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EpetraExt_XMLReader.cpp
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43 
44 #include "EpetraExt_ConfigDefs.h"
45 #ifdef HAVE_MPI
46 #include "Epetra_MpiComm.h"
47 #include "mpi.h"
48 #else
49 #include "Epetra_SerialComm.h"
50 #endif
51 #include "EpetraExt_XMLReader.h"
52 #include "Teuchos_ParameterList.hpp"
53 #include "Teuchos_RCP.hpp"
54 #include "Teuchos_XMLObject.hpp"
55 #include "Teuchos_StringInputSource.hpp"
56 #include "Teuchos_FileInputSource.hpp"
57 #include "Teuchos_ParameterList.hpp"
58 #include "Teuchos_XMLParameterListReader.hpp"
59 #include "Teuchos_Assert.hpp"
60 #include "Epetra_ConfigDefs.h"
61 #include "Epetra_Map.h"
62 #include "Epetra_CrsGraph.h"
63 #include "Epetra_FECrsGraph.h"
64 #include "Epetra_RowMatrix.h"
65 #include "Epetra_CrsMatrix.h"
66 #include "Epetra_FECrsMatrix.h"
67 #include "Epetra_MultiVector.h"
68 #include "Epetra_Import.h"
69 
70 #if defined(__PGI)
71 #include <sstream>
72 #endif
73 
74 // ============================================================================
75 static void Tokenize(const std::string& str, std::vector<std::string>& tokens,
76  const std::string& delimiters = " ")
77 {
78  // Skip delimiters at beginning.
79  std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
80  // Find first "non-delimiter".
81  std::string::size_type pos = str.find_first_of(delimiters, lastPos);
82 
83  while (std::string::npos != pos || std::string::npos != lastPos)
84  {
85  // Found a token, add it to the std::vector.
86  tokens.push_back(str.substr(lastPos, pos - lastPos));
87  // Skip delimiters. Note the "not_of"
88  lastPos = str.find_first_not_of(delimiters, pos);
89  // Find next "non-delimiter"
90  pos = str.find_first_of(delimiters, lastPos);
91  }
92 }
93 using namespace Teuchos;
94 
95 // ============================================================================
96 EpetraExt::XMLReader::XMLReader(const Epetra_Comm& comm, const std::string& FileName) :
97  Comm_(comm)
98 {
99 #ifdef HAVE_TEUCHOS_EXPAT
100  FileInputSource fileSrc(FileName);
101  fileXML_ = rcp(new XMLObject(fileSrc.getObject()));
102  IsOpen_ = true;
103 #else
104  (void)FileName;
105  std::cerr << "Teuchos was not configured with support for expat." << std::endl;
106  std::cerr << "Please reconfigure teuchos with --enable-teuchos-expat." << std::endl;
107  exit(EXIT_FAILURE);
108 #endif
109 }
110 
111 // ============================================================================
112 #ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
113 void EpetraExt::XMLReader::
114 Read(const std::string& Label, Epetra_CrsGraph*& Graph)
115 {
116  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
117  "No file has been opened");
118 
119  Graph = 0;
120 
121  for (int i = 0; i < fileXML_->numChildren(); ++i)
122  {
123  const XMLObject& child = fileXML_->getChild(i);
124  std::string tag = child.getTag();
125 
126  if (tag == "Graph")
127  {
128  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
129  {
130  bool debug = false;
131  int NumGlobalRows = child.getRequiredInt("Rows");
132  int NumGlobalCols = child.getRequiredInt("Columns");
133  int NumGlobalEntries = child.getRequiredInt("Entries");
134  int Offset = child.getRequiredInt("StartingIndex");
135  if (debug) std::cout << NumGlobalCols << NumGlobalEntries << Offset << std::endl;
136 
137  Epetra_Map map(NumGlobalRows, 0, Comm_);
138  Graph = new Epetra_CrsGraph(Copy, map, 0);
139 
140  for (int j = 0; j < child.numContentLines(); ++j)
141  {
142  std::vector<std::string> tokens;
143  const std::string& line = child.getContentLine(j);
144  Tokenize(line, tokens, " \n\r\t");
145  if (tokens.size() < 2) continue;
146 
147  int row, col;
148  row = atoi((char*)tokens[0].c_str());
149  col = atoi((char*)tokens[1].c_str());
150 
151  if (map.LID(row) != -1)
152  Graph->InsertGlobalIndices(row, 1, &col);
153  }
154  Graph->FillComplete();
155  }
156  }
157  }
158 }
159 #endif
160 
161 #ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
162 void EpetraExt::XMLReader::
163 Read64(const std::string& Label, Epetra_CrsGraph*& Graph)
164 {
165  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
166  "No file has been opened");
167 
168  Graph = 0;
169 
170  for (int i = 0; i < fileXML_->numChildren(); ++i)
171  {
172  const XMLObject& child = fileXML_->getChild(i);
173  std::string tag = child.getTag();
174 
175  if (tag == "Graph")
176  {
177  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
178  {
179  bool debug = false;
180  long long NumGlobalRows = child.getRequired<long long>("Rows");
181  long long NumGlobalCols = child.getRequired<long long>("Columns");
182  long long NumGlobalEntries = child.getRequired<long long>("Entries");
183  int Offset = child.getRequiredInt("StartingIndex");
184  if (debug) std::cout << NumGlobalCols << NumGlobalEntries << Offset << std::endl;
185 
186  Epetra_Map map(NumGlobalRows, 0, Comm_);
187  Graph = new Epetra_CrsGraph(Copy, map, 0);
188 
189  for (int j = 0; j < child.numContentLines(); ++j)
190  {
191  std::vector<std::string> tokens;
192  const std::string& line = child.getContentLine(j);
193  Tokenize(line, tokens, " \n\r\t");
194  if (tokens.size() < 2) continue;
195 
196  long long row, col;
197  char *endp;
198  const int base = 10;
199 #if defined(_MSC_VER)
200  row = _strtoi64((char*)tokens[0].c_str(), &endp, base);
201  col = _strtoi64((char*)tokens[1].c_str(), &endp, base);
202 #else
203 #if defined(__PGI)
204  std::istringstream ss_row(tokens[0]);
205  ss_row >> row;
206  std::istringstream ss_col(tokens[1]);
207  ss_col >> col;
208 #else
209  row = strtoll((char*)tokens[0].c_str(), &endp, base);
210  col = strtoll((char*)tokens[1].c_str(), &endp, base);
211 #endif
212 #endif
213 
214  if (map.LID(row) != -1)
215  Graph->InsertGlobalIndices(row, 1, &col);
216  }
217  Graph->FillComplete();
218  }
219  }
220  }
221 }
222 #endif
223 
224 // ============================================================================
225 #ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
226 void EpetraExt::XMLReader::
227 Read(const std::string& Label, Epetra_CrsMatrix*& matrix)
228 {
229  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
230  "No file has been opened");
231 
232  matrix = 0;
233 
234  for (int i = 0; i < fileXML_->numChildren(); ++i)
235  {
236  const XMLObject& child = fileXML_->getChild(i);
237  std::string tag = child.getTag();
238 
239  if (tag == "PointMatrix")
240  {
241  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
242  {
243  bool debug = false;
244  int NumGlobalRows = child.getRequiredInt("Rows");
245  int NumGlobalCols = child.getRequiredInt("Columns");
246  int NumGlobalNonzeros = child.getRequiredInt("Nonzeros");
247  int Offset = child.getRequiredInt("StartingIndex");
248  if (debug) std::cout << NumGlobalCols << NumGlobalNonzeros << Offset << std::endl;
249 
250  Epetra_Map map(NumGlobalRows, 0, Comm_);
251  matrix = new Epetra_CrsMatrix(Copy, map, 0);
252 
253  for (int j = 0; j < child.numContentLines(); ++j)
254  {
255  std::vector<std::string> tokens;
256  const std::string& line = child.getContentLine(j);
257  Tokenize(line, tokens, " \n\r\t");
258  if (tokens.size() < 3) continue;
259 
260  int row, col;
261  double val;
262  row = atoi((char*)tokens[0].c_str());
263  col = atoi((char*)tokens[1].c_str());
264  sscanf((char*)tokens[2].c_str(), "%lg", &val);
265  //val = atof((char*)tokens[2].c_str());
266 
267  if (map.LID(row) != -1)
268  matrix->InsertGlobalValues(row, 1, &val, &col);
269  }
270  matrix->FillComplete();
271  }
272  }
273  }
274 }
275 #endif
276 
277 #ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
278 void EpetraExt::XMLReader::
279 Read64(const std::string& Label, Epetra_CrsMatrix*& matrix)
280 {
281  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
282  "No file has been opened");
283 
284  matrix = 0;
285 
286  for (int i = 0; i < fileXML_->numChildren(); ++i)
287  {
288  const XMLObject& child = fileXML_->getChild(i);
289  std::string tag = child.getTag();
290 
291  if (tag == "PointMatrix")
292  {
293  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
294  {
295  bool debug = false;
296  long long NumGlobalRows = child.getRequiredInt("Rows");
297  long long NumGlobalCols = child.getRequiredInt("Columns");
298  long long NumGlobalNonzeros = child.getRequiredInt("Nonzeros");
299  int Offset = child.getRequiredInt("StartingIndex");
300  if (debug) std::cout << NumGlobalCols << NumGlobalNonzeros << Offset << std::endl;
301 
302  Epetra_Map map(NumGlobalRows, 0, Comm_);
303  matrix = new Epetra_CrsMatrix(Copy, map, 0);
304 
305  for (int j = 0; j < child.numContentLines(); ++j)
306  {
307  std::vector<std::string> tokens;
308  const std::string& line = child.getContentLine(j);
309  Tokenize(line, tokens, " \n\r\t");
310  if (tokens.size() < 3) continue;
311 
312  long long row, col;
313  double val;
314  char *endp;
315  const int base = 10;
316 #if defined(_MSC_VER)
317  row = _strtoi64((char*)tokens[0].c_str(), &endp, base);
318  col = _strtoi64((char*)tokens[1].c_str(), &endp, base);
319 #else
320 #if defined(__PGI)
321  std::istringstream ss_row(tokens[0]);
322  ss_row >> row;
323  std::istringstream ss_col(tokens[1]);
324  ss_col >> col;
325 #else
326  row = strtoll((char*)tokens[0].c_str(), &endp, base);
327  col = strtoll((char*)tokens[1].c_str(), &endp, base);
328 #endif
329 #endif
330  sscanf((char*)tokens[2].c_str(), "%lg", &val);
331  //val = atof((char*)tokens[2].c_str());
332 
333  if (map.LID(row) != -1)
334  matrix->InsertGlobalValues(row, 1, &val, &col);
335  }
336  matrix->FillComplete();
337  }
338  }
339  }
340 }
341 #endif
342 // ============================================================================
343 #ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
344 void EpetraExt::XMLReader::
345 Read(const std::string& Label, Epetra_MultiVector*& MultiVector)
346 {
347  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
348  "No file has been opened");
349 
350  MultiVector = 0;
351 
352  // read all file and create all objects in memory.
353  for (int i = 0; i < fileXML_->numChildren(); ++i)
354  {
355  const XMLObject& child = fileXML_->getChild(i);
356  std::string tag = child.getTag();
357 
358  if (tag == "MultiVector")
359  {
360  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
361  {
362  int GlobalLength = child.getRequiredInt("Length");
363  int NumVectors = child.getRequiredInt("NumVectors");
364 
365  Epetra_Map Map(GlobalLength, 0, Comm_);
366  MultiVector = new Epetra_MultiVector(Map, NumVectors);
367 
368  int count = 0;
369  double val;
370  for (int j = 0; j < child.numContentLines(); ++j)
371  {
372  std::vector<std::string> tokens;
373 
374  const std::string& line = child.getContentLine(j);
375 
376  Tokenize(line, tokens, " \n\r\t");
377 
378  if (tokens.size() == 0) continue;
379 
380  TEUCHOS_TEST_FOR_EXCEPTION(tokens.size() != (unsigned) NumVectors, std::logic_error,
381  "wrong number of tokens in line; "
382  << "tokens.size() = " << tokens.size()
383  << ", NumVectors = " << NumVectors);
384  int tsize = (int) tokens.size();
385  for (int k = 0; k < tsize; ++k)
386  {
387  if (Map.LID(count) != -1)
388  {
389  sscanf((char*)(tokens[k].c_str()), "%lf", &val);
390 
391  (*MultiVector)[k][Map.LID(count)] = val;
392  }
393  }
394  ++count;
395  }
396  }
397  }
398  }
399 }
400 #endif
401 
402 #ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
403 void EpetraExt::XMLReader::
404 Read64(const std::string& Label, Epetra_MultiVector*& MultiVector)
405 {
406  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
407  "No file has been opened");
408 
409  MultiVector = 0;
410 
411  // read all file and create all objects in memory.
412  for (int i = 0; i < fileXML_->numChildren(); ++i)
413  {
414  const XMLObject& child = fileXML_->getChild(i);
415  std::string tag = child.getTag();
416 
417  if (tag == "MultiVector")
418  {
419  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
420  {
421  long long GlobalLength = child.getRequired<long long>("Length");
422  int NumVectors = child.getRequiredInt("NumVectors");
423 
424  Epetra_Map Map(GlobalLength, 0, Comm_);
425  MultiVector = new Epetra_MultiVector(Map, NumVectors);
426 
427  long long count = 0;
428  double val;
429  for (long long j = 0; j < child.numContentLines(); ++j)
430  {
431  std::vector<std::string> tokens;
432 
433  const std::string& line = child.getContentLine(j);
434 
435  Tokenize(line, tokens, " \n\r\t");
436 
437  if (tokens.size() == 0) continue;
438 
439  TEUCHOS_TEST_FOR_EXCEPTION(tokens.size() != (unsigned) NumVectors, std::logic_error,
440  "wrong number of tokens in line; "
441  << "tokens.size() = " << tokens.size()
442  << ", NumVectors = " << NumVectors);
443  int tsize = (int) tokens.size();
444  for (int k = 0; k < tsize; ++k)
445  {
446  if (Map.LID(count) != -1)
447  {
448  sscanf((char*)(tokens[k].c_str()), "%lf", &val);
449 
450  (*MultiVector)[k][Map.LID(count)] = val;
451  }
452  }
453  ++count;
454  }
455  }
456  }
457  }
458 }
459 #endif
460 // ============================================================================
461 #ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
462 void EpetraExt::XMLReader::
463 Read(const std::string& Label, Epetra_Map*& Map)
464 {
465  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
466  "No file has been opened");
467 
468  Map = 0;
469 
470  // read all file and create all objects in memory.
471  for (int i = 0; i < fileXML_->numChildren(); ++i)
472  {
473  const XMLObject& child = fileXML_->getChild(i);
474  std::string tag = child.getTag();
475 
476  if (tag == "Map")
477  {
478  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
479  {
480  int NumGlobalElements = child.getRequiredInt("NumElements");
481  int IndexBase = child.getRequiredInt("IndexBase");
482  int NumProc = child.getRequiredInt("NumProc");
483 
484  TEUCHOS_TEST_FOR_EXCEPTION(NumProc != Comm_.NumProc(), std::logic_error,
485  "Requested map defined with different number of processors, "
486  << "NumProc = " << NumProc << " while "
487  << "Comm.NumProc() = " << Comm_.NumProc());
488 
489  char str[80];
490  sprintf(str, "ElementsOnProc%d", Comm_.MyPID());
491  int NumMyElements = child.getRequiredInt(str);
492 
493  sprintf(str, "ElementsOnProc%d", Comm_.MyPID());
494 
495  std::vector<int> MyGlobalElements(NumMyElements);
496 
497  for (int iproc = 0; iproc < child.numChildren(); ++iproc)
498  {
499  const XMLObject& newChild = child.getChild(iproc);
500  int count = 0;
501 
502  if (newChild.hasAttribute("ID") &&
503  newChild.getRequiredInt("ID") == Comm_.MyPID())
504  {
505  for (int j = 0; j < newChild.numContentLines(); ++j)
506  {
507  std::vector<std::string> tokens;
508 
509  const std::string& line = newChild.getContentLine(j);
510 
511  Tokenize(line, tokens, " \n\r\t");
512  int tsize = (int) tokens.size();
513  for (int k = 0; k < tsize; ++k)
514  {
515  MyGlobalElements[count++] = atoi((char*)tokens[k].c_str());
516  }
517  }
518  }
519  }
520 
521  Map = new Epetra_Map(NumGlobalElements, NumMyElements,
522  &MyGlobalElements[0], IndexBase, Comm_);
523  }
524  }
525  }
526 }
527 #endif
528 
529 #ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
530 void EpetraExt::XMLReader::
531 Read64(const std::string& Label, Epetra_Map*& Map)
532 {
533  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
534  "No file has been opened");
535 
536  Map = 0;
537 
538  // read all file and create all objects in memory.
539  for (int i = 0; i < fileXML_->numChildren(); ++i)
540  {
541  const XMLObject& child = fileXML_->getChild(i);
542  std::string tag = child.getTag();
543 
544  if (tag == "Map")
545  {
546  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
547  {
548  long long NumGlobalElements = child.getRequired<long long>("NumElements");
549  long long IndexBase = child.getRequired<long long>("IndexBase");
550  int NumProc = child.getRequiredInt("NumProc");
551 
552  TEUCHOS_TEST_FOR_EXCEPTION(NumProc != Comm_.NumProc(), std::logic_error,
553  "Requested map defined with different number of processors, "
554  << "NumProc = " << NumProc << " while "
555  << "Comm.NumProc() = " << Comm_.NumProc());
556 
557  char str[80];
558  sprintf(str, "ElementsOnProc%d", Comm_.MyPID());
559  int NumMyElements = child.getRequiredInt(str);
560 
561  sprintf(str, "ElementsOnProc%d", Comm_.MyPID());
562 
563  std::vector<long long> MyGlobalElements(NumMyElements);
564 
565  for (int iproc = 0; iproc < child.numChildren(); ++iproc)
566  {
567  const XMLObject& newChild = child.getChild(iproc);
568  int count = 0;
569 
570  if (newChild.hasAttribute("ID") &&
571  newChild.getRequiredInt("ID") == Comm_.MyPID())
572  {
573  for (int j = 0; j < newChild.numContentLines(); ++j)
574  {
575  std::vector<std::string> tokens;
576 
577  const std::string& line = newChild.getContentLine(j);
578 
579  Tokenize(line, tokens, " \n\r\t");
580  int tsize = (int) tokens.size();
581  for (int k = 0; k < tsize; ++k)
582  {
583  char *endp;
584  const int base = 10;
585 #if defined(_MSC_VER)
586  MyGlobalElements[count++] = _strtoi64((char*)tokens[k].c_str(), &endp, base);
587 #else
588 #if defined(__PGI)
589  std::istringstream ss(tokens[k]);
590  ss >> MyGlobalElements[count++];
591 #else
592  MyGlobalElements[count++] = strtoll((char*)tokens[k].c_str(), &endp, base);
593 #endif
594 #endif
595  }
596  }
597  }
598  }
599 
600  Map = new Epetra_Map(NumGlobalElements, NumMyElements,
601  &MyGlobalElements[0], IndexBase, Comm_);
602  }
603  }
604  }
605 }
606 #endif
607 
608 // ============================================================================
609 void EpetraExt::XMLReader::
610 Read(const std::string& Label, std::vector<std::string>& Content)
611 {
612  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
613  "No file has been opened");
614 
615  for (int i = 0; i < fileXML_->numChildren(); ++i)
616  {
617  const XMLObject& child = fileXML_->getChild(i);
618  std::string tag = child.getTag();
619 
620  if (tag == "Text")
621  {
622  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
623  {
624  for (int j = 0; j < child.numContentLines(); ++j)
625  {
626  const std::string& line = child.getContentLine(j);
627  if (line == "\n") continue;
628  Content.push_back(line);
629  }
630  }
631  }
632  }
633 }
634 
635 // ============================================================================
636 void EpetraExt::XMLReader::
637 Read(const std::string& Label, Teuchos::ParameterList& List)
638 {
639  TEUCHOS_TEST_FOR_EXCEPTION(IsOpen_ == false, std::logic_error,
640  "No file has been opened");
641 
642  for (int i = 0; i < fileXML_->numChildren(); ++i)
643  {
644  const XMLObject& child = fileXML_->getChild(i);
645  std::string tag = child.getTag();
646 
647  if (tag == "List")
648  {
649  if (child.hasAttribute("Label") && child.getRequired("Label") == Label)
650  {
651  Teuchos::XMLParameterListReader ListReader;
652  List = ListReader.toParameterList(child.getChild(0));
653  }
654  }
655  }
656 }
Epetra_MultiVector
Epetra_Map
Epetra_CrsGraph::FillComplete
int FillComplete()
EpetraExt_XMLReader.h
Copy
EpetraExt::XMLReader::Read
void Read(const std::string &Label, Epetra_Map *&Map)
Reads the Epetra_Map stored with label Label.
Definition: EpetraExt_XMLReader.cpp:463
Epetra_CrsMatrix::FillComplete
int FillComplete(bool OptimizeDataStorage=true)
EpetraExt_ConfigDefs.h
Tokenize
static void Tokenize(const std::string &str, std::vector< std::string > &tokens, const std::string &delimiters=" ")
Definition: EpetraExt_XMLReader.cpp:75
Epetra_Comm
EpetraExt::XMLReader::XMLReader
XMLReader(const Epetra_Comm &Comm, const std::string &FileName)
ctor
Definition: EpetraExt_XMLReader.cpp:96
Epetra_BlockMap::LID
int LID(int GID) const
Epetra_CrsGraph::InsertGlobalIndices
int InsertGlobalIndices(int GlobalRow, int NumIndices, int *Indices)
Epetra_CrsMatrix::InsertGlobalValues
virtual int InsertGlobalValues(int GlobalRow, int NumEntries, const double *Values, const int *Indices)
Epetra_CrsMatrix
EpetraExt::XMLReader::Read64
void Read64(const std::string &Label, Epetra_Map *&Map)
Reads the Epetra_Map stored with label Label. Long Long version.
Definition: EpetraExt_XMLReader.cpp:531
Epetra_CrsGraph
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