ProblemVec.cc 34.1 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
#include "ProblemVec.h"
#include "RecoveryEstimator.h"
#include "Serializer.h"
#include "AbstractFunction.h"
#include "Operator.h"
#include "SystemVector.h"
#include "DOFMatrix.h"
#include "FiniteElemSpace.h"
#include "Estimator.h"
#include "Marker.h"
#include "AdaptInfo.h"
#include "FileWriter.h"
#include "CoarseningManager.h"
#include "RefinementManager.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
15
#include "DualTraverse.h"
16
17
18
19
20
21
22
23
#include "Mesh.h"
#include "OEMSolver.h"
#include "Preconditioner.h"
#include "MatVecMultiplier.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
24
#include "Flag.h"
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49

namespace AMDiS {

  ProblemVec *ProblemVec::traversePtr_ = NULL;

  void ProblemVec::initialize(Flag initFlag,
			      ProblemVec *adoptProblem,
			      Flag adoptFlag)
  {
    FUNCNAME("ProblemVec::initialize()");
    
    // === create meshes ===
    if (meshes_.size() != 0) { 
      WARNING("meshes already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
	  ((!adoptFlag.isSet(INIT_MESH))&&
	   (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE)))) {
	createMesh();
      } 
      if (adoptProblem && 
	  (adoptFlag.isSet(INIT_MESH) || 
	   adoptFlag.isSet(INIT_SYSTEM) ||
	   adoptFlag.isSet(INIT_FE_SPACE))) {
	meshes_ = adoptProblem->getMeshes();
Thomas Witkowski's avatar
Thomas Witkowski committed
50
	componentMeshes = adoptProblem->componentMeshes;
51
52
53
54
55
56
57
58
59
	refinementManager_ = adoptProblem->refinementManager_;
	coarseningManager_ = adoptProblem->coarseningManager_;
      }
    }

    if (meshes_.size() == 0) 
      WARNING("no mesh created\n");

    // === create fespace ===
60
    if (feSpaces.size() != 0) {
61
62
63
64
65
66
67
68
      WARNING("feSpaces already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
	  (initFlag.isSet(INIT_SYSTEM)&&!adoptFlag.isSet(INIT_FE_SPACE))) {
	createFESpace();
      } 
      if (adoptProblem &&
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
69
70
	feSpaces = adoptProblem->getFESpaces();
	componentSpaces = adoptProblem->componentSpaces;
71
72
73
      }
    }

74
    if (feSpaces.size() == 0) 
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
      WARNING("no feSpace created\n");

    // === create system ===
    if (initFlag.isSet(INIT_SYSTEM)) {
      createMatricesAndVectors();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
      solution_ = adoptProblem->getSolution();
      rhs_ = adoptProblem->getRHS();
      systemMatrix_ = adoptProblem->getSystemMatrix();
    }

    // === create solver ===
    if (solver_) {
      WARNING("solver already created\n");
    } else {
      if (initFlag.isSet(INIT_SOLVER)) {
	createSolver();
      } 
      if (adoptProblem && adoptFlag.isSet(INIT_SOLVER)) {
	TEST_EXIT(!solver_)("solver already created\n");
	solver_ = adoptProblem->getSolver();
      }
    }

    if (!solver_) 
      WARNING("no solver created\n");

    // === create estimator ===
    if (initFlag.isSet(INIT_ESTIMATOR)) {
      createEstimator();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR)) {
      estimator_ = adoptProblem->getEstimator();
    } 

    // === create marker ===
    if (initFlag.isSet(INIT_MARKER)) {
      createMarker();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_MARKER)) {
116
      marker = adoptProblem->getMarker();
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
    } 


    // === create file writer ===
    if (initFlag.isSet(INIT_FILEWRITER)) {
      createFileWriter();
    }

    
    // === read serialization and init mesh ===
    
    // There are two possiblities where the user can define a serialization
    // to be read from disk. Either by providing the parameter -rs when executing
    // the program or in the init file. The -rs parameter is always checked first,
    // because it can be added automatically when  rescheduling the program
    // before timeout of the runqueue.

    int readSerialization = 0;
135
    std::string serializationFilename = "";
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
    GET_PARAMETER(0, "argv->rs", &serializationFilename);

    // If the parameter -rs is set, we do nothing here, because the problem will be
    // deserialized in the constructor of a following AdaptInstationary initialization.
    if (!serializationFilename.compare("")) {
      int readSerializationWithAdaptInfo = 0;

      GET_PARAMETER(0, name_ + "->input->read serialization", "%d", 
		    &readSerialization);
      GET_PARAMETER(0, name_ + "->input->serialization with adaptinfo", "%d",
		    &readSerializationWithAdaptInfo);

      // The serialization file is only read, if the adaptInfo part should not be used.
      // If the adaptInfo part should be also read, the serialization file will be read
      // in the constructor of the AdaptInstationary problem, because we do not have here
      // the adaptInfo object.
      if (readSerialization && !readSerializationWithAdaptInfo) {
	GET_PARAMETER(0, name_ + "->input->serialization filename", 
		      &serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
158
	std::ifstream in(serializationFilename.c_str());
159
160
161
	deserialize(in);
	in.close();
      } else {
162
163
164
165
	int globalRefinements = 0;
	GET_PARAMETER(0, meshes_[0]->getName() + "->global refinements", "%d", 
		      &globalRefinements);

166
167
168
169
170
	// Initialize the meshes if there is no serialization file.
	for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
	  if (initFlag.isSet(INIT_MESH) && 
	      meshes_[i] && 
	      !(meshes_[i]->isInitialized())) {
171
172
	    meshes_[i]->initialize();	    
	    refinementManager_->globalRefine(meshes_[i], globalRefinements);
173
174
175
176
177
178
179
180
181
182
183
184
	  }
	}	
      }
    }

    doOtherStuff();
  }

  void ProblemVec::createMesh() 
  {
    FUNCNAME("ProblemVec::createMesh()");

Thomas Witkowski's avatar
Thomas Witkowski committed
185
    componentMeshes.resize(nComponents);
186
    std::map<int, Mesh*> meshForRefinementSet;
187
188
    char number[3];

189
    std::string meshName("");
190
    GET_PARAMETER(0, name_ + "->mesh", &meshName);
191
    TEST_EXIT(meshName != "")("no mesh name specified\n");
192
193
    int dim = 0;
    GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
194
    TEST_EXIT(dim)("no problem dimension specified!\n");
195

196
    for (int i = 0; i < nComponents; i++) {
197
      sprintf(number, "%d", i);
198
199
200
      int refSet = -1;
      GET_PARAMETER(0, name_ + "->refinement set[" + number + "]", "%d", &refSet);
      if (refSet < 0) {
201
202
	refSet = 0;
      }
203
      if (meshForRefinementSet[refSet] == NULL) {
204
205
206
207
	Mesh *newMesh = NEW Mesh(meshName, dim);
	meshForRefinementSet[refSet] = newMesh;
	meshes_.push_back(newMesh);
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
208
      componentMeshes[i] = meshForRefinementSet[refSet];
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
    }
    switch(dim) {
    case 1:
      coarseningManager_ = NEW CoarseningManager1d();
      refinementManager_ = NEW RefinementManager1d();
      break;
    case 2:
      coarseningManager_ = NEW CoarseningManager2d();
      refinementManager_ = NEW RefinementManager2d();
      break;
    case 3:
      coarseningManager_ = NEW CoarseningManager3d();
      refinementManager_ = NEW RefinementManager3d();
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

  void ProblemVec::createFESpace()
  {
    FUNCNAME("ProblemVec::createFESpace()");

    int degree = 1;
    char number[3];

235
    std::map< std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
236
    int dim = -1;
237
    GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
238
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");
239

240
    componentSpaces.resize(nComponents, NULL);
241

242
    for (int i = 0; i < nComponents; i++) {
243
244
245
      sprintf(number, "%d", i);
      GET_PARAMETER(0, name_ + "->polynomial degree[" + number + "]","%d", &degree);

246
      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
247

Thomas Witkowski's avatar
Thomas Witkowski committed
248
      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] == NULL) {
249
250
251
	FiniteElemSpace *newFESpace = 
	  FiniteElemSpace::provideFESpace(NULL,
					  Lagrange::getLagrange(dim, degree),
Thomas Witkowski's avatar
Thomas Witkowski committed
252
					  componentMeshes[i],
253
					  name_ + "->feSpace");
Thomas Witkowski's avatar
Thomas Witkowski committed
254
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] = newFESpace;
255
	feSpaces.push_back(newFESpace);
256
      }
257
      componentSpaces[i] = 
Thomas Witkowski's avatar
Thomas Witkowski committed
258
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)];
259
260
261
    }

    // create dof admin for vertex dofs if neccessary
262
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
263
264
265
266
267
268
269
270
271
272
273
274
275
276
      if (meshes_[i]->getNumberOfDOFs(VERTEX) == 0) {
	DimVec<int> ln_dof(meshes_[i]->getDim(), DEFAULT_VALUE, 0);
	ln_dof[VERTEX]= 1;
	meshes_[i]->createDOFAdmin("vertex dofs", ln_dof);      
      }
    }
  }

  void ProblemVec::createMatricesAndVectors()
  {
    FUNCNAME("ProblemVec::createMatricesAndVectors()");

    // === create vectors and system matrix ===

277
    systemMatrix_ = NEW Matrix<DOFMatrix*>(nComponents, nComponents);
278
    systemMatrix_->set(NULL);
279
280
    rhs_ = NEW SystemVector("rhs", componentSpaces, nComponents);
    solution_ = NEW SystemVector("solution", componentSpaces, nComponents);
281
282

    char number[10];
283
    std::string numberedName;
Thomas Witkowski's avatar
Thomas Witkowski committed
284
    for (int i = 0; i < nComponents; i++) {
285
286
      (*systemMatrix_)[i][i] = NEW DOFMatrix(componentSpaces[i], 
					     componentSpaces[i], "A_ii");
287
288
      (*systemMatrix_)[i][i]->setCoupleMatrix(false);
      sprintf(number, "[%d]", i);
289
      numberedName = "rhs" + std::string(number);
290
      rhs_->setDOFVector(i, NEW DOFVector<double>(componentSpaces[i], numberedName));
291
      numberedName = name_ + std::string(number);
292
      solution_->setDOFVector(i, NEW DOFVector<double>(componentSpaces[i], 
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
						       numberedName));
      solution_->getDOFVector(i)->refineInterpol(true);
      solution_->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution_->getDOFVector(i)->set(0.0);
    }

    // === create matVec ===
    matVec_ = NEW StandardMatVec<Matrix<DOFMatrix*>, SystemVector>(systemMatrix_);
  }

  void ProblemVec::createSolver()
  {
    FUNCNAME("ProblemVec::createSolver()");

    // === create solver ===
308
    std::string solverType("no");
309
310
311
312
313
314
315
316
317
318
319
320
    GET_PARAMETER(0, name_ + "->solver", &solverType);
    OEMSolverCreator<SystemVector> *solverCreator = 
      dynamic_cast<OEMSolverCreator<SystemVector>*>(
						    CreatorMap<OEMSolver<SystemVector> >
						    ::getCreator(solverType)
						    );
    TEST_EXIT(solverCreator)("no solver type\n");
    solverCreator->setName(name_ + "->solver");
    solver_ = solverCreator->create();
    solver_->initParameters();

    // === create preconditioners ===
321
    std::string preconType("no");
322
323

    PreconditionerScal *scalPrecon;
324
    PreconditionerVec *vecPrecon = NEW PreconditionerVec(nComponents);
325
326
327
328
329
330
331
332
333
334
335

    GET_PARAMETER(0, name_ + "->solver->left precon", &preconType);
    CreatorInterface<PreconditionerScal> *preconCreator =
      CreatorMap<PreconditionerScal>::getCreator(preconType);

    int i, j;

    if (!preconCreator->isNullCreator()) {
      dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	setName(name_ + "->solver->left precon");

336
      for(i = 0; i < nComponents; i++) {
337
	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
338
	  setSizeAndRow(nComponents, i);
339
340
    
	scalPrecon = preconCreator->create();
341
	for(j = 0; j < nComponents; j++) {
342
343
344
345
346
347
348
349
	  scalPrecon->setMatrix(&(*systemMatrix_)[i][j], j);
	}
	vecPrecon->setScalarPrecon(i, scalPrecon);
      }
      leftPrecon_ = vecPrecon;
    }


350
    vecPrecon = NEW PreconditionerVec(nComponents);
351
352
353
354
355
356
357
358
359
360

    GET_PARAMETER(0, name_ + "->solver->right precon", &preconType);
    preconCreator = 
      CreatorMap<PreconditionerScal>::getCreator(preconType);

    if(!preconCreator->isNullCreator()) {
      dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	setName(name_ + "->solver->left precon");


361
      for(i = 0; i < nComponents; i++) {
362
	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
363
	  setSizeAndRow(nComponents, i);
364
365
    
	scalPrecon = preconCreator->create();
366
	for(j = 0; j < nComponents; j++) {
367
368
369
370
371
372
373
374
375
376
	  scalPrecon->setMatrix(&(*systemMatrix_)[i][j], j);
	}
	vecPrecon->setScalarPrecon(i, scalPrecon);
      }
      rightPrecon_ = vecPrecon;
    }


    // === create vector creator ===
    solver_->setVectorCreator(NEW SystemVector::Creator("temp",
377
							componentSpaces, 
378
							nComponents));
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
  }

  void ProblemVec::createEstimator()
  {
    FUNCNAME("ProblemVec::createEstimator()");

    int i, j;

    // create and set leaf data prototype
    for(i = 0; i < static_cast<int>(meshes_.size()); i++) {
      meshes_[i]->setElementDataPrototype
	(NEW LeafDataEstimatableVec(NEW LeafDataCoarsenableVec));
    }  

    char number[3];
394
    std::string estName;
395

396
    for(i = 0; i < nComponents; i++) {
397
398
      TEST_EXIT(estimator_[i] == NULL)("estimator already created\n");
      sprintf(number, "%d", i);
399
      estName = name_ + "->estimator[" + std::string(number) + "]";
400
401

      // === create estimator ===
402
      std::string estimatorType("no");
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
      GET_PARAMETER(0, estName, &estimatorType);
      EstimatorCreator *estimatorCreator = 
	dynamic_cast<EstimatorCreator*>(
					CreatorMap<Estimator>::getCreator(estimatorType));
      if(estimatorCreator) {
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
	if(estimatorType == "recovery") {
	  dynamic_cast<RecoveryEstimator::Creator*>(estimatorCreator)->
	    setSolution(solution_->getDOFVector(i));
	}
	estimator_[i] = estimatorCreator->create();
      }


      if(estimator_[i]) {
419
	for(j=0; j < nComponents; j++) {
420
421
422
423
424
425
426
427
428
429
430
431
	  estimator_[i]->addSystem((*systemMatrix_)[i][j], 
				   solution_->getDOFVector(j), 
				   rhs_->getDOFVector(j));
	}
      }
    }
  }

  void ProblemVec::createMarker()
  {
    FUNCNAME("ProblemVec::createMarker()");

432
    std::string numberedName;
433
434
    char number[10];
    int numMarkersCreated = 0;
435

436
    for (int i = 0; i < nComponents; i++) {
437
      sprintf(number, "[%d]", i);
438
      numberedName = name_ + "->marker" + std::string(number);
439
440
      marker[i] = Marker::createMarker(numberedName, i);
      if (marker[i]) {
441
442
	numMarkersCreated++;
	if (numMarkersCreated > 1)
443
	  marker[i]->setMaximumMarking(true);
444
445
446
447
448
449
450
451
452
453
      }
    }
  }

  void ProblemVec::createFileWriter()
  {
    FUNCNAME("ProblemVec::createFileWriter()");
  

    // Create one filewriter for all components of the problem
454
455
    std::string numberedName  = name_ + "->output";
    std::string filename = "";
456
457
458
    GET_PARAMETER(0, numberedName + "->filename", &filename);

    if (filename != "") {
459
      std::vector< DOFVector<double>* > solutionList(nComponents);
460

461
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
462
	TEST_EXIT(componentMeshes[0] == componentMeshes[i])
463
464
465
466
467
468
	  ("All Meshes have to be equal to write a vector file.\n");

	solutionList[i] = solution_->getDOFVector(i);
      }

      fileWriters_.push_back(NEW FileWriter(numberedName,
Thomas Witkowski's avatar
Thomas Witkowski committed
469
					    componentMeshes[0],
470
471
472
473
474
475
					    solutionList));
    }


    // Create own filewriters for each components of the problem
    char number[10];
476
    for (int i = 0; i < nComponents; i++) {
477
      sprintf(number, "[%d]", i);
478
      numberedName  = name_ + "->output" + std::string(number);
479
480
481
482
483
      filename = "";
      GET_PARAMETER(0, numberedName + "->filename", &filename);

      if (filename != "") {
	fileWriters_.push_back(NEW FileWriter(numberedName, 
Thomas Witkowski's avatar
Thomas Witkowski committed
484
					      componentMeshes[i], 
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
					      solution_->getDOFVector(i)));
      }
    }


    // Check for serializer
    int writeSerialization = 0;
    GET_PARAMETER(0, name_ + "->write serialization", "%d", &writeSerialization);
    if (writeSerialization) {
      MSG("Use are using the obsolete parameter: %s->write serialization\n", name_.c_str());
      MSG("Please use instead the following parameter: %s->output->write serialization\n", name_.c_str());
      ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
    }

    GET_PARAMETER(0, name_ + "->output->write serialization", "%d", &writeSerialization);
    if (writeSerialization) {
      fileWriters_.push_back(NEW Serializer<ProblemVec>(this));
    }
  }

  void ProblemVec::doOtherStuff()
  {
  }

  void ProblemVec::solve(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("Problem::solve()");

    if (!solver_) {
      WARNING("no solver\n");
      return;
    }

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    clock_t first = clock();
    int iter = solver_->solve(matVec_, solution_, rhs_, leftPrecon_, rightPrecon_);   
524
    
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
#ifdef _OPENMP
    INFO(info_, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
    INFO(info_, 8)("solution of discrete system needed %.5f seconds\n",
		   TIME_USED(first, clock()));
#endif


    adaptInfo->setSolverIterations(iter);
    adaptInfo->setMaxSolverIterations(solver_->getMaxIterations());
    adaptInfo->setSolverTolerance(solver_->getTolerance());
    adaptInfo->setSolverResidual(solver_->getResidual());
  }

  void ProblemVec::estimate(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::estimate()");

    clock_t first = clock();

547
548
549
550
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

551
    if (computeExactError) {
Thomas Witkowski's avatar
Thomas Witkowski committed
552
      computeError(adaptInfo);
553
554
555
556
557
558
559
560
561
562
563
564
565
    } else {
      for (int i = 0; i < nComponents; i++) {
	Estimator *scalEstimator = estimator_[i];
	
	if (scalEstimator) {
	  scalEstimator->estimate(adaptInfo->getTimestep());
	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);
	  adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
	  adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
	} else {
	  WARNING("no estimator for component %d\n" , i);
	}
566
567
568
      }
    }

569
570
571
572
573
574
575
576
577
578
#ifdef _OPENMP
    INFO(info_, 8)("estimation of the error needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
    INFO(info_, 8)("estimation of the error needed %.5f seconds\n",
		   TIME_USED(first, clock()));

#endif

579
580
581
582
583
584
585
586
587
588
589
  }

  Flag ProblemVec::markElements(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::markElements()");

    // to enforce albert-like behavior: refinement even if space tolerance
    // here is reached already because of time adaption
    allowFirstRefinement();

    Flag markFlag = 0;
590
    for (int i = 0; i < nComponents; i++) {
591
      if (marker[i]) {
Thomas Witkowski's avatar
Thomas Witkowski committed
592
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
593
594
595
596
      } else {
	WARNING("no marker for component %d\n", i);
      }
    }
597
    
598
599
600
601
602
603
604
    return markFlag;
  }

  Flag ProblemVec::refineMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::refineMesh()");

605
    int nMeshes = static_cast<int>(meshes_.size());
606
    Flag refineFlag = 0;
607
    for (int i = 0; i < nMeshes; i++) {
608
609
610
611
612
613
614
615
616
      refineFlag |= refinementManager_->refineMesh(meshes_[i]);
    }
    return refineFlag;
  }

  Flag ProblemVec::coarsenMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::coarsenMesh()");

617
    int nMeshes = static_cast<int>(meshes_.size());
618
    Flag coarsenFlag = 0;
619
620
    for (int i = 0; i < nMeshes; i++) {
      if (adaptInfo->isCoarseningAllowed(i)) {
621
622
623
624
625
626
627
628
629
630
631
632
633
	coarsenFlag |= coarseningManager_->coarsenMesh(meshes_[i]);

	WARNING("coarsening for component %d no allowed\n", i);
      }
    }
    return coarsenFlag;
  }

  Flag ProblemVec::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
  {
    FUNCNAME("ProblemVec::oneIteration()");

    if (allowFirstRef_) {
634
      for (int i = 0; i < nComponents; i++) {
635
636
637
638
	adaptInfo->allowRefinement(true, i);
      }
      allowFirstRef_ = false;
    } else {
639
      for (int i = 0; i < nComponents; i++) {
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
	if (adaptInfo->spaceToleranceReached(i)) {
	  adaptInfo->allowRefinement(false, i);
	} else {
	  adaptInfo->allowRefinement(true, i);	
	}
      }
    }

    return StandardProblemIteration::oneIteration(adaptInfo, toDo);
  }

  void ProblemVec::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag) 
  {
    FUNCNAME("ProblemVec::buildAfterCoarsen()");

    clock_t first = clock();

657
658
659
660
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

Thomas Witkowski's avatar
Thomas Witkowski committed
661
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
      meshes_[i]->dofCompress();
    }

    Flag assembleFlag = 
      flag | 
      (*systemMatrix_)[0][0]->getAssembleFlag() | 
      rhs_->getDOFVector(0)->getAssembleFlag()   |
      Mesh::CALL_LEAF_EL                        | 
      Mesh::FILL_COORDS                         |
      Mesh::FILL_DET                            |
      Mesh::FILL_GRD_LAMBDA |
      Mesh::FILL_NEIGH;

    if (useGetBound_) {
      assembleFlag |= Mesh::FILL_BOUND;
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
679

680
    for (int i = 0; i < nComponents; i++) {
681
      MSG("%d DOFs for %s\n", 
682
683
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());
684
685

      rhs_->getDOFVector(i)->set(0.0);
686
      for (int j = 0; j < nComponents; j++) {
687
688
689
690
691
692
693
	if ((*systemMatrix_)[i][j]) {
	  // The matrix should not be deleted, if it was assembled before
	  // and it is marked to be assembled only once.
	  if (!(assembleMatrixOnlyOnce_[i][j] && assembledMatrix_[i][j])) {
	    (*systemMatrix_)[i][j]->clear();
	  }
	}
694
695
696
      }
    }

697
698
699
700
    int i;
#ifdef _OPENMP
#pragma omp parallel for 
#endif
701
702
    for (i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
703
704
705
706
	// Only if this variable is true, the current matrix will be assembled.	
	bool assembleMatrix = true;
	// The DOFMatrix which should be assembled (or not, if assembleMatrix
	// will be set to false).
707
708
	DOFMatrix *matrix = (*systemMatrix_)[i][j];

709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
	// If the matrix was assembled before and it is marked to be assembled
	// only once, it will not be assembled.
	if (assembleMatrixOnlyOnce_[i][j] && assembledMatrix_[i][j]) {
	  assembleMatrix = false;
	}
	// If there is no DOFMatrix (e.g. if it is completly 0), do not assemble.
	if (!matrix) {
	  assembleMatrix = false;
	}

	// If the matrix should not be assembled, the rhs vector has to be considered.
	// This will be only done, if i == j. So, if both is not true, we can jump
	// to the next matrix.
	if (!assembleMatrix && i != j) {
	  continue;
	}

726
727
728
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->initMatrix(matrix);

Thomas Witkowski's avatar
Thomas Witkowski committed
729
	if (componentSpaces[i] == componentSpaces[j]) {
730
	  //	  std::cout << "--- assembleOnOneMesh ---\n";
Thomas Witkowski's avatar
Thomas Witkowski committed
731
732
733
734
	  assembleOnOneMesh(componentSpaces[i],
			    assembleFlag,
			    assembleMatrix ? matrix : NULL,
			    (i == j) ? rhs_->getDOFVector(i) : NULL);
735
736
	  //	  std::cout << "--- Finished ---\n";
	  //	  std::cout << "--- Dim: " << matrix->getUsedSize() << "x" << matrix->getNumCols() << "---\n";
Thomas Witkowski's avatar
Thomas Witkowski committed
737
	} else {
738
	  //	  std::cout << "--- assembleOnDifMesh ---\n";
Thomas Witkowski's avatar
Thomas Witkowski committed
739
740
741
742
	  assembleOnDifMeshes(componentSpaces[i], componentSpaces[j],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
			      (i == j) ? rhs_->getDOFVector(i) : NULL);	  
743
744
	  //	  std::cout << "--- Finished ---\n";
	  //	  std::cout << "--- Dim: " << matrix->getUsedSize() << "x" << matrix->getNumCols() << "---\n";
745
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
746

747
748
749
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->exitMatrix(matrix);	  
	
750
	assembledMatrix_[i][j] = true;
751
752
753
754
      }

      // fill boundary conditions
      if (rhs_->getDOFVector(i)->getBoundaryManager())
755
	rhs_->getDOFVector(i)->getBoundaryManager()->initVector(rhs_->getDOFVector(i));     
756
      
757
      if (solution_->getDOFVector(i)->getBoundaryManager())
758
      	solution_->getDOFVector(i)->getBoundaryManager()->initVector(solution_->getDOFVector(i));
759

Thomas Witkowski's avatar
Thomas Witkowski committed
760
      TraverseStack stack;
Thomas Witkowski's avatar
Thomas Witkowski committed
761
      ElInfo *elInfo = stack.traverseFirst(componentMeshes[i], -1, assembleFlag);
762
      while (elInfo) {
763
	if (rhs_->getDOFVector(i)->getBoundaryManager())
764
765
	  rhs_->getDOFVector(i)->getBoundaryManager()->
	    fillBoundaryConditions(elInfo, rhs_->getDOFVector(i));
766
767

	if (solution_->getDOFVector(i)->getBoundaryManager())
768
769
770
771
	  solution_->getDOFVector(i)->getBoundaryManager()->
	    fillBoundaryConditions(elInfo, solution_->getDOFVector(i));
	elInfo = stack.traverseNext(elInfo);
      }
772
      
773
774
775
      if (rhs_->getDOFVector(i)->getBoundaryManager())
	rhs_->getDOFVector(i)->getBoundaryManager()->exitVector(rhs_->getDOFVector(i));
      if (solution_->getDOFVector(i)->getBoundaryManager())
Thomas Witkowski's avatar
Thomas Witkowski committed
776
      solution_->getDOFVector(i)->getBoundaryManager()->exitVector(solution_->getDOFVector(i));    
777
    }
778
779
780
781
782
783

#ifdef _OPENMP
    INFO(info_, 8)("buildAfterCoarsen needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
784
    INFO(info_, 8)("buildAfterCoarsen needed %.5f seconds\n",
Thomas Witkowski's avatar
Thomas Witkowski committed
785
		   TIME_USED(first, clock()));
786
#endif
787
788
789
790
791
792
  }

  void ProblemVec::writeFiles(AdaptInfo *adaptInfo, bool force) 
  {
    FUNCNAME("ProblemVec::writeFiles()");

793
794
795
796
797
798
799
800
801
802
803
804
805
    clock_t first = clock();

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    int i;
    int size = static_cast<int>(fileWriters_.size());
#ifdef _OPENMP
#pragma omp parallel for schedule(static, 1)
#endif
    for (i = 0; i < size; i++) {
      fileWriters_[i]->writeFiles(adaptInfo, force);
806
    }
807
808
809
810
811
812
813
814
815
    
#ifdef _OPENMP
    INFO(info_, 8)("writeFiles needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
    INFO(info_, 8)("writeFiles needed %.5f seconds\n",
		   TIME_USED(first, clock()));
#endif
816
817
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
818
819
820
821
822
823
824
  void ProblemVec::writeDelayedFiles()
  {
    for (int i = 0; i < static_cast<int>(fileWriters_.size()); i++) {
      fileWriters_[i]->writeDelayedFiles();
    }
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
825
826
827
828
829
830
831
832
833
834
  bool ProblemVec::existsDelayedCalculation()
  {
    for (int i = 0; i < static_cast<int>(fileWriters_.size()); i++) {
      if (fileWriters_[i]->isWritingDelayed())
	return true;   
    }

    return false;
  }

835
  void ProblemVec::interpolInitialSolution(std::vector<AbstractFunction<double, WorldVector<double> >*> *fct) 
836
837
838
839
840
841
842
843
844
845
846
847
848
  {
    FUNCNAME("ProblemVec::interpolInitialSolution()");

    solution_->interpol(fct);
  }

  void ProblemVec::addMatrixOperator(Operator *op, 
				     int i, int j,
				     double *factor,
				     double *estFactor)
  {
    FUNCNAME("ProblemVec::addMatrixOperator()");

849
    if (!(*systemMatrix_)[i][j]) {
850
      TEST_EXIT(i != j)("should have been created already\n");
851
852
      (*systemMatrix_)[i][j] = NEW DOFMatrix(componentSpaces[i],
					     componentSpaces[j],
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
					     "");
      (*systemMatrix_)[i][j]->setCoupleMatrix(true);

      (*systemMatrix_)[i][j]->getBoundaryManager()->
	setBoundaryConditionMap((*systemMatrix_)[i][i]->getBoundaryManager()->
				getBoundaryConditionMap());
    }    
    (*systemMatrix_)[i][j]->addOperator(op, factor, estFactor);
  }

  void ProblemVec::addVectorOperator(Operator *op, int i,
				     double *factor,
				     double *estFactor)
  {
    FUNCNAME("ProblemVec::addVectorOperator()");

    rhs_->getDOFVector(i)->addOperator(op, factor, estFactor);
  }

  void ProblemVec::addDirichletBC(BoundaryType type, int system,
				  AbstractFunction<double, WorldVector<double> >* b)
  {
    FUNCNAME("ProblemVec::addDirichletBC()");

    DirichletBC *dirichlet = new DirichletBC(type, 
					     b, 
879
					     componentSpaces[system]);
880
    for (int i = 0; i < nComponents; i++) {
881
882
883
884
      if (systemMatrix_ && (*systemMatrix_)[system][i]) {
	(*systemMatrix_)[system][i]->getBoundaryManager()->addBoundaryCondition(dirichlet);
      }
    }
885

886
887
    if (rhs_)
      rhs_->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
888

889
890
891
892
893
894
895
896
897
898
899
    if (solution_)
      solution_->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
  }

  void ProblemVec::addNeumannBC(BoundaryType type, int row, int col, 
				AbstractFunction<double, WorldVector<double> > *n)
  {
    FUNCNAME("ProblemVec::addNeumannBC()");

    NeumannBC *neumann = 
      new NeumannBC(type, n, 
900
901
		    componentSpaces[row], 
		    componentSpaces[col]);
902
    if (rhs_)
903
904
905
906
907
908
909
910
911
912
913
      rhs_->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(neumann);
  }

  void ProblemVec::addRobinBC(BoundaryType type, int row, int col, 
			      AbstractFunction<double, WorldVector<double> > *n,
			      AbstractFunction<double, WorldVector<double> > *r)
  {
    FUNCNAME("ProblemVec::addRobinBC()");

    RobinBC *robin = 
      new RobinBC(type, n, r, 
914
915
		  componentSpaces[row], 
		  componentSpaces[col]);
916
    if (rhs_)
917
      rhs_->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(robin);
918
919

    if (systemMatrix_ && (*systemMatrix_)[row][col]) {
920
921
922
923
924
925
926
927
      (*systemMatrix_)[row][col]->getBoundaryManager()->addBoundaryCondition(robin);
    }
  }

  void ProblemVec::addPeriodicBC(BoundaryType type, int row, int col) 
  {
    FUNCNAME("ProblemVec::addPeriodicBC()");

928
    FiniteElemSpace *feSpace = componentSpaces[row];
929
930
931

    PeriodicBC *periodic = new PeriodicBC(type, feSpace);

932
    if (systemMatrix_ && (*systemMatrix_)[row][col]) 
933
      (*systemMatrix_)[row][col]->getBoundaryManager()->addBoundaryCondition(periodic);
934
935

    if (rhs_) 
936
937
938
939
      rhs_->getDOFVector(row)->getBoundaryManager()->
	addBoundaryCondition(periodic);
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
  void ProblemVec::assembleOnOneMesh(FiniteElemSpace *feSpace, Flag assembleFlag,
				     DOFMatrix *matrix, DOFVector<double> *vector)
  {
    Mesh *mesh = feSpace->getMesh();
    const BasisFunction *basisFcts = feSpace->getBasisFcts();

    BoundaryType *bound = NULL;
    if (useGetBound_) {
      bound = GET_MEMORY(BoundaryType, basisFcts->getNumber());
    }

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
    
    while (elInfo) {
      if (useGetBound_) {
	basisFcts->getBound(elInfo, bound);
      }
      
      if (matrix) {
	matrix->assemble(1.0, elInfo, bound);
	
	if (matrix->getBoundaryManager()) {
	  matrix->getBoundaryManager()->
	    fillBoundaryConditions(elInfo, matrix);
	}		      
      }
      
      if (vector) {
	vector->assemble(1.0, elInfo, bound);
      }
      
      elInfo = stack.traverseNext(elInfo);
    }

    if (useGetBound_) {
      FREE_MEMORY(bound, BoundaryType, basisFcts->getNumber());
    }	     
  }

  void ProblemVec::assembleOnDifMeshes(FiniteElemSpace *rowFeSpace, FiniteElemSpace *colFeSpace,
				       Flag assembleFlag,
				       DOFMatrix *matrix, DOFVector<double> *vector)
  {
    Mesh *rowMesh = rowFeSpace->getMesh();
    Mesh *colMesh = colFeSpace->getMesh();

    const BasisFunction *basisFcts = rowFeSpace->getBasisFcts();
    BoundaryType *bound = NULL;
    if (useGetBound_) {
      bound = GET_MEMORY(BoundaryType, basisFcts->getNumber());
    }

    DualTraverse dualTraverse;
    ElInfo *rowElInfo, *colElInfo;
    ElInfo *largeElInfo, *smallElInfo;

997
    dualTraverse.setFillSubElemInfo(true);
Thomas Witkowski's avatar
Thomas Witkowski committed
998
999
1000
1001
1002
1003
1004
1005
1006
    bool cont = dualTraverse.traverseFirst(rowMesh, colMesh, -1, -1,
					   assembleFlag, assembleFlag,
					   &rowElInfo, &colElInfo,
					   &smallElInfo, &largeElInfo);
    while (cont) {
      Element *rowElem = rowElInfo->getElement();
      Element *colElem = colElInfo->getElement();

      if (rowElInfo->getLevel() != colElInfo->getLevel()) {
1007
	if (smallElInfo == rowElInfo) {
Thomas Witkowski's avatar
Thomas Witkowski committed
1008
	  std::cout << "Row = small\n";
1009
1010
	  ERROR_EXIT("NOCH EIN PAAR GEDANKEN MACHEN!\n");
	} else {
Thomas Witkowski's avatar
Thomas Witkowski committed
1011
	  std::cout << "Row = large\n";
1012
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
1013
1014
1015
1016
1017
1018

	if (largeElInfo == colElInfo) 
	  std::cout << "Col = large\n";
	else
	  std::cout << "Col = small\n";

1019
1020
1021
	if (useGetBound_) {
	  basisFcts->getBound(rowElInfo, bound);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
1022

1023
	if (matrix) {
1024
1025
1026
1027
1028
	  matrix->assemble(1.0, rowElInfo, colElInfo, bound);
	}
      } else {
	if (useGetBound_) {
	  basisFcts->getBound(rowElInfo, bound);
1029
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
1030
      
1031
1032
1033
1034
1035
1036
1037
1038
	if (matrix) {
	  matrix->assemble(1.0, rowElInfo, bound);
	  
	  if (matrix->getBoundaryManager()) {
	    matrix->getBoundaryManager()->
	      fillBoundaryConditions(rowElInfo, matrix);
	  }		      
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
      }
      
      if (vector) {
	vector->assemble(1.0, rowElInfo, bound);
      }

      cont = dualTraverse.traverseNext(&rowElInfo, &colElInfo,
				       &smallElInfo, &largeElInfo);
    }

    if (useGetBound_) {
      FREE_MEMORY(bound, BoundaryType, basisFcts->getNumber());
    }
  }

1054
  void ProblemVec::writeResidualMesh(AdaptInfo *adaptInfo, const std::string name)
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
  {
    FUNCNAME("ProblemVec::writeResidualMesh()");

    Mesh *mesh = this->getMesh(0);
    FiniteElemSpace *fe = this->getFESpace(0);
    
    std::map<int, double> vec;
    
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh,
					 -1, 
					 Mesh::CALL_LEAF_EL | 
					 Mesh::FILL_COORDS);
    
    while (elInfo) {		  
      Element *el = elInfo->getElement();
      double lError = el->getEstimation(0);
      
      vec[elInfo->getElement()->getIndex()] = lError;
      elInfo = stack.traverseNext(elInfo);
    }
    
    ElementFileWriter fw(name, mesh, fe, vec);
    fw.writeFiles(adaptInfo, true);    
  }

1081
  void ProblemVec::serialize(std::ostream &out) 
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
  {
    FUNCNAME("ProblemVec::serialize()");

    SerializerUtil::serializeBool(out, &allowFirstRef_);
    
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
      meshes_[i]->serialize(out);
    }

    solution_->serialize(out);
  }

1094
  void ProblemVec::deserialize(std::istream &in) 
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
  {
    FUNCNAME("ProblemVec::deserialize()");

    SerializerUtil::deserializeBool(in, &allowFirstRef_);

    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
      meshes_[i]->deserialize(in);
    }

    solution_->deserialize(in);
  }
Thomas Witkowski's avatar
Thomas Witkowski committed
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161

  void ProblemVec::computeError(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::computeError()");

    for (int i = 0; i < nComponents; i++) {		
      TEST_EXIT(exactSolutionFcts[i])("No solution function given!\n");

      // Compute the difference between exact and computed solution
      DOFVector<double> *tmp = NEW DOFVector<double>(componentSpaces[i], "tmp");
      tmp->interpol(exactSolutionFcts[i]);
      double solMax = tmp->absMax();
      *tmp -= *(solution_->getDOFVector(i));
      
      MSG("L2    error = %.8e\n", tmp->L2Norm());
      MSG("L-inf error = %.8e\n", tmp->absMax() / solMax);
      
      adaptInfo->setEstSum(tmp->absMax() / solMax, i);
      adaptInfo->setEstMax(tmp->absMax() / solMax, i);
      
      // To set element estimates, compute a vector with the difference
      // between exact and computed solution for each DOF.
      DOFVector<double> *sol = NEW DOFVector<double>(componentSpaces[i], "tmp");
      sol->interpol(exactSolutionFcts[i]);
      DOFVector<double>::Iterator it1(sol, USED_DOFS);
      DOFVector<double>::Iterator it2(tmp, USED_DOFS);
      for (it1.reset(), it2.reset(); !it1.end(); ++it1, ++it2) {
	if ((abs(*it1) <= DBL_TOL) || (abs(*it2) <= DBL_TOL)) {
	  *it2 = 0.0;
	} else {
	  *it2 = abs(*it2 / *it1);
	}
      }

      // Compute estimate for every mesh element
      Vector<DegreeOfFreedom> locInd(componentSpaces[i]->getBasisFcts()->getNumber());
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(componentMeshes[i], -1, Mesh::CALL_LEAF_EL);
      while (elInfo) {
	componentSpaces[i]->getBasisFcts()->getLocalIndicesVec(elInfo->getElement(),
							       componentSpaces[i]->getAdmin(),
							       &locInd);
	double estimate = 0.0;
	for (int j = 0; j < componentSpaces[i]->getBasisFcts()->getNumber(); j++) {
	  estimate += (*tmp)[locInd[j]];
	}
	elInfo->getElement()->setEstimation(estimate, i);
	elInfo->getElement()->setMark(0);
								
	elInfo = stack.traverseNext(elInfo);
      }  
      
      DELETE tmp;	
      DELETE sol;
    }						           
  }
1162
1163
}