ProblemVec.cc 48.9 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1
#include <sstream>
Thomas Witkowski's avatar
Thomas Witkowski committed
2
#include <boost/lexical_cast.hpp>
3
4
5
6
7
8
9
10
11
12
13
14
15
16
#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
17
#include "DualTraverse.h"
18
19
20
21
22
23
#include "Mesh.h"
#include "OEMSolver.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
24
#include "Flag.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
25
#include "TraverseParallel.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
26
#include "VtkWriter.h"
27
#include "ValueReader.h"
28
#include "ProblemVecDbg.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
29
#include "Debug.h"
30
31
32

namespace AMDiS {

33
34
  using boost::lexical_cast;

35
36
37
38
39
  void ProblemVec::initialize(Flag initFlag,
			      ProblemVec *adoptProblem,
			      Flag adoptFlag)
  {
    FUNCNAME("ProblemVec::initialize()");
40

41
    // === create meshes ===
Thomas Witkowski's avatar
Thomas Witkowski committed
42
    if (meshes.size() != 0) { 
43
44
45
      WARNING("meshes already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
Thomas Witkowski's avatar
Thomas Witkowski committed
46
	  (!adoptFlag.isSet(INIT_MESH) &&
Thomas Witkowski's avatar
Thomas Witkowski committed
47
	   (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE))))
48
	createMesh();
Thomas Witkowski's avatar
Thomas Witkowski committed
49

50
      if (adoptProblem && 
Thomas Witkowski's avatar
Thomas Witkowski committed
51
	  (adoptFlag.isSet(INIT_MESH) ||
52
53
	   adoptFlag.isSet(INIT_SYSTEM) ||
	   adoptFlag.isSet(INIT_FE_SPACE))) {
Thomas Witkowski's avatar
Thomas Witkowski committed
54
	meshes = adoptProblem->getMeshes();
Thomas Witkowski's avatar
Thomas Witkowski committed
55
	componentMeshes = adoptProblem->componentMeshes;
Thomas Witkowski's avatar
Thomas Witkowski committed
56
57
	refinementManager = adoptProblem->refinementManager;
	coarseningManager = adoptProblem->coarseningManager;
58
59
60

	// If the adopt problem has fewer components than this problem, but only one
	// mesh for all component, than scal up the componentMeshes array.
Thomas Witkowski's avatar
Thomas Witkowski committed
61
	if (adoptProblem->getNumComponents() < nComponents) {
Thomas Witkowski's avatar
Thomas Witkowski committed
62
	  TEST_EXIT(meshes.size() == 1)("Daran muss ich noch arbeiten!\n");
63
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
64
	  componentMeshes.resize(nComponents);
65
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
66
	    componentMeshes[i] = componentMeshes[0];
67
68
	}

69
70
71
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
72
    if (meshes.size() == 0) 
73
74
75
      WARNING("no mesh created\n");

    // === create fespace ===
76
    if (feSpaces.size() != 0) {
77
78
79
      WARNING("feSpaces already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
80
	  (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE)))
81
	createFeSpace(NULL);
82

83
84
      if (adoptProblem &&
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
85
	feSpaces = adoptProblem->getFeSpaces();
86
	componentSpaces = adoptProblem->componentSpaces;
Thomas Witkowski's avatar
Thomas Witkowski committed
87
	traverseInfo = adoptProblem->traverseInfo;
88
89
90

	// If the adopt problem has fewer components than this problem, but only one
	// fe space for all component, than scal up the componentSpaces array.
Thomas Witkowski's avatar
Thomas Witkowski committed
91
92
	if (adoptProblem->getNumComponents() < nComponents) {
	  TEST_EXIT(feSpaces.size() == 1)("Daran muss ich noch arbeiten!\n");
93
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
94
	  componentSpaces.resize(nComponents);
Thomas Witkowski's avatar
Thomas Witkowski committed
95
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
96
	    componentSpaces[i] = componentSpaces[0];
97
98
	}

99
100
101
      }
    }

102
    if (feSpaces.size() == 0) 
103
104
105
      WARNING("no feSpace created\n");

    // === create system ===
106
    if (initFlag.isSet(INIT_SYSTEM)) 
107
      createMatricesAndVectors();
108
    
109
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
110
      solution = adoptProblem->getSolution();
111
      rhs = adoptProblem->getRhs();
Thomas Witkowski's avatar
Thomas Witkowski committed
112
      systemMatrix = adoptProblem->getSystemMatrix();
113
114
115
    }

    // === create solver ===
Thomas Witkowski's avatar
Thomas Witkowski committed
116
    if (solver) {
117
118
119
120
121
122
      WARNING("solver already created\n");
    } else {
      if (initFlag.isSet(INIT_SOLVER)) {
	createSolver();
      } 
      if (adoptProblem && adoptFlag.isSet(INIT_SOLVER)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
123
124
	TEST_EXIT(!solver)("solver already created\n");
	solver = adoptProblem->getSolver();
125
126
127
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
128
    if (!solver) 
129
130
131
      WARNING("no solver created\n");

    // === create estimator ===
Thomas Witkowski's avatar
Thomas Witkowski committed
132
    if (initFlag.isSet(INIT_ESTIMATOR))
133
      createEstimator();
Thomas Witkowski's avatar
Thomas Witkowski committed
134
135

    if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR))
136
      estimator = adoptProblem->getEstimators();
137
138

    // === create marker ===
Thomas Witkowski's avatar
Thomas Witkowski committed
139
    if (initFlag.isSet(INIT_MARKER))
140
      createMarker();
Thomas Witkowski's avatar
Thomas Witkowski committed
141
    if (adoptProblem && adoptFlag.isSet(INIT_MARKER))
142
      marker = adoptProblem->getMarkers();
143
144

    // === create file writer ===
Thomas Witkowski's avatar
Thomas Witkowski committed
145
    if (initFlag.isSet(INIT_FILEWRITER))
146
147
148
149
150
151
152
153
154
155
156
      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;
157
    std::string serializationFilename = "";
158
159
160
161
162
163
164
    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;

165
      GET_PARAMETER(0, name + "->input->read serialization", "%d", &readSerialization);
Thomas Witkowski's avatar
Thomas Witkowski committed
166
      GET_PARAMETER(0, name + "->input->serialization with adaptinfo", "%d",
167
168
169
170
171
172
173
		    &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) {
Thomas Witkowski's avatar
Thomas Witkowski committed
174
	GET_PARAMETER(0, name + "->input->serialization filename", 
175
176
177
		      &serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

178
179
	// If AMDiS is compiled for parallel computations, the deserialization is
	// controlled by the parallel problem object.
180
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
181
	std::ifstream in(serializationFilename.c_str());
182
183
	deserialize(in);
	in.close();
184
185
186

	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
#endif
187
188

	deserialized = true;
189
      } else {
190
	int globalRefinements = 0;
191
192
193
194
195

	// If AMDiS is compied for parallel computations, the global refinements are
	// ignored here. Later, each rank will add the global refinements to its 
	// private mesh.
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
Thomas Witkowski's avatar
Thomas Witkowski committed
196
	GET_PARAMETER(0, meshes[0]->getName() + "->global refinements", "%d", 
197
		      &globalRefinements);
198
#endif
199

200
	// Initialize the meshes if there is no serialization file.
201
202
203
204
205
	for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
	  bool initMesh = initFlag.isSet(INIT_MESH) ||
	    (adoptProblem && adoptFlag.isSet(INIT_MESH));

	  if (initMesh && meshes[i] && !(meshes[i]->isInitialized()))
Thomas Witkowski's avatar
Thomas Witkowski committed
206
	    meshes[i]->initialize();	    
207
	}
208
209
210
211

	// === read value file and use it for the mesh values ===
	std::string valueFilename("");
	GET_PARAMETER(0, meshes[0]->getName() + "->value file name", &valueFilename); 
Thomas Witkowski's avatar
nix.  
Thomas Witkowski committed
212
	if (valueFilename.length()) {
213
214
215
216
217
218
219
220
	  ValueReader::readValue(valueFilename,
				 meshes[0],
				 solution->getDOFVector(0),
				 meshes[0]->getMacroFileInfo());
	  meshes[0]->clearMacroFileInfo();
	}

	// === do global refinements ===
221
222

	for (unsigned int i = 0; i < meshes.size(); i++)
223
	  if (initFlag.isSet(INIT_MESH) && meshes[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
224
	    refinementManager->globalRefine(meshes[i], globalRefinements);
225
226
227
228
229
230
      }
    }

    doOtherStuff();
  }

231

232
233
234
235
  void ProblemVec::createMesh() 
  {
    FUNCNAME("ProblemVec::createMesh()");

Thomas Witkowski's avatar
Thomas Witkowski committed
236
    componentMeshes.resize(nComponents);
237
    std::map<int, Mesh*> meshForRefinementSet;
238

239
    std::string meshName("");
Thomas Witkowski's avatar
Thomas Witkowski committed
240
    GET_PARAMETER(0, name + "->mesh", &meshName);
241
    TEST_EXIT(meshName != "")("no mesh name specified\n");
242
    int dim = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
243
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
244
    TEST_EXIT(dim)("no problem dimension specified!\n");
245

246
    for (int i = 0; i < nComponents; i++) {
247
      int refSet = -1;
248
249
      GET_PARAMETER(0, name + "->refinement set[" + 
		       lexical_cast<std::string>(i) + "]", "%d", &refSet);
250
      if (refSet < 0)
251
	refSet = 0;
252
      
253
      if (meshForRefinementSet[refSet] == NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
254
	Mesh *newMesh = new Mesh(meshName, dim);
255
	meshForRefinementSet[refSet] = newMesh;
Thomas Witkowski's avatar
Thomas Witkowski committed
256
257
	meshes.push_back(newMesh);
	nMeshes++;
258
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
259
      componentMeshes[i] = meshForRefinementSet[refSet];
260
261
262
    }
    switch(dim) {
    case 1:
Thomas Witkowski's avatar
Thomas Witkowski committed
263
264
      coarseningManager = new CoarseningManager1d();
      refinementManager = new RefinementManager1d();
265
266
      break;
    case 2:
Thomas Witkowski's avatar
Thomas Witkowski committed
267
268
      coarseningManager = new CoarseningManager2d();
      refinementManager = new RefinementManager2d();
269
270
      break;
    case 3:
Thomas Witkowski's avatar
Thomas Witkowski committed
271
272
      coarseningManager = new CoarseningManager3d();
      refinementManager = new RefinementManager3d();
273
274
275
276
277
278
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

279

280
  void ProblemVec::createFeSpace(DOFAdmin *admin)
281
  {
282
    FUNCNAME("ProblemVec::createFeSpace()");
283

284
    std::map<std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
285
    int dim = -1;
Thomas Witkowski's avatar
Thomas Witkowski committed
286
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
287
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");
288

289
    componentSpaces.resize(nComponents, NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
290
    traverseInfo.resize(nComponents);
291

292
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
293
      int degree = 1;
294
295
      GET_PARAMETER(0, name + "->polynomial degree[" + 
		    boost::lexical_cast<std::string>(i) + "]","%d", &degree);
296

297
      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
298

Thomas Witkowski's avatar
Thomas Witkowski committed
299
      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] == NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
300
301
302
	stringstream s;
	s << name << "->feSpace[" << i << "]";

303
304
	FiniteElemSpace *newFeSpace = 
	  FiniteElemSpace::provideFeSpace(admin, Lagrange::getLagrange(dim, degree),
Thomas Witkowski's avatar
Thomas Witkowski committed
305
					  componentMeshes[i], s.str());
306
307
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] = newFeSpace;
	feSpaces.push_back(newFeSpace);
308
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
309
310
311
312
      componentSpaces[i] = feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)];
    }

    for (int i = 0; i < nComponents; i++) {
313
      for (int j = 0; j < nComponents; j++)
314
	traverseInfo.getMatrix(i, j).setFeSpace(componentSpaces[i], componentSpaces[j]);
315
      
316
      traverseInfo.getVector(i).setFeSpace(componentSpaces[i]);
317
318
319
    }

    // create dof admin for vertex dofs if neccessary
Thomas Witkowski's avatar
Thomas Witkowski committed
320
321
322
    for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
      if (meshes[i]->getNumberOfDOFs(VERTEX) == 0) {
	DimVec<int> ln_dof(meshes[i]->getDim(), DEFAULT_VALUE, 0);
323
	ln_dof[VERTEX] = 1;
Thomas Witkowski's avatar
Thomas Witkowski committed
324
	meshes[i]->createDOFAdmin("vertex dofs", ln_dof);      
325
326
327
328
      }
    }
  }

329

330
331
332
333
334
335
  void ProblemVec::createMatricesAndVectors()
  {
    FUNCNAME("ProblemVec::createMatricesAndVectors()");

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

Thomas Witkowski's avatar
Thomas Witkowski committed
336
    systemMatrix = new Matrix<DOFMatrix*>(nComponents, nComponents);
Thomas Witkowski's avatar
Thomas Witkowski committed
337
    systemMatrix->set(NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
338
339
    rhs = new SystemVector("rhs", componentSpaces, nComponents);
    solution = new SystemVector("solution", componentSpaces, nComponents);
340

Thomas Witkowski's avatar
Thomas Witkowski committed
341
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
342
      (*systemMatrix)[i][i] = new DOFMatrix(componentSpaces[i], 
Thomas Witkowski's avatar
Thomas Witkowski committed
343
					    componentSpaces[i], "A_ii");
Thomas Witkowski's avatar
Thomas Witkowski committed
344
      (*systemMatrix)[i][i]->setCoupleMatrix(false);
Thomas Witkowski's avatar
Thomas Witkowski committed
345

346
      std::string numberedName = "rhs[" + boost::lexical_cast<std::string>(i) + "]";
Thomas Witkowski's avatar
Thomas Witkowski committed
347
      rhs->setDOFVector(i, new DOFVector<double>(componentSpaces[i], numberedName));
348
349

      numberedName = "solution[" + boost::lexical_cast<std::string>(i) + "]";
Thomas Witkowski's avatar
Thomas Witkowski committed
350
351
      solution->setDOFVector(i, new DOFVector<double>(componentSpaces[i],
      						      numberedName));
Thomas Witkowski's avatar
Thomas Witkowski committed
352
353
      solution->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution->getDOFVector(i)->set(0.0);
354
355
356
    }
  }

357

358
359
360
361
362
  void ProblemVec::createSolver()
  {
    FUNCNAME("ProblemVec::createSolver()");

    // === create solver ===
363
    std::string solverType("0");
Thomas Witkowski's avatar
Thomas Witkowski committed
364
    GET_PARAMETER(0, name + "->solver", &solverType);
365
366
    OEMSolverCreator *solverCreator = 
      dynamic_cast<OEMSolverCreator*>(CreatorMap<OEMSolver>::getCreator(solverType));
367
    TEST_EXIT(solverCreator)("no solver type\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
368
369
370
    solverCreator->setName(name + "->solver");
    solver = solverCreator->create();
    solver->initParameters();
371
372
  }

373

374
375
376
377
378
  void ProblemVec::createEstimator()
  {
    FUNCNAME("ProblemVec::createEstimator()");

    // create and set leaf data prototype
Thomas Witkowski's avatar
Thomas Witkowski committed
379
    for (unsigned int i = 0; i < meshes.size(); i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
380
      meshes[i]->setElementDataPrototype
Thomas Witkowski's avatar
Thomas Witkowski committed
381
	(new LeafDataEstimatableVec(new LeafDataCoarsenableVec));
382

Thomas Witkowski's avatar
Thomas Witkowski committed
383
384
    for (int i = 0; i < nComponents; i++) {
      TEST_EXIT(estimator[i] == NULL)("estimator already created\n");
385
386
      std::string estName = 
	name + "->estimator[" + boost::lexical_cast<std::string>(i) + "]";
387
388

      // === create estimator ===
389
      std::string estimatorType("0");
390
391
      GET_PARAMETER(0, estName, &estimatorType);
      EstimatorCreator *estimatorCreator = 
Thomas Witkowski's avatar
nix.  
Thomas Witkowski committed
392
	dynamic_cast<EstimatorCreator*>(CreatorMap<Estimator>::getCreator(estimatorType));
Thomas Witkowski's avatar
Thomas Witkowski committed
393
      if (estimatorCreator) {
394
395
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
396
	if (estimatorType == "recovery")
397
	  dynamic_cast<RecoveryEstimator::Creator*>(estimatorCreator)->
398
	    setSolution(solution->getDOFVector(i));       
Thomas Witkowski's avatar
Thomas Witkowski committed
399
	estimator[i] = estimatorCreator->create();
400
401
402
      }


Thomas Witkowski's avatar
Thomas Witkowski committed
403
404
405
406
407
      if (estimator[i])
	for (int j = 0; j < nComponents; j++)
	  estimator[i]->addSystem((*systemMatrix)[i][j], 
				  solution->getDOFVector(j), 
				  rhs->getDOFVector(j));      
408
409
410
    }
  }

411

412
413
414
415
  void ProblemVec::createMarker()
  {
    FUNCNAME("ProblemVec::createMarker()");

Thomas Witkowski's avatar
Thomas Witkowski committed
416
    int nMarkersCreated = 0;
417

418
    for (int i = 0; i < nComponents; i++) {
419
420
421
      marker[i] = Marker::createMarker
	(name + "->marker[" + boost::lexical_cast<std::string>(i) + "]", i);

422
      if (marker[i]) {
Thomas Witkowski's avatar
Thomas Witkowski committed
423
424
425
426
	nMarkersCreated++;

	// If there is more than one marker, and all components are defined
	// on the same mesh, the maximum marking has to be enabled.
427
 	if (nMarkersCreated > 1 && nMeshes == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
428
 	  marker[i]->setMaximumMarking(true);
429
430
431
432
      }
    }
  }

433

434
435
436
437
438
  void ProblemVec::createFileWriter()
  {
    FUNCNAME("ProblemVec::createFileWriter()");
  
    // Create one filewriter for all components of the problem
Thomas Witkowski's avatar
Thomas Witkowski committed
439
    std::string numberedName  = name + "->output";
440
    std::string filename = "";
441
442
443
    GET_PARAMETER(0, numberedName + "->filename", &filename);

    if (filename != "") {
444
      std::vector< DOFVector<double>* > solutionList(nComponents);
445

446
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
447
	TEST_EXIT(componentMeshes[0] == componentMeshes[i])
448
449
	  ("All Meshes have to be equal to write a vector file.\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
450
	solutionList[i] = solution->getDOFVector(i);
451
452
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
453
      fileWriters.push_back(new FileWriter(numberedName,
454
455
					   componentMeshes[0],
					   solutionList));
456
457
458
    }

    // Create own filewriters for each components of the problem
459
    for (int i = 0; i < nComponents; i++) {
460
      numberedName = name + "->output[" + boost::lexical_cast<std::string>(i) + "]";
461
462
463
      filename = "";
      GET_PARAMETER(0, numberedName + "->filename", &filename);

464
      if (filename != "")
Thomas Witkowski's avatar
Thomas Witkowski committed
465
	fileWriters.push_back(new FileWriter(numberedName, 
466
					     componentMeshes[i], 
467
					     solution->getDOFVector(i)));      
468
469
470
471
    }

    // Check for serializer
    int writeSerialization = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
472
    GET_PARAMETER(0, name + "->write serialization", "%d", &writeSerialization);
473
    if (writeSerialization) {
Thomas Witkowski's avatar
Thomas Witkowski committed
474
475
      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());
476
477
478
      ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
479
    GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
480

481
    if (writeSerialization)
Thomas Witkowski's avatar
Thomas Witkowski committed
482
      fileWriters.push_back(new Serializer<ProblemVec>(this));
483
484
  }

485

486
487
488
489
  void ProblemVec::doOtherStuff()
  {
  }

490

491
  void ProblemVec::solve(AdaptInfo *adaptInfo, bool fixedMatrix)
492
493
494
  {
    FUNCNAME("Problem::solve()");

Thomas Witkowski's avatar
Thomas Witkowski committed
495
    if (!solver) {
496
497
498
499
500
501
502
503
504
      WARNING("no solver\n");
      return;
    }

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

    clock_t first = clock();
505
    
506
    solver->solveSystem(solverMatrix, *solution, *rhs);
507

508
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
509
510
    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);
511
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
512
513
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
514
515
#endif

516
    adaptInfo->setSolverIterations(solver->getIterations());
Thomas Witkowski's avatar
Thomas Witkowski committed
517
518
519
    adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
    adaptInfo->setSolverTolerance(solver->getTolerance());
    adaptInfo->setSolverResidual(solver->getResidual());
520
521
  }

522

523
524
525
526
527
528
  void ProblemVec::estimate(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::estimate()");

    clock_t first = clock();

529
530
531
532
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

533
    if (computeExactError) {
Thomas Witkowski's avatar
Thomas Witkowski committed
534
      computeError(adaptInfo);
535
536
    } else {
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
537
	Estimator *scalEstimator = estimator[i];
538
539
	
	if (scalEstimator) {
540
541
	  traverseInfo.updateStatus();
	  scalEstimator->setTraverseInfo(traverseInfo);
542
	  scalEstimator->estimate(adaptInfo->getTimestep());
543

544
545
	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);
546
547
548
549
550

	  if (adaptInfo->getRosenbrockMode() == false) {
	    adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
	    adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
	  }
551
	}
552
553
554
      }
    }

555
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
556
557
    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);
558
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
559
560
    INFO(info, 8)("estimation of the error needed %.5f seconds\n",
		  TIME_USED(first, clock()));
561
#endif
562
563
  }

564

565
566
567
568
  Flag ProblemVec::markElements(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::markElements()");

569
    TEST_EXIT_DBG(static_cast<unsigned int>(nComponents) == marker.size())
Thomas Witkowski's avatar
Thomas Witkowski committed
570
571
      ("Wrong number of markers!\n");

572
    Flag markFlag = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
573
    for (int i = 0; i < nComponents; i++) {
574
      if (marker[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
575
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
576
      else
Thomas Witkowski's avatar
Thomas Witkowski committed
577
578
	WARNING("No marker for component %d\n", i);              
    }
579
    
580
581
582
    return markFlag;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
583

584
585
586
587
  Flag ProblemVec::refineMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::refineMesh()");

Thomas Witkowski's avatar
Thomas Witkowski committed
588
    int nMeshes = static_cast<int>(meshes.size());
589
    Flag refineFlag = 0;
590
591
592
593
    for (int i = 0; i < nMeshes; i++)
      if (adaptInfo->isRefinementAllowed(i))
	refineFlag |= refinementManager->refineMesh(meshes[i]);

594
595
596
    return refineFlag;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
597

598
599
600
601
  Flag ProblemVec::coarsenMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::coarsenMesh()");

Thomas Witkowski's avatar
Thomas Witkowski committed
602
    int nMeshes = static_cast<int>(meshes.size());
603
    Flag coarsenFlag = 0;
604
605
    for (int i = 0; i < nMeshes; i++)
      if (adaptInfo->isCoarseningAllowed(i))
Thomas Witkowski's avatar
Thomas Witkowski committed
606
	coarsenFlag |= coarseningManager->coarsenMesh(meshes[i]);
607
608
609
610

    return coarsenFlag;
  }

Thomas Witkowski's avatar
Thomas Witkowski committed
611

612
613
614
615
  Flag ProblemVec::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
  {
    FUNCNAME("ProblemVec::oneIteration()");

616
617
618
619
620
    for (int i = 0; i < nComponents; i++)
      if (adaptInfo->spaceToleranceReached(i))
	adaptInfo->allowRefinement(false, i);
      else
	adaptInfo->allowRefinement(true, i);	
621
622
623
624

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

Thomas Witkowski's avatar
Thomas Witkowski committed
625

626
627
  void ProblemVec::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
				     bool asmMatrix, bool asmVector)
628
629
630
  {
    FUNCNAME("ProblemVec::buildAfterCoarsen()");

631
    if (dualMeshTraverseRequired()) {
632
      dualAssemble(adaptInfo, flag, asmMatrix, asmVector);
633
634
      return;
    }
635

636
    //    printOpenmpTraverseInfo(this, true);
637
638
    //    std::cout << "ElInfo = " << ElInfo::subElemMatrices.size() << std::endl;

Thomas Witkowski's avatar
Thomas Witkowski committed
639
640
641
642
    for (unsigned int i = 0; i < meshes.size(); i++)
      meshes[i]->dofCompress();


643
    clock_t first = clock();
644
645
646
647
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

648
649
650

    Flag assembleFlag = 
      flag | 
Thomas Witkowski's avatar
Thomas Witkowski committed
651
652
      (*systemMatrix)[0][0]->getAssembleFlag() | 
      rhs->getDOFVector(0)->getAssembleFlag()  |
653
654
655
656
      Mesh::CALL_LEAF_EL                        | 
      Mesh::FILL_COORDS                         |
      Mesh::FILL_DET                            |
      Mesh::FILL_GRD_LAMBDA |
657
658
      Mesh::FILL_NEIGH;

Thomas Witkowski's avatar
Thomas Witkowski committed
659
    if (useGetBound)
660
      assembleFlag |= Mesh::FILL_BOUND;
Thomas Witkowski's avatar
Thomas Witkowski committed
661
662

  
Thomas Witkowski's avatar
Thomas Witkowski committed
663
    traverseInfo.updateStatus();
664
665
666
    // Used to calculate the overall number of non zero entries.
    int nnz = 0;

Thomas Witkowski's avatar
Thomas Witkowski committed
667
    for (int i = 0; i < nComponents; i++) {
668

669
670
671
672
673
674
      MSG("%d DOFs for %s\n", 
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());

      rhs->getDOFVector(i)->set(0.0);

675
      for (int j = 0; j < nComponents; j++) {
676

677
678
	//	if (writeAsmInfo)
	//	  MSG("--------- %d %d -------------\n", i, j);
679

680
681
682
683
	// 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).
684
	DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
685

686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
	if (writeAsmInfo && matrix) {
	  for (std::vector<Operator*>::iterator it = matrix->getOperatorsBegin();
	       it != matrix->getOperatorsEnd(); ++it) {
	    Assembler *assembler = (*it)->getAssembler();
	    if (assembler->getZeroOrderAssembler()) 
	      std::cout << "ZOA: " << assembler->getZeroOrderAssembler()->getName() << std::endl;
	    if (assembler->getFirstOrderAssembler(GRD_PSI)) 
	      std::cout << "FOA GRD_PSI: " << assembler->getFirstOrderAssembler(GRD_PSI)->getName() << std::endl;
	    if (assembler->getFirstOrderAssembler(GRD_PHI)) 
	      std::cout << "FOA GRD_PHI: " << assembler->getFirstOrderAssembler(GRD_PHI)->getName() << std::endl;
	    if (assembler->getSecondOrderAssembler()) 
	      std::cout << "SOA: " << assembler->getSecondOrderAssembler()->getName() << std::endl;
	  }
	}

701
702
703
	if (matrix) 
	  matrix->calculateNnz();
	
704
705
	// If the matrix was assembled before and it is marked to be assembled
	// only once, it will not be assembled.
706
	if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) {
707
	  assembleMatrix = false;
708
709
710
711
712
713
714
	} else if (matrix) {
	  matrix->getBaseMatrix().
	    change_dim(componentSpaces[i]->getAdmin()->getUsedSize(), 
		       componentSpaces[j]->getAdmin()->getUsedSize());

	  set_to_zero(matrix->getBaseMatrix());
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
715
716

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
717
	if (!matrix || !assembleMatrix)
718
719
	  assembleMatrix = false;

720
721
722
	// 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.
723
724
725
726
	if (!assembleMatrix && i != j) {
	  if (matrix)
	    nnz += matrix->getBaseMatrix().nnz();

727
	  continue;
728
	}
729

730
731
732
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->initMatrix(matrix);

733
734
735
736
737
738
739
740
	// The simplest case: either the right hand side has no operaters, no aux
	// fe spaces, or all aux fe spaces are equal to the row and col fe space.
	assembleOnOneMesh(componentSpaces[i],
			  assembleFlag,
			  assembleMatrix ? matrix : NULL,
			  ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);
      
	assembledMatrix[i][j] = true;
Thomas Witkowski's avatar
Thomas Witkowski committed
741

Thomas Witkowski's avatar
Thomas Witkowski committed
742
	
743
744
	if (assembleMatrix)
	  matrix->finishInsertion();
Thomas Witkowski's avatar
Thomas Witkowski committed
745

746
747
748
749
 	if (assembleMatrix && matrix->getBoundaryManager())
 	  matrix->getBoundaryManager()->exitMatrix(matrix);	
	
	if (matrix)
Thomas Witkowski's avatar
Thomas Witkowski committed
750
	  nnz += matrix->getBaseMatrix().nnz();
751
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
752

753
754
      // And now assemble boundary conditions on the vectors
      assembleBoundaryConditions(rhs->getDOFVector(i),
Thomas Witkowski's avatar
Thomas Witkowski committed
755
756
757
 				 solution->getDOFVector(i),
 				 componentMeshes[i],
 				 assembleFlag);     
758
    }  
759

760
    if (asmMatrix) {
761
      solverMatrix.setMatrix(*systemMatrix);
762
      createPrecon();
Thomas Witkowski's avatar
Thomas Witkowski committed
763

764
765
      INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
    }
766

767
768
769
770
771
772
773
774
#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
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));    
#endif    
  }
775

776
777
778
779
780
781
782
783
784
785
786

  bool ProblemVec::dualMeshTraverseRequired()
  {
    FUNCNAME("ProblemVec::dualMeshTraverseRequired()");

    TEST_EXIT(meshes.size() <= 2)("More than two mneshes are not supported yet!\n");    

    return (meshes.size() == 2);
  }
  

787
788
  void ProblemVec::dualAssemble(AdaptInfo *adaptInfo, Flag flag, 
				bool asmMatrix, bool asmVector)
789
790
791
  {
    FUNCNAME("ProblemVec::dualAssemble()");

792
793
    TEST_EXIT(asmVector)("Not yet implemented!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
794
795
796
797
    for (unsigned int i = 0; i < meshes.size(); i++)
      meshes[i]->dofCompress();


798
799
800
801
802
    clock_t first = clock();
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

Thomas Witkowski's avatar
Thomas Witkowski committed
803
    
804
805
806
807
    Flag assembleFlag = 
      flag | 
      (*systemMatrix)[0][0]->getAssembleFlag() | 
      rhs->getDOFVector(0)->getAssembleFlag()  |
808
809
810
811
      Mesh::CALL_LEAF_EL                        | 
      Mesh::FILL_COORDS                         |
      Mesh::FILL_DET                            |
      Mesh::FILL_GRD_LAMBDA |
812
813
814
815
      Mesh::FILL_NEIGH;

    if (useGetBound)
      assembleFlag |= Mesh::FILL_BOUND;
Thomas Witkowski's avatar
Thomas Witkowski committed
816

817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
    traverseInfo.updateStatus();

    // Used to calculate the overall number of non zero entries.
    int nnz = 0;

    for (int i = 0; i < nComponents; i++) {

      MSG("%d DOFs for %s\n", 
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());

      rhs->getDOFVector(i)->set(0.0);

      for (int j = 0; j < nComponents; j++) {

	if (writeAsmInfo)
	  std::cout << "-------" << i << " " << j << "----------------" << std::endl;

	// 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).
839
	DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
840
841
842
843
844
845
846
847
848
849
850
851
852

	if (writeAsmInfo && matrix) {
	  for (std::vector<Operator*>::iterator it = matrix->getOperatorsBegin();
	       it != matrix->getOperatorsEnd(); ++it) {
	    Assembler *assembler = (*it)->getAssembler();
	    if (assembler->getZeroOrderAssembler()) 
	      std::cout << "ZOA: " << assembler->getZeroOrderAssembler()->getName() << std::endl;
	    if (assembler->getFirstOrderAssembler(GRD_PSI)) 
	      std::cout << "FOA GRD_PSI: " << assembler->getFirstOrderAssembler(GRD_PSI)->getName() << std::endl;
	    if (assembler->getFirstOrderAssembler(GRD_PHI)) 
	      std::cout << "FOA GRD_PHI: " << assembler->getFirstOrderAssembler(GRD_PHI)->getName() << std::endl;
	    if (assembler->getSecondOrderAssembler()) 
	      std::cout << "SOA: " << assembler->getSecondOrderAssembler()->getName() << std::endl;
Thomas Witkowski's avatar
Thomas Witkowski committed
853
	  }
854
	}