ProblemVec.cc 29.5 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
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
50
51
52
53
54
55
56
57
#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"
#include "Mesh.h"
#include "OEMSolver.h"
#include "Preconditioner.h"
#include "MatVecMultiplier.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"

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();
	componentMeshes_ = adoptProblem->componentMeshes_;
	refinementManager_ = adoptProblem->refinementManager_;
	coarseningManager_ = adoptProblem->coarseningManager_;
      }
    }

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

    // === create fespace ===
58
    if (feSpaces.size() != 0) {
59
60
61
62
63
64
65
66
      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))) {
67
68
	feSpaces = adoptProblem->getFESpaces();
	componentSpaces = adoptProblem->componentSpaces;
69
70
71
      }
    }

72
    if (feSpaces.size() == 0) 
73
74
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
      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)) {
114
      marker = adoptProblem->getMarker();
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
    } 


    // === 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;
133
    std::string serializationFilename = "";
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
    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());
156
	std::ifstream in(serializationFilename.c_str());
157
158
159
	deserialize(in);
	in.close();
      } else {
160
161
162
163
	int globalRefinements = 0;
	GET_PARAMETER(0, meshes_[0]->getName() + "->global refinements", "%d", 
		      &globalRefinements);

164
165
166
167
168
	// 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())) {
169
170
	    meshes_[i]->initialize();	    
	    refinementManager_->globalRefine(meshes_[i], globalRefinements);
171
172
173
174
175
176
177
178
179
180
181
182
	  }
	}	
      }
    }

    doOtherStuff();
  }

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

183
184
    componentMeshes_.resize(nComponents);
    std::map<int, Mesh*> meshForRefinementSet;
185
186
    char number[3];

187
    std::string meshName("");
188
    GET_PARAMETER(0, name_ + "->mesh", &meshName);
189
    TEST_EXIT(meshName != "")("no mesh name specified\n");
190
191
    int dim = 0;
    GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
192
    TEST_EXIT(dim)("no problem dimension specified!\n");
193

194
    for (int i = 0; i < nComponents; i++) {
195
      sprintf(number, "%d", i);
196
197
198
      int refSet = -1;
      GET_PARAMETER(0, name_ + "->refinement set[" + number + "]", "%d", &refSet);
      if (refSet < 0) {
199
200
	refSet = 0;
      }
201
      if (meshForRefinementSet[refSet] == NULL) {
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
	Mesh *newMesh = NEW Mesh(meshName, dim);
	meshForRefinementSet[refSet] = newMesh;
	meshes_.push_back(newMesh);
      }
      componentMeshes_[i] = meshForRefinementSet[refSet];
    }
    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];

233
    std::map< std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
234
    int dim = -1;
235
    GET_PARAMETER(0, name_ + "->dim", "%d", &dim);
236
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");
237

238
    componentSpaces.resize(nComponents, NULL);
239

240
    for (int i = 0; i < nComponents; i++) {
241
242
243
      sprintf(number, "%d", i);
      GET_PARAMETER(0, name_ + "->polynomial degree[" + number + "]","%d", &degree);

244
      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
245

246
      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)] == NULL) {
247
248
249
250
251
	FiniteElemSpace *newFESpace = 
	  FiniteElemSpace::provideFESpace(NULL,
					  Lagrange::getLagrange(dim, degree),
					  componentMeshes_[i],
					  name_ + "->feSpace");
252
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)] = newFESpace;
253
	feSpaces.push_back(newFESpace);
254
      }
255
      componentSpaces[i] = 
256
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes_[i], degree)];
257
258
259
    }

    // create dof admin for vertex dofs if neccessary
260
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
261
262
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()");

    int i;

    // === 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
284
    std::string numberedName;
    for (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++) {
462
463
464
465
466
467
468
469
470
471
472
473
474
475
	TEST_EXIT(componentMeshes_[0] == componentMeshes_[i])
	  ("All Meshes have to be equal to write a vector file.\n");

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

      fileWriters_.push_back(NEW FileWriter(numberedName,
					    componentMeshes_[0],
					    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
484
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
      filename = "";
      GET_PARAMETER(0, numberedName + "->filename", &filename);

      if (filename != "") {
	fileWriters_.push_back(NEW FileWriter(numberedName, 
					      componentMeshes_[i], 
					      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
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
    if (computeExactError) {
      for (int i = 0; i < nComponents; i++) {	
	DOFVector<double> *tmp = NEW DOFVector<double>(componentSpaces[i], "tmp");
	tmp->interpol(exactSolutionFcts[i]);
	*tmp -= *(solution_->getDOFVector(i));
	double l2Error = tmp->L2Norm();
	MSG("L2 error = %.8e\n", l2Error);
	DELETE tmp;	
      }						       
    } 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);
	}
573
574
575
      }
    }

576
577
578
579
580
581
582
583
584
585
#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

586
587
588
589
590
591
592
593
594
595
596
  }

  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;
597
    for (int i = 0; i < nComponents; i++) {
598
599
      if (marker[i]) {
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes_[i]);
600
601
602
603
      } else {
	WARNING("no marker for component %d\n", i);
      }
    }
604
    
605
606
607
608
609
610
611
    return markFlag;
  }

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

612
    int nMeshes = static_cast<int>(meshes_.size());
613
    Flag refineFlag = 0;
614
    for (int i = 0; i < nMeshes; i++) {
615
616
617
618
619
620
621
622
623
      refineFlag |= refinementManager_->refineMesh(meshes_[i]);
    }
    return refineFlag;
  }

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

624
    int nMeshes = static_cast<int>(meshes_.size());
625
    Flag coarsenFlag = 0;
626
627
    for (int i = 0; i < nMeshes; i++) {
      if (adaptInfo->isCoarseningAllowed(i)) {
628
629
630
631
632
633
634
635
636
637
638
639
640
	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_) {
641
      for (int i = 0; i < nComponents; i++) {
642
643
644
645
	adaptInfo->allowRefinement(true, i);
      }
      allowFirstRef_ = false;
    } else {
646
      for (int i = 0; i < nComponents; i++) {
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
	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();

664
665
666
667
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

Thomas Witkowski's avatar
Thomas Witkowski committed
668
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
      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
686

687
    for (int i = 0; i < nComponents; i++) {
688
      MSG("%d DOFs for %s\n", 
689
690
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());
691
692

      rhs_->getDOFVector(i)->set(0.0);
693
      for (int j = 0; j < nComponents; j++) {
694
695
696
697
698
699
700
	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();
	  }
	}
701
702
703
      }
    }

704
705
706
707
    int i;
#ifdef _OPENMP
#pragma omp parallel for 
#endif
708
    for (i = 0; i < nComponents; i++) {
709
      const BasisFunction *basisFcts = componentSpaces[i]->getBasisFcts();
710

711
      for (int j = 0; j < nComponents; j++) {
712
713
714
715
	// 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).
716
717
	DOFMatrix *matrix = (*systemMatrix_)[i][j];

718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
	// 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;
	}

735
736
737
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->initMatrix(matrix);

738
739
740
741
	BoundaryType *bound = NULL;
	if (useGetBound_) {
	  bound = GET_MEMORY(BoundaryType, basisFcts->getNumber());
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
742
	
743
744
745
746
	TraverseStack stack;
	ElInfo *elInfo = stack.traverseFirst(componentMeshes_[i], -1, assembleFlag);
	
	while (elInfo) {
747
	  if (useGetBound_) {
748
	    basisFcts->getBound(elInfo, bound);
749
	  }
Thomas Witkowski's avatar
Thomas Witkowski committed
750
	  
751
752
	  if (assembleMatrix) {
	    matrix->assemble(1.0, elInfo, bound);
Thomas Witkowski's avatar
Thomas Witkowski committed
753
	    
754
755
756
757
758
	    if (matrix->getBoundaryManager()) {
	      matrix->
		getBoundaryManager()->
		fillBoundaryConditions(elInfo, matrix);
	    }		      
759
	  }
760
761
762
763
764
765
	  
	  if (i == j) {
	    rhs_->getDOFVector(i)->assemble(1.0, elInfo, bound);
	  }
	  
	  elInfo = stack.traverseNext(elInfo);
766
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
767
	
768
769
770
771
772
773
774
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->exitMatrix(matrix);	  
	
	if (useGetBound_) {
	  FREE_MEMORY(bound, BoundaryType, basisFcts->getNumber());
	}	  
	
775
	assembledMatrix_[i][j] = true;
776
777
778
779
      }

      // fill boundary conditions
      if (rhs_->getDOFVector(i)->getBoundaryManager())
780
	rhs_->getDOFVector(i)->getBoundaryManager()->initVector(rhs_->getDOFVector(i));     
781
      
782
      if (solution_->getDOFVector(i)->getBoundaryManager())
783
      	solution_->getDOFVector(i)->getBoundaryManager()->initVector(solution_->getDOFVector(i));
784

Thomas Witkowski's avatar
Thomas Witkowski committed
785
786
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(componentMeshes_[i], -1, assembleFlag);
787
      while (elInfo) {
788
	if (rhs_->getDOFVector(i)->getBoundaryManager())
789
790
	  rhs_->getDOFVector(i)->getBoundaryManager()->
	    fillBoundaryConditions(elInfo, rhs_->getDOFVector(i));
791
792

	if (solution_->getDOFVector(i)->getBoundaryManager())
793
794
795
796
	  solution_->getDOFVector(i)->getBoundaryManager()->
	    fillBoundaryConditions(elInfo, solution_->getDOFVector(i));
	elInfo = stack.traverseNext(elInfo);
      }
797
      
798
799
800
      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
801
      solution_->getDOFVector(i)->getBoundaryManager()->exitVector(solution_->getDOFVector(i));    
802
    }
803
804
805
806
807
808

#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
809
    INFO(info_, 8)("buildAfterCoarsen needed %.5f seconds\n",
Thomas Witkowski's avatar
Thomas Witkowski committed
810
		   TIME_USED(first, clock()));
811
#endif
812
813
814
815
816
817
  }

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

818
819
820
821
822
823
824
825
826
827
828
829
830
    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);
831
    }
832
833
834
835
836
837
838
839
840
    
#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
841
842
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
843
844
845
846
847
848
849
  void ProblemVec::writeDelayedFiles()
  {
    for (int i = 0; i < static_cast<int>(fileWriters_.size()); i++) {
      fileWriters_[i]->writeDelayedFiles();
    }
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
850
851
852
853
854
855
856
857
858
859
  bool ProblemVec::existsDelayedCalculation()
  {
    for (int i = 0; i < static_cast<int>(fileWriters_.size()); i++) {
      if (fileWriters_[i]->isWritingDelayed())
	return true;   
    }

    return false;
  }

860
  void ProblemVec::interpolInitialSolution(std::vector<AbstractFunction<double, WorldVector<double> >*> *fct) 
861
862
863
864
865
866
867
868
869
870
871
872
873
  {
    FUNCNAME("ProblemVec::interpolInitialSolution()");

    solution_->interpol(fct);
  }

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

874
    if (!(*systemMatrix_)[i][j]) {
875
      TEST_EXIT(i != j)("should have been created already\n");
876
877
      (*systemMatrix_)[i][j] = NEW DOFMatrix(componentSpaces[i],
					     componentSpaces[j],
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
					     "");
      (*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, 
904
					     componentSpaces[system]);
905
    for (int i = 0; i < nComponents; i++) {
906
907
908
909
      if (systemMatrix_ && (*systemMatrix_)[system][i]) {
	(*systemMatrix_)[system][i]->getBoundaryManager()->addBoundaryCondition(dirichlet);
      }
    }
910

911
912
    if (rhs_)
      rhs_->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
913

914
915
916
917
918
919
920
921
922
923
924
    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, 
925
926
		    componentSpaces[row], 
		    componentSpaces[col]);
927
    if (rhs_)
928
929
930
931
932
933
934
935
936
937
938
      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, 
939
940
		  componentSpaces[row], 
		  componentSpaces[col]);
941
    if (rhs_)
942
      rhs_->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(robin);
943
944

    if (systemMatrix_ && (*systemMatrix_)[row][col]) {
945
946
947
948
949
950
951
952
      (*systemMatrix_)[row][col]->getBoundaryManager()->addBoundaryCondition(robin);
    }
  }

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

953
    FiniteElemSpace *feSpace = componentSpaces[row];
954
955
956

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

957
    if (systemMatrix_ && (*systemMatrix_)[row][col]) 
958
      (*systemMatrix_)[row][col]->getBoundaryManager()->addBoundaryCondition(periodic);
959
960

    if (rhs_) 
961
962
963
964
      rhs_->getDOFVector(row)->getBoundaryManager()->
	addBoundaryCondition(periodic);
  }

965
  void ProblemVec::writeResidualMesh(AdaptInfo *adaptInfo, const std::string name)
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
  {
    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);    
  }

992
  void ProblemVec::serialize(std::ostream &out) 
993
994
995
996
997
998
999
1000
  {
    FUNCNAME("ProblemVec::serialize()");

    SerializerUtil::serializeBool(out, &allowFirstRef_);
    
    for (int i = 0; i < static_cast<int>(meshes_.size()); i++) {
      meshes_[i]->serialize(out);
    }
For faster browsing, not all history is shown. View entire blame