Line data Source code
1 : // The libMesh Finite Element Library.
2 : // Copyright (C) 2002-2025 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
3 :
4 : // This library is free software; you can redistribute it and/or
5 : // modify it under the terms of the GNU Lesser General Public
6 : // License as published by the Free Software Foundation; either
7 : // version 2.1 of the License, or (at your option) any later version.
8 :
9 : // This library is distributed in the hope that it will be useful,
10 : // but WITHOUT ANY WARRANTY; without even the implied warranty of
11 : // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 : // Lesser General Public License for more details.
13 :
14 : // You should have received a copy of the GNU Lesser General Public
15 : // License along with this library; if not, write to the Free Software
16 : // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
17 :
18 :
19 : // Local Includes
20 : #include "libmesh/default_coupling.h" // For downconversion
21 : #include "libmesh/dof_map.h"
22 : #include "libmesh/eigen_system.h"
23 : #include "libmesh/elem.h"
24 : #include "libmesh/explicit_system.h"
25 : #include "libmesh/fe_interface.h"
26 : #include "libmesh/frequency_system.h"
27 : #include "libmesh/int_range.h"
28 : #include "libmesh/libmesh_logging.h"
29 : #include "libmesh/linear_implicit_system.h"
30 : #include "libmesh/mesh_base.h"
31 : #include "libmesh/mesh_refinement.h"
32 : #include "libmesh/newmark_system.h"
33 : #include "libmesh/nonlinear_implicit_system.h"
34 : #include "libmesh/parallel.h"
35 : #include "libmesh/rb_construction.h"
36 : #include "libmesh/remote_elem.h"
37 : #include "libmesh/transient_rb_construction.h"
38 : #include "libmesh/transient_system.h"
39 :
40 : // System includes
41 : #include <functional> // std::plus
42 : #include <numeric> // std::iota
43 : #include <sstream>
44 :
45 : // Include the systems before this one to avoid
46 : // overlapping forward declarations.
47 : #include "libmesh/equation_systems.h"
48 :
49 : namespace libMesh
50 : {
51 :
52 236306 : EquationSystems::EquationSystems (MeshBase & m) :
53 : ParallelObject (m),
54 222814 : _mesh (m),
55 222814 : _refine_in_reinit(true),
56 243052 : _enable_default_ghosting(true)
57 : {
58 : // Set default parameters
59 236306 : this->parameters.set<Real> ("linear solver tolerance") = TOLERANCE * TOLERANCE;
60 236306 : this->parameters.set<unsigned int>("linear solver maximum iterations") = 5000;
61 236306 : }
62 :
63 :
64 :
65 407393 : EquationSystems::~EquationSystems () = default;
66 :
67 :
68 :
69 71 : void EquationSystems::clear ()
70 : {
71 : // Clear any additional parameters
72 2 : parameters.clear ();
73 :
74 : // Clear the systems.
75 2 : _systems.clear();
76 71 : }
77 :
78 :
79 :
80 235975 : void EquationSystems::init ()
81 : {
82 : #ifndef NDEBUG
83 13548 : for (auto i : make_range(this->n_systems()))
84 6810 : libmesh_assert(!this->get_system(i).is_initialized());
85 : #endif
86 :
87 235975 : this->reinit_mesh();
88 235881 : }
89 :
90 :
91 :
92 22188 : void EquationSystems::reinit ()
93 : {
94 22188 : const bool mesh_changed = this->reinit_solutions();
95 :
96 : // If the mesh has changed, systems will need to reinitialize their
97 : // own data on the new mesh.
98 22188 : if (mesh_changed)
99 22188 : this->reinit_systems();
100 22188 : }
101 :
102 236401 : void EquationSystems::reinit_mesh ()
103 : {
104 6750 : const unsigned int n_sys = this->n_systems();
105 :
106 6750 : libmesh_assert_not_equal_to (n_sys, 0);
107 :
108 : // Tell all the \p DofObject entities how many systems
109 : // there are.
110 27135394 : for (auto & node : _mesh.node_ptr_range())
111 14523802 : node->set_n_systems(n_sys);
112 :
113 12297288 : for (auto & elem : _mesh.element_ptr_range())
114 6543315 : elem->set_n_systems(n_sys);
115 :
116 : //for (auto i : make_range(this->n_systems()))
117 : //this->get_system(i).init();
118 :
119 : #ifdef LIBMESH_ENABLE_AMR
120 249901 : MeshRefinement mesh_refine(_mesh);
121 236401 : mesh_refine.clean_refinement_flags();
122 : #endif
123 :
124 : // Now loop over all the systems belonging to this ES
125 : // and call reinit_mesh for each system
126 475324 : for (auto i : make_range(this->n_systems()))
127 239017 : this->get_system(i).reinit_mesh();
128 :
129 236393 : }
130 :
131 22188 : bool EquationSystems::reinit_solutions ()
132 : {
133 754 : parallel_object_only();
134 :
135 754 : const unsigned int n_sys = this->n_systems();
136 754 : libmesh_assert_not_equal_to (n_sys, 0);
137 :
138 : // And any new systems will need initialization
139 45123 : for (unsigned int i=0; i != n_sys; ++i)
140 22935 : if (!this->get_system(i).is_initialized())
141 143 : this->get_system(i).init();
142 :
143 : // We used to assert that all nodes and elements *already* had
144 : // n_systems() properly set; however this is false in the case where
145 : // user code has manually added nodes and/or elements to an
146 : // already-initialized system.
147 :
148 : // Make sure all the \p DofObject entities know how many systems
149 : // there are.
150 : {
151 : // All the nodes
152 15338746 : for (auto & node : _mesh.node_ptr_range())
153 8291830 : node->set_n_systems(n_sys);
154 :
155 : // All the elements
156 16522262 : for (auto & elem : _mesh.element_ptr_range())
157 8758092 : elem->set_n_systems(n_sys);
158 : }
159 :
160 : // Localize each system's vectors
161 45123 : for (unsigned int i=0; i != n_sys; ++i)
162 22935 : this->get_system(i).re_update();
163 :
164 : #ifdef LIBMESH_ENABLE_AMR
165 :
166 754 : bool mesh_changed = false;
167 :
168 : // FIXME: For backwards compatibility, assume
169 : // refine_and_coarsen_elements or refine_uniformly have already
170 : // been called
171 : {
172 45123 : for (unsigned int i=0; i != n_sys; ++i)
173 : {
174 766 : System & sys = this->get_system(i);
175 :
176 : // Even if the system doesn't have any variables in it we want
177 : // consistent behavior; e.g. distribute_dofs should have the
178 : // opportunity to count up zero dofs on each processor.
179 : //
180 : // Who's been adding zero-var systems anyway, outside of my
181 : // unit tests? - RHS
182 : // if (!sys.n_vars())
183 : // continue;
184 :
185 22935 : sys.get_dof_map().distribute_dofs(_mesh);
186 :
187 : // Recreate any user or internal constraints
188 22935 : sys.reinit_constraints();
189 :
190 : // Even if there weren't any constraint changes,
191 : // reinit_constraints() did prepare_send_list() for us.
192 :
193 22935 : sys.prolong_vectors();
194 : }
195 754 : mesh_changed = true;
196 : }
197 :
198 22188 : if (this->_refine_in_reinit)
199 : {
200 : // Don't override any user refinement settings
201 23546 : MeshRefinement mesh_refine(_mesh);
202 22046 : mesh_refine.face_level_mismatch_limit() = 0; // unlimited
203 22046 : mesh_refine.overrefined_boundary_limit() = -1; // unlimited
204 22046 : mesh_refine.underrefined_boundary_limit() = -1; // unlimited
205 :
206 : // Try to coarsen the mesh, then restrict each system's vectors
207 : // if necessary
208 22046 : if (mesh_refine.coarsen_elements())
209 : {
210 0 : for (auto i : make_range(this->n_systems()))
211 : {
212 0 : System & sys = this->get_system(i);
213 0 : sys.get_dof_map().distribute_dofs(_mesh);
214 0 : sys.reinit_constraints();
215 :
216 : // Even if there weren't any constraint changes,
217 : // reinit_constraints() did prepare_send_list() for us.
218 :
219 0 : sys.restrict_vectors();
220 : }
221 0 : mesh_changed = true;
222 : }
223 :
224 : // Once vectors are all restricted, we can delete
225 : // children of coarsened elements
226 750 : if (mesh_changed)
227 22046 : this->get_mesh().contract();
228 :
229 : // Try to refine the mesh, then prolong each system's vectors
230 : // if necessary
231 22046 : if (mesh_refine.refine_elements())
232 : {
233 2414 : for (auto i : make_range(this->n_systems()))
234 : {
235 34 : System & sys = this->get_system(i);
236 1207 : sys.get_dof_map().distribute_dofs(_mesh);
237 1207 : sys.reinit_constraints();
238 :
239 : // Even if there weren't any constraint changes,
240 : // reinit_constraints() did prepare_send_list() for us.
241 :
242 1207 : sys.prolong_vectors();
243 : }
244 34 : mesh_changed = true;
245 : }
246 20546 : }
247 :
248 754 : return mesh_changed;
249 :
250 : #endif // #ifdef LIBMESH_ENABLE_AMR
251 :
252 : return false;
253 : }
254 :
255 :
256 :
257 22188 : void EquationSystems::reinit_systems()
258 : {
259 45123 : for (auto i : make_range(this->n_systems()))
260 22935 : this->get_system(i).reinit();
261 22188 : }
262 :
263 :
264 :
265 0 : void EquationSystems::allgather ()
266 : {
267 : // A serial mesh means nothing needs to be done
268 0 : if (_mesh.is_serial())
269 0 : return;
270 :
271 0 : const unsigned int n_sys = this->n_systems();
272 :
273 0 : libmesh_assert_not_equal_to (n_sys, 0);
274 :
275 : // Gather the mesh
276 0 : _mesh.allgather();
277 :
278 : // Tell all the \p DofObject entities how many systems
279 : // there are.
280 0 : for (auto & node : _mesh.node_ptr_range())
281 0 : node->set_n_systems(n_sys);
282 :
283 0 : for (auto & elem : _mesh.element_ptr_range())
284 0 : elem->set_n_systems(n_sys);
285 :
286 : // And distribute each system's dofs
287 0 : for (auto i : make_range(this->n_systems()))
288 : {
289 0 : System & sys = this->get_system(i);
290 0 : DofMap & dof_map = sys.get_dof_map();
291 0 : dof_map.distribute_dofs(_mesh);
292 :
293 : // The user probably won't need constraint equations or the
294 : // send_list after an allgather, but let's keep it in consistent
295 : // shape just in case.
296 0 : sys.reinit_constraints();
297 :
298 : // Even if there weren't any constraint changes,
299 : // reinit_constraints() did prepare_send_list() for us.
300 : }
301 : }
302 :
303 :
304 :
305 213 : void EquationSystems::enable_default_ghosting (bool enable)
306 : {
307 213 : _enable_default_ghosting = enable;
308 12 : MeshBase &mesh = this->get_mesh();
309 :
310 213 : if (enable)
311 71 : mesh.add_ghosting_functor(mesh.default_ghosting());
312 : else
313 142 : mesh.remove_ghosting_functor(mesh.default_ghosting());
314 :
315 426 : for (auto i : make_range(this->n_systems()))
316 : {
317 6 : DofMap & dof_map = this->get_system(i).get_dof_map();
318 213 : if (enable)
319 71 : dof_map.add_default_ghosting();
320 : else
321 142 : dof_map.remove_default_ghosting();
322 : }
323 213 : }
324 :
325 :
326 :
327 10858 : void EquationSystems::update ()
328 : {
329 624 : LOG_SCOPE("update()", "EquationSystems");
330 :
331 : // Localize each system's vectors
332 22347 : for (auto i : make_range(this->n_systems()))
333 11489 : this->get_system(i).update();
334 10858 : }
335 :
336 :
337 :
338 1339 : System & EquationSystems::add_system (std::string_view sys_type,
339 : std::string_view name)
340 : {
341 : // If the user already built a system with this name, we'll
342 : // trust them and we'll use it. That way they can pre-add
343 : // non-standard derived system classes, and if their restart file
344 : // has some non-standard sys_type we won't throw an error.
345 1339 : if (_systems.count(name))
346 : {
347 145 : return this->get_system(name);
348 : }
349 : // Build a basic System
350 1174 : else if (sys_type == "Basic")
351 701 : this->add_system<System> (name);
352 :
353 : // Build a Newmark system
354 493 : else if (sys_type == "Newmark")
355 0 : this->add_system<NewmarkSystem> (name);
356 :
357 : // Build an Explicit system
358 491 : else if ((sys_type == "Explicit"))
359 71 : this->add_system<ExplicitSystem> (name);
360 :
361 : // Build an Implicit system
362 434 : else if ((sys_type == "Implicit") ||
363 434 : (sys_type == "Steady" ))
364 0 : this->add_system<ImplicitSystem> (name);
365 :
366 : // build a transient implicit linear system
367 1230 : else if ((sys_type == "Transient") ||
368 434 : (sys_type == "TransientImplicit") ||
369 434 : (sys_type == "TransientLinearImplicit"))
370 142 : this->add_system<TransientLinearImplicitSystem> (name);
371 :
372 : // build a transient implicit nonlinear system
373 280 : else if (sys_type == "TransientNonlinearImplicit")
374 0 : this->add_system<TransientNonlinearImplicitSystem> (name);
375 :
376 : // build a transient explicit system
377 280 : else if (sys_type == "TransientExplicit")
378 0 : this->add_system<TransientExplicitSystem> (name);
379 :
380 : // build a linear implicit system
381 280 : else if (sys_type == "LinearImplicit")
382 0 : this->add_system<LinearImplicitSystem> (name);
383 :
384 : // build a nonlinear implicit system
385 272 : else if (sys_type == "NonlinearImplicit")
386 280 : this->add_system<NonlinearImplicitSystem> (name);
387 :
388 : // build a Reduced Basis Construction system
389 0 : else if (sys_type == "RBConstruction")
390 0 : this->add_system<RBConstruction> (name);
391 :
392 : // build a transient Reduced Basis Construction system
393 0 : else if (sys_type == "TransientRBConstruction")
394 0 : this->add_system<TransientRBConstruction> (name);
395 :
396 : #ifdef LIBMESH_HAVE_SLEPC
397 : // build an eigen system
398 0 : else if (sys_type == "Eigen")
399 0 : this->add_system<EigenSystem> (name);
400 0 : else if (sys_type == "TransientEigenSystem")
401 0 : this->add_system<TransientEigenSystem> (name);
402 : #endif
403 :
404 : #if defined(LIBMESH_USE_COMPLEX_NUMBERS)
405 : // build a frequency system
406 0 : else if (sys_type == "Frequency")
407 0 : this->add_system<FrequencySystem> (name);
408 : #endif
409 :
410 : else
411 0 : libmesh_error_msg("ERROR: Unknown system type: " << sys_type);
412 :
413 : // Return a reference to the new system
414 : //return (*this)(name);
415 1194 : return this->get_system(name);
416 : }
417 :
418 :
419 :
420 0 : void EquationSystems::solve ()
421 : {
422 0 : libmesh_assert (this->n_systems());
423 :
424 0 : for (auto i : make_range(this->n_systems()))
425 0 : this->get_system(i).solve();
426 0 : }
427 :
428 :
429 :
430 0 : void EquationSystems::sensitivity_solve (const ParameterVector & parameters_in)
431 : {
432 0 : libmesh_assert (this->n_systems());
433 :
434 0 : for (auto i : make_range(this->n_systems()))
435 0 : this->get_system(i).sensitivity_solve(parameters_in);
436 0 : }
437 :
438 :
439 :
440 0 : void EquationSystems::adjoint_solve (const QoISet & qoi_indices)
441 : {
442 0 : libmesh_assert (this->n_systems());
443 :
444 0 : for (unsigned int i=this->n_systems(); i != 0; --i)
445 0 : this->get_system(i-1).adjoint_solve(qoi_indices);
446 0 : }
447 :
448 :
449 :
450 85751 : void EquationSystems::build_variable_names (std::vector<std::string> & var_names,
451 : const FEType * type,
452 : const std::set<std::string> * system_names) const
453 : {
454 : // start indexing at end of possibly non-empty vector of variable names to avoid overwriting them
455 88463 : unsigned int var_num = var_names.size();
456 :
457 : // We'll want to double-check that we don't have any naming
458 : // conflicts; this API causes problems down the line if so.
459 5424 : std::unordered_multiset<std::string> seen_names;
460 :
461 : // Need to size var_names by scalar variables plus all the
462 : // vector components for all the vector variables
463 : //Could this be replaced by a/some convenience methods?[PB]
464 : {
465 2712 : unsigned int n_scalar_vars = 0;
466 2712 : unsigned int n_vector_vars = 0;
467 :
468 174316 : for (const auto & [sys_name, sys_ptr] : _systems)
469 : {
470 : // Check current system is listed in system_names, and skip pos if not
471 5648 : bool use_current_system = (system_names == nullptr);
472 88565 : if (!use_current_system)
473 846 : use_current_system = system_names->count(sys_name);
474 88565 : if (!use_current_system || sys_ptr->hide_output())
475 : {
476 1552 : for (auto vn : make_range(sys_ptr->n_vars()))
477 776 : seen_names.insert(sys_ptr->variable_name(vn));
478 754 : continue;
479 732 : }
480 :
481 208646 : for (auto vn : make_range(sys_ptr->n_vars()))
482 : {
483 120857 : seen_names.insert(sys_ptr->variable_name(vn));
484 120857 : if (FEInterface::field_type(sys_ptr->variable_type(vn)) == TYPE_VECTOR)
485 6938 : n_vector_vars++;
486 : else
487 113919 : n_scalar_vars++;
488 : }
489 : }
490 :
491 : // Here, we're assuming the number of vector components is the same
492 : // as the mesh spatial dimension.
493 85751 : unsigned int dim = this->get_mesh().spatial_dimension();
494 85751 : unsigned int nv = n_scalar_vars + dim*n_vector_vars;
495 :
496 : // We'd better not have more than dim*this->n_vars() (all vector variables)
497 : // Treat the NodeElem-only mesh case as dim=1
498 2712 : libmesh_assert_less_equal ( nv, (dim > 0 ? dim : 1)*this->n_vars() );
499 :
500 : // 'nv' represents the max possible number of output variables, so allocate enough memory for
501 : // all variables in the system to be populated here. When this is called more than once on a
502 : // single 'var_names' vector, different filters should be used such that duplicates don't occur.
503 85751 : var_names.resize( nv );
504 : }
505 :
506 174245 : for (const auto & [sys_name, sys_ptr] : _systems)
507 : {
508 : // Check current system is listed in system_names, and skip pos if not
509 5648 : bool use_current_system = (system_names == nullptr);
510 88565 : if (!use_current_system)
511 846 : use_current_system = system_names->count(sys_name);
512 88565 : if (!use_current_system || sys_ptr->hide_output())
513 754 : continue;
514 :
515 208575 : for (auto vn : make_range(sys_ptr->n_vars()))
516 : {
517 120857 : const std::string & var_name = sys_ptr->variable_name(vn);
518 120857 : const FEType & fe_type = sys_ptr->variable_type(vn);
519 :
520 120857 : unsigned int n_vec_dim = FEInterface::n_vec_dim( sys_ptr->get_mesh(), fe_type);
521 :
522 : // Filter on the type if requested
523 120857 : if (type == nullptr || (type && *type == fe_type))
524 : {
525 120504 : if (FEInterface::field_type(fe_type) == TYPE_VECTOR)
526 : {
527 6868 : switch(n_vec_dim)
528 : {
529 0 : case 0:
530 : case 1:
531 0 : var_names[var_num++] = var_name;
532 0 : libmesh_error_msg_if(seen_names.count(var_name) > 1,
533 : "Duplicate variable name "+var_name);
534 0 : break;
535 5732 : case 2:
536 5732 : var_names[var_num++] = var_name+"_x";
537 5732 : var_names[var_num++] = var_name+"_y";
538 11509 : libmesh_error_msg_if(seen_names.count(var_name+"_x"),
539 : "Duplicate variable name "+var_name+"_x");
540 11162 : libmesh_error_msg_if(seen_names.count(var_name+"_y"),
541 : "Duplicate variable name "+var_name+"_y");
542 160 : break;
543 1136 : case 3:
544 1136 : var_names[var_num++] = var_name+"_x";
545 1136 : var_names[var_num++] = var_name+"_y";
546 1136 : var_names[var_num++] = var_name+"_z";
547 2240 : libmesh_error_msg_if(seen_names.count(var_name+"_x"),
548 : "Duplicate variable name "+var_name+"_x");
549 2240 : libmesh_error_msg_if(seen_names.count(var_name+"_y"),
550 : "Duplicate variable name "+var_name+"_y");
551 2307 : libmesh_error_msg_if(seen_names.count(var_name+"_z"),
552 : "Duplicate variable name "+var_name+"_z");
553 32 : break;
554 0 : default:
555 0 : libmesh_error_msg("Invalid dim in build_variable_names");
556 : }
557 : }
558 : else
559 113636 : var_names[var_num++] = var_name;
560 : }
561 : }
562 : }
563 : // Now resize again in case we filtered any names
564 85680 : var_names.resize(var_num);
565 85680 : }
566 :
567 :
568 :
569 0 : void EquationSystems::build_solution_vector (std::vector<Number> &,
570 : std::string_view,
571 : std::string_view) const
572 : {
573 : // TODO:[BSK] re-implement this from the method below
574 0 : libmesh_not_implemented();
575 : }
576 :
577 :
578 :
579 :
580 : std::unique_ptr<NumericVector<Number>>
581 79114 : EquationSystems::build_parallel_solution_vector(const std::set<std::string> * system_names,
582 : bool add_sides) const
583 : {
584 4900 : LOG_SCOPE("build_parallel_solution_vector()", "EquationSystems");
585 :
586 : // This function must be run on all processors at once
587 2450 : parallel_object_only();
588 :
589 79114 : const unsigned int dim = _mesh.spatial_dimension();
590 79114 : const dof_id_type max_nn = _mesh.max_node_id();
591 :
592 : // allocate vector storage to hold
593 : // (max_node_id)*(number_of_variables) entries.
594 : //
595 : // If node renumbering is disabled and adaptive coarsening has
596 : // created gaps between node numbers, then this vector will be
597 : // sparse.
598 : //
599 : // We have to differentiate between between scalar and vector
600 : // variables. We intercept vector variables and treat each
601 : // component as a scalar variable (consistently with build_solution_names).
602 :
603 2450 : unsigned int nv = 0;
604 :
605 : //Could this be replaced by a/some convenience methods?[PB]
606 : {
607 2450 : unsigned int n_scalar_vars = 0;
608 2450 : unsigned int n_vector_vars = 0;
609 160900 : for (const auto & [sys_name, sys_ptr] : _systems)
610 : {
611 : // Check current system is listed in system_names, and skip pos if not
612 5116 : bool use_current_system = (system_names == nullptr);
613 81786 : if (!use_current_system)
614 352 : use_current_system = system_names->count(sys_name);
615 81786 : if (!use_current_system || sys_ptr->hide_output())
616 342 : continue;
617 :
618 194516 : for (auto vn : make_range(sys_ptr->n_vars()))
619 : {
620 113082 : if (FEInterface::field_type(sys_ptr->variable_type(vn)) == TYPE_VECTOR)
621 6444 : n_vector_vars++;
622 : else
623 106638 : n_scalar_vars++;
624 : }
625 : }
626 : // Here, we're assuming the number of vector components is the same
627 : // as the mesh spatial dimension.
628 79114 : nv = n_scalar_vars + dim*n_vector_vars;
629 : }
630 :
631 : // Get the number of nodes to store locally.
632 : dof_id_type n_local_nodes = cast_int<dof_id_type>
633 155778 : (std::distance(_mesh.local_nodes_begin(),
634 158228 : _mesh.local_nodes_end()));
635 :
636 : // If node renumbering has been disabled, nodes may not be numbered
637 : // contiguously, and the number of nodes might not match the
638 : // max_node_id. In this case we just do our best.
639 79114 : dof_id_type n_total_nodes = n_local_nodes;
640 79114 : _mesh.comm().sum(n_total_nodes);
641 :
642 79114 : const processor_id_type n_proc = _mesh.comm().size();
643 4900 : const processor_id_type my_pid = _mesh.comm().rank();
644 79114 : const dof_id_type n_gaps = max_nn - n_total_nodes;
645 79114 : const dof_id_type gaps_per_processor = n_gaps / n_proc;
646 79114 : const dof_id_type remainder_gaps = n_gaps % n_proc;
647 :
648 84014 : n_local_nodes = n_local_nodes + // Actual nodes
649 79114 : gaps_per_processor + // Our even share of gaps
650 79114 : (my_pid < remainder_gaps); // Leftovers
651 :
652 : // If we've been asked to build added sides' data, we need space to
653 : // add it. Keep track of how much space.
654 79114 : dof_id_type local_added_side_nodes = 0,
655 2450 : added_side_nodes = 0;
656 :
657 : // others_added_side_nodes[p]: local_added_side_nodes on rank p
658 4900 : std::vector<dof_id_type> others_added_side_nodes;
659 :
660 : // A map of (element_id, side, side_node) pairs to the corresponding
661 : // added side node index.
662 : std::map<std::tuple<dof_id_type, unsigned short, unsigned short>,
663 4900 : dof_id_type> discontinuous_node_indices;
664 :
665 : // If we don't have any added side nodes, we'll have no offsets from
666 : // them, and we won't care about which offsets apply to which node
667 : // ids either.
668 :
669 : // Number of true nodes on processors [0,p]
670 4900 : std::vector<dof_id_type> true_node_offsets;
671 : // Number of added (fake) nodes on processors [0,p)
672 4900 : std::vector<dof_id_type> added_node_offsets;
673 :
674 : auto node_id_to_vec_id =
675 69460109 : [&true_node_offsets, &added_node_offsets]
676 84448817 : (const dof_id_type node_id)
677 : {
678 84438557 : if (true_node_offsets.empty())
679 76926761 : return node_id; // O(1) in the common !add_sides case
680 :
681 : // Find the processor id that has node_id in the parallel vec
682 20520 : const auto lb = std::upper_bound(true_node_offsets.begin(),
683 2052 : true_node_offsets.end(), node_id);
684 2052 : libmesh_assert(lb != true_node_offsets.end());
685 2052 : const processor_id_type p = lb - true_node_offsets.begin();
686 :
687 26676 : return node_id + added_node_offsets[p];
688 79114 : };
689 :
690 79114 : if (add_sides)
691 : {
692 1207 : true_node_offsets.resize(n_proc);
693 1207 : added_node_offsets.resize(n_proc);
694 :
695 : // One loop to count everyone's new side nodes
696 10940 : for (const auto & elem : _mesh.active_element_ptr_range())
697 : {
698 25064 : for (auto s : elem->side_index_range())
699 : {
700 20400 : if (redundant_added_side(*elem,s))
701 5460 : continue;
702 :
703 : const std::vector<unsigned int> side_nodes =
704 15548 : elem->nodes_on_side(s);
705 :
706 15548 : if (elem->processor_id() == this->processor_id())
707 3952 : local_added_side_nodes += side_nodes.size();
708 : }
709 1139 : }
710 :
711 1207 : others_added_side_nodes.resize(n_proc);
712 1207 : _mesh.comm().allgather(local_added_side_nodes,
713 : others_added_side_nodes);
714 :
715 1207 : added_side_nodes = std::accumulate(others_added_side_nodes.begin(),
716 : others_added_side_nodes.end(), 0,
717 : std::plus<>());
718 :
719 1207 : _mesh.comm().allgather(n_local_nodes, true_node_offsets);
720 11781 : for (auto p : make_range(n_proc-1))
721 10642 : true_node_offsets[p+1] += true_node_offsets[p];
722 34 : libmesh_assert_equal_to(true_node_offsets[n_proc-1], _mesh.max_node_id());
723 :
724 : // For nodes that exist in the mesh, we just need an offset to
725 : // tell where to put their solutions.
726 1207 : added_node_offsets[0] = 0;
727 11781 : for (auto p : make_range(n_proc-1))
728 10574 : added_node_offsets[p+1] =
729 10642 : added_node_offsets[p] + others_added_side_nodes[p];
730 :
731 : // For added side nodes, we need to fill a map. Start after all
732 : // the true node for our pid plus all the side nodes for
733 : // previous pids
734 1241 : dof_id_type node_counter = true_node_offsets[my_pid];
735 6494 : for (auto p : make_range(my_pid))
736 5304 : node_counter += others_added_side_nodes[p];
737 :
738 : // One loop to figure out whose added side nodes get which index
739 4492 : for (const auto & elem : _mesh.active_local_element_ptr_range())
740 : {
741 6240 : for (auto s : elem->side_index_range())
742 : {
743 4992 : if (redundant_added_side(*elem,s))
744 1344 : continue;
745 :
746 : const std::vector<unsigned int> side_nodes =
747 3952 : elem->nodes_on_side(s);
748 :
749 27264 : for (auto n : index_range(side_nodes))
750 : discontinuous_node_indices
751 25584 : [std::make_tuple(elem->id(),s,n)] = node_counter++;
752 : }
753 1139 : }
754 : }
755 :
756 : const dof_id_type
757 79114 : n_global_vals = (max_nn + added_side_nodes) * nv,
758 79114 : n_local_vals = (n_local_nodes + local_added_side_nodes) * nv;
759 :
760 : // Create a NumericVector to hold the parallel solution
761 79114 : std::unique_ptr<NumericVector<Number>> parallel_soln_ptr = NumericVector<Number>::build(_communicator);
762 2450 : NumericVector<Number> & parallel_soln = *parallel_soln_ptr;
763 79114 : parallel_soln.init(n_global_vals, n_local_vals, false, PARALLEL);
764 :
765 : // Create a NumericVector to hold the "repeat_count" for each node - this is essentially
766 : // the number of elements contributing to that node's value
767 81564 : std::unique_ptr<NumericVector<Number>> repeat_count_ptr = NumericVector<Number>::build(_communicator);
768 2450 : NumericVector<Number> & repeat_count = *repeat_count_ptr;
769 79114 : repeat_count.init(n_global_vals, n_local_vals, false, PARALLEL);
770 :
771 79114 : repeat_count.close();
772 :
773 2450 : unsigned int var_num=0;
774 :
775 : // For each system in this EquationSystems object,
776 : // update the global solution and if we are on processor 0,
777 : // loop over the elements and build the nodal solution
778 : // from the element solution. Then insert this nodal solution
779 : // into the vector passed to build_solution_vector.
780 160900 : for (const auto & [sys_name, sys_ptr] : _systems)
781 : {
782 : // Check current system is listed in system_names, and skip pos if not
783 5116 : bool use_current_system = (system_names == nullptr);
784 81786 : if (!use_current_system)
785 352 : use_current_system = system_names->count(sys_name);
786 81786 : if (!use_current_system || sys_ptr->hide_output())
787 352 : continue;
788 :
789 2548 : const System & system = *sys_ptr;
790 81434 : const unsigned int nv_sys = system.n_vars();
791 5096 : const unsigned int sys_num = system.number();
792 :
793 : //Could this be replaced by a/some convenience methods?[PB]
794 2548 : unsigned int n_scalar_vars = 0;
795 2548 : unsigned int n_vector_vars = 0;
796 194516 : for (auto vn : make_range(sys_ptr->n_vars()))
797 : {
798 113082 : if (FEInterface::field_type(sys_ptr->variable_type(vn)) == TYPE_VECTOR)
799 6444 : n_vector_vars++;
800 : else
801 106638 : n_scalar_vars++;
802 : }
803 :
804 : // Here, we're assuming the number of vector components is the same
805 : // as the mesh spatial dimension.
806 81434 : unsigned int nv_sys_split = n_scalar_vars + dim*n_vector_vars;
807 :
808 : // Update the current_local_solution
809 : {
810 2548 : System & non_const_sys = const_cast<System &>(system);
811 : // We used to simply call non_const_sys.solution->close()
812 : // here, but that is not allowed when the solution vector is
813 : // locked read-only, for example when printing the solution
814 : // during the middle of a solve... So try to be a bit
815 : // more careful about calling close() unnecessarily.
816 2548 : libmesh_assert(this->comm().verify(non_const_sys.solution->closed()));
817 81434 : if (!non_const_sys.solution->closed())
818 0 : non_const_sys.solution->close();
819 81434 : non_const_sys.update();
820 : }
821 :
822 2548 : NumericVector<Number> & sys_soln(*system.current_local_solution);
823 :
824 2548 : const DofMap & dof_map = system.get_dof_map();
825 :
826 5096 : std::vector<Number> elem_soln; // The finite element solution
827 5096 : std::vector<Number> nodal_soln; // The FE solution interpolated to the nodes
828 2548 : std::vector<dof_id_type> dof_indices; // The DOF indices for the finite element
829 :
830 2548 : unsigned var_inc = 0;
831 194516 : for (unsigned int var=0; var<nv_sys; var++)
832 : {
833 113082 : const FEType & fe_type = system.variable_type(var);
834 113082 : const Variable & var_description = system.variable(var);
835 113082 : unsigned int n_vec_dim = FEInterface::n_vec_dim( sys_ptr->get_mesh(), fe_type );
836 113082 : const auto vg = dof_map.var_group_from_var_number(var);
837 113082 : const bool add_p_level = dof_map.should_p_refine(vg);
838 :
839 28816818 : for (const auto & elem : _mesh.active_local_element_ptr_range())
840 : {
841 15726480 : if (var_description.active_on_subdomain(elem->subdomain_id()))
842 : {
843 15720948 : dof_map.dof_indices (elem, dof_indices, var);
844 15720948 : sys_soln.get(dof_indices, elem_soln);
845 :
846 15720948 : FEInterface::nodal_soln (elem->dim(),
847 : fe_type,
848 : elem,
849 : elem_soln,
850 : nodal_soln,
851 : add_p_level,
852 : n_vec_dim);
853 :
854 : // infinite elements should be skipped...
855 3435990 : if (!elem->infinite())
856 : {
857 1428923 : libmesh_assert_equal_to (nodal_soln.size(), n_vec_dim*elem->n_nodes());
858 :
859 101510248 : for (auto n : elem->node_index_range())
860 : {
861 84360377 : const Node & node = elem->node_ref(n);
862 :
863 : const dof_id_type node_idx =
864 84360377 : nv * node_id_to_vec_id(node.id());
865 :
866 184873978 : for (unsigned int d=0; d < n_vec_dim; d++)
867 : {
868 : // For vector-valued elements, all components are in nodal_soln. For each
869 : // node, the components are stored in order, i.e. node_0 -> s0_x, s0_y, s0_z
870 109342615 : parallel_soln.add(node_idx + (var_inc+d + var_num), nodal_soln[n_vec_dim*n+d]);
871 :
872 : // Increment the repeat count for this position
873 100513601 : repeat_count.add(node_idx + (var_inc+d + var_num), 1);
874 : }
875 : }
876 :
877 15720948 : if (add_sides)
878 : {
879 9020 : for (auto s : elem->side_index_range())
880 : {
881 7200 : if (redundant_added_side(*elem,s))
882 1782 : continue;
883 :
884 : // Compute the FE solution at all the
885 : // side nodes
886 : FEInterface::side_nodal_soln
887 5256 : (fe_type, elem, s, elem_soln,
888 : nodal_soln, add_p_level, n_vec_dim);
889 :
890 : #ifdef DEBUG
891 : const std::vector<unsigned int> side_nodes =
892 876 : elem->nodes_on_side(s);
893 :
894 438 : libmesh_assert_equal_to
895 : (nodal_soln.size(),
896 : side_nodes.size());
897 : #endif
898 :
899 38736 : for (auto n : index_range(nodal_soln))
900 : {
901 : // Retrieve index into global solution vector.
902 : std::size_t node_index =
903 36270 : nv * libmesh_map_find(discontinuous_node_indices,
904 : std::make_tuple(elem->id(), s, n));
905 :
906 66960 : for (unsigned int d=0; d < n_vec_dim; d++)
907 : {
908 36270 : parallel_soln.add(node_index + (var_inc+d + var_num), nodal_soln[n_vec_dim*n+d]);
909 33480 : repeat_count.add(node_index + (var_inc+d + var_num), 1);
910 : }
911 : }
912 : }
913 : }
914 : }
915 : }
916 : else // If this variable doesn't exist on this subdomain we have to still increment repeat_count so that we won't divide by 0 later:
917 100536 : for (auto n : elem->node_index_range())
918 : {
919 95004 : const Node & node = elem->node_ref(n);
920 : // Only do this if this variable has NO DoFs at
921 : // this node... it might have some from an
922 : // adjoining element...
923 95004 : if (!node.n_dofs(sys_num, var))
924 : {
925 : const dof_id_type node_idx =
926 78180 : nv * node_id_to_vec_id(node.id());
927 :
928 156360 : for (unsigned int d=0; d < n_vec_dim; d++)
929 78180 : repeat_count.add(node_idx + (var_inc+d + var_num), 1);
930 : }
931 : }
932 :
933 106006 : } // end loop over elements
934 113082 : var_inc += n_vec_dim;
935 : } // end loop on variables in this system
936 :
937 81434 : var_num += nv_sys_split;
938 : } // end loop over systems
939 :
940 : // Sum the nodal solution values and repeat counts.
941 79114 : parallel_soln.close();
942 79114 : repeat_count.close();
943 :
944 : // If there were gaps in the node numbering, there will be
945 : // corresponding zeros in the parallel_soln and repeat_count
946 : // vectors. We need to set those repeat_count entries to 1
947 : // in order to avoid dividing by zero.
948 79114 : if (n_gaps)
949 : {
950 0 : for (numeric_index_type i=repeat_count.first_local_index();
951 0 : i<repeat_count.last_local_index(); ++i)
952 : {
953 : // repeat_count entries are integral values but let's avoid a
954 : // direct floating point comparison with 0 just in case some
955 : // roundoff noise crept in during vector assembly?
956 0 : if (std::abs(repeat_count(i)) < TOLERANCE)
957 0 : repeat_count.set(i, 1.);
958 : }
959 :
960 : // Make sure the repeat_count vector is up-to-date on all
961 : // processors.
962 0 : repeat_count.close();
963 : }
964 :
965 : // Divide to get the average value at the nodes
966 79114 : parallel_soln /= repeat_count;
967 :
968 81564 : return parallel_soln_ptr;
969 74214 : }
970 :
971 :
972 :
973 79114 : void EquationSystems::build_solution_vector (std::vector<Number> & soln,
974 : const std::set<std::string> * system_names,
975 : bool add_sides) const
976 : {
977 4900 : LOG_SCOPE("build_solution_vector()", "EquationSystems");
978 :
979 : // Call the parallel implementation
980 : std::unique_ptr<NumericVector<Number>> parallel_soln =
981 81564 : this->build_parallel_solution_vector(system_names, add_sides);
982 :
983 : // Localize the NumericVector into the provided std::vector.
984 79114 : parallel_soln->localize_to_one(soln);
985 79114 : }
986 :
987 :
988 :
989 8017 : void EquationSystems::get_vars_active_subdomains(const std::vector<std::string> & names,
990 : std::vector<std::set<subdomain_id_type>> & vars_active_subdomains) const
991 : {
992 8017 : vars_active_subdomains.clear();
993 8243 : vars_active_subdomains.resize(names.size());
994 :
995 16034 : for (const auto & pr : _systems)
996 : {
997 226 : const auto & sys_ptr = pr.second;
998 16034 : for (auto vn : make_range(sys_ptr->n_vars()))
999 : {
1000 8017 : const std::string & var_name = sys_ptr->variable_name(vn);
1001 :
1002 8017 : auto names_it = std::find(names.begin(), names.end(), var_name);
1003 8243 : if(names_it != names.end())
1004 : {
1005 7667 : const Variable & variable = sys_ptr->variable(vn);
1006 216 : const std::set<subdomain_id_type> & active_subdomains = variable.active_subdomains();
1007 7883 : vars_active_subdomains[std::distance(names.begin(), names_it)] = active_subdomains;
1008 : }
1009 : }
1010 : }
1011 8017 : }
1012 :
1013 :
1014 :
1015 : void
1016 352 : EquationSystems::build_elemental_solution_vector (std::vector<Number> & soln,
1017 : std::vector<std::string> & names) const
1018 : {
1019 : // Call the parallel version of this function
1020 : std::unique_ptr<NumericVector<Number>> parallel_soln =
1021 362 : this->build_parallel_elemental_solution_vector(names);
1022 :
1023 : // Localize into 'soln', provided that parallel_soln is not empty.
1024 : // Note: parallel_soln will be empty in the event that none of the
1025 : // input names were CONSTANT, MONOMIAL nor components of CONSTANT,
1026 : // MONOMIAL_VEC variables, or there were simply none of these in
1027 : // the EquationSystems object.
1028 10 : soln.clear();
1029 352 : if (parallel_soln)
1030 352 : parallel_soln->localize_to_one(soln);
1031 352 : }
1032 :
1033 : std::vector<std::pair<unsigned int, unsigned int>>
1034 8231 : EquationSystems::find_variable_numbers
1035 : (std::vector<std::string> & names, const FEType * type, const std::vector<FEType> * types) const
1036 : {
1037 : // This function must be run on all processors at once
1038 232 : parallel_object_only();
1039 :
1040 232 : libmesh_assert (this->n_systems());
1041 :
1042 : // Resolve class of type input and assert that at least one of them is null
1043 232 : libmesh_assert_msg(!type || !types,
1044 : "Input 'type', 'types', or neither in find_variable_numbers, but not both.");
1045 :
1046 464 : std::vector<FEType> type_filter;
1047 8231 : if (type)
1048 0 : type_filter.push_back(*type);
1049 8231 : else if (types)
1050 7947 : type_filter = *types;
1051 :
1052 : // Store a copy of the valid variable names, if any. The names vector will be repopulated with any
1053 : // valid names (or all if 'is_names_empty') in the system that passes through the type filter. If
1054 : // the variable is a vector, its name will be decomposed into its separate components in
1055 : // accordance with build_variable_names().
1056 8695 : std::vector<std::string> name_filter = names;
1057 232 : bool is_names_empty = name_filter.empty();
1058 232 : names.clear();
1059 :
1060 : // initialize convenience variables
1061 232 : FEType var_type;
1062 464 : std::string name;
1063 :
1064 33156 : const std::vector<std::string> component_suffix = {"_x", "_y", "_z"};
1065 8231 : unsigned int dim = _mesh.spatial_dimension();
1066 8231 : libmesh_error_msg_if(dim > 3, "Invalid dim in find_variable_numbers");
1067 :
1068 : // Now filter through the variables in each system and store the system index and their index
1069 : // within that system. This way, we know where to find their data even after we sort them.
1070 464 : std::vector<std::pair<unsigned int, unsigned int>> var_nums;
1071 :
1072 16462 : for (const auto & pr : _systems)
1073 : {
1074 232 : const System & system = *(pr.second);
1075 :
1076 16604 : for (auto var : make_range(system.n_vars()))
1077 : {
1078 : // apply the type filter
1079 8373 : var_type = system.variable_type(var);
1080 8821 : if (type_filter.size() &&
1081 8183 : std::find(type_filter.begin(), type_filter.end(), var_type) == type_filter.end())
1082 0 : continue;
1083 :
1084 : // apply the name filter (note that all variables pass if it is empty)
1085 8373 : if (FEInterface::field_type(var_type) == TYPE_VECTOR)
1086 : {
1087 28 : std::vector<std::string> component_names;
1088 1476 : for (unsigned int comp = 0; comp < dim; ++comp)
1089 : {
1090 1012 : name = system.variable_name(var) + component_suffix[comp];
1091 1008 : if (is_names_empty ||
1092 452 : (std::find(name_filter.begin(), name_filter.end(), name) != name_filter.end()))
1093 984 : component_names.push_back(name);
1094 : }
1095 :
1096 492 : if (! component_names.empty())
1097 492 : names.insert(names.end(), component_names.begin(), component_names.end());
1098 : else
1099 0 : continue;
1100 464 : }
1101 : else /*scalar-valued variable*/
1102 : {
1103 7881 : name = system.variable_name(var);
1104 7897 : if (is_names_empty ||
1105 506 : (std::find(name_filter.begin(), name_filter.end(), name) != name_filter.end()))
1106 7881 : names.push_back(name);
1107 : else
1108 0 : continue;
1109 : }
1110 :
1111 : // if the variable made it through both filters get its system indices
1112 8373 : var_nums.emplace_back(system.number(), var);
1113 : }
1114 : }
1115 :
1116 : // Sort the var_nums vector pairs alphabetically based on the variable name
1117 8695 : std::vector<unsigned int> sort_index(var_nums.size());
1118 232 : std::iota(sort_index.begin(), sort_index.end(), 0);
1119 8231 : std::sort(sort_index.begin(), sort_index.end(),
1120 284 : [&](const unsigned int & lhs, const unsigned int & rhs)
1121 292 : {return this->get_system(var_nums[lhs].first).variable_name(var_nums[lhs].second) <
1122 300 : this->get_system(var_nums[rhs].first).variable_name(var_nums[rhs].second);});
1123 :
1124 8463 : std::vector<std::pair<unsigned int, unsigned int>> var_nums_sorted(var_nums.size());
1125 16604 : for (auto i : index_range(var_nums_sorted))
1126 : {
1127 8845 : var_nums_sorted[i].first = var_nums[sort_index[i]].first;
1128 8609 : var_nums_sorted[i].second = var_nums[sort_index[i]].second;
1129 : }
1130 :
1131 : // Also sort the names vector
1132 8231 : std::sort(names.begin(), names.end());
1133 :
1134 : // Return the sorted vector pairs
1135 8463 : return var_nums_sorted;
1136 31068 : }
1137 :
1138 :
1139 : std::unique_ptr<NumericVector<Number>>
1140 352 : EquationSystems::build_parallel_elemental_solution_vector (std::vector<std::string> & names) const
1141 : {
1142 : // Filter any names that aren't elemental variables and get the system indices for those that are.
1143 : // Note that it's probably fine if the names vector is empty since we'll still at least filter
1144 : // out all non-monomials. If there are no monomials, then nothing is output here.
1145 362 : std::vector<FEType> type = {FEType(CONSTANT, MONOMIAL), FEType(CONSTANT, MONOMIAL_VEC)};
1146 : std::vector<std::pair<unsigned int, unsigned int>> var_nums =
1147 362 : this->find_variable_numbers(names, /*type=*/nullptr, &type);
1148 :
1149 20 : const std::size_t nv = names.size(); /*total number of vars including vector components*/
1150 352 : const dof_id_type ne = _mesh.n_elem();
1151 10 : libmesh_assert_equal_to (ne, _mesh.max_elem_id());
1152 :
1153 : // If there are no variables to write out don't do anything...
1154 352 : if (!nv)
1155 0 : return std::unique_ptr<NumericVector<Number>>(nullptr);
1156 :
1157 : // We can handle the case where there are nullptrs in the Elem vector
1158 : // by just having extra zeros in the solution vector.
1159 352 : numeric_index_type parallel_soln_global_size = ne*nv;
1160 :
1161 352 : numeric_index_type div = parallel_soln_global_size / this->n_processors();
1162 352 : numeric_index_type mod = parallel_soln_global_size % this->n_processors();
1163 :
1164 : // Initialize all processors to the average size.
1165 10 : numeric_index_type parallel_soln_local_size = div;
1166 :
1167 : // The first "mod" processors get an extra entry.
1168 352 : if (this->processor_id() < mod)
1169 136 : parallel_soln_local_size = div+1;
1170 :
1171 : // Create a NumericVector to hold the parallel solution
1172 362 : std::unique_ptr<NumericVector<Number>> parallel_soln_ptr = NumericVector<Number>::build(_communicator);
1173 10 : NumericVector<Number> & parallel_soln = *parallel_soln_ptr;
1174 352 : parallel_soln.init(parallel_soln_global_size,
1175 : parallel_soln_local_size,
1176 : /*fast=*/false,
1177 20 : /*ParallelType=*/PARALLEL);
1178 :
1179 10 : unsigned int sys_ctr = 0;
1180 10 : unsigned int var_ctr = 0;
1181 704 : for (auto i : index_range(var_nums))
1182 : {
1183 362 : std::pair<unsigned int, unsigned int> var_num = var_nums[i];
1184 10 : const System & system = this->get_system(var_num.first);
1185 :
1186 : // Update the current_local_solution if necessary
1187 352 : if (sys_ctr != var_num.first)
1188 : {
1189 0 : System & non_const_sys = const_cast<System &>(system);
1190 : // We used to simply call non_const_sys.solution->close()
1191 : // here, but that is not allowed when the solution vector is
1192 : // locked read-only, for example when printing the solution
1193 : // during during the middle of a solve... So try to be a bit
1194 : // more careful about calling close() unnecessarily.
1195 0 : libmesh_assert(this->comm().verify(non_const_sys.solution->closed()));
1196 0 : if (!non_const_sys.solution->closed())
1197 0 : non_const_sys.solution->close();
1198 0 : non_const_sys.update();
1199 0 : sys_ctr = var_num.first;
1200 : }
1201 :
1202 10 : NumericVector<Number> & sys_soln(*system.current_local_solution);
1203 :
1204 : // The DOF indices for the finite element
1205 10 : std::vector<dof_id_type> dof_indices;
1206 :
1207 10 : const unsigned int var = var_num.second;
1208 :
1209 352 : const Variable & variable = system.variable(var);
1210 10 : const DofMap & dof_map = system.get_dof_map();
1211 :
1212 : // We need to check if the constant monomial is a scalar or a vector and set the number of
1213 : // components as the mesh spatial dimension for the latter as per es.find_variable_numbers().
1214 : // Even for the case where a variable is not active on any subdomain belonging to the
1215 : // processor, we still need to know this number to update 'var_ctr'.
1216 : const unsigned int n_comps =
1217 556 : (system.variable_type(var) == type[1]) ? _mesh.spatial_dimension() : 1;
1218 :
1219 : // Loop over all elements in the mesh and index all components of the variable if it's active
1220 5950 : for (const auto & elem : _mesh.active_local_element_ptr_range())
1221 2889 : if (variable.active_on_subdomain(elem->subdomain_id()))
1222 : {
1223 2889 : dof_map.dof_indices(elem, dof_indices, var);
1224 :
1225 : // The number of DOF components needs to be equal to the expected number so that we know
1226 : // where to store data to correctly correspond to variable names.
1227 261 : libmesh_assert_equal_to(dof_indices.size(), n_comps);
1228 :
1229 8451 : for (unsigned int comp = 0; comp < n_comps; comp++)
1230 6066 : parallel_soln.set(ne * (var_ctr + comp) + elem->id(), sys_soln(dof_indices[comp]));
1231 332 : }
1232 :
1233 352 : var_ctr += n_comps;
1234 : } // end loop over var_nums
1235 :
1236 : // NOTE: number of output names might not be equal to the number passed to this function. Any that
1237 : // aren't CONSTANT MONOMIALS or components of CONSTANT MONOMIAL_VECS have been filtered out (see
1238 : // EquationSystems::find_variable_numbers).
1239 : //
1240 : // But, if everything is accounted for properly, then names.size() == var_ctr
1241 10 : libmesh_assert_equal_to(names.size(), var_ctr);
1242 :
1243 352 : parallel_soln.close();
1244 10 : return parallel_soln_ptr;
1245 332 : }
1246 :
1247 :
1248 :
1249 : void
1250 5507 : EquationSystems::build_discontinuous_solution_vector
1251 : (std::vector<Number> & soln,
1252 : const std::set<std::string> * system_names,
1253 : const std::vector<std::string> * var_names,
1254 : bool vertices_only,
1255 : bool add_sides) const
1256 : {
1257 460 : LOG_SCOPE("build_discontinuous_solution_vector()", "EquationSystems");
1258 :
1259 230 : libmesh_assert (this->n_systems());
1260 :
1261 : // Get the number of variables (nv) by counting the number of variables
1262 : // in each system listed in system_names
1263 230 : unsigned int nv = 0;
1264 :
1265 11085 : for (const auto & [sys_name, sys_ptr] : _systems)
1266 : {
1267 : // Check current system is listed in system_names, and skip pos if not
1268 464 : bool use_current_system = (system_names == nullptr);
1269 5578 : if (!use_current_system)
1270 70 : use_current_system = system_names->count(sys_name);
1271 5578 : if (!use_current_system || sys_ptr->hide_output())
1272 0 : continue;
1273 :
1274 : // Loop over all variables in this System and check whether we
1275 : // are supposed to use each one.
1276 12292 : for (auto var_id : make_range(sys_ptr->n_vars()))
1277 : {
1278 528 : bool use_current_var = (var_names == nullptr);
1279 6714 : if (!use_current_var)
1280 72 : use_current_var = std::count(var_names->begin(),
1281 : var_names->end(),
1282 70 : sys_ptr->variable_name(var_id));
1283 :
1284 : // Only increment the total number of vars if we are
1285 : // supposed to use this one.
1286 6714 : if (use_current_var)
1287 6714 : nv++;
1288 : }
1289 : }
1290 :
1291 : // get the total "weight" - the number of nodal values to write for
1292 : // each variable.
1293 230 : unsigned int tw=0;
1294 408702 : for (const auto & elem : _mesh.active_element_ptr_range())
1295 : {
1296 223087 : tw += vertices_only ? elem->n_vertices() : elem->n_nodes();
1297 :
1298 223087 : if (add_sides)
1299 : {
1300 25064 : for (auto s : elem->side_index_range())
1301 : {
1302 20400 : if (redundant_added_side(*elem,s))
1303 5460 : continue;
1304 :
1305 : const std::vector<unsigned int> side_nodes =
1306 15548 : elem->nodes_on_side(s);
1307 :
1308 14940 : if (!vertices_only)
1309 15548 : tw += side_nodes.size();
1310 : else
1311 0 : for (auto n : index_range(side_nodes))
1312 0 : if (elem->is_vertex(side_nodes[n]))
1313 0 : ++tw;
1314 : }
1315 : }
1316 5047 : }
1317 :
1318 : // Only if we are on processor zero, allocate the storage
1319 : // to hold (number_of_nodes)*(number_of_variables) entries.
1320 5737 : if (_mesh.processor_id() == 0)
1321 986 : soln.resize(tw*nv);
1322 :
1323 460 : std::vector<Number> sys_soln;
1324 :
1325 : // Keep track of the variable "offset". This is used for indexing
1326 : // into the global solution vector.
1327 230 : unsigned int var_offset = 0;
1328 :
1329 : // For each system in this EquationSystems object,
1330 : // update the global solution and if we are on processor 0,
1331 : // loop over the elements and build the nodal solution
1332 : // from the element solution. Then insert this nodal solution
1333 : // into the vector passed to build_solution_vector.
1334 11085 : for (const auto & [sys_name, system] : _systems)
1335 : {
1336 : // Check current system is listed in system_names, and skip pos if not
1337 464 : bool use_current_system = (system_names == nullptr);
1338 5578 : if (!use_current_system)
1339 70 : use_current_system = system_names->count(sys_name);
1340 5578 : if (!use_current_system || system->hide_output())
1341 0 : continue;
1342 :
1343 5578 : const unsigned int nv_sys = system->n_vars();
1344 232 : const auto & dof_map = system->get_dof_map();
1345 :
1346 5578 : system->update_global_solution (sys_soln, 0);
1347 :
1348 : // Keep track of the number of vars actually written.
1349 232 : unsigned int n_vars_written_current_system = 0;
1350 :
1351 5810 : if (_mesh.processor_id() == 0)
1352 : {
1353 232 : std::vector<Number> soln_coeffs; // The finite element solution coeffs
1354 232 : std::vector<Number> nodal_soln; // The FE solution interpolated to the nodes
1355 232 : std::vector<dof_id_type> dof_indices; // The DOF indices for the finite element
1356 :
1357 : // For each variable, determine if we are supposed to
1358 : // write it, then loop over the active elements, compute
1359 : // the nodal_soln and store it to the "soln" vector. We
1360 : // store zeros for subdomain-restricted variables on
1361 : // elements where they are not active.
1362 2188 : for (unsigned int var=0; var<nv_sys; var++)
1363 : {
1364 264 : bool use_current_var = (var_names == nullptr);
1365 1190 : if (!use_current_var)
1366 12 : use_current_var = std::count(var_names->begin(),
1367 : var_names->end(),
1368 11 : system->variable_name(var));
1369 :
1370 : // If we aren't supposed to write this var, go to the
1371 : // next loop iteration.
1372 1190 : if (!use_current_var)
1373 0 : continue;
1374 :
1375 1190 : const FEType & fe_type = system->variable_type(var);
1376 1190 : const Variable & var_description = system->variable(var);
1377 1190 : const auto vg = dof_map.var_group_from_var_number(var);
1378 1190 : const bool add_p_level = dof_map.should_p_refine(vg);
1379 :
1380 132 : unsigned int nn=0;
1381 :
1382 231970 : for (auto & elem : _mesh.active_element_ptr_range())
1383 : {
1384 136185 : if (var_description.active_on_subdomain(elem->subdomain_id()))
1385 : {
1386 136185 : system->get_dof_map().dof_indices (elem, dof_indices, var);
1387 :
1388 157509 : soln_coeffs.resize(dof_indices.size());
1389 :
1390 977562 : for (auto i : index_range(dof_indices))
1391 1082113 : soln_coeffs[i] = sys_soln[dof_indices[i]];
1392 :
1393 : // Compute the FE solution at all the nodes, but
1394 : // only use the first n_vertices() entries if
1395 : // vertices_only == true.
1396 136185 : FEInterface::nodal_soln (elem->dim(),
1397 : fe_type,
1398 : elem,
1399 : soln_coeffs,
1400 : nodal_soln,
1401 : add_p_level,
1402 136185 : FEInterface::n_vec_dim(_mesh, fe_type));
1403 :
1404 : // infinite elements should be skipped...
1405 61626 : if (!elem->infinite())
1406 : {
1407 21324 : libmesh_assert_equal_to (nodal_soln.size(), elem->n_nodes());
1408 :
1409 : const unsigned int n_vals =
1410 136185 : vertices_only ? elem->n_vertices() : elem->n_nodes();
1411 :
1412 1063989 : for (unsigned int n=0; n<n_vals; n++)
1413 : {
1414 : // Compute index into global solution vector.
1415 : std::size_t index =
1416 927804 : nv * (nn++) + (n_vars_written_current_system + var_offset);
1417 :
1418 1207460 : soln[index] += nodal_soln[n];
1419 : }
1420 : }
1421 : }
1422 : else
1423 0 : nn += vertices_only ? elem->n_vertices() : elem->n_nodes();
1424 926 : } // end loop over active elements writing interiors
1425 :
1426 : // Loop writing "fake" sides, if requested
1427 1190 : if (add_sides)
1428 : {
1429 : // We don't build discontinuous solution vectors in
1430 : // parallel yet, but we'll do ordering of fake side
1431 : // values as if we did, for consistency with the
1432 : // parallel continuous ordering and for future
1433 : // compatibility.
1434 : std::vector<std::vector<const Elem *>>
1435 375 : elems_by_pid(_mesh.n_processors());
1436 :
1437 3655 : for (const auto & elem : _mesh.active_element_ptr_range())
1438 2070 : elems_by_pid[elem->processor_id()].push_back(elem);
1439 :
1440 2075 : for (auto p : index_range(elems_by_pid))
1441 3455 : for (const Elem * elem : elems_by_pid[p])
1442 : {
1443 1680 : if (var_description.active_on_subdomain(elem->subdomain_id()))
1444 : {
1445 1680 : system->get_dof_map().dof_indices (elem, dof_indices, var);
1446 :
1447 1820 : soln_coeffs.resize(dof_indices.size());
1448 :
1449 32064 : for (auto i : index_range(dof_indices))
1450 35448 : soln_coeffs[i] = sys_soln[dof_indices[i]];
1451 :
1452 8880 : for (auto s : elem->side_index_range())
1453 : {
1454 7200 : if (redundant_added_side(*elem,s))
1455 1944 : continue;
1456 :
1457 : const std::vector<unsigned int> side_nodes =
1458 5694 : elem->nodes_on_side(s);
1459 :
1460 : // Compute the FE solution at all the
1461 : // side nodes, but only use those for
1462 : // which is_vertex() == true if
1463 : // vertices_only == true.
1464 : FEInterface::side_nodal_soln
1465 5256 : (fe_type, elem, s, soln_coeffs,
1466 : nodal_soln, add_p_level,
1467 5256 : FEInterface::n_vec_dim(_mesh, fe_type));
1468 :
1469 438 : libmesh_assert_equal_to
1470 : (nodal_soln.size(),
1471 : side_nodes.size());
1472 :
1473 : // If we don't have a continuous FE
1474 : // then we want to average between
1475 : // sides, at least in the equal-level
1476 : // case where it's easy. This is
1477 : // analogous to our repeat_count
1478 : // behavior elsewhere.
1479 : const FEContinuity cont =
1480 5256 : FEInterface::get_continuity(fe_type);
1481 876 : const Elem * const neigh = elem->neighbor_ptr(s);
1482 :
1483 5256 : if ((cont == DISCONTINUOUS || cont == H_CURL || cont == H_DIV) &&
1484 0 : neigh &&
1485 5694 : neigh->level() == elem->level() &&
1486 0 : var_description.active_on_subdomain(neigh->subdomain_id()))
1487 : {
1488 0 : std::vector<dof_id_type> neigh_indices;
1489 0 : system->get_dof_map().dof_indices (neigh, neigh_indices, var);
1490 0 : std::vector<Number> neigh_coeffs(neigh_indices.size());
1491 :
1492 0 : for (auto i : index_range(neigh_indices))
1493 0 : neigh_coeffs[i] = sys_soln[neigh_indices[i]];
1494 :
1495 : const unsigned int s_neigh =
1496 0 : neigh->which_neighbor_am_i(elem);
1497 0 : std::vector<Number> neigh_soln;
1498 : FEInterface::side_nodal_soln
1499 0 : (fe_type, neigh, s_neigh,
1500 : neigh_coeffs, neigh_soln, add_p_level,
1501 0 : FEInterface::n_vec_dim(_mesh, fe_type));
1502 :
1503 : const std::vector<unsigned int> neigh_nodes =
1504 0 : neigh->nodes_on_side(s_neigh);
1505 0 : for (auto n : index_range(side_nodes))
1506 0 : for (auto neigh_n : index_range(neigh_nodes))
1507 0 : if (neigh->node_ptr(neigh_nodes[neigh_n])
1508 0 : == elem->node_ptr(side_nodes[n]))
1509 : {
1510 0 : nodal_soln[n] += neigh_soln[neigh_n];
1511 0 : nodal_soln[n] /= 2;
1512 : }
1513 : }
1514 :
1515 38736 : for (auto n : index_range(side_nodes))
1516 : {
1517 33480 : if (vertices_only &&
1518 0 : !elem->is_vertex(n))
1519 0 : continue;
1520 :
1521 : // Compute index into global solution vector.
1522 : std::size_t index =
1523 33480 : nv * (nn++) + (n_vars_written_current_system + var_offset);
1524 :
1525 36270 : soln[index] += nodal_soln[n];
1526 : }
1527 : }
1528 : }
1529 : else
1530 : {
1531 0 : nn += vertices_only ? elem->n_vertices() : elem->n_nodes();
1532 :
1533 0 : for (auto s : elem->side_index_range())
1534 : {
1535 0 : if (redundant_added_side(*elem,s))
1536 0 : continue;
1537 :
1538 : const std::vector<unsigned int> side_nodes =
1539 0 : elem->nodes_on_side(s);
1540 :
1541 0 : for (auto n : index_range(side_nodes))
1542 : {
1543 0 : if (vertices_only &&
1544 0 : !elem->is_vertex(n))
1545 0 : continue;
1546 0 : nn++;
1547 : }
1548 : }
1549 : }
1550 : } // end loop over active elements, writing "fake" sides
1551 250 : }
1552 : // If we made it here, we actually wrote a variable, so increment
1553 : // the number of variables actually written for the current system.
1554 1190 : n_vars_written_current_system++;
1555 :
1556 : } // end loop over vars
1557 : } // end if proc 0
1558 :
1559 : // Update offset for next loop iteration.
1560 5578 : var_offset += n_vars_written_current_system;
1561 : } // end loop over systems
1562 5507 : }
1563 :
1564 :
1565 :
1566 188928 : bool EquationSystems::redundant_added_side(const Elem & elem, unsigned int side)
1567 : {
1568 10536 : libmesh_assert(elem.active());
1569 :
1570 21072 : const Elem * neigh = elem.neighbor_ptr(side);
1571 :
1572 : // Write boundary sides.
1573 188928 : if (!neigh)
1574 4860 : return false;
1575 :
1576 : // Write ghost sides in Nemesis
1577 102432 : if (neigh == remote_elem)
1578 0 : return false;
1579 :
1580 : // Don't write a coarser side if a finer side exists
1581 5676 : if (!neigh->active())
1582 0 : return true;
1583 :
1584 : // Don't write a side redundantly from both of the
1585 : // elements sharing it. We'll disambiguate with id().
1586 101376 : return (neigh->id() < elem.id());
1587 : }
1588 :
1589 :
1590 :
1591 0 : bool EquationSystems::compare (const EquationSystems & other_es,
1592 : const Real threshold,
1593 : const bool verbose) const
1594 : {
1595 : // safety check, whether we handle at least the same number
1596 : // of systems
1597 0 : std::vector<bool> os_result;
1598 :
1599 0 : if (this->n_systems() != other_es.n_systems())
1600 : {
1601 0 : if (verbose)
1602 : {
1603 0 : libMesh::out << " Fatal difference. This system handles "
1604 0 : << this->n_systems() << " systems," << std::endl
1605 0 : << " while the other system handles "
1606 0 : << other_es.n_systems()
1607 0 : << " systems." << std::endl
1608 0 : << " Aborting comparison." << std::endl;
1609 : }
1610 0 : return false;
1611 : }
1612 : else
1613 : {
1614 : // start comparing each system
1615 0 : for (const auto & [sys_name, sys_ptr] : _systems)
1616 : {
1617 : // get the other system
1618 0 : const System & other_system = other_es.get_system (sys_name);
1619 :
1620 0 : os_result.push_back (sys_ptr->compare (other_system, threshold, verbose));
1621 :
1622 : }
1623 :
1624 : }
1625 :
1626 :
1627 : // sum up the results
1628 0 : if (os_result.size()==0)
1629 0 : return true;
1630 : else
1631 : {
1632 : bool os_identical;
1633 0 : unsigned int n = 0;
1634 0 : do
1635 : {
1636 0 : os_identical = os_result[n];
1637 0 : n++;
1638 : }
1639 0 : while (os_identical && n<os_result.size());
1640 0 : return os_identical;
1641 : }
1642 : }
1643 :
1644 :
1645 :
1646 15827 : std::string EquationSystems::get_info () const
1647 : {
1648 16747 : std::ostringstream oss;
1649 :
1650 : oss << " EquationSystems\n"
1651 30734 : << " n_systems()=" << this->n_systems() << '\n';
1652 :
1653 : // Print the info for the individual systems
1654 33348 : for (const auto & pr : _systems)
1655 34534 : oss << pr.second->get_info();
1656 :
1657 :
1658 : // // Possibly print the parameters
1659 : // if (!this->parameters.empty())
1660 : // {
1661 : // oss << " n_parameters()=" << this->n_parameters() << '\n';
1662 : // oss << " Parameters:\n";
1663 :
1664 : // for (const auto & [key, val] : _parameters)
1665 : // oss << " "
1666 : // << "\""
1667 : // << key
1668 : // << "\""
1669 : // << "="
1670 : // << val
1671 : // << '\n';
1672 : // }
1673 :
1674 16287 : return oss.str();
1675 14907 : }
1676 :
1677 :
1678 :
1679 15827 : void EquationSystems::print_info (std::ostream & os) const
1680 : {
1681 16287 : os << this->get_info()
1682 460 : << std::endl;
1683 15827 : }
1684 :
1685 :
1686 :
1687 0 : std::ostream & operator << (std::ostream & os,
1688 : const EquationSystems & es)
1689 : {
1690 0 : es.print_info(os);
1691 0 : return os;
1692 : }
1693 :
1694 :
1695 :
1696 2712 : unsigned int EquationSystems::n_vars () const
1697 : {
1698 2712 : unsigned int tot=0;
1699 :
1700 5536 : for (const auto & pr : _systems)
1701 2824 : tot += pr.second->n_vars();
1702 :
1703 2712 : return tot;
1704 : }
1705 :
1706 :
1707 :
1708 0 : std::size_t EquationSystems::n_dofs () const
1709 : {
1710 0 : std::size_t tot=0;
1711 :
1712 0 : for (const auto & pr : _systems)
1713 0 : tot += pr.second->n_dofs();
1714 :
1715 0 : return tot;
1716 : }
1717 :
1718 :
1719 :
1720 :
1721 22948 : std::size_t EquationSystems::n_active_dofs () const
1722 : {
1723 730 : std::size_t tot=0;
1724 :
1725 45896 : for (const auto & pr : _systems)
1726 22948 : tot += pr.second->n_active_dofs();
1727 :
1728 22948 : return tot;
1729 : }
1730 :
1731 :
1732 239485 : void EquationSystems::_add_system_to_nodes_and_elems()
1733 : {
1734 : // All the nodes
1735 29296810 : for (auto & node : _mesh.node_ptr_range())
1736 15686872 : node->add_system();
1737 :
1738 : // All the elements
1739 13581250 : for (auto & elem : _mesh.element_ptr_range())
1740 7198381 : elem->add_system();
1741 239485 : }
1742 :
1743 71 : void EquationSystems::_remove_default_ghosting(unsigned int sys_num)
1744 : {
1745 71 : this->get_system(sys_num).get_dof_map().remove_default_ghosting();
1746 71 : }
1747 :
1748 : } // namespace libMesh
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