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 203681 : MooseMesh::validParams()
83 : {
84 203681 : InputParameters params = MooseObject::validParams();
85 :
86 814724 : MooseEnum parallel_type("DEFAULT REPLICATED DISTRIBUTED", "DEFAULT");
87 814724 : 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 611043 : params.addParam<bool>(
95 : "allow_renumbering",
96 407362 : true,
97 : "If allow_renumbering=false, node and element numbers are kept fixed until deletion");
98 :
99 611043 : params.addParam<MooseEnum>(
100 : "partitioner",
101 407362 : partitioning(),
102 : "Specifies a mesh partitioner to use when splitting the mesh for a parallel computation.");
103 814724 : MooseEnum direction("x y z radial");
104 814724 : 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 814724 : MooseEnum patch_update_strategy("never always auto iteration", "never");
110 814724 : 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 611043 : params.addParam<bool>(
127 : "construct_node_list_from_side_list",
128 407362 : true,
129 : "Whether or not to generate nodesets from the sidesets (currently often required).");
130 611043 : params.addParam<bool>(
131 : "displace_node_list_by_side_list",
132 407362 : 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 611043 : params.addParam<unsigned int>(
137 407362 : "patch_size", 40, "The number of nodes to consider in the NearestNode neighborhood.");
138 814724 : 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 611043 : params.addParam<unsigned int>("max_leaf_size",
144 407362 : 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 611043 : params.addParam<bool>("build_all_side_lowerd_mesh",
151 407362 : false,
152 : "True to build the lower-dimensional mesh for all sides.");
153 :
154 611043 : params.addParam<bool>("skip_refine_when_use_split",
155 407362 : true,
156 : "True to skip uniform refinements when using a pre-split mesh.");
157 :
158 814724 : 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 814724 : 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 814724 : 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 814724 : 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 814724 : 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 611043 : 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 203681 : 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 407362 : params.addPrivateParam<bool>("_mesh_generator_mesh", false);
205 :
206 : // Whether or not the mesh is pre split
207 611043 : params.addPrivateParam<bool>("_is_split", false);
208 :
209 407362 : params.registerBase("MooseMesh");
210 :
211 : // groups
212 814724 : params.addParamNamesToGroup("patch_update_strategy patch_size max_leaf_size", "Geometric search");
213 814724 : 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 814724 : 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 611043 : params.addParamNamesToGroup("partitioner centroid_partitioner_direction", "Partitioning");
220 :
221 407362 : return params;
222 203681 : }
223 :
224 66973 : MooseMesh::MooseMesh(const InputParameters & parameters)
225 : : MooseObject(parameters),
226 : Restartable(this, "Mesh"),
227 : PerfGraphInterface(this),
228 66973 : _parallel_type(getParam<MooseEnum>("parallel_type").getEnum<MooseMesh::ParallelType>()),
229 66973 : _use_distributed_mesh(false),
230 66973 : _distribution_overridden(false),
231 66973 : _parallel_type_overridden(false),
232 66973 : _mesh(nullptr),
233 133946 : _partitioner_name(getParam<MooseEnum>("partitioner")),
234 66973 : _partitioner_overridden(false),
235 66973 : _custom_partitioner_requested(false),
236 66973 : _uniform_refine_level(0),
237 133946 : _skip_refine_when_use_split(getParam<bool>("skip_refine_when_use_split")),
238 66973 : _skip_deletion_repartition_after_refine(false),
239 66973 : _is_nemesis(false),
240 133946 : _patch_size(getParam<unsigned int>("patch_size")),
241 133946 : _ghosting_patch_size(isParamValid("ghosting_patch_size")
242 133946 : ? getParam<unsigned int>("ghosting_patch_size")
243 66973 : : 5 * _patch_size),
244 133946 : _max_leaf_size(getParam<unsigned int>("max_leaf_size")),
245 66973 : _patch_update_strategy(
246 133946 : getParam<MooseEnum>("patch_update_strategy").getEnum<Moose::PatchUpdateType>()),
247 66973 : _regular_orthogonal_mesh(false),
248 133946 : _is_split(getParam<bool>("_is_split")),
249 66973 : _allow_recovery(true),
250 133946 : _construct_node_list_from_side_list(getParam<bool>("construct_node_list_from_side_list")),
251 133946 : _displace_node_list_by_side_list(getParam<bool>("displace_node_list_by_side_list")),
252 66973 : _need_delete(false),
253 66973 : _allow_remote_element_removal(true),
254 66973 : _need_ghost_ghosted_boundaries(true),
255 66973 : _is_displaced(false),
256 66973 : _coord_sys(
257 133946 : declareRestartableData<std::map<SubdomainID, Moose::CoordinateSystemType>>("coord_sys")),
258 133946 : _rz_coord_axis(getParam<MooseEnum>("rz_coord_axis")),
259 66973 : _coord_system_set(false),
260 653067 : _doing_p_refinement(false)
261 : {
262 200919 : 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 200919 : 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 200847 : else if (isParamValid("block"))
276 765 : _provided_coord_blocks = getParam<std::vector<SubdomainName>>("block");
277 :
278 200919 : if (getParam<bool>("build_all_side_lowerd_mesh"))
279 : // Do not initially allow removal of remote elements
280 223 : allowRemoteElementRemoval(false);
281 :
282 66973 : determineUseDistributedMesh();
283 :
284 : #ifdef MOOSE_KOKKOS_ENABLED
285 50310 : if (_app.isKokkosAvailable())
286 50310 : _kokkos_mesh = std::make_unique<Moose::Kokkos::Mesh>(*this);
287 : #endif
288 66973 : }
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 66007 : MooseMesh::~MooseMesh()
345 : {
346 66007 : freeBndNodes();
347 66007 : freeBndElems();
348 66007 : clearQuadratureNodes();
349 66007 : }
350 :
351 : void
352 220964 : MooseMesh::freeBndNodes()
353 : {
354 : // free memory
355 12599855 : for (auto & bnode : _bnd_nodes)
356 12378891 : delete bnode;
357 :
358 820518 : for (auto & it : _node_set_nodes)
359 599554 : it.second.clear();
360 :
361 220964 : _node_set_nodes.clear();
362 :
363 820669 : for (auto & it : _bnd_node_ids)
364 599705 : it.second.clear();
365 :
366 220964 : _bnd_node_ids.clear();
367 220964 : _bnd_node_range.reset();
368 220964 : }
369 :
370 : void
371 220964 : MooseMesh::freeBndElems()
372 : {
373 : // free memory
374 9628304 : for (auto & belem : _bnd_elems)
375 9407340 : delete belem;
376 :
377 799803 : for (auto & it : _bnd_elem_ids)
378 578839 : it.second.clear();
379 :
380 220964 : _bnd_elem_ids.clear();
381 220964 : _bnd_elem_range.reset();
382 220964 : }
383 :
384 : bool
385 137173 : MooseMesh::prepare(const MeshBase * const mesh_to_clone)
386 : {
387 685865 : TIME_SECTION("prepare", 2, "Preparing Mesh", true);
388 :
389 : parallel_object_only();
390 :
391 137173 : bool libmesh_mesh_prepared = false;
392 :
393 : mooseAssert(_mesh, "The MeshBase has not been constructed");
394 :
395 137173 : 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 114237 : getMesh().allow_renumbering(false);
398 :
399 137173 : 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 137024 : else if (!_mesh->is_prepared())
407 : {
408 18157 : _mesh->complete_preparation();
409 18157 : _moose_mesh_prepared = false;
410 18157 : libmesh_mesh_prepared = true;
411 : }
412 :
413 137173 : if (_moose_mesh_prepared)
414 68647 : return libmesh_mesh_prepared;
415 :
416 : // Collect (local) subdomain IDs
417 68526 : _mesh_subdomains.clear();
418 13333303 : for (const auto & elem : getMesh().element_ptr_range())
419 13333303 : _mesh_subdomains.insert(elem->subdomain_id());
420 :
421 68526 : bool need_subdomain_name_map_sync = false;
422 : // add explicitly requested subdomains
423 205846 : 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 205666 : 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 205176 : 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 68526 : if (need_subdomain_name_map_sync)
467 110 : _mesh->sync_subdomain_name_map();
468 :
469 : // Make sure nodesets have been generated
470 68526 : buildNodeListFromSideList();
471 :
472 : // Collect (local) boundary IDs
473 68526 : const std::set<BoundaryID> & local_bids = getMesh().get_boundary_info().get_boundary_ids();
474 68526 : _mesh_boundary_ids.insert(local_bids.begin(), local_bids.end());
475 :
476 : const std::set<BoundaryID> & local_node_bids =
477 68526 : getMesh().get_boundary_info().get_node_boundary_ids();
478 68526 : _mesh_nodeset_ids.insert(local_node_bids.begin(), local_node_bids.end());
479 :
480 : const std::set<BoundaryID> & local_side_bids =
481 68526 : getMesh().get_boundary_info().get_side_boundary_ids();
482 68526 : _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 137052 : auto add_sets = [this](const bool sidesets, auto & set_ids)
487 : {
488 137052 : const std::string type = sidesets ? "sideset" : "nodeset";
489 137052 : const std::string id_param = "add_" + type + "_ids";
490 137052 : const std::string name_param = "add_" + type + "_names";
491 :
492 137052 : 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 136998 : 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 137052 : };
535 :
536 68526 : add_sets(true, _mesh_sideset_ids);
537 68526 : add_sets(false, _mesh_nodeset_ids);
538 :
539 : // Communicate subdomain and boundary IDs if this is a parallel mesh
540 68526 : if (!getMesh().is_serial())
541 : {
542 8882 : _communicator.set_union(_mesh_subdomains);
543 8882 : _communicator.set_union(_mesh_boundary_ids);
544 8882 : _communicator.set_union(_mesh_nodeset_ids);
545 8882 : _communicator.set_union(_mesh_sideset_ids);
546 : }
547 :
548 68526 : if (!_built_from_other_mesh)
549 : {
550 65713 : if (!_coord_system_set)
551 196911 : setCoordSystem(_provided_coord_blocks, getParam<MultiMooseEnum>("coord_type"));
552 228 : 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 274155 : if (isParamValid("rz_coord_blocks") && isParamValid("rz_coord_origins") &&
562 68577 : 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 479563 : else if (isParamValid("rz_coord_blocks") || isParamValid("rz_coord_origins") ||
585 274036 : 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 68526 : detectOrthogonalDimRanges();
590 :
591 68526 : update();
592 :
593 : // Check if there is subdomain name duplication for the same subdomain ID
594 68526 : checkDuplicateSubdomainNames();
595 :
596 68523 : _moose_mesh_prepared = true;
597 :
598 68523 : return libmesh_mesh_prepared;
599 137170 : }
600 :
601 : bool
602 154957 : 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 154957 : 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 147158 : return false;
610 : }
611 :
612 7799 : _node_to_elem_map.clear();
613 7799 : _node_to_elem_map_built = false;
614 7799 : internalNodeToElemMap();
615 7799 : return true;
616 : }
617 :
618 : void
619 154957 : MooseMesh::update()
620 : {
621 774785 : TIME_SECTION("update", 3, "Updating Mesh", true);
622 :
623 : // Rebuild the boundary conditions
624 154957 : buildNodeListFromSideList();
625 :
626 154957 : buildNodeList();
627 154957 : buildBndElemList();
628 154957 : cacheInfo();
629 154957 : 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 154957 : _max_p_level = 0;
634 154957 : _max_h_level = 0;
635 27753158 : for (const auto & elem : getMesh().active_local_element_ptr_range())
636 : {
637 27598201 : if (elem->p_level() > _max_p_level)
638 658 : _max_p_level = elem->p_level();
639 27598201 : if (elem->level() > _max_h_level)
640 25854 : _max_h_level = elem->level();
641 154957 : }
642 154957 : comm().max(_max_p_level);
643 154957 : comm().max(_max_h_level);
644 :
645 : // the flag might have been set by calling doingPRefinement(true)
646 154957 : _doing_p_refinement = _doing_p_refinement || (_max_p_level > 0);
647 :
648 154957 : computeMaxPerElemAndSide();
649 :
650 : #ifdef MOOSE_KOKKOS_ENABLED
651 128666 : if (_app.getExecutioner() && _app.feProblem().initialized() &&
652 12623 : _app.feProblem().hasKokkosObjects())
653 0 : _kokkos_mesh->update();
654 : #endif
655 :
656 154957 : _finite_volume_info_dirty = true;
657 :
658 154957 : possiblyRebuildNodeToElemMap();
659 154957 : }
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 42688962 : MooseMesh::nodeRef(const dof_id_type i) const
839 : {
840 42688962 : const auto node_ptr = queryNodePtr(i);
841 : mooseAssert(node_ptr, "Missing node");
842 42688962 : return *node_ptr;
843 : }
844 :
845 : Node &
846 24016230 : MooseMesh::nodeRef(const dof_id_type i)
847 : {
848 24016230 : 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 42691706 : MooseMesh::queryNodePtr(const dof_id_type i) const
865 : {
866 42691706 : 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 42494933 : 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 83796 : MooseMesh::meshChanged()
887 : {
888 418980 : TIME_SECTION("meshChanged", 3, "Updating Because Mesh Changed");
889 :
890 83796 : update();
891 :
892 : // Delete all of the cached ranges
893 83796 : _active_node_range.reset();
894 83796 : _active_semilocal_node_range.reset();
895 83796 : _local_node_range.reset();
896 83796 : _bnd_node_range.reset();
897 83796 : _bnd_elem_range.reset();
898 :
899 : // Rebuild the ranges
900 83796 : getActiveLocalElementRange();
901 83796 : getActiveNodeRange();
902 83796 : getLocalNodeRange();
903 83796 : getBoundaryNodeRange();
904 83796 : getBoundaryElementRange();
905 :
906 : // Call the callback function onMeshChanged
907 83796 : onMeshChanged();
908 83796 : }
909 :
910 : void
911 83796 : MooseMesh::onMeshChanged()
912 : {
913 83796 : }
914 :
915 : void
916 208 : MooseMesh::cacheChangedLists()
917 : {
918 1040 : TIME_SECTION("cacheChangedLists", 5, "Caching Changed Lists");
919 :
920 208 : ConstElemRange elem_range(getMesh().local_elements_begin(), getMesh().local_elements_end(), 1);
921 208 : CacheChangedListsThread cclt(*this);
922 208 : Threads::parallel_reduce(elem_range, cclt);
923 :
924 208 : _coarsened_element_children.clear();
925 :
926 416 : _refined_elements = std::make_unique<ConstElemPointerRange>(cclt._refined_elements.begin(),
927 416 : cclt._refined_elements.end());
928 416 : _coarsened_elements = std::make_unique<ConstElemPointerRange>(cclt._coarsened_elements.begin(),
929 416 : cclt._coarsened_elements.end());
930 208 : _coarsened_element_children = cclt._coarsened_element_children;
931 208 : }
932 :
933 : ConstElemPointerRange *
934 208 : MooseMesh::refinedElementRange() const
935 : {
936 208 : return _refined_elements.get();
937 : }
938 :
939 : ConstElemPointerRange *
940 208 : MooseMesh::coarsenedElementRange() const
941 : {
942 208 : return _coarsened_elements.get();
943 : }
944 :
945 : const std::vector<const Elem *> &
946 2468 : MooseMesh::coarsenedElementChildren(const Elem * elem) const
947 : {
948 2468 : auto elem_to_child_pair = _coarsened_element_children.find(elem);
949 : mooseAssert(elem_to_child_pair != _coarsened_element_children.end(), "Missing element in map");
950 4936 : return elem_to_child_pair->second;
951 : }
952 :
953 : void
954 71641 : MooseMesh::updateActiveSemiLocalNodeRange(std::set<dof_id_type> & ghosted_elems)
955 : {
956 358205 : TIME_SECTION("updateActiveSemiLocalNodeRange", 5, "Updating ActiveSemiLocalNode Range");
957 :
958 71641 : _semilocal_node_list.clear();
959 :
960 : // First add the nodes connected to local elems
961 71641 : const ConstElemRange * active_local_elems = getActiveLocalElementRange();
962 13066191 : for (const auto & elem : *active_local_elems)
963 : {
964 82304557 : for (unsigned int n = 0; n < elem->n_nodes(); ++n)
965 : {
966 : // Since elem is const here but we require a non-const Node * to
967 : // store in the _semilocal_node_list (otherwise things like
968 : // UpdateDisplacedMeshThread don't work), we are using a
969 : // const_cast. A more long-term fix would be to have
970 : // getActiveLocalElementRange return a non-const ElemRange.
971 69310007 : Node * node = const_cast<Node *>(elem->node_ptr(n));
972 :
973 69310007 : _semilocal_node_list.insert(node);
974 : }
975 : }
976 :
977 : // Now add the nodes connected to ghosted_elems
978 116852 : for (const auto & ghost_elem_id : ghosted_elems)
979 : {
980 45211 : Elem * elem = getMesh().elem_ptr(ghost_elem_id);
981 250228 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
982 : {
983 205017 : Node * node = elem->node_ptr(n);
984 :
985 205017 : _semilocal_node_list.insert(node);
986 : }
987 : }
988 :
989 : // Now create the actual range
990 143282 : _active_semilocal_node_range = std::make_unique<SemiLocalNodeRange>(_semilocal_node_list.begin(),
991 143282 : _semilocal_node_list.end());
992 71641 : }
993 :
994 : bool
995 26305 : MooseMesh::isSemiLocal(Node * const node) const
996 : {
997 26305 : return _semilocal_node_list.find(node) != _semilocal_node_list.end();
998 : }
999 :
1000 : /**
1001 : * Helper class for sorting Boundary Nodes so that we always get the same
1002 : * order of application for boundary conditions.
1003 : */
1004 : class BndNodeCompare
1005 : {
1006 : public:
1007 154957 : BndNodeCompare() {}
1008 :
1009 121258006 : bool operator()(const BndNode * const & lhs, const BndNode * const & rhs)
1010 : {
1011 121258006 : if (lhs->_bnd_id < rhs->_bnd_id)
1012 22565546 : return true;
1013 :
1014 98692460 : if (lhs->_bnd_id > rhs->_bnd_id)
1015 10253667 : return false;
1016 :
1017 88438793 : if (lhs->_node->id() < rhs->_node->id())
1018 57157697 : return true;
1019 :
1020 31281096 : if (lhs->_node->id() > rhs->_node->id())
1021 31281096 : return false;
1022 :
1023 0 : return false;
1024 : }
1025 : };
1026 :
1027 : void
1028 154957 : MooseMesh::buildNodeList()
1029 : {
1030 774785 : TIME_SECTION("buildNodeList", 5, "Building Node List");
1031 :
1032 154957 : freeBndNodes();
1033 :
1034 154957 : auto bc_tuples = getMesh().get_boundary_info().build_node_list();
1035 :
1036 154957 : int n = bc_tuples.size();
1037 154957 : _bnd_nodes.clear();
1038 154957 : _bnd_nodes.reserve(n);
1039 12661381 : for (const auto & t : bc_tuples)
1040 : {
1041 12506424 : auto node_id = std::get<0>(t);
1042 12506424 : auto bc_id = std::get<1>(t);
1043 :
1044 12506424 : _bnd_nodes.push_back(new BndNode(getMesh().node_ptr(node_id), bc_id));
1045 12506424 : _node_set_nodes[bc_id].push_back(node_id);
1046 12506424 : _bnd_node_ids[bc_id].insert(node_id);
1047 : }
1048 :
1049 154957 : _bnd_nodes.reserve(_bnd_nodes.size() + _extra_bnd_nodes.size());
1050 155011 : for (unsigned int i = 0; i < _extra_bnd_nodes.size(); i++)
1051 : {
1052 54 : BndNode * bnode = new BndNode(_extra_bnd_nodes[i]._node, _extra_bnd_nodes[i]._bnd_id);
1053 54 : _bnd_nodes.push_back(bnode);
1054 54 : _bnd_node_ids[std::get<1>(bc_tuples[i])].insert(_extra_bnd_nodes[i]._node->id());
1055 : }
1056 :
1057 : // This sort is here so that boundary conditions are always applied in the same order
1058 154957 : std::sort(_bnd_nodes.begin(), _bnd_nodes.end(), BndNodeCompare());
1059 154957 : }
1060 :
1061 : void
1062 154957 : MooseMesh::computeMaxPerElemAndSide()
1063 : {
1064 154957 : auto & mesh = getMesh();
1065 :
1066 154957 : _max_sides_per_elem = 0;
1067 154957 : _max_nodes_per_elem = 0;
1068 154957 : _max_nodes_per_side = 0;
1069 :
1070 59545257 : for (auto & elem : as_range(mesh.local_elements_begin(), mesh.local_elements_end()))
1071 : {
1072 29695150 : _max_sides_per_elem = std::max(_max_sides_per_elem, elem->n_sides());
1073 29695150 : _max_nodes_per_elem = std::max(_max_nodes_per_elem, elem->n_nodes());
1074 :
1075 162442146 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
1076 132746996 : _max_nodes_per_side = std::max(_max_nodes_per_side, elem->side_ptr(side)->n_nodes());
1077 154957 : }
1078 :
1079 154957 : mesh.comm().max(_max_sides_per_elem);
1080 154957 : mesh.comm().max(_max_nodes_per_elem);
1081 154957 : mesh.comm().max(_max_nodes_per_side);
1082 154957 : }
1083 :
1084 : void
1085 154957 : MooseMesh::buildElemIDInfo()
1086 : {
1087 154957 : unsigned int n = getMesh().n_elem_integers() + 1;
1088 :
1089 154957 : _block_id_mapping.clear();
1090 154957 : _max_ids.clear();
1091 154957 : _min_ids.clear();
1092 154957 : _id_identical_flag.clear();
1093 :
1094 154957 : _block_id_mapping.resize(n);
1095 154957 : _max_ids.resize(n, std::numeric_limits<dof_id_type>::min());
1096 154957 : _min_ids.resize(n, std::numeric_limits<dof_id_type>::max());
1097 309914 : _id_identical_flag.resize(n, std::vector<bool>(n, true));
1098 27753158 : for (const auto & elem : getMesh().active_local_element_ptr_range())
1099 59317793 : for (unsigned int i = 0; i < n; ++i)
1100 : {
1101 31719592 : auto id = (i == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(i));
1102 31719592 : _block_id_mapping[i][elem->subdomain_id()].insert(id);
1103 31719592 : if (id > _max_ids[i])
1104 118545 : _max_ids[i] = id;
1105 31719592 : if (id < _min_ids[i])
1106 159768 : _min_ids[i] = id;
1107 76369894 : for (unsigned int j = 0; j < n; ++j)
1108 : {
1109 44650302 : auto idj = (j == n - 1 ? elem->subdomain_id() : elem->get_extra_integer(j));
1110 44650302 : if (i != j && _id_identical_flag[i][j] && id != idj)
1111 6742 : _id_identical_flag[i][j] = false;
1112 : }
1113 154957 : }
1114 :
1115 312351 : for (unsigned int i = 0; i < n; ++i)
1116 : {
1117 382969 : for (auto & blk : meshSubdomains())
1118 225575 : comm().set_union(_block_id_mapping[i][blk]);
1119 157394 : comm().min(_id_identical_flag[i]);
1120 : }
1121 154957 : comm().max(_max_ids);
1122 154957 : comm().min(_min_ids);
1123 154957 : }
1124 :
1125 : std::unordered_map<dof_id_type, std::set<dof_id_type>>
1126 11 : MooseMesh::getElemIDMapping(const std::string & from_id_name, const std::string & to_id_name) const
1127 : {
1128 11 : auto & mesh_base = getMesh();
1129 :
1130 11 : if (!mesh_base.has_elem_integer(from_id_name))
1131 0 : mooseError("Mesh does not have the element integer name '", from_id_name, "'");
1132 11 : if (!mesh_base.has_elem_integer(to_id_name))
1133 0 : mooseError("Mesh does not have the element integer name '", to_id_name, "'");
1134 :
1135 11 : const auto id1 = mesh_base.get_elem_integer_index(from_id_name);
1136 11 : const auto id2 = mesh_base.get_elem_integer_index(to_id_name);
1137 :
1138 11 : std::unordered_map<dof_id_type, std::set<dof_id_type>> id_map;
1139 33 : for (const auto id : getAllElemIDs(id1))
1140 33 : id_map[id] = std::set<dof_id_type>();
1141 :
1142 811 : for (const auto & elem : mesh_base.active_local_element_ptr_range())
1143 811 : id_map[elem->get_extra_integer(id1)].insert(elem->get_extra_integer(id2));
1144 :
1145 33 : for (auto & [id, ids] : id_map)
1146 : {
1147 22 : libmesh_ignore(id); // avoid overzealous gcc 9.4 unused var warning
1148 22 : comm().set_union(ids);
1149 : }
1150 :
1151 11 : return id_map;
1152 0 : }
1153 :
1154 : std::set<dof_id_type>
1155 50 : MooseMesh::getAllElemIDs(unsigned int elem_id_index) const
1156 : {
1157 50 : std::set<dof_id_type> unique_ids;
1158 139 : for (auto & pair : _block_id_mapping[elem_id_index])
1159 319 : for (auto & id : pair.second)
1160 230 : unique_ids.insert(id);
1161 50 : return unique_ids;
1162 0 : }
1163 :
1164 : std::set<dof_id_type>
1165 152 : MooseMesh::getElemIDsOnBlocks(unsigned int elem_id_index, const std::set<SubdomainID> & blks) const
1166 : {
1167 152 : std::set<dof_id_type> unique_ids;
1168 379 : for (auto & blk : blks)
1169 : {
1170 227 : auto it = _block_id_mapping[elem_id_index].find(blk);
1171 227 : if (it == _block_id_mapping[elem_id_index].end())
1172 0 : mooseError("Block ", blk, " is not available on the mesh");
1173 :
1174 532 : for (auto & mid : it->second)
1175 305 : unique_ids.insert(mid);
1176 : }
1177 152 : return unique_ids;
1178 0 : }
1179 :
1180 : void
1181 154957 : MooseMesh::buildBndElemList()
1182 : {
1183 774785 : TIME_SECTION("buildBndElemList", 5, "Building Boundary Elements List");
1184 :
1185 154957 : freeBndElems();
1186 :
1187 154957 : auto bc_tuples = getMesh().get_boundary_info().build_active_side_list();
1188 :
1189 154957 : int n = bc_tuples.size();
1190 154957 : _bnd_elems.clear();
1191 154957 : _bnd_elems.reserve(n);
1192 9676135 : for (const auto & t : bc_tuples)
1193 : {
1194 9521178 : auto elem_id = std::get<0>(t);
1195 9521178 : auto side_id = std::get<1>(t);
1196 9521178 : auto bc_id = std::get<2>(t);
1197 :
1198 9521178 : _bnd_elems.push_back(new BndElement(getMesh().elem_ptr(elem_id), side_id, bc_id));
1199 9521178 : _bnd_elem_ids[bc_id].insert(elem_id);
1200 : }
1201 154957 : }
1202 :
1203 : std::unordered_map<dof_id_type, std::vector<dof_id_type>> &
1204 997114 : MooseMesh::internalNodeToElemMap()
1205 : {
1206 997114 : if (!_node_to_elem_map_built) // Guard the creation with a double checked lock
1207 : {
1208 11867 : Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
1209 :
1210 11867 : if (!_node_to_elem_map_built)
1211 : {
1212 : // This is allowing the timing to be run even with threads
1213 : // This is safe because all threads will be waiting on this section when it runs
1214 : // NOTE: Do not copy this construction to other places without thinking REALLY hard about it
1215 : // The PerfGraph is NOT threadsafe and will cause all kinds of havok if care isn't taken
1216 11867 : auto in_threads = Threads::in_threads;
1217 11867 : Threads::in_threads = false;
1218 59335 : TIME_SECTION("nodeToElemMap", 5, "Building Node To Elem Map");
1219 11867 : Threads::in_threads = in_threads;
1220 :
1221 : mooseAssert(_node_to_elem_map.empty(), "Expected empty map before building");
1222 2984309 : for (const auto & elem : getMesh().active_element_ptr_range())
1223 18205478 : for (unsigned int n = 0; n < elem->n_nodes(); n++)
1224 15244903 : _node_to_elem_map[elem->node_id(n)].push_back(elem->id());
1225 :
1226 11867 : _node_to_elem_map_built = true; // MUST be set at the end for double-checked locking to work!
1227 11867 : }
1228 11867 : }
1229 997114 : return _node_to_elem_map;
1230 : }
1231 :
1232 : const std::unordered_map<dof_id_type, std::vector<dof_id_type>> &
1233 983958 : MooseMesh::nodeToElemMap()
1234 : {
1235 983958 : return internalNodeToElemMap();
1236 : }
1237 :
1238 : const ConstElemRange *
1239 10374146 : MooseMesh::getActiveLocalElementRange()
1240 : {
1241 10374146 : return &getMesh().active_local_element_stored_range();
1242 : }
1243 :
1244 : NodeRange *
1245 83860 : MooseMesh::getActiveNodeRange()
1246 : {
1247 83860 : if (!_active_node_range)
1248 : {
1249 251388 : TIME_SECTION("getActiveNodeRange", 5);
1250 :
1251 : _active_node_range =
1252 83796 : std::make_unique<NodeRange>(getMesh().active_nodes_begin(), getMesh().active_nodes_end());
1253 83796 : }
1254 :
1255 83860 : return _active_node_range.get();
1256 : }
1257 :
1258 : SemiLocalNodeRange *
1259 0 : MooseMesh::getActiveSemiLocalNodeRange() const
1260 : {
1261 : mooseAssert(_active_semilocal_node_range,
1262 : "_active_semilocal_node_range has not been created yet!");
1263 :
1264 0 : return _active_semilocal_node_range.get();
1265 : }
1266 :
1267 : ConstNodeRange *
1268 318211 : MooseMesh::getLocalNodeRange()
1269 : {
1270 318211 : if (!_local_node_range)
1271 : {
1272 251388 : TIME_SECTION("getLocalNodeRange", 5);
1273 :
1274 167592 : _local_node_range = std::make_unique<ConstNodeRange>(getMesh().local_nodes_begin(),
1275 251388 : getMesh().local_nodes_end());
1276 83796 : }
1277 :
1278 318211 : return _local_node_range.get();
1279 : }
1280 :
1281 : ConstBndNodeRange *
1282 3672709 : MooseMesh::getBoundaryNodeRange()
1283 : {
1284 3672709 : if (!_bnd_node_range)
1285 : {
1286 251904 : TIME_SECTION("getBoundaryNodeRange", 5);
1287 :
1288 83968 : _bnd_node_range = std::make_unique<ConstBndNodeRange>(bndNodesBegin(), bndNodesEnd());
1289 83968 : }
1290 :
1291 3672709 : return _bnd_node_range.get();
1292 : }
1293 :
1294 : ConstBndElemRange *
1295 188705 : MooseMesh::getBoundaryElementRange()
1296 : {
1297 188705 : if (!_bnd_elem_range)
1298 : {
1299 251388 : TIME_SECTION("getBoundaryElementRange", 5);
1300 :
1301 83796 : _bnd_elem_range = std::make_unique<ConstBndElemRange>(bndElemsBegin(), bndElemsEnd());
1302 83796 : }
1303 :
1304 188705 : return _bnd_elem_range.get();
1305 : }
1306 :
1307 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1308 0 : MooseMesh::getBoundariesToElems() const
1309 : {
1310 0 : mooseDeprecated("MooseMesh::getBoundariesToElems is deprecated, "
1311 : "use MooseMesh::getBoundariesToActiveSemiLocalElemIds");
1312 0 : return getBoundariesToActiveSemiLocalElemIds();
1313 : }
1314 :
1315 : const std::unordered_map<boundary_id_type, std::unordered_set<dof_id_type>> &
1316 61 : MooseMesh::getBoundariesToActiveSemiLocalElemIds() const
1317 : {
1318 61 : return _bnd_elem_ids;
1319 : }
1320 :
1321 : std::unordered_set<dof_id_type>
1322 3501 : MooseMesh::getBoundaryActiveSemiLocalElemIds(BoundaryID bid) const
1323 : {
1324 : // The boundary to element map is computed on every mesh update
1325 3501 : const auto it = _bnd_elem_ids.find(bid);
1326 3501 : if (it == _bnd_elem_ids.end())
1327 : // Boundary is not local to this domain, return an empty set
1328 106 : return std::unordered_set<dof_id_type>{};
1329 3395 : return it->second;
1330 : }
1331 :
1332 : std::unordered_set<dof_id_type>
1333 0 : MooseMesh::getBoundaryActiveNeighborElemIds(BoundaryID bid) const
1334 : {
1335 : // Vector of boundary elems is updated every mesh update
1336 0 : std::unordered_set<dof_id_type> neighbor_elems;
1337 0 : for (const auto & bnd_elem : _bnd_elems)
1338 : {
1339 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1340 0 : if (elem_bid == bid)
1341 : {
1342 0 : const auto * neighbor = elem_ptr->neighbor_ptr(elem_side);
1343 : // Dont add fully remote elements, ghosted is fine
1344 0 : if (neighbor && neighbor != libMesh::remote_elem)
1345 : {
1346 : // handle mesh refinement, only return active elements near the boundary
1347 0 : if (neighbor->active())
1348 0 : neighbor_elems.insert(neighbor->id());
1349 : else
1350 : {
1351 0 : std::vector<const Elem *> family;
1352 0 : neighbor->active_family_tree_by_neighbor(family, elem_ptr);
1353 0 : for (const auto & child_neighbor : family)
1354 0 : neighbor_elems.insert(child_neighbor->id());
1355 0 : }
1356 : }
1357 : }
1358 : }
1359 :
1360 0 : return neighbor_elems;
1361 0 : }
1362 :
1363 : bool
1364 0 : MooseMesh::isBoundaryFullyExternalToSubdomains(BoundaryID bid,
1365 : const std::set<SubdomainID> & blk_group) const
1366 : {
1367 : mooseAssert(_bnd_elem_range, "Boundary element range is not initialized");
1368 :
1369 : // Loop over all side elements of the mesh, select those on the boundary
1370 0 : for (const auto & bnd_elem : *_bnd_elem_range)
1371 : {
1372 0 : const auto & [elem_ptr, elem_side, elem_bid] = *bnd_elem;
1373 0 : if (elem_bid == bid)
1374 : {
1375 : // If an element is internal to the group of subdomain, check the neighbor
1376 0 : if (blk_group.find(elem_ptr->subdomain_id()) != blk_group.end())
1377 : {
1378 0 : const auto * const neighbor = elem_ptr->neighbor_ptr(elem_side);
1379 :
1380 : // If we did not ghost the neighbor, we cannot decide
1381 0 : if (neighbor == libMesh::remote_elem)
1382 0 : mooseError("Insufficient level of geometrical ghosting to determine "
1383 : "if a boundary is internal to the mesh");
1384 : // If the neighbor does not exist, then we are on the edge of the mesh
1385 0 : if (!neighbor)
1386 0 : continue;
1387 : // If the neighbor is also in the group of subdomain,
1388 : // then the boundary cuts the subdomains
1389 0 : if (blk_group.find(neighbor->subdomain_id()) != blk_group.end())
1390 0 : return false;
1391 : }
1392 : }
1393 : }
1394 0 : return true;
1395 : }
1396 :
1397 : void
1398 154957 : MooseMesh::cacheInfo()
1399 : {
1400 464871 : TIME_SECTION("cacheInfo", 3);
1401 :
1402 154957 : _sub_to_data.clear();
1403 154957 : _neighbor_subdomain_boundary_ids.clear();
1404 154957 : _block_node_list.clear();
1405 154957 : _higher_d_elem_side_to_lower_d_elem.clear();
1406 154957 : _lower_d_elem_to_higher_d_elem_side.clear();
1407 154957 : _lower_d_interior_blocks.clear();
1408 154957 : _lower_d_boundary_blocks.clear();
1409 :
1410 154957 : const auto & mesh = getMesh();
1411 :
1412 : // Cache higher and lowerD element information
1413 38310556 : for (const auto & elem : mesh.element_ptr_range())
1414 : {
1415 38155599 : const Elem * ip_elem = elem->interior_parent();
1416 :
1417 38155599 : if (ip_elem)
1418 : {
1419 102485 : unsigned int ip_side = ip_elem->which_side_am_i(elem);
1420 :
1421 : // For some grid sequencing tests: ip_side == libMesh::invalid_uint
1422 102485 : if (ip_side != libMesh::invalid_uint)
1423 : {
1424 102325 : auto pair = std::make_pair(ip_elem, ip_side);
1425 102325 : _higher_d_elem_side_to_lower_d_elem.insert(
1426 102325 : std::pair<std::pair<const Elem *, unsigned short int>, const Elem *>(pair, elem));
1427 102325 : _lower_d_elem_to_higher_d_elem_side.insert(
1428 102325 : std::pair<const Elem *, unsigned short int>(elem, ip_side));
1429 :
1430 102325 : auto id = elem->subdomain_id();
1431 102325 : if (ip_elem->neighbor_ptr(ip_side))
1432 : {
1433 6680 : if (mesh.subdomain_name(id).find("INTERNAL_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1434 6580 : _lower_d_interior_blocks.insert(id);
1435 : }
1436 : else
1437 : {
1438 95645 : if (mesh.subdomain_name(id).find("BOUNDARY_SIDE_LOWERD_SUBDOMAIN_") != std::string::npos)
1439 6890 : _lower_d_boundary_blocks.insert(id);
1440 : }
1441 : }
1442 : }
1443 :
1444 243917838 : for (unsigned int nd = 0; nd < elem->n_nodes(); ++nd)
1445 : {
1446 205762239 : const Node & node = *elem->node_ptr(nd);
1447 205762239 : _block_node_list[node.id()].insert(elem->subdomain_id());
1448 : }
1449 154957 : }
1450 154957 : _communicator.set_union(_lower_d_interior_blocks);
1451 154957 : _communicator.set_union(_lower_d_boundary_blocks);
1452 :
1453 : // Cache the boundaries next to each subdomain
1454 27753158 : for (const auto & elem : mesh.active_local_element_ptr_range())
1455 : {
1456 27598201 : SubdomainID subdomain_id = elem->subdomain_id();
1457 27598201 : auto & sub_data = _sub_to_data[subdomain_id];
1458 27598201 : const auto elem_boundary_ids = getBoundaryIDs(elem);
1459 151896713 : for (unsigned int side = 0; side < elem->n_sides(); side++)
1460 : {
1461 124298512 : const auto & boundary_ids = elem_boundary_ids[side];
1462 124298512 : sub_data.boundary_ids.insert(boundary_ids.begin(), boundary_ids.end());
1463 :
1464 124298512 : const Elem * neig = elem->neighbor_ptr(side);
1465 124298512 : if (neig)
1466 : {
1467 117086363 : _neighbor_subdomain_boundary_ids[neig->subdomain_id()].insert(boundary_ids.begin(),
1468 : boundary_ids.end());
1469 117086363 : SubdomainID neighbor_subdomain_id = neig->subdomain_id();
1470 117086363 : if (neighbor_subdomain_id != subdomain_id)
1471 1819192 : sub_data.neighbor_subs.insert(neighbor_subdomain_id);
1472 : }
1473 : }
1474 27753158 : }
1475 :
1476 374312 : for (const auto blk_id : _mesh_subdomains)
1477 : {
1478 219355 : auto & sub_data = _sub_to_data[blk_id];
1479 219355 : _communicator.set_union(sub_data.neighbor_subs);
1480 219355 : _communicator.set_union(sub_data.boundary_ids);
1481 219355 : _communicator.set_union(_neighbor_subdomain_boundary_ids[blk_id]);
1482 : }
1483 154957 : }
1484 :
1485 : const std::set<SubdomainID> &
1486 95950994 : MooseMesh::getNodeBlockIds(const Node & node) const
1487 : {
1488 95950994 : auto it = _block_node_list.find(node.id());
1489 :
1490 95950994 : if (it == _block_node_list.end())
1491 0 : mooseError("Unable to find node: ", node.id(), " in any block list.");
1492 :
1493 191901988 : return it->second;
1494 : }
1495 :
1496 : MooseMesh::face_info_iterator
1497 164703 : MooseMesh::ownedFaceInfoBegin()
1498 : {
1499 : return face_info_iterator(
1500 164703 : _face_info.begin(),
1501 164703 : _face_info.end(),
1502 329406 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1503 : }
1504 :
1505 : MooseMesh::face_info_iterator
1506 164703 : MooseMesh::ownedFaceInfoEnd()
1507 : {
1508 : return face_info_iterator(
1509 164703 : _face_info.end(),
1510 164703 : _face_info.end(),
1511 329406 : libMesh::Predicates::pid<std::vector<const FaceInfo *>::iterator>(this->processor_id()));
1512 : }
1513 :
1514 : MooseMesh::elem_info_iterator
1515 84250 : MooseMesh::ownedElemInfoBegin()
1516 : {
1517 84250 : return elem_info_iterator(_elem_info.begin(),
1518 84250 : _elem_info.end(),
1519 168500 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1520 : }
1521 :
1522 : MooseMesh::elem_info_iterator
1523 84250 : MooseMesh::ownedElemInfoEnd()
1524 : {
1525 84250 : return elem_info_iterator(_elem_info.end(),
1526 84250 : _elem_info.end(),
1527 168500 : Predicates::NotNull<std::vector<const ElemInfo *>::iterator>());
1528 : }
1529 :
1530 : // default begin() accessor
1531 : MooseMesh::bnd_node_iterator
1532 86428 : MooseMesh::bndNodesBegin()
1533 : {
1534 86428 : Predicates::NotNull<bnd_node_iterator_imp> p;
1535 172856 : return bnd_node_iterator(_bnd_nodes.begin(), _bnd_nodes.end(), p);
1536 86428 : }
1537 :
1538 : // default end() accessor
1539 : MooseMesh::bnd_node_iterator
1540 86428 : MooseMesh::bndNodesEnd()
1541 : {
1542 86428 : Predicates::NotNull<bnd_node_iterator_imp> p;
1543 172856 : return bnd_node_iterator(_bnd_nodes.end(), _bnd_nodes.end(), p);
1544 86428 : }
1545 :
1546 : // default begin() accessor
1547 : MooseMesh::bnd_elem_iterator
1548 83950 : MooseMesh::bndElemsBegin()
1549 : {
1550 83950 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1551 167900 : return bnd_elem_iterator(_bnd_elems.begin(), _bnd_elems.end(), p);
1552 83950 : }
1553 :
1554 : // default end() accessor
1555 : MooseMesh::bnd_elem_iterator
1556 83950 : MooseMesh::bndElemsEnd()
1557 : {
1558 83950 : Predicates::NotNull<bnd_elem_iterator_imp> p;
1559 167900 : return bnd_elem_iterator(_bnd_elems.end(), _bnd_elems.end(), p);
1560 83950 : }
1561 :
1562 : const Node *
1563 0 : MooseMesh::addUniqueNode(const Point & p, Real tol)
1564 : {
1565 : /**
1566 : * Looping through the mesh nodes each time we add a point is very slow. To speed things
1567 : * up we keep a local data structure
1568 : */
1569 0 : if (getMesh().n_nodes() != _node_map.size())
1570 : {
1571 0 : _node_map.clear();
1572 0 : _node_map.reserve(getMesh().n_nodes());
1573 0 : for (const auto & node : getMesh().node_ptr_range())
1574 0 : _node_map.push_back(node);
1575 : }
1576 :
1577 0 : Node * node = nullptr;
1578 0 : for (unsigned int i = 0; i < _node_map.size(); ++i)
1579 : {
1580 0 : if (p.relative_fuzzy_equals(*_node_map[i], tol))
1581 : {
1582 0 : node = _node_map[i];
1583 0 : break;
1584 : }
1585 : }
1586 0 : if (node == nullptr)
1587 : {
1588 0 : node = getMesh().add_node(new Node(p));
1589 0 : _node_map.push_back(node);
1590 : }
1591 :
1592 : mooseAssert(node != nullptr, "Node is NULL");
1593 0 : return node;
1594 : }
1595 :
1596 : Node *
1597 5357 : MooseMesh::addQuadratureNode(const Elem * elem,
1598 : const unsigned short int side,
1599 : const unsigned int qp,
1600 : BoundaryID bid,
1601 : const Point & point)
1602 : {
1603 : Node * qnode;
1604 :
1605 5357 : if (_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) ==
1606 10714 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end())
1607 : {
1608 : // Create a new node id starting from the max node id and counting down. This will be the least
1609 : // likely to collide with an existing node id.
1610 : // Note that we are using numeric_limits<unsigned>::max even
1611 : // though max_id is stored as a dof_id_type. I tried this with
1612 : // numeric_limits<dof_id_type>::max and it broke several tests in
1613 : // MOOSE. So, this is some kind of a magic number that we will
1614 : // just continue to use...
1615 5357 : dof_id_type max_id = std::numeric_limits<unsigned int>::max() - 100;
1616 5357 : dof_id_type new_id = max_id - _quadrature_nodes.size();
1617 :
1618 5357 : if (new_id <= getMesh().max_node_id())
1619 0 : mooseError("Quadrature node id collides with existing node id!");
1620 :
1621 5357 : qnode = new Node(point, new_id);
1622 :
1623 : // Keep track of this new node in two different ways for easy lookup
1624 5357 : _quadrature_nodes[new_id] = qnode;
1625 5357 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp] = qnode;
1626 :
1627 5357 : if (elem->active())
1628 5357 : internalNodeToElemMap()[new_id].push_back(elem->id());
1629 : }
1630 : else
1631 0 : qnode = _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1632 :
1633 5357 : BndNode * bnode = new BndNode(qnode, bid);
1634 5357 : _bnd_nodes.push_back(bnode);
1635 5357 : _bnd_node_ids[bid].insert(qnode->id());
1636 :
1637 5357 : _extra_bnd_nodes.push_back(*bnode);
1638 :
1639 : // Do this so the range will be regenerated next time it is accessed
1640 5357 : _bnd_node_range.reset();
1641 :
1642 5357 : return qnode;
1643 : }
1644 :
1645 : Node *
1646 137880 : MooseMesh::getQuadratureNode(const Elem * elem,
1647 : const unsigned short int side,
1648 : const unsigned int qp)
1649 : {
1650 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes.find(elem->id()) !=
1651 : _elem_to_side_to_qp_to_quadrature_nodes.end(),
1652 : "Elem has no quadrature nodes!");
1653 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()].find(side) !=
1654 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()].end(),
1655 : "Side has no quadrature nodes!");
1656 : mooseAssert(_elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].find(qp) !=
1657 : _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side].end(),
1658 : "qp not found on side!");
1659 :
1660 137880 : return _elem_to_side_to_qp_to_quadrature_nodes[elem->id()][side][qp];
1661 : }
1662 :
1663 : void
1664 74189 : MooseMesh::clearQuadratureNodes()
1665 : {
1666 : // Delete all the quadrature nodes
1667 79534 : for (auto & it : _quadrature_nodes)
1668 5345 : delete it.second;
1669 :
1670 74189 : _quadrature_nodes.clear();
1671 74189 : _elem_to_side_to_qp_to_quadrature_nodes.clear();
1672 74189 : _extra_bnd_nodes.clear();
1673 :
1674 : // NOTE: this does not clear them from the nodeToElem map
1675 74189 : }
1676 :
1677 : BoundaryID
1678 543878 : MooseMesh::getBoundaryID(const BoundaryName & boundary_name) const
1679 : {
1680 543878 : if (boundary_name == "ANY_BOUNDARY_ID")
1681 0 : mooseError("Please use getBoundaryIDs() when passing \"ANY_BOUNDARY_ID\"");
1682 :
1683 543878 : return MooseMeshUtils::getBoundaryID(boundary_name, getMesh());
1684 : }
1685 :
1686 : const Elem *
1687 1577196185 : MooseMesh::getLowerDElem(const Elem * elem, unsigned short int side) const
1688 : {
1689 1577196185 : auto it = _higher_d_elem_side_to_lower_d_elem.find(std::make_pair(elem, side));
1690 :
1691 1577196185 : if (it != _higher_d_elem_side_to_lower_d_elem.end())
1692 280844 : return it->second;
1693 : else
1694 1576915341 : return nullptr;
1695 : }
1696 :
1697 : unsigned int
1698 260 : MooseMesh::getHigherDSide(const Elem * elem) const
1699 : {
1700 260 : auto it = _lower_d_elem_to_higher_d_elem_side.find(elem);
1701 :
1702 260 : if (it != _lower_d_elem_to_higher_d_elem_side.end())
1703 260 : return it->second;
1704 : else
1705 0 : return libMesh::invalid_uint;
1706 : }
1707 :
1708 : std::vector<BoundaryID>
1709 116921 : MooseMesh::getBoundaryIDs(const std::vector<BoundaryName> & boundary_name,
1710 : bool generate_unknown) const
1711 : {
1712 : return MooseMeshUtils::getBoundaryIDs(
1713 116921 : getMesh(), boundary_name, generate_unknown, _mesh_boundary_ids);
1714 : }
1715 :
1716 : SubdomainID
1717 529217 : MooseMesh::getSubdomainID(const SubdomainName & subdomain_name) const
1718 : {
1719 529217 : return MooseMeshUtils::getSubdomainID(subdomain_name, getMesh());
1720 : }
1721 :
1722 : std::vector<SubdomainID>
1723 239989 : MooseMesh::getSubdomainIDs(const std::vector<SubdomainName> & subdomain_name) const
1724 : {
1725 239989 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1726 : }
1727 :
1728 : std::set<SubdomainID>
1729 0 : MooseMesh::getSubdomainIDs(const std::set<SubdomainName> & subdomain_name) const
1730 : {
1731 0 : return MooseMeshUtils::getSubdomainIDs(getMesh(), subdomain_name);
1732 : }
1733 :
1734 : void
1735 253 : MooseMesh::setSubdomainName(SubdomainID subdomain_id, const SubdomainName & name)
1736 : {
1737 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1738 253 : getMesh().subdomain_name(subdomain_id) = name;
1739 253 : }
1740 :
1741 : void
1742 0 : MooseMesh::setSubdomainName(MeshBase & mesh, SubdomainID subdomain_id, const SubdomainName & name)
1743 : {
1744 : mooseAssert(name != "ANY_BLOCK_ID", "Cannot set subdomain name to 'ANY_BLOCK_ID'");
1745 0 : mesh.subdomain_name(subdomain_id) = name;
1746 0 : }
1747 :
1748 : const std::string &
1749 4311396 : MooseMesh::getSubdomainName(SubdomainID subdomain_id) const
1750 : {
1751 4311396 : return getMesh().subdomain_name(subdomain_id);
1752 : }
1753 :
1754 : std::vector<SubdomainName>
1755 71 : MooseMesh::getSubdomainNames(const std::vector<SubdomainID> & subdomain_ids) const
1756 : {
1757 71 : std::vector<SubdomainName> names(subdomain_ids.size());
1758 :
1759 142 : for (unsigned int i = 0; i < subdomain_ids.size(); i++)
1760 71 : names[i] = getSubdomainName(subdomain_ids[i]);
1761 :
1762 71 : return names;
1763 0 : }
1764 :
1765 : void
1766 110 : MooseMesh::setBoundaryName(BoundaryID boundary_id, BoundaryName name)
1767 : {
1768 110 : BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1769 :
1770 : // We need to figure out if this boundary is a sideset or nodeset
1771 110 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1772 30 : boundary_info.sideset_name(boundary_id) = name;
1773 : else
1774 80 : boundary_info.nodeset_name(boundary_id) = name;
1775 110 : }
1776 :
1777 : const std::string &
1778 7597399 : MooseMesh::getBoundaryName(const BoundaryID boundary_id) const
1779 : {
1780 7597399 : const BoundaryInfo & boundary_info = getMesh().get_boundary_info();
1781 :
1782 : // We need to figure out if this boundary is a sideset or nodeset
1783 7597399 : if (boundary_info.get_side_boundary_ids().count(boundary_id))
1784 7477029 : return boundary_info.get_sideset_name(boundary_id);
1785 : else
1786 120370 : return boundary_info.get_nodeset_name(boundary_id);
1787 : }
1788 :
1789 : std::string
1790 27 : MooseMesh::getBoundaryString(BoundaryID boundary_id) const
1791 : {
1792 27 : const auto name = getBoundaryName(boundary_id);
1793 54 : return name.size() ? name : std::to_string(boundary_id);
1794 27 : }
1795 :
1796 : // specialization for PointListAdaptor<MooseMesh::PeriodicNodeInfo>
1797 : template <>
1798 : inline const Point &
1799 173430 : PointListAdaptor<MooseMesh::PeriodicNodeInfo>::getPoint(
1800 : const MooseMesh::PeriodicNodeInfo & item) const
1801 : {
1802 173430 : return *(item.first);
1803 : }
1804 :
1805 : void
1806 27 : MooseMesh::buildPeriodicNodeMap(std::multimap<dof_id_type, dof_id_type> & periodic_node_map,
1807 : unsigned int var_number,
1808 : libMesh::PeriodicBoundaries * pbs) const
1809 : {
1810 81 : TIME_SECTION("buildPeriodicNodeMap", 5);
1811 :
1812 : // clear existing map
1813 27 : periodic_node_map.clear();
1814 :
1815 : // get periodic nodes
1816 27 : std::vector<PeriodicNodeInfo> periodic_nodes;
1817 1575 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1818 : {
1819 : // unfortunately libMesh does not give us a pointer, so we have to look it up ourselves
1820 1548 : auto node = _mesh->node_ptr(std::get<0>(t));
1821 : mooseAssert(node != nullptr,
1822 : "libMesh::BoundaryInfo::build_node_list() returned an ID for a non-existing node");
1823 1548 : auto bc_id = std::get<1>(t);
1824 1548 : periodic_nodes.emplace_back(node, bc_id);
1825 27 : }
1826 :
1827 : // sort by boundary id
1828 27 : std::sort(periodic_nodes.begin(),
1829 : periodic_nodes.end(),
1830 8658 : [](const PeriodicNodeInfo & a, const PeriodicNodeInfo & b) -> bool
1831 8658 : { return a.second > b.second; });
1832 :
1833 : // build kd-tree
1834 : using KDTreeType = nanoflann::KDTreeSingleIndexAdaptor<
1835 : nanoflann::L2_Simple_Adaptor<Real, PointListAdaptor<PeriodicNodeInfo>, Real, std::size_t>,
1836 : PointListAdaptor<PeriodicNodeInfo>,
1837 : LIBMESH_DIM,
1838 : std::size_t>;
1839 27 : const unsigned int max_leaf_size = 20; // slightly affects runtime
1840 : auto point_list =
1841 27 : PointListAdaptor<PeriodicNodeInfo>(periodic_nodes.begin(), periodic_nodes.end());
1842 : auto kd_tree = std::make_unique<KDTreeType>(
1843 27 : LIBMESH_DIM, point_list, nanoflann::KDTreeSingleIndexAdaptorParams(max_leaf_size));
1844 : mooseAssert(kd_tree != nullptr, "KDTree was not properly initialized.");
1845 27 : kd_tree->buildIndex();
1846 :
1847 : // data structures for kd-tree search
1848 27 : nanoflann::SearchParameters search_params;
1849 27 : std::vector<nanoflann::ResultItem<std::size_t, Real>> ret_matches;
1850 :
1851 : // iterate over periodic nodes (boundary ids are in contiguous blocks)
1852 27 : libMesh::PeriodicBoundaryBase * periodic = nullptr;
1853 27 : BoundaryID current_bc_id = BoundaryInfo::invalid_id;
1854 1575 : for (auto & pair : periodic_nodes)
1855 : {
1856 : // entering a new block of boundary IDs
1857 1548 : if (pair.second != current_bc_id)
1858 : {
1859 108 : current_bc_id = pair.second;
1860 108 : periodic = pbs->boundary(current_bc_id);
1861 108 : if (periodic && !periodic->is_my_variable(var_number))
1862 0 : periodic = nullptr;
1863 : }
1864 :
1865 : // variable is not periodic at this node, skip
1866 1548 : if (!periodic)
1867 0 : continue;
1868 :
1869 : // clear result buffer
1870 1548 : ret_matches.clear();
1871 :
1872 : // id of the current node
1873 1548 : const auto id = pair.first->id();
1874 :
1875 : // position where we expect a periodic partner for the current node and boundary
1876 1548 : Point search_point = periodic->get_corresponding_pos(*pair.first);
1877 :
1878 : // search at the expected point
1879 1548 : kd_tree->radiusSearch(&(search_point)(0), libMesh::TOLERANCE, ret_matches, search_params);
1880 4248 : for (auto & match_pair : ret_matches)
1881 : {
1882 2700 : const auto & match = periodic_nodes[match_pair.first];
1883 : // add matched node if the boundary id is the corresponding id in the periodic pair
1884 2700 : if (match.second == periodic->pairedboundary)
1885 1548 : periodic_node_map.emplace(id, match.first->id());
1886 : }
1887 : }
1888 27 : }
1889 :
1890 : void
1891 0 : MooseMesh::buildPeriodicNodeSets(std::map<BoundaryID, std::set<dof_id_type>> & periodic_node_sets,
1892 : unsigned int var_number,
1893 : libMesh::PeriodicBoundaries * pbs) const
1894 : {
1895 0 : TIME_SECTION("buildPeriodicNodeSets", 5);
1896 :
1897 0 : periodic_node_sets.clear();
1898 :
1899 : // Loop over all the boundary nodes adding the periodic nodes to the appropriate set
1900 0 : for (const auto & t : getMesh().get_boundary_info().build_node_list())
1901 : {
1902 0 : auto node_id = std::get<0>(t);
1903 0 : auto bc_id = std::get<1>(t);
1904 :
1905 : // Is this current node on a known periodic boundary?
1906 0 : if (periodic_node_sets.find(bc_id) != periodic_node_sets.end())
1907 0 : periodic_node_sets[bc_id].insert(node_id);
1908 : else // This still might be a periodic node but we just haven't seen this boundary_id yet
1909 : {
1910 0 : const libMesh::PeriodicBoundaryBase * periodic = pbs->boundary(bc_id);
1911 0 : if (periodic && periodic->is_my_variable(var_number))
1912 0 : periodic_node_sets[bc_id].insert(node_id);
1913 : }
1914 0 : }
1915 0 : }
1916 :
1917 : bool
1918 68628 : MooseMesh::detectOrthogonalDimRanges(Real tol)
1919 : {
1920 205884 : TIME_SECTION("detectOrthogonalDimRanges", 5);
1921 :
1922 68628 : if (_regular_orthogonal_mesh)
1923 34404 : return true;
1924 :
1925 34224 : std::vector<Real> min(3, std::numeric_limits<Real>::max());
1926 34224 : std::vector<Real> max(3, std::numeric_limits<Real>::min());
1927 34224 : unsigned int dim = getMesh().mesh_dimension();
1928 :
1929 : // Find the bounding box of our mesh
1930 10257575 : for (const auto & node : getMesh().node_ptr_range())
1931 : // Check all coordinates, we don't know if this mesh might be lying in a higher dim even if the
1932 : // mesh dimension is lower.
1933 40893404 : for (const auto i : make_range(Moose::dim))
1934 : {
1935 30670053 : if ((*node)(i) < min[i])
1936 209985 : min[i] = (*node)(i);
1937 30670053 : if ((*node)(i) > max[i])
1938 469169 : max[i] = (*node)(i);
1939 34224 : }
1940 :
1941 34224 : this->comm().max(max);
1942 34224 : this->comm().min(min);
1943 :
1944 34224 : _extreme_nodes.resize(8); // 2^LIBMESH_DIM
1945 : // Now make sure that there are actual nodes at all of the extremes
1946 34224 : std::vector<bool> extreme_matches(8, false);
1947 34224 : std::vector<unsigned int> comp_map(3);
1948 10257575 : for (const auto & node : getMesh().node_ptr_range())
1949 : {
1950 : // See if the current node is located at one of the extremes
1951 10223351 : unsigned int coord_match = 0;
1952 :
1953 40893404 : for (const auto i : make_range(Moose::dim))
1954 : {
1955 30670053 : if (std::abs((*node)(i)-min[i]) < tol)
1956 : {
1957 6349562 : comp_map[i] = MIN;
1958 6349562 : ++coord_match;
1959 : }
1960 24320491 : else if (std::abs((*node)(i)-max[i]) < tol)
1961 : {
1962 1393901 : comp_map[i] = MAX;
1963 1393901 : ++coord_match;
1964 : }
1965 : }
1966 :
1967 10223351 : if (coord_match == LIBMESH_DIM) // Found a coordinate at one of the extremes
1968 : {
1969 124509 : _extreme_nodes[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = node;
1970 124509 : extreme_matches[comp_map[X] * 4 + comp_map[Y] * 2 + comp_map[Z]] = true;
1971 : }
1972 34224 : }
1973 :
1974 : // See if we matched all of the extremes for the mesh dimension
1975 34224 : this->comm().max(extreme_matches);
1976 34224 : if (std::count(extreme_matches.begin(), extreme_matches.end(), true) == (1 << dim))
1977 29833 : _regular_orthogonal_mesh = true;
1978 :
1979 : // Set the bounds
1980 34224 : _bounds.resize(LIBMESH_DIM);
1981 136896 : for (const auto i : make_range(Moose::dim))
1982 : {
1983 102672 : _bounds[i].resize(2);
1984 102672 : _bounds[i][MIN] = min[i];
1985 102672 : _bounds[i][MAX] = max[i];
1986 : }
1987 :
1988 34224 : return _regular_orthogonal_mesh;
1989 68628 : }
1990 :
1991 : void
1992 538 : MooseMesh::detectPairedSidesets()
1993 : {
1994 1614 : TIME_SECTION("detectPairedSidesets", 5);
1995 :
1996 538 : _paired_boundary = std::vector<std::pair<BoundaryID, BoundaryID>>();
1997 :
1998 : // Loop over level-0 elements (since boundary condition information
1999 : // is only directly stored for them) and find sidesets with normals
2000 : // that point in the -x, +x, -y, +y, and -z, +z direction. If there
2001 : // is a unique sideset id for each direction, then the paired
2002 : // sidesets consist of (-x,+x), (-y,+y), (-z,+z). If there are
2003 : // multiple sideset ids for a given direction, then we can't pick a
2004 : // single pair for that direction. In that case, we'll just return
2005 : // as was done in the original algorithm.
2006 :
2007 : // we need to test all element dimensions from dim down to 1
2008 538 : const unsigned int mesh_dim = getMesh().mesh_dimension();
2009 :
2010 : // Helper for iterating through unit dimensions (0=x, 1=y, 2=z)
2011 : static constexpr std::array<std::size_t, 3> unit_dims{0, 1, 2};
2012 : // Helper for mapping from unit dim -> name
2013 1614 : static const std::array<std::string, 3> unit_dim_names{"x", "y", "z"};
2014 :
2015 : // Boundary id sets for elements of different dimensions
2016 : // First index: side dimension; 0=1D, 1=2D, 2=3D
2017 : // Second index: unit dimension; 0=x, 1=y, 2=z
2018 : // Third index: false for minus, true for plus
2019 16678 : std::array<std::array<std::array<std::set<BoundaryID>, 2>, 3>, 3> ids{};
2020 :
2021 : // Build quadrature needed to evaluate side normals
2022 538 : std::array<std::unique_ptr<FEBase>, 3> fe_faces{};
2023 538 : std::array<std::unique_ptr<libMesh::QGauss>, 3> qfaces{};
2024 1596 : for (const auto side_dim : make_range(mesh_dim))
2025 : {
2026 : // Face is assumed to be flat, therefore normal is assumed to be
2027 : // constant over the face, therefore only compute it at 1 qp.
2028 1058 : qfaces[side_dim] = std::unique_ptr<libMesh::QGauss>(new libMesh::QGauss(side_dim, CONSTANT));
2029 :
2030 : // A first-order Lagrange FE for the face.
2031 1058 : fe_faces[side_dim] = FEBase::build(side_dim + 1, FEType(FIRST, libMesh::LAGRANGE));
2032 1058 : fe_faces[side_dim]->attach_quadrature_rule(qfaces[side_dim].get());
2033 1058 : fe_faces[side_dim]->get_normals();
2034 : }
2035 :
2036 : // Get boundary IDs for each dimension that are in the unit normal
2037 538 : const auto & boundary_info = getMesh().get_boundary_info();
2038 : // Temporary for evaluating boundary_ids
2039 538 : std::vector<boundary_id_type> face_ids;
2040 : // The side dimensions we've come across, so that we only report
2041 : // warnings for side dimensions that we have
2042 538 : std::set<unsigned int> side_dims;
2043 : // Normal dimensions that we found that were nonzero; lets us
2044 : // skip warnings for dimensions that we don't have
2045 538 : std::array<bool, 3> nonzero_dims = periodic_dim_default;
2046 307171 : for (auto & elem : as_range(getMesh().level_elements_begin(0), getMesh().level_elements_end(0)))
2047 : {
2048 : // If not on the boundary, nothing to do
2049 306633 : if (!elem->on_boundary())
2050 259116 : continue;
2051 :
2052 47517 : const auto side_dim = elem->dim() - 1;
2053 47517 : side_dims.insert(side_dim);
2054 :
2055 : // Check for unit normals on each boundary side
2056 265346 : for (const auto s : elem->side_index_range())
2057 217829 : if (!elem->neighbor_ptr(s))
2058 : {
2059 : // Reinit to get the normal
2060 52932 : fe_faces[side_dim]->reinit(elem, s);
2061 52932 : const auto & normal = fe_faces[side_dim]->get_normals()[0];
2062 :
2063 : // Get the boundary ID(s) for this side. If there is more
2064 : // than 1 boundary id, then we already can't determine a
2065 : // unique pairing of sides in this direction, but we'll just
2066 : // keep going to keep the logic simple.
2067 52932 : boundary_info.boundary_ids(elem, s, face_ids);
2068 :
2069 52932 : bool found = false;
2070 211728 : for (const auto unit_dim : unit_dims)
2071 : {
2072 158796 : if (libMesh::absolute_fuzzy_equals(normal(unit_dim), 0.0))
2073 103964 : continue;
2074 54832 : nonzero_dims[unit_dim] = true;
2075 54832 : if (!found)
2076 88072 : for (const auto plus : {false, true})
2077 : {
2078 84272 : if (libMesh::absolute_fuzzy_equals(normal(unit_dim), plus ? 1.0 : -1.0))
2079 : {
2080 51032 : ids[side_dim][unit_dim][plus].insert(face_ids.begin(), face_ids.end());
2081 51032 : found = true;
2082 51032 : break;
2083 : }
2084 : }
2085 : }
2086 : }
2087 538 : }
2088 :
2089 : // For a distributed mesh, boundaries may be distributed as well. We therefore collect information
2090 : // from everyone. If the mesh is already serial, then there is no need to do an allgather. Note
2091 : // that this is just going to gather information about what the periodic bc ids are. We are not
2092 : // gathering any remote elements or anything like that. It's just that the GhostPointNeighbors
2093 : // ghosting functor currently relies on the fact that every process agrees on whether we have
2094 : // periodic boundaries; every process that thinks there are periodic boundaries will call
2095 : // MeshBase::sub_point_locator which makes a parallel_object_only() assertion (right or wrong). So
2096 : // we all need to go there (or not go there)
2097 538 : if (_use_distributed_mesh && !_mesh->is_serial())
2098 : {
2099 : // Communicate id data by packing as [side dim, unit dim, plus (as a char), boundary id]
2100 122 : std::vector<std::tuple<unsigned int, unsigned int, unsigned char, boundary_id_type>> id_data;
2101 244 : for (const auto side_dim : side_dims)
2102 488 : for (const auto unit_dim : unit_dims)
2103 1098 : for (const auto plus : {false, true})
2104 1192 : for (const auto bd : ids[side_dim][unit_dim][plus])
2105 460 : id_data.emplace_back(side_dim, unit_dim, plus, bd);
2106 122 : _communicator.allgather(id_data, false);
2107 1170 : for (const auto & [side_dim, unit_dim, plus_char, bd] : id_data)
2108 1048 : ids[side_dim][unit_dim][bool(plus_char)].insert(bd);
2109 :
2110 : // Gather true-ness of nonzero_dims
2111 488 : for (auto & entry : nonzero_dims)
2112 366 : _communicator.max(entry);
2113 :
2114 : // Gather found side dimensions
2115 122 : _communicator.set_union(side_dims);
2116 122 : } // end if (_use_distributed_mesh && !_need_ghost_ghosted_boundaries)
2117 :
2118 : // Find pairings that have exactly one boundary on each side
2119 538 : std::ostringstream oss_found, oss_missing;
2120 1076 : for (const auto side_dim : side_dims)
2121 : {
2122 2152 : for (const auto unit_dim : unit_dims)
2123 1614 : if (nonzero_dims[unit_dim])
2124 : {
2125 1061 : const auto & unit_name = unit_dim_names[unit_dim];
2126 1061 : const auto & minus = ids[side_dim][unit_dim][false];
2127 1061 : const auto & plus = ids[side_dim][unit_dim][true];
2128 :
2129 1061 : if (minus.size() == 1 && plus.size() == 1)
2130 : {
2131 1904 : const auto get_boundary_name = [this](const auto id)
2132 : {
2133 1904 : const auto & name = getBoundaryName(id);
2134 1904 : return name.size() ? name : std::to_string(id);
2135 952 : };
2136 :
2137 952 : oss_found << "\n " << side_dim + 1 << "D " << unit_name
2138 952 : << "-direction: " << get_boundary_name(*minus.begin()) << " <-> "
2139 1904 : << get_boundary_name(*plus.begin());
2140 952 : _paired_boundary->emplace_back(std::make_pair(*minus.begin(), *plus.begin()));
2141 : }
2142 : else
2143 109 : oss_missing << "\n " << side_dim + 1 << "D -" << unit_name << "/+" << unit_name
2144 109 : << ": Found " << minus.size() << " -" << unit_name << " boundaries and "
2145 109 : << plus.size() << " +" << unit_name << " boundaries";
2146 : }
2147 : }
2148 :
2149 538 : std::ostringstream oss;
2150 538 : const auto found = oss_found.str();
2151 538 : const auto missing = oss_missing.str();
2152 538 : if (found.size())
2153 : oss << "The following paired boundaries were automatically detected for periodicity:\n"
2154 504 : << found << "\n";
2155 538 : if (missing.size())
2156 : {
2157 75 : if (found.size())
2158 41 : oss << "\n";
2159 : oss << "Paired boundaries were not automatically detected for the following:\n"
2160 : << missing
2161 : << "\n\nAutomatic detection requires that exactly one boundary is found in each unit "
2162 75 : "direction.\n";
2163 : }
2164 :
2165 538 : mooseInfoRepeated(oss.str());
2166 538 : }
2167 :
2168 : Real
2169 72760 : MooseMesh::dimensionWidth(unsigned int component) const
2170 : {
2171 72760 : return getMaxInDimension(component) - getMinInDimension(component);
2172 : }
2173 :
2174 : Real
2175 33393 : MooseMesh::getMinInDimension(unsigned int component) const
2176 : {
2177 : mooseAssert(_mesh, "The MeshBase has not been constructed");
2178 : mooseAssert(component < _bounds.size(), "Requested dimension out of bounds");
2179 :
2180 33393 : return _bounds[component][MIN];
2181 : }
2182 :
2183 : Real
2184 33393 : MooseMesh::getMaxInDimension(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 33393 : return _bounds[component][MAX];
2190 : }
2191 :
2192 : void
2193 873 : MooseMesh::addPeriodicVariable(const unsigned int sys_num,
2194 : const unsigned int var_num,
2195 : const BoundaryID primary,
2196 : const BoundaryID secondary)
2197 : {
2198 873 : if (!_regular_orthogonal_mesh)
2199 0 : return;
2200 :
2201 873 : const auto key = std::make_pair(sys_num, var_num);
2202 873 : auto & entry = _periodic_dim.try_emplace(key, periodic_dim_default).first->second;
2203 :
2204 873 : _half_range = Point(dimensionWidth(0) / 2.0, dimensionWidth(1) / 2.0, dimensionWidth(2) / 2.0);
2205 :
2206 873 : bool component_found = false;
2207 2707 : for (const auto component : make_range(dimension()))
2208 : {
2209 1834 : const std::pair<BoundaryID, BoundaryID> * boundary_ids = getPairedBoundaryMapping(component);
2210 :
2211 1834 : if (boundary_ids && ((boundary_ids->first == primary && boundary_ids->second == secondary) ||
2212 976 : (boundary_ids->first == secondary && boundary_ids->second == primary)))
2213 : {
2214 858 : entry[component] = true;
2215 858 : component_found = true;
2216 : }
2217 : }
2218 :
2219 873 : if (!component_found)
2220 30 : mooseWarning("Could not find a match between boundary '",
2221 15 : getBoundaryName(primary),
2222 : "' and '",
2223 15 : getBoundaryName(secondary),
2224 : "' to set periodic boundary conditions for variable (index:",
2225 : var_num,
2226 : ") in either the X, Y or Z direction. The periodic dimension of the mesh for this "
2227 : "variable will not be stored.");
2228 : }
2229 :
2230 : const std::array<bool, 3> &
2231 5076485 : MooseMesh::queryPeriodicDimensions(const unsigned int sys_num, const unsigned int var_num) const
2232 : {
2233 5076485 : const auto key = std::make_pair(sys_num, var_num);
2234 5076485 : if (const auto it = _periodic_dim.find(key); it != _periodic_dim.end())
2235 4972801 : return it->second;
2236 103684 : return periodic_dim_default;
2237 : }
2238 :
2239 : const std::array<bool, 3> &
2240 27 : MooseMesh::queryPeriodicDimensions(const MooseVariableBase & var) const
2241 : {
2242 27 : return queryPeriodicDimensions(var.sys().number(), var.number());
2243 : }
2244 :
2245 : bool
2246 0 : MooseMesh::isTranslatedPeriodic(const unsigned int sys_num,
2247 : const unsigned int var_num,
2248 : const unsigned int component) const
2249 : {
2250 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2251 0 : return queryPeriodicDimensions(sys_num, var_num)[component];
2252 : }
2253 :
2254 : bool
2255 0 : MooseMesh::isTranslatedPeriodic(const MooseVariableBase & var, const unsigned int component) const
2256 : {
2257 0 : return isTranslatedPeriodic(var.sys().number(), var.number(), component);
2258 : }
2259 :
2260 : bool
2261 0 : MooseMesh::isTranslatedPeriodic(const unsigned int var_num, const unsigned int component) const
2262 : {
2263 0 : mooseDoOnce(mooseDeprecated(
2264 : "MooseMesh::isTranslatedPeriodic(const unsigned int, const unsigned int) is deprecated. Use "
2265 : "the method that additionally takes the system number or the MooseVariableBase instead."));
2266 0 : return isTranslatedPeriodic(0, var_num, component);
2267 : }
2268 :
2269 : RealVectorValue
2270 5076458 : MooseMesh::minPeriodicVector(const unsigned int sys_num,
2271 : const unsigned int var_num,
2272 : Point p,
2273 : Point q) const
2274 : {
2275 5076458 : const auto & periodic_dims = queryPeriodicDimensions(sys_num, var_num);
2276 :
2277 15164330 : for (const auto i : make_range(dimension()))
2278 : {
2279 : // check to see if we're closer in real or periodic space in x, y, and z
2280 10087872 : if (periodic_dims[i])
2281 : {
2282 : // Need to test order before differencing
2283 9880504 : if (p(i) > q(i))
2284 : {
2285 6390944 : if (p(i) - q(i) > _half_range(i))
2286 2344164 : p(i) -= _half_range(i) * 2;
2287 : }
2288 : else
2289 : {
2290 3489560 : if (q(i) - p(i) > _half_range(i))
2291 927180 : p(i) += _half_range(i) * 2;
2292 : }
2293 : }
2294 : }
2295 :
2296 5076458 : return q - p;
2297 : }
2298 :
2299 : RealVectorValue
2300 0 : MooseMesh::minPeriodicVector(const MooseVariableBase & var, const Point & p, const Point & q) const
2301 : {
2302 0 : return minPeriodicVector(var.sys().number(), var.number(), p, q);
2303 : }
2304 :
2305 : RealVectorValue
2306 0 : MooseMesh::minPeriodicVector(const unsigned int var_num, const Point & p, const Point & q) const
2307 : {
2308 0 : mooseDoOnce(mooseDeprecated("MooseMesh::minPeriodicVector(const unsigned int, const Point &, "
2309 : "const Point &) is deprecated. Use the method that additionally "
2310 : "takes the system number or the MooseVariableBase instead."));
2311 0 : return minPeriodicVector(0, var_num, p, q);
2312 : }
2313 :
2314 : Real
2315 5076458 : MooseMesh::minPeriodicDistance(const unsigned int sys_num,
2316 : const unsigned int var_num,
2317 : const Point & p,
2318 : const Point & q) const
2319 : {
2320 5076458 : return minPeriodicVector(sys_num, var_num, p, q).norm();
2321 : }
2322 :
2323 : Real
2324 25600 : MooseMesh::minPeriodicDistance(const MooseVariableBase & var,
2325 : const Point & p,
2326 : const Point & q) const
2327 : {
2328 25600 : return minPeriodicDistance(var.sys().number(), var.number(), p, q);
2329 : }
2330 :
2331 : Real
2332 0 : MooseMesh::minPeriodicDistance(const unsigned int var_num, const Point & p, const Point & q) const
2333 : {
2334 0 : mooseDoOnce(mooseDeprecated("MooseMesh::minPeriodicDistance(const unsigned int, const Point &, "
2335 : "const Point &) is deprecated. Use the method that additionally "
2336 : "takes the system number or the MooseVariableBase instead."));
2337 0 : return minPeriodicDistance(0, var_num, p, q);
2338 : }
2339 :
2340 : const std::pair<BoundaryID, BoundaryID> *
2341 2383 : MooseMesh::getPairedBoundaryMapping(unsigned int component) const
2342 : {
2343 2383 : if (!_regular_orthogonal_mesh)
2344 0 : mooseError("Trying to retrieve automatic paired mapping for a mesh that is not regular and "
2345 : "orthogonal");
2346 :
2347 : mooseAssert(component < dimension(), "Requested dimension out of bounds");
2348 :
2349 2383 : if (!hasDetectedPairedSidesets())
2350 0 : mooseError("MooseMesh::getPairedBoundaryMapping(): Paired boundaries not built; must call "
2351 : "detectPairedSidesets() first");
2352 :
2353 2383 : if (component < _paired_boundary->size())
2354 2380 : return &(*_paired_boundary)[component];
2355 : else
2356 3 : return nullptr;
2357 : }
2358 :
2359 : void
2360 33 : MooseMesh::buildHRefinementAndCoarseningMaps(Assembly * const assembly)
2361 : {
2362 33 : std::map<ElemType, Elem *> canonical_elems;
2363 :
2364 : // First, loop over all elements and find a canonical element for each type
2365 : // Doing it this way guarantees that this is going to work in parallel
2366 19937 : for (const auto & elem : getMesh().element_ptr_range()) // TODO: Thread this
2367 : {
2368 9952 : ElemType type = elem->type();
2369 :
2370 9952 : if (canonical_elems.find(type) ==
2371 19904 : canonical_elems.end()) // If we haven't seen this type of elem before save it
2372 42 : canonical_elems[type] = elem;
2373 : else
2374 : {
2375 9910 : Elem * stored = canonical_elems[type];
2376 9910 : if (elem->id() < stored->id()) // Arbitrarily keep the one with a lower id
2377 0 : canonical_elems[type] = elem;
2378 : }
2379 33 : }
2380 : // Now build the maps using these templates
2381 : // Note: This MUST be done NOT threaded!
2382 75 : for (const auto & can_it : canonical_elems)
2383 : {
2384 42 : Elem * elem = can_it.second;
2385 :
2386 : // Need to do this just once to get the right qrules put in place
2387 42 : assembly->setCurrentSubdomainID(elem->subdomain_id());
2388 42 : assembly->reinit(elem);
2389 42 : assembly->reinit(elem, 0);
2390 42 : auto && qrule = assembly->writeableQRule();
2391 42 : auto && qrule_face = assembly->writeableQRuleFace();
2392 :
2393 : // Volume to volume projection for refinement
2394 42 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, -1, -1);
2395 :
2396 : // Volume to volume projection for coarsening
2397 42 : buildCoarseningMap(*elem, *qrule, *qrule_face, -1);
2398 :
2399 : // Map the sides of children
2400 216 : for (unsigned int side = 0; side < elem->n_sides(); side++)
2401 : {
2402 : // Side to side for sides that match parent's sides
2403 174 : buildRefinementMap(*elem, *qrule, *qrule_face, side, -1, side);
2404 174 : buildCoarseningMap(*elem, *qrule, *qrule_face, side);
2405 : }
2406 :
2407 : // Child side to parent volume mapping for "internal" child sides
2408 240 : for (unsigned int child = 0; child < elem->n_children(); ++child)
2409 1146 : for (unsigned int side = 0; side < elem->n_sides();
2410 : ++side) // Assume children have the same number of sides!
2411 948 : if (!elem->is_child_on_side(child, side)) // Otherwise we already computed that map
2412 474 : buildRefinementMap(*elem, *qrule, *qrule_face, -1, child, side);
2413 : }
2414 33 : }
2415 :
2416 : void
2417 90 : MooseMesh::buildPRefinementAndCoarseningMaps(Assembly * const assembly)
2418 : {
2419 90 : _elem_type_to_p_refinement_map.clear();
2420 90 : _elem_type_to_p_refinement_side_map.clear();
2421 90 : _elem_type_to_p_coarsening_map.clear();
2422 90 : _elem_type_to_p_coarsening_side_map.clear();
2423 :
2424 90 : std::map<ElemType, std::pair<Elem *, unsigned int>> elems_and_max_p_level;
2425 :
2426 32218 : for (const auto & elem : getMesh().active_element_ptr_range())
2427 : {
2428 32128 : const auto type = elem->type();
2429 32128 : auto & [picked_elem, max_p_level] = elems_and_max_p_level[type];
2430 32128 : if (!picked_elem)
2431 90 : picked_elem = elem;
2432 32128 : max_p_level = std::max(max_p_level, elem->p_level());
2433 90 : }
2434 :
2435 : // The only requirement on the FEType is that it can be arbitrarily p-refined
2436 90 : const FEType p_refinable_fe_type(CONSTANT, libMesh::MONOMIAL);
2437 90 : std::vector<Point> volume_ref_points_coarse, volume_ref_points_fine, face_ref_points_coarse,
2438 90 : face_ref_points_fine;
2439 90 : std::vector<unsigned int> p_levels;
2440 :
2441 180 : for (auto & [elem_type, elem_p_level_pair] : elems_and_max_p_level)
2442 : {
2443 90 : auto & [moose_elem, max_p_level] = elem_p_level_pair;
2444 90 : const auto dim = moose_elem->dim();
2445 : // Need to do this just once to get the right qrules put in place
2446 90 : assembly->setCurrentSubdomainID(moose_elem->subdomain_id());
2447 90 : assembly->reinit(moose_elem);
2448 90 : assembly->reinit(moose_elem, 0);
2449 90 : auto & qrule = assembly->writeableQRule();
2450 90 : auto & qrule_face = assembly->writeableQRuleFace();
2451 :
2452 90 : libMesh::Parallel::Communicator self_comm{};
2453 90 : ReplicatedMesh mesh(self_comm);
2454 90 : mesh.set_mesh_dimension(dim);
2455 630 : for (const auto & nd : moose_elem->node_ref_range())
2456 540 : mesh.add_point(nd);
2457 :
2458 90 : Elem * const elem = mesh.add_elem(Elem::build(elem_type).release());
2459 630 : for (const auto i : elem->node_index_range())
2460 540 : elem->set_node(i, mesh.node_ptr(i));
2461 :
2462 90 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, p_refinable_fe_type));
2463 90 : fe_face->get_phi();
2464 90 : const auto & face_phys_points = fe_face->get_xyz();
2465 90 : fe_face->attach_quadrature_rule(qrule_face);
2466 :
2467 90 : qrule->init(*elem);
2468 90 : volume_ref_points_coarse = qrule->get_points();
2469 90 : fe_face->reinit(elem, (unsigned int)0);
2470 90 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_coarse);
2471 :
2472 90 : p_levels.resize(max_p_level + 1);
2473 90 : std::iota(p_levels.begin(), p_levels.end(), 0);
2474 90 : libMesh::MeshRefinement mesh_refinement(mesh);
2475 :
2476 306 : for (const auto p_level : p_levels)
2477 : {
2478 216 : mesh_refinement.uniformly_p_refine(1);
2479 216 : qrule->init(*elem);
2480 216 : volume_ref_points_fine = qrule->get_points();
2481 216 : fe_face->reinit(elem, (unsigned int)0);
2482 216 : libMesh::FEMap::inverse_map(dim, elem, face_phys_points, face_ref_points_fine);
2483 :
2484 216 : const auto map_key = std::make_pair(elem_type, p_level);
2485 216 : auto & volume_refine_map = _elem_type_to_p_refinement_map[map_key];
2486 216 : auto & face_refine_map = _elem_type_to_p_refinement_side_map[map_key];
2487 216 : auto & volume_coarsen_map = _elem_type_to_p_coarsening_map[map_key];
2488 216 : auto & face_coarsen_map = _elem_type_to_p_coarsening_side_map[map_key];
2489 :
2490 432 : auto fill_maps = [this](const auto & coarse_ref_points,
2491 : const auto & fine_ref_points,
2492 : auto & coarsen_map,
2493 : auto & refine_map)
2494 : {
2495 432 : mapPoints(fine_ref_points, coarse_ref_points, refine_map);
2496 432 : mapPoints(coarse_ref_points, fine_ref_points, coarsen_map);
2497 648 : };
2498 :
2499 216 : fill_maps(
2500 : volume_ref_points_coarse, volume_ref_points_fine, volume_coarsen_map, volume_refine_map);
2501 216 : fill_maps(face_ref_points_coarse, face_ref_points_fine, face_coarsen_map, face_refine_map);
2502 :
2503 : // With this level's maps filled our fine points now become our coarse points
2504 216 : volume_ref_points_fine.swap(volume_ref_points_coarse);
2505 216 : face_ref_points_fine.swap(face_ref_points_coarse);
2506 : }
2507 90 : }
2508 90 : }
2509 :
2510 : void
2511 57 : MooseMesh::buildRefinementAndCoarseningMaps(Assembly * const assembly)
2512 : {
2513 285 : TIME_SECTION("buildRefinementAndCoarseningMaps", 5, "Building Refinement And Coarsening Maps");
2514 57 : if (doingPRefinement())
2515 24 : buildPRefinementAndCoarseningMaps(assembly);
2516 : else
2517 33 : buildHRefinementAndCoarseningMaps(assembly);
2518 57 : }
2519 :
2520 : void
2521 690 : MooseMesh::buildRefinementMap(const Elem & elem,
2522 : QBase & qrule,
2523 : QBase & qrule_face,
2524 : int parent_side,
2525 : int child,
2526 : int child_side)
2527 : {
2528 3450 : TIME_SECTION("buildRefinementMap", 5, "Building Refinement Map");
2529 :
2530 690 : if (child == -1) // Doing volume mapping or parent side mapping
2531 : {
2532 : mooseAssert(parent_side == child_side,
2533 : "Parent side must match child_side if not passing a specific child!");
2534 :
2535 216 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2536 :
2537 216 : if (_elem_type_to_refinement_map.find(the_pair) != _elem_type_to_refinement_map.end())
2538 0 : mooseError("Already built a qp refinement map!");
2539 :
2540 216 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2541 216 : std::vector<std::vector<QpMap>> & refinement_map = _elem_type_to_refinement_map[the_pair];
2542 216 : findAdaptivityQpMaps(
2543 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2544 216 : }
2545 : else // Need to map a child side to parent volume qps
2546 : {
2547 474 : std::pair<int, int> child_pair(child, child_side);
2548 :
2549 474 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) !=
2550 1380 : _elem_type_to_child_side_refinement_map.end() &&
2551 432 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) !=
2552 906 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2553 0 : mooseError("Already built a qp refinement map!");
2554 :
2555 474 : std::vector<std::pair<unsigned int, QpMap>> coarsen_map;
2556 : std::vector<std::vector<QpMap>> & refinement_map =
2557 474 : _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2558 474 : findAdaptivityQpMaps(
2559 : &elem, qrule, qrule_face, refinement_map, coarsen_map, parent_side, child, child_side);
2560 474 : }
2561 690 : }
2562 :
2563 : const std::vector<std::vector<QpMap>> &
2564 3422 : MooseMesh::getRefinementMap(const Elem & elem, int parent_side, int child, int child_side)
2565 : {
2566 3422 : if (child == -1) // Doing volume mapping or parent side mapping
2567 : {
2568 : mooseAssert(parent_side == child_side,
2569 : "Parent side must match child_side if not passing a specific child!");
2570 :
2571 3422 : std::pair<int, ElemType> the_pair(parent_side, elem.type());
2572 :
2573 3422 : if (_elem_type_to_refinement_map.find(the_pair) == _elem_type_to_refinement_map.end())
2574 0 : mooseError("Could not find a suitable qp refinement map!");
2575 :
2576 3422 : return _elem_type_to_refinement_map[the_pair];
2577 : }
2578 : else // Need to map a child side to parent volume qps
2579 : {
2580 0 : std::pair<int, int> child_pair(child, child_side);
2581 :
2582 0 : if (_elem_type_to_child_side_refinement_map.find(elem.type()) ==
2583 0 : _elem_type_to_child_side_refinement_map.end() ||
2584 0 : _elem_type_to_child_side_refinement_map[elem.type()].find(child_pair) ==
2585 0 : _elem_type_to_child_side_refinement_map[elem.type()].end())
2586 0 : mooseError("Could not find a suitable qp refinement map!");
2587 :
2588 0 : return _elem_type_to_child_side_refinement_map[elem.type()][child_pair];
2589 : }
2590 :
2591 : /**
2592 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2593 : * processor has a complete map. This may require parallel communication. This is likely to
2594 : * happen
2595 : * when running on a mixed element mesh.
2596 : */
2597 : }
2598 :
2599 : void
2600 216 : MooseMesh::buildCoarseningMap(const Elem & elem, QBase & qrule, QBase & qrule_face, int input_side)
2601 : {
2602 1080 : TIME_SECTION("buildCoarseningMap", 5, "Building Coarsening Map");
2603 :
2604 216 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2605 :
2606 216 : if (_elem_type_to_coarsening_map.find(the_pair) != _elem_type_to_coarsening_map.end())
2607 0 : mooseError("Already built a qp coarsening map!");
2608 :
2609 216 : std::vector<std::vector<QpMap>> refinement_map;
2610 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map =
2611 216 : _elem_type_to_coarsening_map[the_pair];
2612 :
2613 : // The -1 here is for a specific child. We don't do that for coarsening maps
2614 : // Also note that we're always mapping the same side to the same side (which is guaranteed by
2615 : // libMesh).
2616 216 : findAdaptivityQpMaps(
2617 : &elem, qrule, qrule_face, refinement_map, coarsen_map, input_side, -1, input_side);
2618 :
2619 : /**
2620 : * TODO: When running with parallel mesh + stateful adaptivty we will need to make sure that each
2621 : * processor has a complete map. This may require parallel communication. This is likely to
2622 : * happen
2623 : * when running on a mixed element mesh.
2624 : */
2625 216 : }
2626 :
2627 : const std::vector<std::pair<unsigned int, QpMap>> &
2628 1288 : MooseMesh::getCoarseningMap(const Elem & elem, int input_side)
2629 : {
2630 1288 : std::pair<int, ElemType> the_pair(input_side, elem.type());
2631 :
2632 1288 : if (_elem_type_to_coarsening_map.find(the_pair) == _elem_type_to_coarsening_map.end())
2633 0 : mooseError("Could not find a suitable qp refinement map!");
2634 :
2635 2576 : return _elem_type_to_coarsening_map[the_pair];
2636 : }
2637 :
2638 : void
2639 7038 : MooseMesh::mapPoints(const std::vector<Point> & from,
2640 : const std::vector<Point> & to,
2641 : std::vector<QpMap> & qp_map)
2642 : {
2643 7038 : unsigned int n_from = from.size();
2644 7038 : unsigned int n_to = to.size();
2645 :
2646 7038 : qp_map.resize(n_from);
2647 :
2648 61340 : for (unsigned int i = 0; i < n_from; ++i)
2649 : {
2650 54302 : const Point & from_point = from[i];
2651 :
2652 54302 : QpMap & current_map = qp_map[i];
2653 :
2654 1247054 : for (unsigned int j = 0; j < n_to; ++j)
2655 : {
2656 1192752 : const Point & to_point = to[j];
2657 1192752 : Real distance = (from_point - to_point).norm();
2658 :
2659 1192752 : if (distance < current_map._distance)
2660 : {
2661 167558 : current_map._distance = distance;
2662 167558 : current_map._from = i;
2663 167558 : current_map._to = j;
2664 : }
2665 : }
2666 : }
2667 7038 : }
2668 :
2669 : void
2670 906 : MooseMesh::findAdaptivityQpMaps(const Elem * template_elem,
2671 : QBase & qrule,
2672 : QBase & qrule_face,
2673 : std::vector<std::vector<QpMap>> & refinement_map,
2674 : std::vector<std::pair<unsigned int, QpMap>> & coarsen_map,
2675 : int parent_side,
2676 : int child,
2677 : int child_side)
2678 : {
2679 2718 : TIME_SECTION("findAdaptivityQpMaps", 5);
2680 :
2681 906 : ReplicatedMesh mesh(_communicator);
2682 906 : mesh.skip_partitioning(true);
2683 :
2684 906 : unsigned int dim = template_elem->dim();
2685 906 : mesh.set_mesh_dimension(dim);
2686 :
2687 7092 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2688 6186 : mesh.add_point(template_elem->point(i));
2689 :
2690 906 : Elem * elem = mesh.add_elem(Elem::build(template_elem->type()).release());
2691 :
2692 7092 : for (unsigned int i = 0; i < template_elem->n_nodes(); ++i)
2693 6186 : elem->set_node(i, mesh.node_ptr(i));
2694 :
2695 906 : std::unique_ptr<FEBase> fe(FEBase::build(dim, FEType()));
2696 906 : fe->get_phi();
2697 906 : const std::vector<Point> & q_points_volume = fe->get_xyz();
2698 :
2699 906 : std::unique_ptr<FEBase> fe_face(FEBase::build(dim, FEType()));
2700 906 : fe_face->get_phi();
2701 906 : const std::vector<Point> & q_points_face = fe_face->get_xyz();
2702 :
2703 906 : fe->attach_quadrature_rule(&qrule);
2704 906 : fe_face->attach_quadrature_rule(&qrule_face);
2705 :
2706 : // The current q_points (locations in *physical* space)
2707 : const std::vector<Point> * q_points;
2708 :
2709 906 : if (parent_side != -1)
2710 : {
2711 348 : fe_face->reinit(elem, parent_side);
2712 348 : q_points = &q_points_face;
2713 : }
2714 : else
2715 : {
2716 558 : fe->reinit(elem);
2717 558 : q_points = &q_points_volume;
2718 : }
2719 :
2720 906 : std::vector<Point> parent_ref_points;
2721 :
2722 906 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, parent_ref_points);
2723 906 : libMesh::MeshRefinement mesh_refinement(mesh);
2724 906 : mesh_refinement.uniformly_refine(1);
2725 :
2726 : // A map from the child element index to the locations of all the child's quadrature points in
2727 : // *reference* space. Note that we use a map here instead of a vector because the caller can
2728 : // pass an explicit child index. We are not guaranteed to have a sequence from [0, n_children)
2729 906 : std::map<unsigned int, std::vector<Point>> child_to_ref_points;
2730 :
2731 906 : unsigned int n_children = elem->n_children();
2732 :
2733 906 : refinement_map.resize(n_children);
2734 :
2735 906 : std::vector<unsigned int> children;
2736 :
2737 906 : if (child != -1) // Passed in a child explicitly
2738 474 : children.push_back(child);
2739 : else
2740 : {
2741 432 : children.resize(n_children);
2742 2724 : for (unsigned int child = 0; child < n_children; ++child)
2743 2292 : children[child] = child;
2744 : }
2745 :
2746 3672 : for (unsigned int i = 0; i < children.size(); ++i)
2747 : {
2748 2766 : unsigned int child = children[i];
2749 :
2750 2766 : if ((parent_side != -1 && !elem->is_child_on_side(child, parent_side)))
2751 948 : continue;
2752 :
2753 1818 : const Elem * child_elem = elem->child_ptr(child);
2754 :
2755 1818 : if (child_side != -1)
2756 : {
2757 1422 : fe_face->reinit(child_elem, child_side);
2758 1422 : q_points = &q_points_face;
2759 : }
2760 : else
2761 : {
2762 396 : fe->reinit(child_elem);
2763 396 : q_points = &q_points_volume;
2764 : }
2765 :
2766 1818 : std::vector<Point> child_ref_points;
2767 :
2768 1818 : libMesh::FEMap::inverse_map(elem->dim(), elem, *q_points, child_ref_points);
2769 1818 : child_to_ref_points[child] = child_ref_points;
2770 :
2771 1818 : std::vector<QpMap> & qp_map = refinement_map[child];
2772 :
2773 : // Find the closest parent_qp to each child_qp
2774 1818 : mapPoints(child_ref_points, parent_ref_points, qp_map);
2775 1818 : }
2776 :
2777 906 : coarsen_map.resize(parent_ref_points.size());
2778 :
2779 : // For each parent qp find the closest child qp
2780 6210 : for (unsigned int child = 0; child < n_children; child++)
2781 : {
2782 5304 : if (parent_side != -1 && !elem->is_child_on_side(child, child_side))
2783 948 : continue;
2784 :
2785 4356 : std::vector<Point> & child_ref_points = child_to_ref_points[child];
2786 :
2787 4356 : std::vector<QpMap> qp_map;
2788 :
2789 : // Find all of the closest points from parent_qp to _THIS_ child's qp
2790 4356 : mapPoints(parent_ref_points, child_ref_points, qp_map);
2791 :
2792 : // Check those to see if they are closer than what we currently have for each point
2793 32856 : for (unsigned int parent_qp = 0; parent_qp < parent_ref_points.size(); ++parent_qp)
2794 : {
2795 28500 : std::pair<unsigned int, QpMap> & child_and_map = coarsen_map[parent_qp];
2796 28500 : unsigned int & closest_child = child_and_map.first;
2797 28500 : QpMap & closest_map = child_and_map.second;
2798 :
2799 28500 : QpMap & current_map = qp_map[parent_qp];
2800 :
2801 28500 : if (current_map._distance < closest_map._distance)
2802 : {
2803 6300 : closest_child = child;
2804 6300 : closest_map = current_map;
2805 : }
2806 : }
2807 4356 : }
2808 906 : }
2809 :
2810 : void
2811 0 : MooseMesh::changeBoundaryId(const boundary_id_type old_id,
2812 : const boundary_id_type new_id,
2813 : bool delete_prev)
2814 : {
2815 0 : TIME_SECTION("changeBoundaryId", 6);
2816 0 : changeBoundaryId(getMesh(), old_id, new_id, delete_prev);
2817 0 : }
2818 :
2819 : void
2820 0 : MooseMesh::changeBoundaryId(MeshBase & mesh,
2821 : const boundary_id_type old_id,
2822 : const boundary_id_type new_id,
2823 : bool delete_prev)
2824 : {
2825 : // Get a reference to our BoundaryInfo object, we will use it several times below...
2826 0 : BoundaryInfo & boundary_info = mesh.get_boundary_info();
2827 :
2828 : // Container to catch ids passed back from BoundaryInfo
2829 0 : std::vector<boundary_id_type> old_ids;
2830 :
2831 : // Only level-0 elements store BCs. Loop over them.
2832 0 : for (auto & elem : as_range(mesh.level_elements_begin(0), mesh.level_elements_end(0)))
2833 : {
2834 0 : unsigned int n_sides = elem->n_sides();
2835 0 : for (unsigned int s = 0; s != n_sides; ++s)
2836 : {
2837 0 : boundary_info.boundary_ids(elem, s, old_ids);
2838 0 : if (std::find(old_ids.begin(), old_ids.end(), old_id) != old_ids.end())
2839 : {
2840 0 : std::vector<boundary_id_type> new_ids(old_ids);
2841 0 : std::replace(new_ids.begin(), new_ids.end(), old_id, new_id);
2842 0 : if (delete_prev)
2843 : {
2844 0 : boundary_info.remove_side(elem, s);
2845 0 : boundary_info.add_side(elem, s, new_ids);
2846 : }
2847 : else
2848 0 : boundary_info.add_side(elem, s, new_ids);
2849 0 : }
2850 : }
2851 0 : }
2852 :
2853 : // Remove any remaining references to the old ID from the
2854 : // BoundaryInfo object. This prevents things like empty sidesets
2855 : // from showing up when printing information, etc.
2856 0 : if (delete_prev)
2857 0 : boundary_info.remove_id(old_id);
2858 :
2859 : // The cached boundary id sets will need re-preparation
2860 0 : mesh.unset_has_boundary_id_sets();
2861 0 : }
2862 :
2863 : const RealVectorValue &
2864 0 : MooseMesh::getNormalByBoundaryID(BoundaryID id) const
2865 : {
2866 : mooseAssert(_boundary_to_normal_map.get() != nullptr, "Boundary To Normal Map not built!");
2867 :
2868 : // Note: Boundaries that are not in the map (existing boundaries) will default
2869 : // construct a new RealVectorValue - (x,y,z)=(0, 0, 0)
2870 0 : return (*_boundary_to_normal_map)[id];
2871 : }
2872 :
2873 : MooseMesh &
2874 0 : MooseMesh::clone() const
2875 : {
2876 0 : mooseError("MooseMesh::clone() is no longer supported, use MooseMesh::safeClone() instead.");
2877 : }
2878 :
2879 : void
2880 73957 : MooseMesh::determineUseDistributedMesh()
2881 : {
2882 73957 : switch (_parallel_type)
2883 : {
2884 69095 : case ParallelType::DEFAULT:
2885 : // The user did not specify 'parallel_type = XYZ' in the input file,
2886 : // so we allow the --distributed-mesh command line arg to possibly turn
2887 : // on DistributedMesh. If the command line arg is not present, we pick ReplicatedMesh.
2888 69095 : if (_app.getDistributedMeshOnCommandLine())
2889 10810 : _use_distributed_mesh = true;
2890 69095 : break;
2891 3515 : case ParallelType::REPLICATED:
2892 3515 : if (_app.getDistributedMeshOnCommandLine() || _is_nemesis || _is_split)
2893 741 : _parallel_type_overridden = true;
2894 3515 : _use_distributed_mesh = false;
2895 3515 : break;
2896 1347 : case ParallelType::DISTRIBUTED:
2897 1347 : _use_distributed_mesh = true;
2898 1347 : break;
2899 : }
2900 :
2901 : // If the user specifies 'nemesis = true' in the Mesh block, or they are using --use-split,
2902 : // we must use DistributedMesh.
2903 73957 : if (_is_nemesis || _is_split)
2904 562 : _use_distributed_mesh = true;
2905 73957 : }
2906 :
2907 : std::unique_ptr<MeshBase>
2908 69197 : MooseMesh::buildMeshBaseObject(unsigned int dim)
2909 : {
2910 69197 : std::unique_ptr<MeshBase> mesh;
2911 69197 : if (_use_distributed_mesh)
2912 10847 : mesh = buildTypedMesh<DistributedMesh>(dim);
2913 : else
2914 58350 : mesh = buildTypedMesh<ReplicatedMesh>(dim);
2915 :
2916 69197 : return mesh;
2917 0 : }
2918 :
2919 : void
2920 66123 : MooseMesh::setMeshBase(std::unique_ptr<MeshBase> mesh_base)
2921 : {
2922 66123 : _mesh = std::move(mesh_base);
2923 66123 : _mesh->allow_remote_element_removal(_allow_remote_element_removal);
2924 66123 : }
2925 :
2926 : void
2927 65635 : MooseMesh::init()
2928 : {
2929 : /**
2930 : * If the mesh base hasn't been constructed by the time init is called, just do it here.
2931 : * This can happen if somebody builds a mesh outside of the normal Action system. Forcing
2932 : * developers to create, construct the MeshBase, and then init separately is a bit much for casual
2933 : * use but it gives us the ability to run MeshGenerators in-between.
2934 : */
2935 65635 : if (!_mesh)
2936 10 : _mesh = buildMeshBaseObject();
2937 :
2938 65635 : if (_app.isSplitMesh() && _use_distributed_mesh)
2939 0 : mooseError("You cannot use the mesh splitter capability with DistributedMesh!");
2940 :
2941 196905 : TIME_SECTION("init", 2);
2942 :
2943 65635 : if (_app.isRecovering() && _allow_recovery && _app.isUltimateMaster())
2944 : {
2945 : // Some partitioners are not idempotent. Some recovery data
2946 : // files require partitioning to match mesh partitioning. This
2947 : // means that, when recovering, we can't safely repartition.
2948 3324 : const bool skip_partitioning_later = getMesh().skip_partitioning();
2949 3324 : getMesh().skip_partitioning(true);
2950 3324 : const bool allow_renumbering_later = getMesh().allow_renumbering();
2951 3324 : getMesh().allow_renumbering(false);
2952 :
2953 : // For now, only read the recovery mesh on the Ultimate Master..
2954 : // sub-apps need to just build their mesh like normal
2955 : {
2956 9972 : TIME_SECTION("readRecoveredMesh", 2);
2957 3324 : getMesh().read(_app.getRestartRecoverFileBase() + MooseApp::checkpointSuffix());
2958 3324 : }
2959 :
2960 3324 : getMesh().allow_renumbering(allow_renumbering_later);
2961 3324 : getMesh().skip_partitioning(skip_partitioning_later);
2962 : }
2963 : else // Normally just build the mesh
2964 : {
2965 : // Don't allow partitioning during building
2966 62311 : if (_app.isSplitMesh())
2967 89 : getMesh().skip_partitioning(true);
2968 62311 : buildMesh();
2969 :
2970 186915 : if (getParam<bool>("build_all_side_lowerd_mesh"))
2971 205 : buildLowerDMesh();
2972 : }
2973 65629 : }
2974 :
2975 : unsigned int
2976 91565110 : MooseMesh::dimension() const
2977 : {
2978 91565110 : return getMesh().mesh_dimension();
2979 : }
2980 :
2981 : unsigned int
2982 37754 : MooseMesh::effectiveSpatialDimension() const
2983 : {
2984 37754 : const Real abs_zero = 1e-12;
2985 :
2986 : // See if the mesh is completely containd in the z and y planes to calculate effective spatial
2987 : // dim
2988 69595 : for (unsigned int dim = LIBMESH_DIM; dim >= 1; --dim)
2989 69595 : if (dimensionWidth(dim - 1) >= abs_zero)
2990 37754 : return dim;
2991 :
2992 : // If we get here, we have a 1D mesh on the x-axis.
2993 0 : return 1;
2994 : }
2995 :
2996 : unsigned int
2997 89958 : MooseMesh::getBlocksMaxDimension(const std::vector<SubdomainName> & blocks) const
2998 : {
2999 89958 : const auto & mesh = getMesh();
3000 :
3001 : // Take a shortcut if possible
3002 89958 : if (const auto & elem_dims = mesh.elem_dimensions(); mesh.is_prepared() && elem_dims.size() == 1)
3003 78814 : return *elem_dims.begin();
3004 :
3005 11144 : unsigned short dim = 0;
3006 11144 : const auto subdomain_ids = getSubdomainIDs(blocks);
3007 11144 : const std::set<SubdomainID> subdomain_ids_set(subdomain_ids.begin(), subdomain_ids.end());
3008 2328536 : for (const auto & elem : mesh.active_subdomain_set_elements_ptr_range(subdomain_ids_set))
3009 2328536 : dim = std::max(dim, elem->dim());
3010 :
3011 : // Get the maximumal globally
3012 11144 : _communicator.max(dim);
3013 11144 : return dim;
3014 11144 : }
3015 :
3016 : std::vector<BoundaryID>
3017 106423470 : MooseMesh::getBoundaryIDs(const Elem * const elem, const unsigned short int side) const
3018 : {
3019 106423470 : std::vector<BoundaryID> ids;
3020 106423470 : getMesh().get_boundary_info().boundary_ids(elem, side, ids);
3021 106423470 : return ids;
3022 0 : }
3023 :
3024 : std::vector<std::vector<BoundaryID>>
3025 406957866 : MooseMesh::getBoundaryIDs(const Elem * const elem) const
3026 : {
3027 406957866 : std::vector<std::vector<BoundaryID>> ids;
3028 406957866 : getMesh().get_boundary_info().side_boundary_ids(elem, ids);
3029 406957866 : return ids;
3030 0 : }
3031 :
3032 : const std::set<BoundaryID> &
3033 506742 : MooseMesh::getBoundaryIDs() const
3034 : {
3035 506742 : return getMesh().get_boundary_info().get_boundary_ids();
3036 : }
3037 :
3038 : void
3039 223483 : MooseMesh::buildNodeListFromSideList()
3040 : {
3041 223483 : auto & boundary_info = getMesh().get_boundary_info();
3042 :
3043 223483 : if (_construct_node_list_from_side_list)
3044 : {
3045 223457 : const std::set<boundary_id_type> & side_bcids = boundary_info.get_side_boundary_ids();
3046 :
3047 223457 : if (_displace_node_list_by_side_list)
3048 : {
3049 : // Don't want to use auto here - the rbegin trick relies on a
3050 : // sorted set and we want the compiler to scream if libMesh ever
3051 : // switches type
3052 223457 : const std::set<boundary_id_type> & node_bcids = boundary_info.get_node_boundary_ids();
3053 :
3054 : // If we've got a reasonable largest BC id, we can just use the
3055 : // subsequent unused ones
3056 223457 : boundary_id_type next_bcid = 0;
3057 223457 : if (!node_bcids.empty())
3058 215055 : next_bcid = std::max(next_bcid, cast_int<boundary_id_type>(*node_bcids.rbegin() + 1));
3059 223457 : if (!side_bcids.empty())
3060 218520 : next_bcid = std::max(next_bcid, cast_int<boundary_id_type>(*side_bcids.rbegin() + 1));
3061 :
3062 : // We need all processors to agree on the id to use, even when
3063 : // each only sees the bcids on their own portions of a
3064 : // distributed mesh.
3065 223457 : _communicator.max(next_bcid);
3066 :
3067 : // If we've got an unreasonably high largest BC id, we should
3068 : // probably just search for unused ones with moderate values, so we
3069 : // don't risk wrapping.
3070 223457 : if (next_bcid > 1000 || next_bcid <= 0)
3071 3047 : next_bcid = 1000;
3072 :
3073 : // If any side bcid is already a node bcid with a different name,
3074 : // that's a different boundary condition that we need to reassign
3075 : // rather than overwrite or merge to.
3076 1077091 : for (auto bcid : side_bcids)
3077 1675166 : if (node_bcids.count(bcid) &&
3078 821532 : (boundary_info.get_sideset_name(bcid) != boundary_info.get_nodeset_name(bcid)))
3079 : {
3080 2002 : boundary_info.renumber_node_id(bcid, next_bcid);
3081 : do
3082 : {
3083 2012 : ++next_bcid;
3084 2012 : } while (node_bcids.count(next_bcid) || side_bcids.count(next_bcid));
3085 : }
3086 : }
3087 :
3088 : // For any side bcid that has a name, make sure that our new node
3089 : // bcid is given the same name. We need to iterate over the
3090 : // actual name map (which is global) here, not over side_bcids
3091 : // (which only includes local ids on a distributed mesh).
3092 1064263 : for (auto & [id, name] : boundary_info.get_sideset_name_map())
3093 840806 : boundary_info.nodeset_name(id) = name;
3094 :
3095 223457 : boundary_info.build_node_list_from_side_list();
3096 : }
3097 223483 : }
3098 :
3099 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3100 218 : MooseMesh::buildSideList()
3101 : {
3102 218 : return getMesh().get_boundary_info().build_side_list();
3103 : }
3104 :
3105 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>>
3106 4742 : MooseMesh::buildActiveSideList() const
3107 : {
3108 4742 : return getMesh().get_boundary_info().build_active_side_list();
3109 : }
3110 :
3111 : unsigned int
3112 23836 : MooseMesh::sideWithBoundaryID(const Elem * const elem, const BoundaryID boundary_id) const
3113 : {
3114 23836 : return getMesh().get_boundary_info().side_with_boundary_id(elem, boundary_id);
3115 : }
3116 :
3117 : MeshBase::node_iterator
3118 3240 : MooseMesh::localNodesBegin()
3119 : {
3120 3240 : return getMesh().local_nodes_begin();
3121 : }
3122 :
3123 : MeshBase::node_iterator
3124 3240 : MooseMesh::localNodesEnd()
3125 : {
3126 3240 : return getMesh().local_nodes_end();
3127 : }
3128 :
3129 : MeshBase::const_node_iterator
3130 0 : MooseMesh::localNodesBegin() const
3131 : {
3132 0 : return getMesh().local_nodes_begin();
3133 : }
3134 :
3135 : MeshBase::const_node_iterator
3136 0 : MooseMesh::localNodesEnd() const
3137 : {
3138 0 : return getMesh().local_nodes_end();
3139 : }
3140 :
3141 : MeshBase::element_iterator
3142 148198 : MooseMesh::activeLocalElementsBegin()
3143 : {
3144 148198 : return getMesh().active_local_elements_begin();
3145 : }
3146 :
3147 : const MeshBase::element_iterator
3148 148198 : MooseMesh::activeLocalElementsEnd()
3149 : {
3150 148198 : return getMesh().active_local_elements_end();
3151 : }
3152 :
3153 : MeshBase::const_element_iterator
3154 0 : MooseMesh::activeLocalElementsBegin() const
3155 : {
3156 0 : return getMesh().active_local_elements_begin();
3157 : }
3158 :
3159 : const MeshBase::const_element_iterator
3160 0 : MooseMesh::activeLocalElementsEnd() const
3161 : {
3162 0 : return getMesh().active_local_elements_end();
3163 : }
3164 :
3165 : dof_id_type
3166 55223 : MooseMesh::nNodes() const
3167 : {
3168 55223 : return getMesh().n_nodes();
3169 : }
3170 :
3171 : dof_id_type
3172 1562 : MooseMesh::nElem() const
3173 : {
3174 1562 : return getMesh().n_elem();
3175 : }
3176 :
3177 : dof_id_type
3178 0 : MooseMesh::maxNodeId() const
3179 : {
3180 0 : return getMesh().max_node_id();
3181 : }
3182 :
3183 : dof_id_type
3184 0 : MooseMesh::maxElemId() const
3185 : {
3186 0 : return getMesh().max_elem_id();
3187 : }
3188 :
3189 : Elem *
3190 0 : MooseMesh::elem(const dof_id_type i)
3191 : {
3192 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3193 0 : return elemPtr(i);
3194 : }
3195 :
3196 : const Elem *
3197 0 : MooseMesh::elem(const dof_id_type i) const
3198 : {
3199 0 : mooseDeprecated("MooseMesh::elem() is deprecated, please use MooseMesh::elemPtr() instead");
3200 0 : return elemPtr(i);
3201 : }
3202 :
3203 : Elem *
3204 15694169 : MooseMesh::elemPtr(const dof_id_type i)
3205 : {
3206 15694169 : return getMesh().elem_ptr(i);
3207 : }
3208 :
3209 : const Elem *
3210 1237286 : MooseMesh::elemPtr(const dof_id_type i) const
3211 : {
3212 1237286 : return getMesh().elem_ptr(i);
3213 : }
3214 :
3215 : Elem *
3216 21675 : MooseMesh::queryElemPtr(const dof_id_type i)
3217 : {
3218 21675 : return getMesh().query_elem_ptr(i);
3219 : }
3220 :
3221 : const Elem *
3222 36374 : MooseMesh::queryElemPtr(const dof_id_type i) const
3223 : {
3224 36374 : return getMesh().query_elem_ptr(i);
3225 : }
3226 :
3227 : bool
3228 0 : MooseMesh::prepared() const
3229 : {
3230 0 : return _mesh->is_prepared() && _moose_mesh_prepared;
3231 : }
3232 :
3233 : void
3234 0 : MooseMesh::prepared(bool state)
3235 : {
3236 0 : if (state)
3237 0 : mooseError("We don't have any right to tell the libmesh mesh that it *is* prepared. Only a "
3238 : "call to prepare_for_use should tell us that");
3239 :
3240 : // Some people may call this even before we have a MeshBase object. This isn't dangerous really
3241 : // because when the MeshBase object is born, it knows it's in an unprepared state
3242 0 : if (_mesh)
3243 0 : _mesh->unset_is_prepared();
3244 :
3245 : // If the libMesh mesh isn't preparead, then our MooseMesh wrapper is also no longer prepared
3246 0 : _moose_mesh_prepared = false;
3247 :
3248 : /**
3249 : * If we are explicitly setting the mesh to not prepared, then we've likely modified the mesh
3250 : * and can no longer make assumptions about orthogonality. We really should recheck.
3251 : */
3252 0 : _regular_orthogonal_mesh = false;
3253 0 : }
3254 :
3255 : void
3256 0 : MooseMesh::needsPrepareForUse()
3257 : {
3258 0 : prepared(false);
3259 0 : }
3260 :
3261 : const std::set<SubdomainID> &
3262 8046534 : MooseMesh::meshSubdomains() const
3263 : {
3264 8046534 : return _mesh_subdomains;
3265 : }
3266 :
3267 : const std::set<BoundaryID> &
3268 11912 : MooseMesh::meshBoundaryIds() const
3269 : {
3270 11912 : return _mesh_boundary_ids;
3271 : }
3272 :
3273 : const std::set<BoundaryID> &
3274 29602 : MooseMesh::meshSidesetIds() const
3275 : {
3276 29602 : return _mesh_sideset_ids;
3277 : }
3278 :
3279 : const std::set<BoundaryID> &
3280 149063 : MooseMesh::meshNodesetIds() const
3281 : {
3282 149063 : return _mesh_nodeset_ids;
3283 : }
3284 :
3285 : void
3286 0 : MooseMesh::setMeshBoundaryIDs(std::set<BoundaryID> boundary_IDs)
3287 : {
3288 0 : _mesh_boundary_ids = boundary_IDs;
3289 0 : }
3290 :
3291 : void
3292 0 : MooseMesh::setBoundaryToNormalMap(
3293 : std::unique_ptr<std::map<BoundaryID, RealVectorValue>> boundary_map)
3294 : {
3295 0 : _boundary_to_normal_map = std::move(boundary_map);
3296 0 : }
3297 :
3298 : void
3299 0 : MooseMesh::setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map)
3300 : {
3301 0 : mooseDeprecated("setBoundaryToNormalMap(std::map<BoundaryID, RealVectorValue> * boundary_map) is "
3302 : "deprecated, use the unique_ptr version instead");
3303 0 : _boundary_to_normal_map.reset(boundary_map);
3304 0 : }
3305 :
3306 : unsigned int
3307 125150 : MooseMesh::uniformRefineLevel() const
3308 : {
3309 125150 : return _uniform_refine_level;
3310 : }
3311 :
3312 : void
3313 67651 : MooseMesh::setUniformRefineLevel(unsigned int level, bool deletion)
3314 : {
3315 67651 : _uniform_refine_level = level;
3316 67651 : _skip_deletion_repartition_after_refine = deletion;
3317 67651 : }
3318 :
3319 : void
3320 56144 : MooseMesh::addGhostedBoundary(BoundaryID boundary_id)
3321 : {
3322 56144 : _ghosted_boundaries.insert(boundary_id);
3323 56144 : }
3324 :
3325 : void
3326 0 : MooseMesh::setGhostedBoundaryInflation(const std::vector<Real> & inflation)
3327 : {
3328 0 : _ghosted_boundaries_inflation = inflation;
3329 0 : }
3330 :
3331 : const std::set<unsigned int> &
3332 0 : MooseMesh::getGhostedBoundaries() const
3333 : {
3334 0 : return _ghosted_boundaries;
3335 : }
3336 :
3337 : const std::vector<Real> &
3338 11484 : MooseMesh::getGhostedBoundaryInflation() const
3339 : {
3340 11484 : return _ghosted_boundaries_inflation;
3341 : }
3342 :
3343 : namespace // Anonymous namespace for helpers
3344 : {
3345 : // A class for templated methods that expect output iterator
3346 : // arguments, which adds objects to the Mesh.
3347 : // Although extra_ghost_elem_inserter can add any object, we
3348 : // template it around object type so that type inference and
3349 : // iterator_traits will work.
3350 : // This object specifically is used to insert extra ghost elems into the mesh
3351 : template <typename T>
3352 : struct extra_ghost_elem_inserter
3353 : {
3354 : using iterator_category = std::output_iterator_tag;
3355 : using value_type = T;
3356 :
3357 44732 : extra_ghost_elem_inserter(DistributedMesh & m) : mesh(m) {}
3358 :
3359 19101 : void operator=(const Elem * e) { mesh.add_extra_ghost_elem(const_cast<Elem *>(e)); }
3360 :
3361 35698 : void operator=(Node * n) { mesh.add_node(n); }
3362 :
3363 : void operator=(Point * p) { mesh.add_point(*p); }
3364 :
3365 : extra_ghost_elem_inserter & operator++() { return *this; }
3366 :
3367 54799 : extra_ghost_elem_inserter operator++(int) { return extra_ghost_elem_inserter(*this); }
3368 :
3369 : // We don't return a reference-to-T here because we don't want to
3370 : // construct one or have any of its methods called. We just want
3371 : // to allow the returned object to be able to do mesh insertions
3372 : // with operator=().
3373 54799 : extra_ghost_elem_inserter & operator*() { return *this; }
3374 :
3375 : private:
3376 : DistributedMesh & mesh;
3377 : };
3378 :
3379 : /**
3380 : * Specific weak ordering for Elem *'s to be used in a set.
3381 : * We use the id, but first sort by level. This guarantees
3382 : * when traversing the set from beginning to end the lower
3383 : * level (parent) elements are encountered first.
3384 : *
3385 : * This was swiped from libMesh mesh_communication.C, and ought to be
3386 : * replaced with libMesh::CompareElemIdsByLevel just as soon as I refactor to
3387 : * create that - @roystgnr
3388 : */
3389 : struct CompareElemsByLevel
3390 : {
3391 104881 : bool operator()(const Elem * a, const Elem * b) const
3392 : {
3393 : libmesh_assert(a);
3394 : libmesh_assert(b);
3395 104881 : const unsigned int al = a->level(), bl = b->level();
3396 104881 : const dof_id_type aid = a->id(), bid = b->id();
3397 :
3398 104881 : return (al == bl) ? aid < bid : al < bl;
3399 : }
3400 : };
3401 :
3402 : } // anonymous namespace
3403 :
3404 : void
3405 138445 : MooseMesh::ghostGhostedBoundaries()
3406 : {
3407 : // No need to do this if using a serial mesh
3408 : // We do not need to ghost boundary elements when _need_ghost_ghosted_boundaries
3409 : // is not true. _need_ghost_ghosted_boundaries can be set by a mesh generator
3410 : // where boundaries are already ghosted accordingly
3411 138445 : if (!_use_distributed_mesh || !_need_ghost_ghosted_boundaries)
3412 116079 : return;
3413 :
3414 67098 : TIME_SECTION("GhostGhostedBoundaries", 3);
3415 :
3416 : parallel_object_only();
3417 :
3418 22366 : DistributedMesh & mesh = dynamic_cast<DistributedMesh &>(getMesh());
3419 :
3420 : // We clear ghosted elements that were added by previous invocations of this
3421 : // method but leave ghosted elements that were added by other code, e.g.
3422 : // OversampleOutput, untouched
3423 22366 : mesh.clear_extra_ghost_elems(_ghost_elems_from_ghost_boundaries);
3424 22366 : _ghost_elems_from_ghost_boundaries.clear();
3425 :
3426 22366 : std::set<const Elem *, CompareElemsByLevel> boundary_elems_to_ghost;
3427 22366 : std::set<Node *> connected_nodes_to_ghost;
3428 :
3429 22366 : std::vector<const Elem *> family_tree;
3430 :
3431 902893 : for (const auto & t : mesh.get_boundary_info().build_side_list())
3432 : {
3433 880527 : auto elem_id = std::get<0>(t);
3434 880527 : auto bc_id = std::get<2>(t);
3435 :
3436 880527 : if (_ghosted_boundaries.find(bc_id) != _ghosted_boundaries.end())
3437 : {
3438 5695 : Elem * elem = mesh.elem_ptr(elem_id);
3439 :
3440 : #ifdef LIBMESH_ENABLE_AMR
3441 5695 : elem->family_tree(family_tree);
3442 5695 : Elem * parent = elem->parent();
3443 5695 : while (parent)
3444 : {
3445 0 : family_tree.push_back(parent);
3446 0 : parent = parent->parent();
3447 : }
3448 : #else
3449 : family_tree.clear();
3450 : family_tree.push_back(elem);
3451 : #endif
3452 15230 : for (const auto & felem : family_tree)
3453 : {
3454 9535 : boundary_elems_to_ghost.insert(felem);
3455 :
3456 : // The entries of connected_nodes_to_ghost need to be
3457 : // non-constant, so that they will work in things like
3458 : // UpdateDisplacedMeshThread. The container returned by
3459 : // family_tree contains const Elems even when the Elem
3460 : // it is called on is non-const, so once that interface
3461 : // gets fixed we can remove this const_cast.
3462 57258 : for (unsigned int n = 0; n < felem->n_nodes(); ++n)
3463 47723 : connected_nodes_to_ghost.insert(const_cast<Node *>(felem->node_ptr(n)));
3464 : }
3465 : }
3466 22366 : }
3467 :
3468 : // We really do want to store this by value instead of by reference
3469 22366 : const auto prior_ghost_elems = mesh.extra_ghost_elems();
3470 :
3471 22366 : mesh.comm().allgather_packed_range(&mesh,
3472 : connected_nodes_to_ghost.begin(),
3473 : connected_nodes_to_ghost.end(),
3474 : extra_ghost_elem_inserter<Node>(mesh));
3475 :
3476 22366 : mesh.comm().allgather_packed_range(&mesh,
3477 : boundary_elems_to_ghost.begin(),
3478 : boundary_elems_to_ghost.end(),
3479 : extra_ghost_elem_inserter<Elem>(mesh));
3480 :
3481 22366 : const auto & current_ghost_elems = mesh.extra_ghost_elems();
3482 :
3483 44732 : std::set_difference(current_ghost_elems.begin(),
3484 : current_ghost_elems.end(),
3485 : prior_ghost_elems.begin(),
3486 : prior_ghost_elems.end(),
3487 22366 : std::inserter(_ghost_elems_from_ghost_boundaries,
3488 : _ghost_elems_from_ghost_boundaries.begin()));
3489 22366 : }
3490 :
3491 : unsigned int
3492 11484 : MooseMesh::getPatchSize() const
3493 : {
3494 11484 : return _patch_size;
3495 : }
3496 :
3497 : void
3498 0 : MooseMesh::setPatchUpdateStrategy(Moose::PatchUpdateType patch_update_strategy)
3499 : {
3500 0 : _patch_update_strategy = patch_update_strategy;
3501 0 : }
3502 :
3503 : const Moose::PatchUpdateType &
3504 36409 : MooseMesh::getPatchUpdateStrategy() const
3505 : {
3506 36409 : return _patch_update_strategy;
3507 : }
3508 :
3509 : BoundingBox
3510 114404 : MooseMesh::getInflatedProcessorBoundingBox(Real inflation_multiplier) const
3511 : {
3512 : // Grab a bounding box to speed things up. Note that
3513 : // local_bounding_box is *not* equivalent to processor_bounding_box
3514 : // with processor_id() except in serial.
3515 114404 : BoundingBox bbox = MeshTools::create_local_bounding_box(getMesh());
3516 :
3517 : // Inflate the bbox just a bit to deal with roundoff
3518 : // Adding 1% of the diagonal size in each direction on each end
3519 114404 : Real inflation_amount = inflation_multiplier * (bbox.max() - bbox.min()).norm();
3520 114404 : Point inflation(inflation_amount, inflation_amount, inflation_amount);
3521 :
3522 114404 : bbox.first -= inflation; // min
3523 114404 : bbox.second += inflation; // max
3524 :
3525 228808 : return bbox;
3526 : }
3527 :
3528 160115 : MooseMesh::operator libMesh::MeshBase &() { return getMesh(); }
3529 :
3530 2990 : MooseMesh::operator const libMesh::MeshBase &() const { return getMesh(); }
3531 :
3532 : const MeshBase *
3533 439965 : MooseMesh::getMeshPtr() const
3534 : {
3535 439965 : return _mesh.get();
3536 : }
3537 :
3538 : MeshBase &
3539 59350858 : MooseMesh::getMesh()
3540 : {
3541 : mooseAssert(_mesh, "Mesh hasn't been created");
3542 59350858 : return *_mesh;
3543 : }
3544 :
3545 : const MeshBase &
3546 707596809 : MooseMesh::getMesh() const
3547 : {
3548 : mooseAssert(_mesh, "Mesh hasn't been created");
3549 707596809 : return *_mesh;
3550 : }
3551 :
3552 : void
3553 0 : MooseMesh::printInfo(std::ostream & os, const unsigned int verbosity /* = 0 */) const
3554 : {
3555 0 : os << '\n';
3556 0 : getMesh().print_info(os, verbosity);
3557 0 : os << std::flush;
3558 0 : }
3559 :
3560 : const std::vector<dof_id_type> &
3561 229 : MooseMesh::getNodeList(boundary_id_type nodeset_id) const
3562 : {
3563 : std::map<boundary_id_type, std::vector<dof_id_type>>::const_iterator it =
3564 229 : _node_set_nodes.find(nodeset_id);
3565 :
3566 229 : if (it == _node_set_nodes.end())
3567 : {
3568 : // On a distributed mesh we might not know about a remote nodeset,
3569 : // so we'll return an empty vector and hope the nodeset exists
3570 : // elsewhere.
3571 0 : if (!getMesh().is_serial())
3572 : {
3573 0 : static const std::vector<dof_id_type> empty_vec;
3574 0 : return empty_vec;
3575 : }
3576 : // On a replicated mesh we should know about every nodeset and if
3577 : // we're asked for one that doesn't exist then it must be a bug.
3578 : else
3579 : {
3580 0 : mooseError("Unable to nodeset ID: ", nodeset_id, '.');
3581 : }
3582 : }
3583 :
3584 229 : return it->second;
3585 : }
3586 :
3587 : const std::set<BoundaryID> &
3588 4681422 : MooseMesh::getSubdomainBoundaryIds(const SubdomainID subdomain_id) const
3589 : {
3590 4681422 : const auto it = _sub_to_data.find(subdomain_id);
3591 :
3592 4681422 : if (it == _sub_to_data.end())
3593 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3594 :
3595 9362844 : return it->second.boundary_ids;
3596 : }
3597 :
3598 : std::set<BoundaryID>
3599 22 : MooseMesh::getSubdomainInterfaceBoundaryIds(const SubdomainID subdomain_id) const
3600 : {
3601 22 : const auto & bnd_ids = getSubdomainBoundaryIds(subdomain_id);
3602 22 : std::set<BoundaryID> boundary_ids(bnd_ids.begin(), bnd_ids.end());
3603 : std::unordered_map<SubdomainID, std::set<BoundaryID>>::const_iterator it =
3604 22 : _neighbor_subdomain_boundary_ids.find(subdomain_id);
3605 :
3606 22 : boundary_ids.insert(it->second.begin(), it->second.end());
3607 :
3608 44 : return boundary_ids;
3609 0 : }
3610 :
3611 : std::set<SubdomainID>
3612 203 : MooseMesh::getBoundaryConnectedBlocks(const BoundaryID bid) const
3613 : {
3614 203 : std::set<SubdomainID> subdomain_ids;
3615 763 : for (const auto & [sub_id, data] : _sub_to_data)
3616 560 : if (data.boundary_ids.find(bid) != data.boundary_ids.end())
3617 203 : subdomain_ids.insert(sub_id);
3618 :
3619 203 : return subdomain_ids;
3620 0 : }
3621 :
3622 : std::set<SubdomainID>
3623 169 : MooseMesh::getBoundaryConnectedSecondaryBlocks(const BoundaryID bid) const
3624 : {
3625 169 : std::set<SubdomainID> subdomain_ids;
3626 507 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3627 338 : if (it.second.find(bid) != it.second.end())
3628 169 : subdomain_ids.insert(it.first);
3629 :
3630 169 : return subdomain_ids;
3631 0 : }
3632 :
3633 : std::set<SubdomainID>
3634 11 : MooseMesh::getInterfaceConnectedBlocks(const BoundaryID bid) const
3635 : {
3636 11 : std::set<SubdomainID> subdomain_ids = getBoundaryConnectedBlocks(bid);
3637 110 : for (const auto & it : _neighbor_subdomain_boundary_ids)
3638 99 : if (it.second.find(bid) != it.second.end())
3639 44 : subdomain_ids.insert(it.first);
3640 :
3641 11 : return subdomain_ids;
3642 0 : }
3643 :
3644 : const std::set<SubdomainID> &
3645 0 : MooseMesh::getBlockConnectedBlocks(const SubdomainID subdomain_id) const
3646 : {
3647 0 : const auto it = _sub_to_data.find(subdomain_id);
3648 :
3649 0 : if (it == _sub_to_data.end())
3650 0 : mooseError("Unable to find subdomain ID: ", subdomain_id, '.');
3651 :
3652 0 : return it->second.neighbor_subs;
3653 : }
3654 :
3655 : bool
3656 1216264 : MooseMesh::isBoundaryNode(dof_id_type node_id) const
3657 : {
3658 1216264 : bool found_node = false;
3659 4992112 : for (const auto & it : _bnd_node_ids)
3660 : {
3661 4053776 : if (it.second.find(node_id) != it.second.end())
3662 : {
3663 277928 : found_node = true;
3664 277928 : break;
3665 : }
3666 : }
3667 1216264 : return found_node;
3668 : }
3669 :
3670 : bool
3671 995742 : MooseMesh::isBoundaryNode(dof_id_type node_id, BoundaryID bnd_id) const
3672 : {
3673 995742 : bool found_node = false;
3674 995742 : std::map<boundary_id_type, std::set<dof_id_type>>::const_iterator it = _bnd_node_ids.find(bnd_id);
3675 995742 : if (it != _bnd_node_ids.end())
3676 935442 : if (it->second.find(node_id) != it->second.end())
3677 11620 : found_node = true;
3678 995742 : return found_node;
3679 : }
3680 :
3681 : bool
3682 0 : MooseMesh::isBoundaryElem(dof_id_type elem_id) const
3683 : {
3684 0 : bool found_elem = false;
3685 0 : for (const auto & it : _bnd_elem_ids)
3686 : {
3687 0 : if (it.second.find(elem_id) != it.second.end())
3688 : {
3689 0 : found_elem = true;
3690 0 : break;
3691 : }
3692 : }
3693 0 : return found_elem;
3694 : }
3695 :
3696 : bool
3697 425114 : MooseMesh::isBoundaryElem(dof_id_type elem_id, BoundaryID bnd_id) const
3698 : {
3699 425114 : bool found_elem = false;
3700 425114 : auto it = _bnd_elem_ids.find(bnd_id);
3701 425114 : if (it != _bnd_elem_ids.end())
3702 393181 : if (it->second.find(elem_id) != it->second.end())
3703 22342 : found_elem = true;
3704 425114 : return found_elem;
3705 : }
3706 :
3707 : void
3708 1276 : MooseMesh::errorIfDistributedMesh(std::string name) const
3709 : {
3710 1276 : if (_use_distributed_mesh)
3711 0 : mooseError("Cannot use ",
3712 : name,
3713 : " with DistributedMesh!\n",
3714 : "Consider specifying parallel_type = 'replicated' in your input file\n",
3715 : "to prevent it from being run with DistributedMesh.");
3716 1276 : }
3717 :
3718 : void
3719 69922 : MooseMesh::setPartitionerHelper(MeshBase * const mesh)
3720 : {
3721 69922 : if (_use_distributed_mesh && (_partitioner_name != "default" && _partitioner_name != "parmetis"))
3722 : {
3723 16 : _partitioner_name = "parmetis";
3724 16 : _partitioner_overridden = true;
3725 : }
3726 :
3727 69922 : setPartitioner(mesh ? *mesh : getMesh(), _partitioner_name, _use_distributed_mesh, _pars, *this);
3728 69922 : }
3729 :
3730 : void
3731 69922 : MooseMesh::setPartitioner(MeshBase & mesh_base,
3732 : MooseEnum & partitioner,
3733 : bool use_distributed_mesh,
3734 : const InputParameters & params,
3735 : MooseObject & context_obj)
3736 : {
3737 : // Set the partitioner based on partitioner name
3738 69922 : switch (partitioner)
3739 : {
3740 64922 : case -3: // default
3741 : // We'll use the default partitioner, but notify the user of which one is being used...
3742 64922 : if (use_distributed_mesh)
3743 21304 : partitioner = "parmetis";
3744 : else
3745 108540 : partitioner = "metis";
3746 64922 : break;
3747 :
3748 : // No need to explicitily create the metis or parmetis partitioners,
3749 : // They are the default for serial and parallel mesh respectively
3750 4888 : case -2: // metis
3751 : case -1: // parmetis
3752 4888 : break;
3753 :
3754 60 : case 0: // linear
3755 60 : mesh_base.partitioner().reset(new libMesh::LinearPartitioner);
3756 60 : break;
3757 52 : case 1: // centroid
3758 : {
3759 104 : if (!params.isParamValid("centroid_partitioner_direction"))
3760 0 : context_obj.paramError(
3761 : "centroid_partitioner_direction",
3762 : "If using the centroid partitioner you _must_ specify centroid_partitioner_direction!");
3763 :
3764 52 : MooseEnum direction = params.get<MooseEnum>("centroid_partitioner_direction");
3765 :
3766 52 : if (direction == "x")
3767 32 : mesh_base.partitioner().reset(
3768 16 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::X));
3769 36 : else if (direction == "y")
3770 72 : mesh_base.partitioner().reset(
3771 36 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Y));
3772 0 : else if (direction == "z")
3773 0 : mesh_base.partitioner().reset(
3774 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::Z));
3775 0 : else if (direction == "radial")
3776 0 : mesh_base.partitioner().reset(
3777 0 : new libMesh::CentroidPartitioner(libMesh::CentroidPartitioner::RADIAL));
3778 52 : break;
3779 52 : }
3780 0 : case 2: // hilbert_sfc
3781 0 : mesh_base.partitioner().reset(new libMesh::HilbertSFCPartitioner);
3782 0 : break;
3783 0 : case 3: // morton_sfc
3784 0 : mesh_base.partitioner().reset(new libMesh::MortonSFCPartitioner);
3785 0 : break;
3786 : }
3787 69922 : }
3788 :
3789 : void
3790 1497 : MooseMesh::setCustomPartitioner(Partitioner * partitioner)
3791 : {
3792 1497 : _custom_partitioner = partitioner->clone();
3793 1497 : setIsCustomPartitionerRequested(true);
3794 1497 : if (_mesh)
3795 12 : _mesh->partitioner() = _custom_partitioner->clone();
3796 1497 : _partitioner_name = "custom";
3797 1497 : }
3798 :
3799 : bool
3800 0 : MooseMesh::isCustomPartitionerRequested() const
3801 : {
3802 0 : return _custom_partitioner_requested;
3803 : }
3804 :
3805 : bool
3806 145939 : MooseMesh::hasSecondOrderElements()
3807 : {
3808 145939 : bool mesh_has_second_order_elements = false;
3809 46315657 : for (auto it = activeLocalElementsBegin(), end = activeLocalElementsEnd(); it != end; ++it)
3810 23101159 : if ((*it)->default_order() == SECOND)
3811 : {
3812 16300 : mesh_has_second_order_elements = true;
3813 16300 : break;
3814 145939 : }
3815 :
3816 : // We checked our local elements, so take the max over all processors.
3817 145939 : comm().max(mesh_has_second_order_elements);
3818 145939 : return mesh_has_second_order_elements;
3819 : }
3820 :
3821 : void
3822 3001 : MooseMesh::setIsCustomPartitionerRequested(bool cpr)
3823 : {
3824 3001 : _custom_partitioner_requested = cpr;
3825 3001 : }
3826 :
3827 : std::unique_ptr<libMesh::PointLocatorBase>
3828 7000 : MooseMesh::getPointLocator() const
3829 : {
3830 7000 : return getMesh().sub_point_locator();
3831 : }
3832 :
3833 : void
3834 4742 : MooseMesh::buildFiniteVolumeInfo() const
3835 : {
3836 : mooseAssert(!Threads::in_threads,
3837 : "This routine has not been implemented for threads. Please query this routine before "
3838 : "a threaded region or contact a MOOSE developer to discuss.");
3839 4742 : _finite_volume_info_dirty = false;
3840 :
3841 : using Keytype = std::pair<const Elem *, unsigned short int>;
3842 :
3843 : // create a map from elem/side --> boundary ids
3844 : std::vector<std::tuple<dof_id_type, unsigned short int, boundary_id_type>> side_list =
3845 4742 : buildActiveSideList();
3846 4742 : std::map<Keytype, std::set<boundary_id_type>> side_map;
3847 164212 : for (auto & [elem_id, side, bc_id] : side_list)
3848 : {
3849 159470 : const Elem * elem = _mesh->elem_ptr(elem_id);
3850 159470 : Keytype key(elem, side);
3851 159470 : auto & bc_set = side_map[key];
3852 159470 : bc_set.insert(bc_id);
3853 : }
3854 :
3855 4742 : _face_info.clear();
3856 4742 : _all_face_info.clear();
3857 4742 : _elem_side_to_face_info.clear();
3858 :
3859 4742 : _elem_to_elem_info.clear();
3860 4742 : _elem_info.clear();
3861 :
3862 : // by performing the element ID comparison check in the below loop, we are ensuring that we never
3863 : // double count face contributions. If a face lies along a process boundary, the only process that
3864 : // will contribute to both sides of the face residuals/Jacobians will be the process that owns the
3865 : // element with the lower ID.
3866 4742 : auto begin = getMesh().active_elements_begin();
3867 4742 : auto end = getMesh().active_elements_end();
3868 :
3869 : // We prepare a map connecting the Elem* and the corresponding ElemInfo
3870 : // for the active elements.
3871 4742 : _elem_to_elem_info.reserve(nActiveLocalElem());
3872 4742 : unsigned int num_sides = 0;
3873 1137318 : for (const Elem * elem : as_range(begin, end))
3874 : {
3875 1132576 : _elem_to_elem_info.emplace(elem->id(), elem);
3876 1132576 : num_sides += elem->n_sides();
3877 4742 : }
3878 :
3879 : // Used to speed up FaceInfo creation:
3880 : // - element side builder that caches per type of element
3881 4742 : libMesh::ElemSideBuilder side_builder;
3882 :
3883 4742 : _all_face_info.reserve(num_sides / 2);
3884 4742 : dof_id_type face_index = 0;
3885 2269894 : for (const Elem * elem : as_range(begin, end))
3886 : {
3887 5035168 : for (unsigned int side = 0; side < elem->n_sides(); ++side)
3888 : {
3889 : // get the neighbor element
3890 3902592 : const Elem * neighbor = elem->neighbor_ptr(side);
3891 :
3892 : // Check if the FaceInfo shall belong to the element. If yes,
3893 : // create and initialize the FaceInfo. We need this to ensure that
3894 : // we do not duplicate FaceInfo-s.
3895 3902592 : if (Moose::FV::elemHasFaceInfo(*elem, neighbor))
3896 : {
3897 : mooseAssert(!neighbor || (neighbor->level() < elem->level() ? neighbor->active() : true),
3898 : "If the neighbor is coarser than the element, we expect that the neighbor must "
3899 : "be active.");
3900 :
3901 : // We construct the faceInfo using the elementinfo and side index
3902 : mooseAssert(elem->default_order() < 4, "Did not expect such high element orders in FV");
3903 4057954 : _all_face_info.emplace_back(
3904 2028977 : &_elem_to_elem_info[elem->id()], side, face_index++, side_builder);
3905 :
3906 2028977 : auto & fi = _all_face_info.back();
3907 :
3908 : // get all the sidesets that this face is contained in and cache them
3909 : // in the face info.
3910 2028977 : std::set<boundary_id_type> & boundary_ids = fi.boundaryIDs();
3911 2028977 : boundary_ids.clear();
3912 :
3913 : // We initialize the weights/other information in faceInfo. If the neighbor does not exist
3914 : // or is remote (so when we are on some sort of mesh boundary), we initialize the ghost
3915 : // cell and use it to compute the weights corresponding to the faceInfo.
3916 2028977 : if (!neighbor || neighbor == libMesh::remote_elem)
3917 152539 : fi.computeBoundaryCoefficients();
3918 : else
3919 1876438 : fi.computeInternalCoefficients(&_elem_to_elem_info[neighbor->id()]);
3920 :
3921 2028977 : auto lit = side_map.find(Keytype(&fi.elem(), fi.elemSideID()));
3922 2028977 : if (lit != side_map.end())
3923 152633 : boundary_ids.insert(lit->second.begin(), lit->second.end());
3924 :
3925 2028977 : if (fi.neighborPtr())
3926 : {
3927 1876438 : auto rit = side_map.find(Keytype(fi.neighborPtr(), fi.neighborSideID()));
3928 1876438 : if (rit != side_map.end())
3929 4220 : boundary_ids.insert(rit->second.begin(), rit->second.end());
3930 : }
3931 : }
3932 : }
3933 4742 : }
3934 :
3935 : // Build the local face info and elem_side to face info maps. We need to do this after
3936 : // _all_face_info is finished being constructed because emplace_back invalidates all iterators and
3937 : // references if ever the new size exceeds capacity
3938 4742 : _elem_side_to_face_info.reserve(_all_face_info.size());
3939 : // heuristic to avoid resizing too much
3940 4742 : _face_info.reserve(_all_face_info.size());
3941 2033719 : for (auto & fi : _all_face_info)
3942 : {
3943 2028977 : const Elem * const elem = &fi.elem();
3944 2028977 : const auto side = fi.elemSideID();
3945 :
3946 : #ifndef NDEBUG
3947 : auto pair_it =
3948 : #endif
3949 2028977 : _elem_side_to_face_info.emplace(std::make_pair(elem, side), &fi);
3950 : mooseAssert(pair_it.second, "We should be adding unique FaceInfo objects.");
3951 :
3952 : // We will add the faces on processor boundaries to the list of face infos on each
3953 : // associated processor.
3954 2583648 : if (fi.elem().processor_id() == this->processor_id() ||
3955 554671 : (fi.neighborPtr() && (fi.neighborPtr()->processor_id() == this->processor_id())))
3956 1745141 : _face_info.push_back(&fi);
3957 : }
3958 :
3959 4742 : _elem_info.reserve(nActiveLocalElem());
3960 1137318 : for (auto & ei : _elem_to_elem_info)
3961 1132576 : if (ei.second.elem()->processor_id() == this->processor_id())
3962 978244 : _elem_info.push_back(&ei.second);
3963 4742 : }
3964 :
3965 : const FaceInfo *
3966 122662946 : MooseMesh::faceInfo(const Elem * elem, unsigned int side) const
3967 : {
3968 122662946 : auto it = _elem_side_to_face_info.find(std::make_pair(elem, side));
3969 :
3970 122662946 : if (it == _elem_side_to_face_info.end())
3971 792 : return nullptr;
3972 : else
3973 : {
3974 : mooseAssert(it->second,
3975 : "For some reason, the FaceInfo object is NULL! Try calling "
3976 : "`buildFiniteVolumeInfo()` before using this accessor!");
3977 122662154 : return it->second;
3978 : }
3979 : }
3980 :
3981 : const ElemInfo &
3982 108299889 : MooseMesh::elemInfo(const dof_id_type id) const
3983 : {
3984 108299889 : return libmesh_map_find(_elem_to_elem_info, id);
3985 : }
3986 :
3987 : void
3988 4722 : MooseMesh::computeFiniteVolumeCoords() const
3989 : {
3990 4722 : if (_finite_volume_info_dirty)
3991 0 : mooseError("Trying to compute face- and elem-info coords when the information is dirty");
3992 :
3993 2032979 : for (auto & fi : _all_face_info)
3994 : {
3995 : // get elem & neighbor elements, and set subdomain ids
3996 2028257 : const SubdomainID elem_subdomain_id = fi.elemSubdomainID();
3997 2028257 : const SubdomainID neighbor_subdomain_id = fi.neighborSubdomainID();
3998 :
3999 2028257 : coordTransformFactor(
4000 2028257 : *this, elem_subdomain_id, fi.faceCentroid(), fi.faceCoord(), neighbor_subdomain_id);
4001 : }
4002 :
4003 1137138 : for (auto & ei : _elem_to_elem_info)
4004 1132416 : coordTransformFactor(
4005 2264832 : *this, ei.second.subdomain_id(), ei.second.centroid(), ei.second.coordFactor());
4006 4722 : }
4007 :
4008 : MooseEnum
4009 203681 : MooseMesh::partitioning()
4010 : {
4011 : MooseEnum partitioning(
4012 611043 : "default=-3 metis=-2 parmetis=-1 linear=0 centroid hilbert_sfc morton_sfc custom", "default");
4013 203681 : return partitioning;
4014 : }
4015 :
4016 : MooseEnum
4017 3421 : MooseMesh::elemTypes()
4018 : {
4019 : MooseEnum elemTypes(
4020 : "EDGE EDGE2 EDGE3 EDGE4 QUAD QUAD4 QUAD8 QUAD9 TRI3 TRI6 HEX HEX8 HEX20 HEX27 TET4 TET10 "
4021 10263 : "PRISM6 PRISM15 PRISM18 PYRAMID5 PYRAMID13 PYRAMID14");
4022 3421 : return elemTypes;
4023 : }
4024 :
4025 : void
4026 35755 : MooseMesh::allowRemoteElementRemoval(const bool allow_remote_element_removal)
4027 : {
4028 35755 : _allow_remote_element_removal = allow_remote_element_removal;
4029 35755 : if (_mesh)
4030 16324 : _mesh->allow_remote_element_removal(allow_remote_element_removal);
4031 :
4032 35755 : if (!allow_remote_element_removal)
4033 : // If we're not allowing remote element removal now, then we will need deletion later after
4034 : // late geoemetric ghosting functors have been added (late geometric ghosting functor addition
4035 : // happens when algebraic ghosting functors are added)
4036 35755 : _need_delete = true;
4037 35755 : }
4038 :
4039 : void
4040 17623 : MooseMesh::deleteRemoteElements()
4041 : {
4042 17623 : _allow_remote_element_removal = true;
4043 17623 : if (!_mesh)
4044 0 : mooseError("Cannot delete remote elements because we have not yet attached a MeshBase");
4045 :
4046 17623 : _mesh->allow_remote_element_removal(true);
4047 :
4048 17623 : _mesh->delete_remote_elements();
4049 17623 : }
4050 :
4051 : void
4052 4718 : MooseMesh::cacheFaceInfoVariableOwnership() const
4053 : {
4054 : mooseAssert(
4055 : !Threads::in_threads,
4056 : "Performing writes to faceInfo variable association maps. This must be done unthreaded!");
4057 :
4058 4718 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
4059 :
4060 4060395 : auto face_lambda = [this](const SubdomainID elem_subdomain_id,
4061 : const SubdomainID neighbor_subdomain_id,
4062 : SystemBase & sys,
4063 : std::vector<std::vector<FaceInfo::VarFaceNeighbors>> & face_type_vector)
4064 : {
4065 4060395 : face_type_vector[sys.number()].resize(sys.nVariables(), FaceInfo::VarFaceNeighbors::NEITHER);
4066 4060395 : const auto & variables = sys.getVariables(0);
4067 :
4068 8732670 : for (const auto & var : variables)
4069 : {
4070 4672275 : const unsigned int var_num = var->number();
4071 4672275 : const unsigned int sys_num = var->sys().number();
4072 4672275 : std::set<SubdomainID> var_subdomains = var->blockIDs();
4073 : /**
4074 : * The following paragraph of code assigns the VarFaceNeighbors
4075 : * 1. The face is an internal face of this variable if it is defined on
4076 : * the elem and neighbor subdomains
4077 : * 2. The face is an invalid face of this variable if it is neither defined
4078 : * on the elem nor the neighbor subdomains
4079 : * 3. If not 1. or 2. then this is a boundary for this variable and the else clause
4080 : * applies
4081 : */
4082 4672275 : bool var_defined_elem = var_subdomains.find(elem_subdomain_id) != var_subdomains.end();
4083 : bool var_defined_neighbor =
4084 4672275 : var_subdomains.find(neighbor_subdomain_id) != var_subdomains.end();
4085 4672275 : if (var_defined_elem && var_defined_neighbor)
4086 3885061 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::BOTH;
4087 787214 : else if (!var_defined_elem && !var_defined_neighbor)
4088 349377 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEITHER;
4089 : else
4090 : {
4091 : // this is a boundary face for this variable, set elem or neighbor
4092 437837 : if (var_defined_elem)
4093 432405 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::ELEM;
4094 5432 : else if (var_defined_neighbor)
4095 5432 : face_type_vector[sys_num][var_num] = FaceInfo::VarFaceNeighbors::NEIGHBOR;
4096 : else
4097 0 : mooseError("Should never get here");
4098 : }
4099 4672275 : }
4100 4060395 : };
4101 :
4102 : // We loop through the faces and check if they are internal, boundary or external to
4103 : // the variables in the problem
4104 2032927 : for (FaceInfo & face : _all_face_info)
4105 : {
4106 2028209 : const SubdomainID elem_subdomain_id = face.elemSubdomainID();
4107 2028209 : const SubdomainID neighbor_subdomain_id = face.neighborSubdomainID();
4108 :
4109 2028209 : auto & face_type_vector = face.faceType();
4110 :
4111 2028209 : face_type_vector.clear();
4112 2028209 : face_type_vector.resize(num_eqs);
4113 :
4114 : // First, we check the variables in the solver systems (linear/nonlinear)
4115 4060395 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4116 2032186 : face_lambda(elem_subdomain_id,
4117 : neighbor_subdomain_id,
4118 2032186 : _app.feProblem().getSolverSystem(i),
4119 : face_type_vector);
4120 :
4121 : // Then we check the variables in the auxiliary system
4122 2028209 : face_lambda(elem_subdomain_id,
4123 : neighbor_subdomain_id,
4124 2028209 : _app.feProblem().getAuxiliarySystem(),
4125 : face_type_vector);
4126 : }
4127 4718 : }
4128 :
4129 : void
4130 4718 : MooseMesh::cacheFVElementalDoFs() const
4131 : {
4132 : mooseAssert(!Threads::in_threads,
4133 : "Performing writes to elemInfo dof indices. This must be done unthreaded!");
4134 :
4135 2267443 : auto elem_lambda = [](const ElemInfo & elem_info,
4136 : SystemBase & sys,
4137 : std::vector<std::vector<dof_id_type>> & dof_vector)
4138 : {
4139 2267443 : if (sys.nFVVariables())
4140 : {
4141 1199180 : dof_vector[sys.number()].resize(sys.nVariables(), libMesh::DofObject::invalid_id);
4142 1199180 : const auto & variables = sys.getVariables(0);
4143 :
4144 3685546 : for (const auto & var : variables)
4145 2486366 : if (var->isFV())
4146 : {
4147 1440695 : const auto & var_subdomains = var->blockIDs();
4148 :
4149 : // We will only cache for FV variables and if they live on the current subdomain
4150 1440695 : if (var_subdomains.find(elem_info.subdomain_id()) != var_subdomains.end())
4151 : {
4152 1333516 : std::vector<dof_id_type> indices;
4153 1333516 : var->dofMap().dof_indices(elem_info.elem(), indices, var->number());
4154 : mooseAssert(indices.size() == 1, "We expect to have only one dof per element!");
4155 1333516 : dof_vector[sys.number()][var->number()] = indices[0];
4156 1333516 : }
4157 : }
4158 : }
4159 2267443 : };
4160 :
4161 4718 : const unsigned int num_eqs = _app.feProblem().es().n_systems();
4162 :
4163 : // We loop through the elements in the mesh and cache the dof indices
4164 : // for the corresponding variables.
4165 1137118 : for (auto & ei_pair : _elem_to_elem_info)
4166 : {
4167 1132400 : auto & elem_info = ei_pair.second;
4168 1132400 : auto & dof_vector = elem_info.dofIndices();
4169 :
4170 1132400 : dof_vector.clear();
4171 1132400 : dof_vector.resize(num_eqs);
4172 :
4173 : // First, we cache the dof indices for the variables in the solver systems (linear, nonlinear)
4174 2267443 : for (const auto i : make_range(_app.feProblem().numSolverSystems()))
4175 1135043 : elem_lambda(elem_info, _app.feProblem().getSolverSystem(i), dof_vector);
4176 :
4177 : // Then we cache the dof indices for the auxvariables
4178 1132400 : elem_lambda(elem_info, _app.feProblem().getAuxiliarySystem(), dof_vector);
4179 : }
4180 4718 : }
4181 :
4182 : void
4183 4718 : MooseMesh::setupFiniteVolumeMeshData() const
4184 : {
4185 4718 : buildFiniteVolumeInfo();
4186 4718 : computeFiniteVolumeCoords();
4187 4718 : cacheFaceInfoVariableOwnership();
4188 4718 : cacheFVElementalDoFs();
4189 4718 : }
4190 :
4191 : void
4192 65641 : MooseMesh::setCoordSystem(const std::vector<SubdomainName> & blocks,
4193 : const MultiMooseEnum & coord_sys)
4194 : {
4195 328205 : TIME_SECTION("setCoordSystem", 5, "Setting Coordinate System");
4196 65641 : if (!_provided_coord_blocks.empty() && (_provided_coord_blocks != blocks))
4197 : {
4198 0 : const std::string param_name = isParamValid("coord_block") ? "coord_block" : "block";
4199 0 : mooseWarning("Supplied blocks in the 'setCoordSystem' method do not match the value of the "
4200 : "'Mesh/",
4201 : param_name,
4202 : "' parameter. Did you provide different parameter values for 'Mesh/",
4203 : param_name,
4204 : "' and 'Problem/block'?. We will honor the parameter value from 'Mesh/",
4205 : param_name,
4206 : "'");
4207 : mooseAssert(_coord_system_set,
4208 : "If we are arriving here due to a bad specification in the Problem block, then we "
4209 : "should have already set our coordinate system subdomains from the Mesh block");
4210 0 : return;
4211 0 : }
4212 198081 : if (_pars.isParamSetByUser("coord_type") && getParam<MultiMooseEnum>("coord_type") != coord_sys)
4213 0 : mooseError("Supplied coordinate systems in the 'setCoordSystem' method do not match the value "
4214 : "of the 'Mesh/coord_type' parameter. Did you provide different parameter values for "
4215 : "'coord_type' to 'Mesh' and 'Problem'?");
4216 :
4217 : // If blocks contain ANY_BLOCK_ID, it should be the only block specified, and coord_sys should
4218 : // have one and only one entry. In that case, the same coordinate system will be set for all
4219 : // subdomains.
4220 65641 : if (blocks.size() == 1 && blocks[0] == "ANY_BLOCK_ID")
4221 : {
4222 0 : if (coord_sys.size() > 1)
4223 0 : mooseError("If you specify ANY_BLOCK_ID as the only block, you must also specify a single "
4224 : "coordinate system for it.");
4225 0 : if (!_mesh->is_prepared())
4226 0 : mooseError(
4227 : "You cannot set the coordinate system for ANY_BLOCK_ID before the mesh is prepared. "
4228 : "Please call this method after the mesh is prepared.");
4229 0 : const auto coord_type = coord_sys.size() == 0
4230 0 : ? Moose::COORD_XYZ
4231 0 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4232 0 : for (const auto sid : meshSubdomains())
4233 0 : _coord_sys[sid] = coord_type;
4234 0 : return;
4235 : }
4236 :
4237 : // If multiple blocks are specified, but one of them is ANY_BLOCK_ID, let's emit a helpful error
4238 65641 : if (std::find(blocks.begin(), blocks.end(), "ANY_BLOCK_ID") != blocks.end())
4239 0 : mooseError("You cannot specify ANY_BLOCK_ID together with other blocks in the "
4240 : "setCoordSystem() method. If you want to set the same coordinate system for all "
4241 : "blocks, use ANY_BLOCK_ID as the only block.");
4242 :
4243 65641 : auto subdomains = meshSubdomains();
4244 : // It's possible that a user has called this API before the mesh is prepared and consequently we
4245 : // don't yet have the subdomains in meshSubdomains()
4246 66040 : for (const auto & sub_name : blocks)
4247 : {
4248 399 : const auto sub_id = getSubdomainID(sub_name);
4249 399 : subdomains.insert(sub_id);
4250 : }
4251 :
4252 65641 : if (coord_sys.size() <= 1)
4253 : {
4254 : // We will specify the same coordinate system for all blocks
4255 65617 : const auto coord_type = coord_sys.size() == 0
4256 65617 : ? Moose::COORD_XYZ
4257 65617 : : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[0]);
4258 157706 : for (const auto sid : subdomains)
4259 92089 : _coord_sys[sid] = coord_type;
4260 : }
4261 : else
4262 : {
4263 24 : if (blocks.size() != coord_sys.size())
4264 0 : mooseError("Number of blocks and coordinate systems does not match.");
4265 :
4266 96 : for (const auto i : index_range(blocks))
4267 : {
4268 72 : SubdomainID sid = getSubdomainID(blocks[i]);
4269 : Moose::CoordinateSystemType coord_type =
4270 72 : Moose::stringToEnum<Moose::CoordinateSystemType>(coord_sys[i]);
4271 72 : _coord_sys[sid] = coord_type;
4272 : }
4273 :
4274 96 : for (const auto & sid : subdomains)
4275 72 : if (_coord_sys.find(sid) == _coord_sys.end())
4276 0 : mooseError("Subdomain '" + Moose::stringify(sid) +
4277 : "' does not have a coordinate system specified.");
4278 : }
4279 :
4280 65641 : _coord_system_set = true;
4281 :
4282 65641 : updateCoordTransform();
4283 65641 : }
4284 :
4285 : Moose::CoordinateSystemType
4286 2290261442 : MooseMesh::getCoordSystem(SubdomainID sid) const
4287 : {
4288 2290261442 : auto it = _coord_sys.find(sid);
4289 2290261442 : if (it != _coord_sys.end())
4290 4580522884 : return (*it).second;
4291 : else
4292 0 : mooseError("Requested subdomain ", sid, " does not exist.");
4293 : }
4294 :
4295 : Moose::CoordinateSystemType
4296 55126 : MooseMesh::getUniqueCoordSystem() const
4297 : {
4298 55126 : const auto unique_system = _coord_sys.find(*meshSubdomains().begin())->second;
4299 : // Check that it is actually unique
4300 55126 : bool result = std::all_of(
4301 55126 : std::next(_coord_sys.begin()),
4302 55126 : _coord_sys.end(),
4303 4346 : [unique_system](
4304 : typename std::unordered_map<SubdomainID, Moose::CoordinateSystemType>::const_reference
4305 4346 : item) { return (item.second == unique_system); });
4306 55126 : if (!result)
4307 0 : mooseError("The unique coordinate system of the mesh was requested by the mesh contains "
4308 : "multiple blocks with different coordinate systems");
4309 :
4310 55126 : if (usingGeneralAxisymmetricCoordAxes())
4311 0 : mooseError("General axisymmetric coordinate axes are being used, and it is currently "
4312 : "conservatively assumed that in this case there is no unique coordinate system.");
4313 :
4314 55126 : return unique_system;
4315 : }
4316 :
4317 : const std::map<SubdomainID, Moose::CoordinateSystemType> &
4318 68645 : MooseMesh::getCoordSystem() const
4319 : {
4320 68645 : return _coord_sys;
4321 : }
4322 :
4323 : void
4324 0 : MooseMesh::setAxisymmetricCoordAxis(const MooseEnum & rz_coord_axis)
4325 : {
4326 0 : _rz_coord_axis = rz_coord_axis;
4327 :
4328 0 : updateCoordTransform();
4329 0 : }
4330 :
4331 : void
4332 17 : MooseMesh::setGeneralAxisymmetricCoordAxes(
4333 : const std::vector<SubdomainName> & blocks,
4334 : const std::vector<std::pair<Point, RealVectorValue>> & axes)
4335 : {
4336 : // Set the axes for the given blocks
4337 : mooseAssert(blocks.size() == axes.size(), "Blocks and axes vectors must be the same length.");
4338 58 : for (const auto i : index_range(blocks))
4339 : {
4340 41 : const auto subdomain_id = getSubdomainID(blocks[i]);
4341 41 : const auto it = _coord_sys.find(subdomain_id);
4342 41 : if (it == _coord_sys.end())
4343 0 : mooseError("The block '",
4344 0 : blocks[i],
4345 : "' has not set a coordinate system. Make sure to call setCoordSystem() before "
4346 : "setGeneralAxisymmetricCoordAxes().");
4347 : else
4348 : {
4349 41 : if (it->second == Moose::COORD_RZ)
4350 : {
4351 41 : const auto direction = axes[i].second;
4352 41 : if (direction.is_zero())
4353 0 : mooseError("Only nonzero vectors may be supplied for RZ directions.");
4354 :
4355 41 : _subdomain_id_to_rz_coord_axis[subdomain_id] =
4356 82 : std::make_pair(axes[i].first, direction.unit());
4357 : }
4358 : else
4359 0 : mooseError("The block '",
4360 0 : blocks[i],
4361 : "' was provided in setGeneralAxisymmetricCoordAxes(), but the coordinate system "
4362 : "for this block is not 'RZ'.");
4363 : }
4364 : }
4365 :
4366 : // Make sure there are no RZ blocks that still do not have axes
4367 17 : const auto all_subdomain_ids = meshSubdomains();
4368 70 : for (const auto subdomain_id : all_subdomain_ids)
4369 94 : if (getCoordSystem(subdomain_id) == Moose::COORD_RZ &&
4370 41 : !_subdomain_id_to_rz_coord_axis.count(subdomain_id))
4371 0 : mooseError("The block '",
4372 0 : getSubdomainName(subdomain_id),
4373 : "' was specified to use the 'RZ' coordinate system but was not given in "
4374 : "setGeneralAxisymmetricCoordAxes().");
4375 :
4376 17 : updateCoordTransform();
4377 17 : }
4378 :
4379 : const std::pair<Point, RealVectorValue> &
4380 1063075 : MooseMesh::getGeneralAxisymmetricCoordAxis(SubdomainID subdomain_id) const
4381 : {
4382 1063075 : auto it = _subdomain_id_to_rz_coord_axis.find(subdomain_id);
4383 1063075 : if (it != _subdomain_id_to_rz_coord_axis.end())
4384 2126150 : return (*it).second;
4385 : else
4386 0 : mooseError("Requested subdomain ", subdomain_id, " does not exist.");
4387 : }
4388 :
4389 : bool
4390 24319265 : MooseMesh::usingGeneralAxisymmetricCoordAxes() const
4391 : {
4392 24319265 : return _subdomain_id_to_rz_coord_axis.size() > 0;
4393 : }
4394 :
4395 : void
4396 68645 : MooseMesh::updateCoordTransform()
4397 : {
4398 68645 : if (!_coord_transform)
4399 68624 : _coord_transform = std::make_unique<MooseAppCoordTransform>(*this);
4400 : else
4401 21 : _coord_transform->setCoordinateSystem(*this);
4402 68645 : }
4403 :
4404 : unsigned int
4405 20684434 : MooseMesh::getAxisymmetricRadialCoord() const
4406 : {
4407 20684434 : if (usingGeneralAxisymmetricCoordAxes())
4408 0 : mooseError("getAxisymmetricRadialCoord() should not be called if "
4409 : "setGeneralAxisymmetricCoordAxes() has been called.");
4410 :
4411 20684434 : if (_rz_coord_axis == 0)
4412 133200 : return 1; // if the rotation axis is x (0), then the radial direction is y (1)
4413 : else
4414 20551234 : return 0; // otherwise the radial direction is assumed to be x, i.e., the rotation axis is y
4415 : }
4416 :
4417 : void
4418 61035 : MooseMesh::checkCoordinateSystems()
4419 : {
4420 27896803 : for (const auto & elem : getMesh().element_ptr_range())
4421 : {
4422 13917887 : SubdomainID sid = elem->subdomain_id();
4423 13917887 : if (_coord_sys[sid] == Moose::COORD_RZ && elem->dim() == 3)
4424 3 : mooseError("An RZ coordinate system was requested for subdomain " + Moose::stringify(sid) +
4425 : " which contains 3D elements.");
4426 13917884 : if (_coord_sys[sid] == Moose::COORD_RSPHERICAL && elem->dim() > 1)
4427 0 : mooseError("An RSPHERICAL coordinate system was requested for subdomain " +
4428 0 : Moose::stringify(sid) + " which contains 2D or 3D elements.");
4429 61032 : }
4430 61032 : }
4431 :
4432 : void
4433 2022 : MooseMesh::setCoordData(const MooseMesh & other_mesh)
4434 : {
4435 2022 : _coord_sys = other_mesh._coord_sys;
4436 2022 : _rz_coord_axis = other_mesh._rz_coord_axis;
4437 2022 : _subdomain_id_to_rz_coord_axis = other_mesh._subdomain_id_to_rz_coord_axis;
4438 2022 : }
4439 :
4440 : const MooseUnits &
4441 2 : MooseMesh::lengthUnit() const
4442 : {
4443 : mooseAssert(_coord_transform, "This must be non-null");
4444 2 : return _coord_transform->lengthUnit();
4445 : }
4446 :
4447 : void
4448 68526 : MooseMesh::checkDuplicateSubdomainNames()
4449 : {
4450 68526 : std::map<SubdomainName, SubdomainID> subdomain;
4451 164755 : for (const auto & sbd_id : _mesh_subdomains)
4452 : {
4453 96232 : std::string sub_name = getSubdomainName(sbd_id);
4454 96232 : if (!sub_name.empty() && subdomain.count(sub_name) > 0)
4455 6 : mooseError("The subdomain name ",
4456 : sub_name,
4457 : " is used for both subdomain with ID=",
4458 3 : subdomain[sub_name],
4459 : " and ID=",
4460 : sbd_id,
4461 : ", Please rename one of them!");
4462 : else
4463 96229 : subdomain[sub_name] = sbd_id;
4464 96229 : }
4465 68523 : }
4466 :
4467 : const std::vector<QpMap> &
4468 800 : MooseMesh::getPRefinementMapHelper(
4469 : const Elem & elem,
4470 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4471 : {
4472 : // We are actually seeking the map stored with the p_level - 1 key, e.g. the refinement map that
4473 : // maps from the previous p_level to this element's p_level
4474 800 : return libmesh_map_find(map,
4475 : std::make_pair(elem.type(), cast_int<unsigned int>(elem.p_level() - 1)));
4476 : }
4477 :
4478 : const std::vector<QpMap> &
4479 0 : MooseMesh::getPCoarseningMapHelper(
4480 : const Elem & elem,
4481 : const std::map<std::pair<ElemType, unsigned int>, std::vector<QpMap>> & map) const
4482 : {
4483 : mooseAssert(elem.active() && elem.p_refinement_flag() == Elem::JUST_COARSENED,
4484 : "These are the conditions that should be met for requesting a coarsening map");
4485 0 : return libmesh_map_find(map, std::make_pair(elem.type(), elem.p_level()));
4486 : }
4487 :
4488 : const std::vector<QpMap> &
4489 800 : MooseMesh::getPRefinementMap(const Elem & elem) const
4490 : {
4491 800 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_map);
4492 : }
4493 :
4494 : const std::vector<QpMap> &
4495 0 : MooseMesh::getPRefinementSideMap(const Elem & elem) const
4496 : {
4497 0 : return getPRefinementMapHelper(elem, _elem_type_to_p_refinement_side_map);
4498 : }
4499 :
4500 : const std::vector<QpMap> &
4501 0 : MooseMesh::getPCoarseningMap(const Elem & elem) const
4502 : {
4503 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_map);
4504 : }
4505 :
4506 : const std::vector<QpMap> &
4507 0 : MooseMesh::getPCoarseningSideMap(const Elem & elem) const
4508 : {
4509 0 : return getPCoarseningMapHelper(elem, _elem_type_to_p_coarsening_side_map);
4510 : }
4511 :
4512 : bool
4513 26973 : MooseMesh::skipNoncriticalPartitioning() const
4514 : {
4515 26973 : return _mesh->skip_noncritical_partitioning();
4516 : }
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