Line data Source code
1 : //* This file is part of the MOOSE framework
2 : //* https://mooseframework.inl.gov
3 : //*
4 : //* All rights reserved, see COPYRIGHT for full restrictions
5 : //* https://github.com/idaholab/moose/blob/master/COPYRIGHT
6 : //*
7 : //* Licensed under LGPL 2.1, please see LICENSE for details
8 : //* https://www.gnu.org/licenses/lgpl-2.1.html
9 :
10 : #include "MooseError.h"
11 : #include "MooseMesh.h"
12 : #include "Factory.h"
13 : #include "CacheChangedListsThread.h"
14 : #include "MooseUtils.h"
15 : #include "MooseApp.h"
16 : #include "RelationshipManager.h"
17 : #include "PointListAdaptor.h"
18 : #include "Executioner.h"
19 : #include "NonlinearSystemBase.h"
20 : #include "LinearSystem.h"
21 : #include "AuxiliarySystem.h"
22 : #include "Assembly.h"
23 : #include "SubProblem.h"
24 : #include "MooseVariableBase.h"
25 : #include "MooseMeshUtils.h"
26 : #include "MooseAppCoordTransform.h"
27 : #include "FEProblemBase.h"
28 :
29 : #include <utility>
30 :
31 : // libMesh
32 : #include "libmesh/bounding_box.h"
33 : #include "libmesh/boundary_info.h"
34 : #include "libmesh/mesh_tools.h"
35 : #include "libmesh/parallel.h"
36 : #include "libmesh/mesh_communication.h"
37 : #include "libmesh/periodic_boundary_base.h"
38 : #include "libmesh/fe_base.h"
39 : #include "libmesh/fe_interface.h"
40 : #include "libmesh/mesh_inserter_iterator.h"
41 : #include "libmesh/mesh_communication.h"
42 : #include "libmesh/mesh_inserter_iterator.h"
43 : #include "libmesh/mesh_tools.h"
44 : #include "libmesh/parallel.h"
45 : #include "libmesh/parallel_elem.h"
46 : #include "libmesh/parallel_node.h"
47 : #include "libmesh/parallel_ghost_sync.h"
48 : #include "libmesh/utility.h"
49 : #include "libmesh/remote_elem.h"
50 : #include "libmesh/linear_partitioner.h"
51 : #include "libmesh/centroid_partitioner.h"
52 : #include "libmesh/parmetis_partitioner.h"
53 : #include "libmesh/hilbert_sfc_partitioner.h"
54 : #include "libmesh/morton_sfc_partitioner.h"
55 : #include "libmesh/edge_edge2.h"
56 : #include "libmesh/mesh_refinement.h"
57 : #include "libmesh/quadrature.h"
58 : #include "libmesh/boundary_info.h"
59 : #include "libmesh/periodic_boundaries.h"
60 : #include "libmesh/quadrature_gauss.h"
61 : #include "libmesh/point_locator_base.h"
62 : #include "libmesh/default_coupling.h"
63 : #include "libmesh/ghost_point_neighbors.h"
64 : #include "libmesh/fe_type.h"
65 : #include "libmesh/enum_to_string.h"
66 :
67 : static const int GRAIN_SIZE =
68 : 1; // the grain_size does not have much influence on our execution speed
69 :
70 : using namespace libMesh;
71 :
72 : // Make newer nanoflann API compatible with older nanoflann versions
73 : #if NANOFLANN_VERSION < 0x150
74 : namespace nanoflann
75 : {
76 : typedef SearchParams SearchParameters;
77 :
78 : template <typename T, typename U>
79 : using ResultItem = std::pair<T, U>;
80 : }
81 : #endif
82 :
83 : InputParameters
84 357709 : MooseMesh::validParams()
85 : {
86 357709 : InputParameters params = MooseObject::validParams();
87 :
88 1788545 : MooseEnum parallel_type("DEFAULT REPLICATED DISTRIBUTED", "DEFAULT");
89 1430836 : params.addParam<MooseEnum>("parallel_type",
90 : parallel_type,
91 : "DEFAULT: Use libMesh::ReplicatedMesh unless --distributed-mesh is "
92 : "specified on the command line "
93 : "REPLICATED: Always use libMesh::ReplicatedMesh "
94 : "DISTRIBUTED: Always use libMesh::DistributedMesh");
95 :
96 1073127 : params.addParam<bool>(
97 : "allow_renumbering",
98 715418 : true,
99 : "If allow_renumbering=false, node and element numbers are kept fixed until deletion");
100 :
101 : // TODO: this parameter does not belong here, it's only for FileMesh
102 1073127 : params.addParam<bool>("nemesis",
103 715418 : false,
104 : "If nemesis=true and file=foo.e, actually reads "
105 : "foo.e.N.0, foo.e.N.1, ... foo.e.N.N-1, "
106 : "where N = # CPUs, with NemesisIO.");
107 :
108 1073127 : params.addParam<MooseEnum>(
109 : "partitioner",
110 715418 : partitioning(),
111 : "Specifies a mesh partitioner to use when splitting the mesh for a parallel computation.");
112 1430836 : MooseEnum direction("x y z radial");
113 1430836 : params.addParam<MooseEnum>("centroid_partitioner_direction",
114 : direction,
115 : "Specifies the sort direction if using the centroid partitioner. "
116 : "Available options: x, y, z, radial");
117 :
118 1430836 : MooseEnum patch_update_strategy("never always auto iteration", "never");
119 1430836 : params.addParam<MooseEnum>(
120 : "patch_update_strategy",
121 : patch_update_strategy,
122 : "How often to update the geometric search 'patch'. The default is to "
123 : "never update it (which is the most efficient but could be a problem "
124 : "with lots of relative motion). 'always' will update the patch for all "
125 : "secondary nodes at the beginning of every timestep which might be time "
126 : "consuming. 'auto' will attempt to determine at the start of which "
127 : "timesteps the patch for all secondary nodes needs to be updated automatically."
128 : "'iteration' updates the patch at every nonlinear iteration for a "
129 : "subset of secondary nodes for which penetration is not detected. If there "
130 : "can be substantial relative motion between the primary and secondary surfaces "
131 : "during the nonlinear iterations within a timestep, it is advisable to use "
132 : "'iteration' option to ensure accurate contact detection.");
133 :
134 : // Note: This parameter is named to match 'construct_side_list_from_node_list' in SetupMeshAction
135 1073127 : params.addParam<bool>(
136 : "construct_node_list_from_side_list",
137 715418 : true,
138 : "Whether or not to generate nodesets from the sidesets (usually a good idea).");
139 1073127 : params.addParam<unsigned int>(
140 715418 : "patch_size", 40, "The number of nodes to consider in the NearestNode neighborhood.");
141 1430836 : params.addParam<unsigned int>("ghosting_patch_size",
142 : "The number of nearest neighbors considered "
143 : "for ghosting purposes when 'iteration' "
144 : "patch update strategy is used. Default is "
145 : "5 * patch_size.");
146 1073127 : params.addParam<unsigned int>("max_leaf_size",
147 715418 : 10,
148 : "The maximum number of points in each leaf of the KDTree used in "
149 : "the nearest neighbor search. As the leaf size becomes larger,"
150 : "KDTree construction becomes faster but the nearest neighbor search"
151 : "becomes slower.");
152 :
153 1073127 : params.addParam<bool>("build_all_side_lowerd_mesh",
154 715418 : false,
155 : "True to build the lower-dimensional mesh for all sides.");
156 :
157 1073127 : params.addParam<bool>("skip_refine_when_use_split",
158 715418 : true,
159 : "True to skip uniform refinements when using a pre-split mesh.");
160 :
161 1430836 : params.addParam<std::vector<SubdomainID>>(
162 : "add_subdomain_ids",
163 : "The listed subdomain ids will be assumed valid for the mesh. This permits setting up "
164 : "subdomain restrictions for subdomains initially containing no elements, which can occur, "
165 : "for example, in additive manufacturing simulations which dynamically add and remove "
166 : "elements. Names for this subdomains may be provided using add_subdomain_names. In this case "
167 : "this list and add_subdomain_names must contain the same number of items.");
168 1430836 : params.addParam<std::vector<SubdomainName>>(
169 : "add_subdomain_names",
170 : "The listed subdomain names will be assumed valid for the mesh. This permits setting up "
171 : "subdomain restrictions for subdomains initially containing no elements, which can occur, "
172 : "for example, in additive manufacturing simulations which dynamically add and remove "
173 : "elements. IDs for this subdomains may be provided using add_subdomain_ids. Otherwise IDs "
174 : "are automatically assigned. In case add_subdomain_ids is set too, both lists must contain "
175 : "the same number of items.");
176 :
177 1430836 : params.addParam<std::vector<BoundaryID>>(
178 : "add_sideset_ids",
179 : "The listed sideset ids will be assumed valid for the mesh. This permits setting up boundary "
180 : "restrictions for sidesets initially containing no sides. Names for this sidesets may be "
181 : "provided using add_sideset_names. In this case this list and add_sideset_names must contain "
182 : "the same number of items.");
183 1430836 : params.addParam<std::vector<BoundaryName>>(
184 : "add_sideset_names",
185 : "The listed sideset names will be assumed valid for the mesh. This permits setting up "
186 : "boundary restrictions for sidesets initially containing no sides. Ids for this sidesets may "
187 : "be provided using add_sideset_ids. In this case this list and add_sideset_ids must contain "
188 : "the same number of items.");
189 :
190 1430836 : params.addParam<std::vector<BoundaryID>>(
191 : "add_nodeset_ids",
192 : "The listed nodeset ids will be assumed valid for the mesh. This permits setting up boundary "
193 : "restrictions for node initially containing no sides. Names for this nodesets may be "
194 : "provided using add_nodeset_names. In this case this list and add_nodeset_names must contain "
195 : "the same number of items.");
196 1073127 : params.addParam<std::vector<BoundaryName>>(
197 : "add_nodeset_names",
198 : "The listed nodeset names will be assumed valid for the mesh. This permits setting up "
199 : "boundary restrictions for nodesets initially containing no sides. Ids for this nodesets may "
200 : "be provided using add_nodesets_ids. In this case this list and add_nodesets_ids must "
201 : "contain the same number of items.");
202 :
203 357709 : params += MooseAppCoordTransform::validParams();
204 :
205 : // This indicates that the derived mesh type accepts a MeshGenerator, and should be set to true in
206 : // derived types that do so.
207 715418 : params.addPrivateParam<bool>("_mesh_generator_mesh", false);
208 :
209 : // Whether or not the mesh is pre split
210 1073127 : params.addPrivateParam<bool>("_is_split", false);
211 :
212 715418 : params.registerBase("MooseMesh");
213 :
214 : // groups
215 1430836 : params.addParamNamesToGroup("patch_update_strategy patch_size max_leaf_size", "Geometric search");
216 1430836 : params.addParamNamesToGroup("nemesis", "Advanced");
217 1430836 : params.addParamNamesToGroup("add_subdomain_ids add_subdomain_names add_sideset_ids "
218 : "add_sideset_names add_nodeset_ids add_nodeset_names",
219 : "Pre-declaration of future mesh sub-entities");
220 1430836 : params.addParamNamesToGroup("construct_node_list_from_side_list build_all_side_lowerd_mesh",
221 : "Automatic definition of mesh element sides entities");
222 1073127 : params.addParamNamesToGroup("partitioner centroid_partitioner_direction", "Partitioning");
223 :
224 715418 : return params;
225 357709 : }
226 :
227 68589 : MooseMesh::MooseMesh(const InputParameters & parameters)
228 : : MooseObject(parameters),
229 : Restartable(this, "Mesh"),
230 : PerfGraphInterface(this),
231 68589 : _parallel_type(getParam<MooseEnum>("parallel_type").getEnum<MooseMesh::ParallelType>()),
232 68589 : _use_distributed_mesh(false),
233 68589 : _distribution_overridden(false),
234 68589 : _parallel_type_overridden(false),
235 68589 : _mesh(nullptr),
236 137178 : _partitioner_name(getParam<MooseEnum>("partitioner")),
237 68589 : _partitioner_overridden(false),
238 68589 : _custom_partitioner_requested(false),
239 68589 : _uniform_refine_level(0),
240 137178 : _skip_refine_when_use_split(getParam<bool>("skip_refine_when_use_split")),
241 68589 : _skip_deletion_repartition_after_refine(false),
242 137178 : _is_nemesis(getParam<bool>("nemesis")),
243 68589 : _node_to_elem_map_built(false),
244 68589 : _node_to_active_semilocal_elem_map_built(false),
245 137178 : _patch_size(getParam<unsigned int>("patch_size")),
246 137178 : _ghosting_patch_size(isParamValid("ghosting_patch_size")
247 137178 : ? getParam<unsigned int>("ghosting_patch_size")
248 68589 : : 5 * _patch_size),
249 137178 : _max_leaf_size(getParam<unsigned int>("max_leaf_size")),
250 68589 : _patch_update_strategy(
251 137178 : getParam<MooseEnum>("patch_update_strategy").getEnum<Moose::PatchUpdateType>()),
252 68589 : _regular_orthogonal_mesh(false),
253 137178 : _is_split(getParam<bool>("_is_split")),
254 68589 : _has_lower_d(false),
255 68589 : _allow_recovery(true),
256 137178 : _construct_node_list_from_side_list(getParam<bool>("construct_node_list_from_side_list")),
257 68589 : _need_delete(false),
258 68589 : _allow_remote_element_removal(true),
259 68589 : _need_ghost_ghosted_boundaries(true),
260 68589 : _is_displaced(false),
261 68589 : _coord_sys(
262 137178 : declareRestartableData<std::map<SubdomainID, Moose::CoordinateSystemType>>("coord_sys")),
263 137178 : _rz_coord_axis(getParam<MooseEnum>("rz_coord_axis")),
264 68589 : _coord_system_set(false),
265 662653 : _doing_p_refinement(false)
266 : {
267 205767 : if (isParamValid("ghosting_patch_size") && (_patch_update_strategy != Moose::Iteration))
268 0 : mooseError("Ghosting patch size parameter has to be set in the mesh block "
269 : "only when 'iteration' patch update strategy is used.");
270 :
271 205767 : if (isParamValid("coord_block"))
272 : {
273 78 : if (isParamValid("block"))
274 0 : paramWarning("block",
275 : "You set both 'Mesh/block' and 'Mesh/coord_block'. The value of "
276 : "'Mesh/coord_block' will be used.");
277 :
278 78 : _provided_coord_blocks = getParam<std::vector<SubdomainName>>("coord_block");
279 : }
280 205689 : else if (isParamValid("block"))
281 789 : _provided_coord_blocks = getParam<std::vector<SubdomainName>>("block");
282 :
283 205767 : if (getParam<bool>("build_all_side_lowerd_mesh"))
284 : // Do not initially allow removal of remote elements
285 244 : allowRemoteElementRemoval(false);
286 :
287 68589 : determineUseDistributedMesh();
288 :
289 : #ifdef MOOSE_KOKKOS_ENABLED
290 45352 : if (_app.isKokkosAvailable())
291 45352 : _kokkos_mesh = std::make_unique<Moose::Kokkos::Mesh>(*this);
292 : #endif
293 68589 : }
294 :
295 3296 : MooseMesh::MooseMesh(const MooseMesh & other_mesh)
296 : : MooseObject(other_mesh._pars),
297 : Restartable(this, "Mesh"),
298 : PerfGraphInterface(this, "CopiedMesh"),
299 3296 : _built_from_other_mesh(true),
300 3296 : _parallel_type(other_mesh._parallel_type),
301 3296 : _use_distributed_mesh(other_mesh._use_distributed_mesh),
302 3296 : _distribution_overridden(other_mesh._distribution_overridden),
303 3296 : _parallel_type_overridden(other_mesh._parallel_type_overridden),
304 3296 : _mesh(other_mesh.getMesh().clone()),
305 3296 : _partitioner_name(other_mesh._partitioner_name),
306 3296 : _partitioner_overridden(other_mesh._partitioner_overridden),
307 3296 : _custom_partitioner_requested(other_mesh._custom_partitioner_requested),
308 3296 : _uniform_refine_level(other_mesh.uniformRefineLevel()),
309 3296 : _skip_refine_when_use_split(other_mesh._skip_refine_when_use_split),
310 3296 : _skip_deletion_repartition_after_refine(other_mesh._skip_deletion_repartition_after_refine),
311 3296 : _is_nemesis(false),
312 3296 : _node_to_elem_map_built(false),
313 3296 : _node_to_active_semilocal_elem_map_built(false),
314 3296 : _patch_size(other_mesh._patch_size),
315 3296 : _ghosting_patch_size(other_mesh._ghosting_patch_size),
316 3296 : _max_leaf_size(other_mesh._max_leaf_size),
317 3296 : _patch_update_strategy(other_mesh._patch_update_strategy),
318 3296 : _regular_orthogonal_mesh(false),
319 3296 : _is_split(other_mesh._is_split),
320 3296 : _lower_d_interior_blocks(other_mesh._lower_d_interior_blocks),
321 3296 : _lower_d_boundary_blocks(other_mesh._lower_d_boundary_blocks),
322 3296 : _has_lower_d(other_mesh._has_lower_d),
323 3296 : _allow_recovery(other_mesh._allow_recovery),
324 3296 : _construct_node_list_from_side_list(other_mesh._construct_node_list_from_side_list),
325 3296 : _need_delete(other_mesh._need_delete),
326 3296 : _allow_remote_element_removal(other_mesh._allow_remote_element_removal),
327 3296 : _need_ghost_ghosted_boundaries(other_mesh._need_ghost_ghosted_boundaries),
328 3296 : _coord_sys(other_mesh._coord_sys),
329 3296 : _rz_coord_axis(other_mesh._rz_coord_axis),
330 3296 : _subdomain_id_to_rz_coord_axis(other_mesh._subdomain_id_to_rz_coord_axis),
331 3296 : _coord_system_set(other_mesh._coord_system_set),
332 3296 : _provided_coord_blocks(other_mesh._provided_coord_blocks),
333 31899 : _doing_p_refinement(other_mesh._doing_p_refinement)
334 : {
335 : // Note: this calls BoundaryInfo::operator= without changing the
336 : // ownership semantics of either Mesh's BoundaryInfo object.
337 3296 : getMesh().get_boundary_info() = other_mesh.getMesh().get_boundary_info();
338 :
339 3296 : const std::set<SubdomainID> & subdomains = other_mesh.meshSubdomains();
340 4468 : for (const auto & sbd_id : subdomains)
341 1172 : setSubdomainName(sbd_id, other_mesh.getMesh().subdomain_name(sbd_id));
342 :
343 : // Get references to BoundaryInfo objects to make the code below cleaner...
344 3296 : const BoundaryInfo & other_boundary_info = other_mesh.getMesh().get_boundary_info();
345 3296 : BoundaryInfo & boundary_info = getMesh().get_boundary_info();
346 :
347 : // Use the other BoundaryInfo object to build the list of side boundary ids
348 3296 : std::vector<BoundaryID> side_boundaries;
349 3296 : other_boundary_info.build_side_boundary_ids(side_boundaries);
350 :
351 : // Assign those boundary ids in our BoundaryInfo object
352 15641 : for (const auto & side_bnd_id : side_boundaries)
353 12345 : boundary_info.sideset_name(side_bnd_id) = other_boundary_info.get_sideset_name(side_bnd_id);
354 :
355 : // Do the same thing for node boundary ids
356 3296 : std::vector<BoundaryID> node_boundaries;
357 3296 : other_boundary_info.build_node_boundary_ids(node_boundaries);
358 :
359 14243 : for (const auto & node_bnd_id : node_boundaries)
360 10947 : boundary_info.nodeset_name(node_bnd_id) = other_boundary_info.get_nodeset_name(node_bnd_id);
361 :
362 3296 : _bounds.resize(other_mesh._bounds.size());
363 3632 : for (std::size_t i = 0; i < _bounds.size(); ++i)
364 : {
365 336 : _bounds[i].resize(other_mesh._bounds[i].size());
366 1008 : for (std::size_t j = 0; j < _bounds[i].size(); ++j)
367 672 : _bounds[i][j] = other_mesh._bounds[i][j];
368 : }
369 :
370 3296 : updateCoordTransform();
371 :
372 : #ifdef MOOSE_KOKKOS_ENABLED
373 2235 : if (_app.isKokkosAvailable())
374 2235 : _kokkos_mesh = std::make_unique<Moose::Kokkos::Mesh>(*this);
375 : #endif
376 3296 : }
377 :
378 66382 : MooseMesh::~MooseMesh()
379 : {
380 66382 : freeBndNodes();
381 66382 : freeBndElems();
382 66382 : clearQuadratureNodes();
383 66382 : }
384 :
385 : void
386 227904 : MooseMesh::freeBndNodes()
387 : {
388 : // free memory
389 12707913 : for (auto & bnode : _bnd_nodes)
390 12480009 : delete bnode;
391 :
392 842301 : for (auto & it : _node_set_nodes)
393 614397 : it.second.clear();
394 :
395 227904 : _node_set_nodes.clear();
396 :
397 842468 : for (auto & it : _bnd_node_ids)
398 614564 : it.second.clear();
399 :
400 227904 : _bnd_node_ids.clear();
401 227904 : _bnd_node_range.reset();
402 227904 : }
403 :
404 : void
405 227904 : MooseMesh::freeBndElems()
406 : {
407 : // free memory
408 10094121 : for (auto & belem : _bnd_elems)
409 9866217 : delete belem;
410 :
411 826956 : for (auto & it : _bnd_elem_ids)
412 599052 : it.second.clear();
413 :
414 227904 : _bnd_elem_ids.clear();
415 227904 : _bnd_elem_range.reset();
416 227904 : }
417 :
418 : bool
419 140727 : MooseMesh::prepare(const MeshBase * const mesh_to_clone)
420 : {
421 703635 : TIME_SECTION("prepare", 2, "Preparing Mesh", true);
422 :
423 140727 : bool called_prepare_for_use = false;
424 :
425 : mooseAssert(_mesh, "The MeshBase has not been constructed");
426 :
427 140727 : if (!dynamic_cast<DistributedMesh *>(&getMesh()) || _is_nemesis)
428 : // For whatever reason we do not want to allow renumbering here nor ever in the future?
429 120303 : getMesh().allow_renumbering(false);
430 :
431 140727 : if (mesh_to_clone)
432 : {
433 : mooseAssert(mesh_to_clone->is_prepared(),
434 : "The mesh we wish to clone from must already be prepared");
435 168 : _mesh = mesh_to_clone->clone();
436 168 : _moose_mesh_prepared = false;
437 : }
438 140559 : else if (!_mesh->is_prepared())
439 : {
440 18141 : _mesh->prepare_for_use();
441 18141 : _moose_mesh_prepared = false;
442 18141 : called_prepare_for_use = true;
443 : }
444 :
445 140727 : if (_moose_mesh_prepared)
446 70374 : return called_prepare_for_use;
447 :
448 : // Collect (local) subdomain IDs
449 70353 : _mesh_subdomains.clear();
450 13228447 : for (const auto & elem : getMesh().element_ptr_range())
451 13228447 : _mesh_subdomains.insert(elem->subdomain_id());
452 :
453 : // add explicitly requested subdomains
454 211351 : if (isParamValid("add_subdomain_ids") && !isParamValid("add_subdomain_names"))
455 : {
456 : // only subdomain ids are explicitly given
457 78 : const auto & add_subdomain_id = getParam<std::vector<SubdomainID>>("add_subdomain_ids");
458 39 : _mesh_subdomains.insert(add_subdomain_id.begin(), add_subdomain_id.end());
459 : }
460 211156 : else if (isParamValid("add_subdomain_ids") && isParamValid("add_subdomain_names"))
461 : {
462 : const auto add_subdomain =
463 428 : getParam<SubdomainID, SubdomainName>("add_subdomain_ids", "add_subdomain_names");
464 266 : for (const auto & [sub_id, sub_name] : add_subdomain)
465 : {
466 : // add subdomain id
467 159 : _mesh_subdomains.insert(sub_id);
468 : // set name of the subdomain just added
469 159 : setSubdomainName(sub_id, sub_name);
470 : }
471 107 : }
472 210621 : else if (isParamValid("add_subdomain_names"))
473 : {
474 : // the user has defined add_subdomain_names, but not add_subdomain_ids
475 26 : const auto & add_subdomain_names = getParam<std::vector<SubdomainName>>("add_subdomain_names");
476 :
477 : // to define subdomain ids, we need the largest subdomain id defined yet.
478 13 : subdomain_id_type offset = 0;
479 13 : if (!_mesh_subdomains.empty())
480 13 : offset = *_mesh_subdomains.rbegin();
481 :
482 : // add all subdomains (and auto-assign ids)
483 52 : for (const SubdomainName & sub_name : add_subdomain_names)
484 : {
485 : // to avoid two subdomains with the same ID (notably on recover)
486 39 : if (getSubdomainID(sub_name) != libMesh::Elem::invalid_subdomain_id)
487 3 : continue;
488 36 : const auto sub_id = ++offset;
489 : // add subdomain id
490 36 : _mesh_subdomains.insert(sub_id);
491 : // set name of the subdomain just added
492 36 : setSubdomainName(sub_id, sub_name);
493 : }
494 : }
495 :
496 : // Make sure nodesets have been generated
497 70353 : buildNodeListFromSideList();
498 :
499 : // Collect (local) boundary IDs
500 70353 : const std::set<BoundaryID> & local_bids = getMesh().get_boundary_info().get_boundary_ids();
501 70353 : _mesh_boundary_ids.insert(local_bids.begin(), local_bids.end());
502 :
503 : const std::set<BoundaryID> & local_node_bids =
504 70353 : getMesh().get_boundary_info().get_node_boundary_ids();
505 70353 : _mesh_nodeset_ids.insert(local_node_bids.begin(), local_node_bids.end());
506 :
507 : const std::set<BoundaryID> & local_side_bids =
508 70353 : getMesh().get_boundary_info().get_side_boundary_ids();
509 70353 : _mesh_sideset_ids.insert(local_side_bids.begin(), local_side_bids.end());
510 :
511 : // Add explicitly requested sidesets/nodesets
512 : // This is done *after* the side boundaries (e.g. "right", ...) have been generated.
513 140706 : auto add_sets = [this](const bool sidesets, auto & set_ids)
514 : {
515 140706 : const std::string type = sidesets ? "sideset" : "nodeset";
516 140706 : const std::string id_param = "add_" + type + "_ids";
517 140706 : const std::string name_param = "add_" + type + "_names";
518 :
519 140706 : if (isParamValid(id_param))
520 : {
521 60 : const auto & add_ids = getParam<std::vector<BoundaryID>>(id_param);
522 60 : _mesh_boundary_ids.insert(add_ids.begin(), add_ids.end());
523 60 : set_ids.insert(add_ids.begin(), add_ids.end());
524 60 : if (isParamValid(name_param))
525 : {
526 47 : const auto & add_names = getParam<std::vector<BoundaryName>>(name_param);
527 : mooseAssert(add_names.size() == add_ids.size(),
528 : "Id and name sets must be the same size when adding.");
529 128 : for (const auto i : index_range(add_ids))
530 81 : setBoundaryName(add_ids[i], add_names[i]);
531 : }
532 : }
533 140646 : else if (isParamValid(name_param))
534 : {
535 : // the user has defined names, but not ids
536 13 : const auto & add_names = getParam<std::vector<BoundaryName>>(name_param);
537 :
538 13 : auto & mesh_ids = sidesets ? _mesh_sideset_ids : _mesh_nodeset_ids;
539 :
540 : // to define ids, we need the largest id defined yet.
541 13 : boundary_id_type offset = 0;
542 13 : if (!mesh_ids.empty())
543 13 : offset = *mesh_ids.rbegin();
544 13 : if (!_mesh_boundary_ids.empty())
545 13 : offset = std::max(offset, *_mesh_boundary_ids.rbegin());
546 :
547 : // add all sidesets/nodesets (and auto-assign ids)
548 26 : for (const auto & name : add_names)
549 : {
550 : // to avoid two sets with the same ID (notably on recover)
551 13 : if (getBoundaryID(name) != Moose::INVALID_BOUNDARY_ID)
552 1 : continue;
553 12 : const auto id = ++offset;
554 : // add sideset id
555 12 : _mesh_boundary_ids.insert(id);
556 12 : set_ids.insert(id);
557 : // set name of the sideset just added
558 12 : setBoundaryName(id, name);
559 : }
560 : }
561 140706 : };
562 :
563 70353 : add_sets(true, _mesh_sideset_ids);
564 70353 : add_sets(false, _mesh_nodeset_ids);
565 :
566 : // Communicate subdomain and boundary IDs if this is a parallel mesh
567 70353 : if (!getMesh().is_serial())
568 : {
569 7791 : _communicator.set_union(_mesh_subdomains);
570 7791 : _communicator.set_union(_mesh_boundary_ids);
571 7791 : _communicator.set_union(_mesh_nodeset_ids);
572 7791 : _communicator.set_union(_mesh_sideset_ids);
573 : }
574 :
575 70353 : if (!_built_from_other_mesh)
576 : {
577 67247 : if (!_coord_system_set)
578 201741 : setCoordSystem(_provided_coord_blocks, getParam<MultiMooseEnum>("coord_type"));
579 0 : else if (_pars.isParamSetByUser("coord_type"))
580 0 : mooseError(
581 : "Trying to set coordinate system type information based on the user input file, but "
582 : "the coordinate system type information has already been set programmatically! "
583 : "Either remove your coordinate system type information from the input file, or contact "
584 : "your application developer");
585 : }
586 :
587 : // Set general axisymmetric axes if provided
588 281475 : if (isParamValid("rz_coord_blocks") && isParamValid("rz_coord_origins") &&
589 70416 : isParamValid("rz_coord_directions"))
590 : {
591 42 : const auto rz_coord_blocks = getParam<std::vector<SubdomainName>>("rz_coord_blocks");
592 42 : const auto rz_coord_origins = getParam<std::vector<Point>>("rz_coord_origins");
593 42 : const auto rz_coord_directions = getParam<std::vector<RealVectorValue>>("rz_coord_directions");
594 42 : if (rz_coord_origins.size() == rz_coord_blocks.size() &&
595 21 : rz_coord_directions.size() == rz_coord_blocks.size())
596 : {
597 21 : std::vector<std::pair<Point, RealVectorValue>> rz_coord_axes;
598 68 : for (unsigned int i = 0; i < rz_coord_origins.size(); ++i)
599 47 : rz_coord_axes.push_back(std::make_pair(rz_coord_origins[i], rz_coord_directions[i]));
600 :
601 21 : setGeneralAxisymmetricCoordAxes(rz_coord_blocks, rz_coord_axes);
602 :
603 63 : if (isParamSetByUser("rz_coord_axis"))
604 0 : mooseError("The parameter 'rz_coord_axis' may not be provided if 'rz_coord_blocks', "
605 : "'rz_coord_origins', and 'rz_coord_directions' are provided.");
606 21 : }
607 : else
608 0 : mooseError("The parameters 'rz_coord_blocks', 'rz_coord_origins', and "
609 : "'rz_coord_directions' must all have the same size.");
610 21 : }
611 492324 : else if (isParamValid("rz_coord_blocks") || isParamValid("rz_coord_origins") ||
612 281328 : isParamValid("rz_coord_directions"))
613 0 : mooseError("If any of the parameters 'rz_coord_blocks', 'rz_coord_origins', and "
614 : "'rz_coord_directions' are provided, then all must be provided.");
615 :
616 70353 : detectOrthogonalDimRanges();
617 :
618 70353 : update();
619 :
620 : // Check if there is subdomain name duplication for the same subdomain ID
621 70353 : checkDuplicateSubdomainNames();
622 :
623 70349 : _moose_mesh_prepared = true;
624 :
625 70349 : return called_prepare_for_use;
626 140723 : }
627 :
628 : void
629 161522 : MooseMesh::update()
630 : {
631 807610 : TIME_SECTION("update", 3, "Updating Mesh", true);
632 :
633 : // Rebuild the boundary conditions
634 161522 : buildNodeListFromSideList();
635 :
636 : // Update the node to elem map
637 161522 : _node_to_elem_map.clear();
638 161522 : _node_to_elem_map_built = false;
639 161522 : _node_to_active_semilocal_elem_map.clear();
640 161522 : _node_to_active_semilocal_elem_map_built = false;
641 :
642 161522 : buildNodeList();
643 161522 : buildBndElemList();
644 161522 : cacheInfo();
645 161522 : buildElemIDInfo();
646 :
647 : // this will make moose mesh aware of p-refinement added by mesh generators including
648 : // a file mesh generator loading a restart checkpoint file
649 161522 : _max_p_level = 0;
650 161522 : _max_h_level = 0;
651 30466494 : for (const auto & elem : getMesh().active_local_element_ptr_range())
652 : {
653 30304972 : if (elem->p_level() > _max_p_level)
654 598 : _max_p_level = elem->p_level();
655 30304972 : if (elem->level() > _max_h_level)
656 29974 : _max_h_level = elem->level();
657 161522 : }
658 161522 : comm().max(_max_p_level);
659 161522 : comm().max(_max_h_level);
660 :
661 : // the flag might have been set by calling doingPRefinement(true)
662 161522 : _doing_p_refinement = _doing_p_refinement || (_max_p_level > 0);
663 :
664 : #ifdef MOOSE_KOKKOS_ENABLED
665 107255 : if (_app.hasKokkosObjects() || (_app.getExecutioner() && _app.feProblem().hasKokkosObjects()))
666 1622 : _kokkos_mesh->update();
667 : #endif
668 :
669 161522 : _finite_volume_info_dirty = true;
670 161522 : }
671 :
672 : void
673 226 : MooseMesh::buildLowerDMesh()
674 : {
675 226 : auto & mesh = getMesh();
676 :
677 226 : if (!mesh.is_serial())
678 0 : mooseError(
679 : "Hybrid finite element method must use replicated mesh.\nCurrently lower-dimensional mesh "
680 : "does not support mesh re-partitioning and a debug assertion being hit related with "
681 : "neighbors of lower-dimensional element, with distributed mesh.");
682 :
683 : // Lower-D element build requires neighboring element information
684 226 : if (!mesh.is_prepared())
685 214 : mesh.find_neighbors();
686 :
687 : // maximum number of sides of all elements
688 226 : unsigned int max_n_sides = 0;
689 :
690 : // remove existing lower-d element first
691 226 : std::set<Elem *> deleteable_elems;
692 4790 : for (auto & elem : mesh.element_ptr_range())
693 4564 : if (_lower_d_interior_blocks.count(elem->subdomain_id()) ||
694 2282 : _lower_d_boundary_blocks.count(elem->subdomain_id()))
695 0 : deleteable_elems.insert(elem);
696 2282 : else if (elem->n_sides() > max_n_sides)
697 452 : max_n_sides = elem->n_sides();
698 :
699 226 : for (auto & elem : deleteable_elems)
700 0 : mesh.delete_elem(elem);
701 226 : for (const auto & id : _lower_d_interior_blocks)
702 0 : _mesh_subdomains.erase(id);
703 226 : for (const auto & id : _lower_d_boundary_blocks)
704 0 : _mesh_subdomains.erase(id);
705 226 : _lower_d_interior_blocks.clear();
706 226 : _lower_d_boundary_blocks.clear();
707 :
708 226 : mesh.comm().max(max_n_sides);
709 :
710 226 : deleteable_elems.clear();
711 :
712 : // get all side types
713 226 : std::set<int> interior_side_types;
714 226 : std::set<int> boundary_side_types;
715 4790 : for (const auto & elem : mesh.active_element_ptr_range())
716 12314 : for (const auto side : elem->side_index_range())
717 : {
718 10032 : Elem * neig = elem->neighbor_ptr(side);
719 10032 : std::unique_ptr<Elem> side_elem(elem->build_side_ptr(side));
720 10032 : if (neig)
721 6560 : interior_side_types.insert(side_elem->type());
722 : else
723 3472 : boundary_side_types.insert(side_elem->type());
724 10258 : }
725 226 : mesh.comm().set_union(interior_side_types);
726 226 : mesh.comm().set_union(boundary_side_types);
727 :
728 : // assign block ids for different side types
729 226 : std::map<ElemType, SubdomainID> interior_block_ids;
730 226 : std::map<ElemType, SubdomainID> boundary_block_ids;
731 : // we assume this id is not used by the mesh
732 226 : auto id = libMesh::Elem::invalid_subdomain_id - 2;
733 468 : for (const auto & tpid : interior_side_types)
734 : {
735 242 : const auto type = ElemType(tpid);
736 242 : mesh.subdomain_name(id) = "INTERNAL_SIDE_LOWERD_SUBDOMAIN_" + Utility::enum_to_string(type);
737 242 : interior_block_ids[type] = id;
738 242 : _lower_d_interior_blocks.insert(id);
739 242 : if (_mesh_subdomains.count(id) > 0)
740 0 : mooseError("Trying to add a mesh block with id ", id, " that has existed in the mesh");
741 242 : _mesh_subdomains.insert(id);
742 242 : --id;
743 : }
744 468 : for (const auto & tpid : boundary_side_types)
745 : {
746 242 : const auto type = ElemType(tpid);
747 242 : mesh.subdomain_name(id) = "BOUNDARY_SIDE_LOWERD_SUBDOMAIN_" + Utility::enum_to_string(type);
748 242 : boundary_block_ids[type] = id;
749 242 : _lower_d_boundary_blocks.insert(id);
750 242 : if (_mesh_subdomains.count(id) > 0)
751 0 : mooseError("Trying to add a mesh block with id ", id, " that has existed in the mesh");
752 242 : _mesh_subdomains.insert(id);
753 242 : --id;
754 : }
755 :
756 226 : dof_id_type max_elem_id = mesh.max_elem_id();
757 226 : unique_id_type max_unique_id = mesh.parallel_max_unique_id();
758 :
759 226 : std::vector<Elem *> side_elems;
760 226 : _higher_d_elem_side_to_lower_d_elem.clear();
761 4790 : for (const auto & elem : mesh.active_element_ptr_range())
762 : {
763 : // skip existing lower-d elements
764 2282 : if (elem->interior_parent())
765 0 : continue;
766 :
767 12314 : for (const auto side : elem->side_index_range())
768 : {
769 10032 : Elem * neig = elem->neighbor_ptr(side);
770 :
771 10032 : bool build_side = false;
772 10032 : if (!neig)
773 3472 : build_side = true;
774 : else
775 : {
776 : mooseAssert(!neig->is_remote(), "We error if the mesh is not serial");
777 6560 : if (!neig->active())
778 0 : build_side = true;
779 6560 : else if (neig->level() == elem->level() && elem->id() < neig->id())
780 3280 : build_side = true;
781 : }
782 :
783 10032 : if (build_side)
784 : {
785 6752 : std::unique_ptr<Elem> side_elem(elem->build_side_ptr(side));
786 :
787 : // The side will be added with the same processor id as the parent.
788 6752 : side_elem->processor_id() = elem->processor_id();
789 :
790 : // Add subdomain ID
791 6752 : if (neig)
792 3280 : side_elem->subdomain_id() = interior_block_ids.at(side_elem->type());
793 : else
794 3472 : side_elem->subdomain_id() = boundary_block_ids.at(side_elem->type());
795 :
796 : // set ids consistently across processors (these ids will be temporary)
797 6752 : side_elem->set_id(max_elem_id + elem->id() * max_n_sides + side);
798 6752 : side_elem->set_unique_id(max_unique_id + elem->id() * max_n_sides + side);
799 :
800 : // Also assign the side's interior parent, so it is always
801 : // easy to figure out the Elem we came from.
802 : // Note: the interior parent could be a ghost element.
803 6752 : side_elem->set_interior_parent(elem);
804 :
805 6752 : side_elems.push_back(side_elem.release());
806 :
807 : // add link between higher d element to lower d element
808 6752 : auto pair = std::make_pair(elem, side);
809 6752 : auto link = std::make_pair(pair, side_elems.back());
810 6752 : auto ilink = std::make_pair(side_elems.back(), side);
811 6752 : _lower_d_elem_to_higher_d_elem_side.insert(ilink);
812 6752 : _higher_d_elem_side_to_lower_d_elem.insert(link);
813 6752 : }
814 : }
815 226 : }
816 :
817 : // finally, add the lower-dimensional element to the mesh
818 : // Note: lower-d interior element will exist on a processor if its associated interior
819 : // parent exists on a processor whether or not being a ghost. Lower-d elements will
820 : // get its interior parent's processor id.
821 6978 : for (auto & elem : side_elems)
822 6752 : mesh.add_elem(elem);
823 :
824 : // we do all the stuff in prepare_for_use such as renumber_nodes_and_elements(),
825 : // update_parallel_id_counts(), cache_elem_dims(), etc. except partitioning here.
826 226 : const bool skip_partitioning_old = mesh.skip_partitioning();
827 226 : mesh.skip_partitioning(true);
828 : // Finding neighbors is ambiguous for lower-dimensional elements on interior faces
829 226 : mesh.allow_find_neighbors(false);
830 226 : mesh.prepare_for_use();
831 226 : mesh.skip_partitioning(skip_partitioning_old);
832 226 : }
833 :
834 : const Node &
835 0 : MooseMesh::node(const dof_id_type i) const
836 : {
837 0 : mooseDeprecated("MooseMesh::node() is deprecated, please use MooseMesh::nodeRef() instead");
838 0 : return nodeRef(i);
839 : }
840 :
841 : Node &
842 0 : MooseMesh::node(const dof_id_type i)
843 : {
844 0 : mooseDeprecated("MooseMesh::node() is deprecated, please use MooseMesh::nodeRef() instead");
845 0 : return nodeRef(i);
846 : }
847 :
848 : const Node &
849 47286888 : MooseMesh::nodeRef(const dof_id_type i) const
850 : {
851 47286888 : const auto node_ptr = queryNodePtr(i);
852 : mooseAssert(node_ptr, "Missing node");
853 47286888 : return *node_ptr;
854 : }
855 :
856 : Node &
857 26683813 : MooseMesh::nodeRef(const dof_id_type i)
858 : {
859 26683813 : return const_cast<Node &>(const_cast<const MooseMesh *>(this)->nodeRef(i));
860 : }
861 :
862 : const Node *
863 0 : MooseMesh::nodePtr(const dof_id_type i) const
864 : {
865 0 : return &nodeRef(i);
866 : }
867 :
868 : Node *
869 2269 : MooseMesh::nodePtr(const dof_id_type i)
870 : {
871 2269 : return &nodeRef(i);
872 : }
873 :
874 : const Node *
875 47290044 : MooseMesh::queryNodePtr(const dof_id_type i) const
876 : {
877 47290044 : if (i > getMesh().max_node_id())
878 : {
879 223340 : auto it = _quadrature_nodes.find(i);
880 223340 : if (it == _quadrature_nodes.end())
881 0 : return nullptr;
882 223340 : auto & node_ptr = it->second;
883 : mooseAssert(node_ptr, "Uninitialized quadrature node");
884 223340 : return node_ptr;
885 : }
886 :
887 47066704 : return getMesh().query_node_ptr(i);
888 : }
889 :
890 : Node *
891 3156 : MooseMesh::queryNodePtr(const dof_id_type i)
892 : {
893 3156 : return const_cast<Node *>(const_cast<const MooseMesh *>(this)->queryNodePtr(i));
894 : }
895 :
896 : void
897 88336 : MooseMesh::meshChanged()
898 : {
899 441680 : TIME_SECTION("meshChanged", 3, "Updating Because Mesh Changed");
900 :
901 88336 : update();
902 :
903 : // Delete all of the cached ranges
904 88336 : _active_local_elem_range.reset();
905 88336 : _active_node_range.reset();
906 88336 : _active_semilocal_node_range.reset();
907 88336 : _local_node_range.reset();
908 88336 : _bnd_node_range.reset();
909 88336 : _bnd_elem_range.reset();
910 :
911 : // Rebuild the ranges
912 88336 : getActiveLocalElementRange();
913 88336 : getActiveNodeRange();
914 88336 : getLocalNodeRange();
915 88336 : getBoundaryNodeRange();
916 88336 : getBoundaryElementRange();
917 :
918 : // Call the callback function onMeshChanged
919 88336 : onMeshChanged();
920 88336 : }
921 :
922 : void
923 88336 : MooseMesh::onMeshChanged()
924 : {
925 88336 : }
926 :
927 : void
928 232 : MooseMesh::cacheChangedLists()
929 : {
930 1160 : TIME_SECTION("cacheChangedLists", 5, "Caching Changed Lists");
931 :
932 232 : ConstElemRange elem_range(getMesh().local_elements_begin(), getMesh().local_elements_end(), 1);
933 232 : CacheChangedListsThread cclt(*this);
934 232 : Threads::parallel_reduce(elem_range, cclt);
935 :
936 232 : _coarsened_element_children.clear();
937 :
938 464 : _refined_elements = std::make_unique<ConstElemPointerRange>(cclt._refined_elements.begin(),
939 464 : cclt._refined_elements.end());
940 464 : _coarsened_elements = std::make_unique<ConstElemPointerRange>(cclt._coarsened_elements.begin(),
941 464 : cclt._coarsened_elements.end());
942 232 : _coarsened_element_children = cclt._coarsened_element_children;
943 232 : }
944 :
945 : ConstElemPointerRange *
946 232 : MooseMesh::refinedElementRange() const
947 : {
948 232 : return _refined_elements.get();
949 : }
950 :
951 : ConstElemPointerRange *
952 232 : MooseMesh::coarsenedElementRange() const
953 : {
954 232 : return _coarsened_elements.get();
955 : }
956 :
957 : const std::vector<const Elem *> &
958 2874 : MooseMesh::coarsenedElementChildren(const Elem * elem) const
959 : {
960 2874 : auto elem_to_child_pair = _coarsened_element_children.find(elem);
961 : mooseAssert(elem_to_child_pair != _coarsened_element_children.end(), "Missing element in map");
962 5748 : return elem_to_child_pair->second;
963 : }
964 :
965 : void
966 74055 : MooseMesh::updateActiveSemiLocalNodeRange(std::set<dof_id_type> & ghosted_elems)
967 : {
968 370275 : TIME_SECTION("updateActiveSemiLocalNodeRange", 5, "Updating ActiveSemiLocalNode Range");
969 :
970 74055 : _semilocal_node_list.clear();
971 :
972 : // First add the nodes connected to local elems
973 74055 : ConstElemRange * active_local_elems = getActiveLocalElementRange();
974 14250674 : for (const auto & elem : *active_local_elems)
975 : {
976 89624685 : for (unsigned int n = 0; n < elem->n_nodes(); ++n)
977 : {
978 : // Since elem is const here but we require a non-const Node * to
979 : // store in the _semilocal_node_list (otherwise things like
980 : // UpdateDisplacedMeshThread don't work), we are using a
981 : // const_cast. A more long-term fix would be to have
982 : // getActiveLocalElementRange return a non-const ElemRange.
983 75448066 : Node * node = const_cast<Node *>(elem->node_ptr(n));
984 :
985 75448066 : _semilocal_node_list.insert(node);
986 : }
987 : }
988 :
989 : // Now add the nodes connected to ghosted_elems
990 119244 : for (const auto & ghost_elem_id : ghosted_elems)
991 : {
992 45189 : Elem * elem = getMesh().elem_ptr(ghost_elem_id);
993 250126 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
994 : {
995 204937 : Node * node = elem->node_ptr(n);
996 :
997 204937 : _semilocal_node_list.insert(node);
998 : }
999 : }
1000 :
1001 : // Now create the actual range
1002 148110 : _active_semilocal_node_range = std::make_unique<SemiLocalNodeRange>(_semilocal_node_list.begin(),
1003 148110 : _semilocal_node_list.end());
1004 74055 : }
1005 :
1006 : bool
1007 34749 : MooseMesh::isSemiLocal(Node * const node) const
1008 : {
1009 34749 : return _semilocal_node_list.find(node) != _semilocal_node_list.end();
1010 : }
1011 :
1012 : /**
1013 : * Helper class for sorting Boundary Nodes so that we always get the same
1014 : * order of application for boundary conditions.
1015 : */
1016 : class BndNodeCompare
1017 : {
1018 : public:
1019 161522 : BndNodeCompare() {}
1020 :
1021 123105273 : bool operator()(const BndNode * const & lhs, const BndNode * const & rhs)
1022 : {
1023 123105273 : if (lhs->_bnd_id < rhs->_bnd_id)
1024 23013630 : return true;
1025 :
1026 100091643 : if (lhs->_bnd_id > rhs->_bnd_id)
1027 10455485 : return false;
1028 :
1029 89636158 : if (lhs->_node->id() < rhs->_node->id())
1030 57787944 : return true;
1031 :
1032 31848214 : if (lhs->_node->id() > rhs->_node->id())
1033 31848214 : return false;
1034 :
1035 0 : return false;
1036 : }
1037 : };
1038 :
1039 : void
1040 161522 : MooseMesh::buildNodeList()
1041 : {
1042 807610 : TIME_SECTION("buildNodeList", 5, "Building Node List");
1043 :
1044 161522 : freeBndNodes();
1045 :
1046 161522 : auto bc_tuples = getMesh().get_boundary_info().build_node_list();
1047 :
1048 161522 : int n = bc_tuples.size();
1049 161522 : _bnd_nodes.clear();
1050 161522 : _bnd_nodes.reserve(n);
1051 12828043 : for (const auto & t : bc_tuples)
1052 : {
1053 12666521 : auto node_id = std::get<0>(t);
1054 12666521 : auto bc_id = std::get<1>(t);
1055 :
1056 12666521 : _bnd_nodes.push_back(new BndNode(getMesh().node_ptr(node_id), bc_id));
1057 12666521 : _node_set_nodes[bc_id].push_back(node_id);
1058 12666521 : _bnd_node_ids[bc_id].insert(node_id);
1059 : }
1060 :
1061 161522 : _bnd_nodes.reserve(_bnd_nodes.size() + _extra_bnd_nodes.size());
1062 161582 : for (unsigned int i = 0; i < _extra_bnd_nodes.size(); i++)
1063 : {
1064 60 : BndNode * bnode = new BndNode(_extra_bnd_nodes[i]._node, _extra_bnd_nodes[i]._bnd_id);
1065 60 : _bnd_nodes.push_back(bnode);
1066 60 : _bnd_node_ids[std::get<1>(bc_tuples[i])].insert(_extra_bnd_nodes[i]._node->id());
1067 : }
1068 :
1069 : // This sort is here so that boundary conditions are always applied in the same order
1070 161522 : std::sort(_bnd_nodes.begin(), _bnd_nodes.end(), BndNodeCompare());
1071 161522 : }
1072 :
1073 : void
1074 67257 : MooseMesh::computeMaxPerElemAndSide()
1075 : {
1076 67257 : auto & mesh = getMesh();
1077 :
1078 67257 : _max_sides_per_elem = 0;
1079 67257 : _max_nodes_per_elem = 0;
1080 67257 : _max_nodes_per_side = 0;
1081 :
1082 19541217 : for (auto & elem : as_range(mesh.local_elements_begin(), mesh.local_elements_end()))
1083 : {
1084 9736980 : _max_sides_per_elem = std::max(_max_sides_per_elem, elem->n_sides());
1085 9736980 : _max_nodes_per_elem = std::max(_max_nodes_per_elem, elem->n_nodes());
1086 :
1087 55243445 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
1088 45506465 : _max_nodes_per_side = std::max(_max_nodes_per_side, elem->side_ptr(side)->n_nodes());
1089 67257 : }
1090 :
1091 67257 : mesh.comm().max(_max_sides_per_elem);
1092 67257 : mesh.comm().max(_max_nodes_per_elem);
1093 67257 : mesh.comm().max(_max_nodes_per_side);
1094 67257 : }
1095 :
1096 : void
1097 161522 : MooseMesh::buildElemIDInfo()
1098 : {
1099 161522 : unsigned int n = getMesh().n_elem_integers() + 1;
1100 :
1101 161522 : _block_id_mapping.clear();
1102 161522 : _max_ids.clear();
1103 161522 : _min_ids.clear();
1104 161522 : _id_identical_flag.clear();
1105 :
1106 161522 : _block_id_mapping.resize(n);
1107 161522 : _max_ids.resize(n, std::numeric_limits<dof_id_type>::min());
1108 161522 : _min_ids.resize(n, std::numeric_limits<dof_id_type>::max());
1109 323044 : _id_identical_flag.resize(n, std::vector<bool>(n, true));
1110 30466494 : for (const auto & elem : getMesh().active_local_element_ptr_range())
1111 62948436 : for (unsigned int i = 0; i < n; ++i)
1112 : {
1113 32643464 : auto id = (i == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(i));
1114 32643464 : _block_id_mapping[i][elem->subdomain_id()].insert(id);
1115 32643464 : if (id > _max_ids[i])
1116 76671 : _max_ids[i] = id;
1117 32643464 : if (id < _min_ids[i])
1118 166349 : _min_ids[i] = id;
1119 72981128 : for (unsigned int j = 0; j < n; ++j)
1120 : {
1121 40337664 : auto idj = (j == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(j));
1122 40337664 : if (i != j && _id_identical_flag[i][j] && id != idj)
1123 4750 : _id_identical_flag[i][j] = false;
1124 : }
1125 161522 : }
1126 :
1127 324638 : for (unsigned int i = 0; i < n; ++i)
1128 : {
1129 395624 : for (auto & blk : meshSubdomains())
1130 232508 : comm().set_union(_block_id_mapping[i][blk]);
1131 163116 : comm().min(_id_identical_flag[i]);
1132 : }
1133 161522 : comm().max(_max_ids);
1134 161522 : comm().min(_min_ids);
1135 161522 : }
1136 :
1137 : std::unordered_map<dof_id_type, std::set<dof_id_type>>
1138 12 : MooseMesh::getElemIDMapping(const std::string & from_id_name, const std::string & to_id_name) const
1139 : {
1140 12 : auto & mesh_base = getMesh();
1141 :
1142 12 : if (!mesh_base.has_elem_integer(from_id_name))
1143 0 : mooseError("Mesh does not have the element integer name '", from_id_name, "'");
1144 12 : if (!mesh_base.has_elem_integer(to_id_name))
1145 0 : mooseError("Mesh does not have the element integer name '", to_id_name, "'");
1146 :
1147 12 : const auto id1 = mesh_base.get_elem_integer_index(from_id_name);
1148 12 : const auto id2 = mesh_base.get_elem_integer_index(to_id_name);
1149 :
1150 12 : std::unordered_map<dof_id_type, std::set<dof_id_type>> id_map;
1151 36 : for (const auto id : getAllElemIDs(id1))
1152 36 : id_map[id] = std::set<dof_id_type>();
1153 :
1154 912 : for (const auto & elem : mesh_base.active_local_element_ptr_range())
1155 912 : id_map[elem->get_extra_integer(id1)].insert(elem->get_extra_integer(id2));
1156 :
1157 36 : for (auto & [id, ids] : id_map)
1158 : {
1159 24 : libmesh_ignore(id); // avoid overzealous gcc 9.4 unused var warning
1160 24 : comm().set_union(ids);
1161 : }
1162 :
1163 12 : return id_map;
1164 0 : }
1165 :
1166 : std::set<dof_id_type>
1167 54 : MooseMesh::getAllElemIDs(unsigned int elem_id_index) const
1168 : {
1169 54 : std::set<dof_id_type> unique_ids;
1170 150 : for (auto & pair : _block_id_mapping[elem_id_index])
1171 344 : for (auto & id : pair.second)
1172 248 : unique_ids.insert(id);
1173 54 : return unique_ids;
1174 0 : }
1175 :
1176 : std::set<dof_id_type>
1177 70 : MooseMesh::getElemIDsOnBlocks(unsigned int elem_id_index, const std::set<SubdomainID> & blks) const
1178 : {
1179 70 : std::set<dof_id_type> unique_ids;
1180 154 : for (auto & blk : blks)
1181 : {
1182 84 : auto it = _block_id_mapping[elem_id_index].find(blk);
1183 84 : if (it == _block_id_mapping[elem_id_index].end())
1184 0 : mooseError("Block ", blk, " is not available on the mesh");
1185 :
1186 252 : for (auto & mid : it->second)
1187 168 : unique_ids.insert(mid);
1188 : }
1189 70 : return unique_ids;
1190 0 : }
1191 :
1192 : void
1193 161522 : MooseMesh::buildBndElemList()
1194 : {
1195 807610 : TIME_SECTION("buildBndElemList", 5, "Building Boundary Elements List");
1196 :
1197 161522 : freeBndElems();
1198 :
1199 161522 : auto bc_tuples = getMesh().get_boundary_info().build_active_side_list();
1200 :
1201 161522 : int n = bc_tuples.size();
1202 161522 : _bnd_elems.clear();
1203 161522 : _bnd_elems.reserve(n);
1204 10194441 : for (const auto & t : bc_tuples)
1205 : {
1206 10032919 : auto elem_id = std::get<0>(t);
1207 10032919 : auto side_id = std::get<1>(t);
1208 10032919 : auto bc_id = std::get<2>(t);
1209 :
1210 10032919 : _bnd_elems.push_back(new BndElement(getMesh().elem_ptr(elem_id), side_id, bc_id));
1211 10032919 : _bnd_elem_ids[bc_id].insert(elem_id);
1212 : }
1213 161522 : }
1214 :
1215 : const std::map<dof_id_type, std::vector<dof_id_type>> &
1216 1061096 : MooseMesh::nodeToElemMap()
1217 : {
1218 1061096 : if (!_node_to_elem_map_built) // Guard the creation with a double checked lock
1219 : {
1220 5959 : Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
1221 :
1222 5959 : if (!_node_to_elem_map_built)
1223 : {
1224 : // This is allowing the timing to be run even with threads
1225 : // This is safe because all threads will be waiting on this section when it runs
1226 : // NOTE: Do not copy this construction to other places without thinking REALLY hard about it
1227 : // The PerfGraph is NOT threadsafe and will cause all kinds of havok if care isn't taken
1228 5943 : auto in_threads = Threads::in_threads;
1229 5943 : Threads::in_threads = false;
1230 29715 : TIME_SECTION("nodeToElemMap", 5, "Building Node To Elem Map");
1231 5943 : Threads::in_threads = in_threads;
1232 :
1233 1354749 : for (const auto & elem : getMesh().active_element_ptr_range())
1234 8110916 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
1235 6768053 : _node_to_elem_map[elem->node_id(n)].push_back(elem->id());
1236 :
1237 5943 : _node_to_elem_map_built = true; // MUST be set at the end for double-checked locking to work!
1238 5943 : }
1239 5959 : }
1240 1061096 : return _node_to_elem_map;
1241 : }
1242 :
1243 : const std::map<dof_id_type, std::vector<dof_id_type>> &
1244 123424 : MooseMesh::nodeToActiveSemilocalElemMap()
1245 : {
1246 123424 : if (!_node_to_active_semilocal_elem_map_built) // Guard the creation with a double checked lock
1247 : {
1248 61718 : Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
1249 :
1250 : // This is allowing the timing to be run even with threads
1251 : // This is safe because all threads will be waiting on this section when it runs
1252 : // NOTE: Do not copy this construction to other places without thinking REALLY hard about it
1253 : // The PerfGraph is NOT threadsafe and will cause all kinds of havok if care isn't taken
1254 61718 : auto in_threads = Threads::in_threads;
1255 61718 : Threads::in_threads = false;
1256 308590 : TIME_SECTION("nodeToActiveSemilocalElemMap", 5, "Building SemiLocalElemMap");
1257 61718 : Threads::in_threads = in_threads;
1258 :
1259 61718 : if (!_node_to_active_semilocal_elem_map_built)
1260 : {
1261 61718 : for (const auto & elem :
1262 11964822 : as_range(getMesh().semilocal_elements_begin(), getMesh().semilocal_elements_end()))
1263 11841386 : if (elem->active())
1264 78530835 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
1265 66751167 : _node_to_active_semilocal_elem_map[elem->node_id(n)].push_back(elem->id());
1266 :
1267 61718 : _node_to_active_semilocal_elem_map_built =
1268 : true; // MUST be set at the end for double-checked locking to work!
1269 : }
1270 61718 : }
1271 :
1272 123424 : return _node_to_active_semilocal_elem_map;
1273 : }
1274 :
1275 : ConstElemRange *
1276 11367767 : MooseMesh::getActiveLocalElementRange()
1277 : {
1278 11367767 : if (!_active_local_elem_range)
1279 : {
1280 443256 : TIME_SECTION("getActiveLocalElementRange", 5);
1281 :
1282 295504 : _active_local_elem_range = std::make_unique<ConstElemRange>(
1283 443256 : getMesh().active_local_elements_begin(), getMesh().active_local_elements_end(), GRAIN_SIZE);
1284 147752 : }
1285 :
1286 11367767 : return _active_local_elem_range.get();
1287 : }
1288 :
1289 : NodeRange *
1290 88406 : MooseMesh::getActiveNodeRange()
1291 : {
1292 88406 : if (!_active_node_range)
1293 : {
1294 265008 : TIME_SECTION("getActiveNodeRange", 5);
1295 :
1296 176672 : _active_node_range = std::make_unique<NodeRange>(
1297 265008 : getMesh().active_nodes_begin(), getMesh().active_nodes_end(), GRAIN_SIZE);
1298 88336 : }
1299 :
1300 88406 : return _active_node_range.get();
1301 : }
1302 :
1303 : SemiLocalNodeRange *
1304 0 : MooseMesh::getActiveSemiLocalNodeRange() const
1305 : {
1306 : mooseAssert(_active_semilocal_node_range,
1307 : "_active_semilocal_node_range has not been created yet!");
1308 :
1309 0 : return _active_semilocal_node_range.get();
1310 : }
1311 :
1312 : ConstNodeRange *
1313 338070 : MooseMesh::getLocalNodeRange()
1314 : {
1315 338070 : if (!_local_node_range)
1316 : {
1317 265008 : TIME_SECTION("getLocalNodeRange", 5);
1318 :
1319 176672 : _local_node_range = std::make_unique<ConstNodeRange>(
1320 265008 : getMesh().local_nodes_begin(), getMesh().local_nodes_end(), GRAIN_SIZE);
1321 88336 : }
1322 :
1323 338070 : return _local_node_range.get();
1324 : }
1325 :
1326 : ConstBndNodeRange *
1327 3960052 : MooseMesh::getBoundaryNodeRange()
1328 : {
1329 3960052 : if (!_bnd_node_range)
1330 : {
1331 265521 : TIME_SECTION("getBoundaryNodeRange", 5);
1332 :
1333 : _bnd_node_range =
1334 88507 : std::make_unique<ConstBndNodeRange>(bndNodesBegin(), bndNodesEnd(), GRAIN_SIZE);
1335 88507 : }
1336 :
1337 3960052 : return _bnd_node_range.get();
1338 : }
1339 :
1340 : ConstBndElemRange *
1341 199158 : MooseMesh::getBoundaryElementRange()
1342 : {
1343 199158 : if (!_bnd_elem_range)
1344 : {
1345 265008 : TIME_SECTION("getBoundaryElementRange", 5);
1346 :
1347 : _bnd_elem_range =
1348 88336 : std::make_unique<ConstBndElemRange>(bndElemsBegin(), bndElemsEnd(), GRAIN_SIZE);
1349 88336 : }
1350 :
1351 199158 : return _bnd_elem_range.get();
1352 : }
1353 :
1354 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1355 0 : MooseMesh::getBoundariesToElems() const
1356 : {
1357 0 : mooseDeprecated("MooseMesh::getBoundariesToElems is deprecated, "
1358 : "use MooseMesh::getBoundariesToActiveSemiLocalElemIds");
1359 0 : return getBoundariesToActiveSemiLocalElemIds();
1360 : }
1361 :
1362 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1363 66 : MooseMesh::getBoundariesToActiveSemiLocalElemIds() const
1364 : {
1365 66 : return _bnd_elem_ids;
1366 : }
1367 :
1368 : std::unordered_set<dof_id_type>
1369 1085 : MooseMesh::getBoundaryActiveSemiLocalElemIds(BoundaryID bid) const
1370 : {
1371 : // The boundary to element map is computed on every mesh update
1372 1085 : const auto it = _bnd_elem_ids.find(bid);
1373 1085 : if (it == _bnd_elem_ids.end())
1374 : // Boundary is not local to this domain, return an empty set
1375 34 : return std::unordered_set<dof_id_type>{};
1376 1051 : return it->second;
1377 : }
1378 :
1379 : std::unordered_set<dof_id_type>
1380 0 : MooseMesh::getBoundaryActiveNeighborElemIds(BoundaryID bid) const
1381 : {
1382 : // Vector of boundary elems is updated every mesh update
1383 0 : std::unordered_set<dof_id_type> neighbor_elems;
1384 0 : for (const auto & bnd_elem : _bnd_elems)
1385 : {
1386 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1387 0 : if (elem_bid == bid)
1388 : {
1389 0 : const auto * neighbor = elem_ptr->neighbor_ptr(elem_side);
1390 : // Dont add fully remote elements, ghosted is fine
1391 0 : if (neighbor && neighbor != libMesh::remote_elem)
1392 : {
1393 : // handle mesh refinement, only return active elements near the boundary
1394 0 : if (neighbor->active())
1395 0 : neighbor_elems.insert(neighbor->id());
1396 : else
1397 : {
1398 0 : std::vector<const Elem *> family;
1399 0 : neighbor->active_family_tree_by_neighbor(family, elem_ptr);
1400 0 : for (const auto & child_neighbor : family)
1401 0 : neighbor_elems.insert(child_neighbor->id());
1402 0 : }
1403 : }
1404 : }
1405 : }
1406 :
1407 0 : return neighbor_elems;
1408 0 : }
1409 :
1410 : bool
1411 0 : MooseMesh::isBoundaryFullyExternalToSubdomains(BoundaryID bid,
1412 : const std::set<SubdomainID> & blk_group) const
1413 : {
1414 : mooseAssert(_bnd_elem_range, "Boundary element range is not initialized");
1415 :
1416 : // Loop over all side elements of the mesh, select those on the boundary
1417 0 : for (const auto & bnd_elem : *_bnd_elem_range)
1418 : {
1419 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1420 0 : if (elem_bid == bid)
1421 : {
1422 : // If an element is internal to the group of subdomain, check the neighbor
1423 0 : if (blk_group.find(elem_ptr->subdomain_id()) != blk_group.end())
1424 : {
1425 0 : const auto * const neighbor = elem_ptr->neighbor_ptr(elem_side);
1426 :
1427 : // If we did not ghost the neighbor, we cannot decide
1428 0 : if (neighbor == libMesh::remote_elem)
1429 0 : mooseError("Insufficient level of geometrical ghosting to determine "
1430 : "if a boundary is internal to the mesh");
1431 : // If the neighbor does not exist, then we are on the edge of the mesh
1432 0 : if (!neighbor)
1433 0 : continue;
1434 : // If the neighbor is also in the group of subdomain,
1435 : // then the boundary cuts the subdomains
1436 0 : if (blk_group.find(neighbor->subdomain_id()) != blk_group.end())
1437 0 : return false;
1438 : }
1439 : }
1440 : }
1441 0 : return true;
1442 : }
1443 :
1444 : void
1445 161522 : MooseMesh::cacheInfo()
1446 : {
1447 484566 : TIME_SECTION("cacheInfo", 3);
1448 :
1449 161522 : _has_lower_d = false;
1450 161522 : _sub_to_data.clear();
1451 161522 : _neighbor_subdomain_boundary_ids.clear();
1452 161522 : _block_node_list.clear();
1453 161522 : _higher_d_elem_side_to_lower_d_elem.clear();
1454 161522 : _lower_d_elem_to_higher_d_elem_side.clear();
1455 161522 : _lower_d_interior_blocks.clear();
1456 161522 : _lower_d_boundary_blocks.clear();
1457 :
1458 161522 : auto & mesh = getMesh();
1459 :
1460 : // TODO: Thread this!
1461 41597262 : for (const auto & elem : mesh.element_ptr_range())
1462 : {
1463 41435740 : const Elem * ip_elem = elem->interior_parent();
1464 :
1465 41435740 : if (ip_elem)
1466 : {
1467 85684 : if (elem->active())
1468 76982 : _sub_to_data[elem->subdomain_id()].is_lower_d = true;
1469 85684 : unsigned int ip_side = ip_elem->which_side_am_i(elem);
1470 :
1471 : // For some grid sequencing tests: ip_side == libMesh::invalid_uint
1472 85684 : if (ip_side != libMesh::invalid_uint)
1473 : {
1474 85484 : auto pair = std::make_pair(ip_elem, ip_side);
1475 85484 : _higher_d_elem_side_to_lower_d_elem.insert(
1476 85484 : std::pair<std::pair<const Elem *, unsigned short int>, const Elem *>(pair, elem));
1477 85484 : _lower_d_elem_to_higher_d_elem_side.insert(
1478 85484 : std::pair<const Elem *, unsigned short int>(elem, ip_side));
1479 :
1480 85484 : auto id = elem->subdomain_id();
1481 85484 : if (ip_elem->neighbor_ptr(ip_side))
1482 : {
1483 7304 : if (mesh.subdomain_name(id).find("INTERNAL_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1484 7196 : _lower_d_interior_blocks.insert(id);
1485 : }
1486 : else
1487 : {
1488 78180 : if (mesh.subdomain_name(id).find("BOUNDARY_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1489 7546 : _lower_d_boundary_blocks.insert(id);
1490 : }
1491 : }
1492 : }
1493 :
1494 264038903 : for (unsigned int nd = 0; nd < elem->n_nodes(); ++nd)
1495 : {
1496 222603163 : Node & node = *elem->node_ptr(nd);
1497 222603163 : _block_node_list[node.id()].insert(elem->subdomain_id());
1498 : }
1499 161522 : }
1500 161522 : _communicator.set_union(_lower_d_interior_blocks);
1501 161522 : _communicator.set_union(_lower_d_boundary_blocks);
1502 :
1503 30466494 : for (const auto & elem : mesh.active_local_element_ptr_range())
1504 : {
1505 30304972 : SubdomainID subdomain_id = elem->subdomain_id();
1506 30304972 : auto & sub_data = _sub_to_data[subdomain_id];
1507 166491342 : for (unsigned int side = 0; side < elem->n_sides(); side++)
1508 : {
1509 136186370 : std::vector<BoundaryID> boundary_ids = getBoundaryIDs(elem, side);
1510 136186370 : sub_data.boundary_ids.insert(boundary_ids.begin(), boundary_ids.end());
1511 :
1512 136186370 : Elem * neig = elem->neighbor_ptr(side);
1513 136186370 : if (neig)
1514 : {
1515 128417658 : _neighbor_subdomain_boundary_ids[neig->subdomain_id()].insert(boundary_ids.begin(),
1516 : boundary_ids.end());
1517 128417658 : SubdomainID neighbor_subdomain_id = neig->subdomain_id();
1518 128417658 : if (neighbor_subdomain_id != subdomain_id)
1519 1630762 : sub_data.neighbor_subs.insert(neighbor_subdomain_id);
1520 : }
1521 136186370 : }
1522 161522 : }
1523 :
1524 388903 : for (const auto blk_id : _mesh_subdomains)
1525 : {
1526 227381 : auto & sub_data = _sub_to_data[blk_id];
1527 227381 : _communicator.set_union(sub_data.neighbor_subs);
1528 227381 : _communicator.set_union(sub_data.boundary_ids);
1529 227381 : _communicator.max(sub_data.is_lower_d);
1530 227381 : if (sub_data.is_lower_d)
1531 8541 : _has_lower_d = true;
1532 227381 : _communicator.set_union(_neighbor_subdomain_boundary_ids[blk_id]);
1533 : }
1534 161522 : }
1535 :
1536 : const std::set<SubdomainID> &
1537 103036674 : MooseMesh::getNodeBlockIds(const Node & node) const
1538 : {
1539 103036674 : auto it = _block_node_list.find(node.id());
1540 :
1541 103036674 : if (it == _block_node_list.end())
1542 0 : mooseError("Unable to find node: ", node.id(), " in any block list.");
1543 :
1544 206073348 : return it->second;
1545 : }
1546 :
1547 : MooseMesh::face_info_iterator
1548 207456 : MooseMesh::ownedFaceInfoBegin()
1549 : {
1550 : return face_info_iterator(
1551 207456 : _face_info.begin(),
1552 207456 : _face_info.end(),
1553 414912 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1554 : }
1555 :
1556 : MooseMesh::face_info_iterator
1557 207456 : MooseMesh::ownedFaceInfoEnd()
1558 : {
1559 : return face_info_iterator(
1560 207456 : _face_info.end(),
1561 207456 : _face_info.end(),
1562 414912 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1563 : }
1564 :
1565 : MooseMesh::elem_info_iterator
1566 22350 : MooseMesh::ownedElemInfoBegin()
1567 : {
1568 22350 : return elem_info_iterator(_elem_info.begin(),
1569 22350 : _elem_info.end(),
1570 44700 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1571 : }
1572 :
1573 : MooseMesh::elem_info_iterator
1574 22350 : MooseMesh::ownedElemInfoEnd()
1575 : {
1576 22350 : return elem_info_iterator(_elem_info.end(),
1577 22350 : _elem_info.end(),
1578 44700 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1579 : }
1580 :
1581 : // default begin() accessor
1582 : MooseMesh::bnd_node_iterator
1583 88507 : MooseMesh::bndNodesBegin()
1584 : {
1585 88507 : Predicates::NotNull<bnd_node_iterator_imp> p;
1586 177014 : return bnd_node_iterator(_bnd_nodes.begin(), _bnd_nodes.end(), p);
1587 88507 : }
1588 :
1589 : // default end() accessor
1590 : MooseMesh::bnd_node_iterator
1591 88507 : MooseMesh::bndNodesEnd()
1592 : {
1593 88507 : Predicates::NotNull<bnd_node_iterator_imp> p;
1594 177014 : return bnd_node_iterator(_bnd_nodes.end(), _bnd_nodes.end(), p);
1595 88507 : }
1596 :
1597 : // default begin() accessor
1598 : MooseMesh::bnd_elem_iterator
1599 88506 : MooseMesh::bndElemsBegin()
1600 : {
1601 88506 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1602 177012 : return bnd_elem_iterator(_bnd_elems.begin(), _bnd_elems.end(), p);
1603 88506 : }
1604 :
1605 : // default end() accessor
1606 : MooseMesh::bnd_elem_iterator
1607 88506 : MooseMesh::bndElemsEnd()
1608 : {
1609 88506 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1610 177012 : return bnd_elem_iterator(_bnd_elems.end(), _bnd_elems.end(), p);
1611 88506 : }
1612 :
1613 : const Node *
1614 0 : MooseMesh::addUniqueNode(const Point & p, Real tol)
1615 : {
1616 : /**
1617 : * Looping through the mesh nodes each time we add a point is very slow. To speed things
1618 : * up we keep a local data structure
1619 : */
1620 0 : if (getMesh().n_nodes() != _node_map.size())
1621 : {
1622 0 : _node_map.clear();
1623 0 : _node_map.reserve(getMesh().n_nodes());
1624 0 : for (const auto & node : getMesh().node_ptr_range())
1625 0 : _node_map.push_back(node);
1626 : }
1627 :
1628 0 : Node * node = nullptr;
1629 0 : for (unsigned int i = 0; i < _node_map.size(); ++i)
1630 : {
1631 0 : if (p.relative_fuzzy_equals(*_node_map[i], tol))
1632 : {
1633 0 : node = _node_map[i];
1634 0 : break;
1635 : }
1636 : }
1637 0 : if (node == nullptr)
1638 : {
1639 0 : node = getMesh().add_node(new Node(p));
1640 0 : _node_map.push_back(node);
1641 : }
1642 :
1643 : mooseAssert(node != nullptr, "Node is NULL");
1644 0 : return node;
1645 : }
1646 :
1647 : Node *
1648 6090 : MooseMesh::addQuadratureNode(const Elem * elem,
1649 : const unsigned short int side,
1650 : const unsigned int qp,
1651 : BoundaryID bid,
1652 : const Point & point)
1653 : {
1654 : Node * qnode;
1655 :
1656 6090 : if (_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) ==
1657 12180 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end())
1658 : {
1659 : // Create a new node id starting from the max node id and counting down. This will be the least
1660 : // likely to collide with an existing node id.
1661 : // Note that we are using numeric_limits<unsigned>::max even
1662 : // though max_id is stored as a dof_id_type. I tried this with
1663 : // numeric_limits<dof_id_type>::max and it broke several tests in
1664 : // MOOSE. So, this is some kind of a magic number that we will
1665 : // just continue to use...
1666 6090 : dof_id_type max_id = std::numeric_limits<unsigned int>::max() - 100;
1667 6090 : dof_id_type new_id = max_id - _quadrature_nodes.size();
1668 :
1669 6090 : if (new_id <= getMesh().max_node_id())
1670 0 : mooseError("Quadrature node id collides with existing node id!");
1671 :
1672 6090 : qnode = new Node(point, new_id);
1673 :
1674 : // Keep track of this new node in two different ways for easy lookup
1675 6090 : _quadrature_nodes[new_id] = qnode;
1676 6090 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp] = qnode;
1677 :
1678 6090 : if (elem->active())
1679 : {
1680 6090 : _node_to_elem_map[new_id].push_back(elem->id());
1681 6090 : _node_to_active_semilocal_elem_map[new_id].push_back(elem->id());
1682 : }
1683 : }
1684 : else
1685 0 : qnode = _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1686 :
1687 6090 : BndNode * bnode = new BndNode(qnode, bid);
1688 6090 : _bnd_nodes.push_back(bnode);
1689 6090 : _bnd_node_ids[bid].insert(qnode->id());
1690 :
1691 6090 : _extra_bnd_nodes.push_back(*bnode);
1692 :
1693 : // Do this so the range will be regenerated next time it is accessed
1694 6090 : _bnd_node_range.reset();
1695 :
1696 6090 : return qnode;
1697 : }
1698 :
1699 : Node *
1700 156789 : MooseMesh::getQuadratureNode(const Elem * elem,
1701 : const unsigned short int side,
1702 : const unsigned int qp)
1703 : {
1704 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes.find(elem->id()) !=
1705 : _elem_to_side_to_qp_to_quadrature_nodes.end(),
1706 : "Elem has no quadrature nodes!");
1707 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()].find(side) !=
1708 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()].end(),
1709 : "Side has no quadrature nodes!");
1710 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) !=
1711 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end(),
1712 : "qp not found on side!");
1713 :
1714 156789 : return _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1715 : }
1716 :
1717 : void
1718 75235 : MooseMesh::clearQuadratureNodes()
1719 : {
1720 : // Delete all the quadrature nodes
1721 81309 : for (auto & it : _quadrature_nodes)
1722 6074 : delete it.second;
1723 :
1724 75235 : _quadrature_nodes.clear();
1725 75235 : _elem_to_side_to_qp_to_quadrature_nodes.clear();
1726 75235 : _extra_bnd_nodes.clear();
1727 75235 : }
1728 :
1729 : BoundaryID
1730 550216 : MooseMesh::getBoundaryID(const BoundaryName & boundary_name) const
1731 : {
1732 550216 : if (boundary_name == "ANY_BOUNDARY_ID")
1733 0 : mooseError("Please use getBoundaryIDs() when passing \"ANY_BOUNDARY_ID\"");
1734 :
1735 550216 : return MooseMeshUtils::getBoundaryID(boundary_name, getMesh());
1736 : }
1737 :
1738 : const Elem *
1739 1799502628 : MooseMesh::getLowerDElem(const Elem * elem, unsigned short int side) const
1740 : {
1741 1799502628 : auto it = _higher_d_elem_side_to_lower_d_elem.find(std::make_pair(elem, side));
1742 :
1743 1799502628 : if (it != _higher_d_elem_side_to_lower_d_elem.end())
1744 273745 : return it->second;
1745 : else
1746 1799228883 : return nullptr;
1747 : }
1748 :
1749 : unsigned int
1750 292 : MooseMesh::getHigherDSide(const Elem * elem) const
1751 : {
1752 292 : auto it = _lower_d_elem_to_higher_d_elem_side.find(elem);
1753 :
1754 292 : if (it != _lower_d_elem_to_higher_d_elem_side.end())
1755 292 : return it->second;
1756 : else
1757 0 : return libMesh::invalid_uint;
1758 : }
1759 :
1760 : std::vector<BoundaryID>
1761 125211 : MooseMesh::getBoundaryIDs(const std::vector<BoundaryName> & boundary_name,
1762 : bool generate_unknown) const
1763 : {
1764 : return MooseMeshUtils::getBoundaryIDs(
1765 125211 : getMesh(), boundary_name, generate_unknown, _mesh_boundary_ids);
1766 : }
1767 :
1768 : SubdomainID
1769 533456 : MooseMesh::getSubdomainID(const SubdomainName & subdomain_name) const
1770 : {
1771 533456 : return MooseMeshUtils::getSubdomainID(subdomain_name, getMesh());
1772 : }
1773 :
1774 : std::vector<SubdomainID>
1775 248980 : MooseMesh::getSubdomainIDs(const std::vector<SubdomainName> & subdomain_name) const
1776 : {
1777 248980 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1778 : }
1779 :
1780 : std::set<SubdomainID>
1781 0 : MooseMesh::getSubdomainIDs(const std::set<SubdomainName> & subdomain_name) const
1782 : {
1783 0 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1784 : }
1785 :
1786 : void
1787 1460 : MooseMesh::setSubdomainName(SubdomainID subdomain_id, const SubdomainName & name)
1788 : {
1789 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1790 1460 : getMesh().subdomain_name(subdomain_id) = name;
1791 1460 : }
1792 :
1793 : void
1794 0 : MooseMesh::setSubdomainName(MeshBase & mesh, SubdomainID subdomain_id, const SubdomainName & name)
1795 : {
1796 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1797 0 : mesh.subdomain_name(subdomain_id) = name;
1798 0 : }
1799 :
1800 : const std::string &
1801 5116858 : MooseMesh::getSubdomainName(SubdomainID subdomain_id) const
1802 : {
1803 5116858 : return getMesh().subdomain_name(subdomain_id);
1804 : }
1805 :
1806 : std::vector<SubdomainName>
1807 81 : MooseMesh::getSubdomainNames(const std::vector<SubdomainID> & subdomain_ids) const
1808 : {
1809 81 : std::vector<SubdomainName> names(subdomain_ids.size());
1810 :
1811 162 : for (unsigned int i = 0; i < subdomain_ids.size(); i++)
1812 81 : names[i] = getSubdomainName(subdomain_ids[i]);
1813 :
1814 81 : return names;
1815 0 : }
1816 :
1817 : void
1818 123 : MooseMesh::setBoundaryName(BoundaryID boundary_id, BoundaryName name)
1819 : {
1820 123 : BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1821 :
1822 : // We need to figure out if this boundary is a sideset or nodeset
1823 123 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1824 33 : boundary_info.sideset_name(boundary_id) = name;
1825 : else
1826 90 : boundary_info.nodeset_name(boundary_id) = name;
1827 123 : }
1828 :
1829 : const std::string &
1830 8774123 : MooseMesh::getBoundaryName(BoundaryID boundary_id) const
1831 : {
1832 8774123 : const BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1833 :
1834 : // We need to figure out if this boundary is a sideset or nodeset
1835 8774123 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1836 8712577 : return boundary_info.get_sideset_name(boundary_id);
1837 : else
1838 61546 : return boundary_info.get_nodeset_name(boundary_id);
1839 : }
1840 :
1841 : // specialization for PointListAdaptor<MooseMesh::PeriodicNodeInfo>
1842 : template <>
1843 : inline const Point &
1844 192700 : PointListAdaptor<MooseMesh::PeriodicNodeInfo>::getPoint(
1845 : const MooseMesh::PeriodicNodeInfo & item) const
1846 : {
1847 192700 : return *(item.first);
1848 : }
1849 :
1850 : void
1851 30 : MooseMesh::buildPeriodicNodeMap(std::multimap<dof_id_type, dof_id_type> & periodic_node_map,
1852 : unsigned int var_number,
1853 : libMesh::PeriodicBoundaries * pbs) const
1854 : {
1855 90 : TIME_SECTION("buildPeriodicNodeMap", 5);
1856 :
1857 : // clear existing map
1858 30 : periodic_node_map.clear();
1859 :
1860 : // get periodic nodes
1861 30 : std::vector<PeriodicNodeInfo> periodic_nodes;
1862 1750 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1863 : {
1864 : // unfortunately libMesh does not give us a pointer, so we have to look it up ourselves
1865 1720 : auto node = _mesh->node_ptr(std::get<0>(t));
1866 : mooseAssert(node != nullptr,
1867 : "libMesh::BoundaryInfo::build_node_list() returned an ID for a non-existing node");
1868 1720 : auto bc_id = std::get<1>(t);
1869 1720 : periodic_nodes.emplace_back(node, bc_id);
1870 30 : }
1871 :
1872 : // sort by boundary id
1873 30 : std::sort(periodic_nodes.begin(),
1874 : periodic_nodes.end(),
1875 9620 : [](const PeriodicNodeInfo & a, const PeriodicNodeInfo & b) -> bool
1876 9620 : { return a.second > b.second; });
1877 :
1878 : // build kd-tree
1879 : using KDTreeType = nanoflann::KDTreeSingleIndexAdaptor<
1880 : nanoflann::L2_Simple_Adaptor<Real, PointListAdaptor<PeriodicNodeInfo>, Real, std::size_t>,
1881 : PointListAdaptor<PeriodicNodeInfo>,
1882 : LIBMESH_DIM,
1883 : std::size_t>;
1884 30 : const unsigned int max_leaf_size = 20; // slightly affects runtime
1885 : auto point_list =
1886 30 : PointListAdaptor<PeriodicNodeInfo>(periodic_nodes.begin(), periodic_nodes.end());
1887 : auto kd_tree = std::make_unique<KDTreeType>(
1888 30 : LIBMESH_DIM, point_list, nanoflann::KDTreeSingleIndexAdaptorParams(max_leaf_size));
1889 : mooseAssert(kd_tree != nullptr, "KDTree was not properly initialized.");
1890 30 : kd_tree->buildIndex();
1891 :
1892 : // data structures for kd-tree search
1893 30 : nanoflann::SearchParameters search_params;
1894 30 : std::vector<nanoflann::ResultItem<std::size_t, Real>> ret_matches;
1895 :
1896 : // iterate over periodic nodes (boundary ids are in contiguous blocks)
1897 30 : libMesh::PeriodicBoundaryBase * periodic = nullptr;
1898 30 : BoundaryID current_bc_id = BoundaryInfo::invalid_id;
1899 1750 : for (auto & pair : periodic_nodes)
1900 : {
1901 : // entering a new block of boundary IDs
1902 1720 : if (pair.second != current_bc_id)
1903 : {
1904 120 : current_bc_id = pair.second;
1905 120 : periodic = pbs->boundary(current_bc_id);
1906 120 : if (periodic && !periodic->is_my_variable(var_number))
1907 0 : periodic = nullptr;
1908 : }
1909 :
1910 : // variable is not periodic at this node, skip
1911 1720 : if (!periodic)
1912 0 : continue;
1913 :
1914 : // clear result buffer
1915 1720 : ret_matches.clear();
1916 :
1917 : // id of the current node
1918 1720 : const auto id = pair.first->id();
1919 :
1920 : // position where we expect a periodic partner for the current node and boundary
1921 1720 : Point search_point = periodic->get_corresponding_pos(*pair.first);
1922 :
1923 : // search at the expected point
1924 1720 : kd_tree->radiusSearch(&(search_point)(0), libMesh::TOLERANCE, ret_matches, search_params);
1925 4720 : for (auto & match_pair : ret_matches)
1926 : {
1927 3000 : const auto & match = periodic_nodes[match_pair.first];
1928 : // add matched node if the boundary id is the corresponding id in the periodic pair
1929 3000 : if (match.second == periodic->pairedboundary)
1930 1720 : periodic_node_map.emplace(id, match.first->id());
1931 : }
1932 : }
1933 30 : }
1934 :
1935 : void
1936 0 : MooseMesh::buildPeriodicNodeSets(std::map<BoundaryID, std::set<dof_id_type>> & periodic_node_sets,
1937 : unsigned int var_number,
1938 : libMesh::PeriodicBoundaries * pbs) const
1939 : {
1940 0 : TIME_SECTION("buildPeriodicNodeSets", 5);
1941 :
1942 0 : periodic_node_sets.clear();
1943 :
1944 : // Loop over all the boundary nodes adding the periodic nodes to the appropriate set
1945 0 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1946 : {
1947 0 : auto node_id = std::get<0>(t);
1948 0 : auto bc_id = std::get<1>(t);
1949 :
1950 : // Is this current node on a known periodic boundary?
1951 0 : if (periodic_node_sets.find(bc_id) != periodic_node_sets.end())
1952 0 : periodic_node_sets[bc_id].insert(node_id);
1953 : else // This still might be a periodic node but we just haven't seen this boundary_id yet
1954 : {
1955 0 : const libMesh::PeriodicBoundaryBase * periodic = pbs->boundary(bc_id);
1956 0 : if (periodic && periodic->is_my_variable(var_number))
1957 0 : periodic_node_sets[bc_id].insert(node_id);
1958 : }
1959 0 : }
1960 0 : }
1961 :
1962 : bool
1963 70468 : MooseMesh::detectOrthogonalDimRanges(Real tol)
1964 : {
1965 211404 : TIME_SECTION("detectOrthogonalDimRanges", 5);
1966 :
1967 70468 : if (_regular_orthogonal_mesh)
1968 37289 : return true;
1969 :
1970 33179 : std::vector<Real> min(3, std::numeric_limits<Real>::max());
1971 33179 : std::vector<Real> max(3, std::numeric_limits<Real>::min());
1972 33179 : unsigned int dim = getMesh().mesh_dimension();
1973 :
1974 : // Find the bounding box of our mesh
1975 9457497 : for (const auto & node : getMesh().node_ptr_range())
1976 : // Check all coordinates, we don't know if this mesh might be lying in a higher dim even if the
1977 : // mesh dimension is lower.
1978 37697272 : for (const auto i : make_range(Moose::dim))
1979 : {
1980 28272954 : if ((*node)(i) < min[i])
1981 186003 : min[i] = (*node)(i);
1982 28272954 : if ((*node)(i) > max[i])
1983 434262 : max[i] = (*node)(i);
1984 33179 : }
1985 :
1986 33179 : this->comm().max(max);
1987 33179 : this->comm().min(min);
1988 :
1989 33179 : _extreme_nodes.resize(8); // 2^LIBMESH_DIM
1990 : // Now make sure that there are actual nodes at all of the extremes
1991 33179 : std::vector<bool> extreme_matches(8, false);
1992 33179 : std::vector<unsigned int> comp_map(3);
1993 9457497 : for (const auto & node : getMesh().node_ptr_range())
1994 : {
1995 : // See if the current node is located at one of the extremes
1996 9424318 : unsigned int coord_match = 0;
1997 :
1998 37697272 : for (const auto i : make_range(Moose::dim))
1999 : {
2000 28272954 : if (std::abs((*node)(i)-min[i]) < tol)
2001 : {
2002 5566989 : comp_map[i] = MIN;
2003 5566989 : ++coord_match;
2004 : }
2005 22705965 : else if (std::abs((*node)(i)-max[i]) < tol)
2006 : {
2007 1312548 : comp_map[i] = MAX;
2008 1312548 : ++coord_match;
2009 : }
2010 : }
2011 :
2012 9424318 : if (coord_match == LIBMESH_DIM) // Found a coordinate at one of the extremes
2013 : {
2014 119079 : _extreme_nodes[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = node;
2015 119079 : extreme_matches[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = true;
2016 : }
2017 33179 : }
2018 :
2019 : // See if we matched all of the extremes for the mesh dimension
2020 33179 : this->comm().max(extreme_matches);
2021 33179 : if (std::count(extreme_matches.begin(), extreme_matches.end(), true) == (1 << dim))
2022 28903 : _regular_orthogonal_mesh = true;
2023 :
2024 : // Set the bounds
2025 33179 : _bounds.resize(LIBMESH_DIM);
2026 132716 : for (const auto i : make_range(Moose::dim))
2027 : {
2028 99537 : _bounds[i].resize(2);
2029 99537 : _bounds[i][MIN] = min[i];
2030 99537 : _bounds[i][MAX] = max[i];
2031 : }
2032 :
2033 33179 : return _regular_orthogonal_mesh;
2034 70468 : }
2035 :
2036 : void
2037 501 : MooseMesh::detectPairedSidesets()
2038 : {
2039 1503 : TIME_SECTION("detectPairedSidesets", 5);
2040 :
2041 : // Loop over level-0 elements (since boundary condition information
2042 : // is only directly stored for them) and find sidesets with normals
2043 : // that point in the -x, +x, -y, +y, and -z, +z direction. If there
2044 : // is a unique sideset id for each direction, then the paired
2045 : // sidesets consist of (-x,+x), (-y,+y), (-z,+z). If there are
2046 : // multiple sideset ids for a given direction, then we can't pick a
2047 : // single pair for that direction. In that case, we'll just return
2048 : // as was done in the original algorithm.
2049 :
2050 : // Points used for direction comparison
2051 501 : const Point minus_x(-1, 0, 0), plus_x(1, 0, 0), minus_y(0, -1, 0), plus_y(0, 1, 0),
2052 501 : minus_z(0, 0, -1), plus_z(0, 0, 1);
2053 :
2054 : // we need to test all element dimensions from dim down to 1
2055 501 : const unsigned int dim = getMesh().mesh_dimension();
2056 :
2057 : // boundary id sets for elements of different dimensions
2058 3006 : std::vector<std::set<BoundaryID>> minus_x_ids(dim), plus_x_ids(dim), minus_y_ids(dim),
2059 3006 : plus_y_ids(dim), minus_z_ids(dim), plus_z_ids(dim);
2060 :
2061 1002 : std::vector<std::unique_ptr<FEBase>> fe_faces(dim);
2062 501 : std::vector<std::unique_ptr<libMesh::QGauss>> qfaces(dim);
2063 1490 : for (unsigned side_dim = 0; side_dim < dim; ++side_dim)
2064 : {
2065 : // Face is assumed to be flat, therefore normal is assumed to be
2066 : // constant over the face, therefore only compute it at 1 qp.
2067 989 : qfaces[side_dim] = std::unique_ptr<libMesh::QGauss>(new libMesh::QGauss(side_dim, CONSTANT));
2068 :
2069 : // A first-order Lagrange FE for the face.
2070 989 : fe_faces[side_dim] = FEBase::build(side_dim + 1, FEType(FIRST, libMesh::LAGRANGE));
2071 989 : fe_faces[side_dim]->attach_quadrature_rule(qfaces[side_dim].get());
2072 : }
2073 :
2074 : // We need this to get boundary ids for each boundary face we encounter.
2075 501 : BoundaryInfo & boundary_info = getMesh().get_boundary_info();
2076 501 : std::vector<boundary_id_type> face_ids;
2077 :
2078 366462 : for (auto & elem : as_range(getMesh().level_elements_begin(0), getMesh().level_elements_end(0)))
2079 : {
2080 : // dimension of the current element and its normals
2081 365961 : unsigned int side_dim = elem->dim() - 1;
2082 365961 : const std::vector<Point> & normals = fe_faces[side_dim]->get_normals();
2083 :
2084 : // loop over element sides
2085 1890001 : for (unsigned int s = 0; s < elem->n_sides(); s++)
2086 : {
2087 : // If side is on the boundary
2088 1524040 : if (elem->neighbor_ptr(s) == nullptr)
2089 : {
2090 57460 : std::unique_ptr<Elem> side = elem->build_side_ptr(s);
2091 :
2092 57460 : fe_faces[side_dim]->reinit(elem, s);
2093 :
2094 : // Get the boundary ID(s) for this side. If there is more
2095 : // than 1 boundary id, then we already can't determine a
2096 : // unique pairing of sides in this direction, but we'll just
2097 : // keep going to keep the logic simple.
2098 57460 : boundary_info.boundary_ids(elem, s, face_ids);
2099 :
2100 : // x-direction faces
2101 57460 : if (normals[0].absolute_fuzzy_equals(minus_x))
2102 12949 : minus_x_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2103 44511 : else if (normals[0].absolute_fuzzy_equals(plus_x))
2104 12949 : plus_x_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2105 :
2106 : // y-direction faces
2107 31562 : else if (normals[0].absolute_fuzzy_equals(minus_y))
2108 12475 : minus_y_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2109 19087 : else if (normals[0].absolute_fuzzy_equals(plus_y))
2110 12475 : plus_y_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2111 :
2112 : // z-direction faces
2113 6612 : else if (normals[0].absolute_fuzzy_equals(minus_z))
2114 3306 : minus_z_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2115 3306 : else if (normals[0].absolute_fuzzy_equals(plus_z))
2116 3306 : plus_z_ids[side_dim].insert(face_ids.begin(), face_ids.end());
2117 57460 : }
2118 : }
2119 501 : }
2120 :
2121 : // For a distributed mesh, boundaries may be distributed as well. We therefore collect information
2122 : // from everyone. If the mesh is already serial, then there is no need to do an allgather. Note
2123 : // that this is just going to gather information about what the periodic bc ids are. We are not
2124 : // gathering any remote elements or anything like that. It's just that the GhostPointNeighbors
2125 : // ghosting functor currently relies on the fact that every process agrees on whether we have
2126 : // periodic boundaries; every process that thinks there are periodic boundaries will call
2127 : // MeshBase::sub_point_locator which makes a parallel_object_only() assertion (right or wrong). So
2128 : // we all need to go there (or not go there)
2129 501 : if (_use_distributed_mesh && !_mesh->is_serial())
2130 : {
2131 : // Pack all data together so that we send them via one communication
2132 : // pair: boundary side --> boundary ids.
2133 139 : std::vector<std::pair<boundary_id_type, boundary_id_type>> vecdata;
2134 : // We check boundaries on all dimensions
2135 417 : for (unsigned side_dim = 0; side_dim < dim; ++side_dim)
2136 : {
2137 : // "6" means: we have at most 6 boundaries. It is true for generated simple mesh
2138 : // "detectPairedSidesets" is designed for only simple meshes
2139 417 : for (auto bd = minus_x_ids[side_dim].begin(); bd != minus_x_ids[side_dim].end(); bd++)
2140 139 : vecdata.emplace_back(side_dim * 6 + 0, *bd);
2141 :
2142 417 : for (auto bd = plus_x_ids[side_dim].begin(); bd != plus_x_ids[side_dim].end(); bd++)
2143 139 : vecdata.emplace_back(side_dim * 6 + 1, *bd);
2144 :
2145 381 : for (auto bd = minus_y_ids[side_dim].begin(); bd != minus_y_ids[side_dim].end(); bd++)
2146 103 : vecdata.emplace_back(side_dim * 6 + 2, *bd);
2147 :
2148 381 : for (auto bd = plus_y_ids[side_dim].begin(); bd != plus_y_ids[side_dim].end(); bd++)
2149 103 : vecdata.emplace_back(side_dim * 6 + 3, *bd);
2150 :
2151 298 : for (auto bd = minus_z_ids[side_dim].begin(); bd != minus_z_ids[side_dim].end(); bd++)
2152 20 : vecdata.emplace_back(side_dim * 6 + 4, *bd);
2153 :
2154 298 : for (auto bd = plus_z_ids[side_dim].begin(); bd != plus_z_ids[side_dim].end(); bd++)
2155 20 : vecdata.emplace_back(side_dim * 6 + 5, *bd);
2156 : }
2157 :
2158 139 : _communicator.allgather(vecdata, false);
2159 :
2160 : // Unpack data, and add them into minus/plus_x/y_ids
2161 1319 : for (auto pair = vecdata.begin(); pair != vecdata.end(); pair++)
2162 : {
2163 : // Convert data from the long vector, and add data to separated sets
2164 1180 : auto side_dim = pair->first / 6;
2165 1180 : auto side = pair->first % 6;
2166 :
2167 1180 : switch (side)
2168 : {
2169 327 : case 0:
2170 327 : minus_x_ids[side_dim].insert(pair->second);
2171 327 : break;
2172 327 : case 1:
2173 327 : plus_x_ids[side_dim].insert(pair->second);
2174 327 : break;
2175 223 : case 2:
2176 223 : minus_y_ids[side_dim].insert(pair->second);
2177 223 : break;
2178 223 : case 3:
2179 223 : plus_y_ids[side_dim].insert(pair->second);
2180 223 : break;
2181 40 : case 4:
2182 40 : minus_z_ids[side_dim].insert(pair->second);
2183 40 : break;
2184 40 : case 5:
2185 40 : plus_z_ids[side_dim].insert(pair->second);
2186 40 : break;
2187 0 : default:
2188 0 : mooseError("Unknown boundary side ", side);
2189 : }
2190 : }
2191 :
2192 139 : } // end if (_use_distributed_mesh && !_need_ghost_ghosted_boundaries)
2193 :
2194 1490 : for (unsigned side_dim = 0; side_dim < dim; ++side_dim)
2195 : {
2196 : // If unique pairings were found, fill up the _paired_boundary data
2197 : // structure with that information.
2198 989 : if (minus_x_ids[side_dim].size() == 1 && plus_x_ids[side_dim].size() == 1)
2199 501 : _paired_boundary.emplace_back(
2200 1002 : std::make_pair(*(minus_x_ids[side_dim].begin()), *(plus_x_ids[side_dim].begin())));
2201 : else
2202 488 : mooseInfoRepeated(
2203 976 : "For side dimension " + std::to_string(side_dim) +
2204 976 : " we did not find paired boundaries (sidesets) in X due to the presence of " +
2205 1952 : std::to_string(minus_x_ids[side_dim].size()) + " -X normal and " +
2206 1952 : std::to_string(plus_x_ids[side_dim].size()) + " +X normal boundaries.");
2207 :
2208 989 : if (minus_y_ids[side_dim].size() == 1 && plus_y_ids[side_dim].size() == 1)
2209 433 : _paired_boundary.emplace_back(
2210 866 : std::make_pair(*(minus_y_ids[side_dim].begin()), *(plus_y_ids[side_dim].begin())));
2211 : else
2212 556 : mooseInfoRepeated(
2213 1112 : "For side dimension " + std::to_string(side_dim) +
2214 1112 : " we did not find paired boundaries (sidesets) in Y due to the presence of " +
2215 2224 : std::to_string(minus_y_ids[side_dim].size()) + " -Y normal and " +
2216 2224 : std::to_string(plus_y_ids[side_dim].size()) + " +Y normal boundaries.");
2217 :
2218 989 : if (minus_z_ids[side_dim].size() == 1 && plus_z_ids[side_dim].size() == 1)
2219 55 : _paired_boundary.emplace_back(
2220 110 : std::make_pair(*(minus_z_ids[side_dim].begin()), *(plus_z_ids[side_dim].begin())));
2221 : else
2222 934 : mooseInfoRepeated(
2223 1868 : "For side dimension " + std::to_string(side_dim) +
2224 1868 : " we did not find paired boundaries (sidesets) in Z due to the presence of " +
2225 3736 : std::to_string(minus_z_ids[side_dim].size()) + " -Z normal and " +
2226 3736 : std::to_string(plus_z_ids[side_dim].size()) + " +Z normal boundaries.");
2227 : }
2228 501 : }
2229 :
2230 : Real
2231 76483 : MooseMesh::dimensionWidth(unsigned int component) const
2232 : {
2233 76483 : return getMaxInDimension(component) - getMinInDimension(component);
2234 : }
2235 :
2236 : Real
2237 33634 : MooseMesh::getMinInDimension(unsigned int component) const
2238 : {
2239 : mooseAssert(_mesh, "The MeshBase has not been constructed");
2240 : mooseAssert(component < _bounds.size(), "Requested dimension out of bounds");
2241 :
2242 33634 : return _bounds[component][MIN];
2243 : }
2244 :
2245 : Real
2246 33634 : MooseMesh::getMaxInDimension(unsigned int component) const
2247 : {
2248 : mooseAssert(_mesh, "The MeshBase has not been constructed");
2249 : mooseAssert(component < _bounds.size(), "Requested dimension out of bounds");
2250 :
2251 33634 : return _bounds[component][MAX];
2252 : }
2253 :
2254 : void
2255 1028 : MooseMesh::addPeriodicVariable(unsigned int var_num, BoundaryID primary, BoundaryID secondary)
2256 : {
2257 1028 : if (!_regular_orthogonal_mesh)
2258 0 : return;
2259 :
2260 1028 : _periodic_dim[var_num].resize(dimension());
2261 :
2262 1028 : _half_range = Point(dimensionWidth(0) / 2.0, dimensionWidth(1) / 2.0, dimensionWidth(2) / 2.0);
2263 :
2264 1028 : bool component_found = false;
2265 3168 : for (unsigned int component = 0; component < dimension(); ++component)
2266 : {
2267 2140 : const std::pair<BoundaryID, BoundaryID> * boundary_ids = getPairedBoundaryMapping(component);
2268 :
2269 2140 : if (boundary_ids != nullptr &&
2270 2140 : ((boundary_ids->first == primary && boundary_ids->second == secondary) ||
2271 1181 : (boundary_ids->first == secondary && boundary_ids->second == primary)))
2272 : {
2273 998 : _periodic_dim[var_num][component] = true;
2274 998 : component_found = true;
2275 : }
2276 : }
2277 1028 : if (!component_found)
2278 60 : mooseWarning("Could not find a match between boundary '",
2279 30 : getBoundaryName(primary),
2280 : "' and '",
2281 30 : getBoundaryName(secondary),
2282 : "' to set periodic boundary conditions for variable (index:",
2283 : var_num,
2284 : ") in either the X, Y or Z direction. The periodic dimension of the mesh for this "
2285 : "variable will not be stored.");
2286 : }
2287 :
2288 : bool
2289 11282342 : MooseMesh::isTranslatedPeriodic(unsigned int nonlinear_var_num, unsigned int component) const
2290 : {
2291 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2292 :
2293 11282342 : if (_periodic_dim.find(nonlinear_var_num) != _periodic_dim.end())
2294 11049582 : return _periodic_dim.at(nonlinear_var_num)[component];
2295 : else
2296 232760 : return false;
2297 : }
2298 :
2299 : RealVectorValue
2300 5677703 : MooseMesh::minPeriodicVector(unsigned int nonlinear_var_num, Point p, Point q) const
2301 : {
2302 16959985 : for (unsigned int i = 0; i < dimension(); ++i)
2303 : {
2304 : // check to see if we're closer in real or periodic space in x, y, and z
2305 11282282 : if (isTranslatedPeriodic(nonlinear_var_num, i))
2306 : {
2307 : // Need to test order before differencing
2308 11049522 : if (p(i) > q(i))
2309 : {
2310 7186638 : if (p(i) - q(i) > _half_range(i))
2311 2646954 : p(i) -= _half_range(i) * 2;
2312 : }
2313 : else
2314 : {
2315 3862884 : if (q(i) - p(i) > _half_range(i))
2316 1020204 : p(i) += _half_range(i) * 2;
2317 : }
2318 : }
2319 : }
2320 :
2321 5677703 : return q - p;
2322 : }
2323 :
2324 : Real
2325 5677703 : MooseMesh::minPeriodicDistance(unsigned int nonlinear_var_num, Point p, Point q) const
2326 : {
2327 5677703 : return minPeriodicVector(nonlinear_var_num, p, q).norm();
2328 : }
2329 :
2330 : const std::pair<BoundaryID, BoundaryID> *
2331 2756 : MooseMesh::getPairedBoundaryMapping(unsigned int component)
2332 : {
2333 2756 : if (!_regular_orthogonal_mesh)
2334 0 : mooseError("Trying to retrieve automatic paired mapping for a mesh that is not regular and "
2335 : "orthogonal");
2336 :
2337 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2338 :
2339 2756 : if (_paired_boundary.empty())
2340 501 : detectPairedSidesets();
2341 :
2342 2756 : if (component < _paired_boundary.size())
2343 2756 : return &_paired_boundary[component];
2344 : else
2345 0 : return nullptr;
2346 : }
2347 :
2348 : void
2349 37 : MooseMesh::buildHRefinementAndCoarseningMaps(Assembly * const assembly)
2350 : {
2351 37 : std::map<ElemType, Elem *> canonical_elems;
2352 :
2353 : // First, loop over all elements and find a canonical element for each type
2354 : // Doing it this way guarantees that this is going to work in parallel
2355 21829 : for (const auto & elem : getMesh().element_ptr_range()) // TODO: Thread this
2356 : {
2357 10896 : ElemType type = elem->type();
2358 :
2359 10896 : if (canonical_elems.find(type) ==
2360 21792 : canonical_elems.end()) // If we haven't seen this type of elem before save it
2361 48 : canonical_elems[type] = elem;
2362 : else
2363 : {
2364 10848 : Elem * stored = canonical_elems[type];
2365 10848 : if (elem->id() < stored->id()) // Arbitrarily keep the one with a lower id
2366 0 : canonical_elems[type] = elem;
2367 : }
2368 37 : }
2369 : // Now build the maps using these templates
2370 : // Note: This MUST be done NOT threaded!
2371 85 : for (const auto & can_it : canonical_elems)
2372 : {
2373 48 : Elem * elem = can_it.second;
2374 :
2375 : // Need to do this just once to get the right qrules put in place
2376 48 : assembly->setCurrentSubdomainID(elem->subdomain_id());
2377 48 : assembly->reinit(elem);
2378 48 : assembly->reinit(elem, 0);
2379 48 : auto && qrule = assembly->writeableQRule();
2380 48 : auto && qrule_face = assembly->writeableQRuleFace();
2381 :
2382 : // Volume to volume projection for refinement
2383 48 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, -1, -1);
2384 :
2385 : // Volume to volume projection for coarsening
2386 48 : buildCoarseningMap(*elem, *qrule, *qrule_face, -1);
2387 :
2388 : // Map the sides of children
2389 244 : for (unsigned int side = 0; side < elem->n_sides(); side++)
2390 : {
2391 : // Side to side for sides that match parent's sides
2392 196 : buildRefinementMap(*elem, *qrule, *qrule_face, side, -1, side);
2393 196 : buildCoarseningMap(*elem, *qrule, *qrule_face, side);
2394 : }
2395 :
2396 : // Child side to parent volume mapping for "internal" child sides
2397 270 : for (unsigned int child = 0; child < elem->n_children(); ++child)
2398 1274 : for (unsigned int side = 0; side < elem->n_sides();
2399 : ++side) // Assume children have the same number of sides!
2400 1052 : if (!elem->is_child_on_side(child, side)) // Otherwise we already computed that map
2401 526 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, child, side);
2402 : }
2403 37 : }
2404 :
2405 : void
2406 98 : MooseMesh::buildPRefinementAndCoarseningMaps(Assembly * const assembly)
2407 : {
2408 98 : _elem_type_to_p_refinement_map.clear();
2409 98 : _elem_type_to_p_refinement_side_map.clear();
2410 98 : _elem_type_to_p_coarsening_map.clear();
2411 98 : _elem_type_to_p_coarsening_side_map.clear();
2412 :
2413 98 : std::map<ElemType, std::pair<Elem *, unsigned int>> elems_and_max_p_level;
2414 :
2415 35298 : for (const auto & elem : getMesh().active_element_ptr_range())
2416 : {
2417 35200 : const auto type = elem->type();
2418 35200 : auto & [picked_elem, max_p_level] = elems_and_max_p_level[type];
2419 35200 : if (!picked_elem)
2420 98 : picked_elem = elem;
2421 35200 : max_p_level = std::max(max_p_level, elem->p_level());
2422 98 : }
2423 :
2424 : // The only requirement on the FEType is that it can be arbitrarily p-refined
2425 98 : const FEType p_refinable_fe_type(CONSTANT, libMesh::MONOMIAL);
2426 98 : std::vector<Point> volume_ref_points_coarse, volume_ref_points_fine, face_ref_points_coarse,
2427 98 : face_ref_points_fine;
2428 98 : std::vector<unsigned int> p_levels;
2429 :
2430 196 : for (auto & [elem_type, elem_p_level_pair] : elems_and_max_p_level)
2431 : {
2432 98 : auto & [moose_elem, max_p_level] = elem_p_level_pair;
2433 98 : const auto dim = moose_elem->dim();
2434 : // Need to do this just once to get the right qrules put in place
2435 98 : assembly->setCurrentSubdomainID(moose_elem->subdomain_id());
2436 98 : assembly->reinit(moose_elem);
2437 98 : assembly->reinit(moose_elem, 0);
2438 98 : auto & qrule = assembly->writeableQRule();
2439 98 : auto & qrule_face = assembly->writeableQRuleFace();
2440 :
2441 98 : libMesh::Parallel::Communicator self_comm{};
2442 98 : ReplicatedMesh mesh(self_comm);
2443 98 : mesh.set_mesh_dimension(dim);
2444 686 : for (const auto & nd : moose_elem->node_ref_range())
2445 588 : mesh.add_point(nd);
2446 :
2447 98 : Elem * const elem = mesh.add_elem(Elem::build(elem_type).release());
2448 686 : for (const auto i : elem->node_index_range())
2449 588 : elem->set_node(i, mesh.node_ptr(i));
2450 :
2451 98 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, p_refinable_fe_type));
2452 98 : fe_face->get_phi();
2453 98 : const auto & face_phys_points = fe_face->get_xyz();
2454 98 : fe_face->attach_quadrature_rule(qrule_face);
2455 :
2456 98 : qrule->init(*elem);
2457 98 : volume_ref_points_coarse = qrule->get_points();
2458 98 : fe_face->reinit(elem, (unsigned int)0);
2459 98 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_coarse);
2460 :
2461 98 : p_levels.resize(max_p_level + 1);
2462 98 : std::iota(p_levels.begin(), p_levels.end(), 0);
2463 98 : libMesh::MeshRefinement mesh_refinement(mesh);
2464 :
2465 334 : for (const auto p_level : p_levels)
2466 : {
2467 236 : mesh_refinement.uniformly_p_refine(1);
2468 236 : qrule->init(*elem);
2469 236 : volume_ref_points_fine = qrule->get_points();
2470 236 : fe_face->reinit(elem, (unsigned int)0);
2471 236 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_fine);
2472 :
2473 236 : const auto map_key = std::make_pair(elem_type, p_level);
2474 236 : auto & volume_refine_map = _elem_type_to_p_refinement_map[map_key];
2475 236 : auto & face_refine_map = _elem_type_to_p_refinement_side_map[map_key];
2476 236 : auto & volume_coarsen_map = _elem_type_to_p_coarsening_map[map_key];
2477 236 : auto & face_coarsen_map = _elem_type_to_p_coarsening_side_map[map_key];
2478 :
2479 472 : auto fill_maps = [this](const auto & coarse_ref_points,
2480 : const auto & fine_ref_points,
2481 : auto & coarsen_map,
2482 : auto & refine_map)
2483 : {
2484 472 : mapPoints(fine_ref_points, coarse_ref_points, refine_map);
2485 472 : mapPoints(coarse_ref_points, fine_ref_points, coarsen_map);
2486 708 : };
2487 :
2488 236 : fill_maps(
2489 : volume_ref_points_coarse, volume_ref_points_fine, volume_coarsen_map, volume_refine_map);
2490 236 : fill_maps(face_ref_points_coarse, face_ref_points_fine, face_coarsen_map, face_refine_map);
2491 :
2492 : // With this level's maps filled our fine points now become our coarse points
2493 236 : volume_ref_points_fine.swap(volume_ref_points_coarse);
2494 236 : face_ref_points_fine.swap(face_ref_points_coarse);
2495 : }
2496 98 : }
2497 98 : }
2498 :
2499 : void
2500 63 : MooseMesh::buildRefinementAndCoarseningMaps(Assembly * const assembly)
2501 : {
2502 315 : TIME_SECTION("buildRefinementAndCoarseningMaps", 5, "Building Refinement And Coarsening Maps");
2503 63 : if (doingPRefinement())
2504 26 : buildPRefinementAndCoarseningMaps(assembly);
2505 : else
2506 37 : buildHRefinementAndCoarseningMaps(assembly);
2507 63 : }
2508 :
2509 : void
2510 770 : MooseMesh::buildRefinementMap(const Elem & elem,
2511 : QBase & qrule,
2512 : QBase & qrule_face,
2513 : int parent_side,
2514 : int child,
2515 : int child_side)
2516 : {
2517 3850 : TIME_SECTION("buildRefinementMap", 5, "Building Refinement Map");
2518 :
2519 770 : if (child == -1) // Doing volume mapping or parent side mapping
2520 : {
2521 : mooseAssert(parent_side == child_side,
2522 : "Parent side must match child_side if not passing a specific child!");
2523 :
2524 244 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2525 :
2526 244 : if (_elem_type_to_refinement_map.find(the_pair) != _elem_type_to_refinement_map.end())
2527 0 : mooseError("Already built a qp refinement map!");
2528 :
2529 244 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2530 244 : std::vector<std::vector<QpMap>> & refinement_map = _elem_type_to_refinement_map[the_pair];
2531 244 : findAdaptivityQpMaps(
2532 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2533 244 : }
2534 : else // Need to map a child side to parent volume qps
2535 : {
2536 526 : std::pair<int, int> child_pair(child, child_side);
2537 :
2538 526 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) !=
2539 1530 : _elem_type_to_child_side_refinement_map.end() &&
2540 478 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) !=
2541 1004 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2542 0 : mooseError("Already built a qp refinement map!");
2543 :
2544 526 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2545 : std::vector<std::vector<QpMap>> & refinement_map =
2546 526 : _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2547 526 : findAdaptivityQpMaps(
2548 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2549 526 : }
2550 770 : }
2551 :
2552 : const std::vector<std::vector<QpMap>> &
2553 3980 : MooseMesh::getRefinementMap(const Elem & elem, int parent_side, int child, int child_side)
2554 : {
2555 3980 : if (child == -1) // Doing volume mapping or parent side mapping
2556 : {
2557 : mooseAssert(parent_side == child_side,
2558 : "Parent side must match child_side if not passing a specific child!");
2559 :
2560 3980 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2561 :
2562 3980 : if (_elem_type_to_refinement_map.find(the_pair) == _elem_type_to_refinement_map.end())
2563 0 : mooseError("Could not find a suitable qp refinement map!");
2564 :
2565 3980 : return _elem_type_to_refinement_map[the_pair];
2566 : }
2567 : else // Need to map a child side to parent volume qps
2568 : {
2569 0 : std::pair<int, int> child_pair(child, child_side);
2570 :
2571 0 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) ==
2572 0 : _elem_type_to_child_side_refinement_map.end() ||
2573 0 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) ==
2574 0 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2575 0 : mooseError("Could not find a suitable qp refinement map!");
2576 :
2577 0 : return _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2578 : }
2579 :
2580 : /**
2581 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2582 : * processor has a complete map. This may require parallel communication. This is likely to
2583 : * happen
2584 : * when running on a mixed element mesh.
2585 : */
2586 : }
2587 :
2588 : void
2589 244 : MooseMesh::buildCoarseningMap(const Elem & elem, QBase & qrule, QBase & qrule_face, int input_side)
2590 : {
2591 1220 : TIME_SECTION("buildCoarseningMap", 5, "Building Coarsening Map");
2592 :
2593 244 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2594 :
2595 244 : if (_elem_type_to_coarsening_map.find(the_pair) != _elem_type_to_coarsening_map.end())
2596 0 : mooseError("Already built a qp coarsening map!");
2597 :
2598 244 : std::vector<std::vector<QpMap>> refinement_map;
2599 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map =
2600 244 : _elem_type_to_coarsening_map[the_pair];
2601 :
2602 : // The -1 here is for a specific child. We don't do that for coarsening maps
2603 : // Also note that we're always mapping the same side to the same side (which is guaranteed by
2604 : // libMesh).
2605 244 : findAdaptivityQpMaps(
2606 : &elem, qrule, qrule_face, refinement_map, coarsen_map, input_side, -1, input_side);
2607 :
2608 : /**
2609 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2610 : * processor has a complete map. This may require parallel communication. This is likely to
2611 : * happen
2612 : * when running on a mixed element mesh.
2613 : */
2614 244 : }
2615 :
2616 : const std::vector<std::pair<unsigned int, QpMap>> &
2617 1509 : MooseMesh::getCoarseningMap(const Elem & elem, int input_side)
2618 : {
2619 1509 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2620 :
2621 1509 : if (_elem_type_to_coarsening_map.find(the_pair) == _elem_type_to_coarsening_map.end())
2622 0 : mooseError("Could not find a suitable qp refinement map!");
2623 :
2624 3018 : return _elem_type_to_coarsening_map[the_pair];
2625 : }
2626 :
2627 : void
2628 7770 : MooseMesh::mapPoints(const std::vector<Point> & from,
2629 : const std::vector<Point> & to,
2630 : std::vector<QpMap> & qp_map)
2631 : {
2632 7770 : unsigned int n_from = from.size();
2633 7770 : unsigned int n_to = to.size();
2634 :
2635 7770 : qp_map.resize(n_from);
2636 :
2637 67554 : for (unsigned int i = 0; i < n_from; ++i)
2638 : {
2639 59784 : const Point & from_point = from[i];
2640 :
2641 59784 : QpMap & current_map = qp_map[i];
2642 :
2643 1369844 : for (unsigned int j = 0; j < n_to; ++j)
2644 : {
2645 1310060 : const Point & to_point = to[j];
2646 1310060 : Real distance = (from_point - to_point).norm();
2647 :
2648 1310060 : if (distance < current_map._distance)
2649 : {
2650 184431 : current_map._distance = distance;
2651 184431 : current_map._from = i;
2652 184431 : current_map._to = j;
2653 : }
2654 : }
2655 : }
2656 7770 : }
2657 :
2658 : void
2659 1014 : MooseMesh::findAdaptivityQpMaps(const Elem * template_elem,
2660 : QBase & qrule,
2661 : QBase & qrule_face,
2662 : std::vector<std::vector<QpMap>> & refinement_map,
2663 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map,
2664 : int parent_side,
2665 : int child,
2666 : int child_side)
2667 : {
2668 3042 : TIME_SECTION("findAdaptivityQpMaps", 5);
2669 :
2670 1014 : ReplicatedMesh mesh(_communicator);
2671 1014 : mesh.skip_partitioning(true);
2672 :
2673 1014 : unsigned int dim = template_elem->dim();
2674 1014 : mesh.set_mesh_dimension(dim);
2675 :
2676 7948 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2677 6934 : mesh.add_point(template_elem->point(i));
2678 :
2679 1014 : Elem * elem = mesh.add_elem(Elem::build(template_elem->type()).release());
2680 :
2681 7948 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2682 6934 : elem->set_node(i, mesh.node_ptr(i));
2683 :
2684 1014 : std::unique_ptr<FEBase> fe(FEBase::build(dim, FEType()));
2685 1014 : fe->get_phi();
2686 1014 : const std::vector<Point> & q_points_volume = fe->get_xyz();
2687 :
2688 1014 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, FEType()));
2689 1014 : fe_face->get_phi();
2690 1014 : const std::vector<Point> & q_points_face = fe_face->get_xyz();
2691 :
2692 1014 : fe->attach_quadrature_rule(&qrule);
2693 1014 : fe_face->attach_quadrature_rule(&qrule_face);
2694 :
2695 : // The current q_points (locations in *physical* space)
2696 : const std::vector<Point> * q_points;
2697 :
2698 1014 : if (parent_side != -1)
2699 : {
2700 392 : fe_face->reinit(elem, parent_side);
2701 392 : q_points = &q_points_face;
2702 : }
2703 : else
2704 : {
2705 622 : fe->reinit(elem);
2706 622 : q_points = &q_points_volume;
2707 : }
2708 :
2709 1014 : std::vector<Point> parent_ref_points;
2710 :
2711 1014 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, parent_ref_points);
2712 1014 : libMesh::MeshRefinement mesh_refinement(mesh);
2713 1014 : mesh_refinement.uniformly_refine(1);
2714 :
2715 : // A map from the child element index to the locations of all the child's quadrature points in
2716 : // *reference* space. Note that we use a map here instead of a vector because the caller can
2717 : // pass an explicit child index. We are not guaranteed to have a sequence from [0, n_children)
2718 1014 : std::map<unsigned int, std::vector<Point>> child_to_ref_points;
2719 :
2720 1014 : unsigned int n_children = elem->n_children();
2721 :
2722 1014 : refinement_map.resize(n_children);
2723 :
2724 1014 : std::vector<unsigned int> children;
2725 :
2726 1014 : if (child != -1) // Passed in a child explicitly
2727 526 : children.push_back(child);
2728 : else
2729 : {
2730 488 : children.resize(n_children);
2731 3036 : for (unsigned int child = 0; child < n_children; ++child)
2732 2548 : children[child] = child;
2733 : }
2734 :
2735 4088 : for (unsigned int i = 0; i < children.size(); ++i)
2736 : {
2737 3074 : unsigned int child = children[i];
2738 :
2739 3074 : if ((parent_side != -1 && !elem->is_child_on_side(child, parent_side)))
2740 1052 : continue;
2741 :
2742 2022 : const Elem * child_elem = elem->child_ptr(child);
2743 :
2744 2022 : if (child_side != -1)
2745 : {
2746 1578 : fe_face->reinit(child_elem, child_side);
2747 1578 : q_points = &q_points_face;
2748 : }
2749 : else
2750 : {
2751 444 : fe->reinit(child_elem);
2752 444 : q_points = &q_points_volume;
2753 : }
2754 :
2755 2022 : std::vector<Point> child_ref_points;
2756 :
2757 2022 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, child_ref_points);
2758 2022 : child_to_ref_points[child] = child_ref_points;
2759 :
2760 2022 : std::vector<QpMap> & qp_map = refinement_map[child];
2761 :
2762 : // Find the closest parent_qp to each child_qp
2763 2022 : mapPoints(child_ref_points, parent_ref_points, qp_map);
2764 2022 : }
2765 :
2766 1014 : coarsen_map.resize(parent_ref_points.size());
2767 :
2768 : // For each parent qp find the closest child qp
2769 6870 : for (unsigned int child = 0; child < n_children; child++)
2770 : {
2771 5856 : if (parent_side != -1 && !elem->is_child_on_side(child, child_side))
2772 1052 : continue;
2773 :
2774 4804 : std::vector<Point> & child_ref_points = child_to_ref_points[child];
2775 :
2776 4804 : std::vector<QpMap> qp_map;
2777 :
2778 : // Find all of the closest points from parent_qp to _THIS_ child's qp
2779 4804 : mapPoints(parent_ref_points, child_ref_points, qp_map);
2780 :
2781 : // Check those to see if they are closer than what we currently have for each point
2782 36224 : for (unsigned int parent_qp = 0; parent_qp < parent_ref_points.size(); ++parent_qp)
2783 : {
2784 31420 : std::pair<unsigned int, QpMap> & child_and_map = coarsen_map[parent_qp];
2785 31420 : unsigned int & closest_child = child_and_map.first;
2786 31420 : QpMap & closest_map = child_and_map.second;
2787 :
2788 31420 : QpMap & current_map = qp_map[parent_qp];
2789 :
2790 31420 : if (current_map._distance < closest_map._distance)
2791 : {
2792 7030 : closest_child = child;
2793 7030 : closest_map = current_map;
2794 : }
2795 : }
2796 4804 : }
2797 1014 : }
2798 :
2799 : void
2800 0 : MooseMesh::changeBoundaryId(const boundary_id_type old_id,
2801 : const boundary_id_type new_id,
2802 : bool delete_prev)
2803 : {
2804 0 : TIME_SECTION("changeBoundaryId", 6);
2805 0 : changeBoundaryId(getMesh(), old_id, new_id, delete_prev);
2806 0 : }
2807 :
2808 : void
2809 0 : MooseMesh::changeBoundaryId(MeshBase & mesh,
2810 : const boundary_id_type old_id,
2811 : const boundary_id_type new_id,
2812 : bool delete_prev)
2813 : {
2814 : // Get a reference to our BoundaryInfo object, we will use it several times below...
2815 0 : BoundaryInfo & boundary_info = mesh.get_boundary_info();
2816 :
2817 : // Container to catch ids passed back from BoundaryInfo
2818 0 : std::vector<boundary_id_type> old_ids;
2819 :
2820 : // Only level-0 elements store BCs. Loop over them.
2821 0 : for (auto & elem : as_range(mesh.level_elements_begin(0), mesh.level_elements_end(0)))
2822 : {
2823 0 : unsigned int n_sides = elem->n_sides();
2824 0 : for (unsigned int s = 0; s != n_sides; ++s)
2825 : {
2826 0 : boundary_info.boundary_ids(elem, s, old_ids);
2827 0 : if (std::find(old_ids.begin(), old_ids.end(), old_id) != old_ids.end())
2828 : {
2829 0 : std::vector<boundary_id_type> new_ids(old_ids);
2830 0 : std::replace(new_ids.begin(), new_ids.end(), old_id, new_id);
2831 0 : if (delete_prev)
2832 : {
2833 0 : boundary_info.remove_side(elem, s);
2834 0 : boundary_info.add_side(elem, s, new_ids);
2835 : }
2836 : else
2837 0 : boundary_info.add_side(elem, s, new_ids);
2838 0 : }
2839 : }
2840 0 : }
2841 :
2842 : // Remove any remaining references to the old ID from the
2843 : // BoundaryInfo object. This prevents things like empty sidesets
2844 : // from showing up when printing information, etc.
2845 0 : if (delete_prev)
2846 0 : boundary_info.remove_id(old_id);
2847 0 : }
2848 :
2849 : const RealVectorValue &
2850 0 : MooseMesh::getNormalByBoundaryID(BoundaryID id) const
2851 : {
2852 : mooseAssert(_boundary_to_normal_map.get() != nullptr, "Boundary To Normal Map not built!");
2853 :
2854 : // Note: Boundaries that are not in the map (existing boundaries) will default
2855 : // construct a new RealVectorValue - (x,y,z)=(0, 0, 0)
2856 0 : return (*_boundary_to_normal_map)[id];
2857 : }
2858 :
2859 : MooseMesh &
2860 0 : MooseMesh::clone() const
2861 : {
2862 0 : mooseError("MooseMesh::clone() is no longer supported, use MooseMesh::safeClone() instead.");
2863 : }
2864 :
2865 : void
2866 69491 : MooseMesh::determineUseDistributedMesh()
2867 : {
2868 69491 : switch (_parallel_type)
2869 : {
2870 64649 : case ParallelType::DEFAULT:
2871 : // The user did not specify 'parallel_type = XYZ' in the input file,
2872 : // so we allow the --distributed-mesh command line arg to possibly turn
2873 : // on DistributedMesh. If the command line arg is not present, we pick ReplicatedMesh.
2874 64649 : if (_app.getDistributedMeshOnCommandLine())
2875 8133 : _use_distributed_mesh = true;
2876 64649 : break;
2877 3333 : case ParallelType::REPLICATED:
2878 3333 : if (_app.getDistributedMeshOnCommandLine() || _is_nemesis || _is_split)
2879 562 : _parallel_type_overridden = true;
2880 3333 : _use_distributed_mesh = false;
2881 3333 : break;
2882 1509 : case ParallelType::DISTRIBUTED:
2883 1509 : _use_distributed_mesh = true;
2884 1509 : break;
2885 : }
2886 :
2887 : // If the user specifies 'nemesis = true' in the Mesh block, or they are using --use-split,
2888 : // we must use DistributedMesh.
2889 69491 : if (_is_nemesis || _is_split)
2890 354 : _use_distributed_mesh = true;
2891 69491 : }
2892 :
2893 : std::unique_ptr<MeshBase>
2894 70577 : MooseMesh::buildMeshBaseObject(unsigned int dim)
2895 : {
2896 70577 : std::unique_ptr<MeshBase> mesh;
2897 70577 : if (_use_distributed_mesh)
2898 9452 : mesh = buildTypedMesh<DistributedMesh>(dim);
2899 : else
2900 61125 : mesh = buildTypedMesh<ReplicatedMesh>(dim);
2901 :
2902 70577 : return mesh;
2903 0 : }
2904 :
2905 : void
2906 67586 : MooseMesh::setMeshBase(std::unique_ptr<MeshBase> mesh_base)
2907 : {
2908 67586 : _mesh = std::move(mesh_base);
2909 67586 : _mesh->allow_remote_element_removal(_allow_remote_element_removal);
2910 67586 : }
2911 :
2912 : void
2913 67265 : MooseMesh::init()
2914 : {
2915 : /**
2916 : * If the mesh base hasn't been constructed by the time init is called, just do it here.
2917 : * This can happen if somebody builds a mesh outside of the normal Action system. Forcing
2918 : * developers to create, construct the MeshBase, and then init separately is a bit much for casual
2919 : * use but it gives us the ability to run MeshGenerators in-between.
2920 : */
2921 67265 : if (!_mesh)
2922 11 : _mesh = buildMeshBaseObject();
2923 :
2924 67265 : if (_app.isSplitMesh() && _use_distributed_mesh)
2925 0 : mooseError("You cannot use the mesh splitter capability with DistributedMesh!");
2926 :
2927 201795 : TIME_SECTION("init", 2);
2928 :
2929 67265 : if (_app.isRecovering() && _allow_recovery && _app.isUltimateMaster())
2930 : {
2931 : // Some partitioners are not idempotent. Some recovery data
2932 : // files require partitioning to match mesh partitioning. This
2933 : // means that, when recovering, we can't safely repartition.
2934 3119 : const bool skip_partitioning_later = getMesh().skip_partitioning();
2935 3119 : getMesh().skip_partitioning(true);
2936 3119 : const bool allow_renumbering_later = getMesh().allow_renumbering();
2937 3119 : getMesh().allow_renumbering(false);
2938 :
2939 : // For now, only read the recovery mesh on the Ultimate Master..
2940 : // sub-apps need to just build their mesh like normal
2941 : {
2942 9357 : TIME_SECTION("readRecoveredMesh", 2);
2943 3119 : getMesh().read(_app.getRestartRecoverFileBase() + MooseApp::checkpointSuffix());
2944 3119 : }
2945 :
2946 3119 : getMesh().allow_renumbering(allow_renumbering_later);
2947 3119 : getMesh().skip_partitioning(skip_partitioning_later);
2948 : }
2949 : else // Normally just build the mesh
2950 : {
2951 : // Don't allow partitioning during building
2952 64146 : if (_app.isSplitMesh())
2953 101 : getMesh().skip_partitioning(true);
2954 64146 : buildMesh();
2955 :
2956 : // Re-enable partitioning so the splitter can partition!
2957 64138 : if (_app.isSplitMesh())
2958 101 : getMesh().skip_partitioning(false);
2959 :
2960 192414 : if (getParam<bool>("build_all_side_lowerd_mesh"))
2961 226 : buildLowerDMesh();
2962 : }
2963 :
2964 67257 : computeMaxPerElemAndSide();
2965 67257 : }
2966 :
2967 : unsigned int
2968 36218996 : MooseMesh::dimension() const
2969 : {
2970 36218996 : return getMesh().mesh_dimension();
2971 : }
2972 :
2973 : unsigned int
2974 39259 : MooseMesh::effectiveSpatialDimension() const
2975 : {
2976 39259 : const Real abs_zero = 1e-12;
2977 :
2978 : // See if the mesh is completely containd in the z and y planes to calculate effective spatial
2979 : // dim
2980 72783 : for (unsigned int dim = LIBMESH_DIM; dim >= 1; --dim)
2981 72783 : if (dimensionWidth(dim - 1) >= abs_zero)
2982 39259 : return dim;
2983 :
2984 : // If we get here, we have a 1D mesh on the x-axis.
2985 0 : return 1;
2986 : }
2987 :
2988 : unsigned int
2989 94096 : MooseMesh::getBlocksMaxDimension(const std::vector<SubdomainName> & blocks) const
2990 : {
2991 94096 : const auto & mesh = getMesh();
2992 :
2993 : // Take a shortcut if possible
2994 94096 : if (const auto & elem_dims = mesh.elem_dimensions(); mesh.is_prepared() && elem_dims.size() == 1)
2995 82996 : return *elem_dims.begin();
2996 :
2997 11100 : unsigned short dim = 0;
2998 11100 : const auto subdomain_ids = getSubdomainIDs(blocks);
2999 11100 : const std::set<SubdomainID> subdomain_ids_set(subdomain_ids.begin(), subdomain_ids.end());
3000 2476175 : for (const auto & elem : mesh.active_subdomain_set_elements_ptr_range(subdomain_ids_set))
3001 2476175 : dim = std::max(dim, elem->dim());
3002 :
3003 : // Get the maximumal globally
3004 11100 : _communicator.max(dim);
3005 11100 : return dim;
3006 11100 : }
3007 :
3008 : std::vector<BoundaryID>
3009 1930543903 : MooseMesh::getBoundaryIDs(const Elem * const elem, const unsigned short int side) const
3010 : {
3011 1930543903 : std::vector<BoundaryID> ids;
3012 1930543903 : getMesh().get_boundary_info().boundary_ids(elem, side, ids);
3013 1930543903 : return ids;
3014 0 : }
3015 :
3016 : const std::set<BoundaryID> &
3017 553428 : MooseMesh::getBoundaryIDs() const
3018 : {
3019 553428 : return getMesh().get_boundary_info().get_boundary_ids();
3020 : }
3021 :
3022 : void
3023 231875 : MooseMesh::buildNodeListFromSideList()
3024 : {
3025 231875 : if (_construct_node_list_from_side_list)
3026 231845 : getMesh().get_boundary_info().build_node_list_from_side_list();
3027 231875 : }
3028 :
3029 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3030 253 : MooseMesh::buildSideList()
3031 : {
3032 253 : return getMesh().get_boundary_info().build_side_list();
3033 : }
3034 :
3035 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3036 5823 : MooseMesh::buildActiveSideList() const
3037 : {
3038 5823 : return getMesh().get_boundary_info().build_active_side_list();
3039 : }
3040 :
3041 : unsigned int
3042 9220 : MooseMesh::sideWithBoundaryID(const Elem * const elem, const BoundaryID boundary_id) const
3043 : {
3044 9220 : return getMesh().get_boundary_info().side_with_boundary_id(elem, boundary_id);
3045 : }
3046 :
3047 : MeshBase::node_iterator
3048 710 : MooseMesh::localNodesBegin()
3049 : {
3050 710 : return getMesh().local_nodes_begin();
3051 : }
3052 :
3053 : MeshBase::node_iterator
3054 710 : MooseMesh::localNodesEnd()
3055 : {
3056 710 : return getMesh().local_nodes_end();
3057 : }
3058 :
3059 : MeshBase::const_node_iterator
3060 0 : MooseMesh::localNodesBegin() const
3061 : {
3062 0 : return getMesh().local_nodes_begin();
3063 : }
3064 :
3065 : MeshBase::const_node_iterator
3066 0 : MooseMesh::localNodesEnd() const
3067 : {
3068 0 : return getMesh().local_nodes_end();
3069 : }
3070 :
3071 : MeshBase::element_iterator
3072 153644 : MooseMesh::activeLocalElementsBegin()
3073 : {
3074 153644 : return getMesh().active_local_elements_begin();
3075 : }
3076 :
3077 : const MeshBase::element_iterator
3078 153644 : MooseMesh::activeLocalElementsEnd()
3079 : {
3080 153644 : return getMesh().active_local_elements_end();
3081 : }
3082 :
3083 : MeshBase::const_element_iterator
3084 0 : MooseMesh::activeLocalElementsBegin() const
3085 : {
3086 0 : return getMesh().active_local_elements_begin();
3087 : }
3088 :
3089 : const MeshBase::const_element_iterator
3090 0 : MooseMesh::activeLocalElementsEnd() const
3091 : {
3092 0 : return getMesh().active_local_elements_end();
3093 : }
3094 :
3095 : dof_id_type
3096 57426 : MooseMesh::nNodes() const
3097 : {
3098 57426 : return getMesh().n_nodes();
3099 : }
3100 :
3101 : dof_id_type
3102 1758 : MooseMesh::nElem() const
3103 : {
3104 1758 : return getMesh().n_elem();
3105 : }
3106 :
3107 : dof_id_type
3108 0 : MooseMesh::maxNodeId() const
3109 : {
3110 0 : return getMesh().max_node_id();
3111 : }
3112 :
3113 : dof_id_type
3114 0 : MooseMesh::maxElemId() const
3115 : {
3116 0 : return getMesh().max_elem_id();
3117 : }
3118 :
3119 : Elem *
3120 0 : MooseMesh::elem(const dof_id_type i)
3121 : {
3122 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3123 0 : return elemPtr(i);
3124 : }
3125 :
3126 : const Elem *
3127 0 : MooseMesh::elem(const dof_id_type i) const
3128 : {
3129 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3130 0 : return elemPtr(i);
3131 : }
3132 :
3133 : Elem *
3134 17382437 : MooseMesh::elemPtr(const dof_id_type i)
3135 : {
3136 17382437 : return getMesh().elem_ptr(i);
3137 : }
3138 :
3139 : const Elem *
3140 1361242 : MooseMesh::elemPtr(const dof_id_type i) const
3141 : {
3142 1361242 : return getMesh().elem_ptr(i);
3143 : }
3144 :
3145 : Elem *
3146 7728 : MooseMesh::queryElemPtr(const dof_id_type i)
3147 : {
3148 7728 : return getMesh().query_elem_ptr(i);
3149 : }
3150 :
3151 : const Elem *
3152 219 : MooseMesh::queryElemPtr(const dof_id_type i) const
3153 : {
3154 219 : return getMesh().query_elem_ptr(i);
3155 : }
3156 :
3157 : bool
3158 0 : MooseMesh::prepared() const
3159 : {
3160 0 : return _mesh->is_prepared() && _moose_mesh_prepared;
3161 : }
3162 :
3163 : void
3164 0 : MooseMesh::prepared(bool state)
3165 : {
3166 0 : if (state)
3167 0 : mooseError("We don't have any right to tell the libmesh mesh that it *is* prepared. Only a "
3168 : "call to prepare_for_use should tell us that");
3169 :
3170 : // Some people may call this even before we have a MeshBase object. This isn't dangerous really
3171 : // because when the MeshBase object is born, it knows it's in an unprepared state
3172 0 : if (_mesh)
3173 0 : _mesh->set_isnt_prepared();
3174 :
3175 : // If the libMesh mesh isn't preparead, then our MooseMesh wrapper is also no longer prepared
3176 0 : _moose_mesh_prepared = false;
3177 :
3178 : /**
3179 : * If we are explicitly setting the mesh to not prepared, then we've likely modified the mesh
3180 : * and can no longer make assumptions about orthogonality. We really should recheck.
3181 : */
3182 0 : _regular_orthogonal_mesh = false;
3183 0 : }
3184 :
3185 : void
3186 0 : MooseMesh::needsPrepareForUse()
3187 : {
3188 0 : prepared(false);
3189 0 : }
3190 :
3191 : const std::set<SubdomainID> &
3192 8431969 : MooseMesh::meshSubdomains() const
3193 : {
3194 8431969 : return _mesh_subdomains;
3195 : }
3196 :
3197 : const std::set<BoundaryID> &
3198 111040 : MooseMesh::meshBoundaryIds() const
3199 : {
3200 111040 : return _mesh_boundary_ids;
3201 : }
3202 :
3203 : const std::set<BoundaryID> &
3204 32750 : MooseMesh::meshSidesetIds() const
3205 : {
3206 32750 : return _mesh_sideset_ids;
3207 : }
3208 :
3209 : const std::set<BoundaryID> &
3210 156383 : MooseMesh::meshNodesetIds() const
3211 : {
3212 156383 : return _mesh_nodeset_ids;
3213 : }
3214 :
3215 : void
3216 0 : MooseMesh::setMeshBoundaryIDs(std::set<BoundaryID> boundary_IDs)
3217 : {
3218 0 : _mesh_boundary_ids = boundary_IDs;
3219 0 : }
3220 :
3221 : void
3222 0 : MooseMesh::setBoundaryToNormalMap(
3223 : std::unique_ptr<std::map<BoundaryID, RealVectorValue>> boundary_map)
3224 : {
3225 0 : _boundary_to_normal_map = std::move(boundary_map);
3226 0 : }
3227 :
3228 : void
3229 0 : MooseMesh::setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map)
3230 : {
3231 0 : mooseDeprecated("setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map) is "
3232 : "deprecated, use the unique_ptr version instead");
3233 0 : _boundary_to_normal_map.reset(boundary_map);
3234 0 : }
3235 :
3236 : unsigned int
3237 129982 : MooseMesh::uniformRefineLevel() const
3238 : {
3239 129982 : return _uniform_refine_level;
3240 : }
3241 :
3242 : void
3243 69503 : MooseMesh::setUniformRefineLevel(unsigned int level, bool deletion)
3244 : {
3245 69503 : _uniform_refine_level = level;
3246 69503 : _skip_deletion_repartition_after_refine = deletion;
3247 69503 : }
3248 :
3249 : void
3250 60498 : MooseMesh::addGhostedBoundary(BoundaryID boundary_id)
3251 : {
3252 60498 : _ghosted_boundaries.insert(boundary_id);
3253 60498 : }
3254 :
3255 : void
3256 0 : MooseMesh::setGhostedBoundaryInflation(const std::vector<Real> & inflation)
3257 : {
3258 0 : _ghosted_boundaries_inflation = inflation;
3259 0 : }
3260 :
3261 : const std::set<unsigned int> &
3262 0 : MooseMesh::getGhostedBoundaries() const
3263 : {
3264 0 : return _ghosted_boundaries;
3265 : }
3266 :
3267 : const std::vector<Real> &
3268 12477 : MooseMesh::getGhostedBoundaryInflation() const
3269 : {
3270 12477 : return _ghosted_boundaries_inflation;
3271 : }
3272 :
3273 : namespace // Anonymous namespace for helpers
3274 : {
3275 : // A class for templated methods that expect output iterator
3276 : // arguments, which adds objects to the Mesh.
3277 : // Although any mesh_inserter_iterator can add any object, we
3278 : // template it around object type so that type inference and
3279 : // iterator_traits will work.
3280 : // This object specifically is used to insert extra ghost elems into the mesh
3281 : template <typename T>
3282 : struct extra_ghost_elem_inserter
3283 : {
3284 : using iterator_category = std::output_iterator_tag;
3285 : using value_type = T;
3286 :
3287 39504 : extra_ghost_elem_inserter(DistributedMesh & m) : mesh(m) {}
3288 :
3289 18777 : void operator=(const Elem * e) { mesh.add_extra_ghost_elem(const_cast<Elem *>(e)); }
3290 :
3291 35594 : void operator=(Node * n) { mesh.add_node(n); }
3292 :
3293 : void operator=(Point * p) { mesh.add_point(*p); }
3294 :
3295 : extra_ghost_elem_inserter & operator++() { return *this; }
3296 :
3297 54371 : extra_ghost_elem_inserter operator++(int) { return extra_ghost_elem_inserter(*this); }
3298 :
3299 : // We don't return a reference-to-T here because we don't want to
3300 : // construct one or have any of its methods called. We just want
3301 : // to allow the returned object to be able to do mesh insertions
3302 : // with operator=().
3303 54371 : extra_ghost_elem_inserter & operator*() { return *this; }
3304 :
3305 : private:
3306 : DistributedMesh & mesh;
3307 : };
3308 :
3309 : /**
3310 : * Specific weak ordering for Elem *'s to be used in a set.
3311 : * We use the id, but first sort by level. This guarantees
3312 : * when traversing the set from beginning to end the lower
3313 : * level (parent) elements are encountered first.
3314 : *
3315 : * This was swiped from libMesh mesh_communication.C, and ought to be
3316 : * replaced with libMesh::CompareElemIdsByLevel just as soon as I refactor to
3317 : * create that - @roystgnr
3318 : */
3319 : struct CompareElemsByLevel
3320 : {
3321 103489 : bool operator()(const Elem * a, const Elem * b) const
3322 : {
3323 : libmesh_assert(a);
3324 : libmesh_assert(b);
3325 103489 : const unsigned int al = a->level(), bl = b->level();
3326 103489 : const dof_id_type aid = a->id(), bid = b->id();
3327 :
3328 103489 : return (al == bl) ? aid < bid : al < bl;
3329 : }
3330 : };
3331 :
3332 : } // anonymous namespace
3333 :
3334 : void
3335 142766 : MooseMesh::ghostGhostedBoundaries()
3336 : {
3337 : // No need to do this if using a serial mesh
3338 : // We do not need to ghost boundary elements when _need_ghost_ghosted_boundaries
3339 : // is not true. _need_ghost_ghosted_boundaries can be set by a mesh generator
3340 : // where boundaries are already ghosted accordingly
3341 142766 : if (!_use_distributed_mesh || !_need_ghost_ghosted_boundaries)
3342 123014 : return;
3343 :
3344 59256 : TIME_SECTION("GhostGhostedBoundaries", 3);
3345 :
3346 : parallel_object_only();
3347 :
3348 19752 : DistributedMesh & mesh = dynamic_cast<DistributedMesh &>(getMesh());
3349 :
3350 : // We clear ghosted elements that were added by previous invocations of this
3351 : // method but leave ghosted elements that were added by other code, e.g.
3352 : // OversampleOutput, untouched
3353 19752 : mesh.clear_extra_ghost_elems(_ghost_elems_from_ghost_boundaries);
3354 19752 : _ghost_elems_from_ghost_boundaries.clear();
3355 :
3356 19752 : std::set<const Elem *, CompareElemsByLevel> boundary_elems_to_ghost;
3357 19752 : std::set<Node *> connected_nodes_to_ghost;
3358 :
3359 19752 : std::vector<const Elem *> family_tree;
3360 :
3361 833302 : for (const auto & t : mesh.get_boundary_info().build_side_list())
3362 : {
3363 813550 : auto elem_id = std::get<0>(t);
3364 813550 : auto bc_id = std::get<2>(t);
3365 :
3366 813550 : if (_ghosted_boundaries.find(bc_id) != _ghosted_boundaries.end())
3367 : {
3368 5725 : Elem * elem = mesh.elem_ptr(elem_id);
3369 :
3370 : #ifdef LIBMESH_ENABLE_AMR
3371 5725 : elem->family_tree(family_tree);
3372 5725 : Elem * parent = elem->parent();
3373 5725 : while (parent)
3374 : {
3375 0 : family_tree.push_back(parent);
3376 0 : parent = parent->parent();
3377 : }
3378 : #else
3379 : family_tree.clear();
3380 : family_tree.push_back(elem);
3381 : #endif
3382 15098 : for (const auto & felem : family_tree)
3383 : {
3384 9373 : boundary_elems_to_ghost.insert(felem);
3385 :
3386 : // The entries of connected_nodes_to_ghost need to be
3387 : // non-constant, so that they will work in things like
3388 : // UpdateDisplacedMeshThread. The container returned by
3389 : // family_tree contains const Elems even when the Elem
3390 : // it is called on is non-const, so once that interface
3391 : // gets fixed we can remove this const_cast.
3392 56448 : for (unsigned int n = 0; n < felem->n_nodes(); ++n)
3393 47075 : connected_nodes_to_ghost.insert(const_cast<Node *>(felem->node_ptr(n)));
3394 : }
3395 : }
3396 19752 : }
3397 :
3398 : // We really do want to store this by value instead of by reference
3399 19752 : const auto prior_ghost_elems = mesh.extra_ghost_elems();
3400 :
3401 19752 : mesh.comm().allgather_packed_range(&mesh,
3402 : connected_nodes_to_ghost.begin(),
3403 : connected_nodes_to_ghost.end(),
3404 : extra_ghost_elem_inserter<Node>(mesh));
3405 :
3406 19752 : mesh.comm().allgather_packed_range(&mesh,
3407 : boundary_elems_to_ghost.begin(),
3408 : boundary_elems_to_ghost.end(),
3409 : extra_ghost_elem_inserter<Elem>(mesh));
3410 :
3411 19752 : const auto & current_ghost_elems = mesh.extra_ghost_elems();
3412 :
3413 39504 : std::set_difference(current_ghost_elems.begin(),
3414 : current_ghost_elems.end(),
3415 : prior_ghost_elems.begin(),
3416 : prior_ghost_elems.end(),
3417 19752 : std::inserter(_ghost_elems_from_ghost_boundaries,
3418 : _ghost_elems_from_ghost_boundaries.begin()));
3419 19752 : }
3420 :
3421 : unsigned int
3422 12477 : MooseMesh::getPatchSize() const
3423 : {
3424 12477 : return _patch_size;
3425 : }
3426 :
3427 : void
3428 0 : MooseMesh::setPatchUpdateStrategy(Moose::PatchUpdateType patch_update_strategy)
3429 : {
3430 0 : _patch_update_strategy = patch_update_strategy;
3431 0 : }
3432 :
3433 : const Moose::PatchUpdateType &
3434 39716 : MooseMesh::getPatchUpdateStrategy() const
3435 : {
3436 39716 : return _patch_update_strategy;
3437 : }
3438 :
3439 : BoundingBox
3440 123157 : MooseMesh::getInflatedProcessorBoundingBox(Real inflation_multiplier) const
3441 : {
3442 : // Grab a bounding box to speed things up. Note that
3443 : // local_bounding_box is *not* equivalent to processor_bounding_box
3444 : // with processor_id() except in serial.
3445 123157 : BoundingBox bbox = MeshTools::create_local_bounding_box(getMesh());
3446 :
3447 : // Inflate the bbox just a bit to deal with roundoff
3448 : // Adding 1% of the diagonal size in each direction on each end
3449 123157 : Real inflation_amount = inflation_multiplier * (bbox.max() - bbox.min()).norm();
3450 123157 : Point inflation(inflation_amount, inflation_amount, inflation_amount);
3451 :
3452 123157 : bbox.first -= inflation; // min
3453 123157 : bbox.second += inflation; // max
3454 :
3455 246314 : return bbox;
3456 : }
3457 :
3458 167098 : MooseMesh::operator libMesh::MeshBase &() { return getMesh(); }
3459 :
3460 3211 : MooseMesh::operator const libMesh::MeshBase &() const { return getMesh(); }
3461 :
3462 : const MeshBase *
3463 446589 : MooseMesh::getMeshPtr() const
3464 : {
3465 446589 : return _mesh.get();
3466 : }
3467 :
3468 : MeshBase &
3469 58800664 : MooseMesh::getMesh()
3470 : {
3471 : mooseAssert(_mesh, "Mesh hasn't been created");
3472 58800664 : return *_mesh;
3473 : }
3474 :
3475 : const MeshBase &
3476 2080938263 : MooseMesh::getMesh() const
3477 : {
3478 : mooseAssert(_mesh, "Mesh hasn't been created");
3479 2080938263 : return *_mesh;
3480 : }
3481 :
3482 : void
3483 0 : MooseMesh::printInfo(std::ostream & os, const unsigned int verbosity /* = 0 */) const
3484 : {
3485 0 : os << '\n';
3486 0 : getMesh().print_info(os, verbosity);
3487 0 : os << std::flush;
3488 0 : }
3489 :
3490 : const std::vector<dof_id_type> &
3491 234 : MooseMesh::getNodeList(boundary_id_type nodeset_id) const
3492 : {
3493 : std::map<boundary_id_type, std::vector<dof_id_type>>::const_iterator it =
3494 234 : _node_set_nodes.find(nodeset_id);
3495 :
3496 234 : if (it == _node_set_nodes.end())
3497 : {
3498 : // On a distributed mesh we might not know about a remote nodeset,
3499 : // so we'll return an empty vector and hope the nodeset exists
3500 : // elsewhere.
3501 0 : if (!getMesh().is_serial())
3502 : {
3503 0 : static const std::vector<dof_id_type> empty_vec;
3504 0 : return empty_vec;
3505 : }
3506 : // On a replicated mesh we should know about every nodeset and if
3507 : // we're asked for one that doesn't exist then it must be a bug.
3508 : else
3509 : {
3510 0 : mooseError("Unable to nodeset ID: ", nodeset_id, '.');
3511 : }
3512 : }
3513 :
3514 234 : return it->second;
3515 : }
3516 :
3517 : const std::set<BoundaryID> &
3518 5605471 : MooseMesh::getSubdomainBoundaryIds(const SubdomainID subdomain_id) const
3519 : {
3520 5605471 : const auto it = _sub_to_data.find(subdomain_id);
3521 :
3522 5605471 : if (it == _sub_to_data.end())
3523 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3524 :
3525 11210942 : return it->second.boundary_ids;
3526 : }
3527 :
3528 : std::set<BoundaryID>
3529 24 : MooseMesh::getSubdomainInterfaceBoundaryIds(const SubdomainID subdomain_id) const
3530 : {
3531 24 : const auto & bnd_ids = getSubdomainBoundaryIds(subdomain_id);
3532 24 : std::set<BoundaryID> boundary_ids(bnd_ids.begin(), bnd_ids.end());
3533 : std::unordered_map<SubdomainID, std::set<BoundaryID>>::const_iterator it =
3534 24 : _neighbor_subdomain_boundary_ids.find(subdomain_id);
3535 :
3536 24 : boundary_ids.insert(it->second.begin(), it->second.end());
3537 :
3538 48 : return boundary_ids;
3539 0 : }
3540 :
3541 : std::set<SubdomainID>
3542 225 : MooseMesh::getBoundaryConnectedBlocks(const BoundaryID bid) const
3543 : {
3544 225 : std::set<SubdomainID> subdomain_ids;
3545 843 : for (const auto & [sub_id, data] : _sub_to_data)
3546 618 : if (data.boundary_ids.find(bid) != data.boundary_ids.end())
3547 225 : subdomain_ids.insert(sub_id);
3548 :
3549 225 : return subdomain_ids;
3550 0 : }
3551 :
3552 : std::set<SubdomainID>
3553 188 : MooseMesh::getBoundaryConnectedSecondaryBlocks(const BoundaryID bid) const
3554 : {
3555 188 : std::set<SubdomainID> subdomain_ids;
3556 564 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3557 376 : if (it.second.find(bid) != it.second.end())
3558 188 : subdomain_ids.insert(it.first);
3559 :
3560 188 : return subdomain_ids;
3561 0 : }
3562 :
3563 : std::set<SubdomainID>
3564 12 : MooseMesh::getInterfaceConnectedBlocks(const BoundaryID bid) const
3565 : {
3566 12 : std::set<SubdomainID> subdomain_ids = getBoundaryConnectedBlocks(bid);
3567 120 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3568 108 : if (it.second.find(bid) != it.second.end())
3569 48 : subdomain_ids.insert(it.first);
3570 :
3571 12 : return subdomain_ids;
3572 0 : }
3573 :
3574 : const std::set<SubdomainID> &
3575 0 : MooseMesh::getBlockConnectedBlocks(const SubdomainID subdomain_id) const
3576 : {
3577 0 : const auto it = _sub_to_data.find(subdomain_id);
3578 :
3579 0 : if (it == _sub_to_data.end())
3580 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3581 :
3582 0 : return it->second.neighbor_subs;
3583 : }
3584 :
3585 : bool
3586 1368264 : MooseMesh::isBoundaryNode(dof_id_type node_id) const
3587 : {
3588 1368264 : bool found_node = false;
3589 5616082 : for (const auto & it : _bnd_node_ids)
3590 : {
3591 4560454 : if (it.second.find(node_id) != it.second.end())
3592 : {
3593 312636 : found_node = true;
3594 312636 : break;
3595 : }
3596 : }
3597 1368264 : return found_node;
3598 : }
3599 :
3600 : bool
3601 1121256 : MooseMesh::isBoundaryNode(dof_id_type node_id, BoundaryID bnd_id) const
3602 : {
3603 1121256 : bool found_node = false;
3604 1121256 : std::map<boundary_id_type, std::set<dof_id_type>>::const_iterator it = _bnd_node_ids.find(bnd_id);
3605 1121256 : if (it != _bnd_node_ids.end())
3606 1060956 : if (it->second.find(node_id) != it->second.end())
3607 13112 : found_node = true;
3608 1121256 : return found_node;
3609 : }
3610 :
3611 : bool
3612 0 : MooseMesh::isBoundaryElem(dof_id_type elem_id) const
3613 : {
3614 0 : bool found_elem = false;
3615 0 : for (const auto & it : _bnd_elem_ids)
3616 : {
3617 0 : if (it.second.find(elem_id) != it.second.end())
3618 : {
3619 0 : found_elem = true;
3620 0 : break;
3621 : }
3622 : }
3623 0 : return found_elem;
3624 : }
3625 :
3626 : bool
3627 478233 : MooseMesh::isBoundaryElem(dof_id_type elem_id, BoundaryID bnd_id) const
3628 : {
3629 478233 : bool found_elem = false;
3630 478233 : auto it = _bnd_elem_ids.find(bnd_id);
3631 478233 : if (it != _bnd_elem_ids.end())
3632 442310 : if (it->second.find(elem_id) != it->second.end())
3633 25128 : found_elem = true;
3634 478233 : return found_elem;
3635 : }
3636 :
3637 : void
3638 1417 : MooseMesh::errorIfDistributedMesh(std::string name) const
3639 : {
3640 1417 : if (_use_distributed_mesh)
3641 0 : mooseError("Cannot use ",
3642 : name,
3643 : " with DistributedMesh!\n",
3644 : "Consider specifying parallel_type = 'replicated' in your input file\n",
3645 : "to prevent it from being run with DistributedMesh.");
3646 1417 : }
3647 :
3648 : void
3649 70507 : MooseMesh::setPartitionerHelper(MeshBase * const mesh)
3650 : {
3651 70507 : if (_use_distributed_mesh && (_partitioner_name != "default" && _partitioner_name != "parmetis"))
3652 : {
3653 13 : _partitioner_name = "parmetis";
3654 13 : _partitioner_overridden = true;
3655 : }
3656 :
3657 70507 : setPartitioner(mesh ? *mesh : getMesh(), _partitioner_name, _use_distributed_mesh, _pars, *this);
3658 70507 : }
3659 :
3660 : void
3661 70507 : MooseMesh::setPartitioner(MeshBase & mesh_base,
3662 : MooseEnum & partitioner,
3663 : bool use_distributed_mesh,
3664 : const InputParameters & params,
3665 : MooseObject & context_obj)
3666 : {
3667 : // Set the partitioner based on partitioner name
3668 70507 : switch (partitioner)
3669 : {
3670 66338 : case -3: // default
3671 : // We'll use the default partitioner, but notify the user of which one is being used...
3672 66338 : if (use_distributed_mesh)
3673 18706 : partitioner = "parmetis";
3674 : else
3675 113970 : partitioner = "metis";
3676 66338 : break;
3677 :
3678 : // No need to explicitily create the metis or parmetis partitioners,
3679 : // They are the default for serial and parallel mesh respectively
3680 4066 : case -2: // metis
3681 : case -1: // parmetis
3682 4066 : break;
3683 :
3684 45 : case 0: // linear
3685 45 : mesh_base.partitioner().reset(new libMesh::LinearPartitioner);
3686 45 : break;
3687 58 : case 1: // centroid
3688 : {
3689 116 : if (!params.isParamValid("centroid_partitioner_direction"))
3690 0 : context_obj.paramError(
3691 : "centroid_partitioner_direction",
3692 : "If using the centroid partitioner you _must_ specify centroid_partitioner_direction!");
3693 :
3694 58 : MooseEnum direction = params.get<MooseEnum>("centroid_partitioner_direction");
3695 :
3696 58 : if (direction == "x")
3697 36 : mesh_base.partitioner().reset(
3698 18 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::X));
3699 40 : else if (direction == "y")
3700 80 : mesh_base.partitioner().reset(
3701 40 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Y));
3702 0 : else if (direction == "z")
3703 0 : mesh_base.partitioner().reset(
3704 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Z));
3705 0 : else if (direction == "radial")
3706 0 : mesh_base.partitioner().reset(
3707 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::RADIAL));
3708 58 : break;
3709 58 : }
3710 0 : case 2: // hilbert_sfc
3711 0 : mesh_base.partitioner().reset(new libMesh::HilbertSFCPartitioner);
3712 0 : break;
3713 0 : case 3: // morton_sfc
3714 0 : mesh_base.partitioner().reset(new libMesh::MortonSFCPartitioner);
3715 0 : break;
3716 : }
3717 70507 : }
3718 :
3719 : void
3720 1661 : MooseMesh::setCustomPartitioner(Partitioner * partitioner)
3721 : {
3722 1661 : _custom_partitioner = partitioner->clone();
3723 1661 : }
3724 :
3725 : bool
3726 0 : MooseMesh::isCustomPartitionerRequested() const
3727 : {
3728 0 : return _custom_partitioner_requested;
3729 : }
3730 :
3731 : bool
3732 151282 : MooseMesh::hasSecondOrderElements()
3733 : {
3734 151282 : bool mesh_has_second_order_elements = false;
3735 49293488 : for (auto it = activeLocalElementsBegin(), end = activeLocalElementsEnd(); it != end; ++it)
3736 24583636 : if ((*it)->default_order() == SECOND)
3737 : {
3738 12533 : mesh_has_second_order_elements = true;
3739 12533 : break;
3740 151282 : }
3741 :
3742 : // We checked our local elements, so take the max over all processors.
3743 151282 : comm().max(mesh_has_second_order_elements);
3744 151282 : return mesh_has_second_order_elements;
3745 : }
3746 :
3747 : void
3748 1672 : MooseMesh::setIsCustomPartitionerRequested(bool cpr)
3749 : {
3750 1672 : _custom_partitioner_requested = cpr;
3751 1672 : }
3752 :
3753 : std::unique_ptr<libMesh::PointLocatorBase>
3754 6236 : MooseMesh::getPointLocator() const
3755 : {
3756 6236 : return getMesh().sub_point_locator();
3757 : }
3758 :
3759 : void
3760 5823 : MooseMesh::buildFiniteVolumeInfo() const
3761 : {
3762 : mooseAssert(!Threads::in_threads,
3763 : "This routine has not been implemented for threads. Please query this routine before "
3764 : "a threaded region or contact a MOOSE developer to discuss.");
3765 5823 : _finite_volume_info_dirty = false;
3766 :
3767 : using Keytype = std::pair<const Elem *, unsigned short int>;
3768 :
3769 : // create a map from elem/side --> boundary ids
3770 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>> side_list =
3771 5823 : buildActiveSideList();
3772 5823 : std::map<Keytype, std::set<boundary_id_type>> side_map;
3773 193949 : for (auto & [elem_id, side, bc_id] : side_list)
3774 : {
3775 188126 : const Elem * elem = _mesh->elem_ptr(elem_id);
3776 188126 : Keytype key(elem, side);
3777 188126 : auto & bc_set = side_map[key];
3778 188126 : bc_set.insert(bc_id);
3779 : }
3780 :
3781 5823 : _face_info.clear();
3782 5823 : _all_face_info.clear();
3783 5823 : _elem_side_to_face_info.clear();
3784 :
3785 5823 : _elem_to_elem_info.clear();
3786 5823 : _elem_info.clear();
3787 :
3788 : // by performing the element ID comparison check in the below loop, we are ensuring that we never
3789 : // double count face contributions. If a face lies along a process boundary, the only process that
3790 : // will contribute to both sides of the face residuals/Jacobians will be the process that owns the
3791 : // element with the lower ID.
3792 5823 : auto begin = getMesh().active_elements_begin();
3793 5823 : auto end = getMesh().active_elements_end();
3794 :
3795 : // We prepare a map connecting the Elem* and the corresponding ElemInfo
3796 : // for the active elements.
3797 1274579 : for (const Elem * elem : as_range(begin, end))
3798 1274579 : _elem_to_elem_info.emplace(elem->id(), elem);
3799 :
3800 5823 : dof_id_type face_index = 0;
3801 2543335 : for (const Elem * elem : as_range(begin, end))
3802 : {
3803 5447963 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
3804 : {
3805 : // get the neighbor element
3806 4179207 : const Elem * neighbor = elem->neighbor_ptr(side);
3807 :
3808 : // Check if the FaceInfo shall belong to the element. If yes,
3809 : // create and initialize the FaceInfo. We need this to ensure that
3810 : // we do not duplicate FaceInfo-s.
3811 4179207 : if (Moose::FV::elemHasFaceInfo(*elem, neighbor))
3812 : {
3813 : mooseAssert(!neighbor || (neighbor->level() < elem->level() ? neighbor->active() : true),
3814 : "If the neighbor is coarser than the element, we expect that the neighbor must "
3815 : "be active.");
3816 :
3817 : // We construct the faceInfo using the elementinfo and side index
3818 2178251 : _all_face_info.emplace_back(&_elem_to_elem_info[elem->id()], side, face_index++);
3819 :
3820 2178251 : auto & fi = _all_face_info.back();
3821 :
3822 : // get all the sidesets that this face is contained in and cache them
3823 : // in the face info.
3824 2178251 : std::set<boundary_id_type> & boundary_ids = fi.boundaryIDs();
3825 2178251 : boundary_ids.clear();
3826 :
3827 : // We initialize the weights/other information in faceInfo. If the neighbor does not exist
3828 : // or is remote (so when we are on some sort of mesh boundary), we initialize the ghost
3829 : // cell and use it to compute the weights corresponding to the faceInfo.
3830 2178251 : if (!neighbor || neighbor == libMesh::remote_elem)
3831 174207 : fi.computeBoundaryCoefficients();
3832 : else
3833 2004044 : fi.computeInternalCoefficients(&_elem_to_elem_info[neighbor->id()]);
3834 :
3835 2178251 : auto lit = side_map.find(Keytype(&fi.elem(), fi.elemSideID()));
3836 2178251 : if (lit != side_map.end())
3837 176438 : boundary_ids.insert(lit->second.begin(), lit->second.end());
3838 :
3839 2178251 : if (fi.neighborPtr())
3840 : {
3841 2004044 : auto rit = side_map.find(Keytype(fi.neighborPtr(), fi.neighborSideID()));
3842 2004044 : if (rit != side_map.end())
3843 5077 : boundary_ids.insert(rit->second.begin(), rit->second.end());
3844 : }
3845 : }
3846 : }
3847 5823 : }
3848 :
3849 : // Build the local face info and elem_side to face info maps. We need to do this after
3850 : // _all_face_info is finished being constructed because emplace_back invalidates all iterators and
3851 : // references if ever the new size exceeds capacity
3852 2184074 : for (auto & fi : _all_face_info)
3853 : {
3854 2178251 : const Elem * const elem = &fi.elem();
3855 2178251 : const auto side = fi.elemSideID();
3856 :
3857 : #ifndef NDEBUG
3858 : auto pair_it =
3859 : #endif
3860 2178251 : _elem_side_to_face_info.emplace(std::make_pair(elem, side), &fi);
3861 : mooseAssert(pair_it.second, "We should be adding unique FaceInfo objects.");
3862 :
3863 : // We will add the faces on processor boundaries to the list of face infos on each
3864 : // associated processor.
3865 2449151 : if (fi.elem().processor_id() == this->processor_id() ||
3866 270900 : (fi.neighborPtr() && (fi.neighborPtr()->processor_id() == this->processor_id())))
3867 2037008 : _face_info.push_back(&fi);
3868 : }
3869 :
3870 1274579 : for (auto & ei : _elem_to_elem_info)
3871 1268756 : if (ei.second.elem()->processor_id() == this->processor_id())
3872 1193657 : _elem_info.push_back(&ei.second);
3873 5823 : }
3874 :
3875 : const FaceInfo *
3876 86993182 : MooseMesh::faceInfo(const Elem * elem, unsigned int side) const
3877 : {
3878 86993182 : auto it = _elem_side_to_face_info.find(std::make_pair(elem, side));
3879 :
3880 86993182 : if (it == _elem_side_to_face_info.end())
3881 891 : return nullptr;
3882 : else
3883 : {
3884 : mooseAssert(it->second,
3885 : "For some reason, the FaceInfo object is NULL! Try calling "
3886 : "`buildFiniteVolumeInfo()` before using this accessor!");
3887 86992291 : return it->second;
3888 : }
3889 : }
3890 :
3891 : const ElemInfo &
3892 302196 : MooseMesh::elemInfo(const dof_id_type id) const
3893 : {
3894 302196 : return libmesh_map_find(_elem_to_elem_info, id);
3895 : }
3896 :
3897 : void
3898 5821 : MooseMesh::computeFiniteVolumeCoords() const
3899 : {
3900 5821 : if (_finite_volume_info_dirty)
3901 0 : mooseError("Trying to compute face- and elem-info coords when the information is dirty");
3902 :
3903 2184000 : for (auto & fi : _all_face_info)
3904 : {
3905 : // get elem & neighbor elements, and set subdomain ids
3906 2178179 : const SubdomainID elem_subdomain_id = fi.elemSubdomainID();
3907 2178179 : const SubdomainID neighbor_subdomain_id = fi.neighborSubdomainID();
3908 :
3909 2178179 : coordTransformFactor(
3910 2178179 : *this, elem_subdomain_id, fi.faceCentroid(), fi.faceCoord(), neighbor_subdomain_id);
3911 : }
3912 :
3913 1274561 : for (auto & ei : _elem_to_elem_info)
3914 1268740 : coordTransformFactor(
3915 2537480 : *this, ei.second.subdomain_id(), ei.second.centroid(), ei.second.coordFactor());
3916 5821 : }
3917 :
3918 : MooseEnum
3919 357709 : MooseMesh::partitioning()
3920 : {
3921 : MooseEnum partitioning("default=-3 metis=-2 parmetis=-1 linear=0 centroid hilbert_sfc morton_sfc",
3922 1073127 : "default");
3923 357709 : return partitioning;
3924 : }
3925 :
3926 : MooseEnum
3927 0 : MooseMesh::elemTypes()
3928 : {
3929 : MooseEnum elemTypes(
3930 : "EDGE EDGE2 EDGE3 EDGE4 QUAD QUAD4 QUAD8 QUAD9 TRI3 TRI6 HEX HEX8 HEX20 HEX27 TET4 TET10 "
3931 0 : "PRISM6 PRISM15 PRISM18 PYRAMID5 PYRAMID13 PYRAMID14");
3932 0 : return elemTypes;
3933 : }
3934 :
3935 : void
3936 37112 : MooseMesh::allowRemoteElementRemoval(const bool allow_remote_element_removal)
3937 : {
3938 37112 : _allow_remote_element_removal = allow_remote_element_removal;
3939 37112 : if (_mesh)
3940 16889 : _mesh->allow_remote_element_removal(allow_remote_element_removal);
3941 :
3942 37112 : if (!allow_remote_element_removal)
3943 : // If we're not allowing remote element removal now, then we will need deletion later after
3944 : // late geoemetric ghosting functors have been added (late geometric ghosting functor addition
3945 : // happens when algebraic ghosting functors are added)
3946 37112 : _need_delete = true;
3947 37112 : }
3948 :
3949 : void
3950 18498 : MooseMesh::deleteRemoteElements()
3951 : {
3952 18498 : _allow_remote_element_removal = true;
3953 18498 : if (!_mesh)
3954 0 : mooseError("Cannot delete remote elements because we have not yet attached a MeshBase");
3955 :
3956 18498 : _mesh->allow_remote_element_removal(true);
3957 :
3958 18498 : _mesh->delete_remote_elements();
3959 18498 : }
3960 :
3961 : void
3962 5817 : MooseMesh::cacheFaceInfoVariableOwnership() const
3963 : {
3964 : mooseAssert(
3965 : !Threads::in_threads,
3966 : "Performing writes to faceInfo variable association maps. This must be done unthreaded!");
3967 :
3968 5817 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
3969 :
3970 4360774 : auto face_lambda = [this](const SubdomainID elem_subdomain_id,
3971 : const SubdomainID neighbor_subdomain_id,
3972 : SystemBase & sys,
3973 : std::vector<std::vector<FaceInfo::VarFaceNeighbors>> & face_type_vector)
3974 : {
3975 4360774 : face_type_vector[sys.number()].resize(sys.nVariables(), FaceInfo::VarFaceNeighbors::NEITHER);
3976 4360774 : const auto & variables = sys.getVariables(0);
3977 :
3978 9572539 : for (const auto & var : variables)
3979 : {
3980 5211765 : const unsigned int var_num = var->number();
3981 5211765 : const unsigned int sys_num = var->sys().number();
3982 5211765 : std::set<SubdomainID> var_subdomains = var->blockIDs();
3983 : /**
3984 : * The following paragraph of code assigns the VarFaceNeighbors
3985 : * 1. The face is an internal face of this variable if it is defined on
3986 : * the elem and neighbor subdomains
3987 : * 2. The face is an invalid face of this variable if it is neither defined
3988 : * on the elem nor the neighbor subdomains
3989 : * 3. If not 1. or 2. then this is a boundary for this variable and the else clause
3990 : * applies
3991 : */
3992 5211765 : bool var_defined_elem = var_subdomains.find(elem_subdomain_id) != var_subdomains.end();
3993 : bool var_defined_neighbor =
3994 5211765 : var_subdomains.find(neighbor_subdomain_id) != var_subdomains.end();
3995 5211765 : if (var_defined_elem && var_defined_neighbor)
3996 4148427 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::BOTH;
3997 1063338 : else if (!var_defined_elem && !var_defined_neighbor)
3998 580622 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEITHER;
3999 : else
4000 : {
4001 : // this is a boundary face for this variable, set elem or neighbor
4002 482716 : if (var_defined_elem)
4003 476325 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::ELEM;
4004 6391 : else if (var_defined_neighbor)
4005 6391 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEIGHBOR;
4006 : else
4007 0 : mooseError("Should never get here");
4008 : }
4009 5211765 : }
4010 4360774 : };
4011 :
4012 : // We loop through the faces and check if they are internal, boundary or external to
4013 : // the variables in the problem
4014 2183948 : for (FaceInfo & face : _all_face_info)
4015 : {
4016 2178131 : const SubdomainID elem_subdomain_id = face.elemSubdomainID();
4017 2178131 : const SubdomainID neighbor_subdomain_id = face.neighborSubdomainID();
4018 :
4019 2178131 : auto & face_type_vector = face.faceType();
4020 :
4021 2178131 : face_type_vector.clear();
4022 2178131 : face_type_vector.resize(num_eqs);
4023 :
4024 : // First, we check the variables in the solver systems (linear/nonlinear)
4025 4360774 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4026 2182643 : face_lambda(elem_subdomain_id,
4027 : neighbor_subdomain_id,
4028 2182643 : _app.feProblem().getSolverSystem(i),
4029 : face_type_vector);
4030 :
4031 : // Then we check the variables in the auxiliary system
4032 2178131 : face_lambda(elem_subdomain_id,
4033 : neighbor_subdomain_id,
4034 2178131 : _app.feProblem().getAuxiliarySystem(),
4035 : face_type_vector);
4036 : }
4037 5817 : }
4038 :
4039 : void
4040 5817 : MooseMesh::cacheFVElementalDoFs() const
4041 : {
4042 : mooseAssert(!Threads::in_threads,
4043 : "Performing writes to elemInfo dof indices. This must be done unthreaded!");
4044 :
4045 2540390 : auto elem_lambda = [](const ElemInfo & elem_info,
4046 : SystemBase & sys,
4047 : std::vector<std::vector<dof_id_type>> & dof_vector)
4048 : {
4049 2540390 : if (sys.nFVVariables())
4050 : {
4051 1341671 : dof_vector[sys.number()].resize(sys.nVariables(), libMesh::DofObject::invalid_id);
4052 1341671 : const auto & variables = sys.getVariables(0);
4053 :
4054 4164488 : for (const auto & var : variables)
4055 2822817 : if (var->isFV())
4056 : {
4057 1599244 : const auto & var_subdomains = var->blockIDs();
4058 :
4059 : // We will only cache for FV variables and if they live on the current subdomain
4060 1599244 : if (var_subdomains.find(elem_info.subdomain_id()) != var_subdomains.end())
4061 : {
4062 1464421 : std::vector<dof_id_type> indices;
4063 1464421 : var->dofMap().dof_indices(elem_info.elem(), indices, var->number());
4064 : mooseAssert(indices.size() == 1, "We expect to have only one dof per element!");
4065 1464421 : dof_vector[sys.number()][var->number()] = indices[0];
4066 1464421 : }
4067 : }
4068 : }
4069 2540390 : };
4070 :
4071 5817 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
4072 :
4073 : // We loop through the elements in the mesh and cache the dof indices
4074 : // for the corresponding variables.
4075 1274541 : for (auto & ei_pair : _elem_to_elem_info)
4076 : {
4077 1268724 : auto & elem_info = ei_pair.second;
4078 1268724 : auto & dof_vector = elem_info.dofIndices();
4079 :
4080 1268724 : dof_vector.clear();
4081 1268724 : dof_vector.resize(num_eqs);
4082 :
4083 : // First, we cache the dof indices for the variables in the solver systems (linear, nonlinear)
4084 2540390 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4085 1271666 : elem_lambda(elem_info, _app.feProblem().getSolverSystem(i), dof_vector);
4086 :
4087 : // Then we cache the dof indices for the auxvariables
4088 1268724 : elem_lambda(elem_info, _app.feProblem().getAuxiliarySystem(), dof_vector);
4089 : }
4090 5817 : }
4091 :
4092 : void
4093 5817 : MooseMesh::setupFiniteVolumeMeshData() const
4094 : {
4095 5817 : buildFiniteVolumeInfo();
4096 5817 : computeFiniteVolumeCoords();
4097 5817 : cacheFaceInfoVariableOwnership();
4098 5817 : cacheFVElementalDoFs();
4099 5817 : }
4100 :
4101 : void
4102 67251 : MooseMesh::setCoordSystem(const std::vector<SubdomainName> & blocks,
4103 : const MultiMooseEnum & coord_sys)
4104 : {
4105 336255 : TIME_SECTION("setCoordSystem", 5, "Setting Coordinate System");
4106 67251 : if (!_provided_coord_blocks.empty() && (_provided_coord_blocks != blocks))
4107 : {
4108 0 : const std::string param_name = isParamValid("coord_block") ? "coord_block" : "block";
4109 0 : mooseWarning("Supplied blocks in the 'setCoordSystem' method do not match the value of the "
4110 : "'Mesh/",
4111 : param_name,
4112 : "' parameter. Did you provide different parameter values for 'Mesh/",
4113 : param_name,
4114 : "' and 'Problem/block'?. We will honor the parameter value from 'Mesh/",
4115 : param_name,
4116 : "'");
4117 : mooseAssert(_coord_system_set,
4118 : "If we are arriving here due to a bad specification in the Problem block, then we "
4119 : "should have already set our coordinate system subdomains from the Mesh block");
4120 0 : return;
4121 0 : }
4122 202941 : if (_pars.isParamSetByUser("coord_type") && getParam<MultiMooseEnum>("coord_type") != coord_sys)
4123 0 : mooseError("Supplied coordinate systems in the 'setCoordSystem' method do not match the value "
4124 : "of the 'Mesh/coord_type' parameter. Did you provide different parameter values for "
4125 : "'coord_type' to 'Mesh' and 'Problem'?");
4126 :
4127 : // If blocks contain ANY_BLOCK_ID, it should be the only block specified, and coord_sys should
4128 : // have one and only one entry. In that case, the same coordinate system will be set for all
4129 : // subdomains.
4130 67251 : if (blocks.size() == 1 && blocks[0] == "ANY_BLOCK_ID")
4131 : {
4132 0 : if (coord_sys.size() > 1)
4133 0 : mooseError("If you specify ANY_BLOCK_ID as the only block, you must also specify a single "
4134 : "coordinate system for it.");
4135 0 : if (!_mesh->is_prepared())
4136 0 : mooseError(
4137 : "You cannot set the coordinate system for ANY_BLOCK_ID before the mesh is prepared. "
4138 : "Please call this method after the mesh is prepared.");
4139 0 : const auto coord_type = coord_sys.size() == 0
4140 0 : ? Moose::COORD_XYZ
4141 0 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4142 0 : for (const auto sid : meshSubdomains())
4143 0 : _coord_sys[sid] = coord_type;
4144 0 : return;
4145 : }
4146 :
4147 : // If multiple blocks are specified, but one of them is ANY_BLOCK_ID, let's emit a helpful error
4148 67251 : if (std::find(blocks.begin(), blocks.end(), "ANY_BLOCK_ID") != blocks.end())
4149 0 : mooseError("You cannot specify ANY_BLOCK_ID together with other blocks in the "
4150 : "setCoordSystem() method. If you want to set the same coordinate system for all "
4151 : "blocks, use ANY_BLOCK_ID as the only block.");
4152 :
4153 67251 : auto subdomains = meshSubdomains();
4154 : // It's possible that a user has called this API before the mesh is prepared and consequently we
4155 : // don't yet have the subdomains in meshSubdomains()
4156 67670 : for (const auto & sub_name : blocks)
4157 : {
4158 419 : const auto sub_id = getSubdomainID(sub_name);
4159 419 : subdomains.insert(sub_id);
4160 : }
4161 :
4162 67251 : if (coord_sys.size() <= 1)
4163 : {
4164 : // We will specify the same coordinate system for all blocks
4165 67225 : const auto coord_type = coord_sys.size() == 0
4166 67225 : ? Moose::COORD_XYZ
4167 67225 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4168 160303 : for (const auto sid : subdomains)
4169 93078 : _coord_sys[sid] = coord_type;
4170 : }
4171 : else
4172 : {
4173 26 : if (blocks.size() != coord_sys.size())
4174 0 : mooseError("Number of blocks and coordinate systems does not match.");
4175 :
4176 104 : for (const auto i : index_range(blocks))
4177 : {
4178 78 : SubdomainID sid = getSubdomainID(blocks[i]);
4179 : Moose::CoordinateSystemType coord_type =
4180 78 : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[i]);
4181 78 : _coord_sys[sid] = coord_type;
4182 : }
4183 :
4184 104 : for (const auto & sid : subdomains)
4185 78 : if (_coord_sys.find(sid) == _coord_sys.end())
4186 0 : mooseError("Subdomain '" + Moose::stringify(sid) +
4187 : "' does not have a coordinate system specified.");
4188 : }
4189 :
4190 67251 : _coord_system_set = true;
4191 :
4192 67251 : updateCoordTransform();
4193 67251 : }
4194 :
4195 : Moose::CoordinateSystemType
4196 2563857250 : MooseMesh::getCoordSystem(SubdomainID sid) const
4197 : {
4198 2563857250 : auto it = _coord_sys.find(sid);
4199 2563857250 : if (it != _coord_sys.end())
4200 5127714500 : return (*it).second;
4201 : else
4202 0 : mooseError("Requested subdomain ", sid, " does not exist.");
4203 : }
4204 :
4205 : Moose::CoordinateSystemType
4206 59816 : MooseMesh::getUniqueCoordSystem() const
4207 : {
4208 59816 : const auto unique_system = _coord_sys.find(*meshSubdomains().begin())->second;
4209 : // Check that it is actually unique
4210 59816 : bool result = std::all_of(
4211 59816 : std::next(_coord_sys.begin()),
4212 59816 : _coord_sys.end(),
4213 3818 : [unique_system](
4214 : typename std::unordered_map<SubdomainID, Moose::CoordinateSystemType>::const_reference
4215 3818 : item) { return (item.second == unique_system); });
4216 59816 : if (!result)
4217 0 : mooseError("The unique coordinate system of the mesh was requested by the mesh contains "
4218 : "multiple blocks with different coordinate systems");
4219 :
4220 59816 : if (usingGeneralAxisymmetricCoordAxes())
4221 0 : mooseError("General axisymmetric coordinate axes are being used, and it is currently "
4222 : "conservatively assumed that in this case there is no unique coordinate system.");
4223 :
4224 59816 : return unique_system;
4225 : }
4226 :
4227 : const std::map<SubdomainID, Moose::CoordinateSystemType> &
4228 70568 : MooseMesh::getCoordSystem() const
4229 : {
4230 70568 : return _coord_sys;
4231 : }
4232 :
4233 : void
4234 0 : MooseMesh::setAxisymmetricCoordAxis(const MooseEnum & rz_coord_axis)
4235 : {
4236 0 : _rz_coord_axis = rz_coord_axis;
4237 :
4238 0 : updateCoordTransform();
4239 0 : }
4240 :
4241 : void
4242 21 : MooseMesh::setGeneralAxisymmetricCoordAxes(
4243 : const std::vector<SubdomainName> & blocks,
4244 : const std::vector<std::pair<Point, RealVectorValue>> & axes)
4245 : {
4246 : // Set the axes for the given blocks
4247 : mooseAssert(blocks.size() == axes.size(), "Blocks and axes vectors must be the same length.");
4248 68 : for (const auto i : index_range(blocks))
4249 : {
4250 47 : const auto subdomain_id = getSubdomainID(blocks[i]);
4251 47 : const auto it = _coord_sys.find(subdomain_id);
4252 47 : if (it == _coord_sys.end())
4253 0 : mooseError("The block '",
4254 0 : blocks[i],
4255 : "' has not set a coordinate system. Make sure to call setCoordSystem() before "
4256 : "setGeneralAxisymmetricCoordAxes().");
4257 : else
4258 : {
4259 47 : if (it->second == Moose::COORD_RZ)
4260 : {
4261 47 : const auto direction = axes[i].second;
4262 47 : if (direction.is_zero())
4263 0 : mooseError("Only nonzero vectors may be supplied for RZ directions.");
4264 :
4265 47 : _subdomain_id_to_rz_coord_axis[subdomain_id] =
4266 94 : std::make_pair(axes[i].first, direction.unit());
4267 : }
4268 : else
4269 0 : mooseError("The block '",
4270 0 : blocks[i],
4271 : "' was provided in setGeneralAxisymmetricCoordAxes(), but the coordinate system "
4272 : "for this block is not 'RZ'.");
4273 : }
4274 : }
4275 :
4276 : // Make sure there are no RZ blocks that still do not have axes
4277 21 : const auto all_subdomain_ids = meshSubdomains();
4278 81 : for (const auto subdomain_id : all_subdomain_ids)
4279 107 : if (getCoordSystem(subdomain_id) == Moose::COORD_RZ &&
4280 47 : !_subdomain_id_to_rz_coord_axis.count(subdomain_id))
4281 0 : mooseError("The block '",
4282 0 : getSubdomainName(subdomain_id),
4283 : "' was specified to use the 'RZ' coordinate system but was not given in "
4284 : "setGeneralAxisymmetricCoordAxes().");
4285 :
4286 21 : updateCoordTransform();
4287 21 : }
4288 :
4289 : const std::pair<Point, RealVectorValue> &
4290 1212256 : MooseMesh::getGeneralAxisymmetricCoordAxis(SubdomainID subdomain_id) const
4291 : {
4292 1212256 : auto it = _subdomain_id_to_rz_coord_axis.find(subdomain_id);
4293 1212256 : if (it != _subdomain_id_to_rz_coord_axis.end())
4294 2424512 : return (*it).second;
4295 : else
4296 0 : mooseError("Requested subdomain ", subdomain_id, " does not exist.");
4297 : }
4298 :
4299 : bool
4300 30443778 : MooseMesh::usingGeneralAxisymmetricCoordAxes() const
4301 : {
4302 30443778 : return _subdomain_id_to_rz_coord_axis.size() > 0;
4303 : }
4304 :
4305 : void
4306 70568 : MooseMesh::updateCoordTransform()
4307 : {
4308 70568 : if (!_coord_transform)
4309 70543 : _coord_transform = std::make_unique<MooseAppCoordTransform>(*this);
4310 : else
4311 25 : _coord_transform->setCoordinateSystem(*this);
4312 70568 : }
4313 :
4314 : unsigned int
4315 26202063 : MooseMesh::getAxisymmetricRadialCoord() const
4316 : {
4317 26202063 : if (usingGeneralAxisymmetricCoordAxes())
4318 0 : mooseError("getAxisymmetricRadialCoord() should not be called if "
4319 : "setGeneralAxisymmetricCoordAxes() has been called.");
4320 :
4321 26202063 : if (_rz_coord_axis == 0)
4322 156000 : return 1; // if the rotation axis is x (0), then the radial direction is y (1)
4323 : else
4324 26046063 : return 0; // otherwise the radial direction is assumed to be x, i.e., the rotation axis is y
4325 : }
4326 :
4327 : void
4328 62634 : MooseMesh::checkCoordinateSystems()
4329 : {
4330 30019976 : for (const auto & elem : getMesh().element_ptr_range())
4331 : {
4332 14978675 : SubdomainID sid = elem->subdomain_id();
4333 14978675 : if (_coord_sys[sid] == Moose::COORD_RZ && elem->dim() == 3)
4334 4 : mooseError("An RZ coordinate system was requested for subdomain " + Moose::stringify(sid) +
4335 : " which contains 3D elements.");
4336 14978671 : if (_coord_sys[sid] == Moose::COORD_RSPHERICAL && elem->dim() > 1)
4337 0 : mooseError("An RSPHERICAL coordinate system was requested for subdomain " +
4338 0 : Moose::stringify(sid) + " which contains 2D or 3D elements.");
4339 62630 : }
4340 62630 : }
4341 :
4342 : void
4343 2246 : MooseMesh::setCoordData(const MooseMesh & other_mesh)
4344 : {
4345 2246 : _coord_sys = other_mesh._coord_sys;
4346 2246 : _rz_coord_axis = other_mesh._rz_coord_axis;
4347 2246 : _subdomain_id_to_rz_coord_axis = other_mesh._subdomain_id_to_rz_coord_axis;
4348 2246 : }
4349 :
4350 : const MooseUnits &
4351 2 : MooseMesh::lengthUnit() const
4352 : {
4353 : mooseAssert(_coord_transform, "This must be non-null");
4354 2 : return _coord_transform->lengthUnit();
4355 : }
4356 :
4357 : void
4358 70353 : MooseMesh::checkDuplicateSubdomainNames()
4359 : {
4360 70353 : std::map<SubdomainName, SubdomainID> subdomain;
4361 167905 : for (const auto & sbd_id : _mesh_subdomains)
4362 : {
4363 97556 : std::string sub_name = getSubdomainName(sbd_id);
4364 97556 : if (!sub_name.empty() && subdomain.count(sub_name) > 0)
4365 8 : mooseError("The subdomain name ",
4366 : sub_name,
4367 : " is used for both subdomain with ID=",
4368 4 : subdomain[sub_name],
4369 : " and ID=",
4370 : sbd_id,
4371 : ", Please rename one of them!");
4372 : else
4373 97552 : subdomain[sub_name] = sbd_id;
4374 97552 : }
4375 70349 : }
4376 :
4377 : const std::vector<QpMap> &
4378 900 : MooseMesh::getPRefinementMapHelper(
4379 : const Elem & elem,
4380 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4381 : {
4382 : // We are actually seeking the map stored with the p_level - 1 key, e.g. the refinement map that
4383 : // maps from the previous p_level to this element's p_level
4384 900 : return libmesh_map_find(map,
4385 : std::make_pair(elem.type(), cast_int<unsigned int>(elem.p_level() - 1)));
4386 : }
4387 :
4388 : const std::vector<QpMap> &
4389 0 : MooseMesh::getPCoarseningMapHelper(
4390 : const Elem & elem,
4391 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4392 : {
4393 : mooseAssert(elem.active() && elem.p_refinement_flag() == Elem::JUST_COARSENED,
4394 : "These are the conditions that should be met for requesting a coarsening map");
4395 0 : return libmesh_map_find(map, std::make_pair(elem.type(), elem.p_level()));
4396 : }
4397 :
4398 : const std::vector<QpMap> &
4399 900 : MooseMesh::getPRefinementMap(const Elem & elem) const
4400 : {
4401 900 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_map);
4402 : }
4403 :
4404 : const std::vector<QpMap> &
4405 0 : MooseMesh::getPRefinementSideMap(const Elem & elem) const
4406 : {
4407 0 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_side_map);
4408 : }
4409 :
4410 : const std::vector<QpMap> &
4411 0 : MooseMesh::getPCoarseningMap(const Elem & elem) const
4412 : {
4413 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_map);
4414 : }
4415 :
4416 : const std::vector<QpMap> &
4417 0 : MooseMesh::getPCoarseningSideMap(const Elem & elem) const
4418 : {
4419 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_side_map);
4420 : }
4421 :
4422 : bool
4423 25074 : MooseMesh::skipNoncriticalPartitioning() const
4424 : {
4425 25074 : return _mesh->skip_noncritical_partitioning();
4426 : }
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