Reference documentation for deal.II version GIT c1ddcf411d 2023-11-30 16:30:02+00:00
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dynamic_sparsity_pattern.cc
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15 
17 #include <deal.II/base/utilities.h>
18 
21 
22 #include <algorithm>
23 #include <cmath>
24 #include <functional>
25 #include <numeric>
26 #include <set>
27 
29 
30 
31 
32 template <typename ForwardIterator>
33 void
35  ForwardIterator end,
36  const bool indices_are_sorted)
37 {
38  const int n_elements = end - begin;
39  if (n_elements <= 0)
40  return;
41 
42  const size_type stop_size = entries.size() + n_elements;
43 
44  if (indices_are_sorted == true && n_elements > 3)
45  {
46  // in debug mode, check whether the
47  // indices really are sorted.
48 #ifdef DEBUG
49  {
50  ForwardIterator test = begin, test1 = begin;
51  ++test1;
52  for (; test1 != end; ++test, ++test1)
53  Assert(*test1 > *test, ExcInternalError());
54  }
55 #endif
56 
57  if (entries.empty() || entries.back() < *begin)
58  {
59  entries.insert(entries.end(), begin, end);
60  return;
61  }
62 
63  // find a possible insertion point for
64  // the first entry. check whether the
65  // first entry is a duplicate before
66  // actually doing something.
67  ForwardIterator my_it = begin;
68  size_type col = *my_it;
69  std::vector<size_type>::iterator it =
70  Utilities::lower_bound(entries.begin(), entries.end(), col);
71  while (*it == col)
72  {
73  ++my_it;
74  if (my_it == end)
75  break;
76  col = *my_it;
77  // check the very next entry in the
78  // current array
79  ++it;
80  if (it == entries.end())
81  break;
82  if (*it > col)
83  break;
84  if (*it == col)
85  continue;
86  // ok, it wasn't the very next one, do a
87  // binary search to find the insert point
88  it = Utilities::lower_bound(it, entries.end(), col);
89  if (it == entries.end())
90  break;
91  }
92  // all input entries were duplicates.
93  if (my_it == end)
94  return;
95 
96  // resize vector by just inserting the
97  // list
98  const size_type pos1 = it - entries.begin();
99  Assert(pos1 <= entries.size(), ExcInternalError());
100  entries.insert(it, my_it, end);
101  it = entries.begin() + pos1;
102  Assert(entries.size() >= static_cast<size_type>(it - entries.begin()),
103  ExcInternalError());
104 
105  // now merge the two lists.
106  std::vector<size_type>::iterator it2 = it + (end - my_it);
107 
108  // as long as there are indices both in
109  // the end of the entries list and in the
110  // input list
111  while (my_it != end && it2 != entries.end())
112  {
113  if (*my_it < *it2)
114  *it++ = *my_it++;
115  else if (*my_it == *it2)
116  {
117  *it++ = *it2++;
118  ++my_it;
119  }
120  else
121  *it++ = *it2++;
122  }
123  // in case there are indices left in the
124  // input list
125  while (my_it != end)
126  *it++ = *my_it++;
127 
128  // in case there are indices left in the
129  // end of entries
130  while (it2 != entries.end())
131  *it++ = *it2++;
132 
133  // resize and return
134  const size_type new_size = it - entries.begin();
135  Assert(new_size <= stop_size, ExcInternalError());
136  entries.resize(new_size);
137  return;
138  }
139 
140  // unsorted case or case with too few
141  // elements
142  ForwardIterator my_it = begin;
143 
144  // If necessary, increase the size of the
145  // array.
146  if (stop_size > entries.capacity())
147  entries.reserve(stop_size);
148 
149  size_type col = *my_it;
150  std::vector<size_type>::iterator it, it2;
151  // insert the first element as for one
152  // entry only first check the last
153  // element (or if line is still empty)
154  if ((entries.empty()) || (entries.back() < col))
155  {
156  entries.push_back(col);
157  it = entries.end() - 1;
158  }
159  else
160  {
161  // do a binary search to find the place
162  // where to insert:
163  it2 = Utilities::lower_bound(entries.begin(), entries.end(), col);
164 
165  // If this entry is a duplicate, continue
166  // immediately Insert at the right place
167  // in the vector. Vector grows
168  // automatically to fit elements. Always
169  // doubles its size.
170  if (*it2 != col)
171  it = entries.insert(it2, col);
172  else
173  it = it2;
174  }
175 
176  ++my_it;
177  // Now try to be smart and insert with
178  // bias in the direction we are
179  // walking. This has the advantage that
180  // for sorted lists, we always search in
181  // the right direction, what should
182  // decrease the work needed in here.
183  for (; my_it != end; ++my_it)
184  {
185  col = *my_it;
186  // need a special insertion command when
187  // we're at the end of the list
188  if (col > entries.back())
189  {
190  entries.push_back(col);
191  it = entries.end() - 1;
192  }
193  // search to the right (preferred search
194  // direction)
195  else if (col > *it)
196  {
197  it2 = Utilities::lower_bound(it++, entries.end(), col);
198  if (*it2 != col)
199  it = entries.insert(it2, col);
200  }
201  // search to the left
202  else if (col < *it)
203  {
204  it2 = Utilities::lower_bound(entries.begin(), it, col);
205  if (*it2 != col)
206  it = entries.insert(it2, col);
207  }
208  // if we're neither larger nor smaller,
209  // then this was a duplicate and we can
210  // just continue.
211  }
212 }
213 
214 
217 {
218  return entries.capacity() * sizeof(size_type) + sizeof(Line);
219 }
220 
221 
224  , have_entries(false)
225  , rowset(0)
226 {}
227 
228 
229 
232  , have_entries(false)
233  , rowset(0)
234 {
235  (void)s;
236  Assert(s.rows == 0 && s.cols == 0,
237  ExcMessage(
238  "This constructor can only be called if the provided argument "
239  "is the sparsity pattern for an empty matrix. This constructor can "
240  "not be used to copy-construct a non-empty sparsity pattern."));
241 }
242 
243 
244 
246  const size_type n,
247  const IndexSet &rowset_)
249  , have_entries(false)
250  , rowset(0)
251 {
252  reinit(m, n, rowset_);
253 }
254 
255 
257  : DynamicSparsityPattern(rowset_.size(), rowset_.size(), rowset_)
258 {}
259 
260 
263  , have_entries(false)
264  , rowset(0)
265 {
266  reinit(n, n);
267 }
268 
269 
270 
273 {
274  (void)s;
275  Assert(s.n_rows() == 0 && s.n_cols() == 0,
276  ExcMessage(
277  "This operator can only be called if the provided argument "
278  "is the sparsity pattern for an empty matrix. This operator can "
279  "not be used to copy a non-empty sparsity pattern."));
280 
281  Assert(n_rows() == 0 && n_cols() == 0,
282  ExcMessage("This operator can only be called if the current object is "
283  "empty."));
284 
285  return *this;
286 }
287 
288 
289 
290 void
292  const size_type n,
293  const IndexSet &rowset_)
294 {
295  resize(m, n);
296  have_entries = false;
297  rowset = rowset_;
298 
299  Assert(rowset.size() == 0 || rowset.size() == m,
300  ExcMessage(
301  "The IndexSet argument to this function needs to either "
302  "be empty (indicating the complete set of rows), or have size "
303  "equal to the desired number of rows as specified by the "
304  "first argument to this function. (Of course, the number "
305  "of indices in this IndexSet may be less than the number "
306  "of rows, but the *size* of the IndexSet must be equal.)"));
307 
308  std::vector<Line> new_lines(rowset.size() == 0 ? n_rows() :
309  rowset.n_elements());
310  lines.swap(new_lines);
311 }
312 
313 
314 
315 void
317 {}
318 
319 
320 
321 bool
323 {
324  return ((rows == 0) && (cols == 0));
325 }
326 
327 
328 
331 {
332  if (!have_entries)
333  return 0;
334 
335  size_type m = 0;
336  for (const auto &line : lines)
337  {
338  m = std::max(m, static_cast<size_type>(line.entries.size()));
339  }
340 
341  return m;
342 }
343 
344 
345 
346 void
348  const size_type &row,
349  const ArrayView<const size_type> &columns,
350  const bool indices_are_sorted)
351 {
352  add_entries(row, columns.begin(), columns.end(), indices_are_sorted);
353 }
354 
355 
356 
357 bool
359 {
362  Assert(
363  rowset.size() == 0 || rowset.is_element(i),
364  ExcMessage(
365  "The row IndexSet does not contain the index i. This sparsity pattern "
366  "object cannot know whether the entry (i, j) exists or not."));
367 
368  // Avoid a segmentation fault in below code if the row index happens to
369  // not be present in the IndexSet rowset:
370  if (!(rowset.size() == 0 || rowset.is_element(i)))
371  return false;
372 
373  if (!have_entries)
374  return false;
375 
376  const size_type rowindex =
377  rowset.size() == 0 ? i : rowset.index_within_set(i);
378 
379  return std::binary_search(lines[rowindex].entries.begin(),
380  lines[rowindex].entries.end(),
381  j);
382 }
383 
384 
385 
386 void
388 {
390 
391  // loop over all elements presently in the sparsity pattern and add the
392  // transpose element. note:
393  //
394  // 1. that the sparsity pattern changes which we work on, but not the present
395  // row
396  //
397  // 2. that the @p{add} function can be called on elements that already exist
398  // without any harm
399  for (size_type row = 0; row < lines.size(); ++row)
400  {
401  const size_type rowindex =
402  rowset.size() == 0 ? row : rowset.nth_index_in_set(row);
403 
404  for (const size_type row_entry : lines[row].entries)
405  // add the transpose entry if this is not the diagonal
406  if (rowindex != row_entry)
407  add(row_entry, rowindex);
408  }
409 }
410 
411 
412 
413 void
415 {
416  AssertIndexRange(row, n_rows());
417  if (!have_entries)
418  return;
419 
420  if (rowset.size() > 0 && !rowset.is_element(row))
421  return;
422 
423  const size_type rowindex =
424  rowset.size() == 0 ? row : rowset.index_within_set(row);
425 
426  AssertIndexRange(rowindex, lines.size());
427  lines[rowindex].entries = std::vector<size_type>();
428 }
429 
430 
431 
434 {
436  view.reinit(rows.n_elements(), this->n_cols());
437  AssertDimension(rows.size(), this->n_rows());
438 
439  const auto end = rows.end();
441  for (auto it = rows.begin(); it != end; ++it, ++view_row)
442  {
443  const size_type rowindex =
444  rowset.size() == 0 ? *it : rowset.index_within_set(*it);
445 
446  view.lines[view_row].entries = lines[rowindex].entries;
447  view.have_entries |= (lines[rowindex].entries.size() > 0);
448  }
449  return view;
450 }
451 
452 
453 
454 template <typename SparsityPatternTypeLeft, typename SparsityPatternTypeRight>
455 void
457  const SparsityPatternTypeLeft &sp_A,
458  const SparsityPatternTypeRight &sp_B)
459 {
460  Assert(sp_A.n_rows() == sp_B.n_rows(),
461  ExcDimensionMismatch(sp_A.n_rows(), sp_B.n_rows()));
462 
463  this->reinit(sp_A.n_cols(), sp_B.n_cols());
464  // we will go through all the
465  // rows in the matrix A, and for each column in a row we add the whole
466  // row of matrix B with that row number. This means that we will insert
467  // a lot of entries to each row, which is best handled by the
468  // DynamicSparsityPattern class.
469 
470  std::vector<size_type> new_cols;
471  new_cols.reserve(sp_B.max_entries_per_row());
472 
473  // C_{kl} = A_{ik} B_{il}
474  for (size_type i = 0; i < sp_A.n_rows(); ++i)
475  {
476  // get all column numbers from sp_B in a temporary vector:
477  new_cols.resize(sp_B.row_length(i));
478  {
479  const auto last_il = sp_B.end(i);
480  auto *col_ptr = new_cols.data();
481  for (auto il = sp_B.begin(i); il != last_il; ++il)
482  *col_ptr++ = il->column();
483  }
484  std::sort(new_cols.begin(), new_cols.end());
485 
486  // now for each k, add new_cols to the target sparsity
487  const auto last_ik = sp_A.end(i);
488  for (auto ik = sp_A.begin(i); ik != last_ik; ++ik)
489  this->add_entries(ik->column(), new_cols.begin(), new_cols.end(), true);
490  }
491 }
492 
493 
494 
495 template <typename SparsityPatternTypeLeft, typename SparsityPatternTypeRight>
496 void
498  const SparsityPatternTypeLeft &left,
499  const SparsityPatternTypeRight &right)
500 {
501  Assert(left.n_cols() == right.n_rows(),
502  ExcDimensionMismatch(left.n_cols(), right.n_rows()));
503 
504  this->reinit(left.n_rows(), right.n_cols());
505 
506  typename SparsityPatternTypeLeft::iterator it_left = left.begin(),
507  end_left = left.end();
508  for (; it_left != end_left; ++it_left)
509  {
510  const unsigned int j = it_left->column();
511 
512  // We are sitting on entry (i,j) of the left sparsity pattern. We then
513  // need to add all entries (i,k) to the final sparsity pattern where (j,k)
514  // exists in the right sparsity pattern -- i.e., we need to iterate over
515  // row j.
516  typename SparsityPatternTypeRight::iterator it_right = right.begin(j),
517  end_right = right.end(j);
518  for (; it_right != end_right; ++it_right)
519  this->add(it_left->row(), it_right->column());
520  }
521 }
522 
523 
524 
525 void
526 DynamicSparsityPattern::print(std::ostream &out) const
527 {
528  for (size_type row = 0; row < lines.size(); ++row)
529  {
530  out << '[' << (rowset.size() == 0 ? row : rowset.nth_index_in_set(row));
531 
532  for (const auto entry : lines[row].entries)
533  out << ',' << entry;
534 
535  out << ']' << std::endl;
536  }
537 
538  AssertThrow(out.fail() == false, ExcIO());
539 }
540 
541 
542 
543 void
545 {
546  for (size_type row = 0; row < lines.size(); ++row)
547  {
548  const size_type rowindex =
549  rowset.size() == 0 ? row : rowset.nth_index_in_set(row);
550 
551  for (const auto entry : lines[row].entries)
552  // while matrix entries are usually
553  // written (i,j), with i vertical and
554  // j horizontal, gnuplot output is
555  // x-y, that is we have to exchange
556  // the order of output
557  out << entry << " " << -static_cast<signed int>(rowindex) << std::endl;
558  }
559 
560 
561  AssertThrow(out.fail() == false, ExcIO());
562 }
563 
564 
565 
568 {
569  size_type b = 0;
570  for (size_type row = 0; row < lines.size(); ++row)
571  {
572  const size_type rowindex =
573  rowset.size() == 0 ? row : rowset.nth_index_in_set(row);
574 
575  for (const auto entry : lines[row].entries)
576  if (static_cast<size_type>(
577  std::abs(static_cast<int>(rowindex - entry))) > b)
578  b = std::abs(static_cast<signed int>(rowindex - entry));
579  }
580 
581  return b;
582 }
583 
584 
585 
588 {
589  if (!have_entries)
590  return 0;
591 
592  size_type n = 0;
593  for (const auto &line : lines)
594  {
595  n += line.entries.size();
596  }
597 
598  return n;
599 }
600 
601 
602 
603 IndexSet
605 {
606  std::set<types::global_dof_index> cols;
607  for (const auto &line : lines)
608  cols.insert(line.entries.begin(), line.entries.end());
609 
610  IndexSet res(this->n_cols());
611  res.add_indices(cols.begin(), cols.end());
612  return res;
613 }
614 
615 
616 
617 IndexSet
619 {
620  const IndexSet all_rows = complete_index_set(this->n_rows());
621  const IndexSet &locally_stored_rows = rowset.size() == 0 ? all_rows : rowset;
622 
623  std::vector<types::global_dof_index> rows;
624  auto line = lines.begin();
625  AssertDimension(locally_stored_rows.n_elements(), lines.size());
626  for (const auto row : locally_stored_rows)
627  {
628  if (line->entries.size() > 0)
629  rows.push_back(row);
630 
631  ++line;
632  }
633 
634  IndexSet res(this->n_rows());
635  res.add_indices(rows.begin(), rows.end());
636  return res;
637 }
638 
639 
640 
643 {
644  size_type mem = sizeof(DynamicSparsityPattern) +
646  sizeof(rowset);
647 
648  for (const auto &line : lines)
650 
651  return mem;
652 }
653 
654 
655 
659  const DynamicSparsityPattern::size_type col) const
660 {
661  AssertIndexRange(row, n_rows());
662  AssertIndexRange(col, n_cols());
663  Assert(rowset.size() == 0 || rowset.is_element(row), ExcInternalError());
664 
665  const DynamicSparsityPattern::size_type local_row =
666  rowset.size() != 0u ? rowset.index_within_set(row) : row;
667 
668  // now we need to do a binary search. Note that col indices are assumed to
669  // be sorted.
670  const auto &cols = lines[local_row].entries;
671  auto it = Utilities::lower_bound(cols.begin(), cols.end(), col);
672 
673  if ((it != cols.end()) && (*it == col))
674  return (it - cols.begin());
675  else
677 }
678 
679 
680 
681 // explicit instantiations
682 template void
684 template void
686  const size_type *,
687  const bool);
688 #ifndef DEAL_II_VECTOR_ITERATOR_IS_POINTER
689 template void
690 DynamicSparsityPattern::Line::add_entries(std::vector<size_type>::iterator,
691  std::vector<size_type>::iterator,
692  const bool);
693 template void
695  std::vector<size_type>::const_iterator,
696  std::vector<size_type>::const_iterator,
697  const bool);
698 #endif
699 
700 template void
702  const DynamicSparsityPattern &);
703 template void
705  const SparsityPattern &);
706 template void
708  const DynamicSparsityPattern &);
709 template void
711  const SparsityPattern &);
712 
713 template void
715  const SparsityPattern &);
716 template void
718  const SparsityPattern &);
719 template void
721  const DynamicSparsityPattern &);
722 template void
724  const DynamicSparsityPattern &);
725 
iterator begin() const
Definition: array_view.h:703
iterator end() const
Definition: array_view.h:712
DynamicSparsityPattern get_view(const IndexSet &rows) const
types::global_dof_index size_type
void compute_mmult_pattern(const SparsityPatternTypeLeft &left, const SparsityPatternTypeRight &right)
virtual void add_row_entries(const size_type &row, const ArrayView< const size_type > &columns, const bool indices_are_sorted=false) override
size_type column_index(const size_type row, const size_type col) const
DynamicSparsityPattern & operator=(const DynamicSparsityPattern &)
virtual void add_entries(const ArrayView< const std::pair< size_type, size_type >> &entries)
void print(std::ostream &out) const
void reinit(const size_type m, const size_type n, const IndexSet &rowset=IndexSet())
void clear_row(const size_type row)
void print_gnuplot(std::ostream &out) const
void compute_Tmmult_pattern(const SparsityPatternTypeLeft &left, const SparsityPatternTypeRight &right)
bool exists(const size_type i, const size_type j) const
void add(const size_type i, const size_type j)
size_type size() const
Definition: index_set.h:1761
size_type index_within_set(const size_type global_index) const
Definition: index_set.h:1986
size_type n_elements() const
Definition: index_set.h:1919
bool is_element(const size_type index) const
Definition: index_set.h:1879
size_type nth_index_in_set(const size_type local_index) const
Definition: index_set.h:1967
void add_indices(const ForwardIterator &begin, const ForwardIterator &end)
Definition: index_set.h:1816
virtual void resize(const size_type rows, const size_type cols)
size_type n_rows() const
size_type n_cols() const
#define DEAL_II_NAMESPACE_OPEN
Definition: config.h:477
#define DEAL_II_NAMESPACE_CLOSE
Definition: config.h:478
static ::ExceptionBase & ExcInternalError()
static ::ExceptionBase & ExcDimensionMismatch(std::size_t arg1, std::size_t arg2)
#define Assert(cond, exc)
Definition: exceptions.h:1631
#define AssertDimension(dim1, dim2)
Definition: exceptions.h:1820
#define AssertIndexRange(index, range)
Definition: exceptions.h:1888
static ::ExceptionBase & ExcIO()
static ::ExceptionBase & ExcMessage(std::string arg1)
static ::ExceptionBase & ExcNotQuadratic()
#define AssertThrow(cond, exc)
Definition: exceptions.h:1732
IndexSet complete_index_set(const IndexSet::size_type N)
Definition: index_set.h:1189
types::global_dof_index size_type
Definition: cuda_kernels.h:45
std::enable_if_t< std::is_fundamental_v< T >, std::size_t > memory_consumption(const T &t)
SymmetricTensor< 2, dim, Number > b(const Tensor< 2, dim, Number > &F)
VectorType::value_type * begin(VectorType &V)
VectorType::value_type * end(VectorType &V)
Iterator lower_bound(Iterator first, Iterator last, const T &val)
Definition: utilities.h:1008
const types::global_dof_index invalid_size_type
Definition: types.h:234
unsigned int global_dof_index
Definition: types.h:82
void add_entries(ForwardIterator begin, ForwardIterator end, const bool indices_are_sorted)