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_communication.h"
41 : #include "libmesh/mesh_tools.h"
42 : #include "libmesh/parallel.h"
43 : #include "libmesh/parallel_elem.h"
44 : #include "libmesh/parallel_node.h"
45 : #include "libmesh/parallel_ghost_sync.h"
46 : #include "libmesh/utility.h"
47 : #include "libmesh/remote_elem.h"
48 : #include "libmesh/linear_partitioner.h"
49 : #include "libmesh/centroid_partitioner.h"
50 : #include "libmesh/parmetis_partitioner.h"
51 : #include "libmesh/hilbert_sfc_partitioner.h"
52 : #include "libmesh/morton_sfc_partitioner.h"
53 : #include "libmesh/edge_edge2.h"
54 : #include "libmesh/mesh_refinement.h"
55 : #include "libmesh/quadrature.h"
56 : #include "libmesh/boundary_info.h"
57 : #include "libmesh/periodic_boundaries.h"
58 : #include "libmesh/quadrature_gauss.h"
59 : #include "libmesh/point_locator_base.h"
60 : #include "libmesh/default_coupling.h"
61 : #include "libmesh/ghost_point_neighbors.h"
62 : #include "libmesh/fe_type.h"
63 : #include "libmesh/enum_to_string.h"
64 : #include "libmesh/elem_side_builder.h"
65 :
66 : using namespace libMesh;
67 :
68 : // Make newer nanoflann API compatible with older nanoflann versions
69 : #if NANOFLANN_VERSION < 0x150
70 : namespace nanoflann
71 : {
72 : typedef SearchParams SearchParameters;
73 :
74 : template <typename T, typename U>
75 : using ResultItem = std::pair<T, U>;
76 : }
77 : #endif
78 :
79 : const std::array<bool, 3> MooseMesh::periodic_dim_default{false, false, false};
80 :
81 : InputParameters
82 201466 : MooseMesh::validParams()
83 : {
84 201466 : InputParameters params = MooseObject::validParams();
85 :
86 805864 : MooseEnum parallel_type("DEFAULT REPLICATED DISTRIBUTED", "DEFAULT");
87 805864 : params.addParam<MooseEnum>("parallel_type",
88 : parallel_type,
89 : "DEFAULT: Use libMesh::ReplicatedMesh unless --distributed-mesh is "
90 : "specified on the command line "
91 : "REPLICATED: Always use libMesh::ReplicatedMesh "
92 : "DISTRIBUTED: Always use libMesh::DistributedMesh");
93 :
94 604398 : params.addParam<bool>(
95 : "allow_renumbering",
96 402932 : true,
97 : "If allow_renumbering=false, node and element numbers are kept fixed until deletion");
98 :
99 604398 : params.addParam<MooseEnum>(
100 : "partitioner",
101 402932 : partitioning(),
102 : "Specifies a mesh partitioner to use when splitting the mesh for a parallel computation.");
103 805864 : MooseEnum direction("x y z radial");
104 805864 : params.addParam<MooseEnum>("centroid_partitioner_direction",
105 : direction,
106 : "Specifies the sort direction if using the centroid partitioner. "
107 : "Available options: x, y, z, radial");
108 :
109 805864 : MooseEnum patch_update_strategy("never always auto iteration", "never");
110 805864 : params.addParam<MooseEnum>(
111 : "patch_update_strategy",
112 : patch_update_strategy,
113 : "How often to update the geometric search 'patch'. The default is to "
114 : "never update it (which is the most efficient but could be a problem "
115 : "with lots of relative motion). 'always' will update the patch for all "
116 : "secondary nodes at the beginning of every timestep which might be time "
117 : "consuming. 'auto' will attempt to determine at the start of which "
118 : "timesteps the patch for all secondary nodes needs to be updated automatically."
119 : "'iteration' updates the patch at every nonlinear iteration for a "
120 : "subset of secondary nodes for which penetration is not detected. If there "
121 : "can be substantial relative motion between the primary and secondary surfaces "
122 : "during the nonlinear iterations within a timestep, it is advisable to use "
123 : "'iteration' option to ensure accurate contact detection.");
124 :
125 : // Note: This parameter is named to match 'construct_side_list_from_node_list' in SetupMeshAction
126 604398 : params.addParam<bool>(
127 : "construct_node_list_from_side_list",
128 402932 : true,
129 : "Whether or not to generate nodesets from the sidesets (currently often required).");
130 604398 : params.addParam<bool>(
131 : "displace_node_list_by_side_list",
132 402932 : true,
133 : "Whether to renumber existing nodesets with ids matching sidesets that "
134 : "lack names matching sidesets, when constructing nodesets from sidesets via the default "
135 : "'construct_node_list_from_side_list' option, rather than to merge them with the sideset.");
136 604398 : params.addParam<unsigned int>(
137 402932 : "patch_size", 40, "The number of nodes to consider in the NearestNode neighborhood.");
138 805864 : params.addParam<unsigned int>("ghosting_patch_size",
139 : "The number of nearest neighbors considered "
140 : "for ghosting purposes when 'iteration' "
141 : "patch update strategy is used. Default is "
142 : "5 * patch_size.");
143 604398 : params.addParam<unsigned int>("max_leaf_size",
144 402932 : 10,
145 : "The maximum number of points in each leaf of the KDTree used in "
146 : "the nearest neighbor search. As the leaf size becomes larger,"
147 : "KDTree construction becomes faster but the nearest neighbor search"
148 : "becomes slower.");
149 :
150 604398 : params.addParam<bool>("build_all_side_lowerd_mesh",
151 402932 : false,
152 : "True to build the lower-dimensional mesh for all sides.");
153 :
154 604398 : params.addParam<bool>("skip_refine_when_use_split",
155 402932 : true,
156 : "True to skip uniform refinements when using a pre-split mesh.");
157 :
158 805864 : params.addParam<std::vector<SubdomainID>>(
159 : "add_subdomain_ids",
160 : "The listed subdomain ids will be assumed valid for the mesh. This permits setting up "
161 : "subdomain restrictions for subdomains initially containing no elements, which can occur, "
162 : "for example, in additive manufacturing simulations which dynamically add and remove "
163 : "elements. Names for this subdomains may be provided using add_subdomain_names. In this case "
164 : "this list and add_subdomain_names must contain the same number of items.");
165 805864 : params.addParam<std::vector<SubdomainName>>(
166 : "add_subdomain_names",
167 : "The listed subdomain names will be assumed valid for the mesh. This permits setting up "
168 : "subdomain restrictions for subdomains initially containing no elements, which can occur, "
169 : "for example, in additive manufacturing simulations which dynamically add and remove "
170 : "elements. IDs for this subdomains may be provided using add_subdomain_ids. Otherwise IDs "
171 : "are automatically assigned. In case add_subdomain_ids is set too, both lists must contain "
172 : "the same number of items.");
173 :
174 805864 : params.addParam<std::vector<BoundaryID>>(
175 : "add_sideset_ids",
176 : "The listed sideset ids will be assumed valid for the mesh. This permits setting up boundary "
177 : "restrictions for sidesets initially containing no sides. Names for this sidesets may be "
178 : "provided using add_sideset_names. In this case this list and add_sideset_names must contain "
179 : "the same number of items.");
180 805864 : params.addParam<std::vector<BoundaryName>>(
181 : "add_sideset_names",
182 : "The listed sideset names will be assumed valid for the mesh. This permits setting up "
183 : "boundary restrictions for sidesets initially containing no sides. Ids for this sidesets may "
184 : "be provided using add_sideset_ids. In this case this list and add_sideset_ids must contain "
185 : "the same number of items.");
186 :
187 805864 : params.addParam<std::vector<BoundaryID>>(
188 : "add_nodeset_ids",
189 : "The listed nodeset ids will be assumed valid for the mesh. This permits setting up boundary "
190 : "restrictions for node initially containing no sides. Names for this nodesets may be "
191 : "provided using add_nodeset_names. In this case this list and add_nodeset_names must contain "
192 : "the same number of items.");
193 604398 : params.addParam<std::vector<BoundaryName>>(
194 : "add_nodeset_names",
195 : "The listed nodeset names will be assumed valid for the mesh. This permits setting up "
196 : "boundary restrictions for nodesets initially containing no sides. Ids for this nodesets may "
197 : "be provided using add_nodesets_ids. In this case this list and add_nodesets_ids must "
198 : "contain the same number of items.");
199 :
200 201466 : params += MooseAppCoordTransform::validParams();
201 :
202 : // This indicates that the derived mesh type accepts a MeshGenerator, and should be set to true in
203 : // derived types that do so.
204 402932 : params.addPrivateParam<bool>("_mesh_generator_mesh", false);
205 :
206 : // Whether or not the mesh is pre split
207 604398 : params.addPrivateParam<bool>("_is_split", false);
208 :
209 402932 : params.registerBase("MooseMesh");
210 :
211 : // groups
212 805864 : params.addParamNamesToGroup("patch_update_strategy patch_size max_leaf_size", "Geometric search");
213 805864 : params.addParamNamesToGroup("add_subdomain_ids add_subdomain_names add_sideset_ids "
214 : "add_sideset_names add_nodeset_ids add_nodeset_names",
215 : "Pre-declaration of future mesh sub-entities");
216 805864 : params.addParamNamesToGroup("construct_node_list_from_side_list build_all_side_lowerd_mesh "
217 : "displace_node_list_by_side_list",
218 : "Automatic definition of mesh element sides entities");
219 604398 : params.addParamNamesToGroup("partitioner centroid_partitioner_direction", "Partitioning");
220 :
221 402932 : return params;
222 201466 : }
223 :
224 66289 : MooseMesh::MooseMesh(const InputParameters & parameters)
225 : : MooseObject(parameters),
226 : Restartable(this, "Mesh"),
227 : PerfGraphInterface(this),
228 66289 : _parallel_type(getParam<MooseEnum>("parallel_type").getEnum<MooseMesh::ParallelType>()),
229 66289 : _use_distributed_mesh(false),
230 66289 : _distribution_overridden(false),
231 66289 : _parallel_type_overridden(false),
232 66289 : _mesh(nullptr),
233 132578 : _partitioner_name(getParam<MooseEnum>("partitioner")),
234 66289 : _partitioner_overridden(false),
235 66289 : _custom_partitioner_requested(false),
236 66289 : _uniform_refine_level(0),
237 132578 : _skip_refine_when_use_split(getParam<bool>("skip_refine_when_use_split")),
238 66289 : _skip_deletion_repartition_after_refine(false),
239 66289 : _is_nemesis(false),
240 132578 : _patch_size(getParam<unsigned int>("patch_size")),
241 132578 : _ghosting_patch_size(isParamValid("ghosting_patch_size")
242 132578 : ? getParam<unsigned int>("ghosting_patch_size")
243 66289 : : 5 * _patch_size),
244 132578 : _max_leaf_size(getParam<unsigned int>("max_leaf_size")),
245 66289 : _patch_update_strategy(
246 132578 : getParam<MooseEnum>("patch_update_strategy").getEnum<Moose::PatchUpdateType>()),
247 66289 : _regular_orthogonal_mesh(false),
248 132578 : _is_split(getParam<bool>("_is_split")),
249 66289 : _allow_recovery(true),
250 132578 : _construct_node_list_from_side_list(getParam<bool>("construct_node_list_from_side_list")),
251 132578 : _displace_node_list_by_side_list(getParam<bool>("displace_node_list_by_side_list")),
252 66289 : _need_delete(false),
253 66289 : _allow_remote_element_removal(true),
254 66289 : _need_ghost_ghosted_boundaries(true),
255 66289 : _is_displaced(false),
256 66289 : _coord_sys(
257 132578 : declareRestartableData<std::map<SubdomainID, Moose::CoordinateSystemType>>("coord_sys")),
258 132578 : _rz_coord_axis(getParam<MooseEnum>("rz_coord_axis")),
259 66289 : _coord_system_set(false),
260 646330 : _doing_p_refinement(false)
261 : {
262 198867 : if (isParamValid("ghosting_patch_size") && (_patch_update_strategy != Moose::Iteration))
263 0 : mooseError("Ghosting patch size parameter has to be set in the mesh block "
264 : "only when 'iteration' patch update strategy is used.");
265 :
266 198867 : if (isParamValid("coord_block"))
267 : {
268 72 : if (isParamValid("block"))
269 0 : paramWarning("block",
270 : "You set both 'Mesh/block' and 'Mesh/coord_block'. The value of "
271 : "'Mesh/coord_block' will be used.");
272 :
273 72 : _provided_coord_blocks = getParam<std::vector<SubdomainName>>("coord_block");
274 : }
275 198795 : else if (isParamValid("block"))
276 765 : _provided_coord_blocks = getParam<std::vector<SubdomainName>>("block");
277 :
278 198867 : if (getParam<bool>("build_all_side_lowerd_mesh"))
279 : // Do not initially allow removal of remote elements
280 223 : allowRemoteElementRemoval(false);
281 :
282 66289 : determineUseDistributedMesh();
283 :
284 : #ifdef MOOSE_KOKKOS_ENABLED
285 49729 : if (_app.isKokkosAvailable())
286 49729 : _kokkos_mesh = std::make_unique<Moose::Kokkos::Mesh>(*this);
287 : #endif
288 66289 : }
289 :
290 2987 : MooseMesh::MooseMesh(const MooseMesh & other_mesh)
291 : : MooseObject(other_mesh._pars),
292 : Restartable(this, "Mesh"),
293 : PerfGraphInterface(this, "CopiedMesh"),
294 2987 : _built_from_other_mesh(true),
295 2987 : _parallel_type(other_mesh._parallel_type),
296 2987 : _use_distributed_mesh(other_mesh._use_distributed_mesh),
297 2987 : _distribution_overridden(other_mesh._distribution_overridden),
298 2987 : _parallel_type_overridden(other_mesh._parallel_type_overridden),
299 2987 : _mesh(other_mesh.getMesh().clone()),
300 2987 : _partitioner_name(other_mesh._partitioner_name),
301 2987 : _partitioner_overridden(other_mesh._partitioner_overridden),
302 2987 : _custom_partitioner_requested(other_mesh._custom_partitioner_requested),
303 2987 : _uniform_refine_level(other_mesh.uniformRefineLevel()),
304 2987 : _skip_refine_when_use_split(other_mesh._skip_refine_when_use_split),
305 2987 : _skip_deletion_repartition_after_refine(other_mesh._skip_deletion_repartition_after_refine),
306 2987 : _is_nemesis(other_mesh._is_nemesis),
307 2987 : _patch_size(other_mesh._patch_size),
308 2987 : _ghosting_patch_size(other_mesh._ghosting_patch_size),
309 2987 : _max_leaf_size(other_mesh._max_leaf_size),
310 2987 : _patch_update_strategy(other_mesh._patch_update_strategy),
311 2987 : _regular_orthogonal_mesh(false),
312 2987 : _is_split(other_mesh._is_split),
313 2987 : _lower_d_interior_blocks(other_mesh._lower_d_interior_blocks),
314 2987 : _lower_d_boundary_blocks(other_mesh._lower_d_boundary_blocks),
315 2987 : _allow_recovery(other_mesh._allow_recovery),
316 2987 : _construct_node_list_from_side_list(other_mesh._construct_node_list_from_side_list),
317 2987 : _displace_node_list_by_side_list(other_mesh._displace_node_list_by_side_list),
318 2987 : _need_delete(other_mesh._need_delete),
319 2987 : _allow_remote_element_removal(other_mesh._allow_remote_element_removal),
320 2987 : _need_ghost_ghosted_boundaries(other_mesh._need_ghost_ghosted_boundaries),
321 2987 : _coord_sys(other_mesh._coord_sys),
322 2987 : _rz_coord_axis(other_mesh._rz_coord_axis),
323 2987 : _subdomain_id_to_rz_coord_axis(other_mesh._subdomain_id_to_rz_coord_axis),
324 2987 : _coord_system_set(other_mesh._coord_system_set),
325 2987 : _provided_coord_blocks(other_mesh._provided_coord_blocks),
326 29110 : _doing_p_refinement(other_mesh._doing_p_refinement)
327 : {
328 2987 : _bounds.resize(other_mesh._bounds.size());
329 3296 : for (std::size_t i = 0; i < _bounds.size(); ++i)
330 : {
331 309 : _bounds[i].resize(other_mesh._bounds[i].size());
332 927 : for (std::size_t j = 0; j < _bounds[i].size(); ++j)
333 618 : _bounds[i][j] = other_mesh._bounds[i][j];
334 : }
335 :
336 2987 : updateCoordTransform();
337 :
338 : #ifdef MOOSE_KOKKOS_ENABLED
339 2227 : if (_app.isKokkosAvailable())
340 2227 : _kokkos_mesh = std::make_unique<Moose::Kokkos::Mesh>(*this);
341 : #endif
342 2987 : }
343 :
344 65356 : MooseMesh::~MooseMesh()
345 : {
346 65356 : freeBndNodes();
347 65356 : freeBndElems();
348 65356 : clearQuadratureNodes();
349 65356 : }
350 :
351 : void
352 218826 : MooseMesh::freeBndNodes()
353 : {
354 : // free memory
355 12325728 : for (auto & bnode : _bnd_nodes)
356 12106902 : delete bnode;
357 :
358 812385 : for (auto & it : _node_set_nodes)
359 593559 : it.second.clear();
360 :
361 218826 : _node_set_nodes.clear();
362 :
363 812536 : for (auto & it : _bnd_node_ids)
364 593710 : it.second.clear();
365 :
366 218826 : _bnd_node_ids.clear();
367 218826 : _bnd_node_range.reset();
368 218826 : }
369 :
370 : void
371 218826 : MooseMesh::freeBndElems()
372 : {
373 : // free memory
374 9451807 : for (auto & belem : _bnd_elems)
375 9232981 : delete belem;
376 :
377 791708 : for (auto & it : _bnd_elem_ids)
378 572882 : it.second.clear();
379 :
380 218826 : _bnd_elem_ids.clear();
381 218826 : _bnd_elem_range.reset();
382 218826 : }
383 :
384 : bool
385 135861 : MooseMesh::prepare(const MeshBase * const mesh_to_clone)
386 : {
387 679305 : TIME_SECTION("prepare", 2, "Preparing Mesh", true);
388 :
389 : parallel_object_only();
390 :
391 135861 : bool libmesh_mesh_prepared = false;
392 :
393 : mooseAssert(_mesh, "The MeshBase has not been constructed");
394 :
395 135861 : if (!dynamic_cast<DistributedMesh *>(&getMesh()) || _is_nemesis)
396 : // For whatever reason we do not want to allow renumbering here nor ever in the future?
397 113129 : getMesh().allow_renumbering(false);
398 :
399 135861 : if (mesh_to_clone)
400 : {
401 : mooseAssert(mesh_to_clone->is_prepared(),
402 : "The mesh we wish to clone from must already be prepared");
403 149 : _mesh = mesh_to_clone->clone();
404 149 : _moose_mesh_prepared = false;
405 : }
406 135712 : else if (!_mesh->is_prepared())
407 : {
408 17835 : _mesh->complete_preparation();
409 17835 : _moose_mesh_prepared = false;
410 17835 : libmesh_mesh_prepared = true;
411 : }
412 :
413 135861 : if (_moose_mesh_prepared)
414 67999 : return libmesh_mesh_prepared;
415 :
416 : // Collect (local) subdomain IDs
417 67862 : _mesh_subdomains.clear();
418 13266664 : for (const auto & elem : getMesh().element_ptr_range())
419 13266664 : _mesh_subdomains.insert(elem->subdomain_id());
420 :
421 67862 : bool need_subdomain_name_map_sync = false;
422 : // add explicitly requested subdomains
423 203854 : if (isParamValid("add_subdomain_ids") && !isParamValid("add_subdomain_names"))
424 : {
425 : // only subdomain ids are explicitly given
426 72 : const auto & add_subdomain_id = getParam<std::vector<SubdomainID>>("add_subdomain_ids");
427 36 : _mesh_subdomains.insert(add_subdomain_id.begin(), add_subdomain_id.end());
428 : }
429 203674 : else if (isParamValid("add_subdomain_ids") && isParamValid("add_subdomain_names"))
430 : {
431 : const auto add_subdomain =
432 392 : getParam<SubdomainID, SubdomainName>("add_subdomain_ids", "add_subdomain_names");
433 244 : for (const auto & [sub_id, sub_name] : add_subdomain)
434 : {
435 : // add subdomain id
436 146 : _mesh_subdomains.insert(sub_id);
437 : // set name of the subdomain just added
438 146 : setSubdomainName(sub_id, sub_name);
439 : }
440 98 : need_subdomain_name_map_sync = true;
441 98 : }
442 203184 : else if (isParamValid("add_subdomain_names"))
443 : {
444 : // the user has defined add_subdomain_names, but not add_subdomain_ids
445 24 : const auto & add_subdomain_names = getParam<std::vector<SubdomainName>>("add_subdomain_names");
446 :
447 : // to define subdomain ids, we need the largest subdomain id defined yet.
448 12 : subdomain_id_type offset = 0;
449 12 : if (!_mesh_subdomains.empty())
450 12 : offset = *_mesh_subdomains.rbegin();
451 :
452 : // add all subdomains (and auto-assign ids)
453 48 : for (const SubdomainName & sub_name : add_subdomain_names)
454 : {
455 : // to avoid two subdomains with the same ID (notably on recover)
456 36 : if (getSubdomainID(sub_name) != libMesh::Elem::invalid_subdomain_id)
457 3 : continue;
458 33 : const auto sub_id = ++offset;
459 : // add subdomain id
460 33 : _mesh_subdomains.insert(sub_id);
461 : // set name of the subdomain just added
462 33 : setSubdomainName(sub_id, sub_name);
463 : }
464 12 : need_subdomain_name_map_sync = true;
465 : }
466 67862 : if (need_subdomain_name_map_sync)
467 110 : _mesh->sync_subdomain_name_map();
468 :
469 : // Make sure nodesets have been generated
470 67862 : buildNodeListFromSideList();
471 :
472 : // Collect (local) boundary IDs
473 67862 : const std::set<BoundaryID> & local_bids = getMesh().get_boundary_info().get_boundary_ids();
474 67862 : _mesh_boundary_ids.insert(local_bids.begin(), local_bids.end());
475 :
476 : const std::set<BoundaryID> & local_node_bids =
477 67862 : getMesh().get_boundary_info().get_node_boundary_ids();
478 67862 : _mesh_nodeset_ids.insert(local_node_bids.begin(), local_node_bids.end());
479 :
480 : const std::set<BoundaryID> & local_side_bids =
481 67862 : getMesh().get_boundary_info().get_side_boundary_ids();
482 67862 : _mesh_sideset_ids.insert(local_side_bids.begin(), local_side_bids.end());
483 :
484 : // Add explicitly requested sidesets/nodesets
485 : // This is done *after* the side boundaries (e.g. "right", ...) have been generated.
486 135724 : auto add_sets = [this](const bool sidesets, auto & set_ids)
487 : {
488 135724 : const std::string type = sidesets ? "sideset" : "nodeset";
489 135724 : const std::string id_param = "add_" + type + "_ids";
490 135724 : const std::string name_param = "add_" + type + "_names";
491 :
492 135724 : if (isParamValid(id_param))
493 : {
494 54 : const auto & add_ids = getParam<std::vector<BoundaryID>>(id_param);
495 54 : _mesh_boundary_ids.insert(add_ids.begin(), add_ids.end());
496 54 : set_ids.insert(add_ids.begin(), add_ids.end());
497 54 : if (isParamValid(name_param))
498 : {
499 42 : const auto & add_names = getParam<std::vector<BoundaryName>>(name_param);
500 : mooseAssert(add_names.size() == add_ids.size(),
501 : "Id and name sets must be the same size when adding.");
502 114 : for (const auto i : index_range(add_ids))
503 72 : setBoundaryName(add_ids[i], add_names[i]);
504 : }
505 : }
506 135670 : else if (isParamValid(name_param))
507 : {
508 : // the user has defined names, but not ids
509 12 : const auto & add_names = getParam<std::vector<BoundaryName>>(name_param);
510 :
511 12 : auto & mesh_ids = sidesets ? _mesh_sideset_ids : _mesh_nodeset_ids;
512 :
513 : // to define ids, we need the largest id defined yet.
514 12 : boundary_id_type offset = 0;
515 12 : if (!mesh_ids.empty())
516 12 : offset = *mesh_ids.rbegin();
517 12 : if (!_mesh_boundary_ids.empty())
518 12 : offset = std::max(offset, *_mesh_boundary_ids.rbegin());
519 :
520 : // add all sidesets/nodesets (and auto-assign ids)
521 24 : for (const auto & name : add_names)
522 : {
523 : // to avoid two sets with the same ID (notably on recover)
524 12 : if (getBoundaryID(name) != Moose::INVALID_BOUNDARY_ID)
525 1 : continue;
526 11 : const auto id = ++offset;
527 : // add sideset id
528 11 : _mesh_boundary_ids.insert(id);
529 11 : set_ids.insert(id);
530 : // set name of the sideset just added
531 11 : setBoundaryName(id, name);
532 : }
533 : }
534 135724 : };
535 :
536 67862 : add_sets(true, _mesh_sideset_ids);
537 67862 : add_sets(false, _mesh_nodeset_ids);
538 :
539 : // Communicate subdomain and boundary IDs if this is a parallel mesh
540 67862 : if (!getMesh().is_serial())
541 : {
542 8820 : _communicator.set_union(_mesh_subdomains);
543 8820 : _communicator.set_union(_mesh_boundary_ids);
544 8820 : _communicator.set_union(_mesh_nodeset_ids);
545 8820 : _communicator.set_union(_mesh_sideset_ids);
546 : }
547 :
548 67862 : if (!_built_from_other_mesh)
549 : {
550 65049 : if (!_coord_system_set)
551 194925 : setCoordSystem(_provided_coord_blocks, getParam<MultiMooseEnum>("coord_type"));
552 222 : else if (_pars.isParamSetByUser("coord_type"))
553 0 : mooseError(
554 : "Trying to set coordinate system type information based on the user input file, but "
555 : "the coordinate system type information has already been set programmatically! "
556 : "Either remove your coordinate system type information from the input file, or contact "
557 : "your application developer");
558 : }
559 :
560 : // Set general axisymmetric axes if provided
561 271499 : if (isParamValid("rz_coord_blocks") && isParamValid("rz_coord_origins") &&
562 67913 : isParamValid("rz_coord_directions"))
563 : {
564 34 : const auto rz_coord_blocks = getParam<std::vector<SubdomainName>>("rz_coord_blocks");
565 34 : const auto rz_coord_origins = getParam<std::vector<Point>>("rz_coord_origins");
566 34 : const auto rz_coord_directions = getParam<std::vector<RealVectorValue>>("rz_coord_directions");
567 34 : if (rz_coord_origins.size() == rz_coord_blocks.size() &&
568 17 : rz_coord_directions.size() == rz_coord_blocks.size())
569 : {
570 17 : std::vector<std::pair<Point, RealVectorValue>> rz_coord_axes;
571 58 : for (unsigned int i = 0; i < rz_coord_origins.size(); ++i)
572 41 : rz_coord_axes.push_back(std::make_pair(rz_coord_origins[i], rz_coord_directions[i]));
573 :
574 17 : setGeneralAxisymmetricCoordAxes(rz_coord_blocks, rz_coord_axes);
575 :
576 51 : if (isParamSetByUser("rz_coord_axis"))
577 0 : mooseError("The parameter 'rz_coord_axis' may not be provided if 'rz_coord_blocks', "
578 : "'rz_coord_origins', and 'rz_coord_directions' are provided.");
579 17 : }
580 : else
581 0 : mooseError("The parameters 'rz_coord_blocks', 'rz_coord_origins', and "
582 : "'rz_coord_directions' must all have the same size.");
583 17 : }
584 474915 : else if (isParamValid("rz_coord_blocks") || isParamValid("rz_coord_origins") ||
585 271380 : isParamValid("rz_coord_directions"))
586 0 : mooseError("If any of the parameters 'rz_coord_blocks', 'rz_coord_origins', and "
587 : "'rz_coord_directions' are provided, then all must be provided.");
588 :
589 67862 : detectOrthogonalDimRanges();
590 :
591 67862 : update();
592 :
593 : // Check if there is subdomain name duplication for the same subdomain ID
594 67862 : checkDuplicateSubdomainNames();
595 :
596 67859 : _moose_mesh_prepared = true;
597 :
598 67859 : return libmesh_mesh_prepared;
599 135858 : }
600 :
601 : bool
602 153470 : MooseMesh::possiblyRebuildNodeToElemMap()
603 : {
604 : // *Rebuild* the node to element map. I emphasize rebuild because if it has not been built
605 : // previously we won't do anything
606 153470 : if (!_node_to_elem_map_built)
607 : {
608 : mooseAssert(_node_to_elem_map.empty(), "If it hasn't been built, it better well be empty");
609 145695 : return false;
610 : }
611 :
612 7775 : _node_to_elem_map.clear();
613 7775 : _node_to_elem_map_built = false;
614 7775 : internalNodeToElemMap();
615 7775 : return true;
616 : }
617 :
618 : void
619 153470 : MooseMesh::update()
620 : {
621 767350 : TIME_SECTION("update", 3, "Updating Mesh", true);
622 :
623 : // Rebuild the boundary conditions
624 153470 : buildNodeListFromSideList();
625 :
626 153470 : buildNodeList();
627 153470 : buildBndElemList();
628 153470 : cacheInfo();
629 153470 : buildElemIDInfo();
630 :
631 : // this will make moose mesh aware of p-refinement added by mesh generators including
632 : // a file mesh generator loading a restart checkpoint file
633 153470 : _max_p_level = 0;
634 153470 : _max_h_level = 0;
635 27661945 : for (const auto & elem : getMesh().active_local_element_ptr_range())
636 : {
637 27508475 : if (elem->p_level() > _max_p_level)
638 658 : _max_p_level = elem->p_level();
639 27508475 : if (elem->level() > _max_h_level)
640 25506 : _max_h_level = elem->level();
641 153470 : }
642 153470 : comm().max(_max_p_level);
643 153470 : comm().max(_max_h_level);
644 :
645 : // the flag might have been set by calling doingPRefinement(true)
646 153470 : _doing_p_refinement = _doing_p_refinement || (_max_p_level > 0);
647 :
648 153470 : computeMaxPerElemAndSide();
649 :
650 : #ifdef MOOSE_KOKKOS_ENABLED
651 127363 : if (_app.getExecutioner() && _app.feProblem().initialized() &&
652 12589 : _app.feProblem().hasKokkosObjects())
653 0 : _kokkos_mesh->update();
654 : #endif
655 :
656 153470 : _finite_volume_info_dirty = true;
657 :
658 153470 : possiblyRebuildNodeToElemMap();
659 153470 : }
660 :
661 : void
662 205 : MooseMesh::buildLowerDMesh()
663 : {
664 205 : auto & mesh = getMesh();
665 :
666 205 : if (!mesh.is_serial())
667 0 : mooseError(
668 : "Hybrid finite element method must use replicated mesh.\nCurrently lower-dimensional mesh "
669 : "does not support mesh re-partitioning and a debug assertion being hit related with "
670 : "neighbors of lower-dimensional element, with distributed mesh.");
671 :
672 : // Lower-D element build requires neighboring element information
673 205 : if (!mesh.is_prepared())
674 194 : mesh.find_neighbors();
675 :
676 : // maximum number of sides of all elements
677 205 : unsigned int max_n_sides = 0;
678 :
679 : // remove existing lower-d element first
680 205 : std::set<Elem *> deleteable_elems;
681 4347 : for (auto & elem : mesh.element_ptr_range())
682 4142 : if (_lower_d_interior_blocks.count(elem->subdomain_id()) ||
683 2071 : _lower_d_boundary_blocks.count(elem->subdomain_id()))
684 0 : deleteable_elems.insert(elem);
685 2071 : else if (elem->n_sides() > max_n_sides)
686 410 : max_n_sides = elem->n_sides();
687 :
688 205 : for (auto & elem : deleteable_elems)
689 0 : mesh.delete_elem(elem);
690 205 : for (const auto & id : _lower_d_interior_blocks)
691 0 : _mesh_subdomains.erase(id);
692 205 : for (const auto & id : _lower_d_boundary_blocks)
693 0 : _mesh_subdomains.erase(id);
694 205 : _lower_d_interior_blocks.clear();
695 205 : _lower_d_boundary_blocks.clear();
696 :
697 205 : mesh.comm().max(max_n_sides);
698 :
699 205 : deleteable_elems.clear();
700 :
701 : // get all side types
702 205 : std::set<int> interior_side_types;
703 205 : std::set<int> boundary_side_types;
704 4347 : for (const auto & elem : mesh.active_element_ptr_range())
705 11173 : for (const auto side : elem->side_index_range())
706 : {
707 9102 : Elem * neig = elem->neighbor_ptr(side);
708 9102 : std::unique_ptr<Elem> side_elem(elem->build_side_ptr(side));
709 9102 : if (neig)
710 5956 : interior_side_types.insert(side_elem->type());
711 : else
712 3146 : boundary_side_types.insert(side_elem->type());
713 9307 : }
714 205 : mesh.comm().set_union(interior_side_types);
715 205 : mesh.comm().set_union(boundary_side_types);
716 :
717 : // assign block ids for different side types
718 205 : std::map<ElemType, SubdomainID> interior_block_ids;
719 205 : std::map<ElemType, SubdomainID> boundary_block_ids;
720 : // we assume this id is not used by the mesh
721 205 : auto id = libMesh::Elem::invalid_subdomain_id - 2;
722 424 : for (const auto & tpid : interior_side_types)
723 : {
724 219 : const auto type = ElemType(tpid);
725 219 : mesh.subdomain_name(id) = "INTERNAL_SIDE_LOWERD_SUBDOMAIN_" + Utility::enum_to_string(type);
726 219 : interior_block_ids[type] = id;
727 219 : _lower_d_interior_blocks.insert(id);
728 219 : if (_mesh_subdomains.count(id) > 0)
729 0 : mooseError("Trying to add a mesh block with id ", id, " that has existed in the mesh");
730 219 : _mesh_subdomains.insert(id);
731 219 : --id;
732 : }
733 424 : for (const auto & tpid : boundary_side_types)
734 : {
735 219 : const auto type = ElemType(tpid);
736 219 : mesh.subdomain_name(id) = "BOUNDARY_SIDE_LOWERD_SUBDOMAIN_" + Utility::enum_to_string(type);
737 219 : boundary_block_ids[type] = id;
738 219 : _lower_d_boundary_blocks.insert(id);
739 219 : if (_mesh_subdomains.count(id) > 0)
740 0 : mooseError("Trying to add a mesh block with id ", id, " that has existed in the mesh");
741 219 : _mesh_subdomains.insert(id);
742 219 : --id;
743 : }
744 :
745 205 : dof_id_type max_elem_id = mesh.max_elem_id();
746 205 : unique_id_type max_unique_id = mesh.parallel_max_unique_id();
747 :
748 205 : std::vector<Elem *> side_elems;
749 205 : _higher_d_elem_side_to_lower_d_elem.clear();
750 4347 : for (const auto & elem : mesh.active_element_ptr_range())
751 : {
752 : // skip existing lower-d elements
753 2071 : if (elem->interior_parent())
754 0 : continue;
755 :
756 11173 : for (const auto side : elem->side_index_range())
757 : {
758 9102 : Elem * neig = elem->neighbor_ptr(side);
759 :
760 9102 : bool build_side = false;
761 9102 : if (!neig)
762 3146 : build_side = true;
763 : else
764 : {
765 : mooseAssert(!neig->is_remote(), "We error if the mesh is not serial");
766 5956 : if (!neig->active())
767 0 : build_side = true;
768 5956 : else if (neig->level() == elem->level() && elem->id() < neig->id())
769 2978 : build_side = true;
770 : }
771 :
772 9102 : if (build_side)
773 : {
774 6124 : std::unique_ptr<Elem> side_elem(elem->build_side_ptr(side));
775 :
776 : // The side will be added with the same processor id as the parent.
777 6124 : side_elem->processor_id() = elem->processor_id();
778 :
779 : // Add subdomain ID
780 6124 : if (neig)
781 2978 : side_elem->subdomain_id() = interior_block_ids.at(side_elem->type());
782 : else
783 3146 : side_elem->subdomain_id() = boundary_block_ids.at(side_elem->type());
784 :
785 : // set ids consistently across processors (these ids will be temporary)
786 6124 : side_elem->set_id(max_elem_id + elem->id() * max_n_sides + side);
787 6124 : side_elem->set_unique_id(max_unique_id + elem->id() * max_n_sides + side);
788 :
789 : // Also assign the side's interior parent, so it is always
790 : // easy to figure out the Elem we came from.
791 : // Note: the interior parent could be a ghost element.
792 6124 : side_elem->set_interior_parent(elem);
793 :
794 6124 : side_elems.push_back(side_elem.release());
795 :
796 : // add link between higher d element to lower d element
797 6124 : auto pair = std::make_pair(elem, side);
798 6124 : auto link = std::make_pair(pair, side_elems.back());
799 6124 : auto ilink = std::make_pair(side_elems.back(), side);
800 6124 : _lower_d_elem_to_higher_d_elem_side.insert(ilink);
801 6124 : _higher_d_elem_side_to_lower_d_elem.insert(link);
802 6124 : }
803 : }
804 205 : }
805 :
806 : // finally, add the lower-dimensional element to the mesh
807 : // Note: lower-d interior element will exist on a processor if its associated interior
808 : // parent exists on a processor whether or not being a ghost. Lower-d elements will
809 : // get its interior parent's processor id.
810 6329 : for (auto & elem : side_elems)
811 6124 : mesh.add_elem(elem);
812 :
813 : // we do all the stuff in prepare_for_use such as renumber_nodes_and_elements(),
814 : // update_parallel_id_counts(), cache_elem_dims(), etc. except partitioning here.
815 205 : const bool skip_partitioning_old = mesh.skip_partitioning();
816 205 : mesh.skip_partitioning(true);
817 : // Finding neighbors is ambiguous for lower-dimensional elements on interior faces
818 205 : mesh.allow_find_neighbors(false);
819 205 : mesh.prepare_for_use();
820 205 : mesh.skip_partitioning(skip_partitioning_old);
821 205 : }
822 :
823 : const Node &
824 0 : MooseMesh::node(const dof_id_type i) const
825 : {
826 0 : mooseDeprecated("MooseMesh::node() is deprecated, please use MooseMesh::nodeRef() instead");
827 0 : return nodeRef(i);
828 : }
829 :
830 : Node &
831 0 : MooseMesh::node(const dof_id_type i)
832 : {
833 0 : mooseDeprecated("MooseMesh::node() is deprecated, please use MooseMesh::nodeRef() instead");
834 0 : return nodeRef(i);
835 : }
836 :
837 : const Node &
838 42687596 : MooseMesh::nodeRef(const dof_id_type i) const
839 : {
840 42687596 : const auto node_ptr = queryNodePtr(i);
841 : mooseAssert(node_ptr, "Missing node");
842 42687596 : return *node_ptr;
843 : }
844 :
845 : Node &
846 24014864 : MooseMesh::nodeRef(const dof_id_type i)
847 : {
848 24014864 : return const_cast<Node &>(const_cast<const MooseMesh *>(this)->nodeRef(i));
849 : }
850 :
851 : const Node *
852 0 : MooseMesh::nodePtr(const dof_id_type i) const
853 : {
854 0 : return &nodeRef(i);
855 : }
856 :
857 : Node *
858 2096 : MooseMesh::nodePtr(const dof_id_type i)
859 : {
860 2096 : return &nodeRef(i);
861 : }
862 :
863 : const Node *
864 42690340 : MooseMesh::queryNodePtr(const dof_id_type i) const
865 : {
866 42690340 : if (i > getMesh().max_node_id())
867 : {
868 196773 : auto it = _quadrature_nodes.find(i);
869 196773 : if (it == _quadrature_nodes.end())
870 0 : return nullptr;
871 196773 : auto & node_ptr = it->second;
872 : mooseAssert(node_ptr, "Uninitialized quadrature node");
873 196773 : return node_ptr;
874 : }
875 :
876 42493567 : return getMesh().query_node_ptr(i);
877 : }
878 :
879 : Node *
880 2744 : MooseMesh::queryNodePtr(const dof_id_type i)
881 : {
882 2744 : return const_cast<Node *>(const_cast<const MooseMesh *>(this)->queryNodePtr(i));
883 : }
884 :
885 : void
886 82973 : MooseMesh::meshChanged()
887 : {
888 414865 : TIME_SECTION("meshChanged", 3, "Updating Because Mesh Changed");
889 :
890 82973 : update();
891 :
892 : // Delete all of the cached ranges
893 82973 : _active_local_elem_range.reset();
894 82973 : _active_node_range.reset();
895 82973 : _active_semilocal_node_range.reset();
896 82973 : _local_node_range.reset();
897 82973 : _bnd_node_range.reset();
898 82973 : _bnd_elem_range.reset();
899 :
900 : // Rebuild the ranges
901 82973 : getActiveLocalElementRange();
902 82973 : getActiveNodeRange();
903 82973 : getLocalNodeRange();
904 82973 : getBoundaryNodeRange();
905 82973 : getBoundaryElementRange();
906 :
907 : // Call the callback function onMeshChanged
908 82973 : onMeshChanged();
909 82973 : }
910 :
911 : void
912 82973 : MooseMesh::onMeshChanged()
913 : {
914 82973 : }
915 :
916 : void
917 208 : MooseMesh::cacheChangedLists()
918 : {
919 1040 : TIME_SECTION("cacheChangedLists", 5, "Caching Changed Lists");
920 :
921 208 : ConstElemRange elem_range(getMesh().local_elements_begin(), getMesh().local_elements_end(), 1);
922 208 : CacheChangedListsThread cclt(*this);
923 208 : Threads::parallel_reduce(elem_range, cclt);
924 :
925 208 : _coarsened_element_children.clear();
926 :
927 416 : _refined_elements = std::make_unique<ConstElemPointerRange>(cclt._refined_elements.begin(),
928 416 : cclt._refined_elements.end());
929 416 : _coarsened_elements = std::make_unique<ConstElemPointerRange>(cclt._coarsened_elements.begin(),
930 416 : cclt._coarsened_elements.end());
931 208 : _coarsened_element_children = cclt._coarsened_element_children;
932 208 : }
933 :
934 : ConstElemPointerRange *
935 208 : MooseMesh::refinedElementRange() const
936 : {
937 208 : return _refined_elements.get();
938 : }
939 :
940 : ConstElemPointerRange *
941 208 : MooseMesh::coarsenedElementRange() const
942 : {
943 208 : return _coarsened_elements.get();
944 : }
945 :
946 : const std::vector<const Elem *> &
947 2468 : MooseMesh::coarsenedElementChildren(const Elem * elem) const
948 : {
949 2468 : auto elem_to_child_pair = _coarsened_element_children.find(elem);
950 : mooseAssert(elem_to_child_pair != _coarsened_element_children.end(), "Missing element in map");
951 4936 : return elem_to_child_pair->second;
952 : }
953 :
954 : void
955 70995 : MooseMesh::updateActiveSemiLocalNodeRange(std::set<dof_id_type> & ghosted_elems)
956 : {
957 354975 : TIME_SECTION("updateActiveSemiLocalNodeRange", 5, "Updating ActiveSemiLocalNode Range");
958 :
959 70995 : _semilocal_node_list.clear();
960 :
961 : // First add the nodes connected to local elems
962 70995 : ConstElemRange * active_local_elems = getActiveLocalElementRange();
963 13021418 : for (const auto & elem : *active_local_elems)
964 : {
965 81739045 : for (unsigned int n = 0; n < elem->n_nodes(); ++n)
966 : {
967 : // Since elem is const here but we require a non-const Node * to
968 : // store in the _semilocal_node_list (otherwise things like
969 : // UpdateDisplacedMeshThread don't work), we are using a
970 : // const_cast. A more long-term fix would be to have
971 : // getActiveLocalElementRange return a non-const ElemRange.
972 68788622 : Node * node = const_cast<Node *>(elem->node_ptr(n));
973 :
974 68788622 : _semilocal_node_list.insert(node);
975 : }
976 : }
977 :
978 : // Now add the nodes connected to ghosted_elems
979 116206 : for (const auto & ghost_elem_id : ghosted_elems)
980 : {
981 45211 : Elem * elem = getMesh().elem_ptr(ghost_elem_id);
982 250228 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
983 : {
984 205017 : Node * node = elem->node_ptr(n);
985 :
986 205017 : _semilocal_node_list.insert(node);
987 : }
988 : }
989 :
990 : // Now create the actual range
991 141990 : _active_semilocal_node_range = std::make_unique<SemiLocalNodeRange>(_semilocal_node_list.begin(),
992 141990 : _semilocal_node_list.end());
993 70995 : }
994 :
995 : bool
996 26313 : MooseMesh::isSemiLocal(Node * const node) const
997 : {
998 26313 : return _semilocal_node_list.find(node) != _semilocal_node_list.end();
999 : }
1000 :
1001 : /**
1002 : * Helper class for sorting Boundary Nodes so that we always get the same
1003 : * order of application for boundary conditions.
1004 : */
1005 : class BndNodeCompare
1006 : {
1007 : public:
1008 153470 : BndNodeCompare() {}
1009 :
1010 118488277 : bool operator()(const BndNode * const & lhs, const BndNode * const & rhs)
1011 : {
1012 118488277 : if (lhs->_bnd_id < rhs->_bnd_id)
1013 22144427 : return true;
1014 :
1015 96343850 : if (lhs->_bnd_id > rhs->_bnd_id)
1016 10071488 : return false;
1017 :
1018 86272362 : if (lhs->_node->id() < rhs->_node->id())
1019 55725377 : return true;
1020 :
1021 30546985 : if (lhs->_node->id() > rhs->_node->id())
1022 30546985 : return false;
1023 :
1024 0 : return false;
1025 : }
1026 : };
1027 :
1028 : void
1029 153470 : MooseMesh::buildNodeList()
1030 : {
1031 767350 : TIME_SECTION("buildNodeList", 5, "Building Node List");
1032 :
1033 153470 : freeBndNodes();
1034 :
1035 153470 : auto bc_tuples = getMesh().get_boundary_info().build_node_list();
1036 :
1037 153470 : int n = bc_tuples.size();
1038 153470 : _bnd_nodes.clear();
1039 153470 : _bnd_nodes.reserve(n);
1040 12386213 : for (const auto & t : bc_tuples)
1041 : {
1042 12232743 : auto node_id = std::get<0>(t);
1043 12232743 : auto bc_id = std::get<1>(t);
1044 :
1045 12232743 : _bnd_nodes.push_back(new BndNode(getMesh().node_ptr(node_id), bc_id));
1046 12232743 : _node_set_nodes[bc_id].push_back(node_id);
1047 12232743 : _bnd_node_ids[bc_id].insert(node_id);
1048 : }
1049 :
1050 153470 : _bnd_nodes.reserve(_bnd_nodes.size() + _extra_bnd_nodes.size());
1051 153524 : for (unsigned int i = 0; i < _extra_bnd_nodes.size(); i++)
1052 : {
1053 54 : BndNode * bnode = new BndNode(_extra_bnd_nodes[i]._node, _extra_bnd_nodes[i]._bnd_id);
1054 54 : _bnd_nodes.push_back(bnode);
1055 54 : _bnd_node_ids[std::get<1>(bc_tuples[i])].insert(_extra_bnd_nodes[i]._node->id());
1056 : }
1057 :
1058 : // This sort is here so that boundary conditions are always applied in the same order
1059 153470 : std::sort(_bnd_nodes.begin(), _bnd_nodes.end(), BndNodeCompare());
1060 153470 : }
1061 :
1062 : void
1063 153470 : MooseMesh::computeMaxPerElemAndSide()
1064 : {
1065 153470 : auto & mesh = getMesh();
1066 :
1067 153470 : _max_sides_per_elem = 0;
1068 153470 : _max_nodes_per_elem = 0;
1069 153470 : _max_nodes_per_side = 0;
1070 :
1071 59328570 : for (auto & elem : as_range(mesh.local_elements_begin(), mesh.local_elements_end()))
1072 : {
1073 29587550 : _max_sides_per_elem = std::max(_max_sides_per_elem, elem->n_sides());
1074 29587550 : _max_nodes_per_elem = std::max(_max_nodes_per_elem, elem->n_nodes());
1075 :
1076 161717602 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
1077 132130052 : _max_nodes_per_side = std::max(_max_nodes_per_side, elem->side_ptr(side)->n_nodes());
1078 153470 : }
1079 :
1080 153470 : mesh.comm().max(_max_sides_per_elem);
1081 153470 : mesh.comm().max(_max_nodes_per_elem);
1082 153470 : mesh.comm().max(_max_nodes_per_side);
1083 153470 : }
1084 :
1085 : void
1086 153470 : MooseMesh::buildElemIDInfo()
1087 : {
1088 153470 : unsigned int n = getMesh().n_elem_integers() + 1;
1089 :
1090 153470 : _block_id_mapping.clear();
1091 153470 : _max_ids.clear();
1092 153470 : _min_ids.clear();
1093 153470 : _id_identical_flag.clear();
1094 :
1095 153470 : _block_id_mapping.resize(n);
1096 153470 : _max_ids.resize(n, std::numeric_limits<dof_id_type>::min());
1097 153470 : _min_ids.resize(n, std::numeric_limits<dof_id_type>::max());
1098 306940 : _id_identical_flag.resize(n, std::vector<bool>(n, true));
1099 27661945 : for (const auto & elem : getMesh().active_local_element_ptr_range())
1100 59138249 : for (unsigned int i = 0; i < n; ++i)
1101 : {
1102 31629774 : auto id = (i == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(i));
1103 31629774 : _block_id_mapping[i][elem->subdomain_id()].insert(id);
1104 31629774 : if (id > _max_ids[i])
1105 117455 : _max_ids[i] = id;
1106 31629774 : if (id < _min_ids[i])
1107 158357 : _min_ids[i] = id;
1108 76190074 : for (unsigned int j = 0; j < n; ++j)
1109 : {
1110 44560300 : auto idj = (j == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(j));
1111 44560300 : if (i != j && _id_identical_flag[i][j] && id != idj)
1112 6718 : _id_identical_flag[i][j] = false;
1113 : }
1114 153470 : }
1115 :
1116 309365 : for (unsigned int i = 0; i < n; ++i)
1117 : {
1118 379041 : for (auto & blk : meshSubdomains())
1119 223146 : comm().set_union(_block_id_mapping[i][blk]);
1120 155895 : comm().min(_id_identical_flag[i]);
1121 : }
1122 153470 : comm().max(_max_ids);
1123 153470 : comm().min(_min_ids);
1124 153470 : }
1125 :
1126 : std::unordered_map<dof_id_type, std::set<dof_id_type>>
1127 11 : MooseMesh::getElemIDMapping(const std::string & from_id_name, const std::string & to_id_name) const
1128 : {
1129 11 : auto & mesh_base = getMesh();
1130 :
1131 11 : if (!mesh_base.has_elem_integer(from_id_name))
1132 0 : mooseError("Mesh does not have the element integer name '", from_id_name, "'");
1133 11 : if (!mesh_base.has_elem_integer(to_id_name))
1134 0 : mooseError("Mesh does not have the element integer name '", to_id_name, "'");
1135 :
1136 11 : const auto id1 = mesh_base.get_elem_integer_index(from_id_name);
1137 11 : const auto id2 = mesh_base.get_elem_integer_index(to_id_name);
1138 :
1139 11 : std::unordered_map<dof_id_type, std::set<dof_id_type>> id_map;
1140 33 : for (const auto id : getAllElemIDs(id1))
1141 33 : id_map[id] = std::set<dof_id_type>();
1142 :
1143 811 : for (const auto & elem : mesh_base.active_local_element_ptr_range())
1144 811 : id_map[elem->get_extra_integer(id1)].insert(elem->get_extra_integer(id2));
1145 :
1146 33 : for (auto & [id, ids] : id_map)
1147 : {
1148 22 : libmesh_ignore(id); // avoid overzealous gcc 9.4 unused var warning
1149 22 : comm().set_union(ids);
1150 : }
1151 :
1152 11 : return id_map;
1153 0 : }
1154 :
1155 : std::set<dof_id_type>
1156 50 : MooseMesh::getAllElemIDs(unsigned int elem_id_index) const
1157 : {
1158 50 : std::set<dof_id_type> unique_ids;
1159 139 : for (auto & pair : _block_id_mapping[elem_id_index])
1160 319 : for (auto & id : pair.second)
1161 230 : unique_ids.insert(id);
1162 50 : return unique_ids;
1163 0 : }
1164 :
1165 : std::set<dof_id_type>
1166 152 : MooseMesh::getElemIDsOnBlocks(unsigned int elem_id_index, const std::set<SubdomainID> & blks) const
1167 : {
1168 152 : std::set<dof_id_type> unique_ids;
1169 379 : for (auto & blk : blks)
1170 : {
1171 227 : auto it = _block_id_mapping[elem_id_index].find(blk);
1172 227 : if (it == _block_id_mapping[elem_id_index].end())
1173 0 : mooseError("Block ", blk, " is not available on the mesh");
1174 :
1175 532 : for (auto & mid : it->second)
1176 305 : unique_ids.insert(mid);
1177 : }
1178 152 : return unique_ids;
1179 0 : }
1180 :
1181 : void
1182 153470 : MooseMesh::buildBndElemList()
1183 : {
1184 767350 : TIME_SECTION("buildBndElemList", 5, "Building Boundary Elements List");
1185 :
1186 153470 : freeBndElems();
1187 :
1188 153470 : auto bc_tuples = getMesh().get_boundary_info().build_active_side_list();
1189 :
1190 153470 : int n = bc_tuples.size();
1191 153470 : _bnd_elems.clear();
1192 153470 : _bnd_elems.reserve(n);
1193 9499335 : for (const auto & t : bc_tuples)
1194 : {
1195 9345865 : auto elem_id = std::get<0>(t);
1196 9345865 : auto side_id = std::get<1>(t);
1197 9345865 : auto bc_id = std::get<2>(t);
1198 :
1199 9345865 : _bnd_elems.push_back(new BndElement(getMesh().elem_ptr(elem_id), side_id, bc_id));
1200 9345865 : _bnd_elem_ids[bc_id].insert(elem_id);
1201 : }
1202 153470 : }
1203 :
1204 : std::unordered_map<dof_id_type, std::vector<dof_id_type>> &
1205 966827 : MooseMesh::internalNodeToElemMap()
1206 : {
1207 966827 : if (!_node_to_elem_map_built) // Guard the creation with a double checked lock
1208 : {
1209 11634 : Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
1210 :
1211 11634 : if (!_node_to_elem_map_built)
1212 : {
1213 : // This is allowing the timing to be run even with threads
1214 : // This is safe because all threads will be waiting on this section when it runs
1215 : // NOTE: Do not copy this construction to other places without thinking REALLY hard about it
1216 : // The PerfGraph is NOT threadsafe and will cause all kinds of havok if care isn't taken
1217 11634 : auto in_threads = Threads::in_threads;
1218 11634 : Threads::in_threads = false;
1219 58170 : TIME_SECTION("nodeToElemMap", 5, "Building Node To Elem Map");
1220 11634 : Threads::in_threads = in_threads;
1221 :
1222 : mooseAssert(_node_to_elem_map.empty(), "Expected empty map before building");
1223 2850522 : for (const auto & elem : getMesh().active_element_ptr_range())
1224 16865975 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
1225 14038721 : _node_to_elem_map[elem->node_id(n)].push_back(elem->id());
1226 :
1227 11634 : _node_to_elem_map_built = true; // MUST be set at the end for double-checked locking to work!
1228 11634 : }
1229 11634 : }
1230 966827 : return _node_to_elem_map;
1231 : }
1232 :
1233 : const std::unordered_map<dof_id_type, std::vector<dof_id_type>> &
1234 953695 : MooseMesh::nodeToElemMap()
1235 : {
1236 953695 : return internalNodeToElemMap();
1237 : }
1238 :
1239 : ConstElemRange *
1240 10368482 : MooseMesh::getActiveLocalElementRange()
1241 : {
1242 10368482 : if (!_active_local_elem_range)
1243 : {
1244 423807 : TIME_SECTION("getActiveLocalElementRange", 5);
1245 :
1246 282538 : _active_local_elem_range = std::make_unique<ConstElemRange>(
1247 423807 : getMesh().active_local_elements_begin(), getMesh().active_local_elements_end());
1248 141269 : }
1249 :
1250 10368482 : return _active_local_elem_range.get();
1251 : }
1252 :
1253 : NodeRange *
1254 83037 : MooseMesh::getActiveNodeRange()
1255 : {
1256 83037 : if (!_active_node_range)
1257 : {
1258 248919 : TIME_SECTION("getActiveNodeRange", 5);
1259 :
1260 : _active_node_range =
1261 82973 : std::make_unique<NodeRange>(getMesh().active_nodes_begin(), getMesh().active_nodes_end());
1262 82973 : }
1263 :
1264 83037 : return _active_node_range.get();
1265 : }
1266 :
1267 : SemiLocalNodeRange *
1268 0 : MooseMesh::getActiveSemiLocalNodeRange() const
1269 : {
1270 : mooseAssert(_active_semilocal_node_range,
1271 : "_active_semilocal_node_range has not been created yet!");
1272 :
1273 0 : return _active_semilocal_node_range.get();
1274 : }
1275 :
1276 : ConstNodeRange *
1277 315741 : MooseMesh::getLocalNodeRange()
1278 : {
1279 315741 : if (!_local_node_range)
1280 : {
1281 248919 : TIME_SECTION("getLocalNodeRange", 5);
1282 :
1283 165946 : _local_node_range = std::make_unique<ConstNodeRange>(getMesh().local_nodes_begin(),
1284 248919 : getMesh().local_nodes_end());
1285 82973 : }
1286 :
1287 315741 : return _local_node_range.get();
1288 : }
1289 :
1290 : ConstBndNodeRange *
1291 3669320 : MooseMesh::getBoundaryNodeRange()
1292 : {
1293 3669320 : if (!_bnd_node_range)
1294 : {
1295 249435 : TIME_SECTION("getBoundaryNodeRange", 5);
1296 :
1297 83145 : _bnd_node_range = std::make_unique<ConstBndNodeRange>(bndNodesBegin(), bndNodesEnd());
1298 83145 : }
1299 :
1300 3669320 : return _bnd_node_range.get();
1301 : }
1302 :
1303 : ConstBndElemRange *
1304 187258 : MooseMesh::getBoundaryElementRange()
1305 : {
1306 187258 : if (!_bnd_elem_range)
1307 : {
1308 248919 : TIME_SECTION("getBoundaryElementRange", 5);
1309 :
1310 82973 : _bnd_elem_range = std::make_unique<ConstBndElemRange>(bndElemsBegin(), bndElemsEnd());
1311 82973 : }
1312 :
1313 187258 : return _bnd_elem_range.get();
1314 : }
1315 :
1316 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1317 0 : MooseMesh::getBoundariesToElems() const
1318 : {
1319 0 : mooseDeprecated("MooseMesh::getBoundariesToElems is deprecated, "
1320 : "use MooseMesh::getBoundariesToActiveSemiLocalElemIds");
1321 0 : return getBoundariesToActiveSemiLocalElemIds();
1322 : }
1323 :
1324 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1325 61 : MooseMesh::getBoundariesToActiveSemiLocalElemIds() const
1326 : {
1327 61 : return _bnd_elem_ids;
1328 : }
1329 :
1330 : std::unordered_set<dof_id_type>
1331 2963 : MooseMesh::getBoundaryActiveSemiLocalElemIds(BoundaryID bid) const
1332 : {
1333 : // The boundary to element map is computed on every mesh update
1334 2963 : const auto it = _bnd_elem_ids.find(bid);
1335 2963 : if (it == _bnd_elem_ids.end())
1336 : // Boundary is not local to this domain, return an empty set
1337 94 : return std::unordered_set<dof_id_type>{};
1338 2869 : return it->second;
1339 : }
1340 :
1341 : std::unordered_set<dof_id_type>
1342 0 : MooseMesh::getBoundaryActiveNeighborElemIds(BoundaryID bid) const
1343 : {
1344 : // Vector of boundary elems is updated every mesh update
1345 0 : std::unordered_set<dof_id_type> neighbor_elems;
1346 0 : for (const auto & bnd_elem : _bnd_elems)
1347 : {
1348 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1349 0 : if (elem_bid == bid)
1350 : {
1351 0 : const auto * neighbor = elem_ptr->neighbor_ptr(elem_side);
1352 : // Dont add fully remote elements, ghosted is fine
1353 0 : if (neighbor && neighbor != libMesh::remote_elem)
1354 : {
1355 : // handle mesh refinement, only return active elements near the boundary
1356 0 : if (neighbor->active())
1357 0 : neighbor_elems.insert(neighbor->id());
1358 : else
1359 : {
1360 0 : std::vector<const Elem *> family;
1361 0 : neighbor->active_family_tree_by_neighbor(family, elem_ptr);
1362 0 : for (const auto & child_neighbor : family)
1363 0 : neighbor_elems.insert(child_neighbor->id());
1364 0 : }
1365 : }
1366 : }
1367 : }
1368 :
1369 0 : return neighbor_elems;
1370 0 : }
1371 :
1372 : bool
1373 0 : MooseMesh::isBoundaryFullyExternalToSubdomains(BoundaryID bid,
1374 : const std::set<SubdomainID> & blk_group) const
1375 : {
1376 : mooseAssert(_bnd_elem_range, "Boundary element range is not initialized");
1377 :
1378 : // Loop over all side elements of the mesh, select those on the boundary
1379 0 : for (const auto & bnd_elem : *_bnd_elem_range)
1380 : {
1381 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1382 0 : if (elem_bid == bid)
1383 : {
1384 : // If an element is internal to the group of subdomain, check the neighbor
1385 0 : if (blk_group.find(elem_ptr->subdomain_id()) != blk_group.end())
1386 : {
1387 0 : const auto * const neighbor = elem_ptr->neighbor_ptr(elem_side);
1388 :
1389 : // If we did not ghost the neighbor, we cannot decide
1390 0 : if (neighbor == libMesh::remote_elem)
1391 0 : mooseError("Insufficient level of geometrical ghosting to determine "
1392 : "if a boundary is internal to the mesh");
1393 : // If the neighbor does not exist, then we are on the edge of the mesh
1394 0 : if (!neighbor)
1395 0 : continue;
1396 : // If the neighbor is also in the group of subdomain,
1397 : // then the boundary cuts the subdomains
1398 0 : if (blk_group.find(neighbor->subdomain_id()) != blk_group.end())
1399 0 : return false;
1400 : }
1401 : }
1402 : }
1403 0 : return true;
1404 : }
1405 :
1406 : void
1407 153470 : MooseMesh::cacheInfo()
1408 : {
1409 460410 : TIME_SECTION("cacheInfo", 3);
1410 :
1411 153470 : _sub_to_data.clear();
1412 153470 : _neighbor_subdomain_boundary_ids.clear();
1413 153470 : _block_node_list.clear();
1414 153470 : _higher_d_elem_side_to_lower_d_elem.clear();
1415 153470 : _lower_d_elem_to_higher_d_elem_side.clear();
1416 153470 : _lower_d_interior_blocks.clear();
1417 153470 : _lower_d_boundary_blocks.clear();
1418 :
1419 153470 : const auto & mesh = getMesh();
1420 :
1421 : // Cache higher and lowerD element information
1422 38119446 : for (const auto & elem : mesh.element_ptr_range())
1423 : {
1424 37965976 : const Elem * ip_elem = elem->interior_parent();
1425 :
1426 37965976 : if (ip_elem)
1427 : {
1428 73327 : unsigned int ip_side = ip_elem->which_side_am_i(elem);
1429 :
1430 : // For some grid sequencing tests: ip_side == libMesh::invalid_uint
1431 73327 : if (ip_side != libMesh::invalid_uint)
1432 : {
1433 73167 : auto pair = std::make_pair(ip_elem, ip_side);
1434 73167 : _higher_d_elem_side_to_lower_d_elem.insert(
1435 73167 : std::pair<std::pair<const Elem *, unsigned short int>, const Elem *>(pair, elem));
1436 73167 : _lower_d_elem_to_higher_d_elem_side.insert(
1437 73167 : std::pair<const Elem *, unsigned short int>(elem, ip_side));
1438 :
1439 73167 : auto id = elem->subdomain_id();
1440 73167 : if (ip_elem->neighbor_ptr(ip_side))
1441 : {
1442 6680 : if (mesh.subdomain_name(id).find("INTERNAL_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1443 6580 : _lower_d_interior_blocks.insert(id);
1444 : }
1445 : else
1446 : {
1447 66487 : if (mesh.subdomain_name(id).find("BOUNDARY_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1448 6890 : _lower_d_boundary_blocks.insert(id);
1449 : }
1450 : }
1451 : }
1452 :
1453 241766744 : for (unsigned int nd = 0; nd < elem->n_nodes(); ++nd)
1454 : {
1455 203800768 : const Node & node = *elem->node_ptr(nd);
1456 203800768 : _block_node_list[node.id()].insert(elem->subdomain_id());
1457 : }
1458 153470 : }
1459 153470 : _communicator.set_union(_lower_d_interior_blocks);
1460 153470 : _communicator.set_union(_lower_d_boundary_blocks);
1461 :
1462 : // Cache the boundaries next to each subdomain
1463 27661945 : for (const auto & elem : mesh.active_local_element_ptr_range())
1464 : {
1465 27508475 : SubdomainID subdomain_id = elem->subdomain_id();
1466 27508475 : auto & sub_data = _sub_to_data[subdomain_id];
1467 27508475 : const auto elem_boundary_ids = getBoundaryIDs(elem);
1468 151253731 : for (unsigned int side = 0; side < elem->n_sides(); side++)
1469 : {
1470 123745256 : const auto & boundary_ids = elem_boundary_ids[side];
1471 123745256 : sub_data.boundary_ids.insert(boundary_ids.begin(), boundary_ids.end());
1472 :
1473 123745256 : const Elem * neig = elem->neighbor_ptr(side);
1474 123745256 : if (neig)
1475 : {
1476 116636785 : _neighbor_subdomain_boundary_ids[neig->subdomain_id()].insert(boundary_ids.begin(),
1477 : boundary_ids.end());
1478 116636785 : SubdomainID neighbor_subdomain_id = neig->subdomain_id();
1479 116636785 : if (neighbor_subdomain_id != subdomain_id)
1480 1818116 : sub_data.neighbor_subs.insert(neighbor_subdomain_id);
1481 : }
1482 : }
1483 27661945 : }
1484 :
1485 370408 : for (const auto blk_id : _mesh_subdomains)
1486 : {
1487 216938 : auto & sub_data = _sub_to_data[blk_id];
1488 216938 : _communicator.set_union(sub_data.neighbor_subs);
1489 216938 : _communicator.set_union(sub_data.boundary_ids);
1490 216938 : _communicator.set_union(_neighbor_subdomain_boundary_ids[blk_id]);
1491 : }
1492 153470 : }
1493 :
1494 : const std::set<SubdomainID> &
1495 95327261 : MooseMesh::getNodeBlockIds(const Node & node) const
1496 : {
1497 95327261 : auto it = _block_node_list.find(node.id());
1498 :
1499 95327261 : if (it == _block_node_list.end())
1500 0 : mooseError("Unable to find node: ", node.id(), " in any block list.");
1501 :
1502 190654522 : return it->second;
1503 : }
1504 :
1505 : MooseMesh::face_info_iterator
1506 165335 : MooseMesh::ownedFaceInfoBegin()
1507 : {
1508 : return face_info_iterator(
1509 165335 : _face_info.begin(),
1510 165335 : _face_info.end(),
1511 330670 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1512 : }
1513 :
1514 : MooseMesh::face_info_iterator
1515 165335 : MooseMesh::ownedFaceInfoEnd()
1516 : {
1517 : return face_info_iterator(
1518 165335 : _face_info.end(),
1519 165335 : _face_info.end(),
1520 330670 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1521 : }
1522 :
1523 : MooseMesh::elem_info_iterator
1524 85539 : MooseMesh::ownedElemInfoBegin()
1525 : {
1526 85539 : return elem_info_iterator(_elem_info.begin(),
1527 85539 : _elem_info.end(),
1528 171078 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1529 : }
1530 :
1531 : MooseMesh::elem_info_iterator
1532 85539 : MooseMesh::ownedElemInfoEnd()
1533 : {
1534 85539 : return elem_info_iterator(_elem_info.end(),
1535 85539 : _elem_info.end(),
1536 171078 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1537 : }
1538 :
1539 : // default begin() accessor
1540 : MooseMesh::bnd_node_iterator
1541 85410 : MooseMesh::bndNodesBegin()
1542 : {
1543 85410 : Predicates::NotNull<bnd_node_iterator_imp> p;
1544 170820 : return bnd_node_iterator(_bnd_nodes.begin(), _bnd_nodes.end(), p);
1545 85410 : }
1546 :
1547 : // default end() accessor
1548 : MooseMesh::bnd_node_iterator
1549 85410 : MooseMesh::bndNodesEnd()
1550 : {
1551 85410 : Predicates::NotNull<bnd_node_iterator_imp> p;
1552 170820 : return bnd_node_iterator(_bnd_nodes.end(), _bnd_nodes.end(), p);
1553 85410 : }
1554 :
1555 : // default begin() accessor
1556 : MooseMesh::bnd_elem_iterator
1557 83127 : MooseMesh::bndElemsBegin()
1558 : {
1559 83127 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1560 166254 : return bnd_elem_iterator(_bnd_elems.begin(), _bnd_elems.end(), p);
1561 83127 : }
1562 :
1563 : // default end() accessor
1564 : MooseMesh::bnd_elem_iterator
1565 83127 : MooseMesh::bndElemsEnd()
1566 : {
1567 83127 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1568 166254 : return bnd_elem_iterator(_bnd_elems.end(), _bnd_elems.end(), p);
1569 83127 : }
1570 :
1571 : const Node *
1572 0 : MooseMesh::addUniqueNode(const Point & p, Real tol)
1573 : {
1574 : /**
1575 : * Looping through the mesh nodes each time we add a point is very slow. To speed things
1576 : * up we keep a local data structure
1577 : */
1578 0 : if (getMesh().n_nodes() != _node_map.size())
1579 : {
1580 0 : _node_map.clear();
1581 0 : _node_map.reserve(getMesh().n_nodes());
1582 0 : for (const auto & node : getMesh().node_ptr_range())
1583 0 : _node_map.push_back(node);
1584 : }
1585 :
1586 0 : Node * node = nullptr;
1587 0 : for (unsigned int i = 0; i < _node_map.size(); ++i)
1588 : {
1589 0 : if (p.relative_fuzzy_equals(*_node_map[i], tol))
1590 : {
1591 0 : node = _node_map[i];
1592 0 : break;
1593 : }
1594 : }
1595 0 : if (node == nullptr)
1596 : {
1597 0 : node = getMesh().add_node(new Node(p));
1598 0 : _node_map.push_back(node);
1599 : }
1600 :
1601 : mooseAssert(node != nullptr, "Node is NULL");
1602 0 : return node;
1603 : }
1604 :
1605 : Node *
1606 5357 : MooseMesh::addQuadratureNode(const Elem * elem,
1607 : const unsigned short int side,
1608 : const unsigned int qp,
1609 : BoundaryID bid,
1610 : const Point & point)
1611 : {
1612 : Node * qnode;
1613 :
1614 5357 : if (_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) ==
1615 10714 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end())
1616 : {
1617 : // Create a new node id starting from the max node id and counting down. This will be the least
1618 : // likely to collide with an existing node id.
1619 : // Note that we are using numeric_limits<unsigned>::max even
1620 : // though max_id is stored as a dof_id_type. I tried this with
1621 : // numeric_limits<dof_id_type>::max and it broke several tests in
1622 : // MOOSE. So, this is some kind of a magic number that we will
1623 : // just continue to use...
1624 5357 : dof_id_type max_id = std::numeric_limits<unsigned int>::max() - 100;
1625 5357 : dof_id_type new_id = max_id - _quadrature_nodes.size();
1626 :
1627 5357 : if (new_id <= getMesh().max_node_id())
1628 0 : mooseError("Quadrature node id collides with existing node id!");
1629 :
1630 5357 : qnode = new Node(point, new_id);
1631 :
1632 : // Keep track of this new node in two different ways for easy lookup
1633 5357 : _quadrature_nodes[new_id] = qnode;
1634 5357 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp] = qnode;
1635 :
1636 5357 : if (elem->active())
1637 5357 : internalNodeToElemMap()[new_id].push_back(elem->id());
1638 : }
1639 : else
1640 0 : qnode = _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1641 :
1642 5357 : BndNode * bnode = new BndNode(qnode, bid);
1643 5357 : _bnd_nodes.push_back(bnode);
1644 5357 : _bnd_node_ids[bid].insert(qnode->id());
1645 :
1646 5357 : _extra_bnd_nodes.push_back(*bnode);
1647 :
1648 : // Do this so the range will be regenerated next time it is accessed
1649 5357 : _bnd_node_range.reset();
1650 :
1651 5357 : return qnode;
1652 : }
1653 :
1654 : Node *
1655 137880 : MooseMesh::getQuadratureNode(const Elem * elem,
1656 : const unsigned short int side,
1657 : const unsigned int qp)
1658 : {
1659 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes.find(elem->id()) !=
1660 : _elem_to_side_to_qp_to_quadrature_nodes.end(),
1661 : "Elem has no quadrature nodes!");
1662 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()].find(side) !=
1663 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()].end(),
1664 : "Side has no quadrature nodes!");
1665 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) !=
1666 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end(),
1667 : "qp not found on side!");
1668 :
1669 137880 : return _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1670 : }
1671 :
1672 : void
1673 73516 : MooseMesh::clearQuadratureNodes()
1674 : {
1675 : // Delete all the quadrature nodes
1676 78861 : for (auto & it : _quadrature_nodes)
1677 5345 : delete it.second;
1678 :
1679 73516 : _quadrature_nodes.clear();
1680 73516 : _elem_to_side_to_qp_to_quadrature_nodes.clear();
1681 73516 : _extra_bnd_nodes.clear();
1682 :
1683 : // NOTE: this does not clear them from the nodeToElem map
1684 73516 : }
1685 :
1686 : BoundaryID
1687 361088 : MooseMesh::getBoundaryID(const BoundaryName & boundary_name) const
1688 : {
1689 361088 : if (boundary_name == "ANY_BOUNDARY_ID")
1690 0 : mooseError("Please use getBoundaryIDs() when passing \"ANY_BOUNDARY_ID\"");
1691 :
1692 361088 : return MooseMeshUtils::getBoundaryID(boundary_name, getMesh());
1693 : }
1694 :
1695 : const Elem *
1696 1577719579 : MooseMesh::getLowerDElem(const Elem * elem, unsigned short int side) const
1697 : {
1698 1577719579 : auto it = _higher_d_elem_side_to_lower_d_elem.find(std::make_pair(elem, side));
1699 :
1700 1577719579 : if (it != _higher_d_elem_side_to_lower_d_elem.end())
1701 231516 : return it->second;
1702 : else
1703 1577488063 : return nullptr;
1704 : }
1705 :
1706 : unsigned int
1707 260 : MooseMesh::getHigherDSide(const Elem * elem) const
1708 : {
1709 260 : auto it = _lower_d_elem_to_higher_d_elem_side.find(elem);
1710 :
1711 260 : if (it != _lower_d_elem_to_higher_d_elem_side.end())
1712 260 : return it->second;
1713 : else
1714 0 : return libMesh::invalid_uint;
1715 : }
1716 :
1717 : std::vector<BoundaryID>
1718 116137 : MooseMesh::getBoundaryIDs(const std::vector<BoundaryName> & boundary_name,
1719 : bool generate_unknown) const
1720 : {
1721 : return MooseMeshUtils::getBoundaryIDs(
1722 116137 : getMesh(), boundary_name, generate_unknown, _mesh_boundary_ids);
1723 : }
1724 :
1725 : SubdomainID
1726 346216 : MooseMesh::getSubdomainID(const SubdomainName & subdomain_name) const
1727 : {
1728 346216 : return MooseMeshUtils::getSubdomainID(subdomain_name, getMesh());
1729 : }
1730 :
1731 : std::vector<SubdomainID>
1732 236564 : MooseMesh::getSubdomainIDs(const std::vector<SubdomainName> & subdomain_name) const
1733 : {
1734 236564 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1735 : }
1736 :
1737 : std::set<SubdomainID>
1738 0 : MooseMesh::getSubdomainIDs(const std::set<SubdomainName> & subdomain_name) const
1739 : {
1740 0 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1741 : }
1742 :
1743 : void
1744 253 : MooseMesh::setSubdomainName(SubdomainID subdomain_id, const SubdomainName & name)
1745 : {
1746 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1747 253 : getMesh().subdomain_name(subdomain_id) = name;
1748 253 : }
1749 :
1750 : void
1751 0 : MooseMesh::setSubdomainName(MeshBase & mesh, SubdomainID subdomain_id, const SubdomainName & name)
1752 : {
1753 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1754 0 : mesh.subdomain_name(subdomain_id) = name;
1755 0 : }
1756 :
1757 : const std::string &
1758 4308531 : MooseMesh::getSubdomainName(SubdomainID subdomain_id) const
1759 : {
1760 4308531 : return getMesh().subdomain_name(subdomain_id);
1761 : }
1762 :
1763 : std::vector<SubdomainName>
1764 71 : MooseMesh::getSubdomainNames(const std::vector<SubdomainID> & subdomain_ids) const
1765 : {
1766 71 : std::vector<SubdomainName> names(subdomain_ids.size());
1767 :
1768 142 : for (unsigned int i = 0; i < subdomain_ids.size(); i++)
1769 71 : names[i] = getSubdomainName(subdomain_ids[i]);
1770 :
1771 71 : return names;
1772 0 : }
1773 :
1774 : void
1775 110 : MooseMesh::setBoundaryName(BoundaryID boundary_id, BoundaryName name)
1776 : {
1777 110 : BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1778 :
1779 : // We need to figure out if this boundary is a sideset or nodeset
1780 110 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1781 30 : boundary_info.sideset_name(boundary_id) = name;
1782 : else
1783 80 : boundary_info.nodeset_name(boundary_id) = name;
1784 110 : }
1785 :
1786 : const std::string &
1787 7478876 : MooseMesh::getBoundaryName(const BoundaryID boundary_id) const
1788 : {
1789 7478876 : const BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1790 :
1791 : // We need to figure out if this boundary is a sideset or nodeset
1792 7478876 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1793 7358506 : return boundary_info.get_sideset_name(boundary_id);
1794 : else
1795 120370 : return boundary_info.get_nodeset_name(boundary_id);
1796 : }
1797 :
1798 : std::string
1799 27 : MooseMesh::getBoundaryString(BoundaryID boundary_id) const
1800 : {
1801 27 : const auto name = getBoundaryName(boundary_id);
1802 54 : return name.size() ? name : std::to_string(boundary_id);
1803 27 : }
1804 :
1805 : // specialization for PointListAdaptor<MooseMesh::PeriodicNodeInfo>
1806 : template <>
1807 : inline const Point &
1808 173430 : PointListAdaptor<MooseMesh::PeriodicNodeInfo>::getPoint(
1809 : const MooseMesh::PeriodicNodeInfo & item) const
1810 : {
1811 173430 : return *(item.first);
1812 : }
1813 :
1814 : void
1815 27 : MooseMesh::buildPeriodicNodeMap(std::multimap<dof_id_type, dof_id_type> & periodic_node_map,
1816 : unsigned int var_number,
1817 : libMesh::PeriodicBoundaries * pbs) const
1818 : {
1819 81 : TIME_SECTION("buildPeriodicNodeMap", 5);
1820 :
1821 : // clear existing map
1822 27 : periodic_node_map.clear();
1823 :
1824 : // get periodic nodes
1825 27 : std::vector<PeriodicNodeInfo> periodic_nodes;
1826 1575 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1827 : {
1828 : // unfortunately libMesh does not give us a pointer, so we have to look it up ourselves
1829 1548 : auto node = _mesh->node_ptr(std::get<0>(t));
1830 : mooseAssert(node != nullptr,
1831 : "libMesh::BoundaryInfo::build_node_list() returned an ID for a non-existing node");
1832 1548 : auto bc_id = std::get<1>(t);
1833 1548 : periodic_nodes.emplace_back(node, bc_id);
1834 27 : }
1835 :
1836 : // sort by boundary id
1837 27 : std::sort(periodic_nodes.begin(),
1838 : periodic_nodes.end(),
1839 8658 : [](const PeriodicNodeInfo & a, const PeriodicNodeInfo & b) -> bool
1840 8658 : { return a.second > b.second; });
1841 :
1842 : // build kd-tree
1843 : using KDTreeType = nanoflann::KDTreeSingleIndexAdaptor<
1844 : nanoflann::L2_Simple_Adaptor<Real, PointListAdaptor<PeriodicNodeInfo>, Real, std::size_t>,
1845 : PointListAdaptor<PeriodicNodeInfo>,
1846 : LIBMESH_DIM,
1847 : std::size_t>;
1848 27 : const unsigned int max_leaf_size = 20; // slightly affects runtime
1849 : auto point_list =
1850 27 : PointListAdaptor<PeriodicNodeInfo>(periodic_nodes.begin(), periodic_nodes.end());
1851 : auto kd_tree = std::make_unique<KDTreeType>(
1852 27 : LIBMESH_DIM, point_list, nanoflann::KDTreeSingleIndexAdaptorParams(max_leaf_size));
1853 : mooseAssert(kd_tree != nullptr, "KDTree was not properly initialized.");
1854 27 : kd_tree->buildIndex();
1855 :
1856 : // data structures for kd-tree search
1857 27 : nanoflann::SearchParameters search_params;
1858 27 : std::vector<nanoflann::ResultItem<std::size_t, Real>> ret_matches;
1859 :
1860 : // iterate over periodic nodes (boundary ids are in contiguous blocks)
1861 27 : libMesh::PeriodicBoundaryBase * periodic = nullptr;
1862 27 : BoundaryID current_bc_id = BoundaryInfo::invalid_id;
1863 1575 : for (auto & pair : periodic_nodes)
1864 : {
1865 : // entering a new block of boundary IDs
1866 1548 : if (pair.second != current_bc_id)
1867 : {
1868 108 : current_bc_id = pair.second;
1869 108 : periodic = pbs->boundary(current_bc_id);
1870 108 : if (periodic && !periodic->is_my_variable(var_number))
1871 0 : periodic = nullptr;
1872 : }
1873 :
1874 : // variable is not periodic at this node, skip
1875 1548 : if (!periodic)
1876 0 : continue;
1877 :
1878 : // clear result buffer
1879 1548 : ret_matches.clear();
1880 :
1881 : // id of the current node
1882 1548 : const auto id = pair.first->id();
1883 :
1884 : // position where we expect a periodic partner for the current node and boundary
1885 1548 : Point search_point = periodic->get_corresponding_pos(*pair.first);
1886 :
1887 : // search at the expected point
1888 1548 : kd_tree->radiusSearch(&(search_point)(0), libMesh::TOLERANCE, ret_matches, search_params);
1889 4248 : for (auto & match_pair : ret_matches)
1890 : {
1891 2700 : const auto & match = periodic_nodes[match_pair.first];
1892 : // add matched node if the boundary id is the corresponding id in the periodic pair
1893 2700 : if (match.second == periodic->pairedboundary)
1894 1548 : periodic_node_map.emplace(id, match.first->id());
1895 : }
1896 : }
1897 27 : }
1898 :
1899 : void
1900 0 : MooseMesh::buildPeriodicNodeSets(std::map<BoundaryID, std::set<dof_id_type>> & periodic_node_sets,
1901 : unsigned int var_number,
1902 : libMesh::PeriodicBoundaries * pbs) const
1903 : {
1904 0 : TIME_SECTION("buildPeriodicNodeSets", 5);
1905 :
1906 0 : periodic_node_sets.clear();
1907 :
1908 : // Loop over all the boundary nodes adding the periodic nodes to the appropriate set
1909 0 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1910 : {
1911 0 : auto node_id = std::get<0>(t);
1912 0 : auto bc_id = std::get<1>(t);
1913 :
1914 : // Is this current node on a known periodic boundary?
1915 0 : if (periodic_node_sets.find(bc_id) != periodic_node_sets.end())
1916 0 : periodic_node_sets[bc_id].insert(node_id);
1917 : else // This still might be a periodic node but we just haven't seen this boundary_id yet
1918 : {
1919 0 : const libMesh::PeriodicBoundaryBase * periodic = pbs->boundary(bc_id);
1920 0 : if (periodic && periodic->is_my_variable(var_number))
1921 0 : periodic_node_sets[bc_id].insert(node_id);
1922 : }
1923 0 : }
1924 0 : }
1925 :
1926 : bool
1927 67964 : MooseMesh::detectOrthogonalDimRanges(Real tol)
1928 : {
1929 203892 : TIME_SECTION("detectOrthogonalDimRanges", 5);
1930 :
1931 67964 : if (_regular_orthogonal_mesh)
1932 34350 : return true;
1933 :
1934 33614 : std::vector<Real> min(3, std::numeric_limits<Real>::max());
1935 33614 : std::vector<Real> max(3, std::numeric_limits<Real>::min());
1936 33614 : unsigned int dim = getMesh().mesh_dimension();
1937 :
1938 : // Find the bounding box of our mesh
1939 10092451 : for (const auto & node : getMesh().node_ptr_range())
1940 : // Check all coordinates, we don't know if this mesh might be lying in a higher dim even if the
1941 : // mesh dimension is lower.
1942 40235348 : for (const auto i : make_range(Moose::dim))
1943 : {
1944 30176511 : if ((*node)(i) < min[i])
1945 205419 : min[i] = (*node)(i);
1946 30176511 : if ((*node)(i) > max[i])
1947 453469 : max[i] = (*node)(i);
1948 33614 : }
1949 :
1950 33614 : this->comm().max(max);
1951 33614 : this->comm().min(min);
1952 :
1953 33614 : _extreme_nodes.resize(8); // 2^LIBMESH_DIM
1954 : // Now make sure that there are actual nodes at all of the extremes
1955 33614 : std::vector<bool> extreme_matches(8, false);
1956 33614 : std::vector<unsigned int> comp_map(3);
1957 10092451 : for (const auto & node : getMesh().node_ptr_range())
1958 : {
1959 : // See if the current node is located at one of the extremes
1960 10058837 : unsigned int coord_match = 0;
1961 :
1962 40235348 : for (const auto i : make_range(Moose::dim))
1963 : {
1964 30176511 : if (std::abs((*node)(i)-min[i]) < tol)
1965 : {
1966 6337969 : comp_map[i] = MIN;
1967 6337969 : ++coord_match;
1968 : }
1969 23838542 : else if (std::abs((*node)(i)-max[i]) < tol)
1970 : {
1971 1371472 : comp_map[i] = MAX;
1972 1371472 : ++coord_match;
1973 : }
1974 : }
1975 :
1976 10058837 : if (coord_match == LIBMESH_DIM) // Found a coordinate at one of the extremes
1977 : {
1978 121985 : _extreme_nodes[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = node;
1979 121985 : extreme_matches[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = true;
1980 : }
1981 33614 : }
1982 :
1983 : // See if we matched all of the extremes for the mesh dimension
1984 33614 : this->comm().max(extreme_matches);
1985 33614 : if (std::count(extreme_matches.begin(), extreme_matches.end(), true) == (1 << dim))
1986 29316 : _regular_orthogonal_mesh = true;
1987 :
1988 : // Set the bounds
1989 33614 : _bounds.resize(LIBMESH_DIM);
1990 134456 : for (const auto i : make_range(Moose::dim))
1991 : {
1992 100842 : _bounds[i].resize(2);
1993 100842 : _bounds[i][MIN] = min[i];
1994 100842 : _bounds[i][MAX] = max[i];
1995 : }
1996 :
1997 33614 : return _regular_orthogonal_mesh;
1998 67964 : }
1999 :
2000 : void
2001 538 : MooseMesh::detectPairedSidesets()
2002 : {
2003 1614 : TIME_SECTION("detectPairedSidesets", 5);
2004 :
2005 538 : _paired_boundary = std::vector<std::pair<BoundaryID, BoundaryID>>();
2006 :
2007 : // Loop over level-0 elements (since boundary condition information
2008 : // is only directly stored for them) and find sidesets with normals
2009 : // that point in the -x, +x, -y, +y, and -z, +z direction. If there
2010 : // is a unique sideset id for each direction, then the paired
2011 : // sidesets consist of (-x,+x), (-y,+y), (-z,+z). If there are
2012 : // multiple sideset ids for a given direction, then we can't pick a
2013 : // single pair for that direction. In that case, we'll just return
2014 : // as was done in the original algorithm.
2015 :
2016 : // we need to test all element dimensions from dim down to 1
2017 538 : const unsigned int mesh_dim = getMesh().mesh_dimension();
2018 :
2019 : // Helper for iterating through unit dimensions (0=x, 1=y, 2=z)
2020 : static constexpr std::array<std::size_t, 3> unit_dims{0, 1, 2};
2021 : // Helper for mapping from unit dim -> name
2022 1614 : static const std::array<std::string, 3> unit_dim_names{"x", "y", "z"};
2023 :
2024 : // Boundary id sets for elements of different dimensions
2025 : // First index: side dimension; 0=1D, 1=2D, 2=3D
2026 : // Second index: unit dimension; 0=x, 1=y, 2=z
2027 : // Third index: false for minus, true for plus
2028 16678 : std::array<std::array<std::array<std::set<BoundaryID>, 2>, 3>, 3> ids{};
2029 :
2030 : // Build quadrature needed to evaluate side normals
2031 538 : std::array<std::unique_ptr<FEBase>, 3> fe_faces{};
2032 538 : std::array<std::unique_ptr<libMesh::QGauss>, 3> qfaces{};
2033 1596 : for (const auto side_dim : make_range(mesh_dim))
2034 : {
2035 : // Face is assumed to be flat, therefore normal is assumed to be
2036 : // constant over the face, therefore only compute it at 1 qp.
2037 1058 : qfaces[side_dim] = std::unique_ptr<libMesh::QGauss>(new libMesh::QGauss(side_dim, CONSTANT));
2038 :
2039 : // A first-order Lagrange FE for the face.
2040 1058 : fe_faces[side_dim] = FEBase::build(side_dim + 1, FEType(FIRST, libMesh::LAGRANGE));
2041 1058 : fe_faces[side_dim]->attach_quadrature_rule(qfaces[side_dim].get());
2042 1058 : fe_faces[side_dim]->get_normals();
2043 : }
2044 :
2045 : // Get boundary IDs for each dimension that are in the unit normal
2046 538 : const auto & boundary_info = getMesh().get_boundary_info();
2047 : // Temporary for evaluating boundary_ids
2048 538 : std::vector<boundary_id_type> face_ids;
2049 : // The side dimensions we've come across, so that we only report
2050 : // warnings for side dimensions that we have
2051 538 : std::set<unsigned int> side_dims;
2052 : // Normal dimensions that we found that were nonzero; lets us
2053 : // skip warnings for dimensions that we don't have
2054 538 : std::array<bool, 3> nonzero_dims = periodic_dim_default;
2055 336871 : for (auto & elem : as_range(getMesh().level_elements_begin(0), getMesh().level_elements_end(0)))
2056 : {
2057 : // If not on the boundary, nothing to do
2058 336333 : if (!elem->on_boundary())
2059 286656 : continue;
2060 :
2061 49677 : const auto side_dim = elem->dim() - 1;
2062 49677 : side_dims.insert(side_dim);
2063 :
2064 : // Check for unit normals on each boundary side
2065 276146 : for (const auto s : elem->side_index_range())
2066 226469 : if (!elem->neighbor_ptr(s))
2067 : {
2068 : // Reinit to get the normal
2069 55092 : fe_faces[side_dim]->reinit(elem, s);
2070 55092 : const auto & normal = fe_faces[side_dim]->get_normals()[0];
2071 :
2072 : // Get the boundary ID(s) for this side. If there is more
2073 : // than 1 boundary id, then we already can't determine a
2074 : // unique pairing of sides in this direction, but we'll just
2075 : // keep going to keep the logic simple.
2076 55092 : boundary_info.boundary_ids(elem, s, face_ids);
2077 :
2078 55092 : bool found = false;
2079 220368 : for (const auto unit_dim : unit_dims)
2080 : {
2081 165276 : if (libMesh::absolute_fuzzy_equals(normal(unit_dim), 0.0))
2082 108284 : continue;
2083 56992 : nonzero_dims[unit_dim] = true;
2084 56992 : if (!found)
2085 91312 : for (const auto plus : {false, true})
2086 : {
2087 87512 : if (libMesh::absolute_fuzzy_equals(normal(unit_dim), plus ? 1.0 : -1.0))
2088 : {
2089 53192 : ids[side_dim][unit_dim][plus].insert(face_ids.begin(), face_ids.end());
2090 53192 : found = true;
2091 53192 : break;
2092 : }
2093 : }
2094 : }
2095 : }
2096 538 : }
2097 :
2098 : // For a distributed mesh, boundaries may be distributed as well. We therefore collect information
2099 : // from everyone. If the mesh is already serial, then there is no need to do an allgather. Note
2100 : // that this is just going to gather information about what the periodic bc ids are. We are not
2101 : // gathering any remote elements or anything like that. It's just that the GhostPointNeighbors
2102 : // ghosting functor currently relies on the fact that every process agrees on whether we have
2103 : // periodic boundaries; every process that thinks there are periodic boundaries will call
2104 : // MeshBase::sub_point_locator which makes a parallel_object_only() assertion (right or wrong). So
2105 : // we all need to go there (or not go there)
2106 538 : if (_use_distributed_mesh && !_mesh->is_serial())
2107 : {
2108 : // Communicate id data by packing as [side dim, unit dim, plus (as a char), boundary id]
2109 122 : std::vector<std::tuple<unsigned int, unsigned int, unsigned char, boundary_id_type>> id_data;
2110 244 : for (const auto side_dim : side_dims)
2111 488 : for (const auto unit_dim : unit_dims)
2112 1098 : for (const auto plus : {false, true})
2113 1192 : for (const auto bd : ids[side_dim][unit_dim][plus])
2114 460 : id_data.emplace_back(side_dim, unit_dim, plus, bd);
2115 122 : _communicator.allgather(id_data, false);
2116 1170 : for (const auto & [side_dim, unit_dim, plus_char, bd] : id_data)
2117 1048 : ids[side_dim][unit_dim][bool(plus_char)].insert(bd);
2118 :
2119 : // Gather true-ness of nonzero_dims
2120 488 : for (auto & entry : nonzero_dims)
2121 366 : _communicator.max(entry);
2122 :
2123 : // Gather found side dimensions
2124 122 : _communicator.set_union(side_dims);
2125 122 : } // end if (_use_distributed_mesh && !_need_ghost_ghosted_boundaries)
2126 :
2127 : // Find pairings that have exactly one boundary on each side
2128 538 : std::ostringstream oss_found, oss_missing;
2129 1076 : for (const auto side_dim : side_dims)
2130 : {
2131 2152 : for (const auto unit_dim : unit_dims)
2132 1614 : if (nonzero_dims[unit_dim])
2133 : {
2134 1061 : const auto & unit_name = unit_dim_names[unit_dim];
2135 1061 : const auto & minus = ids[side_dim][unit_dim][false];
2136 1061 : const auto & plus = ids[side_dim][unit_dim][true];
2137 :
2138 1061 : if (minus.size() == 1 && plus.size() == 1)
2139 : {
2140 1904 : const auto get_boundary_name = [this](const auto id)
2141 : {
2142 1904 : const auto & name = getBoundaryName(id);
2143 1904 : return name.size() ? name : std::to_string(id);
2144 952 : };
2145 :
2146 952 : oss_found << "\n " << side_dim + 1 << "D " << unit_name
2147 952 : << "-direction: " << get_boundary_name(*minus.begin()) << " <-> "
2148 1904 : << get_boundary_name(*plus.begin());
2149 952 : _paired_boundary->emplace_back(std::make_pair(*minus.begin(), *plus.begin()));
2150 : }
2151 : else
2152 109 : oss_missing << "\n " << side_dim + 1 << "D -" << unit_name << "/+" << unit_name
2153 109 : << ": Found " << minus.size() << " -" << unit_name << " boundaries and "
2154 109 : << plus.size() << " +" << unit_name << " boundaries";
2155 : }
2156 : }
2157 :
2158 538 : std::ostringstream oss;
2159 538 : const auto found = oss_found.str();
2160 538 : const auto missing = oss_missing.str();
2161 538 : if (found.size())
2162 : oss << "The following paired boundaries were automatically detected for periodicity:\n"
2163 504 : << found << "\n";
2164 538 : if (missing.size())
2165 : {
2166 75 : if (found.size())
2167 41 : oss << "\n";
2168 : oss << "Paired boundaries were not automatically detected for the following:\n"
2169 : << missing
2170 : << "\n\nAutomatic detection requires that exactly one boundary is found in each unit "
2171 75 : "direction.\n";
2172 : }
2173 :
2174 538 : mooseInfoRepeated(oss.str());
2175 538 : }
2176 :
2177 : Real
2178 72688 : MooseMesh::dimensionWidth(unsigned int component) const
2179 : {
2180 72688 : return getMaxInDimension(component) - getMinInDimension(component);
2181 : }
2182 :
2183 : Real
2184 33299 : MooseMesh::getMinInDimension(unsigned int component) const
2185 : {
2186 : mooseAssert(_mesh, "The MeshBase has not been constructed");
2187 : mooseAssert(component < _bounds.size(), "Requested dimension out of bounds");
2188 :
2189 33299 : return _bounds[component][MIN];
2190 : }
2191 :
2192 : Real
2193 33299 : MooseMesh::getMaxInDimension(unsigned int component) const
2194 : {
2195 : mooseAssert(_mesh, "The MeshBase has not been constructed");
2196 : mooseAssert(component < _bounds.size(), "Requested dimension out of bounds");
2197 :
2198 33299 : return _bounds[component][MAX];
2199 : }
2200 :
2201 : void
2202 873 : MooseMesh::addPeriodicVariable(const unsigned int sys_num,
2203 : const unsigned int var_num,
2204 : const BoundaryID primary,
2205 : const BoundaryID secondary)
2206 : {
2207 873 : if (!_regular_orthogonal_mesh)
2208 0 : return;
2209 :
2210 873 : const auto key = std::make_pair(sys_num, var_num);
2211 873 : auto & entry = _periodic_dim.try_emplace(key, periodic_dim_default).first->second;
2212 :
2213 873 : _half_range = Point(dimensionWidth(0) / 2.0, dimensionWidth(1) / 2.0, dimensionWidth(2) / 2.0);
2214 :
2215 873 : bool component_found = false;
2216 2707 : for (const auto component : make_range(dimension()))
2217 : {
2218 1834 : const std::pair<BoundaryID, BoundaryID> * boundary_ids = getPairedBoundaryMapping(component);
2219 :
2220 1834 : if (boundary_ids && ((boundary_ids->first == primary && boundary_ids->second == secondary) ||
2221 976 : (boundary_ids->first == secondary && boundary_ids->second == primary)))
2222 : {
2223 858 : entry[component] = true;
2224 858 : component_found = true;
2225 : }
2226 : }
2227 :
2228 873 : if (!component_found)
2229 30 : mooseWarning("Could not find a match between boundary '",
2230 15 : getBoundaryName(primary),
2231 : "' and '",
2232 15 : getBoundaryName(secondary),
2233 : "' to set periodic boundary conditions for variable (index:",
2234 : var_num,
2235 : ") in either the X, Y or Z direction. The periodic dimension of the mesh for this "
2236 : "variable will not be stored.");
2237 : }
2238 :
2239 : const std::array<bool, 3> &
2240 5075618 : MooseMesh::queryPeriodicDimensions(const unsigned int sys_num, const unsigned int var_num) const
2241 : {
2242 5075618 : const auto key = std::make_pair(sys_num, var_num);
2243 5075618 : if (const auto it = _periodic_dim.find(key); it != _periodic_dim.end())
2244 4971934 : return it->second;
2245 103684 : return periodic_dim_default;
2246 : }
2247 :
2248 : const std::array<bool, 3> &
2249 27 : MooseMesh::queryPeriodicDimensions(const MooseVariableBase & var) const
2250 : {
2251 27 : return queryPeriodicDimensions(var.sys().number(), var.number());
2252 : }
2253 :
2254 : bool
2255 0 : MooseMesh::isTranslatedPeriodic(const unsigned int sys_num,
2256 : const unsigned int var_num,
2257 : const unsigned int component) const
2258 : {
2259 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2260 0 : return queryPeriodicDimensions(sys_num, var_num)[component];
2261 : }
2262 :
2263 : bool
2264 0 : MooseMesh::isTranslatedPeriodic(const MooseVariableBase & var, const unsigned int component) const
2265 : {
2266 0 : return isTranslatedPeriodic(var.sys().number(), var.number(), component);
2267 : }
2268 :
2269 : bool
2270 0 : MooseMesh::isTranslatedPeriodic(const unsigned int var_num, const unsigned int component) const
2271 : {
2272 0 : mooseDoOnce(mooseDeprecated(
2273 : "MooseMesh::isTranslatedPeriodic(const unsigned int, const unsigned int) is deprecated. Use "
2274 : "the method that additionally takes the system number or the MooseVariableBase instead."));
2275 0 : return isTranslatedPeriodic(0, var_num, component);
2276 : }
2277 :
2278 : RealVectorValue
2279 5075591 : MooseMesh::minPeriodicVector(const unsigned int sys_num,
2280 : const unsigned int var_num,
2281 : Point p,
2282 : Point q) const
2283 : {
2284 5075591 : const auto & periodic_dims = queryPeriodicDimensions(sys_num, var_num);
2285 :
2286 15161729 : for (const auto i : make_range(dimension()))
2287 : {
2288 : // check to see if we're closer in real or periodic space in x, y, and z
2289 10086138 : if (periodic_dims[i])
2290 : {
2291 : // Need to test order before differencing
2292 9878770 : if (p(i) > q(i))
2293 : {
2294 6390485 : if (p(i) - q(i) > _half_range(i))
2295 2344164 : p(i) -= _half_range(i) * 2;
2296 : }
2297 : else
2298 : {
2299 3488285 : if (q(i) - p(i) > _half_range(i))
2300 926721 : p(i) += _half_range(i) * 2;
2301 : }
2302 : }
2303 : }
2304 :
2305 5075591 : return q - p;
2306 : }
2307 :
2308 : RealVectorValue
2309 0 : MooseMesh::minPeriodicVector(const MooseVariableBase & var, const Point & p, const Point & q) const
2310 : {
2311 0 : return minPeriodicVector(var.sys().number(), var.number(), p, q);
2312 : }
2313 :
2314 : RealVectorValue
2315 0 : MooseMesh::minPeriodicVector(const unsigned int var_num, const Point & p, const Point & q) const
2316 : {
2317 0 : mooseDoOnce(mooseDeprecated("MooseMesh::minPeriodicVector(const unsigned int, const Point &, "
2318 : "const Point &) is deprecated. Use the method that additionally "
2319 : "takes the system number or the MooseVariableBase instead."));
2320 0 : return minPeriodicVector(0, var_num, p, q);
2321 : }
2322 :
2323 : Real
2324 5075591 : MooseMesh::minPeriodicDistance(const unsigned int sys_num,
2325 : const unsigned int var_num,
2326 : const Point & p,
2327 : const Point & q) const
2328 : {
2329 5075591 : return minPeriodicVector(sys_num, var_num, p, q).norm();
2330 : }
2331 :
2332 : Real
2333 25600 : MooseMesh::minPeriodicDistance(const MooseVariableBase & var,
2334 : const Point & p,
2335 : const Point & q) const
2336 : {
2337 25600 : return minPeriodicDistance(var.sys().number(), var.number(), p, q);
2338 : }
2339 :
2340 : Real
2341 0 : MooseMesh::minPeriodicDistance(const unsigned int var_num, const Point & p, const Point & q) const
2342 : {
2343 0 : mooseDoOnce(mooseDeprecated("MooseMesh::minPeriodicDistance(const unsigned int, const Point &, "
2344 : "const Point &) is deprecated. Use the method that additionally "
2345 : "takes the system number or the MooseVariableBase instead."));
2346 0 : return minPeriodicDistance(0, var_num, p, q);
2347 : }
2348 :
2349 : const std::pair<BoundaryID, BoundaryID> *
2350 2383 : MooseMesh::getPairedBoundaryMapping(unsigned int component) const
2351 : {
2352 2383 : if (!_regular_orthogonal_mesh)
2353 0 : mooseError("Trying to retrieve automatic paired mapping for a mesh that is not regular and "
2354 : "orthogonal");
2355 :
2356 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2357 :
2358 2383 : if (!hasDetectedPairedSidesets())
2359 0 : mooseError("MooseMesh::getPairedBoundaryMapping(): Paired boundaries not built; must call "
2360 : "detectPairedSidesets() first");
2361 :
2362 2383 : if (component < _paired_boundary->size())
2363 2380 : return &(*_paired_boundary)[component];
2364 : else
2365 3 : return nullptr;
2366 : }
2367 :
2368 : void
2369 33 : MooseMesh::buildHRefinementAndCoarseningMaps(Assembly * const assembly)
2370 : {
2371 33 : std::map<ElemType, Elem *> canonical_elems;
2372 :
2373 : // First, loop over all elements and find a canonical element for each type
2374 : // Doing it this way guarantees that this is going to work in parallel
2375 19937 : for (const auto & elem : getMesh().element_ptr_range()) // TODO: Thread this
2376 : {
2377 9952 : ElemType type = elem->type();
2378 :
2379 9952 : if (canonical_elems.find(type) ==
2380 19904 : canonical_elems.end()) // If we haven't seen this type of elem before save it
2381 42 : canonical_elems[type] = elem;
2382 : else
2383 : {
2384 9910 : Elem * stored = canonical_elems[type];
2385 9910 : if (elem->id() < stored->id()) // Arbitrarily keep the one with a lower id
2386 0 : canonical_elems[type] = elem;
2387 : }
2388 33 : }
2389 : // Now build the maps using these templates
2390 : // Note: This MUST be done NOT threaded!
2391 75 : for (const auto & can_it : canonical_elems)
2392 : {
2393 42 : Elem * elem = can_it.second;
2394 :
2395 : // Need to do this just once to get the right qrules put in place
2396 42 : assembly->setCurrentSubdomainID(elem->subdomain_id());
2397 42 : assembly->reinit(elem);
2398 42 : assembly->reinit(elem, 0);
2399 42 : auto && qrule = assembly->writeableQRule();
2400 42 : auto && qrule_face = assembly->writeableQRuleFace();
2401 :
2402 : // Volume to volume projection for refinement
2403 42 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, -1, -1);
2404 :
2405 : // Volume to volume projection for coarsening
2406 42 : buildCoarseningMap(*elem, *qrule, *qrule_face, -1);
2407 :
2408 : // Map the sides of children
2409 216 : for (unsigned int side = 0; side < elem->n_sides(); side++)
2410 : {
2411 : // Side to side for sides that match parent's sides
2412 174 : buildRefinementMap(*elem, *qrule, *qrule_face, side, -1, side);
2413 174 : buildCoarseningMap(*elem, *qrule, *qrule_face, side);
2414 : }
2415 :
2416 : // Child side to parent volume mapping for "internal" child sides
2417 240 : for (unsigned int child = 0; child < elem->n_children(); ++child)
2418 1146 : for (unsigned int side = 0; side < elem->n_sides();
2419 : ++side) // Assume children have the same number of sides!
2420 948 : if (!elem->is_child_on_side(child, side)) // Otherwise we already computed that map
2421 474 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, child, side);
2422 : }
2423 33 : }
2424 :
2425 : void
2426 90 : MooseMesh::buildPRefinementAndCoarseningMaps(Assembly * const assembly)
2427 : {
2428 90 : _elem_type_to_p_refinement_map.clear();
2429 90 : _elem_type_to_p_refinement_side_map.clear();
2430 90 : _elem_type_to_p_coarsening_map.clear();
2431 90 : _elem_type_to_p_coarsening_side_map.clear();
2432 :
2433 90 : std::map<ElemType, std::pair<Elem *, unsigned int>> elems_and_max_p_level;
2434 :
2435 32218 : for (const auto & elem : getMesh().active_element_ptr_range())
2436 : {
2437 32128 : const auto type = elem->type();
2438 32128 : auto & [picked_elem, max_p_level] = elems_and_max_p_level[type];
2439 32128 : if (!picked_elem)
2440 90 : picked_elem = elem;
2441 32128 : max_p_level = std::max(max_p_level, elem->p_level());
2442 90 : }
2443 :
2444 : // The only requirement on the FEType is that it can be arbitrarily p-refined
2445 90 : const FEType p_refinable_fe_type(CONSTANT, libMesh::MONOMIAL);
2446 90 : std::vector<Point> volume_ref_points_coarse, volume_ref_points_fine, face_ref_points_coarse,
2447 90 : face_ref_points_fine;
2448 90 : std::vector<unsigned int> p_levels;
2449 :
2450 180 : for (auto & [elem_type, elem_p_level_pair] : elems_and_max_p_level)
2451 : {
2452 90 : auto & [moose_elem, max_p_level] = elem_p_level_pair;
2453 90 : const auto dim = moose_elem->dim();
2454 : // Need to do this just once to get the right qrules put in place
2455 90 : assembly->setCurrentSubdomainID(moose_elem->subdomain_id());
2456 90 : assembly->reinit(moose_elem);
2457 90 : assembly->reinit(moose_elem, 0);
2458 90 : auto & qrule = assembly->writeableQRule();
2459 90 : auto & qrule_face = assembly->writeableQRuleFace();
2460 :
2461 90 : libMesh::Parallel::Communicator self_comm{};
2462 90 : ReplicatedMesh mesh(self_comm);
2463 90 : mesh.set_mesh_dimension(dim);
2464 630 : for (const auto & nd : moose_elem->node_ref_range())
2465 540 : mesh.add_point(nd);
2466 :
2467 90 : Elem * const elem = mesh.add_elem(Elem::build(elem_type).release());
2468 630 : for (const auto i : elem->node_index_range())
2469 540 : elem->set_node(i, mesh.node_ptr(i));
2470 :
2471 90 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, p_refinable_fe_type));
2472 90 : fe_face->get_phi();
2473 90 : const auto & face_phys_points = fe_face->get_xyz();
2474 90 : fe_face->attach_quadrature_rule(qrule_face);
2475 :
2476 90 : qrule->init(*elem);
2477 90 : volume_ref_points_coarse = qrule->get_points();
2478 90 : fe_face->reinit(elem, (unsigned int)0);
2479 90 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_coarse);
2480 :
2481 90 : p_levels.resize(max_p_level + 1);
2482 90 : std::iota(p_levels.begin(), p_levels.end(), 0);
2483 90 : libMesh::MeshRefinement mesh_refinement(mesh);
2484 :
2485 306 : for (const auto p_level : p_levels)
2486 : {
2487 216 : mesh_refinement.uniformly_p_refine(1);
2488 216 : qrule->init(*elem);
2489 216 : volume_ref_points_fine = qrule->get_points();
2490 216 : fe_face->reinit(elem, (unsigned int)0);
2491 216 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_fine);
2492 :
2493 216 : const auto map_key = std::make_pair(elem_type, p_level);
2494 216 : auto & volume_refine_map = _elem_type_to_p_refinement_map[map_key];
2495 216 : auto & face_refine_map = _elem_type_to_p_refinement_side_map[map_key];
2496 216 : auto & volume_coarsen_map = _elem_type_to_p_coarsening_map[map_key];
2497 216 : auto & face_coarsen_map = _elem_type_to_p_coarsening_side_map[map_key];
2498 :
2499 432 : auto fill_maps = [this](const auto & coarse_ref_points,
2500 : const auto & fine_ref_points,
2501 : auto & coarsen_map,
2502 : auto & refine_map)
2503 : {
2504 432 : mapPoints(fine_ref_points, coarse_ref_points, refine_map);
2505 432 : mapPoints(coarse_ref_points, fine_ref_points, coarsen_map);
2506 648 : };
2507 :
2508 216 : fill_maps(
2509 : volume_ref_points_coarse, volume_ref_points_fine, volume_coarsen_map, volume_refine_map);
2510 216 : fill_maps(face_ref_points_coarse, face_ref_points_fine, face_coarsen_map, face_refine_map);
2511 :
2512 : // With this level's maps filled our fine points now become our coarse points
2513 216 : volume_ref_points_fine.swap(volume_ref_points_coarse);
2514 216 : face_ref_points_fine.swap(face_ref_points_coarse);
2515 : }
2516 90 : }
2517 90 : }
2518 :
2519 : void
2520 57 : MooseMesh::buildRefinementAndCoarseningMaps(Assembly * const assembly)
2521 : {
2522 285 : TIME_SECTION("buildRefinementAndCoarseningMaps", 5, "Building Refinement And Coarsening Maps");
2523 57 : if (doingPRefinement())
2524 24 : buildPRefinementAndCoarseningMaps(assembly);
2525 : else
2526 33 : buildHRefinementAndCoarseningMaps(assembly);
2527 57 : }
2528 :
2529 : void
2530 690 : MooseMesh::buildRefinementMap(const Elem & elem,
2531 : QBase & qrule,
2532 : QBase & qrule_face,
2533 : int parent_side,
2534 : int child,
2535 : int child_side)
2536 : {
2537 3450 : TIME_SECTION("buildRefinementMap", 5, "Building Refinement Map");
2538 :
2539 690 : if (child == -1) // Doing volume mapping or parent side mapping
2540 : {
2541 : mooseAssert(parent_side == child_side,
2542 : "Parent side must match child_side if not passing a specific child!");
2543 :
2544 216 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2545 :
2546 216 : if (_elem_type_to_refinement_map.find(the_pair) != _elem_type_to_refinement_map.end())
2547 0 : mooseError("Already built a qp refinement map!");
2548 :
2549 216 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2550 216 : std::vector<std::vector<QpMap>> & refinement_map = _elem_type_to_refinement_map[the_pair];
2551 216 : findAdaptivityQpMaps(
2552 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2553 216 : }
2554 : else // Need to map a child side to parent volume qps
2555 : {
2556 474 : std::pair<int, int> child_pair(child, child_side);
2557 :
2558 474 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) !=
2559 1380 : _elem_type_to_child_side_refinement_map.end() &&
2560 432 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) !=
2561 906 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2562 0 : mooseError("Already built a qp refinement map!");
2563 :
2564 474 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2565 : std::vector<std::vector<QpMap>> & refinement_map =
2566 474 : _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2567 474 : findAdaptivityQpMaps(
2568 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2569 474 : }
2570 690 : }
2571 :
2572 : const std::vector<std::vector<QpMap>> &
2573 3422 : MooseMesh::getRefinementMap(const Elem & elem, int parent_side, int child, int child_side)
2574 : {
2575 3422 : if (child == -1) // Doing volume mapping or parent side mapping
2576 : {
2577 : mooseAssert(parent_side == child_side,
2578 : "Parent side must match child_side if not passing a specific child!");
2579 :
2580 3422 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2581 :
2582 3422 : if (_elem_type_to_refinement_map.find(the_pair) == _elem_type_to_refinement_map.end())
2583 0 : mooseError("Could not find a suitable qp refinement map!");
2584 :
2585 3422 : return _elem_type_to_refinement_map[the_pair];
2586 : }
2587 : else // Need to map a child side to parent volume qps
2588 : {
2589 0 : std::pair<int, int> child_pair(child, child_side);
2590 :
2591 0 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) ==
2592 0 : _elem_type_to_child_side_refinement_map.end() ||
2593 0 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) ==
2594 0 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2595 0 : mooseError("Could not find a suitable qp refinement map!");
2596 :
2597 0 : return _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2598 : }
2599 :
2600 : /**
2601 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2602 : * processor has a complete map. This may require parallel communication. This is likely to
2603 : * happen
2604 : * when running on a mixed element mesh.
2605 : */
2606 : }
2607 :
2608 : void
2609 216 : MooseMesh::buildCoarseningMap(const Elem & elem, QBase & qrule, QBase & qrule_face, int input_side)
2610 : {
2611 1080 : TIME_SECTION("buildCoarseningMap", 5, "Building Coarsening Map");
2612 :
2613 216 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2614 :
2615 216 : if (_elem_type_to_coarsening_map.find(the_pair) != _elem_type_to_coarsening_map.end())
2616 0 : mooseError("Already built a qp coarsening map!");
2617 :
2618 216 : std::vector<std::vector<QpMap>> refinement_map;
2619 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map =
2620 216 : _elem_type_to_coarsening_map[the_pair];
2621 :
2622 : // The -1 here is for a specific child. We don't do that for coarsening maps
2623 : // Also note that we're always mapping the same side to the same side (which is guaranteed by
2624 : // libMesh).
2625 216 : findAdaptivityQpMaps(
2626 : &elem, qrule, qrule_face, refinement_map, coarsen_map, input_side, -1, input_side);
2627 :
2628 : /**
2629 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2630 : * processor has a complete map. This may require parallel communication. This is likely to
2631 : * happen
2632 : * when running on a mixed element mesh.
2633 : */
2634 216 : }
2635 :
2636 : const std::vector<std::pair<unsigned int, QpMap>> &
2637 1288 : MooseMesh::getCoarseningMap(const Elem & elem, int input_side)
2638 : {
2639 1288 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2640 :
2641 1288 : if (_elem_type_to_coarsening_map.find(the_pair) == _elem_type_to_coarsening_map.end())
2642 0 : mooseError("Could not find a suitable qp refinement map!");
2643 :
2644 2576 : return _elem_type_to_coarsening_map[the_pair];
2645 : }
2646 :
2647 : void
2648 7038 : MooseMesh::mapPoints(const std::vector<Point> & from,
2649 : const std::vector<Point> & to,
2650 : std::vector<QpMap> & qp_map)
2651 : {
2652 7038 : unsigned int n_from = from.size();
2653 7038 : unsigned int n_to = to.size();
2654 :
2655 7038 : qp_map.resize(n_from);
2656 :
2657 61340 : for (unsigned int i = 0; i < n_from; ++i)
2658 : {
2659 54302 : const Point & from_point = from[i];
2660 :
2661 54302 : QpMap & current_map = qp_map[i];
2662 :
2663 1247054 : for (unsigned int j = 0; j < n_to; ++j)
2664 : {
2665 1192752 : const Point & to_point = to[j];
2666 1192752 : Real distance = (from_point - to_point).norm();
2667 :
2668 1192752 : if (distance < current_map._distance)
2669 : {
2670 167558 : current_map._distance = distance;
2671 167558 : current_map._from = i;
2672 167558 : current_map._to = j;
2673 : }
2674 : }
2675 : }
2676 7038 : }
2677 :
2678 : void
2679 906 : MooseMesh::findAdaptivityQpMaps(const Elem * template_elem,
2680 : QBase & qrule,
2681 : QBase & qrule_face,
2682 : std::vector<std::vector<QpMap>> & refinement_map,
2683 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map,
2684 : int parent_side,
2685 : int child,
2686 : int child_side)
2687 : {
2688 2718 : TIME_SECTION("findAdaptivityQpMaps", 5);
2689 :
2690 906 : ReplicatedMesh mesh(_communicator);
2691 906 : mesh.skip_partitioning(true);
2692 :
2693 906 : unsigned int dim = template_elem->dim();
2694 906 : mesh.set_mesh_dimension(dim);
2695 :
2696 7092 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2697 6186 : mesh.add_point(template_elem->point(i));
2698 :
2699 906 : Elem * elem = mesh.add_elem(Elem::build(template_elem->type()).release());
2700 :
2701 7092 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2702 6186 : elem->set_node(i, mesh.node_ptr(i));
2703 :
2704 906 : std::unique_ptr<FEBase> fe(FEBase::build(dim, FEType()));
2705 906 : fe->get_phi();
2706 906 : const std::vector<Point> & q_points_volume = fe->get_xyz();
2707 :
2708 906 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, FEType()));
2709 906 : fe_face->get_phi();
2710 906 : const std::vector<Point> & q_points_face = fe_face->get_xyz();
2711 :
2712 906 : fe->attach_quadrature_rule(&qrule);
2713 906 : fe_face->attach_quadrature_rule(&qrule_face);
2714 :
2715 : // The current q_points (locations in *physical* space)
2716 : const std::vector<Point> * q_points;
2717 :
2718 906 : if (parent_side != -1)
2719 : {
2720 348 : fe_face->reinit(elem, parent_side);
2721 348 : q_points = &q_points_face;
2722 : }
2723 : else
2724 : {
2725 558 : fe->reinit(elem);
2726 558 : q_points = &q_points_volume;
2727 : }
2728 :
2729 906 : std::vector<Point> parent_ref_points;
2730 :
2731 906 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, parent_ref_points);
2732 906 : libMesh::MeshRefinement mesh_refinement(mesh);
2733 906 : mesh_refinement.uniformly_refine(1);
2734 :
2735 : // A map from the child element index to the locations of all the child's quadrature points in
2736 : // *reference* space. Note that we use a map here instead of a vector because the caller can
2737 : // pass an explicit child index. We are not guaranteed to have a sequence from [0, n_children)
2738 906 : std::map<unsigned int, std::vector<Point>> child_to_ref_points;
2739 :
2740 906 : unsigned int n_children = elem->n_children();
2741 :
2742 906 : refinement_map.resize(n_children);
2743 :
2744 906 : std::vector<unsigned int> children;
2745 :
2746 906 : if (child != -1) // Passed in a child explicitly
2747 474 : children.push_back(child);
2748 : else
2749 : {
2750 432 : children.resize(n_children);
2751 2724 : for (unsigned int child = 0; child < n_children; ++child)
2752 2292 : children[child] = child;
2753 : }
2754 :
2755 3672 : for (unsigned int i = 0; i < children.size(); ++i)
2756 : {
2757 2766 : unsigned int child = children[i];
2758 :
2759 2766 : if ((parent_side != -1 && !elem->is_child_on_side(child, parent_side)))
2760 948 : continue;
2761 :
2762 1818 : const Elem * child_elem = elem->child_ptr(child);
2763 :
2764 1818 : if (child_side != -1)
2765 : {
2766 1422 : fe_face->reinit(child_elem, child_side);
2767 1422 : q_points = &q_points_face;
2768 : }
2769 : else
2770 : {
2771 396 : fe->reinit(child_elem);
2772 396 : q_points = &q_points_volume;
2773 : }
2774 :
2775 1818 : std::vector<Point> child_ref_points;
2776 :
2777 1818 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, child_ref_points);
2778 1818 : child_to_ref_points[child] = child_ref_points;
2779 :
2780 1818 : std::vector<QpMap> & qp_map = refinement_map[child];
2781 :
2782 : // Find the closest parent_qp to each child_qp
2783 1818 : mapPoints(child_ref_points, parent_ref_points, qp_map);
2784 1818 : }
2785 :
2786 906 : coarsen_map.resize(parent_ref_points.size());
2787 :
2788 : // For each parent qp find the closest child qp
2789 6210 : for (unsigned int child = 0; child < n_children; child++)
2790 : {
2791 5304 : if (parent_side != -1 && !elem->is_child_on_side(child, child_side))
2792 948 : continue;
2793 :
2794 4356 : std::vector<Point> & child_ref_points = child_to_ref_points[child];
2795 :
2796 4356 : std::vector<QpMap> qp_map;
2797 :
2798 : // Find all of the closest points from parent_qp to _THIS_ child's qp
2799 4356 : mapPoints(parent_ref_points, child_ref_points, qp_map);
2800 :
2801 : // Check those to see if they are closer than what we currently have for each point
2802 32856 : for (unsigned int parent_qp = 0; parent_qp < parent_ref_points.size(); ++parent_qp)
2803 : {
2804 28500 : std::pair<unsigned int, QpMap> & child_and_map = coarsen_map[parent_qp];
2805 28500 : unsigned int & closest_child = child_and_map.first;
2806 28500 : QpMap & closest_map = child_and_map.second;
2807 :
2808 28500 : QpMap & current_map = qp_map[parent_qp];
2809 :
2810 28500 : if (current_map._distance < closest_map._distance)
2811 : {
2812 6300 : closest_child = child;
2813 6300 : closest_map = current_map;
2814 : }
2815 : }
2816 4356 : }
2817 906 : }
2818 :
2819 : void
2820 0 : MooseMesh::changeBoundaryId(const boundary_id_type old_id,
2821 : const boundary_id_type new_id,
2822 : bool delete_prev)
2823 : {
2824 0 : TIME_SECTION("changeBoundaryId", 6);
2825 0 : changeBoundaryId(getMesh(), old_id, new_id, delete_prev);
2826 0 : }
2827 :
2828 : void
2829 0 : MooseMesh::changeBoundaryId(MeshBase & mesh,
2830 : const boundary_id_type old_id,
2831 : const boundary_id_type new_id,
2832 : bool delete_prev)
2833 : {
2834 : // Get a reference to our BoundaryInfo object, we will use it several times below...
2835 0 : BoundaryInfo & boundary_info = mesh.get_boundary_info();
2836 :
2837 : // Container to catch ids passed back from BoundaryInfo
2838 0 : std::vector<boundary_id_type> old_ids;
2839 :
2840 : // Only level-0 elements store BCs. Loop over them.
2841 0 : for (auto & elem : as_range(mesh.level_elements_begin(0), mesh.level_elements_end(0)))
2842 : {
2843 0 : unsigned int n_sides = elem->n_sides();
2844 0 : for (unsigned int s = 0; s != n_sides; ++s)
2845 : {
2846 0 : boundary_info.boundary_ids(elem, s, old_ids);
2847 0 : if (std::find(old_ids.begin(), old_ids.end(), old_id) != old_ids.end())
2848 : {
2849 0 : std::vector<boundary_id_type> new_ids(old_ids);
2850 0 : std::replace(new_ids.begin(), new_ids.end(), old_id, new_id);
2851 0 : if (delete_prev)
2852 : {
2853 0 : boundary_info.remove_side(elem, s);
2854 0 : boundary_info.add_side(elem, s, new_ids);
2855 : }
2856 : else
2857 0 : boundary_info.add_side(elem, s, new_ids);
2858 0 : }
2859 : }
2860 0 : }
2861 :
2862 : // Remove any remaining references to the old ID from the
2863 : // BoundaryInfo object. This prevents things like empty sidesets
2864 : // from showing up when printing information, etc.
2865 0 : if (delete_prev)
2866 0 : boundary_info.remove_id(old_id);
2867 :
2868 : // The cached boundary id sets will need re-preparation
2869 0 : mesh.unset_has_boundary_id_sets();
2870 0 : }
2871 :
2872 : const RealVectorValue &
2873 0 : MooseMesh::getNormalByBoundaryID(BoundaryID id) const
2874 : {
2875 : mooseAssert(_boundary_to_normal_map.get() != nullptr, "Boundary To Normal Map not built!");
2876 :
2877 : // Note: Boundaries that are not in the map (existing boundaries) will default
2878 : // construct a new RealVectorValue - (x,y,z)=(0, 0, 0)
2879 0 : return (*_boundary_to_normal_map)[id];
2880 : }
2881 :
2882 : MooseMesh &
2883 0 : MooseMesh::clone() const
2884 : {
2885 0 : mooseError("MooseMesh::clone() is no longer supported, use MooseMesh::safeClone() instead.");
2886 : }
2887 :
2888 : void
2889 73146 : MooseMesh::determineUseDistributedMesh()
2890 : {
2891 73146 : switch (_parallel_type)
2892 : {
2893 68284 : case ParallelType::DEFAULT:
2894 : // The user did not specify 'parallel_type = XYZ' in the input file,
2895 : // so we allow the --distributed-mesh command line arg to possibly turn
2896 : // on DistributedMesh. If the command line arg is not present, we pick ReplicatedMesh.
2897 68284 : if (_app.getDistributedMeshOnCommandLine())
2898 10674 : _use_distributed_mesh = true;
2899 68284 : break;
2900 3515 : case ParallelType::REPLICATED:
2901 3515 : if (_app.getDistributedMeshOnCommandLine() || _is_nemesis || _is_split)
2902 741 : _parallel_type_overridden = true;
2903 3515 : _use_distributed_mesh = false;
2904 3515 : break;
2905 1347 : case ParallelType::DISTRIBUTED:
2906 1347 : _use_distributed_mesh = true;
2907 1347 : break;
2908 : }
2909 :
2910 : // If the user specifies 'nemesis = true' in the Mesh block, or they are using --use-split,
2911 : // we must use DistributedMesh.
2912 73146 : if (_is_nemesis || _is_split)
2913 562 : _use_distributed_mesh = true;
2914 73146 : }
2915 :
2916 : std::unique_ptr<MeshBase>
2917 68458 : MooseMesh::buildMeshBaseObject(unsigned int dim)
2918 : {
2919 68458 : std::unique_ptr<MeshBase> mesh;
2920 68458 : if (_use_distributed_mesh)
2921 10737 : mesh = buildTypedMesh<DistributedMesh>(dim);
2922 : else
2923 57721 : mesh = buildTypedMesh<ReplicatedMesh>(dim);
2924 :
2925 68458 : return mesh;
2926 0 : }
2927 :
2928 : void
2929 65439 : MooseMesh::setMeshBase(std::unique_ptr<MeshBase> mesh_base)
2930 : {
2931 65439 : _mesh = std::move(mesh_base);
2932 65439 : _mesh->allow_remote_element_removal(_allow_remote_element_removal);
2933 65439 : }
2934 :
2935 : void
2936 64987 : MooseMesh::init()
2937 : {
2938 : /**
2939 : * If the mesh base hasn't been constructed by the time init is called, just do it here.
2940 : * This can happen if somebody builds a mesh outside of the normal Action system. Forcing
2941 : * developers to create, construct the MeshBase, and then init separately is a bit much for casual
2942 : * use but it gives us the ability to run MeshGenerators in-between.
2943 : */
2944 64987 : if (!_mesh)
2945 10 : _mesh = buildMeshBaseObject();
2946 :
2947 64987 : if (_app.isSplitMesh() && _use_distributed_mesh)
2948 0 : mooseError("You cannot use the mesh splitter capability with DistributedMesh!");
2949 :
2950 194961 : TIME_SECTION("init", 2);
2951 :
2952 64987 : if (_app.isRecovering() && _allow_recovery && _app.isUltimateMaster())
2953 : {
2954 : // Some partitioners are not idempotent. Some recovery data
2955 : // files require partitioning to match mesh partitioning. This
2956 : // means that, when recovering, we can't safely repartition.
2957 3307 : const bool skip_partitioning_later = getMesh().skip_partitioning();
2958 3307 : getMesh().skip_partitioning(true);
2959 3307 : const bool allow_renumbering_later = getMesh().allow_renumbering();
2960 3307 : getMesh().allow_renumbering(false);
2961 :
2962 : // For now, only read the recovery mesh on the Ultimate Master..
2963 : // sub-apps need to just build their mesh like normal
2964 : {
2965 9921 : TIME_SECTION("readRecoveredMesh", 2);
2966 3307 : getMesh().read(_app.getRestartRecoverFileBase() + MooseApp::checkpointSuffix());
2967 3307 : }
2968 :
2969 3307 : getMesh().allow_renumbering(allow_renumbering_later);
2970 3307 : getMesh().skip_partitioning(skip_partitioning_later);
2971 : }
2972 : else // Normally just build the mesh
2973 : {
2974 : // Don't allow partitioning during building
2975 61680 : if (_app.isSplitMesh())
2976 89 : getMesh().skip_partitioning(true);
2977 61680 : buildMesh();
2978 :
2979 185022 : if (getParam<bool>("build_all_side_lowerd_mesh"))
2980 205 : buildLowerDMesh();
2981 : }
2982 64981 : }
2983 :
2984 : unsigned int
2985 92447372 : MooseMesh::dimension() const
2986 : {
2987 92447372 : return getMesh().mesh_dimension();
2988 : }
2989 :
2990 : unsigned int
2991 37660 : MooseMesh::effectiveSpatialDimension() const
2992 : {
2993 37660 : const Real abs_zero = 1e-12;
2994 :
2995 : // See if the mesh is completely containd in the z and y planes to calculate effective spatial
2996 : // dim
2997 69523 : for (unsigned int dim = LIBMESH_DIM; dim >= 1; --dim)
2998 69523 : if (dimensionWidth(dim - 1) >= abs_zero)
2999 37660 : return dim;
3000 :
3001 : // If we get here, we have a 1D mesh on the x-axis.
3002 0 : return 1;
3003 : }
3004 :
3005 : unsigned int
3006 88693 : MooseMesh::getBlocksMaxDimension(const std::vector<SubdomainName> & blocks) const
3007 : {
3008 88693 : const auto & mesh = getMesh();
3009 :
3010 : // Take a shortcut if possible
3011 88693 : if (const auto & elem_dims = mesh.elem_dimensions(); mesh.is_prepared() && elem_dims.size() == 1)
3012 78662 : return *elem_dims.begin();
3013 :
3014 10031 : unsigned short dim = 0;
3015 10031 : const auto subdomain_ids = getSubdomainIDs(blocks);
3016 10031 : const std::set<SubdomainID> subdomain_ids_set(subdomain_ids.begin(), subdomain_ids.end());
3017 1848683 : for (const auto & elem : mesh.active_subdomain_set_elements_ptr_range(subdomain_ids_set))
3018 1848683 : dim = std::max(dim, elem->dim());
3019 :
3020 : // Get the maximumal globally
3021 10031 : _communicator.max(dim);
3022 10031 : return dim;
3023 10031 : }
3024 :
3025 : std::vector<BoundaryID>
3026 106280032 : MooseMesh::getBoundaryIDs(const Elem * const elem, const unsigned short int side) const
3027 : {
3028 106280032 : std::vector<BoundaryID> ids;
3029 106280032 : getMesh().get_boundary_info().boundary_ids(elem, side, ids);
3030 106280032 : return ids;
3031 0 : }
3032 :
3033 : std::vector<std::vector<BoundaryID>>
3034 407122124 : MooseMesh::getBoundaryIDs(const Elem * const elem) const
3035 : {
3036 407122124 : std::vector<std::vector<BoundaryID>> ids;
3037 407122124 : getMesh().get_boundary_info().side_boundary_ids(elem, ids);
3038 407122124 : return ids;
3039 0 : }
3040 :
3041 : const std::set<BoundaryID> &
3042 504980 : MooseMesh::getBoundaryIDs() const
3043 : {
3044 504980 : return getMesh().get_boundary_info().get_boundary_ids();
3045 : }
3046 :
3047 : void
3048 221332 : MooseMesh::buildNodeListFromSideList()
3049 : {
3050 221332 : auto & boundary_info = getMesh().get_boundary_info();
3051 :
3052 221332 : if (_construct_node_list_from_side_list)
3053 : {
3054 221306 : const std::set<boundary_id_type> & side_bcids = boundary_info.get_side_boundary_ids();
3055 :
3056 221306 : if (_displace_node_list_by_side_list)
3057 : {
3058 : // Don't want to use auto here - the rbegin trick relies on a
3059 : // sorted set and we want the compiler to scream if libMesh ever
3060 : // switches type
3061 221306 : const std::set<boundary_id_type> & node_bcids = boundary_info.get_node_boundary_ids();
3062 :
3063 : // If we've got a reasonable largest BC id, we can just use the
3064 : // subsequent unused ones
3065 221306 : boundary_id_type next_bcid = 0;
3066 221306 : if (!node_bcids.empty())
3067 213095 : next_bcid = std::max(next_bcid, cast_int<boundary_id_type>(*node_bcids.rbegin() + 1));
3068 221306 : if (!side_bcids.empty())
3069 216471 : next_bcid = std::max(next_bcid, cast_int<boundary_id_type>(*side_bcids.rbegin() + 1));
3070 :
3071 : // We need all processors to agree on the id to use, even when
3072 : // each only sees the bcids on their own portions of a
3073 : // distributed mesh.
3074 221306 : _communicator.max(next_bcid);
3075 :
3076 : // If we've got an unreasonably high largest BC id, we should
3077 : // probably just search for unused ones with moderate values, so we
3078 : // don't risk wrapping.
3079 221306 : if (next_bcid > 1000 || next_bcid <= 0)
3080 2999 : next_bcid = 1000;
3081 :
3082 : // If any side bcid is already a node bcid with a different name,
3083 : // that's a different boundary condition that we need to reassign
3084 : // rather than overwrite or merge to.
3085 1065815 : for (auto bcid : side_bcids)
3086 1657486 : if (node_bcids.count(bcid) &&
3087 812977 : (boundary_info.get_sideset_name(bcid) != boundary_info.get_nodeset_name(bcid)))
3088 : {
3089 2002 : boundary_info.renumber_node_id(bcid, next_bcid);
3090 : do
3091 : {
3092 2012 : ++next_bcid;
3093 2012 : } while (node_bcids.count(next_bcid) || side_bcids.count(next_bcid));
3094 : }
3095 : }
3096 :
3097 : // For any side bcid that has a name, make sure that our new node
3098 : // bcid is given the same name. We need to iterate over the
3099 : // actual name map (which is global) here, not over side_bcids
3100 : // (which only includes local ids on a distributed mesh).
3101 1053820 : for (auto & [id, name] : boundary_info.get_sideset_name_map())
3102 832514 : boundary_info.nodeset_name(id) = name;
3103 :
3104 221306 : boundary_info.build_node_list_from_side_list();
3105 : }
3106 221332 : }
3107 :
3108 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3109 218 : MooseMesh::buildSideList()
3110 : {
3111 218 : return getMesh().get_boundary_info().build_side_list();
3112 : }
3113 :
3114 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3115 4528 : MooseMesh::buildActiveSideList() const
3116 : {
3117 4528 : return getMesh().get_boundary_info().build_active_side_list();
3118 : }
3119 :
3120 : unsigned int
3121 20736 : MooseMesh::sideWithBoundaryID(const Elem * const elem, const BoundaryID boundary_id) const
3122 : {
3123 20736 : return getMesh().get_boundary_info().side_with_boundary_id(elem, boundary_id);
3124 : }
3125 :
3126 : MeshBase::node_iterator
3127 3045 : MooseMesh::localNodesBegin()
3128 : {
3129 3045 : return getMesh().local_nodes_begin();
3130 : }
3131 :
3132 : MeshBase::node_iterator
3133 3045 : MooseMesh::localNodesEnd()
3134 : {
3135 3045 : return getMesh().local_nodes_end();
3136 : }
3137 :
3138 : MeshBase::const_node_iterator
3139 0 : MooseMesh::localNodesBegin() const
3140 : {
3141 0 : return getMesh().local_nodes_begin();
3142 : }
3143 :
3144 : MeshBase::const_node_iterator
3145 0 : MooseMesh::localNodesEnd() const
3146 : {
3147 0 : return getMesh().local_nodes_end();
3148 : }
3149 :
3150 : MeshBase::element_iterator
3151 146546 : MooseMesh::activeLocalElementsBegin()
3152 : {
3153 146546 : return getMesh().active_local_elements_begin();
3154 : }
3155 :
3156 : const MeshBase::element_iterator
3157 146546 : MooseMesh::activeLocalElementsEnd()
3158 : {
3159 146546 : return getMesh().active_local_elements_end();
3160 : }
3161 :
3162 : MeshBase::const_element_iterator
3163 0 : MooseMesh::activeLocalElementsBegin() const
3164 : {
3165 0 : return getMesh().active_local_elements_begin();
3166 : }
3167 :
3168 : const MeshBase::const_element_iterator
3169 0 : MooseMesh::activeLocalElementsEnd() const
3170 : {
3171 0 : return getMesh().active_local_elements_end();
3172 : }
3173 :
3174 : dof_id_type
3175 54714 : MooseMesh::nNodes() const
3176 : {
3177 54714 : return getMesh().n_nodes();
3178 : }
3179 :
3180 : dof_id_type
3181 1562 : MooseMesh::nElem() const
3182 : {
3183 1562 : return getMesh().n_elem();
3184 : }
3185 :
3186 : dof_id_type
3187 0 : MooseMesh::maxNodeId() const
3188 : {
3189 0 : return getMesh().max_node_id();
3190 : }
3191 :
3192 : dof_id_type
3193 0 : MooseMesh::maxElemId() const
3194 : {
3195 0 : return getMesh().max_elem_id();
3196 : }
3197 :
3198 : Elem *
3199 0 : MooseMesh::elem(const dof_id_type i)
3200 : {
3201 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3202 0 : return elemPtr(i);
3203 : }
3204 :
3205 : const Elem *
3206 0 : MooseMesh::elem(const dof_id_type i) const
3207 : {
3208 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3209 0 : return elemPtr(i);
3210 : }
3211 :
3212 : Elem *
3213 15517999 : MooseMesh::elemPtr(const dof_id_type i)
3214 : {
3215 15517999 : return getMesh().elem_ptr(i);
3216 : }
3217 :
3218 : const Elem *
3219 1244668 : MooseMesh::elemPtr(const dof_id_type i) const
3220 : {
3221 1244668 : return getMesh().elem_ptr(i);
3222 : }
3223 :
3224 : Elem *
3225 21673 : MooseMesh::queryElemPtr(const dof_id_type i)
3226 : {
3227 21673 : return getMesh().query_elem_ptr(i);
3228 : }
3229 :
3230 : const Elem *
3231 36392 : MooseMesh::queryElemPtr(const dof_id_type i) const
3232 : {
3233 36392 : return getMesh().query_elem_ptr(i);
3234 : }
3235 :
3236 : bool
3237 0 : MooseMesh::prepared() const
3238 : {
3239 0 : return _mesh->is_prepared() && _moose_mesh_prepared;
3240 : }
3241 :
3242 : void
3243 0 : MooseMesh::prepared(bool state)
3244 : {
3245 0 : if (state)
3246 0 : mooseError("We don't have any right to tell the libmesh mesh that it *is* prepared. Only a "
3247 : "call to prepare_for_use should tell us that");
3248 :
3249 : // Some people may call this even before we have a MeshBase object. This isn't dangerous really
3250 : // because when the MeshBase object is born, it knows it's in an unprepared state
3251 0 : if (_mesh)
3252 0 : _mesh->unset_is_prepared();
3253 :
3254 : // If the libMesh mesh isn't preparead, then our MooseMesh wrapper is also no longer prepared
3255 0 : _moose_mesh_prepared = false;
3256 :
3257 : /**
3258 : * If we are explicitly setting the mesh to not prepared, then we've likely modified the mesh
3259 : * and can no longer make assumptions about orthogonality. We really should recheck.
3260 : */
3261 0 : _regular_orthogonal_mesh = false;
3262 0 : }
3263 :
3264 : void
3265 0 : MooseMesh::needsPrepareForUse()
3266 : {
3267 0 : prepared(false);
3268 0 : }
3269 :
3270 : const std::set<SubdomainID> &
3271 8185995 : MooseMesh::meshSubdomains() const
3272 : {
3273 8185995 : return _mesh_subdomains;
3274 : }
3275 :
3276 : const std::set<BoundaryID> &
3277 11197 : MooseMesh::meshBoundaryIds() const
3278 : {
3279 11197 : return _mesh_boundary_ids;
3280 : }
3281 :
3282 : const std::set<BoundaryID> &
3283 29185 : MooseMesh::meshSidesetIds() const
3284 : {
3285 29185 : return _mesh_sideset_ids;
3286 : }
3287 :
3288 : const std::set<BoundaryID> &
3289 148012 : MooseMesh::meshNodesetIds() const
3290 : {
3291 148012 : return _mesh_nodeset_ids;
3292 : }
3293 :
3294 : void
3295 0 : MooseMesh::setMeshBoundaryIDs(std::set<BoundaryID> boundary_IDs)
3296 : {
3297 0 : _mesh_boundary_ids = boundary_IDs;
3298 0 : }
3299 :
3300 : void
3301 0 : MooseMesh::setBoundaryToNormalMap(
3302 : std::unique_ptr<std::map<BoundaryID, RealVectorValue>> boundary_map)
3303 : {
3304 0 : _boundary_to_normal_map = std::move(boundary_map);
3305 0 : }
3306 :
3307 : void
3308 0 : MooseMesh::setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map)
3309 : {
3310 0 : mooseDeprecated("setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map) is "
3311 : "deprecated, use the unique_ptr version instead");
3312 0 : _boundary_to_normal_map.reset(boundary_map);
3313 0 : }
3314 :
3315 : unsigned int
3316 123757 : MooseMesh::uniformRefineLevel() const
3317 : {
3318 123757 : return _uniform_refine_level;
3319 : }
3320 :
3321 : void
3322 67003 : MooseMesh::setUniformRefineLevel(unsigned int level, bool deletion)
3323 : {
3324 67003 : _uniform_refine_level = level;
3325 67003 : _skip_deletion_repartition_after_refine = deletion;
3326 67003 : }
3327 :
3328 : void
3329 56144 : MooseMesh::addGhostedBoundary(BoundaryID boundary_id)
3330 : {
3331 56144 : _ghosted_boundaries.insert(boundary_id);
3332 56144 : }
3333 :
3334 : void
3335 0 : MooseMesh::setGhostedBoundaryInflation(const std::vector<Real> & inflation)
3336 : {
3337 0 : _ghosted_boundaries_inflation = inflation;
3338 0 : }
3339 :
3340 : const std::set<unsigned int> &
3341 0 : MooseMesh::getGhostedBoundaries() const
3342 : {
3343 0 : return _ghosted_boundaries;
3344 : }
3345 :
3346 : const std::vector<Real> &
3347 11484 : MooseMesh::getGhostedBoundaryInflation() const
3348 : {
3349 11484 : return _ghosted_boundaries_inflation;
3350 : }
3351 :
3352 : namespace // Anonymous namespace for helpers
3353 : {
3354 : // A class for templated methods that expect output iterator
3355 : // arguments, which adds objects to the Mesh.
3356 : // Although extra_ghost_elem_inserter can add any object, we
3357 : // template it around object type so that type inference and
3358 : // iterator_traits will work.
3359 : // This object specifically is used to insert extra ghost elems into the mesh
3360 : template <typename T>
3361 : struct extra_ghost_elem_inserter
3362 : {
3363 : using iterator_category = std::output_iterator_tag;
3364 : using value_type = T;
3365 :
3366 44316 : extra_ghost_elem_inserter(DistributedMesh & m) : mesh(m) {}
3367 :
3368 19101 : void operator=(const Elem * e) { mesh.add_extra_ghost_elem(const_cast<Elem *>(e)); }
3369 :
3370 35698 : void operator=(Node * n) { mesh.add_node(n); }
3371 :
3372 : void operator=(Point * p) { mesh.add_point(*p); }
3373 :
3374 : extra_ghost_elem_inserter & operator++() { return *this; }
3375 :
3376 54799 : extra_ghost_elem_inserter operator++(int) { return extra_ghost_elem_inserter(*this); }
3377 :
3378 : // We don't return a reference-to-T here because we don't want to
3379 : // construct one or have any of its methods called. We just want
3380 : // to allow the returned object to be able to do mesh insertions
3381 : // with operator=().
3382 54799 : extra_ghost_elem_inserter & operator*() { return *this; }
3383 :
3384 : private:
3385 : DistributedMesh & mesh;
3386 : };
3387 :
3388 : /**
3389 : * Specific weak ordering for Elem *'s to be used in a set.
3390 : * We use the id, but first sort by level. This guarantees
3391 : * when traversing the set from beginning to end the lower
3392 : * level (parent) elements are encountered first.
3393 : *
3394 : * This was swiped from libMesh mesh_communication.C, and ought to be
3395 : * replaced with libMesh::CompareElemIdsByLevel just as soon as I refactor to
3396 : * create that - @roystgnr
3397 : */
3398 : struct CompareElemsByLevel
3399 : {
3400 104881 : bool operator()(const Elem * a, const Elem * b) const
3401 : {
3402 : libmesh_assert(a);
3403 : libmesh_assert(b);
3404 104881 : const unsigned int al = a->level(), bl = b->level();
3405 104881 : const dof_id_type aid = a->id(), bid = b->id();
3406 :
3407 104881 : return (al == bl) ? aid < bid : al < bl;
3408 : }
3409 : };
3410 :
3411 : } // anonymous namespace
3412 :
3413 : void
3414 137151 : MooseMesh::ghostGhostedBoundaries()
3415 : {
3416 : // No need to do this if using a serial mesh
3417 : // We do not need to ghost boundary elements when _need_ghost_ghosted_boundaries
3418 : // is not true. _need_ghost_ghosted_boundaries can be set by a mesh generator
3419 : // where boundaries are already ghosted accordingly
3420 137151 : if (!_use_distributed_mesh || !_need_ghost_ghosted_boundaries)
3421 114993 : return;
3422 :
3423 66474 : TIME_SECTION("GhostGhostedBoundaries", 3);
3424 :
3425 : parallel_object_only();
3426 :
3427 22158 : DistributedMesh & mesh = dynamic_cast<DistributedMesh &>(getMesh());
3428 :
3429 : // We clear ghosted elements that were added by previous invocations of this
3430 : // method but leave ghosted elements that were added by other code, e.g.
3431 : // OversampleOutput, untouched
3432 22158 : mesh.clear_extra_ghost_elems(_ghost_elems_from_ghost_boundaries);
3433 22158 : _ghost_elems_from_ghost_boundaries.clear();
3434 :
3435 22158 : std::set<const Elem *, CompareElemsByLevel> boundary_elems_to_ghost;
3436 22158 : std::set<Node *> connected_nodes_to_ghost;
3437 :
3438 22158 : std::vector<const Elem *> family_tree;
3439 :
3440 882378 : for (const auto & t : mesh.get_boundary_info().build_side_list())
3441 : {
3442 860220 : auto elem_id = std::get<0>(t);
3443 860220 : auto bc_id = std::get<2>(t);
3444 :
3445 860220 : if (_ghosted_boundaries.find(bc_id) != _ghosted_boundaries.end())
3446 : {
3447 5695 : Elem * elem = mesh.elem_ptr(elem_id);
3448 :
3449 : #ifdef LIBMESH_ENABLE_AMR
3450 5695 : elem->family_tree(family_tree);
3451 5695 : Elem * parent = elem->parent();
3452 5695 : while (parent)
3453 : {
3454 0 : family_tree.push_back(parent);
3455 0 : parent = parent->parent();
3456 : }
3457 : #else
3458 : family_tree.clear();
3459 : family_tree.push_back(elem);
3460 : #endif
3461 15230 : for (const auto & felem : family_tree)
3462 : {
3463 9535 : boundary_elems_to_ghost.insert(felem);
3464 :
3465 : // The entries of connected_nodes_to_ghost need to be
3466 : // non-constant, so that they will work in things like
3467 : // UpdateDisplacedMeshThread. The container returned by
3468 : // family_tree contains const Elems even when the Elem
3469 : // it is called on is non-const, so once that interface
3470 : // gets fixed we can remove this const_cast.
3471 57258 : for (unsigned int n = 0; n < felem->n_nodes(); ++n)
3472 47723 : connected_nodes_to_ghost.insert(const_cast<Node *>(felem->node_ptr(n)));
3473 : }
3474 : }
3475 22158 : }
3476 :
3477 : // We really do want to store this by value instead of by reference
3478 22158 : const auto prior_ghost_elems = mesh.extra_ghost_elems();
3479 :
3480 22158 : mesh.comm().allgather_packed_range(&mesh,
3481 : connected_nodes_to_ghost.begin(),
3482 : connected_nodes_to_ghost.end(),
3483 : extra_ghost_elem_inserter<Node>(mesh));
3484 :
3485 22158 : mesh.comm().allgather_packed_range(&mesh,
3486 : boundary_elems_to_ghost.begin(),
3487 : boundary_elems_to_ghost.end(),
3488 : extra_ghost_elem_inserter<Elem>(mesh));
3489 :
3490 22158 : const auto & current_ghost_elems = mesh.extra_ghost_elems();
3491 :
3492 44316 : std::set_difference(current_ghost_elems.begin(),
3493 : current_ghost_elems.end(),
3494 : prior_ghost_elems.begin(),
3495 : prior_ghost_elems.end(),
3496 22158 : std::inserter(_ghost_elems_from_ghost_boundaries,
3497 : _ghost_elems_from_ghost_boundaries.begin()));
3498 22158 : }
3499 :
3500 : unsigned int
3501 11484 : MooseMesh::getPatchSize() const
3502 : {
3503 11484 : return _patch_size;
3504 : }
3505 :
3506 : void
3507 0 : MooseMesh::setPatchUpdateStrategy(Moose::PatchUpdateType patch_update_strategy)
3508 : {
3509 0 : _patch_update_strategy = patch_update_strategy;
3510 0 : }
3511 :
3512 : const Moose::PatchUpdateType &
3513 36409 : MooseMesh::getPatchUpdateStrategy() const
3514 : {
3515 36409 : return _patch_update_strategy;
3516 : }
3517 :
3518 : BoundingBox
3519 114404 : MooseMesh::getInflatedProcessorBoundingBox(Real inflation_multiplier) const
3520 : {
3521 : // Grab a bounding box to speed things up. Note that
3522 : // local_bounding_box is *not* equivalent to processor_bounding_box
3523 : // with processor_id() except in serial.
3524 114404 : BoundingBox bbox = MeshTools::create_local_bounding_box(getMesh());
3525 :
3526 : // Inflate the bbox just a bit to deal with roundoff
3527 : // Adding 1% of the diagonal size in each direction on each end
3528 114404 : Real inflation_amount = inflation_multiplier * (bbox.max() - bbox.min()).norm();
3529 114404 : Point inflation(inflation_amount, inflation_amount, inflation_amount);
3530 :
3531 114404 : bbox.first -= inflation; // min
3532 114404 : bbox.second += inflation; // max
3533 :
3534 228808 : return bbox;
3535 : }
3536 :
3537 158630 : MooseMesh::operator libMesh::MeshBase &() { return getMesh(); }
3538 :
3539 2990 : MooseMesh::operator const libMesh::MeshBase &() const { return getMesh(); }
3540 :
3541 : const MeshBase *
3542 346857 : MooseMesh::getMeshPtr() const
3543 : {
3544 346857 : return _mesh.get();
3545 : }
3546 :
3547 : MeshBase &
3548 48558357 : MooseMesh::getMesh()
3549 : {
3550 : mooseAssert(_mesh, "Mesh hasn't been created");
3551 48558357 : return *_mesh;
3552 : }
3553 :
3554 : const MeshBase &
3555 708004760 : MooseMesh::getMesh() const
3556 : {
3557 : mooseAssert(_mesh, "Mesh hasn't been created");
3558 708004760 : return *_mesh;
3559 : }
3560 :
3561 : void
3562 0 : MooseMesh::printInfo(std::ostream & os, const unsigned int verbosity /* = 0 */) const
3563 : {
3564 0 : os << '\n';
3565 0 : getMesh().print_info(os, verbosity);
3566 0 : os << std::flush;
3567 0 : }
3568 :
3569 : const std::vector<dof_id_type> &
3570 229 : MooseMesh::getNodeList(boundary_id_type nodeset_id) const
3571 : {
3572 : std::map<boundary_id_type, std::vector<dof_id_type>>::const_iterator it =
3573 229 : _node_set_nodes.find(nodeset_id);
3574 :
3575 229 : if (it == _node_set_nodes.end())
3576 : {
3577 : // On a distributed mesh we might not know about a remote nodeset,
3578 : // so we'll return an empty vector and hope the nodeset exists
3579 : // elsewhere.
3580 0 : if (!getMesh().is_serial())
3581 : {
3582 0 : static const std::vector<dof_id_type> empty_vec;
3583 0 : return empty_vec;
3584 : }
3585 : // On a replicated mesh we should know about every nodeset and if
3586 : // we're asked for one that doesn't exist then it must be a bug.
3587 : else
3588 : {
3589 0 : mooseError("Unable to nodeset ID: ", nodeset_id, '.');
3590 : }
3591 : }
3592 :
3593 229 : return it->second;
3594 : }
3595 :
3596 : const std::set<BoundaryID> &
3597 4678728 : MooseMesh::getSubdomainBoundaryIds(const SubdomainID subdomain_id) const
3598 : {
3599 4678728 : const auto it = _sub_to_data.find(subdomain_id);
3600 :
3601 4678728 : if (it == _sub_to_data.end())
3602 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3603 :
3604 9357456 : return it->second.boundary_ids;
3605 : }
3606 :
3607 : std::set<BoundaryID>
3608 22 : MooseMesh::getSubdomainInterfaceBoundaryIds(const SubdomainID subdomain_id) const
3609 : {
3610 22 : const auto & bnd_ids = getSubdomainBoundaryIds(subdomain_id);
3611 22 : std::set<BoundaryID> boundary_ids(bnd_ids.begin(), bnd_ids.end());
3612 : std::unordered_map<SubdomainID, std::set<BoundaryID>>::const_iterator it =
3613 22 : _neighbor_subdomain_boundary_ids.find(subdomain_id);
3614 :
3615 22 : boundary_ids.insert(it->second.begin(), it->second.end());
3616 :
3617 44 : return boundary_ids;
3618 0 : }
3619 :
3620 : std::set<SubdomainID>
3621 203 : MooseMesh::getBoundaryConnectedBlocks(const BoundaryID bid) const
3622 : {
3623 203 : std::set<SubdomainID> subdomain_ids;
3624 763 : for (const auto & [sub_id, data] : _sub_to_data)
3625 560 : if (data.boundary_ids.find(bid) != data.boundary_ids.end())
3626 203 : subdomain_ids.insert(sub_id);
3627 :
3628 203 : return subdomain_ids;
3629 0 : }
3630 :
3631 : std::set<SubdomainID>
3632 169 : MooseMesh::getBoundaryConnectedSecondaryBlocks(const BoundaryID bid) const
3633 : {
3634 169 : std::set<SubdomainID> subdomain_ids;
3635 507 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3636 338 : if (it.second.find(bid) != it.second.end())
3637 169 : subdomain_ids.insert(it.first);
3638 :
3639 169 : return subdomain_ids;
3640 0 : }
3641 :
3642 : std::set<SubdomainID>
3643 11 : MooseMesh::getInterfaceConnectedBlocks(const BoundaryID bid) const
3644 : {
3645 11 : std::set<SubdomainID> subdomain_ids = getBoundaryConnectedBlocks(bid);
3646 110 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3647 99 : if (it.second.find(bid) != it.second.end())
3648 44 : subdomain_ids.insert(it.first);
3649 :
3650 11 : return subdomain_ids;
3651 0 : }
3652 :
3653 : const std::set<SubdomainID> &
3654 0 : MooseMesh::getBlockConnectedBlocks(const SubdomainID subdomain_id) const
3655 : {
3656 0 : const auto it = _sub_to_data.find(subdomain_id);
3657 :
3658 0 : if (it == _sub_to_data.end())
3659 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3660 :
3661 0 : return it->second.neighbor_subs;
3662 : }
3663 :
3664 : bool
3665 1216264 : MooseMesh::isBoundaryNode(dof_id_type node_id) const
3666 : {
3667 1216264 : bool found_node = false;
3668 4992112 : for (const auto & it : _bnd_node_ids)
3669 : {
3670 4053776 : if (it.second.find(node_id) != it.second.end())
3671 : {
3672 277928 : found_node = true;
3673 277928 : break;
3674 : }
3675 : }
3676 1216264 : return found_node;
3677 : }
3678 :
3679 : bool
3680 995742 : MooseMesh::isBoundaryNode(dof_id_type node_id, BoundaryID bnd_id) const
3681 : {
3682 995742 : bool found_node = false;
3683 995742 : std::map<boundary_id_type, std::set<dof_id_type>>::const_iterator it = _bnd_node_ids.find(bnd_id);
3684 995742 : if (it != _bnd_node_ids.end())
3685 935442 : if (it->second.find(node_id) != it->second.end())
3686 11620 : found_node = true;
3687 995742 : return found_node;
3688 : }
3689 :
3690 : bool
3691 0 : MooseMesh::isBoundaryElem(dof_id_type elem_id) const
3692 : {
3693 0 : bool found_elem = false;
3694 0 : for (const auto & it : _bnd_elem_ids)
3695 : {
3696 0 : if (it.second.find(elem_id) != it.second.end())
3697 : {
3698 0 : found_elem = true;
3699 0 : break;
3700 : }
3701 : }
3702 0 : return found_elem;
3703 : }
3704 :
3705 : bool
3706 425114 : MooseMesh::isBoundaryElem(dof_id_type elem_id, BoundaryID bnd_id) const
3707 : {
3708 425114 : bool found_elem = false;
3709 425114 : auto it = _bnd_elem_ids.find(bnd_id);
3710 425114 : if (it != _bnd_elem_ids.end())
3711 393181 : if (it->second.find(elem_id) != it->second.end())
3712 22342 : found_elem = true;
3713 425114 : return found_elem;
3714 : }
3715 :
3716 : void
3717 1276 : MooseMesh::errorIfDistributedMesh(std::string name) const
3718 : {
3719 1276 : if (_use_distributed_mesh)
3720 0 : mooseError("Cannot use ",
3721 : name,
3722 : " with DistributedMesh!\n",
3723 : "Consider specifying parallel_type = 'replicated' in your input file\n",
3724 : "to prevent it from being run with DistributedMesh.");
3725 1276 : }
3726 :
3727 : void
3728 69183 : MooseMesh::setPartitionerHelper(MeshBase * const mesh)
3729 : {
3730 69183 : if (_use_distributed_mesh && (_partitioner_name != "default" && _partitioner_name != "parmetis"))
3731 : {
3732 16 : _partitioner_name = "parmetis";
3733 16 : _partitioner_overridden = true;
3734 : }
3735 :
3736 69183 : setPartitioner(mesh ? *mesh : getMesh(), _partitioner_name, _use_distributed_mesh, _pars, *this);
3737 69183 : }
3738 :
3739 : void
3740 69183 : MooseMesh::setPartitioner(MeshBase & mesh_base,
3741 : MooseEnum & partitioner,
3742 : bool use_distributed_mesh,
3743 : const InputParameters & params,
3744 : MooseObject & context_obj)
3745 : {
3746 : // Set the partitioner based on partitioner name
3747 69183 : switch (partitioner)
3748 : {
3749 64238 : case -3: // default
3750 : // We'll use the default partitioner, but notify the user of which one is being used...
3751 64238 : if (use_distributed_mesh)
3752 21100 : partitioner = "parmetis";
3753 : else
3754 107376 : partitioner = "metis";
3755 64238 : break;
3756 :
3757 : // No need to explicitily create the metis or parmetis partitioners,
3758 : // They are the default for serial and parallel mesh respectively
3759 4833 : case -2: // metis
3760 : case -1: // parmetis
3761 4833 : break;
3762 :
3763 60 : case 0: // linear
3764 60 : mesh_base.partitioner().reset(new libMesh::LinearPartitioner);
3765 60 : break;
3766 52 : case 1: // centroid
3767 : {
3768 104 : if (!params.isParamValid("centroid_partitioner_direction"))
3769 0 : context_obj.paramError(
3770 : "centroid_partitioner_direction",
3771 : "If using the centroid partitioner you _must_ specify centroid_partitioner_direction!");
3772 :
3773 52 : MooseEnum direction = params.get<MooseEnum>("centroid_partitioner_direction");
3774 :
3775 52 : if (direction == "x")
3776 32 : mesh_base.partitioner().reset(
3777 16 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::X));
3778 36 : else if (direction == "y")
3779 72 : mesh_base.partitioner().reset(
3780 36 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Y));
3781 0 : else if (direction == "z")
3782 0 : mesh_base.partitioner().reset(
3783 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Z));
3784 0 : else if (direction == "radial")
3785 0 : mesh_base.partitioner().reset(
3786 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::RADIAL));
3787 52 : break;
3788 52 : }
3789 0 : case 2: // hilbert_sfc
3790 0 : mesh_base.partitioner().reset(new libMesh::HilbertSFCPartitioner);
3791 0 : break;
3792 0 : case 3: // morton_sfc
3793 0 : mesh_base.partitioner().reset(new libMesh::MortonSFCPartitioner);
3794 0 : break;
3795 : }
3796 69183 : }
3797 :
3798 : void
3799 1497 : MooseMesh::setCustomPartitioner(Partitioner * partitioner)
3800 : {
3801 1497 : _custom_partitioner = partitioner->clone();
3802 1497 : setIsCustomPartitionerRequested(true);
3803 1497 : if (_mesh)
3804 12 : _mesh->partitioner() = _custom_partitioner->clone();
3805 1497 : _partitioner_name = "custom";
3806 1497 : }
3807 :
3808 : bool
3809 0 : MooseMesh::isCustomPartitionerRequested() const
3810 : {
3811 0 : return _custom_partitioner_requested;
3812 : }
3813 :
3814 : bool
3815 144287 : MooseMesh::hasSecondOrderElements()
3816 : {
3817 144287 : bool mesh_has_second_order_elements = false;
3818 46159433 : for (auto it = activeLocalElementsBegin(), end = activeLocalElementsEnd(); it != end; ++it)
3819 23023701 : if ((*it)->default_order() == SECOND)
3820 : {
3821 16128 : mesh_has_second_order_elements = true;
3822 16128 : break;
3823 144287 : }
3824 :
3825 : // We checked our local elements, so take the max over all processors.
3826 144287 : comm().max(mesh_has_second_order_elements);
3827 144287 : return mesh_has_second_order_elements;
3828 : }
3829 :
3830 : void
3831 3001 : MooseMesh::setIsCustomPartitionerRequested(bool cpr)
3832 : {
3833 3001 : _custom_partitioner_requested = cpr;
3834 3001 : }
3835 :
3836 : std::unique_ptr<libMesh::PointLocatorBase>
3837 7000 : MooseMesh::getPointLocator() const
3838 : {
3839 7000 : return getMesh().sub_point_locator();
3840 : }
3841 :
3842 : void
3843 4528 : MooseMesh::buildFiniteVolumeInfo() const
3844 : {
3845 : mooseAssert(!Threads::in_threads,
3846 : "This routine has not been implemented for threads. Please query this routine before "
3847 : "a threaded region or contact a MOOSE developer to discuss.");
3848 4528 : _finite_volume_info_dirty = false;
3849 :
3850 : using Keytype = std::pair<const Elem *, unsigned short int>;
3851 :
3852 : // create a map from elem/side --> boundary ids
3853 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>> side_list =
3854 4528 : buildActiveSideList();
3855 4528 : std::map<Keytype, std::set<boundary_id_type>> side_map;
3856 160910 : for (auto & [elem_id, side, bc_id] : side_list)
3857 : {
3858 156382 : const Elem * elem = _mesh->elem_ptr(elem_id);
3859 156382 : Keytype key(elem, side);
3860 156382 : auto & bc_set = side_map[key];
3861 156382 : bc_set.insert(bc_id);
3862 : }
3863 :
3864 4528 : _face_info.clear();
3865 4528 : _all_face_info.clear();
3866 4528 : _elem_side_to_face_info.clear();
3867 :
3868 4528 : _elem_to_elem_info.clear();
3869 4528 : _elem_info.clear();
3870 :
3871 : // by performing the element ID comparison check in the below loop, we are ensuring that we never
3872 : // double count face contributions. If a face lies along a process boundary, the only process that
3873 : // will contribute to both sides of the face residuals/Jacobians will be the process that owns the
3874 : // element with the lower ID.
3875 4528 : auto begin = getMesh().active_elements_begin();
3876 4528 : auto end = getMesh().active_elements_end();
3877 :
3878 : // We prepare a map connecting the Elem* and the corresponding ElemInfo
3879 : // for the active elements.
3880 4528 : _elem_to_elem_info.reserve(nActiveLocalElem());
3881 4528 : unsigned int num_sides = 0;
3882 1146389 : for (const Elem * elem : as_range(begin, end))
3883 : {
3884 1141861 : _elem_to_elem_info.emplace(elem->id(), elem);
3885 1141861 : num_sides += elem->n_sides();
3886 4528 : }
3887 :
3888 : // Used to speed up FaceInfo creation:
3889 : // - element side builder that caches per type of element
3890 4528 : libMesh::ElemSideBuilder side_builder;
3891 :
3892 4528 : _all_face_info.reserve(num_sides / 2);
3893 4528 : dof_id_type face_index = 0;
3894 2288250 : for (const Elem * elem : as_range(begin, end))
3895 : {
3896 5086275 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
3897 : {
3898 : // get the neighbor element
3899 3944414 : const Elem * neighbor = elem->neighbor_ptr(side);
3900 :
3901 : // Check if the FaceInfo shall belong to the element. If yes,
3902 : // create and initialize the FaceInfo. We need this to ensure that
3903 : // we do not duplicate FaceInfo-s.
3904 3944414 : if (Moose::FV::elemHasFaceInfo(*elem, neighbor))
3905 : {
3906 : mooseAssert(!neighbor || (neighbor->level() < elem->level() ? neighbor->active() : true),
3907 : "If the neighbor is coarser than the element, we expect that the neighbor must "
3908 : "be active.");
3909 :
3910 : // We construct the faceInfo using the elementinfo and side index
3911 : mooseAssert(elem->default_order() < 4, "Did not expect such high element orders in FV");
3912 4097254 : _all_face_info.emplace_back(
3913 2048627 : &_elem_to_elem_info[elem->id()], side, face_index++, side_builder);
3914 :
3915 2048627 : auto & fi = _all_face_info.back();
3916 :
3917 : // get all the sidesets that this face is contained in and cache them
3918 : // in the face info.
3919 2048627 : std::set<boundary_id_type> & boundary_ids = fi.boundaryIDs();
3920 2048627 : boundary_ids.clear();
3921 :
3922 : // We initialize the weights/other information in faceInfo. If the neighbor does not exist
3923 : // or is remote (so when we are on some sort of mesh boundary), we initialize the ghost
3924 : // cell and use it to compute the weights corresponding to the faceInfo.
3925 2048627 : if (!neighbor || neighbor == libMesh::remote_elem)
3926 150017 : fi.computeBoundaryCoefficients();
3927 : else
3928 1898610 : fi.computeInternalCoefficients(&_elem_to_elem_info[neighbor->id()]);
3929 :
3930 2048627 : auto lit = side_map.find(Keytype(&fi.elem(), fi.elemSideID()));
3931 2048627 : if (lit != side_map.end())
3932 149793 : boundary_ids.insert(lit->second.begin(), lit->second.end());
3933 :
3934 2048627 : if (fi.neighborPtr())
3935 : {
3936 1898610 : auto rit = side_map.find(Keytype(fi.neighborPtr(), fi.neighborSideID()));
3937 1898610 : if (rit != side_map.end())
3938 3972 : boundary_ids.insert(rit->second.begin(), rit->second.end());
3939 : }
3940 : }
3941 : }
3942 4528 : }
3943 :
3944 : // Build the local face info and elem_side to face info maps. We need to do this after
3945 : // _all_face_info is finished being constructed because emplace_back invalidates all iterators and
3946 : // references if ever the new size exceeds capacity
3947 4528 : _elem_side_to_face_info.reserve(_all_face_info.size());
3948 : // heuristic to avoid resizing too much
3949 4528 : _face_info.reserve(_all_face_info.size());
3950 2053155 : for (auto & fi : _all_face_info)
3951 : {
3952 2048627 : const Elem * const elem = &fi.elem();
3953 2048627 : const auto side = fi.elemSideID();
3954 :
3955 : #ifndef NDEBUG
3956 : auto pair_it =
3957 : #endif
3958 2048627 : _elem_side_to_face_info.emplace(std::make_pair(elem, side), &fi);
3959 : mooseAssert(pair_it.second, "We should be adding unique FaceInfo objects.");
3960 :
3961 : // We will add the faces on processor boundaries to the list of face infos on each
3962 : // associated processor.
3963 2629614 : if (fi.elem().processor_id() == this->processor_id() ||
3964 580987 : (fi.neighborPtr() && (fi.neighborPtr()->processor_id() == this->processor_id())))
3965 1751577 : _face_info.push_back(&fi);
3966 : }
3967 :
3968 4528 : _elem_info.reserve(nActiveLocalElem());
3969 1146389 : for (auto & ei : _elem_to_elem_info)
3970 1141861 : if (ei.second.elem()->processor_id() == this->processor_id())
3971 980987 : _elem_info.push_back(&ei.second);
3972 4528 : }
3973 :
3974 : const FaceInfo *
3975 123061313 : MooseMesh::faceInfo(const Elem * elem, unsigned int side) const
3976 : {
3977 123061313 : auto it = _elem_side_to_face_info.find(std::make_pair(elem, side));
3978 :
3979 123061313 : if (it == _elem_side_to_face_info.end())
3980 792 : return nullptr;
3981 : else
3982 : {
3983 : mooseAssert(it->second,
3984 : "For some reason, the FaceInfo object is NULL! Try calling "
3985 : "`buildFiniteVolumeInfo()` before using this accessor!");
3986 123060521 : return it->second;
3987 : }
3988 : }
3989 :
3990 : const ElemInfo &
3991 109109413 : MooseMesh::elemInfo(const dof_id_type id) const
3992 : {
3993 109109413 : return libmesh_map_find(_elem_to_elem_info, id);
3994 : }
3995 :
3996 : void
3997 4508 : MooseMesh::computeFiniteVolumeCoords() const
3998 : {
3999 4508 : if (_finite_volume_info_dirty)
4000 0 : mooseError("Trying to compute face- and elem-info coords when the information is dirty");
4001 :
4002 2052415 : for (auto & fi : _all_face_info)
4003 : {
4004 : // get elem & neighbor elements, and set subdomain ids
4005 2047907 : const SubdomainID elem_subdomain_id = fi.elemSubdomainID();
4006 2047907 : const SubdomainID neighbor_subdomain_id = fi.neighborSubdomainID();
4007 :
4008 2047907 : coordTransformFactor(
4009 2047907 : *this, elem_subdomain_id, fi.faceCentroid(), fi.faceCoord(), neighbor_subdomain_id);
4010 : }
4011 :
4012 1146209 : for (auto & ei : _elem_to_elem_info)
4013 1141701 : coordTransformFactor(
4014 2283402 : *this, ei.second.subdomain_id(), ei.second.centroid(), ei.second.coordFactor());
4015 4508 : }
4016 :
4017 : MooseEnum
4018 201466 : MooseMesh::partitioning()
4019 : {
4020 : MooseEnum partitioning(
4021 604398 : "default=-3 metis=-2 parmetis=-1 linear=0 centroid hilbert_sfc morton_sfc custom", "default");
4022 201466 : return partitioning;
4023 : }
4024 :
4025 : MooseEnum
4026 3393 : MooseMesh::elemTypes()
4027 : {
4028 : MooseEnum elemTypes(
4029 : "EDGE EDGE2 EDGE3 EDGE4 QUAD QUAD4 QUAD8 QUAD9 TRI3 TRI6 HEX HEX8 HEX20 HEX27 TET4 TET10 "
4030 10179 : "PRISM6 PRISM15 PRISM18 PYRAMID5 PYRAMID13 PYRAMID14");
4031 3393 : return elemTypes;
4032 : }
4033 :
4034 : void
4035 34845 : MooseMesh::allowRemoteElementRemoval(const bool allow_remote_element_removal)
4036 : {
4037 34845 : _allow_remote_element_removal = allow_remote_element_removal;
4038 34845 : if (_mesh)
4039 15924 : _mesh->allow_remote_element_removal(allow_remote_element_removal);
4040 :
4041 34845 : if (!allow_remote_element_removal)
4042 : // If we're not allowing remote element removal now, then we will need deletion later after
4043 : // late geoemetric ghosting functors have been added (late geometric ghosting functor addition
4044 : // happens when algebraic ghosting functors are added)
4045 34845 : _need_delete = true;
4046 34845 : }
4047 :
4048 : void
4049 17384 : MooseMesh::deleteRemoteElements()
4050 : {
4051 17384 : _allow_remote_element_removal = true;
4052 17384 : if (!_mesh)
4053 0 : mooseError("Cannot delete remote elements because we have not yet attached a MeshBase");
4054 :
4055 17384 : _mesh->allow_remote_element_removal(true);
4056 :
4057 17384 : _mesh->delete_remote_elements();
4058 17384 : }
4059 :
4060 : void
4061 4504 : MooseMesh::cacheFaceInfoVariableOwnership() const
4062 : {
4063 : mooseAssert(
4064 : !Threads::in_threads,
4065 : "Performing writes to faceInfo variable association maps. This must be done unthreaded!");
4066 :
4067 4504 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
4068 :
4069 4099611 : auto face_lambda = [this](const SubdomainID elem_subdomain_id,
4070 : const SubdomainID neighbor_subdomain_id,
4071 : SystemBase & sys,
4072 : std::vector<std::vector<FaceInfo::VarFaceNeighbors>> & face_type_vector)
4073 : {
4074 4099611 : face_type_vector[sys.number()].resize(sys.nVariables(), FaceInfo::VarFaceNeighbors::NEITHER);
4075 4099611 : const auto & variables = sys.getVariables(0);
4076 :
4077 8768127 : for (const auto & var : variables)
4078 : {
4079 4668516 : const unsigned int var_num = var->number();
4080 4668516 : const unsigned int sys_num = var->sys().number();
4081 4668516 : std::set<SubdomainID> var_subdomains = var->blockIDs();
4082 : /**
4083 : * The following paragraph of code assigns the VarFaceNeighbors
4084 : * 1. The face is an internal face of this variable if it is defined on
4085 : * the elem and neighbor subdomains
4086 : * 2. The face is an invalid face of this variable if it is neither defined
4087 : * on the elem nor the neighbor subdomains
4088 : * 3. If not 1. or 2. then this is a boundary for this variable and the else clause
4089 : * applies
4090 : */
4091 4668516 : bool var_defined_elem = var_subdomains.find(elem_subdomain_id) != var_subdomains.end();
4092 : bool var_defined_neighbor =
4093 4668516 : var_subdomains.find(neighbor_subdomain_id) != var_subdomains.end();
4094 4668516 : if (var_defined_elem && var_defined_neighbor)
4095 3906932 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::BOTH;
4096 761584 : else if (!var_defined_elem && !var_defined_neighbor)
4097 327057 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEITHER;
4098 : else
4099 : {
4100 : // this is a boundary face for this variable, set elem or neighbor
4101 434527 : if (var_defined_elem)
4102 429343 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::ELEM;
4103 5184 : else if (var_defined_neighbor)
4104 5184 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEIGHBOR;
4105 : else
4106 0 : mooseError("Should never get here");
4107 : }
4108 4668516 : }
4109 4099611 : };
4110 :
4111 : // We loop through the faces and check if they are internal, boundary or external to
4112 : // the variables in the problem
4113 2052363 : for (FaceInfo & face : _all_face_info)
4114 : {
4115 2047859 : const SubdomainID elem_subdomain_id = face.elemSubdomainID();
4116 2047859 : const SubdomainID neighbor_subdomain_id = face.neighborSubdomainID();
4117 :
4118 2047859 : auto & face_type_vector = face.faceType();
4119 :
4120 2047859 : face_type_vector.clear();
4121 2047859 : face_type_vector.resize(num_eqs);
4122 :
4123 : // First, we check the variables in the solver systems (linear/nonlinear)
4124 4099611 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4125 2051752 : face_lambda(elem_subdomain_id,
4126 : neighbor_subdomain_id,
4127 2051752 : _app.feProblem().getSolverSystem(i),
4128 : face_type_vector);
4129 :
4130 : // Then we check the variables in the auxiliary system
4131 2047859 : face_lambda(elem_subdomain_id,
4132 : neighbor_subdomain_id,
4133 2047859 : _app.feProblem().getAuxiliarySystem(),
4134 : face_type_vector);
4135 : }
4136 4504 : }
4137 :
4138 : void
4139 4504 : MooseMesh::cacheFVElementalDoFs() const
4140 : {
4141 : mooseAssert(!Threads::in_threads,
4142 : "Performing writes to elemInfo dof indices. This must be done unthreaded!");
4143 :
4144 2285944 : auto elem_lambda = [](const ElemInfo & elem_info,
4145 : SystemBase & sys,
4146 : std::vector<std::vector<dof_id_type>> & dof_vector)
4147 : {
4148 2285944 : if (sys.nFVVariables())
4149 : {
4150 1208331 : dof_vector[sys.number()].resize(sys.nVariables(), libMesh::DofObject::invalid_id);
4151 1208331 : const auto & variables = sys.getVariables(0);
4152 :
4153 3692668 : for (const auto & var : variables)
4154 2484337 : if (var->isFV())
4155 : {
4156 1438666 : const auto & var_subdomains = var->blockIDs();
4157 :
4158 : // We will only cache for FV variables and if they live on the current subdomain
4159 1438666 : if (var_subdomains.find(elem_info.subdomain_id()) != var_subdomains.end())
4160 : {
4161 1342399 : std::vector<dof_id_type> indices;
4162 1342399 : var->dofMap().dof_indices(elem_info.elem(), indices, var->number());
4163 : mooseAssert(indices.size() == 1, "We expect to have only one dof per element!");
4164 1342399 : dof_vector[sys.number()][var->number()] = indices[0];
4165 1342399 : }
4166 : }
4167 : }
4168 2285944 : };
4169 :
4170 4504 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
4171 :
4172 : // We loop through the elements in the mesh and cache the dof indices
4173 : // for the corresponding variables.
4174 1146189 : for (auto & ei_pair : _elem_to_elem_info)
4175 : {
4176 1141685 : auto & elem_info = ei_pair.second;
4177 1141685 : auto & dof_vector = elem_info.dofIndices();
4178 :
4179 1141685 : dof_vector.clear();
4180 1141685 : dof_vector.resize(num_eqs);
4181 :
4182 : // First, we cache the dof indices for the variables in the solver systems (linear, nonlinear)
4183 2285944 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4184 1144259 : elem_lambda(elem_info, _app.feProblem().getSolverSystem(i), dof_vector);
4185 :
4186 : // Then we cache the dof indices for the auxvariables
4187 1141685 : elem_lambda(elem_info, _app.feProblem().getAuxiliarySystem(), dof_vector);
4188 : }
4189 4504 : }
4190 :
4191 : void
4192 4504 : MooseMesh::setupFiniteVolumeMeshData() const
4193 : {
4194 4504 : buildFiniteVolumeInfo();
4195 4504 : computeFiniteVolumeCoords();
4196 4504 : cacheFaceInfoVariableOwnership();
4197 4504 : cacheFVElementalDoFs();
4198 4504 : }
4199 :
4200 : void
4201 64979 : MooseMesh::setCoordSystem(const std::vector<SubdomainName> & blocks,
4202 : const MultiMooseEnum & coord_sys)
4203 : {
4204 324895 : TIME_SECTION("setCoordSystem", 5, "Setting Coordinate System");
4205 64979 : if (!_provided_coord_blocks.empty() && (_provided_coord_blocks != blocks))
4206 : {
4207 0 : const std::string param_name = isParamValid("coord_block") ? "coord_block" : "block";
4208 0 : mooseWarning("Supplied blocks in the 'setCoordSystem' method do not match the value of the "
4209 : "'Mesh/",
4210 : param_name,
4211 : "' parameter. Did you provide different parameter values for 'Mesh/",
4212 : param_name,
4213 : "' and 'Problem/block'?. We will honor the parameter value from 'Mesh/",
4214 : param_name,
4215 : "'");
4216 : mooseAssert(_coord_system_set,
4217 : "If we are arriving here due to a bad specification in the Problem block, then we "
4218 : "should have already set our coordinate system subdomains from the Mesh block");
4219 0 : return;
4220 0 : }
4221 195999 : if (_pars.isParamSetByUser("coord_type") && getParam<MultiMooseEnum>("coord_type") != coord_sys)
4222 0 : mooseError("Supplied coordinate systems in the 'setCoordSystem' method do not match the value "
4223 : "of the 'Mesh/coord_type' parameter. Did you provide different parameter values for "
4224 : "'coord_type' to 'Mesh' and 'Problem'?");
4225 :
4226 : // If blocks contain ANY_BLOCK_ID, it should be the only block specified, and coord_sys should
4227 : // have one and only one entry. In that case, the same coordinate system will be set for all
4228 : // subdomains.
4229 64979 : if (blocks.size() == 1 && blocks[0] == "ANY_BLOCK_ID")
4230 : {
4231 0 : if (coord_sys.size() > 1)
4232 0 : mooseError("If you specify ANY_BLOCK_ID as the only block, you must also specify a single "
4233 : "coordinate system for it.");
4234 0 : if (!_mesh->is_prepared())
4235 0 : mooseError(
4236 : "You cannot set the coordinate system for ANY_BLOCK_ID before the mesh is prepared. "
4237 : "Please call this method after the mesh is prepared.");
4238 0 : const auto coord_type = coord_sys.size() == 0
4239 0 : ? Moose::COORD_XYZ
4240 0 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4241 0 : for (const auto sid : meshSubdomains())
4242 0 : _coord_sys[sid] = coord_type;
4243 0 : return;
4244 : }
4245 :
4246 : // If multiple blocks are specified, but one of them is ANY_BLOCK_ID, let's emit a helpful error
4247 64979 : if (std::find(blocks.begin(), blocks.end(), "ANY_BLOCK_ID") != blocks.end())
4248 0 : mooseError("You cannot specify ANY_BLOCK_ID together with other blocks in the "
4249 : "setCoordSystem() method. If you want to set the same coordinate system for all "
4250 : "blocks, use ANY_BLOCK_ID as the only block.");
4251 :
4252 64979 : auto subdomains = meshSubdomains();
4253 : // It's possible that a user has called this API before the mesh is prepared and consequently we
4254 : // don't yet have the subdomains in meshSubdomains()
4255 65378 : for (const auto & sub_name : blocks)
4256 : {
4257 399 : const auto sub_id = getSubdomainID(sub_name);
4258 399 : subdomains.insert(sub_id);
4259 : }
4260 :
4261 64979 : if (coord_sys.size() <= 1)
4262 : {
4263 : // We will specify the same coordinate system for all blocks
4264 64955 : const auto coord_type = coord_sys.size() == 0
4265 64955 : ? Moose::COORD_XYZ
4266 64955 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4267 155907 : for (const auto sid : subdomains)
4268 90952 : _coord_sys[sid] = coord_type;
4269 : }
4270 : else
4271 : {
4272 24 : if (blocks.size() != coord_sys.size())
4273 0 : mooseError("Number of blocks and coordinate systems does not match.");
4274 :
4275 96 : for (const auto i : index_range(blocks))
4276 : {
4277 72 : SubdomainID sid = getSubdomainID(blocks[i]);
4278 : Moose::CoordinateSystemType coord_type =
4279 72 : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[i]);
4280 72 : _coord_sys[sid] = coord_type;
4281 : }
4282 :
4283 96 : for (const auto & sid : subdomains)
4284 72 : if (_coord_sys.find(sid) == _coord_sys.end())
4285 0 : mooseError("Subdomain '" + Moose::stringify(sid) +
4286 : "' does not have a coordinate system specified.");
4287 : }
4288 :
4289 64979 : _coord_system_set = true;
4290 :
4291 64979 : updateCoordTransform();
4292 64979 : }
4293 :
4294 : Moose::CoordinateSystemType
4295 2285885020 : MooseMesh::getCoordSystem(SubdomainID sid) const
4296 : {
4297 2285885020 : auto it = _coord_sys.find(sid);
4298 2285885020 : if (it != _coord_sys.end())
4299 4571770040 : return (*it).second;
4300 : else
4301 0 : mooseError("Requested subdomain ", sid, " does not exist.");
4302 : }
4303 :
4304 : Moose::CoordinateSystemType
4305 55126 : MooseMesh::getUniqueCoordSystem() const
4306 : {
4307 55126 : const auto unique_system = _coord_sys.find(*meshSubdomains().begin())->second;
4308 : // Check that it is actually unique
4309 55126 : bool result = std::all_of(
4310 55126 : std::next(_coord_sys.begin()),
4311 55126 : _coord_sys.end(),
4312 4346 : [unique_system](
4313 : typename std::unordered_map<SubdomainID, Moose::CoordinateSystemType>::const_reference
4314 4346 : item) { return (item.second == unique_system); });
4315 55126 : if (!result)
4316 0 : mooseError("The unique coordinate system of the mesh was requested by the mesh contains "
4317 : "multiple blocks with different coordinate systems");
4318 :
4319 55126 : if (usingGeneralAxisymmetricCoordAxes())
4320 0 : mooseError("General axisymmetric coordinate axes are being used, and it is currently "
4321 : "conservatively assumed that in this case there is no unique coordinate system.");
4322 :
4323 55126 : return unique_system;
4324 : }
4325 :
4326 : const std::map<SubdomainID, Moose::CoordinateSystemType> &
4327 67983 : MooseMesh::getCoordSystem() const
4328 : {
4329 67983 : return _coord_sys;
4330 : }
4331 :
4332 : void
4333 0 : MooseMesh::setAxisymmetricCoordAxis(const MooseEnum & rz_coord_axis)
4334 : {
4335 0 : _rz_coord_axis = rz_coord_axis;
4336 :
4337 0 : updateCoordTransform();
4338 0 : }
4339 :
4340 : void
4341 17 : MooseMesh::setGeneralAxisymmetricCoordAxes(
4342 : const std::vector<SubdomainName> & blocks,
4343 : const std::vector<std::pair<Point, RealVectorValue>> & axes)
4344 : {
4345 : // Set the axes for the given blocks
4346 : mooseAssert(blocks.size() == axes.size(), "Blocks and axes vectors must be the same length.");
4347 58 : for (const auto i : index_range(blocks))
4348 : {
4349 41 : const auto subdomain_id = getSubdomainID(blocks[i]);
4350 41 : const auto it = _coord_sys.find(subdomain_id);
4351 41 : if (it == _coord_sys.end())
4352 0 : mooseError("The block '",
4353 0 : blocks[i],
4354 : "' has not set a coordinate system. Make sure to call setCoordSystem() before "
4355 : "setGeneralAxisymmetricCoordAxes().");
4356 : else
4357 : {
4358 41 : if (it->second == Moose::COORD_RZ)
4359 : {
4360 41 : const auto direction = axes[i].second;
4361 41 : if (direction.is_zero())
4362 0 : mooseError("Only nonzero vectors may be supplied for RZ directions.");
4363 :
4364 41 : _subdomain_id_to_rz_coord_axis[subdomain_id] =
4365 82 : std::make_pair(axes[i].first, direction.unit());
4366 : }
4367 : else
4368 0 : mooseError("The block '",
4369 0 : blocks[i],
4370 : "' was provided in setGeneralAxisymmetricCoordAxes(), but the coordinate system "
4371 : "for this block is not 'RZ'.");
4372 : }
4373 : }
4374 :
4375 : // Make sure there are no RZ blocks that still do not have axes
4376 17 : const auto all_subdomain_ids = meshSubdomains();
4377 70 : for (const auto subdomain_id : all_subdomain_ids)
4378 94 : if (getCoordSystem(subdomain_id) == Moose::COORD_RZ &&
4379 41 : !_subdomain_id_to_rz_coord_axis.count(subdomain_id))
4380 0 : mooseError("The block '",
4381 0 : getSubdomainName(subdomain_id),
4382 : "' was specified to use the 'RZ' coordinate system but was not given in "
4383 : "setGeneralAxisymmetricCoordAxes().");
4384 :
4385 17 : updateCoordTransform();
4386 17 : }
4387 :
4388 : const std::pair<Point, RealVectorValue> &
4389 1052515 : MooseMesh::getGeneralAxisymmetricCoordAxis(SubdomainID subdomain_id) const
4390 : {
4391 1052515 : auto it = _subdomain_id_to_rz_coord_axis.find(subdomain_id);
4392 1052515 : if (it != _subdomain_id_to_rz_coord_axis.end())
4393 2105030 : return (*it).second;
4394 : else
4395 0 : mooseError("Requested subdomain ", subdomain_id, " does not exist.");
4396 : }
4397 :
4398 : bool
4399 24301557 : MooseMesh::usingGeneralAxisymmetricCoordAxes() const
4400 : {
4401 24301557 : return _subdomain_id_to_rz_coord_axis.size() > 0;
4402 : }
4403 :
4404 : void
4405 67983 : MooseMesh::updateCoordTransform()
4406 : {
4407 67983 : if (!_coord_transform)
4408 67962 : _coord_transform = std::make_unique<MooseAppCoordTransform>(*this);
4409 : else
4410 21 : _coord_transform->setCoordinateSystem(*this);
4411 67983 : }
4412 :
4413 : unsigned int
4414 20681695 : MooseMesh::getAxisymmetricRadialCoord() const
4415 : {
4416 20681695 : if (usingGeneralAxisymmetricCoordAxes())
4417 0 : mooseError("getAxisymmetricRadialCoord() should not be called if "
4418 : "setGeneralAxisymmetricCoordAxes() has been called.");
4419 :
4420 20681695 : if (_rz_coord_axis == 0)
4421 133200 : return 1; // if the rotation axis is x (0), then the radial direction is y (1)
4422 : else
4423 20548495 : return 0; // otherwise the radial direction is assumed to be x, i.e., the rotation axis is y
4424 : }
4425 :
4426 : void
4427 60411 : MooseMesh::checkCoordinateSystems()
4428 : {
4429 27714113 : for (const auto & elem : getMesh().element_ptr_range())
4430 : {
4431 13826854 : SubdomainID sid = elem->subdomain_id();
4432 13826854 : if (_coord_sys[sid] == Moose::COORD_RZ && elem->dim() == 3)
4433 3 : mooseError("An RZ coordinate system was requested for subdomain " + Moose::stringify(sid) +
4434 : " which contains 3D elements.");
4435 13826851 : if (_coord_sys[sid] == Moose::COORD_RSPHERICAL && elem->dim() > 1)
4436 0 : mooseError("An RSPHERICAL coordinate system was requested for subdomain " +
4437 0 : Moose::stringify(sid) + " which contains 2D or 3D elements.");
4438 60408 : }
4439 60408 : }
4440 :
4441 : void
4442 2022 : MooseMesh::setCoordData(const MooseMesh & other_mesh)
4443 : {
4444 2022 : _coord_sys = other_mesh._coord_sys;
4445 2022 : _rz_coord_axis = other_mesh._rz_coord_axis;
4446 2022 : _subdomain_id_to_rz_coord_axis = other_mesh._subdomain_id_to_rz_coord_axis;
4447 2022 : }
4448 :
4449 : const MooseUnits &
4450 2 : MooseMesh::lengthUnit() const
4451 : {
4452 : mooseAssert(_coord_transform, "This must be non-null");
4453 2 : return _coord_transform->lengthUnit();
4454 : }
4455 :
4456 : void
4457 67862 : MooseMesh::checkDuplicateSubdomainNames()
4458 : {
4459 67862 : std::map<SubdomainName, SubdomainID> subdomain;
4460 162952 : for (const auto & sbd_id : _mesh_subdomains)
4461 : {
4462 95093 : std::string sub_name = getSubdomainName(sbd_id);
4463 95093 : if (!sub_name.empty() && subdomain.count(sub_name) > 0)
4464 6 : mooseError("The subdomain name ",
4465 : sub_name,
4466 : " is used for both subdomain with ID=",
4467 3 : subdomain[sub_name],
4468 : " and ID=",
4469 : sbd_id,
4470 : ", Please rename one of them!");
4471 : else
4472 95090 : subdomain[sub_name] = sbd_id;
4473 95090 : }
4474 67859 : }
4475 :
4476 : const std::vector<QpMap> &
4477 800 : MooseMesh::getPRefinementMapHelper(
4478 : const Elem & elem,
4479 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4480 : {
4481 : // We are actually seeking the map stored with the p_level - 1 key, e.g. the refinement map that
4482 : // maps from the previous p_level to this element's p_level
4483 800 : return libmesh_map_find(map,
4484 : std::make_pair(elem.type(), cast_int<unsigned int>(elem.p_level() - 1)));
4485 : }
4486 :
4487 : const std::vector<QpMap> &
4488 0 : MooseMesh::getPCoarseningMapHelper(
4489 : const Elem & elem,
4490 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4491 : {
4492 : mooseAssert(elem.active() && elem.p_refinement_flag() == Elem::JUST_COARSENED,
4493 : "These are the conditions that should be met for requesting a coarsening map");
4494 0 : return libmesh_map_find(map, std::make_pair(elem.type(), elem.p_level()));
4495 : }
4496 :
4497 : const std::vector<QpMap> &
4498 800 : MooseMesh::getPRefinementMap(const Elem & elem) const
4499 : {
4500 800 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_map);
4501 : }
4502 :
4503 : const std::vector<QpMap> &
4504 0 : MooseMesh::getPRefinementSideMap(const Elem & elem) const
4505 : {
4506 0 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_side_map);
4507 : }
4508 :
4509 : const std::vector<QpMap> &
4510 0 : MooseMesh::getPCoarseningMap(const Elem & elem) const
4511 : {
4512 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_map);
4513 : }
4514 :
4515 : const std::vector<QpMap> &
4516 0 : MooseMesh::getPCoarseningSideMap(const Elem & elem) const
4517 : {
4518 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_side_map);
4519 : }
4520 :
4521 : bool
4522 26727 : MooseMesh::skipNoncriticalPartitioning() const
4523 : {
4524 26727 : return _mesh->skip_noncritical_partitioning();
4525 : }
|
