
618 70092 : Node * nd = _nodes[old_id];
619 23364 : libmesh_assert (nd);
620 :
621 93456 : if (new_id >= _nodes.size())
622 288 : _nodes.resize(new_id+1, nullptr);
623 :
624 23364 : nd->set_id(new_id);
625 23364 : libmesh_assert (!_nodes[new_id]);
626 93456 : _nodes[new_id] = nd;
627 70092 : _nodes[old_id] = nullptr;
628 : }
629 :
630 :
631 :
632 117566 : void ReplicatedMesh::clear ()
633 : {
634 : // Call parent clear function
635 117566 : MeshBase::clear();
636 :
637 : // Clear our elements and nodes
638 : // There is no need to remove them from
639 : // the BoundaryInfo data structure since we
640 : // already cleared it.
641 117566 : this->ReplicatedMesh::clear_elems();
642 :
643 13050747 : for (auto & node : _nodes)
644 21779076 : delete node;
645 :
646 117566 : _n_nodes = 0;
647 31557 : _nodes.clear();
648 117566 : }
649 :
650 :
651 :
652 118264 : void ReplicatedMesh::clear_elems ()
653 : {
654 15703707 : for (auto & elem : _elements)
655 15585443 : delete elem;
656 :
657 118264 : _n_elem = 0;
658 31759 : _elements.clear();
659 118264 : }
660 :
661 :
662 :
663 210422 : void ReplicatedMesh::update_parallel_id_counts()
664 : {
665 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
666 210422 : _next_unique_id = this->parallel_max_unique_id();
667 : #endif
668 :
669 210422 : this->_preparation.has_synched_id_counts = true;
670 210422 : }
671 :
672 :
673 :
674 : #ifdef LIBMESH_ENABLE_UNIQUE_ID
675 238966 : unique_id_type ReplicatedMesh::parallel_max_unique_id() const
676 : {
677 : // This function must be run on all processors at once
678 59884 : parallel_object_only();
679 :
680 238966 : unique_id_type max_local = _next_unique_id;
681 238966 : this->comm().max(max_local);
682 238966 : return max_local;
683 : }
684 :
685 :
686 :
687 32215 : void ReplicatedMesh::set_next_unique_id(unique_id_type id)
688 : {
689 32215 : _next_unique_id = id;
690 32215 : }
691 : #endif
692 :
693 :
694 :
695 163209 : void ReplicatedMesh::renumber_nodes_and_elements ()
696 : {
697 59640 : LOG_SCOPE("renumber_nodes_and_elem()", "Mesh");
698 :
699 : // node and element id counters
700 29820 : dof_id_type next_free_elem = 0;
701 29820 : dof_id_type next_free_node = 0;
702 :
703 : // Will hold the set of nodes that are currently connected to elements
704 59640 : std::unordered_set<Node *> connected_nodes;
705 :
706 : // Loop over the elements. Note that there may
707 : // be nullptrs in the _elements vector from the coarsening
708 : // process. Pack the elements in to a contiguous array
709 : // and then trim any excess.
710 : {
711 29820 : std::vector<Elem *>::iterator in = _elements.begin();
712 29820 : std::vector<Elem *>::iterator out_iter = _elements.begin();
713 29820 : const std::vector<Elem *>::iterator end = _elements.end();
714 :
715 40248653 : for (; in != end; ++in)
716 40085444 : if (*in != nullptr)
717 : {
718 3046930 : Elem * el = *in;
719 :
720 38626322 : *out_iter = *in;
721 3046930 : ++out_iter;
722 :
723 : // Increment the element counter
724 38626322 : el->set_id (next_free_elem++);
725 :
726 38626322 : if (_skip_renumber_nodes_and_elements)
727 : {
728 : // Add this elements nodes to the connected list
729 2145255 : for (auto & n : el->node_ref_range())
730 1934776 : connected_nodes.insert(&n);
731 : }
732 : else // We DO want node renumbering
733 : {
734 : // Loop over this element's nodes. Number them,
735 : // if they have not been numbered already. Also,
736 : // position them in the _nodes vector so that they
737 : // are packed contiguously from the beginning.
738 237266840 : for (auto & n : el->node_ref_range())
739 198850997 : if (n.id() == next_free_node) // don't need to process
740 37770676 : next_free_node++; // [(src == dst) below]
741 :
742 161080321 : else if (n.id() > next_free_node) // need to process
743 : {
744 : // The source and destination indices
745 : // for this node
746 1093566 : const dof_id_type src_idx = n.id();
747 8806824 : const dof_id_type dst_idx = next_free_node++;
748 :
749 : // ensure we want to swap a valid nodes
750 1093566 : libmesh_assert(_nodes[src_idx]);
751 :
752 : // Swap the source and destination nodes
753 2701347 : std::swap(_nodes[src_idx],
754 2701347 : _nodes[dst_idx] );
755 :
756 : // Set proper indices where that makes sense
757 8806824 : if (_nodes[src_idx] != nullptr)
758 1078820 : _nodes[src_idx]->set_id (src_idx);
759 1093566 : _nodes[dst_idx]->set_id (dst_idx);
760 : }
761 : }
762 : }
763 :
764 : // Erase any additional storage. These elements have been
765 : // copied into nullptr voids by the procedure above, and are
766 : // thus repeated and unnecessary.
767 163209 : _elements.erase (out_iter, end);
768 : }
769 :
770 :
771 163209 : if (_skip_renumber_nodes_and_elements)
772 : {
773 : // Loop over the nodes. Note that there may
774 : // be nullptrs in the _nodes vector from the coarsening
775 : // process. Pack the nodes in to a contiguous array
776 : // and then trim any excess.
777 :
778 60 : std::vector<Node *>::iterator in = _nodes.begin();
779 60 : std::vector<Node *>::iterator out_iter = _nodes.begin();
780 60 : const std::vector<Node *>::iterator end = _nodes.end();
781 :
782 925936 : for (; in != end; ++in)
783 925541 : if (*in != nullptr)
784 : {
785 : // This is a reference so that if we change the pointer it will change in the vector
786 209684 : Node * & nd = *in;
787 :
788 : // If this node is still connected to an elem, put it in the list
789 419368 : if (connected_nodes.count(nd))
790 : {
791 673877 : *out_iter = nd;
792 137780 : ++out_iter;
793 :
794 : // Increment the node counter
795 673877 : nd->set_id (next_free_node++);
796 : }
797 : else // This node is orphaned, delete it!
798 : {
799 251664 : this->get_boundary_info().remove (nd);
800 143808 : _constraint_rows.erase(nd);
801 :
802 : // delete the node
803 251664 : --_n_nodes;
804 431424 : delete nd;
805 251664 : nd = nullptr;
806 : }
807 : }
808 :
809 : // Erase any additional storage. Whatever was
810 395 : _nodes.erase (out_iter, end);
811 : }
812 : else // We really DO want node renumbering
813 : {
814 : // Any nodes in the vector >= _nodes[next_free_node]
815 : // are not connected to any elements and may be deleted
816 : // if desired.
817 :
818 : // Now, delete the unused nodes
819 : {
820 133054 : std::vector<Node *>::iterator nd = _nodes.begin();
821 29760 : const std::vector<Node *>::iterator end = _nodes.end();
822 :
823 29760 : std::advance (nd, next_free_node);
824 :
825 1746697 : for (auto & node : as_range(nd, end))
826 : {
827 : // Mesh modification code might have already deleted some
828 : // nodes
829 1583883 : if (node == nullptr)
830 168342 : continue;
831 :
832 : // remove any boundary information associated with
833 : // this node
834 1350519 : this->get_boundary_info().remove (node);
835 195108 : _constraint_rows.erase(node);
836 :
837 : // delete the node
838 1350519 : --_n_nodes;
839 2603484 : delete node;
840 1350519 : node = nullptr;
841 : }
842 :
843 162814 : _nodes.erase (nd, end);
844 : }
845 : }
846 :
847 163209 : this->_preparation.has_removed_orphaned_nodes = true;
848 :
849 29820 : libmesh_assert_equal_to (next_free_elem, _elements.size());
850 29820 : libmesh_assert_equal_to (next_free_node, _nodes.size());
851 :
852 163209 : this->update_parallel_id_counts();
853 163209 : }
854 :
855 :
856 :
857 2220 : void ReplicatedMesh::fix_broken_node_and_element_numbering ()
858 : {
859 : // Nodes first
860 3180410 : for (auto n : index_range(_nodes))
861 3178190 : if (this->_nodes[n] != nullptr)
862 3178190 : this->_nodes[n]->set_id() = cast_int<dof_id_type>(n);
863 :
864 : // Elements next
865 3664758 : for (auto e : index_range(_elements))
866 3662538 : if (this->_elements[e] != nullptr)
867 3662538 : this->_elements[e]->set_id() = cast_int<dof_id_type>(e);
868 2220 : }
869 :
870 :
871 98371 : dof_id_type ReplicatedMesh::n_active_elem () const
872 : {
873 180242 : return static_cast<dof_id_type>(std::distance (this->active_elements_begin(),
874 278613 : this->active_elements_end()));
875 : }
876 :
877 : std::vector<dof_id_type>
878 142 : ReplicatedMesh::get_disconnected_subdomains(std::vector<subdomain_id_type> * subdomain_ids) const
879 : {
880 : // find number of disconnected subdomains
881 4 : std::vector<dof_id_type> representative_elem_ids;
882 :
883 : // use subdomain_ids as markers for all elements to indicate if the elements
884 : // have been visited. Note: here subdomain ID is unrelated with element
885 : // subdomain_id().
886 8 : std::vector<subdomain_id_type> subdomains;
887 142 : if (!subdomain_ids)
888 0 : subdomain_ids = &subdomains;
889 4 : subdomain_ids->clear();
890 142 : subdomain_ids->resize(max_elem_id() + 1, Elem::invalid_subdomain_id);
891 :
892 : // counter of disconnected subdomains
893 4 : subdomain_id_type subdomain_counter = 0;
894 :
895 : // a stack for visiting elements, make its capacity sufficiently large to avoid
896 : // memory allocation and deallocation when the vector size changes
897 8 : std::vector<const Elem *> list;
898 142 : list.reserve(n_elem());
899 :
900 : // counter of visited elements
901 4 : dof_id_type visited = 0;
902 142 : dof_id_type n_active = n_active_elem();
903 4 : do
904 : {
905 1672 : for (const auto & elem : active_element_ptr_range())
906 876 : if ((*subdomain_ids)[elem->id()] == Elem::invalid_subdomain_id)
907 : {
908 284 : list.push_back(elem);
909 284 : (*subdomain_ids)[elem->id()] = subdomain_counter;
910 284 : break;
911 268 : }
912 : // we should be able to find a seed here
913 8 : libmesh_assert(list.size() > 0);
914 :
915 284 : dof_id_type min_id = std::numeric_limits<dof_id_type>::max();
916 1988 : while (list.size() > 0)
917 : {
918 : // pop up an element
919 1704 : const Elem * elem = list.back(); list.pop_back(); ++visited;
920 :
921 3084 : min_id = std::min(elem->id(), min_id);
922 :
923 8520 : for (auto s : elem->side_index_range())
924 : {
925 6816 : const Elem * neighbor = elem->neighbor_ptr(s);
926 6816 : if (neighbor != nullptr && (*subdomain_ids)[neighbor->id()] == Elem::invalid_subdomain_id)
927 : {
928 : // neighbor must be active
929 40 : libmesh_assert(neighbor->active());
930 1420 : list.push_back(neighbor);
931 1460 : (*subdomain_ids)[neighbor->id()] = subdomain_counter;
932 : }
933 : }
934 : }
935 :
936 284 : representative_elem_ids.push_back(min_id);
937 284 : subdomain_counter++;
938 : }
939 284 : while (visited != n_active);
940 :
941 146 : return representative_elem_ids;
942 : }
943 :
944 : std::unordered_map<dof_id_type, std::vector<std::vector<Point>>>
945 142 : ReplicatedMesh::get_boundary_points() const
946 : {
947 142 : libmesh_error_msg_if(mesh_dimension() != 2,
948 : "Error: get_boundary_points only works for 2D now");
949 :
950 : // find number of disconnected subdomains
951 : // subdomains will hold the IDs of disconnected subdomains for all elements.
952 8 : std::vector<subdomain_id_type> subdomains;
953 146 : std::vector<dof_id_type> elem_ids = get_disconnected_subdomains(&subdomains);
954 :
955 4 : std::unordered_map<dof_id_type, std::vector<std::vector<Point>>> boundary_points;
956 :
957 : // get all boundary sides that are to be erased later during visiting
958 : // use a comparison functor to avoid run-time randomness due to pointers
959 : struct boundary_side_compare
960 : {
961 1584 : bool operator()(const std::pair<const Elem *, unsigned int> & lhs,
962 : const std::pair<const Elem *, unsigned int> & rhs) const
963 : {
964 42340 : if (lhs.first->id() < rhs.first->id())
965 328 : return true;
966 29298 : else if (lhs.first->id() == rhs.first->id())
967 : {
968 14668 : if (lhs.second < rhs.second)
969 112 : return true;
970 : }
971 1144 : return false;
972 : }
973 : };
974 8 : std::set<std::pair<const Elem *, unsigned int>, boundary_side_compare> boundary_elements;
975 3592 : for (const auto & elem : active_element_ptr_range())
976 8568 : for (auto s : elem->side_index_range())
977 7008 : if (elem->neighbor_ptr(s) == nullptr)
978 3542 : boundary_elements.insert(std::pair<const Elem *, unsigned int>(elem, s));
979 :
980 568 : while (!boundary_elements.empty())
981 : {
982 : // get the first entry as the seed
983 426 : const Elem * eseed = boundary_elements.begin()->first;
984 426 : unsigned int sseed = boundary_elements.begin()->second;
985 :
986 : // get the subdomain ID that these boundary sides attached to
987 438 : subdomain_id_type subdomain_id = subdomains[eseed->id()];
988 :
989 : // start visiting the mesh to find all boundary nodes with the seed
990 24 : std::vector<Point> bpoints;
991 426 : const Elem * elem = eseed;
992 12 : unsigned int s = sseed;
993 438 : std::vector<unsigned int> local_side_nodes = elem->nodes_on_side(s);
994 : while (true)
995 : {
996 96 : std::pair<const Elem *, unsigned int> side(elem, s);
997 96 : libmesh_assert(boundary_elements.count(side));
998 96 : boundary_elements.erase(side);
999 :
1000 : // push all nodes on the side except the node on the other end of the side (index 1)
1001 11928 : for (auto i : index_range(local_side_nodes))
1002 8520 : if (i != 1)
1003 5400 : bpoints.push_back(*static_cast<const Point *>(elem->node_ptr(local_side_nodes[i])));
1004 :
1005 : // use the last node to find next element and side
1006 3408 : const Node * node = elem->node_ptr(local_side_nodes[1]);
1007 96 : std::set<const Elem *> neighbors;
1008 3408 : elem->find_point_neighbors(*node, neighbors);
1009 :
1010 : // if only one neighbor is found (itself), this node is a cornor node on boundary
1011 3408 : if (neighbors.size() != 1)
1012 64 : neighbors.erase(elem);
1013 :
1014 : // find the connecting side
1015 96 : bool found = false;
1016 3676 : for (const auto & neighbor : neighbors)
1017 : {
1018 9966 : for (auto ss : neighbor->side_index_range())
1019 9872 : if (neighbor->neighbor_ptr(ss) == nullptr && !(elem == neighbor && s == ss))
1020 : {
1021 4938 : local_side_nodes = neighbor->nodes_on_side(ss);
1022 : // we expect the starting point of the side to be the same as the end of the previous side
1023 5082 : if (neighbor->node_ptr(local_side_nodes[0]) == node)
1024 : {
1025 3408 : elem = neighbor;
1026 96 : s = ss;
1027 96 : found = true;
1028 96 : break;
1029 : }
1030 1578 : else if (neighbor->node_ptr(local_side_nodes[1]) == node)
1031 : {
1032 0 : elem = neighbor;
1033 0 : s = ss;
1034 0 : found = true;
1035 : // flip nodes in local_side_nodes because the side is in an opposite direction
1036 0 : auto temp(local_side_nodes);
1037 0 : local_side_nodes[0] = temp[1];
1038 0 : local_side_nodes[1] = temp[0];
1039 0 : for (unsigned int i = 2; i < temp.size(); ++i)
1040 0 : local_side_nodes[temp.size() + 1 - i] = temp[i];
1041 0 : break;
1042 : }
1043 : }
1044 101 : if (found)
1045 96 : break;
1046 : }
1047 :
1048 3408 : libmesh_error_msg_if(!found, "ERROR: mesh topology error on visiting boundary sides");
1049 :
1050 : // exit if we reach the starting point
1051 3408 : if (elem == eseed && s == sseed)
1052 12 : break;
1053 84 : }
1054 426 : boundary_points[elem_ids[subdomain_id]].push_back(bpoints);
1055 : }
1056 :
1057 146 : return boundary_points;
1058 : }
1059 :
1060 : } // namespace libMesh
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