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dofhandler.cc
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1 /*!
2  *
3  * Copyright (C) 2015 Technical University of Liberec. All rights reserved.
4  *
5  * This program is free software; you can redistribute it and/or modify it under
6  * the terms of the GNU General Public License version 3 as published by the
7  * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
8  *
9  * This program is distributed in the hope that it will be useful, but WITHOUT
10  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11  * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
12  *
13  *
14  * @file dofhandler.cc
15  * @brief Declaration of class which handles the ordering of degrees of freedom (dof) and mappings between local and global dofs.
16  * @author Jan Stebel
17  */
18 
19 #include "fem/dofhandler.hh"
20 #include "fem/finite_element.hh"
21 #include "fem/dh_cell_accessor.hh"
22 #include "mesh/mesh.h"
23 #include "mesh/duplicate_nodes.h"
24 #include "mesh/partitioning.hh"
25 #include "mesh/long_idx.hh"
26 #include "mesh/accessors.hh"
27 #include "mesh/range_wrapper.hh"
28 #include "mesh/neighbours.h"
29 #include "la/distribution.hh"
30 
31 
32 
33 
35 {}
36 
37 
38 
39 
40 
41 
42 DOFHandlerMultiDim::DOFHandlerMultiDim(Mesh& _mesh, bool make_elem_part)
43  : DOFHandlerBase(_mesh),
44  ds_(nullptr),
45  is_parallel_(true),
46  dh_seq_(nullptr),
47  scatter_to_seq_(nullptr),
48  el_ds_(nullptr)
49 {
50  if (make_elem_part) make_elem_partitioning();
51 }
52 
53 
54 std::shared_ptr<DOFHandlerMultiDim> DOFHandlerMultiDim::sequential()
55 {
57  return dh_seq_;
58 }
59 
60 
61 std::shared_ptr<VecScatter> DOFHandlerMultiDim::sequential_scatter()
62 {
64  return scatter_to_seq_;
65 }
66 
67 
69 {
70  // get number of dofs per element and then set up cell_starts
72  for (auto cell : this->local_range())
73  {
74  cell_starts[cell.local_idx()+1] = cell.n_dofs();
75  max_elem_dofs_ = max( (int)max_elem_dofs_, (int)cell.n_dofs() );
76  }
77  for (unsigned int i=0; i<cell_starts.size()-1; ++i)
78  cell_starts[i+1] += cell_starts[i];
79 }
80 
81 
83  std::vector<LongIdx> &node_dof_starts,
84  std::vector<LongIdx> &edge_dof_starts)
85 {
86  // initialize dofs on nodes
87  // We must separate dofs for dimensions because FE functions
88  // may be discontinuous on nodes shared by different
89  // dimensions.
90  unsigned int n_node_dofs = 0;
91  for (unsigned int nid=0; nid<mesh_->tree->n_nodes(); nid++)
92  {
93  node_dof_starts.push_back(n_node_dofs);
94  n_node_dofs += ds_->n_node_dofs(nid);
95  }
96  node_dof_starts.push_back(n_node_dofs);
97 
98  unsigned int n_edge_dofs = 0;
99  for (unsigned int i=0; i<mesh_->n_edges(); i++)
100  {
101  edge_dof_starts.push_back(n_edge_dofs);
102  n_edge_dofs += ds_->n_edge_dofs(mesh_->edges[i]);
103  }
104  edge_dof_starts.push_back(n_edge_dofs);
105 }
106 
107 
109  std::vector<short int> &node_status,
110  std::vector<short int> &edge_status)
111 {
112  // mark local dofs
113  for (auto cell : this->own_range())
114  {
115  for (unsigned int n=0; n<cell.dim()+1; n++)
116  {
117  unsigned int nid = mesh_->tree->objects(cell.dim())[mesh_->tree->obj_4_el()[cell.elm_idx()]].nodes[n];
118  node_status[nid] = VALID_NFACE;
119  }
120  }
121 
122  // unmark dofs on ghost cells from lower procs
123  for (auto cell : this->ghost_range())
124  {
125  if (cell.elm().proc() < el_ds_->myp())
126  {
127  for (unsigned int n=0; n<cell.dim()+1; n++)
128  {
129  unsigned int nid = mesh_->tree->objects(cell.dim())[mesh_->tree->obj_4_el()[cell.elm_idx()]].nodes[n];
130  node_status[nid] = INVALID_NFACE;
131  }
132  }
133  }
134 
135  // mark local edges
136  for (auto eid : edg_4_loc)
137  edge_status[eid] = VALID_NFACE;
138 
139  // unmark dofs on ghost cells from lower procs
140  for (auto cell : this->ghost_range())
141  {
142  if (cell.elm().proc() < el_ds_->myp())
143  {
144  for (unsigned int n=0; n<cell.dim()+1; n++)
145  {
146  unsigned int eid = cell.elm().side(n)->edge_idx();
147  edge_status[eid] = INVALID_NFACE;
148  }
149  }
150  }
151 }
152 
153 
155 {
156  // send number of elements required from the other processor
157  unsigned int n_elems = ghost_proc_el[proc].size();
158  MPI_Send(&n_elems, 1, MPI_UNSIGNED, proc, 0, MPI_COMM_WORLD);
159 
160  // send indices of elements required
161  MPI_Send(&(ghost_proc_el[proc][0]), n_elems, MPI_LONG_IDX, proc, 1, MPI_COMM_WORLD);
162 
163  // receive numbers of dofs on required elements
164  vector<unsigned int> n_dofs(n_elems);
165  MPI_Recv(&(n_dofs[0]), n_elems, MPI_UNSIGNED, proc, 2, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
166 
167  // receive dofs on required elements
168  unsigned int n_dofs_sum = 0;
169  for (auto nd : n_dofs) n_dofs_sum += nd;
170  dofs.resize(n_dofs_sum);
171  MPI_Recv(&(dofs[0]), n_dofs_sum, MPI_LONG_IDX, proc, 3, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
172 }
173 
174 
175 void DOFHandlerMultiDim::send_ghost_dofs(unsigned int proc)
176 {
177  // receive number of elements required by the other processor
178  unsigned int n_elems;
179  MPI_Recv(&n_elems, 1, MPI_UNSIGNED, proc, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
180 
181  // receive indices of elements required
182  vector<LongIdx> elems(n_elems);
183  MPI_Recv(&(elems[0]), n_elems, MPI_LONG_IDX, proc, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
184 
185  // send numbers of dofs on required elements
186  vector<unsigned int> n_dofs;
187  for (LongIdx el : elems)
188  {
189  auto cell = this->cell_accessor_from_element(el);
190  n_dofs.push_back(cell_starts[cell.local_idx()+1] - cell_starts[cell.local_idx()]);
191  }
192  MPI_Send(&(n_dofs[0]), n_elems, MPI_UNSIGNED, proc, 2, MPI_COMM_WORLD);
193 
194  // send dofs on the required elements
195  vector<LongIdx> dofs;
196  for (LongIdx el : elems)
197  {
198  auto cell = this->cell_accessor_from_element(el);
199  dofs.insert(dofs.end(), dof_indices.begin()+cell_starts[cell.local_idx()], dof_indices.begin()+cell_starts[cell.local_idx()+1]);
200  }
201  MPI_Send(&(dofs[0]), dofs.size(), MPI_LONG_IDX, proc, 3, MPI_COMM_WORLD);
202 }
203 
204 
206  const std::vector<bool> &update_cells,
207  const std::vector<LongIdx> &dofs,
208  const std::vector<LongIdx> &node_dof_starts,
209  std::vector<LongIdx> &node_dofs,
210  const std::vector<LongIdx> &edge_dof_starts,
211  std::vector<LongIdx> &edge_dofs)
212 {
213  // update dof_indices on ghost cells
214  unsigned int dof_offset=0;
215  for (unsigned int gid=0; gid<ghost_proc_el[proc].size(); gid++)
216  {
217  DHCellAccessor dh_cell = this->cell_accessor_from_element( ghost_proc_el[proc][gid] );
218 
219  for (unsigned dof=0; dof<dh_cell.n_dofs(); dof++)
220  dof_indices[cell_starts[dh_cell.local_idx()]+dof] = dofs[dof_offset+dof];
221 
222  vector<unsigned int> loc_node_dof_count(dh_cell.elm()->n_nodes(), 0);
223  vector<unsigned int> loc_edge_dof_count(dh_cell.elm()->n_sides(), 0);
224  for (unsigned int idof = 0; idof<dh_cell.n_dofs(); ++idof)
225  {
226  if (dh_cell.cell_dof(idof).dim == 0)
227  { // update nodal dof
228  unsigned int dof_nface_idx = dh_cell.cell_dof(idof).n_face_idx;
229  unsigned int nid = mesh_->tree->objects(dh_cell.dim())[mesh_->tree->obj_4_el()[dh_cell.elm_idx()]].nodes[dof_nface_idx];
230 
231  if (node_dofs[node_dof_starts[nid]+loc_node_dof_count[dof_nface_idx]] == INVALID_DOF)
232  {
233  node_dofs[node_dof_starts[nid]+loc_node_dof_count[dof_nface_idx]] = dofs[dof_offset+idof];
234  local_to_global_dof_idx_.push_back(dofs[dof_offset+idof]);
235  }
236 
237  loc_node_dof_count[dof_nface_idx]++;
238  }
239  else if (dh_cell.cell_dof(idof).dim == dh_cell.dim()-1)
240  { // update edge dof
241  unsigned int dof_nface_idx = dh_cell.cell_dof(idof).n_face_idx;
242  unsigned int eid = dh_cell.elm().side(dof_nface_idx)->edge_idx();
243 
244  if (edge_dofs[edge_dof_starts[eid]+loc_edge_dof_count[dof_nface_idx]] == INVALID_DOF)
245  {
246  edge_dofs[edge_dof_starts[eid]+loc_edge_dof_count[dof_nface_idx]] = dofs[dof_offset+idof];
247  local_to_global_dof_idx_.push_back(dofs[dof_offset+idof]);
248  }
249 
250  loc_edge_dof_count[dof_nface_idx]++;
251  }
252  else if (dh_cell.cell_dof(idof).dim == dh_cell.dim())
253  {
254  local_to_global_dof_idx_.push_back(dofs[dof_offset+idof]);
255  }
256  }
257 
258  dof_offset += dh_cell.n_dofs();
259  }
260 
261  // update dof_indices on local elements
262  for (auto cell : this->own_range())
263  {
264  if (!update_cells[cell.local_idx()]) continue;
265 
266  // loop over element dofs
267  vector<unsigned int> loc_node_dof_count(cell.elm()->n_nodes(), 0);
268  vector<unsigned int> loc_edge_dof_count(cell.elm()->n_sides(), 0);
269  for (unsigned int idof = 0; idof<cell.n_dofs(); ++idof)
270  {
271  unsigned int dof_nface_idx = cell.cell_dof(idof).n_face_idx;
272  if (cell.cell_dof(idof).dim == 0)
273  {
274  if (dof_indices[cell_starts[cell.local_idx()]+idof] == INVALID_DOF)
275  { // update nodal dof
276  unsigned int nid = mesh_->tree->objects(cell.dim())[mesh_->tree->obj_4_el()[cell.elm_idx()]].nodes[dof_nface_idx];
277  dof_indices[cell_starts[cell.local_idx()]+idof] = node_dofs[node_dof_starts[nid]+loc_node_dof_count[dof_nface_idx]];
278  }
279  loc_node_dof_count[dof_nface_idx]++;
280  } else if (cell.cell_dof(idof).dim == cell.dim()-1)
281  {
282  if (dof_indices[cell_starts[cell.local_idx()]+idof] == INVALID_DOF)
283  { // update edge dof
284  unsigned int eid = cell.elm().side(dof_nface_idx)->edge_idx();
285  dof_indices[cell_starts[cell.local_idx()]+idof] = edge_dofs[edge_dof_starts[eid]+loc_edge_dof_count[dof_nface_idx]];
286  }
287  loc_edge_dof_count[dof_nface_idx]++;
288  }
289  }
290  }
291 }
292 
293 
294 void DOFHandlerMultiDim::distribute_dofs(std::shared_ptr<DiscreteSpace> ds)
295 {
296  // First check if dofs are already distributed.
297  OLD_ASSERT(ds_ == nullptr, "Attempt to distribute DOFs multiple times!");
298 
299  ds_ = ds;
300 
301  std::vector<LongIdx> node_dofs, node_dof_starts, edge_dofs, edge_dof_starts;
303  edge_status(mesh_->n_edges(), INVALID_NFACE);
304  std::vector<bool> update_cells(el_ds_->lsize(), false);
305  unsigned int next_free_dof = 0;
306 
308  init_dof_starts(node_dof_starts, edge_dof_starts);
309  node_dofs.resize(node_dof_starts[node_dof_starts.size()-1], (LongIdx)INVALID_DOF);
310  edge_dofs.resize(edge_dof_starts[edge_dof_starts.size()-1], (LongIdx)INVALID_DOF);
311  init_status(node_status, edge_status);
312 
313  // Distribute dofs on local elements.
314  dof_indices.resize(cell_starts[cell_starts.size()-1]);
315  local_to_global_dof_idx_.reserve(dof_indices.size());
316  for (auto cell : this->own_range())
317  {
318 
319  // loop over element dofs
320  vector<unsigned int> loc_node_dof_count(cell.elm()->n_nodes(), 0);
321  vector<unsigned int> loc_edge_dof_count(cell.elm()->dim()+1, 0);
322  for (unsigned int idof = 0; idof<cell.n_dofs(); ++idof)
323  {
324  unsigned int dof_dim = cell.cell_dof(idof).dim;
325  unsigned int dof_nface_idx = cell.cell_dof(idof).n_face_idx;
326 
327  if (dof_dim == 0)
328  { // add dofs shared by nodes
329  unsigned int nid = mesh_->tree->objects(cell.dim())[mesh_->tree->obj_4_el()[cell.elm_idx()]].nodes[dof_nface_idx];
330  unsigned int node_dof_idx = node_dof_starts[nid]+loc_node_dof_count[dof_nface_idx];
331 
332  switch (node_status[nid])
333  {
334  case VALID_NFACE:
335  for (int i=0; i<node_dof_starts[nid+1] - node_dof_starts[nid]; i++)
336  {
337  local_to_global_dof_idx_.push_back(next_free_dof);
338  node_dofs[node_dof_starts[nid]+i] = next_free_dof++;
339  }
340  node_status[nid] = ASSIGNED_NFACE;
341  break;
342  case INVALID_NFACE:
343  node_dofs[node_dof_idx] = INVALID_DOF;
344  update_cells[cell.local_idx()] = true;
345  break;
346  }
347  dof_indices[cell_starts[cell.local_idx()]+idof] = node_dofs[node_dof_idx];
348  loc_node_dof_count[dof_nface_idx]++;
349  }
350  else if (dof_dim == cell.dim()-1)
351  { // add dofs shared by edges
352  unsigned int eid = cell.elm().side(dof_nface_idx)->edge_idx();
353  unsigned int edge_dof_idx = edge_dof_starts[eid]+loc_edge_dof_count[dof_nface_idx];
354  switch (edge_status[eid])
355  {
356  case VALID_NFACE:
357  for (int i=0; i<edge_dof_starts[eid+1] - edge_dof_starts[eid]; i++)
358  {
359  local_to_global_dof_idx_.push_back(next_free_dof);
360  edge_dofs[edge_dof_starts[eid]+i] = next_free_dof++;
361  }
362  edge_status[eid] = ASSIGNED_NFACE;
363  break;
364  case INVALID_NFACE:
365  edge_dofs[edge_dof_idx] = INVALID_DOF;
366  update_cells[cell.local_idx()] = true;
367  break;
368  }
369  dof_indices[cell_starts[cell.local_idx()]+idof] = edge_dofs[edge_dof_idx];
370  loc_edge_dof_count[dof_nface_idx]++;
371  }
372  else if (dof_dim == cell.dim())
373  { // add dofs owned only by the element
374  local_to_global_dof_idx_.push_back(next_free_dof);
375  dof_indices[cell_starts[cell.local_idx()]+idof] = next_free_dof++;
376  }
377  else
378  ASSERT(false).error("Unsupported dof n_face.");
379  }
380  }
381  node_status.clear();
382  edge_status.clear();
383 
384  lsize_ = next_free_dof;
385 
386  // communicate n_dofs across all processes
387  dof_ds_ = std::make_shared<Distribution>(lsize_, PETSC_COMM_WORLD);
388  n_global_dofs_ = dof_ds_->size();
389 
390  // shift dof indices
391  loffset_ = dof_ds_->get_starts_array()[dof_ds_->myp()];
392  if (loffset_ > 0)
393  {
394  for (unsigned int i=0; i<dof_indices.size(); i++)
395  if (dof_indices[i] != INVALID_DOF)
396  dof_indices[i] += loffset_;
397  for (auto &i : local_to_global_dof_idx_)
398  i += loffset_;
399  }
400 
401  // communicate dofs from ghost cells
402  // first propagate from lower procs to higher procs and then vice versa
403  for (unsigned int from_higher = 0; from_higher < 2; from_higher++)
404  {
405  for (unsigned int proc : ghost_proc)
406  {
407  if ((proc > el_ds_->myp()) == from_higher)
408  { // receive dofs from master processor
409  vector<LongIdx> dofs;
410  receive_ghost_dofs(proc, dofs);
411 
412  // update dof_indices and node_dofs on ghost elements
413  update_local_dofs(proc,
414  update_cells,
415  dofs,
416  node_dof_starts,
417  node_dofs,
418  edge_dof_starts,
419  edge_dofs
420  );
421 
422  }
423  else
424  send_ghost_dofs(proc);
425  }
426  }
427  update_cells.clear();
428  node_dofs.clear();
429  node_dof_starts.clear();
430  edge_dofs.clear();
431  edge_dof_starts.clear();
432 }
433 
434 
436 {
437  if (dh_seq_ != nullptr) return;
438 
439  if ( !is_parallel_ )
440  {
441  dh_seq_ = std::make_shared<DOFHandlerMultiDim>(*this);
442  return;
443  }
444 
445  dh_seq_ = std::make_shared<DOFHandlerMultiDim>(*mesh_);
446 
447  dh_seq_->n_global_dofs_ = n_global_dofs_;
448  dh_seq_->lsize_ = n_global_dofs_;
449  dh_seq_->loffset_ = 0;
450  dh_seq_->mesh_ = mesh_;
451  dh_seq_->dof_ds_ = dof_ds_; // should be sequential distribution
452  dh_seq_->ds_ = ds_;
453  dh_seq_->is_parallel_ = false;
454 
457  &dh_seq_->max_elem_dofs_,
458  1,
459  MPI_UNSIGNED,
460  MPI_MAX,
462 
463  for (unsigned int i=0; i<mesh_->n_elements(); i++) dh_seq_->global_to_local_el_idx_[i] = mesh_->get_row_4_el()[i];
464 
465  // Auxiliary vectors cell_starts_loc and dof_indices_loc contain
466  // only local element data (without ghost elements).
467  // Then it is possible to create sequential vectors by simple reduce/gather operation.
468  vector<LongIdx> cell_starts_loc(mesh_->n_elements()+1, 0);
469  vector<LongIdx> dof_indices_loc;
470 
471  // construct cell_starts_loc
472  for (auto cell : this->own_range())
473  {
474  cell_starts_loc[mesh_->get_row_4_el()[cell.elm_idx()]+1] = cell.n_dofs();
475  }
476  for (unsigned int i=0; i<mesh_->n_elements(); ++i)
477  cell_starts_loc[i+1] += cell_starts_loc[i];
478 
479  // construct dof_indices_loc
480  dof_indices_loc.resize(cell_starts_loc[mesh_->n_elements()]);
481  for (auto cell : this->own_range())
482  {
483  for (unsigned int idof=0; idof<cell.n_dofs(); idof++)
484  dof_indices_loc[cell_starts_loc[mesh_->get_row_4_el()[cell.elm_idx()]]+idof] = dof_indices[cell_starts[cell.local_idx()]+idof];
485  }
486 
487  Distribution distr(dof_indices_loc.size(), PETSC_COMM_WORLD);
488  dh_seq_->cell_starts.resize(mesh_->n_elements()+1);
489  dh_seq_->dof_indices.resize(distr.size());
490 
491  MPI_Allreduce( cell_starts_loc.data(),
492  dh_seq_->cell_starts.data(),
493  cell_starts_loc.size(),
494  MPI_LONG_IDX,
495  MPI_SUM,
496  MPI_COMM_WORLD );
497 
498  MPI_Allgatherv( dof_indices_loc.data(),
499  dof_indices_loc.size(),
500  MPI_LONG_IDX,
501  dh_seq_->dof_indices.data(),
502  (const int *)distr.get_lsizes_array(),
503  (const int *)distr.get_starts_array(),
504  MPI_LONG_IDX,
505  MPI_COMM_WORLD );
506 
507  // create scatter from parallel to sequential vector
508  Vec v_from;
509  VecCreateMPI(PETSC_COMM_WORLD, lsize_, PETSC_DETERMINE, &v_from);
510  scatter_to_seq_ = std::make_shared<VecScatter>();
511  VecScatterCreateToAll(v_from, scatter_to_seq_.get(), NULL);
512  VecDestroy(&v_from);
513 
514  // create scatter for sequential dof handler (Warning: not tested)
515  Vec v_seq;
516  VecCreateSeq(PETSC_COMM_SELF, n_global_dofs_, &v_seq);
517  dh_seq_->scatter_to_seq_ = std::make_shared<VecScatter>();
518  VecScatterCreateToAll(v_seq, dh_seq_->scatter_to_seq_.get(), NULL);
519  VecDestroy(&v_seq);
520 }
521 
522 
524 {
525  if (is_parallel_ && el_ds_->np() > 1)
526  { // for parallel DH create vector with ghost values
528  VectorMPI vec(lsize_, ghost_dofs);
529  return vec;
530  } else {
531  VectorMPI vec(lsize_, PETSC_COMM_SELF);
532  return vec;
533  }
534 }
535 
536 
538 {
539  unsigned int ndofs = 0;
540  LongIdx cell_idx = global_to_local_el_idx_.at(cell.idx());
541  ndofs = cell_starts[cell_idx+1]-cell_starts[cell_idx];
542  for (unsigned int k=0; k<ndofs; k++)
543  indices[k] = dof_indices[cell_starts[cell_idx]+k];
544 
545  return ndofs;
546 }
547 
548 
549 
551 {
552  unsigned int ndofs = 0;
553  LongIdx cell_idx = global_to_local_el_idx_.at(cell.idx());
554  ndofs = cell_starts[cell_idx+1]-cell_starts[cell_idx];
555  for (unsigned int k=0; k<ndofs; k++)
556  indices[k] = cell_starts[cell_idx]+k;
557 
558  return ndofs;
559 }
560 
561 
563 {}
564 
565 
566 
568 {
569  // create local arrays of elements
570  el_ds_ = mesh_->get_el_ds();
571 
572  // create local array of edges
573  for (unsigned int iedg=0; iedg<mesh_->n_edges(); iedg++)
574  {
575  bool is_edge_local = false;
576  Edge *edg = &mesh_->edges[iedg];
577  for (int sid=0; sid<edg->n_sides; sid++)
578  if ( el_is_local(edg->side(sid)->element().idx()) )
579  {
580  is_edge_local = true;
581  break;
582  }
583  if (is_edge_local)
584  edg_4_loc.push_back(iedg);
585  }
586 
587  // create local array of neighbours
588  for (unsigned int inb=0; inb<mesh_->n_vb_neighbours(); inb++)
589  {
590  Neighbour *nb = &mesh_->vb_neighbours_[inb];
591  if ( el_is_local(nb->element().idx())
592  || el_is_local(nb->side()->element().idx()) )
593  nb_4_loc.push_back(inb);
594  }
595 
596  // create array of local nodes
597  std::vector<bool> node_is_local(mesh_->tree->n_nodes(), false);
598  for (auto cell : this->own_range())
599  {
600  unsigned int obj_idx = mesh_->tree->obj_4_el()[cell.elm_idx()];
601  for (unsigned int nid=0; nid<cell.elm()->n_nodes(); nid++)
602  node_is_local[mesh_->tree->objects(cell.dim())[obj_idx].nodes[nid]] = true;
603  }
604 
605  // init global to local element map with locally owned elements (later add ghost elements)
606  for ( unsigned int iel = 0; iel < el_ds_->lsize(); iel++ )
608 
609  // create array of local ghost cells
610  for ( auto cell : mesh_->elements_range() )
611  {
612  if (cell.proc() != el_ds_->myp())
613  {
614  bool has_local_node = false;
615  unsigned int obj_idx = mesh_->tree->obj_4_el()[cell.idx()];
616  for (unsigned int nid=0; nid<cell->n_nodes(); nid++)
617  if (node_is_local[mesh_->tree->objects(cell->dim())[obj_idx].nodes[nid]])
618  {
619  has_local_node = true;
620  break;
621  }
622  if (has_local_node)
623  {
624  ghost_4_loc.push_back(cell.idx());
625  ghost_proc.insert(cell.proc());
626  ghost_proc_el[cell.proc()].push_back(cell.idx());
627  global_to_local_el_idx_[cell.idx()] = el_ds_->lsize() - 1 + ghost_4_loc.size();
628  }
629  }
630  }
631  for (auto nb : nb_4_loc)
632  {
633  auto cell = mesh_->vb_neighbours_[nb].element();
634  if (!el_is_local(cell.idx()) && find(ghost_4_loc.begin(), ghost_4_loc.end(), cell.idx()) == ghost_4_loc.end())
635  {
636  ghost_4_loc.push_back(cell.idx());
637  ghost_proc.insert(cell.proc());
638  ghost_proc_el[cell.proc()].push_back(cell.idx());
639  global_to_local_el_idx_[cell.idx()] = el_ds_->lsize() - 1 + ghost_4_loc.size();
640  }
641  cell = mesh_->vb_neighbours_[nb].side()->element();
642  if (!el_is_local(cell.idx()) && find(ghost_4_loc.begin(), ghost_4_loc.end(), cell.idx()) == ghost_4_loc.end())
643  {
644  ghost_4_loc.push_back(cell.idx());
645  ghost_proc.insert(cell.proc());
646  ghost_proc_el[cell.proc()].push_back(cell.idx());
647  global_to_local_el_idx_[cell.idx()] = el_ds_->lsize() - 1 + ghost_4_loc.size();
648  }
649  }
650 }
651 
652 
653 bool DOFHandlerMultiDim::el_is_local(int index) const
654 {
655  return el_ds_->is_local(mesh_->get_row_4_el()[index]);
656 }
657 
658 
659 std::size_t DOFHandlerMultiDim::hash() const {
660  return this->n_global_dofs_;
661 }
662 
663 
665  auto bgn_it = make_iter<DHCellAccessor>( DHCellAccessor(this, 0) );
666  auto end_it = make_iter<DHCellAccessor>( DHCellAccessor(this, el_ds_->lsize()) );
667  return Range<DHCellAccessor>(bgn_it, end_it);
668 }
669 
670 
672  auto bgn_it = make_iter<DHCellAccessor>( DHCellAccessor(this, 0) );
673  auto end_it = make_iter<DHCellAccessor>( DHCellAccessor(this, el_ds_->lsize()+ghost_4_loc.size()) );
674  return Range<DHCellAccessor>(bgn_it, end_it);
675 }
676 
677 
679  auto bgn_it = make_iter<DHCellAccessor>( DHCellAccessor(this, el_ds_->lsize()) );
680  auto end_it = make_iter<DHCellAccessor>( DHCellAccessor(this, el_ds_->lsize()+ghost_4_loc.size()) );
681  return Range<DHCellAccessor>(bgn_it, end_it);
682 }
683 
684 
686  auto map_it = global_to_local_el_idx_.find((LongIdx)elm_idx); // find in global to local map
687  ASSERT( map_it != global_to_local_el_idx_.end() )(elm_idx).error("DH accessor can be create only for own or ghost elements!\n");
688  return DHCellAccessor(this, map_it->second);
689 }
690 
691 
693  stringstream s;
695 
696  s << "DOFHandlerMultiDim structure:" << endl;
697  s << "- is parallel: " << (is_parallel_?"true":"false") << endl;
698  s << "- proc id: " << el_ds_->myp() << endl;
699  s << "- global number of dofs: " << n_global_dofs_ << endl;
700  s << "- number of locally owned cells: " << el_ds_->lsize() << endl;
701  s << "- number of ghost cells: " << ghost_4_loc.size() << endl;
702  s << "- dofs on locally owned cells:" << endl;
703 
704  for (auto cell : own_range())
705  {
706  auto ndofs = cell.get_dof_indices(dofs);
707  s << "-- cell " << cell.elm().index() << ": ";
708  for (unsigned int idof=0; idof<ndofs; idof++) s << dofs[idof] << " "; s << endl;
709  }
710  s << "- dofs on ghost cells:" << endl;
711  for (auto cell : ghost_range())
712  {
713  auto ndofs = cell.get_dof_indices(dofs);
714  s << "-- cell " << cell.elm().index() << ": ";
715  for (unsigned int idof=0; idof<ndofs; idof++) s << dofs[idof] << " "; s << endl;
716  }
717  s << "- locally owned dofs (" << lsize_ << "): ";
718  for (unsigned int i=0; i<lsize_; i++) s << local_to_global_dof_idx_[i] << " "; s << endl;
719  s << "- ghost dofs (" << local_to_global_dof_idx_.size() - lsize_ << "): ";
720  for (unsigned int i=lsize_; i<local_to_global_dof_idx_.size(); i++) s << local_to_global_dof_idx_[i] << " "; s << endl;
721  s << "- global-to-local-cell map:" << endl;
722  for (auto cell : global_to_local_el_idx_) s << "-- " << cell.first << " -> " << cell.second << " " << endl;
723  s << endl;
724 
725  printf("%s", s.str().c_str());
726 }
727 
728 
729 
730 
731 
732 
733 
734 
735 
736 
737 
738 
739 
740 
741 
742 
743 
#define MPI_Recv(buf, count, datatype, source, tag, comm, status)
Definition: mpi.h:271
void receive_ghost_dofs(unsigned int proc, std::vector< LongIdx > &dofs)
Obtain dof numbers on ghost elements from other processor.
Definition: dofhandler.cc:154
int LongIdx
Define type that represents indices of large arrays (elements, nodes, dofs etc.)
Definition: long_idx.hh:22
std::shared_ptr< DOFHandlerMultiDim > sequential()
Returns sequential version of the current dof handler.
Definition: dofhandler.cc:54
const Dof & cell_dof(unsigned int idof) const
Return dof on a given cell.
virtual ~DOFHandlerBase()
Destructor.
Definition: dofhandler.cc:34
void create_sequential()
Communicate local dof indices to all processors and create new sequential dof handler.
Definition: dofhandler.cc:435
void init_cell_starts()
Initialize vector of starting indices for elements.
Definition: dofhandler.cc:68
Declaration of class which handles the ordering of degrees of freedom (dof) and mappings between loca...
unsigned int n_nodes() const
Definition: elements.h:129
unsigned int elm_idx() const
Return serial idx to element of loc_ele_idx_.
unsigned int get_loc_dof_indices(const ElementAccessor< 3 > &cell, std::vector< LongIdx > &indices) const override
Returns the indices of dofs associated to the cell on the local process.
Definition: dofhandler.cc:550
const DHCellAccessor cell_accessor_from_element(unsigned int elm_idx) const
Return DHCellAccessor appropriate to ElementAccessor of given idx.
Definition: dofhandler.cc:685
LongIdx * get_row_4_el() const
Definition: mesh.h:167
void init_dof_starts(std::vector< LongIdx > &node_dof_starts, std::vector< LongIdx > &edge_dof_starts)
Initialize auxiliary vector of starting indices of nodal/edge dofs.
Definition: dofhandler.cc:82
const std::vector< MeshObject > & objects(unsigned int dim) const
#define MPI_LONG_IDX
Definition: long_idx.hh:24
unsigned int edge_idx() const
Definition: side_impl.hh:62
DuplicateNodes * tree
Definition: mesh.h:268
Distribution * el_ds_
Distribution of elements.
Definition: dofhandler.hh:420
static const int INVALID_NFACE
Definition: dofhandler.hh:363
unsigned int dim() const
Return dimension of element appropriate to cell.
unsigned int dim
Association to n-face of given dimension (point, line, triangle, tetrahedron.
unsigned int local_idx() const
Return local index to element (index of DOF handler).
void distribute_dofs(std::shared_ptr< DiscreteSpace > ds)
Distributes degrees of freedom on the mesh needed for the given discrete space.
Definition: dofhandler.cc:294
#define MPI_SUM
Definition: mpi.h:196
Definition: mesh.h:76
Cell accessor allow iterate over DOF handler cells.
std::shared_ptr< VecScatter > sequential_scatter()
Returns scatter context from parallel to sequential vectors.
Definition: dofhandler.cc:61
std::vector< LongIdx > local_to_global_dof_idx_
Maps local and ghost dof indices to global ones.
Definition: dofhandler.hh:412
int n_sides
Definition: edges.h:36
Definition: edges.h:26
SideIter side(const unsigned int loc_index)
Definition: accessors.hh:137
#define MPI_Send(buf, count, datatype, dest, tag, comm)
Definition: mpi.h:263
#define ASSERT(expr)
Allow use shorter versions of macro names if these names is not used with external library...
Definition: asserts.hh:346
void init_status(std::vector< short int > &node_status, std::vector< short int > &edge_status)
Initialize node_status and edge_status.
Definition: dofhandler.cc:108
std::shared_ptr< Distribution > dof_ds_
Distribution of dofs associated to local process.
Definition: dofhandler.hh:132
#define MPI_Allgatherv(sendbuf, sendcount, sendtype, recvbuf, recvcounts, displs, recvtype, comm)
Definition: mpi.h:587
unsigned int n_dofs() const
Return number of dofs on given cell.
ElementAccessor< 3 > element() const
Definition: side_impl.hh:53
std::shared_ptr< DOFHandlerMultiDim > dh_seq_
Sequential dof handler associated to the current (parallel) one.
Definition: dofhandler.hh:376
unsigned int lsize_
Number of dofs associated to local process.
Definition: dofhandler.hh:114
unsigned int n_face_idx
Index of n-face to which the dof is associated.
map< unsigned int, vector< LongIdx > > ghost_proc_el
Arrays of ghost cells for each neighbouring processor.
Definition: dofhandler.hh:435
static const int ASSIGNED_NFACE
Definition: dofhandler.hh:365
void send_ghost_dofs(unsigned int proc)
Send dof numbers to other processor.
Definition: dofhandler.cc:175
std::vector< LongIdx > cell_starts
Starting indices for local (owned+ghost) element dofs.
Definition: dofhandler.hh:396
#define OLD_ASSERT(...)
Definition: global_defs.h:131
unsigned int n_vb_neighbours() const
Definition: mesh.cc:235
ElementAccessor< 3 > element()
Definition: neighbours.h:163
const ElementAccessor< 3 > elm() const
Return ElementAccessor to element of loc_ele_idx_.
unsigned int get_dof_indices(const ElementAccessor< 3 > &cell, std::vector< LongIdx > &indices) const override
Returns the global indices of dofs associated to the cell.
Definition: dofhandler.cc:537
bool is_local(unsigned int idx) const
identify local index
Mesh * mesh_
Pointer to the mesh to which the dof handler is associated.
Definition: dofhandler.hh:127
Range helper class.
SideIter side()
Definition: neighbours.h:147
std::vector< LongIdx > dof_indices
Dof numbers on local and ghost elements.
Definition: dofhandler.hh:404
unsigned int n_sides() const
Definition: elements.h:135
static const int VALID_NFACE
Definition: dofhandler.hh:364
Range< DHCellAccessor > ghost_range() const
Returns range over ghosts DOF handler cells.
Definition: dofhandler.cc:678
vector< LongIdx > nb_4_loc
Local neighbour index -> global neighbour index.
Definition: dofhandler.hh:426
unsigned int max_elem_dofs_
Max. number of dofs per element.
Definition: dofhandler.hh:122
vector< LongIdx > ghost_4_loc
Indices of ghost cells (neighbouring with local elements).
Definition: dofhandler.hh:429
std::unordered_map< LongIdx, LongIdx > global_to_local_el_idx_
Maps global element index into local/ghost index (obsolete).
Definition: dofhandler.hh:417
virtual Range< ElementAccessor< 3 > > elements_range() const
Returns range of bulk elements.
Definition: mesh.cc:1040
unsigned int n_nodes() const
unsigned int np() const
get num of processors
Distribution * get_el_ds() const
Definition: mesh.h:164
void make_elem_partitioning()
Prepare parallel distribution of elements, edges and neighbours.
Definition: dofhandler.cc:567
void print() const
Output structure of dof handler.
Definition: dofhandler.cc:692
std::shared_ptr< Distribution > distr() const
Definition: dofhandler.hh:73
unsigned int myp() const
get my processor
Support classes for parallel programing.
#define MPI_Allreduce(sendbuf, recvbuf, count, datatype, op, comm)
Definition: mpi.h:612
vector< Neighbour > vb_neighbours_
Definition: mesh.h:273
#define MPI_STATUS_IGNORE
Definition: mpi.h:203
vector< LongIdx > edg_4_loc
Local edge index -> global edge index.
Definition: dofhandler.hh:423
Range< DHCellAccessor > own_range() const
Returns range of DOF handler cells (only range of own without ghost cells)
Definition: dofhandler.cc:664
unsigned int loffset_
Index of the first dof on the local process.
Definition: dofhandler.hh:119
static const int INVALID_DOF
Definition: dofhandler.hh:366
set< unsigned int > ghost_proc
Processors of ghost elements.
Definition: dofhandler.hh:432
~DOFHandlerMultiDim() override
Destructor.
Definition: dofhandler.cc:562
std::vector< Edge > edges
Vector of MH edges, this should not be part of the geometrical mesh.
Definition: mesh.h:252
#define MPI_COMM_WORLD
Definition: mpi.h:123
std::shared_ptr< DiscreteSpace > ds_
Pointer to the discrete space for which the handler distributes dofs.
Definition: dofhandler.hh:370
#define MPI_MAX
Definition: mpi.h:197
#define MPI_UNSIGNED
Definition: mpi.h:165
Abstract class for description of finite elements.
VectorMPI create_vector()
Allocates PETSc vector according to the dof distribution.
Definition: dofhandler.cc:523
unsigned int n_global_dofs_
Number of global dofs assigned by the handler.
Definition: dofhandler.hh:109
unsigned int n_edges() const
Definition: mesh.h:137
bool el_is_local(int index) const
Definition: dofhandler.cc:653
DOFHandlerMultiDim(Mesh &_mesh, bool make_elem_part=true)
Constructor.
Definition: dofhandler.cc:42
void update_local_dofs(unsigned int proc, const std::vector< bool > &update_cells, const std::vector< LongIdx > &dofs, const std::vector< LongIdx > &node_dof_starts, std::vector< LongIdx > &node_dofs, const std::vector< LongIdx > &edge_dof_starts, std::vector< LongIdx > &edge_dofs)
Update dofs on local elements from ghost element dofs.
Definition: dofhandler.cc:205
Range< DHCellAccessor > local_range() const
Returns range over own and ghost cells of DOF handler.
Definition: dofhandler.cc:671
const std::vector< unsigned int > & obj_4_el() const
bool is_parallel_
Indicator for parallel/sequential dof handler.
Definition: dofhandler.hh:373
unsigned int idx() const
Return local idx of element in boundary / bulk part of element vector.
Definition: accessors.hh:111
std::shared_ptr< VecScatter > scatter_to_seq_
Scatter context for parallel to sequential vectors.
Definition: dofhandler.hh:379
LongIdx * get_el_4_loc() const
Definition: mesh.h:170
SideIter side(const unsigned int i) const
Definition: edges.h:31
Implementation of range helper class.
friend class DHCellAccessor
Definition: dofhandler.hh:267
std::size_t hash() const override
Definition: dofhandler.cc:659
void printf(BasicWriter< Char > &w, BasicCStringRef< Char > format, ArgList args)
Definition: printf.h:444
std::shared_ptr< DiscreteSpace > ds() const
Return pointer to discrete space for which the handler distributes dofs.
Definition: dofhandler.hh:259
unsigned int lsize(int proc) const
get local size