ProblemVec.cc 43.1 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1
#include <sstream>
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"
29
30
31

namespace AMDiS {

32
33
  using boost::lexical_cast;

34
35
36
37
38
  void ProblemVec::initialize(Flag initFlag,
			      ProblemVec *adoptProblem,
			      Flag adoptFlag)
  {
    FUNCNAME("ProblemVec::initialize()");
39

40
    // === create meshes ===
Thomas Witkowski's avatar
Thomas Witkowski committed
41
    if (meshes.size() != 0) { 
42
43
44
      WARNING("meshes already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
Thomas Witkowski's avatar
Thomas Witkowski committed
45
	  (!adoptFlag.isSet(INIT_MESH) &&
46
47
48
49
50
51
52
	   (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))) {
Thomas Witkowski's avatar
Thomas Witkowski committed
53
	meshes = adoptProblem->getMeshes();
Thomas Witkowski's avatar
Thomas Witkowski committed
54
	componentMeshes = adoptProblem->componentMeshes;
Thomas Witkowski's avatar
Thomas Witkowski committed
55
56
	refinementManager = adoptProblem->refinementManager;
	coarseningManager = adoptProblem->coarseningManager;
57
58
59

	// 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
60
	if (adoptProblem->getNumComponents() < nComponents) {
Thomas Witkowski's avatar
Thomas Witkowski committed
61
	  TEST_EXIT(meshes.size() == 1)("Daran muss ich noch arbeiten!\n");
62
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
63
	  componentMeshes.resize(nComponents);
64
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
65
	    componentMeshes[i] = componentMeshes[0];
66
67
	}

68
69
70
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
71
    if (meshes.size() == 0) 
72
73
74
      WARNING("no mesh created\n");

    // === create fespace ===
75
    if (feSpaces.size() != 0) {
76
77
78
      WARNING("feSpaces already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
79
80
	  (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE)))
	createFESpace(NULL);
81

82
83
      if (adoptProblem &&
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
84
85
	feSpaces = adoptProblem->getFESpaces();
	componentSpaces = adoptProblem->componentSpaces;
Thomas Witkowski's avatar
Thomas Witkowski committed
86
	traverseInfo = adoptProblem->traverseInfo;
87
88
89

	// 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
90
91
	if (adoptProblem->getNumComponents() < nComponents) {
	  TEST_EXIT(feSpaces.size() == 1)("Daran muss ich noch arbeiten!\n");
92
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
93
	  componentSpaces.resize(nComponents);
Thomas Witkowski's avatar
Thomas Witkowski committed
94
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
95
	    componentSpaces[i] = componentSpaces[0];
96
97
	}

98
99
100
      }
    }

101
    if (feSpaces.size() == 0) 
102
103
104
      WARNING("no feSpace created\n");

    // === create system ===
105
    if (initFlag.isSet(INIT_SYSTEM)) 
106
      createMatricesAndVectors();
107
    
108
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
109
110
111
      solution = adoptProblem->getSolution();
      rhs = adoptProblem->getRHS();
      systemMatrix = adoptProblem->getSystemMatrix();
112
113
114
    }

    // === create solver ===
Thomas Witkowski's avatar
Thomas Witkowski committed
115
    if (solver) {
116
117
118
119
120
121
      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
122
123
	TEST_EXIT(!solver)("solver already created\n");
	solver = adoptProblem->getSolver();
124
125
126
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
127
    if (!solver) 
128
129
130
      WARNING("no solver created\n");

    // === create estimator ===
Thomas Witkowski's avatar
Thomas Witkowski committed
131
    if (initFlag.isSet(INIT_ESTIMATOR))
132
      createEstimator();
Thomas Witkowski's avatar
Thomas Witkowski committed
133
134

    if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR))
Thomas Witkowski's avatar
Thomas Witkowski committed
135
      estimator = adoptProblem->getEstimator();
136
137

    // === create marker ===
Thomas Witkowski's avatar
Thomas Witkowski committed
138
    if (initFlag.isSet(INIT_MARKER))
139
      createMarker();
Thomas Witkowski's avatar
Thomas Witkowski committed
140
    if (adoptProblem && adoptFlag.isSet(INIT_MARKER))
141
      marker = adoptProblem->getMarker();
142
143

    // === create file writer ===
Thomas Witkowski's avatar
Thomas Witkowski committed
144
    if (initFlag.isSet(INIT_FILEWRITER))
145
146
147
148
149
150
151
152
153
154
155
      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;
156
    std::string serializationFilename = "";
157
158
159
160
161
162
163
    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;

164
      GET_PARAMETER(0, name + "->input->read serialization", "%d", &readSerialization);
Thomas Witkowski's avatar
Thomas Witkowski committed
165
      GET_PARAMETER(0, name + "->input->serialization with adaptinfo", "%d",
166
167
168
169
170
171
172
		    &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
173
	GET_PARAMETER(0, name + "->input->serialization filename", 
174
175
176
		      &serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

177
178
	// If AMDiS is compiled for parallel computations, the deserialization is
	// controlled by the parallel problem object.
179
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
180
	std::ifstream in(serializationFilename.c_str());
181
182
	deserialize(in);
	in.close();
183
184
185

	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
#endif
186
      } else {
187
	int globalRefinements = 0;
188
189
190
191
192

	// 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
193
	GET_PARAMETER(0, meshes[0]->getName() + "->global refinements", "%d", 
194
		      &globalRefinements);
195
#endif
196

197
	// Initialize the meshes if there is no serialization file.
198
199
200
201
202
	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
203
	    meshes[i]->initialize();	    
204
	}
205
206
207
208

	// === 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
209
	if (valueFilename.length()) {
210
211
212
213
214
215
216
217
218
219
	  ValueReader::readValue(valueFilename,
				 meshes[0],
				 solution->getDOFVector(0),
				 meshes[0]->getMacroFileInfo());
	  meshes[0]->clearMacroFileInfo();
	}

	// === do global refinements ===
	for (int i = 0; i < static_cast<int>(meshes.size()); i++)
	  if (initFlag.isSet(INIT_MESH) && meshes[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
220
	    refinementManager->globalRefine(meshes[i], globalRefinements);
221
222
223
224
225
226
227
228
229
230
      }
    }

    doOtherStuff();
  }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
231
    componentMeshes.resize(nComponents);
232
    std::map<int, Mesh*> meshForRefinementSet;
233

234
    std::string meshName("");
Thomas Witkowski's avatar
Thomas Witkowski committed
235
    GET_PARAMETER(0, name + "->mesh", &meshName);
236
    TEST_EXIT(meshName != "")("no mesh name specified\n");
237
    int dim = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
238
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
239
    TEST_EXIT(dim)("no problem dimension specified!\n");
240

241
    for (int i = 0; i < nComponents; i++) {
242
      int refSet = -1;
243
244
      GET_PARAMETER(0, name + "->refinement set[" + 
		       lexical_cast<std::string>(i) + "]", "%d", &refSet);
245
      if (refSet < 0)
246
	refSet = 0;
247
      
248
      if (meshForRefinementSet[refSet] == NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
249
	Mesh *newMesh = new Mesh(meshName, dim);
250
	meshForRefinementSet[refSet] = newMesh;
Thomas Witkowski's avatar
Thomas Witkowski committed
251
252
	meshes.push_back(newMesh);
	nMeshes++;
253
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
254
      componentMeshes[i] = meshForRefinementSet[refSet];
255
256
257
    }
    switch(dim) {
    case 1:
Thomas Witkowski's avatar
Thomas Witkowski committed
258
259
      coarseningManager = new CoarseningManager1d();
      refinementManager = new RefinementManager1d();
260
261
      break;
    case 2:
Thomas Witkowski's avatar
Thomas Witkowski committed
262
263
      coarseningManager = new CoarseningManager2d();
      refinementManager = new RefinementManager2d();
264
265
      break;
    case 3:
Thomas Witkowski's avatar
Thomas Witkowski committed
266
267
      coarseningManager = new CoarseningManager3d();
      refinementManager = new RefinementManager3d();
268
269
270
271
272
273
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

274
  void ProblemVec::createFESpace(DOFAdmin *admin)
275
276
277
  {
    FUNCNAME("ProblemVec::createFESpace()");

278
    std::map<std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
279
    int dim = -1;
Thomas Witkowski's avatar
Thomas Witkowski committed
280
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
281
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");
282

283
    componentSpaces.resize(nComponents, NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
284
    traverseInfo.resize(nComponents);
285

286
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
287
      int degree = 1;
288
289
      GET_PARAMETER(0, name + "->polynomial degree[" + 
		    boost::lexical_cast<std::string>(i) + "]","%d", &degree);
290

291
      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
292

Thomas Witkowski's avatar
Thomas Witkowski committed
293
      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] == NULL) {
Thomas Witkowski's avatar
Thomas Witkowski committed
294
295
296
	stringstream s;
	s << name << "->feSpace[" << i << "]";

297
	FiniteElemSpace *newFESpace = 
298
	  FiniteElemSpace::provideFESpace(admin, Lagrange::getLagrange(dim, degree),
Thomas Witkowski's avatar
Thomas Witkowski committed
299
					  componentMeshes[i], s.str());
Thomas Witkowski's avatar
Thomas Witkowski committed
300
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] = newFESpace;
301
	feSpaces.push_back(newFESpace);
302
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
303
304
305
306
      componentSpaces[i] = feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)];
    }

    for (int i = 0; i < nComponents; i++) {
307
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Thomas Witkowski committed
308
	traverseInfo.getMatrix(i, j).setFESpace(componentSpaces[i], componentSpaces[j]);
309
      
Thomas Witkowski's avatar
Thomas Witkowski committed
310
      traverseInfo.getVector(i).setFESpace(componentSpaces[i]);
311
312
313
    }

    // create dof admin for vertex dofs if neccessary
Thomas Witkowski's avatar
Thomas Witkowski committed
314
315
316
    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);
317
	ln_dof[VERTEX] = 1;
Thomas Witkowski's avatar
Thomas Witkowski committed
318
	meshes[i]->createDOFAdmin("vertex dofs", ln_dof);      
319
320
321
322
323
324
325
326
327
328
      }
    }
  }

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

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

Thomas Witkowski's avatar
Thomas Witkowski committed
329
    systemMatrix = new Matrix<DOFMatrix*>(nComponents, nComponents);
Thomas Witkowski's avatar
Thomas Witkowski committed
330
    systemMatrix->set(NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
331
332
    rhs = new SystemVector("rhs", componentSpaces, nComponents);
    solution = new SystemVector("solution", componentSpaces, nComponents);
333

Thomas Witkowski's avatar
Thomas Witkowski committed
334
    for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
335
      (*systemMatrix)[i][i] = new DOFMatrix(componentSpaces[i], 
Thomas Witkowski's avatar
Thomas Witkowski committed
336
					    componentSpaces[i], "A_ii");
Thomas Witkowski's avatar
Thomas Witkowski committed
337
      (*systemMatrix)[i][i]->setCoupleMatrix(false);
Thomas Witkowski's avatar
Thomas Witkowski committed
338

339
      std::string numberedName = "rhs[" + boost::lexical_cast<std::string>(i) + "]";
Thomas Witkowski's avatar
Thomas Witkowski committed
340
      rhs->setDOFVector(i, new DOFVector<double>(componentSpaces[i], numberedName));
341
342

      numberedName = "solution[" + boost::lexical_cast<std::string>(i) + "]";
Thomas Witkowski's avatar
Thomas Witkowski committed
343
344
      solution->setDOFVector(i, new DOFVector<double>(componentSpaces[i],
      						      numberedName));
Thomas Witkowski's avatar
Thomas Witkowski committed
345
346
      solution->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution->getDOFVector(i)->set(0.0);
347
348
349
350
351
352
353
354
    }
  }

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

    // === create solver ===
355
    std::string solverType("0");
Thomas Witkowski's avatar
Thomas Witkowski committed
356
    GET_PARAMETER(0, name + "->solver", &solverType);
357
358
    OEMSolverCreator *solverCreator = 
      dynamic_cast<OEMSolverCreator*>(CreatorMap<OEMSolver>::getCreator(solverType));
359
    TEST_EXIT(solverCreator)("no solver type\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
360
361
362
    solverCreator->setName(name + "->solver");
    solver = solverCreator->create();
    solver->initParameters();
363
364
365
366
367
368
369
  }

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

    // create and set leaf data prototype
370
    for (int i = 0; i < static_cast<int>(meshes.size()); i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
371
      meshes[i]->setElementDataPrototype
Thomas Witkowski's avatar
Thomas Witkowski committed
372
	(new LeafDataEstimatableVec(new LeafDataCoarsenableVec));
373

Thomas Witkowski's avatar
Thomas Witkowski committed
374
375
    for (int i = 0; i < nComponents; i++) {
      TEST_EXIT(estimator[i] == NULL)("estimator already created\n");
376
377
      std::string estName = 
	name + "->estimator[" + boost::lexical_cast<std::string>(i) + "]";
378
379

      // === create estimator ===
380
      std::string estimatorType("0");
381
382
      GET_PARAMETER(0, estName, &estimatorType);
      EstimatorCreator *estimatorCreator = 
Thomas Witkowski's avatar
nix.    
Thomas Witkowski committed
383
	dynamic_cast<EstimatorCreator*>(CreatorMap<Estimator>::getCreator(estimatorType));
Thomas Witkowski's avatar
Thomas Witkowski committed
384
      if (estimatorCreator) {
385
386
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
Thomas Witkowski's avatar
Thomas Witkowski committed
387
	if (estimatorType == "recovery") {
388
	  dynamic_cast<RecoveryEstimator::Creator*>(estimatorCreator)->
Thomas Witkowski's avatar
Thomas Witkowski committed
389
	    setSolution(solution->getDOFVector(i));
390
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
391
	estimator[i] = estimatorCreator->create();
392
393
394
      }


Thomas Witkowski's avatar
Thomas Witkowski committed
395
      if (estimator[i]) {
396
	for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Thomas Witkowski committed
397
398
399
	  estimator[i]->addSystem((*systemMatrix)[i][j], 
				   solution->getDOFVector(j), 
				   rhs->getDOFVector(j));
400
401
402
403
404
405
406
407
      }
    }
  }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
408
    int nMarkersCreated = 0;
409

410
    for (int i = 0; i < nComponents; i++) {
411
412
413
      marker[i] = Marker::createMarker
	(name + "->marker[" + boost::lexical_cast<std::string>(i) + "]", i);

414
      if (marker[i]) {
Thomas Witkowski's avatar
Thomas Witkowski committed
415
416
417
418
	nMarkersCreated++;

	// If there is more than one marker, and all components are defined
	// on the same mesh, the maximum marking has to be enabled.
419
 	if (nMarkersCreated > 1 && nMeshes == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
420
 	  marker[i]->setMaximumMarking(true);
421
422
423
424
425
426
427
428
429
      }
    }
  }

  void ProblemVec::createFileWriter()
  {
    FUNCNAME("ProblemVec::createFileWriter()");
  
    // Create one filewriter for all components of the problem
Thomas Witkowski's avatar
Thomas Witkowski committed
430
    std::string numberedName  = name + "->output";
431
    std::string filename = "";
432
433
434
    GET_PARAMETER(0, numberedName + "->filename", &filename);

    if (filename != "") {
435
      std::vector< DOFVector<double>* > solutionList(nComponents);
436

437
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
438
	TEST_EXIT(componentMeshes[0] == componentMeshes[i])
439
440
	  ("All Meshes have to be equal to write a vector file.\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
441
	solutionList[i] = solution->getDOFVector(i);
442
443
      }

Thomas Witkowski's avatar
Thomas Witkowski committed
444
      fileWriters.push_back(new FileWriter(numberedName,
Thomas Witkowski's avatar
Thomas Witkowski committed
445
					    componentMeshes[0],
446
447
448
449
					    solutionList));
    }

    // Create own filewriters for each components of the problem
450
    for (int i = 0; i < nComponents; i++) {
451
      numberedName = name + "->output[" + boost::lexical_cast<std::string>(i) + "]";
452
453
454
      filename = "";
      GET_PARAMETER(0, numberedName + "->filename", &filename);

455
      if (filename != "")
Thomas Witkowski's avatar
Thomas Witkowski committed
456
	fileWriters.push_back(new FileWriter(numberedName, 
457
458
					     componentMeshes[i], 
					     solution->getDOFVector(i)));
459
460
461
462
    }

    // Check for serializer
    int writeSerialization = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
463
    GET_PARAMETER(0, name + "->write serialization", "%d", &writeSerialization);
464
    if (writeSerialization) {
Thomas Witkowski's avatar
Thomas Witkowski committed
465
466
      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());
467
468
469
      ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
470
    GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
471
472
473
474

    // Serialization is not allowed to be done by the problem, if its part of a parallel
    // problem definition. Than, the parallel problem object must be serialized.
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
475
    if (writeSerialization)
Thomas Witkowski's avatar
Thomas Witkowski committed
476
      fileWriters.push_back(new Serializer<ProblemVec>(this));
477
#endif
478
479
480
481
482
483
  }

  void ProblemVec::doOtherStuff()
  {
  }

484
  void ProblemVec::solve(AdaptInfo *adaptInfo, bool fixedMatrix)
485
486
487
  {
    FUNCNAME("Problem::solve()");

Thomas Witkowski's avatar
Thomas Witkowski committed
488
    if (!solver) {
489
490
491
492
493
494
495
496
497
      WARNING("no solver\n");
      return;
    }

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

    clock_t first = clock();
498
    solver->solveSystem(solverMatrix, *solution, *rhs);
499

500
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
501
502
    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);
503
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
504
505
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
506
507
#endif

508
    adaptInfo->setSolverIterations(solver->getIterations());
Thomas Witkowski's avatar
Thomas Witkowski committed
509
510
511
    adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
    adaptInfo->setSolverTolerance(solver->getTolerance());
    adaptInfo->setSolverResidual(solver->getResidual());
512
513
514
515
516
517
518
519
  }

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

    clock_t first = clock();

520
521
522
523
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

524
    if (computeExactError) {
Thomas Witkowski's avatar
Thomas Witkowski committed
525
      computeError(adaptInfo);
526
527
    } else {
      for (int i = 0; i < nComponents; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
528
	Estimator *scalEstimator = estimator[i];
529
530
531
532
533
534
535
536
537
538
	
	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);
	}
539
540
541
      }
    }

542
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
543
544
    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);
545
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
546
547
    INFO(info, 8)("estimation of the error needed %.5f seconds\n",
		  TIME_USED(first, clock()));
548
549

#endif
550
551
552
553
554
555
556
557
558
559
560
  }

  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;
561
562
    for (int i = 0; i < nComponents; i++)
      if (marker[i])
Thomas Witkowski's avatar
Thomas Witkowski committed
563
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
564
565
      else
	WARNING("no marker for component %d\n", i);         
566
    
567
568
569
570
571
572
573
    return markFlag;
  }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
574
    int nMeshes = static_cast<int>(meshes.size());
575
    Flag refineFlag = 0;
576
577
578
579
    for (int i = 0; i < nMeshes; i++)
      if (adaptInfo->isRefinementAllowed(i))
	refineFlag |= refinementManager->refineMesh(meshes[i]);

580
581
582
583
584
585
586
    return refineFlag;
  }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
587
    int nMeshes = static_cast<int>(meshes.size());
588
    Flag coarsenFlag = 0;
589
590
    for (int i = 0; i < nMeshes; i++)
      if (adaptInfo->isCoarseningAllowed(i))
Thomas Witkowski's avatar
Thomas Witkowski committed
591
	coarsenFlag |= coarseningManager->coarsenMesh(meshes[i]);
592
593
594
595
596
597
598
599

    return coarsenFlag;
  }

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

Thomas Witkowski's avatar
Thomas Witkowski committed
600
    if (allowFirstRef) {
Thomas Witkowski's avatar
Thomas Witkowski committed
601
      for (int i = 0; i < nComponents; i++)
602
	adaptInfo->allowRefinement(true, i);
Thomas Witkowski's avatar
Thomas Witkowski committed
603

Thomas Witkowski's avatar
Thomas Witkowski committed
604
      allowFirstRef = false;
605
    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
606
607
      for (int i = 0; i < nComponents; i++)
	if (adaptInfo->spaceToleranceReached(i))
608
	  adaptInfo->allowRefinement(false, i);
Thomas Witkowski's avatar
Thomas Witkowski committed
609
	else
610
611
612
613
614
615
	  adaptInfo->allowRefinement(true, i);	
    }

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

616
617
  void ProblemVec::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
				     bool asmMatrix, bool asmVector)
618
619
620
  {
    FUNCNAME("ProblemVec::buildAfterCoarsen()");

621
    //    printOpenmpTraverseInfo(this, true);
622

623
    clock_t first = clock();
624
625
626
627
#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

628
    for (int i = 0; i < static_cast<int>(meshes.size()); i++)
Thomas Witkowski's avatar
Thomas Witkowski committed
629
      meshes[i]->dofCompress();
630
631
632

    Flag assembleFlag = 
      flag | 
Thomas Witkowski's avatar
Thomas Witkowski committed
633
634
      (*systemMatrix)[0][0]->getAssembleFlag() | 
      rhs->getDOFVector(0)->getAssembleFlag()  |
635
636
637
638
639
640
      Mesh::CALL_LEAF_EL                        | 
      Mesh::FILL_COORDS                         |
      Mesh::FILL_DET                            |
      Mesh::FILL_GRD_LAMBDA |
      Mesh::FILL_NEIGH;

Thomas Witkowski's avatar
Thomas Witkowski committed
641
    if (useGetBound)
642
      assembleFlag |= Mesh::FILL_BOUND;
Thomas Witkowski's avatar
Thomas Witkowski committed
643

Thomas Witkowski's avatar
Thomas Witkowski committed
644
645
    traverseInfo.updateStatus();

646
647
648
    // Used to calculate the overall number of non zero entries.
    int nnz = 0;

Thomas Witkowski's avatar
Thomas Witkowski committed
649
    for (int i = 0; i < nComponents; i++) {
650

651
652
653
654
655
656
      MSG("%d DOFs for %s\n", 
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());

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

657
      for (int j = 0; j < nComponents; j++) {
658

659
660
661
662
	// 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).
Thomas Witkowski's avatar
Thomas Witkowski committed
663
	DOFMatrix *matrix = (*systemMatrix)[i][j];
664

665
666
667
	if (matrix) 
	  matrix->calculateNnz();
	
668
669
	// If the matrix was assembled before and it is marked to be assembled
	// only once, it will not be assembled.
670
	if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) {
671
	  assembleMatrix = false;
672
673
674
675
676
677
678
	} 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
679
680

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
681
	if (!matrix || !assembleMatrix)
682
683
	  assembleMatrix = false;

684
685
686
	// 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.
687
688
689
690
	if (!assembleMatrix && i != j) {
	  if (matrix)
	    nnz += matrix->getBaseMatrix().nnz();

691
	  continue;
692
	}
693

694
695
696
	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->initMatrix(matrix);

Thomas Witkowski's avatar
Thomas Witkowski committed
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
	if (traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_NO_AUX ||
	    traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_WITH_AUX) {

	  // Row fe space and col fe space are both equal

	  if (traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_NO_AUX ||
	      traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_WITH_AUX) {

	    // 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);

	  } else if (traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_WITH_DIF_AUX) {

	    // Row fe space and col fe space are both equal, but right hand side has at
716
	    // least one another aux fe space. 
Thomas Witkowski's avatar
Thomas Witkowski committed
717
718
719
720
721
722

	    assembleOnOneMesh(componentSpaces[i],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
			      ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);

723
724
	    assembleOnDifMeshes2(componentSpaces[i], 
				 traverseInfo.getAuxFESpace(i, j),
Thomas Witkowski's avatar
Thomas Witkowski committed
725
726
				 assembleFlag,
				 NULL,
727
				 ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
728
729
730
731
732
733
734

	  } else {
	    ERROR_EXIT("Possible? If yes, not yet implemented!\n");
	  }

	} else if (traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_WITH_DIF_AUX) {
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
735
736
737
	  assembleOnOneMesh(componentSpaces[i],
			    assembleFlag,
			    assembleMatrix ? matrix : NULL,
Thomas Witkowski's avatar
Thomas Witkowski committed
738
			    ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);
739
	  
Thomas Witkowski's avatar
Thomas Witkowski committed
740
741
742
743
	  assembleOnDifMeshes2(componentSpaces[i],
			       traverseInfo.getAuxFESpace(i, j),
			       assembleFlag,
			       assembleMatrix ? matrix : NULL,
744
			       ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
745
746
747
748

	} else if (traverseInfo.getStatus(i, j) ==  SingleComponentInfo::DIF_SPACES_NO_AUX ||
		   traverseInfo.getStatus(i, j) ==  SingleComponentInfo::DIF_SPACES_WITH_AUX) {

Thomas Witkowski's avatar
Thomas Witkowski committed
749
750
751
	  assembleOnDifMeshes(componentSpaces[i], componentSpaces[j],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
Thomas Witkowski's avatar
Thomas Witkowski committed
752
753
754
			      ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);	  
	} else {
	  ERROR_EXIT("Not yet implemented!\n");
755
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
756

Thomas Witkowski's avatar
Thomas Witkowski committed
757
	assembledMatrix[i][j] = true;
758
759
760

	if (assembleMatrix)
	  matrix->finishInsertion();
761
762

 	if (assembleMatrix && matrix->getBoundaryManager())
763
 	  matrix->getBoundaryManager()->exitMatrix(matrix);	
764
765
	
	if (matrix)
766
	  nnz += matrix->getBaseMatrix().nnz();	  
767
768
      }

769
      // And now assemble boundary conditions on the vectors
Thomas Witkowski's avatar
Thomas Witkowski committed
770
771
      assembleBoundaryConditions(rhs->getDOFVector(i),
				 solution->getDOFVector(i),
772
				 componentMeshes[i],
773
				 assembleFlag);     
774
    }
775

776
    solverMatrix.setMatrix(*systemMatrix);
777

Thomas Witkowski's avatar
Thomas Witkowski committed
778
    createPrecon();
779

780
    INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
781

782
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
783
784
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()), omp_get_wtime() - wtime);
785
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
786
787
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
788
#endif    
789
790
  }

791

792
793
  void ProblemVec::createPrecon()
  {
794
    std::string preconType("no");
795
796
797
798
799
    GET_PARAMETER(0, name + "->solver->left precon", &preconType);

    CreatorInterface<ITL_BasePreconditioner> *preconCreator = 
      CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);

Thomas Witkowski's avatar
Thomas Witkowski committed
800
    solver->setLeftPrecon(preconCreator->create(solverMatrix.getMatrix()));
801
802
803
804
805

    preconType= "no";
    GET_PARAMETER(0, name + "->solver->right precon", &preconType);

    preconCreator = CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
Thomas Witkowski's avatar
Thomas Witkowski committed
806
    solver->setRightPrecon(preconCreator->create(solverMatrix.getMatrix()));
807
808
809
  }


810
811
812
813
  void ProblemVec::writeFiles(AdaptInfo *adaptInfo, bool force) 
  {
    FUNCNAME("ProblemVec::writeFiles()");

814
815
816
817
818
819
820
    clock_t first = clock();

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

    int i;
Thomas Witkowski's avatar
Thomas Witkowski committed
821
    int size = static_cast<int>(fileWriters.size());
822
823
824
825
#ifdef _OPENMP
#pragma omp parallel for schedule(static, 1)
#endif
    for (i = 0; i < size; i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
826
      fileWriters[i]->writeFiles(adaptInfo, force);
827
    }
828
829
    
#ifdef _OPENMP
Thomas Witkowski's avatar
Thomas Witkowski committed
830
831
832
    INFO(info, 8)("writeFiles needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()),
		  omp_get_wtime() - wtime);
833
#else
Thomas Witkowski's avatar
Thomas Witkowski committed
834
835
    INFO(info, 8)("writeFiles needed %.5f seconds\n",
		  TIME_USED(first, clock()));
836
#endif
837
838
  }

839
840
841
842
843
  void ProblemVec::writeFiles(AdaptInfo &adaptInfo, bool force) 
  {
    writeFiles(&adaptInfo, force);
  }

844
  void ProblemVec::interpolInitialSolution(std::vector<AbstractFunction<double, WorldVector<double> >*> *fct) 
845
846
847
  {
    FUNCNAME("ProblemVec::interpolInitialSolution()");

Thomas Witkowski's avatar
Thomas Witkowski committed
848
    solution->interpol(fct);
849
850
  }

851
852
  void ProblemVec::addMatrixOperator(Operator *op, int i, int j,
				     double *factor, double *estFactor)
853
854
  {
    FUNCNAME("ProblemVec::addMatrixOperator()");
Thomas Witkowski's avatar
Thomas Witkowski committed
855
   
Thomas Witkowski's avatar
Thomas Witkowski committed
856
    if (!(*systemMatrix)[i][j]) {
857
      TEST_EXIT(i != j)("should have been created already\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
858
      (*systemMatrix)[i][j] = new DOFMatrix(componentSpaces[i], componentSpaces[j], "");
Thomas Witkowski's avatar
Thomas Witkowski committed
859
860
861
      (*systemMatrix)[i][j]->setCoupleMatrix(true);
      (*systemMatrix)[i][j]->getBoundaryManager()->
	setBoundaryConditionMap((*systemMatrix)[i][i]->getBoundaryManager()->
862
				getBoundaryConditionMap());
Thomas Witkowski's avatar
Thomas Witkowski committed
863
864
865

      if (estimator[i])
	estimator[i]->setNewMatrix(j, (*systemMatrix)[i][j]);
866
    }    
Thomas Witkowski's avatar
Thomas Witkowski committed
867

868
    (*systemMatrix)[i][j]->addOperator(op, factor, estFactor);
Thomas Witkowski's avatar
Thomas Witkowski committed
869

870
    traverseInfo.getMatrix(i, j).setAuxFESpaces(op->getAuxFESpaces()); 
871
      
872
873
874
875
876
877
    for (int k = 0; k < static_cast<int>(op->getAuxFESpaces().size()); k++) {
      if ((op->getAuxFESpaces())[k]->getMesh() != componentSpaces[i]->getMesh() ||
	  (op->getAuxFESpaces())[k]->getMesh() != componentSpaces[j]->getMesh()) {
	op->setNeedDualTraverse(true);
	break;
      }          
878
    } 
879
880
881
882

    OperatorPos opPos = {i, j, factor, estFactor, Operator::MATRIX_OPERATOR};
    operators[op].push_back(opPos);
    opFlags[op].setFlag(Operator::MATRIX_OPERATOR);
883
884
  }

885
886
887
888
889
890
891
892
  void ProblemVec::addMatrixOperator(Operator &op, int i, int j,
				     double *factor, double *estFactor)
  {
    addMatrixOperator(&op, i, j, factor, estFactor);
  }

  void ProblemVec::addVectorOperator(Operator *op, int i, 
				     double *factor, double *estFactor)	
893
894
895
  {
    FUNCNAME("ProblemVec::addVectorOperator()");

Thomas Witkowski's avatar
Thomas Witkowski committed
896
897
    rhs->getDOFVector(i)->addOperator(op, factor, estFactor);

898
    traverseInfo.getVector(i).setAuxFESpaces(op->getAuxFESpaces()); 
899
      
900
901
902
903
    for (int j = 0; j < static_cast<int>(op->getAuxFESpaces().size()); j++) {
      if ((op->getAuxFESpaces())[j]->getMesh() != componentSpaces[i]->getMesh()) {
	op->setNeedDualTraverse(true);
	break;      
904
905
      }    
    }
906
907
908
909

    OperatorPos opPos = {i, -1, factor, estFactor, Operator::VECTOR_OPERATOR};
    operators[op].push_back(opPos);
    opFlags[op].setFlag(Operator::VECTOR_OPERATOR);
910
911
  }

912
913
914
915
916
917
  void ProblemVec::addVectorOperator(Operator &op, int i, 
				     double *factor, double *estFactor)	
  {
    addVectorOperator(&op, i, factor, estFactor);
  }

918
  void ProblemVec::addDirichletBC(BoundaryType type, int row, int col,
919
920
921
922
				  AbstractFunction<double, WorldVector<double> >* b)
  {
    FUNCNAME("ProblemVec::addDirichletBC()");

923
924
925
926
927
928
929
930
931
932
933
934
    DirichletBC *dirichletApply = 
      new DirichletBC(type, b, componentSpaces[row], componentSpaces[col], true);
    DirichletBC *dirichletNotApply = 
      new DirichletBC(type, b, componentSpaces[row], componentSpaces[col], false);

    for (int i = 0; i < nComponents; i++) 
      if (systemMatrix && (*systemMatrix)[row][i])
	if (i == col)
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletApply);
	else
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletNotApply);

Thomas Witkowski's avatar
Thomas Witkowski committed
935
    if (rhs)
936
      rhs->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(dirichletApply);
Thomas Witkowski's avatar
Thomas Witkowski committed
937
    if (solution)
938
      solution->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(dirichletApply);
939
940
941
942
943
944
945
946
  }

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

    NeumannBC *neumann = 
947
948
      new NeumannBC(type, n, componentSpaces[row], componentSpaces[col]);

Thomas Witkowski's avatar
Thomas Witkowski committed
949
950
    if (rhs)
      rhs->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(neumann);
951
952
953
954
955
956
957
958
959
  }

  void ProblemVec::addRobinBC(BoundaryType type, int