Reference documentation for deal.II version GIT 196b8d1939 2022-07-03 13:35:01+00:00
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utilities.cc
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2 //
3 // Copyright (C) 2005 - 2022 by the deal.II authors
4 //
5 // This file is part of the deal.II library.
6 //
7 // The deal.II library is free software; you can use it, redistribute
8 // it, and/or modify it under the terms of the GNU Lesser General
9 // Public License as published by the Free Software Foundation; either
10 // version 2.1 of the License, or (at your option) any later version.
11 // The full text of the license can be found in the file LICENSE.md at
12 // the top level directory of deal.II.
13 //
14 // ---------------------------------------------------------------------
15 
16 #include <deal.II/base/config.h>
17 
18 // It's necessary to include winsock2.h before thread_local_storage.h,
19 // because Intel implementation of TBB includes winsock.h,
20 // and we'll get a conflict between winsock.h and winsock2.h otherwise.
21 #ifdef DEAL_II_MSVC
22 # include <winsock2.h>
23 #endif
24 
26 #include <deal.II/base/mpi.h>
27 #include <deal.II/base/point.h>
29 #include <deal.II/base/utilities.h>
30 
32 #define BOOST_BIND_GLOBAL_PLACEHOLDERS
33 #include <boost/archive/iterators/base64_from_binary.hpp>
34 #include <boost/archive/iterators/binary_from_base64.hpp>
35 #include <boost/archive/iterators/transform_width.hpp>
36 #include <boost/iostreams/copy.hpp>
37 #include <boost/lexical_cast.hpp>
38 #include <boost/random.hpp>
39 #undef BOOST_BIND_GLOBAL_PLACEHOLDERS
41 
42 #include <algorithm>
43 #include <bitset>
44 #include <cctype>
45 #include <cerrno>
46 #include <cmath>
47 #include <cstddef>
48 #include <cstdio>
49 #include <ctime>
50 #include <fstream>
51 #include <iomanip>
52 #include <iostream>
53 #include <limits>
54 #include <sstream>
55 #include <string>
56 
57 #if defined(DEAL_II_HAVE_UNISTD_H) && defined(DEAL_II_HAVE_GETHOSTNAME)
58 # include <unistd.h>
59 #endif
60 
61 #ifndef DEAL_II_MSVC
62 # include <cstdlib>
63 #endif
64 
65 
66 #ifdef DEAL_II_WITH_TRILINOS
67 # ifdef DEAL_II_WITH_MPI
71 
72 # include <Epetra_MpiComm.h>
73 # include <Teuchos_DefaultComm.hpp>
74 # endif
75 # include <Epetra_SerialComm.h>
76 # include <Teuchos_RCP.hpp>
77 #endif
78 
80 
81 
82 namespace Utilities
83 {
85  unsigned int,
86  unsigned int,
87  << "When trying to convert " << arg1 << " to a string with "
88  << arg2 << " digits");
89  DeclException1(ExcInvalidNumber, unsigned int, << "Invalid number " << arg1);
91  std::string,
92  << "Can't convert the string " << arg1
93  << " to the desired type");
94 
95 
96  std::string
98  {
100  }
101 
102 
103  namespace
104  {
105  template <int dim,
106  typename Number,
107  int effective_dim,
108  typename LongDouble,
109  typename Integer>
110  std::vector<std::array<std::uint64_t, effective_dim>>
111  inverse_Hilbert_space_filling_curve_effective(
112  const std::vector<Point<dim, Number>> &points,
113  const Point<dim, Number> & bl,
114  const std::array<LongDouble, dim> & extents,
115  const std::bitset<dim> & valid_extents,
116  const int min_bits,
117  const Integer max_int)
118  {
119  std::vector<std::array<Integer, effective_dim>> int_points(points.size());
120 
121  for (unsigned int i = 0; i < points.size(); ++i)
122  {
123  // convert into integers:
124  unsigned int eff_d = 0;
125  for (unsigned int d = 0; d < dim; ++d)
126  if (valid_extents[d])
127  {
128  Assert(extents[d] > 0, ExcInternalError());
129  const LongDouble v = (static_cast<LongDouble>(points[i][d]) -
130  static_cast<LongDouble>(bl[d])) /
131  extents[d];
132  Assert(v >= 0. && v <= 1., ExcInternalError());
133  AssertIndexRange(eff_d, effective_dim);
134  int_points[i][eff_d] =
135  static_cast<Integer>(v * static_cast<LongDouble>(max_int));
136  ++eff_d;
137  }
138  }
139 
140  // note that we call this with "min_bits"
141  return inverse_Hilbert_space_filling_curve<effective_dim>(int_points,
142  min_bits);
143  }
144  } // namespace
145 
146  template <int dim, typename Number>
147  std::vector<std::array<std::uint64_t, dim>>
149  const std::vector<Point<dim, Number>> &points,
150  const int bits_per_dim)
151  {
152  using Integer = std::uint64_t;
153  // take floating point number hopefully with mantissa >= 64bit
154  using LongDouble = long double;
155 
156  // return if there is nothing to do
157  if (points.size() == 0)
158  return std::vector<std::array<std::uint64_t, dim>>();
159 
160  // get bounding box:
161  Point<dim, Number> bl = points[0], tr = points[0];
162  for (const auto &p : points)
163  for (unsigned int d = 0; d < dim; ++d)
164  {
165  const double cid = p[d];
166  bl[d] = std::min(cid, bl[d]);
167  tr[d] = std::max(cid, tr[d]);
168  }
169 
170  std::array<LongDouble, dim> extents;
171  std::bitset<dim> valid_extents;
172  for (unsigned int i = 0; i < dim; ++i)
173  {
174  extents[i] =
175  static_cast<LongDouble>(tr[i]) - static_cast<LongDouble>(bl[i]);
176  valid_extents[i] = (extents[i] > 0.);
177  }
178 
179  // make sure our conversion from fractional coordinates to
180  // Integers work as expected, namely our cast (LongDouble)max_int
181  const int min_bits =
182  std::min(bits_per_dim,
183  std::min(std::numeric_limits<Integer>::digits,
184  std::numeric_limits<LongDouble>::digits));
185 
186  // based on that get the maximum integer:
187  const Integer max_int = (min_bits == std::numeric_limits<Integer>::digits ?
189  (Integer(1) << min_bits) - 1);
190 
191  const unsigned int effective_dim = valid_extents.count();
192  if (effective_dim == dim)
193  {
194  return inverse_Hilbert_space_filling_curve_effective<dim,
195  Number,
196  dim,
197  LongDouble,
198  Integer>(
199  points, bl, extents, valid_extents, min_bits, max_int);
200  }
201 
202  // various degenerate cases
203  std::array<std::uint64_t, dim> zero_ind;
204  for (unsigned int d = 0; d < dim; ++d)
205  zero_ind[d] = 0;
206 
207  std::vector<std::array<std::uint64_t, dim>> ind(points.size(), zero_ind);
208  // manually check effective_dim == 1 and effective_dim == 2
209  if (dim == 3 && effective_dim == 2)
210  {
211  const auto ind2 =
212  inverse_Hilbert_space_filling_curve_effective<dim,
213  Number,
214  2,
215  LongDouble,
216  Integer>(
217  points, bl, extents, valid_extents, min_bits, max_int);
218 
219  for (unsigned int i = 0; i < ind.size(); ++i)
220  for (unsigned int d = 0; d < 2; ++d)
221  ind[i][d + 1] = ind2[i][d];
222 
223  return ind;
224  }
225  else if (effective_dim == 1)
226  {
227  const auto ind1 =
228  inverse_Hilbert_space_filling_curve_effective<dim,
229  Number,
230  1,
231  LongDouble,
232  Integer>(
233  points, bl, extents, valid_extents, min_bits, max_int);
234 
235  for (unsigned int i = 0; i < ind.size(); ++i)
236  ind[i][dim - 1] = ind1[i][0];
237 
238  return ind;
239  }
240 
241  // we should get here only if effective_dim == 0
242  Assert(effective_dim == 0, ExcInternalError());
243 
244  // if the bounding box is degenerate in all dimensions,
245  // can't do much but exit gracefully by setting index according
246  // to the index of each point so that there is no re-ordering
247  for (unsigned int i = 0; i < points.size(); ++i)
248  ind[i][dim - 1] = i;
249 
250  return ind;
251  }
252 
253 
254 
255  template <int dim>
256  std::vector<std::array<std::uint64_t, dim>>
258  const std::vector<std::array<std::uint64_t, dim>> &points,
259  const int bits_per_dim)
260  {
261  using Integer = std::uint64_t;
262 
263  std::vector<std::array<Integer, dim>> int_points(points);
264 
265  std::vector<std::array<Integer, dim>> res(int_points.size());
266 
267  // follow
268  // J. Skilling, Programming the Hilbert curve, AIP Conf. Proc. 707, 381
269  // (2004); http://dx.doi.org/10.1063/1.1751381 also see
270  // https://stackoverflow.com/questions/499166/mapping-n-dimensional-value-to-a-point-on-hilbert-curve
271  // https://gitlab.com/octopus-code/octopus/blob/develop/src/grid/hilbert.c
272  // https://github.com/trilinos/Trilinos/blob/master/packages/zoltan/src/hsfc/hsfc_hilbert.c
273  // (Zoltan_HSFC_InvHilbertXd)
274  // https://github.com/aditi137/Hilbert/blob/master/Hilbert/hilbert.cpp
275 
276  // now we can map to 1D coordinate stored in Transpose format
277  // adopt AxestoTranspose function from the paper, that
278  // transforms in-place between geometrical axes and Hilbert transpose.
279  // Example: b=5 bits for each of n=3 coordinates.
280  // 15-bit Hilbert integer = A B C D E F G H I J K L M N O is
281  // stored as its Transpose
282  // X[0] = A D G J M X[2]|
283  // X[1] = B E H K N <-------> | /X[1]
284  // X[2] = C F I L O axes |/
285  // high low 0------ X[0]
286 
287  // Depth of the Hilbert curve
288  Assert(bits_per_dim <= std::numeric_limits<Integer>::digits,
289  ExcMessage("This integer type can not hold " +
290  std::to_string(bits_per_dim) + " bits."));
291 
292  const Integer M = Integer(1) << (bits_per_dim - 1); // largest bit
293 
294  for (unsigned int index = 0; index < int_points.size(); ++index)
295  {
296  auto &X = int_points[index];
297  auto &L = res[index];
298 
299  // Inverse undo
300  for (Integer q = M; q > 1; q >>= 1)
301  {
302  const Integer p = q - 1;
303  for (unsigned int i = 0; i < dim; ++i)
304  {
305  // invert
306  if (X[i] & q)
307  {
308  X[0] ^= p;
309  }
310  // exchange
311  else
312  {
313  const Integer t = (X[0] ^ X[i]) & p;
314  X[0] ^= t;
315  X[i] ^= t;
316  }
317  }
318  }
319 
320  // Gray encode (inverse of decode)
321  for (unsigned int i = 1; i < dim; ++i)
322  X[i] ^= X[i - 1];
323 
324  Integer t = 0;
325  for (Integer q = M; q > 1; q >>= 1)
326  if (X[dim - 1] & q)
327  t ^= q - 1;
328  for (unsigned int i = 0; i < dim; ++i)
329  X[i] ^= t;
330 
331  // now we need to go from index stored in transpose format to
332  // consecutive format, which is better suited for comparators.
333  // we could interleave into some big unsigned int...
334  // https://www.forceflow.be/2013/10/07/morton-encodingdecoding-through-bit-interleaving-implementations/
335  // https://stackoverflow.com/questions/4431522/given-2-16-bit-ints-can-i-interleave-those-bits-to-form-a-single-32-bit-int
336  // ...but we would loose spatial resolution!
337 
338  // interleave using brute force, follow TransposetoLine from
339  // https://github.com/aditi137/Hilbert/blob/master/Hilbert/hilbert.cpp
340  {
341  Integer p = M;
342  unsigned int j = 0;
343  for (unsigned int i = 0; i < dim; ++i)
344  {
345  L[i] = 0;
346  // go through bits using a mask q
347  for (Integer q = M; q > 0; q >>= 1)
348  {
349  if (X[j] & p)
350  L[i] |= q;
351  if (++j == dim)
352  {
353  j = 0;
354  p >>= 1;
355  }
356  }
357  }
358  }
359 
360  } // end of the loop over points
361 
362  return res;
363  }
364 
365 
366 
367  template <int dim>
368  std::uint64_t
369  pack_integers(const std::array<std::uint64_t, dim> &index,
370  const int bits_per_dim)
371  {
372  using Integer = std::uint64_t;
373 
374  AssertIndexRange(bits_per_dim * dim, 65);
375  Assert(bits_per_dim > 0, ExcMessage("bits_per_dim should be positive"));
376 
377  const Integer mask = (Integer(1) << bits_per_dim) - 1;
378 
379  Integer res = 0;
380  for (unsigned int i = 0; i < dim; ++i)
381  {
382  // take bits_per_dim from each integer and shift them
383  const Integer v = (mask & index[dim - 1 - i]) << (bits_per_dim * i);
384  res |= v;
385  }
386  return res;
387  }
388 
389 
390 
391  std::string
392  compress(const std::string &input)
393  {
394 #ifdef DEAL_II_WITH_ZLIB
395  namespace bio = boost::iostreams;
396 
397  std::stringstream compressed;
398  std::stringstream origin(input);
399 
400  bio::filtering_streambuf<bio::input> out;
401  out.push(bio::gzip_compressor());
402  out.push(origin);
403  bio::copy(out, compressed);
404 
405  return compressed.str();
406 #else
407  return input;
408 #endif
409  }
410 
411 
412 
413  std::string
414  decompress(const std::string &compressed_input)
415  {
416 #ifdef DEAL_II_WITH_ZLIB
417  namespace bio = boost::iostreams;
418 
419  std::stringstream compressed(compressed_input);
420  std::stringstream decompressed;
421 
422  bio::filtering_streambuf<bio::input> out;
423  out.push(bio::gzip_decompressor());
424  out.push(compressed);
425  bio::copy(out, decompressed);
426 
427  return decompressed.str();
428 #else
429  return compressed_input;
430 #endif
431  }
432 
433 
434 
435  std::string
436  encode_base64(const std::vector<unsigned char> &binary_input)
437  {
438  using namespace boost::archive::iterators;
439  using It = base64_from_binary<
440  transform_width<std::vector<unsigned char>::const_iterator, 6, 8>>;
441  auto base64 = std::string(It(binary_input.begin()), It(binary_input.end()));
442  // Add padding.
443  return base64.append((3 - binary_input.size() % 3) % 3, '=');
444  }
445 
446 
447 
448  std::vector<unsigned char>
449  decode_base64(const std::string &base64_input)
450  {
451  using namespace boost::archive::iterators;
452  using It =
453  transform_width<binary_from_base64<std::string::const_iterator>, 8, 6>;
454  auto binary = std::vector<unsigned char>(It(base64_input.begin()),
455  It(base64_input.end()));
456  // Remove padding.
457  auto length = base64_input.size();
458  if (binary.size() > 2 && base64_input[length - 1] == '=' &&
459  base64_input[length - 2] == '=')
460  {
461  binary.erase(binary.end() - 2, binary.end());
462  }
463  else if (binary.size() > 1 && base64_input[length - 1] == '=')
464  {
465  binary.erase(binary.end() - 1, binary.end());
466  }
467  return binary;
468  }
469 
470 
471 
472  std::string
473  int_to_string(const unsigned int value, const unsigned int digits)
474  {
475  return to_string(value, digits);
476  }
477 
478 
479 
480  template <typename number>
481  std::string
482  to_string(const number value, const unsigned int digits)
483  {
484  // For integer data types, use the standard std::to_string()
485  // function. On the other hand, that function is defined in terms
486  // of std::sprintf, which does not use the usual std::iostream
487  // interface and tries to render floating point numbers in awkward
488  // ways (see
489  // https://en.cppreference.com/w/cpp/string/basic_string/to_string). So
490  // resort to boost::lexical_cast for all other types (in
491  // particular for floating point types.
492  std::string lc_string = (std::is_integral<number>::value ?
493  std::to_string(value) :
494  boost::lexical_cast<std::string>(value));
495 
496  if ((digits != numbers::invalid_unsigned_int) &&
497  (lc_string.size() < digits))
498  {
499  // We have to add the padding zeroes in front of the number
500  const unsigned int padding_position = (lc_string[0] == '-') ? 1 : 0;
501 
502  const std::string padding(digits - lc_string.size(), '0');
503  lc_string.insert(padding_position, padding);
504  }
505 
506  return lc_string;
507  }
508 
509 
510 
511  std::string
512  replace_in_string(const std::string &input,
513  const std::string &from,
514  const std::string &to)
515  {
516  if (from.empty())
517  return input;
518 
519  std::string out = input;
520  std::string::size_type pos = out.find(from);
521 
522  while (pos != std::string::npos)
523  {
524  out.replace(pos, from.size(), to);
525  pos = out.find(from, pos + to.size());
526  }
527  return out;
528  }
529 
530  std::string
531  trim(const std::string &input)
532  {
533  std::string::size_type left = 0;
534  std::string::size_type right = input.size() > 0 ? input.size() - 1 : 0;
535 
536  for (; left < input.size(); ++left)
537  {
538  if (std::isspace(input[left]) == 0)
539  {
540  break;
541  }
542  }
543 
544  for (; right >= left; --right)
545  {
546  if (std::isspace(input[right]) == 0)
547  {
548  break;
549  }
550  }
551 
552  return std::string(input, left, right - left + 1);
553  }
554 
555 
556 
557  std::string
558  dim_string(const int dim, const int spacedim)
559  {
560  if (dim == spacedim)
561  return int_to_string(dim);
562  else
563  return int_to_string(dim) + "," + int_to_string(spacedim);
564  }
565 
566 
567  unsigned int
568  needed_digits(const unsigned int max_number)
569  {
570  if (max_number > 0)
571  return static_cast<int>(
572  std::ceil(std::log10(std::fabs(max_number + 0.1))));
573 
574  return 1;
575  }
576 
577 
578 
579  template <typename Number>
580  Number
581  truncate_to_n_digits(const Number number, const unsigned int n_digits)
582  {
583  AssertThrow(n_digits >= 1, ExcMessage("invalid parameter."));
584 
585  if (!(std::fabs(number) > std::numeric_limits<Number>::min()))
586  return number;
587 
588  const int order =
589  static_cast<int>(std::floor(std::log10(std::fabs(number))));
590 
591  const int shift = -order + static_cast<int>(n_digits) - 1;
592 
593  Assert(shift <= static_cast<int>(std::floor(
595  ExcMessage(
596  "Overflow. Use a smaller value for n_digits and/or make sure "
597  "that the absolute value of 'number' does not become too small."));
598 
599  const Number factor = std::pow(10.0, static_cast<Number>(shift));
600 
601  const Number number_cutoff = std::trunc(number * factor) / factor;
602 
603  return number_cutoff;
604  }
605 
606 
607  int
608  string_to_int(const std::string &s_)
609  {
610  // trim whitespace on either side of the text if necessary
611  std::string s = s_;
612  while ((s.size() > 0) && (s[0] == ' '))
613  s.erase(s.begin());
614  while ((s.size() > 0) && (s.back() == ' '))
615  s.erase(s.end() - 1);
616 
617  // Now convert and see whether we succeed. Note that strtol only
618  // touches errno if an error occurred, so if we want to check
619  // whether an error happened, we need to make sure that errno==0
620  // before calling strtol since otherwise it may be that the
621  // conversion succeeds and that errno remains at the value it
622  // was before, whatever that was.
623  char *p;
624  errno = 0;
625  const int i = std::strtol(s.c_str(), &p, 10);
626 
627  // We have an error if one of the following conditions is true:
628  // - strtol sets errno != 0
629  // - The original string was empty (we could have checked that
630  // earlier already)
631  // - The string has non-zero length and strtol converted the
632  // first part to something useful, but stopped converting short
633  // of the terminating '\0' character. This happens, for example,
634  // if the given string is "1234 abc".
635  AssertThrow(!((errno != 0) || (s.size() == 0) ||
636  ((s.size() > 0) && (*p != '\0'))),
637  ExcMessage("Can't convert <" + s + "> to an integer."));
638 
639  return i;
640  }
641 
642 
643 
644  std::vector<int>
645  string_to_int(const std::vector<std::string> &s)
646  {
647  std::vector<int> tmp(s.size());
648  for (unsigned int i = 0; i < s.size(); ++i)
649  tmp[i] = string_to_int(s[i]);
650  return tmp;
651  }
652 
653 
654 
655  double
656  string_to_double(const std::string &s_)
657  {
658  // trim whitespace on either side of the text if necessary
659  std::string s = s_;
660  while ((s.size() > 0) && (s[0] == ' '))
661  s.erase(s.begin());
662  while ((s.size() > 0) && (s.back() == ' '))
663  s.erase(s.end() - 1);
664 
665  // Now convert and see whether we succeed. Note that strtol only
666  // touches errno if an error occurred, so if we want to check
667  // whether an error happened, we need to make sure that errno==0
668  // before calling strtol since otherwise it may be that the
669  // conversion succeeds and that errno remains at the value it
670  // was before, whatever that was.
671  char *p;
672  errno = 0;
673  const double d = std::strtod(s.c_str(), &p);
674 
675  // We have an error if one of the following conditions is true:
676  // - strtod sets errno != 0
677  // - The original string was empty (we could have checked that
678  // earlier already)
679  // - The string has non-zero length and strtod converted the
680  // first part to something useful, but stopped converting short
681  // of the terminating '\0' character. This happens, for example,
682  // if the given string is "1.234 abc".
683  AssertThrow(!((errno != 0) || (s.size() == 0) ||
684  ((s.size() > 0) && (*p != '\0'))),
685  ExcMessage("Can't convert <" + s + "> to a double."));
686 
687  return d;
688  }
689 
690 
691 
692  std::vector<double>
693  string_to_double(const std::vector<std::string> &s)
694  {
695  std::vector<double> tmp(s.size());
696  for (unsigned int i = 0; i < s.size(); ++i)
697  tmp[i] = string_to_double(s[i]);
698  return tmp;
699  }
700 
701 
702 
703  std::vector<std::string>
704  split_string_list(const std::string &s, const std::string &delimiter)
705  {
706  // keep the currently remaining part of the input string in 'tmp' and
707  // keep chopping elements of the list off the front
708  std::string tmp = s;
709 
710  // as discussed in the documentation, eat whitespace from the end
711  // of the string
712  while (tmp.size() != 0 && tmp.back() == ' ')
713  tmp.erase(tmp.size() - 1, 1);
714 
715  // split the input list until it is empty. since in every iteration
716  // 'tmp' is what's left of the string after the next delimiter,
717  // and since we've stripped trailing space already, 'tmp' will
718  // be empty at one point if 's' ended in a delimiter, even if
719  // there was space after the last delimiter. this matches what's
720  // discussed in the documentation
721  std::vector<std::string> split_list;
722  while (tmp.size() != 0)
723  {
724  std::string name;
725  name = tmp;
726 
727  if (name.find(delimiter) != std::string::npos)
728  {
729  name.erase(name.find(delimiter), std::string::npos);
730  tmp.erase(0, tmp.find(delimiter) + delimiter.size());
731  }
732  else
733  tmp = "";
734 
735  // strip spaces from this element's front and end
736  while ((name.size() != 0) && (name[0] == ' '))
737  name.erase(0, 1);
738  while (name.size() != 0 && name.back() == ' ')
739  name.erase(name.size() - 1, 1);
740 
741  split_list.push_back(name);
742  }
743 
744  return split_list;
745  }
746 
747 
748  std::vector<std::string>
749  split_string_list(const std::string &s, const char delimiter)
750  {
751  std::string d = ",";
752  d[0] = delimiter;
753  return split_string_list(s, d);
754  }
755 
756 
757  std::vector<std::string>
758  break_text_into_lines(const std::string &original_text,
759  const unsigned int width,
760  const char delimiter)
761  {
762  std::string text = original_text;
763  std::vector<std::string> lines;
764 
765  // remove trailing spaces
766  while ((text.size() != 0) && (text.back() == delimiter))
767  text.erase(text.size() - 1, 1);
768 
769  // then split the text into lines
770  while (text.size() != 0)
771  {
772  // in each iteration, first remove
773  // leading spaces
774  while ((text.size() != 0) && (text[0] == delimiter))
775  text.erase(0, 1);
776 
777  std::size_t pos_newline = text.find_first_of('\n', 0);
778  if (pos_newline != std::string::npos && pos_newline <= width)
779  {
780  std::string line(text, 0, pos_newline);
781  while ((line.size() != 0) && (line.back() == delimiter))
782  line.erase(line.size() - 1, 1);
783  lines.push_back(line);
784  text.erase(0, pos_newline + 1);
785  continue;
786  }
787 
788  // if we can fit everything into one
789  // line, then do so. otherwise, we have
790  // to keep breaking
791  if (text.size() < width)
792  {
793  // remove trailing spaces
794  while ((text.size() != 0) && (text.back() == delimiter))
795  text.erase(text.size() - 1, 1);
796  lines.push_back(text);
797  text = "";
798  }
799  else
800  {
801  // starting at position width, find the
802  // location of the previous space, so
803  // that we can break around there
804  int location = std::min<int>(width, text.size() - 1);
805  for (; location > 0; --location)
806  if (text[location] == delimiter)
807  break;
808 
809  // if there are no spaces, then try if
810  // there are spaces coming up
811  if (location == 0)
812  for (location = std::min<int>(width, text.size() - 1);
813  location < static_cast<int>(text.size());
814  ++location)
815  if (text[location] == delimiter)
816  break;
817 
818  // now take the text up to the found
819  // location and put it into a single
820  // line, and remove it from 'text'
821  std::string line(text, 0, location);
822  while ((line.size() != 0) && (line.back() == delimiter))
823  line.erase(line.size() - 1, 1);
824  lines.push_back(line);
825  text.erase(0, location);
826  }
827  }
828 
829  return lines;
830  }
831 
832 
833 
834  bool
835  match_at_string_start(const std::string &name, const std::string &pattern)
836  {
837  if (pattern.size() > name.size())
838  return false;
839 
840  for (unsigned int i = 0; i < pattern.size(); ++i)
841  if (pattern[i] != name[i])
842  return false;
843 
844  return true;
845  }
846 
847 
848 
849  std::pair<int, unsigned int>
850  get_integer_at_position(const std::string &name, const unsigned int position)
851  {
852  Assert(position < name.size(), ExcInternalError());
853 
854  const std::string test_string(name.begin() + position, name.end());
855 
856  std::istringstream str(test_string);
857 
858  int i;
859  if (str >> i)
860  {
861  // compute the number of
862  // digits of i. assuming it
863  // is less than 8 is likely
864  // ok
865  if (i < 10)
866  return std::make_pair(i, 1U);
867  else if (i < 100)
868  return std::make_pair(i, 2U);
869  else if (i < 1000)
870  return std::make_pair(i, 3U);
871  else if (i < 10000)
872  return std::make_pair(i, 4U);
873  else if (i < 100000)
874  return std::make_pair(i, 5U);
875  else if (i < 1000000)
876  return std::make_pair(i, 6U);
877  else if (i < 10000000)
878  return std::make_pair(i, 7U);
879  else
880  {
881  Assert(false, ExcNotImplemented());
882  return std::make_pair(-1, numbers::invalid_unsigned_int);
883  }
884  }
885  else
886  return std::make_pair(-1, numbers::invalid_unsigned_int);
887  }
888 
889 
890 
891  double
892  generate_normal_random_number(const double a, const double sigma)
893  {
894  // if no noise: return now
895  if (sigma == 0)
896  return a;
897 
898  // we would want to use rand(), but that function is not reentrant
899  // in a thread context. one could use rand_r, but this does not
900  // produce reproducible results between threads either (though at
901  // least it is reentrant). these two approaches being
902  // non-workable, use a thread-local random number generator here.
903  // we could use std::mt19937 but doing so results in compiler-dependent
904  // output.
905  static Threads::ThreadLocalStorage<boost::mt19937> random_number_generator;
906  return boost::normal_distribution<>(a,
907  sigma)(random_number_generator.get());
908  }
909 
910 
911 
912  namespace System
913  {
914 #ifdef __linux__
915 
916  double
917  get_cpu_load()
918  {
919  std::ifstream cpuinfo;
920  cpuinfo.open("/proc/loadavg");
921 
922  AssertThrow(cpuinfo.fail() == false, ExcIO());
923 
924  double load;
925  cpuinfo >> load;
926 
927  return load;
928  }
929 
930 #else
931 
932  double
934  {
935  return 0.;
936  }
937 
938 #endif
939 
940  const std::string
942  {
944  {
945  case 0:
946  return "disabled";
947  case 128:
948 #ifdef __ALTIVEC__
949  return "AltiVec";
950 #else
951  return "SSE2";
952 #endif
953  case 256:
954  return "AVX";
955  case 512:
956  return "AVX512";
957  default:
958  AssertThrow(false,
960  "Invalid DEAL_II_VECTORIZATION_WIDTH_IN_BITS."));
961  return "ERROR";
962  }
963  }
964 
965 
966  void
968  {
969  stats.VmPeak = stats.VmSize = stats.VmHWM = stats.VmRSS = 0;
970 
971  // parsing /proc/self/stat would be a
972  // lot easier, but it does not contain
973  // VmHWM, so we use /status instead.
974 #ifdef __linux__
975  std::ifstream file("/proc/self/status");
976  std::string line;
977  std::string name;
978  while (!file.eof())
979  {
980  file >> name;
981  if (name == "VmPeak:")
982  file >> stats.VmPeak;
983  else if (name == "VmSize:")
984  file >> stats.VmSize;
985  else if (name == "VmHWM:")
986  file >> stats.VmHWM;
987  else if (name == "VmRSS:")
988  {
989  file >> stats.VmRSS;
990  break; // this is always the last entry
991  }
992 
993  getline(file, line);
994  }
995 #endif
996  }
997 
998 
999 
1000  std::string
1002  {
1003 #if defined(DEAL_II_HAVE_UNISTD_H) && defined(DEAL_II_HAVE_GETHOSTNAME)
1004  const unsigned int N = 1024;
1005  char hostname[N];
1006  gethostname(&(hostname[0]), N - 1);
1007 #else
1008  std::string hostname("unknown");
1009 #endif
1010  return hostname;
1011  }
1012 
1013 
1014 
1015  std::string
1017  {
1018  std::time_t time1 = std::time(nullptr);
1019  std::tm * time = std::localtime(&time1);
1020 
1021  std::ostringstream o;
1022  o << time->tm_hour << ":" << (time->tm_min < 10 ? "0" : "")
1023  << time->tm_min << ":" << (time->tm_sec < 10 ? "0" : "")
1024  << time->tm_sec;
1025 
1026  return o.str();
1027  }
1028 
1029 
1030 
1031  std::string
1033  {
1034  std::time_t time1 = std::time(nullptr);
1035  std::tm * time = std::localtime(&time1);
1036 
1037  std::ostringstream o;
1038  o << time->tm_year + 1900 << "/" << time->tm_mon + 1 << "/"
1039  << time->tm_mday;
1040 
1041  return o.str();
1042  }
1043 
1044 
1045 
1046  void
1047  posix_memalign(void **memptr, std::size_t alignment, std::size_t size)
1048  {
1049 #ifndef DEAL_II_MSVC
1050  const int ierr = ::posix_memalign(memptr, alignment, size);
1051 
1052  AssertThrow(ierr == 0, ExcOutOfMemory(size));
1053  AssertThrow(*memptr != nullptr, ExcOutOfMemory(size));
1054 #else
1055  // Windows does not appear to have posix_memalign. just use the
1056  // regular malloc in that case
1057  *memptr = malloc(size);
1058  (void)alignment;
1059  AssertThrow(*memptr != 0, ExcOutOfMemory(size));
1060 #endif
1061  }
1062 
1063 
1064 
1065  bool
1067  {
1069  }
1070  } // namespace System
1071 
1072 
1073 #ifdef DEAL_II_WITH_TRILINOS
1074 
1075  namespace Trilinos
1076  {
1077  const Epetra_Comm &
1079  {
1080 # ifdef DEAL_II_WITH_MPI
1081  static Teuchos::RCP<Epetra_MpiComm> communicator =
1082  Teuchos::rcp(new Epetra_MpiComm(MPI_COMM_WORLD), true);
1083 # else
1084  static Teuchos::RCP<Epetra_SerialComm> communicator =
1085  Teuchos::rcp(new Epetra_SerialComm(), true);
1086 # endif
1087 
1088  return *communicator;
1089  }
1090 
1091 
1092 
1093  const Teuchos::RCP<const Teuchos::Comm<int>> &
1095  {
1096 # ifdef DEAL_II_WITH_MPI
1097  static auto communicator = Teuchos::RCP<const Teuchos::Comm<int>>(
1098  new Teuchos::MpiComm<int>(MPI_COMM_SELF));
1099 # else
1100  static auto communicator =
1101  Teuchos::RCP<const Teuchos::Comm<int>>(new Teuchos::Comm<int>());
1102 # endif
1103 
1104  return communicator;
1105  }
1106 
1107 
1108 
1109  const Epetra_Comm &
1111  {
1112 # ifdef DEAL_II_WITH_MPI
1113  static Teuchos::RCP<Epetra_MpiComm> communicator =
1114  Teuchos::rcp(new Epetra_MpiComm(MPI_COMM_SELF), true);
1115 # else
1116  static Teuchos::RCP<Epetra_SerialComm> communicator =
1117  Teuchos::rcp(new Epetra_SerialComm(), true);
1118 # endif
1119 
1120  return *communicator;
1121  }
1122 
1123 
1124 
1125  Epetra_Comm *
1126  duplicate_communicator(const Epetra_Comm &communicator)
1127  {
1128 # ifdef DEAL_II_WITH_MPI
1129 
1130  // see if the communicator is in fact a
1131  // parallel MPI communicator; if so,
1132  // return a duplicate of it
1133  const Epetra_MpiComm *mpi_comm =
1134  dynamic_cast<const Epetra_MpiComm *>(&communicator);
1135  if (mpi_comm != nullptr)
1136  return new Epetra_MpiComm(
1137  Utilities::MPI::duplicate_communicator(mpi_comm->GetMpiComm()));
1138 # endif
1139 
1140  // if we don't support MPI, or if the
1141  // communicator in question was in fact
1142  // not an MPI communicator, return a
1143  // copy of the same object again
1144  Assert(dynamic_cast<const Epetra_SerialComm *>(&communicator) != nullptr,
1145  ExcInternalError());
1146  return new Epetra_SerialComm(
1147  dynamic_cast<const Epetra_SerialComm &>(communicator));
1148  }
1149 
1150 
1151 
1152  void
1153  destroy_communicator(Epetra_Comm &communicator)
1154  {
1155  // save the communicator, reset the map, and delete the communicator if
1156  // this whole thing was created as an MPI communicator
1157 # ifdef DEAL_II_WITH_MPI
1158  Epetra_MpiComm *mpi_comm = dynamic_cast<Epetra_MpiComm *>(&communicator);
1159  if (mpi_comm != nullptr)
1160  {
1161  MPI_Comm comm = mpi_comm->GetMpiComm();
1162  *mpi_comm = Epetra_MpiComm(MPI_COMM_SELF);
1163 
1165  }
1166 # endif
1167  }
1168 
1169 
1170 
1171  unsigned int
1172  get_n_mpi_processes(const Epetra_Comm &mpi_communicator)
1173  {
1174  return mpi_communicator.NumProc();
1175  }
1176 
1177 
1178  unsigned int
1179  get_this_mpi_process(const Epetra_Comm &mpi_communicator)
1180  {
1181  return static_cast<unsigned int>(mpi_communicator.MyPID());
1182  }
1183 
1184 
1185 
1186  Epetra_Map
1187  duplicate_map(const Epetra_BlockMap &map, const Epetra_Comm &comm)
1188  {
1189  if (map.LinearMap() == true)
1190  {
1191  // each processor stores a
1192  // contiguous range of
1193  // elements in the
1194  // following constructor
1195  // call
1196  return Epetra_Map(map.NumGlobalElements(),
1197  map.NumMyElements(),
1198  map.IndexBase(),
1199  comm);
1200  }
1201  else
1202  {
1203  // the range is not
1204  // contiguous
1205  return Epetra_Map(map.NumGlobalElements(),
1206  map.NumMyElements(),
1207  map.MyGlobalElements(),
1208  0,
1209  comm);
1210  }
1211  }
1212  } // namespace Trilinos
1213 
1214 #endif
1215 
1216 #ifndef DOXYGEN
1217  template std::string
1218  to_string<int>(int, unsigned int);
1219  template std::string
1220  to_string<long int>(long int, unsigned int);
1221  template std::string
1222  to_string<long long int>(long long int, unsigned int);
1223  template std::string
1224  to_string<unsigned int>(unsigned int, unsigned int);
1225  template std::string
1226  to_string<unsigned long int>(unsigned long int, unsigned int);
1227  template std::string
1228  to_string<unsigned long long int>(unsigned long long int, unsigned int);
1229  template std::string
1230  to_string<float>(float, unsigned int);
1231  template std::string
1232  to_string<double>(double, unsigned int);
1233  template std::string
1234  to_string<long double>(long double, unsigned int);
1235 
1236  template double
1237  truncate_to_n_digits(const double, const unsigned int);
1238  template float
1239  truncate_to_n_digits(const float, const unsigned int);
1240 
1241  template std::vector<std::array<std::uint64_t, 1>>
1242  inverse_Hilbert_space_filling_curve<1, double>(
1243  const std::vector<Point<1, double>> &,
1244  const int);
1245  template std::vector<std::array<std::uint64_t, 1>>
1246  inverse_Hilbert_space_filling_curve<1>(
1247  const std::vector<std::array<std::uint64_t, 1>> &,
1248  const int);
1249  template std::vector<std::array<std::uint64_t, 2>>
1250  inverse_Hilbert_space_filling_curve<2, double>(
1251  const std::vector<Point<2, double>> &,
1252  const int);
1253  template std::vector<std::array<std::uint64_t, 2>>
1254  inverse_Hilbert_space_filling_curve<2>(
1255  const std::vector<std::array<std::uint64_t, 2>> &,
1256  const int);
1257  template std::vector<std::array<std::uint64_t, 3>>
1258  inverse_Hilbert_space_filling_curve<3, double>(
1259  const std::vector<Point<3, double>> &,
1260  const int);
1261  template std::vector<std::array<std::uint64_t, 3>>
1262  inverse_Hilbert_space_filling_curve<3>(
1263  const std::vector<std::array<std::uint64_t, 3>> &,
1264  const int);
1265 
1266  template std::uint64_t
1267  pack_integers<1>(const std::array<std::uint64_t, 1> &, const int);
1268  template std::uint64_t
1269  pack_integers<2>(const std::array<std::uint64_t, 2> &, const int);
1270  template std::uint64_t
1271  pack_integers<3>(const std::array<std::uint64_t, 3> &, const int);
1272 
1273 #endif
1274 
1275 } // namespace Utilities
1276 
A class that provides a separate storage location on each thread that accesses the object.
#define DEAL_II_NAMESPACE_OPEN
Definition: config.h:442
#define DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
Definition: config.h:456
#define DEAL_II_PACKAGE_VERSION
Definition: config.h:26
#define DEAL_II_VECTORIZATION_WIDTH_IN_BITS
Definition: config.h:127
#define DEAL_II_NAMESPACE_CLOSE
Definition: config.h:443
#define DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
Definition: config.h:495
#define DEAL_II_PACKAGE_NAME
Definition: config.h:24
static ::ExceptionBase & ExcInternalError()
static ::ExceptionBase & ExcOutOfMemory(std::size_t arg1)
#define Assert(cond, exc)
Definition: exceptions.h:1473
std::string to_string(const T &t)
Definition: patterns.h:2403
static ::ExceptionBase & ExcNotImplemented()
static ::ExceptionBase & ExcCantConvertString(std::string arg1)
#define DeclException2(Exception2, type1, type2, outsequence)
Definition: exceptions.h:532
#define AssertIndexRange(index, range)
Definition: exceptions.h:1732
static ::ExceptionBase & ExcIO()
static ::ExceptionBase & ExcInvalidNumber(unsigned int arg1)
#define DeclException1(Exception1, type1, outsequence)
Definition: exceptions.h:509
static ::ExceptionBase & ExcInvalidNumber2StringConversersion(unsigned int arg1, unsigned int arg2)
static ::ExceptionBase & ExcMessage(std::string arg1)
#define AssertThrow(cond, exc)
Definition: exceptions.h:1583
Expression fabs(const Expression &x)
Expression ceil(const Expression &x)
Expression floor(const Expression &x)
Expression log10(const Expression &x)
void shift(const Tensor< 1, spacedim > &shift_vector, Triangulation< dim, spacedim > &triangulation)
Definition: grid_tools.cc:2050
static const char L
static const char N
types::global_dof_index size_type
Definition: cuda_kernels.h:45
SymmetricTensor< 2, dim, Number > d(const Tensor< 2, dim, Number > &F, const Tensor< 2, dim, Number > &dF_dt)
void malloc(T *&pointer, const unsigned int n_elements)
Definition: cuda.h:85
void free_communicator(MPI_Comm &mpi_communicator)
Definition: mpi.cc:199
bool job_supports_mpi()
Definition: mpi.cc:1027
MPI_Comm duplicate_communicator(const MPI_Comm &mpi_communicator)
Definition: mpi.cc:188
void get_memory_stats(MemoryStats &stats)
Definition: utilities.cc:967
std::string get_hostname()
Definition: utilities.cc:1001
std::string get_time()
Definition: utilities.cc:1016
void posix_memalign(void **memptr, std::size_t alignment, std::size_t size)
Definition: utilities.cc:1047
double get_cpu_load()
Definition: utilities.cc:933
bool job_supports_mpi()
Definition: utilities.cc:1066
const std::string get_current_vectorization_level()
Definition: utilities.cc:941
std::string get_date()
Definition: utilities.cc:1032
void destroy_communicator(Epetra_Comm &communicator)
Definition: utilities.cc:1153
Epetra_Map duplicate_map(const Epetra_BlockMap &map, const Epetra_Comm &comm)
Definition: utilities.cc:1187
unsigned int get_this_mpi_process(const Epetra_Comm &mpi_communicator)
Definition: utilities.cc:1179
unsigned int get_n_mpi_processes(const Epetra_Comm &mpi_communicator)
Definition: utilities.cc:1172
const Epetra_Comm & comm_self()
Definition: utilities.cc:1110
const Teuchos::RCP< const Teuchos::Comm< int > > & tpetra_comm_self()
Definition: utilities.cc:1094
Epetra_Comm * duplicate_communicator(const Epetra_Comm &communicator)
Definition: utilities.cc:1126
const Epetra_Comm & comm_world()
Definition: utilities.cc:1078
std::vector< std::string > split_string_list(const std::string &s, const std::string &delimiter=",")
Definition: utilities.cc:704
Number truncate_to_n_digits(const Number number, const unsigned int n_digits)
Definition: utilities.cc:581
std::string dim_string(const int dim, const int spacedim)
Definition: utilities.cc:558
std::uint64_t pack_integers(const std::array< std::uint64_t, dim > &index, const int bits_per_dim)
Definition: utilities.cc:369
std::pair< int, unsigned int > get_integer_at_position(const std::string &name, const unsigned int position)
Definition: utilities.cc:850
std::string encode_base64(const std::vector< unsigned char > &binary_input)
Definition: utilities.cc:436
std::vector< std::array< std::uint64_t, dim > > inverse_Hilbert_space_filling_curve(const std::vector< Point< dim, Number >> &points, const int bits_per_dim=64)
Definition: utilities.cc:148
std::string replace_in_string(const std::string &input, const std::string &from, const std::string &to)
Definition: utilities.cc:512
std::vector< unsigned char > decode_base64(const std::string &base64_input)
Definition: utilities.cc:449
std::vector< std::string > break_text_into_lines(const std::string &original_text, const unsigned int width, const char delimiter=' ')
Definition: utilities.cc:758
std::string to_string(const number value, const unsigned int digits=numbers::invalid_unsigned_int)
Definition: utilities.cc:482
std::string compress(const std::string &input)
Definition: utilities.cc:392
std::string int_to_string(const unsigned int value, const unsigned int digits=numbers::invalid_unsigned_int)
Definition: utilities.cc:473
bool match_at_string_start(const std::string &name, const std::string &pattern)
Definition: utilities.cc:835
std::string decompress(const std::string &compressed_input)
Definition: utilities.cc:414
unsigned int needed_digits(const unsigned int max_number)
Definition: utilities.cc:568
double string_to_double(const std::string &s)
Definition: utilities.cc:656
std::string dealii_version_string()
Definition: utilities.cc:97
std::string trim(const std::string &input)
Definition: utilities.cc:531
double generate_normal_random_number(const double a, const double sigma)
Definition: utilities.cc:892
int string_to_int(const std::string &s)
Definition: utilities.cc:608
void copy(const T *begin, const T *end, U *dest)
static const unsigned int invalid_unsigned_int
Definition: types.h:201
unsigned long int VmRSS
Definition: utilities.h:923
unsigned long int VmPeak
Definition: utilities.h:907
unsigned long int VmSize
Definition: utilities.h:912
unsigned long int VmHWM
Definition: utilities.h:917
const MPI_Comm & comm